diff --git a/_modules/index.html b/_modules/index.html
index b44c3a30a..962ca4804 100644
--- a/_modules/index.html
+++ b/_modules/index.html
@@ -496,36 +496,72 @@
                   
   <h1>All modules for which code is available</h1>
 <ul><li><a href="pypath.html">pypath</a></li>
-<ul><li><a href="pypath/core/attrs.html">pypath.core.attrs</a></li>
+<ul><li><a href="pypath/core/annot.html">pypath.core.annot</a></li>
+<li><a href="pypath/core/attrs.html">pypath.core.attrs</a></li>
 <li><a href="pypath/core/common.html">pypath.core.common</a></li>
+<li><a href="pypath/core/complex.html">pypath.core.complex</a></li>
+<li><a href="pypath/core/entity.html">pypath.core.entity</a></li>
+<li><a href="pypath/core/enz_sub.html">pypath.core.enz_sub</a></li>
+<li><a href="pypath/core/evidence.html">pypath.core.evidence</a></li>
+<li><a href="pypath/core/interaction.html">pypath.core.interaction</a></li>
+<li><a href="pypath/core/intercell.html">pypath.core.intercell</a></li>
+<li><a href="pypath/core/network.html">pypath.core.network</a></li>
 <li><a href="pypath/inputs.html">pypath.inputs</a></li>
 <ul><li><a href="pypath/inputs/abs.html">pypath.inputs.abs</a></li>
 <li><a href="pypath/inputs/acsn.html">pypath.inputs.acsn</a></li>
+<li><a href="pypath/inputs/adhesome.html">pypath.inputs.adhesome</a></li>
 <li><a href="pypath/inputs/adrecs.html">pypath.inputs.adrecs</a></li>
+<li><a href="pypath/inputs/almen2009.html">pypath.inputs.almen2009</a></li>
+<li><a href="pypath/inputs/baccin2019.html">pypath.inputs.baccin2019</a></li>
+<li><a href="pypath/inputs/biogps.html">pypath.inputs.biogps</a></li>
 <li><a href="pypath/inputs/biogrid.html">pypath.inputs.biogrid</a></li>
 <li><a href="pypath/inputs/biomart.html">pypath.inputs.biomart</a></li>
 <li><a href="pypath/inputs/biomodels.html">pypath.inputs.biomodels</a></li>
 <li><a href="pypath/inputs/ca1.html">pypath.inputs.ca1</a></li>
 <li><a href="pypath/inputs/cancercellmap.html">pypath.inputs.cancercellmap</a></li>
+<li><a href="pypath/inputs/cancerdrugsdb.html">pypath.inputs.cancerdrugsdb</a></li>
+<li><a href="pypath/inputs/cancersea.html">pypath.inputs.cancersea</a></li>
 <li><a href="pypath/inputs/cell.html">pypath.inputs.cell</a></li>
+<li><a href="pypath/inputs/cellcall.html">pypath.inputs.cellcall</a></li>
+<li><a href="pypath/inputs/cellcellinteractions.html">pypath.inputs.cellcellinteractions</a></li>
+<li><a href="pypath/inputs/cellchatdb.html">pypath.inputs.cellchatdb</a></li>
+<li><a href="pypath/inputs/cellinker.html">pypath.inputs.cellinker</a></li>
+<li><a href="pypath/inputs/cellphonedb.html">pypath.inputs.cellphonedb</a></li>
+<li><a href="pypath/inputs/celltalkdb.html">pypath.inputs.celltalkdb</a></li>
+<li><a href="pypath/inputs/celltypist.html">pypath.inputs.celltypist</a></li>
 <li><a href="pypath/inputs/chembl.html">pypath.inputs.chembl</a></li>
 <li><a href="pypath/inputs/clinvar.html">pypath.inputs.clinvar</a></li>
+<li><a href="pypath/inputs/collectri.html">pypath.inputs.collectri</a></li>
 <li><a href="pypath/inputs/common.html">pypath.inputs.common</a></li>
 <li><a href="pypath/inputs/compath.html">pypath.inputs.compath</a></li>
+<li><a href="pypath/inputs/compleat.html">pypath.inputs.compleat</a></li>
+<li><a href="pypath/inputs/complexportal.html">pypath.inputs.complexportal</a></li>
+<li><a href="pypath/inputs/comppi.html">pypath.inputs.comppi</a></li>
+<li><a href="pypath/inputs/connectomedb.html">pypath.inputs.connectomedb</a></li>
+<li><a href="pypath/inputs/corum.html">pypath.inputs.corum</a></li>
+<li><a href="pypath/inputs/cosmic.html">pypath.inputs.cosmic</a></li>
+<li><a href="pypath/inputs/cpad.html">pypath.inputs.cpad</a></li>
 <li><a href="pypath/inputs/cpdb.html">pypath.inputs.cpdb</a></li>
 <li><a href="pypath/inputs/credentials.html">pypath.inputs.credentials</a></li>
+<li><a href="pypath/inputs/csa.html">pypath.inputs.csa</a></li>
+<li><a href="pypath/inputs/cspa.html">pypath.inputs.cspa</a></li>
 <li><a href="pypath/inputs/ctdbase.html">pypath.inputs.ctdbase</a></li>
+<li><a href="pypath/inputs/cytosig.html">pypath.inputs.cytosig</a></li>
 <li><a href="pypath/inputs/dbptm.html">pypath.inputs.dbptm</a></li>
 <li><a href="pypath/inputs/ddinter.html">pypath.inputs.ddinter</a></li>
 <li><a href="pypath/inputs/deathdomain.html">pypath.inputs.deathdomain</a></li>
+<li><a href="pypath/inputs/depod.html">pypath.inputs.depod</a></li>
+<li><a href="pypath/inputs/dgidb.html">pypath.inputs.dgidb</a></li>
 <li><a href="pypath/inputs/dip.html">pypath.inputs.dip</a></li>
 <li><a href="pypath/inputs/diseases.html">pypath.inputs.diseases</a></li>
+<li><a href="pypath/inputs/domino.html">pypath.inputs.domino</a></li>
 <li><a href="pypath/inputs/dorothea.html">pypath.inputs.dorothea</a></li>
 <li><a href="pypath/inputs/drugbank.html">pypath.inputs.drugbank</a></li>
 <li><a href="pypath/inputs/drugcentral.html">pypath.inputs.drugcentral</a></li>
 <li><a href="pypath/inputs/ebi.html">pypath.inputs.ebi</a></li>
 <li><a href="pypath/inputs/elm.html">pypath.inputs.elm</a></li>
 <li><a href="pypath/inputs/embopress.html">pypath.inputs.embopress</a></li>
+<li><a href="pypath/inputs/embrace.html">pypath.inputs.embrace</a></li>
 <li><a href="pypath/inputs/encode.html">pypath.inputs.encode</a></li>
 <li><a href="pypath/inputs/ensembl.html">pypath.inputs.ensembl</a></li>
 <li><a href="pypath/inputs/eutils.html">pypath.inputs.eutils</a></li>
@@ -535,6 +571,11 @@ <h1>All modules for which code is available</h1>
 <li><a href="pypath/inputs/go.html">pypath.inputs.go</a></li>
 <li><a href="pypath/inputs/gpcrdb.html">pypath.inputs.gpcrdb</a></li>
 <li><a href="pypath/inputs/graphviz.html">pypath.inputs.graphviz</a></li>
+<li><a href="pypath/inputs/guide2pharma.html">pypath.inputs.guide2pharma</a></li>
+<li><a href="pypath/inputs/gutmgene.html">pypath.inputs.gutmgene</a></li>
+<li><a href="pypath/inputs/havugimana.html">pypath.inputs.havugimana</a></li>
+<li><a href="pypath/inputs/hgnc.html">pypath.inputs.hgnc</a></li>
+<li><a href="pypath/inputs/hippie.html">pypath.inputs.hippie</a></li>
 <li><a href="pypath/inputs/hmdb/common.html">pypath.inputs.hmdb.common</a></li>
 <li><a href="pypath/inputs/hmdb/metabolites.html">pypath.inputs.hmdb.metabolites</a></li>
 <li><a href="pypath/inputs/hmdb/proteins.html">pypath.inputs.hmdb.proteins</a></li>
@@ -542,24 +583,47 @@ <h1>All modules for which code is available</h1>
 <li><a href="pypath/inputs/hmdb/structures.html">pypath.inputs.hmdb.structures</a></li>
 <li><a href="pypath/inputs/hmdb/visual.html">pypath.inputs.hmdb.visual</a></li>
 <li><a href="pypath/inputs/hmdb/xml.html">pypath.inputs.hmdb.xml</a></li>
+<li><a href="pypath/inputs/homologene.html">pypath.inputs.homologene</a></li>
+<li><a href="pypath/inputs/hpmr.html">pypath.inputs.hpmr</a></li>
+<li><a href="pypath/inputs/hpo.html">pypath.inputs.hpo</a></li>
 <li><a href="pypath/inputs/hprd.html">pypath.inputs.hprd</a></li>
 <li><a href="pypath/inputs/htri.html">pypath.inputs.htri</a></li>
+<li><a href="pypath/inputs/humancellmap.html">pypath.inputs.humancellmap</a></li>
+<li><a href="pypath/inputs/humap.html">pypath.inputs.humap</a></li>
 <li><a href="pypath/inputs/humsavar.html">pypath.inputs.humsavar</a></li>
+<li><a href="pypath/inputs/huri.html">pypath.inputs.huri</a></li>
 <li><a href="pypath/inputs/i3d.html">pypath.inputs.i3d</a></li>
+<li><a href="pypath/inputs/icellnet.html">pypath.inputs.icellnet</a></li>
 <li><a href="pypath/inputs/ielm.html">pypath.inputs.ielm</a></li>
 <li><a href="pypath/inputs/imweb.html">pypath.inputs.imweb</a></li>
 <li><a href="pypath/inputs/innatedb.html">pypath.inputs.innatedb</a></li>
 <li><a href="pypath/inputs/instruct.html">pypath.inputs.instruct</a></li>
 <li><a href="pypath/inputs/intact.html">pypath.inputs.intact</a></li>
+<li><a href="pypath/inputs/integrins.html">pypath.inputs.integrins</a></li>
 <li><a href="pypath/inputs/interpro.html">pypath.inputs.interpro</a></li>
+<li><a href="pypath/inputs/intogen.html">pypath.inputs.intogen</a></li>
 <li><a href="pypath/inputs/ipi.html">pypath.inputs.ipi</a></li>
+<li><a href="pypath/inputs/iptmnet.html">pypath.inputs.iptmnet</a></li>
+<li><a href="pypath/inputs/italk.html">pypath.inputs.italk</a></li>
+<li><a href="pypath/inputs/kea.html">pypath.inputs.kea</a></li>
+<li><a href="pypath/inputs/kegg.html">pypath.inputs.kegg</a></li>
 <li><a href="pypath/inputs/kegg_api.html">pypath.inputs.kegg_api</a></li>
+<li><a href="pypath/inputs/kinasedotcom.html">pypath.inputs.kinasedotcom</a></li>
 <li><a href="pypath/inputs/kirouac2010.html">pypath.inputs.kirouac2010</a></li>
+<li><a href="pypath/inputs/lambert2018.html">pypath.inputs.lambert2018</a></li>
 <li><a href="pypath/inputs/laudanna.html">pypath.inputs.laudanna</a></li>
+<li><a href="pypath/inputs/li2012.html">pypath.inputs.li2012</a></li>
 <li><a href="pypath/inputs/lincs.html">pypath.inputs.lincs</a></li>
+<li><a href="pypath/inputs/lmpid.html">pypath.inputs.lmpid</a></li>
 <li><a href="pypath/inputs/lncdisease.html">pypath.inputs.lncdisease</a></li>
 <li><a href="pypath/inputs/lncrnadb.html">pypath.inputs.lncrnadb</a></li>
+<li><a href="pypath/inputs/locate.html">pypath.inputs.locate</a></li>
+<li><a href="pypath/inputs/lrdb.html">pypath.inputs.lrdb</a></li>
 <li><a href="pypath/inputs/macrophage.html">pypath.inputs.macrophage</a></li>
+<li><a href="pypath/inputs/matrisome.html">pypath.inputs.matrisome</a></li>
+<li><a href="pypath/inputs/matrixdb.html">pypath.inputs.matrixdb</a></li>
+<li><a href="pypath/inputs/mcam.html">pypath.inputs.mcam</a></li>
+<li><a href="pypath/inputs/membranome.html">pypath.inputs.membranome</a></li>
 <li><a href="pypath/inputs/mimp.html">pypath.inputs.mimp</a></li>
 <li><a href="pypath/inputs/mir2disease.html">pypath.inputs.mir2disease</a></li>
 <li><a href="pypath/inputs/mirbase.html">pypath.inputs.mirbase</a></li>
@@ -568,37 +632,60 @@ <h1>All modules for which code is available</h1>
 <li><a href="pypath/inputs/mirtarbase.html">pypath.inputs.mirtarbase</a></li>
 <li><a href="pypath/inputs/mitab.html">pypath.inputs.mitab</a></li>
 <li><a href="pypath/inputs/mppi.html">pypath.inputs.mppi</a></li>
+<li><a href="pypath/inputs/msigdb.html">pypath.inputs.msigdb</a></li>
 <li><a href="pypath/inputs/ncrdeathdb.html">pypath.inputs.ncrdeathdb</a></li>
 <li><a href="pypath/inputs/negatome.html">pypath.inputs.negatome</a></li>
 <li><a href="pypath/inputs/netbiol.html">pypath.inputs.netbiol</a></li>
+<li><a href="pypath/inputs/netpath.html">pypath.inputs.netpath</a></li>
 <li><a href="pypath/inputs/offsides.html">pypath.inputs.offsides</a></li>
+<li><a href="pypath/inputs/oma.html">pypath.inputs.oma</a></li>
 <li><a href="pypath/inputs/ontology.html">pypath.inputs.ontology</a></li>
 <li><a href="pypath/inputs/opentargets.html">pypath.inputs.opentargets</a></li>
+<li><a href="pypath/inputs/opm.html">pypath.inputs.opm</a></li>
 <li><a href="pypath/inputs/oreganno.html">pypath.inputs.oreganno</a></li>
+<li><a href="pypath/inputs/panglaodb.html">pypath.inputs.panglaodb</a></li>
 <li><a href="pypath/inputs/pathophenodb.html">pypath.inputs.pathophenodb</a></li>
 <li><a href="pypath/inputs/pathwaycommons.html">pypath.inputs.pathwaycommons</a></li>
 <li><a href="pypath/inputs/pazar.html">pypath.inputs.pazar</a></li>
+<li><a href="pypath/inputs/pdb.html">pypath.inputs.pdb</a></li>
 <li><a href="pypath/inputs/pdzbase.html">pypath.inputs.pdzbase</a></li>
 <li><a href="pypath/inputs/pepcyber.html">pypath.inputs.pepcyber</a></li>
 <li><a href="pypath/inputs/pfam.html">pypath.inputs.pfam</a></li>
 <li><a href="pypath/inputs/pharos.html">pypath.inputs.pharos</a></li>
 <li><a href="pypath/inputs/phobius.html">pypath.inputs.phobius</a></li>
+<li><a href="pypath/inputs/phosphatome.html">pypath.inputs.phosphatome</a></li>
 <li><a href="pypath/inputs/phosphoelm.html">pypath.inputs.phosphoelm</a></li>
 <li><a href="pypath/inputs/phosphonetworks.html">pypath.inputs.phosphonetworks</a></li>
 <li><a href="pypath/inputs/phosphopoint.html">pypath.inputs.phosphopoint</a></li>
+<li><a href="pypath/inputs/phosphosite.html">pypath.inputs.phosphosite</a></li>
+<li><a href="pypath/inputs/pisa.html">pypath.inputs.pisa</a></li>
 <li><a href="pypath/inputs/pro.html">pypath.inputs.pro</a></li>
+<li><a href="pypath/inputs/progeny.html">pypath.inputs.progeny</a></li>
+<li><a href="pypath/inputs/proteinatlas.html">pypath.inputs.proteinatlas</a></li>
 <li><a href="pypath/inputs/proteins.html">pypath.inputs.proteins</a></li>
 <li><a href="pypath/inputs/protmapper.html">pypath.inputs.protmapper</a></li>
 <li><a href="pypath/inputs/pubchem.html">pypath.inputs.pubchem</a></li>
 <li><a href="pypath/inputs/pubmed.html">pypath.inputs.pubmed</a></li>
+<li><a href="pypath/inputs/ramilowski2015.html">pypath.inputs.ramilowski2015</a></li>
 <li><a href="pypath/inputs/ramp.html">pypath.inputs.ramp</a></li>
 <li><a href="pypath/inputs/reaction.html">pypath.inputs.reaction</a></li>
 <li><a href="pypath/inputs/reactome.html">pypath.inputs.reactome</a></li>
+<li><a href="pypath/inputs/scconnect.html">pypath.inputs.scconnect</a></li>
 <li><a href="pypath/inputs/science.html">pypath.inputs.science</a></li>
 <li><a href="pypath/inputs/sider.html">pypath.inputs.sider</a></li>
+<li><a href="pypath/inputs/signalink.html">pypath.inputs.signalink</a></li>
+<li><a href="pypath/inputs/signor.html">pypath.inputs.signor</a></li>
+<li><a href="pypath/inputs/spike.html">pypath.inputs.spike</a></li>
 <li><a href="pypath/inputs/stitch.html">pypath.inputs.stitch</a></li>
 <li><a href="pypath/inputs/string.html">pypath.inputs.string</a></li>
+<li><a href="pypath/inputs/surfaceome.html">pypath.inputs.surfaceome</a></li>
 <li><a href="pypath/inputs/switches_elm.html">pypath.inputs.switches_elm</a></li>
+<li><a href="pypath/inputs/talklr.html">pypath.inputs.talklr</a></li>
+<li><a href="pypath/inputs/tcdb.html">pypath.inputs.tcdb</a></li>
+<li><a href="pypath/inputs/tfcensus.html">pypath.inputs.tfcensus</a></li>
+<li><a href="pypath/inputs/threedcomplex.html">pypath.inputs.threedcomplex</a></li>
+<li><a href="pypath/inputs/threedid.html">pypath.inputs.threedid</a></li>
+<li><a href="pypath/inputs/topdb.html">pypath.inputs.topdb</a></li>
 <li><a href="pypath/inputs/transmir.html">pypath.inputs.transmir</a></li>
 <li><a href="pypath/inputs/trip.html">pypath.inputs.trip</a></li>
 <li><a href="pypath/inputs/trrust.html">pypath.inputs.trrust</a></li>
@@ -606,26 +693,46 @@ <h1>All modules for which code is available</h1>
 <li><a href="pypath/inputs/unichem.html">pypath.inputs.unichem</a></li>
 <li><a href="pypath/inputs/uniprot.html">pypath.inputs.uniprot</a></li>
 <li><a href="pypath/inputs/uniprot_db.html">pypath.inputs.uniprot_db</a></li>
-</ul><li><a href="pypath/internals/input_formats.html">pypath.internals.input_formats</a></li>
+<li><a href="pypath/inputs/wang.html">pypath.inputs.wang</a></li>
+<li><a href="pypath/inputs/wojtowicz2020.html">pypath.inputs.wojtowicz2020</a></li>
+<li><a href="pypath/inputs/zhong2015.html">pypath.inputs.zhong2015</a></li>
+</ul><li><a href="pypath/internals/annot_formats.html">pypath.internals.annot_formats</a></li>
+<li><a href="pypath/internals/input_formats.html">pypath.internals.input_formats</a></li>
+<li><a href="pypath/internals/intera.html">pypath.internals.intera</a></li>
 <li><a href="pypath/internals/license.html">pypath.internals.license</a></li>
 <li><a href="pypath/internals/refs.html">pypath.internals.refs</a></li>
 <li><a href="pypath/internals/resource.html">pypath.internals.resource</a></li>
 <li><a href="pypath/legacy/db_categories.html">pypath.legacy.db_categories</a></li>
-<li><a href="pypath/resources.html">pypath.resources</a></li>
+<li><a href="pypath/omnipath.html">pypath.omnipath</a></li>
+<ul><li><a href="pypath/omnipath/app.html">pypath.omnipath.app</a></li>
+<li><a href="pypath/omnipath/databases.html">pypath.omnipath.databases</a></li>
+<ul><li><a href="pypath/omnipath/databases/define.html">pypath.omnipath.databases.define</a></li>
+</ul><li><a href="pypath/omnipath/export.html">pypath.omnipath.export</a></li>
+<li><a href="pypath/omnipath/param.html">pypath.omnipath.param</a></li>
+<li><a href="pypath/omnipath/server/build.html">pypath.omnipath.server.build</a></li>
+<li><a href="pypath/omnipath/server/generate_about_page.html">pypath.omnipath.server.generate_about_page</a></li>
+<li><a href="pypath/omnipath/server/legacy.html">pypath.omnipath.server.legacy</a></li>
+<li><a href="pypath/omnipath/server/run.html">pypath.omnipath.server.run</a></li>
+</ul><li><a href="pypath/resources.html">pypath.resources</a></li>
 <ul><li><a href="pypath/resources/controller.html">pypath.resources.controller</a></li>
+<li><a href="pypath/resources/descriptions.html">pypath.resources.descriptions</a></li>
 <li><a href="pypath/resources/licenses.html">pypath.resources.licenses</a></li>
 <li><a href="pypath/resources/network.html">pypath.resources.network</a></li>
 </ul><li><a href="pypath/share/cache.html">pypath.share.cache</a></li>
 <li><a href="pypath/share/curl.html">pypath.share.curl</a></li>
 <li><a href="pypath/share/progress.html">pypath.share.progress</a></li>
 <li><a href="pypath/utils/go.html">pypath.utils.go</a></li>
+<li><a href="pypath/utils/mapping.html">pypath.utils.mapping</a></li>
+<li><a href="pypath/utils/orthology.html">pypath.utils.orthology</a></li>
 <li><a href="pypath/utils/pdb.html">pypath.utils.pdb</a></li>
 <li><a href="pypath/utils/proteomicsdb.html">pypath.utils.proteomicsdb</a></li>
+<li><a href="pypath/utils/pyreact.html">pypath.utils.pyreact</a></li>
 <li><a href="pypath/utils/reflists.html">pypath.utils.reflists</a></li>
 <li><a href="pypath/utils/residues.html">pypath.utils.residues</a></li>
 <li><a href="pypath/utils/seq.html">pypath.utils.seq</a></li>
 <li><a href="pypath/utils/taxonomy.html">pypath.utils.taxonomy</a></li>
 <li><a href="pypath/utils/unichem.html">pypath.utils.unichem</a></li>
+<li><a href="pypath/utils/uniprot.html">pypath.utils.uniprot</a></li>
 <li><a href="pypath/visual/drawing.html">pypath.visual.drawing</a></li>
 <li><a href="pypath/visual/igraph_drawing.html">pypath.visual.igraph_drawing</a></li>
 <ul><li><a href="pypath/visual/igraph_drawing/edge.html">pypath.visual.igraph_drawing.edge</a></li>
diff --git a/_modules/pypath/core/annot.html b/_modules/pypath/core/annot.html
new file mode 100644
index 000000000..4886cdbc8
--- /dev/null
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@@ -0,0 +1,8282 @@
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+                  
+  <h1>Source code for pypath.core.annot</h1><div class="highlight"><pre>
+<span></span><span class="ch">#!/usr/bin/env python</span>
+<span class="c1"># -*- coding: utf-8 -*-</span>
+
+<span class="c1">#</span>
+<span class="c1">#  This file is part of the `pypath` python module</span>
+<span class="c1">#</span>
+<span class="c1">#  Copyright 2014-2023</span>
+<span class="c1">#  EMBL, EMBL-EBI, Uniklinik RWTH Aachen, Heidelberg University</span>
+<span class="c1">#</span>
+<span class="c1">#  Authors: see the file `README.rst`</span>
+<span class="c1">#  Contact: Dénes Türei (turei.denes@gmail.com)</span>
+<span class="c1">#</span>
+<span class="c1">#  Distributed under the GPLv3 License.</span>
+<span class="c1">#  See accompanying file LICENSE.txt or copy at</span>
+<span class="c1">#      https://www.gnu.org/licenses/gpl-3.0.html</span>
+<span class="c1">#</span>
+<span class="c1">#  Website: https://pypath.omnipathdb.org/</span>
+<span class="c1">#</span>
+
+<span class="kn">from</span> <span class="nn">__future__</span> <span class="kn">import</span> <span class="n">annotations</span>
+
+<span class="kn">from</span> <span class="nn">future.utils</span> <span class="kn">import</span> <span class="n">iteritems</span>
+<span class="kn">from</span> <span class="nn">past.builtins</span> <span class="kn">import</span> <span class="n">xrange</span><span class="p">,</span> <span class="nb">range</span><span class="p">,</span> <span class="n">reduce</span>
+
+<span class="kn">import</span> <span class="nn">os</span>
+<span class="kn">import</span> <span class="nn">sys</span>
+<span class="kn">import</span> <span class="nn">copy</span>
+<span class="kn">import</span> <span class="nn">importlib</span> <span class="k">as</span> <span class="nn">imp</span>
+<span class="kn">import</span> <span class="nn">collections</span>
+<span class="kn">import</span> <span class="nn">itertools</span>
+<span class="kn">import</span> <span class="nn">traceback</span>
+
+<span class="kn">import</span> <span class="nn">dill</span> <span class="k">as</span> <span class="nn">pickle</span>
+<span class="kn">import</span> <span class="nn">numpy</span> <span class="k">as</span> <span class="nn">np</span>
+<span class="kn">import</span> <span class="nn">pandas</span> <span class="k">as</span> <span class="nn">pd</span>
+
+<span class="kn">import</span> <span class="nn">pypath.inputs.cellphonedb</span> <span class="k">as</span> <span class="nn">cellphonedb</span>
+<span class="kn">import</span> <span class="nn">pypath.inputs.lrdb</span> <span class="k">as</span> <span class="nn">lrdb</span>
+<span class="kn">import</span> <span class="nn">pypath.inputs.uniprot_db</span> <span class="k">as</span> <span class="nn">uniprot_db</span>
+<span class="kn">import</span> <span class="nn">pypath.share.common</span> <span class="k">as</span> <span class="nn">common</span>
+<span class="kn">import</span> <span class="nn">pypath_common._constants</span> <span class="k">as</span> <span class="nn">_const</span>
+<span class="kn">import</span> <span class="nn">pypath.share.settings</span> <span class="k">as</span> <span class="nn">settings</span>
+<span class="kn">import</span> <span class="nn">pypath.utils.mapping</span> <span class="k">as</span> <span class="nn">mapping</span>
+<span class="kn">import</span> <span class="nn">pypath.utils.reflists</span> <span class="k">as</span> <span class="nn">reflists</span>
+<span class="kn">import</span> <span class="nn">pypath.utils.uniprot</span> <span class="k">as</span> <span class="nn">utils_uniprot</span>
+<span class="kn">import</span> <span class="nn">pypath.internals.resource</span> <span class="k">as</span> <span class="nn">resource</span>
+<span class="kn">import</span> <span class="nn">pypath.utils.go</span> <span class="k">as</span> <span class="nn">go</span>
+<span class="kn">import</span> <span class="nn">pypath.core.intercell_annot</span> <span class="k">as</span> <span class="nn">intercell_annot</span>
+<span class="kn">import</span> <span class="nn">pypath.core.common</span> <span class="k">as</span> <span class="nn">core_common</span>
+<span class="kn">import</span> <span class="nn">pypath.share.session</span> <span class="k">as</span> <span class="nn">session_mod</span>
+<span class="kn">import</span> <span class="nn">pypath.internals.annot_formats</span> <span class="k">as</span> <span class="nn">annot_formats</span>
+<span class="kn">import</span> <span class="nn">pypath.core.complex</span> <span class="k">as</span> <span class="nn">complex</span>
+<span class="kn">import</span> <span class="nn">pypath.internals.intera</span> <span class="k">as</span> <span class="nn">intera</span>
+<span class="kn">import</span> <span class="nn">pypath.core.entity</span> <span class="k">as</span> <span class="nn">entity</span>
+
+<span class="c1">#TODO this should be part of json files</span>
+<span class="n">protein_sources_default</span> <span class="o">=</span> <span class="p">{</span>
+    <span class="s1">&#39;Dgidb&#39;</span><span class="p">,</span>
+    <span class="s1">&#39;Membranome&#39;</span><span class="p">,</span>
+    <span class="s1">&#39;Exocarta&#39;</span><span class="p">,</span>
+    <span class="s1">&#39;Vesiclepedia&#39;</span><span class="p">,</span>
+    <span class="s1">&#39;Matrisome&#39;</span><span class="p">,</span>
+    <span class="s1">&#39;Surfaceome&#39;</span><span class="p">,</span>
+    <span class="s1">&#39;CellSurfaceProteinAtlas&#39;</span><span class="p">,</span>
+    <span class="s1">&#39;CellSurfaceProteinAtlasCellType&#39;</span><span class="p">,</span>
+    <span class="s1">&#39;HumanPlasmaMembraneReceptome&#39;</span><span class="p">,</span>
+    <span class="s1">&#39;Matrixdb&#39;</span><span class="p">,</span>
+    <span class="s1">&#39;Locate&#39;</span><span class="p">,</span>
+    <span class="s1">&#39;GOIntercell&#39;</span><span class="p">,</span>
+    <span class="s1">&#39;CellPhoneDB&#39;</span><span class="p">,</span>
+    <span class="s1">&#39;Ramilowski2015&#39;</span><span class="p">,</span>
+    <span class="s1">&#39;Ramilowski2015Location&#39;</span><span class="p">,</span>
+    <span class="s1">&#39;Kirouac2010&#39;</span><span class="p">,</span>
+    <span class="s1">&#39;GuideToPharmacology&#39;</span><span class="p">,</span>
+    <span class="s1">&#39;Adhesome&#39;</span><span class="p">,</span>
+    <span class="s1">&#39;Integrins&#39;</span><span class="p">,</span>
+    <span class="s1">&#39;Opm&#39;</span><span class="p">,</span>
+    <span class="s1">&#39;Topdb&#39;</span><span class="p">,</span>
+    <span class="s1">&#39;Hgnc&#39;</span><span class="p">,</span>
+    <span class="s1">&#39;Zhong2015&#39;</span><span class="p">,</span>
+    <span class="s1">&#39;HumanProteinAtlas&#39;</span><span class="p">,</span>
+    <span class="s1">&#39;HumanProteinAtlasSubcellular&#39;</span><span class="p">,</span>
+    <span class="s1">&#39;HumanProteinAtlasSecretome&#39;</span><span class="p">,</span>
+    <span class="s1">&#39;Comppi&#39;</span><span class="p">,</span>
+    <span class="s1">&#39;SignorPathways&#39;</span><span class="p">,</span>
+    <span class="s1">&#39;SignalinkPathways&#39;</span><span class="p">,</span>
+    <span class="s1">&#39;SignalinkFunctions&#39;</span><span class="p">,</span>
+    <span class="s1">&#39;KeggPathways&#39;</span><span class="p">,</span>
+    <span class="s1">&#39;KeggPathwaysPC&#39;</span><span class="p">,</span>
+    <span class="s1">&#39;NetpathPathways&#39;</span><span class="p">,</span>
+    <span class="s1">&#39;Cpad&#39;</span><span class="p">,</span>
+    <span class="s1">&#39;Disgenet&#39;</span><span class="p">,</span>
+    <span class="s1">&#39;Kinasedotcom&#39;</span><span class="p">,</span>
+    <span class="s1">&#39;Phosphatome&#39;</span><span class="p">,</span>
+    <span class="s1">&#39;Tfcensus&#39;</span><span class="p">,</span>
+    <span class="s1">&#39;Intogen&#39;</span><span class="p">,</span>
+    <span class="s1">&#39;CancerGeneCensus&#39;</span><span class="p">,</span>
+    <span class="s1">&#39;Cancersea&#39;</span><span class="p">,</span>
+    <span class="s1">&#39;Msigdb&#39;</span><span class="p">,</span>
+    <span class="s1">&#39;Lrdb&#39;</span><span class="p">,</span>
+    <span class="s1">&#39;Baccin2019&#39;</span><span class="p">,</span>
+    <span class="s1">&#39;Almen2009&#39;</span><span class="p">,</span>
+    <span class="s1">&#39;Phobius&#39;</span><span class="p">,</span>
+    <span class="s1">&#39;Icellnet&#39;</span><span class="p">,</span>
+    <span class="s1">&#39;Cellcellinteractions&#39;</span><span class="p">,</span>
+    <span class="s1">&#39;Italk&#39;</span><span class="p">,</span>
+    <span class="s1">&#39;Embrace&#39;</span><span class="p">,</span>
+    <span class="s1">&#39;UniprotLocations&#39;</span><span class="p">,</span>
+    <span class="s1">&#39;UniprotFamilies&#39;</span><span class="p">,</span>
+    <span class="s1">&#39;UniprotTopologies&#39;</span><span class="p">,</span>
+    <span class="s1">&#39;UniprotTissues&#39;</span><span class="p">,</span>
+    <span class="s1">&#39;UniprotKeywords&#39;</span><span class="p">,</span>
+    <span class="s1">&#39;Tcdb&#39;</span><span class="p">,</span>
+    <span class="s1">&#39;Mcam&#39;</span><span class="p">,</span>
+    <span class="s1">&#39;Gpcrdb&#39;</span><span class="p">,</span>
+    <span class="s1">&#39;Celltalkdb&#39;</span><span class="p">,</span>
+    <span class="s1">&#39;Cellchatdb&#39;</span><span class="p">,</span>
+    <span class="s1">&#39;Connectomedb&#39;</span><span class="p">,</span>
+    <span class="s1">&#39;Talklr&#39;</span><span class="p">,</span>
+    <span class="s1">&#39;Humancellmap&#39;</span><span class="p">,</span>
+    <span class="s1">&#39;Cellcall&#39;</span><span class="p">,</span>
+    <span class="c1">#&#39;Biogps&#39;,</span>
+    <span class="s1">&#39;Cellinker&#39;</span><span class="p">,</span>
+    <span class="s1">&#39;Scconnect&#39;</span><span class="p">,</span>
+    <span class="s1">&#39;Cancerdrugsdb&#39;</span><span class="p">,</span>
+    <span class="s1">&#39;Progeny&#39;</span><span class="p">,</span>
+    <span class="s1">&#39;Celltypist&#39;</span><span class="p">,</span>
+    <span class="s1">&#39;Cytosig&#39;</span><span class="p">,</span>
+    <span class="s1">&#39;Wang&#39;</span><span class="p">,</span>
+    <span class="s1">&#39;Panglaodb&#39;</span><span class="p">,</span>
+    <span class="s1">&#39;Lambert2018&#39;</span><span class="p">,</span>
+    <span class="s1">&#39;InterPro&#39;</span><span class="p">,</span>
+<span class="p">}</span>
+
+<span class="c1">#TODO this should be part of json files</span>
+<span class="n">complex_sources_default</span> <span class="o">=</span> <span class="p">{</span>
+    <span class="s1">&#39;CellPhoneDBComplex&#39;</span><span class="p">,</span>
+    <span class="s1">&#39;CorumFuncat&#39;</span><span class="p">,</span>
+    <span class="s1">&#39;CorumGO&#39;</span><span class="p">,</span>
+    <span class="s1">&#39;IcellnetComplex&#39;</span><span class="p">,</span>
+    <span class="s1">&#39;CellchatdbComplex&#39;</span><span class="p">,</span>
+    <span class="s1">&#39;CellinkerComplex&#39;</span><span class="p">,</span>
+    <span class="s1">&#39;ScconnectComplex&#39;</span><span class="p">,</span>
+<span class="p">}</span>
+
+<span class="c1">#TODO this should be part of json files</span>
+<span class="n">default_fields</span> <span class="o">=</span> <span class="p">{</span>
+    <span class="s1">&#39;Matrisome&#39;</span><span class="p">:</span> <span class="p">(</span><span class="s1">&#39;mainclass&#39;</span><span class="p">,</span> <span class="s1">&#39;subclass&#39;</span><span class="p">),</span>
+    <span class="s1">&#39;Locate&#39;</span><span class="p">:</span> <span class="p">(</span><span class="s1">&#39;location&#39;</span><span class="p">,),</span>
+    <span class="s1">&#39;Vesiclepedia&#39;</span><span class="p">:</span> <span class="p">(</span><span class="s1">&#39;vesicle&#39;</span><span class="p">,),</span>
+    <span class="s1">&#39;Exocarta&#39;</span><span class="p">:</span> <span class="p">(</span><span class="s1">&#39;vesicle&#39;</span><span class="p">,),</span>
+    <span class="s1">&#39;Ramilowski_location&#39;</span><span class="p">:</span> <span class="p">(</span><span class="s1">&#39;location&#39;</span><span class="p">,),</span>
+    <span class="s1">&#39;HPA&#39;</span><span class="p">:</span> <span class="p">(</span><span class="s1">&#39;tissue&#39;</span><span class="p">,</span> <span class="s1">&#39;level&#39;</span><span class="p">),</span>
+    <span class="s1">&#39;CellPhoneDB&#39;</span><span class="p">:</span> <span class="p">(</span>
+        <span class="s1">&#39;receptor&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;adhesion&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;cytoplasm&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;peripheral&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;secretion&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;secreted&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;transporter&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;transmembrane&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;extracellular&#39;</span><span class="p">,</span>
+    <span class="p">),</span>
+    <span class="s1">&#39;CellPhoneDB_Complex&#39;</span><span class="p">:</span> <span class="p">(</span>
+        <span class="s1">&#39;receptor&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;adhesion&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;cytoplasm&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;peripheral&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;secretion&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;secreted&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;transporter&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;transmembrane&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;extracellular&#39;</span><span class="p">,</span>
+    <span class="p">),</span>
+    <span class="s1">&#39;Cpad&#39;</span><span class="p">:</span> <span class="p">(</span>
+        <span class="s1">&#39;cancer&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;effect_on_cancer&#39;</span><span class="p">,</span>
+    <span class="p">),</span>
+    <span class="s1">&#39;Disgenet&#39;</span><span class="p">:</span> <span class="p">(</span>
+        <span class="s1">&#39;disease&#39;</span><span class="p">,</span>
+    <span class="p">),</span>
+<span class="p">}</span>
+
+
+<div class="viewcode-block" id="CustomAnnotation">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.CustomAnnotation.html#pypath.core.annot.CustomAnnotation">[docs]</a>
+<span class="k">class</span> <span class="nc">CustomAnnotation</span><span class="p">(</span><span class="n">session_mod</span><span class="o">.</span><span class="n">Logger</span><span class="p">):</span>
+
+
+<div class="viewcode-block" id="CustomAnnotation.__init__">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.CustomAnnotation.html#pypath.core.annot.CustomAnnotation.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">class_definitions</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">excludes</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">excludes_extra</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">build</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
+            <span class="n">pickle_file</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">annotdb_pickle_file</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">composite_resource_name</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+        <span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        :param tuple class_definitions:</span>
+<span class="sd">            A series of annotation class definitions, each represented by</span>
+<span class="sd">            an instance of ``pypath.internals.annot_formats.AnnotDef``.</span>
+<span class="sd">            These definitions carry the attributes and instructions to</span>
+<span class="sd">            populate the classes.</span>
+<span class="sd">        :param dict excludes:</span>
+<span class="sd">            A dict with parent category names (strings) or category keys</span>
+<span class="sd">            (tuples) as keys and sets if identifiers as values.</span>
+<span class="sd">            The identifiers in this dict will be excluded from all the</span>
+<span class="sd">            respective categories while building the database. E.g. if</span>
+<span class="sd">            the UniProt ID `P00533` (EGFR) is in the set under the key of</span>
+<span class="sd">            `adhesion` it will be excluded from the category `adhesion` and</span>
+<span class="sd">            all it&#39;s direct children.</span>
+<span class="sd">        :param dict excludes_extra:</span>
+<span class="sd">            Same kind of dict as `excludes` but it will be added to the</span>
+<span class="sd">            built-in default. The built in and the provided extra sets</span>
+<span class="sd">            will be merged. If you want to overwrite or modify the built-in</span>
+<span class="sd">            sets provide your custom dict as `excludes`.</span>
+<span class="sd">        :param bool build:</span>
+<span class="sd">            Execute the build upon instantiation or set up an empty object</span>
+<span class="sd">            the build can be executed on later.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">if</span> <span class="ow">not</span> <span class="nb">hasattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">&#39;_log_name&#39;</span><span class="p">):</span>
+
+            <span class="n">session_mod</span><span class="o">.</span><span class="n">Logger</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">name</span> <span class="o">=</span> <span class="s1">&#39;annot&#39;</span><span class="p">)</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">pickle_file</span> <span class="o">=</span> <span class="n">pickle_file</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">annotdb_pickle_file</span> <span class="o">=</span> <span class="n">annotdb_pickle_file</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">_class_definitions_provided</span> <span class="o">=</span> <span class="n">class_definitions</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">_excludes_original</span> <span class="o">=</span> <span class="n">excludes</span> <span class="ow">or</span> <span class="p">{}</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">_excludes_extra_original</span> <span class="o">=</span> <span class="n">excludes_extra</span> <span class="ow">or</span> <span class="p">{}</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">network</span> <span class="o">=</span> <span class="kc">None</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">classes</span> <span class="o">=</span> <span class="p">{}</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">consensus_scores</span> <span class="o">=</span> <span class="p">{}</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">composite_numof_resources</span> <span class="o">=</span> <span class="p">{}</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">composite_resource_name</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="n">composite_resource_name</span> <span class="ow">or</span>
+            <span class="n">settings</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">&#39;annot_composite_database_name&#39;</span><span class="p">)</span>
+        <span class="p">)</span>
+
+        <span class="k">if</span> <span class="n">build</span><span class="p">:</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">load</span><span class="p">()</span></div>
+
+
+
+<div class="viewcode-block" id="CustomAnnotation.reload">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.CustomAnnotation.html#pypath.core.annot.CustomAnnotation.reload">[docs]</a>
+    <span class="k">def</span> <span class="nf">reload</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Reloads the object from the module level.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">imp</span><span class="o">.</span><span class="n">reload</span><span class="p">(</span><span class="n">core_common</span><span class="p">)</span>
+        <span class="n">modname</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="vm">__class__</span><span class="o">.</span><span class="vm">__module__</span>
+        <span class="n">mod</span> <span class="o">=</span> <span class="nb">__import__</span><span class="p">(</span><span class="n">modname</span><span class="p">,</span> <span class="n">fromlist</span> <span class="o">=</span> <span class="p">[</span><span class="n">modname</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;.&#39;</span><span class="p">)[</span><span class="mi">0</span><span class="p">]])</span>
+        <span class="n">imp</span><span class="o">.</span><span class="n">reload</span><span class="p">(</span><span class="n">mod</span><span class="p">)</span>
+        <span class="n">new</span> <span class="o">=</span> <span class="nb">getattr</span><span class="p">(</span><span class="n">mod</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="vm">__class__</span><span class="o">.</span><span class="vm">__name__</span><span class="p">)</span>
+        <span class="nb">setattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">&#39;__class__&#39;</span><span class="p">,</span> <span class="n">new</span><span class="p">)</span>
+
+        <span class="n">imp</span><span class="o">.</span><span class="n">reload</span><span class="p">(</span><span class="n">annot_formats</span><span class="p">)</span>
+        <span class="n">new_annotkey</span> <span class="o">=</span> <span class="n">annot_formats</span><span class="o">.</span><span class="n">AnnotDefKey</span>
+        <span class="n">new_annotgroup</span> <span class="o">=</span> <span class="n">annot_formats</span><span class="o">.</span><span class="n">AnnotationGroup</span>
+
+        <span class="k">for</span> <span class="n">key</span><span class="p">,</span> <span class="bp">cls</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">classes</span><span class="p">):</span>
+
+            <span class="n">key</span><span class="o">.</span><span class="vm">__class__</span> <span class="o">=</span> <span class="n">new_annotkey</span>
+            <span class="bp">cls</span><span class="o">.</span><span class="vm">__class__</span> <span class="o">=</span> <span class="n">new_annotgroup</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">load</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">pickle_file</span> <span class="ow">and</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">exists</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">pickle_file</span><span class="p">):</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">load_from_pickle</span><span class="p">(</span><span class="n">pickle_file</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">pickle_file</span><span class="p">)</span>
+
+        <span class="k">else</span><span class="p">:</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">pre_build</span><span class="p">()</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">build</span><span class="p">()</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">post_load</span><span class="p">()</span>
+
+
+    <span class="k">def</span> <span class="nf">pre_build</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">update_excludes</span><span class="p">()</span>
+
+
+    <span class="k">def</span> <span class="nf">build</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">ensure_annotdb</span><span class="p">()</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_class_definitions</span> <span class="o">=</span> <span class="p">{}</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">add_class_definitions</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_class_definitions_provided</span> <span class="ow">or</span> <span class="p">{})</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">classes</span> <span class="o">=</span> <span class="p">{}</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">populate_classes</span><span class="p">()</span>
+
+
+    <span class="k">def</span> <span class="nf">post_load</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">pass</span>
+
+
+    <span class="k">def</span> <span class="nf">update_excludes</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_excludes</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">defaultdict</span><span class="p">(</span><span class="nb">set</span><span class="p">)</span>
+
+        <span class="k">for</span> <span class="n">label</span><span class="p">,</span> <span class="n">group</span> <span class="ow">in</span> <span class="n">itertools</span><span class="o">.</span><span class="n">chain</span><span class="p">(</span>
+            <span class="n">iteritems</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_excludes_original</span><span class="p">),</span>
+            <span class="n">iteritems</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_excludes_extra_original</span><span class="p">),</span>
+        <span class="p">):</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">_excludes</span><span class="p">[</span><span class="n">label</span><span class="p">]</span><span class="o">.</span><span class="n">update</span><span class="p">(</span><span class="n">group</span><span class="p">)</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_excludes</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_excludes</span><span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">ensure_annotdb</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">annotdb</span> <span class="o">=</span> <span class="n">get_db</span><span class="p">(</span><span class="n">pickle_file</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">annotdb_pickle_file</span><span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">add_class_definitions</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">class_definitions</span><span class="p">):</span>
+
+        <span class="n">class_definitions</span> <span class="o">=</span> <span class="n">copy</span><span class="o">.</span><span class="n">deepcopy</span><span class="p">(</span><span class="n">class_definitions</span><span class="p">)</span>
+
+        <span class="k">if</span> <span class="ow">not</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">class_definitions</span><span class="p">,</span> <span class="nb">dict</span><span class="p">):</span>
+
+            <span class="n">class_definitions</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">(</span>
+                <span class="p">(</span>
+                    <span class="n">classdef</span><span class="o">.</span><span class="n">key</span><span class="p">,</span>
+                    <span class="n">classdef</span>
+                <span class="p">)</span> <span class="k">for</span> <span class="n">classdef</span> <span class="ow">in</span> <span class="n">class_definitions</span>
+            <span class="p">)</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_class_definitions</span><span class="o">.</span><span class="n">update</span><span class="p">(</span><span class="n">class_definitions</span><span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">update_parents</span><span class="p">()</span>
+
+
+<div class="viewcode-block" id="CustomAnnotation.update_parents">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.CustomAnnotation.html#pypath.core.annot.CustomAnnotation.update_parents">[docs]</a>
+    <span class="k">def</span> <span class="nf">update_parents</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Creates a dict :py:attr:``children`` with parent class names as keys</span>
+<span class="sd">        and sets of children class keys as values. Also a dict</span>
+<span class="sd">        :py:attr:``parents`` with children class keys as keys and parent</span>
+<span class="sd">        class keys as values.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">children</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">defaultdict</span><span class="p">(</span><span class="nb">set</span><span class="p">)</span>
+        <span class="n">parents</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">defaultdict</span><span class="p">(</span><span class="nb">set</span><span class="p">)</span>
+        <span class="n">collect_parents</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">defaultdict</span><span class="p">(</span><span class="nb">set</span><span class="p">)</span>
+
+        <span class="c1"># collecting the potential parents</span>
+        <span class="k">for</span> <span class="n">key</span><span class="p">,</span> <span class="n">classdef</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_class_definitions</span><span class="p">):</span>
+
+            <span class="k">if</span> <span class="n">classdef</span><span class="o">.</span><span class="n">source</span> <span class="o">==</span> <span class="s1">&#39;composite&#39;</span><span class="p">:</span>
+
+                <span class="n">collect_parents</span><span class="p">[</span><span class="n">classdef</span><span class="o">.</span><span class="n">name</span><span class="p">]</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">key</span><span class="p">)</span>
+
+        <span class="c1"># assigning children to parents</span>
+        <span class="k">for</span> <span class="n">key</span><span class="p">,</span> <span class="n">classdef</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_class_definitions</span><span class="p">):</span>
+
+            <span class="n">parent</span> <span class="o">=</span> <span class="n">key</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span>
+            <span class="k">if</span> <span class="n">parent</span> <span class="ow">in</span> <span class="n">collect_parents</span><span class="p">:</span>
+
+                <span class="k">for</span> <span class="n">parent_key</span> <span class="ow">in</span> <span class="n">collect_parents</span><span class="p">[</span><span class="n">parent</span><span class="p">]:</span>
+
+                    <span class="n">children</span><span class="p">[</span><span class="n">parent_key</span><span class="p">]</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">key</span><span class="p">)</span>
+                    <span class="n">parents</span><span class="p">[</span><span class="n">key</span><span class="p">]</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">parent_key</span><span class="p">)</span>
+                    <span class="n">parents</span><span class="p">[</span><span class="n">key</span><span class="p">[</span><span class="mi">0</span><span class="p">]]</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">parent_key</span><span class="p">)</span>
+                    <span class="n">parents</span><span class="p">[(</span><span class="n">key</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">key</span><span class="p">[</span><span class="mi">1</span><span class="p">])]</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">parent_key</span><span class="p">)</span>
+                    <span class="n">parents</span><span class="p">[(</span><span class="n">key</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">key</span><span class="p">[</span><span class="mi">2</span><span class="p">])]</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">parent_key</span><span class="p">)</span>
+                    <span class="n">parents</span><span class="p">[</span><span class="n">key</span><span class="p">[</span><span class="mi">2</span><span class="p">]]</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">parent_key</span><span class="p">)</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">children</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">(</span><span class="n">children</span><span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">parents</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">(</span><span class="n">parents</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="CustomAnnotation.populate_classes">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.CustomAnnotation.html#pypath.core.annot.CustomAnnotation.populate_classes">[docs]</a>
+    <span class="k">def</span> <span class="nf">populate_classes</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">update</span> <span class="o">=</span> <span class="kc">False</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Creates a classification of proteins according to the custom</span>
+<span class="sd">        annotation definitions.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">pickle_file</span><span class="p">:</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">load_from_pickle</span><span class="p">(</span><span class="n">pickle_file</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">pickle_file</span><span class="p">)</span>
+            <span class="k">return</span>
+
+        <span class="k">for</span> <span class="n">classdef</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">_class_definitions</span><span class="o">.</span><span class="n">values</span><span class="p">():</span>
+
+            <span class="k">if</span> <span class="n">classdef</span><span class="o">.</span><span class="n">key</span> <span class="ow">not</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">classes</span> <span class="ow">or</span> <span class="n">update</span><span class="p">:</span>
+
+                <span class="bp">self</span><span class="o">.</span><span class="n">create_class</span><span class="p">(</span><span class="n">classdef</span><span class="p">)</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">populate_scores</span><span class="p">()</span></div>
+
+
+
+<div class="viewcode-block" id="CustomAnnotation.populate_scores">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.CustomAnnotation.html#pypath.core.annot.CustomAnnotation.populate_scores">[docs]</a>
+    <span class="k">def</span> <span class="nf">populate_scores</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Creates the consensus score dictionaries based on the number of</span>
+<span class="sd">        resources annotating an entity for each composite category.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">for</span> <span class="n">classdef</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">_class_definitions</span><span class="o">.</span><span class="n">values</span><span class="p">():</span>
+
+
+            <span class="k">if</span> <span class="n">classdef</span><span class="o">.</span><span class="n">source</span> <span class="o">!=</span> <span class="s1">&#39;composite&#39;</span><span class="p">:</span>
+
+                <span class="k">continue</span>
+
+            <span class="n">components</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_execute_operation</span><span class="p">(</span>
+                <span class="n">classdef</span><span class="o">.</span><span class="n">resource</span><span class="p">,</span>
+                <span class="n">execute</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+                <span class="n">only_generic</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
+            <span class="p">)</span>
+
+            <span class="n">name</span> <span class="o">=</span> <span class="n">classdef</span><span class="o">.</span><span class="n">name</span>
+            <span class="c1">#components = self._collect_by_parent(</span>
+                <span class="c1">#classdef.resource,</span>
+                <span class="c1">#only_generic = True,</span>
+            <span class="c1">#)</span>
+
+            <span class="n">n_resources</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="n">components</span><span class="p">)</span>
+
+            <span class="n">n_resources_by_entity</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">(</span>
+                <span class="n">collections</span><span class="o">.</span><span class="n">Counter</span><span class="p">(</span>
+                    <span class="n">itertools</span><span class="o">.</span><span class="n">chain</span><span class="p">(</span><span class="o">*</span><span class="n">components</span><span class="p">)</span>
+                <span class="p">)</span>
+            <span class="p">)</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">composite_numof_resources</span><span class="p">[</span><span class="n">name</span><span class="p">]</span> <span class="o">=</span> <span class="n">n_resources</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">consensus_scores</span><span class="p">[</span><span class="n">name</span><span class="p">]</span> <span class="o">=</span> <span class="n">n_resources_by_entity</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">load_from_pickle</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">pickle_file</span><span class="p">):</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span><span class="s1">&#39;Loading from pickle `</span><span class="si">%s</span><span class="s1">`.&#39;</span> <span class="o">%</span> <span class="n">pickle_file</span><span class="p">)</span>
+
+        <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">pickle_file</span><span class="p">,</span> <span class="s1">&#39;rb&#39;</span><span class="p">)</span> <span class="k">as</span> <span class="n">fp</span><span class="p">:</span>
+
+            <span class="p">(</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">classes</span><span class="p">,</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">consensus_scores</span><span class="p">,</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">composite_numof_resources</span><span class="p">,</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">parents</span><span class="p">,</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">children</span><span class="p">,</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">composite_resource_name</span><span class="p">,</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">_class_definitions</span><span class="p">,</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">_excludes</span><span class="p">,</span>
+            <span class="p">)</span> <span class="o">=</span> <span class="n">pickle</span><span class="o">.</span><span class="n">load</span><span class="p">(</span><span class="n">fp</span><span class="p">)</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_update_complex_attribute_classes</span><span class="p">()</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span><span class="s1">&#39;Loaded from pickle `</span><span class="si">%s</span><span class="s1">`.&#39;</span> <span class="o">%</span> <span class="n">pickle_file</span><span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">save_to_pickle</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">pickle_file</span><span class="p">):</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span><span class="s1">&#39;Saving to pickle `</span><span class="si">%s</span><span class="s1">`.&#39;</span> <span class="o">%</span> <span class="n">pickle_file</span><span class="p">)</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_update_complex_attribute_classes</span><span class="p">()</span>
+
+        <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">pickle_file</span><span class="p">,</span> <span class="s1">&#39;wb&#39;</span><span class="p">)</span> <span class="k">as</span> <span class="n">fp</span><span class="p">:</span>
+
+            <span class="n">pickle</span><span class="o">.</span><span class="n">dump</span><span class="p">(</span>
+                <span class="n">obj</span> <span class="o">=</span> <span class="p">(</span>
+                    <span class="bp">self</span><span class="o">.</span><span class="n">classes</span><span class="p">,</span>
+                    <span class="bp">self</span><span class="o">.</span><span class="n">consensus_scores</span><span class="p">,</span>
+                    <span class="bp">self</span><span class="o">.</span><span class="n">composite_numof_resources</span><span class="p">,</span>
+                    <span class="bp">self</span><span class="o">.</span><span class="n">parents</span><span class="p">,</span>
+                    <span class="bp">self</span><span class="o">.</span><span class="n">children</span><span class="p">,</span>
+                    <span class="bp">self</span><span class="o">.</span><span class="n">composite_resource_name</span><span class="p">,</span>
+                    <span class="bp">self</span><span class="o">.</span><span class="n">_class_definitions</span><span class="p">,</span>
+                    <span class="bp">self</span><span class="o">.</span><span class="n">_excludes</span><span class="p">,</span>
+                <span class="p">),</span>
+                <span class="n">file</span> <span class="o">=</span> <span class="n">fp</span><span class="p">,</span>
+                <span class="n">protocol</span> <span class="o">=</span> <span class="n">pickle</span><span class="o">.</span><span class="n">HIGHEST_PROTOCOL</span><span class="p">,</span>
+            <span class="p">)</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span><span class="s1">&#39;Saved to pickle `</span><span class="si">%s</span><span class="s1">`.&#39;</span> <span class="o">%</span> <span class="n">pickle_file</span><span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">_update_complex_attribute_classes</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="nb">complex</span><span class="o">.</span><span class="n">ComplexAggregator</span><span class="o">.</span><span class="n">_update_complex_attribute_classes_static</span><span class="p">(</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">classes</span><span class="o">.</span><span class="n">keys</span><span class="p">(),</span>
+            <span class="n">mod</span> <span class="o">=</span> <span class="n">sys</span><span class="o">.</span><span class="n">modules</span><span class="p">[</span><span class="vm">__name__</span><span class="p">],</span>
+        <span class="p">)</span>
+
+
+<div class="viewcode-block" id="CustomAnnotation.create_class">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.CustomAnnotation.html#pypath.core.annot.CustomAnnotation.create_class">[docs]</a>
+    <span class="k">def</span> <span class="nf">create_class</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">classdef</span><span class="p">,</span> <span class="n">override</span> <span class="o">=</span> <span class="kc">False</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Creates a category of entities by processing a custom definition.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">if</span> <span class="n">classdef</span><span class="o">.</span><span class="n">enabled</span> <span class="ow">or</span> <span class="n">override</span><span class="p">:</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">classes</span><span class="p">[</span><span class="n">classdef</span><span class="o">.</span><span class="n">key</span><span class="p">]</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">process_annot</span><span class="p">(</span><span class="n">classdef</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="CustomAnnotation.process_annot">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.CustomAnnotation.html#pypath.core.annot.CustomAnnotation.process_annot">[docs]</a>
+    <span class="k">def</span> <span class="nf">process_annot</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">classdef</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Processes an annotation definition and returns a set of identifiers.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">members</span> <span class="o">=</span> <span class="nb">set</span><span class="p">()</span>
+
+        <span class="k">if</span> <span class="ow">not</span> <span class="n">classdef</span><span class="o">.</span><span class="n">enabled</span><span class="p">:</span>
+
+            <span class="k">return</span> <span class="n">members</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span>
+            <span class="s1">&#39;Processing custom annotation definition &#39;</span>
+            <span class="s1">&#39;`</span><span class="si">%s</span><span class="s1">` (parent: `</span><span class="si">%s</span><span class="s1">`, resource: `</span><span class="si">%s</span><span class="s1">`).&#39;</span> <span class="o">%</span> <span class="n">classdef</span><span class="o">.</span><span class="n">key</span>
+        <span class="p">)</span>
+
+        <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">classdef</span><span class="o">.</span><span class="n">resource</span><span class="p">,</span> <span class="nb">set</span><span class="p">):</span>
+
+            <span class="n">members</span> <span class="o">=</span> <span class="n">classdef</span><span class="o">.</span><span class="n">resource</span>
+
+        <span class="k">elif</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">classdef</span><span class="o">.</span><span class="n">resource</span><span class="p">,</span> <span class="nb">str</span><span class="p">):</span>
+
+            <span class="k">if</span> <span class="n">classdef</span><span class="o">.</span><span class="n">resource</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">annotdb</span><span class="o">.</span><span class="n">annots</span><span class="p">:</span>
+
+                <span class="k">if</span> <span class="ow">not</span> <span class="n">classdef</span><span class="o">.</span><span class="n">args</span><span class="p">:</span>
+
+                    <span class="n">members</span> <span class="o">=</span> <span class="p">(</span>
+                        <span class="bp">self</span><span class="o">.</span><span class="n">annotdb</span><span class="o">.</span><span class="n">annots</span><span class="p">[</span><span class="n">classdef</span><span class="o">.</span><span class="n">resource</span><span class="p">]</span><span class="o">.</span><span class="n">to_set</span><span class="p">()</span>
+                    <span class="p">)</span>
+
+                <span class="k">else</span><span class="p">:</span>
+
+                    <span class="n">members</span> <span class="o">=</span> <span class="p">(</span>
+                        <span class="bp">self</span><span class="o">.</span><span class="n">annotdb</span><span class="o">.</span><span class="n">annots</span><span class="p">[</span><span class="n">classdef</span><span class="o">.</span><span class="n">resource</span><span class="p">]</span><span class="o">.</span><span class="n">select</span><span class="p">(</span>
+                            <span class="o">**</span><span class="n">classdef</span><span class="o">.</span><span class="n">args</span>
+                        <span class="p">)</span>
+                    <span class="p">)</span>
+
+                <span class="c1"># Automatically include direct complex annotations</span>
+                <span class="n">cplex_resource</span> <span class="o">=</span> <span class="s1">&#39;</span><span class="si">%s</span><span class="s1">_complex&#39;</span> <span class="o">%</span> <span class="n">classdef</span><span class="o">.</span><span class="n">resource</span>
+
+                <span class="k">if</span> <span class="n">cplex_resource</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">annotdb</span><span class="o">.</span><span class="n">annots</span><span class="p">:</span>
+
+                    <span class="n">classdef_args</span> <span class="o">=</span> <span class="n">classdef</span><span class="o">.</span><span class="n">_asdict</span><span class="p">()</span>
+                    <span class="n">classdef_args</span><span class="p">[</span><span class="s1">&#39;resource&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">cplex_resource</span>
+                    <span class="n">cplex_classdef</span> <span class="o">=</span> <span class="n">annot_formats</span><span class="o">.</span><span class="n">AnnotDef</span><span class="p">(</span><span class="o">**</span><span class="n">classdef_args</span><span class="p">)</span>
+
+                    <span class="n">members</span><span class="o">.</span><span class="n">update</span><span class="p">(</span>
+                        <span class="bp">self</span><span class="o">.</span><span class="n">process_annot</span><span class="p">(</span><span class="n">cplex_classdef</span><span class="p">)</span>
+                    <span class="p">)</span>
+
+            <span class="k">elif</span> <span class="p">(</span>
+                <span class="n">classdef</span><span class="o">.</span><span class="n">resource</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s1">&#39;~&#39;</span><span class="p">)</span> <span class="ow">or</span>
+                <span class="n">classdef</span><span class="o">.</span><span class="n">resource</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s1">&#39;#&#39;</span><span class="p">)</span>
+            <span class="p">):</span>
+
+                <span class="n">members</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_execute_operation</span><span class="p">(</span>
+                    <span class="n">annot_formats</span><span class="o">.</span><span class="n">AnnotOp</span><span class="p">(</span><span class="n">annots</span> <span class="o">=</span> <span class="n">classdef</span><span class="o">.</span><span class="n">resource</span><span class="p">)</span>
+                <span class="p">)</span>
+
+            <span class="k">else</span><span class="p">:</span>
+
+                <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span><span class="s1">&#39;Resource not found: </span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="n">classdef</span><span class="o">.</span><span class="n">resource</span><span class="p">)</span>
+
+        <span class="k">elif</span> <span class="nb">callable</span><span class="p">(</span><span class="n">classdef</span><span class="o">.</span><span class="n">resource</span><span class="p">):</span>
+
+            <span class="n">members</span> <span class="o">=</span> <span class="n">classdef</span><span class="o">.</span><span class="n">resource</span><span class="p">(</span><span class="o">**</span><span class="p">(</span><span class="n">classdef</span><span class="o">.</span><span class="n">args</span> <span class="ow">or</span> <span class="p">{}))</span>
+
+        <span class="k">elif</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">classdef</span><span class="o">.</span><span class="n">resource</span><span class="p">,</span> <span class="n">annot_formats</span><span class="o">.</span><span class="n">AnnotOp</span><span class="p">):</span>
+
+            <span class="n">members</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_execute_operation</span><span class="p">(</span><span class="n">classdef</span><span class="o">.</span><span class="n">resource</span><span class="p">)</span>
+
+        <span class="k">for</span> <span class="n">avoid</span> <span class="ow">in</span> <span class="n">classdef</span><span class="o">.</span><span class="n">avoid</span><span class="p">:</span>
+
+            <span class="n">op</span> <span class="o">=</span> <span class="n">annot_formats</span><span class="o">.</span><span class="n">AnnotOp</span><span class="p">(</span>
+                <span class="n">annots</span> <span class="o">=</span> <span class="p">(</span>
+                    <span class="n">members</span><span class="p">,</span>
+                    <span class="bp">self</span><span class="o">.</span><span class="n">select</span><span class="p">(</span><span class="n">avoid</span><span class="p">)</span>
+                <span class="p">),</span>
+                <span class="n">op</span> <span class="o">=</span> <span class="nb">set</span><span class="o">.</span><span class="n">difference</span><span class="p">,</span>
+            <span class="p">)</span>
+
+            <span class="n">members</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_execute_operation</span><span class="p">(</span><span class="n">op</span><span class="p">)</span>
+
+        <span class="k">for</span> <span class="n">limit</span> <span class="ow">in</span> <span class="n">classdef</span><span class="o">.</span><span class="n">limit</span><span class="p">:</span>
+
+            <span class="n">op</span> <span class="o">=</span> <span class="n">annot_formats</span><span class="o">.</span><span class="n">AnnotOp</span><span class="p">(</span>
+                <span class="n">annots</span> <span class="o">=</span> <span class="p">(</span>
+                    <span class="n">members</span><span class="p">,</span>
+                    <span class="bp">self</span><span class="o">.</span><span class="n">select</span><span class="p">(</span><span class="n">limit</span><span class="p">)</span>
+                <span class="p">),</span>
+                <span class="n">op</span> <span class="o">=</span> <span class="nb">set</span><span class="o">.</span><span class="n">intersection</span><span class="p">,</span>
+            <span class="p">)</span>
+
+            <span class="n">members</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_execute_operation</span><span class="p">(</span><span class="n">op</span><span class="p">)</span>
+
+        <span class="k">if</span> <span class="n">classdef</span><span class="o">.</span><span class="n">exclude</span><span class="p">:</span>
+
+            <span class="n">members</span> <span class="o">=</span> <span class="n">members</span> <span class="o">-</span> <span class="n">classdef</span><span class="o">.</span><span class="n">exclude</span>
+
+        <span class="k">if</span> <span class="n">classdef</span><span class="o">.</span><span class="n">parent</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">_excludes</span><span class="p">:</span>
+
+            <span class="n">members</span> <span class="o">=</span> <span class="n">members</span> <span class="o">-</span> <span class="bp">self</span><span class="o">.</span><span class="n">_excludes</span><span class="p">[</span><span class="n">classdef</span><span class="o">.</span><span class="n">parent</span><span class="p">]</span>
+
+        <span class="k">if</span> <span class="n">classdef</span><span class="o">.</span><span class="n">key</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">_excludes</span><span class="p">:</span>
+
+            <span class="n">members</span> <span class="o">=</span> <span class="n">members</span> <span class="o">-</span> <span class="bp">self</span><span class="o">.</span><span class="n">_excludes</span><span class="p">[</span><span class="n">classdef</span><span class="o">.</span><span class="n">key</span><span class="p">]</span>
+
+        <span class="n">transmitter</span><span class="p">,</span> <span class="n">receiver</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_get_transmitter_receiver</span><span class="p">(</span><span class="n">classdef</span><span class="p">)</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span>
+            <span class="s1">&#39;Finished processing custom annotation definition &#39;</span>
+            <span class="s1">&#39;`</span><span class="si">%s</span><span class="s1">` (parent: `</span><span class="si">%s</span><span class="s1">`, resource: `</span><span class="si">%s</span><span class="s1">`). Resulted a set of </span><span class="si">%u</span><span class="s1"> &#39;</span>
+            <span class="s1">&#39;entities.&#39;</span> <span class="o">%</span> <span class="p">(</span><span class="n">classdef</span><span class="o">.</span><span class="n">key</span> <span class="o">+</span> <span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">members</span><span class="p">),))</span>
+        <span class="p">)</span>
+
+        <span class="k">return</span> <span class="n">annot_formats</span><span class="o">.</span><span class="n">AnnotationGroup</span><span class="p">(</span>
+            <span class="n">members</span> <span class="o">=</span> <span class="n">members</span><span class="p">,</span>
+            <span class="n">name</span> <span class="o">=</span> <span class="n">classdef</span><span class="o">.</span><span class="n">name</span><span class="p">,</span>
+            <span class="n">parent</span> <span class="o">=</span> <span class="n">classdef</span><span class="o">.</span><span class="n">parent</span><span class="p">,</span>
+            <span class="n">aspect</span> <span class="o">=</span> <span class="n">classdef</span><span class="o">.</span><span class="n">aspect</span><span class="p">,</span>
+            <span class="n">resource</span> <span class="o">=</span> <span class="n">classdef</span><span class="o">.</span><span class="n">resource_name</span><span class="p">,</span> <span class="c1"># the actual database name</span>
+            <span class="n">scope</span> <span class="o">=</span> <span class="n">classdef</span><span class="o">.</span><span class="n">scope</span><span class="p">,</span>
+            <span class="n">source</span> <span class="o">=</span> <span class="n">classdef</span><span class="o">.</span><span class="n">source</span><span class="p">,</span> <span class="c1"># resource_specific / composite</span>
+            <span class="n">transmitter</span> <span class="o">=</span> <span class="n">transmitter</span><span class="p">,</span>
+            <span class="n">receiver</span> <span class="o">=</span> <span class="n">receiver</span><span class="p">,</span>
+        <span class="p">)</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">_execute_operation</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">annotop</span><span class="p">,</span> <span class="n">execute</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Executes a set operation on anntation sets.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">_is_short_notation</span><span class="p">(</span><span class="n">annotop</span><span class="p">):</span>
+
+            <span class="n">annots</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_collect_by_parent</span><span class="p">(</span><span class="n">annotop</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
+            <span class="n">op</span> <span class="o">=</span> <span class="nb">set</span><span class="o">.</span><span class="n">union</span>
+
+        <span class="k">elif</span> <span class="bp">self</span><span class="o">.</span><span class="n">_is_short_notation</span><span class="p">(</span><span class="n">annotop</span><span class="o">.</span><span class="n">annots</span><span class="p">):</span>
+
+            <span class="n">annots</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_collect_by_parent</span><span class="p">(</span><span class="n">annotop</span><span class="o">.</span><span class="n">annots</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
+            <span class="n">op</span> <span class="o">=</span> <span class="n">annotop</span><span class="o">.</span><span class="n">op</span>
+
+        <span class="k">else</span><span class="p">:</span>
+
+            <span class="n">annots</span> <span class="o">=</span> <span class="nb">tuple</span><span class="p">(</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">select</span><span class="p">(</span><span class="n">_annot</span><span class="p">,</span> <span class="n">execute</span> <span class="o">=</span> <span class="n">execute</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
+                <span class="k">for</span> <span class="n">_annot</span> <span class="ow">in</span> <span class="n">annotop</span><span class="o">.</span><span class="n">annots</span>
+                <span class="k">if</span> <span class="p">(</span>
+                    <span class="ow">not</span> <span class="nb">hasattr</span><span class="p">(</span><span class="n">_annot</span><span class="p">,</span> <span class="s1">&#39;enabled&#39;</span><span class="p">)</span> <span class="ow">or</span>
+                    <span class="n">_annot</span><span class="o">.</span><span class="n">enabled</span>
+                <span class="p">)</span>
+            <span class="p">)</span>
+            <span class="n">annots</span> <span class="o">=</span> <span class="nb">tuple</span><span class="p">(</span><span class="n">itertools</span><span class="o">.</span><span class="n">chain</span><span class="p">(</span><span class="o">*</span><span class="p">(</span>
+                <span class="p">(</span><span class="n">a</span><span class="p">,)</span> <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">a</span><span class="p">,</span> <span class="nb">set</span><span class="p">)</span> <span class="k">else</span> <span class="n">a</span>
+                <span class="k">for</span> <span class="n">a</span> <span class="ow">in</span> <span class="n">annots</span>
+            <span class="p">)))</span>
+            <span class="n">op</span> <span class="o">=</span> <span class="n">annotop</span><span class="o">.</span><span class="n">op</span>
+
+        <span class="k">if</span> <span class="n">execute</span><span class="p">:</span>
+
+            <span class="n">annots</span> <span class="o">=</span> <span class="n">op</span><span class="p">(</span><span class="o">*</span><span class="p">(</span>
+                <span class="n">a</span> <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">a</span><span class="p">,</span> <span class="nb">set</span><span class="p">)</span> <span class="k">else</span> <span class="nb">set</span><span class="p">(</span><span class="n">a</span><span class="p">)</span>
+                <span class="k">for</span> <span class="n">a</span> <span class="ow">in</span> <span class="n">annots</span>
+            <span class="p">))</span>
+
+        <span class="k">return</span> <span class="n">annots</span>
+
+
+    <span class="k">def</span> <span class="nf">_collect_by_parent</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">parent</span><span class="p">,</span> <span class="n">only_generic</span> <span class="o">=</span> <span class="kc">False</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Processes the shorthand (single string) notation</span>
+<span class="sd">        `[#name]~parent[~resource]`.</span>
+<span class="sd">        Returns tuple of sets.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">name</span><span class="p">,</span> <span class="n">parent</span><span class="p">,</span> <span class="n">resource</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_process_short_notation</span><span class="p">(</span><span class="n">parent</span><span class="p">)</span>
+
+        <span class="k">return</span> <span class="nb">tuple</span><span class="p">(</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">select</span><span class="p">(</span><span class="n">classdef</span><span class="o">.</span><span class="n">key</span><span class="p">)</span>
+            <span class="k">for</span> <span class="n">classdef</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">_class_definitions</span><span class="o">.</span><span class="n">values</span><span class="p">()</span>
+            <span class="k">if</span> <span class="p">(</span>
+                <span class="n">classdef</span><span class="o">.</span><span class="n">parent</span> <span class="o">==</span> <span class="n">parent</span> <span class="ow">and</span>
+                <span class="p">(</span>
+                    <span class="ow">not</span> <span class="n">resource</span> <span class="ow">or</span>
+                    <span class="n">classdef</span><span class="o">.</span><span class="n">resource_name</span> <span class="o">==</span> <span class="n">resource</span>
+                <span class="p">)</span> <span class="ow">and</span>
+                <span class="n">classdef</span><span class="o">.</span><span class="n">enabled</span> <span class="ow">and</span>
+                <span class="ow">not</span> <span class="p">(</span>
+                    <span class="n">classdef</span><span class="o">.</span><span class="n">name</span> <span class="o">==</span> <span class="n">classdef</span><span class="o">.</span><span class="n">parent</span> <span class="ow">and</span> <span class="p">(</span>
+                        <span class="n">classdef</span><span class="o">.</span><span class="n">source</span> <span class="o">==</span> <span class="s1">&#39;composite&#39;</span> <span class="ow">or</span>
+                        <span class="n">classdef</span><span class="o">.</span><span class="n">resource_name</span> <span class="o">==</span> <span class="n">resource</span>
+                    <span class="p">)</span>
+                <span class="p">)</span> <span class="ow">and</span>
+                <span class="p">(</span>
+                    <span class="ow">not</span> <span class="n">only_generic</span> <span class="ow">or</span>
+                    <span class="n">classdef</span><span class="o">.</span><span class="n">scope</span> <span class="o">==</span> <span class="s1">&#39;generic&#39;</span>
+                <span class="p">)</span>
+            <span class="p">)</span>
+        <span class="p">)</span>
+
+
+    <span class="nd">@staticmethod</span>
+    <span class="k">def</span> <span class="nf">_process_short_notation</span><span class="p">(</span><span class="n">shortdef</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Extracts name, parent and resource froms the shorthand (single string)</span>
+<span class="sd">        notation `[#name]~parent[~resource]`.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">parent</span> <span class="o">=</span> <span class="n">shortdef</span>
+        <span class="n">name</span> <span class="o">=</span> <span class="kc">None</span>
+        <span class="n">resource</span> <span class="o">=</span> <span class="kc">None</span>
+
+        <span class="k">if</span> <span class="n">parent</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s1">&#39;#&#39;</span><span class="p">):</span>
+
+            <span class="n">name</span><span class="p">,</span> <span class="n">parent</span> <span class="o">=</span> <span class="n">parent</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;~&#39;</span><span class="p">,</span> <span class="n">maxsplit</span> <span class="o">=</span> <span class="mi">1</span><span class="p">)</span>
+            <span class="n">name</span> <span class="o">=</span> <span class="n">name</span><span class="o">.</span><span class="n">strip</span><span class="p">(</span><span class="s1">&#39;#&#39;</span><span class="p">)</span>
+
+        <span class="n">parent</span> <span class="o">=</span> <span class="n">parent</span><span class="o">.</span><span class="n">strip</span><span class="p">(</span><span class="s1">&#39;~&#39;</span><span class="p">)</span>
+        <span class="n">parent_resource</span> <span class="o">=</span> <span class="n">parent</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;~&#39;</span><span class="p">)</span>
+
+        <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">parent_resource</span><span class="p">)</span> <span class="o">==</span> <span class="mi">2</span><span class="p">:</span>
+
+            <span class="n">parent</span><span class="p">,</span> <span class="n">resource</span> <span class="o">=</span> <span class="n">parent_resource</span>
+
+        <span class="k">return</span> <span class="n">name</span><span class="p">,</span> <span class="n">parent</span><span class="p">,</span> <span class="n">resource</span>
+
+
+    <span class="nd">@staticmethod</span>
+    <span class="k">def</span> <span class="nf">_is_short_notation</span><span class="p">(</span><span class="n">obj</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="p">(</span>
+            <span class="nb">isinstance</span><span class="p">(</span><span class="n">obj</span><span class="p">,</span> <span class="nb">str</span><span class="p">)</span> <span class="ow">and</span> <span class="p">(</span>
+                <span class="n">obj</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s1">&#39;~&#39;</span><span class="p">)</span> <span class="ow">or</span>
+                <span class="n">obj</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s1">&#39;#&#39;</span><span class="p">)</span>
+            <span class="p">)</span>
+        <span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">_get_transmitter_receiver</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">classdef</span><span class="p">):</span>
+
+        <span class="n">transmitter</span> <span class="o">=</span> <span class="n">classdef</span><span class="o">.</span><span class="n">transmitter</span>
+        <span class="n">receiver</span> <span class="o">=</span> <span class="n">classdef</span><span class="o">.</span><span class="n">receiver</span>
+
+        <span class="k">if</span> <span class="n">transmitter</span> <span class="ow">is</span> <span class="kc">None</span> <span class="ow">or</span> <span class="n">receiver</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
+
+            <span class="n">name</span><span class="p">,</span> <span class="n">parent</span><span class="p">,</span> <span class="n">resource</span> <span class="o">=</span> <span class="n">classdef</span><span class="o">.</span><span class="n">key</span>
+
+            <span class="k">for</span> <span class="n">key</span><span class="p">,</span> <span class="n">parentdef</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_class_definitions</span><span class="p">):</span>
+
+                <span class="k">if</span> <span class="p">(</span>
+                    <span class="n">parentdef</span><span class="o">.</span><span class="n">name</span> <span class="o">==</span> <span class="n">parent</span> <span class="ow">and</span>
+                    <span class="p">(</span>
+                        <span class="n">parentdef</span><span class="o">.</span><span class="n">source</span> <span class="o">==</span> <span class="s1">&#39;composite&#39;</span> <span class="ow">or</span>
+                        <span class="n">parentdef</span><span class="o">.</span><span class="n">resource</span> <span class="o">==</span> <span class="bp">self</span><span class="o">.</span><span class="n">composite_resource_name</span>
+                    <span class="p">)</span>
+                <span class="p">):</span>
+
+                    <span class="n">transmitter</span> <span class="o">=</span> <span class="p">(</span>
+                        <span class="n">transmitter</span>
+                            <span class="k">if</span> <span class="n">transmitter</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span> <span class="k">else</span>
+                        <span class="n">parentdef</span><span class="o">.</span><span class="n">transmitter</span>
+                    <span class="p">)</span>
+                    <span class="n">receiver</span> <span class="o">=</span> <span class="p">(</span>
+                        <span class="n">receiver</span>
+                            <span class="k">if</span> <span class="n">receiver</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span> <span class="k">else</span>
+                        <span class="n">parentdef</span><span class="o">.</span><span class="n">receiver</span>
+                    <span class="p">)</span>
+                    <span class="k">break</span>
+
+        <span class="k">return</span> <span class="n">transmitter</span><span class="p">,</span> <span class="n">receiver</span>
+
+
+    <span class="k">def</span> <span class="nf">_select</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">name</span><span class="p">,</span>
+            <span class="n">parent</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">resource</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">entity_type</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">execute</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
+            <span class="o">**</span><span class="n">kwargs</span>
+        <span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Retrieves a class by its name and loads it if hasn&#39;t been loaded yet</span>
+<span class="sd">        but the name present in the class definitions.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">selected</span> <span class="o">=</span> <span class="kc">None</span>
+
+        <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">_is_short_notation</span><span class="p">(</span><span class="n">name</span><span class="p">):</span>
+
+            <span class="n">annots</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_collect_by_parent</span><span class="p">(</span><span class="n">name</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
+            <span class="n">annots</span> <span class="o">=</span> <span class="nb">tuple</span><span class="p">(</span>
+                <span class="n">a</span> <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">a</span><span class="p">,</span> <span class="nb">set</span><span class="p">)</span> <span class="k">else</span> <span class="nb">set</span><span class="p">(</span><span class="n">a</span><span class="p">)</span>
+                <span class="k">for</span> <span class="n">a</span> <span class="ow">in</span> <span class="n">annots</span>
+            <span class="p">)</span>
+
+            <span class="n">selected</span> <span class="o">=</span> <span class="nb">set</span><span class="o">.</span><span class="n">union</span><span class="p">(</span><span class="o">*</span><span class="n">annots</span><span class="p">)</span> <span class="k">if</span> <span class="n">execute</span> <span class="k">else</span> <span class="n">annots</span>
+
+        <span class="k">else</span><span class="p">:</span>
+
+            <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">name</span><span class="p">,</span> <span class="nb">tuple</span><span class="p">):</span>
+
+                <span class="n">name</span><span class="p">,</span> <span class="n">parent</span><span class="p">,</span> <span class="n">resource</span> <span class="o">=</span> <span class="n">name</span>
+
+            <span class="k">if</span> <span class="ow">not</span> <span class="n">parent</span> <span class="ow">or</span> <span class="ow">not</span> <span class="n">resource</span><span class="p">:</span>
+
+                <span class="k">if</span> <span class="ow">not</span> <span class="n">parent</span><span class="p">:</span>
+
+                    <span class="n">parent</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">get_parent</span><span class="p">(</span><span class="n">name</span> <span class="o">=</span> <span class="n">name</span><span class="p">,</span> <span class="n">resource</span> <span class="o">=</span> <span class="n">resource</span><span class="p">)</span>
+                    <span class="n">parent</span> <span class="o">=</span> <span class="n">parent</span><span class="o">.</span><span class="n">name</span> <span class="k">if</span> <span class="n">parent</span> <span class="k">else</span> <span class="kc">None</span>
+
+                <span class="k">if</span> <span class="ow">not</span> <span class="n">resource</span><span class="p">:</span>
+
+                    <span class="n">resource</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">get_resource</span><span class="p">(</span><span class="n">name</span> <span class="o">=</span> <span class="n">name</span><span class="p">,</span> <span class="n">parent</span> <span class="o">=</span> <span class="n">parent</span><span class="p">)</span>
+
+            <span class="n">key</span> <span class="o">=</span> <span class="n">annot_formats</span><span class="o">.</span><span class="n">AnnotDefKey</span><span class="p">(</span><span class="n">name</span><span class="p">,</span> <span class="n">parent</span><span class="p">,</span> <span class="n">resource</span><span class="p">)</span>
+
+            <span class="k">if</span> <span class="n">key</span> <span class="ow">not</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">classes</span> <span class="ow">and</span> <span class="n">key</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">_class_definitions</span><span class="p">:</span>
+
+                <span class="bp">self</span><span class="o">.</span><span class="n">create_class</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_class_definitions</span><span class="p">[</span><span class="n">key</span><span class="p">])</span>
+
+            <span class="k">if</span> <span class="n">key</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">classes</span><span class="p">:</span>
+
+                <span class="n">selected</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">classes</span><span class="p">[</span><span class="n">key</span><span class="p">]</span>
+
+        <span class="k">if</span> <span class="n">selected</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
+
+            <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_filter_entity_type</span><span class="p">(</span>
+                <span class="n">selected</span><span class="p">,</span>
+                <span class="n">entity_type</span> <span class="o">=</span> <span class="n">entity_type</span><span class="p">,</span>
+            <span class="p">)</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span>
+            <span class="s1">&#39;No such annotation class: `name=</span><span class="si">%s</span><span class="s1">, &#39;</span>
+            <span class="s1">&#39;parent=</span><span class="si">%s</span><span class="s1">, resource=</span><span class="si">%s</span><span class="s1">`&#39;</span> <span class="o">%</span> <span class="n">key</span>
+        <span class="p">)</span>
+
+
+<div class="viewcode-block" id="CustomAnnotation.select">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.CustomAnnotation.html#pypath.core.annot.CustomAnnotation.select">[docs]</a>
+    <span class="k">def</span> <span class="nf">select</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">definition</span><span class="p">,</span>
+            <span class="n">parent</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">resource</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">entity_type</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="o">**</span><span class="n">kwargs</span>
+        <span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Retrieves a class by its name or definition. The definition can be</span>
+<span class="sd">        a class name (string) or a set of entities, or an AnnotDef object</span>
+<span class="sd">        defining the contents based on original resources or an AnnotOp</span>
+<span class="sd">        which defines the contents as an operation over other definitions.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">selected</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">_execute_operation</span><span class="p">(</span><span class="n">definition</span><span class="p">)</span>
+                <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">definition</span><span class="p">,</span> <span class="n">annot_formats</span><span class="o">.</span><span class="n">AnnotOp</span><span class="p">)</span> <span class="k">else</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">process_annot</span><span class="p">(</span><span class="n">definition</span><span class="p">)</span>
+                <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">definition</span><span class="p">,</span> <span class="n">annot_formats</span><span class="o">.</span><span class="n">AnnotDef</span><span class="p">)</span> <span class="k">else</span>
+            <span class="n">definition</span>
+                <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">definition</span><span class="p">,</span> <span class="n">annot_formats</span><span class="o">.</span><span class="n">_set_type</span><span class="p">)</span> <span class="k">else</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">_select</span><span class="p">(</span><span class="o">*</span><span class="n">definition</span><span class="p">)</span>
+                <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">definition</span><span class="p">,</span> <span class="p">(</span><span class="nb">tuple</span><span class="p">,</span> <span class="nb">list</span><span class="p">))</span> <span class="k">else</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">_select</span><span class="p">(</span><span class="o">**</span><span class="n">definition</span><span class="p">)</span>
+                <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">definition</span><span class="p">,</span> <span class="nb">dict</span><span class="p">)</span> <span class="k">else</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">_select</span><span class="p">(</span>
+                <span class="n">definition</span><span class="p">,</span>
+                <span class="n">parent</span> <span class="o">=</span> <span class="n">parent</span><span class="p">,</span>
+                <span class="n">resource</span> <span class="o">=</span> <span class="n">resource</span><span class="p">,</span>
+                <span class="o">**</span><span class="n">kwargs</span>
+            <span class="p">)</span>
+        <span class="p">)</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_filter_entity_type</span><span class="p">(</span><span class="n">selected</span><span class="p">,</span> <span class="n">entity_type</span> <span class="o">=</span> <span class="n">entity_type</span><span class="p">)</span></div>
+
+
+
+    <span class="c1"># synonym for old name</span>
+    <span class="n">get_class</span> <span class="o">=</span> <span class="n">select</span>
+
+
+<div class="viewcode-block" id="CustomAnnotation.labels">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.CustomAnnotation.html#pypath.core.annot.CustomAnnotation.labels">[docs]</a>
+    <span class="k">def</span> <span class="nf">labels</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">name</span><span class="p">,</span>
+            <span class="n">parent</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">resource</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">entity_type</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+        <span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Same as ``select`` but returns a list of labels (more human readable).</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">return</span> <span class="n">mapping</span><span class="o">.</span><span class="n">label</span><span class="p">(</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">select</span><span class="p">(</span>
+                <span class="n">name</span> <span class="o">=</span> <span class="n">name</span><span class="p">,</span>
+                <span class="n">parent</span> <span class="o">=</span> <span class="n">parent</span><span class="p">,</span>
+                <span class="n">resource</span> <span class="o">=</span> <span class="n">resource</span><span class="p">,</span>
+                <span class="n">entity_type</span> <span class="o">=</span> <span class="n">entity_type</span><span class="p">,</span>
+            <span class="p">)</span>
+        <span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="CustomAnnotation.show">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.CustomAnnotation.html#pypath.core.annot.CustomAnnotation.show">[docs]</a>
+    <span class="k">def</span> <span class="nf">show</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">name</span><span class="p">,</span>
+            <span class="n">parent</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">resource</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="o">**</span><span class="n">kwargs</span>
+        <span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Same as ``select`` but prints a table to the console with basic</span>
+<span class="sd">        information from the UniProt datasheets.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">utils_uniprot</span><span class="o">.</span><span class="n">info</span><span class="p">(</span>
+            <span class="o">*</span><span class="bp">self</span><span class="o">.</span><span class="n">select</span><span class="p">(</span>
+                <span class="n">definition</span> <span class="o">=</span> <span class="n">name</span><span class="p">,</span>
+                <span class="n">parent</span> <span class="o">=</span> <span class="n">parent</span><span class="p">,</span>
+                <span class="n">resource</span> <span class="o">=</span> <span class="n">resource</span><span class="p">,</span>
+                <span class="n">entity_type</span> <span class="o">=</span> <span class="s1">&#39;protein&#39;</span><span class="p">,</span>
+            <span class="p">),</span>
+            <span class="o">**</span><span class="n">kwargs</span>
+        <span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="CustomAnnotation.quality_check_table">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.CustomAnnotation.html#pypath.core.annot.CustomAnnotation.quality_check_table">[docs]</a>
+    <span class="k">def</span> <span class="nf">quality_check_table</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">path</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">fmt</span> <span class="o">=</span> <span class="s1">&#39;tsv&#39;</span><span class="p">,</span>
+            <span class="n">only_swissprot</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
+            <span class="n">top</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="o">**</span><span class="n">kwargs</span>
+        <span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Exports a table in tsv format for quality check and browsing purposes.</span>
+<span class="sd">        Each protein represented in one row of this table with basic data</span>
+<span class="sd">        from UniProt and the list of annotation categories from this</span>
+<span class="sd">        database.</span>
+
+<span class="sd">        :param str path:</span>
+<span class="sd">            Path for the exported file.</span>
+<span class="sd">        :param str fmt:</span>
+<span class="sd">            Format: either `tsv` or `latex`.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">features</span> <span class="o">=</span> <span class="n">kwargs</span><span class="p">[</span><span class="s1">&#39;features&#39;</span><span class="p">]</span> <span class="k">if</span> <span class="s1">&#39;features&#39;</span> <span class="ow">in</span> <span class="n">kwargs</span> <span class="k">else</span> <span class="p">()</span>
+        <span class="n">proteins</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">get_proteins</span><span class="p">())</span>
+
+        <span class="k">if</span> <span class="n">only_swissprot</span><span class="p">:</span>
+
+            <span class="n">proteins</span> <span class="o">=</span> <span class="n">reflists</span><span class="o">.</span><span class="n">select</span><span class="p">(</span><span class="n">proteins</span><span class="p">,</span> <span class="s1">&#39;swissprot&#39;</span><span class="p">)</span>
+
+        <span class="n">genesymbols</span> <span class="o">=</span> <span class="p">[</span><span class="n">mapping</span><span class="o">.</span><span class="n">label</span><span class="p">(</span><span class="n">uniprot</span><span class="p">)</span> <span class="k">for</span> <span class="n">uniprot</span> <span class="ow">in</span> <span class="n">proteins</span><span class="p">]</span>
+        <span class="n">proteins</span> <span class="o">=</span> <span class="p">[</span>
+            <span class="n">uniprot</span>
+            <span class="k">for</span> <span class="n">uniprot</span><span class="p">,</span> <span class="n">genesymbol</span> <span class="ow">in</span>
+            <span class="nb">sorted</span><span class="p">(</span>
+                <span class="p">(</span>
+                    <span class="p">(</span><span class="n">uniprot</span><span class="p">,</span> <span class="n">genesymbol</span><span class="p">)</span>
+                    <span class="k">for</span> <span class="n">uniprot</span><span class="p">,</span> <span class="n">genesymbol</span> <span class="ow">in</span>
+                    <span class="nb">zip</span><span class="p">(</span><span class="n">proteins</span><span class="p">,</span> <span class="n">genesymbols</span><span class="p">)</span>
+                <span class="p">),</span>
+                <span class="n">key</span> <span class="o">=</span> <span class="k">lambda</span> <span class="n">it</span><span class="p">:</span> <span class="n">it</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span>
+            <span class="p">)</span>
+        <span class="p">][:</span><span class="n">top</span><span class="p">]</span>
+
+        <span class="n">tbl</span> <span class="o">=</span> <span class="n">utils_uniprot</span><span class="o">.</span><span class="n">collect</span><span class="p">(</span><span class="n">proteins</span><span class="p">,</span> <span class="o">*</span><span class="n">features</span><span class="p">)</span>
+
+        <span class="n">tbl</span><span class="p">[</span><span class="s1">&#39;intercell_composite&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="p">[</span>
+            <span class="s1">&#39;, &#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span>
+                <span class="bp">cls</span>
+                <span class="k">for</span> <span class="bp">cls</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">classes_by_entity</span><span class="p">(</span><span class="n">uniprot</span><span class="p">,</span> <span class="n">labels</span> <span class="o">=</span> <span class="kc">True</span><span class="p">)</span>
+                <span class="k">if</span> <span class="bp">cls</span><span class="o">.</span><span class="n">endswith</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">composite_resource_name</span><span class="p">)</span>
+            <span class="p">)</span>
+            <span class="k">for</span> <span class="n">uniprot</span> <span class="ow">in</span> <span class="n">proteins</span>
+        <span class="p">]</span>
+        <span class="n">tbl</span><span class="p">[</span><span class="s1">&#39;intercell_all&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="p">[</span>
+            <span class="s1">&#39;, &#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span>
+                <span class="bp">cls</span>
+                <span class="k">for</span> <span class="bp">cls</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">classes_by_entity</span><span class="p">(</span><span class="n">uniprot</span><span class="p">,</span> <span class="n">labels</span> <span class="o">=</span> <span class="kc">True</span><span class="p">)</span>
+                <span class="k">if</span> <span class="ow">not</span> <span class="bp">cls</span><span class="o">.</span><span class="n">endswith</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">composite_resource_name</span><span class="p">)</span>
+            <span class="p">)</span>
+            <span class="k">for</span> <span class="n">uniprot</span> <span class="ow">in</span> <span class="n">proteins</span>
+        <span class="p">]</span>
+
+        <span class="k">if</span> <span class="n">fmt</span> <span class="o">==</span> <span class="s1">&#39;tsv&#39;</span><span class="p">:</span>
+
+            <span class="n">result</span> <span class="o">=</span> <span class="n">common</span><span class="o">.</span><span class="n">tsv_table</span><span class="p">(</span><span class="n">tbl</span> <span class="o">=</span> <span class="n">tbl</span><span class="p">,</span> <span class="n">path</span> <span class="o">=</span> <span class="n">path</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
+
+        <span class="k">elif</span> <span class="s1">&#39;tex&#39;</span> <span class="ow">in</span> <span class="n">fmt</span><span class="p">:</span>
+
+            <span class="k">if</span> <span class="s1">&#39;colformat&#39;</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">kwargs</span><span class="p">:</span>
+
+                <span class="n">kwargs</span><span class="p">[</span><span class="s1">&#39;colformat&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="sa">r</span><span class="s1">&#39;rllrrK</span><span class="si">{25mm}</span><span class="s1">LK</span><span class="si">{20mm}</span><span class="s1">K</span><span class="si">{20mm}</span><span class="s1">K</span><span class="si">{25mm}</span><span class="s1">L&#39;</span>
+
+            <span class="n">result</span> <span class="o">=</span> <span class="n">common</span><span class="o">.</span><span class="n">latex_table</span><span class="p">(</span><span class="n">tbl</span> <span class="o">=</span> <span class="n">tbl</span><span class="p">,</span> <span class="n">path</span> <span class="o">=</span> <span class="n">path</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
+
+        <span class="k">else</span><span class="p">:</span>
+
+            <span class="n">result</span> <span class="o">=</span> <span class="n">tbl</span>
+
+        <span class="k">return</span> <span class="n">result</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">_key</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">name</span><span class="p">,</span> <span class="n">parent</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span> <span class="n">resource</span> <span class="o">=</span> <span class="kc">None</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="n">name</span> <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">name</span><span class="p">,</span> <span class="nb">tuple</span><span class="p">)</span> <span class="k">else</span> <span class="p">(</span><span class="n">name</span><span class="p">,</span> <span class="n">parent</span><span class="p">,</span> <span class="n">resource</span><span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">get_class_scope</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">name</span><span class="p">,</span> <span class="n">parent</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span> <span class="n">resource</span> <span class="o">=</span> <span class="kc">None</span><span class="p">):</span>
+
+        <span class="n">key</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_key</span><span class="p">(</span><span class="n">name</span><span class="p">,</span> <span class="n">parent</span><span class="p">,</span> <span class="n">resource</span><span class="p">)</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">classes</span><span class="p">[</span><span class="n">key</span><span class="p">]</span><span class="o">.</span><span class="n">scope</span>
+
+
+    <span class="k">def</span> <span class="nf">get_resource</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">name</span><span class="p">,</span> <span class="n">parent</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span> <span class="n">resource</span> <span class="o">=</span> <span class="kc">None</span><span class="p">):</span>
+
+        <span class="n">key</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_key</span><span class="p">(</span><span class="n">name</span><span class="p">,</span> <span class="n">parent</span><span class="p">,</span> <span class="n">resource</span><span class="p">)</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">classes</span><span class="p">[</span><span class="n">key</span><span class="p">]</span><span class="o">.</span><span class="n">resource</span>
+
+
+    <span class="k">def</span> <span class="nf">get_aspect</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">name</span><span class="p">,</span> <span class="n">parent</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span> <span class="n">resource</span> <span class="o">=</span> <span class="kc">None</span><span class="p">):</span>
+
+        <span class="n">key</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_key</span><span class="p">(</span><span class="n">name</span><span class="p">,</span> <span class="n">parent</span><span class="p">,</span> <span class="n">resource</span><span class="p">)</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">classes</span><span class="p">[</span><span class="n">key</span><span class="p">]</span><span class="o">.</span><span class="n">aspect</span>
+
+
+    <span class="k">def</span> <span class="nf">get_source</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">name</span><span class="p">,</span> <span class="n">parent</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span> <span class="n">resource</span> <span class="o">=</span> <span class="kc">None</span><span class="p">):</span>
+
+        <span class="n">key</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_key</span><span class="p">(</span><span class="n">name</span><span class="p">,</span> <span class="n">parent</span><span class="p">,</span> <span class="n">resource</span><span class="p">)</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">classes</span><span class="p">[</span><span class="n">key</span><span class="p">]</span><span class="o">.</span><span class="n">source</span>
+
+
+<div class="viewcode-block" id="CustomAnnotation.get_parents">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.CustomAnnotation.html#pypath.core.annot.CustomAnnotation.get_parents">[docs]</a>
+    <span class="k">def</span> <span class="nf">get_parents</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">name</span><span class="p">,</span> <span class="n">parent</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span> <span class="n">resource</span> <span class="o">=</span> <span class="kc">None</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        As names should be unique for resources, a combination of a name and</span>
+<span class="sd">        resource determines the parent category. This method looks up the</span>
+<span class="sd">        parent for a pair of name and resource.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">parent</span> <span class="o">=</span> <span class="n">parent</span> <span class="ow">or</span> <span class="n">name</span>
+
+        <span class="n">keys</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="p">(</span><span class="n">name</span><span class="p">,</span> <span class="n">parent</span><span class="p">,</span> <span class="n">resource</span><span class="p">),</span>
+            <span class="p">(</span><span class="n">name</span><span class="p">,</span> <span class="n">name</span><span class="p">,</span> <span class="n">resource</span><span class="p">),</span>
+            <span class="p">(</span><span class="n">name</span><span class="p">,</span> <span class="n">resource</span><span class="p">),</span>
+            <span class="p">(</span><span class="n">name</span><span class="p">,</span> <span class="n">parent</span><span class="p">),</span>
+            <span class="p">(</span><span class="n">parent</span><span class="p">,</span> <span class="n">resource</span><span class="p">),</span>
+        <span class="p">)</span>
+
+        <span class="k">for</span> <span class="n">key</span> <span class="ow">in</span> <span class="n">keys</span><span class="p">:</span>
+
+            <span class="k">if</span> <span class="n">key</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">parents</span><span class="p">:</span>
+
+                <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">parents</span><span class="p">[</span><span class="n">key</span><span class="p">]</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">get_parent</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">name</span><span class="p">,</span> <span class="n">parent</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span> <span class="n">resource</span> <span class="o">=</span> <span class="kc">None</span><span class="p">):</span>
+
+        <span class="n">parents</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">get_parents</span><span class="p">(</span>
+            <span class="n">name</span> <span class="o">=</span> <span class="n">name</span><span class="p">,</span>
+            <span class="n">parent</span> <span class="o">=</span> <span class="n">parent</span><span class="p">,</span>
+            <span class="n">resource</span> <span class="o">=</span> <span class="n">resource</span><span class="p">,</span>
+        <span class="p">)</span>
+
+        <span class="k">return</span> <span class="p">(</span>
+            <span class="nb">sorted</span><span class="p">(</span><span class="n">parents</span><span class="p">,</span> <span class="n">key</span> <span class="o">=</span> <span class="k">lambda</span> <span class="n">par</span><span class="p">:</span> <span class="n">par</span><span class="p">[</span><span class="mi">0</span><span class="p">])[</span><span class="mi">0</span><span class="p">]</span>
+                <span class="k">if</span> <span class="n">parents</span> <span class="k">else</span>
+            <span class="kc">None</span>
+        <span class="p">)</span>
+
+
+<div class="viewcode-block" id="CustomAnnotation.get_resources">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.CustomAnnotation.html#pypath.core.annot.CustomAnnotation.get_resources">[docs]</a>
+    <span class="k">def</span> <span class="nf">get_resources</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">name</span><span class="p">,</span> <span class="n">parent</span> <span class="o">=</span> <span class="kc">None</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Returns a set with the names of all resources defining a category</span>
+<span class="sd">        with the given name and parent.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">parent</span> <span class="o">=</span> <span class="n">parent</span> <span class="ow">or</span> <span class="n">name</span>
+
+        <span class="k">return</span> <span class="p">{</span>
+            <span class="n">key</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span>
+            <span class="k">for</span> <span class="n">key</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">_class_definitions</span><span class="o">.</span><span class="n">keys</span><span class="p">()</span>
+            <span class="k">if</span> <span class="n">key</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">==</span> <span class="n">name</span> <span class="ow">and</span> <span class="n">key</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="o">==</span> <span class="n">parent</span>
+        <span class="p">}</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">consensus_score</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">name</span><span class="p">,</span> <span class="n">entity</span><span class="p">):</span>
+
+        <span class="k">if</span> <span class="n">name</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">consensus_scores</span><span class="p">:</span>
+
+            <span class="k">if</span> <span class="n">entity</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">consensus_scores</span><span class="p">[</span><span class="n">name</span><span class="p">]:</span>
+
+                <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">consensus_scores</span><span class="p">[</span><span class="n">name</span><span class="p">][</span><span class="n">entity</span><span class="p">]</span>
+
+        <span class="k">return</span> <span class="mi">0</span>
+
+
+    <span class="k">def</span> <span class="nf">consensus_score_normalized</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">name</span><span class="p">,</span> <span class="n">entity</span><span class="p">):</span>
+
+        <span class="n">score</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">consensus_score</span><span class="p">(</span><span class="n">name</span><span class="p">,</span> <span class="n">entity</span><span class="p">)</span>
+
+        <span class="k">if</span> <span class="ow">not</span> <span class="n">np</span><span class="o">.</span><span class="n">isnan</span><span class="p">(</span><span class="n">score</span><span class="p">):</span>
+
+            <span class="n">n_resources</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">composite_numof_resources</span><span class="p">[</span><span class="n">name</span><span class="p">]</span>
+            <span class="n">score</span> <span class="o">=</span> <span class="n">score</span> <span class="o">/</span> <span class="nb">float</span><span class="p">(</span><span class="n">n_resources</span><span class="p">)</span>
+
+        <span class="k">return</span> <span class="n">score</span>
+
+
+<div class="viewcode-block" id="CustomAnnotation.get_resource">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.CustomAnnotation.html#pypath.core.annot.CustomAnnotation.get_resource">[docs]</a>
+    <span class="k">def</span> <span class="nf">get_resource</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">name</span><span class="p">,</span> <span class="n">parent</span> <span class="o">=</span> <span class="kc">None</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        For a category name and its parent returns a single resource name.</span>
+<span class="sd">        If a category belonging to the composite database matches the name</span>
+<span class="sd">        and the parent the name of the composite database will be returned,</span>
+<span class="sd">        otherwise the resource name first in alphabetic order.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">resources</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">get_resources</span><span class="p">(</span><span class="n">name</span> <span class="o">=</span> <span class="n">name</span><span class="p">,</span> <span class="n">parent</span> <span class="o">=</span> <span class="n">parent</span><span class="p">)</span>
+
+
+        <span class="k">return</span> <span class="p">(</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">composite_resource_name</span>
+                <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">composite_resource_name</span> <span class="ow">in</span> <span class="n">resources</span> <span class="k">else</span>
+            <span class="nb">sorted</span><span class="p">(</span><span class="n">resources</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span>
+                <span class="k">if</span> <span class="n">resources</span> <span class="k">else</span>
+            <span class="kc">None</span>
+        <span class="p">)</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">get_class_label</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">name</span><span class="p">,</span> <span class="n">parent</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span> <span class="n">resource</span> <span class="o">=</span> <span class="kc">None</span><span class="p">):</span>
+
+        <span class="bp">cls</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">select</span><span class="p">(</span><span class="n">name</span><span class="p">,</span> <span class="n">parent</span> <span class="o">=</span> <span class="n">parent</span><span class="p">,</span> <span class="n">resource</span> <span class="o">=</span> <span class="n">resource</span><span class="p">)</span>
+
+        <span class="k">return</span> <span class="bp">cls</span><span class="o">.</span><span class="n">label</span>
+
+
+    <span class="k">def</span> <span class="fm">__len__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">classes</span><span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="fm">__contains__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">other</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="p">(</span>
+            <span class="n">other</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">classes</span> <span class="ow">or</span>
+            <span class="nb">any</span><span class="p">(</span><span class="n">other</span> <span class="ow">in</span> <span class="n">v</span> <span class="k">for</span> <span class="n">v</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">classes</span><span class="o">.</span><span class="n">values</span><span class="p">)</span>
+        <span class="p">)</span>
+
+
+    <span class="nd">@staticmethod</span>
+    <span class="k">def</span> <span class="nf">sets</span><span class="p">(</span><span class="o">*</span><span class="n">args</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="n">annot_formats</span><span class="o">.</span><span class="n">AnnotationGroup</span><span class="o">.</span><span class="n">sets</span><span class="p">(</span><span class="o">*</span><span class="n">args</span><span class="p">)</span>
+
+
+    <span class="nd">@staticmethod</span>
+    <span class="k">def</span> <span class="nf">union</span><span class="p">(</span><span class="o">*</span><span class="n">args</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="n">annot_formats</span><span class="o">.</span><span class="n">AnnotationGroup</span><span class="o">.</span><span class="n">union</span><span class="p">(</span><span class="o">*</span><span class="n">args</span><span class="p">)</span>
+
+
+    <span class="nd">@staticmethod</span>
+    <span class="k">def</span> <span class="nf">intersection</span><span class="p">(</span><span class="o">*</span><span class="n">args</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="n">annot_formats</span><span class="o">.</span><span class="n">AnnotationGroup</span><span class="o">.</span><span class="n">intersection</span><span class="p">(</span><span class="o">*</span><span class="n">args</span><span class="p">)</span>
+
+
+    <span class="nd">@staticmethod</span>
+    <span class="k">def</span> <span class="nf">difference</span><span class="p">(</span><span class="o">*</span><span class="n">args</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="n">annot_formats</span><span class="o">.</span><span class="n">AnnotationGroup</span><span class="o">.</span><span class="n">difference</span><span class="p">(</span><span class="o">*</span><span class="n">args</span><span class="p">)</span>
+
+
+    <span class="nd">@staticmethod</span>
+    <span class="k">def</span> <span class="nf">symmetric_difference</span><span class="p">(</span><span class="o">*</span><span class="n">args</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="n">annot_formats</span><span class="o">.</span><span class="n">AnnotationGroup</span><span class="o">.</span><span class="n">symmetric_difference</span><span class="p">(</span><span class="o">*</span><span class="n">args</span><span class="p">)</span>
+
+
+    <span class="nd">@staticmethod</span>
+    <span class="k">def</span> <span class="nf">isdisjoint</span><span class="p">(</span><span class="o">*</span><span class="n">args</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="n">annot_formats</span><span class="o">.</span><span class="n">AnnotationGroup</span><span class="o">.</span><span class="n">isdisjoint</span><span class="p">(</span><span class="o">*</span><span class="n">args</span><span class="p">)</span>
+
+
+    <span class="nd">@staticmethod</span>
+    <span class="k">def</span> <span class="nf">_filter_entity_type</span><span class="p">(</span><span class="n">group</span><span class="p">,</span> <span class="n">entity_type</span><span class="p">):</span>
+
+        <span class="k">if</span> <span class="nb">hasattr</span><span class="p">(</span><span class="n">group</span><span class="p">,</span> <span class="s1">&#39;filter_entity_type&#39;</span><span class="p">):</span>
+
+            <span class="n">group</span> <span class="o">=</span> <span class="n">group</span><span class="o">.</span><span class="n">filter_entity_type</span><span class="p">(</span><span class="n">entity_type</span> <span class="o">=</span> <span class="n">entity_type</span><span class="p">)</span>
+
+        <span class="k">else</span><span class="p">:</span>
+
+            <span class="n">group</span> <span class="o">=</span> <span class="n">entity</span><span class="o">.</span><span class="n">Entity</span><span class="o">.</span><span class="n">filter_entity_type</span><span class="p">(</span>
+                <span class="n">group</span><span class="p">,</span>
+                <span class="n">entity_type</span> <span class="o">=</span> <span class="n">entity_type</span><span class="p">,</span>
+            <span class="p">)</span>
+
+        <span class="k">return</span> <span class="n">group</span>
+
+
+<div class="viewcode-block" id="CustomAnnotation.make_df">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.CustomAnnotation.html#pypath.core.annot.CustomAnnotation.make_df">[docs]</a>
+    <span class="k">def</span> <span class="nf">make_df</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">all_annotations</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span> <span class="n">full_name</span> <span class="o">=</span> <span class="kc">False</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Creates a ``pandas.DataFrame`` where each record assigns a</span>
+<span class="sd">        molecular entity to an annotation category. The data frame will</span>
+<span class="sd">        be assigned to the ``df`` attribute.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span><span class="s1">&#39;Creating data frame from custom annotation.&#39;</span><span class="p">)</span>
+
+        <span class="n">header</span> <span class="o">=</span> <span class="p">[</span>
+            <span class="s1">&#39;category&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;parent&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;database&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;scope&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;aspect&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;source&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;uniprot&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;genesymbol&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;entity_type&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;consensus_score&#39;</span><span class="p">,</span>
+        <span class="p">]</span>
+
+        <span class="n">dtypes</span> <span class="o">=</span> <span class="p">{</span>
+            <span class="s1">&#39;category&#39;</span><span class="p">:</span>    <span class="s1">&#39;category&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;parent&#39;</span><span class="p">:</span>      <span class="s1">&#39;category&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;database&#39;</span><span class="p">:</span>    <span class="s1">&#39;category&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;scope&#39;</span><span class="p">:</span>       <span class="s1">&#39;category&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;aspect&#39;</span><span class="p">:</span>      <span class="s1">&#39;category&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;source&#39;</span><span class="p">:</span>      <span class="s1">&#39;category&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;uniprot&#39;</span><span class="p">:</span>     <span class="s1">&#39;category&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;genesymbol&#39;</span><span class="p">:</span>  <span class="s1">&#39;category&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;entity_type&#39;</span><span class="p">:</span> <span class="s1">&#39;category&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;consensus_score&#39;</span><span class="p">:</span> <span class="s1">&#39;uint16&#39;</span><span class="p">,</span>
+        <span class="p">}</span>
+
+        <span class="k">if</span> <span class="n">full_name</span><span class="p">:</span>
+
+            <span class="n">header</span><span class="o">.</span><span class="n">insert</span><span class="p">(</span><span class="o">-</span><span class="mi">1</span><span class="p">,</span> <span class="s1">&#39;full_name&#39;</span><span class="p">)</span>
+            <span class="n">dtypes</span><span class="p">[</span><span class="s1">&#39;full_name&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="s1">&#39;category&#39;</span>
+
+        <span class="c1"># this won&#39;t be needed any more I guess</span>
+        <span class="c1">#self.collect_classes()</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">df</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">(</span>
+            <span class="p">[</span>
+                <span class="c1"># annotation category, entity id</span>
+                <span class="p">[</span>
+                    <span class="n">annotgroup</span><span class="o">.</span><span class="n">name</span><span class="p">,</span>
+                    <span class="n">annotgroup</span><span class="o">.</span><span class="n">parent</span><span class="p">,</span>
+                    <span class="n">annotgroup</span><span class="o">.</span><span class="n">resource</span><span class="p">,</span>
+                    <span class="n">annotgroup</span><span class="o">.</span><span class="n">scope</span><span class="p">,</span>
+                    <span class="n">annotgroup</span><span class="o">.</span><span class="n">aspect</span><span class="p">,</span>
+                    <span class="n">annotgroup</span><span class="o">.</span><span class="n">source</span><span class="p">,</span>
+                    <span class="n">uniprot</span><span class="o">.</span><span class="fm">__str__</span><span class="p">(),</span>
+                    <span class="p">(</span>
+                        <span class="n">mapping</span><span class="o">.</span><span class="n">map_name0</span><span class="p">(</span><span class="n">uniprot</span><span class="p">,</span> <span class="s1">&#39;uniprot&#39;</span><span class="p">,</span> <span class="s1">&#39;genesymbol&#39;</span><span class="p">)</span>
+                            <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">uniprot</span><span class="p">,</span> <span class="nb">str</span><span class="p">)</span> <span class="k">else</span>
+                        <span class="s1">&#39;COMPLEX:</span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="n">uniprot</span><span class="o">.</span><span class="n">genesymbol_str</span>
+                            <span class="k">if</span> <span class="nb">hasattr</span><span class="p">(</span><span class="n">uniprot</span><span class="p">,</span> <span class="s1">&#39;genesymbol_str&#39;</span><span class="p">)</span> <span class="k">else</span>
+                        <span class="n">uniprot</span><span class="o">.</span><span class="fm">__str__</span><span class="p">()</span>
+                    <span class="p">),</span>
+                <span class="p">]</span> <span class="o">+</span>
+                <span class="c1"># full name</span>
+                <span class="p">(</span>
+                    <span class="p">[</span>
+                        <span class="s1">&#39;; &#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span>
+                            <span class="n">mapping</span><span class="o">.</span><span class="n">map_name</span><span class="p">(</span>
+                                <span class="n">uniprot</span><span class="p">,</span>
+                                <span class="s1">&#39;uniprot&#39;</span><span class="p">,</span>
+                                <span class="s1">&#39;protein-name&#39;</span><span class="p">,</span>
+                            <span class="p">)</span>
+                        <span class="p">),</span>
+                    <span class="p">]</span>
+                    <span class="k">if</span> <span class="n">full_name</span> <span class="k">else</span> <span class="p">[]</span>
+                <span class="p">)</span> <span class="o">+</span>
+                <span class="c1"># entity type and consensus score</span>
+                <span class="p">[</span>
+                    <span class="p">(</span>
+                        <span class="s1">&#39;complex&#39;</span>
+                            <span class="k">if</span> <span class="nb">hasattr</span><span class="p">(</span><span class="n">uniprot</span><span class="p">,</span> <span class="s1">&#39;genesymbol_str&#39;</span><span class="p">)</span> <span class="k">else</span>
+                        <span class="s1">&#39;mirna&#39;</span>
+                            <span class="k">if</span> <span class="n">uniprot</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s1">&#39;MIMAT&#39;</span><span class="p">)</span> <span class="k">else</span>
+                        <span class="s1">&#39;protein&#39;</span>
+                    <span class="p">),</span>
+                    <span class="bp">self</span><span class="o">.</span><span class="n">consensus_score</span><span class="p">(</span>
+                        <span class="n">annotgroup</span><span class="o">.</span><span class="n">name</span><span class="p">,</span>
+                        <span class="n">uniprot</span><span class="p">,</span>
+                    <span class="p">),</span>
+                <span class="p">]</span> <span class="o">+</span>
+                <span class="c1"># all annotations</span>
+                <span class="p">(</span>
+                    <span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">annotdb</span><span class="o">.</span><span class="n">all_annotations_str</span><span class="p">(</span><span class="n">uniprot</span><span class="p">)]</span>
+                        <span class="k">if</span> <span class="n">all_annotations</span> <span class="k">else</span>
+                    <span class="p">[]</span>
+                <span class="p">)</span>
+                <span class="k">for</span> <span class="n">key</span><span class="p">,</span> <span class="n">annotgroup</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">classes</span><span class="p">)</span>
+                <span class="k">for</span> <span class="n">uniprot</span> <span class="ow">in</span> <span class="n">annotgroup</span>
+            <span class="p">],</span>
+            <span class="n">columns</span> <span class="o">=</span> <span class="n">header</span> <span class="o">+</span> <span class="p">(</span>
+                <span class="p">[</span><span class="s1">&#39;all_annotations&#39;</span><span class="p">]</span> <span class="k">if</span> <span class="n">all_annotations</span> <span class="k">else</span> <span class="p">[]</span>
+            <span class="p">),</span>
+        <span class="p">)</span><span class="o">.</span><span class="n">astype</span><span class="p">(</span><span class="n">dtypes</span><span class="p">)</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span>
+            <span class="s1">&#39;Custom annotation data frame has been created. &#39;</span>
+            <span class="s1">&#39;Memory usage: </span><span class="si">%s</span><span class="s1">.&#39;</span> <span class="o">%</span> <span class="n">common</span><span class="o">.</span><span class="n">df_memory_usage</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">df</span><span class="p">)</span>
+        <span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="CustomAnnotation.get_df">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.CustomAnnotation.html#pypath.core.annot.CustomAnnotation.get_df">[docs]</a>
+    <span class="k">def</span> <span class="nf">get_df</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Returns the data frame of custom annotations. If it does not exist yet</span>
+<span class="sd">        builds the data frame.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">if</span> <span class="ow">not</span> <span class="nb">hasattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">&#39;df&#39;</span><span class="p">):</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">make_df</span><span class="p">()</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">df</span></div>
+
+
+
+<div class="viewcode-block" id="CustomAnnotation.counts">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.CustomAnnotation.html#pypath.core.annot.CustomAnnotation.counts">[docs]</a>
+    <span class="k">def</span> <span class="nf">counts</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">entity_type</span> <span class="o">=</span> <span class="s1">&#39;protein&#39;</span><span class="p">,</span> <span class="n">labels</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Returns a dict with number of elements in each class.</span>
+
+<span class="sd">        :param bool labels:</span>
+<span class="sd">            Use keys or labels as keys in the returned dict.</span>
+
+<span class="sd">        All other arguments passed to ``iter_classes``.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">return</span> <span class="nb">dict</span><span class="p">(</span>
+            <span class="p">(</span>
+                <span class="bp">cls</span><span class="o">.</span><span class="n">label</span> <span class="k">if</span> <span class="n">labels</span> <span class="k">else</span> <span class="bp">cls</span><span class="o">.</span><span class="n">key</span><span class="p">,</span>
+                <span class="bp">cls</span><span class="o">.</span><span class="n">count_entity_type</span><span class="p">(</span><span class="n">entity_type</span> <span class="o">=</span> <span class="n">entity_type</span><span class="p">)</span>
+            <span class="p">)</span>
+            <span class="k">for</span> <span class="bp">cls</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">iter_classes</span><span class="p">(</span><span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
+            <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="bp">cls</span><span class="p">)</span> <span class="o">&gt;</span> <span class="mi">0</span>
+        <span class="p">)</span></div>
+
+
+    <span class="c1"># synonym</span>
+    <span class="n">counts_by_class</span> <span class="o">=</span> <span class="n">counts</span>
+
+
+    <span class="k">def</span> <span class="nf">counts_df</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">groupby</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+
+        <span class="n">df</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">filtered</span><span class="p">(</span><span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
+
+        <span class="c1"># n.b. pandas is horrible, I can&#39;t understand how it could got</span>
+        <span class="c1"># released for production use, how one can build business on it???</span>
+        <span class="n">groupby</span> <span class="o">=</span> <span class="n">groupby</span> <span class="ow">or</span> <span class="p">[</span><span class="s1">&#39;category&#39;</span><span class="p">,</span> <span class="s1">&#39;parent&#39;</span><span class="p">,</span> <span class="s1">&#39;database&#39;</span><span class="p">]</span>
+        <span class="n">df</span> <span class="o">=</span> <span class="n">df</span><span class="o">.</span><span class="n">groupby</span><span class="p">(</span><span class="n">groupby</span><span class="p">)</span>
+        <span class="n">counts</span> <span class="o">=</span> <span class="n">df</span><span class="o">.</span><span class="n">uniprot</span><span class="o">.</span><span class="n">nunique</span><span class="p">()</span><span class="o">.</span><span class="n">reset_index</span><span class="p">()</span>
+        <span class="n">counts</span><span class="o">.</span><span class="n">rename</span><span class="p">(</span><span class="n">columns</span> <span class="o">=</span> <span class="p">{</span><span class="s1">&#39;uniprot&#39;</span><span class="p">:</span> <span class="s1">&#39;n_uniprot&#39;</span><span class="p">},</span> <span class="n">inplace</span> <span class="o">=</span> <span class="kc">True</span><span class="p">)</span>
+        <span class="n">df</span> <span class="o">=</span> <span class="n">df</span><span class="o">.</span><span class="n">agg</span><span class="p">(</span><span class="s1">&#39;head&#39;</span><span class="p">,</span> <span class="n">n</span> <span class="o">=</span> <span class="mi">1</span><span class="p">)</span><span class="o">.</span><span class="n">reset_index</span><span class="p">()</span>
+        <span class="n">df</span><span class="o">.</span><span class="n">drop</span><span class="p">(</span>
+            <span class="p">[</span><span class="s1">&#39;uniprot&#39;</span><span class="p">,</span> <span class="s1">&#39;entity_type&#39;</span><span class="p">,</span> <span class="s1">&#39;genesymbol&#39;</span><span class="p">,</span> <span class="s1">&#39;index&#39;</span><span class="p">],</span>
+            <span class="n">axis</span> <span class="o">=</span> <span class="mi">1</span><span class="p">,</span>
+            <span class="n">inplace</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
+        <span class="p">)</span>
+        <span class="n">df</span> <span class="o">=</span> <span class="n">df</span><span class="o">.</span><span class="n">merge</span><span class="p">(</span><span class="n">counts</span><span class="p">,</span> <span class="n">on</span> <span class="o">=</span> <span class="n">groupby</span><span class="p">)</span>
+
+        <span class="k">return</span> <span class="n">df</span>
+
+
+    <span class="k">def</span> <span class="nf">iter_classes</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">filter_classes</span><span class="p">(</span>
+            <span class="n">classes</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">classes</span><span class="o">.</span><span class="n">values</span><span class="p">(),</span>
+            <span class="o">**</span><span class="n">kwargs</span>
+        <span class="p">)</span>
+
+
+<div class="viewcode-block" id="CustomAnnotation.filter_classes">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.CustomAnnotation.html#pypath.core.annot.CustomAnnotation.filter_classes">[docs]</a>
+    <span class="nd">@staticmethod</span>
+    <span class="k">def</span> <span class="nf">filter_classes</span><span class="p">(</span><span class="n">classes</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Returns a list of annotation classes filtered by their attributes.</span>
+<span class="sd">        ``kwargs`` contains attributes and values.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">classes</span> <span class="o">=</span> <span class="n">classes</span>
+
+        <span class="k">return</span> <span class="p">(</span>
+            <span class="bp">cls</span>
+            <span class="k">for</span> <span class="bp">cls</span> <span class="ow">in</span> <span class="n">classes</span>
+            <span class="k">if</span> <span class="nb">all</span><span class="p">(</span>
+                <span class="n">common</span><span class="o">.</span><span class="n">eq</span><span class="p">(</span><span class="n">val</span><span class="p">,</span> <span class="nb">getattr</span><span class="p">(</span><span class="bp">cls</span><span class="p">,</span> <span class="n">attr</span><span class="p">))</span>
+                <span class="k">for</span> <span class="n">attr</span><span class="p">,</span> <span class="n">val</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="n">kwargs</span><span class="p">)</span>
+            <span class="p">)</span>
+        <span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="CustomAnnotation.filter">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.CustomAnnotation.html#pypath.core.annot.CustomAnnotation.filter">[docs]</a>
+    <span class="k">def</span> <span class="nf">filter</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">entity_type</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Filters the annotated entities by annotation class attributes and</span>
+<span class="sd">        ``entity_type``. ``kwargs`` passed to ``filter_classes``.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">return</span> <span class="nb">set</span><span class="p">(</span>
+            <span class="n">itertools</span><span class="o">.</span><span class="n">chain</span><span class="p">(</span><span class="o">*</span><span class="p">(</span>
+                <span class="bp">cls</span><span class="o">.</span><span class="n">filter_entity_type</span><span class="p">(</span><span class="n">entity_type</span> <span class="o">=</span> <span class="n">entity_type</span><span class="p">)</span>
+                <span class="k">for</span> <span class="bp">cls</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">iter_classes</span><span class="p">(</span><span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
+            <span class="p">))</span>
+        <span class="p">)</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">filter_entity_type</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="bp">cls</span><span class="p">,</span> <span class="n">entity_type</span> <span class="o">=</span> <span class="kc">None</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="bp">cls</span><span class="o">.</span><span class="n">filter_entity_type</span><span class="p">(</span><span class="n">entity_type</span> <span class="o">=</span> <span class="n">entity_type</span><span class="p">)</span>
+
+
+<div class="viewcode-block" id="CustomAnnotation.network_df">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.CustomAnnotation.html#pypath.core.annot.CustomAnnotation.network_df">[docs]</a>
+    <span class="k">def</span> <span class="nf">network_df</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">annot_df</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">network</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">combined_df</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">network_args</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">annot_args</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">annot_args_source</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">annot_args_target</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">entities</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">entities_source</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">entities_target</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">only_directed</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+            <span class="n">only_undirected</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+            <span class="n">only_signed</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">only_effect</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">only_proteins</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+            <span class="n">swap_undirected</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
+            <span class="n">undirected_orientation</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">entities_or</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+        <span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Combines the annotation data frame and a network data frame.</span>
+<span class="sd">        Creates a ``pandas.DataFrame`` where each record is an interaction</span>
+<span class="sd">        between a pair of molecular enitities labeled by their annotations.</span>
+
+<span class="sd">        network : pypath.network.Network,pandas.DataFrame</span>
+<span class="sd">            A ``pypath.network.Network`` object or a data frame with network</span>
+<span class="sd">            data.</span>
+<span class="sd">        combined_df : pandas.DataFrame</span>
+<span class="sd">            Optional, a network data frame already combined with annotations</span>
+<span class="sd">            for filtering only.</span>
+<span class="sd">        resources : set,None</span>
+<span class="sd">            Use only these network resources.</span>
+<span class="sd">        entities : set,None</span>
+<span class="sd">            Limit the network only to these molecular entities.</span>
+<span class="sd">        entities_source : set,None</span>
+<span class="sd">            Limit the source side of network connections only to these</span>
+<span class="sd">            molecular entities.</span>
+<span class="sd">        entities_target : set,None</span>
+<span class="sd">            Limit the target side of network connections only to these</span>
+<span class="sd">            molecular entities.</span>
+<span class="sd">        annot_args : dict,None</span>
+<span class="sd">            Parameters for filtering annotation classes; note, the defaults</span>
+<span class="sd">            might include some filtering, provide an empty dict if you want</span>
+<span class="sd">            no filtering at all; however this might result in huge data</span>
+<span class="sd">            frame and consequently memory issues. Passed to the ``filtered``</span>
+<span class="sd">            method.</span>
+<span class="sd">        annot_args_source : dict,None</span>
+<span class="sd">            Same as ``annot_args`` but only for the source side of the</span>
+<span class="sd">            network connections. These override ``annot_args`` but all the</span>
+<span class="sd">            criteria not defined here will be applied from ``annot_args``.</span>
+<span class="sd">        annot_args_target : dict,None</span>
+<span class="sd">            Same as ``annot_args`` but only for the target side of the</span>
+<span class="sd">            network connections. These override ``annot_args`` but all the</span>
+<span class="sd">            criteria not defined here will be applied from ``annot_args``.</span>
+<span class="sd">        only_directed : bool</span>
+<span class="sd">            Use only the directed interactions.</span>
+<span class="sd">        only_undirected : bool</span>
+<span class="sd">            Use only the undirected interactions. Specifically for retrieving</span>
+<span class="sd">            and counting the interactions without direction information.</span>
+<span class="sd">        only_effect : int,None</span>
+<span class="sd">            Use only the interactions with this effect. Either -1 or 1.</span>
+<span class="sd">        only_proteins : bool</span>
+<span class="sd">            Use only the interactions where each of the partners is a protein</span>
+<span class="sd">            (i.e. not complex, miRNA, small molecule or other kind of entity).</span>
+<span class="sd">        swap_undirected : bool</span>
+<span class="sd">            Convert undirected interactions to a pair of mutual interactions.</span>
+<span class="sd">        undirected_orientation : str,None</span>
+<span class="sd">            Ignore the direction at all interactions and make sure all of</span>
+<span class="sd">            them have a uniform orientation. If `id`, all interactions will</span>
+<span class="sd">            be oriented by the identifiers of the partenrs; if `category`,</span>
+<span class="sd">            the interactions will be oriented by the categories of the</span>
+<span class="sd">            partners.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">if</span> <span class="nb">hasattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">&#39;interclass_network&#39;</span><span class="p">):</span>
+
+            <span class="n">combined_df</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">interclass_network</span>
+
+        <span class="n">param_str</span> <span class="o">=</span> <span class="s1">&#39;, &#39;</span><span class="o">.</span><span class="n">join</span><span class="p">([</span>
+            <span class="s1">&#39;network_args=[</span><span class="si">%s</span><span class="s1">]&#39;</span> <span class="o">%</span> <span class="n">common</span><span class="o">.</span><span class="n">dict_str</span><span class="p">(</span><span class="n">network_args</span><span class="p">),</span>
+            <span class="s1">&#39;annot_args=[</span><span class="si">%s</span><span class="s1">]&#39;</span> <span class="o">%</span> <span class="n">common</span><span class="o">.</span><span class="n">dict_str</span><span class="p">(</span><span class="n">annot_args</span><span class="p">),</span>
+            <span class="s1">&#39;annot_args_source=[</span><span class="si">%s</span><span class="s1">]&#39;</span> <span class="o">%</span> <span class="n">common</span><span class="o">.</span><span class="n">dict_str</span><span class="p">(</span><span class="n">annot_args_source</span><span class="p">),</span>
+            <span class="s1">&#39;annot_args_target=[</span><span class="si">%s</span><span class="s1">]&#39;</span> <span class="o">%</span> <span class="n">common</span><span class="o">.</span><span class="n">dict_str</span><span class="p">(</span><span class="n">annot_args_target</span><span class="p">),</span>
+            <span class="s1">&#39;entities=</span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="n">common</span><span class="o">.</span><span class="n">none_or_len</span><span class="p">(</span><span class="n">entities</span><span class="p">),</span>
+            <span class="s1">&#39;entities_source=</span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="n">common</span><span class="o">.</span><span class="n">none_or_len</span><span class="p">(</span><span class="n">entities_source</span><span class="p">),</span>
+            <span class="s1">&#39;entities_target=</span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="n">common</span><span class="o">.</span><span class="n">none_or_len</span><span class="p">(</span><span class="n">entities_target</span><span class="p">),</span>
+            <span class="s1">&#39;only_directed=</span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="n">only_directed</span><span class="p">,</span>
+            <span class="s1">&#39;only_undirected=</span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="n">only_undirected</span><span class="p">,</span>
+            <span class="s1">&#39;only_signed=</span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="n">only_signed</span><span class="p">,</span>
+            <span class="s1">&#39;only_effect=</span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="n">only_effect</span><span class="p">,</span>
+            <span class="s1">&#39;only_proteins=</span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="n">only_proteins</span><span class="p">,</span>
+            <span class="s1">&#39;swap_undirected=</span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="n">swap_undirected</span><span class="p">,</span>
+            <span class="s1">&#39;entities_or=</span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="n">entities_or</span><span class="p">,</span>
+        <span class="p">])</span>
+
+        <span class="k">if</span> <span class="n">combined_df</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span>
+                <span class="s1">&#39;Using previously created network-annotation data frame. &#39;</span>
+                <span class="s1">&#39;Parameters </span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="n">param_str</span>
+            <span class="p">)</span>
+            <span class="n">network_df</span> <span class="o">=</span> <span class="kc">None</span>
+
+        <span class="k">else</span><span class="p">:</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span>
+                <span class="s1">&#39;Combining custom annotation with network data frame. &#39;</span>
+                <span class="s1">&#39;Parameters </span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="n">param_str</span>
+            <span class="p">)</span>
+
+            <span class="n">network_df</span> <span class="o">=</span> <span class="p">(</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">_network_df</span><span class="p">(</span><span class="n">network</span><span class="p">)</span>
+                    <span class="k">if</span> <span class="n">network</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span> <span class="k">else</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">network</span>
+            <span class="p">)</span>
+
+        <span class="k">if</span> <span class="n">network_df</span> <span class="ow">is</span> <span class="kc">None</span> <span class="ow">and</span> <span class="n">combined_df</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span><span class="s1">&#39;No network provided, no default network set.&#39;</span><span class="p">)</span>
+
+            <span class="k">return</span>
+
+        <span class="n">_network_args</span> <span class="o">=</span> <span class="p">{</span>
+            <span class="s1">&#39;only_proteins&#39;</span><span class="p">:</span> <span class="n">only_proteins</span><span class="p">,</span>
+            <span class="s1">&#39;only_effect&#39;</span><span class="p">:</span> <span class="n">only_effect</span><span class="p">,</span>
+            <span class="s1">&#39;only_signed&#39;</span><span class="p">:</span> <span class="n">only_signed</span><span class="p">,</span>
+            <span class="s1">&#39;only_directed&#39;</span><span class="p">:</span> <span class="n">only_directed</span><span class="p">,</span>
+            <span class="s1">&#39;only_undirected&#39;</span><span class="p">:</span> <span class="n">only_undirected</span><span class="p">,</span>
+            <span class="s1">&#39;entities&#39;</span><span class="p">:</span> <span class="n">entities</span><span class="p">,</span>
+            <span class="s1">&#39;source_entities&#39;</span><span class="p">:</span> <span class="n">entities_source</span><span class="p">,</span>
+            <span class="s1">&#39;target_entities&#39;</span><span class="p">:</span> <span class="n">entities_target</span><span class="p">,</span>
+            <span class="s1">&#39;swap_undirected&#39;</span><span class="p">:</span> <span class="n">swap_undirected</span><span class="p">,</span>
+            <span class="s1">&#39;entities_or&#39;</span><span class="p">:</span> <span class="n">entities_or</span><span class="p">,</span>
+        <span class="p">}</span>
+        <span class="n">_network_args</span><span class="o">.</span><span class="n">update</span><span class="p">(</span><span class="n">network_args</span> <span class="ow">or</span> <span class="p">{})</span>
+
+        <span class="k">if</span> <span class="ow">not</span> <span class="n">entities_or</span><span class="p">:</span>
+
+            <span class="n">entities_source</span> <span class="o">=</span> <span class="n">entities_source</span> <span class="ow">or</span> <span class="n">entities</span> <span class="ow">or</span> <span class="nb">set</span><span class="p">()</span>
+            <span class="n">entities_target</span> <span class="o">=</span> <span class="n">entities_target</span> <span class="ow">or</span> <span class="n">entities</span> <span class="ow">or</span> <span class="nb">set</span><span class="p">()</span>
+
+        <span class="n">_annot_args_source</span> <span class="o">=</span> <span class="p">(</span><span class="n">annot_args</span> <span class="ow">or</span> <span class="p">{})</span><span class="o">.</span><span class="n">copy</span><span class="p">()</span>
+        <span class="n">_annot_args_source</span><span class="o">.</span><span class="n">update</span><span class="p">(</span><span class="n">annot_args_source</span><span class="p">)</span>
+        <span class="n">_annot_args_source</span><span class="p">[</span><span class="s1">&#39;entities&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">entities_source</span>
+        <span class="n">_annot_args_target</span> <span class="o">=</span> <span class="p">(</span><span class="n">annot_args</span> <span class="ow">or</span> <span class="p">{})</span><span class="o">.</span><span class="n">copy</span><span class="p">()</span>
+        <span class="n">_annot_args_target</span><span class="o">.</span><span class="n">update</span><span class="p">(</span><span class="n">annot_args_target</span><span class="p">)</span>
+        <span class="n">_annot_args_target</span><span class="p">[</span><span class="s1">&#39;entities&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">entities_target</span>
+
+        <span class="k">if</span> <span class="n">only_proteins</span><span class="p">:</span>
+
+            <span class="n">_annot_args_source</span><span class="p">[</span><span class="s1">&#39;entity_type&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="s1">&#39;protein&#39;</span>
+            <span class="n">_annot_args_target</span><span class="p">[</span><span class="s1">&#39;entity_type&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="s1">&#39;protein&#39;</span>
+
+        <span class="k">if</span> <span class="n">combined_df</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
+
+            <span class="n">network_df</span> <span class="o">=</span> <span class="n">core_common</span><span class="o">.</span><span class="n">filter_network_df</span><span class="p">(</span>
+                <span class="n">df</span> <span class="o">=</span> <span class="n">network_df</span><span class="p">,</span>
+                <span class="o">**</span><span class="n">_network_args</span>
+            <span class="p">)</span>
+            <span class="n">annot_df_source</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">filtered</span><span class="p">(</span>
+                <span class="n">annot_df</span> <span class="o">=</span> <span class="n">annot_df</span><span class="p">,</span>
+                <span class="o">**</span><span class="n">_annot_args_source</span>
+            <span class="p">)</span>
+            <span class="n">annot_df_target</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">filtered</span><span class="p">(</span>
+                <span class="n">annot_df</span> <span class="o">=</span> <span class="n">annot_df</span><span class="p">,</span>
+                <span class="o">**</span><span class="n">_annot_args_target</span>
+            <span class="p">)</span>
+
+            <span class="n">annot_network_df</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">merge</span><span class="p">(</span>
+                <span class="n">network_df</span><span class="p">,</span>
+                <span class="n">annot_df_source</span><span class="p">,</span>
+                <span class="n">suffixes</span> <span class="o">=</span> <span class="p">[</span><span class="s1">&#39;&#39;</span><span class="p">,</span> <span class="s1">&#39;_a&#39;</span><span class="p">],</span>
+                <span class="n">how</span> <span class="o">=</span> <span class="s1">&#39;inner&#39;</span><span class="p">,</span>
+                <span class="n">left_on</span> <span class="o">=</span> <span class="s1">&#39;id_a&#39;</span><span class="p">,</span>
+                <span class="n">right_on</span> <span class="o">=</span> <span class="s1">&#39;uniprot&#39;</span><span class="p">,</span>
+            <span class="p">)</span>
+
+            <span class="n">annot_network_df</span><span class="o">.</span><span class="n">id_a</span> <span class="o">=</span> <span class="n">annot_network_df</span><span class="o">.</span><span class="n">id_a</span><span class="o">.</span><span class="n">astype</span><span class="p">(</span><span class="s1">&#39;category&#39;</span><span class="p">)</span>
+
+            <span class="n">annot_network_df</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">merge</span><span class="p">(</span>
+                <span class="n">annot_network_df</span><span class="p">,</span>
+                <span class="n">annot_df_target</span><span class="p">,</span>
+                <span class="n">suffixes</span> <span class="o">=</span> <span class="p">[</span><span class="s1">&#39;_a&#39;</span><span class="p">,</span> <span class="s1">&#39;_b&#39;</span><span class="p">],</span>
+                <span class="n">how</span> <span class="o">=</span> <span class="s1">&#39;inner&#39;</span><span class="p">,</span>
+                <span class="n">left_on</span> <span class="o">=</span> <span class="s1">&#39;id_b&#39;</span><span class="p">,</span>
+                <span class="n">right_on</span> <span class="o">=</span> <span class="s1">&#39;uniprot&#39;</span><span class="p">,</span>
+            <span class="p">)</span>
+
+            <span class="n">annot_network_df</span><span class="o">.</span><span class="n">id_b</span> <span class="o">=</span> <span class="n">annot_network_df</span><span class="o">.</span><span class="n">id_b</span><span class="o">.</span><span class="n">astype</span><span class="p">(</span><span class="s1">&#39;category&#39;</span><span class="p">)</span>
+
+            <span class="c1"># these columns are duplicates</span>
+            <span class="n">annot_network_df</span><span class="o">.</span><span class="n">drop</span><span class="p">(</span>
+                <span class="n">labels</span> <span class="o">=</span> <span class="p">[</span><span class="s1">&#39;type_a&#39;</span><span class="p">,</span> <span class="s1">&#39;type_b&#39;</span><span class="p">,</span> <span class="s1">&#39;uniprot_a&#39;</span><span class="p">,</span> <span class="s1">&#39;uniprot_b&#39;</span><span class="p">],</span>
+                <span class="n">inplace</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
+                <span class="n">axis</span> <span class="o">=</span> <span class="s1">&#39;columns&#39;</span><span class="p">,</span>
+            <span class="p">)</span>
+
+        <span class="k">else</span><span class="p">:</span>
+
+            <span class="n">combined_df</span> <span class="o">=</span> <span class="n">core_common</span><span class="o">.</span><span class="n">filter_network_df</span><span class="p">(</span>
+                <span class="n">df</span> <span class="o">=</span> <span class="n">combined_df</span><span class="p">,</span>
+                <span class="o">**</span><span class="n">_network_args</span>
+            <span class="p">)</span>
+            <span class="n">combined_df</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">filtered</span><span class="p">(</span>
+                <span class="n">annot_df</span> <span class="o">=</span> <span class="n">combined_df</span><span class="p">,</span>
+                <span class="n">postfix</span> <span class="o">=</span> <span class="s1">&#39;_a&#39;</span><span class="p">,</span>
+                <span class="o">**</span><span class="n">_annot_args_source</span>
+            <span class="p">)</span>
+            <span class="n">combined_df</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">filtered</span><span class="p">(</span>
+                <span class="n">annot_df</span> <span class="o">=</span> <span class="n">combined_df</span><span class="p">,</span>
+                <span class="n">postfix</span> <span class="o">=</span> <span class="s1">&#39;_b&#39;</span><span class="p">,</span>
+                <span class="o">**</span><span class="n">_annot_args_target</span>
+            <span class="p">)</span>
+
+            <span class="n">annot_network_df</span> <span class="o">=</span> <span class="n">combined_df</span>
+
+        <span class="k">if</span> <span class="n">undirected_orientation</span><span class="p">:</span>
+
+            <span class="c1"># which columns we consider for the orientation</span>
+            <span class="n">by</span> <span class="o">=</span> <span class="n">undirected_orientation</span>
+            <span class="n">by</span> <span class="o">=</span> <span class="n">by</span> <span class="k">if</span> <span class="n">by</span> <span class="ow">in</span> <span class="p">{</span><span class="s1">&#39;id&#39;</span><span class="p">,</span> <span class="s1">&#39;category&#39;</span><span class="p">}</span> <span class="k">else</span> <span class="s1">&#39;category&#39;</span>
+            <span class="n">by_col_a</span> <span class="o">=</span> <span class="nb">getattr</span><span class="p">(</span><span class="n">annot_network_df</span><span class="p">,</span> <span class="s1">&#39;</span><span class="si">%s</span><span class="s1">_a&#39;</span> <span class="o">%</span> <span class="n">by</span><span class="p">)</span>
+            <span class="n">by_col_b</span> <span class="o">=</span> <span class="nb">getattr</span><span class="p">(</span><span class="n">annot_network_df</span><span class="p">,</span> <span class="s1">&#39;</span><span class="si">%s</span><span class="s1">_b&#39;</span> <span class="o">%</span> <span class="n">by</span><span class="p">)</span>
+            <span class="c1"># indices of the records with the wrong orientation</span>
+            <span class="n">idx_wrong_orient</span> <span class="o">=</span> <span class="p">[</span><span class="n">a</span> <span class="o">&gt;</span> <span class="n">b</span> <span class="k">for</span> <span class="n">a</span><span class="p">,</span> <span class="n">b</span> <span class="ow">in</span> <span class="nb">zip</span><span class="p">(</span><span class="n">by_col_a</span><span class="p">,</span> <span class="n">by_col_b</span><span class="p">)]</span>
+            <span class="c1"># split the data frame</span>
+            <span class="n">wrong_orient</span> <span class="o">=</span> <span class="n">annot_network_df</span><span class="o">.</span><span class="n">iloc</span><span class="p">[</span><span class="n">idx_wrong_orient</span><span class="p">]</span><span class="o">.</span><span class="n">copy</span><span class="p">()</span>
+            <span class="n">good_orient</span> <span class="o">=</span> <span class="n">annot_network_df</span><span class="o">.</span><span class="n">iloc</span><span class="p">[</span>
+                <span class="n">np</span><span class="o">.</span><span class="n">logical_not</span><span class="p">(</span><span class="n">idx_wrong_orient</span><span class="p">)</span>
+            <span class="p">]</span><span class="o">.</span><span class="n">copy</span><span class="p">()</span>
+            <span class="n">column_order</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="n">annot_network_df</span><span class="o">.</span><span class="n">columns</span><span class="p">)</span>
+            <span class="c1"># swap the orientation</span>
+            <span class="n">column_map</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">(</span>
+                <span class="p">(</span>
+                    <span class="n">col</span><span class="p">,</span>
+                    <span class="n">common</span><span class="o">.</span><span class="n">swap_suffix</span><span class="p">(</span><span class="n">col</span><span class="p">)</span>
+                <span class="p">)</span>
+                <span class="k">for</span> <span class="n">col</span> <span class="ow">in</span> <span class="n">column_order</span>
+            <span class="p">)</span>
+            <span class="n">wrong_orient</span> <span class="o">=</span> <span class="n">wrong_orient</span><span class="o">.</span><span class="n">rename</span><span class="p">(</span><span class="n">columns</span> <span class="o">=</span> <span class="n">column_map</span><span class="p">)</span>
+            <span class="c1"># make sure the column order is correct</span>
+            <span class="n">wrong_orient</span> <span class="o">=</span> <span class="n">wrong_orient</span><span class="p">[</span><span class="n">column_order</span><span class="p">]</span>
+            <span class="c1"># concatenate the slices</span>
+            <span class="n">orientation_swapped</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">concat</span><span class="p">([</span><span class="n">good_orient</span><span class="p">,</span> <span class="n">wrong_orient</span><span class="p">])</span>
+            <span class="n">orientation_swapped</span> <span class="o">=</span> <span class="n">orientation_swapped</span><span class="o">.</span><span class="n">drop_duplicates</span><span class="p">(</span>
+                <span class="n">subset</span> <span class="o">=</span> <span class="p">[</span>
+                    <span class="s1">&#39;id_a&#39;</span><span class="p">,</span>
+                    <span class="s1">&#39;id_b&#39;</span><span class="p">,</span>
+                    <span class="s1">&#39;type&#39;</span><span class="p">,</span>
+                    <span class="s1">&#39;category_a&#39;</span><span class="p">,</span>
+                    <span class="s1">&#39;category_b&#39;</span><span class="p">,</span>
+                    <span class="s1">&#39;parent_a&#39;</span><span class="p">,</span>
+                    <span class="s1">&#39;parent_b&#39;</span><span class="p">,</span>
+                    <span class="s1">&#39;source_a&#39;</span><span class="p">,</span>
+                    <span class="s1">&#39;source_b&#39;</span><span class="p">,</span>
+                    <span class="s1">&#39;scope_a&#39;</span><span class="p">,</span>
+                    <span class="s1">&#39;scope_b&#39;</span><span class="p">,</span>
+                    <span class="s1">&#39;entity_type_a&#39;</span><span class="p">,</span>
+                    <span class="s1">&#39;entity_type_b&#39;</span><span class="p">,</span>
+                <span class="p">]</span>
+            <span class="p">)</span>
+            <span class="c1"># removing direction and effect columns</span>
+            <span class="c1"># as they are not valid any more</span>
+            <span class="n">orientation_swapped</span><span class="o">.</span><span class="n">drop</span><span class="p">(</span>
+                <span class="p">[</span><span class="s1">&#39;directed&#39;</span><span class="p">,</span> <span class="s1">&#39;effect&#39;</span><span class="p">],</span>
+                <span class="n">axis</span> <span class="o">=</span> <span class="mi">1</span><span class="p">,</span>
+                <span class="n">inplace</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
+            <span class="p">)</span>
+            <span class="n">annot_network_df</span> <span class="o">=</span> <span class="n">orientation_swapped</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span>
+            <span class="s1">&#39;Combined custom annotation data frame with network data frame. &#39;</span>
+            <span class="s1">&#39;Memory usage: </span><span class="si">%s</span><span class="s1">.&#39;</span> <span class="o">%</span> <span class="n">common</span><span class="o">.</span><span class="n">df_memory_usage</span><span class="p">(</span><span class="n">annot_network_df</span><span class="p">)</span>
+        <span class="p">)</span>
+
+        <span class="k">return</span> <span class="n">annot_network_df</span></div>
+
+
+
+    <span class="c1"># this became a synonym</span>
+    <span class="n">filter_interclass_network</span> <span class="o">=</span> <span class="n">network_df</span>
+
+
+<div class="viewcode-block" id="CustomAnnotation.set_interclass_network_df">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.CustomAnnotation.html#pypath.core.annot.CustomAnnotation.set_interclass_network_df">[docs]</a>
+    <span class="k">def</span> <span class="nf">set_interclass_network_df</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Creates a data frame of the whole inter-class network and keeps it</span>
+<span class="sd">        assigned to the instance in order to make subsequent queries faster.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">unset_interclass_network_df</span><span class="p">()</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">interclass_network</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">get_interclass_network_df</span><span class="p">(</span><span class="o">**</span><span class="n">kwargs</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="CustomAnnotation.get_interclass_network_df">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.CustomAnnotation.html#pypath.core.annot.CustomAnnotation.get_interclass_network_df">[docs]</a>
+    <span class="k">def</span> <span class="nf">get_interclass_network_df</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        If the an interclass network is already present the ``network``</span>
+<span class="sd">        and other ``kwargs`` provided not considered. Otherwise these</span>
+<span class="sd">        are passed to ``network_df``.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">return</span> <span class="p">(</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">interclass_network</span>
+                <span class="k">if</span> <span class="nb">hasattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">&#39;interclass_network&#39;</span><span class="p">)</span> <span class="k">else</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">network_df</span><span class="p">(</span><span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
+        <span class="p">)</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">unset_interclass_network_df</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">if</span> <span class="nb">hasattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">&#39;interclass_network&#39;</span><span class="p">):</span>
+
+            <span class="k">del</span> <span class="bp">self</span><span class="o">.</span><span class="n">interclass_network</span>
+
+
+    <span class="c1">#</span>
+    <span class="c1"># Below only thin wrappers to make the interface more intuitive</span>
+    <span class="c1"># without knowing the argument names</span>
+    <span class="c1">#</span>
+
+    <span class="c1">#</span>
+    <span class="c1"># Building a network of connections between classes</span>
+    <span class="c1">#</span>
+
+    <span class="k">def</span> <span class="nf">inter_class_network</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">annot_args_source</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">annot_args_target</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">network</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="o">**</span><span class="n">kwargs</span>
+        <span class="p">):</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">network_df</span><span class="p">(</span>
+            <span class="n">network</span> <span class="o">=</span> <span class="n">network</span><span class="p">,</span>
+            <span class="n">annot_args_source</span> <span class="o">=</span> <span class="n">annot_args_source</span><span class="p">,</span>
+            <span class="n">annot_args_target</span> <span class="o">=</span> <span class="n">annot_args_target</span><span class="p">,</span>
+            <span class="o">**</span><span class="n">kwargs</span>
+        <span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">inter_class_network_undirected</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">annot_args_source</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">annot_args_target</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">network</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="o">**</span><span class="n">kwargs</span>
+        <span class="p">):</span>
+
+        <span class="n">kwargs</span><span class="o">.</span><span class="n">update</span><span class="p">({</span><span class="s1">&#39;only_undirected&#39;</span><span class="p">:</span> <span class="kc">True</span><span class="p">})</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">network_df</span><span class="p">(</span>
+            <span class="n">network</span> <span class="o">=</span> <span class="n">network</span><span class="p">,</span>
+            <span class="n">annot_args_source</span> <span class="o">=</span> <span class="n">annot_args_source</span><span class="p">,</span>
+            <span class="n">annot_args_target</span> <span class="o">=</span> <span class="n">annot_args_target</span><span class="p">,</span>
+            <span class="o">**</span><span class="n">kwargs</span>
+        <span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">inter_class_network_directed</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">annot_args_source</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">annot_args_target</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">network</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="o">**</span><span class="n">kwargs</span>
+        <span class="p">):</span>
+
+        <span class="n">kwargs</span><span class="o">.</span><span class="n">update</span><span class="p">({</span><span class="s1">&#39;only_directed&#39;</span><span class="p">:</span> <span class="kc">True</span><span class="p">})</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">network_df</span><span class="p">(</span>
+            <span class="n">network</span> <span class="o">=</span> <span class="n">network</span><span class="p">,</span>
+            <span class="n">annot_args_source</span> <span class="o">=</span> <span class="n">annot_args_source</span><span class="p">,</span>
+            <span class="n">annot_args_target</span> <span class="o">=</span> <span class="n">annot_args_target</span><span class="p">,</span>
+            <span class="o">**</span><span class="n">kwargs</span>
+        <span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">inter_class_network_signed</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">annot_args_source</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">annot_args_target</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">network</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="o">**</span><span class="n">kwargs</span>
+        <span class="p">):</span>
+
+        <span class="n">kwargs</span><span class="o">.</span><span class="n">update</span><span class="p">({</span><span class="s1">&#39;only_signed&#39;</span><span class="p">:</span> <span class="kc">True</span><span class="p">})</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">network_df</span><span class="p">(</span>
+            <span class="n">network</span> <span class="o">=</span> <span class="n">network</span><span class="p">,</span>
+            <span class="n">annot_args_source</span> <span class="o">=</span> <span class="n">annot_args_source</span><span class="p">,</span>
+            <span class="n">annot_args_target</span> <span class="o">=</span> <span class="n">annot_args_target</span><span class="p">,</span>
+            <span class="o">**</span><span class="n">kwargs</span>
+        <span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">inter_class_network_stimulatory</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">annot_args_source</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">annot_args_target</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">network</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="o">**</span><span class="n">kwargs</span>
+        <span class="p">):</span>
+
+        <span class="n">kwargs</span><span class="o">.</span><span class="n">update</span><span class="p">({</span>
+            <span class="s1">&#39;only_directed&#39;</span><span class="p">:</span> <span class="kc">True</span><span class="p">,</span>
+            <span class="s1">&#39;only_effect&#39;</span><span class="p">:</span> <span class="mi">1</span><span class="p">,</span>
+        <span class="p">})</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">network_df</span><span class="p">(</span>
+            <span class="n">network</span> <span class="o">=</span> <span class="n">network</span><span class="p">,</span>
+            <span class="n">annot_args_source</span> <span class="o">=</span> <span class="n">annot_args_source</span><span class="p">,</span>
+            <span class="n">annot_args_target</span> <span class="o">=</span> <span class="n">annot_args_target</span><span class="p">,</span>
+            <span class="o">**</span><span class="n">kwargs</span>
+        <span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">inter_class_network_inhibitory</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">annot_args_source</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">annot_args_target</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">network</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="o">**</span><span class="n">kwargs</span>
+        <span class="p">):</span>
+
+        <span class="n">kwargs</span><span class="o">.</span><span class="n">update</span><span class="p">({</span>
+            <span class="s1">&#39;only_directed&#39;</span><span class="p">:</span> <span class="kc">True</span><span class="p">,</span>
+            <span class="s1">&#39;only_effect&#39;</span><span class="p">:</span> <span class="o">-</span><span class="mi">1</span><span class="p">,</span>
+        <span class="p">})</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">network_df</span><span class="p">(</span>
+            <span class="n">network</span> <span class="o">=</span> <span class="n">network</span><span class="p">,</span>
+            <span class="n">annot_args_source</span> <span class="o">=</span> <span class="n">annot_args_source</span><span class="p">,</span>
+            <span class="n">annot_args_target</span> <span class="o">=</span> <span class="n">annot_args_target</span><span class="p">,</span>
+            <span class="o">**</span><span class="n">kwargs</span>
+        <span class="p">)</span>
+
+    <span class="c1">#</span>
+    <span class="c1"># Counting connections between classes (total)</span>
+    <span class="c1">#</span>
+
+    <span class="k">def</span> <span class="nf">count_inter_class_connections</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">annot_args_source</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">annot_args_target</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="o">**</span><span class="n">kwargs</span>
+        <span class="p">):</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">inter_class_network</span><span class="p">(</span>
+            <span class="n">annot_args_source</span> <span class="o">=</span> <span class="n">annot_args_source</span><span class="p">,</span>
+            <span class="n">annot_args_target</span> <span class="o">=</span> <span class="n">annot_args_target</span><span class="p">,</span>
+            <span class="o">**</span><span class="n">kwargs</span>
+        <span class="p">)</span><span class="o">.</span><span class="n">groupby</span><span class="p">([</span><span class="s1">&#39;id_a&#39;</span><span class="p">,</span> <span class="s1">&#39;id_b&#39;</span><span class="p">],</span> <span class="n">as_index</span> <span class="o">=</span> <span class="kc">False</span><span class="p">)</span><span class="o">.</span><span class="n">ngroups</span>
+
+
+    <span class="c1"># synonym</span>
+    <span class="n">count_inter_class_connections_all</span> <span class="o">=</span> <span class="n">count_inter_class_connections</span>
+
+
+    <span class="k">def</span> <span class="nf">count_inter_class_connections_undirected</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">annot_args_source</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">annot_args_target</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="o">**</span><span class="n">kwargs</span>
+        <span class="p">):</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">inter_class_network_undirected</span><span class="p">(</span>
+            <span class="n">annot_args_source</span> <span class="o">=</span> <span class="n">annot_args_source</span><span class="p">,</span>
+            <span class="n">annot_args_target</span> <span class="o">=</span> <span class="n">annot_args_target</span><span class="p">,</span>
+            <span class="o">**</span><span class="n">kwargs</span>
+        <span class="p">)</span><span class="o">.</span><span class="n">groupby</span><span class="p">([</span><span class="s1">&#39;id_a&#39;</span><span class="p">,</span> <span class="s1">&#39;id_b&#39;</span><span class="p">],</span> <span class="n">as_index</span> <span class="o">=</span> <span class="kc">False</span><span class="p">)</span><span class="o">.</span><span class="n">ngroups</span>
+
+
+    <span class="k">def</span> <span class="nf">count_inter_class_connections_directed</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">annot_args_source</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">annot_args_target</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="o">**</span><span class="n">kwargs</span>
+        <span class="p">):</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">inter_class_network_directed</span><span class="p">(</span>
+            <span class="n">annot_args_source</span> <span class="o">=</span> <span class="n">annot_args_source</span><span class="p">,</span>
+            <span class="n">annot_args_target</span> <span class="o">=</span> <span class="n">annot_args_target</span><span class="p">,</span>
+            <span class="o">**</span><span class="n">kwargs</span>
+        <span class="p">)</span><span class="o">.</span><span class="n">groupby</span><span class="p">([</span><span class="s1">&#39;id_a&#39;</span><span class="p">,</span> <span class="s1">&#39;id_b&#39;</span><span class="p">],</span> <span class="n">as_index</span> <span class="o">=</span> <span class="kc">False</span><span class="p">)</span><span class="o">.</span><span class="n">ngroups</span>
+
+
+    <span class="k">def</span> <span class="nf">count_inter_class_connections_signed</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">annot_args_source</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">annot_args_target</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="o">**</span><span class="n">kwargs</span>
+        <span class="p">):</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">inter_class_network_signed</span><span class="p">(</span>
+            <span class="n">annot_args_source</span> <span class="o">=</span> <span class="n">annot_args_source</span><span class="p">,</span>
+            <span class="n">annot_args_target</span> <span class="o">=</span> <span class="n">annot_args_target</span><span class="p">,</span>
+            <span class="o">**</span><span class="n">kwargs</span>
+        <span class="p">)</span><span class="o">.</span><span class="n">groupby</span><span class="p">([</span><span class="s1">&#39;id_a&#39;</span><span class="p">,</span> <span class="s1">&#39;id_b&#39;</span><span class="p">],</span> <span class="n">as_index</span> <span class="o">=</span> <span class="kc">False</span><span class="p">)</span><span class="o">.</span><span class="n">ngroups</span>
+
+
+    <span class="k">def</span> <span class="nf">count_inter_class_connections_stimulatory</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">annot_args_source</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">annot_args_target</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="o">**</span><span class="n">kwargs</span>
+        <span class="p">):</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">inter_class_network_stimulatory</span><span class="p">(</span>
+            <span class="n">annot_args_source</span> <span class="o">=</span> <span class="n">annot_args_source</span><span class="p">,</span>
+            <span class="n">annot_args_target</span> <span class="o">=</span> <span class="n">annot_args_target</span><span class="p">,</span>
+            <span class="o">**</span><span class="n">kwargs</span>
+        <span class="p">)</span><span class="o">.</span><span class="n">groupby</span><span class="p">([</span><span class="s1">&#39;id_a&#39;</span><span class="p">,</span> <span class="s1">&#39;id_b&#39;</span><span class="p">],</span> <span class="n">as_index</span> <span class="o">=</span> <span class="kc">False</span><span class="p">)</span><span class="o">.</span><span class="n">ngroups</span>
+
+
+    <span class="k">def</span> <span class="nf">count_inter_class_connections_inhibitory</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">annot_args_source</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">annot_args_target</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="o">**</span><span class="n">kwargs</span>
+        <span class="p">):</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">inter_class_network_inhibitory</span><span class="p">(</span>
+            <span class="n">annot_args_source</span> <span class="o">=</span> <span class="n">annot_args_source</span><span class="p">,</span>
+            <span class="n">annot_args_target</span> <span class="o">=</span> <span class="n">annot_args_target</span><span class="p">,</span>
+            <span class="o">**</span><span class="n">kwargs</span>
+        <span class="p">)</span><span class="o">.</span><span class="n">groupby</span><span class="p">([</span><span class="s1">&#39;id_a&#39;</span><span class="p">,</span> <span class="s1">&#39;id_b&#39;</span><span class="p">],</span> <span class="n">as_index</span> <span class="o">=</span> <span class="kc">False</span><span class="p">)</span><span class="o">.</span><span class="n">ngroups</span>
+
+
+    <span class="c1">#</span>
+    <span class="c1"># Class to class connection counts</span>
+    <span class="c1">#</span>
+
+<div class="viewcode-block" id="CustomAnnotation.class_to_class_connections">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.CustomAnnotation.html#pypath.core.annot.CustomAnnotation.class_to_class_connections">[docs]</a>
+    <span class="k">def</span> <span class="nf">class_to_class_connections</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        ``kwargs`` passed to ``filter_interclass_network``.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">network</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">network_df</span><span class="p">(</span><span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span><span class="s1">&#39;Counting connections between classes.&#39;</span><span class="p">)</span>
+
+        <span class="k">return</span> <span class="p">(</span>
+            <span class="n">network</span><span class="o">.</span><span class="n">groupby</span><span class="p">(</span>
+                <span class="p">[</span><span class="s1">&#39;category_a&#39;</span><span class="p">,</span> <span class="s1">&#39;category_b&#39;</span><span class="p">,</span> <span class="s1">&#39;id_a&#39;</span><span class="p">,</span> <span class="s1">&#39;id_b&#39;</span><span class="p">]</span>
+            <span class="p">)</span><span class="o">.</span><span class="n">size</span><span class="p">()</span><span class="o">.</span><span class="n">groupby</span><span class="p">(</span>
+                <span class="n">level</span> <span class="o">=</span> <span class="p">[</span><span class="s1">&#39;category_a&#39;</span><span class="p">,</span> <span class="s1">&#39;category_b&#39;</span><span class="p">]</span>
+            <span class="p">)</span><span class="o">.</span><span class="n">size</span><span class="p">()</span>
+        <span class="p">)</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">class_to_class_connections_undirected</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+
+        <span class="n">param</span> <span class="o">=</span> <span class="p">{</span>
+            <span class="s1">&#39;only_undirected&#39;</span><span class="p">:</span> <span class="kc">True</span><span class="p">,</span>
+        <span class="p">}</span>
+        <span class="n">kwargs</span><span class="o">.</span><span class="n">update</span><span class="p">(</span><span class="n">param</span><span class="p">)</span>
+
+        <span class="n">c2c</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">class_to_class_connections</span><span class="p">(</span><span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
+
+        <span class="n">c2c_rev</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">(</span>
+            <span class="p">(</span>
+                <span class="p">(</span><span class="n">cls1</span><span class="p">,</span> <span class="n">cls0</span><span class="p">),</span>
+                <span class="n">val</span>
+            <span class="p">)</span>
+            <span class="k">for</span> <span class="p">(</span><span class="n">cls0</span><span class="p">,</span> <span class="n">cls1</span><span class="p">),</span> <span class="n">val</span> <span class="ow">in</span> <span class="nb">zip</span><span class="p">(</span><span class="n">c2c</span><span class="o">.</span><span class="n">index</span><span class="p">,</span> <span class="n">c2c</span><span class="p">)</span>
+            <span class="k">if</span> <span class="n">cls0</span> <span class="o">!=</span> <span class="n">cls1</span>
+        <span class="p">)</span>
+
+        <span class="k">return</span> <span class="n">common</span><span class="o">.</span><span class="n">sum_dicts</span><span class="p">(</span><span class="n">c2c</span><span class="p">,</span> <span class="n">c2c_rev</span><span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">class_to_class_connections_directed</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+
+        <span class="n">param</span> <span class="o">=</span> <span class="p">{</span>
+            <span class="s1">&#39;only_directed&#39;</span><span class="p">:</span> <span class="kc">True</span><span class="p">,</span>
+        <span class="p">}</span>
+        <span class="n">kwargs</span><span class="o">.</span><span class="n">update</span><span class="p">(</span><span class="n">param</span><span class="p">)</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">class_to_class_connections</span><span class="p">(</span><span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">class_to_class_connections_signed</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+
+        <span class="n">param</span> <span class="o">=</span> <span class="p">{</span>
+            <span class="s1">&#39;only_signed&#39;</span><span class="p">:</span> <span class="kc">True</span><span class="p">,</span>
+        <span class="p">}</span>
+        <span class="n">kwargs</span><span class="o">.</span><span class="n">update</span><span class="p">(</span><span class="n">param</span><span class="p">)</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">class_to_class_connections</span><span class="p">(</span><span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">class_to_class_connections_stimulatory</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+
+        <span class="n">param</span> <span class="o">=</span> <span class="p">{</span>
+            <span class="s1">&#39;only_effect&#39;</span><span class="p">:</span> <span class="mi">1</span><span class="p">,</span>
+        <span class="p">}</span>
+        <span class="n">kwargs</span><span class="o">.</span><span class="n">update</span><span class="p">(</span><span class="n">param</span><span class="p">)</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">class_to_class_connections</span><span class="p">(</span><span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">class_to_class_connections_inhibitory</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+
+        <span class="n">param</span> <span class="o">=</span> <span class="p">{</span>
+            <span class="s1">&#39;only_effect&#39;</span><span class="p">:</span> <span class="o">-</span><span class="mi">1</span><span class="p">,</span>
+        <span class="p">}</span>
+        <span class="n">kwargs</span><span class="o">.</span><span class="n">update</span><span class="p">(</span><span class="n">param</span><span class="p">)</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">class_to_class_connections</span><span class="p">(</span><span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
+
+
+    <span class="c1">#</span>
+    <span class="c1"># Inter-class degrees</span>
+    <span class="c1">#</span>
+
+<div class="viewcode-block" id="CustomAnnotation.degree_inter_class_network">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.CustomAnnotation.html#pypath.core.annot.CustomAnnotation.degree_inter_class_network">[docs]</a>
+    <span class="k">def</span> <span class="nf">degree_inter_class_network</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">annot_args_source</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">annot_args_target</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">degrees_of</span> <span class="o">=</span> <span class="s1">&#39;target&#39;</span><span class="p">,</span>
+            <span class="o">**</span><span class="n">kwargs</span>
+        <span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        degrees_of : str</span>
+<span class="sd">            Either *source* or *target*. Count the degrees for the source</span>
+<span class="sd">            or the target class.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">id_cols</span> <span class="o">=</span> <span class="p">(</span><span class="s1">&#39;id_a&#39;</span><span class="p">,</span> <span class="s1">&#39;id_b&#39;</span><span class="p">)</span>
+        <span class="n">groupby</span><span class="p">,</span> <span class="n">unique</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="n">id_cols</span>
+                <span class="k">if</span> <span class="n">degrees_of</span> <span class="o">==</span> <span class="s1">&#39;source&#39;</span> <span class="k">else</span>
+            <span class="nb">reversed</span><span class="p">(</span><span class="n">id_cols</span><span class="p">)</span>
+        <span class="p">)</span>
+
+        <span class="n">degrees</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">inter_class_network</span><span class="p">(</span>
+                <span class="n">annot_args_source</span> <span class="o">=</span> <span class="n">annot_args_source</span><span class="p">,</span>
+                <span class="n">annot_args_target</span> <span class="o">=</span> <span class="n">annot_args_target</span><span class="p">,</span>
+                <span class="o">**</span><span class="n">kwargs</span>
+            <span class="p">)</span><span class="o">.</span><span class="n">groupby</span><span class="p">(</span><span class="n">groupby</span><span class="p">)[</span><span class="n">unique</span><span class="p">]</span><span class="o">.</span><span class="n">nunique</span><span class="p">()</span>
+        <span class="p">)</span>
+
+        <span class="k">return</span> <span class="n">degrees</span><span class="p">[</span><span class="n">degrees</span> <span class="o">!=</span> <span class="mi">0</span><span class="p">]</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">degree_inter_class_network_undirected</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">annot_args_source</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">annot_args_target</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="o">**</span><span class="n">kwargs</span>
+        <span class="p">):</span>
+
+        <span class="n">kwargs</span><span class="o">.</span><span class="n">update</span><span class="p">({</span><span class="s1">&#39;only_undirected&#39;</span><span class="p">:</span> <span class="kc">True</span><span class="p">})</span>
+
+        <span class="k">return</span> <span class="p">(</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">degree_inter_class_network</span><span class="p">(</span>
+                <span class="n">annot_args_source</span> <span class="o">=</span> <span class="n">annot_args_source</span><span class="p">,</span>
+                <span class="n">annot_args_target</span> <span class="o">=</span> <span class="n">annot_args_target</span><span class="p">,</span>
+                <span class="o">**</span><span class="n">kwargs</span>
+            <span class="p">)</span>
+        <span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">degree_inter_class_network_directed</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">annot_args_source</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">annot_args_target</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="o">**</span><span class="n">kwargs</span>
+        <span class="p">):</span>
+
+        <span class="n">kwargs</span><span class="o">.</span><span class="n">update</span><span class="p">({</span><span class="s1">&#39;only_directed&#39;</span><span class="p">:</span> <span class="kc">True</span><span class="p">})</span>
+
+        <span class="k">return</span> <span class="p">(</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">degree_inter_class_network</span><span class="p">(</span>
+                <span class="n">annot_args_source</span> <span class="o">=</span> <span class="n">annot_args_source</span><span class="p">,</span>
+                <span class="n">annot_args_target</span> <span class="o">=</span> <span class="n">annot_args_target</span><span class="p">,</span>
+                <span class="o">**</span><span class="n">kwargs</span>
+            <span class="p">)</span>
+        <span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">degree_inter_class_network_stimulatory</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">annot_args_source</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">annot_args_target</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="o">**</span><span class="n">kwargs</span>
+        <span class="p">):</span>
+
+        <span class="n">kwargs</span><span class="o">.</span><span class="n">update</span><span class="p">({</span>
+            <span class="s1">&#39;only_directed&#39;</span><span class="p">:</span> <span class="kc">True</span><span class="p">,</span>
+            <span class="s1">&#39;only_effect&#39;</span><span class="p">:</span> <span class="mi">1</span><span class="p">,</span>
+        <span class="p">})</span>
+
+        <span class="k">return</span> <span class="p">(</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">degree_inter_class_network</span><span class="p">(</span>
+                <span class="n">annot_args_source</span> <span class="o">=</span> <span class="n">annot_args_source</span><span class="p">,</span>
+                <span class="n">annot_args_target</span> <span class="o">=</span> <span class="n">annot_args_target</span><span class="p">,</span>
+                <span class="o">**</span><span class="n">kwargs</span>
+            <span class="p">)</span>
+        <span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">degree_inter_class_network_inhibitory</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">annot_args_source</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">annot_args_target</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="o">**</span><span class="n">kwargs</span>
+        <span class="p">):</span>
+
+        <span class="n">kwargs</span><span class="o">.</span><span class="n">update</span><span class="p">({</span>
+            <span class="s1">&#39;only_directed&#39;</span><span class="p">:</span> <span class="kc">True</span><span class="p">,</span>
+            <span class="s1">&#39;only_effect&#39;</span><span class="p">:</span> <span class="o">-</span><span class="mi">1</span><span class="p">,</span>
+        <span class="p">})</span>
+
+        <span class="k">return</span> <span class="p">(</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">degree_inter_class_network</span><span class="p">(</span>
+                <span class="n">annot_args_source</span> <span class="o">=</span> <span class="n">annot_args_source</span><span class="p">,</span>
+                <span class="n">annot_args_target</span> <span class="o">=</span> <span class="n">annot_args_target</span><span class="p">,</span>
+                <span class="o">**</span><span class="n">kwargs</span>
+            <span class="p">)</span>
+        <span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">degree_inter_class_network_2</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">degrees_of</span> <span class="o">=</span> <span class="s1">&#39;target&#39;</span><span class="p">,</span>
+            <span class="n">sum_by_class</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
+            <span class="o">**</span><span class="n">kwargs</span>
+        <span class="p">):</span>
+
+        <span class="n">network</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">network_df</span><span class="p">(</span><span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
+
+        <span class="n">id_cols</span> <span class="o">=</span> <span class="p">(</span><span class="s1">&#39;id_a&#39;</span><span class="p">,</span> <span class="s1">&#39;id_b&#39;</span><span class="p">)</span>
+        <span class="n">groupby</span><span class="p">,</span> <span class="n">unique</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="n">id_cols</span>
+                <span class="k">if</span> <span class="n">degrees_of</span> <span class="o">==</span> <span class="s1">&#39;source&#39;</span> <span class="k">else</span>
+            <span class="nb">reversed</span><span class="p">(</span><span class="n">id_cols</span><span class="p">)</span>
+        <span class="p">)</span>
+
+        <span class="k">if</span> <span class="n">sum_by_class</span><span class="p">:</span>
+
+            <span class="n">groupby_cat</span> <span class="o">=</span> <span class="p">(</span>
+                <span class="s1">&#39;category_a&#39;</span>
+                    <span class="k">if</span> <span class="n">degrees_of</span> <span class="o">==</span> <span class="s1">&#39;source&#39;</span> <span class="k">else</span>
+                <span class="s1">&#39;category_b&#39;</span>
+            <span class="p">)</span>
+            <span class="n">groupby</span> <span class="o">=</span> <span class="p">[</span><span class="n">groupby</span><span class="p">,</span> <span class="n">groupby_cat</span><span class="p">]</span>
+
+        <span class="n">degrees</span> <span class="o">=</span> <span class="n">network</span><span class="o">.</span><span class="n">groupby</span><span class="p">(</span><span class="n">groupby</span><span class="p">)[</span><span class="n">unique</span><span class="p">]</span><span class="o">.</span><span class="n">nunique</span><span class="p">()</span>
+
+        <span class="k">if</span> <span class="n">sum_by_class</span><span class="p">:</span>
+
+            <span class="n">degrees</span> <span class="o">=</span> <span class="n">degrees</span><span class="o">.</span><span class="n">groupby</span><span class="p">(</span><span class="n">groupby_cat</span><span class="p">)</span><span class="o">.</span><span class="n">sum</span><span class="p">()</span>
+
+        <span class="k">return</span> <span class="n">degrees</span><span class="p">[</span><span class="n">degrees</span> <span class="o">!=</span> <span class="mi">0</span><span class="p">]</span>
+
+
+    <span class="k">def</span> <span class="nf">degree_inter_class_network_undirected_2</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+
+        <span class="n">kwargs</span><span class="o">.</span><span class="n">update</span><span class="p">({</span><span class="s1">&#39;only_undirected&#39;</span><span class="p">:</span> <span class="kc">True</span><span class="p">,</span> <span class="s1">&#39;degrees_of&#39;</span><span class="p">:</span> <span class="s1">&#39;source&#39;</span><span class="p">})</span>
+        <span class="n">deg_source</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">degree_inter_class_network_2</span><span class="p">(</span><span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
+
+        <span class="n">kwargs</span><span class="o">.</span><span class="n">update</span><span class="p">({</span><span class="s1">&#39;only_undirected&#39;</span><span class="p">:</span> <span class="kc">True</span><span class="p">,</span> <span class="s1">&#39;degrees_of&#39;</span><span class="p">:</span> <span class="s1">&#39;target&#39;</span><span class="p">})</span>
+        <span class="n">deg_target</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">degree_inter_class_network_2</span><span class="p">(</span><span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
+
+        <span class="k">return</span> <span class="n">common</span><span class="o">.</span><span class="n">sum_dicts</span><span class="p">(</span><span class="n">deg_source</span><span class="p">,</span> <span class="n">deg_target</span><span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">degree_inter_class_network_directed_2</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+
+        <span class="n">kwargs</span><span class="o">.</span><span class="n">update</span><span class="p">({</span><span class="s1">&#39;only_directed&#39;</span><span class="p">:</span> <span class="kc">True</span><span class="p">})</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">degree_inter_class_network_2</span><span class="p">(</span><span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">degree_inter_class_network_stimulatory_2</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+
+        <span class="n">kwargs</span><span class="o">.</span><span class="n">update</span><span class="p">({</span><span class="s1">&#39;only_effect&#39;</span><span class="p">:</span> <span class="mi">1</span><span class="p">})</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">degree_inter_class_network_2</span><span class="p">(</span><span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">degree_inter_class_network_inhibitory_2</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+
+        <span class="n">kwargs</span><span class="o">.</span><span class="n">update</span><span class="p">({</span><span class="s1">&#39;only_effect&#39;</span><span class="p">:</span> <span class="o">-</span><span class="mi">1</span><span class="p">})</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">degree_inter_class_network_2</span><span class="p">(</span><span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
+
+    <span class="c1">#</span>
+    <span class="c1"># End of wrappers</span>
+    <span class="c1">#</span>
+
+
+<div class="viewcode-block" id="CustomAnnotation.register_network">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.CustomAnnotation.html#pypath.core.annot.CustomAnnotation.register_network">[docs]</a>
+    <span class="k">def</span> <span class="nf">register_network</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">network</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Sets ``network`` as the default network dataset for the instance.</span>
+<span class="sd">        All methods afterwards will use this network.</span>
+<span class="sd">        Also it discards the interclass network data frame if it present to</span>
+<span class="sd">        make sure future queries will address the network registered here.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">unset_interclass_network_df</span><span class="p">()</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">network</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_network_df</span><span class="p">(</span><span class="n">network</span><span class="p">)</span></div>
+
+
+
+    <span class="nd">@staticmethod</span>
+    <span class="k">def</span> <span class="nf">_network_df</span><span class="p">(</span><span class="n">network</span><span class="p">):</span>
+
+        <span class="k">if</span> <span class="ow">not</span> <span class="nb">hasattr</span><span class="p">(</span><span class="n">network</span><span class="p">,</span> <span class="s1">&#39;df&#39;</span><span class="p">)</span> <span class="ow">and</span> <span class="nb">hasattr</span><span class="p">(</span><span class="n">network</span><span class="p">,</span> <span class="s1">&#39;make_df&#39;</span><span class="p">):</span>
+
+            <span class="n">network</span><span class="o">.</span><span class="n">make_df</span><span class="p">()</span>
+
+        <span class="k">return</span> <span class="p">(</span>
+            <span class="n">network</span><span class="o">.</span><span class="n">df</span>
+                <span class="k">if</span> <span class="nb">hasattr</span><span class="p">(</span><span class="n">network</span><span class="p">,</span> <span class="s1">&#39;df&#39;</span><span class="p">)</span> <span class="k">else</span>
+            <span class="n">network</span>
+        <span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">filtered</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">annot_df</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">entities</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="o">**</span><span class="n">kwargs</span>
+        <span class="p">):</span>
+
+        <span class="n">annot_df</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">get_df</span><span class="p">()</span> <span class="k">if</span> <span class="n">annot_df</span> <span class="ow">is</span> <span class="kc">None</span> <span class="k">else</span> <span class="n">annot_df</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">filter_df</span><span class="p">(</span>
+            <span class="n">annot_df</span> <span class="o">=</span> <span class="n">annot_df</span><span class="p">,</span>
+            <span class="n">entities</span> <span class="o">=</span> <span class="n">entities</span><span class="p">,</span>
+            <span class="o">**</span><span class="n">kwargs</span>
+        <span class="p">)</span>
+
+
+    <span class="nd">@classmethod</span>
+    <span class="k">def</span> <span class="nf">filter_df</span><span class="p">(</span>
+            <span class="bp">cls</span><span class="p">,</span>
+            <span class="n">annot_df</span><span class="p">,</span>
+            <span class="n">entities</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">postfix</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="o">**</span><span class="n">kwargs</span>
+        <span class="p">):</span>
+
+        <span class="n">query</span> <span class="o">=</span> <span class="bp">cls</span><span class="o">.</span><span class="n">_process_query_args</span><span class="p">(</span>
+            <span class="n">df</span> <span class="o">=</span> <span class="n">annot_df</span><span class="p">,</span>
+            <span class="n">entities</span> <span class="o">=</span> <span class="n">entities</span><span class="p">,</span>
+            <span class="n">args</span> <span class="o">=</span> <span class="n">kwargs</span><span class="p">,</span>
+            <span class="n">postfix</span> <span class="o">=</span> <span class="n">postfix</span><span class="p">,</span>
+        <span class="p">)</span>
+
+        <span class="n">args</span> <span class="o">=</span> <span class="bp">cls</span><span class="o">.</span><span class="n">_args_add_postfix</span><span class="p">(</span><span class="n">args</span><span class="p">,</span> <span class="n">postfix</span><span class="p">)</span>
+
+        <span class="n">query</span> <span class="o">=</span> <span class="s1">&#39; and &#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">query</span><span class="p">)</span>
+
+        <span class="k">return</span> <span class="n">annot_df</span><span class="o">.</span><span class="n">query</span><span class="p">(</span><span class="n">query</span><span class="p">)</span> <span class="k">if</span> <span class="n">query</span> <span class="k">else</span> <span class="n">annot_df</span>
+
+
+    <span class="nd">@staticmethod</span>
+    <span class="k">def</span> <span class="nf">_process_query_args</span><span class="p">(</span><span class="n">df</span><span class="p">,</span> <span class="n">args</span><span class="p">,</span> <span class="n">entities</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span> <span class="n">postfix</span> <span class="o">=</span> <span class="kc">None</span><span class="p">):</span>
+
+        <span class="n">query</span> <span class="o">=</span> <span class="p">[]</span>
+
+        <span class="k">for</span> <span class="n">col</span><span class="p">,</span> <span class="n">val</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="n">args</span><span class="p">):</span>
+
+            <span class="n">col</span> <span class="o">=</span> <span class="s1">&#39;</span><span class="si">%s%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="p">(</span><span class="n">col</span><span class="p">,</span> <span class="n">postfix</span><span class="p">)</span> <span class="k">if</span> <span class="n">postfix</span> <span class="k">else</span> <span class="n">col</span>
+
+            <span class="k">if</span> <span class="n">val</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span> <span class="ow">and</span> <span class="n">col</span> <span class="ow">in</span> <span class="n">df</span><span class="o">.</span><span class="n">columns</span><span class="p">:</span>
+
+                <span class="n">op</span> <span class="o">=</span> <span class="s1">&#39;==&#39;</span> <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">val</span><span class="p">,</span> <span class="n">_const</span><span class="o">.</span><span class="n">SIMPLE_TYPES</span><span class="p">)</span> <span class="k">else</span> <span class="s1">&#39;in&#39;</span>
+
+                <span class="n">q</span> <span class="o">=</span> <span class="s1">&#39;</span><span class="si">%s</span><span class="s1"> </span><span class="si">%s</span><span class="s1"> </span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="p">(</span><span class="n">col</span><span class="p">,</span> <span class="n">op</span><span class="p">,</span> <span class="s1">&#39;@args[&quot;</span><span class="si">%s</span><span class="s1">&quot;]&#39;</span> <span class="o">%</span> <span class="n">col</span><span class="p">)</span>
+
+                <span class="n">query</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">q</span><span class="p">)</span>
+
+        <span class="k">if</span> <span class="n">entities</span><span class="p">:</span>
+
+            <span class="n">entity_cols</span> <span class="o">=</span> <span class="p">{</span><span class="s1">&#39;id&#39;</span><span class="p">,</span> <span class="s1">&#39;genesymbol&#39;</span><span class="p">,</span> <span class="s1">&#39;uniprot&#39;</span><span class="p">}</span>
+
+            <span class="k">if</span> <span class="n">postfix</span><span class="p">:</span>
+
+                <span class="n">entity_cols</span> <span class="o">=</span> <span class="p">{</span>
+                    <span class="s1">&#39;</span><span class="si">%s%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="p">(</span><span class="n">col</span><span class="p">,</span> <span class="n">postfix</span><span class="p">)</span>
+                    <span class="k">for</span> <span class="n">col</span> <span class="ow">in</span> <span class="n">entity_cols</span>
+                <span class="p">}</span>
+
+            <span class="n">entity_cols</span> <span class="o">=</span> <span class="n">entity_cols</span> <span class="o">&amp;</span> <span class="nb">set</span><span class="p">(</span><span class="n">df</span><span class="o">.</span><span class="n">columns</span><span class="p">)</span>
+
+            <span class="n">q</span> <span class="o">=</span> <span class="s1">&#39;(</span><span class="si">%s</span><span class="s1">)&#39;</span> <span class="o">%</span> <span class="p">(</span>
+                <span class="s1">&#39; or &#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span>
+                    <span class="s1">&#39;</span><span class="si">%s</span><span class="s1"> in @entities&#39;</span> <span class="o">%</span> <span class="n">col</span>
+                    <span class="k">for</span> <span class="n">col</span> <span class="ow">in</span> <span class="n">entity_cols</span>
+                <span class="p">)</span>
+            <span class="p">)</span>
+            <span class="n">query</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">q</span><span class="p">)</span>
+
+        <span class="k">return</span> <span class="n">query</span>
+
+
+    <span class="nd">@staticmethod</span>
+    <span class="k">def</span> <span class="nf">_args_add_postfix</span><span class="p">(</span><span class="n">args</span><span class="p">,</span> <span class="n">postfix</span><span class="p">):</span>
+
+        <span class="k">if</span> <span class="n">postfix</span><span class="p">:</span>
+
+            <span class="n">args</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">(</span>
+                <span class="p">(</span>
+                    <span class="s1">&#39;</span><span class="si">%s%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="p">(</span><span class="n">key</span><span class="p">,</span> <span class="n">postfix</span><span class="p">),</span>
+                    <span class="n">val</span>
+                <span class="p">)</span>
+                <span class="k">for</span> <span class="n">key</span><span class="p">,</span> <span class="n">val</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="n">args</span><span class="p">)</span>
+            <span class="p">)</span>
+
+        <span class="k">return</span> <span class="n">args</span>
+
+
+    <span class="k">def</span> <span class="nf">export</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">fname</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">make_df</span><span class="p">()</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">df</span><span class="o">.</span><span class="n">to_csv</span><span class="p">(</span><span class="n">fname</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
+
+
+<div class="viewcode-block" id="CustomAnnotation.classes_by_entity">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.CustomAnnotation.html#pypath.core.annot.CustomAnnotation.classes_by_entity">[docs]</a>
+    <span class="k">def</span> <span class="nf">classes_by_entity</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">element</span><span class="p">,</span> <span class="n">labels</span> <span class="o">=</span> <span class="kc">False</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Returns a set of class keys with the classes containing at least</span>
+<span class="sd">        one of the elements.</span>
+
+<span class="sd">        :param str,set element:</span>
+<span class="sd">            One or more element (entity) to search for in the classes.</span>
+<span class="sd">        :param bool labels:</span>
+<span class="sd">            Return labels instead of keys.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">element</span> <span class="o">=</span> <span class="n">common</span><span class="o">.</span><span class="n">to_set</span><span class="p">(</span><span class="n">element</span><span class="p">)</span>
+
+        <span class="k">return</span> <span class="nb">set</span><span class="p">(</span>
+            <span class="bp">cls</span><span class="o">.</span><span class="n">label</span> <span class="k">if</span> <span class="n">labels</span> <span class="k">else</span> <span class="n">key</span>
+            <span class="k">for</span> <span class="n">key</span><span class="p">,</span> <span class="bp">cls</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">classes</span><span class="p">)</span>
+            <span class="k">if</span> <span class="n">element</span> <span class="o">&amp;</span> <span class="bp">cls</span>
+        <span class="p">)</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">entities_by_resource</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">entity_types</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+
+        <span class="n">by_resource</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">defaultdict</span><span class="p">(</span><span class="nb">set</span><span class="p">)</span>
+
+        <span class="k">for</span> <span class="n">key</span><span class="p">,</span> <span class="bp">cls</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">classes</span><span class="p">):</span>
+
+            <span class="n">by_resource</span><span class="p">[</span><span class="bp">cls</span><span class="o">.</span><span class="n">resource</span><span class="p">]</span><span class="o">.</span><span class="n">update</span><span class="p">(</span>
+                <span class="bp">cls</span><span class="o">.</span><span class="n">filter_entity_type</span><span class="p">(</span><span class="n">entity_type</span> <span class="o">=</span> <span class="n">entity_types</span><span class="p">)</span>
+            <span class="p">)</span>
+
+        <span class="k">return</span> <span class="nb">dict</span><span class="p">(</span><span class="n">by_resource</span><span class="p">)</span>
+
+
+    <span class="c1"># TODO: this kind of methods should be implemented by metaprogramming</span>
+    <span class="k">def</span> <span class="nf">proteins_by_resource</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">entities_by_resource</span><span class="p">(</span><span class="n">entity_types</span> <span class="o">=</span> <span class="s1">&#39;protein&#39;</span><span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">complexes_by_resource</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">entities_by_resource</span><span class="p">(</span><span class="n">entity_types</span> <span class="o">=</span> <span class="s1">&#39;complex&#39;</span><span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">mirnas_by_resource</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">entities_by_resource</span><span class="p">(</span><span class="n">entity_types</span> <span class="o">=</span> <span class="s1">&#39;mirna&#39;</span><span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">counts_by_resource</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">entity_types</span> <span class="o">=</span> <span class="kc">None</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="nb">dict</span><span class="p">(</span>
+            <span class="p">(</span>
+                <span class="n">resource</span><span class="p">,</span>
+                <span class="nb">len</span><span class="p">(</span><span class="n">entities</span><span class="p">)</span>
+            <span class="p">)</span>
+            <span class="k">for</span> <span class="n">resource</span><span class="p">,</span> <span class="n">entities</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">entities_by_resource</span><span class="p">(</span><span class="n">entity_types</span> <span class="o">=</span> <span class="n">entity_types</span><span class="p">)</span>
+            <span class="p">)</span>
+        <span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">get_entities</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">entity_types</span> <span class="o">=</span> <span class="kc">None</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="n">entity</span><span class="o">.</span><span class="n">Entity</span><span class="o">.</span><span class="n">filter_entity_type</span><span class="p">(</span>
+            <span class="nb">set</span><span class="o">.</span><span class="n">union</span><span class="p">(</span><span class="o">*</span><span class="p">(</span><span class="nb">set</span><span class="p">(</span><span class="n">a</span><span class="p">)</span> <span class="k">for</span> <span class="n">a</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">classes</span><span class="o">.</span><span class="n">values</span><span class="p">()))</span>
+                <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">classes</span> <span class="k">else</span>
+            <span class="p">(),</span>
+            <span class="n">entity_type</span> <span class="o">=</span> <span class="n">entity_types</span><span class="p">,</span>
+        <span class="p">)</span>
+
+
+    <span class="c1"># TODO: this kind of methods should be implemented by metaprogramming</span>
+    <span class="k">def</span> <span class="nf">get_proteins</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">get_entities</span><span class="p">(</span><span class="n">entity_types</span> <span class="o">=</span> <span class="s1">&#39;protein&#39;</span><span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">get_complexes</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">get_entities</span><span class="p">(</span><span class="n">entity_types</span> <span class="o">=</span> <span class="s1">&#39;complex&#39;</span><span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">get_mirnas</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">get_entities</span><span class="p">(</span><span class="n">entity_types</span> <span class="o">=</span> <span class="s1">&#39;mirna&#39;</span><span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">numof_entities</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">entity_types</span> <span class="o">=</span> <span class="kc">None</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">get_entities</span><span class="p">(</span><span class="n">entity_types</span> <span class="o">=</span> <span class="n">entity_types</span><span class="p">))</span>
+
+
+    <span class="c1"># TODO: this kind of methods should be implemented by metaprogramming</span>
+    <span class="k">def</span> <span class="nf">numof_proteins</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">numof_entities</span><span class="p">(</span><span class="n">entity_types</span> <span class="o">=</span> <span class="s1">&#39;protein&#39;</span><span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">numof_complexes</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">numof_entities</span><span class="p">(</span><span class="n">entity_types</span> <span class="o">=</span> <span class="s1">&#39;complex&#39;</span><span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">numof_mirnas</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">numof_entities</span><span class="p">(</span><span class="n">entity_types</span> <span class="o">=</span> <span class="s1">&#39;mirna&#39;</span><span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">numof_classes</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">classes</span><span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">numof_records</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">entity_types</span> <span class="o">=</span> <span class="kc">None</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="nb">sum</span><span class="p">(</span>
+            <span class="bp">cls</span><span class="o">.</span><span class="n">count_entity_type</span><span class="p">(</span><span class="n">entity_type</span> <span class="o">=</span> <span class="n">entity_types</span><span class="p">)</span>
+            <span class="k">for</span> <span class="bp">cls</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">classes</span><span class="o">.</span><span class="n">values</span><span class="p">()</span>
+        <span class="p">)</span>
+
+
+    <span class="c1"># TODO: this kind of methods should be implemented by metaprogramming</span>
+    <span class="k">def</span> <span class="nf">numof_protein_records</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">numof_records</span><span class="p">(</span><span class="n">entity_types</span> <span class="o">=</span> <span class="s1">&#39;protein&#39;</span><span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">numof_complex_records</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">numof_records</span><span class="p">(</span><span class="n">entity_types</span> <span class="o">=</span> <span class="s1">&#39;complex&#39;</span><span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">numof_mirna_records</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">numof_records</span><span class="p">(</span><span class="n">entity_types</span> <span class="o">=</span> <span class="s1">&#39;mirna&#39;</span><span class="p">)</span>
+
+
+<div class="viewcode-block" id="CustomAnnotation.resources_in_category">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.CustomAnnotation.html#pypath.core.annot.CustomAnnotation.resources_in_category">[docs]</a>
+    <span class="k">def</span> <span class="nf">resources_in_category</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">key</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Returns a list of resources contributing to the definition of</span>
+<span class="sd">        a category.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">if</span> <span class="ow">not</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">key</span><span class="p">,</span> <span class="nb">tuple</span><span class="p">):</span>
+
+            <span class="n">key</span> <span class="o">=</span> <span class="p">(</span><span class="n">key</span><span class="p">,</span> <span class="n">key</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">composite_resource_name</span><span class="p">)</span>
+
+        <span class="k">if</span> <span class="n">key</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">children</span><span class="p">:</span>
+
+            <span class="k">return</span> <span class="nb">sorted</span><span class="p">({</span><span class="n">child</span><span class="o">.</span><span class="n">resource</span> <span class="k">for</span> <span class="n">child</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">children</span><span class="p">[</span><span class="n">key</span><span class="p">]})</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">all_resources</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="nb">sorted</span><span class="p">({</span><span class="n">grp</span><span class="o">.</span><span class="n">resource</span> <span class="k">for</span> <span class="n">grp</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">classes</span><span class="o">.</span><span class="n">values</span><span class="p">()})</span>
+
+
+    <span class="k">def</span> <span class="fm">__getitem__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">item</span><span class="p">):</span>
+
+        <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">item</span><span class="p">,</span> <span class="nb">tuple</span><span class="p">)</span> <span class="ow">and</span> <span class="n">item</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">classes</span><span class="p">:</span>
+
+            <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">classes</span><span class="p">[</span><span class="n">item</span><span class="p">]</span>
+
+        <span class="k">else</span><span class="p">:</span>
+
+            <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">classes_by_entity</span><span class="p">(</span><span class="n">item</span><span class="p">)</span>
+
+
+<div class="viewcode-block" id="CustomAnnotation.browse">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.CustomAnnotation.html#pypath.core.annot.CustomAnnotation.browse">[docs]</a>
+    <span class="k">def</span> <span class="nf">browse</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">start</span><span class="p">:</span> <span class="nb">int</span> <span class="o">=</span> <span class="mi">0</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Print gene information as a table.</span>
+
+<span class="sd">        Presents information about annotation classes as ascii tables printed</span>
+<span class="sd">        in the terminal. If one class provided, prints one table. If multiple</span>
+<span class="sd">        classes provided, prints a table for each of them one by one</span>
+<span class="sd">        proceeding to the next one once you hit return. If no classes</span>
+<span class="sd">        provided goes through all classes.</span>
+
+<span class="sd">        ``kwargs`` passed to ``pypath.utils.uniprot.info``.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">classes</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">(</span>
+            <span class="p">(</span>
+                <span class="bp">cls</span><span class="o">.</span><span class="n">label</span><span class="p">,</span>
+                <span class="bp">cls</span><span class="o">.</span><span class="n">filter_entity_type</span><span class="p">(</span><span class="n">entity_type</span> <span class="o">=</span> <span class="s1">&#39;protein&#39;</span><span class="p">)</span>
+            <span class="p">)</span>
+            <span class="k">for</span> <span class="bp">cls</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">iter_classes</span><span class="p">(</span><span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
+        <span class="p">)</span>
+
+        <span class="n">utils_uniprot</span><span class="o">.</span><span class="n">browse</span><span class="p">(</span><span class="n">groups</span> <span class="o">=</span> <span class="n">classes</span><span class="p">,</span> <span class="n">start</span> <span class="o">=</span> <span class="n">start</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">)</span></div>
+</div>
+
+
+
+<div class="viewcode-block" id="AnnotationBase">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.AnnotationBase.html#pypath.core.annot.AnnotationBase">[docs]</a>
+<span class="k">class</span> <span class="nc">AnnotationBase</span><span class="p">(</span><span class="n">resource</span><span class="o">.</span><span class="n">AbstractResource</span><span class="p">):</span>
+
+    <span class="n">_dtypes</span> <span class="o">=</span> <span class="p">{</span>
+        <span class="s1">&#39;uniprot&#39;</span><span class="p">:</span> <span class="s1">&#39;category&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;genesymbol&#39;</span><span class="p">:</span> <span class="s1">&#39;category&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;entity_type&#39;</span><span class="p">:</span> <span class="s1">&#39;category&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;source&#39;</span><span class="p">:</span> <span class="s1">&#39;category&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;label&#39;</span><span class="p">:</span> <span class="s1">&#39;category&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;value&#39;</span><span class="p">:</span> <span class="s1">&#39;object&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;record_id&#39;</span><span class="p">:</span> <span class="s1">&#39;int32&#39;</span><span class="p">,</span>
+    <span class="p">}</span>
+
+
+<div class="viewcode-block" id="AnnotationBase.__init__">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.AnnotationBase.html#pypath.core.annot.AnnotationBase.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">name</span><span class="p">,</span>
+            <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">,</span>
+            <span class="n">input_method</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">input_args</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">entity_type</span> <span class="o">=</span> <span class="s1">&#39;protein&#39;</span><span class="p">,</span>
+            <span class="n">swissprot_only</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
+            <span class="n">proteins</span> <span class="o">=</span> <span class="p">(),</span>
+            <span class="n">complexes</span> <span class="o">=</span> <span class="p">(),</span>
+            <span class="n">reference_set</span> <span class="o">=</span> <span class="p">(),</span>
+            <span class="n">infer_complexes</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">dump</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">primary_field</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">check_ids</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
+            <span class="o">**</span><span class="n">kwargs</span>
+        <span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Represents annotations for a set of proteins.</span>
+<span class="sd">        Loads the data from the original resource and provides methods</span>
+<span class="sd">        to query the annotations.</span>
+
+<span class="sd">        :arg str name:</span>
+<span class="sd">            A custom name for the annotation resource.</span>
+<span class="sd">        :arg int ncbi_tax_id:</span>
+<span class="sd">            NCBI Taxonomy identifier.</span>
+<span class="sd">        :arg callable,str input_method:</span>
+<span class="sd">            Either a callable or the name of a method in any submodules of</span>
+<span class="sd">            the ``pypath.inputs``  module. Should return a dict with</span>
+<span class="sd">            UniProt IDs as keys or an object suitable for ``process_method``.</span>
+<span class="sd">        :arg dict input_args:</span>
+<span class="sd">            Arguments for the ``input_method``.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">session_mod</span><span class="o">.</span><span class="n">Logger</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">name</span> <span class="o">=</span> <span class="s1">&#39;annot&#39;</span><span class="p">)</span>
+
+        <span class="n">input_args</span> <span class="o">=</span> <span class="n">input_args</span> <span class="ow">or</span> <span class="p">{}</span>
+        <span class="n">input_args</span><span class="o">.</span><span class="n">update</span><span class="p">(</span><span class="n">kwargs</span><span class="p">)</span>
+
+        <span class="n">resource</span><span class="o">.</span><span class="n">AbstractResource</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">name</span> <span class="o">=</span> <span class="n">name</span><span class="p">,</span>
+            <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">,</span>
+            <span class="n">input_method</span> <span class="o">=</span> <span class="n">input_method</span><span class="p">,</span>
+            <span class="n">input_args</span> <span class="o">=</span> <span class="n">input_args</span><span class="p">,</span>
+            <span class="n">dump</span> <span class="o">=</span> <span class="n">dump</span><span class="p">,</span>
+            <span class="n">data_attr_name</span> <span class="o">=</span> <span class="s1">&#39;annot&#39;</span><span class="p">,</span>
+        <span class="p">)</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">entity_type</span> <span class="o">=</span> <span class="n">entity_type</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">primary_field</span> <span class="o">=</span> <span class="n">primary_field</span>
+        <span class="n">infer_complexes</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="n">infer_complexes</span>
+                <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">infer_complexes</span><span class="p">,</span> <span class="nb">bool</span><span class="p">)</span> <span class="k">else</span>
+            <span class="n">settings</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">&#39;annot_infer_complexes&#39;</span><span class="p">)</span>
+        <span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">infer_complexes</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="n">infer_complexes</span> <span class="ow">and</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">entity_type</span> <span class="o">==</span> <span class="s1">&#39;protein&#39;</span>
+        <span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">proteins</span> <span class="o">=</span> <span class="n">proteins</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">complexes</span> <span class="o">=</span> <span class="n">complexes</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">reference_set</span> <span class="o">=</span> <span class="n">reference_set</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">swissprot_only</span> <span class="o">=</span> <span class="n">swissprot_only</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">check_ids</span> <span class="o">=</span> <span class="n">check_ids</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">load</span><span class="p">()</span></div>
+
+
+
+<div class="viewcode-block" id="AnnotationBase.reload">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.AnnotationBase.html#pypath.core.annot.AnnotationBase.reload">[docs]</a>
+    <span class="k">def</span> <span class="nf">reload</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Reloads the object from the module level.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">modname</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="vm">__class__</span><span class="o">.</span><span class="vm">__module__</span>
+        <span class="n">mod</span> <span class="o">=</span> <span class="nb">__import__</span><span class="p">(</span><span class="n">modname</span><span class="p">,</span> <span class="n">fromlist</span> <span class="o">=</span> <span class="p">[</span><span class="n">modname</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;.&#39;</span><span class="p">)[</span><span class="mi">0</span><span class="p">]])</span>
+        <span class="n">imp</span><span class="o">.</span><span class="n">reload</span><span class="p">(</span><span class="n">mod</span><span class="p">)</span>
+        <span class="n">new</span> <span class="o">=</span> <span class="nb">getattr</span><span class="p">(</span><span class="n">mod</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="vm">__class__</span><span class="o">.</span><span class="vm">__name__</span><span class="p">)</span>
+        <span class="nb">setattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">&#39;__class__&#39;</span><span class="p">,</span> <span class="n">new</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="AnnotationBase.load">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.AnnotationBase.html#pypath.core.annot.AnnotationBase.load">[docs]</a>
+    <span class="k">def</span> <span class="nf">load</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Loads the annotation data by calling the input method.</span>
+<span class="sd">        Infers annotations for complexes in the complex database if</span>
+<span class="sd">        py:attr:``infer_complexes`` is True.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span><span class="s1">&#39;Loading annotations from `</span><span class="si">%s</span><span class="s1">`.&#39;</span> <span class="o">%</span> <span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">)</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">set_reference_set</span><span class="p">()</span>
+        <span class="n">resource</span><span class="o">.</span><span class="n">AbstractResource</span><span class="o">.</span><span class="n">load</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">_ensure_swissprot</span><span class="p">()</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_update_primary_field</span><span class="p">()</span>
+
+        <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">infer_complexes</span><span class="p">:</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">add_complexes_by_inference</span><span class="p">()</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span>
+            <span class="s1">&#39;Loaded annotations from `</span><span class="si">%s</span><span class="s1">`: </span><span class="si">%u</span><span class="s1"> molecules, </span><span class="si">%u</span><span class="s1"> annotations.&#39;</span> <span class="o">%</span> <span class="p">(</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">,</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">numof_entities</span><span class="p">(),</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">numof_records</span><span class="p">(),</span>
+            <span class="p">)</span>
+        <span class="p">)</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">_update_primary_field</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">primary_field</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">primary_field</span> <span class="ow">or</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">get_names</span><span class="p">()[</span><span class="mi">0</span><span class="p">]</span>
+                <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">get_names</span><span class="p">()</span> <span class="k">else</span>
+            <span class="kc">None</span>
+        <span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">_ensure_swissprot</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">if</span> <span class="p">(</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">ncbi_tax_id</span> <span class="o">==</span> <span class="n">_const</span><span class="o">.</span><span class="n">NOT_ORGANISM_SPECIFIC</span> <span class="ow">or</span>
+            <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">check_ids</span>
+        <span class="p">):</span>
+
+            <span class="k">return</span>
+
+        <span class="n">new</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">defaultdict</span><span class="p">(</span><span class="nb">set</span><span class="p">)</span>
+
+        <span class="k">for</span> <span class="n">uniprot</span><span class="p">,</span> <span class="n">annots</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">annot</span><span class="p">):</span>
+
+            <span class="k">if</span> <span class="n">entity</span><span class="o">.</span><span class="n">Entity</span><span class="o">.</span><span class="n">_is_protein</span><span class="p">(</span><span class="n">uniprot</span><span class="p">):</span>
+
+                <span class="n">swissprots</span> <span class="o">=</span> <span class="n">mapping</span><span class="o">.</span><span class="n">map_name</span><span class="p">(</span>
+                    <span class="n">uniprot</span><span class="p">,</span>
+                    <span class="s1">&#39;uniprot&#39;</span><span class="p">,</span>
+                    <span class="s1">&#39;uniprot&#39;</span><span class="p">,</span>
+                    <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">ncbi_tax_id</span><span class="p">,</span>
+                <span class="p">)</span>
+
+                <span class="k">for</span> <span class="n">swissprot</span> <span class="ow">in</span> <span class="n">swissprots</span><span class="p">:</span>
+
+                    <span class="n">new</span><span class="p">[</span><span class="n">swissprot</span><span class="p">]</span><span class="o">.</span><span class="n">update</span><span class="p">(</span><span class="n">annots</span><span class="p">)</span>
+
+            <span class="k">else</span><span class="p">:</span>
+
+                <span class="n">new</span><span class="p">[</span><span class="n">uniprot</span><span class="p">]</span><span class="o">.</span><span class="n">update</span><span class="p">(</span><span class="n">annots</span><span class="p">)</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">annot</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">(</span><span class="n">new</span><span class="p">)</span>
+
+
+<div class="viewcode-block" id="AnnotationBase.add_complexes_by_inference">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.AnnotationBase.html#pypath.core.annot.AnnotationBase.add_complexes_by_inference">[docs]</a>
+    <span class="k">def</span> <span class="nf">add_complexes_by_inference</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">complexes</span> <span class="o">=</span> <span class="kc">None</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Creates complex annotations by in silico inference and adds them</span>
+<span class="sd">        to this annotation set.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">complex_annotation</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">complex_inference</span><span class="p">(</span><span class="n">complexes</span> <span class="o">=</span> <span class="n">complexes</span><span class="p">)</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">annot</span><span class="o">.</span><span class="n">update</span><span class="p">(</span><span class="n">complex_annotation</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="AnnotationBase.complex_inference">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.AnnotationBase.html#pypath.core.annot.AnnotationBase.complex_inference">[docs]</a>
+    <span class="k">def</span> <span class="nf">complex_inference</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">complexes</span> <span class="o">=</span> <span class="kc">None</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Annotates all complexes in `complexes`, by default in the default</span>
+<span class="sd">        complex database (existing in the `complex` module or generated</span>
+<span class="sd">        on demand according to the module&#39;s current settings).</span>
+
+<span class="sd">        Returns</span>
+<span class="sd">        -------</span>
+<span class="sd">        Dict with complexes as keys and sets of annotations as values.</span>
+<span class="sd">        Complexes with no valid information in this annotation resource</span>
+<span class="sd">        won&#39;t be in the dict.</span>
+
+<span class="sd">        Parameters</span>
+<span class="sd">        ----------</span>
+<span class="sd">        complexes : iterable</span>
+<span class="sd">            Iterable yielding complexes.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span><span class="s1">&#39;Inferring complex annotations from `</span><span class="si">%s</span><span class="s1">`.&#39;</span> <span class="o">%</span> <span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">)</span>
+
+        <span class="k">if</span> <span class="ow">not</span> <span class="n">complexes</span><span class="p">:</span>
+
+            <span class="kn">import</span> <span class="nn">pypath.core.complex</span> <span class="k">as</span> <span class="nn">complex</span>
+
+            <span class="n">complexdb</span> <span class="o">=</span> <span class="nb">complex</span><span class="o">.</span><span class="n">get_db</span><span class="p">()</span>
+
+            <span class="n">complexes</span> <span class="o">=</span> <span class="n">complexdb</span><span class="o">.</span><span class="n">complexes</span><span class="o">.</span><span class="n">values</span><span class="p">()</span>
+
+        <span class="n">complex_annotation</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">defaultdict</span><span class="p">(</span><span class="nb">set</span><span class="p">)</span>
+
+        <span class="k">for</span> <span class="n">cplex</span> <span class="ow">in</span> <span class="n">complexes</span><span class="p">:</span>
+
+            <span class="n">this_cplex_annot</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">annotate_complex</span><span class="p">(</span><span class="n">cplex</span><span class="p">)</span>
+
+            <span class="k">if</span> <span class="n">this_cplex_annot</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
+
+                <span class="n">complex_annotation</span><span class="p">[</span><span class="n">cplex</span><span class="p">]</span><span class="o">.</span><span class="n">update</span><span class="p">(</span><span class="n">this_cplex_annot</span><span class="p">)</span>
+
+        <span class="k">return</span> <span class="n">complex_annotation</span></div>
+
+
+
+<div class="viewcode-block" id="AnnotationBase.annotate_complex">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.AnnotationBase.html#pypath.core.annot.AnnotationBase.annotate_complex">[docs]</a>
+    <span class="k">def</span> <span class="nf">annotate_complex</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">cplex</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Infers annotations for a single complex.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">if</span> <span class="p">(</span>
+            <span class="ow">not</span> <span class="nb">all</span><span class="p">(</span><span class="n">comp</span> <span class="ow">in</span> <span class="bp">self</span> <span class="k">for</span> <span class="n">comp</span> <span class="ow">in</span> <span class="n">cplex</span><span class="o">.</span><span class="n">components</span><span class="o">.</span><span class="n">keys</span><span class="p">())</span> <span class="ow">or</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">_eq_fields</span> <span class="ow">is</span> <span class="kc">None</span>
+        <span class="p">):</span>
+            <span class="c1"># this means no annotation for this complex</span>
+            <span class="k">return</span> <span class="kc">None</span>
+
+        <span class="k">elif</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">_eq_fields</span><span class="p">:</span>
+            <span class="c1"># here empty set means the complex belongs</span>
+            <span class="c1"># to the class of enitities covered by this</span>
+            <span class="c1"># annotation</span>
+            <span class="k">return</span> <span class="nb">set</span><span class="p">()</span>
+
+        <span class="k">elif</span> <span class="nb">callable</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_eq_fields</span><span class="p">):</span>
+
+            <span class="c1"># here a custom method combines the annotations</span>
+            <span class="c1"># we look at all possible combinations of the annotations</span>
+            <span class="c1"># of the components, but most likely each component have</span>
+            <span class="c1"># only one annotation in this case</span>
+            <span class="k">return</span> <span class="nb">set</span><span class="p">(</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">_eq_fields</span><span class="p">(</span><span class="o">*</span><span class="n">annots</span><span class="p">)</span>
+                <span class="k">for</span> <span class="n">annots</span> <span class="ow">in</span> <span class="n">itertools</span><span class="o">.</span><span class="n">product</span><span class="p">(</span>
+                    <span class="o">*</span><span class="p">(</span>
+                        <span class="bp">self</span><span class="o">.</span><span class="n">annot</span><span class="p">[</span><span class="n">comp</span><span class="p">]</span>
+                        <span class="k">for</span> <span class="n">comp</span> <span class="ow">in</span> <span class="n">cplex</span><span class="o">.</span><span class="n">components</span><span class="o">.</span><span class="n">keys</span><span class="p">()</span>
+                    <span class="p">)</span>
+                <span class="p">)</span>
+            <span class="p">)</span>
+
+        <span class="k">elif</span> <span class="nb">hasattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">&#39;_merge&#39;</span><span class="p">):</span>
+
+            <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_merge</span><span class="p">(</span><span class="o">*</span><span class="p">(</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">annot</span><span class="p">[</span><span class="n">comp</span><span class="p">]</span>
+                <span class="k">for</span> <span class="n">comp</span> <span class="ow">in</span> <span class="n">cplex</span><span class="o">.</span><span class="n">components</span><span class="o">.</span><span class="n">keys</span><span class="p">()</span>
+            <span class="p">))</span>
+
+        <span class="k">else</span><span class="p">:</span>
+
+            <span class="n">groups</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">defaultdict</span><span class="p">(</span><span class="nb">set</span><span class="p">)</span>
+            <span class="n">empty_args</span> <span class="o">=</span> <span class="p">{}</span>
+            <span class="bp">cls</span> <span class="o">=</span> <span class="kc">None</span>
+            <span class="n">components</span> <span class="o">=</span> <span class="nb">set</span><span class="p">(</span><span class="n">cplex</span><span class="o">.</span><span class="n">components</span><span class="o">.</span><span class="n">keys</span><span class="p">())</span>
+
+            <span class="k">for</span> <span class="n">comp</span> <span class="ow">in</span> <span class="n">cplex</span><span class="o">.</span><span class="n">components</span><span class="o">.</span><span class="n">keys</span><span class="p">():</span>
+
+                <span class="k">for</span> <span class="n">comp_annot</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">annot</span><span class="p">[</span><span class="n">comp</span><span class="p">]:</span>
+
+                    <span class="k">if</span> <span class="bp">cls</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
+
+                        <span class="bp">cls</span> <span class="o">=</span> <span class="n">comp_annot</span><span class="o">.</span><span class="vm">__class__</span>
+                        <span class="n">empty_args</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">(</span>
+                            <span class="p">(</span><span class="n">f</span><span class="p">,</span> <span class="kc">None</span><span class="p">)</span>
+                            <span class="k">for</span> <span class="n">f</span> <span class="ow">in</span> <span class="n">comp_annot</span><span class="o">.</span><span class="n">_fields</span>
+                            <span class="k">if</span> <span class="n">f</span> <span class="ow">not</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">_eq_fields</span>
+                        <span class="p">)</span>
+
+                    <span class="n">groups</span><span class="p">[</span>
+                        <span class="nb">tuple</span><span class="p">(</span>
+                            <span class="nb">getattr</span><span class="p">(</span><span class="n">comp_annot</span><span class="p">,</span> <span class="n">f</span><span class="p">)</span>
+                            <span class="k">for</span> <span class="n">f</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">_eq_fields</span>
+                        <span class="p">)</span>
+                    <span class="p">]</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">comp</span><span class="p">)</span>
+
+            <span class="k">return</span> <span class="nb">set</span><span class="p">(</span>
+                <span class="c1"># the characteristic attributes of the group</span>
+                <span class="c1"># and the remaining left empty</span>
+                <span class="bp">cls</span><span class="p">(</span>
+                    <span class="o">**</span><span class="nb">dict</span><span class="p">(</span><span class="nb">zip</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_eq_fields</span><span class="p">,</span> <span class="n">key</span><span class="p">)),</span>
+                    <span class="o">**</span><span class="n">empty_args</span>
+                <span class="p">)</span>
+                <span class="c1"># checking all groups</span>
+                <span class="k">for</span> <span class="n">key</span><span class="p">,</span> <span class="n">group</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="n">groups</span><span class="p">)</span>
+                <span class="c1"># and accepting the ones covering all members of the complex</span>
+                <span class="k">if</span> <span class="n">group</span> <span class="o">==</span> <span class="n">components</span>
+            <span class="p">)</span> <span class="ow">or</span> <span class="kc">None</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">_update_complex_attribute_classes</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="nb">complex</span><span class="o">.</span><span class="n">ComplexAggregator</span><span class="o">.</span><span class="n">_update_complex_attribute_classes_static</span><span class="p">(</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">annot</span><span class="o">.</span><span class="n">keys</span><span class="p">(),</span>
+            <span class="n">mod</span> <span class="o">=</span> <span class="n">sys</span><span class="o">.</span><span class="n">modules</span><span class="p">[</span><span class="vm">__name__</span><span class="p">],</span>
+        <span class="p">)</span>
+
+
+<div class="viewcode-block" id="AnnotationBase.load_proteins">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.AnnotationBase.html#pypath.core.annot.AnnotationBase.load_proteins">[docs]</a>
+    <span class="k">def</span> <span class="nf">load_proteins</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Retrieves a set of all UniProt IDs to have a base set of the entire</span>
+<span class="sd">        proteome.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">uniprots</span> <span class="o">=</span> <span class="nb">set</span><span class="p">(</span>
+            <span class="n">uniprot_db</span><span class="o">.</span><span class="n">all_uniprots</span><span class="p">(</span><span class="n">organism</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">ncbi_tax_id</span><span class="p">)</span>
+        <span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="AnnotationBase.get_reference_set">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.AnnotationBase.html#pypath.core.annot.AnnotationBase.get_reference_set">[docs]</a>
+    <span class="nd">@staticmethod</span>
+    <span class="k">def</span> <span class="nf">get_reference_set</span><span class="p">(</span>
+            <span class="n">proteins</span> <span class="o">=</span> <span class="p">(),</span>
+            <span class="n">complexes</span> <span class="o">=</span> <span class="p">(),</span>
+            <span class="n">use_complexes</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+            <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">,</span>
+            <span class="n">swissprot_only</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
+        <span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Retrieves the reference set i.e. the set of all entities which</span>
+<span class="sd">        potentially have annotation in this resource. Typically this is the</span>
+<span class="sd">        proteome of the organism from UniProt optionally with all the protein</span>
+<span class="sd">        complexes from the complex database.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">proteins</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="n">proteins</span> <span class="ow">or</span>
+            <span class="nb">sorted</span><span class="p">(</span>
+                <span class="n">uniprot_db</span><span class="o">.</span><span class="n">all_uniprots</span><span class="p">(</span>
+                    <span class="n">organism</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">,</span>
+                    <span class="n">swissprot</span> <span class="o">=</span> <span class="n">swissprot_only</span><span class="p">,</span>
+                <span class="p">)</span>
+            <span class="p">)</span>
+        <span class="p">)</span>
+
+        <span class="k">if</span> <span class="n">use_complexes</span><span class="p">:</span>
+
+            <span class="kn">import</span> <span class="nn">pypath.core.complex</span> <span class="k">as</span> <span class="nn">complex</span>
+
+            <span class="n">complexes</span> <span class="o">=</span> <span class="p">(</span>
+                <span class="n">complexes</span> <span class="ow">or</span>
+                <span class="nb">sorted</span><span class="p">(</span><span class="nb">complex</span><span class="o">.</span><span class="n">all_complexes</span><span class="p">())</span>
+            <span class="p">)</span>
+
+        <span class="n">reference_set</span> <span class="o">=</span> <span class="nb">sorted</span><span class="p">(</span>
+            <span class="n">itertools</span><span class="o">.</span><span class="n">chain</span><span class="p">(</span>
+                <span class="n">proteins</span><span class="p">,</span>
+                <span class="n">complexes</span><span class="p">,</span>
+            <span class="p">)</span>
+        <span class="p">)</span>
+
+        <span class="k">return</span> <span class="n">proteins</span><span class="p">,</span> <span class="n">complexes</span><span class="p">,</span> <span class="n">reference_set</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">_get_reference_set</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">get_reference_set</span><span class="p">(</span>
+            <span class="n">proteins</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">proteins</span><span class="p">,</span>
+            <span class="n">complexes</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">complexes</span><span class="p">,</span>
+            <span class="n">use_complexes</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">has_complexes</span><span class="p">(),</span>
+            <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">ncbi_tax_id</span><span class="p">,</span>
+            <span class="n">swissprot_only</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">swissprot_only</span><span class="p">,</span>
+        <span class="p">)</span>
+
+
+<div class="viewcode-block" id="AnnotationBase.set_reference_set">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.AnnotationBase.html#pypath.core.annot.AnnotationBase.set_reference_set">[docs]</a>
+    <span class="k">def</span> <span class="nf">set_reference_set</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Assigns the reference set to the :py:attr``reference_set`` attribute.</span>
+<span class="sd">        The reference set is the set of all entities which</span>
+<span class="sd">        potentially have annotation in this resource. Typically this is the</span>
+<span class="sd">        proteome of the organism from UniProt optionally with all the protein</span>
+<span class="sd">        complexes from the complex database.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">if</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">reference_set</span><span class="p">:</span>
+
+            <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">ncbi_tax_id</span> <span class="o">==</span> <span class="n">_const</span><span class="o">.</span><span class="n">NOT_ORGANISM_SPECIFIC</span><span class="p">:</span>
+
+                <span class="n">proteins</span><span class="p">,</span> <span class="n">complexes</span><span class="p">,</span> <span class="n">reference_set</span> <span class="o">=</span> <span class="p">(</span><span class="nb">set</span><span class="p">(),)</span> <span class="o">*</span> <span class="mi">3</span>
+
+            <span class="k">else</span><span class="p">:</span>
+
+                <span class="n">proteins</span><span class="p">,</span> <span class="n">complexes</span><span class="p">,</span> <span class="n">reference_set</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_get_reference_set</span><span class="p">()</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">proteins</span> <span class="o">=</span> <span class="n">proteins</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">complexes</span> <span class="o">=</span> <span class="n">complexes</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">reference_set</span> <span class="o">=</span> <span class="n">reference_set</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">has_complexes</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">entity_type</span> <span class="o">==</span> <span class="s1">&#39;complex&#39;</span> <span class="ow">or</span> <span class="bp">self</span><span class="o">.</span><span class="n">infer_complexes</span>
+
+
+    <span class="k">def</span> <span class="nf">_process_method</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">*</span><span class="n">args</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        By default it converts a set to dict of empty sets in order to make</span>
+<span class="sd">        it compatible with other methods.</span>
+<span class="sd">        Derived classes might override.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">annot</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">((</span><span class="n">u</span><span class="p">,</span> <span class="nb">set</span><span class="p">())</span> <span class="k">for</span> <span class="n">u</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span><span class="p">)</span>
+
+
+<div class="viewcode-block" id="AnnotationBase.select">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.AnnotationBase.html#pypath.core.annot.AnnotationBase.select">[docs]</a>
+    <span class="k">def</span> <span class="nf">select</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">method</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span> <span class="n">entity_type</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Retrieves a subset by filtering based on ``kwargs``.</span>
+<span class="sd">        Each argument should be a name and a value or set of values.</span>
+<span class="sd">        Elements having the provided values in the annotation will be</span>
+<span class="sd">        returned.</span>
+<span class="sd">        Returns a set of UniProt IDs.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">result</span> <span class="o">=</span> <span class="nb">set</span><span class="p">()</span>
+
+        <span class="n">names</span> <span class="o">=</span> <span class="nb">set</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">get_names</span><span class="p">())</span>
+
+        <span class="k">if</span> <span class="ow">not</span> <span class="nb">all</span><span class="p">(</span><span class="n">k</span> <span class="ow">in</span> <span class="n">names</span> <span class="k">for</span> <span class="n">k</span> <span class="ow">in</span> <span class="n">kwargs</span><span class="o">.</span><span class="n">keys</span><span class="p">()):</span>
+
+            <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s1">&#39;Unknown field names: </span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="p">(</span>
+                    <span class="s1">&#39;, &#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="nb">sorted</span><span class="p">(</span><span class="nb">set</span><span class="p">(</span><span class="n">kwargs</span><span class="o">.</span><span class="n">keys</span><span class="p">())</span> <span class="o">-</span> <span class="n">names</span><span class="p">))</span>
+                <span class="p">)</span>
+            <span class="p">)</span>
+
+        <span class="k">for</span> <span class="n">uniprot</span><span class="p">,</span> <span class="n">annot</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">annot</span><span class="p">):</span>
+
+            <span class="k">for</span> <span class="n">a</span> <span class="ow">in</span> <span class="n">annot</span><span class="p">:</span>
+
+                <span class="c1"># we either call a method on all records</span>
+                <span class="c1"># or check against conditions provided in **kwargs</span>
+                <span class="k">if</span> <span class="p">(</span>
+                    <span class="ow">not</span> <span class="nb">callable</span><span class="p">(</span><span class="n">method</span><span class="p">)</span> <span class="ow">or</span>
+                    <span class="n">method</span><span class="p">(</span><span class="n">a</span><span class="p">)</span>
+                <span class="p">)</span> <span class="ow">and</span> <span class="nb">all</span><span class="p">(</span>
+                    <span class="p">(</span>
+                        <span class="c1"># simple agreement</span>
+                        <span class="p">(</span>
+                            <span class="nb">getattr</span><span class="p">(</span><span class="n">a</span><span class="p">,</span> <span class="n">name</span><span class="p">)</span> <span class="o">==</span> <span class="n">value</span>
+                        <span class="p">)</span>
+                        <span class="c1"># custom method returns bool</span>
+                        <span class="ow">or</span>
+                        <span class="p">(</span>
+                            <span class="nb">callable</span><span class="p">(</span><span class="n">value</span><span class="p">)</span>
+                            <span class="ow">and</span>
+                            <span class="n">value</span><span class="p">(</span><span class="nb">getattr</span><span class="p">(</span><span class="n">a</span><span class="p">,</span> <span class="n">name</span><span class="p">))</span>
+                        <span class="p">)</span>
+                        <span class="c1"># multiple value in annotation slot</span>
+                        <span class="c1"># and value is a set: checking if they have</span>
+                        <span class="c1"># any in common</span>
+                        <span class="ow">or</span>
+                        <span class="p">(</span>
+                            <span class="nb">isinstance</span><span class="p">(</span><span class="nb">getattr</span><span class="p">(</span><span class="n">a</span><span class="p">,</span> <span class="n">name</span><span class="p">),</span> <span class="n">_const</span><span class="o">.</span><span class="n">LIST_LIKE</span><span class="p">)</span>
+                            <span class="ow">and</span>
+                            <span class="nb">isinstance</span><span class="p">(</span><span class="n">value</span><span class="p">,</span> <span class="nb">set</span><span class="p">)</span>
+                            <span class="ow">and</span>
+                            <span class="nb">set</span><span class="p">(</span><span class="nb">getattr</span><span class="p">(</span><span class="n">a</span><span class="p">,</span> <span class="n">name</span><span class="p">))</span> <span class="o">&amp;</span> <span class="n">value</span>
+                        <span class="p">)</span>
+                        <span class="c1"># search value is a set, checking if contains</span>
+                        <span class="c1"># the record&#39;s value</span>
+                        <span class="ow">or</span>
+                        <span class="p">(</span>
+                            <span class="nb">isinstance</span><span class="p">(</span><span class="n">value</span><span class="p">,</span> <span class="nb">set</span><span class="p">)</span>
+                            <span class="ow">and</span>
+                            <span class="nb">getattr</span><span class="p">(</span><span class="n">a</span><span class="p">,</span> <span class="n">name</span><span class="p">)</span> <span class="ow">in</span> <span class="n">value</span>
+                        <span class="p">)</span>
+                        <span class="c1"># record&#39;s value contains multiple elements</span>
+                        <span class="c1"># (set, list or tuple), checking if it contains</span>
+                        <span class="c1"># the search value</span>
+                        <span class="ow">or</span>
+                        <span class="p">(</span>
+                            <span class="nb">isinstance</span><span class="p">(</span><span class="nb">getattr</span><span class="p">(</span><span class="n">a</span><span class="p">,</span> <span class="n">name</span><span class="p">),</span> <span class="n">_const</span><span class="o">.</span><span class="n">LIST_LIKE</span><span class="p">)</span>
+                            <span class="ow">and</span>
+                            <span class="n">value</span> <span class="ow">in</span> <span class="nb">getattr</span><span class="p">(</span><span class="n">a</span><span class="p">,</span> <span class="n">name</span><span class="p">)</span>
+                        <span class="p">)</span>
+                    <span class="p">)</span>
+                    <span class="k">for</span> <span class="n">name</span><span class="p">,</span> <span class="n">value</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="n">kwargs</span><span class="p">)</span>
+                <span class="p">):</span>
+
+                    <span class="n">result</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">uniprot</span><span class="p">)</span>
+                    <span class="k">break</span>
+
+        <span class="n">result</span> <span class="o">=</span> <span class="n">entity</span><span class="o">.</span><span class="n">Entity</span><span class="o">.</span><span class="n">filter_entity_type</span><span class="p">(</span><span class="n">result</span><span class="p">,</span> <span class="n">entity_type</span><span class="p">)</span>
+
+        <span class="k">return</span> <span class="n">result</span></div>
+
+
+
+    <span class="c1"># synonym for old name</span>
+    <span class="n">get_subset</span> <span class="o">=</span> <span class="n">select</span>
+
+
+<div class="viewcode-block" id="AnnotationBase.labels">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.AnnotationBase.html#pypath.core.annot.AnnotationBase.labels">[docs]</a>
+    <span class="k">def</span> <span class="nf">labels</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">method</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Same as ``select`` but returns a list of labels (more human readable).</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">return</span> <span class="n">mapping</span><span class="o">.</span><span class="n">label</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">select</span><span class="p">(</span><span class="n">method</span> <span class="o">=</span> <span class="n">method</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">))</span></div>
+
+
+
+<div class="viewcode-block" id="AnnotationBase.show">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.AnnotationBase.html#pypath.core.annot.AnnotationBase.show">[docs]</a>
+    <span class="k">def</span> <span class="nf">show</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">method</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span> <span class="n">table_param</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Same as ``select`` but prints a table to the console with basic</span>
+<span class="sd">        information from the UniProt datasheets.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">table_param</span> <span class="o">=</span> <span class="n">table_param</span> <span class="ow">or</span> <span class="p">{}</span>
+
+        <span class="n">utils_uniprot</span><span class="o">.</span><span class="n">info</span><span class="p">(</span>
+            <span class="o">*</span><span class="bp">self</span><span class="o">.</span><span class="n">select</span><span class="p">(</span><span class="n">method</span> <span class="o">=</span> <span class="n">method</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">),</span>
+            <span class="o">**</span><span class="n">table_param</span>
+        <span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="AnnotationBase.get_subset_bool_array">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.AnnotationBase.html#pypath.core.annot.AnnotationBase.get_subset_bool_array">[docs]</a>
+    <span class="k">def</span> <span class="nf">get_subset_bool_array</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">reference_set</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Returns a boolean vector with True and False values for each entity</span>
+<span class="sd">        in the reference set. The values represent presence absence data</span>
+<span class="sd">        in the simplest case, but by providing ``kwargs`` any kind of matching</span>
+<span class="sd">        and filtering is possible. ``kwargs`` are passed to the ``select``</span>
+<span class="sd">        method.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">reference_set</span> <span class="o">=</span> <span class="n">reference_set</span> <span class="ow">or</span> <span class="bp">self</span><span class="o">.</span><span class="n">reference_set</span>
+
+        <span class="n">subset</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">get_subset</span><span class="p">(</span><span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
+
+        <span class="k">return</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">([</span>
+            <span class="n">entity</span> <span class="ow">in</span> <span class="n">subset</span>
+            <span class="k">for</span> <span class="n">entity</span> <span class="ow">in</span> <span class="n">reference_set</span>
+        <span class="p">])</span></div>
+
+
+
+<div class="viewcode-block" id="AnnotationBase.to_bool_array">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.AnnotationBase.html#pypath.core.annot.AnnotationBase.to_bool_array">[docs]</a>
+    <span class="k">def</span> <span class="nf">to_bool_array</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">reference_set</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Returns a presence/absence boolean array for a reference set.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">total</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">to_set</span><span class="p">()</span>
+
+        <span class="k">return</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">([</span>
+            <span class="n">entity</span> <span class="ow">in</span> <span class="n">total</span>
+            <span class="k">for</span> <span class="n">entity</span> <span class="ow">in</span> <span class="n">reference_set</span>
+        <span class="p">])</span></div>
+
+
+
+<div class="viewcode-block" id="AnnotationBase.to_set">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.AnnotationBase.html#pypath.core.annot.AnnotationBase.to_set">[docs]</a>
+    <span class="k">def</span> <span class="nf">to_set</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Returns the entities present in this annotation resource as a set.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">return</span> <span class="nb">set</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">annot</span><span class="o">.</span><span class="n">keys</span><span class="p">())</span></div>
+
+
+
+    <span class="nd">@staticmethod</span>
+    <span class="k">def</span> <span class="nf">_entity_types</span><span class="p">(</span><span class="n">entity_types</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="p">(</span>
+            <span class="p">{</span><span class="n">entity_types</span><span class="p">}</span>
+                <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">entity_types</span><span class="p">,</span> <span class="nb">str</span><span class="p">)</span> <span class="k">else</span>
+            <span class="n">entity_types</span>
+        <span class="p">)</span>
+
+
+<div class="viewcode-block" id="AnnotationBase.all_entities">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.AnnotationBase.html#pypath.core.annot.AnnotationBase.all_entities">[docs]</a>
+    <span class="k">def</span> <span class="nf">all_entities</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">entity_types</span> <span class="o">=</span> <span class="kc">None</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        All entities annotated in this resource.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">entity_types</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_entity_types</span><span class="p">(</span><span class="n">entity_types</span><span class="p">)</span>
+
+        <span class="k">return</span> <span class="nb">sorted</span><span class="p">((</span>
+            <span class="n">k</span> <span class="k">for</span> <span class="n">k</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">annot</span><span class="o">.</span><span class="n">keys</span><span class="p">()</span>
+            <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">_match_entity_type</span><span class="p">(</span><span class="n">k</span><span class="p">,</span> <span class="n">entity_types</span><span class="p">)</span>
+        <span class="p">))</span></div>
+
+
+
+<div class="viewcode-block" id="AnnotationBase.all_proteins">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.AnnotationBase.html#pypath.core.annot.AnnotationBase.all_proteins">[docs]</a>
+    <span class="k">def</span> <span class="nf">all_proteins</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        All UniProt IDs annotated in this resource.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">return</span> <span class="nb">sorted</span><span class="p">((</span>
+            <span class="n">k</span> <span class="k">for</span> <span class="n">k</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">annot</span><span class="o">.</span><span class="n">keys</span><span class="p">()</span>
+            <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">is_protein</span><span class="p">(</span><span class="n">k</span><span class="p">)</span>
+        <span class="p">))</span></div>
+
+
+
+<div class="viewcode-block" id="AnnotationBase.all_complexes">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.AnnotationBase.html#pypath.core.annot.AnnotationBase.all_complexes">[docs]</a>
+    <span class="k">def</span> <span class="nf">all_complexes</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        All protein complexes annotated in this resource.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">return</span> <span class="nb">sorted</span><span class="p">((</span>
+            <span class="n">k</span>
+            <span class="k">for</span> <span class="n">k</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">annot</span><span class="o">.</span><span class="n">keys</span><span class="p">()</span>
+            <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">is_complex</span><span class="p">(</span><span class="n">k</span><span class="p">)</span>
+        <span class="p">))</span></div>
+
+
+
+<div class="viewcode-block" id="AnnotationBase.all_mirnas">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.AnnotationBase.html#pypath.core.annot.AnnotationBase.all_mirnas">[docs]</a>
+    <span class="k">def</span> <span class="nf">all_mirnas</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        All miRNAs annotated in this resource.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">return</span> <span class="nb">sorted</span><span class="p">((</span>
+            <span class="n">k</span> <span class="k">for</span> <span class="n">k</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">annot</span><span class="o">.</span><span class="n">keys</span><span class="p">()</span>
+            <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">is_mirna</span><span class="p">(</span><span class="n">k</span><span class="p">)</span>
+        <span class="p">))</span></div>
+
+
+
+    <span class="nd">@staticmethod</span>
+    <span class="k">def</span> <span class="nf">is_protein</span><span class="p">(</span><span class="n">key</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="n">entity</span><span class="o">.</span><span class="n">Entity</span><span class="o">.</span><span class="n">_is_protein</span><span class="p">(</span><span class="n">key</span><span class="p">)</span>
+
+
+    <span class="nd">@staticmethod</span>
+    <span class="k">def</span> <span class="nf">is_mirna</span><span class="p">(</span><span class="n">key</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="n">entity</span><span class="o">.</span><span class="n">Entity</span><span class="o">.</span><span class="n">_is_mirna</span><span class="p">(</span><span class="n">key</span><span class="p">)</span>
+
+
+    <span class="nd">@staticmethod</span>
+    <span class="k">def</span> <span class="nf">is_complex</span><span class="p">(</span><span class="n">key</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="n">entity</span><span class="o">.</span><span class="n">Entity</span><span class="o">.</span><span class="n">_is_complex</span><span class="p">(</span><span class="n">key</span><span class="p">)</span>
+
+
+    <span class="nd">@classmethod</span>
+    <span class="k">def</span> <span class="nf">get_entity_type</span><span class="p">(</span><span class="bp">cls</span><span class="p">,</span> <span class="n">key</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="n">entity</span><span class="o">.</span><span class="n">Entity</span><span class="o">.</span><span class="n">_get_entity_type</span><span class="p">(</span><span class="n">key</span><span class="p">)</span>
+
+
+    <span class="nd">@classmethod</span>
+    <span class="k">def</span> <span class="nf">_match_entity_type</span><span class="p">(</span><span class="bp">cls</span><span class="p">,</span> <span class="n">key</span><span class="p">,</span> <span class="n">entity_types</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="ow">not</span> <span class="n">entity_types</span> <span class="ow">or</span> <span class="bp">cls</span><span class="o">.</span><span class="n">get_entity_type</span><span class="p">(</span><span class="n">key</span><span class="p">)</span> <span class="ow">in</span> <span class="n">entity_types</span>
+
+
+<div class="viewcode-block" id="AnnotationBase.numof_records">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.AnnotationBase.html#pypath.core.annot.AnnotationBase.numof_records">[docs]</a>
+    <span class="k">def</span> <span class="nf">numof_records</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">entity_types</span> <span class="o">=</span> <span class="kc">None</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        The total number of annotation records.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">entity_types</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_entity_types</span><span class="p">(</span><span class="n">entity_types</span><span class="p">)</span>
+
+        <span class="k">return</span> <span class="nb">sum</span><span class="p">(</span>
+            <span class="nb">max</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">a</span><span class="p">),</span> <span class="mi">1</span><span class="p">)</span>
+            <span class="k">for</span> <span class="n">k</span><span class="p">,</span> <span class="n">a</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">annot</span><span class="p">)</span>
+            <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">_match_entity_type</span><span class="p">(</span><span class="n">k</span><span class="p">,</span> <span class="n">entity_types</span><span class="p">)</span>
+        <span class="p">)</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">numof_protein_records</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">numof_records</span><span class="p">(</span><span class="n">entity_types</span> <span class="o">=</span> <span class="p">{</span><span class="s1">&#39;protein&#39;</span><span class="p">})</span>
+
+
+    <span class="k">def</span> <span class="nf">numof_mirna_records</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">numof_records</span><span class="p">(</span><span class="n">entity_types</span> <span class="o">=</span> <span class="p">{</span><span class="s1">&#39;mirna&#39;</span><span class="p">})</span>
+
+
+    <span class="k">def</span> <span class="nf">numof_complex_records</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">numof_records</span><span class="p">(</span><span class="n">entity_types</span> <span class="o">=</span> <span class="p">{</span><span class="s1">&#39;complex&#39;</span><span class="p">})</span>
+
+
+<div class="viewcode-block" id="AnnotationBase.numof_entities">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.AnnotationBase.html#pypath.core.annot.AnnotationBase.numof_entities">[docs]</a>
+    <span class="k">def</span> <span class="nf">numof_entities</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        The number of annotated entities in the resource.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">return</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">annot</span><span class="p">)</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">_numof_entities</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">entity_types</span> <span class="o">=</span> <span class="kc">None</span><span class="p">):</span>
+
+        <span class="n">entity_types</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_entity_types</span><span class="p">(</span><span class="n">entity_types</span><span class="p">)</span>
+
+        <span class="k">return</span> <span class="nb">len</span><span class="p">([</span>
+            <span class="n">k</span> <span class="k">for</span> <span class="n">k</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">annot</span><span class="o">.</span><span class="n">keys</span><span class="p">()</span>
+            <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">_match_entity_type</span><span class="p">(</span><span class="n">k</span><span class="p">,</span> <span class="n">entity_types</span><span class="p">)</span>
+        <span class="p">])</span>
+
+
+    <span class="k">def</span> <span class="nf">numof_proteins</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_numof_entities</span><span class="p">(</span><span class="n">entity_types</span> <span class="o">=</span> <span class="p">{</span><span class="s1">&#39;protein&#39;</span><span class="p">})</span>
+
+
+    <span class="k">def</span> <span class="nf">numof_mirnas</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_numof_entities</span><span class="p">(</span><span class="n">entity_types</span> <span class="o">=</span> <span class="p">{</span><span class="s1">&#39;mirna&#39;</span><span class="p">})</span>
+
+
+    <span class="k">def</span> <span class="nf">numof_complexes</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_numof_entities</span><span class="p">(</span><span class="n">entity_types</span> <span class="o">=</span> <span class="p">{</span><span class="s1">&#39;complex&#39;</span><span class="p">})</span>
+
+
+    <span class="k">def</span> <span class="fm">__repr__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="p">(</span>
+            <span class="s1">&#39;&lt;</span><span class="si">%s</span><span class="s1"> annotations: </span><span class="si">%u</span><span class="s1"> records about </span><span class="si">%u</span><span class="s1"> entities&gt;&#39;</span> <span class="o">%</span> <span class="p">(</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">,</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">numof_records</span><span class="p">(),</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">numof_entities</span><span class="p">(),</span>
+            <span class="p">)</span>
+        <span class="p">)</span>
+
+
+<div class="viewcode-block" id="AnnotationBase.to_array">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.AnnotationBase.html#pypath.core.annot.AnnotationBase.to_array">[docs]</a>
+    <span class="k">def</span> <span class="nf">to_array</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">reference_set</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span> <span class="n">use_fields</span> <span class="o">=</span> <span class="kc">None</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Returns an entity vs feature array. In case of more complex</span>
+<span class="sd">        annotations this might be huge.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">use_fields</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="n">use_fields</span> <span class="ow">or</span> <span class="p">(</span>
+                <span class="n">default_fields</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">]</span>
+                    <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">name</span> <span class="ow">in</span> <span class="n">default_fields</span> <span class="k">else</span>
+                <span class="kc">None</span>
+            <span class="p">)</span>
+        <span class="p">)</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span>
+            <span class="s1">&#39;Creating boolean array from `</span><span class="si">%s</span><span class="s1">` annotation data.&#39;</span> <span class="o">%</span> <span class="bp">self</span><span class="o">.</span><span class="n">name</span>
+        <span class="p">)</span>
+
+        <span class="n">reference_set</span> <span class="o">=</span> <span class="n">reference_set</span> <span class="ow">or</span> <span class="bp">self</span><span class="o">.</span><span class="n">reference_set</span>
+
+        <span class="n">all_fields</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">get_names</span><span class="p">()</span>
+        <span class="n">fields</span> <span class="o">=</span> <span class="n">use_fields</span> <span class="ow">or</span> <span class="n">all_fields</span>
+        <span class="n">ifields</span> <span class="o">=</span> <span class="nb">tuple</span><span class="p">(</span>
+            <span class="n">i</span> <span class="k">for</span> <span class="n">i</span><span class="p">,</span> <span class="n">field</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">all_fields</span><span class="p">)</span> <span class="k">if</span> <span class="n">field</span> <span class="ow">in</span> <span class="n">fields</span>
+        <span class="p">)</span>
+        <span class="n">result</span> <span class="o">=</span> <span class="p">[</span>
+            <span class="p">(</span>
+                <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">,),</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">to_bool_array</span><span class="p">(</span><span class="n">reference_set</span> <span class="o">=</span> <span class="n">reference_set</span><span class="p">)</span>
+            <span class="p">)</span>
+        <span class="p">]</span>
+
+        <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="n">xrange</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">fields</span><span class="p">)):</span>
+
+            <span class="n">this_ifields</span> <span class="o">=</span> <span class="n">ifields</span><span class="p">[:</span><span class="n">i</span> <span class="o">+</span> <span class="mi">1</span><span class="p">]</span>
+            <span class="n">this_fields</span>  <span class="o">=</span>  <span class="n">fields</span><span class="p">[:</span><span class="n">i</span> <span class="o">+</span> <span class="mi">1</span><span class="p">]</span>
+
+            <span class="n">value_combinations</span> <span class="o">=</span> <span class="nb">set</span><span class="p">(</span>
+                <span class="nb">tuple</span><span class="p">(</span><span class="n">annot</span><span class="p">[</span><span class="n">j</span><span class="p">]</span> <span class="k">for</span> <span class="n">j</span> <span class="ow">in</span> <span class="n">this_ifields</span><span class="p">)</span>
+                <span class="k">for</span> <span class="n">annots</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">annot</span><span class="o">.</span><span class="n">values</span><span class="p">()</span>
+                <span class="k">for</span> <span class="n">annot</span> <span class="ow">in</span> <span class="n">annots</span>
+            <span class="p">)</span>
+            <span class="n">value_combinations</span> <span class="o">=</span> <span class="nb">sorted</span><span class="p">(</span>
+                <span class="n">values</span>
+                <span class="k">for</span> <span class="n">values</span> <span class="ow">in</span> <span class="n">value_combinations</span>
+                <span class="k">if</span> <span class="ow">not</span> <span class="nb">any</span><span class="p">(</span>
+                    <span class="nb">isinstance</span><span class="p">(</span><span class="n">v</span><span class="p">,</span> <span class="p">(</span><span class="nb">type</span><span class="p">(</span><span class="kc">None</span><span class="p">),</span> <span class="nb">float</span><span class="p">,</span> <span class="nb">int</span><span class="p">))</span>
+                    <span class="k">for</span> <span class="n">v</span> <span class="ow">in</span> <span class="n">values</span>
+                <span class="p">)</span>
+            <span class="p">)</span>
+
+            <span class="k">for</span> <span class="n">values</span> <span class="ow">in</span> <span class="n">value_combinations</span><span class="p">:</span>
+
+                <span class="n">labels</span> <span class="o">=</span> <span class="nb">tuple</span><span class="p">(</span>
+                    <span class="s1">&#39;not-</span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="n">this_fields</span><span class="p">[</span><span class="n">ival</span><span class="p">]</span>
+                        <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">val</span><span class="p">,</span> <span class="nb">bool</span><span class="p">)</span> <span class="ow">and</span> <span class="ow">not</span> <span class="n">val</span> <span class="k">else</span>
+                    <span class="n">this_fields</span><span class="p">[</span><span class="n">ival</span><span class="p">]</span>
+                        <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">val</span><span class="p">,</span> <span class="nb">bool</span><span class="p">)</span> <span class="ow">and</span> <span class="n">val</span> <span class="k">else</span>
+                    <span class="n">val</span>
+                    <span class="k">for</span> <span class="n">ival</span><span class="p">,</span> <span class="n">val</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">values</span><span class="p">)</span>
+                <span class="p">)</span>
+
+                <span class="n">this_values</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">(</span><span class="nb">zip</span><span class="p">(</span><span class="n">this_fields</span><span class="p">,</span> <span class="n">values</span><span class="p">))</span>
+
+                <span class="n">this_array</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">get_subset_bool_array</span><span class="p">(</span>
+                    <span class="n">reference_set</span> <span class="o">=</span> <span class="n">reference_set</span><span class="p">,</span>
+                    <span class="o">**</span><span class="n">this_values</span>
+                <span class="p">)</span>
+
+                <span class="n">result</span><span class="o">.</span><span class="n">append</span><span class="p">(</span>
+                    <span class="p">(</span>
+                        <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">,)</span> <span class="o">+</span> <span class="n">labels</span><span class="p">,</span>
+                        <span class="n">this_array</span><span class="p">,</span>
+                    <span class="p">)</span>
+                <span class="p">)</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span>
+            <span class="s1">&#39;Boolean array has been created from &#39;</span>
+            <span class="s1">&#39;`</span><span class="si">%s</span><span class="s1">` annotation data.&#39;</span> <span class="o">%</span> <span class="bp">self</span><span class="o">.</span><span class="n">name</span>
+        <span class="p">)</span>
+
+        <span class="k">return</span> <span class="p">(</span>
+            <span class="nb">tuple</span><span class="p">(</span><span class="n">r</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="k">for</span> <span class="n">r</span> <span class="ow">in</span> <span class="n">result</span><span class="p">),</span>
+            <span class="n">np</span><span class="o">.</span><span class="n">vstack</span><span class="p">([</span><span class="n">r</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="k">for</span> <span class="n">r</span> <span class="ow">in</span> <span class="n">result</span><span class="p">])</span><span class="o">.</span><span class="n">T</span>
+        <span class="p">)</span></div>
+
+
+
+    <span class="nd">@property</span>
+    <span class="k">def</span> <span class="nf">has_fields</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="nb">any</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">annot</span><span class="o">.</span><span class="n">values</span><span class="p">())</span>
+
+
+<div class="viewcode-block" id="AnnotationBase.make_df">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.AnnotationBase.html#pypath.core.annot.AnnotationBase.make_df">[docs]</a>
+    <span class="k">def</span> <span class="nf">make_df</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">rebuild</span> <span class="o">=</span> <span class="kc">False</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Compiles a ``pandas.DataFrame`` from the annotation data.</span>
+<span class="sd">        The data frame will be assigned to :py:attr``df``.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span><span class="s1">&#39;Creating dataframe from `</span><span class="si">%s</span><span class="s1">` annotations.&#39;</span> <span class="o">%</span> <span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">)</span>
+
+        <span class="k">if</span> <span class="nb">hasattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">&#39;df&#39;</span><span class="p">)</span> <span class="ow">and</span> <span class="ow">not</span> <span class="n">rebuild</span><span class="p">:</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span><span class="s1">&#39;Data frame already exists, rebuild not requested.&#39;</span><span class="p">)</span>
+            <span class="k">return</span>
+
+        <span class="n">discard</span> <span class="o">=</span> <span class="p">{</span><span class="s1">&#39;n/a&#39;</span><span class="p">,</span> <span class="kc">None</span><span class="p">}</span>
+
+        <span class="n">columns</span> <span class="o">=</span> <span class="p">[</span>
+            <span class="s1">&#39;uniprot&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;genesymbol&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;entity_type&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;source&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;label&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;value&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;record_id&#39;</span><span class="p">,</span>
+        <span class="p">]</span>
+
+        <span class="n">has_fields</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">has_fields</span>
+        <span class="n">records</span> <span class="o">=</span> <span class="p">[]</span>
+        <span class="n">irec</span> <span class="o">=</span> <span class="mi">0</span>
+
+        <span class="k">for</span> <span class="n">element</span><span class="p">,</span> <span class="n">annots</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">annot</span><span class="p">):</span>
+
+            <span class="k">if</span> <span class="ow">not</span> <span class="n">element</span><span class="p">:</span>
+
+                <span class="k">continue</span>
+
+            <span class="n">entity_type</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">get_entity_type</span><span class="p">(</span><span class="n">element</span><span class="p">)</span>
+
+            <span class="n">genesymbol_str</span> <span class="o">=</span> <span class="p">(</span>
+                <span class="s1">&#39;COMPLEX:</span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="n">element</span><span class="o">.</span><span class="n">genesymbol_str</span>
+                    <span class="k">if</span> <span class="nb">hasattr</span><span class="p">(</span><span class="n">element</span><span class="p">,</span> <span class="s1">&#39;genesymbol_str&#39;</span><span class="p">)</span> <span class="k">else</span>
+                <span class="s1">&#39;COMPLEX:</span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="p">(</span>
+                    <span class="nb">complex</span><span class="o">.</span><span class="n">get_db</span><span class="p">()</span><span class="o">.</span><span class="n">complexes</span><span class="p">[</span><span class="n">element</span><span class="p">]</span><span class="o">.</span><span class="n">genesymbol_str</span>
+                <span class="p">)</span>
+                    <span class="k">if</span> <span class="n">element</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s1">&#39;COMPLEX:&#39;</span><span class="p">)</span> <span class="k">else</span>
+                <span class="p">(</span>
+                    <span class="n">mapping</span><span class="o">.</span><span class="n">label</span><span class="p">(</span>
+                        <span class="n">element</span><span class="p">,</span>
+                        <span class="n">entity_type</span> <span class="o">=</span> <span class="n">entity_type</span><span class="p">,</span>
+                        <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">ncbi_tax_id</span><span class="p">,</span>
+                    <span class="p">)</span> <span class="ow">or</span>
+                    <span class="s1">&#39;&#39;</span>
+                <span class="p">)</span>
+            <span class="p">)</span>
+
+            <span class="k">if</span> <span class="ow">not</span> <span class="n">has_fields</span><span class="p">:</span>
+
+                <span class="n">records</span><span class="o">.</span><span class="n">append</span><span class="p">([</span>
+                    <span class="n">element</span><span class="o">.</span><span class="fm">__str__</span><span class="p">(),</span>
+                    <span class="n">genesymbol_str</span><span class="p">,</span>
+                    <span class="n">entity_type</span><span class="p">,</span>
+                    <span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">,</span>
+                    <span class="s1">&#39;in </span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">,</span>
+                    <span class="s1">&#39;yes&#39;</span><span class="p">,</span>
+                    <span class="n">irec</span><span class="p">,</span>
+                <span class="p">])</span>
+
+                <span class="n">irec</span> <span class="o">+=</span> <span class="mi">1</span>
+
+            <span class="k">for</span> <span class="n">annot</span> <span class="ow">in</span> <span class="n">annots</span><span class="p">:</span>
+
+                <span class="k">for</span> <span class="n">label</span><span class="p">,</span> <span class="n">value</span> <span class="ow">in</span> <span class="nb">zip</span><span class="p">(</span><span class="n">annot</span><span class="o">.</span><span class="n">_fields</span><span class="p">,</span> <span class="n">annot</span><span class="p">):</span>
+
+                    <span class="k">if</span> <span class="n">value</span> <span class="ow">in</span> <span class="n">discard</span><span class="p">:</span>
+
+                        <span class="k">continue</span>
+
+                    <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">value</span><span class="p">,</span> <span class="p">(</span><span class="nb">set</span><span class="p">,</span> <span class="nb">list</span><span class="p">,</span> <span class="nb">tuple</span><span class="p">)):</span>
+
+                        <span class="n">value</span> <span class="o">=</span> <span class="s1">&#39;;&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="nb">map</span><span class="p">(</span><span class="nb">str</span><span class="p">,</span> <span class="n">value</span><span class="p">))</span>
+
+                    <span class="n">records</span><span class="o">.</span><span class="n">append</span><span class="p">([</span>
+                        <span class="n">element</span><span class="o">.</span><span class="fm">__str__</span><span class="p">(),</span>
+                        <span class="n">genesymbol_str</span><span class="p">,</span>
+                        <span class="n">entity_type</span><span class="p">,</span>
+                        <span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">,</span>
+                        <span class="n">label</span><span class="p">,</span>
+                        <span class="nb">str</span><span class="p">(</span><span class="n">value</span><span class="p">),</span>
+                        <span class="n">irec</span><span class="p">,</span>
+                    <span class="p">])</span>
+
+                <span class="n">irec</span> <span class="o">+=</span> <span class="mi">1</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">df</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">(</span>
+            <span class="n">records</span><span class="p">,</span>
+            <span class="n">columns</span> <span class="o">=</span> <span class="n">columns</span><span class="p">,</span>
+        <span class="p">)</span><span class="o">.</span><span class="n">astype</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_dtypes</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="AnnotationBase.coverage">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.AnnotationBase.html#pypath.core.annot.AnnotationBase.coverage">[docs]</a>
+    <span class="k">def</span> <span class="nf">coverage</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">other</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Calculates the coverage of the annotation i.e. the proportion of</span>
+<span class="sd">        entities having at least one record in this annotation resource</span>
+<span class="sd">        for an arbitrary set of entities.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">other</span> <span class="o">=</span> <span class="n">other</span> <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">other</span><span class="p">,</span> <span class="nb">set</span><span class="p">)</span> <span class="k">else</span> <span class="nb">set</span><span class="p">(</span><span class="n">other</span><span class="p">)</span>
+
+        <span class="k">return</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span> <span class="o">&amp;</span> <span class="n">other</span><span class="p">)</span> <span class="o">/</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">proportion</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">other</span><span class="p">):</span>
+
+        <span class="n">other</span> <span class="o">=</span> <span class="n">other</span> <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">other</span><span class="p">,</span> <span class="nb">set</span><span class="p">)</span> <span class="k">else</span> <span class="nb">set</span><span class="p">(</span><span class="n">other</span><span class="p">)</span>
+
+        <span class="k">return</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span> <span class="o">&amp;</span> <span class="n">other</span><span class="p">)</span> <span class="o">/</span> <span class="nb">len</span><span class="p">(</span><span class="n">other</span><span class="p">)</span> <span class="k">if</span> <span class="n">other</span> <span class="k">else</span> <span class="mf">.0</span>
+
+
+<div class="viewcode-block" id="AnnotationBase.subset_intersection">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.AnnotationBase.html#pypath.core.annot.AnnotationBase.subset_intersection">[docs]</a>
+    <span class="k">def</span> <span class="nf">subset_intersection</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">universe</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Calculates the proportion of entities in a subset occuring in the</span>
+<span class="sd">        set ``universe``. The subset is selected by passing ``kwargs`` to the</span>
+<span class="sd">        ``select`` method.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">subset</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">get_subset</span><span class="p">(</span><span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
+
+        <span class="k">return</span> <span class="nb">len</span><span class="p">(</span><span class="n">subset</span> <span class="o">&amp;</span> <span class="n">universe</span><span class="p">)</span> <span class="o">/</span> <span class="nb">len</span><span class="p">(</span><span class="n">subset</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="AnnotationBase.get_values">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.AnnotationBase.html#pypath.core.annot.AnnotationBase.get_values">[docs]</a>
+    <span class="k">def</span> <span class="nf">get_values</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">name</span><span class="p">,</span> <span class="n">exclude_none</span> <span class="o">=</span> <span class="kc">True</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Returns the set of all possible values of a field. E.g. if the</span>
+<span class="sd">        records of this annotation have a field ``cell_type`` then calling</span>
+<span class="sd">        this method can tell you that across all records the values of</span>
+<span class="sd">        this field might be ``{&#39;macrophage&#39;, &#39;epithelial_cell&#39;, ...}``.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">values</span> <span class="o">=</span>  <span class="p">{</span>
+            <span class="n">val</span>
+            <span class="k">for</span> <span class="n">aset</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">annot</span><span class="o">.</span><span class="n">values</span><span class="p">()</span>
+            <span class="k">for</span> <span class="n">a</span> <span class="ow">in</span> <span class="n">aset</span>
+            <span class="k">for</span> <span class="n">val</span> <span class="ow">in</span> <span class="p">(</span>
+                <span class="c1"># to support tuple values</span>
+                <span class="nb">getattr</span><span class="p">(</span><span class="n">a</span><span class="p">,</span> <span class="n">name</span><span class="p">)</span>
+                    <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="nb">getattr</span><span class="p">(</span><span class="n">a</span><span class="p">,</span> <span class="n">name</span><span class="p">),</span> <span class="n">_const</span><span class="o">.</span><span class="n">LIST_LIKE</span><span class="p">)</span> <span class="k">else</span>
+                <span class="p">(</span><span class="nb">getattr</span><span class="p">(</span><span class="n">a</span><span class="p">,</span> <span class="n">name</span><span class="p">),)</span>
+            <span class="p">)</span>
+        <span class="p">}</span>
+
+        <span class="k">if</span> <span class="n">exclude_none</span><span class="p">:</span>
+
+            <span class="n">values</span><span class="o">.</span><span class="n">discard</span><span class="p">(</span><span class="kc">None</span><span class="p">)</span>
+
+        <span class="k">return</span> <span class="n">values</span></div>
+
+
+
+<div class="viewcode-block" id="AnnotationBase.get_names">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.AnnotationBase.html#pypath.core.annot.AnnotationBase.get_names">[docs]</a>
+    <span class="k">def</span> <span class="nf">get_names</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Returns the list of field names in the records. The annotation</span>
+<span class="sd">        consists of uniform records and each entity might be annotated</span>
+<span class="sd">        with one or more records. Each record is a tuple of fields, for</span>
+<span class="sd">        example ``(&#39;cell_type&#39;, &#39;expression_level&#39;, &#39;score&#39;)``.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">names</span> <span class="o">=</span> <span class="p">()</span>
+
+        <span class="k">for</span> <span class="n">values</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">annot</span><span class="o">.</span><span class="n">values</span><span class="p">():</span>
+
+            <span class="k">if</span> <span class="n">values</span><span class="p">:</span>
+
+                <span class="k">for</span> <span class="n">val</span> <span class="ow">in</span> <span class="n">values</span><span class="p">:</span>
+
+                    <span class="n">names</span> <span class="o">=</span> <span class="n">val</span><span class="o">.</span><span class="n">_fields</span>
+                    <span class="k">break</span>
+
+            <span class="k">break</span>
+
+        <span class="k">return</span> <span class="n">names</span></div>
+
+
+
+    <span class="k">def</span> <span class="fm">__and__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">other</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="n">other</span> <span class="o">&amp;</span> <span class="bp">self</span><span class="o">.</span><span class="n">to_set</span><span class="p">()</span>
+
+
+    <span class="k">def</span> <span class="fm">__or__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">other</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="n">other</span> <span class="o">|</span> <span class="bp">self</span><span class="o">.</span><span class="n">to_set</span><span class="p">()</span>
+
+
+    <span class="k">def</span> <span class="fm">__sub__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">other</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">to_set</span><span class="p">()</span> <span class="o">-</span> <span class="n">other</span>
+
+
+    <span class="k">def</span> <span class="fm">__len__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">numof_entities</span><span class="p">()</span>
+
+
+    <span class="k">def</span> <span class="fm">__getitem__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">item</span><span class="p">):</span>
+
+        <span class="k">if</span> <span class="ow">not</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">item</span><span class="p">,</span> <span class="n">_const</span><span class="o">.</span><span class="n">SIMPLE_TYPES</span><span class="p">):</span>
+
+            <span class="k">return</span> <span class="nb">set</span><span class="o">.</span><span class="n">union</span><span class="p">(</span>
+                <span class="o">*</span><span class="p">(</span>
+                    <span class="bp">self</span><span class="o">.</span><span class="n">annot</span><span class="p">[</span><span class="n">it</span><span class="p">]</span>
+                    <span class="k">for</span> <span class="n">it</span> <span class="ow">in</span> <span class="n">item</span>
+                    <span class="k">if</span> <span class="n">it</span> <span class="ow">in</span> <span class="bp">self</span>
+                <span class="p">)</span>
+            <span class="p">)</span>
+
+        <span class="k">elif</span> <span class="n">item</span> <span class="ow">in</span> <span class="bp">self</span><span class="p">:</span>
+
+            <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">annot</span><span class="p">[</span><span class="n">item</span><span class="p">]</span>
+
+        <span class="k">elif</span> <span class="bp">self</span><span class="o">.</span><span class="n">primary_field</span><span class="p">:</span>
+
+            <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">select</span><span class="p">(</span><span class="o">**</span><span class="p">{</span><span class="bp">self</span><span class="o">.</span><span class="n">primary_field</span><span class="p">:</span> <span class="n">item</span><span class="p">})</span>
+
+
+    <span class="k">def</span> <span class="fm">__contains__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">item</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="n">item</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">annot</span>
+
+
+<div class="viewcode-block" id="AnnotationBase.numof_references">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.AnnotationBase.html#pypath.core.annot.AnnotationBase.numof_references">[docs]</a>
+    <span class="k">def</span> <span class="nf">numof_references</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Some annotations contain references. The field name for references</span>
+<span class="sd">        is always ``pmid`` (PubMed ID). This method collects and counts the</span>
+<span class="sd">        references across all records.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">return</span> <span class="nb">len</span><span class="p">(</span><span class="nb">set</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">all_refs</span><span class="p">()))</span></div>
+
+
+
+<div class="viewcode-block" id="AnnotationBase.curation_effort">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.AnnotationBase.html#pypath.core.annot.AnnotationBase.curation_effort">[docs]</a>
+    <span class="k">def</span> <span class="nf">curation_effort</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Counts the reference-record pairs.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">return</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">all_refs</span><span class="p">())</span></div>
+
+
+
+<div class="viewcode-block" id="AnnotationBase.all_refs">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.AnnotationBase.html#pypath.core.annot.AnnotationBase.all_refs">[docs]</a>
+    <span class="k">def</span> <span class="nf">all_refs</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Some annotations contain references. The field name for references</span>
+<span class="sd">        is always ``pmid`` (PubMed ID). This method collects the references</span>
+<span class="sd">        across all records. Returns *list*.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">if</span> <span class="s1">&#39;pmid&#39;</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">get_names</span><span class="p">():</span>
+
+            <span class="k">return</span> <span class="p">[</span>
+                <span class="n">a</span><span class="o">.</span><span class="n">pmid</span>
+                <span class="k">for</span> <span class="n">aa</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">annot</span><span class="o">.</span><span class="n">values</span><span class="p">()</span>
+                <span class="k">for</span> <span class="n">a</span> <span class="ow">in</span> <span class="n">aa</span>
+                <span class="k">if</span> <span class="n">a</span><span class="o">.</span><span class="n">pmid</span>
+            <span class="p">]</span>
+
+        <span class="k">return</span> <span class="p">[]</span></div>
+
+
+
+    <span class="nd">@property</span>
+    <span class="k">def</span> <span class="nf">summary</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="p">{</span>
+            <span class="s1">&#39;n_total&#39;</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">numof_entities</span><span class="p">(),</span>
+            <span class="s1">&#39;n_records_total&#39;</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">numof_records</span><span class="p">(),</span>
+            <span class="s1">&#39;n_proteins&#39;</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">numof_proteins</span><span class="p">(),</span>
+            <span class="s1">&#39;pct_proteins&#39;</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">proportion</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">proteins</span><span class="p">)</span> <span class="o">*</span> <span class="mi">100</span><span class="p">,</span>
+            <span class="s1">&#39;n_complexes&#39;</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">numof_complexes</span><span class="p">(),</span>
+            <span class="s1">&#39;pct_complexes&#39;</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">proportion</span><span class="p">(</span>
+                <span class="nb">complex</span><span class="o">.</span><span class="n">get_db</span><span class="p">()</span><span class="o">.</span><span class="n">complexes</span><span class="o">.</span><span class="n">keys</span><span class="p">()</span>
+            <span class="p">)</span> <span class="o">*</span> <span class="mi">100</span><span class="p">,</span>
+            <span class="s1">&#39;n_mirnas&#39;</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">numof_mirnas</span><span class="p">(),</span>
+            <span class="s1">&#39;pct_mirnas&#39;</span><span class="p">:</span> <span class="p">(</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">proportion</span><span class="p">(</span><span class="n">reflists</span><span class="o">.</span><span class="n">get_reflist</span><span class="p">(</span><span class="s1">&#39;mirbase&#39;</span><span class="p">))</span> <span class="o">*</span> <span class="mi">100</span>
+            <span class="p">),</span>
+            <span class="s1">&#39;n_protein_records&#39;</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">numof_protein_records</span><span class="p">(),</span>
+            <span class="s1">&#39;n_complex_records&#39;</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">numof_complex_records</span><span class="p">(),</span>
+            <span class="s1">&#39;n_mirna_records&#39;</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">numof_mirna_records</span><span class="p">(),</span>
+            <span class="s1">&#39;references&#39;</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">numof_references</span><span class="p">(),</span>
+            <span class="s1">&#39;curation_effort&#39;</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">curation_effort</span><span class="p">(),</span>
+            <span class="s1">&#39;records_per_entity&#39;</span><span class="p">:</span> <span class="p">(</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">numof_protein_records</span><span class="p">()</span> <span class="o">/</span> <span class="bp">self</span><span class="o">.</span><span class="n">numof_proteins</span><span class="p">()</span>
+                    <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">numof_proteins</span><span class="p">()</span> <span class="k">else</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">numof_records</span><span class="p">()</span> <span class="o">/</span> <span class="bp">self</span><span class="o">.</span><span class="n">numof_entities</span><span class="p">()</span>
+                    <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">numof_entities</span><span class="p">()</span> <span class="k">else</span>
+                <span class="mi">0</span>
+            <span class="p">),</span>
+            <span class="s1">&#39;complex_annotations_inferred&#39;</span><span class="p">:</span> <span class="nb">bool</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">numof_proteins</span><span class="p">()),</span>
+            <span class="s1">&#39;fields&#39;</span><span class="p">:</span> <span class="s1">&#39;, &#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">get_names</span><span class="p">()),</span>
+            <span class="s1">&#39;name&#39;</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">,</span>
+        <span class="p">}</span>
+
+
+<div class="viewcode-block" id="AnnotationBase.browse">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.AnnotationBase.html#pypath.core.annot.AnnotationBase.browse">[docs]</a>
+    <span class="k">def</span> <span class="nf">browse</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">field</span><span class="p">:</span> <span class="nb">str</span> <span class="o">|</span> <span class="nb">list</span><span class="p">[</span><span class="nb">str</span><span class="p">]</span> <span class="o">|</span> <span class="nb">dict</span><span class="p">[</span><span class="nb">str</span><span class="p">,</span> <span class="nb">str</span><span class="p">]</span> <span class="o">|</span> <span class="kc">None</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">start</span><span class="p">:</span> <span class="nb">int</span> <span class="o">=</span> <span class="mi">0</span><span class="p">,</span>
+            <span class="o">**</span><span class="n">kwargs</span>
+        <span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Print gene information as a table.</span>
+
+<span class="sd">        Presents information about annotation categories as ascii tables</span>
+<span class="sd">        printed in the terminal. If one category provided, prints one table.</span>
+<span class="sd">        If multiple categories provided, prints a table for each of them one</span>
+<span class="sd">        by one proceeding to the next one once you hit return. If no categories</span>
+<span class="sd">        provided goes through all levels of the primary category.</span>
+
+<span class="sd">        Args</span>
+<span class="sd">            field:</span>
+<span class="sd">                The field to browse categories by.</span>
+
+<span class="sd">                * If None the primary field will be selected.</span>
+<span class="sd">                  If this annotation resource doesn&#39;t have fields, all proteins</span>
+<span class="sd">                  will be presented as one single category.</span>
+<span class="sd">                * If a string it will be considered a field name and it will</span>
+<span class="sd">                  browse through all levels of this field.</span>
+<span class="sd">                * If a ``list``, set or tuple, it will be considered either a</span>
+<span class="sd">                  ``list`` of field names or a list of values from the primary</span>
+<span class="sd">                  field. In the former case all combinations of the values of</span>
+<span class="sd">                  the fields will be presented, in the latter case the browsing</span>
+<span class="sd">                  will be limited to the levels of the primary field contained</span>
+<span class="sd">                  in ``field``.</span>
+<span class="sd">                * If a ``dict``, keys are supposed to be field names and values</span>
+<span class="sd">                  as list of levels. If any of the values are None, all levels</span>
+<span class="sd">                  from that field will be used.</span>
+
+<span class="sd">            start:</span>
+<span class="sd">                Start browsing from this category. E.g. if there are 500</span>
+<span class="sd">                categories and start is 250 it will skip everything before the</span>
+<span class="sd">                250th.</span>
+<span class="sd">            kwargs:</span>
+<span class="sd">                Passed to ``pypath.utils.uniprot.info``.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">if</span> <span class="ow">not</span> <span class="n">field</span> <span class="ow">and</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">primary_field</span><span class="p">:</span>
+
+            <span class="n">uniprots</span> <span class="o">=</span> <span class="n">entity</span><span class="o">.</span><span class="n">Entity</span><span class="o">.</span><span class="n">only_proteins</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">to_set</span><span class="p">())</span>
+
+            <span class="n">utils_uniprot</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="n">uniprots</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
+
+            <span class="k">return</span>
+
+        <span class="n">field</span> <span class="o">=</span> <span class="n">field</span> <span class="ow">or</span> <span class="bp">self</span><span class="o">.</span><span class="n">primary_field</span>
+
+        <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">field</span><span class="p">,</span> <span class="nb">str</span><span class="p">):</span>
+
+            <span class="c1"># all values of the field</span>
+            <span class="n">field</span> <span class="o">=</span> <span class="p">{</span><span class="n">field</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">get_values</span><span class="p">(</span><span class="n">field</span><span class="p">)}</span>
+
+        <span class="k">elif</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">field</span><span class="p">,</span> <span class="n">_const</span><span class="o">.</span><span class="n">LIST_LIKE</span><span class="p">):</span>
+
+            <span class="k">if</span> <span class="nb">set</span><span class="p">(</span><span class="n">field</span><span class="p">)</span> <span class="o">&amp;</span> <span class="nb">set</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">get_names</span><span class="p">()):</span>
+
+                <span class="c1"># a set of fields provided</span>
+                <span class="n">field</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">(</span>
+                    <span class="p">(</span>
+                        <span class="n">fi</span><span class="p">,</span>
+                        <span class="bp">self</span><span class="o">.</span><span class="n">get_values</span><span class="p">(</span><span class="n">fi</span><span class="p">)</span>
+                    <span class="p">)</span>
+                    <span class="k">for</span> <span class="n">fi</span> <span class="ow">in</span> <span class="n">field</span>
+                <span class="p">)</span>
+
+            <span class="k">else</span><span class="p">:</span>
+
+                <span class="c1"># a set of values provided</span>
+                <span class="n">field</span> <span class="o">=</span> <span class="p">{</span><span class="bp">self</span><span class="o">.</span><span class="n">primary_field</span><span class="p">:</span> <span class="n">field</span><span class="p">}</span>
+
+        <span class="k">elif</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">field</span><span class="p">,</span> <span class="nb">dict</span><span class="p">):</span>
+
+            <span class="n">field</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">(</span>
+                <span class="p">(</span>
+                    <span class="n">fi</span><span class="p">,</span>
+                    <span class="n">vals</span> <span class="ow">or</span> <span class="bp">self</span><span class="o">.</span><span class="n">get_values</span><span class="p">(</span><span class="n">fi</span><span class="p">)</span>
+                <span class="p">)</span>
+                <span class="k">for</span> <span class="n">fi</span><span class="p">,</span> <span class="n">vals</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="n">field</span><span class="p">)</span>
+            <span class="p">)</span>
+
+        <span class="k">else</span><span class="p">:</span>
+
+            <span class="n">sys</span><span class="o">.</span><span class="n">stdout</span><span class="o">.</span><span class="n">write</span><span class="p">(</span>
+                <span class="s1">&#39;Could not recognize field definition, &#39;</span>
+                <span class="s1">&#39;please refer to the docs.</span><span class="se">\n</span><span class="s1">&#39;</span>
+            <span class="p">)</span>
+            <span class="n">sys</span><span class="o">.</span><span class="n">stdout</span><span class="o">.</span><span class="n">flush</span><span class="p">()</span>
+            <span class="k">return</span>
+
+        <span class="c1"># otherwise we assume `field` is a dict of fields and values</span>
+
+        <span class="n">field_keys</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="n">field</span><span class="o">.</span><span class="n">keys</span><span class="p">())</span>
+        <span class="n">field_values</span> <span class="o">=</span> <span class="p">[</span><span class="n">field</span><span class="p">[</span><span class="n">k</span><span class="p">]</span> <span class="k">for</span> <span class="n">k</span> <span class="ow">in</span> <span class="n">field_keys</span><span class="p">]</span>
+
+        <span class="n">values</span> <span class="o">=</span> <span class="nb">sorted</span><span class="p">(</span><span class="n">itertools</span><span class="o">.</span><span class="n">product</span><span class="p">(</span><span class="o">*</span><span class="n">field_values</span><span class="p">))</span>
+        <span class="n">total</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="n">values</span><span class="p">)</span>
+
+        <span class="n">groups</span> <span class="o">=</span> <span class="p">{}</span>
+
+        <span class="k">for</span> <span class="n">vals</span> <span class="ow">in</span> <span class="n">values</span><span class="p">:</span>
+
+            <span class="n">args</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">(</span><span class="nb">zip</span><span class="p">(</span><span class="n">field_keys</span><span class="p">,</span> <span class="n">vals</span><span class="p">))</span>
+
+            <span class="n">proteins</span> <span class="o">=</span> <span class="n">entity</span><span class="o">.</span><span class="n">Entity</span><span class="o">.</span><span class="n">only_proteins</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">select</span><span class="p">(</span><span class="o">**</span><span class="n">args</span><span class="p">))</span>
+
+            <span class="k">if</span> <span class="ow">not</span> <span class="n">proteins</span><span class="p">:</span>
+
+                <span class="k">continue</span>
+
+            <span class="n">label</span> <span class="o">=</span> <span class="p">(</span>
+                <span class="n">vals</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span>
+                    <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">vals</span><span class="p">)</span> <span class="o">==</span> <span class="mi">1</span> <span class="k">else</span>
+                <span class="s1">&#39;, &#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span>
+                    <span class="s1">&#39;</span><span class="si">%s</span><span class="s1">: </span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="p">(</span>
+                        <span class="n">key</span><span class="p">,</span>
+                        <span class="nb">str</span><span class="p">(</span><span class="n">val</span><span class="p">)</span>
+                    <span class="p">)</span>
+                    <span class="k">for</span> <span class="n">key</span><span class="p">,</span> <span class="n">val</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="n">args</span><span class="p">)</span>
+                <span class="p">)</span>
+            <span class="p">)</span>
+
+            <span class="n">groups</span><span class="p">[</span><span class="n">label</span><span class="p">]</span> <span class="o">=</span> <span class="n">proteins</span>
+
+        <span class="n">utils_uniprot</span><span class="o">.</span><span class="n">browse</span><span class="p">(</span><span class="n">groups</span> <span class="o">=</span> <span class="n">groups</span><span class="p">,</span> <span class="n">start</span> <span class="o">=</span> <span class="n">start</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">)</span></div>
+</div>
+
+
+
+<div class="viewcode-block" id="Membranome">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.Membranome.html#pypath.core.annot.Membranome">[docs]</a>
+<span class="k">class</span> <span class="nc">Membranome</span><span class="p">(</span><span class="n">AnnotationBase</span><span class="p">):</span>
+
+    <span class="n">_eq_fields</span> <span class="o">=</span> <span class="p">(</span><span class="s1">&#39;membrane&#39;</span><span class="p">,</span> <span class="s1">&#39;side&#39;</span><span class="p">)</span>
+
+
+<div class="viewcode-block" id="Membranome.__init__">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.Membranome.html#pypath.core.annot.Membranome.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+
+        <span class="n">AnnotationBase</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">name</span> <span class="o">=</span> <span class="s1">&#39;Membranome&#39;</span><span class="p">,</span>
+            <span class="n">input_method</span> <span class="o">=</span> <span class="s1">&#39;membranome.membranome_annotations&#39;</span><span class="p">,</span>
+            <span class="o">**</span><span class="n">kwargs</span>
+        <span class="p">)</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">_process_method</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="n">record</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">namedtuple</span><span class="p">(</span>
+            <span class="s1">&#39;MembranomeAnnotation&#39;</span><span class="p">,</span>
+            <span class="p">[</span><span class="s1">&#39;membrane&#39;</span><span class="p">,</span> <span class="s1">&#39;side&#39;</span><span class="p">],</span>
+        <span class="p">)</span>
+
+        <span class="n">_annot</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">defaultdict</span><span class="p">(</span><span class="nb">set</span><span class="p">)</span>
+
+        <span class="k">for</span> <span class="n">a</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span><span class="p">:</span>
+
+            <span class="n">_annot</span><span class="p">[</span><span class="n">a</span><span class="p">[</span><span class="mi">0</span><span class="p">]]</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">record</span><span class="p">(</span><span class="n">a</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span> <span class="n">a</span><span class="p">[</span><span class="mi">2</span><span class="p">]))</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">annot</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">(</span><span class="n">_annot</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="Exocarta">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.Exocarta.html#pypath.core.annot.Exocarta">[docs]</a>
+<span class="k">class</span> <span class="nc">Exocarta</span><span class="p">(</span><span class="n">AnnotationBase</span><span class="p">):</span>
+
+    <span class="n">_eq_fields</span> <span class="o">=</span> <span class="p">(</span><span class="s1">&#39;tissue&#39;</span><span class="p">,</span> <span class="s1">&#39;vesicle&#39;</span><span class="p">)</span>
+
+
+<div class="viewcode-block" id="Exocarta.__init__">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.Exocarta.html#pypath.core.annot.Exocarta.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+
+        <span class="k">if</span> <span class="s1">&#39;organism&#39;</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">kwargs</span><span class="p">:</span>
+
+            <span class="n">kwargs</span><span class="p">[</span><span class="s1">&#39;organism&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span>
+
+        <span class="k">if</span> <span class="s1">&#39;database&#39;</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">kwargs</span><span class="p">:</span>
+
+            <span class="n">kwargs</span><span class="p">[</span><span class="s1">&#39;database&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="s1">&#39;exocarta&#39;</span>
+
+        <span class="n">AnnotationBase</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">name</span> <span class="o">=</span> <span class="n">kwargs</span><span class="p">[</span><span class="s1">&#39;database&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">capitalize</span><span class="p">(),</span>
+            <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">,</span>
+            <span class="n">input_method</span> <span class="o">=</span> <span class="s1">&#39;exocarta._get_exocarta_vesiclepedia&#39;</span><span class="p">,</span>
+            <span class="o">**</span><span class="n">kwargs</span><span class="p">,</span>
+        <span class="p">)</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">_process_method</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="n">record</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">namedtuple</span><span class="p">(</span>
+            <span class="s1">&#39;</span><span class="si">%s</span><span class="s1">Annotation&#39;</span> <span class="o">%</span> <span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">,</span>
+            <span class="p">[</span><span class="s1">&#39;pmid&#39;</span><span class="p">,</span> <span class="s1">&#39;tissue&#39;</span><span class="p">,</span> <span class="s1">&#39;vesicle&#39;</span><span class="p">],</span>
+        <span class="p">)</span>
+
+        <span class="n">_annot</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">defaultdict</span><span class="p">(</span><span class="nb">set</span><span class="p">)</span>
+
+        <span class="n">missing_name</span> <span class="o">=</span> <span class="kc">False</span>
+
+        <span class="k">for</span> <span class="n">a</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span><span class="p">:</span>
+
+            <span class="k">if</span> <span class="ow">not</span> <span class="n">a</span><span class="p">[</span><span class="mi">1</span><span class="p">]:</span>
+
+                <span class="n">missing_name</span> <span class="o">=</span> <span class="kc">True</span>
+                <span class="k">continue</span>
+
+            <span class="n">uniprots</span> <span class="o">=</span> <span class="n">mapping</span><span class="o">.</span><span class="n">map_name</span><span class="p">(</span><span class="n">a</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span> <span class="s1">&#39;genesymbol&#39;</span><span class="p">,</span> <span class="s1">&#39;uniprot&#39;</span><span class="p">)</span>
+
+            <span class="k">for</span> <span class="n">u</span> <span class="ow">in</span> <span class="n">uniprots</span><span class="p">:</span>
+
+                <span class="k">for</span> <span class="n">vesicle</span> <span class="ow">in</span> <span class="p">(</span>
+                    <span class="n">a</span><span class="p">[</span><span class="mi">3</span><span class="p">][</span><span class="mi">3</span><span class="p">]</span>
+                        <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">name</span> <span class="o">==</span> <span class="s1">&#39;Vesiclepedia&#39;</span> <span class="k">else</span>
+                    <span class="p">(</span><span class="s1">&#39;Exosomes&#39;</span><span class="p">,)</span>
+                <span class="p">):</span>
+
+                    <span class="n">_annot</span><span class="p">[</span><span class="n">u</span><span class="p">]</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">record</span><span class="p">(</span><span class="n">a</span><span class="p">[</span><span class="mi">3</span><span class="p">][</span><span class="mi">0</span><span class="p">],</span> <span class="n">a</span><span class="p">[</span><span class="mi">3</span><span class="p">][</span><span class="mi">2</span><span class="p">],</span> <span class="n">vesicle</span><span class="p">))</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">annot</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">(</span><span class="n">_annot</span><span class="p">)</span>
+
+        <span class="k">if</span> <span class="n">missing_name</span><span class="p">:</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span>
+                <span class="s1">&#39;One or more names were missing while processing &#39;</span>
+                <span class="s1">&#39;annotations from </span><span class="si">%s</span><span class="s1">. Best if you check your cache &#39;</span>
+                <span class="s1">&#39;file and re-download the data if it</span><span class="se">\&#39;</span><span class="s1"> corrupted.&#39;</span> <span class="o">%</span> <span class="p">(</span>
+                    <span class="bp">self</span><span class="o">.</span><span class="n">name</span>
+                <span class="p">)</span>
+            <span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="Vesiclepedia">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.Vesiclepedia.html#pypath.core.annot.Vesiclepedia">[docs]</a>
+<span class="k">class</span> <span class="nc">Vesiclepedia</span><span class="p">(</span><span class="n">Exocarta</span><span class="p">):</span>
+
+    <span class="n">_eq_fields</span> <span class="o">=</span> <span class="p">(</span><span class="s1">&#39;tissue&#39;</span><span class="p">,</span> <span class="s1">&#39;vesicle&#39;</span><span class="p">)</span>
+
+
+<div class="viewcode-block" id="Vesiclepedia.__init__">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.Vesiclepedia.html#pypath.core.annot.Vesiclepedia.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+
+        <span class="n">Exocarta</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">,</span>
+            <span class="n">database</span> <span class="o">=</span> <span class="s1">&#39;vesiclepedia&#39;</span><span class="p">,</span>
+            <span class="o">**</span><span class="n">kwargs</span>
+        <span class="p">)</span></div>
+</div>
+
+
+
+<div class="viewcode-block" id="Embrace">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.Embrace.html#pypath.core.annot.Embrace">[docs]</a>
+<span class="k">class</span> <span class="nc">Embrace</span><span class="p">(</span><span class="n">AnnotationBase</span><span class="p">):</span>
+
+    <span class="n">_eq_fields</span> <span class="o">=</span> <span class="p">(</span><span class="s1">&#39;mainclass&#39;</span><span class="p">,)</span>
+
+
+<div class="viewcode-block" id="Embrace.__init__">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.Embrace.html#pypath.core.annot.Embrace.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+
+        <span class="n">AnnotationBase</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">name</span> <span class="o">=</span> <span class="s1">&#39;EMBRACE&#39;</span><span class="p">,</span>
+            <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">,</span>
+            <span class="n">input_method</span> <span class="o">=</span> <span class="s1">&#39;embrace.embrace_annotations&#39;</span><span class="p">,</span>
+            <span class="o">**</span><span class="n">kwargs</span>
+        <span class="p">)</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">_process_method</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">annot</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span>
+        <span class="nb">delattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">&#39;data&#39;</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="Baccin2019">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.Baccin2019.html#pypath.core.annot.Baccin2019">[docs]</a>
+<span class="k">class</span> <span class="nc">Baccin2019</span><span class="p">(</span><span class="n">AnnotationBase</span><span class="p">):</span>
+
+    <span class="n">_eq_fields</span> <span class="o">=</span> <span class="p">(</span><span class="s1">&#39;mainclass&#39;</span><span class="p">,</span> <span class="s1">&#39;subclass&#39;</span><span class="p">,</span> <span class="s1">&#39;location&#39;</span><span class="p">)</span>
+
+
+<div class="viewcode-block" id="Baccin2019.__init__">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.Baccin2019.html#pypath.core.annot.Baccin2019.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+
+        <span class="n">AnnotationBase</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">name</span> <span class="o">=</span> <span class="s1">&#39;Baccin2019&#39;</span><span class="p">,</span>
+            <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">,</span>
+            <span class="n">input_method</span> <span class="o">=</span> <span class="s1">&#39;baccin2019.baccin2019_annotations&#39;</span><span class="p">,</span>
+            <span class="o">**</span><span class="n">kwargs</span>
+        <span class="p">)</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">_process_method</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">annot</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span>
+        <span class="nb">delattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">&#39;data&#39;</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="Almen2009">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.Almen2009.html#pypath.core.annot.Almen2009">[docs]</a>
+<span class="k">class</span> <span class="nc">Almen2009</span><span class="p">(</span><span class="n">AnnotationBase</span><span class="p">):</span>
+
+    <span class="n">_eq_fields</span> <span class="o">=</span> <span class="p">(</span><span class="s1">&#39;mainclass&#39;</span><span class="p">,)</span>
+
+
+<div class="viewcode-block" id="Almen2009.__init__">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.Almen2009.html#pypath.core.annot.Almen2009.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+
+        <span class="n">AnnotationBase</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">name</span> <span class="o">=</span> <span class="s1">&#39;Almen2009&#39;</span><span class="p">,</span>
+            <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">,</span>
+            <span class="n">input_method</span> <span class="o">=</span> <span class="s1">&#39;almen2009.almen2009_annotations&#39;</span><span class="p">,</span>
+            <span class="o">**</span><span class="n">kwargs</span>
+        <span class="p">)</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">_process_method</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">annot</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span>
+        <span class="nb">delattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">&#39;data&#39;</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="Italk">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.Italk.html#pypath.core.annot.Italk">[docs]</a>
+<span class="k">class</span> <span class="nc">Italk</span><span class="p">(</span><span class="n">AnnotationBase</span><span class="p">):</span>
+
+    <span class="n">_eq_fields</span> <span class="o">=</span> <span class="p">(</span><span class="s1">&#39;mainclass&#39;</span><span class="p">,</span> <span class="s1">&#39;subclass&#39;</span><span class="p">)</span>
+
+
+<div class="viewcode-block" id="Italk.__init__">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.Italk.html#pypath.core.annot.Italk.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+
+        <span class="n">AnnotationBase</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">name</span> <span class="o">=</span> <span class="s1">&#39;iTALK&#39;</span><span class="p">,</span>
+            <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">,</span>
+            <span class="n">input_method</span> <span class="o">=</span> <span class="s1">&#39;italk.italk_annotations&#39;</span><span class="p">,</span>
+            <span class="o">**</span><span class="n">kwargs</span>
+        <span class="p">)</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">_process_method</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">annot</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span>
+        <span class="nb">delattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">&#39;data&#39;</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="Cellcellinteractions">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.Cellcellinteractions.html#pypath.core.annot.Cellcellinteractions">[docs]</a>
+<span class="k">class</span> <span class="nc">Cellcellinteractions</span><span class="p">(</span><span class="n">AnnotationBase</span><span class="p">):</span>
+
+    <span class="n">_eq_fields</span> <span class="o">=</span> <span class="p">(</span><span class="s1">&#39;mainclass&#39;</span><span class="p">,)</span>
+
+
+<div class="viewcode-block" id="Cellcellinteractions.__init__">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.Cellcellinteractions.html#pypath.core.annot.Cellcellinteractions.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+
+        <span class="n">AnnotationBase</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">name</span> <span class="o">=</span> <span class="s1">&#39;CellCellInteractions&#39;</span><span class="p">,</span>
+            <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">,</span>
+            <span class="n">input_method</span> <span class="o">=</span> <span class="p">(</span>
+                <span class="s1">&#39;cellcellinteractions.&#39;</span>
+                <span class="s1">&#39;cellcellinteractions_annotations&#39;</span>
+            <span class="p">),</span>
+            <span class="o">**</span><span class="n">kwargs</span>
+        <span class="p">)</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">_process_method</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">annot</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span>
+        <span class="nb">delattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">&#39;data&#39;</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="Matrisome">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.Matrisome.html#pypath.core.annot.Matrisome">[docs]</a>
+<span class="k">class</span> <span class="nc">Matrisome</span><span class="p">(</span><span class="n">AnnotationBase</span><span class="p">):</span>
+
+    <span class="n">_eq_fields</span> <span class="o">=</span> <span class="p">(</span><span class="s1">&#39;mainclass&#39;</span><span class="p">,</span> <span class="s1">&#39;subclass&#39;</span><span class="p">)</span>
+
+
+<div class="viewcode-block" id="Matrisome.__init__">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.Matrisome.html#pypath.core.annot.Matrisome.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+
+        <span class="k">if</span> <span class="s1">&#39;organism&#39;</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">kwargs</span><span class="p">:</span>
+
+            <span class="n">kwargs</span><span class="p">[</span><span class="s1">&#39;organism&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span>
+
+        <span class="n">AnnotationBase</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">name</span> <span class="o">=</span> <span class="s1">&#39;Matrisome&#39;</span><span class="p">,</span>
+            <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">,</span>
+            <span class="n">input_method</span> <span class="o">=</span> <span class="s1">&#39;matrisome.matrisome_annotations&#39;</span><span class="p">,</span>
+            <span class="o">**</span><span class="n">kwargs</span><span class="p">,</span>
+        <span class="p">)</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">_process_method</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">annot</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span>
+        <span class="nb">delattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">&#39;data&#39;</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="Surfaceome">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.Surfaceome.html#pypath.core.annot.Surfaceome">[docs]</a>
+<span class="k">class</span> <span class="nc">Surfaceome</span><span class="p">(</span><span class="n">AnnotationBase</span><span class="p">):</span>
+
+    <span class="n">_eq_fields</span> <span class="o">=</span> <span class="p">(</span><span class="s1">&#39;mainclass&#39;</span><span class="p">,)</span>
+
+
+<div class="viewcode-block" id="Surfaceome.__init__">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.Surfaceome.html#pypath.core.annot.Surfaceome.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+
+        <span class="n">AnnotationBase</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">name</span> <span class="o">=</span> <span class="s1">&#39;Surfaceome&#39;</span><span class="p">,</span>
+            <span class="n">input_method</span> <span class="o">=</span> <span class="s1">&#39;surfaceome.surfaceome_annotations&#39;</span><span class="p">,</span>
+            <span class="o">**</span><span class="n">kwargs</span>
+        <span class="p">)</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">_process_method</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="n">_annot</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">defaultdict</span><span class="p">(</span><span class="nb">set</span><span class="p">)</span>
+
+        <span class="n">record</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">namedtuple</span><span class="p">(</span>
+            <span class="s1">&#39;SurfaceomeAnnotation&#39;</span><span class="p">,</span>
+            <span class="p">[</span><span class="s1">&#39;score&#39;</span><span class="p">,</span> <span class="s1">&#39;mainclass&#39;</span><span class="p">,</span> <span class="s1">&#39;subclasses&#39;</span><span class="p">]</span>
+        <span class="p">)</span>
+        <span class="n">record</span><span class="o">.</span><span class="vm">__defaults__</span> <span class="o">=</span> <span class="p">(</span><span class="kc">None</span><span class="p">,</span> <span class="kc">None</span><span class="p">)</span>
+
+        <span class="k">for</span> <span class="n">uniprot</span><span class="p">,</span> <span class="n">a</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">data</span><span class="p">):</span>
+
+            <span class="n">_annot</span><span class="p">[</span><span class="n">uniprot</span><span class="p">]</span><span class="o">.</span><span class="n">add</span><span class="p">(</span>
+                <span class="n">record</span><span class="p">(</span>
+                    <span class="n">a</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span>
+                    <span class="n">a</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span>
+                    <span class="nb">tuple</span><span class="p">(</span><span class="nb">sorted</span><span class="p">(</span><span class="n">a</span><span class="p">[</span><span class="mi">2</span><span class="p">]))</span> <span class="k">if</span> <span class="n">a</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="k">else</span> <span class="kc">None</span><span class="p">,</span>
+                <span class="p">)</span>
+            <span class="p">)</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">annot</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">(</span><span class="n">_annot</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="Adhesome">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.Adhesome.html#pypath.core.annot.Adhesome">[docs]</a>
+<span class="k">class</span> <span class="nc">Adhesome</span><span class="p">(</span><span class="n">AnnotationBase</span><span class="p">):</span>
+
+    <span class="n">_eq_fields</span> <span class="o">=</span> <span class="p">(</span><span class="s1">&#39;mainclass&#39;</span><span class="p">,)</span>
+
+
+<div class="viewcode-block" id="Adhesome.__init__">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.Adhesome.html#pypath.core.annot.Adhesome.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+
+        <span class="n">AnnotationBase</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">name</span> <span class="o">=</span> <span class="s1">&#39;Adhesome&#39;</span><span class="p">,</span>
+            <span class="n">input_method</span> <span class="o">=</span> <span class="s1">&#39;adhesome.adhesome_annotations&#39;</span><span class="p">,</span>
+            <span class="o">**</span><span class="n">kwargs</span>
+        <span class="p">)</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">_process_method</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">annot</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span>
+        <span class="nb">delattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">&#39;data&#39;</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="Cancersea">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.Cancersea.html#pypath.core.annot.Cancersea">[docs]</a>
+<span class="k">class</span> <span class="nc">Cancersea</span><span class="p">(</span><span class="n">AnnotationBase</span><span class="p">):</span>
+
+    <span class="n">_eq_fields</span> <span class="o">=</span> <span class="p">(</span><span class="s1">&#39;state&#39;</span><span class="p">,)</span>
+
+
+<div class="viewcode-block" id="Cancersea.__init__">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.Cancersea.html#pypath.core.annot.Cancersea.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+
+        <span class="n">AnnotationBase</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">name</span> <span class="o">=</span> <span class="s1">&#39;CancerSEA&#39;</span><span class="p">,</span>
+            <span class="n">input_method</span> <span class="o">=</span> <span class="s1">&#39;cancersea.cancersea_annotations&#39;</span><span class="p">,</span>
+            <span class="o">**</span><span class="n">kwargs</span>
+        <span class="p">)</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">_process_method</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">annot</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span>
+        <span class="nb">delattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">&#39;data&#39;</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="Hgnc">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.Hgnc.html#pypath.core.annot.Hgnc">[docs]</a>
+<span class="k">class</span> <span class="nc">Hgnc</span><span class="p">(</span><span class="n">AnnotationBase</span><span class="p">):</span>
+
+    <span class="n">_eq_fields</span> <span class="o">=</span> <span class="p">(</span><span class="s1">&#39;mainclass&#39;</span><span class="p">,)</span>
+
+
+<div class="viewcode-block" id="Hgnc.__init__">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.Hgnc.html#pypath.core.annot.Hgnc.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+
+        <span class="n">AnnotationBase</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">name</span> <span class="o">=</span> <span class="s1">&#39;HGNC&#39;</span><span class="p">,</span>
+            <span class="n">input_method</span> <span class="o">=</span> <span class="s1">&#39;hgnc.hgnc_genegroups&#39;</span><span class="p">,</span>
+            <span class="o">**</span><span class="n">kwargs</span>
+        <span class="p">)</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">_process_method</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">annot</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span>
+        <span class="nb">delattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">&#39;data&#39;</span><span class="p">)</span></div>
+
+
+
+
+<div class="viewcode-block" id="Zhong2015">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.Zhong2015.html#pypath.core.annot.Zhong2015">[docs]</a>
+<span class="k">class</span> <span class="nc">Zhong2015</span><span class="p">(</span><span class="n">AnnotationBase</span><span class="p">):</span>
+
+    <span class="n">_eq_fields</span> <span class="o">=</span> <span class="p">(</span><span class="s1">&#39;type&#39;</span><span class="p">,)</span>
+
+
+<div class="viewcode-block" id="Zhong2015.__init__">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.Zhong2015.html#pypath.core.annot.Zhong2015.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+
+        <span class="n">AnnotationBase</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">name</span> <span class="o">=</span> <span class="s1">&#39;Zhong2015&#39;</span><span class="p">,</span>
+            <span class="n">input_method</span> <span class="o">=</span> <span class="s1">&#39;zhong2015.zhong2015_annotations&#39;</span><span class="p">,</span>
+            <span class="o">**</span><span class="n">kwargs</span>
+        <span class="p">)</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">_process_method</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">annot</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span>
+        <span class="nb">delattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">&#39;data&#39;</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="Opm">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.Opm.html#pypath.core.annot.Opm">[docs]</a>
+<span class="k">class</span> <span class="nc">Opm</span><span class="p">(</span><span class="n">AnnotationBase</span><span class="p">):</span>
+
+    <span class="n">_eq_fields</span> <span class="o">=</span> <span class="p">(</span><span class="s1">&#39;membrane&#39;</span><span class="p">,)</span>
+
+
+<div class="viewcode-block" id="Opm.__init__">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.Opm.html#pypath.core.annot.Opm.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+
+        <span class="k">if</span> <span class="s1">&#39;organism&#39;</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">kwargs</span><span class="p">:</span>
+
+            <span class="n">kwargs</span><span class="p">[</span><span class="s1">&#39;organism&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span>
+
+        <span class="n">AnnotationBase</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">name</span> <span class="o">=</span> <span class="s1">&#39;OPM&#39;</span><span class="p">,</span>
+            <span class="n">input_method</span> <span class="o">=</span> <span class="s1">&#39;opm.opm_annotations&#39;</span><span class="p">,</span>
+            <span class="o">**</span><span class="n">kwargs</span>
+        <span class="p">)</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">_process_method</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">annot</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span>
+        <span class="nb">delattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">&#39;data&#39;</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="Phobius">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.Phobius.html#pypath.core.annot.Phobius">[docs]</a>
+<span class="k">class</span> <span class="nc">Phobius</span><span class="p">(</span><span class="n">AnnotationBase</span><span class="p">):</span>
+
+    <span class="n">_eq_fields</span> <span class="o">=</span> <span class="p">(</span>
+        <span class="s1">&#39;tm_helices&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;signal_peptide&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;cytoplasmic&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;non_cytoplasmic&#39;</span><span class="p">,</span>
+    <span class="p">)</span>
+
+
+<div class="viewcode-block" id="Phobius.__init__">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.Phobius.html#pypath.core.annot.Phobius.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+
+        <span class="n">AnnotationBase</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">name</span> <span class="o">=</span> <span class="s1">&#39;Phobius&#39;</span><span class="p">,</span>
+            <span class="n">input_method</span> <span class="o">=</span> <span class="s1">&#39;phobius.phobius_annotations&#39;</span><span class="p">,</span>
+            <span class="o">**</span><span class="n">kwargs</span>
+        <span class="p">)</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">_process_method</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">annot</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span>
+        <span class="nb">delattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">&#39;data&#39;</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="Topdb">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.Topdb.html#pypath.core.annot.Topdb">[docs]</a>
+<span class="k">class</span> <span class="nc">Topdb</span><span class="p">(</span><span class="n">AnnotationBase</span><span class="p">):</span>
+
+    <span class="n">_eq_fields</span> <span class="o">=</span> <span class="p">(</span><span class="s1">&#39;membrane&#39;</span><span class="p">,)</span>
+
+
+<div class="viewcode-block" id="Topdb.__init__">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.Topdb.html#pypath.core.annot.Topdb.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+
+        <span class="n">AnnotationBase</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">name</span> <span class="o">=</span> <span class="s1">&#39;TopDB&#39;</span><span class="p">,</span>
+            <span class="n">input_method</span> <span class="o">=</span> <span class="s1">&#39;topdb.topdb_annotations&#39;</span><span class="p">,</span>
+            <span class="n">input_args</span> <span class="o">=</span> <span class="p">{</span>
+                <span class="s1">&#39;ncbi_tax_id&#39;</span><span class="p">:</span> <span class="n">ncbi_tax_id</span><span class="p">,</span>
+            <span class="p">},</span>
+            <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">,</span>
+            <span class="o">**</span><span class="n">kwargs</span>
+        <span class="p">)</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">_process_method</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">annot</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span>
+        <span class="nb">delattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">&#39;data&#39;</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="Cpad">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.Cpad.html#pypath.core.annot.Cpad">[docs]</a>
+<span class="k">class</span> <span class="nc">Cpad</span><span class="p">(</span><span class="n">AnnotationBase</span><span class="p">):</span>
+
+    <span class="n">_eq_fields</span> <span class="o">=</span> <span class="p">(</span>
+        <span class="s1">&#39;effect_on_pathway&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;pathway&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;effect_on_cancer&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;cancer&#39;</span> <span class="p">,</span>
+    <span class="p">)</span>
+
+
+<div class="viewcode-block" id="Cpad.__init__">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.Cpad.html#pypath.core.annot.Cpad.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+
+        <span class="n">AnnotationBase</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">name</span> <span class="o">=</span> <span class="s1">&#39;CPAD&#39;</span><span class="p">,</span>
+            <span class="n">input_method</span> <span class="o">=</span> <span class="s1">&#39;cpad.cpad_annotations&#39;</span><span class="p">,</span>
+            <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">,</span>
+            <span class="o">**</span><span class="n">kwargs</span>
+        <span class="p">)</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">_process_method</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">annot</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span>
+        <span class="nb">delattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">&#39;data&#39;</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="Disgenet">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.Disgenet.html#pypath.core.annot.Disgenet">[docs]</a>
+<span class="k">class</span> <span class="nc">Disgenet</span><span class="p">(</span><span class="n">AnnotationBase</span><span class="p">):</span>
+
+    <span class="n">_eq_fields</span> <span class="o">=</span> <span class="p">(</span>
+        <span class="s1">&#39;disease&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;type&#39;</span><span class="p">,</span>
+    <span class="p">)</span>
+
+
+<div class="viewcode-block" id="Disgenet.__init__">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.Disgenet.html#pypath.core.annot.Disgenet.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+
+        <span class="n">AnnotationBase</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">name</span> <span class="o">=</span> <span class="s1">&#39;DisGeNet&#39;</span><span class="p">,</span>
+            <span class="n">input_method</span> <span class="o">=</span> <span class="s1">&#39;disgenet.disgenet_annotations&#39;</span><span class="p">,</span>
+            <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">,</span>
+            <span class="o">**</span><span class="n">kwargs</span>
+        <span class="p">)</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">_process_method</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">annot</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span>
+        <span class="nb">delattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">&#39;data&#39;</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="Msigdb">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.Msigdb.html#pypath.core.annot.Msigdb">[docs]</a>
+<span class="k">class</span> <span class="nc">Msigdb</span><span class="p">(</span><span class="n">AnnotationBase</span><span class="p">):</span>
+
+    <span class="n">_eq_fields</span> <span class="o">=</span> <span class="p">(</span>
+        <span class="s1">&#39;collection&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;geneset&#39;</span><span class="p">,</span>
+    <span class="p">)</span>
+
+
+<div class="viewcode-block" id="Msigdb.__init__">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.Msigdb.html#pypath.core.annot.Msigdb.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+
+        <span class="n">AnnotationBase</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">name</span> <span class="o">=</span> <span class="s1">&#39;MSigDB&#39;</span><span class="p">,</span>
+            <span class="n">input_method</span> <span class="o">=</span> <span class="s1">&#39;msigdb.msigdb_annotations&#39;</span><span class="p">,</span>
+            <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">,</span>
+            <span class="n">input_args</span> <span class="o">=</span> <span class="p">{</span><span class="s1">&#39;exclude&#39;</span><span class="p">:</span> <span class="p">()},</span>
+            <span class="o">**</span><span class="n">kwargs</span>
+        <span class="p">)</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">_process_method</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">annot</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span>
+        <span class="nb">delattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">&#39;data&#39;</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="Integrins">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.Integrins.html#pypath.core.annot.Integrins">[docs]</a>
+<span class="k">class</span> <span class="nc">Integrins</span><span class="p">(</span><span class="n">AnnotationBase</span><span class="p">):</span>
+
+    <span class="n">_eq_fields</span> <span class="o">=</span> <span class="p">()</span>
+
+
+<div class="viewcode-block" id="Integrins.__init__">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.Integrins.html#pypath.core.annot.Integrins.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+
+        <span class="n">AnnotationBase</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">name</span> <span class="o">=</span> <span class="s1">&#39;Integrins&#39;</span><span class="p">,</span>
+            <span class="n">input_method</span> <span class="o">=</span> <span class="s1">&#39;integrins.get_integrins&#39;</span><span class="p">,</span>
+            <span class="o">**</span><span class="n">kwargs</span>
+        <span class="p">)</span></div>
+</div>
+
+
+
+<div class="viewcode-block" id="Lrdb">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.Lrdb.html#pypath.core.annot.Lrdb">[docs]</a>
+<span class="k">class</span> <span class="nc">Lrdb</span><span class="p">(</span><span class="n">AnnotationBase</span><span class="p">):</span>
+
+
+    <span class="n">_eq_fields</span> <span class="o">=</span> <span class="p">(</span><span class="s1">&#39;role&#39;</span><span class="p">,)</span>
+
+
+<div class="viewcode-block" id="Lrdb.__init__">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.Lrdb.html#pypath.core.annot.Lrdb.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+
+        <span class="n">AnnotationBase</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">name</span> <span class="o">=</span> <span class="s1">&#39;LRdb&#39;</span><span class="p">,</span>
+            <span class="n">input_method</span> <span class="o">=</span> <span class="s1">&#39;lrdb.lrdb_annotations&#39;</span><span class="p">,</span>
+            <span class="o">**</span><span class="n">kwargs</span>
+        <span class="p">)</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">_process_method</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">annot</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span>
+        <span class="nb">delattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">&#39;data&#39;</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="HumanProteinAtlas">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.HumanProteinAtlas.html#pypath.core.annot.HumanProteinAtlas">[docs]</a>
+<span class="k">class</span> <span class="nc">HumanProteinAtlas</span><span class="p">(</span><span class="n">AnnotationBase</span><span class="p">):</span>
+
+    <span class="n">_eq_fields</span> <span class="o">=</span> <span class="p">(</span><span class="s1">&#39;organ&#39;</span><span class="p">,</span> <span class="s1">&#39;tissue&#39;</span><span class="p">,</span> <span class="s1">&#39;status&#39;</span><span class="p">,</span> <span class="s1">&#39;level&#39;</span><span class="p">,</span> <span class="s1">&#39;pathology&#39;</span><span class="p">)</span>
+
+
+<div class="viewcode-block" id="HumanProteinAtlas.__init__">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.HumanProteinAtlas.html#pypath.core.annot.HumanProteinAtlas.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+
+        <span class="n">AnnotationBase</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">name</span> <span class="o">=</span> <span class="s1">&#39;HPA_tissue&#39;</span><span class="p">,</span>
+            <span class="n">input_method</span> <span class="o">=</span> <span class="s1">&#39;proteinatlas.proteinatlas_annotations&#39;</span><span class="p">,</span>
+            <span class="o">**</span><span class="n">kwargs</span>
+        <span class="p">)</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">_process_method</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">annot</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span>
+        <span class="nb">delattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">&#39;data&#39;</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="HumanProteinAtlasSubcellular">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.HumanProteinAtlasSubcellular.html#pypath.core.annot.HumanProteinAtlasSubcellular">[docs]</a>
+<span class="k">class</span> <span class="nc">HumanProteinAtlasSubcellular</span><span class="p">(</span><span class="n">AnnotationBase</span><span class="p">):</span>
+
+    <span class="n">_eq_fields</span> <span class="o">=</span> <span class="p">(</span><span class="s1">&#39;location&#39;</span><span class="p">,)</span>
+
+
+<div class="viewcode-block" id="HumanProteinAtlasSubcellular.__init__">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.HumanProteinAtlasSubcellular.html#pypath.core.annot.HumanProteinAtlasSubcellular.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+
+        <span class="n">AnnotationBase</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">name</span> <span class="o">=</span> <span class="s1">&#39;HPA_subcellular&#39;</span><span class="p">,</span>
+            <span class="n">input_method</span> <span class="o">=</span> <span class="p">(</span>
+                <span class="s1">&#39;proteinatlas.proteinatlas_subcellular_annotations&#39;</span>
+            <span class="p">),</span>
+            <span class="o">**</span><span class="n">kwargs</span>
+        <span class="p">)</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">_process_method</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">annot</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span>
+        <span class="nb">delattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">&#39;data&#39;</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="HumanProteinAtlasSecretome">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.HumanProteinAtlasSecretome.html#pypath.core.annot.HumanProteinAtlasSecretome">[docs]</a>
+<span class="k">class</span> <span class="nc">HumanProteinAtlasSecretome</span><span class="p">(</span><span class="n">AnnotationBase</span><span class="p">):</span>
+
+    <span class="n">_eq_fields</span> <span class="o">=</span> <span class="p">(</span><span class="s1">&#39;mainclass&#39;</span><span class="p">,)</span>
+
+
+<div class="viewcode-block" id="HumanProteinAtlasSecretome.__init__">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.HumanProteinAtlasSecretome.html#pypath.core.annot.HumanProteinAtlasSecretome.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+
+        <span class="n">AnnotationBase</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">name</span> <span class="o">=</span> <span class="s1">&#39;HPA_secretome&#39;</span><span class="p">,</span>
+            <span class="n">input_method</span> <span class="o">=</span> <span class="s1">&#39;proteinatlas.proteinatlas_secretome_annotations&#39;</span><span class="p">,</span>
+            <span class="o">**</span><span class="n">kwargs</span>
+        <span class="p">)</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">_process_method</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">annot</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span>
+        <span class="nb">delattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">&#39;data&#39;</span><span class="p">)</span></div>
+
+
+
+
+<div class="viewcode-block" id="CancerGeneCensus">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.CancerGeneCensus.html#pypath.core.annot.CancerGeneCensus">[docs]</a>
+<span class="k">class</span> <span class="nc">CancerGeneCensus</span><span class="p">(</span><span class="n">AnnotationBase</span><span class="p">):</span>
+
+    <span class="n">_eq_fields</span> <span class="o">=</span> <span class="kc">None</span>
+
+
+<div class="viewcode-block" id="CancerGeneCensus.__init__">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.CancerGeneCensus.html#pypath.core.annot.CancerGeneCensus.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+
+        <span class="n">AnnotationBase</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">name</span> <span class="o">=</span> <span class="s1">&#39;CancerGeneCensus&#39;</span><span class="p">,</span>
+            <span class="n">input_method</span> <span class="o">=</span> <span class="s1">&#39;cosmic.cancer_gene_census_annotations&#39;</span><span class="p">,</span>
+            <span class="o">**</span><span class="n">kwargs</span>
+        <span class="p">)</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">_process_method</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">annot</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span>
+        <span class="nb">delattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">&#39;data&#39;</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="Intogen">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.Intogen.html#pypath.core.annot.Intogen">[docs]</a>
+<span class="k">class</span> <span class="nc">Intogen</span><span class="p">(</span><span class="n">AnnotationBase</span><span class="p">):</span>
+
+    <span class="n">_eq_fields</span> <span class="o">=</span> <span class="p">(</span><span class="s1">&#39;type&#39;</span><span class="p">,</span> <span class="s1">&#39;role&#39;</span><span class="p">)</span>
+
+
+<div class="viewcode-block" id="Intogen.__init__">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.Intogen.html#pypath.core.annot.Intogen.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+
+        <span class="n">AnnotationBase</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">name</span> <span class="o">=</span> <span class="s1">&#39;IntOGen&#39;</span><span class="p">,</span>
+            <span class="n">input_method</span> <span class="o">=</span> <span class="s1">&#39;intogen.intogen_annotations&#39;</span><span class="p">,</span>
+            <span class="o">**</span><span class="n">kwargs</span>
+        <span class="p">)</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">_process_method</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">annot</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span>
+        <span class="nb">delattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">&#39;data&#39;</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="Comppi">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.Comppi.html#pypath.core.annot.Comppi">[docs]</a>
+<span class="k">class</span> <span class="nc">Comppi</span><span class="p">(</span><span class="n">AnnotationBase</span><span class="p">):</span>
+
+    <span class="n">_eq_fields</span> <span class="o">=</span> <span class="p">(</span><span class="s1">&#39;location&#39;</span><span class="p">,)</span>
+
+
+<div class="viewcode-block" id="Comppi.__init__">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.Comppi.html#pypath.core.annot.Comppi.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+
+        <span class="n">AnnotationBase</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">name</span> <span class="o">=</span> <span class="s1">&#39;ComPPI&#39;</span><span class="p">,</span>
+            <span class="n">input_method</span> <span class="o">=</span> <span class="s1">&#39;comppi.comppi_locations&#39;</span><span class="p">,</span>
+            <span class="o">**</span><span class="n">kwargs</span>
+        <span class="p">)</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">_process_method</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">annot</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span>
+        <span class="nb">delattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">&#39;data&#39;</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="Ramilowski2015Location">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.Ramilowski2015Location.html#pypath.core.annot.Ramilowski2015Location">[docs]</a>
+<span class="k">class</span> <span class="nc">Ramilowski2015Location</span><span class="p">(</span><span class="n">AnnotationBase</span><span class="p">):</span>
+
+    <span class="n">_eq_fields</span> <span class="o">=</span> <span class="p">(</span><span class="s1">&#39;location&#39;</span><span class="p">,)</span>
+
+
+<div class="viewcode-block" id="Ramilowski2015Location.__init__">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.Ramilowski2015Location.html#pypath.core.annot.Ramilowski2015Location.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+
+        <span class="n">AnnotationBase</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">name</span> <span class="o">=</span> <span class="s1">&#39;Ramilowski_location&#39;</span><span class="p">,</span>
+            <span class="n">input_method</span> <span class="o">=</span> <span class="s1">&#39;ramilowski2015.ramilowski_locations&#39;</span><span class="p">,</span>
+            <span class="o">**</span><span class="n">kwargs</span>
+        <span class="p">)</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">_process_method</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">annot</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span>
+        <span class="nb">delattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">&#39;data&#39;</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="CellSurfaceProteinAtlas">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.CellSurfaceProteinAtlas.html#pypath.core.annot.CellSurfaceProteinAtlas">[docs]</a>
+<span class="k">class</span> <span class="nc">CellSurfaceProteinAtlas</span><span class="p">(</span><span class="n">AnnotationBase</span><span class="p">):</span>
+
+
+    <span class="n">_eq_fields</span> <span class="o">=</span> <span class="p">(</span><span class="s1">&#39;high_confidence&#39;</span><span class="p">,</span> <span class="s1">&#39;tm&#39;</span><span class="p">,</span> <span class="s1">&#39;gpi&#39;</span><span class="p">,</span> <span class="s1">&#39;uniprot_cell_surface&#39;</span><span class="p">)</span>
+
+
+<div class="viewcode-block" id="CellSurfaceProteinAtlas.__init__">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.CellSurfaceProteinAtlas.html#pypath.core.annot.CellSurfaceProteinAtlas.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">,</span>
+            <span class="o">**</span><span class="n">kwargs</span>
+        <span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        The name of this resource abbreviated as `CSPA`.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">if</span> <span class="s1">&#39;organism&#39;</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">kwargs</span><span class="p">:</span>
+
+            <span class="n">kwargs</span><span class="p">[</span><span class="s1">&#39;organism&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span>
+
+        <span class="n">AnnotationBase</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">name</span> <span class="o">=</span> <span class="s1">&#39;CSPA&#39;</span><span class="p">,</span>
+            <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">,</span>
+            <span class="n">input_method</span> <span class="o">=</span> <span class="s1">&#39;cspa.cspa_annotations&#39;</span><span class="p">,</span>
+            <span class="o">**</span><span class="n">kwargs</span>
+        <span class="p">)</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">_process_method</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">annot</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span>
+        <span class="nb">delattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">&#39;data&#39;</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="CellSurfaceProteinAtlasCellType">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.CellSurfaceProteinAtlasCellType.html#pypath.core.annot.CellSurfaceProteinAtlasCellType">[docs]</a>
+<span class="k">class</span> <span class="nc">CellSurfaceProteinAtlasCellType</span><span class="p">(</span><span class="n">AnnotationBase</span><span class="p">):</span>
+
+
+    <span class="n">_eq_fields</span> <span class="o">=</span> <span class="p">(</span><span class="s1">&#39;cell_type&#39;</span><span class="p">,)</span>
+
+
+<div class="viewcode-block" id="CellSurfaceProteinAtlasCellType.__init__">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.CellSurfaceProteinAtlasCellType.html#pypath.core.annot.CellSurfaceProteinAtlasCellType.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">,</span>
+            <span class="o">**</span><span class="n">kwargs</span>
+        <span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        The name of this resource abbreviated as `CSPA`.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">if</span> <span class="s1">&#39;organism&#39;</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">kwargs</span><span class="p">:</span>
+
+            <span class="n">kwargs</span><span class="p">[</span><span class="s1">&#39;organism&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span>
+
+        <span class="n">AnnotationBase</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">name</span> <span class="o">=</span> <span class="s1">&#39;CSPA_celltype&#39;</span><span class="p">,</span>
+            <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">,</span>
+            <span class="n">input_method</span> <span class="o">=</span> <span class="s1">&#39;cspa.cspa_cell_type_annotations&#39;</span><span class="p">,</span>
+            <span class="o">**</span><span class="n">kwargs</span>
+        <span class="p">)</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">_process_method</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">annot</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span>
+        <span class="nb">delattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">&#39;data&#39;</span><span class="p">)</span></div>
+
+
+
+
+<div class="viewcode-block" id="HumanPlasmaMembraneReceptome">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.HumanPlasmaMembraneReceptome.html#pypath.core.annot.HumanPlasmaMembraneReceptome">[docs]</a>
+<span class="k">class</span> <span class="nc">HumanPlasmaMembraneReceptome</span><span class="p">(</span><span class="n">AnnotationBase</span><span class="p">):</span>
+
+    <span class="n">_eq_fields</span> <span class="o">=</span> <span class="p">(</span><span class="s1">&#39;role&#39;</span><span class="p">,)</span>
+
+
+<div class="viewcode-block" id="HumanPlasmaMembraneReceptome.__init__">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.HumanPlasmaMembraneReceptome.html#pypath.core.annot.HumanPlasmaMembraneReceptome.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        The name of this resource abbreviated as `HPMR`.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">AnnotationBase</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">name</span> <span class="o">=</span> <span class="s1">&#39;HPMR&#39;</span><span class="p">,</span>
+            <span class="n">input_method</span> <span class="o">=</span> <span class="s1">&#39;hpmr.hpmr_annotations&#39;</span><span class="p">,</span>
+            <span class="o">**</span><span class="n">kwargs</span>
+        <span class="p">)</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">_process_method</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">annot</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span>
+        <span class="k">del</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span></div>
+
+
+
+<div class="viewcode-block" id="Kinasedotcom">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.Kinasedotcom.html#pypath.core.annot.Kinasedotcom">[docs]</a>
+<span class="k">class</span> <span class="nc">Kinasedotcom</span><span class="p">(</span><span class="n">AnnotationBase</span><span class="p">):</span>
+
+    <span class="n">_eq_fields</span> <span class="o">=</span> <span class="p">(</span><span class="s1">&#39;group&#39;</span><span class="p">,</span> <span class="s1">&#39;family&#39;</span><span class="p">)</span>
+
+
+<div class="viewcode-block" id="Kinasedotcom.__init__">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.Kinasedotcom.html#pypath.core.annot.Kinasedotcom.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Kinases from `kinase.com`.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">AnnotationBase</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">name</span> <span class="o">=</span> <span class="s1">&#39;kinase.com&#39;</span><span class="p">,</span>
+            <span class="n">input_method</span> <span class="o">=</span> <span class="s1">&#39;kinasedotcom.kinasedotcom_annotations&#39;</span><span class="p">,</span>
+            <span class="o">**</span><span class="n">kwargs</span>
+        <span class="p">)</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">_process_method</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="c1">#  already the appropriate format, no processing needed</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">annot</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span>
+
+        <span class="nb">delattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">&#39;data&#39;</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="Tfcensus">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.Tfcensus.html#pypath.core.annot.Tfcensus">[docs]</a>
+<span class="k">class</span> <span class="nc">Tfcensus</span><span class="p">(</span><span class="n">AnnotationBase</span><span class="p">):</span>
+
+    <span class="n">_eq_fields</span> <span class="o">=</span> <span class="p">()</span>
+
+
+<div class="viewcode-block" id="Tfcensus.__init__">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.Tfcensus.html#pypath.core.annot.Tfcensus.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Transcription factors from TF census (Vaquerizas et al 2009).</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">AnnotationBase</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">name</span> <span class="o">=</span> <span class="s1">&#39;TFcensus&#39;</span><span class="p">,</span>
+            <span class="n">input_method</span> <span class="o">=</span> <span class="s1">&#39;tfcensus.tfcensus_annotations&#39;</span><span class="p">,</span>
+            <span class="o">**</span><span class="n">kwargs</span>
+        <span class="p">)</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">_process_method</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="c1">#  already the appropriate format, no processing needed</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">annot</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span>
+
+        <span class="nb">delattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">&#39;data&#39;</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="Dgidb">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.Dgidb.html#pypath.core.annot.Dgidb">[docs]</a>
+<span class="k">class</span> <span class="nc">Dgidb</span><span class="p">(</span><span class="n">AnnotationBase</span><span class="p">):</span>
+
+    <span class="n">_eq_fields</span> <span class="o">=</span> <span class="p">(</span><span class="s1">&#39;category&#39;</span><span class="p">,)</span>
+
+
+<div class="viewcode-block" id="Dgidb.__init__">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.Dgidb.html#pypath.core.annot.Dgidb.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Druggable proteins from DGIdb (Drug Gene Interaction Database).</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">AnnotationBase</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">name</span> <span class="o">=</span> <span class="s1">&#39;DGIdb&#39;</span><span class="p">,</span>
+            <span class="n">input_method</span> <span class="o">=</span> <span class="s1">&#39;dgidb.dgidb_annotations&#39;</span><span class="p">,</span>
+            <span class="o">**</span><span class="n">kwargs</span>
+        <span class="p">)</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">_process_method</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="c1">#  already the appropriate format, no processing needed</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">annot</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span>
+
+        <span class="nb">delattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">&#39;data&#39;</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="Phosphatome">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.Phosphatome.html#pypath.core.annot.Phosphatome">[docs]</a>
+<span class="k">class</span> <span class="nc">Phosphatome</span><span class="p">(</span><span class="n">AnnotationBase</span><span class="p">):</span>
+
+    <span class="n">_eq_fields</span> <span class="o">=</span> <span class="p">()</span>
+
+
+<div class="viewcode-block" id="Phosphatome.__init__">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.Phosphatome.html#pypath.core.annot.Phosphatome.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        The list of phosphatases from Chen et al, Science Signaling (2017)</span>
+<span class="sd">        Table S1.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">AnnotationBase</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">name</span> <span class="o">=</span> <span class="s1">&#39;Phosphatome&#39;</span><span class="p">,</span>
+            <span class="n">input_method</span> <span class="o">=</span> <span class="s1">&#39;phosphatome.phosphatome_annotations&#39;</span><span class="p">,</span>
+            <span class="o">**</span><span class="n">kwargs</span>
+        <span class="p">)</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">_process_method</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">annot</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span>
+        <span class="k">del</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span></div>
+
+
+
+<div class="viewcode-block" id="Matrixdb">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.Matrixdb.html#pypath.core.annot.Matrixdb">[docs]</a>
+<span class="k">class</span> <span class="nc">Matrixdb</span><span class="p">(</span><span class="n">AnnotationBase</span><span class="p">):</span>
+
+    <span class="n">_eq_fields</span> <span class="o">=</span> <span class="p">(</span><span class="s1">&#39;mainclass&#39;</span><span class="p">,)</span>
+
+
+<div class="viewcode-block" id="Matrixdb.__init__">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.Matrixdb.html#pypath.core.annot.Matrixdb.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Protein annotations from MatrixDB.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">AnnotationBase</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">name</span> <span class="o">=</span> <span class="s1">&#39;MatrixDB&#39;</span><span class="p">,</span>
+            <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">,</span>
+            <span class="n">input_method</span> <span class="o">=</span> <span class="s1">&#39;matrixdb.matrixdb_annotations&#39;</span><span class="p">,</span>
+            <span class="o">**</span><span class="n">kwargs</span>
+        <span class="p">)</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">_process_method</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="c1">#  already the appropriate format, no processing needed</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">annot</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span>
+
+        <span class="nb">delattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">&#39;data&#39;</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="SignorPathways">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.SignorPathways.html#pypath.core.annot.SignorPathways">[docs]</a>
+<span class="k">class</span> <span class="nc">SignorPathways</span><span class="p">(</span><span class="n">AnnotationBase</span><span class="p">):</span>
+
+    <span class="n">_eq_fields</span> <span class="o">=</span> <span class="p">(</span><span class="s1">&#39;pathway&#39;</span><span class="p">,)</span>
+
+
+<div class="viewcode-block" id="SignorPathways.__init__">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.SignorPathways.html#pypath.core.annot.SignorPathways.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Pathway annotations from Signor.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">AnnotationBase</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">name</span> <span class="o">=</span> <span class="s1">&#39;SIGNOR&#39;</span><span class="p">,</span>
+            <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">,</span>
+            <span class="n">input_method</span> <span class="o">=</span> <span class="s1">&#39;signor.signor_pathway_annotations&#39;</span><span class="p">,</span>
+            <span class="o">**</span><span class="n">kwargs</span>
+        <span class="p">)</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">_process_method</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="c1">#  already the appropriate format, no processing needed</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">annot</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span>
+
+        <span class="nb">delattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">&#39;data&#39;</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="SignalinkPathways">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.SignalinkPathways.html#pypath.core.annot.SignalinkPathways">[docs]</a>
+<span class="k">class</span> <span class="nc">SignalinkPathways</span><span class="p">(</span><span class="n">AnnotationBase</span><span class="p">):</span>
+
+    <span class="n">_eq_fields</span> <span class="o">=</span> <span class="p">(</span><span class="s1">&#39;pathway&#39;</span><span class="p">,)</span>
+
+
+<div class="viewcode-block" id="SignalinkPathways.__init__">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.SignalinkPathways.html#pypath.core.annot.SignalinkPathways.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Pathway annotations from SignaLink.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">AnnotationBase</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">name</span> <span class="o">=</span> <span class="s1">&#39;SignaLink_pathway&#39;</span><span class="p">,</span>
+            <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">,</span>
+            <span class="n">input_method</span> <span class="o">=</span> <span class="s1">&#39;signalink.signalink_pathway_annotations&#39;</span><span class="p">,</span>
+            <span class="o">**</span><span class="n">kwargs</span>
+        <span class="p">)</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">_process_method</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="c1">#  already the appropriate format, no processing needed</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">annot</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span>
+
+        <span class="nb">delattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">&#39;data&#39;</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="SignalinkFunctions">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.SignalinkFunctions.html#pypath.core.annot.SignalinkFunctions">[docs]</a>
+<span class="k">class</span> <span class="nc">SignalinkFunctions</span><span class="p">(</span><span class="n">AnnotationBase</span><span class="p">):</span>
+
+    <span class="n">_eq_fields</span> <span class="o">=</span> <span class="p">(</span><span class="s1">&#39;function&#39;</span><span class="p">,)</span>
+
+
+<div class="viewcode-block" id="SignalinkFunctions.__init__">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.SignalinkFunctions.html#pypath.core.annot.SignalinkFunctions.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Functional annotations from SignaLink.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">AnnotationBase</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">name</span> <span class="o">=</span> <span class="s1">&#39;SignaLink_function&#39;</span><span class="p">,</span>
+            <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">,</span>
+            <span class="n">input_method</span> <span class="o">=</span> <span class="s1">&#39;signalink.signalink_function_annotations&#39;</span><span class="p">,</span>
+            <span class="o">**</span><span class="n">kwargs</span>
+        <span class="p">)</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">_process_method</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="c1">#  already the appropriate format, no processing needed</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">annot</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span>
+
+        <span class="nb">delattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">&#39;data&#39;</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="KeggPathways">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.KeggPathways.html#pypath.core.annot.KeggPathways">[docs]</a>
+<span class="k">class</span> <span class="nc">KeggPathways</span><span class="p">(</span><span class="n">AnnotationBase</span><span class="p">):</span>
+
+    <span class="n">_eq_fields</span> <span class="o">=</span> <span class="p">(</span><span class="s1">&#39;pathway&#39;</span><span class="p">,)</span>
+
+
+<div class="viewcode-block" id="KeggPathways.__init__">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.KeggPathways.html#pypath.core.annot.KeggPathways.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Pathway annotations from KEGG.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">AnnotationBase</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">name</span> <span class="o">=</span> <span class="s1">&#39;KEGG&#39;</span><span class="p">,</span>
+            <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">,</span>
+            <span class="n">input_method</span> <span class="o">=</span> <span class="s1">&#39;kegg.kegg_pathway_annotations&#39;</span><span class="p">,</span>
+            <span class="o">**</span><span class="n">kwargs</span>
+        <span class="p">)</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">_process_method</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="c1">#  already the appropriate format, no processing needed</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">annot</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span>
+
+        <span class="nb">delattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">&#39;data&#39;</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="KeggPathwaysPC">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.KeggPathwaysPC.html#pypath.core.annot.KeggPathwaysPC">[docs]</a>
+<span class="k">class</span> <span class="nc">KeggPathwaysPC</span><span class="p">(</span><span class="n">AnnotationBase</span><span class="p">):</span>
+
+    <span class="n">_eq_fields</span> <span class="o">=</span> <span class="p">(</span><span class="s1">&#39;pathway&#39;</span><span class="p">,)</span>
+
+
+<div class="viewcode-block" id="KeggPathwaysPC.__init__">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.KeggPathwaysPC.html#pypath.core.annot.KeggPathwaysPC.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Pathway annotations from KEGG via PathwayCommons.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">AnnotationBase</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">name</span> <span class="o">=</span> <span class="s1">&#39;KEGG-PC&#39;</span><span class="p">,</span>
+            <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">,</span>
+            <span class="n">input_method</span> <span class="o">=</span> <span class="s1">&#39;kegg.kegg_pathway_annotations_pathwaycommons&#39;</span><span class="p">,</span>
+            <span class="o">**</span><span class="n">kwargs</span>
+        <span class="p">)</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">_process_method</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="c1">#  already the appropriate format, no processing needed</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">annot</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span>
+
+        <span class="nb">delattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">&#39;data&#39;</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="NetpathPathways">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.NetpathPathways.html#pypath.core.annot.NetpathPathways">[docs]</a>
+<span class="k">class</span> <span class="nc">NetpathPathways</span><span class="p">(</span><span class="n">AnnotationBase</span><span class="p">):</span>
+
+    <span class="n">_eq_fields</span> <span class="o">=</span> <span class="p">(</span><span class="s1">&#39;pathway&#39;</span><span class="p">,)</span>
+
+
+<div class="viewcode-block" id="NetpathPathways.__init__">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.NetpathPathways.html#pypath.core.annot.NetpathPathways.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Pathway annotations from NetPath.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">AnnotationBase</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">name</span> <span class="o">=</span> <span class="s1">&#39;NetPath&#39;</span><span class="p">,</span>
+            <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">,</span>
+            <span class="n">input_method</span> <span class="o">=</span> <span class="s1">&#39;netpath.netpath_pathway_annotations&#39;</span><span class="p">,</span>
+            <span class="o">**</span><span class="n">kwargs</span>
+        <span class="p">)</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">_process_method</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="c1">#  already the appropriate format, no processing needed</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">annot</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span>
+
+        <span class="nb">delattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">&#39;data&#39;</span><span class="p">)</span></div>
+
+
+
+
+<div class="viewcode-block" id="Locate">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.Locate.html#pypath.core.annot.Locate">[docs]</a>
+<span class="k">class</span> <span class="nc">Locate</span><span class="p">(</span><span class="n">AnnotationBase</span><span class="p">):</span>
+
+    <span class="n">_eq_fields</span> <span class="o">=</span> <span class="p">(</span><span class="s1">&#39;location&#39;</span><span class="p">,)</span>
+
+
+<div class="viewcode-block" id="Locate.__init__">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.Locate.html#pypath.core.annot.Locate.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">,</span>
+            <span class="n">literature</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
+            <span class="n">external</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
+            <span class="n">predictions</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+            <span class="o">**</span><span class="n">kwargs</span>
+        <span class="p">):</span>
+
+        <span class="n">input_args</span> <span class="o">=</span> <span class="p">{</span>
+            <span class="s1">&#39;organism&#39;</span><span class="p">:</span> <span class="n">ncbi_tax_id</span> <span class="ow">or</span> <span class="mi">9606</span><span class="p">,</span>
+            <span class="s1">&#39;literature&#39;</span><span class="p">:</span> <span class="n">literature</span><span class="p">,</span>
+            <span class="s1">&#39;external&#39;</span><span class="p">:</span> <span class="n">external</span><span class="p">,</span>
+            <span class="s1">&#39;predictions&#39;</span><span class="p">:</span> <span class="n">predictions</span><span class="p">,</span>
+        <span class="p">}</span>
+
+        <span class="n">AnnotationBase</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">name</span> <span class="o">=</span> <span class="s1">&#39;LOCATE&#39;</span><span class="p">,</span>
+            <span class="n">input_method</span> <span class="o">=</span> <span class="s1">&#39;locate.locate_localizations&#39;</span><span class="p">,</span>
+            <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">,</span>
+            <span class="n">input_args</span> <span class="o">=</span> <span class="n">input_args</span><span class="p">,</span>
+            <span class="o">**</span><span class="n">kwargs</span>
+        <span class="p">)</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">_process_method</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="c1">#  already the appropriate format, no processing needed</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">annot</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span>
+
+        <span class="nb">delattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">&#39;data&#39;</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="GOCustomIntercell">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.GOCustomIntercell.html#pypath.core.annot.GOCustomIntercell">[docs]</a>
+<span class="k">class</span> <span class="nc">GOCustomIntercell</span><span class="p">(</span><span class="n">go</span><span class="o">.</span><span class="n">GOCustomAnnotation</span><span class="p">):</span>
+
+
+<div class="viewcode-block" id="GOCustomIntercell.__init__">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.GOCustomIntercell.html#pypath.core.annot.GOCustomIntercell.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">categories</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">go_annot</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">,</span>
+            <span class="o">**</span><span class="n">kwargs</span>
+        <span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Same as :class:``pypath.go.GOCustomAnnotation``</span>
+<span class="sd">        initialized with the categories defined in</span>
+<span class="sd">        ``pypath.intercell_annot.intercell_categories``.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">categories</span> <span class="o">=</span> <span class="n">categories</span> <span class="ow">or</span> <span class="n">intercell_annot</span><span class="o">.</span><span class="n">go_combined_classes</span>
+
+        <span class="n">go</span><span class="o">.</span><span class="n">GOCustomAnnotation</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">categories</span> <span class="o">=</span> <span class="n">categories</span><span class="p">,</span>
+            <span class="n">go_annot</span> <span class="o">=</span> <span class="n">go_annot</span><span class="p">,</span>
+            <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">,</span>
+        <span class="p">)</span></div>
+</div>
+
+
+
+<div class="viewcode-block" id="GOIntercell">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.GOIntercell.html#pypath.core.annot.GOIntercell">[docs]</a>
+<span class="k">class</span> <span class="nc">GOIntercell</span><span class="p">(</span><span class="n">AnnotationBase</span><span class="p">):</span>
+
+    <span class="n">_eq_fields</span> <span class="o">=</span> <span class="p">(</span><span class="s1">&#39;mainclass&#39;</span><span class="p">,)</span>
+
+
+<div class="viewcode-block" id="GOIntercell.__init__">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.GOIntercell.html#pypath.core.annot.GOIntercell.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">categories</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">go_annot</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">,</span>
+            <span class="o">**</span><span class="n">kwargs</span>
+        <span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Annotation of proteins based on their roles in intercellular</span>
+<span class="sd">        communication from Gene Ontology.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">categories</span> <span class="o">=</span> <span class="n">categories</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">go_annot</span> <span class="o">=</span> <span class="n">go_annot</span>
+
+        <span class="n">AnnotationBase</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">name</span> <span class="o">=</span> <span class="s1">&#39;GO_Intercell&#39;</span><span class="p">,</span>
+            <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">,</span>
+            <span class="o">**</span><span class="n">kwargs</span>
+        <span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="GOIntercell.load">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.GOIntercell.html#pypath.core.annot.GOIntercell.load">[docs]</a>
+    <span class="k">def</span> <span class="nf">load</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="n">record</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">namedtuple</span><span class="p">(</span>
+            <span class="s1">&#39;GOIntercellAnnotation&#39;</span><span class="p">,</span>
+            <span class="p">(</span><span class="s1">&#39;mainclass&#39;</span><span class="p">,),</span>
+        <span class="p">)</span>
+
+        <span class="n">annot</span> <span class="o">=</span> <span class="n">GOCustomIntercell</span><span class="p">(</span>
+            <span class="n">categories</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">categories</span><span class="p">,</span>
+            <span class="n">go_annot</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">go_annot</span><span class="p">,</span>
+            <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">ncbi_tax_id</span><span class="p">,</span>
+        <span class="p">)</span>
+
+        <span class="n">annot_uniprots</span> <span class="o">=</span> <span class="n">annot</span><span class="o">.</span><span class="n">get_annotations</span><span class="p">()</span>
+
+        <span class="n">_annot</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">defaultdict</span><span class="p">(</span><span class="nb">set</span><span class="p">)</span>
+
+        <span class="k">for</span> <span class="n">mainclass</span><span class="p">,</span> <span class="n">uniprots</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="n">annot_uniprots</span><span class="p">):</span>
+
+            <span class="k">for</span> <span class="n">uniprot</span> <span class="ow">in</span> <span class="n">uniprots</span><span class="p">:</span>
+
+                <span class="n">_annot</span><span class="p">[</span><span class="n">uniprot</span><span class="p">]</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">record</span><span class="p">(</span><span class="n">mainclass</span> <span class="o">=</span> <span class="n">mainclass</span><span class="p">))</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">annot</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">(</span><span class="n">_annot</span><span class="p">)</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">_process_method</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">*</span><span class="n">args</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+
+        <span class="k">pass</span></div>
+
+
+
+<div class="viewcode-block" id="CellPhoneDB">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.CellPhoneDB.html#pypath.core.annot.CellPhoneDB">[docs]</a>
+<span class="k">class</span> <span class="nc">CellPhoneDB</span><span class="p">(</span><span class="n">AnnotationBase</span><span class="p">):</span>
+
+
+    <span class="n">_eq_fields</span> <span class="o">=</span> <span class="p">(</span><span class="s1">&#39;receptor&#39;</span><span class="p">,</span> <span class="s1">&#39;peripheral&#39;</span><span class="p">,</span> <span class="s1">&#39;secreted&#39;</span><span class="p">,</span> <span class="s1">&#39;transmembrane&#39;</span><span class="p">)</span>
+
+
+<div class="viewcode-block" id="CellPhoneDB.__init__">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.CellPhoneDB.html#pypath.core.annot.CellPhoneDB.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+
+        <span class="n">_</span> <span class="o">=</span> <span class="n">kwargs</span><span class="o">.</span><span class="n">pop</span><span class="p">(</span><span class="s1">&#39;ncbi_tax_id&#39;</span><span class="p">,</span> <span class="kc">None</span><span class="p">)</span>
+
+        <span class="n">AnnotationBase</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">name</span> <span class="o">=</span> <span class="s1">&#39;CellPhoneDB&#39;</span><span class="p">,</span>
+            <span class="n">input_method</span> <span class="o">=</span> <span class="s1">&#39;cellphonedb.cellphonedb_protein_annotations&#39;</span><span class="p">,</span>
+            <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">,</span>
+            <span class="o">**</span><span class="n">kwargs</span>
+        <span class="p">)</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">_process_method</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">*</span><span class="n">args</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">annot</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">(</span>
+            <span class="p">(</span><span class="n">uniprot</span><span class="p">,</span> <span class="p">{</span><span class="n">annot</span><span class="p">,</span> <span class="p">})</span>
+            <span class="k">for</span> <span class="n">uniprot</span><span class="p">,</span> <span class="n">annot</span> <span class="ow">in</span>
+            <span class="n">iteritems</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">data</span><span class="p">)</span>
+        <span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="Icellnet">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.Icellnet.html#pypath.core.annot.Icellnet">[docs]</a>
+<span class="k">class</span> <span class="nc">Icellnet</span><span class="p">(</span><span class="n">AnnotationBase</span><span class="p">):</span>
+
+    <span class="n">_eq_fields</span> <span class="o">=</span> <span class="p">(</span><span class="s1">&#39;role&#39;</span><span class="p">,)</span>
+
+
+<div class="viewcode-block" id="Icellnet.__init__">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.Icellnet.html#pypath.core.annot.Icellnet.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+
+        <span class="n">_</span> <span class="o">=</span> <span class="n">kwargs</span><span class="o">.</span><span class="n">pop</span><span class="p">(</span><span class="s1">&#39;ncbi_tax_id&#39;</span><span class="p">,</span> <span class="kc">None</span><span class="p">)</span>
+
+        <span class="n">AnnotationBase</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">name</span> <span class="o">=</span> <span class="s1">&#39;ICELLNET&#39;</span><span class="p">,</span>
+            <span class="n">input_method</span> <span class="o">=</span> <span class="s1">&#39;icellnet.icellnet_annotations&#39;</span><span class="p">,</span>
+            <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">,</span>
+            <span class="n">complexes</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+        <span class="p">)</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">_process_method</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">*</span><span class="n">args</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+
+        <span class="c1">#  already the appropriate format, no processing needed</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">annot</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span>
+
+        <span class="nb">delattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">&#39;data&#39;</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="Cellcall">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.Cellcall.html#pypath.core.annot.Cellcall">[docs]</a>
+<span class="k">class</span> <span class="nc">Cellcall</span><span class="p">(</span><span class="n">AnnotationBase</span><span class="p">):</span>
+
+    <span class="n">_eq_fields</span> <span class="o">=</span> <span class="p">(</span><span class="s1">&#39;role&#39;</span><span class="p">,)</span>
+
+
+<div class="viewcode-block" id="Cellcall.__init__">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.Cellcall.html#pypath.core.annot.Cellcall.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+
+        <span class="n">_</span> <span class="o">=</span> <span class="n">kwargs</span><span class="o">.</span><span class="n">pop</span><span class="p">(</span><span class="s1">&#39;ncbi_tax_id&#39;</span><span class="p">,</span> <span class="kc">None</span><span class="p">)</span>
+
+        <span class="n">AnnotationBase</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">name</span> <span class="o">=</span> <span class="s1">&#39;CellCall&#39;</span><span class="p">,</span>
+            <span class="n">input_method</span> <span class="o">=</span> <span class="s1">&#39;cellcall.cellcall_annotations&#39;</span><span class="p">,</span>
+            <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">,</span>
+            <span class="n">complexes</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+        <span class="p">)</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">_process_method</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">*</span><span class="n">args</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+
+        <span class="c1">#  already the appropriate format, no processing needed</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">annot</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span>
+
+        <span class="nb">delattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">&#39;data&#39;</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="Cellinker">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.Cellinker.html#pypath.core.annot.Cellinker">[docs]</a>
+<span class="k">class</span> <span class="nc">Cellinker</span><span class="p">(</span><span class="n">AnnotationBase</span><span class="p">):</span>
+
+    <span class="n">_eq_fields</span> <span class="o">=</span> <span class="p">(</span><span class="s1">&#39;role&#39;</span><span class="p">,</span> <span class="s1">&#39;location&#39;</span><span class="p">,</span> <span class="s1">&#39;type&#39;</span><span class="p">)</span>
+
+
+<div class="viewcode-block" id="Cellinker.__init__">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.Cellinker.html#pypath.core.annot.Cellinker.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+
+        <span class="n">kwargs</span><span class="p">[</span><span class="s1">&#39;organism&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span>
+
+        <span class="n">AnnotationBase</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">name</span> <span class="o">=</span> <span class="s1">&#39;Cellinker&#39;</span><span class="p">,</span>
+            <span class="n">input_method</span> <span class="o">=</span> <span class="s1">&#39;cellinker.cellinker_annotations&#39;</span><span class="p">,</span>
+            <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">,</span>
+            <span class="n">complexes</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+        <span class="p">)</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">_process_method</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">*</span><span class="n">args</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+
+        <span class="c1">#  already the appropriate format, no processing needed</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">annot</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span>
+
+        <span class="nb">delattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">&#39;data&#39;</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="Scconnect">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.Scconnect.html#pypath.core.annot.Scconnect">[docs]</a>
+<span class="k">class</span> <span class="nc">Scconnect</span><span class="p">(</span><span class="n">AnnotationBase</span><span class="p">):</span>
+
+    <span class="n">_eq_fields</span> <span class="o">=</span> <span class="p">(</span><span class="s1">&#39;role&#39;</span><span class="p">,)</span>
+
+
+<div class="viewcode-block" id="Scconnect.__init__">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.Scconnect.html#pypath.core.annot.Scconnect.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+
+        <span class="n">kwargs</span><span class="p">[</span><span class="s1">&#39;organism&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span>
+
+        <span class="n">AnnotationBase</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">name</span> <span class="o">=</span> <span class="s1">&#39;scConnect&#39;</span><span class="p">,</span>
+            <span class="n">input_method</span> <span class="o">=</span> <span class="s1">&#39;scconnect.scconnect_annotations&#39;</span><span class="p">,</span>
+            <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">,</span>
+            <span class="n">complexes</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+        <span class="p">)</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">_process_method</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">*</span><span class="n">args</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">annot</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">(</span>
+            <span class="p">(</span><span class="n">k</span><span class="p">,</span> <span class="n">v</span><span class="p">)</span>
+            <span class="k">for</span> <span class="n">k</span><span class="p">,</span> <span class="n">v</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">data</span><span class="p">)</span>
+            <span class="k">if</span> <span class="ow">not</span> <span class="n">entity</span><span class="o">.</span><span class="n">Entity</span><span class="o">.</span><span class="n">_is_complex</span><span class="p">(</span><span class="n">k</span><span class="p">)</span>
+        <span class="p">)</span>
+
+        <span class="nb">delattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">&#39;data&#39;</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="Biogps">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.Biogps.html#pypath.core.annot.Biogps">[docs]</a>
+<span class="k">class</span> <span class="nc">Biogps</span><span class="p">(</span><span class="n">AnnotationBase</span><span class="p">):</span>
+
+    <span class="n">_eq_fields</span> <span class="o">=</span> <span class="p">(</span><span class="s1">&#39;dataset&#39;</span><span class="p">,</span> <span class="s1">&#39;sample&#39;</span><span class="p">,</span> <span class="s1">&#39;probe&#39;</span><span class="p">)</span>
+
+
+<div class="viewcode-block" id="Biogps.__init__">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.Biogps.html#pypath.core.annot.Biogps.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+
+        <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span> <span class="ow">or</span> <span class="mi">9606</span>
+
+        <span class="n">AnnotationBase</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">name</span> <span class="o">=</span> <span class="s1">&#39;BioGPS&#39;</span><span class="p">,</span>
+            <span class="n">input_method</span> <span class="o">=</span> <span class="s1">&#39;biogps.biogps_annotations&#39;</span><span class="p">,</span>
+            <span class="n">input_args</span> <span class="o">=</span> <span class="p">{</span>
+                <span class="s1">&#39;organism&#39;</span><span class="p">:</span> <span class="n">ncbi_tax_id</span><span class="p">,</span>
+            <span class="p">},</span>
+            <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">,</span>
+            <span class="n">complexes</span> <span class="o">=</span> <span class="p">(),</span>
+            <span class="n">infer_complexes</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+        <span class="p">)</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">_process_method</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">*</span><span class="n">args</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+
+        <span class="c1">#  already the appropriate format, no processing needed</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">annot</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span>
+
+        <span class="nb">delattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">&#39;data&#39;</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="Cellchatdb">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.Cellchatdb.html#pypath.core.annot.Cellchatdb">[docs]</a>
+<span class="k">class</span> <span class="nc">Cellchatdb</span><span class="p">(</span><span class="n">AnnotationBase</span><span class="p">):</span>
+
+    <span class="n">_eq_fields</span> <span class="o">=</span> <span class="p">(</span><span class="s1">&#39;role&#39;</span><span class="p">,</span> <span class="s1">&#39;category&#39;</span><span class="p">)</span>
+
+
+<div class="viewcode-block" id="Cellchatdb.__init__">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.Cellchatdb.html#pypath.core.annot.Cellchatdb.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+
+        <span class="n">_</span> <span class="o">=</span> <span class="n">kwargs</span><span class="o">.</span><span class="n">pop</span><span class="p">(</span><span class="s1">&#39;ncbi_tax_id&#39;</span><span class="p">,</span> <span class="kc">None</span><span class="p">)</span>
+
+        <span class="n">AnnotationBase</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">name</span> <span class="o">=</span> <span class="s1">&#39;CellChatDB&#39;</span><span class="p">,</span>
+            <span class="n">input_method</span> <span class="o">=</span> <span class="s1">&#39;cellchatdb.cellchatdb_annotations&#39;</span><span class="p">,</span>
+            <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">,</span>
+            <span class="n">complexes</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+        <span class="p">)</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">_process_method</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">*</span><span class="n">args</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+
+        <span class="c1">#  already the appropriate format, no processing needed</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">annot</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span>
+
+        <span class="nb">delattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">&#39;data&#39;</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="Celltalkdb">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.Celltalkdb.html#pypath.core.annot.Celltalkdb">[docs]</a>
+<span class="k">class</span> <span class="nc">Celltalkdb</span><span class="p">(</span><span class="n">AnnotationBase</span><span class="p">):</span>
+
+    <span class="n">_eq_fields</span> <span class="o">=</span> <span class="p">(</span><span class="s1">&#39;role&#39;</span><span class="p">,)</span>
+
+
+<div class="viewcode-block" id="Celltalkdb.__init__">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.Celltalkdb.html#pypath.core.annot.Celltalkdb.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+
+        <span class="n">_</span> <span class="o">=</span> <span class="n">kwargs</span><span class="o">.</span><span class="n">pop</span><span class="p">(</span><span class="s1">&#39;ncbi_tax_id&#39;</span><span class="p">,</span> <span class="kc">None</span><span class="p">)</span>
+
+        <span class="n">AnnotationBase</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">name</span> <span class="o">=</span> <span class="s1">&#39;CellTalkDB&#39;</span><span class="p">,</span>
+            <span class="n">input_method</span> <span class="o">=</span> <span class="s1">&#39;celltalkdb.celltalkdb_annotations&#39;</span><span class="p">,</span>
+            <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">,</span>
+            <span class="n">complexes</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+        <span class="p">)</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">_process_method</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">*</span><span class="n">args</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+
+        <span class="c1">#  already the appropriate format, no processing needed</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">annot</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span>
+
+        <span class="nb">delattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">&#39;data&#39;</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="Connectomedb">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.Connectomedb.html#pypath.core.annot.Connectomedb">[docs]</a>
+<span class="k">class</span> <span class="nc">Connectomedb</span><span class="p">(</span><span class="n">AnnotationBase</span><span class="p">):</span>
+
+    <span class="n">_eq_fields</span> <span class="o">=</span> <span class="p">(</span><span class="s1">&#39;role&#39;</span><span class="p">,</span> <span class="s1">&#39;location&#39;</span><span class="p">)</span>
+
+
+<div class="viewcode-block" id="Connectomedb.__init__">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.Connectomedb.html#pypath.core.annot.Connectomedb.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+
+        <span class="n">_</span> <span class="o">=</span> <span class="n">kwargs</span><span class="o">.</span><span class="n">pop</span><span class="p">(</span><span class="s1">&#39;ncbi_tax_id&#39;</span><span class="p">,</span> <span class="kc">None</span><span class="p">)</span>
+
+        <span class="n">AnnotationBase</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">name</span> <span class="o">=</span> <span class="s1">&#39;connectomeDB2020&#39;</span><span class="p">,</span>
+            <span class="n">input_method</span> <span class="o">=</span> <span class="s1">&#39;connectomedb.connectomedb_annotations&#39;</span><span class="p">,</span>
+            <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">,</span>
+            <span class="n">complexes</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+        <span class="p">)</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">_process_method</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">*</span><span class="n">args</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+
+        <span class="c1">#  already the appropriate format, no processing needed</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">annot</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span>
+
+        <span class="nb">delattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">&#39;data&#39;</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="Talklr">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.Talklr.html#pypath.core.annot.Talklr">[docs]</a>
+<span class="k">class</span> <span class="nc">Talklr</span><span class="p">(</span><span class="n">AnnotationBase</span><span class="p">):</span>
+
+    <span class="n">_eq_fields</span> <span class="o">=</span> <span class="p">(</span><span class="s1">&#39;role&#39;</span><span class="p">,)</span>
+
+
+<div class="viewcode-block" id="Talklr.__init__">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.Talklr.html#pypath.core.annot.Talklr.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+
+        <span class="n">_</span> <span class="o">=</span> <span class="n">kwargs</span><span class="o">.</span><span class="n">pop</span><span class="p">(</span><span class="s1">&#39;ncbi_tax_id&#39;</span><span class="p">,</span> <span class="kc">None</span><span class="p">)</span>
+
+        <span class="n">AnnotationBase</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">name</span> <span class="o">=</span> <span class="s1">&#39;talklr&#39;</span><span class="p">,</span>
+            <span class="n">input_method</span> <span class="o">=</span> <span class="s1">&#39;talklr.talklr_annotations&#39;</span><span class="p">,</span>
+            <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">,</span>
+            <span class="n">complexes</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+        <span class="p">)</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">_process_method</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">*</span><span class="n">args</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+
+        <span class="c1">#  already the appropriate format, no processing needed</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">annot</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span>
+
+        <span class="nb">delattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">&#39;data&#39;</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="IcellnetComplex">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.IcellnetComplex.html#pypath.core.annot.IcellnetComplex">[docs]</a>
+<span class="k">class</span> <span class="nc">IcellnetComplex</span><span class="p">(</span><span class="n">AnnotationBase</span><span class="p">):</span>
+
+    <span class="n">_eq_fields</span> <span class="o">=</span> <span class="p">(</span><span class="s1">&#39;role&#39;</span><span class="p">,)</span>
+
+
+<div class="viewcode-block" id="IcellnetComplex.__init__">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.IcellnetComplex.html#pypath.core.annot.IcellnetComplex.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+
+        <span class="n">_</span> <span class="o">=</span> <span class="n">kwargs</span><span class="o">.</span><span class="n">pop</span><span class="p">(</span><span class="s1">&#39;ncbi_tax_id&#39;</span><span class="p">,</span> <span class="kc">None</span><span class="p">)</span>
+
+        <span class="n">AnnotationBase</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">name</span> <span class="o">=</span> <span class="s1">&#39;ICELLNET_complex&#39;</span><span class="p">,</span>
+            <span class="n">input_method</span> <span class="o">=</span> <span class="s1">&#39;icellnet.icellnet_annotations&#39;</span><span class="p">,</span>
+            <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">,</span>
+            <span class="n">entity_type</span> <span class="o">=</span> <span class="s1">&#39;complex&#39;</span><span class="p">,</span>
+        <span class="p">)</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">_process_method</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">*</span><span class="n">args</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+
+        <span class="c1">#  already the appropriate format, no processing needed</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">annot</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span>
+
+        <span class="nb">delattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">&#39;data&#39;</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="CellchatdbComplex">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.CellchatdbComplex.html#pypath.core.annot.CellchatdbComplex">[docs]</a>
+<span class="k">class</span> <span class="nc">CellchatdbComplex</span><span class="p">(</span><span class="n">AnnotationBase</span><span class="p">):</span>
+
+    <span class="n">_eq_fields</span> <span class="o">=</span> <span class="p">(</span><span class="s1">&#39;role&#39;</span><span class="p">,</span> <span class="s1">&#39;category&#39;</span><span class="p">)</span>
+
+
+<div class="viewcode-block" id="CellchatdbComplex.__init__">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.CellchatdbComplex.html#pypath.core.annot.CellchatdbComplex.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+
+        <span class="n">_</span> <span class="o">=</span> <span class="n">kwargs</span><span class="o">.</span><span class="n">pop</span><span class="p">(</span><span class="s1">&#39;ncbi_tax_id&#39;</span><span class="p">,</span> <span class="kc">None</span><span class="p">)</span>
+
+        <span class="n">AnnotationBase</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">name</span> <span class="o">=</span> <span class="s1">&#39;CellChatDB_complex&#39;</span><span class="p">,</span>
+            <span class="n">input_method</span> <span class="o">=</span> <span class="s1">&#39;cellchatdb.cellchatdb_annotations&#39;</span><span class="p">,</span>
+            <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">,</span>
+            <span class="n">entity_type</span> <span class="o">=</span> <span class="s1">&#39;complex&#39;</span><span class="p">,</span>
+        <span class="p">)</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">_process_method</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">*</span><span class="n">args</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+
+        <span class="c1">#  already the appropriate format, no processing needed</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">annot</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span>
+
+        <span class="nb">delattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">&#39;data&#39;</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="CellPhoneDBComplex">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.CellPhoneDBComplex.html#pypath.core.annot.CellPhoneDBComplex">[docs]</a>
+<span class="k">class</span> <span class="nc">CellPhoneDBComplex</span><span class="p">(</span><span class="n">CellPhoneDB</span><span class="p">):</span>
+
+
+<div class="viewcode-block" id="CellPhoneDBComplex.__init__">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.CellPhoneDBComplex.html#pypath.core.annot.CellPhoneDBComplex.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+
+        <span class="n">_</span> <span class="o">=</span> <span class="n">kwargs</span><span class="o">.</span><span class="n">pop</span><span class="p">(</span><span class="s1">&#39;ncbi_tax_id&#39;</span><span class="p">,</span> <span class="kc">None</span><span class="p">)</span>
+
+        <span class="n">AnnotationBase</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">name</span> <span class="o">=</span> <span class="s1">&#39;CellPhoneDB_complex&#39;</span><span class="p">,</span>
+            <span class="n">input_method</span> <span class="o">=</span> <span class="s1">&#39;cellphonedb.cellphonedb_complex_annotations&#39;</span><span class="p">,</span>
+            <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">,</span>
+            <span class="n">entity_type</span> <span class="o">=</span> <span class="s1">&#39;complex&#39;</span><span class="p">,</span>
+            <span class="o">**</span><span class="n">kwargs</span>
+        <span class="p">)</span></div>
+</div>
+
+
+
+<div class="viewcode-block" id="CellinkerComplex">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.CellinkerComplex.html#pypath.core.annot.CellinkerComplex">[docs]</a>
+<span class="k">class</span> <span class="nc">CellinkerComplex</span><span class="p">(</span><span class="n">AnnotationBase</span><span class="p">):</span>
+
+    <span class="n">_eq_fields</span> <span class="o">=</span> <span class="p">(</span><span class="s1">&#39;role&#39;</span><span class="p">,</span> <span class="s1">&#39;location&#39;</span><span class="p">,</span> <span class="s1">&#39;type&#39;</span><span class="p">)</span>
+
+
+<div class="viewcode-block" id="CellinkerComplex.__init__">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.CellinkerComplex.html#pypath.core.annot.CellinkerComplex.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+
+        <span class="n">kwargs</span><span class="p">[</span><span class="s1">&#39;organism&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span>
+
+        <span class="n">AnnotationBase</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">name</span> <span class="o">=</span> <span class="s1">&#39;Cellinker_complex&#39;</span><span class="p">,</span>
+            <span class="n">input_method</span> <span class="o">=</span> <span class="s1">&#39;cellinker.cellinker_complex_annotations&#39;</span><span class="p">,</span>
+            <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">,</span>
+            <span class="n">entity_type</span> <span class="o">=</span> <span class="s1">&#39;complex&#39;</span><span class="p">,</span>
+        <span class="p">)</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">_process_method</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">*</span><span class="n">args</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+
+        <span class="c1">#  already the appropriate format, no processing needed</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">annot</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span>
+
+        <span class="nb">delattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">&#39;data&#39;</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="ScconnectComplex">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.ScconnectComplex.html#pypath.core.annot.ScconnectComplex">[docs]</a>
+<span class="k">class</span> <span class="nc">ScconnectComplex</span><span class="p">(</span><span class="n">AnnotationBase</span><span class="p">):</span>
+
+    <span class="n">_eq_fields</span> <span class="o">=</span> <span class="p">(</span><span class="s1">&#39;role&#39;</span><span class="p">,)</span>
+
+
+<div class="viewcode-block" id="ScconnectComplex.__init__">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.ScconnectComplex.html#pypath.core.annot.ScconnectComplex.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+
+        <span class="n">kwargs</span><span class="p">[</span><span class="s1">&#39;organism&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span>
+
+        <span class="n">AnnotationBase</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">name</span> <span class="o">=</span> <span class="s1">&#39;scConnect_complex&#39;</span><span class="p">,</span>
+            <span class="n">input_method</span> <span class="o">=</span> <span class="s1">&#39;scconnect.scconnect_annotations&#39;</span><span class="p">,</span>
+            <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">,</span>
+            <span class="n">entity_type</span> <span class="o">=</span> <span class="s1">&#39;complex&#39;</span><span class="p">,</span>
+        <span class="p">)</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">_process_method</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">*</span><span class="n">args</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">annot</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">(</span>
+            <span class="p">(</span><span class="n">k</span><span class="p">,</span> <span class="n">v</span><span class="p">)</span>
+            <span class="k">for</span> <span class="n">k</span><span class="p">,</span> <span class="n">v</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">data</span><span class="p">)</span>
+            <span class="k">if</span> <span class="n">entity</span><span class="o">.</span><span class="n">Entity</span><span class="o">.</span><span class="n">_is_complex</span><span class="p">(</span><span class="n">k</span><span class="p">)</span>
+        <span class="p">)</span>
+
+        <span class="nb">delattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">&#39;data&#39;</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="HpmrComplex">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.HpmrComplex.html#pypath.core.annot.HpmrComplex">[docs]</a>
+<span class="k">class</span> <span class="nc">HpmrComplex</span><span class="p">(</span><span class="n">AnnotationBase</span><span class="p">):</span>
+
+
+<div class="viewcode-block" id="HpmrComplex.__init__">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.HpmrComplex.html#pypath.core.annot.HpmrComplex.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+
+        <span class="n">_</span> <span class="o">=</span> <span class="n">kwargs</span><span class="o">.</span><span class="n">pop</span><span class="p">(</span><span class="s1">&#39;ncbi_tax_id&#39;</span><span class="p">,</span> <span class="kc">None</span><span class="p">)</span>
+
+        <span class="n">AnnotationBase</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">name</span> <span class="o">=</span> <span class="s1">&#39;HPMR_complex&#39;</span><span class="p">,</span>
+            <span class="n">input_method</span> <span class="o">=</span> <span class="s1">&#39;hpmr.hpmr_complexes&#39;</span><span class="p">,</span>
+            <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">,</span>
+            <span class="n">entity_type</span> <span class="o">=</span> <span class="s1">&#39;complex&#39;</span><span class="p">,</span>
+            <span class="o">**</span><span class="n">kwargs</span>
+        <span class="p">)</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">_process_method</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">*</span><span class="n">args</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">annot</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">(</span>
+            <span class="p">(</span><span class="n">cplex</span><span class="o">.</span><span class="fm">__str__</span><span class="p">(),</span> <span class="nb">set</span><span class="p">())</span>
+            <span class="k">for</span> <span class="n">cplex</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span>
+        <span class="p">)</span>
+        <span class="k">del</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span></div>
+
+
+
+<div class="viewcode-block" id="Corum">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.Corum.html#pypath.core.annot.Corum">[docs]</a>
+<span class="k">class</span> <span class="nc">Corum</span><span class="p">(</span><span class="n">AnnotationBase</span><span class="p">):</span>
+
+
+<div class="viewcode-block" id="Corum.__init__">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.Corum.html#pypath.core.annot.Corum.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">name</span><span class="p">,</span> <span class="n">annot_attr</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_annot_attr</span> <span class="o">=</span> <span class="n">annot_attr</span>
+
+        <span class="n">AnnotationBase</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">name</span> <span class="o">=</span> <span class="n">name</span><span class="p">,</span>
+            <span class="n">input_method</span> <span class="o">=</span> <span class="s1">&#39;corum.corum_complexes&#39;</span><span class="p">,</span>
+            <span class="n">entity_type</span> <span class="o">=</span> <span class="s1">&#39;complex&#39;</span><span class="p">,</span>
+            <span class="o">**</span><span class="n">kwargs</span>
+        <span class="p">)</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">_process_method</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">*</span><span class="n">args</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+
+        <span class="n">record</span> <span class="o">=</span> <span class="n">CorumAnnotation</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="n">collections</span><span class="o">.</span><span class="n">namedtuple</span><span class="p">(</span>
+                <span class="s1">&#39;CorumAnnotation</span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="bp">self</span><span class="o">.</span><span class="n">_annot_attr</span><span class="o">.</span><span class="n">capitalize</span><span class="p">(),</span>
+                <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_annot_attr</span><span class="p">,),</span>
+            <span class="p">)</span>
+        <span class="p">)</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">annot</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">(</span>
+            <span class="p">(</span>
+                <span class="n">cplex</span><span class="o">.</span><span class="fm">__str__</span><span class="p">(),</span>
+                <span class="nb">set</span><span class="p">(</span>
+                    <span class="n">record</span><span class="p">(</span><span class="n">annot_val</span><span class="p">)</span>
+                    <span class="k">for</span> <span class="n">annot_val</span> <span class="ow">in</span> <span class="n">cplex</span><span class="o">.</span><span class="n">attrs</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">_annot_attr</span><span class="p">]</span>
+                    <span class="k">if</span> <span class="n">annot_val</span> <span class="o">!=</span> <span class="s1">&#39;None&#39;</span>
+                <span class="p">)</span>
+            <span class="p">)</span>
+            <span class="k">for</span> <span class="n">cplex</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span><span class="o">.</span><span class="n">values</span><span class="p">()</span>
+        <span class="p">)</span>
+
+        <span class="k">del</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span></div>
+
+
+
+<div class="viewcode-block" id="CorumFuncat">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.CorumFuncat.html#pypath.core.annot.CorumFuncat">[docs]</a>
+<span class="k">class</span> <span class="nc">CorumFuncat</span><span class="p">(</span><span class="n">Corum</span><span class="p">):</span>
+
+
+<div class="viewcode-block" id="CorumFuncat.__init__">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.CorumFuncat.html#pypath.core.annot.CorumFuncat.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+
+        <span class="n">Corum</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">name</span> <span class="o">=</span> <span class="s1">&#39;CORUM_Funcat&#39;</span><span class="p">,</span>
+            <span class="n">annot_attr</span> <span class="o">=</span> <span class="s1">&#39;funcat&#39;</span><span class="p">,</span>
+            <span class="o">**</span><span class="n">kwargs</span>
+        <span class="p">)</span></div>
+</div>
+
+
+
+<div class="viewcode-block" id="CorumGO">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.CorumGO.html#pypath.core.annot.CorumGO">[docs]</a>
+<span class="k">class</span> <span class="nc">CorumGO</span><span class="p">(</span><span class="n">Corum</span><span class="p">):</span>
+
+
+<div class="viewcode-block" id="CorumGO.__init__">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.CorumGO.html#pypath.core.annot.CorumGO.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+
+        <span class="n">Corum</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">name</span> <span class="o">=</span> <span class="s1">&#39;CORUM_GO&#39;</span><span class="p">,</span>
+            <span class="n">annot_attr</span> <span class="o">=</span> <span class="s1">&#39;go&#39;</span><span class="p">,</span>
+            <span class="o">**</span><span class="n">kwargs</span>
+        <span class="p">)</span></div>
+</div>
+
+
+
+<div class="viewcode-block" id="LigandReceptor">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.LigandReceptor.html#pypath.core.annot.LigandReceptor">[docs]</a>
+<span class="k">class</span> <span class="nc">LigandReceptor</span><span class="p">(</span><span class="n">AnnotationBase</span><span class="p">):</span>
+
+    <span class="n">_eq_fields</span> <span class="o">=</span> <span class="p">(</span><span class="s1">&#39;mainclass&#39;</span><span class="p">,)</span>
+
+
+<div class="viewcode-block" id="LigandReceptor.__init__">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.LigandReceptor.html#pypath.core.annot.LigandReceptor.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">name</span><span class="p">,</span>
+            <span class="n">ligand_col</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">receptor_col</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">ligand_id_type</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">receptor_id_type</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">record_processor_method</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">record_extra_fields</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">record_defaults</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">extra_fields_methods</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="o">**</span><span class="n">kwargs</span>
+        <span class="p">):</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">name</span> <span class="o">=</span> <span class="n">name</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">ligand_col</span> <span class="o">=</span> <span class="n">ligand_col</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">receptor_col</span> <span class="o">=</span> <span class="n">receptor_col</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">ligand_id_type</span> <span class="o">=</span> <span class="n">ligand_id_type</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">receptor_id_type</span> <span class="o">=</span> <span class="n">receptor_id_type</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">_record_extra_fields</span> <span class="o">=</span> <span class="n">record_extra_fields</span> <span class="ow">or</span> <span class="p">()</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">_record_defaults</span> <span class="o">=</span> <span class="n">record_defaults</span> <span class="ow">or</span> <span class="p">()</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">_extra_fields_methods</span> <span class="o">=</span> <span class="n">extra_fields_methods</span> <span class="ow">or</span> <span class="p">{}</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">_set_record_template</span><span class="p">()</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">record_processor_method</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="n">record_processor_method</span> <span class="ow">or</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">_default_record_processor</span>
+        <span class="p">)</span>
+
+        <span class="k">if</span> <span class="s1">&#39;ncbi_tax_id&#39;</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">kwargs</span><span class="p">:</span>
+
+            <span class="n">kwargs</span><span class="p">[</span><span class="s1">&#39;ncbi_tax_id&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="mi">9606</span>
+
+        <span class="n">AnnotationBase</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">name</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">,</span>
+            <span class="o">**</span><span class="n">kwargs</span>
+        <span class="p">)</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">_set_record_template</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">record</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">namedtuple</span><span class="p">(</span>
+            <span class="s1">&#39;</span><span class="si">%s</span><span class="s1">Annotation&#39;</span> <span class="o">%</span> <span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">,</span>
+            <span class="p">(</span><span class="s1">&#39;mainclass&#39;</span><span class="p">,)</span> <span class="o">+</span> <span class="bp">self</span><span class="o">.</span><span class="n">_record_extra_fields</span><span class="p">,</span>
+        <span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">record</span><span class="o">.</span><span class="fm">__new__</span><span class="o">.</span><span class="vm">__defaults__</span> <span class="o">=</span> <span class="p">()</span> <span class="o">+</span> <span class="bp">self</span><span class="o">.</span><span class="n">_record_defaults</span>
+
+
+    <span class="k">def</span> <span class="nf">_default_record_processor</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">record</span><span class="p">,</span> <span class="n">typ</span><span class="p">,</span> <span class="n">annot</span><span class="p">):</span>
+
+        <span class="n">i_id</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">ligand_col</span> <span class="k">if</span> <span class="n">typ</span> <span class="o">==</span> <span class="s1">&#39;ligand&#39;</span> <span class="k">else</span> <span class="bp">self</span><span class="o">.</span><span class="n">receptor_col</span>
+        <span class="n">id_type</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">ligand_id_type</span> <span class="k">if</span> <span class="n">typ</span> <span class="o">==</span> <span class="s1">&#39;ligand&#39;</span> <span class="k">else</span> <span class="bp">self</span><span class="o">.</span><span class="n">receptor_id_type</span>
+        <span class="p">)</span>
+        <span class="n">original_id</span> <span class="o">=</span> <span class="n">record</span><span class="p">[</span><span class="n">i_id</span><span class="p">]</span>
+        <span class="n">uniprots</span> <span class="o">=</span> <span class="n">mapping</span><span class="o">.</span><span class="n">map_name</span><span class="p">(</span><span class="n">original_id</span><span class="p">,</span> <span class="n">id_type</span><span class="p">,</span> <span class="s1">&#39;uniprot&#39;</span><span class="p">)</span>
+
+        <span class="k">for</span> <span class="n">uniprot</span> <span class="ow">in</span> <span class="n">uniprots</span><span class="p">:</span>
+
+            <span class="n">annot</span><span class="p">[</span><span class="n">uniprot</span><span class="p">]</span><span class="o">.</span><span class="n">add</span><span class="p">(</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">record</span><span class="p">(</span>
+                    <span class="n">mainclass</span> <span class="o">=</span> <span class="n">typ</span><span class="p">,</span>
+                    <span class="o">**</span><span class="bp">self</span><span class="o">.</span><span class="n">_get_extra_fields</span><span class="p">(</span><span class="n">record</span><span class="p">)</span>
+                <span class="p">)</span>
+            <span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">_get_extra_fields</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">record</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="nb">dict</span><span class="p">(</span>
+            <span class="p">(</span>
+                <span class="n">name</span><span class="p">,</span>
+                <span class="n">method</span><span class="p">(</span><span class="n">record</span><span class="p">),</span>
+            <span class="p">)</span>
+            <span class="k">for</span> <span class="n">name</span><span class="p">,</span> <span class="n">method</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_extra_fields_methods</span><span class="p">)</span>
+        <span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">_process_method</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">*</span><span class="n">args</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+
+        <span class="n">annot</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">defaultdict</span><span class="p">(</span><span class="nb">set</span><span class="p">)</span>
+
+        <span class="k">for</span> <span class="n">record</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span><span class="p">:</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">record_processor_method</span><span class="p">(</span>
+                <span class="n">record</span><span class="p">,</span>
+                <span class="n">typ</span> <span class="o">=</span> <span class="s1">&#39;ligand&#39;</span><span class="p">,</span>
+                <span class="n">annot</span> <span class="o">=</span> <span class="n">annot</span><span class="p">,</span>
+            <span class="p">)</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">record_processor_method</span><span class="p">(</span>
+                <span class="n">record</span><span class="p">,</span>
+                <span class="n">typ</span> <span class="o">=</span> <span class="s1">&#39;receptor&#39;</span><span class="p">,</span>
+                <span class="n">annot</span> <span class="o">=</span> <span class="n">annot</span><span class="p">,</span>
+            <span class="p">)</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">annot</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">(</span><span class="n">annot</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="Ramilowski2015">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.Ramilowski2015.html#pypath.core.annot.Ramilowski2015">[docs]</a>
+<span class="k">class</span> <span class="nc">Ramilowski2015</span><span class="p">(</span><span class="n">LigandReceptor</span><span class="p">):</span>
+
+
+<div class="viewcode-block" id="Ramilowski2015.__init__">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.Ramilowski2015.html#pypath.core.annot.Ramilowski2015.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">load_sources</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+
+        <span class="n">extra_fields_methods</span> <span class="o">=</span> <span class="p">{</span>
+            <span class="s1">&#39;sources&#39;</span><span class="p">:</span>
+                <span class="k">lambda</span> <span class="n">record</span><span class="p">:</span> <span class="p">(</span>
+                    <span class="nb">tuple</span><span class="p">(</span><span class="n">record</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;;&#39;</span><span class="p">))</span> <span class="k">if</span> <span class="n">load_sources</span> <span class="k">else</span> <span class="kc">None</span>
+                <span class="p">),</span>
+        <span class="p">}</span>
+
+
+        <span class="n">LigandReceptor</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">name</span> <span class="o">=</span> <span class="s1">&#39;Ramilowski2015&#39;</span><span class="p">,</span>
+            <span class="n">input_method</span> <span class="o">=</span> <span class="s1">&#39;ramilowski2015.ramilowski_interactions&#39;</span><span class="p">,</span>
+            <span class="n">record_extra_fields</span> <span class="o">=</span> <span class="p">(</span><span class="s1">&#39;sources&#39;</span><span class="p">,),</span>
+            <span class="n">extra_fields_methods</span> <span class="o">=</span> <span class="n">extra_fields_methods</span><span class="p">,</span>
+            <span class="n">ligand_col</span> <span class="o">=</span> <span class="mi">0</span><span class="p">,</span>
+            <span class="n">receptor_col</span> <span class="o">=</span> <span class="mi">1</span><span class="p">,</span>
+            <span class="n">ligand_id_type</span> <span class="o">=</span> <span class="s1">&#39;genesymbol&#39;</span><span class="p">,</span>
+            <span class="n">receptor_id_type</span> <span class="o">=</span> <span class="s1">&#39;genesymbol&#39;</span><span class="p">,</span>
+            <span class="o">**</span><span class="n">kwargs</span>
+        <span class="p">)</span></div>
+</div>
+
+
+
+<div class="viewcode-block" id="Kirouac2010">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.Kirouac2010.html#pypath.core.annot.Kirouac2010">[docs]</a>
+<span class="k">class</span> <span class="nc">Kirouac2010</span><span class="p">(</span><span class="n">LigandReceptor</span><span class="p">):</span>
+
+
+<div class="viewcode-block" id="Kirouac2010.__init__">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.Kirouac2010.html#pypath.core.annot.Kirouac2010.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">load_sources</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+
+        <span class="n">LigandReceptor</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">name</span> <span class="o">=</span> <span class="s1">&#39;Kirouac2010&#39;</span><span class="p">,</span>
+            <span class="n">input_method</span> <span class="o">=</span> <span class="s1">&#39;kirouac2010.kirouac2010_interactions&#39;</span><span class="p">,</span>
+            <span class="n">ligand_col</span> <span class="o">=</span> <span class="mi">0</span><span class="p">,</span>
+            <span class="n">receptor_col</span> <span class="o">=</span> <span class="mi">1</span><span class="p">,</span>
+            <span class="n">ligand_id_type</span> <span class="o">=</span> <span class="s1">&#39;genesymbol&#39;</span><span class="p">,</span>
+            <span class="n">receptor_id_type</span> <span class="o">=</span> <span class="s1">&#39;genesymbol&#39;</span><span class="p">,</span>
+            <span class="o">**</span><span class="n">kwargs</span>
+        <span class="p">)</span></div>
+</div>
+
+
+
+<div class="viewcode-block" id="GuideToPharmacology">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.GuideToPharmacology.html#pypath.core.annot.GuideToPharmacology">[docs]</a>
+<span class="k">class</span> <span class="nc">GuideToPharmacology</span><span class="p">(</span><span class="n">LigandReceptor</span><span class="p">):</span>
+
+
+<div class="viewcode-block" id="GuideToPharmacology.__init__">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.GuideToPharmacology.html#pypath.core.annot.GuideToPharmacology.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">load_sources</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+
+        <span class="n">LigandReceptor</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">name</span> <span class="o">=</span> <span class="s1">&#39;Guide2Pharma&#39;</span><span class="p">,</span>
+            <span class="n">input_method</span> <span class="o">=</span> <span class="s1">&#39;guide2pharma.guide2pharma_interactions&#39;</span><span class="p">,</span>
+            <span class="n">ligand_col</span> <span class="o">=</span> <span class="mi">0</span><span class="p">,</span>
+            <span class="n">receptor_col</span> <span class="o">=</span> <span class="mi">2</span><span class="p">,</span>
+            <span class="n">ligand_id_type</span> <span class="o">=</span> <span class="s1">&#39;genesymbol&#39;</span><span class="p">,</span>
+            <span class="n">receptor_id_type</span> <span class="o">=</span> <span class="s1">&#39;uniprot&#39;</span><span class="p">,</span>
+            <span class="o">**</span><span class="n">kwargs</span>
+        <span class="p">)</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">_default_record_processor</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">record</span><span class="p">,</span> <span class="n">typ</span><span class="p">,</span> <span class="n">annot</span><span class="p">):</span>
+
+        <span class="k">if</span> <span class="p">(</span>
+            <span class="n">record</span><span class="o">.</span><span class="n">ligand_id_type</span> <span class="o">!=</span> <span class="s1">&#39;genesymbol&#39;</span> <span class="ow">or</span>
+            <span class="n">record</span><span class="o">.</span><span class="n">target_id_type</span> <span class="o">!=</span> <span class="s1">&#39;uniprot&#39;</span>
+        <span class="p">):</span>
+
+            <span class="k">return</span>
+
+        <span class="n">LigandReceptor</span><span class="o">.</span><span class="n">_default_record_processor</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">record</span><span class="p">,</span> <span class="n">typ</span><span class="p">,</span> <span class="n">annot</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="UniprotLocations">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.UniprotLocations.html#pypath.core.annot.UniprotLocations">[docs]</a>
+<span class="k">class</span> <span class="nc">UniprotLocations</span><span class="p">(</span><span class="n">AnnotationBase</span><span class="p">):</span>
+
+    <span class="n">_eq_fields</span> <span class="o">=</span> <span class="p">(</span><span class="s1">&#39;location&#39;</span><span class="p">,)</span>
+
+
+<div class="viewcode-block" id="UniprotLocations.__init__">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.UniprotLocations.html#pypath.core.annot.UniprotLocations.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Subcellular localizations from UniProt.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">if</span> <span class="s1">&#39;organism&#39;</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">kwargs</span><span class="p">:</span>
+
+            <span class="n">kwargs</span><span class="p">[</span><span class="s1">&#39;organism&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span>
+
+        <span class="n">AnnotationBase</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">name</span> <span class="o">=</span> <span class="s1">&#39;UniProt_location&#39;</span><span class="p">,</span>
+            <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">,</span>
+            <span class="n">input_method</span> <span class="o">=</span> <span class="s1">&#39;uniprot.uniprot_locations&#39;</span><span class="p">,</span>
+            <span class="o">**</span><span class="n">kwargs</span>
+        <span class="p">)</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">_process_method</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="c1">#  already the appropriate format, no processing needed</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">annot</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span>
+
+        <span class="nb">delattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">&#39;data&#39;</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="UniprotFamilies">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.UniprotFamilies.html#pypath.core.annot.UniprotFamilies">[docs]</a>
+<span class="k">class</span> <span class="nc">UniprotFamilies</span><span class="p">(</span><span class="n">AnnotationBase</span><span class="p">):</span>
+
+    <span class="n">_eq_fields</span> <span class="o">=</span> <span class="p">(</span><span class="s1">&#39;family&#39;</span><span class="p">,</span> <span class="s1">&#39;subfamily&#39;</span><span class="p">)</span>
+
+
+<div class="viewcode-block" id="UniprotFamilies.__init__">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.UniprotFamilies.html#pypath.core.annot.UniprotFamilies.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Protein families from UniProt.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">if</span> <span class="s1">&#39;organism&#39;</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">kwargs</span><span class="p">:</span>
+
+            <span class="n">kwargs</span><span class="p">[</span><span class="s1">&#39;organism&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span>
+
+        <span class="n">AnnotationBase</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">name</span> <span class="o">=</span> <span class="s1">&#39;UniProt_family&#39;</span><span class="p">,</span>
+            <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">,</span>
+            <span class="n">input_method</span> <span class="o">=</span> <span class="s1">&#39;uniprot.uniprot_families&#39;</span><span class="p">,</span>
+            <span class="o">**</span><span class="n">kwargs</span>
+        <span class="p">)</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">_process_method</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="c1">#  already the appropriate format, no processing needed</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">annot</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span>
+
+        <span class="nb">delattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">&#39;data&#39;</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="UniprotTissues">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.UniprotTissues.html#pypath.core.annot.UniprotTissues">[docs]</a>
+<span class="k">class</span> <span class="nc">UniprotTissues</span><span class="p">(</span><span class="n">AnnotationBase</span><span class="p">):</span>
+
+    <span class="n">_eq_fields</span> <span class="o">=</span> <span class="p">(</span><span class="s1">&#39;tissue&#39;</span><span class="p">,</span> <span class="s1">&#39;level&#39;</span><span class="p">)</span>
+
+
+<div class="viewcode-block" id="UniprotTissues.__init__">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.UniprotTissues.html#pypath.core.annot.UniprotTissues.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Tissue expression levels from UniProt.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">if</span> <span class="s1">&#39;organism&#39;</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">kwargs</span><span class="p">:</span>
+
+            <span class="n">kwargs</span><span class="p">[</span><span class="s1">&#39;organism&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span>
+
+        <span class="n">AnnotationBase</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">name</span> <span class="o">=</span> <span class="s1">&#39;UniProt_tissue&#39;</span><span class="p">,</span>
+            <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">,</span>
+            <span class="n">input_method</span> <span class="o">=</span> <span class="s1">&#39;uniprot.uniprot_tissues&#39;</span><span class="p">,</span>
+            <span class="o">**</span><span class="n">kwargs</span>
+        <span class="p">)</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">_process_method</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="c1">#  already the appropriate format, no processing needed</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">annot</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span>
+
+        <span class="nb">delattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">&#39;data&#39;</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="UniprotKeywords">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.UniprotKeywords.html#pypath.core.annot.UniprotKeywords">[docs]</a>
+<span class="k">class</span> <span class="nc">UniprotKeywords</span><span class="p">(</span><span class="n">AnnotationBase</span><span class="p">):</span>
+
+    <span class="n">_eq_fields</span> <span class="o">=</span> <span class="p">(</span><span class="s1">&#39;keyword&#39;</span><span class="p">,)</span>
+
+
+<div class="viewcode-block" id="UniprotKeywords.__init__">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.UniprotKeywords.html#pypath.core.annot.UniprotKeywords.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Tissue expression levels from UniProt.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">if</span> <span class="s1">&#39;organism&#39;</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">kwargs</span><span class="p">:</span>
+
+            <span class="n">kwargs</span><span class="p">[</span><span class="s1">&#39;organism&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span>
+
+        <span class="n">AnnotationBase</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">name</span> <span class="o">=</span> <span class="s1">&#39;UniProt_keyword&#39;</span><span class="p">,</span>
+            <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">,</span>
+            <span class="n">input_method</span> <span class="o">=</span> <span class="s1">&#39;uniprot.uniprot_keywords&#39;</span><span class="p">,</span>
+            <span class="o">**</span><span class="n">kwargs</span>
+        <span class="p">)</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">_process_method</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="c1">#  already the appropriate format, no processing needed</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">annot</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span>
+
+        <span class="nb">delattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">&#39;data&#39;</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="UniprotTopologies">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.UniprotTopologies.html#pypath.core.annot.UniprotTopologies">[docs]</a>
+<span class="k">class</span> <span class="nc">UniprotTopologies</span><span class="p">(</span><span class="n">AnnotationBase</span><span class="p">):</span>
+
+    <span class="n">_eq_fields</span> <span class="o">=</span> <span class="p">(</span><span class="s1">&#39;topology&#39;</span><span class="p">,</span> <span class="s1">&#39;start&#39;</span><span class="p">,</span> <span class="s1">&#39;end&#39;</span><span class="p">)</span>
+
+
+<div class="viewcode-block" id="UniprotTopologies.__init__">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.UniprotTopologies.html#pypath.core.annot.UniprotTopologies.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Topological domains and transmembrane segments from UniProt.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">if</span> <span class="s1">&#39;organism&#39;</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">kwargs</span><span class="p">:</span>
+
+            <span class="n">kwargs</span><span class="p">[</span><span class="s1">&#39;organism&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span>
+
+        <span class="n">AnnotationBase</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">name</span> <span class="o">=</span> <span class="s1">&#39;UniProt_topology&#39;</span><span class="p">,</span>
+            <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">,</span>
+            <span class="n">input_method</span> <span class="o">=</span> <span class="s1">&#39;uniprot.uniprot_topology&#39;</span><span class="p">,</span>
+            <span class="o">**</span><span class="n">kwargs</span>
+        <span class="p">)</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">_process_method</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="c1">#  already the appropriate format, no processing needed</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">annot</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span>
+
+        <span class="nb">delattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">&#39;data&#39;</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="Humancellmap">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.Humancellmap.html#pypath.core.annot.Humancellmap">[docs]</a>
+<span class="k">class</span> <span class="nc">Humancellmap</span><span class="p">(</span><span class="n">AnnotationBase</span><span class="p">):</span>
+
+    <span class="n">_eq_fields</span> <span class="o">=</span> <span class="p">(</span><span class="s1">&#39;localization&#39;</span><span class="p">,</span> <span class="s1">&#39;method&#39;</span><span class="p">)</span>
+
+
+<div class="viewcode-block" id="Humancellmap.__init__">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.Humancellmap.html#pypath.core.annot.Humancellmap.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Protein families from UniProt.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">AnnotationBase</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">name</span> <span class="o">=</span> <span class="s1">&#39;HumanCellMap&#39;</span><span class="p">,</span>
+            <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">,</span>
+            <span class="n">input_method</span> <span class="o">=</span> <span class="s1">&#39;humancellmap.humancellmap_annotations&#39;</span><span class="p">,</span>
+            <span class="o">**</span><span class="n">kwargs</span>
+        <span class="p">)</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">_process_method</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="c1">#  already the appropriate format, no processing needed</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">annot</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span>
+
+        <span class="nb">delattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">&#39;data&#39;</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="Tcdb">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.Tcdb.html#pypath.core.annot.Tcdb">[docs]</a>
+<span class="k">class</span> <span class="nc">Tcdb</span><span class="p">(</span><span class="n">AnnotationBase</span><span class="p">):</span>
+
+    <span class="n">_eq_fields</span> <span class="o">=</span> <span class="p">(</span><span class="s1">&#39;family&#39;</span><span class="p">,</span> <span class="s1">&#39;tcid&#39;</span><span class="p">)</span>
+
+
+<div class="viewcode-block" id="Tcdb.__init__">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.Tcdb.html#pypath.core.annot.Tcdb.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Topological domains and transmembrane segments from UniProt.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">if</span> <span class="s1">&#39;organism&#39;</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">kwargs</span><span class="p">:</span>
+
+            <span class="n">kwargs</span><span class="p">[</span><span class="s1">&#39;organism&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span>
+
+        <span class="n">AnnotationBase</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">name</span> <span class="o">=</span> <span class="s1">&#39;TCDB&#39;</span><span class="p">,</span>
+            <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">,</span>
+            <span class="n">input_method</span> <span class="o">=</span> <span class="s1">&#39;tcdb.tcdb_annotations&#39;</span><span class="p">,</span>
+            <span class="o">**</span><span class="n">kwargs</span>
+        <span class="p">)</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">_process_method</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="c1">#  already the appropriate format, no processing needed</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">annot</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span>
+
+        <span class="nb">delattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">&#39;data&#39;</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="Mcam">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.Mcam.html#pypath.core.annot.Mcam">[docs]</a>
+<span class="k">class</span> <span class="nc">Mcam</span><span class="p">(</span><span class="n">AnnotationBase</span><span class="p">):</span>
+
+    <span class="n">_eq_fields</span> <span class="o">=</span> <span class="p">()</span>
+
+
+<div class="viewcode-block" id="Mcam.__init__">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.Mcam.html#pypath.core.annot.Mcam.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        List of cell adhesion molecules (CAMs) from 10.4137/cin.s341.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">AnnotationBase</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">name</span> <span class="o">=</span> <span class="s1">&#39;MCAM&#39;</span><span class="p">,</span>
+            <span class="n">input_method</span> <span class="o">=</span> <span class="s1">&#39;mcam.mcam_cell_adhesion_molecules&#39;</span><span class="p">,</span>
+            <span class="o">**</span><span class="n">kwargs</span>
+        <span class="p">)</span></div>
+</div>
+
+
+
+<div class="viewcode-block" id="Gpcrdb">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.Gpcrdb.html#pypath.core.annot.Gpcrdb">[docs]</a>
+<span class="k">class</span> <span class="nc">Gpcrdb</span><span class="p">(</span><span class="n">AnnotationBase</span><span class="p">):</span>
+
+    <span class="n">_eq_fields</span> <span class="o">=</span> <span class="p">(</span><span class="s1">&#39;gpcr_class&#39;</span><span class="p">,</span> <span class="s1">&#39;family&#39;</span><span class="p">,</span> <span class="s1">&#39;subfamily&#39;</span><span class="p">)</span>
+
+
+<div class="viewcode-block" id="Gpcrdb.__init__">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.Gpcrdb.html#pypath.core.annot.Gpcrdb.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        GPCR classification from GPCRdb - https://gpcrdb.org/.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">if</span> <span class="s1">&#39;organism&#39;</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">kwargs</span><span class="p">:</span>
+
+            <span class="n">kwargs</span><span class="p">[</span><span class="s1">&#39;organism&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span>
+
+        <span class="n">AnnotationBase</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">name</span> <span class="o">=</span> <span class="s1">&#39;GPCRdb&#39;</span><span class="p">,</span>
+            <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">,</span>
+            <span class="n">input_method</span> <span class="o">=</span> <span class="s1">&#39;gpcrdb.gpcrdb_annotations&#39;</span><span class="p">,</span>
+            <span class="o">**</span><span class="n">kwargs</span>
+        <span class="p">)</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">_process_method</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="c1">#  already the appropriate format, no processing needed</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">annot</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span>
+
+        <span class="nb">delattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">&#39;data&#39;</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="Progeny">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.Progeny.html#pypath.core.annot.Progeny">[docs]</a>
+<span class="k">class</span> <span class="nc">Progeny</span><span class="p">(</span><span class="n">AnnotationBase</span><span class="p">):</span>
+
+    <span class="n">_eq_fields</span> <span class="o">=</span> <span class="p">(</span><span class="s1">&#39;pathway&#39;</span><span class="p">,)</span>
+
+
+<div class="viewcode-block" id="Progeny.__init__">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.Progeny.html#pypath.core.annot.Progeny.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Pathway responsive genes: signatures based on transcriptomics data</span>
+<span class="sd">        from PROGENy (https://github.com/saezlab/progeny).</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">if</span> <span class="s1">&#39;organism&#39;</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">kwargs</span><span class="p">:</span>
+
+            <span class="n">kwargs</span><span class="p">[</span><span class="s1">&#39;organism&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span>
+
+        <span class="n">AnnotationBase</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">name</span> <span class="o">=</span> <span class="s1">&#39;PROGENy&#39;</span><span class="p">,</span>
+            <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">,</span>
+            <span class="n">input_method</span> <span class="o">=</span> <span class="s1">&#39;progeny.progeny_annotations&#39;</span><span class="p">,</span>
+            <span class="n">infer_complexes</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+            <span class="o">**</span><span class="n">kwargs</span>
+        <span class="p">)</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">_process_method</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="c1">#  already the appropriate format, no processing needed</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">annot</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span>
+
+        <span class="nb">delattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">&#39;data&#39;</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="Celltypist">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.Celltypist.html#pypath.core.annot.Celltypist">[docs]</a>
+<span class="k">class</span> <span class="nc">Celltypist</span><span class="p">(</span><span class="n">AnnotationBase</span><span class="p">):</span>
+
+    <span class="n">_eq_fields</span> <span class="o">=</span> <span class="p">(</span><span class="s1">&#39;cell_type&#39;</span><span class="p">,</span> <span class="s1">&#39;cell_subtype&#39;</span><span class="p">)</span>
+
+
+<div class="viewcode-block" id="Celltypist.__init__">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.Celltypist.html#pypath.core.annot.Celltypist.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Cell type markers from the CellTypist database.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">AnnotationBase</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">name</span> <span class="o">=</span> <span class="s1">&#39;CellTypist&#39;</span><span class="p">,</span>
+            <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">,</span>
+            <span class="n">input_method</span> <span class="o">=</span> <span class="s1">&#39;celltypist.celltypist_annotations&#39;</span><span class="p">,</span>
+            <span class="n">infer_complexes</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+            <span class="o">**</span><span class="n">kwargs</span>
+        <span class="p">)</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">_process_method</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="c1">#  already the appropriate format, no processing needed</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">annot</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span>
+
+        <span class="nb">delattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">&#39;data&#39;</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="Cytosig">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.Cytosig.html#pypath.core.annot.Cytosig">[docs]</a>
+<span class="k">class</span> <span class="nc">Cytosig</span><span class="p">(</span><span class="n">AnnotationBase</span><span class="p">):</span>
+
+    <span class="n">_eq_fields</span> <span class="o">=</span> <span class="p">(</span><span class="s1">&#39;cytokine&#39;</span><span class="p">,)</span>
+
+
+<div class="viewcode-block" id="Cytosig.__init__">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.Cytosig.html#pypath.core.annot.Cytosig.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Cytokine perturbation signatures from the CytoSig database.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">AnnotationBase</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">name</span> <span class="o">=</span> <span class="s1">&#39;CytoSig&#39;</span><span class="p">,</span>
+            <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">,</span>
+            <span class="n">input_method</span> <span class="o">=</span> <span class="s1">&#39;cytosig.cytosig_annotations&#39;</span><span class="p">,</span>
+            <span class="n">infer_complexes</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+            <span class="o">**</span><span class="n">kwargs</span>
+        <span class="p">)</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">_process_method</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="c1">#  already the appropriate format, no processing needed</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">annot</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span>
+
+        <span class="nb">delattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">&#39;data&#39;</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="Panglaodb">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.Panglaodb.html#pypath.core.annot.Panglaodb">[docs]</a>
+<span class="k">class</span> <span class="nc">Panglaodb</span><span class="p">(</span><span class="n">AnnotationBase</span><span class="p">):</span>
+
+    <span class="n">_eq_fields</span> <span class="o">=</span> <span class="p">(</span><span class="s1">&#39;cell_type&#39;</span><span class="p">,</span> <span class="s1">&#39;organ&#39;</span><span class="p">)</span>
+
+
+<div class="viewcode-block" id="Panglaodb.__init__">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.Panglaodb.html#pypath.core.annot.Panglaodb.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Cell type markers from PanglaoDB</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">AnnotationBase</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">name</span> <span class="o">=</span> <span class="s1">&#39;PanglaoDB&#39;</span><span class="p">,</span>
+            <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">,</span>
+            <span class="n">input_method</span> <span class="o">=</span> <span class="s1">&#39;panglaodb.panglaodb_annotations&#39;</span><span class="p">,</span>
+            <span class="n">infer_complexes</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+            <span class="n">check_ids</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+            <span class="o">**</span><span class="n">kwargs</span>
+        <span class="p">)</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">_process_method</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="c1">#  already the appropriate format, no processing needed</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">annot</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span>
+
+        <span class="nb">delattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">&#39;data&#39;</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="Lambert2018">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.Lambert2018.html#pypath.core.annot.Lambert2018">[docs]</a>
+<span class="k">class</span> <span class="nc">Lambert2018</span><span class="p">(</span><span class="n">AnnotationBase</span><span class="p">):</span>
+
+    <span class="n">_eq_fields</span> <span class="o">=</span> <span class="p">(</span><span class="s1">&#39;genesymbol&#39;</span><span class="p">,</span> <span class="s1">&#39;is_tf&#39;</span><span class="p">)</span>
+
+
+<div class="viewcode-block" id="Lambert2018.__init__">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.Lambert2018.html#pypath.core.annot.Lambert2018.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Cell type markers from PanglaoDB</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">AnnotationBase</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">name</span> <span class="o">=</span> <span class="s1">&#39;Lambert2018&#39;</span><span class="p">,</span>
+            <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">,</span>
+            <span class="n">input_method</span> <span class="o">=</span> <span class="s1">&#39;lambert2018.lambert2018_annotations&#39;</span><span class="p">,</span>
+            <span class="n">infer_complexes</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
+            <span class="n">check_ids</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+            <span class="o">**</span><span class="n">kwargs</span>
+        <span class="p">)</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">_process_method</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="c1">#  already the appropriate format, no processing needed</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">annot</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span>
+
+        <span class="nb">delattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">&#39;data&#39;</span><span class="p">)</span></div>
+
+
+
+
+<div class="viewcode-block" id="Wang">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.Wang.html#pypath.core.annot.Wang">[docs]</a>
+<span class="k">class</span> <span class="nc">Wang</span><span class="p">(</span><span class="n">AnnotationBase</span><span class="p">):</span>
+
+    <span class="n">_eq_fields</span> <span class="o">=</span> <span class="p">(</span><span class="s1">&#39;function&#39;</span><span class="p">,</span> <span class="s1">&#39;location&#39;</span><span class="p">)</span>
+
+
+<div class="viewcode-block" id="Wang.__init__">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.Wang.html#pypath.core.annot.Wang.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Cytokine perturbation signatures from the CytoSig database.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">AnnotationBase</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">name</span> <span class="o">=</span> <span class="s1">&#39;Wang&#39;</span><span class="p">,</span>
+            <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">,</span>
+            <span class="n">input_method</span> <span class="o">=</span> <span class="s1">&#39;wang.wang_annotations&#39;</span><span class="p">,</span>
+            <span class="o">**</span><span class="n">kwargs</span>
+        <span class="p">)</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">_process_method</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="c1">#  already the appropriate format, no processing needed</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">annot</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span>
+
+        <span class="nb">delattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">&#39;data&#39;</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="Cancerdrugsdb">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.Cancerdrugsdb.html#pypath.core.annot.Cancerdrugsdb">[docs]</a>
+<span class="k">class</span> <span class="nc">Cancerdrugsdb</span><span class="p">(</span><span class="n">AnnotationBase</span><span class="p">):</span>
+
+
+<div class="viewcode-block" id="Cancerdrugsdb.__init__">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.Cancerdrugsdb.html#pypath.core.annot.Cancerdrugsdb.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Approved cancer drugs from the Cancer Drugs Database</span>
+<span class="sd">        (https://www.anticancerfund.org/en/cancerdrugs-db).</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">kwargs</span><span class="o">.</span><span class="n">pop</span><span class="p">(</span><span class="s1">&#39;ncbi_tax_id&#39;</span><span class="p">,</span> <span class="kc">None</span><span class="p">)</span>
+
+        <span class="n">AnnotationBase</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">name</span> <span class="o">=</span> <span class="s1">&#39;CancerDrugsDB&#39;</span><span class="p">,</span>
+            <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">_const</span><span class="o">.</span><span class="n">NOT_ORGANISM_SPECIFIC</span><span class="p">,</span>
+            <span class="n">input_method</span> <span class="o">=</span> <span class="s1">&#39;cancerdrugsdb.cancerdrugsdb_annotations&#39;</span><span class="p">,</span>
+            <span class="n">entity_type</span> <span class="o">=</span> <span class="s1">&#39;small_molecule&#39;</span><span class="p">,</span>
+            <span class="o">**</span><span class="n">kwargs</span>
+        <span class="p">)</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">_process_method</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="c1">#  already the appropriate format, no processing needed</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">annot</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span>
+
+        <span class="nb">delattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">&#39;data&#39;</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="InterPro">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.InterPro.html#pypath.core.annot.InterPro">[docs]</a>
+<span class="k">class</span> <span class="nc">InterPro</span><span class="p">(</span><span class="n">AnnotationBase</span><span class="p">):</span>
+
+    <span class="n">_eq_fields</span> <span class="o">=</span> <span class="p">(</span><span class="s1">&#39;interpro_id&#39;</span><span class="p">,</span> <span class="s1">&#39;start&#39;</span><span class="p">,</span> <span class="s1">&#39;end&#39;</span><span class="p">)</span>
+
+
+<div class="viewcode-block" id="InterPro.__init__">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.InterPro.html#pypath.core.annot.InterPro.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Protein signatures from the InterPro database.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">AnnotationBase</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">name</span> <span class="o">=</span> <span class="s1">&#39;InterPro&#39;</span><span class="p">,</span>
+            <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">,</span>
+            <span class="n">input_method</span> <span class="o">=</span> <span class="s1">&#39;interpro.interpro_annotations&#39;</span><span class="p">,</span>
+            <span class="o">**</span><span class="n">kwargs</span>
+        <span class="p">)</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">_process_method</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">annot</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span>
+        <span class="nb">delattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">&#39;data&#39;</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="AnnotationTable">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.AnnotationTable.html#pypath.core.annot.AnnotationTable">[docs]</a>
+<span class="k">class</span> <span class="nc">AnnotationTable</span><span class="p">(</span><span class="n">session_mod</span><span class="o">.</span><span class="n">Logger</span><span class="p">):</span>
+
+
+<div class="viewcode-block" id="AnnotationTable.__init__">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.AnnotationTable.html#pypath.core.annot.AnnotationTable.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">proteins</span> <span class="o">=</span> <span class="p">(),</span>
+            <span class="n">complexes</span> <span class="o">=</span> <span class="p">(),</span>
+            <span class="n">protein_sources</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">complex_sources</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">use_fields</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">,</span>
+            <span class="n">swissprot_only</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
+            <span class="n">use_complexes</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
+            <span class="n">keep_annotators</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
+            <span class="n">create_dataframe</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+            <span class="n">load</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
+            <span class="n">pickle_file</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+        <span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Manages a custom set of annotation resources. Loads data and</span>
+<span class="sd">        accepts queries, provides methods for converting the data to</span>
+<span class="sd">        data frame.</span>
+
+<span class="sd">        :arg set proteins:</span>
+<span class="sd">            A reference set of proteins (UniProt IDs).</span>
+<span class="sd">        :arg set complexes:</span>
+<span class="sd">            A reference set of complexes.</span>
+<span class="sd">        :arg set protein_sources:</span>
+<span class="sd">            Class names providing the protein annotations. If not provided</span>
+<span class="sd">            the module&#39;s ``protein_sources_default`` attribute will be used.</span>
+<span class="sd">        :arg set complex_sources:</span>
+<span class="sd">            Class names providing the complex annotations. If not provided</span>
+<span class="sd">            the module&#39;s ``complex_sources_default`` attribute will be used.</span>
+<span class="sd">        :arg dict use_fields:</span>
+<span class="sd">            A dict with resource names as keys and tuple of field labels as</span>
+<span class="sd">            values. If provided for any resource only these fields will be</span>
+<span class="sd">            used for constructing the data frame. If `None`, the module&#39;s</span>
+<span class="sd">            ``default_fields`` settings will be used.</span>
+<span class="sd">        :arg bool use_complexes:</span>
+<span class="sd">            Whether to include complexes in the annotations.</span>
+<span class="sd">        :arg bool create_dataframe:</span>
+<span class="sd">            Whether to create a boolean data frame of annotations, apart</span>
+<span class="sd">            from having the annotator objects.</span>
+<span class="sd">        :arg bool load:</span>
+<span class="sd">            Load the data upon initialization. If `False`, you will have a</span>
+<span class="sd">            chance to call the ``load`` method later.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">session_mod</span><span class="o">.</span><span class="n">Logger</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">name</span> <span class="o">=</span> <span class="s1">&#39;annot&#39;</span><span class="p">)</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_module</span> <span class="o">=</span> <span class="n">sys</span><span class="o">.</span><span class="n">modules</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="vm">__module__</span><span class="p">]</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">pickle_file</span> <span class="o">=</span> <span class="n">pickle_file</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">complexes</span> <span class="o">=</span> <span class="n">complexes</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">protein_sources</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="n">protein_sources</span>
+                <span class="k">if</span> <span class="n">protein_sources</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span> <span class="k">else</span>
+            <span class="n">protein_sources_default</span>
+        <span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">complex_sources</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="n">complex_sources</span>
+                <span class="k">if</span> <span class="n">complex_sources</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span> <span class="k">else</span>
+            <span class="n">complex_sources_default</span>
+        <span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">use_fields</span> <span class="o">=</span> <span class="n">use_fields</span> <span class="ow">or</span> <span class="n">default_fields</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">keep_annotators</span> <span class="o">=</span> <span class="n">keep_annotators</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">create_dataframe</span> <span class="o">=</span> <span class="n">create_dataframe</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">proteins</span> <span class="o">=</span> <span class="n">proteins</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">swissprot_only</span> <span class="o">=</span> <span class="n">swissprot_only</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">use_complexes</span> <span class="o">=</span> <span class="n">use_complexes</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">set_reference_set</span><span class="p">()</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">annots</span> <span class="o">=</span> <span class="p">{}</span>
+
+        <span class="k">if</span> <span class="n">load</span><span class="p">:</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">load</span><span class="p">()</span></div>
+
+
+
+<div class="viewcode-block" id="AnnotationTable.reload">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.AnnotationTable.html#pypath.core.annot.AnnotationTable.reload">[docs]</a>
+    <span class="k">def</span> <span class="nf">reload</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Reloads the object from the module level.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">modname</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="vm">__class__</span><span class="o">.</span><span class="vm">__module__</span>
+        <span class="n">mod</span> <span class="o">=</span> <span class="nb">__import__</span><span class="p">(</span><span class="n">modname</span><span class="p">,</span> <span class="n">fromlist</span> <span class="o">=</span> <span class="p">[</span><span class="n">modname</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;.&#39;</span><span class="p">)[</span><span class="mi">0</span><span class="p">]])</span>
+        <span class="n">imp</span><span class="o">.</span><span class="n">reload</span><span class="p">(</span><span class="n">mod</span><span class="p">)</span>
+        <span class="n">new</span> <span class="o">=</span> <span class="nb">getattr</span><span class="p">(</span><span class="n">mod</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="vm">__class__</span><span class="o">.</span><span class="vm">__name__</span><span class="p">)</span>
+        <span class="nb">setattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">&#39;__class__&#39;</span><span class="p">,</span> <span class="n">new</span><span class="p">)</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">load</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">pickle_file</span><span class="p">:</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">load_from_pickle</span><span class="p">(</span><span class="n">pickle_file</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">pickle_file</span><span class="p">)</span>
+            <span class="k">return</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">set_reference_set</span><span class="p">()</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">load_protein_resources</span><span class="p">()</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">load_complex_resources</span><span class="p">()</span>
+
+        <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">create_dataframe</span><span class="p">:</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">make_dataframe</span><span class="p">()</span>
+
+
+    <span class="k">def</span> <span class="nf">load_from_pickle</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">pickle_file</span><span class="p">):</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span><span class="s1">&#39;Loading from pickle `</span><span class="si">%s</span><span class="s1">`.&#39;</span> <span class="o">%</span> <span class="n">pickle_file</span><span class="p">)</span>
+
+        <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">pickle_file</span><span class="p">,</span> <span class="s1">&#39;rb&#39;</span><span class="p">)</span> <span class="k">as</span> <span class="n">fp</span><span class="p">:</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">proteins</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">complexes</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">reference_set</span><span class="p">,</span> <span class="n">annots</span> <span class="o">=</span> <span class="p">(</span>
+                <span class="n">pickle</span><span class="o">.</span><span class="n">load</span><span class="p">(</span><span class="n">fp</span><span class="p">)</span>
+            <span class="p">)</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">annots</span> <span class="o">=</span> <span class="p">{}</span>
+
+            <span class="k">for</span> <span class="n">name</span><span class="p">,</span> <span class="p">(</span><span class="n">cls_name</span><span class="p">,</span> <span class="n">data</span><span class="p">,</span> <span class="n">record_cls</span><span class="p">)</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="n">annots</span><span class="p">):</span>
+
+                <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span>
+                    <span class="s1">&#39;Loading from pickle: annotation class `</span><span class="si">%s</span><span class="s1">`.&#39;</span> <span class="o">%</span> <span class="n">cls_name</span>
+                <span class="p">)</span>
+
+                <span class="k">if</span> <span class="n">record_cls</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
+
+                    <span class="n">modname</span> <span class="o">=</span> <span class="n">record_cls</span><span class="p">[</span><span class="s1">&#39;module&#39;</span><span class="p">]</span>
+
+                    <span class="k">if</span> <span class="n">modname</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">sys</span><span class="o">.</span><span class="n">modules</span><span class="p">:</span>
+
+                        <span class="n">mod</span> <span class="o">=</span> <span class="nb">__import__</span><span class="p">(</span>
+                            <span class="n">modname</span><span class="p">,</span>
+                            <span class="n">fromlist</span> <span class="o">=</span> <span class="p">[</span><span class="n">modname</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;.&#39;</span><span class="p">)[</span><span class="mi">0</span><span class="p">]],</span>
+                        <span class="p">)</span>
+
+                    <span class="nb">setattr</span><span class="p">(</span>
+                        <span class="n">sys</span><span class="o">.</span><span class="n">modules</span><span class="p">[</span><span class="n">modname</span><span class="p">],</span>
+                        <span class="n">record_cls</span><span class="p">[</span><span class="s1">&#39;name&#39;</span><span class="p">],</span>
+                        <span class="n">collections</span><span class="o">.</span><span class="n">namedtuple</span><span class="p">(</span>
+                            <span class="n">record_cls</span><span class="p">[</span><span class="s1">&#39;name&#39;</span><span class="p">],</span>
+                            <span class="n">record_cls</span><span class="p">[</span><span class="s1">&#39;fields&#39;</span><span class="p">],</span>
+                        <span class="p">),</span>
+                    <span class="p">)</span>
+
+                    <span class="n">record_cls_new</span> <span class="o">=</span> <span class="nb">getattr</span><span class="p">(</span>
+                        <span class="n">sys</span><span class="o">.</span><span class="n">modules</span><span class="p">[</span><span class="n">modname</span><span class="p">],</span>
+                        <span class="n">record_cls</span><span class="p">[</span><span class="s1">&#39;name&#39;</span><span class="p">],</span>
+                    <span class="p">)</span>
+
+                    <span class="n">data</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">(</span>
+                        <span class="p">(</span>
+                            <span class="n">key</span><span class="p">,</span>
+                            <span class="nb">set</span><span class="p">(</span>
+                                <span class="n">record_cls_new</span><span class="p">(</span><span class="o">*</span><span class="n">this_annot</span><span class="p">)</span>
+                                <span class="k">for</span> <span class="n">this_annot</span> <span class="ow">in</span> <span class="n">these_annots</span>
+                            <span class="p">)</span>
+                        <span class="p">)</span>
+                        <span class="k">for</span> <span class="n">key</span><span class="p">,</span> <span class="n">these_annots</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="n">data</span><span class="p">)</span>
+                    <span class="p">)</span>
+
+                    <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span>
+                        <span class="s1">&#39;Reconstituted annotation data for `</span><span class="si">%s</span><span class="s1">`: &#39;</span>
+                        <span class="s1">&#39;dict of length </span><span class="si">%u</span><span class="s1">.&#39;</span> <span class="o">%</span> <span class="p">(</span>
+                            <span class="n">name</span><span class="p">,</span>
+                            <span class="nb">len</span><span class="p">(</span><span class="n">data</span><span class="p">),</span>
+                        <span class="p">)</span>
+                    <span class="p">)</span>
+
+                <span class="bp">cls</span> <span class="o">=</span> <span class="nb">globals</span><span class="p">()[</span><span class="n">cls_name</span><span class="p">]</span>
+
+                <span class="k">try</span><span class="p">:</span>
+
+                    <span class="bp">self</span><span class="o">.</span><span class="n">annots</span><span class="p">[</span><span class="n">name</span><span class="p">]</span> <span class="o">=</span> <span class="bp">cls</span><span class="p">(</span><span class="n">dump</span> <span class="o">=</span> <span class="n">data</span><span class="p">)</span>
+                    <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span>
+                        <span class="s1">&#39;Instance of annotation class `</span><span class="si">%s</span><span class="s1">` (resource </span><span class="si">%s</span><span class="s1">) &#39;</span>
+                        <span class="s1">&#39;successfully loaded from pickle.&#39;</span> <span class="o">%</span> <span class="p">(</span>
+                            <span class="n">cls_name</span><span class="p">,</span>
+                            <span class="n">name</span><span class="p">,</span>
+                        <span class="p">)</span>
+                    <span class="p">)</span>
+
+                <span class="c1"># we never want to fail due to any issue with</span>
+                <span class="c1"># one resource:</span>
+                <span class="k">except</span> <span class="ne">Exception</span> <span class="k">as</span> <span class="n">e</span><span class="p">:</span>
+
+                    <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span>
+                        <span class="s1">&#39;ERROR: Failed to create instance of `</span><span class="si">%s</span><span class="s1">` &#39;</span>
+                        <span class="s1">&#39;with data loaded from the pickle.&#39;</span> <span class="o">%</span> <span class="n">cls_name</span>
+                    <span class="p">)</span>
+                    <span class="bp">self</span><span class="o">.</span><span class="n">_log_traceback</span><span class="p">()</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span><span class="s1">&#39;Loaded from pickle `</span><span class="si">%s</span><span class="s1">`.&#39;</span> <span class="o">%</span> <span class="n">pickle_file</span><span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">save_to_pickle</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">pickle_file</span><span class="p">):</span>
+
+        <span class="k">def</span> <span class="nf">get_record_class</span><span class="p">(</span><span class="n">annot</span><span class="p">):</span>
+
+            <span class="k">for</span> <span class="n">val</span> <span class="ow">in</span> <span class="n">annot</span><span class="o">.</span><span class="n">values</span><span class="p">():</span>
+
+                <span class="k">for</span> <span class="n">elem</span> <span class="ow">in</span> <span class="n">val</span><span class="p">:</span>
+
+                    <span class="k">return</span> <span class="n">elem</span><span class="o">.</span><span class="vm">__class__</span>
+
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span><span class="s1">&#39;Saving to pickle `</span><span class="si">%s</span><span class="s1">`.&#39;</span> <span class="o">%</span> <span class="n">pickle_file</span><span class="p">)</span>
+
+        <span class="k">for</span> <span class="n">annot</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">annots</span><span class="o">.</span><span class="n">values</span><span class="p">():</span>
+
+            <span class="n">annot</span><span class="o">.</span><span class="n">_update_complex_attribute_classes</span><span class="p">()</span>
+
+        <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">pickle_file</span><span class="p">,</span> <span class="s1">&#39;wb&#39;</span><span class="p">)</span> <span class="k">as</span> <span class="n">fp</span><span class="p">:</span>
+
+            <span class="n">classes</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">(</span>
+                <span class="p">(</span>
+                    <span class="n">name</span><span class="p">,</span>
+                    <span class="n">get_record_class</span><span class="p">(</span><span class="n">annot</span><span class="o">.</span><span class="n">annot</span><span class="p">)</span>
+                <span class="p">)</span>
+                <span class="k">for</span> <span class="n">name</span><span class="p">,</span> <span class="n">annot</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">annots</span><span class="p">)</span>
+            <span class="p">)</span>
+
+            <span class="n">annots</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">(</span>
+                <span class="p">(</span>
+                    <span class="n">name</span><span class="p">,</span>
+                    <span class="p">(</span>
+                        <span class="n">annot</span><span class="o">.</span><span class="vm">__class__</span><span class="o">.</span><span class="vm">__name__</span><span class="p">,</span>
+                        <span class="nb">dict</span><span class="p">(</span>
+                            <span class="p">(</span>
+                                <span class="n">key</span><span class="p">,</span>
+                                <span class="nb">set</span><span class="p">(</span>
+                                    <span class="nb">tuple</span><span class="p">(</span><span class="n">this_annot</span><span class="p">)</span>
+                                    <span class="k">for</span> <span class="n">this_annot</span> <span class="ow">in</span> <span class="n">these_annots</span>
+                                <span class="p">)</span>
+                            <span class="p">)</span>
+                            <span class="k">for</span> <span class="n">key</span><span class="p">,</span> <span class="n">these_annots</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="n">annot</span><span class="o">.</span><span class="n">annot</span><span class="p">)</span>
+                        <span class="p">),</span>
+                        <span class="p">{</span>
+                            <span class="s1">&#39;name&#39;</span><span class="p">:</span> <span class="n">classes</span><span class="p">[</span><span class="n">name</span><span class="p">]</span><span class="o">.</span><span class="vm">__name__</span><span class="p">,</span>
+                            <span class="s1">&#39;module&#39;</span><span class="p">:</span> <span class="n">classes</span><span class="p">[</span><span class="n">name</span><span class="p">]</span><span class="o">.</span><span class="vm">__module__</span><span class="p">,</span>
+                            <span class="s1">&#39;fields&#39;</span><span class="p">:</span> <span class="n">classes</span><span class="p">[</span><span class="n">name</span><span class="p">]</span><span class="o">.</span><span class="n">_fields</span><span class="p">,</span>
+                        <span class="p">}</span>
+                        <span class="k">if</span> <span class="n">classes</span><span class="p">[</span><span class="n">name</span><span class="p">]</span> <span class="k">else</span> <span class="kc">None</span>
+                    <span class="p">)</span>
+                <span class="p">)</span>
+                <span class="k">for</span> <span class="n">name</span><span class="p">,</span> <span class="n">annot</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">annots</span><span class="p">)</span>
+            <span class="p">)</span>
+
+            <span class="n">pickle</span><span class="o">.</span><span class="n">dump</span><span class="p">(</span>
+                <span class="n">obj</span> <span class="o">=</span> <span class="p">(</span>
+                    <span class="bp">self</span><span class="o">.</span><span class="n">proteins</span><span class="p">,</span>
+                    <span class="bp">self</span><span class="o">.</span><span class="n">complexes</span><span class="p">,</span>
+                    <span class="bp">self</span><span class="o">.</span><span class="n">reference_set</span><span class="p">,</span>
+                    <span class="n">annots</span><span class="p">,</span>
+                <span class="p">),</span>
+                <span class="n">file</span> <span class="o">=</span> <span class="n">fp</span><span class="p">,</span>
+                <span class="n">protocol</span> <span class="o">=</span> <span class="n">pickle</span><span class="o">.</span><span class="n">HIGHEST_PROTOCOL</span><span class="p">,</span>
+            <span class="p">)</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span><span class="s1">&#39;Saved to pickle `</span><span class="si">%s</span><span class="s1">`.&#39;</span> <span class="o">%</span> <span class="n">pickle_file</span><span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">set_reference_set</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">proteins</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">complexes</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">reference_set</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="n">AnnotationBase</span><span class="o">.</span><span class="n">get_reference_set</span><span class="p">(</span>
+                <span class="n">proteins</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">proteins</span><span class="p">,</span>
+                <span class="n">complexes</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">complexes</span><span class="p">,</span>
+                <span class="n">use_complexes</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">use_complexes</span><span class="p">,</span>
+                <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">ncbi_tax_id</span><span class="p">,</span>
+                <span class="n">swissprot_only</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">swissprot_only</span><span class="p">,</span>
+            <span class="p">)</span>
+        <span class="p">)</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">rows</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">(</span>
+            <span class="nb">reversed</span><span class="p">(</span><span class="n">i</span><span class="p">)</span>
+            <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">reference_set</span><span class="p">)</span>
+        <span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">load_protein_resources</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_load_resources</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">protein_sources</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">proteins</span><span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">load_complex_resources</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_load_resources</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">complex_sources</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">complexes</span><span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">_load_resources</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">definitions</span><span class="p">,</span> <span class="n">reference_set</span><span class="p">):</span>
+
+        <span class="k">for</span> <span class="bp">cls</span> <span class="ow">in</span> <span class="n">definitions</span><span class="p">:</span>
+
+            <span class="bp">cls</span> <span class="o">=</span> <span class="bp">cls</span> <span class="k">if</span> <span class="nb">callable</span><span class="p">(</span><span class="bp">cls</span><span class="p">)</span> <span class="k">else</span> <span class="nb">getattr</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_module</span><span class="p">,</span> <span class="bp">cls</span><span class="p">)</span>
+
+            <span class="n">total_attempts</span> <span class="o">=</span> <span class="n">settings</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">&#39;annot_load_resource_attempts&#39;</span><span class="p">)</span>
+
+            <span class="k">for</span> <span class="n">attempt</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">total_attempts</span><span class="p">):</span>
+
+                <span class="k">try</span><span class="p">:</span>
+
+                    <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span>
+                        <span class="sa">f</span><span class="s1">&#39;Loading annotation resource `</span><span class="si">{</span><span class="bp">cls</span><span class="o">.</span><span class="vm">__name__</span><span class="si">}</span><span class="s1">`; &#39;</span>
+                        <span class="sa">f</span><span class="s1">&#39;attempt </span><span class="si">{</span><span class="n">attempt</span><span class="w"> </span><span class="o">+</span><span class="w"> </span><span class="mi">1</span><span class="si">}</span><span class="s1"> of </span><span class="si">{</span><span class="n">total_attempts</span><span class="si">}</span><span class="s1">.&#39;</span>
+                    <span class="p">)</span>
+
+                    <span class="n">annot</span> <span class="o">=</span> <span class="bp">cls</span><span class="p">(</span>
+                        <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">ncbi_tax_id</span><span class="p">,</span>
+                        <span class="n">reference_set</span> <span class="o">=</span> <span class="n">reference_set</span><span class="p">,</span>
+                    <span class="p">)</span>
+
+                    <span class="bp">self</span><span class="o">.</span><span class="n">annots</span><span class="p">[</span><span class="n">annot</span><span class="o">.</span><span class="n">name</span><span class="p">]</span> <span class="o">=</span> <span class="n">annot</span>
+
+                    <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span>
+                        <span class="sa">f</span><span class="s1">&#39;Successfully loaded resource `</span><span class="si">{</span><span class="bp">cls</span><span class="o">.</span><span class="vm">__name__</span><span class="si">}</span><span class="s1">` &#39;</span>
+                        <span class="sa">f</span><span class="s1">&#39;(</span><span class="si">{</span><span class="n">annot</span><span class="o">.</span><span class="n">name</span><span class="si">}</span><span class="s1">).&#39;</span>
+                    <span class="p">)</span>
+                    <span class="k">break</span>
+
+                <span class="k">except</span> <span class="ne">Exception</span> <span class="k">as</span> <span class="n">e</span><span class="p">:</span>
+
+                    <span class="n">exc</span> <span class="o">=</span> <span class="n">sys</span><span class="o">.</span><span class="n">exc_info</span><span class="p">()</span>
+                    <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span>
+                        <span class="s1">&#39;Failed to load annotations from resource `</span><span class="si">%s</span><span class="s1">`:&#39;</span> <span class="o">%</span> <span class="p">(</span>
+                            <span class="bp">cls</span><span class="o">.</span><span class="vm">__name__</span> <span class="k">if</span> <span class="nb">hasattr</span><span class="p">(</span><span class="bp">cls</span><span class="p">,</span> <span class="s1">&#39;__name__&#39;</span><span class="p">)</span> <span class="k">else</span> <span class="nb">str</span><span class="p">(</span><span class="bp">cls</span><span class="p">)</span>
+                        <span class="p">)</span>
+                    <span class="p">)</span>
+                    <span class="bp">self</span><span class="o">.</span><span class="n">_log_traceback</span><span class="p">()</span>
+
+
+    <span class="k">def</span> <span class="nf">make_dataframe</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">reference_set</span> <span class="o">=</span> <span class="kc">None</span><span class="p">):</span>
+
+        <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">create_dataframe</span><span class="p">:</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">df</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">to_dataframe</span><span class="p">(</span><span class="n">reference_set</span> <span class="o">=</span> <span class="n">reference_set</span><span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">ensure_array</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">reference_set</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span> <span class="n">rebuild</span> <span class="o">=</span> <span class="kc">False</span><span class="p">):</span>
+
+        <span class="k">if</span> <span class="ow">not</span> <span class="nb">hasattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">&#39;data&#39;</span><span class="p">)</span> <span class="ow">or</span> <span class="n">rebuild</span><span class="p">:</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">make_array</span><span class="p">(</span><span class="n">reference_set</span> <span class="o">=</span> <span class="n">reference_set</span><span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">to_array</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">reference_set</span> <span class="o">=</span> <span class="kc">None</span><span class="p">):</span>
+
+        <span class="n">reference_set</span> <span class="o">=</span> <span class="n">reference_set</span> <span class="ow">or</span> <span class="bp">self</span><span class="o">.</span><span class="n">reference_set</span>
+
+        <span class="n">names</span>  <span class="o">=</span> <span class="p">[]</span>
+        <span class="n">arrays</span> <span class="o">=</span> <span class="p">[]</span>
+
+        <span class="k">for</span> <span class="n">resource</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">annots</span><span class="o">.</span><span class="n">values</span><span class="p">():</span>
+
+            <span class="c1"># skipping HPA for now because too large number of</span>
+            <span class="c1"># annotations, it would take very long:</span>
+            <span class="k">if</span> <span class="n">resource</span><span class="o">.</span><span class="n">name</span> <span class="o">==</span> <span class="s1">&#39;HPA&#39;</span><span class="p">:</span>
+
+                <span class="k">continue</span>
+
+            <span class="n">use_fields</span> <span class="o">=</span> <span class="p">(</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">use_fields</span><span class="p">[</span><span class="n">resource</span><span class="o">.</span><span class="n">name</span><span class="p">]</span>
+                    <span class="k">if</span> <span class="n">resource</span><span class="o">.</span><span class="n">name</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">use_fields</span> <span class="k">else</span>
+                <span class="kc">None</span>
+            <span class="p">)</span>
+
+            <span class="n">this_names</span><span class="p">,</span> <span class="n">this_array</span> <span class="o">=</span> <span class="n">resource</span><span class="o">.</span><span class="n">to_array</span><span class="p">(</span>
+                    <span class="n">reference_set</span> <span class="o">=</span> <span class="n">reference_set</span><span class="p">,</span>
+                    <span class="n">use_fields</span> <span class="o">=</span> <span class="p">(</span>
+                        <span class="bp">self</span><span class="o">.</span><span class="n">use_fields</span><span class="p">[</span><span class="n">resource</span><span class="o">.</span><span class="n">name</span><span class="p">]</span>
+                            <span class="k">if</span> <span class="n">resource</span><span class="o">.</span><span class="n">name</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">use_fields</span> <span class="k">else</span>
+                        <span class="kc">None</span>
+                    <span class="p">),</span>
+                <span class="p">)</span>
+
+            <span class="n">names</span><span class="o">.</span><span class="n">extend</span><span class="p">(</span><span class="n">this_names</span><span class="p">)</span>
+            <span class="n">arrays</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">this_array</span><span class="p">)</span>
+
+        <span class="n">names</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">(</span><span class="nb">list</span><span class="p">(</span><span class="n">itertools</span><span class="o">.</span><span class="n">chain</span><span class="p">(</span><span class="n">names</span><span class="p">)))</span>
+        <span class="n">data</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">hstack</span><span class="p">(</span><span class="n">arrays</span><span class="p">)</span>
+
+        <span class="k">return</span> <span class="n">names</span><span class="p">,</span> <span class="n">data</span>
+
+
+    <span class="k">def</span> <span class="nf">make_array</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">reference_set</span> <span class="o">=</span> <span class="kc">None</span><span class="p">):</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">names</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">to_array</span><span class="p">(</span><span class="n">reference_set</span> <span class="o">=</span> <span class="n">reference_set</span><span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">set_cols</span><span class="p">()</span>
+
+
+    <span class="k">def</span> <span class="nf">set_cols</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">cols</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">((</span><span class="n">name</span><span class="p">,</span> <span class="n">i</span><span class="p">)</span> <span class="k">for</span> <span class="n">i</span><span class="p">,</span> <span class="n">name</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">names</span><span class="p">))</span>
+
+
+    <span class="k">def</span> <span class="nf">keep</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">keep</span><span class="p">):</span>
+
+        <span class="n">ikeep</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">([</span>
+            <span class="n">i</span> <span class="k">for</span> <span class="n">i</span><span class="p">,</span> <span class="n">name</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">names</span><span class="p">)</span> <span class="k">if</span> <span class="n">name</span> <span class="ow">in</span> <span class="n">keep</span>
+        <span class="p">])</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">names</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">names</span><span class="p">[</span><span class="n">ikeep</span><span class="p">]</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">data</span>  <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span><span class="p">[:,</span> <span class="n">ikeep</span><span class="p">]</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">set_cols</span><span class="p">()</span>
+
+
+    <span class="k">def</span> <span class="nf">make_sets</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">ensure_array</span><span class="p">()</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">sets</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">(</span>
+            <span class="p">(</span>
+                <span class="n">name</span><span class="p">,</span>
+                <span class="nb">set</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">reference_set</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">data</span><span class="p">[:,</span> <span class="n">i</span><span class="p">]])</span>
+            <span class="p">)</span>
+            <span class="k">for</span> <span class="n">i</span><span class="p">,</span> <span class="n">name</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">names</span><span class="p">)</span>
+        <span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">annotate_network</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">pa</span><span class="p">):</span>
+
+        <span class="n">nodes</span> <span class="o">=</span> <span class="n">pa</span><span class="o">.</span><span class="n">graph</span><span class="o">.</span><span class="n">vs</span><span class="p">[</span><span class="s1">&#39;name&#39;</span><span class="p">]</span>
+        <span class="n">edges</span> <span class="o">=</span> <span class="p">[</span>
+            <span class="p">(</span>
+                <span class="n">nodes</span><span class="p">[</span><span class="n">e</span><span class="o">.</span><span class="n">source</span><span class="p">],</span>
+                <span class="n">nodes</span><span class="p">[</span><span class="n">e</span><span class="o">.</span><span class="n">target</span><span class="p">]</span>
+            <span class="p">)</span>
+            <span class="k">for</span> <span class="n">e</span> <span class="ow">in</span> <span class="n">pa</span><span class="o">.</span><span class="n">graph</span><span class="o">.</span><span class="n">es</span>
+        <span class="p">]</span>
+
+        <span class="n">nodeannot</span> <span class="o">=</span> <span class="p">[]</span>
+        <span class="n">edgeannot</span> <span class="o">=</span> <span class="p">[]</span>
+
+        <span class="k">for</span> <span class="n">i</span><span class="p">,</span> <span class="n">uniprot</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">nodes</span><span class="p">):</span>
+
+            <span class="k">for</span> <span class="n">name</span><span class="p">,</span> <span class="n">uniprots</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">sets</span><span class="p">):</span>
+
+                <span class="k">if</span> <span class="n">uniprot</span> <span class="ow">in</span> <span class="n">uniprots</span><span class="p">:</span>
+
+                    <span class="n">nodeannot</span><span class="o">.</span><span class="n">append</span><span class="p">((</span><span class="n">name</span><span class="p">,</span> <span class="n">i</span><span class="p">))</span>
+
+        <span class="k">for</span> <span class="n">i</span><span class="p">,</span> <span class="p">(</span><span class="n">uniprot1</span><span class="p">,</span> <span class="n">uniprot2</span><span class="p">)</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">edges</span><span class="p">):</span>
+
+            <span class="k">for</span> <span class="n">name1</span><span class="p">,</span> <span class="n">uniprots1</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">sets</span><span class="p">):</span>
+
+                <span class="k">for</span> <span class="n">name2</span><span class="p">,</span> <span class="n">uniprots2</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">sets</span><span class="p">):</span>
+
+                    <span class="k">if</span> <span class="n">uniprot1</span> <span class="ow">in</span> <span class="n">uniprots1</span> <span class="ow">and</span> <span class="n">uniprot2</span> <span class="ow">in</span> <span class="n">uniprots2</span><span class="p">:</span>
+
+                        <span class="n">edgeannot</span><span class="o">.</span><span class="n">append</span><span class="p">((</span><span class="n">name1</span><span class="p">,</span> <span class="n">name2</span><span class="p">,</span> <span class="n">i</span><span class="p">))</span>
+
+        <span class="k">return</span> <span class="n">nodeannot</span><span class="p">,</span> <span class="n">edgeannot</span>
+
+
+    <span class="k">def</span> <span class="nf">network_stats</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">pa</span><span class="p">):</span>
+
+        <span class="n">nodeannot</span><span class="p">,</span> <span class="n">edgeannot</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">annotate_network</span><span class="p">(</span><span class="n">pa</span><span class="p">)</span>
+
+        <span class="n">nodestats</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">Counter</span><span class="p">(</span><span class="s1">&#39;__&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">n</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span> <span class="k">for</span> <span class="n">n</span> <span class="ow">in</span> <span class="n">nodeannot</span><span class="p">)</span>
+
+        <span class="n">edgestats</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">Counter</span><span class="p">(</span>
+            <span class="nb">tuple</span><span class="p">(</span><span class="nb">sorted</span><span class="p">((</span><span class="s1">&#39;__&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">e</span><span class="p">[</span><span class="mi">0</span><span class="p">]),</span> <span class="s1">&#39;__&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">e</span><span class="p">[</span><span class="mi">1</span><span class="p">]))))</span>
+            <span class="k">for</span> <span class="n">e</span> <span class="ow">in</span> <span class="n">edgeannot</span>
+        <span class="p">)</span>
+
+        <span class="k">return</span> <span class="n">nodestats</span><span class="p">,</span> <span class="n">edgestats</span>
+
+
+    <span class="k">def</span> <span class="nf">export_network_stats</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">pa</span><span class="p">):</span>
+
+        <span class="n">nodestats</span><span class="p">,</span> <span class="n">edgestats</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">network_stats</span><span class="p">(</span><span class="n">pa</span><span class="p">)</span>
+
+        <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="s1">&#39;annot_edgestats2.tsv&#39;</span><span class="p">,</span> <span class="s1">&#39;w&#39;</span><span class="p">)</span> <span class="k">as</span> <span class="n">fp</span><span class="p">:</span>
+
+            <span class="n">_</span> <span class="o">=</span> <span class="n">fp</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\t</span><span class="s1">&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">((</span><span class="s1">&#39;name1&#39;</span><span class="p">,</span> <span class="s1">&#39;name2&#39;</span><span class="p">,</span> <span class="s1">&#39;count&#39;</span><span class="p">)))</span>
+            <span class="n">_</span> <span class="o">=</span> <span class="n">fp</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\n</span><span class="s1">&#39;</span><span class="p">)</span>
+
+            <span class="n">_</span> <span class="o">=</span> <span class="n">fp</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\n</span><span class="s1">&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span>
+                <span class="s1">&#39;</span><span class="si">%s</span><span class="se">\t</span><span class="si">%s</span><span class="se">\t</span><span class="si">%u</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="p">(</span><span class="n">name1</span><span class="p">,</span> <span class="n">name2</span><span class="p">,</span> <span class="n">cnt</span><span class="p">)</span>
+                <span class="k">for</span> <span class="p">(</span><span class="n">name1</span><span class="p">,</span> <span class="n">name2</span><span class="p">),</span> <span class="n">cnt</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="n">edgestats</span><span class="p">)</span>
+            <span class="p">))</span>
+
+        <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="s1">&#39;annot_nodestats2.tsv&#39;</span><span class="p">,</span> <span class="s1">&#39;w&#39;</span><span class="p">)</span> <span class="k">as</span> <span class="n">fp</span><span class="p">:</span>
+
+            <span class="n">_</span> <span class="o">=</span> <span class="n">fp</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\t</span><span class="s1">&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">((</span><span class="s1">&#39;name&#39;</span><span class="p">,</span> <span class="s1">&#39;count&#39;</span><span class="p">)))</span>
+            <span class="n">_</span> <span class="o">=</span> <span class="n">fp</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\n</span><span class="s1">&#39;</span><span class="p">)</span>
+
+            <span class="n">_</span> <span class="o">=</span> <span class="n">fp</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\n</span><span class="s1">&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span>
+                <span class="s1">&#39;</span><span class="si">%s</span><span class="se">\t</span><span class="si">%u</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="p">(</span><span class="n">name</span><span class="p">,</span> <span class="n">cnt</span><span class="p">)</span>
+                <span class="k">for</span> <span class="n">name</span><span class="p">,</span> <span class="n">cnt</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="n">nodestats</span><span class="p">)</span>
+            <span class="p">))</span>
+
+
+    <span class="k">def</span> <span class="nf">to_dataframe</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">reference_set</span> <span class="o">=</span> <span class="kc">None</span><span class="p">):</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span><span class="s1">&#39;Creating data frame from AnnotationTable.&#39;</span><span class="p">)</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">ensure_array</span><span class="p">(</span>
+            <span class="n">reference_set</span> <span class="o">=</span> <span class="n">reference_set</span><span class="p">,</span>
+            <span class="n">rebuild</span> <span class="o">=</span> <span class="n">reference_set</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">,</span>
+        <span class="p">)</span>
+
+        <span class="n">colnames</span> <span class="o">=</span> <span class="p">[</span><span class="s1">&#39;__&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">name</span><span class="p">)</span> <span class="k">for</span> <span class="n">name</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">names</span><span class="p">]</span>
+
+        <span class="n">df</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">(</span>
+            <span class="n">data</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span><span class="p">,</span>
+            <span class="n">index</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">reference_set</span><span class="p">,</span>
+            <span class="n">columns</span> <span class="o">=</span> <span class="n">colnames</span><span class="p">,</span>
+        <span class="p">)</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span>
+            <span class="s1">&#39;Created annotation data frame, memory usage: </span><span class="si">%s</span><span class="s1">.&#39;</span> <span class="o">%</span> <span class="p">(</span>
+                <span class="n">common</span><span class="o">.</span><span class="n">df_memory_usage</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">df</span><span class="p">)</span>
+            <span class="p">)</span>
+        <span class="p">)</span>
+
+        <span class="k">return</span> <span class="n">df</span>
+
+
+    <span class="k">def</span> <span class="nf">make_narrow_df</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span><span class="s1">&#39;Creating narrow data frame from AnnotationTable.&#39;</span><span class="p">)</span>
+
+        <span class="k">for</span> <span class="n">annot</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">annots</span><span class="o">.</span><span class="n">values</span><span class="p">():</span>
+
+            <span class="n">annot</span><span class="o">.</span><span class="n">make_df</span><span class="p">()</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">narrow_df</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">concat</span><span class="p">(</span>
+            <span class="n">annot</span><span class="o">.</span><span class="n">df</span> <span class="k">for</span> <span class="n">annot</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">annots</span><span class="o">.</span><span class="n">values</span><span class="p">()</span>
+        <span class="p">)</span><span class="o">.</span><span class="n">astype</span><span class="p">(</span><span class="n">AnnotationBase</span><span class="o">.</span><span class="n">_dtypes</span><span class="p">)</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span>
+            <span class="s1">&#39;Created annotation data frame, memory usage: </span><span class="si">%s</span><span class="s1">.&#39;</span> <span class="o">%</span> <span class="p">(</span>
+                <span class="n">common</span><span class="o">.</span><span class="n">df_memory_usage</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">narrow_df</span><span class="p">)</span>
+            <span class="p">)</span>
+        <span class="p">)</span>
+
+
+<div class="viewcode-block" id="AnnotationTable.search">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.AnnotationTable.html#pypath.core.annot.AnnotationTable.search">[docs]</a>
+    <span class="k">def</span> <span class="nf">search</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">protein</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Returns a dictionary with all annotations of a protein. Keys are the</span>
+<span class="sd">        resource names.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">return</span> <span class="nb">dict</span><span class="p">(</span>
+            <span class="p">(</span>
+                <span class="n">resource</span><span class="p">,</span>
+                <span class="n">annot</span><span class="o">.</span><span class="n">annot</span><span class="p">[</span><span class="n">protein</span><span class="p">]</span>
+            <span class="p">)</span>
+            <span class="k">for</span> <span class="n">resource</span><span class="p">,</span> <span class="n">annot</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">annots</span><span class="p">)</span>
+            <span class="k">if</span> <span class="n">protein</span> <span class="ow">in</span> <span class="n">annot</span><span class="o">.</span><span class="n">annot</span>
+        <span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="AnnotationTable.all_annotations">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.AnnotationTable.html#pypath.core.annot.AnnotationTable.all_annotations">[docs]</a>
+    <span class="k">def</span> <span class="nf">all_annotations</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">entity</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Returns all annotation records for one protein in a single list.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">return</span> <span class="p">[</span>
+            <span class="n">aa</span>
+            <span class="k">for</span> <span class="n">a</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">annots</span><span class="o">.</span><span class="n">values</span><span class="p">()</span>
+            <span class="k">if</span> <span class="n">entity</span> <span class="ow">in</span> <span class="n">a</span><span class="o">.</span><span class="n">annot</span>
+            <span class="k">for</span> <span class="n">aa</span> <span class="ow">in</span> <span class="n">a</span><span class="o">.</span><span class="n">annot</span><span class="p">[</span><span class="n">entity</span><span class="p">]</span>
+        <span class="p">]</span></div>
+
+
+
+<div class="viewcode-block" id="AnnotationTable.all_annotations_str">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.AnnotationTable.html#pypath.core.annot.AnnotationTable.all_annotations_str">[docs]</a>
+    <span class="k">def</span> <span class="nf">all_annotations_str</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">protein</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Returns all annotation records for one protein serialized.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">return</span> <span class="s1">&#39;; &#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span>
+            <span class="nb">str</span><span class="p">(</span><span class="n">a</span><span class="p">)</span> <span class="k">for</span> <span class="n">a</span> <span class="ow">in</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">all_annotations</span><span class="p">(</span><span class="n">protein</span> <span class="o">=</span> <span class="n">protein</span><span class="p">)</span>
+        <span class="p">)</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">update_summaries</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">summaries</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">(</span>
+            <span class="p">(</span>
+                <span class="n">name</span><span class="p">,</span>
+                <span class="n">a</span><span class="o">.</span><span class="n">summary</span>
+            <span class="p">)</span>
+            <span class="k">for</span> <span class="n">name</span><span class="p">,</span> <span class="n">a</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">annots</span><span class="p">)</span>
+        <span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">summaries_tab</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">outfile</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span> <span class="n">return_table</span> <span class="o">=</span> <span class="kc">False</span><span class="p">):</span>
+
+        <span class="n">columns</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="p">(</span><span class="s1">&#39;name&#39;</span><span class="p">,</span> <span class="s1">&#39;Resource&#39;</span><span class="p">),</span>
+            <span class="p">(</span><span class="s1">&#39;n_total&#39;</span><span class="p">,</span> <span class="s1">&#39;Entities&#39;</span><span class="p">),</span>
+            <span class="p">(</span><span class="s1">&#39;n_records_total&#39;</span><span class="p">,</span> <span class="s1">&#39;Records&#39;</span><span class="p">),</span>
+            <span class="p">(</span><span class="s1">&#39;records_per_entity&#39;</span><span class="p">,</span> <span class="s1">&#39;Records per entity&#39;</span><span class="p">),</span>
+            <span class="p">(</span><span class="s1">&#39;n_proteins&#39;</span><span class="p">,</span> <span class="s1">&#39;Proteins&#39;</span><span class="p">),</span>
+            <span class="p">(</span><span class="s1">&#39;pct_proteins&#39;</span><span class="p">,</span> <span class="s1">&#39;Proteins [%]&#39;</span><span class="p">),</span>
+            <span class="p">(</span><span class="s1">&#39;n_protein_records&#39;</span><span class="p">,</span> <span class="s1">&#39;Protein records&#39;</span><span class="p">),</span>
+            <span class="p">(</span><span class="s1">&#39;n_complexes&#39;</span><span class="p">,</span> <span class="s1">&#39;Complexes&#39;</span><span class="p">),</span>
+            <span class="p">(</span><span class="s1">&#39;pct_complexes&#39;</span><span class="p">,</span> <span class="s1">&#39;Complexes [%]&#39;</span><span class="p">),</span>
+            <span class="p">(</span><span class="s1">&#39;n_complex_records&#39;</span><span class="p">,</span> <span class="s1">&#39;Complex records&#39;</span><span class="p">),</span>
+            <span class="p">(</span><span class="s1">&#39;complex_annotations_inferred&#39;</span><span class="p">,</span> <span class="s1">&#39;Inferred complex annotations&#39;</span><span class="p">),</span>
+            <span class="p">(</span><span class="s1">&#39;n_mirnas&#39;</span><span class="p">,</span> <span class="s1">&#39;miRNA&#39;</span><span class="p">),</span>
+            <span class="p">(</span><span class="s1">&#39;pct_mirnas&#39;</span><span class="p">,</span> <span class="s1">&#39;miRNA [%]&#39;</span><span class="p">),</span>
+            <span class="p">(</span><span class="s1">&#39;n_mirna_records&#39;</span><span class="p">,</span> <span class="s1">&#39;miRNA records&#39;</span><span class="p">),</span>
+            <span class="p">(</span><span class="s1">&#39;references&#39;</span><span class="p">,</span> <span class="s1">&#39;References&#39;</span><span class="p">),</span>
+            <span class="p">(</span><span class="s1">&#39;curation_effort&#39;</span><span class="p">,</span> <span class="s1">&#39;Curation effort&#39;</span><span class="p">),</span>
+            <span class="p">(</span><span class="s1">&#39;fields&#39;</span><span class="p">,</span> <span class="s1">&#39;Fields&#39;</span><span class="p">),</span>
+        <span class="p">)</span>
+
+        <span class="n">tab</span> <span class="o">=</span> <span class="p">[]</span>
+        <span class="n">tab</span><span class="o">.</span><span class="n">append</span><span class="p">([</span><span class="n">f</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="k">for</span> <span class="n">f</span> <span class="ow">in</span> <span class="n">columns</span><span class="p">])</span>
+
+        <span class="n">tab</span><span class="o">.</span><span class="n">extend</span><span class="p">([</span>
+            <span class="p">[</span>
+                <span class="nb">str</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">summaries</span><span class="p">[</span><span class="n">src</span><span class="p">][</span><span class="n">f</span><span class="p">[</span><span class="mi">0</span><span class="p">]])</span>
+                <span class="k">for</span> <span class="n">f</span> <span class="ow">in</span> <span class="n">columns</span>
+            <span class="p">]</span>
+            <span class="k">for</span> <span class="n">src</span> <span class="ow">in</span> <span class="nb">sorted</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">summaries</span><span class="o">.</span><span class="n">keys</span><span class="p">())</span>
+        <span class="p">])</span>
+
+        <span class="k">if</span> <span class="n">outfile</span><span class="p">:</span>
+
+            <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">outfile</span><span class="p">,</span> <span class="s1">&#39;w&#39;</span><span class="p">)</span> <span class="k">as</span> <span class="n">fp</span><span class="p">:</span>
+
+                <span class="n">fp</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\n</span><span class="s1">&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\t</span><span class="s1">&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">row</span><span class="p">)</span> <span class="k">for</span> <span class="n">row</span> <span class="ow">in</span> <span class="n">tab</span><span class="p">))</span>
+
+        <span class="k">if</span> <span class="n">return_table</span><span class="p">:</span>
+
+            <span class="k">return</span> <span class="n">tab</span>
+
+
+    <span class="k">def</span> <span class="nf">get_entities</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">entity_type</span> <span class="o">=</span> <span class="kc">None</span><span class="p">):</span>
+
+        <span class="n">entity_type</span> <span class="o">=</span> <span class="n">common</span><span class="o">.</span><span class="n">to_set</span><span class="p">(</span><span class="n">entity_type</span><span class="p">)</span>
+
+        <span class="n">entities</span> <span class="o">=</span> <span class="nb">set</span><span class="o">.</span><span class="n">union</span><span class="p">(</span><span class="o">*</span><span class="p">(</span>
+            <span class="nb">set</span><span class="p">(</span><span class="n">an</span><span class="o">.</span><span class="n">annot</span><span class="o">.</span><span class="n">keys</span><span class="p">())</span>
+            <span class="k">for</span> <span class="n">an</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">annots</span><span class="o">.</span><span class="n">values</span><span class="p">()</span>
+        <span class="p">))</span>
+
+        <span class="k">return</span> <span class="n">entity</span><span class="o">.</span><span class="n">Entity</span><span class="o">.</span><span class="n">filter_entity_type</span><span class="p">(</span>
+            <span class="n">entities</span><span class="p">,</span>
+            <span class="n">entity_type</span> <span class="o">=</span> <span class="n">entity_type</span><span class="p">,</span>
+        <span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">get_proteins</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">get_entities</span><span class="p">(</span><span class="n">entity_type</span> <span class="o">=</span> <span class="s1">&#39;protein&#39;</span><span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">get_complexes</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">get_entities</span><span class="p">(</span><span class="n">entity_type</span> <span class="o">=</span> <span class="s1">&#39;complex&#39;</span><span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">get_mirnas</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">get_entities</span><span class="p">(</span><span class="n">entity_type</span> <span class="o">=</span> <span class="s1">&#39;mirna&#39;</span><span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">numof_entities</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">entity_type</span> <span class="o">=</span> <span class="kc">None</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">get_entities</span><span class="p">(</span><span class="n">entity_type</span> <span class="o">=</span> <span class="n">entity_type</span><span class="p">))</span>
+
+
+    <span class="k">def</span> <span class="nf">numof_proteins</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">get_proteins</span><span class="p">())</span>
+
+
+    <span class="k">def</span> <span class="nf">numof_complexes</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">get_complexes</span><span class="p">())</span>
+
+
+    <span class="k">def</span> <span class="nf">numof_mirnas</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">get_mirnas</span><span class="p">())</span>
+
+
+    <span class="k">def</span> <span class="nf">numof_records</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">entity_type</span> <span class="o">=</span> <span class="kc">None</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="nb">sum</span><span class="p">(</span>
+            <span class="n">an</span><span class="o">.</span><span class="n">numof_records</span><span class="p">(</span><span class="n">entity_types</span> <span class="o">=</span> <span class="n">entity_type</span><span class="p">)</span>
+            <span class="k">for</span> <span class="n">an</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">annots</span><span class="o">.</span><span class="n">values</span><span class="p">()</span>
+        <span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">numof_resources</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">annots</span><span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="fm">__repr__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="p">(</span>
+            <span class="s1">&#39;&lt;Annotation database: </span><span class="si">%u</span><span class="s1"> records about </span><span class="si">%u</span><span class="s1"> &#39;</span>
+            <span class="s1">&#39;entities from </span><span class="si">%u</span><span class="s1"> resources&gt;&#39;</span> <span class="o">%</span> <span class="p">(</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">numof_records</span><span class="p">(),</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">numof_entities</span><span class="p">(),</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">numof_resources</span><span class="p">(),</span>
+            <span class="p">)</span>
+        <span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="fm">__getitem__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">item</span><span class="p">):</span>
+
+        <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">item</span><span class="p">,</span> <span class="n">_const</span><span class="o">.</span><span class="n">SIMPLE_TYPES</span><span class="p">):</span>
+
+            <span class="k">if</span> <span class="n">item</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">annots</span><span class="p">:</span>
+
+                <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">annots</span><span class="p">[</span><span class="n">item</span><span class="p">]</span>
+
+            <span class="k">elif</span> <span class="n">item</span> <span class="ow">in</span> <span class="bp">self</span><span class="p">:</span>
+
+                <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">search</span><span class="p">(</span><span class="n">item</span><span class="p">)</span>
+
+        <span class="k">else</span><span class="p">:</span>
+
+            <span class="k">return</span> <span class="nb">dict</span><span class="p">(</span>
+                <span class="p">(</span><span class="n">it</span><span class="p">,</span> <span class="bp">self</span><span class="p">[</span><span class="n">it</span><span class="p">])</span>
+                <span class="k">for</span> <span class="n">it</span> <span class="ow">in</span> <span class="n">item</span>
+            <span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="fm">__contains__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">item</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="p">(</span>
+            <span class="n">item</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">annots</span> <span class="ow">or</span>
+            <span class="nb">any</span><span class="p">(</span><span class="n">item</span> <span class="ow">in</span> <span class="n">a</span> <span class="k">for</span> <span class="n">a</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">annots</span><span class="o">.</span><span class="n">values</span><span class="p">())</span>
+        <span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="init_db">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.init_db.html#pypath.core.annot.init_db">[docs]</a>
+<span class="k">def</span> <span class="nf">init_db</span><span class="p">(</span>
+        <span class="n">keep_annotators</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
+        <span class="n">create_dataframe</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+        <span class="n">use_complexes</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
+        <span class="o">**</span><span class="n">kwargs</span>
+    <span class="p">):</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Initializes or reloads the annotation database.</span>
+<span class="sd">    The database will be assigned to the ``db`` attribute of this module.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="nb">globals</span><span class="p">()[</span><span class="s1">&#39;db&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">AnnotationTable</span><span class="p">(</span>
+        <span class="n">keep_annotators</span> <span class="o">=</span> <span class="n">keep_annotators</span><span class="p">,</span>
+        <span class="n">create_dataframe</span> <span class="o">=</span> <span class="n">create_dataframe</span><span class="p">,</span>
+        <span class="n">use_complexes</span> <span class="o">=</span> <span class="n">use_complexes</span><span class="p">,</span>
+        <span class="o">**</span><span class="n">kwargs</span>
+    <span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="get_db">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.get_db.html#pypath.core.annot.get_db">[docs]</a>
+<span class="k">def</span> <span class="nf">get_db</span><span class="p">(</span>
+        <span class="n">keep_annotators</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
+        <span class="n">create_dataframe</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+        <span class="n">use_complexes</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
+        <span class="o">**</span><span class="n">kwargs</span>
+    <span class="p">):</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Retrieves the current database instance and initializes it if does</span>
+<span class="sd">    not exist yet.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="k">if</span> <span class="s1">&#39;db&#39;</span> <span class="ow">not</span> <span class="ow">in</span> <span class="nb">globals</span><span class="p">():</span>
+
+        <span class="n">init_db</span><span class="p">(</span>
+            <span class="n">keep_annotators</span> <span class="o">=</span> <span class="n">keep_annotators</span><span class="p">,</span>
+            <span class="n">create_dataframe</span> <span class="o">=</span> <span class="n">create_dataframe</span><span class="p">,</span>
+            <span class="n">use_complexes</span> <span class="o">=</span> <span class="n">use_complexes</span><span class="p">,</span>
+            <span class="o">**</span><span class="n">kwargs</span>
+        <span class="p">)</span>
+
+    <span class="k">return</span> <span class="nb">globals</span><span class="p">()[</span><span class="s1">&#39;db&#39;</span><span class="p">]</span></div>
+
+
+<div class="viewcode-block" id="HPO">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.HPO.html#pypath.core.annot.HPO">[docs]</a>
+<span class="k">class</span> <span class="nc">HPO</span><span class="p">(</span><span class="n">AnnotationBase</span><span class="p">):</span>
+
+    <span class="n">_eq_fields</span> <span class="o">=</span> <span class="p">()</span>
+
+<div class="viewcode-block" id="HPO.__init__">
+<a class="viewcode-back" href="../../../api/pypath.core.annot.HPO.html#pypath.core.annot.HPO.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        HPO Gene Annotations from the HPO database.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">kwargs</span><span class="o">.</span><span class="n">pop</span><span class="p">(</span><span class="s1">&#39;ncbi_tax_id&#39;</span><span class="p">,</span> <span class="kc">None</span><span class="p">)</span>
+
+        <span class="n">AnnotationBase</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">name</span> <span class="o">=</span> <span class="s1">&#39;HPO&#39;</span><span class="p">,</span>
+            <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">_const</span><span class="o">.</span><span class="n">NOT_ORGANISM_SPECIFIC</span><span class="p">,</span>
+            <span class="n">input_method</span> <span class="o">=</span> <span class="s1">&#39;hpo.hpo_annotations&#39;</span><span class="p">,</span>
+            <span class="o">**</span><span class="n">kwargs</span>
+        <span class="p">)</span></div>
+
+
+    <span class="k">def</span> <span class="nf">_process_method</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+        <span class="c1">#  already the appropriate format, no processing needed</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">annot</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span>
+        <span class="nb">delattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">&#39;data&#39;</span><span class="p">)</span></div>
+
+</pre></div>
+
+                </article>
+              
+              
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+              
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diff --git a/_modules/pypath/core/complex.html b/_modules/pypath/core/complex.html
new file mode 100644
index 000000000..b815209fd
--- /dev/null
+++ b/_modules/pypath/core/complex.html
@@ -0,0 +1,1535 @@
+
+<!DOCTYPE html>
+
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+                  
+  <h1>Source code for pypath.core.complex</h1><div class="highlight"><pre>
+<span></span><span class="ch">#!/usr/bin/env python</span>
+<span class="c1"># -*- coding: utf-8 -*-</span>
+
+<span class="c1">#</span>
+<span class="c1">#  This file is part of the `pypath` python module</span>
+<span class="c1">#</span>
+<span class="c1">#  Copyright 2014-2023</span>
+<span class="c1">#  EMBL, EMBL-EBI, Uniklinik RWTH Aachen, Heidelberg University</span>
+<span class="c1">#</span>
+<span class="c1">#  Authors: see the file `README.rst`</span>
+<span class="c1">#  Contact: Dénes Türei (turei.denes@gmail.com)</span>
+<span class="c1">#</span>
+<span class="c1">#  Distributed under the GPLv3 License.</span>
+<span class="c1">#  See accompanying file LICENSE.txt or copy at</span>
+<span class="c1">#      https://www.gnu.org/licenses/gpl-3.0.html</span>
+<span class="c1">#</span>
+<span class="c1">#  Website: https://pypath.omnipathdb.org/</span>
+<span class="c1">#</span>
+
+<span class="kn">from</span> <span class="nn">future.utils</span> <span class="kn">import</span> <span class="n">iteritems</span>
+
+<span class="kn">import</span> <span class="nn">sys</span>
+<span class="kn">import</span> <span class="nn">importlib</span> <span class="k">as</span> <span class="nn">imp</span>
+<span class="kn">import</span> <span class="nn">traceback</span>
+<span class="kn">import</span> <span class="nn">collections</span>
+
+<span class="k">try</span><span class="p">:</span>
+    <span class="kn">import</span> <span class="nn">cPickle</span> <span class="k">as</span> <span class="nn">pickle</span>
+<span class="k">except</span><span class="p">:</span>
+    <span class="kn">import</span> <span class="nn">pickle</span>
+
+<span class="kn">import</span> <span class="nn">numpy</span> <span class="k">as</span> <span class="nn">np</span>
+<span class="kn">import</span> <span class="nn">pandas</span> <span class="k">as</span> <span class="nn">pd</span>
+
+<span class="kn">import</span> <span class="nn">pypath.inputs</span> <span class="k">as</span> <span class="nn">inputs</span>
+<span class="kn">import</span> <span class="nn">pypath.internals.intera</span> <span class="k">as</span> <span class="nn">intera</span>
+<span class="kn">import</span> <span class="nn">pypath.internals.resource</span> <span class="k">as</span> <span class="nn">resource</span>
+<span class="kn">import</span> <span class="nn">pypath.share.settings</span> <span class="k">as</span> <span class="nn">settings</span>
+<span class="kn">import</span> <span class="nn">pypath.share.session</span> <span class="k">as</span> <span class="nn">session_mod</span>
+<span class="kn">import</span> <span class="nn">pypath.share.common</span> <span class="k">as</span> <span class="nn">common</span>
+
+
+<span class="n">complex_resources</span> <span class="o">=</span> <span class="p">(</span>
+    <span class="s1">&#39;Signor&#39;</span><span class="p">,</span>
+    <span class="s1">&#39;Corum&#39;</span><span class="p">,</span>
+    <span class="s1">&#39;CellPhoneDB&#39;</span><span class="p">,</span>
+    <span class="s1">&#39;Havugimana&#39;</span><span class="p">,</span>
+    <span class="s1">&#39;Compleat&#39;</span><span class="p">,</span>
+    <span class="s1">&#39;ComplexPortal&#39;</span><span class="p">,</span>
+    <span class="s1">&#39;Pdb&#39;</span><span class="p">,</span>
+    <span class="s1">&#39;GuideToPharmacology&#39;</span><span class="p">,</span>
+    <span class="s1">&#39;Humap&#39;</span><span class="p">,</span>
+    <span class="s1">&#39;Humap2&#39;</span><span class="p">,</span>
+    <span class="s1">&#39;Icellnet&#39;</span><span class="p">,</span>
+    <span class="s1">&#39;Kegg&#39;</span><span class="p">,</span>
+    <span class="s1">&#39;Cellchatdb&#39;</span><span class="p">,</span>
+    <span class="s1">&#39;Cellinker&#39;</span><span class="p">,</span>
+    <span class="s1">&#39;Spike&#39;</span><span class="p">,</span>
+<span class="p">)</span>
+
+
+<div class="viewcode-block" id="AbstractComplexResource">
+<a class="viewcode-back" href="../../../api/pypath.core.complex.AbstractComplexResource.html#pypath.core.complex.AbstractComplexResource">[docs]</a>
+<span class="k">class</span> <span class="nc">AbstractComplexResource</span><span class="p">(</span><span class="n">resource</span><span class="o">.</span><span class="n">AbstractResource</span><span class="p">):</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    A resource which provides information about molecular complexes.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+
+<div class="viewcode-block" id="AbstractComplexResource.__init__">
+<a class="viewcode-back" href="../../../api/pypath.core.complex.AbstractComplexResource.html#pypath.core.complex.AbstractComplexResource.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">name</span><span class="p">,</span>
+            <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">,</span>
+            <span class="n">input_method</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">input_args</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">dump</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="o">**</span><span class="n">kwargs</span>
+        <span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        name : str</span>
+<span class="sd">            Custom name for the resource.</span>
+<span class="sd">        input_method : callable</span>
+<span class="sd">            Method providing the input data.</span>
+<span class="sd">        process_method : callable</span>
+<span class="sd">            Method processing the data and yielding ``intera.Complex``</span>
+<span class="sd">            instances.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">session_mod</span><span class="o">.</span><span class="n">Logger</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">name</span> <span class="o">=</span> <span class="s1">&#39;complex&#39;</span><span class="p">)</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">complexes</span> <span class="o">=</span> <span class="p">{}</span>
+
+        <span class="n">resource</span><span class="o">.</span><span class="n">AbstractResource</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">name</span> <span class="o">=</span> <span class="n">name</span><span class="p">,</span>
+            <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">,</span>
+            <span class="n">input_method</span> <span class="o">=</span> <span class="n">input_method</span><span class="p">,</span>
+            <span class="n">input_args</span> <span class="o">=</span> <span class="n">input_args</span><span class="p">,</span>
+            <span class="n">dump</span> <span class="o">=</span> <span class="n">dump</span><span class="p">,</span>
+            <span class="n">data_attr_name</span> <span class="o">=</span> <span class="s1">&#39;complexes&#39;</span><span class="p">,</span>
+        <span class="p">)</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">load</span><span class="p">()</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">load</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="n">resource</span><span class="o">.</span><span class="n">AbstractResource</span><span class="o">.</span><span class="n">load</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">update_index</span><span class="p">()</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span>
+            <span class="s1">&#39;Loaded resource `</span><span class="si">%s</span><span class="s1">`: </span><span class="si">%u</span><span class="s1"> proteins, </span><span class="si">%u</span><span class="s1"> complexes.&#39;</span> <span class="o">%</span> <span class="p">(</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">,</span>
+                <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">proteins</span><span class="p">),</span>
+                <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">complexes</span><span class="p">),</span>
+            <span class="p">)</span>
+        <span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">_process_method</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">complexes</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span>
+
+        <span class="nb">delattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">&#39;data&#39;</span><span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="fm">__iter__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">for</span> <span class="n">cplex</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">complexes</span><span class="o">.</span><span class="n">values</span><span class="p">():</span>
+
+            <span class="k">yield</span> <span class="n">cplex</span>
+
+
+    <span class="k">def</span> <span class="nf">update_index</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">proteins</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">defaultdict</span><span class="p">(</span><span class="nb">set</span><span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">resources</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">defaultdict</span><span class="p">(</span><span class="nb">set</span><span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">ids</span> <span class="o">=</span> <span class="p">{}</span>
+
+        <span class="k">for</span> <span class="n">cplex</span> <span class="ow">in</span> <span class="bp">self</span><span class="p">:</span>
+
+            <span class="k">for</span> <span class="n">protein</span> <span class="ow">in</span> <span class="n">cplex</span><span class="p">:</span>
+
+                <span class="bp">self</span><span class="o">.</span><span class="n">proteins</span><span class="p">[</span><span class="n">protein</span><span class="p">]</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">cplex</span><span class="p">)</span>
+
+            <span class="k">for</span> <span class="n">db</span> <span class="ow">in</span> <span class="n">cplex</span><span class="o">.</span><span class="n">sources</span><span class="p">:</span>
+
+                <span class="bp">self</span><span class="o">.</span><span class="n">resources</span><span class="p">[</span><span class="n">protein</span><span class="p">]</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">cplex</span><span class="p">)</span>
+
+            <span class="k">for</span> <span class="n">db</span><span class="p">,</span> <span class="n">ids</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="n">cplex</span><span class="o">.</span><span class="n">ids</span><span class="p">):</span>
+
+                <span class="k">for</span> <span class="n">_id</span> <span class="ow">in</span> <span class="n">ids</span><span class="p">:</span>
+
+                    <span class="bp">self</span><span class="o">.</span><span class="n">ids</span><span class="p">[(</span><span class="n">db</span><span class="p">,</span> <span class="n">_id</span><span class="p">)]</span> <span class="o">=</span> <span class="n">cplex</span>
+
+
+    <span class="k">def</span> <span class="fm">__contains__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">other</span><span class="p">):</span>
+
+        <span class="c1"># a Complex instance</span>
+        <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">other</span><span class="p">,</span> <span class="n">intera</span><span class="o">.</span><span class="n">Complex</span><span class="p">):</span>
+
+            <span class="n">other</span> <span class="o">=</span> <span class="n">other</span><span class="o">.</span><span class="fm">__str__</span><span class="p">()</span>
+
+        <span class="c1"># either a UniProt ID or</span>
+        <span class="c1"># a complex string representation</span>
+        <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">other</span><span class="p">,</span> <span class="nb">str</span><span class="p">):</span>
+
+            <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">other</span><span class="p">)</span> <span class="o">&lt;=</span> <span class="mi">10</span><span class="p">:</span>
+
+                <span class="k">return</span> <span class="n">other</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">proteins</span>
+
+            <span class="k">else</span><span class="p">:</span>
+
+                <span class="k">return</span> <span class="n">other</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">complexes</span>
+
+        <span class="k">return</span> <span class="kc">False</span>
+
+
+    <span class="k">def</span> <span class="fm">__len__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">complexes</span><span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="fm">__repr__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="s1">&#39;&lt;Complex database: </span><span class="si">%u</span><span class="s1"> complexes&gt;&#39;</span> <span class="o">%</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span>
+
+
+    <span class="nd">@property</span>
+    <span class="k">def</span> <span class="nf">numof_references</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="nb">len</span><span class="p">(</span>
+            <span class="nb">set</span><span class="o">.</span><span class="n">union</span><span class="p">(</span><span class="o">*</span><span class="p">(</span>
+                <span class="n">cplex</span><span class="o">.</span><span class="n">references</span> <span class="k">for</span> <span class="n">cplex</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">complexes</span><span class="o">.</span><span class="n">values</span><span class="p">()</span>
+            <span class="p">))</span>
+        <span class="p">)</span>
+
+
+    <span class="nd">@property</span>
+    <span class="k">def</span> <span class="nf">curation_effort</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="nb">len</span><span class="p">(</span>
+            <span class="nb">set</span><span class="o">.</span><span class="n">union</span><span class="p">(</span><span class="o">*</span><span class="p">(</span>
+                <span class="p">{(</span><span class="n">key</span><span class="p">,</span> <span class="n">ref</span><span class="p">)</span> <span class="k">for</span> <span class="n">ref</span> <span class="ow">in</span> <span class="n">cplex</span><span class="o">.</span><span class="n">references</span><span class="p">}</span>
+                <span class="k">for</span> <span class="n">key</span><span class="p">,</span> <span class="n">cplex</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">complexes</span><span class="p">)</span>
+            <span class="p">))</span>
+        <span class="p">)</span>
+
+
+    <span class="nd">@property</span>
+    <span class="k">def</span> <span class="nf">has_stoichiometry</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="nb">any</span><span class="p">(</span>
+            <span class="n">cnt</span> <span class="o">&gt;</span> <span class="mi">1</span>
+            <span class="k">for</span> <span class="n">cplex</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">complexes</span><span class="o">.</span><span class="n">values</span><span class="p">()</span>
+            <span class="k">for</span> <span class="n">cnt</span> <span class="ow">in</span> <span class="n">cplex</span><span class="o">.</span><span class="n">components</span><span class="o">.</span><span class="n">values</span><span class="p">()</span>
+        <span class="p">)</span>
+
+
+    <span class="nd">@property</span>
+    <span class="k">def</span> <span class="nf">all_sources</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="nb">set</span><span class="o">.</span><span class="n">union</span><span class="p">(</span><span class="o">*</span><span class="p">(</span>
+            <span class="n">cplex</span><span class="o">.</span><span class="n">sources</span>
+            <span class="k">for</span> <span class="n">cplex</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">complexes</span><span class="o">.</span><span class="n">values</span><span class="p">()</span>
+        <span class="p">))</span>
+
+
+    <span class="nd">@property</span>
+    <span class="k">def</span> <span class="nf">homomers</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="nb">sum</span><span class="p">(</span>
+            <span class="mi">1</span> <span class="k">for</span> <span class="n">cplex</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">complexes</span><span class="o">.</span><span class="n">values</span><span class="p">()</span>
+            <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">cplex</span><span class="o">.</span><span class="n">components</span><span class="p">)</span> <span class="o">==</span> <span class="mi">1</span>
+        <span class="p">)</span>
+
+
+    <span class="nd">@property</span>
+    <span class="k">def</span> <span class="nf">heteromers</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="nb">sum</span><span class="p">(</span>
+            <span class="mi">1</span> <span class="k">for</span> <span class="n">cplex</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">complexes</span><span class="o">.</span><span class="n">values</span><span class="p">()</span>
+            <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">cplex</span><span class="o">.</span><span class="n">components</span><span class="p">)</span> <span class="o">&gt;</span> <span class="mi">1</span>
+        <span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">make_df</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="n">colnames</span> <span class="o">=</span> <span class="p">[</span>
+            <span class="s1">&#39;name&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;components&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;components_genesymbols&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;stoichiometry&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;sources&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;references&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;identifiers&#39;</span><span class="p">,</span>
+        <span class="p">]</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span><span class="s1">&#39;Creating a data frame of complexes.&#39;</span><span class="p">)</span>
+
+        <span class="n">records</span> <span class="o">=</span> <span class="p">[]</span>
+
+        <span class="k">for</span> <span class="n">cplex</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">complexes</span><span class="o">.</span><span class="n">values</span><span class="p">():</span>
+
+            <span class="n">records</span><span class="o">.</span><span class="n">append</span><span class="p">([</span>
+                <span class="n">cplex</span><span class="o">.</span><span class="n">name</span> <span class="k">if</span> <span class="n">cplex</span><span class="o">.</span><span class="n">name</span> <span class="k">else</span> <span class="kc">None</span><span class="p">,</span>
+                <span class="n">cplex</span><span class="o">.</span><span class="fm">__str__</span><span class="p">()[</span><span class="mi">8</span><span class="p">:],</span>
+                <span class="n">cplex</span><span class="o">.</span><span class="n">genesymbol_str</span><span class="p">,</span>
+                <span class="n">cplex</span><span class="o">.</span><span class="n">stoichiometry</span><span class="p">,</span>
+                <span class="s1">&#39;;&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">cplex</span><span class="o">.</span><span class="n">sources</span><span class="p">),</span>
+                <span class="s1">&#39;;&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">cplex</span><span class="o">.</span><span class="n">references</span><span class="p">),</span>
+                <span class="s1">&#39;;&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span>
+                    <span class="s1">&#39;</span><span class="si">%s</span><span class="s1">:</span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="p">(</span><span class="n">db</span><span class="p">,</span> <span class="n">_id</span><span class="p">)</span>
+                    <span class="k">for</span> <span class="n">db</span><span class="p">,</span> <span class="n">ids</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="n">cplex</span><span class="o">.</span><span class="n">ids</span><span class="p">)</span>
+                    <span class="k">for</span> <span class="n">_id</span> <span class="ow">in</span> <span class="n">ids</span>
+                <span class="p">),</span>
+            <span class="p">])</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">df</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">(</span>
+            <span class="n">records</span><span class="p">,</span>
+            <span class="n">columns</span> <span class="o">=</span> <span class="n">colnames</span><span class="p">,</span>
+        <span class="p">)</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span>
+            <span class="s1">&#39;Created data frame of complexes. &#39;</span>
+            <span class="s1">&#39;Memory usage: </span><span class="si">%s</span><span class="s1">.&#39;</span> <span class="o">%</span> <span class="n">common</span><span class="o">.</span><span class="n">df_memory_usage</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">df</span><span class="p">)</span>
+        <span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">_from_dump_callback</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">if</span> <span class="nb">hasattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">&#39;_from_dump&#39;</span><span class="p">):</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">complexes</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_from_dump</span>
+            <span class="nb">delattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">&#39;_from_dump&#39;</span><span class="p">)</span>
+            <span class="nb">delattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">&#39;dump&#39;</span><span class="p">)</span>
+
+
+    <span class="nd">@property</span>
+    <span class="k">def</span> <span class="nf">summary</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="p">{</span>
+            <span class="s1">&#39;n_complexes&#39;</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="fm">__len__</span><span class="p">(),</span>
+            <span class="s1">&#39;n_references&#39;</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">numof_references</span><span class="p">,</span>
+            <span class="s1">&#39;curation_effort&#39;</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">curation_effort</span><span class="p">,</span>
+            <span class="s1">&#39;has_stoichiometry&#39;</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">has_stoichiometry</span><span class="p">,</span>
+            <span class="s1">&#39;name&#39;</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">,</span>
+            <span class="s1">&#39;sources&#39;</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">all_sources</span><span class="p">,</span>
+            <span class="s1">&#39;homomers&#39;</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">homomers</span><span class="p">,</span>
+            <span class="s1">&#39;heteromers&#39;</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">heteromers</span><span class="p">,</span>
+        <span class="p">}</span>
+
+
+    <span class="nd">@property</span>
+    <span class="k">def</span> <span class="nf">summary_str</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="n">s</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">summary</span>
+        <span class="n">bar</span> <span class="o">=</span> <span class="s1">&#39;=&#39;</span> <span class="o">*</span> <span class="mi">70</span>
+
+        <span class="k">return</span> <span class="p">(</span>
+            <span class="s1">&#39;</span><span class="se">\n</span><span class="si">%s</span><span class="se">\n</span><span class="s1">&#39;</span>
+            <span class="s1">&#39;Complex resource `</span><span class="si">%s</span><span class="s1">`</span><span class="se">\n</span><span class="s1">&#39;</span>
+            <span class="s1">&#39;</span><span class="si">%s</span><span class="se">\n</span><span class="s1">&#39;</span>
+            <span class="s1">&#39;</span><span class="se">\t</span><span class="s1">Number of complexes: </span><span class="si">%u</span><span class="se">\n</span><span class="s1">&#39;</span>
+            <span class="s1">&#39;</span><span class="se">\t</span><span class="s1">Homomers: </span><span class="si">%u</span><span class="se">\n</span><span class="s1">&#39;</span>
+            <span class="s1">&#39;</span><span class="se">\t</span><span class="s1">Heteromers: </span><span class="si">%u</span><span class="se">\n</span><span class="s1">&#39;</span>
+            <span class="s1">&#39;</span><span class="se">\t</span><span class="s1">Number of literature references: </span><span class="si">%u</span><span class="se">\n</span><span class="s1">&#39;</span>
+            <span class="s1">&#39;</span><span class="se">\t</span><span class="s1">Curation effort (reference-entity pairs): </span><span class="si">%u</span><span class="se">\n</span><span class="s1">&#39;</span>
+            <span class="s1">&#39;</span><span class="se">\t</span><span class="s1">Has stoichiometry: </span><span class="si">%s</span><span class="se">\n</span><span class="s1">&#39;</span>
+            <span class="s1">&#39;</span><span class="se">\t</span><span class="s1">Sources: </span><span class="si">%s</span><span class="se">\n</span><span class="s1">&#39;</span>
+            <span class="s1">&#39;</span><span class="si">%s</span><span class="se">\n\n</span><span class="s1">&#39;</span>
+        <span class="p">)</span> <span class="o">%</span> <span class="p">(</span>
+            <span class="n">bar</span><span class="p">,</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">,</span>
+            <span class="n">bar</span><span class="p">,</span>
+            <span class="n">s</span><span class="p">[</span><span class="s1">&#39;n_complexes&#39;</span><span class="p">],</span>
+            <span class="n">s</span><span class="p">[</span><span class="s1">&#39;homomers&#39;</span><span class="p">],</span>
+            <span class="n">s</span><span class="p">[</span><span class="s1">&#39;heteromers&#39;</span><span class="p">],</span>
+            <span class="n">s</span><span class="p">[</span><span class="s1">&#39;n_references&#39;</span><span class="p">],</span>
+            <span class="n">s</span><span class="p">[</span><span class="s1">&#39;curation_effort&#39;</span><span class="p">],</span>
+            <span class="nb">str</span><span class="p">(</span><span class="n">s</span><span class="p">[</span><span class="s1">&#39;has_stoichiometry&#39;</span><span class="p">]),</span>
+            <span class="s1">&#39;, &#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">s</span><span class="p">[</span><span class="s1">&#39;sources&#39;</span><span class="p">]),</span>
+            <span class="n">bar</span>
+        <span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="CellPhoneDB">
+<a class="viewcode-back" href="../../../api/pypath.core.complex.CellPhoneDB.html#pypath.core.complex.CellPhoneDB">[docs]</a>
+<span class="k">class</span> <span class="nc">CellPhoneDB</span><span class="p">(</span><span class="n">AbstractComplexResource</span><span class="p">):</span>
+
+
+<div class="viewcode-block" id="CellPhoneDB.__init__">
+<a class="viewcode-back" href="../../../api/pypath.core.complex.CellPhoneDB.html#pypath.core.complex.CellPhoneDB.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+
+        <span class="n">AbstractComplexResource</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">name</span> <span class="o">=</span> <span class="s1">&#39;CellPhoneDB&#39;</span><span class="p">,</span>
+            <span class="n">input_method</span> <span class="o">=</span> <span class="s1">&#39;cellphonedb.cellphonedb_complexes&#39;</span><span class="p">,</span>
+        <span class="p">)</span></div>
+</div>
+
+
+
+<div class="viewcode-block" id="Corum">
+<a class="viewcode-back" href="../../../api/pypath.core.complex.Corum.html#pypath.core.complex.Corum">[docs]</a>
+<span class="k">class</span> <span class="nc">Corum</span><span class="p">(</span><span class="n">AbstractComplexResource</span><span class="p">):</span>
+
+
+<div class="viewcode-block" id="Corum.__init__">
+<a class="viewcode-back" href="../../../api/pypath.core.complex.Corum.html#pypath.core.complex.Corum.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">input_args</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+
+        <span class="n">AbstractComplexResource</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">name</span> <span class="o">=</span> <span class="s1">&#39;CORUM&#39;</span><span class="p">,</span>
+            <span class="n">input_method</span> <span class="o">=</span> <span class="s1">&#39;corum.corum_complexes&#39;</span><span class="p">,</span>
+            <span class="n">input_args</span> <span class="o">=</span> <span class="n">input_args</span> <span class="ow">or</span> <span class="p">{},</span>
+        <span class="p">)</span></div>
+</div>
+
+
+
+<div class="viewcode-block" id="Havugimana">
+<a class="viewcode-back" href="../../../api/pypath.core.complex.Havugimana.html#pypath.core.complex.Havugimana">[docs]</a>
+<span class="k">class</span> <span class="nc">Havugimana</span><span class="p">(</span><span class="n">AbstractComplexResource</span><span class="p">):</span>
+
+
+<div class="viewcode-block" id="Havugimana.__init__">
+<a class="viewcode-back" href="../../../api/pypath.core.complex.Havugimana.html#pypath.core.complex.Havugimana.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">input_args</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+
+        <span class="n">AbstractComplexResource</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">name</span> <span class="o">=</span> <span class="s1">&#39;Havugimana2012&#39;</span><span class="p">,</span>
+            <span class="n">input_method</span> <span class="o">=</span> <span class="s1">&#39;havugimana.havugimana_complexes&#39;</span><span class="p">,</span>
+            <span class="n">input_args</span> <span class="o">=</span> <span class="n">input_args</span> <span class="ow">or</span> <span class="p">{},</span>
+        <span class="p">)</span></div>
+</div>
+
+
+
+<div class="viewcode-block" id="Compleat">
+<a class="viewcode-back" href="../../../api/pypath.core.complex.Compleat.html#pypath.core.complex.Compleat">[docs]</a>
+<span class="k">class</span> <span class="nc">Compleat</span><span class="p">(</span><span class="n">AbstractComplexResource</span><span class="p">):</span>
+
+
+<div class="viewcode-block" id="Compleat.__init__">
+<a class="viewcode-back" href="../../../api/pypath.core.complex.Compleat.html#pypath.core.complex.Compleat.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">input_args</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+
+        <span class="n">AbstractComplexResource</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">name</span> <span class="o">=</span> <span class="s1">&#39;Compleat&#39;</span><span class="p">,</span>
+            <span class="n">input_method</span> <span class="o">=</span> <span class="s1">&#39;compleat.compleat_complexes&#39;</span><span class="p">,</span>
+            <span class="n">input_args</span> <span class="o">=</span> <span class="n">input_args</span> <span class="ow">or</span> <span class="p">{},</span>
+        <span class="p">)</span></div>
+</div>
+
+
+
+<div class="viewcode-block" id="ComplexPortal">
+<a class="viewcode-back" href="../../../api/pypath.core.complex.ComplexPortal.html#pypath.core.complex.ComplexPortal">[docs]</a>
+<span class="k">class</span> <span class="nc">ComplexPortal</span><span class="p">(</span><span class="n">AbstractComplexResource</span><span class="p">):</span>
+
+
+<div class="viewcode-block" id="ComplexPortal.__init__">
+<a class="viewcode-back" href="../../../api/pypath.core.complex.ComplexPortal.html#pypath.core.complex.ComplexPortal.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">input_args</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+
+        <span class="n">AbstractComplexResource</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">name</span> <span class="o">=</span> <span class="s1">&#39;ComplexPortal&#39;</span><span class="p">,</span>
+            <span class="n">input_method</span> <span class="o">=</span> <span class="s1">&#39;complexportal.complexportal_complexes&#39;</span><span class="p">,</span>
+            <span class="n">input_args</span> <span class="o">=</span> <span class="n">input_args</span> <span class="ow">or</span> <span class="p">{},</span>
+        <span class="p">)</span></div>
+</div>
+
+
+
+<div class="viewcode-block" id="Kegg">
+<a class="viewcode-back" href="../../../api/pypath.core.complex.Kegg.html#pypath.core.complex.Kegg">[docs]</a>
+<span class="k">class</span> <span class="nc">Kegg</span><span class="p">(</span><span class="n">AbstractComplexResource</span><span class="p">):</span>
+
+
+<div class="viewcode-block" id="Kegg.__init__">
+<a class="viewcode-back" href="../../../api/pypath.core.complex.Kegg.html#pypath.core.complex.Kegg.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">input_args</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+
+        <span class="n">AbstractComplexResource</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">name</span> <span class="o">=</span> <span class="s1">&#39;KEGG&#39;</span><span class="p">,</span>
+            <span class="n">input_method</span> <span class="o">=</span> <span class="s1">&#39;kegg.kegg_medicus_complexes&#39;</span><span class="p">,</span>
+            <span class="n">input_args</span> <span class="o">=</span> <span class="n">input_args</span> <span class="ow">or</span> <span class="p">{},</span>
+        <span class="p">)</span></div>
+</div>
+
+
+
+<div class="viewcode-block" id="Pdb">
+<a class="viewcode-back" href="../../../api/pypath.core.complex.Pdb.html#pypath.core.complex.Pdb">[docs]</a>
+<span class="k">class</span> <span class="nc">Pdb</span><span class="p">(</span><span class="n">AbstractComplexResource</span><span class="p">):</span>
+
+
+<div class="viewcode-block" id="Pdb.__init__">
+<a class="viewcode-back" href="../../../api/pypath.core.complex.Pdb.html#pypath.core.complex.Pdb.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">input_args</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+
+        <span class="n">input_args</span> <span class="o">=</span> <span class="n">input_args</span> <span class="ow">or</span> <span class="p">{}</span>
+
+        <span class="k">if</span> <span class="s1">&#39;organism&#39;</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">input_args</span><span class="p">:</span>
+
+            <span class="n">input_args</span><span class="p">[</span><span class="s1">&#39;organism&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">settings</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">&#39;default_organism&#39;</span><span class="p">)</span>
+
+        <span class="n">AbstractComplexResource</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">name</span> <span class="o">=</span> <span class="s1">&#39;PDB&#39;</span><span class="p">,</span>
+            <span class="n">input_method</span> <span class="o">=</span> <span class="s1">&#39;pdb.pdb_complexes&#39;</span><span class="p">,</span>
+            <span class="n">input_args</span> <span class="o">=</span> <span class="n">input_args</span> <span class="ow">or</span> <span class="p">{},</span>
+        <span class="p">)</span></div>
+</div>
+
+
+
+<div class="viewcode-block" id="Signor">
+<a class="viewcode-back" href="../../../api/pypath.core.complex.Signor.html#pypath.core.complex.Signor">[docs]</a>
+<span class="k">class</span> <span class="nc">Signor</span><span class="p">(</span><span class="n">AbstractComplexResource</span><span class="p">):</span>
+
+
+<div class="viewcode-block" id="Signor.__init__">
+<a class="viewcode-back" href="../../../api/pypath.core.complex.Signor.html#pypath.core.complex.Signor.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">input_args</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+
+        <span class="n">input_args</span> <span class="o">=</span> <span class="n">input_args</span> <span class="ow">or</span> <span class="p">{}</span>
+
+        <span class="k">if</span> <span class="s1">&#39;organism&#39;</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">input_args</span><span class="p">:</span>
+
+            <span class="n">input_args</span><span class="p">[</span><span class="s1">&#39;organism&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">settings</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">&#39;default_organism&#39;</span><span class="p">)</span>
+
+        <span class="n">AbstractComplexResource</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">name</span> <span class="o">=</span> <span class="s1">&#39;SIGNOR&#39;</span><span class="p">,</span>
+            <span class="n">input_method</span> <span class="o">=</span> <span class="s1">&#39;signor.signor_complexes&#39;</span><span class="p">,</span>
+            <span class="n">input_args</span> <span class="o">=</span> <span class="n">input_args</span> <span class="ow">or</span> <span class="p">{},</span>
+        <span class="p">)</span></div>
+</div>
+
+
+
+<div class="viewcode-block" id="Hpmr">
+<a class="viewcode-back" href="../../../api/pypath.core.complex.Hpmr.html#pypath.core.complex.Hpmr">[docs]</a>
+<span class="k">class</span> <span class="nc">Hpmr</span><span class="p">(</span><span class="n">AbstractComplexResource</span><span class="p">):</span>
+
+
+<div class="viewcode-block" id="Hpmr.__init__">
+<a class="viewcode-back" href="../../../api/pypath.core.complex.Hpmr.html#pypath.core.complex.Hpmr.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">input_args</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+
+        <span class="n">input_args</span> <span class="o">=</span> <span class="n">input_args</span> <span class="ow">or</span> <span class="p">{}</span>
+
+        <span class="n">AbstractComplexResource</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">name</span> <span class="o">=</span> <span class="s1">&#39;HPMR&#39;</span><span class="p">,</span>
+            <span class="n">input_method</span> <span class="o">=</span> <span class="s1">&#39;hpmr.hpmr_complexes&#39;</span><span class="p">,</span>
+            <span class="n">input_args</span> <span class="o">=</span> <span class="n">input_args</span> <span class="ow">or</span> <span class="p">{},</span>
+        <span class="p">)</span></div>
+</div>
+
+
+
+<div class="viewcode-block" id="Humap">
+<a class="viewcode-back" href="../../../api/pypath.core.complex.Humap.html#pypath.core.complex.Humap">[docs]</a>
+<span class="k">class</span> <span class="nc">Humap</span><span class="p">(</span><span class="n">AbstractComplexResource</span><span class="p">):</span>
+
+
+<div class="viewcode-block" id="Humap.__init__">
+<a class="viewcode-back" href="../../../api/pypath.core.complex.Humap.html#pypath.core.complex.Humap.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">input_args</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+
+        <span class="n">AbstractComplexResource</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">name</span> <span class="o">=</span> <span class="s1">&#39;hu.MAP&#39;</span><span class="p">,</span>
+            <span class="n">input_method</span> <span class="o">=</span> <span class="s1">&#39;humap.humap_complexes&#39;</span><span class="p">,</span>
+        <span class="p">)</span></div>
+</div>
+
+
+
+<div class="viewcode-block" id="Humap2">
+<a class="viewcode-back" href="../../../api/pypath.core.complex.Humap2.html#pypath.core.complex.Humap2">[docs]</a>
+<span class="k">class</span> <span class="nc">Humap2</span><span class="p">(</span><span class="n">AbstractComplexResource</span><span class="p">):</span>
+
+
+<div class="viewcode-block" id="Humap2.__init__">
+<a class="viewcode-back" href="../../../api/pypath.core.complex.Humap2.html#pypath.core.complex.Humap2.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">input_args</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+
+        <span class="n">AbstractComplexResource</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">name</span> <span class="o">=</span> <span class="s1">&#39;hu.MAP2&#39;</span><span class="p">,</span>
+            <span class="n">input_method</span> <span class="o">=</span> <span class="s1">&#39;humap.humap2_complexes&#39;</span><span class="p">,</span>
+        <span class="p">)</span></div>
+</div>
+
+
+
+<div class="viewcode-block" id="GuideToPharmacology">
+<a class="viewcode-back" href="../../../api/pypath.core.complex.GuideToPharmacology.html#pypath.core.complex.GuideToPharmacology">[docs]</a>
+<span class="k">class</span> <span class="nc">GuideToPharmacology</span><span class="p">(</span><span class="n">AbstractComplexResource</span><span class="p">):</span>
+
+
+<div class="viewcode-block" id="GuideToPharmacology.__init__">
+<a class="viewcode-back" href="../../../api/pypath.core.complex.GuideToPharmacology.html#pypath.core.complex.GuideToPharmacology.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">input_args</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+
+        <span class="n">input_args</span> <span class="o">=</span> <span class="n">input_args</span> <span class="ow">or</span> <span class="p">{}</span>
+
+        <span class="n">AbstractComplexResource</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">name</span> <span class="o">=</span> <span class="s1">&#39;Guide2Pharma&#39;</span><span class="p">,</span>
+            <span class="n">input_method</span> <span class="o">=</span> <span class="s1">&#39;guide2pharma.guide2pharma_complexes&#39;</span><span class="p">,</span>
+            <span class="n">input_args</span> <span class="o">=</span> <span class="n">input_args</span> <span class="ow">or</span> <span class="p">{},</span>
+        <span class="p">)</span></div>
+</div>
+
+
+
+<div class="viewcode-block" id="Icellnet">
+<a class="viewcode-back" href="../../../api/pypath.core.complex.Icellnet.html#pypath.core.complex.Icellnet">[docs]</a>
+<span class="k">class</span> <span class="nc">Icellnet</span><span class="p">(</span><span class="n">AbstractComplexResource</span><span class="p">):</span>
+
+
+<div class="viewcode-block" id="Icellnet.__init__">
+<a class="viewcode-back" href="../../../api/pypath.core.complex.Icellnet.html#pypath.core.complex.Icellnet.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">input_args</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+
+        <span class="n">input_args</span> <span class="o">=</span> <span class="n">input_args</span> <span class="ow">or</span> <span class="p">{}</span>
+
+        <span class="n">AbstractComplexResource</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">name</span> <span class="o">=</span> <span class="s1">&#39;ICELLNET&#39;</span><span class="p">,</span>
+            <span class="n">input_method</span> <span class="o">=</span> <span class="s1">&#39;icellnet.icellnet_complexes&#39;</span><span class="p">,</span>
+            <span class="n">input_args</span> <span class="o">=</span> <span class="n">input_args</span> <span class="ow">or</span> <span class="p">{},</span>
+        <span class="p">)</span></div>
+</div>
+
+
+
+<div class="viewcode-block" id="Spike">
+<a class="viewcode-back" href="../../../api/pypath.core.complex.Spike.html#pypath.core.complex.Spike">[docs]</a>
+<span class="k">class</span> <span class="nc">Spike</span><span class="p">(</span><span class="n">AbstractComplexResource</span><span class="p">):</span>
+
+
+<div class="viewcode-block" id="Spike.__init__">
+<a class="viewcode-back" href="../../../api/pypath.core.complex.Spike.html#pypath.core.complex.Spike.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">input_args</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+
+        <span class="n">input_args</span> <span class="o">=</span> <span class="n">input_args</span> <span class="ow">or</span> <span class="p">{}</span>
+
+        <span class="n">AbstractComplexResource</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">name</span> <span class="o">=</span> <span class="s1">&#39;SPIKE&#39;</span><span class="p">,</span>
+            <span class="n">input_method</span> <span class="o">=</span> <span class="s1">&#39;spike.spike_complexes&#39;</span><span class="p">,</span>
+            <span class="n">input_args</span> <span class="o">=</span> <span class="n">input_args</span> <span class="ow">or</span> <span class="p">{},</span>
+        <span class="p">)</span></div>
+</div>
+
+
+
+<div class="viewcode-block" id="Cellchatdb">
+<a class="viewcode-back" href="../../../api/pypath.core.complex.Cellchatdb.html#pypath.core.complex.Cellchatdb">[docs]</a>
+<span class="k">class</span> <span class="nc">Cellchatdb</span><span class="p">(</span><span class="n">AbstractComplexResource</span><span class="p">):</span>
+
+
+<div class="viewcode-block" id="Cellchatdb.__init__">
+<a class="viewcode-back" href="../../../api/pypath.core.complex.Cellchatdb.html#pypath.core.complex.Cellchatdb.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">input_args</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+
+        <span class="n">input_args</span> <span class="o">=</span> <span class="n">input_args</span> <span class="ow">or</span> <span class="p">{}</span>
+
+        <span class="k">if</span> <span class="s1">&#39;organism&#39;</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">input_args</span><span class="p">:</span>
+
+            <span class="n">input_args</span><span class="p">[</span><span class="s1">&#39;organism&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">settings</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">&#39;default_organism&#39;</span><span class="p">)</span>
+
+        <span class="n">AbstractComplexResource</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">name</span> <span class="o">=</span> <span class="s1">&#39;CellChatDB&#39;</span><span class="p">,</span>
+            <span class="n">input_method</span> <span class="o">=</span> <span class="s1">&#39;cellchatdb.cellchatdb_complexes&#39;</span><span class="p">,</span>
+            <span class="n">input_args</span> <span class="o">=</span> <span class="n">input_args</span> <span class="ow">or</span> <span class="p">{},</span>
+        <span class="p">)</span></div>
+</div>
+
+
+
+<div class="viewcode-block" id="Cellinker">
+<a class="viewcode-back" href="../../../api/pypath.core.complex.Cellinker.html#pypath.core.complex.Cellinker">[docs]</a>
+<span class="k">class</span> <span class="nc">Cellinker</span><span class="p">(</span><span class="n">AbstractComplexResource</span><span class="p">):</span>
+
+
+<div class="viewcode-block" id="Cellinker.__init__">
+<a class="viewcode-back" href="../../../api/pypath.core.complex.Cellinker.html#pypath.core.complex.Cellinker.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">input_args</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+
+        <span class="n">input_args</span> <span class="o">=</span> <span class="n">input_args</span> <span class="ow">or</span> <span class="p">{}</span>
+
+        <span class="k">if</span> <span class="s1">&#39;organism&#39;</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">input_args</span><span class="p">:</span>
+
+            <span class="n">input_args</span><span class="p">[</span><span class="s1">&#39;organism&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">settings</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">&#39;default_organism&#39;</span><span class="p">)</span>
+
+        <span class="n">AbstractComplexResource</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">name</span> <span class="o">=</span> <span class="s1">&#39;Cellinker&#39;</span><span class="p">,</span>
+            <span class="n">input_method</span> <span class="o">=</span> <span class="s1">&#39;cellinker.cellinker_complexes&#39;</span><span class="p">,</span>
+            <span class="n">input_args</span> <span class="o">=</span> <span class="n">input_args</span> <span class="ow">or</span> <span class="p">{},</span>
+        <span class="p">)</span></div>
+</div>
+
+
+
+<div class="viewcode-block" id="ComplexAggregator">
+<a class="viewcode-back" href="../../../api/pypath.core.complex.ComplexAggregator.html#pypath.core.complex.ComplexAggregator">[docs]</a>
+<span class="k">class</span> <span class="nc">ComplexAggregator</span><span class="p">(</span><span class="n">AbstractComplexResource</span><span class="p">):</span>
+
+
+<div class="viewcode-block" id="ComplexAggregator.__init__">
+<a class="viewcode-back" href="../../../api/pypath.core.complex.ComplexAggregator.html#pypath.core.complex.ComplexAggregator.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">resources</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">pickle_file</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+        <span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Combines complexes from multiple resources.</span>
+
+<span class="sd">        :arg list resources:</span>
+<span class="sd">            List of resources. Names of complex resource classes in this</span>
+<span class="sd">            module or custom</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">pickle_file</span> <span class="o">=</span> <span class="n">pickle_file</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">resources</span> <span class="o">=</span> <span class="n">resources</span> <span class="ow">or</span> <span class="n">complex_resources</span>
+
+        <span class="n">AbstractComplexResource</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">name</span> <span class="o">=</span> <span class="s1">&#39;OmniPath&#39;</span><span class="p">,</span>
+        <span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="ComplexAggregator.reload">
+<a class="viewcode-back" href="../../../api/pypath.core.complex.ComplexAggregator.html#pypath.core.complex.ComplexAggregator.reload">[docs]</a>
+    <span class="k">def</span> <span class="nf">reload</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Reloads the object from the module level.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">modname</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="vm">__class__</span><span class="o">.</span><span class="vm">__module__</span>
+        <span class="n">mod</span> <span class="o">=</span> <span class="nb">__import__</span><span class="p">(</span><span class="n">modname</span><span class="p">,</span> <span class="n">fromlist</span> <span class="o">=</span> <span class="p">[</span><span class="n">modname</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;.&#39;</span><span class="p">)[</span><span class="mi">0</span><span class="p">]])</span>
+        <span class="n">imp</span><span class="o">.</span><span class="n">reload</span><span class="p">(</span><span class="n">mod</span><span class="p">)</span>
+        <span class="n">new</span> <span class="o">=</span> <span class="nb">getattr</span><span class="p">(</span><span class="n">mod</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="vm">__class__</span><span class="o">.</span><span class="vm">__name__</span><span class="p">)</span>
+        <span class="nb">setattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">&#39;__class__&#39;</span><span class="p">,</span> <span class="n">new</span><span class="p">)</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">load</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">pickle_file</span><span class="p">:</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span><span class="s1">&#39;Loading database from pickle `</span><span class="si">%s</span><span class="s1">`.&#39;</span> <span class="o">%</span> <span class="bp">self</span><span class="o">.</span><span class="n">pickle_file</span><span class="p">)</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">load_from_pickle</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">pickle_file</span><span class="p">)</span>
+            <span class="k">return</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">data</span> <span class="o">=</span> <span class="p">{}</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">summaries</span> <span class="o">=</span> <span class="p">{}</span>
+
+        <span class="k">for</span> <span class="n">res</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">resources</span><span class="p">:</span>
+
+            <span class="n">total_attempts</span> <span class="o">=</span> <span class="n">settings</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">&#39;complex_load_resource_attempts&#39;</span><span class="p">)</span>
+
+            <span class="k">for</span> <span class="n">attempt</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">total_attempts</span><span class="p">):</span>
+
+                <span class="k">try</span><span class="p">:</span>
+
+                    <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span>
+                        <span class="sa">f</span><span class="s1">&#39;Loading resource `</span><span class="si">{</span><span class="nb">str</span><span class="p">(</span><span class="n">res</span><span class="p">)</span><span class="si">}</span><span class="s1">`; &#39;</span>
+                        <span class="sa">f</span><span class="s1">&#39;attempt </span><span class="si">{</span><span class="n">attempt</span><span class="w"> </span><span class="o">+</span><span class="w"> </span><span class="mi">1</span><span class="si">}</span><span class="s1">/</span><span class="si">{</span><span class="n">total_attempts</span><span class="si">}</span><span class="s1">.&#39;</span>
+                    <span class="p">)</span>
+
+                    <span class="k">if</span> <span class="ow">not</span> <span class="nb">callable</span><span class="p">(</span><span class="n">res</span><span class="p">):</span>
+
+                        <span class="k">if</span> <span class="n">res</span> <span class="ow">in</span> <span class="nb">globals</span><span class="p">():</span>
+
+                            <span class="n">res</span> <span class="o">=</span> <span class="nb">globals</span><span class="p">()[</span><span class="n">res</span><span class="p">]</span>
+
+                    <span class="k">if</span> <span class="nb">callable</span><span class="p">(</span><span class="n">res</span><span class="p">):</span>
+
+                        <span class="n">processor</span> <span class="o">=</span> <span class="n">res</span><span class="p">()</span>
+
+                    <span class="k">elif</span> <span class="nb">hasattr</span><span class="p">(</span><span class="n">res</span><span class="p">,</span> <span class="s1">&#39;complexes&#39;</span><span class="p">):</span>
+
+                        <span class="n">processor</span> <span class="o">=</span> <span class="n">res</span>
+
+                    <span class="k">if</span> <span class="nb">hasattr</span><span class="p">(</span><span class="n">processor</span><span class="p">,</span> <span class="s1">&#39;summary&#39;</span><span class="p">):</span>
+
+                        <span class="bp">self</span><span class="o">.</span><span class="n">summaries</span><span class="p">[</span><span class="n">processor</span><span class="o">.</span><span class="n">name</span><span class="p">]</span> <span class="o">=</span> <span class="n">processor</span><span class="o">.</span><span class="n">summary</span>
+
+                    <span class="k">for</span> <span class="n">key</span><span class="p">,</span> <span class="n">cplex</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="n">processor</span><span class="o">.</span><span class="n">complexes</span><span class="p">):</span>
+
+                        <span class="k">if</span> <span class="n">key</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span><span class="p">:</span>
+
+                            <span class="bp">self</span><span class="o">.</span><span class="n">data</span><span class="p">[</span><span class="n">key</span><span class="p">]</span> <span class="o">+=</span> <span class="n">cplex</span>
+
+                        <span class="k">else</span><span class="p">:</span>
+
+                            <span class="bp">self</span><span class="o">.</span><span class="n">data</span><span class="p">[</span><span class="n">key</span><span class="p">]</span> <span class="o">=</span> <span class="n">cplex</span>
+
+                    <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span><span class="sa">f</span><span class="s1">&#39;Successfully loaded resource `</span><span class="si">{</span><span class="nb">str</span><span class="p">(</span><span class="n">res</span><span class="p">)</span><span class="si">}</span><span class="s1">`.&#39;</span><span class="p">)</span>
+                    <span class="k">break</span>
+
+                <span class="k">except</span> <span class="ne">Exception</span><span class="p">:</span>
+
+                    <span class="n">exc</span> <span class="o">=</span> <span class="n">sys</span><span class="o">.</span><span class="n">exc_info</span><span class="p">()</span>
+                    <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span><span class="s1">&#39;Failed to load resource `</span><span class="si">%s</span><span class="s1">`:&#39;</span> <span class="o">%</span> <span class="nb">str</span><span class="p">(</span><span class="n">res</span><span class="p">))</span>
+                    <span class="bp">self</span><span class="o">.</span><span class="n">_log_traceback</span><span class="p">()</span>
+
+        <span class="n">resource</span><span class="o">.</span><span class="n">AbstractResource</span><span class="o">.</span><span class="n">load</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">update_index</span><span class="p">()</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">update_summaries</span><span class="p">()</span>
+
+
+    <span class="k">def</span> <span class="nf">load_from_pickle</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">pickle_file</span><span class="p">):</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span><span class="s1">&#39;Loading from pickle `</span><span class="si">%s</span><span class="s1">`.&#39;</span> <span class="o">%</span> <span class="n">pickle_file</span><span class="p">)</span>
+
+        <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">pickle_file</span><span class="p">,</span> <span class="s1">&#39;rb&#39;</span><span class="p">)</span> <span class="k">as</span> <span class="n">fp</span><span class="p">:</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">complexes</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">summaries</span> <span class="o">=</span> <span class="n">pickle</span><span class="o">.</span><span class="n">load</span><span class="p">(</span><span class="n">fp</span><span class="p">)</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span><span class="s1">&#39;Loaded from pickle `</span><span class="si">%s</span><span class="s1">`.&#39;</span> <span class="o">%</span> <span class="n">pickle_file</span><span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">update_summaries</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">for</span> <span class="n">src</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">summaries</span><span class="o">.</span><span class="n">keys</span><span class="p">():</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">summaries</span><span class="p">[</span><span class="n">src</span><span class="p">][</span><span class="s1">&#39;unique_complexes&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="nb">sum</span><span class="p">(</span>
+                <span class="mi">1</span> <span class="k">for</span> <span class="n">cplex</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">complexes</span><span class="o">.</span><span class="n">values</span><span class="p">()</span>
+                <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">cplex</span><span class="o">.</span><span class="n">sources</span><span class="p">)</span> <span class="o">==</span> <span class="mi">1</span> <span class="ow">and</span> <span class="n">src</span> <span class="ow">in</span> <span class="n">cplex</span><span class="o">.</span><span class="n">sources</span>
+            <span class="p">)</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">summaries</span><span class="p">[</span><span class="n">src</span><span class="p">][</span><span class="s1">&#39;shared_complexes&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="nb">sum</span><span class="p">(</span>
+                <span class="mi">1</span> <span class="k">for</span> <span class="n">cplex</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">complexes</span><span class="o">.</span><span class="n">values</span><span class="p">()</span>
+                <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">cplex</span><span class="o">.</span><span class="n">sources</span><span class="p">)</span> <span class="o">&gt;</span> <span class="mi">1</span> <span class="ow">and</span> <span class="n">src</span> <span class="ow">in</span> <span class="n">cplex</span><span class="o">.</span><span class="n">sources</span>
+            <span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">summaries_tab</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">outfile</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span> <span class="n">return_table</span> <span class="o">=</span> <span class="kc">False</span><span class="p">):</span>
+
+        <span class="n">columns</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="p">(</span><span class="s1">&#39;name&#39;</span><span class="p">,</span> <span class="s1">&#39;Resource&#39;</span><span class="p">),</span>
+            <span class="p">(</span><span class="s1">&#39;n_complexes&#39;</span><span class="p">,</span> <span class="s1">&#39;All complexes&#39;</span><span class="p">),</span>
+            <span class="p">(</span><span class="s1">&#39;homomers&#39;</span><span class="p">,</span> <span class="s1">&#39;Homomers&#39;</span><span class="p">),</span>
+            <span class="p">(</span><span class="s1">&#39;heteromers&#39;</span><span class="p">,</span> <span class="s1">&#39;Heteromers&#39;</span><span class="p">),</span>
+            <span class="p">(</span><span class="s1">&#39;has_stoichiometry&#39;</span><span class="p">,</span> <span class="s1">&#39;Stoichiometry&#39;</span><span class="p">),</span>
+            <span class="p">(</span><span class="s1">&#39;unique_complexes&#39;</span><span class="p">,</span> <span class="s1">&#39;Unique complexes&#39;</span><span class="p">),</span>
+            <span class="p">(</span><span class="s1">&#39;shared_complexes&#39;</span><span class="p">,</span> <span class="s1">&#39;Shared complexes&#39;</span><span class="p">),</span>
+            <span class="p">(</span><span class="s1">&#39;n_references&#39;</span><span class="p">,</span> <span class="s1">&#39;References&#39;</span><span class="p">),</span>
+            <span class="p">(</span><span class="s1">&#39;curation_effort&#39;</span><span class="p">,</span> <span class="s1">&#39;Curation effort&#39;</span><span class="p">),</span>
+        <span class="p">)</span>
+
+        <span class="n">tab</span> <span class="o">=</span> <span class="p">[]</span>
+        <span class="n">tab</span><span class="o">.</span><span class="n">append</span><span class="p">([</span><span class="n">f</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="k">for</span> <span class="n">f</span> <span class="ow">in</span> <span class="n">columns</span><span class="p">])</span>
+
+        <span class="n">tab</span><span class="o">.</span><span class="n">extend</span><span class="p">([</span>
+            <span class="p">[</span>
+                <span class="nb">str</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">summaries</span><span class="p">[</span><span class="n">src</span><span class="p">][</span><span class="n">f</span><span class="p">[</span><span class="mi">0</span><span class="p">]])</span>
+                <span class="k">for</span> <span class="n">f</span> <span class="ow">in</span> <span class="n">columns</span>
+            <span class="p">]</span>
+            <span class="k">for</span> <span class="n">src</span> <span class="ow">in</span> <span class="nb">sorted</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">summaries</span><span class="o">.</span><span class="n">keys</span><span class="p">())</span>
+        <span class="p">])</span>
+
+        <span class="k">if</span> <span class="n">outfile</span><span class="p">:</span>
+
+            <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">outfile</span><span class="p">,</span> <span class="s1">&#39;w&#39;</span><span class="p">)</span> <span class="k">as</span> <span class="n">fp</span><span class="p">:</span>
+
+                <span class="n">fp</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\n</span><span class="s1">&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\t</span><span class="s1">&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">row</span><span class="p">)</span> <span class="k">for</span> <span class="n">row</span> <span class="ow">in</span> <span class="n">tab</span><span class="p">))</span>
+
+        <span class="k">if</span> <span class="n">return_table</span><span class="p">:</span>
+
+            <span class="k">return</span> <span class="n">tab</span>
+
+
+    <span class="k">def</span> <span class="nf">_update_complex_attribute_classes</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_update_complex_attribute_classes_static</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">complexes</span><span class="p">)</span>
+
+
+    <span class="nd">@staticmethod</span>
+    <span class="k">def</span> <span class="nf">_update_complex_attribute_classes_static</span><span class="p">(</span><span class="n">cplexes</span><span class="p">,</span> <span class="n">mod</span> <span class="o">=</span> <span class="kc">None</span><span class="p">):</span>
+
+        <span class="n">mod</span> <span class="o">=</span> <span class="n">mod</span> <span class="ow">or</span> <span class="n">sys</span><span class="o">.</span><span class="n">modules</span><span class="p">[</span><span class="vm">__name__</span><span class="p">]</span>
+
+        <span class="k">for</span> <span class="n">key</span> <span class="ow">in</span> <span class="n">cplexes</span><span class="p">:</span>
+
+            <span class="k">if</span> <span class="nb">hasattr</span><span class="p">(</span><span class="n">key</span><span class="p">,</span> <span class="s1">&#39;attrs&#39;</span><span class="p">):</span>
+
+                <span class="k">for</span> <span class="n">attr</span><span class="p">,</span> <span class="n">val</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="n">key</span><span class="o">.</span><span class="n">attrs</span><span class="p">):</span>
+
+                    <span class="bp">cls</span> <span class="o">=</span> <span class="n">val</span><span class="o">.</span><span class="vm">__class__</span><span class="o">.</span><span class="vm">__name__</span>
+
+                    <span class="k">if</span> <span class="nb">hasattr</span><span class="p">(</span><span class="n">mod</span><span class="p">,</span> <span class="bp">cls</span><span class="p">):</span>
+
+                        <span class="n">val</span><span class="o">.</span><span class="vm">__class__</span> <span class="o">=</span> <span class="nb">getattr</span><span class="p">(</span><span class="n">mod</span><span class="p">,</span> <span class="bp">cls</span><span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">save_to_pickle</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">pickle_file</span><span class="p">):</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span><span class="s1">&#39;Saving to pickle `</span><span class="si">%s</span><span class="s1">`.&#39;</span> <span class="o">%</span> <span class="n">pickle_file</span><span class="p">)</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_update_complex_attribute_classes</span><span class="p">()</span>
+
+        <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">pickle_file</span><span class="p">,</span> <span class="s1">&#39;wb&#39;</span><span class="p">)</span> <span class="k">as</span> <span class="n">fp</span><span class="p">:</span>
+
+            <span class="n">pickle</span><span class="o">.</span><span class="n">dump</span><span class="p">(</span>
+                <span class="n">obj</span> <span class="o">=</span> <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">complexes</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">summaries</span><span class="p">),</span>
+                <span class="n">file</span> <span class="o">=</span> <span class="n">fp</span><span class="p">,</span>
+            <span class="p">)</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span><span class="s1">&#39;Saved to pickle `</span><span class="si">%s</span><span class="s1">`.&#39;</span> <span class="o">%</span> <span class="n">pickle_file</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="init_db">
+<a class="viewcode-back" href="../../../api/pypath.core.complex.init_db.html#pypath.core.complex.init_db">[docs]</a>
+<span class="k">def</span> <span class="nf">init_db</span><span class="p">(</span><span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Initializes or reloads the complex database.</span>
+<span class="sd">    The database will be assigned to the ``db`` attribute of this module.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="nb">globals</span><span class="p">()[</span><span class="s1">&#39;db&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">ComplexAggregator</span><span class="p">(</span><span class="o">**</span><span class="n">kwargs</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="get_db">
+<a class="viewcode-back" href="../../../api/pypath.core.complex.get_db.html#pypath.core.complex.get_db">[docs]</a>
+<span class="k">def</span> <span class="nf">get_db</span><span class="p">(</span><span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Retrieves the current database instance and initializes it if does</span>
+<span class="sd">    not exist yet.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="k">if</span> <span class="s1">&#39;db&#39;</span> <span class="ow">not</span> <span class="ow">in</span> <span class="nb">globals</span><span class="p">():</span>
+
+        <span class="n">init_db</span><span class="p">(</span><span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
+
+    <span class="k">return</span> <span class="nb">globals</span><span class="p">()[</span><span class="s1">&#39;db&#39;</span><span class="p">]</span></div>
+
+
+
+<div class="viewcode-block" id="all_complexes">
+<a class="viewcode-back" href="../../../api/pypath.core.complex.all_complexes.html#pypath.core.complex.all_complexes">[docs]</a>
+<span class="k">def</span> <span class="nf">all_complexes</span><span class="p">():</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Returns a set of all complexes in the database which serves as a</span>
+<span class="sd">    reference set for many methods, just like</span>
+<span class="sd">    ``inputs.uniprot_db.all_uniprots`` represents the proteome.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="n">db</span> <span class="o">=</span> <span class="n">get_db</span><span class="p">()</span>
+
+    <span class="k">return</span> <span class="nb">set</span><span class="p">(</span><span class="n">db</span><span class="o">.</span><span class="n">complexes</span><span class="o">.</span><span class="n">values</span><span class="p">())</span></div>
+
+</pre></div>
+
+                </article>
+              
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+    <li class="breadcrumb-item active" aria-current="page">pypath.core.entity</li>
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+      
+    </div>
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+                  
+  <h1>Source code for pypath.core.entity</h1><div class="highlight"><pre>
+<span></span><span class="ch">#!/usr/bin/env python</span>
+<span class="c1"># -*- coding: utf-8 -*-</span>
+
+<span class="c1">#</span>
+<span class="c1">#  This file is part of the `pypath` python module</span>
+<span class="c1">#</span>
+<span class="c1">#  Copyright 2014-2023</span>
+<span class="c1">#  EMBL, EMBL-EBI, Uniklinik RWTH Aachen, Heidelberg University</span>
+<span class="c1">#</span>
+<span class="c1">#  Authors: see the file `README.rst`</span>
+<span class="c1">#  Contact: Dénes Türei (turei.denes@gmail.com)</span>
+<span class="c1">#</span>
+<span class="c1">#  Distributed under the GPLv3 License.</span>
+<span class="c1">#  See accompanying file LICENSE.txt or copy at</span>
+<span class="c1">#      https://www.gnu.org/licenses/gpl-3.0.html</span>
+<span class="c1">#</span>
+<span class="c1">#  Website: https://pypath.omnipathdb.org/</span>
+<span class="c1">#</span>
+
+<span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">Provides classes for representing molecular entities and their collections.</span>
+<span class="sd">A molecular entity is defined by its identifier, type and taxon.</span>
+<span class="sd">&quot;&quot;&quot;</span>
+
+<span class="kn">from</span> <span class="nn">future.utils</span> <span class="kn">import</span> <span class="n">iteritems</span>
+
+<span class="kn">import</span> <span class="nn">itertools</span>
+<span class="kn">import</span> <span class="nn">importlib</span> <span class="k">as</span> <span class="nn">imp</span>
+<span class="kn">import</span> <span class="nn">collections</span>
+
+<span class="kn">import</span> <span class="nn">pypath.share.common</span> <span class="k">as</span> <span class="nn">common</span>
+<span class="kn">import</span> <span class="nn">pypath_common._constants</span> <span class="k">as</span> <span class="nn">_const</span>
+<span class="kn">import</span> <span class="nn">pypath.share.session</span> <span class="k">as</span> <span class="nn">session_mod</span>
+<span class="kn">import</span> <span class="nn">pypath.utils.mapping</span> <span class="k">as</span> <span class="nn">mapping</span>
+<span class="kn">import</span> <span class="nn">pypath.share.settings</span> <span class="k">as</span> <span class="nn">settings</span>
+<span class="kn">import</span> <span class="nn">pypath.core.attrs</span> <span class="k">as</span> <span class="nn">attrs_mod</span>
+
+
+<span class="n">EntityKey</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">namedtuple</span><span class="p">(</span>
+    <span class="s1">&#39;EntityKey&#39;</span><span class="p">,</span>
+    <span class="p">[</span>
+        <span class="s1">&#39;identifier&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;id_type&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;entity_type&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;taxon&#39;</span><span class="p">,</span>
+    <span class="p">]</span>
+<span class="p">)</span>
+
+
+<div class="viewcode-block" id="Entity">
+<a class="viewcode-back" href="../../../api/pypath.core.entity.Entity.html#pypath.core.entity.Entity">[docs]</a>
+<span class="k">class</span> <span class="nc">Entity</span><span class="p">(</span><span class="n">session_mod</span><span class="o">.</span><span class="n">Logger</span><span class="p">,</span> <span class="n">attrs_mod</span><span class="o">.</span><span class="n">AttributeHandler</span><span class="p">):</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Represents a molecular entity such as protein, miRNA, lncRNA or small</span>
+<span class="sd">    molecule.</span>
+
+<span class="sd">    :arg str identifier:</span>
+<span class="sd">        An identifier from the reference database e.g. UniProt ID for</span>
+<span class="sd">        proteins.</span>
+<span class="sd">    :arg str entity_type:</span>
+<span class="sd">        The type of the molecular entity, defaults to ``&#39;protein&#39;``.</span>
+<span class="sd">    :arg str id_type:</span>
+<span class="sd">        The type of the identifier (the reference database), default is</span>
+<span class="sd">        ``&#39;uniprot&#39;``.</span>
+<span class="sd">    :arg int taxon:</span>
+<span class="sd">        The NCBI Taxonomy Identifier of the molecular entity, e.g. ``9606``</span>
+<span class="sd">        for human. Use ``0`` for non taxon specific molecules e.g. metabolites</span>
+<span class="sd">        or drug compounds.</span>
+<span class="sd">    :arg NoneType,dict attrs:</span>
+<span class="sd">        A dictionary of additional attributes.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="vm">__slots__</span> <span class="o">=</span> <span class="p">[</span>
+        <span class="s1">&#39;identifier&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;entity_type&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;id_type&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;taxon&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;label&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;key&#39;</span><span class="p">,</span>
+    <span class="p">]</span>
+
+
+    <span class="n">_default_id_types</span> <span class="o">=</span> <span class="n">settings</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">&#39;default_name_types&#39;</span><span class="p">)</span>
+    <span class="n">_smol_types</span> <span class="o">=</span> <span class="n">settings</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">&#39;small_molecule_entity_types&#39;</span><span class="p">)</span>
+
+    <span class="n">_id_type_to_entity_type</span> <span class="o">=</span> <span class="p">{</span>
+        <span class="s1">&#39;uniprot&#39;</span><span class="p">:</span> <span class="s1">&#39;protein&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;genesymbol&#39;</span><span class="p">:</span> <span class="s1">&#39;protein&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;mir-name&#39;</span><span class="p">:</span> <span class="s1">&#39;mirna&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;mir-mat-name&#39;</span><span class="p">:</span> <span class="s1">&#39;mirna&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;mir-pre&#39;</span><span class="p">:</span> <span class="s1">&#39;mirna&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;mir-mat&#39;</span><span class="p">:</span> <span class="s1">&#39;mirna&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;lncrna-genesymbol&#39;</span><span class="p">:</span> <span class="s1">&#39;lncrna&#39;</span><span class="p">,</span>
+    <span class="p">}</span>
+
+    <span class="n">_label_types</span> <span class="o">=</span> <span class="nb">set</span><span class="p">(</span><span class="n">mapping</span><span class="o">.</span><span class="n">Mapper</span><span class="o">.</span><span class="n">label_type_to_id_type</span><span class="o">.</span><span class="n">keys</span><span class="p">())</span>
+
+
+<div class="viewcode-block" id="Entity.__init__">
+<a class="viewcode-back" href="../../../api/pypath.core.entity.Entity.html#pypath.core.entity.Entity.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">identifier</span><span class="p">,</span>
+            <span class="n">entity_type</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">id_type</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">taxon</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">,</span>
+            <span class="n">attrs</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+        <span class="p">):</span>
+
+        <span class="k">if</span> <span class="p">(</span>
+            <span class="nb">isinstance</span><span class="p">(</span><span class="n">identifier</span><span class="p">,</span> <span class="n">Entity</span><span class="p">)</span> <span class="ow">or</span>
+            <span class="nb">hasattr</span><span class="p">(</span><span class="n">identifier</span><span class="p">,</span> <span class="s1">&#39;identifier&#39;</span><span class="p">)</span>
+        <span class="p">):</span>
+
+            <span class="p">(</span>
+                <span class="n">identifier</span><span class="p">,</span>
+                <span class="n">entity_type</span><span class="p">,</span>
+                <span class="n">id_type</span><span class="p">,</span>
+                <span class="n">taxon</span><span class="p">,</span>
+            <span class="p">)</span> <span class="o">=</span> <span class="p">(</span>
+                <span class="n">identifier</span><span class="o">.</span><span class="n">identifier</span><span class="p">,</span>
+                <span class="n">identifier</span><span class="o">.</span><span class="n">entity_type</span><span class="p">,</span>
+                <span class="n">identifier</span><span class="o">.</span><span class="n">id_type</span><span class="p">,</span>
+                <span class="n">identifier</span><span class="o">.</span><span class="n">taxon</span><span class="p">,</span>
+            <span class="p">)</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_bootstrap</span><span class="p">(</span><span class="n">identifier</span><span class="p">,</span> <span class="n">id_type</span><span class="p">,</span> <span class="n">entity_type</span><span class="p">,</span> <span class="n">taxon</span><span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">key</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_key</span>
+
+        <span class="n">attrs_mod</span><span class="o">.</span><span class="n">AttributeHandler</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">attrs</span><span class="p">)</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">set_label</span><span class="p">()</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">reload</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="n">modname</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="vm">__class__</span><span class="o">.</span><span class="vm">__module__</span>
+        <span class="n">mod</span> <span class="o">=</span> <span class="nb">__import__</span><span class="p">(</span><span class="n">modname</span><span class="p">,</span> <span class="n">fromlist</span> <span class="o">=</span> <span class="p">[</span><span class="n">modname</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;.&#39;</span><span class="p">)[</span><span class="mi">0</span><span class="p">]])</span>
+        <span class="kn">import</span> <span class="nn">importlib</span> <span class="k">as</span> <span class="nn">imp</span>
+        <span class="n">imp</span><span class="o">.</span><span class="n">reload</span><span class="p">(</span><span class="n">mod</span><span class="p">)</span>
+        <span class="n">new</span> <span class="o">=</span> <span class="nb">getattr</span><span class="p">(</span><span class="n">mod</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="vm">__class__</span><span class="o">.</span><span class="vm">__name__</span><span class="p">)</span>
+        <span class="nb">setattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">&#39;__class__&#39;</span><span class="p">,</span> <span class="n">new</span><span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">_bootstrap</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">identifier</span><span class="p">,</span> <span class="n">id_type</span><span class="p">,</span> <span class="n">entity_type</span><span class="p">,</span> <span class="n">taxon</span><span class="p">):</span>
+
+        <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">_is_complex</span><span class="p">(</span><span class="n">identifier</span><span class="p">):</span>
+
+            <span class="n">entity_type</span> <span class="o">=</span> <span class="s1">&#39;complex&#39;</span>
+            <span class="n">id_type</span> <span class="o">=</span> <span class="s1">&#39;complex&#39;</span>
+            <span class="n">taxon</span> <span class="o">=</span> <span class="p">(</span>
+                <span class="n">identifier</span><span class="o">.</span><span class="n">ncbi_tax_id</span>
+                    <span class="k">if</span> <span class="nb">hasattr</span><span class="p">(</span><span class="n">identifier</span><span class="p">,</span> <span class="s1">&#39;ncbi_tax_id&#39;</span><span class="p">)</span> <span class="k">else</span>
+                <span class="n">taxon</span>
+            <span class="p">)</span>
+
+        <span class="k">if</span> <span class="n">entity_type</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">_smol_types</span><span class="p">:</span>
+
+            <span class="n">taxon</span> <span class="o">=</span> <span class="n">_const</span><span class="o">.</span><span class="n">NOT_ORGANISM_SPECIFIC</span>
+
+        <span class="n">taxon</span> <span class="o">=</span> <span class="n">settings</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">&#39;default_organism&#39;</span><span class="p">)</span> <span class="k">if</span> <span class="n">taxon</span> <span class="ow">is</span> <span class="kc">None</span> <span class="k">else</span> <span class="n">taxon</span>
+
+        <span class="k">if</span> <span class="ow">not</span> <span class="n">entity_type</span><span class="p">:</span>
+
+            <span class="k">if</span> <span class="n">id_type</span> <span class="ow">and</span> <span class="n">id_type</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">_id_type_to_entity_type</span><span class="p">:</span>
+
+                <span class="n">entity_type</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_id_type_to_entity_type</span><span class="p">[</span><span class="n">id_type</span><span class="p">]</span>
+
+
+        <span class="k">if</span> <span class="ow">not</span> <span class="n">id_type</span><span class="p">:</span>
+
+            <span class="n">id_type</span><span class="p">,</span> <span class="n">entity_type</span> <span class="o">=</span> <span class="n">mapping</span><span class="o">.</span><span class="n">guess_type</span><span class="p">(</span>
+                <span class="n">identifier</span><span class="p">,</span>
+                <span class="n">entity_type</span> <span class="o">=</span> <span class="n">entity_type</span><span class="p">,</span>
+            <span class="p">)</span>
+
+        <span class="k">if</span> <span class="ow">not</span> <span class="n">id_type</span> <span class="ow">and</span> <span class="p">(</span><span class="ow">not</span> <span class="n">entity_type</span> <span class="ow">or</span> <span class="n">entity_type</span> <span class="o">==</span> <span class="s1">&#39;protein&#39;</span><span class="p">):</span>
+
+            <span class="n">id_type</span><span class="p">,</span> <span class="n">entity_type</span> <span class="o">=</span> <span class="s1">&#39;genesymbol&#39;</span><span class="p">,</span> <span class="s1">&#39;protein&#39;</span>
+
+        <span class="k">if</span> <span class="n">id_type</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">_label_types</span><span class="p">:</span>
+
+            <span class="n">_identifier</span> <span class="o">=</span> <span class="n">mapping</span><span class="o">.</span><span class="n">id_from_label0</span><span class="p">(</span>
+                <span class="n">label</span> <span class="o">=</span> <span class="n">identifier</span><span class="p">,</span>
+                <span class="n">label_id_type</span> <span class="o">=</span> <span class="n">id_type</span><span class="p">,</span>
+                <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">taxon</span><span class="p">,</span>
+            <span class="p">)</span>
+
+
+
+            <span class="k">if</span> <span class="n">_identifier</span> <span class="ow">and</span> <span class="n">_identifier</span> <span class="o">!=</span> <span class="n">identifier</span><span class="p">:</span>
+
+                <span class="n">id_type</span> <span class="o">=</span> <span class="n">mapping</span><span class="o">.</span><span class="n">mapper</span><span class="o">.</span><span class="n">label_type_to_id_type</span><span class="p">[</span><span class="n">id_type</span><span class="p">]</span>
+                <span class="n">identifier</span> <span class="o">=</span> <span class="n">_identifier</span>
+
+            <span class="k">if</span> <span class="n">id_type</span> <span class="o">==</span> <span class="s1">&#39;mir-pre&#39;</span><span class="p">:</span>
+
+                <span class="n">_identifier</span> <span class="o">=</span> <span class="n">mapping</span><span class="o">.</span><span class="n">map_name0</span><span class="p">(</span>
+                    <span class="n">identifier</span><span class="p">,</span>
+                    <span class="n">id_type</span><span class="p">,</span>
+                    <span class="s1">&#39;mirbase&#39;</span><span class="p">,</span>
+                    <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">taxon</span><span class="p">,</span>
+                <span class="p">)</span>
+
+                <span class="k">if</span> <span class="n">_identifier</span> <span class="ow">and</span> <span class="n">_identifier</span> <span class="o">!=</span> <span class="n">identifier</span><span class="p">:</span>
+
+                    <span class="n">identifier</span> <span class="o">=</span> <span class="n">_identifier</span>
+                    <span class="n">id_type</span> <span class="o">=</span> <span class="s1">&#39;mirbase&#39;</span>
+
+        <span class="n">entity_type</span> <span class="o">=</span> <span class="n">entity_type</span> <span class="ow">or</span> <span class="bp">self</span><span class="o">.</span><span class="n">_get_entity_type</span><span class="p">(</span><span class="n">identifier</span><span class="p">)</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">identifier</span> <span class="o">=</span> <span class="n">identifier</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">id_type</span> <span class="o">=</span> <span class="n">id_type</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">entity_type</span> <span class="o">=</span> <span class="n">entity_type</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">taxon</span> <span class="o">=</span> <span class="n">taxon</span>
+
+
+    <span class="nd">@staticmethod</span>
+    <span class="k">def</span> <span class="nf">entity_name_str</span><span class="p">(</span><span class="n">entity</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="p">(</span>
+            <span class="n">entity</span>
+                <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">entity</span><span class="p">,</span> <span class="nb">str</span><span class="p">)</span> <span class="k">else</span>
+            <span class="nb">str</span><span class="p">(</span><span class="n">entity</span><span class="p">)</span>
+        <span class="p">)</span>
+
+
+    <span class="nd">@classmethod</span>
+    <span class="k">def</span> <span class="nf">igraph_vertex_name</span><span class="p">(</span><span class="bp">cls</span><span class="p">,</span> <span class="n">igraph_v</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="bp">cls</span><span class="o">.</span><span class="n">entity_name_str</span><span class="p">(</span><span class="n">igraph_v</span><span class="p">[</span><span class="s1">&#39;name&#39;</span><span class="p">])</span>
+
+
+    <span class="nd">@staticmethod</span>
+    <span class="k">def</span> <span class="nf">igraph_vertex_label</span><span class="p">(</span><span class="n">igraph_v</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="n">igraph_v</span><span class="p">[</span><span class="s1">&#39;label&#39;</span><span class="p">]</span>
+
+
+    <span class="nd">@classmethod</span>
+    <span class="k">def</span> <span class="nf">igraph_vertex_name_label</span><span class="p">(</span><span class="bp">cls</span><span class="p">,</span> <span class="n">igraph_v</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="p">(</span>
+            <span class="bp">cls</span><span class="o">.</span><span class="n">igraph_vertex_name</span><span class="p">(</span><span class="n">igraph_v</span><span class="p">),</span>
+            <span class="bp">cls</span><span class="o">.</span><span class="n">igraph_vertex_label</span><span class="p">(</span><span class="n">igraph_v</span><span class="p">),</span>
+        <span class="p">)</span>
+
+
+    <span class="nd">@staticmethod</span>
+    <span class="k">def</span> <span class="nf">_is_protein</span><span class="p">(</span><span class="n">key</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="p">(</span>
+            <span class="nb">isinstance</span><span class="p">(</span><span class="n">key</span><span class="p">,</span> <span class="nb">str</span><span class="p">)</span> <span class="ow">and</span> <span class="p">(</span>
+                <span class="ow">not</span> <span class="n">key</span><span class="o">.</span><span class="n">isdigit</span><span class="p">()</span> <span class="ow">or</span>
+                <span class="n">settings</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">&#39;default_name_types&#39;</span><span class="p">)[</span><span class="s1">&#39;protein&#39;</span><span class="p">]</span> <span class="o">==</span> <span class="s1">&#39;entrez&#39;</span>
+            <span class="p">)</span> <span class="ow">and</span>
+            <span class="ow">not</span> <span class="n">key</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s1">&#39;MIMAT&#39;</span><span class="p">)</span> <span class="ow">and</span>
+            <span class="ow">not</span> <span class="n">key</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s1">&#39;COMPLEX&#39;</span><span class="p">)</span>
+        <span class="p">)</span>
+
+
+    <span class="nd">@staticmethod</span>
+    <span class="k">def</span> <span class="nf">_is_small_molecule</span><span class="p">(</span><span class="n">key</span><span class="p">):</span>
+
+        <span class="k">return</span><span class="p">(</span>
+            <span class="nb">isinstance</span><span class="p">(</span><span class="n">key</span><span class="p">,</span> <span class="nb">str</span><span class="p">)</span> <span class="ow">and</span>
+            <span class="n">key</span><span class="o">.</span><span class="n">isdigit</span><span class="p">()</span> <span class="ow">and</span>
+            <span class="n">settings</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">&#39;default_name_types&#39;</span><span class="p">)[</span><span class="s1">&#39;protein&#39;</span><span class="p">]</span> <span class="o">!=</span> <span class="s1">&#39;entrez&#39;</span>
+        <span class="p">)</span>
+
+
+    <span class="nd">@staticmethod</span>
+    <span class="k">def</span> <span class="nf">_is_mirna</span><span class="p">(</span><span class="n">key</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="p">(</span>
+            <span class="nb">isinstance</span><span class="p">(</span><span class="n">key</span><span class="p">,</span> <span class="nb">str</span><span class="p">)</span> <span class="ow">and</span>
+            <span class="n">key</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s1">&#39;MIMAT&#39;</span><span class="p">)</span>
+        <span class="p">)</span>
+
+
+    <span class="nd">@staticmethod</span>
+    <span class="k">def</span> <span class="nf">_is_complex</span><span class="p">(</span><span class="n">key</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="n">key</span><span class="o">.</span><span class="vm">__class__</span><span class="o">.</span><span class="vm">__name__</span> <span class="o">==</span> <span class="s1">&#39;Complex&#39;</span> <span class="ow">or</span> <span class="p">(</span>
+            <span class="nb">isinstance</span><span class="p">(</span><span class="n">key</span><span class="p">,</span> <span class="nb">str</span><span class="p">)</span> <span class="ow">and</span>
+            <span class="n">key</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s1">&#39;COMPLEX&#39;</span><span class="p">)</span>
+        <span class="p">)</span>
+
+
+    <span class="nd">@classmethod</span>
+    <span class="k">def</span> <span class="nf">_get_entity_type</span><span class="p">(</span><span class="bp">cls</span><span class="p">,</span> <span class="n">key</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="p">(</span>
+            <span class="s1">&#39;complex&#39;</span>
+                <span class="k">if</span> <span class="bp">cls</span><span class="o">.</span><span class="n">_is_complex</span><span class="p">(</span><span class="n">key</span><span class="p">)</span> <span class="k">else</span>
+            <span class="s1">&#39;mirna&#39;</span>
+                <span class="k">if</span> <span class="bp">cls</span><span class="o">.</span><span class="n">_is_mirna</span><span class="p">(</span><span class="n">key</span><span class="p">)</span> <span class="k">else</span>
+            <span class="s1">&#39;small_molecule&#39;</span>
+                <span class="k">if</span> <span class="bp">cls</span><span class="o">.</span><span class="n">_is_small_molecule</span><span class="p">(</span><span class="n">key</span><span class="p">)</span> <span class="k">else</span>
+            <span class="s1">&#39;protein&#39;</span>
+        <span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">is_small_molecule</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="p">(</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">entity_type</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">_smol_types</span> <span class="ow">or</span> <span class="p">(</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">identifier</span><span class="o">.</span><span class="n">isdigit</span><span class="p">()</span> <span class="ow">and</span> <span class="p">(</span>
+                    <span class="bp">self</span><span class="o">.</span><span class="n">_default_id_types</span><span class="p">[</span><span class="s1">&#39;protein&#39;</span><span class="p">]</span> <span class="o">!=</span> <span class="s1">&#39;entrez&#39;</span> <span class="ow">or</span>
+                    <span class="bp">self</span><span class="o">.</span><span class="n">id_type</span> <span class="o">==</span> <span class="s1">&#39;pubchem&#39;</span>
+                <span class="p">)</span>
+            <span class="p">)</span>
+        <span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">is_protein</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="p">(</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">entity_type</span> <span class="ow">not</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">_smol_types</span> <span class="ow">and</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">id_type</span> <span class="o">!=</span> <span class="s1">&#39;pubchem&#39;</span> <span class="ow">and</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">_is_protein</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">identifier</span><span class="p">)</span>
+        <span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">is_mirna</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_is_mirna</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">identifier</span><span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">is_complex</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_is_complex</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">identifier</span><span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">get_entity_type</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_get_entity_type</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">identifier</span><span class="p">)</span>
+
+
+<div class="viewcode-block" id="Entity.filter_entity_type">
+<a class="viewcode-back" href="../../../api/pypath.core.entity.Entity.html#pypath.core.entity.Entity.filter_entity_type">[docs]</a>
+    <span class="nd">@classmethod</span>
+    <span class="k">def</span> <span class="nf">filter_entity_type</span><span class="p">(</span><span class="bp">cls</span><span class="p">,</span> <span class="n">entities</span><span class="p">,</span> <span class="n">entity_type</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Filters an iterable of entities or identifiers keeping only the ones</span>
+<span class="sd">        of type(s) in ``entity_type``.</span>
+
+<span class="sd">        :param iterable entities:</span>
+<span class="sd">            A list, set, tuple or other iterable yielding entities or</span>
+<span class="sd">            identifiers.</span>
+<span class="sd">        :param str,set entity_type:</span>
+<span class="sd">            One or more entity types e.g. ``{&#39;protein&#39;, &#39;mirna&#39;}``.</span>
+
+<span class="sd">        :returns:</span>
+<span class="sd">            Same type of object as ``entities`` if the type of the object is</span>
+<span class="sd">            list, set or tuple, otherwise a generator.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">if</span> <span class="ow">not</span> <span class="n">entity_type</span> <span class="ow">or</span> <span class="ow">not</span> <span class="n">entities</span><span class="p">:</span>
+
+            <span class="k">return</span> <span class="n">entities</span>
+
+        <span class="n">entity_type</span> <span class="o">=</span> <span class="n">common</span><span class="o">.</span><span class="n">to_set</span><span class="p">(</span><span class="n">entity_type</span><span class="p">)</span>
+        <span class="n">obj_type</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="nb">type</span><span class="p">(</span><span class="n">entities</span><span class="p">)</span>
+                <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">entities</span><span class="p">,</span> <span class="n">_const</span><span class="o">.</span><span class="n">LIST_LIKE</span><span class="p">)</span> <span class="k">else</span>
+            <span class="k">lambda</span> <span class="n">x</span><span class="p">:</span> <span class="n">x</span>
+        <span class="p">)</span>
+
+        <span class="k">return</span> <span class="n">obj_type</span><span class="p">(</span>
+            <span class="n">e</span>
+            <span class="k">for</span> <span class="n">e</span> <span class="ow">in</span> <span class="n">entities</span>
+            <span class="k">if</span> <span class="bp">cls</span><span class="o">.</span><span class="n">_get_entity_type</span><span class="p">(</span><span class="n">e</span><span class="p">)</span> <span class="ow">in</span> <span class="n">entity_type</span>
+        <span class="p">)</span></div>
+
+
+
+    <span class="nd">@classmethod</span>
+    <span class="k">def</span> <span class="nf">only_proteins</span><span class="p">(</span><span class="bp">cls</span><span class="p">,</span> <span class="n">entities</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="bp">cls</span><span class="o">.</span><span class="n">filter_entity_type</span><span class="p">(</span><span class="n">entities</span><span class="p">,</span> <span class="n">entity_type</span> <span class="o">=</span> <span class="s1">&#39;protein&#39;</span><span class="p">)</span>
+
+
+    <span class="nd">@classmethod</span>
+    <span class="k">def</span> <span class="nf">only_complexes</span><span class="p">(</span><span class="bp">cls</span><span class="p">,</span> <span class="n">entities</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="bp">cls</span><span class="o">.</span><span class="n">filter_entity_type</span><span class="p">(</span><span class="n">entities</span><span class="p">,</span> <span class="n">entity_type</span> <span class="o">=</span> <span class="s1">&#39;complex&#39;</span><span class="p">)</span>
+
+
+    <span class="nd">@classmethod</span>
+    <span class="k">def</span> <span class="nf">only_mirnas</span><span class="p">(</span><span class="bp">cls</span><span class="p">,</span> <span class="n">entities</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="bp">cls</span><span class="o">.</span><span class="n">filter_entity_type</span><span class="p">(</span><span class="n">entities</span><span class="p">,</span> <span class="n">entity_type</span> <span class="o">=</span> <span class="s1">&#39;mirna&#39;</span><span class="p">)</span>
+
+
+<div class="viewcode-block" id="Entity.count_entity_type">
+<a class="viewcode-back" href="../../../api/pypath.core.entity.Entity.html#pypath.core.entity.Entity.count_entity_type">[docs]</a>
+    <span class="nd">@classmethod</span>
+    <span class="k">def</span> <span class="nf">count_entity_type</span><span class="p">(</span><span class="bp">cls</span><span class="p">,</span> <span class="n">entities</span><span class="p">,</span> <span class="n">entity_type</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Counts elements in an iterable of entities or identifiers of type(s)</span>
+<span class="sd">        in ``entity_type``.</span>
+
+<span class="sd">        :param iterable entities:</span>
+<span class="sd">            A list, set, tuple or other iterable yielding entities or</span>
+<span class="sd">            identifiers.</span>
+<span class="sd">        :param str,set entity_type:</span>
+<span class="sd">            One or more entity types e.g. ``{&#39;protein&#39;, &#39;mirna&#39;}``.</span>
+
+<span class="sd">        :returns:</span>
+<span class="sd">            int</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">entities</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="n">entities</span>
+                <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">entities</span><span class="p">,</span> <span class="n">_const</span><span class="o">.</span><span class="n">LIST_LIKE</span><span class="p">)</span> <span class="k">else</span>
+            <span class="nb">list</span><span class="p">(</span><span class="n">entities</span><span class="p">)</span>
+        <span class="p">)</span>
+
+        <span class="k">return</span> <span class="nb">len</span><span class="p">(</span>
+            <span class="bp">cls</span><span class="o">.</span><span class="n">filter_entity_type</span><span class="p">(</span>
+                <span class="n">entities</span><span class="p">,</span>
+                <span class="n">entity_type</span> <span class="o">=</span> <span class="n">entity_type</span><span class="p">,</span>
+            <span class="p">)</span>
+        <span class="p">)</span></div>
+
+
+
+    <span class="nd">@property</span>
+    <span class="k">def</span> <span class="nf">_key</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="n">EntityKey</span><span class="p">(</span>
+            <span class="n">identifier</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">identifier</span><span class="p">,</span>
+            <span class="n">id_type</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">id_type</span><span class="p">,</span>
+            <span class="n">entity_type</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">entity_type</span><span class="p">,</span>
+            <span class="n">taxon</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">taxon</span><span class="p">,</span>
+        <span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="fm">__hash__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="nb">hash</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">key</span><span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="fm">__eq__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">other</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="p">(</span>
+            <span class="bp">self</span><span class="o">.</span><span class="fm">__hash__</span><span class="p">()</span> <span class="o">==</span> <span class="n">other</span><span class="o">.</span><span class="fm">__hash__</span><span class="p">()</span>
+                <span class="k">if</span> <span class="nb">hasattr</span><span class="p">(</span><span class="n">other</span><span class="p">,</span> <span class="s1">&#39;key&#39;</span><span class="p">)</span> <span class="k">else</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">identifier</span> <span class="o">==</span> <span class="n">other</span> <span class="ow">or</span> <span class="bp">self</span><span class="o">.</span><span class="n">label</span> <span class="o">==</span> <span class="n">other</span>
+        <span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="fm">__lt__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">other</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="p">(</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">key</span> <span class="o">&lt;</span> <span class="n">other</span><span class="o">.</span><span class="n">key</span>
+                <span class="k">if</span> <span class="nb">hasattr</span><span class="p">(</span><span class="n">other</span><span class="p">,</span> <span class="s1">&#39;key&#39;</span><span class="p">)</span> <span class="k">else</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">identifier</span> <span class="o">&lt;</span> <span class="n">other</span>
+        <span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="fm">__gt__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">other</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="p">(</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">key</span> <span class="o">&lt;</span> <span class="n">other</span><span class="o">.</span><span class="n">key</span>
+                <span class="k">if</span> <span class="nb">hasattr</span><span class="p">(</span><span class="n">other</span><span class="p">,</span> <span class="s1">&#39;key&#39;</span><span class="p">)</span> <span class="k">else</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">identifier</span> <span class="o">&lt;</span> <span class="n">other</span>
+        <span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">set_label</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">label</span> <span class="o">=</span> <span class="n">mapping</span><span class="o">.</span><span class="n">label</span><span class="p">(</span>
+            <span class="n">name</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">identifier</span><span class="p">,</span>
+            <span class="n">id_type</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">id_type</span><span class="p">,</span>
+            <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">taxon</span><span class="p">,</span>
+            <span class="n">entity_type</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">entity_type</span><span class="p">,</span>
+        <span class="p">)</span> <span class="ow">or</span> <span class="bp">self</span><span class="o">.</span><span class="n">identifier</span>
+
+
+    <span class="k">def</span> <span class="fm">__repr__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="s1">&#39;&lt;Entity: </span><span class="si">%s</span><span class="s1">&gt;&#39;</span> <span class="o">%</span> <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">label</span> <span class="ow">or</span> <span class="bp">self</span><span class="o">.</span><span class="n">identifier</span><span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="fm">__iadd__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">other</span><span class="p">):</span>
+
+        <span class="k">if</span> <span class="bp">self</span> <span class="o">==</span> <span class="n">other</span><span class="p">:</span>
+
+            <span class="n">attrs_mod</span><span class="o">.</span><span class="n">AttributeHandler</span><span class="o">.</span><span class="fm">__iadd__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">other</span><span class="p">)</span>
+
+        <span class="k">return</span> <span class="bp">self</span>
+
+
+    <span class="nd">@classmethod</span>
+    <span class="k">def</span> <span class="nf">entity_info</span><span class="p">(</span><span class="bp">cls</span><span class="p">,</span> <span class="n">identifier</span><span class="p">):</span>
+
+        <span class="k">if</span> <span class="bp">cls</span><span class="o">.</span><span class="n">_is_protein</span><span class="p">(</span><span class="n">identifier</span><span class="p">):</span>
+
+            <span class="kn">import</span> <span class="nn">pypath.utils.uniprot</span> <span class="k">as</span> <span class="nn">uniprot</span>
+            <span class="k">return</span> <span class="n">uniprot</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="n">identifier</span><span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">info</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">entity_info</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">identifier</span><span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="fm">__bool__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="nb">bool</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">identifier</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="EntityList">
+<a class="viewcode-back" href="../../../api/pypath.core.entity.EntityList.html#pypath.core.entity.EntityList">[docs]</a>
+<span class="k">class</span> <span class="nc">EntityList</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span>
+
+
+<div class="viewcode-block" id="EntityList.__init__">
+<a class="viewcode-back" href="../../../api/pypath.core.entity.EntityList.html#pypath.core.entity.EntityList.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">entities</span><span class="p">):</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_entities</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="n">entities</span>
+                <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">entities</span><span class="p">,</span> <span class="p">(</span><span class="nb">list</span><span class="p">,</span> <span class="nb">tuple</span><span class="p">,</span> <span class="nb">set</span><span class="p">))</span> <span class="k">else</span>
+            <span class="nb">list</span><span class="p">(</span><span class="n">entities</span><span class="p">)</span>
+        <span class="p">)</span></div>
+
+
+
+    <span class="k">def</span> <span class="fm">__iter__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">for</span> <span class="n">e</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">_entities</span><span class="p">:</span>
+
+            <span class="k">yield</span> <span class="n">e</span>
+
+
+    <span class="k">def</span> <span class="fm">__len__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_entities</span><span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="fm">__repr__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="s1">&#39;&lt;EntityList (</span><span class="si">%u</span><span class="s1"> elements)&gt;&#39;</span> <span class="o">%</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="fm">__add__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">other</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="n">EntityList</span><span class="p">(</span><span class="nb">set</span><span class="p">(</span><span class="n">itertools</span><span class="o">.</span><span class="n">chain</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_entities</span><span class="p">,</span> <span class="nb">list</span><span class="p">(</span><span class="n">other</span><span class="p">))))</span>
+
+
+    <span class="k">def</span> <span class="fm">__iadd__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">other</span><span class="p">):</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_entities</span> <span class="o">=</span> <span class="nb">set</span><span class="p">(</span><span class="n">itertools</span><span class="o">.</span><span class="n">chain</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_entities</span><span class="p">,</span> <span class="nb">list</span><span class="p">(</span><span class="n">other</span><span class="p">)))</span>
+
+        <span class="k">return</span> <span class="bp">self</span>
+
+
+    <span class="nd">@property</span>
+    <span class="k">def</span> <span class="nf">labels</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">for</span> <span class="n">e</span> <span class="ow">in</span> <span class="bp">self</span><span class="p">:</span>
+
+            <span class="k">yield</span> <span class="n">e</span><span class="o">.</span><span class="n">label</span>
+
+
+    <span class="nd">@property</span>
+    <span class="k">def</span> <span class="nf">ids</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">for</span> <span class="n">e</span> <span class="ow">in</span> <span class="bp">self</span><span class="p">:</span>
+
+            <span class="k">yield</span> <span class="n">e</span><span class="o">.</span><span class="n">identifier</span>
+
+
+    <span class="n">identifiers</span> <span class="o">=</span> <span class="n">ids</span>
+
+
+    <span class="nd">@property</span>
+    <span class="k">def</span> <span class="nf">entities</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">for</span> <span class="n">e</span> <span class="ow">in</span> <span class="bp">self</span><span class="p">:</span>
+
+            <span class="k">yield</span> <span class="n">e</span>
+
+
+    <span class="nd">@property</span>
+    <span class="k">def</span> <span class="nf">list_ids</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="nb">list</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">ids</span><span class="p">)</span>
+
+
+    <span class="nd">@property</span>
+    <span class="k">def</span> <span class="nf">list_labels</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="nb">list</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">labels</span><span class="p">)</span>
+
+
+    <span class="nd">@property</span>
+    <span class="k">def</span> <span class="nf">list_entities</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="nb">list</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">entities</span><span class="p">)</span>
+
+
+    <span class="n">l</span> <span class="o">=</span> <span class="n">labels</span>
+    <span class="n">i</span> <span class="o">=</span> <span class="n">ids</span>
+    <span class="n">e</span> <span class="o">=</span> <span class="n">entities</span>
+    <span class="n">ll</span> <span class="o">=</span> <span class="n">list_labels</span>
+    <span class="n">li</span> <span class="o">=</span> <span class="n">list_ids</span>
+    <span class="n">le</span> <span class="o">=</span> <span class="n">list_entities</span></div>
+
+</pre></div>
+
+                </article>
+              
+              
+              
+              
+              
+                <footer class="prev-next-footer">
+                  
+<div class="prev-next-area">
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+    
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+      <br/>
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diff --git a/_modules/pypath/core/enz_sub.html b/_modules/pypath/core/enz_sub.html
new file mode 100644
index 000000000..9980b0f28
--- /dev/null
+++ b/_modules/pypath/core/enz_sub.html
@@ -0,0 +1,1967 @@
+
+<!DOCTYPE html>
+
+
+<html lang="en" data-content_root="../../../" >
+
+  <head>
+    <meta charset="utf-8" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+    <title>pypath.core.enz_sub &#8212; pypath 0.16.9 documentation</title>
+  
+  
+  
+  <script data-cfasync="false">
+    document.documentElement.dataset.mode = localStorage.getItem("mode") || "";
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+      
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+                  
+  <h1>Source code for pypath.core.enz_sub</h1><div class="highlight"><pre>
+<span></span><span class="ch">#!/usr/bin/env python</span>
+<span class="c1"># -*- coding: utf-8 -*-</span>
+
+<span class="c1">#</span>
+<span class="c1">#  This file is part of the `pypath` python module</span>
+<span class="c1">#</span>
+<span class="c1">#  Copyright 2014-2023</span>
+<span class="c1">#  EMBL, EMBL-EBI, Uniklinik RWTH Aachen, Heidelberg University</span>
+<span class="c1">#</span>
+<span class="c1">#  Authors: see the file `README.rst`</span>
+<span class="c1">#  Contact: Dénes Türei (turei.denes@gmail.com)</span>
+<span class="c1">#</span>
+<span class="c1">#  Distributed under the GPLv3 License.</span>
+<span class="c1">#  See accompanying file LICENSE.txt or copy at</span>
+<span class="c1">#      https://www.gnu.org/licenses/gpl-3.0.html</span>
+<span class="c1">#</span>
+<span class="c1">#  Website: https://pypath.omnipathdb.org/</span>
+<span class="c1">#</span>
+
+<span class="kn">from</span> <span class="nn">future.utils</span> <span class="kn">import</span> <span class="n">iteritems</span>
+<span class="kn">from</span> <span class="nn">past.builtins</span> <span class="kn">import</span> <span class="n">xrange</span><span class="p">,</span> <span class="nb">range</span>
+
+<span class="kn">import</span> <span class="nn">sys</span>
+<span class="kn">import</span> <span class="nn">importlib</span> <span class="k">as</span> <span class="nn">imp</span>
+<span class="kn">import</span> <span class="nn">itertools</span>
+<span class="kn">import</span> <span class="nn">collections</span>
+<span class="kn">import</span> <span class="nn">pickle</span>
+<span class="kn">import</span> <span class="nn">traceback</span>
+
+<span class="kn">import</span> <span class="nn">pandas</span> <span class="k">as</span> <span class="nn">pd</span>
+
+<span class="kn">import</span> <span class="nn">pypath.share.common</span> <span class="k">as</span> <span class="nn">common</span>
+<span class="kn">import</span> <span class="nn">pypath_common._constants</span> <span class="k">as</span> <span class="nn">_const</span>
+<span class="kn">import</span> <span class="nn">pypath.utils.mapping</span> <span class="k">as</span> <span class="nn">mapping</span>
+<span class="kn">import</span> <span class="nn">pypath.utils.orthology</span> <span class="k">as</span> <span class="nn">orthology</span>
+<span class="kn">import</span> <span class="nn">pypath.inputs.uniprot</span> <span class="k">as</span> <span class="nn">uniprot_input</span>
+<span class="kn">import</span> <span class="nn">pypath.internals.intera</span> <span class="k">as</span> <span class="nn">intera</span>
+<span class="kn">import</span> <span class="nn">pypath.share.progress</span> <span class="k">as</span> <span class="nn">progress</span>
+<span class="kn">import</span> <span class="nn">pypath.share.session</span> <span class="k">as</span> <span class="nn">session_mod</span>
+<span class="kn">import</span> <span class="nn">pypath.utils.taxonomy</span> <span class="k">as</span> <span class="nn">taxonomy</span>
+<span class="kn">import</span> <span class="nn">pypath.inputs</span> <span class="k">as</span> <span class="nn">inputs</span>
+<span class="kn">import</span> <span class="nn">pypath.core.evidence</span> <span class="k">as</span> <span class="nn">evidence</span>
+<span class="kn">import</span> <span class="nn">pypath.core.entity</span> <span class="k">as</span> <span class="nn">entity</span>
+<span class="kn">import</span> <span class="nn">pypath.resources</span> <span class="k">as</span> <span class="nn">resources</span>
+
+
+<div class="viewcode-block" id="EnzymeSubstrateProcessor">
+<a class="viewcode-back" href="../../../api/pypath.core.enz_sub.EnzymeSubstrateProcessor.html#pypath.core.enz_sub.EnzymeSubstrateProcessor">[docs]</a>
+<span class="k">class</span> <span class="nc">EnzymeSubstrateProcessor</span><span class="p">(</span>
+        <span class="n">orthology</span><span class="o">.</span><span class="n">Proteomes</span><span class="p">,</span>
+        <span class="n">orthology</span><span class="o">.</span><span class="n">SequenceContainer</span>
+    <span class="p">):</span>
+
+
+<div class="viewcode-block" id="EnzymeSubstrateProcessor.__init__">
+<a class="viewcode-back" href="../../../api/pypath.core.enz_sub.EnzymeSubstrateProcessor.html#pypath.core.enz_sub.EnzymeSubstrateProcessor.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">input_param</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">input_method</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">trace</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+            <span class="n">id_type_enzyme</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">id_type_substrate</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">name</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">allow_mixed_organisms</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">organisms_supported</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+            <span class="o">**</span><span class="n">kwargs</span>
+        <span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Processes enzyme-substrate interaction data from various databases.</span>
+<span class="sd">        Provides generators to iterate over these interactions.</span>
+<span class="sd">        For organisms other than human obtains the organism specific</span>
+<span class="sd">        interactions from databases.</span>
+
+<span class="sd">        :param str input_method:</span>
+<span class="sd">            Either a method name in the ``inputs`` module or a database</span>
+<span class="sd">            name e.g. `PhosphoSite` or a callable which returns data in</span>
+<span class="sd">            list of dicts format.</span>
+<span class="sd">        :param int ncbi_tax_id: NCBI Taxonomy ID used at the database lookups.</span>
+<span class="sd">        :param bool trace: Keep data about ambiguous ID mappings and PTM data</span>
+<span class="sd">                           in mismatch with UniProt sequences.</span>
+<span class="sd">        :param pypath.mapping.Mapper: A `Mapper` instance. If `None` a new</span>
+<span class="sd">                                      instance will be created.</span>
+<span class="sd">        :param str id_type_enzyme: The ID type of the enzyme in the database.</span>
+<span class="sd">        :param str id_type_substrate: The ID type of the substrate in the</span>
+<span class="sd">                                      database.</span>
+
+<span class="sd">        :param bool nonhuman_direct_lookup: Use direct lookup at non-human</span>
+<span class="sd">                                            target species.</span>
+<span class="sd">        :param **kwargs: Args to be forwarded to the input method.</span>
+
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">if</span> <span class="ow">not</span> <span class="nb">hasattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">&#39;_logger&#39;</span><span class="p">):</span>
+
+            <span class="n">session_mod</span><span class="o">.</span><span class="n">Logger</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">name</span> <span class="o">=</span> <span class="s1">&#39;enz_sub&#39;</span><span class="p">)</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">mammal_taxa</span> <span class="o">=</span> <span class="p">{</span><span class="mi">9606</span><span class="p">,</span> <span class="mi">10090</span><span class="p">,</span> <span class="mi">10116</span><span class="p">}</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">nomatch</span> <span class="o">=</span> <span class="p">[]</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">kin_ambig</span> <span class="o">=</span> <span class="p">{}</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">sub_ambig</span> <span class="o">=</span> <span class="p">{}</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">input_param</span> <span class="o">=</span> <span class="n">input_param</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">name</span> <span class="o">=</span> <span class="n">name</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">id_type_enzyme</span> <span class="o">=</span> <span class="n">id_type_enzyme</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">id_type_substrate</span> <span class="o">=</span> <span class="n">id_type_substrate</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">allow_mixed_organisms</span> <span class="o">=</span> <span class="n">allow_mixed_organisms</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">input_method</span> <span class="o">=</span> <span class="n">input_method</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">trace</span> <span class="o">=</span> <span class="n">trace</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">organisms_supported</span> <span class="o">=</span> <span class="n">organisms_supported</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">setup</span><span class="p">()</span>
+
+        <span class="n">orthology</span><span class="o">.</span><span class="n">SequenceContainer</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">load_seq</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">ncbi_tax_id</span><span class="p">)</span>
+
+        <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">allow_mixed_organisms</span><span class="p">:</span>
+
+            <span class="k">for</span> <span class="n">taxon</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">mammal_taxa</span><span class="p">:</span>
+
+                <span class="bp">self</span><span class="o">.</span><span class="n">load_seq</span><span class="p">(</span><span class="n">taxon</span> <span class="o">=</span> <span class="n">taxon</span><span class="p">)</span>
+
+        <span class="n">orthology</span><span class="o">.</span><span class="n">Proteomes</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">set_inputargs</span><span class="p">(</span><span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">load_enz_sub</span><span class="p">()</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">setup</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">name</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_get_param</span><span class="p">(</span><span class="s1">&#39;name&#39;</span><span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">id_type_enzyme</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_get_param</span><span class="p">(</span><span class="s1">&#39;id_type_enzyme&#39;</span><span class="p">,</span> <span class="s1">&#39;genesymbol&#39;</span><span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">id_type_substrate</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_get_param</span><span class="p">(</span>
+            <span class="s1">&#39;id_type_substrate&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;genesymbol&#39;</span><span class="p">,</span>
+        <span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">id_type_substrate</span> <span class="o">=</span> <span class="n">common</span><span class="o">.</span><span class="n">to_list</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">id_type_substrate</span><span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_get_param</span><span class="p">(</span><span class="s1">&#39;ncbi_tax_id&#39;</span><span class="p">,</span> <span class="mi">9606</span><span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">organisms_supported</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_get_param</span><span class="p">(</span>
+            <span class="s1">&#39;organisms_supported&#39;</span><span class="p">,</span>
+            <span class="kc">False</span><span class="p">,</span>
+        <span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">allow_mixed_organisms</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_get_param</span><span class="p">(</span>
+            <span class="s1">&#39;allow_mixed_organisms&#39;</span><span class="p">,</span>
+            <span class="kc">False</span><span class="p">,</span>
+        <span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">input_method</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_get_param</span><span class="p">(</span><span class="s1">&#39;input_method&#39;</span><span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">set_method</span><span class="p">()</span>
+
+
+    <span class="k">def</span> <span class="nf">_get_param</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">label</span><span class="p">,</span> <span class="n">default</span> <span class="o">=</span> <span class="kc">None</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="p">(</span>
+            <span class="nb">getattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">label</span><span class="p">)</span> <span class="ow">or</span> <span class="p">(</span>
+                <span class="nb">getattr</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">input_param</span><span class="p">,</span> <span class="n">label</span><span class="p">)</span>
+                    <span class="k">if</span> <span class="nb">hasattr</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">input_param</span><span class="p">,</span> <span class="n">label</span><span class="p">)</span> <span class="k">else</span>
+                <span class="n">default</span>
+            <span class="p">)</span>
+        <span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">load_enz_sub</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_setup</span><span class="p">()</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">load_data</span><span class="p">()</span>
+
+
+    <span class="k">def</span> <span class="nf">reload</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="n">modname</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="vm">__class__</span><span class="o">.</span><span class="vm">__module__</span>
+        <span class="n">mod</span> <span class="o">=</span> <span class="nb">__import__</span><span class="p">(</span><span class="n">modname</span><span class="p">,</span> <span class="n">fromlist</span><span class="o">=</span><span class="p">[</span><span class="n">modname</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;.&#39;</span><span class="p">)[</span><span class="mi">0</span><span class="p">]])</span>
+        <span class="n">imp</span><span class="o">.</span><span class="n">reload</span><span class="p">(</span><span class="n">mod</span><span class="p">)</span>
+        <span class="n">new</span> <span class="o">=</span> <span class="nb">getattr</span><span class="p">(</span><span class="n">mod</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="vm">__class__</span><span class="o">.</span><span class="vm">__name__</span><span class="p">)</span>
+        <span class="nb">setattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">&#39;__class__&#39;</span><span class="p">,</span> <span class="n">new</span><span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">reset_ptmprocessor</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">seq</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span> <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="kc">None</span><span class="p">):</span>
+
+        <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span> <span class="ow">or</span> <span class="bp">self</span><span class="o">.</span><span class="n">ncbi_tax_id</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">set_taxon</span><span class="p">(</span><span class="n">ncbi_tax_id</span><span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">load_seq</span><span class="p">(</span><span class="n">ncbi_tax_id</span><span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">load_data</span><span class="p">()</span>
+
+
+    <span class="k">def</span> <span class="nf">set_taxon</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">ncbi_tax_id</span><span class="p">):</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">_organism_setup</span><span class="p">()</span>
+
+
+<div class="viewcode-block" id="EnzymeSubstrateProcessor.set_method">
+<a class="viewcode-back" href="../../../api/pypath.core.enz_sub.EnzymeSubstrateProcessor.html#pypath.core.enz_sub.EnzymeSubstrateProcessor.set_method">[docs]</a>
+    <span class="k">def</span> <span class="nf">set_method</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Selects the input method.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">def</span> <span class="nf">empty_input</span><span class="p">(</span><span class="o">*</span><span class="n">args</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span> <span class="k">return</span> <span class="p">[]</span>
+
+
+        <span class="c1"># attempting to look up the method in the inputs module</span>
+        <span class="k">if</span> <span class="ow">not</span> <span class="nb">hasattr</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">input_method</span><span class="p">,</span> <span class="s1">&#39;__call__&#39;</span><span class="p">):</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">input_method</span> <span class="o">=</span> <span class="p">(</span>
+                <span class="n">inputs</span><span class="o">.</span><span class="n">get_method</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">input_method</span><span class="p">)</span> <span class="ow">or</span>
+                <span class="n">empty_input</span>
+            <span class="p">)</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">name</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">name</span> <span class="ow">or</span> <span class="bp">self</span><span class="o">.</span><span class="n">input_method</span><span class="o">.</span><span class="vm">__name__</span></div>
+
+
+
+<div class="viewcode-block" id="EnzymeSubstrateProcessor.set_inputargs">
+<a class="viewcode-back" href="../../../api/pypath.core.enz_sub.EnzymeSubstrateProcessor.html#pypath.core.enz_sub.EnzymeSubstrateProcessor.set_inputargs">[docs]</a>
+    <span class="k">def</span> <span class="nf">set_inputargs</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">**</span><span class="n">inputargs</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Sets the arguments to be provided for the input method.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">inputargs</span> <span class="o">=</span> <span class="n">inputargs</span></div>
+
+
+
+<div class="viewcode-block" id="EnzymeSubstrateProcessor.load_data">
+<a class="viewcode-back" href="../../../api/pypath.core.enz_sub.EnzymeSubstrateProcessor.html#pypath.core.enz_sub.EnzymeSubstrateProcessor.load_data">[docs]</a>
+    <span class="k">def</span> <span class="nf">load_data</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Loads the data by the defined input method.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">input_method_name</span> <span class="o">=</span> <span class="s1">&#39;</span><span class="si">%s</span><span class="s1">.</span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="p">(</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">input_method</span><span class="o">.</span><span class="vm">__module__</span><span class="p">,</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">input_method</span><span class="o">.</span><span class="vm">__name__</span><span class="p">,</span>
+        <span class="p">)</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span>
+            <span class="s1">&#39;Calling `</span><span class="si">%s</span><span class="s1">` with arguments </span><span class="si">%s</span><span class="s1">.&#39;</span> <span class="o">%</span> <span class="p">(</span>
+                <span class="n">input_method_name</span><span class="p">,</span>
+                <span class="nb">str</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">inputargs</span><span class="p">)</span>
+            <span class="p">)</span>
+        <span class="p">)</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">data</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">input_method</span><span class="p">(</span><span class="o">**</span><span class="bp">self</span><span class="o">.</span><span class="n">inputargs</span><span class="p">)</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span>
+            <span class="s1">&#39;Loaded data by `</span><span class="si">%s</span><span class="s1">`, resulted </span><span class="si">%u</span><span class="s1"> records.&#39;</span> <span class="o">%</span> <span class="p">(</span>
+                <span class="n">input_method_name</span><span class="p">,</span>
+                <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">data</span><span class="p">),</span>
+            <span class="p">)</span>
+        <span class="p">)</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">_phosphosite_setup</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">if</span> <span class="s1">&#39;strict&#39;</span> <span class="ow">not</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">inputargs</span><span class="p">:</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">inputargs</span><span class="p">[</span><span class="s1">&#39;strict&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="kc">False</span>
+
+        <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">inputargs</span><span class="p">[</span><span class="s1">&#39;organism&#39;</span><span class="p">]</span> <span class="ow">in</span> <span class="n">taxonomy</span><span class="o">.</span><span class="n">taxids</span><span class="p">:</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">inputargs</span><span class="p">[</span><span class="s1">&#39;organism&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="p">(</span>
+                <span class="n">taxonomy</span><span class="o">.</span><span class="n">taxids</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">inputargs</span><span class="p">[</span><span class="s1">&#39;organism&#39;</span><span class="p">]]</span>
+            <span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">_phosphoelm_setup</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">ncbi_tax_id</span> <span class="o">!=</span> <span class="mi">9606</span> <span class="ow">and</span> <span class="s1">&#39;ltp_only&#39;</span> <span class="ow">not</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">inputargs</span><span class="p">:</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">inputargs</span><span class="p">[</span><span class="s1">&#39;ltp_only&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="kc">False</span>
+
+
+    <span class="k">def</span> <span class="nf">_setup</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="n">setupmethod</span> <span class="o">=</span> <span class="s1">&#39;_</span><span class="si">%s</span><span class="s1">_setup&#39;</span> <span class="o">%</span> <span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_organism_setup</span><span class="p">()</span>
+
+        <span class="k">if</span> <span class="nb">hasattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">setupmethod</span><span class="p">):</span>
+
+            <span class="nb">getattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">setupmethod</span><span class="p">)()</span>
+
+
+    <span class="k">def</span> <span class="nf">_organism_setup</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">organisms_supported</span><span class="p">:</span>
+
+            <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">ncbi_tax_id</span> <span class="ow">in</span> <span class="n">taxonomy</span><span class="o">.</span><span class="n">taxa</span><span class="p">:</span>
+
+                <span class="bp">self</span><span class="o">.</span><span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">taxonomy</span><span class="o">.</span><span class="n">taxa</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">ncbi_tax_id</span><span class="p">]</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">inputargs</span><span class="p">[</span><span class="s1">&#39;organism&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">ncbi_tax_id</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">load_proteome</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">ncbi_tax_id</span><span class="p">,</span> <span class="kc">False</span><span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">_process</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">p</span><span class="p">):</span>
+
+        <span class="c1"># human leukocyte antigenes result a result an</span>
+        <span class="c1"># extremely high number of combinations</span>
+        <span class="k">if</span> <span class="p">(</span>
+            <span class="ow">not</span> <span class="n">p</span><span class="p">[</span><span class="s1">&#39;kinase&#39;</span><span class="p">]</span> <span class="ow">or</span> <span class="p">(</span>
+                <span class="nb">isinstance</span><span class="p">(</span><span class="n">p</span><span class="p">[</span><span class="s1">&#39;substrate&#39;</span><span class="p">],</span> <span class="nb">str</span><span class="p">)</span> <span class="ow">and</span>
+                <span class="n">p</span><span class="p">[</span><span class="s1">&#39;substrate&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s1">&#39;HLA&#39;</span><span class="p">)</span>
+            <span class="p">)</span>
+        <span class="p">):</span>
+
+            <span class="k">return</span>
+
+        <span class="k">if</span> <span class="ow">not</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">p</span><span class="p">[</span><span class="s1">&#39;kinase&#39;</span><span class="p">],</span> <span class="nb">list</span><span class="p">):</span>
+            <span class="n">p</span><span class="p">[</span><span class="s1">&#39;kinase&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="p">[</span><span class="n">p</span><span class="p">[</span><span class="s1">&#39;kinase&#39;</span><span class="p">]]</span>
+
+        <span class="n">kinase_ups</span> <span class="o">=</span> <span class="n">mapping</span><span class="o">.</span><span class="n">map_names</span><span class="p">(</span>
+            <span class="n">p</span><span class="p">[</span><span class="s1">&#39;kinase&#39;</span><span class="p">],</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">id_type_enzyme</span><span class="p">,</span>
+            <span class="s1">&#39;uniprot&#39;</span><span class="p">,</span>
+            <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">ncbi_tax_id</span><span class="p">,</span>
+        <span class="p">)</span>
+
+        <span class="n">substrate_ups_all</span> <span class="o">=</span> <span class="nb">set</span><span class="p">()</span>
+
+        <span class="k">for</span> <span class="n">sub_id_type</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">id_type_substrate</span><span class="p">:</span>
+
+            <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">sub_id_type</span><span class="p">,</span> <span class="p">(</span><span class="nb">list</span><span class="p">,</span> <span class="nb">tuple</span><span class="p">)):</span>
+                <span class="n">sub_id_type</span><span class="p">,</span> <span class="n">sub_id_attr</span> <span class="o">=</span> <span class="n">sub_id_type</span>
+            <span class="k">else</span><span class="p">:</span>
+                <span class="n">sub_id_attr</span> <span class="o">=</span> <span class="s1">&#39;substrate&#39;</span>
+
+            <span class="n">substrate_ups_all</span><span class="o">.</span><span class="n">update</span><span class="p">(</span>
+                <span class="nb">set</span><span class="p">(</span>
+                    <span class="n">mapping</span><span class="o">.</span><span class="n">map_name</span><span class="p">(</span>
+                        <span class="n">p</span><span class="p">[</span><span class="n">sub_id_attr</span><span class="p">],</span>
+                        <span class="n">sub_id_type</span><span class="p">,</span>
+                        <span class="s1">&#39;uniprot&#39;</span><span class="p">,</span>
+                        <span class="bp">self</span><span class="o">.</span><span class="n">ncbi_tax_id</span><span class="p">,</span>
+                    <span class="p">)</span>
+                <span class="p">)</span>
+            <span class="p">)</span>
+
+        <span class="c1"># looking up sequences in all isoforms:</span>
+        <span class="n">substrate_ups</span> <span class="o">=</span> <span class="p">[]</span>
+
+        <span class="k">for</span> <span class="n">s</span> <span class="ow">in</span> <span class="n">substrate_ups_all</span><span class="p">:</span>
+
+            <span class="k">if</span> <span class="s1">&#39;substrate_isoform&#39;</span> <span class="ow">in</span> <span class="n">p</span> <span class="ow">and</span> <span class="n">p</span><span class="p">[</span><span class="s1">&#39;substrate_isoform&#39;</span><span class="p">]:</span>
+
+                <span class="n">substrate_ups</span><span class="o">.</span><span class="n">append</span><span class="p">((</span><span class="n">s</span><span class="p">,</span> <span class="n">p</span><span class="p">[</span><span class="s1">&#39;substrate_isoform&#39;</span><span class="p">]))</span>
+
+            <span class="k">else</span><span class="p">:</span>
+
+                <span class="n">se</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">get_seq</span><span class="p">(</span><span class="n">s</span><span class="p">)</span>
+
+                <span class="k">if</span> <span class="n">se</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
+                    <span class="k">continue</span>
+
+                <span class="k">for</span> <span class="n">isof</span> <span class="ow">in</span> <span class="n">se</span><span class="o">.</span><span class="n">isoforms</span><span class="p">():</span>
+
+                    <span class="k">if</span> <span class="s1">&#39;instance&#39;</span> <span class="ow">in</span> <span class="n">p</span> <span class="ow">and</span> <span class="n">p</span><span class="p">[</span><span class="s1">&#39;instance&#39;</span><span class="p">]</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
+
+                        <span class="k">if</span> <span class="n">se</span><span class="o">.</span><span class="n">match</span><span class="p">(</span>
+                            <span class="n">p</span><span class="p">[</span><span class="s1">&#39;instance&#39;</span><span class="p">],</span>
+                            <span class="n">p</span><span class="p">[</span><span class="s1">&#39;start&#39;</span><span class="p">],</span>
+                            <span class="n">p</span><span class="p">[</span><span class="s1">&#39;end&#39;</span><span class="p">],</span>
+                            <span class="n">isoform</span> <span class="o">=</span> <span class="n">isof</span><span class="p">,</span>
+                        <span class="p">):</span>
+
+                            <span class="n">substrate_ups</span><span class="o">.</span><span class="n">append</span><span class="p">((</span><span class="n">s</span><span class="p">,</span> <span class="n">isof</span><span class="p">))</span>
+
+                    <span class="k">else</span><span class="p">:</span>
+
+                        <span class="k">if</span> <span class="n">se</span><span class="o">.</span><span class="n">match</span><span class="p">(</span>
+                            <span class="n">p</span><span class="p">[</span><span class="s1">&#39;resaa&#39;</span><span class="p">],</span>
+                            <span class="n">p</span><span class="p">[</span><span class="s1">&#39;resnum&#39;</span><span class="p">],</span>
+                            <span class="n">isoform</span> <span class="o">=</span> <span class="n">isof</span><span class="p">,</span>
+                        <span class="p">):</span>
+
+                            <span class="n">substrate_ups</span><span class="o">.</span><span class="n">append</span><span class="p">((</span><span class="n">s</span><span class="p">,</span> <span class="n">isof</span><span class="p">))</span>
+
+        <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">trace</span><span class="p">:</span>
+
+            <span class="k">if</span> <span class="n">p</span><span class="p">[</span><span class="s1">&#39;substrate&#39;</span><span class="p">]</span> <span class="ow">not</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">sub_ambig</span><span class="p">:</span>
+
+                <span class="bp">self</span><span class="o">.</span><span class="n">sub_ambig</span><span class="p">[</span><span class="n">p</span><span class="p">[</span><span class="s1">&#39;substrate&#39;</span><span class="p">]]</span> <span class="o">=</span> <span class="n">substrate_ups</span>
+
+            <span class="k">for</span> <span class="n">k</span> <span class="ow">in</span> <span class="n">p</span><span class="p">[</span><span class="s1">&#39;kinase&#39;</span><span class="p">]:</span>
+
+                <span class="k">if</span> <span class="n">k</span> <span class="ow">not</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">kin_ambig</span><span class="p">:</span>
+
+                    <span class="bp">self</span><span class="o">.</span><span class="n">kin_ambig</span><span class="p">[</span><span class="n">k</span><span class="p">]</span> <span class="o">=</span> <span class="n">kinase_ups</span>
+            <span class="c1"># generating report on non matching substrates</span>
+            <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">substrate_ups</span><span class="p">)</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
+
+                <span class="k">for</span> <span class="n">s</span> <span class="ow">in</span> <span class="n">substrate_ups_all</span><span class="p">:</span>
+
+                    <span class="n">se</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">get_seq</span><span class="p">(</span><span class="n">s</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span>
+
+                    <span class="k">if</span> <span class="n">se</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
+                        <span class="k">continue</span>
+
+                    <span class="bp">self</span><span class="o">.</span><span class="n">nomatch</span><span class="o">.</span><span class="n">append</span><span class="p">(</span>
+                        <span class="p">(</span>
+                            <span class="n">s</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span>
+                            <span class="n">s</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span>
+                            <span class="p">(</span>
+                                <span class="n">p</span><span class="p">[</span><span class="s1">&#39;substrate_refseq&#39;</span><span class="p">]</span>
+                                    <span class="k">if</span> <span class="s1">&#39;substrate_refseq&#39;</span> <span class="ow">in</span> <span class="n">p</span> <span class="k">else</span>
+                                <span class="s1">&#39;&#39;</span><span class="p">,</span>
+                                <span class="n">s</span><span class="p">,</span>
+                                <span class="n">p</span><span class="p">[</span><span class="s1">&#39;instance&#39;</span><span class="p">],</span>
+                                <span class="n">se</span><span class="o">.</span><span class="n">get</span><span class="p">(</span>
+                                    <span class="n">p</span><span class="p">[</span><span class="s1">&#39;start&#39;</span><span class="p">],</span>
+                                    <span class="n">p</span><span class="p">[</span><span class="s1">&#39;end&#39;</span><span class="p">]</span>
+                                <span class="p">),</span>
+                            <span class="p">),</span>
+                        <span class="p">)</span>
+                    <span class="p">)</span>
+
+        <span class="c1"># building objects representing the enzyme-substrate interaction(s)</span>
+
+        <span class="k">if</span> <span class="s1">&#39;typ&#39;</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">p</span><span class="p">:</span>
+            <span class="n">p</span><span class="p">[</span><span class="s1">&#39;typ&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="s1">&#39;phosphorylation&#39;</span>
+
+        <span class="n">_resources</span> <span class="o">=</span> <span class="nb">tuple</span><span class="p">(</span>
+            <span class="p">(</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">input_param</span><span class="o">.</span><span class="n">get_via</span><span class="p">(</span><span class="n">name</span><span class="p">)</span>
+                    <span class="k">if</span> <span class="nb">hasattr</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">input_param</span><span class="p">,</span> <span class="s1">&#39;get_via&#39;</span><span class="p">)</span> <span class="k">else</span>
+                <span class="n">name</span>
+            <span class="p">)</span>
+            <span class="k">for</span> <span class="n">name</span> <span class="ow">in</span> <span class="p">(</span>
+                <span class="n">p</span><span class="p">[</span><span class="s1">&#39;databases&#39;</span><span class="p">]</span> <span class="k">if</span> <span class="s1">&#39;databases&#39;</span> <span class="ow">in</span> <span class="n">p</span> <span class="k">else</span> <span class="p">()</span>
+            <span class="p">)</span>
+        <span class="p">)</span>
+        <span class="n">_resources</span> <span class="o">+=</span> <span class="p">(</span>
+            <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">,)</span>
+                <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">input_param</span><span class="p">,</span> <span class="nb">str</span><span class="p">)</span> <span class="k">else</span>
+            <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">input_param</span><span class="p">,)</span>
+        <span class="p">)</span>
+
+        <span class="c1"># collecting the evidences</span>
+        <span class="n">evidences</span> <span class="o">=</span> <span class="n">evidence</span><span class="o">.</span><span class="n">Evidences</span><span class="p">(</span>
+            <span class="n">evidence</span><span class="o">.</span><span class="n">Evidence</span><span class="p">(</span>
+                <span class="n">resource</span> <span class="o">=</span> <span class="n">_res</span><span class="p">,</span>
+                <span class="n">references</span> <span class="o">=</span> <span class="n">p</span><span class="p">[</span><span class="s1">&#39;references&#39;</span><span class="p">]</span> <span class="k">if</span> <span class="s1">&#39;references&#39;</span> <span class="ow">in</span> <span class="n">p</span> <span class="k">else</span> <span class="kc">None</span>
+            <span class="p">)</span>
+            <span class="k">for</span> <span class="n">_res</span> <span class="ow">in</span> <span class="n">_resources</span>
+        <span class="p">)</span>
+
+        <span class="k">for</span> <span class="n">s</span> <span class="ow">in</span> <span class="n">substrate_ups</span><span class="p">:</span>
+
+            <span class="c1"># building the objects representing the substrate</span>
+            <span class="n">se</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">get_seq</span><span class="p">(</span><span class="n">s</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span>
+
+            <span class="k">if</span> <span class="n">se</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
+                <span class="k">continue</span>
+
+            <span class="n">res</span> <span class="o">=</span> <span class="n">intera</span><span class="o">.</span><span class="n">Residue</span><span class="p">(</span>
+                <span class="n">p</span><span class="p">[</span><span class="s1">&#39;resnum&#39;</span><span class="p">],</span>
+                <span class="n">p</span><span class="p">[</span><span class="s1">&#39;resaa&#39;</span><span class="p">],</span>
+                <span class="n">s</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span>
+                <span class="n">isoform</span> <span class="o">=</span> <span class="n">s</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span>
+                <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">ncbi_tax_id</span><span class="p">,</span>
+            <span class="p">)</span>
+
+            <span class="k">if</span> <span class="s1">&#39;instance&#39;</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">p</span> <span class="ow">or</span> <span class="n">p</span><span class="p">[</span><span class="s1">&#39;instance&#39;</span><span class="p">]</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
+
+                <span class="n">reg</span> <span class="o">=</span> <span class="n">se</span><span class="o">.</span><span class="n">get_region</span><span class="p">(</span>
+                    <span class="n">p</span><span class="p">[</span><span class="s1">&#39;resnum&#39;</span><span class="p">],</span>
+                    <span class="n">p</span><span class="p">[</span><span class="s1">&#39;start&#39;</span><span class="p">]</span> <span class="k">if</span> <span class="s1">&#39;start&#39;</span> <span class="ow">in</span> <span class="n">p</span> <span class="k">else</span> <span class="kc">None</span><span class="p">,</span>
+                    <span class="n">p</span><span class="p">[</span><span class="s1">&#39;end&#39;</span><span class="p">]</span> <span class="k">if</span> <span class="s1">&#39;end&#39;</span> <span class="ow">in</span> <span class="n">p</span> <span class="k">else</span> <span class="kc">None</span><span class="p">,</span>
+                    <span class="n">isoform</span> <span class="o">=</span> <span class="n">s</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span>
+                <span class="p">)</span>
+
+                <span class="k">if</span> <span class="n">reg</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
+
+                    <span class="n">p</span><span class="p">[</span><span class="s1">&#39;start&#39;</span><span class="p">],</span> <span class="n">p</span><span class="p">[</span><span class="s1">&#39;end&#39;</span><span class="p">],</span> <span class="n">p</span><span class="p">[</span><span class="s1">&#39;instance&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">reg</span>
+
+            <span class="n">mot</span> <span class="o">=</span> <span class="n">intera</span><span class="o">.</span><span class="n">Motif</span><span class="p">(</span>
+                    <span class="n">s</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span>
+                    <span class="n">p</span><span class="p">[</span><span class="s1">&#39;start&#39;</span><span class="p">],</span>
+                    <span class="n">p</span><span class="p">[</span><span class="s1">&#39;end&#39;</span><span class="p">],</span>
+                    <span class="n">instance</span> <span class="o">=</span> <span class="n">p</span><span class="p">[</span><span class="s1">&#39;instance&#39;</span><span class="p">],</span>
+                    <span class="n">isoform</span> <span class="o">=</span> <span class="n">s</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span>
+                    <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">ncbi_tax_id</span><span class="p">,</span>
+                <span class="p">)</span>
+
+            <span class="n">ptm</span> <span class="o">=</span> <span class="n">intera</span><span class="o">.</span><span class="n">Ptm</span><span class="p">(</span>
+                <span class="n">s</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span>
+                <span class="n">motif</span> <span class="o">=</span> <span class="n">mot</span><span class="p">,</span>
+                <span class="n">residue</span> <span class="o">=</span> <span class="n">res</span><span class="p">,</span>
+                <span class="n">typ</span> <span class="o">=</span> <span class="n">p</span><span class="p">[</span><span class="s1">&#39;typ&#39;</span><span class="p">],</span>
+                <span class="n">evidences</span> <span class="o">=</span> <span class="n">evidences</span><span class="p">,</span>
+                <span class="n">isoform</span> <span class="o">=</span> <span class="n">s</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span>
+                <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">ncbi_tax_id</span><span class="p">,</span>
+            <span class="p">)</span>
+
+            <span class="k">for</span> <span class="n">k</span> <span class="ow">in</span> <span class="n">kinase_ups</span><span class="p">:</span>
+
+                <span class="k">if</span> <span class="p">(</span>
+                    <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">allow_mixed_organisms</span> <span class="ow">and</span> <span class="p">(</span>
+                        <span class="bp">self</span><span class="o">.</span><span class="n">get_taxon</span><span class="p">(</span><span class="n">k</span><span class="p">)</span> <span class="o">!=</span> <span class="bp">self</span><span class="o">.</span><span class="n">ncbi_tax_id</span> <span class="ow">or</span>
+                        <span class="bp">self</span><span class="o">.</span><span class="n">get_taxon</span><span class="p">(</span><span class="n">s</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span> <span class="o">!=</span> <span class="bp">self</span><span class="o">.</span><span class="n">ncbi_tax_id</span>
+                    <span class="p">)</span>
+                <span class="p">):</span>
+                    <span class="k">continue</span>
+
+                <span class="c1"># the enzyme (kinase)</span>
+                <span class="n">dom</span> <span class="o">=</span> <span class="n">intera</span><span class="o">.</span><span class="n">Domain</span><span class="p">(</span>
+                    <span class="n">protein</span> <span class="o">=</span> <span class="n">k</span><span class="p">,</span>
+                    <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">ncbi_tax_id</span><span class="p">,</span>
+                <span class="p">)</span>
+
+                <span class="n">dommot</span> <span class="o">=</span> <span class="n">intera</span><span class="o">.</span><span class="n">DomainMotif</span><span class="p">(</span>
+                    <span class="n">domain</span> <span class="o">=</span> <span class="n">dom</span><span class="p">,</span>
+                    <span class="n">ptm</span> <span class="o">=</span> <span class="n">ptm</span><span class="p">,</span>
+                    <span class="n">evidences</span> <span class="o">=</span> <span class="n">evidences</span><span class="p">,</span>
+                <span class="p">)</span>
+
+                <span class="k">if</span> <span class="nb">hasattr</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">input_param</span><span class="p">,</span> <span class="s1">&#39;extra_attrs&#39;</span><span class="p">):</span>
+
+                    <span class="k">for</span> <span class="n">attr</span><span class="p">,</span> <span class="n">key</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">input_param</span><span class="o">.</span><span class="n">extra_attrs</span><span class="p">):</span>
+
+                        <span class="k">if</span> <span class="n">key</span> <span class="ow">in</span> <span class="n">p</span><span class="p">:</span>
+
+                            <span class="nb">setattr</span><span class="p">(</span><span class="n">dommot</span><span class="p">,</span> <span class="n">attr</span><span class="p">,</span> <span class="n">p</span><span class="p">[</span><span class="n">key</span><span class="p">])</span>
+
+                <span class="k">yield</span> <span class="n">dommot</span>
+
+
+    <span class="k">def</span> <span class="nf">input_is</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">i</span><span class="p">,</span> <span class="n">op</span> <span class="o">=</span> <span class="s1">&#39;__eq__&#39;</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="p">(</span>
+            <span class="nb">type</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">)</span> <span class="ow">in</span> <span class="n">_const</span><span class="o">.</span><span class="n">CHAR_TYPES</span> <span class="ow">and</span>
+            <span class="nb">getattr</span><span class="p">(</span><span class="n">i</span><span class="p">,</span> <span class="n">op</span><span class="p">)(</span><span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="o">.</span><span class="n">lower</span><span class="p">())</span>
+        <span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="fm">__iter__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Iterates through the enzyme-substrate interactions.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">for</span> <span class="n">p</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span><span class="p">:</span>
+
+            <span class="k">for</span> <span class="n">enz_sub</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">_process</span><span class="p">(</span><span class="n">p</span><span class="p">):</span>
+
+                <span class="k">yield</span> <span class="n">enz_sub</span>
+
+
+    <span class="k">def</span> <span class="fm">__len__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">data</span><span class="p">)</span> <span class="k">if</span> <span class="nb">hasattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">&#39;data&#39;</span><span class="p">)</span> <span class="k">else</span> <span class="mi">0</span>
+
+
+    <span class="k">def</span> <span class="fm">__repr__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="s1">&#39;&lt;Enzyme-substrate processor: </span><span class="si">%u</span><span class="s1"> records&gt;&#39;</span> <span class="o">%</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="EnzymeSubstrateOrthologyProcessor">
+<a class="viewcode-back" href="../../../api/pypath.core.enz_sub.EnzymeSubstrateOrthologyProcessor.html#pypath.core.enz_sub.EnzymeSubstrateOrthologyProcessor">[docs]</a>
+<span class="k">class</span> <span class="nc">EnzymeSubstrateOrthologyProcessor</span><span class="p">(</span>
+        <span class="n">orthology</span><span class="o">.</span><span class="n">PtmOrthology</span><span class="p">,</span>
+        <span class="n">EnzymeSubstrateProcessor</span><span class="p">,</span>
+        <span class="n">session_mod</span><span class="o">.</span><span class="n">Logger</span>
+    <span class="p">):</span>
+
+
+<div class="viewcode-block" id="EnzymeSubstrateOrthologyProcessor.__init__">
+<a class="viewcode-back" href="../../../api/pypath.core.enz_sub.EnzymeSubstrateOrthologyProcessor.html#pypath.core.enz_sub.EnzymeSubstrateOrthologyProcessor.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">ncbi_tax_id</span><span class="p">,</span>
+            <span class="n">input_param</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">input_method</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">map_by_orthology_from</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">trace</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+            <span class="n">id_type_enzyme</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">id_type_substrate</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">name</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">orthology_only_swissprot</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
+            <span class="n">ptm_orthology_strict</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+            <span class="o">**</span><span class="n">kwargs</span>
+        <span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Unifies a `pypath.core.enz_sub.EnzymeSubstrateProcessor` and</span>
+<span class="sd">        a `pypath.utils.orthology.PtmOrthology` object to build</span>
+<span class="sd">        a set of enzyme-substrate interactions from a database and</span>
+<span class="sd">        subsequently translate them by orthology to one different organism.</span>
+<span class="sd">        Multiple organism can be chosen as the source of the</span>
+<span class="sd">        enzyme-substrate interactions. For example if you want mouse</span>
+<span class="sd">        interactions, you can translate them from human and from rat.</span>
+<span class="sd">        To get the original mouse interactions themselves, use an</span>
+<span class="sd">        other instance of the `EnzymeSubstrateProcessor`.</span>
+<span class="sd">        To have both the original and the orthology translated set,</span>
+<span class="sd">        and also from multiple databases, whatmore all these merged</span>
+<span class="sd">        into a single set, use the `EnzymeSubstrateAggregator`.</span>
+
+<span class="sd">        :param str input_method: Data source for `EnzymeSubstrateProcessor`.</span>
+<span class="sd">        :param int ncbi_tax_id: The NCBI Taxonomy ID the interactions</span>
+<span class="sd">                                should be translated to.</span>
+<span class="sd">        :param bool orthology_only_swissprot: Use only SwissProt</span>
+<span class="sd">                                             (i.e. not Trembl) at orthology</span>
+<span class="sd">                                             translation.</span>
+<span class="sd">        :param bool ptm_orthology_strict: Use only those homologous PTM pairs</span>
+<span class="sd">                                         which are in PhosphoSite data, i.e.</span>
+<span class="sd">                                         do not look for residues with same</span>
+<span class="sd">                                         offset in protein sequence.</span>
+
+<span class="sd">        See further options at `EnzymeSubstrateProcessor`.</span>
+
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">if</span> <span class="ow">not</span> <span class="nb">hasattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">&#39;_logger&#39;</span><span class="p">):</span>
+
+            <span class="n">session_mod</span><span class="o">.</span><span class="n">Logger</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">name</span> <span class="o">=</span> <span class="s1">&#39;enz_sub_orthology&#39;</span><span class="p">)</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">target_taxon</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">map_by_orthology_from</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="n">map_by_orthology_from</span> <span class="ow">or</span>
+            <span class="p">{</span><span class="mi">9606</span><span class="p">,</span> <span class="mi">10090</span><span class="p">,</span> <span class="mi">10116</span><span class="p">}</span>
+        <span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">map_by_orthology_from</span> <span class="o">=</span> <span class="n">common</span><span class="o">.</span><span class="n">to_set</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">map_by_orthology_from</span><span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">map_by_orthology_from</span><span class="o">.</span><span class="n">discard</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">target_taxon</span><span class="p">)</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">input_param</span> <span class="o">=</span> <span class="n">input_param</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">input_method</span> <span class="o">=</span> <span class="n">input_method</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">trace</span> <span class="o">=</span> <span class="n">trace</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">id_type_enzyme</span> <span class="o">=</span> <span class="n">id_type_enzyme</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">id_type_substrate</span> <span class="o">=</span> <span class="n">id_type_substrate</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">name</span> <span class="o">=</span> <span class="n">name</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">ptmprocargs</span> <span class="o">=</span> <span class="n">kwargs</span>
+
+        <span class="n">orthology</span><span class="o">.</span><span class="n">PtmOrthology</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">target</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">,</span>
+            <span class="n">only_swissprot</span> <span class="o">=</span> <span class="n">orthology_only_swissprot</span><span class="p">,</span>
+            <span class="n">strict</span> <span class="o">=</span> <span class="n">ptm_orthology_strict</span><span class="p">,</span>
+        <span class="p">)</span></div>
+
+
+
+    <span class="k">def</span> <span class="fm">__iter__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Iterates through enzyme-substrate interactions</span>
+<span class="sd">        translated to another organism by orthology.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">for</span> <span class="n">source_taxon</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">map_by_orthology_from</span><span class="p">:</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span>
+                <span class="s1">&#39;Translating enzyme-substrate interactions &#39;</span>
+                <span class="s1">&#39;from organism </span><span class="si">%u</span><span class="s1"> to </span><span class="si">%u</span><span class="s1">.&#39;</span> <span class="o">%</span> <span class="p">(</span>
+                    <span class="n">source_taxon</span><span class="p">,</span>
+                    <span class="bp">self</span><span class="o">.</span><span class="n">target_taxon</span><span class="p">,</span>
+                <span class="p">)</span>
+            <span class="p">)</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">set_default_source</span><span class="p">(</span><span class="n">source_taxon</span><span class="p">)</span>
+
+            <span class="n">EnzymeSubstrateProcessor</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span>
+                <span class="bp">self</span><span class="p">,</span>
+                <span class="n">input_param</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">input_param</span><span class="p">,</span>
+                <span class="n">input_method</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">input_method</span><span class="p">,</span>
+                <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">source_taxon</span><span class="p">,</span>
+                <span class="n">trace</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">trace</span><span class="p">,</span>
+                <span class="n">id_type_enzyme</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">id_type_enzyme</span><span class="p">,</span>
+                <span class="n">id_type_substrate</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">id_type_substrate</span><span class="p">,</span>
+                <span class="n">name</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">,</span>
+                <span class="n">allow_mixed_organisms</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
+                <span class="o">**</span><span class="bp">self</span><span class="o">.</span><span class="n">ptmprocargs</span><span class="p">,</span>
+            <span class="p">)</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span>
+                <span class="s1">&#39;Enzyme-substrate interactions loaded from resource `</span><span class="si">%s</span><span class="s1">` &#39;</span>
+                <span class="s1">&#39;for organism </span><span class="si">%s</span><span class="s1">, </span><span class="si">%u</span><span class="s1"> raw records.&#39;</span> <span class="o">%</span> <span class="p">(</span>
+                    <span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">,</span>
+                    <span class="n">source_taxon</span><span class="p">,</span>
+                    <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="p">),</span>
+                <span class="p">)</span>
+            <span class="p">)</span>
+
+            <span class="k">for</span> <span class="n">es</span> <span class="ow">in</span> <span class="n">EnzymeSubstrateProcessor</span><span class="o">.</span><span class="fm">__iter__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+                <span class="k">for</span> <span class="n">target_es</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">translate</span><span class="p">(</span><span class="n">es</span><span class="p">):</span>
+
+                    <span class="k">yield</span> <span class="n">target_es</span>
+
+
+    <span class="k">def</span> <span class="fm">__repr__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="p">(</span>
+            <span class="s1">&#39;&lt;Enzyme-substrate orthology processor, &#39;</span>
+            <span class="s1">&#39;target taxon: </span><span class="si">%u</span><span class="s1">, source taxon(s): </span><span class="si">%s</span><span class="s1">&gt;&#39;</span> <span class="o">%</span> <span class="p">(</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">target_taxon</span><span class="p">,</span>
+                <span class="s1">&#39;, &#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="nb">str</span><span class="p">(</span><span class="n">tax</span><span class="p">)</span> <span class="k">for</span> <span class="n">tax</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">map_by_orthology_from</span><span class="p">),</span>
+            <span class="p">)</span>
+        <span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="EnzymeSubstrateAggregator">
+<a class="viewcode-back" href="../../../api/pypath.core.enz_sub.EnzymeSubstrateAggregator.html#pypath.core.enz_sub.EnzymeSubstrateAggregator">[docs]</a>
+<span class="k">class</span> <span class="nc">EnzymeSubstrateAggregator</span><span class="p">(</span><span class="n">session_mod</span><span class="o">.</span><span class="n">Logger</span><span class="p">):</span>
+
+
+<div class="viewcode-block" id="EnzymeSubstrateAggregator.__init__">
+<a class="viewcode-back" href="../../../api/pypath.core.enz_sub.EnzymeSubstrateAggregator.html#pypath.core.enz_sub.EnzymeSubstrateAggregator.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span>
+            <span class="n">input_param</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">exclude</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">,</span>
+            <span class="n">map_by_orthology_from</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">trace</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+            <span class="n">orthology_only_swissprot</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
+            <span class="n">ptm_orthology_strict</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+            <span class="n">nonhuman_direct_lookup</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
+            <span class="n">inputargs</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">pickle_file</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+        <span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Docs not written yet.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">session_mod</span><span class="o">.</span><span class="n">Logger</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">name</span> <span class="o">=</span> <span class="s1">&#39;enz_sub&#39;</span><span class="p">)</span>
+
+        <span class="k">for</span> <span class="n">k</span><span class="p">,</span> <span class="n">v</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="nb">locals</span><span class="p">()):</span>
+            <span class="nb">setattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">k</span><span class="p">,</span> <span class="n">v</span><span class="p">)</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">main</span><span class="p">()</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">reload</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="n">modname</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="vm">__class__</span><span class="o">.</span><span class="vm">__module__</span>
+        <span class="n">mod</span> <span class="o">=</span> <span class="nb">__import__</span><span class="p">(</span><span class="n">modname</span><span class="p">,</span> <span class="n">fromlist</span> <span class="o">=</span> <span class="p">[</span><span class="n">modname</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;.&#39;</span><span class="p">)[</span><span class="mi">0</span><span class="p">]])</span>
+        <span class="n">imp</span><span class="o">.</span><span class="n">reload</span><span class="p">(</span><span class="n">mod</span><span class="p">)</span>
+        <span class="n">new</span> <span class="o">=</span> <span class="nb">getattr</span><span class="p">(</span><span class="n">mod</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="vm">__class__</span><span class="o">.</span><span class="vm">__name__</span><span class="p">)</span>
+        <span class="nb">setattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">&#39;__class__&#39;</span><span class="p">,</span> <span class="n">new</span><span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">main</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">pickle_file</span><span class="p">:</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">load_from_pickle</span><span class="p">(</span><span class="n">pickle_file</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">pickle_file</span><span class="p">)</span>
+
+        <span class="k">else</span><span class="p">:</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">build</span><span class="p">()</span>
+
+
+    <span class="k">def</span> <span class="nf">load_from_pickle</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">pickle_file</span> <span class="o">=</span> <span class="kc">None</span><span class="p">):</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span><span class="s1">&#39;Loading from file `</span><span class="si">%s</span><span class="s1">`.&#39;</span> <span class="o">%</span> <span class="n">pickle_file</span><span class="p">)</span>
+
+        <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">pickle_file</span><span class="p">,</span> <span class="s1">&#39;rb&#39;</span><span class="p">)</span> <span class="k">as</span> <span class="n">fp</span><span class="p">:</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">enz_sub</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">references</span> <span class="o">=</span> <span class="n">pickle</span><span class="o">.</span><span class="n">load</span><span class="p">(</span><span class="n">fp</span><span class="p">)</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">update_ptm_lookup_dict</span><span class="p">()</span>
+
+
+    <span class="k">def</span> <span class="nf">save_to_pickle</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">pickle_file</span><span class="p">):</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span><span class="s1">&#39;Saving to file file `</span><span class="si">%s</span><span class="s1">`.&#39;</span> <span class="o">%</span> <span class="n">pickle_file</span><span class="p">)</span>
+
+        <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">pickle_file</span><span class="p">,</span> <span class="s1">&#39;wb&#39;</span><span class="p">)</span> <span class="k">as</span> <span class="n">fp</span><span class="p">:</span>
+
+            <span class="n">pickle</span><span class="o">.</span><span class="n">dump</span><span class="p">(</span>
+                <span class="n">obj</span> <span class="o">=</span> <span class="p">(</span>
+                    <span class="bp">self</span><span class="o">.</span><span class="n">enz_sub</span><span class="p">,</span>
+                    <span class="bp">self</span><span class="o">.</span><span class="n">references</span><span class="p">,</span>
+                <span class="p">),</span>
+                <span class="n">file</span> <span class="o">=</span> <span class="n">fp</span><span class="p">,</span>
+            <span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">build</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">inputargs</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">inputargs</span> <span class="ow">or</span> <span class="p">{}</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">map_by_orthology_from</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="p">(</span>
+                <span class="p">{</span><span class="mi">9606</span><span class="p">,</span> <span class="mi">10090</span><span class="p">,</span> <span class="mi">10116</span><span class="p">}</span>
+                    <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">ncbi_tax_id</span> <span class="o">!=</span> <span class="mi">9606</span> <span class="k">else</span>
+                <span class="nb">set</span><span class="p">()</span>
+            <span class="p">)</span>
+                <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">map_by_orthology_from</span> <span class="ow">is</span> <span class="kc">None</span> <span class="k">else</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">map_by_orthology_from</span>
+        <span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">map_by_orthology_from</span> <span class="o">=</span> <span class="nb">set</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">map_by_orthology_from</span><span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">map_by_orthology_from</span><span class="o">.</span><span class="n">discard</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">ncbi_tax_id</span><span class="p">)</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">set_inputs</span><span class="p">()</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">build_list</span><span class="p">()</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">unique</span><span class="p">()</span>
+
+
+    <span class="k">def</span> <span class="fm">__iter__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">for</span> <span class="n">ptm</span> <span class="ow">in</span> <span class="n">itertools</span><span class="o">.</span><span class="n">chain</span><span class="p">(</span><span class="o">*</span><span class="bp">self</span><span class="o">.</span><span class="n">enz_sub</span><span class="o">.</span><span class="n">values</span><span class="p">()):</span>
+
+            <span class="k">yield</span> <span class="n">ptm</span>
+
+
+    <span class="k">def</span> <span class="fm">__len__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="nb">sum</span><span class="p">([</span><span class="nb">len</span><span class="p">(</span><span class="n">esub</span><span class="p">)</span> <span class="k">for</span> <span class="n">esub</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">enz_sub</span><span class="o">.</span><span class="n">values</span><span class="p">()])</span>
+
+
+    <span class="k">def</span> <span class="fm">__repr__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="s1">&#39;&lt;Enzyme-substrate database: </span><span class="si">%s</span><span class="s1"> relationships&gt;&#39;</span> <span class="o">%</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="fm">__getitem__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">*</span><span class="n">args</span><span class="p">):</span>
+
+        <span class="n">args</span> <span class="o">=</span> <span class="n">args</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">args</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="nb">tuple</span><span class="p">)</span> <span class="k">else</span> <span class="n">args</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">get_enzyme_substrate</span><span class="p">(</span><span class="o">*</span><span class="n">args</span><span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">get_enzyme_substrate</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">enzyme</span><span class="p">,</span> <span class="n">substrate</span><span class="p">):</span>
+
+        <span class="n">enzyme</span> <span class="o">=</span> <span class="n">entity</span><span class="o">.</span><span class="n">Entity</span><span class="p">(</span><span class="n">enzyme</span><span class="p">)</span>
+        <span class="n">substrate</span> <span class="o">=</span> <span class="n">entity</span><span class="o">.</span><span class="n">Entity</span><span class="p">(</span><span class="n">substrate</span><span class="p">)</span>
+
+        <span class="n">key</span> <span class="o">=</span> <span class="p">(</span><span class="n">enzyme</span><span class="p">,</span> <span class="n">substrate</span><span class="p">)</span>
+
+        <span class="k">if</span> <span class="n">key</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">enz_sub</span><span class="p">:</span>
+
+            <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">enz_sub</span><span class="p">[</span><span class="n">key</span><span class="p">]</span>
+
+
+    <span class="k">def</span> <span class="nf">set_inputs</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">input_param</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">input_param</span> <span class="ow">or</span>
+            <span class="n">resources</span><span class="o">.</span><span class="n">get_controller</span><span class="p">()</span><span class="o">.</span><span class="n">collect_enzyme_substrate</span><span class="p">()</span>
+        <span class="p">)</span>
+
+
+<div class="viewcode-block" id="EnzymeSubstrateAggregator.build_list">
+<a class="viewcode-back" href="../../../api/pypath.core.enz_sub.EnzymeSubstrateAggregator.html#pypath.core.enz_sub.EnzymeSubstrateAggregator.build_list">[docs]</a>
+    <span class="k">def</span> <span class="nf">build_list</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Builds a full list of enzyme-substrate interactions from</span>
+<span class="sd">        all the requested sources. This list might contain redundant</span>
+<span class="sd">        elements which later will be merged by `unique`.</span>
+<span class="sd">        This &#39;full list&#39; is organised into a dict by pairs of proteins</span>
+<span class="sd">        in order to make it more efficient to compile a unique set</span>
+<span class="sd">        for each pair.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">def</span> <span class="nf">extend_lists</span><span class="p">(</span><span class="n">enz_sub</span><span class="p">):</span>
+
+            <span class="k">for</span> <span class="n">es</span> <span class="ow">in</span> <span class="n">enz_sub</span><span class="p">:</span>
+
+                <span class="n">key</span> <span class="o">=</span> <span class="p">(</span><span class="n">es</span><span class="o">.</span><span class="n">domain</span><span class="o">.</span><span class="n">protein</span><span class="p">,</span> <span class="n">es</span><span class="o">.</span><span class="n">ptm</span><span class="o">.</span><span class="n">protein</span><span class="p">)</span>
+
+                <span class="k">if</span> <span class="n">key</span> <span class="ow">not</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">enz_sub</span><span class="p">:</span>
+
+                    <span class="bp">self</span><span class="o">.</span><span class="n">enz_sub</span><span class="p">[</span><span class="n">key</span><span class="p">]</span> <span class="o">=</span> <span class="p">[]</span>
+
+                <span class="bp">self</span><span class="o">.</span><span class="n">enz_sub</span><span class="p">[</span><span class="n">key</span><span class="p">]</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">es</span><span class="p">)</span>
+
+                <span class="k">for</span> <span class="n">ev</span> <span class="ow">in</span> <span class="n">es</span><span class="o">.</span><span class="n">evidences</span><span class="p">:</span>
+
+                    <span class="n">resource_key</span> <span class="o">=</span> <span class="p">(</span><span class="n">ev</span><span class="o">.</span><span class="n">resource</span><span class="o">.</span><span class="n">name</span><span class="p">,</span> <span class="n">ev</span><span class="o">.</span><span class="n">resource</span><span class="o">.</span><span class="n">via</span><span class="p">)</span>
+
+                    <span class="bp">self</span><span class="o">.</span><span class="n">references</span><span class="p">[</span><span class="n">resource_key</span><span class="p">][</span><span class="n">es</span><span class="o">.</span><span class="n">key</span><span class="p">()]</span><span class="o">.</span><span class="n">update</span><span class="p">(</span>
+                        <span class="n">ev</span><span class="o">.</span><span class="n">references</span>
+                    <span class="p">)</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span>
+            <span class="s1">&#39;Starting to build enzyme-substrate &#39;</span>
+            <span class="s1">&#39;database for organism `</span><span class="si">%u</span><span class="s1">`.&#39;</span> <span class="o">%</span> <span class="bp">self</span><span class="o">.</span><span class="n">ncbi_tax_id</span>
+        <span class="p">)</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">enz_sub</span> <span class="o">=</span> <span class="p">{}</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">references</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">defaultdict</span><span class="p">(</span>
+            <span class="k">lambda</span><span class="p">:</span> <span class="n">collections</span><span class="o">.</span><span class="n">defaultdict</span><span class="p">(</span><span class="nb">set</span><span class="p">)</span>
+        <span class="p">)</span>
+
+        <span class="k">for</span> <span class="n">input_param</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">input_param</span><span class="p">:</span>
+
+            <span class="n">name</span> <span class="o">=</span> <span class="p">(</span>
+                <span class="n">input_param</span><span class="p">[</span><span class="s1">&#39;name&#39;</span><span class="p">]</span>
+                    <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">input_param</span><span class="p">,</span> <span class="nb">dict</span><span class="p">)</span> <span class="k">else</span>
+                <span class="n">input_param</span><span class="o">.</span><span class="n">name</span>
+            <span class="p">)</span>
+
+            <span class="k">try</span><span class="p">:</span>
+
+                <span class="n">input_method</span> <span class="o">=</span> <span class="p">(</span>
+                    <span class="n">input_param</span><span class="p">[</span><span class="s1">&#39;input_method&#39;</span><span class="p">]</span>
+                        <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">input_param</span><span class="p">,</span> <span class="nb">dict</span><span class="p">)</span> <span class="k">else</span>
+                    <span class="n">input_param</span><span class="o">.</span><span class="n">input_method</span>
+                <span class="p">)</span>
+
+                <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span>
+                    <span class="s1">&#39;Loading enzyme-substrate interactions &#39;</span>
+                    <span class="s1">&#39;from resource `</span><span class="si">%s</span><span class="s1">` by method `</span><span class="si">%s</span><span class="s1">`.&#39;</span> <span class="o">%</span> <span class="p">(</span>
+                        <span class="n">name</span><span class="p">,</span>
+                        <span class="n">input_method</span><span class="p">,</span>
+                    <span class="p">)</span>
+                <span class="p">)</span>
+
+                <span class="n">args</span> <span class="o">=</span> <span class="p">(</span>
+                    <span class="n">input_param</span>
+                        <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">input_param</span><span class="p">,</span> <span class="nb">dict</span><span class="p">)</span> <span class="k">else</span>
+                    <span class="p">{</span><span class="s1">&#39;input_param&#39;</span><span class="p">:</span> <span class="n">input_param</span><span class="p">}</span>
+                <span class="p">)</span>
+
+                <span class="k">if</span> <span class="p">(</span>
+                    <span class="bp">self</span><span class="o">.</span><span class="n">ncbi_tax_id</span> <span class="o">==</span> <span class="mi">9606</span> <span class="ow">or</span> <span class="p">(</span>
+                        <span class="bp">self</span><span class="o">.</span><span class="n">nonhuman_direct_lookup</span> <span class="ow">and</span>
+                        <span class="n">input_param</span><span class="o">.</span><span class="n">organisms_supported</span>
+                    <span class="p">)</span>
+                <span class="p">):</span>
+
+                    <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span>
+                        <span class="s1">&#39;Loading enzyme-substrate interactions &#39;</span>
+                        <span class="s1">&#39;for taxon `</span><span class="si">%u</span><span class="s1">`.&#39;</span> <span class="o">%</span> <span class="bp">self</span><span class="o">.</span><span class="n">ncbi_tax_id</span>
+                    <span class="p">)</span>
+
+                    <span class="n">proc</span> <span class="o">=</span> <span class="n">EnzymeSubstrateProcessor</span><span class="p">(</span>
+                        <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">ncbi_tax_id</span><span class="p">,</span>
+                        <span class="n">trace</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">trace</span><span class="p">,</span>
+                        <span class="o">**</span><span class="n">args</span><span class="p">,</span>
+                    <span class="p">)</span>
+
+                    <span class="n">extend_lists</span><span class="p">(</span><span class="n">proc</span><span class="o">.</span><span class="fm">__iter__</span><span class="p">())</span>
+
+                <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">map_by_orthology_from</span><span class="p">:</span>
+
+                    <span class="n">source_taxons_str</span> <span class="o">=</span> <span class="s1">&#39;, &#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span>
+                        <span class="s1">&#39;</span><span class="si">%u</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="n">tax</span> <span class="k">for</span> <span class="n">tax</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">map_by_orthology_from</span>
+                    <span class="p">)</span>
+
+                    <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span>
+                        <span class="s1">&#39;Mapping `</span><span class="si">%s</span><span class="s1">` by orthology from taxons </span><span class="si">%s</span><span class="s1"> to </span><span class="si">%u</span><span class="s1">.&#39;</span> <span class="o">%</span> <span class="p">(</span>
+                            <span class="n">input_method</span><span class="p">,</span>
+                            <span class="n">source_taxons_str</span><span class="p">,</span>
+                            <span class="bp">self</span><span class="o">.</span><span class="n">ncbi_tax_id</span><span class="p">,</span>
+                        <span class="p">)</span>
+                    <span class="p">)</span>
+
+                    <span class="n">proc</span> <span class="o">=</span> <span class="n">EnzymeSubstrateOrthologyProcessor</span><span class="p">(</span>
+                        <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">ncbi_tax_id</span><span class="p">,</span>
+                        <span class="n">map_by_orthology_from</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">map_by_orthology_from</span><span class="p">,</span>
+                        <span class="n">trace</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">trace</span><span class="p">,</span>
+                        <span class="n">orthology_only_swissprot</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">orthology_only_swissprot</span><span class="p">,</span>
+                        <span class="n">ptm_orthology_strict</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">ptm_orthology_strict</span><span class="p">,</span>
+                        <span class="o">**</span><span class="n">args</span>
+                    <span class="p">)</span>
+
+                    <span class="n">extend_lists</span><span class="p">(</span><span class="n">proc</span><span class="o">.</span><span class="fm">__iter__</span><span class="p">())</span>
+
+                    <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span>
+                        <span class="s1">&#39;Finished translating `</span><span class="si">%s</span><span class="s1">` by orthology &#39;</span>
+                        <span class="s1">&#39;from </span><span class="si">%s</span><span class="s1"> to </span><span class="si">%u</span><span class="s1">.&#39;</span> <span class="o">%</span> <span class="p">(</span>
+                            <span class="n">input_method</span><span class="p">,</span>
+                            <span class="n">source_taxons_str</span><span class="p">,</span>
+                            <span class="bp">self</span><span class="o">.</span><span class="n">ncbi_tax_id</span><span class="p">,</span>
+                        <span class="p">)</span>
+                    <span class="p">)</span>
+
+                <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span>
+                    <span class="s1">&#39;Finished loading enzyme-substrate data &#39;</span>
+                    <span class="s1">&#39;from resource `</span><span class="si">%s</span><span class="s1">`.&#39;</span> <span class="o">%</span> <span class="n">name</span>
+                <span class="p">)</span>
+
+            <span class="k">except</span> <span class="ne">Exception</span> <span class="k">as</span> <span class="n">e</span><span class="p">:</span>
+
+                <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span><span class="s1">&#39;Failed to load resource `</span><span class="si">%s</span><span class="s1">`.&#39;</span> <span class="o">%</span> <span class="n">name</span><span class="p">)</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">_log_traceback</span><span class="p">()</span>
+
+                <span class="k">try</span><span class="p">:</span>
+
+                    <span class="n">traceback</span><span class="o">.</span><span class="n">print_tb</span><span class="p">(</span>
+                        <span class="n">e</span><span class="o">.</span><span class="n">__traceback__</span><span class="p">,</span>
+                        <span class="n">file</span> <span class="o">=</span> <span class="n">sys</span><span class="o">.</span><span class="n">stdout</span><span class="p">,</span>
+                    <span class="p">)</span>
+
+                <span class="k">except</span> <span class="ne">Exception</span> <span class="k">as</span> <span class="n">e</span><span class="p">:</span>
+
+                    <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span><span class="s1">&#39;Failed handling exception.&#39;</span><span class="p">)</span>
+                    <span class="bp">self</span><span class="o">.</span><span class="n">_log_traceback</span><span class="p">()</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">references</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">references</span><span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">update_ptm_lookup_dict</span><span class="p">()</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span>
+            <span class="s1">&#39;Finished building enzyme-substrate database &#39;</span>
+            <span class="s1">&#39;for organism `</span><span class="si">%u</span><span class="s1">`, resulted </span><span class="si">%u</span><span class="s1"> relationships.&#39;</span> <span class="o">%</span> <span class="p">(</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">ncbi_tax_id</span><span class="p">,</span>
+                <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="p">),</span>
+            <span class="p">)</span>
+        <span class="p">)</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">update_ptm_lookup_dict</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">ptm_to_enzyme</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">defaultdict</span><span class="p">(</span><span class="nb">set</span><span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">ptms</span> <span class="o">=</span> <span class="p">{}</span>
+
+        <span class="k">for</span> <span class="p">(</span><span class="n">enz</span><span class="p">,</span> <span class="n">sub</span><span class="p">),</span> <span class="n">ptms</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">enz_sub</span><span class="p">):</span>
+
+            <span class="k">for</span> <span class="n">ptm</span> <span class="ow">in</span> <span class="n">ptms</span><span class="p">:</span>
+
+                <span class="bp">self</span><span class="o">.</span><span class="n">ptm_to_enzyme</span><span class="p">[</span><span class="n">ptm</span><span class="o">.</span><span class="n">ptm</span><span class="p">]</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">enz</span><span class="p">)</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">ptms</span><span class="p">[</span><span class="n">ptm</span><span class="o">.</span><span class="n">ptm</span><span class="p">]</span> <span class="o">=</span> <span class="n">ptm</span><span class="o">.</span><span class="n">ptm</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">ptm_to_enzyme</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">ptm_to_enzyme</span><span class="p">)</span>
+
+
+<div class="viewcode-block" id="EnzymeSubstrateAggregator.unique">
+<a class="viewcode-back" href="../../../api/pypath.core.enz_sub.EnzymeSubstrateAggregator.html#pypath.core.enz_sub.EnzymeSubstrateAggregator.unique">[docs]</a>
+    <span class="k">def</span> <span class="nf">unique</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Merges the redundant elements of the interaction list.</span>
+<span class="sd">        Elements are redundant if they agree in all their attributes</span>
+<span class="sd">        except the sources, references and isoforms.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">unique_list</span> <span class="o">=</span> <span class="nb">set</span><span class="p">()</span>
+
+        <span class="k">for</span> <span class="n">key</span><span class="p">,</span> <span class="n">enz_sub</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">enz_sub</span><span class="p">):</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">enz_sub</span><span class="p">[</span><span class="n">key</span><span class="p">]</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">uniq_enz_sub</span><span class="p">(</span><span class="n">enz_sub</span><span class="p">)</span></div>
+
+
+
+    <span class="nd">@staticmethod</span>
+    <span class="k">def</span> <span class="nf">uniq_enz_sub</span><span class="p">(</span><span class="n">enz_sub</span><span class="p">):</span>
+
+        <span class="n">enz_sub_uniq</span> <span class="o">=</span> <span class="p">[]</span>
+
+        <span class="k">for</span> <span class="n">es</span> <span class="ow">in</span> <span class="n">enz_sub</span><span class="p">:</span>
+
+            <span class="n">merged</span> <span class="o">=</span> <span class="kc">False</span>
+
+            <span class="k">for</span> <span class="n">i</span><span class="p">,</span> <span class="n">es_u</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">enz_sub_uniq</span><span class="p">):</span>
+
+                <span class="k">if</span> <span class="n">es</span> <span class="o">==</span> <span class="n">es_u</span><span class="p">:</span>
+
+                    <span class="n">enz_sub_uniq</span><span class="p">[</span><span class="n">i</span><span class="p">]</span><span class="o">.</span><span class="n">merge</span><span class="p">(</span><span class="n">es</span><span class="p">)</span>
+                    <span class="n">merged</span> <span class="o">=</span> <span class="kc">True</span>
+
+            <span class="k">if</span> <span class="ow">not</span> <span class="n">merged</span><span class="p">:</span>
+
+                <span class="n">enz_sub_uniq</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">es</span><span class="p">)</span>
+
+        <span class="k">return</span> <span class="n">enz_sub_uniq</span>
+
+
+    <span class="k">def</span> <span class="nf">make_df</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">tax_id</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span> <span class="n">resources_only_primary</span> <span class="o">=</span> <span class="kc">False</span><span class="p">):</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span><span class="s1">&#39;Creating enzyme-substrate interaction data frame.&#39;</span><span class="p">)</span>
+
+
+        <span class="n">hdr</span> <span class="o">=</span> <span class="p">[</span>
+            <span class="s1">&#39;enzyme&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;enzyme_genesymbol&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;substrate&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;substrate_genesymbol&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;isoforms&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;residue_type&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;residue_offset&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;modification&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;sources&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;references&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;curation_effort&#39;</span><span class="p">,</span>
+        <span class="p">]</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">df</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">(</span>
+            <span class="p">[</span>
+                <span class="n">dm</span><span class="o">.</span><span class="n">get_line</span><span class="p">(</span><span class="n">resources_only_primary</span> <span class="o">=</span> <span class="n">resources_only_primary</span><span class="p">)</span>
+                <span class="k">for</span> <span class="n">dm</span> <span class="ow">in</span> <span class="bp">self</span>
+            <span class="p">],</span>
+            <span class="n">columns</span> <span class="o">=</span> <span class="n">hdr</span><span class="p">,</span>
+        <span class="p">)</span><span class="o">.</span><span class="n">astype</span><span class="p">(</span>
+            <span class="p">{</span>
+                <span class="s1">&#39;enzyme&#39;</span><span class="p">:</span> <span class="s1">&#39;category&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;substrate&#39;</span><span class="p">:</span> <span class="s1">&#39;category&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;isoforms&#39;</span><span class="p">:</span> <span class="s1">&#39;category&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;residue_type&#39;</span><span class="p">:</span> <span class="s1">&#39;category&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;residue_offset&#39;</span><span class="p">:</span> <span class="s1">&#39;int32&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;modification&#39;</span><span class="p">:</span> <span class="s1">&#39;category&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;sources&#39;</span><span class="p">:</span> <span class="s1">&#39;category&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;references&#39;</span><span class="p">:</span> <span class="s1">&#39;category&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;curation_effort&#39;</span><span class="p">:</span> <span class="s1">&#39;int32&#39;</span><span class="p">,</span>
+            <span class="p">}</span>
+        <span class="p">)</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">df</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">df</span><span class="o">.</span><span class="n">loc</span><span class="p">[:,</span><span class="n">hdr</span><span class="p">]</span>
+
+        <span class="k">if</span> <span class="n">tax_id</span><span class="p">:</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">df</span><span class="p">[</span><span class="s1">&#39;ncbi_tax_id&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">ncbi_tax_id</span><span class="p">]</span> <span class="o">*</span> <span class="bp">self</span><span class="o">.</span><span class="n">df</span><span class="o">.</span><span class="n">shape</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span>
+            <span class="s1">&#39;Created enzyme-substrate interaction data frame. &#39;</span>
+            <span class="s1">&#39;Memory usage: </span><span class="si">%s</span><span class="s1">.&#39;</span> <span class="o">%</span> <span class="n">common</span><span class="o">.</span><span class="n">df_memory_usage</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">df</span><span class="p">)</span>
+        <span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">export_table</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">fname</span><span class="p">):</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">make_df</span><span class="p">()</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">df</span><span class="o">.</span><span class="n">to_csv</span><span class="p">(</span><span class="n">fname</span><span class="p">,</span> <span class="n">sep</span> <span class="o">=</span> <span class="s1">&#39;</span><span class="se">\t</span><span class="s1">&#39;</span><span class="p">,</span> <span class="n">index</span> <span class="o">=</span> <span class="kc">False</span><span class="p">)</span>
+
+
+<div class="viewcode-block" id="EnzymeSubstrateAggregator.assign_to_network">
+<a class="viewcode-back" href="../../../api/pypath.core.enz_sub.EnzymeSubstrateAggregator.html#pypath.core.enz_sub.EnzymeSubstrateAggregator.assign_to_network">[docs]</a>
+    <span class="k">def</span> <span class="nf">assign_to_network</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">pa</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Assigns enzyme-substrate interactions to the edges of a</span>
+<span class="sd">        network in a py:class:``pypath.legacy.main.PyPath`` instance.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">pa</span><span class="o">.</span><span class="n">update_vname</span><span class="p">()</span>
+
+        <span class="k">if</span> <span class="s1">&#39;ptm&#39;</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">pa</span><span class="o">.</span><span class="n">graph</span><span class="o">.</span><span class="n">es</span><span class="o">.</span><span class="n">attributes</span><span class="p">():</span>
+            <span class="n">pa</span><span class="o">.</span><span class="n">graph</span><span class="o">.</span><span class="n">es</span><span class="p">[</span><span class="s1">&#39;ptm&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="p">[[]</span> <span class="k">for</span> <span class="n">_</span> <span class="ow">in</span> <span class="n">pa</span><span class="o">.</span><span class="n">graph</span><span class="o">.</span><span class="n">es</span><span class="p">]</span>
+
+        <span class="k">for</span> <span class="n">key</span><span class="p">,</span> <span class="n">ptms</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">enz_sub</span><span class="p">):</span>
+
+            <span class="n">nodes</span> <span class="o">=</span> <span class="n">pa</span><span class="o">.</span><span class="n">get_node_pair</span><span class="p">(</span><span class="n">key</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">key</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span>
+                    <span class="n">directed</span> <span class="o">=</span> <span class="n">pa</span><span class="o">.</span><span class="n">graph</span><span class="o">.</span><span class="n">is_directed</span><span class="p">())</span>
+
+            <span class="n">e</span> <span class="o">=</span> <span class="kc">None</span>
+
+            <span class="k">if</span> <span class="n">nodes</span><span class="p">:</span>
+                <span class="n">e</span> <span class="o">=</span> <span class="n">pa</span><span class="o">.</span><span class="n">graph</span><span class="o">.</span><span class="n">get_eid</span><span class="p">(</span>
+                    <span class="n">nodes</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">nodes</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span> <span class="n">error</span> <span class="o">=</span> <span class="kc">False</span><span class="p">)</span>
+
+            <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">e</span><span class="p">,</span> <span class="nb">int</span><span class="p">)</span> <span class="ow">and</span> <span class="n">e</span> <span class="o">&gt;</span> <span class="mi">0</span><span class="p">:</span>
+
+                <span class="k">if</span> <span class="n">pa</span><span class="o">.</span><span class="n">graph</span><span class="o">.</span><span class="n">es</span><span class="p">[</span><span class="n">e</span><span class="p">][</span><span class="s1">&#39;ptm&#39;</span><span class="p">]</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
+                    <span class="n">pa</span><span class="o">.</span><span class="n">graph</span><span class="o">.</span><span class="n">es</span><span class="p">[</span><span class="n">e</span><span class="p">][</span><span class="s1">&#39;ptm&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="p">[]</span>
+
+                <span class="n">pa</span><span class="o">.</span><span class="n">graph</span><span class="o">.</span><span class="n">es</span><span class="p">[</span><span class="n">e</span><span class="p">][</span><span class="s1">&#39;ptm&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">extend</span><span class="p">(</span><span class="n">ptms</span><span class="p">)</span></div>
+
+
+
+    <span class="nd">@property</span>
+    <span class="k">def</span> <span class="nf">resources</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="nb">set</span><span class="o">.</span><span class="n">union</span><span class="p">(</span><span class="o">*</span><span class="p">(</span>
+            <span class="n">es</span><span class="o">.</span><span class="n">evidences</span><span class="o">.</span><span class="n">get_resource_names_via</span><span class="p">(</span><span class="n">via</span> <span class="o">=</span> <span class="kc">None</span><span class="p">)</span>
+            <span class="k">for</span> <span class="n">es</span> <span class="ow">in</span> <span class="bp">self</span>
+        <span class="p">))</span>
+
+
+    <span class="nd">@property</span>
+    <span class="k">def</span> <span class="nf">resources_sorted</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="nb">sorted</span><span class="p">(</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">resources</span><span class="p">,</span>
+            <span class="n">key</span> <span class="o">=</span> <span class="k">lambda</span> <span class="n">res</span><span class="p">:</span> <span class="p">(</span><span class="n">res</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="s1">&#39;&#39;</span><span class="p">)</span> <span class="k">if</span> <span class="n">res</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="ow">is</span> <span class="kc">None</span> <span class="k">else</span> <span class="n">res</span>
+        <span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">update_summaries</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">collect_args</span> <span class="o">=</span> <span class="kc">None</span><span class="p">):</span>
+
+        <span class="n">collect_args</span> <span class="o">=</span> <span class="n">collect_args</span> <span class="ow">or</span> <span class="p">{</span><span class="s1">&#39;via&#39;</span><span class="p">:</span> <span class="kc">False</span><span class="p">}</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">summaries</span> <span class="o">=</span> <span class="p">{}</span>
+
+        <span class="n">resources</span> <span class="o">=</span> <span class="p">[</span>
+            <span class="n">res</span> <span class="k">for</span> <span class="n">res</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">resources_sorted</span>
+            <span class="k">if</span> <span class="p">(</span>
+                <span class="n">res</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="ow">is</span> <span class="kc">None</span> <span class="ow">or</span>
+                <span class="s1">&#39;via&#39;</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">collect_args</span> <span class="ow">or</span>
+                <span class="n">collect_args</span><span class="p">[</span><span class="s1">&#39;via&#39;</span><span class="p">]</span> <span class="o">!=</span> <span class="kc">False</span>
+            <span class="p">)</span>
+        <span class="p">]</span>
+
+        <span class="n">refs_by_resource</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">(</span>
+            <span class="p">(</span>
+                <span class="n">resource</span><span class="p">,</span>
+                <span class="nb">set</span><span class="o">.</span><span class="n">union</span><span class="p">(</span>
+                    <span class="o">*</span><span class="n">itertools</span><span class="o">.</span><span class="n">chain</span><span class="p">(</span>
+                        <span class="bp">self</span><span class="o">.</span><span class="n">references</span><span class="p">[</span><span class="n">resource</span><span class="p">]</span><span class="o">.</span><span class="n">values</span><span class="p">()</span>
+                    <span class="p">)</span>
+                <span class="p">)</span>
+            <span class="p">)</span>
+            <span class="k">for</span> <span class="n">resource</span> <span class="ow">in</span> <span class="n">resources</span>
+        <span class="p">)</span>
+        <span class="n">curation_effort_by_resource</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">(</span>
+            <span class="p">(</span>
+                <span class="n">resource</span><span class="p">,</span>
+                <span class="p">{</span>
+                    <span class="n">key</span> <span class="o">+</span> <span class="p">(</span><span class="n">ref</span><span class="p">,)</span>
+                    <span class="k">for</span> <span class="n">key</span><span class="p">,</span> <span class="n">refs</span> <span class="ow">in</span>
+                    <span class="n">itertools</span><span class="o">.</span><span class="n">chain</span><span class="p">(</span>
+                        <span class="n">iteritems</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">references</span><span class="p">[</span><span class="n">resource</span><span class="p">])</span>
+                    <span class="p">)</span>
+                    <span class="k">for</span> <span class="n">ref</span> <span class="ow">in</span> <span class="n">refs</span>
+                <span class="p">}</span>
+            <span class="p">)</span>
+            <span class="k">for</span> <span class="n">resource</span> <span class="ow">in</span> <span class="n">resources</span>
+        <span class="p">)</span>
+
+        <span class="n">resources_sorted</span> <span class="o">=</span> <span class="nb">sorted</span><span class="p">(</span><span class="n">resources</span><span class="p">)</span>
+
+        <span class="k">for</span> <span class="n">resource</span> <span class="ow">in</span> <span class="n">resources</span><span class="p">:</span>
+
+            <span class="n">n_total</span> <span class="o">=</span> <span class="nb">sum</span><span class="p">(</span>
+                <span class="mi">1</span>
+                <span class="k">for</span> <span class="n">es</span> <span class="ow">in</span> <span class="bp">self</span>
+                <span class="k">if</span> <span class="n">resource</span> <span class="ow">in</span> <span class="n">es</span><span class="o">.</span><span class="n">evidences</span><span class="o">.</span><span class="n">get_resource_names</span><span class="p">(</span><span class="o">**</span><span class="n">collect_args</span><span class="p">)</span>
+            <span class="p">)</span>
+
+            <span class="n">n_unique</span> <span class="o">=</span> <span class="nb">sum</span><span class="p">(</span>
+                <span class="mi">1</span> <span class="k">for</span> <span class="n">es</span> <span class="ow">in</span> <span class="bp">self</span>
+                <span class="k">if</span> <span class="p">(</span>
+                    <span class="n">resource</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="ow">in</span> <span class="n">es</span><span class="o">.</span><span class="n">evidences</span> <span class="ow">and</span>
+                    <span class="n">es</span><span class="o">.</span><span class="n">evidences</span><span class="o">.</span><span class="n">count_resources</span><span class="p">(</span><span class="o">**</span><span class="n">collect_args</span><span class="p">)</span> <span class="o">==</span> <span class="mi">1</span>
+                <span class="p">)</span>
+            <span class="p">)</span>
+            <span class="n">n_shared</span> <span class="o">=</span> <span class="nb">sum</span><span class="p">(</span>
+                <span class="mi">1</span> <span class="k">for</span> <span class="n">es</span> <span class="ow">in</span> <span class="bp">self</span>
+                <span class="k">if</span> <span class="p">(</span>
+                    <span class="n">resource</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="ow">in</span> <span class="n">es</span><span class="o">.</span><span class="n">evidences</span> <span class="ow">and</span>
+                    <span class="n">es</span><span class="o">.</span><span class="n">evidences</span><span class="o">.</span><span class="n">count_resources</span><span class="p">(</span><span class="o">**</span><span class="n">collect_args</span><span class="p">)</span> <span class="o">&gt;</span> <span class="mi">1</span>
+                <span class="p">)</span>
+            <span class="p">)</span>
+
+            <span class="n">curation_effort</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="n">curation_effort_by_resource</span><span class="p">[</span><span class="n">resource</span><span class="p">])</span>
+            <span class="n">ce_others</span> <span class="o">=</span> <span class="nb">set</span><span class="o">.</span><span class="n">union</span><span class="p">(</span><span class="o">*</span><span class="p">(</span>
+                <span class="n">ce</span>
+                <span class="k">for</span> <span class="n">res</span><span class="p">,</span> <span class="n">ce</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="n">curation_effort_by_resource</span><span class="p">)</span>
+                <span class="k">if</span> <span class="n">res</span> <span class="o">!=</span> <span class="n">resource</span>
+            <span class="p">))</span>
+            <span class="n">curation_effort_shared</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span>
+                <span class="n">curation_effort_by_resource</span><span class="p">[</span><span class="n">resource</span><span class="p">]</span> <span class="o">&amp;</span>
+                <span class="n">ce_others</span>
+            <span class="p">)</span>
+            <span class="n">curation_effort_unique</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span>
+                <span class="n">curation_effort_by_resource</span><span class="p">[</span><span class="n">resource</span><span class="p">]</span> <span class="o">-</span>
+                <span class="n">ce_others</span>
+            <span class="p">)</span>
+
+            <span class="n">references</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="n">refs_by_resource</span><span class="p">[</span><span class="n">resource</span><span class="p">])</span>
+            <span class="n">refs_others</span> <span class="o">=</span> <span class="nb">set</span><span class="o">.</span><span class="n">union</span><span class="p">(</span><span class="o">*</span><span class="p">(</span>
+                <span class="n">refs</span>
+                <span class="k">for</span> <span class="n">res</span><span class="p">,</span> <span class="n">refs</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="n">refs_by_resource</span><span class="p">)</span>
+                <span class="k">if</span> <span class="n">res</span> <span class="o">!=</span> <span class="n">resource</span>
+            <span class="p">))</span>
+            <span class="n">references_shared</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="n">refs_by_resource</span><span class="p">[</span><span class="n">resource</span><span class="p">]</span> <span class="o">&amp;</span> <span class="n">refs_others</span><span class="p">)</span>
+            <span class="n">references_unique</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="n">refs_by_resource</span><span class="p">[</span><span class="n">resource</span><span class="p">]</span> <span class="o">-</span> <span class="n">refs_others</span><span class="p">)</span>
+
+            <span class="n">enzymes</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="nb">set</span><span class="p">(</span>
+                <span class="n">es</span><span class="o">.</span><span class="n">domain</span><span class="o">.</span><span class="n">protein</span>
+                <span class="k">for</span> <span class="n">es</span> <span class="ow">in</span> <span class="bp">self</span>
+                <span class="k">if</span> <span class="n">resource</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="ow">in</span> <span class="n">es</span><span class="o">.</span><span class="n">evidences</span>
+            <span class="p">))</span>
+            <span class="n">substrates</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="nb">set</span><span class="p">(</span>
+                <span class="n">es</span><span class="o">.</span><span class="n">ptm</span><span class="o">.</span><span class="n">protein</span>
+                <span class="k">for</span> <span class="n">es</span> <span class="ow">in</span> <span class="bp">self</span>
+                <span class="k">if</span> <span class="n">resource</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="ow">in</span> <span class="n">es</span><span class="o">.</span><span class="n">evidences</span>
+            <span class="p">))</span>
+
+            <span class="n">modification_types</span> <span class="o">=</span> <span class="s1">&#39;, &#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span>
+                <span class="p">(</span>
+                    <span class="s1">&#39;</span><span class="si">%s</span><span class="s1"> (</span><span class="si">%u</span><span class="s1">)&#39;</span> <span class="o">%</span> <span class="p">(</span><span class="n">typ</span><span class="p">,</span> <span class="n">cnt</span><span class="p">)</span>
+                    <span class="k">for</span> <span class="n">typ</span><span class="p">,</span> <span class="n">cnt</span> <span class="ow">in</span>
+                    <span class="nb">sorted</span><span class="p">(</span>
+                        <span class="n">iteritems</span><span class="p">(</span><span class="n">collections</span><span class="o">.</span><span class="n">Counter</span><span class="p">(</span>
+                            <span class="n">es</span><span class="o">.</span><span class="n">ptm</span><span class="o">.</span><span class="n">typ</span>
+                            <span class="k">for</span> <span class="n">es</span> <span class="ow">in</span> <span class="bp">self</span>
+                            <span class="k">if</span> <span class="n">resource</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="ow">in</span> <span class="n">es</span><span class="o">.</span><span class="n">evidences</span>
+                        <span class="p">)),</span>
+                        <span class="n">key</span> <span class="o">=</span> <span class="k">lambda</span> <span class="n">type_cnt</span><span class="p">:</span> <span class="n">type_cnt</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span>
+                        <span class="n">reverse</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
+                    <span class="p">)</span>
+                    <span class="k">if</span> <span class="n">typ</span>
+                <span class="p">)</span>
+            <span class="p">)</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">summaries</span><span class="p">[</span><span class="n">resource</span><span class="p">]</span> <span class="o">=</span> <span class="p">{</span>
+                <span class="s1">&#39;name&#39;</span><span class="p">:</span> <span class="n">resource</span><span class="p">,</span>
+                <span class="s1">&#39;n_es_total&#39;</span><span class="p">:</span> <span class="n">n_total</span><span class="p">,</span>
+                <span class="s1">&#39;n_es_unique&#39;</span><span class="p">:</span> <span class="n">n_unique</span><span class="p">,</span>
+                <span class="s1">&#39;n_es_shared&#39;</span><span class="p">:</span> <span class="n">n_shared</span><span class="p">,</span>
+                <span class="s1">&#39;n_enzymes&#39;</span><span class="p">:</span> <span class="n">enzymes</span><span class="p">,</span>
+                <span class="s1">&#39;n_substrates&#39;</span><span class="p">:</span> <span class="n">substrates</span><span class="p">,</span>
+                <span class="s1">&#39;references&#39;</span><span class="p">:</span> <span class="n">references</span><span class="p">,</span>
+                <span class="s1">&#39;references_unique&#39;</span><span class="p">:</span> <span class="n">references_unique</span><span class="p">,</span>
+                <span class="s1">&#39;references_shared&#39;</span><span class="p">:</span> <span class="n">references_shared</span><span class="p">,</span>
+                <span class="s1">&#39;curation_effort&#39;</span><span class="p">:</span> <span class="n">curation_effort</span><span class="p">,</span>
+                <span class="s1">&#39;curation_effort_unique&#39;</span><span class="p">:</span> <span class="n">curation_effort_shared</span><span class="p">,</span>
+                <span class="s1">&#39;curation_effort_shared&#39;</span><span class="p">:</span> <span class="n">curation_effort_shared</span><span class="p">,</span>
+                <span class="s1">&#39;modification_types&#39;</span><span class="p">:</span> <span class="n">modification_types</span><span class="p">,</span>
+            <span class="p">}</span>
+
+
+    <span class="k">def</span> <span class="nf">summaries_tab</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">outfile</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span> <span class="n">return_table</span> <span class="o">=</span> <span class="kc">False</span><span class="p">):</span>
+
+        <span class="n">columns</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="p">(</span><span class="s1">&#39;name&#39;</span><span class="p">,</span> <span class="s1">&#39;Resource&#39;</span><span class="p">),</span>
+            <span class="p">(</span><span class="s1">&#39;n_es_total&#39;</span><span class="p">,</span> <span class="s1">&#39;E-S interactions&#39;</span><span class="p">),</span>
+            <span class="p">(</span><span class="s1">&#39;n_es_shared&#39;</span><span class="p">,</span> <span class="s1">&#39;Shared E-S interactions&#39;</span><span class="p">),</span>
+            <span class="p">(</span><span class="s1">&#39;n_es_unique&#39;</span><span class="p">,</span> <span class="s1">&#39;Unique E-S interactions&#39;</span><span class="p">),</span>
+            <span class="p">(</span><span class="s1">&#39;n_enzymes&#39;</span><span class="p">,</span> <span class="s1">&#39;Enzymes&#39;</span><span class="p">),</span>
+            <span class="p">(</span><span class="s1">&#39;n_substrates&#39;</span><span class="p">,</span> <span class="s1">&#39;Substrates&#39;</span><span class="p">),</span>
+            <span class="p">(</span><span class="s1">&#39;references&#39;</span><span class="p">,</span> <span class="s1">&#39;References&#39;</span><span class="p">),</span>
+            <span class="p">(</span><span class="s1">&#39;references_shared&#39;</span><span class="p">,</span> <span class="s1">&#39;Shared references&#39;</span><span class="p">),</span>
+            <span class="p">(</span><span class="s1">&#39;references_unique&#39;</span><span class="p">,</span> <span class="s1">&#39;Unique references&#39;</span><span class="p">),</span>
+            <span class="p">(</span><span class="s1">&#39;curation_effort&#39;</span><span class="p">,</span> <span class="s1">&#39;Curation effort&#39;</span><span class="p">),</span>
+            <span class="p">(</span><span class="s1">&#39;curation_effort_shared&#39;</span><span class="p">,</span> <span class="s1">&#39;Shared curation effort&#39;</span><span class="p">),</span>
+            <span class="p">(</span><span class="s1">&#39;curation_effort_unique&#39;</span><span class="p">,</span> <span class="s1">&#39;Unique curation effort&#39;</span><span class="p">),</span>
+            <span class="p">(</span><span class="s1">&#39;modification_types&#39;</span><span class="p">,</span> <span class="s1">&#39;Modification types&#39;</span><span class="p">),</span>
+        <span class="p">)</span>
+
+        <span class="n">tab</span> <span class="o">=</span> <span class="p">[]</span>
+        <span class="n">tab</span><span class="o">.</span><span class="n">append</span><span class="p">([</span><span class="n">f</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="k">for</span> <span class="n">f</span> <span class="ow">in</span> <span class="n">columns</span><span class="p">])</span>
+
+        <span class="n">tab</span><span class="o">.</span><span class="n">extend</span><span class="p">([</span>
+            <span class="p">[</span>
+                <span class="nb">str</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">summaries</span><span class="p">[</span><span class="n">src</span><span class="p">][</span><span class="n">f</span><span class="p">[</span><span class="mi">0</span><span class="p">]])</span>
+                <span class="k">for</span> <span class="n">f</span> <span class="ow">in</span> <span class="n">columns</span>
+            <span class="p">]</span>
+            <span class="k">for</span> <span class="n">src</span> <span class="ow">in</span> <span class="nb">sorted</span><span class="p">(</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">summaries</span><span class="o">.</span><span class="n">keys</span><span class="p">(),</span>
+                <span class="n">key</span> <span class="o">=</span> <span class="k">lambda</span> <span class="n">res</span><span class="p">:</span> <span class="p">(</span><span class="n">res</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="s1">&#39;&#39;</span><span class="p">)</span> <span class="k">if</span> <span class="n">res</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="ow">is</span> <span class="kc">None</span> <span class="k">else</span> <span class="n">res</span><span class="p">,</span>
+            <span class="p">)</span>
+        <span class="p">])</span>
+
+        <span class="k">if</span> <span class="n">outfile</span><span class="p">:</span>
+
+            <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">outfile</span><span class="p">,</span> <span class="s1">&#39;w&#39;</span><span class="p">)</span> <span class="k">as</span> <span class="n">fp</span><span class="p">:</span>
+
+                <span class="n">fp</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\n</span><span class="s1">&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\t</span><span class="s1">&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">row</span><span class="p">)</span> <span class="k">for</span> <span class="n">row</span> <span class="ow">in</span> <span class="n">tab</span><span class="p">))</span>
+
+        <span class="k">if</span> <span class="n">return_table</span><span class="p">:</span>
+
+            <span class="k">return</span> <span class="n">tab</span></div>
+
+
+
+
+<div class="viewcode-block" id="init_db">
+<a class="viewcode-back" href="../../../api/pypath.core.enz_sub.init_db.html#pypath.core.enz_sub.init_db">[docs]</a>
+<span class="k">def</span> <span class="nf">init_db</span><span class="p">(</span><span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+
+    <span class="nb">globals</span><span class="p">()[</span><span class="s1">&#39;db&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">EnzymeSubstrateAggregator</span><span class="p">(</span><span class="o">**</span><span class="n">kwargs</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="get_db">
+<a class="viewcode-back" href="../../../api/pypath.core.enz_sub.get_db.html#pypath.core.enz_sub.get_db">[docs]</a>
+<span class="k">def</span> <span class="nf">get_db</span><span class="p">(</span><span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+
+    <span class="k">if</span> <span class="s1">&#39;db&#39;</span> <span class="ow">not</span> <span class="ow">in</span> <span class="nb">globals</span><span class="p">():</span>
+
+        <span class="n">init_db</span><span class="p">(</span><span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
+
+    <span class="k">return</span> <span class="nb">globals</span><span class="p">()[</span><span class="s1">&#39;db&#39;</span><span class="p">]</span></div>
+
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+  <h1>Source code for pypath.core.evidence</h1><div class="highlight"><pre>
+<span></span><span class="ch">#!/usr/bin/env python</span>
+<span class="c1"># -*- coding: utf-8 -*-</span>
+
+<span class="c1">#</span>
+<span class="c1">#  This file is part of the `pypath` python module</span>
+<span class="c1">#</span>
+<span class="c1">#  Copyright 2014-2023</span>
+<span class="c1">#  EMBL, EMBL-EBI, Uniklinik RWTH Aachen, Heidelberg University</span>
+<span class="c1">#</span>
+<span class="c1">#  Authors: see the file `README.rst`</span>
+<span class="c1">#  Contact: Dénes Türei (turei.denes@gmail.com)</span>
+<span class="c1">#</span>
+<span class="c1">#  Distributed under the GPLv3 License.</span>
+<span class="c1">#  See accompanying file LICENSE.txt or copy at</span>
+<span class="c1">#      https://www.gnu.org/licenses/gpl-3.0.html</span>
+<span class="c1">#</span>
+<span class="c1">#  Website: https://pypath.omnipathdb.org/</span>
+<span class="c1">#</span>
+
+<span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">Provides classes for representing and processing evidences supporting</span>
+<span class="sd">relationships. The evidences hold information about the databases and</span>
+<span class="sd">literature references, they can be organized into collections. A number</span>
+<span class="sd">of operations are available on evidences and their collections, for</span>
+<span class="sd">example they can be combined or filtered.</span>
+<span class="sd">&quot;&quot;&quot;</span>
+
+<span class="kn">from</span> <span class="nn">__future__</span> <span class="kn">import</span> <span class="n">annotations</span>
+
+<span class="kn">from</span> <span class="nn">future.utils</span> <span class="kn">import</span> <span class="n">iteritems</span>
+
+<span class="kn">import</span> <span class="nn">importlib</span> <span class="k">as</span> <span class="nn">imp</span>
+<span class="kn">import</span> <span class="nn">copy</span>
+
+<span class="kn">import</span> <span class="nn">pypath.internals.refs</span> <span class="k">as</span> <span class="nn">refs</span>
+<span class="kn">import</span> <span class="nn">pypath.share.common</span> <span class="k">as</span> <span class="nn">common</span>
+<span class="kn">import</span> <span class="nn">pypath.share.session</span> <span class="k">as</span> <span class="nn">session_mod</span>
+<span class="kn">import</span> <span class="nn">pypath.core.entity</span> <span class="k">as</span> <span class="nn">entity</span>
+<span class="kn">import</span> <span class="nn">pypath.core.attrs</span> <span class="k">as</span> <span class="nn">attrs_mod</span>
+<span class="kn">import</span> <span class="nn">pypath.resources.network</span> <span class="k">as</span> <span class="nn">netres</span>
+
+<span class="n">_logger</span> <span class="o">=</span> <span class="n">session_mod</span><span class="o">.</span><span class="n">Logger</span><span class="p">(</span><span class="n">name</span> <span class="o">=</span> <span class="s1">&#39;evidence&#39;</span><span class="p">)</span>
+<span class="n">_log</span> <span class="o">=</span> <span class="n">_logger</span><span class="o">.</span><span class="n">_log</span>
+
+
+<div class="viewcode-block" id="Evidence">
+<a class="viewcode-back" href="../../../api/pypath.core.evidence.Evidence.html#pypath.core.evidence.Evidence">[docs]</a>
+<span class="k">class</span> <span class="nc">Evidence</span><span class="p">(</span><span class="n">attrs_mod</span><span class="o">.</span><span class="n">AttributeHandler</span><span class="p">):</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Represents an evidence supporting a relationship such as molecular</span>
+<span class="sd">    interaction, molecular complex, enzyme-PTM interaction, annotation, etc.</span>
+
+<span class="sd">    The evidence consists of two main parts: the database and the literature</span>
+<span class="sd">    references. If a relationship is supported by multiple databases, for</span>
+<span class="sd">    each one `Evidence` object should be created and</span>
+
+<span class="sd">    :arg pypath.resource.ResourceAttributes resource:</span>
+<span class="sd">        An object derived from :py:class:`pypath.resource.ResourceAttributes`.</span>
+<span class="sd">    :arg str,list,set,NoneType references:</span>
+<span class="sd">        Optional, one or more literature references (preferably PubMed IDs).</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="vm">__slots__</span> <span class="o">=</span> <span class="p">[</span>
+        <span class="s1">&#39;resource&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;references&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;dataset&#39;</span><span class="p">,</span>
+    <span class="p">]</span>
+
+
+<div class="viewcode-block" id="Evidence.__init__">
+<a class="viewcode-back" href="../../../api/pypath.core.evidence.Evidence.html#pypath.core.evidence.Evidence.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">resource</span><span class="p">,</span> <span class="n">references</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span> <span class="n">attrs</span> <span class="o">=</span> <span class="kc">None</span><span class="p">):</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">resource</span> <span class="o">=</span> <span class="n">resource</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">dataset</span> <span class="o">=</span> <span class="nb">getattr</span><span class="p">(</span><span class="n">resource</span><span class="p">,</span> <span class="s1">&#39;dataset&#39;</span><span class="p">,</span> <span class="kc">None</span><span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">references</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_process_references</span><span class="p">(</span><span class="n">references</span><span class="p">)</span>
+        <span class="n">attrs_mod</span><span class="o">.</span><span class="n">AttributeHandler</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">attrs</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="Evidence.reload">
+<a class="viewcode-back" href="../../../api/pypath.core.evidence.Evidence.html#pypath.core.evidence.Evidence.reload">[docs]</a>
+    <span class="k">def</span> <span class="nf">reload</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Reloads the object from the module level.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">modname</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="vm">__class__</span><span class="o">.</span><span class="vm">__module__</span>
+        <span class="n">mod</span> <span class="o">=</span> <span class="nb">__import__</span><span class="p">(</span><span class="n">modname</span><span class="p">,</span> <span class="n">fromlist</span> <span class="o">=</span> <span class="p">[</span><span class="n">modname</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;.&#39;</span><span class="p">)[</span><span class="mi">0</span><span class="p">]])</span>
+        <span class="n">imp</span><span class="o">.</span><span class="n">reload</span><span class="p">(</span><span class="n">mod</span><span class="p">)</span>
+        <span class="n">new</span> <span class="o">=</span> <span class="nb">getattr</span><span class="p">(</span><span class="n">mod</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="vm">__class__</span><span class="o">.</span><span class="vm">__name__</span><span class="p">)</span>
+        <span class="nb">setattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">&#39;__class__&#39;</span><span class="p">,</span> <span class="n">new</span><span class="p">)</span></div>
+
+
+
+    <span class="nd">@staticmethod</span>
+    <span class="k">def</span> <span class="nf">_process_references</span><span class="p">(</span><span class="n">references</span><span class="p">):</span>
+
+        <span class="n">references</span> <span class="o">=</span> <span class="n">common</span><span class="o">.</span><span class="n">to_set</span><span class="p">(</span><span class="n">references</span><span class="p">)</span>
+
+        <span class="k">return</span> <span class="p">(</span>
+            <span class="nb">set</span><span class="p">(</span>
+                <span class="p">(</span>
+                    <span class="n">refs</span><span class="o">.</span><span class="n">Reference</span><span class="p">(</span><span class="n">ref</span><span class="p">)</span>
+                        <span class="k">if</span> <span class="ow">not</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">ref</span><span class="p">,</span> <span class="n">refs</span><span class="o">.</span><span class="n">Reference</span><span class="p">)</span> <span class="k">else</span>
+                    <span class="n">ref</span>
+                <span class="p">)</span>
+                <span class="k">for</span> <span class="n">ref</span> <span class="ow">in</span> <span class="n">references</span>
+            <span class="p">)</span>
+        <span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="fm">__hash__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">resource</span><span class="o">.</span><span class="fm">__hash__</span><span class="p">()</span>
+
+
+    <span class="k">def</span> <span class="fm">__eq__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">other</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="p">(</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">resource</span> <span class="o">==</span> <span class="n">other</span> <span class="ow">or</span>
+            <span class="p">(</span>
+                <span class="nb">hasattr</span><span class="p">(</span><span class="n">other</span><span class="p">,</span> <span class="s1">&#39;resource&#39;</span><span class="p">)</span> <span class="ow">and</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">resource</span> <span class="o">==</span> <span class="n">other</span><span class="o">.</span><span class="n">resource</span> <span class="ow">and</span>
+                <span class="p">(</span>
+                    <span class="bp">self</span><span class="o">.</span><span class="n">resource</span><span class="o">.</span><span class="n">interaction_type</span> <span class="o">==</span>
+                    <span class="bp">self</span><span class="o">.</span><span class="n">resource</span><span class="o">.</span><span class="n">interaction_type</span>
+                <span class="p">)</span>
+            <span class="p">)</span>
+        <span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="fm">__iadd__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">other</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        This will ignore if the other evidence is from different resource:</span>
+<span class="sd">        still better than attributing wrong references to a resource.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">if</span> <span class="bp">self</span> <span class="o">==</span> <span class="n">other</span><span class="p">:</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">dataset</span> <span class="o">=</span> <span class="n">netres</span><span class="o">.</span><span class="n">choose_dataset</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">dataset</span><span class="p">,</span> <span class="n">other</span><span class="o">.</span><span class="n">dataset</span><span class="p">)</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">references</span><span class="o">.</span><span class="n">update</span><span class="p">(</span><span class="n">other</span><span class="o">.</span><span class="n">references</span><span class="p">)</span>
+            <span class="n">attrs_mod</span><span class="o">.</span><span class="n">AttributeHandler</span><span class="o">.</span><span class="fm">__iadd__</span><span class="p">(</span><span class="n">other</span><span class="p">)</span>
+
+        <span class="k">else</span><span class="p">:</span>
+
+            <span class="n">_log</span><span class="p">(</span>
+                <span class="s1">&#39;Warning: attempt to merge evidences from different &#39;</span>
+                <span class="s1">&#39;resources. Ignoring the second evidence.&#39;</span>
+            <span class="p">)</span>
+
+        <span class="k">return</span> <span class="bp">self</span>
+
+
+    <span class="k">def</span> <span class="fm">__add__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">other</span><span class="p">):</span>
+
+        <span class="n">dataset</span> <span class="o">=</span> <span class="n">netres</span><span class="o">.</span><span class="n">choose_dataset</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">dataset</span><span class="p">,</span> <span class="n">other</span><span class="o">.</span><span class="n">dataset</span><span class="p">)</span>
+
+        <span class="n">new</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="vm">__class__</span><span class="p">(</span>
+            <span class="n">resource</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">resource</span><span class="p">,</span>
+            <span class="n">references</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">references</span> <span class="o">|</span> <span class="n">other</span><span class="o">.</span><span class="n">references</span><span class="p">,</span>
+        <span class="p">)</span>
+        <span class="n">new</span><span class="o">.</span><span class="n">dataset</span> <span class="o">=</span> <span class="n">dataset</span>
+        <span class="n">new</span><span class="o">.</span><span class="n">update_attrs</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">attrs</span><span class="o">.</span><span class="n">copy</span><span class="p">())</span>
+        <span class="n">new</span><span class="o">.</span><span class="n">update_attrs</span><span class="p">(</span><span class="n">other</span><span class="o">.</span><span class="n">attrs</span><span class="o">.</span><span class="n">copy</span><span class="p">())</span>
+
+        <span class="k">return</span> <span class="n">new</span>
+
+
+    <span class="nd">@property</span>
+    <span class="k">def</span> <span class="nf">key</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">resource</span><span class="o">.</span><span class="n">key</span>
+
+
+<div class="viewcode-block" id="Evidence.merge">
+<a class="viewcode-back" href="../../../api/pypath.core.evidence.Evidence.html#pypath.core.evidence.Evidence.merge">[docs]</a>
+    <span class="k">def</span> <span class="nf">merge</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">other</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Merges two evidences. Returns set of either one or two evidences</span>
+<span class="sd">        depending on whether the two evidences are from the same resource.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">if</span> <span class="bp">self</span> <span class="o">==</span> <span class="n">other</span><span class="p">:</span>
+
+            <span class="bp">self</span> <span class="o">+=</span> <span class="n">other</span>
+            <span class="k">return</span> <span class="p">{</span><span class="bp">self</span><span class="p">}</span>
+
+        <span class="k">else</span><span class="p">:</span>
+
+            <span class="k">return</span> <span class="p">{</span><span class="bp">self</span><span class="p">,</span> <span class="n">other</span><span class="p">}</span></div>
+
+
+
+    <span class="k">def</span> <span class="fm">__repr__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="s1">&#39;&lt;Evidence </span><span class="si">%s</span><span class="s1"> (</span><span class="si">%s%u</span><span class="s1"> references)&gt;&#39;</span> <span class="o">%</span> <span class="p">(</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">resource</span><span class="o">.</span><span class="n">name</span><span class="p">,</span>
+            <span class="s1">&#39;via </span><span class="si">%s</span><span class="s1">, &#39;</span> <span class="o">%</span> <span class="bp">self</span><span class="o">.</span><span class="n">resource</span><span class="o">.</span><span class="n">via</span> <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">resource</span><span class="o">.</span><span class="n">via</span> <span class="k">else</span> <span class="s1">&#39;&#39;</span><span class="p">,</span>
+            <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">references</span><span class="p">),</span>
+        <span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="fm">__str__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">resource</span><span class="o">.</span><span class="n">name</span>
+
+
+    <span class="k">def</span> <span class="nf">__copy__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="vm">__class__</span><span class="p">(</span>
+            <span class="n">resource</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">resource</span><span class="p">,</span>
+            <span class="n">references</span> <span class="o">=</span> <span class="n">copy</span><span class="o">.</span><span class="n">copy</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">references</span><span class="p">),</span>
+            <span class="n">attrs</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">attrs</span><span class="o">.</span><span class="n">copy</span><span class="p">(),</span>
+        <span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="fm">__contains__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">other</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        :arg str,tuple,Reference other:</span>
+<span class="sd">            Either a reference or a database name, or a tuple of a database</span>
+<span class="sd">            name and an interaction type or a tuple of a database, interaction</span>
+<span class="sd">            type and a primary database (or None if the query should be</span>
+<span class="sd">            limited only to primary databases).</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">return</span> <span class="p">(</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">_contains</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">other</span><span class="p">)</span> <span class="ow">or</span>
+            <span class="n">attrs_mod</span><span class="o">.</span><span class="n">AttributeHandler</span><span class="o">.</span><span class="fm">__contains__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">other</span><span class="p">)</span>
+        <span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">contains_database</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">database</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">resource</span><span class="o">.</span><span class="n">name</span> <span class="o">==</span> <span class="n">database</span>
+
+
+    <span class="k">def</span> <span class="nf">contains_reference</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">reference</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="n">reference</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">references</span>
+
+
+    <span class="k">def</span> <span class="nf">has_database_via</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">database</span><span class="p">,</span> <span class="n">via</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="p">(</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">resource</span><span class="o">.</span><span class="n">name</span> <span class="o">==</span> <span class="n">database</span> <span class="ow">and</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">resource</span><span class="o">.</span><span class="n">via</span> <span class="o">==</span> <span class="n">via</span>
+        <span class="p">)</span>
+
+
+<div class="viewcode-block" id="Evidence.has_interaction_type">
+<a class="viewcode-back" href="../../../api/pypath.core.evidence.Evidence.html#pypath.core.evidence.Evidence.has_interaction_type">[docs]</a>
+    <span class="k">def</span> <span class="nf">has_interaction_type</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">interaction_type</span><span class="p">,</span>
+            <span class="n">database</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">via</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+        <span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        If ``via`` is ``False`` then it will be ignored, otherwise if ``None``</span>
+<span class="sd">        only primary resources are considered.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">return</span> <span class="p">(</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">resource</span><span class="o">.</span><span class="n">interaction_type</span> <span class="o">==</span> <span class="n">interaction_type</span> <span class="ow">and</span>
+            <span class="p">(</span>
+                <span class="ow">not</span> <span class="n">database</span> <span class="ow">or</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">resource</span><span class="o">.</span><span class="n">name</span> <span class="o">==</span> <span class="n">database</span>
+            <span class="p">)</span> <span class="ow">and</span>
+            <span class="p">(</span>
+                <span class="n">via</span> <span class="o">==</span> <span class="kc">False</span> <span class="ow">or</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">resource</span><span class="o">.</span><span class="n">via</span> <span class="o">==</span> <span class="n">via</span>
+            <span class="p">)</span>
+        <span class="p">)</span></div>
+
+
+
+    <span class="nd">@staticmethod</span>
+    <span class="k">def</span> <span class="nf">_contains</span><span class="p">(</span><span class="n">obj</span><span class="p">,</span> <span class="n">other</span><span class="p">):</span>
+
+        <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">other</span><span class="p">,</span> <span class="nb">int</span><span class="p">):</span>
+
+            <span class="n">other</span> <span class="o">=</span> <span class="s1">&#39;</span><span class="si">%u</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="n">other</span>
+
+        <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">other</span><span class="p">,</span> <span class="nb">str</span><span class="p">)</span> <span class="ow">and</span> <span class="n">other</span><span class="o">.</span><span class="n">isdigit</span><span class="p">():</span>
+
+            <span class="n">other</span> <span class="o">=</span> <span class="n">refs</span><span class="o">.</span><span class="n">Reference</span><span class="p">(</span><span class="n">other</span><span class="p">)</span>
+
+        <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">other</span><span class="p">,</span> <span class="n">refs</span><span class="o">.</span><span class="n">Reference</span><span class="p">):</span>
+
+            <span class="k">return</span> <span class="n">obj</span><span class="o">.</span><span class="n">contains_reference</span><span class="p">(</span><span class="n">other</span><span class="p">)</span>
+
+        <span class="c1"># this makes possible to accept a NetworkResource or a</span>
+        <span class="c1"># NetworkResourceKey:</span>
+        <span class="k">if</span> <span class="p">(</span>
+            <span class="nb">hasattr</span><span class="p">(</span><span class="n">other</span><span class="p">,</span> <span class="s1">&#39;name&#39;</span><span class="p">)</span> <span class="ow">and</span>
+            <span class="nb">hasattr</span><span class="p">(</span><span class="n">other</span><span class="p">,</span> <span class="s1">&#39;interaction_type&#39;</span><span class="p">)</span> <span class="ow">and</span>
+            <span class="nb">hasattr</span><span class="p">(</span><span class="n">other</span><span class="p">,</span> <span class="s1">&#39;via&#39;</span><span class="p">)</span>
+        <span class="p">):</span>
+
+            <span class="n">other</span> <span class="o">=</span> <span class="p">(</span><span class="n">other</span><span class="o">.</span><span class="n">name</span><span class="p">,</span> <span class="n">other</span><span class="o">.</span><span class="n">interaction_type</span><span class="p">,</span> <span class="n">other</span><span class="o">.</span><span class="n">via</span><span class="p">)</span>
+
+        <span class="n">other</span> <span class="o">=</span> <span class="n">other</span> <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">other</span><span class="p">,</span> <span class="nb">tuple</span><span class="p">)</span> <span class="k">else</span> <span class="p">(</span><span class="n">other</span><span class="p">,)</span>
+
+        <span class="k">return</span> <span class="p">(</span>
+            <span class="n">obj</span><span class="o">.</span><span class="n">contains_database</span><span class="p">(</span><span class="n">other</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span> <span class="ow">and</span>
+            <span class="p">(</span>
+                <span class="nb">len</span><span class="p">(</span><span class="n">other</span><span class="p">)</span> <span class="o">==</span> <span class="mi">1</span> <span class="ow">or</span>
+                <span class="n">obj</span><span class="o">.</span><span class="n">has_interaction_type</span><span class="p">(</span><span class="n">other</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span> <span class="n">other</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span>
+            <span class="p">)</span> <span class="ow">and</span>
+            <span class="p">(</span>
+                <span class="nb">len</span><span class="p">(</span><span class="n">other</span><span class="p">)</span> <span class="o">&lt;=</span> <span class="mi">2</span> <span class="ow">or</span>
+                <span class="n">obj</span><span class="o">.</span><span class="n">has_database_via</span><span class="p">(</span><span class="n">other</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">other</span><span class="p">[</span><span class="mi">2</span><span class="p">])</span>
+            <span class="p">)</span>
+        <span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">has_data_model</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">data_model</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">resource</span><span class="o">.</span><span class="n">data_model</span> <span class="o">==</span> <span class="n">data_model</span>
+
+
+    <span class="k">def</span> <span class="nf">match</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">resource</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">data_model</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">interaction_type</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">via</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+            <span class="n">references</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">datasets</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+        <span class="p">):</span>
+
+        <span class="k">def</span> <span class="nf">_match</span><span class="p">(</span><span class="n">attr</span><span class="p">,</span> <span class="n">value</span><span class="p">):</span>
+
+            <span class="k">return</span> <span class="p">(</span>
+                <span class="nb">getattr</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">resource</span><span class="p">,</span> <span class="n">attr</span><span class="p">)</span> <span class="ow">in</span> <span class="n">value</span>
+                    <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">value</span><span class="p">,</span> <span class="n">_const</span><span class="o">.</span><span class="n">LIST_LIKE</span><span class="p">)</span> <span class="k">else</span>
+                <span class="nb">getattr</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">resource</span><span class="p">,</span> <span class="n">attr</span><span class="p">)</span> <span class="o">==</span> <span class="n">value</span>
+            <span class="p">)</span>
+
+
+        <span class="n">resource</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="n">resource</span><span class="o">.</span><span class="n">resource</span>
+                <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">resource</span><span class="p">,</span> <span class="n">Evidence</span><span class="p">)</span> <span class="k">else</span>
+            <span class="n">resource</span>
+        <span class="p">)</span>
+
+        <span class="n">interaction_type</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="n">resource</span><span class="o">.</span><span class="n">interaction_type</span>
+                <span class="k">if</span> <span class="p">(</span>
+                    <span class="n">interaction_type</span> <span class="ow">is</span> <span class="kc">None</span> <span class="ow">and</span>
+                    <span class="nb">hasattr</span><span class="p">(</span><span class="n">resource</span><span class="p">,</span> <span class="s1">&#39;interaction_type&#39;</span><span class="p">)</span>
+                <span class="p">)</span> <span class="k">else</span>
+            <span class="n">interaction_type</span>
+        <span class="p">)</span>
+
+        <span class="n">via</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="n">resource</span><span class="o">.</span><span class="n">via</span>
+                <span class="k">if</span> <span class="p">(</span>
+                    <span class="n">via</span> <span class="ow">is</span> <span class="kc">None</span> <span class="ow">and</span>
+                    <span class="nb">hasattr</span><span class="p">(</span><span class="n">resource</span><span class="p">,</span> <span class="s1">&#39;via&#39;</span><span class="p">)</span>
+                <span class="p">)</span> <span class="k">else</span>
+            <span class="n">via</span>
+        <span class="p">)</span>
+
+        <span class="n">data_model</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="n">resource</span><span class="o">.</span><span class="n">data_model</span>
+                <span class="k">if</span> <span class="nb">hasattr</span><span class="p">(</span><span class="n">resource</span><span class="p">,</span> <span class="s1">&#39;data_model&#39;</span><span class="p">)</span> <span class="k">else</span>
+            <span class="n">data_model</span>
+        <span class="p">)</span>
+
+        <span class="n">references</span> <span class="o">=</span> <span class="n">common</span><span class="o">.</span><span class="n">to_set</span><span class="p">(</span><span class="n">references</span><span class="p">)</span>
+
+        <span class="k">return</span> <span class="p">(</span>
+            <span class="p">(</span>
+                <span class="n">resource</span> <span class="ow">is</span> <span class="kc">None</span> <span class="ow">or</span> <span class="p">(</span>
+                    <span class="bp">self</span><span class="o">.</span><span class="n">resource</span><span class="o">.</span><span class="n">name</span> <span class="ow">in</span> <span class="n">resource</span>
+                        <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">resource</span><span class="p">,</span> <span class="nb">set</span><span class="p">)</span> <span class="k">else</span>
+                    <span class="bp">self</span><span class="o">.</span><span class="n">resource</span> <span class="o">==</span> <span class="n">resource</span>
+                <span class="p">)</span>
+            <span class="p">)</span> <span class="ow">and</span>
+            <span class="p">(</span>
+                <span class="n">interaction_type</span> <span class="ow">is</span> <span class="kc">None</span> <span class="ow">or</span>
+                <span class="n">_match</span><span class="p">(</span><span class="s1">&#39;interaction_type&#39;</span><span class="p">,</span> <span class="n">interaction_type</span><span class="p">)</span>
+            <span class="p">)</span> <span class="ow">and</span>
+            <span class="p">(</span>
+                <span class="n">via</span> <span class="ow">is</span> <span class="kc">None</span> <span class="ow">or</span>
+                <span class="p">(</span><span class="n">via</span> <span class="o">==</span> <span class="kc">False</span> <span class="ow">and</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">resource</span><span class="o">.</span><span class="n">via</span><span class="p">)</span> <span class="ow">or</span>
+                <span class="p">(</span><span class="n">via</span> <span class="o">==</span> <span class="kc">True</span> <span class="ow">and</span> <span class="bp">self</span><span class="o">.</span><span class="n">resource</span><span class="o">.</span><span class="n">via</span><span class="p">)</span> <span class="ow">or</span>
+                <span class="n">_match</span><span class="p">(</span><span class="s1">&#39;via&#39;</span><span class="p">,</span> <span class="n">via</span><span class="p">)</span>
+            <span class="p">)</span> <span class="ow">and</span>
+            <span class="p">(</span>
+                <span class="ow">not</span> <span class="n">references</span> <span class="ow">or</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">references</span> <span class="o">&amp;</span> <span class="n">references</span>
+            <span class="p">)</span> <span class="ow">and</span>
+            <span class="p">(</span>
+                <span class="ow">not</span> <span class="n">data_model</span> <span class="ow">or</span>
+                <span class="n">_match</span><span class="p">(</span><span class="s1">&#39;data_model&#39;</span><span class="p">,</span> <span class="n">data_model</span><span class="p">)</span>
+            <span class="p">)</span> <span class="ow">and</span>
+            <span class="p">(</span>
+                <span class="n">datasets</span> <span class="ow">is</span> <span class="kc">None</span> <span class="ow">or</span>
+                <span class="n">_match</span><span class="p">(</span><span class="s1">&#39;dataset&#39;</span><span class="p">,</span> <span class="n">datasets</span><span class="p">)</span>
+            <span class="p">)</span>
+        <span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="fm">__str__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">resource</span><span class="o">.</span><span class="n">name</span>
+
+
+    <span class="nd">@property</span>
+    <span class="k">def</span> <span class="nf">pubmeds</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">list</span><span class="p">[</span><span class="nb">str</span><span class="p">]:</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        PubMed IDs of the references supporting this evidence.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">return</span> <span class="p">[</span><span class="n">r</span><span class="o">.</span><span class="n">pmid</span> <span class="k">for</span> <span class="n">r</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">references</span><span class="p">]</span>
+
+
+<div class="viewcode-block" id="Evidence.asdict">
+<a class="viewcode-back" href="../../../api/pypath.core.evidence.Evidence.html#pypath.core.evidence.Evidence.asdict">[docs]</a>
+    <span class="k">def</span> <span class="nf">asdict</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">dict</span><span class="p">:</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Dictionary representation of the evidence.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">return</span> <span class="p">{</span>
+            <span class="s1">&#39;resource&#39;</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">resource</span><span class="o">.</span><span class="n">name</span><span class="p">,</span>
+            <span class="s1">&#39;references&#39;</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">pubmeds</span><span class="p">,</span>
+            <span class="s1">&#39;dataset&#39;</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">dataset</span><span class="p">,</span>
+            <span class="s1">&#39;via&#39;</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">resource</span><span class="o">.</span><span class="n">via</span><span class="p">,</span>
+            <span class="s1">&#39;attrs&#39;</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">attrs</span><span class="p">,</span>
+        <span class="p">}</span></div>
+</div>
+
+
+
+<div class="viewcode-block" id="Evidences">
+<a class="viewcode-back" href="../../../api/pypath.core.evidence.Evidences.html#pypath.core.evidence.Evidences">[docs]</a>
+<span class="k">class</span> <span class="nc">Evidences</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    A collection of evidences. All evidences supporting a relationship such</span>
+<span class="sd">    as molecular interaction, molecular complex, enzyme-PTM interaction,</span>
+<span class="sd">    annotation, etc should be collected in one `Evidences` object. This way</span>
+<span class="sd">    the set of evidences can be queried a comprehensive way.</span>
+
+<span class="sd">    :arg tuple,list,set,Evidences evidences:</span>
+<span class="sd">        An iterable providing :py:class:`Evidence` instances. It is possible</span>
+<span class="sd">        to create an empty evidence collection and populate it later or to</span>
+<span class="sd">        show this way that certain relationship has no supporting evidences.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="vm">__slots__</span> <span class="o">=</span> <span class="p">[</span>
+        <span class="s1">&#39;evidences&#39;</span><span class="p">,</span>
+    <span class="p">]</span>
+
+
+<div class="viewcode-block" id="Evidences.__init__">
+<a class="viewcode-back" href="../../../api/pypath.core.evidence.Evidences.html#pypath.core.evidence.Evidences.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">evidences</span> <span class="o">=</span> <span class="p">()):</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">evidences</span> <span class="o">=</span> <span class="p">{}</span>
+        <span class="bp">self</span><span class="o">.</span><span class="fm">__iadd__</span><span class="p">(</span><span class="n">evidences</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="Evidences.reload">
+<a class="viewcode-back" href="../../../api/pypath.core.evidence.Evidences.html#pypath.core.evidence.Evidences.reload">[docs]</a>
+    <span class="k">def</span> <span class="nf">reload</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Reloads the object from the module level.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">modname</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="vm">__class__</span><span class="o">.</span><span class="vm">__module__</span>
+        <span class="n">mod</span> <span class="o">=</span> <span class="nb">__import__</span><span class="p">(</span><span class="n">modname</span><span class="p">,</span> <span class="n">fromlist</span> <span class="o">=</span> <span class="p">[</span><span class="n">modname</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;.&#39;</span><span class="p">)[</span><span class="mi">0</span><span class="p">]])</span>
+        <span class="n">imp</span><span class="o">.</span><span class="n">reload</span><span class="p">(</span><span class="n">mod</span><span class="p">)</span>
+        <span class="n">new</span> <span class="o">=</span> <span class="nb">getattr</span><span class="p">(</span><span class="n">mod</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="vm">__class__</span><span class="o">.</span><span class="vm">__name__</span><span class="p">)</span>
+        <span class="nb">setattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">&#39;__class__&#39;</span><span class="p">,</span> <span class="n">new</span><span class="p">)</span>
+
+        <span class="n">new_ev_class</span> <span class="o">=</span> <span class="nb">getattr</span><span class="p">(</span><span class="n">mod</span><span class="p">,</span> <span class="s1">&#39;Evidence&#39;</span><span class="p">)</span>
+
+        <span class="k">for</span> <span class="n">ev</span> <span class="ow">in</span> <span class="bp">self</span><span class="p">:</span>
+
+            <span class="n">ev</span><span class="o">.</span><span class="vm">__class__</span> <span class="o">=</span> <span class="n">new_ev_class</span></div>
+
+
+
+    <span class="k">def</span> <span class="fm">__iadd__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">other</span><span class="p">):</span>
+
+        <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">other</span><span class="p">,</span> <span class="nb">str</span><span class="p">):</span>
+
+            <span class="n">other</span> <span class="o">=</span> <span class="n">Evidence</span><span class="p">(</span><span class="n">other</span><span class="p">)</span>
+
+        <span class="n">other</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="n">other</span>
+                <span class="k">if</span> <span class="p">(</span>
+                    <span class="nb">hasattr</span><span class="p">(</span><span class="n">other</span><span class="p">,</span> <span class="s1">&#39;__iter__&#39;</span><span class="p">)</span> <span class="ow">and</span>
+                    <span class="ow">not</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">other</span><span class="p">,</span> <span class="n">Evidence</span><span class="p">)</span>
+                <span class="p">)</span> <span class="k">else</span>
+            <span class="p">(</span><span class="n">other</span><span class="p">,)</span>
+                <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">other</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="vm">__class__</span><span class="p">)</span> <span class="k">else</span>
+            <span class="p">()</span>
+        <span class="p">)</span>
+
+        <span class="k">for</span> <span class="n">ev</span> <span class="ow">in</span> <span class="n">other</span><span class="p">:</span>
+
+            <span class="k">if</span> <span class="n">ev</span><span class="o">.</span><span class="n">key</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">evidences</span><span class="p">:</span>
+
+                <span class="bp">self</span><span class="o">.</span><span class="n">evidences</span><span class="p">[</span><span class="n">ev</span><span class="o">.</span><span class="n">key</span><span class="p">]</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">evidences</span><span class="p">[</span><span class="n">ev</span><span class="o">.</span><span class="n">key</span><span class="p">]</span> <span class="o">+</span> <span class="n">ev</span>
+
+            <span class="k">else</span><span class="p">:</span>
+
+                <span class="bp">self</span><span class="o">.</span><span class="n">evidences</span><span class="p">[</span><span class="n">ev</span><span class="o">.</span><span class="n">key</span><span class="p">]</span> <span class="o">=</span> <span class="n">ev</span><span class="o">.</span><span class="n">__copy__</span><span class="p">()</span>
+
+        <span class="k">return</span> <span class="bp">self</span>
+
+
+    <span class="k">def</span> <span class="fm">__add__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">other</span><span class="p">):</span>
+
+        <span class="k">if</span> <span class="ow">not</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">other</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="vm">__class__</span><span class="p">):</span>
+
+            <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">__copy__</span><span class="p">()</span>
+
+        <span class="k">return</span> <span class="n">Evidences</span><span class="p">(</span>
+            <span class="p">(</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">evidences</span><span class="p">[</span><span class="n">key</span><span class="p">]</span><span class="o">.</span><span class="n">__copy__</span><span class="p">()</span>
+                    <span class="k">if</span> <span class="n">key</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">other</span><span class="o">.</span><span class="n">evidences</span> <span class="k">else</span>
+                <span class="n">other</span><span class="o">.</span><span class="n">evidences</span><span class="p">[</span><span class="n">key</span><span class="p">]</span><span class="o">.</span><span class="n">__copy__</span><span class="p">()</span>
+                    <span class="k">if</span> <span class="n">key</span> <span class="ow">not</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">evidences</span> <span class="k">else</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">evidences</span><span class="p">[</span><span class="n">key</span><span class="p">]</span> <span class="o">+</span> <span class="n">other</span><span class="o">.</span><span class="n">evidences</span><span class="p">[</span><span class="n">key</span><span class="p">]</span>
+            <span class="p">)</span>
+            <span class="k">for</span> <span class="n">key</span> <span class="ow">in</span>
+            <span class="nb">set</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">evidences</span><span class="o">.</span><span class="n">keys</span><span class="p">())</span> <span class="o">|</span> <span class="nb">set</span><span class="p">(</span><span class="n">other</span><span class="o">.</span><span class="n">evidences</span><span class="o">.</span><span class="n">keys</span><span class="p">())</span>
+        <span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="fm">__radd__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">other</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="fm">__add__</span><span class="p">(</span><span class="n">other</span><span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="fm">__sub__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">other</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="n">Evidences</span><span class="p">(</span>
+            <span class="n">ev</span>
+            <span class="k">for</span> <span class="n">ev</span> <span class="ow">in</span> <span class="bp">self</span>
+            <span class="k">if</span> <span class="n">ev</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">other</span>
+        <span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">intersection</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">other</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="n">Evidences</span><span class="p">(</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">evidences</span><span class="p">[</span><span class="n">key</span><span class="p">]</span> <span class="o">+</span> <span class="n">other</span><span class="o">.</span><span class="n">evidences</span><span class="p">[</span><span class="n">key</span><span class="p">]</span>
+            <span class="k">for</span> <span class="n">key</span> <span class="ow">in</span>
+            <span class="nb">set</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">evidences</span><span class="o">.</span><span class="n">keys</span><span class="p">())</span> <span class="o">&amp;</span> <span class="nb">set</span><span class="p">(</span><span class="n">other</span><span class="o">.</span><span class="n">evidences</span><span class="o">.</span><span class="n">keys</span><span class="p">())</span>
+        <span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="fm">__iter__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">for</span> <span class="n">ev</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">evidences</span><span class="o">.</span><span class="n">values</span><span class="p">():</span>
+
+            <span class="k">yield</span> <span class="n">ev</span>
+
+
+    <span class="k">def</span> <span class="fm">__repr__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="s1">&#39;&lt;Evidences: </span><span class="si">%s</span><span class="s1"> (</span><span class="si">%u</span><span class="s1"> references)&gt;&#39;</span> <span class="o">%</span> <span class="p">(</span>
+            <span class="p">(</span>
+                <span class="s1">&#39;, &#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="nb">sorted</span><span class="p">(</span><span class="nb">set</span><span class="p">(</span><span class="n">ev</span><span class="o">.</span><span class="n">resource</span><span class="o">.</span><span class="n">name</span> <span class="k">for</span> <span class="n">ev</span> <span class="ow">in</span> <span class="bp">self</span><span class="p">)))</span>
+                    <span class="k">if</span> <span class="bp">self</span> <span class="k">else</span>
+                <span class="s1">&#39;None&#39;</span>
+            <span class="p">),</span>
+            <span class="p">(</span>
+                <span class="nb">len</span><span class="p">(</span><span class="nb">set</span><span class="o">.</span><span class="n">union</span><span class="p">(</span><span class="o">*</span><span class="p">(</span><span class="n">ev</span><span class="o">.</span><span class="n">references</span> <span class="k">for</span> <span class="n">ev</span> <span class="ow">in</span> <span class="bp">self</span><span class="p">)))</span>
+                    <span class="k">if</span> <span class="bp">self</span> <span class="k">else</span>
+                <span class="mi">0</span>
+            <span class="p">),</span>
+        <span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">__copy__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="n">Evidences</span><span class="p">((</span><span class="n">ev</span><span class="o">.</span><span class="n">__copy__</span><span class="p">()</span> <span class="k">for</span> <span class="n">ev</span> <span class="ow">in</span> <span class="bp">self</span><span class="p">))</span>
+
+
+    <span class="k">def</span> <span class="fm">__bool__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="nb">bool</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">evidences</span><span class="p">))</span>
+
+
+    <span class="k">def</span> <span class="fm">__contains__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">other</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        :arg str,tuple,Reference other:</span>
+<span class="sd">            Either a reference or a database name, or a tuple of a database</span>
+<span class="sd">            name and an interaction type or a tuple of a database, interaction</span>
+<span class="sd">            type and a primary database (or None if the query should be</span>
+<span class="sd">            limited only to primary databases).</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">return</span> <span class="n">Evidence</span><span class="o">.</span><span class="n">_contains</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">other</span><span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="fm">__and__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">other</span><span class="p">):</span>
+
+        <span class="n">other</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_foreign_resources_set</span><span class="p">(</span><span class="n">other</span><span class="p">)</span>
+        <span class="n">this</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_resident_resources_set</span><span class="p">(</span><span class="n">other</span><span class="p">)</span>
+
+        <span class="k">return</span> <span class="n">this</span> <span class="o">&amp;</span> <span class="n">other</span>
+
+
+    <span class="k">def</span> <span class="fm">__or__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">other</span><span class="p">):</span>
+
+        <span class="n">other</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_foreign_resources_set</span><span class="p">(</span><span class="n">other</span><span class="p">)</span>
+        <span class="n">this</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_resident_resources_set</span><span class="p">(</span><span class="n">other</span><span class="p">)</span>
+
+        <span class="k">return</span> <span class="n">this</span> <span class="o">|</span> <span class="n">other</span>
+
+
+    <span class="nd">@staticmethod</span>
+    <span class="k">def</span> <span class="nf">_foreign_resources_set</span><span class="p">(</span><span class="n">resources</span><span class="p">):</span>
+
+        <span class="n">other</span> <span class="o">=</span> <span class="n">common</span><span class="o">.</span><span class="n">to_set</span><span class="p">(</span><span class="n">resources</span><span class="p">)</span>
+
+        <span class="k">return</span> <span class="p">{</span>
+            <span class="p">(</span>
+                <span class="n">res</span><span class="o">.</span><span class="n">resource</span>
+                    <span class="k">if</span> <span class="nb">hasattr</span><span class="p">(</span><span class="n">res</span><span class="p">,</span> <span class="s1">&#39;resource&#39;</span><span class="p">)</span> <span class="k">else</span>
+                <span class="n">res</span>
+            <span class="p">)</span>
+            <span class="k">for</span> <span class="n">res</span> <span class="ow">in</span> <span class="n">resources</span>
+        <span class="p">}</span>
+
+
+    <span class="k">def</span> <span class="nf">_resident_resources_set</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">other</span> <span class="o">=</span> <span class="kc">None</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="p">(</span>
+            <span class="p">{</span><span class="n">ev</span><span class="o">.</span><span class="n">resource</span><span class="o">.</span><span class="n">name</span> <span class="k">for</span> <span class="n">ev</span> <span class="ow">in</span> <span class="bp">self</span><span class="p">}</span>
+                <span class="k">if</span> <span class="p">(</span>
+                    <span class="nb">hasattr</span><span class="p">(</span><span class="n">other</span><span class="p">,</span> <span class="s1">&#39;__iter__&#39;</span><span class="p">)</span> <span class="ow">and</span>
+                    <span class="nb">all</span><span class="p">(</span><span class="nb">isinstance</span><span class="p">(</span><span class="n">res</span><span class="p">,</span> <span class="nb">str</span><span class="p">)</span> <span class="k">for</span> <span class="n">res</span> <span class="ow">in</span> <span class="n">other</span><span class="p">)</span>
+                <span class="p">)</span> <span class="k">else</span>
+            <span class="p">{</span><span class="n">ev</span><span class="o">.</span><span class="n">resource</span> <span class="k">for</span> <span class="n">ev</span> <span class="ow">in</span> <span class="bp">self</span><span class="p">}</span>
+        <span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="fm">__eq__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">other</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="p">{</span><span class="n">ev</span><span class="o">.</span><span class="n">resource</span> <span class="k">for</span> <span class="n">ev</span> <span class="ow">in</span> <span class="bp">self</span><span class="p">}</span> <span class="o">==</span> <span class="p">{</span><span class="n">ev</span><span class="o">.</span><span class="n">resource</span> <span class="k">for</span> <span class="n">ev</span> <span class="ow">in</span> <span class="n">other</span><span class="p">}</span>
+
+
+    <span class="k">def</span> <span class="fm">__len__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">count_resources</span><span class="p">()</span>
+
+
+    <span class="k">def</span> <span class="nf">count_resources</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="nb">len</span><span class="p">(</span><span class="nb">list</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">filter</span><span class="p">(</span><span class="o">**</span><span class="n">kwargs</span><span class="p">)))</span>
+
+
+    <span class="k">def</span> <span class="nf">get_resources</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="p">{</span>
+            <span class="n">ev</span><span class="o">.</span><span class="n">resource</span>
+            <span class="k">for</span> <span class="n">ev</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">filter</span><span class="p">(</span><span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
+        <span class="p">}</span>
+
+
+    <span class="k">def</span> <span class="nf">get_resources_via</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="p">{</span>
+            <span class="p">(</span><span class="n">ev</span><span class="o">.</span><span class="n">resource</span><span class="p">,</span> <span class="n">ev</span><span class="o">.</span><span class="n">resource</span><span class="o">.</span><span class="n">via</span><span class="p">)</span>
+            <span class="k">for</span> <span class="n">ev</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">filter</span><span class="p">(</span><span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
+        <span class="p">}</span>
+
+
+    <span class="k">def</span> <span class="nf">get_resource_names_via</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="p">{</span>
+            <span class="p">(</span><span class="n">ev</span><span class="o">.</span><span class="n">resource</span><span class="o">.</span><span class="n">name</span><span class="p">,</span> <span class="n">ev</span><span class="o">.</span><span class="n">resource</span><span class="o">.</span><span class="n">via</span><span class="p">)</span>
+            <span class="k">for</span> <span class="n">ev</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">filter</span><span class="p">(</span><span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
+        <span class="p">}</span>
+
+
+    <span class="k">def</span> <span class="nf">count_references</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">get_references</span><span class="p">(</span><span class="o">**</span><span class="n">kwargs</span><span class="p">))</span>
+
+
+    <span class="k">def</span> <span class="nf">get_references</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+
+        <span class="n">evidences</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">filter</span><span class="p">(</span><span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
+
+        <span class="k">return</span> <span class="p">{</span>
+            <span class="n">ref</span>
+            <span class="k">for</span> <span class="n">ev</span> <span class="ow">in</span> <span class="n">evidences</span>
+            <span class="k">for</span> <span class="n">ref</span> <span class="ow">in</span> <span class="n">ev</span><span class="o">.</span><span class="n">references</span>
+        <span class="p">}</span>
+
+
+    <span class="k">def</span> <span class="nf">count_curation_effort</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">get_curation_effort</span><span class="p">(</span><span class="o">**</span><span class="n">kwargs</span><span class="p">))</span>
+
+
+    <span class="k">def</span> <span class="nf">get_curation_effort</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+
+        <span class="n">evidences</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">filter</span><span class="p">(</span><span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
+
+        <span class="k">return</span> <span class="p">{</span>
+            <span class="p">(</span><span class="n">ev</span><span class="o">.</span><span class="n">resource</span><span class="p">,</span> <span class="n">ref</span><span class="p">)</span>
+            <span class="k">for</span> <span class="n">ev</span> <span class="ow">in</span> <span class="n">evidences</span>
+            <span class="k">for</span> <span class="n">ref</span> <span class="ow">in</span> <span class="n">ev</span><span class="o">.</span><span class="n">references</span>
+        <span class="p">}</span>
+
+
+    <span class="k">def</span> <span class="nf">contains_database</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">database</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="nb">any</span><span class="p">(</span>
+            <span class="n">ev</span><span class="o">.</span><span class="n">resource</span><span class="o">.</span><span class="n">name</span> <span class="o">==</span> <span class="n">database</span>
+            <span class="k">for</span> <span class="n">ev</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">filter</span><span class="p">(</span><span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
+        <span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">contains_reference</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">reference</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="nb">any</span><span class="p">(</span><span class="n">reference</span> <span class="ow">in</span> <span class="n">ev</span><span class="o">.</span><span class="n">references</span> <span class="k">for</span> <span class="n">ev</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">filter</span><span class="p">(</span><span class="o">**</span><span class="n">kwargs</span><span class="p">))</span>
+
+
+    <span class="k">def</span> <span class="nf">has_database_via</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">database</span><span class="p">,</span> <span class="n">via</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="nb">any</span><span class="p">(</span>
+            <span class="n">ev</span><span class="o">.</span><span class="n">has_database_via</span><span class="p">(</span><span class="n">database</span><span class="p">,</span> <span class="n">via</span><span class="p">)</span>
+            <span class="k">for</span> <span class="n">ev</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">filter</span><span class="p">(</span><span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
+        <span class="p">)</span>
+
+
+<div class="viewcode-block" id="Evidences.has_interaction_type">
+<a class="viewcode-back" href="../../../api/pypath.core.evidence.Evidences.html#pypath.core.evidence.Evidences.has_interaction_type">[docs]</a>
+    <span class="k">def</span> <span class="nf">has_interaction_type</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">interaction_type</span><span class="p">,</span>
+            <span class="n">database</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">via</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+        <span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        If ``via`` is ``False`` then it will be ignored, otherwise if ``None``</span>
+<span class="sd">        only primary resources are considered.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">return</span> <span class="nb">any</span><span class="p">(</span>
+            <span class="n">ev</span><span class="o">.</span><span class="n">has_interaction_type</span><span class="p">(</span><span class="n">interaction_type</span><span class="p">,</span> <span class="n">database</span><span class="p">,</span> <span class="n">via</span><span class="p">)</span>
+            <span class="k">for</span> <span class="n">ev</span> <span class="ow">in</span> <span class="bp">self</span>
+        <span class="p">)</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">has_data_model</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">data_model</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="nb">any</span><span class="p">(</span>
+            <span class="n">ev</span><span class="o">.</span><span class="n">has_data_model</span><span class="p">(</span><span class="n">data_model</span><span class="p">)</span>
+            <span class="k">for</span> <span class="n">ev</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">filter</span><span class="p">(</span><span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
+        <span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">get_resources</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="p">{</span><span class="n">ev</span><span class="o">.</span><span class="n">resource</span> <span class="k">for</span> <span class="n">ev</span> <span class="ow">in</span> <span class="bp">self</span><span class="p">}</span>
+
+
+    <span class="k">def</span> <span class="nf">get_resource_names</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="p">{</span><span class="n">ev</span><span class="o">.</span><span class="n">resource</span><span class="o">.</span><span class="n">name</span> <span class="k">for</span> <span class="n">ev</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">filter</span><span class="p">(</span><span class="o">**</span><span class="n">kwargs</span><span class="p">)}</span>
+
+
+    <span class="k">def</span> <span class="nf">get_interaction_types</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="p">{</span><span class="n">ev</span><span class="o">.</span><span class="n">resource</span><span class="o">.</span><span class="n">interaction_type</span> <span class="k">for</span> <span class="n">ev</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">filter</span><span class="p">(</span><span class="o">**</span><span class="n">kwargs</span><span class="p">)}</span>
+
+
+    <span class="k">def</span> <span class="nf">get_data_models</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="p">{</span><span class="n">ev</span><span class="o">.</span><span class="n">resource</span><span class="o">.</span><span class="n">data_model</span> <span class="k">for</span> <span class="n">ev</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">filter</span><span class="p">(</span><span class="o">**</span><span class="n">kwargs</span><span class="p">)}</span>
+
+
+    <span class="k">def</span> <span class="nf">get_datasets</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="p">{</span>
+            <span class="n">ds</span> <span class="k">for</span> <span class="n">ds</span> <span class="ow">in</span>
+            <span class="p">(</span><span class="n">ev</span><span class="o">.</span><span class="n">dataset</span> <span class="k">for</span> <span class="n">ev</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">filter</span><span class="p">(</span><span class="o">**</span><span class="n">kwargs</span><span class="p">))</span>
+            <span class="k">if</span> <span class="n">ds</span>
+        <span class="p">}</span>
+
+
+<div class="viewcode-block" id="Evidences.has_dataset">
+<a class="viewcode-back" href="../../../api/pypath.core.evidence.Evidences.html#pypath.core.evidence.Evidences.has_dataset">[docs]</a>
+    <span class="k">def</span> <span class="nf">has_dataset</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">dataset</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">bool</span><span class="p">:</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Contains evidence(s) from a given dataset meeting the criteria.</span>
+
+<span class="sd">        Args:</span>
+<span class="sd">            dataset:</span>
+<span class="sd">                Name of the dataset.</span>
+<span class="sd">            kwargs:</span>
+<span class="sd">                Filtering criteria for evidences.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">return</span> <span class="n">dataset</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">get_datasets</span><span class="p">(</span><span class="o">**</span><span class="n">kwargs</span><span class="p">)</span></div>
+
+
+
+    <span class="k">def</span> <span class="fm">__isub__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">other</span><span class="p">):</span>
+
+        <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">other</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="vm">__class__</span><span class="p">):</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">evidences</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">(</span>
+                <span class="p">(</span><span class="n">key</span><span class="p">,</span> <span class="n">ev</span><span class="p">)</span>
+                <span class="k">for</span> <span class="n">key</span><span class="p">,</span> <span class="n">ev</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">evidences</span><span class="p">)</span>
+                <span class="k">if</span> <span class="n">key</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">other</span><span class="o">.</span><span class="n">evidences</span> <span class="ow">or</span> <span class="n">other</span><span class="o">.</span><span class="n">evidences</span><span class="p">[</span><span class="n">key</span><span class="p">]</span> <span class="o">!=</span> <span class="n">ev</span>
+            <span class="p">)</span>
+
+        <span class="k">else</span><span class="p">:</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">remove</span><span class="p">(</span><span class="n">other</span><span class="p">)</span>
+
+        <span class="k">return</span> <span class="bp">self</span>
+
+
+    <span class="k">def</span> <span class="nf">remove</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">resource</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span> <span class="n">interaction_type</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span> <span class="n">via</span> <span class="o">=</span> <span class="kc">False</span><span class="p">):</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">evidences</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">(</span>
+            <span class="p">(</span><span class="n">key</span><span class="p">,</span> <span class="n">ev</span><span class="p">)</span>
+            <span class="k">for</span> <span class="n">key</span><span class="p">,</span> <span class="n">ev</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">evidences</span><span class="p">)</span>
+            <span class="k">if</span> <span class="ow">not</span> <span class="n">ev</span><span class="o">.</span><span class="n">match</span><span class="p">(</span>
+                <span class="n">resource</span> <span class="o">=</span> <span class="n">resource</span><span class="p">,</span>
+                <span class="n">interaction_type</span> <span class="o">=</span> <span class="n">interaction_type</span><span class="p">,</span>
+                <span class="n">via</span> <span class="o">=</span> <span class="n">via</span><span class="p">,</span>
+            <span class="p">)</span>
+        <span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">filter</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">resource</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">data_model</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">interaction_type</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">via</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+            <span class="n">references</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">datasets</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+        <span class="p">):</span>
+
+        <span class="k">return</span> <span class="p">(</span>
+            <span class="n">ev</span> <span class="k">for</span> <span class="n">ev</span> <span class="ow">in</span> <span class="bp">self</span>
+            <span class="k">if</span> <span class="n">ev</span><span class="o">.</span><span class="n">match</span><span class="p">(</span>
+                <span class="n">resource</span> <span class="o">=</span> <span class="n">resource</span><span class="p">,</span>
+                <span class="n">data_model</span> <span class="o">=</span> <span class="n">data_model</span><span class="p">,</span>
+                <span class="n">interaction_type</span> <span class="o">=</span> <span class="n">interaction_type</span><span class="p">,</span>
+                <span class="n">via</span> <span class="o">=</span> <span class="n">via</span><span class="p">,</span>
+                <span class="n">references</span> <span class="o">=</span> <span class="n">references</span><span class="p">,</span>
+                <span class="n">datasets</span> <span class="o">=</span> <span class="n">datasets</span><span class="p">,</span>
+            <span class="p">)</span>
+        <span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">match</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">resource</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">data_model</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">interaction_type</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">via</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+            <span class="n">references</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">datasets</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+        <span class="p">):</span>
+
+        <span class="k">return</span> <span class="nb">bool</span><span class="p">(</span>
+            <span class="nb">tuple</span><span class="p">(</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">filter</span><span class="p">(</span>
+                    <span class="n">resource</span> <span class="o">=</span> <span class="n">resource</span><span class="p">,</span>
+                    <span class="n">data_model</span> <span class="o">=</span> <span class="n">data_model</span><span class="p">,</span>
+                    <span class="n">interaction_type</span> <span class="o">=</span> <span class="n">interaction_type</span><span class="p">,</span>
+                    <span class="n">via</span> <span class="o">=</span> <span class="n">via</span><span class="p">,</span>
+                    <span class="n">references</span> <span class="o">=</span> <span class="n">references</span><span class="p">,</span>
+                    <span class="n">datasets</span> <span class="o">=</span> <span class="n">datasets</span><span class="p">,</span>
+                <span class="p">)</span>
+            <span class="p">)</span>
+        <span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="fm">__getitem__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">key</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Key is a :py:class:`pypath.internals.resource.NetworkResourceKey` or</span>
+<span class="sd">        an equivalent tuple.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">evidences</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="n">key</span><span class="p">,</span> <span class="kc">None</span><span class="p">)</span> <span class="ow">or</span> <span class="bp">self</span><span class="o">.</span><span class="n">simple_dict</span><span class="p">[</span><span class="n">key</span><span class="p">]</span>
+
+
+<div class="viewcode-block" id="Evidences.keys">
+<a class="viewcode-back" href="../../../api/pypath.core.evidence.Evidences.html#pypath.core.evidence.Evidences.keys">[docs]</a>
+    <span class="k">def</span> <span class="nf">keys</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Returns</span>
+<span class="sd">            (dict_keys): The keys of this dictionary are</span>
+<span class="sd">                :py:class:`pypath.internals.resource.NetworkResourceKey`</span>
+<span class="sd">                objects.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">evidences</span><span class="o">.</span><span class="n">keys</span><span class="p">()</span></div>
+
+
+
+<div class="viewcode-block" id="Evidences.items">
+<a class="viewcode-back" href="../../../api/pypath.core.evidence.Evidences.html#pypath.core.evidence.Evidences.items">[docs]</a>
+    <span class="k">def</span> <span class="nf">items</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Returns</span>
+<span class="sd">            (dict_items): The evidences as a mapping, with</span>
+<span class="sd">                :py:class:`pypath.internals.resource.NetworkResourceKey`</span>
+<span class="sd">                objects as keys and :py:class:`pypath.core.evidence.Evidence`</span>
+<span class="sd">                objects as values.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">evidences</span><span class="o">.</span><span class="n">items</span><span class="p">()</span></div>
+
+
+
+    <span class="nd">@property</span>
+    <span class="k">def</span> <span class="nf">simple_dict</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">dict</span><span class="p">[</span><span class="nb">str</span><span class="p">,</span> <span class="n">evidence</span><span class="o">.</span><span class="n">Evidence</span><span class="p">]:</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Returns</span>
+<span class="sd">            Keys are resource labels, values are ``Evidence`` objects.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">return</span> <span class="nb">dict</span><span class="p">(</span>
+            <span class="p">(</span><span class="n">res</span><span class="o">.</span><span class="n">last</span><span class="p">,</span> <span class="n">ev</span><span class="p">)</span>
+            <span class="k">for</span> <span class="n">res</span><span class="p">,</span> <span class="n">ev</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span>
+        <span class="p">)</span>
+
+
+<div class="viewcode-block" id="Evidences.serialize_attrs">
+<a class="viewcode-back" href="../../../api/pypath.core.evidence.Evidences.html#pypath.core.evidence.Evidences.serialize_attrs">[docs]</a>
+    <span class="k">def</span> <span class="nf">serialize_attrs</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">top_key_prefix</span><span class="p">:</span> <span class="nb">bool</span> <span class="o">=</span> <span class="kc">True</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">str</span><span class="p">:</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Serialize the extra attributes of the evidences as a JSON string.</span>
+
+<span class="sd">        Returns</span>
+<span class="sd">            A JSON serialized string with the evidences from each resource.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">return</span> <span class="n">attrs_mod</span><span class="o">.</span><span class="n">AttributeHandler</span><span class="o">.</span><span class="n">_serialize</span><span class="p">(</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">simple_dict</span><span class="p">,</span>
+            <span class="n">top_key_prefix</span> <span class="o">=</span> <span class="n">top_key_prefix</span><span class="p">,</span>
+            <span class="n">default</span> <span class="o">=</span> <span class="k">lambda</span> <span class="n">obj</span><span class="p">:</span> <span class="n">obj</span><span class="o">.</span><span class="n">serialize</span><span class="p">(),</span>
+        <span class="p">)</span></div>
+
+
+
+    <span class="nd">@property</span>
+    <span class="k">def</span> <span class="nf">datasets</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">set</span><span class="p">:</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Datasets in this evidence set.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">return</span> <span class="p">{</span><span class="n">ev</span><span class="o">.</span><span class="n">dataset</span> <span class="k">for</span> <span class="n">ev</span> <span class="ow">in</span> <span class="bp">self</span><span class="p">}</span>
+
+
+    <span class="nd">@property</span>
+    <span class="k">def</span> <span class="nf">attrs</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">dict</span><span class="p">:</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Combines the custom attributes from all evidences within this set.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">return</span> <span class="n">common</span><span class="o">.</span><span class="n">combine_attrs</span><span class="p">([</span><span class="n">ev</span><span class="o">.</span><span class="n">attrs</span> <span class="k">for</span> <span class="n">ev</span> <span class="ow">in</span> <span class="bp">self</span><span class="p">])</span>
+
+
+<div class="viewcode-block" id="Evidences.asdict">
+<a class="viewcode-back" href="../../../api/pypath.core.evidence.Evidences.html#pypath.core.evidence.Evidences.asdict">[docs]</a>
+    <span class="k">def</span> <span class="nf">asdict</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">list</span><span class="p">[</span><span class="nb">dict</span><span class="p">]:</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Evidence set as a list of dictionaries.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">return</span> <span class="p">[</span><span class="n">ev</span><span class="o">.</span><span class="n">asdict</span><span class="p">()</span> <span class="k">for</span> <span class="n">ev</span> <span class="ow">in</span> <span class="bp">self</span><span class="p">]</span></div>
+</div>
+
+</pre></div>
+
+                </article>
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+                  
+  <h1>Source code for pypath.core.interaction</h1><div class="highlight"><pre>
+<span></span><span class="ch">#!/usr/bin/env python</span>
+<span class="c1"># -*- coding: utf-8 -*-</span>
+
+<span class="c1">#</span>
+<span class="c1">#  This file is part of the `pypath` python module</span>
+<span class="c1">#</span>
+<span class="c1">#  Copyright 2014-2023</span>
+<span class="c1">#  EMBL, EMBL-EBI, Uniklinik RWTH Aachen, Heidelberg University</span>
+<span class="c1">#</span>
+<span class="c1">#  Authors: see the file `README.rst`</span>
+<span class="c1">#  Contact: Dénes Türei (turei.denes@gmail.com)</span>
+<span class="c1">#</span>
+<span class="c1">#  Distributed under the GPLv3 License.</span>
+<span class="c1">#  See accompanying file LICENSE.txt or copy at</span>
+<span class="c1">#      https://www.gnu.org/licenses/gpl-3.0.html</span>
+<span class="c1">#</span>
+<span class="c1">#  Website: https://pypath.omnipathdb.org/</span>
+<span class="c1">#</span>
+
+<span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">Here we define one class, the :py:class:`Interaction`` which provides a</span>
+<span class="sd">rich API for representing and querying molecular interactions. The</span>
+<span class="sd">interactions serve as the building elements of the network and the</span>
+<span class="sd">:py:class:`pypath.network.Network` object largely relies on methods</span>
+<span class="sd">of the :py:class:`Interaction`` objects.</span>
+<span class="sd">&quot;&quot;&quot;</span>
+
+<span class="kn">from</span> <span class="nn">__future__</span> <span class="kn">import</span> <span class="n">annotations</span>
+
+<span class="kn">from</span> <span class="nn">future.utils</span> <span class="kn">import</span> <span class="n">iteritems</span>
+
+<span class="kn">from</span> <span class="nn">typing</span> <span class="kn">import</span> <span class="n">Literal</span>
+
+<span class="kn">import</span> <span class="nn">importlib</span> <span class="k">as</span> <span class="nn">imp</span>
+<span class="kn">import</span> <span class="nn">collections</span>
+<span class="kn">import</span> <span class="nn">operator</span>
+<span class="kn">import</span> <span class="nn">itertools</span>
+<span class="kn">import</span> <span class="nn">functools</span>
+<span class="kn">import</span> <span class="nn">json</span>
+
+<span class="kn">import</span> <span class="nn">pypath.core.evidence</span> <span class="k">as</span> <span class="nn">pypath_evidence</span>
+<span class="kn">import</span> <span class="nn">pypath.internals.resource</span> <span class="k">as</span> <span class="nn">pypath_resource</span>
+<span class="kn">import</span> <span class="nn">pypath.share.session</span> <span class="k">as</span> <span class="nn">session_mod</span>
+<span class="kn">import</span> <span class="nn">pypath.share.common</span> <span class="k">as</span> <span class="nn">common</span>
+<span class="kn">import</span> <span class="nn">pypath.utils.mapping</span> <span class="k">as</span> <span class="nn">mapping</span>
+<span class="kn">import</span> <span class="nn">pypath.core.entity</span> <span class="k">as</span> <span class="nn">entity</span>
+<span class="kn">import</span> <span class="nn">pypath.core.attrs</span> <span class="k">as</span> <span class="nn">attrs_mod</span>
+<span class="kn">import</span> <span class="nn">pypath.utils.orthology</span> <span class="k">as</span> <span class="nn">orthology</span>
+
+<span class="n">_logger</span> <span class="o">=</span> <span class="n">session_mod</span><span class="o">.</span><span class="n">Logger</span><span class="p">(</span><span class="n">name</span> <span class="o">=</span> <span class="s1">&#39;interaction&#39;</span><span class="p">)</span>
+<span class="n">_log</span> <span class="o">=</span> <span class="n">_logger</span><span class="o">.</span><span class="n">_log</span>
+
+
+<span class="n">InteractionKey</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">namedtuple</span><span class="p">(</span>
+    <span class="s1">&#39;InteractionKey&#39;</span><span class="p">,</span>
+    <span class="p">[</span>
+        <span class="s1">&#39;entity_a&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;entity_b&#39;</span><span class="p">,</span>
+    <span class="p">],</span>
+<span class="p">)</span>
+
+
+<span class="n">InteractionDataFrameRecord</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">namedtuple</span><span class="p">(</span>
+    <span class="s1">&#39;InteractionDataFrameRecord&#39;</span><span class="p">,</span>
+    <span class="p">[</span>
+        <span class="s1">&#39;id_a&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;id_b&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;type_a&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;type_b&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;directed&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;effect&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;type&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;dmodel&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;sources&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;references&#39;</span><span class="p">,</span>
+    <span class="p">],</span>
+<span class="p">)</span>
+<span class="n">InteractionDataFrameRecord</span><span class="o">.</span><span class="fm">__new__</span><span class="o">.</span><span class="vm">__defaults__</span> <span class="o">=</span> <span class="p">(</span><span class="kc">None</span><span class="p">,)</span> <span class="o">*</span> <span class="mi">8</span>
+
+
+<div class="viewcode-block" id="Interaction">
+<a class="viewcode-back" href="../../../api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction">[docs]</a>
+<span class="k">class</span> <span class="nc">Interaction</span><span class="p">(</span><span class="n">attrs_mod</span><span class="o">.</span><span class="n">AttributeHandler</span><span class="p">):</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Represents a unique pair of molecular entities interacting with each</span>
+<span class="sd">    other. One :py:class:`Interaction` object might represent multiple</span>
+<span class="sd">    interactions i.e. with different direction or effect or type (e.g.</span>
+<span class="sd">    transcriptional regulation and post-translational regulation),</span>
+<span class="sd">    each supported by different evidences.</span>
+
+<span class="sd">    :arg str,pypath.entity.Entity a,b:</span>
+<span class="sd">        The two interacting partners. If an :py:class:`pypath.entity.Entity`</span>
+<span class="sd">        objects provided the other attributes (entity_type, id_type, taxon)</span>
+<span class="sd">        will be ignored.</span>
+<span class="sd">    :arg str id_type_a,id_type_b:</span>
+<span class="sd">        The identifier types for partner ``a`` and ``b`` e.g. ``&#39;uniprot&#39;``.</span>
+<span class="sd">    :arg str entity_type_a,entity_type_b:</span>
+<span class="sd">        The types of the molecular entities ``a`` and ``b``</span>
+<span class="sd">        e.g. ``&#39;protein&#39;``.</span>
+<span class="sd">    :arg int taxon_a,taxon_b:</span>
+<span class="sd">        The NCBI Taxonomy Identifiers of partner ``a`` and ``b``</span>
+<span class="sd">        e.g. ``9606`` for human.</span>
+
+<span class="sd">    :details:</span>
+<span class="sd">        The arguments ``a`` and ``b`` will be assigned to the attribute ``a``</span>
+<span class="sd">        and ``b`` in an alphabetical order, hence it&#39;s possible that</span>
+<span class="sd">        argument ``a`` becomes attribute ``b``.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="vm">__slots__</span> <span class="o">=</span> <span class="p">[</span>
+        <span class="s1">&#39;a&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;b&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;a_b&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;b_a&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;nodes&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;key&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;evidences&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;direction&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;positive&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;negative&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;unknown_effect&#39;</span><span class="p">,</span>
+    <span class="p">]</span>
+
+    <span class="n">_get_methods</span> <span class="o">=</span> <span class="p">{</span>
+        <span class="s1">&#39;datasets&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;entities&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;evidences&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;references&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;curation_effort&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;resource_names&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;resources&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;data_models&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;interaction_types&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;interactions&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;interactions_0&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;interactions_directed&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;interactions_undirected&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;interactions_non_directed&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;interactions_undirected_0&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;interactions_non_directed_0&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;interactions_signed&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;interactions_positive&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;interactions_negative&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;interactions_mutual&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;resources_via&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;resource_names_via&#39;</span><span class="p">,</span>
+    <span class="p">}</span>
+
+    <span class="n">_get_methods_autogen</span> <span class="o">=</span> <span class="p">(</span>
+        <span class="s1">&#39;references&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;resources&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;resources_via&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;resource_names&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;resource_names_via&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;data_models&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;interaction_types&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;datasets&#39;</span><span class="p">,</span>
+    <span class="p">)</span>
+
+    <span class="n">_by_methods</span> <span class="o">=</span> <span class="p">(</span>
+        <span class="s1">&#39;resource&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;reference&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;data_model&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;interaction_type&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;interaction_type_and_data_model&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;interaction_type_and_data_model_and_resource&#39;</span><span class="p">,</span>
+    <span class="p">)</span>
+
+    <span class="n">_count_methods</span> <span class="o">=</span> <span class="p">{</span>
+        <span class="s1">&#39;references&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;resources&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;resources_via&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;resource_names_via&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;resource_names&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;curation_effort&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;entities&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;proteins&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;complexes&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;mirnas&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;interactions&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;interactions_0&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;interactions_directed&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;interactions_signed&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;interactions_positive&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;interactions_negative&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;data_models&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;interaction_types&#39;</span><span class="p">,</span>
+    <span class="p">}</span>
+
+    <span class="n">_get_method_signature</span> <span class="o">=</span> <span class="p">[</span>
+        <span class="p">(</span><span class="s1">&#39;direction&#39;</span><span class="p">,</span> <span class="kc">None</span><span class="p">),</span>
+        <span class="p">(</span><span class="s1">&#39;effect&#39;</span><span class="p">,</span> <span class="kc">None</span><span class="p">),</span>
+        <span class="p">(</span><span class="s1">&#39;resources&#39;</span><span class="p">,</span> <span class="kc">None</span><span class="p">),</span>
+        <span class="p">(</span><span class="s1">&#39;data_model&#39;</span><span class="p">,</span> <span class="kc">None</span><span class="p">),</span>
+        <span class="p">(</span><span class="s1">&#39;interaction_type&#39;</span><span class="p">,</span> <span class="kc">None</span><span class="p">),</span>
+        <span class="p">(</span><span class="s1">&#39;via&#39;</span><span class="p">,</span> <span class="kc">None</span><span class="p">),</span>
+        <span class="p">(</span><span class="s1">&#39;references&#39;</span><span class="p">,</span> <span class="kc">None</span><span class="p">),</span>
+    <span class="p">]</span>
+
+    <span class="n">_degree_modes</span> <span class="o">=</span> <span class="p">(</span>
+        <span class="s1">&#39;ALL&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;IN&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;OUT&#39;</span><span class="p">,</span>
+    <span class="p">)</span>
+
+    <span class="n">_degree_directions</span> <span class="o">=</span> <span class="p">{</span>
+        <span class="s1">&#39;undirected&#39;</span><span class="p">:</span> <span class="p">(</span><span class="kc">None</span><span class="p">,</span> <span class="kc">None</span><span class="p">),</span>
+        <span class="s1">&#39;non_directed&#39;</span><span class="p">:</span> <span class="p">(</span><span class="kc">False</span><span class="p">,</span> <span class="kc">None</span><span class="p">),</span>
+        <span class="s1">&#39;directed&#39;</span><span class="p">:</span> <span class="p">(</span><span class="kc">True</span><span class="p">,</span> <span class="kc">None</span><span class="p">),</span>
+        <span class="s1">&#39;signed&#39;</span><span class="p">:</span> <span class="p">(</span><span class="kc">True</span><span class="p">,</span> <span class="kc">True</span><span class="p">),</span>
+        <span class="s1">&#39;positive&#39;</span><span class="p">:</span> <span class="p">(</span><span class="kc">True</span><span class="p">,</span> <span class="s1">&#39;positive&#39;</span><span class="p">),</span>
+        <span class="s1">&#39;negative&#39;</span><span class="p">:</span> <span class="p">(</span><span class="kc">True</span><span class="p">,</span> <span class="s1">&#39;negative&#39;</span><span class="p">),</span>
+    <span class="p">}</span>
+
+    <span class="n">_entity_types</span> <span class="o">=</span> <span class="p">{</span>
+        <span class="s1">&#39;protein&#39;</span><span class="p">,</span>
+        <span class="p">(</span><span class="s1">&#39;complex&#39;</span><span class="p">,</span> <span class="s1">&#39;complexes&#39;</span><span class="p">),</span>
+        <span class="s1">&#39;mirna&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;lncrna&#39;</span><span class="p">,</span>
+        <span class="c1"># ugly :(</span>
+        <span class="p">((</span><span class="s1">&#39;small_molecule&#39;</span><span class="p">,</span> <span class="s1">&#39;drug&#39;</span><span class="p">,</span> <span class="s1">&#39;metabolite&#39;</span><span class="p">),),</span>
+        <span class="kc">None</span><span class="p">,</span>
+    <span class="p">}</span>
+
+    <span class="n">_entity_values</span> <span class="o">=</span> <span class="p">{</span>
+        <span class="s1">&#39;identifiers&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;labels&#39;</span><span class="p">,</span>
+        <span class="kc">None</span><span class="p">,</span>
+    <span class="p">}</span>
+
+
+<div class="viewcode-block" id="Interaction.__init__">
+<a class="viewcode-back" href="../../../api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">a</span><span class="p">,</span>
+            <span class="n">b</span><span class="p">,</span>
+            <span class="n">id_type_a</span> <span class="o">=</span> <span class="s1">&#39;uniprot&#39;</span><span class="p">,</span>
+            <span class="n">id_type_b</span> <span class="o">=</span> <span class="s1">&#39;uniprot&#39;</span><span class="p">,</span>
+            <span class="n">entity_type_a</span> <span class="o">=</span> <span class="s1">&#39;protein&#39;</span><span class="p">,</span>
+            <span class="n">entity_type_b</span> <span class="o">=</span> <span class="s1">&#39;protein&#39;</span><span class="p">,</span>
+            <span class="n">taxon_a</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">,</span>
+            <span class="n">taxon_b</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">,</span>
+            <span class="n">attrs</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+        <span class="p">):</span>
+
+        <span class="n">a</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_get_entity</span><span class="p">(</span>
+            <span class="n">identifier</span> <span class="o">=</span> <span class="n">a</span><span class="p">,</span>
+            <span class="n">id_type</span> <span class="o">=</span> <span class="n">id_type_a</span><span class="p">,</span>
+            <span class="n">entity_type</span> <span class="o">=</span> <span class="n">entity_type_a</span><span class="p">,</span>
+            <span class="n">taxon</span> <span class="o">=</span> <span class="n">taxon_a</span><span class="p">,</span>
+        <span class="p">)</span>
+        <span class="n">b</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_get_entity</span><span class="p">(</span>
+            <span class="n">identifier</span> <span class="o">=</span> <span class="n">b</span><span class="p">,</span>
+            <span class="n">id_type</span> <span class="o">=</span> <span class="n">id_type_b</span><span class="p">,</span>
+            <span class="n">entity_type</span> <span class="o">=</span> <span class="n">entity_type_b</span><span class="p">,</span>
+            <span class="n">taxon</span> <span class="o">=</span> <span class="n">taxon_b</span><span class="p">,</span>
+        <span class="p">)</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">nodes</span> <span class="o">=</span> <span class="nb">tuple</span><span class="p">(</span><span class="nb">sorted</span><span class="p">((</span><span class="n">a</span><span class="p">,</span> <span class="n">b</span><span class="p">)))</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">a</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">nodes</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">b</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">nodes</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">key</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_key</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">a_b</span> <span class="o">=</span> <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">nodes</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="bp">self</span><span class="o">.</span><span class="n">nodes</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">b_a</span> <span class="o">=</span> <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">nodes</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span> <span class="bp">self</span><span class="o">.</span><span class="n">nodes</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">evidences</span> <span class="o">=</span> <span class="n">pypath_evidence</span><span class="o">.</span><span class="n">Evidences</span><span class="p">()</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">direction</span> <span class="o">=</span> <span class="p">{</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">a_b</span><span class="p">:</span> <span class="n">pypath_evidence</span><span class="o">.</span><span class="n">Evidences</span><span class="p">(),</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">b_a</span><span class="p">:</span> <span class="n">pypath_evidence</span><span class="o">.</span><span class="n">Evidences</span><span class="p">(),</span>
+            <span class="s1">&#39;undirected&#39;</span><span class="p">:</span> <span class="n">pypath_evidence</span><span class="o">.</span><span class="n">Evidences</span><span class="p">(),</span>
+        <span class="p">}</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">positive</span> <span class="o">=</span> <span class="p">{</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">a_b</span><span class="p">:</span> <span class="n">pypath_evidence</span><span class="o">.</span><span class="n">Evidences</span><span class="p">(),</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">b_a</span><span class="p">:</span> <span class="n">pypath_evidence</span><span class="o">.</span><span class="n">Evidences</span><span class="p">(),</span>
+        <span class="p">}</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">negative</span> <span class="o">=</span> <span class="p">{</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">a_b</span><span class="p">:</span> <span class="n">pypath_evidence</span><span class="o">.</span><span class="n">Evidences</span><span class="p">(),</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">b_a</span><span class="p">:</span> <span class="n">pypath_evidence</span><span class="o">.</span><span class="n">Evidences</span><span class="p">(),</span>
+        <span class="p">}</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">unknown_effect</span> <span class="o">=</span> <span class="p">{</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">a_b</span><span class="p">:</span> <span class="n">pypath_evidence</span><span class="o">.</span><span class="n">Evidences</span><span class="p">(),</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">b_a</span><span class="p">:</span> <span class="n">pypath_evidence</span><span class="o">.</span><span class="n">Evidences</span><span class="p">(),</span>
+        <span class="p">}</span>
+
+        <span class="n">attrs_mod</span><span class="o">.</span><span class="n">AttributeHandler</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">attrs</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="Interaction.reload">
+<a class="viewcode-back" href="../../../api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.reload">[docs]</a>
+    <span class="k">def</span> <span class="nf">reload</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Reloads the object from the module level.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">modname</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="vm">__class__</span><span class="o">.</span><span class="vm">__module__</span>
+        <span class="n">evmodname</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">evidences</span><span class="o">.</span><span class="vm">__class__</span><span class="o">.</span><span class="vm">__module__</span>
+        <span class="n">enmodname</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">a</span><span class="o">.</span><span class="vm">__class__</span><span class="o">.</span><span class="vm">__module__</span>
+        <span class="n">mod</span> <span class="o">=</span> <span class="nb">__import__</span><span class="p">(</span><span class="n">modname</span><span class="p">,</span> <span class="n">fromlist</span> <span class="o">=</span> <span class="p">[</span><span class="n">modname</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;.&#39;</span><span class="p">)[</span><span class="mi">0</span><span class="p">]])</span>
+        <span class="n">evmod</span> <span class="o">=</span> <span class="nb">__import__</span><span class="p">(</span><span class="n">evmodname</span><span class="p">,</span> <span class="n">fromlist</span> <span class="o">=</span> <span class="p">[</span><span class="n">evmodname</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;.&#39;</span><span class="p">)[</span><span class="mi">0</span><span class="p">]])</span>
+        <span class="n">enmod</span> <span class="o">=</span> <span class="nb">__import__</span><span class="p">(</span><span class="n">enmodname</span><span class="p">,</span> <span class="n">fromlist</span> <span class="o">=</span> <span class="p">[</span><span class="n">enmodname</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;.&#39;</span><span class="p">)[</span><span class="mi">0</span><span class="p">]])</span>
+        <span class="n">imp</span><span class="o">.</span><span class="n">reload</span><span class="p">(</span><span class="n">mod</span><span class="p">)</span>
+        <span class="n">imp</span><span class="o">.</span><span class="n">reload</span><span class="p">(</span><span class="n">evmod</span><span class="p">)</span>
+        <span class="n">imp</span><span class="o">.</span><span class="n">reload</span><span class="p">(</span><span class="n">enmod</span><span class="p">)</span>
+        <span class="n">new</span> <span class="o">=</span> <span class="nb">getattr</span><span class="p">(</span><span class="n">mod</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="vm">__class__</span><span class="o">.</span><span class="vm">__name__</span><span class="p">)</span>
+        <span class="n">evsnew</span> <span class="o">=</span> <span class="nb">getattr</span><span class="p">(</span><span class="n">evmod</span><span class="p">,</span> <span class="s1">&#39;Evidences&#39;</span><span class="p">)</span>
+        <span class="n">evnew</span> <span class="o">=</span> <span class="nb">getattr</span><span class="p">(</span><span class="n">evmod</span><span class="p">,</span> <span class="s1">&#39;Evidence&#39;</span><span class="p">)</span>
+        <span class="n">ennew</span> <span class="o">=</span> <span class="nb">getattr</span><span class="p">(</span><span class="n">enmod</span><span class="p">,</span> <span class="s1">&#39;Entity&#39;</span><span class="p">)</span>
+        <span class="nb">setattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">&#39;__class__&#39;</span><span class="p">,</span> <span class="n">new</span><span class="p">)</span>
+
+        <span class="k">for</span> <span class="n">evs</span> <span class="ow">in</span> <span class="n">itertools</span><span class="o">.</span><span class="n">chain</span><span class="p">(</span>
+            <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">evidences</span><span class="p">,),</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">direction</span><span class="o">.</span><span class="n">values</span><span class="p">(),</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">positive</span><span class="o">.</span><span class="n">values</span><span class="p">(),</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">negative</span><span class="o">.</span><span class="n">values</span><span class="p">(),</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">unknown_effect</span><span class="o">.</span><span class="n">values</span><span class="p">(),</span>
+        <span class="p">):</span>
+
+            <span class="n">evs</span><span class="o">.</span><span class="vm">__class__</span> <span class="o">=</span> <span class="n">evsnew</span>
+
+            <span class="k">for</span> <span class="n">ev</span> <span class="ow">in</span> <span class="n">evs</span><span class="p">:</span>
+
+                <span class="n">ev</span><span class="o">.</span><span class="vm">__class__</span> <span class="o">=</span> <span class="n">evnew</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">a</span><span class="o">.</span><span class="vm">__class__</span> <span class="o">=</span> <span class="n">ennew</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">b</span><span class="o">.</span><span class="vm">__class__</span> <span class="o">=</span> <span class="n">ennew</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_generate_get_methods</span><span class="p">()</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">_generate_count_methods</span><span class="p">()</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">_generate_by_methods</span><span class="p">()</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">_get_entity</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">identifier</span><span class="p">,</span>
+            <span class="n">id_type</span> <span class="o">=</span> <span class="s1">&#39;uniprot&#39;</span><span class="p">,</span>
+            <span class="n">entity_type</span> <span class="o">=</span> <span class="s1">&#39;protein&#39;</span><span class="p">,</span>
+            <span class="n">taxon</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">,</span>
+        <span class="p">):</span>
+
+        <span class="k">if</span> <span class="ow">not</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">identifier</span><span class="p">,</span> <span class="n">entity</span><span class="o">.</span><span class="n">Entity</span><span class="p">):</span>
+
+            <span class="n">identifier</span> <span class="o">=</span> <span class="n">entity</span><span class="o">.</span><span class="n">Entity</span><span class="p">(</span>
+                <span class="n">identifier</span> <span class="o">=</span> <span class="n">identifier</span><span class="p">,</span>
+                <span class="n">id_type</span> <span class="o">=</span> <span class="n">id_type</span><span class="p">,</span>
+                <span class="n">entity_type</span> <span class="o">=</span> <span class="n">entity_type</span><span class="p">,</span>
+                <span class="n">taxon</span> <span class="o">=</span> <span class="n">taxon</span><span class="p">,</span>
+            <span class="p">)</span>
+
+        <span class="k">return</span> <span class="n">identifier</span>
+
+
+    <span class="k">def</span> <span class="nf">_check_nodes_key</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">nodes</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;Checks if *nodes* is contained in the edge.</span>
+
+<span class="sd">        :arg list nodes:</span>
+<span class="sd">             Or [tuple], contains the names of the nodes to be checked.</span>
+
+<span class="sd">        :return:</span>
+<span class="sd">            (*bool*) -- ``True`` if all elements in *nodes* are</span>
+<span class="sd">            contained in the object :py:attr:`nodes` list.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">return</span> <span class="n">nodes</span> <span class="o">==</span> <span class="bp">self</span><span class="o">.</span><span class="n">a_b</span> <span class="ow">or</span> <span class="n">nodes</span> <span class="o">==</span> <span class="bp">self</span><span class="o">.</span><span class="n">b_a</span>
+
+
+    <span class="k">def</span> <span class="nf">_check_direction_key</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">direction</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Checks if *direction* is ``&#39;undirected&#39;`` or contains the nodes of</span>
+<span class="sd">        the current edge. Used internally to check that *di* is a valid</span>
+<span class="sd">        key for the object attributes declared on dictionaries.</span>
+
+<span class="sd">        :arg tuple di:</span>
+<span class="sd">            Or [str], key to be tested for validity.</span>
+
+<span class="sd">        :return:</span>
+<span class="sd">            (*bool*) -- ``True`` if *di* is ``&#39;undirected&#39;`` or a tuple</span>
+<span class="sd">              of node names contained in the edge, ``False`` otherwise.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">return</span> <span class="p">(</span>
+            <span class="n">direction</span> <span class="o">==</span> <span class="s1">&#39;undirected&#39;</span> <span class="ow">or</span> <span class="p">(</span>
+                <span class="nb">isinstance</span><span class="p">(</span><span class="n">direction</span><span class="p">,</span> <span class="nb">tuple</span><span class="p">)</span> <span class="ow">and</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">_check_nodes_key</span><span class="p">(</span><span class="n">direction</span><span class="p">)</span>
+            <span class="p">)</span>
+        <span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">id_to_entity</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">identifier</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="p">(</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">a</span>
+                <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">a</span> <span class="o">==</span> <span class="n">identifier</span> <span class="k">else</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">b</span>
+                <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">b</span> <span class="o">==</span> <span class="n">identifier</span> <span class="k">else</span>
+            <span class="kc">None</span>
+        <span class="p">)</span>
+
+
+<div class="viewcode-block" id="Interaction.direction_key">
+<a class="viewcode-back" href="../../../api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.direction_key">[docs]</a>
+    <span class="k">def</span> <span class="nf">direction_key</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">direction</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        The direction keys are tuples of `Entity` objects; this method</span>
+<span class="sd">        creates these tuples from a tuple of strings. The two strings</span>
+<span class="sd">        can be labels or identifiers.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">if</span> <span class="n">direction</span> <span class="o">==</span> <span class="s1">&#39;undirected&#39;</span><span class="p">:</span>
+
+            <span class="k">return</span> <span class="n">direction</span>
+
+        <span class="n">direction</span> <span class="o">=</span> <span class="nb">tuple</span><span class="p">(</span><span class="nb">map</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">id_to_entity</span><span class="p">,</span> <span class="n">direction</span><span class="p">))</span>
+
+        <span class="k">return</span> <span class="p">(</span>
+            <span class="n">direction</span>
+                <span class="k">if</span> <span class="n">direction</span> <span class="o">==</span> <span class="bp">self</span><span class="o">.</span><span class="n">a_b</span> <span class="ow">or</span> <span class="n">direction</span> <span class="o">==</span> <span class="bp">self</span><span class="o">.</span><span class="n">b_a</span> <span class="k">else</span>
+            <span class="kc">None</span>
+        <span class="p">)</span></div>
+
+
+
+    <span class="nd">@staticmethod</span>
+    <span class="k">def</span> <span class="nf">direction_key_identifiers</span><span class="p">(</span><span class="n">direction</span><span class="p">):</span>
+
+        <span class="k">if</span> <span class="n">direction</span> <span class="o">==</span> <span class="s1">&#39;undirected&#39;</span><span class="p">:</span>
+
+            <span class="k">return</span> <span class="n">direction</span>
+
+        <span class="k">return</span> <span class="nb">tuple</span><span class="p">(</span><span class="n">ent</span><span class="o">.</span><span class="n">identifier</span> <span class="k">for</span> <span class="n">ent</span> <span class="ow">in</span> <span class="n">direction</span><span class="p">)</span>
+
+
+    <span class="nd">@staticmethod</span>
+    <span class="k">def</span> <span class="nf">_directed_key</span><span class="p">(</span><span class="n">direction</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="n">direction</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span> <span class="ow">and</span> <span class="n">direction</span> <span class="o">!=</span> <span class="s1">&#39;undirected&#39;</span>
+
+
+<div class="viewcode-block" id="Interaction.add_evidence">
+<a class="viewcode-back" href="../../../api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.add_evidence">[docs]</a>
+    <span class="k">def</span> <span class="nf">add_evidence</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">evidence</span><span class="p">,</span>
+            <span class="n">direction</span> <span class="o">=</span> <span class="s1">&#39;undirected&#39;</span><span class="p">,</span>
+            <span class="n">effect</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">references</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">attrs</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+        <span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Adds directionality information with the corresponding data</span>
+<span class="sd">        source named. Modifies self attributes :py:attr:`dirs` and</span>
+<span class="sd">        :py:attr:`sources`.</span>
+
+<span class="sd">        :arg resource.NetworkResource,evidence.Evidence evidence:</span>
+<span class="sd">            Either a ``pypath.evidence.Evidence`` object or a resource as</span>
+<span class="sd">            ``pypath.resource.NetworkResource`` object. In the latter case</span>
+<span class="sd">            the references can be provided in a separate argument.</span>
+<span class="sd">        :arg tuple direction:</span>
+<span class="sd">            Or [str], the directionality key for which the value on</span>
+<span class="sd">            :py:attr:`dirs` has to be set ``True``.</span>
+<span class="sd">        :arg int effect:</span>
+<span class="sd">            The causal effect of the interaction. 1 or &#39;stimulation&#39;</span>
+<span class="sd">            corresponds to a stimulatory, -1 or &#39;inhibition&#39; to an</span>
+<span class="sd">            inhibitory while 0 to an unknown or neutral effect.</span>
+<span class="sd">        :arg set,NoneType references:</span>
+<span class="sd">            A set of references, used only if the resource have been provided</span>
+<span class="sd">            as ``NetworkResource`` object.</span>
+<span class="sd">        :arg dict attrs:</span>
+<span class="sd">            Custom (resource specific) attributes.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">direction</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">direction_key</span><span class="p">(</span><span class="n">direction</span><span class="p">)</span>
+
+        <span class="k">if</span> <span class="n">direction</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
+
+            <span class="n">_log</span><span class="p">(</span>
+                <span class="s1">&#39;Attempting to add evidence with non matching &#39;</span>
+                <span class="s1">&#39;interaction partners.&#39;</span>
+            <span class="p">)</span>
+            <span class="k">return</span>
+
+        <span class="n">evidence</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="n">evidence</span>
+                <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span>
+                    <span class="n">evidence</span><span class="p">,</span>
+                    <span class="p">(</span>
+                        <span class="n">pypath_evidence</span><span class="o">.</span><span class="n">Evidence</span><span class="p">,</span>
+                        <span class="n">pypath_evidence</span><span class="o">.</span><span class="n">Evidences</span><span class="p">,</span>
+                    <span class="p">)</span>
+                <span class="p">)</span> <span class="k">else</span>
+            <span class="n">pypath_evidence</span><span class="o">.</span><span class="n">Evidence</span><span class="p">(</span>
+                <span class="n">resource</span> <span class="o">=</span> <span class="n">evidence</span><span class="p">,</span>
+                <span class="n">references</span> <span class="o">=</span> <span class="n">references</span><span class="p">,</span>
+            <span class="p">)</span>
+        <span class="p">)</span>
+
+        <span class="k">if</span> <span class="nb">hasattr</span><span class="p">(</span><span class="n">evidence</span><span class="p">,</span> <span class="s1">&#39;update_attrs&#39;</span><span class="p">):</span>
+
+            <span class="n">evidence</span><span class="o">.</span><span class="n">update_attrs</span><span class="p">(</span><span class="n">attrs</span><span class="p">)</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">evidences</span> <span class="o">+=</span> <span class="n">evidence</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">direction</span><span class="p">[</span><span class="n">direction</span><span class="p">]</span> <span class="o">+=</span> <span class="n">evidence</span>
+
+        <span class="k">if</span> <span class="n">direction</span> <span class="o">!=</span> <span class="s1">&#39;undirected&#39;</span><span class="p">:</span>
+
+            <span class="k">if</span> <span class="n">effect</span> <span class="ow">in</span> <span class="p">{</span><span class="mi">1</span><span class="p">,</span> <span class="s1">&#39;positive&#39;</span><span class="p">,</span> <span class="s1">&#39;stimulation&#39;</span><span class="p">}:</span>
+
+                <span class="bp">self</span><span class="o">.</span><span class="n">positive</span><span class="p">[</span><span class="n">direction</span><span class="p">]</span> <span class="o">+=</span> <span class="n">evidence</span>
+
+            <span class="k">elif</span> <span class="n">effect</span> <span class="ow">in</span> <span class="p">{</span><span class="o">-</span><span class="mi">1</span><span class="p">,</span> <span class="s1">&#39;negative&#39;</span><span class="p">,</span> <span class="s1">&#39;inhibition&#39;</span><span class="p">}:</span>
+
+                <span class="bp">self</span><span class="o">.</span><span class="n">negative</span><span class="p">[</span><span class="n">direction</span><span class="p">]</span> <span class="o">+=</span> <span class="n">evidence</span>
+
+            <span class="k">elif</span> <span class="n">effect</span> <span class="ow">in</span> <span class="p">{</span><span class="mi">0</span><span class="p">,</span> <span class="s1">&#39;unknown&#39;</span><span class="p">}:</span>
+
+                <span class="bp">self</span><span class="o">.</span><span class="n">unknown_effect</span><span class="p">[</span><span class="n">direction</span><span class="p">]</span> <span class="o">+=</span> <span class="n">evidence</span></div>
+
+
+
+    <span class="k">def</span> <span class="fm">__hash__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="nb">hash</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">key</span><span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="fm">__eq__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">other</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="nb">hasattr</span><span class="p">(</span><span class="n">other</span><span class="p">,</span> <span class="s1">&#39;key&#39;</span><span class="p">)</span> <span class="ow">and</span> <span class="bp">self</span><span class="o">.</span><span class="n">key</span> <span class="o">==</span> <span class="n">other</span><span class="o">.</span><span class="n">key</span>
+
+
+    <span class="nd">@property</span>
+    <span class="k">def</span> <span class="nf">_key</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="n">InteractionKey</span><span class="p">(</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">a</span><span class="o">.</span><span class="n">key</span><span class="p">,</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">b</span><span class="o">.</span><span class="n">key</span><span class="p">,</span>
+        <span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="fm">__iadd__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">other</span><span class="p">):</span>
+
+        <span class="k">if</span> <span class="bp">self</span> <span class="o">!=</span> <span class="n">other</span><span class="p">:</span>
+
+            <span class="n">_log</span><span class="p">(</span>
+                <span class="s1">&#39;Attempt to merge interactions with &#39;</span>
+                <span class="s1">&#39;non matching interaction partners.&#39;</span>
+            <span class="p">)</span>
+            <span class="k">return</span> <span class="bp">self</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_merge_evidences</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">other</span><span class="p">)</span>
+        <span class="n">attrs_mod</span><span class="o">.</span><span class="n">AttributeHandler</span><span class="o">.</span><span class="fm">__iadd__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">other</span><span class="p">)</span>
+
+        <span class="k">return</span> <span class="bp">self</span>
+
+
+    <span class="k">def</span> <span class="fm">__add__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">other</span><span class="p">):</span>
+
+        <span class="n">new</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">__copy__</span><span class="p">()</span>
+
+        <span class="n">new</span> <span class="o">+=</span> <span class="n">other</span>
+
+        <span class="k">return</span> <span class="n">new</span>
+
+
+    <span class="k">def</span> <span class="nf">__copy__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="n">new</span> <span class="o">=</span> <span class="n">Interaction</span><span class="p">(</span><span class="o">*</span><span class="bp">self</span><span class="o">.</span><span class="n">key</span><span class="p">)</span>
+        <span class="n">new</span> <span class="o">+=</span> <span class="bp">self</span>
+        <span class="n">new</span><span class="o">.</span><span class="n">update_attrs</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span>
+
+        <span class="k">return</span> <span class="n">new</span>
+
+
+    <span class="nd">@staticmethod</span>
+    <span class="k">def</span> <span class="nf">_merge_evidences</span><span class="p">(</span><span class="n">one</span><span class="p">,</span> <span class="n">other</span><span class="p">):</span>
+
+        <span class="n">one</span><span class="o">.</span><span class="n">evidences</span> <span class="o">+=</span> <span class="n">other</span><span class="o">.</span><span class="n">evidences</span>
+
+        <span class="k">for</span> <span class="n">dir_key</span> <span class="ow">in</span> <span class="n">one</span><span class="o">.</span><span class="n">direction</span><span class="o">.</span><span class="n">keys</span><span class="p">():</span>
+
+            <span class="n">one</span><span class="o">.</span><span class="n">direction</span><span class="p">[</span><span class="n">dir_key</span><span class="p">]</span> <span class="o">+=</span> <span class="n">other</span><span class="o">.</span><span class="n">direction</span><span class="p">[</span><span class="n">dir_key</span><span class="p">]</span>
+
+        <span class="k">for</span> <span class="n">eff_key</span> <span class="ow">in</span> <span class="n">one</span><span class="o">.</span><span class="n">positive</span><span class="o">.</span><span class="n">keys</span><span class="p">():</span>
+
+            <span class="n">one</span><span class="o">.</span><span class="n">positive</span><span class="p">[</span><span class="n">eff_key</span><span class="p">]</span> <span class="o">+=</span> <span class="n">other</span><span class="o">.</span><span class="n">positive</span><span class="p">[</span><span class="n">eff_key</span><span class="p">]</span>
+
+        <span class="k">for</span> <span class="n">eff_key</span> <span class="ow">in</span> <span class="n">one</span><span class="o">.</span><span class="n">negative</span><span class="o">.</span><span class="n">keys</span><span class="p">():</span>
+
+            <span class="n">one</span><span class="o">.</span><span class="n">negative</span><span class="p">[</span><span class="n">eff_key</span><span class="p">]</span> <span class="o">+=</span> <span class="n">other</span><span class="o">.</span><span class="n">negative</span><span class="p">[</span><span class="n">eff_key</span><span class="p">]</span>
+
+        <span class="k">for</span> <span class="n">eff_key</span> <span class="ow">in</span> <span class="n">one</span><span class="o">.</span><span class="n">unknown_effect</span><span class="o">.</span><span class="n">keys</span><span class="p">():</span>
+
+            <span class="n">one</span><span class="o">.</span><span class="n">unknown_effect</span><span class="p">[</span><span class="n">eff_key</span><span class="p">]</span> <span class="o">+=</span> <span class="n">other</span><span class="o">.</span><span class="n">unknown_effect</span><span class="p">[</span><span class="n">eff_key</span><span class="p">]</span>
+
+
+    <span class="k">def</span> <span class="fm">__repr__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="s1">&#39;&lt;Interaction: </span><span class="si">%s</span><span class="s1"> [</span><span class="si">%s</span><span class="s1">]&gt;&#39;</span> <span class="o">%</span> <span class="p">(</span>
+            <span class="bp">self</span><span class="o">.</span><span class="fm">__str__</span><span class="p">(),</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">evidences</span><span class="o">.</span><span class="fm">__repr__</span><span class="p">()</span><span class="o">.</span><span class="n">strip</span><span class="p">(</span><span class="s1">&#39;&lt;&gt;&#39;</span><span class="p">),</span>
+        <span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="fm">__str__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="s1">&#39;</span><span class="si">%s</span><span class="s1"> </span><span class="si">%s</span><span class="s1">=</span><span class="si">%s</span><span class="s1">=</span><span class="si">%s</span><span class="s1">=</span><span class="si">%s</span><span class="s1"> </span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="p">(</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">a</span><span class="o">.</span><span class="n">label</span> <span class="ow">or</span> <span class="bp">self</span><span class="o">.</span><span class="n">a</span><span class="o">.</span><span class="n">identifier</span><span class="p">,</span>
+            <span class="s1">&#39;&lt;&#39;</span> <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">direction</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">b_a</span><span class="p">]</span> <span class="k">else</span> <span class="s1">&#39;=&#39;</span><span class="p">,</span>
+            <span class="p">(</span>
+                <span class="s1">&#39;(+-)&#39;</span> <span class="k">if</span> <span class="p">(</span>
+                    <span class="bp">self</span><span class="o">.</span><span class="n">positive</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">b_a</span><span class="p">]</span> <span class="ow">and</span>
+                    <span class="bp">self</span><span class="o">.</span><span class="n">negative</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">b_a</span><span class="p">]</span>
+                <span class="p">)</span> <span class="k">else</span>
+                <span class="s1">&#39;(+)=&#39;</span> <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">positive</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">b_a</span><span class="p">]</span> <span class="k">else</span>
+                <span class="s1">&#39;(-)=&#39;</span> <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">negative</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">b_a</span><span class="p">]</span> <span class="k">else</span>
+                <span class="s1">&#39;====&#39;</span>
+            <span class="p">),</span>
+            <span class="p">(</span>
+                <span class="s1">&#39;(+-)&#39;</span> <span class="k">if</span> <span class="p">(</span>
+                    <span class="bp">self</span><span class="o">.</span><span class="n">positive</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">a_b</span><span class="p">]</span> <span class="ow">and</span>
+                    <span class="bp">self</span><span class="o">.</span><span class="n">negative</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">a_b</span><span class="p">]</span>
+                <span class="p">)</span> <span class="k">else</span>
+                <span class="s1">&#39;(+)=&#39;</span> <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">positive</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">a_b</span><span class="p">]</span> <span class="k">else</span>
+                <span class="s1">&#39;(-)=&#39;</span> <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">negative</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">a_b</span><span class="p">]</span> <span class="k">else</span>
+                <span class="s1">&#39;====&#39;</span>
+            <span class="p">),</span>
+            <span class="s1">&#39;&gt;&#39;</span> <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">direction</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">a_b</span><span class="p">]</span> <span class="k">else</span> <span class="s1">&#39;=&#39;</span><span class="p">,</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">b</span><span class="o">.</span><span class="n">label</span> <span class="ow">or</span> <span class="bp">self</span><span class="o">.</span><span class="n">b</span><span class="o">.</span><span class="n">identifier</span><span class="p">,</span>
+        <span class="p">)</span>
+
+    <span class="k">def</span> <span class="fm">__contains__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">other</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="p">(</span>
+            <span class="n">other</span> <span class="o">==</span> <span class="bp">self</span><span class="o">.</span><span class="n">a</span> <span class="ow">or</span>
+            <span class="n">other</span> <span class="o">==</span> <span class="bp">self</span><span class="o">.</span><span class="n">b</span> <span class="ow">or</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">evidences</span><span class="o">.</span><span class="fm">__contains__</span><span class="p">(</span><span class="n">other</span><span class="p">)</span> <span class="ow">or</span>
+            <span class="n">attrs_mod</span><span class="o">.</span><span class="n">AttributeHandler</span><span class="o">.</span><span class="fm">__contains__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">other</span><span class="p">)</span>
+        <span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">has_data_model</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">data_model</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">evidences</span><span class="o">.</span><span class="n">has_data_model</span><span class="p">(</span><span class="n">data_model</span><span class="p">)</span>
+
+
+    <span class="nd">@property</span>
+    <span class="k">def</span> <span class="nf">data_models</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="p">{</span>
+            <span class="n">ev</span><span class="o">.</span><span class="n">resource</span><span class="o">.</span><span class="n">data_model</span>
+            <span class="k">for</span> <span class="n">ev</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">evidences</span>
+        <span class="p">}</span>
+
+
+    <span class="k">def</span> <span class="nf">has_dataset</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">dataset</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
+            <span class="n">direction</span><span class="p">:</span> <span class="nb">str</span> <span class="o">|</span> <span class="nb">tuple</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">effect</span><span class="p">:</span> <span class="n">Literal</span><span class="p">[</span><span class="s1">&#39;positive&#39;</span><span class="p">,</span> <span class="s1">&#39;negative&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="o">**</span><span class="n">kwargs</span><span class="p">,</span>
+        <span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">bool</span><span class="p">:</span>
+
+        <span class="k">return</span> <span class="p">(</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">get_evidences</span><span class="p">(</span><span class="n">direction</span> <span class="o">=</span> <span class="n">direction</span><span class="p">,</span> <span class="n">effect</span> <span class="o">=</span> <span class="n">effect</span><span class="p">)</span><span class="o">.</span>
+            <span class="n">has_dataset</span><span class="p">(</span><span class="n">dataset</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
+        <span class="p">)</span>
+
+
+<div class="viewcode-block" id="Interaction.get_direction">
+<a class="viewcode-back" href="../../../api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.get_direction">[docs]</a>
+    <span class="k">def</span> <span class="nf">get_direction</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">direction</span><span class="p">,</span>
+            <span class="n">resources</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+            <span class="n">evidences</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+            <span class="n">sources</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+            <span class="n">resource_names</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+        <span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Returns the state (or *resources* if specified) of the given</span>
+<span class="sd">        *direction*.</span>
+
+<span class="sd">        :arg tuple direction:</span>
+<span class="sd">            Or [str] (if ``&#39;undirected&#39;``). Pair of nodes from which</span>
+<span class="sd">            direction information is to be retrieved.</span>
+<span class="sd">        :arg bool resources:</span>
+<span class="sd">            Optional, ``&#39;False&#39;`` by default. Specifies if the</span>
+<span class="sd">            :py:attr:`resources` information of the given direction is to</span>
+<span class="sd">            be retrieved instead.</span>
+
+<span class="sd">        :return:</span>
+<span class="sd">            (*bool* or *set*) -- (if ``resources=True``). Presence/absence</span>
+<span class="sd">            of the requested direction (or the list of resources if</span>
+<span class="sd">            specified). Returns ``None`` if *direction* is not valid.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">direction</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">direction_key</span><span class="p">(</span><span class="n">direction</span><span class="p">)</span>
+
+        <span class="k">if</span> <span class="n">direction</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
+
+            <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_select_answer_type</span><span class="p">(</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">direction</span><span class="p">[</span><span class="n">direction</span><span class="p">],</span>
+                <span class="n">resources</span> <span class="o">=</span> <span class="n">resources</span><span class="p">,</span>
+                <span class="n">evidences</span> <span class="o">=</span> <span class="n">evidences</span><span class="p">,</span>
+                <span class="n">resource_names</span> <span class="o">=</span> <span class="n">resource_names</span><span class="p">,</span>
+                <span class="n">sources</span> <span class="o">=</span> <span class="n">sources</span><span class="p">,</span>
+            <span class="p">)</span>
+
+        <span class="k">else</span><span class="p">:</span>
+            <span class="k">return</span> <span class="kc">None</span></div>
+
+
+
+<div class="viewcode-block" id="Interaction.get_directions">
+<a class="viewcode-back" href="../../../api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.get_directions">[docs]</a>
+    <span class="k">def</span> <span class="nf">get_directions</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">src</span><span class="p">,</span>
+            <span class="n">tgt</span><span class="p">,</span>
+            <span class="n">resources</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+            <span class="n">evidences</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+            <span class="n">resource_names</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+            <span class="n">sources</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+        <span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Returns all directions with boolean values or list of sources.</span>
+
+<span class="sd">        :arg str src:</span>
+<span class="sd">            Source node.</span>
+<span class="sd">        :arg str tgt:</span>
+<span class="sd">            Target node.</span>
+<span class="sd">        :arg bool resources:</span>
+<span class="sd">            Optional, ``False`` by default. Specifies whether to return</span>
+<span class="sd">            the :py:attr:`resources` attribute instead of :py:attr:`dirs`.</span>
+
+<span class="sd">        :return:</span>
+<span class="sd">            Contains the :py:attr:`dirs` (or :py:attr:`resources` if</span>
+<span class="sd">            specified) of the given edge.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">query</span> <span class="o">=</span> <span class="p">(</span><span class="n">src</span><span class="p">,</span> <span class="n">tgt</span><span class="p">)</span>
+
+        <span class="n">answer_type_args</span> <span class="o">=</span> <span class="p">{</span>
+            <span class="s1">&#39;resources&#39;</span><span class="p">:</span> <span class="n">resources</span><span class="p">,</span>
+            <span class="s1">&#39;evidences&#39;</span><span class="p">:</span> <span class="n">evidences</span><span class="p">,</span>
+            <span class="s1">&#39;resource_names&#39;</span><span class="p">:</span> <span class="n">resource_names</span><span class="p">,</span>
+            <span class="s1">&#39;sources&#39;</span><span class="p">:</span> <span class="n">sources</span><span class="p">,</span>
+        <span class="p">}</span>
+
+        <span class="n">query</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">direction_key</span><span class="p">(</span><span class="n">query</span><span class="p">)</span>
+
+        <span class="k">if</span> <span class="n">query</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
+
+            <span class="k">return</span> <span class="p">[</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">_select_answer_type</span><span class="p">(</span>
+                    <span class="bp">self</span><span class="o">.</span><span class="n">direction</span><span class="p">[</span><span class="n">query</span><span class="p">],</span>
+                    <span class="o">**</span><span class="n">answer_type_args</span>
+                <span class="p">),</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">_select_answer_type</span><span class="p">(</span>
+                    <span class="bp">self</span><span class="o">.</span><span class="n">direction</span><span class="p">[</span><span class="nb">tuple</span><span class="p">(</span><span class="nb">reversed</span><span class="p">(</span><span class="n">query</span><span class="p">))],</span>
+                    <span class="o">**</span><span class="n">answer_type_args</span>
+                <span class="p">),</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">_select_answer_type</span><span class="p">(</span>
+                    <span class="bp">self</span><span class="o">.</span><span class="n">direction</span><span class="p">[</span><span class="s1">&#39;undirected&#39;</span><span class="p">],</span>
+                    <span class="o">**</span><span class="n">answer_type_args</span>
+                <span class="p">),</span>
+            <span class="p">]</span>
+
+        <span class="k">else</span><span class="p">:</span>
+            <span class="k">return</span> <span class="kc">None</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">_select_answer_type</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">answer</span><span class="p">,</span>
+            <span class="n">resources</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+            <span class="n">evidences</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+            <span class="n">resource_names</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+            <span class="n">sources</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+        <span class="p">):</span>
+
+        <span class="k">return</span> <span class="p">(</span>
+            <span class="n">answer</span>
+                <span class="k">if</span> <span class="n">evidences</span> <span class="k">else</span>
+            <span class="n">answer</span><span class="o">.</span><span class="n">get_resources</span><span class="p">()</span>
+                <span class="k">if</span> <span class="n">resources</span> <span class="k">else</span>
+            <span class="n">answer</span><span class="o">.</span><span class="n">get_resource_names</span><span class="p">()</span>
+                <span class="k">if</span> <span class="n">sources</span> <span class="ow">or</span> <span class="n">resource_names</span> <span class="k">else</span>
+            <span class="nb">bool</span><span class="p">(</span><span class="n">answer</span><span class="p">)</span>
+        <span class="p">)</span>
+
+
+<div class="viewcode-block" id="Interaction.which_directions">
+<a class="viewcode-back" href="../../../api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.which_directions">[docs]</a>
+    <span class="k">def</span> <span class="nf">which_directions</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">resources</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">effect</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+        <span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Returns the pair(s) of nodes for which there is information</span>
+<span class="sd">        about their directionality.</span>
+
+<span class="sd">        :arg str effect:</span>
+<span class="sd">            Either *positive* or *negative*.</span>
+<span class="sd">        :arg str,set resources:</span>
+<span class="sd">            Limits the query to one or more resources. Optional.</span>
+
+<span class="sd">        :return:</span>
+<span class="sd">            (*tuple*) -- Tuple of tuples with pairs of nodes where the</span>
+<span class="sd">            first element is the source and the second is the target</span>
+<span class="sd">            entity, according to the given resources and limited to the</span>
+<span class="sd">            effect.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">resources</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_resources_set</span><span class="p">(</span><span class="n">resources</span><span class="p">)</span>
+        <span class="n">effect</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_effect_synonyms</span><span class="p">(</span><span class="n">effect</span><span class="p">)</span>
+
+        <span class="k">return</span> <span class="nb">tuple</span><span class="p">(</span>
+            <span class="n">_dir</span>
+            <span class="k">for</span> <span class="n">_dir</span><span class="p">,</span> <span class="n">_evidences</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">direction</span><span class="p">)</span>
+            <span class="k">if</span> <span class="n">_dir</span> <span class="o">!=</span> <span class="s1">&#39;undirected&#39;</span> <span class="ow">and</span>
+            <span class="n">_evidences</span> <span class="ow">and</span> <span class="p">(</span>
+                <span class="ow">not</span> <span class="n">resources</span> <span class="ow">or</span>
+                <span class="n">_evidences</span> <span class="o">&amp;</span> <span class="n">resources</span>
+            <span class="p">)</span> <span class="ow">and</span> <span class="p">(</span>
+                <span class="ow">not</span> <span class="n">effect</span>
+                <span class="ow">or</span> <span class="p">(</span>
+                    <span class="ow">not</span> <span class="n">resources</span> <span class="ow">and</span>
+                    <span class="nb">getattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">effect</span><span class="p">)[</span><span class="n">_dir</span><span class="p">]</span>
+                <span class="p">)</span> <span class="ow">or</span>
+                <span class="nb">getattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">effect</span><span class="p">)[</span><span class="n">_dir</span><span class="p">]</span> <span class="o">&amp;</span> <span class="n">resources</span>
+            <span class="p">)</span>
+        <span class="p">)</span></div>
+
+
+
+    <span class="c1"># synonym: old name</span>
+    <span class="n">which_dirs</span> <span class="o">=</span> <span class="n">which_directions</span>
+
+
+<div class="viewcode-block" id="Interaction.which_signs">
+<a class="viewcode-back" href="../../../api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.which_signs">[docs]</a>
+    <span class="k">def</span> <span class="nf">which_signs</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">resources</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span> <span class="n">effect</span> <span class="o">=</span> <span class="kc">None</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Returns the pair(s) of nodes for which there is information</span>
+<span class="sd">        about their effect signs.</span>
+
+<span class="sd">        :param str,set resources:</span>
+<span class="sd">            Limits the query to one or more resources. Optional.</span>
+<span class="sd">        :param str effect:</span>
+<span class="sd">            Either *positive* or *negative*, limiting the query to positive</span>
+<span class="sd">            or negative effects; for any other values effects of both</span>
+<span class="sd">            signs will be returned.</span>
+
+<span class="sd">        :return:</span>
+<span class="sd">            (*tuple*) -- Tuple of tuples with pairs of nodes where the</span>
+<span class="sd">            first element is a tuple of the source and the target entity,</span>
+<span class="sd">            while the second element is the effect sign, according to</span>
+<span class="sd">            the given resources. E.g. (((&#39;A&#39;, &#39;B&#39;), &#39;positive&#39;),)</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">resources</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_resources_set</span><span class="p">(</span><span class="n">resources</span><span class="p">)</span>
+        <span class="n">effect</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_effect_synonyms</span><span class="p">(</span><span class="n">effect</span><span class="p">)</span>
+        <span class="n">effects</span> <span class="o">=</span> <span class="p">(</span><span class="n">effect</span><span class="p">,)</span> <span class="k">if</span> <span class="n">effect</span> <span class="k">else</span> <span class="p">(</span><span class="s1">&#39;positive&#39;</span><span class="p">,</span> <span class="s1">&#39;negative&#39;</span><span class="p">)</span>
+
+        <span class="k">return</span> <span class="nb">tuple</span><span class="p">(</span>
+            <span class="p">(</span><span class="n">_dir</span><span class="p">,</span> <span class="n">_effect</span><span class="p">)</span>
+            <span class="k">for</span> <span class="n">_effect</span> <span class="ow">in</span> <span class="n">effects</span>
+            <span class="k">for</span> <span class="n">_dir</span><span class="p">,</span> <span class="n">_evidences</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="nb">getattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">_effect</span><span class="p">))</span>
+            <span class="k">if</span> <span class="n">_evidences</span> <span class="ow">and</span> <span class="p">(</span>
+                <span class="ow">not</span> <span class="n">resources</span> <span class="ow">or</span>
+                <span class="n">_evidences</span> <span class="o">&amp;</span> <span class="n">resources</span>
+            <span class="p">)</span>
+        <span class="p">)</span></div>
+
+
+
+    <span class="nd">@staticmethod</span>
+    <span class="k">def</span> <span class="nf">_effect_synonyms</span><span class="p">(</span><span class="n">effect</span><span class="p">):</span>
+
+        <span class="k">if</span> <span class="ow">not</span> <span class="n">effect</span> <span class="ow">or</span> <span class="n">effect</span> <span class="o">==</span> <span class="kc">True</span><span class="p">:</span>
+
+            <span class="k">return</span> <span class="n">effect</span>
+
+        <span class="k">if</span> <span class="n">effect</span> <span class="ow">in</span> <span class="p">{</span><span class="s1">&#39;positive&#39;</span><span class="p">,</span> <span class="s1">&#39;stimulation&#39;</span><span class="p">,</span> <span class="s1">&#39;stimulatory&#39;</span><span class="p">}:</span>
+
+            <span class="k">return</span> <span class="s1">&#39;positive&#39;</span>
+
+        <span class="k">if</span> <span class="n">effect</span> <span class="ow">in</span> <span class="p">{</span><span class="s1">&#39;negative&#39;</span><span class="p">,</span> <span class="s1">&#39;inhibition&#39;</span><span class="p">,</span> <span class="s1">&#39;inhibitory&#39;</span><span class="p">}:</span>
+
+            <span class="k">return</span> <span class="s1">&#39;negative&#39;</span>
+
+        <span class="k">if</span> <span class="n">effect</span> <span class="ow">in</span> <span class="p">{</span><span class="s1">&#39;unknown&#39;</span><span class="p">}:</span>
+
+            <span class="k">return</span> <span class="s1">&#39;unknown&#39;</span>
+
+
+    <span class="k">def</span> <span class="nf">_resources_set</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">resources</span> <span class="o">=</span> <span class="kc">None</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="n">common</span><span class="o">.</span><span class="n">to_set</span><span class="p">(</span><span class="n">resources</span><span class="p">)</span>
+
+
+<div class="viewcode-block" id="Interaction.unset_direction">
+<a class="viewcode-back" href="../../../api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.unset_direction">[docs]</a>
+    <span class="k">def</span> <span class="nf">unset_direction</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">direction</span><span class="p">,</span>
+            <span class="n">only_sign</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+            <span class="n">resource</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">interaction_type</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">via</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+            <span class="n">source</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+        <span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Removes directionality and/or source information of the</span>
+<span class="sd">        specified *direction*. Modifies attribute :py:attr:`dirs` and</span>
+<span class="sd">        :py:attr:`sources`.</span>
+
+<span class="sd">        :arg tuple direction:</span>
+<span class="sd">            Or [str] (if ``&#39;undirected&#39;``) the pair of nodes specifying</span>
+<span class="sd">            the directionality from which the information is to be</span>
+<span class="sd">            removed.</span>
+<span class="sd">        :arg set resource:</span>
+<span class="sd">            Optional, ``None`` by default. If specified, determines</span>
+<span class="sd">            which specific source(s) is(are) to be removed from</span>
+<span class="sd">            :py:attr:`sources` attribute in the specified *direction*.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">direction</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">direction_key</span><span class="p">(</span><span class="n">direction</span><span class="p">)</span>
+
+        <span class="k">if</span> <span class="n">direction</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
+
+            <span class="n">attrs</span> <span class="o">=</span> <span class="p">(</span>
+                <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_effect_synonyms</span><span class="p">(</span><span class="n">only_sign</span><span class="p">),)</span>
+                    <span class="k">if</span> <span class="n">only_sign</span> <span class="k">else</span>
+                <span class="p">(</span><span class="s1">&#39;direction&#39;</span><span class="p">,</span> <span class="s1">&#39;positive&#39;</span><span class="p">,</span> <span class="s1">&#39;negative&#39;</span><span class="p">,</span> <span class="s1">&#39;unknown_effect&#39;</span><span class="p">)</span>
+            <span class="p">)</span>
+            <span class="n">resource</span> <span class="o">=</span> <span class="n">resource</span> <span class="ow">or</span> <span class="n">source</span>
+
+            <span class="k">for</span> <span class="n">attr</span> <span class="ow">in</span> <span class="n">attrs</span><span class="p">:</span>
+
+                <span class="k">if</span> <span class="n">resource</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
+
+                    <span class="nb">getattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">attr</span><span class="p">)[</span><span class="n">direction</span><span class="p">]</span><span class="o">.</span><span class="n">remove</span><span class="p">(</span>
+                        <span class="n">resource</span> <span class="o">=</span> <span class="n">resource</span><span class="p">,</span>
+                        <span class="n">interaction_type</span> <span class="o">=</span> <span class="n">interaction_type</span><span class="p">,</span>
+                        <span class="n">via</span> <span class="o">=</span> <span class="n">via</span><span class="p">,</span>
+                    <span class="p">)</span>
+
+                <span class="k">else</span><span class="p">:</span>
+                    <span class="nb">getattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">attr</span><span class="p">)[</span><span class="n">direction</span><span class="p">]</span> <span class="o">=</span> <span class="p">(</span>
+                        <span class="n">pypath_evidence</span><span class="o">.</span><span class="n">Evidences</span><span class="p">()</span>
+                    <span class="p">)</span></div>
+
+
+
+    <span class="c1"># synonym: old name</span>
+    <span class="n">unset_dir</span> <span class="o">=</span> <span class="n">unset_direction</span>
+
+
+<div class="viewcode-block" id="Interaction.unset_sign">
+<a class="viewcode-back" href="../../../api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.unset_sign">[docs]</a>
+    <span class="k">def</span> <span class="nf">unset_sign</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">direction</span><span class="p">,</span>
+            <span class="n">sign</span><span class="p">,</span>
+            <span class="n">resource</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">interaction_type</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">via</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+            <span class="n">source</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+        <span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Removes sign and/or source information of the specified</span>
+<span class="sd">        *direction* and *sign*. Modifies attribute :py:attr:`positive`</span>
+<span class="sd">        and :py:attr:`positive_sources` or :py:attr:`negative` and</span>
+<span class="sd">        :py:attr:`negative_sources` (or</span>
+<span class="sd">        :py:attr:`positive_attributes`/:py:attr:`negative_sources`</span>
+<span class="sd">        only if ``source=True``).</span>
+
+<span class="sd">        :arg tuple direction:</span>
+<span class="sd">            The pair of nodes specifying the directionality from which</span>
+<span class="sd">            the information is to be removed.</span>
+<span class="sd">        :arg str sign:</span>
+<span class="sd">            Sign from which the information is to be removed. Must be</span>
+<span class="sd">            either ``&#39;positive&#39;`` or ``&#39;negative&#39;``.</span>
+<span class="sd">        :arg set source:</span>
+<span class="sd">            Optional, ``None`` by default. If specified, determines</span>
+<span class="sd">            which source(s) is(are) to be removed from the sources in</span>
+<span class="sd">            the specified *direction* and *sign*.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">unset_direction</span><span class="p">(</span>
+            <span class="n">direction</span> <span class="o">=</span> <span class="n">direction</span><span class="p">,</span>
+            <span class="n">only_sign</span> <span class="o">=</span> <span class="n">sign</span><span class="p">,</span>
+            <span class="n">resource</span> <span class="o">=</span> <span class="n">resource</span><span class="p">,</span>
+            <span class="n">interaction_type</span> <span class="o">=</span> <span class="n">interaction_type</span><span class="p">,</span>
+            <span class="n">via</span> <span class="o">=</span> <span class="n">via</span><span class="p">,</span>
+            <span class="n">source</span> <span class="o">=</span> <span class="n">source</span><span class="p">,</span>
+        <span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="Interaction.unset_interaction_type">
+<a class="viewcode-back" href="../../../api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.unset_interaction_type">[docs]</a>
+    <span class="k">def</span> <span class="nf">unset_interaction_type</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">interaction_type</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Removes all evidences with a certain ``interaction_type``.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">for</span> <span class="n">ev</span> <span class="ow">in</span> <span class="nb">tuple</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">evidences</span><span class="p">):</span>
+
+            <span class="k">if</span> <span class="n">ev</span><span class="o">.</span><span class="n">resource</span><span class="o">.</span><span class="n">interaction_type</span> <span class="o">==</span> <span class="n">interaction_type</span><span class="p">:</span>
+
+                <span class="bp">self</span><span class="o">.</span><span class="n">evidences</span> <span class="o">-=</span> <span class="n">ev</span>
+
+        <span class="k">for</span> <span class="n">attr</span> <span class="ow">in</span> <span class="p">(</span><span class="s1">&#39;direction&#39;</span><span class="p">,</span> <span class="s1">&#39;positive&#39;</span><span class="p">,</span> <span class="s1">&#39;negative&#39;</span><span class="p">):</span>
+
+            <span class="k">for</span> <span class="n">key</span><span class="p">,</span> <span class="n">evs</span> <span class="ow">in</span> <span class="nb">getattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">attr</span><span class="p">):</span>
+
+                <span class="k">for</span> <span class="n">ev</span> <span class="ow">in</span> <span class="nb">tuple</span><span class="p">(</span><span class="n">evs</span><span class="p">):</span>
+
+                    <span class="k">if</span> <span class="n">ev</span><span class="o">.</span><span class="n">resource</span><span class="o">.</span><span class="n">interaction_type</span> <span class="o">==</span> <span class="n">interaction_type</span><span class="p">:</span>
+
+                        <span class="n">evs</span> <span class="o">-=</span> <span class="n">ev</span></div>
+
+
+
+<div class="viewcode-block" id="Interaction.is_directed">
+<a class="viewcode-back" href="../../../api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.is_directed">[docs]</a>
+    <span class="k">def</span> <span class="nf">is_directed</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Checks if edge has any directionality information.</span>
+
+<span class="sd">        :return:</span>
+<span class="sd">            (*bool*) -- Returns ``True`` if any of the :py:attr:`dirs`</span>
+<span class="sd">            attribute values is ``True`` (except ``&#39;undirected&#39;``),</span>
+<span class="sd">            ``False`` otherwise.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">return</span> <span class="nb">any</span><span class="p">(</span>
+            <span class="n">evs</span>
+            <span class="k">for</span> <span class="n">dkey</span><span class="p">,</span> <span class="n">evs</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">direction</span><span class="p">)</span>
+            <span class="k">if</span> <span class="n">dkey</span> <span class="o">!=</span> <span class="s1">&#39;undirected&#39;</span>
+        <span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="Interaction.is_directed_by_resources">
+<a class="viewcode-back" href="../../../api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.is_directed_by_resources">[docs]</a>
+    <span class="k">def</span> <span class="nf">is_directed_by_resources</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">resources</span> <span class="o">=</span> <span class="kc">None</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Checks if edge has any directionality information from some</span>
+<span class="sd">        resource(s).</span>
+
+<span class="sd">        :return:</span>
+<span class="sd">            (*bool*) -- Returns ``True`` if any of the :py:attr:`dirs`</span>
+<span class="sd">            attribute values is ``True`` (except ``&#39;undirected&#39;``),</span>
+<span class="sd">            ``False`` otherwise.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_dir_by_resource</span><span class="p">(</span><span class="n">resources</span><span class="p">,</span> <span class="n">op</span> <span class="o">=</span> <span class="n">operator</span><span class="o">.</span><span class="n">or_</span><span class="p">)</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">is_mutual</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">resources</span> <span class="o">=</span> <span class="kc">None</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Checks if the edge has mutual directions (both A--&gt;B and B--&gt;A).</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">return</span> <span class="p">(</span>
+            <span class="nb">bool</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">direction</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">a_b</span><span class="p">])</span> <span class="ow">and</span> <span class="nb">bool</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">direction</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">b_a</span><span class="p">])</span>
+                <span class="k">if</span> <span class="ow">not</span> <span class="n">resources</span> <span class="k">else</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">is_mutual_by_resources</span><span class="p">(</span><span class="n">resources</span> <span class="o">=</span> <span class="n">resources</span><span class="p">)</span>
+        <span class="p">)</span>
+
+
+<div class="viewcode-block" id="Interaction.is_mutual_by_resources">
+<a class="viewcode-back" href="../../../api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.is_mutual_by_resources">[docs]</a>
+    <span class="k">def</span> <span class="nf">is_mutual_by_resources</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">resources</span> <span class="o">=</span> <span class="kc">None</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Checks if the edge has mutual directions (both A--&gt;B and B--&gt;A)</span>
+<span class="sd">        according to some resource(s).</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_dir_by_resource</span><span class="p">(</span><span class="n">resources</span><span class="p">,</span> <span class="n">op</span> <span class="o">=</span> <span class="n">operator</span><span class="o">.</span><span class="n">and_</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="Interaction.is_loop">
+<a class="viewcode-back" href="../../../api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.is_loop">[docs]</a>
+    <span class="k">def</span> <span class="nf">is_loop</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        :returns:</span>
+<span class="sd">        ``True`` if the interaction is a loop edge i.e. its endpoints are the</span>
+<span class="sd">        same node.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">a</span> <span class="o">==</span> <span class="bp">self</span><span class="o">.</span><span class="n">b</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">_dir_by_resource</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">resources</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span> <span class="n">op</span> <span class="o">=</span> <span class="n">operator</span><span class="o">.</span><span class="n">or_</span><span class="p">):</span>
+
+        <span class="n">resources</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_resources_set</span><span class="p">(</span><span class="n">resources</span><span class="p">)</span>
+
+        <span class="k">return</span> <span class="n">op</span><span class="p">(</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">direction</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">a_b</span><span class="p">]</span> <span class="o">&amp;</span> <span class="n">resources</span><span class="p">,</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">direction</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">b_a</span><span class="p">]</span> <span class="o">&amp;</span> <span class="n">resources</span><span class="p">,</span>
+        <span class="p">)</span>
+
+
+<div class="viewcode-block" id="Interaction.is_stimulation">
+<a class="viewcode-back" href="../../../api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.is_stimulation">[docs]</a>
+    <span class="k">def</span> <span class="nf">is_stimulation</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">direction</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span> <span class="n">resources</span> <span class="o">=</span> <span class="kc">None</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Checks if any (or for a specific *direction*) interaction is</span>
+<span class="sd">        activation (positive interaction).</span>
+
+<span class="sd">        :arg tuple direction:</span>
+<span class="sd">            Optional, ``None`` by default. If specified, checks the</span>
+<span class="sd">            :py:attr:`positive` attribute of that specific</span>
+<span class="sd">            directionality. If not specified, checks both.</span>
+
+<span class="sd">        :return:</span>
+<span class="sd">            (*bool*) -- ``True`` if any interaction (or the specified</span>
+<span class="sd">            *direction*) is activatory (positive).</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_is_effect</span><span class="p">(</span>
+            <span class="n">sign</span> <span class="o">=</span> <span class="s1">&#39;positive&#39;</span><span class="p">,</span>
+            <span class="n">direction</span> <span class="o">=</span> <span class="n">direction</span><span class="p">,</span>
+            <span class="n">resources</span> <span class="o">=</span> <span class="n">resources</span><span class="p">,</span>
+        <span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="Interaction.is_inhibition">
+<a class="viewcode-back" href="../../../api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.is_inhibition">[docs]</a>
+    <span class="k">def</span> <span class="nf">is_inhibition</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">direction</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span> <span class="n">resources</span> <span class="o">=</span> <span class="kc">None</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Checks if any (or for a specific *direction*) interaction is</span>
+<span class="sd">        inhibition (negative interaction).</span>
+
+<span class="sd">        :arg tuple direction:</span>
+<span class="sd">            Optional, ``None`` by default. If specified, checks the</span>
+<span class="sd">            :py:attr:`negative` attribute of that specific</span>
+<span class="sd">            directionality. If not specified, checks both.</span>
+
+<span class="sd">        :return:</span>
+<span class="sd">            (*bool*) -- ``True`` if any interaction (or the specified</span>
+<span class="sd">            *direction*) is inhibitory (negative).</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_is_effect</span><span class="p">(</span>
+            <span class="n">sign</span> <span class="o">=</span> <span class="s1">&#39;negative&#39;</span><span class="p">,</span>
+            <span class="n">direction</span> <span class="o">=</span> <span class="n">direction</span><span class="p">,</span>
+            <span class="n">resources</span> <span class="o">=</span> <span class="n">resources</span><span class="p">,</span>
+        <span class="p">)</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">_is_effect</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">sign</span><span class="p">,</span> <span class="n">direction</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span> <span class="n">resources</span> <span class="o">=</span> <span class="kc">None</span><span class="p">):</span>
+
+        <span class="n">_sign</span> <span class="o">=</span> <span class="nb">getattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">sign</span><span class="p">)</span>
+        <span class="n">_resources</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_resources_set</span><span class="p">(</span><span class="n">resources</span><span class="p">)</span>
+
+        <span class="k">return</span> <span class="p">(</span>
+            <span class="nb">any</span><span class="p">(</span>
+                <span class="nb">bool</span><span class="p">(</span>
+                    <span class="n">_evidences</span>
+                        <span class="k">if</span> <span class="ow">not</span> <span class="n">_resources</span> <span class="k">else</span>
+                    <span class="n">_evidences</span> <span class="o">&amp;</span> <span class="n">_resources</span>
+                <span class="p">)</span>
+                <span class="k">for</span> <span class="n">_direction</span><span class="p">,</span> <span class="n">_evidences</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="n">_sign</span><span class="p">)</span>
+                <span class="k">if</span> <span class="ow">not</span> <span class="n">direction</span> <span class="ow">or</span> <span class="n">direction</span> <span class="o">==</span> <span class="n">_direction</span>
+            <span class="p">)</span>
+        <span class="p">)</span>
+
+
+<div class="viewcode-block" id="Interaction.has_sign">
+<a class="viewcode-back" href="../../../api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.has_sign">[docs]</a>
+    <span class="k">def</span> <span class="nf">has_sign</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">direction</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span> <span class="n">resources</span> <span class="o">=</span> <span class="kc">None</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Checks whether the edge (or for a specific *direction*) has</span>
+<span class="sd">        any signed information (about positive/negative interactions).</span>
+
+<span class="sd">        :arg tuple direction:</span>
+<span class="sd">            Optional, ``None`` by default. If specified, only the</span>
+<span class="sd">            information of that direction is checked for sign.</span>
+
+<span class="sd">        :return:</span>
+<span class="sd">            (*bool*) -- ``True`` if there exist any information on the</span>
+<span class="sd">              sign of the interaction, ``False`` otherwise.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">return</span> <span class="p">(</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">is_stimulation</span><span class="p">(</span><span class="n">direction</span> <span class="o">=</span> <span class="n">direction</span><span class="p">,</span> <span class="n">resources</span> <span class="o">=</span> <span class="n">resources</span><span class="p">)</span>
+                <span class="ow">or</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">is_inhibition</span><span class="p">(</span><span class="n">direction</span> <span class="o">=</span> <span class="n">direction</span><span class="p">,</span> <span class="n">resources</span> <span class="o">=</span> <span class="n">resources</span><span class="p">)</span>
+        <span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="Interaction.add_sign">
+<a class="viewcode-back" href="../../../api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.add_sign">[docs]</a>
+    <span class="k">def</span> <span class="nf">add_sign</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">direction</span><span class="p">:</span> <span class="nb">tuple</span><span class="p">,</span>
+            <span class="n">sign</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
+            <span class="n">resource</span><span class="p">:</span> <span class="nb">str</span> <span class="o">|</span> <span class="nb">set</span><span class="p">[</span><span class="nb">str</span><span class="p">]</span> <span class="o">|</span> <span class="kc">None</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">resource_name</span><span class="p">:</span> <span class="nb">str</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">interaction_type</span><span class="p">:</span> <span class="nb">str</span> <span class="o">=</span> <span class="s1">&#39;PPI&#39;</span><span class="p">,</span>
+            <span class="n">data_model</span><span class="p">:</span> <span class="nb">str</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">attrs</span><span class="p">:</span> <span class="nb">dict</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="o">**</span><span class="n">kwargs</span>
+        <span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Sets sign and source information on a given direction of the</span>
+<span class="sd">        edge. Modifies the attributes :py:attr:`positive` and</span>
+<span class="sd">        :py:attr:`positive_sources` or :py:attr:`negative` and</span>
+<span class="sd">        :py:attr:`negative_sources` depending on the sign. Direction is</span>
+<span class="sd">        also updated accordingly, which also modifies the attributes</span>
+<span class="sd">        :py:attr:`dirs` and :py:attr:`sources`.</span>
+
+<span class="sd">        Args</span>
+<span class="sd">            direction:</span>
+<span class="sd">                Pair of edge nodes specifying the direction from which the</span>
+<span class="sd">                information is to be set/updated.</span>
+<span class="sd">            sign:</span>
+<span class="sd">                Specifies the type of interaction. Either ``&#39;positive&#39;`` or</span>
+<span class="sd">                ``&#39;negative&#39;``.</span>
+<span class="sd">            resource:</span>
+<span class="sd">                Contains the name(s) of the source(s) from which the</span>
+<span class="sd">                information was obtained.</span>
+<span class="sd">            attrs:</span>
+<span class="sd">                Custom (resource specific) edge attributes.</span>
+<span class="sd">            kwargs:</span>
+<span class="sd">                Passed to ``pypath.resource.NetworkResource`` if ``resource``</span>
+<span class="sd">                is not already a ``NetworkResource`` or ``Evidence``</span>
+<span class="sd">                instance.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">sign</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_effect_synonyms</span><span class="p">(</span><span class="n">sign</span><span class="p">)</span>
+
+        <span class="n">evidence</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="n">resource</span>
+                <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">resource</span><span class="p">,</span> <span class="n">pypath_evidence</span><span class="o">.</span><span class="n">Evidence</span><span class="p">)</span> <span class="k">else</span>
+            <span class="n">pypath_evidence</span><span class="o">.</span><span class="n">Evidence</span><span class="p">(</span>
+                <span class="n">resource</span> <span class="o">=</span> <span class="n">resource</span><span class="p">,</span>
+                <span class="n">references</span> <span class="o">=</span> <span class="n">references</span><span class="p">,</span>
+            <span class="p">)</span>
+                <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">resource</span><span class="p">,</span> <span class="n">pypath_resource</span><span class="o">.</span><span class="n">NetworkResource</span><span class="p">)</span> <span class="k">else</span>
+            <span class="n">pypath_evidence</span><span class="o">.</span><span class="n">Evidence</span><span class="p">(</span>
+                <span class="n">resource</span> <span class="o">=</span> <span class="n">pypath_resource</span><span class="o">.</span><span class="n">NetworkResource</span><span class="p">(</span>
+                    <span class="n">name</span> <span class="o">=</span> <span class="n">resource_name</span><span class="p">,</span>
+                    <span class="n">interaction_type</span> <span class="o">=</span> <span class="n">interaction_type</span><span class="p">,</span>
+                    <span class="n">data_model</span> <span class="o">=</span> <span class="n">data_model</span><span class="p">,</span>
+                    <span class="o">**</span><span class="n">kwargs</span>
+                <span class="p">)</span>
+            <span class="p">)</span>
+                <span class="k">if</span> <span class="n">resource_name</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span> <span class="k">else</span>
+            <span class="kc">None</span>
+        <span class="p">)</span>
+
+        <span class="n">evidence</span><span class="o">.</span><span class="n">update_attrs</span><span class="p">(</span><span class="n">attrs</span><span class="p">)</span>
+
+        <span class="n">direction</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">direction_key</span><span class="p">(</span><span class="n">direction</span><span class="p">)</span>
+
+        <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">_directed_key</span><span class="p">(</span><span class="n">direction</span><span class="p">)</span> <span class="ow">and</span> <span class="n">evidence</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
+
+            <span class="n">ev_attr</span> <span class="o">=</span> <span class="nb">getattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">sign</span><span class="p">)</span>
+            <span class="n">ev_attr</span> <span class="o">+=</span> <span class="n">evidence</span></div>
+
+
+
+<div class="viewcode-block" id="Interaction.get_sign">
+<a class="viewcode-back" href="../../../api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.get_sign">[docs]</a>
+    <span class="k">def</span> <span class="nf">get_sign</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">direction</span><span class="p">:</span> <span class="nb">tuple</span><span class="p">,</span>
+            <span class="n">sign</span><span class="p">:</span> <span class="nb">str</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">evidences</span><span class="p">:</span> <span class="nb">bool</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+            <span class="n">resources</span><span class="p">:</span> <span class="nb">bool</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+            <span class="n">resource_names</span><span class="p">:</span> <span class="nb">bool</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+            <span class="n">sources</span><span class="p">:</span> <span class="nb">bool</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+        <span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">list</span><span class="p">[</span><span class="nb">bool</span> <span class="o">|</span> <span class="nb">str</span><span class="p">]:</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Retrieves the sign information of the edge in the given</span>
+<span class="sd">        diretion. If specified in *sign*, only that sign&#39;s information</span>
+<span class="sd">        will be retrieved. If specified in *sources*, the sources of</span>
+<span class="sd">        that information will be retrieved instead.</span>
+
+<span class="sd">        Args</span>
+<span class="sd">            direction:</span>
+<span class="sd">                Contains the pair of nodes specifying the directionality of</span>
+<span class="sd">                the edge from which th information is to be retrieved.</span>
+<span class="sd">            sign:</span>
+<span class="sd">                Optional, ``None`` by default. Denotes whether to retrieve</span>
+<span class="sd">                the ``&#39;positive&#39;`` or ``&#39;negative&#39;`` specific information.</span>
+<span class="sd">            resources:</span>
+<span class="sd">                Optional, ``False`` by default. Specifies whether to return</span>
+<span class="sd">                the resources instead of sign.</span>
+
+<span class="sd">        Returns</span>
+<span class="sd">            If ``sign=None`` containing [bool] values</span>
+<span class="sd">            denoting the presence of positive and negative sign on that</span>
+<span class="sd">            direction, if ``sources=True`` the [set] of sources for each</span>
+<span class="sd">            of them will be returned instead. If *sign* is specified,</span>
+<span class="sd">            returns [bool] or [set] (if ``sources=True``) of that</span>
+<span class="sd">            specific direction and sign.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">sign</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_effect_synonyms</span><span class="p">(</span><span class="n">sign</span><span class="p">)</span>
+
+        <span class="n">answer_type_args</span> <span class="o">=</span> <span class="p">{</span>
+            <span class="s1">&#39;resources&#39;</span><span class="p">:</span> <span class="n">resources</span><span class="p">,</span>
+            <span class="s1">&#39;evidences&#39;</span><span class="p">:</span> <span class="n">evidences</span><span class="p">,</span>
+            <span class="s1">&#39;resource_names&#39;</span><span class="p">:</span> <span class="n">resource_names</span><span class="p">,</span>
+            <span class="s1">&#39;sources&#39;</span><span class="p">:</span> <span class="n">sources</span><span class="p">,</span>
+        <span class="p">}</span>
+
+        <span class="n">direction</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">direction_key</span><span class="p">(</span><span class="n">direction</span><span class="p">)</span>
+
+        <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">_directed_key</span><span class="p">(</span><span class="n">direction</span><span class="p">):</span>
+
+            <span class="k">return</span> <span class="p">(</span>
+
+                <span class="bp">self</span><span class="o">.</span><span class="n">_select_answer_type</span><span class="p">(</span>
+                    <span class="nb">getattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">sign</span><span class="p">)[</span><span class="n">direction</span><span class="p">],</span>
+                    <span class="o">**</span><span class="n">answer_type_args</span>
+                <span class="p">)</span>
+
+                    <span class="k">if</span> <span class="n">sign</span> <span class="k">else</span>
+
+                <span class="p">[</span>
+                    <span class="bp">self</span><span class="o">.</span><span class="n">_select_answer_type</span><span class="p">(</span>
+                        <span class="bp">self</span><span class="o">.</span><span class="n">positive</span><span class="p">[</span><span class="n">direction</span><span class="p">],</span>
+                        <span class="o">**</span><span class="n">answer_type_args</span>
+                    <span class="p">),</span>
+                    <span class="bp">self</span><span class="o">.</span><span class="n">_select_answer_type</span><span class="p">(</span>
+                        <span class="bp">self</span><span class="o">.</span><span class="n">negative</span><span class="p">[</span><span class="n">direction</span><span class="p">],</span>
+                        <span class="o">**</span><span class="n">answer_type_args</span>
+                    <span class="p">)</span>
+                <span class="p">]</span>
+
+            <span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="Interaction.source">
+<a class="viewcode-back" href="../../../api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.source">[docs]</a>
+    <span class="k">def</span> <span class="nf">source</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">undirected</span><span class="p">:</span> <span class="nb">bool</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+            <span class="n">resources</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="o">**</span><span class="n">kwargs</span>
+        <span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Returns the name(s) of the source node(s) for each existing</span>
+<span class="sd">        direction on the interaction.</span>
+
+<span class="sd">        Args</span>
+<span class="sd">            undirected:</span>
+<span class="sd">                Optional, ``False`` by default.</span>
+
+<span class="sd">        Returns</span>
+<span class="sd">            (*list*) -- Contains the name(s) for the source node(s).</span>
+<span class="sd">            This means if the interaction is bidirectional, the list</span>
+<span class="sd">            will contain both identifiers on the edge. If the</span>
+<span class="sd">            interaction is undirected, an empty list will be returned.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_partner</span><span class="p">(</span>
+            <span class="n">source_target</span> <span class="o">=</span> <span class="s1">&#39;source&#39;</span><span class="p">,</span>
+            <span class="n">undirected</span> <span class="o">=</span> <span class="n">undirected</span><span class="p">,</span>
+            <span class="n">resources</span> <span class="o">=</span> <span class="n">resources</span><span class="p">,</span>
+            <span class="o">**</span><span class="n">kwargs</span>
+        <span class="p">)</span></div>
+
+
+
+    <span class="c1"># synonym: old name</span>
+    <span class="n">src</span> <span class="o">=</span> <span class="n">source</span>
+
+
+<div class="viewcode-block" id="Interaction.target">
+<a class="viewcode-back" href="../../../api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.target">[docs]</a>
+    <span class="k">def</span> <span class="nf">target</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">undirected</span><span class="p">:</span> <span class="nb">bool</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+            <span class="n">resources</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="o">**</span><span class="n">kwargs</span>
+        <span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Returns the name(s) of the target node(s) for each existing</span>
+<span class="sd">        direction on the interaction.</span>
+
+<span class="sd">        Args</span>
+<span class="sd">            undirected:</span>
+<span class="sd">                Optional, ``False`` by default.</span>
+
+<span class="sd">        Returns</span>
+<span class="sd">            (*list*) -- Contains the name(s) for the target node(s).</span>
+<span class="sd">            This means if the interaction is bidirectional, the list</span>
+<span class="sd">            will contain both identifiers on the edge. If the</span>
+<span class="sd">            interaction is undirected, an empty list will be returned.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_partner</span><span class="p">(</span>
+            <span class="n">source_target</span> <span class="o">=</span> <span class="s1">&#39;target&#39;</span><span class="p">,</span>
+            <span class="n">undirected</span> <span class="o">=</span> <span class="n">undirected</span><span class="p">,</span>
+            <span class="n">resources</span> <span class="o">=</span> <span class="n">resources</span><span class="p">,</span>
+            <span class="o">**</span><span class="n">kwargs</span>
+        <span class="p">)</span></div>
+
+
+
+    <span class="c1"># synonym: old name</span>
+    <span class="n">tgt</span> <span class="o">=</span> <span class="n">target</span>
+
+
+    <span class="k">def</span> <span class="nf">_partner</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">source_target</span><span class="p">,</span>
+            <span class="n">undirected</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+            <span class="n">resources</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="o">**</span><span class="n">kwargs</span>
+        <span class="p">):</span>
+
+        <span class="n">resources</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_resources_set</span><span class="p">(</span><span class="n">resources</span><span class="p">)</span>
+        <span class="n">_slice</span> <span class="o">=</span> <span class="nb">slice</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="mi">1</span><span class="p">)</span> <span class="k">if</span> <span class="n">source_target</span> <span class="o">==</span> <span class="s1">&#39;source&#39;</span> <span class="k">else</span> <span class="nb">slice</span><span class="p">(</span><span class="mi">1</span><span class="p">,</span> <span class="mi">2</span><span class="p">)</span>
+
+        <span class="k">return</span> <span class="nb">tuple</span><span class="p">(</span><span class="n">itertools</span><span class="o">.</span><span class="n">chain</span><span class="p">(</span>
+            <span class="p">(</span>
+                <span class="n">_direction</span><span class="p">[</span><span class="n">_slice</span><span class="p">]</span>
+                    <span class="k">if</span> <span class="n">_direction</span> <span class="o">!=</span> <span class="s1">&#39;undirected&#39;</span> <span class="k">else</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">nodes</span>
+                    <span class="k">if</span> <span class="n">undirected</span> <span class="k">else</span>
+                <span class="p">()</span>
+            <span class="p">)</span>
+            <span class="k">for</span> <span class="n">_direction</span><span class="p">,</span> <span class="n">_evidences</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">direction</span><span class="p">)</span>
+            <span class="k">if</span> <span class="p">(</span>
+                <span class="p">(</span>
+                    <span class="p">(</span>
+                        <span class="ow">not</span> <span class="n">resources</span> <span class="ow">and</span>
+                        <span class="ow">not</span> <span class="n">kwargs</span> <span class="ow">and</span>
+                        <span class="nb">bool</span><span class="p">(</span><span class="n">_evidences</span><span class="p">)</span>
+                    <span class="p">)</span> <span class="ow">or</span>
+                    <span class="p">(</span>
+                        <span class="nb">any</span><span class="p">(</span>
+                            <span class="n">ev</span><span class="o">.</span><span class="n">match</span><span class="p">(</span>
+                                <span class="n">resource</span> <span class="o">=</span> <span class="n">res</span><span class="p">,</span>
+                                <span class="o">**</span><span class="n">kwargs</span>
+                            <span class="p">)</span>
+                            <span class="k">for</span> <span class="n">res</span> <span class="ow">in</span> <span class="n">resources</span> <span class="ow">or</span> <span class="p">(</span><span class="kc">None</span><span class="p">,)</span>
+                            <span class="k">for</span> <span class="n">ev</span> <span class="ow">in</span> <span class="n">_evidences</span>
+                        <span class="p">)</span>
+                    <span class="p">)</span>
+                <span class="p">)</span>
+            <span class="p">)</span>
+        <span class="p">))</span>
+
+
+<div class="viewcode-block" id="Interaction.src_by_resource">
+<a class="viewcode-back" href="../../../api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.src_by_resource">[docs]</a>
+    <span class="k">def</span> <span class="nf">src_by_resource</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">resource</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Returns the name(s) of the source node(s) for each existing</span>
+<span class="sd">        direction on the interaction for a specific *resource*.</span>
+
+<span class="sd">        :arg str resource:</span>
+<span class="sd">            Name of the resource according to which the information is to</span>
+<span class="sd">            be retrieved.</span>
+
+<span class="sd">        :return:</span>
+<span class="sd">            (*list*) -- Contains the name(s) for the source node(s)</span>
+<span class="sd">            according to the specified *resource*. This means if the</span>
+<span class="sd">            interaction is bidirectional, the list will contain both</span>
+<span class="sd">            identifiers on the edge. If the specified *source* is not</span>
+<span class="sd">            found or invalid, an empty list will be returned.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">return</span> <span class="p">[</span>
+            <span class="n">_dir</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span>
+            <span class="k">for</span> <span class="n">_dir</span><span class="p">,</span> <span class="n">_evidences</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">direction</span><span class="p">)</span>
+            <span class="k">if</span> <span class="p">(</span>
+                <span class="n">_dir</span> <span class="o">!=</span> <span class="s1">&#39;undirected&#39;</span> <span class="ow">and</span>
+                <span class="n">resource</span> <span class="ow">in</span> <span class="n">_evidences</span>
+            <span class="p">)</span>
+        <span class="p">]</span></div>
+
+
+
+<div class="viewcode-block" id="Interaction.tgt_by_resource">
+<a class="viewcode-back" href="../../../api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.tgt_by_resource">[docs]</a>
+    <span class="k">def</span> <span class="nf">tgt_by_resource</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">resource</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Returns the name(s) of the target node(s) for each existing</span>
+<span class="sd">        direction on the interaction for a specific *resource*.</span>
+
+<span class="sd">        :arg str resource:</span>
+<span class="sd">            Name of the resource according to which the information is to</span>
+<span class="sd">            be retrieved.</span>
+
+<span class="sd">        :return:</span>
+<span class="sd">            (*list*) -- Contains the name(s) for the target node(s)</span>
+<span class="sd">            according to the specified *resource*. This means if the</span>
+<span class="sd">            interaction is bidirectional, the list will contain both</span>
+<span class="sd">            identifiers on the edge. If the specified *source* is not</span>
+<span class="sd">            found or invalid, an empty list will be returned.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">return</span> <span class="p">[</span>
+            <span class="n">_dir</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span>
+            <span class="k">for</span> <span class="n">_dir</span><span class="p">,</span> <span class="n">_evidences</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">direction</span><span class="p">)</span>
+            <span class="k">if</span> <span class="p">(</span>
+                <span class="n">_dir</span> <span class="o">!=</span> <span class="s1">&#39;undirected&#39;</span> <span class="ow">and</span>
+                <span class="n">resource</span> <span class="ow">in</span> <span class="n">_evidences</span>
+            <span class="p">)</span>
+        <span class="p">]</span></div>
+
+
+
+<div class="viewcode-block" id="Interaction.resources_a_b">
+<a class="viewcode-back" href="../../../api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.resources_a_b">[docs]</a>
+    <span class="k">def</span> <span class="nf">resources_a_b</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">resources</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+            <span class="n">evidences</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+            <span class="n">resource_names</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+            <span class="n">sources</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+        <span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Retrieves the list of resources for the :py:attr:`a_b`</span>
+<span class="sd">        direction.</span>
+
+<span class="sd">        :return:</span>
+<span class="sd">            (*set*) -- Contains the names of the sources supporting the</span>
+<span class="sd">            :py:attr:`a_b` directionality of the edge.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">answer_type_args</span> <span class="o">=</span> <span class="p">{</span>
+            <span class="s1">&#39;resources&#39;</span><span class="p">:</span> <span class="n">resources</span><span class="p">,</span>
+            <span class="s1">&#39;evidences&#39;</span><span class="p">:</span> <span class="n">evidences</span><span class="p">,</span>
+            <span class="s1">&#39;resource_names&#39;</span><span class="p">:</span> <span class="n">resource_names</span><span class="p">,</span>
+            <span class="s1">&#39;sources&#39;</span><span class="p">:</span> <span class="n">sources</span><span class="p">,</span>
+        <span class="p">}</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_select_answer_type</span><span class="p">(</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">direction</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">a_b</span><span class="p">],</span>
+            <span class="o">**</span><span class="n">answer_type_args</span>
+        <span class="p">)</span></div>
+
+
+
+    <span class="c1"># synonym for old method name</span>
+    <span class="n">sources_straight</span> <span class="o">=</span> <span class="n">resources_a_b</span>
+
+
+<div class="viewcode-block" id="Interaction.resources_b_a">
+<a class="viewcode-back" href="../../../api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.resources_b_a">[docs]</a>
+    <span class="k">def</span> <span class="nf">resources_b_a</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">resources</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+            <span class="n">evidences</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+            <span class="n">resource_names</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+            <span class="n">sources</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+        <span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Retrieves the list of sources for the :py:attr:`b_a` direction.</span>
+
+<span class="sd">        :return:</span>
+<span class="sd">            (*set*) -- Contains the names of the sources supporting the</span>
+<span class="sd">            :py:attr:`b_a` directionality of the edge.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">answer_type_args</span> <span class="o">=</span> <span class="p">{</span>
+            <span class="s1">&#39;resources&#39;</span><span class="p">:</span> <span class="n">resources</span><span class="p">,</span>
+            <span class="s1">&#39;evidences&#39;</span><span class="p">:</span> <span class="n">evidences</span><span class="p">,</span>
+            <span class="s1">&#39;resource_names&#39;</span><span class="p">:</span> <span class="n">resource_names</span><span class="p">,</span>
+            <span class="s1">&#39;sources&#39;</span><span class="p">:</span> <span class="n">sources</span><span class="p">,</span>
+        <span class="p">}</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_select_answer_type</span><span class="p">(</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">direction</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">b_a</span><span class="p">],</span>
+            <span class="o">**</span><span class="n">answer_type_args</span>
+        <span class="p">)</span></div>
+
+
+
+    <span class="c1"># synonym for old method name</span>
+    <span class="n">sources_reverse</span> <span class="o">=</span> <span class="n">resources_b_a</span>
+
+
+<div class="viewcode-block" id="Interaction.resources_undirected">
+<a class="viewcode-back" href="../../../api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.resources_undirected">[docs]</a>
+    <span class="k">def</span> <span class="nf">resources_undirected</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">resources</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+            <span class="n">evidences</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+            <span class="n">resource_names</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+            <span class="n">sources</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+        <span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Retrieves the list of resources without directed information.</span>
+
+<span class="sd">        :return:</span>
+<span class="sd">            (*set*) -- Contains the names of the sources supporting the</span>
+<span class="sd">            edge presence but without specific directionality</span>
+<span class="sd">            information.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">answer_type_args</span> <span class="o">=</span> <span class="p">{</span>
+            <span class="s1">&#39;resources&#39;</span><span class="p">:</span> <span class="n">resources</span><span class="p">,</span>
+            <span class="s1">&#39;evidences&#39;</span><span class="p">:</span> <span class="n">evidences</span><span class="p">,</span>
+            <span class="s1">&#39;resource_names&#39;</span><span class="p">:</span> <span class="n">resource_names</span><span class="p">,</span>
+            <span class="s1">&#39;sources&#39;</span><span class="p">:</span> <span class="n">sources</span><span class="p">,</span>
+        <span class="p">}</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_select_answer_type</span><span class="p">(</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">direction</span><span class="p">[</span><span class="s1">&#39;undirected&#39;</span><span class="p">],</span>
+            <span class="o">**</span><span class="n">answer_type_args</span>
+        <span class="p">)</span></div>
+
+
+
+    <span class="n">sources_undirected</span> <span class="o">=</span> <span class="n">resources_undirected</span>
+
+
+<div class="viewcode-block" id="Interaction.positive_a_b">
+<a class="viewcode-back" href="../../../api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.positive_a_b">[docs]</a>
+    <span class="k">def</span> <span class="nf">positive_a_b</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Checks if the :py:attr:`a_b` directionality is a positive</span>
+<span class="sd">        interaction.</span>
+
+<span class="sd">        :return:</span>
+<span class="sd">            (*bool*) -- ``True`` if there is supporting information on</span>
+<span class="sd">            the :py:attr:`a_b` direction of the edge as activation.</span>
+<span class="sd">            ``False`` otherwise.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">return</span> <span class="nb">bool</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">positive</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">a_b</span><span class="p">])</span></div>
+
+
+
+    <span class="n">positive_straight</span> <span class="o">=</span> <span class="n">positive_a_b</span>
+
+
+<div class="viewcode-block" id="Interaction.positive_b_a">
+<a class="viewcode-back" href="../../../api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.positive_b_a">[docs]</a>
+    <span class="k">def</span> <span class="nf">positive_b_a</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Checks if the :py:attr:`b_a` directionality is a positive</span>
+<span class="sd">        interaction.</span>
+
+<span class="sd">        :return:</span>
+<span class="sd">            (*bool*) -- ``True`` if there is supporting information on</span>
+<span class="sd">            the :py:attr:`b_a` direction of the edge as activation.</span>
+<span class="sd">            ``False`` otherwise.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">return</span> <span class="nb">bool</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">positive</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">b_a</span><span class="p">])</span></div>
+
+
+
+    <span class="n">positive_reverse</span> <span class="o">=</span> <span class="n">positive_b_a</span>
+
+
+<div class="viewcode-block" id="Interaction.negative_a_b">
+<a class="viewcode-back" href="../../../api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.negative_a_b">[docs]</a>
+    <span class="k">def</span> <span class="nf">negative_a_b</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Checks if the :py:attr:`a_b` directionality is a negative</span>
+<span class="sd">        interaction.</span>
+
+<span class="sd">        :return:</span>
+<span class="sd">            (*bool*) -- ``True`` if there is supporting information on</span>
+<span class="sd">            the :py:attr:`a_b` direction of the edge as inhibition.</span>
+<span class="sd">            ``False`` otherwise.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">return</span> <span class="nb">bool</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">negative</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">a_b</span><span class="p">])</span></div>
+
+
+
+    <span class="n">negative_straight</span> <span class="o">=</span> <span class="n">negative_a_b</span>
+
+
+<div class="viewcode-block" id="Interaction.negative_b_a">
+<a class="viewcode-back" href="../../../api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.negative_b_a">[docs]</a>
+    <span class="k">def</span> <span class="nf">negative_b_a</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Checks if the :py:attr:`b_a` directionality is a negative</span>
+<span class="sd">        interaction.</span>
+
+<span class="sd">        :return:</span>
+<span class="sd">            (*bool*) -- ``True`` if there is supporting information on</span>
+<span class="sd">            the :py:attr:`b_a` direction of the edge as inhibition.</span>
+<span class="sd">            ``False`` otherwise.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">return</span> <span class="nb">bool</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">negative</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">b_a</span><span class="p">])</span></div>
+
+
+
+    <span class="n">negative_reverse</span> <span class="o">=</span> <span class="n">negative_b_a</span>
+
+
+<div class="viewcode-block" id="Interaction.negative_resources_a_b">
+<a class="viewcode-back" href="../../../api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.negative_resources_a_b">[docs]</a>
+    <span class="k">def</span> <span class="nf">negative_resources_a_b</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Retrieves the list of resources for the :py:attr:`a_b`</span>
+<span class="sd">        direction and negative sign.</span>
+
+<span class="sd">        :return:</span>
+<span class="sd">            (*set*) -- Contains the names of the resources supporting the</span>
+<span class="sd">            :py:attr:`a_b` directionality of the edge with a</span>
+<span class="sd">            negative sign.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">answer_type_args</span> <span class="o">=</span> <span class="p">{</span>
+            <span class="s1">&#39;resource_names&#39;</span><span class="p">:</span> <span class="kc">True</span>
+        <span class="p">}</span>
+        <span class="n">answer_type_args</span><span class="o">.</span><span class="n">update</span><span class="p">(</span><span class="n">kwargs</span><span class="p">)</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_select_answer_type</span><span class="p">(</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">negative</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">a_b</span><span class="p">],</span>
+            <span class="o">**</span><span class="n">answer_type_args</span>
+        <span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="Interaction.negative_resources_b_a">
+<a class="viewcode-back" href="../../../api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.negative_resources_b_a">[docs]</a>
+    <span class="k">def</span> <span class="nf">negative_resources_b_a</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Retrieves the list of resources for the :py:attr:`b_a`</span>
+<span class="sd">        direction and negative sign.</span>
+
+<span class="sd">        :return:</span>
+<span class="sd">            (*set*) -- Contains the names of the resources supporting the</span>
+<span class="sd">            :py:attr:`b_a` directionality of the edge with a</span>
+<span class="sd">            negative sign.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">answer_type_args</span> <span class="o">=</span> <span class="p">{</span>
+            <span class="s1">&#39;resource_names&#39;</span><span class="p">:</span> <span class="kc">True</span>
+        <span class="p">}</span>
+        <span class="n">answer_type_args</span><span class="o">.</span><span class="n">update</span><span class="p">(</span><span class="n">kwargs</span><span class="p">)</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_select_answer_type</span><span class="p">(</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">negative</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">b_a</span><span class="p">],</span>
+            <span class="o">**</span><span class="n">answer_type_args</span>
+        <span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="Interaction.positive_resources_a_b">
+<a class="viewcode-back" href="../../../api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.positive_resources_a_b">[docs]</a>
+    <span class="k">def</span> <span class="nf">positive_resources_a_b</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Retrieves the list of resources for the :py:attr:`a_b`</span>
+<span class="sd">        direction and positive sign.</span>
+
+<span class="sd">        :return:</span>
+<span class="sd">            (*set*) -- Contains the names of the resources supporting the</span>
+<span class="sd">            :py:attr:`a_b` directionality of the edge with a</span>
+<span class="sd">            positive sign.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">answer_type_args</span> <span class="o">=</span> <span class="p">{</span>
+            <span class="s1">&#39;resource_names&#39;</span><span class="p">:</span> <span class="kc">True</span>
+        <span class="p">}</span>
+        <span class="n">answer_type_args</span><span class="o">.</span><span class="n">update</span><span class="p">(</span><span class="n">kwargs</span><span class="p">)</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_select_answer_type</span><span class="p">(</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">positive</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">a_b</span><span class="p">],</span>
+            <span class="o">**</span><span class="n">answer_type_args</span>
+        <span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="Interaction.positive_resources_b_a">
+<a class="viewcode-back" href="../../../api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.positive_resources_b_a">[docs]</a>
+    <span class="k">def</span> <span class="nf">positive_resources_b_a</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Retrieves the list of resources for the :py:attr:`b_a`</span>
+<span class="sd">        direction and positive sign.</span>
+
+<span class="sd">        :return:</span>
+<span class="sd">            (*set*) -- Contains the names of the resources supporting the</span>
+<span class="sd">            :py:attr:`b_a` directionality of the edge with a</span>
+<span class="sd">            positive sign.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">answer_type_args</span> <span class="o">=</span> <span class="p">{</span>
+            <span class="s1">&#39;resource_names&#39;</span><span class="p">:</span> <span class="kc">True</span>
+        <span class="p">}</span>
+        <span class="n">answer_type_args</span><span class="o">.</span><span class="n">update</span><span class="p">(</span><span class="n">kwargs</span><span class="p">)</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_select_answer_type</span><span class="p">(</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">positive</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">b_a</span><span class="p">],</span>
+            <span class="o">**</span><span class="n">answer_type_args</span>
+        <span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="Interaction.majority_dir">
+<a class="viewcode-back" href="../../../api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.majority_dir">[docs]</a>
+    <span class="k">def</span> <span class="nf">majority_dir</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">only_interaction_type</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">only_primary</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
+            <span class="n">by_references</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+            <span class="n">by_reference_resource_pairs</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
+        <span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Infers which is the major directionality of the edge by number</span>
+<span class="sd">        of supporting sources.</span>
+
+<span class="sd">        :return:</span>
+<span class="sd">            (*tuple*) -- Contains the pair of nodes denoting the</span>
+<span class="sd">            consensus directionality. If the number of sources on both</span>
+<span class="sd">            directions is equal, ``None`` is returned. If there is no</span>
+<span class="sd">            directionality information, ``&#39;undirected&#39;``` will be</span>
+<span class="sd">            returned.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+
+        <span class="n">a_b</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">direction</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">a_b</span><span class="p">]</span>
+        <span class="n">b_a</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">direction</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">b_a</span><span class="p">]</span>
+
+        <span class="k">if</span> <span class="ow">not</span> <span class="n">a_b</span> <span class="ow">and</span> <span class="ow">not</span> <span class="n">b_a</span><span class="p">:</span>
+
+            <span class="k">return</span> <span class="s1">&#39;undirected&#39;</span>
+
+        <span class="n">method</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="s1">&#39;count_references&#39;</span>
+                <span class="k">if</span> <span class="n">by_references</span> <span class="k">else</span>
+            <span class="s1">&#39;count_curation_effort&#39;</span>
+                <span class="k">if</span> <span class="n">by_reference_resource_pairs</span> <span class="k">else</span>
+            <span class="s1">&#39;count_resources&#39;</span>
+        <span class="p">)</span>
+
+        <span class="n">n_a_b</span> <span class="o">=</span> <span class="nb">getattr</span><span class="p">(</span><span class="n">a_b</span><span class="p">,</span> <span class="n">method</span><span class="p">)(</span>
+            <span class="n">interaction_type</span> <span class="o">=</span> <span class="n">only_interaction_type</span><span class="p">,</span>
+            <span class="n">via</span> <span class="o">=</span> <span class="kc">False</span> <span class="k">if</span> <span class="n">only_primary</span> <span class="k">else</span> <span class="kc">None</span><span class="p">,</span>
+        <span class="p">)</span>
+        <span class="n">n_b_a</span> <span class="o">=</span> <span class="nb">getattr</span><span class="p">(</span><span class="n">b_a</span><span class="p">,</span> <span class="n">method</span><span class="p">)(</span>
+            <span class="n">interaction_type</span> <span class="o">=</span> <span class="n">only_interaction_type</span><span class="p">,</span>
+            <span class="n">via</span> <span class="o">=</span> <span class="kc">False</span> <span class="k">if</span> <span class="n">only_primary</span> <span class="k">else</span> <span class="kc">None</span><span class="p">,</span>
+        <span class="p">)</span>
+
+        <span class="k">return</span> <span class="p">(</span>
+            <span class="s1">&#39;undirected&#39;</span>
+                <span class="k">if</span> <span class="n">n_a_b</span> <span class="o">==</span> <span class="mi">0</span> <span class="ow">and</span> <span class="n">n_b_a</span> <span class="o">==</span> <span class="mi">0</span> <span class="k">else</span>
+            <span class="kc">None</span>
+                <span class="k">if</span> <span class="n">n_a_b</span> <span class="o">==</span> <span class="n">n_b_a</span> <span class="k">else</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">a_b</span>
+                <span class="k">if</span> <span class="n">n_a_b</span> <span class="o">&gt;</span> <span class="n">n_b_a</span> <span class="k">else</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">b_a</span>
+        <span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="Interaction.majority_sign">
+<a class="viewcode-back" href="../../../api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.majority_sign">[docs]</a>
+    <span class="k">def</span> <span class="nf">majority_sign</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">only_interaction_type</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">only_primary</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
+            <span class="n">by_references</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+            <span class="n">by_reference_resource_pairs</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
+        <span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Infers which is the major sign (activation/inhibition) of the</span>
+<span class="sd">        edge by number of supporting sources on both directions.</span>
+
+<span class="sd">        :return:</span>
+<span class="sd">            (*dict*) -- Keys are the node tuples on both directions</span>
+<span class="sd">            (:py:attr:`straight`/:py:attr:`reverse`) and values can be</span>
+<span class="sd">            either ``None`` if that direction has no sign information or</span>
+<span class="sd">            a list of two [bool] elements corresponding to majority of</span>
+<span class="sd">            positive and majority of negative support. In case both</span>
+<span class="sd">            elements of the list are ``True``, this means the number of</span>
+<span class="sd">            supporting sources for both signs in that direction is</span>
+<span class="sd">            equal.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">result</span> <span class="o">=</span> <span class="p">{}</span>
+
+        <span class="n">method</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="s1">&#39;count_references&#39;</span>
+                <span class="k">if</span> <span class="n">by_references</span> <span class="k">else</span>
+            <span class="s1">&#39;count_curation_effort&#39;</span>
+                <span class="k">if</span> <span class="n">by_reference_resource_pairs</span> <span class="k">else</span>
+            <span class="s1">&#39;count_resources&#39;</span>
+        <span class="p">)</span>
+
+        <span class="k">for</span> <span class="n">_dir</span> <span class="ow">in</span> <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">a_b</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">b_a</span><span class="p">):</span>
+
+            <span class="n">n_pos</span> <span class="o">=</span> <span class="nb">getattr</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">positive</span><span class="p">[</span><span class="n">_dir</span><span class="p">],</span> <span class="n">method</span><span class="p">)(</span>
+                <span class="n">interaction_type</span> <span class="o">=</span> <span class="n">only_interaction_type</span><span class="p">,</span>
+                <span class="n">via</span> <span class="o">=</span> <span class="kc">False</span> <span class="k">if</span> <span class="n">only_primary</span> <span class="k">else</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="p">)</span>
+            <span class="n">n_neg</span> <span class="o">=</span> <span class="nb">getattr</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">negative</span><span class="p">[</span><span class="n">_dir</span><span class="p">],</span> <span class="n">method</span><span class="p">)(</span>
+                <span class="n">interaction_type</span> <span class="o">=</span> <span class="n">only_interaction_type</span><span class="p">,</span>
+                <span class="n">via</span> <span class="o">=</span> <span class="kc">False</span> <span class="k">if</span> <span class="n">only_primary</span> <span class="k">else</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="p">)</span>
+
+            <span class="n">result</span><span class="p">[</span><span class="n">_dir</span><span class="p">]</span> <span class="o">=</span> <span class="p">[</span>
+                <span class="mi">0</span> <span class="o">&lt;</span> <span class="n">n_pos</span> <span class="o">&gt;=</span> <span class="n">n_neg</span><span class="p">,</span>
+                <span class="mi">0</span> <span class="o">&lt;</span> <span class="n">n_neg</span> <span class="o">&gt;=</span> <span class="n">n_pos</span><span class="p">,</span>
+            <span class="p">]</span>
+
+        <span class="k">return</span> <span class="n">result</span></div>
+
+
+
+<div class="viewcode-block" id="Interaction.consensus">
+<a class="viewcode-back" href="../../../api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.consensus">[docs]</a>
+    <span class="k">def</span> <span class="nf">consensus</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">only_interaction_type</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">only_primary</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+            <span class="n">by_references</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+            <span class="n">by_reference_resource_pairs</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
+        <span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Infers the consensus edge(s) according to the number of</span>
+<span class="sd">        supporting sources. This includes direction and sign.</span>
+
+<span class="sd">        :return:</span>
+<span class="sd">            (*list*) -- Contains the consensus edge(s) along with the</span>
+<span class="sd">            consensus sign. If there is no major directionality, both</span>
+<span class="sd">            are returned. The structure is as follows:</span>
+<span class="sd">            ``[&#39;&lt;source&gt;&#39;, &#39;&lt;target&gt;&#39;, &#39;&lt;(un)directed&gt;&#39;, &#39;&lt;sign&gt;&#39;]``</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">result</span> <span class="o">=</span> <span class="p">[]</span>
+
+        <span class="n">_dir</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">majority_dir</span><span class="p">(</span>
+            <span class="n">only_interaction_type</span> <span class="o">=</span> <span class="n">only_interaction_type</span><span class="p">,</span>
+            <span class="n">only_primary</span> <span class="o">=</span> <span class="n">only_primary</span><span class="p">,</span>
+            <span class="n">by_references</span> <span class="o">=</span> <span class="n">by_references</span><span class="p">,</span>
+            <span class="n">by_reference_resource_pairs</span> <span class="o">=</span> <span class="n">by_reference_resource_pairs</span><span class="p">,</span>
+        <span class="p">)</span>
+
+        <span class="k">if</span> <span class="n">_dir</span> <span class="o">==</span> <span class="s1">&#39;undirected&#39;</span> <span class="ow">or</span> <span class="n">_dir</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
+
+            <span class="n">_dir</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">majority_dir</span><span class="p">(</span>
+                <span class="n">only_interaction_type</span> <span class="o">=</span> <span class="n">only_interaction_type</span><span class="p">,</span>
+                <span class="n">only_primary</span> <span class="o">=</span> <span class="n">only_primary</span><span class="p">,</span>
+                <span class="n">by_references</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+                <span class="n">by_reference_resource_pairs</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+            <span class="p">)</span>
+
+        <span class="n">_effect</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">majority_sign</span><span class="p">(</span>
+            <span class="n">only_interaction_type</span> <span class="o">=</span> <span class="n">only_interaction_type</span><span class="p">,</span>
+            <span class="n">only_primary</span> <span class="o">=</span> <span class="n">only_primary</span><span class="p">,</span>
+            <span class="n">by_references</span> <span class="o">=</span> <span class="n">by_references</span><span class="p">,</span>
+            <span class="n">by_reference_resource_pairs</span> <span class="o">=</span> <span class="n">by_reference_resource_pairs</span><span class="p">,</span>
+        <span class="p">)</span>
+        <span class="n">_effect_noref</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">majority_sign</span><span class="p">(</span>
+            <span class="n">only_interaction_type</span> <span class="o">=</span> <span class="n">only_interaction_type</span><span class="p">,</span>
+            <span class="n">only_primary</span> <span class="o">=</span> <span class="n">only_primary</span><span class="p">,</span>
+            <span class="n">by_references</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+            <span class="n">by_reference_resource_pairs</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+        <span class="p">)</span>
+
+        <span class="k">if</span> <span class="n">_dir</span> <span class="o">==</span> <span class="s1">&#39;undirected&#39;</span><span class="p">:</span>
+
+            <span class="n">result</span><span class="o">.</span><span class="n">append</span><span class="p">([</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">a_b</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">a_b</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span>
+                <span class="s1">&#39;undirected&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;unknown&#39;</span><span class="p">,</span>
+            <span class="p">])</span>
+
+        <span class="k">else</span><span class="p">:</span>
+
+            <span class="n">dirs</span> <span class="o">=</span> <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">a_b</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">b_a</span><span class="p">)</span> <span class="k">if</span> <span class="n">_dir</span> <span class="ow">is</span> <span class="kc">None</span> <span class="k">else</span> <span class="p">(</span><span class="n">_dir</span><span class="p">,)</span>
+
+            <span class="k">for</span> <span class="n">d</span> <span class="ow">in</span> <span class="n">dirs</span><span class="p">:</span>
+
+                <span class="n">d_effect</span> <span class="o">=</span> <span class="p">(</span>
+                    <span class="n">_effect</span><span class="p">[</span><span class="n">d</span><span class="p">]</span>
+                        <span class="k">if</span> <span class="p">(</span>
+                            <span class="n">_effect</span><span class="p">[</span><span class="n">d</span><span class="p">]</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span> <span class="ow">and</span>
+                            <span class="n">_effect</span><span class="p">[</span><span class="n">d</span><span class="p">][</span><span class="mi">0</span><span class="p">]</span> <span class="o">!=</span> <span class="n">_effect</span><span class="p">[</span><span class="n">d</span><span class="p">][</span><span class="mi">1</span><span class="p">]</span>
+                        <span class="p">)</span> <span class="k">else</span>
+                    <span class="n">_effect_noref</span><span class="p">[</span><span class="n">d</span><span class="p">]</span>
+                <span class="p">)</span>
+
+                <span class="k">if</span> <span class="n">d_effect</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
+
+                    <span class="c1"># index #0 is positive</span>
+                    <span class="k">if</span> <span class="n">d_effect</span><span class="p">[</span><span class="mi">0</span><span class="p">]:</span>
+
+                        <span class="n">result</span><span class="o">.</span><span class="n">append</span><span class="p">([</span>
+                            <span class="n">d</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span>
+                            <span class="n">d</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span>
+                            <span class="s1">&#39;directed&#39;</span><span class="p">,</span>
+                            <span class="s1">&#39;positive&#39;</span><span class="p">,</span>
+                        <span class="p">])</span>
+
+                    <span class="c1"># can not be elif bc of the case of equal weight of</span>
+                    <span class="c1"># evidences for both positive and negative</span>
+                    <span class="k">if</span> <span class="n">d_effect</span><span class="p">[</span><span class="mi">1</span><span class="p">]:</span>
+
+                        <span class="n">result</span><span class="o">.</span><span class="n">append</span><span class="p">([</span>
+                            <span class="n">d</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span>
+                            <span class="n">d</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span>
+                            <span class="s1">&#39;directed&#39;</span><span class="p">,</span>
+                            <span class="s1">&#39;negative&#39;</span><span class="p">,</span>
+                        <span class="p">])</span>
+
+                <span class="c1"># directed with unknown effect</span>
+                <span class="k">else</span><span class="p">:</span>
+
+                    <span class="n">result</span><span class="o">.</span><span class="n">append</span><span class="p">([</span>
+                        <span class="n">d</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span>
+                        <span class="n">d</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span>
+                        <span class="s1">&#39;directed&#39;</span><span class="p">,</span>
+                        <span class="s1">&#39;unknown&#39;</span><span class="p">,</span>
+                    <span class="p">])</span>
+
+        <span class="k">return</span> <span class="n">result</span></div>
+
+
+
+    <span class="n">consensus_edges</span> <span class="o">=</span> <span class="n">consensus</span>
+
+
+<div class="viewcode-block" id="Interaction.merge">
+<a class="viewcode-back" href="../../../api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.merge">[docs]</a>
+    <span class="k">def</span> <span class="nf">merge</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">other</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Merges current Interaction with another (if and only if they are the</span>
+<span class="sd">        same class and contain the same nodes). Updates the attributes</span>
+<span class="sd">        :py:attr:`direction`, :py:attr:`positive` and :py:attr:`negative`.</span>
+
+<span class="sd">        :arg pypath.interaction.Interaction other:</span>
+<span class="sd">            The new Interaction object to be merged with the current one.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+
+        <span class="k">if</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">_check_nodes_key</span><span class="p">(</span><span class="n">other</span><span class="o">.</span><span class="n">nodes</span><span class="p">):</span>
+
+            <span class="n">_log</span><span class="p">(</span>
+                <span class="s1">&#39;Attempting to merge Interaction instances with different &#39;</span>
+                <span class="s1">&#39;interacting partners.&#39;</span>
+            <span class="p">)</span>
+            <span class="k">return</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">evidences</span> <span class="o">+=</span> <span class="n">other</span><span class="o">.</span><span class="n">evidences</span>
+
+        <span class="k">for</span> <span class="n">attr</span><span class="p">,</span> <span class="n">_dir</span> <span class="ow">in</span> <span class="n">itertools</span><span class="o">.</span><span class="n">product</span><span class="p">(</span>
+            <span class="p">(</span><span class="s1">&#39;direction&#39;</span><span class="p">,</span> <span class="s1">&#39;positive&#39;</span><span class="p">,</span> <span class="s1">&#39;negative&#39;</span><span class="p">),</span>
+            <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">a_b</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">b_a</span><span class="p">,</span> <span class="s1">&#39;undirected&#39;</span><span class="p">)</span>
+        <span class="p">):</span>
+
+            <span class="k">if</span> <span class="n">attr</span> <span class="o">!=</span> <span class="s1">&#39;direction&#39;</span> <span class="ow">and</span> <span class="n">_dir</span> <span class="o">==</span> <span class="s1">&#39;undirected&#39;</span><span class="p">:</span>
+
+                <span class="k">continue</span>
+
+            <span class="nb">getattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">attr</span><span class="p">)[</span><span class="n">_dir</span><span class="p">]</span> <span class="o">+=</span> <span class="nb">getattr</span><span class="p">(</span><span class="n">other</span><span class="p">,</span> <span class="n">attr</span><span class="p">)[</span><span class="n">_dir</span><span class="p">]</span></div>
+
+
+
+<div class="viewcode-block" id="Interaction.translate">
+<a class="viewcode-back" href="../../../api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.translate">[docs]</a>
+    <span class="k">def</span> <span class="nf">translate</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">ids</span><span class="p">,</span> <span class="n">new_attrs</span> <span class="o">=</span> <span class="kc">None</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Translates the node names/identifiers according to the</span>
+<span class="sd">        dictionary *ids*. Also is able to change attributes like `id_type`,</span>
+<span class="sd">        `taxon` and `entity_type`.</span>
+
+<span class="sd">        :arg dict ids:</span>
+<span class="sd">            Dictionary containing (at least) the current names of the</span>
+<span class="sd">            nodes as keys and their translation as values.</span>
+<span class="sd">        :arg dict new_attrs:</span>
+<span class="sd">            Dictionary with new IDs as keys and their dicts of their new</span>
+<span class="sd">            attributes as values. For any attribute not provided here</span>
+<span class="sd">            the attributes from the original instance will be used.</span>
+<span class="sd">            E.g. you can provide `{&#39;1956&#39;: {&#39;id_type&#39;: &#39;entrez&#39;}}&#39; if the</span>
+<span class="sd">            new ID type for protein EGFR is Entrez Gene ID.</span>
+
+<span class="sd">        :return:</span>
+<span class="sd">            (*pypath.main.Direction*) -- The copy of current edge object</span>
+<span class="sd">            with translated node names.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">new_a</span> <span class="o">=</span> <span class="n">ids</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">nodes</span><span class="p">[</span><span class="mi">0</span><span class="p">]]</span>
+        <span class="n">new_b</span> <span class="o">=</span> <span class="n">ids</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">nodes</span><span class="p">[</span><span class="mi">1</span><span class="p">]]</span>
+        <span class="n">new_ids</span> <span class="o">=</span> <span class="p">{</span><span class="s1">&#39;a&#39;</span><span class="p">:</span> <span class="n">new_a</span><span class="p">,</span> <span class="s1">&#39;b&#39;</span><span class="p">:</span> <span class="n">new_b</span><span class="p">}</span>
+        <span class="n">to_old</span> <span class="o">=</span> <span class="n">common</span><span class="o">.</span><span class="n">swap_dict_simple</span><span class="p">(</span><span class="n">ids</span><span class="p">)</span>
+
+        <span class="n">all_new_attrs</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">(</span>
+            <span class="p">(</span>
+                <span class="s1">&#39;</span><span class="si">%s</span><span class="s1">_</span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="p">(</span><span class="n">attr</span><span class="p">,</span> <span class="n">label</span><span class="p">),</span>
+                <span class="n">new_attrs</span><span class="p">[</span><span class="n">new_ids</span><span class="p">[</span><span class="n">label</span><span class="p">]][</span><span class="n">attr</span><span class="p">]</span>
+                    <span class="k">if</span> <span class="p">(</span>
+                        <span class="n">new_ids</span><span class="p">[</span><span class="n">label</span><span class="p">]</span> <span class="ow">in</span> <span class="n">new_attrs</span> <span class="ow">and</span>
+                        <span class="n">attr</span> <span class="ow">in</span> <span class="n">new_attrs</span><span class="p">[</span><span class="n">new_ids</span><span class="p">[</span><span class="n">label</span><span class="p">]]</span>
+                    <span class="p">)</span> <span class="k">else</span>
+                <span class="nb">getattr</span><span class="p">(</span><span class="nb">getattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">label</span><span class="p">),</span> <span class="n">attr</span><span class="p">)</span>
+            <span class="p">)</span>
+            <span class="k">for</span> <span class="n">attr</span> <span class="ow">in</span> <span class="p">(</span><span class="s1">&#39;id_type&#39;</span><span class="p">,</span> <span class="s1">&#39;entity_type&#39;</span><span class="p">,</span> <span class="s1">&#39;taxon&#39;</span><span class="p">)</span>
+            <span class="k">for</span> <span class="n">label</span> <span class="ow">in</span> <span class="p">(</span><span class="s1">&#39;a&#39;</span><span class="p">,</span> <span class="s1">&#39;b&#39;</span><span class="p">)</span>
+        <span class="p">)</span>
+
+        <span class="n">all_new_attrs</span><span class="p">[</span><span class="s1">&#39;attrs&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">new_attrs</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">&#39;attrs&#39;</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">attrs</span><span class="p">)</span>
+
+        <span class="n">new</span> <span class="o">=</span> <span class="n">Interaction</span><span class="p">(</span>
+            <span class="n">a</span> <span class="o">=</span> <span class="n">new_a</span><span class="p">,</span>
+            <span class="n">b</span> <span class="o">=</span> <span class="n">new_b</span><span class="p">,</span>
+            <span class="o">**</span><span class="n">all_new_attrs</span>
+        <span class="p">)</span>
+
+        <span class="n">new</span><span class="o">.</span><span class="n">evidences</span> <span class="o">+=</span> <span class="bp">self</span><span class="o">.</span><span class="n">evidences</span>
+
+        <span class="n">to_old</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">(</span>
+            <span class="p">(</span>
+                <span class="n">new_id</span><span class="p">,</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">id_to_entity</span><span class="p">(</span><span class="n">old_id</span><span class="p">)</span>
+            <span class="p">)</span>
+            <span class="k">for</span> <span class="n">new_id</span><span class="p">,</span> <span class="n">old_id</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="n">to_old</span><span class="p">)</span>
+        <span class="p">)</span>
+
+        <span class="c1"># this is required to handle also loop edges</span>
+        <span class="n">new_old_a_b</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="p">(</span>
+                <span class="n">to_old</span><span class="p">[</span><span class="n">new</span><span class="o">.</span><span class="n">a</span><span class="o">.</span><span class="n">identifier</span><span class="p">],</span>
+                <span class="n">to_old</span><span class="p">[</span><span class="n">new</span><span class="o">.</span><span class="n">b</span><span class="o">.</span><span class="n">identifier</span><span class="p">],</span>
+            <span class="p">)</span>
+                <span class="k">if</span> <span class="n">new</span><span class="o">.</span><span class="n">a</span> <span class="o">!=</span> <span class="n">new</span><span class="o">.</span><span class="n">b</span> <span class="k">else</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">a_b</span>
+        <span class="p">)</span>
+        <span class="n">new_old_b_a</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="p">(</span>
+                <span class="n">to_old</span><span class="p">[</span><span class="n">new</span><span class="o">.</span><span class="n">b</span><span class="o">.</span><span class="n">identifier</span><span class="p">],</span>
+                <span class="n">to_old</span><span class="p">[</span><span class="n">new</span><span class="o">.</span><span class="n">a</span><span class="o">.</span><span class="n">identifier</span><span class="p">],</span>
+            <span class="p">)</span>
+                <span class="k">if</span> <span class="n">new</span><span class="o">.</span><span class="n">a</span> <span class="o">!=</span> <span class="n">new</span><span class="o">.</span><span class="n">b</span> <span class="k">else</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">b_a</span>
+        <span class="p">)</span>
+
+        <span class="k">for</span> <span class="p">(</span><span class="n">old_dir</span><span class="p">,</span> <span class="n">new_dir</span><span class="p">),</span> <span class="n">attr</span> <span class="ow">in</span> <span class="n">itertools</span><span class="o">.</span><span class="n">product</span><span class="p">(</span>
+            <span class="nb">zip</span><span class="p">(</span>
+                <span class="p">(</span>
+                    <span class="n">new_old_a_b</span><span class="p">,</span>
+                    <span class="n">new_old_b_a</span><span class="p">,</span>
+                    <span class="s1">&#39;undirected&#39;</span>
+                <span class="p">),</span>
+                <span class="p">(</span>
+                    <span class="n">new</span><span class="o">.</span><span class="n">a_b</span><span class="p">,</span>
+                    <span class="n">new</span><span class="o">.</span><span class="n">b_a</span><span class="p">,</span>
+                    <span class="s1">&#39;undirected&#39;</span><span class="p">,</span>
+                <span class="p">),</span>
+            <span class="p">),</span>
+            <span class="p">(</span><span class="s1">&#39;direction&#39;</span><span class="p">,</span> <span class="s1">&#39;positive&#39;</span><span class="p">,</span> <span class="s1">&#39;negative&#39;</span><span class="p">),</span>
+        <span class="p">):</span>
+
+            <span class="k">if</span> <span class="n">old_dir</span> <span class="o">==</span> <span class="s1">&#39;undirected&#39;</span> <span class="ow">and</span> <span class="n">attr</span> <span class="o">!=</span> <span class="s1">&#39;direction&#39;</span><span class="p">:</span>
+
+                <span class="k">continue</span>
+
+            <span class="nb">getattr</span><span class="p">(</span><span class="n">new</span><span class="p">,</span> <span class="n">attr</span><span class="p">)[</span><span class="n">new_dir</span><span class="p">]</span> <span class="o">+=</span> <span class="nb">getattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">attr</span><span class="p">)[</span><span class="n">old_dir</span><span class="p">]</span>
+
+        <span class="k">return</span> <span class="n">new</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">orthology_translate_one</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">id_a</span><span class="p">,</span> <span class="n">id_b</span><span class="p">,</span> <span class="n">taxon</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">translate</span><span class="p">(</span>
+            <span class="n">ids</span> <span class="o">=</span> <span class="p">{</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">a</span><span class="p">:</span> <span class="n">id_a</span><span class="p">,</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">b</span><span class="p">:</span> <span class="n">id_b</span><span class="p">,</span>
+            <span class="p">},</span>
+            <span class="n">new_attrs</span> <span class="o">=</span> <span class="p">{</span>
+                <span class="n">id_a</span><span class="p">:</span> <span class="p">{</span>
+                    <span class="s1">&#39;taxon&#39;</span><span class="p">:</span> <span class="p">(</span>
+                        <span class="bp">self</span><span class="o">.</span><span class="n">a</span><span class="o">.</span><span class="n">taxon</span>
+                            <span class="k">if</span> <span class="n">id_a</span> <span class="o">==</span> <span class="bp">self</span><span class="o">.</span><span class="n">a</span><span class="o">.</span><span class="n">identifier</span> <span class="k">else</span>
+                        <span class="n">taxon</span>
+                    <span class="p">),</span>
+                <span class="p">},</span>
+                <span class="n">id_b</span><span class="p">:</span> <span class="p">{</span>
+                    <span class="s1">&#39;taxon&#39;</span><span class="p">:</span> <span class="p">(</span>
+                        <span class="bp">self</span><span class="o">.</span><span class="n">b</span><span class="o">.</span><span class="n">taxon</span>
+                            <span class="k">if</span> <span class="n">id_b</span> <span class="o">==</span> <span class="bp">self</span><span class="o">.</span><span class="n">b</span><span class="o">.</span><span class="n">identifier</span> <span class="k">else</span>
+                        <span class="n">taxon</span>
+                    <span class="p">),</span>
+                <span class="p">},</span>
+            <span class="p">},</span>
+        <span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">orthology_translate</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">taxon</span><span class="p">,</span> <span class="n">exclude</span> <span class="o">=</span> <span class="kc">None</span><span class="p">):</span>
+
+        <span class="n">exclude</span> <span class="o">=</span> <span class="n">exclude</span> <span class="ow">or</span> <span class="nb">set</span><span class="p">()</span>
+        <span class="n">exclude</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="mi">0</span><span class="p">)</span>
+
+        <span class="k">for</span> <span class="n">new_a</span><span class="p">,</span> <span class="n">new_b</span> <span class="ow">in</span> <span class="n">itertools</span><span class="o">.</span><span class="n">product</span><span class="p">(</span>
+            <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">a</span><span class="o">.</span><span class="n">identifier</span><span class="p">,)</span>
+                <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">a</span><span class="o">.</span><span class="n">taxon</span> <span class="ow">in</span> <span class="n">exclude</span> <span class="k">else</span>
+            <span class="n">orthology</span><span class="o">.</span><span class="n">translate</span><span class="p">(</span>
+                <span class="n">source_id</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">a</span><span class="o">.</span><span class="n">identifier</span><span class="p">,</span>
+                <span class="n">target</span> <span class="o">=</span> <span class="n">taxon</span><span class="p">,</span>
+                <span class="n">source</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">a</span><span class="o">.</span><span class="n">taxon</span><span class="p">,</span>
+            <span class="p">),</span>
+            <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">b</span><span class="o">.</span><span class="n">identifier</span><span class="p">,)</span>
+                <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">b</span><span class="o">.</span><span class="n">taxon</span> <span class="ow">in</span> <span class="n">exclude</span> <span class="k">else</span>
+            <span class="n">orthology</span><span class="o">.</span><span class="n">translate</span><span class="p">(</span>
+                <span class="n">source_id</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">b</span><span class="o">.</span><span class="n">identifier</span><span class="p">,</span>
+                <span class="n">target</span> <span class="o">=</span> <span class="n">taxon</span><span class="p">,</span>
+                <span class="n">source</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">b</span><span class="o">.</span><span class="n">taxon</span><span class="p">,</span>
+            <span class="p">),</span>
+        <span class="p">):</span>
+
+            <span class="k">yield</span> <span class="bp">self</span><span class="o">.</span><span class="n">orthology_translate_one</span><span class="p">(</span>
+                <span class="n">id_a</span> <span class="o">=</span> <span class="n">new_a</span><span class="p">,</span>
+                <span class="n">id_b</span> <span class="o">=</span> <span class="n">new_b</span><span class="p">,</span>
+                <span class="n">taxon</span> <span class="o">=</span> <span class="n">taxon</span><span class="p">,</span>
+            <span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">get_evidences</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">direction</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">effect</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">resources</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">data_model</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">interaction_type</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">via</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">references</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">datasets</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+        <span class="p">):</span>
+
+        <span class="n">effect</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_effect_synonyms</span><span class="p">(</span><span class="n">effect</span><span class="p">)</span>
+
+        <span class="n">evidences</span> <span class="o">=</span> <span class="p">(</span>
+
+            <span class="c1"># any signed</span>
+            <span class="nb">sum</span><span class="p">(</span><span class="n">itertools</span><span class="o">.</span><span class="n">chain</span><span class="p">(</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">positive</span><span class="o">.</span><span class="n">values</span><span class="p">(),</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">negative</span><span class="o">.</span><span class="n">values</span><span class="p">(),</span>
+            <span class="p">))</span>
+
+                <span class="k">if</span> <span class="n">effect</span> <span class="o">==</span> <span class="kc">True</span> <span class="k">else</span>
+
+            <span class="c1"># only positive</span>
+            <span class="p">(</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">positive</span><span class="p">[</span><span class="n">direction</span><span class="p">]</span>
+                    <span class="k">if</span> <span class="n">direction</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">positive</span> <span class="k">else</span>
+                <span class="nb">sum</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">positive</span><span class="o">.</span><span class="n">values</span><span class="p">())</span>
+            <span class="p">)</span>
+
+                <span class="k">if</span> <span class="n">effect</span> <span class="o">==</span> <span class="s1">&#39;positive&#39;</span> <span class="k">else</span>
+
+            <span class="c1"># only negative</span>
+            <span class="p">(</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">negative</span><span class="p">[</span><span class="n">direction</span><span class="p">]</span>
+                    <span class="k">if</span> <span class="n">direction</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">negative</span> <span class="k">else</span>
+                <span class="nb">sum</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">negative</span><span class="o">.</span><span class="n">values</span><span class="p">())</span>
+            <span class="p">)</span>
+
+                <span class="k">if</span> <span class="n">effect</span> <span class="o">==</span> <span class="s1">&#39;negative&#39;</span> <span class="k">else</span>
+
+            <span class="c1"># any directed</span>
+            <span class="nb">sum</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">direction</span><span class="p">[</span><span class="n">_dir</span><span class="p">]</span> <span class="k">for</span> <span class="n">_dir</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">which_dirs</span><span class="p">())</span>
+
+                <span class="k">if</span> <span class="n">direction</span> <span class="o">==</span> <span class="kc">True</span> <span class="k">else</span>
+
+            <span class="c1"># one specific direction</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">direction</span><span class="p">[</span><span class="n">direction</span><span class="p">]</span>
+
+                <span class="k">if</span> <span class="n">direction</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">direction</span> <span class="k">else</span>
+
+            <span class="c1"># all evidences (default)</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">evidences</span>
+
+        <span class="p">)</span>
+
+        <span class="k">return</span> <span class="p">(</span>
+            <span class="n">pypath_evidence</span><span class="o">.</span><span class="n">Evidences</span><span class="p">(</span>
+                <span class="n">evidences</span><span class="o">.</span><span class="n">filter</span><span class="p">(</span>
+                    <span class="n">resource</span> <span class="o">=</span> <span class="n">resources</span><span class="p">,</span>
+                    <span class="n">interaction_type</span> <span class="o">=</span> <span class="n">interaction_type</span><span class="p">,</span>
+                    <span class="n">via</span> <span class="o">=</span> <span class="n">via</span><span class="p">,</span>
+                    <span class="n">data_model</span> <span class="o">=</span> <span class="n">data_model</span><span class="p">,</span>
+                    <span class="n">references</span> <span class="o">=</span> <span class="n">references</span><span class="p">,</span>
+                    <span class="n">datasets</span> <span class="o">=</span> <span class="n">datasets</span><span class="p">,</span>
+                <span class="p">)</span>
+            <span class="p">)</span>
+        <span class="p">)</span>
+
+
+<div class="viewcode-block" id="Interaction.get_entities">
+<a class="viewcode-back" href="../../../api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.get_entities">[docs]</a>
+    <span class="k">def</span> <span class="nf">get_entities</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">entity_type</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">direction</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">effect</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">resources</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">data_model</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">interaction_type</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">via</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">references</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">datasets</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">return_type</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+        <span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Retrieves the entities involved in interactions matching the criteria.</span>
+<span class="sd">        It either returns both interacting entities in a *set* or an empty</span>
+<span class="sd">        *set*. This may not sound so useful at the level of this object but</span>
+<span class="sd">        becomes more useful once we want to collect entities having certain</span>
+<span class="sd">        kind of interactions across a series of `Interaction` objects.</span>
+
+<span class="sd">        :arg str entity_type:</span>
+<span class="sd">            The type of the molecular entity. Possible values: `protein`,</span>
+<span class="sd">            `complex`, `mirna`, `small_molecule`.</span>
+<span class="sd">        :arg str return_type:</span>
+<span class="sd">            The type of values to return. Default is</span>
+<span class="sd">            py:class:``pypath.entity.Entity`` objects, alternatives are</span>
+<span class="sd">            ``labels``  ``identifiers``.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="c1"># TODO: this method could be made slightly more efficient by using</span>
+        <span class="c1"># not ``get_interactions`` but a simpler logic as here we don&#39;t need</span>
+        <span class="c1"># to handle the directions separately; however this is not very</span>
+        <span class="c1"># important and for the time being it&#39;s good as it is.</span>
+
+        <span class="n">kwargs</span> <span class="o">=</span> <span class="nb">locals</span><span class="p">()</span>
+        <span class="n">_</span> <span class="o">=</span> <span class="n">kwargs</span><span class="o">.</span><span class="n">pop</span><span class="p">(</span><span class="s1">&#39;self&#39;</span><span class="p">)</span>
+        <span class="n">entity_type</span> <span class="o">=</span> <span class="n">common</span><span class="o">.</span><span class="n">to_set</span><span class="p">(</span><span class="n">kwargs</span><span class="o">.</span><span class="n">pop</span><span class="p">(</span><span class="s1">&#39;entity_type&#39;</span><span class="p">))</span>
+        <span class="n">return_type</span> <span class="o">=</span> <span class="n">kwargs</span><span class="o">.</span><span class="n">pop</span><span class="p">(</span><span class="s1">&#39;return_type&#39;</span><span class="p">)</span>
+
+        <span class="n">return_types</span> <span class="o">=</span> <span class="p">{</span>
+            <span class="s1">&#39;entity&#39;</span><span class="p">:</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="s1">&#39;entities&#39;</span><span class="p">:</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="s1">&#39;id&#39;</span><span class="p">:</span> <span class="s1">&#39;identifier&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;name&#39;</span><span class="p">:</span> <span class="s1">&#39;identifier&#39;</span><span class="p">,</span>
+        <span class="p">}</span>
+
+        <span class="c1"># allow plurals</span>
+        <span class="n">return_type</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="n">return_type</span><span class="p">[:</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span>
+                <span class="k">if</span> <span class="p">(</span>
+                    <span class="nb">isinstance</span><span class="p">(</span><span class="n">return_type</span><span class="p">,</span> <span class="nb">str</span><span class="p">)</span> <span class="ow">and</span>
+                    <span class="n">return_type</span><span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span> <span class="o">==</span> <span class="s1">&#39;s&#39;</span>
+                <span class="p">)</span> <span class="k">else</span>
+            <span class="n">return_type</span>
+        <span class="p">)</span>
+        <span class="c1"># allow some synonyms</span>
+        <span class="n">return_type</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="n">return_types</span><span class="p">[</span><span class="n">return_type</span><span class="p">]</span>
+                <span class="k">if</span> <span class="n">return_type</span> <span class="ow">in</span> <span class="n">return_types</span> <span class="k">else</span>
+            <span class="n">return_type</span>
+        <span class="p">)</span>
+
+        <span class="k">return</span> <span class="p">(</span>
+            <span class="nb">set</span><span class="p">(</span>
+                <span class="p">(</span>
+                    <span class="nb">getattr</span><span class="p">(</span><span class="n">en</span><span class="p">,</span> <span class="n">return_type</span><span class="p">)</span>
+                        <span class="k">if</span> <span class="n">return_type</span> <span class="ow">and</span> <span class="nb">hasattr</span><span class="p">(</span><span class="n">en</span><span class="p">,</span> <span class="n">return_type</span><span class="p">)</span> <span class="k">else</span>
+                    <span class="n">en</span>
+                <span class="p">)</span>
+                <span class="k">for</span> <span class="n">en</span> <span class="ow">in</span>
+                <span class="n">itertools</span><span class="o">.</span><span class="n">chain</span><span class="p">(</span>
+                    <span class="o">*</span><span class="bp">self</span><span class="o">.</span><span class="n">get_interactions</span><span class="p">(</span><span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
+                <span class="p">)</span>
+                <span class="k">if</span> <span class="ow">not</span> <span class="n">entity_type</span> <span class="ow">or</span> <span class="n">en</span><span class="o">.</span><span class="n">entity_type</span> <span class="ow">in</span> <span class="n">entity_type</span>
+            <span class="p">)</span>
+        <span class="p">)</span></div>
+
+
+
+    <span class="nd">@classmethod</span>
+    <span class="k">def</span> <span class="nf">_generate_entity_methods</span><span class="p">(</span><span class="bp">cls</span><span class="p">):</span>
+
+        <span class="k">def</span> <span class="nf">_create_entity_method</span><span class="p">(</span><span class="n">entity_type</span><span class="p">,</span> <span class="n">return_type</span><span class="p">):</span>
+
+
+            <span class="k">def</span> <span class="nf">_entity_method</span><span class="p">(</span><span class="o">*</span><span class="n">args</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+
+                <span class="bp">self</span> <span class="o">=</span> <span class="n">args</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span>
+                <span class="n">kwargs</span><span class="p">[</span><span class="s1">&#39;entity_type&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">entity_type</span>
+                <span class="n">kwargs</span><span class="p">[</span><span class="s1">&#39;return_type&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">return_type</span>
+
+                <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">get_entities</span><span class="p">(</span><span class="o">*</span><span class="n">args</span><span class="p">[</span><span class="mi">1</span><span class="p">:],</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
+
+
+            <span class="k">return</span> <span class="n">_entity_method</span>
+
+
+        <span class="k">for</span> <span class="n">etype</span><span class="p">,</span> <span class="n">vtype</span> <span class="ow">in</span> <span class="n">itertools</span><span class="o">.</span><span class="n">product</span><span class="p">(</span>
+            <span class="bp">cls</span><span class="o">.</span><span class="n">_entity_types</span><span class="p">,</span>
+            <span class="bp">cls</span><span class="o">.</span><span class="n">_entity_values</span><span class="p">,</span>
+        <span class="p">):</span>
+
+            <span class="k">if</span> <span class="n">etype</span> <span class="ow">is</span> <span class="kc">None</span> <span class="ow">and</span> <span class="n">vtype</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
+
+                <span class="k">continue</span>
+
+            <span class="n">entity_type</span> <span class="o">=</span> <span class="n">common</span><span class="o">.</span><span class="n">sfirst</span><span class="p">(</span><span class="n">etype</span><span class="p">)</span>
+            <span class="n">entity_type_label</span> <span class="o">=</span> <span class="n">common</span><span class="o">.</span><span class="n">sfirst</span><span class="p">(</span><span class="n">entity_type</span><span class="p">)</span>
+            <span class="n">return_type</span> <span class="o">=</span> <span class="n">vtype</span>
+
+            <span class="n">etype_part</span> <span class="o">=</span> <span class="p">(</span>
+                <span class="s1">&#39;&#39;</span>
+                    <span class="k">if</span> <span class="ow">not</span> <span class="n">entity_type_label</span> <span class="k">else</span>
+                <span class="n">entity_type_label</span>
+                    <span class="k">if</span> <span class="n">vtype</span> <span class="k">else</span>
+                <span class="n">etype</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span>
+                    <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">etype</span><span class="p">,</span> <span class="nb">tuple</span><span class="p">)</span> <span class="ow">and</span> <span class="nb">len</span><span class="p">(</span><span class="n">etype</span><span class="p">)</span> <span class="o">&gt;</span> <span class="mi">1</span> <span class="k">else</span>
+                <span class="s1">&#39;</span><span class="si">%s</span><span class="s1">s&#39;</span> <span class="o">%</span> <span class="n">entity_type_label</span>
+            <span class="p">)</span>
+            <span class="n">vtype_part</span> <span class="o">=</span> <span class="s1">&#39;</span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="n">vtype</span> <span class="k">if</span> <span class="n">vtype</span> <span class="k">else</span> <span class="s1">&#39;&#39;</span>
+
+            <span class="n">_method_name</span> <span class="o">=</span> <span class="s1">&#39;</span><span class="si">%s%s%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="p">(</span>
+                <span class="n">etype_part</span><span class="p">,</span>
+                <span class="s1">&#39;_&#39;</span> <span class="k">if</span> <span class="n">etype_part</span> <span class="ow">and</span> <span class="n">vtype_part</span> <span class="k">else</span> <span class="s1">&#39;&#39;</span><span class="p">,</span>
+                <span class="n">vtype_part</span><span class="p">,</span>
+            <span class="p">)</span>
+            <span class="n">method_name</span> <span class="o">=</span> <span class="s1">&#39;get_</span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="n">_method_name</span>
+            <span class="n">method</span> <span class="o">=</span> <span class="n">_create_entity_method</span><span class="p">(</span>
+                <span class="n">entity_type</span> <span class="o">=</span> <span class="n">entity_type</span><span class="p">,</span>
+                <span class="n">return_type</span> <span class="o">=</span> <span class="n">return_type</span><span class="p">,</span>
+            <span class="p">)</span>
+
+            <span class="bp">cls</span><span class="o">.</span><span class="n">_add_method</span><span class="p">(</span>
+                <span class="n">method_name</span><span class="p">,</span>
+                <span class="n">method</span><span class="p">,</span>
+                <span class="n">signature</span> <span class="o">=</span> <span class="p">(</span>
+                    <span class="p">[</span><span class="s1">&#39;self&#39;</span><span class="p">,</span> <span class="p">(</span><span class="s1">&#39;entity_type&#39;</span><span class="p">,</span> <span class="kc">None</span><span class="p">)]</span> <span class="o">+</span>
+                    <span class="bp">cls</span><span class="o">.</span><span class="n">_get_method_signature</span> <span class="o">+</span>
+                    <span class="p">[(</span><span class="s1">&#39;return_type&#39;</span><span class="p">,</span> <span class="kc">None</span><span class="p">)]</span>
+                <span class="p">),</span>
+                <span class="n">doc</span> <span class="o">=</span> <span class="bp">cls</span><span class="o">.</span><span class="n">get_entities</span><span class="o">.</span><span class="vm">__doc__</span><span class="p">,</span>
+            <span class="p">)</span>
+            <span class="bp">cls</span><span class="o">.</span><span class="n">_get_methods</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">_method_name</span><span class="p">)</span>
+            <span class="bp">cls</span><span class="o">.</span><span class="n">_count_methods</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">_method_name</span><span class="p">)</span>
+
+
+<div class="viewcode-block" id="Interaction.get_interactions">
+<a class="viewcode-back" href="../../../api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.get_interactions">[docs]</a>
+    <span class="k">def</span> <span class="nf">get_interactions</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">direction</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">effect</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">resources</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">data_model</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">interaction_type</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">via</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">references</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">entity_type</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">source_entity_type</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">target_entity_type</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">datasets</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+        <span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Returns one or two tuples of the interacting partners: one if only</span>
+<span class="sd">        one direction, two if both directions match the query criteria.</span>
+<span class="sd">        The tuple will be empty if no evidence matches the criteria.</span>
+
+<span class="sd">        :arg NontType,bool,tuple direction:</span>
+<span class="sd">            If `None` both undirected and directed, if `True` only directed,</span>
+<span class="sd">            if a *tuple* of entities only the interactions with that specific</span>
+<span class="sd">            direction will be considered. Unless you set this parameter to</span>
+<span class="sd">            `True` this method will return both directions if one or more</span>
+<span class="sd">            undirected resources present.</span>
+<span class="sd">            If `False`, only the undirected interactions will be considered,</span>
+<span class="sd">            and if any resource annotates this interaction as undirected</span>
+<span class="sd">            both directions will be returned. However the</span>
+<span class="sd">            ``count_interactions_undirected`` method will return `1`</span>
+<span class="sd">            in this case.</span>
+<span class="sd">        :arg NoneType,bool,str effect:</span>
+<span class="sd">            If `None` also interactions without effect, if `True` only</span>
+<span class="sd">            the ones with any effect, if a string naming an effect only the</span>
+<span class="sd">            interactions with that specific effect will be considered.</span>
+<span class="sd">        :arg NontType,str,set resources:</span>
+<span class="sd">            Optionally limit the query to one or more resources.</span>
+<span class="sd">        :arg NontType,str,set data_model:</span>
+<span class="sd">            Optionally limit the query to one or more data models e.g.</span>
+<span class="sd">            `activity_flow`.</span>
+<span class="sd">        :arg NontType,str,set interaction_type:</span>
+<span class="sd">            Optionally limit the query to one or more interaction types</span>
+<span class="sd">            e.g. `PPI`.</span>
+<span class="sd">        :arg NontType,bool,str,set via:</span>
+<span class="sd">            Optionally limit the query to certain secondary databases or</span>
+<span class="sd">            if `False` consider only data from primary databases.</span>
+<span class="sd">        :arg str entity_type:</span>
+<span class="sd">            Molecule type for both of the entities.</span>
+<span class="sd">        :arg str source_entity_type:</span>
+<span class="sd">            Molecule type for the source entity.</span>
+<span class="sd">        :arg str target_entity_type:</span>
+<span class="sd">            Molecule type for the target entity.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">effect</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_effect_synonyms</span><span class="p">(</span><span class="n">effect</span><span class="p">)</span>
+        <span class="n">direction</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">direction_key</span><span class="p">(</span><span class="n">direction</span><span class="p">)</span>
+                <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">direction</span><span class="p">,</span> <span class="nb">tuple</span><span class="p">)</span> <span class="k">else</span>
+            <span class="n">direction</span>
+        <span class="p">)</span>
+
+        <span class="n">entity_type</span> <span class="o">=</span> <span class="n">common</span><span class="o">.</span><span class="n">to_set</span><span class="p">(</span><span class="n">entity_type</span><span class="p">)</span>
+        <span class="n">source_entity_type</span> <span class="o">=</span> <span class="n">common</span><span class="o">.</span><span class="n">to_set</span><span class="p">(</span><span class="n">source_entity_type</span><span class="p">)</span> <span class="ow">or</span> <span class="n">entity_type</span>
+        <span class="n">target_entity_type</span> <span class="o">=</span> <span class="n">common</span><span class="o">.</span><span class="n">to_set</span><span class="p">(</span><span class="n">target_entity_type</span><span class="p">)</span> <span class="ow">or</span> <span class="n">entity_type</span>
+
+        <span class="k">return</span> <span class="nb">tuple</span><span class="p">(</span>
+
+            <span class="c1"># direction key</span>
+            <span class="n">_dir</span>
+
+            <span class="c1"># possible directions</span>
+            <span class="k">for</span> <span class="n">_dir</span> <span class="ow">in</span> <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">a_b</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">b_a</span><span class="p">)</span>
+
+            <span class="c1"># conditions by selecting and evaluating evidence collections</span>
+            <span class="k">if</span> <span class="p">(</span>
+                <span class="p">(</span>
+                    <span class="ow">not</span> <span class="n">source_entity_type</span> <span class="ow">or</span>
+                    <span class="n">_dir</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">entity_type</span> <span class="ow">in</span> <span class="n">source_entity_type</span>
+                <span class="p">)</span> <span class="ow">and</span>
+                <span class="p">(</span>
+                    <span class="ow">not</span> <span class="n">target_entity_type</span> <span class="ow">or</span>
+                    <span class="n">_dir</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">entity_type</span> <span class="ow">in</span> <span class="n">target_entity_type</span>
+                <span class="p">)</span>
+            <span class="p">)</span>
+            <span class="ow">and</span>
+            <span class="p">(</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">evaluate_evidences</span><span class="p">(</span>
+                    <span class="n">this_direction</span> <span class="o">=</span> <span class="n">_dir</span><span class="p">,</span>
+                    <span class="n">direction</span> <span class="o">=</span> <span class="n">direction</span><span class="p">,</span>
+                    <span class="n">effect</span> <span class="o">=</span> <span class="n">effect</span><span class="p">,</span>
+                    <span class="n">resources</span> <span class="o">=</span> <span class="n">resources</span><span class="p">,</span>
+                    <span class="n">data_model</span> <span class="o">=</span> <span class="n">data_model</span><span class="p">,</span>
+                    <span class="n">interaction_type</span> <span class="o">=</span> <span class="n">interaction_type</span><span class="p">,</span>
+                    <span class="n">via</span> <span class="o">=</span> <span class="n">via</span><span class="p">,</span>
+                    <span class="n">references</span> <span class="o">=</span> <span class="n">references</span><span class="p">,</span>
+                    <span class="n">datasets</span> <span class="o">=</span> <span class="n">datasets</span><span class="p">,</span>
+                <span class="p">)</span>
+            <span class="p">)</span>
+
+        <span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="Interaction.evaluate_evidences">
+<a class="viewcode-back" href="../../../api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.evaluate_evidences">[docs]</a>
+    <span class="k">def</span> <span class="nf">evaluate_evidences</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">this_direction</span><span class="p">,</span>
+            <span class="n">direction</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">effect</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">resources</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">data_model</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">interaction_type</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">via</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">references</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">datasets</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+        <span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Selects the evidence collections matching the direction and effect</span>
+<span class="sd">        criteria and then evaluates if any of the evidences in these</span>
+<span class="sd">        collections match the evidence criteria.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">kwargs</span> <span class="o">=</span> <span class="nb">locals</span><span class="p">()</span>
+        <span class="n">_</span> <span class="o">=</span> <span class="n">kwargs</span><span class="o">.</span><span class="n">pop</span><span class="p">(</span><span class="s1">&#39;self&#39;</span><span class="p">)</span>
+
+        <span class="k">return</span> <span class="nb">any</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">iter_match_evidences</span><span class="p">(</span><span class="o">**</span><span class="n">kwargs</span><span class="p">))</span></div>
+
+
+
+<div class="viewcode-block" id="Interaction.iter_match_evidences">
+<a class="viewcode-back" href="../../../api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.iter_match_evidences">[docs]</a>
+    <span class="k">def</span> <span class="nf">iter_match_evidences</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">this_direction</span><span class="p">,</span>
+            <span class="n">direction</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">effect</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">resources</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">data_model</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">interaction_type</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">via</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">references</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">datasets</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+        <span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Selects the evidence collections matching the direction and effect</span>
+<span class="sd">        criteria and yields collections matching the evidence criteria.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">for</span> <span class="n">evs</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">iter_evidences</span><span class="p">(</span>
+            <span class="n">this_direction</span> <span class="o">=</span> <span class="n">this_direction</span><span class="p">,</span>
+            <span class="n">direction</span> <span class="o">=</span> <span class="n">direction</span><span class="p">,</span>
+            <span class="n">effect</span> <span class="o">=</span> <span class="n">effect</span><span class="p">,</span>
+        <span class="p">):</span>
+
+            <span class="k">if</span> <span class="n">evs</span><span class="o">.</span><span class="n">match</span><span class="p">(</span>
+                <span class="n">resource</span> <span class="o">=</span> <span class="n">resources</span><span class="p">,</span>
+                <span class="n">data_model</span> <span class="o">=</span> <span class="n">data_model</span><span class="p">,</span>
+                <span class="n">interaction_type</span> <span class="o">=</span> <span class="n">interaction_type</span><span class="p">,</span>
+                <span class="n">via</span> <span class="o">=</span> <span class="n">via</span><span class="p">,</span>
+                <span class="n">references</span> <span class="o">=</span> <span class="n">references</span><span class="p">,</span>
+                <span class="n">datasets</span> <span class="o">=</span> <span class="n">datasets</span><span class="p">,</span>
+            <span class="p">):</span>
+
+                <span class="k">yield</span> <span class="n">evs</span></div>
+
+
+
+<div class="viewcode-block" id="Interaction.iter_evidences">
+<a class="viewcode-back" href="../../../api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.iter_evidences">[docs]</a>
+    <span class="k">def</span> <span class="nf">iter_evidences</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">this_direction</span><span class="p">,</span>
+            <span class="n">direction</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">effect</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+        <span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Selects and yields evidence collections matching the direction and</span>
+<span class="sd">        effect criteria.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="c1"># evidence keys</span>
+        <span class="k">for</span> <span class="n">evs_key</span> <span class="ow">in</span> <span class="p">(</span><span class="s1">&#39;undirected&#39;</span><span class="p">,</span> <span class="n">this_direction</span><span class="p">):</span>
+
+            <span class="c1"># evidence dicts</span>
+            <span class="k">for</span> <span class="n">this_effect</span> <span class="ow">in</span> <span class="p">(</span><span class="s1">&#39;direction&#39;</span><span class="p">,</span> <span class="s1">&#39;positive&#39;</span><span class="p">,</span> <span class="s1">&#39;negative&#39;</span><span class="p">):</span>
+
+                <span class="k">if</span> <span class="p">(</span>
+                    <span class="c1"># only undirected</span>
+                    <span class="p">(</span>
+                        <span class="n">direction</span> <span class="o">==</span> <span class="kc">False</span> <span class="ow">and</span>
+                        <span class="n">evs_key</span> <span class="o">==</span> <span class="s1">&#39;undirected&#39;</span> <span class="ow">and</span>
+                        <span class="n">this_effect</span> <span class="o">==</span> <span class="s1">&#39;direction&#39;</span>
+                    <span class="p">)</span> <span class="ow">or</span>
+                    <span class="c1"># undirected</span>
+                    <span class="p">(</span>
+                        <span class="n">direction</span> <span class="ow">is</span> <span class="kc">None</span> <span class="ow">and</span>
+                        <span class="ow">not</span> <span class="n">effect</span> <span class="ow">and</span>
+                        <span class="n">this_effect</span> <span class="o">==</span> <span class="s1">&#39;direction&#39;</span>
+                    <span class="p">)</span> <span class="ow">or</span>
+                    <span class="c1"># directed</span>
+                    <span class="p">(</span>
+                        <span class="n">direction</span> <span class="o">!=</span> <span class="kc">False</span> <span class="ow">and</span>
+                        <span class="n">evs_key</span> <span class="o">!=</span> <span class="s1">&#39;undirected&#39;</span> <span class="ow">and</span>
+                        <span class="n">this_effect</span> <span class="o">==</span> <span class="s1">&#39;direction&#39;</span> <span class="ow">and</span>
+                        <span class="ow">not</span> <span class="n">effect</span> <span class="ow">and</span> <span class="p">(</span>
+                            <span class="c1"># any direction</span>
+                            <span class="n">direction</span> <span class="o">==</span> <span class="kc">True</span> <span class="ow">or</span>
+                            <span class="c1"># specific direction</span>
+                            <span class="n">direction</span> <span class="o">==</span> <span class="n">this_direction</span>
+                        <span class="p">)</span>
+                    <span class="p">)</span> <span class="ow">or</span>
+                    <span class="c1"># with effect</span>
+                    <span class="p">(</span>
+                        <span class="n">direction</span> <span class="o">!=</span> <span class="kc">False</span> <span class="ow">and</span>
+                        <span class="n">evs_key</span> <span class="o">!=</span> <span class="s1">&#39;undirected&#39;</span> <span class="ow">and</span>
+                        <span class="n">this_effect</span> <span class="o">!=</span> <span class="s1">&#39;direction&#39;</span> <span class="ow">and</span> <span class="p">(</span>
+                            <span class="c1"># any effect</span>
+                            <span class="n">effect</span> <span class="o">==</span> <span class="kc">True</span> <span class="ow">or</span>
+                            <span class="c1"># specific effect</span>
+                            <span class="n">effect</span> <span class="o">==</span> <span class="n">this_effect</span>
+                        <span class="p">)</span>
+                    <span class="p">)</span>
+                <span class="p">):</span>
+
+                    <span class="c1"># getting the evidence dict and the key from it</span>
+                    <span class="k">yield</span> <span class="nb">getattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">this_effect</span><span class="p">)[</span><span class="n">evs_key</span><span class="p">]</span></div>
+
+
+
+<div class="viewcode-block" id="Interaction.get_interactions_0">
+<a class="viewcode-back" href="../../../api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.get_interactions_0">[docs]</a>
+    <span class="k">def</span> <span class="nf">get_interactions_0</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Returns unique interacting pairs without being aware of the direction.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">kwargs</span><span class="p">[</span><span class="s1">&#39;direction&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="kc">None</span>
+        <span class="n">kwargs</span><span class="p">[</span><span class="s1">&#39;effect&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="kc">None</span>
+
+        <span class="n">result</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">get_interactions</span><span class="p">(</span><span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
+
+        <span class="k">return</span> <span class="n">result</span><span class="p">[:</span><span class="mi">1</span><span class="p">]</span> <span class="k">if</span> <span class="n">result</span> <span class="k">else</span> <span class="p">()</span></div>
+
+
+
+<div class="viewcode-block" id="Interaction.get_interactions_directed">
+<a class="viewcode-back" href="../../../api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.get_interactions_directed">[docs]</a>
+    <span class="k">def</span> <span class="nf">get_interactions_directed</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Args</span>
+<span class="sd">            kwargs:</span>
+<span class="sd">                See the docs of method ``get_interactions``.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">if</span> <span class="s1">&#39;direction&#39;</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">kwargs</span> <span class="ow">or</span> <span class="n">kwargs</span><span class="p">[</span><span class="s1">&#39;direction&#39;</span><span class="p">]</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
+
+            <span class="n">kwargs</span><span class="p">[</span><span class="s1">&#39;direction&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="kc">True</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">get_interactions</span><span class="p">(</span><span class="o">**</span><span class="n">kwargs</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="Interaction.get_interactions_undirected">
+<a class="viewcode-back" href="../../../api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.get_interactions_undirected">[docs]</a>
+    <span class="k">def</span> <span class="nf">get_interactions_undirected</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Only the undirected interactions will be considered, if any resource</span>
+<span class="sd">        annotates this interaction as undirected both directions will be</span>
+<span class="sd">        returned, no matter if certain resources provide direction. However</span>
+<span class="sd">        the ``count_interactions_undirected`` method will return `1` in this</span>
+<span class="sd">        case.</span>
+
+<span class="sd">        Args</span>
+<span class="sd">            kwargs:</span>
+<span class="sd">                See the docs of method ``get_interactions``.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">kwargs</span><span class="p">[</span><span class="s1">&#39;direction&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="kc">False</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">get_interactions</span><span class="p">(</span><span class="o">**</span><span class="n">kwargs</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="Interaction.get_interactions_undirected_0">
+<a class="viewcode-back" href="../../../api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.get_interactions_undirected_0">[docs]</a>
+    <span class="k">def</span> <span class="nf">get_interactions_undirected_0</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Only the undirected interactions will be considered, if any resource</span>
+<span class="sd">        annotates this interaction as undirected the interacting pair as</span>
+<span class="sd">        a sorted tuple will be returned inside a one element tuple.</span>
+
+<span class="sd">        Args</span>
+<span class="sd">            kwargs:</span>
+<span class="sd">                See the docs of method ``get_interactions``.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">undir</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">get_interactions_undirected</span><span class="p">(</span><span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
+
+        <span class="k">return</span> <span class="n">undir</span><span class="p">[:</span><span class="mi">1</span><span class="p">]</span> <span class="k">if</span> <span class="n">undir</span> <span class="k">else</span> <span class="p">()</span></div>
+
+
+
+<div class="viewcode-block" id="Interaction.get_interactions_non_directed">
+<a class="viewcode-back" href="../../../api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.get_interactions_non_directed">[docs]</a>
+    <span class="k">def</span> <span class="nf">get_interactions_non_directed</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Only the undirected interactions will be considered, if any resource</span>
+<span class="sd">        annotates this interaction as undirected both directions will be</span>
+<span class="sd">        returned, but only if no resource provide direction. However</span>
+<span class="sd">        the ``count_interactions_non_directed`` method will return `1` in</span>
+<span class="sd">        this case.</span>
+
+<span class="sd">        Args</span>
+<span class="sd">            kwargs:</span>
+<span class="sd">                See the docs of method ``get_interactions``.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">kwargs</span><span class="p">[</span><span class="s1">&#39;direction&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="kc">True</span>
+
+        <span class="k">return</span> <span class="p">(</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">get_interactions_undirected</span><span class="p">(</span><span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
+                <span class="k">if</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">get_interactions</span><span class="p">(</span><span class="o">**</span><span class="n">kwargs</span><span class="p">)</span> <span class="k">else</span>
+            <span class="p">()</span>
+        <span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="Interaction.get_interactions_non_directed_0">
+<a class="viewcode-back" href="../../../api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.get_interactions_non_directed_0">[docs]</a>
+    <span class="k">def</span> <span class="nf">get_interactions_non_directed_0</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Only the undirected interactions will be considered, if any resource</span>
+<span class="sd">        annotates this interaction as undirected and none as directed, the</span>
+<span class="sd">        interacting pair as a sorted tuple will be returned inside a one</span>
+<span class="sd">        element tuple.</span>
+
+<span class="sd">        Args</span>
+<span class="sd">            kwargs:</span>
+<span class="sd">                See the docs of method ``get_interactions``.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">nondir</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">get_interactions_non_directed</span><span class="p">(</span><span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
+
+        <span class="k">return</span> <span class="n">nondir</span><span class="p">[:</span><span class="mi">1</span><span class="p">]</span> <span class="k">if</span> <span class="n">nondir</span> <span class="k">else</span> <span class="p">()</span></div>
+
+
+
+<div class="viewcode-block" id="Interaction.get_interactions_signed">
+<a class="viewcode-back" href="../../../api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.get_interactions_signed">[docs]</a>
+    <span class="k">def</span> <span class="nf">get_interactions_signed</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Args</span>
+<span class="sd">            kwargs:</span>
+<span class="sd">                See the docs of method ``get_interactions``.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">if</span> <span class="s1">&#39;effect&#39;</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">kwargs</span> <span class="ow">or</span> <span class="n">kwargs</span><span class="p">[</span><span class="s1">&#39;effect&#39;</span><span class="p">]</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
+
+            <span class="n">kwargs</span><span class="p">[</span><span class="s1">&#39;effect&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="kc">True</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">get_interactions</span><span class="p">(</span><span class="o">**</span><span class="n">kwargs</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="Interaction.get_interactions_positive">
+<a class="viewcode-back" href="../../../api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.get_interactions_positive">[docs]</a>
+    <span class="k">def</span> <span class="nf">get_interactions_positive</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Args</span>
+<span class="sd">            kwargs:</span>
+<span class="sd">                See the docs of method ``get_interactions``.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">kwargs</span><span class="p">[</span><span class="s1">&#39;effect&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="s1">&#39;positive&#39;</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">get_interactions</span><span class="p">(</span><span class="o">**</span><span class="n">kwargs</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="Interaction.get_interactions_negative">
+<a class="viewcode-back" href="../../../api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.get_interactions_negative">[docs]</a>
+    <span class="k">def</span> <span class="nf">get_interactions_negative</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Args</span>
+<span class="sd">            kwargs:</span>
+<span class="sd">                See the docs of method ``get_interactions``.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">kwargs</span><span class="p">[</span><span class="s1">&#39;effect&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="s1">&#39;negative&#39;</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">get_interactions</span><span class="p">(</span><span class="o">**</span><span class="n">kwargs</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="Interaction.get_interactions_mutual">
+<a class="viewcode-back" href="../../../api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.get_interactions_mutual">[docs]</a>
+    <span class="k">def</span> <span class="nf">get_interactions_mutual</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Note: undirected interactions does not count as mutual but only</span>
+<span class="sd">        interactions with explicit direction information for both directions.</span>
+
+<span class="sd">        Args</span>
+<span class="sd">            kwargs:</span>
+<span class="sd">                See the docs of method ``get_interactions``.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">if</span> <span class="s1">&#39;direction&#39;</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">kwargs</span> <span class="ow">or</span> <span class="n">kwargs</span><span class="p">[</span><span class="s1">&#39;direction&#39;</span><span class="p">]</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
+
+            <span class="n">kwargs</span><span class="p">[</span><span class="s1">&#39;direction&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="kc">True</span>
+
+        <span class="n">interactions</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">get_interactions</span><span class="p">(</span><span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
+
+        <span class="k">return</span> <span class="n">interactions</span> <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">interactions</span><span class="p">)</span> <span class="o">==</span> <span class="mi">2</span> <span class="k">else</span> <span class="p">()</span></div>
+
+
+
+<div class="viewcode-block" id="Interaction.is_mutual">
+<a class="viewcode-back" href="../../../api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.is_mutual">[docs]</a>
+    <span class="k">def</span> <span class="nf">is_mutual</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Note: undirected interactions does not count as mutual but only</span>
+<span class="sd">        interactions with explicit direction information for both directions.</span>
+
+<span class="sd">        Args</span>
+<span class="sd">            kwargs:</span>
+<span class="sd">                See the docs of method ``get_interactions``.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">return</span> <span class="nb">bool</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">get_interactions_mutual</span><span class="p">(</span><span class="o">**</span><span class="n">kwargs</span><span class="p">))</span></div>
+
+
+
+<div class="viewcode-block" id="Interaction.count_interactions_mutual">
+<a class="viewcode-back" href="../../../api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.count_interactions_mutual">[docs]</a>
+    <span class="k">def</span> <span class="nf">count_interactions_mutual</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Note: undirected interactions does not count as mutual but only</span>
+<span class="sd">        interactions with explicit direction information for both directions.</span>
+
+<span class="sd">        Args</span>
+<span class="sd">            kwargs:</span>
+<span class="sd">                See the docs of method ``get_interactions``.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">return</span> <span class="nb">int</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">is_mutual</span><span class="p">(</span><span class="o">**</span><span class="n">kwargs</span><span class="p">))</span></div>
+
+
+
+<div class="viewcode-block" id="Interaction.count_interactions_undirected">
+<a class="viewcode-back" href="../../../api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.count_interactions_undirected">[docs]</a>
+    <span class="k">def</span> <span class="nf">count_interactions_undirected</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Returns `True` if any resource annotates this interaction without</span>
+<span class="sd">        direction.</span>
+
+<span class="sd">        Args</span>
+<span class="sd">            kwargs:</span>
+<span class="sd">                See the docs of method ``get_interactions``.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">return</span> <span class="nb">bool</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">get_interactions_undirected</span><span class="p">(</span><span class="o">**</span><span class="n">kwargs</span><span class="p">))</span></div>
+
+
+
+<div class="viewcode-block" id="Interaction.count_interactions_non_directed">
+<a class="viewcode-back" href="../../../api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.count_interactions_non_directed">[docs]</a>
+    <span class="k">def</span> <span class="nf">count_interactions_non_directed</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Returns `True` if any resource annotates this interaction without</span>
+<span class="sd">        and no resource with direction.</span>
+
+<span class="sd">        Args</span>
+<span class="sd">            kwargs:</span>
+<span class="sd">                See the docs of method ``get_interactions``.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">return</span> <span class="nb">bool</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">get_interactions_non_directed</span><span class="p">(</span><span class="o">**</span><span class="n">kwargs</span><span class="p">))</span></div>
+
+
+
+<div class="viewcode-block" id="Interaction.get_degrees">
+<a class="viewcode-back" href="../../../api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.get_degrees">[docs]</a>
+    <span class="k">def</span> <span class="nf">get_degrees</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">mode</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
+            <span class="n">direction</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">effect</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">resources</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">data_model</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">interaction_type</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">via</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">references</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+        <span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Returns a *set* of nodes with the connections matching the direction,</span>
+<span class="sd">        effect and evidence criteria. E.g. if the query concerns the incoming</span>
+<span class="sd">        degrees with positive effect and the matching evidences show A</span>
+<span class="sd">        activates B, but not the other way around, only &quot;B&quot; will be returned.</span>
+
+<span class="sd">        Args</span>
+<span class="sd">            mode:</span>
+<span class="sd">                The type of degrees to be considered. Three possible values are</span>
+<span class="sd">                ``&#39;IN&#39;``, `&#39;OUT&#39;`` and ``&#39;ALL&#39;`` for incoming, outgoing and all</span>
+<span class="sd">                connections, respectively. If the ``direction`` is ``False``</span>
+<span class="sd">                the only possible mode is ``ALL``. If the ``direction`` is</span>
+<span class="sd">                ``None`` and also directed evidence(s) match the criteria these</span>
+<span class="sd">                will overwrite the undirected evidences and only the directed</span>
+<span class="sd">                result will be returned.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">kwargs</span> <span class="o">=</span> <span class="nb">locals</span><span class="p">()</span>
+        <span class="n">_</span> <span class="o">=</span> <span class="n">kwargs</span><span class="o">.</span><span class="n">pop</span><span class="p">(</span><span class="s1">&#39;self&#39;</span><span class="p">)</span>
+        <span class="n">mode</span> <span class="o">=</span> <span class="n">kwargs</span><span class="o">.</span><span class="n">pop</span><span class="p">(</span><span class="s1">&#39;mode&#39;</span><span class="p">)</span>
+
+        <span class="n">idx</span> <span class="o">=</span> <span class="p">{</span>
+            <span class="s1">&#39;ALL&#39;</span><span class="p">:</span> <span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="mi">2</span><span class="p">),</span>
+            <span class="s1">&#39;OUT&#39;</span><span class="p">:</span> <span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="mi">1</span><span class="p">),</span>
+            <span class="s1">&#39;IN&#39;</span><span class="p">:</span>  <span class="p">(</span><span class="mi">1</span><span class="p">,</span> <span class="mi">2</span><span class="p">),</span>
+        <span class="p">}</span>
+
+        <span class="k">if</span> <span class="n">direction</span> <span class="o">==</span> <span class="kc">False</span><span class="p">:</span>
+
+            <span class="n">mode</span> <span class="o">=</span> <span class="s1">&#39;ALL&#39;</span>
+
+        <span class="k">if</span> <span class="n">direction</span> <span class="ow">is</span> <span class="kc">None</span> <span class="ow">and</span> <span class="ow">not</span> <span class="n">effect</span><span class="p">:</span>
+
+            <span class="n">_</span> <span class="o">=</span> <span class="n">kwargs</span><span class="o">.</span><span class="n">pop</span><span class="p">(</span><span class="s1">&#39;direction&#39;</span><span class="p">)</span>
+
+            <span class="k">return</span> <span class="p">(</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">get_degrees</span><span class="p">(</span><span class="n">mode</span> <span class="o">=</span> <span class="n">mode</span><span class="p">,</span> <span class="n">direction</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">)</span> <span class="ow">or</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">get_degrees</span><span class="p">(</span><span class="n">mode</span> <span class="o">=</span> <span class="n">mode</span><span class="p">,</span> <span class="n">direction</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
+            <span class="p">)</span>
+
+        <span class="n">result</span> <span class="o">=</span> <span class="nb">set</span><span class="p">()</span>
+
+        <span class="n">node_pairs</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">get_interactions</span><span class="p">(</span><span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
+
+        <span class="k">for</span> <span class="n">pair</span> <span class="ow">in</span> <span class="n">node_pairs</span><span class="p">:</span>
+
+            <span class="n">result</span><span class="o">.</span><span class="n">update</span><span class="p">(</span>
+                <span class="n">pair</span><span class="p">[</span>
+                    <span class="n">idx</span><span class="p">[</span><span class="n">mode</span><span class="p">][</span><span class="mi">0</span><span class="p">]:</span>
+                    <span class="n">idx</span><span class="p">[</span><span class="n">mode</span><span class="p">][</span><span class="mi">1</span><span class="p">]</span>
+                <span class="p">]</span>
+            <span class="p">)</span>
+
+        <span class="k">return</span> <span class="n">result</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">get_curation_effort</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="nb">tuple</span><span class="p">(</span>
+            <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">a</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">b</span><span class="p">,</span> <span class="n">res</span><span class="p">,</span> <span class="n">ref</span><span class="p">)</span>
+            <span class="k">for</span> <span class="n">res</span><span class="p">,</span> <span class="n">refs</span> <span class="ow">in</span>
+            <span class="n">iteritems</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">references_by_resource</span><span class="p">(</span><span class="o">**</span><span class="n">kwargs</span><span class="p">))</span>
+            <span class="k">for</span> <span class="n">ref</span> <span class="ow">in</span> <span class="n">refs</span>
+        <span class="p">)</span>
+
+
+    <span class="nd">@staticmethod</span>
+    <span class="k">def</span> <span class="nf">_get</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">method</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+
+        <span class="n">via</span> <span class="o">=</span> <span class="n">kwargs</span><span class="p">[</span><span class="s1">&#39;via&#39;</span><span class="p">]</span> <span class="k">if</span> <span class="s1">&#39;via&#39;</span> <span class="ow">in</span> <span class="n">kwargs</span> <span class="k">else</span> <span class="kc">False</span>
+
+        <span class="k">return</span> <span class="nb">getattr</span><span class="p">(</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">get_evidences</span><span class="p">(</span>
+                <span class="o">**</span><span class="n">kwargs</span>
+            <span class="p">),</span>
+            <span class="s1">&#39;get_</span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="n">method</span><span class="p">,</span>
+        <span class="p">)(</span><span class="n">via</span> <span class="o">=</span> <span class="n">via</span><span class="p">)</span>
+
+
+    <span class="nd">@staticmethod</span>
+    <span class="k">def</span> <span class="nf">_count</span><span class="p">(</span><span class="n">method</span><span class="p">):</span>
+
+        <span class="nd">@functools</span><span class="o">.</span><span class="n">wraps</span><span class="p">(</span><span class="n">method</span><span class="p">)</span>
+        <span class="k">def</span> <span class="nf">count_method</span><span class="p">(</span><span class="o">*</span><span class="n">args</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+
+            <span class="k">return</span> <span class="nb">len</span><span class="p">(</span><span class="n">method</span><span class="p">(</span><span class="o">*</span><span class="n">args</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">))</span>
+
+        <span class="k">return</span> <span class="n">count_method</span>
+
+
+    <span class="nd">@staticmethod</span>
+    <span class="k">def</span> <span class="nf">_by</span><span class="p">(</span><span class="n">method</span><span class="p">,</span> <span class="n">by</span> <span class="o">=</span> <span class="s1">&#39;resources&#39;</span><span class="p">):</span>
+
+        <span class="n">by</span> <span class="o">=</span> <span class="p">(</span><span class="n">by</span><span class="p">,)</span> <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">by</span><span class="p">,</span> <span class="nb">str</span><span class="p">)</span> <span class="k">else</span> <span class="n">by</span>
+
+        <span class="nd">@functools</span><span class="o">.</span><span class="n">wraps</span><span class="p">(</span><span class="n">method</span><span class="p">)</span>
+        <span class="k">def</span> <span class="nf">by_method</span><span class="p">(</span><span class="o">*</span><span class="n">args</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+
+            <span class="bp">self</span> <span class="o">=</span> <span class="n">args</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span>
+            <span class="n">name_keys</span> <span class="o">=</span> <span class="n">kwargs</span><span class="o">.</span><span class="n">pop</span><span class="p">(</span><span class="s1">&#39;name_keys&#39;</span><span class="p">,</span> <span class="kc">True</span><span class="p">)</span>
+
+            <span class="k">for</span> <span class="n">_by</span> <span class="ow">in</span> <span class="n">by</span><span class="p">:</span>
+
+                <span class="n">_</span> <span class="o">=</span> <span class="n">kwargs</span><span class="o">.</span><span class="n">pop</span><span class="p">(</span><span class="n">_by</span><span class="p">,</span> <span class="kc">None</span><span class="p">)</span>
+
+            <span class="n">levels_methods</span> <span class="o">=</span> <span class="p">(</span>
+                <span class="s1">&#39;get_</span><span class="si">%s%s</span><span class="s1">s&#39;</span> <span class="o">%</span> <span class="p">(</span>
+                    <span class="n">_by</span><span class="p">[:</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span> <span class="k">if</span> <span class="n">_by</span> <span class="ow">in</span> <span class="p">{</span><span class="s1">&#39;resources&#39;</span><span class="p">,</span> <span class="s1">&#39;references&#39;</span><span class="p">}</span> <span class="k">else</span> <span class="n">_by</span><span class="p">,</span>
+                    <span class="s1">&#39;_name&#39;</span> <span class="k">if</span> <span class="n">_by</span> <span class="o">==</span> <span class="s1">&#39;resources&#39;</span> <span class="ow">and</span> <span class="n">name_keys</span> <span class="k">else</span> <span class="s1">&#39;&#39;</span>
+                <span class="p">)</span>
+                <span class="k">for</span> <span class="n">_by</span> <span class="ow">in</span> <span class="n">by</span>
+            <span class="p">)</span>
+
+            <span class="n">levels</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="n">itertools</span><span class="o">.</span><span class="n">product</span><span class="p">(</span><span class="o">*</span><span class="p">(</span>
+                <span class="nb">getattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">levels_method</span><span class="p">)(</span><span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
+                <span class="k">for</span> <span class="n">levels_method</span> <span class="ow">in</span> <span class="n">levels_methods</span>
+            <span class="p">)))</span>
+
+            <span class="n">result</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">(</span>
+                <span class="p">(</span>
+                    <span class="n">_levels</span> <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">_levels</span><span class="p">)</span> <span class="o">&gt;</span> <span class="mi">1</span> <span class="k">else</span> <span class="n">_levels</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span>
+                    <span class="n">method</span><span class="p">(</span>
+                        <span class="o">*</span><span class="n">args</span><span class="p">,</span>
+                        <span class="o">**</span><span class="nb">dict</span><span class="p">(</span><span class="nb">zip</span><span class="p">(</span><span class="n">by</span><span class="p">,</span> <span class="n">_levels</span><span class="p">)),</span>
+                        <span class="o">**</span><span class="n">kwargs</span>
+                    <span class="p">)</span>
+                <span class="p">)</span>
+                <span class="k">for</span> <span class="n">_levels</span> <span class="ow">in</span> <span class="n">levels</span>
+            <span class="p">)</span>
+
+            <span class="k">return</span> <span class="nb">dict</span><span class="p">((</span><span class="n">k</span><span class="p">,</span> <span class="n">v</span><span class="p">)</span> <span class="k">for</span> <span class="n">k</span><span class="p">,</span> <span class="n">v</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="n">result</span><span class="p">)</span> <span class="k">if</span> <span class="n">v</span><span class="p">)</span>
+
+        <span class="k">return</span> <span class="n">by_method</span>
+
+
+    <span class="nd">@classmethod</span>
+    <span class="k">def</span> <span class="nf">_by_resource</span><span class="p">(</span><span class="bp">cls</span><span class="p">,</span> <span class="n">method</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="bp">cls</span><span class="o">.</span><span class="n">_by</span><span class="p">(</span><span class="n">method</span><span class="p">,</span> <span class="n">by</span> <span class="o">=</span> <span class="s1">&#39;resources&#39;</span><span class="p">)</span>
+
+
+    <span class="nd">@classmethod</span>
+    <span class="k">def</span> <span class="nf">_by_data_model</span><span class="p">(</span><span class="bp">cls</span><span class="p">,</span> <span class="n">method</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="bp">cls</span><span class="o">.</span><span class="n">_by</span><span class="p">(</span><span class="n">method</span><span class="p">,</span> <span class="n">by</span> <span class="o">=</span> <span class="s1">&#39;data_model&#39;</span><span class="p">)</span>
+
+
+    <span class="nd">@classmethod</span>
+    <span class="k">def</span> <span class="nf">_by_interaction_type_and_data_model</span><span class="p">(</span><span class="bp">cls</span><span class="p">,</span> <span class="n">method</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="bp">cls</span><span class="o">.</span><span class="n">_by</span><span class="p">(</span><span class="n">method</span><span class="p">,</span> <span class="n">by</span> <span class="o">=</span> <span class="p">(</span><span class="s1">&#39;interaction_type&#39;</span><span class="p">,</span> <span class="s1">&#39;data_model&#39;</span><span class="p">))</span>
+
+
+    <span class="nd">@classmethod</span>
+    <span class="k">def</span> <span class="nf">_by_interaction_type_and_data_model_and_resource</span><span class="p">(</span><span class="bp">cls</span><span class="p">,</span> <span class="n">method</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="bp">cls</span><span class="o">.</span><span class="n">_by</span><span class="p">(</span>
+            <span class="n">method</span><span class="p">,</span>
+            <span class="n">by</span> <span class="o">=</span> <span class="p">(</span><span class="s1">&#39;interaction_type&#39;</span><span class="p">,</span> <span class="s1">&#39;data_model&#39;</span><span class="p">,</span> <span class="s1">&#39;resources&#39;</span><span class="p">),</span>
+        <span class="p">)</span>
+
+
+    <span class="nd">@classmethod</span>
+    <span class="k">def</span> <span class="nf">_by_interaction_type</span><span class="p">(</span><span class="bp">cls</span><span class="p">,</span> <span class="n">method</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="bp">cls</span><span class="o">.</span><span class="n">_by</span><span class="p">(</span><span class="n">method</span><span class="p">,</span> <span class="n">by</span> <span class="o">=</span> <span class="s1">&#39;interaction_type&#39;</span><span class="p">)</span>
+
+
+    <span class="nd">@classmethod</span>
+    <span class="k">def</span> <span class="nf">_by_reference</span><span class="p">(</span><span class="bp">cls</span><span class="p">,</span> <span class="n">method</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="bp">cls</span><span class="o">.</span><span class="n">_by</span><span class="p">(</span><span class="n">method</span><span class="p">,</span> <span class="n">by</span> <span class="o">=</span> <span class="s1">&#39;references&#39;</span><span class="p">)</span>
+
+
+    <span class="nd">@classmethod</span>
+    <span class="k">def</span> <span class="nf">_generate_get_methods</span><span class="p">(</span><span class="bp">cls</span><span class="p">):</span>
+
+        <span class="k">def</span> <span class="nf">_create_get_method</span><span class="p">(</span><span class="n">method</span><span class="p">):</span>
+
+            <span class="nd">@functools</span><span class="o">.</span><span class="n">wraps</span><span class="p">(</span><span class="n">method</span><span class="p">)</span>
+            <span class="k">def</span> <span class="nf">_get_method</span><span class="p">(</span><span class="o">*</span><span class="n">args</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+
+                <span class="k">return</span> <span class="bp">cls</span><span class="o">.</span><span class="n">_get</span><span class="p">(</span><span class="bp">self</span> <span class="o">=</span> <span class="n">args</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">method</span> <span class="o">=</span> <span class="n">method</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
+
+            <span class="k">return</span> <span class="n">_get_method</span>
+
+        <span class="k">for</span> <span class="n">_get</span> <span class="ow">in</span> <span class="bp">cls</span><span class="o">.</span><span class="n">_get_methods_autogen</span><span class="p">:</span>
+
+            <span class="n">method_name</span> <span class="o">=</span> <span class="s1">&#39;get_</span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="n">_get</span>
+
+            <span class="n">signature</span> <span class="o">=</span> <span class="bp">cls</span><span class="o">.</span><span class="n">_update_get_method_signature</span><span class="p">(</span><span class="n">method_name</span><span class="p">)</span>
+
+            <span class="bp">cls</span><span class="o">.</span><span class="n">_add_method</span><span class="p">(</span>
+                <span class="n">method_name</span> <span class="o">=</span> <span class="n">method_name</span><span class="p">,</span>
+                <span class="n">method</span> <span class="o">=</span> <span class="n">_create_get_method</span><span class="p">(</span><span class="n">_get</span><span class="p">),</span>
+                <span class="c1"># this is not always correct, to be fixed later</span>
+                <span class="n">signature</span> <span class="o">=</span> <span class="n">signature</span><span class="p">,</span>
+                <span class="n">doc</span> <span class="o">=</span> <span class="p">(</span>
+                    <span class="s1">&#39;Retrieves </span><span class="si">%s</span><span class="s1"> matching the criteria.&#39;</span> <span class="o">%</span> <span class="p">(</span>
+                        <span class="n">_get</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s1">&#39;_&#39;</span><span class="p">,</span> <span class="s1">&#39; &#39;</span><span class="p">)</span>
+                    <span class="p">)</span>
+                <span class="p">),</span>
+            <span class="p">)</span>
+
+
+    <span class="nd">@classmethod</span>
+    <span class="k">def</span> <span class="nf">_generate_degree_methods</span><span class="p">(</span><span class="bp">cls</span><span class="p">):</span>
+
+        <span class="k">def</span> <span class="nf">_create_degree_method</span><span class="p">(</span><span class="n">mode</span><span class="p">,</span> <span class="n">direction</span><span class="p">,</span> <span class="n">effect</span><span class="p">):</span>
+
+            <span class="n">wrap_args</span> <span class="o">=</span> <span class="n">mode</span><span class="p">,</span> <span class="n">direction</span><span class="p">,</span> <span class="n">effect</span>
+
+            <span class="nd">@functools</span><span class="o">.</span><span class="n">wraps</span><span class="p">(</span><span class="n">wrap_args</span><span class="p">)</span>
+            <span class="k">def</span> <span class="nf">_degree_method</span><span class="p">(</span><span class="o">*</span><span class="n">args</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+
+                <span class="n">mode</span><span class="p">,</span> <span class="n">direction</span><span class="p">,</span> <span class="n">effect</span> <span class="o">=</span> <span class="n">wrap_args</span>
+
+                <span class="n">kwargs</span><span class="p">[</span><span class="s1">&#39;direction&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">direction</span>
+                <span class="n">kwargs</span><span class="p">[</span><span class="s1">&#39;effect&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">effect</span>
+
+                <span class="k">return</span> <span class="bp">cls</span><span class="o">.</span><span class="n">get_degrees</span><span class="p">(</span><span class="bp">self</span> <span class="o">=</span> <span class="n">args</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">mode</span> <span class="o">=</span> <span class="n">mode</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
+
+            <span class="k">return</span> <span class="n">_degree_method</span>
+
+        <span class="k">for</span> <span class="n">mode</span><span class="p">,</span> <span class="p">(</span><span class="n">dir_label</span><span class="p">,</span> <span class="n">dir_args</span><span class="p">)</span> <span class="ow">in</span> <span class="n">itertools</span><span class="o">.</span><span class="n">product</span><span class="p">(</span>
+            <span class="bp">cls</span><span class="o">.</span><span class="n">_degree_modes</span><span class="p">,</span>
+            <span class="n">iteritems</span><span class="p">(</span><span class="bp">cls</span><span class="o">.</span><span class="n">_degree_directions</span><span class="p">)</span>
+        <span class="p">):</span>
+
+            <span class="k">if</span> <span class="n">dir_label</span> <span class="ow">in</span> <span class="p">{</span><span class="s1">&#39;undirected&#39;</span><span class="p">,</span> <span class="s1">&#39;non_directed&#39;</span><span class="p">}</span> <span class="ow">and</span> <span class="n">mode</span> <span class="o">!=</span> <span class="s1">&#39;ALL&#39;</span><span class="p">:</span>
+
+                <span class="k">continue</span>
+
+            <span class="n">method_name</span> <span class="o">=</span> <span class="s1">&#39;degrees_</span><span class="si">%s%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="p">(</span>
+                <span class="n">dir_label</span><span class="p">,</span>
+                <span class="s1">&#39;_</span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="n">mode</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span> <span class="k">if</span> <span class="n">mode</span> <span class="o">!=</span> <span class="s1">&#39;ALL&#39;</span> <span class="k">else</span> <span class="s1">&#39;&#39;</span>
+            <span class="p">)</span>
+
+            <span class="bp">cls</span><span class="o">.</span><span class="n">_count_methods</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">method_name</span><span class="p">)</span>
+            <span class="bp">cls</span><span class="o">.</span><span class="n">_get_methods</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">method_name</span><span class="p">)</span>
+
+            <span class="n">method</span> <span class="o">=</span> <span class="n">_create_degree_method</span><span class="p">(</span><span class="n">mode</span><span class="p">,</span> <span class="o">*</span><span class="n">dir_args</span><span class="p">)</span>
+            <span class="n">_method_name</span> <span class="o">=</span> <span class="s1">&#39;get_</span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="n">method_name</span>
+
+            <span class="bp">cls</span><span class="o">.</span><span class="n">_add_method</span><span class="p">(</span>
+                <span class="n">method_name</span> <span class="o">=</span> <span class="n">_method_name</span><span class="p">,</span>
+                <span class="n">method</span> <span class="o">=</span> <span class="n">method</span><span class="p">,</span>
+                <span class="n">signature</span> <span class="o">=</span> <span class="p">[</span><span class="s1">&#39;mode&#39;</span><span class="p">]</span> <span class="o">+</span> <span class="bp">cls</span><span class="o">.</span><span class="n">_get_method_signature</span><span class="p">,</span>
+                <span class="n">doc</span> <span class="o">=</span> <span class="bp">cls</span><span class="o">.</span><span class="n">get_degrees</span><span class="o">.</span><span class="vm">__doc__</span><span class="p">,</span>
+            <span class="p">)</span>
+
+
+    <span class="nd">@classmethod</span>
+    <span class="k">def</span> <span class="nf">_generate_count_methods</span><span class="p">(</span><span class="bp">cls</span><span class="p">):</span>
+
+        <span class="k">for</span> <span class="n">_get</span> <span class="ow">in</span> <span class="bp">cls</span><span class="o">.</span><span class="n">_count_methods</span><span class="p">:</span>
+
+            <span class="n">_get_method</span> <span class="o">=</span> <span class="nb">getattr</span><span class="p">(</span><span class="bp">cls</span><span class="p">,</span> <span class="s1">&#39;get_</span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="n">_get</span><span class="p">)</span>
+
+            <span class="n">method_name</span> <span class="o">=</span> <span class="s1">&#39;count_</span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="n">_get</span>
+
+            <span class="n">signature</span> <span class="o">=</span> <span class="bp">cls</span><span class="o">.</span><span class="n">_update_get_method_signature</span><span class="p">(</span><span class="n">method_name</span><span class="p">)</span>
+
+            <span class="bp">cls</span><span class="o">.</span><span class="n">_add_method</span><span class="p">(</span>
+                <span class="n">method_name</span> <span class="o">=</span> <span class="n">method_name</span><span class="p">,</span>
+                <span class="n">method</span> <span class="o">=</span> <span class="bp">cls</span><span class="o">.</span><span class="n">_count</span><span class="p">(</span><span class="n">_get_method</span><span class="p">),</span>
+                <span class="n">signature</span> <span class="o">=</span> <span class="bp">cls</span><span class="o">.</span><span class="n">_get_method_signature</span><span class="p">,</span>
+                <span class="n">doc</span> <span class="o">=</span> <span class="n">_get_method</span><span class="o">.</span><span class="vm">__doc__</span><span class="p">,</span>
+            <span class="p">)</span>
+
+
+    <span class="nd">@classmethod</span>
+    <span class="k">def</span> <span class="nf">_update_get_method_signature</span><span class="p">(</span><span class="bp">cls</span><span class="p">,</span> <span class="n">method_name</span><span class="p">):</span>
+
+        <span class="n">signature</span> <span class="o">=</span> <span class="bp">cls</span><span class="o">.</span><span class="n">_get_method_signature</span>
+
+        <span class="k">if</span> <span class="s1">&#39;interaction&#39;</span> <span class="ow">in</span> <span class="n">method_name</span><span class="p">:</span>
+
+            <span class="n">signature</span> <span class="o">=</span> <span class="n">signature</span> <span class="o">+</span> <span class="p">[</span>
+                <span class="p">(</span><span class="s1">&#39;entity_type&#39;</span><span class="p">,</span> <span class="kc">None</span><span class="p">),</span>
+                <span class="p">(</span><span class="s1">&#39;source_entity_type&#39;</span><span class="p">,</span> <span class="kc">None</span><span class="p">),</span>
+                <span class="p">(</span><span class="s1">&#39;target_entity_type&#39;</span><span class="p">,</span> <span class="kc">None</span><span class="p">),</span>
+            <span class="p">]</span>
+
+        <span class="k">return</span> <span class="n">signature</span>
+
+
+    <span class="nd">@classmethod</span>
+    <span class="k">def</span> <span class="nf">_generate_by_methods</span><span class="p">(</span><span class="bp">cls</span><span class="p">):</span>
+
+        <span class="k">for</span> <span class="n">_get</span><span class="p">,</span> <span class="n">_by</span> <span class="ow">in</span> <span class="n">itertools</span><span class="o">.</span><span class="n">product</span><span class="p">(</span>
+            <span class="bp">cls</span><span class="o">.</span><span class="n">_get_methods</span><span class="p">,</span>
+            <span class="bp">cls</span><span class="o">.</span><span class="n">_by_methods</span><span class="p">,</span>
+        <span class="p">):</span>
+
+            <span class="n">_get_method</span> <span class="o">=</span> <span class="nb">getattr</span><span class="p">(</span><span class="bp">cls</span><span class="p">,</span> <span class="s1">&#39;get_</span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="n">_get</span><span class="p">)</span>
+            <span class="n">method_name</span> <span class="o">=</span> <span class="s1">&#39;</span><span class="si">%s</span><span class="s1">_by_</span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="p">(</span><span class="n">_get</span><span class="p">,</span> <span class="n">_by</span><span class="p">)</span>
+            <span class="n">method</span> <span class="o">=</span> <span class="nb">getattr</span><span class="p">(</span><span class="bp">cls</span><span class="p">,</span> <span class="s1">&#39;_by_</span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="n">_by</span><span class="p">)(</span><span class="n">_get_method</span><span class="p">)</span>
+
+            <span class="bp">cls</span><span class="o">.</span><span class="n">_add_method</span><span class="p">(</span>
+                <span class="n">method_name</span> <span class="o">=</span> <span class="n">method_name</span><span class="p">,</span>
+                <span class="n">method</span> <span class="o">=</span> <span class="n">method</span><span class="p">,</span>
+                <span class="n">signature</span> <span class="o">=</span> <span class="bp">cls</span><span class="o">.</span><span class="n">_get_method_signature</span><span class="p">,</span>
+                <span class="n">doc</span> <span class="o">=</span> <span class="n">_get_method</span><span class="o">.</span><span class="vm">__doc__</span><span class="p">,</span>
+            <span class="p">)</span>
+
+
+    <span class="nd">@classmethod</span>
+    <span class="k">def</span> <span class="nf">_add_method</span><span class="p">(</span><span class="bp">cls</span><span class="p">,</span> <span class="n">method_name</span><span class="p">,</span> <span class="n">method</span><span class="p">,</span> <span class="n">signature</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span> <span class="n">doc</span> <span class="o">=</span> <span class="kc">None</span><span class="p">):</span>
+
+        <span class="n">common</span><span class="o">.</span><span class="n">add_method</span><span class="p">(</span>
+            <span class="bp">cls</span><span class="p">,</span>
+            <span class="n">method_name</span><span class="p">,</span>
+            <span class="n">method</span><span class="p">,</span>
+            <span class="n">signature</span> <span class="o">=</span> <span class="n">signature</span><span class="p">,</span>
+            <span class="n">doc</span> <span class="o">=</span> <span class="n">doc</span><span class="p">,</span>
+        <span class="p">)</span>
+
+
+<div class="viewcode-block" id="Interaction.generate_df_records">
+<a class="viewcode-back" href="../../../api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.generate_df_records">[docs]</a>
+    <span class="k">def</span> <span class="nf">generate_df_records</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">by_source</span><span class="p">:</span> <span class="nb">bool</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+            <span class="n">with_references</span><span class="p">:</span> <span class="nb">bool</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+        <span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Yields interaction records. It is a generator because one edge can</span>
+<span class="sd">        be represented by one or more records depending on the signs and</span>
+<span class="sd">        directions and other parameters</span>
+
+<span class="sd">        Args</span>
+<span class="sd">            by_source:</span>
+<span class="sd">                Yield separate records by resources. This way the node pairs</span>
+<span class="sd">                will be redundant and you need to group later if you want</span>
+<span class="sd">                unique interacting pairs. By default is ``False`` because for</span>
+<span class="sd">                most applications unique interactions are preferred.</span>
+<span class="sd">                If ``False`` the *refrences* field will still be present</span>
+<span class="sd">                but with ``None`` values.</span>
+<span class="sd">            with_references:</span>
+<span class="sd">                Include the literature references. By default is ``False``</span>
+<span class="sd">                because you rarely need these and they increase the data size</span>
+<span class="sd">                significantly.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">def</span> <span class="nf">source_add_via</span><span class="p">(</span><span class="n">source</span><span class="p">,</span> <span class="n">via</span><span class="p">):</span>
+
+            <span class="k">return</span> <span class="s1">&#39;</span><span class="si">%s%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="p">(</span><span class="n">source</span><span class="p">,</span> <span class="s1">&#39;_</span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="n">via</span> <span class="k">if</span> <span class="n">via</span> <span class="k">else</span> <span class="s1">&#39;&#39;</span><span class="p">)</span>
+
+
+        <span class="k">def</span> <span class="nf">iter_sources</span><span class="p">(</span><span class="n">evs</span><span class="p">):</span>
+
+            <span class="n">sources</span> <span class="o">=</span> <span class="n">evs</span><span class="o">.</span><span class="n">get_resource_names_via</span><span class="p">()</span>
+
+            <span class="k">if</span> <span class="n">by_source</span><span class="p">:</span>
+
+                <span class="k">for</span> <span class="n">source</span><span class="p">,</span> <span class="n">via</span> <span class="ow">in</span> <span class="n">sources</span><span class="p">:</span>
+
+                    <span class="n">refs</span> <span class="o">=</span> <span class="p">(</span>
+                        <span class="p">{</span>
+                            <span class="n">ref</span><span class="o">.</span><span class="n">pmid</span>
+                            <span class="k">for</span> <span class="n">ref</span> <span class="ow">in</span>
+                            <span class="bp">self</span><span class="o">.</span><span class="n">get_references</span><span class="p">(</span>
+                                <span class="n">resources</span> <span class="o">=</span> <span class="n">source</span><span class="p">,</span>
+                                <span class="n">interaction_type</span> <span class="o">=</span> <span class="n">interaction_type</span><span class="p">,</span>
+                                <span class="n">via</span> <span class="o">=</span> <span class="n">via</span><span class="p">,</span>
+                            <span class="p">)</span>
+                        <span class="p">}</span>
+                            <span class="k">if</span> <span class="n">with_references</span> <span class="k">else</span>
+                        <span class="kc">None</span>
+                    <span class="p">)</span>
+
+                    <span class="n">_source</span> <span class="o">=</span> <span class="n">source_add_via</span><span class="p">(</span><span class="n">source</span><span class="p">,</span> <span class="n">via</span><span class="p">)</span>
+
+                    <span class="k">yield</span> <span class="n">_source</span><span class="p">,</span> <span class="n">refs</span>
+
+            <span class="k">else</span><span class="p">:</span>
+
+                <span class="n">_sources</span> <span class="o">=</span> <span class="p">{</span>
+                    <span class="n">source_add_via</span><span class="p">(</span><span class="n">source</span><span class="p">,</span> <span class="n">via</span><span class="p">)</span>
+                    <span class="k">for</span> <span class="n">source</span><span class="p">,</span> <span class="n">via</span> <span class="ow">in</span> <span class="n">sources</span>
+                <span class="p">}</span>
+
+                <span class="n">refs</span> <span class="o">=</span> <span class="p">(</span>
+                    <span class="p">{</span>
+                        <span class="n">ref</span><span class="o">.</span><span class="n">pmid</span>
+                        <span class="k">for</span> <span class="n">ref</span> <span class="ow">in</span>
+                        <span class="bp">self</span><span class="o">.</span><span class="n">get_references</span><span class="p">(</span>
+                            <span class="n">resources</span> <span class="o">=</span> <span class="p">{</span><span class="n">s</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="k">for</span> <span class="n">s</span> <span class="ow">in</span> <span class="n">sources</span><span class="p">},</span>
+                            <span class="n">interaction_type</span> <span class="o">=</span> <span class="n">interaction_type</span><span class="p">,</span>
+                        <span class="p">)</span>
+                    <span class="p">}</span>
+                        <span class="k">if</span> <span class="n">with_references</span> <span class="k">else</span>
+                    <span class="kc">None</span>
+                <span class="p">)</span>
+
+                <span class="k">if</span> <span class="n">_sources</span><span class="p">:</span>
+
+                    <span class="k">yield</span> <span class="n">_sources</span><span class="p">,</span> <span class="n">refs</span>
+
+
+        <span class="k">for</span> <span class="n">interaction_type</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">get_interaction_types</span><span class="p">():</span>
+
+            <span class="n">dmodels</span> <span class="o">=</span> <span class="p">(</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">get_data_models</span><span class="p">(</span><span class="n">interaction_type</span> <span class="o">=</span> <span class="n">interaction_type</span><span class="p">)</span>
+            <span class="p">)</span>
+            <span class="n">dmodels</span> <span class="o">=</span> <span class="n">dmodels</span> <span class="k">if</span> <span class="n">by_source</span> <span class="k">else</span> <span class="p">(</span><span class="n">dmodels</span><span class="p">,)</span>
+
+            <span class="k">for</span> <span class="n">data_model</span> <span class="ow">in</span> <span class="n">dmodels</span><span class="p">:</span>
+
+                <span class="n">evs_undirected</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">get_evidences</span><span class="p">(</span>
+                    <span class="n">direction</span> <span class="o">=</span> <span class="s1">&#39;undirected&#39;</span><span class="p">,</span>
+                    <span class="n">interaction_type</span> <span class="o">=</span> <span class="n">interaction_type</span><span class="p">,</span>
+                    <span class="n">data_model</span> <span class="o">=</span> <span class="n">data_model</span><span class="p">,</span>
+                <span class="p">)</span>
+
+                <span class="k">for</span> <span class="n">_dir</span> <span class="ow">in</span> <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">a_b</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">b_a</span><span class="p">):</span>
+
+                    <span class="n">evs_dir</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">get_evidences</span><span class="p">(</span>
+                        <span class="n">direction</span> <span class="o">=</span> <span class="n">_dir</span><span class="p">,</span>
+                        <span class="n">interaction_type</span> <span class="o">=</span> <span class="n">interaction_type</span><span class="p">,</span>
+                        <span class="n">data_model</span> <span class="o">=</span> <span class="n">data_model</span><span class="p">,</span>
+                    <span class="p">)</span>
+                    <span class="n">evs_without_sign</span> <span class="o">=</span> <span class="n">evs_dir</span><span class="o">.</span><span class="n">__copy__</span><span class="p">()</span>
+
+                    <span class="k">for</span> <span class="n">_effect</span><span class="p">,</span> <span class="n">effect</span> <span class="ow">in</span> <span class="nb">zip</span><span class="p">(</span>
+                        <span class="p">(</span><span class="mi">1</span><span class="p">,</span> <span class="o">-</span><span class="mi">1</span><span class="p">),</span>
+                        <span class="p">(</span><span class="s1">&#39;positive&#39;</span><span class="p">,</span> <span class="s1">&#39;negative&#39;</span><span class="p">)</span>
+                    <span class="p">):</span>
+
+                        <span class="n">evs_sign</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">get_evidences</span><span class="p">(</span>
+                            <span class="n">direction</span> <span class="o">=</span> <span class="n">_dir</span><span class="p">,</span>
+                            <span class="n">effect</span> <span class="o">=</span> <span class="n">effect</span><span class="p">,</span>
+                            <span class="n">interaction_type</span> <span class="o">=</span> <span class="n">interaction_type</span><span class="p">,</span>
+                            <span class="n">data_model</span> <span class="o">=</span> <span class="n">data_model</span><span class="p">,</span>
+                        <span class="p">)</span>
+                        <span class="c1"># to make sure we keep all references:</span>
+                        <span class="n">evs_sign</span> <span class="o">+=</span> <span class="n">evs_sign</span><span class="o">.</span><span class="n">intersection</span><span class="p">(</span><span class="n">evs_dir</span><span class="p">)</span>
+                        <span class="n">evs_without_sign</span> <span class="o">-=</span> <span class="n">evs_sign</span>
+                        <span class="n">evs_undirected</span> <span class="o">-=</span> <span class="n">evs_sign</span>
+
+                        <span class="k">for</span> <span class="n">sources</span><span class="p">,</span> <span class="n">refs</span> <span class="ow">in</span> <span class="n">iter_sources</span><span class="p">(</span><span class="n">evs_sign</span><span class="p">):</span>
+
+                            <span class="k">yield</span> <span class="n">InteractionDataFrameRecord</span><span class="p">(</span>
+                                <span class="n">id_a</span> <span class="o">=</span> <span class="n">_dir</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">identifier</span><span class="p">,</span>
+                                <span class="n">id_b</span> <span class="o">=</span> <span class="n">_dir</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">identifier</span><span class="p">,</span>
+                                <span class="n">type_a</span> <span class="o">=</span> <span class="n">_dir</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">entity_type</span><span class="p">,</span>
+                                <span class="n">type_b</span> <span class="o">=</span> <span class="n">_dir</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">entity_type</span><span class="p">,</span>
+                                <span class="n">directed</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
+                                <span class="n">effect</span> <span class="o">=</span> <span class="n">_effect</span><span class="p">,</span>
+                                <span class="nb">type</span> <span class="o">=</span> <span class="n">interaction_type</span><span class="p">,</span>
+                                <span class="n">dmodel</span> <span class="o">=</span> <span class="n">data_model</span><span class="p">,</span>
+                                <span class="n">sources</span> <span class="o">=</span> <span class="n">sources</span><span class="p">,</span>
+                                <span class="n">references</span> <span class="o">=</span> <span class="n">refs</span><span class="p">,</span>
+                            <span class="p">)</span>
+
+                    <span class="k">if</span> <span class="n">evs_without_sign</span><span class="p">:</span>
+
+                        <span class="n">evs_undirected</span> <span class="o">-=</span> <span class="n">evs_without_sign</span>
+
+                        <span class="k">for</span> <span class="n">sources</span><span class="p">,</span> <span class="n">refs</span> <span class="ow">in</span> <span class="n">iter_sources</span><span class="p">(</span><span class="n">evs_without_sign</span><span class="p">):</span>
+
+                            <span class="k">yield</span> <span class="n">InteractionDataFrameRecord</span><span class="p">(</span>
+                                <span class="n">id_a</span> <span class="o">=</span> <span class="n">_dir</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">identifier</span><span class="p">,</span>
+                                <span class="n">id_b</span> <span class="o">=</span> <span class="n">_dir</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">identifier</span><span class="p">,</span>
+                                <span class="n">type_a</span> <span class="o">=</span> <span class="n">_dir</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">entity_type</span><span class="p">,</span>
+                                <span class="n">type_b</span> <span class="o">=</span> <span class="n">_dir</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">entity_type</span><span class="p">,</span>
+                                <span class="n">directed</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
+                                <span class="n">effect</span> <span class="o">=</span> <span class="mi">0</span><span class="p">,</span>
+                                <span class="nb">type</span> <span class="o">=</span> <span class="n">interaction_type</span><span class="p">,</span>
+                                <span class="n">dmodel</span> <span class="o">=</span> <span class="n">data_model</span><span class="p">,</span>
+                                <span class="n">sources</span> <span class="o">=</span> <span class="n">sources</span><span class="p">,</span>
+                                <span class="n">references</span> <span class="o">=</span> <span class="n">refs</span><span class="p">,</span>
+                            <span class="p">)</span>
+
+                <span class="k">if</span> <span class="n">evs_undirected</span><span class="p">:</span>
+
+                    <span class="k">for</span> <span class="n">sources</span><span class="p">,</span> <span class="n">refs</span> <span class="ow">in</span> <span class="n">iter_sources</span><span class="p">(</span><span class="n">evs_undirected</span><span class="p">):</span>
+
+                        <span class="k">yield</span> <span class="n">InteractionDataFrameRecord</span><span class="p">(</span>
+                            <span class="n">id_a</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">a</span><span class="o">.</span><span class="n">identifier</span><span class="p">,</span>
+                            <span class="n">id_b</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">b</span><span class="o">.</span><span class="n">identifier</span><span class="p">,</span>
+                            <span class="n">type_a</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">a</span><span class="o">.</span><span class="n">entity_type</span><span class="p">,</span>
+                            <span class="n">type_b</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">b</span><span class="o">.</span><span class="n">entity_type</span><span class="p">,</span>
+                            <span class="n">directed</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+                            <span class="n">effect</span> <span class="o">=</span> <span class="mi">0</span><span class="p">,</span>
+                            <span class="nb">type</span> <span class="o">=</span> <span class="n">interaction_type</span><span class="p">,</span>
+                            <span class="n">dmodel</span> <span class="o">=</span> <span class="n">data_model</span><span class="p">,</span>
+                            <span class="n">sources</span> <span class="o">=</span> <span class="n">sources</span><span class="p">,</span>
+                            <span class="n">references</span> <span class="o">=</span> <span class="n">refs</span><span class="p">,</span>
+                        <span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="Interaction.asdict">
+<a class="viewcode-back" href="../../../api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.asdict">[docs]</a>
+    <span class="k">def</span> <span class="nf">asdict</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">direction</span><span class="p">:</span> <span class="nb">tuple</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">dict</span><span class="p">:</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Dictionary representation of the evidences.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">direction</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">a_b</span> <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">a_b</span> <span class="o">==</span> <span class="n">direction</span> <span class="k">else</span> <span class="bp">self</span><span class="o">.</span><span class="n">b_a</span>
+
+        <span class="k">return</span> <span class="p">{</span>
+            <span class="s1">&#39;id_a&#39;</span><span class="p">:</span> <span class="nb">str</span><span class="p">(</span><span class="n">direction</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">identifier</span><span class="p">),</span>
+            <span class="s1">&#39;id_b&#39;</span><span class="p">:</span> <span class="nb">str</span><span class="p">(</span><span class="n">direction</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">identifier</span><span class="p">),</span>
+            <span class="s1">&#39;positive&#39;</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">positive</span><span class="p">[</span><span class="n">direction</span><span class="p">]</span><span class="o">.</span><span class="n">asdict</span><span class="p">(),</span>
+            <span class="s1">&#39;negative&#39;</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">negative</span><span class="p">[</span><span class="n">direction</span><span class="p">]</span><span class="o">.</span><span class="n">asdict</span><span class="p">(),</span>
+            <span class="s1">&#39;directed&#39;</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">unknown_effect</span><span class="p">[</span><span class="n">direction</span><span class="p">]</span><span class="o">.</span><span class="n">asdict</span><span class="p">(),</span>
+            <span class="s1">&#39;undirected&#39;</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">direction</span><span class="p">[</span><span class="s1">&#39;undirected&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">asdict</span><span class="p">(),</span>
+        <span class="p">}</span></div>
+
+
+
+<div class="viewcode-block" id="Interaction.serialize_attrs">
+<a class="viewcode-back" href="../../../api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.serialize_attrs">[docs]</a>
+    <span class="k">def</span> <span class="nf">serialize_attrs</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">direction</span><span class="p">:</span> <span class="nb">tuple</span> <span class="o">|</span> <span class="nb">str</span> <span class="o">|</span> <span class="kc">None</span> <span class="o">=</span> <span class="kc">None</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">str</span><span class="p">:</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Serialize the resource specific attributes into a JSON string.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">evs</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">evidences</span> <span class="k">if</span> <span class="ow">not</span> <span class="n">direction</span> <span class="k">else</span> <span class="bp">self</span><span class="o">.</span><span class="n">direction</span><span class="p">[</span><span class="n">direction</span><span class="p">]</span>
+
+        <span class="k">return</span> <span class="n">evs</span><span class="o">.</span><span class="n">serialize_attrs</span><span class="p">()</span></div>
+
+
+
+<div class="viewcode-block" id="Interaction.serialize_evidences">
+<a class="viewcode-back" href="../../../api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.serialize_evidences">[docs]</a>
+    <span class="k">def</span> <span class="nf">serialize_evidences</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">direction</span><span class="p">:</span> <span class="nb">tuple</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">str</span><span class="p">:</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Serialize the evidences into a JSON string.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_serialize</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">asdict</span><span class="p">(</span><span class="n">direction</span> <span class="o">=</span> <span class="n">direction</span><span class="p">))</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">_get_attr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">resource</span><span class="p">,</span> <span class="n">key</span><span class="p">,</span> <span class="n">direction</span><span class="p">):</span>
+
+        <span class="k">if</span> <span class="n">resource</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">direction</span><span class="p">[</span><span class="n">direction</span><span class="p">]:</span>
+
+            <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">direction</span><span class="p">[</span><span class="n">direction</span><span class="p">][</span><span class="n">resource</span><span class="p">][</span><span class="n">key</span><span class="p">]</span>
+
+
+<div class="viewcode-block" id="Interaction.get_attr">
+<a class="viewcode-back" href="../../../api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.get_attr">[docs]</a>
+    <span class="k">def</span> <span class="nf">get_attr</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">resource</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
+            <span class="n">key</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
+            <span class="n">direction</span><span class="p">:</span> <span class="nb">tuple</span> <span class="o">|</span> <span class="nb">str</span> <span class="o">|</span> <span class="kc">None</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+        <span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Extracts the values of one specific attribute.</span>
+
+<span class="sd">        Args</span>
+<span class="sd">            resource:</span>
+<span class="sd">                Name of the resource.</span>
+<span class="sd">            key:</span>
+<span class="sd">                Name of the attribute.</span>
+<span class="sd">            direction:</span>
+<span class="sd">                Direction(s) to consider, either a tuple of entities or</span>
+<span class="sd">                entity names, or the string `undirected`.</span>
+
+<span class="sd">        Returns</span>
+<span class="sd">            Depends on the arguments. The value of the attribute if direction</span>
+<span class="sd">            is defined. Otherwise a dict with the value of the attribute for</span>
+<span class="sd">            each direction. The value of the attribute is `None` if the</span>
+<span class="sd">            resource or the attribute does not belong to this interaction.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">if</span> <span class="n">direction</span><span class="p">:</span>
+
+            <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_get_attr</span><span class="p">(</span><span class="n">resource</span><span class="p">,</span> <span class="n">key</span><span class="p">,</span> <span class="n">direction</span><span class="p">)</span>
+
+        <span class="k">else</span><span class="p">:</span>
+
+            <span class="k">return</span> <span class="nb">dict</span><span class="p">(</span>
+                <span class="p">(</span>
+                    <span class="n">d</span><span class="p">,</span>
+                    <span class="bp">self</span><span class="o">.</span><span class="n">_get_attr</span><span class="p">(</span><span class="n">resource</span><span class="p">,</span> <span class="n">key</span><span class="p">,</span> <span class="n">d</span><span class="p">)</span>
+                <span class="p">)</span>
+                <span class="k">for</span> <span class="n">d</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">direction</span><span class="o">.</span><span class="n">keys</span><span class="p">()</span>
+            <span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="Interaction.dorothea_levels">
+<a class="viewcode-back" href="../../../api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.dorothea_levels">[docs]</a>
+    <span class="k">def</span> <span class="nf">dorothea_levels</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">direction</span><span class="p">:</span> <span class="nb">str</span> <span class="o">|</span> <span class="nb">tuple</span> <span class="o">|</span> <span class="kc">None</span> <span class="o">=</span> <span class="kc">None</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Retrieves the DoRothEA confidence levels.</span>
+
+<span class="sd">        Args</span>
+<span class="sd">            direction:</span>
+<span class="sd">                Direction(s) to consider, either a tuple of entities or</span>
+<span class="sd">                entity names, or the string `undirected`.</span>
+
+<span class="sd">        Returns</span>
+<span class="sd">            List of unique single letter strings representing the five</span>
+<span class="sd">            confidence levels (A-E).</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">directions</span> <span class="o">=</span> <span class="p">(</span><span class="n">direction</span><span class="p">,)</span> <span class="k">if</span> <span class="n">direction</span> <span class="k">else</span> <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">a_b</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">b_a</span><span class="p">)</span>
+
+        <span class="k">return</span> <span class="nb">sorted</span><span class="p">(</span>
+            <span class="p">{</span>
+                <span class="n">level</span>
+                <span class="k">for</span> <span class="n">direction</span> <span class="ow">in</span> <span class="n">directions</span>
+                <span class="k">for</span> <span class="n">level</span> <span class="ow">in</span> <span class="p">(</span>
+                    <span class="bp">self</span><span class="o">.</span><span class="n">_get_attr</span><span class="p">(</span><span class="s1">&#39;DoRothEA&#39;</span><span class="p">,</span> <span class="s1">&#39;level&#39;</span><span class="p">,</span> <span class="n">direction</span><span class="p">)</span> <span class="ow">or</span>
+                    <span class="p">()</span>
+                <span class="p">)</span>
+            <span class="p">}</span>
+        <span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="Interaction.dorothea_level">
+<a class="viewcode-back" href="../../../api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.dorothea_level">[docs]</a>
+    <span class="k">def</span> <span class="nf">dorothea_level</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">direction</span><span class="p">:</span> <span class="nb">str</span> <span class="o">|</span> <span class="nb">tuple</span><span class="p">,</span>
+        <span class="p">)</span> <span class="o">-&gt;</span> <span class="n">Literal</span><span class="p">[</span><span class="s1">&#39;A&#39;</span><span class="p">,</span> <span class="s1">&#39;B&#39;</span><span class="p">,</span> <span class="s1">&#39;C&#39;</span><span class="p">,</span> <span class="s1">&#39;D&#39;</span><span class="p">,</span> <span class="s1">&#39;E&#39;</span><span class="p">]:</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        DoRothEA confidence level for one direction as a single letter.</span>
+
+<span class="sd">        Some interactions might have multiple levels due to the ambiguous</span>
+<span class="sd">        nature of translating gene symbols to UniProt IDs. Here we take the</span>
+<span class="sd">        highest level and drop the rest. For interactions without DoRothEA</span>
+<span class="sd">        levels None is returned.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">levels</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">dorothea_levels</span><span class="p">(</span><span class="n">direction</span> <span class="o">=</span> <span class="n">direction</span><span class="p">)</span>
+
+        <span class="k">return</span> <span class="n">common</span><span class="o">.</span><span class="n">first</span><span class="p">(</span><span class="n">levels</span><span class="p">)</span></div>
+</div>
+
+
+
+<span class="n">Interaction</span><span class="o">.</span><span class="n">_generate_entity_methods</span><span class="p">()</span>
+<span class="n">Interaction</span><span class="o">.</span><span class="n">_generate_get_methods</span><span class="p">()</span>
+<span class="n">Interaction</span><span class="o">.</span><span class="n">_generate_degree_methods</span><span class="p">()</span>
+<span class="n">Interaction</span><span class="o">.</span><span class="n">_generate_count_methods</span><span class="p">()</span>
+<span class="n">Interaction</span><span class="o">.</span><span class="n">_generate_by_methods</span><span class="p">()</span>
+</pre></div>
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+                <article class="bd-article">
+                  
+  <h1>Source code for pypath.core.intercell</h1><div class="highlight"><pre>
+<span></span><span class="ch">#!/usr/bin/env python</span>
+<span class="c1"># -*- coding: utf-8 -*-</span>
+
+<span class="c1">#</span>
+<span class="c1">#  This file is part of the `pypath` python module</span>
+<span class="c1">#</span>
+<span class="c1">#  Copyright 2014-2023</span>
+<span class="c1">#  EMBL, EMBL-EBI, Uniklinik RWTH Aachen, Heidelberg University</span>
+<span class="c1">#</span>
+<span class="c1">#  Authors: see the file `README.rst`</span>
+<span class="c1">#  Contact: Dénes Türei (turei.denes@gmail.com)</span>
+<span class="c1">#</span>
+<span class="c1">#  Distributed under the GPLv3 License.</span>
+<span class="c1">#  See accompanying file LICENSE.txt or copy at</span>
+<span class="c1">#      https://www.gnu.org/licenses/gpl-3.0.html</span>
+<span class="c1">#</span>
+<span class="c1">#  Website: https://pypath.omnipathdb.org/</span>
+<span class="c1">#</span>
+
+<span class="kn">from</span> <span class="nn">future.utils</span> <span class="kn">import</span> <span class="n">iteritems</span>
+
+<span class="kn">import</span> <span class="nn">re</span>
+<span class="kn">import</span> <span class="nn">importlib</span> <span class="k">as</span> <span class="nn">imp</span>
+<span class="kn">import</span> <span class="nn">collections</span>
+<span class="kn">import</span> <span class="nn">itertools</span>
+
+<span class="kn">import</span> <span class="nn">numpy</span> <span class="k">as</span> <span class="nn">np</span>
+<span class="kn">import</span> <span class="nn">pandas</span> <span class="k">as</span> <span class="nn">pd</span>
+
+<span class="kn">import</span> <span class="nn">pypath.share.settings</span> <span class="k">as</span> <span class="nn">settings</span>
+<span class="kn">import</span> <span class="nn">pypath.share.common</span> <span class="k">as</span> <span class="nn">common</span>
+<span class="kn">import</span> <span class="nn">pypath.share.session</span> <span class="k">as</span> <span class="nn">session</span>
+<span class="kn">import</span> <span class="nn">pypath.core.annot</span> <span class="k">as</span> <span class="nn">annot</span>
+<span class="kn">import</span> <span class="nn">pypath.core.intercell_annot</span> <span class="k">as</span> <span class="nn">intercell_annot</span>
+<span class="kn">import</span> <span class="nn">pypath.core.network</span> <span class="k">as</span> <span class="nn">network_mod</span>
+<span class="kn">import</span> <span class="nn">pypath.internals.annot_formats</span> <span class="k">as</span> <span class="nn">af</span>
+
+
+<div class="viewcode-block" id="IntercellAnnotation">
+<a class="viewcode-back" href="../../../api/pypath.core.intercell.IntercellAnnotation.html#pypath.core.intercell.IntercellAnnotation">[docs]</a>
+<span class="k">class</span> <span class="nc">IntercellAnnotation</span><span class="p">(</span><span class="n">annot</span><span class="o">.</span><span class="n">CustomAnnotation</span><span class="p">):</span>
+
+
+<div class="viewcode-block" id="IntercellAnnotation.__init__">
+<a class="viewcode-back" href="../../../api/pypath.core.intercell.IntercellAnnotation.html#pypath.core.intercell.IntercellAnnotation.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">class_definitions</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">excludes</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">excludes_extra</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">cellphonedb_categories</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">baccin_categories</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">hpmr_categories</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">surfaceome_categories</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">gpcrdb_categories</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">icellnet_categories</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">build</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
+            <span class="n">composite_resource_name</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="o">**</span><span class="n">kwargs</span>
+        <span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Builds a database about roles of proteins and complexes in</span>
+<span class="sd">        intercellular communication. The built-in category definitions</span>
+<span class="sd">        defining the default contents of this database can be found in the</span>
+<span class="sd">        ``pypath.core.intercell_annot`` module.</span>
+
+<span class="sd">        :param tuple class_definitions:</span>
+<span class="sd">            A series of annotation class definitions, each represented by</span>
+<span class="sd">            an instance of ``pypath.internals.annot_formats.AnnotDef``.</span>
+<span class="sd">            These definitions carry the attributes and instructions to</span>
+<span class="sd">            populate the classes.</span>
+<span class="sd">        :param dict excludes:</span>
+<span class="sd">            A dict with parent category names (strings) or category keys</span>
+<span class="sd">            (tuples) as keys and sets if identifiers as values.</span>
+<span class="sd">            The identifiers in this dict will be excluded from all the</span>
+<span class="sd">            respective categories while building the database. E.g. if</span>
+<span class="sd">            the UniProt ID `P00533` (EGFR) is in the set under the key of</span>
+<span class="sd">            `adhesion` it will be excluded from the category `adhesion` and</span>
+<span class="sd">            all it&#39;s direct children.</span>
+<span class="sd">        :param dict excludes_extra:</span>
+<span class="sd">            Same kind of dict as `excludes` but it will be added to the</span>
+<span class="sd">            built-in default. The built in and the provided extra sets</span>
+<span class="sd">            will be merged. If you want to overwrite or modify the built-in</span>
+<span class="sd">            sets provide your custom dict as `excludes`.</span>
+<span class="sd">        :param bool build:</span>
+<span class="sd">            Execute the build upon instantiation or set up an empty object</span>
+<span class="sd">            the build can be executed on later.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">if</span> <span class="ow">not</span> <span class="nb">hasattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">&#39;_log_name&#39;</span><span class="p">):</span>
+
+            <span class="n">session</span><span class="o">.</span><span class="n">Logger</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">name</span> <span class="o">=</span> <span class="s1">&#39;intercell&#39;</span><span class="p">)</span>
+
+        <span class="n">class_definitions</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="n">class_definitions</span> <span class="ow">or</span>
+            <span class="n">intercell_annot</span><span class="o">.</span><span class="n">annot_combined_classes</span>
+        <span class="p">)</span>
+        <span class="n">excludes</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="n">excludes</span> <span class="ow">or</span>
+            <span class="n">intercell_annot</span><span class="o">.</span><span class="n">excludes</span>
+        <span class="p">)</span>
+
+        <span class="n">locals_</span> <span class="o">=</span> <span class="nb">locals</span><span class="p">()</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">_resource_categories</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">(</span>
+            <span class="p">(</span>
+                <span class="n">res</span><span class="p">,</span>
+                <span class="n">locals_</span><span class="p">[</span><span class="s1">&#39;</span><span class="si">%s</span><span class="s1">_categories&#39;</span> <span class="o">%</span> <span class="n">res</span><span class="p">]</span>
+                    <span class="k">if</span> <span class="n">locals_</span><span class="p">[</span><span class="s1">&#39;</span><span class="si">%s</span><span class="s1">_categories&#39;</span> <span class="o">%</span> <span class="n">res</span><span class="p">]</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span> <span class="k">else</span>
+                <span class="n">settings</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">&#39;intercell_</span><span class="si">%s</span><span class="s1">_categories&#39;</span> <span class="o">%</span> <span class="n">res</span><span class="p">)</span>
+            <span class="p">)</span>
+            <span class="k">for</span> <span class="n">res</span> <span class="ow">in</span> <span class="p">(</span>
+                <span class="s1">&#39;baccin&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;cellphonedb&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;hpmr&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;surfaceome&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;gpcrdb&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;icellnet&#39;</span><span class="p">,</span>
+            <span class="p">)</span>
+        <span class="p">)</span>
+
+        <span class="n">annot</span><span class="o">.</span><span class="n">CustomAnnotation</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">class_definitions</span> <span class="o">=</span> <span class="n">class_definitions</span><span class="p">,</span>
+            <span class="n">excludes</span> <span class="o">=</span> <span class="n">excludes</span><span class="p">,</span>
+            <span class="n">excludes_extra</span> <span class="o">=</span> <span class="n">excludes_extra</span><span class="p">,</span>
+            <span class="n">build</span> <span class="o">=</span> <span class="n">build</span><span class="p">,</span>
+            <span class="n">composite_resource_name</span> <span class="o">=</span> <span class="n">composite_resource_name</span><span class="p">,</span>
+            <span class="o">**</span><span class="n">kwargs</span>
+        <span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="IntercellAnnotation.reload">
+<a class="viewcode-back" href="../../../api/pypath.core.intercell.IntercellAnnotation.html#pypath.core.intercell.IntercellAnnotation.reload">[docs]</a>
+    <span class="k">def</span> <span class="nf">reload</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Reloads the object from the module level.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">imp</span><span class="o">.</span><span class="n">reload</span><span class="p">(</span><span class="n">af</span><span class="p">)</span>
+        <span class="n">imp</span><span class="o">.</span><span class="n">reload</span><span class="p">(</span><span class="n">annot</span><span class="p">)</span>
+        <span class="n">modname</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="vm">__class__</span><span class="o">.</span><span class="vm">__module__</span>
+        <span class="n">mod</span> <span class="o">=</span> <span class="nb">__import__</span><span class="p">(</span><span class="n">modname</span><span class="p">,</span> <span class="n">fromlist</span> <span class="o">=</span> <span class="p">[</span><span class="n">modname</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;.&#39;</span><span class="p">)[</span><span class="mi">0</span><span class="p">]])</span>
+        <span class="n">imp</span><span class="o">.</span><span class="n">reload</span><span class="p">(</span><span class="n">mod</span><span class="p">)</span>
+        <span class="n">new</span> <span class="o">=</span> <span class="nb">getattr</span><span class="p">(</span><span class="n">mod</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="vm">__class__</span><span class="o">.</span><span class="vm">__name__</span><span class="p">)</span>
+        <span class="nb">setattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">&#39;__class__&#39;</span><span class="p">,</span> <span class="n">new</span><span class="p">)</span>
+
+        <span class="k">for</span> <span class="n">k</span><span class="p">,</span> <span class="n">v</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">classes</span><span class="p">):</span>
+
+            <span class="n">k</span><span class="o">.</span><span class="vm">__class__</span> <span class="o">=</span> <span class="nb">getattr</span><span class="p">(</span><span class="n">af</span><span class="p">,</span> <span class="n">k</span><span class="o">.</span><span class="vm">__class__</span><span class="o">.</span><span class="vm">__name__</span><span class="p">)</span>
+            <span class="n">v</span><span class="o">.</span><span class="vm">__class__</span> <span class="o">=</span> <span class="nb">getattr</span><span class="p">(</span><span class="n">af</span><span class="p">,</span> <span class="n">v</span><span class="o">.</span><span class="vm">__class__</span><span class="o">.</span><span class="vm">__name__</span><span class="p">)</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">set_classes</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">class_names</span> <span class="o">=</span> <span class="nb">set</span><span class="p">(</span><span class="n">itertools</span><span class="o">.</span><span class="n">chain</span><span class="p">(</span>
+            <span class="o">*</span><span class="n">intercell_annot</span><span class="o">.</span><span class="n">class_types</span><span class="o">.</span><span class="n">values</span><span class="p">()</span>
+        <span class="p">))</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">class_types</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">(</span>
+            <span class="p">(</span><span class="bp">cls</span><span class="p">,</span> <span class="n">typ</span><span class="p">)</span>
+            <span class="k">for</span> <span class="n">typ</span><span class="p">,</span> <span class="n">ccls</span> <span class="ow">in</span> <span class="n">intercell_annot</span><span class="o">.</span><span class="n">class_types</span><span class="o">.</span><span class="n">items</span><span class="p">()</span>
+            <span class="k">for</span> <span class="bp">cls</span> <span class="ow">in</span> <span class="n">ccls</span>
+        <span class="p">)</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">main_classes</span> <span class="o">=</span> <span class="p">{}</span>
+
+        <span class="k">for</span> <span class="bp">cls</span> <span class="ow">in</span> <span class="nb">set</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">classes</span><span class="o">.</span><span class="n">keys</span><span class="p">()):</span>
+
+            <span class="n">mainclass</span> <span class="o">=</span> <span class="kc">None</span>
+
+            <span class="n">cls_split</span> <span class="o">=</span> <span class="bp">cls</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;_&#39;</span><span class="p">)</span>
+
+            <span class="k">for</span> <span class="n">j</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">cls_split</span><span class="p">)):</span>
+
+                <span class="n">this_part</span> <span class="o">=</span> <span class="s1">&#39;_&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">cls_split</span><span class="p">[:</span><span class="n">j</span><span class="p">])</span>
+
+                <span class="k">if</span> <span class="n">this_part</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">class_names</span><span class="p">:</span>
+
+                    <span class="n">mainclass</span> <span class="o">=</span> <span class="n">this_part</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">main_classes</span><span class="p">[</span><span class="bp">cls</span><span class="p">]</span> <span class="o">=</span> <span class="n">mainclass</span>
+
+
+    <span class="k">def</span> <span class="nf">add_classes_to_df</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">if</span> <span class="ow">not</span> <span class="nb">hasattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">&#39;df&#39;</span><span class="p">):</span>
+
+            <span class="k">return</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">df</span><span class="p">[</span><span class="s1">&#39;mainclass&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">([</span><span class="bp">self</span><span class="o">.</span><span class="n">main_classes</span><span class="p">[</span><span class="n">c</span><span class="p">]</span> <span class="k">for</span> <span class="n">c</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">df</span><span class="o">.</span><span class="n">category</span><span class="p">])</span>
+        <span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">df</span><span class="p">[</span><span class="s1">&#39;mainclass&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">df</span><span class="p">[</span><span class="s1">&#39;mainclass&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">astype</span><span class="p">(</span><span class="s1">&#39;category&#39;</span><span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">df</span><span class="p">[</span><span class="s1">&#39;class_type&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">([</span>
+                <span class="p">(</span>
+                    <span class="bp">self</span><span class="o">.</span><span class="n">class_types</span><span class="p">[</span><span class="n">c</span><span class="p">]</span>
+                        <span class="k">if</span> <span class="n">c</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">class_types</span> <span class="k">else</span>
+                    <span class="s1">&#39;sub&#39;</span>
+                <span class="p">)</span>
+                <span class="k">for</span> <span class="n">c</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">df</span><span class="o">.</span><span class="n">category</span>
+            <span class="p">])</span>
+        <span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">df</span><span class="p">[</span><span class="s1">&#39;class_type&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">df</span><span class="p">[</span><span class="s1">&#39;class_type&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">astype</span><span class="p">(</span><span class="s1">&#39;category&#39;</span><span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">collect_classes</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">class_names</span> <span class="o">=</span> <span class="nb">set</span><span class="p">(</span>
+            <span class="n">itertools</span><span class="o">.</span><span class="n">chain</span><span class="p">(</span>
+                <span class="o">*</span><span class="n">intercell_annot</span><span class="o">.</span><span class="n">class_types</span><span class="o">.</span><span class="n">values</span><span class="p">()</span>
+            <span class="p">)</span>
+        <span class="p">)</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">class_types</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">(</span>
+            <span class="p">(</span><span class="bp">cls</span><span class="p">,</span> <span class="n">typ</span><span class="p">)</span>
+            <span class="k">for</span> <span class="n">typ</span><span class="p">,</span> <span class="n">ccls</span> <span class="ow">in</span> <span class="n">intercell_annot</span><span class="o">.</span><span class="n">class_types</span><span class="o">.</span><span class="n">items</span><span class="p">()</span>
+            <span class="k">for</span> <span class="bp">cls</span> <span class="ow">in</span> <span class="n">ccls</span>
+        <span class="p">)</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">children</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">defaultdict</span><span class="p">(</span><span class="nb">set</span><span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">parents</span> <span class="o">=</span> <span class="p">{}</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">class_labels</span> <span class="o">=</span> <span class="p">{}</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">resource_labels</span> <span class="o">=</span> <span class="p">{}</span>
+
+        <span class="k">for</span> <span class="bp">cls</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">classes</span><span class="o">.</span><span class="n">keys</span><span class="p">():</span>
+
+            <span class="n">mainclass</span> <span class="o">=</span> <span class="kc">None</span>
+
+            <span class="k">if</span> <span class="bp">cls</span> <span class="ow">in</span> <span class="n">intercell_annot</span><span class="o">.</span><span class="n">class_types</span><span class="p">[</span><span class="s1">&#39;misc&#39;</span><span class="p">]:</span>
+
+                <span class="bp">self</span><span class="o">.</span><span class="n">parents</span><span class="p">[</span><span class="bp">cls</span><span class="p">]</span> <span class="o">=</span> <span class="kc">None</span>
+
+            <span class="k">else</span><span class="p">:</span>
+
+                <span class="n">cls_split</span> <span class="o">=</span> <span class="bp">cls</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;_&#39;</span><span class="p">)</span>
+
+                <span class="k">for</span> <span class="n">j</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">cls_split</span><span class="p">)</span> <span class="o">+</span> <span class="mi">1</span><span class="p">):</span>
+
+                    <span class="n">this_part</span> <span class="o">=</span> <span class="s1">&#39;_&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">cls_split</span><span class="p">[:</span><span class="n">j</span><span class="p">])</span>
+
+                    <span class="k">if</span> <span class="n">this_part</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">class_names</span><span class="p">:</span>
+
+                        <span class="n">mainclass</span> <span class="o">=</span> <span class="n">this_part</span>
+
+                <span class="bp">self</span><span class="o">.</span><span class="n">children</span><span class="p">[</span><span class="n">mainclass</span><span class="p">]</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="bp">cls</span><span class="p">)</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">parents</span><span class="p">[</span><span class="bp">cls</span><span class="p">]</span> <span class="o">=</span> <span class="n">mainclass</span>
+
+                <span class="n">resource</span> <span class="o">=</span> <span class="n">cls_split</span><span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span>
+
+            <span class="k">if</span> <span class="n">mainclass</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span> <span class="ow">and</span> <span class="n">resource</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">mainclass</span><span class="p">:</span>
+
+                <span class="bp">self</span><span class="o">.</span><span class="n">resource_labels</span><span class="p">[</span><span class="bp">cls</span><span class="p">]</span> <span class="o">=</span> <span class="p">(</span>
+                    <span class="n">intercell_annot</span><span class="o">.</span><span class="n">get_resource_label</span><span class="p">(</span><span class="n">resource</span><span class="p">)</span>
+                <span class="p">)</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">class_labels</span><span class="p">[</span><span class="bp">cls</span><span class="p">]</span> <span class="o">=</span> <span class="p">(</span>
+                <span class="n">intercell_annot</span><span class="o">.</span><span class="n">get_class_label</span><span class="p">(</span><span class="n">mainclass</span> <span class="ow">or</span> <span class="bp">cls</span><span class="p">)</span>
+            <span class="p">)</span>
+
+
+<div class="viewcode-block" id="IntercellAnnotation.make_df">
+<a class="viewcode-back" href="../../../api/pypath.core.intercell.IntercellAnnotation.html#pypath.core.intercell.IntercellAnnotation.make_df">[docs]</a>
+    <span class="k">def</span> <span class="nf">make_df</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="n">annot</span><span class="o">.</span><span class="n">CustomAnnotation</span><span class="o">.</span><span class="n">make_df</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">df_add_causality</span><span class="p">()</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">df_add_locations</span><span class="p">()</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">load_from_pickle</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">pickle_file</span><span class="p">):</span>
+
+        <span class="n">annot</span><span class="o">.</span><span class="n">CustomAnnotation</span><span class="o">.</span><span class="n">load_from_pickle</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">pickle_file</span> <span class="o">=</span> <span class="n">pickle_file</span><span class="p">,</span>
+        <span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">df_add_causality</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">if</span> <span class="ow">not</span> <span class="nb">hasattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">&#39;df&#39;</span><span class="p">):</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">make_df</span><span class="p">()</span>
+            <span class="k">return</span>
+
+        <span class="k">for</span> <span class="n">causality</span> <span class="ow">in</span> <span class="p">(</span><span class="s1">&#39;transmitter&#39;</span><span class="p">,</span> <span class="s1">&#39;receiver&#39;</span><span class="p">):</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">df</span><span class="p">[</span><span class="n">causality</span><span class="p">]</span> <span class="o">=</span> <span class="p">[</span>
+                <span class="nb">bool</span><span class="p">(</span><span class="nb">getattr</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">classes</span><span class="p">[</span><span class="n">key</span><span class="p">],</span> <span class="n">causality</span><span class="p">))</span>
+                <span class="k">for</span> <span class="n">key</span> <span class="ow">in</span> <span class="nb">zip</span><span class="p">(</span>
+                    <span class="bp">self</span><span class="o">.</span><span class="n">df</span><span class="o">.</span><span class="n">category</span><span class="p">,</span>
+                    <span class="bp">self</span><span class="o">.</span><span class="n">df</span><span class="o">.</span><span class="n">parent</span><span class="p">,</span>
+                    <span class="bp">self</span><span class="o">.</span><span class="n">df</span><span class="o">.</span><span class="n">database</span><span class="p">,</span>
+                <span class="p">)</span>
+            <span class="p">]</span>
+
+
+    <span class="k">def</span> <span class="nf">df_add_locations</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">locations</span> <span class="o">=</span> <span class="kc">None</span><span class="p">):</span>
+
+        <span class="k">if</span> <span class="ow">not</span> <span class="nb">hasattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">&#39;df&#39;</span><span class="p">):</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">make_df</span><span class="p">()</span>
+            <span class="k">return</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span><span class="s1">&#39;Adding location columns to data frame.&#39;</span><span class="p">)</span>
+
+        <span class="n">locations</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="n">locations</span> <span class="ow">or</span>
+            <span class="p">(</span>
+                <span class="s1">&#39;secreted&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;plasma_membrane_transmembrane&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;plasma_membrane_peripheral&#39;</span><span class="p">,</span>
+            <span class="p">)</span>
+        <span class="p">)</span>
+        <span class="n">location_classes</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">(</span>
+            <span class="p">(</span>
+                <span class="n">location</span><span class="p">,</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">select</span><span class="p">(</span><span class="n">location</span><span class="p">),</span>
+            <span class="p">)</span>
+            <span class="k">for</span> <span class="n">location</span> <span class="ow">in</span> <span class="n">locations</span>
+        <span class="p">)</span>
+
+        <span class="k">for</span> <span class="n">location</span><span class="p">,</span> <span class="n">entities</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="n">location_classes</span><span class="p">):</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">df</span><span class="p">[</span><span class="n">location</span><span class="p">]</span> <span class="o">=</span> <span class="p">[</span>
+                <span class="n">uniprot</span> <span class="ow">in</span> <span class="n">entities</span>
+                <span class="k">for</span> <span class="n">uniprot</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">df</span><span class="o">.</span><span class="n">uniprot</span>
+            <span class="p">]</span>
+
+
+    <span class="k">def</span> <span class="nf">pre_build</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="n">annot</span><span class="o">.</span><span class="n">CustomAnnotation</span><span class="o">.</span><span class="n">pre_build</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">add_extra_categories</span><span class="p">()</span>
+
+
+    <span class="k">def</span> <span class="nf">add_extra_categories</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">add_cellphonedb_categories</span><span class="p">()</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">add_baccin_categories</span><span class="p">()</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">add_hpmr_categories</span><span class="p">()</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">add_surfaceome_categories</span><span class="p">()</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">add_gpcrdb_categories</span><span class="p">()</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">add_icellnet_categories</span><span class="p">()</span>
+
+
+    <span class="k">def</span> <span class="nf">add_cellphonedb_categories</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">_resource_categories</span><span class="p">[</span><span class="s1">&#39;cellphonedb&#39;</span><span class="p">]:</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">ensure_annotdb</span><span class="p">()</span>
+
+            <span class="n">cellphonedb_categories</span> <span class="o">=</span> <span class="p">[]</span>
+
+            <span class="k">for</span> <span class="n">mainclass</span> <span class="ow">in</span> <span class="p">(</span><span class="s1">&#39;receptor&#39;</span><span class="p">,</span> <span class="s1">&#39;secreted&#39;</span><span class="p">):</span>
+
+                <span class="n">cpdb</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">annotdb</span><span class="o">.</span><span class="n">annots</span><span class="p">[</span><span class="s1">&#39;CellPhoneDB&#39;</span><span class="p">]</span>
+                <span class="n">attr</span> <span class="o">=</span> <span class="s1">&#39;</span><span class="si">%s</span><span class="s1">_class&#39;</span> <span class="o">%</span> <span class="n">mainclass</span>
+
+                <span class="n">categories</span> <span class="o">=</span> <span class="n">cpdb</span><span class="o">.</span><span class="n">get_values</span><span class="p">(</span><span class="n">attr</span><span class="p">)</span>
+
+                <span class="k">for</span> <span class="n">category</span> <span class="ow">in</span> <span class="n">categories</span><span class="p">:</span>
+
+                    <span class="k">if</span> <span class="n">category</span> <span class="ow">in</span> <span class="p">{</span><span class="s1">&#39;secreted&#39;</span><span class="p">,</span> <span class="s1">&#39;receptor&#39;</span><span class="p">}:</span>
+
+                        <span class="k">continue</span>
+
+                    <span class="n">parent</span> <span class="o">=</span> <span class="p">(</span>
+                        <span class="s1">&#39;receptor&#39;</span>
+                            <span class="k">if</span> <span class="n">mainclass</span> <span class="o">==</span> <span class="s1">&#39;receptor&#39;</span> <span class="k">else</span>
+                        <span class="s1">&#39;ligand&#39;</span>
+                    <span class="p">)</span>
+
+                    <span class="n">cellphonedb_categories</span><span class="o">.</span><span class="n">append</span><span class="p">(</span>
+                        <span class="n">af</span><span class="o">.</span><span class="n">AnnotDef</span><span class="p">(</span>
+                            <span class="n">name</span> <span class="o">=</span> <span class="n">category</span><span class="p">,</span>
+                            <span class="n">parent</span> <span class="o">=</span> <span class="n">parent</span><span class="p">,</span>
+                            <span class="n">resource</span> <span class="o">=</span> <span class="s1">&#39;CellPhoneDB&#39;</span><span class="p">,</span>
+                            <span class="n">args</span> <span class="o">=</span> <span class="p">{</span>
+                                <span class="n">mainclass</span><span class="p">:</span> <span class="nb">bool</span><span class="p">,</span>
+                                <span class="n">attr</span><span class="p">:</span> <span class="n">category</span><span class="p">,</span>
+                            <span class="p">},</span>
+                        <span class="p">)</span>
+                    <span class="p">)</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">_class_definitions_provided</span> <span class="o">+=</span> <span class="nb">tuple</span><span class="p">(</span><span class="n">cellphonedb_categories</span><span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">add_baccin_categories</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">_resource_categories</span><span class="p">[</span><span class="s1">&#39;baccin&#39;</span><span class="p">]:</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">ensure_annotdb</span><span class="p">()</span>
+            <span class="n">baccin_categories</span> <span class="o">=</span> <span class="p">[]</span>
+            <span class="n">baccin</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">annotdb</span><span class="o">.</span><span class="n">annots</span><span class="p">[</span><span class="s1">&#39;Baccin2019&#39;</span><span class="p">]</span>
+            <span class="n">fields</span> <span class="o">=</span> <span class="n">baccin</span><span class="o">.</span><span class="n">get_names</span><span class="p">()</span>
+            <span class="n">locations</span> <span class="o">=</span> <span class="p">{</span>
+                <span class="s1">&#39;surface&#39;</span><span class="p">:</span> <span class="p">{</span><span class="s1">&#39;membrane&#39;</span><span class="p">,</span> <span class="s1">&#39;both&#39;</span><span class="p">},</span>
+                <span class="s1">&#39;secreted&#39;</span><span class="p">:</span> <span class="p">{</span><span class="s1">&#39;secreted&#39;</span><span class="p">,</span> <span class="s1">&#39;both&#39;</span><span class="p">,</span> <span class="s1">&#39;ecm&#39;</span><span class="p">},</span>
+            <span class="p">}</span>
+
+            <span class="n">subclasses</span> <span class="o">=</span> <span class="n">baccin</span><span class="o">.</span><span class="n">get_values</span><span class="p">(</span><span class="s1">&#39;subclass&#39;</span><span class="p">)</span> <span class="o">-</span> <span class="p">{</span><span class="s1">&#39;other&#39;</span><span class="p">,</span> <span class="kc">None</span><span class="p">}</span>
+
+            <span class="n">this_fields</span> <span class="o">=</span> <span class="n">fields</span><span class="p">[</span><span class="mi">1</span><span class="p">:]</span>
+
+            <span class="k">for</span> <span class="n">subclass</span> <span class="ow">in</span> <span class="n">subclasses</span><span class="p">:</span>
+
+                <span class="n">receptor</span> <span class="o">=</span> <span class="s1">&#39;receptor&#39;</span> <span class="ow">in</span> <span class="n">subclass</span>
+
+                <span class="n">args</span> <span class="o">=</span> <span class="p">{</span><span class="s1">&#39;subclass&#39;</span><span class="p">:</span> <span class="n">subclass</span><span class="p">}</span>
+
+                <span class="k">for</span> <span class="n">location</span> <span class="ow">in</span> <span class="p">(</span><span class="s1">&#39;surface&#39;</span><span class="p">,</span> <span class="s1">&#39;secreted&#39;</span><span class="p">):</span>
+
+                    <span class="k">if</span> <span class="n">receptor</span> <span class="ow">and</span> <span class="n">location</span> <span class="o">==</span> <span class="s1">&#39;secreted&#39;</span><span class="p">:</span>
+
+                        <span class="k">continue</span>
+
+                    <span class="k">if</span> <span class="ow">not</span> <span class="n">receptor</span><span class="p">:</span>
+
+                        <span class="n">args</span><span class="p">[</span><span class="s1">&#39;location&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">location</span>
+
+                    <span class="n">members</span> <span class="o">=</span> <span class="n">baccin</span><span class="o">.</span><span class="n">select</span><span class="p">(</span><span class="o">**</span><span class="n">args</span><span class="p">)</span>
+
+                    <span class="k">if</span> <span class="ow">not</span> <span class="n">members</span><span class="p">:</span>
+
+                        <span class="k">continue</span>
+
+                    <span class="n">parent</span> <span class="o">=</span> <span class="p">(</span>
+                        <span class="s1">&#39;receptor&#39;</span>
+                        <span class="k">if</span> <span class="n">receptor</span> <span class="k">else</span>
+                        <span class="p">(</span>
+                            <span class="s1">&#39;cell_surface_ligand&#39;</span>
+                                <span class="k">if</span> <span class="n">location</span> <span class="o">==</span> <span class="s1">&#39;surface&#39;</span> <span class="k">else</span>
+                            <span class="s1">&#39;ligand&#39;</span>
+                        <span class="p">)</span>
+                    <span class="p">)</span>
+
+                    <span class="n">name</span> <span class="o">=</span> <span class="n">subclass</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s1">&#39;_receptor&#39;</span><span class="p">,</span> <span class="s1">&#39;&#39;</span><span class="p">)</span>
+
+                    <span class="n">baccin_categories</span><span class="o">.</span><span class="n">append</span><span class="p">(</span>
+                        <span class="n">af</span><span class="o">.</span><span class="n">AnnotDef</span><span class="p">(</span>
+                            <span class="n">name</span> <span class="o">=</span> <span class="n">name</span><span class="p">,</span>
+                            <span class="n">parent</span> <span class="o">=</span> <span class="n">parent</span><span class="p">,</span>
+                            <span class="n">resource</span> <span class="o">=</span> <span class="s1">&#39;Baccin2019&#39;</span><span class="p">,</span>
+                            <span class="n">args</span> <span class="o">=</span> <span class="n">args</span><span class="p">,</span>
+                        <span class="p">)</span>
+                    <span class="p">)</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">_class_definitions_provided</span> <span class="o">+=</span> <span class="nb">tuple</span><span class="p">(</span><span class="n">baccin_categories</span><span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">add_hpmr_categories</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="n">resep</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">compile</span><span class="p">(</span><span class="sa">r</span><span class="s1">&#39;[- /\(\),]+&#39;</span><span class="p">)</span>
+
+        <span class="n">hpmr_categories</span> <span class="o">=</span> <span class="p">[]</span>
+
+        <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">_resource_categories</span><span class="p">[</span><span class="s1">&#39;hpmr&#39;</span><span class="p">]:</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">ensure_annotdb</span><span class="p">()</span>
+
+            <span class="n">hpmr</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">annotdb</span><span class="p">[</span><span class="s1">&#39;HPMR&#39;</span><span class="p">]</span>
+
+            <span class="n">fields</span> <span class="o">=</span> <span class="n">hpmr</span><span class="o">.</span><span class="n">get_names</span><span class="p">()</span>
+
+            <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">2</span><span class="p">,</span> <span class="nb">len</span><span class="p">(</span><span class="n">fields</span><span class="p">)</span> <span class="o">+</span> <span class="mi">1</span><span class="p">):</span>
+
+                <span class="n">combinations</span> <span class="o">=</span> <span class="p">{</span>
+                    <span class="n">a</span><span class="p">[:</span><span class="n">i</span><span class="p">]</span>
+                    <span class="k">for</span> <span class="n">entity</span><span class="p">,</span> <span class="n">annots</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="n">hpmr</span><span class="o">.</span><span class="n">annot</span><span class="p">)</span>
+                    <span class="k">for</span> <span class="n">a</span> <span class="ow">in</span> <span class="n">annots</span>
+                <span class="p">}</span>
+
+                <span class="k">for</span> <span class="n">values</span> <span class="ow">in</span> <span class="n">combinations</span><span class="p">:</span>
+
+                    <span class="k">if</span> <span class="ow">not</span> <span class="n">values</span><span class="p">[</span><span class="mi">0</span><span class="p">]:</span>
+
+                        <span class="k">continue</span>
+
+                    <span class="n">this_fields</span> <span class="o">=</span> <span class="n">fields</span><span class="p">[</span><span class="mi">1</span><span class="p">:</span><span class="n">i</span><span class="p">]</span>
+                    <span class="n">this_values</span> <span class="o">=</span> <span class="n">values</span><span class="p">[</span><span class="mi">1</span><span class="p">:</span><span class="n">i</span><span class="p">]</span>
+
+                    <span class="k">if</span> <span class="ow">not</span> <span class="n">this_values</span><span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">]:</span>
+
+                        <span class="k">continue</span>
+
+                    <span class="n">args</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">(</span><span class="nb">zip</span><span class="p">(</span>
+                        <span class="n">this_fields</span><span class="p">,</span>
+                        <span class="n">this_values</span><span class="p">,</span>
+                    <span class="p">))</span>
+
+                    <span class="n">members</span> <span class="o">=</span> <span class="n">hpmr</span><span class="o">.</span><span class="n">select</span><span class="p">(</span><span class="o">**</span><span class="n">args</span><span class="p">)</span>
+                    <span class="n">parent</span> <span class="o">=</span> <span class="n">values</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span>
+
+                    <span class="k">if</span> <span class="ow">not</span> <span class="n">members</span><span class="p">:</span>
+
+                        <span class="k">continue</span>
+
+                    <span class="n">name_parts</span> <span class="o">=</span> <span class="p">(</span>
+                        <span class="n">this_values</span><span class="p">[</span><span class="mi">1</span><span class="p">:]</span>
+                            <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">this_values</span><span class="p">)</span> <span class="o">&gt;</span> <span class="mi">1</span> <span class="k">else</span>
+                        <span class="n">this_values</span>
+                    <span class="p">)</span>
+
+                    <span class="n">name</span> <span class="o">=</span> <span class="s1">&#39;_&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span>
+                        <span class="n">name_part</span><span class="o">.</span><span class="n">strip</span><span class="p">(</span><span class="s1">&#39;_&#39;</span><span class="p">)</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s1">&#39;_receptors&#39;</span><span class="p">,</span> <span class="s1">&#39;&#39;</span><span class="p">)</span>
+                        <span class="k">for</span> <span class="n">name_part</span> <span class="ow">in</span>
+                        <span class="p">(</span>
+                            <span class="n">resep</span><span class="o">.</span><span class="n">sub</span><span class="p">(</span><span class="s1">&#39;_&#39;</span><span class="p">,</span> <span class="n">val</span><span class="p">)</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span>
+                                <span class="k">if</span> <span class="n">val</span> <span class="k">else</span>
+                            <span class="kc">None</span>
+                            <span class="k">for</span> <span class="n">val</span> <span class="ow">in</span> <span class="nb">reversed</span><span class="p">(</span><span class="n">name_parts</span><span class="p">)</span>
+                        <span class="p">)</span>
+                        <span class="k">if</span> <span class="n">name_part</span>
+                    <span class="p">)</span>
+
+                    <span class="n">hpmr_categories</span><span class="o">.</span><span class="n">append</span><span class="p">(</span>
+                        <span class="n">af</span><span class="o">.</span><span class="n">AnnotDef</span><span class="p">(</span>
+                            <span class="n">name</span> <span class="o">=</span> <span class="n">name</span><span class="p">,</span>
+                            <span class="n">resource</span> <span class="o">=</span> <span class="s1">&#39;HPMR&#39;</span><span class="p">,</span>
+                            <span class="n">args</span> <span class="o">=</span> <span class="n">args</span><span class="p">,</span>
+                            <span class="n">parent</span> <span class="o">=</span> <span class="n">parent</span><span class="p">,</span>
+                        <span class="p">)</span>
+                    <span class="p">)</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">_class_definitions_provided</span> <span class="o">+=</span> <span class="nb">tuple</span><span class="p">(</span><span class="n">hpmr_categories</span><span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">add_gpcrdb_categories</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="n">resep</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">compile</span><span class="p">(</span><span class="sa">r</span><span class="s1">&#39;[- /\(\),]+&#39;</span><span class="p">)</span>
+
+        <span class="n">gpcrdb_categories</span> <span class="o">=</span> <span class="p">[]</span>
+
+        <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">_resource_categories</span><span class="p">[</span><span class="s1">&#39;gpcrdb&#39;</span><span class="p">]:</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">ensure_annotdb</span><span class="p">()</span>
+
+            <span class="n">gpcrdb</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">annotdb</span><span class="p">[</span><span class="s1">&#39;GPCRdb&#39;</span><span class="p">]</span>
+
+            <span class="n">fields</span> <span class="o">=</span> <span class="n">gpcrdb</span><span class="o">.</span><span class="n">get_names</span><span class="p">()</span>
+
+            <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">1</span><span class="p">,</span> <span class="nb">len</span><span class="p">(</span><span class="n">fields</span><span class="p">)</span> <span class="o">+</span> <span class="mi">1</span><span class="p">):</span>
+
+                <span class="n">combinations</span> <span class="o">=</span> <span class="p">{</span>
+                    <span class="n">a</span><span class="p">[:</span><span class="n">i</span><span class="p">]</span>
+                    <span class="k">for</span> <span class="n">entity</span><span class="p">,</span> <span class="n">annots</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="n">gpcrdb</span><span class="o">.</span><span class="n">annot</span><span class="p">)</span>
+                    <span class="k">for</span> <span class="n">a</span> <span class="ow">in</span> <span class="n">annots</span>
+                <span class="p">}</span>
+
+                <span class="k">for</span> <span class="n">values</span> <span class="ow">in</span> <span class="n">combinations</span><span class="p">:</span>
+
+                    <span class="k">if</span> <span class="ow">not</span> <span class="n">values</span><span class="p">[</span><span class="mi">0</span><span class="p">]:</span>
+
+                        <span class="k">continue</span>
+
+                    <span class="n">this_fields</span> <span class="o">=</span> <span class="n">fields</span><span class="p">[:</span><span class="n">i</span><span class="p">]</span>
+                    <span class="n">this_values</span> <span class="o">=</span> <span class="n">values</span><span class="p">[:</span><span class="n">i</span><span class="p">]</span>
+
+                    <span class="n">args</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">(</span><span class="nb">zip</span><span class="p">(</span>
+                        <span class="n">this_fields</span><span class="p">,</span>
+                        <span class="n">this_values</span><span class="p">,</span>
+                    <span class="p">))</span>
+
+                    <span class="n">members</span> <span class="o">=</span> <span class="n">gpcrdb</span><span class="o">.</span><span class="n">select</span><span class="p">(</span><span class="o">**</span><span class="n">args</span><span class="p">)</span>
+
+                    <span class="k">if</span> <span class="ow">not</span> <span class="n">members</span><span class="p">:</span>
+
+                        <span class="k">continue</span>
+
+                    <span class="n">name</span> <span class="o">=</span> <span class="s1">&#39;_&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span>
+                        <span class="n">resep</span><span class="o">.</span><span class="n">sub</span><span class="p">(</span><span class="s1">&#39;_&#39;</span><span class="p">,</span> <span class="n">val</span><span class="p">)</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span><span class="o">.</span><span class="n">strip</span><span class="p">(</span><span class="s1">&#39;_&#39;</span><span class="p">)</span>
+                        <span class="k">for</span> <span class="n">val</span> <span class="ow">in</span>
+                        <span class="n">this_values</span>
+                    <span class="p">)</span>
+                    <span class="n">name</span> <span class="o">=</span> <span class="n">name</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s1">&#39;_receptors&#39;</span><span class="p">,</span> <span class="s1">&#39;&#39;</span><span class="p">)</span>
+
+                    <span class="n">gpcrdb_categories</span><span class="o">.</span><span class="n">append</span><span class="p">(</span>
+                        <span class="n">af</span><span class="o">.</span><span class="n">AnnotDef</span><span class="p">(</span>
+                            <span class="n">name</span> <span class="o">=</span> <span class="n">name</span><span class="p">,</span>
+                            <span class="n">resource</span> <span class="o">=</span> <span class="s1">&#39;GPCRdb&#39;</span><span class="p">,</span>
+                            <span class="n">args</span> <span class="o">=</span> <span class="n">args</span><span class="p">,</span>
+                            <span class="n">parent</span> <span class="o">=</span> <span class="s1">&#39;receptor&#39;</span><span class="p">,</span>
+                        <span class="p">)</span>
+                    <span class="p">)</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">_class_definitions_provided</span> <span class="o">+=</span> <span class="nb">tuple</span><span class="p">(</span><span class="n">gpcrdb_categories</span><span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">add_surfaceome_categories</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="n">resep</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">compile</span><span class="p">(</span><span class="sa">r</span><span class="s1">&#39;[- /\(\),\.]+&#39;</span><span class="p">)</span>
+        <span class="n">recls</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">compile</span><span class="p">(</span><span class="sa">r</span><span class="s1">&#39;_(?:transporters|receptors|ion_channels)&#39;</span><span class="p">)</span>
+
+        <span class="n">mainclasses</span> <span class="o">=</span> <span class="p">{</span>
+            <span class="s1">&#39;Receptors&#39;</span><span class="p">:</span> <span class="s1">&#39;receptor&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;Transporters&#39;</span><span class="p">:</span> <span class="s1">&#39;transporter&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;Enzymes&#39;</span><span class="p">:</span> <span class="s1">&#39;surface_enzyme&#39;</span><span class="p">,</span>
+        <span class="p">}</span>
+
+        <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">_resource_categories</span><span class="p">[</span><span class="s1">&#39;surfaceome&#39;</span><span class="p">]:</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">ensure_annotdb</span><span class="p">()</span>
+            <span class="n">surfaceome</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">annotdb</span><span class="p">[</span><span class="s1">&#39;Surfaceome&#39;</span><span class="p">]</span>
+            <span class="n">surfaceome_categories</span> <span class="o">=</span> <span class="p">[]</span>
+
+            <span class="k">for</span> <span class="n">mainclass</span><span class="p">,</span> <span class="n">parent</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="n">mainclasses</span><span class="p">):</span>
+
+                <span class="n">subclasses</span> <span class="o">=</span> <span class="p">{</span>
+                    <span class="n">sc</span>
+                    <span class="k">for</span> <span class="n">annots</span> <span class="ow">in</span> <span class="n">surfaceome</span><span class="o">.</span><span class="n">annot</span><span class="o">.</span><span class="n">values</span><span class="p">()</span>
+                    <span class="k">for</span> <span class="n">a</span> <span class="ow">in</span> <span class="n">annots</span>
+                    <span class="k">for</span> <span class="n">sc</span> <span class="ow">in</span> <span class="p">(</span><span class="n">a</span><span class="o">.</span><span class="n">subclasses</span> <span class="ow">or</span> <span class="p">())</span>
+                    <span class="k">if</span> <span class="p">(</span>
+                        <span class="n">a</span><span class="o">.</span><span class="n">mainclass</span> <span class="o">==</span> <span class="n">mainclass</span> <span class="ow">and</span>
+                        <span class="n">sc</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span> <span class="ow">and</span>
+                        <span class="ow">not</span> <span class="n">sc</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">isdigit</span><span class="p">()</span>
+                    <span class="p">)</span>
+                <span class="p">}</span>
+
+                <span class="k">for</span> <span class="n">subclass</span> <span class="ow">in</span> <span class="n">subclasses</span><span class="p">:</span>
+
+                    <span class="k">if</span> <span class="n">subclass</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s1">&#39;Other&#39;</span><span class="p">):</span>
+
+                        <span class="k">continue</span>
+
+                    <span class="n">name</span> <span class="o">=</span> <span class="s1">&#39;</span><span class="si">%s</span><span class="s1">_</span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="p">(</span>
+                        <span class="n">resep</span><span class="o">.</span><span class="n">sub</span><span class="p">(</span><span class="s1">&#39;_&#39;</span><span class="p">,</span> <span class="n">subclass</span><span class="p">)</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span><span class="o">.</span><span class="n">strip</span><span class="p">(</span><span class="s1">&#39;_&#39;</span><span class="p">),</span>
+                        <span class="n">mainclass</span><span class="o">.</span><span class="n">lower</span><span class="p">(),</span>
+                    <span class="p">)</span>
+                    <span class="n">_parent</span> <span class="o">=</span> <span class="p">(</span>
+                        <span class="s1">&#39;ion_channel&#39;</span>
+                            <span class="k">if</span> <span class="s1">&#39;ion_channel&#39;</span> <span class="ow">in</span> <span class="n">name</span> <span class="k">else</span>
+                        <span class="n">parent</span>
+                    <span class="p">)</span>
+                    <span class="n">name</span> <span class="o">=</span> <span class="n">recls</span><span class="o">.</span><span class="n">sub</span><span class="p">(</span><span class="s1">&#39;&#39;</span><span class="p">,</span> <span class="n">name</span><span class="p">)</span>
+
+                    <span class="n">surfaceome_categories</span><span class="o">.</span><span class="n">append</span><span class="p">(</span>
+                        <span class="n">af</span><span class="o">.</span><span class="n">AnnotDef</span><span class="p">(</span>
+                            <span class="n">name</span> <span class="o">=</span> <span class="n">name</span><span class="p">,</span>
+                            <span class="n">resource</span> <span class="o">=</span> <span class="s1">&#39;Surfaceome&#39;</span><span class="p">,</span>
+                            <span class="n">args</span> <span class="o">=</span> <span class="p">{</span>
+                                <span class="s1">&#39;mainclass&#39;</span><span class="p">:</span> <span class="n">mainclass</span><span class="p">,</span>
+                                <span class="s1">&#39;subclasses&#39;</span><span class="p">:</span> <span class="n">subclass</span><span class="p">,</span>
+                            <span class="p">},</span>
+                            <span class="n">parent</span> <span class="o">=</span> <span class="n">_parent</span><span class="p">,</span>
+                        <span class="p">)</span>
+                    <span class="p">)</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">_class_definitions_provided</span> <span class="o">+=</span> <span class="nb">tuple</span><span class="p">(</span><span class="n">surfaceome_categories</span><span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">add_icellnet_categories</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="n">icellnet_categories</span> <span class="o">=</span> <span class="p">[]</span>
+
+        <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">_resource_categories</span><span class="p">[</span><span class="s1">&#39;icellnet&#39;</span><span class="p">]:</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">ensure_annotdb</span><span class="p">()</span>
+
+            <span class="n">icellnet</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">annotdb</span><span class="p">[</span><span class="s1">&#39;ICELLNET&#39;</span><span class="p">]</span>
+
+            <span class="n">names</span> <span class="o">=</span> <span class="n">icellnet</span><span class="o">.</span><span class="n">get_names</span><span class="p">()[:</span><span class="mi">3</span><span class="p">]</span>
+
+            <span class="n">combinations</span> <span class="o">=</span> <span class="p">{</span>
+                <span class="n">a</span><span class="p">[:</span><span class="mi">3</span><span class="p">]</span>
+                <span class="k">for</span> <span class="n">aa</span> <span class="ow">in</span> <span class="n">icellnet</span><span class="o">.</span><span class="n">annot</span><span class="o">.</span><span class="n">values</span><span class="p">()</span>
+                <span class="k">for</span> <span class="n">a</span> <span class="ow">in</span> <span class="n">aa</span>
+            <span class="p">}</span>
+
+            <span class="k">for</span> <span class="n">values</span> <span class="ow">in</span> <span class="n">combinations</span><span class="p">:</span>
+
+                <span class="k">for</span> <span class="n">l</span> <span class="ow">in</span> <span class="p">(</span><span class="mi">2</span><span class="p">,</span> <span class="mi">3</span><span class="p">):</span>
+
+                    <span class="n">_fields</span> <span class="o">=</span> <span class="n">names</span><span class="p">[:</span><span class="n">l</span><span class="p">]</span>
+                    <span class="n">_values</span> <span class="o">=</span> <span class="n">values</span><span class="p">[:</span><span class="n">l</span><span class="p">]</span>
+
+                    <span class="k">if</span> <span class="n">_values</span><span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
+
+                        <span class="k">continue</span>
+
+                    <span class="n">args</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">(</span><span class="nb">zip</span><span class="p">(</span><span class="n">_fields</span><span class="p">,</span> <span class="n">_values</span><span class="p">))</span>
+
+                    <span class="n">members</span> <span class="o">=</span> <span class="n">icellnet</span><span class="o">.</span><span class="n">select</span><span class="p">(</span><span class="o">**</span><span class="n">args</span><span class="p">)</span>
+
+                    <span class="k">if</span> <span class="ow">not</span> <span class="n">members</span><span class="p">:</span>
+
+                        <span class="k">continue</span>
+
+                    <span class="n">name</span> <span class="o">=</span> <span class="s1">&#39;_&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span>
+                        <span class="n">val</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s1">&#39;.&#39;</span><span class="p">,</span> <span class="s1">&#39;&#39;</span><span class="p">)</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s1">&#39; &#39;</span><span class="p">,</span> <span class="s1">&#39;_&#39;</span><span class="p">)</span>
+                        <span class="k">for</span> <span class="n">val</span> <span class="ow">in</span> <span class="n">_values</span><span class="p">[</span><span class="mi">1</span><span class="p">:]</span>
+                        <span class="k">if</span> <span class="n">val</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span>
+                    <span class="p">)</span>
+
+                    <span class="n">icellnet_categories</span><span class="o">.</span><span class="n">append</span><span class="p">(</span>
+                        <span class="n">af</span><span class="o">.</span><span class="n">AnnotDef</span><span class="p">(</span>
+                            <span class="n">name</span> <span class="o">=</span> <span class="n">name</span><span class="p">,</span>
+                            <span class="n">resource</span> <span class="o">=</span> <span class="s1">&#39;ICELLNET&#39;</span><span class="p">,</span>
+                            <span class="n">args</span> <span class="o">=</span> <span class="n">args</span><span class="p">,</span>
+                            <span class="n">parent</span> <span class="o">=</span> <span class="n">values</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span>
+                        <span class="p">)</span>
+                    <span class="p">)</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">_class_definitions_provided</span> <span class="o">+=</span> <span class="nb">tuple</span><span class="p">(</span><span class="n">icellnet_categories</span><span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">post_load</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">make_df</span><span class="p">()</span>
+
+
+    <span class="k">def</span> <span class="fm">__repr__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="p">(</span>
+            <span class="s1">&#39;&lt;Intercell annotations: </span><span class="si">%s</span><span class="s1"> records about </span><span class="si">%s</span><span class="s1"> entities&gt;&#39;</span> <span class="o">%</span> <span class="p">(</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">numof_records</span><span class="p">(),</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">numof_entities</span><span class="p">(),</span>
+            <span class="p">)</span>
+        <span class="p">)</span>
+
+
+    <span class="nd">@classmethod</span>
+    <span class="k">def</span> <span class="nf">filter_df</span><span class="p">(</span>
+            <span class="bp">cls</span><span class="p">,</span>
+            <span class="n">annot_df</span><span class="p">,</span>
+            <span class="n">category</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">name</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">parent</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">database</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">scope</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">aspect</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">source</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">entities</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">entity_type</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">causality</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">topology</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">postfix</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+        <span class="p">):</span>
+
+        <span class="n">category</span> <span class="o">=</span> <span class="n">category</span> <span class="ow">or</span> <span class="n">name</span>
+        <span class="n">args</span> <span class="o">=</span> <span class="nb">locals</span><span class="p">()</span>
+
+        <span class="n">_topologies</span> <span class="o">=</span> <span class="p">{</span>
+            <span class="s1">&#39;pmtm&#39;</span><span class="p">:</span> <span class="s1">&#39;plasma_membrane_transmembrane&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;pmp&#39;</span><span class="p">:</span> <span class="s1">&#39;plasma_membrane_peripheral&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;sec&#39;</span><span class="p">:</span> <span class="s1">&#39;secreted&#39;</span><span class="p">,</span>
+        <span class="p">}</span>
+
+        <span class="n">entities</span> <span class="o">=</span> <span class="n">args</span><span class="o">.</span><span class="n">pop</span><span class="p">(</span><span class="s1">&#39;entities&#39;</span><span class="p">)</span>
+        <span class="n">causality</span> <span class="o">=</span> <span class="n">args</span><span class="o">.</span><span class="n">pop</span><span class="p">(</span><span class="s1">&#39;causality&#39;</span><span class="p">)</span> <span class="ow">or</span> <span class="p">()</span>
+        <span class="n">topology</span> <span class="o">=</span> <span class="n">args</span><span class="o">.</span><span class="n">pop</span><span class="p">(</span><span class="s1">&#39;topology&#39;</span><span class="p">)</span> <span class="ow">or</span> <span class="p">()</span>
+
+        <span class="n">topology</span> <span class="o">=</span> <span class="p">[</span>
+            <span class="n">_topologies</span><span class="p">[</span><span class="n">top</span><span class="p">]</span> <span class="k">if</span> <span class="n">top</span> <span class="ow">in</span> <span class="n">_topologies</span> <span class="k">else</span> <span class="n">top</span>
+            <span class="k">for</span> <span class="n">top</span> <span class="ow">in</span> <span class="n">common</span><span class="o">.</span><span class="n">to_set</span><span class="p">(</span><span class="n">topology</span><span class="p">)</span>
+        <span class="p">]</span>
+
+        <span class="n">query</span> <span class="o">=</span> <span class="bp">cls</span><span class="o">.</span><span class="n">_process_query_args</span><span class="p">(</span>
+            <span class="n">df</span> <span class="o">=</span> <span class="n">annot_df</span><span class="p">,</span>
+            <span class="n">entities</span> <span class="o">=</span> <span class="n">entities</span><span class="p">,</span>
+            <span class="n">args</span> <span class="o">=</span> <span class="n">args</span><span class="p">,</span>
+            <span class="n">postfix</span> <span class="o">=</span> <span class="n">postfix</span><span class="p">,</span>
+        <span class="p">)</span>
+
+        <span class="k">if</span> <span class="n">causality</span><span class="p">:</span>
+
+            <span class="n">query</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="bp">cls</span><span class="o">.</span><span class="n">_process_boolean_group_args</span><span class="p">(</span><span class="n">causality</span><span class="p">,</span> <span class="n">postfix</span><span class="p">))</span>
+
+        <span class="k">if</span> <span class="n">topology</span><span class="p">:</span>
+
+            <span class="n">query</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="bp">cls</span><span class="o">.</span><span class="n">_process_boolean_group_args</span><span class="p">(</span><span class="n">topology</span><span class="p">,</span> <span class="n">postfix</span><span class="p">))</span>
+
+        <span class="n">args</span> <span class="o">=</span> <span class="bp">cls</span><span class="o">.</span><span class="n">_args_add_postfix</span><span class="p">(</span><span class="n">args</span><span class="p">,</span> <span class="n">postfix</span><span class="p">)</span>
+
+        <span class="n">query</span> <span class="o">=</span> <span class="s1">&#39; and &#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">query</span><span class="p">)</span>
+
+        <span class="k">return</span> <span class="n">annot_df</span><span class="o">.</span><span class="n">query</span><span class="p">(</span><span class="n">query</span><span class="p">)</span> <span class="k">if</span> <span class="n">query</span> <span class="k">else</span> <span class="n">annot_df</span>
+
+
+    <span class="nd">@staticmethod</span>
+    <span class="k">def</span> <span class="nf">_process_boolean_group_args</span><span class="p">(</span><span class="n">values</span><span class="p">,</span> <span class="n">postfix</span><span class="p">):</span>
+
+        <span class="k">if</span> <span class="n">postfix</span><span class="p">:</span>
+
+            <span class="n">values</span> <span class="o">=</span> <span class="p">{</span>
+                <span class="s1">&#39;</span><span class="si">%s%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="p">(</span><span class="n">val</span><span class="p">,</span> <span class="n">postfix</span><span class="p">)</span>
+                <span class="k">for</span> <span class="n">val</span> <span class="ow">in</span> <span class="n">common</span><span class="o">.</span><span class="n">to_list</span><span class="p">(</span><span class="n">values</span><span class="p">)</span>
+            <span class="p">}</span>
+
+        <span class="k">return</span> <span class="s1">&#39; or &#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">common</span><span class="o">.</span><span class="n">to_set</span><span class="p">(</span><span class="n">values</span><span class="p">))</span>
+
+
+<div class="viewcode-block" id="IntercellAnnotation.network_df">
+<a class="viewcode-back" href="../../../api/pypath.core.intercell.IntercellAnnotation.html#pypath.core.intercell.IntercellAnnotation.network_df">[docs]</a>
+    <span class="k">def</span> <span class="nf">network_df</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">annot_df</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">network</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">combined_df</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">network_args</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">annot_args</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">annot_args_source</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">annot_args_target</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">entities</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">only_directed</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+            <span class="n">only_undirected</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+            <span class="n">undirected_orientation</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">only_signed</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">only_effect</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">only_proteins</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+            <span class="n">swap_undirected</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
+            <span class="n">entities_or</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+            <span class="n">transmitter_receiver</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+            <span class="n">only_generic</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
+            <span class="n">only_composite</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
+            <span class="n">only_functional</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
+            <span class="n">exclude_intracellular</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
+        <span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Combines the annotation data frame and a network data frame.</span>
+<span class="sd">        Creates a ``pandas.DataFrame`` where each record is an interaction</span>
+<span class="sd">        between a pair of molecular enitities labeled by their annotations.</span>
+
+<span class="sd">        network : pypath.network.Network,pandas.DataFrame</span>
+<span class="sd">            A ``pypath.network.Network`` object or a data frame with network</span>
+<span class="sd">            data.</span>
+<span class="sd">        combined_df : pandas.DataFrame</span>
+<span class="sd">            Optional, a network data frame already combined with annotations</span>
+<span class="sd">            for filtering only.</span>
+<span class="sd">        resources : set,None</span>
+<span class="sd">            Use only these network resources.</span>
+<span class="sd">        entities : set,None</span>
+<span class="sd">            Limit the network only to these molecular entities.</span>
+<span class="sd">        entities_source : set,None</span>
+<span class="sd">            Limit the source side of network connections only to these</span>
+<span class="sd">            molecular entities.</span>
+<span class="sd">        entities_target : set,None</span>
+<span class="sd">            Limit the target side of network connections only to these</span>
+<span class="sd">            molecular entities.</span>
+<span class="sd">        annot_args : dict,None</span>
+<span class="sd">            Parameters for filtering annotation classes; note, the defaults</span>
+<span class="sd">            might include some filtering, provide an empty dict if you want</span>
+<span class="sd">            no filtering at all; however this might result in huge data</span>
+<span class="sd">            frame and consequently memory issues. Passed to the ``filtered``</span>
+<span class="sd">            method.</span>
+<span class="sd">        annot_args_source : dict,None</span>
+<span class="sd">            Same as ``annot_args`` but only for the source side of the</span>
+<span class="sd">            network connections.</span>
+<span class="sd">        annot_args_target : dict,None</span>
+<span class="sd">            Same as ``annot_args`` but only for the target side of the</span>
+<span class="sd">            network connections.</span>
+<span class="sd">        only_directed : bool</span>
+<span class="sd">            Use only the directed interactions.</span>
+<span class="sd">        only_undirected : bool</span>
+<span class="sd">            Use only the undirected interactions. Specifically for retrieving</span>
+<span class="sd">            and counting the interactions without direction information.</span>
+<span class="sd">        undirected_orientation : str,None</span>
+<span class="sd">            Ignore the direction at all interactions and make sure all of</span>
+<span class="sd">            them have a uniform orientation. If `id`, all interactions will</span>
+<span class="sd">            be oriented by the identifiers of the partenrs; if `category`,</span>
+<span class="sd">            the interactions will be oriented by the categories of the</span>
+<span class="sd">            partners.</span>
+<span class="sd">        only_effect : int,None</span>
+<span class="sd">            Use only the interactions with this effect. Either -1 or 1.</span>
+<span class="sd">        only_signed : bool</span>
+<span class="sd">            Use only the interactions with effect sign.</span>
+<span class="sd">        only_proteins : bool</span>
+<span class="sd">            Use only the interactions where each of the partners is a protein</span>
+<span class="sd">            (i.e. not complex, miRNA, small molecule or other kind of entity).</span>
+<span class="sd">        transmitter_receiver : bool</span>
+<span class="sd">            On the source side only transmitters, on the target side only</span>
+<span class="sd">            receivers.</span>
+<span class="sd">        only_generic : bool</span>
+<span class="sd">            Use only the generic classes. If specific classes allowed the</span>
+<span class="sd">            size of the combined data frame might be huge.</span>
+<span class="sd">        only_composite : bool</span>
+<span class="sd">            Use only the composite classes. If resource_specific classes</span>
+<span class="sd">            allowed the size of the combined data frame might be huge.</span>
+<span class="sd">        only_functional : bool</span>
+<span class="sd">            Use only the functional classes. Locational classes are often</span>
+<span class="sd">            not relevant and they largely increase the size of the</span>
+<span class="sd">            combined data frame.</span>
+<span class="sd">        exclude_intracellular : bool</span>
+<span class="sd">            Remove the intracellular parent class and it&#39;s children. These</span>
+<span class="sd">            classes are not relevant in intercellular signaling and having</span>
+<span class="sd">            them largely increases the size of the combined data frame.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">annot_df</span> <span class="o">=</span> <span class="n">annot_df</span> <span class="ow">or</span> <span class="bp">self</span><span class="o">.</span><span class="n">get_df</span><span class="p">()</span>
+
+        <span class="k">if</span> <span class="n">exclude_intracellular</span><span class="p">:</span>
+
+            <span class="k">if</span> <span class="n">combined_df</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
+
+                <span class="n">annot_df</span> <span class="o">=</span> <span class="n">annot_df</span><span class="p">[</span><span class="n">annot_df</span><span class="o">.</span><span class="n">parent</span> <span class="o">!=</span> <span class="s1">&#39;intracellular&#39;</span><span class="p">]</span>
+
+            <span class="k">else</span><span class="p">:</span>
+
+                <span class="n">combined_df</span> <span class="o">=</span> <span class="n">combined_df</span><span class="o">.</span><span class="n">query</span><span class="p">(</span>
+                    <span class="s1">&#39;parent_a != &quot;intracellular&quot; and &#39;</span>
+                    <span class="s1">&#39;parent_b != &quot;intracellular&quot;&#39;</span>
+                <span class="p">)</span>
+
+        <span class="n">annot_args</span> <span class="o">=</span> <span class="n">annot_args</span> <span class="ow">or</span> <span class="p">{}</span>
+        <span class="n">annot_args_source</span> <span class="o">=</span> <span class="n">annot_args_source</span> <span class="ow">or</span> <span class="p">{}</span>
+        <span class="n">annot_args_target</span> <span class="o">=</span> <span class="n">annot_args_target</span> <span class="ow">or</span> <span class="p">{}</span>
+
+        <span class="k">if</span> <span class="n">only_generic</span><span class="p">:</span>
+
+            <span class="n">annot_args</span><span class="p">[</span><span class="s1">&#39;scope&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="s1">&#39;generic&#39;</span>
+
+        <span class="k">if</span> <span class="n">only_composite</span><span class="p">:</span>
+
+            <span class="n">annot_args</span><span class="p">[</span><span class="s1">&#39;source&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="s1">&#39;composite&#39;</span>
+
+        <span class="k">if</span> <span class="n">only_functional</span><span class="p">:</span>
+
+            <span class="n">annot_args</span><span class="p">[</span><span class="s1">&#39;aspect&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="s1">&#39;functional&#39;</span>
+
+        <span class="k">if</span> <span class="n">transmitter_receiver</span><span class="p">:</span>
+
+            <span class="n">annot_args_source</span><span class="p">[</span><span class="s1">&#39;causality&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="s1">&#39;transmitter&#39;</span>
+            <span class="n">annot_args_target</span><span class="p">[</span><span class="s1">&#39;causality&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="s1">&#39;receiver&#39;</span>
+
+        <span class="k">return</span> <span class="n">annot</span><span class="o">.</span><span class="n">CustomAnnotation</span><span class="o">.</span><span class="n">network_df</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">annot_df</span> <span class="o">=</span> <span class="n">annot_df</span><span class="p">,</span>
+            <span class="n">network</span> <span class="o">=</span> <span class="n">network</span><span class="p">,</span>
+            <span class="n">combined_df</span> <span class="o">=</span> <span class="n">combined_df</span><span class="p">,</span>
+            <span class="n">network_args</span> <span class="o">=</span> <span class="n">network_args</span><span class="p">,</span>
+            <span class="n">annot_args</span> <span class="o">=</span> <span class="n">annot_args</span><span class="p">,</span>
+            <span class="n">annot_args_source</span> <span class="o">=</span> <span class="n">annot_args_source</span><span class="p">,</span>
+            <span class="n">annot_args_target</span> <span class="o">=</span> <span class="n">annot_args_target</span><span class="p">,</span>
+            <span class="n">entities</span> <span class="o">=</span> <span class="n">entities</span><span class="p">,</span>
+            <span class="n">only_directed</span> <span class="o">=</span> <span class="n">only_directed</span><span class="p">,</span>
+            <span class="n">only_undirected</span> <span class="o">=</span> <span class="n">only_undirected</span><span class="p">,</span>
+            <span class="n">only_signed</span> <span class="o">=</span> <span class="n">only_signed</span><span class="p">,</span>
+            <span class="n">only_effect</span> <span class="o">=</span> <span class="n">only_effect</span><span class="p">,</span>
+            <span class="n">only_proteins</span> <span class="o">=</span> <span class="n">only_proteins</span><span class="p">,</span>
+            <span class="n">swap_undirected</span> <span class="o">=</span> <span class="n">swap_undirected</span><span class="p">,</span>
+            <span class="n">entities_or</span> <span class="o">=</span> <span class="n">entities_or</span><span class="p">,</span>
+            <span class="n">undirected_orientation</span> <span class="o">=</span> <span class="n">undirected_orientation</span><span class="p">,</span>
+        <span class="p">)</span></div>
+
+
+
+    <span class="c1"># this became a synonym</span>
+    <span class="n">filter_interclass_network</span> <span class="o">=</span> <span class="n">network_df</span>
+
+
+    <span class="k">def</span> <span class="nf">update_summaries</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">summaries</span> <span class="o">=</span> <span class="p">{}</span>
+
+        <span class="k">for</span> <span class="n">key</span><span class="p">,</span> <span class="n">group</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">classes</span><span class="p">):</span>
+
+            <span class="k">if</span> <span class="n">group</span><span class="o">.</span><span class="n">source</span> <span class="o">==</span> <span class="s1">&#39;resource_specific&#39;</span><span class="p">:</span>
+
+                <span class="k">continue</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">summaries</span><span class="p">[</span><span class="n">key</span><span class="p">]</span> <span class="o">=</span> <span class="p">{</span>
+                <span class="s1">&#39;name&#39;</span><span class="p">:</span> <span class="n">group</span><span class="o">.</span><span class="n">name</span><span class="p">,</span>
+                <span class="s1">&#39;aspect&#39;</span><span class="p">:</span> <span class="n">group</span><span class="o">.</span><span class="n">aspect</span><span class="p">,</span>
+                <span class="s1">&#39;transmitter&#39;</span><span class="p">:</span> <span class="n">group</span><span class="o">.</span><span class="n">transmitter</span><span class="p">,</span>
+                <span class="s1">&#39;receiver&#39;</span><span class="p">:</span> <span class="n">group</span><span class="o">.</span><span class="n">receiver</span><span class="p">,</span>
+                <span class="s1">&#39;resources&#39;</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">resources_in_category</span><span class="p">(</span><span class="n">key</span><span class="p">),</span>
+                <span class="s1">&#39;n_proteins&#39;</span><span class="p">:</span> <span class="n">group</span><span class="o">.</span><span class="n">n_proteins</span><span class="p">,</span>
+                <span class="s1">&#39;n_mirnas&#39;</span><span class="p">:</span> <span class="n">group</span><span class="o">.</span><span class="n">n_mirnas</span><span class="p">,</span>
+                <span class="s1">&#39;n_complexes&#39;</span><span class="p">:</span> <span class="n">group</span><span class="o">.</span><span class="n">n_complexes</span><span class="p">,</span>
+            <span class="p">}</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">summaries</span><span class="p">[(</span><span class="s1">&#39;Total&#39;</span><span class="p">,</span> <span class="s1">&#39;Total&#39;</span><span class="p">,</span> <span class="s1">&#39;OmniPath&#39;</span><span class="p">)]</span> <span class="o">=</span> <span class="p">{</span>
+            <span class="s1">&#39;name&#39;</span><span class="p">:</span> <span class="s1">&#39;Total&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;aspect&#39;</span><span class="p">:</span> <span class="s1">&#39;&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;transmitter&#39;</span><span class="p">:</span> <span class="s1">&#39;&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;receiver&#39;</span><span class="p">:</span> <span class="s1">&#39;&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;resources&#39;</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">all_resources</span><span class="p">(),</span>
+            <span class="s1">&#39;n_proteins&#39;</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">numof_proteins</span><span class="p">(),</span>
+            <span class="s1">&#39;n_mirnas&#39;</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">numof_mirnas</span><span class="p">(),</span>
+            <span class="s1">&#39;n_complexes&#39;</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">numof_complexes</span><span class="p">(),</span>
+        <span class="p">}</span>
+
+
+    <span class="k">def</span> <span class="nf">summaries_tab</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">outfile</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span> <span class="n">return_table</span> <span class="o">=</span> <span class="kc">False</span><span class="p">):</span>
+
+        <span class="n">columns</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="p">(</span><span class="s1">&#39;name&#39;</span><span class="p">,</span> <span class="s1">&#39;Category&#39;</span><span class="p">),</span>
+            <span class="p">(</span><span class="s1">&#39;aspect&#39;</span><span class="p">,</span> <span class="s1">&#39;Aspect&#39;</span><span class="p">),</span>
+            <span class="p">(</span><span class="s1">&#39;transmitter&#39;</span><span class="p">,</span> <span class="s1">&#39;Transmitter&#39;</span><span class="p">),</span>
+            <span class="p">(</span><span class="s1">&#39;receiver&#39;</span><span class="p">,</span> <span class="s1">&#39;Receiver&#39;</span><span class="p">),</span>
+            <span class="p">(</span><span class="s1">&#39;n_proteins&#39;</span><span class="p">,</span> <span class="s1">&#39;Proteins&#39;</span><span class="p">),</span>
+            <span class="p">(</span><span class="s1">&#39;n_mirnas&#39;</span><span class="p">,</span> <span class="s1">&#39;miRNAs&#39;</span><span class="p">),</span>
+            <span class="p">(</span><span class="s1">&#39;n_complexes&#39;</span><span class="p">,</span> <span class="s1">&#39;Complexes&#39;</span><span class="p">),</span>
+            <span class="p">(</span><span class="s1">&#39;resources&#39;</span><span class="p">,</span> <span class="s1">&#39;Resources&#39;</span><span class="p">),</span>
+        <span class="p">)</span>
+
+        <span class="n">tab</span> <span class="o">=</span> <span class="p">[]</span>
+        <span class="n">tab</span><span class="o">.</span><span class="n">append</span><span class="p">([</span><span class="n">f</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="k">for</span> <span class="n">f</span> <span class="ow">in</span> <span class="n">columns</span><span class="p">])</span>
+
+        <span class="n">tab</span><span class="o">.</span><span class="n">extend</span><span class="p">([</span>
+            <span class="p">[</span>
+                <span class="p">(</span>
+                    <span class="s1">&#39;, &#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">summaries</span><span class="p">[</span><span class="n">key</span><span class="p">][</span><span class="n">f</span><span class="p">[</span><span class="mi">0</span><span class="p">]])</span>
+                        <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">summaries</span><span class="p">[</span><span class="n">key</span><span class="p">][</span><span class="n">f</span><span class="p">[</span><span class="mi">0</span><span class="p">]],</span> <span class="nb">list</span><span class="p">)</span> <span class="k">else</span>
+                    <span class="nb">str</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">summaries</span><span class="p">[</span><span class="n">key</span><span class="p">][</span><span class="n">f</span><span class="p">[</span><span class="mi">0</span><span class="p">]])</span>
+                <span class="p">)</span>
+                <span class="k">for</span> <span class="n">f</span> <span class="ow">in</span> <span class="n">columns</span>
+            <span class="p">]</span>
+            <span class="k">for</span> <span class="n">key</span> <span class="ow">in</span> <span class="nb">sorted</span><span class="p">(</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">summaries</span><span class="o">.</span><span class="n">keys</span><span class="p">(),</span>
+                <span class="n">key</span> <span class="o">=</span> <span class="k">lambda</span> <span class="n">k</span><span class="p">:</span> <span class="n">k</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="k">if</span> <span class="n">k</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">!=</span> <span class="s1">&#39;Total&#39;</span> <span class="k">else</span> <span class="s1">&#39;zzzz&#39;</span><span class="p">,</span>
+            <span class="p">)</span>
+        <span class="p">])</span>
+
+        <span class="k">if</span> <span class="n">outfile</span><span class="p">:</span>
+
+            <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">outfile</span><span class="p">,</span> <span class="s1">&#39;w&#39;</span><span class="p">)</span> <span class="k">as</span> <span class="n">fp</span><span class="p">:</span>
+
+                <span class="n">fp</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\n</span><span class="s1">&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\t</span><span class="s1">&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">row</span><span class="p">)</span> <span class="k">for</span> <span class="n">row</span> <span class="ow">in</span> <span class="n">tab</span><span class="p">))</span>
+
+        <span class="k">if</span> <span class="n">return_table</span><span class="p">:</span>
+
+            <span class="k">return</span> <span class="n">tab</span></div>
+
+
+
+<div class="viewcode-block" id="init_db">
+<a class="viewcode-back" href="../../../api/pypath.core.intercell.init_db.html#pypath.core.intercell.init_db">[docs]</a>
+<span class="k">def</span> <span class="nf">init_db</span><span class="p">(</span><span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+
+    <span class="nb">globals</span><span class="p">()[</span><span class="s1">&#39;db&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">IntercellAnnotation</span><span class="p">(</span><span class="o">**</span><span class="n">kwargs</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="get_db">
+<a class="viewcode-back" href="../../../api/pypath.core.intercell.get_db.html#pypath.core.intercell.get_db">[docs]</a>
+<span class="k">def</span> <span class="nf">get_db</span><span class="p">(</span><span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+
+    <span class="k">if</span> <span class="s1">&#39;db&#39;</span> <span class="ow">not</span> <span class="ow">in</span> <span class="nb">globals</span><span class="p">():</span>
+
+        <span class="n">init_db</span><span class="p">(</span><span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
+
+    <span class="k">return</span> <span class="nb">globals</span><span class="p">()[</span><span class="s1">&#39;db&#39;</span><span class="p">]</span></div>
+
+</pre></div>
+
+                </article>
+              
+              
+              
+              
+              
+                <footer class="prev-next-footer">
+                  
+<div class="prev-next-area">
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diff --git a/_modules/pypath/core/network.html b/_modules/pypath/core/network.html
new file mode 100644
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@@ -0,0 +1,5539 @@
+
+<!DOCTYPE html>
+
+
+<html lang="en" data-content_root="../../../" >
+
+  <head>
+    <meta charset="utf-8" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+    <title>pypath.core.network &#8212; pypath 0.16.9 documentation</title>
+  
+  
+  
+  <script data-cfasync="false">
+    document.documentElement.dataset.mode = localStorage.getItem("mode") || "";
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+                  
+  <h1>Source code for pypath.core.network</h1><div class="highlight"><pre>
+<span></span><span class="ch">#!/usr/bin/env python</span>
+<span class="c1"># -*- coding: utf-8 -*-</span>
+
+<span class="c1">#</span>
+<span class="c1">#  This file is part of the `pypath` python module</span>
+<span class="c1">#</span>
+<span class="c1">#  Copyright 2014-2023</span>
+<span class="c1">#  EMBL, EMBL-EBI, Uniklinik RWTH Aachen, Heidelberg University</span>
+<span class="c1">#</span>
+<span class="c1">#  Authors: see the file `README.rst`</span>
+<span class="c1">#  Contact: Dénes Türei (turei.denes@gmail.com)</span>
+<span class="c1">#</span>
+<span class="c1">#  Distributed under the GPLv3 License.</span>
+<span class="c1">#  See accompanying file LICENSE.txt or copy at</span>
+<span class="c1">#      https://www.gnu.org/licenses/gpl-3.0.html</span>
+<span class="c1">#</span>
+<span class="c1">#  Website: https://pypath.omnipathdb.org/</span>
+<span class="c1">#</span>
+
+<span class="kn">from</span> <span class="nn">__future__</span> <span class="kn">import</span> <span class="n">annotations</span>
+
+<span class="kn">from</span> <span class="nn">future.utils</span> <span class="kn">import</span> <span class="n">iteritems</span>
+
+<span class="kn">from</span> <span class="nn">typing</span> <span class="kn">import</span> <span class="n">Mapping</span>
+
+<span class="kn">import</span> <span class="nn">importlib</span> <span class="k">as</span> <span class="nn">imp</span>
+<span class="kn">import</span> <span class="nn">re</span>
+<span class="kn">import</span> <span class="nn">os</span>
+<span class="kn">import</span> <span class="nn">sys</span>
+<span class="kn">import</span> <span class="nn">collections</span>
+<span class="kn">import</span> <span class="nn">itertools</span>
+<span class="kn">import</span> <span class="nn">functools</span>
+<span class="kn">import</span> <span class="nn">copy</span> <span class="k">as</span> <span class="nn">copy_mod</span>
+<span class="kn">import</span> <span class="nn">pickle</span>
+<span class="kn">import</span> <span class="nn">random</span>
+<span class="kn">import</span> <span class="nn">traceback</span>
+<span class="kn">from</span> <span class="nn">typing_extensions</span> <span class="kn">import</span> <span class="n">Literal</span>
+
+<span class="kn">import</span> <span class="nn">numpy</span> <span class="k">as</span> <span class="nn">np</span>
+<span class="kn">import</span> <span class="nn">pandas</span> <span class="k">as</span> <span class="nn">pd</span>
+
+<span class="kn">import</span> <span class="nn">pypath.share.session</span> <span class="k">as</span> <span class="nn">session_mod</span>
+<span class="kn">import</span> <span class="nn">pypath.share.progress</span> <span class="k">as</span> <span class="nn">progress</span>
+<span class="kn">import</span> <span class="nn">pypath.core.interaction</span> <span class="k">as</span> <span class="nn">interaction_mod</span>
+<span class="kn">import</span> <span class="nn">pypath.core.evidence</span> <span class="k">as</span> <span class="nn">evidence</span>
+<span class="kn">import</span> <span class="nn">pypath.core.entity</span> <span class="k">as</span> <span class="nn">entity_mod</span>
+<span class="kn">import</span> <span class="nn">pypath.core.common</span> <span class="k">as</span> <span class="nn">core_common</span>
+<span class="kn">import</span> <span class="nn">pypath.share.common</span> <span class="k">as</span> <span class="nn">common</span>
+<span class="kn">import</span> <span class="nn">pypath_common._constants</span> <span class="k">as</span> <span class="nn">_const</span>
+<span class="kn">import</span> <span class="nn">pypath.share.settings</span> <span class="k">as</span> <span class="nn">settings</span>
+<span class="kn">import</span> <span class="nn">pypath.share.cache</span> <span class="k">as</span> <span class="nn">cache_mod</span>
+<span class="kn">import</span> <span class="nn">pypath.utils.mapping</span> <span class="k">as</span> <span class="nn">mapping</span>
+<span class="kn">import</span> <span class="nn">pypath.inputs.pubmed</span> <span class="k">as</span> <span class="nn">pubmed_input</span>
+<span class="kn">import</span> <span class="nn">pypath.share.curl</span> <span class="k">as</span> <span class="nn">curl</span>
+<span class="kn">import</span> <span class="nn">pypath.internals.refs</span> <span class="k">as</span> <span class="nn">refs_mod</span>
+<span class="kn">import</span> <span class="nn">pypath.internals.resource</span> <span class="k">as</span> <span class="nn">resource_mod</span>
+<span class="kn">import</span> <span class="nn">pypath.utils.reflists</span> <span class="k">as</span> <span class="nn">reflists</span>
+<span class="kn">import</span> <span class="nn">pypath.resources.network</span> <span class="k">as</span> <span class="nn">network_resources</span>
+<span class="kn">import</span> <span class="nn">pypath.inputs</span> <span class="k">as</span> <span class="nn">inputs</span>
+
+<span class="c1"># Py 2/3</span>
+<span class="k">try</span><span class="p">:</span>
+    <span class="nb">input</span> <span class="o">=</span> <span class="n">raw_input</span>
+<span class="k">except</span> <span class="ne">NameError</span><span class="p">:</span>
+    <span class="k">pass</span>
+
+<span class="n">NetworkEntityCollection</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">namedtuple</span><span class="p">(</span>
+    <span class="s1">&#39;NetworkEntityCollection&#39;</span><span class="p">,</span>
+    <span class="p">[</span>
+        <span class="s1">&#39;total&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;by_resource&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;by_category&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;shared&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;unique&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;shared_res_cat&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;unique_res_cat&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;shared_cat&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;unique_cat&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;resource_cat&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;cat_resource&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;method&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;label&#39;</span><span class="p">,</span>
+    <span class="p">],</span>
+<span class="p">)</span>
+<span class="n">NetworkEntityCollection</span><span class="o">.</span><span class="fm">__new__</span><span class="o">.</span><span class="vm">__defaults__</span> <span class="o">=</span> <span class="p">(</span><span class="kc">None</span><span class="p">,)</span> <span class="o">*</span> <span class="mi">8</span>
+
+
+<div class="viewcode-block" id="NetworkEntityCollection">
+<a class="viewcode-back" href="../../../api/pypath.core.network.NetworkEntityCollection.html#pypath.core.network.NetworkEntityCollection">[docs]</a>
+<span class="k">class</span> <span class="nc">NetworkEntityCollection</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span>
+
+    <span class="vm">__slots__</span> <span class="o">=</span> <span class="p">[</span>
+        <span class="s1">&#39;collection&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;_collection&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;label&#39;</span><span class="p">,</span>
+
+        <span class="s1">&#39;shared_within_data_model&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;unique_within_data_model&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;shared_within_interaction_type&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;unique_within_interaction_type&#39;</span><span class="p">,</span>
+
+        <span class="s1">&#39;n_collection&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;n_shared_within_data_model&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;n_unique_within_data_model&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;n_shared_within_interaction_type&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;n_unique_within_interaction_type&#39;</span><span class="p">,</span>
+
+        <span class="s1">&#39;pct_collection&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;pct_within_data_model&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;pct_within_interaction_type&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;pct_shared_within_data_model&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;pct_unique_within_data_model&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;pct_shared_within_interaction_type&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;pct_unique_within_interaction_type&#39;</span><span class="p">,</span>
+
+        <span class="s1">&#39;by_data_model&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;by_interaction_type&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;unique_by_data_model&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;shared_by_data_model&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;unique_by_interaction_type&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;shared_by_interaction_type&#39;</span><span class="p">,</span>
+
+        <span class="s1">&#39;n_by_data_model&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;n_by_interaction_type&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;n_unique_by_data_model&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;n_shared_by_data_model&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;n_unique_by_interaction_type&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;n_shared_by_interaction_type&#39;</span><span class="p">,</span>
+
+        <span class="s1">&#39;pct_by_data_model&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;pct_by_interaction_type&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;pct_unique_by_data_model&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;pct_shared_by_data_model&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;pct_unique_by_interaction_type&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;pct_shared_by_interaction_type&#39;</span><span class="p">,</span>
+
+    <span class="p">]</span>
+
+
+<div class="viewcode-block" id="NetworkEntityCollection.__init__">
+<a class="viewcode-back" href="../../../api/pypath.core.network.NetworkEntityCollection.html#pypath.core.network.NetworkEntityCollection.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">collection</span><span class="p">,</span> <span class="n">label</span> <span class="o">=</span> <span class="kc">None</span><span class="p">):</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">collection</span> <span class="o">=</span> <span class="n">collection</span><span class="o">.</span><span class="n">copy</span><span class="p">()</span>
+        <span class="c1"># we need a copy where we don&#39;t add the totals</span>
+        <span class="c1"># so these don&#39;t bother the shared and unique methods</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">_collection</span> <span class="o">=</span> <span class="n">collection</span><span class="o">.</span><span class="n">copy</span><span class="p">()</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">label</span> <span class="o">=</span> <span class="n">label</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">main</span><span class="p">()</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">main</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">setup</span><span class="p">()</span>
+
+
+    <span class="k">def</span> <span class="nf">setup</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">update</span><span class="p">()</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">collection_add_total</span><span class="p">()</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">update_collection_counts</span><span class="p">()</span>
+
+
+    <span class="k">def</span> <span class="nf">update_collection_counts</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">n_collection</span> <span class="o">=</span> <span class="n">common</span><span class="o">.</span><span class="n">dict_counts</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">collection</span><span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">pct_collection</span> <span class="o">=</span> <span class="n">common</span><span class="o">.</span><span class="n">dict_set_percent</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">collection</span><span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">collection_add_total</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">collection</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_add_total</span><span class="p">(</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">collection</span><span class="p">,</span>
+            <span class="n">key</span> <span class="o">=</span> <span class="p">(</span><span class="s1">&#39;all&#39;</span><span class="p">,</span> <span class="s1">&#39;all&#39;</span><span class="p">,</span> <span class="s1">&#39;Total&#39;</span><span class="p">)</span>
+        <span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">update</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">for</span> <span class="n">level</span> <span class="ow">in</span> <span class="p">(</span><span class="s1">&#39;interaction_type&#39;</span><span class="p">,</span> <span class="s1">&#39;data_model&#39;</span><span class="p">):</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">_update</span><span class="p">(</span><span class="n">level</span> <span class="o">=</span> <span class="n">level</span><span class="p">)</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">_update</span><span class="p">(</span><span class="n">level</span> <span class="o">=</span> <span class="n">level</span><span class="p">,</span> <span class="n">summarize_groups</span> <span class="o">=</span> <span class="kc">True</span><span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">_update</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">level</span><span class="p">,</span> <span class="n">summarize_groups</span> <span class="o">=</span> <span class="kc">False</span><span class="p">):</span>
+
+        <span class="n">midpart</span> <span class="o">=</span> <span class="s1">&#39;_by_&#39;</span> <span class="k">if</span> <span class="n">summarize_groups</span> <span class="k">else</span> <span class="s1">&#39;_within_&#39;</span>
+
+        <span class="k">if</span> <span class="n">summarize_groups</span><span class="p">:</span>
+
+            <span class="n">collection</span> <span class="o">=</span> <span class="n">common</span><span class="o">.</span><span class="n">dict_subtotals</span><span class="p">(</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">_expand_keys</span><span class="p">(</span><span class="n">level</span> <span class="o">=</span> <span class="n">level</span><span class="p">)</span>
+            <span class="p">)</span>
+
+            <span class="n">by</span> <span class="o">=</span> <span class="s1">&#39;by_</span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="n">level</span>
+
+            <span class="nb">setattr</span><span class="p">(</span>
+                <span class="bp">self</span><span class="p">,</span>
+                <span class="n">by</span><span class="p">,</span>
+                <span class="n">collection</span>
+            <span class="p">)</span>
+            <span class="nb">setattr</span><span class="p">(</span>
+                <span class="bp">self</span><span class="p">,</span>
+                <span class="s1">&#39;n</span><span class="si">%s%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="p">(</span><span class="n">midpart</span><span class="p">,</span> <span class="n">level</span><span class="p">),</span>
+                <span class="n">common</span><span class="o">.</span><span class="n">dict_counts</span><span class="p">(</span><span class="n">collection</span><span class="p">)</span>
+            <span class="p">)</span>
+
+            <span class="k">for</span> <span class="n">k</span><span class="p">,</span> <span class="n">v</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="nb">getattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">by</span><span class="p">)):</span>
+
+                <span class="n">k</span> <span class="o">=</span> <span class="n">k</span> <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">k</span><span class="p">,</span> <span class="nb">tuple</span><span class="p">)</span> <span class="k">else</span> <span class="p">(</span><span class="n">k</span><span class="p">,</span> <span class="s1">&#39;all&#39;</span><span class="p">)</span>
+
+                <span class="n">k</span> <span class="o">+=</span> <span class="p">(</span><span class="s1">&#39;Total&#39;</span><span class="p">,)</span>
+
+                <span class="bp">self</span><span class="o">.</span><span class="n">collection</span><span class="p">[</span><span class="n">k</span><span class="p">]</span> <span class="o">=</span> <span class="n">v</span>
+
+        <span class="k">else</span><span class="p">:</span>
+
+            <span class="n">collection</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_expand_keys</span><span class="p">(</span><span class="n">level</span> <span class="o">=</span> <span class="n">level</span><span class="p">)</span>
+
+        <span class="nb">setattr</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="s1">&#39;pct</span><span class="si">%s%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="p">(</span><span class="n">midpart</span><span class="p">,</span> <span class="n">level</span><span class="p">),</span>
+            <span class="p">(</span>
+                <span class="n">common</span><span class="o">.</span><span class="n">dict_set_percent</span><span class="p">(</span><span class="n">collection</span><span class="p">)</span>
+                    <span class="k">if</span> <span class="n">summarize_groups</span> <span class="k">else</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">_percent_and_collapse</span><span class="p">(</span><span class="n">collection</span><span class="p">)</span>
+            <span class="p">)</span>
+        <span class="p">)</span>
+
+        <span class="k">for</span> <span class="n">method</span> <span class="ow">in</span> <span class="p">(</span><span class="s1">&#39;shared&#39;</span><span class="p">,</span> <span class="s1">&#39;unique&#39;</span><span class="p">):</span>
+
+            <span class="n">shared_unique</span> <span class="o">=</span> <span class="p">(</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">_add_total</span><span class="p">(</span>
+                    <span class="n">common</span><span class="o">.</span><span class="n">shared_unique_foreach</span><span class="p">(</span><span class="n">collection</span><span class="p">,</span> <span class="n">op</span> <span class="o">=</span> <span class="n">method</span><span class="p">),</span>
+                    <span class="n">key</span> <span class="o">=</span> <span class="p">(</span>
+                        <span class="s1">&#39;all&#39;</span>
+                            <span class="k">if</span> <span class="n">level</span> <span class="o">==</span> <span class="s1">&#39;interaction_type&#39;</span> <span class="k">else</span>
+                        <span class="p">(</span><span class="s1">&#39;all&#39;</span><span class="p">,</span> <span class="s1">&#39;all&#39;</span><span class="p">)</span>
+                    <span class="p">)</span>
+                <span class="p">)</span>
+                    <span class="k">if</span> <span class="n">summarize_groups</span> <span class="k">else</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">_shared_unique</span><span class="p">(</span>
+                    <span class="n">dct</span> <span class="o">=</span> <span class="n">collection</span><span class="p">,</span>
+                    <span class="n">method</span> <span class="o">=</span> <span class="n">method</span><span class="p">,</span>
+                    <span class="n">total_key</span> <span class="o">=</span> <span class="p">(</span>
+                        <span class="p">(</span><span class="s1">&#39;all&#39;</span><span class="p">,</span> <span class="s1">&#39;Total&#39;</span><span class="p">)</span>
+                            <span class="k">if</span> <span class="n">level</span> <span class="o">==</span> <span class="s1">&#39;interaction_type&#39;</span> <span class="k">else</span>
+                        <span class="kc">None</span>
+                    <span class="p">),</span>
+                <span class="p">)</span>
+            <span class="p">)</span>
+
+            <span class="k">if</span> <span class="ow">not</span> <span class="n">summarize_groups</span><span class="p">:</span>
+
+                <span class="n">shared_unique_flat</span> <span class="o">=</span> <span class="n">common</span><span class="o">.</span><span class="n">dict_collapse_keys</span><span class="p">(</span><span class="n">shared_unique</span><span class="p">)</span>
+
+            <span class="n">attr</span> <span class="o">=</span> <span class="s1">&#39;</span><span class="si">%s%s%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="p">(</span><span class="n">method</span><span class="p">,</span> <span class="n">midpart</span><span class="p">,</span> <span class="n">level</span><span class="p">)</span>
+            <span class="n">n_attr</span> <span class="o">=</span> <span class="s1">&#39;n_</span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="n">attr</span>
+            <span class="n">pct_attr</span> <span class="o">=</span> <span class="s1">&#39;pct_</span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="n">attr</span>
+
+            <span class="nb">setattr</span><span class="p">(</span>
+                <span class="bp">self</span><span class="p">,</span>
+                <span class="n">attr</span><span class="p">,</span>
+                <span class="n">shared_unique</span>
+            <span class="p">)</span>
+            <span class="nb">setattr</span><span class="p">(</span>
+                <span class="bp">self</span><span class="p">,</span>
+                <span class="n">n_attr</span><span class="p">,</span>
+                <span class="n">common</span><span class="o">.</span><span class="n">dict_collapse_keys</span><span class="p">(</span>
+                    <span class="n">common</span><span class="o">.</span><span class="n">dict_counts</span><span class="p">(</span><span class="n">shared_unique</span><span class="p">)</span>
+                <span class="p">)</span>
+            <span class="p">)</span>
+            <span class="nb">setattr</span><span class="p">(</span>
+                <span class="bp">self</span><span class="p">,</span>
+                <span class="n">pct_attr</span><span class="p">,</span>
+                <span class="n">common</span><span class="o">.</span><span class="n">dict_collapse_keys</span><span class="p">(</span>
+                    <span class="n">common</span><span class="o">.</span><span class="n">dict_set_percent</span><span class="p">(</span><span class="n">shared_unique</span><span class="p">)</span>
+                        <span class="k">if</span> <span class="n">summarize_groups</span> <span class="k">else</span>
+                    <span class="bp">self</span><span class="o">.</span><span class="n">_percent_and_collapse</span><span class="p">(</span><span class="n">shared_unique</span><span class="p">)</span>
+                <span class="p">)</span>
+            <span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">_expand_keys</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">level</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="n">common</span><span class="o">.</span><span class="n">dict_expand_keys</span><span class="p">(</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">_collection</span><span class="p">,</span>
+            <span class="n">depth</span> <span class="o">=</span> <span class="mi">1</span><span class="p">,</span>
+            <span class="n">front</span> <span class="o">=</span> <span class="n">level</span> <span class="o">==</span> <span class="s1">&#39;interaction_type&#39;</span><span class="p">,</span>
+        <span class="p">)</span>
+
+
+    <span class="nd">@classmethod</span>
+    <span class="k">def</span> <span class="nf">_shared_unique</span><span class="p">(</span><span class="bp">cls</span><span class="p">,</span> <span class="n">dct</span><span class="p">,</span> <span class="n">method</span><span class="p">,</span> <span class="n">total_key</span> <span class="o">=</span> <span class="kc">None</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="nb">dict</span><span class="p">(</span>
+            <span class="p">(</span>
+                <span class="n">key</span><span class="p">,</span>
+                <span class="bp">cls</span><span class="o">.</span><span class="n">_add_total</span><span class="p">(</span>
+                    <span class="n">common</span><span class="o">.</span><span class="n">shared_unique_foreach</span><span class="p">(</span><span class="n">val</span><span class="p">,</span> <span class="n">op</span> <span class="o">=</span> <span class="n">method</span><span class="p">),</span>
+                    <span class="n">key</span> <span class="o">=</span> <span class="n">total_key</span>
+                <span class="p">)</span>
+            <span class="p">)</span>
+            <span class="k">for</span> <span class="n">key</span><span class="p">,</span> <span class="n">val</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="n">dct</span><span class="p">)</span>
+        <span class="p">)</span>
+
+
+    <span class="nd">@staticmethod</span>
+    <span class="k">def</span> <span class="nf">_add_total</span><span class="p">(</span><span class="n">dct</span><span class="p">,</span> <span class="n">key</span> <span class="o">=</span> <span class="kc">None</span><span class="p">):</span>
+
+        <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">key</span><span class="p">,</span> <span class="p">(</span><span class="nb">str</span><span class="p">,</span> <span class="nb">tuple</span><span class="p">)):</span>
+
+            <span class="n">_key</span> <span class="o">=</span> <span class="n">key</span>
+
+        <span class="k">else</span><span class="p">:</span>
+
+            <span class="n">first_key</span> <span class="o">=</span> <span class="nb">next</span><span class="p">(</span><span class="n">dct</span><span class="o">.</span><span class="n">keys</span><span class="p">()</span><span class="o">.</span><span class="fm">__iter__</span><span class="p">())</span>
+
+            <span class="k">if</span> <span class="nb">callable</span><span class="p">(</span><span class="n">key</span><span class="p">):</span>
+
+                <span class="n">_key</span> <span class="o">=</span> <span class="n">key</span><span class="p">(</span><span class="n">first_key</span><span class="p">)</span>
+
+            <span class="k">else</span><span class="p">:</span>
+
+                <span class="n">_key</span> <span class="o">=</span> <span class="p">(</span>
+                    <span class="s1">&#39;Total&#39;</span>
+                        <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">first_key</span><span class="p">,</span> <span class="nb">str</span><span class="p">)</span> <span class="k">else</span>
+                    <span class="n">first_key</span><span class="p">[:</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span> <span class="o">+</span> <span class="p">(</span><span class="s1">&#39;Total&#39;</span><span class="p">,)</span>
+                <span class="p">)</span>
+
+        <span class="n">dct</span><span class="p">[</span><span class="n">_key</span><span class="p">]</span> <span class="o">=</span> <span class="n">common</span><span class="o">.</span><span class="n">dict_union</span><span class="p">(</span><span class="n">dct</span><span class="p">)</span>
+
+        <span class="k">return</span> <span class="n">dct</span>
+
+
+    <span class="nd">@classmethod</span>
+    <span class="k">def</span> <span class="nf">_percent_and_collapse</span><span class="p">(</span><span class="bp">cls</span><span class="p">,</span> <span class="n">dct</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="p">(</span>
+            <span class="n">common</span><span class="o">.</span><span class="n">dict_collapse_keys</span><span class="p">(</span>
+                <span class="nb">dict</span><span class="p">(</span>
+                    <span class="p">(</span>
+                        <span class="n">key</span><span class="p">,</span>
+                        <span class="n">common</span><span class="o">.</span><span class="n">dict_set_percent</span><span class="p">(</span><span class="n">val</span><span class="p">)</span>
+                    <span class="p">)</span>
+                    <span class="k">for</span> <span class="n">key</span><span class="p">,</span> <span class="n">val</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="n">dct</span><span class="p">)</span>
+                <span class="p">)</span>
+            <span class="p">)</span>
+        <span class="p">)</span></div>
+
+
+
+<span class="n">NetworkStatsRecord</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">namedtuple</span><span class="p">(</span>
+    <span class="s1">&#39;NetworkStatsRecord&#39;</span><span class="p">,</span>
+    <span class="p">[</span>
+        <span class="s1">&#39;total&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;by_resource&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;by_category&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;shared&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;unique&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;percent&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;shared_res_cat&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;unique_res_cat&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;percent_res_cat&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;shared_cat&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;unique_cat&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;percent_cat&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;resource_cat&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;cat_resource&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;method&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;label&#39;</span><span class="p">,</span>
+    <span class="p">],</span>
+<span class="p">)</span>
+<span class="n">NetworkStatsRecord</span><span class="o">.</span><span class="fm">__new__</span><span class="o">.</span><span class="vm">__defaults__</span> <span class="o">=</span> <span class="p">(</span><span class="kc">None</span><span class="p">,)</span> <span class="o">*</span> <span class="mi">11</span>
+
+
+<div class="viewcode-block" id="Network">
+<a class="viewcode-back" href="../../../api/pypath.core.network.Network.html#pypath.core.network.Network">[docs]</a>
+<span class="k">class</span> <span class="nc">Network</span><span class="p">(</span><span class="n">session_mod</span><span class="o">.</span><span class="n">Logger</span><span class="p">):</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Represents a molecular interaction network. Provides various methods to</span>
+<span class="sd">    query the network and its components. Optionally converts the network</span>
+<span class="sd">    to a ``pandas.DataFrame`` of interactions.</span>
+
+<span class="sd">    :arg list,dict resources:</span>
+<span class="sd">        One or more lists or dictionaries containing</span>
+<span class="sd">        ``pypath.resource.NetworkResource`` objects.</span>
+<span class="sd">    :arg bool make_df:</span>
+<span class="sd">        Create a ``pandas.DataFrame`` already when creating the instance.</span>
+<span class="sd">        If no network data loaded no data frame will be created.</span>
+<span class="sd">    :arg int ncbi_tax_id:</span>
+<span class="sd">        Restrict the network only to this organism. If ``None`` identifiers</span>
+<span class="sd">        from any organism will be allowed.</span>
+<span class="sd">    :arg bool allow_loops:</span>
+<span class="sd">        Allow interactions with the their two endpoints being the same entity.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="n">_partners_methods</span> <span class="o">=</span> <span class="p">(</span>
+        <span class="p">{</span>
+            <span class="s1">&#39;&#39;</span><span class="p">:</span> <span class="p">{},</span>
+            <span class="s1">&#39;transcriptionally_&#39;</span><span class="p">:</span> <span class="p">{</span>
+                <span class="s1">&#39;interaction_type&#39;</span><span class="p">:</span> <span class="p">{</span>
+                    <span class="s1">&#39;transcriptional&#39;</span><span class="p">,</span>
+                    <span class="s1">&#39;mirna_transcriptional&#39;</span><span class="p">,</span>
+                <span class="p">},</span>
+            <span class="p">},</span>
+            <span class="s1">&#39;post_transcriptionally_&#39;</span><span class="p">:</span> <span class="p">{</span>
+                <span class="s1">&#39;interaction_type&#39;</span><span class="p">:</span> <span class="p">{</span>
+                    <span class="s1">&#39;post_transcriptional&#39;</span><span class="p">,</span>
+                    <span class="s1">&#39;lncrna_post_transcriptional&#39;</span><span class="p">,</span>
+                <span class="p">},</span>
+            <span class="p">},</span>
+            <span class="s1">&#39;post_translationally_&#39;</span><span class="p">:</span> <span class="p">{</span>
+                <span class="s1">&#39;interaction_type&#39;</span><span class="p">:</span> <span class="s1">&#39;post_translational&#39;</span><span class="p">,</span>
+            <span class="p">},</span>
+        <span class="p">},</span>
+        <span class="p">{</span>
+            <span class="s1">&#39;regulat&#39;</span><span class="p">:</span> <span class="p">{</span>
+                <span class="s1">&#39;direction&#39;</span><span class="p">:</span> <span class="kc">True</span><span class="p">,</span>
+            <span class="p">},</span>
+            <span class="s1">&#39;activat&#39;</span><span class="p">:</span> <span class="p">{</span>
+                <span class="s1">&#39;effect&#39;</span><span class="p">:</span> <span class="s1">&#39;positive&#39;</span><span class="p">,</span>
+            <span class="p">},</span>
+            <span class="s1">&#39;suppress&#39;</span><span class="p">:</span> <span class="p">{</span>
+                <span class="s1">&#39;effect&#39;</span><span class="p">:</span> <span class="s1">&#39;negative&#39;</span><span class="p">,</span>
+            <span class="p">},</span>
+        <span class="p">},</span>
+        <span class="p">{</span>
+            <span class="s1">&#39;es&#39;</span><span class="p">:</span> <span class="p">{</span>
+                <span class="s1">&#39;mode&#39;</span><span class="p">:</span> <span class="s1">&#39;IN&#39;</span><span class="p">,</span>
+            <span class="p">},</span>
+            <span class="s1">&#39;ed_by&#39;</span><span class="p">:</span> <span class="p">{</span>
+                <span class="s1">&#39;mode&#39;</span><span class="p">:</span> <span class="s1">&#39;OUT&#39;</span><span class="p">,</span>
+            <span class="p">}</span>
+        <span class="p">},</span>
+    <span class="p">)</span>
+
+
+<div class="viewcode-block" id="Network.__init__">
+<a class="viewcode-back" href="../../../api/pypath.core.network.Network.html#pypath.core.network.Network.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">resources</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">make_df</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+            <span class="n">df_by_source</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+            <span class="n">df_with_references</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+            <span class="n">df_columns</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">df_dtype</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">pickle_file</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">,</span>
+            <span class="n">allow_loops</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="o">**</span><span class="n">kwargs</span>
+        <span class="p">):</span>
+
+        <span class="n">session_mod</span><span class="o">.</span><span class="n">Logger</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">name</span> <span class="o">=</span> <span class="s1">&#39;network&#39;</span><span class="p">)</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span><span class="s1">&#39;Creating network object.&#39;</span><span class="p">)</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">df_by_source</span> <span class="o">=</span> <span class="n">df_by_source</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">df_with_references</span> <span class="o">=</span> <span class="n">df_with_references</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">df_columns</span> <span class="o">=</span> <span class="n">df_columns</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">df_dtype</span> <span class="o">=</span> <span class="n">df_dtype</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">allow_loops</span> <span class="o">=</span> <span class="n">allow_loops</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">cache_dir</span> <span class="o">=</span> <span class="n">cache_mod</span><span class="o">.</span><span class="n">get_cachedir</span><span class="p">()</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">keep_original_names</span> <span class="o">=</span> <span class="n">settings</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">&#39;network_keep_original_names&#39;</span><span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">default_name_types</span> <span class="o">=</span> <span class="n">settings</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">&#39;default_name_types&#39;</span><span class="p">)</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">reset</span><span class="p">()</span>
+
+        <span class="k">if</span> <span class="n">pickle_file</span> <span class="ow">and</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">exists</span><span class="p">(</span><span class="n">pickle_file</span><span class="p">):</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">load_from_pickle</span><span class="p">(</span><span class="n">pickle_file</span> <span class="o">=</span> <span class="n">pickle_file</span><span class="p">)</span>
+            <span class="k">return</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">load</span><span class="p">(</span><span class="n">resources</span> <span class="o">=</span> <span class="n">resources</span><span class="p">,</span> <span class="n">make_df</span> <span class="o">=</span> <span class="n">make_df</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="Network.reload">
+<a class="viewcode-back" href="../../../api/pypath.core.network.Network.html#pypath.core.network.Network.reload">[docs]</a>
+    <span class="k">def</span> <span class="nf">reload</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">recursive</span><span class="p">:</span> <span class="nb">bool</span> <span class="o">=</span> <span class="kc">False</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Reloads the object from the module level.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">modname</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="vm">__class__</span><span class="o">.</span><span class="vm">__module__</span>
+        <span class="n">mod</span> <span class="o">=</span> <span class="nb">__import__</span><span class="p">(</span><span class="n">modname</span><span class="p">,</span> <span class="n">fromlist</span> <span class="o">=</span> <span class="p">[</span><span class="n">modname</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;.&#39;</span><span class="p">)[</span><span class="mi">0</span><span class="p">]])</span>
+        <span class="n">imp</span><span class="o">.</span><span class="n">reload</span><span class="p">(</span><span class="n">mod</span><span class="p">)</span>
+        <span class="n">new</span> <span class="o">=</span> <span class="nb">getattr</span><span class="p">(</span><span class="n">mod</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="vm">__class__</span><span class="o">.</span><span class="vm">__name__</span><span class="p">)</span>
+        <span class="nb">setattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">&#39;__class__&#39;</span><span class="p">,</span> <span class="n">new</span><span class="p">)</span>
+
+        <span class="k">if</span> <span class="n">recursive</span><span class="p">:</span>
+
+            <span class="n">imp</span><span class="o">.</span><span class="n">reload</span><span class="p">(</span><span class="n">entity_mod</span><span class="p">)</span>
+            <span class="n">imp</span><span class="o">.</span><span class="n">reload</span><span class="p">(</span><span class="n">interaction_mod</span><span class="p">)</span>
+
+            <span class="k">for</span> <span class="n">entity</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">nodes</span><span class="o">.</span><span class="n">values</span><span class="p">():</span>
+
+                <span class="n">entity</span><span class="o">.</span><span class="vm">__class__</span> <span class="o">=</span> <span class="n">entity_mod</span><span class="o">.</span><span class="n">Entity</span>
+
+            <span class="k">for</span> <span class="n">interaction</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">interactions</span><span class="o">.</span><span class="n">values</span><span class="p">():</span>
+
+                <span class="n">interaction</span><span class="o">.</span><span class="vm">__class__</span> <span class="o">=</span> <span class="n">interaction_mod</span><span class="o">.</span><span class="n">Interaction</span>
+                <span class="n">interaction</span><span class="o">.</span><span class="n">a</span><span class="o">.</span><span class="vm">__class__</span> <span class="o">=</span> <span class="n">entity_mod</span><span class="o">.</span><span class="n">Entity</span>
+                <span class="n">interaction</span><span class="o">.</span><span class="n">b</span><span class="o">.</span><span class="vm">__class__</span> <span class="o">=</span> <span class="n">entity_mod</span><span class="o">.</span><span class="n">Entity</span></div>
+
+
+
+    <span class="k">def</span> <span class="fm">__len__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">interactions</span><span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="fm">__bool__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="nb">bool</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">interactions</span><span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="fm">__iter__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">for</span> <span class="n">ia</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">interactions</span><span class="o">.</span><span class="n">values</span><span class="p">():</span>
+
+            <span class="k">yield</span> <span class="n">ia</span>
+
+
+    <span class="k">def</span> <span class="fm">__contains__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">other</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="nb">any</span><span class="p">(</span><span class="n">other</span> <span class="ow">in</span> <span class="n">ia</span> <span class="k">for</span> <span class="n">ia</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">interactions</span><span class="o">.</span><span class="n">values</span><span class="p">())</span>
+
+
+<div class="viewcode-block" id="Network.reset">
+<a class="viewcode-back" href="../../../api/pypath.core.network.Network.html#pypath.core.network.Network.reset">[docs]</a>
+    <span class="k">def</span> <span class="nf">reset</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Removes network data i.e. creates empty interaction and node</span>
+<span class="sd">        dictionaries.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">raw_data</span> <span class="o">=</span> <span class="p">{}</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">interactions</span> <span class="o">=</span> <span class="p">{}</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">nodes</span> <span class="o">=</span> <span class="p">{}</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">nodes_by_label</span> <span class="o">=</span> <span class="p">{}</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">interactions_by_nodes</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">defaultdict</span><span class="p">(</span><span class="nb">set</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="Network.load">
+<a class="viewcode-back" href="../../../api/pypath.core.network.Network.html#pypath.core.network.Network.load">[docs]</a>
+    <span class="k">def</span> <span class="nf">load</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">resources</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">make_df</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+            <span class="n">exclude</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">reread</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+            <span class="n">redownload</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+            <span class="n">keep_raw</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+            <span class="n">top_call</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
+            <span class="n">cache_files</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">only_directions</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+            <span class="n">pickle_file</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">allow_loops</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">first_n</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+        <span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Loads data from a network resource or a collection of resources.</span>
+
+<span class="sd">        :arg str,dict,list,resource.NetworkResource resources:</span>
+<span class="sd">            An object defining one or more network resources. If *str* it</span>
+<span class="sd">            will be looked up among the collections in the</span>
+<span class="sd">            ``pypath.resources.network`` module (e.g. ``&#39;pathway&#39;`` will load</span>
+<span class="sd">            all resources in the `pathway` collection). If *dict* or *list*</span>
+<span class="sd">            it will be processed recursively i.e. the ``load`` method will be</span>
+<span class="sd">            called for each element. If it is a</span>
+<span class="sd">            ``pypath.resource.NetworkResource`` object it will be processed</span>
+<span class="sd">            and added to the network.</span>
+<span class="sd">        :arg bool make_df:</span>
+<span class="sd">            Whether to create a ``pandas.DataFrame`` after loading all</span>
+<span class="sd">            resources.</span>
+<span class="sd">        :arg NoneType,set exclude:</span>
+<span class="sd">            A *set* of resource names to be ignored. It is useful if you want</span>
+<span class="sd">            to load a collection with the exception of a few resources.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">if</span> <span class="n">pickle_file</span><span class="p">:</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">load_from_pickle</span><span class="p">(</span><span class="n">pickle_file</span> <span class="o">=</span> <span class="n">pickle_file</span><span class="p">)</span>
+            <span class="k">return</span>
+
+        <span class="n">kwargs</span> <span class="o">=</span> <span class="p">{</span>
+            <span class="s1">&#39;reread&#39;</span><span class="p">:</span> <span class="n">reread</span><span class="p">,</span>
+            <span class="s1">&#39;redownload&#39;</span><span class="p">:</span> <span class="n">redownload</span><span class="p">,</span>
+            <span class="s1">&#39;keep_raw&#39;</span><span class="p">:</span> <span class="n">keep_raw</span><span class="p">,</span>
+            <span class="s1">&#39;top_call&#39;</span><span class="p">:</span> <span class="kc">False</span><span class="p">,</span>
+            <span class="s1">&#39;only_directions&#39;</span><span class="p">:</span> <span class="n">only_directions</span><span class="p">,</span>
+            <span class="s1">&#39;allow_loops&#39;</span><span class="p">:</span> <span class="n">allow_loops</span><span class="p">,</span>
+            <span class="s1">&#39;first_n&#39;</span><span class="p">:</span> <span class="n">first_n</span><span class="p">,</span>
+        <span class="p">}</span>
+
+        <span class="n">exclude</span> <span class="o">=</span> <span class="n">common</span><span class="o">.</span><span class="n">to_set</span><span class="p">(</span><span class="n">exclude</span><span class="p">)</span>
+
+        <span class="n">resources</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="p">(</span><span class="n">resources</span><span class="p">,)</span>
+                <span class="k">if</span> <span class="ow">not</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">resources</span><span class="p">,</span> <span class="p">(</span><span class="nb">list</span><span class="p">,</span> <span class="n">Mapping</span><span class="p">,</span> <span class="nb">tuple</span><span class="p">,</span> <span class="nb">set</span><span class="p">))</span> <span class="k">else</span>
+            <span class="n">resources</span><span class="o">.</span><span class="n">values</span><span class="p">()</span>
+                <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">resources</span><span class="p">,</span> <span class="n">Mapping</span><span class="p">)</span> <span class="k">else</span>
+            <span class="n">resources</span>
+        <span class="p">)</span>
+
+        <span class="k">for</span> <span class="n">resource</span> <span class="ow">in</span> <span class="n">resources</span><span class="p">:</span>
+
+            <span class="k">if</span> <span class="p">(</span>
+                <span class="nb">isinstance</span><span class="p">(</span><span class="n">resource</span><span class="p">,</span> <span class="nb">str</span><span class="p">)</span> <span class="ow">and</span>
+                <span class="nb">hasattr</span><span class="p">(</span><span class="n">network_resources</span><span class="p">,</span> <span class="n">resource</span><span class="p">)</span>
+            <span class="p">):</span>
+
+                <span class="bp">self</span><span class="o">.</span><span class="n">load</span><span class="p">(</span>
+                    <span class="n">resources</span> <span class="o">=</span> <span class="nb">getattr</span><span class="p">(</span><span class="n">network_resources</span><span class="p">,</span> <span class="n">resource</span><span class="p">),</span>
+                    <span class="o">**</span><span class="n">kwargs</span>
+                <span class="p">)</span>
+
+            <span class="k">elif</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">resource</span><span class="p">,</span> <span class="p">(</span><span class="nb">list</span><span class="p">,</span> <span class="nb">dict</span><span class="p">,</span> <span class="nb">tuple</span><span class="p">,</span> <span class="nb">set</span><span class="p">)):</span>
+
+                <span class="bp">self</span><span class="o">.</span><span class="n">load</span><span class="p">(</span>
+                    <span class="n">resources</span> <span class="o">=</span> <span class="n">resource</span><span class="p">,</span>
+                    <span class="o">**</span><span class="n">kwargs</span>
+                <span class="p">)</span>
+
+            <span class="k">elif</span> <span class="p">(</span>
+                <span class="nb">isinstance</span><span class="p">(</span>
+                    <span class="n">resource</span><span class="p">,</span>
+                    <span class="p">(</span>
+                        <span class="n">network_resources</span><span class="o">.</span><span class="n">data_formats</span><span class="o">.</span>\
+                            <span class="n">input_formats</span><span class="o">.</span><span class="n">NetworkInput</span><span class="p">,</span>
+                        <span class="n">network_resources</span><span class="o">.</span><span class="n">resource</span><span class="o">.</span><span class="n">NetworkResource</span><span class="p">,</span>
+                    <span class="p">)</span>
+                <span class="p">)</span> <span class="ow">and</span> <span class="n">resource</span><span class="o">.</span><span class="n">name</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">exclude</span>
+            <span class="p">):</span>
+
+                <span class="bp">self</span><span class="o">.</span><span class="n">load_resource</span><span class="p">(</span><span class="n">resource</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
+
+            <span class="k">elif</span> <span class="n">resource</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
+
+                <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span>
+                    <span class="s1">&#39;Could not recognize network input &#39;</span>
+                    <span class="s1">&#39;definition: `</span><span class="si">%s</span><span class="s1">`.&#39;</span> <span class="o">%</span> <span class="nb">str</span><span class="p">(</span><span class="n">resource</span><span class="p">)</span>
+                <span class="p">)</span>
+
+        <span class="k">if</span> <span class="n">make_df</span> <span class="ow">and</span> <span class="n">top_call</span><span class="p">:</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">make_df</span><span class="p">()</span></div>
+
+
+
+    <span class="c1"># synonyms (old method names of PyPath)</span>
+    <span class="n">load_resources</span> <span class="o">=</span> <span class="n">load</span>
+    <span class="n">init_network</span> <span class="o">=</span> <span class="n">load</span>
+
+
+<div class="viewcode-block" id="Network.load_resource">
+<a class="viewcode-back" href="../../../api/pypath.core.network.Network.html#pypath.core.network.Network.load_resource">[docs]</a>
+    <span class="k">def</span> <span class="nf">load_resource</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">resource</span><span class="p">,</span>
+            <span class="n">clean</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
+            <span class="n">reread</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">redownload</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">keep_raw</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+            <span class="n">only_directions</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+            <span class="n">allow_loops</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">first_n</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="o">**</span><span class="n">kwargs</span>
+        <span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Loads the data from a single resource and attaches it to the</span>
+<span class="sd">        network</span>
+
+<span class="sd">        :arg pypath.input_formats.NetworkInput resource:</span>
+<span class="sd">            :py:class:`pypath.input_formats.NetworkInput` instance</span>
+<span class="sd">            containing the detailed definition of the input format to</span>
+<span class="sd">            the downloaded file.</span>
+<span class="sd">        :arg bool clean:</span>
+<span class="sd">            Legacy parameter, has no effect at the moment.</span>
+<span class="sd">            Optional, ``True`` by default. Whether to clean the graph</span>
+<span class="sd">            after importing the data or not. See</span>
+<span class="sd">            :py:meth:`pypath.main.PyPath.clean_graph` for more</span>
+<span class="sd">            information.</span>
+<span class="sd">        :arg dict cache_files:</span>
+<span class="sd">            Legacy parameter, has no effect at the moment.</span>
+<span class="sd">            Optional, ``{}`` by default. Contains the resource name(s)</span>
+<span class="sd">            [str] (keys) and the corresponding cached file name [str].</span>
+<span class="sd">            If provided (and file exists) bypasses the download of the</span>
+<span class="sd">            data for that resource and uses the cache file instead.</span>
+<span class="sd">        :arg bool reread:</span>
+<span class="sd">            Optional, ``False`` by default. Specifies whether to reread</span>
+<span class="sd">            the data files from the cache or omit them (similar to</span>
+<span class="sd">            *redownload*).</span>
+<span class="sd">        :arg bool redownload:</span>
+<span class="sd">            Optional, ``False`` by default. Specifies whether to</span>
+<span class="sd">            re-download the data and ignore the cache.</span>
+<span class="sd">        :arg bool only_directions:</span>
+<span class="sd">            If ``True``, no new interactions will be created but direction</span>
+<span class="sd">            and effect sign evidences will be added to existing interactions.</span>
+<span class="sd">        :arg int first_n:</span>
+<span class="sd">            Load only the first n interactions.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">total_attempts</span> <span class="o">=</span> <span class="n">settings</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">&#39;network_load_resource_attempts&#39;</span><span class="p">)</span>
+
+        <span class="k">for</span> <span class="n">attempt</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">total_attempts</span><span class="p">):</span>
+
+            <span class="k">try</span><span class="p">:</span>
+
+                <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span>
+                    <span class="sa">f</span><span class="s1">&#39;Loading network data from resource `</span><span class="si">{</span><span class="n">resource</span><span class="o">.</span><span class="n">name</span><span class="si">}</span><span class="s1">`&#39;</span>
+                    <span class="sa">f</span><span class="s1">&#39; (dataset: </span><span class="si">{</span><span class="n">resource</span><span class="o">.</span><span class="n">dataset</span><span class="si">}</span><span class="s1">); &#39;</span>
+                    <span class="sa">f</span><span class="s1">&#39;attempt </span><span class="si">{</span><span class="n">attempt</span><span class="w"> </span><span class="o">+</span><span class="w"> </span><span class="mi">1</span><span class="si">}</span><span class="s1"> of </span><span class="si">{</span><span class="n">total_attempts</span><span class="si">}</span><span class="s1">.&#39;</span>
+                <span class="p">)</span>
+
+                <span class="bp">self</span><span class="o">.</span><span class="n">_read_resource</span><span class="p">(</span>
+                    <span class="n">resource</span><span class="p">,</span>
+                    <span class="n">reread</span> <span class="o">=</span> <span class="n">reread</span><span class="p">,</span>
+                    <span class="n">redownload</span> <span class="o">=</span> <span class="n">redownload</span><span class="p">,</span>
+                    <span class="n">keep_raw</span> <span class="o">=</span> <span class="n">keep_raw</span><span class="p">,</span>
+                    <span class="n">first_n</span> <span class="o">=</span> <span class="n">first_n</span><span class="p">,</span>
+                <span class="p">)</span>
+
+                <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span>
+                    <span class="s1">&#39;Successfully read interactions &#39;</span>
+                    <span class="sa">f</span><span class="s1">&#39;from resource `</span><span class="si">{</span><span class="n">resource</span><span class="o">.</span><span class="n">name</span><span class="si">}</span><span class="s1">`.&#39;</span>
+                <span class="p">)</span>
+                <span class="k">break</span>
+
+            <span class="k">except</span> <span class="ne">Exception</span> <span class="k">as</span> <span class="n">e</span><span class="p">:</span>
+
+                <span class="n">exc</span> <span class="o">=</span> <span class="n">sys</span><span class="o">.</span><span class="n">exc_info</span><span class="p">()</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span>
+                    <span class="s1">&#39;Failed to read interactions &#39;</span>
+                    <span class="sa">f</span><span class="s1">&#39;from resource `</span><span class="si">{</span><span class="n">resource</span><span class="o">.</span><span class="n">name</span><span class="si">}</span><span class="s1">`:&#39;</span>
+                <span class="p">)</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">_log_traceback</span><span class="p">(</span><span class="n">console</span> <span class="o">=</span> <span class="kc">True</span><span class="p">)</span>
+
+                <span class="k">if</span> <span class="n">attempt</span> <span class="o">==</span> <span class="n">total_attempts</span> <span class="o">-</span> <span class="mi">1</span><span class="p">:</span>
+
+                    <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span>
+                        <span class="sa">f</span><span class="s1">&#39;Not loading `</span><span class="si">{</span><span class="n">resource</span><span class="o">.</span><span class="n">name</span><span class="si">}</span><span class="s1">`: giving up after &#39;</span>
+                        <span class="sa">f</span><span class="s1">&#39;</span><span class="si">{</span><span class="n">total_attempts</span><span class="si">}</span><span class="s1"> attempts.&#39;</span>
+                    <span class="p">)</span>
+                    <span class="k">return</span>
+
+        <span class="n">allow_loops</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_allow_loops</span><span class="p">(</span>
+            <span class="n">allow_loops</span> <span class="o">=</span> <span class="n">allow_loops</span><span class="p">,</span>
+            <span class="n">resource</span> <span class="o">=</span> <span class="n">resource</span><span class="p">,</span>
+        <span class="p">)</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span><span class="s1">&#39;Loops allowed for resource `</span><span class="si">%s</span><span class="s1">`: </span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="p">(</span>
+            <span class="n">resource</span><span class="o">.</span><span class="n">name</span><span class="p">,</span>
+            <span class="n">allow_loops</span><span class="p">,</span>
+        <span class="p">))</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_add_edge_list</span><span class="p">(</span>
+            <span class="n">only_directions</span> <span class="o">=</span> <span class="n">only_directions</span><span class="p">,</span>
+            <span class="n">allow_loops</span> <span class="o">=</span> <span class="n">allow_loops</span><span class="p">,</span>
+        <span class="p">)</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">organisms_check</span><span class="p">()</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">remove_zero_degree</span><span class="p">()</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span>
+            <span class="s1">&#39;Completed: loading network data from &#39;</span>
+            <span class="s1">&#39;resource `</span><span class="si">%s</span><span class="s1">`.&#39;</span> <span class="o">%</span> <span class="n">resource</span><span class="o">.</span><span class="n">name</span>
+        <span class="p">)</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">_read_resource</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">resource</span><span class="p">,</span>
+            <span class="n">reread</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+            <span class="n">redownload</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+            <span class="n">keep_raw</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+            <span class="n">cache_files</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">first_n</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+        <span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Reads interaction data file containing node and edge attributes</span>
+<span class="sd">        that can be read from simple text based files and adds it to the</span>
+<span class="sd">        networkdata. This function works not only with files, but with</span>
+<span class="sd">        lists as well. Any other function can be written to download and</span>
+<span class="sd">        preprocess data, and then give it to this function to finally</span>
+<span class="sd">        attach to the network.</span>
+
+<span class="sd">        :arg pypath.input_formats.NetworkInput resource:</span>
+<span class="sd">            :py:class:`pypath.input_formats.NetworkInput` instance</span>
+<span class="sd">            containing the detailed definition of the input format of</span>
+<span class="sd">            the file. Instead of the file name (on the</span>
+<span class="sd">            :py:attr:`pypath.input_formats.NetworkInput.input`</span>
+<span class="sd">            attribute) you can give a custom function name, which will</span>
+<span class="sd">            be executed, and the returned data will be used instead.</span>
+<span class="sd">        :arg bool keep_raw:</span>
+<span class="sd">            Optional, ``False`` by default. Whether to keep the raw data</span>
+<span class="sd">            read by this function, in order for debugging purposes, or</span>
+<span class="sd">            further use.</span>
+<span class="sd">        :arg dict cache_files:</span>
+<span class="sd">            Optional, ``{}`` by default. Contains the resource name(s)</span>
+<span class="sd">            [str] (keys) and the corresponding cached file name [str].</span>
+<span class="sd">            If provided (and file exists) bypasses the download of the</span>
+<span class="sd">            data for that resource and uses the cache file instead.</span>
+<span class="sd">        :arg bool reread:</span>
+<span class="sd">            Optional, ``False`` by default. Specifies whether to reread</span>
+<span class="sd">            the data files from the cache or omit them (similar to</span>
+<span class="sd">            *redownload*).</span>
+<span class="sd">        :arg bool redownload:</span>
+<span class="sd">            Optional, ``False`` by default. Specifies whether to</span>
+<span class="sd">            re-download the data and ignore the cache.</span>
+<span class="sd">        :arg int first_n:</span>
+<span class="sd">            Load only the first n interactions.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span><span class="s1">&#39;Reading network data from `</span><span class="si">%s</span><span class="s1">`.&#39;</span> <span class="o">%</span> <span class="n">resource</span><span class="o">.</span><span class="n">name</span><span class="p">)</span>
+
+        <span class="n">SMOL_TYPES</span> <span class="o">=</span> <span class="n">settings</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">&#39;small_molecule_entity_types&#39;</span><span class="p">)</span>
+
+        <span class="c1"># workaround in order to make it work with both NetworkInput</span>
+        <span class="c1"># and NetworkResource type param</span>
+        <span class="n">_resource</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="n">resource</span>
+                <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span>
+                    <span class="n">resource</span><span class="p">,</span>
+                    <span class="n">network_resources</span><span class="o">.</span><span class="n">resource</span><span class="o">.</span><span class="n">NetworkResource</span>
+                <span class="p">)</span> <span class="k">else</span>
+            <span class="n">network_resources</span><span class="o">.</span><span class="n">resource</span><span class="o">.</span><span class="n">NetworkResource</span><span class="p">(</span>
+                <span class="n">name</span> <span class="o">=</span> <span class="n">resource</span><span class="o">.</span><span class="n">name</span><span class="p">,</span>
+                <span class="n">interaction_type</span> <span class="o">=</span> <span class="n">resource</span><span class="o">.</span><span class="n">interaction_type</span><span class="p">,</span>
+                <span class="n">networkinput</span> <span class="o">=</span> <span class="n">resource</span><span class="p">,</span>
+                <span class="n">data_model</span> <span class="o">=</span> <span class="n">resource</span><span class="o">.</span><span class="n">data_model</span> <span class="ow">or</span> <span class="s1">&#39;unknown&#39;</span><span class="p">,</span>
+            <span class="p">)</span>
+        <span class="p">)</span>
+
+        <span class="n">networkinput</span> <span class="o">=</span> <span class="n">_resource</span><span class="o">.</span><span class="n">networkinput</span>
+
+        <span class="n">_resources_secondary</span> <span class="o">=</span> <span class="p">()</span>
+
+        <span class="n">expand_complexes</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="n">networkinput</span><span class="o">.</span><span class="n">expand_complexes</span>
+                <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">networkinput</span><span class="o">.</span><span class="n">expand_complexes</span><span class="p">,</span> <span class="nb">bool</span><span class="p">)</span> <span class="k">else</span>
+            <span class="n">settings</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">&#39;network_expand_complexes&#39;</span><span class="p">)</span>
+        <span class="p">)</span>
+        <span class="n">reread</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="n">reread</span>
+                <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">reread</span><span class="p">,</span> <span class="nb">bool</span><span class="p">)</span> <span class="k">else</span>
+            <span class="ow">not</span> <span class="n">settings</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">&#39;network_pickle_cache&#39;</span><span class="p">)</span>
+        <span class="p">)</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span><span class="s1">&#39;Expanding complexes for `</span><span class="si">%s</span><span class="s1">`: </span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="p">(</span>
+            <span class="n">networkinput</span><span class="o">.</span><span class="n">name</span><span class="p">,</span> <span class="nb">str</span><span class="p">(</span><span class="n">expand_complexes</span><span class="p">),</span>
+        <span class="p">))</span>
+
+        <span class="n">edge_list</span> <span class="o">=</span> <span class="p">[]</span>
+        <span class="n">edge_list_mapped</span> <span class="o">=</span> <span class="p">[]</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">edge_list_mapped</span> <span class="o">=</span> <span class="p">[]</span>
+        <span class="n">infile</span> <span class="o">=</span> <span class="kc">None</span>
+        <span class="n">_name</span> <span class="o">=</span> <span class="n">networkinput</span><span class="o">.</span><span class="n">name</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span>
+
+        <span class="n">edges_cache</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">cache_dir</span><span class="p">,</span>
+            <span class="s1">&#39;</span><span class="si">%s</span><span class="s1">_</span><span class="si">%s</span><span class="s1">_</span><span class="si">%s</span><span class="s1">.edges.pickle&#39;</span> <span class="o">%</span> <span class="p">(</span>
+                <span class="n">_name</span><span class="p">,</span>
+                <span class="n">_resource</span><span class="o">.</span><span class="n">data_model</span><span class="p">,</span>
+                <span class="n">_resource</span><span class="o">.</span><span class="n">interaction_type</span><span class="p">,</span>
+            <span class="p">)</span>
+        <span class="p">)</span>
+
+        <span class="n">interaction_cache</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">cache_dir</span><span class="p">,</span>
+            <span class="s1">&#39;</span><span class="si">%s</span><span class="s1">_</span><span class="si">%s</span><span class="s1">_</span><span class="si">%s</span><span class="s1">.interactions.pickle&#39;</span> <span class="o">%</span> <span class="p">(</span>
+                <span class="n">_name</span><span class="p">,</span>
+                <span class="n">_resource</span><span class="o">.</span><span class="n">data_model</span><span class="p">,</span>
+                <span class="n">_resource</span><span class="o">.</span><span class="n">interaction_type</span><span class="p">,</span>
+            <span class="p">)</span>
+        <span class="p">)</span>
+
+        <span class="k">if</span> <span class="ow">not</span> <span class="n">reread</span> <span class="ow">and</span> <span class="ow">not</span> <span class="n">redownload</span><span class="p">:</span>
+
+            <span class="n">infile</span><span class="p">,</span> <span class="n">edge_list_mapped</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_lookup_cache</span><span class="p">(</span>
+                <span class="n">_name</span><span class="p">,</span>
+                <span class="n">cache_files</span><span class="p">,</span>
+                <span class="n">interaction_cache</span><span class="p">,</span>
+                <span class="n">edges_cache</span><span class="p">,</span>
+            <span class="p">)</span>
+
+        <span class="k">if</span> <span class="ow">not</span> <span class="nb">len</span><span class="p">(</span><span class="n">edge_list_mapped</span><span class="p">):</span>
+
+            <span class="k">if</span> <span class="n">infile</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
+
+                <span class="k">if</span> <span class="ow">not</span> <span class="nb">isinstance</span><span class="p">(</span>
+                    <span class="n">resource</span><span class="p">,</span>
+                    <span class="p">(</span>
+                        <span class="n">network_resources</span><span class="o">.</span><span class="n">data_formats</span><span class="o">.</span>\
+                            <span class="n">input_formats</span><span class="o">.</span><span class="n">NetworkInput</span><span class="p">,</span>
+                        <span class="n">network_resources</span><span class="o">.</span><span class="n">resource</span><span class="o">.</span><span class="n">NetworkResource</span><span class="p">,</span>
+                    <span class="p">)</span>
+                <span class="p">):</span>
+
+                    <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span>
+                        <span class="s1">&#39;_read_network_data: No proper input file &#39;</span>
+                        <span class="s1">&#39;definition. `param` should be either &#39;</span>
+                        <span class="s1">&#39;a `pypath.input_formats.NetworkInput` or a &#39;</span>
+                        <span class="s1">&#39;`pypath.resource.NetworkResource` instance.&#39;</span><span class="p">,</span>
+                        <span class="o">-</span><span class="mi">5</span><span class="p">,</span>
+                    <span class="p">)</span>
+
+                    <span class="k">return</span> <span class="kc">None</span>
+
+                <span class="k">if</span> <span class="n">networkinput</span><span class="o">.</span><span class="n">huge</span><span class="p">:</span>
+
+                    <span class="n">sys</span><span class="o">.</span><span class="n">stdout</span><span class="o">.</span><span class="n">write</span><span class="p">(</span>
+                        <span class="s1">&#39;</span><span class="se">\n\t</span><span class="s1">Processing </span><span class="si">%s</span><span class="s1"> requires huge memory.</span><span class="se">\n</span><span class="s1">&#39;</span>
+                        <span class="s1">&#39;</span><span class="se">\t</span><span class="s1">Please hit `y` if you have at &#39;</span>
+                        <span class="s1">&#39;least 2G free memory,</span><span class="se">\n</span><span class="s1">&#39;</span>
+                        <span class="s1">&#39;</span><span class="se">\t</span><span class="s1">or `n` to omit </span><span class="si">%s</span><span class="s1">.</span><span class="se">\n</span><span class="s1">&#39;</span>
+                        <span class="s1">&#39;</span><span class="se">\t</span><span class="s1">After processing once, it will be saved in </span><span class="se">\n</span><span class="s1">&#39;</span>
+                        <span class="s1">&#39;</span><span class="se">\t</span><span class="si">%s</span><span class="s1">, so next time can be loaded quickly.</span><span class="se">\n\n</span><span class="s1">&#39;</span>
+                        <span class="s1">&#39;</span><span class="se">\t</span><span class="s1">Process </span><span class="si">%s</span><span class="s1"> now? [y/n]</span><span class="se">\n</span><span class="s1">&#39;</span> <span class="o">%</span>
+                        <span class="p">(</span>
+                            <span class="n">networkinput</span><span class="o">.</span><span class="n">name</span><span class="p">,</span>
+                            <span class="n">networkinput</span><span class="o">.</span><span class="n">name</span><span class="p">,</span>
+                            <span class="n">edges_cache</span><span class="p">,</span>
+                            <span class="n">networkinput</span><span class="o">.</span><span class="n">name</span>
+                        <span class="p">)</span>
+                    <span class="p">)</span>
+                    <span class="n">sys</span><span class="o">.</span><span class="n">stdout</span><span class="o">.</span><span class="n">flush</span><span class="p">()</span>
+
+                    <span class="k">while</span> <span class="kc">True</span><span class="p">:</span>
+                        <span class="n">answer</span> <span class="o">=</span> <span class="nb">input</span><span class="p">()</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span>
+
+                        <span class="k">if</span> <span class="n">answer</span> <span class="o">==</span> <span class="s1">&#39;n&#39;</span><span class="p">:</span>
+                            <span class="k">return</span> <span class="kc">None</span>
+
+                        <span class="k">elif</span> <span class="n">answer</span> <span class="o">==</span> <span class="s1">&#39;y&#39;</span><span class="p">:</span>
+                            <span class="k">break</span>
+
+                        <span class="k">else</span><span class="p">:</span>
+                            <span class="n">sys</span><span class="o">.</span><span class="n">stdout</span><span class="o">.</span><span class="n">write</span><span class="p">(</span>
+                                <span class="s1">&#39;</span><span class="se">\n\t</span><span class="s1">Please answer `y` or `n`:</span><span class="se">\n\t</span><span class="s1">&#39;</span><span class="p">)</span>
+                            <span class="n">sys</span><span class="o">.</span><span class="n">stdout</span><span class="o">.</span><span class="n">flush</span><span class="p">()</span>
+
+                <span class="c1"># if no method available it gonna be None</span>
+                <span class="n">input_func</span> <span class="o">=</span> <span class="n">inputs</span><span class="o">.</span><span class="n">get_method</span><span class="p">(</span><span class="n">networkinput</span><span class="o">.</span><span class="n">input</span><span class="p">)</span>
+
+                <span class="c1"># reading from remote or local file, or executing import</span>
+                <span class="c1"># function:</span>
+                <span class="k">if</span> <span class="p">(</span>
+                    <span class="nb">isinstance</span><span class="p">(</span><span class="n">networkinput</span><span class="o">.</span><span class="n">input</span><span class="p">,</span> <span class="nb">str</span><span class="p">)</span> <span class="ow">and</span> <span class="p">(</span>
+                        <span class="n">networkinput</span><span class="o">.</span><span class="n">input</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s1">&#39;http&#39;</span><span class="p">)</span> <span class="ow">or</span>
+                        <span class="n">networkinput</span><span class="o">.</span><span class="n">input</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s1">&#39;ftp&#39;</span><span class="p">)</span>
+                    <span class="p">)</span>
+                <span class="p">):</span>
+
+                    <span class="n">curl_use_cache</span> <span class="o">=</span> <span class="ow">not</span> <span class="n">redownload</span>
+                    <span class="n">c</span> <span class="o">=</span> <span class="n">curl</span><span class="o">.</span><span class="n">Curl</span><span class="p">(</span>
+                        <span class="n">networkinput</span><span class="o">.</span><span class="n">input</span><span class="p">,</span>
+                        <span class="n">silent</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+                        <span class="n">large</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
+                        <span class="n">cache</span> <span class="o">=</span> <span class="n">curl_use_cache</span>
+                    <span class="p">)</span>
+                    <span class="n">infile</span> <span class="o">=</span> <span class="n">c</span><span class="o">.</span><span class="n">fileobj</span><span class="o">.</span><span class="n">read</span><span class="p">()</span>
+
+                    <span class="k">if</span> <span class="nb">type</span><span class="p">(</span><span class="n">infile</span><span class="p">)</span> <span class="ow">is</span> <span class="nb">bytes</span><span class="p">:</span>
+
+                        <span class="k">try</span><span class="p">:</span>
+                            <span class="n">infile</span> <span class="o">=</span> <span class="n">infile</span><span class="o">.</span><span class="n">decode</span><span class="p">(</span><span class="s1">&#39;utf-8&#39;</span><span class="p">)</span>
+
+                        <span class="k">except</span> <span class="ne">UnicodeDecodeError</span> <span class="k">as</span> <span class="n">e</span><span class="p">:</span>
+
+                            <span class="k">try</span><span class="p">:</span>
+                                <span class="n">infile</span> <span class="o">=</span> <span class="n">infile</span><span class="o">.</span><span class="n">decode</span><span class="p">(</span><span class="s1">&#39;iso-8859-1&#39;</span><span class="p">)</span>
+
+                            <span class="k">except</span> <span class="ne">UnicodeDecodeError</span><span class="p">:</span>
+
+                                <span class="k">raise</span> <span class="n">e</span>
+
+                    <span class="n">infile</span> <span class="o">=</span> <span class="p">[</span>
+                        <span class="n">x</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">infile</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\r</span><span class="s1">&#39;</span><span class="p">,</span> <span class="s1">&#39;&#39;</span><span class="p">)</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\n</span><span class="s1">&#39;</span><span class="p">)</span>
+                        <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">x</span><span class="p">)</span> <span class="o">&gt;</span> <span class="mi">0</span>
+                    <span class="p">]</span>
+                    <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span>
+                        <span class="s2">&quot;Retrieving data from `</span><span class="si">%s</span><span class="s2">` ...&quot;</span> <span class="o">%</span> <span class="n">networkinput</span><span class="o">.</span><span class="n">input</span>
+                    <span class="p">)</span>
+
+                <span class="k">elif</span> <span class="n">input_func</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
+
+                    <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span>
+                        <span class="s1">&#39;Retrieving data by method `</span><span class="si">%s</span><span class="s1">` of the &#39;</span>
+                        <span class="s1">&#39;pypath.inputs module...&#39;</span> <span class="o">%</span> <span class="n">input_func</span><span class="o">.</span><span class="vm">__name__</span>
+                    <span class="p">)</span>
+
+                    <span class="n">_store_cache</span> <span class="o">=</span> <span class="n">curl</span><span class="o">.</span><span class="n">CACHE</span>
+
+                    <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">redownload</span><span class="p">,</span> <span class="nb">bool</span><span class="p">):</span>
+
+                        <span class="n">curl</span><span class="o">.</span><span class="n">CACHE</span> <span class="o">=</span> <span class="ow">not</span> <span class="n">redownload</span>
+
+                    <span class="k">try</span><span class="p">:</span>
+
+                        <span class="n">infile</span> <span class="o">=</span> <span class="n">input_func</span><span class="p">(</span><span class="o">**</span><span class="n">networkinput</span><span class="o">.</span><span class="n">input_args</span><span class="p">)</span>
+
+                    <span class="k">except</span> <span class="ne">Exception</span> <span class="k">as</span> <span class="n">e</span><span class="p">:</span>
+
+                        <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span>
+                            <span class="sa">f</span><span class="s1">&#39;Error in method `</span><span class="si">{</span><span class="n">input_func</span><span class="o">.</span><span class="vm">__name__</span><span class="si">}</span><span class="s1">` of the &#39;</span>
+                            <span class="s1">&#39;pypath.inputs module. &#39;</span>
+                        <span class="p">)</span>
+
+                        <span class="k">raise</span> <span class="n">e</span>
+
+                    <span class="k">finally</span><span class="p">:</span>
+
+                        <span class="n">curl</span><span class="o">.</span><span class="n">CACHE</span> <span class="o">=</span> <span class="n">_store_cache</span>
+
+                <span class="k">elif</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">isfile</span><span class="p">(</span><span class="n">networkinput</span><span class="o">.</span><span class="n">input</span><span class="p">):</span>
+
+                    <span class="n">infile</span> <span class="o">=</span> <span class="n">curl</span><span class="o">.</span><span class="n">Curl</span><span class="p">(</span>
+                        <span class="n">networkinput</span><span class="o">.</span><span class="n">input</span><span class="p">,</span>
+                        <span class="n">large</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
+                        <span class="n">silent</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+                    <span class="p">)</span><span class="o">.</span><span class="n">result</span>
+
+                    <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span><span class="s1">&#39;</span><span class="si">%s</span><span class="s1"> opened...&#39;</span> <span class="o">%</span> <span class="n">networkinput</span><span class="o">.</span><span class="n">input</span><span class="p">)</span>
+
+                <span class="k">if</span> <span class="n">infile</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
+
+                    <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span>
+                        <span class="s1">&#39;`</span><span class="si">%s</span><span class="s1">`: Could not find file or input function &#39;</span>
+                        <span class="s1">&#39;or failed preprocessing.&#39;</span> <span class="o">%</span>
+                        <span class="n">networkinput</span><span class="o">.</span><span class="n">input</span><span class="p">,</span>
+                        <span class="o">-</span><span class="mi">5</span><span class="p">,</span>
+                    <span class="p">)</span>
+                    <span class="k">return</span> <span class="kc">None</span>
+
+            <span class="n">is_directed</span> <span class="o">=</span> <span class="n">networkinput</span><span class="o">.</span><span class="n">is_directed</span>
+            <span class="n">sign</span> <span class="o">=</span> <span class="n">networkinput</span><span class="o">.</span><span class="n">sign</span>
+            <span class="n">ref_col</span> <span class="o">=</span> <span class="p">(</span>
+                <span class="n">networkinput</span><span class="o">.</span><span class="n">refs</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span>
+                    <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">networkinput</span><span class="o">.</span><span class="n">refs</span><span class="p">,</span> <span class="nb">tuple</span><span class="p">)</span> <span class="k">else</span>
+                <span class="n">networkinput</span><span class="o">.</span><span class="n">refs</span>
+                    <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">networkinput</span><span class="o">.</span><span class="n">refs</span><span class="p">,</span> <span class="nb">int</span><span class="p">)</span> <span class="k">else</span>
+                <span class="kc">None</span>
+            <span class="p">)</span>
+            <span class="n">ref_sep</span> <span class="o">=</span> <span class="p">(</span>
+                <span class="n">networkinput</span><span class="o">.</span><span class="n">refs</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span>
+                    <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">networkinput</span><span class="o">.</span><span class="n">refs</span><span class="p">,</span> <span class="nb">tuple</span><span class="p">)</span> <span class="k">else</span>
+                <span class="s1">&#39;;&#39;</span>
+            <span class="p">)</span>
+            <span class="c1"># column index of the sign</span>
+            <span class="n">sig_col</span> <span class="o">=</span> <span class="kc">None</span> <span class="k">if</span> <span class="ow">not</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">sign</span><span class="p">,</span> <span class="nb">tuple</span><span class="p">)</span> <span class="k">else</span> <span class="n">sign</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span>
+            <span class="c1"># column index and value(s) for the direction</span>
+            <span class="n">dir_col</span> <span class="o">=</span> <span class="kc">None</span>
+            <span class="n">dir_val</span> <span class="o">=</span> <span class="kc">None</span>
+            <span class="n">dir_sep</span> <span class="o">=</span> <span class="kc">None</span>
+
+            <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">is_directed</span><span class="p">,</span> <span class="nb">tuple</span><span class="p">):</span>
+
+                <span class="n">dir_col</span> <span class="o">=</span> <span class="n">is_directed</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span>
+                <span class="n">dir_val</span> <span class="o">=</span> <span class="n">is_directed</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span>
+                <span class="n">dir_sep</span> <span class="o">=</span> <span class="n">is_directed</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">is_directed</span><span class="p">)</span> <span class="o">&gt;</span> <span class="mi">2</span> <span class="k">else</span> <span class="kc">None</span>
+
+            <span class="k">elif</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">sign</span><span class="p">,</span> <span class="nb">tuple</span><span class="p">):</span>
+
+                <span class="n">dir_col</span> <span class="o">=</span> <span class="n">sign</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span>
+                <span class="n">dir_val</span> <span class="o">=</span> <span class="n">sign</span><span class="p">[</span><span class="mi">1</span><span class="p">:</span><span class="mi">3</span><span class="p">]</span>
+                <span class="n">dir_val</span> <span class="o">=</span> <span class="p">(</span>
+                    <span class="n">dir_val</span>
+                        <span class="k">if</span> <span class="nb">type</span><span class="p">(</span><span class="n">dir_val</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span> <span class="ow">in</span> <span class="n">_const</span><span class="o">.</span><span class="n">SIMPLE_TYPES</span> <span class="k">else</span>
+                    <span class="n">common</span><span class="o">.</span><span class="n">flat_list</span><span class="p">(</span><span class="n">dir_val</span><span class="p">)</span>
+                <span class="p">)</span>
+                <span class="n">dir_sep</span> <span class="o">=</span> <span class="n">sign</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span> <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">sign</span><span class="p">)</span> <span class="o">&gt;</span> <span class="mi">3</span> <span class="k">else</span> <span class="kc">None</span>
+
+            <span class="n">dir_val</span> <span class="o">=</span> <span class="n">common</span><span class="o">.</span><span class="n">to_set</span><span class="p">(</span><span class="n">dir_val</span><span class="p">)</span>
+
+            <span class="n">must_have_references</span> <span class="o">=</span> <span class="p">(</span>
+                <span class="n">settings</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">&#39;keep_noref&#39;</span><span class="p">)</span> <span class="ow">or</span>
+                <span class="n">networkinput</span><span class="o">.</span><span class="n">must_have_references</span>
+            <span class="p">)</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span>
+                <span class="s1">&#39;Resource `</span><span class="si">%s</span><span class="s1">` </span><span class="si">%s</span><span class="s1"> have literature references &#39;</span>
+                <span class="s1">&#39;for all interactions. Interactions without references &#39;</span>
+                <span class="s1">&#39;will be </span><span class="si">%s</span><span class="s1">. You can alter this condition globally by &#39;</span>
+                <span class="s1">&#39;`pypath.settings.keep_noref` or for individual resources &#39;</span>
+                <span class="s1">&#39;by the `must_have_references` attribute of their &#39;</span>
+                <span class="s1">&#39;`NetworkInput` object.&#39;</span> <span class="o">%</span> <span class="p">(</span>
+                    <span class="n">networkinput</span><span class="o">.</span><span class="n">name</span><span class="p">,</span>
+                    <span class="s1">&#39;must&#39;</span> <span class="k">if</span> <span class="n">must_have_references</span> <span class="k">else</span> <span class="s1">&#39;does not need to&#39;</span><span class="p">,</span>
+                    <span class="s1">&#39;dropped&#39;</span> <span class="k">if</span> <span class="n">must_have_references</span> <span class="k">else</span> <span class="s1">&#39;included&#39;</span><span class="p">,</span>
+                <span class="p">),</span>
+                <span class="mi">1</span><span class="p">,</span>
+            <span class="p">)</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span>
+                <span class="s1">&#39;`</span><span class="si">%s</span><span class="s1">` must have references: </span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="p">(</span>
+                    <span class="n">networkinput</span><span class="o">.</span><span class="n">name</span><span class="p">,</span>
+                    <span class="nb">str</span><span class="p">(</span><span class="n">must_have_references</span><span class="p">)</span>
+                <span class="p">)</span>
+            <span class="p">)</span>
+
+            <span class="c1"># iterating lines from input file</span>
+            <span class="n">input_filtered</span> <span class="o">=</span> <span class="mi">0</span>
+            <span class="n">ref_filtered</span> <span class="o">=</span> <span class="mi">0</span>
+            <span class="n">taxon_filtered</span> <span class="o">=</span> <span class="mi">0</span>
+            <span class="n">read_error</span> <span class="o">=</span> <span class="kc">False</span>
+            <span class="n">lnum</span> <span class="o">=</span> <span class="mi">0</span> <span class="c1"># we need to define it here to avoid errors if the</span>
+                     <span class="c1"># loop below runs zero cycles</span>
+
+            <span class="n">prg</span> <span class="o">=</span> <span class="n">progress</span><span class="o">.</span><span class="n">Progress</span><span class="p">(</span>
+                <span class="n">iterable</span> <span class="o">=</span> <span class="n">infile</span><span class="p">,</span>
+                <span class="n">name</span> <span class="o">=</span> <span class="s1">&#39;Reading network data - </span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="n">networkinput</span><span class="o">.</span><span class="n">name</span><span class="p">,</span>
+            <span class="p">)</span>
+
+            <span class="k">try</span><span class="p">:</span>
+
+                <span class="k">for</span> <span class="n">lnum</span><span class="p">,</span> <span class="n">line</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">prg</span><span class="p">):</span>
+
+                    <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">line</span><span class="p">)</span> <span class="o">&lt;=</span> <span class="mi">1</span> <span class="ow">or</span> <span class="p">(</span><span class="n">lnum</span> <span class="o">==</span> <span class="mi">1</span> <span class="ow">and</span> <span class="n">networkinput</span><span class="o">.</span><span class="n">header</span><span class="p">):</span>
+                        <span class="c1"># empty lines</span>
+                        <span class="c1"># or header row</span>
+                        <span class="k">continue</span>
+
+                    <span class="k">if</span> <span class="ow">not</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">line</span><span class="p">,</span> <span class="p">(</span><span class="nb">list</span><span class="p">,</span> <span class="nb">tuple</span><span class="p">)):</span>
+
+                        <span class="k">if</span> <span class="nb">hasattr</span><span class="p">(</span><span class="n">line</span><span class="p">,</span> <span class="s1">&#39;decode&#39;</span><span class="p">):</span>
+                            <span class="n">line</span> <span class="o">=</span> <span class="n">line</span><span class="o">.</span><span class="n">decode</span><span class="p">(</span><span class="s1">&#39;utf-8&#39;</span><span class="p">)</span>
+
+                        <span class="n">line</span> <span class="o">=</span> <span class="n">line</span><span class="o">.</span><span class="n">strip</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\n\r</span><span class="s1">&#39;</span><span class="p">)</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="n">networkinput</span><span class="o">.</span><span class="n">separator</span><span class="p">)</span>
+
+                    <span class="k">else</span><span class="p">:</span>
+                        <span class="n">line</span> <span class="o">=</span> <span class="p">[</span>
+                            <span class="n">x</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\n</span><span class="s1">&#39;</span><span class="p">,</span> <span class="s1">&#39;&#39;</span><span class="p">)</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\r</span><span class="s1">&#39;</span><span class="p">,</span> <span class="s1">&#39;&#39;</span><span class="p">)</span>
+                                <span class="k">if</span> <span class="nb">hasattr</span><span class="p">(</span><span class="n">x</span><span class="p">,</span> <span class="s1">&#39;replace&#39;</span><span class="p">)</span> <span class="k">else</span>
+                            <span class="n">x</span>
+                            <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">line</span>
+                        <span class="p">]</span>
+
+                    <span class="c1"># 1) filters</span>
+                    <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">_filters</span><span class="p">(</span>
+                        <span class="n">line</span><span class="p">,</span>
+                        <span class="n">networkinput</span><span class="o">.</span><span class="n">positive_filters</span><span class="p">,</span>
+                        <span class="n">networkinput</span><span class="o">.</span><span class="n">negative_filters</span>
+                    <span class="p">):</span>
+
+                        <span class="n">input_filtered</span> <span class="o">+=</span> <span class="mi">1</span>
+                        <span class="k">continue</span>
+
+                    <span class="c1"># 2) direction</span>
+                    <span class="c1"># reading names and attributes:</span>
+                    <span class="k">if</span> <span class="n">is_directed</span> <span class="ow">and</span> <span class="ow">not</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">is_directed</span><span class="p">,</span> <span class="nb">tuple</span><span class="p">):</span>
+
+                        <span class="n">this_edge_dir</span> <span class="o">=</span> <span class="kc">True</span>
+
+                    <span class="k">else</span><span class="p">:</span>
+
+                        <span class="n">this_edge_dir</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_process_direction</span><span class="p">(</span>
+                            <span class="n">line</span><span class="p">,</span>
+                            <span class="n">dir_col</span><span class="p">,</span>
+                            <span class="n">dir_val</span><span class="p">,</span>
+                            <span class="n">dir_sep</span><span class="p">,</span>
+                        <span class="p">)</span>
+
+                    <span class="c1"># 3) references</span>
+                    <span class="n">refs</span> <span class="o">=</span> <span class="p">[]</span>
+
+                    <span class="k">if</span> <span class="n">ref_col</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
+
+                        <span class="k">if</span> <span class="n">line</span><span class="p">[</span><span class="n">ref_col</span><span class="p">]</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
+
+                            <span class="n">refs</span> <span class="o">=</span> <span class="p">()</span>
+
+                        <span class="k">elif</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">line</span><span class="p">[</span><span class="n">ref_col</span><span class="p">],</span> <span class="p">(</span><span class="nb">list</span><span class="p">,</span> <span class="nb">set</span><span class="p">,</span> <span class="nb">tuple</span><span class="p">)):</span>
+
+                            <span class="n">refs</span> <span class="o">=</span> <span class="n">line</span><span class="p">[</span><span class="n">ref_col</span><span class="p">]</span>
+
+                        <span class="k">elif</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">line</span><span class="p">[</span><span class="n">ref_col</span><span class="p">],</span> <span class="nb">int</span><span class="p">):</span>
+
+                            <span class="n">refs</span> <span class="o">=</span> <span class="p">(</span><span class="n">line</span><span class="p">[</span><span class="n">ref_col</span><span class="p">],)</span>
+
+                        <span class="k">else</span><span class="p">:</span>
+
+                            <span class="n">refs</span> <span class="o">=</span> <span class="n">line</span><span class="p">[</span><span class="n">ref_col</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="n">ref_sep</span><span class="p">)</span>
+
+                        <span class="n">refs</span> <span class="o">=</span> <span class="n">common</span><span class="o">.</span><span class="n">del_empty</span><span class="p">(</span><span class="nb">list</span><span class="p">(</span><span class="nb">set</span><span class="p">(</span><span class="n">refs</span><span class="p">)))</span>
+
+                    <span class="n">refs</span> <span class="o">=</span> <span class="n">pubmed_input</span><span class="o">.</span><span class="n">only_pmids</span><span class="p">(</span>
+                        <span class="p">[</span><span class="nb">str</span><span class="p">(</span><span class="n">r</span><span class="p">)</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span> <span class="k">for</span> <span class="n">r</span> <span class="ow">in</span> <span class="n">refs</span><span class="p">]</span>
+                    <span class="p">)</span>
+
+                    <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">refs</span><span class="p">)</span> <span class="o">==</span> <span class="mi">0</span> <span class="ow">and</span> <span class="n">must_have_references</span><span class="p">:</span>
+
+                        <span class="n">ref_filtered</span> <span class="o">+=</span> <span class="mi">1</span>
+                        <span class="k">continue</span>
+
+                    <span class="c1"># 4) entity types</span>
+                    <span class="n">entity_type_a</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_process_field</span><span class="p">(</span>
+                        <span class="n">networkinput</span><span class="o">.</span><span class="n">entity_type_a</span><span class="p">,</span>
+                        <span class="n">line</span><span class="p">,</span>
+                    <span class="p">)</span>
+                    <span class="n">entity_type_b</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_process_field</span><span class="p">(</span>
+                        <span class="n">networkinput</span><span class="o">.</span><span class="n">entity_type_b</span><span class="p">,</span>
+                        <span class="n">line</span><span class="p">,</span>
+                    <span class="p">)</span>
+
+                    <span class="c1"># 5) ID types</span>
+                    <span class="n">id_type_a</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_process_field</span><span class="p">(</span><span class="n">networkinput</span><span class="o">.</span><span class="n">id_type_a</span><span class="p">,</span> <span class="n">line</span><span class="p">)</span>
+                    <span class="n">id_type_b</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_process_field</span><span class="p">(</span><span class="n">networkinput</span><span class="o">.</span><span class="n">id_type_b</span><span class="p">,</span> <span class="n">line</span><span class="p">)</span>
+
+                    <span class="c1"># 6) organisms</span>
+                    <span class="c1"># to give an easy way for input definition:</span>
+                    <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">networkinput</span><span class="o">.</span><span class="n">ncbi_tax_id</span><span class="p">,</span> <span class="nb">int</span><span class="p">):</span>
+
+                        <span class="n">taxon_a</span> <span class="o">=</span> <span class="p">(</span>
+                            <span class="n">_const</span><span class="o">.</span><span class="n">NOT_ORGANISM_SPECIFIC</span>
+                                <span class="k">if</span> <span class="n">entity_type_a</span> <span class="ow">in</span> <span class="n">SMOL_TYPES</span> <span class="k">else</span>
+                            <span class="n">networkinput</span><span class="o">.</span><span class="n">ncbi_tax_id</span>
+                        <span class="p">)</span>
+                        <span class="n">taxon_b</span> <span class="o">=</span> <span class="p">(</span>
+                            <span class="n">_const</span><span class="o">.</span><span class="n">NOT_ORGANISM_SPECIFIC</span>
+                                <span class="k">if</span> <span class="n">entity_type_b</span> <span class="ow">in</span> <span class="n">SMOL_TYPES</span> <span class="k">else</span>
+                            <span class="n">networkinput</span><span class="o">.</span><span class="n">ncbi_tax_id</span>
+                        <span class="p">)</span>
+
+                    <span class="c1"># to enable more sophisticated inputs:</span>
+                    <span class="k">elif</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">networkinput</span><span class="o">.</span><span class="n">ncbi_tax_id</span><span class="p">,</span> <span class="nb">dict</span><span class="p">):</span>
+
+                        <span class="n">taxx</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_process_taxon</span><span class="p">(</span>
+                            <span class="n">networkinput</span><span class="o">.</span><span class="n">ncbi_tax_id</span><span class="p">,</span>
+                            <span class="n">line</span><span class="p">,</span>
+                        <span class="p">)</span>
+
+                        <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">taxx</span><span class="p">,</span> <span class="nb">tuple</span><span class="p">):</span>
+
+                            <span class="n">taxon_a</span><span class="p">,</span> <span class="n">taxon_b</span> <span class="o">=</span> <span class="n">taxx</span>
+
+                        <span class="k">else</span><span class="p">:</span>
+
+                            <span class="n">taxon_a</span> <span class="o">=</span> <span class="n">taxon_b</span> <span class="o">=</span> <span class="n">taxx</span>
+
+                        <span class="n">taxd_a</span> <span class="o">=</span> <span class="p">(</span>
+                            <span class="n">networkinput</span><span class="o">.</span><span class="n">ncbi_tax_id</span><span class="p">[</span><span class="s1">&#39;A&#39;</span><span class="p">]</span>
+                                <span class="k">if</span> <span class="s1">&#39;A&#39;</span> <span class="ow">in</span> <span class="n">networkinput</span><span class="o">.</span><span class="n">ncbi_tax_id</span> <span class="k">else</span>
+                            <span class="n">_const</span><span class="o">.</span><span class="n">NOT_ORGANISM_SPECIFIC</span>
+                                <span class="k">if</span> <span class="n">entity_type_a</span> <span class="ow">in</span> <span class="n">SMOL_TYPES</span> <span class="k">else</span>
+                            <span class="n">networkinput</span><span class="o">.</span><span class="n">ncbi_tax_id</span>
+                        <span class="p">)</span>
+                        <span class="n">taxd_b</span> <span class="o">=</span> <span class="p">(</span>
+                            <span class="n">networkinput</span><span class="o">.</span><span class="n">ncbi_tax_id</span><span class="p">[</span><span class="s1">&#39;B&#39;</span><span class="p">]</span>
+                                <span class="k">if</span> <span class="s1">&#39;B&#39;</span> <span class="ow">in</span> <span class="n">networkinput</span><span class="o">.</span><span class="n">ncbi_tax_id</span> <span class="k">else</span>
+                            <span class="n">_const</span><span class="o">.</span><span class="n">NOT_ORGANISM_SPECIFIC</span>
+                                <span class="k">if</span> <span class="n">entity_type_b</span> <span class="ow">in</span> <span class="n">SMOL_TYPES</span> <span class="k">else</span>
+                            <span class="n">networkinput</span><span class="o">.</span><span class="n">ncbi_tax_id</span>
+                        <span class="p">)</span>
+
+                        <span class="n">only_default</span> <span class="o">=</span> <span class="n">networkinput</span><span class="o">.</span><span class="n">only_default_organism</span>
+
+                        <span class="k">if</span> <span class="ow">not</span> <span class="p">(</span>
+                            <span class="bp">self</span><span class="o">.</span><span class="n">_match_taxon</span><span class="p">(</span><span class="n">taxd_a</span><span class="p">,</span> <span class="n">taxon_a</span><span class="p">,</span> <span class="n">only_default</span><span class="p">)</span> <span class="ow">and</span>
+                            <span class="bp">self</span><span class="o">.</span><span class="n">_match_taxon</span><span class="p">(</span><span class="n">taxd_b</span><span class="p">,</span> <span class="n">taxon_b</span><span class="p">,</span> <span class="n">only_default</span><span class="p">)</span>
+                        <span class="p">):</span>
+
+                            <span class="n">taxon_filtered</span> <span class="o">+=</span> <span class="mi">1</span>
+                            <span class="k">continue</span>
+
+                    <span class="c1"># assuming by default the default organism</span>
+                    <span class="k">else</span><span class="p">:</span>
+
+                        <span class="n">taxon_a</span> <span class="o">=</span> <span class="n">taxon_b</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">ncbi_tax_id</span>
+
+                    <span class="k">if</span> <span class="n">taxon_a</span> <span class="ow">is</span> <span class="kc">None</span> <span class="ow">or</span> <span class="n">taxon_b</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
+
+                        <span class="n">taxon_filtered</span> <span class="o">+=</span> <span class="mi">1</span>
+                        <span class="k">continue</span>
+
+                    <span class="c1"># 7) effect (sign)</span>
+                    <span class="n">positive</span> <span class="o">=</span> <span class="kc">False</span>
+                    <span class="n">negative</span> <span class="o">=</span> <span class="kc">False</span>
+
+                    <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">sign</span><span class="p">,</span> <span class="nb">tuple</span><span class="p">):</span>
+
+                        <span class="n">positive</span><span class="p">,</span> <span class="n">negative</span> <span class="o">=</span> <span class="p">(</span>
+                            <span class="bp">self</span><span class="o">.</span><span class="n">_process_sign</span><span class="p">(</span><span class="n">line</span><span class="p">[</span><span class="n">sign</span><span class="p">[</span><span class="mi">0</span><span class="p">]],</span> <span class="n">sign</span><span class="p">)</span>
+                        <span class="p">)</span>
+
+                    <span class="c1"># 8) resources (source databases)</span>
+                    <span class="n">resource</span> <span class="o">=</span> <span class="p">(</span>
+                        <span class="n">line</span><span class="p">[</span><span class="n">networkinput</span><span class="o">.</span><span class="n">resource</span><span class="p">]</span>
+                            <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">networkinput</span><span class="o">.</span><span class="n">resource</span><span class="p">,</span> <span class="nb">int</span><span class="p">)</span> <span class="k">else</span>
+                        <span class="n">line</span><span class="p">[</span><span class="n">networkinput</span><span class="o">.</span><span class="n">resource</span><span class="p">[</span><span class="mi">0</span><span class="p">]]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span>
+                            <span class="n">networkinput</span><span class="o">.</span><span class="n">resource</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span>
+                        <span class="p">)</span>
+                            <span class="k">if</span> <span class="p">(</span>
+                                <span class="nb">isinstance</span><span class="p">(</span><span class="n">networkinput</span><span class="o">.</span><span class="n">resource</span><span class="p">,</span> <span class="nb">tuple</span><span class="p">)</span> <span class="ow">and</span>
+                                <span class="nb">hasattr</span><span class="p">(</span><span class="n">line</span><span class="p">[</span><span class="n">networkinput</span><span class="o">.</span><span class="n">resource</span><span class="p">[</span><span class="mi">0</span><span class="p">]],</span> <span class="s1">&#39;split&#39;</span><span class="p">)</span>
+                            <span class="p">)</span> <span class="k">else</span>
+                        <span class="p">[]</span>
+                            <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">networkinput</span><span class="o">.</span><span class="n">resource</span><span class="p">,</span> <span class="nb">tuple</span><span class="p">)</span> <span class="k">else</span>
+                        <span class="n">networkinput</span><span class="o">.</span><span class="n">resource</span>
+                    <span class="p">)</span>
+
+                    <span class="n">resource</span> <span class="o">=</span> <span class="n">common</span><span class="o">.</span><span class="n">to_set</span><span class="p">(</span><span class="n">resource</span><span class="p">)</span>
+
+                    <span class="n">_resources_secondary</span> <span class="o">=</span> <span class="nb">tuple</span><span class="p">(</span>
+                        <span class="n">network_resources</span><span class="o">.</span><span class="n">resource</span><span class="o">.</span><span class="n">NetworkResource</span><span class="p">(</span>
+                            <span class="n">name</span> <span class="o">=</span> <span class="n">sec_res</span><span class="p">,</span>
+                            <span class="n">interaction_type</span> <span class="o">=</span> <span class="n">_resource</span><span class="o">.</span><span class="n">interaction_type</span><span class="p">,</span>
+                            <span class="n">data_model</span> <span class="o">=</span> <span class="n">_resource</span><span class="o">.</span><span class="n">data_model</span><span class="p">,</span>
+                            <span class="n">via</span> <span class="o">=</span> <span class="n">_resource</span><span class="o">.</span><span class="n">name</span><span class="p">,</span>
+                            <span class="n">dataset</span> <span class="o">=</span> <span class="n">_resource</span><span class="o">.</span><span class="n">dataset</span><span class="p">,</span>
+                        <span class="p">)</span>
+                        <span class="k">for</span> <span class="n">sec_res</span> <span class="ow">in</span> <span class="n">resource</span>
+                        <span class="k">if</span> <span class="n">sec_res</span> <span class="o">!=</span> <span class="n">_resource</span><span class="o">.</span><span class="n">name</span>
+                    <span class="p">)</span>
+
+                    <span class="n">resource</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">networkinput</span><span class="o">.</span><span class="n">name</span><span class="p">)</span>
+
+                    <span class="c1"># 9) interacting partners</span>
+                    <span class="n">id_a</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_process_partner</span><span class="p">(</span><span class="n">networkinput</span><span class="o">.</span><span class="n">id_col_a</span><span class="p">,</span> <span class="n">line</span><span class="p">)</span>
+                    <span class="n">id_b</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_process_partner</span><span class="p">(</span><span class="n">networkinput</span><span class="o">.</span><span class="n">id_col_b</span><span class="p">,</span> <span class="n">line</span><span class="p">)</span>
+
+                    <span class="c1"># 10) further attributes</span>
+                    <span class="c1"># getting additional edge and node attributes</span>
+                    <span class="n">attrs_edge</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_process_attrs</span><span class="p">(</span>
+                        <span class="n">line</span><span class="p">,</span>
+                        <span class="n">networkinput</span><span class="o">.</span><span class="n">extra_edge_attrs</span><span class="p">,</span>
+                        <span class="n">lnum</span><span class="p">,</span>
+                    <span class="p">)</span>
+                    <span class="n">attrs_node_a</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_process_attrs</span><span class="p">(</span>
+                        <span class="n">line</span><span class="p">,</span>
+                        <span class="n">networkinput</span><span class="o">.</span><span class="n">extra_node_attrs_a</span><span class="p">,</span>
+                        <span class="n">lnum</span><span class="p">,</span>
+                    <span class="p">)</span>
+                    <span class="n">attrs_node_b</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_process_attrs</span><span class="p">(</span>
+                        <span class="n">line</span><span class="p">,</span>
+                        <span class="n">networkinput</span><span class="o">.</span><span class="n">extra_node_attrs_b</span><span class="p">,</span>
+                        <span class="n">lnum</span><span class="p">,</span>
+                    <span class="p">)</span>
+
+                    <span class="c1"># 11) creating the Evidence object</span>
+                    <span class="n">evidences</span> <span class="o">=</span> <span class="n">evidence</span><span class="o">.</span><span class="n">Evidences</span><span class="p">(</span>
+                        <span class="n">evidences</span> <span class="o">=</span> <span class="p">(</span>
+                            <span class="n">evidence</span><span class="o">.</span><span class="n">Evidence</span><span class="p">(</span>
+                                <span class="n">resource</span> <span class="o">=</span> <span class="n">_res</span><span class="p">,</span>
+                                <span class="n">references</span> <span class="o">=</span> <span class="kc">None</span> <span class="k">if</span> <span class="n">_res</span><span class="o">.</span><span class="n">via</span> <span class="k">else</span> <span class="n">refs</span><span class="p">,</span>
+                                <span class="n">attrs</span> <span class="o">=</span> <span class="n">attrs_edge</span><span class="p">,</span>
+                            <span class="p">)</span>
+                            <span class="k">for</span> <span class="n">_res</span> <span class="ow">in</span>
+                            <span class="n">_resources_secondary</span> <span class="o">+</span> <span class="p">(</span><span class="n">_resource</span><span class="p">,)</span>
+                        <span class="p">)</span>
+                    <span class="p">)</span>
+
+                    <span class="c1"># 12) node attributes that</span>
+                    <span class="c1">#     depend on the interaction direction</span>
+                    <span class="k">if</span> <span class="n">networkinput</span><span class="o">.</span><span class="n">mark_source</span><span class="p">:</span>
+
+                        <span class="n">attrs_node_a</span><span class="p">[</span><span class="n">networkinput</span><span class="o">.</span><span class="n">mark_source</span><span class="p">]</span> <span class="o">=</span> <span class="n">this_edge_dir</span>
+
+                    <span class="k">if</span> <span class="n">networkinput</span><span class="o">.</span><span class="n">mark_target</span><span class="p">:</span>
+
+                        <span class="n">attrs_node_b</span><span class="p">[</span><span class="n">networkinput</span><span class="o">.</span><span class="n">mark_target</span><span class="p">]</span> <span class="o">=</span> <span class="n">this_edge_dir</span>
+
+                    <span class="c1"># 13) all interaction data goes into a dict</span>
+                    <span class="n">new_edge</span> <span class="o">=</span> <span class="p">{</span>
+                        <span class="s1">&#39;id_a&#39;</span><span class="p">:</span> <span class="n">id_a</span><span class="p">,</span>
+                        <span class="s1">&#39;id_b&#39;</span><span class="p">:</span> <span class="n">id_b</span><span class="p">,</span>
+                        <span class="s1">&#39;id_type_a&#39;</span><span class="p">:</span> <span class="n">id_type_a</span><span class="p">,</span>
+                        <span class="s1">&#39;id_type_b&#39;</span><span class="p">:</span> <span class="n">id_type_b</span><span class="p">,</span>
+                        <span class="s1">&#39;entity_type_a&#39;</span><span class="p">:</span> <span class="n">entity_type_a</span><span class="p">,</span>
+                        <span class="s1">&#39;entity_type_b&#39;</span><span class="p">:</span> <span class="n">entity_type_b</span><span class="p">,</span>
+                        <span class="s1">&#39;source&#39;</span><span class="p">:</span> <span class="n">resource</span><span class="p">,</span>
+                        <span class="s1">&#39;is_directed&#39;</span><span class="p">:</span> <span class="n">this_edge_dir</span><span class="p">,</span>
+                        <span class="s1">&#39;references&#39;</span><span class="p">:</span> <span class="n">refs</span><span class="p">,</span>
+                        <span class="s1">&#39;positive&#39;</span><span class="p">:</span> <span class="n">positive</span><span class="p">,</span>
+                        <span class="s1">&#39;negative&#39;</span><span class="p">:</span> <span class="n">negative</span><span class="p">,</span>
+                        <span class="s1">&#39;taxon_a&#39;</span><span class="p">:</span> <span class="n">taxon_a</span><span class="p">,</span>
+                        <span class="s1">&#39;taxon_b&#39;</span><span class="p">:</span> <span class="n">taxon_b</span><span class="p">,</span>
+                        <span class="s1">&#39;interaction_type&#39;</span><span class="p">:</span> <span class="n">networkinput</span><span class="o">.</span><span class="n">interaction_type</span><span class="p">,</span>
+                        <span class="s1">&#39;evidences&#39;</span><span class="p">:</span> <span class="n">evidences</span><span class="p">,</span>
+                        <span class="s1">&#39;attrs_node_a&#39;</span><span class="p">:</span> <span class="n">attrs_node_a</span><span class="p">,</span>
+                        <span class="s1">&#39;attrs_node_b&#39;</span><span class="p">:</span> <span class="n">attrs_node_b</span><span class="p">,</span>
+                        <span class="s1">&#39;attrs_edge&#39;</span><span class="p">:</span> <span class="n">attrs_edge</span><span class="p">,</span>
+                    <span class="p">}</span>
+
+                    <span class="k">if</span> <span class="n">read_error</span><span class="p">:</span>
+
+                        <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span>
+                            <span class="s1">&#39;Errors occured, certain lines skipped.&#39;</span>
+                            <span class="s1">&#39;Trying to read the remaining.</span><span class="se">\n</span><span class="s1">&#39;</span><span class="p">,</span>
+                            <span class="mi">5</span><span class="p">,</span>
+                        <span class="p">)</span>
+
+                    <span class="n">edge_list</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">new_edge</span><span class="p">)</span>
+
+                    <span class="k">if</span> <span class="n">first_n</span> <span class="ow">and</span> <span class="nb">len</span><span class="p">(</span><span class="n">edge_list</span><span class="p">)</span> <span class="o">&gt;=</span> <span class="n">first_n</span><span class="p">:</span>
+
+                        <span class="k">break</span>
+
+            <span class="k">except</span> <span class="ne">Exception</span> <span class="k">as</span> <span class="n">e</span><span class="p">:</span>
+
+                <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span>
+                    <span class="s1">&#39;Error at loading resource `</span><span class="si">%s</span><span class="s1">`.&#39;</span> <span class="o">%</span> <span class="n">networkinput</span><span class="o">.</span><span class="n">name</span>
+                <span class="p">)</span>
+
+                <span class="k">raise</span> <span class="n">e</span>
+
+            <span class="k">if</span> <span class="nb">hasattr</span><span class="p">(</span><span class="n">infile</span><span class="p">,</span> <span class="s1">&#39;close&#39;</span><span class="p">):</span>
+
+                <span class="n">infile</span><span class="o">.</span><span class="n">close</span><span class="p">()</span>
+
+            <span class="c1"># 14) ID translation of edges</span>
+            <span class="n">edge_list_mapped</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_map_list</span><span class="p">(</span>
+                <span class="n">edge_list</span><span class="p">,</span>
+                <span class="n">expand_complexes</span> <span class="o">=</span> <span class="n">expand_complexes</span><span class="p">,</span>
+            <span class="p">)</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span>
+                <span class="s1">&#39;</span><span class="si">%u</span><span class="s1"> lines have been read from </span><span class="si">%s</span><span class="s1">, &#39;</span>
+                <span class="s1">&#39;</span><span class="si">%u</span><span class="s1"> links after mapping; &#39;</span>
+                <span class="s1">&#39;</span><span class="si">%u</span><span class="s1"> lines filtered by filters; &#39;</span>
+                <span class="s1">&#39;</span><span class="si">%u</span><span class="s1"> lines filtered because lack of references; &#39;</span>
+                <span class="s1">&#39;</span><span class="si">%u</span><span class="s1"> lines filtered by taxon filters.&#39;</span> <span class="o">%</span>
+                <span class="p">(</span>
+                    <span class="n">lnum</span> <span class="o">-</span> <span class="mi">1</span><span class="p">,</span>
+                    <span class="n">networkinput</span><span class="o">.</span><span class="n">input</span><span class="p">,</span>
+                    <span class="nb">len</span><span class="p">(</span><span class="n">edge_list_mapped</span><span class="p">),</span>
+                    <span class="n">input_filtered</span><span class="p">,</span>
+                    <span class="n">ref_filtered</span><span class="p">,</span>
+                    <span class="n">taxon_filtered</span><span class="p">,</span>
+                <span class="p">)</span>
+            <span class="p">)</span>
+
+            <span class="k">if</span> <span class="n">reread</span> <span class="ow">or</span> <span class="n">redownload</span><span class="p">:</span>
+
+                <span class="n">pickle</span><span class="o">.</span><span class="n">dump</span><span class="p">(</span><span class="n">edge_list_mapped</span><span class="p">,</span> <span class="nb">open</span><span class="p">(</span><span class="n">edges_cache</span><span class="p">,</span> <span class="s1">&#39;wb&#39;</span><span class="p">),</span> <span class="o">-</span><span class="mi">1</span><span class="p">)</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span><span class="s1">&#39;ID translated edge list saved to </span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="n">edges_cache</span><span class="p">)</span>
+
+        <span class="k">else</span><span class="p">:</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span>
+                <span class="s1">&#39;Previously ID translated edge list &#39;</span>
+                <span class="s1">&#39;has been loaded from `</span><span class="si">%s</span><span class="s1">`.&#39;</span> <span class="o">%</span> <span class="n">edges_cache</span>
+            <span class="p">)</span>
+
+        <span class="k">if</span> <span class="n">keep_raw</span><span class="p">:</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">raw_data</span><span class="p">[</span><span class="n">networkinput</span><span class="o">.</span><span class="n">name</span><span class="p">]</span> <span class="o">=</span> <span class="n">edge_list_mapped</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">edge_list_mapped</span> <span class="o">=</span> <span class="n">edge_list_mapped</span>
+
+
+    <span class="k">def</span> <span class="nf">_lookup_cache</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">name</span><span class="p">,</span> <span class="n">cache_files</span><span class="p">,</span> <span class="n">int_cache</span><span class="p">,</span> <span class="n">edges_cache</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Checks up the cache folder for the files of a given resource.</span>
+<span class="sd">        First checks if *name* is on the *cache_files* dictionary.</span>
+<span class="sd">        If so, loads either the interactions or edges otherwise. If</span>
+<span class="sd">        not, checks *edges_cache* or *int_cache* otherwise.</span>
+
+<span class="sd">        :arg str name:</span>
+<span class="sd">            Name of the resource (lower-case).</span>
+<span class="sd">        :arg dict cache_files:</span>
+<span class="sd">            Contains the resource name(s) [str] (keys) and the</span>
+<span class="sd">            corresponding cached file name [str] (values).</span>
+<span class="sd">        :arg str int_cache:</span>
+<span class="sd">            Path to the interactions cache file of the resource.</span>
+<span class="sd">        :arg str edges_cache:</span>
+<span class="sd">            Path to the edges cache file of the resource.</span>
+
+<span class="sd">        :return:</span>
+<span class="sd">            * (*file*) -- The loaded pickle file from the cache if the</span>
+<span class="sd">              file is contains the interactions. ``None`` otherwise.</span>
+<span class="sd">            * (*list*) -- List of mapped edges if the file contains the</span>
+<span class="sd">              information from the edges. ``[]`` otherwise.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">cache_files</span> <span class="o">=</span> <span class="n">cache_files</span> <span class="ow">or</span> <span class="p">{}</span>
+        <span class="n">infile</span> <span class="o">=</span> <span class="kc">None</span>
+        <span class="n">edge_list_mapped</span> <span class="o">=</span> <span class="p">[]</span>
+        <span class="n">cache_file</span> <span class="o">=</span> <span class="n">cache_files</span><span class="p">[</span><span class="n">name</span><span class="p">]</span> <span class="k">if</span> <span class="n">name</span> <span class="ow">in</span> <span class="n">cache_files</span> <span class="k">else</span> <span class="kc">None</span>
+
+        <span class="k">if</span> <span class="n">cache_file</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span> <span class="ow">and</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">exists</span><span class="p">(</span><span class="n">cache_file</span><span class="p">):</span>
+            <span class="n">cache_type</span> <span class="o">=</span> <span class="n">cache_file</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;.&#39;</span><span class="p">)[</span><span class="o">-</span><span class="mi">2</span><span class="p">]</span>
+
+            <span class="k">if</span> <span class="n">cache_type</span> <span class="o">==</span> <span class="s1">&#39;interactions&#39;</span><span class="p">:</span>
+                <span class="n">infile</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">read_from_cache</span><span class="p">(</span><span class="n">int_cache</span><span class="p">)</span>
+
+            <span class="k">elif</span> <span class="n">cache_type</span> <span class="o">==</span> <span class="s1">&#39;edges&#39;</span><span class="p">:</span>
+                <span class="n">edge_list_mapped</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">read_from_cache</span><span class="p">(</span><span class="n">edges_cache</span><span class="p">)</span>
+
+        <span class="k">elif</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">exists</span><span class="p">(</span><span class="n">edges_cache</span><span class="p">):</span>
+            <span class="n">edge_list_mapped</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">read_from_cache</span><span class="p">(</span><span class="n">edges_cache</span><span class="p">)</span>
+
+        <span class="k">elif</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">exists</span><span class="p">(</span><span class="n">int_cache</span><span class="p">):</span>
+            <span class="n">infile</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">read_from_cache</span><span class="p">(</span><span class="n">int_cache</span><span class="p">)</span>
+
+        <span class="k">return</span> <span class="n">infile</span><span class="p">,</span> <span class="n">edge_list_mapped</span>
+
+
+    <span class="nd">@classmethod</span>
+    <span class="k">def</span> <span class="nf">_filters</span><span class="p">(</span>
+            <span class="bp">cls</span><span class="p">,</span>
+            <span class="n">line</span><span class="p">,</span>
+            <span class="n">positive_filters</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">negative_filters</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+        <span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Applies negative and positive filters on a line (record from an</span>
+<span class="sd">        interaction database). If returns ``True`` the interaction will be</span>
+<span class="sd">        discarded, if ``False`` the interaction will be further processed</span>
+<span class="sd">        and if all other criteria fit then will be added to the network</span>
+<span class="sd">        after identifier translation.</span>
+
+<span class="sd">        Return</span>
+<span class="sd">            (bool): True if the line should be filtered (removed), False</span>
+<span class="sd">                if all filters passed, the record can be further processed.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">return</span> <span class="p">(</span>
+            <span class="bp">cls</span><span class="o">.</span><span class="n">_process_filters</span><span class="p">(</span><span class="n">line</span><span class="p">,</span> <span class="n">negative_filters</span><span class="p">,</span> <span class="kc">False</span><span class="p">)</span> <span class="ow">or</span>
+            <span class="bp">cls</span><span class="o">.</span><span class="n">_process_filters</span><span class="p">(</span><span class="n">line</span><span class="p">,</span> <span class="n">positive_filters</span><span class="p">,</span> <span class="kc">True</span><span class="p">)</span>
+        <span class="p">)</span>
+
+
+    <span class="nd">@classmethod</span>
+    <span class="k">def</span> <span class="nf">_process_filters</span><span class="p">(</span><span class="bp">cls</span><span class="p">,</span> <span class="n">line</span><span class="p">,</span> <span class="n">filters</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span> <span class="n">negate</span> <span class="o">=</span> <span class="kc">False</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Args</span>
+<span class="sd">            negate (bool): Whether to negate the filter matches. Sorry for</span>
+<span class="sd">                the confusion, but it should be True for positive filters</span>
+<span class="sd">                and False for negatives.</span>
+
+
+<span class="sd">        Return</span>
+<span class="sd">            (bool): True if the line should be filtered (removed), False</span>
+<span class="sd">                if all filters passed, the record can be further processed.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">_negate</span> <span class="o">=</span> <span class="p">(</span><span class="k">lambda</span> <span class="n">x</span><span class="p">:</span> <span class="ow">not</span> <span class="n">x</span><span class="p">)</span> <span class="k">if</span> <span class="n">negate</span> <span class="k">else</span> <span class="p">(</span><span class="k">lambda</span> <span class="n">x</span><span class="p">:</span> <span class="n">x</span><span class="p">)</span>
+
+        <span class="n">filters</span> <span class="o">=</span> <span class="n">filters</span> <span class="ow">or</span> <span class="p">()</span>
+
+        <span class="k">for</span> <span class="n">filtr</span> <span class="ow">in</span> <span class="n">filters</span><span class="p">:</span>
+
+            <span class="k">if</span> <span class="n">_negate</span><span class="p">(</span><span class="bp">cls</span><span class="o">.</span><span class="n">_process_filter</span><span class="p">(</span><span class="n">line</span><span class="p">,</span> <span class="n">filtr</span><span class="p">)):</span>
+
+                <span class="k">return</span> <span class="kc">True</span>
+
+        <span class="k">return</span> <span class="kc">False</span>
+
+
+    <span class="nd">@classmethod</span>
+    <span class="k">def</span> <span class="nf">_process_filter</span><span class="p">(</span><span class="bp">cls</span><span class="p">,</span> <span class="n">line</span><span class="p">,</span> <span class="n">filtr</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Return</span>
+<span class="sd">            (bool): True if the filter matches.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">if</span> <span class="nb">callable</span><span class="p">(</span><span class="n">filtr</span><span class="p">):</span>
+
+            <span class="k">if</span> <span class="n">filtr</span><span class="p">(</span><span class="n">line</span><span class="p">):</span>
+
+                <span class="k">return</span> <span class="kc">True</span>
+
+        <span class="k">else</span><span class="p">:</span>
+
+            <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">filtr</span><span class="p">)</span> <span class="o">&gt;</span> <span class="mi">2</span><span class="p">:</span>
+
+                <span class="n">sep</span> <span class="o">=</span> <span class="n">filtr</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span>
+                <span class="n">thisVal</span> <span class="o">=</span> <span class="nb">set</span><span class="p">(</span><span class="n">line</span><span class="p">[</span><span class="n">filtr</span><span class="p">[</span><span class="mi">0</span><span class="p">]]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="n">sep</span><span class="p">))</span>
+
+            <span class="k">else</span><span class="p">:</span>
+
+                <span class="n">thisVal</span> <span class="o">=</span> <span class="n">common</span><span class="o">.</span><span class="n">to_set</span><span class="p">(</span><span class="n">line</span><span class="p">[</span><span class="n">filtr</span><span class="p">[</span><span class="mi">0</span><span class="p">]])</span>
+
+            <span class="n">filtrVal</span> <span class="o">=</span> <span class="n">common</span><span class="o">.</span><span class="n">to_set</span><span class="p">(</span><span class="n">filtr</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span>
+
+            <span class="k">return</span> <span class="nb">bool</span><span class="p">(</span><span class="n">thisVal</span> <span class="o">&amp;</span> <span class="n">filtrVal</span><span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">_process_sign</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">sign_data</span><span class="p">,</span> <span class="n">sign_def</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Processes the sign of an interaction, used when processing an</span>
+<span class="sd">        input file.</span>
+
+<span class="sd">        :arg str sign_data:</span>
+<span class="sd">            Data regarding the sign to be processed.</span>
+<span class="sd">        :arg tuple sign_def:</span>
+<span class="sd">            Contains information about how to process *sign_data*. This</span>
+<span class="sd">            is defined in :py:mod:`pypath.data_formats`. First element</span>
+<span class="sd">            determines the position on the direction information of each</span>
+<span class="sd">            line on the data file [int], second element is either [str]</span>
+<span class="sd">            or [list] and defines the terms for which an interaction is</span>
+<span class="sd">            defined as stimulation, third element is similar but for the</span>
+<span class="sd">            inhibition and third (optional) element determines the</span>
+<span class="sd">            separator for *sign_data* if contains more than one element.</span>
+
+<span class="sd">        :return:</span>
+<span class="sd">            * (*bool*) -- Determines whether the processed interaction</span>
+<span class="sd">              is considered stimulation (positive) or not.</span>
+<span class="sd">            * (*bool*) -- Determines whether the processed interaction</span>
+<span class="sd">              is considered inhibition (negative) or not.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">positive</span> <span class="o">=</span> <span class="kc">False</span>
+        <span class="n">negative</span> <span class="o">=</span> <span class="kc">False</span>
+        <span class="n">sign_sep</span> <span class="o">=</span> <span class="n">sign_def</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span> <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">sign_def</span><span class="p">)</span> <span class="o">&gt;</span> <span class="mi">3</span> <span class="k">else</span> <span class="kc">None</span>
+        <span class="n">sign_data</span> <span class="o">=</span> <span class="n">sign_data</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="n">sign_sep</span><span class="p">)</span> <span class="k">if</span> <span class="n">sign_sep</span> <span class="k">else</span> <span class="n">sign_data</span>
+        <span class="n">sign_data</span> <span class="o">=</span> <span class="n">common</span><span class="o">.</span><span class="n">to_set</span><span class="p">(</span><span class="n">sign_data</span><span class="p">)</span>
+        <span class="n">pos</span> <span class="o">=</span> <span class="n">common</span><span class="o">.</span><span class="n">to_set</span><span class="p">(</span><span class="n">sign_def</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span>
+        <span class="n">neg</span> <span class="o">=</span> <span class="n">common</span><span class="o">.</span><span class="n">to_set</span><span class="p">(</span><span class="n">sign_def</span><span class="p">[</span><span class="mi">2</span><span class="p">])</span>
+
+        <span class="k">if</span> <span class="nb">bool</span><span class="p">(</span><span class="n">sign_data</span> <span class="o">&amp;</span> <span class="n">pos</span><span class="p">):</span>
+
+            <span class="n">positive</span> <span class="o">=</span> <span class="kc">True</span>
+
+        <span class="k">if</span> <span class="nb">bool</span><span class="p">(</span><span class="n">sign_data</span> <span class="o">&amp;</span> <span class="n">neg</span><span class="p">):</span>
+
+            <span class="n">negative</span> <span class="o">=</span> <span class="kc">True</span>
+
+        <span class="k">return</span> <span class="n">positive</span><span class="p">,</span> <span class="n">negative</span>
+
+
+    <span class="k">def</span> <span class="nf">_process_direction</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">line</span><span class="p">,</span> <span class="n">dir_col</span><span class="p">,</span> <span class="n">dir_val</span><span class="p">,</span> <span class="n">dir_sep</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Processes the direction information of an interaction according</span>
+<span class="sd">        to a data file from a source.</span>
+
+<span class="sd">        :arg list line:</span>
+<span class="sd">            The stripped and separated line from the resource data file</span>
+<span class="sd">            containing the information of an interaction.</span>
+<span class="sd">        :arg int dir_col:</span>
+<span class="sd">            The column/position number where the information about the</span>
+<span class="sd">            direction is to be found (on *line*).</span>
+<span class="sd">        :arg list dir_val:</span>
+<span class="sd">            Contains the terms [str] for which that interaction is to be</span>
+<span class="sd">            considered directed.</span>
+<span class="sd">        :arg str dir_sep:</span>
+<span class="sd">            Separator for the field in *line* containing the direction</span>
+<span class="sd">            information (if any).</span>
+
+<span class="sd">        :return:</span>
+<span class="sd">            (*bool*) -- Determines whether the given interaction is</span>
+<span class="sd">            directed or not.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">dir_col</span><span class="p">,</span> <span class="nb">bool</span><span class="p">):</span>
+
+            <span class="k">return</span> <span class="n">dic_col</span>
+
+        <span class="k">if</span> <span class="p">(</span>
+            <span class="n">dir_val</span> <span class="ow">is</span> <span class="kc">None</span> <span class="ow">and</span>
+            <span class="nb">isinstance</span><span class="p">(</span><span class="n">dir_col</span><span class="p">,</span> <span class="nb">int</span><span class="p">)</span> <span class="ow">and</span>
+            <span class="nb">isinstance</span><span class="p">(</span><span class="n">line</span><span class="p">[</span><span class="n">dir_col</span><span class="p">],</span> <span class="nb">bool</span><span class="p">)</span>
+        <span class="p">):</span>
+
+            <span class="k">return</span> <span class="n">line</span><span class="p">[</span><span class="n">dir_col</span><span class="p">]</span>
+
+        <span class="k">if</span> <span class="n">dir_col</span> <span class="ow">is</span> <span class="kc">None</span> <span class="ow">or</span> <span class="n">dir_val</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
+
+            <span class="k">return</span> <span class="kc">False</span>
+
+        <span class="k">else</span><span class="p">:</span>
+
+            <span class="n">value</span> <span class="o">=</span> <span class="n">line</span><span class="p">[</span><span class="n">dir_col</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="n">dir_sep</span><span class="p">)</span> <span class="k">if</span> <span class="n">dir_sep</span> <span class="k">else</span> <span class="n">line</span><span class="p">[</span><span class="n">dir_col</span><span class="p">]</span>
+            <span class="n">value</span> <span class="o">=</span> <span class="n">common</span><span class="o">.</span><span class="n">to_set</span><span class="p">(</span><span class="n">value</span><span class="p">)</span>
+
+            <span class="k">return</span> <span class="nb">bool</span><span class="p">(</span><span class="n">value</span> <span class="o">&amp;</span> <span class="n">dir_val</span><span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">_process_field</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">fmt</span><span class="p">,</span> <span class="n">line</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Extract a value from a line describing an interaction.</span>
+
+<span class="sd">        Args</span>
+<span class="sd">            fmt (str, tuple, callable): The value, or a definition how to</span>
+<span class="sd">                process it.</span>
+<span class="sd">            line (list): The raw interaction record.</span>
+
+<span class="sd">        Return</span>
+<span class="sd">            (str): The extracted value.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">if</span> <span class="n">common</span><span class="o">.</span><span class="n">is_str</span><span class="p">(</span><span class="n">fmt</span><span class="p">)</span> <span class="ow">or</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">fmt</span><span class="p">,</span> <span class="nb">list</span><span class="p">):</span>
+
+            <span class="k">return</span> <span class="n">fmt</span>
+
+        <span class="k">elif</span> <span class="nb">callable</span><span class="p">(</span><span class="n">fmt</span><span class="p">):</span>
+
+            <span class="k">return</span> <span class="n">fmt</span><span class="p">(</span><span class="n">line</span><span class="p">)</span>
+
+        <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">fmt</span><span class="p">,</span> <span class="nb">int</span><span class="p">):</span>
+
+            <span class="n">idx</span><span class="p">,</span> <span class="n">dct</span> <span class="o">=</span> <span class="n">fmt</span><span class="p">,</span> <span class="p">{}</span>
+
+        <span class="k">elif</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">fmt</span><span class="p">,</span> <span class="nb">tuple</span><span class="p">):</span>
+
+            <span class="n">idx</span><span class="p">,</span> <span class="n">dct</span> <span class="o">=</span> <span class="n">fmt</span>
+
+        <span class="n">val</span> <span class="o">=</span> <span class="n">line</span><span class="p">[</span><span class="n">idx</span><span class="p">]</span>
+        <span class="n">val</span> <span class="o">=</span> <span class="n">dct</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="n">val</span><span class="p">,</span> <span class="n">val</span><span class="p">)</span>
+
+        <span class="k">return</span> <span class="n">val</span>
+
+
+    <span class="nd">@staticmethod</span>
+    <span class="k">def</span> <span class="nf">_process_partner</span><span class="p">(</span><span class="n">fmt</span><span class="p">,</span> <span class="n">line</span><span class="p">):</span>
+
+        <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">fmt</span><span class="p">,</span> <span class="nb">int</span><span class="p">):</span>
+
+            <span class="n">partner</span> <span class="o">=</span> <span class="n">line</span><span class="p">[</span><span class="n">fmt</span><span class="p">]</span>
+
+        <span class="k">elif</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">fmt</span><span class="p">,</span> <span class="nb">tuple</span><span class="p">):</span>
+
+            <span class="n">idx</span><span class="p">,</span> <span class="n">proc</span> <span class="o">=</span> <span class="n">fmt</span>
+            <span class="n">obj</span> <span class="o">=</span> <span class="n">line</span> <span class="k">if</span> <span class="n">idx</span> <span class="ow">is</span> <span class="kc">None</span> <span class="k">else</span> <span class="n">line</span><span class="p">[</span><span class="n">idx</span><span class="p">]</span>
+
+            <span class="n">partner</span> <span class="o">=</span> <span class="n">proc</span><span class="p">(</span><span class="n">obj</span><span class="p">)</span>
+
+        <span class="k">return</span> <span class="n">partner</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span> <span class="k">if</span> <span class="nb">hasattr</span><span class="p">(</span><span class="n">partner</span><span class="p">,</span> <span class="s1">&#39;strip&#39;</span><span class="p">)</span> <span class="k">else</span> <span class="n">partner</span>
+
+
+    <span class="k">def</span> <span class="nf">_map_list</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">lst</span><span class="p">,</span>
+            <span class="n">single_list</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+            <span class="n">expand_complexes</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
+        <span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Maps the names from a list of edges or items (molecules).</span>
+
+<span class="sd">        :arg list lst:</span>
+<span class="sd">            List of items or edge dictionaries whose names have to be</span>
+<span class="sd">            mapped.</span>
+<span class="sd">        :arg bool single_list:</span>
+<span class="sd">            Optional, ``False`` by default. Determines whether the</span>
+<span class="sd">            provided elements are items or edges. This is, either calls</span>
+<span class="sd">            :py:meth:`pypath.main.PyPath.map_edge` or</span>
+<span class="sd">            :py:meth:`pypath.main.PyPath.map_item` to map the item</span>
+<span class="sd">            names.</span>
+<span class="sd">        :arg bool expand_complexes:</span>
+<span class="sd">            Expand complexes, i.e. create links between each member of</span>
+<span class="sd">            the complex and the interacting partner.</span>
+
+<span class="sd">        :return:</span>
+<span class="sd">            (*list*) -- Copy of *lst* with their elements&#39; names mapped.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">list_mapped</span> <span class="o">=</span> <span class="p">[]</span>
+
+        <span class="k">if</span> <span class="n">single_list</span><span class="p">:</span>
+
+            <span class="k">for</span> <span class="n">item</span> <span class="ow">in</span> <span class="n">lst</span><span class="p">:</span>
+
+                <span class="n">list_mapped</span> <span class="o">+=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_map_item</span><span class="p">(</span>
+                    <span class="n">item</span><span class="p">,</span>
+                    <span class="n">expand_complexes</span> <span class="o">=</span> <span class="n">expand_complexes</span><span class="p">,</span>
+                <span class="p">)</span>
+
+        <span class="k">else</span><span class="p">:</span>
+
+            <span class="k">for</span> <span class="n">edge</span> <span class="ow">in</span> <span class="n">lst</span><span class="p">:</span>
+
+                <span class="n">list_mapped</span> <span class="o">+=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_map_edge</span><span class="p">(</span>
+                    <span class="n">edge</span><span class="p">,</span>
+                    <span class="n">expand_complexes</span> <span class="o">=</span> <span class="n">expand_complexes</span><span class="p">,</span>
+                <span class="p">)</span>
+
+        <span class="k">return</span> <span class="n">list_mapped</span>
+
+
+    <span class="k">def</span> <span class="nf">_map_item</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">item</span><span class="p">,</span> <span class="n">expand_complexes</span> <span class="o">=</span> <span class="kc">True</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Translates the name in *item* representing a molecule. Default</span>
+<span class="sd">        name types are defined in</span>
+<span class="sd">        :py:attr:`pypath.main.PyPath.default_name_type` If the mapping</span>
+<span class="sd">        is unsuccessful, the item will be added to</span>
+<span class="sd">        :py:attr:`pypath.main.PyPath.unmapped` list.</span>
+
+<span class="sd">        :arg dict item:</span>
+<span class="sd">            Item whose name is to be mapped to a default name type.</span>
+<span class="sd">        :arg bool expand_complexes:</span>
+<span class="sd">            Expand complexes, i.e. create links between each member of</span>
+<span class="sd">            the complex and the interacting partner.</span>
+
+<span class="sd">        :return:</span>
+<span class="sd">            (*list*) -- The default mapped name(s) [str] of *item*.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="c1"># TODO: include</span>
+        <span class="n">default_id</span> <span class="o">=</span> <span class="n">mapping</span><span class="o">.</span><span class="n">map_name</span><span class="p">(</span>
+            <span class="n">item</span><span class="p">[</span><span class="s1">&#39;name&#39;</span><span class="p">],</span> <span class="n">item</span><span class="p">[</span><span class="s1">&#39;id_type&#39;</span><span class="p">],</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">default_name_types</span><span class="p">[</span><span class="n">item</span><span class="p">[</span><span class="s1">&#39;type&#39;</span><span class="p">]],</span>
+            <span class="n">expand_complexes</span> <span class="o">=</span> <span class="n">expand_complexes</span><span class="p">,</span>
+        <span class="p">)</span>
+
+        <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">default_id</span><span class="p">)</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">unmapped</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">item</span><span class="p">[</span><span class="s1">&#39;name&#39;</span><span class="p">])</span>
+
+        <span class="k">return</span> <span class="n">default_id</span>
+
+
+    <span class="k">def</span> <span class="nf">_map_edge</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">edge</span><span class="p">,</span> <span class="n">expand_complexes</span> <span class="o">=</span> <span class="kc">True</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Translates the identifiers in *edge* representing an edge. Default</span>
+<span class="sd">        name types are defined in</span>
+<span class="sd">        :py:attr:`pypath.main.PyPath.default_name_type` If the mapping</span>
+<span class="sd">        is unsuccessful, the item will be added to</span>
+<span class="sd">        :py:attr:`pypath.main.PyPath.unmapped` list.</span>
+
+<span class="sd">        :arg dict edge:</span>
+<span class="sd">            Item whose name is to be mapped to a default name type.</span>
+<span class="sd">        :arg bool expand_complexes:</span>
+<span class="sd">            Expand complexes, i.e. create links between each member of</span>
+<span class="sd">            the complex and the interacting partner.</span>
+
+<span class="sd">        :return:</span>
+<span class="sd">            (*list*) -- Contains the edge(s) [dict] with default mapped</span>
+<span class="sd">            names.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">edge_stack</span> <span class="o">=</span> <span class="p">[]</span>
+
+        <span class="n">defnt</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">default_name_types</span>
+        <span class="n">def_name_type_a</span> <span class="o">=</span> <span class="n">defnt</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="n">edge</span><span class="p">[</span><span class="s1">&#39;entity_type_a&#39;</span><span class="p">],</span> <span class="n">edge</span><span class="p">[</span><span class="s1">&#39;id_type_a&#39;</span><span class="p">])</span>
+        <span class="n">def_name_type_b</span> <span class="o">=</span> <span class="n">defnt</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="n">edge</span><span class="p">[</span><span class="s1">&#39;entity_type_b&#39;</span><span class="p">],</span> <span class="n">edge</span><span class="p">[</span><span class="s1">&#39;id_type_b&#39;</span><span class="p">])</span>
+
+        <span class="n">default_id_a</span> <span class="o">=</span> <span class="n">mapping</span><span class="o">.</span><span class="n">map_name</span><span class="p">(</span>
+            <span class="n">edge</span><span class="p">[</span><span class="s1">&#39;id_a&#39;</span><span class="p">],</span>
+            <span class="n">edge</span><span class="p">[</span><span class="s1">&#39;id_type_a&#39;</span><span class="p">],</span>
+            <span class="n">def_name_type_a</span><span class="p">,</span>
+            <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">edge</span><span class="p">[</span><span class="s1">&#39;taxon_a&#39;</span><span class="p">],</span>
+            <span class="n">expand_complexes</span> <span class="o">=</span> <span class="n">expand_complexes</span><span class="p">,</span>
+        <span class="p">)</span>
+
+        <span class="n">default_id_b</span> <span class="o">=</span> <span class="n">mapping</span><span class="o">.</span><span class="n">map_name</span><span class="p">(</span>
+            <span class="n">edge</span><span class="p">[</span><span class="s1">&#39;id_b&#39;</span><span class="p">],</span>
+            <span class="n">edge</span><span class="p">[</span><span class="s1">&#39;id_type_b&#39;</span><span class="p">],</span>
+            <span class="n">def_name_type_b</span><span class="p">,</span>
+            <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">edge</span><span class="p">[</span><span class="s1">&#39;taxon_b&#39;</span><span class="p">],</span>
+            <span class="n">expand_complexes</span> <span class="o">=</span> <span class="n">expand_complexes</span><span class="p">,</span>
+        <span class="p">)</span>
+
+        <span class="c1"># this is needed because the possibility ambigous mapping</span>
+        <span class="c1"># and expansion of complexes</span>
+        <span class="c1"># one name can be mapped to multiple ones</span>
+        <span class="c1"># this multiplies the nodes and edges</span>
+        <span class="c1"># in case of proteins this does not happen too often</span>
+        <span class="k">for</span> <span class="n">id_a</span><span class="p">,</span> <span class="n">id_b</span> <span class="ow">in</span> <span class="n">itertools</span><span class="o">.</span><span class="n">product</span><span class="p">(</span><span class="n">default_id_a</span><span class="p">,</span> <span class="n">default_id_b</span><span class="p">):</span>
+
+            <span class="n">this_edge</span> <span class="o">=</span> <span class="n">copy_mod</span><span class="o">.</span><span class="n">copy</span><span class="p">(</span><span class="n">edge</span><span class="p">)</span>
+            <span class="n">this_edge</span><span class="p">[</span><span class="s1">&#39;default_name_a&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">id_a</span>
+            <span class="n">this_edge</span><span class="p">[</span><span class="s1">&#39;default_name_type_a&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">def_name_type_a</span>
+
+            <span class="n">this_edge</span><span class="p">[</span><span class="s1">&#39;default_name_b&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">id_b</span>
+            <span class="n">this_edge</span><span class="p">[</span><span class="s1">&#39;default_name_type_b&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">def_name_type_b</span>
+
+            <span class="n">edge_stack</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">this_edge</span><span class="p">)</span>
+
+        <span class="k">return</span> <span class="n">edge_stack</span>
+
+
+    <span class="k">def</span> <span class="nf">_process_attrs</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">line</span><span class="p">,</span> <span class="n">spec</span><span class="p">,</span> <span class="n">lnum</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Extracts the extra (custom, resource specific) attributes from a</span>
+<span class="sd">        line of the input based on the given specification (defined in the</span>
+<span class="sd">        network input definition).</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">attrs</span> <span class="o">=</span> <span class="p">{}</span>
+
+        <span class="k">for</span> <span class="n">col</span> <span class="ow">in</span> <span class="n">spec</span><span class="o">.</span><span class="n">keys</span><span class="p">():</span>
+            <span class="c1"># extra_edge_attrs and extra_node_attrs are dicts</span>
+            <span class="c1"># of additional parameters assigned to edges and nodes</span>
+            <span class="c1"># respectively;</span>
+            <span class="c1"># key is the name of the parameter, value is the col number,</span>
+            <span class="c1"># or a tuple of col number and the separator,</span>
+            <span class="c1"># if the column contains additional subfields e.g. (5, &quot;;&quot;)</span>
+
+            <span class="k">try</span><span class="p">:</span>
+
+                <span class="k">if</span> <span class="n">spec</span><span class="p">[</span><span class="n">col</span><span class="p">]</span><span class="o">.</span><span class="vm">__class__</span> <span class="ow">is</span> <span class="nb">tuple</span><span class="p">:</span>
+
+                    <span class="k">if</span> <span class="nb">hasattr</span><span class="p">(</span><span class="n">spec</span><span class="p">[</span><span class="n">col</span><span class="p">][</span><span class="mi">1</span><span class="p">],</span> <span class="s1">&#39;__call__&#39;</span><span class="p">):</span>
+                        <span class="n">field_value</span> <span class="o">=</span> <span class="n">spec</span><span class="p">[</span><span class="n">col</span><span class="p">][</span><span class="mi">1</span><span class="p">](</span><span class="n">line</span><span class="p">[</span><span class="n">spec</span><span class="p">[</span><span class="n">col</span><span class="p">][</span><span class="mi">0</span><span class="p">]])</span>
+
+                    <span class="k">else</span><span class="p">:</span>
+                        <span class="n">field_value</span> <span class="o">=</span> <span class="n">line</span><span class="p">[</span><span class="n">spec</span><span class="p">[</span><span class="n">col</span><span class="p">][</span><span class="mi">0</span><span class="p">]]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="n">spec</span><span class="p">[</span><span class="n">col</span><span class="p">][</span><span class="mi">1</span><span class="p">])</span>
+
+                <span class="k">else</span><span class="p">:</span>
+                    <span class="n">field_value</span> <span class="o">=</span> <span class="n">line</span><span class="p">[</span><span class="n">spec</span><span class="p">[</span><span class="n">col</span><span class="p">]]</span>
+
+            <span class="k">except</span><span class="p">:</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span>
+                    <span class="s1">&#39;Wrong column index (</span><span class="si">%s</span><span class="s1">) in extra attributes? &#39;</span>
+                    <span class="s1">&#39;Line #</span><span class="si">%u</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="p">(</span><span class="nb">str</span><span class="p">(</span><span class="n">col</span><span class="p">),</span> <span class="n">lnum</span><span class="p">),</span>
+                    <span class="o">-</span><span class="mi">5</span><span class="p">,</span>
+                <span class="p">)</span>
+
+            <span class="n">field_name</span> <span class="o">=</span> <span class="n">col</span>
+            <span class="n">attrs</span><span class="p">[</span><span class="n">field_name</span><span class="p">]</span> <span class="o">=</span> <span class="n">field_value</span>
+
+        <span class="k">return</span> <span class="n">attrs</span>
+
+
+    <span class="k">def</span> <span class="nf">_process_taxon</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">tax_dict</span><span class="p">,</span> <span class="n">fields</span><span class="p">):</span> <span class="c1"># TODO</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">tax_dict</span><span class="p">,</span> <span class="nb">int</span><span class="p">):</span>
+
+            <span class="k">return</span> <span class="n">tax_dict</span>
+
+        <span class="k">elif</span> <span class="s1">&#39;A&#39;</span> <span class="ow">in</span> <span class="n">tax_dict</span> <span class="ow">and</span> <span class="s1">&#39;B&#39;</span> <span class="ow">in</span> <span class="n">tax_dict</span><span class="p">:</span>
+
+            <span class="k">return</span> <span class="p">(</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">_process_taxon</span><span class="p">(</span><span class="n">tax_dict</span><span class="p">[</span><span class="s1">&#39;A&#39;</span><span class="p">],</span> <span class="n">fields</span><span class="p">),</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">_process_taxon</span><span class="p">(</span><span class="n">tax_dict</span><span class="p">[</span><span class="s1">&#39;B&#39;</span><span class="p">],</span> <span class="n">fields</span><span class="p">),</span>
+            <span class="p">)</span>
+
+        <span class="k">else</span><span class="p">:</span>
+
+            <span class="k">if</span> <span class="s1">&#39;dict&#39;</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">tax_dict</span><span class="p">:</span>
+                <span class="k">return</span> <span class="nb">int</span><span class="p">(</span><span class="n">fields</span><span class="p">[</span><span class="n">tax_dict</span><span class="p">[</span><span class="s1">&#39;col&#39;</span><span class="p">]])</span>
+
+            <span class="k">elif</span> <span class="n">fields</span><span class="p">[</span><span class="n">tax_dict</span><span class="p">[</span><span class="s1">&#39;col&#39;</span><span class="p">]]</span> <span class="ow">in</span> <span class="n">tax_dict</span><span class="p">[</span><span class="s1">&#39;dict&#39;</span><span class="p">]:</span>
+                <span class="k">return</span> <span class="n">tax_dict</span><span class="p">[</span><span class="s1">&#39;dict&#39;</span><span class="p">][</span><span class="n">fields</span><span class="p">[</span><span class="n">tax_dict</span><span class="p">[</span><span class="s1">&#39;col&#39;</span><span class="p">]]]</span>
+
+            <span class="k">else</span><span class="p">:</span>
+                <span class="k">return</span> <span class="kc">None</span>
+
+
+    <span class="k">def</span> <span class="nf">_match_taxon</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">tax_dict</span><span class="p">,</span> <span class="n">taxon</span><span class="p">,</span> <span class="n">only_default_organism</span> <span class="o">=</span> <span class="kc">False</span><span class="p">):</span>
+
+        <span class="n">has_dict</span> <span class="o">=</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">tax_dict</span><span class="p">,</span> <span class="nb">dict</span><span class="p">)</span>
+        <span class="n">has_include</span> <span class="o">=</span> <span class="n">has_dict</span> <span class="ow">and</span> <span class="s1">&#39;include&#39;</span> <span class="ow">in</span> <span class="n">tax_dict</span>
+        <span class="n">has_exclude</span> <span class="o">=</span> <span class="n">has_dict</span> <span class="ow">and</span> <span class="s1">&#39;exclude&#39;</span> <span class="ow">in</span> <span class="n">tax_dict</span>
+
+        <span class="k">return</span> <span class="p">(</span>
+            <span class="p">(</span>
+                <span class="n">taxon</span> <span class="o">==</span> <span class="n">_const</span><span class="o">.</span><span class="n">NOT_ORGANISM_SPECIFIC</span>
+            <span class="p">)</span> <span class="ow">or</span> <span class="p">(</span>
+                <span class="n">has_include</span> <span class="ow">and</span>
+                <span class="n">taxon</span> <span class="ow">in</span> <span class="n">tax_dict</span><span class="p">[</span><span class="s1">&#39;include&#39;</span><span class="p">]</span>
+            <span class="p">)</span> <span class="ow">or</span> <span class="p">(</span>
+                <span class="n">has_exclude</span> <span class="ow">and</span>
+                <span class="n">taxon</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">tax_dict</span><span class="p">[</span><span class="s1">&#39;exclude&#39;</span><span class="p">]</span>
+            <span class="p">)</span> <span class="ow">or</span> <span class="p">(</span>
+                <span class="ow">not</span> <span class="n">has_include</span> <span class="ow">and</span>
+                <span class="ow">not</span> <span class="n">has_exclude</span> <span class="ow">and</span>
+                <span class="p">(</span>
+                    <span class="ow">not</span> <span class="n">only_default_organism</span> <span class="ow">or</span>
+                    <span class="n">taxon</span> <span class="o">==</span> <span class="bp">self</span><span class="o">.</span><span class="n">ncbi_tax_id</span>
+                <span class="p">)</span>
+            <span class="p">)</span>
+        <span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">_add_edge_list</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">edge_list</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+            <span class="n">regulator</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+            <span class="n">only_directions</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+            <span class="n">allow_loops</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+        <span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Adds edges to the network from *edge_list* obtained from file or</span>
+<span class="sd">        other input method. If none is passed, checks for such data in</span>
+<span class="sd">        :py:attr:`pypath.network.Network.edge_list_mapped`.</span>
+
+<span class="sd">        :arg str edge_list:</span>
+<span class="sd">            Optional, ``False`` by default. The source name of the list</span>
+<span class="sd">            of edges to be added. This must have been loaded previously</span>
+<span class="sd">            (e.g.: with :py:meth:`pypath.main.PyPath.read_data_file`).</span>
+<span class="sd">            If none is passed, loads the data directly from</span>
+<span class="sd">            :py:attr:`pypath.main.PyPath.raw_data`.</span>
+<span class="sd">        :arg bool regulator:</span>
+<span class="sd">            Optional, ``False`` by default. If set to ``True``, non</span>
+<span class="sd">            previously existing nodes, will not be added (and hence, the</span>
+<span class="sd">            edges involved).</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span><span class="s1">&#39;Adding preprocessed edge list to existing network.&#39;</span><span class="p">)</span>
+
+        <span class="n">allow_loops</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_allow_loops</span><span class="p">(</span><span class="n">allow_loops</span> <span class="o">=</span> <span class="n">allow_loops</span><span class="p">)</span>
+
+        <span class="k">if</span> <span class="ow">not</span> <span class="n">edge_list</span><span class="p">:</span>
+
+            <span class="k">if</span> <span class="p">(</span>
+                <span class="nb">hasattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">&#39;edge_list_mapped&#39;</span><span class="p">)</span> <span class="ow">and</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">edge_list_mapped</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span>
+            <span class="p">):</span>
+
+                <span class="n">edge_list</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">edge_list_mapped</span>
+
+            <span class="k">else</span><span class="p">:</span>
+
+                <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span><span class="s1">&#39;_add_edge_list(): No data, nothing to do.&#39;</span><span class="p">)</span>
+                <span class="k">return</span> <span class="kc">True</span>
+
+        <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">edge_list</span><span class="p">,</span> <span class="nb">str</span><span class="p">):</span>
+
+            <span class="k">if</span> <span class="n">edge_list</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">raw_data</span><span class="p">:</span>
+
+                <span class="n">edge_list</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">raw_data</span><span class="p">[</span><span class="n">edge_list</span><span class="p">]</span>
+
+            <span class="k">else</span><span class="p">:</span>
+
+                <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span>
+                    <span class="s1">&#39;`</span><span class="si">%s</span><span class="s1">` looks like a source name, but no data &#39;</span>
+                    <span class="s1">&#39;available under this name.&#39;</span> <span class="o">%</span> <span class="n">edge_list</span>
+                <span class="p">)</span>
+
+                <span class="k">return</span> <span class="kc">False</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_filtered_loops</span> <span class="o">=</span> <span class="mi">0</span>
+
+        <span class="n">prg</span> <span class="o">=</span> <span class="n">progress</span><span class="o">.</span><span class="n">Progress</span><span class="p">(</span>
+            <span class="n">iterable</span> <span class="o">=</span> <span class="n">edge_list</span><span class="p">,</span>
+            <span class="n">name</span> <span class="o">=</span> <span class="s1">&#39;Processing interactions&#39;</span><span class="p">,</span>
+        <span class="p">)</span>
+
+        <span class="k">for</span> <span class="n">e</span> <span class="ow">in</span> <span class="n">prg</span><span class="p">:</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">_add_update_edge</span><span class="p">(</span>
+                <span class="n">e</span><span class="p">,</span>
+                <span class="n">allow_loops</span> <span class="o">=</span> <span class="n">allow_loops</span><span class="p">,</span>
+                <span class="n">only_directions</span> <span class="o">=</span> <span class="n">only_directions</span><span class="p">,</span>
+            <span class="p">)</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span>
+            <span class="s1">&#39;New network resource added, current number &#39;</span>
+            <span class="s1">&#39;of nodes: </span><span class="si">%u</span><span class="s1">, edges: </span><span class="si">%u</span><span class="s1">.&#39;</span> <span class="o">%</span> <span class="p">(</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">vcount</span><span class="p">,</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">ecount</span>
+            <span class="p">)</span>
+        <span class="p">)</span>
+
+        <span class="k">if</span> <span class="ow">not</span> <span class="n">allow_loops</span><span class="p">:</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span><span class="s1">&#39;Loop edges discarded: </span><span class="si">%u</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="bp">self</span><span class="o">.</span><span class="n">_filtered_loops</span><span class="p">)</span>
+
+        <span class="nb">delattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">&#39;_filtered_loops&#39;</span><span class="p">)</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">raw_data</span> <span class="o">=</span> <span class="kc">None</span>
+
+
+    <span class="k">def</span> <span class="nf">_add_update_edge</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">edge</span><span class="p">,</span>
+            <span class="n">allow_loops</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">only_directions</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+        <span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Adds a new interaction (edge) or updates the attributes of the edge</span>
+<span class="sd">        if it already exists.</span>
+
+<span class="sd">        :arg dict edge:</span>
+<span class="sd">            A dictionary describing an edge (interaction) with the following</span>
+<span class="sd">            items:</span>
+<span class="sd">            :item str id_a:</span>
+<span class="sd">                Name of the source node of the edge to be added/updated.</span>
+<span class="sd">            :item str id_b:</span>
+<span class="sd">                Name of the source node of the edge to be added/updated.</span>
+<span class="sd">            :item set source:</span>
+<span class="sd">                Or [list], contains the names [str] of the resources</span>
+<span class="sd">                supporting that edge.</span>
+<span class="sd">            :item pypath.evidence.Evidence evidence:</span>
+<span class="sd">                A ``pypath.evidence.Evidence`` object.</span>
+<span class="sd">            :item bool is_directed:</span>
+<span class="sd">                Whether if the edge is directed or not.</span>
+<span class="sd">            :item set refs:</span>
+<span class="sd">                Or [list], contains the instances of the references</span>
+<span class="sd">                :py:class:`pypath.refs.Reference` for that edge.</span>
+<span class="sd">            :item bool stim:</span>
+<span class="sd">                Whether the edge is stimulatory or not.</span>
+<span class="sd">            :item bool inh:</span>
+<span class="sd">                Whether the edge is inhibitory or note</span>
+<span class="sd">            :item int taxon_a:</span>
+<span class="sd">                NCBI Taxonomic identifier of the source molecule.</span>
+<span class="sd">            :item int taxon_b:</span>
+<span class="sd">                NCBI Taxonomic identifier of the target molecule.</span>
+<span class="sd">            :item str typ:</span>
+<span class="sd">                The type of interaction (e.g.: ``&#39;trascriptional&#39;``)</span>
+<span class="sd">            :item dict extra_attrs:</span>
+<span class="sd">                Optional, ``{}`` by default. Contains any extra attributes</span>
+<span class="sd">                for the edge to be updated.</span>
+
+<span class="sd">        :arg bool only_directions:</span>
+<span class="sd">            Optional, ``False`` by default. If set to ``True`` and the</span>
+<span class="sd">            edge is not in the network, it won&#39;t be created. If it already</span>
+<span class="sd">            exists the attributes of the new edge will be added to the</span>
+<span class="sd">            existing one.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="p">(</span>
+            <span class="n">id_a</span><span class="p">,</span>
+            <span class="n">id_b</span><span class="p">,</span>
+            <span class="n">id_type_a</span><span class="p">,</span>
+            <span class="n">id_type_b</span><span class="p">,</span>
+            <span class="n">entity_type_a</span><span class="p">,</span>
+            <span class="n">entity_type_b</span><span class="p">,</span>
+            <span class="n">source</span><span class="p">,</span>
+            <span class="n">evidences</span><span class="p">,</span>
+            <span class="n">is_directed</span><span class="p">,</span>
+            <span class="n">refs</span><span class="p">,</span>
+            <span class="n">positive</span><span class="p">,</span>
+            <span class="n">negative</span><span class="p">,</span>
+            <span class="n">taxon_a</span><span class="p">,</span>
+            <span class="n">taxon_b</span><span class="p">,</span>
+            <span class="n">interaction_type</span><span class="p">,</span>
+            <span class="n">extra_attrs</span><span class="p">,</span>
+            <span class="n">extra_attrs_a</span><span class="p">,</span>
+            <span class="n">extra_attrs_b</span><span class="p">,</span>
+        <span class="p">)</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="n">edge</span><span class="p">[</span><span class="s1">&#39;default_name_a&#39;</span><span class="p">],</span>
+            <span class="n">edge</span><span class="p">[</span><span class="s1">&#39;default_name_b&#39;</span><span class="p">],</span>
+            <span class="n">edge</span><span class="p">[</span><span class="s1">&#39;default_name_type_a&#39;</span><span class="p">],</span>
+            <span class="n">edge</span><span class="p">[</span><span class="s1">&#39;default_name_type_b&#39;</span><span class="p">],</span>
+            <span class="n">edge</span><span class="p">[</span><span class="s1">&#39;entity_type_a&#39;</span><span class="p">],</span>
+            <span class="n">edge</span><span class="p">[</span><span class="s1">&#39;entity_type_b&#39;</span><span class="p">],</span>
+            <span class="n">edge</span><span class="p">[</span><span class="s1">&#39;source&#39;</span><span class="p">],</span>
+            <span class="n">edge</span><span class="p">[</span><span class="s1">&#39;evidences&#39;</span><span class="p">],</span>
+            <span class="n">edge</span><span class="p">[</span><span class="s1">&#39;is_directed&#39;</span><span class="p">],</span>
+            <span class="n">edge</span><span class="p">[</span><span class="s1">&#39;references&#39;</span><span class="p">],</span>
+            <span class="n">edge</span><span class="p">[</span><span class="s1">&#39;positive&#39;</span><span class="p">],</span>
+            <span class="n">edge</span><span class="p">[</span><span class="s1">&#39;negative&#39;</span><span class="p">],</span>
+            <span class="n">edge</span><span class="p">[</span><span class="s1">&#39;taxon_a&#39;</span><span class="p">],</span>
+            <span class="n">edge</span><span class="p">[</span><span class="s1">&#39;taxon_b&#39;</span><span class="p">],</span>
+            <span class="n">edge</span><span class="p">[</span><span class="s1">&#39;interaction_type&#39;</span><span class="p">],</span>
+            <span class="n">edge</span><span class="p">[</span><span class="s1">&#39;attrs_edge&#39;</span><span class="p">],</span>
+            <span class="n">edge</span><span class="p">[</span><span class="s1">&#39;attrs_node_a&#39;</span><span class="p">],</span>
+            <span class="n">edge</span><span class="p">[</span><span class="s1">&#39;attrs_node_b&#39;</span><span class="p">],</span>
+        <span class="p">)</span>
+
+        <span class="n">allow_loops</span> <span class="o">=</span> <span class="n">allow_loops</span> <span class="ow">or</span> <span class="bp">self</span><span class="o">.</span><span class="n">allow_loops</span>
+
+        <span class="n">refs</span> <span class="o">=</span> <span class="p">{</span><span class="n">refs_mod</span><span class="o">.</span><span class="n">Reference</span><span class="p">(</span><span class="n">pmid</span><span class="p">)</span> <span class="k">for</span> <span class="n">pmid</span> <span class="ow">in</span> <span class="n">refs</span><span class="p">}</span>
+
+        <span class="n">entity_a</span> <span class="o">=</span> <span class="n">entity_mod</span><span class="o">.</span><span class="n">Entity</span><span class="p">(</span>
+            <span class="n">identifier</span> <span class="o">=</span> <span class="n">id_a</span><span class="p">,</span>
+            <span class="n">id_type</span> <span class="o">=</span> <span class="n">id_type_a</span><span class="p">,</span>
+            <span class="n">entity_type</span> <span class="o">=</span> <span class="n">entity_type_a</span><span class="p">,</span>
+            <span class="n">taxon</span> <span class="o">=</span> <span class="n">taxon_a</span><span class="p">,</span>
+            <span class="n">attrs</span> <span class="o">=</span> <span class="n">extra_attrs_a</span><span class="p">,</span>
+        <span class="p">)</span>
+        <span class="n">entity_b</span> <span class="o">=</span> <span class="n">entity_mod</span><span class="o">.</span><span class="n">Entity</span><span class="p">(</span>
+            <span class="n">identifier</span> <span class="o">=</span> <span class="n">id_b</span><span class="p">,</span>
+            <span class="n">id_type</span> <span class="o">=</span> <span class="n">id_type_b</span><span class="p">,</span>
+            <span class="n">entity_type</span> <span class="o">=</span> <span class="n">entity_type_b</span><span class="p">,</span>
+            <span class="n">taxon</span> <span class="o">=</span> <span class="n">taxon_b</span><span class="p">,</span>
+            <span class="n">attrs</span> <span class="o">=</span> <span class="n">extra_attrs_b</span><span class="p">,</span>
+        <span class="p">)</span>
+
+        <span class="n">interaction</span> <span class="o">=</span> <span class="n">interaction_mod</span><span class="o">.</span><span class="n">Interaction</span><span class="p">(</span>
+            <span class="n">a</span> <span class="o">=</span> <span class="n">entity_a</span><span class="p">,</span>
+            <span class="n">b</span> <span class="o">=</span> <span class="n">entity_b</span><span class="p">,</span>
+            <span class="n">attrs</span> <span class="o">=</span> <span class="n">extra_attrs</span><span class="p">,</span>
+        <span class="p">)</span>
+
+        <span class="k">if</span> <span class="ow">not</span> <span class="n">allow_loops</span> <span class="ow">and</span> <span class="n">interaction</span><span class="o">.</span><span class="n">is_loop</span><span class="p">():</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">_filtered_loops</span> <span class="o">+=</span> <span class="mi">1</span>
+            <span class="k">return</span>
+
+        <span class="k">if</span> <span class="n">is_directed</span><span class="p">:</span>
+
+            <span class="n">interaction</span><span class="o">.</span><span class="n">add_evidence</span><span class="p">(</span>
+                <span class="n">evidence</span> <span class="o">=</span> <span class="n">evidences</span><span class="p">,</span>
+                <span class="n">direction</span> <span class="o">=</span> <span class="p">(</span><span class="n">entity_a</span><span class="p">,</span> <span class="n">entity_b</span><span class="p">),</span>
+            <span class="p">)</span>
+
+        <span class="k">else</span><span class="p">:</span>
+
+            <span class="n">interaction</span><span class="o">.</span><span class="n">add_evidence</span><span class="p">(</span>
+                <span class="n">evidence</span> <span class="o">=</span> <span class="n">evidences</span><span class="p">,</span>
+                <span class="n">direction</span> <span class="o">=</span> <span class="s1">&#39;undirected&#39;</span><span class="p">,</span>
+            <span class="p">)</span>
+
+        <span class="c1"># setting signs:</span>
+        <span class="k">if</span> <span class="n">positive</span><span class="p">:</span>
+
+            <span class="n">interaction</span><span class="o">.</span><span class="n">add_evidence</span><span class="p">(</span>
+                <span class="n">evidence</span> <span class="o">=</span> <span class="n">evidences</span><span class="p">,</span>
+                <span class="n">direction</span> <span class="o">=</span> <span class="p">(</span><span class="n">entity_a</span><span class="p">,</span> <span class="n">entity_b</span><span class="p">),</span>
+                <span class="n">effect</span> <span class="o">=</span> <span class="mi">1</span><span class="p">,</span>
+            <span class="p">)</span>
+
+        <span class="k">if</span> <span class="n">negative</span><span class="p">:</span>
+
+            <span class="n">interaction</span><span class="o">.</span><span class="n">add_evidence</span><span class="p">(</span>
+                <span class="n">evidence</span> <span class="o">=</span> <span class="n">evidences</span><span class="p">,</span>
+                <span class="n">direction</span> <span class="o">=</span> <span class="p">(</span><span class="n">entity_a</span><span class="p">,</span> <span class="n">entity_b</span><span class="p">),</span>
+                <span class="n">effect</span> <span class="o">=</span> <span class="o">-</span><span class="mi">1</span><span class="p">,</span>
+            <span class="p">)</span>
+
+        <span class="k">if</span> <span class="n">is_directed</span> <span class="ow">and</span> <span class="ow">not</span> <span class="n">positive</span> <span class="ow">and</span> <span class="ow">not</span> <span class="n">negative</span><span class="p">:</span>
+
+            <span class="n">interaction</span><span class="o">.</span><span class="n">add_evidence</span><span class="p">(</span>
+                <span class="n">evidence</span> <span class="o">=</span> <span class="n">evidences</span><span class="p">,</span>
+                <span class="n">direction</span> <span class="o">=</span> <span class="p">(</span><span class="n">entity_a</span><span class="p">,</span> <span class="n">entity_b</span><span class="p">),</span>
+                <span class="n">effect</span> <span class="o">=</span> <span class="mi">0</span><span class="p">,</span>
+            <span class="p">)</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">add_interaction</span><span class="p">(</span>
+            <span class="n">interaction</span><span class="p">,</span>
+            <span class="n">attrs</span> <span class="o">=</span> <span class="n">extra_attrs</span><span class="p">,</span>
+            <span class="n">only_directions</span> <span class="o">=</span> <span class="n">only_directions</span><span class="p">,</span>
+        <span class="p">)</span>
+
+
+<div class="viewcode-block" id="Network.organisms_check">
+<a class="viewcode-back" href="../../../api/pypath.core.network.Network.html#pypath.core.network.Network.organisms_check">[docs]</a>
+    <span class="k">def</span> <span class="nf">organisms_check</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">organisms</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">remove_mismatches</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
+            <span class="n">remove_nonspecific</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+        <span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Scans the network for one or more organisms and removes the nodes</span>
+<span class="sd">        and interactions which belong to any other organism.</span>
+
+<span class="sd">        :arg int,set,NoneType organisms:</span>
+<span class="sd">            One or more NCBI Taxonomy IDs. If ``None`` the value in</span>
+<span class="sd">            :py:attr:`ncbi_tax_id` will be used. If that&#39;s too is ``None``</span>
+<span class="sd">            then only the entities with discrepancy between their stated</span>
+<span class="sd">            organism and their identifier.</span>
+<span class="sd">        :arg bool remove_mismatches:</span>
+<span class="sd">            Remove the entities where their ``identifier`` can not be found</span>
+<span class="sd">            in the reference list from the database for their ``taxon``.</span>
+<span class="sd">        :arg bool remove_nonspecific:</span>
+<span class="sd">            Remove the entities with taxonomy ID zero, which is used to</span>
+<span class="sd">            represent the non taxon specific entities such as metabolites</span>
+<span class="sd">            or drug compounds.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span>
+            <span class="s1">&#39;Checking organisms. </span><span class="si">%u</span><span class="s1"> nodes and </span><span class="si">%u</span><span class="s1"> interactions before.&#39;</span> <span class="o">%</span> <span class="p">(</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">vcount</span><span class="p">,</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">ecount</span><span class="p">,</span>
+            <span class="p">)</span>
+        <span class="p">)</span>
+
+        <span class="n">organisms</span> <span class="o">=</span> <span class="n">common</span><span class="o">.</span><span class="n">to_set</span><span class="p">(</span><span class="n">organisms</span> <span class="ow">or</span> <span class="bp">self</span><span class="o">.</span><span class="n">ncbi_tax_id</span><span class="p">)</span>
+
+        <span class="n">to_remove</span> <span class="o">=</span> <span class="nb">set</span><span class="p">()</span>
+
+        <span class="k">for</span> <span class="n">node</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">nodes</span><span class="o">.</span><span class="n">values</span><span class="p">():</span>
+
+            <span class="k">if</span> <span class="p">(</span>
+                <span class="n">organisms</span> <span class="ow">and</span>
+                <span class="n">node</span><span class="o">.</span><span class="n">taxon</span> <span class="o">!=</span> <span class="n">_const</span><span class="o">.</span><span class="n">NOT_ORGANISM_SPECIFIC</span> <span class="ow">and</span>
+                <span class="n">node</span><span class="o">.</span><span class="n">taxon</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">organisms</span>
+            <span class="p">):</span>
+
+                <span class="n">to_remove</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">node</span><span class="p">)</span>
+
+            <span class="k">if</span> <span class="p">(</span>
+                <span class="p">(</span>
+                    <span class="n">remove_mismatches</span> <span class="ow">and</span>
+                    <span class="ow">not</span> <span class="n">node</span><span class="o">.</span><span class="n">entity_type</span> <span class="ow">in</span> <span class="p">{</span>
+                        <span class="s1">&#39;complex&#39;</span><span class="p">,</span>
+                        <span class="s1">&#39;lncrna&#39;</span><span class="p">,</span>
+                        <span class="s1">&#39;drug&#39;</span><span class="p">,</span>
+                        <span class="s1">&#39;small_molecule&#39;</span>
+                    <span class="p">}</span> <span class="ow">and</span>
+                    <span class="ow">not</span> <span class="n">reflists</span><span class="o">.</span><span class="n">check</span><span class="p">(</span>
+                        <span class="n">name</span> <span class="o">=</span> <span class="n">node</span><span class="o">.</span><span class="n">identifier</span><span class="p">,</span>
+                        <span class="n">id_type</span> <span class="o">=</span> <span class="n">node</span><span class="o">.</span><span class="n">id_type</span><span class="p">,</span>
+                        <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">node</span><span class="o">.</span><span class="n">taxon</span><span class="p">,</span>
+                    <span class="p">)</span>
+                <span class="p">)</span> <span class="ow">or</span> <span class="p">(</span>
+                    <span class="n">remove_nonspecific</span> <span class="ow">and</span>
+                    <span class="ow">not</span> <span class="n">node</span><span class="o">.</span><span class="n">taxon</span>
+                <span class="p">)</span>
+            <span class="p">):</span>
+
+                <span class="n">to_remove</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">node</span><span class="p">)</span>
+
+        <span class="k">for</span> <span class="n">node</span> <span class="ow">in</span> <span class="n">to_remove</span><span class="p">:</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">remove_node</span><span class="p">(</span><span class="n">node</span><span class="p">)</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span>
+            <span class="s1">&#39;Finished checking organisms. &#39;</span>
+            <span class="s1">&#39;</span><span class="si">%u</span><span class="s1"> nodes have been removed, &#39;</span>
+            <span class="s1">&#39;</span><span class="si">%u</span><span class="s1"> nodes and </span><span class="si">%u</span><span class="s1"> interactions remained.&#39;</span> <span class="o">%</span> <span class="p">(</span>
+                <span class="nb">len</span><span class="p">(</span><span class="n">to_remove</span><span class="p">),</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">vcount</span><span class="p">,</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">ecount</span><span class="p">,</span>
+            <span class="p">)</span>
+        <span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="Network.get_organisms">
+<a class="viewcode-back" href="../../../api/pypath.core.network.Network.html#pypath.core.network.Network.get_organisms">[docs]</a>
+    <span class="k">def</span> <span class="nf">get_organisms</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Returns the set of all NCBI Taxonomy IDs occurring in the network.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">return</span> <span class="p">{</span><span class="n">n</span><span class="o">.</span><span class="n">taxon</span> <span class="k">for</span> <span class="n">n</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">nodes</span><span class="o">.</span><span class="n">values</span><span class="p">()}</span></div>
+
+
+
+    <span class="nd">@property</span>
+    <span class="k">def</span> <span class="nf">vcount</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">nodes</span><span class="p">)</span>
+
+
+    <span class="nd">@property</span>
+    <span class="k">def</span> <span class="nf">ecount</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">interactions</span><span class="p">)</span>
+
+
+<div class="viewcode-block" id="Network.make_df">
+<a class="viewcode-back" href="../../../api/pypath.core.network.Network.html#pypath.core.network.Network.make_df">[docs]</a>
+    <span class="k">def</span> <span class="nf">make_df</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">records</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">by_source</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">with_references</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">columns</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">dtype</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+        <span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Creates a ``pandas.DataFrame`` from the interactions.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span><span class="s1">&#39;Creating interactions data frame.&#39;</span><span class="p">)</span>
+
+        <span class="n">by_source</span> <span class="o">=</span> <span class="n">by_source</span> <span class="k">if</span> <span class="n">by_source</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span> <span class="k">else</span> <span class="bp">self</span><span class="o">.</span><span class="n">df_by_source</span>
+        <span class="n">with_references</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="n">with_references</span>
+                <span class="k">if</span> <span class="n">with_references</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span> <span class="k">else</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">df_with_references</span>
+        <span class="p">)</span>
+        <span class="n">columns</span> <span class="o">=</span> <span class="n">columns</span> <span class="ow">or</span> <span class="bp">self</span><span class="o">.</span><span class="n">df_columns</span>
+        <span class="n">dtype</span> <span class="o">=</span> <span class="n">dtype</span> <span class="ow">or</span> <span class="bp">self</span><span class="o">.</span><span class="n">df_dtype</span>
+
+        <span class="k">if</span> <span class="ow">not</span> <span class="n">dtype</span><span class="p">:</span>
+
+            <span class="n">dtype</span> <span class="o">=</span> <span class="p">{</span>
+                <span class="s1">&#39;id_a&#39;</span><span class="p">:</span> <span class="s1">&#39;category&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;id_b&#39;</span><span class="p">:</span> <span class="s1">&#39;category&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;type_a&#39;</span><span class="p">:</span> <span class="s1">&#39;category&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;type_b&#39;</span><span class="p">:</span> <span class="s1">&#39;category&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;effect&#39;</span><span class="p">:</span> <span class="s1">&#39;int8&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;type&#39;</span><span class="p">:</span> <span class="s1">&#39;category&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;dmodel&#39;</span><span class="p">:</span> <span class="s1">&#39;category&#39;</span> <span class="k">if</span> <span class="n">by_source</span> <span class="k">else</span> <span class="s1">&#39;object&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;sources&#39;</span><span class="p">:</span> <span class="s1">&#39;category&#39;</span> <span class="k">if</span> <span class="n">by_source</span> <span class="k">else</span> <span class="s1">&#39;object&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;references&#39;</span><span class="p">:</span> <span class="s1">&#39;object&#39;</span> <span class="k">if</span> <span class="n">with_references</span> <span class="k">else</span> <span class="s1">&#39;category&#39;</span><span class="p">,</span>
+            <span class="p">}</span>
+
+        <span class="k">if</span> <span class="ow">not</span> <span class="n">records</span><span class="p">:</span>
+
+            <span class="n">records</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">generate_df_records</span><span class="p">(</span>
+                <span class="n">by_source</span> <span class="o">=</span> <span class="n">by_source</span><span class="p">,</span>
+                <span class="n">with_references</span> <span class="o">=</span> <span class="n">with_references</span><span class="p">,</span>
+            <span class="p">)</span>
+
+        <span class="k">if</span> <span class="ow">not</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">records</span><span class="p">,</span> <span class="p">(</span><span class="nb">list</span><span class="p">,</span> <span class="nb">tuple</span><span class="p">,</span> <span class="n">np</span><span class="o">.</span><span class="n">ndarray</span><span class="p">)):</span>
+
+            <span class="n">records</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="n">records</span><span class="p">)</span>
+
+        <span class="k">if</span> <span class="ow">not</span> <span class="n">columns</span> <span class="ow">and</span> <span class="nb">hasattr</span><span class="p">(</span><span class="n">records</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="s1">&#39;_fields&#39;</span><span class="p">):</span>
+
+            <span class="n">columns</span> <span class="o">=</span> <span class="n">records</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">_fields</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">records</span> <span class="o">=</span> <span class="n">records</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">dtype</span> <span class="o">=</span> <span class="n">dtype</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">df</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">(</span>
+            <span class="n">records</span><span class="p">,</span>
+            <span class="n">columns</span> <span class="o">=</span> <span class="n">columns</span><span class="p">,</span>
+        <span class="p">)</span>
+
+        <span class="c1">### why?</span>
+        <span class="k">if</span> <span class="n">dtype</span><span class="p">:</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">df</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">df</span><span class="o">.</span><span class="n">astype</span><span class="p">(</span><span class="n">dtype</span><span class="p">)</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span>
+            <span class="s1">&#39;Interaction data frame ready. &#39;</span>
+            <span class="s1">&#39;Memory usage: </span><span class="si">%s</span><span class="s1"> &#39;</span> <span class="o">%</span> <span class="n">common</span><span class="o">.</span><span class="n">df_memory_usage</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">df</span><span class="p">)</span>
+        <span class="p">)</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">get_df</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">if</span> <span class="ow">not</span> <span class="nb">hasattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">&#39;df&#39;</span><span class="p">):</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">make_df</span><span class="p">()</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">df</span>
+
+
+    <span class="k">def</span> <span class="nf">filtered</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">resource</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">entity_type</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">data_model</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">interaction_type</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">only_directed</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">only_undirected</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">only_signed</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">only_proteins</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">effect</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">entities</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">source_entities</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">target_entities</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">swap_undirected</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
+            <span class="o">**</span><span class="n">kwargs</span>
+        <span class="p">):</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">filter_df</span><span class="p">(</span>
+            <span class="n">df</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">get_df</span><span class="p">(),</span>
+            <span class="n">resource</span> <span class="o">=</span> <span class="n">resource</span><span class="p">,</span>
+            <span class="n">entity_type</span> <span class="o">=</span> <span class="n">entity_type</span><span class="p">,</span>
+            <span class="n">data_model</span> <span class="o">=</span> <span class="n">data_model</span><span class="p">,</span>
+            <span class="n">interaction_type</span> <span class="o">=</span> <span class="n">interaction_type</span><span class="p">,</span>
+            <span class="n">only_directed</span> <span class="o">=</span> <span class="n">only_directed</span><span class="p">,</span>
+            <span class="n">only_undirected</span> <span class="o">=</span> <span class="n">only_undirected</span><span class="p">,</span>
+            <span class="n">only_signed</span> <span class="o">=</span> <span class="n">only_signed</span><span class="p">,</span>
+            <span class="n">only_proteins</span> <span class="o">=</span> <span class="n">only_proteins</span><span class="p">,</span>
+            <span class="n">effect</span> <span class="o">=</span> <span class="n">effect</span><span class="p">,</span>
+            <span class="n">entities</span> <span class="o">=</span> <span class="n">entities</span><span class="p">,</span>
+            <span class="n">source_entities</span> <span class="o">=</span> <span class="n">source_entities</span><span class="p">,</span>
+            <span class="n">target_entities</span> <span class="o">=</span> <span class="n">target_entities</span><span class="p">,</span>
+            <span class="n">swap_undirected</span> <span class="o">=</span> <span class="n">swap_undirected</span><span class="p">,</span>
+            <span class="o">**</span><span class="n">kwargs</span>
+        <span class="p">)</span>
+
+
+    <span class="nd">@staticmethod</span>
+    <span class="k">def</span> <span class="nf">filter_df</span><span class="p">(</span><span class="o">*</span><span class="n">args</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="n">core_common</span><span class="o">.</span><span class="n">filter_network_df</span><span class="p">(</span><span class="o">*</span><span class="n">args</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">generate_df_records</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">by_source</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span> <span class="n">with_references</span> <span class="o">=</span> <span class="kc">False</span><span class="p">):</span>
+
+        <span class="k">for</span> <span class="n">ia</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">interactions</span><span class="o">.</span><span class="n">values</span><span class="p">():</span>
+
+            <span class="k">for</span> <span class="n">rec</span> <span class="ow">in</span> <span class="n">ia</span><span class="o">.</span><span class="n">generate_df_records</span><span class="p">(</span>
+                <span class="n">by_source</span> <span class="o">=</span> <span class="n">by_source</span><span class="p">,</span>
+                <span class="n">with_references</span> <span class="o">=</span> <span class="n">with_references</span><span class="p">,</span>
+            <span class="p">):</span>
+
+                <span class="k">yield</span> <span class="n">rec</span>
+
+
+<div class="viewcode-block" id="Network.from_igraph">
+<a class="viewcode-back" href="../../../api/pypath.core.network.Network.html#pypath.core.network.Network.from_igraph">[docs]</a>
+    <span class="nd">@classmethod</span>
+    <span class="k">def</span> <span class="nf">from_igraph</span><span class="p">(</span><span class="bp">cls</span><span class="p">,</span> <span class="n">pa</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Creates an instance from an ``igraph.Graph`` based</span>
+<span class="sd">        ``pypath.main.PyPath`` object.</span>
+
+<span class="sd">        :arg pypath.main.PyPath pa:</span>
+<span class="sd">            A ``pypath.main.PyPath`` object with network data loaded.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">obj</span> <span class="o">=</span> <span class="bp">cls</span><span class="p">(</span><span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
+
+        <span class="k">for</span> <span class="n">ia</span> <span class="ow">in</span> <span class="n">pa</span><span class="o">.</span><span class="n">graph</span><span class="o">.</span><span class="n">es</span><span class="p">[</span><span class="s1">&#39;attrs&#39;</span><span class="p">]:</span>
+
+            <span class="n">obj</span><span class="o">.</span><span class="n">add_interaction</span><span class="p">(</span><span class="n">ia</span><span class="p">)</span>
+
+        <span class="k">return</span> <span class="n">obj</span></div>
+
+
+
+<div class="viewcode-block" id="Network.add_interaction">
+<a class="viewcode-back" href="../../../api/pypath.core.network.Network.html#pypath.core.network.Network.add_interaction">[docs]</a>
+    <span class="k">def</span> <span class="nf">add_interaction</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">interaction</span><span class="p">,</span>
+            <span class="n">attrs</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">only_directions</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+        <span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Adds a ready ``pypath.interaction.Interaction`` object to the network.</span>
+<span class="sd">        If an interaction between the two endpoints already exists, the</span>
+<span class="sd">        interactions will be merged: this stands for the directions, signs,</span>
+<span class="sd">        evidences and other attributes.</span>
+
+<span class="sd">        :arg interaction.Interaction interaction:</span>
+<span class="sd">            A ``pypath.interaction.Interaction`` object.</span>
+<span class="sd">        :arg NoneType,dict attrs:</span>
+<span class="sd">            Optional, a dictionary of extra (usually resource specific)</span>
+<span class="sd">            attributes.</span>
+<span class="sd">        :arg bool only_directions:</span>
+<span class="sd">            If the interaction between the two endpoints does not exist it</span>
+<span class="sd">            won&#39;t be added to the network. Otherwise all attributes</span>
+<span class="sd">            (direction, effect sign, evidences, etc) will be merged to the</span>
+<span class="sd">            existing interaction. Apart from the endpoints also the</span>
+<span class="sd">            ``interaction_type`` of the existing interaction has to match the</span>
+<span class="sd">            interaction added here.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">attrs</span> <span class="o">=</span> <span class="n">attrs</span> <span class="ow">or</span> <span class="p">{}</span>
+
+        <span class="n">key</span> <span class="o">=</span> <span class="p">(</span><span class="n">interaction</span><span class="o">.</span><span class="n">a</span><span class="p">,</span> <span class="n">interaction</span><span class="o">.</span><span class="n">b</span><span class="p">)</span>
+
+        <span class="k">if</span> <span class="n">key</span> <span class="ow">not</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">interactions</span><span class="p">:</span>
+
+            <span class="k">if</span> <span class="n">only_directions</span><span class="p">:</span>
+
+                <span class="k">return</span>
+
+            <span class="k">else</span><span class="p">:</span>
+
+                <span class="bp">self</span><span class="o">.</span><span class="n">interactions</span><span class="p">[</span><span class="n">key</span><span class="p">]</span> <span class="o">=</span> <span class="n">interaction</span>
+
+        <span class="k">else</span><span class="p">:</span>
+
+            <span class="k">if</span> <span class="n">only_directions</span><span class="p">:</span>
+
+                <span class="k">if</span> <span class="p">(</span>
+                    <span class="bp">self</span><span class="o">.</span><span class="n">interactions</span><span class="p">[</span><span class="n">key</span><span class="p">]</span><span class="o">.</span><span class="n">get_interaction_types</span><span class="p">()</span> <span class="o">&amp;</span>
+                    <span class="n">interaction</span><span class="o">.</span><span class="n">get_interaction_types</span><span class="p">()</span>
+                <span class="p">):</span>
+
+                    <span class="k">for</span> <span class="n">itype_to_remove</span> <span class="ow">in</span> <span class="p">(</span>
+                        <span class="n">interaction</span><span class="o">.</span><span class="n">get_interaction_types</span><span class="p">()</span> <span class="o">-</span>
+                        <span class="bp">self</span><span class="o">.</span><span class="n">interactions</span><span class="p">[</span><span class="n">key</span><span class="p">]</span><span class="o">.</span><span class="n">get_interaction_types</span><span class="p">()</span>
+                    <span class="p">):</span>
+
+                        <span class="n">interaction</span><span class="o">.</span><span class="n">unset_interaction_type</span><span class="p">(</span><span class="n">itype_to_remove</span><span class="p">)</span>
+
+                <span class="k">else</span><span class="p">:</span>
+
+                    <span class="k">return</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">interactions</span><span class="p">[</span><span class="n">key</span><span class="p">]</span> <span class="o">+=</span> <span class="n">interaction</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">interactions</span><span class="p">[</span><span class="n">key</span><span class="p">]</span><span class="o">.</span><span class="n">update_attrs</span><span class="p">(</span><span class="o">**</span><span class="n">attrs</span><span class="p">)</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">add_node</span><span class="p">(</span><span class="n">interaction</span><span class="o">.</span><span class="n">a</span><span class="p">,</span> <span class="n">add</span> <span class="o">=</span> <span class="ow">not</span> <span class="n">only_directions</span><span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">add_node</span><span class="p">(</span><span class="n">interaction</span><span class="o">.</span><span class="n">b</span><span class="p">,</span> <span class="n">add</span> <span class="o">=</span> <span class="ow">not</span> <span class="n">only_directions</span><span class="p">)</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">interactions_by_nodes</span><span class="p">[</span><span class="n">interaction</span><span class="o">.</span><span class="n">a</span><span class="p">]</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">key</span><span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">interactions_by_nodes</span><span class="p">[</span><span class="n">interaction</span><span class="o">.</span><span class="n">b</span><span class="p">]</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">key</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="Network.add_node">
+<a class="viewcode-back" href="../../../api/pypath.core.network.Network.html#pypath.core.network.Network.add_node">[docs]</a>
+    <span class="k">def</span> <span class="nf">add_node</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">entity</span><span class="p">,</span> <span class="n">attrs</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span> <span class="n">add</span> <span class="o">=</span> <span class="kc">True</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Adds a molecular entity to the py:attr:``nodes`` and</span>
+<span class="sd">        py:attr:``nodes_by_label`` dictionaries.</span>
+
+<span class="sd">        :arg entity.Entity entity:</span>
+<span class="sd">            An object representing a molecular entity.</span>
+<span class="sd">        :arg NoneType,dict attrs:</span>
+<span class="sd">            Optional extra attributes to be assigned to the entity.</span>
+<span class="sd">        :arg bool add:</span>
+<span class="sd">            Whether to add a new molecular entity to the network if it does</span>
+<span class="sd">            not exist yet. If ``False`` will only update attributes for</span>
+<span class="sd">            existing entities otherwise will do nothing.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">if</span> <span class="n">attrs</span><span class="p">:</span>
+
+            <span class="n">entity</span><span class="o">.</span><span class="n">update_attrs</span><span class="p">(</span><span class="o">**</span><span class="n">attrs</span><span class="p">)</span>
+
+        <span class="k">if</span> <span class="n">entity</span><span class="o">.</span><span class="n">identifier</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">nodes</span><span class="p">:</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">nodes</span><span class="p">[</span><span class="n">entity</span><span class="o">.</span><span class="n">identifier</span><span class="p">]</span> <span class="o">+=</span> <span class="n">entity</span>
+
+        <span class="k">elif</span> <span class="n">add</span><span class="p">:</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">nodes</span><span class="p">[</span><span class="n">entity</span><span class="o">.</span><span class="n">identifier</span><span class="p">]</span> <span class="o">=</span> <span class="n">entity</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">nodes_by_label</span><span class="p">[</span><span class="n">entity</span><span class="o">.</span><span class="n">label</span> <span class="ow">or</span> <span class="n">entity</span><span class="o">.</span><span class="n">identifier</span><span class="p">]</span> <span class="o">=</span> <span class="n">entity</span></div>
+
+
+
+<div class="viewcode-block" id="Network.remove_node">
+<a class="viewcode-back" href="../../../api/pypath.core.network.Network.html#pypath.core.network.Network.remove_node">[docs]</a>
+    <span class="k">def</span> <span class="nf">remove_node</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">entity</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Removes a node with all its interactions.</span>
+<span class="sd">        If the removal of the interactions leaves any of the partner nodes</span>
+<span class="sd">        without interactions it will be removed too.</span>
+
+<span class="sd">        :arg str,Entity entity:</span>
+<span class="sd">            A molecular entity identifier, label or ``Entity`` object.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">entity</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">entity</span><span class="p">(</span><span class="n">entity</span><span class="p">)</span>
+
+        <span class="k">if</span> <span class="ow">not</span> <span class="n">entity</span><span class="p">:</span>
+
+            <span class="k">return</span>
+
+        <span class="n">_</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">nodes</span><span class="o">.</span><span class="n">pop</span><span class="p">(</span><span class="n">entity</span><span class="o">.</span><span class="n">identifier</span><span class="p">,</span> <span class="kc">None</span><span class="p">)</span>
+        <span class="n">_</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">nodes_by_label</span><span class="o">.</span><span class="n">pop</span><span class="p">(</span><span class="n">entity</span><span class="o">.</span><span class="n">label</span><span class="p">,</span> <span class="kc">None</span><span class="p">)</span>
+
+        <span class="k">if</span> <span class="n">entity</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">interactions_by_nodes</span><span class="p">:</span>
+
+            <span class="n">partners</span> <span class="o">=</span> <span class="nb">set</span><span class="p">()</span>
+
+            <span class="k">for</span> <span class="n">i_key</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">interactions_by_nodes</span><span class="p">[</span><span class="n">entity</span><span class="p">]</span><span class="o">.</span><span class="n">copy</span><span class="p">():</span>
+
+                <span class="bp">self</span><span class="o">.</span><span class="n">remove_interaction</span><span class="p">(</span><span class="o">*</span><span class="n">i_key</span><span class="p">)</span>
+
+            <span class="n">_</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">interactions_by_nodes</span><span class="o">.</span><span class="n">pop</span><span class="p">(</span><span class="n">entity</span><span class="p">,</span> <span class="kc">None</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="Network.remove_interaction">
+<a class="viewcode-back" href="../../../api/pypath.core.network.Network.html#pypath.core.network.Network.remove_interaction">[docs]</a>
+    <span class="k">def</span> <span class="nf">remove_interaction</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">entity_a</span><span class="p">,</span> <span class="n">entity_b</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Removes the interaction between two nodes if exists.</span>
+
+<span class="sd">        :arg str,Entity entity_a,entity_b:</span>
+<span class="sd">            A pair of molecular entity identifiers, labels or ``Entity``</span>
+<span class="sd">            objects.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">entity_a</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">entity</span><span class="p">(</span><span class="n">entity_a</span><span class="p">)</span>
+        <span class="n">entity_b</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">entity</span><span class="p">(</span><span class="n">entity_b</span><span class="p">)</span>
+
+        <span class="n">key_ab</span> <span class="o">=</span> <span class="p">(</span><span class="n">entity_a</span><span class="p">,</span> <span class="n">entity_b</span><span class="p">)</span>
+        <span class="n">key_ba</span> <span class="o">=</span> <span class="p">(</span><span class="n">entity_b</span><span class="p">,</span> <span class="n">entity_a</span><span class="p">)</span>
+
+        <span class="n">_</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">interactions</span><span class="o">.</span><span class="n">pop</span><span class="p">(</span><span class="n">key_ab</span><span class="p">,</span> <span class="kc">None</span><span class="p">)</span>
+        <span class="n">_</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">interactions</span><span class="o">.</span><span class="n">pop</span><span class="p">(</span><span class="n">key_ba</span><span class="p">,</span> <span class="kc">None</span><span class="p">)</span>
+
+        <span class="n">keys</span> <span class="o">=</span> <span class="p">{</span><span class="n">key_ab</span><span class="p">,</span> <span class="n">key_ba</span><span class="p">}</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">interactions_by_nodes</span><span class="p">[</span><span class="n">entity_a</span><span class="p">]</span> <span class="o">-=</span> <span class="n">keys</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">interactions_by_nodes</span><span class="p">[</span><span class="n">entity_b</span><span class="p">]</span> <span class="o">-=</span> <span class="n">keys</span>
+
+        <span class="k">if</span> <span class="p">(</span>
+            <span class="n">entity_a</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">interactions_by_nodes</span> <span class="ow">and</span>
+            <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">interactions_by_nodes</span><span class="p">[</span><span class="n">entity_a</span><span class="p">]</span>
+        <span class="p">):</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">remove_node</span><span class="p">(</span><span class="n">entity_a</span><span class="p">)</span>
+
+        <span class="k">if</span> <span class="p">(</span>
+            <span class="n">entity_b</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">interactions_by_nodes</span> <span class="ow">and</span>
+            <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">interactions_by_nodes</span><span class="p">[</span><span class="n">entity_b</span><span class="p">]</span>
+        <span class="p">):</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">remove_node</span><span class="p">(</span><span class="n">entity_b</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="Network.remove_zero_degree">
+<a class="viewcode-back" href="../../../api/pypath.core.network.Network.html#pypath.core.network.Network.remove_zero_degree">[docs]</a>
+    <span class="k">def</span> <span class="nf">remove_zero_degree</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Removes all nodes with no interaction.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span>
+            <span class="s1">&#39;Removing zero degree nodes. &#39;</span>
+            <span class="s1">&#39;</span><span class="si">%u</span><span class="s1"> nodes and </span><span class="si">%u</span><span class="s1"> interactions before.&#39;</span> <span class="o">%</span> <span class="p">(</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">vcount</span><span class="p">,</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">ecount</span><span class="p">,</span>
+            <span class="p">)</span>
+        <span class="p">)</span>
+
+        <span class="n">to_remove</span> <span class="o">=</span> <span class="nb">set</span><span class="p">()</span>
+
+        <span class="k">for</span> <span class="n">node</span><span class="p">,</span> <span class="n">interactions</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">interactions_by_nodes</span><span class="p">):</span>
+
+            <span class="k">if</span> <span class="ow">not</span> <span class="n">interactions</span><span class="p">:</span>
+
+                <span class="n">to_remove</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">node</span><span class="p">)</span>
+
+        <span class="k">for</span> <span class="n">node</span> <span class="ow">in</span> <span class="n">to_remove</span><span class="p">:</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">remove_node</span><span class="p">(</span><span class="n">node</span><span class="p">)</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span>
+            <span class="s1">&#39;Finished removing zero degree nodes. &#39;</span>
+            <span class="s1">&#39;</span><span class="si">%u</span><span class="s1"> nodes have been removed, &#39;</span>
+            <span class="s1">&#39;</span><span class="si">%u</span><span class="s1"> nodes and </span><span class="si">%u</span><span class="s1"> interactions remained.&#39;</span> <span class="o">%</span> <span class="p">(</span>
+                <span class="nb">len</span><span class="p">(</span><span class="n">to_remove</span><span class="p">),</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">vcount</span><span class="p">,</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">ecount</span><span class="p">,</span>
+            <span class="p">)</span>
+        <span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="Network.remove_loops">
+<a class="viewcode-back" href="../../../api/pypath.core.network.Network.html#pypath.core.network.Network.remove_loops">[docs]</a>
+    <span class="k">def</span> <span class="nf">remove_loops</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Removes the loop interactions from the network i.e. the ones with</span>
+<span class="sd">        their two endpoints being the same entity.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span>
+            <span class="s1">&#39;Removing loop edges. Number of edges before: </span><span class="si">%u</span><span class="s1">.&#39;</span> <span class="o">%</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span>
+        <span class="p">)</span>
+
+        <span class="k">for</span> <span class="n">ia</span> <span class="ow">in</span> <span class="nb">list</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+            <span class="k">if</span> <span class="n">ia</span><span class="o">.</span><span class="n">is_loop</span><span class="p">():</span>
+
+                <span class="bp">self</span><span class="o">.</span><span class="n">remove_interaction</span><span class="p">(</span><span class="n">ia</span><span class="o">.</span><span class="n">a</span><span class="p">,</span> <span class="n">ia</span><span class="o">.</span><span class="n">b</span><span class="p">)</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span>
+            <span class="s1">&#39;Removed loop edges. Number of edges after: </span><span class="si">%u</span><span class="s1">.&#39;</span> <span class="o">%</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span>
+        <span class="p">)</span></div>
+
+
+
+    <span class="nd">@property</span>
+    <span class="k">def</span> <span class="nf">resources</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Returns a set of all resources.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">return</span> <span class="nb">set</span><span class="o">.</span><span class="n">union</span><span class="p">(</span><span class="o">*</span><span class="p">(</span><span class="n">ia</span><span class="o">.</span><span class="n">get_resources</span><span class="p">()</span> <span class="k">for</span> <span class="n">ia</span> <span class="ow">in</span> <span class="bp">self</span><span class="p">))</span>
+
+
+    <span class="nd">@property</span>
+    <span class="k">def</span> <span class="nf">resource_names</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Returns a set of all resource names.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">return</span> <span class="nb">set</span><span class="o">.</span><span class="n">union</span><span class="p">(</span><span class="o">*</span><span class="p">(</span><span class="n">ia</span><span class="o">.</span><span class="n">get_resource_names</span><span class="p">()</span> <span class="k">for</span> <span class="n">ia</span> <span class="ow">in</span> <span class="bp">self</span><span class="p">))</span>
+
+
+<div class="viewcode-block" id="Network.entities_by_resource">
+<a class="viewcode-back" href="../../../api/pypath.core.network.Network.html#pypath.core.network.Network.entities_by_resource">[docs]</a>
+    <span class="k">def</span> <span class="nf">entities_by_resource</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Returns a dict of sets with resources as keys and sets of entity IDs</span>
+<span class="sd">        as values.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">return</span> <span class="nb">dict</span><span class="p">(</span>
+            <span class="p">(</span>
+                <span class="n">resource</span><span class="p">,</span>
+                <span class="nb">set</span><span class="p">(</span>
+                    <span class="n">itertools</span><span class="o">.</span><span class="n">chain</span><span class="p">(</span>
+                        <span class="o">*</span><span class="bp">self</span><span class="o">.</span><span class="n">df</span><span class="p">[</span>
+                            <span class="p">[</span>
+                                <span class="n">resource</span> <span class="ow">in</span> <span class="n">resources</span>
+                                <span class="k">for</span> <span class="n">resources</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">df</span><span class="o">.</span><span class="n">sources</span>
+                            <span class="p">]</span>
+                        <span class="p">][[</span><span class="s1">&#39;id_a&#39;</span><span class="p">,</span> <span class="s1">&#39;id_b&#39;</span><span class="p">]]</span><span class="o">.</span><span class="n">values</span>
+                    <span class="p">)</span>
+                <span class="p">)</span>
+            <span class="p">)</span>
+            <span class="k">for</span> <span class="n">resource</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">resources</span>
+        <span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="Network.entity_by_id">
+<a class="viewcode-back" href="../../../api/pypath.core.network.Network.html#pypath.core.network.Network.entity_by_id">[docs]</a>
+    <span class="k">def</span> <span class="nf">entity_by_id</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">identifier</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Returns a ``pypath.entity.Entity`` object representing a molecular</span>
+<span class="sd">        entity by looking it up by its identifier. If the molecule does not</span>
+<span class="sd">        present in the current network ``None`` will be returned.</span>
+
+<span class="sd">        :arg str identifier:</span>
+<span class="sd">            The identifier of a molecular entity. Unless it&#39;s been set</span>
+<span class="sd">            otherwise for genes/proteins it is the UniProt ID.</span>
+<span class="sd">            E.g. ``&#39;P00533&#39;``.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">if</span> <span class="n">identifier</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">nodes</span><span class="p">:</span>
+
+            <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">nodes</span><span class="p">[</span><span class="n">identifier</span><span class="p">]</span></div>
+
+
+
+<div class="viewcode-block" id="Network.entity_by_label">
+<a class="viewcode-back" href="../../../api/pypath.core.network.Network.html#pypath.core.network.Network.entity_by_label">[docs]</a>
+    <span class="k">def</span> <span class="nf">entity_by_label</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">label</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Returns a ``pypath.entity.Entity`` object representing a molecular</span>
+<span class="sd">        entity by looking it up by its label. If the molecule does not</span>
+<span class="sd">        present in the current network ``None`` will be returned.</span>
+
+<span class="sd">        :arg str label:</span>
+<span class="sd">            The label of a molecular entity. Unless it&#39;s been set otherwise</span>
+<span class="sd">            for genes/proteins it is the Gene Symbol. E.g. ``&#39;EGFR&#39;``.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">if</span> <span class="n">label</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">nodes_by_label</span><span class="p">:</span>
+
+            <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">nodes_by_label</span><span class="p">[</span><span class="n">label</span><span class="p">]</span></div>
+
+
+
+<div class="viewcode-block" id="Network.interaction">
+<a class="viewcode-back" href="../../../api/pypath.core.network.Network.html#pypath.core.network.Network.interaction">[docs]</a>
+    <span class="k">def</span> <span class="nf">interaction</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">a</span><span class="p">,</span> <span class="n">b</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Retrieves the interaction `a --&gt; b` if it exists in the network,</span>
+<span class="sd">        otherwise `b --&gt; a`. If no interaction exist between `a` and `b`</span>
+<span class="sd">        returns `None`.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">entity_a</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">entity</span><span class="p">(</span><span class="n">a</span><span class="p">)</span>
+        <span class="n">entity_b</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">entity</span><span class="p">(</span><span class="n">b</span><span class="p">)</span>
+
+        <span class="n">key_ab</span> <span class="o">=</span> <span class="p">(</span><span class="n">entity_a</span><span class="p">,</span> <span class="n">entity_b</span><span class="p">)</span>
+        <span class="n">key_ba</span> <span class="o">=</span> <span class="p">(</span><span class="n">entity_b</span><span class="p">,</span> <span class="n">entity_a</span><span class="p">)</span>
+
+        <span class="k">if</span> <span class="n">key_ab</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">interactions</span><span class="p">:</span>
+
+            <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">interactions</span><span class="p">[</span><span class="n">key_ab</span><span class="p">]</span>
+
+        <span class="k">elif</span> <span class="n">key_ba</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">interactions</span><span class="p">:</span>
+
+            <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">interactions</span><span class="p">[</span><span class="n">key_ba</span><span class="p">]</span></div>
+
+
+
+<div class="viewcode-block" id="Network.random_interaction">
+<a class="viewcode-back" href="../../../api/pypath.core.network.Network.html#pypath.core.network.Network.random_interaction">[docs]</a>
+    <span class="k">def</span> <span class="nf">random_interaction</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Picks a random interaction from the network.</span>
+
+<span class="sd">        Returns</span>
+<span class="sd">            An Interaction object, or None if the network is empty.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">key</span> <span class="o">=</span> <span class="kc">None</span>
+
+        <span class="n">keys</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">get_interactions</span><span class="p">(</span><span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
+                <span class="k">if</span> <span class="n">kwargs</span> <span class="k">else</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">interactions</span><span class="o">.</span><span class="n">keys</span><span class="p">()</span>
+        <span class="p">)</span>
+
+        <span class="k">for</span> <span class="n">_</span><span class="p">,</span> <span class="n">key</span> <span class="ow">in</span> <span class="nb">zip</span><span class="p">(</span><span class="nb">range</span><span class="p">(</span><span class="n">random</span><span class="o">.</span><span class="n">randint</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="p">))</span> <span class="o">+</span> <span class="mi">1</span><span class="p">),</span> <span class="n">keys</span><span class="p">):</span>
+
+            <span class="k">pass</span>
+
+        <span class="k">if</span> <span class="n">key</span><span class="p">:</span>
+
+            <span class="n">key</span> <span class="o">=</span> <span class="nb">tuple</span><span class="p">(</span><span class="nb">sorted</span><span class="p">(</span><span class="n">key</span><span class="p">,</span> <span class="n">key</span> <span class="o">=</span> <span class="k">lambda</span> <span class="n">e</span><span class="p">:</span> <span class="n">e</span><span class="o">.</span><span class="n">identifier</span><span class="p">))</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">interactions</span><span class="p">[</span><span class="n">key</span><span class="p">]</span> <span class="k">if</span> <span class="n">key</span> <span class="k">else</span> <span class="kc">None</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">_get_interaction</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">id_a</span><span class="p">,</span> <span class="n">id_b</span><span class="p">,</span> <span class="n">name_type</span> <span class="o">=</span> <span class="s1">&#39;id&#39;</span><span class="p">):</span>
+
+        <span class="n">method</span> <span class="o">=</span> <span class="s1">&#39;entity_by_</span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="n">name_type</span>
+
+        <span class="n">entity_a</span> <span class="o">=</span> <span class="nb">getattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">method</span><span class="p">)(</span><span class="n">id_a</span><span class="p">)</span>
+        <span class="n">entity_b</span> <span class="o">=</span> <span class="nb">getattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">method</span><span class="p">)(</span><span class="n">id_b</span><span class="p">)</span>
+
+        <span class="n">a_b</span> <span class="o">=</span> <span class="p">(</span><span class="n">entity_a</span><span class="p">,</span> <span class="n">entity_b</span><span class="p">)</span>
+        <span class="n">b_a</span> <span class="o">=</span> <span class="p">(</span><span class="n">entity_b</span><span class="p">,</span> <span class="n">entity_a</span><span class="p">)</span>
+
+        <span class="k">if</span> <span class="n">a_b</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">interactions</span><span class="p">:</span>
+
+            <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">interactions</span><span class="p">[</span><span class="n">a_b</span><span class="p">]</span>
+
+        <span class="k">elif</span> <span class="n">b_a</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">interactions</span><span class="p">:</span>
+
+            <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">interactions</span><span class="p">[</span><span class="n">b_a</span><span class="p">]</span>
+
+
+    <span class="k">def</span> <span class="nf">entity</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">entity</span><span class="p">):</span>
+
+        <span class="k">if</span> <span class="ow">not</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">entity</span><span class="p">,</span> <span class="n">entity_mod</span><span class="o">.</span><span class="n">Entity</span><span class="p">):</span>
+
+            <span class="n">entity</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">entity_by_id</span><span class="p">(</span><span class="n">entity</span><span class="p">)</span> <span class="ow">or</span> <span class="bp">self</span><span class="o">.</span><span class="n">entity_by_label</span><span class="p">(</span><span class="n">entity</span><span class="p">)</span>
+
+        <span class="k">return</span> <span class="n">entity</span>
+
+
+<div class="viewcode-block" id="Network.interaction_by_id">
+<a class="viewcode-back" href="../../../api/pypath.core.network.Network.html#pypath.core.network.Network.interaction_by_id">[docs]</a>
+    <span class="k">def</span> <span class="nf">interaction_by_id</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">id_a</span><span class="p">,</span> <span class="n">id_b</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Returns a ``pypath.interaction.Interaction`` object by looking it up</span>
+<span class="sd">        based on a pair of identifiers. If the interaction does not exist</span>
+<span class="sd">        in the network ``None`` will be returned.</span>
+
+<span class="sd">        :arg str id_a:</span>
+<span class="sd">            The identifier of one of the partners in the interaction. Unless</span>
+<span class="sd">            it&#39;s been set otherwise for genes/proteins it is the UniProt ID.</span>
+<span class="sd">            E.g. ``&#39;P00533&#39;``.</span>
+<span class="sd">        :arg str id_b:</span>
+<span class="sd">            The other partner, similarly to ``id_a``. The order of the</span>
+<span class="sd">            partners does not matter here.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_get_interaction</span><span class="p">(</span><span class="n">id_a</span><span class="p">,</span> <span class="n">id_b</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="Network.interaction_by_label">
+<a class="viewcode-back" href="../../../api/pypath.core.network.Network.html#pypath.core.network.Network.interaction_by_label">[docs]</a>
+    <span class="k">def</span> <span class="nf">interaction_by_label</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">label_a</span><span class="p">,</span> <span class="n">label_b</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Returns a ``pypath.interaction.Interaction`` object by looking it up</span>
+<span class="sd">        based on a pair of labels. If the interaction does not exist</span>
+<span class="sd">        in the network ``None`` will be returned.</span>
+
+<span class="sd">        :arg str label_a:</span>
+<span class="sd">            The label of one of the partners in the interaction. Unless</span>
+<span class="sd">            it&#39;s been set otherwise for genes/proteins it is the Gene Symbol.</span>
+<span class="sd">            E.g. ``&#39;EGFR&#39;``.</span>
+<span class="sd">        :arg str label_b:</span>
+<span class="sd">            The other partner, similarly to ``label_a``. The order of the</span>
+<span class="sd">            partners does not matter here.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_get_interaction</span><span class="p">(</span><span class="n">label_a</span><span class="p">,</span> <span class="n">label_b</span><span class="p">,</span> <span class="n">name_type</span> <span class="o">=</span> <span class="s1">&#39;label&#39;</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="Network.to_igraph">
+<a class="viewcode-back" href="../../../api/pypath.core.network.Network.html#pypath.core.network.Network.to_igraph">[docs]</a>
+    <span class="k">def</span> <span class="nf">to_igraph</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Converts the network to the legacy ``igraph.Graph`` based ``PyPath``</span>
+<span class="sd">        object.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">raise</span> <span class="ne">NotImplementedError</span></div>
+
+
+
+    <span class="k">def</span> <span class="fm">__repr__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="s1">&#39;&lt;Network: </span><span class="si">%u</span><span class="s1"> nodes, </span><span class="si">%u</span><span class="s1"> interactions&gt;&#39;</span> <span class="o">%</span> <span class="p">(</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">vcount</span><span class="p">,</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">ecount</span><span class="p">,</span>
+        <span class="p">)</span>
+
+
+<div class="viewcode-block" id="Network.save_to_pickle">
+<a class="viewcode-back" href="../../../api/pypath.core.network.Network.html#pypath.core.network.Network.save_to_pickle">[docs]</a>
+    <span class="k">def</span> <span class="nf">save_to_pickle</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">pickle_file</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Saves the network to a pickle file.</span>
+
+<span class="sd">        :arg str pickle_file:</span>
+<span class="sd">            Path to the pickle file.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span><span class="s1">&#39;Saving to pickle `</span><span class="si">%s</span><span class="s1">`.&#39;</span> <span class="o">%</span> <span class="n">pickle_file</span><span class="p">)</span>
+
+        <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">pickle_file</span><span class="p">,</span> <span class="s1">&#39;wb&#39;</span><span class="p">)</span> <span class="k">as</span> <span class="n">fp</span><span class="p">:</span>
+
+            <span class="n">pickle</span><span class="o">.</span><span class="n">dump</span><span class="p">(</span>
+                <span class="n">obj</span> <span class="o">=</span> <span class="p">(</span>
+                    <span class="bp">self</span><span class="o">.</span><span class="n">interactions</span><span class="p">,</span>
+                    <span class="bp">self</span><span class="o">.</span><span class="n">nodes</span><span class="p">,</span>
+                    <span class="bp">self</span><span class="o">.</span><span class="n">nodes_by_label</span><span class="p">,</span>
+                <span class="p">),</span>
+                <span class="n">file</span> <span class="o">=</span> <span class="n">fp</span><span class="p">,</span>
+            <span class="p">)</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_update_interactions_by_nodes</span><span class="p">()</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span><span class="s1">&#39;Saved to pickle `</span><span class="si">%s</span><span class="s1">`.&#39;</span> <span class="o">%</span> <span class="n">pickle_file</span><span class="p">)</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">_update_interactions_by_nodes</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">interactions_by_nodes</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">defaultdict</span><span class="p">(</span><span class="nb">set</span><span class="p">)</span>
+
+        <span class="k">for</span> <span class="n">key</span><span class="p">,</span> <span class="n">ia</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">interactions</span><span class="p">):</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">interactions_by_nodes</span><span class="p">[</span><span class="n">ia</span><span class="o">.</span><span class="n">a</span><span class="p">]</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">key</span><span class="p">)</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">interactions_by_nodes</span><span class="p">[</span><span class="n">ia</span><span class="o">.</span><span class="n">b</span><span class="p">]</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">key</span><span class="p">)</span>
+
+
+<div class="viewcode-block" id="Network.load_from_pickle">
+<a class="viewcode-back" href="../../../api/pypath.core.network.Network.html#pypath.core.network.Network.load_from_pickle">[docs]</a>
+    <span class="k">def</span> <span class="nf">load_from_pickle</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">pickle_file</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Loads the network to a pickle file.</span>
+
+<span class="sd">        :arg str pickle_file:</span>
+<span class="sd">            Path to the pickle file.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span><span class="s1">&#39;Loading from pickle `</span><span class="si">%s</span><span class="s1">`.&#39;</span> <span class="o">%</span> <span class="n">pickle_file</span><span class="p">)</span>
+
+        <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">pickle_file</span><span class="p">,</span> <span class="s1">&#39;rb&#39;</span><span class="p">)</span> <span class="k">as</span> <span class="n">fp</span><span class="p">:</span>
+
+            <span class="p">(</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">interactions</span><span class="p">,</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">nodes</span><span class="p">,</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">nodes_by_label</span><span class="p">,</span>
+            <span class="p">)</span> <span class="o">=</span> <span class="n">pickle</span><span class="o">.</span><span class="n">load</span><span class="p">(</span><span class="n">fp</span><span class="p">)</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_update_interactions_by_nodes</span><span class="p">()</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span><span class="s1">&#39;Loaded from pickle `</span><span class="si">%s</span><span class="s1">`.&#39;</span> <span class="o">%</span> <span class="n">pickle_file</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="Network.from_pickle">
+<a class="viewcode-back" href="../../../api/pypath.core.network.Network.html#pypath.core.network.Network.from_pickle">[docs]</a>
+    <span class="nd">@classmethod</span>
+    <span class="k">def</span> <span class="nf">from_pickle</span><span class="p">(</span><span class="bp">cls</span><span class="p">,</span> <span class="n">pickle_file</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Initializes a new ``Network`` object by loading it from a pickle</span>
+<span class="sd">        file. Returns a ``Network`` object.</span>
+
+<span class="sd">        Args</span>
+<span class="sd">            pickle_file:</span>
+<span class="sd">                Path to a pickle file.</span>
+<span class="sd">            kwargs:</span>
+<span class="sd">                Passed to ``Network.__init__``.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">new</span> <span class="o">=</span> <span class="bp">cls</span><span class="p">(</span>
+            <span class="n">pickle_file</span> <span class="o">=</span> <span class="n">pickle_file</span><span class="p">,</span>
+            <span class="o">**</span><span class="n">kwargs</span>
+        <span class="p">)</span>
+
+        <span class="k">return</span> <span class="n">new</span></div>
+
+
+
+<div class="viewcode-block" id="Network.extra_directions">
+<a class="viewcode-back" href="../../../api/pypath.core.network.Network.html#pypath.core.network.Network.extra_directions">[docs]</a>
+    <span class="k">def</span> <span class="nf">extra_directions</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">resources</span> <span class="o">=</span> <span class="s1">&#39;extra_directions&#39;</span><span class="p">,</span>
+            <span class="n">use_laudanna</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+            <span class="n">use_string</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+            <span class="n">dataset</span> <span class="o">=</span> <span class="s1">&#39;directionextra&#39;</span><span class="p">,</span>
+        <span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Adds additional direction &amp; effect information from resources having</span>
+<span class="sd">        no literature curated references, but giving sufficient evidence</span>
+<span class="sd">        about the directionality for interactions already supported by</span>
+<span class="sd">        literature evidences from other sources.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">resources</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="nb">getattr</span><span class="p">(</span><span class="n">network_resources</span><span class="p">,</span> <span class="n">resources</span><span class="p">)</span>
+                <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">resources</span><span class="p">,</span> <span class="nb">str</span><span class="p">)</span> <span class="k">else</span>
+            <span class="nb">list</span><span class="p">(</span><span class="n">resources</span><span class="p">)</span>
+        <span class="p">)</span>
+
+        <span class="k">if</span> <span class="n">use_laudanna</span><span class="p">:</span>
+
+            <span class="n">resources</span><span class="o">.</span><span class="n">append</span><span class="p">(</span>
+                <span class="n">network_resources</span><span class="o">.</span><span class="n">pathway_bad</span><span class="p">[</span><span class="s1">&#39;laudanna_effects&#39;</span><span class="p">]</span>
+            <span class="p">)</span>
+            <span class="n">resources</span><span class="o">.</span><span class="n">append</span><span class="p">(</span>
+                <span class="n">network_resources</span><span class="o">.</span><span class="n">pathway_bad</span><span class="p">[</span><span class="s1">&#39;laudanna_directions&#39;</span><span class="p">]</span>
+            <span class="p">)</span>
+
+        <span class="k">if</span> <span class="n">use_string</span><span class="p">:</span>
+
+            <span class="k">pass</span>
+
+        <span class="n">resources</span> <span class="o">=</span> <span class="n">resource_mod</span><span class="o">.</span><span class="n">NetworkDataset</span><span class="p">(</span>
+            <span class="n">name</span> <span class="o">=</span> <span class="n">dataset</span><span class="p">,</span>
+            <span class="n">resources</span> <span class="o">=</span> <span class="n">resources</span><span class="p">,</span>
+        <span class="p">)</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">load</span><span class="p">(</span><span class="n">resources</span> <span class="o">=</span> <span class="n">resources</span><span class="p">,</span> <span class="n">only_directions</span> <span class="o">=</span> <span class="kc">True</span><span class="p">)</span></div>
+
+
+
+    <span class="nd">@staticmethod</span>
+    <span class="k">def</span> <span class="nf">omnipath_resources</span><span class="p">(</span>
+            <span class="n">omnipath</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">kinase_substrate_extra</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+            <span class="n">ligand_receptor_extra</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+            <span class="n">pathway_extra</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+            <span class="n">old_omnipath_resources</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+            <span class="n">exclude</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+        <span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">list</span><span class="p">[</span><span class="n">network_resoruces</span><span class="o">.</span><span class="n">resource</span><span class="o">.</span><span class="n">NetworkResource</span><span class="p">]:</span>
+
+
+        <span class="k">def</span> <span class="nf">reference_constraints</span><span class="p">(</span><span class="n">resources</span><span class="p">,</span> <span class="n">data_model</span><span class="p">,</span> <span class="n">relax</span> <span class="o">=</span> <span class="kc">True</span><span class="p">):</span>
+
+            <span class="n">result</span> <span class="o">=</span> <span class="p">[]</span>
+
+            <span class="n">resources</span> <span class="o">=</span> <span class="p">(</span>
+                <span class="n">resources</span><span class="o">.</span><span class="n">values</span><span class="p">()</span>
+                    <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">resources</span><span class="p">,</span> <span class="nb">dict</span><span class="p">)</span> <span class="k">else</span>
+                <span class="n">resources</span>
+            <span class="p">)</span>
+
+            <span class="n">resources</span> <span class="o">=</span> <span class="n">copy_mod</span><span class="o">.</span><span class="n">deepcopy</span><span class="p">(</span><span class="n">resources</span><span class="p">)</span>
+
+            <span class="k">for</span> <span class="n">res</span> <span class="ow">in</span> <span class="n">resources</span><span class="p">:</span>
+
+                <span class="k">if</span> <span class="n">res</span><span class="o">.</span><span class="n">data_model</span> <span class="o">==</span> <span class="n">data_model</span><span class="p">:</span>
+
+                    <span class="n">res</span><span class="o">.</span><span class="n">networkinput</span><span class="o">.</span><span class="n">must_have_references</span> <span class="o">=</span> <span class="ow">not</span> <span class="n">relax</span>
+                    <span class="n">result</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">res</span><span class="p">)</span>
+
+            <span class="k">return</span> <span class="n">result</span>
+
+
+        <span class="n">omnipath</span> <span class="o">=</span> <span class="n">omnipath</span> <span class="ow">or</span> <span class="n">copy_mod</span><span class="o">.</span><span class="n">deepcopy</span><span class="p">(</span><span class="n">network_resources</span><span class="o">.</span><span class="n">omnipath</span><span class="p">)</span>
+        <span class="n">exclude</span> <span class="o">=</span> <span class="n">common</span><span class="o">.</span><span class="n">to_set</span><span class="p">(</span><span class="n">exclude</span><span class="p">)</span>
+
+        <span class="k">if</span> <span class="n">old_omnipath_resources</span><span class="p">:</span>
+
+            <span class="n">interaction_resources</span> <span class="o">=</span> <span class="p">(</span>
+                <span class="n">copy_mod</span><span class="o">.</span><span class="n">deepcopy</span><span class="p">(</span><span class="n">network_resources</span><span class="o">.</span><span class="n">interaction</span><span class="p">)</span>
+            <span class="p">)</span>
+
+            <span class="n">omnipath</span> <span class="o">=</span> <span class="n">copy_mod</span><span class="o">.</span><span class="n">deepcopy</span><span class="p">(</span><span class="n">omnipath</span><span class="p">)</span>
+            <span class="n">omnipath</span><span class="p">[</span><span class="s1">&#39;biogrid&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">interaction_resources</span><span class="p">[</span><span class="s1">&#39;biogrid&#39;</span><span class="p">]</span>
+            <span class="n">omnipath</span><span class="p">[</span><span class="s1">&#39;alz&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">interaction_resources</span><span class="p">[</span><span class="s1">&#39;alz&#39;</span><span class="p">]</span>
+            <span class="n">omnipath</span><span class="p">[</span><span class="s1">&#39;netpath&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">interaction_resources</span><span class="p">[</span><span class="s1">&#39;netpath&#39;</span><span class="p">]</span>
+            <span class="n">exclude</span><span class="o">.</span><span class="n">update</span><span class="p">({</span><span class="s1">&#39;IntAct&#39;</span><span class="p">,</span> <span class="s1">&#39;HPRD&#39;</span><span class="p">})</span>
+
+        <span class="k">else</span><span class="p">:</span>
+
+            <span class="n">omnipath</span><span class="p">[</span><span class="s1">&#39;huri&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">copy_mod</span><span class="o">.</span><span class="n">deepcopy</span><span class="p">(</span>
+                <span class="n">network_resources</span><span class="o">.</span><span class="n">interaction_misc</span><span class="p">[</span><span class="s1">&#39;huri&#39;</span><span class="p">]</span>
+            <span class="p">)</span>
+
+        <span class="n">omnipath</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="n">omnipath</span><span class="o">.</span><span class="n">without</span><span class="p">(</span><span class="n">exclude</span><span class="p">))</span>
+
+        <span class="k">for</span> <span class="n">dataset</span><span class="p">,</span> <span class="n">data_model</span><span class="p">,</span> <span class="n">enabled</span> <span class="ow">in</span> <span class="p">(</span>
+            <span class="p">(</span><span class="s1">&#39;pathwayextra&#39;</span><span class="p">,</span> <span class="s1">&#39;activity_flow&#39;</span><span class="p">,</span> <span class="n">pathway_extra</span><span class="p">),</span>
+            <span class="p">(</span><span class="s1">&#39;ligrecextra&#39;</span><span class="p">,</span> <span class="s1">&#39;ligand_receptor&#39;</span><span class="p">,</span> <span class="n">ligand_receptor_extra</span><span class="p">),</span>
+            <span class="p">(</span><span class="s1">&#39;kinaseextra&#39;</span><span class="p">,</span> <span class="s1">&#39;enzyme_substrate&#39;</span><span class="p">,</span> <span class="n">kinase_substrate_extra</span><span class="p">),</span>
+        <span class="p">):</span>
+
+            <span class="k">if</span> <span class="n">enabled</span><span class="p">:</span>
+
+                <span class="n">extra</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span>
+                    <span class="n">resource_mod</span><span class="o">.</span><span class="n">NetworkDataset</span><span class="p">(</span>
+                        <span class="n">name</span> <span class="o">=</span> <span class="n">dataset</span><span class="p">,</span>
+                        <span class="n">resources</span> <span class="o">=</span> <span class="n">reference_constraints</span><span class="p">(</span>
+                            <span class="n">omnipath</span><span class="p">,</span>
+                            <span class="n">data_model</span><span class="p">,</span>
+                        <span class="p">),</span>
+                    <span class="p">)</span>
+                <span class="p">)</span>
+
+                <span class="n">omnipath</span><span class="o">.</span><span class="n">extend</span><span class="p">(</span><span class="n">extra</span><span class="p">)</span>
+
+        <span class="k">return</span> <span class="n">omnipath</span>
+
+
+    <span class="k">def</span> <span class="nf">load_omnipath</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">omnipath</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">kinase_substrate_extra</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+            <span class="n">ligand_receptor_extra</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+            <span class="n">pathway_extra</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+            <span class="n">extra_directions</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
+            <span class="n">remove_htp</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+            <span class="n">htp_threshold</span> <span class="o">=</span> <span class="mi">1</span><span class="p">,</span>
+            <span class="n">keep_directed</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
+            <span class="n">remove_undirected</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
+            <span class="n">min_refs_undirected</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">min_resources_undirected</span> <span class="o">=</span> <span class="mi">2</span><span class="p">,</span>
+            <span class="n">old_omnipath_resources</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+            <span class="n">exclude</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">pickle_file</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">allow_loops</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+        <span class="p">):</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span><span class="s1">&#39;Loading the `OmniPath` network.&#39;</span><span class="p">)</span>
+
+        <span class="k">if</span> <span class="n">pickle_file</span><span class="p">:</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">load</span><span class="p">(</span><span class="n">pickle_file</span> <span class="o">=</span> <span class="n">pickle_file</span><span class="p">)</span>
+            <span class="k">return</span>
+
+        <span class="n">omnipath</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">omnipath_resources</span><span class="p">(</span>
+            <span class="n">omnipath</span> <span class="o">=</span> <span class="n">omnipath</span><span class="p">,</span>
+            <span class="n">kinase_substrate_extra</span> <span class="o">=</span> <span class="n">kinase_substrate_extra</span><span class="p">,</span>
+            <span class="n">ligand_receptor_extra</span> <span class="o">=</span> <span class="n">ligand_receptor_extra</span><span class="p">,</span>
+            <span class="n">pathway_extra</span> <span class="o">=</span> <span class="n">pathway_extra</span><span class="p">,</span>
+            <span class="n">old_omnipath_resources</span> <span class="o">=</span> <span class="n">old_omnipath_resources</span><span class="p">,</span>
+            <span class="n">exclude</span> <span class="o">=</span> <span class="n">exclude</span><span class="p">,</span>
+        <span class="p">)</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">load</span><span class="p">(</span><span class="n">omnipath</span><span class="p">,</span> <span class="n">exclude</span> <span class="o">=</span> <span class="n">exclude</span><span class="p">,</span> <span class="n">allow_loops</span> <span class="o">=</span> <span class="n">allow_loops</span><span class="p">)</span>
+
+
+        <span class="k">for</span> <span class="n">dataset</span><span class="p">,</span> <span class="n">label</span><span class="p">,</span> <span class="n">enabled</span> <span class="ow">in</span> <span class="p">(</span>
+            <span class="p">(</span><span class="s1">&#39;pathwayextra&#39;</span><span class="p">,</span> <span class="s1">&#39;activity flow&#39;</span><span class="p">,</span> <span class="n">pathway_extra</span><span class="p">),</span>
+            <span class="p">(</span><span class="s1">&#39;ligrecextra&#39;</span><span class="p">,</span> <span class="s1">&#39;ligand-receptor&#39;</span><span class="p">,</span> <span class="n">ligand_receptor_extra</span><span class="p">),</span>
+            <span class="p">(</span><span class="s1">&#39;kinaseextra&#39;</span><span class="p">,</span> <span class="s1">&#39;enzyme-PTM&#39;</span><span class="p">,</span> <span class="n">kinase_substrate_extra</span><span class="p">),</span>
+        <span class="p">):</span>
+
+            <span class="k">if</span> <span class="n">enabled</span><span class="p">:</span>
+
+                <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span><span class="sa">f</span><span class="s1">&#39;Loading extra </span><span class="si">{</span><span class="n">label</span><span class="si">}</span><span class="s1"> interactions.&#39;</span><span class="p">)</span>
+
+                <span class="bp">self</span><span class="o">.</span><span class="n">load</span><span class="p">(</span>
+                    <span class="nb">getattr</span><span class="p">(</span><span class="n">network_resources</span><span class="p">,</span> <span class="n">dataset</span><span class="p">)</span><span class="o">.</span><span class="n">rename</span><span class="p">(</span><span class="n">dataset</span><span class="p">),</span>
+                    <span class="n">exclude</span> <span class="o">=</span> <span class="n">exclude</span><span class="p">,</span>
+                <span class="p">)</span>
+
+        <span class="k">if</span> <span class="n">extra_directions</span><span class="p">:</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">extra_directions</span><span class="p">()</span>
+
+        <span class="k">if</span> <span class="n">remove_htp</span><span class="p">:</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">remove_htp</span><span class="p">(</span>
+                <span class="n">threshold</span> <span class="o">=</span> <span class="n">htp_threshold</span><span class="p">,</span>
+                <span class="n">keep_directed</span> <span class="o">=</span> <span class="n">keep_directed</span><span class="p">,</span>
+            <span class="p">)</span>
+
+        <span class="k">if</span> <span class="n">remove_undirected</span><span class="p">:</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">remove_undirected</span><span class="p">(</span>
+                <span class="n">min_refs</span> <span class="o">=</span> <span class="n">min_refs_undirected</span><span class="p">,</span>
+                <span class="n">min_resources</span> <span class="o">=</span> <span class="n">min_resources_undirected</span><span class="p">,</span>
+            <span class="p">)</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span><span class="s1">&#39;Finished loading the `OmniPath` network.&#39;</span><span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">remove_htp</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">threshold</span> <span class="o">=</span> <span class="mi">50</span><span class="p">,</span> <span class="n">keep_directed</span> <span class="o">=</span> <span class="kc">False</span><span class="p">):</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span>
+            <span class="s1">&#39;Removing high-throughput interactions above threshold </span><span class="si">%u</span><span class="s1">&#39;</span>
+            <span class="s1">&#39; interactions per reference. Directed interactions </span><span class="si">%s</span><span class="s1">.&#39;</span> <span class="o">%</span> <span class="p">(</span>
+                <span class="n">threshold</span><span class="p">,</span>
+                <span class="s1">&#39;will be kept&#39;</span> <span class="k">if</span> <span class="n">keep_directed</span> <span class="k">else</span> <span class="s1">&#39;also will be removed&#39;</span>
+            <span class="p">)</span>
+        <span class="p">)</span>
+
+        <span class="n">to_remove</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">htp_interactions</span><span class="p">(</span>
+            <span class="n">threshold</span> <span class="o">=</span> <span class="n">threshold</span><span class="p">,</span>
+            <span class="n">ignore_directed</span> <span class="o">=</span> <span class="n">keep_directed</span><span class="p">,</span>
+        <span class="p">)</span>
+
+        <span class="n">ecount_before</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">ecount</span>
+        <span class="n">vcount_before</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">vcount</span>
+
+        <span class="k">for</span> <span class="n">key</span> <span class="ow">in</span> <span class="n">to_remove</span><span class="p">:</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">remove_interaction</span><span class="p">(</span><span class="o">*</span><span class="n">key</span><span class="p">)</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span>
+            <span class="s1">&#39;Interactions with only high-throughput references &#39;</span>
+            <span class="s1">&#39;have been removed. </span><span class="si">%u</span><span class="s1"> interactions removed. &#39;</span>
+            <span class="s1">&#39;Number of edges decreased from </span><span class="si">%u</span><span class="s1"> to </span><span class="si">%u</span><span class="s1">, &#39;</span>
+            <span class="s1">&#39;number of nodes from </span><span class="si">%u</span><span class="s1"> to </span><span class="si">%u</span><span class="s1">.&#39;</span> <span class="o">%</span> <span class="p">(</span>
+                <span class="nb">len</span><span class="p">(</span><span class="n">to_remove</span><span class="p">),</span>
+                <span class="n">ecount_before</span><span class="p">,</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">ecount</span><span class="p">,</span>
+                <span class="n">vcount_before</span><span class="p">,</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">vcount</span><span class="p">,</span>
+            <span class="p">)</span>
+        <span class="p">)</span>
+
+
+<div class="viewcode-block" id="Network.htp_references">
+<a class="viewcode-back" href="../../../api/pypath.core.network.Network.html#pypath.core.network.Network.htp_references">[docs]</a>
+    <span class="k">def</span> <span class="nf">htp_references</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">threshold</span> <span class="o">=</span> <span class="mi">50</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Collects the high-throughput references i.e. the ones cited at a</span>
+<span class="sd">        higher number of interactions than ``threshold``.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">interactions_per_reference</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">numof_interactions_per_reference</span><span class="p">()</span>
+
+        <span class="n">htp_refs</span> <span class="o">=</span> <span class="p">{</span>
+            <span class="n">ref</span>
+            <span class="k">for</span> <span class="n">ref</span><span class="p">,</span> <span class="n">cnt</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="n">interactions_per_reference</span><span class="p">)</span>
+            <span class="k">if</span> <span class="n">cnt</span> <span class="o">&gt;</span> <span class="n">threshold</span>
+        <span class="p">}</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span><span class="s1">&#39;High-throughput references collected: </span><span class="si">%u</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="nb">len</span><span class="p">(</span><span class="n">htp_refs</span><span class="p">))</span>
+
+        <span class="k">return</span> <span class="n">htp_refs</span></div>
+
+
+
+<div class="viewcode-block" id="Network.htp_interactions">
+<a class="viewcode-back" href="../../../api/pypath.core.network.Network.html#pypath.core.network.Network.htp_interactions">[docs]</a>
+    <span class="k">def</span> <span class="nf">htp_interactions</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">threshold</span> <span class="o">=</span> <span class="mi">50</span><span class="p">,</span> <span class="n">ignore_directed</span> <span class="o">=</span> <span class="kc">False</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Collects the interactions only from high-throughput studies.</span>
+
+<span class="sd">        :returns:</span>
+<span class="sd">            Set of interaction keys (tuples of entities).</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">htp_refs</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">htp_references</span><span class="p">(</span><span class="n">threshold</span> <span class="o">=</span> <span class="n">threshold</span><span class="p">)</span>
+
+        <span class="n">htp_int</span> <span class="o">=</span> <span class="nb">set</span><span class="p">()</span>
+
+        <span class="k">for</span> <span class="n">key</span><span class="p">,</span> <span class="n">ia</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">interactions</span><span class="p">):</span>
+
+            <span class="k">if</span> <span class="p">(</span>
+                <span class="p">(</span>
+                    <span class="ow">not</span> <span class="n">ignore_directed</span> <span class="ow">or</span>
+                    <span class="ow">not</span> <span class="n">ia</span><span class="o">.</span><span class="n">is_directed</span><span class="p">()</span>
+                <span class="p">)</span> <span class="ow">and</span>
+                <span class="ow">not</span> <span class="n">ia</span><span class="o">.</span><span class="n">get_references</span><span class="p">()</span> <span class="o">-</span> <span class="n">htp_refs</span>
+            <span class="p">):</span>
+
+                <span class="n">htp_int</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">key</span><span class="p">)</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span><span class="s1">&#39;High-throughput interactions collected: </span><span class="si">%u</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="nb">len</span><span class="p">(</span><span class="n">htp_int</span><span class="p">))</span>
+
+        <span class="k">return</span> <span class="n">htp_int</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">remove_undirected</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">min_refs</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span> <span class="n">min_resources</span> <span class="o">=</span> <span class="kc">None</span><span class="p">):</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span>
+            <span class="s1">&#39;Removing undirected interactions</span><span class="si">%s%s%s</span><span class="s1">.&#39;</span> <span class="o">%</span> <span class="p">(</span>
+                <span class="p">(</span>
+                    <span class="s1">&#39; with less than </span><span class="si">%u</span><span class="s1"> references&#39;</span> <span class="o">%</span> <span class="n">min_refs</span>
+                <span class="p">)</span>
+                <span class="k">if</span> <span class="n">min_refs</span> <span class="k">else</span> <span class="s1">&#39;&#39;</span><span class="p">,</span>
+                <span class="s1">&#39; and&#39;</span> <span class="k">if</span> <span class="n">min_refs</span> <span class="ow">and</span> <span class="n">min_resources</span> <span class="k">else</span> <span class="s1">&#39;&#39;</span><span class="p">,</span>
+                <span class="p">(</span>
+                    <span class="s1">&#39; with less than </span><span class="si">%u</span><span class="s1"> resources &#39;</span> <span class="o">%</span> <span class="n">min_resources</span>
+                <span class="p">),</span>
+            <span class="p">)</span>
+        <span class="p">)</span>
+
+        <span class="n">ecount_before</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">ecount</span>
+        <span class="n">vcount_before</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">vcount</span>
+
+        <span class="n">to_remove</span> <span class="o">=</span> <span class="nb">set</span><span class="p">()</span>
+
+        <span class="k">for</span> <span class="n">key</span><span class="p">,</span> <span class="n">ia</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">interactions</span><span class="p">):</span>
+
+            <span class="k">if</span> <span class="p">(</span>
+                <span class="ow">not</span> <span class="n">ia</span><span class="o">.</span><span class="n">is_directed</span><span class="p">()</span> <span class="ow">and</span>
+                <span class="p">(</span>
+                    <span class="ow">not</span> <span class="n">min_refs</span> <span class="ow">or</span>
+                    <span class="n">ia</span><span class="o">.</span><span class="n">count_references</span><span class="p">()</span> <span class="o">&lt;</span> <span class="n">min_refs</span>
+                <span class="p">)</span> <span class="ow">and</span>
+                <span class="p">(</span>
+                    <span class="ow">not</span> <span class="n">min_resources</span> <span class="ow">or</span>
+                    <span class="n">ia</span><span class="o">.</span><span class="n">count_resource_names</span><span class="p">()</span> <span class="o">&lt;</span> <span class="n">min_resources</span>
+                <span class="p">)</span>
+            <span class="p">):</span>
+
+                <span class="n">to_remove</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">key</span><span class="p">)</span>
+
+        <span class="k">for</span> <span class="n">key</span> <span class="ow">in</span> <span class="n">to_remove</span><span class="p">:</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">remove_interaction</span><span class="p">(</span><span class="o">*</span><span class="n">key</span><span class="p">)</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span>
+            <span class="s1">&#39;Undirected interactions </span><span class="si">%s</span><span class="s1"> have been removed. &#39;</span>
+            <span class="s1">&#39;</span><span class="si">%u</span><span class="s1"> interactions removed. Number of edges &#39;</span>
+            <span class="s1">&#39;decreased from </span><span class="si">%u</span><span class="s1"> to </span><span class="si">%u</span><span class="s1">, number of vertices &#39;</span>
+            <span class="s1">&#39;from </span><span class="si">%u</span><span class="s1"> to </span><span class="si">%u</span><span class="s1">.&#39;</span> <span class="o">%</span> <span class="p">(</span>
+                <span class="s1">&#39;&#39;</span>
+                    <span class="k">if</span> <span class="n">min_refs</span> <span class="ow">is</span> <span class="kc">None</span> <span class="k">else</span>
+                <span class="s1">&#39;with less than </span><span class="si">%u</span><span class="s1"> references&#39;</span> <span class="o">%</span> <span class="n">min_refs</span><span class="p">,</span>
+                <span class="nb">len</span><span class="p">(</span><span class="n">to_remove</span><span class="p">),</span>
+                <span class="n">ecount_before</span><span class="p">,</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">ecount</span><span class="p">,</span>
+                <span class="n">vcount_before</span><span class="p">,</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">vcount</span><span class="p">,</span>
+            <span class="p">)</span>
+        <span class="p">)</span>
+
+
+<div class="viewcode-block" id="Network.numof_interactions_per_reference">
+<a class="viewcode-back" href="../../../api/pypath.core.network.Network.html#pypath.core.network.Network.numof_interactions_per_reference">[docs]</a>
+    <span class="k">def</span> <span class="nf">numof_interactions_per_reference</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Counts the number of interactions for each literature reference.</span>
+<span class="sd">        Returns a ``collections.Counter`` object (similar to ``dict``).</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">return</span> <span class="n">collections</span><span class="o">.</span><span class="n">Counter</span><span class="p">(</span>
+            <span class="n">itertools</span><span class="o">.</span><span class="n">chain</span><span class="p">(</span>
+                <span class="o">*</span><span class="p">(</span>
+                    <span class="n">ia</span><span class="o">.</span><span class="n">get_references</span><span class="p">()</span>
+                    <span class="k">for</span> <span class="n">ia</span> <span class="ow">in</span> <span class="bp">self</span>
+                <span class="p">)</span>
+            <span class="p">)</span>
+        <span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="Network.interactions_by_reference">
+<a class="viewcode-back" href="../../../api/pypath.core.network.Network.html#pypath.core.network.Network.interactions_by_reference">[docs]</a>
+    <span class="k">def</span> <span class="nf">interactions_by_reference</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Creates a ``dict`` with literature references as keys and interactions</span>
+<span class="sd">        described by each reference as values.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">interactions_by_reference</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">defaultdict</span><span class="p">(</span><span class="nb">set</span><span class="p">)</span>
+
+        <span class="k">for</span> <span class="n">i_key</span><span class="p">,</span> <span class="n">ia</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">interactions</span><span class="p">):</span>
+
+            <span class="k">for</span> <span class="n">ref</span> <span class="ow">in</span> <span class="n">ia</span><span class="o">.</span><span class="n">get_references</span><span class="p">():</span>
+
+                <span class="n">interactions_by_reference</span><span class="p">[</span><span class="n">ref</span><span class="p">]</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">i_key</span><span class="p">)</span>
+
+        <span class="k">return</span> <span class="nb">dict</span><span class="p">(</span><span class="n">interactions_by_reference</span><span class="p">)</span></div>
+
+
+    <span class="c1">#</span>
+    <span class="c1"># Methods for loading specific datasets or initializing the object</span>
+    <span class="c1"># with loading datasets</span>
+    <span class="c1">#</span>
+
+    <span class="nd">@classmethod</span>
+    <span class="k">def</span> <span class="nf">omnipath</span><span class="p">(</span>
+            <span class="bp">cls</span><span class="p">,</span>
+            <span class="n">omnipath</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">kinase_substrate_extra</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+            <span class="n">ligand_receptor_extra</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+            <span class="n">pathway_extra</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+            <span class="n">extra_directions</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
+            <span class="n">remove_htp</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+            <span class="n">htp_threshold</span> <span class="o">=</span> <span class="mi">1</span><span class="p">,</span>
+            <span class="n">keep_directed</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
+            <span class="n">min_refs_undirected</span> <span class="o">=</span> <span class="mi">2</span><span class="p">,</span>
+            <span class="n">old_omnipath_resources</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+            <span class="n">exclude</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">,</span>
+            <span class="o">**</span><span class="n">kwargs</span>
+        <span class="p">):</span>
+
+        <span class="n">make_df</span> <span class="o">=</span> <span class="n">kwargs</span><span class="o">.</span><span class="n">pop</span><span class="p">(</span><span class="s1">&#39;make_df&#39;</span><span class="p">,</span> <span class="kc">None</span><span class="p">)</span>
+
+        <span class="n">new</span> <span class="o">=</span> <span class="bp">cls</span><span class="p">(</span><span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
+
+        <span class="n">new</span><span class="o">.</span><span class="n">load_omnipath</span><span class="p">(</span>
+            <span class="n">omnipath</span> <span class="o">=</span> <span class="n">omnipath</span><span class="p">,</span>
+            <span class="n">kinase_substrate_extra</span> <span class="o">=</span> <span class="n">kinase_substrate_extra</span><span class="p">,</span>
+            <span class="n">ligand_receptor_extra</span> <span class="o">=</span> <span class="n">ligand_receptor_extra</span><span class="p">,</span>
+            <span class="n">pathway_extra</span> <span class="o">=</span> <span class="n">pathway_extra</span><span class="p">,</span>
+            <span class="n">extra_directions</span> <span class="o">=</span> <span class="n">extra_directions</span><span class="p">,</span>
+            <span class="n">remove_htp</span> <span class="o">=</span> <span class="n">remove_htp</span><span class="p">,</span>
+            <span class="n">htp_threshold</span> <span class="o">=</span> <span class="n">htp_threshold</span><span class="p">,</span>
+            <span class="n">keep_directed</span> <span class="o">=</span> <span class="n">keep_directed</span><span class="p">,</span>
+            <span class="n">min_refs_undirected</span> <span class="o">=</span> <span class="n">min_refs_undirected</span><span class="p">,</span>
+            <span class="n">old_omnipath_resources</span> <span class="o">=</span> <span class="n">old_omnipath_resources</span><span class="p">,</span>
+            <span class="n">exclude</span> <span class="o">=</span> <span class="n">exclude</span><span class="p">,</span>
+        <span class="p">)</span>
+
+        <span class="k">if</span> <span class="n">make_df</span><span class="p">:</span>
+
+            <span class="bp">cls</span><span class="o">.</span><span class="n">make_df</span><span class="p">()</span>
+
+        <span class="k">return</span> <span class="n">new</span>
+
+
+    <span class="nd">@staticmethod</span>
+    <span class="k">def</span> <span class="nf">dorothea_resources</span><span class="p">(</span><span class="n">levels</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span> <span class="n">expand_levels</span> <span class="o">=</span> <span class="kc">None</span><span class="p">):</span>
+
+        <span class="n">expand_levels</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="n">expand_levels</span>
+                <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">expand_levels</span><span class="p">,</span> <span class="nb">bool</span><span class="p">)</span> <span class="k">else</span>
+            <span class="n">settings</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">&#39;dorothea_expand_levels&#39;</span><span class="p">)</span>
+        <span class="p">)</span>
+
+        <span class="n">dorothea</span> <span class="o">=</span> <span class="n">copy_mod</span><span class="o">.</span><span class="n">deepcopy</span><span class="p">(</span><span class="n">network_resources</span><span class="o">.</span><span class="n">transcription_dorothea</span><span class="p">)</span>
+
+        <span class="k">if</span> <span class="n">levels</span><span class="p">:</span>
+
+            <span class="n">dorothea</span><span class="p">[</span><span class="s1">&#39;dorothea&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">networkinput</span><span class="o">.</span><span class="n">input_args</span><span class="p">[</span><span class="s1">&#39;levels&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">levels</span>
+
+        <span class="n">dorothea</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="n">network_resources</span><span class="o">.</span><span class="n">dorothea_expand_levels</span><span class="p">(</span><span class="n">dorothea</span><span class="p">,</span> <span class="n">levels</span> <span class="o">=</span> <span class="n">levels</span><span class="p">)</span>
+                <span class="k">if</span> <span class="n">expand_levels</span> <span class="k">else</span>
+            <span class="n">dorothea</span>
+        <span class="p">)</span>
+
+        <span class="n">dorothea</span> <span class="o">=</span> <span class="n">dorothea</span><span class="o">.</span><span class="n">rename</span><span class="p">(</span><span class="s1">&#39;dorothea&#39;</span><span class="p">)</span>
+
+        <span class="k">return</span> <span class="n">dorothea</span>
+
+
+    <span class="k">def</span> <span class="nf">load_dorothea</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">levels</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span> <span class="n">expand_levels</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+
+        <span class="n">dorothea</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">dorothea_resources</span><span class="p">(</span>
+            <span class="n">levels</span> <span class="o">=</span> <span class="n">levels</span><span class="p">,</span>
+            <span class="n">expand_levels</span> <span class="o">=</span> <span class="n">expand_levels</span><span class="p">,</span>
+        <span class="p">)</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">load</span><span class="p">(</span><span class="n">dorothea</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
+
+
+<div class="viewcode-block" id="Network.dorothea">
+<a class="viewcode-back" href="../../../api/pypath.core.network.Network.html#pypath.core.network.Network.dorothea">[docs]</a>
+    <span class="nd">@classmethod</span>
+    <span class="k">def</span> <span class="nf">dorothea</span><span class="p">(</span><span class="bp">cls</span><span class="p">,</span> <span class="n">levels</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span> <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Initializes a new ``Network`` object with loading the transcriptional</span>
+<span class="sd">        regulation network from DoRothEA.</span>
+
+<span class="sd">        :arg NontType,set levels:</span>
+<span class="sd">            The confidence levels to include.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">make_df</span> <span class="o">=</span> <span class="n">kwargs</span><span class="o">.</span><span class="n">pop</span><span class="p">(</span><span class="s1">&#39;make_df&#39;</span><span class="p">,</span> <span class="kc">False</span><span class="p">)</span>
+
+        <span class="n">new</span> <span class="o">=</span> <span class="bp">cls</span><span class="p">(</span><span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
+
+        <span class="n">new</span><span class="o">.</span><span class="n">load_dorothea</span><span class="p">(</span><span class="n">levels</span> <span class="o">=</span> <span class="n">levels</span><span class="p">,</span> <span class="n">make_df</span> <span class="o">=</span> <span class="n">make_df</span><span class="p">)</span>
+
+        <span class="k">return</span> <span class="n">new</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">load_collectri</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">load</span><span class="p">(</span><span class="n">network_resources</span><span class="o">.</span><span class="n">collectri</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
+
+
+<div class="viewcode-block" id="Network.collectri">
+<a class="viewcode-back" href="../../../api/pypath.core.network.Network.html#pypath.core.network.Network.collectri">[docs]</a>
+    <span class="nd">@classmethod</span>
+    <span class="k">def</span> <span class="nf">collectri</span><span class="p">(</span><span class="bp">cls</span><span class="p">,</span> <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Initializes a new ``Network`` object with loading the transcriptional</span>
+<span class="sd">        regulation network from CollecTRI.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">make_df</span> <span class="o">=</span> <span class="n">kwargs</span><span class="o">.</span><span class="n">pop</span><span class="p">(</span><span class="s1">&#39;make_df&#39;</span><span class="p">,</span> <span class="kc">False</span><span class="p">)</span>
+
+        <span class="n">new</span> <span class="o">=</span> <span class="bp">cls</span><span class="p">(</span><span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
+
+        <span class="n">new</span><span class="o">.</span><span class="n">load_collectri</span><span class="p">(</span><span class="n">make_df</span> <span class="o">=</span> <span class="n">make_df</span><span class="p">)</span>
+
+        <span class="k">return</span> <span class="n">new</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">load_transcription</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">collectri</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
+            <span class="n">dorothea</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
+            <span class="n">original_resources</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
+            <span class="n">dorothea_levels</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">exclude</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">reread</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+            <span class="n">redownload</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+            <span class="n">allow_loops</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="o">**</span><span class="n">kwargs</span>
+        <span class="p">):</span>
+
+        <span class="n">make_df</span> <span class="o">=</span> <span class="n">kwargs</span><span class="o">.</span><span class="n">pop</span><span class="p">(</span><span class="s1">&#39;make_df&#39;</span><span class="p">,</span> <span class="kc">None</span><span class="p">)</span>
+
+        <span class="k">if</span> <span class="n">collectri</span><span class="p">:</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">load_collectri</span><span class="p">(</span>
+                <span class="n">reread</span> <span class="o">=</span> <span class="n">reread</span><span class="p">,</span>
+                <span class="n">redownload</span> <span class="o">=</span> <span class="n">redownload</span><span class="p">,</span>
+                <span class="n">allow_loops</span> <span class="o">=</span> <span class="n">allow_loops</span><span class="p">,</span>
+            <span class="p">)</span>
+
+        <span class="k">if</span> <span class="n">dorothea</span><span class="p">:</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">load_dorothea</span><span class="p">(</span>
+                <span class="n">levels</span> <span class="o">=</span> <span class="n">dorothea_levels</span><span class="p">,</span>
+                <span class="n">reread</span> <span class="o">=</span> <span class="n">reread</span><span class="p">,</span>
+                <span class="n">redownload</span> <span class="o">=</span> <span class="n">redownload</span><span class="p">,</span>
+                <span class="n">allow_loops</span> <span class="o">=</span> <span class="n">allow_loops</span><span class="p">,</span>
+            <span class="p">)</span>
+
+        <span class="k">if</span> <span class="n">original_resources</span><span class="p">:</span>
+
+            <span class="n">transcription</span> <span class="o">=</span> <span class="p">(</span>
+                <span class="n">original_resources</span>
+                    <span class="k">if</span> <span class="ow">not</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">original_resources</span><span class="p">,</span> <span class="nb">bool</span><span class="p">)</span> <span class="k">else</span>
+                <span class="n">network_resources</span><span class="o">.</span><span class="n">transcription_onebyone</span><span class="o">.</span><span class="n">rename</span><span class="p">(</span><span class="s1">&#39;tf_target&#39;</span><span class="p">)</span>
+            <span class="p">)</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">load</span><span class="p">(</span>
+                <span class="n">resources</span> <span class="o">=</span> <span class="n">transcription</span><span class="p">,</span>
+                <span class="n">reread</span> <span class="o">=</span> <span class="n">reread</span><span class="p">,</span>
+                <span class="n">redownload</span> <span class="o">=</span> <span class="n">redownload</span><span class="p">,</span>
+                <span class="n">exclude</span> <span class="o">=</span> <span class="n">exclude</span><span class="p">,</span>
+                <span class="n">allow_loops</span> <span class="o">=</span> <span class="n">allow_loops</span><span class="p">,</span>
+            <span class="p">)</span>
+
+        <span class="k">if</span> <span class="n">make_df</span><span class="p">:</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">make_df</span><span class="p">()</span>
+
+
+<div class="viewcode-block" id="Network.transcription">
+<a class="viewcode-back" href="../../../api/pypath.core.network.Network.html#pypath.core.network.Network.transcription">[docs]</a>
+    <span class="nd">@classmethod</span>
+    <span class="k">def</span> <span class="nf">transcription</span><span class="p">(</span>
+            <span class="bp">cls</span><span class="p">,</span>
+            <span class="n">dorothea</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
+            <span class="n">original_resources</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
+            <span class="n">dorothea_levels</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">exclude</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">reread</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+            <span class="n">redownload</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+            <span class="n">make_df</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+            <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">,</span>
+            <span class="n">allow_loops</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="o">**</span><span class="n">kwargs</span>
+        <span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Initializes a new ``Network`` object with loading a transcriptional</span>
+<span class="sd">        regulation network from all databases by default.</span>
+
+<span class="sd">        Args</span>
+<span class="sd">            kwargs:</span>
+<span class="sd">                Passed to ``Network.__init__``.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">load_args</span> <span class="o">=</span> <span class="nb">locals</span><span class="p">()</span>
+        <span class="n">kwargs</span> <span class="o">=</span> <span class="n">load_args</span><span class="o">.</span><span class="n">pop</span><span class="p">(</span><span class="s1">&#39;kwargs&#39;</span><span class="p">)</span>
+        <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">load_args</span><span class="o">.</span><span class="n">pop</span><span class="p">(</span><span class="s1">&#39;ncbi_tax_id&#39;</span><span class="p">)</span>
+        <span class="n">kwargs</span><span class="p">[</span><span class="s1">&#39;ncbi_tax_id&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span>
+        <span class="bp">cls</span> <span class="o">=</span> <span class="n">load_args</span><span class="o">.</span><span class="n">pop</span><span class="p">(</span><span class="s1">&#39;cls&#39;</span><span class="p">)</span>
+
+        <span class="n">new</span> <span class="o">=</span> <span class="bp">cls</span><span class="p">(</span><span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
+
+        <span class="n">new</span><span class="o">.</span><span class="n">load_transcription</span><span class="p">(</span><span class="o">**</span><span class="n">load_args</span><span class="p">)</span>
+
+        <span class="k">return</span> <span class="n">new</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">load_mirna_target</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+
+        <span class="k">if</span> <span class="s1">&#39;resources&#39;</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">kwargs</span><span class="p">:</span>
+
+            <span class="n">kwargs</span><span class="p">[</span><span class="s1">&#39;resources&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="p">(</span>
+                <span class="n">network_resources</span><span class="o">.</span><span class="n">mirna_target</span><span class="o">.</span><span class="n">rename</span><span class="p">(</span><span class="s1">&#39;mirnatarget&#39;</span><span class="p">)</span>
+            <span class="p">)</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">load</span><span class="p">(</span><span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
+
+
+<div class="viewcode-block" id="Network.mirna_target">
+<a class="viewcode-back" href="../../../api/pypath.core.network.Network.html#pypath.core.network.Network.mirna_target">[docs]</a>
+    <span class="nd">@classmethod</span>
+    <span class="k">def</span> <span class="nf">mirna_target</span><span class="p">(</span>
+            <span class="bp">cls</span><span class="p">,</span>
+            <span class="n">resources</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">make_df</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">reread</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+            <span class="n">redownload</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+            <span class="n">exclude</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">,</span>
+            <span class="o">**</span><span class="n">kwargs</span>
+        <span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Initializes a new ``Network`` object with loading a miRNA-mRNA</span>
+<span class="sd">        regulation network from all databases by default.</span>
+
+<span class="sd">        Args</span>
+<span class="sd">            kwargs:</span>
+<span class="sd">                Passed to ``Network.__init__``.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">new</span> <span class="o">=</span> <span class="bp">cls</span><span class="p">(</span><span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
+
+        <span class="n">new</span><span class="o">.</span><span class="n">load_mirna_target</span><span class="p">(</span>
+            <span class="n">exclude</span> <span class="o">=</span> <span class="n">exclude</span><span class="p">,</span>
+            <span class="n">make_df</span> <span class="o">=</span> <span class="n">make_df</span><span class="p">,</span>
+            <span class="n">reread</span> <span class="o">=</span> <span class="n">reread</span><span class="p">,</span>
+            <span class="n">redownload</span> <span class="o">=</span> <span class="n">redownload</span><span class="p">,</span>
+        <span class="p">)</span>
+
+        <span class="k">return</span> <span class="n">new</span></div>
+
+
+    <span class="c1">#</span>
+    <span class="c1"># Methods for querying partners by node</span>
+    <span class="c1">#</span>
+
+<div class="viewcode-block" id="Network.partners">
+<a class="viewcode-back" href="../../../api/pypath.core.network.Network.html#pypath.core.network.Network.partners">[docs]</a>
+    <span class="k">def</span> <span class="nf">partners</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">entity</span><span class="p">,</span>
+            <span class="n">mode</span> <span class="o">=</span> <span class="s1">&#39;ALL&#39;</span><span class="p">,</span>
+            <span class="n">direction</span><span class="p">:</span> <span class="nb">bool</span> <span class="o">|</span> <span class="nb">tuple</span> <span class="o">|</span> <span class="kc">None</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">effect</span><span class="p">:</span> <span class="nb">bool</span> <span class="o">|</span> <span class="nb">str</span> <span class="o">|</span> <span class="kc">None</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">resources</span><span class="p">:</span> <span class="nb">str</span> <span class="o">|</span> <span class="nb">set</span><span class="p">[</span><span class="nb">str</span><span class="p">]</span> <span class="o">|</span> <span class="kc">None</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">interaction_type</span><span class="p">:</span> <span class="nb">str</span> <span class="o">|</span> <span class="nb">set</span><span class="p">[</span><span class="nb">str</span><span class="p">]</span> <span class="o">|</span> <span class="kc">None</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">data_model</span><span class="p">:</span> <span class="nb">str</span> <span class="o">|</span> <span class="nb">set</span><span class="p">[</span><span class="nb">str</span><span class="p">]</span> <span class="o">|</span> <span class="kc">None</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">via</span><span class="p">:</span> <span class="nb">bool</span> <span class="o">|</span> <span class="nb">str</span> <span class="o">|</span> <span class="nb">set</span><span class="p">[</span><span class="nb">str</span><span class="p">]</span> <span class="o">|</span> <span class="kc">None</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">references</span><span class="p">:</span> <span class="nb">bool</span> <span class="o">|</span> <span class="nb">str</span> <span class="o">|</span> <span class="nb">set</span><span class="p">[</span><span class="nb">str</span><span class="p">]</span> <span class="o">|</span> <span class="kc">None</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">return_interactions</span><span class="p">:</span> <span class="nb">bool</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+        <span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        :arg str,Entity,list,set,tuple,EntityList entity:</span>
+<span class="sd">            An identifier or label of a molecular entity or an</span>
+<span class="sd">            :py:class:`Entity` object. Alternatively an iterator with the</span>
+<span class="sd">            elements of any of the types valid for a single entity argument,</span>
+<span class="sd">            e.g. a list of gene symbols.</span>
+<span class="sd">        :arg str mode:</span>
+<span class="sd">            Mode of counting the interactions: `IN`, `OUT` or `ALL` , whether</span>
+<span class="sd">            to consider incoming, outgoing or all edges, respectively,</span>
+<span class="sd">            respective to the `node defined in `entity``.</span>
+
+<span class="sd">        :returns:</span>
+<span class="sd">            :py:class:`EntityList` object containing the partners having</span>
+<span class="sd">            interactions to the queried node(s) matching all the criteria.</span>
+<span class="sd">            If ``entity`` doesn&#39;t present in the network the returned</span>
+<span class="sd">            ``EntityList`` will be empty just like if no interaction matches</span>
+<span class="sd">            the criteria.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">if</span> <span class="p">(</span>
+            <span class="ow">not</span> <span class="n">common</span><span class="o">.</span><span class="n">is_str</span><span class="p">(</span><span class="n">entity</span><span class="p">)</span> <span class="ow">and</span>
+            <span class="ow">not</span> <span class="nb">hasattr</span><span class="p">(</span><span class="n">entity</span><span class="p">,</span> <span class="s1">&#39;identifier&#39;</span><span class="p">)</span> <span class="ow">and</span>
+            <span class="nb">hasattr</span><span class="p">(</span><span class="n">entity</span><span class="p">,</span> <span class="s1">&#39;__iter__&#39;</span><span class="p">)</span>
+        <span class="p">):</span>
+
+            <span class="n">kwargs</span> <span class="o">=</span> <span class="nb">locals</span><span class="p">()</span>
+            <span class="n">_</span> <span class="o">=</span> <span class="n">kwargs</span><span class="o">.</span><span class="n">pop</span><span class="p">(</span><span class="s1">&#39;self&#39;</span><span class="p">)</span>
+            <span class="n">_</span> <span class="o">=</span> <span class="n">kwargs</span><span class="o">.</span><span class="n">pop</span><span class="p">(</span><span class="s1">&#39;entity&#39;</span><span class="p">)</span>
+            <span class="n">_</span> <span class="o">=</span> <span class="n">kwargs</span><span class="o">.</span><span class="n">pop</span><span class="p">(</span><span class="s1">&#39;return_interactions&#39;</span><span class="p">)</span>
+
+            <span class="k">return</span> <span class="n">entity_mod</span><span class="o">.</span><span class="n">EntityList</span><span class="p">(</span>
+                <span class="nb">set</span><span class="p">(</span><span class="n">itertools</span><span class="o">.</span><span class="n">chain</span><span class="p">(</span><span class="o">*</span><span class="p">(</span>
+                    <span class="bp">self</span><span class="o">.</span><span class="n">partners</span><span class="p">(</span><span class="n">_entity</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
+                    <span class="k">for</span> <span class="n">_entity</span> <span class="ow">in</span> <span class="n">entity</span>
+                <span class="p">)))</span>
+            <span class="p">)</span>
+
+        <span class="n">entity</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">entity</span><span class="p">(</span><span class="n">entity</span><span class="p">)</span>
+
+        <span class="c1"># we need to swap it to make it work relative to the queried entity</span>
+        <span class="n">_mode</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="s1">&#39;IN&#39;</span>
+                <span class="k">if</span> <span class="n">mode</span> <span class="o">==</span> <span class="s1">&#39;OUT&#39;</span> <span class="k">else</span>
+            <span class="s1">&#39;OUT&#39;</span>
+                <span class="k">if</span> <span class="n">mode</span> <span class="o">==</span> <span class="s1">&#39;IN&#39;</span> <span class="k">else</span>
+            <span class="s1">&#39;ALL&#39;</span>
+        <span class="p">)</span>
+
+        <span class="k">return</span> <span class="p">(</span>
+            <span class="n">entity_mod</span><span class="o">.</span><span class="n">EntityList</span><span class="p">(</span>
+                <span class="p">{</span>
+                    <span class="n">partner</span>
+                    <span class="k">for</span> <span class="n">ia</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">interactions_by_nodes</span><span class="p">[</span><span class="n">entity</span><span class="p">]</span>
+                    <span class="k">for</span> <span class="n">partner</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">interactions</span><span class="p">[</span><span class="n">ia</span><span class="p">]</span><span class="o">.</span><span class="n">get_degrees</span><span class="p">(</span>
+                        <span class="n">mode</span> <span class="o">=</span> <span class="n">_mode</span><span class="p">,</span>
+                        <span class="n">direction</span> <span class="o">=</span> <span class="n">direction</span><span class="p">,</span>
+                        <span class="n">effect</span> <span class="o">=</span> <span class="n">effect</span><span class="p">,</span>
+                        <span class="n">resources</span> <span class="o">=</span> <span class="n">resources</span><span class="p">,</span>
+                        <span class="n">interaction_type</span> <span class="o">=</span> <span class="n">interaction_type</span><span class="p">,</span>
+                        <span class="n">data_model</span> <span class="o">=</span> <span class="n">data_model</span><span class="p">,</span>
+                        <span class="n">via</span> <span class="o">=</span> <span class="n">via</span><span class="p">,</span>
+                        <span class="n">references</span> <span class="o">=</span> <span class="n">references</span><span class="p">,</span>
+                    <span class="p">)</span>
+                    <span class="k">if</span> <span class="n">partner</span> <span class="o">!=</span> <span class="n">entity</span> <span class="ow">or</span> <span class="bp">self</span><span class="o">.</span><span class="n">interactions</span><span class="p">[</span><span class="n">ia</span><span class="p">]</span><span class="o">.</span><span class="n">is_loop</span><span class="p">()</span>
+                <span class="p">}</span>
+                <span class="k">if</span> <span class="n">entity</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">interactions_by_nodes</span> <span class="k">else</span>
+                <span class="p">()</span>
+            <span class="p">)</span>
+        <span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="Network.count_partners">
+<a class="viewcode-back" href="../../../api/pypath.core.network.Network.html#pypath.core.network.Network.count_partners">[docs]</a>
+    <span class="k">def</span> <span class="nf">count_partners</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">entity</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Returns the count of the interacting partners for one or more</span>
+<span class="sd">        entities according to the specified criteria.</span>
+<span class="sd">        Please refer to the docs of the ``partners`` method.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">return</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">partners</span><span class="p">(</span><span class="n">entity</span> <span class="o">=</span> <span class="n">entity</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">))</span></div>
+
+
+
+    <span class="nd">@classmethod</span>
+    <span class="k">def</span> <span class="nf">_generate_partners_methods</span><span class="p">(</span><span class="bp">cls</span><span class="p">):</span>
+
+        <span class="k">def</span> <span class="nf">_create_partners_method</span><span class="p">(</span><span class="n">method_args</span><span class="p">):</span>
+
+            <span class="n">count</span> <span class="o">=</span> <span class="n">method_args</span><span class="o">.</span><span class="n">pop</span><span class="p">(</span><span class="s1">&#39;count&#39;</span><span class="p">)</span>
+            <span class="n">method</span> <span class="o">=</span> <span class="s1">&#39;count_partners&#39;</span> <span class="k">if</span> <span class="n">count</span> <span class="k">else</span> <span class="s1">&#39;partners&#39;</span>
+
+            <span class="nd">@functools</span><span class="o">.</span><span class="n">wraps</span><span class="p">(</span><span class="n">method_args</span><span class="p">)</span>
+            <span class="k">def</span> <span class="nf">_partners_method</span><span class="p">(</span><span class="o">*</span><span class="n">args</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+
+                <span class="bp">self</span> <span class="o">=</span> <span class="n">args</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span>
+                <span class="n">kwargs</span><span class="o">.</span><span class="n">update</span><span class="p">(</span><span class="n">method_args</span><span class="p">)</span>
+
+                <span class="k">return</span> <span class="nb">getattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">method</span><span class="p">)(</span><span class="o">*</span><span class="n">args</span><span class="p">[</span><span class="mi">1</span><span class="p">:],</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
+
+            <span class="n">_partners_method</span><span class="o">.</span><span class="vm">__doc__</span> <span class="o">=</span> <span class="nb">getattr</span><span class="p">(</span><span class="bp">cls</span><span class="p">,</span> <span class="n">method</span><span class="p">)</span><span class="o">.</span><span class="vm">__doc__</span>
+
+            <span class="k">return</span> <span class="n">_partners_method</span>
+
+        <span class="k">for</span> <span class="n">name_parts</span><span class="p">,</span> <span class="n">arg_parts</span> <span class="ow">in</span> <span class="p">(</span>
+            <span class="nb">zip</span><span class="p">(</span><span class="o">*</span><span class="n">param</span><span class="p">)</span>
+            <span class="k">for</span> <span class="n">param</span> <span class="ow">in</span>
+            <span class="n">itertools</span><span class="o">.</span><span class="n">product</span><span class="p">(</span>
+                <span class="o">*</span><span class="p">(</span><span class="n">iteritems</span><span class="p">(</span><span class="n">variety</span><span class="p">)</span> <span class="k">for</span> <span class="n">variety</span> <span class="ow">in</span> <span class="bp">cls</span><span class="o">.</span><span class="n">_partners_methods</span><span class="p">)</span>
+            <span class="p">)</span>
+        <span class="p">):</span>
+
+            <span class="k">for</span> <span class="n">count</span> <span class="ow">in</span> <span class="p">(</span><span class="kc">False</span><span class="p">,</span> <span class="kc">True</span><span class="p">):</span>
+
+                <span class="n">method_args</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">(</span>
+                    <span class="n">itertools</span><span class="o">.</span><span class="n">chain</span><span class="p">(</span>
+                        <span class="o">*</span><span class="p">(</span><span class="n">iteritems</span><span class="p">(</span><span class="n">part</span><span class="p">)</span> <span class="k">for</span> <span class="n">part</span> <span class="ow">in</span> <span class="n">arg_parts</span><span class="p">)</span>
+                    <span class="p">)</span>
+                <span class="p">)</span>
+                <span class="n">method_name</span> <span class="o">=</span> <span class="s1">&#39;&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">name_parts</span><span class="p">)</span>
+                <span class="n">method_name</span> <span class="o">=</span> <span class="p">(</span>
+                    <span class="s1">&#39;count_</span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="n">method_name</span> <span class="k">if</span> <span class="n">count</span> <span class="k">else</span> <span class="n">method_name</span>
+                <span class="p">)</span>
+                <span class="n">method_args</span><span class="p">[</span><span class="s1">&#39;count&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">count</span>
+                <span class="n">method</span> <span class="o">=</span> <span class="n">_create_partners_method</span><span class="p">(</span><span class="n">method_args</span><span class="p">)</span>
+                <span class="n">method</span><span class="o">.</span><span class="vm">__name__</span> <span class="o">=</span> <span class="n">method_name</span>
+
+                <span class="nb">setattr</span><span class="p">(</span>
+                    <span class="bp">cls</span><span class="p">,</span>
+                    <span class="n">method_name</span><span class="p">,</span>
+                    <span class="n">method</span><span class="p">,</span>
+                <span class="p">)</span>
+
+    <span class="c1">#</span>
+    <span class="c1"># Methods for selecting paths and motives in the network</span>
+    <span class="c1">#</span>
+
+<div class="viewcode-block" id="Network.find_paths">
+<a class="viewcode-back" href="../../../api/pypath.core.network.Network.html#pypath.core.network.Network.find_paths">[docs]</a>
+    <span class="k">def</span> <span class="nf">find_paths</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">start</span><span class="p">:</span> <span class="p">(</span>
+                <span class="nb">str</span> <span class="o">|</span> <span class="n">entity</span><span class="o">.</span><span class="n">Entity</span> <span class="o">|</span> <span class="n">entity</span><span class="o">.</span><span class="n">EntityList</span> <span class="o">|</span>
+                <span class="n">Iterable</span><span class="p">[</span><span class="nb">str</span> <span class="o">|</span> <span class="n">entity</span><span class="o">.</span><span class="n">Entity</span><span class="p">]</span>
+            <span class="p">),</span>
+            <span class="n">end</span><span class="p">:</span> <span class="p">(</span>
+                <span class="nb">str</span> <span class="o">|</span> <span class="n">entity</span><span class="o">.</span><span class="n">Entity</span> <span class="o">|</span> <span class="n">entity</span><span class="o">.</span><span class="n">EntityList</span> <span class="o">|</span>
+                <span class="n">Iterable</span><span class="p">[</span><span class="nb">str</span> <span class="o">|</span> <span class="n">entity</span><span class="o">.</span><span class="n">Entity</span><span class="p">]</span> <span class="o">|</span>
+                <span class="kc">None</span>
+            <span class="p">)</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">loops</span><span class="p">:</span> <span class="nb">bool</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+            <span class="n">mode</span><span class="p">:</span> <span class="n">Literal</span><span class="p">[</span><span class="s1">&#39;OUT&#39;</span><span class="p">,</span> <span class="s1">&#39;IN&#39;</span><span class="p">,</span> <span class="s1">&#39;ALL&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="s1">&#39;OUT&#39;</span><span class="p">,</span>
+            <span class="n">maxlen</span><span class="p">:</span> <span class="nb">int</span> <span class="o">=</span> <span class="mi">2</span><span class="p">,</span>
+            <span class="n">minlen</span><span class="p">:</span> <span class="nb">int</span> <span class="o">=</span> <span class="mi">1</span><span class="p">,</span>
+            <span class="n">direction</span><span class="p">:</span> <span class="nb">bool</span> <span class="o">|</span> <span class="nb">tuple</span> <span class="o">|</span> <span class="kc">None</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">effect</span><span class="p">:</span> <span class="nb">bool</span> <span class="o">|</span> <span class="nb">str</span> <span class="o">|</span> <span class="kc">None</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">resources</span><span class="p">:</span> <span class="nb">str</span> <span class="o">|</span> <span class="nb">set</span><span class="p">[</span><span class="nb">str</span><span class="p">]</span> <span class="o">|</span> <span class="kc">None</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">interaction_type</span><span class="p">:</span> <span class="nb">str</span> <span class="o">|</span> <span class="nb">set</span><span class="p">[</span><span class="nb">str</span><span class="p">]</span> <span class="o">|</span> <span class="kc">None</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">data_model</span><span class="p">:</span> <span class="nb">str</span> <span class="o">|</span> <span class="nb">set</span><span class="p">[</span><span class="nb">str</span><span class="p">]</span> <span class="o">|</span> <span class="kc">None</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">via</span><span class="p">:</span> <span class="nb">bool</span> <span class="o">|</span> <span class="nb">str</span> <span class="o">|</span> <span class="nb">set</span><span class="p">[</span><span class="nb">str</span><span class="p">]</span> <span class="o">|</span> <span class="kc">None</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">references</span><span class="p">:</span> <span class="nb">bool</span> <span class="o">|</span> <span class="nb">str</span> <span class="o">|</span> <span class="nb">set</span><span class="p">[</span><span class="nb">str</span><span class="p">]</span> <span class="o">|</span> <span class="kc">None</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">silent</span><span class="p">:</span> <span class="nb">bool</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+        <span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Find paths or motifs in a network.</span>
+
+<span class="sd">        Finds all paths up to length ``maxlen`` between groups of nodes.</span>
+<span class="sd">        In addition is able to search for motifs or select the nodes of a</span>
+<span class="sd">        subnetwork around certain nodes.</span>
+
+<span class="sd">        Args</span>
+<span class="sd">            start:</span>
+<span class="sd">                Starting node(s) of the paths.</span>
+<span class="sd">            end:</span>
+<span class="sd">                Target node(s) of the paths. If ``None`` any target node will</span>
+<span class="sd">                be accepted and all paths from the starting nodes with length</span>
+<span class="sd">                ``maxlen`` will be returned.</span>
+<span class="sd">            loops:</span>
+<span class="sd">                Search for loops, i.e. the start and end nodes of each path</span>
+<span class="sd">                should be the same.</span>
+<span class="sd">            mode:</span>
+<span class="sd">                Direction of the paths. ``&#39;OUT&#39;`` means from ``start`` to ``end``,</span>
+<span class="sd">                ``&#39;IN&#39;`` the opposite direction while ``&#39;ALL&#39;`` both directions.</span>
+<span class="sd">            maxlen:</span>
+<span class="sd">                Maximum length of paths in steps, i.e. if maxlen = 3, then</span>
+<span class="sd">                the longest path may consist of 3 edges and 4 nodes.</span>
+<span class="sd">            minlen:</span>
+<span class="sd">                Minimum length of the path.</span>
+<span class="sd">            silent:</span>
+<span class="sd">                Indicate progress by showing a progress bar.</span>
+
+<span class="sd">        Details</span>
+<span class="sd">            The arguments: ``direction``, ``effect``, ``resources``,</span>
+<span class="sd">            ``interaction_type``, ``data_model``, ``via`` and ``references``</span>
+<span class="sd">            will be passed to the ``partners`` method of this object and from</span>
+<span class="sd">            there to the relevant methods of the ``Interaction`` and</span>
+<span class="sd">            ``Evidence`` objects. By these arguments it is possible to filter</span>
+<span class="sd">            the interactions in the paths according to custom criteria. If any</span>
+<span class="sd">            of these arguments is a ``tuple`` or ``list``, its first value will</span>
+<span class="sd">            be used to match the first interaction in the path, the second for</span>
+<span class="sd">            the second one and so on. If the list or tuple is shorter then</span>
+<span class="sd">            ``maxlen``, its last element will be used for all interactions.</span>
+<span class="sd">            If it&#39;s longer than ``maxlen``, the remaining elements will be</span>
+<span class="sd">            discarded. This way the method is able to search for custom</span>
+<span class="sd">            motives. For example, let&#39;s say you want to find the motives</span>
+<span class="sd">            where the estrogen receptor transcription factor *ESR1*</span>
+<span class="sd">            transcriptionally regulates a gene encoding a protein which</span>
+<span class="sd">            then has some effect post-translationally on *ESR1*:</span>
+
+<span class="sd">        Examples</span>
+
+<span class="sd">            n.find_paths(</span>
+<span class="sd">                &#39;ESR1&#39;,</span>
+<span class="sd">                loops = True,</span>
+<span class="sd">                minlen = 2,</span>
+<span class="sd">                interaction_type = (&#39;transcriptional&#39;, &#39;post_translational&#39;),</span>
+<span class="sd">            )</span>
+
+<span class="sd">            # Or if you are interested only in the -/+ feedback loops i.e.</span>
+<span class="sd">            # *ESR1 --(-)--&gt; X --(+)--&gt; ESR1*:</span>
+
+<span class="sd">            n.find_paths(</span>
+<span class="sd">                &#39;ESR1&#39;,</span>
+<span class="sd">                loops = True,</span>
+<span class="sd">                minlen = 2,</span>
+<span class="sd">                interaction_type = (&#39;transcriptional&#39;, &#39;post_translational&#39;),</span>
+<span class="sd">                effect = (&#39;negative&#39;, &#39;positive&#39;),</span>
+<span class="sd">            )</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">def</span> <span class="nf">list_of_entities</span><span class="p">(</span><span class="n">entities</span><span class="p">):</span>
+
+            <span class="n">entities</span> <span class="o">=</span> <span class="p">(</span>
+                <span class="p">(</span><span class="n">entities</span><span class="p">,)</span>
+                    <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span>
+                        <span class="n">entities</span><span class="p">,</span>
+                        <span class="p">(</span><span class="nb">str</span><span class="p">,</span> <span class="n">entity_mod</span><span class="o">.</span><span class="n">Entity</span><span class="p">)</span>
+                    <span class="p">)</span> <span class="k">else</span>
+                <span class="n">entities</span>
+            <span class="p">)</span>
+
+            <span class="n">entities</span> <span class="o">=</span> <span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">entity</span><span class="p">(</span><span class="n">en</span><span class="p">)</span> <span class="k">for</span> <span class="n">en</span> <span class="ow">in</span> <span class="n">entities</span><span class="p">]</span>
+
+            <span class="k">return</span> <span class="n">entities</span>
+
+
+        <span class="k">def</span> <span class="nf">interaction_arg</span><span class="p">(</span><span class="n">value</span><span class="p">):</span>
+
+            <span class="n">value</span> <span class="o">=</span> <span class="p">(</span>
+                <span class="nb">tuple</span><span class="p">(</span><span class="n">value</span><span class="p">)</span>
+                    <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">value</span><span class="p">,</span> <span class="p">(</span><span class="nb">tuple</span><span class="p">,</span> <span class="nb">list</span><span class="p">))</span> <span class="k">else</span>
+                <span class="p">(</span><span class="n">value</span><span class="p">,)</span>
+            <span class="p">)</span>
+
+            <span class="n">value</span> <span class="o">=</span> <span class="n">value</span> <span class="o">+</span> <span class="p">(</span><span class="n">value</span><span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">],)</span> <span class="o">*</span> <span class="p">(</span><span class="n">maxlen</span> <span class="o">-</span> <span class="nb">len</span><span class="p">(</span><span class="n">value</span><span class="p">))</span>
+            <span class="n">value</span> <span class="o">=</span> <span class="n">value</span><span class="p">[:</span><span class="n">maxlen</span><span class="p">]</span>
+
+            <span class="k">return</span> <span class="n">value</span>
+
+
+        <span class="k">def</span> <span class="nf">find_all_paths_aux</span><span class="p">(</span><span class="n">start</span><span class="p">,</span> <span class="n">end</span><span class="p">,</span> <span class="n">path</span><span class="p">,</span> <span class="n">maxlen</span> <span class="o">=</span> <span class="kc">None</span><span class="p">):</span>
+
+            <span class="n">path</span> <span class="o">=</span> <span class="n">path</span> <span class="o">+</span> <span class="p">[</span><span class="n">start</span><span class="p">]</span>
+
+            <span class="k">if</span> <span class="p">(</span>
+                <span class="nb">len</span><span class="p">(</span><span class="n">path</span><span class="p">)</span> <span class="o">&gt;=</span> <span class="n">minlen</span> <span class="o">+</span> <span class="mi">1</span> <span class="ow">and</span>
+                <span class="p">(</span>
+                    <span class="n">start</span> <span class="o">==</span> <span class="n">end</span> <span class="ow">or</span>
+                    <span class="p">(</span>
+                        <span class="n">end</span> <span class="ow">is</span> <span class="kc">None</span> <span class="ow">and</span>
+                        <span class="ow">not</span> <span class="n">loops</span> <span class="ow">and</span>
+                        <span class="nb">len</span><span class="p">(</span><span class="n">path</span><span class="p">)</span> <span class="o">==</span> <span class="n">maxlen</span> <span class="o">+</span> <span class="mi">1</span>
+                    <span class="p">)</span> <span class="ow">or</span>
+                    <span class="p">(</span>
+                        <span class="n">loops</span> <span class="ow">and</span>
+                        <span class="n">path</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">==</span> <span class="n">path</span><span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span>
+                    <span class="p">)</span>
+                <span class="p">)</span>
+            <span class="p">):</span>
+
+                <span class="k">return</span> <span class="p">[</span><span class="n">path</span><span class="p">]</span>
+
+            <span class="n">paths</span> <span class="o">=</span> <span class="p">[]</span>
+
+            <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">path</span><span class="p">)</span> <span class="o">&lt;=</span> <span class="n">maxlen</span><span class="p">:</span>
+
+                <span class="n">next_steps</span> <span class="o">=</span> <span class="nb">set</span><span class="p">(</span>
+                    <span class="bp">self</span><span class="o">.</span><span class="n">partners</span><span class="p">(</span>
+                        <span class="n">entity</span> <span class="o">=</span> <span class="n">start</span><span class="p">,</span>
+                        <span class="o">**</span><span class="n">interaction_args</span><span class="p">[</span><span class="nb">len</span><span class="p">(</span><span class="n">path</span><span class="p">)</span> <span class="o">-</span> <span class="mi">1</span><span class="p">]</span>
+                    <span class="p">)</span>
+                <span class="p">)</span>
+
+                <span class="n">next_steps</span> <span class="o">=</span> <span class="n">next_steps</span> <span class="k">if</span> <span class="n">loops</span> <span class="k">else</span> <span class="n">next_steps</span> <span class="o">-</span> <span class="nb">set</span><span class="p">(</span><span class="n">path</span><span class="p">)</span>
+
+                <span class="k">for</span> <span class="n">node</span> <span class="ow">in</span> <span class="n">next_steps</span><span class="p">:</span>
+
+                    <span class="n">paths</span><span class="o">.</span><span class="n">extend</span><span class="p">(</span>
+                        <span class="n">find_all_paths_aux</span><span class="p">(</span>
+                            <span class="n">node</span><span class="p">,</span>
+                            <span class="n">end</span><span class="p">,</span>
+                            <span class="n">path</span><span class="p">,</span> <span class="n">maxlen</span>
+                        <span class="p">)</span>
+                    <span class="p">)</span>
+
+            <span class="k">return</span> <span class="n">paths</span>
+
+
+        <span class="n">minlen</span> <span class="o">=</span> <span class="nb">max</span><span class="p">(</span><span class="mi">1</span><span class="p">,</span> <span class="n">minlen</span><span class="p">)</span>
+        <span class="n">start</span> <span class="o">=</span> <span class="n">list_of_entities</span><span class="p">(</span><span class="n">start</span><span class="p">)</span>
+        <span class="n">end</span> <span class="o">=</span> <span class="n">list_of_entities</span><span class="p">(</span><span class="n">end</span><span class="p">)</span> <span class="k">if</span> <span class="n">end</span> <span class="k">else</span> <span class="p">(</span><span class="kc">None</span><span class="p">,)</span>
+
+        <span class="n">interaction_args</span> <span class="o">=</span> <span class="p">{</span>
+            <span class="s1">&#39;mode&#39;</span><span class="p">:</span> <span class="n">interaction_arg</span><span class="p">(</span><span class="n">mode</span><span class="p">),</span>
+            <span class="s1">&#39;direction&#39;</span><span class="p">:</span> <span class="n">interaction_arg</span><span class="p">(</span><span class="n">direction</span><span class="p">),</span>
+            <span class="s1">&#39;effect&#39;</span><span class="p">:</span> <span class="n">interaction_arg</span><span class="p">(</span><span class="n">effect</span><span class="p">),</span>
+            <span class="s1">&#39;resources&#39;</span><span class="p">:</span> <span class="n">interaction_arg</span><span class="p">(</span><span class="n">resources</span><span class="p">),</span>
+            <span class="s1">&#39;interaction_type&#39;</span><span class="p">:</span> <span class="n">interaction_arg</span><span class="p">(</span><span class="n">interaction_type</span><span class="p">),</span>
+            <span class="s1">&#39;data_model&#39;</span><span class="p">:</span> <span class="n">interaction_arg</span><span class="p">(</span><span class="n">data_model</span><span class="p">),</span>
+            <span class="s1">&#39;via&#39;</span><span class="p">:</span> <span class="n">interaction_arg</span><span class="p">(</span><span class="n">via</span><span class="p">),</span>
+            <span class="s1">&#39;references&#39;</span><span class="p">:</span> <span class="n">interaction_arg</span><span class="p">(</span><span class="n">references</span><span class="p">),</span>
+        <span class="p">}</span>
+        <span class="n">interaction_args</span> <span class="o">=</span> <span class="nb">tuple</span><span class="p">(</span>
+            <span class="nb">dict</span><span class="p">(</span>
+                <span class="p">(</span><span class="n">key</span><span class="p">,</span> <span class="n">interaction_args</span><span class="p">[</span><span class="n">key</span><span class="p">][</span><span class="n">i</span><span class="p">])</span>
+                <span class="k">for</span> <span class="n">key</span> <span class="ow">in</span> <span class="n">interaction_args</span><span class="o">.</span><span class="n">keys</span><span class="p">()</span>
+            <span class="p">)</span>
+            <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">maxlen</span><span class="p">)</span>
+        <span class="p">)</span>
+
+        <span class="n">all_paths</span> <span class="o">=</span> <span class="p">[]</span>
+
+        <span class="k">if</span> <span class="ow">not</span> <span class="n">silent</span><span class="p">:</span>
+            <span class="n">prg</span> <span class="o">=</span> <span class="n">progress</span><span class="o">.</span><span class="n">Progress</span><span class="p">(</span>
+                <span class="nb">len</span><span class="p">(</span><span class="n">start</span><span class="p">)</span> <span class="o">*</span> <span class="nb">len</span><span class="p">(</span><span class="n">end</span><span class="p">),</span>
+                <span class="s1">&#39;Looking up all paths up to length </span><span class="si">%u</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="n">maxlen</span><span class="p">,</span> <span class="mi">1</span><span class="p">)</span>
+
+        <span class="k">for</span> <span class="n">s</span> <span class="ow">in</span> <span class="n">start</span><span class="p">:</span>
+
+            <span class="k">for</span> <span class="n">e</span> <span class="ow">in</span> <span class="n">end</span><span class="p">:</span>
+
+                <span class="k">if</span> <span class="ow">not</span> <span class="n">silent</span><span class="p">:</span>
+                    <span class="n">prg</span><span class="o">.</span><span class="n">step</span><span class="p">()</span>
+
+                <span class="n">all_paths</span><span class="o">.</span><span class="n">extend</span><span class="p">(</span><span class="n">find_all_paths_aux</span><span class="p">(</span><span class="n">s</span><span class="p">,</span> <span class="n">e</span><span class="p">,</span> <span class="p">[],</span> <span class="n">maxlen</span><span class="p">))</span>
+
+        <span class="k">if</span> <span class="ow">not</span> <span class="n">silent</span><span class="p">:</span>
+            <span class="n">prg</span><span class="o">.</span><span class="n">terminate</span><span class="p">()</span>
+
+        <span class="k">return</span> <span class="n">all_paths</span></div>
+
+
+    <span class="c1">#</span>
+    <span class="c1"># Methods for collecting interaction attributes across the network</span>
+    <span class="c1">#</span>
+
+    <span class="k">def</span> <span class="nf">_collect</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">what</span><span class="p">,</span>
+            <span class="n">by</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">add_total</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+            <span class="o">**</span><span class="n">kwargs</span>
+        <span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Collects the values of an attribute over all interactions in the</span>
+<span class="sd">        network.</span>
+
+<span class="sd">        Args</span>
+<span class="sd">            kwargs:</span>
+<span class="sd">                Passed to methods of</span>
+<span class="sd">                :py:class:`pypath.interaction.Interaction`.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">result</span> <span class="o">=</span> <span class="nb">set</span><span class="p">()</span> <span class="k">if</span> <span class="ow">not</span> <span class="n">by</span> <span class="k">else</span> <span class="n">collections</span><span class="o">.</span><span class="n">defaultdict</span><span class="p">(</span><span class="nb">set</span><span class="p">)</span>
+
+        <span class="n">method</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_get_by_method_name</span><span class="p">(</span><span class="n">what</span><span class="p">,</span> <span class="n">by</span><span class="p">)</span>
+
+        <span class="k">if</span> <span class="ow">not</span> <span class="nb">hasattr</span><span class="p">(</span><span class="n">interaction_mod</span><span class="o">.</span><span class="n">Interaction</span><span class="p">,</span> <span class="n">method</span><span class="p">):</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span><span class="s1">&#39;Collecting attributes: no such method: `</span><span class="si">%s</span><span class="s1">`.&#39;</span> <span class="o">%</span> <span class="n">method</span><span class="p">)</span>
+
+        <span class="k">else</span><span class="p">:</span>
+
+            <span class="k">for</span> <span class="n">ia</span> <span class="ow">in</span> <span class="bp">self</span><span class="p">:</span>
+
+                <span class="n">ia_attrs</span> <span class="o">=</span> <span class="nb">getattr</span><span class="p">(</span><span class="n">ia</span><span class="p">,</span> <span class="n">method</span><span class="p">)(</span><span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
+
+                <span class="k">if</span> <span class="n">by</span><span class="p">:</span>
+
+                    <span class="k">for</span> <span class="n">grp</span><span class="p">,</span> <span class="n">val</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="n">ia_attrs</span><span class="p">):</span>
+
+                        <span class="n">result</span><span class="p">[</span><span class="n">grp</span><span class="p">]</span><span class="o">.</span><span class="n">update</span><span class="p">(</span><span class="n">val</span><span class="p">)</span>
+
+                <span class="k">else</span><span class="p">:</span>
+
+                    <span class="n">result</span><span class="o">.</span><span class="n">update</span><span class="p">(</span><span class="n">ia_attrs</span><span class="p">)</span>
+
+        <span class="k">if</span> <span class="n">by</span> <span class="ow">and</span> <span class="n">add_total</span><span class="p">:</span>
+
+            <span class="n">result</span><span class="p">[</span><span class="s1">&#39;total&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="nb">set</span><span class="o">.</span><span class="n">union</span><span class="p">(</span><span class="o">*</span><span class="n">result</span><span class="o">.</span><span class="n">values</span><span class="p">())</span>
+
+        <span class="k">return</span> <span class="nb">dict</span><span class="p">(</span><span class="n">result</span><span class="p">)</span> <span class="k">if</span> <span class="n">by</span> <span class="k">else</span> <span class="n">result</span>
+
+
+    <span class="nd">@classmethod</span>
+    <span class="k">def</span> <span class="nf">_generate_collect_methods</span><span class="p">(</span><span class="bp">cls</span><span class="p">):</span>
+
+        <span class="k">def</span> <span class="nf">_create_collect_method</span><span class="p">(</span><span class="n">what</span><span class="p">):</span>
+
+            <span class="nd">@functools</span><span class="o">.</span><span class="n">wraps</span><span class="p">(</span><span class="n">what</span><span class="p">)</span>
+            <span class="k">def</span> <span class="nf">_collect_method</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+
+                <span class="n">kwargs</span><span class="p">[</span><span class="s1">&#39;what&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">what</span>
+
+                <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span><span class="s1">&#39;Collecting `</span><span class="si">%s</span><span class="s1">`.&#39;</span> <span class="o">%</span> <span class="n">what</span><span class="p">)</span>
+
+                <span class="n">collection</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_collect</span><span class="p">(</span>
+                    <span class="n">by</span> <span class="o">=</span> <span class="s1">&#39;interaction_type_and_data_model_and_resource&#39;</span><span class="p">,</span>
+                    <span class="o">**</span><span class="n">kwargs</span>
+                <span class="p">)</span>
+
+                <span class="k">return</span> <span class="p">(</span>
+                    <span class="n">NetworkEntityCollection</span><span class="p">(</span>
+                        <span class="n">collection</span> <span class="o">=</span> <span class="n">collection</span><span class="p">,</span>
+                        <span class="n">label</span> <span class="o">=</span> <span class="n">what</span><span class="p">,</span>
+                    <span class="p">)</span>
+                <span class="p">)</span>
+
+            <span class="k">return</span> <span class="n">_collect_method</span>
+
+
+        <span class="k">for</span> <span class="n">_get</span> <span class="ow">in</span> <span class="n">interaction_mod</span><span class="o">.</span><span class="n">Interaction</span><span class="o">.</span><span class="n">_get_methods</span><span class="p">:</span>
+
+            <span class="n">method</span> <span class="o">=</span> <span class="n">_create_collect_method</span><span class="p">(</span><span class="n">_get</span><span class="p">)</span>
+            <span class="n">method_name</span> <span class="o">=</span> <span class="s1">&#39;collect_</span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="n">_get</span>
+            <span class="n">doc</span> <span class="o">=</span> <span class="p">(</span>
+                <span class="s1">&#39;Builds a comprehensive collection of `</span><span class="si">%s</span><span class="s1">` entities &#39;</span>
+                <span class="s1">&#39;across the network, counts unique and shared objects &#39;</span>
+                <span class="s1">&#39;by resource, data model and interaction types.&#39;</span> <span class="o">%</span> <span class="n">_get</span>
+            <span class="p">)</span>
+            <span class="n">signature</span> <span class="o">=</span> <span class="n">interaction_mod</span><span class="o">.</span><span class="n">Interaction</span><span class="o">.</span><span class="n">_get_method_signature</span>
+
+            <span class="k">if</span> <span class="s1">&#39;degree&#39;</span> <span class="ow">in</span> <span class="n">_get</span><span class="p">:</span>
+
+                <span class="n">signature</span> <span class="o">=</span> <span class="p">[(</span><span class="s1">&#39;mode&#39;</span><span class="p">,)]</span> <span class="o">+</span> <span class="n">signature</span>
+
+            <span class="bp">cls</span><span class="o">.</span><span class="n">_add_method</span><span class="p">(</span>
+                <span class="n">method_name</span><span class="p">,</span>
+                <span class="n">method</span><span class="p">,</span>
+                <span class="n">signature</span> <span class="o">=</span> <span class="n">signature</span><span class="p">,</span>
+                <span class="n">doc</span> <span class="o">=</span> <span class="n">doc</span><span class="p">,</span>
+            <span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">update_summaries</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">collect_args</span> <span class="o">=</span> <span class="kc">None</span><span class="p">):</span>
+
+
+        <span class="k">def</span> <span class="nf">get_labels</span><span class="p">(</span><span class="n">lab</span><span class="p">,</span> <span class="n">key</span><span class="p">,</span> <span class="n">segments</span><span class="p">):</span>
+
+            <span class="k">return</span> <span class="nb">tuple</span><span class="p">(</span>
+                <span class="p">(</span>
+                    <span class="s1">&#39;</span><span class="si">%s%s%s%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="p">(</span>
+                        <span class="n">key</span><span class="p">,</span>
+                        <span class="s1">&#39;_&#39;</span> <span class="k">if</span> <span class="n">seg</span> <span class="k">else</span> <span class="s1">&#39;&#39;</span><span class="p">,</span>
+                        <span class="n">seg</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s1">&#39; &#39;</span><span class="p">,</span> <span class="s1">&#39;_&#39;</span><span class="p">),</span>
+                        <span class="s1">&#39;_pct&#39;</span> <span class="k">if</span> <span class="n">pct</span> <span class="k">else</span> <span class="s1">&#39;_n&#39;</span><span class="p">,</span>
+                    <span class="p">),</span>
+                    <span class="s1">&#39;</span><span class="si">%s%s%s%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="p">(</span><span class="n">lab</span><span class="p">,</span> <span class="s1">&#39; &#39;</span> <span class="k">if</span> <span class="n">seg</span> <span class="k">else</span> <span class="s1">&#39;&#39;</span><span class="p">,</span> <span class="n">seg</span><span class="p">,</span> <span class="n">pct</span><span class="p">)</span>
+                <span class="p">)</span>
+                <span class="k">for</span> <span class="n">seg</span> <span class="ow">in</span> <span class="n">segments</span>
+                <span class="k">for</span> <span class="n">pct</span> <span class="ow">in</span> <span class="p">(</span><span class="s1">&#39;&#39;</span><span class="p">,</span> <span class="sa">r</span><span class="s1">&#39; [%]&#39;</span><span class="p">)</span>
+            <span class="p">)</span>
+
+
+        <span class="k">def</span> <span class="nf">add_resource_segments</span><span class="p">(</span><span class="n">rec</span><span class="p">,</span> <span class="n">res</span><span class="p">,</span> <span class="n">key</span><span class="p">,</span> <span class="n">lab</span><span class="p">,</span> <span class="n">segments</span><span class="p">,</span> <span class="n">coll</span><span class="p">):</span>
+
+            <span class="n">get</span> <span class="o">=</span> <span class="n">coll</span><span class="p">[</span><span class="n">key</span><span class="p">]</span><span class="o">.</span><span class="fm">__getattribute__</span>
+
+            <span class="n">values</span> <span class="o">=</span> <span class="nb">tuple</span><span class="p">(</span><span class="n">itertools</span><span class="o">.</span><span class="n">chain</span><span class="p">(</span><span class="o">*</span><span class="nb">zip</span><span class="p">(</span><span class="o">*</span><span class="p">(</span>
+                <span class="p">(</span>
+                    <span class="n">get</span><span class="p">(</span><span class="s1">&#39;</span><span class="si">%s</span><span class="s1">_collection&#39;</span> <span class="o">%</span> <span class="n">n_pct</span><span class="p">)</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="n">res</span><span class="p">,</span> <span class="mi">0</span><span class="p">),</span>
+                    <span class="n">get</span><span class="p">(</span><span class="s1">&#39;</span><span class="si">%s</span><span class="s1">_shared_within_data_model&#39;</span> <span class="o">%</span> <span class="n">n_pct</span><span class="p">)</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="n">res</span><span class="p">,</span> <span class="mi">0</span><span class="p">),</span>
+                    <span class="n">get</span><span class="p">(</span><span class="s1">&#39;</span><span class="si">%s</span><span class="s1">_unique_within_data_model&#39;</span> <span class="o">%</span> <span class="n">n_pct</span><span class="p">)</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="n">res</span><span class="p">,</span> <span class="mi">0</span><span class="p">),</span>
+                    <span class="n">get</span><span class="p">(</span>
+                        <span class="s1">&#39;</span><span class="si">%s</span><span class="s1">_shared_within_interaction_type&#39;</span> <span class="o">%</span> <span class="n">n_pct</span>
+                    <span class="p">)</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="n">res</span><span class="p">,</span> <span class="mi">0</span><span class="p">),</span>
+                    <span class="n">get</span><span class="p">(</span>
+                        <span class="s1">&#39;</span><span class="si">%s</span><span class="s1">_unique_within_interaction_type&#39;</span> <span class="o">%</span> <span class="n">n_pct</span>
+                    <span class="p">)</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="n">res</span><span class="p">,</span> <span class="mi">0</span><span class="p">),</span>
+                <span class="p">)</span>
+                <span class="k">for</span> <span class="n">n_pct</span> <span class="ow">in</span> <span class="p">(</span><span class="s1">&#39;n&#39;</span><span class="p">,</span> <span class="s1">&#39;pct&#39;</span><span class="p">)</span>
+            <span class="p">))))</span>
+
+            <span class="n">labels</span> <span class="o">=</span> <span class="n">get_labels</span><span class="p">(</span><span class="n">lab</span><span class="p">,</span> <span class="n">key</span><span class="p">,</span> <span class="n">segments</span><span class="p">)</span>
+
+            <span class="n">rec</span><span class="o">.</span><span class="n">extend</span><span class="p">(</span><span class="nb">list</span><span class="p">(</span><span class="nb">zip</span><span class="p">(</span><span class="n">labels</span><span class="p">,</span> <span class="n">values</span><span class="p">)))</span>
+
+            <span class="k">return</span> <span class="n">rec</span>
+
+
+        <span class="k">def</span> <span class="nf">add_dmodel_segments</span><span class="p">(</span><span class="n">rec</span><span class="p">,</span> <span class="n">itype</span><span class="p">,</span> <span class="n">dmodel</span><span class="p">,</span> <span class="n">key</span><span class="p">,</span> <span class="n">lab</span><span class="p">,</span> <span class="n">segments</span><span class="p">,</span> <span class="n">coll</span><span class="p">):</span>
+
+            <span class="n">it_dm_key</span> <span class="o">=</span> <span class="p">(</span><span class="n">itype</span><span class="p">,</span> <span class="n">dmodel</span><span class="p">)</span>
+            <span class="n">total_key</span> <span class="o">=</span> <span class="n">it_dm_key</span> <span class="o">+</span> <span class="p">(</span><span class="s1">&#39;Total&#39;</span><span class="p">,)</span>
+
+            <span class="n">get</span> <span class="o">=</span> <span class="n">coll</span><span class="p">[</span><span class="n">key</span><span class="p">]</span><span class="o">.</span><span class="fm">__getattribute__</span>
+
+            <span class="n">values</span> <span class="o">=</span> <span class="nb">tuple</span><span class="p">(</span><span class="n">itertools</span><span class="o">.</span><span class="n">chain</span><span class="p">(</span><span class="o">*</span><span class="nb">zip</span><span class="p">(</span><span class="o">*</span><span class="p">(</span>
+                <span class="p">(</span>
+                    <span class="n">get</span><span class="p">(</span><span class="s1">&#39;</span><span class="si">%s</span><span class="s1">_by_data_model&#39;</span> <span class="o">%</span> <span class="n">n_pct</span><span class="p">)</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="n">it_dm_key</span><span class="p">,</span> <span class="mi">0</span><span class="p">),</span>
+                    <span class="n">get</span><span class="p">(</span>
+                        <span class="s1">&#39;</span><span class="si">%s</span><span class="s1">_shared_within_data_model&#39;</span> <span class="o">%</span> <span class="n">n_pct</span>
+                    <span class="p">)</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="n">total_key</span><span class="p">,</span> <span class="mi">0</span><span class="p">),</span>
+                    <span class="n">get</span><span class="p">(</span>
+                        <span class="s1">&#39;</span><span class="si">%s</span><span class="s1">_unique_within_data_model&#39;</span> <span class="o">%</span> <span class="n">n_pct</span>
+                    <span class="p">)</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="n">total_key</span><span class="p">,</span> <span class="mi">0</span><span class="p">),</span>
+                    <span class="n">get</span><span class="p">(</span><span class="s1">&#39;</span><span class="si">%s</span><span class="s1">_shared_by_data_model&#39;</span> <span class="o">%</span> <span class="n">n_pct</span><span class="p">)</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="n">it_dm_key</span><span class="p">,</span> <span class="mi">0</span><span class="p">),</span>
+                    <span class="n">get</span><span class="p">(</span><span class="s1">&#39;</span><span class="si">%s</span><span class="s1">_unique_by_data_model&#39;</span> <span class="o">%</span> <span class="n">n_pct</span><span class="p">)</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="n">it_dm_key</span><span class="p">,</span> <span class="mi">0</span><span class="p">),</span>
+                <span class="p">)</span>
+                <span class="k">for</span> <span class="n">n_pct</span> <span class="ow">in</span> <span class="p">(</span><span class="s1">&#39;n&#39;</span><span class="p">,</span> <span class="s1">&#39;pct&#39;</span><span class="p">)</span>
+            <span class="p">))))</span>
+
+            <span class="n">labels</span> <span class="o">=</span> <span class="n">get_labels</span><span class="p">(</span><span class="n">lab</span><span class="p">,</span> <span class="n">key</span><span class="p">,</span> <span class="n">segments</span><span class="p">)</span>
+
+            <span class="n">rec</span><span class="o">.</span><span class="n">extend</span><span class="p">(</span><span class="nb">list</span><span class="p">(</span><span class="nb">zip</span><span class="p">(</span><span class="n">labels</span><span class="p">,</span> <span class="n">values</span><span class="p">)))</span>
+
+            <span class="k">return</span> <span class="n">rec</span>
+
+
+        <span class="k">def</span> <span class="nf">add_itype_segments</span><span class="p">(</span><span class="n">rec</span><span class="p">,</span> <span class="n">itype</span><span class="p">,</span> <span class="n">key</span><span class="p">,</span> <span class="n">lab</span><span class="p">,</span> <span class="n">segments</span><span class="p">,</span> <span class="n">coll</span><span class="p">):</span>
+
+            <span class="n">get</span> <span class="o">=</span> <span class="n">coll</span><span class="p">[</span><span class="n">key</span><span class="p">]</span><span class="o">.</span><span class="fm">__getattribute__</span>
+            <span class="n">total_key</span> <span class="o">=</span> <span class="p">(</span><span class="n">itype</span><span class="p">,</span> <span class="s1">&#39;all&#39;</span><span class="p">,</span> <span class="s1">&#39;Total&#39;</span><span class="p">)</span>
+
+            <span class="n">values</span> <span class="o">=</span> <span class="nb">tuple</span><span class="p">(</span><span class="n">itertools</span><span class="o">.</span><span class="n">chain</span><span class="p">(</span><span class="o">*</span><span class="nb">zip</span><span class="p">(</span><span class="o">*</span><span class="p">(</span>
+                <span class="p">(</span>
+                    <span class="n">get</span><span class="p">(</span><span class="s1">&#39;</span><span class="si">%s</span><span class="s1">_by_interaction_type&#39;</span> <span class="o">%</span> <span class="n">n_pct</span><span class="p">)</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="n">itype</span><span class="p">,</span> <span class="mi">0</span><span class="p">),</span>
+                    <span class="n">get</span><span class="p">(</span>
+                        <span class="s1">&#39;</span><span class="si">%s</span><span class="s1">_shared_within_interaction_type&#39;</span> <span class="o">%</span> <span class="n">n_pct</span>
+                    <span class="p">)</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="n">total_key</span><span class="p">,</span> <span class="mi">0</span><span class="p">),</span>
+                    <span class="n">get</span><span class="p">(</span>
+                        <span class="s1">&#39;</span><span class="si">%s</span><span class="s1">_unique_within_interaction_type&#39;</span> <span class="o">%</span> <span class="n">n_pct</span>
+                    <span class="p">)</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="n">total_key</span><span class="p">,</span> <span class="mi">0</span><span class="p">),</span>
+                    <span class="n">get</span><span class="p">(</span><span class="s1">&#39;</span><span class="si">%s</span><span class="s1">_shared_by_data_model&#39;</span> <span class="o">%</span> <span class="n">n_pct</span><span class="p">)</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="n">total_key</span><span class="p">,</span> <span class="mi">0</span><span class="p">),</span>
+                    <span class="n">get</span><span class="p">(</span><span class="s1">&#39;</span><span class="si">%s</span><span class="s1">_unique_by_data_model&#39;</span> <span class="o">%</span> <span class="n">n_pct</span><span class="p">)</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="n">total_key</span><span class="p">,</span> <span class="mi">0</span><span class="p">),</span>
+                <span class="p">)</span>
+                <span class="k">for</span> <span class="n">n_pct</span> <span class="ow">in</span> <span class="p">(</span><span class="s1">&#39;n&#39;</span><span class="p">,</span> <span class="s1">&#39;pct&#39;</span><span class="p">)</span>
+            <span class="p">))))</span>
+
+            <span class="n">labels</span> <span class="o">=</span> <span class="n">get_labels</span><span class="p">(</span><span class="n">lab</span><span class="p">,</span> <span class="n">key</span><span class="p">,</span> <span class="n">segments</span><span class="p">)</span>
+
+            <span class="n">rec</span><span class="o">.</span><span class="n">extend</span><span class="p">(</span><span class="nb">list</span><span class="p">(</span><span class="nb">zip</span><span class="p">(</span><span class="n">labels</span><span class="p">,</span> <span class="n">values</span><span class="p">)))</span>
+
+            <span class="k">return</span> <span class="n">rec</span>
+
+
+        <span class="n">collect_args</span> <span class="o">=</span> <span class="n">collect_args</span> <span class="ow">or</span> <span class="p">{</span><span class="s1">&#39;via&#39;</span><span class="p">:</span> <span class="kc">False</span><span class="p">}</span>
+
+
+        <span class="n">required</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">OrderedDict</span><span class="p">(</span>
+            <span class="n">entities</span> <span class="o">=</span> <span class="s1">&#39;Entities&#39;</span><span class="p">,</span>
+            <span class="n">proteins</span> <span class="o">=</span> <span class="s1">&#39;Proteins&#39;</span><span class="p">,</span>
+            <span class="n">mirnas</span> <span class="o">=</span> <span class="s1">&#39;miRNAs&#39;</span><span class="p">,</span>
+            <span class="n">interactions_0</span> <span class="o">=</span> <span class="s1">&#39;Edges&#39;</span><span class="p">,</span>
+            <span class="n">references</span> <span class="o">=</span> <span class="s1">&#39;References&#39;</span><span class="p">,</span>
+            <span class="n">curation_effort</span> <span class="o">=</span> <span class="s1">&#39;Curation effort&#39;</span><span class="p">,</span>
+            <span class="n">interactions_non_directed_0</span> <span class="o">=</span> <span class="s1">&#39;Undirected interactions&#39;</span><span class="p">,</span>
+            <span class="n">interactions_directed</span> <span class="o">=</span> <span class="s1">&#39;Directed interactions&#39;</span><span class="p">,</span>
+            <span class="n">interactions_positive</span> <span class="o">=</span> <span class="s1">&#39;Stimulatory interactions&#39;</span><span class="p">,</span>
+            <span class="n">interactions_negative</span> <span class="o">=</span> <span class="s1">&#39;Inhibitory interactions&#39;</span><span class="p">,</span>
+            <span class="n">interactions_mutual</span> <span class="o">=</span> <span class="s1">&#39;Mutual interactions&#39;</span><span class="p">,</span>
+        <span class="p">)</span>
+
+        <span class="n">segments</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="s1">&#39;&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;shared within database category&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;unique within database category&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;shared within interaction type&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;unique within interaction type&#39;</span><span class="p">,</span>
+        <span class="p">)</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">summaries</span> <span class="o">=</span> <span class="p">[]</span>
+
+        <span class="n">coll</span> <span class="o">=</span> <span class="p">{}</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span><span class="s1">&#39;Updating summaries.&#39;</span><span class="p">)</span>
+
+        <span class="k">for</span> <span class="n">method</span> <span class="ow">in</span> <span class="n">required</span><span class="o">.</span><span class="n">keys</span><span class="p">():</span>
+
+            <span class="n">coll</span><span class="p">[</span><span class="n">method</span><span class="p">]</span> <span class="o">=</span> <span class="nb">getattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">&#39;collect_</span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="n">method</span><span class="p">)(</span>
+                <span class="o">**</span><span class="n">collect_args</span>
+            <span class="p">)</span>
+
+        <span class="k">for</span> <span class="n">itype</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">get_interaction_types</span><span class="p">():</span>
+
+            <span class="k">for</span> <span class="n">dmodel</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">get_data_models</span><span class="p">(</span><span class="n">interaction_type</span> <span class="o">=</span> <span class="n">itype</span><span class="p">):</span>
+
+                <span class="k">for</span> <span class="n">res</span> <span class="ow">in</span> <span class="nb">sorted</span><span class="p">(</span>
+                    <span class="bp">self</span><span class="o">.</span><span class="n">get_resource_names</span><span class="p">(</span>
+                        <span class="n">interaction_type</span> <span class="o">=</span> <span class="n">itype</span><span class="p">,</span>
+                        <span class="n">data_model</span> <span class="o">=</span> <span class="n">dmodel</span><span class="p">,</span>
+                        <span class="o">**</span><span class="n">collect_args</span>
+                    <span class="p">),</span>
+                    <span class="n">key</span> <span class="o">=</span> <span class="k">lambda</span> <span class="n">r</span><span class="p">:</span> <span class="n">r</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span>
+                <span class="p">):</span>
+
+                    <span class="c1"># compiling a record for each resource</span>
+                    <span class="c1"># within the data model</span>
+
+                    <span class="n">rec</span> <span class="o">=</span> <span class="p">[((</span><span class="s1">&#39;resource&#39;</span><span class="p">,</span> <span class="s1">&#39;Resource&#39;</span><span class="p">),</span> <span class="n">res</span><span class="p">)]</span>
+
+                    <span class="n">_res</span> <span class="o">=</span> <span class="p">(</span><span class="n">itype</span><span class="p">,</span> <span class="n">dmodel</span><span class="p">,</span> <span class="n">res</span><span class="p">)</span>
+
+                    <span class="k">for</span> <span class="n">key</span><span class="p">,</span> <span class="n">lab</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="n">required</span><span class="p">):</span>
+
+                        <span class="n">rec</span> <span class="o">=</span> <span class="n">add_resource_segments</span><span class="p">(</span>
+                            <span class="n">rec</span><span class="p">,</span> <span class="n">_res</span><span class="p">,</span> <span class="n">key</span><span class="p">,</span> <span class="n">lab</span><span class="p">,</span> <span class="n">segments</span><span class="p">,</span> <span class="n">coll</span><span class="p">,</span>
+                        <span class="p">)</span>
+
+                    <span class="bp">self</span><span class="o">.</span><span class="n">summaries</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">rec</span><span class="p">)</span>
+
+                <span class="c1"># compiling a summary record for the data model</span>
+
+                <span class="n">rec</span> <span class="o">=</span> <span class="p">[(</span>
+                    <span class="p">(</span><span class="s1">&#39;resource&#39;</span><span class="p">,</span> <span class="s1">&#39;Resource&#39;</span><span class="p">),</span>
+                    <span class="s1">&#39;</span><span class="si">%s</span><span class="s1"> total&#39;</span> <span class="o">%</span> <span class="n">dmodel</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s1">&#39;_&#39;</span><span class="p">,</span> <span class="s1">&#39; &#39;</span><span class="p">)</span><span class="o">.</span><span class="n">capitalize</span><span class="p">()</span>
+                <span class="p">)]</span>
+
+                <span class="k">for</span> <span class="n">key</span><span class="p">,</span> <span class="n">lab</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="n">required</span><span class="p">):</span>
+
+                    <span class="n">rec</span> <span class="o">=</span> <span class="n">add_dmodel_segments</span><span class="p">(</span>
+                        <span class="n">rec</span><span class="p">,</span> <span class="n">itype</span><span class="p">,</span> <span class="n">dmodel</span><span class="p">,</span> <span class="n">key</span><span class="p">,</span> <span class="n">lab</span><span class="p">,</span> <span class="n">segments</span><span class="p">,</span> <span class="n">coll</span><span class="p">,</span>
+                    <span class="p">)</span>
+
+                <span class="bp">self</span><span class="o">.</span><span class="n">summaries</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">rec</span><span class="p">)</span>
+
+            <span class="c1"># compiling a summary record for the interaction type</span>
+
+            <span class="n">rec</span> <span class="o">=</span> <span class="p">[(</span>
+                <span class="p">(</span><span class="s1">&#39;resource&#39;</span><span class="p">,</span> <span class="s1">&#39;Resource&#39;</span><span class="p">),</span>
+                <span class="s1">&#39;</span><span class="si">%s</span><span class="s1"> total&#39;</span> <span class="o">%</span> <span class="n">itype</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s1">&#39;_&#39;</span><span class="p">,</span> <span class="s1">&#39; &#39;</span><span class="p">)</span><span class="o">.</span><span class="n">capitalize</span><span class="p">()</span>
+            <span class="p">)]</span>
+
+            <span class="k">for</span> <span class="n">key</span><span class="p">,</span> <span class="n">lab</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="n">required</span><span class="p">):</span>
+
+                <span class="n">rec</span> <span class="o">=</span> <span class="n">add_itype_segments</span><span class="p">(</span><span class="n">rec</span><span class="p">,</span> <span class="n">itype</span><span class="p">,</span> <span class="n">key</span><span class="p">,</span> <span class="n">lab</span><span class="p">,</span> <span class="n">segments</span><span class="p">,</span> <span class="n">coll</span><span class="p">)</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">summaries</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">rec</span><span class="p">)</span>
+
+        <span class="c1"># maybe we could compile a summary record for the entire network</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">summaries</span> <span class="o">=</span> <span class="p">[</span>
+            <span class="n">collections</span><span class="o">.</span><span class="n">OrderedDict</span><span class="p">(</span><span class="n">rec</span><span class="p">)</span>
+            <span class="k">for</span> <span class="n">rec</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">summaries</span>
+        <span class="p">]</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span><span class="s1">&#39;Finished updating summaries.&#39;</span><span class="p">)</span>
+
+
+<div class="viewcode-block" id="Network.summaries_tab">
+<a class="viewcode-back" href="../../../api/pypath.core.network.Network.html#pypath.core.network.Network.summaries_tab">[docs]</a>
+    <span class="k">def</span> <span class="nf">summaries_tab</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">outfile</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">return_table</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+            <span class="n">label_type</span> <span class="o">=</span> <span class="mi">1</span><span class="p">,</span>
+        <span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Creates a table from resource vs. entity counts and optionally</span>
+<span class="sd">        writes it to ``outfile`` and returns it.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">tab</span> <span class="o">=</span> <span class="p">[]</span>
+
+        <span class="n">tab</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">key</span><span class="p">[</span><span class="n">label_type</span><span class="p">]</span> <span class="k">for</span> <span class="n">key</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">summaries</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">keys</span><span class="p">())</span>
+
+        <span class="k">for</span> <span class="n">rec</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">summaries</span><span class="p">:</span>
+
+            <span class="n">tab</span><span class="o">.</span><span class="n">append</span><span class="p">([</span><span class="nb">str</span><span class="p">(</span><span class="n">val</span><span class="p">)</span> <span class="k">for</span> <span class="n">val</span> <span class="ow">in</span> <span class="n">rec</span><span class="o">.</span><span class="n">values</span><span class="p">()])</span>
+
+        <span class="k">if</span> <span class="n">outfile</span><span class="p">:</span>
+
+            <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">outfile</span><span class="p">,</span> <span class="s1">&#39;w&#39;</span><span class="p">)</span> <span class="k">as</span> <span class="n">fp</span><span class="p">:</span>
+
+                <span class="n">fp</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\n</span><span class="s1">&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\t</span><span class="s1">&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">row</span><span class="p">)</span> <span class="k">for</span> <span class="n">row</span> <span class="ow">in</span> <span class="n">tab</span><span class="p">))</span>
+
+        <span class="k">if</span> <span class="n">return_table</span><span class="p">:</span>
+
+            <span class="k">return</span> <span class="n">tab</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">homology_translate</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">taxon</span><span class="p">,</span> <span class="n">exclude</span> <span class="o">=</span> <span class="kc">None</span><span class="p">):</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span>
+            <span class="s1">&#39;Translating network by homology from organism `</span><span class="si">%u</span><span class="s1">` to `</span><span class="si">%u</span><span class="s1">`.&#39;</span> <span class="o">%</span> <span class="p">(</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">ncbi_tax_id</span><span class="p">,</span>
+                <span class="n">taxon</span><span class="p">,</span>
+            <span class="p">)</span>
+        <span class="p">)</span>
+
+        <span class="n">new</span> <span class="o">=</span> <span class="n">Network</span><span class="p">(</span><span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">taxon</span><span class="p">)</span>
+
+        <span class="n">n_ia_translated</span> <span class="o">=</span> <span class="mi">0</span>
+        <span class="n">entities_translated</span> <span class="o">=</span> <span class="nb">set</span><span class="p">()</span>
+
+        <span class="k">for</span> <span class="n">ia</span> <span class="ow">in</span> <span class="bp">self</span><span class="p">:</span>
+
+            <span class="n">ia_translated</span> <span class="o">=</span> <span class="kc">False</span>
+
+            <span class="k">for</span> <span class="n">new_ia</span> <span class="ow">in</span> <span class="n">ia</span><span class="o">.</span><span class="n">homology_translate</span><span class="p">(</span>
+                <span class="n">taxon</span> <span class="o">=</span> <span class="n">taxon</span><span class="p">,</span>
+                <span class="n">exclude</span> <span class="o">=</span> <span class="n">exclude</span><span class="p">,</span>
+            <span class="p">):</span>
+
+                <span class="n">new</span><span class="o">.</span><span class="n">add_interaction</span><span class="p">(</span><span class="n">new_ia</span><span class="p">)</span>
+                <span class="n">ia_translated</span> <span class="o">=</span> <span class="kc">True</span>
+                <span class="n">entities_translated</span><span class="o">.</span><span class="n">update</span><span class="p">(</span><span class="n">ia</span><span class="o">.</span><span class="n">get_entities</span><span class="p">())</span>
+
+            <span class="n">n_ia_translated</span> <span class="o">+=</span> <span class="n">ia_translated</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span>
+            <span class="s1">&#39;Orthology translation ready. &#39;</span>
+            <span class="s1">&#39;</span><span class="si">%u</span><span class="s1"> out of </span><span class="si">%u</span><span class="s1"> interactions (</span><span class="si">%.02f%%</span><span class="s1">), &#39;</span>
+            <span class="s1">&#39;</span><span class="si">%u</span><span class="s1"> out of </span><span class="si">%u</span><span class="s1"> entities (</span><span class="si">%.02f%%</span><span class="s1">) &#39;</span>
+            <span class="s1">&#39;have been translated.&#39;</span> <span class="o">%</span> <span class="p">(</span>
+                <span class="n">n_ia_translated</span><span class="p">,</span>
+                <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="p">),</span>
+                <span class="n">n_ia_translated</span> <span class="o">/</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span> <span class="o">*</span> <span class="mi">100</span><span class="p">,</span>
+                <span class="nb">len</span><span class="p">(</span><span class="n">entities_translated</span><span class="p">),</span>
+                <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">nodes</span><span class="p">),</span>
+                <span class="nb">len</span><span class="p">(</span><span class="n">entities_translated</span><span class="p">)</span> <span class="o">/</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">nodes</span><span class="p">)</span> <span class="o">*</span> <span class="mi">100</span><span class="p">,</span>
+            <span class="p">)</span>
+        <span class="p">)</span>
+
+        <span class="k">return</span> <span class="n">new</span>
+
+
+    <span class="nd">@staticmethod</span>
+    <span class="k">def</span> <span class="nf">_get_by_method_name</span><span class="p">(</span><span class="n">get</span><span class="p">,</span> <span class="n">by</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="p">(</span>
+            <span class="s1">&#39;&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span>
+                <span class="p">(</span>
+                    <span class="s1">&#39;get_&#39;</span> <span class="k">if</span> <span class="ow">not</span> <span class="n">by</span> <span class="k">else</span> <span class="s1">&#39;&#39;</span><span class="p">,</span>
+                    <span class="n">get</span><span class="p">,</span>
+                    <span class="s1">&#39;_by_&#39;</span> <span class="k">if</span> <span class="n">by</span> <span class="k">else</span> <span class="s1">&#39;&#39;</span><span class="p">,</span>
+                    <span class="n">by</span> <span class="ow">or</span> <span class="s1">&#39;&#39;</span><span class="p">,</span>
+                <span class="p">)</span>
+            <span class="p">)</span>
+        <span class="p">)</span>
+
+
+    <span class="nd">@staticmethod</span>
+    <span class="k">def</span> <span class="nf">_iter_get_by_methods</span><span class="p">():</span>
+
+        <span class="k">return</span> <span class="p">(</span>
+            <span class="n">itertools</span><span class="o">.</span><span class="n">product</span><span class="p">(</span>
+                <span class="n">interaction_mod</span><span class="o">.</span><span class="n">Interaction</span><span class="o">.</span><span class="n">_get_methods</span> <span class="o">|</span> <span class="p">{</span><span class="s1">&#39;entities&#39;</span><span class="p">},</span>
+                <span class="n">interaction_mod</span><span class="o">.</span><span class="n">Interaction</span><span class="o">.</span><span class="n">_by_methods</span> <span class="o">+</span> <span class="p">(</span><span class="kc">None</span><span class="p">,),</span>
+            <span class="p">)</span>
+        <span class="p">)</span>
+
+    <span class="nd">@classmethod</span>
+    <span class="k">def</span> <span class="nf">_generate_get_methods</span><span class="p">(</span><span class="bp">cls</span><span class="p">):</span>
+
+        <span class="k">def</span> <span class="nf">_create_get_method</span><span class="p">(</span><span class="n">what</span><span class="p">,</span> <span class="n">by</span><span class="p">):</span>
+
+            <span class="n">wrap_args</span> <span class="o">=</span> <span class="p">(</span><span class="n">what</span><span class="p">,</span> <span class="n">by</span><span class="p">)</span>
+
+            <span class="nd">@functools</span><span class="o">.</span><span class="n">wraps</span><span class="p">(</span><span class="n">wrap_args</span><span class="p">)</span>
+            <span class="k">def</span> <span class="nf">_get_by_method</span><span class="p">(</span><span class="o">*</span><span class="n">args</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+
+                <span class="n">what</span><span class="p">,</span> <span class="n">by</span> <span class="o">=</span> <span class="n">wrap_args</span>
+
+                <span class="bp">self</span> <span class="o">=</span> <span class="n">args</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span>
+                <span class="n">kwargs</span><span class="p">[</span><span class="s1">&#39;what&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">what</span>
+                <span class="n">kwargs</span><span class="p">[</span><span class="s1">&#39;by&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">by</span>
+
+                <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_collect</span><span class="p">(</span><span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
+
+            <span class="k">return</span> <span class="n">_get_by_method</span>
+
+
+        <span class="k">for</span> <span class="n">_get</span><span class="p">,</span> <span class="n">_by</span> <span class="ow">in</span> <span class="bp">cls</span><span class="o">.</span><span class="n">_iter_get_by_methods</span><span class="p">():</span>
+
+            <span class="n">method_name</span> <span class="o">=</span> <span class="bp">cls</span><span class="o">.</span><span class="n">_get_by_method_name</span><span class="p">(</span><span class="n">_get</span><span class="p">,</span> <span class="n">_by</span><span class="p">)</span>
+
+            <span class="nb">setattr</span><span class="p">(</span>
+                <span class="bp">cls</span><span class="p">,</span>
+                <span class="n">method_name</span><span class="p">,</span>
+                <span class="n">_create_get_method</span><span class="p">(</span><span class="n">what</span> <span class="o">=</span> <span class="n">_get</span><span class="p">,</span> <span class="n">by</span> <span class="o">=</span> <span class="n">_by</span><span class="p">),</span>
+            <span class="p">)</span>
+
+
+    <span class="nd">@classmethod</span>
+    <span class="k">def</span> <span class="nf">_generate_count_methods</span><span class="p">(</span><span class="bp">cls</span><span class="p">):</span>
+
+        <span class="k">def</span> <span class="nf">_create_count_method</span><span class="p">(</span><span class="n">what</span><span class="p">,</span> <span class="n">by</span><span class="p">):</span>
+
+            <span class="n">method_name</span> <span class="o">=</span> <span class="bp">cls</span><span class="o">.</span><span class="n">_get_by_method_name</span><span class="p">(</span><span class="n">what</span><span class="p">,</span> <span class="n">by</span><span class="p">)</span>
+
+            <span class="nd">@functools</span><span class="o">.</span><span class="n">wraps</span><span class="p">(</span><span class="n">method_name</span><span class="p">)</span>
+            <span class="k">def</span> <span class="nf">_count_method</span><span class="p">(</span><span class="o">*</span><span class="n">args</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+
+                <span class="bp">self</span> <span class="o">=</span> <span class="n">args</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span>
+
+                <span class="n">collection</span> <span class="o">=</span> <span class="nb">getattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">method_name</span><span class="p">)(</span><span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
+
+                <span class="k">return</span> <span class="p">(</span>
+                    <span class="nb">len</span><span class="p">(</span><span class="n">collection</span><span class="p">)</span>
+                        <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">collection</span><span class="p">,</span> <span class="nb">set</span><span class="p">)</span> <span class="k">else</span>
+                    <span class="n">common</span><span class="o">.</span><span class="n">dict_counts</span><span class="p">(</span><span class="n">collection</span><span class="p">)</span>
+                <span class="p">)</span>
+
+            <span class="k">return</span> <span class="n">_count_method</span>
+
+
+        <span class="k">for</span> <span class="n">_get</span><span class="p">,</span> <span class="n">_by</span> <span class="ow">in</span> <span class="bp">cls</span><span class="o">.</span><span class="n">_iter_get_by_methods</span><span class="p">():</span>
+
+            <span class="n">method_name</span> <span class="o">=</span> <span class="p">(</span>
+                <span class="s1">&#39;count_</span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="p">(</span>
+                    <span class="bp">cls</span><span class="o">.</span><span class="n">_get_by_method_name</span><span class="p">(</span><span class="n">_get</span><span class="p">,</span> <span class="n">_by</span><span class="p">)</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s1">&#39;get_&#39;</span><span class="p">,</span> <span class="s1">&#39;&#39;</span><span class="p">)</span>
+                <span class="p">)</span>
+            <span class="p">)</span>
+
+            <span class="nb">setattr</span><span class="p">(</span>
+                <span class="bp">cls</span><span class="p">,</span>
+                <span class="n">method_name</span><span class="p">,</span>
+                <span class="n">_create_count_method</span><span class="p">(</span><span class="n">what</span> <span class="o">=</span> <span class="n">_get</span><span class="p">,</span> <span class="n">by</span> <span class="o">=</span> <span class="n">_by</span><span class="p">)</span>
+            <span class="p">)</span>
+
+
+    <span class="nd">@classmethod</span>
+    <span class="k">def</span> <span class="nf">_add_method</span><span class="p">(</span><span class="bp">cls</span><span class="p">,</span> <span class="n">method_name</span><span class="p">,</span> <span class="n">method</span><span class="p">,</span> <span class="n">signature</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span> <span class="n">doc</span> <span class="o">=</span> <span class="kc">None</span><span class="p">):</span>
+
+        <span class="n">common</span><span class="o">.</span><span class="n">add_method</span><span class="p">(</span>
+            <span class="bp">cls</span><span class="p">,</span>
+            <span class="n">method_name</span><span class="p">,</span>
+            <span class="n">method</span><span class="p">,</span>
+            <span class="n">signature</span> <span class="o">=</span> <span class="n">signature</span><span class="p">,</span>
+            <span class="n">doc</span> <span class="o">=</span> <span class="n">doc</span><span class="p">,</span>
+        <span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">_allow_loops</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">allow_loops</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span> <span class="n">resource</span> <span class="o">=</span> <span class="kc">None</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Integrates settings for the `allow_loops` parameter from the</span>
+<span class="sd">        method, instance and module level settings.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">default</span> <span class="o">=</span> <span class="n">settings</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">&#39;network_allow_loops&#39;</span><span class="p">)</span>
+
+        <span class="k">return</span> <span class="p">(</span>
+            <span class="c1"># from the arguments of the actual `load` call</span>
+            <span class="n">allow_loops</span>
+                <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">allow_loops</span><span class="p">,</span> <span class="nb">bool</span><span class="p">)</span> <span class="k">else</span>
+            <span class="c1"># from the current instance</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">allow_loops</span>
+                <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">allow_loops</span><span class="p">,</span> <span class="nb">bool</span><span class="p">)</span> <span class="k">else</span>
+            <span class="c1"># resource specific settings</span>
+            <span class="n">resource</span><span class="o">.</span><span class="n">networkinput</span><span class="o">.</span><span class="n">allow_loops</span>
+                <span class="k">if</span> <span class="p">(</span>
+                    <span class="nb">hasattr</span><span class="p">(</span><span class="n">resource</span><span class="p">,</span> <span class="s1">&#39;networkinput&#39;</span><span class="p">)</span> <span class="ow">and</span>
+                    <span class="nb">isinstance</span><span class="p">(</span><span class="n">resource</span><span class="o">.</span><span class="n">networkinput</span><span class="o">.</span><span class="n">allow_loops</span><span class="p">,</span> <span class="nb">bool</span><span class="p">)</span>
+                <span class="p">)</span> <span class="k">else</span>
+            <span class="c1"># interaction type specific settings from the module level</span>
+            <span class="n">resource</span><span class="o">.</span><span class="n">networkinput</span><span class="o">.</span><span class="n">interaction_type</span> <span class="ow">in</span> <span class="n">default</span>
+                <span class="k">if</span> <span class="p">(</span>
+                    <span class="nb">isinstance</span><span class="p">(</span><span class="n">default</span><span class="p">,</span> <span class="n">_const</span><span class="o">.</span><span class="n">LIST_LIKE</span><span class="p">)</span> <span class="ow">and</span>
+                    <span class="nb">hasattr</span><span class="p">(</span><span class="n">resource</span><span class="p">,</span> <span class="s1">&#39;networkinput&#39;</span><span class="p">)</span>
+                <span class="p">)</span> <span class="k">else</span>
+            <span class="c1"># general settings from the module level</span>
+            <span class="nb">bool</span><span class="p">(</span><span class="n">default</span><span class="p">)</span>
+        <span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">count_loops</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="nb">sum</span><span class="p">(</span><span class="n">ia</span><span class="o">.</span><span class="n">is_loop</span><span class="p">()</span> <span class="k">for</span> <span class="n">ia</span> <span class="ow">in</span> <span class="bp">self</span><span class="p">)</span>
+
+
+<div class="viewcode-block" id="Network.direction_consistency">
+<a class="viewcode-back" href="../../../api/pypath.core.network.Network.html#pypath.core.network.Network.direction_consistency">[docs]</a>
+    <span class="k">def</span> <span class="nf">direction_consistency</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Collects statistics about the consistency of interaction</span>
+<span class="sd">        directions between resources.</span>
+<span class="sd">        * total_directed: number of directed edges</span>
+<span class="sd">        * shared_directed: number of directed edges in overlap with other</span>
+<span class="sd">          resources</span>
+<span class="sd">        * consistent_edges: number of edges consistent with other resources</span>
+<span class="sd">        * inconsistent_edges: number of edges inconsistent with other</span>
+<span class="sd">          resources</span>
+<span class="sd">        * total_consistency: sum of consistencies (for all edges and all</span>
+<span class="sd">          resources)</span>
+<span class="sd">        * total_inconsistency: sum of inconsistencies (for all edges and all</span>
+<span class="sd">          resources)</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">def</span> <span class="nf">dd_matrix</span><span class="p">(</span><span class="n">dd</span><span class="p">):</span>
+
+            <span class="n">names</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="n">dd</span><span class="o">.</span><span class="n">keys</span><span class="p">())</span>
+
+            <span class="k">return</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">(</span>
+                <span class="p">[</span>
+                    <span class="p">[</span><span class="n">key</span><span class="p">]</span> <span class="o">+</span> <span class="nb">list</span><span class="p">(</span><span class="n">val</span><span class="o">.</span><span class="n">values</span><span class="p">())</span>
+                    <span class="k">for</span> <span class="n">key</span><span class="p">,</span> <span class="n">val</span> <span class="ow">in</span> <span class="n">dd</span><span class="o">.</span><span class="n">items</span><span class="p">()</span>
+                <span class="p">],</span>
+                <span class="n">columns</span> <span class="o">=</span> <span class="p">[</span><span class="s1">&#39;resource&#39;</span><span class="p">]</span> <span class="o">+</span> <span class="n">names</span><span class="p">,</span>
+            <span class="p">)</span>
+
+
+        <span class="n">DirectionConsistency</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">namedtuple</span><span class="p">(</span>
+            <span class="s1">&#39;DirectionConsistency&#39;</span><span class="p">,</span>
+            <span class="p">[</span>
+                <span class="s1">&#39;total_directed&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;shared_directed&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;consistent_edges&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;inconsistent_edges&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;total_consistency&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;total_inconsistency&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;total_signed&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;shared_signed&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;consistent_signed_edges&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;inconsistent_signed_edges&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;total_sign_consistency&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;total_sign_inconsistency&#39;</span><span class="p">,</span>
+            <span class="p">]</span>
+        <span class="p">)</span>
+
+        <span class="n">summary</span> <span class="o">=</span> <span class="p">{}</span>
+
+        <span class="n">resources</span> <span class="o">=</span> <span class="nb">sorted</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">get_resource_names</span><span class="p">(</span><span class="n">via</span> <span class="o">=</span> <span class="kc">False</span><span class="p">))</span>
+        <span class="n">consistencies</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">OrderedDict</span><span class="p">(</span>
+            <span class="p">(</span>
+                <span class="n">resource1</span><span class="p">,</span>
+                <span class="n">collections</span><span class="o">.</span><span class="n">OrderedDict</span><span class="p">(</span>
+                    <span class="p">(</span><span class="n">resource2</span><span class="p">,</span> <span class="mi">0</span><span class="p">)</span>
+                    <span class="k">for</span> <span class="n">resource2</span> <span class="ow">in</span> <span class="n">resources</span>
+                <span class="p">)</span>
+            <span class="p">)</span>
+            <span class="k">for</span> <span class="n">resource1</span> <span class="ow">in</span> <span class="n">resources</span>
+        <span class="p">)</span>
+        <span class="n">inconsistencies</span> <span class="o">=</span> <span class="n">copy_mod</span><span class="o">.</span><span class="n">deepcopy</span><span class="p">(</span><span class="n">consistencies</span><span class="p">)</span>
+        <span class="n">sign_consistencies</span> <span class="o">=</span> <span class="n">copy_mod</span><span class="o">.</span><span class="n">deepcopy</span><span class="p">(</span><span class="n">consistencies</span><span class="p">)</span>
+        <span class="n">sign_inconsistencies</span> <span class="o">=</span> <span class="n">copy_mod</span><span class="o">.</span><span class="n">deepcopy</span><span class="p">(</span><span class="n">consistencies</span><span class="p">)</span>
+
+        <span class="k">for</span> <span class="n">resource</span> <span class="ow">in</span> <span class="n">resources</span><span class="p">:</span>
+
+            <span class="n">total_directed</span> <span class="o">=</span> <span class="mi">0</span>
+            <span class="n">shared_directed</span> <span class="o">=</span> <span class="mi">0</span>
+            <span class="n">consistent_edges</span> <span class="o">=</span> <span class="mi">0</span>
+            <span class="n">inconsistent_edges</span> <span class="o">=</span> <span class="mi">0</span>
+            <span class="n">total_consistency</span> <span class="o">=</span> <span class="mi">0</span>
+            <span class="n">total_inconsistency</span> <span class="o">=</span> <span class="mi">0</span>
+            <span class="n">total_signed</span> <span class="o">=</span> <span class="mi">0</span>
+            <span class="n">shared_signed</span> <span class="o">=</span> <span class="mi">0</span>
+            <span class="n">consistent_signed_edges</span> <span class="o">=</span> <span class="mi">0</span>
+            <span class="n">inconsistent_signed_edges</span> <span class="o">=</span> <span class="mi">0</span>
+            <span class="n">total_sign_consistency</span> <span class="o">=</span> <span class="mi">0</span>
+            <span class="n">total_sign_inconsistency</span> <span class="o">=</span> <span class="mi">0</span>
+
+            <span class="k">for</span> <span class="n">ia</span> <span class="ow">in</span> <span class="bp">self</span><span class="p">:</span>
+
+                <span class="k">if</span> <span class="ow">not</span> <span class="n">ia</span><span class="o">.</span><span class="n">is_directed</span><span class="p">():</span>
+
+                    <span class="k">continue</span>
+
+                <span class="n">res_a_b</span> <span class="o">=</span> <span class="n">ia</span><span class="o">.</span><span class="n">direction</span><span class="p">[</span><span class="n">ia</span><span class="o">.</span><span class="n">a_b</span><span class="p">]</span><span class="o">.</span><span class="n">get_resource_names</span><span class="p">(</span><span class="n">via</span> <span class="o">=</span> <span class="kc">False</span><span class="p">)</span>
+                <span class="n">res_b_a</span> <span class="o">=</span> <span class="n">ia</span><span class="o">.</span><span class="n">direction</span><span class="p">[</span><span class="n">ia</span><span class="o">.</span><span class="n">b_a</span><span class="p">]</span><span class="o">.</span><span class="n">get_resource_names</span><span class="p">(</span><span class="n">via</span> <span class="o">=</span> <span class="kc">False</span><span class="p">)</span>
+                <span class="n">res_a_b_pos</span> <span class="o">=</span> <span class="n">ia</span><span class="o">.</span><span class="n">positive</span><span class="p">[</span><span class="n">ia</span><span class="o">.</span><span class="n">a_b</span><span class="p">]</span><span class="o">.</span><span class="n">get_resource_names</span><span class="p">(</span>
+                    <span class="n">via</span> <span class="o">=</span> <span class="kc">False</span>
+                <span class="p">)</span>
+                <span class="n">res_a_b_neg</span> <span class="o">=</span> <span class="n">ia</span><span class="o">.</span><span class="n">negative</span><span class="p">[</span><span class="n">ia</span><span class="o">.</span><span class="n">a_b</span><span class="p">]</span><span class="o">.</span><span class="n">get_resource_names</span><span class="p">(</span>
+                    <span class="n">via</span> <span class="o">=</span> <span class="kc">False</span>
+                <span class="p">)</span>
+                <span class="n">res_b_a_pos</span> <span class="o">=</span> <span class="n">ia</span><span class="o">.</span><span class="n">positive</span><span class="p">[</span><span class="n">ia</span><span class="o">.</span><span class="n">b_a</span><span class="p">]</span><span class="o">.</span><span class="n">get_resource_names</span><span class="p">(</span>
+                    <span class="n">via</span> <span class="o">=</span> <span class="kc">False</span>
+                <span class="p">)</span>
+                <span class="n">res_b_a_neg</span> <span class="o">=</span> <span class="n">ia</span><span class="o">.</span><span class="n">negative</span><span class="p">[</span><span class="n">ia</span><span class="o">.</span><span class="n">b_a</span><span class="p">]</span><span class="o">.</span><span class="n">get_resource_names</span><span class="p">(</span>
+                    <span class="n">via</span> <span class="o">=</span> <span class="kc">False</span>
+                <span class="p">)</span>
+
+                <span class="k">if</span> <span class="n">resource</span> <span class="ow">in</span> <span class="n">res_a_b</span> <span class="ow">or</span> <span class="n">resource</span> <span class="ow">in</span> <span class="n">res_b_a</span><span class="p">:</span>
+
+                    <span class="n">total_directed</span> <span class="o">+=</span> <span class="mi">1</span>
+
+                <span class="k">else</span><span class="p">:</span>
+
+                    <span class="k">continue</span>
+
+                <span class="k">if</span> <span class="n">resource</span> <span class="ow">in</span> <span class="n">res_a_b_pos</span> <span class="ow">or</span> <span class="n">resource</span> <span class="ow">in</span> <span class="n">res_a_b_neg</span><span class="p">:</span>
+
+                    <span class="n">total_signed</span> <span class="o">+=</span> <span class="mi">1</span>
+
+                <span class="k">if</span> <span class="n">resource</span> <span class="ow">in</span> <span class="n">res_b_a_pos</span> <span class="ow">or</span> <span class="n">resource</span> <span class="ow">in</span> <span class="n">res_b_a_neg</span><span class="p">:</span>
+
+                    <span class="n">total_signed</span> <span class="o">+=</span> <span class="mi">1</span>
+
+                <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">res_a_b</span> <span class="o">|</span> <span class="n">res_b_a</span><span class="p">)</span> <span class="o">&gt;</span> <span class="mi">1</span><span class="p">:</span>
+
+                    <span class="n">shared_directed</span> <span class="o">+=</span> <span class="mi">1</span>
+
+                <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">res_a_b_pos</span> <span class="o">|</span> <span class="n">res_a_b_neg</span><span class="p">)</span> <span class="o">&gt;</span> <span class="mi">1</span><span class="p">:</span>
+
+                    <span class="n">shared_signed</span> <span class="o">+=</span> <span class="mi">1</span>
+
+                <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">res_b_a_pos</span> <span class="o">|</span> <span class="n">res_b_a_neg</span><span class="p">)</span> <span class="o">&gt;</span> <span class="mi">1</span><span class="p">:</span>
+
+                    <span class="n">shared_signed</span> <span class="o">+=</span> <span class="mi">1</span>
+
+                <span class="k">if</span> <span class="p">(</span>
+                    <span class="p">(</span><span class="n">resource</span> <span class="ow">in</span> <span class="n">res_a_b</span> <span class="ow">and</span> <span class="nb">len</span><span class="p">(</span><span class="n">res_a_b</span><span class="p">)</span> <span class="o">&gt;</span> <span class="mi">1</span><span class="p">)</span> <span class="ow">or</span>
+                    <span class="p">(</span><span class="n">resource</span> <span class="ow">in</span> <span class="n">res_b_a</span> <span class="ow">and</span> <span class="nb">len</span><span class="p">(</span><span class="n">res_b_a</span><span class="p">)</span> <span class="o">&gt;</span> <span class="mi">1</span><span class="p">)</span>
+                <span class="p">):</span>
+
+                    <span class="n">consistent_edges</span> <span class="o">+=</span> <span class="mi">1</span>
+
+                <span class="k">if</span> <span class="p">(</span>
+                    <span class="p">(</span><span class="n">resource</span> <span class="ow">in</span> <span class="n">res_a_b_pos</span> <span class="ow">and</span> <span class="nb">len</span><span class="p">(</span><span class="n">res_a_b_pos</span><span class="p">)</span> <span class="o">&gt;</span> <span class="mi">1</span><span class="p">)</span> <span class="ow">or</span>
+                    <span class="p">(</span><span class="n">resource</span> <span class="ow">in</span> <span class="n">res_a_b_neg</span> <span class="ow">and</span> <span class="nb">len</span><span class="p">(</span><span class="n">res_a_b_neg</span><span class="p">)</span> <span class="o">&gt;</span> <span class="mi">1</span><span class="p">)</span>
+                <span class="p">):</span>
+
+                    <span class="n">consistent_signed_edges</span> <span class="o">+=</span> <span class="mi">1</span>
+
+                <span class="k">if</span> <span class="p">(</span>
+                    <span class="p">(</span><span class="n">resource</span> <span class="ow">in</span> <span class="n">res_b_a_pos</span> <span class="ow">and</span> <span class="nb">len</span><span class="p">(</span><span class="n">res_b_a_pos</span><span class="p">)</span> <span class="o">&gt;</span> <span class="mi">1</span><span class="p">)</span> <span class="ow">or</span>
+                    <span class="p">(</span><span class="n">resource</span> <span class="ow">in</span> <span class="n">res_b_a_neg</span> <span class="ow">and</span> <span class="nb">len</span><span class="p">(</span><span class="n">res_b_a_neg</span><span class="p">)</span> <span class="o">&gt;</span> <span class="mi">1</span><span class="p">)</span>
+                <span class="p">):</span>
+
+                    <span class="n">consistent_signed_edges</span> <span class="o">+=</span> <span class="mi">1</span>
+
+                <span class="k">if</span> <span class="p">(</span>
+                    <span class="p">(</span>
+                        <span class="n">resource</span> <span class="ow">in</span> <span class="n">res_a_b</span> <span class="ow">and</span>
+                        <span class="n">resource</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">res_b_a</span> <span class="ow">and</span>
+                        <span class="n">res_b_a</span>
+                    <span class="p">)</span> <span class="ow">or</span>
+                    <span class="p">(</span>
+                        <span class="n">resource</span> <span class="ow">in</span> <span class="n">res_b_a</span> <span class="ow">and</span>
+                        <span class="n">resource</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">res_a_b</span> <span class="ow">and</span>
+                        <span class="n">res_a_b</span>
+                    <span class="p">)</span>
+                <span class="p">):</span>
+
+                    <span class="n">inconsistent_edges</span> <span class="o">+=</span> <span class="mi">1</span>
+
+                <span class="k">if</span> <span class="p">(</span>
+                    <span class="p">(</span>
+                        <span class="n">resource</span> <span class="ow">in</span> <span class="n">res_a_b_pos</span> <span class="ow">and</span>
+                        <span class="n">resource</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">res_a_b_neg</span> <span class="ow">and</span>
+                        <span class="n">res_a_b_neg</span>
+                    <span class="p">)</span> <span class="ow">or</span>
+                    <span class="p">(</span>
+                        <span class="n">resource</span> <span class="ow">in</span> <span class="n">res_a_b_neg</span> <span class="ow">and</span>
+                        <span class="n">resource</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">res_a_b_pos</span> <span class="ow">and</span>
+                        <span class="n">res_a_b_pos</span>
+                    <span class="p">)</span>
+                <span class="p">):</span>
+
+                    <span class="n">inconsistent_signed_edges</span> <span class="o">+=</span> <span class="mi">1</span>
+
+                <span class="k">if</span> <span class="p">(</span>
+                    <span class="p">(</span>
+                        <span class="n">resource</span> <span class="ow">in</span> <span class="n">res_b_a_pos</span> <span class="ow">and</span>
+                        <span class="n">resource</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">res_b_a_neg</span> <span class="ow">and</span>
+                        <span class="n">res_b_a_neg</span>
+                    <span class="p">)</span> <span class="ow">or</span>
+                    <span class="p">(</span>
+                        <span class="n">resource</span> <span class="ow">in</span> <span class="n">res_b_a_neg</span> <span class="ow">and</span>
+                        <span class="n">resource</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">res_b_a_pos</span> <span class="ow">and</span>
+                        <span class="n">res_b_a_pos</span>
+                    <span class="p">)</span>
+                <span class="p">):</span>
+
+                    <span class="n">inconsistent_signed_edges</span> <span class="o">+=</span> <span class="mi">1</span>
+
+                <span class="k">if</span> <span class="n">resource</span> <span class="ow">in</span> <span class="n">res_a_b</span><span class="p">:</span>
+
+                    <span class="n">total_consistency</span> <span class="o">+=</span> <span class="nb">len</span><span class="p">(</span><span class="n">res_a_b</span><span class="p">)</span> <span class="o">-</span> <span class="mi">1</span>
+
+                <span class="k">else</span><span class="p">:</span>
+
+                    <span class="n">total_inconsistency</span> <span class="o">+=</span> <span class="nb">len</span><span class="p">(</span><span class="n">res_a_b</span><span class="p">)</span>
+
+                <span class="k">if</span> <span class="n">resource</span> <span class="ow">in</span> <span class="n">res_a_b_pos</span><span class="p">:</span>
+
+                    <span class="n">total_sign_consistency</span> <span class="o">+=</span> <span class="nb">len</span><span class="p">(</span><span class="n">res_a_b_pos</span><span class="p">)</span> <span class="o">-</span> <span class="mi">1</span>
+
+                <span class="k">if</span> <span class="n">resource</span> <span class="ow">in</span> <span class="n">res_a_b_neg</span><span class="p">:</span>
+
+                    <span class="n">total_sign_consistency</span> <span class="o">+=</span> <span class="nb">len</span><span class="p">(</span><span class="n">res_a_b_neg</span><span class="p">)</span> <span class="o">-</span> <span class="mi">1</span>
+
+                <span class="k">if</span> <span class="n">resource</span> <span class="ow">in</span> <span class="n">res_b_a_pos</span><span class="p">:</span>
+
+                    <span class="n">total_sign_consistency</span> <span class="o">+=</span> <span class="nb">len</span><span class="p">(</span><span class="n">res_b_a_pos</span><span class="p">)</span> <span class="o">-</span> <span class="mi">1</span>
+
+                <span class="k">if</span> <span class="n">resource</span> <span class="ow">in</span> <span class="n">res_b_a_neg</span><span class="p">:</span>
+
+                    <span class="n">total_sign_consistency</span> <span class="o">+=</span> <span class="nb">len</span><span class="p">(</span><span class="n">res_b_a_neg</span><span class="p">)</span> <span class="o">-</span> <span class="mi">1</span>
+
+                <span class="k">if</span> <span class="n">resource</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">res_a_b_pos</span><span class="p">:</span>
+
+                    <span class="n">total_sign_inconsistency</span> <span class="o">+=</span> <span class="nb">len</span><span class="p">(</span><span class="n">res_a_b_pos</span><span class="p">)</span>
+
+                <span class="k">if</span> <span class="n">resource</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">res_a_b_neg</span><span class="p">:</span>
+
+                    <span class="n">total_sign_inconsistency</span> <span class="o">+=</span> <span class="nb">len</span><span class="p">(</span><span class="n">res_a_b_neg</span><span class="p">)</span>
+
+                <span class="k">if</span> <span class="n">resource</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">res_b_a_pos</span><span class="p">:</span>
+
+                    <span class="n">total_sign_inconsistency</span> <span class="o">+=</span> <span class="nb">len</span><span class="p">(</span><span class="n">res_b_a_pos</span><span class="p">)</span>
+
+                <span class="k">if</span> <span class="n">resource</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">res_b_a_neg</span><span class="p">:</span>
+
+                    <span class="n">total_sign_inconsistency</span> <span class="o">+=</span> <span class="nb">len</span><span class="p">(</span><span class="n">res_b_a_neg</span><span class="p">)</span>
+
+                <span class="k">if</span> <span class="n">resource</span> <span class="ow">in</span> <span class="n">res_b_a</span><span class="p">:</span>
+
+                    <span class="n">total_consistency</span> <span class="o">+=</span> <span class="nb">len</span><span class="p">(</span><span class="n">res_b_a</span><span class="p">)</span> <span class="o">-</span> <span class="mi">1</span>
+
+                <span class="k">else</span><span class="p">:</span>
+
+                    <span class="n">total_inconsistency</span> <span class="o">+=</span> <span class="nb">len</span><span class="p">(</span><span class="n">res_b_a</span><span class="p">)</span>
+
+                <span class="k">for</span> <span class="n">dir_resources</span> <span class="ow">in</span> <span class="p">(</span><span class="n">res_a_b</span><span class="p">,</span> <span class="n">res_b_a</span><span class="p">):</span>
+
+                    <span class="k">for</span> <span class="n">res_other</span> <span class="ow">in</span> <span class="n">dir_resources</span><span class="p">:</span>
+
+                        <span class="k">if</span> <span class="n">resource</span> <span class="ow">in</span> <span class="n">dir_resources</span><span class="p">:</span>
+
+                            <span class="n">consistencies</span><span class="p">[</span><span class="n">resource</span><span class="p">][</span><span class="n">res_other</span><span class="p">]</span> <span class="o">+=</span> <span class="mi">1</span>
+
+                        <span class="k">else</span><span class="p">:</span>
+
+                            <span class="n">inconsistencies</span><span class="p">[</span><span class="n">resource</span><span class="p">][</span><span class="n">res_other</span><span class="p">]</span> <span class="o">+=</span> <span class="mi">1</span>
+
+                <span class="k">for</span> <span class="n">sign_resources</span> <span class="ow">in</span> <span class="p">(</span>
+                    <span class="n">res_a_b_pos</span><span class="p">,</span>
+                    <span class="n">res_a_b_neg</span><span class="p">,</span>
+                    <span class="n">res_b_a_pos</span><span class="p">,</span>
+                    <span class="n">res_a_b_neg</span><span class="p">,</span>
+                <span class="p">):</span>
+
+                    <span class="k">for</span> <span class="n">res_other</span> <span class="ow">in</span> <span class="n">sign_resources</span><span class="p">:</span>
+
+                        <span class="k">if</span> <span class="n">resource</span> <span class="ow">in</span> <span class="n">sign_resources</span><span class="p">:</span>
+
+                            <span class="n">sign_consistencies</span><span class="p">[</span><span class="n">resource</span><span class="p">][</span><span class="n">res_other</span><span class="p">]</span> <span class="o">+=</span> <span class="mi">1</span>
+
+                        <span class="k">else</span><span class="p">:</span>
+
+                            <span class="n">sign_inconsistencies</span><span class="p">[</span><span class="n">resource</span><span class="p">][</span><span class="n">res_other</span><span class="p">]</span> <span class="o">+=</span> <span class="mi">1</span>
+
+            <span class="n">summary</span><span class="p">[</span><span class="n">resource</span><span class="p">]</span> <span class="o">=</span> <span class="n">DirectionConsistency</span><span class="p">(</span>
+                <span class="n">total_directed</span> <span class="o">=</span> <span class="n">total_directed</span><span class="p">,</span>
+                <span class="n">shared_directed</span> <span class="o">=</span> <span class="n">shared_directed</span><span class="p">,</span>
+                <span class="n">consistent_edges</span> <span class="o">=</span> <span class="n">consistent_edges</span><span class="p">,</span>
+                <span class="n">inconsistent_edges</span> <span class="o">=</span> <span class="n">inconsistent_edges</span><span class="p">,</span>
+                <span class="n">total_consistency</span> <span class="o">=</span> <span class="n">total_consistency</span><span class="p">,</span>
+                <span class="n">total_inconsistency</span> <span class="o">=</span> <span class="n">total_inconsistency</span><span class="p">,</span>
+                <span class="n">total_signed</span> <span class="o">=</span> <span class="n">total_signed</span><span class="p">,</span>
+                <span class="n">shared_signed</span> <span class="o">=</span> <span class="n">shared_signed</span><span class="p">,</span>
+                <span class="n">consistent_signed_edges</span> <span class="o">=</span> <span class="n">consistent_signed_edges</span><span class="p">,</span>
+                <span class="n">inconsistent_signed_edges</span> <span class="o">=</span> <span class="n">inconsistent_signed_edges</span><span class="p">,</span>
+                <span class="n">total_sign_consistency</span> <span class="o">=</span> <span class="n">total_sign_consistency</span><span class="p">,</span>
+                <span class="n">total_sign_inconsistency</span> <span class="o">=</span> <span class="n">total_sign_inconsistency</span><span class="p">,</span>
+            <span class="p">)</span>
+
+        <span class="n">consistencies</span> <span class="o">=</span> <span class="n">dd_matrix</span><span class="p">(</span><span class="n">consistencies</span><span class="p">)</span>
+        <span class="n">inconsistencies</span> <span class="o">=</span> <span class="n">dd_matrix</span><span class="p">(</span><span class="n">inconsistencies</span><span class="p">)</span>
+        <span class="n">sign_consistencies</span> <span class="o">=</span> <span class="n">dd_matrix</span><span class="p">(</span><span class="n">sign_consistencies</span><span class="p">)</span>
+        <span class="n">sign_inconsistencies</span> <span class="o">=</span> <span class="n">dd_matrix</span><span class="p">(</span><span class="n">sign_inconsistencies</span><span class="p">)</span>
+
+        <span class="n">summary</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">(</span>
+            <span class="p">[</span>
+                <span class="p">[</span><span class="n">resource</span><span class="p">]</span> <span class="o">+</span> <span class="nb">list</span><span class="p">(</span><span class="n">values</span><span class="p">)</span>
+                <span class="k">for</span> <span class="n">resource</span><span class="p">,</span> <span class="n">values</span> <span class="ow">in</span> <span class="n">summary</span><span class="o">.</span><span class="n">items</span><span class="p">()</span>
+            <span class="p">],</span>
+            <span class="n">columns</span> <span class="o">=</span> <span class="p">[</span><span class="s1">&#39;resource&#39;</span><span class="p">]</span> <span class="o">+</span> <span class="nb">list</span><span class="p">(</span><span class="n">DirectionConsistency</span><span class="o">.</span><span class="n">_fields</span><span class="p">),</span>
+        <span class="p">)</span>
+
+        <span class="k">return</span> <span class="p">{</span>
+            <span class="s1">&#39;summary&#39;</span><span class="p">:</span> <span class="n">summary</span><span class="p">,</span>
+            <span class="s1">&#39;consistencies&#39;</span><span class="p">:</span> <span class="n">consistencies</span><span class="p">,</span>
+            <span class="s1">&#39;inconsistencies&#39;</span><span class="p">:</span> <span class="n">inconsistencies</span><span class="p">,</span>
+            <span class="s1">&#39;sign_consistencies&#39;</span><span class="p">:</span> <span class="n">sign_consistencies</span><span class="p">,</span>
+            <span class="s1">&#39;sign_inconsistencies&#39;</span><span class="p">:</span> <span class="n">sign_inconsistencies</span><span class="p">,</span>
+        <span class="p">}</span></div>
+</div>
+
+
+
+<span class="n">Network</span><span class="o">.</span><span class="n">_generate_get_methods</span><span class="p">()</span>
+<span class="n">Network</span><span class="o">.</span><span class="n">_generate_partners_methods</span><span class="p">()</span>
+<span class="n">Network</span><span class="o">.</span><span class="n">_generate_count_methods</span><span class="p">()</span>
+<span class="n">Network</span><span class="o">.</span><span class="n">_generate_collect_methods</span><span class="p">()</span>
+
+
+<div class="viewcode-block" id="init_db">
+<a class="viewcode-back" href="../../../api/pypath.core.network.init_db.html#pypath.core.network.init_db">[docs]</a>
+<span class="k">def</span> <span class="nf">init_db</span><span class="p">(</span><span class="n">use_omnipath</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span> <span class="n">method</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+
+    <span class="n">method_name</span> <span class="o">=</span> <span class="p">(</span>
+        <span class="s1">&#39;load_omnipath&#39;</span>
+            <span class="k">if</span> <span class="n">use_omnipath</span> <span class="k">else</span>
+        <span class="p">(</span><span class="n">method</span> <span class="ow">or</span> <span class="s1">&#39;load&#39;</span><span class="p">)</span>
+    <span class="p">)</span>
+
+    <span class="n">new_network</span> <span class="o">=</span> <span class="n">Network</span><span class="p">()</span>
+    <span class="n">maybe_network</span> <span class="o">=</span> <span class="nb">getattr</span><span class="p">(</span><span class="n">new_network</span><span class="p">,</span> <span class="n">method_name</span><span class="p">)(</span><span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
+
+    <span class="nb">globals</span><span class="p">()[</span><span class="s1">&#39;db&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">maybe_network</span> <span class="ow">or</span> <span class="n">new_network</span></div>
+
+
+
+<div class="viewcode-block" id="get_db">
+<a class="viewcode-back" href="../../../api/pypath.core.network.get_db.html#pypath.core.network.get_db">[docs]</a>
+<span class="k">def</span> <span class="nf">get_db</span><span class="p">(</span><span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+
+    <span class="k">if</span> <span class="s1">&#39;db&#39;</span> <span class="ow">not</span> <span class="ow">in</span> <span class="nb">globals</span><span class="p">():</span>
+
+        <span class="n">init_db</span><span class="p">(</span><span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
+
+    <span class="k">return</span> <span class="nb">globals</span><span class="p">()[</span><span class="s1">&#39;db&#39;</span><span class="p">]</span></div>
+
+</pre></div>
+
+                </article>
+              
+              
+              
+              
+              
+                <footer class="prev-next-footer">
+                  
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diff --git a/_modules/pypath/inputs/adhesome.html b/_modules/pypath/inputs/adhesome.html
new file mode 100644
index 000000000..f10776b3a
--- /dev/null
+++ b/_modules/pypath/inputs/adhesome.html
@@ -0,0 +1,699 @@
+
+<!DOCTYPE html>
+
+
+<html lang="en" data-content_root="../../../" >
+
+  <head>
+    <meta charset="utf-8" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+    <title>pypath.inputs.adhesome &#8212; pypath 0.16.9 documentation</title>
+  
+  
+  
+  <script data-cfasync="false">
+    document.documentElement.dataset.mode = localStorage.getItem("mode") || "";
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+</form></div>
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+                  
+  <h1>Source code for pypath.inputs.adhesome</h1><div class="highlight"><pre>
+<span></span><span class="ch">#!/usr/bin/env python</span>
+<span class="c1"># -*- coding: utf-8 -*-</span>
+
+<span class="c1">#</span>
+<span class="c1">#  This file is part of the `pypath` python module</span>
+<span class="c1">#</span>
+<span class="c1">#  Copyright 2014-2023</span>
+<span class="c1">#  EMBL, EMBL-EBI, Uniklinik RWTH Aachen, Heidelberg University</span>
+<span class="c1">#</span>
+<span class="c1">#  Authors: see the file `README.rst`</span>
+<span class="c1">#  Contact: Dénes Türei (turei.denes@gmail.com)</span>
+<span class="c1">#</span>
+<span class="c1">#  Distributed under the GPLv3 License.</span>
+<span class="c1">#  See accompanying file LICENSE.txt or copy at</span>
+<span class="c1">#      https://www.gnu.org/licenses/gpl-3.0.html</span>
+<span class="c1">#</span>
+<span class="c1">#  Website: https://pypath.omnipathdb.org/</span>
+<span class="c1">#</span>
+
+<span class="kn">import</span> <span class="nn">csv</span>
+<span class="kn">import</span> <span class="nn">collections</span>
+
+<span class="kn">import</span> <span class="nn">pypath.share.curl</span> <span class="k">as</span> <span class="nn">curl</span>
+<span class="kn">import</span> <span class="nn">pypath.share.common</span> <span class="k">as</span> <span class="nn">common</span>
+<span class="kn">import</span> <span class="nn">pypath.resources.urls</span> <span class="k">as</span> <span class="nn">urls</span>
+<span class="kn">import</span> <span class="nn">pypath.utils.mapping</span> <span class="k">as</span> <span class="nn">mapping</span>
+
+
+<div class="viewcode-block" id="adhesome_interactions">
+<a class="viewcode-back" href="../../../api/pypath.inputs.adhesome.adhesome_interactions.html#pypath.inputs.adhesome.adhesome_interactions">[docs]</a>
+<span class="k">def</span> <span class="nf">adhesome_interactions</span><span class="p">():</span>
+
+    <span class="n">AdhesomeInteraction</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">namedtuple</span><span class="p">(</span>
+        <span class="s1">&#39;AdhesomeInteraction&#39;</span><span class="p">,</span>
+        <span class="p">[</span><span class="s1">&#39;source&#39;</span><span class="p">,</span> <span class="s1">&#39;target&#39;</span><span class="p">,</span> <span class="s1">&#39;effect&#39;</span><span class="p">,</span> <span class="s1">&#39;type&#39;</span><span class="p">,</span> <span class="s1">&#39;pmid&#39;</span><span class="p">],</span>
+    <span class="p">)</span>
+
+    <span class="n">url</span> <span class="o">=</span> <span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;adhesome&#39;</span><span class="p">][</span><span class="s1">&#39;interactions&#39;</span><span class="p">]</span>
+
+    <span class="n">c</span> <span class="o">=</span> <span class="n">curl</span><span class="o">.</span><span class="n">Curl</span><span class="p">(</span><span class="n">url</span><span class="p">,</span> <span class="n">large</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span> <span class="n">silent</span> <span class="o">=</span> <span class="kc">False</span><span class="p">)</span>
+
+    <span class="n">data</span> <span class="o">=</span> <span class="n">csv</span><span class="o">.</span><span class="n">DictReader</span><span class="p">(</span><span class="n">c</span><span class="o">.</span><span class="n">result</span><span class="p">,</span> <span class="n">delimiter</span> <span class="o">=</span> <span class="s1">&#39;,&#39;</span><span class="p">)</span>
+
+    <span class="n">result</span> <span class="o">=</span> <span class="p">[]</span>
+
+    <span class="k">for</span> <span class="n">rec</span> <span class="ow">in</span> <span class="n">data</span><span class="p">:</span>
+
+        <span class="n">result</span><span class="o">.</span><span class="n">append</span><span class="p">(</span>
+            <span class="n">AdhesomeInteraction</span><span class="p">(</span>
+                <span class="n">source</span> <span class="o">=</span> <span class="n">rec</span><span class="p">[</span><span class="s1">&#39;Source&#39;</span><span class="p">],</span>
+                <span class="n">target</span> <span class="o">=</span> <span class="n">rec</span><span class="p">[</span><span class="s1">&#39;Target&#39;</span><span class="p">],</span>
+                <span class="n">effect</span> <span class="o">=</span> <span class="n">rec</span><span class="p">[</span><span class="s1">&#39;Effect&#39;</span><span class="p">],</span>
+                <span class="nb">type</span>   <span class="o">=</span> <span class="n">common</span><span class="o">.</span><span class="n">upper0</span><span class="p">(</span><span class="n">rec</span><span class="p">[</span><span class="s1">&#39;Type&#39;</span><span class="p">]),</span>
+                <span class="n">pmid</span>   <span class="o">=</span> <span class="n">rec</span><span class="p">[</span><span class="s1">&#39;PMID&#39;</span><span class="p">],</span>
+            <span class="p">)</span>
+        <span class="p">)</span>
+
+    <span class="k">return</span> <span class="n">result</span></div>
+
+
+
+<div class="viewcode-block" id="adhesome_annotations">
+<a class="viewcode-back" href="../../../api/pypath.inputs.adhesome.adhesome_annotations.html#pypath.inputs.adhesome.adhesome_annotations">[docs]</a>
+<span class="k">def</span> <span class="nf">adhesome_annotations</span><span class="p">():</span>
+
+    <span class="n">AdhesomeAnnotation</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">namedtuple</span><span class="p">(</span>
+        <span class="s1">&#39;AdhesomeAnnotation&#39;</span><span class="p">,</span>
+        <span class="p">[</span><span class="s1">&#39;mainclass&#39;</span><span class="p">,</span> <span class="s1">&#39;intrinsic&#39;</span><span class="p">],</span>
+    <span class="p">)</span>
+
+    <span class="n">result</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">defaultdict</span><span class="p">(</span><span class="nb">set</span><span class="p">)</span>
+
+    <span class="n">url</span> <span class="o">=</span> <span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;adhesome&#39;</span><span class="p">][</span><span class="s1">&#39;components&#39;</span><span class="p">]</span>
+    <span class="n">c</span> <span class="o">=</span> <span class="n">curl</span><span class="o">.</span><span class="n">Curl</span><span class="p">(</span><span class="n">url</span><span class="p">,</span> <span class="n">large</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span> <span class="n">silent</span> <span class="o">=</span> <span class="kc">False</span><span class="p">)</span>
+
+    <span class="n">data</span> <span class="o">=</span> <span class="n">csv</span><span class="o">.</span><span class="n">DictReader</span><span class="p">(</span><span class="n">c</span><span class="o">.</span><span class="n">result</span><span class="p">,</span> <span class="n">delimiter</span> <span class="o">=</span> <span class="s1">&#39;,&#39;</span><span class="p">)</span>
+
+    <span class="k">for</span> <span class="n">rec</span> <span class="ow">in</span> <span class="n">data</span><span class="p">:</span>
+        <span class="n">uniprots</span> <span class="o">=</span> <span class="n">rec</span><span class="p">[</span><span class="s1">&#39;Swiss-Prot ID&#39;</span><span class="p">]</span>
+
+        <span class="k">for</span> <span class="n">uniprot</span> <span class="ow">in</span> <span class="n">uniprots</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;,&#39;</span><span class="p">):</span>
+            <span class="n">uniprot</span> <span class="o">=</span> <span class="n">uniprot</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span>
+
+            <span class="k">if</span> <span class="n">uniprot</span> <span class="o">==</span> <span class="s1">&#39;null&#39;</span><span class="p">:</span>
+                <span class="k">continue</span>
+
+            <span class="k">for</span> <span class="n">_uniprot</span> <span class="ow">in</span> <span class="n">mapping</span><span class="o">.</span><span class="n">map_name</span><span class="p">(</span><span class="n">uniprot</span><span class="p">,</span> <span class="s1">&#39;uniprot&#39;</span><span class="p">,</span> <span class="s1">&#39;uniprot&#39;</span><span class="p">):</span>
+                <span class="n">result</span><span class="p">[</span><span class="n">uniprot</span><span class="p">]</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">AdhesomeAnnotation</span><span class="p">(</span>
+                    <span class="n">mainclass</span> <span class="o">=</span> <span class="p">(</span>
+                        <span class="n">common</span><span class="o">.</span><span class="n">upper0</span><span class="p">(</span><span class="n">rec</span><span class="p">[</span><span class="s1">&#39;Functional Category&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">strip</span><span class="p">())</span>
+                    <span class="p">),</span>
+                    <span class="n">intrinsic</span> <span class="o">=</span> <span class="n">rec</span><span class="p">[</span><span class="s1">&#39;FA&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span> <span class="o">==</span> <span class="s1">&#39;Intrinsic Proteins&#39;</span><span class="p">,</span>
+                <span class="p">))</span>
+
+    <span class="k">return</span> <span class="nb">dict</span><span class="p">(</span><span class="n">result</span><span class="p">)</span></div>
+
+</pre></div>
+
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diff --git a/_modules/pypath/inputs/almen2009.html b/_modules/pypath/inputs/almen2009.html
new file mode 100644
index 000000000..e2b912023
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+  <h1>Source code for pypath.inputs.almen2009</h1><div class="highlight"><pre>
+<span></span><span class="ch">#!/usr/bin/env python</span>
+<span class="c1"># -*- coding: utf-8 -*-</span>
+
+<span class="c1">#</span>
+<span class="c1">#  This file is part of the `pypath` python module</span>
+<span class="c1">#</span>
+<span class="c1">#  Copyright 2014-2023</span>
+<span class="c1">#  EMBL, EMBL-EBI, Uniklinik RWTH Aachen, Heidelberg University</span>
+<span class="c1">#</span>
+<span class="c1">#  Authors: see the file `README.rst`</span>
+<span class="c1">#  Contact: Dénes Türei (turei.denes@gmail.com)</span>
+<span class="c1">#</span>
+<span class="c1">#  Distributed under the GPLv3 License.</span>
+<span class="c1">#  See accompanying file LICENSE.txt or copy at</span>
+<span class="c1">#      https://www.gnu.org/licenses/gpl-3.0.html</span>
+<span class="c1">#</span>
+<span class="c1">#  Website: https://pypath.omnipathdb.org/</span>
+<span class="c1">#</span>
+
+<span class="kn">from</span> <span class="nn">future.utils</span> <span class="kn">import</span> <span class="n">iteritems</span>
+
+<span class="kn">import</span> <span class="nn">re</span>
+<span class="kn">import</span> <span class="nn">collections</span>
+
+<span class="kn">import</span> <span class="nn">pypath.inputs.common</span> <span class="k">as</span> <span class="nn">inputs_common</span>
+<span class="kn">import</span> <span class="nn">pypath.resources.urls</span> <span class="k">as</span> <span class="nn">urls</span>
+<span class="kn">import</span> <span class="nn">pypath.share.curl</span> <span class="k">as</span> <span class="nn">curl</span>
+<span class="kn">import</span> <span class="nn">pypath.utils.mapping</span> <span class="k">as</span> <span class="nn">mapping</span>
+
+
+<div class="viewcode-block" id="almen2009_annotations">
+<a class="viewcode-back" href="../../../api/pypath.inputs.almen2009.almen2009_annotations.html#pypath.inputs.almen2009.almen2009_annotations">[docs]</a>
+<span class="k">def</span> <span class="nf">almen2009_annotations</span><span class="p">():</span>
+
+
+    <span class="n">resep</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">compile</span><span class="p">(</span><span class="sa">r</span><span class="s1">&#39;[;/]&#39;</span><span class="p">)</span>
+
+
+    <span class="n">Almen2009Annotation</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">namedtuple</span><span class="p">(</span>
+        <span class="s1">&#39;Almen2009Annotation&#39;</span><span class="p">,</span>
+        <span class="p">[</span>
+            <span class="s1">&#39;mainclass&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;classes&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;phobius_secreted&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;phobius_transmembrane&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;sosui_transmembrane&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;tmhmm_transmembrane&#39;</span><span class="p">,</span>
+        <span class="p">]</span>
+    <span class="p">)</span>
+
+
+    <span class="n">url</span> <span class="o">=</span> <span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;almen2009&#39;</span><span class="p">][</span><span class="s1">&#39;url&#39;</span><span class="p">]</span>
+
+    <span class="n">c</span> <span class="o">=</span> <span class="n">curl</span><span class="o">.</span><span class="n">Curl</span><span class="p">(</span><span class="n">url</span><span class="p">,</span> <span class="n">silent</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span> <span class="n">large</span> <span class="o">=</span> <span class="kc">True</span><span class="p">)</span>
+
+    <span class="n">xls</span> <span class="o">=</span> <span class="n">c</span><span class="o">.</span><span class="n">fileobj</span>
+    <span class="n">xlsfile</span> <span class="o">=</span> <span class="n">xls</span><span class="o">.</span><span class="n">name</span>
+    <span class="n">xls</span><span class="o">.</span><span class="n">close</span><span class="p">()</span>
+    <span class="n">tbl</span> <span class="o">=</span> <span class="n">inputs_common</span><span class="o">.</span><span class="n">read_xls</span><span class="p">(</span><span class="n">xlsfile</span><span class="p">,</span> <span class="n">sheet</span> <span class="o">=</span> <span class="s1">&#39;Data&#39;</span><span class="p">)[</span><span class="mi">1</span><span class="p">:]</span>
+
+    <span class="n">result</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">defaultdict</span><span class="p">(</span><span class="nb">set</span><span class="p">)</span>
+
+    <span class="k">for</span> <span class="n">row</span> <span class="ow">in</span> <span class="n">tbl</span><span class="p">:</span>
+
+        <span class="n">uniprots</span> <span class="o">=</span> <span class="n">mapping</span><span class="o">.</span><span class="n">map_name</span><span class="p">(</span><span class="n">row</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="s1">&#39;ipi&#39;</span><span class="p">,</span> <span class="s1">&#39;uniprot&#39;</span><span class="p">)</span>
+
+        <span class="n">mainclass</span> <span class="o">=</span> <span class="n">row</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span>
+        <span class="n">classes</span> <span class="o">=</span> <span class="n">row</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s1">&#39;KInase&#39;</span><span class="p">,</span> <span class="s1">&#39;Kinase&#39;</span><span class="p">)</span>
+        <span class="n">classes</span> <span class="o">=</span> <span class="nb">tuple</span><span class="p">(</span><span class="nb">sorted</span><span class="p">(</span><span class="n">resep</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="n">classes</span><span class="p">)))</span>
+        <span class="n">phobius_transmembrane</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="nb">float</span><span class="p">(</span><span class="n">row</span><span class="p">[</span><span class="mi">5</span><span class="p">]))</span>
+        <span class="n">phobius_secreted</span> <span class="o">=</span> <span class="n">row</span><span class="p">[</span><span class="mi">6</span><span class="p">]</span> <span class="o">==</span> <span class="s1">&#39;Y&#39;</span>
+        <span class="n">sosui_transmembrane</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="nb">float</span><span class="p">(</span><span class="n">row</span><span class="p">[</span><span class="mi">8</span><span class="p">]))</span> <span class="k">if</span> <span class="n">row</span><span class="p">[</span><span class="mi">8</span><span class="p">]</span> <span class="o">!=</span> <span class="s1">&#39;ERROR&#39;</span> <span class="k">else</span> <span class="mi">0</span>
+        <span class="n">tmhmm_transmembrane</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="nb">float</span><span class="p">(</span><span class="n">row</span><span class="p">[</span><span class="mi">10</span><span class="p">]))</span>
+
+        <span class="k">for</span> <span class="n">uniprot</span> <span class="ow">in</span> <span class="n">uniprots</span><span class="p">:</span>
+
+            <span class="n">result</span><span class="p">[</span><span class="n">uniprot</span><span class="p">]</span><span class="o">.</span><span class="n">add</span><span class="p">(</span>
+                <span class="n">Almen2009Annotation</span><span class="p">(</span>
+                    <span class="n">mainclass</span> <span class="o">=</span> <span class="n">mainclass</span><span class="p">,</span>
+                    <span class="n">classes</span> <span class="o">=</span> <span class="n">classes</span><span class="p">,</span>
+                    <span class="n">phobius_secreted</span> <span class="o">=</span> <span class="n">phobius_secreted</span><span class="p">,</span>
+                    <span class="n">phobius_transmembrane</span> <span class="o">=</span> <span class="n">phobius_transmembrane</span><span class="p">,</span>
+                    <span class="n">sosui_transmembrane</span> <span class="o">=</span> <span class="n">sosui_transmembrane</span><span class="p">,</span>
+                    <span class="n">tmhmm_transmembrane</span> <span class="o">=</span> <span class="n">tmhmm_transmembrane</span><span class="p">,</span>
+                <span class="p">)</span>
+            <span class="p">)</span>
+
+    <span class="k">return</span> <span class="nb">dict</span><span class="p">(</span><span class="n">result</span><span class="p">)</span></div>
+
+</pre></div>
+
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diff --git a/_modules/pypath/inputs/baccin2019.html b/_modules/pypath/inputs/baccin2019.html
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+                  
+  <h1>Source code for pypath.inputs.baccin2019</h1><div class="highlight"><pre>
+<span></span><span class="ch">#!/usr/bin/env python</span>
+<span class="c1"># -*- coding: utf-8 -*-</span>
+
+<span class="c1">#</span>
+<span class="c1">#  This file is part of the `pypath` python module</span>
+<span class="c1">#</span>
+<span class="c1">#  Copyright 2014-2023</span>
+<span class="c1">#  EMBL, EMBL-EBI, Uniklinik RWTH Aachen, Heidelberg University</span>
+<span class="c1">#</span>
+<span class="c1">#  Authors: see the file `README.rst`</span>
+<span class="c1">#  Contact: Dénes Türei (turei.denes@gmail.com)</span>
+<span class="c1">#</span>
+<span class="c1">#  Distributed under the GPLv3 License.</span>
+<span class="c1">#  See accompanying file LICENSE.txt or copy at</span>
+<span class="c1">#      https://www.gnu.org/licenses/gpl-3.0.html</span>
+<span class="c1">#</span>
+<span class="c1">#  Website: https://pypath.omnipathdb.org/</span>
+<span class="c1">#</span>
+
+<span class="kn">import</span> <span class="nn">re</span>
+<span class="kn">import</span> <span class="nn">collections</span>
+<span class="kn">import</span> <span class="nn">itertools</span>
+
+<span class="kn">import</span> <span class="nn">pypath.share.curl</span> <span class="k">as</span> <span class="nn">curl</span>
+<span class="kn">import</span> <span class="nn">pypath.resources.urls</span> <span class="k">as</span> <span class="nn">urls</span>
+<span class="kn">import</span> <span class="nn">pypath.utils.mapping</span> <span class="k">as</span> <span class="nn">mapping</span>
+<span class="kn">import</span> <span class="nn">pypath.utils.orthology</span> <span class="k">as</span> <span class="nn">orthology_mod</span>
+<span class="kn">import</span> <span class="nn">pypath.internals.intera</span> <span class="k">as</span> <span class="nn">intera</span>
+<span class="kn">import</span> <span class="nn">pypath.inputs.common</span> <span class="k">as</span> <span class="nn">inputs_common</span>
+
+
+<div class="viewcode-block" id="baccin2019_interactions">
+<a class="viewcode-back" href="../../../api/pypath.inputs.baccin2019.baccin2019_interactions.html#pypath.inputs.baccin2019.baccin2019_interactions">[docs]</a>
+<span class="k">def</span> <span class="nf">baccin2019_interactions</span><span class="p">(</span><span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">):</span>
+
+    <span class="n">recamel</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">compile</span><span class="p">(</span><span class="sa">r</span><span class="s1">&#39;(.+?)([A-Z][a-z])&#39;</span><span class="p">)</span>
+    <span class="n">recap</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">compile</span><span class="p">(</span><span class="sa">r</span><span class="s1">&#39;(^[A-Z][a-z]|_[A-Z][a-z])(.+)&#39;</span><span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">camel_to_snake</span><span class="p">(</span><span class="n">value</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="p">(</span>
+            <span class="n">recamel</span><span class="o">.</span><span class="n">sub</span><span class="p">(</span>
+                <span class="k">lambda</span> <span class="n">m</span><span class="p">:</span> <span class="n">m</span><span class="o">.</span><span class="n">group</span><span class="p">(</span><span class="mi">1</span><span class="p">)</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span> <span class="o">+</span> <span class="s1">&#39;_&#39;</span> <span class="o">+</span> <span class="n">m</span><span class="o">.</span><span class="n">group</span><span class="p">(</span><span class="mi">2</span><span class="p">),</span>
+                <span class="n">value</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span>
+            <span class="p">)</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span>
+        <span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">id_translate</span><span class="p">(</span><span class="n">mouse_gs</span><span class="p">):</span>
+
+        <span class="n">uniprots</span> <span class="o">=</span> <span class="n">mapping</span><span class="o">.</span><span class="n">map_name</span><span class="p">(</span>
+            <span class="n">mouse_gs</span><span class="p">,</span>
+            <span class="s1">&#39;genesymbol&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;uniprot&#39;</span><span class="p">,</span>
+            <span class="mi">10090</span><span class="p">,</span>
+        <span class="p">)</span>
+
+        <span class="k">if</span> <span class="n">ncbi_tax_id</span> <span class="o">!=</span> <span class="mi">10090</span><span class="p">:</span>
+
+            <span class="n">uniprots</span> <span class="o">=</span> <span class="nb">set</span><span class="p">(</span>
+                <span class="n">itertools</span><span class="o">.</span><span class="n">chain</span><span class="p">(</span><span class="o">*</span><span class="p">(</span>
+                    <span class="n">orthology_mod</span><span class="o">.</span><span class="n">translate</span><span class="p">(</span>
+                        <span class="n">uniprot</span><span class="p">,</span>
+                        <span class="n">target</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">,</span>
+                        <span class="n">source</span> <span class="o">=</span> <span class="mi">10090</span><span class="p">,</span>
+                    <span class="p">)</span>
+                    <span class="k">for</span> <span class="n">uniprot</span> <span class="ow">in</span> <span class="n">uniprots</span>
+                <span class="p">))</span>
+            <span class="p">)</span>
+
+        <span class="k">return</span> <span class="n">uniprots</span>
+
+
+    <span class="k">def</span> <span class="nf">raw_to_uniprots</span><span class="p">(</span><span class="n">raw</span><span class="p">):</span>
+
+        <span class="n">components</span> <span class="o">=</span> <span class="n">raw</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;&amp;&#39;</span><span class="p">)</span>
+
+        <span class="k">return</span> <span class="nb">set</span><span class="p">(</span>
+            <span class="n">itertools</span><span class="o">.</span><span class="n">product</span><span class="p">(</span>
+                <span class="o">*</span><span class="p">(</span><span class="n">id_translate</span><span class="p">(</span><span class="n">comp</span><span class="p">)</span> <span class="k">for</span> <span class="n">comp</span> <span class="ow">in</span> <span class="n">components</span><span class="p">)</span>
+            <span class="p">)</span>
+        <span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">get_partners</span><span class="p">(</span><span class="n">components</span><span class="p">,</span> <span class="n">sources</span><span class="p">,</span> <span class="n">references</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="p">{</span>
+            <span class="p">(</span>
+                <span class="n">comp</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span>
+                    <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">comp</span><span class="p">)</span> <span class="o">==</span> <span class="mi">1</span> <span class="k">else</span>
+                <span class="n">intera</span><span class="o">.</span><span class="n">Complex</span><span class="p">(</span>
+                    <span class="n">components</span> <span class="o">=</span> <span class="n">comp</span><span class="p">,</span>
+                    <span class="n">sources</span> <span class="o">=</span> <span class="n">sources</span><span class="p">,</span>
+                    <span class="n">references</span> <span class="o">=</span> <span class="n">references</span><span class="p">,</span>
+                <span class="p">)</span>
+            <span class="p">)</span>
+            <span class="k">for</span> <span class="n">comp</span> <span class="ow">in</span> <span class="n">components</span>
+        <span class="p">}</span>
+
+
+    <span class="n">Baccin2019Interaction</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">namedtuple</span><span class="p">(</span>
+        <span class="s1">&#39;Baccin2019Interaction&#39;</span><span class="p">,</span>
+        <span class="p">[</span>
+            <span class="s1">&#39;ligand&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;receptor&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;correct&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;ligand_location&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;ligand_category&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;resources&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;references&#39;</span><span class="p">,</span>
+        <span class="p">]</span>
+    <span class="p">)</span>
+
+
+    <span class="n">source_names</span> <span class="o">=</span> <span class="p">{</span>
+        <span class="s1">&#39;Baccin&#39;</span><span class="p">:</span> <span class="s1">&#39;Baccin2019&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;Ramilowski&#39;</span><span class="p">:</span> <span class="s1">&#39;Ramilowski2015&#39;</span><span class="p">,</span>
+    <span class="p">}</span>
+
+    <span class="n">url</span> <span class="o">=</span> <span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;baccin2019&#39;</span><span class="p">][</span><span class="s1">&#39;url&#39;</span><span class="p">]</span>
+    <span class="n">c</span> <span class="o">=</span> <span class="n">curl</span><span class="o">.</span><span class="n">Curl</span><span class="p">(</span><span class="n">url</span><span class="p">,</span> <span class="n">silent</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span> <span class="n">large</span> <span class="o">=</span> <span class="kc">True</span><span class="p">)</span>
+    <span class="n">data</span> <span class="o">=</span> <span class="n">inputs_common</span><span class="o">.</span><span class="n">read_xls</span><span class="p">(</span><span class="n">c</span><span class="o">.</span><span class="n">fileobj</span><span class="o">.</span><span class="n">name</span><span class="p">,</span> <span class="n">sheet</span> <span class="o">=</span> <span class="s1">&#39;SuppTable3&#39;</span><span class="p">)</span>
+
+    <span class="n">result</span> <span class="o">=</span> <span class="p">[]</span>
+
+    <span class="k">for</span> <span class="n">rec</span> <span class="ow">in</span> <span class="n">data</span><span class="p">[</span><span class="mi">3</span><span class="p">:]:</span>
+
+        <span class="k">if</span> <span class="n">rec</span><span class="p">[</span><span class="mi">4</span><span class="p">]</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span> <span class="o">==</span> <span class="s1">&#39;incorrect&#39;</span><span class="p">:</span>
+
+            <span class="k">continue</span>
+
+        <span class="n">ligand_components</span> <span class="o">=</span> <span class="n">raw_to_uniprots</span><span class="p">(</span><span class="n">rec</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span>
+
+        <span class="k">if</span> <span class="ow">not</span> <span class="n">ligand_components</span><span class="p">:</span>
+
+            <span class="k">continue</span>
+
+        <span class="n">receptor_components</span> <span class="o">=</span> <span class="n">raw_to_uniprots</span><span class="p">(</span><span class="n">rec</span><span class="p">[</span><span class="mi">2</span><span class="p">])</span>
+
+        <span class="k">if</span> <span class="ow">not</span> <span class="n">receptor_components</span><span class="p">:</span>
+
+            <span class="k">continue</span>
+
+        <span class="n">sources</span> <span class="o">=</span> <span class="p">{</span><span class="s1">&#39;Baccin2019&#39;</span><span class="p">,</span> <span class="n">rec</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span><span class="o">.</span><span class="n">strip</span><span class="p">()}</span>
+        <span class="n">sources</span> <span class="o">=</span> <span class="p">{</span>
+            <span class="n">source_names</span><span class="p">[</span><span class="n">s</span><span class="p">]</span> <span class="k">if</span> <span class="n">s</span> <span class="ow">in</span> <span class="n">source_names</span> <span class="k">else</span> <span class="n">s</span>
+            <span class="k">for</span> <span class="n">s</span> <span class="ow">in</span> <span class="n">sources</span>
+        <span class="p">}</span>
+
+        <span class="n">references</span> <span class="o">=</span> <span class="p">{</span>
+            <span class="n">_ref</span> <span class="k">for</span> <span class="n">_ref</span> <span class="ow">in</span>
+            <span class="p">(</span>
+                <span class="n">ref</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s1">&#39;.0&#39;</span><span class="p">,</span> <span class="s1">&#39;&#39;</span><span class="p">)</span>
+                <span class="k">for</span> <span class="n">ref</span> <span class="ow">in</span> <span class="n">rec</span><span class="p">[</span><span class="mi">7</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;,&#39;</span><span class="p">)</span>
+            <span class="p">)</span>
+            <span class="k">if</span> <span class="n">_ref</span><span class="o">.</span><span class="n">isdigit</span><span class="p">()</span>
+        <span class="p">}</span>
+
+        <span class="n">ligands</span> <span class="o">=</span> <span class="n">get_partners</span><span class="p">(</span><span class="n">ligand_components</span><span class="p">,</span> <span class="n">sources</span><span class="p">,</span> <span class="n">references</span><span class="p">)</span>
+        <span class="n">receptors</span> <span class="o">=</span> <span class="n">get_partners</span><span class="p">(</span><span class="n">receptor_components</span><span class="p">,</span> <span class="n">sources</span><span class="p">,</span> <span class="n">references</span><span class="p">)</span>
+
+        <span class="k">for</span> <span class="n">ligand</span><span class="p">,</span> <span class="n">receptor</span> <span class="ow">in</span> <span class="n">itertools</span><span class="o">.</span><span class="n">product</span><span class="p">(</span><span class="n">ligands</span><span class="p">,</span> <span class="n">receptors</span><span class="p">):</span>
+            <span class="n">result</span><span class="o">.</span><span class="n">append</span><span class="p">(</span>
+                <span class="n">Baccin2019Interaction</span><span class="p">(</span>
+                    <span class="n">ligand</span> <span class="o">=</span> <span class="n">ligand</span><span class="p">,</span>
+                    <span class="n">receptor</span> <span class="o">=</span> <span class="n">receptor</span><span class="p">,</span>
+                    <span class="n">correct</span> <span class="o">=</span> <span class="n">rec</span><span class="p">[</span><span class="mi">4</span><span class="p">]</span><span class="o">.</span><span class="n">strip</span><span class="p">(),</span>
+                    <span class="n">ligand_location</span> <span class="o">=</span> <span class="n">camel_to_snake</span><span class="p">(</span><span class="n">rec</span><span class="p">[</span><span class="mi">5</span><span class="p">]),</span>
+                    <span class="n">ligand_category</span> <span class="o">=</span> <span class="n">camel_to_snake</span><span class="p">(</span><span class="n">rec</span><span class="p">[</span><span class="mi">6</span><span class="p">]),</span>
+                    <span class="n">resources</span> <span class="o">=</span> <span class="n">sources</span><span class="p">,</span>
+                    <span class="n">references</span> <span class="o">=</span> <span class="n">references</span><span class="p">,</span>
+                <span class="p">)</span>
+            <span class="p">)</span>
+
+    <span class="k">return</span> <span class="n">result</span></div>
+
+
+
+<div class="viewcode-block" id="baccin2019_annotations">
+<a class="viewcode-back" href="../../../api/pypath.inputs.baccin2019.baccin2019_annotations.html#pypath.inputs.baccin2019.baccin2019_annotations">[docs]</a>
+<span class="k">def</span> <span class="nf">baccin2019_annotations</span><span class="p">(</span><span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">):</span>
+
+
+    <span class="n">Baccin2019Annotation</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">namedtuple</span><span class="p">(</span>
+        <span class="s1">&#39;Baccin2019Annotation&#39;</span><span class="p">,</span>
+        <span class="p">[</span>
+            <span class="s1">&#39;mainclass&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;subclass&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;location&#39;</span><span class="p">,</span>
+        <span class="p">]</span>
+    <span class="p">)</span>
+
+
+    <span class="n">ia_all</span> <span class="o">=</span> <span class="n">baccin2019_interactions</span><span class="p">(</span><span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">)</span>
+
+    <span class="n">result</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">defaultdict</span><span class="p">(</span><span class="nb">set</span><span class="p">)</span>
+
+    <span class="k">for</span> <span class="n">ia</span> <span class="ow">in</span> <span class="n">ia_all</span><span class="p">:</span>
+
+        <span class="n">result</span><span class="p">[</span><span class="n">ia</span><span class="o">.</span><span class="n">ligand</span><span class="p">]</span><span class="o">.</span><span class="n">add</span><span class="p">(</span>
+            <span class="n">Baccin2019Annotation</span><span class="p">(</span>
+                <span class="n">mainclass</span> <span class="o">=</span> <span class="s1">&#39;ligand&#39;</span><span class="p">,</span>
+                <span class="n">subclass</span> <span class="o">=</span> <span class="n">ia</span><span class="o">.</span><span class="n">ligand_category</span><span class="p">,</span>
+                <span class="n">location</span> <span class="o">=</span> <span class="n">ia</span><span class="o">.</span><span class="n">ligand_location</span><span class="p">,</span>
+            <span class="p">)</span>
+        <span class="p">)</span>
+
+        <span class="n">result</span><span class="p">[</span><span class="n">ia</span><span class="o">.</span><span class="n">receptor</span><span class="p">]</span><span class="o">.</span><span class="n">add</span><span class="p">(</span>
+            <span class="n">Baccin2019Annotation</span><span class="p">(</span>
+                <span class="n">mainclass</span> <span class="o">=</span> <span class="s1">&#39;receptor&#39;</span><span class="p">,</span>
+                <span class="n">subclass</span> <span class="o">=</span> <span class="p">(</span>
+                    <span class="s1">&#39;</span><span class="si">%s</span><span class="s1">_receptor&#39;</span> <span class="o">%</span> <span class="n">ia</span><span class="o">.</span><span class="n">ligand_category</span>
+                        <span class="k">if</span> <span class="n">ia</span><span class="o">.</span><span class="n">ligand_category</span> <span class="o">!=</span> <span class="s1">&#39;other&#39;</span> <span class="k">else</span>
+                    <span class="kc">None</span>
+                <span class="p">),</span>
+                <span class="n">location</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="p">)</span>
+        <span class="p">)</span>
+
+    <span class="k">return</span> <span class="nb">dict</span><span class="p">(</span><span class="n">result</span><span class="p">)</span></div>
+
+</pre></div>
+
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+  <h1>Source code for pypath.inputs.biogps</h1><div class="highlight"><pre>
+<span></span><span class="ch">#!/usr/bin/env python</span>
+<span class="c1"># -*- coding: utf-8 -*-</span>
+
+<span class="c1">#</span>
+<span class="c1">#  This file is part of the `pypath` python module</span>
+<span class="c1">#</span>
+<span class="c1">#  Copyright 2014-2023</span>
+<span class="c1">#  EMBL, EMBL-EBI, Uniklinik RWTH Aachen, Heidelberg University</span>
+<span class="c1">#</span>
+<span class="c1">#  Authors: see the file `README.rst`</span>
+<span class="c1">#  Contact: Dénes Türei (turei.denes@gmail.com)</span>
+<span class="c1">#</span>
+<span class="c1">#  Distributed under the GPLv3 License.</span>
+<span class="c1">#  See accompanying file LICENSE.txt or copy at</span>
+<span class="c1">#      https://www.gnu.org/licenses/gpl-3.0.html</span>
+<span class="c1">#</span>
+<span class="c1">#  Website: https://pypath.omnipathdb.org/</span>
+<span class="c1">#</span>
+
+<span class="kn">from</span> <span class="nn">future.utils</span> <span class="kn">import</span> <span class="n">iteritems</span>
+<span class="kn">from</span> <span class="nn">past.builtins</span> <span class="kn">import</span> <span class="n">xrange</span><span class="p">,</span> <span class="nb">range</span>
+
+<span class="kn">import</span> <span class="nn">re</span>
+<span class="kn">import</span> <span class="nn">collections</span>
+
+<span class="kn">import</span> <span class="nn">pandas</span> <span class="k">as</span> <span class="nn">pd</span>
+
+<span class="kn">import</span> <span class="nn">pypath.resources.urls</span> <span class="k">as</span> <span class="nn">urls</span>
+<span class="kn">import</span> <span class="nn">pypath.share.curl</span> <span class="k">as</span> <span class="nn">curl</span>
+<span class="kn">import</span> <span class="nn">pypath.share.common</span> <span class="k">as</span> <span class="nn">common</span>
+<span class="kn">import</span> <span class="nn">pypath.utils.taxonomy</span> <span class="k">as</span> <span class="nn">taxonomy</span>
+<span class="kn">import</span> <span class="nn">pypath.utils.mapping</span> <span class="k">as</span> <span class="nn">mapping</span>
+
+
+<span class="n">BiogpsDataset</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">namedtuple</span><span class="p">(</span>
+    <span class="s1">&#39;BiogpsDataset&#39;</span><span class="p">,</span>
+    <span class="p">(</span>
+        <span class="s1">&#39;organism&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;label&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;url&#39;</span><span class="p">,</span>
+    <span class="p">),</span>
+<span class="p">)</span>
+
+
+<div class="viewcode-block" id="biogps_datasets">
+<a class="viewcode-back" href="../../../api/pypath.inputs.biogps.biogps_datasets.html#pypath.inputs.biogps.biogps_datasets">[docs]</a>
+<span class="k">def</span> <span class="nf">biogps_datasets</span><span class="p">():</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    List the expression profile datasets available from BioGPS.</span>
+
+<span class="sd">    Returns</span>
+<span class="sd">        (list): Named tuples with the label, organism and URL of the datasets.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="n">biogps_urls</span> <span class="o">=</span> <span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;biogps&#39;</span><span class="p">]</span>
+    <span class="n">url</span> <span class="o">=</span> <span class="n">biogps_urls</span><span class="p">[</span><span class="s1">&#39;url&#39;</span><span class="p">]</span>
+    <span class="n">datasets</span> <span class="o">=</span> <span class="n">biogps_urls</span><span class="p">[</span><span class="s1">&#39;datasets&#39;</span><span class="p">]</span>
+
+
+    <span class="k">return</span> <span class="p">[</span>
+        <span class="n">BiogpsDataset</span><span class="p">(</span>
+            <span class="n">organism</span> <span class="o">=</span> <span class="n">label</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;_&#39;</span><span class="p">,</span> <span class="n">maxsplit</span> <span class="o">=</span> <span class="mi">1</span><span class="p">)[</span><span class="mi">0</span><span class="p">],</span>
+            <span class="n">label</span> <span class="o">=</span> <span class="n">label</span><span class="p">,</span>
+            <span class="n">url</span> <span class="o">=</span> <span class="n">url</span> <span class="o">%</span> <span class="n">fname</span><span class="p">,</span>
+        <span class="p">)</span>
+        <span class="k">for</span> <span class="n">label</span><span class="p">,</span> <span class="n">fname</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="n">datasets</span><span class="p">)</span>
+    <span class="p">]</span></div>
+
+
+
+<div class="viewcode-block" id="biogps_download">
+<a class="viewcode-back" href="../../../api/pypath.inputs.biogps.biogps_download.html#pypath.inputs.biogps.biogps_download">[docs]</a>
+<span class="k">def</span> <span class="nf">biogps_download</span><span class="p">(</span><span class="n">dataset</span><span class="p">):</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Retrieve one BioGPS expression profile dataset.</span>
+
+<span class="sd">    Args</span>
+<span class="sd">        dataset (str,BiogpsDataset): Either the label of a dataset or a</span>
+<span class="sd">            `BiogpsDataset` object. For a list of available datasets, see</span>
+<span class="sd">            `biogps_datasets`.</span>
+
+<span class="sd">    Returns</span>
+<span class="sd">        (pandas.DataFrame): A data frame of expression values, columns are</span>
+<span class="sd">            tissues, cell types or cell lines, rows are microarray probes</span>
+<span class="sd">            representing transcripts.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="n">biogps_urls</span> <span class="o">=</span> <span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;biogps&#39;</span><span class="p">]</span>
+    <span class="n">label</span> <span class="o">=</span> <span class="n">dataset</span><span class="o">.</span><span class="n">label</span> <span class="k">if</span> <span class="nb">hasattr</span><span class="p">(</span><span class="n">dataset</span><span class="p">,</span> <span class="s1">&#39;label&#39;</span><span class="p">)</span> <span class="k">else</span> <span class="n">dataset</span>
+    <span class="n">url</span> <span class="o">=</span> <span class="n">biogps_urls</span><span class="p">[</span><span class="s1">&#39;url&#39;</span><span class="p">]</span> <span class="o">%</span> <span class="n">biogps_urls</span><span class="p">[</span><span class="s1">&#39;datasets&#39;</span><span class="p">][</span><span class="n">label</span><span class="p">]</span>
+    <span class="n">c</span> <span class="o">=</span> <span class="n">curl</span><span class="o">.</span><span class="n">Curl</span><span class="p">(</span><span class="n">url</span><span class="p">,</span> <span class="n">silent</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span> <span class="n">large</span> <span class="o">=</span> <span class="kc">True</span><span class="p">)</span>
+
+    <span class="n">the_file</span> <span class="o">=</span> <span class="p">(</span>
+        <span class="n">common</span><span class="o">.</span><span class="n">first</span><span class="p">(</span><span class="n">c</span><span class="o">.</span><span class="n">result</span><span class="o">.</span><span class="n">values</span><span class="p">())</span>
+            <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">c</span><span class="o">.</span><span class="n">result</span><span class="p">,</span> <span class="nb">dict</span><span class="p">)</span> <span class="k">else</span>
+        <span class="n">c</span><span class="o">.</span><span class="n">result</span>
+    <span class="p">)</span>
+
+    <span class="n">fileobj</span> <span class="o">=</span> <span class="n">the_file</span> <span class="k">if</span> <span class="nb">hasattr</span><span class="p">(</span><span class="n">the_file</span><span class="p">,</span> <span class="s1">&#39;name&#39;</span><span class="p">)</span> <span class="k">else</span> <span class="n">c</span><span class="o">.</span><span class="n">fileobj</span>
+    <span class="n">sep</span> <span class="o">=</span> <span class="s1">&#39;,&#39;</span> <span class="k">if</span> <span class="n">fileobj</span><span class="o">.</span><span class="n">name</span><span class="o">.</span><span class="n">endswith</span><span class="p">(</span><span class="s1">&#39;csv&#39;</span><span class="p">)</span> <span class="k">else</span> <span class="s1">&#39;</span><span class="se">\t</span><span class="s1">&#39;</span>
+    <span class="n">header</span> <span class="o">=</span> <span class="nb">next</span><span class="p">(</span><span class="n">the_file</span><span class="p">)</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="n">sep</span><span class="p">)</span>
+    <span class="n">header</span> <span class="o">=</span> <span class="p">[</span>
+        <span class="n">re</span><span class="o">.</span><span class="n">sub</span><span class="p">(</span>
+            <span class="s1">&#39;\W+&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;_&#39;</span><span class="p">,</span>
+            <span class="n">re</span><span class="o">.</span><span class="n">sub</span><span class="p">(</span><span class="s1">&#39;^\d+&#39;</span><span class="p">,</span> <span class="s1">&#39;&#39;</span><span class="p">,</span> <span class="n">h</span><span class="p">)</span><span class="o">.</span><span class="n">strip</span><span class="p">(</span><span class="s1">&#39;&#39;</span><span class="p">)</span>
+        <span class="p">)</span><span class="o">.</span><span class="n">strip</span><span class="p">(</span><span class="s1">&#39;_&#39;</span><span class="p">)</span>
+        <span class="k">for</span> <span class="n">h</span> <span class="ow">in</span> <span class="n">header</span>
+    <span class="p">]</span>
+    <span class="n">header</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">=</span> <span class="s1">&#39;probe&#39;</span>
+
+    <span class="n">hdr_dup</span> <span class="o">=</span> <span class="p">{}</span>
+
+    <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="n">xrange</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">header</span><span class="p">)):</span>
+
+        <span class="n">field</span> <span class="o">=</span> <span class="n">header</span><span class="p">[</span><span class="n">i</span><span class="p">]</span>
+        <span class="n">header</span><span class="p">[</span><span class="n">i</span><span class="p">]</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="n">field</span>
+                <span class="k">if</span> <span class="n">field</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">hdr_dup</span> <span class="k">else</span>
+            <span class="s1">&#39;</span><span class="si">%s</span><span class="s1">_</span><span class="si">%u</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="p">(</span><span class="n">field</span><span class="p">,</span> <span class="n">hdr_dup</span><span class="p">[</span><span class="n">field</span><span class="p">])</span>
+        <span class="p">)</span>
+        <span class="n">hdr_dup</span><span class="p">[</span><span class="n">field</span><span class="p">]</span> <span class="o">=</span> <span class="n">hdr_dup</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="n">field</span><span class="p">,</span> <span class="mi">0</span><span class="p">)</span>
+        <span class="n">hdr_dup</span><span class="p">[</span><span class="n">field</span><span class="p">]</span> <span class="o">+=</span> <span class="mi">1</span>
+
+    <span class="n">content</span> <span class="o">=</span> <span class="p">[</span>
+        <span class="p">[</span>
+            <span class="n">value</span> <span class="k">if</span> <span class="n">j</span> <span class="o">==</span> <span class="mi">0</span> <span class="k">else</span> <span class="nb">float</span><span class="p">(</span><span class="n">value</span><span class="p">)</span>
+            <span class="k">for</span> <span class="n">j</span><span class="p">,</span> <span class="n">value</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">row</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="n">sep</span><span class="p">))</span>
+        <span class="p">]</span>
+        <span class="k">for</span> <span class="n">row</span> <span class="ow">in</span> <span class="n">the_file</span>
+    <span class="p">]</span>
+
+    <span class="n">df</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">(</span><span class="n">content</span><span class="p">,</span> <span class="n">columns</span> <span class="o">=</span> <span class="n">header</span><span class="p">)</span>
+
+    <span class="k">return</span> <span class="n">df</span></div>
+
+
+
+<div class="viewcode-block" id="biogps_download_all">
+<a class="viewcode-back" href="../../../api/pypath.inputs.biogps.biogps_download_all.html#pypath.inputs.biogps.biogps_download_all">[docs]</a>
+<span class="k">def</span> <span class="nf">biogps_download_all</span><span class="p">(</span><span class="n">organism</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span> <span class="n">exclude</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span> <span class="n">only</span> <span class="o">=</span> <span class="kc">None</span><span class="p">):</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Downloads all expression data from BioGPS.</span>
+
+<span class="sd">    Args</span>
+<span class="sd">        organism (str,int): Restrict the download to this organism. Human,</span>
+<span class="sd">            mouse and rat datasets are available.</span>
+<span class="sd">        exclude (str,set): One or more datasets to exclude. Should be</span>
+<span class="sd">            dataset labels as shown by `biogps_datasets`.</span>
+<span class="sd">        only (str,set): Restrict the download only to these datasets.</span>
+
+<span class="sd">    Returns</span>
+<span class="sd">        (dict): Dict of pandas data frames, keys are dataset labels, values</span>
+<span class="sd">            are data frames of expression values, columns are tissues, cell</span>
+<span class="sd">            types or cell lines, rows are microarray probes representing</span>
+<span class="sd">            transcripts.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="k">if</span> <span class="n">organism</span><span class="p">:</span>
+
+        <span class="n">organism</span> <span class="o">=</span> <span class="n">taxonomy</span><span class="o">.</span><span class="n">ensure_common_name</span><span class="p">(</span><span class="n">organism</span><span class="p">)</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span>
+
+    <span class="n">exclude</span> <span class="o">=</span> <span class="n">common</span><span class="o">.</span><span class="n">to_set</span><span class="p">(</span><span class="n">exclude</span><span class="p">)</span>
+    <span class="n">only</span> <span class="o">=</span> <span class="n">common</span><span class="o">.</span><span class="n">to_set</span><span class="p">(</span><span class="n">only</span><span class="p">)</span>
+    <span class="n">datasets</span> <span class="o">=</span> <span class="n">biogps_datasets</span><span class="p">()</span>
+
+    <span class="n">result</span> <span class="o">=</span> <span class="p">{}</span>
+
+    <span class="k">for</span> <span class="n">dataset</span> <span class="ow">in</span> <span class="n">datasets</span><span class="p">:</span>
+
+        <span class="k">if</span> <span class="p">(</span>
+            <span class="p">(</span>
+                <span class="ow">not</span> <span class="n">organism</span> <span class="ow">or</span>
+                <span class="n">dataset</span><span class="o">.</span><span class="n">organism</span> <span class="o">==</span> <span class="n">organism</span>
+            <span class="p">)</span> <span class="ow">and</span> <span class="p">(</span>
+                <span class="ow">not</span> <span class="n">only</span> <span class="ow">or</span>
+                <span class="n">dataset</span><span class="o">.</span><span class="n">label</span> <span class="ow">in</span> <span class="n">only</span>
+            <span class="p">)</span> <span class="ow">and</span>
+            <span class="n">dataset</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">exclude</span>
+        <span class="p">):</span>
+
+            <span class="n">result</span><span class="p">[</span><span class="n">dataset</span><span class="o">.</span><span class="n">label</span><span class="p">]</span> <span class="o">=</span> <span class="n">biogps_download</span><span class="p">(</span><span class="n">dataset</span><span class="p">)</span>
+
+    <span class="k">return</span> <span class="n">result</span></div>
+
+
+
+<div class="viewcode-block" id="biogps_annotations">
+<a class="viewcode-back" href="../../../api/pypath.inputs.biogps.biogps_annotations.html#pypath.inputs.biogps.biogps_annotations">[docs]</a>
+<span class="k">def</span> <span class="nf">biogps_annotations</span><span class="p">(</span><span class="n">organism</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">,</span> <span class="n">exclude</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span> <span class="n">only</span> <span class="o">=</span> <span class="kc">None</span><span class="p">):</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Expression data from BioGPS compiled in the annotation format commonly</span>
+<span class="sd">    used in this module.</span>
+
+<span class="sd">    Args</span>
+<span class="sd">        organism (int,str): Name or ID of the organism. This function</span>
+<span class="sd">            is able to process data for one organism at once.</span>
+<span class="sd">        exclude (str,set): One or more datasets to exclude. Should be</span>
+<span class="sd">            dataset labels as shown by `biogps_datasets`.</span>
+<span class="sd">        only (str,set): Restrict the download only to these datasets.</span>
+
+<span class="sd">    Returns</span>
+<span class="sd">        (dict): Dict of annotations, keys are UniProt IDs, values are</span>
+<span class="sd">            sets of named tuples of annotations.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="n">BiogpsAnnotation</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">namedtuple</span><span class="p">(</span>
+        <span class="s1">&#39;BiogpsAnnotation&#39;</span><span class="p">,</span>
+        <span class="p">(</span>
+            <span class="s1">&#39;dataset&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;sample&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;probe&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;expression&#39;</span><span class="p">,</span>
+        <span class="p">),</span>
+    <span class="p">)</span>
+
+    <span class="n">data</span> <span class="o">=</span> <span class="n">biogps_download_all</span><span class="p">(</span>
+        <span class="n">organism</span> <span class="o">=</span> <span class="n">organism</span><span class="p">,</span>
+        <span class="n">exclude</span> <span class="o">=</span> <span class="n">exclude</span><span class="p">,</span>
+        <span class="n">only</span> <span class="o">=</span> <span class="n">only</span><span class="p">,</span>
+    <span class="p">)</span>
+
+    <span class="n">result</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">defaultdict</span><span class="p">(</span><span class="nb">set</span><span class="p">)</span>
+
+    <span class="k">for</span> <span class="n">label</span><span class="p">,</span> <span class="n">df</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="n">data</span><span class="p">):</span>
+
+        <span class="k">for</span> <span class="n">row</span> <span class="ow">in</span> <span class="n">df</span><span class="o">.</span><span class="n">itertuples</span><span class="p">(</span><span class="n">index</span> <span class="o">=</span> <span class="kc">False</span><span class="p">):</span>
+
+            <span class="n">uniprots</span> <span class="o">=</span> <span class="n">mapping</span><span class="o">.</span><span class="n">map_name</span><span class="p">(</span>
+                <span class="n">row</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span>
+                <span class="s1">&#39;affy&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;uniprot&#39;</span><span class="p">,</span>
+                <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">organism</span><span class="p">,</span>
+            <span class="p">)</span>
+
+            <span class="k">for</span> <span class="n">uniprot</span> <span class="ow">in</span> <span class="n">uniprots</span><span class="p">:</span>
+
+                <span class="n">result</span><span class="p">[</span><span class="n">uniprot</span><span class="p">]</span><span class="o">.</span><span class="n">update</span><span class="p">(</span>
+                    <span class="p">{</span>
+                        <span class="n">BiogpsAnnotation</span><span class="p">(</span>
+                            <span class="n">dataset</span> <span class="o">=</span> <span class="n">label</span><span class="p">,</span>
+                            <span class="n">sample</span> <span class="o">=</span> <span class="n">sample</span><span class="p">,</span>
+                            <span class="n">probe</span> <span class="o">=</span> <span class="n">row</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span>
+                            <span class="n">expression</span> <span class="o">=</span> <span class="n">expr</span><span class="p">,</span>
+                        <span class="p">)</span>
+                        <span class="k">for</span> <span class="n">sample</span><span class="p">,</span> <span class="n">expr</span> <span class="ow">in</span> <span class="nb">zip</span><span class="p">(</span><span class="n">row</span><span class="o">.</span><span class="n">_fields</span><span class="p">[</span><span class="mi">1</span><span class="p">:],</span> <span class="n">row</span><span class="p">[</span><span class="mi">1</span><span class="p">:])</span>
+                    <span class="p">}</span>
+                <span class="p">)</span>
+
+    <span class="k">return</span> <span class="n">result</span></div>
+
+</pre></div>
+
+                </article>
+              
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diff --git a/_modules/pypath/inputs/cancerdrugsdb.html b/_modules/pypath/inputs/cancerdrugsdb.html
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+        
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+  <h1>Source code for pypath.inputs.cancerdrugsdb</h1><div class="highlight"><pre>
+<span></span><span class="ch">#!/usr/bin/env python</span>
+<span class="c1"># -*- coding: utf-8 -*-</span>
+
+<span class="c1">#</span>
+<span class="c1">#  This file is part of the `pypath` python module</span>
+<span class="c1">#</span>
+<span class="c1">#  Copyright 2014-2023</span>
+<span class="c1">#  EMBL, EMBL-EBI, Uniklinik RWTH Aachen, Heidelberg University</span>
+<span class="c1">#</span>
+<span class="c1">#  Authors: see the file `README.rst`</span>
+<span class="c1">#  Contact: Dénes Türei (turei.denes@gmail.com)</span>
+<span class="c1">#</span>
+<span class="c1">#  Distributed under the GPLv3 License.</span>
+<span class="c1">#  See accompanying file LICENSE.txt or copy at</span>
+<span class="c1">#      https://www.gnu.org/licenses/gpl-3.0.html</span>
+<span class="c1">#</span>
+<span class="c1">#  Website: https://pypath.omnipathdb.org/</span>
+<span class="c1">#</span>
+
+<span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">Web scraper for the CancerDrugs_DB database.</span>
+<span class="sd">&quot;&quot;&quot;</span>
+
+<span class="kn">import</span> <span class="nn">csv</span>
+<span class="kn">import</span> <span class="nn">collections</span>
+<span class="kn">import</span> <span class="nn">itertools</span>
+<span class="kn">import</span> <span class="nn">re</span>
+
+<span class="kn">import</span> <span class="nn">pypath.share.curl</span> <span class="k">as</span> <span class="nn">curl</span>
+<span class="kn">import</span> <span class="nn">pypath.share.common</span> <span class="k">as</span> <span class="nn">common</span>
+<span class="kn">import</span> <span class="nn">pypath.resources.urls</span> <span class="k">as</span> <span class="nn">urls</span>
+<span class="kn">import</span> <span class="nn">pypath.utils.mapping</span> <span class="k">as</span> <span class="nn">mapping</span>
+<span class="kn">import</span> <span class="nn">pypath.share.session</span> <span class="k">as</span> <span class="nn">session</span>
+
+<span class="n">_logger</span> <span class="o">=</span> <span class="n">session</span><span class="o">.</span><span class="n">Logger</span><span class="p">(</span><span class="n">name</span> <span class="o">=</span> <span class="s1">&#39;cancerdrugsdb_input&#39;</span><span class="p">)</span>
+<span class="n">_log</span> <span class="o">=</span> <span class="n">_logger</span><span class="o">.</span><span class="n">_log</span>
+
+
+<div class="viewcode-block" id="cancerdrugsdb_download">
+<a class="viewcode-back" href="../../../api/pypath.inputs.cancerdrugsdb.cancerdrugsdb_download.html#pypath.inputs.cancerdrugsdb.cancerdrugsdb_download">[docs]</a>
+<span class="k">def</span> <span class="nf">cancerdrugsdb_download</span><span class="p">():</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Downloads a curated set of interactions of cancer drugs licensed</span>
+<span class="sd">    in most parts of the world with gene targets (where available).</span>
+<span class="sd">    From https://www.anticancerfund.org/en/cancerdrugs-db.</span>
+<span class="sd">    This function downloads a single dataset.</span>
+
+<span class="sd">    Args</span>
+<span class="sd">        None.</span>
+
+<span class="sd">    Returns</span>
+<span class="sd">        A list of dicts, each is a record as it provided by the database.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="n">url</span> <span class="o">=</span> <span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;cancerdrugs_db&#39;</span><span class="p">][</span><span class="s1">&#39;url&#39;</span><span class="p">]</span>
+
+    <span class="n">c</span> <span class="o">=</span> <span class="n">curl</span><span class="o">.</span><span class="n">Curl</span><span class="p">(</span><span class="n">url</span><span class="p">,</span> <span class="n">large</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span> <span class="n">silent</span> <span class="o">=</span> <span class="kc">False</span><span class="p">)</span>
+
+    <span class="k">return</span> <span class="nb">list</span><span class="p">(</span><span class="n">csv</span><span class="o">.</span><span class="n">DictReader</span><span class="p">(</span><span class="n">c</span><span class="o">.</span><span class="n">result</span><span class="p">,</span> <span class="n">delimiter</span> <span class="o">=</span> <span class="s1">&#39;</span><span class="se">\t</span><span class="s1">&#39;</span><span class="p">))</span></div>
+
+
+
+<div class="viewcode-block" id="cancerdrugsdb_interactions">
+<a class="viewcode-back" href="../../../api/pypath.inputs.cancerdrugsdb.cancerdrugsdb_interactions.html#pypath.inputs.cancerdrugsdb.cancerdrugsdb_interactions">[docs]</a>
+<span class="k">def</span> <span class="nf">cancerdrugsdb_interactions</span><span class="p">():</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Returns drug-gene interactions from Cancer Drugs Database</span>
+<span class="sd">    (https://www.anticancerfund.org/en/cancerdrugs-db).</span>
+
+<span class="sd">    Args</span>
+<span class="sd">        None.</span>
+
+<span class="sd">    Returns</span>
+<span class="sd">        List of named tuples, each describing a drug-gene interaction.</span>
+<span class="sd">        Identifiers of type PubChem and UniProt.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="c1"># note: drug-target interactions are from GDIdb. if they&#39;re in OnmiPath</span>
+    <span class="c1"># already, do we skip the interactions altogether, or is it better to</span>
+    <span class="c1"># keep them here for consistency? the dataset is very small anyways.</span>
+    <span class="c1"># if we keep them, do we test for consistency between the interactions?</span>
+
+    <span class="n">reid</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">compile</span><span class="p">(</span><span class="sa">r</span><span class="s1">&#39;&gt;(\w+)&lt;&#39;</span><span class="p">)</span>
+
+    <span class="k">def</span> <span class="nf">strip_id</span><span class="p">(</span><span class="n">field</span><span class="p">):</span>
+
+        <span class="n">match</span> <span class="o">=</span> <span class="n">reid</span><span class="o">.</span><span class="n">search</span><span class="p">(</span><span class="n">field</span><span class="p">)</span>
+
+        <span class="k">return</span> <span class="n">match</span><span class="o">.</span><span class="n">group</span><span class="p">(</span><span class="mi">1</span><span class="p">)</span> <span class="k">if</span> <span class="n">match</span> <span class="k">else</span> <span class="kc">None</span>
+
+
+    <span class="k">def</span> <span class="nf">yes_no</span><span class="p">(</span><span class="n">field</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="n">field</span> <span class="o">==</span> <span class="s1">&#39;Y&#39;</span>
+
+
+    <span class="n">CancerDrugsInteraction</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">namedtuple</span><span class="p">(</span>
+        <span class="s1">&#39;CancerdrugsdbInteraction&#39;</span><span class="p">,</span>
+        <span class="p">(</span>
+            <span class="s1">&#39;drug_pubchem&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;drug_chembl&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;drug_drugbank&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;drug_label&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;target_uniprot&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;ema_approved&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;fda_approved&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;european_national_approved&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;who_approved&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;generic&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;approval_year&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;indications&#39;</span><span class="p">,</span>
+        <span class="p">),</span>
+    <span class="p">)</span>
+
+    <span class="n">result</span> <span class="o">=</span> <span class="p">[]</span>
+    <span class="n">unmapped_drug</span> <span class="o">=</span> <span class="p">[]</span>
+    <span class="n">no_targets</span> <span class="o">=</span> <span class="p">[]</span>
+
+    <span class="n">data</span> <span class="o">=</span> <span class="n">cancerdrugsdb_download</span><span class="p">()</span>
+
+    <span class="k">for</span> <span class="n">rec</span> <span class="ow">in</span> <span class="n">data</span><span class="p">:</span>
+
+        <span class="n">chembl</span> <span class="o">=</span> <span class="n">strip_id</span><span class="p">(</span><span class="n">rec</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">&#39;ChEMBL&#39;</span><span class="p">))</span>
+        <span class="n">drugbank</span> <span class="o">=</span> <span class="n">strip_id</span><span class="p">(</span><span class="n">rec</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">&#39;DrugBank ID&#39;</span><span class="p">))</span>
+
+        <span class="k">if</span> <span class="n">chembl</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
+
+            <span class="n">unmapped_drug</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">rec</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">&#39;Product&#39;</span><span class="p">))</span>
+            <span class="k">continue</span>
+
+        <span class="n">pubchems</span> <span class="o">=</span> <span class="n">mapping</span><span class="o">.</span><span class="n">map_name</span><span class="p">(</span><span class="n">chembl</span><span class="p">,</span> <span class="s1">&#39;chembl&#39;</span><span class="p">,</span> <span class="s1">&#39;pubchem&#39;</span><span class="p">)</span>
+
+        <span class="n">targets</span> <span class="o">=</span> <span class="n">rec</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">&#39;Targets&#39;</span><span class="p">)</span>
+
+        <span class="k">if</span> <span class="ow">not</span> <span class="n">targets</span><span class="p">:</span>
+
+            <span class="n">no_targets</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">rec</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">&#39;Product&#39;</span><span class="p">))</span>
+            <span class="k">continue</span>
+
+        <span class="n">target_uniprots</span> <span class="o">=</span> <span class="n">mapping</span><span class="o">.</span><span class="n">map_names</span><span class="p">(</span>
+            <span class="p">(</span><span class="n">tar</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span> <span class="k">for</span> <span class="n">tar</span> <span class="ow">in</span> <span class="n">targets</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;;&#39;</span><span class="p">)),</span>
+            <span class="s1">&#39;genesymbol&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;uniprot&#39;</span><span class="p">,</span>
+        <span class="p">)</span>
+
+        <span class="k">for</span> <span class="n">pubchem</span><span class="p">,</span> <span class="n">uniprot</span> <span class="ow">in</span> <span class="n">itertools</span><span class="o">.</span><span class="n">product</span><span class="p">(</span><span class="n">pubchems</span><span class="p">,</span> <span class="n">target_uniprots</span><span class="p">):</span>
+
+            <span class="n">result</span><span class="o">.</span><span class="n">append</span><span class="p">(</span>
+                <span class="n">CancerDrugsInteraction</span><span class="p">(</span>
+                    <span class="n">drug_pubchem</span> <span class="o">=</span> <span class="n">pubchem</span><span class="p">,</span>
+                    <span class="n">drug_chembl</span> <span class="o">=</span> <span class="n">chembl</span><span class="p">,</span>
+                    <span class="n">drug_drugbank</span> <span class="o">=</span> <span class="n">drugbank</span><span class="p">,</span>
+                    <span class="n">drug_label</span> <span class="o">=</span> <span class="n">rec</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">&#39;Product&#39;</span><span class="p">),</span>
+                    <span class="n">target_uniprot</span> <span class="o">=</span> <span class="n">uniprot</span><span class="p">,</span>
+                    <span class="n">ema_approved</span> <span class="o">=</span> <span class="n">yes_no</span><span class="p">(</span><span class="n">rec</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">&#39;EMA&#39;</span><span class="p">)),</span>
+                    <span class="n">fda_approved</span> <span class="o">=</span> <span class="n">yes_no</span><span class="p">(</span><span class="n">rec</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">&#39;FDA&#39;</span><span class="p">)),</span>
+                    <span class="n">european_national_approved</span> <span class="o">=</span> <span class="n">yes_no</span><span class="p">(</span><span class="n">rec</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">&#39;EN&#39;</span><span class="p">)),</span>
+                    <span class="n">who_approved</span> <span class="o">=</span> <span class="n">yes_no</span><span class="p">(</span><span class="n">rec</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">&#39;WHO&#39;</span><span class="p">)),</span>
+                    <span class="n">generic</span> <span class="o">=</span> <span class="n">yes_no</span><span class="p">(</span><span class="n">rec</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">&#39;Generic&#39;</span><span class="p">)),</span>
+                    <span class="n">approval_year</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">rec</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">&#39;Year&#39;</span><span class="p">))</span> <span class="k">if</span> <span class="n">rec</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">&#39;Year&#39;</span><span class="p">)</span> <span class="k">else</span> <span class="kc">None</span><span class="p">,</span>
+                    <span class="n">indications</span> <span class="o">=</span> <span class="nb">tuple</span><span class="p">(</span>
+                        <span class="n">i</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span>
+                        <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="n">rec</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">&#39;Indications&#39;</span><span class="p">)</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;;&#39;</span><span class="p">)</span>
+                    <span class="p">),</span>
+                <span class="p">)</span>
+            <span class="p">)</span>
+
+
+    <span class="n">_log</span><span class="p">(</span>
+        <span class="s1">&#39;Could not find CHEMBL IDs for </span><span class="si">%u</span><span class="s1"> &#39;</span>
+        <span class="s1">&#39;CancerDrugs_DB Products.&#39;</span> <span class="o">%</span> <span class="nb">len</span><span class="p">(</span><span class="n">unmapped_drug</span><span class="p">)</span>
+    <span class="p">)</span>
+
+    <span class="n">_log</span><span class="p">(</span>
+        <span class="s1">&#39;</span><span class="si">%u</span><span class="s1"> CancerDrugs_DB Products had no targets.&#39;</span>
+        <span class="o">%</span> <span class="nb">len</span><span class="p">(</span><span class="n">no_targets</span><span class="p">)</span>
+    <span class="p">)</span>
+
+    <span class="k">return</span> <span class="n">result</span></div>
+
+
+
+<div class="viewcode-block" id="cancerdrugsdb_annotations">
+<a class="viewcode-back" href="../../../api/pypath.inputs.cancerdrugsdb.cancerdrugsdb_annotations.html#pypath.inputs.cancerdrugsdb.cancerdrugsdb_annotations">[docs]</a>
+<span class="k">def</span> <span class="nf">cancerdrugsdb_annotations</span><span class="p">():</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Returns drug annotations from CancerDrugs_DB.</span>
+
+<span class="sd">    Args</span>
+<span class="sd">        None.</span>
+
+<span class="sd">    Returns</span>
+<span class="sd">        (dict): Keys are PubChem IDs, values are sets of annotations.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="n">record</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">namedtuple</span><span class="p">(</span>
+        <span class="s1">&#39;CancerdrugsdbAnnotation&#39;</span><span class="p">,</span>
+        <span class="p">(</span>
+            <span class="s1">&#39;drug_label&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;ema_approved&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;fda_approved&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;european_national_approved&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;who_approved&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;generic&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;approval_year&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;indications&#39;</span><span class="p">,</span>
+        <span class="p">),</span>
+    <span class="p">)</span>
+
+    <span class="n">result</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">defaultdict</span><span class="p">(</span><span class="nb">set</span><span class="p">)</span>
+    <span class="n">data</span> <span class="o">=</span> <span class="n">cancerdrugsdb_interactions</span><span class="p">()</span>
+
+    <span class="k">for</span> <span class="n">rec</span> <span class="ow">in</span> <span class="n">data</span><span class="p">:</span>
+
+        <span class="n">result</span><span class="p">[</span><span class="n">rec</span><span class="o">.</span><span class="n">drug_pubchem</span><span class="p">]</span><span class="o">.</span><span class="n">add</span><span class="p">(</span>
+            <span class="n">record</span><span class="p">(</span>
+                <span class="o">**</span><span class="nb">dict</span><span class="p">(</span>
+                    <span class="n">i</span>
+                    <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="n">rec</span><span class="o">.</span><span class="n">_asdict</span><span class="p">()</span><span class="o">.</span><span class="n">items</span><span class="p">()</span>
+                    <span class="k">if</span> <span class="n">i</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="ow">in</span> <span class="n">record</span><span class="o">.</span><span class="n">_fields</span>
+                <span class="p">)</span>
+            <span class="p">)</span>
+        <span class="p">)</span>
+
+    <span class="k">return</span> <span class="nb">dict</span><span class="p">(</span><span class="n">result</span><span class="p">)</span></div>
+
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+  <h1>Source code for pypath.inputs.cancersea</h1><div class="highlight"><pre>
+<span></span><span class="ch">#!/usr/bin/env python</span>
+<span class="c1"># -*- coding: utf-8 -*-</span>
+
+<span class="c1">#</span>
+<span class="c1">#  This file is part of the `pypath` python module</span>
+<span class="c1">#</span>
+<span class="c1">#  Copyright 2014-2023</span>
+<span class="c1">#  EMBL, EMBL-EBI, Uniklinik RWTH Aachen, Heidelberg University</span>
+<span class="c1">#</span>
+<span class="c1">#  Authors: see the file `README.rst`</span>
+<span class="c1">#  Contact: Dénes Türei (turei.denes@gmail.com)</span>
+<span class="c1">#</span>
+<span class="c1">#  Distributed under the GPLv3 License.</span>
+<span class="c1">#  See accompanying file LICENSE.txt or copy at</span>
+<span class="c1">#      https://www.gnu.org/licenses/gpl-3.0.html</span>
+<span class="c1">#</span>
+<span class="c1">#  Website: https://pypath.omnipathdb.org/</span>
+<span class="c1">#</span>
+
+<span class="kn">import</span> <span class="nn">os</span>
+<span class="kn">import</span> <span class="nn">collections</span>
+
+<span class="kn">import</span> <span class="nn">bs4</span>
+
+<span class="kn">import</span> <span class="nn">pypath.share.curl</span> <span class="k">as</span> <span class="nn">curl</span>
+<span class="kn">import</span> <span class="nn">pypath.resources.urls</span> <span class="k">as</span> <span class="nn">urls</span>
+<span class="kn">import</span> <span class="nn">pypath.utils.mapping</span> <span class="k">as</span> <span class="nn">mapping</span>
+
+
+<div class="viewcode-block" id="cancersea_annotations">
+<a class="viewcode-back" href="../../../api/pypath.inputs.cancersea.cancersea_annotations.html#pypath.inputs.cancersea.cancersea_annotations">[docs]</a>
+<span class="k">def</span> <span class="nf">cancersea_annotations</span><span class="p">():</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Retrieves genes annotated with cancer funcitonal states from the</span>
+<span class="sd">    CancerSEA database.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="n">CancerseaAnnotation</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">namedtuple</span><span class="p">(</span>
+        <span class="s1">&#39;CancerseaAnnotation&#39;</span><span class="p">,</span>
+        <span class="p">[</span>
+            <span class="s1">&#39;state&#39;</span><span class="p">,</span>
+        <span class="p">],</span>
+    <span class="p">)</span>
+
+    <span class="n">annotations</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">defaultdict</span><span class="p">(</span><span class="nb">set</span><span class="p">)</span>
+
+    <span class="n">url</span> <span class="o">=</span> <span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;cancersea&#39;</span><span class="p">][</span><span class="s1">&#39;rescued&#39;</span><span class="p">]</span>
+    <span class="n">c</span> <span class="o">=</span> <span class="n">curl</span><span class="o">.</span><span class="n">Curl</span><span class="p">(</span><span class="n">url</span><span class="p">,</span> <span class="n">silent</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span> <span class="n">large</span> <span class="o">=</span> <span class="kc">False</span><span class="p">)</span>
+    <span class="n">soup</span> <span class="o">=</span> <span class="n">bs4</span><span class="o">.</span><span class="n">BeautifulSoup</span><span class="p">(</span><span class="n">c</span><span class="o">.</span><span class="n">result</span><span class="p">,</span> <span class="s1">&#39;html.parser&#39;</span><span class="p">)</span>
+
+    <span class="k">for</span> <span class="n">row</span> <span class="ow">in</span> <span class="n">soup</span><span class="o">.</span><span class="n">find_all</span><span class="p">(</span><span class="s1">&#39;tbody&#39;</span><span class="p">)[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">find_all</span><span class="p">(</span><span class="s1">&#39;tr&#39;</span><span class="p">):</span>
+
+        <span class="n">state</span> <span class="o">=</span> <span class="n">row</span><span class="o">.</span><span class="n">find_all</span><span class="p">(</span><span class="s1">&#39;td&#39;</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">text</span>
+        <span class="n">url_end</span> <span class="o">=</span> <span class="n">row</span><span class="o">.</span><span class="n">find_all</span><span class="p">(</span><span class="s1">&#39;td&#39;</span><span class="p">)[</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">find</span><span class="p">(</span><span class="s1">&#39;a&#39;</span><span class="p">)</span><span class="o">.</span><span class="n">attrs</span><span class="p">[</span><span class="s1">&#39;href&#39;</span><span class="p">]</span>
+        <span class="n">url_end</span> <span class="o">=</span> <span class="n">url_end</span><span class="o">.</span><span class="n">rsplit</span><span class="p">(</span><span class="s1">&#39;/&#39;</span><span class="p">,</span> <span class="n">maxsplit</span> <span class="o">=</span> <span class="mi">1</span><span class="p">)[</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span>
+        <span class="n">data_url</span> <span class="o">=</span> <span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;cancersea&#39;</span><span class="p">][</span><span class="s1">&#39;rescued_data&#39;</span><span class="p">]</span> <span class="o">%</span> <span class="n">url_end</span>
+        <span class="n">c</span> <span class="o">=</span> <span class="n">curl</span><span class="o">.</span><span class="n">Curl</span><span class="p">(</span><span class="n">data_url</span><span class="p">,</span> <span class="n">silent</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span> <span class="n">large</span> <span class="o">=</span> <span class="kc">True</span><span class="p">)</span>
+
+        <span class="n">_</span> <span class="o">=</span> <span class="nb">next</span><span class="p">(</span><span class="n">c</span><span class="o">.</span><span class="n">result</span><span class="p">)</span>
+
+        <span class="k">for</span> <span class="n">line</span> <span class="ow">in</span> <span class="n">c</span><span class="o">.</span><span class="n">result</span><span class="p">:</span>
+
+            <span class="n">line</span> <span class="o">=</span> <span class="n">line</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\t</span><span class="s1">&#39;</span><span class="p">)</span>
+
+            <span class="n">uniprots</span> <span class="o">=</span> <span class="n">mapping</span><span class="o">.</span><span class="n">map_name</span><span class="p">(</span><span class="n">line</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span> <span class="s1">&#39;genesymbol&#39;</span><span class="p">,</span> <span class="s1">&#39;uniprot&#39;</span><span class="p">)</span>
+
+            <span class="k">for</span> <span class="n">uniprot</span> <span class="ow">in</span> <span class="n">uniprots</span><span class="p">:</span>
+
+                <span class="n">annotations</span><span class="p">[</span><span class="n">uniprot</span><span class="p">]</span><span class="o">.</span><span class="n">add</span><span class="p">(</span>
+                    <span class="n">CancerseaAnnotation</span><span class="p">(</span><span class="n">state</span> <span class="o">=</span> <span class="n">state</span><span class="p">)</span>
+                <span class="p">)</span>
+
+    <span class="k">return</span> <span class="nb">dict</span><span class="p">(</span><span class="n">annotations</span><span class="p">)</span></div>
+
+</pre></div>
+
+                </article>
+              
+              
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+            
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+        
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+  <script src="../../../_static/scripts/bootstrap.js?digest=8d27b9dea8ad943066ae"></script>
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+    
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+</p></div>
+      
+    </div>
+  
+</div>
+
+  </footer>
+  </body>
+</html>
\ No newline at end of file
diff --git a/_modules/pypath/inputs/cellcall.html b/_modules/pypath/inputs/cellcall.html
new file mode 100644
index 000000000..fa898055a
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+                  
+  <h1>Source code for pypath.inputs.cellcall</h1><div class="highlight"><pre>
+<span></span><span class="ch">#!/usr/bin/env python</span>
+<span class="c1"># -*- coding: utf-8 -*-</span>
+
+<span class="c1">#</span>
+<span class="c1">#  This file is part of the `pypath` python module</span>
+<span class="c1">#</span>
+<span class="c1">#  Copyright 2014-2023</span>
+<span class="c1">#  EMBL, EMBL-EBI, Uniklinik RWTH Aachen, Heidelberg University</span>
+<span class="c1">#</span>
+<span class="c1">#  Authors: see the file `README.rst`</span>
+<span class="c1">#  Contact: Dénes Türei (turei.denes@gmail.com)</span>
+<span class="c1">#</span>
+<span class="c1">#  Distributed under the GPLv3 License.</span>
+<span class="c1">#  See accompanying file LICENSE.txt or copy at</span>
+<span class="c1">#      https://www.gnu.org/licenses/gpl-3.0.html</span>
+<span class="c1">#</span>
+<span class="c1">#  Website: https://pypath.omnipathdb.org/</span>
+<span class="c1">#</span>
+
+<span class="kn">import</span> <span class="nn">csv</span>
+<span class="kn">import</span> <span class="nn">itertools</span>
+<span class="kn">import</span> <span class="nn">collections</span>
+
+<span class="kn">import</span> <span class="nn">pypath.resources.urls</span> <span class="k">as</span> <span class="nn">urls</span>
+<span class="kn">import</span> <span class="nn">pypath.share.curl</span> <span class="k">as</span> <span class="nn">curl</span>
+<span class="kn">import</span> <span class="nn">pypath.utils.mapping</span> <span class="k">as</span> <span class="nn">mapping</span>
+<span class="kn">import</span> <span class="nn">pypath.utils.taxonomy</span> <span class="k">as</span> <span class="nn">taxonomy</span>
+<span class="kn">import</span> <span class="nn">pypath.share.session</span> <span class="k">as</span> <span class="nn">session</span>
+
+<span class="n">_logger</span> <span class="o">=</span> <span class="n">session</span><span class="o">.</span><span class="n">Logger</span><span class="p">(</span><span class="n">name</span> <span class="o">=</span> <span class="s1">&#39;cellcall_input&#39;</span><span class="p">)</span>
+<span class="n">_log</span> <span class="o">=</span> <span class="n">_logger</span><span class="o">.</span><span class="n">_log</span>
+
+
+<div class="viewcode-block" id="cellcall_download">
+<a class="viewcode-back" href="../../../api/pypath.inputs.cellcall.cellcall_download.html#pypath.inputs.cellcall.cellcall_download">[docs]</a>
+<span class="k">def</span> <span class="nf">cellcall_download</span><span class="p">(</span><span class="n">extended</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span> <span class="n">mouse</span> <span class="o">=</span> <span class="kc">False</span><span class="p">):</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Downloads a ligand-receptor-TF pathway dataset from CellCall</span>
+<span class="sd">    (https://github.com/ShellyCoder/cellcall). This function downloads a</span>
+<span class="sd">    single dataset, to download multiple datasets, see</span>
+<span class="sd">    ``cellcall_download_all``. The pathway identifiers refer to KEGG</span>
+<span class="sd">    pathways.</span>
+
+<span class="sd">    Args</span>
+<span class="sd">        extended (bool): CellCall has core and extended datasets, if this</span>
+<span class="sd">            argument is True, the extended dataset will be retrieved.</span>
+<span class="sd">        mouse (bool): CellCall has human and homology inferred mouse</span>
+<span class="sd">            datasets. If this argument is True, the homology inferred</span>
+<span class="sd">            dataset will be retrieved with mouse identifiers.</span>
+
+<span class="sd">    Returns</span>
+<span class="sd">        A list of dicts, each is a record as it provided by the CellCall</span>
+<span class="sd">        database.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="n">dataset</span> <span class="o">=</span> <span class="s1">&#39;</span><span class="si">%s%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="p">(</span>
+        <span class="s1">&#39;_homology&#39;</span> <span class="k">if</span> <span class="n">mouse</span> <span class="k">else</span> <span class="s1">&#39;&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;_extended&#39;</span> <span class="k">if</span> <span class="n">extended</span> <span class="k">else</span> <span class="s1">&#39;&#39;</span><span class="p">,</span>
+    <span class="p">)</span>
+
+    <span class="n">url</span> <span class="o">=</span> <span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;cellcall&#39;</span><span class="p">][</span><span class="s1">&#39;url&#39;</span><span class="p">]</span> <span class="o">%</span> <span class="n">dataset</span>
+    <span class="n">c</span> <span class="o">=</span> <span class="n">curl</span><span class="o">.</span><span class="n">Curl</span><span class="p">(</span><span class="n">url</span><span class="p">,</span> <span class="n">large</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span> <span class="n">silent</span> <span class="o">=</span> <span class="kc">False</span><span class="p">)</span>
+
+    <span class="k">return</span> <span class="nb">list</span><span class="p">(</span><span class="n">csv</span><span class="o">.</span><span class="n">DictReader</span><span class="p">(</span><span class="n">c</span><span class="o">.</span><span class="n">result</span><span class="p">,</span> <span class="n">delimiter</span> <span class="o">=</span> <span class="s1">&#39;</span><span class="se">\t</span><span class="s1">&#39;</span><span class="p">))</span></div>
+
+
+
+<div class="viewcode-block" id="cellcall_download_all">
+<a class="viewcode-back" href="../../../api/pypath.inputs.cellcall.cellcall_download_all.html#pypath.inputs.cellcall.cellcall_download_all">[docs]</a>
+<span class="k">def</span> <span class="nf">cellcall_download_all</span><span class="p">(</span><span class="n">extended</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span> <span class="n">human</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span> <span class="n">mouse</span> <span class="o">=</span> <span class="kc">True</span><span class="p">):</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Downloads ligand-receptor-TF pathway data from CellCall</span>
+<span class="sd">    (https://github.com/ShellyCoder/cellcall). CellCall has core (high</span>
+<span class="sd">    confidence) and extended datasets, human and homology inferred mouse</span>
+<span class="sd">    datasets, 4 datasets in total. By default all these are downloaded</span>
+<span class="sd">    here, with the parameters you can exclude the extended part and select</span>
+<span class="sd">    the organism. The pathway identifiers refer to KEGG pathways.</span>
+
+<span class="sd">    Args</span>
+<span class="sd">        extended (bool): Use also the extended datasets.</span>
+<span class="sd">        human (bool): Include human interactions.</span>
+<span class="sd">        mouse (bool): Include mouse interactions.</span>
+
+<span class="sd">    Returns</span>
+<span class="sd">        A list of dicts, each is a record as it provided by the CellCall</span>
+<span class="sd">        database.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="n">result</span> <span class="o">=</span> <span class="p">[]</span>
+
+    <span class="k">for</span> <span class="n">ext</span><span class="p">,</span> <span class="n">homo</span> <span class="ow">in</span> <span class="n">itertools</span><span class="o">.</span><span class="n">product</span><span class="p">(</span><span class="o">*</span><span class="p">((</span><span class="kc">True</span><span class="p">,</span> <span class="kc">False</span><span class="p">),)</span> <span class="o">*</span> <span class="mi">2</span><span class="p">):</span>
+
+        <span class="k">if</span> <span class="p">(</span>
+            <span class="p">(</span><span class="n">extended</span> <span class="ow">or</span> <span class="ow">not</span> <span class="n">ext</span><span class="p">)</span> <span class="ow">and</span>
+            <span class="p">(</span>
+                <span class="p">(</span><span class="n">human</span> <span class="ow">and</span> <span class="ow">not</span> <span class="n">homo</span><span class="p">)</span> <span class="ow">or</span>
+                <span class="p">(</span><span class="n">mouse</span> <span class="ow">and</span> <span class="n">homo</span><span class="p">)</span>
+            <span class="p">)</span>
+        <span class="p">):</span>
+
+            <span class="n">dataset</span> <span class="o">=</span> <span class="n">cellcall_download</span><span class="p">(</span><span class="n">extended</span> <span class="o">=</span> <span class="n">ext</span><span class="p">,</span> <span class="n">mouse</span> <span class="o">=</span> <span class="n">homo</span><span class="p">)</span>
+            <span class="n">_</span> <span class="o">=</span> <span class="p">[</span>
+                <span class="p">(</span>
+                    <span class="n">rec</span><span class="o">.</span><span class="n">update</span><span class="p">(</span><span class="n">extended</span> <span class="o">=</span> <span class="n">ext</span><span class="p">),</span>
+                    <span class="n">rec</span><span class="o">.</span><span class="n">update</span><span class="p">(</span><span class="n">organism</span> <span class="o">=</span> <span class="mi">10090</span> <span class="k">if</span> <span class="n">homo</span> <span class="k">else</span> <span class="mi">9606</span><span class="p">),</span>
+                <span class="p">)</span>
+                <span class="k">for</span> <span class="n">rec</span> <span class="ow">in</span> <span class="n">dataset</span>
+            <span class="p">]</span>
+            <span class="n">result</span><span class="o">.</span><span class="n">extend</span><span class="p">(</span><span class="n">dataset</span><span class="p">)</span>
+
+    <span class="k">return</span> <span class="n">result</span></div>
+
+
+
+<div class="viewcode-block" id="cellcall_interactions">
+<a class="viewcode-back" href="../../../api/pypath.inputs.cellcall.cellcall_interactions.html#pypath.inputs.cellcall.cellcall_interactions">[docs]</a>
+<span class="k">def</span> <span class="nf">cellcall_interactions</span><span class="p">(</span><span class="n">extended</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span> <span class="n">organism</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">):</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Ligand-receptor interactions from the CellCall database</span>
+<span class="sd">    (https://github.com/ShellyCoder/cellcall).</span>
+
+<span class="sd">    Args</span>
+<span class="sd">        extended (bool): Include not only the core but also the extended</span>
+<span class="sd">            set of interactions.</span>
+<span class="sd">        organism (int,str): The organism to use, human (9606) and mouse</span>
+<span class="sd">            (10090) are supported.</span>
+
+<span class="sd">    Returns</span>
+<span class="sd">        List of named tuples, each describing a ligand-receptor interaction.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="n">record</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">namedtuple</span><span class="p">(</span>
+        <span class="s1">&#39;CellcallInteraction&#39;</span><span class="p">,</span>
+        <span class="p">(</span>
+            <span class="s1">&#39;ligand_uniprot&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;receptor_uniprot&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;core&#39;</span><span class="p">,</span>
+        <span class="p">),</span>
+    <span class="p">)</span>
+
+
+    <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">taxonomy</span><span class="o">.</span><span class="n">ensure_ncbi_tax_id</span><span class="p">(</span><span class="n">organism</span><span class="p">)</span>
+
+    <span class="k">if</span> <span class="n">ncbi_tax_id</span> <span class="ow">not</span> <span class="ow">in</span> <span class="p">{</span><span class="mi">9606</span><span class="p">,</span> <span class="mi">10090</span><span class="p">}:</span>
+
+        <span class="n">msg</span> <span class="o">=</span> <span class="s1">&#39;Unknown organism: `</span><span class="si">%s</span><span class="s1">`.&#39;</span> <span class="o">%</span> <span class="nb">str</span><span class="p">(</span><span class="n">organism</span><span class="p">)</span>
+        <span class="n">_log</span><span class="p">(</span><span class="n">msg</span><span class="p">)</span>
+        <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="n">msg</span><span class="p">)</span>
+
+    <span class="n">human</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span> <span class="o">==</span> <span class="mi">9606</span>
+    <span class="n">mouse</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span> <span class="o">==</span> <span class="mi">10090</span>
+    <span class="n">raw</span> <span class="o">=</span> <span class="n">cellcall_download_all</span><span class="p">(</span>
+        <span class="n">extended</span> <span class="o">=</span> <span class="n">extended</span><span class="p">,</span>
+        <span class="n">human</span> <span class="o">=</span> <span class="n">human</span><span class="p">,</span>
+        <span class="n">mouse</span> <span class="o">=</span> <span class="n">mouse</span><span class="p">,</span>
+    <span class="p">)</span>
+
+    <span class="n">result</span> <span class="o">=</span> <span class="nb">set</span><span class="p">()</span>
+    <span class="n">unmapped</span> <span class="o">=</span> <span class="nb">set</span><span class="p">()</span>
+
+    <span class="k">for</span> <span class="n">r</span> <span class="ow">in</span> <span class="n">raw</span><span class="p">:</span>
+
+        <span class="n">ligands</span> <span class="o">=</span> <span class="n">mapping</span><span class="o">.</span><span class="n">map_name</span><span class="p">(</span>
+            <span class="n">r</span><span class="p">[</span><span class="s1">&#39;Ligand_ID&#39;</span><span class="p">],</span>
+            <span class="s1">&#39;entrez&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;uniprot&#39;</span><span class="p">,</span>
+            <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">,</span>
+        <span class="p">)</span>
+
+        <span class="n">receptors</span> <span class="o">=</span> <span class="n">mapping</span><span class="o">.</span><span class="n">map_name</span><span class="p">(</span>
+            <span class="n">r</span><span class="p">[</span><span class="s1">&#39;Receptor_ID&#39;</span><span class="p">],</span>
+            <span class="s1">&#39;entrez&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;uniprot&#39;</span><span class="p">,</span>
+            <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">,</span>
+        <span class="p">)</span>
+
+        <span class="k">if</span> <span class="ow">not</span> <span class="n">ligands</span><span class="p">:</span>
+
+            <span class="n">unmapped</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">r</span><span class="p">[</span><span class="s1">&#39;Ligand_ID&#39;</span><span class="p">])</span>
+
+        <span class="k">if</span> <span class="ow">not</span> <span class="n">receptors</span><span class="p">:</span>
+
+            <span class="n">unmapped</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">r</span><span class="p">[</span><span class="s1">&#39;Receptor_ID&#39;</span><span class="p">])</span>
+
+        <span class="k">for</span> <span class="n">lig_up</span><span class="p">,</span> <span class="n">rec_up</span> <span class="ow">in</span> <span class="n">itertools</span><span class="o">.</span><span class="n">product</span><span class="p">(</span><span class="n">ligands</span><span class="p">,</span> <span class="n">receptors</span><span class="p">):</span>
+
+            <span class="n">result</span><span class="o">.</span><span class="n">add</span><span class="p">(</span>
+                <span class="n">record</span><span class="p">(</span>
+                    <span class="n">ligand_uniprot</span> <span class="o">=</span> <span class="n">lig_up</span><span class="p">,</span>
+                    <span class="n">receptor_uniprot</span> <span class="o">=</span> <span class="n">rec_up</span><span class="p">,</span>
+                    <span class="n">core</span> <span class="o">=</span> <span class="ow">not</span> <span class="n">r</span><span class="p">[</span><span class="s1">&#39;extended&#39;</span><span class="p">],</span>
+                <span class="p">)</span>
+            <span class="p">)</span>
+
+    <span class="n">_log</span><span class="p">(</span>
+        <span class="s1">&#39;Could not find UniProt IDs for </span><span class="si">%u</span><span class="s1"> &#39;</span>
+        <span class="s1">&#39;CellCall proteins.&#39;</span> <span class="o">%</span> <span class="nb">len</span><span class="p">(</span><span class="n">unmapped</span><span class="p">)</span>
+    <span class="p">)</span>
+
+    <span class="k">return</span> <span class="nb">list</span><span class="p">(</span><span class="n">result</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="cellcall_annotations">
+<a class="viewcode-back" href="../../../api/pypath.inputs.cellcall.cellcall_annotations.html#pypath.inputs.cellcall.cellcall_annotations">[docs]</a>
+<span class="k">def</span> <span class="nf">cellcall_annotations</span><span class="p">(</span><span class="n">extended</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span> <span class="n">organism</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">):</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Ligand and receptor annotations from the CellCall database</span>
+<span class="sd">    (https://github.com/ShellyCoder/cellcall).</span>
+
+<span class="sd">    Args</span>
+<span class="sd">        extended (bool): Include not only the core but also the extended</span>
+<span class="sd">            set of interactions.</span>
+<span class="sd">        organism (int,str): The organism to use, human (9606) and mouse</span>
+<span class="sd">            (10090) are supported.</span>
+
+<span class="sd">    Returns</span>
+<span class="sd">        Dict of annotations, keys are UniProt IDs, values are sets of</span>
+<span class="sd">        annotations.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="n">record</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">namedtuple</span><span class="p">(</span>
+        <span class="s1">&#39;CellcallAnnotation&#39;</span><span class="p">,</span>
+        <span class="p">(</span>
+            <span class="s1">&#39;role&#39;</span><span class="p">,</span>
+        <span class="p">),</span>
+    <span class="p">)</span>
+
+
+    <span class="n">interactions</span> <span class="o">=</span> <span class="n">cellcall_interactions</span><span class="p">(</span>
+        <span class="n">extended</span> <span class="o">=</span> <span class="n">extended</span><span class="p">,</span>
+        <span class="n">organism</span> <span class="o">=</span> <span class="n">organism</span><span class="p">,</span>
+    <span class="p">)</span>
+    <span class="n">result</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">defaultdict</span><span class="p">(</span><span class="nb">set</span><span class="p">)</span>
+
+    <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="n">interactions</span><span class="p">:</span>
+
+        <span class="n">result</span><span class="p">[</span><span class="n">i</span><span class="o">.</span><span class="n">ligand_uniprot</span><span class="p">]</span><span class="o">.</span><span class="n">add</span><span class="p">(</span>
+            <span class="n">record</span><span class="p">(</span><span class="n">role</span> <span class="o">=</span> <span class="s1">&#39;ligand&#39;</span><span class="p">)</span>
+        <span class="p">)</span>
+        <span class="n">result</span><span class="p">[</span><span class="n">i</span><span class="o">.</span><span class="n">receptor_uniprot</span><span class="p">]</span><span class="o">.</span><span class="n">add</span><span class="p">(</span>
+            <span class="n">record</span><span class="p">(</span><span class="n">role</span> <span class="o">=</span> <span class="s1">&#39;receptor&#39;</span><span class="p">)</span>
+        <span class="p">)</span>
+
+    <span class="k">return</span> <span class="nb">dict</span><span class="p">(</span><span class="n">result</span><span class="p">)</span></div>
+
+</pre></div>
+
+                </article>
+              
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diff --git a/_modules/pypath/inputs/cellcellinteractions.html b/_modules/pypath/inputs/cellcellinteractions.html
new file mode 100644
index 000000000..f695ae004
--- /dev/null
+++ b/_modules/pypath/inputs/cellcellinteractions.html
@@ -0,0 +1,667 @@
+
+<!DOCTYPE html>
+
+
+<html lang="en" data-content_root="../../../" >
+
+  <head>
+    <meta charset="utf-8" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
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+  
+  
+  
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+                  
+  <h1>Source code for pypath.inputs.cellcellinteractions</h1><div class="highlight"><pre>
+<span></span><span class="ch">#!/usr/bin/env python</span>
+<span class="c1"># -*- coding: utf-8 -*-</span>
+
+<span class="c1">#</span>
+<span class="c1">#  This file is part of the `pypath` python module</span>
+<span class="c1">#</span>
+<span class="c1">#  Copyright 2014-2023</span>
+<span class="c1">#  EMBL, EMBL-EBI, Uniklinik RWTH Aachen, Heidelberg University</span>
+<span class="c1">#</span>
+<span class="c1">#  Authors: see the file `README.rst`</span>
+<span class="c1">#  Contact: Dénes Türei (turei.denes@gmail.com)</span>
+<span class="c1">#</span>
+<span class="c1">#  Distributed under the GPLv3 License.</span>
+<span class="c1">#  See accompanying file LICENSE.txt or copy at</span>
+<span class="c1">#      https://www.gnu.org/licenses/gpl-3.0.html</span>
+<span class="c1">#</span>
+<span class="c1">#  Website: https://pypath.omnipathdb.org/</span>
+<span class="c1">#</span>
+
+<span class="kn">import</span> <span class="nn">collections</span>
+
+<span class="kn">import</span> <span class="nn">pypath.resources.urls</span> <span class="k">as</span> <span class="nn">urls</span>
+<span class="kn">import</span> <span class="nn">pypath.share.curl</span> <span class="k">as</span> <span class="nn">curl</span>
+<span class="kn">import</span> <span class="nn">pypath.utils.mapping</span> <span class="k">as</span> <span class="nn">mapping</span>
+
+
+<div class="viewcode-block" id="cellcellinteractions_annotations">
+<a class="viewcode-back" href="../../../api/pypath.inputs.cellcellinteractions.cellcellinteractions_annotations.html#pypath.inputs.cellcellinteractions.cellcellinteractions_annotations">[docs]</a>
+<span class="k">def</span> <span class="nf">cellcellinteractions_annotations</span><span class="p">():</span>
+    
+    
+    <span class="n">CellcellinteractionsAnnotation</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">namedtuple</span><span class="p">(</span>
+        <span class="s1">&#39;CellcellinteractionsAnnotation&#39;</span><span class="p">,</span>
+        <span class="p">[</span>
+            <span class="s1">&#39;mainclass&#39;</span><span class="p">,</span>
+        <span class="p">]</span>
+    <span class="p">)</span>
+    
+    
+    <span class="n">url</span> <span class="o">=</span> <span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;cellcellinteractions&#39;</span><span class="p">][</span><span class="s1">&#39;url&#39;</span><span class="p">]</span>
+    
+    <span class="n">c</span> <span class="o">=</span> <span class="n">curl</span><span class="o">.</span><span class="n">Curl</span><span class="p">(</span><span class="n">url</span><span class="p">,</span> <span class="n">silent</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span> <span class="n">large</span> <span class="o">=</span> <span class="kc">True</span><span class="p">)</span>
+    
+    <span class="n">_</span> <span class="o">=</span> <span class="nb">next</span><span class="p">(</span><span class="n">c</span><span class="o">.</span><span class="n">result</span><span class="p">)</span>
+    
+    <span class="n">result</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">defaultdict</span><span class="p">(</span><span class="nb">set</span><span class="p">)</span>
+    
+    <span class="k">for</span> <span class="n">row</span> <span class="ow">in</span> <span class="n">c</span><span class="o">.</span><span class="n">result</span><span class="p">:</span>
+        
+        <span class="n">row</span> <span class="o">=</span> <span class="n">row</span><span class="o">.</span><span class="n">strip</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\r\n</span><span class="s1">&#39;</span><span class="p">)</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\t</span><span class="s1">&#39;</span><span class="p">)</span>
+        
+        <span class="n">uniprots</span> <span class="o">=</span> <span class="n">mapping</span><span class="o">.</span><span class="n">map_name</span><span class="p">(</span><span class="n">row</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="s1">&#39;genesymbol&#39;</span><span class="p">,</span> <span class="s1">&#39;uniprot&#39;</span><span class="p">)</span>
+        <span class="n">classes</span> <span class="o">=</span> <span class="n">row</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;/&#39;</span><span class="p">)</span>
+        
+        <span class="k">for</span> <span class="n">uniprot</span> <span class="ow">in</span> <span class="n">uniprots</span><span class="p">:</span>
+            
+            <span class="k">for</span> <span class="bp">cls</span> <span class="ow">in</span> <span class="n">classes</span><span class="p">:</span>
+                
+                <span class="n">result</span><span class="p">[</span><span class="n">uniprot</span><span class="p">]</span><span class="o">.</span><span class="n">add</span><span class="p">(</span>
+                    <span class="n">CellcellinteractionsAnnotation</span><span class="p">(</span><span class="n">mainclass</span> <span class="o">=</span> <span class="bp">cls</span><span class="p">)</span>
+                <span class="p">)</span>
+    
+    <span class="k">return</span> <span class="nb">dict</span><span class="p">(</span><span class="n">result</span><span class="p">)</span></div>
+
+</pre></div>
+
+                </article>
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diff --git a/_modules/pypath/inputs/cellchatdb.html b/_modules/pypath/inputs/cellchatdb.html
new file mode 100644
index 000000000..9b13c008d
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@@ -0,0 +1,962 @@
+
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+                  
+  <h1>Source code for pypath.inputs.cellchatdb</h1><div class="highlight"><pre>
+<span></span><span class="ch">#!/usr/bin/env python</span>
+<span class="c1"># -*- coding: utf-8 -*-</span>
+
+<span class="c1">#</span>
+<span class="c1">#  This file is part of the `pypath` python module</span>
+<span class="c1">#</span>
+<span class="c1">#  Copyright 2014-2023</span>
+<span class="c1">#  EMBL, EMBL-EBI, Uniklinik RWTH Aachen, Heidelberg University</span>
+<span class="c1">#</span>
+<span class="c1">#  Authors: see the file `README.rst`</span>
+<span class="c1">#  Contact: Dénes Türei (turei.denes@gmail.com)</span>
+<span class="c1">#</span>
+<span class="c1">#  Distributed under the GPLv3 License.</span>
+<span class="c1">#  See accompanying file LICENSE.txt or copy at</span>
+<span class="c1">#      https://www.gnu.org/licenses/gpl-3.0.html</span>
+<span class="c1">#</span>
+<span class="c1">#  Website: https://pypath.omnipathdb.org/</span>
+<span class="c1">#</span>
+
+<span class="kn">import</span> <span class="nn">re</span>
+<span class="kn">import</span> <span class="nn">itertools</span>
+<span class="kn">import</span> <span class="nn">collections</span>
+
+<span class="kn">import</span> <span class="nn">pypath.share.curl</span> <span class="k">as</span> <span class="nn">curl</span>
+<span class="kn">import</span> <span class="nn">pypath.resources.urls</span> <span class="k">as</span> <span class="nn">urls</span>
+<span class="kn">import</span> <span class="nn">pypath.utils.taxonomy</span> <span class="k">as</span> <span class="nn">taxonomy</span>
+<span class="kn">import</span> <span class="nn">pypath.utils.mapping</span> <span class="k">as</span> <span class="nn">mapping</span>
+<span class="kn">import</span> <span class="nn">pypath.internals.intera</span> <span class="k">as</span> <span class="nn">intera</span>
+<span class="kn">import</span> <span class="nn">pypath.inputs.pubmed</span> <span class="k">as</span> <span class="nn">pubmed</span>
+<span class="kn">import</span> <span class="nn">pypath.inputs.rdata</span> <span class="k">as</span> <span class="nn">rdata</span>
+
+
+<div class="viewcode-block" id="cellchatdb_download">
+<a class="viewcode-back" href="../../../api/pypath.inputs.cellchatdb.cellchatdb_download.html#pypath.inputs.cellchatdb.cellchatdb_download">[docs]</a>
+<span class="k">def</span> <span class="nf">cellchatdb_download</span><span class="p">(</span><span class="n">organism</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">,</span> <span class="n">dataset</span> <span class="o">=</span> <span class="s1">&#39;CellChatDB&#39;</span><span class="p">):</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Retrieves data from CellChatDB, extracts fhe R objects from the RDA</span>
+<span class="sd">    format and returns the raw data.</span>
+
+<span class="sd">    :param int,str organism:</span>
+<span class="sd">        Human and mouse are available, for incomprehensive values falls back</span>
+<span class="sd">        to human.</span>
+<span class="sd">    :param str dataset:</span>
+<span class="sd">        Either *CellChatDB* or *PPI*.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="n">organism</span> <span class="o">=</span> <span class="n">taxonomy</span><span class="o">.</span><span class="n">ensure_common_name</span><span class="p">(</span><span class="n">organism</span><span class="p">)</span>
+    <span class="n">organism</span> <span class="o">=</span> <span class="p">(</span>
+        <span class="s1">&#39;mouse&#39;</span>
+            <span class="k">if</span> <span class="n">organism</span> <span class="ow">and</span> <span class="n">organism</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span> <span class="o">==</span> <span class="s1">&#39;mouse&#39;</span> <span class="k">else</span>
+        <span class="s1">&#39;human&#39;</span>
+    <span class="p">)</span>
+    <span class="n">dataset</span> <span class="o">=</span> <span class="s1">&#39;PPI&#39;</span> <span class="k">if</span> <span class="n">dataset</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span> <span class="o">==</span> <span class="s1">&#39;ppi&#39;</span> <span class="k">else</span> <span class="s1">&#39;CellChatDB&#39;</span>
+
+    <span class="n">key</span> <span class="o">=</span> <span class="s1">&#39;</span><span class="si">%s</span><span class="s1">.</span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="p">(</span><span class="n">dataset</span><span class="p">,</span> <span class="n">organism</span><span class="p">)</span>
+    <span class="n">url</span> <span class="o">=</span> <span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;cellchatdb&#39;</span><span class="p">][</span><span class="s1">&#39;url&#39;</span><span class="p">]</span> <span class="o">%</span> <span class="n">key</span>
+
+    <span class="n">c</span> <span class="o">=</span> <span class="n">curl</span><span class="o">.</span><span class="n">Curl</span><span class="p">(</span><span class="n">url</span><span class="p">,</span> <span class="n">silent</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span> <span class="n">large</span> <span class="o">=</span> <span class="kc">True</span><span class="p">)</span>
+    <span class="n">rdata_path</span> <span class="o">=</span> <span class="n">c</span><span class="o">.</span><span class="n">fileobj</span><span class="o">.</span><span class="n">name</span>
+    <span class="n">c</span><span class="o">.</span><span class="n">fileobj</span><span class="o">.</span><span class="n">close</span><span class="p">()</span>
+
+    <span class="n">rdata_parsed</span> <span class="o">=</span> <span class="n">rdata</span><span class="o">.</span><span class="n">rdata</span><span class="o">.</span><span class="n">parser</span><span class="o">.</span><span class="n">parse_file</span><span class="p">(</span><span class="n">rdata_path</span><span class="p">)</span>
+    <span class="n">rdata_converted</span> <span class="o">=</span> <span class="n">rdata</span><span class="o">.</span><span class="n">rdata</span><span class="o">.</span><span class="n">conversion</span><span class="o">.</span><span class="n">convert</span><span class="p">(</span><span class="n">rdata_parsed</span><span class="p">)[</span><span class="n">key</span><span class="p">]</span>
+
+    <span class="k">if</span> <span class="n">dataset</span> <span class="o">==</span> <span class="s1">&#39;CellChatDB&#39;</span><span class="p">:</span>
+
+        <span class="n">df_names</span> <span class="o">=</span> <span class="n">rdata</span><span class="o">.</span><span class="n">_rdata_list_get_names</span><span class="p">(</span><span class="n">rdata_parsed</span><span class="o">.</span><span class="n">object</span><span class="o">.</span><span class="n">value</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span>
+
+        <span class="n">rownames</span> <span class="o">=</span> <span class="p">[</span>
+            <span class="n">rdata</span><span class="o">.</span><span class="n">_rdata_data_frame_get_rownames</span><span class="p">(</span><span class="n">df_obj</span><span class="p">)</span>
+            <span class="k">for</span> <span class="n">df_obj</span> <span class="ow">in</span> <span class="n">rdata_parsed</span><span class="o">.</span><span class="n">object</span><span class="o">.</span><span class="n">value</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">value</span>
+        <span class="p">]</span>
+
+        <span class="n">rownames</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">(</span><span class="nb">zip</span><span class="p">(</span><span class="n">df_names</span><span class="p">,</span> <span class="n">rownames</span><span class="p">))</span>
+
+        <span class="k">for</span> <span class="n">name</span><span class="p">,</span> <span class="n">df</span> <span class="ow">in</span> <span class="n">rdata_converted</span><span class="o">.</span><span class="n">items</span><span class="p">():</span>
+
+            <span class="n">df</span><span class="p">[</span><span class="s1">&#39;rownames&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">rownames</span><span class="p">[</span><span class="n">name</span><span class="p">]</span>
+
+    <span class="k">return</span> <span class="n">rdata_converted</span></div>
+
+
+
+<div class="viewcode-block" id="cellchatdb_complexes">
+<a class="viewcode-back" href="../../../api/pypath.inputs.cellchatdb.cellchatdb_complexes.html#pypath.inputs.cellchatdb.cellchatdb_complexes">[docs]</a>
+<span class="k">def</span> <span class="nf">cellchatdb_complexes</span><span class="p">(</span><span class="n">organism</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">):</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Retrieves data from CellChatDB and processes protein complexes.</span>
+
+<span class="sd">    :param int,str organism:</span>
+<span class="sd">        Human and mouse are available, for incomprehensive values falls back</span>
+<span class="sd">        to human.</span>
+
+<span class="sd">    :return:</span>
+<span class="sd">        Dictionary of complexes.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="n">raw</span> <span class="o">=</span> <span class="n">cellchatdb_download</span><span class="p">(</span><span class="n">organism</span> <span class="o">=</span> <span class="n">organism</span><span class="p">)[</span><span class="s1">&#39;complex&#39;</span><span class="p">]</span>
+
+    <span class="k">return</span> <span class="n">_cellchatdb_process_complexes</span><span class="p">(</span><span class="n">raw</span><span class="p">,</span> <span class="n">organism</span> <span class="o">=</span> <span class="n">organism</span><span class="p">)</span></div>
+
+
+
+<span class="k">def</span> <span class="nf">_cellchatdb_process_complexes</span><span class="p">(</span><span class="n">raw</span><span class="p">,</span> <span class="n">organism</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">):</span>
+
+    <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">raw</span><span class="p">,</span> <span class="nb">dict</span><span class="p">):</span>
+
+        <span class="n">raw</span> <span class="o">=</span> <span class="n">raw</span><span class="p">[</span><span class="s1">&#39;complex&#39;</span><span class="p">]</span>
+
+    <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">_cellchatdb_organism</span><span class="p">(</span><span class="n">organism</span><span class="p">)</span>
+
+    <span class="n">complexes</span> <span class="o">=</span> <span class="p">{}</span>
+
+    <span class="k">for</span> <span class="n">row</span> <span class="ow">in</span> <span class="n">raw</span><span class="o">.</span><span class="n">itertuples</span><span class="p">():</span>
+
+        <span class="n">genesymbols</span> <span class="o">=</span> <span class="p">[</span><span class="n">c</span> <span class="k">for</span> <span class="n">c</span> <span class="ow">in</span> <span class="n">row</span><span class="p">[</span><span class="mi">1</span><span class="p">:</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span> <span class="k">if</span> <span class="n">c</span><span class="p">]</span>
+
+        <span class="n">uniprots</span> <span class="o">=</span> <span class="p">[</span>
+            <span class="n">mapping</span><span class="o">.</span><span class="n">map_name</span><span class="p">(</span>
+                <span class="n">gs</span><span class="p">,</span>
+                <span class="s1">&#39;genesymbol&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;uniprot&#39;</span><span class="p">,</span>
+                <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">,</span>
+            <span class="p">)</span>
+            <span class="k">for</span> <span class="n">gs</span> <span class="ow">in</span> <span class="n">genesymbols</span>
+        <span class="p">]</span>
+
+        <span class="n">uniprots</span> <span class="o">=</span> <span class="p">[</span><span class="n">up</span> <span class="k">for</span> <span class="n">up</span> <span class="ow">in</span> <span class="n">uniprots</span> <span class="k">if</span> <span class="n">up</span><span class="p">]</span>
+
+        <span class="k">for</span> <span class="n">components</span> <span class="ow">in</span> <span class="n">itertools</span><span class="o">.</span><span class="n">product</span><span class="p">(</span><span class="o">*</span><span class="n">uniprots</span><span class="p">):</span>
+
+            <span class="n">cplex</span> <span class="o">=</span> <span class="n">intera</span><span class="o">.</span><span class="n">Complex</span><span class="p">(</span>
+                <span class="n">name</span> <span class="o">=</span> <span class="n">row</span><span class="o">.</span><span class="n">rownames</span><span class="p">,</span>
+                <span class="n">components</span> <span class="o">=</span> <span class="n">components</span><span class="p">,</span>
+                <span class="n">sources</span> <span class="o">=</span> <span class="s1">&#39;CellChatDB&#39;</span><span class="p">,</span>
+                <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">,</span>
+            <span class="p">)</span>
+            <span class="n">complexes</span><span class="p">[</span><span class="n">cplex</span><span class="o">.</span><span class="fm">__str__</span><span class="p">()]</span> <span class="o">=</span> <span class="n">cplex</span>
+
+    <span class="k">return</span> <span class="n">complexes</span>
+
+
+<div class="viewcode-block" id="cellchatdb_cofactors">
+<a class="viewcode-back" href="../../../api/pypath.inputs.cellchatdb.cellchatdb_cofactors.html#pypath.inputs.cellchatdb.cellchatdb_cofactors">[docs]</a>
+<span class="k">def</span> <span class="nf">cellchatdb_cofactors</span><span class="p">(</span><span class="n">organism</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">):</span>
+
+    <span class="n">raw</span> <span class="o">=</span> <span class="n">cellchatdb_download</span><span class="p">(</span><span class="n">organism</span> <span class="o">=</span> <span class="n">organism</span><span class="p">)</span>
+
+    <span class="k">return</span> <span class="n">_cellchatdb_process_cofactors</span><span class="p">(</span><span class="n">raw</span><span class="p">,</span> <span class="n">organism</span> <span class="o">=</span> <span class="n">organism</span><span class="p">)</span></div>
+
+
+
+<span class="k">def</span> <span class="nf">_cellchatdb_process_cofactors</span><span class="p">(</span><span class="n">raw</span><span class="p">,</span> <span class="n">organism</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">):</span>
+
+    <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">raw</span><span class="p">,</span> <span class="nb">dict</span><span class="p">):</span>
+
+        <span class="n">raw</span> <span class="o">=</span> <span class="n">raw</span><span class="p">[</span><span class="s1">&#39;cofactor&#39;</span><span class="p">]</span>
+
+    <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">_cellchatdb_organism</span><span class="p">(</span><span class="n">organism</span><span class="p">)</span>
+
+    <span class="n">cofactors</span> <span class="o">=</span> <span class="p">{}</span>
+
+    <span class="k">for</span> <span class="n">row</span> <span class="ow">in</span> <span class="n">raw</span><span class="o">.</span><span class="n">itertuples</span><span class="p">():</span>
+
+        <span class="n">genesymbols</span> <span class="o">=</span> <span class="p">[</span><span class="n">c</span> <span class="k">for</span> <span class="n">c</span> <span class="ow">in</span> <span class="n">row</span><span class="p">[</span><span class="mi">1</span><span class="p">:</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span> <span class="k">if</span> <span class="n">c</span><span class="p">]</span>
+
+        <span class="n">uniprots</span> <span class="o">=</span> <span class="n">mapping</span><span class="o">.</span><span class="n">map_names</span><span class="p">(</span>
+            <span class="n">genesymbols</span><span class="p">,</span>
+            <span class="s1">&#39;genesymbol&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;uniprot&#39;</span><span class="p">,</span>
+            <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">,</span>
+        <span class="p">)</span>
+
+        <span class="n">cofactors</span><span class="p">[</span><span class="n">row</span><span class="o">.</span><span class="n">rownames</span><span class="p">]</span> <span class="o">=</span> <span class="n">uniprots</span>
+
+    <span class="k">return</span> <span class="n">cofactors</span>
+
+
+<div class="viewcode-block" id="cellchatdb_interactions">
+<a class="viewcode-back" href="../../../api/pypath.inputs.cellchatdb.cellchatdb_interactions.html#pypath.inputs.cellchatdb.cellchatdb_interactions">[docs]</a>
+<span class="k">def</span> <span class="nf">cellchatdb_interactions</span><span class="p">(</span>
+    <span class="n">organism</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">,</span>
+    <span class="n">ligand_receptor</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
+    <span class="n">cofactors</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
+<span class="p">):</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Retrieves data from CellChatDB and processes interactions.</span>
+
+<span class="sd">    :param int,str organism:</span>
+<span class="sd">        Human and mouse are available, for incomprehensive values falls back</span>
+<span class="sd">        to human.</span>
+<span class="sd">    :param bool ligand_receptor:</span>
+<span class="sd">        Include ligand-receptor interactions.</span>
+<span class="sd">    :param bool cofactors:</span>
+<span class="sd">        Include interactions between cofactors (agonists, antagonists),</span>
+<span class="sd">        coreceptors and receptors.</span>
+
+<span class="sd">    :return:</span>
+<span class="sd">        Interactions as list of named tuples.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="k">def</span> <span class="nf">process_name</span><span class="p">(</span><span class="n">name</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="p">(</span>
+            <span class="p">(</span><span class="n">complexes_by_name</span><span class="p">[</span><span class="n">name</span><span class="p">],)</span>
+                <span class="k">if</span> <span class="n">name</span> <span class="ow">in</span> <span class="n">complexes_by_name</span> <span class="k">else</span>
+            <span class="n">mapping</span><span class="o">.</span><span class="n">map_name</span><span class="p">(</span>
+                <span class="n">name</span><span class="p">,</span>
+                <span class="s1">&#39;genesymbol&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;uniprot&#39;</span><span class="p">,</span>
+                <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">,</span>
+            <span class="p">)</span>
+        <span class="p">)</span>
+
+
+    <span class="n">CellChatDBInteraction</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">namedtuple</span><span class="p">(</span>
+        <span class="s1">&#39;CellChatDBInteraction&#39;</span><span class="p">,</span>
+        <span class="p">[</span>
+            <span class="s1">&#39;id_a&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;id_b&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;role_a&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;role_b&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;effect&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;pathway&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;refs&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;category&#39;</span><span class="p">,</span>
+        <span class="p">]</span>
+    <span class="p">)</span>
+
+    <span class="n">repmid</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">compile</span><span class="p">(</span><span class="s1">&#39;PMID:\s*?(\d+)&#39;</span><span class="p">)</span>
+    <span class="n">repmcid</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">compile</span><span class="p">(</span><span class="s1">&#39;PMC\d+&#39;</span><span class="p">)</span>
+
+    <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">_cellchatdb_organism</span><span class="p">(</span><span class="n">organism</span><span class="p">)</span>
+
+    <span class="n">raw</span> <span class="o">=</span> <span class="n">cellchatdb_download</span><span class="p">(</span><span class="n">organism</span> <span class="o">=</span> <span class="n">organism</span><span class="p">)</span>
+
+    <span class="n">_complexes</span> <span class="o">=</span> <span class="n">_cellchatdb_process_complexes</span><span class="p">(</span><span class="n">raw</span><span class="p">,</span> <span class="n">organism</span> <span class="o">=</span> <span class="n">organism</span><span class="p">)</span>
+    <span class="n">_cofactors</span> <span class="o">=</span> <span class="n">_cellchatdb_process_cofactors</span><span class="p">(</span><span class="n">raw</span><span class="p">,</span> <span class="n">organism</span> <span class="o">=</span> <span class="n">organism</span><span class="p">)</span>
+
+    <span class="n">complexes_by_name</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">(</span>
+        <span class="p">(</span><span class="n">cplex</span><span class="o">.</span><span class="n">name</span><span class="p">,</span> <span class="n">cplex</span><span class="p">)</span>
+        <span class="k">for</span> <span class="n">cplex</span> <span class="ow">in</span> <span class="n">_complexes</span><span class="o">.</span><span class="n">values</span><span class="p">()</span>
+    <span class="p">)</span>
+
+    <span class="n">raw_ia</span> <span class="o">=</span> <span class="n">raw</span><span class="p">[</span><span class="s1">&#39;interaction&#39;</span><span class="p">]</span>
+
+    <span class="n">result</span> <span class="o">=</span> <span class="p">[]</span>
+
+    <span class="k">for</span> <span class="n">row</span> <span class="ow">in</span> <span class="n">raw_ia</span><span class="o">.</span><span class="n">itertuples</span><span class="p">():</span>
+
+        <span class="n">refs</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="nb">set</span><span class="p">(</span><span class="n">repmid</span><span class="o">.</span><span class="n">findall</span><span class="p">(</span><span class="n">row</span><span class="o">.</span><span class="n">evidence</span><span class="p">))</span> <span class="o">|</span>
+            <span class="nb">set</span><span class="p">(</span><span class="n">pubmed</span><span class="o">.</span><span class="n">only_pmids</span><span class="p">(</span><span class="n">repmcid</span><span class="o">.</span><span class="n">findall</span><span class="p">(</span><span class="n">row</span><span class="o">.</span><span class="n">evidence</span><span class="p">)))</span>
+        <span class="p">)</span>
+        <span class="c1"># PMIDs starting with 23209 are a mistake in CellChatDB</span>
+        <span class="n">refs</span> <span class="o">=</span> <span class="nb">sorted</span><span class="p">(</span><span class="n">pmid</span> <span class="k">for</span> <span class="n">pmid</span> <span class="ow">in</span> <span class="n">refs</span> <span class="k">if</span> <span class="ow">not</span> <span class="n">pmid</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s1">&#39;23209&#39;</span><span class="p">))</span>
+
+        <span class="n">ligands</span> <span class="o">=</span> <span class="n">process_name</span><span class="p">(</span><span class="n">row</span><span class="o">.</span><span class="n">ligand</span><span class="p">)</span>
+        <span class="n">receptors</span> <span class="o">=</span> <span class="n">process_name</span><span class="p">(</span><span class="n">row</span><span class="o">.</span><span class="n">receptor</span><span class="p">)</span>
+
+        <span class="k">if</span> <span class="n">ligand_receptor</span><span class="p">:</span>
+
+            <span class="n">i</span> <span class="o">=</span> <span class="mi">0</span>
+
+            <span class="k">for</span> <span class="n">ligand</span><span class="p">,</span> <span class="n">receptor</span> <span class="ow">in</span> <span class="n">itertools</span><span class="o">.</span><span class="n">product</span><span class="p">(</span><span class="n">ligands</span><span class="p">,</span> <span class="n">receptors</span><span class="p">):</span>
+
+                <span class="n">result</span><span class="o">.</span><span class="n">append</span><span class="p">(</span>
+                    <span class="n">CellChatDBInteraction</span><span class="p">(</span>
+                        <span class="n">id_a</span> <span class="o">=</span> <span class="n">ligand</span><span class="p">,</span>
+                        <span class="n">id_b</span> <span class="o">=</span> <span class="n">receptor</span><span class="p">,</span>
+                        <span class="n">role_a</span> <span class="o">=</span> <span class="s1">&#39;ligand&#39;</span><span class="p">,</span>
+                        <span class="n">role_b</span> <span class="o">=</span> <span class="s1">&#39;receptor&#39;</span><span class="p">,</span>
+                        <span class="n">effect</span> <span class="o">=</span> <span class="s1">&#39;unknown&#39;</span><span class="p">,</span>
+                        <span class="n">pathway</span> <span class="o">=</span> <span class="n">row</span><span class="o">.</span><span class="n">pathway_name</span><span class="p">,</span>
+                        <span class="n">refs</span> <span class="o">=</span> <span class="n">refs</span><span class="p">,</span>
+                        <span class="n">category</span> <span class="o">=</span> <span class="n">row</span><span class="o">.</span><span class="n">annotation</span><span class="p">,</span>
+                    <span class="p">)</span>
+                <span class="p">)</span>
+
+        <span class="k">if</span> <span class="n">cofactors</span><span class="p">:</span>
+
+            <span class="k">for</span> <span class="n">cofactor_col</span><span class="p">,</span> <span class="n">effect</span><span class="p">,</span> <span class="n">targets</span> <span class="ow">in</span> <span class="p">(</span>
+                <span class="p">(</span><span class="s1">&#39;agonist&#39;</span><span class="p">,</span> <span class="s1">&#39;stimulation&#39;</span><span class="p">,</span> <span class="n">ligands</span><span class="p">),</span>
+                <span class="p">(</span><span class="s1">&#39;antagonist&#39;</span><span class="p">,</span> <span class="s1">&#39;inhibition&#39;</span><span class="p">,</span> <span class="n">ligands</span><span class="p">),</span>
+                <span class="p">(</span><span class="s1">&#39;co_A_receptor&#39;</span><span class="p">,</span> <span class="s1">&#39;stimulation&#39;</span><span class="p">,</span> <span class="n">receptors</span><span class="p">),</span>
+                <span class="p">(</span><span class="s1">&#39;co_I_receptor&#39;</span><span class="p">,</span> <span class="s1">&#39;inhibition&#39;</span><span class="p">,</span> <span class="n">receptors</span><span class="p">),</span>
+            <span class="p">):</span>
+
+                <span class="n">cofact_label</span> <span class="o">=</span> <span class="nb">getattr</span><span class="p">(</span><span class="n">row</span><span class="p">,</span> <span class="n">cofactor_col</span><span class="p">)</span>
+
+                <span class="k">if</span> <span class="n">cofact_label</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">_cofactors</span><span class="p">:</span>
+
+                    <span class="k">continue</span>
+
+                <span class="k">for</span> <span class="n">cofactor</span><span class="p">,</span> <span class="n">target</span> <span class="ow">in</span> <span class="n">itertools</span><span class="o">.</span><span class="n">product</span><span class="p">(</span>
+                    <span class="n">_cofactors</span><span class="p">[</span><span class="n">cofact_label</span><span class="p">],</span>
+                    <span class="n">targets</span>
+                <span class="p">):</span>
+
+                    <span class="n">result</span><span class="o">.</span><span class="n">append</span><span class="p">(</span>
+                        <span class="n">CellChatDBInteraction</span><span class="p">(</span>
+                            <span class="n">id_a</span> <span class="o">=</span> <span class="n">cofactor</span><span class="p">,</span>
+                            <span class="n">id_b</span> <span class="o">=</span> <span class="n">target</span><span class="p">,</span>
+                            <span class="n">role_a</span> <span class="o">=</span> <span class="n">cofactor_col</span><span class="p">,</span>
+                            <span class="n">role_b</span> <span class="o">=</span> <span class="p">(</span>
+                                <span class="s1">&#39;ligand&#39;</span>
+                                    <span class="k">if</span> <span class="n">cofactor_col</span><span class="o">.</span><span class="n">endswith</span><span class="p">(</span><span class="s1">&#39;onist&#39;</span><span class="p">)</span> <span class="k">else</span>
+                                <span class="s1">&#39;receptor&#39;</span>
+                            <span class="p">),</span>
+                            <span class="n">effect</span> <span class="o">=</span> <span class="n">effect</span><span class="p">,</span>
+                            <span class="n">pathway</span> <span class="o">=</span> <span class="n">row</span><span class="o">.</span><span class="n">pathway_name</span><span class="p">,</span>
+                            <span class="n">refs</span> <span class="o">=</span> <span class="nb">set</span><span class="p">(),</span>
+                            <span class="n">category</span> <span class="o">=</span> <span class="n">row</span><span class="o">.</span><span class="n">annotation</span><span class="p">,</span>
+                        <span class="p">)</span>
+                    <span class="p">)</span>
+
+    <span class="k">return</span> <span class="n">result</span></div>
+
+
+
+<div class="viewcode-block" id="cellchatdb_annotations">
+<a class="viewcode-back" href="../../../api/pypath.inputs.cellchatdb.cellchatdb_annotations.html#pypath.inputs.cellchatdb.cellchatdb_annotations">[docs]</a>
+<span class="k">def</span> <span class="nf">cellchatdb_annotations</span><span class="p">(</span><span class="n">organism</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">):</span>
+
+    <span class="n">CellChatDBAnnotation</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">namedtuple</span><span class="p">(</span>
+        <span class="s1">&#39;CellChatDBAnnotation&#39;</span><span class="p">,</span>
+        <span class="p">[</span>
+            <span class="s1">&#39;role&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;pathway&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;category&#39;</span><span class="p">,</span>
+        <span class="p">]</span>
+    <span class="p">)</span>
+
+
+    <span class="n">annotations</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">defaultdict</span><span class="p">(</span><span class="nb">set</span><span class="p">)</span>
+    <span class="n">interactions</span> <span class="o">=</span> <span class="n">cellchatdb_interactions</span><span class="p">(</span><span class="n">organism</span> <span class="o">=</span> <span class="n">organism</span><span class="p">)</span>
+
+    <span class="k">for</span> <span class="n">ia</span> <span class="ow">in</span> <span class="n">interactions</span><span class="p">:</span>
+
+        <span class="k">for</span> <span class="n">side</span> <span class="ow">in</span> <span class="p">(</span><span class="s1">&#39;a&#39;</span><span class="p">,</span> <span class="s1">&#39;b&#39;</span><span class="p">):</span>
+
+            <span class="n">annotations</span><span class="p">[</span><span class="nb">getattr</span><span class="p">(</span><span class="n">ia</span><span class="p">,</span> <span class="s1">&#39;id_</span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="n">side</span><span class="p">)]</span><span class="o">.</span><span class="n">add</span><span class="p">(</span>
+                <span class="n">CellChatDBAnnotation</span><span class="p">(</span>
+                    <span class="n">role</span> <span class="o">=</span> <span class="nb">getattr</span><span class="p">(</span><span class="n">ia</span><span class="p">,</span> <span class="s1">&#39;role_</span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="n">side</span><span class="p">),</span>
+                    <span class="n">pathway</span> <span class="o">=</span> <span class="n">ia</span><span class="o">.</span><span class="n">pathway</span><span class="p">,</span>
+                    <span class="n">category</span> <span class="o">=</span> <span class="n">ia</span><span class="o">.</span><span class="n">category</span><span class="p">,</span>
+                <span class="p">)</span>
+            <span class="p">)</span>
+
+    <span class="k">return</span> <span class="nb">dict</span><span class="p">(</span><span class="n">annotations</span><span class="p">)</span></div>
+
+
+
+<span class="k">def</span> <span class="nf">_cellchatdb_organism</span><span class="p">(</span><span class="n">organism</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">):</span>
+
+    <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">taxonomy</span><span class="o">.</span><span class="n">ensure_ncbi_tax_id</span><span class="p">(</span><span class="n">organism</span><span class="p">)</span>
+    <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="mi">10090</span> <span class="k">if</span> <span class="n">ncbi_tax_id</span> <span class="o">==</span> <span class="mi">10090</span> <span class="k">else</span> <span class="mi">9606</span>
+
+    <span class="k">return</span> <span class="n">ncbi_tax_id</span>
+</pre></div>
+
+                </article>
+              
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diff --git a/_modules/pypath/inputs/cellinker.html b/_modules/pypath/inputs/cellinker.html
new file mode 100644
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+    <span class="theme-switch nav-link" data-mode="auto"><i class="fa-solid fa-circle-half-stroke fa-lg"></i></span>
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+                <article class="bd-article">
+                  
+  <h1>Source code for pypath.inputs.cellinker</h1><div class="highlight"><pre>
+<span></span><span class="ch">#!/usr/bin/env python</span>
+<span class="c1"># -*- coding: utf-8 -*-</span>
+
+<span class="c1">#</span>
+<span class="c1">#  This file is part of the `pypath` python module</span>
+<span class="c1">#</span>
+<span class="c1">#  Copyright 2014-2023</span>
+<span class="c1">#  EMBL, EMBL-EBI, Uniklinik RWTH Aachen, Heidelberg University</span>
+<span class="c1">#</span>
+<span class="c1">#  Authors: see the file `README.rst`</span>
+<span class="c1">#  Contact: Dénes Türei (turei.denes@gmail.com)</span>
+<span class="c1">#</span>
+<span class="c1">#  Distributed under the GPLv3 License.</span>
+<span class="c1">#  See accompanying file LICENSE.txt or copy at</span>
+<span class="c1">#      https://www.gnu.org/licenses/gpl-3.0.html</span>
+<span class="c1">#</span>
+<span class="c1">#  Website: https://pypath.omnipathdb.org/</span>
+<span class="c1">#</span>
+
+<span class="kn">import</span> <span class="nn">csv</span>
+<span class="kn">import</span> <span class="nn">itertools</span>
+<span class="kn">import</span> <span class="nn">collections</span>
+
+<span class="kn">import</span> <span class="nn">pypath.resources.urls</span> <span class="k">as</span> <span class="nn">urls</span>
+<span class="kn">import</span> <span class="nn">pypath.share.curl</span> <span class="k">as</span> <span class="nn">curl</span>
+<span class="kn">import</span> <span class="nn">pypath.utils.taxonomy</span> <span class="k">as</span> <span class="nn">taxonomy</span>
+<span class="kn">import</span> <span class="nn">pypath.utils.mapping</span> <span class="k">as</span> <span class="nn">mapping</span>
+<span class="kn">import</span> <span class="nn">pypath.internals.intera</span> <span class="k">as</span> <span class="nn">intera</span>
+<span class="kn">import</span> <span class="nn">pypath.share.session</span> <span class="k">as</span> <span class="nn">session</span>
+<span class="kn">import</span> <span class="nn">pypath.core.entity</span> <span class="k">as</span> <span class="nn">entity</span>
+
+<span class="n">_logger</span> <span class="o">=</span> <span class="n">session</span><span class="o">.</span><span class="n">Logger</span><span class="p">(</span><span class="n">name</span> <span class="o">=</span> <span class="s1">&#39;cellinker_input&#39;</span><span class="p">)</span>
+<span class="n">_log</span> <span class="o">=</span> <span class="n">_logger</span><span class="o">.</span><span class="n">_log</span>
+
+
+<span class="n">CellinkerInteraction</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">namedtuple</span><span class="p">(</span>
+    <span class="s1">&#39;CellinkerInteraction&#39;</span><span class="p">,</span>
+    <span class="p">(</span>
+        <span class="s1">&#39;ligand&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;receptor&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;ligand_location&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;receptor_location&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;resources&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;pmids&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;type&#39;</span><span class="p">,</span>
+    <span class="p">),</span>
+<span class="p">)</span>
+
+
+<div class="viewcode-block" id="cellinker_complexes_raw">
+<a class="viewcode-back" href="../../../api/pypath.inputs.cellinker.cellinker_complexes_raw.html#pypath.inputs.cellinker.cellinker_complexes_raw">[docs]</a>
+<span class="k">def</span> <span class="nf">cellinker_complexes_raw</span><span class="p">(</span><span class="n">organism</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">):</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Downloads protein complex data from the Cellinker database</span>
+<span class="sd">    (http://www.rna-society.org/cellinker/).</span>
+
+<span class="sd">    Args</span>
+<span class="sd">        organism (int,str): Name or identifier of the organism. Only mouse</span>
+<span class="sd">            and human are available.</span>
+
+<span class="sd">    Returns</span>
+<span class="sd">        (list): List of tuples each describing a protein complex with its</span>
+<span class="sd">            role (ligand or receptor), components, localization and</span>
+<span class="sd">            Cellinker ID.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="n">CellinkerComplex</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">namedtuple</span><span class="p">(</span>
+        <span class="s1">&#39;CellinkerComplex&#39;</span><span class="p">,</span>
+        <span class="p">(</span>
+            <span class="s1">&#39;role&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;cellinker_id&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;components&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;location&#39;</span><span class="p">,</span>
+        <span class="p">),</span>
+    <span class="p">)</span>
+
+    <span class="n">CellinkerComplexComponent</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">namedtuple</span><span class="p">(</span>
+        <span class="s1">&#39;CellinkerComplexComponent&#39;</span><span class="p">,</span>
+        <span class="p">(</span>
+            <span class="s1">&#39;genesymbol&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;entrez&#39;</span><span class="p">,</span>
+        <span class="p">),</span>
+    <span class="p">)</span>
+
+    <span class="n">organism_common</span> <span class="o">=</span> <span class="n">taxonomy</span><span class="o">.</span><span class="n">ensure_common_name</span><span class="p">(</span><span class="n">organism</span><span class="p">)</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span>
+
+    <span class="k">if</span> <span class="n">organism_common</span> <span class="ow">not</span> <span class="ow">in</span> <span class="p">{</span><span class="s1">&#39;human&#39;</span><span class="p">,</span> <span class="s1">&#39;mouse&#39;</span><span class="p">}:</span>
+
+        <span class="n">msg</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="s1">&#39;Unknown organism: </span><span class="si">%s</span><span class="s1"> (</span><span class="si">%s</span><span class="s1">). Only human and mouse &#39;</span>
+            <span class="s1">&#39;are available.&#39;</span> <span class="o">%</span> <span class="p">(</span><span class="nb">str</span><span class="p">(</span><span class="n">organism_common</span><span class="p">),</span> <span class="nb">str</span><span class="p">(</span><span class="n">organism</span><span class="p">))</span>
+        <span class="p">)</span>
+        <span class="n">_log</span><span class="p">(</span><span class="n">msg</span><span class="p">)</span>
+        <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="n">msg</span><span class="p">)</span>
+
+    <span class="n">url</span> <span class="o">=</span> <span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;cellinker_rescued&#39;</span><span class="p">][</span><span class="s1">&#39;complex&#39;</span><span class="p">]</span> <span class="o">%</span> <span class="n">organism_common</span>
+    <span class="n">c</span> <span class="o">=</span> <span class="n">curl</span><span class="o">.</span><span class="n">Curl</span><span class="p">(</span><span class="n">url</span><span class="p">,</span> <span class="n">large</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span> <span class="n">silent</span> <span class="o">=</span> <span class="kc">False</span><span class="p">)</span>
+
+    <span class="n">result</span> <span class="o">=</span> <span class="p">[]</span>
+
+    <span class="n">_</span> <span class="o">=</span> <span class="nb">next</span><span class="p">(</span><span class="n">c</span><span class="o">.</span><span class="n">result</span><span class="p">)</span>
+
+    <span class="k">for</span> <span class="n">r</span> <span class="ow">in</span> <span class="n">c</span><span class="o">.</span><span class="n">result</span><span class="p">:</span>
+
+        <span class="n">r</span> <span class="o">=</span> <span class="n">r</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;,&#39;</span><span class="p">)</span>
+
+        <span class="n">components</span> <span class="o">=</span> <span class="nb">tuple</span><span class="p">(</span>
+            <span class="n">CellinkerComplexComponent</span><span class="p">(</span>
+                <span class="n">genesymbol</span> <span class="o">=</span> <span class="n">r</span><span class="p">[</span><span class="n">i</span><span class="p">],</span>
+                <span class="n">entrez</span> <span class="o">=</span> <span class="n">r</span><span class="p">[</span><span class="n">i</span> <span class="o">+</span> <span class="mi">1</span><span class="p">],</span>
+            <span class="p">)</span>
+            <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">3</span><span class="p">,</span> <span class="mi">13</span><span class="p">,</span> <span class="mi">2</span><span class="p">)</span>
+            <span class="k">if</span> <span class="n">r</span><span class="p">[</span><span class="n">i</span><span class="p">]</span>
+        <span class="p">)</span>
+
+        <span class="n">result</span><span class="o">.</span><span class="n">append</span><span class="p">(</span>
+            <span class="n">CellinkerComplex</span><span class="p">(</span>
+                <span class="n">role</span> <span class="o">=</span> <span class="s1">&#39;ligand&#39;</span> <span class="k">if</span> <span class="n">r</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="k">else</span> <span class="s1">&#39;receptor&#39;</span><span class="p">,</span>
+                <span class="n">cellinker_id</span> <span class="o">=</span> <span class="n">r</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="ow">or</span> <span class="n">r</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span>
+                <span class="n">components</span> <span class="o">=</span> <span class="n">components</span><span class="p">,</span>
+                <span class="n">location</span> <span class="o">=</span> <span class="n">r</span><span class="p">[</span><span class="mi">13</span><span class="p">],</span>
+            <span class="p">)</span>
+        <span class="p">)</span>
+
+    <span class="k">return</span> <span class="n">result</span></div>
+
+
+
+<div class="viewcode-block" id="components_to_complex">
+<a class="viewcode-back" href="../../../api/pypath.inputs.cellinker.components_to_complex.html#pypath.inputs.cellinker.components_to_complex">[docs]</a>
+<span class="k">def</span> <span class="nf">components_to_complex</span><span class="p">(</span><span class="n">components</span><span class="p">,</span> <span class="n">organism</span> <span class="o">=</span> <span class="kc">None</span><span class="p">):</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Converts a set of components to `pypath.internals.intera.Complex`</span>
+<span class="sd">    objects.</span>
+
+<span class="sd">    Args</span>
+<span class="sd">        components (tuple): Components of a complex, as returned by</span>
+<span class="sd">            `cellinker_complexes_raw`.</span>
+<span class="sd">        organism (int,str): Name or identifier of the organism. Only mouse</span>
+<span class="sd">            and human are available. Optional, because organism can be</span>
+<span class="sd">            guessed from the identifiers.</span>
+
+<span class="sd">    Returns</span>
+<span class="sd">        (set): A set of `pypath.internals.intera.Complex` objects.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="k">if</span> <span class="ow">not</span> <span class="n">organism</span><span class="p">:</span>
+
+        <span class="n">organism</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="mi">9606</span> <span class="k">if</span> <span class="p">(</span>
+                <span class="nb">all</span><span class="p">(</span><span class="n">c</span><span class="o">.</span><span class="n">genesymbol</span><span class="o">.</span><span class="n">upper</span><span class="p">()</span> <span class="o">==</span> <span class="n">c</span><span class="o">.</span><span class="n">genesymbol</span> <span class="k">for</span> <span class="n">c</span> <span class="ow">in</span> <span class="n">components</span><span class="p">)</span>
+            <span class="p">)</span> <span class="k">else</span> <span class="mi">10090</span>
+        <span class="p">)</span>
+
+    <span class="n">_organism</span> <span class="o">=</span> <span class="n">taxonomy</span><span class="o">.</span><span class="n">ensure_ncbi_tax_id</span><span class="p">(</span><span class="n">organism</span><span class="p">)</span>
+
+    <span class="k">if</span> <span class="n">_organism</span> <span class="ow">not</span> <span class="ow">in</span> <span class="p">{</span><span class="mi">9606</span><span class="p">,</span> <span class="mi">10090</span><span class="p">}:</span>
+
+        <span class="n">msg</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="s1">&#39;Unknown organism: </span><span class="si">%s</span><span class="s1"> (</span><span class="si">%s</span><span class="s1">). Only human and mouse &#39;</span>
+            <span class="s1">&#39;are available.&#39;</span> <span class="o">%</span> <span class="p">(</span><span class="nb">str</span><span class="p">(</span><span class="n">_organism</span><span class="p">),</span> <span class="nb">str</span><span class="p">(</span><span class="n">organism</span><span class="p">))</span>
+        <span class="p">)</span>
+        <span class="n">_log</span><span class="p">(</span><span class="n">msg</span><span class="p">)</span>
+        <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="n">msg</span><span class="p">)</span>
+
+    <span class="n">result</span> <span class="o">=</span> <span class="nb">set</span><span class="p">()</span>
+
+    <span class="k">for</span> <span class="n">uniprots</span> <span class="ow">in</span> <span class="n">itertools</span><span class="o">.</span><span class="n">product</span><span class="p">(</span><span class="o">*</span><span class="p">(</span>
+        <span class="n">_cellinker_uniprots</span><span class="p">(</span><span class="n">c</span><span class="o">.</span><span class="n">genesymbol</span><span class="p">,</span> <span class="n">c</span><span class="o">.</span><span class="n">entrez</span><span class="p">,</span> <span class="n">_organism</span><span class="p">)</span>
+        <span class="k">for</span> <span class="n">c</span> <span class="ow">in</span> <span class="n">components</span>
+    <span class="p">)):</span>
+
+        <span class="n">result</span><span class="o">.</span><span class="n">add</span><span class="p">(</span>
+            <span class="n">intera</span><span class="o">.</span><span class="n">Complex</span><span class="p">(</span>
+                <span class="n">components</span> <span class="o">=</span> <span class="n">uniprots</span><span class="p">,</span>
+                <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">_organism</span><span class="p">,</span>
+                <span class="n">sources</span> <span class="o">=</span> <span class="s1">&#39;Cellinker&#39;</span><span class="p">,</span>
+            <span class="p">)</span>
+        <span class="p">)</span>
+
+    <span class="k">return</span> <span class="n">result</span></div>
+
+
+
+<div class="viewcode-block" id="cellinker_complexes">
+<a class="viewcode-back" href="../../../api/pypath.inputs.cellinker.cellinker_complexes.html#pypath.inputs.cellinker.cellinker_complexes">[docs]</a>
+<span class="k">def</span> <span class="nf">cellinker_complexes</span><span class="p">(</span><span class="n">organism</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">):</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Protein complex information from the Cellinker database</span>
+<span class="sd">    (http://www.rna-society.org/cellinker/).</span>
+
+<span class="sd">    Args</span>
+<span class="sd">        organism (int,str): Name or identifier of the organism. Only mouse</span>
+<span class="sd">            and human are available.</span>
+
+<span class="sd">    Returns</span>
+<span class="sd">        (dict): A dict of complexes, with string representations as keys and</span>
+<span class="sd">            `pypath.internals.intera.Complex` objects as values.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="n">result</span> <span class="o">=</span> <span class="p">{}</span>
+
+    <span class="k">for</span> <span class="n">c</span> <span class="ow">in</span> <span class="n">cellinker_complexes_raw</span><span class="p">(</span><span class="n">organism</span> <span class="o">=</span> <span class="n">organism</span><span class="p">):</span>
+
+        <span class="k">for</span> <span class="n">cplex</span> <span class="ow">in</span> <span class="n">components_to_complex</span><span class="p">(</span><span class="n">c</span><span class="o">.</span><span class="n">components</span><span class="p">,</span> <span class="n">organism</span> <span class="o">=</span> <span class="n">organism</span><span class="p">):</span>
+
+            <span class="n">result</span><span class="p">[</span><span class="n">cplex</span><span class="o">.</span><span class="fm">__str__</span><span class="p">()]</span> <span class="o">=</span> <span class="n">cplex</span>
+
+    <span class="k">return</span> <span class="n">result</span></div>
+
+
+
+<div class="viewcode-block" id="cellinker_lr_interactions_raw">
+<a class="viewcode-back" href="../../../api/pypath.inputs.cellinker.cellinker_lr_interactions_raw.html#pypath.inputs.cellinker.cellinker_lr_interactions_raw">[docs]</a>
+<span class="k">def</span> <span class="nf">cellinker_lr_interactions_raw</span><span class="p">(</span><span class="n">organism</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">):</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Ligand-receptor interactions from the Cellinker database</span>
+<span class="sd">    (http://www.rna-society.org/cellinker/).</span>
+
+<span class="sd">    Args</span>
+<span class="sd">        organism (int,str): Name or identifier of the organism. Only mouse</span>
+<span class="sd">            and human are available.</span>
+
+<span class="sd">    Returns</span>
+<span class="sd">        (list): A list of dicts, each representing an interaction records</span>
+<span class="sd">            as it is provided by the database.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="k">return</span> <span class="n">_cellinker_interactions_raw</span><span class="p">(</span><span class="n">organism</span> <span class="o">=</span> <span class="n">organism</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="cellinker_smol_interactions_raw">
+<a class="viewcode-back" href="../../../api/pypath.inputs.cellinker.cellinker_smol_interactions_raw.html#pypath.inputs.cellinker.cellinker_smol_interactions_raw">[docs]</a>
+<span class="k">def</span> <span class="nf">cellinker_smol_interactions_raw</span><span class="p">(</span><span class="n">organism</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">):</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Small molecule ligand-protein receptor interactions from the Cellinker</span>
+<span class="sd">    database (http://www.rna-society.org/cellinker/).</span>
+
+<span class="sd">    Args</span>
+<span class="sd">        organism (int,str): Name or identifier of the organism. Only mouse</span>
+<span class="sd">            and human are available.</span>
+
+<span class="sd">    Returns</span>
+<span class="sd">        (list): A list of dicts, each representing an interaction records</span>
+<span class="sd">            as it is provided by the database.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="k">return</span> <span class="n">_cellinker_interactions_raw</span><span class="p">(</span><span class="n">dataset</span> <span class="o">=</span> <span class="s1">&#39;smol&#39;</span><span class="p">,</span> <span class="n">organism</span> <span class="o">=</span> <span class="n">organism</span><span class="p">)</span></div>
+
+
+
+<span class="k">def</span> <span class="nf">_cellinker_interactions_raw</span><span class="p">(</span><span class="n">dataset</span> <span class="o">=</span> <span class="s1">&#39;lr&#39;</span><span class="p">,</span> <span class="n">organism</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">):</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Downloads either the ligand-receptor or the small molecule ligand-receptor</span>
+<span class="sd">    dataset from the Cellinker database.</span>
+
+<span class="sd">    Args</span>
+<span class="sd">        dataset (str): Either `lr` or `smol`, meainng protein-protein or</span>
+<span class="sd">            small molecule-protein ligand-receptor interactions.</span>
+<span class="sd">        organism (int,str): Name or identifier of the organism. Only mouse</span>
+<span class="sd">            and human are available.</span>
+
+<span class="sd">    Returns</span>
+<span class="sd">        (list): A list of dicts, each representing an interaction records</span>
+<span class="sd">            as it is provided by the database.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="k">if</span> <span class="n">dataset</span> <span class="ow">not</span> <span class="ow">in</span> <span class="p">{</span><span class="s1">&#39;lr&#39;</span><span class="p">,</span> <span class="s1">&#39;smol&#39;</span><span class="p">}:</span>
+
+        <span class="n">msg</span> <span class="o">=</span> <span class="s1">&#39;Unknown Cellinker interaction dataset: `</span><span class="si">%s</span><span class="s1">`.&#39;</span> <span class="o">%</span> <span class="nb">str</span><span class="p">(</span><span class="n">dataset</span><span class="p">)</span>
+        <span class="n">_log</span><span class="p">(</span><span class="n">msg</span><span class="p">)</span>
+        <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="n">msg</span><span class="p">)</span>
+
+    <span class="n">org_name_type</span> <span class="o">=</span> <span class="s1">&#39;latin&#39;</span> <span class="k">if</span> <span class="n">dataset</span> <span class="o">==</span> <span class="s1">&#39;lr&#39;</span> <span class="k">else</span> <span class="s1">&#39;common&#39;</span>
+
+    <span class="n">organisms_allowed</span> <span class="o">=</span> <span class="p">(</span>
+        <span class="p">{</span><span class="s1">&#39;Homo sapiens&#39;</span><span class="p">,</span> <span class="s1">&#39;Mus musculus&#39;</span><span class="p">}</span>
+            <span class="k">if</span> <span class="n">org_name_type</span> <span class="o">==</span> <span class="s1">&#39;latin&#39;</span> <span class="k">else</span>
+        <span class="p">{</span><span class="s1">&#39;Human&#39;</span><span class="p">,</span> <span class="s1">&#39;Mouse&#39;</span><span class="p">}</span>
+    <span class="p">)</span>
+
+    <span class="n">_organism</span> <span class="o">=</span> <span class="nb">getattr</span><span class="p">(</span><span class="n">taxonomy</span><span class="p">,</span> <span class="s1">&#39;ensure_</span><span class="si">%s</span><span class="s1">_name&#39;</span> <span class="o">%</span> <span class="n">org_name_type</span><span class="p">)(</span><span class="n">organism</span><span class="p">)</span>
+
+    <span class="k">if</span> <span class="n">_organism</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">organisms_allowed</span><span class="p">:</span>
+
+        <span class="n">msg</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="s1">&#39;Unknown organism: </span><span class="si">%s</span><span class="s1"> (</span><span class="si">%s</span><span class="s1">). Only human and mouse &#39;</span>
+            <span class="s1">&#39;are available.&#39;</span> <span class="o">%</span> <span class="p">(</span><span class="nb">str</span><span class="p">(</span><span class="n">_organism</span><span class="p">),</span> <span class="nb">str</span><span class="p">(</span><span class="n">organism</span><span class="p">))</span>
+        <span class="p">)</span>
+        <span class="n">_log</span><span class="p">(</span><span class="n">msg</span><span class="p">)</span>
+        <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="n">msg</span><span class="p">)</span>
+
+    <span class="k">if</span> <span class="n">org_name_type</span> <span class="o">==</span> <span class="s1">&#39;common&#39;</span><span class="p">:</span> <span class="n">_organism</span> <span class="o">=</span> <span class="n">_organism</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span>
+
+    <span class="n">url</span> <span class="o">=</span> <span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;cellinker_rescued&#39;</span><span class="p">][</span><span class="n">dataset</span><span class="p">]</span> <span class="o">%</span> <span class="n">_organism</span>
+    <span class="n">c</span> <span class="o">=</span> <span class="n">curl</span><span class="o">.</span><span class="n">Curl</span><span class="p">(</span><span class="n">url</span><span class="p">,</span> <span class="n">large</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span> <span class="n">silent</span> <span class="o">=</span> <span class="kc">False</span><span class="p">)</span>
+
+    <span class="n">result</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="n">csv</span><span class="o">.</span><span class="n">DictReader</span><span class="p">(</span><span class="n">c</span><span class="o">.</span><span class="n">result</span><span class="p">,</span> <span class="n">delimiter</span> <span class="o">=</span> <span class="s1">&#39;</span><span class="se">\t</span><span class="s1">&#39;</span><span class="p">))</span>
+
+    <span class="k">return</span> <span class="n">result</span>
+
+
+<div class="viewcode-block" id="cellinker_lr_interactions">
+<a class="viewcode-back" href="../../../api/pypath.inputs.cellinker.cellinker_lr_interactions.html#pypath.inputs.cellinker.cellinker_lr_interactions">[docs]</a>
+<span class="k">def</span> <span class="nf">cellinker_lr_interactions</span><span class="p">(</span><span class="n">organism</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">):</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Ligand-receptor interactions from the Cellinker database</span>
+<span class="sd">    (http://www.rna-society.org/cellinker/).</span>
+
+<span class="sd">    Args</span>
+<span class="sd">        organism (int,str): Name or identifier of the organism. Only mouse</span>
+<span class="sd">            and human are available.</span>
+
+<span class="sd">    Returns</span>
+<span class="sd">        (set): A set of tuples, each representing a preprocessed Cellinker</span>
+<span class="sd">            interaction. The proteins are represented by their UniProt IDs,</span>
+<span class="sd">            while the protein complexes by `Complex` objects.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="n">db_names</span> <span class="o">=</span> <span class="p">{</span>
+        <span class="s1">&#39;IUPHAR&#39;</span><span class="p">:</span> <span class="s1">&#39;Guide2Pharma&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;CellphoneDB&#39;</span><span class="p">:</span> <span class="s1">&#39;CellPhoneDB&#39;</span><span class="p">,</span>
+    <span class="p">}</span>
+
+    <span class="n">result</span> <span class="o">=</span> <span class="nb">set</span><span class="p">()</span>
+
+    <span class="n">raw</span> <span class="o">=</span> <span class="n">cellinker_lr_interactions_raw</span><span class="p">(</span><span class="n">organism</span> <span class="o">=</span> <span class="n">organism</span><span class="p">)</span>
+    <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">taxonomy</span><span class="o">.</span><span class="n">ensure_ncbi_tax_id</span><span class="p">(</span><span class="n">organism</span><span class="p">)</span>
+    <span class="n">complexes</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">(</span>
+        <span class="p">(</span>
+            <span class="n">c</span><span class="o">.</span><span class="n">cellinker_id</span><span class="p">,</span>
+            <span class="n">components_to_complex</span><span class="p">(</span><span class="n">c</span><span class="o">.</span><span class="n">components</span><span class="p">,</span> <span class="n">organism</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">)</span>
+        <span class="p">)</span>
+        <span class="k">for</span> <span class="n">c</span> <span class="ow">in</span> <span class="n">cellinker_complexes_raw</span><span class="p">(</span><span class="n">organism</span> <span class="o">=</span> <span class="n">organism</span><span class="p">)</span>
+    <span class="p">)</span>
+
+    <span class="k">for</span> <span class="n">r</span> <span class="ow">in</span> <span class="n">raw</span><span class="p">:</span>
+
+        <span class="n">ligands</span> <span class="o">=</span> <span class="n">_cellinker_uniprots</span><span class="p">(</span>
+            <span class="n">r</span><span class="p">[</span><span class="s1">&#39;Ligand_symbol&#39;</span><span class="p">],</span>
+            <span class="n">r</span><span class="p">[</span><span class="s1">&#39;Ligand_id&#39;</span><span class="p">],</span>
+            <span class="n">ncbi_tax_id</span><span class="p">,</span>
+            <span class="n">complexes</span> <span class="o">=</span> <span class="n">complexes</span><span class="p">,</span>
+        <span class="p">)</span>
+        <span class="n">receptors</span> <span class="o">=</span> <span class="n">_cellinker_uniprots</span><span class="p">(</span>
+            <span class="n">r</span><span class="p">[</span><span class="s1">&#39;Receptor_symbol&#39;</span><span class="p">],</span>
+            <span class="n">r</span><span class="p">[</span><span class="s1">&#39;Receptor_id&#39;</span><span class="p">],</span>
+            <span class="n">ncbi_tax_id</span><span class="p">,</span>
+            <span class="n">complexes</span> <span class="o">=</span> <span class="n">complexes</span><span class="p">,</span>
+        <span class="p">)</span>
+
+        <span class="n">resources</span> <span class="o">=</span> <span class="s1">&#39;;&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span>
+            <span class="n">db_names</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="n">db</span><span class="p">,</span> <span class="n">db</span><span class="p">)</span>
+            <span class="k">for</span> <span class="n">db</span> <span class="ow">in</span> <span class="n">r</span><span class="p">[</span><span class="s1">&#39;Other.DB&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;;&#39;</span><span class="p">)</span>
+        <span class="p">)</span> <span class="ow">or</span> <span class="kc">None</span>
+
+        <span class="k">for</span> <span class="n">ligand</span><span class="p">,</span> <span class="n">receptor</span> <span class="ow">in</span> <span class="n">itertools</span><span class="o">.</span><span class="n">product</span><span class="p">(</span><span class="n">ligands</span><span class="p">,</span> <span class="n">receptors</span><span class="p">):</span>
+
+            <span class="n">result</span><span class="o">.</span><span class="n">add</span><span class="p">(</span>
+                <span class="n">CellinkerInteraction</span><span class="p">(</span>
+                    <span class="n">ligand</span> <span class="o">=</span> <span class="n">ligand</span><span class="p">,</span>
+                    <span class="n">receptor</span> <span class="o">=</span> <span class="n">receptor</span><span class="p">,</span>
+                    <span class="n">ligand_location</span> <span class="o">=</span> <span class="n">r</span><span class="p">[</span><span class="s1">&#39;Ligand_location&#39;</span><span class="p">],</span>
+                    <span class="c1"># yes, labels are not consistent</span>
+                    <span class="n">receptor_location</span> <span class="o">=</span> <span class="n">r</span><span class="p">[</span><span class="s1">&#39;Receptor.location&#39;</span><span class="p">],</span>
+                    <span class="n">resources</span> <span class="o">=</span> <span class="n">resources</span><span class="p">,</span>
+                    <span class="n">pmids</span> <span class="o">=</span> <span class="n">r</span><span class="p">[</span><span class="s1">&#39;Pmubmed.ID&#39;</span><span class="p">]</span> <span class="ow">or</span> <span class="kc">None</span><span class="p">,</span> <span class="c1"># typo</span>
+                    <span class="nb">type</span> <span class="o">=</span> <span class="n">r</span><span class="p">[</span><span class="s1">&#39;Type&#39;</span><span class="p">],</span>
+                <span class="p">)</span>
+            <span class="p">)</span>
+
+    <span class="k">return</span> <span class="n">result</span></div>
+
+
+
+<div class="viewcode-block" id="cellinker_smol_interactions">
+<a class="viewcode-back" href="../../../api/pypath.inputs.cellinker.cellinker_smol_interactions.html#pypath.inputs.cellinker.cellinker_smol_interactions">[docs]</a>
+<span class="k">def</span> <span class="nf">cellinker_smol_interactions</span><span class="p">(</span><span class="n">organism</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">):</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Small molecule ligand-protein receptor interactions from the Cellinker</span>
+<span class="sd">    database (http://www.rna-society.org/cellinker/).</span>
+
+<span class="sd">    Args</span>
+<span class="sd">        organism (int,str): Name or identifier of the organism. Only mouse</span>
+<span class="sd">            and human are available.</span>
+
+<span class="sd">    Returns</span>
+<span class="sd">        (set): A set of tuples, each representing a preprocessed Cellinker</span>
+<span class="sd">            interaction. The proteins are represented by their UniProt IDs,</span>
+<span class="sd">            the small molecules by PubChem CIDs, while the protein complexes</span>
+<span class="sd">            by `Complex` objects.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="n">db_names</span> <span class="o">=</span> <span class="p">{</span>
+        <span class="s1">&#39;IUPHAR&#39;</span><span class="p">:</span> <span class="s1">&#39;Guide2Pharma&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;CellphoneDB&#39;</span><span class="p">:</span> <span class="s1">&#39;CellPhoneDB&#39;</span><span class="p">,</span>
+    <span class="p">}</span>
+
+    <span class="n">result</span> <span class="o">=</span> <span class="nb">set</span><span class="p">()</span>
+
+    <span class="n">raw</span> <span class="o">=</span> <span class="n">cellinker_smol_interactions_raw</span><span class="p">(</span><span class="n">organism</span> <span class="o">=</span> <span class="n">organism</span><span class="p">)</span>
+    <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">taxonomy</span><span class="o">.</span><span class="n">ensure_ncbi_tax_id</span><span class="p">(</span><span class="n">organism</span><span class="p">)</span>
+    <span class="n">complexes</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">(</span>
+        <span class="p">(</span>
+            <span class="n">c</span><span class="o">.</span><span class="n">cellinker_id</span><span class="p">,</span>
+            <span class="n">components_to_complex</span><span class="p">(</span><span class="n">c</span><span class="o">.</span><span class="n">components</span><span class="p">,</span> <span class="n">organism</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">)</span>
+        <span class="p">)</span>
+        <span class="k">for</span> <span class="n">c</span> <span class="ow">in</span> <span class="n">cellinker_complexes_raw</span><span class="p">(</span><span class="n">organism</span> <span class="o">=</span> <span class="n">organism</span><span class="p">)</span>
+    <span class="p">)</span>
+
+    <span class="k">for</span> <span class="n">r</span> <span class="ow">in</span> <span class="n">raw</span><span class="p">:</span>
+
+        <span class="k">if</span> <span class="ow">not</span> <span class="n">r</span><span class="p">[</span><span class="s1">&#39;ligand_pubchem_cid&#39;</span><span class="p">]:</span>
+
+            <span class="k">continue</span>
+
+        <span class="n">ligands</span> <span class="o">=</span> <span class="p">(</span><span class="n">r</span><span class="p">[</span><span class="s1">&#39;ligand_pubchem_cid&#39;</span><span class="p">],)</span>
+
+        <span class="n">receptors</span> <span class="o">=</span> <span class="n">_cellinker_uniprots</span><span class="p">(</span>
+            <span class="n">r</span><span class="p">[</span><span class="s1">&#39;Receptor_symbol&#39;</span><span class="p">],</span>
+            <span class="n">r</span><span class="p">[</span><span class="s1">&#39;Receptor_id&#39;</span><span class="p">],</span>
+            <span class="n">ncbi_tax_id</span><span class="p">,</span>
+            <span class="n">complexes</span> <span class="o">=</span> <span class="n">complexes</span><span class="p">,</span>
+        <span class="p">)</span>
+
+        <span class="n">resources</span> <span class="o">=</span> <span class="s1">&#39;;&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span>
+            <span class="n">db_names</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="n">db</span><span class="p">,</span> <span class="n">db</span><span class="p">)</span>
+            <span class="k">for</span> <span class="n">db</span> <span class="ow">in</span> <span class="n">r</span><span class="p">[</span><span class="s1">&#39;Other.DB&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;;&#39;</span><span class="p">)</span>
+        <span class="p">)</span> <span class="ow">or</span> <span class="kc">None</span>
+
+        <span class="k">for</span> <span class="n">ligand</span><span class="p">,</span> <span class="n">receptor</span> <span class="ow">in</span> <span class="n">itertools</span><span class="o">.</span><span class="n">product</span><span class="p">(</span><span class="n">ligands</span><span class="p">,</span> <span class="n">receptors</span><span class="p">):</span>
+
+            <span class="n">result</span><span class="o">.</span><span class="n">add</span><span class="p">(</span>
+                <span class="n">CellinkerInteraction</span><span class="p">(</span>
+                    <span class="n">ligand</span> <span class="o">=</span> <span class="n">ligand</span><span class="p">,</span>
+                    <span class="n">receptor</span> <span class="o">=</span> <span class="n">receptor</span><span class="p">,</span>
+                    <span class="n">ligand_location</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+                    <span class="n">receptor_location</span> <span class="o">=</span> <span class="n">r</span><span class="p">[</span><span class="s1">&#39;Receptor_location&#39;</span><span class="p">],</span>
+                    <span class="n">resources</span> <span class="o">=</span> <span class="n">resources</span><span class="p">,</span>
+                    <span class="n">pmids</span> <span class="o">=</span> <span class="n">r</span><span class="p">[</span><span class="s1">&#39;pubmed_id&#39;</span><span class="p">]</span> <span class="ow">or</span> <span class="kc">None</span><span class="p">,</span>
+                    <span class="nb">type</span> <span class="o">=</span> <span class="n">r</span><span class="p">[</span><span class="s1">&#39;Type&#39;</span><span class="p">],</span>
+                <span class="p">)</span>
+            <span class="p">)</span>
+
+    <span class="k">return</span> <span class="n">result</span></div>
+
+
+
+<div class="viewcode-block" id="cellinker_annotations">
+<a class="viewcode-back" href="../../../api/pypath.inputs.cellinker.cellinker_annotations.html#pypath.inputs.cellinker.cellinker_annotations">[docs]</a>
+<span class="k">def</span> <span class="nf">cellinker_annotations</span><span class="p">(</span><span class="n">organism</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">,</span> <span class="n">entity_type</span> <span class="o">=</span> <span class="kc">None</span><span class="p">):</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Ligand and receptor annotations from the Cellinker database</span>
+<span class="sd">    (http://www.rna-society.org/cellinker/).</span>
+
+<span class="sd">    Args</span>
+<span class="sd">        organism (int,str): Name or identifier of the organism. Only mouse</span>
+<span class="sd">            and human are available.</span>
+<span class="sd">        entity_type (str): Either `protein` or `complex`. If `None`, both</span>
+<span class="sd">            proteins and protein complexes will be included.</span>
+
+<span class="sd">    Returns</span>
+<span class="sd">        (dict): A dict of sets of tuples, keys are UniProt IDs for proteins</span>
+<span class="sd">            and `Complex` objects for protein complexes. The tuples are</span>
+<span class="sd">            annotations with ligand or receptor role, localization and</span>
+<span class="sd">            type.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="n">CellinkerAnnotation</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">namedtuple</span><span class="p">(</span>
+        <span class="s1">&#39;CellinkerAnnotation&#39;</span><span class="p">,</span>
+        <span class="p">(</span>
+            <span class="s1">&#39;role&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;location&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;type&#39;</span><span class="p">,</span>
+        <span class="p">),</span>
+    <span class="p">)</span>
+
+    <span class="n">ia</span> <span class="o">=</span> <span class="n">cellinker_lr_interactions</span><span class="p">(</span><span class="n">organism</span> <span class="o">=</span> <span class="n">organism</span><span class="p">)</span>
+
+    <span class="n">result</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">defaultdict</span><span class="p">(</span><span class="nb">set</span><span class="p">)</span>
+
+    <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="n">ia</span><span class="p">:</span>
+
+        <span class="k">for</span> <span class="n">role</span> <span class="ow">in</span> <span class="p">(</span><span class="s1">&#39;ligand&#39;</span><span class="p">,</span> <span class="s1">&#39;receptor&#39;</span><span class="p">):</span>
+
+            <span class="n">this_entity</span> <span class="o">=</span> <span class="nb">getattr</span><span class="p">(</span><span class="n">i</span><span class="p">,</span> <span class="n">role</span><span class="p">)</span>
+            <span class="n">this_entity_type</span> <span class="o">=</span> <span class="n">entity</span><span class="o">.</span><span class="n">Entity</span><span class="o">.</span><span class="n">_get_entity_type</span><span class="p">(</span><span class="n">this_entity</span><span class="p">)</span>
+
+            <span class="k">if</span> <span class="ow">not</span> <span class="n">entity_type</span> <span class="ow">or</span> <span class="n">entity_type</span> <span class="o">==</span> <span class="n">this_entity_type</span><span class="p">:</span>
+
+                <span class="n">result</span><span class="p">[</span><span class="n">this_entity</span><span class="p">]</span><span class="o">.</span><span class="n">add</span><span class="p">(</span>
+                    <span class="n">CellinkerAnnotation</span><span class="p">(</span>
+                        <span class="n">role</span> <span class="o">=</span> <span class="n">role</span><span class="p">,</span>
+                        <span class="n">location</span> <span class="o">=</span> <span class="nb">getattr</span><span class="p">(</span><span class="n">i</span><span class="p">,</span> <span class="s1">&#39;</span><span class="si">%s</span><span class="s1">_location&#39;</span> <span class="o">%</span> <span class="n">role</span><span class="p">),</span>
+                        <span class="nb">type</span> <span class="o">=</span> <span class="n">i</span><span class="o">.</span><span class="n">type</span><span class="p">,</span>
+                    <span class="p">)</span>
+                <span class="p">)</span>
+
+    <span class="k">return</span> <span class="nb">dict</span><span class="p">(</span><span class="n">result</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="cellinker_protein_annotations">
+<a class="viewcode-back" href="../../../api/pypath.inputs.cellinker.cellinker_protein_annotations.html#pypath.inputs.cellinker.cellinker_protein_annotations">[docs]</a>
+<span class="k">def</span> <span class="nf">cellinker_protein_annotations</span><span class="p">(</span><span class="n">organism</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">):</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Ligand and receptor annotations from the Cellinker database</span>
+<span class="sd">    (http://www.rna-society.org/cellinker/).</span>
+
+<span class="sd">    Args</span>
+<span class="sd">        organism (int,str): Name or identifier of the organism. Only mouse</span>
+<span class="sd">            and human are available.</span>
+
+<span class="sd">    Returns</span>
+<span class="sd">        (dict): A dict of sets of tuples, keys are UniProt IDs. The tuples</span>
+<span class="sd">            are annotations with ligand or receptor role, localization and</span>
+<span class="sd">            type.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="k">return</span> <span class="n">cellinker_annotations</span><span class="p">(</span><span class="n">organism</span> <span class="o">=</span> <span class="n">organism</span><span class="p">,</span> <span class="n">entity_type</span> <span class="o">=</span> <span class="s1">&#39;protein&#39;</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="cellinker_complex_annotations">
+<a class="viewcode-back" href="../../../api/pypath.inputs.cellinker.cellinker_complex_annotations.html#pypath.inputs.cellinker.cellinker_complex_annotations">[docs]</a>
+<span class="k">def</span> <span class="nf">cellinker_complex_annotations</span><span class="p">(</span><span class="n">organism</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">):</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Ligand and receptor annotations from the Cellinker database</span>
+<span class="sd">    (http://www.rna-society.org/cellinker/).</span>
+
+<span class="sd">    Args</span>
+<span class="sd">        organism (int,str): Name or identifier of the organism. Only mouse</span>
+<span class="sd">            and human are available.</span>
+
+<span class="sd">    Returns</span>
+<span class="sd">        (dict): A dict of sets of tuples, keys are `Complex` objects.</span>
+<span class="sd">            The tuples are annotations with ligand or receptor role,</span>
+<span class="sd">            localization and type.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="k">return</span> <span class="n">cellinker_annotations</span><span class="p">(</span><span class="n">organism</span> <span class="o">=</span> <span class="n">organism</span><span class="p">,</span> <span class="n">entity_type</span> <span class="o">=</span> <span class="s1">&#39;complex&#39;</span><span class="p">)</span></div>
+
+
+
+<span class="k">def</span> <span class="nf">_cellinker_uniprots</span><span class="p">(</span><span class="n">gsymbol</span><span class="p">,</span> <span class="n">entrez</span><span class="p">,</span> <span class="n">ncbi_tax_id</span><span class="p">,</span> <span class="n">complexes</span> <span class="o">=</span> <span class="kc">None</span><span class="p">):</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Translates the Gene Symbols and Entrez Gene IDs to UniProt IDs.</span>
+
+<span class="sd">    Returns</span>
+<span class="sd">        (set): Set of UniProt IDs.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="k">return</span> <span class="p">(</span>
+        <span class="n">complexes</span><span class="p">[</span><span class="n">entrez</span><span class="p">]</span>
+            <span class="k">if</span> <span class="n">complexes</span> <span class="ow">and</span> <span class="n">entrez</span> <span class="ow">in</span> <span class="n">complexes</span> <span class="k">else</span>
+        <span class="p">(</span>
+            <span class="n">mapping</span><span class="o">.</span><span class="n">map_name</span><span class="p">(</span>
+                <span class="n">gsymbol</span><span class="p">,</span>
+                <span class="s1">&#39;genesymbol&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;uniprot&#39;</span><span class="p">,</span>
+                <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">,</span>
+            <span class="p">)</span> <span class="o">|</span>
+            <span class="n">mapping</span><span class="o">.</span><span class="n">map_name</span><span class="p">(</span>
+                <span class="n">entrez</span><span class="p">,</span>
+                <span class="s1">&#39;entrez&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;uniprot&#39;</span><span class="p">,</span>
+                <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">,</span>
+            <span class="p">)</span>
+        <span class="p">)</span>
+    <span class="p">)</span>
+</pre></div>
+
+                </article>
+              
+              
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diff --git a/_modules/pypath/inputs/cellphonedb.html b/_modules/pypath/inputs/cellphonedb.html
new file mode 100644
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@@ -0,0 +1,984 @@
+
+<!DOCTYPE html>
+
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+<html lang="en" data-content_root="../../../" >
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+                  
+  <h1>Source code for pypath.inputs.cellphonedb</h1><div class="highlight"><pre>
+<span></span><span class="ch">#!/usr/bin/env python</span>
+<span class="c1"># -*- coding: utf-8 -*-</span>
+
+<span class="c1">#</span>
+<span class="c1">#  This file is part of the `pypath` python module</span>
+<span class="c1">#</span>
+<span class="c1">#  Copyright 2014-2023</span>
+<span class="c1">#  EMBL, EMBL-EBI, Uniklinik RWTH Aachen, Heidelberg University</span>
+<span class="c1">#</span>
+<span class="c1">#  Authors: see the file `README.rst`</span>
+<span class="c1">#  Contact: Dénes Türei (turei.denes@gmail.com)</span>
+<span class="c1">#</span>
+<span class="c1">#  Distributed under the GPLv3 License.</span>
+<span class="c1">#  See accompanying file LICENSE.txt or copy at</span>
+<span class="c1">#      https://www.gnu.org/licenses/gpl-3.0.html</span>
+<span class="c1">#</span>
+<span class="c1">#  Website: https://pypath.omnipathdb.org/</span>
+<span class="c1">#</span>
+
+<span class="kn">from</span> <span class="nn">future.utils</span> <span class="kn">import</span> <span class="n">iteritems</span>
+<span class="kn">from</span> <span class="nn">past.builtins</span> <span class="kn">import</span> <span class="n">xrange</span><span class="p">,</span> <span class="nb">range</span>
+
+<span class="kn">import</span> <span class="nn">re</span>
+<span class="kn">import</span> <span class="nn">csv</span>
+<span class="kn">import</span> <span class="nn">collections</span>
+<span class="kn">import</span> <span class="nn">itertools</span>
+
+<span class="kn">import</span> <span class="nn">pypath.share.curl</span> <span class="k">as</span> <span class="nn">curl</span>
+<span class="kn">import</span> <span class="nn">pypath.resources.urls</span> <span class="k">as</span> <span class="nn">urls</span>
+<span class="kn">import</span> <span class="nn">pypath.utils.mapping</span> <span class="k">as</span> <span class="nn">mapping</span>
+<span class="kn">import</span> <span class="nn">pypath.internals.intera</span> <span class="k">as</span> <span class="nn">intera</span>
+<span class="kn">import</span> <span class="nn">pypath.share.common</span> <span class="k">as</span> <span class="nn">common</span>
+<span class="kn">import</span> <span class="nn">pypath.share.session</span> <span class="k">as</span> <span class="nn">session</span>
+<span class="kn">import</span> <span class="nn">pypath.inputs.uniprot_db</span> <span class="k">as</span> <span class="nn">uniprot_db</span>
+
+<span class="n">_logger</span> <span class="o">=</span> <span class="n">session</span><span class="o">.</span><span class="n">Logger</span><span class="p">(</span><span class="n">name</span> <span class="o">=</span> <span class="s1">&#39;cellphonedb_input&#39;</span><span class="p">)</span>
+<span class="n">_log</span> <span class="o">=</span> <span class="n">_logger</span><span class="o">.</span><span class="n">_log</span>
+
+<span class="n">CellPhoneDBAnnotation</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">namedtuple</span><span class="p">(</span>
+    <span class="s1">&#39;CellPhoneDBAnnotation&#39;</span><span class="p">,</span>
+    <span class="p">(</span>
+        <span class="s1">&#39;receptor&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;receptor_class&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;peripheral&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;secreted&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;secreted_class&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;transmembrane&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;integrin&#39;</span><span class="p">,</span>
+    <span class="p">)</span>
+<span class="p">)</span>
+
+
+<div class="viewcode-block" id="cellphonedb_ligands_receptors">
+<a class="viewcode-back" href="../../../api/pypath.inputs.cellphonedb.cellphonedb_ligands_receptors.html#pypath.inputs.cellphonedb.cellphonedb_ligands_receptors">[docs]</a>
+<span class="k">def</span> <span class="nf">cellphonedb_ligands_receptors</span><span class="p">():</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Retrieves the set of ligands and receptors from CellPhoneDB.</span>
+<span class="sd">    Returns tuple of sets.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="n">receptors</span> <span class="o">=</span> <span class="nb">set</span><span class="p">()</span>
+    <span class="n">ligands</span>   <span class="o">=</span> <span class="nb">set</span><span class="p">()</span>
+
+    <span class="n">proteins</span> <span class="o">=</span> <span class="n">cellphonedb_protein_annotations</span><span class="p">()</span>
+    <span class="n">complexes</span> <span class="o">=</span> <span class="n">cellphonedb_complex_annotations</span><span class="p">()</span>
+
+    <span class="k">for</span> <span class="n">_id</span><span class="p">,</span> <span class="n">annot</span> <span class="ow">in</span> <span class="n">itertools</span><span class="o">.</span><span class="n">chain</span><span class="p">(</span>
+        <span class="n">iteritems</span><span class="p">(</span><span class="n">proteins</span><span class="p">),</span>
+        <span class="n">iteritems</span><span class="p">(</span><span class="n">complexes</span><span class="p">)</span>
+    <span class="p">):</span>
+        <span class="k">if</span> <span class="n">annot</span><span class="o">.</span><span class="n">receptor</span><span class="p">:</span>
+            <span class="n">receptors</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">_id</span><span class="p">)</span>
+
+        <span class="k">if</span> <span class="n">annot</span><span class="o">.</span><span class="n">secreted</span> <span class="ow">or</span> <span class="p">(</span>
+            <span class="ow">not</span> <span class="n">annot</span><span class="o">.</span><span class="n">receptor</span> <span class="ow">and</span> <span class="p">(</span>
+                <span class="n">annot</span><span class="o">.</span><span class="n">transmembrane</span> <span class="ow">or</span>
+                <span class="n">annot</span><span class="o">.</span><span class="n">peripheral</span>
+            <span class="p">)</span>
+        <span class="p">):</span>
+            <span class="n">ligands</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">_id</span><span class="p">)</span>
+
+    <span class="k">return</span> <span class="n">ligands</span><span class="p">,</span> <span class="n">receptors</span></div>
+
+
+
+<span class="k">def</span> <span class="nf">_cellphonedb_annotations</span><span class="p">(</span><span class="n">url</span><span class="p">,</span> <span class="n">name_method</span><span class="p">):</span>
+
+    <span class="n">replacements</span> <span class="o">=</span> <span class="p">{</span>
+        <span class="s1">&#39;_add&#39;</span><span class="p">:</span> <span class="s1">&#39;&#39;</span><span class="p">,</span>
+        <span class="s1">&#39; | &#39;</span><span class="p">:</span> <span class="s1">&#39;,&#39;</span><span class="p">,</span>
+        <span class="s1">&#39; &#39;</span><span class="p">:</span> <span class="s1">&#39;_&#39;</span><span class="p">,</span>
+    <span class="p">}</span>
+
+    <span class="k">def</span> <span class="nf">get_bool</span><span class="p">(</span><span class="n">rec</span><span class="p">,</span> <span class="n">attr</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="n">attr</span> <span class="ow">in</span> <span class="n">rec</span> <span class="ow">and</span> <span class="n">rec</span><span class="p">[</span><span class="n">attr</span><span class="p">]</span><span class="o">.</span><span class="n">upper</span><span class="p">()</span> <span class="o">==</span> <span class="s1">&#39;TRUE&#39;</span>
+
+    <span class="k">def</span> <span class="nf">get_desc</span><span class="p">(</span><span class="n">rec</span><span class="p">,</span> <span class="n">attr</span><span class="p">):</span>
+
+        <span class="n">desc</span> <span class="o">=</span> <span class="s1">&#39;</span><span class="si">%s</span><span class="s1">_desc&#39;</span> <span class="o">%</span> <span class="n">attr</span>
+
+        <span class="n">value</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="s1">&#39;&#39;</span>
+                <span class="k">if</span> <span class="p">(</span>
+                    <span class="n">attr</span> <span class="ow">in</span> <span class="n">rec</span> <span class="ow">and</span> <span class="n">rec</span><span class="p">[</span><span class="n">attr</span><span class="p">]</span><span class="o">.</span><span class="n">upper</span><span class="p">()</span> <span class="o">==</span> <span class="s1">&#39;FALSE&#39;</span> <span class="ow">or</span>
+                    <span class="n">attr</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">rec</span> <span class="ow">and</span> <span class="ow">not</span> <span class="n">rec</span><span class="p">[</span><span class="n">desc</span><span class="p">]</span>
+                <span class="p">)</span> <span class="k">else</span>
+            <span class="n">rec</span><span class="p">[</span><span class="n">desc</span><span class="p">]</span>
+                <span class="k">if</span> <span class="n">rec</span><span class="p">[</span><span class="n">desc</span><span class="p">]</span> <span class="k">else</span>
+            <span class="n">attr</span>
+        <span class="p">)</span>
+
+        <span class="k">for</span> <span class="n">pattern</span><span class="p">,</span> <span class="n">repl</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="n">replacements</span><span class="p">):</span>
+
+            <span class="n">value</span> <span class="o">=</span> <span class="n">value</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="n">pattern</span><span class="p">,</span> <span class="n">repl</span><span class="p">)</span>
+
+        <span class="n">value</span> <span class="o">=</span> <span class="n">value</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;,&#39;</span><span class="p">)</span> <span class="k">if</span> <span class="n">value</span> <span class="k">else</span> <span class="kc">None</span>
+
+        <span class="k">return</span> <span class="nb">tuple</span><span class="p">(</span><span class="nb">sorted</span><span class="p">(</span><span class="n">common</span><span class="o">.</span><span class="n">to_set</span><span class="p">(</span><span class="n">value</span><span class="p">)))</span>
+
+    <span class="n">record</span> <span class="o">=</span> <span class="n">CellPhoneDBAnnotation</span>
+
+    <span class="n">annot</span> <span class="o">=</span> <span class="p">{}</span>
+
+    <span class="n">c</span> <span class="o">=</span> <span class="n">curl</span><span class="o">.</span><span class="n">Curl</span><span class="p">(</span><span class="n">url</span><span class="p">,</span> <span class="n">large</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span> <span class="n">silent</span> <span class="o">=</span> <span class="kc">False</span><span class="p">)</span>
+    <span class="n">tab</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="n">csv</span><span class="o">.</span><span class="n">DictReader</span><span class="p">(</span><span class="n">c</span><span class="o">.</span><span class="n">result</span><span class="p">))</span>
+
+    <span class="k">for</span> <span class="n">rec</span> <span class="ow">in</span> <span class="n">tab</span><span class="p">:</span>
+
+        <span class="n">names</span> <span class="o">=</span> <span class="n">name_method</span><span class="p">(</span><span class="n">rec</span><span class="p">)</span>
+
+        <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">names</span><span class="p">,</span> <span class="p">(</span><span class="nb">str</span><span class="p">,</span> <span class="n">intera</span><span class="o">.</span><span class="n">Complex</span><span class="p">)):</span>
+
+            <span class="n">names</span> <span class="o">=</span> <span class="p">(</span><span class="n">names</span><span class="p">,)</span>
+
+        <span class="k">for</span> <span class="n">name</span> <span class="ow">in</span> <span class="n">names</span><span class="p">:</span>
+
+            <span class="n">annot</span><span class="p">[</span><span class="n">name</span><span class="p">]</span> <span class="o">=</span> <span class="n">record</span><span class="p">(</span>
+                <span class="n">receptor</span> <span class="o">=</span> <span class="n">get_bool</span><span class="p">(</span><span class="n">rec</span><span class="p">,</span> <span class="s1">&#39;receptor&#39;</span><span class="p">),</span>
+                <span class="n">receptor_class</span> <span class="o">=</span> <span class="n">get_desc</span><span class="p">(</span><span class="n">rec</span><span class="p">,</span> <span class="s1">&#39;receptor&#39;</span><span class="p">),</span>
+                <span class="n">peripheral</span> <span class="o">=</span> <span class="n">get_bool</span><span class="p">(</span><span class="n">rec</span><span class="p">,</span> <span class="s1">&#39;peripheral&#39;</span><span class="p">),</span>
+                <span class="n">secreted</span> <span class="o">=</span> <span class="n">get_bool</span><span class="p">(</span><span class="n">rec</span><span class="p">,</span> <span class="s1">&#39;secreted&#39;</span><span class="p">),</span>
+                <span class="n">secreted_class</span> <span class="o">=</span> <span class="n">get_desc</span><span class="p">(</span><span class="n">rec</span><span class="p">,</span> <span class="s1">&#39;secreted&#39;</span><span class="p">),</span>
+                <span class="n">transmembrane</span> <span class="o">=</span> <span class="n">get_bool</span><span class="p">(</span><span class="n">rec</span><span class="p">,</span> <span class="s1">&#39;transmembrane&#39;</span><span class="p">),</span>
+                <span class="n">integrin</span> <span class="o">=</span> <span class="n">get_bool</span><span class="p">(</span><span class="n">rec</span><span class="p">,</span> <span class="s1">&#39;integrin&#39;</span><span class="p">),</span>
+            <span class="p">)</span>
+
+    <span class="k">return</span> <span class="n">annot</span>
+
+
+<div class="viewcode-block" id="cellphonedb_protein_annotations">
+<a class="viewcode-back" href="../../../api/pypath.inputs.cellphonedb.cellphonedb_protein_annotations.html#pypath.inputs.cellphonedb.cellphonedb_protein_annotations">[docs]</a>
+<span class="k">def</span> <span class="nf">cellphonedb_protein_annotations</span><span class="p">(</span><span class="n">add_complex_annotations</span> <span class="o">=</span> <span class="kc">False</span><span class="p">):</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    :arg bool add_complex_annotations:</span>
+<span class="sd">        Deprecated because results wrong annotations.</span>
+<span class="sd">        Copy the annotations of complexes to each of their member proteins.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="k">def</span> <span class="nf">name_method</span><span class="p">(</span><span class="n">rec</span><span class="p">):</span>
+        <span class="n">uniprot</span> <span class="o">=</span> <span class="n">rec</span><span class="p">[</span><span class="s1">&#39;uniprot&#39;</span><span class="p">]</span>
+        <span class="n">uniprot</span> <span class="o">=</span> <span class="n">_cellphonedb_hla</span><span class="p">(</span><span class="n">uniprot</span><span class="p">)</span>
+        <span class="n">uniprot</span> <span class="o">=</span> <span class="n">mapping</span><span class="o">.</span><span class="n">map_names</span><span class="p">(</span><span class="n">uniprot</span><span class="p">,</span> <span class="s1">&#39;uniprot&#39;</span><span class="p">,</span> <span class="s1">&#39;uniprot&#39;</span><span class="p">)</span>
+
+        <span class="k">return</span> <span class="n">uniprot</span>
+
+    <span class="n">protein_annotations</span> <span class="o">=</span> <span class="n">_cellphonedb_annotations</span><span class="p">(</span>
+        <span class="n">url</span> <span class="o">=</span> <span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;cellphonedb_git&#39;</span><span class="p">][</span><span class="s1">&#39;proteins&#39;</span><span class="p">],</span>
+        <span class="n">name_method</span> <span class="o">=</span> <span class="n">name_method</span><span class="p">,</span>
+    <span class="p">)</span>
+
+    <span class="k">return</span> <span class="n">protein_annotations</span></div>
+
+
+
+<span class="k">def</span> <span class="nf">_cellphonedb_hla</span><span class="p">(</span><span class="n">uniprot</span><span class="p">):</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Returns *set*.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="n">uniprots</span> <span class="o">=</span> <span class="kc">None</span>
+
+    <span class="c1"># for HLA genes in the uniprot column we have &quot;HLA...&quot; gene symbols</span>
+    <span class="c1"># but not always in the standard format (with dash)</span>
+    <span class="k">if</span> <span class="n">uniprot</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s1">&#39;HLA&#39;</span><span class="p">)</span> <span class="ow">and</span> <span class="s1">&#39;-&#39;</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">uniprot</span><span class="p">:</span>
+        <span class="n">genesymbol</span> <span class="o">=</span> <span class="s1">&#39;HLA-</span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="n">uniprot</span><span class="p">[</span><span class="mi">3</span><span class="p">:]</span>
+        <span class="n">uniprots</span> <span class="o">=</span> <span class="n">mapping</span><span class="o">.</span><span class="n">map_name</span><span class="p">(</span><span class="n">genesymbol</span><span class="p">,</span> <span class="s1">&#39;genesymbol&#39;</span><span class="p">,</span> <span class="s1">&#39;uniprot&#39;</span><span class="p">)</span>
+
+    <span class="k">return</span> <span class="n">uniprots</span> <span class="ow">or</span> <span class="p">{</span><span class="n">uniprot</span><span class="p">}</span>
+
+
+<div class="viewcode-block" id="cellphonedb_complex_annotations">
+<a class="viewcode-back" href="../../../api/pypath.inputs.cellphonedb.cellphonedb_complex_annotations.html#pypath.inputs.cellphonedb.cellphonedb_complex_annotations">[docs]</a>
+<span class="k">def</span> <span class="nf">cellphonedb_complex_annotations</span><span class="p">():</span>
+
+    <span class="k">def</span> <span class="nf">get_uniprots</span><span class="p">(</span><span class="n">rec</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="nb">tuple</span><span class="p">(</span>
+            <span class="n">uniprot</span>
+            <span class="k">for</span> <span class="n">uniprot</span> <span class="ow">in</span>
+            <span class="p">(</span><span class="n">rec</span><span class="p">[</span><span class="s1">&#39;uniprot_</span><span class="si">%u</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="n">i</span><span class="p">]</span> <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="n">xrange</span><span class="p">(</span><span class="mi">1</span><span class="p">,</span> <span class="mi">5</span><span class="p">))</span>
+            <span class="k">if</span> <span class="n">uniprot</span>
+        <span class="p">)</span>
+
+    <span class="k">def</span> <span class="nf">get_stoichiometry</span><span class="p">(</span><span class="n">rec</span><span class="p">):</span>
+
+        <span class="k">if</span> <span class="ow">not</span> <span class="n">rec</span><span class="p">[</span><span class="s1">&#39;stoichiometry&#39;</span><span class="p">]:</span>
+            <span class="k">return</span> <span class="n">get_uniprots</span><span class="p">(</span><span class="n">rec</span><span class="p">)</span>
+
+        <span class="k">return</span> <span class="nb">tuple</span><span class="p">(</span>
+            <span class="n">mapping</span><span class="o">.</span><span class="n">map_name0</span><span class="p">(</span><span class="n">genesymbol</span><span class="p">,</span> <span class="s1">&#39;genesymbol&#39;</span><span class="p">,</span> <span class="s1">&#39;uniprot&#39;</span><span class="p">)</span>
+            <span class="k">for</span> <span class="n">genesymbol</span> <span class="ow">in</span> <span class="n">rec</span><span class="p">[</span><span class="s1">&#39;stoichiometry&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;;&#39;</span><span class="p">)</span>
+        <span class="p">)</span>
+
+    <span class="k">def</span> <span class="nf">name_method</span><span class="p">(</span><span class="n">rec</span><span class="p">):</span>
+        <span class="n">comp</span> <span class="o">=</span> <span class="n">get_stoichiometry</span><span class="p">(</span><span class="n">rec</span><span class="p">)</span>
+
+        <span class="n">cplex</span> <span class="o">=</span> <span class="n">intera</span><span class="o">.</span><span class="n">Complex</span><span class="p">(</span>
+            <span class="n">name</span> <span class="o">=</span> <span class="n">rec</span><span class="p">[</span><span class="s1">&#39;complex_name&#39;</span><span class="p">],</span>
+            <span class="n">components</span> <span class="o">=</span> <span class="n">comp</span><span class="p">,</span>
+            <span class="n">sources</span> <span class="o">=</span> <span class="s1">&#39;CellPhoneDB&#39;</span><span class="p">,</span>
+            <span class="n">ids</span> <span class="o">=</span> <span class="n">rec</span><span class="p">[</span><span class="s1">&#39;complex_name&#39;</span><span class="p">],</span>
+        <span class="p">)</span>
+
+        <span class="k">return</span> <span class="n">cplex</span>
+
+    <span class="k">return</span> <span class="n">_cellphonedb_annotations</span><span class="p">(</span>
+        <span class="n">url</span> <span class="o">=</span> <span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;cellphonedb_git&#39;</span><span class="p">][</span><span class="s1">&#39;complexes&#39;</span><span class="p">],</span>
+        <span class="n">name_method</span> <span class="o">=</span> <span class="n">name_method</span><span class="p">,</span>
+    <span class="p">)</span></div>
+
+
+
+<span class="k">def</span> <span class="nf">_cellphonedb_get_entity</span><span class="p">(</span><span class="n">name</span><span class="p">,</span> <span class="n">complexes</span><span class="p">):</span>
+
+    <span class="k">if</span> <span class="n">name</span> <span class="ow">in</span> <span class="n">complexes</span><span class="p">:</span>
+        <span class="k">return</span> <span class="p">(</span><span class="n">complexes</span><span class="p">[</span><span class="n">name</span><span class="p">],)</span>
+
+    <span class="k">if</span> <span class="s1">&#39;_by&#39;</span> <span class="ow">in</span> <span class="n">name</span><span class="p">:</span>
+        <span class="n">_log</span><span class="p">(</span><span class="sa">f</span><span class="s1">&#39;Ignoring entity: `</span><span class="si">{</span><span class="n">name</span><span class="si">}</span><span class="s1">`.&#39;</span><span class="p">)</span>
+        <span class="k">return</span> <span class="p">()</span>
+
+    <span class="k">if</span> <span class="s1">&#39;:&#39;</span> <span class="ow">in</span> <span class="n">name</span><span class="p">:</span>
+        <span class="n">name</span> <span class="o">=</span> <span class="n">name</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;:&#39;</span><span class="p">)[</span><span class="mi">1</span><span class="p">]</span>
+
+    <span class="k">if</span> <span class="s1">&#39;_&#39;</span> <span class="ow">in</span> <span class="n">name</span><span class="p">:</span>
+        <span class="n">name</span> <span class="o">=</span> <span class="n">mapping</span><span class="o">.</span><span class="n">map_name0</span><span class="p">(</span><span class="n">name</span><span class="p">,</span> <span class="s1">&#39;name-entry&#39;</span><span class="p">,</span> <span class="s1">&#39;name&#39;</span><span class="p">)</span>
+
+    <span class="k">if</span> <span class="ow">not</span> <span class="n">uniprot_db</span><span class="o">.</span><span class="n">is_uniprot</span><span class="p">(</span><span class="n">name</span><span class="p">):</span>
+        <span class="n">uniprot</span> <span class="o">=</span> <span class="n">mapping</span><span class="o">.</span><span class="n">map_name0</span><span class="p">(</span><span class="n">name</span><span class="p">,</span> <span class="s1">&#39;genesymbol&#39;</span><span class="p">,</span> <span class="s1">&#39;uniprot&#39;</span><span class="p">)</span>
+        <span class="n">name</span> <span class="o">=</span> <span class="n">uniprot</span> <span class="ow">or</span> <span class="n">name</span>
+
+    <span class="n">name</span> <span class="o">=</span> <span class="n">_cellphonedb_hla</span><span class="p">(</span><span class="n">name</span><span class="p">)</span>
+
+    <span class="k">return</span> <span class="p">(</span><span class="n">name</span><span class="p">,)</span> <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">name</span><span class="p">,</span> <span class="nb">str</span><span class="p">)</span> <span class="k">else</span> <span class="n">name</span>
+
+
+<div class="viewcode-block" id="cellphonedb_interactions">
+<a class="viewcode-back" href="../../../api/pypath.inputs.cellphonedb.cellphonedb_interactions.html#pypath.inputs.cellphonedb.cellphonedb_interactions">[docs]</a>
+<span class="k">def</span> <span class="nf">cellphonedb_interactions</span><span class="p">():</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Interactions between ligands and receptors from CellPhoneDB.</span>
+
+<span class="sd">    Yields:</span>
+<span class="sd">        Named tuples representing interactions.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="k">def</span> <span class="nf">get_type</span><span class="p">(</span><span class="n">entity</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="p">(</span>
+            <span class="s1">&#39;ligand&#39;</span>
+                <span class="k">if</span> <span class="n">entity</span> <span class="ow">in</span> <span class="n">ligands</span> <span class="k">else</span>
+            <span class="s1">&#39;receptor&#39;</span>
+                <span class="k">if</span> <span class="n">entity</span> <span class="ow">in</span> <span class="n">receptors</span> <span class="k">else</span>
+            <span class="s1">&#39;unknown&#39;</span>
+        <span class="p">)</span>
+
+    <span class="k">def</span> <span class="nf">get_bool</span><span class="p">(</span><span class="n">rec</span><span class="p">,</span> <span class="n">attr</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="n">attr</span> <span class="ow">in</span> <span class="n">rec</span> <span class="ow">and</span> <span class="n">rec</span><span class="p">[</span><span class="n">attr</span><span class="p">]</span><span class="o">.</span><span class="n">upper</span><span class="p">()</span> <span class="o">==</span> <span class="s1">&#39;TRUE&#39;</span>
+
+    <span class="n">CellphonedbInteraction</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">namedtuple</span><span class="p">(</span>
+        <span class="s1">&#39;CellphonedbInteraction&#39;</span><span class="p">,</span>
+        <span class="p">[</span>
+            <span class="s1">&#39;id_a&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;id_b&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;sources&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;references&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;interaction_type&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;type_a&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;type_b&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;is_ppi&#39;</span><span class="p">,</span>
+        <span class="p">]</span>
+    <span class="p">)</span>
+
+    <span class="n">repmid</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">compile</span><span class="p">(</span><span class="sa">r</span><span class="s1">&#39;PMID: ([0-9]+)&#39;</span><span class="p">)</span>
+    <span class="n">recomma</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">compile</span><span class="p">(</span><span class="sa">r</span><span class="s1">&#39;[,;]&#39;</span><span class="p">)</span>
+
+    <span class="n">ligands</span><span class="p">,</span> <span class="n">receptors</span> <span class="o">=</span> <span class="n">cellphonedb_ligands_receptors</span><span class="p">()</span>
+    <span class="n">complexes</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">(</span>
+        <span class="p">(</span>
+            <span class="n">_id</span><span class="p">,</span>
+            <span class="n">cplex</span>
+        <span class="p">)</span>
+        <span class="k">for</span> <span class="n">cplex</span> <span class="ow">in</span> <span class="n">cellphonedb_complexes</span><span class="p">()</span><span class="o">.</span><span class="n">values</span><span class="p">()</span>
+        <span class="k">for</span> <span class="n">_id</span> <span class="ow">in</span> <span class="n">cplex</span><span class="o">.</span><span class="n">ids</span><span class="p">[</span><span class="s1">&#39;CellPhoneDB&#39;</span><span class="p">]</span>
+    <span class="p">)</span>
+
+    <span class="n">url</span> <span class="o">=</span> <span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;cellphonedb_git&#39;</span><span class="p">][</span><span class="s1">&#39;interactions&#39;</span><span class="p">]</span>
+    <span class="n">c</span> <span class="o">=</span> <span class="n">curl</span><span class="o">.</span><span class="n">Curl</span><span class="p">(</span><span class="n">url</span><span class="p">,</span> <span class="n">silent</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span> <span class="n">large</span> <span class="o">=</span> <span class="kc">True</span><span class="p">)</span>
+    <span class="n">reader</span> <span class="o">=</span> <span class="n">csv</span><span class="o">.</span><span class="n">DictReader</span><span class="p">(</span><span class="n">c</span><span class="o">.</span><span class="n">result</span><span class="p">)</span>
+
+    <span class="k">for</span> <span class="n">rec</span> <span class="ow">in</span> <span class="n">reader</span><span class="p">:</span>
+
+        <span class="n">_partner_a</span> <span class="o">=</span> <span class="n">_cellphonedb_get_entity</span><span class="p">(</span>
+            <span class="n">rec</span><span class="p">[</span><span class="s1">&#39;partner_a&#39;</span><span class="p">],</span>
+            <span class="n">complexes</span> <span class="o">=</span> <span class="n">complexes</span><span class="p">,</span>
+        <span class="p">)</span>
+        <span class="n">_partner_b</span> <span class="o">=</span> <span class="n">_cellphonedb_get_entity</span><span class="p">(</span>
+            <span class="n">rec</span><span class="p">[</span><span class="s1">&#39;partner_b&#39;</span><span class="p">],</span>
+            <span class="n">complexes</span> <span class="o">=</span> <span class="n">complexes</span><span class="p">,</span>
+        <span class="p">)</span>
+        <span class="n">_is_ppi</span> <span class="o">=</span> <span class="n">get_bool</span><span class="p">(</span><span class="n">rec</span><span class="p">,</span> <span class="s1">&#39;is_ppi&#39;</span><span class="p">)</span>
+
+        <span class="k">for</span> <span class="n">partner_a</span><span class="p">,</span> <span class="n">partner_b</span> <span class="ow">in</span> <span class="n">itertools</span><span class="o">.</span><span class="n">product</span><span class="p">(</span><span class="n">_partner_a</span><span class="p">,</span> <span class="n">_partner_b</span><span class="p">):</span>
+
+            <span class="n">type_a</span> <span class="o">=</span> <span class="n">get_type</span><span class="p">(</span><span class="n">partner_a</span><span class="p">)</span>
+            <span class="n">type_b</span> <span class="o">=</span> <span class="n">get_type</span><span class="p">(</span><span class="n">partner_b</span><span class="p">)</span>
+            <span class="n">rev</span> <span class="o">=</span> <span class="n">type_b</span> <span class="o">==</span> <span class="s1">&#39;ligand&#39;</span> <span class="ow">and</span> <span class="n">type_a</span> <span class="o">==</span> <span class="s1">&#39;receptor&#39;</span>
+            <span class="n">_type_a</span> <span class="o">=</span> <span class="n">type_b</span> <span class="k">if</span> <span class="n">rev</span> <span class="k">else</span> <span class="n">type_a</span>
+            <span class="n">_type_b</span> <span class="o">=</span> <span class="n">type_a</span> <span class="k">if</span> <span class="n">rev</span> <span class="k">else</span> <span class="n">type_b</span>
+
+            <span class="n">sources</span> <span class="o">=</span> <span class="p">(</span>
+                <span class="s1">&#39;CellPhoneDB&#39;</span>
+                    <span class="k">if</span> <span class="n">rec</span><span class="p">[</span><span class="s1">&#39;annotation_strategy&#39;</span><span class="p">]</span> <span class="o">==</span> <span class="s1">&#39;curated&#39;</span> <span class="k">else</span>
+                <span class="s1">&#39;</span><span class="si">%s</span><span class="s1">;CellPhoneDB&#39;</span> <span class="o">%</span> <span class="p">(</span>
+                    <span class="s1">&#39;;&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span>
+                        <span class="n">recomma</span><span class="o">.</span><span class="n">split</span><span class="p">(</span>
+                            <span class="n">rec</span><span class="p">[</span><span class="s1">&#39;annotation_strategy&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span>
+                                <span class="s1">&#39;guidetopharmacology.org&#39;</span><span class="p">,</span>
+                                <span class="s1">&#39;Guide2Pharma&#39;</span>
+                            <span class="p">)</span>
+                        <span class="p">)</span>
+                    <span class="p">)</span>
+                <span class="p">)</span>
+            <span class="p">)</span>
+            <span class="n">refs</span>   <span class="o">=</span> <span class="s1">&#39;;&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">repmid</span><span class="o">.</span><span class="n">findall</span><span class="p">(</span><span class="n">rec</span><span class="p">[</span><span class="s1">&#39;source&#39;</span><span class="p">]))</span>
+
+            <span class="k">yield</span> <span class="p">(</span>
+                <span class="n">CellphonedbInteraction</span><span class="p">(</span>
+                    <span class="n">id_a</span> <span class="o">=</span> <span class="n">partner_b</span> <span class="k">if</span> <span class="n">rev</span> <span class="k">else</span> <span class="n">partner_a</span><span class="p">,</span>
+                    <span class="n">id_b</span> <span class="o">=</span> <span class="n">partner_a</span> <span class="k">if</span> <span class="n">rev</span> <span class="k">else</span> <span class="n">partner_b</span><span class="p">,</span>
+                    <span class="n">sources</span> <span class="o">=</span> <span class="n">sources</span><span class="p">,</span>
+                    <span class="n">references</span> <span class="o">=</span> <span class="n">refs</span><span class="p">,</span>
+                    <span class="n">interaction_type</span> <span class="o">=</span> <span class="s1">&#39;</span><span class="si">%s</span><span class="s1">-</span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="p">(</span><span class="n">_type_a</span><span class="p">,</span> <span class="n">_type_b</span><span class="p">),</span>
+                    <span class="n">type_a</span> <span class="o">=</span> <span class="n">_type_a</span><span class="p">,</span>
+                    <span class="n">type_b</span> <span class="o">=</span> <span class="n">_type_b</span><span class="p">,</span>
+                    <span class="n">is_ppi</span> <span class="o">=</span> <span class="n">_is_ppi</span><span class="p">,</span>
+                <span class="p">)</span>
+            <span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="cellphonedb_complexes">
+<a class="viewcode-back" href="../../../api/pypath.inputs.cellphonedb.cellphonedb_complexes.html#pypath.inputs.cellphonedb.cellphonedb_complexes">[docs]</a>
+<span class="k">def</span> <span class="nf">cellphonedb_complexes</span><span class="p">():</span>
+
+    <span class="n">annot</span> <span class="o">=</span> <span class="n">cellphonedb_complex_annotations</span><span class="p">()</span>
+
+    <span class="n">complexes</span> <span class="o">=</span> <span class="p">{}</span>
+
+    <span class="k">for</span> <span class="n">cplex</span> <span class="ow">in</span> <span class="n">annot</span><span class="o">.</span><span class="n">keys</span><span class="p">():</span>
+        <span class="n">key</span> <span class="o">=</span> <span class="n">cplex</span><span class="o">.</span><span class="fm">__str__</span><span class="p">()</span>
+
+        <span class="k">if</span> <span class="n">key</span> <span class="ow">in</span> <span class="n">annot</span><span class="p">:</span>
+            <span class="n">cplex</span><span class="o">.</span><span class="n">add_attr</span><span class="p">(</span><span class="s1">&#39;CellPhoneDB&#39;</span><span class="p">,</span> <span class="n">annot</span><span class="p">[</span><span class="n">key</span><span class="p">])</span>
+
+        <span class="n">complexes</span><span class="p">[</span><span class="n">key</span><span class="p">]</span> <span class="o">=</span> <span class="n">cplex</span>
+
+    <span class="k">return</span> <span class="n">complexes</span></div>
+
+</pre></div>
+
+                </article>
+              
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+  <h1>Source code for pypath.inputs.celltalkdb</h1><div class="highlight"><pre>
+<span></span><span class="ch">#!/usr/bin/env python</span>
+<span class="c1"># -*- coding: utf-8 -*-</span>
+
+<span class="c1">#</span>
+<span class="c1">#  This file is part of the `pypath` python module</span>
+<span class="c1">#</span>
+<span class="c1">#  Copyright 2014-2023</span>
+<span class="c1">#  EMBL, EMBL-EBI, Uniklinik RWTH Aachen, Heidelberg University</span>
+<span class="c1">#</span>
+<span class="c1">#  Authors: see the file `README.rst`</span>
+<span class="c1">#  Contact: Dénes Türei (turei.denes@gmail.com)</span>
+<span class="c1">#</span>
+<span class="c1">#  Distributed under the GPLv3 License.</span>
+<span class="c1">#  See accompanying file LICENSE.txt or copy at</span>
+<span class="c1">#      https://www.gnu.org/licenses/gpl-3.0.html</span>
+<span class="c1">#</span>
+<span class="c1">#  Website: https://pypath.omnipathdb.org/</span>
+<span class="c1">#</span>
+
+<span class="kn">import</span> <span class="nn">os</span>
+<span class="kn">import</span> <span class="nn">datetime</span>
+<span class="kn">import</span> <span class="nn">collections</span>
+
+<span class="kn">import</span> <span class="nn">bs4</span>
+
+<span class="kn">import</span> <span class="nn">pypath.resources.urls</span> <span class="k">as</span> <span class="nn">urls</span>
+<span class="kn">import</span> <span class="nn">pypath.share.curl</span> <span class="k">as</span> <span class="nn">curl</span>
+<span class="kn">import</span> <span class="nn">pypath.share.cache</span> <span class="k">as</span> <span class="nn">cache</span>
+<span class="kn">import</span> <span class="nn">pypath.utils.taxonomy</span> <span class="k">as</span> <span class="nn">taxonomy</span>
+<span class="kn">import</span> <span class="nn">pypath.utils.mapping</span> <span class="k">as</span> <span class="nn">mapping</span>
+
+
+<div class="viewcode-block" id="celltalkdb_download">
+<a class="viewcode-back" href="../../../api/pypath.inputs.celltalkdb.celltalkdb_download.html#pypath.inputs.celltalkdb.celltalkdb_download">[docs]</a>
+<span class="k">def</span> <span class="nf">celltalkdb_download</span><span class="p">(</span><span class="n">filename</span> <span class="o">=</span> <span class="s1">&#39;lr_pair&#39;</span><span class="p">,</span> <span class="n">organism</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">):</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Downloads a file from CellTalkDB.</span>
+
+<span class="sd">    :param str filename:</span>
+<span class="sd">        The file name of the dataset to download. Possible values:</span>
+<span class="sd">        lr_pair, gene_info, gene2ensembl, uniprot.</span>
+<span class="sd">    :param int,str organism:</span>
+<span class="sd">        Human and mouse supported, in case of incomprehensible value will</span>
+<span class="sd">        fall back to human.</span>
+
+<span class="sd">    :return:</span>
+<span class="sd">        Generator yielding dataset specific records as named tuples.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="n">taxid</span> <span class="o">=</span> <span class="n">taxonomy</span><span class="o">.</span><span class="n">ensure_common_name</span><span class="p">(</span><span class="n">organism</span><span class="p">)</span>
+    <span class="n">organism</span> <span class="o">=</span> <span class="n">taxid</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span> <span class="k">if</span> <span class="n">taxid</span> <span class="ow">in</span> <span class="p">{</span><span class="s1">&#39;Mouse&#39;</span><span class="p">,</span> <span class="s1">&#39;Human&#39;</span><span class="p">}</span> <span class="k">else</span> <span class="s1">&#39;human&#39;</span>
+
+    <span class="n">cache_fname</span> <span class="o">=</span> <span class="s1">&#39;celltalkdb_</span><span class="si">%s</span><span class="s1">_</span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="p">(</span><span class="n">organism</span><span class="p">,</span> <span class="n">filename</span><span class="p">)</span>
+    <span class="n">cache_path</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">cache</span><span class="o">.</span><span class="n">get_cachedir</span><span class="p">(),</span> <span class="n">cache_fname</span><span class="p">)</span>
+
+    <span class="k">if</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">exists</span><span class="p">(</span><span class="n">cache_path</span><span class="p">):</span>
+
+        <span class="n">result</span> <span class="o">=</span> <span class="n">curl</span><span class="o">.</span><span class="n">FileOpener</span><span class="p">(</span><span class="n">cache_path</span><span class="p">)</span><span class="o">.</span><span class="n">result</span>
+
+    <span class="k">else</span><span class="p">:</span>
+
+        <span class="n">url</span> <span class="o">=</span> <span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;celltalkdb&#39;</span><span class="p">][</span><span class="s1">&#39;url&#39;</span><span class="p">]</span>
+        <span class="n">ref_url</span> <span class="o">=</span> <span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;celltalkdb&#39;</span><span class="p">][</span><span class="s1">&#39;ref_url&#39;</span><span class="p">]</span>
+        <span class="n">init_url</span> <span class="o">=</span> <span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;celltalkdb&#39;</span><span class="p">][</span><span class="s1">&#39;init_url&#39;</span><span class="p">]</span>
+
+        <span class="n">cookie</span> <span class="o">=</span> <span class="s1">&#39;&#39;</span>
+
+        <span class="n">c_init</span> <span class="o">=</span> <span class="n">curl</span><span class="o">.</span><span class="n">Curl</span><span class="p">(</span>
+            <span class="n">init_url</span><span class="p">,</span>
+            <span class="n">silent</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
+            <span class="n">large</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
+            <span class="n">cache</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+            <span class="n">follow</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+            <span class="n">bypass_url_encoding</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
+            <span class="n">retries</span> <span class="o">=</span> <span class="mi">1</span><span class="p">,</span>
+            <span class="n">empty_attempt_again</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+        <span class="p">)</span>
+
+        <span class="k">for</span> <span class="n">h</span> <span class="ow">in</span> <span class="n">c_init</span><span class="o">.</span><span class="n">resp_headers</span><span class="p">:</span>
+
+            <span class="k">if</span> <span class="n">h</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="sa">b</span><span class="s1">&#39;set-cookie&#39;</span><span class="p">):</span>
+
+                <span class="n">cookie</span> <span class="o">=</span> <span class="n">h</span><span class="o">.</span><span class="n">decode</span><span class="p">()</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;:&#39;</span><span class="p">)[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;;&#39;</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span>
+
+        <span class="n">soup</span> <span class="o">=</span> <span class="n">bs4</span><span class="o">.</span><span class="n">BeautifulSoup</span><span class="p">(</span><span class="n">c_init</span><span class="o">.</span><span class="n">fileobj</span><span class="p">,</span> <span class="s1">&#39;html.parser&#39;</span><span class="p">)</span>
+        <span class="n">form</span> <span class="o">=</span> <span class="n">soup</span><span class="o">.</span><span class="n">find</span><span class="p">(</span><span class="s1">&#39;form&#39;</span><span class="p">,</span> <span class="p">{</span><span class="s1">&#39;action&#39;</span><span class="p">:</span> <span class="s1">&#39;handler/download.php&#39;</span><span class="p">})</span>
+        <span class="n">inputs</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">(</span>
+            <span class="p">(</span>
+                <span class="n">field</span><span class="o">.</span><span class="n">attrs</span><span class="p">[</span><span class="s1">&#39;name&#39;</span><span class="p">],</span>
+                <span class="n">field</span><span class="o">.</span><span class="n">attrs</span><span class="p">[</span><span class="s1">&#39;value&#39;</span><span class="p">]</span>
+            <span class="p">)</span>
+            <span class="k">for</span> <span class="n">field</span> <span class="ow">in</span> <span class="n">form</span><span class="o">.</span><span class="n">find_all</span><span class="p">(</span><span class="s1">&#39;input&#39;</span><span class="p">)</span>
+        <span class="p">)</span>
+
+        <span class="n">inputs</span><span class="p">[</span><span class="s1">&#39;ref&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">ref_url</span>
+        <span class="n">inputs</span><span class="p">[</span><span class="s1">&#39;filename&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="s1">&#39;</span><span class="si">%s</span><span class="s1">_</span><span class="si">%s</span><span class="s1">.txt&#39;</span> <span class="o">%</span> <span class="p">(</span><span class="n">organism</span><span class="p">,</span> <span class="n">filename</span><span class="p">)</span>
+
+        <span class="n">c</span> <span class="o">=</span> <span class="n">curl</span><span class="o">.</span><span class="n">Curl</span><span class="p">(</span>
+            <span class="n">url</span> <span class="o">=</span> <span class="n">url</span><span class="p">,</span>
+            <span class="n">cache</span> <span class="o">=</span> <span class="n">cache_path</span><span class="p">,</span>
+            <span class="n">post</span> <span class="o">=</span> <span class="n">inputs</span><span class="p">,</span>
+            <span class="n">silent</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+            <span class="n">large</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
+            <span class="n">req_headers</span> <span class="o">=</span> <span class="p">[</span>
+                <span class="s1">&#39;Cookie: </span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="n">cookie</span><span class="p">,</span>
+                <span class="s1">&#39;Referer: http://tcm.zju.edu.cn/celltalkdb/download.php&#39;</span><span class="p">,</span>
+            <span class="p">],</span>
+        <span class="p">)</span>
+
+        <span class="n">result</span> <span class="o">=</span> <span class="n">c</span><span class="o">.</span><span class="n">result</span>
+
+    <span class="n">header</span> <span class="o">=</span> <span class="nb">next</span><span class="p">(</span><span class="n">result</span><span class="p">)</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\t</span><span class="s1">&#39;</span><span class="p">)</span>
+
+    <span class="n">record</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">namedtuple</span><span class="p">(</span><span class="s1">&#39;CellTalkDbRecord&#39;</span><span class="p">,</span> <span class="n">header</span><span class="p">)</span>
+
+    <span class="k">for</span> <span class="n">values</span> <span class="ow">in</span> <span class="n">result</span><span class="p">:</span>
+
+        <span class="k">yield</span> <span class="n">record</span><span class="p">(</span><span class="o">*</span><span class="n">values</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\t</span><span class="s1">&#39;</span><span class="p">))</span></div>
+
+
+
+<div class="viewcode-block" id="celltalkdb_interactions">
+<a class="viewcode-back" href="../../../api/pypath.inputs.celltalkdb.celltalkdb_interactions.html#pypath.inputs.celltalkdb.celltalkdb_interactions">[docs]</a>
+<span class="k">def</span> <span class="nf">celltalkdb_interactions</span><span class="p">(</span><span class="n">organism</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">):</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Retrieves ligand-receptor interactions from CellTalkDB</span>
+<span class="sd">    http://tcm.zju.edu.cn/celltalkdb/index.php</span>
+
+<span class="sd">    :param int,str organism:</span>
+<span class="sd">        Human and mouse supported, in case of incomprehensible value will</span>
+<span class="sd">        fall back to human.</span>
+
+<span class="sd">    :return:</span>
+<span class="sd">        List of interactions as named tuples.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="n">CellTalkDBInteraction</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">namedtuple</span><span class="p">(</span>
+        <span class="s1">&#39;CellTalkDBInteraction&#39;</span><span class="p">,</span>
+        <span class="p">[</span>
+            <span class="s1">&#39;ligand_genesymbol&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;receptor_genesymbol&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;reference&#39;</span><span class="p">,</span>
+        <span class="p">]</span>
+    <span class="p">)</span>
+
+    <span class="k">return</span> <span class="p">[</span>
+        <span class="n">CellTalkDBInteraction</span><span class="p">(</span>
+            <span class="n">ligand_genesymbol</span> <span class="o">=</span> <span class="n">rec</span><span class="o">.</span><span class="n">ligand_gene_symbol</span><span class="p">,</span>
+            <span class="n">receptor_genesymbol</span> <span class="o">=</span> <span class="n">rec</span><span class="o">.</span><span class="n">receptor_gene_symbol</span><span class="p">,</span>
+            <span class="n">reference</span> <span class="o">=</span> <span class="n">rec</span><span class="o">.</span><span class="n">evidence</span><span class="p">,</span>
+        <span class="p">)</span>
+        <span class="k">for</span> <span class="n">rec</span> <span class="ow">in</span> <span class="n">celltalkdb_download</span><span class="p">(</span><span class="n">organism</span> <span class="o">=</span> <span class="n">organism</span><span class="p">)</span>
+    <span class="p">]</span></div>
+
+
+
+<div class="viewcode-block" id="celltalkdb_annotations">
+<a class="viewcode-back" href="../../../api/pypath.inputs.celltalkdb.celltalkdb_annotations.html#pypath.inputs.celltalkdb.celltalkdb_annotations">[docs]</a>
+<span class="k">def</span> <span class="nf">celltalkdb_annotations</span><span class="p">(</span><span class="n">organism</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">):</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Retrieves annotation of protein ligand and receptor roles from CellTalkDB</span>
+<span class="sd">    http://tcm.zju.edu.cn/celltalkdb/index.php</span>
+
+<span class="sd">    :param int,str organism:</span>
+<span class="sd">        Human and mouse supported, in case of incomprehensible value will</span>
+<span class="sd">        fall back to human.</span>
+
+<span class="sd">    :return:</span>
+<span class="sd">        Dictionary of annotations with UniProt IDs as keys.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="n">CellTalkDBAnnotation</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">namedtuple</span><span class="p">(</span>
+        <span class="s1">&#39;CellTalkDBAnnotation&#39;</span><span class="p">,</span>
+        <span class="p">[</span>
+            <span class="s1">&#39;role&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;pmid&#39;</span><span class="p">,</span>
+        <span class="p">]</span>
+    <span class="p">)</span>
+
+    <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">taxonomy</span><span class="o">.</span><span class="n">ensure_ncbi_tax_id</span><span class="p">(</span><span class="n">organism</span><span class="p">)</span>
+    <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span> <span class="k">if</span> <span class="n">ncbi_tax_id</span> <span class="ow">in</span> <span class="p">{</span><span class="mi">9606</span><span class="p">,</span> <span class="mi">10090</span><span class="p">}</span> <span class="k">else</span> <span class="mi">9606</span>
+
+    <span class="n">annot</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">defaultdict</span><span class="p">(</span><span class="nb">set</span><span class="p">)</span>
+
+    <span class="k">for</span> <span class="n">rec</span> <span class="ow">in</span> <span class="n">celltalkdb_download</span><span class="p">(</span><span class="n">organism</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">):</span>
+
+        <span class="k">for</span> <span class="n">role</span> <span class="ow">in</span> <span class="p">(</span><span class="s1">&#39;ligand&#39;</span><span class="p">,</span> <span class="s1">&#39;receptor&#39;</span><span class="p">):</span>
+
+            <span class="n">uniprots</span> <span class="o">=</span> <span class="n">mapping</span><span class="o">.</span><span class="n">map_name</span><span class="p">(</span>
+                <span class="nb">getattr</span><span class="p">(</span><span class="n">rec</span><span class="p">,</span> <span class="s1">&#39;</span><span class="si">%s</span><span class="s1">_gene_symbol&#39;</span> <span class="o">%</span> <span class="n">role</span><span class="p">),</span>
+                <span class="s1">&#39;genesymbol&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;uniprot&#39;</span><span class="p">,</span>
+                <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">,</span>
+            <span class="p">)</span>
+
+            <span class="k">for</span> <span class="n">uniprot</span> <span class="ow">in</span> <span class="n">uniprots</span><span class="p">:</span>
+
+                <span class="n">annot</span><span class="p">[</span><span class="n">uniprot</span><span class="p">]</span><span class="o">.</span><span class="n">add</span><span class="p">(</span>
+                    <span class="n">CellTalkDBAnnotation</span><span class="p">(</span>
+                        <span class="n">role</span> <span class="o">=</span> <span class="n">role</span><span class="p">,</span>
+                        <span class="n">pmid</span> <span class="o">=</span> <span class="n">rec</span><span class="o">.</span><span class="n">evidence</span><span class="p">,</span>
+                    <span class="p">)</span>
+                <span class="p">)</span>
+
+    <span class="k">return</span> <span class="nb">dict</span><span class="p">(</span><span class="n">annot</span><span class="p">)</span></div>
+
+</pre></div>
+
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diff --git a/_modules/pypath/inputs/celltypist.html b/_modules/pypath/inputs/celltypist.html
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+                <article class="bd-article">
+                  
+  <h1>Source code for pypath.inputs.celltypist</h1><div class="highlight"><pre>
+<span></span><span class="ch">#!/usr/bin/env python</span>
+<span class="c1"># -*- coding: utf-8 -*-</span>
+
+<span class="c1">#</span>
+<span class="c1">#  This file is part of the `pypath` python module</span>
+<span class="c1">#</span>
+<span class="c1">#  Copyright 2014-2023</span>
+<span class="c1">#  EMBL, EMBL-EBI, Uniklinik RWTH Aachen, Heidelberg University</span>
+<span class="c1">#</span>
+<span class="c1">#  Authors: see the file `README.rst`</span>
+<span class="c1">#  Contact: Dénes Türei (turei.denes@gmail.com)</span>
+<span class="c1">#</span>
+<span class="c1">#  Distributed under the GPLv3 License.</span>
+<span class="c1">#  See accompanying file LICENSE.txt or copy at</span>
+<span class="c1">#      https://www.gnu.org/licenses/gpl-3.0.html</span>
+<span class="c1">#</span>
+<span class="c1">#  Website: https://pypath.omnipathdb.org/</span>
+<span class="c1">#</span>
+
+<span class="kn">import</span> <span class="nn">re</span>
+<span class="kn">import</span> <span class="nn">collections</span>
+
+<span class="kn">import</span> <span class="nn">pypath.inputs.common</span> <span class="k">as</span> <span class="nn">inputs_common</span>
+<span class="kn">import</span> <span class="nn">pypath.resources.urls</span> <span class="k">as</span> <span class="nn">urls</span>
+<span class="kn">import</span> <span class="nn">pypath.share.curl</span> <span class="k">as</span> <span class="nn">curl</span>
+<span class="kn">import</span> <span class="nn">pypath.utils.mapping</span> <span class="k">as</span> <span class="nn">mapping</span>
+
+
+<div class="viewcode-block" id="celltypist_annotations">
+<a class="viewcode-back" href="../../../api/pypath.inputs.celltypist.celltypist_annotations.html#pypath.inputs.celltypist.celltypist_annotations">[docs]</a>
+<span class="k">def</span> <span class="nf">celltypist_annotations</span><span class="p">():</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Immune cell type marker genes from Celltypist</span>
+<span class="sd">    (https://github.com/Teichlab/celltypist_wiki).</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="n">recomma</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">compile</span><span class="p">(</span><span class="sa">r</span><span class="s1">&#39;\s?,\s?&#39;</span><span class="p">)</span>
+
+    <span class="k">def</span> <span class="nf">multi_value_field</span><span class="p">(</span><span class="n">value</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="nb">tuple</span><span class="p">(</span><span class="nb">sorted</span><span class="p">(</span><span class="n">recomma</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="n">value</span><span class="o">.</span><span class="n">strip</span><span class="p">())))</span>
+
+    <span class="n">record</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">namedtuple</span><span class="p">(</span>
+        <span class="s1">&#39;CelltypistAnnotation&#39;</span><span class="p">,</span>
+        <span class="p">(</span>
+            <span class="s1">&#39;cell_type&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;cell_subtype&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;cell_ontology&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;marker_type&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;tissues&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;datasets&#39;</span><span class="p">,</span>
+        <span class="p">)</span>
+    <span class="p">)</span>
+
+    <span class="n">result</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">defaultdict</span><span class="p">(</span><span class="nb">set</span><span class="p">)</span>
+
+    <span class="n">url</span> <span class="o">=</span> <span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;celltypist&#39;</span><span class="p">][</span><span class="s1">&#39;url&#39;</span><span class="p">]</span>
+
+    <span class="n">c</span> <span class="o">=</span> <span class="n">curl</span><span class="o">.</span><span class="n">Curl</span><span class="p">(</span><span class="n">url</span><span class="p">,</span> <span class="n">silent</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span> <span class="n">large</span> <span class="o">=</span> <span class="kc">True</span><span class="p">)</span>
+
+    <span class="n">xls</span> <span class="o">=</span> <span class="n">c</span><span class="o">.</span><span class="n">fileobj</span>
+    <span class="n">xlsfile</span> <span class="o">=</span> <span class="n">xls</span><span class="o">.</span><span class="n">name</span>
+    <span class="n">xls</span><span class="o">.</span><span class="n">close</span><span class="p">()</span>
+    <span class="n">tbl</span> <span class="o">=</span> <span class="n">inputs_common</span><span class="o">.</span><span class="n">read_xls</span><span class="p">(</span><span class="n">xlsfile</span><span class="p">)[</span><span class="mi">1</span><span class="p">:]</span>
+
+    <span class="n">marker_columns</span> <span class="o">=</span> <span class="p">((</span><span class="mi">6</span><span class="p">,</span> <span class="s1">&#39;curated_marker&#39;</span><span class="p">),</span> <span class="p">(</span><span class="mi">7</span><span class="p">,</span> <span class="s1">&#39;celltypist_model&#39;</span><span class="p">))</span>
+
+    <span class="k">for</span> <span class="n">r</span> <span class="ow">in</span> <span class="n">tbl</span><span class="p">:</span>
+
+        <span class="k">for</span> <span class="n">col</span><span class="p">,</span> <span class="n">marker_type</span> <span class="ow">in</span> <span class="n">marker_columns</span><span class="p">:</span>
+
+            <span class="n">genesymbols</span> <span class="o">=</span> <span class="n">recomma</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="n">r</span><span class="p">[</span><span class="n">col</span><span class="p">]</span><span class="o">.</span><span class="n">strip</span><span class="p">())</span>
+            <span class="n">uniprots</span> <span class="o">=</span> <span class="n">mapping</span><span class="o">.</span><span class="n">map_names</span><span class="p">(</span><span class="n">genesymbols</span><span class="p">,</span> <span class="s1">&#39;genesymbol&#39;</span><span class="p">,</span> <span class="s1">&#39;uniprot&#39;</span><span class="p">)</span>
+
+            <span class="n">annot</span> <span class="o">=</span> <span class="n">record</span><span class="p">(</span>
+                <span class="n">cell_type</span> <span class="o">=</span> <span class="n">r</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span>
+                <span class="n">cell_subtype</span> <span class="o">=</span> <span class="n">r</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span>
+                <span class="n">cell_ontology</span> <span class="o">=</span> <span class="n">r</span><span class="p">[</span><span class="mi">3</span><span class="p">],</span>
+                <span class="n">marker_type</span> <span class="o">=</span> <span class="n">marker_type</span><span class="p">,</span>
+                <span class="n">tissues</span> <span class="o">=</span> <span class="n">multi_value_field</span><span class="p">(</span><span class="n">r</span><span class="p">[</span><span class="mi">4</span><span class="p">]),</span>
+                <span class="n">datasets</span> <span class="o">=</span> <span class="n">multi_value_field</span><span class="p">(</span><span class="n">r</span><span class="p">[</span><span class="mi">5</span><span class="p">]),</span>
+            <span class="p">)</span>
+
+            <span class="k">for</span> <span class="n">u</span> <span class="ow">in</span> <span class="n">uniprots</span><span class="p">:</span>
+
+                <span class="n">result</span><span class="p">[</span><span class="n">u</span><span class="p">]</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">annot</span><span class="p">)</span>
+
+    <span class="k">return</span> <span class="nb">dict</span><span class="p">(</span><span class="n">result</span><span class="p">)</span></div>
+
+</pre></div>
+
+                </article>
+              
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+              
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+            
+          </footer>
+        
+      </main>
+    </div>
+  </div>
+  
+  <!-- Scripts loaded after <body> so the DOM is not blocked -->
+  <script src="../../../_static/scripts/bootstrap.js?digest=8d27b9dea8ad943066ae"></script>
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+    
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+      
+    </div>
+  
+</div>
+
+  </footer>
+  </body>
+</html>
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diff --git a/_modules/pypath/inputs/collectri.html b/_modules/pypath/inputs/collectri.html
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+                  
+  <h1>Source code for pypath.inputs.collectri</h1><div class="highlight"><pre>
+<span></span><span class="ch">#!/usr/bin/env python</span>
+<span class="c1"># -*- coding: utf-8 -*-</span>
+
+<span class="c1">#</span>
+<span class="c1">#  This file is part of the `pypath` python module</span>
+<span class="c1">#</span>
+<span class="c1">#  Copyright 2014-2023</span>
+<span class="c1">#  EMBL, EMBL-EBI, Uniklinik RWTH Aachen, Heidelberg University</span>
+<span class="c1">#</span>
+<span class="c1">#  Authors: see the file `README.rst`</span>
+<span class="c1">#  Contact: Dénes Türei (turei.denes@gmail.com)</span>
+<span class="c1">#</span>
+<span class="c1">#  Distributed under the GPLv3 License.</span>
+<span class="c1">#  See accompanying file LICENSE.txt or copy at</span>
+<span class="c1">#      https://www.gnu.org/licenses/gpl-3.0.html</span>
+<span class="c1">#</span>
+<span class="c1">#  Website: https://pypath.omnipathdb.org/</span>
+<span class="c1">#</span>
+
+<span class="kn">from</span> <span class="nn">__future__</span> <span class="kn">import</span> <span class="n">annotations</span>
+
+<span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">CollecTRI is a comprehensive resource of TF-target interactions.</span>
+<span class="sd">&quot;&quot;&quot;</span>
+
+<span class="kn">from</span> <span class="nn">typing</span> <span class="kn">import</span> <span class="n">Literal</span>
+
+<span class="kn">import</span> <span class="nn">re</span>
+<span class="kn">import</span> <span class="nn">collections</span>
+<span class="kn">import</span> <span class="nn">itertools</span>
+
+<span class="kn">import</span> <span class="nn">pypath.resources.urls</span> <span class="k">as</span> <span class="nn">urls</span>
+<span class="kn">import</span> <span class="nn">pypath.share.curl</span> <span class="k">as</span> <span class="nn">curl</span>
+<span class="kn">import</span> <span class="nn">pypath.internals.intera</span> <span class="k">as</span> <span class="nn">intera</span>
+<span class="kn">import</span> <span class="nn">pypath.utils.mapping</span> <span class="k">as</span> <span class="nn">mapping</span>
+<span class="kn">import</span> <span class="nn">pypath.share.session</span> <span class="k">as</span> <span class="nn">session</span>
+
+<span class="n">_log</span> <span class="o">=</span> <span class="n">session</span><span class="o">.</span><span class="n">Logger</span><span class="p">(</span><span class="n">name</span> <span class="o">=</span> <span class="s1">&#39;collectri_input&#39;</span><span class="p">)</span><span class="o">.</span><span class="n">_log</span>
+
+<span class="c1"># Based on literature by Sophia</span>
+<span class="c1"># https://www.sciencedirect.com/science/article/abs/pii/S0304419X19300526</span>
+<span class="c1"># https://www.nature.com/articles/1209933</span>
+<span class="n">COMPLEXES</span> <span class="o">=</span> <span class="p">{</span>
+    <span class="s1">&#39;AP1&#39;</span><span class="p">:</span> <span class="p">{</span>
+        <span class="s1">&#39;JUN-FOS&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;JUNB-FOS&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;JUND-FOS&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;JUN-FOSB&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;JUNB-FOSB&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;JUND-FOSB&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;JUN-FOSL1&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;JUNB-FOSL1&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;JUND-FOSL1&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;JUN-FOSL2&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;JUNB-FOSL2&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;JUND-FOSL2&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;JUN-JUN&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;JUN-JUNB&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;JUN-JUND&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;JUNB-JUNB&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;JUNB-JUND&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;JUND-JUND&#39;</span><span class="p">,</span>
+    <span class="p">},</span>
+    <span class="s1">&#39;NFKB&#39;</span><span class="p">:</span> <span class="p">{</span>
+        <span class="s1">&#39;RELA-RELA&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;RELA-REL&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;RELA-RELB&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;RELA-NFKB1&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;RELA-NFKB2&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;REL-REL&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;REL-RELB&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;REL-NFKB1&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;REL-NFKB2&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;RELB-RELB&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;RELB-NFKB1&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;RELB-NFKB2&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;NFKB1-NFKB1&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;NFKB1-NFKB2&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;NFKB2-NFKB2&#39;</span><span class="p">,</span>
+    <span class="p">},</span>
+<span class="p">}</span>
+
+
+<div class="viewcode-block" id="collectri_raw">
+<a class="viewcode-back" href="../../../api/pypath.inputs.collectri.collectri_raw.html#pypath.inputs.collectri.collectri_raw">[docs]</a>
+<span class="k">def</span> <span class="nf">collectri_raw</span><span class="p">(</span>
+        <span class="n">protein_coding</span><span class="p">:</span> <span class="nb">bool</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
+        <span class="n">mirna</span><span class="p">:</span> <span class="nb">bool</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+    <span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">list</span><span class="p">[</span><span class="nb">tuple</span><span class="p">]:</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    TF-target interactions from the CollecTRI database.</span>
+
+<span class="sd">    Args:</span>
+<span class="sd">        protein_coding:</span>
+<span class="sd">            Include regulation of protein coding genes.</span>
+<span class="sd">        mirna:</span>
+<span class="sd">            Include regulation of miRNA coding genes.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+
+    <span class="n">remirna</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">compile</span><span class="p">(</span><span class="s1">&#39;^MIR(\d+)$&#39;</span><span class="p">)</span>
+
+    <span class="n">CollectriRecord</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">namedtuple</span><span class="p">(</span>
+        <span class="s1">&#39;CollectriRecord&#39;</span><span class="p">,</span>
+        <span class="p">(</span>
+            <span class="s1">&#39;tf&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;target&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;effect&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;tf_category&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;resources&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;pubmed&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;sign_decision&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;target_type&#39;</span><span class="p">,</span>
+        <span class="p">),</span>
+    <span class="p">)</span>
+
+    <span class="n">url</span> <span class="o">=</span> <span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;collectri&#39;</span><span class="p">][</span><span class="s1">&#39;url&#39;</span><span class="p">]</span>
+    <span class="n">c</span> <span class="o">=</span> <span class="n">curl</span><span class="o">.</span><span class="n">Curl</span><span class="p">(</span>
+        <span class="n">url</span><span class="p">,</span>
+        <span class="n">silent</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+        <span class="n">large</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
+    <span class="p">)</span>
+    <span class="n">_</span> <span class="o">=</span> <span class="nb">next</span><span class="p">(</span><span class="n">c</span><span class="o">.</span><span class="n">result</span><span class="p">)</span>
+
+    <span class="n">result</span> <span class="o">=</span> <span class="p">[]</span>
+
+    <span class="k">for</span> <span class="n">l</span> <span class="ow">in</span> <span class="n">c</span><span class="o">.</span><span class="n">result</span><span class="p">:</span>
+
+        <span class="n">l</span> <span class="o">=</span> <span class="n">l</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;,&#39;</span><span class="p">)</span>
+        <span class="n">mmirna</span> <span class="o">=</span> <span class="n">remirna</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="n">l</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span>
+
+        <span class="k">if</span> <span class="p">(</span>
+            <span class="p">(</span><span class="n">mmirna</span> <span class="ow">and</span> <span class="ow">not</span> <span class="n">mirna</span><span class="p">)</span> <span class="ow">or</span>
+            <span class="p">(</span><span class="ow">not</span> <span class="n">mmirna</span> <span class="ow">and</span> <span class="ow">not</span> <span class="n">protein_coding</span><span class="p">)</span>
+        <span class="p">):</span>
+
+            <span class="k">continue</span>
+
+        <span class="n">target_id</span> <span class="o">=</span> <span class="sa">f</span><span class="s1">&#39;hsa-miR-</span><span class="si">{</span><span class="n">mmirna</span><span class="o">.</span><span class="n">group</span><span class="p">(</span><span class="mi">1</span><span class="p">)</span><span class="si">}</span><span class="s1">&#39;</span> <span class="k">if</span> <span class="n">mmirna</span> <span class="k">else</span> <span class="n">l</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span>
+
+        <span class="n">result</span><span class="o">.</span><span class="n">append</span><span class="p">(</span>
+            <span class="n">CollectriRecord</span><span class="p">(</span>
+                <span class="n">tf</span> <span class="o">=</span> <span class="n">l</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span>
+                <span class="n">target</span> <span class="o">=</span> <span class="n">target_id</span><span class="p">,</span>
+                <span class="n">effect</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">l</span><span class="p">[</span><span class="mi">2</span><span class="p">]),</span>
+                <span class="n">tf_category</span> <span class="o">=</span> <span class="n">l</span><span class="p">[</span><span class="mi">3</span><span class="p">],</span>
+                <span class="n">resources</span> <span class="o">=</span> <span class="n">l</span><span class="p">[</span><span class="mi">4</span><span class="p">]</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s1">&#39;DoRothEA_A&#39;</span><span class="p">,</span> <span class="s1">&#39;DoRothEA-A&#39;</span><span class="p">),</span>
+                <span class="n">pubmed</span> <span class="o">=</span> <span class="n">l</span><span class="p">[</span><span class="mi">5</span><span class="p">],</span>
+                <span class="n">sign_decision</span> <span class="o">=</span> <span class="n">l</span><span class="p">[</span><span class="mi">6</span><span class="p">],</span>
+                <span class="n">target_type</span> <span class="o">=</span> <span class="s1">&#39;mirna&#39;</span> <span class="k">if</span> <span class="n">mmirna</span> <span class="k">else</span> <span class="s1">&#39;protein&#39;</span><span class="p">,</span>
+            <span class="p">)</span>
+        <span class="p">)</span>
+
+    <span class="k">return</span> <span class="n">result</span></div>
+
+
+
+<div class="viewcode-block" id="collectri_interactions">
+<a class="viewcode-back" href="../../../api/pypath.inputs.collectri.collectri_interactions.html#pypath.inputs.collectri.collectri_interactions">[docs]</a>
+<span class="k">def</span> <span class="nf">collectri_interactions</span><span class="p">(</span>
+        <span class="n">protein_coding</span><span class="p">:</span> <span class="nb">bool</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
+        <span class="n">mirna</span><span class="p">:</span> <span class="nb">bool</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+    <span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">list</span><span class="p">[</span><span class="nb">tuple</span><span class="p">]:</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    TF-target interactions from the CollecTRI database.</span>
+
+<span class="sd">    While `collectri_raw` returns the records in the same format as in the</span>
+<span class="sd">    original data, here we translate identifiers to UniProt IDs, and use</span>
+<span class="sd">    `Complex` objects to represent protein complexes.</span>
+
+<span class="sd">    Args:</span>
+<span class="sd">        protein_coding:</span>
+<span class="sd">            Include regulation of protein coding genes.</span>
+<span class="sd">        mirna:</span>
+<span class="sd">            Include regulation of miRNA coding genes.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="n">CollectriInteraction</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">namedtuple</span><span class="p">(</span>
+        <span class="s1">&#39;CollectriInteraction&#39;</span><span class="p">,</span>
+        <span class="p">(</span>
+            <span class="s1">&#39;tf&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;target&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;effect&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;tf_category&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;resources&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;pubmed&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;sign_decision&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;target_type&#39;</span><span class="p">,</span>
+        <span class="p">),</span>
+    <span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">process_complex</span><span class="p">(</span><span class="n">name</span><span class="p">):</span>
+
+        <span class="n">result</span> <span class="o">=</span> <span class="p">[]</span>
+
+        <span class="k">for</span> <span class="n">var</span> <span class="ow">in</span> <span class="n">COMPLEXES</span><span class="p">[</span><span class="n">name</span><span class="p">]:</span>
+
+            <span class="n">uniprots</span> <span class="o">=</span> <span class="p">[</span>
+                <span class="n">mapping</span><span class="o">.</span><span class="n">map_name</span><span class="p">(</span><span class="n">comp</span><span class="p">,</span> <span class="s1">&#39;genesymbol&#39;</span><span class="p">,</span> <span class="s1">&#39;uniprot&#39;</span><span class="p">)</span>
+                <span class="k">for</span> <span class="n">comp</span> <span class="ow">in</span> <span class="n">var</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;-&#39;</span><span class="p">)</span>
+            <span class="p">]</span>
+
+            <span class="k">if</span> <span class="nb">all</span><span class="p">(</span><span class="n">uniprots</span><span class="p">):</span>
+
+                <span class="n">result</span><span class="o">.</span><span class="n">extend</span><span class="p">(</span><span class="nb">list</span><span class="p">(</span><span class="n">itertools</span><span class="o">.</span><span class="n">product</span><span class="p">(</span><span class="o">*</span><span class="n">uniprots</span><span class="p">)))</span>
+
+            <span class="k">else</span><span class="p">:</span>
+
+                <span class="n">_log</span><span class="p">(</span>
+                    <span class="s1">&#39;Failed to translate all components of &#39;</span>
+                    <span class="sa">f</span><span class="s1">&#39;complex `</span><span class="si">{</span><span class="n">name</span><span class="si">}</span><span class="s1">` (components: </span><span class="si">{</span><span class="n">var</span><span class="si">}</span><span class="s1">).&#39;</span>
+                <span class="p">)</span>
+
+        <span class="k">return</span> <span class="nb">set</span><span class="p">(</span><span class="n">result</span><span class="p">)</span>
+
+
+    <span class="k">for</span> <span class="n">rec</span> <span class="ow">in</span> <span class="n">collectri_raw</span><span class="p">(</span><span class="n">protein_coding</span> <span class="o">=</span> <span class="n">protein_coding</span><span class="p">,</span> <span class="n">mirna</span> <span class="o">=</span> <span class="n">mirna</span><span class="p">):</span>
+
+        <span class="n">tf_uniprots</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="n">process_complex</span><span class="p">(</span><span class="n">rec</span><span class="o">.</span><span class="n">tf</span><span class="p">)</span>
+                <span class="k">if</span> <span class="n">rec</span><span class="o">.</span><span class="n">tf</span> <span class="ow">in</span> <span class="n">COMPLEXES</span> <span class="k">else</span>
+            <span class="n">mapping</span><span class="o">.</span><span class="n">map_name</span><span class="p">(</span><span class="n">rec</span><span class="o">.</span><span class="n">tf</span><span class="p">,</span> <span class="s1">&#39;genesymbol&#39;</span><span class="p">,</span> <span class="s1">&#39;uniprot&#39;</span><span class="p">)</span>
+        <span class="p">)</span>
+
+        <span class="n">target_uniprots</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="p">(</span><span class="n">rec</span><span class="o">.</span><span class="n">target</span><span class="p">,)</span>
+                <span class="k">if</span> <span class="n">rec</span><span class="o">.</span><span class="n">target_type</span> <span class="o">==</span> <span class="s1">&#39;mirna&#39;</span> <span class="k">else</span>
+            <span class="n">mapping</span><span class="o">.</span><span class="n">map_name</span><span class="p">(</span><span class="n">rec</span><span class="o">.</span><span class="n">target</span><span class="p">,</span> <span class="s1">&#39;genesymbol&#39;</span><span class="p">,</span> <span class="s1">&#39;uniprot&#39;</span><span class="p">)</span>
+        <span class="p">)</span>
+
+        <span class="k">for</span> <span class="n">tf_u</span><span class="p">,</span> <span class="n">t_u</span> <span class="ow">in</span> <span class="n">itertools</span><span class="o">.</span><span class="n">product</span><span class="p">(</span><span class="n">tf_uniprots</span><span class="p">,</span> <span class="n">target_uniprots</span><span class="p">):</span>
+
+            <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">tf_u</span><span class="p">,</span> <span class="nb">tuple</span><span class="p">):</span>
+
+                <span class="n">tf_u</span> <span class="o">=</span> <span class="n">intera</span><span class="o">.</span><span class="n">Complex</span><span class="p">(</span>
+                    <span class="n">components</span> <span class="o">=</span> <span class="n">tf_u</span><span class="p">,</span>
+                    <span class="n">sources</span> <span class="o">=</span> <span class="s1">&#39;CollecTRI&#39;</span><span class="p">,</span>
+                <span class="p">)</span>
+
+            <span class="k">yield</span> <span class="n">CollectriInteraction</span><span class="p">(</span><span class="n">tf_u</span><span class="p">,</span> <span class="n">t_u</span><span class="p">,</span> <span class="o">*</span><span class="n">rec</span><span class="p">[</span><span class="mi">2</span><span class="p">:])</span></div>
+
+
+</pre></div>
+
+                </article>
+              
+              
+              
+              
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+  <h1>Source code for pypath.inputs.compleat</h1><div class="highlight"><pre>
+<span></span><span class="ch">#!/usr/bin/env python</span>
+<span class="c1"># -*- coding: utf-8 -*-</span>
+
+<span class="c1">#</span>
+<span class="c1">#  This file is part of the `pypath` python module</span>
+<span class="c1">#</span>
+<span class="c1">#  Copyright 2014-2023</span>
+<span class="c1">#  EMBL, EMBL-EBI, Uniklinik RWTH Aachen, Heidelberg University</span>
+<span class="c1">#</span>
+<span class="c1">#  Authors: see the file `README.rst`</span>
+<span class="c1">#  Contact: Dénes Türei (turei.denes@gmail.com)</span>
+<span class="c1">#</span>
+<span class="c1">#  Distributed under the GPLv3 License.</span>
+<span class="c1">#  See accompanying file LICENSE.txt or copy at</span>
+<span class="c1">#      https://www.gnu.org/licenses/gpl-3.0.html</span>
+<span class="c1">#</span>
+<span class="c1">#  Website: https://pypath.omnipathdb.org/</span>
+<span class="c1">#</span>
+
+<span class="kn">import</span> <span class="nn">csv</span>
+
+<span class="kn">import</span> <span class="nn">pypath.share.curl</span> <span class="k">as</span> <span class="nn">curl</span>
+<span class="kn">import</span> <span class="nn">pypath.resources.urls</span> <span class="k">as</span> <span class="nn">urls</span>
+<span class="kn">import</span> <span class="nn">pypath.internals.intera</span> <span class="k">as</span> <span class="nn">intera</span>
+<span class="kn">import</span> <span class="nn">pypath.utils.mapping</span> <span class="k">as</span> <span class="nn">mapping</span>
+
+
+<div class="viewcode-block" id="compleat_raw">
+<a class="viewcode-back" href="../../../api/pypath.inputs.compleat.compleat_raw.html#pypath.inputs.compleat.compleat_raw">[docs]</a>
+<span class="k">def</span> <span class="nf">compleat_raw</span><span class="p">():</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Raw protein complex data from the Compleat database.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="n">url</span> <span class="o">=</span> <span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;compleat&#39;</span><span class="p">][</span><span class="s1">&#39;rescued&#39;</span><span class="p">]</span>
+    <span class="n">c</span> <span class="o">=</span> <span class="n">curl</span><span class="o">.</span><span class="n">Curl</span><span class="p">(</span><span class="n">url</span><span class="p">,</span> <span class="n">large</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span> <span class="n">silent</span> <span class="o">=</span> <span class="kc">False</span><span class="p">)</span>
+    <span class="n">tab</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="n">csv</span><span class="o">.</span><span class="n">DictReader</span><span class="p">(</span>
+        <span class="n">c</span><span class="o">.</span><span class="n">result</span><span class="p">,</span>
+        <span class="n">delimiter</span> <span class="o">=</span> <span class="s1">&#39;</span><span class="se">\t</span><span class="s1">&#39;</span><span class="p">,</span>
+        <span class="n">fieldnames</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="s1">&#39;compleat_id&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;member_count&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;predicted&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;functions&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;functions2&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;nothing&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;sources&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;name&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;method&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;organisms&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;pubmeds&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;members&#39;</span><span class="p">,</span>
+        <span class="p">)</span>
+    <span class="p">))</span>
+
+    <span class="k">return</span> <span class="n">tab</span></div>
+
+
+
+<div class="viewcode-block" id="compleat_complexes">
+<a class="viewcode-back" href="../../../api/pypath.inputs.compleat.compleat_complexes.html#pypath.inputs.compleat.compleat_complexes">[docs]</a>
+<span class="k">def</span> <span class="nf">compleat_complexes</span><span class="p">(</span><span class="n">predicted</span> <span class="o">=</span> <span class="kc">True</span><span class="p">):</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Retrieves and processes protein complexes from the Compleat database.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="n">raw</span> <span class="o">=</span> <span class="n">compleat_raw</span><span class="p">()</span>
+    <span class="n">complexes</span> <span class="o">=</span> <span class="p">{}</span>
+
+    <span class="k">for</span> <span class="n">rec</span> <span class="ow">in</span> <span class="n">raw</span><span class="p">:</span>
+
+        <span class="n">is_predicted</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="n">rec</span><span class="p">[</span><span class="s1">&#39;predicted&#39;</span><span class="p">]</span> <span class="ow">and</span>
+            <span class="n">rec</span><span class="p">[</span><span class="s1">&#39;predicted&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span> <span class="o">==</span> <span class="s1">&#39;Predicted&#39;</span>
+        <span class="p">)</span>
+
+        <span class="k">if</span> <span class="n">is_predicted</span> <span class="ow">and</span> <span class="ow">not</span> <span class="n">predicted</span><span class="p">:</span>
+
+            <span class="k">continue</span>
+
+        <span class="k">if</span> <span class="ow">not</span> <span class="n">rec</span><span class="p">[</span><span class="s1">&#39;members&#39;</span><span class="p">]:</span>
+
+            <span class="k">continue</span>
+
+        <span class="n">uniprots</span> <span class="o">=</span> <span class="p">[]</span>
+
+        <span class="k">for</span> <span class="n">entrez</span> <span class="ow">in</span> <span class="n">rec</span><span class="p">[</span><span class="s1">&#39;members&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">():</span>
+
+            <span class="n">uniprot</span> <span class="o">=</span> <span class="n">mapping</span><span class="o">.</span><span class="n">map_name0</span><span class="p">(</span><span class="n">entrez</span><span class="o">.</span><span class="n">strip</span><span class="p">(),</span> <span class="s1">&#39;entrez&#39;</span><span class="p">,</span> <span class="s1">&#39;uniprot&#39;</span><span class="p">)</span>
+
+            <span class="k">if</span> <span class="n">uniprot</span><span class="p">:</span>
+                <span class="n">uniprots</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">uniprot</span><span class="p">)</span>
+
+        <span class="k">if</span> <span class="ow">not</span> <span class="n">uniprots</span><span class="p">:</span>
+            <span class="k">continue</span>
+
+        <span class="n">name</span> <span class="o">=</span> <span class="n">rec</span><span class="p">[</span><span class="s1">&#39;name&#39;</span><span class="p">]</span>
+        <span class="n">references</span> <span class="o">=</span> <span class="n">rec</span><span class="p">[</span><span class="s1">&#39;pubmeds&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;,&#39;</span><span class="p">)</span> <span class="k">if</span> <span class="n">rec</span><span class="p">[</span><span class="s1">&#39;pubmeds&#39;</span><span class="p">]</span> <span class="k">else</span> <span class="kc">None</span>
+        <span class="n">sources</span> <span class="o">=</span> <span class="nb">set</span><span class="p">(</span><span class="n">rec</span><span class="p">[</span><span class="s1">&#39;sources&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;,&#39;</span><span class="p">))</span> <span class="k">if</span> <span class="n">is_predicted</span> <span class="k">else</span> <span class="nb">set</span><span class="p">()</span>
+        <span class="n">sources</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="s1">&#39;Compleat&#39;</span><span class="p">)</span>
+
+        <span class="n">cplex</span> <span class="o">=</span> <span class="n">intera</span><span class="o">.</span><span class="n">Complex</span><span class="p">(</span>
+            <span class="n">components</span> <span class="o">=</span> <span class="n">uniprots</span><span class="p">,</span>
+            <span class="n">sources</span> <span class="o">=</span> <span class="n">sources</span><span class="p">,</span>
+            <span class="n">references</span> <span class="o">=</span> <span class="n">references</span><span class="p">,</span>
+            <span class="n">name</span> <span class="o">=</span> <span class="n">name</span><span class="p">,</span>
+            <span class="n">ids</span> <span class="o">=</span> <span class="p">{</span><span class="s1">&#39;Compleat&#39;</span><span class="p">:</span> <span class="n">rec</span><span class="p">[</span><span class="s1">&#39;compleat_id&#39;</span><span class="p">]},</span>
+        <span class="p">)</span>
+
+        <span class="k">if</span> <span class="n">cplex</span><span class="o">.</span><span class="fm">__str__</span><span class="p">()</span> <span class="ow">in</span> <span class="n">complexes</span><span class="p">:</span>
+
+            <span class="n">complexes</span><span class="p">[</span><span class="n">cplex</span><span class="o">.</span><span class="fm">__str__</span><span class="p">()]</span> <span class="o">+=</span> <span class="n">cplex</span>
+
+        <span class="k">else</span><span class="p">:</span>
+
+            <span class="n">complexes</span><span class="p">[</span><span class="n">cplex</span><span class="o">.</span><span class="fm">__str__</span><span class="p">()]</span> <span class="o">=</span> <span class="n">cplex</span>
+
+    <span class="k">return</span> <span class="n">complexes</span></div>
+
+</pre></div>
+
+                </article>
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diff --git a/_modules/pypath/inputs/complexportal.html b/_modules/pypath/inputs/complexportal.html
new file mode 100644
index 000000000..134d268b7
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+  <h1>Source code for pypath.inputs.complexportal</h1><div class="highlight"><pre>
+<span></span><span class="ch">#!/usr/bin/env python</span>
+<span class="c1"># -*- coding: utf-8 -*-</span>
+
+<span class="c1">#</span>
+<span class="c1">#  This file is part of the `pypath` python module</span>
+<span class="c1">#</span>
+<span class="c1">#  Copyright 2014-2023</span>
+<span class="c1">#  EMBL, EMBL-EBI, Uniklinik RWTH Aachen, Heidelberg University</span>
+<span class="c1">#</span>
+<span class="c1">#  Authors: see the file `README.rst`</span>
+<span class="c1">#  Contact: Dénes Türei (turei.denes@gmail.com)</span>
+<span class="c1">#</span>
+<span class="c1">#  Distributed under the GPLv3 License.</span>
+<span class="c1">#  See accompanying file LICENSE.txt or copy at</span>
+<span class="c1">#      https://www.gnu.org/licenses/gpl-3.0.html</span>
+<span class="c1">#</span>
+<span class="c1">#  Website: https://pypath.omnipathdb.org/</span>
+<span class="c1">#</span>
+
+<span class="kn">from</span> <span class="nn">future.utils</span> <span class="kn">import</span> <span class="n">iteritems</span>
+
+<span class="kn">import</span> <span class="nn">collections</span>
+
+<span class="kn">import</span> <span class="nn">bs4</span>
+
+<span class="kn">import</span> <span class="nn">pypath.share.curl</span> <span class="k">as</span> <span class="nn">curl</span>
+<span class="kn">import</span> <span class="nn">pypath.resources.urls</span> <span class="k">as</span> <span class="nn">urls</span>
+<span class="kn">import</span> <span class="nn">pypath.internals.intera</span> <span class="k">as</span> <span class="nn">intera</span>
+
+
+<div class="viewcode-block" id="complexportal_complexes">
+<a class="viewcode-back" href="../../../api/pypath.inputs.complexportal.complexportal_complexes.html#pypath.inputs.complexportal.complexportal_complexes">[docs]</a>
+<span class="k">def</span> <span class="nf">complexportal_complexes</span><span class="p">(</span><span class="n">organism</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">,</span> <span class="n">return_details</span> <span class="o">=</span> <span class="kc">False</span><span class="p">):</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Complex dataset from IntAct.</span>
+<span class="sd">    See more:</span>
+<span class="sd">    http://www.ebi.ac.uk/intact/complex/</span>
+<span class="sd">    http://nar.oxfordjournals.org/content/early/2014/10/13/nar.gku975.full.pdf</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="n">spec</span> <span class="o">=</span> <span class="p">{</span><span class="mi">9606</span><span class="p">:</span> <span class="s1">&#39;Homo_sapiens&#39;</span><span class="p">}</span>
+
+    <span class="n">zipurl</span> <span class="o">=</span> <span class="s1">&#39;</span><span class="si">%s</span><span class="s1">/</span><span class="si">%s</span><span class="s1">.zip&#39;</span> <span class="o">%</span> <span class="p">(</span>
+        <span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;complex_portal&#39;</span><span class="p">][</span><span class="s1">&#39;url&#39;</span><span class="p">],</span>
+        <span class="n">spec</span><span class="p">[</span><span class="n">organism</span><span class="p">],</span>
+    <span class="p">)</span>
+    <span class="n">c</span> <span class="o">=</span> <span class="n">curl</span><span class="o">.</span><span class="n">Curl</span><span class="p">(</span><span class="n">zipurl</span><span class="p">,</span> <span class="n">large</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span> <span class="n">silent</span> <span class="o">=</span> <span class="kc">False</span><span class="p">)</span>
+    <span class="n">files</span> <span class="o">=</span> <span class="n">c</span><span class="o">.</span><span class="n">result</span>
+
+    <span class="n">errors</span> <span class="o">=</span> <span class="p">[]</span>
+    <span class="n">complexes</span> <span class="o">=</span> <span class="p">{}</span>
+    <span class="n">details</span> <span class="o">=</span> <span class="p">[]</span>
+    <span class="n">name_key</span> <span class="o">=</span> <span class="s1">&#39;complex recommended name&#39;</span>
+
+    <span class="k">for</span> <span class="n">xmlname</span><span class="p">,</span> <span class="n">xml</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="n">c</span><span class="o">.</span><span class="n">result</span><span class="p">):</span>
+
+        <span class="n">soup</span> <span class="o">=</span> <span class="n">bs4</span><span class="o">.</span><span class="n">BeautifulSoup</span><span class="p">(</span><span class="n">xml</span><span class="p">,</span> <span class="s1">&#39;html.parser&#39;</span><span class="p">)</span>
+        <span class="n">interactors_xml</span> <span class="o">=</span> <span class="n">soup</span><span class="o">.</span><span class="n">find_all</span><span class="p">(</span><span class="s1">&#39;interactor&#39;</span><span class="p">)</span>
+        <span class="n">interactors</span> <span class="o">=</span> <span class="p">{}</span>
+        <span class="n">interactions</span> <span class="o">=</span> <span class="p">{}</span>
+
+        <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="n">interactors_xml</span><span class="p">:</span>
+
+            <span class="k">if</span> <span class="n">i</span><span class="o">.</span><span class="n">find</span><span class="p">(</span><span class="s1">&#39;primaryref&#39;</span><span class="p">)</span><span class="o">.</span><span class="n">attrs</span><span class="p">[</span><span class="s1">&#39;db&#39;</span><span class="p">]</span> <span class="o">==</span> <span class="s1">&#39;uniprotkb&#39;</span><span class="p">:</span>
+
+                <span class="n">interactors</span><span class="p">[</span><span class="n">i</span><span class="o">.</span><span class="n">attrs</span><span class="p">[</span><span class="s1">&#39;id&#39;</span><span class="p">]]</span> <span class="o">=</span> <span class="n">i</span><span class="o">.</span><span class="n">find</span><span class="p">(</span><span class="s1">&#39;primaryref&#39;</span><span class="p">)</span><span class="o">.</span><span class="n">attrs</span><span class="p">[</span><span class="s1">&#39;id&#39;</span><span class="p">]</span>
+
+        <span class="n">interactions_xml</span> <span class="o">=</span> <span class="n">soup</span><span class="o">.</span><span class="n">find_all</span><span class="p">(</span><span class="s1">&#39;interaction&#39;</span><span class="p">)</span>
+
+        <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="n">interactions_xml</span><span class="p">:</span>
+
+            <span class="n">description</span> <span class="o">=</span> <span class="s1">&#39;&#39;</span>
+            <span class="n">pubmeds</span> <span class="o">=</span> <span class="p">[]</span>
+            <span class="n">fullname</span> <span class="o">=</span> <span class="s1">&#39;&#39;</span>
+            <span class="n">names</span> <span class="o">=</span> <span class="p">{}</span>
+            <span class="n">pdbs</span> <span class="o">=</span> <span class="p">[]</span>
+            <span class="n">uniprots</span> <span class="o">=</span> <span class="p">[]</span>
+            <span class="n">ids</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">defaultdict</span><span class="p">(</span><span class="nb">set</span><span class="p">)</span>
+
+            <span class="k">for</span> <span class="n">a</span> <span class="ow">in</span> <span class="n">i</span><span class="o">.</span><span class="n">find_all</span><span class="p">(</span><span class="s1">&#39;attribute&#39;</span><span class="p">):</span>
+                <span class="k">if</span> <span class="n">a</span><span class="o">.</span><span class="n">attrs</span><span class="p">[</span><span class="s1">&#39;name&#39;</span><span class="p">]</span> <span class="o">==</span> <span class="s1">&#39;curated-complex&#39;</span><span class="p">:</span>
+                    <span class="n">description</span> <span class="o">=</span> <span class="n">a</span><span class="o">.</span><span class="n">text</span>
+
+            <span class="k">for</span> <span class="n">sr</span> <span class="ow">in</span> <span class="n">i</span><span class="o">.</span><span class="n">find_all</span><span class="p">(</span><span class="s1">&#39;secondaryref&#39;</span><span class="p">):</span>
+                <span class="k">if</span> <span class="n">sr</span><span class="o">.</span><span class="n">attrs</span><span class="p">[</span><span class="s1">&#39;db&#39;</span><span class="p">]</span> <span class="o">==</span> <span class="s1">&#39;pubmed&#39;</span><span class="p">:</span>
+                    <span class="n">pubmeds</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">sr</span><span class="o">.</span><span class="n">attrs</span><span class="p">[</span><span class="s1">&#39;id&#39;</span><span class="p">])</span>
+
+                <span class="k">if</span> <span class="n">sr</span><span class="o">.</span><span class="n">attrs</span><span class="p">[</span><span class="s1">&#39;db&#39;</span><span class="p">]</span> <span class="o">==</span> <span class="s1">&#39;wwpdb&#39;</span><span class="p">:</span>
+                    <span class="n">pdbs</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">sr</span><span class="o">.</span><span class="n">attrs</span><span class="p">[</span><span class="s1">&#39;id&#39;</span><span class="p">])</span>
+
+            <span class="k">for</span> <span class="n">pr</span> <span class="ow">in</span> <span class="n">i</span><span class="o">.</span><span class="n">find_all</span><span class="p">(</span><span class="s1">&#39;primaryref&#39;</span><span class="p">):</span>
+                <span class="k">if</span> <span class="n">pr</span><span class="o">.</span><span class="n">attrs</span><span class="p">[</span><span class="s1">&#39;db&#39;</span><span class="p">]</span> <span class="ow">in</span> <span class="p">{</span><span class="s1">&#39;wwpdb&#39;</span><span class="p">,</span> <span class="s1">&#39;rcsb pdb&#39;</span><span class="p">,</span> <span class="s1">&#39;pdbe&#39;</span><span class="p">}:</span>
+                    <span class="n">pdbs</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">pr</span><span class="o">.</span><span class="n">attrs</span><span class="p">[</span><span class="s1">&#39;id&#39;</span><span class="p">])</span>
+
+            <span class="k">for</span> <span class="n">sr</span> <span class="ow">in</span> <span class="n">i</span><span class="o">.</span><span class="n">find</span><span class="p">(</span><span class="s1">&#39;xref&#39;</span><span class="p">)</span><span class="o">.</span><span class="n">find_all</span><span class="p">(</span><span class="s1">&#39;secondaryref&#39;</span><span class="p">):</span>
+
+                <span class="k">if</span> <span class="p">(</span>
+                    <span class="s1">&#39;reftype&#39;</span> <span class="ow">in</span> <span class="n">sr</span><span class="o">.</span><span class="n">attrs</span> <span class="ow">and</span>
+                    <span class="n">sr</span><span class="o">.</span><span class="n">attrs</span><span class="p">[</span><span class="s1">&#39;db&#39;</span><span class="p">]</span> <span class="ow">in</span> <span class="p">{</span><span class="s1">&#39;intact&#39;</span><span class="p">,</span> <span class="s1">&#39;reactome&#39;</span><span class="p">}</span> <span class="ow">and</span>
+                    <span class="n">sr</span><span class="o">.</span><span class="n">attrs</span><span class="p">[</span><span class="s1">&#39;reftype&#39;</span><span class="p">]</span> <span class="o">==</span> <span class="s1">&#39;identity&#39;</span>
+                <span class="p">):</span>
+
+                    <span class="n">ids</span><span class="p">[</span><span class="n">sr</span><span class="o">.</span><span class="n">attrs</span><span class="p">[</span><span class="s1">&#39;db&#39;</span><span class="p">]]</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">sr</span><span class="o">.</span><span class="n">attrs</span><span class="p">[</span><span class="s1">&#39;id&#39;</span><span class="p">])</span>
+
+            <span class="n">pubmeds</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="nb">set</span><span class="p">(</span><span class="n">pubmeds</span><span class="p">))</span>
+            <span class="n">pdbs</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="nb">set</span><span class="p">(</span><span class="n">pdbs</span><span class="p">))</span>
+            <span class="n">fullname</span> <span class="o">=</span> <span class="p">(</span>
+                <span class="kc">None</span>
+                    <span class="k">if</span> <span class="n">i</span><span class="o">.</span><span class="n">find</span><span class="p">(</span><span class="s1">&#39;fullname&#39;</span><span class="p">)</span> <span class="ow">is</span> <span class="kc">None</span> <span class="k">else</span>
+                <span class="n">i</span><span class="o">.</span><span class="n">find</span><span class="p">(</span><span class="s1">&#39;fullname&#39;</span><span class="p">)</span><span class="o">.</span><span class="n">text</span>
+            <span class="p">)</span>
+
+            <span class="k">for</span> <span class="n">a</span> <span class="ow">in</span> <span class="n">i</span><span class="o">.</span><span class="n">find_all</span><span class="p">(</span><span class="s1">&#39;alias&#39;</span><span class="p">):</span>
+                <span class="n">names</span><span class="p">[</span><span class="n">a</span><span class="o">.</span><span class="n">attrs</span><span class="p">[</span><span class="s1">&#39;type&#39;</span><span class="p">]]</span> <span class="o">=</span> <span class="n">a</span><span class="o">.</span><span class="n">text</span>
+
+            <span class="k">for</span> <span class="n">intref</span> <span class="ow">in</span> <span class="n">i</span><span class="o">.</span><span class="n">find_all</span><span class="p">(</span><span class="s1">&#39;interactorref&#39;</span><span class="p">):</span>
+                <span class="n">int_id</span> <span class="o">=</span> <span class="n">intref</span><span class="o">.</span><span class="n">text</span>
+
+                <span class="k">if</span> <span class="n">int_id</span> <span class="ow">in</span> <span class="n">interactors</span><span class="p">:</span>
+                    <span class="n">uniprot</span> <span class="o">=</span> <span class="n">interactors</span><span class="p">[</span><span class="n">int_id</span><span class="p">]</span>
+
+                    <span class="k">if</span> <span class="n">uniprot</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s1">&#39;PRO&#39;</span><span class="p">):</span>
+                        <span class="k">continue</span>
+
+                    <span class="n">uniprot</span> <span class="o">=</span> <span class="n">uniprot</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;-&#39;</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span>
+                    <span class="n">uniprots</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">uniprot</span><span class="p">)</span>
+
+            <span class="k">if</span> <span class="n">uniprots</span><span class="p">:</span>
+
+                <span class="k">if</span> <span class="n">pdbs</span><span class="p">:</span>
+                    <span class="n">ids</span><span class="p">[</span><span class="s1">&#39;PDB&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">update</span><span class="p">(</span><span class="nb">set</span><span class="p">(</span><span class="n">pdbs</span><span class="p">))</span>
+
+                <span class="n">cplex</span> <span class="o">=</span> <span class="n">intera</span><span class="o">.</span><span class="n">Complex</span><span class="p">(</span>
+                    <span class="n">components</span> <span class="o">=</span> <span class="n">uniprots</span><span class="p">,</span>
+                    <span class="n">name</span> <span class="o">=</span> <span class="n">names</span><span class="p">[</span><span class="n">name_key</span><span class="p">]</span> <span class="k">if</span> <span class="n">name_key</span> <span class="ow">in</span> <span class="n">names</span> <span class="k">else</span> <span class="kc">None</span><span class="p">,</span>
+                    <span class="n">references</span> <span class="o">=</span> <span class="nb">set</span><span class="p">(</span><span class="n">pubmeds</span><span class="p">),</span>
+                    <span class="n">sources</span> <span class="o">=</span> <span class="s1">&#39;ComplexPortal&#39;</span><span class="p">,</span>
+                    <span class="n">ids</span> <span class="o">=</span> <span class="n">ids</span><span class="p">,</span>
+                <span class="p">)</span>
+
+                <span class="k">if</span> <span class="n">cplex</span><span class="o">.</span><span class="fm">__str__</span><span class="p">()</span> <span class="ow">in</span> <span class="n">complexes</span><span class="p">:</span>
+                    <span class="n">complexes</span><span class="p">[</span><span class="n">cplex</span><span class="o">.</span><span class="fm">__str__</span><span class="p">()]</span> <span class="o">+=</span> <span class="n">cplex</span>
+
+                <span class="k">else</span><span class="p">:</span>
+                    <span class="n">complexes</span><span class="p">[</span><span class="n">cplex</span><span class="o">.</span><span class="fm">__str__</span><span class="p">()]</span> <span class="o">=</span> <span class="n">cplex</span>
+
+            <span class="n">details</span><span class="o">.</span><span class="n">append</span><span class="p">({</span>
+                <span class="s1">&#39;uniprots&#39;</span><span class="p">:</span> <span class="n">uniprots</span><span class="p">,</span>
+                <span class="s1">&#39;pdbs&#39;</span><span class="p">:</span> <span class="n">pdbs</span><span class="p">,</span>
+                <span class="s1">&#39;pubmeds&#39;</span><span class="p">:</span> <span class="n">pubmeds</span><span class="p">,</span>
+                <span class="s1">&#39;fullname&#39;</span><span class="p">:</span> <span class="n">fullname</span><span class="p">,</span>
+                <span class="s1">&#39;names&#39;</span><span class="p">:</span> <span class="n">names</span><span class="p">,</span>
+                <span class="s1">&#39;description&#39;</span><span class="p">:</span> <span class="n">description</span>
+            <span class="p">})</span>
+
+    <span class="k">if</span> <span class="n">return_details</span><span class="p">:</span>
+        <span class="k">return</span> <span class="n">complexes</span><span class="p">,</span> <span class="n">details</span>
+
+    <span class="k">else</span><span class="p">:</span>
+        <span class="k">return</span> <span class="n">complexes</span></div>
+
+</pre></div>
+
+                </article>
+              
+              
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+                <article class="bd-article">
+                  
+  <h1>Source code for pypath.inputs.comppi</h1><div class="highlight"><pre>
+<span></span><span class="ch">#!/usr/bin/env python</span>
+<span class="c1"># -*- coding: utf-8 -*-</span>
+
+<span class="c1">#</span>
+<span class="c1">#  This file is part of the `pypath` python module</span>
+<span class="c1">#</span>
+<span class="c1">#  Copyright 2014-2023</span>
+<span class="c1">#  EMBL, EMBL-EBI, Uniklinik RWTH Aachen, Heidelberg University</span>
+<span class="c1">#</span>
+<span class="c1">#  Authors: see the file `README.rst`</span>
+<span class="c1">#  Contact: Dénes Türei (turei.denes@gmail.com)</span>
+<span class="c1">#</span>
+<span class="c1">#  Distributed under the GPLv3 License.</span>
+<span class="c1">#  See accompanying file LICENSE.txt or copy at</span>
+<span class="c1">#      https://www.gnu.org/licenses/gpl-3.0.html</span>
+<span class="c1">#</span>
+<span class="c1">#  Website: https://pypath.omnipathdb.org/</span>
+<span class="c1">#</span>
+
+<span class="kn">import</span> <span class="nn">itertools</span>
+<span class="kn">import</span> <span class="nn">collections</span>
+
+<span class="kn">import</span> <span class="nn">pypath.share.curl</span> <span class="k">as</span> <span class="nn">curl</span>
+<span class="kn">import</span> <span class="nn">pypath.share.session</span> <span class="k">as</span> <span class="nn">session</span>
+<span class="kn">import</span> <span class="nn">pypath.share.settings</span> <span class="k">as</span> <span class="nn">settings</span>
+<span class="kn">import</span> <span class="nn">pypath.resources.urls</span> <span class="k">as</span> <span class="nn">urls</span>
+<span class="kn">import</span> <span class="nn">pypath.utils.mapping</span> <span class="k">as</span> <span class="nn">mapping</span>
+<span class="kn">import</span> <span class="nn">pypath.utils.taxonomy</span> <span class="k">as</span> <span class="nn">taxonomy</span>
+
+<span class="n">_logger</span> <span class="o">=</span> <span class="n">session</span><span class="o">.</span><span class="n">Logger</span><span class="p">(</span><span class="n">name</span> <span class="o">=</span> <span class="s1">&#39;comppi_input&#39;</span><span class="p">)</span>
+<span class="n">_log</span> <span class="o">=</span> <span class="n">_logger</span><span class="o">.</span><span class="n">_log</span>
+
+
+<div class="viewcode-block" id="comppi_interaction_locations">
+<a class="viewcode-back" href="../../../api/pypath.inputs.comppi.comppi_interaction_locations.html#pypath.inputs.comppi.comppi_interaction_locations">[docs]</a>
+<span class="k">def</span> <span class="nf">comppi_interaction_locations</span><span class="p">(</span><span class="n">organism</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">):</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Downloads and preprocesses protein interaction and cellular compartment</span>
+<span class="sd">    association data from the ComPPI database.</span>
+<span class="sd">    This data provides scores for occurrence of protein-protein interactions</span>
+<span class="sd">    in various compartments.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="n">ComppiLocation</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">namedtuple</span><span class="p">(</span>
+        <span class="s1">&#39;ComppiLocation&#39;</span><span class="p">,</span>
+        <span class="p">[</span>
+            <span class="s1">&#39;location&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;score&#39;</span><span class="p">,</span>
+        <span class="p">],</span>
+    <span class="p">)</span>
+
+    <span class="n">ComppiInteraction</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">namedtuple</span><span class="p">(</span>
+        <span class="s1">&#39;ComppiInteraction&#39;</span><span class="p">,</span>
+        <span class="p">[</span>
+            <span class="s1">&#39;id_a&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;id_b&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;loc_a&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;loc_b&#39;</span><span class="p">,</span>
+        <span class="p">],</span>
+    <span class="p">)</span>
+
+    <span class="k">def</span> <span class="nf">process_locations</span><span class="p">(</span><span class="n">loc</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="nb">tuple</span><span class="p">(</span>
+            <span class="n">ComppiLocation</span><span class="p">(</span><span class="n">location</span> <span class="o">=</span> <span class="n">llloc</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">score</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">llloc</span><span class="p">[</span><span class="mi">1</span><span class="p">]))</span>
+            <span class="k">for</span> <span class="n">llloc</span> <span class="ow">in</span>
+            <span class="p">(</span><span class="n">lloc</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;:&#39;</span><span class="p">)</span> <span class="k">for</span> <span class="n">lloc</span> <span class="ow">in</span> <span class="n">loc</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;|&#39;</span><span class="p">))</span>
+        <span class="p">)</span>
+
+
+    <span class="n">organisms</span> <span class="o">=</span> <span class="p">{</span>
+        <span class="mi">9606</span><span class="p">:</span> <span class="mi">0</span><span class="p">,</span>
+        <span class="mi">7227</span><span class="p">:</span> <span class="mi">1</span><span class="p">,</span>
+        <span class="mi">6239</span><span class="p">:</span> <span class="mi">2</span><span class="p">,</span>
+        <span class="mi">4932</span><span class="p">:</span> <span class="mi">3</span><span class="p">,</span>
+    <span class="p">}</span>
+
+    <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">taxonomy</span><span class="o">.</span><span class="n">ensure_ncbi_tax_id</span><span class="p">(</span><span class="n">organism</span><span class="p">)</span>
+
+    <span class="k">if</span> <span class="n">ncbi_tax_id</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">organisms</span><span class="p">:</span>
+
+        <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span>
+            <span class="s1">&#39;Can not recognize organism: `</span><span class="si">%s</span><span class="s1">`. &#39;</span>
+            <span class="s1">&#39;Available organisms are human (9606), Drosophila (7227), &#39;</span>
+            <span class="s1">&#39;C. elegans (6239) and S. cerevisiae (4932).&#39;</span> <span class="o">%</span> <span class="nb">str</span><span class="p">(</span><span class="n">organism</span><span class="p">)</span>
+        <span class="p">)</span>
+
+    <span class="n">url</span> <span class="o">=</span> <span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;comppi&#39;</span><span class="p">][</span><span class="s1">&#39;url&#39;</span><span class="p">]</span>
+    <span class="n">headers</span> <span class="o">=</span> <span class="p">[</span><span class="n">settings</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">&#39;user_agent&#39;</span><span class="p">)]</span>
+
+    <span class="c1"># obtaining cookie</span>
+    <span class="n">c</span> <span class="o">=</span> <span class="n">curl</span><span class="o">.</span><span class="n">Curl</span><span class="p">(</span><span class="n">url</span><span class="p">,</span> <span class="n">cache</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span> <span class="n">req_headers</span> <span class="o">=</span> <span class="n">headers</span><span class="p">)</span>
+    <span class="n">cookie</span> <span class="o">=</span> <span class="s1">&#39;;&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">([</span>
+        <span class="n">h</span><span class="o">.</span><span class="n">decode</span><span class="p">()</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;:&#39;</span><span class="p">)[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;;&#39;</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span>
+        <span class="k">for</span> <span class="n">h</span> <span class="ow">in</span> <span class="n">c</span><span class="o">.</span><span class="n">resp_headers</span>
+        <span class="k">if</span> <span class="n">h</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="sa">b</span><span class="s1">&#39;Set-Cookie&#39;</span><span class="p">)</span>
+    <span class="p">])</span>
+    <span class="n">cookie_hdr</span> <span class="o">=</span> <span class="p">[</span><span class="s1">&#39;Cookie: </span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="n">cookie</span><span class="p">]</span>
+    <span class="n">_log</span><span class="p">(</span><span class="s1">&#39;Cookie from ComPPI: </span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="n">cookie</span><span class="p">)</span>
+
+    <span class="c1"># performing the download</span>
+    <span class="n">post</span> <span class="o">=</span> <span class="p">{</span>
+        <span class="s1">&#39;fDlSet&#39;</span><span class="p">:</span> <span class="s1">&#39;comp&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;fDlSpec&#39;</span><span class="p">:</span> <span class="s1">&#39;</span><span class="si">%u</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="n">ncbi_tax_id</span><span class="p">,</span>
+        <span class="s1">&#39;fDlMLoc&#39;</span><span class="p">:</span> <span class="s1">&#39;all&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;fDlSubmit&#39;</span><span class="p">:</span> <span class="s1">&#39;Download&#39;</span>
+    <span class="p">}</span>
+    <span class="n">c</span> <span class="o">=</span> <span class="n">curl</span><span class="o">.</span><span class="n">Curl</span><span class="p">(</span>
+        <span class="n">url</span><span class="p">,</span>
+        <span class="n">req_headers</span> <span class="o">=</span> <span class="n">headers</span> <span class="o">+</span> <span class="n">cookie_hdr</span><span class="p">,</span>
+        <span class="n">post</span> <span class="o">=</span> <span class="n">post</span><span class="p">,</span>
+        <span class="n">large</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
+        <span class="n">silent</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+        <span class="n">compr</span> <span class="o">=</span> <span class="s1">&#39;gz&#39;</span><span class="p">,</span>
+    <span class="p">)</span>
+
+    <span class="n">_</span> <span class="o">=</span> <span class="nb">next</span><span class="p">(</span><span class="n">c</span><span class="o">.</span><span class="n">result</span><span class="p">)</span>
+
+    <span class="k">for</span> <span class="n">l</span> <span class="ow">in</span> <span class="n">c</span><span class="o">.</span><span class="n">result</span><span class="p">:</span>
+
+        <span class="n">l</span> <span class="o">=</span> <span class="n">l</span><span class="o">.</span><span class="n">strip</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\r\n</span><span class="s1">&#39;</span><span class="p">)</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\t</span><span class="s1">&#39;</span><span class="p">)</span>
+
+        <span class="n">organism_a</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">l</span><span class="p">[</span><span class="mi">7</span><span class="p">])</span>
+        <span class="n">organism_b</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">l</span><span class="p">[</span><span class="mi">15</span><span class="p">])</span>
+
+        <span class="k">if</span> <span class="n">organism</span> <span class="ow">and</span> <span class="p">(</span><span class="n">organism_a</span> <span class="o">!=</span> <span class="n">organism</span> <span class="ow">or</span> <span class="n">organism_b</span> <span class="o">!=</span> <span class="n">organism</span><span class="p">):</span>
+            <span class="k">continue</span>
+
+        <span class="k">for</span> <span class="n">uniprot1</span><span class="p">,</span> <span class="n">uniprot2</span> <span class="ow">in</span> <span class="n">itertools</span><span class="o">.</span><span class="n">product</span><span class="p">(</span>
+            <span class="n">mapping</span><span class="o">.</span><span class="n">map_name</span><span class="p">(</span><span class="n">l</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="s1">&#39;uniprot&#39;</span><span class="p">,</span> <span class="s1">&#39;uniprot&#39;</span><span class="p">),</span>
+            <span class="n">mapping</span><span class="o">.</span><span class="n">map_name</span><span class="p">(</span><span class="n">l</span><span class="p">[</span><span class="mi">8</span><span class="p">],</span> <span class="s1">&#39;uniprot&#39;</span><span class="p">,</span> <span class="s1">&#39;uniprot&#39;</span><span class="p">),</span>
+        <span class="p">):</span>
+
+            <span class="k">yield</span> <span class="n">ComppiInteraction</span><span class="p">(</span>
+                <span class="n">id_a</span> <span class="o">=</span> <span class="n">uniprot1</span><span class="p">,</span>
+                <span class="n">id_b</span> <span class="o">=</span> <span class="n">uniprot2</span><span class="p">,</span>
+                <span class="n">loc_a</span> <span class="o">=</span> <span class="n">process_locations</span><span class="p">(</span><span class="n">l</span><span class="p">[</span><span class="mi">2</span><span class="p">]),</span>
+                <span class="n">loc_b</span> <span class="o">=</span> <span class="n">process_locations</span><span class="p">(</span><span class="n">l</span><span class="p">[</span><span class="mi">10</span><span class="p">]),</span>
+            <span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="comppi_locations">
+<a class="viewcode-back" href="../../../api/pypath.inputs.comppi.comppi_locations.html#pypath.inputs.comppi.comppi_locations">[docs]</a>
+<span class="k">def</span> <span class="nf">comppi_locations</span><span class="p">(</span><span class="n">organism</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">,</span> <span class="n">score_threshold</span> <span class="o">=</span> <span class="mf">.7</span><span class="p">):</span>
+
+    <span class="n">result</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">defaultdict</span><span class="p">(</span><span class="nb">set</span><span class="p">)</span>
+
+    <span class="k">for</span> <span class="n">iloc</span> <span class="ow">in</span> <span class="n">comppi_interaction_locations</span><span class="p">(</span><span class="n">organism</span> <span class="o">=</span> <span class="n">organism</span><span class="p">):</span>
+
+        <span class="k">for</span> <span class="n">label</span> <span class="ow">in</span> <span class="p">(</span><span class="s1">&#39;a&#39;</span><span class="p">,</span> <span class="s1">&#39;b&#39;</span><span class="p">):</span>
+
+            <span class="k">for</span> <span class="n">loc</span> <span class="ow">in</span> <span class="nb">getattr</span><span class="p">(</span><span class="n">iloc</span><span class="p">,</span> <span class="s1">&#39;loc_</span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="n">label</span><span class="p">):</span>
+
+                <span class="k">if</span> <span class="n">loc</span><span class="o">.</span><span class="n">location</span> <span class="o">==</span> <span class="s1">&#39;N/A&#39;</span> <span class="ow">or</span> <span class="n">loc</span><span class="o">.</span><span class="n">score</span> <span class="o">&lt;</span> <span class="n">score_threshold</span><span class="p">:</span>
+
+                    <span class="k">continue</span>
+
+                <span class="n">result</span><span class="p">[</span><span class="nb">getattr</span><span class="p">(</span><span class="n">iloc</span><span class="p">,</span> <span class="s1">&#39;id_</span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="n">label</span><span class="p">)]</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">loc</span><span class="p">)</span>
+
+    <span class="k">return</span> <span class="nb">dict</span><span class="p">(</span><span class="n">result</span><span class="p">)</span></div>
+
+</pre></div>
+
+                </article>
+              
+              
+              
+              
+              
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diff --git a/_modules/pypath/inputs/connectomedb.html b/_modules/pypath/inputs/connectomedb.html
new file mode 100644
index 000000000..6ebc245c0
--- /dev/null
+++ b/_modules/pypath/inputs/connectomedb.html
@@ -0,0 +1,717 @@
+
+<!DOCTYPE html>
+
+
+<html lang="en" data-content_root="../../../" >
+
+  <head>
+    <meta charset="utf-8" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
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+  
+  
+  
+  <script data-cfasync="false">
+    document.documentElement.dataset.mode = localStorage.getItem("mode") || "";
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+                  
+  <h1>Source code for pypath.inputs.connectomedb</h1><div class="highlight"><pre>
+<span></span><span class="ch">#!/usr/bin/env python</span>
+<span class="c1"># -*- coding: utf-8 -*-</span>
+
+<span class="c1">#</span>
+<span class="c1">#  This file is part of the `pypath` python module</span>
+<span class="c1">#</span>
+<span class="c1">#  Copyright 2014-2023</span>
+<span class="c1">#  EMBL, EMBL-EBI, Uniklinik RWTH Aachen, Heidelberg University</span>
+<span class="c1">#</span>
+<span class="c1">#  Authors: see the file `README.rst`</span>
+<span class="c1">#  Contact: Dénes Türei (turei.denes@gmail.com)</span>
+<span class="c1">#</span>
+<span class="c1">#  Distributed under the GPLv3 License.</span>
+<span class="c1">#  See accompanying file LICENSE.txt or copy at</span>
+<span class="c1">#      https://www.gnu.org/licenses/gpl-3.0.html</span>
+<span class="c1">#</span>
+<span class="c1">#  Website: https://pypath.omnipathdb.org/</span>
+<span class="c1">#</span>
+
+<span class="kn">import</span> <span class="nn">re</span>
+<span class="kn">import</span> <span class="nn">csv</span>
+<span class="kn">import</span> <span class="nn">collections</span>
+<span class="kn">import</span> <span class="nn">itertools</span>
+
+<span class="kn">import</span> <span class="nn">pypath.resources.urls</span> <span class="k">as</span> <span class="nn">urls</span>
+<span class="kn">import</span> <span class="nn">pypath.share.curl</span> <span class="k">as</span> <span class="nn">curl</span>
+<span class="kn">import</span> <span class="nn">pypath.utils.mapping</span> <span class="k">as</span> <span class="nn">mapping</span>
+
+
+<div class="viewcode-block" id="connectomedb_interactions">
+<a class="viewcode-back" href="../../../api/pypath.inputs.connectomedb.connectomedb_interactions.html#pypath.inputs.connectomedb.connectomedb_interactions">[docs]</a>
+<span class="k">def</span> <span class="nf">connectomedb_interactions</span><span class="p">():</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Retrieves ligand-receptor interactions from connectomeDB2020</span>
+<span class="sd">    https://asrhou.github.io/NATMI/</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="n">ConnectomedbInteraction</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">namedtuple</span><span class="p">(</span>
+        <span class="s1">&#39;ConnectomedbInteraction&#39;</span><span class="p">,</span>
+        <span class="p">[</span>
+            <span class="s1">&#39;ligand&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;ligand_location&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;receptor&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;references&#39;</span><span class="p">,</span>
+        <span class="p">]</span>
+    <span class="p">)</span>
+
+    <span class="n">rea</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">compile</span><span class="p">(</span><span class="sa">r</span><span class="s1">&#39;&lt;a[^&gt;]+&gt;([^&lt;]*)&lt;/a&gt;&#39;</span><span class="p">)</span>
+    <span class="n">resemicol</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">compile</span><span class="p">(</span><span class="sa">r</span><span class="s1">&#39;; ?&#39;</span><span class="p">)</span>
+
+    <span class="n">url</span> <span class="o">=</span> <span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;connectomedb2020&#39;</span><span class="p">][</span><span class="s1">&#39;url&#39;</span><span class="p">]</span>
+    <span class="n">c</span> <span class="o">=</span> <span class="n">curl</span><span class="o">.</span><span class="n">Curl</span><span class="p">(</span><span class="n">url</span><span class="p">,</span> <span class="n">large</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span> <span class="n">silent</span> <span class="o">=</span> <span class="kc">False</span><span class="p">)</span>
+    <span class="n">tab</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="n">csv</span><span class="o">.</span><span class="n">DictReader</span><span class="p">(</span><span class="n">c</span><span class="o">.</span><span class="n">result</span><span class="p">))</span>
+
+    <span class="k">return</span> <span class="p">[</span>
+        <span class="n">ConnectomedbInteraction</span><span class="p">(</span>
+            <span class="n">ligand</span> <span class="o">=</span> <span class="n">row</span><span class="p">[</span><span class="s1">&#39;Ligand gene symbol&#39;</span><span class="p">],</span>
+            <span class="n">ligand_location</span> <span class="o">=</span> <span class="n">resemicol</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="n">row</span><span class="p">[</span><span class="s1">&#39;Ligand location&#39;</span><span class="p">]),</span>
+            <span class="n">receptor</span> <span class="o">=</span> <span class="n">row</span><span class="p">[</span><span class="s1">&#39;Receptor gene symbol&#39;</span><span class="p">],</span>
+            <span class="n">references</span> <span class="o">=</span> <span class="n">rea</span><span class="o">.</span><span class="n">findall</span><span class="p">(</span><span class="n">row</span><span class="p">[</span><span class="s1">&#39;PMID support&#39;</span><span class="p">]),</span>
+        <span class="p">)</span>
+        <span class="k">for</span> <span class="n">row</span> <span class="ow">in</span> <span class="n">tab</span>
+    <span class="p">]</span></div>
+
+
+
+<div class="viewcode-block" id="connectomedb_annotations">
+<a class="viewcode-back" href="../../../api/pypath.inputs.connectomedb.connectomedb_annotations.html#pypath.inputs.connectomedb.connectomedb_annotations">[docs]</a>
+<span class="k">def</span> <span class="nf">connectomedb_annotations</span><span class="p">():</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Retrieves ligand and receptor annotations from connectomeDB2020</span>
+<span class="sd">    https://asrhou.github.io/NATMI/</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="n">ConnectomedbAnnotation</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">namedtuple</span><span class="p">(</span>
+        <span class="s1">&#39;ConnectomedbAnnotation&#39;</span><span class="p">,</span>
+        <span class="p">[</span>
+            <span class="s1">&#39;role&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;location&#39;</span><span class="p">,</span>
+        <span class="p">]</span>
+    <span class="p">)</span>
+
+    <span class="n">interactions</span> <span class="o">=</span> <span class="n">connectomedb_interactions</span><span class="p">()</span>
+
+    <span class="n">result</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">defaultdict</span><span class="p">(</span><span class="nb">set</span><span class="p">)</span>
+
+    <span class="k">for</span> <span class="n">ia</span> <span class="ow">in</span> <span class="n">interactions</span><span class="p">:</span>
+
+        <span class="k">for</span> <span class="n">role</span> <span class="ow">in</span> <span class="p">(</span><span class="s1">&#39;ligand&#39;</span><span class="p">,</span> <span class="s1">&#39;receptor&#39;</span><span class="p">):</span>
+
+            <span class="n">loc_attr</span> <span class="o">=</span> <span class="s1">&#39;</span><span class="si">%s</span><span class="s1">_location&#39;</span> <span class="o">%</span> <span class="n">role</span>
+            <span class="n">locations</span> <span class="o">=</span> <span class="p">(</span>
+                <span class="nb">getattr</span><span class="p">(</span><span class="n">ia</span><span class="p">,</span> <span class="n">loc_attr</span><span class="p">)</span>
+                    <span class="k">if</span> <span class="nb">hasattr</span><span class="p">(</span><span class="n">ia</span><span class="p">,</span> <span class="n">loc_attr</span><span class="p">)</span> <span class="k">else</span>
+                <span class="p">(</span><span class="s1">&#39;plasma membrane&#39;</span><span class="p">,)</span>
+            <span class="p">)</span>
+
+            <span class="n">uniprots</span> <span class="o">=</span> <span class="n">mapping</span><span class="o">.</span><span class="n">map_name</span><span class="p">(</span>
+                <span class="nb">getattr</span><span class="p">(</span><span class="n">ia</span><span class="p">,</span> <span class="n">role</span><span class="p">),</span>
+                <span class="s1">&#39;genesymbol&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;uniprot&#39;</span><span class="p">,</span>
+            <span class="p">)</span>
+
+            <span class="k">for</span> <span class="n">uniprot</span><span class="p">,</span> <span class="n">location</span> <span class="ow">in</span> <span class="n">itertools</span><span class="o">.</span><span class="n">product</span><span class="p">(</span><span class="n">uniprots</span><span class="p">,</span> <span class="n">locations</span><span class="p">):</span>
+
+                <span class="n">result</span><span class="p">[</span><span class="n">uniprot</span><span class="p">]</span><span class="o">.</span><span class="n">add</span><span class="p">(</span>
+                    <span class="n">ConnectomedbAnnotation</span><span class="p">(</span>
+                        <span class="n">role</span> <span class="o">=</span> <span class="n">role</span><span class="p">,</span>
+                        <span class="n">location</span> <span class="o">=</span> <span class="n">location</span><span class="p">,</span>
+                    <span class="p">)</span>
+                <span class="p">)</span>
+
+    <span class="k">return</span> <span class="nb">dict</span><span class="p">(</span><span class="n">result</span><span class="p">)</span></div>
+
+</pre></div>
+
+                </article>
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+  <h1>Source code for pypath.inputs.corum</h1><div class="highlight"><pre>
+<span></span><span class="ch">#!/usr/bin/env python</span>
+<span class="c1"># -*- coding: utf-8 -*-</span>
+
+<span class="c1">#</span>
+<span class="c1">#  This file is part of the `pypath` python module</span>
+<span class="c1">#</span>
+<span class="c1">#  Copyright 2014-2023</span>
+<span class="c1">#  EMBL, EMBL-EBI, Uniklinik RWTH Aachen, Heidelberg University</span>
+<span class="c1">#</span>
+<span class="c1">#  Authors: see the file `README.rst`</span>
+<span class="c1">#  Contact: Dénes Türei (turei.denes@gmail.com)</span>
+<span class="c1">#</span>
+<span class="c1">#  Distributed under the GPLv3 License.</span>
+<span class="c1">#  See accompanying file LICENSE.txt or copy at</span>
+<span class="c1">#      https://www.gnu.org/licenses/gpl-3.0.html</span>
+<span class="c1">#</span>
+<span class="c1">#  Website: https://pypath.omnipathdb.org/</span>
+<span class="c1">#</span>
+
+<span class="kn">import</span> <span class="nn">csv</span>
+
+<span class="kn">import</span> <span class="nn">pypath.share.curl</span> <span class="k">as</span> <span class="nn">curl</span>
+<span class="kn">import</span> <span class="nn">pypath.resources.urls</span> <span class="k">as</span> <span class="nn">urls</span>
+<span class="kn">import</span> <span class="nn">pypath.internals.intera</span> <span class="k">as</span> <span class="nn">intera</span>
+<span class="kn">import</span> <span class="nn">pypath.utils.taxonomy</span> <span class="k">as</span> <span class="nn">taxonomy</span>
+
+
+<div class="viewcode-block" id="corum_complexes">
+<a class="viewcode-back" href="../../../api/pypath.inputs.corum.corum_complexes.html#pypath.inputs.corum.corum_complexes">[docs]</a>
+<span class="k">def</span> <span class="nf">corum_complexes</span><span class="p">(</span><span class="n">organism</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">):</span>
+    <span class="n">annots</span> <span class="o">=</span> <span class="p">(</span>
+        <span class="s1">&#39;mithocondr&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;nucleus&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;endoplasmic reticulum&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;cytoplasm&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;transcriptional control&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;vesicle docking&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;extracellular matrix component&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;cell-matrix adhesion&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;cytokines&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;cell death&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;integrin receptor signalling pathway&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;eukaryotic plasma membrane&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;nuclear membrane&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;cellular export and secretion&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;cell-substrate adherens junction&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;cytoskeleton&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;receptor binding&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;nucleolus&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;transmembrane signal transduction&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;transcription&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;modification by phosphorylation&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;cell-cell adhesion&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;intercellular junction&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;ion transport&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;cell adhesion&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;cell junction&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;endocytosis&#39;</span><span class="p">,</span>
+    <span class="p">)</span>
+
+    <span class="n">organism</span> <span class="o">=</span> <span class="n">taxonomy</span><span class="o">.</span><span class="n">ensure_ncbi_tax_id</span><span class="p">(</span><span class="n">organism</span><span class="p">)</span>
+
+    <span class="n">complexes</span> <span class="o">=</span> <span class="p">{}</span>
+
+    <span class="n">c</span> <span class="o">=</span> <span class="n">curl</span><span class="o">.</span><span class="n">Curl</span><span class="p">(</span>
+        <span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;corum&#39;</span><span class="p">][</span><span class="s1">&#39;url_rescued&#39;</span><span class="p">],</span>
+        <span class="n">silent</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+        <span class="n">large</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
+        <span class="n">files_needed</span> <span class="o">=</span> <span class="p">[</span><span class="s1">&#39;allComplexes.txt&#39;</span><span class="p">],</span>
+    <span class="p">)</span>
+
+    <span class="n">tab</span> <span class="o">=</span> <span class="n">csv</span><span class="o">.</span><span class="n">DictReader</span><span class="p">(</span><span class="n">c</span><span class="o">.</span><span class="n">result</span><span class="p">[</span><span class="s1">&#39;allComplexes.txt&#39;</span><span class="p">],</span> <span class="n">delimiter</span> <span class="o">=</span> <span class="s1">&#39;</span><span class="se">\t</span><span class="s1">&#39;</span><span class="p">)</span>
+
+    <span class="k">for</span> <span class="n">rec</span> <span class="ow">in</span> <span class="n">tab</span><span class="p">:</span>
+
+        <span class="n">cplex_organism</span> <span class="o">=</span> <span class="n">rec</span><span class="p">[</span><span class="s1">&#39;Organism&#39;</span><span class="p">]</span>
+
+        <span class="k">if</span> <span class="n">taxonomy</span><span class="o">.</span><span class="n">ensure_ncbi_tax_id</span><span class="p">(</span><span class="n">cplex_organism</span><span class="p">)</span> <span class="o">!=</span> <span class="n">organism</span><span class="p">:</span>
+
+            <span class="k">continue</span>
+
+        <span class="n">uniprots</span> <span class="o">=</span> <span class="n">rec</span><span class="p">[</span><span class="s1">&#39;subunits(UniProt IDs)&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;;&#39;</span><span class="p">)</span>
+
+        <span class="n">pubmeds</span>  <span class="o">=</span> <span class="n">rec</span><span class="p">[</span><span class="s1">&#39;PubMed ID&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;;&#39;</span><span class="p">)</span>
+        <span class="n">name</span>     <span class="o">=</span> <span class="n">rec</span><span class="p">[</span><span class="s1">&#39;ComplexName&#39;</span><span class="p">]</span>
+
+        <span class="n">cplex</span> <span class="o">=</span> <span class="n">intera</span><span class="o">.</span><span class="n">Complex</span><span class="p">(</span>
+            <span class="n">name</span> <span class="o">=</span> <span class="n">name</span><span class="p">,</span>
+            <span class="n">components</span> <span class="o">=</span> <span class="n">uniprots</span><span class="p">,</span>
+            <span class="n">sources</span> <span class="o">=</span> <span class="s1">&#39;CORUM&#39;</span><span class="p">,</span>
+            <span class="n">references</span> <span class="o">=</span> <span class="n">pubmeds</span><span class="p">,</span>
+            <span class="n">ids</span> <span class="o">=</span> <span class="n">rec</span><span class="p">[</span><span class="s1">&#39;ComplexID&#39;</span><span class="p">],</span>
+            <span class="n">attrs</span> <span class="o">=</span> <span class="p">{</span>
+                <span class="s1">&#39;funcat&#39;</span><span class="p">:</span> <span class="nb">set</span><span class="p">(</span><span class="n">rec</span><span class="p">[</span><span class="s1">&#39;FunCat description&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;;&#39;</span><span class="p">)),</span>
+                <span class="s1">&#39;go&#39;</span><span class="p">:</span> <span class="nb">set</span><span class="p">(</span><span class="n">rec</span><span class="p">[</span><span class="s1">&#39;GO description&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;;&#39;</span><span class="p">)),</span>
+            <span class="p">},</span>
+        <span class="p">)</span>
+
+        <span class="k">if</span> <span class="n">cplex</span><span class="o">.</span><span class="fm">__str__</span><span class="p">()</span> <span class="ow">in</span> <span class="n">complexes</span><span class="p">:</span>
+
+            <span class="n">complexes</span><span class="p">[</span><span class="n">cplex</span><span class="o">.</span><span class="fm">__str__</span><span class="p">()]</span><span class="o">.</span><span class="n">references</span><span class="o">.</span><span class="n">update</span><span class="p">(</span><span class="nb">set</span><span class="p">(</span><span class="n">pubmeds</span><span class="p">))</span>
+
+        <span class="k">else</span><span class="p">:</span>
+
+            <span class="n">complexes</span><span class="p">[</span><span class="n">cplex</span><span class="o">.</span><span class="fm">__str__</span><span class="p">()]</span> <span class="o">=</span> <span class="n">cplex</span>
+
+    <span class="k">return</span> <span class="n">complexes</span></div>
+
+</pre></div>
+
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+                  
+  <h1>Source code for pypath.inputs.cosmic</h1><div class="highlight"><pre>
+<span></span><span class="ch">#!/usr/bin/env python</span>
+<span class="c1"># -*- coding: utf-8 -*-</span>
+
+<span class="c1">#</span>
+<span class="c1">#  This file is part of the `pypath` python module</span>
+<span class="c1">#</span>
+<span class="c1">#  Copyright 2014-2023</span>
+<span class="c1">#  EMBL, EMBL-EBI, Uniklinik RWTH Aachen, Heidelberg University</span>
+<span class="c1">#</span>
+<span class="c1">#  Authors: see the file `README.rst`</span>
+<span class="c1">#  Contact: Dénes Türei (turei.denes@gmail.com)</span>
+<span class="c1">#</span>
+<span class="c1">#  Distributed under the GPLv3 License.</span>
+<span class="c1">#  See accompanying file LICENSE.txt or copy at</span>
+<span class="c1">#      https://www.gnu.org/licenses/gpl-3.0.html</span>
+<span class="c1">#</span>
+<span class="c1">#  Website: https://pypath.omnipathdb.org/</span>
+<span class="c1">#</span>
+
+<span class="kn">import</span> <span class="nn">os</span>
+<span class="kn">import</span> <span class="nn">csv</span>
+<span class="kn">import</span> <span class="nn">collections</span>
+<span class="kn">import</span> <span class="nn">base64</span>
+<span class="kn">import</span> <span class="nn">json</span>
+
+<span class="kn">import</span> <span class="nn">pypath.resources.urls</span> <span class="k">as</span> <span class="nn">urls</span>
+<span class="kn">import</span> <span class="nn">pypath.share.curl</span> <span class="k">as</span> <span class="nn">curl</span>
+<span class="kn">import</span> <span class="nn">pypath.share.session</span> <span class="k">as</span> <span class="nn">session_mod</span>
+<span class="kn">import</span> <span class="nn">pypath.share.settings</span> <span class="k">as</span> <span class="nn">settings</span>
+<span class="kn">import</span> <span class="nn">pypath.utils.mapping</span> <span class="k">as</span> <span class="nn">mapping</span>
+<span class="kn">import</span> <span class="nn">pypath.inputs.credentials</span> <span class="k">as</span> <span class="nn">credentials</span>
+
+<span class="n">_logger</span> <span class="o">=</span> <span class="n">session_mod</span><span class="o">.</span><span class="n">Logger</span><span class="p">(</span><span class="n">name</span> <span class="o">=</span> <span class="s1">&#39;cosmic_input&#39;</span><span class="p">)</span>
+<span class="n">_log</span> <span class="o">=</span> <span class="n">_logger</span><span class="o">.</span><span class="n">_log</span>
+
+
+<div class="viewcode-block" id="cancer_gene_census_annotations">
+<a class="viewcode-back" href="../../../api/pypath.inputs.cosmic.cancer_gene_census_annotations.html#pypath.inputs.cosmic.cancer_gene_census_annotations">[docs]</a>
+<span class="k">def</span> <span class="nf">cancer_gene_census_annotations</span><span class="p">(</span>
+        <span class="n">user</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+        <span class="n">passwd</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+        <span class="n">credentials_fname</span> <span class="o">=</span> <span class="s1">&#39;cosmic_credentials&#39;</span><span class="p">,</span>
+    <span class="p">):</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Retrieves a list of cancer driver genes (Cancer Gene Census) from</span>
+<span class="sd">    the Sanger COSMIC (Catalogue of Somatic Mutations in Cancer) database.</span>
+<span class="sd">    Returns dict of annotations.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="k">try</span><span class="p">:</span>
+
+        <span class="n">cosmic_cred</span> <span class="o">=</span> <span class="n">credentials</span><span class="o">.</span><span class="n">credentials</span><span class="p">(</span>
+            <span class="n">user</span> <span class="o">=</span> <span class="n">user</span><span class="p">,</span>
+            <span class="n">passwd</span> <span class="o">=</span> <span class="n">passwd</span><span class="p">,</span>
+            <span class="n">resource</span> <span class="o">=</span> <span class="s1">&#39;COSMIC&#39;</span><span class="p">,</span>
+            <span class="n">from_file</span> <span class="o">=</span> <span class="n">credentials_fname</span><span class="p">,</span>
+        <span class="p">)</span>
+
+    <span class="k">except</span> <span class="ne">RuntimeError</span><span class="p">:</span>
+
+        <span class="n">_log</span><span class="p">(</span>
+            <span class="s1">&#39;No credentials available for the COSMIC website. &#39;</span>
+            <span class="s1">&#39;Either set the `cosmic_credentials` key in the `settings` &#39;</span>
+            <span class="s1">&#39;module (e.g. `{</span><span class="se">\&#39;</span><span class="s1">user</span><span class="se">\&#39;</span><span class="s1">: </span><span class="se">\&#39;</span><span class="s1">myuser</span><span class="se">\&#39;</span><span class="s1">, &#39;</span>
+            <span class="s1">&#39;</span><span class="se">\&#39;</span><span class="s1">passwd</span><span class="se">\&#39;</span><span class="s1">: </span><span class="se">\&#39;</span><span class="s1">mypassword</span><span class="se">\&#39;</span><span class="s1">}`), or pass them directly to the &#39;</span>
+            <span class="s1">&#39;`pypath.inputs.cosmic.cancer_gene_census_annotations` &#39;</span>
+            <span class="s1">&#39;method.&#39;</span>
+        <span class="p">)</span>
+
+        <span class="k">return</span> <span class="p">{}</span>
+
+    <span class="n">CancerGeneCensusAnnotation</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">namedtuple</span><span class="p">(</span>
+        <span class="s1">&#39;CancerGeneCensusAnnotation&#39;</span><span class="p">,</span>
+        <span class="p">(</span>
+            <span class="s1">&#39;tier&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;hallmark&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;somatic&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;germline&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;tumour_types_somatic&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;tumour_types_germline&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;cancer_syndrome&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;tissue_type&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;genetics&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;role&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;mutation_type&#39;</span><span class="p">,</span>
+        <span class="p">),</span>
+    <span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">multi_field</span><span class="p">(</span><span class="n">content</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="p">(</span>
+            <span class="nb">tuple</span><span class="p">(</span><span class="nb">sorted</span><span class="p">(</span><span class="n">i</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span> <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="n">content</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;,&#39;</span><span class="p">)))</span>
+                <span class="k">if</span> <span class="n">content</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span> <span class="k">else</span>
+            <span class="p">()</span>
+        <span class="p">)</span>
+
+
+    <span class="n">url</span> <span class="o">=</span> <span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;cgc&#39;</span><span class="p">][</span><span class="s1">&#39;url_new&#39;</span><span class="p">]</span>
+
+    <span class="n">auth_str</span> <span class="o">=</span> <span class="n">base64</span><span class="o">.</span><span class="n">b64encode</span><span class="p">(</span>
+        <span class="p">(</span><span class="s1">&#39;</span><span class="si">%s</span><span class="s1">:</span><span class="si">%s</span><span class="se">\n</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="p">(</span><span class="n">cosmic_cred</span><span class="p">[</span><span class="s1">&#39;user&#39;</span><span class="p">],</span> <span class="n">cosmic_cred</span><span class="p">[</span><span class="s1">&#39;passwd&#39;</span><span class="p">]))</span><span class="o">.</span><span class="n">encode</span><span class="p">()</span>
+    <span class="p">)</span>
+
+    <span class="n">req_hdrs</span> <span class="o">=</span> <span class="p">[</span><span class="s1">&#39;Authorization: Basic </span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="n">auth_str</span><span class="o">.</span><span class="n">decode</span><span class="p">()]</span>
+
+    <span class="n">c</span> <span class="o">=</span> <span class="n">curl</span><span class="o">.</span><span class="n">Curl</span><span class="p">(</span>
+        <span class="n">url</span><span class="p">,</span>
+        <span class="n">large</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+        <span class="n">silent</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+        <span class="n">req_headers</span> <span class="o">=</span> <span class="n">req_hdrs</span><span class="p">,</span>
+        <span class="n">cache</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+    <span class="p">)</span>
+
+    <span class="n">access_url</span> <span class="o">=</span> <span class="n">json</span><span class="o">.</span><span class="n">loads</span><span class="p">(</span><span class="n">c</span><span class="o">.</span><span class="n">result</span><span class="p">)</span>
+
+    <span class="k">if</span> <span class="s1">&#39;url&#39;</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">access_url</span><span class="p">:</span>
+
+        <span class="n">_log</span><span class="p">(</span>
+            <span class="s1">&#39;Could not retrieve COSMIC access URL. &#39;</span>
+            <span class="s1">&#39;Most likely the authentication failed. &#39;</span>
+            <span class="s1">&#39;The reply was: `</span><span class="si">%s</span><span class="s1">`&#39;</span> <span class="o">%</span> <span class="n">c</span><span class="o">.</span><span class="n">result</span>
+        <span class="p">)</span>
+
+        <span class="k">return</span> <span class="kc">None</span>
+
+    <span class="n">c</span> <span class="o">=</span> <span class="n">curl</span><span class="o">.</span><span class="n">Curl</span><span class="p">(</span>
+        <span class="n">access_url</span><span class="p">[</span><span class="s1">&#39;url&#39;</span><span class="p">],</span>
+        <span class="n">large</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
+        <span class="n">silent</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+        <span class="n">bypass_url_encoding</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
+    <span class="p">)</span>
+
+    <span class="n">data</span> <span class="o">=</span> <span class="n">csv</span><span class="o">.</span><span class="n">DictReader</span><span class="p">(</span><span class="n">c</span><span class="o">.</span><span class="n">fileobj</span><span class="p">,</span> <span class="n">delimiter</span> <span class="o">=</span> <span class="s1">&#39;,&#39;</span><span class="p">)</span>
+    <span class="n">result</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">defaultdict</span><span class="p">(</span><span class="nb">set</span><span class="p">)</span>
+
+    <span class="k">for</span> <span class="n">rec</span> <span class="ow">in</span> <span class="n">data</span><span class="p">:</span>
+
+        <span class="n">uniprots</span> <span class="o">=</span> <span class="n">mapping</span><span class="o">.</span><span class="n">map_name</span><span class="p">(</span>
+            <span class="n">rec</span><span class="p">[</span><span class="s1">&#39;Gene Symbol&#39;</span><span class="p">],</span>
+            <span class="s1">&#39;genesymbol&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;uniprot&#39;</span><span class="p">,</span>
+        <span class="p">)</span>
+
+        <span class="k">for</span> <span class="n">uniprot</span> <span class="ow">in</span> <span class="n">uniprots</span><span class="p">:</span>
+
+            <span class="n">result</span><span class="p">[</span><span class="n">uniprot</span><span class="p">]</span><span class="o">.</span><span class="n">add</span><span class="p">(</span>
+                <span class="n">CancerGeneCensusAnnotation</span><span class="p">(</span>
+                    <span class="n">tier</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">rec</span><span class="p">[</span><span class="s1">&#39;Tier&#39;</span><span class="p">]),</span>
+                    <span class="n">hallmark</span> <span class="o">=</span> <span class="n">rec</span><span class="p">[</span><span class="s1">&#39;Hallmark&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span> <span class="o">==</span> <span class="s1">&#39;yes&#39;</span><span class="p">,</span>
+                    <span class="n">somatic</span> <span class="o">=</span> <span class="n">rec</span><span class="p">[</span><span class="s1">&#39;Somatic&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span> <span class="o">==</span> <span class="s1">&#39;yes&#39;</span><span class="p">,</span>
+                    <span class="n">germline</span> <span class="o">=</span> <span class="n">rec</span><span class="p">[</span><span class="s1">&#39;Germline&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span> <span class="o">==</span> <span class="s1">&#39;yes&#39;</span><span class="p">,</span>
+                    <span class="n">tumour_types_somatic</span> <span class="o">=</span> <span class="p">(</span>
+                        <span class="n">multi_field</span><span class="p">(</span><span class="n">rec</span><span class="p">[</span><span class="s1">&#39;Tumour Types(Somatic)&#39;</span><span class="p">])</span>
+                    <span class="p">),</span>
+                    <span class="n">tumour_types_germline</span> <span class="o">=</span> <span class="p">(</span>
+                        <span class="n">multi_field</span><span class="p">(</span><span class="n">rec</span><span class="p">[</span><span class="s1">&#39;Tumour Types(Germline)&#39;</span><span class="p">])</span>
+                    <span class="p">),</span>
+                    <span class="n">cancer_syndrome</span> <span class="o">=</span> <span class="p">(</span>
+                        <span class="n">multi_field</span><span class="p">(</span><span class="n">rec</span><span class="p">[</span><span class="s1">&#39;Cancer Syndrome&#39;</span><span class="p">])</span>
+                    <span class="p">),</span>
+                    <span class="n">tissue_type</span> <span class="o">=</span> <span class="p">(</span>
+                        <span class="n">multi_field</span><span class="p">(</span><span class="n">rec</span><span class="p">[</span><span class="s1">&#39;Tissue Type&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s1">&#39; &#39;</span><span class="p">,</span> <span class="s1">&#39;&#39;</span><span class="p">))</span>
+                    <span class="p">),</span>
+                    <span class="n">genetics</span> <span class="o">=</span> <span class="n">rec</span><span class="p">[</span><span class="s1">&#39;Molecular Genetics&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span> <span class="ow">or</span> <span class="kc">None</span><span class="p">,</span>
+                    <span class="n">role</span> <span class="o">=</span> <span class="p">(</span>
+                        <span class="n">multi_field</span><span class="p">(</span><span class="n">rec</span><span class="p">[</span><span class="s1">&#39;Role in Cancer&#39;</span><span class="p">])</span>
+                    <span class="p">),</span>
+                    <span class="n">mutation_type</span> <span class="o">=</span> <span class="p">(</span>
+                        <span class="n">multi_field</span><span class="p">(</span><span class="n">rec</span><span class="p">[</span><span class="s1">&#39;Mutation Types&#39;</span><span class="p">])</span>
+                    <span class="p">),</span>
+                <span class="p">)</span>
+            <span class="p">)</span>
+
+    <span class="k">return</span> <span class="nb">dict</span><span class="p">(</span><span class="n">result</span><span class="p">)</span></div>
+
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diff --git a/_modules/pypath/inputs/cpad.html b/_modules/pypath/inputs/cpad.html
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+  <h1>Source code for pypath.inputs.cpad</h1><div class="highlight"><pre>
+<span></span><span class="ch">#!/usr/bin/env python</span>
+<span class="c1"># -*- coding: utf-8 -*-</span>
+
+<span class="c1">#</span>
+<span class="c1">#  This file is part of the `pypath` python module</span>
+<span class="c1">#</span>
+<span class="c1">#  Copyright 2014-2023</span>
+<span class="c1">#  EMBL, EMBL-EBI, Uniklinik RWTH Aachen, Heidelberg University</span>
+<span class="c1">#</span>
+<span class="c1">#  Authors: see the file `README.rst`</span>
+<span class="c1">#  Contact: Dénes Türei (turei.denes@gmail.com)</span>
+<span class="c1">#</span>
+<span class="c1">#  Distributed under the GPLv3 License.</span>
+<span class="c1">#  See accompanying file LICENSE.txt or copy at</span>
+<span class="c1">#      https://www.gnu.org/licenses/gpl-3.0.html</span>
+<span class="c1">#</span>
+<span class="c1">#  Website: https://pypath.omnipathdb.org/</span>
+<span class="c1">#</span>
+
+<span class="kn">import</span> <span class="nn">csv</span>
+<span class="kn">import</span> <span class="nn">collections</span>
+
+<span class="kn">import</span> <span class="nn">pypath.share.curl</span> <span class="k">as</span> <span class="nn">curl</span>
+<span class="kn">import</span> <span class="nn">pypath.share.common</span> <span class="k">as</span> <span class="nn">common</span>
+<span class="kn">import</span> <span class="nn">pypath.resources.urls</span> <span class="k">as</span> <span class="nn">urls</span>
+<span class="kn">import</span> <span class="nn">pypath.utils.mapping</span> <span class="k">as</span> <span class="nn">mapping</span>
+
+
+<div class="viewcode-block" id="get_cpad">
+<a class="viewcode-back" href="../../../api/pypath.inputs.cpad.get_cpad.html#pypath.inputs.cpad.get_cpad">[docs]</a>
+<span class="k">def</span> <span class="nf">get_cpad</span><span class="p">():</span>
+
+    <span class="n">url</span> <span class="o">=</span> <span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;cpad&#39;</span><span class="p">][</span><span class="s1">&#39;url&#39;</span><span class="p">]</span>
+    <span class="n">c</span> <span class="o">=</span> <span class="n">curl</span><span class="o">.</span><span class="n">Curl</span><span class="p">(</span><span class="n">url</span><span class="p">,</span> <span class="n">silent</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span> <span class="n">large</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span> <span class="n">encoding</span> <span class="o">=</span> <span class="s1">&#39;iso-8859-1&#39;</span><span class="p">)</span>
+    <span class="n">reader</span> <span class="o">=</span> <span class="n">csv</span><span class="o">.</span><span class="n">DictReader</span><span class="p">(</span><span class="n">c</span><span class="o">.</span><span class="n">result</span><span class="p">,</span> <span class="n">delimiter</span> <span class="o">=</span> <span class="s1">&#39;</span><span class="se">\t</span><span class="s1">&#39;</span><span class="p">)</span>
+
+    <span class="k">return</span> <span class="n">reader</span></div>
+
+
+
+<div class="viewcode-block" id="cpad_annotations">
+<a class="viewcode-back" href="../../../api/pypath.inputs.cpad.cpad_annotations.html#pypath.inputs.cpad.cpad_annotations">[docs]</a>
+<span class="k">def</span> <span class="nf">cpad_annotations</span><span class="p">(</span><span class="n">include_unknown_type</span> <span class="o">=</span> <span class="kc">False</span><span class="p">):</span>
+
+    <span class="n">CpadAnnotation</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">namedtuple</span><span class="p">(</span>
+        <span class="s1">&#39;CpadAnnotation&#39;</span><span class="p">,</span>
+        <span class="p">[</span>
+            <span class="s1">&#39;regulator_type&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;effect_on_pathway&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;pathway&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;effect_on_cancer&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;effect_on_cancer_outcome&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;cancer&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;pathway_category&#39;</span><span class="p">,</span>
+        <span class="p">]</span>
+    <span class="p">)</span>
+
+    <span class="n">cpad</span> <span class="o">=</span> <span class="n">get_cpad</span><span class="p">()</span>
+
+    <span class="n">result</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">defaultdict</span><span class="p">(</span><span class="nb">set</span><span class="p">)</span>
+
+    <span class="k">for</span> <span class="n">rec</span> <span class="ow">in</span> <span class="n">cpad</span><span class="p">:</span>
+        <span class="k">if</span> <span class="n">rec</span><span class="p">[</span><span class="s1">&#39;Regulator&#39;</span><span class="p">]</span> <span class="o">==</span> <span class="s1">&#39;NULL&#39;</span><span class="p">:</span>
+            <span class="k">continue</span>
+
+        <span class="k">for</span> <span class="n">regulator</span> <span class="ow">in</span> <span class="n">rec</span><span class="p">[</span><span class="s1">&#39;Regulator&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39; and &#39;</span><span class="p">):</span>
+            <span class="n">uniprot</span> <span class="o">=</span> <span class="n">mapping</span><span class="o">.</span><span class="n">map_name0</span><span class="p">(</span><span class="n">regulator</span><span class="p">,</span> <span class="s1">&#39;genesymbol&#39;</span><span class="p">,</span> <span class="s1">&#39;uniprot&#39;</span><span class="p">)</span>
+
+            <span class="k">if</span> <span class="n">uniprot</span><span class="p">:</span>
+                <span class="n">regulator_name</span> <span class="o">=</span> <span class="n">uniprot</span>
+                <span class="n">regulator_type</span> <span class="o">=</span> <span class="s1">&#39;protein&#39;</span>
+
+            <span class="k">else</span><span class="p">:</span>
+                <span class="n">mirbase</span> <span class="o">=</span> <span class="n">mapping</span><span class="o">.</span><span class="n">map_name</span><span class="p">(</span>
+                    <span class="s1">&#39;hsa-</span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="n">regulator</span><span class="p">,</span>
+                    <span class="s1">&#39;mir-mat-name&#39;</span><span class="p">,</span>
+                    <span class="s1">&#39;mirbase&#39;</span><span class="p">,</span>
+                <span class="p">)</span>
+
+                <span class="k">if</span> <span class="ow">not</span> <span class="n">mirbase</span><span class="p">:</span>
+                    <span class="n">mirbase</span> <span class="o">=</span> <span class="n">mapping</span><span class="o">.</span><span class="n">map_name</span><span class="p">(</span>
+                        <span class="s1">&#39;hsa-</span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="n">regulator</span><span class="p">,</span>
+                        <span class="s1">&#39;mir-name&#39;</span><span class="p">,</span>
+                        <span class="s1">&#39;mirbase&#39;</span><span class="p">,</span>
+                    <span class="p">)</span>
+
+                <span class="k">if</span> <span class="n">mirbase</span><span class="p">:</span>
+                    <span class="n">regulator_name</span> <span class="o">=</span> <span class="n">mirbase</span>
+                    <span class="n">regulator_type</span> <span class="o">=</span> <span class="s1">&#39;mirna&#39;</span>
+
+                <span class="k">else</span><span class="p">:</span>
+                    <span class="k">if</span> <span class="n">include_unknown_type</span><span class="p">:</span>
+                        <span class="n">regulator_name</span> <span class="o">=</span> <span class="n">regulator</span>
+                        <span class="n">regulator_type</span> <span class="o">=</span> <span class="s1">&#39;unknown&#39;</span>
+
+                    <span class="k">else</span><span class="p">:</span>
+                        <span class="k">continue</span>
+
+            <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">regulator_name</span><span class="p">,</span> <span class="nb">str</span><span class="p">):</span>
+                <span class="n">regulator_name</span> <span class="o">=</span> <span class="p">(</span><span class="n">regulator_name</span><span class="p">,)</span>
+
+            <span class="k">for</span> <span class="n">regulator_name_0</span> <span class="ow">in</span> <span class="n">regulator_name</span><span class="p">:</span>
+                <span class="n">record</span> <span class="o">=</span> <span class="n">CpadAnnotation</span><span class="p">(</span>
+                    <span class="n">regulator_type</span> <span class="o">=</span> <span class="n">regulator_type</span><span class="p">,</span>
+                    <span class="n">effect_on_pathway</span> <span class="o">=</span> <span class="n">rec</span><span class="p">[</span><span class="s1">&#39;Regulator_Type&#39;</span><span class="p">],</span>
+                    <span class="n">effect_on_cancer</span> <span class="o">=</span> <span class="n">rec</span><span class="p">[</span><span class="s1">&#39;Regulation_Type&#39;</span><span class="p">],</span>
+                    <span class="n">effect_on_cancer_outcome</span> <span class="o">=</span> <span class="n">rec</span><span class="p">[</span><span class="s1">&#39;Outcome_Description&#39;</span><span class="p">],</span>
+                    <span class="n">pathway</span> <span class="o">=</span> <span class="n">rec</span><span class="p">[</span><span class="s1">&#39;Pathway&#39;</span><span class="p">],</span>
+                    <span class="n">pathway_category</span> <span class="o">=</span> <span class="n">rec</span><span class="p">[</span><span class="s1">&#39;Pathway_Category&#39;</span><span class="p">],</span>
+                    <span class="n">cancer</span> <span class="o">=</span> <span class="n">rec</span><span class="p">[</span><span class="s1">&#39;Cancer&#39;</span><span class="p">],</span>
+                <span class="p">)</span>
+
+                <span class="n">result</span><span class="p">[</span><span class="n">regulator_name_0</span><span class="p">]</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">record</span><span class="p">)</span>
+
+    <span class="k">return</span> <span class="nb">dict</span><span class="p">(</span><span class="n">result</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="cpad_pathway_cancer">
+<a class="viewcode-back" href="../../../api/pypath.inputs.cpad.cpad_pathway_cancer.html#pypath.inputs.cpad.cpad_pathway_cancer">[docs]</a>
+<span class="k">def</span> <span class="nf">cpad_pathway_cancer</span><span class="p">():</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Collects only the pathway-cancer relationships. Returns sets of records</span>
+<span class="sd">    grouped in dicts by cancer and by pathway.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="n">CpadPathwayCancer</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">namedtuple</span><span class="p">(</span>
+        <span class="s1">&#39;CpadPathwayCancer&#39;</span><span class="p">,</span>
+        <span class="p">[</span>
+            <span class="s1">&#39;pathway&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;cancer&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;pathway_category&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;effect_on_cancer&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;effect_on_cancer_outcome&#39;</span><span class="p">,</span>
+        <span class="p">]</span>
+    <span class="p">)</span>
+
+    <span class="n">cpad</span> <span class="o">=</span> <span class="n">get_cpad</span><span class="p">()</span>
+
+    <span class="n">by_cancer</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">defaultdict</span><span class="p">(</span><span class="nb">set</span><span class="p">)</span>
+    <span class="n">by_pathway</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">defaultdict</span><span class="p">(</span><span class="nb">set</span><span class="p">)</span>
+
+    <span class="k">for</span> <span class="n">rec</span> <span class="ow">in</span> <span class="n">cpad</span><span class="p">:</span>
+
+        <span class="n">record</span> <span class="o">=</span> <span class="n">CpadPathwayCancer</span><span class="p">(</span>
+            <span class="n">pathway</span> <span class="o">=</span> <span class="n">rec</span><span class="p">[</span><span class="s1">&#39;Pathway&#39;</span><span class="p">],</span>
+            <span class="n">cancer</span> <span class="o">=</span> <span class="n">rec</span><span class="p">[</span><span class="s1">&#39;Cancer&#39;</span><span class="p">],</span>
+            <span class="n">pathway_category</span> <span class="o">=</span> <span class="n">rec</span><span class="p">[</span><span class="s1">&#39;Pathway_Category&#39;</span><span class="p">],</span>
+            <span class="n">effect_on_cancer</span> <span class="o">=</span> <span class="n">rec</span><span class="p">[</span><span class="s1">&#39;Regulation_Type&#39;</span><span class="p">],</span>
+            <span class="n">effect_on_cancer_outcome</span> <span class="o">=</span> <span class="n">rec</span><span class="p">[</span><span class="s1">&#39;Outcome_Description&#39;</span><span class="p">],</span>
+        <span class="p">)</span>
+
+        <span class="n">by_cancer</span><span class="p">[</span><span class="n">rec</span><span class="p">[</span><span class="s1">&#39;Cancer&#39;</span><span class="p">]]</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">record</span><span class="p">)</span>
+        <span class="n">by_pathway</span><span class="p">[</span><span class="n">rec</span><span class="p">[</span><span class="s1">&#39;Pathway&#39;</span><span class="p">]]</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">record</span><span class="p">)</span>
+
+    <span class="k">return</span> <span class="nb">dict</span><span class="p">(</span><span class="n">by_cancer</span><span class="p">),</span> <span class="nb">dict</span><span class="p">(</span><span class="n">by_pathway</span><span class="p">)</span></div>
+
+
+</pre></div>
+
+                </article>
+              
+              
+              
+              
+              
+                <footer class="prev-next-footer">
+                  
+<div class="prev-next-area">
+</div>
+                </footer>
+              
+            </div>
+            
+            
+              
+                <div class="bd-sidebar-secondary bd-toc"><div class="sidebar-secondary-items sidebar-secondary__inner">
+
+
+  <div class="sidebar-secondary-item">
+<div
+    id="pst-page-navigation-heading-2"
+    class="page-toc tocsection onthispage">
+    <i class="fa-solid fa-list"></i> On this page
+  </div>
+  <nav class="bd-toc-nav page-toc" aria-labelledby="pst-page-navigation-heading-2">
+    <ul class="visible nav section-nav flex-column">
+<li class="toctree-l1 toc-h1 nav-item toc-entry"><a class="reference internal nav-link" href="../../../index.html">Welcome to pypath!</a></li>
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+<li class="toctree-l1 toc-h1 nav-item toc-entry"><a class="reference internal nav-link" href="../../../notebooks/manual.html">The pypath book</a></li>
+</ul>
+
+  </nav></div>
+
+</div></div>
+              
+            
+          </div>
+          <footer class="bd-footer-content">
+            
+          </footer>
+        
+      </main>
+    </div>
+  </div>
+  
+  <!-- Scripts loaded after <body> so the DOM is not blocked -->
+  <script src="../../../_static/scripts/bootstrap.js?digest=8d27b9dea8ad943066ae"></script>
+<script src="../../../_static/scripts/pydata-sphinx-theme.js?digest=8d27b9dea8ad943066ae"></script>
+
+  <footer class="bd-footer">
+<div class="bd-footer__inner bd-page-width">
+  
+    <div class="footer-items__start">
+      
+        <div class="footer-item">
+
+  <p class="copyright">
+    
+      © Copyright 2024, Denes Turei &lt;turei.denes@gmail.com&gt;, Nicolàs Palacio, Sebastian Lobentanzer, Olga Ivanova, Melih Darcan, Erva Ulusoy, Tennur Kilic, Omer Kaan Vural, Ahmet Rifaioglu, Charles Tapley Hoyt.
+      <br/>
+    
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+
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+      
+    </div>
+  
+  
+  
+    <div class="footer-items__end">
+      
+        <div class="footer-item">
+<p class="theme-version">
+  Built with the <a href="https://pydata-sphinx-theme.readthedocs.io/en/stable/index.html">PyData Sphinx Theme</a> 0.15.2.
+</p></div>
+      
+    </div>
+  
+</div>
+
+  </footer>
+  </body>
+</html>
\ No newline at end of file
diff --git a/_modules/pypath/inputs/csa.html b/_modules/pypath/inputs/csa.html
new file mode 100644
index 000000000..b14bd0f80
--- /dev/null
+++ b/_modules/pypath/inputs/csa.html
@@ -0,0 +1,732 @@
+
+<!DOCTYPE html>
+
+
+<html lang="en" data-content_root="../../../" >
+
+  <head>
+    <meta charset="utf-8" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+    <title>pypath.inputs.csa &#8212; pypath 0.16.9 documentation</title>
+  
+  
+  
+  <script data-cfasync="false">
+    document.documentElement.dataset.mode = localStorage.getItem("mode") || "";
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+                  
+  <h1>Source code for pypath.inputs.csa</h1><div class="highlight"><pre>
+<span></span><span class="ch">#!/usr/bin/env python</span>
+<span class="c1"># -*- coding: utf-8 -*-</span>
+
+<span class="c1">#</span>
+<span class="c1">#  This file is part of the `pypath` python module</span>
+<span class="c1">#</span>
+<span class="c1">#  Copyright 2014-2023</span>
+<span class="c1">#  EMBL, EMBL-EBI, Uniklinik RWTH Aachen, Heidelberg University</span>
+<span class="c1">#</span>
+<span class="c1">#  Authors: see the file `README.rst`</span>
+<span class="c1">#  Contact: Dénes Türei (turei.denes@gmail.com)</span>
+<span class="c1">#</span>
+<span class="c1">#  Distributed under the GPLv3 License.</span>
+<span class="c1">#  See accompanying file LICENSE.txt or copy at</span>
+<span class="c1">#      https://www.gnu.org/licenses/gpl-3.0.html</span>
+<span class="c1">#</span>
+<span class="c1">#  Website: https://pypath.omnipathdb.org/</span>
+<span class="c1">#</span>
+
+<span class="k">try</span><span class="p">:</span>
+    <span class="kn">from</span> <span class="nn">cStringIO</span> <span class="kn">import</span> <span class="n">StringIO</span>
+<span class="k">except</span> <span class="ne">ModuleNotFoundError</span><span class="p">:</span>
+    <span class="kn">from</span> <span class="nn">io</span> <span class="kn">import</span> <span class="n">StringIO</span>
+
+<span class="kn">import</span> <span class="nn">pypath.resources.urls</span> <span class="k">as</span> <span class="nn">urls</span>
+<span class="kn">import</span> <span class="nn">pypath.share.curl</span> <span class="k">as</span> <span class="nn">curl</span>
+<span class="kn">import</span> <span class="nn">pypath.share.progress</span> <span class="k">as</span> <span class="nn">progress</span>
+<span class="kn">import</span> <span class="nn">pypath.inputs.pdb</span> <span class="k">as</span> <span class="nn">pdb_input</span>
+<span class="kn">import</span> <span class="nn">pypath.inputs.common</span> <span class="k">as</span> <span class="nn">inputs_common</span>
+<span class="kn">import</span> <span class="nn">pypath.utils.pdb</span> <span class="k">as</span> <span class="nn">pdb_utils</span>
+<span class="kn">import</span> <span class="nn">pypath.internals.intera</span> <span class="k">as</span> <span class="nn">intera</span>
+
+
+<div class="viewcode-block" id="get_csa">
+<a class="viewcode-back" href="../../../api/pypath.inputs.csa.get_csa.html#pypath.inputs.csa.get_csa">[docs]</a>
+<span class="k">def</span> <span class="nf">get_csa</span><span class="p">(</span><span class="n">uniprots</span> <span class="o">=</span> <span class="kc">None</span><span class="p">):</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Downloads and preprocesses catalytic sites data.</span>
+<span class="sd">    This data tells which residues are involved in the catalytic</span>
+<span class="sd">    activity of one protein.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="n">url</span> <span class="o">=</span> <span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;catalytic_sites&#39;</span><span class="p">][</span><span class="s1">&#39;url&#39;</span><span class="p">]</span>
+    <span class="n">c</span> <span class="o">=</span> <span class="n">curl</span><span class="o">.</span><span class="n">Curl</span><span class="p">(</span><span class="n">url</span><span class="p">,</span> <span class="n">silent</span> <span class="o">=</span> <span class="kc">False</span><span class="p">)</span>
+    <span class="n">data</span> <span class="o">=</span> <span class="n">c</span><span class="o">.</span><span class="n">result</span>
+
+    <span class="k">if</span> <span class="n">data</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
+
+        <span class="k">return</span> <span class="kc">None</span>
+
+    <span class="n">u_pdb</span><span class="p">,</span> <span class="n">pdb_u</span> <span class="o">=</span> <span class="n">pdb_input</span><span class="o">.</span><span class="n">pdb_chains</span><span class="p">()</span>
+    <span class="n">buff</span> <span class="o">=</span> <span class="n">StringIO</span><span class="p">()</span>
+    <span class="n">buff</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="n">data</span><span class="p">)</span>
+    <span class="n">cols</span> <span class="o">=</span> <span class="p">{</span>
+        <span class="s1">&#39;pdb&#39;</span><span class="p">:</span> <span class="mi">0</span><span class="p">,</span>
+        <span class="s1">&#39;id&#39;</span><span class="p">:</span> <span class="mi">1</span><span class="p">,</span>
+        <span class="s1">&#39;resname&#39;</span><span class="p">:</span> <span class="mi">2</span><span class="p">,</span>
+        <span class="s1">&#39;chain&#39;</span><span class="p">:</span> <span class="mi">3</span><span class="p">,</span>
+        <span class="s1">&#39;resnum&#39;</span><span class="p">:</span> <span class="mi">4</span><span class="p">,</span>
+        <span class="s1">&#39;chem_fun&#39;</span><span class="p">:</span> <span class="mi">5</span><span class="p">,</span>
+        <span class="s1">&#39;evidence&#39;</span><span class="p">:</span> <span class="mi">6</span><span class="p">,</span>
+    <span class="p">}</span>
+    <span class="n">table</span> <span class="o">=</span> <span class="n">inputs_common</span><span class="o">.</span><span class="n">read_table</span><span class="p">(</span>
+        <span class="n">cols</span> <span class="o">=</span> <span class="n">cols</span><span class="p">,</span>
+        <span class="n">fileObject</span> <span class="o">=</span> <span class="n">buff</span><span class="p">,</span>
+        <span class="n">sep</span> <span class="o">=</span> <span class="s1">&#39;,&#39;</span><span class="p">,</span>
+        <span class="n">hdr</span> <span class="o">=</span> <span class="mi">1</span><span class="p">,</span>
+    <span class="p">)</span>
+    <span class="n">css</span> <span class="o">=</span> <span class="p">{}</span>
+    <span class="n">prg</span> <span class="o">=</span> <span class="n">progress</span><span class="o">.</span><span class="n">Progress</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">table</span><span class="p">),</span> <span class="s1">&#39;Processing catalytic sites&#39;</span><span class="p">,</span> <span class="mi">11</span><span class="p">)</span>
+
+    <span class="k">for</span> <span class="n">l</span> <span class="ow">in</span> <span class="n">table</span><span class="p">:</span>
+
+        <span class="k">if</span> <span class="n">l</span><span class="p">[</span><span class="s1">&#39;pdb&#39;</span><span class="p">]</span> <span class="ow">in</span> <span class="n">pdb_u</span><span class="p">:</span>
+
+            <span class="k">if</span> <span class="n">l</span><span class="p">[</span><span class="s1">&#39;chain&#39;</span><span class="p">]</span> <span class="ow">in</span> <span class="n">pdb_u</span><span class="p">[</span><span class="n">l</span><span class="p">[</span><span class="s1">&#39;pdb&#39;</span><span class="p">]]:</span>
+
+                <span class="n">uniprot</span> <span class="o">=</span> <span class="n">pdb_u</span><span class="p">[</span><span class="n">l</span><span class="p">[</span><span class="s1">&#39;pdb&#39;</span><span class="p">]][</span><span class="n">l</span><span class="p">[</span><span class="s1">&#39;chain&#39;</span><span class="p">]][</span><span class="s1">&#39;uniprot&#39;</span><span class="p">]</span>
+
+                <span class="k">if</span> <span class="n">uniprots</span> <span class="ow">is</span> <span class="kc">None</span> <span class="ow">or</span> <span class="n">uniprot</span> <span class="ow">in</span> <span class="n">uniprots</span><span class="p">:</span>
+
+                    <span class="n">offset</span> <span class="o">=</span> <span class="n">pdb_u</span><span class="p">[</span><span class="n">l</span><span class="p">[</span><span class="s1">&#39;pdb&#39;</span><span class="p">]][</span><span class="n">l</span><span class="p">[</span><span class="s1">&#39;chain&#39;</span><span class="p">]][</span><span class="s1">&#39;offset&#39;</span><span class="p">]</span>
+
+                    <span class="k">if</span> <span class="n">offset</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
+
+                        <span class="n">l</span><span class="p">[</span><span class="s1">&#39;resnum&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">l</span><span class="p">[</span><span class="s1">&#39;resnum&#39;</span><span class="p">])</span> <span class="o">+</span> <span class="n">offset</span>
+
+                    <span class="k">else</span><span class="p">:</span>
+
+                        <span class="n">this_res</span> <span class="o">=</span> <span class="n">pdb_utils</span><span class="o">.</span><span class="n">residue_pdb</span><span class="p">(</span>
+                            <span class="n">l</span><span class="p">[</span><span class="s1">&#39;pdb&#39;</span><span class="p">],</span>
+                            <span class="n">l</span><span class="p">[</span><span class="s1">&#39;chain&#39;</span><span class="p">],</span>
+                            <span class="n">l</span><span class="p">[</span><span class="s1">&#39;resnum&#39;</span><span class="p">],</span>
+                        <span class="p">)</span>
+
+                        <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">this_res</span><span class="p">)</span> <span class="o">&gt;</span> <span class="mi">0</span><span class="p">:</span>
+                            <span class="n">l</span><span class="p">[</span><span class="s1">&#39;resnum&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">this_res</span><span class="p">[</span><span class="s1">&#39;UPCOUNT&#39;</span><span class="p">])</span>
+
+                        <span class="k">else</span><span class="p">:</span>
+                            <span class="n">l</span><span class="p">[</span><span class="s1">&#39;resnum&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="kc">None</span>
+
+                    <span class="k">if</span> <span class="n">l</span><span class="p">[</span><span class="s1">&#39;resnum&#39;</span><span class="p">]</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
+
+                        <span class="k">if</span> <span class="n">uniprot</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">css</span><span class="p">:</span>
+
+                            <span class="n">css</span><span class="p">[</span><span class="n">uniprot</span><span class="p">]</span> <span class="o">=</span> <span class="p">{}</span>
+
+                        <span class="k">if</span> <span class="n">l</span><span class="p">[</span><span class="s1">&#39;pdb&#39;</span><span class="p">]</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">css</span><span class="p">[</span><span class="n">uniprot</span><span class="p">]:</span>
+
+                            <span class="n">css</span><span class="p">[</span><span class="n">uniprot</span><span class="p">][</span><span class="n">l</span><span class="p">[</span><span class="s1">&#39;pdb&#39;</span><span class="p">]]</span> <span class="o">=</span> <span class="p">{}</span>
+
+                        <span class="k">if</span> <span class="n">l</span><span class="p">[</span><span class="s1">&#39;id&#39;</span><span class="p">]</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">css</span><span class="p">[</span><span class="n">uniprot</span><span class="p">][</span><span class="n">l</span><span class="p">[</span><span class="s1">&#39;pdb&#39;</span><span class="p">]]:</span>
+
+                            <span class="n">css</span><span class="p">[</span><span class="n">uniprot</span><span class="p">][</span><span class="n">l</span><span class="p">[</span><span class="s1">&#39;pdb&#39;</span><span class="p">]][</span><span class="n">l</span><span class="p">[</span><span class="s1">&#39;id&#39;</span><span class="p">]]</span> <span class="o">=</span> <span class="p">[]</span>
+
+                        <span class="n">css</span><span class="p">[</span><span class="n">uniprot</span><span class="p">][</span><span class="n">l</span><span class="p">[</span><span class="s1">&#39;pdb&#39;</span><span class="p">]][</span><span class="n">l</span><span class="p">[</span><span class="s1">&#39;id&#39;</span><span class="p">]]</span><span class="o">.</span><span class="n">append</span><span class="p">(</span>
+                            <span class="n">intera</span><span class="o">.</span><span class="n">Residue</span><span class="p">(</span>
+                                <span class="n">name</span> <span class="o">=</span> <span class="n">l</span><span class="p">[</span><span class="s1">&#39;resname&#39;</span><span class="p">],</span>
+                                <span class="n">number</span> <span class="o">=</span> <span class="n">l</span><span class="p">[</span><span class="s1">&#39;resnum&#39;</span><span class="p">],</span>
+                                <span class="n">protein</span> <span class="o">=</span> <span class="n">uniprot</span><span class="p">,</span>
+                            <span class="p">)</span>
+                        <span class="p">)</span>
+
+        <span class="n">prg</span><span class="o">.</span><span class="n">step</span><span class="p">()</span>
+
+    <span class="n">prg</span><span class="o">.</span><span class="n">terminate</span><span class="p">()</span>
+
+    <span class="k">return</span> <span class="n">css</span></div>
+
+</pre></div>
+
+                </article>
+              
+              
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diff --git a/_modules/pypath/inputs/cspa.html b/_modules/pypath/inputs/cspa.html
new file mode 100644
index 000000000..3a7d50e3d
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@@ -0,0 +1,757 @@
+
+<!DOCTYPE html>
+
+
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+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
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+  
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+                  
+  <h1>Source code for pypath.inputs.cspa</h1><div class="highlight"><pre>
+<span></span><span class="ch">#!/usr/bin/env python</span>
+<span class="c1"># -*- coding: utf-8 -*-</span>
+
+<span class="c1">#</span>
+<span class="c1">#  This file is part of the `pypath` python module</span>
+<span class="c1">#</span>
+<span class="c1">#  Copyright 2014-2023</span>
+<span class="c1">#  EMBL, EMBL-EBI, Uniklinik RWTH Aachen, Heidelberg University</span>
+<span class="c1">#</span>
+<span class="c1">#  Authors: see the file `README.rst`</span>
+<span class="c1">#  Contact: Dénes Türei (turei.denes@gmail.com)</span>
+<span class="c1">#</span>
+<span class="c1">#  Distributed under the GPLv3 License.</span>
+<span class="c1">#  See accompanying file LICENSE.txt or copy at</span>
+<span class="c1">#      https://www.gnu.org/licenses/gpl-3.0.html</span>
+<span class="c1">#</span>
+<span class="c1">#  Website: https://pypath.omnipathdb.org/</span>
+<span class="c1">#</span>
+
+<span class="kn">from</span> <span class="nn">future.utils</span> <span class="kn">import</span> <span class="n">iteritems</span>
+
+<span class="kn">import</span> <span class="nn">collections</span>
+
+<span class="kn">import</span> <span class="nn">pypath.share.curl</span> <span class="k">as</span> <span class="nn">curl</span>
+<span class="kn">import</span> <span class="nn">pypath.share.common</span> <span class="k">as</span> <span class="nn">common</span>
+<span class="kn">import</span> <span class="nn">pypath.resources.urls</span> <span class="k">as</span> <span class="nn">urls</span>
+<span class="kn">import</span> <span class="nn">pypath.inputs.common</span> <span class="k">as</span> <span class="nn">inputs_common</span>
+<span class="kn">import</span> <span class="nn">pypath.utils.mapping</span> <span class="k">as</span> <span class="nn">mapping</span>
+<span class="kn">import</span> <span class="nn">pypath.utils.taxonomy</span> <span class="k">as</span> <span class="nn">taxonomy</span>
+
+
+<div class="viewcode-block" id="cspa_annotations">
+<a class="viewcode-back" href="../../../api/pypath.inputs.cspa.cspa_annotations.html#pypath.inputs.cspa.cspa_annotations">[docs]</a>
+<span class="k">def</span> <span class="nf">cspa_annotations</span><span class="p">(</span><span class="n">organism</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">):</span>
+
+
+    <span class="n">CspaAnnotation</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">namedtuple</span><span class="p">(</span>
+        <span class="s1">&#39;CspaAnnotation&#39;</span><span class="p">,</span>
+        <span class="p">[</span>
+            <span class="s1">&#39;high_confidence&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;n_cell_types&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;tm&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;gpi&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;uniprot_cell_surface&#39;</span><span class="p">,</span>
+        <span class="p">],</span>
+    <span class="p">)</span>
+
+
+    <span class="n">sheets</span> <span class="o">=</span> <span class="p">{</span>
+        <span class="s1">&#39;Human&#39;</span><span class="p">:</span> <span class="s1">&#39;Table A&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;Mouse&#39;</span><span class="p">:</span> <span class="s1">&#39;Table B&#39;</span><span class="p">,</span>
+    <span class="p">}</span>
+
+    <span class="n">str_organism</span> <span class="o">=</span> <span class="n">taxonomy</span><span class="o">.</span><span class="n">taxids</span><span class="p">[</span><span class="n">organism</span><span class="p">]</span><span class="o">.</span><span class="n">capitalize</span><span class="p">()</span>
+
+    <span class="n">url</span> <span class="o">=</span> <span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;cspa&#39;</span><span class="p">][</span><span class="s1">&#39;url_s2&#39;</span><span class="p">]</span>
+    <span class="n">c</span> <span class="o">=</span> <span class="n">curl</span><span class="o">.</span><span class="n">Curl</span><span class="p">(</span><span class="n">url</span><span class="p">,</span> <span class="n">large</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span> <span class="n">silent</span> <span class="o">=</span> <span class="kc">False</span><span class="p">)</span>
+    <span class="n">xlsname</span> <span class="o">=</span> <span class="n">c</span><span class="o">.</span><span class="n">fname</span>
+    <span class="k">del</span><span class="p">(</span><span class="n">c</span><span class="p">)</span>
+    <span class="n">raw</span> <span class="o">=</span> <span class="n">inputs_common</span><span class="o">.</span><span class="n">read_xls</span><span class="p">(</span><span class="n">xlsname</span><span class="p">,</span> <span class="n">sheets</span><span class="p">[</span><span class="n">str_organism</span><span class="p">])[</span><span class="mi">1</span><span class="p">:]</span>
+
+    <span class="n">result</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">defaultdict</span><span class="p">(</span><span class="nb">set</span><span class="p">)</span>
+
+    <span class="k">for</span> <span class="n">row</span> <span class="ow">in</span> <span class="n">raw</span><span class="p">:</span>
+
+        <span class="k">for</span> <span class="n">uniprot</span> <span class="ow">in</span> <span class="n">mapping</span><span class="o">.</span><span class="n">map_name</span><span class="p">(</span><span class="n">row</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span> <span class="s1">&#39;uniprot&#39;</span><span class="p">,</span> <span class="s1">&#39;uniprot&#39;</span><span class="p">):</span>
+
+            <span class="n">result</span><span class="p">[</span><span class="n">uniprot</span><span class="p">]</span><span class="o">.</span><span class="n">add</span><span class="p">(</span>
+                <span class="n">CspaAnnotation</span><span class="p">(</span>
+                    <span class="n">high_confidence</span> <span class="o">=</span> <span class="s1">&#39;high confidence&#39;</span> <span class="ow">in</span> <span class="n">row</span><span class="p">[</span><span class="mi">2</span><span class="p">],</span>
+                    <span class="n">n_cell_types</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="nb">float</span><span class="p">(</span><span class="n">row</span><span class="p">[</span><span class="mi">9</span><span class="p">])),</span>
+                    <span class="n">tm</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="nb">float</span><span class="p">(</span><span class="n">row</span><span class="p">[</span><span class="mi">11</span><span class="p">])),</span>
+                    <span class="n">gpi</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="nb">float</span><span class="p">(</span><span class="n">row</span><span class="p">[</span><span class="mi">12</span><span class="p">])),</span>
+                    <span class="n">uniprot_cell_surface</span> <span class="o">=</span> <span class="n">row</span><span class="p">[</span><span class="mi">13</span><span class="p">]</span> <span class="o">==</span> <span class="s1">&#39;yes&#39;</span><span class="p">,</span>
+                <span class="p">)</span>
+            <span class="p">)</span>
+
+    <span class="k">return</span> <span class="nb">dict</span><span class="p">(</span><span class="n">result</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="cspa_cell_types">
+<a class="viewcode-back" href="../../../api/pypath.inputs.cspa.cspa_cell_types.html#pypath.inputs.cspa.cspa_cell_types">[docs]</a>
+<span class="k">def</span> <span class="nf">cspa_cell_types</span><span class="p">(</span><span class="n">organism</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">):</span>
+
+    <span class="n">sheets</span> <span class="o">=</span> <span class="p">{</span>
+        <span class="s1">&#39;Human&#39;</span><span class="p">:</span> <span class="s1">&#39;Table_E&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;Mouse&#39;</span><span class="p">:</span> <span class="s1">&#39;Table_F&#39;</span><span class="p">,</span>
+    <span class="p">}</span>
+
+    <span class="n">str_organism</span> <span class="o">=</span> <span class="n">taxonomy</span><span class="o">.</span><span class="n">taxids</span><span class="p">[</span><span class="n">organism</span><span class="p">]</span><span class="o">.</span><span class="n">capitalize</span><span class="p">()</span>
+
+    <span class="n">url</span> <span class="o">=</span> <span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;cspa&#39;</span><span class="p">][</span><span class="s1">&#39;url_s1&#39;</span><span class="p">]</span>
+    <span class="n">c</span> <span class="o">=</span> <span class="n">curl</span><span class="o">.</span><span class="n">Curl</span><span class="p">(</span><span class="n">url</span><span class="p">,</span> <span class="n">large</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span> <span class="n">silent</span> <span class="o">=</span> <span class="kc">False</span><span class="p">)</span>
+    <span class="n">xlsname</span> <span class="o">=</span> <span class="n">c</span><span class="o">.</span><span class="n">fname</span>
+    <span class="k">del</span><span class="p">(</span><span class="n">c</span><span class="p">)</span>
+    <span class="n">raw</span> <span class="o">=</span> <span class="n">inputs_common</span><span class="o">.</span><span class="n">read_xls</span><span class="p">(</span><span class="n">xlsname</span><span class="p">,</span> <span class="n">sheets</span><span class="p">[</span><span class="n">str_organism</span><span class="p">])</span>
+
+    <span class="n">result</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">defaultdict</span><span class="p">(</span><span class="k">lambda</span><span class="p">:</span> <span class="n">collections</span><span class="o">.</span><span class="n">defaultdict</span><span class="p">(</span><span class="nb">dict</span><span class="p">))</span>
+
+    <span class="n">cell_types</span> <span class="o">=</span> <span class="n">raw</span><span class="p">[</span><span class="mi">0</span><span class="p">][</span><span class="mi">1</span><span class="p">:]</span>
+
+    <span class="k">for</span> <span class="n">row</span> <span class="ow">in</span> <span class="n">raw</span><span class="p">[</span><span class="mi">1</span><span class="p">:]:</span>
+
+        <span class="k">for</span> <span class="n">uniprot</span> <span class="ow">in</span> <span class="n">mapping</span><span class="o">.</span><span class="n">map_name</span><span class="p">(</span><span class="n">row</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="s1">&#39;uniprot&#39;</span><span class="p">,</span> <span class="s1">&#39;uniprot&#39;</span><span class="p">):</span>
+
+            <span class="k">for</span> <span class="n">col</span><span class="p">,</span> <span class="n">cell_type</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">cell_types</span><span class="p">):</span>
+
+                <span class="n">value</span> <span class="o">=</span> <span class="n">row</span><span class="p">[</span><span class="n">col</span> <span class="o">+</span> <span class="mi">1</span><span class="p">]</span>
+
+                <span class="n">result</span><span class="p">[</span><span class="n">cell_type</span><span class="p">][</span><span class="n">uniprot</span><span class="p">]</span> <span class="o">=</span> <span class="p">(</span>
+                    <span class="nb">float</span><span class="p">(</span><span class="n">value</span><span class="p">)</span>
+                        <span class="k">if</span> <span class="n">common</span><span class="o">.</span><span class="n">is_float</span><span class="p">(</span><span class="n">value</span><span class="p">)</span> <span class="k">else</span>
+                    <span class="kc">None</span>
+                <span class="p">)</span>
+
+    <span class="k">return</span> <span class="nb">dict</span><span class="p">((</span><span class="n">k</span><span class="p">,</span> <span class="nb">dict</span><span class="p">(</span><span class="n">v</span><span class="p">))</span> <span class="k">for</span> <span class="n">k</span><span class="p">,</span> <span class="n">v</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="n">result</span><span class="p">))</span></div>
+
+
+
+<div class="viewcode-block" id="cspa_cell_type_annotations">
+<a class="viewcode-back" href="../../../api/pypath.inputs.cspa.cspa_cell_type_annotations.html#pypath.inputs.cspa.cspa_cell_type_annotations">[docs]</a>
+<span class="k">def</span> <span class="nf">cspa_cell_type_annotations</span><span class="p">(</span><span class="n">organism</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">):</span>
+
+
+    <span class="n">CspaCellType</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">namedtuple</span><span class="p">(</span>
+        <span class="s1">&#39;CspaCellType&#39;</span><span class="p">,</span>
+        <span class="p">[</span>
+            <span class="s1">&#39;cell_type&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;value&#39;</span><span class="p">,</span>
+        <span class="p">],</span>
+    <span class="p">)</span>
+
+
+    <span class="n">cell_type_data</span> <span class="o">=</span> <span class="n">cspa_cell_types</span><span class="p">(</span><span class="n">organism</span> <span class="o">=</span> <span class="n">organism</span><span class="p">)</span>
+
+
+    <span class="n">result</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">defaultdict</span><span class="p">(</span><span class="nb">set</span><span class="p">)</span>
+
+    <span class="k">for</span> <span class="n">cell_type</span><span class="p">,</span> <span class="n">data</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="n">cell_type_data</span><span class="p">):</span>
+
+        <span class="k">for</span> <span class="n">uniprot</span><span class="p">,</span> <span class="n">value</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="n">data</span><span class="p">):</span>
+
+            <span class="k">if</span> <span class="n">value</span><span class="p">:</span>
+
+                <span class="n">result</span><span class="p">[</span><span class="n">uniprot</span><span class="p">]</span><span class="o">.</span><span class="n">add</span><span class="p">(</span>
+                    <span class="n">CspaCellType</span><span class="p">(</span>
+                        <span class="n">cell_type</span> <span class="o">=</span> <span class="n">cell_type</span><span class="p">,</span>
+                        <span class="n">value</span> <span class="o">=</span> <span class="n">value</span><span class="p">,</span>
+                    <span class="p">)</span>
+                <span class="p">)</span>
+
+    <span class="k">return</span> <span class="nb">dict</span><span class="p">(</span><span class="n">result</span><span class="p">)</span></div>
+
+</pre></div>
+
+                </article>
+              
+              
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+  <h1>Source code for pypath.inputs.cytosig</h1><div class="highlight"><pre>
+<span></span><span class="ch">#!/usr/bin/env python</span>
+<span class="c1"># -*- coding: utf-8 -*-</span>
+
+<span class="c1">#</span>
+<span class="c1">#  This file is part of the `pypath` python module</span>
+<span class="c1">#</span>
+<span class="c1">#  Copyright 2014-2023</span>
+<span class="c1">#  EMBL, EMBL-EBI, Uniklinik RWTH Aachen, Heidelberg University</span>
+<span class="c1">#</span>
+<span class="c1">#  Authors: see the file `README.rst`</span>
+<span class="c1">#  Contact: Dénes Türei (turei.denes@gmail.com)</span>
+<span class="c1">#</span>
+<span class="c1">#  Distributed under the GPLv3 License.</span>
+<span class="c1">#  See accompanying file LICENSE.txt or copy at</span>
+<span class="c1">#      https://www.gnu.org/licenses/gpl-3.0.html</span>
+<span class="c1">#</span>
+<span class="c1">#  Website: https://pypath.omnipathdb.org/</span>
+<span class="c1">#</span>
+
+<span class="kn">from</span> <span class="nn">typing</span> <span class="kn">import</span> <span class="n">Union</span>
+<span class="kn">import</span> <span class="nn">collections</span>
+<span class="kn">import</span> <span class="nn">itertools</span>
+
+<span class="kn">import</span> <span class="nn">pandas</span> <span class="k">as</span> <span class="nn">pd</span>
+
+<span class="kn">import</span> <span class="nn">pypath.resources.urls</span> <span class="k">as</span> <span class="nn">urls</span>
+<span class="kn">import</span> <span class="nn">pypath.share.curl</span> <span class="k">as</span> <span class="nn">curl</span>
+<span class="kn">import</span> <span class="nn">pypath.share.session</span> <span class="k">as</span> <span class="nn">session</span>
+<span class="kn">import</span> <span class="nn">pypath.utils.mapping</span> <span class="k">as</span> <span class="nn">mapping</span>
+
+
+<span class="n">_log</span> <span class="o">=</span> <span class="n">session</span><span class="o">.</span><span class="n">Logger</span><span class="p">(</span><span class="n">name</span> <span class="o">=</span> <span class="s1">&#39;cytosig_input&#39;</span><span class="p">)</span><span class="o">.</span><span class="n">_log</span>
+
+
+<span class="n">CUSTOM_MAPPINGS</span> <span class="o">=</span> <span class="p">{</span>
+    <span class="s1">&#39;Activin A&#39;</span><span class="p">:</span> <span class="p">(</span><span class="s1">&#39;P08476&#39;</span><span class="p">,</span> <span class="s1">&#39;INHBA&#39;</span><span class="p">),</span>
+    <span class="s1">&#39;IL12&#39;</span><span class="p">:</span> <span class="p">(</span><span class="s1">&#39;P29459&#39;</span><span class="p">,</span> <span class="s1">&#39;IL12A&#39;</span><span class="p">),</span>
+    <span class="s1">&#39;IL36&#39;</span><span class="p">:</span> <span class="p">(</span><span class="s1">&#39;Q9UHA7&#39;</span><span class="p">,</span> <span class="s1">&#39;IL36A&#39;</span><span class="p">),</span>
+    <span class="s1">&#39;MCSF&#39;</span><span class="p">:</span> <span class="p">(</span><span class="s1">&#39;P09603&#39;</span><span class="p">,</span> <span class="s1">&#39;CSF1&#39;</span><span class="p">),</span>
+    <span class="s1">&#39;TWEAK&#39;</span><span class="p">:</span> <span class="p">(</span><span class="s1">&#39;O43508&#39;</span><span class="p">,</span> <span class="s1">&#39;TNFSF12&#39;</span><span class="p">),</span>
+<span class="p">}</span>
+
+
+<div class="viewcode-block" id="cytosig_df">
+<a class="viewcode-back" href="../../../api/pypath.inputs.cytosig.cytosig_df.html#pypath.inputs.cytosig.cytosig_df">[docs]</a>
+<span class="k">def</span> <span class="nf">cytosig_df</span><span class="p">(</span><span class="n">long</span><span class="p">:</span> <span class="nb">bool</span> <span class="o">=</span> <span class="kc">False</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">Union</span><span class="p">[</span><span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">,</span> <span class="n">pd</span><span class="o">.</span><span class="n">Series</span><span class="p">]:</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    CytoSig core data is a matrix of cytokines vs. targets. Here this matrix</span>
+<span class="sd">    is returned as a pandas data frame, either in a wide or long format.</span>
+
+<span class="sd">    Args</span>
+<span class="sd">        long: Convert the data frame to long format.</span>
+
+<span class="sd">    Returns</span>
+<span class="sd">        The original matrix format data frame (rows are signature genes,</span>
+<span class="sd">        columns are cytokines) by default; if `long` is `True`, a series</span>
+<span class="sd">        with multi index is returned.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="n">url</span> <span class="o">=</span> <span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;cytosig&#39;</span><span class="p">][</span><span class="s1">&#39;url&#39;</span><span class="p">]</span>
+    <span class="n">c</span> <span class="o">=</span> <span class="n">curl</span><span class="o">.</span><span class="n">Curl</span><span class="p">(</span><span class="n">url</span><span class="p">,</span> <span class="n">large</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span> <span class="n">silent</span> <span class="o">=</span> <span class="kc">False</span><span class="p">)</span>
+
+    <span class="c1"># bravo pandas!</span>
+    <span class="c1"># I would&#39;ve never expected that anything in pandas works this smooth</span>
+    <span class="n">df</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">read_csv</span><span class="p">(</span><span class="n">c</span><span class="o">.</span><span class="n">fileobj</span><span class="p">,</span> <span class="n">sep</span> <span class="o">=</span> <span class="s1">&#39;</span><span class="se">\t</span><span class="s1">&#39;</span><span class="p">)</span>
+
+    <span class="k">if</span> <span class="n">long</span><span class="p">:</span>
+
+        <span class="c1"># well done, pandas.</span>
+        <span class="c1"># your api and docs though are still an ugly mess</span>
+        <span class="n">df</span> <span class="o">=</span> <span class="n">df</span><span class="o">.</span><span class="n">stack</span><span class="p">()</span>
+
+    <span class="k">return</span> <span class="n">df</span></div>
+
+
+
+<div class="viewcode-block" id="cytosig_annotations">
+<a class="viewcode-back" href="../../../api/pypath.inputs.cytosig.cytosig_annotations.html#pypath.inputs.cytosig.cytosig_annotations">[docs]</a>
+<span class="k">def</span> <span class="nf">cytosig_annotations</span><span class="p">()</span> <span class="o">-&gt;</span> <span class="nb">dict</span><span class="p">:</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    CytoSig is a compendium of expression signatures from cytokine</span>
+<span class="sd">    perturbation experiments.</span>
+
+<span class="sd">    Returns</span>
+<span class="sd">        Dict of sets of annotations.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="k">def</span> <span class="nf">map_to_uniprot</span><span class="p">(</span><span class="n">genesymbol</span><span class="p">):</span>
+
+        <span class="n">uniprots</span> <span class="o">=</span> <span class="n">mapping</span><span class="o">.</span><span class="n">map_name</span><span class="p">(</span><span class="n">genesymbol</span><span class="p">,</span> <span class="s1">&#39;genesymbol&#39;</span><span class="p">,</span> <span class="s1">&#39;uniprot&#39;</span><span class="p">)</span>
+
+        <span class="k">if</span> <span class="ow">not</span> <span class="n">uniprots</span> <span class="ow">and</span> <span class="n">genesymbol</span> <span class="ow">in</span> <span class="n">CUSTOM_MAPPINGS</span><span class="p">:</span>
+
+            <span class="n">uniprots</span> <span class="o">=</span> <span class="p">{</span><span class="n">CUSTOM_MAPPINGS</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="n">genesymbol</span><span class="p">)[</span><span class="mi">0</span><span class="p">]}</span>
+
+        <span class="k">return</span> <span class="n">uniprots</span>
+
+
+    <span class="n">cytosig</span> <span class="o">=</span> <span class="n">cytosig_df</span><span class="p">(</span><span class="n">long</span> <span class="o">=</span> <span class="kc">True</span><span class="p">)</span>
+
+    <span class="n">record</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">namedtuple</span><span class="p">(</span>
+        <span class="s1">&#39;CytosigAnnotation&#39;</span><span class="p">,</span>
+        <span class="p">(</span><span class="s1">&#39;cytokine&#39;</span><span class="p">,</span> <span class="s1">&#39;score&#39;</span><span class="p">,</span> <span class="s1">&#39;cytokine_genesymbol&#39;</span><span class="p">,</span> <span class="s1">&#39;target_genesymbol&#39;</span><span class="p">),</span>
+    <span class="p">)</span>
+    <span class="n">result</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">defaultdict</span><span class="p">(</span><span class="nb">set</span><span class="p">)</span>
+    <span class="n">unmapped</span> <span class="o">=</span> <span class="nb">set</span><span class="p">()</span>
+
+    <span class="k">for</span> <span class="p">(</span><span class="n">target</span><span class="p">,</span> <span class="n">cytokine</span><span class="p">),</span> <span class="n">score</span> <span class="ow">in</span> <span class="n">cytosig</span><span class="o">.</span><span class="n">items</span><span class="p">():</span>
+
+        <span class="n">u_target</span> <span class="o">=</span> <span class="n">map_to_uniprot</span><span class="p">(</span><span class="n">target</span><span class="p">)</span>
+        <span class="n">u_cytokine</span> <span class="o">=</span> <span class="n">map_to_uniprot</span><span class="p">(</span><span class="n">cytokine</span><span class="p">)</span>
+
+        <span class="k">if</span> <span class="ow">not</span> <span class="n">u_cytokine</span><span class="p">:</span>
+
+            <span class="n">unmapped</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">cytokine</span><span class="p">)</span>
+
+        <span class="k">for</span> <span class="n">u_t</span><span class="p">,</span> <span class="n">u_c</span> <span class="ow">in</span> <span class="n">itertools</span><span class="o">.</span><span class="n">product</span><span class="p">(</span><span class="n">u_target</span><span class="p">,</span> <span class="n">u_cytokine</span><span class="p">):</span>
+
+            <span class="n">result</span><span class="p">[</span><span class="n">u_t</span><span class="p">]</span><span class="o">.</span><span class="n">add</span><span class="p">(</span>
+                <span class="n">record</span><span class="p">(</span>
+                    <span class="n">cytokine</span> <span class="o">=</span> <span class="n">u_c</span><span class="p">,</span>
+                    <span class="n">score</span> <span class="o">=</span> <span class="n">score</span><span class="p">,</span>
+                    <span class="n">cytokine_genesymbol</span> <span class="o">=</span> <span class="n">cytokine</span><span class="p">,</span>
+                    <span class="n">target_genesymbol</span> <span class="o">=</span> <span class="n">target</span><span class="p">,</span>
+                <span class="p">)</span>
+            <span class="p">)</span>
+
+    <span class="k">if</span> <span class="n">unmapped</span><span class="p">:</span>
+
+        <span class="n">_log</span><span class="p">(</span>
+            <span class="s1">&#39;Could not translate to UniProt IDs the following cytokines: &#39;</span> <span class="o">+</span>
+            <span class="s1">&#39;, &#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="nb">sorted</span><span class="p">(</span><span class="n">unmapped</span><span class="p">))</span>
+        <span class="p">)</span>
+
+    <span class="k">return</span> <span class="nb">dict</span><span class="p">(</span><span class="n">result</span><span class="p">)</span></div>
+
+</pre></div>
+
+                </article>
+              
+              
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+                  
+  <h1>Source code for pypath.inputs.depod</h1><div class="highlight"><pre>
+<span></span><span class="ch">#!/usr/bin/env python</span>
+<span class="c1"># -*- coding: utf-8 -*-</span>
+
+<span class="c1">#</span>
+<span class="c1">#  This file is part of the `pypath` python module</span>
+<span class="c1">#</span>
+<span class="c1">#  Copyright 2014-2023</span>
+<span class="c1">#  EMBL, EMBL-EBI, Uniklinik RWTH Aachen, Heidelberg University</span>
+<span class="c1">#</span>
+<span class="c1">#  Authors: see the file `README.rst`</span>
+<span class="c1">#  Contact: Dénes Türei (turei.denes@gmail.com)</span>
+<span class="c1">#</span>
+<span class="c1">#  Distributed under the GPLv3 License.</span>
+<span class="c1">#  See accompanying file LICENSE.txt or copy at</span>
+<span class="c1">#      https://www.gnu.org/licenses/gpl-3.0.html</span>
+<span class="c1">#</span>
+<span class="c1">#  Website: https://pypath.omnipathdb.org/</span>
+<span class="c1">#</span>
+
+<span class="kn">import</span> <span class="nn">re</span>
+<span class="kn">import</span> <span class="nn">itertools</span>
+
+<span class="kn">import</span> <span class="nn">pypath.resources.urls</span> <span class="k">as</span> <span class="nn">urls</span>
+<span class="kn">import</span> <span class="nn">pypath.share.curl</span> <span class="k">as</span> <span class="nn">curl</span>
+<span class="kn">import</span> <span class="nn">pypath.utils.mapping</span> <span class="k">as</span> <span class="nn">mapping</span>
+<span class="kn">import</span> <span class="nn">pypath.utils.taxonomy</span> <span class="k">as</span> <span class="nn">taxonomy</span>
+<span class="kn">import</span> <span class="nn">pypath.share.common</span> <span class="k">as</span> <span class="nn">common</span>
+
+
+<div class="viewcode-block" id="depod_interactions">
+<a class="viewcode-back" href="../../../api/pypath.inputs.depod.depod_interactions.html#pypath.inputs.depod.depod_interactions">[docs]</a>
+<span class="k">def</span> <span class="nf">depod_interactions</span><span class="p">(</span><span class="n">organism</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">):</span>
+
+    <span class="n">url</span> <span class="o">=</span> <span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;depod&#39;</span><span class="p">][</span><span class="s1">&#39;urls&#39;</span><span class="p">][</span><span class="mi">1</span><span class="p">]</span>
+    <span class="n">c</span> <span class="o">=</span> <span class="n">curl</span><span class="o">.</span><span class="n">Curl</span><span class="p">(</span><span class="n">url</span><span class="p">,</span> <span class="n">silent</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span> <span class="n">large</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span> <span class="n">encoding</span> <span class="o">=</span> <span class="s1">&#39;iso-8859-1&#39;</span><span class="p">)</span>
+    <span class="n">data</span> <span class="o">=</span> <span class="n">c</span><span class="o">.</span><span class="n">result</span>
+    <span class="n">result</span> <span class="o">=</span> <span class="p">[]</span>
+    <span class="n">i</span> <span class="o">=</span> <span class="p">[]</span>
+    <span class="n">lnum</span> <span class="o">=</span> <span class="mi">0</span>
+
+    <span class="k">for</span> <span class="n">l</span> <span class="ow">in</span> <span class="n">data</span><span class="p">:</span>
+
+        <span class="k">if</span> <span class="n">lnum</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
+            <span class="n">lnum</span> <span class="o">+=</span> <span class="mi">1</span>
+            <span class="k">continue</span>
+        <span class="n">l</span> <span class="o">=</span> <span class="n">l</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\n</span><span class="s1">&#39;</span><span class="p">,</span> <span class="s1">&#39;&#39;</span><span class="p">)</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\r</span><span class="s1">&#39;</span><span class="p">,</span> <span class="s1">&#39;&#39;</span><span class="p">)</span>
+        <span class="n">l</span> <span class="o">=</span> <span class="n">l</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\t</span><span class="s1">&#39;</span><span class="p">)</span>
+        <span class="n">specA</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">l</span><span class="p">[</span><span class="mi">9</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;:&#39;</span><span class="p">)[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;(&#39;</span><span class="p">)[</span><span class="mi">0</span><span class="p">])</span>
+        <span class="n">specB</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">l</span><span class="p">[</span><span class="mi">10</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;:&#39;</span><span class="p">)[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;(&#39;</span><span class="p">)[</span><span class="mi">0</span><span class="p">])</span>
+
+        <span class="k">if</span> <span class="n">organism</span> <span class="ow">is</span> <span class="kc">None</span> <span class="ow">or</span> <span class="p">(</span><span class="n">specA</span> <span class="o">==</span> <span class="n">organism</span> <span class="ow">and</span> <span class="n">specB</span> <span class="o">==</span> <span class="n">organism</span><span class="p">):</span>
+
+            <span class="n">pm</span> <span class="o">=</span> <span class="n">l</span><span class="p">[</span><span class="mi">8</span><span class="p">]</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s1">&#39;pubmed:&#39;</span><span class="p">,</span> <span class="s1">&#39;&#39;</span><span class="p">)</span>
+            <span class="n">sc</span> <span class="o">=</span> <span class="n">l</span><span class="p">[</span><span class="mi">14</span><span class="p">]</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s1">&#39;curator score:&#39;</span><span class="p">,</span> <span class="s1">&#39;&#39;</span><span class="p">)</span>
+            <span class="n">ty</span> <span class="o">=</span> <span class="n">l</span><span class="p">[</span><span class="mi">11</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;(&#39;</span><span class="p">)[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s1">&#39;)&#39;</span><span class="p">,</span> <span class="s1">&#39;&#39;</span><span class="p">)</span>
+            <span class="n">l</span> <span class="o">=</span> <span class="p">[</span><span class="n">l</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">l</span><span class="p">[</span><span class="mi">1</span><span class="p">]]</span>
+            <span class="n">interaction</span> <span class="o">=</span> <span class="p">()</span>
+
+            <span class="k">for</span> <span class="n">ll</span> <span class="ow">in</span> <span class="n">l</span><span class="p">:</span>
+
+                <span class="n">ll</span> <span class="o">=</span> <span class="n">ll</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;|&#39;</span><span class="p">)</span>
+                <span class="n">uniprot</span> <span class="o">=</span> <span class="s1">&#39;&#39;</span>
+                <span class="k">for</span> <span class="n">lll</span> <span class="ow">in</span> <span class="n">ll</span><span class="p">:</span>
+                    <span class="n">nm</span> <span class="o">=</span> <span class="n">lll</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;:&#39;</span><span class="p">)</span>
+                    <span class="n">u</span> <span class="o">=</span> <span class="n">nm</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span>
+                    <span class="k">if</span> <span class="n">nm</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">==</span> <span class="s1">&#39;uniprotkb&#39;</span> <span class="ow">and</span> <span class="nb">len</span><span class="p">(</span><span class="n">u</span><span class="p">)</span> <span class="o">==</span> <span class="mi">6</span><span class="p">:</span>
+                        <span class="n">uniprot</span> <span class="o">=</span> <span class="n">u</span>
+                <span class="n">interaction</span> <span class="o">+=</span> <span class="p">(</span><span class="n">uniprot</span><span class="p">,</span> <span class="p">)</span>
+
+            <span class="n">interaction</span> <span class="o">+=</span> <span class="p">(</span><span class="n">pm</span><span class="p">,</span> <span class="n">sc</span><span class="p">,</span> <span class="n">ty</span><span class="p">)</span>
+            <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">interaction</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span> <span class="o">&gt;</span> <span class="mi">1</span> <span class="ow">and</span> <span class="nb">len</span><span class="p">(</span><span class="n">interaction</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span> <span class="o">&gt;</span> <span class="mi">1</span><span class="p">:</span>
+                <span class="n">i</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">interaction</span><span class="p">)</span>
+
+        <span class="n">lnum</span> <span class="o">+=</span> <span class="mi">1</span>
+
+    <span class="k">return</span> <span class="n">i</span></div>
+
+
+
+<div class="viewcode-block" id="depod_enzyme_substrate">
+<a class="viewcode-back" href="../../../api/pypath.inputs.depod.depod_enzyme_substrate.html#pypath.inputs.depod.depod_enzyme_substrate">[docs]</a>
+<span class="k">def</span> <span class="nf">depod_enzyme_substrate</span><span class="p">(</span><span class="n">organism</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">):</span>
+
+    <span class="n">result</span> <span class="o">=</span> <span class="p">[]</span>
+
+    <span class="n">reunip</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">compile</span><span class="p">(</span><span class="sa">r</span><span class="s1">&#39;uniprotkb:([A-Z0-9]+)&#39;</span><span class="p">)</span>
+    <span class="n">reptm</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">compile</span><span class="p">(</span><span class="sa">r</span><span class="s1">&#39;([A-Z][a-z]</span><span class="si">{2}</span><span class="s1">)-([0-9]+)&#39;</span><span class="p">)</span>
+    <span class="n">repmidsep</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">compile</span><span class="p">(</span><span class="sa">r</span><span class="s1">&#39;[,|]\s?&#39;</span><span class="p">)</span>
+
+    <span class="n">url</span> <span class="o">=</span> <span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;depod&#39;</span><span class="p">][</span><span class="s1">&#39;urls&#39;</span><span class="p">][</span><span class="mi">0</span><span class="p">]</span>
+    <span class="n">c</span> <span class="o">=</span> <span class="n">curl</span><span class="o">.</span><span class="n">Curl</span><span class="p">(</span><span class="n">url</span><span class="p">,</span> <span class="n">silent</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span> <span class="n">encoding</span> <span class="o">=</span> <span class="s1">&#39;ascii&#39;</span><span class="p">)</span>
+    <span class="n">data</span> <span class="o">=</span> <span class="n">c</span><span class="o">.</span><span class="n">result</span>
+    <span class="n">data</span> <span class="o">=</span> <span class="p">[</span><span class="n">x</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\t</span><span class="s1">&#39;</span><span class="p">)</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">data</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\n</span><span class="s1">&#39;</span><span class="p">)]</span>
+    <span class="k">del</span> <span class="n">data</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span>
+
+    <span class="n">url_mitab</span> <span class="o">=</span> <span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;depod&#39;</span><span class="p">][</span><span class="s1">&#39;urls&#39;</span><span class="p">][</span><span class="mi">1</span><span class="p">]</span>
+    <span class="n">c_mitab</span> <span class="o">=</span> <span class="n">curl</span><span class="o">.</span><span class="n">Curl</span><span class="p">(</span><span class="n">url_mitab</span><span class="p">,</span> <span class="n">silent</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span> <span class="n">encoding</span> <span class="o">=</span> <span class="s1">&#39;iso-8859-1&#39;</span><span class="p">)</span>
+    <span class="n">data_mitab</span> <span class="o">=</span> <span class="n">c_mitab</span><span class="o">.</span><span class="n">result</span>
+    <span class="n">data_mitab</span> <span class="o">=</span> <span class="p">[</span><span class="n">x</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\t</span><span class="s1">&#39;</span><span class="p">)</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">data_mitab</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\n</span><span class="s1">&#39;</span><span class="p">)]</span>
+    <span class="k">del</span> <span class="n">data_mitab</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span>
+
+    <span class="k">for</span> <span class="n">i</span><span class="p">,</span> <span class="n">l</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">data</span><span class="p">):</span>
+
+        <span class="k">if</span> <span class="p">(</span>
+            <span class="nb">len</span><span class="p">(</span><span class="n">l</span><span class="p">)</span> <span class="o">&gt;</span> <span class="mi">6</span> <span class="ow">and</span>
+            <span class="n">l</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="o">==</span> <span class="s1">&#39;protein substrate&#39;</span> <span class="ow">and</span>
+            <span class="n">taxonomy</span><span class="o">.</span><span class="n">ensure_ncbi_tax_id</span><span class="p">(</span>
+                <span class="n">l</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;(&#39;</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span>
+            <span class="p">)</span> <span class="o">==</span> <span class="n">organism</span> <span class="ow">and</span>
+            <span class="n">l</span><span class="p">[</span><span class="mi">4</span><span class="p">]</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span> <span class="o">!=</span> <span class="s1">&#39;N/A&#39;</span>
+        <span class="p">):</span>
+
+            <span class="n">enzyme_uniprot</span> <span class="o">=</span> <span class="n">reunip</span><span class="o">.</span><span class="n">search</span><span class="p">(</span><span class="n">data_mitab</span><span class="p">[</span><span class="n">i</span><span class="p">][</span><span class="mi">0</span><span class="p">])</span><span class="o">.</span><span class="n">groups</span><span class="p">()[</span><span class="mi">0</span><span class="p">]</span>
+            <span class="n">substrate_uniprot</span> <span class="o">=</span> <span class="n">reunip</span><span class="o">.</span><span class="n">search</span><span class="p">(</span><span class="n">data_mitab</span><span class="p">[</span><span class="n">i</span><span class="p">][</span><span class="mi">1</span><span class="p">])</span><span class="o">.</span><span class="n">groups</span><span class="p">()[</span><span class="mi">0</span><span class="p">]</span>
+
+            <span class="k">for</span> <span class="n">enzyme_up</span><span class="p">,</span> <span class="n">substrate_up</span> <span class="ow">in</span> <span class="n">itertools</span><span class="o">.</span><span class="n">product</span><span class="p">(</span>
+                    <span class="n">mapping</span><span class="o">.</span><span class="n">map_name</span><span class="p">(</span>
+                        <span class="n">enzyme_uniprot</span><span class="p">,</span>
+                        <span class="s1">&#39;uniprot&#39;</span><span class="p">,</span>
+                        <span class="s1">&#39;uniprot&#39;</span>
+                    <span class="p">),</span>
+                    <span class="n">mapping</span><span class="o">.</span><span class="n">map_name</span><span class="p">(</span>
+                        <span class="n">substrate_uniprot</span><span class="p">,</span>
+                        <span class="s1">&#39;uniprot&#39;</span><span class="p">,</span>
+                        <span class="s1">&#39;uniprot&#39;</span>
+                    <span class="p">),</span>
+                <span class="p">):</span>
+
+                <span class="k">for</span> <span class="n">resaa</span><span class="p">,</span> <span class="n">resnum</span> <span class="ow">in</span> <span class="n">reptm</span><span class="o">.</span><span class="n">findall</span><span class="p">(</span><span class="n">l</span><span class="p">[</span><span class="mi">4</span><span class="p">]):</span>
+
+                    <span class="n">resnum</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">resnum</span><span class="p">)</span>
+                    <span class="n">resaa</span> <span class="o">=</span> <span class="p">(</span>
+                        <span class="n">common</span><span class="o">.</span><span class="n">aminoa_3_to_1_letter</span><span class="p">[</span><span class="n">resaa</span><span class="p">]</span>
+                            <span class="k">if</span> <span class="n">resaa</span> <span class="ow">in</span> <span class="n">common</span><span class="o">.</span><span class="n">aminoa_3_to_1_letter</span> <span class="k">else</span>
+                        <span class="n">resaa</span>
+                    <span class="p">)</span>
+
+                    <span class="n">result</span><span class="o">.</span><span class="n">append</span><span class="p">({</span>
+                        <span class="s1">&#39;instance&#39;</span><span class="p">:</span> <span class="kc">None</span><span class="p">,</span>
+                        <span class="s1">&#39;kinase&#39;</span><span class="p">:</span> <span class="n">enzyme_up</span><span class="p">,</span>
+                        <span class="s1">&#39;resaa&#39;</span><span class="p">:</span> <span class="n">resaa</span><span class="p">,</span>
+                        <span class="s1">&#39;resnum&#39;</span><span class="p">:</span> <span class="n">resnum</span><span class="p">,</span>
+                        <span class="s1">&#39;references&#39;</span><span class="p">:</span> <span class="n">repmidsep</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="n">l</span><span class="p">[</span><span class="mi">6</span><span class="p">]</span><span class="o">.</span><span class="n">strip</span><span class="p">()),</span>
+                        <span class="s1">&#39;substrate&#39;</span><span class="p">:</span> <span class="n">substrate_up</span><span class="p">,</span>
+                        <span class="s1">&#39;start&#39;</span><span class="p">:</span> <span class="kc">None</span><span class="p">,</span>
+                        <span class="s1">&#39;end&#39;</span><span class="p">:</span> <span class="kc">None</span><span class="p">,</span>
+                        <span class="s1">&#39;typ&#39;</span><span class="p">:</span> <span class="s1">&#39;dephosphorylation&#39;</span><span class="p">,</span>
+                    <span class="p">})</span>
+
+    <span class="k">return</span> <span class="n">result</span></div>
+
+</pre></div>
+
+                </article>
+              
+              
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+                  
+  <h1>Source code for pypath.inputs.dgidb</h1><div class="highlight"><pre>
+<span></span><span class="ch">#!/usr/bin/env python</span>
+<span class="c1"># -*- coding: utf-8 -*-</span>
+
+<span class="c1">#</span>
+<span class="c1">#  This file is part of the `pypath` python module</span>
+<span class="c1">#</span>
+<span class="c1">#  Copyright 2014-2023</span>
+<span class="c1">#  EMBL, EMBL-EBI, Uniklinik RWTH Aachen, Heidelberg University</span>
+<span class="c1">#</span>
+<span class="c1">#  Authors: see the file `README.rst`</span>
+<span class="c1">#  Contact: Dénes Türei (turei.denes@gmail.com)</span>
+<span class="c1">#</span>
+<span class="c1">#  Distributed under the GPLv3 License.</span>
+<span class="c1">#  See accompanying file LICENSE.txt or copy at</span>
+<span class="c1">#      https://www.gnu.org/licenses/gpl-3.0.html</span>
+<span class="c1">#</span>
+<span class="c1">#  Website: https://pypath.omnipathdb.org/</span>
+<span class="c1">#</span>
+
+<span class="kn">from</span> <span class="nn">__future__</span> <span class="kn">import</span> <span class="n">annotations</span>
+
+<span class="kn">import</span> <span class="nn">csv</span>
+<span class="kn">import</span> <span class="nn">collections</span>
+
+<span class="kn">import</span> <span class="nn">bs4</span>
+
+<span class="kn">import</span> <span class="nn">pypath.share.curl</span> <span class="k">as</span> <span class="nn">curl</span>
+<span class="kn">import</span> <span class="nn">pypath.resources.urls</span> <span class="k">as</span> <span class="nn">urls</span>
+<span class="kn">import</span> <span class="nn">pypath.utils.mapping</span> <span class="k">as</span> <span class="nn">mapping</span>
+
+
+<div class="viewcode-block" id="dgidb_interactions">
+<a class="viewcode-back" href="../../../api/pypath.inputs.dgidb.dgidb_interactions.html#pypath.inputs.dgidb.dgidb_interactions">[docs]</a>
+<span class="k">def</span> <span class="nf">dgidb_interactions</span><span class="p">()</span> <span class="o">-&gt;</span> <span class="nb">list</span><span class="p">[</span><span class="nb">tuple</span><span class="p">]:</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Retrieves drug-gene interactions from DGIdb.</span>
+
+<span class="sd">    Returns:</span>
+<span class="sd">        A list with tuples. Tuples are dgidb interactons</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="n">result</span> <span class="o">=</span> <span class="nb">set</span><span class="p">()</span>
+
+    <span class="n">DgidbInteraction</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">namedtuple</span><span class="p">(</span>
+        <span class="s1">&#39;DgidbInteraction&#39;</span><span class="p">,</span>
+        <span class="p">[</span>
+            <span class="s1">&#39;genesymbol&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;entrez&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;resource&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;type&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;drug_name&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;drug_chembl&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;score&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;pmid&#39;</span>
+        <span class="p">],</span>
+    <span class="p">)</span>
+
+    <span class="n">url</span> <span class="o">=</span> <span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;dgidb&#39;</span><span class="p">][</span><span class="s1">&#39;interactions&#39;</span><span class="p">]</span>
+    <span class="n">c</span> <span class="o">=</span> <span class="n">curl</span><span class="o">.</span><span class="n">Curl</span><span class="p">(</span><span class="n">url</span> <span class="o">=</span> <span class="n">url</span><span class="p">,</span> <span class="n">silent</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span> <span class="n">large</span> <span class="o">=</span> <span class="kc">True</span><span class="p">)</span>
+    <span class="n">interactions</span> <span class="o">=</span> <span class="n">csv</span><span class="o">.</span><span class="n">DictReader</span><span class="p">(</span><span class="n">c</span><span class="o">.</span><span class="n">result</span><span class="p">,</span> <span class="n">delimiter</span> <span class="o">=</span> <span class="s1">&#39;</span><span class="se">\t</span><span class="s1">&#39;</span><span class="p">)</span>
+
+    <span class="k">for</span> <span class="n">interaction</span> <span class="ow">in</span> <span class="n">interactions</span><span class="p">:</span>
+
+        <span class="n">interaction</span> <span class="o">=</span> <span class="p">{</span><span class="n">k</span><span class="p">:</span> <span class="n">v</span> <span class="ow">or</span> <span class="kc">None</span> <span class="k">for</span> <span class="n">k</span><span class="p">,</span> <span class="n">v</span> <span class="ow">in</span> <span class="n">interaction</span><span class="o">.</span><span class="n">items</span><span class="p">()}</span>
+
+        <span class="n">dgidb_interaction</span> <span class="o">=</span> <span class="n">DgidbInteraction</span><span class="p">(</span>
+            <span class="n">genesymbol</span> <span class="o">=</span> <span class="n">interaction</span><span class="p">[</span><span class="s1">&#39;gene_name&#39;</span><span class="p">],</span>
+            <span class="n">entrez</span> <span class="o">=</span> <span class="n">interaction</span><span class="p">[</span><span class="s1">&#39;entrez_id&#39;</span><span class="p">],</span>
+            <span class="n">resource</span> <span class="o">=</span> <span class="n">interaction</span><span class="p">[</span><span class="s1">&#39;interaction_claim_source&#39;</span><span class="p">],</span>
+            <span class="nb">type</span> <span class="o">=</span> <span class="n">interaction</span><span class="p">[</span><span class="s1">&#39;interaction_types&#39;</span><span class="p">],</span>
+            <span class="n">drug_name</span> <span class="o">=</span> <span class="n">interaction</span><span class="p">[</span><span class="s1">&#39;drug_claim_primary_name&#39;</span><span class="p">],</span>
+            <span class="n">drug_chembl</span> <span class="o">=</span> <span class="n">interaction</span><span class="p">[</span><span class="s1">&#39;drug_concept_id&#39;</span><span class="p">],</span>
+            <span class="n">score</span> <span class="o">=</span> <span class="n">interaction</span><span class="p">[</span><span class="s1">&#39;interaction_group_score&#39;</span><span class="p">],</span>
+            <span class="n">pmid</span> <span class="o">=</span> <span class="n">interaction</span><span class="p">[</span><span class="s1">&#39;PMIDs&#39;</span><span class="p">],</span>
+        <span class="p">)</span>
+
+        <span class="n">result</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">dgidb_interaction</span><span class="p">)</span>
+
+    <span class="k">return</span> <span class="nb">list</span><span class="p">(</span><span class="n">result</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="dgidb_annotations">
+<a class="viewcode-back" href="../../../api/pypath.inputs.dgidb.dgidb_annotations.html#pypath.inputs.dgidb.dgidb_annotations">[docs]</a>
+<span class="k">def</span> <span class="nf">dgidb_annotations</span><span class="p">():</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Downloads druggable protein annotations from DGIdb.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="n">DgidbAnnotation</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">namedtuple</span><span class="p">(</span>
+        <span class="s1">&#39;DgidbAnnotation&#39;</span><span class="p">,</span>
+        <span class="p">[</span><span class="s1">&#39;category&#39;</span><span class="p">],</span>
+    <span class="p">)</span>
+
+
+    <span class="n">url</span> <span class="o">=</span> <span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;dgidb&#39;</span><span class="p">][</span><span class="s1">&#39;categories&#39;</span><span class="p">]</span>
+    <span class="n">c</span> <span class="o">=</span> <span class="n">curl</span><span class="o">.</span><span class="n">Curl</span><span class="p">(</span><span class="n">url</span> <span class="o">=</span> <span class="n">url</span><span class="p">,</span> <span class="n">silent</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span> <span class="n">large</span> <span class="o">=</span> <span class="kc">True</span><span class="p">)</span>
+    <span class="n">data</span> <span class="o">=</span> <span class="n">csv</span><span class="o">.</span><span class="n">DictReader</span><span class="p">(</span><span class="n">c</span><span class="o">.</span><span class="n">result</span><span class="p">,</span> <span class="n">delimiter</span> <span class="o">=</span> <span class="s1">&#39;</span><span class="se">\t</span><span class="s1">&#39;</span><span class="p">)</span>
+
+    <span class="n">result</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">defaultdict</span><span class="p">(</span><span class="nb">set</span><span class="p">)</span>
+
+    <span class="k">for</span> <span class="n">rec</span> <span class="ow">in</span> <span class="n">data</span><span class="p">:</span>
+
+        <span class="n">uniprots</span> <span class="o">=</span> <span class="n">mapping</span><span class="o">.</span><span class="n">map_name</span><span class="p">(</span>
+            <span class="n">rec</span><span class="p">[</span><span class="s1">&#39;entrez_gene_symbol&#39;</span><span class="p">],</span>
+            <span class="s1">&#39;genesymbol&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;uniprot&#39;</span><span class="p">,</span>
+        <span class="p">)</span>
+
+        <span class="k">for</span> <span class="n">uniprot</span> <span class="ow">in</span> <span class="n">uniprots</span><span class="p">:</span>
+            <span class="n">result</span><span class="p">[</span><span class="n">uniprot</span><span class="p">]</span><span class="o">.</span><span class="n">add</span><span class="p">(</span>
+                <span class="n">DgidbAnnotation</span><span class="p">(</span>
+                    <span class="n">category</span> <span class="o">=</span> <span class="n">rec</span><span class="p">[</span><span class="s1">&#39;category&#39;</span><span class="p">]</span>
+                <span class="p">)</span>
+            <span class="p">)</span>
+
+    <span class="k">return</span> <span class="nb">dict</span><span class="p">(</span><span class="n">result</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="get_dgidb_old">
+<a class="viewcode-back" href="../../../api/pypath.inputs.dgidb.get_dgidb_old.html#pypath.inputs.dgidb.get_dgidb_old">[docs]</a>
+<span class="k">def</span> <span class="nf">get_dgidb_old</span><span class="p">():</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Deprecated. Will be removed soon.</span>
+
+<span class="sd">    Downloads and processes the list of all human druggable proteins.</span>
+<span class="sd">    Returns a list of GeneSymbols.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="n">genesymbols</span> <span class="o">=</span> <span class="p">[]</span>
+    <span class="n">url</span> <span class="o">=</span> <span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;dgidb&#39;</span><span class="p">][</span><span class="s1">&#39;main_url&#39;</span><span class="p">]</span>
+    <span class="n">c</span> <span class="o">=</span> <span class="n">curl</span><span class="o">.</span><span class="n">Curl</span><span class="p">(</span><span class="n">url</span><span class="p">,</span> <span class="n">silent</span> <span class="o">=</span> <span class="kc">False</span><span class="p">)</span>
+    <span class="n">html</span> <span class="o">=</span> <span class="n">c</span><span class="o">.</span><span class="n">result</span>
+    <span class="n">soup</span> <span class="o">=</span> <span class="n">bs4</span><span class="o">.</span><span class="n">BeautifulSoup</span><span class="p">(</span><span class="n">html</span><span class="p">,</span> <span class="s1">&#39;html.parser&#39;</span><span class="p">)</span>
+    <span class="n">cats</span> <span class="o">=</span> <span class="p">[</span>
+        <span class="n">o</span><span class="o">.</span><span class="n">attrs</span><span class="p">[</span><span class="s1">&#39;value&#39;</span><span class="p">]</span>
+        <span class="k">for</span> <span class="n">o</span> <span class="ow">in</span> <span class="n">soup</span><span class="o">.</span><span class="n">find</span><span class="p">(</span><span class="s1">&#39;select&#39;</span><span class="p">,</span> <span class="p">{</span><span class="s1">&#39;id&#39;</span><span class="p">:</span> <span class="s1">&#39;gene_categories&#39;</span><span class="p">})</span>
+        <span class="o">.</span><span class="n">find_all</span><span class="p">(</span><span class="s1">&#39;option&#39;</span><span class="p">)</span>
+    <span class="p">]</span>
+
+    <span class="k">for</span> <span class="n">cat</span> <span class="ow">in</span> <span class="n">cats</span><span class="p">:</span>
+        <span class="n">url</span> <span class="o">=</span> <span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;dgidb&#39;</span><span class="p">][</span><span class="s1">&#39;url&#39;</span><span class="p">]</span> <span class="o">%</span> <span class="n">cat</span>
+        <span class="n">c</span> <span class="o">=</span> <span class="n">curl</span><span class="o">.</span><span class="n">Curl</span><span class="p">(</span><span class="n">url</span><span class="p">)</span>
+        <span class="n">html</span> <span class="o">=</span> <span class="n">c</span><span class="o">.</span><span class="n">result</span>
+        <span class="n">soup</span> <span class="o">=</span> <span class="n">bs4</span><span class="o">.</span><span class="n">BeautifulSoup</span><span class="p">(</span><span class="n">html</span><span class="p">,</span> <span class="s1">&#39;html.parser&#39;</span><span class="p">)</span>
+        <span class="n">trs</span> <span class="o">=</span> <span class="n">soup</span><span class="o">.</span><span class="n">find</span><span class="p">(</span><span class="s1">&#39;tbody&#39;</span><span class="p">)</span><span class="o">.</span><span class="n">find_all</span><span class="p">(</span><span class="s1">&#39;tr&#39;</span><span class="p">)</span>
+        <span class="n">genesymbols</span><span class="o">.</span><span class="n">extend</span><span class="p">([</span><span class="n">tr</span><span class="o">.</span><span class="n">find</span><span class="p">(</span><span class="s1">&#39;td&#39;</span><span class="p">)</span><span class="o">.</span><span class="n">text</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span> <span class="k">for</span> <span class="n">tr</span> <span class="ow">in</span> <span class="n">trs</span><span class="p">])</span>
+
+    <span class="k">return</span> <span class="n">mapping</span><span class="o">.</span><span class="n">map_names</span><span class="p">(</span><span class="n">genesymbols</span><span class="p">,</span> <span class="s1">&#39;genesymbol&#39;</span><span class="p">,</span> <span class="s1">&#39;uniprot&#39;</span><span class="p">)</span></div>
+
+</pre></div>
+
+                </article>
+              
+              
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diff --git a/_modules/pypath/inputs/domino.html b/_modules/pypath/inputs/domino.html
new file mode 100644
index 000000000..8a60110eb
--- /dev/null
+++ b/_modules/pypath/inputs/domino.html
@@ -0,0 +1,1141 @@
+
+<!DOCTYPE html>
+
+
+<html lang="en" data-content_root="../../../" >
+
+  <head>
+    <meta charset="utf-8" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+    <title>pypath.inputs.domino &#8212; pypath 0.16.9 documentation</title>
+  
+  
+  
+  <script data-cfasync="false">
+    document.documentElement.dataset.mode = localStorage.getItem("mode") || "";
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+  <link href="../../../_static/vendor/fontawesome/6.5.1/css/all.min.css?digest=8d27b9dea8ad943066ae" rel="stylesheet" />
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+<link rel="preload" as="font" type="font/woff2" crossorigin href="../../../_static/vendor/fontawesome/6.5.1/webfonts/fa-regular-400.woff2" />
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+  
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+
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+    <script>DOCUMENTATION_OPTIONS.pagename = '_modules/pypath/inputs/domino';</script>
+    <link rel="icon" href="../../../_static/omnipath-logo.svg"/>
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+  <meta name="viewport" content="width=device-width, initial-scale=1"/>
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+  <body data-bs-spy="scroll" data-bs-target=".bd-toc-nav" data-offset="180" data-bs-root-margin="0px 0px -60%" data-default-mode="">
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+  
+  <div id="pst-scroll-pixel-helper"></div>
+  
+  <button type="button" class="btn rounded-pill" id="pst-back-to-top">
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+  <label class="overlay overlay-primary" for="__primary"></label>
+  
+  <input type="checkbox"
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+          name="__secondary"
+          id="__secondary"/>
+  <label class="overlay overlay-secondary" for="__secondary"></label>
+  
+  <div class="search-button__wrapper">
+    <div class="search-button__overlay"></div>
+    <div class="search-button__search-container">
+<form class="bd-search d-flex align-items-center"
+      action="../../../search.html"
+      method="get">
+  <i class="fa-solid fa-magnifying-glass"></i>
+  <input type="search"
+         class="form-control"
+         name="q"
+         id="search-input"
+         placeholder="Search the docs ..."
+         aria-label="Search the docs ..."
+         autocomplete="off"
+         autocorrect="off"
+         autocapitalize="off"
+         spellcheck="false"/>
+  <span class="search-button__kbd-shortcut"><kbd class="kbd-shortcut__modifier">Ctrl</kbd>+<kbd>K</kbd></span>
+</form></div>
+  </div>
+  
+    <header class="bd-header navbar navbar-expand-lg bd-navbar">
+<div class="bd-header__inner bd-page-width">
+  <label class="sidebar-toggle primary-toggle" for="__primary">
+    <span class="fa-solid fa-bars"></span>
+  </label>
+  
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+  <div class=" navbar-header-items__start">
+    
+      <div class="navbar-item">
+
+  
+
+<a class="navbar-brand logo" href="../../../contents.html">
+  
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+  
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+  
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+    
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+      
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+  <ul class="bd-navbar-elements navbar-nav">
+    
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+                      </a>
+                    </li>
+                
+
+                    <li class="nav-item">
+                      <a class="nav-link nav-internal" href="../../../webservice.html">
+                        Webservice
+                      </a>
+                    </li>
+                
+
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+                      <a class="nav-link nav-internal" href="../../../releasehistory.html">
+                        Release history
+                      </a>
+                    </li>
+                
+
+                    <li class="nav-item">
+                      <a class="nav-link nav-internal" href="../../../reference.html">
+                        Reference
+                      </a>
+                    </li>
+                
+
+                    <li class="nav-item">
+                      <a class="nav-link nav-internal" href="../../../notebooks/manual.html">
+                        The pypath book
+                      </a>
+                    </li>
+                
+  </ul>
+</nav></div>
+      
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+    
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+    <div class="navbar-header-items__end">
+      
+        <div class="navbar-item navbar-persistent--container">
+          
+
+ <script>
+ document.write(`
+   <button class="btn navbar-btn search-button-field search-button__button" title="Search" aria-label="Search" data-bs-placement="bottom" data-bs-toggle="tooltip">
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+   </button>
+ `);
+ </script>
+        </div>
+      
+      
+        <div class="navbar-item">
+
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+document.write(`
+  <button class="btn btn-sm navbar-btn theme-switch-button" title="light/dark" aria-label="light/dark" data-bs-placement="bottom" data-bs-toggle="tooltip">
+    <span class="theme-switch nav-link" data-mode="light"><i class="fa-solid fa-sun fa-lg"></i></span>
+    <span class="theme-switch nav-link" data-mode="dark"><i class="fa-solid fa-moon fa-lg"></i></span>
+    <span class="theme-switch nav-link" data-mode="auto"><i class="fa-solid fa-circle-half-stroke fa-lg"></i></span>
+  </button>
+`);
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+      
+        <div class="navbar-item"><ul class="navbar-icon-links navbar-nav"
+    aria-label="Icon Links">
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+            <span class="sr-only">PyPI</span></a>
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+          
+          
+          
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+          
+          
+          
+          
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+            <span class="sr-only">OmniPath</span></a>
+        </li>
+        <li class="nav-item">
+          
+          
+          
+          
+          
+          
+          
+          
+          <a href="https://saezlab.org/" title="Saez Lab" class="nav-link" rel="noopener" target="_blank" data-bs-toggle="tooltip" data-bs-placement="bottom"><span><i class="fa-solid fa-users fa-lg" aria-hidden="true"></i></span>
+            <span class="sr-only">Saez Lab</span></a>
+        </li>
+</ul></div>
+      
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+    
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+  
+  
+    <div class="navbar-persistent--mobile">
+
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+ document.write(`
+   <button class="btn navbar-btn search-button-field search-button__button" title="Search" aria-label="Search" data-bs-placement="bottom" data-bs-toggle="tooltip">
+    <i class="fa-solid fa-magnifying-glass"></i>
+    <span class="search-button__default-text">Search</span>
+    <span class="search-button__kbd-shortcut"><kbd class="kbd-shortcut__modifier">Ctrl</kbd>+<kbd class="kbd-shortcut__modifier">K</kbd></span>
+   </button>
+ `);
+ </script>
+    </div>
+  
+
+  
+    <label class="sidebar-toggle secondary-toggle" for="__secondary" tabindex="0">
+      <span class="fa-solid fa-outdent"></span>
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+  
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+    <div class="bd-container__inner bd-page-width">
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+        
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+        
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+<nav class="navbar-nav">
+  <ul class="bd-navbar-elements navbar-nav">
+    
+                    <li class="nav-item">
+                      <a class="nav-link nav-internal" href="../../../index.html">
+                        Welcome to pypath!
+                      </a>
+                    </li>
+                
+
+                    <li class="nav-item">
+                      <a class="nav-link nav-internal" href="../../../webservice.html">
+                        Webservice
+                      </a>
+                    </li>
+                
+
+                    <li class="nav-item">
+                      <a class="nav-link nav-internal" href="../../../releasehistory.html">
+                        Release history
+                      </a>
+                    </li>
+                
+
+                    <li class="nav-item">
+                      <a class="nav-link nav-internal" href="../../../reference.html">
+                        Reference
+                      </a>
+                    </li>
+                
+
+                    <li class="nav-item">
+                      <a class="nav-link nav-internal" href="../../../notebooks/manual.html">
+                        The pypath book
+                      </a>
+                    </li>
+                
+  </ul>
+</nav></div>
+        
+      </div>
+    
+    
+    
+      <div class="sidebar-header-items__end">
+        
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+
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+document.write(`
+  <button class="btn btn-sm navbar-btn theme-switch-button" title="light/dark" aria-label="light/dark" data-bs-placement="bottom" data-bs-toggle="tooltip">
+    <span class="theme-switch nav-link" data-mode="light"><i class="fa-solid fa-sun fa-lg"></i></span>
+    <span class="theme-switch nav-link" data-mode="dark"><i class="fa-solid fa-moon fa-lg"></i></span>
+    <span class="theme-switch nav-link" data-mode="auto"><i class="fa-solid fa-circle-half-stroke fa-lg"></i></span>
+  </button>
+`);
+</script></div>
+        
+          <div class="navbar-item"><ul class="navbar-icon-links navbar-nav"
+    aria-label="Icon Links">
+        <li class="nav-item">
+          
+          
+          
+          
+          
+          
+          
+          
+          <a href="https://github.com/saezlab/pypath" title="GitHub" class="nav-link" rel="noopener" target="_blank" data-bs-toggle="tooltip" data-bs-placement="bottom"><span><i class="fa-brands fa-square-github fa-lg" aria-hidden="true"></i></span>
+            <span class="sr-only">GitHub</span></a>
+        </li>
+        <li class="nav-item">
+          
+          
+          
+          
+          
+          
+          
+          
+          <a href="https://twitter.com/omnipathdb" title="Twitter" class="nav-link" rel="noopener" target="_blank" data-bs-toggle="tooltip" data-bs-placement="bottom"><span><i class="fa-brands fa-square-twitter fa-lg" aria-hidden="true"></i></span>
+            <span class="sr-only">Twitter</span></a>
+        </li>
+        <li class="nav-item">
+          
+          
+          
+          
+          
+          
+          
+          
+          <a href="https://pypi.org/project/pypath-omnipath" title="PyPI" class="nav-link" rel="noopener" target="_blank" data-bs-toggle="tooltip" data-bs-placement="bottom"><span><i class="fa-solid fa-box fa-lg" aria-hidden="true"></i></span>
+            <span class="sr-only">PyPI</span></a>
+        </li>
+        <li class="nav-item">
+          
+          
+          
+          
+          
+          
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+  <h1>Source code for pypath.inputs.domino</h1><div class="highlight"><pre>
+<span></span><span class="ch">#!/usr/bin/env python</span>
+<span class="c1"># -*- coding: utf-8 -*-</span>
+
+<span class="c1">#</span>
+<span class="c1">#  This file is part of the `pypath` python module</span>
+<span class="c1">#</span>
+<span class="c1">#  Copyright 2014-2023</span>
+<span class="c1">#  EMBL, EMBL-EBI, Uniklinik RWTH Aachen, Heidelberg University</span>
+<span class="c1">#</span>
+<span class="c1">#  Authors: see the file `README.rst`</span>
+<span class="c1">#  Contact: Dénes Türei (turei.denes@gmail.com)</span>
+<span class="c1">#</span>
+<span class="c1">#  Distributed under the GPLv3 License.</span>
+<span class="c1">#  See accompanying file LICENSE.txt or copy at</span>
+<span class="c1">#      https://www.gnu.org/licenses/gpl-3.0.html</span>
+<span class="c1">#</span>
+<span class="c1">#  Website: https://pypath.omnipathdb.org/</span>
+<span class="c1">#</span>
+
+<span class="kn">from</span> <span class="nn">past.builtins</span> <span class="kn">import</span> <span class="n">xrange</span><span class="p">,</span> <span class="nb">range</span>
+
+<span class="kn">import</span> <span class="nn">re</span>
+<span class="kn">import</span> <span class="nn">itertools</span>
+<span class="kn">import</span> <span class="nn">collections</span>
+
+<span class="kn">import</span> <span class="nn">pypath.resources.urls</span> <span class="k">as</span> <span class="nn">urls</span>
+<span class="kn">import</span> <span class="nn">pypath.share.curl</span> <span class="k">as</span> <span class="nn">curl</span>
+<span class="kn">import</span> <span class="nn">pypath.share.session</span> <span class="k">as</span> <span class="nn">session</span>
+<span class="kn">import</span> <span class="nn">pypath.share.progress</span> <span class="k">as</span> <span class="nn">progress</span>
+<span class="kn">import</span> <span class="nn">pypath.inputs.ontology</span> <span class="k">as</span> <span class="nn">ontology</span>
+<span class="kn">import</span> <span class="nn">pypath.internals.intera</span> <span class="k">as</span> <span class="nn">intera</span>
+<span class="kn">import</span> <span class="nn">pypath.internals.resource</span> <span class="k">as</span> <span class="nn">resource_internals</span>
+<span class="kn">import</span> <span class="nn">pypath.core.evidence</span> <span class="k">as</span> <span class="nn">evidence</span>
+
+<span class="n">_logger</span> <span class="o">=</span> <span class="n">session</span><span class="o">.</span><span class="n">Logger</span><span class="p">(</span><span class="n">name</span> <span class="o">=</span> <span class="s1">&#39;domino_input&#39;</span><span class="p">)</span>
+<span class="n">_log</span> <span class="o">=</span> <span class="n">_logger</span><span class="o">.</span><span class="n">_log</span>
+
+
+<div class="viewcode-block" id="get_domino">
+<a class="viewcode-back" href="../../../api/pypath.inputs.domino.get_domino.html#pypath.inputs.domino.get_domino">[docs]</a>
+<span class="k">def</span> <span class="nf">get_domino</span><span class="p">(</span><span class="n">none_values</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span> <span class="n">outfile</span> <span class="o">=</span> <span class="kc">None</span><span class="p">):</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Returns</span>
+<span class="sd">        A list of records with the following fields:</span>
+<span class="sd">        header = [&#39;uniprot_A&#39;, &#39;uniprot_B&#39;, &#39;isoform_A&#39;, &#39;isoform_B&#39;, #3</span>
+<span class="sd">        &#39;exp_method&#39;, &#39;references&#39;, &#39;taxon_A&#39;, &#39;taxon_B&#39;, #7</span>
+<span class="sd">        &#39;role_A&#39;, &#39;role_B&#39;, &#39;binding_site_range_A&#39;, &#39;binding_site_range_B&#39;, #11</span>
+<span class="sd">        &#39;domains_A&#39;, &#39;domains_B&#39;, &#39;ptm_residue_A&#39;, &#39;ptm_residue_B&#39;, #15</span>
+<span class="sd">        &#39;ptm_type_mi_A&#39;, &#39;ptm_type_mi_B&#39;, &#39;ptm_type_A&#39;, &#39;ptm_type_B&#39;, #19</span>
+<span class="sd">        &#39;ptm_res_name_A&#39;, &#39;ptm_res_name_B&#39;, &#39;mutations_A&#39;, &#39;mutations_B&#39;, #23</span>
+<span class="sd">        &#39;mutation_effects_A&#39;, &#39;mutation_effects_B&#39;, &#39;domains_interpro_A&#39;, #26</span>
+<span class="sd">        &#39;domains_interpro_B&#39;, &#39;negative&#39;] #28</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="n">DominoRecord</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">namedtuple</span><span class="p">(</span>
+        <span class="s1">&#39;DominoRecord&#39;</span><span class="p">,</span>
+        <span class="p">(</span>
+            <span class="s1">&#39;uniprot_A&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;uniprot_B&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;isoform_A&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;isoform_B&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;exp_method&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;references&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;taxon_A&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;taxon_B&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;role_A&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;role_B&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;binding_site_range_A&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;binding_site_range_B&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;domains_A&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;domains_B&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;ptm_residue_A&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;ptm_residue_B&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;ptm_type_mi_A&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;ptm_type_mi_B&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;ptm_type_A&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;ptm_type_B&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;ptm_res_name_A&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;ptm_res_name_B&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;mutations_A&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;mutations_B&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;mutation_effects_A&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;mutation_effects_B&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;domains_interpro_A&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;domains_interpro_B&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;negative&#39;</span><span class="p">,</span>
+        <span class="p">),</span>
+    <span class="p">)</span>
+
+    <span class="n">result</span> <span class="o">=</span> <span class="p">[]</span>
+    <span class="n">taxid</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">compile</span><span class="p">(</span><span class="sa">r</span><span class="s1">&#39;taxid:(.*)\([a-zA-Z ]*\)&#39;</span><span class="p">)</span>
+    <span class="n">miont</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">compile</span><span class="p">(</span><span class="sa">r</span><span class="s1">&#39;MI:[0-9]</span><span class="si">{4}</span><span class="s1">\((.*)\)&#39;</span><span class="p">)</span>
+    <span class="n">binds</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">compile</span><span class="p">(</span><span class="sa">r</span><span class="s1">&#39;([-0-9]*);.*&#39;</span><span class="p">)</span>
+    <span class="n">domai</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">compile</span><span class="p">(</span><span class="sa">r</span><span class="s1">&#39;.*;.*;.*\((.*)\)&#39;</span><span class="p">)</span>
+    <span class="n">dipro</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">compile</span><span class="p">(</span><span class="sa">r</span><span class="s1">&#39;.*;.*;.+:(IPR[0-9]*).*&#39;</span><span class="p">)</span>
+    <span class="n">ptmrs</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">compile</span><span class="p">(</span><span class="sa">r</span><span class="s1">&#39;([-0-9]*);.*&#39;</span><span class="p">)</span>
+    <span class="n">ptmmi</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">compile</span><span class="p">(</span><span class="sa">r</span><span class="s1">&#39;[0-9]*;(MI:[0-9]*)\(.*\);.*;.*&#39;</span><span class="p">)</span>
+    <span class="n">ptmrn</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">compile</span><span class="p">(</span>
+        <span class="sa">r</span><span class="s1">&#39;.*sequence:[\s]*[0-9]+-[0-9]+[\s]*:[\s]*([A-Z]{10,}).*&#39;</span><span class="p">)</span>
+    <span class="n">ptmty</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">compile</span><span class="p">(</span><span class="sa">r</span><span class="s1">&#39;[0-9]*;MI:[0-9]*\((.*)\);.*;.*&#39;</span><span class="p">)</span>
+    <span class="n">refrs</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">compile</span><span class="p">(</span><span class="sa">r</span><span class="s1">&#39;(pubmed|doi):[&quot;]*([-0-9a-zA-Z\.\(\)/]*)[&quot;]*&#39;</span><span class="p">)</span>
+    <span class="n">url</span> <span class="o">=</span> <span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;domino&#39;</span><span class="p">][</span><span class="s1">&#39;rescued&#39;</span><span class="p">]</span>
+    <span class="n">c</span> <span class="o">=</span> <span class="n">curl</span><span class="o">.</span><span class="n">Curl</span><span class="p">(</span><span class="n">url</span><span class="p">,</span> <span class="n">silent</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span> <span class="n">large</span> <span class="o">=</span> <span class="kc">True</span><span class="p">)</span>
+    <span class="n">data</span> <span class="o">=</span> <span class="n">c</span><span class="o">.</span><span class="n">result</span>
+    <span class="n">_</span> <span class="o">=</span> <span class="nb">next</span><span class="p">(</span><span class="n">data</span><span class="p">)</span>
+
+    <span class="k">for</span> <span class="n">r</span> <span class="ow">in</span> <span class="n">data</span><span class="p">:</span>
+
+        <span class="n">r</span> <span class="o">=</span> <span class="n">r</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\t</span><span class="s1">&#39;</span><span class="p">)</span>
+
+        <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">r</span><span class="p">)</span> <span class="o">&lt;</span> <span class="mi">39</span><span class="p">:</span>
+
+            <span class="k">continue</span>
+
+        <span class="n">this_row</span> <span class="o">=</span> <span class="p">[</span>
+            <span class="kc">None</span> <span class="k">if</span> <span class="s1">&#39;:&#39;</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">r</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="k">else</span> <span class="n">r</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;:&#39;</span><span class="p">)[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;-&#39;</span><span class="p">)[</span><span class="mi">0</span><span class="p">],</span>
+            <span class="kc">None</span> <span class="k">if</span> <span class="s1">&#39;:&#39;</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">r</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="k">else</span> <span class="n">r</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;:&#39;</span><span class="p">)[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;-&#39;</span><span class="p">)[</span><span class="mi">0</span><span class="p">],</span>
+            <span class="s1">&#39;1&#39;</span>  <span class="k">if</span> <span class="s1">&#39;-&#39;</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">r</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="k">else</span> <span class="n">r</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;-&#39;</span><span class="p">)[</span><span class="mi">1</span><span class="p">],</span>
+            <span class="s1">&#39;1&#39;</span>  <span class="k">if</span> <span class="s1">&#39;-&#39;</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">r</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="k">else</span> <span class="n">r</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;-&#39;</span><span class="p">)[</span><span class="mi">1</span><span class="p">],</span>
+            <span class="n">miont</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="n">r</span><span class="p">[</span><span class="mi">6</span><span class="p">])</span><span class="o">.</span><span class="n">groups</span><span class="p">(</span><span class="mi">1</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span> <span class="k">if</span> <span class="n">miont</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="n">r</span><span class="p">[</span><span class="mi">6</span><span class="p">])</span> <span class="k">else</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">refrs</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="n">r</span><span class="p">[</span><span class="mi">8</span><span class="p">])</span><span class="o">.</span><span class="n">groups</span><span class="p">(</span><span class="mi">1</span><span class="p">)[</span><span class="mi">1</span><span class="p">]</span> <span class="k">if</span> <span class="n">refrs</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="n">r</span><span class="p">[</span><span class="mi">8</span><span class="p">])</span> <span class="k">else</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">taxid</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="n">r</span><span class="p">[</span><span class="mi">9</span><span class="p">])</span><span class="o">.</span><span class="n">groups</span><span class="p">(</span><span class="mi">1</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span> <span class="k">if</span> <span class="n">taxid</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="n">r</span><span class="p">[</span><span class="mi">9</span><span class="p">])</span> <span class="k">else</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">taxid</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="n">r</span><span class="p">[</span><span class="mi">10</span><span class="p">])</span><span class="o">.</span><span class="n">groups</span><span class="p">(</span><span class="mi">1</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span> <span class="k">if</span> <span class="n">taxid</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="n">r</span><span class="p">[</span><span class="mi">10</span><span class="p">])</span> <span class="k">else</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">miont</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="n">r</span><span class="p">[</span><span class="mi">11</span><span class="p">])</span><span class="o">.</span><span class="n">groups</span><span class="p">(</span><span class="mi">1</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span> <span class="k">if</span> <span class="n">miont</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="n">r</span><span class="p">[</span><span class="mi">11</span><span class="p">])</span> <span class="k">else</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">miont</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="n">r</span><span class="p">[</span><span class="mi">17</span><span class="p">])</span><span class="o">.</span><span class="n">groups</span><span class="p">(</span><span class="mi">1</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span> <span class="k">if</span> <span class="n">miont</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="n">r</span><span class="p">[</span><span class="mi">16</span><span class="p">])</span> <span class="k">else</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="s1">&#39;;&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span>
+                <span class="n">binds</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="n">x</span><span class="p">)</span><span class="o">.</span><span class="n">groups</span><span class="p">(</span><span class="mi">1</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span> <span class="k">if</span> <span class="n">binds</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="n">x</span><span class="p">)</span> <span class="k">else</span> <span class="s1">&#39;&#39;</span>
+                <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">r</span><span class="p">[</span><span class="mi">32</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;,&#39;</span><span class="p">)</span>
+            <span class="p">),</span>
+            <span class="s1">&#39;;&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span>
+                <span class="n">binds</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="n">x</span><span class="p">)</span><span class="o">.</span><span class="n">groups</span><span class="p">(</span><span class="mi">1</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span> <span class="k">if</span> <span class="n">binds</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="n">x</span><span class="p">)</span> <span class="k">else</span> <span class="s1">&#39;&#39;</span>
+                <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">r</span><span class="p">[</span><span class="mi">33</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;,&#39;</span><span class="p">)</span>
+            <span class="p">),</span>
+            <span class="s1">&#39;;&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span>
+                <span class="n">domai</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="n">x</span><span class="p">)</span><span class="o">.</span><span class="n">groups</span><span class="p">(</span><span class="mi">1</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span> <span class="k">if</span> <span class="n">domai</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="n">x</span><span class="p">)</span> <span class="k">else</span> <span class="s1">&#39;&#39;</span>
+                <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">r</span><span class="p">[</span><span class="mi">32</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;,&#39;</span><span class="p">)</span>
+            <span class="p">),</span>
+            <span class="s1">&#39;;&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span>
+                <span class="n">domai</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="n">x</span><span class="p">)</span><span class="o">.</span><span class="n">groups</span><span class="p">(</span><span class="mi">1</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span> <span class="k">if</span> <span class="n">domai</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="n">x</span><span class="p">)</span> <span class="k">else</span> <span class="s1">&#39;&#39;</span>
+                <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">r</span><span class="p">[</span><span class="mi">33</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;,&#39;</span><span class="p">)</span>
+            <span class="p">),</span>
+            <span class="s1">&#39;;&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span>
+                <span class="n">ptmrs</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="n">x</span><span class="p">)</span><span class="o">.</span><span class="n">groups</span><span class="p">(</span><span class="mi">1</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span> <span class="k">if</span> <span class="n">ptmrs</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="n">x</span><span class="p">)</span> <span class="k">else</span> <span class="s1">&#39;&#39;</span>
+                <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">r</span><span class="p">[</span><span class="mi">34</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;|&#39;</span><span class="p">)</span>
+            <span class="p">),</span>
+            <span class="s1">&#39;;&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span>
+                <span class="n">ptmrs</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="n">x</span><span class="p">)</span><span class="o">.</span><span class="n">groups</span><span class="p">(</span><span class="mi">1</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span> <span class="k">if</span> <span class="n">ptmrs</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="n">x</span><span class="p">)</span> <span class="k">else</span> <span class="s1">&#39;&#39;</span>
+                <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">r</span><span class="p">[</span><span class="mi">35</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;|&#39;</span><span class="p">)</span>
+            <span class="p">),</span>
+            <span class="s1">&#39;;&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span>
+                <span class="n">ptmmi</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="n">x</span><span class="p">)</span><span class="o">.</span><span class="n">groups</span><span class="p">(</span><span class="mi">1</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span> <span class="k">if</span> <span class="n">ptmmi</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="n">x</span><span class="p">)</span> <span class="k">else</span> <span class="s1">&#39;&#39;</span>
+                <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">r</span><span class="p">[</span><span class="mi">34</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;|&#39;</span><span class="p">)</span>
+            <span class="p">),</span>
+            <span class="s1">&#39;;&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span>
+                <span class="n">ptmmi</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="n">x</span><span class="p">)</span><span class="o">.</span><span class="n">groups</span><span class="p">(</span><span class="mi">1</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span> <span class="k">if</span> <span class="n">ptmmi</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="n">x</span><span class="p">)</span> <span class="k">else</span> <span class="s1">&#39;&#39;</span>
+                <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">r</span><span class="p">[</span><span class="mi">35</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;|&#39;</span><span class="p">)</span>
+            <span class="p">),</span>
+            <span class="s1">&#39;;&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span>
+                <span class="n">ptmty</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="n">x</span><span class="p">)</span><span class="o">.</span><span class="n">groups</span><span class="p">(</span><span class="mi">1</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span> <span class="k">if</span> <span class="n">ptmty</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="n">x</span><span class="p">)</span> <span class="k">else</span> <span class="s1">&#39;&#39;</span>
+                <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">r</span><span class="p">[</span><span class="mi">34</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;|&#39;</span><span class="p">)</span>
+            <span class="p">),</span>
+            <span class="s1">&#39;;&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span>
+                <span class="n">ptmty</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="n">x</span><span class="p">)</span><span class="o">.</span><span class="n">groups</span><span class="p">(</span><span class="mi">1</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span> <span class="k">if</span> <span class="n">ptmty</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="n">x</span><span class="p">)</span> <span class="k">else</span> <span class="s1">&#39;&#39;</span>
+                <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">r</span><span class="p">[</span><span class="mi">35</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;|&#39;</span><span class="p">)</span>
+            <span class="p">),</span>
+            <span class="s1">&#39;;&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span>
+                <span class="n">ptmrn</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="n">x</span><span class="p">)</span><span class="o">.</span><span class="n">groups</span><span class="p">(</span><span class="mi">1</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span> <span class="k">if</span> <span class="n">ptmrn</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="n">x</span><span class="p">)</span> <span class="k">else</span> <span class="s1">&#39;&#39;</span>
+                <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">r</span><span class="p">[</span><span class="mi">34</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;|&#39;</span><span class="p">)</span>
+            <span class="p">),</span>
+            <span class="s1">&#39;;&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span>
+                <span class="n">ptmrn</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="n">x</span><span class="p">)</span><span class="o">.</span><span class="n">groups</span><span class="p">(</span><span class="mi">1</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span> <span class="k">if</span> <span class="n">ptmrn</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="n">x</span><span class="p">)</span> <span class="k">else</span> <span class="s1">&#39;&#39;</span>
+                <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">r</span><span class="p">[</span><span class="mi">35</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;|&#39;</span><span class="p">)</span>
+            <span class="p">),</span>
+            <span class="s1">&#39;;&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span>
+                <span class="n">ptmrs</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="n">x</span><span class="p">)</span><span class="o">.</span><span class="n">groups</span><span class="p">(</span><span class="mi">1</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span> <span class="k">if</span> <span class="n">ptmrs</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="n">x</span><span class="p">)</span> <span class="k">else</span> <span class="s1">&#39;&#39;</span>
+                <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">r</span><span class="p">[</span><span class="mi">36</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;|&#39;</span><span class="p">)</span>
+            <span class="p">),</span> <span class="s1">&#39;;&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span>
+                <span class="n">ptmrs</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="n">x</span><span class="p">)</span><span class="o">.</span><span class="n">groups</span><span class="p">(</span><span class="mi">1</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span> <span class="k">if</span> <span class="n">ptmrs</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="n">x</span><span class="p">)</span> <span class="k">else</span> <span class="s1">&#39;&#39;</span>
+                <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">r</span><span class="p">[</span><span class="mi">37</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;|&#39;</span><span class="p">)</span>
+            <span class="p">),</span>
+            <span class="s1">&#39;;&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span>
+                <span class="n">ptmty</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="n">x</span><span class="p">)</span><span class="o">.</span><span class="n">groups</span><span class="p">(</span><span class="mi">1</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span> <span class="k">if</span> <span class="n">ptmty</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="n">x</span><span class="p">)</span> <span class="k">else</span> <span class="s1">&#39;&#39;</span>
+                <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">r</span><span class="p">[</span><span class="mi">36</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;|&#39;</span><span class="p">)</span>
+            <span class="p">),</span>
+            <span class="s1">&#39;;&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span>
+                <span class="n">ptmty</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="n">x</span><span class="p">)</span><span class="o">.</span><span class="n">groups</span><span class="p">(</span><span class="mi">1</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span> <span class="k">if</span> <span class="n">ptmty</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="n">x</span><span class="p">)</span> <span class="k">else</span> <span class="s1">&#39;&#39;</span>
+                <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">r</span><span class="p">[</span><span class="mi">37</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;|&#39;</span><span class="p">)</span>
+            <span class="p">),</span>
+            <span class="n">dipro</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="n">r</span><span class="p">[</span><span class="mi">32</span><span class="p">])</span><span class="o">.</span><span class="n">groups</span><span class="p">(</span><span class="mi">1</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span> <span class="k">if</span> <span class="n">dipro</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="n">r</span><span class="p">[</span><span class="mi">32</span><span class="p">])</span> <span class="k">else</span> <span class="s1">&#39;&#39;</span><span class="p">,</span>
+            <span class="n">dipro</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="n">r</span><span class="p">[</span><span class="mi">33</span><span class="p">])</span><span class="o">.</span><span class="n">groups</span><span class="p">(</span><span class="mi">1</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span> <span class="k">if</span> <span class="n">dipro</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="n">r</span><span class="p">[</span><span class="mi">33</span><span class="p">])</span> <span class="k">else</span> <span class="s1">&#39;&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;0&#39;</span> <span class="k">if</span> <span class="n">r</span><span class="p">[</span><span class="mi">38</span><span class="p">]</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span> <span class="o">==</span> <span class="s1">&#39;-&#39;</span> <span class="k">else</span> <span class="s1">&#39;1&#39;</span><span class="p">,</span>
+        <span class="p">]</span>
+
+        <span class="k">if</span> <span class="ow">not</span> <span class="n">none_values</span><span class="p">:</span>
+
+            <span class="n">this_row</span> <span class="o">=</span> <span class="p">[</span><span class="s1">&#39;&#39;</span> <span class="k">if</span> <span class="n">x</span> <span class="ow">is</span> <span class="kc">None</span> <span class="k">else</span> <span class="n">x</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">this_row</span><span class="p">]</span>
+            <span class="n">this_row</span> <span class="o">=</span> <span class="n">DominoRecord</span><span class="p">(</span><span class="o">*</span><span class="n">this_row</span><span class="p">)</span>
+
+        <span class="n">result</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">this_row</span><span class="p">)</span>
+
+    <span class="k">if</span> <span class="n">outfile</span><span class="p">:</span>
+
+        <span class="n">_log</span><span class="p">(</span><span class="s1">&#39;Saving data into `</span><span class="si">%s</span><span class="s1">`.&#39;</span> <span class="o">%</span> <span class="n">outfile</span><span class="p">)</span>
+
+        <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">outfile</span><span class="p">,</span> <span class="s1">&#39;w&#39;</span><span class="p">)</span> <span class="k">as</span> <span class="n">outf</span><span class="p">:</span>
+
+            <span class="n">outf</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\t</span><span class="s1">&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">header</span><span class="p">)</span> <span class="o">+</span> <span class="s1">&#39;</span><span class="se">\n</span><span class="s1">&#39;</span><span class="p">)</span>
+
+            <span class="k">for</span> <span class="n">r</span> <span class="ow">in</span> <span class="n">result</span><span class="p">:</span>
+
+                <span class="n">outf</span><span class="o">.</span><span class="n">write</span><span class="p">(</span>
+                    <span class="s1">&#39;</span><span class="se">\t</span><span class="s1">&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="s1">&#39;&#39;</span> <span class="k">if</span> <span class="n">x</span> <span class="ow">is</span> <span class="kc">None</span> <span class="k">else</span> <span class="n">x</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">r</span><span class="p">)</span> <span class="o">+</span> <span class="s1">&#39;</span><span class="se">\n</span><span class="s1">&#39;</span>
+                <span class="p">)</span>
+
+    <span class="k">return</span> <span class="n">result</span></div>
+
+
+
+<div class="viewcode-block" id="domino_interactions">
+<a class="viewcode-back" href="../../../api/pypath.inputs.domino.domino_interactions.html#pypath.inputs.domino.domino_interactions">[docs]</a>
+<span class="k">def</span> <span class="nf">domino_interactions</span><span class="p">():</span>
+
+    <span class="n">domino</span> <span class="o">=</span> <span class="n">get_domino</span><span class="p">()</span>
+
+    <span class="n">interactions</span> <span class="o">=</span> <span class="p">[</span>
+        <span class="n">l</span> <span class="k">for</span> <span class="n">l</span> <span class="ow">in</span> <span class="n">domino</span>
+        <span class="k">if</span> <span class="p">(</span>
+            <span class="n">l</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="ow">and</span>
+            <span class="n">l</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="ow">and</span>
+            <span class="s1">&#39;&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">l</span><span class="p">[</span><span class="mi">5</span><span class="p">])</span> <span class="ow">and</span>
+            <span class="s1">&#39;&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">([</span>
+                <span class="n">l</span><span class="p">[</span><span class="n">i</span><span class="p">]</span>
+                <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">10</span><span class="p">,</span> <span class="mi">12</span><span class="p">)</span> <span class="o">+</span> <span class="nb">range</span><span class="p">(</span><span class="mi">14</span><span class="p">,</span> <span class="mi">22</span><span class="p">)</span> <span class="o">+</span> <span class="nb">range</span><span class="p">(</span><span class="mi">24</span><span class="p">,</span> <span class="mi">26</span><span class="p">)</span>
+            <span class="p">])</span> <span class="ow">and</span>
+            <span class="n">l</span><span class="p">[</span><span class="mi">28</span><span class="p">]</span> <span class="o">!=</span> <span class="s1">&#39;1&#39;</span>
+        <span class="p">)</span>
+    <span class="p">]</span>
+
+    <span class="k">return</span> <span class="n">interactions</span></div>
+
+
+
+<div class="viewcode-block" id="domino_ddi">
+<a class="viewcode-back" href="../../../api/pypath.inputs.domino.domino_ddi.html#pypath.inputs.domino.domino_ddi">[docs]</a>
+<span class="k">def</span> <span class="nf">domino_ddi</span><span class="p">():</span>
+
+    <span class="n">domi</span> <span class="o">=</span> <span class="n">domino_enzsub</span><span class="p">()</span>
+
+    <span class="k">return</span> <span class="n">domi</span><span class="p">[</span><span class="s1">&#39;ddi&#39;</span><span class="p">]</span></div>
+
+
+
+<div class="viewcode-block" id="domino_enzsub">
+<a class="viewcode-back" href="../../../api/pypath.inputs.domino.domino_enzsub.html#pypath.inputs.domino.domino_enzsub">[docs]</a>
+<span class="k">def</span> <span class="nf">domino_enzsub</span><span class="p">():</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Returns</span>
+<span class="sd">        A dict of two elements: `ddi` contains domain-domain, while `dmi`</span>
+<span class="sd">        domain-motif interactions. The latter includes protein-PTM</span>
+<span class="sd">        interactions.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="n">domino_resource</span> <span class="o">=</span> <span class="n">resource_internals</span><span class="o">.</span><span class="n">EnzymeSubstrateResource</span><span class="p">(</span>
+        <span class="n">name</span> <span class="o">=</span> <span class="s1">&#39;DOMINO&#39;</span><span class="p">,</span>
+        <span class="n">input_method</span> <span class="o">=</span> <span class="s1">&#39;domino.domino_enzsub&#39;</span><span class="p">,</span>
+    <span class="p">)</span>
+
+    <span class="n">domino</span> <span class="o">=</span> <span class="n">get_domino</span><span class="p">()</span>
+
+    <span class="k">try</span><span class="p">:</span>
+
+        <span class="n">miont</span> <span class="o">=</span> <span class="n">ontology</span><span class="o">.</span><span class="n">ontology</span><span class="p">(</span><span class="s1">&#39;MI&#39;</span><span class="p">)</span>
+
+    <span class="k">except</span><span class="p">:</span>
+
+        <span class="n">miont</span> <span class="o">=</span> <span class="p">{}</span>
+
+    <span class="n">dmi</span> <span class="o">=</span> <span class="p">[]</span>
+    <span class="n">ddi</span> <span class="o">=</span> <span class="p">[]</span>
+    <span class="n">prg</span> <span class="o">=</span> <span class="n">progress</span><span class="o">.</span><span class="n">Progress</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">domino</span><span class="p">),</span> <span class="s1">&#39;Processing DOMINO&#39;</span><span class="p">,</span> <span class="mi">11</span><span class="p">)</span>
+
+    <span class="n">ptm_types</span> <span class="o">=</span> <span class="p">{</span>
+        <span class="s2">&quot;o4&#39;-phospho-tyrosine&quot;</span><span class="p">:</span> <span class="s1">&#39;phosphorylation&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;phosphorylated residue&#39;</span><span class="p">:</span> <span class="s1">&#39;phosphorylation&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;o-phospho-threonine&#39;</span><span class="p">:</span> <span class="s1">&#39;phosphorylation&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;o-phospho-serine&#39;</span><span class="p">:</span> <span class="s1">&#39;phosphorylation&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;n6-methyl-lysine&#39;</span><span class="p">:</span> <span class="s1">&#39;methylation&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;n6,n6,n6-trimethyl-lysine&#39;</span><span class="p">:</span> <span class="s1">&#39;trimethylation&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;n6,n6-dimethyl-lysine&#39;</span><span class="p">:</span> <span class="s1">&#39;dimethylation&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;acetylated residue&#39;</span><span class="p">:</span> <span class="s1">&#39;acetylation&#39;</span><span class="p">,</span>
+    <span class="p">}</span>
+
+    <span class="k">for</span> <span class="n">l</span> <span class="ow">in</span> <span class="n">domino</span><span class="p">:</span>
+
+        <span class="n">prg</span><span class="o">.</span><span class="n">step</span><span class="p">()</span>
+
+        <span class="k">if</span> <span class="p">(</span>
+            <span class="p">(</span>
+                <span class="n">l</span><span class="p">[</span><span class="mi">14</span><span class="p">]</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span> <span class="o">!=</span> <span class="s1">&#39;&#39;</span> <span class="ow">or</span>
+                <span class="n">l</span><span class="p">[</span><span class="mi">15</span><span class="p">]</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span> <span class="o">!=</span> <span class="s1">&#39;&#39;</span> <span class="ow">or</span>
+                <span class="p">(</span>
+                    <span class="n">l</span><span class="p">[</span><span class="mi">10</span><span class="p">]</span> <span class="o">!=</span> <span class="s1">&#39;&#39;</span> <span class="ow">and</span>
+                    <span class="n">l</span><span class="p">[</span><span class="mi">11</span><span class="p">]</span> <span class="o">!=</span> <span class="s1">&#39;&#39;</span>
+                <span class="p">)</span>
+            <span class="p">)</span> <span class="ow">and</span>
+            <span class="nb">len</span><span class="p">(</span><span class="n">l</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span> <span class="o">&gt;</span> <span class="mi">0</span> <span class="ow">and</span>
+            <span class="nb">len</span><span class="p">(</span><span class="n">l</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span> <span class="o">&gt;</span> <span class="mi">0</span>
+        <span class="p">):</span>
+
+            <span class="n">uniprot1</span> <span class="o">=</span> <span class="n">l</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span>
+            <span class="n">uniprot2</span> <span class="o">=</span> <span class="n">l</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span>
+
+            <span class="c1"># ptms</span>
+            <span class="k">if</span> <span class="p">(</span>
+                <span class="s1">&#39;-&#39;</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">l</span><span class="p">[</span><span class="mi">14</span><span class="p">]</span> <span class="ow">and</span>
+                <span class="s1">&#39;-&#39;</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">l</span><span class="p">[</span><span class="mi">15</span><span class="p">]</span>
+            <span class="p">):</span>
+
+                <span class="n">ptmre12</span> <span class="o">=</span> <span class="p">[</span><span class="nb">int</span><span class="p">(</span><span class="n">x</span><span class="p">)</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">l</span><span class="p">[</span><span class="mi">14</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;;&#39;</span><span class="p">)]</span> <span class="k">if</span> <span class="n">l</span><span class="p">[</span><span class="mi">14</span><span class="p">]</span> <span class="k">else</span> <span class="p">[]</span>
+                <span class="n">ptmre21</span> <span class="o">=</span> <span class="p">[</span><span class="nb">int</span><span class="p">(</span><span class="n">x</span><span class="p">)</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">l</span><span class="p">[</span><span class="mi">15</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;;&#39;</span><span class="p">)]</span> <span class="k">if</span> <span class="n">l</span><span class="p">[</span><span class="mi">15</span><span class="p">]</span> <span class="k">else</span> <span class="p">[]</span>
+                <span class="n">ptmty12</span> <span class="o">=</span> <span class="n">l</span><span class="p">[</span><span class="mi">16</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;;&#39;</span><span class="p">)</span> <span class="k">if</span> <span class="n">l</span><span class="p">[</span><span class="mi">16</span><span class="p">]</span> <span class="k">else</span> <span class="p">[</span><span class="kc">None</span><span class="p">]</span> <span class="o">*</span> <span class="nb">len</span><span class="p">(</span><span class="n">ptmre12</span><span class="p">)</span>
+                <span class="n">ptmty12</span> <span class="o">=</span> <span class="p">[</span>
+                    <span class="n">ptm_types</span><span class="p">[</span><span class="n">miont</span><span class="p">[</span><span class="n">x</span><span class="p">]]</span> <span class="k">if</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">miont</span> <span class="k">else</span> <span class="kc">None</span>
+                    <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">ptmty12</span>
+                <span class="p">]</span>
+                <span class="n">ptmrn12</span> <span class="o">=</span> <span class="n">l</span><span class="p">[</span><span class="mi">20</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;;&#39;</span><span class="p">)</span> <span class="k">if</span> <span class="n">l</span><span class="p">[</span><span class="mi">20</span><span class="p">]</span> <span class="k">else</span> <span class="p">[</span><span class="kc">None</span><span class="p">]</span> <span class="o">*</span> <span class="nb">len</span><span class="p">(</span><span class="n">ptmre12</span><span class="p">)</span>
+
+                <span class="n">ptmrn12</span> <span class="o">=</span> <span class="p">[</span>
+                    <span class="kc">None</span>
+                        <span class="k">if</span> <span class="p">(</span>
+                            <span class="n">x</span> <span class="ow">is</span> <span class="kc">None</span> <span class="ow">or</span>
+                            <span class="n">x</span> <span class="o">==</span> <span class="s1">&#39;&#39;</span> <span class="ow">or</span>
+                            <span class="nb">len</span><span class="p">(</span><span class="n">x</span><span class="p">)</span> <span class="o">&lt;</span> <span class="nb">min</span><span class="p">(</span><span class="n">ptmre12</span><span class="p">[</span><span class="n">i</span><span class="p">]</span> <span class="o">-</span> <span class="mi">1</span><span class="p">,</span> <span class="mi">11</span><span class="p">)</span>
+                        <span class="p">)</span> <span class="k">else</span>
+                    <span class="n">x</span><span class="p">[</span><span class="mi">10</span><span class="p">]</span>
+                        <span class="k">if</span> <span class="n">ptmre12</span><span class="p">[</span><span class="n">i</span><span class="p">]</span> <span class="o">&gt;</span> <span class="mi">10</span> <span class="k">else</span>
+                    <span class="n">x</span><span class="p">[</span><span class="n">ptmre12</span><span class="p">[</span><span class="n">i</span><span class="p">]</span> <span class="o">-</span> <span class="mi">1</span><span class="p">]</span>
+                    <span class="k">for</span> <span class="n">i</span><span class="p">,</span> <span class="n">x</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">ptmrn12</span><span class="p">)</span>
+                <span class="p">]</span>
+                <span class="n">ptmty21</span> <span class="o">=</span> <span class="n">l</span><span class="p">[</span><span class="mi">17</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;;&#39;</span><span class="p">)</span> <span class="k">if</span> <span class="n">l</span><span class="p">[</span><span class="mi">17</span><span class="p">]</span> <span class="k">else</span> <span class="p">[</span><span class="kc">None</span><span class="p">]</span> <span class="o">*</span> <span class="nb">len</span><span class="p">(</span><span class="n">ptmre12</span><span class="p">)</span>
+                <span class="n">ptmty21</span> <span class="o">=</span> <span class="p">[</span>
+                    <span class="n">ptm_types</span><span class="p">[</span><span class="n">miont</span><span class="p">[</span><span class="n">x</span><span class="p">]]</span> <span class="k">if</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">miont</span> <span class="k">else</span> <span class="kc">None</span>
+                    <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">ptmty21</span>
+                <span class="p">]</span>
+                <span class="n">ptmrn21</span> <span class="o">=</span> <span class="n">l</span><span class="p">[</span><span class="mi">21</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;;&#39;</span><span class="p">)</span> <span class="k">if</span> <span class="n">l</span><span class="p">[</span><span class="mi">21</span><span class="p">]</span> <span class="k">else</span> <span class="p">[</span><span class="kc">None</span><span class="p">]</span> <span class="o">*</span> <span class="nb">len</span><span class="p">(</span><span class="n">ptmre21</span><span class="p">)</span>
+                <span class="n">ptmrn21</span> <span class="o">=</span> <span class="p">[</span>
+                    <span class="kc">None</span>
+                        <span class="k">if</span> <span class="p">(</span>
+                            <span class="n">x</span> <span class="ow">is</span> <span class="kc">None</span> <span class="ow">or</span>
+                            <span class="n">x</span> <span class="o">==</span> <span class="s1">&#39;&#39;</span> <span class="ow">or</span>
+                            <span class="nb">len</span><span class="p">(</span><span class="n">x</span><span class="p">)</span> <span class="o">&lt;</span> <span class="nb">min</span><span class="p">(</span><span class="n">ptmre21</span><span class="p">[</span><span class="n">i</span><span class="p">]</span> <span class="o">-</span> <span class="mi">1</span><span class="p">,</span> <span class="mi">11</span><span class="p">)</span>
+                        <span class="p">)</span> <span class="k">else</span>
+                    <span class="n">x</span><span class="p">[</span><span class="mi">10</span><span class="p">]</span>
+                        <span class="k">if</span> <span class="n">ptmre21</span><span class="p">[</span><span class="n">i</span><span class="p">]</span> <span class="o">&gt;</span> <span class="mi">10</span> <span class="k">else</span>
+                    <span class="n">x</span><span class="p">[</span><span class="n">ptmre21</span><span class="p">[</span><span class="n">i</span><span class="p">]</span> <span class="o">-</span> <span class="mi">1</span><span class="p">]</span>
+                    <span class="k">for</span> <span class="n">i</span><span class="p">,</span> <span class="n">x</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">ptmrn21</span><span class="p">)</span>
+                <span class="p">]</span>
+
+                <span class="k">for</span> <span class="n">i</span><span class="p">,</span> <span class="n">resnum</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">ptmre12</span><span class="p">):</span>
+
+                    <span class="n">res</span> <span class="o">=</span> <span class="n">intera</span><span class="o">.</span><span class="n">Residue</span><span class="p">(</span><span class="n">resnum</span><span class="p">,</span> <span class="n">ptmrn12</span><span class="p">[</span><span class="n">i</span><span class="p">],</span> <span class="n">uniprot2</span><span class="p">)</span>
+                    <span class="n">ptm</span> <span class="o">=</span> <span class="n">intera</span><span class="o">.</span><span class="n">Ptm</span><span class="p">(</span>
+                        <span class="n">uniprot2</span><span class="p">,</span>
+                        <span class="n">typ</span> <span class="o">=</span> <span class="n">ptmty12</span><span class="p">[</span><span class="n">i</span><span class="p">]</span> <span class="ow">or</span> <span class="s1">&#39;unknown&#39;</span><span class="p">,</span>
+                        <span class="n">residue</span> <span class="o">=</span> <span class="n">res</span><span class="p">,</span>
+                        <span class="n">evidences</span> <span class="o">=</span> <span class="n">evidence</span><span class="o">.</span><span class="n">Evidence</span><span class="p">(</span>
+                            <span class="n">resource</span> <span class="o">=</span> <span class="n">domino_resource</span><span class="p">,</span>
+                        <span class="p">),</span>
+                    <span class="p">)</span>
+                    <span class="n">dom</span> <span class="o">=</span> <span class="n">intera</span><span class="o">.</span><span class="n">Domain</span><span class="p">(</span><span class="n">uniprot1</span><span class="p">)</span>
+                    <span class="n">dm</span> <span class="o">=</span> <span class="n">intera</span><span class="o">.</span><span class="n">DomainMotif</span><span class="p">(</span>
+                        <span class="n">domain</span> <span class="o">=</span> <span class="n">dom</span><span class="p">,</span>
+                        <span class="n">ptm</span> <span class="o">=</span> <span class="n">ptm</span><span class="p">,</span>
+                        <span class="n">evidences</span> <span class="o">=</span> <span class="n">evidence</span><span class="o">.</span><span class="n">Evidence</span><span class="p">(</span>
+                            <span class="n">resource</span> <span class="o">=</span> <span class="n">domino_resource</span><span class="p">,</span>
+                            <span class="n">references</span> <span class="o">=</span> <span class="n">l</span><span class="p">[</span><span class="mi">5</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;;&#39;</span><span class="p">),</span>
+                        <span class="p">),</span>
+                    <span class="p">)</span>
+                    <span class="n">dmi</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">dm</span><span class="p">)</span>
+
+            <span class="c1"># binding sites</span>
+            <span class="k">if</span> <span class="n">l</span><span class="p">[</span><span class="mi">10</span><span class="p">]</span> <span class="ow">and</span> <span class="n">l</span><span class="p">[</span><span class="mi">11</span><span class="p">]:</span>
+
+                <span class="k">try</span><span class="p">:</span>
+
+                    <span class="n">bssrt1</span> <span class="o">=</span> <span class="p">[</span>
+                        <span class="nb">int</span><span class="p">(</span><span class="n">x</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;-&#39;</span><span class="p">)[</span><span class="mi">0</span><span class="p">])</span>
+                        <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">l</span><span class="p">[</span><span class="mi">10</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;;&#39;</span><span class="p">)</span>
+                        <span class="k">if</span> <span class="n">x</span> <span class="o">!=</span> <span class="s1">&#39;&#39;</span> <span class="ow">and</span> <span class="n">x</span> <span class="o">!=</span> <span class="s1">&#39;0&#39;</span>
+                    <span class="p">]</span>
+                    <span class="n">bsend1</span> <span class="o">=</span> <span class="p">[</span>
+                        <span class="nb">int</span><span class="p">(</span><span class="n">x</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;-&#39;</span><span class="p">)[</span><span class="mi">1</span><span class="p">])</span>
+                        <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">l</span><span class="p">[</span><span class="mi">10</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;;&#39;</span><span class="p">)</span>
+                        <span class="k">if</span> <span class="n">x</span> <span class="o">!=</span> <span class="s1">&#39;&#39;</span> <span class="ow">and</span> <span class="n">x</span> <span class="o">!=</span> <span class="s1">&#39;0&#39;</span>
+                    <span class="p">]</span>
+                    <span class="n">bssrt2</span> <span class="o">=</span> <span class="p">[</span>
+                        <span class="nb">int</span><span class="p">(</span><span class="n">x</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;-&#39;</span><span class="p">)[</span><span class="mi">0</span><span class="p">])</span>
+                        <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">l</span><span class="p">[</span><span class="mi">11</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;;&#39;</span><span class="p">)</span>
+                        <span class="k">if</span> <span class="n">x</span> <span class="o">!=</span> <span class="s1">&#39;&#39;</span> <span class="ow">and</span> <span class="n">x</span> <span class="o">!=</span> <span class="s1">&#39;0&#39;</span>
+                    <span class="p">]</span>
+                    <span class="n">bsend2</span> <span class="o">=</span> <span class="p">[</span>
+                        <span class="nb">int</span><span class="p">(</span><span class="n">x</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;-&#39;</span><span class="p">)[</span><span class="mi">1</span><span class="p">])</span>
+                        <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">l</span><span class="p">[</span><span class="mi">11</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;;&#39;</span><span class="p">)</span>
+                        <span class="k">if</span> <span class="n">x</span> <span class="o">!=</span> <span class="s1">&#39;&#39;</span> <span class="ow">and</span> <span class="n">x</span> <span class="o">!=</span> <span class="s1">&#39;0&#39;</span>
+                    <span class="p">]</span>
+
+                <span class="k">except</span><span class="p">:</span>
+
+                    <span class="n">sys</span><span class="o">.</span><span class="n">stdout</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s1">&#39;Error processing line:</span><span class="se">\n</span><span class="s1">&#39;</span><span class="p">)</span>
+                    <span class="n">sys</span><span class="o">.</span><span class="n">stdout</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="n">l</span><span class="p">)</span>
+                    <span class="n">sys</span><span class="o">.</span><span class="n">stdout</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\n</span><span class="s1">&#39;</span><span class="p">)</span>
+                    <span class="n">sys</span><span class="o">.</span><span class="n">stdout</span><span class="o">.</span><span class="n">flush</span><span class="p">()</span>
+
+                    <span class="k">return</span> <span class="kc">None</span>
+
+                <span class="n">bs1</span> <span class="o">=</span> <span class="p">[]</span>
+                <span class="n">bs2</span> <span class="o">=</span> <span class="p">[]</span>
+
+                <span class="k">if</span> <span class="n">l</span><span class="p">[</span><span class="mi">26</span><span class="p">]:</span>
+
+                    <span class="k">for</span> <span class="n">i</span><span class="p">,</span> <span class="n">n</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">bssrt1</span><span class="p">):</span>
+
+                        <span class="n">bs1</span><span class="o">.</span><span class="n">append</span><span class="p">(</span>
+                            <span class="n">intera</span><span class="o">.</span><span class="n">Domain</span><span class="p">(</span>
+                                <span class="n">protein</span> <span class="o">=</span> <span class="n">uniprot1</span><span class="p">,</span>
+                                <span class="n">domain</span> <span class="o">=</span> <span class="n">l</span><span class="p">[</span><span class="mi">26</span><span class="p">],</span>
+                                <span class="n">start</span> <span class="o">=</span> <span class="n">bssrt1</span><span class="p">[</span><span class="n">i</span><span class="p">],</span>
+                                <span class="n">end</span> <span class="o">=</span> <span class="n">bsend1</span><span class="p">[</span><span class="n">i</span><span class="p">],</span>
+                                <span class="n">domain_id_type</span> <span class="o">=</span> <span class="s1">&#39;interpro&#39;</span><span class="p">,</span>
+                                <span class="n">isoform</span> <span class="o">=</span> <span class="n">l</span><span class="p">[</span><span class="mi">2</span><span class="p">],</span>
+                            <span class="p">)</span>
+                        <span class="p">)</span>
+
+                <span class="k">else</span><span class="p">:</span>
+
+                    <span class="k">for</span> <span class="n">i</span><span class="p">,</span> <span class="n">n</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">bssrt1</span><span class="p">):</span>
+
+                        <span class="n">mot</span> <span class="o">=</span> <span class="n">intera</span><span class="o">.</span><span class="n">Motif</span><span class="p">(</span>
+                            <span class="n">protein</span> <span class="o">=</span> <span class="n">uniprot1</span><span class="p">,</span>
+                            <span class="n">start</span> <span class="o">=</span> <span class="n">bssrt1</span><span class="p">[</span><span class="n">i</span><span class="p">],</span>
+                            <span class="n">end</span> <span class="o">=</span> <span class="n">bsend1</span><span class="p">[</span><span class="n">i</span><span class="p">],</span>
+                            <span class="n">isoform</span> <span class="o">=</span> <span class="n">l</span><span class="p">[</span><span class="mi">2</span><span class="p">],</span>
+                        <span class="p">)</span>
+                        <span class="n">bs1</span><span class="o">.</span><span class="n">append</span><span class="p">(</span>
+                            <span class="n">intera</span><span class="o">.</span><span class="n">Ptm</span><span class="p">(</span>
+                                <span class="n">protein</span> <span class="o">=</span> <span class="n">uniprot1</span><span class="p">,</span>
+                                <span class="n">motif</span> <span class="o">=</span> <span class="n">mot</span><span class="p">,</span>
+                                <span class="n">evidences</span> <span class="o">=</span> <span class="n">evidence</span><span class="o">.</span><span class="n">Evidence</span><span class="p">(</span>
+                                    <span class="n">resource</span> <span class="o">=</span> <span class="n">domino_resource</span><span class="p">,</span>
+                                <span class="p">),</span>
+                                <span class="n">isoform</span> <span class="o">=</span> <span class="n">l</span><span class="p">[</span><span class="mi">2</span><span class="p">],</span>
+                            <span class="p">)</span>
+                        <span class="p">)</span>
+
+                <span class="k">if</span> <span class="n">l</span><span class="p">[</span><span class="mi">27</span><span class="p">]:</span>
+
+                    <span class="k">for</span> <span class="n">i</span><span class="p">,</span> <span class="n">n</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">bssrt2</span><span class="p">):</span>
+
+                        <span class="n">bs2</span><span class="o">.</span><span class="n">append</span><span class="p">(</span>
+                            <span class="n">intera</span><span class="o">.</span><span class="n">Domain</span><span class="p">(</span>
+                                <span class="n">protein</span> <span class="o">=</span> <span class="n">uniprot2</span><span class="p">,</span>
+                                <span class="n">domain</span> <span class="o">=</span> <span class="n">l</span><span class="p">[</span><span class="mi">27</span><span class="p">],</span>
+                                <span class="n">start</span> <span class="o">=</span> <span class="n">bssrt2</span><span class="p">[</span><span class="n">i</span><span class="p">],</span>
+                                <span class="n">end</span> <span class="o">=</span> <span class="n">bsend2</span><span class="p">[</span><span class="n">i</span><span class="p">],</span>
+                                <span class="n">domain_id_type</span> <span class="o">=</span> <span class="s1">&#39;interpro&#39;</span><span class="p">,</span>
+                                <span class="n">isoform</span> <span class="o">=</span> <span class="n">l</span><span class="p">[</span><span class="mi">3</span><span class="p">],</span>
+                            <span class="p">)</span>
+                        <span class="p">)</span>
+
+                <span class="k">else</span><span class="p">:</span>
+
+                    <span class="k">for</span> <span class="n">i</span><span class="p">,</span> <span class="n">n</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">bssrt2</span><span class="p">):</span>
+
+                        <span class="n">mot</span> <span class="o">=</span> <span class="n">intera</span><span class="o">.</span><span class="n">Motif</span><span class="p">(</span>
+                            <span class="n">protein</span> <span class="o">=</span> <span class="n">uniprot2</span><span class="p">,</span>
+                            <span class="n">start</span> <span class="o">=</span> <span class="n">bssrt2</span><span class="p">[</span><span class="n">i</span><span class="p">],</span>
+                            <span class="n">end</span> <span class="o">=</span> <span class="n">bsend2</span><span class="p">[</span><span class="n">i</span><span class="p">],</span>
+                            <span class="n">isoform</span> <span class="o">=</span> <span class="n">l</span><span class="p">[</span><span class="mi">3</span><span class="p">],</span>
+                        <span class="p">)</span>
+                        <span class="n">bs2</span><span class="o">.</span><span class="n">append</span><span class="p">(</span>
+                            <span class="n">intera</span><span class="o">.</span><span class="n">Ptm</span><span class="p">(</span>
+                                <span class="n">protein</span> <span class="o">=</span> <span class="n">uniprot2</span><span class="p">,</span>
+                                <span class="n">motif</span> <span class="o">=</span> <span class="n">mot</span><span class="p">,</span>
+                                <span class="n">evidences</span> <span class="o">=</span> <span class="n">evidence</span><span class="o">.</span><span class="n">Evidence</span><span class="p">(</span>
+                                    <span class="n">resource</span> <span class="o">=</span> <span class="n">domino_resource</span><span class="p">,</span>
+                                <span class="p">),</span>
+                            <span class="p">)</span>
+                        <span class="p">)</span>
+
+                <span class="k">for</span> <span class="n">one</span><span class="p">,</span> <span class="n">two</span> <span class="ow">in</span> <span class="n">itertools</span><span class="o">.</span><span class="n">product</span><span class="p">(</span><span class="n">bs1</span><span class="p">,</span> <span class="n">bs2</span><span class="p">):</span>
+
+
+                    <span class="k">if</span> <span class="p">(</span>
+                        <span class="n">one</span><span class="o">.</span><span class="vm">__class__</span><span class="o">.</span><span class="vm">__name__</span> <span class="o">==</span> <span class="s1">&#39;Domain&#39;</span> <span class="ow">and</span>
+                        <span class="n">two</span><span class="o">.</span><span class="vm">__class__</span><span class="o">.</span><span class="vm">__name__</span> <span class="o">==</span> <span class="s1">&#39;Domain&#39;</span>
+                    <span class="p">):</span>
+
+                        <span class="n">dd</span> <span class="o">=</span> <span class="n">intera</span><span class="o">.</span><span class="n">DomainDomain</span><span class="p">(</span>
+                            <span class="n">one</span><span class="p">,</span>
+                            <span class="n">two</span><span class="p">,</span>
+                            <span class="n">sources</span> <span class="o">=</span> <span class="s1">&#39;DOMINO&#39;</span><span class="p">,</span>
+                        <span class="p">)</span>
+                        <span class="n">ddi</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">dd</span><span class="p">)</span>
+
+                    <span class="k">if</span> <span class="p">(</span>
+                        <span class="n">one</span><span class="o">.</span><span class="vm">__class__</span><span class="o">.</span><span class="vm">__name__</span> <span class="o">==</span> <span class="s1">&#39;Domain&#39;</span> <span class="ow">and</span>
+                        <span class="n">two</span><span class="o">.</span><span class="vm">__class__</span><span class="o">.</span><span class="vm">__name__</span> <span class="o">==</span> <span class="s1">&#39;Ptm&#39;</span>
+                    <span class="p">):</span>
+
+                        <span class="n">dm</span> <span class="o">=</span> <span class="n">intera</span><span class="o">.</span><span class="n">DomainMotif</span><span class="p">(</span>
+                            <span class="n">domain</span> <span class="o">=</span> <span class="n">one</span><span class="p">,</span>
+                            <span class="n">ptm</span> <span class="o">=</span> <span class="n">two</span><span class="p">,</span>
+                            <span class="n">evidences</span> <span class="o">=</span> <span class="n">evidence</span><span class="o">.</span><span class="n">Evidence</span><span class="p">(</span>
+                                <span class="n">resource</span> <span class="o">=</span> <span class="n">domino_resource</span><span class="p">,</span>
+                                <span class="n">references</span> <span class="o">=</span> <span class="n">l</span><span class="p">[</span><span class="mi">6</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;;&#39;</span><span class="p">)</span>
+                            <span class="p">),</span>
+                        <span class="p">)</span>
+                        <span class="n">dmi</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">dm</span><span class="p">)</span>
+
+                    <span class="k">if</span> <span class="p">(</span>
+                        <span class="n">two</span><span class="o">.</span><span class="vm">__class__</span><span class="o">.</span><span class="vm">__name__</span> <span class="o">==</span> <span class="s1">&#39;Domain&#39;</span> <span class="ow">and</span>
+                        <span class="n">one</span><span class="o">.</span><span class="vm">__class__</span><span class="o">.</span><span class="vm">__name__</span> <span class="o">==</span> <span class="s1">&#39;Ptm&#39;</span>
+                    <span class="p">):</span>
+
+                        <span class="n">dm</span> <span class="o">=</span> <span class="n">intera</span><span class="o">.</span><span class="n">DomainMotif</span><span class="p">(</span>
+                            <span class="n">domain</span> <span class="o">=</span> <span class="n">two</span><span class="p">,</span>
+                            <span class="n">ptm</span> <span class="o">=</span> <span class="n">one</span><span class="p">,</span>
+                            <span class="n">evidences</span> <span class="o">=</span> <span class="n">evidence</span><span class="o">.</span><span class="n">Evidence</span><span class="p">(</span>
+                                <span class="n">resource</span> <span class="o">=</span> <span class="n">domino_resource</span><span class="p">,</span>
+                                <span class="n">references</span> <span class="o">=</span> <span class="n">l</span><span class="p">[</span><span class="mi">6</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;;&#39;</span><span class="p">)</span>
+                            <span class="p">),</span>
+                        <span class="p">)</span>
+                        <span class="n">dmi</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">dm</span><span class="p">)</span>
+
+    <span class="n">prg</span><span class="o">.</span><span class="n">terminate</span><span class="p">()</span>
+
+    <span class="k">return</span> <span class="p">{</span><span class="s1">&#39;ddi&#39;</span><span class="p">:</span> <span class="n">ddi</span><span class="p">,</span> <span class="s1">&#39;dmi&#39;</span><span class="p">:</span> <span class="n">dmi</span><span class="p">}</span></div>
+
+</pre></div>
+
+                </article>
+              
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+  <h1>Source code for pypath.inputs.embrace</h1><div class="highlight"><pre>
+<span></span><span class="ch">#!/usr/bin/env python</span>
+<span class="c1"># -*- coding: utf-8 -*-</span>
+
+<span class="c1">#</span>
+<span class="c1">#  This file is part of the `pypath` python module</span>
+<span class="c1">#</span>
+<span class="c1">#  Copyright 2014-2023</span>
+<span class="c1">#  EMBL, EMBL-EBI, Uniklinik RWTH Aachen, Heidelberg University</span>
+<span class="c1">#</span>
+<span class="c1">#  Authors: see the file `README.rst`</span>
+<span class="c1">#  Contact: Dénes Türei (turei.denes@gmail.com)</span>
+<span class="c1">#</span>
+<span class="c1">#  Distributed under the GPLv3 License.</span>
+<span class="c1">#  See accompanying file LICENSE.txt or copy at</span>
+<span class="c1">#      https://www.gnu.org/licenses/gpl-3.0.html</span>
+<span class="c1">#</span>
+<span class="c1">#  Website: https://pypath.omnipathdb.org/</span>
+<span class="c1">#</span>
+
+<span class="kn">import</span> <span class="nn">itertools</span>
+<span class="kn">import</span> <span class="nn">collections</span>
+
+<span class="kn">import</span> <span class="nn">pypath.inputs.common</span> <span class="k">as</span> <span class="nn">inputs_common</span>
+<span class="kn">import</span> <span class="nn">pypath.resources.urls</span> <span class="k">as</span> <span class="nn">urls</span>
+<span class="kn">import</span> <span class="nn">pypath.utils.mapping</span> <span class="k">as</span> <span class="nn">mapping</span>
+<span class="kn">import</span> <span class="nn">pypath.utils.orthology</span> <span class="k">as</span> <span class="nn">orthology</span>
+<span class="kn">import</span> <span class="nn">pypath.share.common</span> <span class="k">as</span> <span class="nn">common</span>
+<span class="kn">import</span> <span class="nn">pypath.inputs.cell</span> <span class="k">as</span> <span class="nn">cell_input</span>
+
+
+<div class="viewcode-block" id="embrace_raw">
+<a class="viewcode-back" href="../../../api/pypath.inputs.embrace.embrace_raw.html#pypath.inputs.embrace.embrace_raw">[docs]</a>
+<span class="k">def</span> <span class="nf">embrace_raw</span><span class="p">():</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Returns Supplementary Table S11 from 10.1016/j.isci.2019.10.026</span>
+<span class="sd">    (Sheikh et al. 2019) as a list of tuples.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="n">path</span> <span class="o">=</span> <span class="n">cell_input</span><span class="o">.</span><span class="n">cell_supplementary</span><span class="p">(</span>
+        <span class="n">supp_url</span> <span class="o">=</span> <span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;embrace&#39;</span><span class="p">][</span><span class="s1">&#39;url&#39;</span><span class="p">],</span>
+        <span class="n">article_url</span> <span class="o">=</span> <span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;embrace&#39;</span><span class="p">][</span><span class="s1">&#39;article&#39;</span><span class="p">],</span>
+    <span class="p">)</span>
+
+    <span class="n">content</span> <span class="o">=</span> <span class="n">inputs_common</span><span class="o">.</span><span class="n">read_xls</span><span class="p">(</span><span class="n">path</span><span class="p">)</span>
+
+    <span class="n">EmbraceRawRecord</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">namedtuple</span><span class="p">(</span>
+        <span class="s1">&#39;EmbraceRawRecord&#39;</span><span class="p">,</span>
+        <span class="n">content</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span>
+    <span class="p">)</span>
+
+    <span class="k">return</span> <span class="p">[</span>
+        <span class="n">EmbraceRawRecord</span><span class="p">(</span><span class="o">*</span><span class="p">(</span><span class="n">line</span><span class="p">[:</span><span class="mi">2</span><span class="p">]</span> <span class="o">+</span> <span class="p">[</span><span class="nb">int</span><span class="p">(</span><span class="nb">float</span><span class="p">(</span><span class="n">n</span><span class="p">))</span> <span class="k">for</span> <span class="n">n</span> <span class="ow">in</span> <span class="n">line</span><span class="p">[</span><span class="mi">2</span><span class="p">:]]))</span>
+        <span class="k">for</span> <span class="n">line</span> <span class="ow">in</span>
+        <span class="n">content</span><span class="p">[</span><span class="mi">1</span><span class="p">:]</span>
+    <span class="p">]</span></div>
+
+
+
+<span class="k">def</span> <span class="nf">_embrace_id_translation</span><span class="p">(</span><span class="n">mouse_genesymbol</span><span class="p">,</span> <span class="n">organism</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">):</span>
+
+    <span class="n">uniprots</span> <span class="o">=</span> <span class="n">mapping</span><span class="o">.</span><span class="n">map_name</span><span class="p">(</span>
+        <span class="n">mouse_genesymbol</span><span class="p">,</span>
+        <span class="s1">&#39;genesymbol&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;uniprot&#39;</span><span class="p">,</span>
+        <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="mi">10090</span><span class="p">,</span>
+    <span class="p">)</span>
+
+    <span class="k">if</span> <span class="n">organism</span> <span class="o">!=</span> <span class="mi">10090</span><span class="p">:</span>
+
+        <span class="n">uniprots</span> <span class="o">=</span> <span class="n">orthology</span><span class="o">.</span><span class="n">translate</span><span class="p">(</span>
+            <span class="n">uniprots</span><span class="p">,</span>
+            <span class="n">target</span> <span class="o">=</span> <span class="n">organism</span><span class="p">,</span>
+            <span class="n">source</span> <span class="o">=</span> <span class="mi">10090</span><span class="p">,</span>
+        <span class="p">)</span>
+
+    <span class="k">return</span> <span class="n">uniprots</span> <span class="ow">or</span> <span class="p">[</span><span class="kc">None</span><span class="p">]</span>
+
+
+<div class="viewcode-block" id="embrace_translated">
+<a class="viewcode-back" href="../../../api/pypath.inputs.embrace.embrace_translated.html#pypath.inputs.embrace.embrace_translated">[docs]</a>
+<span class="k">def</span> <span class="nf">embrace_translated</span><span class="p">(</span><span class="n">organism</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">):</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Returns Supplementary Table S11 from 10.1016/j.isci.2019.10.026</span>
+<span class="sd">    (Sheikh et al. 2019) translated to UniProt IDs of the requested organism.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="n">raw</span> <span class="o">=</span> <span class="n">embrace_raw</span><span class="p">()</span>
+    <span class="n">record</span> <span class="o">=</span> <span class="n">raw</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="vm">__class__</span>
+    <span class="n">result</span> <span class="o">=</span> <span class="p">[]</span>
+
+    <span class="k">for</span> <span class="n">row</span> <span class="ow">in</span> <span class="n">raw</span><span class="p">:</span>
+
+        <span class="n">ligands</span> <span class="o">=</span> <span class="n">_embrace_id_translation</span><span class="p">(</span>
+            <span class="n">row</span><span class="o">.</span><span class="n">ligand_symbol</span><span class="p">,</span>
+            <span class="n">organism</span> <span class="o">=</span> <span class="n">organism</span><span class="p">,</span>
+        <span class="p">)</span>
+        <span class="n">receptors</span> <span class="o">=</span> <span class="n">_embrace_id_translation</span><span class="p">(</span>
+            <span class="n">row</span><span class="o">.</span><span class="n">receptor_symbol</span><span class="p">,</span>
+            <span class="n">organism</span> <span class="o">=</span> <span class="n">organism</span><span class="p">,</span>
+        <span class="p">)</span>
+
+        <span class="k">for</span> <span class="n">ligand</span><span class="p">,</span> <span class="n">receptor</span> <span class="ow">in</span> <span class="n">itertools</span><span class="o">.</span><span class="n">product</span><span class="p">(</span><span class="n">ligands</span><span class="p">,</span> <span class="n">receptors</span><span class="p">):</span>
+
+            <span class="n">result</span><span class="o">.</span><span class="n">append</span><span class="p">(</span>
+                <span class="n">record</span><span class="p">(</span><span class="o">*</span><span class="p">((</span><span class="n">ligand</span><span class="p">,</span> <span class="n">receptor</span><span class="p">)</span> <span class="o">+</span> <span class="n">row</span><span class="p">[</span><span class="mi">2</span><span class="p">:]))</span>
+            <span class="p">)</span>
+
+    <span class="k">return</span> <span class="n">result</span></div>
+
+
+
+<div class="viewcode-block" id="embrace_interactions">
+<a class="viewcode-back" href="../../../api/pypath.inputs.embrace.embrace_interactions.html#pypath.inputs.embrace.embrace_interactions">[docs]</a>
+<span class="k">def</span> <span class="nf">embrace_interactions</span><span class="p">(</span><span class="n">organism</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">):</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Returns ligand-receptor interactions from Supplementary Table S11 of</span>
+<span class="sd">    10.1016/j.isci.2019.10.026 (Sheikh et al. 2019) translated to UniProt IDs</span>
+<span class="sd">    of the requested organism.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+
+    <span class="n">EmbraceInteraction</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">namedtuple</span><span class="p">(</span>
+        <span class="s1">&#39;EmbraceInteraction&#39;</span><span class="p">,</span>
+        <span class="p">[</span>
+            <span class="s1">&#39;ligand&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;receptor&#39;</span><span class="p">,</span>
+        <span class="p">]</span>
+    <span class="p">)</span>
+
+    <span class="k">return</span> <span class="p">[</span>
+        <span class="n">EmbraceInteraction</span><span class="p">(</span><span class="o">*</span><span class="n">rec</span><span class="p">[:</span><span class="mi">2</span><span class="p">])</span>
+        <span class="k">for</span> <span class="n">rec</span> <span class="ow">in</span> <span class="n">embrace_translated</span><span class="p">(</span><span class="n">organism</span> <span class="o">=</span> <span class="n">organism</span><span class="p">)</span>
+        <span class="k">if</span> <span class="n">rec</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="ow">and</span> <span class="n">rec</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span>
+    <span class="p">]</span></div>
+
+
+
+<div class="viewcode-block" id="embrace_annotations">
+<a class="viewcode-back" href="../../../api/pypath.inputs.embrace.embrace_annotations.html#pypath.inputs.embrace.embrace_annotations">[docs]</a>
+<span class="k">def</span> <span class="nf">embrace_annotations</span><span class="p">(</span><span class="n">organism</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">,</span> <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="kc">None</span><span class="p">):</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Returns protein annotations from Supplementary Table S11 of</span>
+<span class="sd">    10.1016/j.isci.2019.10.026 (Sheikh et al. 2019) translated to UniProt IDs</span>
+<span class="sd">    of the requested organism.</span>
+<span class="sd">    Returns dict with UniProt IDs as keys and sets of annotation tuples as</span>
+<span class="sd">    values.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="k">def</span> <span class="nf">_get_value</span><span class="p">(</span><span class="n">rec</span><span class="p">,</span> <span class="n">mainclass</span><span class="p">,</span> <span class="n">celltype</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="nb">bool</span><span class="p">(</span><span class="nb">getattr</span><span class="p">(</span><span class="n">rec</span><span class="p">,</span> <span class="s1">&#39;</span><span class="si">%s</span><span class="s1">_</span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="p">(</span><span class="n">celltype</span><span class="p">,</span> <span class="n">mainclass</span><span class="p">)))</span>
+
+
+    <span class="n">EmbraceAnnotation</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">namedtuple</span><span class="p">(</span>
+        <span class="s1">&#39;EmbraceAnnotation&#39;</span><span class="p">,</span>
+        <span class="p">[</span>
+            <span class="s1">&#39;mainclass&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;neuron&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;mural_cell&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;microglia&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;endothelial_cell&#39;</span><span class="p">,</span>
+        <span class="p">]</span>
+    <span class="p">)</span>
+
+
+    <span class="n">organism</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span> <span class="ow">or</span> <span class="n">organism</span>
+    <span class="n">result</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">defaultdict</span><span class="p">(</span><span class="nb">set</span><span class="p">)</span>
+
+    <span class="k">for</span> <span class="n">rec</span> <span class="ow">in</span> <span class="n">embrace_translated</span><span class="p">(</span><span class="n">organism</span> <span class="o">=</span> <span class="n">organism</span><span class="p">):</span>
+
+        <span class="k">for</span> <span class="n">mainclass</span> <span class="ow">in</span> <span class="p">(</span><span class="s1">&#39;ligand&#39;</span><span class="p">,</span> <span class="s1">&#39;receptor&#39;</span><span class="p">):</span>
+
+            <span class="n">identifier</span> <span class="o">=</span> <span class="nb">getattr</span><span class="p">(</span><span class="n">rec</span><span class="p">,</span> <span class="s1">&#39;</span><span class="si">%s</span><span class="s1">_symbol&#39;</span> <span class="o">%</span> <span class="n">mainclass</span><span class="p">)</span>
+
+            <span class="k">if</span> <span class="ow">not</span> <span class="n">identifier</span><span class="p">:</span>
+
+                <span class="k">continue</span>
+
+            <span class="n">result</span><span class="p">[</span><span class="n">identifier</span><span class="p">]</span><span class="o">.</span><span class="n">add</span><span class="p">(</span>
+                <span class="n">EmbraceAnnotation</span><span class="p">(</span>
+                    <span class="n">mainclass</span> <span class="o">=</span> <span class="n">mainclass</span><span class="p">,</span>
+                    <span class="n">neuron</span> <span class="o">=</span> <span class="n">_get_value</span><span class="p">(</span><span class="n">rec</span><span class="p">,</span> <span class="n">mainclass</span><span class="p">,</span> <span class="s1">&#39;N&#39;</span><span class="p">),</span>
+                    <span class="n">mural_cell</span> <span class="o">=</span> <span class="n">_get_value</span><span class="p">(</span><span class="n">rec</span><span class="p">,</span> <span class="n">mainclass</span><span class="p">,</span> <span class="s1">&#39;P&#39;</span><span class="p">),</span>
+                    <span class="n">microglia</span> <span class="o">=</span> <span class="n">_get_value</span><span class="p">(</span><span class="n">rec</span><span class="p">,</span> <span class="n">mainclass</span><span class="p">,</span> <span class="s1">&#39;M&#39;</span><span class="p">),</span>
+                    <span class="n">endothelial_cell</span> <span class="o">=</span> <span class="n">_get_value</span><span class="p">(</span><span class="n">rec</span><span class="p">,</span> <span class="n">mainclass</span><span class="p">,</span> <span class="s1">&#39;EC&#39;</span><span class="p">),</span>
+                <span class="p">)</span>
+            <span class="p">)</span>
+
+    <span class="k">return</span> <span class="nb">dict</span><span class="p">(</span><span class="n">result</span><span class="p">)</span></div>
+
+</pre></div>
+
+                </article>
+              
+              
+              
+              
+              
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diff --git a/_modules/pypath/inputs/guide2pharma.html b/_modules/pypath/inputs/guide2pharma.html
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+                  
+  <h1>Source code for pypath.inputs.guide2pharma</h1><div class="highlight"><pre>
+<span></span><span class="ch">#!/usr/bin/env python</span>
+<span class="c1"># -*- coding: utf-8 -*-</span>
+
+<span class="c1">#</span>
+<span class="c1">#  This file is part of the `pypath` python module</span>
+<span class="c1">#</span>
+<span class="c1">#  Copyright 2014-2023</span>
+<span class="c1">#  EMBL, EMBL-EBI, Uniklinik RWTH Aachen, Heidelberg University</span>
+<span class="c1">#</span>
+<span class="c1">#  Authors: see the file `README.rst`</span>
+<span class="c1">#  Contact: Dénes Türei (turei.denes@gmail.com)</span>
+<span class="c1">#</span>
+<span class="c1">#  Distributed under the GPLv3 License.</span>
+<span class="c1">#  See accompanying file LICENSE.txt or copy at</span>
+<span class="c1">#      https://www.gnu.org/licenses/gpl-3.0.html</span>
+<span class="c1">#</span>
+<span class="c1">#  Website: https://pypath.omnipathdb.org/</span>
+<span class="c1">#</span>
+
+<span class="kn">from</span> <span class="nn">__future__</span> <span class="kn">import</span> <span class="n">annotations</span>
+
+<span class="kn">import</span> <span class="nn">csv</span>
+<span class="kn">import</span> <span class="nn">collections</span>
+<span class="kn">import</span> <span class="nn">itertools</span>
+
+<span class="kn">import</span> <span class="nn">pypath.share.curl</span> <span class="k">as</span> <span class="nn">curl</span>
+<span class="kn">import</span> <span class="nn">pypath.share.common</span> <span class="k">as</span> <span class="nn">common</span>
+<span class="kn">import</span> <span class="nn">pypath_common._constants</span> <span class="k">as</span> <span class="nn">_const</span>
+<span class="kn">import</span> <span class="nn">pypath.resources.urls</span> <span class="k">as</span> <span class="nn">urls</span>
+<span class="kn">import</span> <span class="nn">pypath.utils.mapping</span> <span class="k">as</span> <span class="nn">mapping</span>
+<span class="kn">import</span> <span class="nn">pypath.utils.taxonomy</span> <span class="k">as</span> <span class="nn">taxonomy</span>
+<span class="kn">import</span> <span class="nn">pypath.internals.intera</span> <span class="k">as</span> <span class="nn">intera</span>
+
+
+<div class="viewcode-block" id="guide2pharma_download">
+<a class="viewcode-back" href="../../../api/pypath.inputs.guide2pharma.guide2pharma_download.html#pypath.inputs.guide2pharma.guide2pharma_download">[docs]</a>
+<span class="k">def</span> <span class="nf">guide2pharma_download</span><span class="p">(</span>
+        <span class="n">organism</span><span class="p">:</span> <span class="nb">str</span> <span class="o">|</span> <span class="nb">int</span> <span class="o">=</span> <span class="s1">&#39;human&#39;</span><span class="p">,</span>
+        <span class="n">endogenous</span><span class="p">:</span> <span class="nb">bool</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
+        <span class="n">process_interactions</span><span class="p">:</span> <span class="nb">bool</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
+        <span class="n">process_complexes</span><span class="p">:</span> <span class="nb">bool</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
+    <span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">tuple</span><span class="p">[</span><span class="nb">list</span><span class="p">,</span> <span class="nb">dict</span><span class="p">]:</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Downloads and processes Guide to Pharmacology data.</span>
+<span class="sd">    Returns list of dicts.</span>
+
+<span class="sd">    Args:</span>
+<span class="sd">        organism</span>
+<span class="sd">            Name of the organism, e.g. `human`.</span>
+<span class="sd">        endogenous</span>
+<span class="sd">            Whether to include only endogenous ligands interactions.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="n">get_taxid</span> <span class="o">=</span> <span class="k">lambda</span> <span class="n">x</span><span class="p">:</span> <span class="p">(</span>
+        <span class="n">_const</span><span class="o">.</span><span class="n">NOT_ORGANISM_SPECIFIC</span>
+            <span class="k">if</span> <span class="n">x</span> <span class="ow">in</span> <span class="p">{</span><span class="s1">&#39;&#39;</span><span class="p">,</span> <span class="s1">&#39;None&#39;</span><span class="p">}</span> <span class="k">else</span>
+        <span class="n">taxonomy</span><span class="o">.</span><span class="n">ensure_ncbi_tax_id</span><span class="p">(</span><span class="n">x</span><span class="p">)</span>
+    <span class="p">)</span>
+    <span class="n">organism_</span> <span class="o">=</span> <span class="kc">None</span>
+    <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="kc">None</span>
+
+    <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">organism</span><span class="p">,</span> <span class="nb">str</span><span class="p">):</span>
+
+        <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">get_taxid</span><span class="p">(</span><span class="n">organism</span><span class="p">)</span>
+
+        <span class="k">try</span><span class="p">:</span>
+
+            <span class="n">organism_</span> <span class="o">=</span> <span class="n">taxonomy</span><span class="o">.</span><span class="n">ensure_common_name</span><span class="p">(</span><span class="n">ncbi_tax_id</span><span class="p">)</span>
+            <span class="n">organism_</span> <span class="o">=</span> <span class="n">organism_</span><span class="o">.</span><span class="n">capitalize</span><span class="p">()</span> <span class="k">if</span> <span class="n">organism_</span> <span class="k">else</span> <span class="kc">None</span>
+
+        <span class="k">except</span> <span class="ne">KeyError</span><span class="p">:</span>
+
+            <span class="k">pass</span>  <span class="c1"># no organism specified</span>
+
+    <span class="n">positives</span> <span class="o">=</span> <span class="p">{</span>
+        <span class="s1">&#39;agonist&#39;</span><span class="p">,</span> <span class="s1">&#39;activator&#39;</span><span class="p">,</span> <span class="s1">&#39;potentiation&#39;</span><span class="p">,</span> <span class="s1">&#39;partial agonist&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;inverse antagonist&#39;</span><span class="p">,</span> <span class="s1">&#39;full agonist&#39;</span><span class="p">,</span> <span class="s1">&#39;activation&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;irreversible agonist&#39;</span><span class="p">,</span> <span class="s1">&#39;positive&#39;</span><span class="p">,</span>
+    <span class="p">}</span>
+    <span class="n">negatives</span> <span class="o">=</span> <span class="p">{</span>
+        <span class="s1">&#39;inhibitor&#39;</span><span class="p">,</span> <span class="s1">&#39;antagonist&#39;</span><span class="p">,</span> <span class="s1">&#39;inhibition&#39;</span><span class="p">,</span> <span class="s1">&#39;irreversible inhibition&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;inverse agonist&#39;</span><span class="p">,</span> <span class="s1">&#39;negative&#39;</span><span class="p">,</span> <span class="s1">&#39;weak inhibition&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;reversible inhibition&#39;</span><span class="p">,</span>
+    <span class="p">}</span>
+
+
+    <span class="n">GuideToPharmacologyInteraction</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">namedtuple</span><span class="p">(</span>
+        <span class="s1">&#39;GuideToPharmacologyInteraction&#39;</span><span class="p">,</span>
+        <span class="p">[</span>
+            <span class="s1">&#39;ligand&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;ligand_id_type&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;target&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;target_id_type&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;target_is_ligand&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;ligand_organism&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;target_organism&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;effect&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;ligand_location&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;target_type&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;ligand_endogenous&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;pubmed_ids&#39;</span><span class="p">,</span>
+        <span class="p">]</span>
+    <span class="p">)</span>
+
+    <span class="k">def</span> <span class="nf">is_positive</span><span class="p">(</span><span class="n">term</span><span class="p">):</span>
+        <span class="k">return</span> <span class="n">term</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span> <span class="ow">in</span> <span class="n">positives</span>
+
+    <span class="k">def</span> <span class="nf">is_negative</span><span class="p">(</span><span class="n">term</span><span class="p">):</span>
+        <span class="k">return</span> <span class="n">term</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span> <span class="ow">in</span> <span class="n">negatives</span>
+
+    <span class="n">interactions</span> <span class="o">=</span> <span class="p">[]</span>
+    <span class="n">complexes</span> <span class="o">=</span> <span class="p">{}</span>
+
+    <span class="n">url</span> <span class="o">=</span> <span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;gtp&#39;</span><span class="p">][</span><span class="s1">&#39;url&#39;</span><span class="p">]</span>
+
+    <span class="n">c</span> <span class="o">=</span> <span class="n">curl</span><span class="o">.</span><span class="n">Curl</span><span class="p">(</span><span class="n">url</span><span class="p">,</span> <span class="n">silent</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span> <span class="n">large</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span> <span class="n">encoding</span> <span class="o">=</span> <span class="s1">&#39;utf-8&#39;</span><span class="p">)</span>
+
+    <span class="n">line0</span> <span class="o">=</span> <span class="nb">next</span><span class="p">(</span><span class="n">c</span><span class="o">.</span><span class="n">result</span><span class="p">)</span>
+
+    <span class="k">if</span> <span class="n">line0</span><span class="p">[:</span><span class="mi">2</span><span class="p">]</span> <span class="o">!=</span> <span class="s1">&#39;&quot;#&#39;</span><span class="p">:</span>
+
+        <span class="n">c</span><span class="o">.</span><span class="n">fileobj</span><span class="o">.</span><span class="n">seek</span><span class="p">(</span><span class="mi">0</span><span class="p">)</span>
+
+    <span class="n">data</span> <span class="o">=</span> <span class="n">csv</span><span class="o">.</span><span class="n">DictReader</span><span class="p">(</span><span class="n">c</span><span class="o">.</span><span class="n">result</span><span class="p">)</span>
+
+    <span class="k">if</span> <span class="n">organism_</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
+
+        <span class="n">data</span> <span class="o">=</span> <span class="p">[</span>
+            <span class="n">d</span> <span class="k">for</span> <span class="n">d</span> <span class="ow">in</span> <span class="n">data</span>
+            <span class="k">if</span> <span class="p">(</span>
+                <span class="n">get_taxid</span><span class="p">(</span><span class="n">d</span><span class="p">[</span><span class="s1">&#39;Target Species&#39;</span><span class="p">])</span> <span class="o">==</span> <span class="n">ncbi_tax_id</span> <span class="ow">and</span>
+                <span class="n">ncbi_tax_id</span> <span class="ow">in</span> <span class="nb">set</span><span class="p">(</span>
+                    <span class="n">get_taxid</span><span class="p">(</span><span class="n">t</span><span class="p">)</span>
+                    <span class="k">for</span> <span class="n">t</span> <span class="ow">in</span> <span class="n">d</span><span class="p">[</span><span class="s1">&#39;Ligand Species&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;|&#39;</span><span class="p">)</span>
+                <span class="p">)</span>
+            <span class="p">)</span>
+        <span class="p">]</span>
+
+    <span class="k">if</span> <span class="n">endogenous</span><span class="p">:</span>
+
+        <span class="n">data</span> <span class="o">=</span> <span class="p">[</span><span class="n">d</span> <span class="k">for</span> <span class="n">d</span> <span class="ow">in</span> <span class="n">data</span> <span class="k">if</span> <span class="n">d</span><span class="p">[</span><span class="s1">&#39;Endogenous&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span> <span class="o">==</span> <span class="s1">&#39;true&#39;</span><span class="p">]</span>
+
+    <span class="k">for</span> <span class="n">d</span> <span class="ow">in</span> <span class="n">data</span><span class="p">:</span>
+
+        <span class="k">if</span> <span class="n">is_positive</span><span class="p">(</span><span class="n">d</span><span class="p">[</span><span class="s1">&#39;Type&#39;</span><span class="p">])</span> <span class="ow">or</span> <span class="n">is_positive</span><span class="p">(</span><span class="n">d</span><span class="p">[</span><span class="s1">&#39;Action&#39;</span><span class="p">]):</span>
+            <span class="n">effect</span> <span class="o">=</span> <span class="mi">1</span>
+
+        <span class="k">elif</span> <span class="n">is_negative</span><span class="p">(</span><span class="n">d</span><span class="p">[</span><span class="s1">&#39;Type&#39;</span><span class="p">])</span> <span class="ow">or</span> <span class="n">is_negative</span><span class="p">(</span><span class="n">d</span><span class="p">[</span><span class="s1">&#39;Action&#39;</span><span class="p">]):</span>
+            <span class="n">effect</span> <span class="o">=</span> <span class="o">-</span><span class="mi">1</span>
+
+        <span class="k">else</span><span class="p">:</span>
+            <span class="n">effect</span> <span class="o">=</span> <span class="mi">0</span>
+
+        <span class="n">ligands</span> <span class="o">=</span> <span class="n">d</span><span class="p">[</span><span class="s1">&#39;Ligand Gene Symbol&#39;</span><span class="p">]</span> <span class="ow">or</span> <span class="n">d</span><span class="p">[</span><span class="s1">&#39;Ligand PubChem SID&#39;</span><span class="p">]</span>
+        <span class="n">ligands</span> <span class="o">=</span> <span class="n">ligands</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;|&#39;</span><span class="p">)</span>
+        <span class="n">ligand_taxons</span> <span class="o">=</span> <span class="p">[</span><span class="n">get_taxid</span><span class="p">(</span><span class="n">l</span><span class="p">)</span> <span class="k">for</span> <span class="n">l</span> <span class="ow">in</span> <span class="n">d</span><span class="p">[</span><span class="s1">&#39;Ligand Species&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;|&#39;</span><span class="p">)]</span>
+
+        <span class="k">for</span> <span class="n">ligand_taxon</span> <span class="ow">in</span> <span class="nb">zip</span><span class="p">(</span><span class="n">ligands</span><span class="p">,</span> <span class="n">ligand_taxons</span><span class="p">):</span>
+
+            <span class="n">targets</span> <span class="o">=</span> <span class="p">(</span>
+                <span class="n">d</span><span class="p">[</span><span class="s1">&#39;Target UniProt ID&#39;</span><span class="p">]</span> <span class="ow">or</span>
+                <span class="n">d</span><span class="p">[</span><span class="s1">&#39;Target Ligand UniProt ID&#39;</span><span class="p">]</span> <span class="ow">or</span>
+                <span class="n">d</span><span class="p">[</span><span class="s1">&#39;Target Ligand PubChem SID&#39;</span><span class="p">]</span>
+            <span class="p">)</span>
+            <span class="n">targets</span> <span class="o">=</span> <span class="n">targets</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;|&#39;</span><span class="p">)</span>
+            <span class="n">references</span> <span class="o">=</span> <span class="n">d</span><span class="p">[</span><span class="s1">&#39;PubMed ID&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;|&#39;</span><span class="p">)</span> <span class="k">if</span> <span class="n">d</span><span class="p">[</span><span class="s1">&#39;PubMed ID&#39;</span><span class="p">]</span> <span class="k">else</span> <span class="p">[]</span>
+
+            <span class="k">if</span> <span class="n">process_interactions</span><span class="p">:</span>
+
+                <span class="k">for</span> <span class="n">ligand</span><span class="p">,</span> <span class="n">target</span> <span class="ow">in</span> <span class="n">itertools</span><span class="o">.</span><span class="n">product</span><span class="p">(</span><span class="n">ligands</span><span class="p">,</span> <span class="n">targets</span><span class="p">):</span>
+
+                    <span class="n">interactions</span><span class="o">.</span><span class="n">append</span><span class="p">(</span>
+                        <span class="n">GuideToPharmacologyInteraction</span><span class="p">(</span>
+                            <span class="n">ligand</span> <span class="o">=</span> <span class="n">ligand</span><span class="p">,</span>
+                            <span class="n">ligand_id_type</span> <span class="o">=</span> <span class="p">(</span>
+                                <span class="s1">&#39;genesymbol&#39;</span>
+                                    <span class="k">if</span> <span class="n">d</span><span class="p">[</span><span class="s1">&#39;Ligand Gene Symbol&#39;</span><span class="p">]</span> <span class="k">else</span>
+                                <span class="s1">&#39;pubchem_sid&#39;</span>
+                                    <span class="k">if</span> <span class="n">d</span><span class="p">[</span><span class="s1">&#39;Ligand PubChem SID&#39;</span><span class="p">]</span> <span class="k">else</span>
+                                <span class="kc">None</span>
+                            <span class="p">),</span>
+                            <span class="n">target</span> <span class="o">=</span> <span class="n">target</span><span class="p">,</span>
+                            <span class="n">target_id_type</span> <span class="o">=</span> <span class="p">(</span>
+                                <span class="s1">&#39;uniprot&#39;</span>
+                                    <span class="k">if</span> <span class="p">(</span>
+                                        <span class="n">d</span><span class="p">[</span><span class="s1">&#39;Target UniProt ID&#39;</span><span class="p">]</span> <span class="ow">or</span>
+                                        <span class="n">d</span><span class="p">[</span><span class="s1">&#39;Target Ligand UniProt ID&#39;</span><span class="p">]</span>
+                                    <span class="p">)</span> <span class="k">else</span>
+                                <span class="s1">&#39;pubchem_sid&#39;</span>
+                                    <span class="k">if</span> <span class="n">d</span><span class="p">[</span><span class="s1">&#39;Target Ligand PubChem SID&#39;</span><span class="p">]</span> <span class="k">else</span>
+                                <span class="kc">None</span>
+                            <span class="p">),</span>
+                            <span class="n">target_is_ligand</span> <span class="o">=</span> <span class="nb">bool</span><span class="p">(</span><span class="n">d</span><span class="p">[</span><span class="s1">&#39;Target Ligand&#39;</span><span class="p">]),</span>
+                            <span class="n">ligand_organism</span> <span class="o">=</span> <span class="n">ligand_taxon</span><span class="p">,</span>
+                            <span class="n">target_organism</span> <span class="o">=</span> <span class="n">get_taxid</span><span class="p">(</span><span class="n">d</span><span class="p">[</span><span class="s1">&#39;Target Species&#39;</span><span class="p">]),</span>
+                            <span class="n">effect</span> <span class="o">=</span> <span class="n">effect</span><span class="p">,</span>
+                            <span class="n">ligand_location</span> <span class="o">=</span> <span class="p">(</span>
+                                <span class="n">d</span><span class="p">[</span><span class="s1">&#39;Ligand Context&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span> <span class="ow">or</span> <span class="kc">None</span>
+                            <span class="p">),</span>
+                            <span class="n">target_type</span> <span class="o">=</span> <span class="p">(</span>
+                                <span class="n">d</span><span class="p">[</span><span class="s1">&#39;Receptor Site&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span> <span class="ow">or</span> <span class="kc">None</span>
+                            <span class="p">),</span>
+                            <span class="n">ligand_endogenous</span> <span class="o">=</span> <span class="p">(</span>
+                                <span class="n">d</span><span class="p">[</span><span class="s1">&#39;Endogenous&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span> <span class="o">==</span> <span class="s1">&#39;t&#39;</span>
+                            <span class="p">),</span>
+                            <span class="n">pubmed_ids</span> <span class="o">=</span> <span class="n">references</span><span class="p">,</span>
+                        <span class="p">)</span>
+                    <span class="p">)</span>
+
+            <span class="k">if</span> <span class="n">process_complexes</span><span class="p">:</span>
+                <span class="k">if</span> <span class="p">(</span>
+                    <span class="nb">len</span><span class="p">(</span><span class="n">targets</span><span class="p">)</span> <span class="o">&gt;</span> <span class="mi">1</span> <span class="ow">and</span> <span class="p">(</span>
+                        <span class="n">d</span><span class="p">[</span><span class="s1">&#39;Target UniProt ID&#39;</span><span class="p">]</span> <span class="ow">or</span>
+                        <span class="n">d</span><span class="p">[</span><span class="s1">&#39;Target Ligand UniProt ID&#39;</span><span class="p">]</span>
+                    <span class="p">)</span>
+                <span class="p">):</span>
+                    <span class="n">cplex</span> <span class="o">=</span> <span class="n">intera</span><span class="o">.</span><span class="n">Complex</span><span class="p">(</span>
+                        <span class="n">components</span> <span class="o">=</span> <span class="n">targets</span><span class="p">,</span>
+                        <span class="n">sources</span> <span class="o">=</span> <span class="s1">&#39;Guide2Pharma&#39;</span><span class="p">,</span>
+                        <span class="n">references</span> <span class="o">=</span> <span class="n">references</span><span class="p">,</span>
+                    <span class="p">)</span>
+                    <span class="n">key</span> <span class="o">=</span> <span class="n">cplex</span><span class="o">.</span><span class="fm">__str__</span><span class="p">()</span>
+
+                    <span class="k">if</span> <span class="n">key</span> <span class="ow">in</span> <span class="n">complexes</span><span class="p">:</span>
+                        <span class="n">complexes</span><span class="p">[</span><span class="n">key</span><span class="p">]</span> <span class="o">+=</span> <span class="n">cplex</span>
+
+                    <span class="k">else</span><span class="p">:</span>
+                        <span class="n">complexes</span><span class="p">[</span><span class="n">key</span><span class="p">]</span> <span class="o">=</span> <span class="n">cplex</span>
+
+                <span class="k">if</span> <span class="p">(</span>
+                    <span class="nb">len</span><span class="p">(</span><span class="n">ligands</span><span class="p">)</span> <span class="o">&gt;</span> <span class="mi">1</span> <span class="ow">and</span>
+                    <span class="n">d</span><span class="p">[</span><span class="s1">&#39;Ligand Gene Symbol&#39;</span><span class="p">]</span>
+                <span class="p">):</span>
+                    <span class="n">ligand_uniprots</span> <span class="o">=</span> <span class="p">[</span>
+                        <span class="n">mapping</span><span class="o">.</span><span class="n">map_name0</span><span class="p">(</span><span class="n">ligand</span><span class="p">,</span> <span class="s1">&#39;genesymbol&#39;</span><span class="p">,</span> <span class="s1">&#39;uniprot&#39;</span><span class="p">)</span>
+                        <span class="k">for</span> <span class="n">ligand</span> <span class="ow">in</span> <span class="n">ligands</span>
+                    <span class="p">]</span>
+                    <span class="n">ligand_uniprots</span> <span class="o">=</span> <span class="p">[</span><span class="n">u</span> <span class="k">for</span> <span class="n">u</span> <span class="ow">in</span> <span class="n">ligand_uniprots</span> <span class="k">if</span> <span class="n">u</span><span class="p">]</span>
+
+                    <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">ligand_uniprots</span><span class="p">)</span> <span class="o">&gt;</span> <span class="mi">1</span><span class="p">:</span>
+                        <span class="n">cplex</span> <span class="o">=</span> <span class="n">intera</span><span class="o">.</span><span class="n">Complex</span><span class="p">(</span>
+                            <span class="n">components</span> <span class="o">=</span> <span class="n">ligand_uniprots</span><span class="p">,</span>
+                            <span class="n">sources</span> <span class="o">=</span> <span class="s1">&#39;Guide2Pharma&#39;</span><span class="p">,</span>
+                            <span class="n">references</span> <span class="o">=</span> <span class="n">references</span><span class="p">,</span>
+                        <span class="p">)</span>
+                        <span class="n">key</span> <span class="o">=</span> <span class="n">cplex</span><span class="o">.</span><span class="fm">__str__</span><span class="p">()</span>
+
+                        <span class="k">if</span> <span class="n">key</span> <span class="ow">in</span> <span class="n">complexes</span><span class="p">:</span>
+                            <span class="n">complexes</span><span class="p">[</span><span class="n">key</span><span class="p">]</span> <span class="o">+=</span> <span class="n">cplex</span>
+
+                        <span class="k">else</span><span class="p">:</span>
+                            <span class="n">complexes</span><span class="p">[</span><span class="n">key</span><span class="p">]</span> <span class="o">=</span> <span class="n">cplex</span>
+
+    <span class="k">return</span> <span class="n">interactions</span><span class="p">,</span> <span class="n">complexes</span></div>
+
+
+
+<div class="viewcode-block" id="guide2pharma_interactions">
+<a class="viewcode-back" href="../../../api/pypath.inputs.guide2pharma.guide2pharma_interactions.html#pypath.inputs.guide2pharma.guide2pharma_interactions">[docs]</a>
+<span class="k">def</span> <span class="nf">guide2pharma_interactions</span><span class="p">(</span><span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+
+    <span class="n">interactions</span><span class="p">,</span> <span class="n">complexes</span> <span class="o">=</span> <span class="n">guide2pharma_download</span><span class="p">(</span>
+        <span class="n">process_complexes</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+        <span class="o">**</span><span class="n">kwargs</span>
+    <span class="p">)</span>
+
+    <span class="k">return</span> <span class="n">interactions</span></div>
+
+
+
+<div class="viewcode-block" id="guide2pharma_complexes">
+<a class="viewcode-back" href="../../../api/pypath.inputs.guide2pharma.guide2pharma_complexes.html#pypath.inputs.guide2pharma.guide2pharma_complexes">[docs]</a>
+<span class="k">def</span> <span class="nf">guide2pharma_complexes</span><span class="p">(</span><span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+
+    <span class="n">interactions</span><span class="p">,</span> <span class="n">complexes</span> <span class="o">=</span> <span class="n">guide2pharma_download</span><span class="p">(</span>
+        <span class="n">process_interactions</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+        <span class="o">**</span><span class="n">kwargs</span>
+    <span class="p">)</span>
+
+    <span class="k">return</span> <span class="n">complexes</span></div>
+
+</pre></div>
+
+                </article>
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+  <h1>Source code for pypath.inputs.gutmgene</h1><div class="highlight"><pre>
+<span></span><span class="ch">#!/usr/bin/env python</span>
+<span class="c1"># -*- coding: utf-8 -*-</span>
+
+<span class="c1">#</span>
+<span class="c1">#  This file is part of the `pypath` python module</span>
+<span class="c1">#</span>
+<span class="c1">#  Copyright 2014-2023</span>
+<span class="c1">#  EMBL, EMBL-EBI, Uniklinik RWTH Aachen, Heidelberg University</span>
+<span class="c1">#</span>
+<span class="c1">#  Authors: see the file `README.rst`</span>
+<span class="c1">#  Contact: Dénes Türei (turei.denes@gmail.com)</span>
+<span class="c1">#</span>
+<span class="c1">#  Distributed under the GPLv3 License.</span>
+<span class="c1">#  See accompanying file LICENSE.txt or copy at</span>
+<span class="c1">#      https://www.gnu.org/licenses/gpl-3.0.html</span>
+<span class="c1">#</span>
+<span class="c1">#  Website: https://pypath.omnipathdb.org/</span>
+<span class="c1">#</span>
+
+<span class="kn">from</span> <span class="nn">__future__</span> <span class="kn">import</span> <span class="n">annotations</span>
+
+<span class="kn">from</span> <span class="nn">typing</span> <span class="kn">import</span> <span class="n">Literal</span><span class="p">,</span> <span class="n">NamedTuple</span>
+
+<span class="kn">import</span> <span class="nn">collections</span>
+
+<span class="kn">import</span> <span class="nn">pypath.share.curl</span> <span class="k">as</span> <span class="nn">curl</span>
+<span class="kn">import</span> <span class="nn">pypath.utils.taxonomy</span> <span class="k">as</span> <span class="nn">taxonomy</span>
+<span class="kn">import</span> <span class="nn">pypath.utils.mapping</span> <span class="k">as</span> <span class="nn">mapping</span>
+<span class="kn">import</span> <span class="nn">pypath.resources.urls</span> <span class="k">as</span> <span class="nn">urls</span>
+<span class="kn">import</span> <span class="nn">pypath.share.session</span> <span class="k">as</span> <span class="nn">session</span>
+
+<span class="n">_log</span> <span class="o">=</span> <span class="n">session</span><span class="o">.</span><span class="n">Logger</span><span class="p">(</span><span class="n">name</span> <span class="o">=</span> <span class="s1">&#39;gutmgene_input&#39;</span><span class="p">)</span><span class="o">.</span><span class="n">_log</span>
+
+
+<div class="viewcode-block" id="GutmgeneRaw">
+<a class="viewcode-back" href="../../../api/pypath.inputs.gutmgene.GutmgeneRaw.html#pypath.inputs.gutmgene.GutmgeneRaw">[docs]</a>
+<span class="k">class</span> <span class="nc">GutmgeneRaw</span><span class="p">(</span><span class="n">NamedTuple</span><span class="p">):</span>
+    <span class="n">microbe_taxon</span><span class="p">:</span> <span class="nb">str</span>
+    <span class="n">microbe_ncbi_tax_id</span><span class="p">:</span> <span class="nb">str</span>
+    <span class="n">gut_microbiota_id</span><span class="p">:</span> <span class="nb">str</span>
+    <span class="n">classification</span><span class="p">:</span> <span class="nb">str</span>
+    <span class="n">genesymbol</span><span class="p">:</span> <span class="nb">str</span>
+    <span class="n">entrez</span><span class="p">:</span> <span class="nb">str</span>
+    <span class="n">effect</span><span class="p">:</span> <span class="nb">str</span>
+    <span class="n">throughput</span><span class="p">:</span> <span class="nb">str</span></div>
+
+
+
+<div class="viewcode-block" id="GutmgeneAnnotation">
+<a class="viewcode-back" href="../../../api/pypath.inputs.gutmgene.GutmgeneAnnotation.html#pypath.inputs.gutmgene.GutmgeneAnnotation">[docs]</a>
+<span class="k">class</span> <span class="nc">GutmgeneAnnotation</span><span class="p">(</span><span class="n">NamedTuple</span><span class="p">):</span>
+    <span class="n">microbe_taxon</span><span class="p">:</span> <span class="nb">str</span>
+    <span class="n">microbe_ncbi_tax_id</span><span class="p">:</span> <span class="nb">str</span>
+    <span class="n">gut_microbiota_id</span><span class="p">:</span> <span class="nb">str</span>
+    <span class="n">classification</span><span class="p">:</span> <span class="nb">str</span>
+    <span class="n">effect</span><span class="p">:</span> <span class="nb">str</span>
+    <span class="n">throughput</span><span class="p">:</span> <span class="nb">str</span></div>
+
+
+
+<div class="viewcode-block" id="gutmgene_raw">
+<a class="viewcode-back" href="../../../api/pypath.inputs.gutmgene.gutmgene_raw.html#pypath.inputs.gutmgene.gutmgene_raw">[docs]</a>
+<span class="k">def</span> <span class="nf">gutmgene_raw</span><span class="p">(</span><span class="n">organism</span><span class="p">:</span> <span class="n">Literal</span><span class="p">[</span><span class="s1">&#39;human&#39;</span><span class="p">,</span> <span class="s1">&#39;mouse&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="s1">&#39;human&#39;</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">list</span><span class="p">[</span><span class="nb">tuple</span><span class="p">]:</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Gut microbiota genes from the gut microbiota gene database (gutMGene).</span>
+
+<span class="sd">    Args:</span>
+<span class="sd">        organism: Organism ID or name; human and mouse are available.</span>
+
+<span class="sd">    Returns:</span>
+<span class="sd">        A list of named tuples containing information about gut microbiota</span>
+<span class="sd">        genes in human.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="n">organism_</span> <span class="o">=</span> <span class="n">taxonomy</span><span class="o">.</span><span class="n">ensure_common_name</span><span class="p">(</span><span class="n">organism</span><span class="p">,</span> <span class="n">lower</span> <span class="o">=</span> <span class="kc">True</span><span class="p">)</span>
+
+    <span class="k">if</span> <span class="n">organism</span> <span class="ow">not</span> <span class="ow">in</span> <span class="p">(</span><span class="s1">&#39;human&#39;</span><span class="p">,</span> <span class="s1">&#39;mouse&#39;</span><span class="p">):</span>
+
+        <span class="n">err</span> <span class="o">=</span> <span class="s1">&#39;`organism` must be either `human` or `mouse`, not `</span><span class="si">{organism}</span><span class="s1">`.&#39;</span>
+        <span class="n">_log</span><span class="p">(</span><span class="n">err</span><span class="p">)</span>
+        <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="n">err</span><span class="p">)</span>
+
+    <span class="n">url</span> <span class="o">=</span> <span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;gutmgene&#39;</span><span class="p">][</span><span class="sa">f</span><span class="s1">&#39;url_</span><span class="si">{</span><span class="n">organism_</span><span class="si">}</span><span class="s1">&#39;</span><span class="p">]</span>
+    <span class="n">c</span> <span class="o">=</span> <span class="n">curl</span><span class="o">.</span><span class="n">Curl</span><span class="p">(</span><span class="n">url</span><span class="p">,</span> <span class="n">silent</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span> <span class="n">large</span> <span class="o">=</span> <span class="kc">True</span><span class="p">)</span>
+
+    <span class="n">result</span> <span class="o">=</span> <span class="nb">set</span><span class="p">()</span>
+
+    <span class="k">for</span> <span class="n">l</span> <span class="ow">in</span> <span class="n">c</span><span class="o">.</span><span class="n">result</span><span class="p">:</span>
+
+        <span class="k">if</span> <span class="n">l</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s1">&#39;&quot;&#39;</span><span class="p">):</span>
+            <span class="k">continue</span>
+
+        <span class="n">l</span> <span class="o">=</span> <span class="n">l</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s1">&#39;&quot;&#39;</span><span class="p">,</span> <span class="s1">&#39;&#39;</span><span class="p">)</span>
+        <span class="n">l</span> <span class="o">=</span> <span class="n">l</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\t</span><span class="s1">&#39;</span><span class="p">)</span>
+        <span class="n">l</span> <span class="o">=</span> <span class="p">(</span><span class="kc">None</span> <span class="k">if</span> <span class="ow">not</span> <span class="n">i</span> <span class="k">else</span> <span class="n">i</span> <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="n">l</span><span class="p">)</span>
+
+        <span class="k">if</span> <span class="n">l</span><span class="p">:</span>
+
+            <span class="n">result</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">GutmgeneRaw</span><span class="p">(</span><span class="o">*</span><span class="n">l</span><span class="p">))</span>
+
+    <span class="k">return</span> <span class="nb">list</span><span class="p">(</span><span class="n">result</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="gutmgene_annotations">
+<a class="viewcode-back" href="../../../api/pypath.inputs.gutmgene.gutmgene_annotations.html#pypath.inputs.gutmgene.gutmgene_annotations">[docs]</a>
+<span class="k">def</span> <span class="nf">gutmgene_annotations</span><span class="p">(</span>
+        <span class="n">organism</span><span class="p">:</span> <span class="n">Literal</span><span class="p">[</span><span class="s1">&#39;human&#39;</span><span class="p">,</span> <span class="s1">&#39;mouse&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="s1">&#39;human&#39;</span><span class="p">,</span>
+    <span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">dict</span><span class="p">[</span><span class="nb">str</span><span class="p">,</span> <span class="nb">set</span><span class="p">[</span><span class="n">GutmgeneAnnotation</span><span class="p">]]:</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Microbial effectors of human or mouse genes from the gutMGene database.</span>
+
+<span class="sd">    Args:</span>
+<span class="sd">        organism:</span>
+<span class="sd">            Organism ID or name; human and mouse are available.</span>
+
+<span class="sd">    Return:</span>
+<span class="sd">        A dict of sets of named tuples representing microbial relationships;</span>
+<span class="sd">        top level keys are UniProt IDs.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="n">raw</span> <span class="o">=</span> <span class="n">gutmgene_raw</span><span class="p">(</span><span class="n">organism</span><span class="p">)</span>
+    <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">taxonomy</span><span class="o">.</span><span class="n">ensure_ncbi_tax_id</span><span class="p">(</span><span class="n">organism</span><span class="p">)</span>
+    <span class="n">result</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">defaultdict</span><span class="p">(</span><span class="nb">set</span><span class="p">)</span>
+
+    <span class="k">for</span> <span class="n">rec</span> <span class="ow">in</span> <span class="n">raw</span><span class="p">:</span>
+
+        <span class="n">uniprots</span> <span class="o">=</span> <span class="n">mapping</span><span class="o">.</span><span class="n">map_name</span><span class="p">(</span>
+            <span class="n">rec</span><span class="o">.</span><span class="n">genesymbol</span><span class="p">,</span>
+            <span class="s1">&#39;genesymbol&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;uniprot&#39;</span><span class="p">,</span>
+            <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">,</span>
+        <span class="p">)</span>
+
+        <span class="k">for</span> <span class="n">uniprot</span> <span class="ow">in</span> <span class="n">uniprots</span><span class="p">:</span>
+
+            <span class="n">result</span><span class="p">[</span><span class="n">uniprot</span><span class="p">]</span><span class="o">.</span><span class="n">add</span><span class="p">(</span>
+                <span class="n">GutmgeneAnnotation</span><span class="p">(</span>
+                    <span class="n">microbe_taxon</span> <span class="o">=</span> <span class="n">rec</span><span class="o">.</span><span class="n">microbe_taxon</span><span class="p">,</span>
+                    <span class="n">microbe_ncbi_tax_id</span> <span class="o">=</span> <span class="n">rec</span><span class="o">.</span><span class="n">microbe_ncbi_tax_id</span><span class="p">,</span>
+                    <span class="n">gut_microbiota_id</span> <span class="o">=</span> <span class="n">rec</span><span class="o">.</span><span class="n">gut_microbiota_id</span><span class="p">,</span>
+                    <span class="n">classification</span> <span class="o">=</span> <span class="n">rec</span><span class="o">.</span><span class="n">classification</span><span class="p">,</span>
+                    <span class="n">effect</span> <span class="o">=</span> <span class="n">rec</span><span class="o">.</span><span class="n">effect</span><span class="p">,</span>
+                    <span class="n">throughput</span> <span class="o">=</span> <span class="n">rec</span><span class="o">.</span><span class="n">throughput</span><span class="p">,</span>
+                <span class="p">)</span>
+            <span class="p">)</span>
+
+    <span class="k">return</span> <span class="nb">dict</span><span class="p">(</span><span class="n">result</span><span class="p">)</span></div>
+
+</pre></div>
+
+                </article>
+              
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diff --git a/_modules/pypath/inputs/havugimana.html b/_modules/pypath/inputs/havugimana.html
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+
+<!DOCTYPE html>
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+                  
+  <h1>Source code for pypath.inputs.havugimana</h1><div class="highlight"><pre>
+<span></span><span class="ch">#!/usr/bin/env python</span>
+<span class="c1"># -*- coding: utf-8 -*-</span>
+
+<span class="c1">#</span>
+<span class="c1">#  This file is part of the `pypath` python module</span>
+<span class="c1">#</span>
+<span class="c1">#  Copyright 2014-2023</span>
+<span class="c1">#  EMBL, EMBL-EBI, Uniklinik RWTH Aachen, Heidelberg University</span>
+<span class="c1">#</span>
+<span class="c1">#  Authors: see the file `README.rst`</span>
+<span class="c1">#  Contact: Dénes Türei (turei.denes@gmail.com)</span>
+<span class="c1">#</span>
+<span class="c1">#  Distributed under the GPLv3 License.</span>
+<span class="c1">#  See accompanying file LICENSE.txt or copy at</span>
+<span class="c1">#      https://www.gnu.org/licenses/gpl-3.0.html</span>
+<span class="c1">#</span>
+<span class="c1">#  Website: https://pypath.omnipathdb.org/</span>
+<span class="c1">#</span>
+
+<span class="kn">import</span> <span class="nn">collections</span>
+<span class="kn">import</span> <span class="nn">itertools</span>
+
+<span class="kn">import</span> <span class="nn">pypath.share.curl</span> <span class="k">as</span> <span class="nn">curl</span>
+<span class="kn">import</span> <span class="nn">pypath.inputs.cell</span> <span class="k">as</span> <span class="nn">cell_input</span>
+<span class="kn">import</span> <span class="nn">pypath.inputs.common</span> <span class="k">as</span> <span class="nn">inputs_common</span>
+<span class="kn">import</span> <span class="nn">pypath.resources.urls</span> <span class="k">as</span> <span class="nn">urls</span>
+<span class="kn">import</span> <span class="nn">pypath.internals.intera</span> <span class="k">as</span> <span class="nn">intera</span>
+
+
+<div class="viewcode-block" id="get_havugimana">
+<a class="viewcode-back" href="../../../api/pypath.inputs.havugimana.get_havugimana.html#pypath.inputs.havugimana.get_havugimana">[docs]</a>
+<span class="k">def</span> <span class="nf">get_havugimana</span><span class="p">():</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Downloads data from</span>
+<span class="sd">    Supplement Table S3/1 from Havugimana 2012</span>
+<span class="sd">    Cell. 150(5): 1068–1081.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="n">supp_url</span> <span class="o">=</span> <span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;havugimana&#39;</span><span class="p">][</span><span class="s1">&#39;url&#39;</span><span class="p">]</span>
+    <span class="n">article_url</span> <span class="o">=</span> <span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;havugimana&#39;</span><span class="p">][</span><span class="s1">&#39;article&#39;</span><span class="p">]</span>
+    <span class="n">path</span> <span class="o">=</span> <span class="n">cell_input</span><span class="o">.</span><span class="n">cell_supplementary</span><span class="p">(</span><span class="n">supp_url</span><span class="p">,</span> <span class="n">article_url</span><span class="p">)</span>
+    <span class="n">table</span> <span class="o">=</span> <span class="n">inputs_common</span><span class="o">.</span><span class="n">read_xls</span><span class="p">(</span><span class="n">path</span><span class="p">)</span>
+
+    <span class="k">return</span> <span class="n">table</span><span class="p">[</span><span class="mi">3</span><span class="p">:]</span></div>
+
+
+
+<div class="viewcode-block" id="havugimana_complexes">
+<a class="viewcode-back" href="../../../api/pypath.inputs.havugimana.havugimana_complexes.html#pypath.inputs.havugimana.havugimana_complexes">[docs]</a>
+<span class="k">def</span> <span class="nf">havugimana_complexes</span><span class="p">():</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Retrieves complexes from</span>
+<span class="sd">    Supplement Table S3/1 from Havugimana 2012</span>
+<span class="sd">    Cell. 150(5): 1068–1081.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="n">complexes</span> <span class="o">=</span> <span class="p">{}</span>
+
+    <span class="k">for</span> <span class="n">rec</span> <span class="ow">in</span> <span class="n">get_havugimana</span><span class="p">():</span>
+
+        <span class="n">cplex</span> <span class="o">=</span> <span class="n">intera</span><span class="o">.</span><span class="n">Complex</span><span class="p">(</span>
+            <span class="n">components</span> <span class="o">=</span> <span class="n">rec</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;,&#39;</span><span class="p">),</span>
+            <span class="n">sources</span> <span class="o">=</span> <span class="s1">&#39;Havugimana2012&#39;</span><span class="p">,</span>
+            <span class="n">ids</span> <span class="o">=</span> <span class="n">rec</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span>
+        <span class="p">)</span>
+
+        <span class="n">complexes</span><span class="p">[</span><span class="n">cplex</span><span class="o">.</span><span class="fm">__str__</span><span class="p">()]</span> <span class="o">=</span> <span class="n">cplex</span>
+
+    <span class="k">return</span> <span class="n">complexes</span></div>
+
+</pre></div>
+
+                </article>
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diff --git a/_modules/pypath/inputs/hgnc.html b/_modules/pypath/inputs/hgnc.html
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+                  
+  <h1>Source code for pypath.inputs.hgnc</h1><div class="highlight"><pre>
+<span></span><span class="ch">#!/usr/bin/env python</span>
+<span class="c1"># -*- coding: utf-8 -*-</span>
+
+<span class="c1">#</span>
+<span class="c1">#  This file is part of the `pypath` python module</span>
+<span class="c1">#</span>
+<span class="c1">#  Copyright 2014-2023</span>
+<span class="c1">#  EMBL, EMBL-EBI, Uniklinik RWTH Aachen, Heidelberg University</span>
+<span class="c1">#</span>
+<span class="c1">#  Authors: see the file `README.rst`</span>
+<span class="c1">#  Contact: Dénes Türei (turei.denes@gmail.com)</span>
+<span class="c1">#</span>
+<span class="c1">#  Distributed under the GPLv3 License.</span>
+<span class="c1">#  See accompanying file LICENSE.txt or copy at</span>
+<span class="c1">#      https://www.gnu.org/licenses/gpl-3.0.html</span>
+<span class="c1">#</span>
+<span class="c1">#  Website: https://pypath.omnipathdb.org/</span>
+<span class="c1">#</span>
+
+<span class="kn">import</span> <span class="nn">collections</span>
+
+<span class="kn">import</span> <span class="nn">pypath.share.curl</span> <span class="k">as</span> <span class="nn">curl</span>
+<span class="kn">import</span> <span class="nn">pypath.resources.urls</span> <span class="k">as</span> <span class="nn">urls</span>
+<span class="kn">import</span> <span class="nn">pypath.utils.mapping</span> <span class="k">as</span> <span class="nn">mapping</span>
+
+<div class="viewcode-block" id="hgnc_genegroups">
+<a class="viewcode-back" href="../../../api/pypath.inputs.hgnc.hgnc_genegroups.html#pypath.inputs.hgnc.hgnc_genegroups">[docs]</a>
+<span class="k">def</span> <span class="nf">hgnc_genegroups</span><span class="p">():</span>
+
+    <span class="n">HGNCGeneGroupAnnotation</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">namedtuple</span><span class="p">(</span>
+        <span class="s1">&#39;HGNCGeneGroupAnnotation&#39;</span><span class="p">,</span>
+        <span class="p">[</span><span class="s1">&#39;mainclass&#39;</span><span class="p">],</span>
+    <span class="p">)</span>
+
+
+    <span class="n">result</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">defaultdict</span><span class="p">(</span><span class="nb">set</span><span class="p">)</span>
+
+    <span class="n">url</span> <span class="o">=</span> <span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;hgnc&#39;</span><span class="p">][</span><span class="s1">&#39;groups&#39;</span><span class="p">]</span>
+    <span class="n">c</span> <span class="o">=</span> <span class="n">curl</span><span class="o">.</span><span class="n">Curl</span><span class="p">(</span><span class="n">url</span><span class="p">,</span> <span class="n">large</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span> <span class="n">silent</span> <span class="o">=</span> <span class="kc">False</span><span class="p">)</span>
+
+    <span class="n">_</span> <span class="o">=</span> <span class="nb">next</span><span class="p">(</span><span class="n">c</span><span class="o">.</span><span class="n">result</span><span class="p">)</span>
+
+    <span class="k">for</span> <span class="n">rec</span> <span class="ow">in</span> <span class="n">c</span><span class="o">.</span><span class="n">result</span><span class="p">:</span>
+
+        <span class="n">rec</span> <span class="o">=</span> <span class="n">rec</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\t</span><span class="s1">&#39;</span><span class="p">)</span>
+        <span class="n">uniprots</span> <span class="o">=</span> <span class="p">{</span><span class="n">u</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span> <span class="k">for</span> <span class="n">u</span> <span class="ow">in</span> <span class="n">rec</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;,&#39;</span><span class="p">)}</span>
+        <span class="n">uniprots</span><span class="o">.</span><span class="n">discard</span><span class="p">(</span><span class="s1">&#39;&#39;</span><span class="p">)</span>
+
+        <span class="k">if</span> <span class="ow">not</span> <span class="n">uniprots</span><span class="p">:</span>
+            <span class="k">continue</span>
+
+        <span class="n">uniprots</span> <span class="o">=</span> <span class="n">mapping</span><span class="o">.</span><span class="n">map_names</span><span class="p">(</span><span class="n">uniprots</span><span class="p">,</span> <span class="s1">&#39;uniprot&#39;</span><span class="p">,</span> <span class="s1">&#39;uniprot&#39;</span><span class="p">)</span>
+
+        <span class="k">if</span> <span class="ow">not</span> <span class="n">uniprots</span><span class="p">:</span>
+            <span class="k">continue</span>
+
+        <span class="n">groups</span> <span class="o">=</span> <span class="n">rec</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;|&#39;</span><span class="p">)</span>
+
+        <span class="k">for</span> <span class="n">group</span> <span class="ow">in</span> <span class="n">groups</span><span class="p">:</span>
+            <span class="n">group</span> <span class="o">=</span> <span class="n">group</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span>
+
+            <span class="k">if</span> <span class="n">group</span><span class="p">:</span>
+                <span class="k">for</span> <span class="n">uniprot</span> <span class="ow">in</span> <span class="n">uniprots</span><span class="p">:</span>
+                    <span class="n">result</span><span class="p">[</span><span class="n">uniprot</span><span class="p">]</span><span class="o">.</span><span class="n">add</span><span class="p">(</span>
+                        <span class="n">HGNCGeneGroupAnnotation</span><span class="p">(</span><span class="n">mainclass</span> <span class="o">=</span> <span class="n">group</span><span class="p">)</span>
+                    <span class="p">)</span>
+
+    <span class="k">return</span> <span class="nb">dict</span><span class="p">(</span><span class="n">result</span><span class="p">)</span></div>
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+  <h1>Source code for pypath.inputs.hippie</h1><div class="highlight"><pre>
+<span></span><span class="ch">#!/usr/bin/env python</span>
+<span class="c1"># -*- coding: utf-8 -*-</span>
+
+<span class="c1">#</span>
+<span class="c1">#  This file is part of the `pypath` python module</span>
+<span class="c1">#</span>
+<span class="c1">#  Copyright 2014-2023</span>
+<span class="c1">#  EMBL, EMBL-EBI, Uniklinik RWTH Aachen, Heidelberg University</span>
+<span class="c1">#</span>
+<span class="c1">#  Authors: see the file `README.rst`</span>
+<span class="c1">#  Contact: Dénes Türei (turei.denes@gmail.com)</span>
+<span class="c1">#</span>
+<span class="c1">#  Distributed under the GPLv3 License.</span>
+<span class="c1">#  See accompanying file LICENSE.txt or copy at</span>
+<span class="c1">#      https://www.gnu.org/licenses/gpl-3.0.html</span>
+<span class="c1">#</span>
+<span class="c1">#  Website: https://pypath.omnipathdb.org/</span>
+<span class="c1">#</span>
+
+<span class="kn">import</span> <span class="nn">collections</span>
+<span class="kn">import</span> <span class="nn">itertools</span>
+
+<span class="kn">import</span> <span class="nn">pypath.resources.urls</span> <span class="k">as</span> <span class="nn">urls</span>
+<span class="kn">import</span> <span class="nn">pypath.share.curl</span> <span class="k">as</span> <span class="nn">curl</span>
+<span class="kn">import</span> <span class="nn">pypath.share.common</span> <span class="k">as</span> <span class="nn">common</span>
+<span class="kn">import</span> <span class="nn">pypath.utils.mapping</span> <span class="k">as</span> <span class="nn">mapping</span>
+<span class="kn">import</span> <span class="nn">pypath.utils.taxonomy</span> <span class="k">as</span> <span class="nn">taxonomy</span>
+
+
+<div class="viewcode-block" id="hippie_interactions">
+<a class="viewcode-back" href="../../../api/pypath.inputs.hippie.hippie_interactions.html#pypath.inputs.hippie.hippie_interactions">[docs]</a>
+<span class="k">def</span> <span class="nf">hippie_interactions</span><span class="p">(</span>
+        <span class="n">score_threshold</span> <span class="o">=</span> <span class="mf">.75</span><span class="p">,</span>
+        <span class="n">only_human</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+        <span class="n">only_sources</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+        <span class="n">only_methods</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+        <span class="n">methods</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+        <span class="n">sources</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+        <span class="n">references</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
+        <span class="n">organisms</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+    <span class="p">):</span>
+
+    <span class="n">only_sources</span> <span class="o">=</span> <span class="n">common</span><span class="o">.</span><span class="n">to_set</span><span class="p">(</span><span class="n">only_sources</span><span class="p">)</span>
+    <span class="n">only_methods</span> <span class="o">=</span> <span class="n">common</span><span class="o">.</span><span class="n">to_set</span><span class="p">(</span><span class="n">only_methods</span><span class="p">)</span>
+
+    <span class="n">HippieInteraction</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">namedtuple</span><span class="p">(</span>
+        <span class="s1">&#39;HippieInteraction&#39;</span><span class="p">,</span>
+        <span class="p">[</span>
+            <span class="s1">&#39;id_a&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;id_b&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;score&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;methods&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;references&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;sources&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;organisms&#39;</span><span class="p">,</span>
+        <span class="p">],</span>
+    <span class="p">)</span>
+
+    <span class="n">tps</span> <span class="o">=</span> <span class="k">lambda</span> <span class="n">i</span><span class="p">:</span> <span class="nb">tuple</span><span class="p">(</span><span class="nb">sorted</span><span class="p">(</span><span class="n">i</span><span class="p">))</span>
+
+    <span class="n">url</span> <span class="o">=</span> <span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;hippie&#39;</span><span class="p">][</span><span class="s1">&#39;url&#39;</span><span class="p">]</span>
+    <span class="n">c</span> <span class="o">=</span> <span class="n">curl</span><span class="o">.</span><span class="n">Curl</span><span class="p">(</span><span class="n">url</span><span class="p">,</span> <span class="n">large</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span> <span class="n">silent</span> <span class="o">=</span> <span class="kc">False</span><span class="p">)</span>
+
+    <span class="n">result</span> <span class="o">=</span> <span class="nb">set</span><span class="p">()</span>
+
+    <span class="k">for</span> <span class="n">i</span><span class="p">,</span> <span class="n">l</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">c</span><span class="o">.</span><span class="n">result</span><span class="p">):</span>
+
+        <span class="n">l</span> <span class="o">=</span> <span class="n">l</span><span class="o">.</span><span class="n">strip</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\r\n</span><span class="s1">&#39;</span><span class="p">)</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\t</span><span class="s1">&#39;</span><span class="p">)</span>
+
+        <span class="n">score</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">l</span><span class="p">[</span><span class="mi">4</span><span class="p">])</span>
+
+        <span class="k">if</span> <span class="n">score</span> <span class="o">&lt;</span> <span class="n">score_threshold</span><span class="p">:</span>
+
+            <span class="k">continue</span>
+
+        <span class="n">ids_a_1</span> <span class="o">=</span> <span class="n">mapping</span><span class="o">.</span><span class="n">map_name</span><span class="p">(</span><span class="n">l</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="s1">&#39;uniprot-entry&#39;</span><span class="p">,</span> <span class="s1">&#39;uniprot&#39;</span><span class="p">)</span>
+        <span class="n">ids_a_2</span> <span class="o">=</span> <span class="n">mapping</span><span class="o">.</span><span class="n">map_name</span><span class="p">(</span><span class="n">l</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span> <span class="s1">&#39;entrez&#39;</span><span class="p">,</span> <span class="s1">&#39;uniprot&#39;</span><span class="p">)</span>
+        <span class="n">ids_b_1</span> <span class="o">=</span> <span class="n">mapping</span><span class="o">.</span><span class="n">map_name</span><span class="p">(</span><span class="n">l</span><span class="p">[</span><span class="mi">2</span><span class="p">],</span> <span class="s1">&#39;uniprot-entry&#39;</span><span class="p">,</span> <span class="s1">&#39;uniprot&#39;</span><span class="p">)</span>
+        <span class="n">ids_b_2</span> <span class="o">=</span> <span class="n">mapping</span><span class="o">.</span><span class="n">map_name</span><span class="p">(</span><span class="n">l</span><span class="p">[</span><span class="mi">3</span><span class="p">],</span> <span class="s1">&#39;entrez&#39;</span><span class="p">,</span> <span class="s1">&#39;uniprot&#39;</span><span class="p">)</span>
+
+        <span class="k">for</span> <span class="n">id_a</span><span class="p">,</span> <span class="n">id_b</span> <span class="ow">in</span> <span class="n">itertools</span><span class="o">.</span><span class="n">product</span><span class="p">(</span>
+            <span class="n">ids_a_1</span> <span class="o">|</span> <span class="n">ids_a_2</span><span class="p">,</span>
+            <span class="n">ids_b_1</span> <span class="o">|</span> <span class="n">ids_b_2</span>
+        <span class="p">):</span>
+
+            <span class="n">details</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">(</span>
+                <span class="p">(</span>
+                    <span class="n">dd</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span>
+                    <span class="nb">set</span><span class="p">(</span><span class="n">dd</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;,&#39;</span><span class="p">)),</span>
+                <span class="p">)</span>
+                <span class="k">for</span> <span class="n">dd</span> <span class="ow">in</span>
+                <span class="p">(</span><span class="n">d</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;:&#39;</span><span class="p">)</span> <span class="k">for</span> <span class="n">d</span> <span class="ow">in</span> <span class="n">l</span><span class="p">[</span><span class="mi">5</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;;&#39;</span><span class="p">))</span>
+            <span class="p">)</span>
+
+            <span class="n">_sources</span> <span class="o">=</span> <span class="n">details</span><span class="p">[</span><span class="s1">&#39;sources&#39;</span><span class="p">]</span> <span class="k">if</span> <span class="s1">&#39;sources&#39;</span> <span class="ow">in</span> <span class="n">details</span> <span class="k">else</span> <span class="nb">set</span><span class="p">()</span>
+            <span class="n">experiments</span> <span class="o">=</span> <span class="p">(</span>
+                <span class="n">details</span><span class="p">[</span><span class="s1">&#39;experiments&#39;</span><span class="p">]</span> <span class="k">if</span> <span class="s1">&#39;experiments&#39;</span> <span class="ow">in</span> <span class="n">details</span> <span class="k">else</span> <span class="nb">set</span><span class="p">()</span>
+            <span class="p">)</span>
+
+            <span class="k">if</span> <span class="ow">not</span> <span class="nb">all</span><span class="p">((</span>
+                <span class="ow">not</span> <span class="n">only_methods</span> <span class="ow">or</span> <span class="n">experiments</span> <span class="o">&amp;</span> <span class="n">only_methods</span><span class="p">,</span>
+                <span class="ow">not</span> <span class="n">only_methods</span> <span class="ow">or</span> <span class="n">_sources</span> <span class="o">&amp;</span> <span class="n">only_sources</span><span class="p">,</span>
+            <span class="p">)):</span>
+
+                <span class="k">continue</span>
+
+            <span class="n">_organisms</span> <span class="o">=</span> <span class="p">{</span><span class="mi">9606</span><span class="p">}</span>
+
+            <span class="k">if</span> <span class="s1">&#39;species&#39;</span> <span class="ow">in</span> <span class="n">details</span><span class="p">:</span>
+
+                <span class="n">names</span> <span class="o">=</span> <span class="p">{</span>
+                    <span class="n">spec</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;(&#39;</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span>
+                    <span class="k">for</span> <span class="n">spec</span> <span class="ow">in</span> <span class="n">details</span><span class="p">[</span><span class="s1">&#39;species&#39;</span><span class="p">]</span>
+                <span class="p">}</span>
+                <span class="n">_organisms</span> <span class="o">=</span> <span class="p">{</span>
+                    <span class="n">taxonomy</span><span class="o">.</span><span class="n">ensure_ncbi_tax_id</span><span class="p">(</span><span class="n">name</span><span class="p">)</span>
+                    <span class="k">for</span> <span class="n">name</span> <span class="ow">in</span> <span class="n">names</span>
+                <span class="p">}</span>
+                <span class="n">_organisms</span><span class="o">.</span><span class="n">discard</span><span class="p">(</span><span class="kc">None</span><span class="p">)</span>
+
+                <span class="k">if</span> <span class="n">only_human</span> <span class="ow">and</span> <span class="mi">9606</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">_organisms</span><span class="p">:</span>
+
+                    <span class="k">continue</span>
+
+            <span class="n">result</span><span class="o">.</span><span class="n">add</span><span class="p">(</span>
+                <span class="n">HippieInteraction</span><span class="p">(</span>
+                    <span class="n">id_a</span> <span class="o">=</span> <span class="n">id_a</span><span class="p">,</span>
+                    <span class="n">id_b</span> <span class="o">=</span> <span class="n">id_b</span><span class="p">,</span>
+                    <span class="n">score</span> <span class="o">=</span> <span class="n">score</span><span class="p">,</span>
+                    <span class="n">methods</span> <span class="o">=</span> <span class="n">tps</span><span class="p">(</span><span class="n">experiments</span><span class="p">)</span> <span class="k">if</span> <span class="n">methods</span> <span class="k">else</span> <span class="kc">None</span><span class="p">,</span>
+                    <span class="n">references</span> <span class="o">=</span> <span class="p">(</span>
+                        <span class="n">tps</span><span class="p">(</span><span class="n">details</span><span class="p">[</span><span class="s1">&#39;pmids&#39;</span><span class="p">])</span> <span class="k">if</span> <span class="n">references</span> <span class="k">else</span> <span class="kc">None</span>
+                    <span class="p">),</span>
+                    <span class="n">sources</span> <span class="o">=</span> <span class="n">tps</span><span class="p">(</span><span class="n">_sources</span><span class="p">)</span> <span class="k">if</span> <span class="n">sources</span> <span class="k">else</span> <span class="kc">None</span><span class="p">,</span>
+                    <span class="n">organisms</span> <span class="o">=</span> <span class="n">tps</span><span class="p">(</span><span class="n">_organisms</span><span class="p">)</span> <span class="k">if</span> <span class="n">organisms</span> <span class="k">else</span> <span class="kc">None</span><span class="p">,</span>
+                <span class="p">)</span>
+            <span class="p">)</span>
+
+    <span class="k">return</span> <span class="nb">list</span><span class="p">(</span><span class="n">result</span><span class="p">)</span></div>
+
+</pre></div>
+
+                </article>
+              
+              
+              
+              
+              
+                <footer class="prev-next-footer">
+                  
+<div class="prev-next-area">
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diff --git a/_modules/pypath/inputs/homologene.html b/_modules/pypath/inputs/homologene.html
new file mode 100644
index 000000000..fc83f3b1f
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@@ -0,0 +1,810 @@
+
+<!DOCTYPE html>
+
+
+<html lang="en" data-content_root="../../../" >
+
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+                  
+  <h1>Source code for pypath.inputs.homologene</h1><div class="highlight"><pre>
+<span></span><span class="ch">#!/usr/bin/env python</span>
+<span class="c1"># -*- coding: utf-8 -*-</span>
+
+<span class="c1">#</span>
+<span class="c1">#  This file is part of the `pypath` python module</span>
+<span class="c1">#</span>
+<span class="c1">#  Copyright 2014-2023</span>
+<span class="c1">#  EMBL, EMBL-EBI, Uniklinik RWTH Aachen, Heidelberg University</span>
+<span class="c1">#</span>
+<span class="c1">#  Authors: see the file `README.rst`</span>
+<span class="c1">#  Contact: Dénes Türei (turei.denes@gmail.com)</span>
+<span class="c1">#</span>
+<span class="c1">#  Distributed under the GPLv3 License.</span>
+<span class="c1">#  See accompanying file LICENSE.txt or copy at</span>
+<span class="c1">#      https://www.gnu.org/licenses/gpl-3.0.html</span>
+<span class="c1">#</span>
+<span class="c1">#  Website: https://pypath.omnipathdb.org/</span>
+<span class="c1">#</span>
+
+<span class="kn">import</span> <span class="nn">collections</span>
+<span class="kn">import</span> <span class="nn">itertools</span>
+
+<span class="kn">import</span> <span class="nn">pypath.utils.mapping</span> <span class="k">as</span> <span class="nn">mapping</span>
+<span class="kn">import</span> <span class="nn">pypath.resources.urls</span> <span class="k">as</span> <span class="nn">urls</span>
+<span class="kn">import</span> <span class="nn">pypath.share.curl</span> <span class="k">as</span> <span class="nn">curl</span>
+<span class="kn">import</span> <span class="nn">pypath.inputs.uniprot_db</span> <span class="k">as</span> <span class="nn">uniprot_db</span>
+<span class="kn">import</span> <span class="nn">pypath.share.session</span> <span class="k">as</span> <span class="nn">session</span>
+
+<span class="n">_logger</span> <span class="o">=</span> <span class="n">session</span><span class="o">.</span><span class="n">Logger</span><span class="p">(</span><span class="n">name</span> <span class="o">=</span> <span class="s1">&#39;homologene_input&#39;</span><span class="p">)</span>
+<span class="n">_log</span> <span class="o">=</span> <span class="n">_logger</span><span class="o">.</span><span class="n">_log</span>
+
+
+<div class="viewcode-block" id="get_homologene">
+<a class="viewcode-back" href="../../../api/pypath.inputs.homologene.get_homologene.html#pypath.inputs.homologene.get_homologene">[docs]</a>
+<span class="k">def</span> <span class="nf">get_homologene</span><span class="p">():</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Downloads the latest release of the NCBI HomoloGene database.</span>
+<span class="sd">    Returns file pointer.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="n">url</span> <span class="o">=</span> <span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;homologene&#39;</span><span class="p">][</span><span class="s1">&#39;url_rescued&#39;</span><span class="p">]</span>
+
+    <span class="n">c</span> <span class="o">=</span> <span class="n">curl</span><span class="o">.</span><span class="n">Curl</span><span class="p">(</span>
+        <span class="n">url</span> <span class="o">=</span> <span class="n">url</span><span class="p">,</span>
+        <span class="n">silent</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+        <span class="n">large</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
+        <span class="n">timeout</span> <span class="o">=</span> <span class="mi">1800</span><span class="p">,</span>
+        <span class="n">ignore_content_length</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
+    <span class="p">)</span>
+
+    <span class="k">return</span> <span class="n">c</span><span class="o">.</span><span class="n">result</span></div>
+
+
+
+<div class="viewcode-block" id="homologene_dict">
+<a class="viewcode-back" href="../../../api/pypath.inputs.homologene.homologene_dict.html#pypath.inputs.homologene.homologene_dict">[docs]</a>
+<span class="k">def</span> <span class="nf">homologene_dict</span><span class="p">(</span><span class="n">source</span><span class="p">,</span> <span class="n">target</span><span class="p">,</span> <span class="n">id_type</span><span class="p">):</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Returns orthology translation table as dict, obtained</span>
+<span class="sd">    from NCBI HomoloGene data.</span>
+
+<span class="sd">    Args</span>
+<span class="sd">        source (int): NCBI Taxonomy ID of the source species (keys).</span>
+<span class="sd">        target (int): NCBI Taxonomy ID of the target species (values).</span>
+<span class="sd">        id_type (str): ID type to be used in the dict. Possible values:</span>
+<span class="sd">            &#39;RefSeq&#39;, &#39;Entrez&#39;, &#39;GI&#39;, &#39;GeneSymbol&#39;.</span>
+
+<span class="sd">    Returns</span>
+<span class="sd">        Dict of sets: keys are IDs of the source organism, values are sets</span>
+<span class="sd">        of IDs of the target organism.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+    <span class="n">ids</span> <span class="o">=</span> <span class="p">{</span>
+        <span class="s1">&#39;refseq&#39;</span><span class="p">:</span> <span class="mi">5</span><span class="p">,</span>
+        <span class="s1">&#39;refseqp&#39;</span><span class="p">:</span> <span class="mi">5</span><span class="p">,</span>
+        <span class="s1">&#39;genesymbol&#39;</span><span class="p">:</span> <span class="mi">3</span><span class="p">,</span>
+        <span class="s1">&#39;gi&#39;</span><span class="p">:</span> <span class="mi">4</span><span class="p">,</span>
+        <span class="s1">&#39;entrez&#39;</span><span class="p">:</span> <span class="mi">2</span>
+    <span class="p">}</span>
+
+    <span class="k">try</span><span class="p">:</span>
+        <span class="n">id_col</span> <span class="o">=</span> <span class="n">ids</span><span class="p">[</span><span class="n">id_type</span><span class="o">.</span><span class="n">lower</span><span class="p">()]</span>
+    <span class="k">except</span> <span class="ne">KeyError</span><span class="p">:</span>
+        <span class="n">_log</span><span class="p">(</span>
+            <span class="s1">&#39;Unknown ID type: `</span><span class="si">%s</span><span class="s1">`. Please use RefSeq, &#39;</span>
+            <span class="s1">&#39;Entrez, GI or GeneSymbol.&#39;</span> <span class="o">%</span> <span class="n">id_type</span>
+        <span class="p">)</span>
+        <span class="k">raise</span>
+
+    <span class="n">hg</span> <span class="o">=</span> <span class="n">get_homologene</span><span class="p">()</span>
+    <span class="n">hgroup</span> <span class="o">=</span> <span class="kc">None</span>
+    <span class="n">result</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">defaultdict</span><span class="p">(</span><span class="nb">set</span><span class="p">)</span>
+
+    <span class="k">for</span> <span class="n">l</span> <span class="ow">in</span> <span class="n">hg</span><span class="p">:</span>
+
+        <span class="n">l</span> <span class="o">=</span> <span class="n">l</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\t</span><span class="s1">&#39;</span><span class="p">)</span>
+        <span class="n">this_hgroup</span> <span class="o">=</span> <span class="n">l</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span>
+
+        <span class="k">if</span> <span class="n">this_hgroup</span> <span class="o">!=</span> <span class="n">hgroup</span><span class="p">:</span>
+
+            <span class="n">this_source</span> <span class="o">=</span> <span class="kc">None</span>
+            <span class="n">this_target</span> <span class="o">=</span> <span class="kc">None</span>
+            <span class="n">hgroup</span> <span class="o">=</span> <span class="n">this_hgroup</span>
+
+        <span class="n">this_taxon</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">l</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">strip</span><span class="p">())</span>
+
+        <span class="k">if</span> <span class="n">this_taxon</span> <span class="o">==</span> <span class="n">source</span><span class="p">:</span>
+
+            <span class="n">this_source</span> <span class="o">=</span> <span class="n">l</span><span class="p">[</span><span class="n">id_col</span><span class="p">]</span>
+
+        <span class="k">elif</span> <span class="n">this_taxon</span> <span class="o">==</span> <span class="n">target</span><span class="p">:</span>
+
+            <span class="n">this_target</span> <span class="o">=</span> <span class="n">l</span><span class="p">[</span><span class="n">id_col</span><span class="p">]</span>
+
+        <span class="k">if</span> <span class="p">(</span>
+            <span class="n">this_source</span> <span class="ow">and</span>
+            <span class="n">this_target</span>
+        <span class="p">):</span>
+
+            <span class="n">result</span><span class="p">[</span><span class="n">this_source</span><span class="p">]</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">this_target</span><span class="p">)</span>
+
+    <span class="k">return</span> <span class="nb">dict</span><span class="p">(</span><span class="n">result</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="homologene_uniprot_dict">
+<a class="viewcode-back" href="../../../api/pypath.inputs.homologene.homologene_uniprot_dict.html#pypath.inputs.homologene.homologene_uniprot_dict">[docs]</a>
+<span class="k">def</span> <span class="nf">homologene_uniprot_dict</span><span class="p">(</span><span class="n">source</span><span class="p">,</span> <span class="n">target</span><span class="p">,</span> <span class="n">only_swissprot</span> <span class="o">=</span> <span class="kc">True</span><span class="p">):</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Returns orthology translation table as dict from UniProt to Uniprot,</span>
+<span class="sd">    obtained from NCBI HomoloGene data. Uses RefSeq and Entrez IDs for</span>
+<span class="sd">    translation.</span>
+
+<span class="sd">    Args</span>
+<span class="sd">        source (int): NCBI Taxonomy ID of the source species (keys).</span>
+<span class="sd">        target(int): NCBI Taxonomy ID of the target species (values).</span>
+<span class="sd">        only_swissprot (bool): Use only SwissProt IDs.</span>
+
+<span class="sd">    Returns</span>
+<span class="sd">        Dict of sets: keys are UniProt IDs of the source organism, values</span>
+<span class="sd">        are sets of UniProt IDs of the target organism.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="n">result</span> <span class="o">=</span> <span class="p">{}</span>
+
+    <span class="n">hge</span> <span class="o">=</span> <span class="n">homologene_dict</span><span class="p">(</span><span class="n">source</span><span class="p">,</span> <span class="n">target</span><span class="p">,</span> <span class="s1">&#39;entrez&#39;</span><span class="p">)</span>
+    <span class="n">hgr</span> <span class="o">=</span> <span class="n">homologene_dict</span><span class="p">(</span><span class="n">source</span><span class="p">,</span> <span class="n">target</span><span class="p">,</span> <span class="s1">&#39;refseq&#39;</span><span class="p">)</span>
+
+    <span class="n">all_source</span> <span class="o">=</span> <span class="nb">set</span><span class="p">(</span><span class="n">uniprot_db</span><span class="o">.</span><span class="n">all_uniprots</span><span class="p">(</span>
+        <span class="n">organism</span> <span class="o">=</span> <span class="n">source</span><span class="p">,</span>
+        <span class="n">swissprot</span> <span class="o">=</span> <span class="s1">&#39;YES&#39;</span><span class="p">,</span>
+    <span class="p">))</span>
+
+    <span class="k">if</span> <span class="ow">not</span> <span class="n">only_swissprot</span><span class="p">:</span>
+
+        <span class="n">all_source_trembl</span> <span class="o">=</span> <span class="n">uniprot_db</span><span class="o">.</span><span class="n">all_uniprots</span><span class="p">(</span>
+            <span class="n">organism</span> <span class="o">=</span> <span class="n">source</span><span class="p">,</span>
+            <span class="n">swissprot</span> <span class="o">=</span> <span class="s1">&#39;NO&#39;</span><span class="p">,</span>
+        <span class="p">)</span>
+        <span class="n">all_source</span><span class="o">.</span><span class="n">update</span><span class="p">(</span><span class="nb">set</span><span class="p">(</span><span class="n">all_source_trembl</span><span class="p">))</span>
+
+    <span class="k">for</span> <span class="n">u</span> <span class="ow">in</span> <span class="n">all_source</span><span class="p">:</span>
+
+        <span class="n">source_e</span> <span class="o">=</span> <span class="n">mapping</span><span class="o">.</span><span class="n">map_name</span><span class="p">(</span><span class="n">u</span><span class="p">,</span> <span class="s1">&#39;uniprot&#39;</span><span class="p">,</span> <span class="s1">&#39;entrez&#39;</span><span class="p">,</span> <span class="n">source</span><span class="p">)</span>
+        <span class="n">source_r</span> <span class="o">=</span> <span class="n">mapping</span><span class="o">.</span><span class="n">map_name</span><span class="p">(</span><span class="n">u</span><span class="p">,</span> <span class="s1">&#39;uniprot&#39;</span><span class="p">,</span> <span class="s1">&#39;refseqp&#39;</span><span class="p">,</span> <span class="n">source</span><span class="p">)</span>
+        <span class="n">target_u</span> <span class="o">=</span> <span class="nb">set</span><span class="p">()</span>
+        <span class="n">target_r</span> <span class="o">=</span> <span class="nb">set</span><span class="p">()</span>
+        <span class="n">target_e</span> <span class="o">=</span> <span class="nb">set</span><span class="p">()</span>
+
+        <span class="k">for</span> <span class="n">e</span> <span class="ow">in</span> <span class="n">source_e</span><span class="p">:</span>
+
+            <span class="k">if</span> <span class="n">e</span> <span class="ow">in</span> <span class="n">hge</span><span class="p">:</span>
+
+                <span class="n">target_e</span><span class="o">.</span><span class="n">update</span><span class="p">(</span><span class="n">hge</span><span class="p">[</span><span class="n">e</span><span class="p">])</span>
+
+        <span class="k">for</span> <span class="n">r</span> <span class="ow">in</span> <span class="n">source_r</span><span class="p">:</span>
+
+            <span class="k">if</span> <span class="n">r</span> <span class="ow">in</span> <span class="n">hgr</span><span class="p">:</span>
+
+                <span class="n">target_r</span><span class="o">.</span><span class="n">update</span><span class="p">(</span><span class="n">hgr</span><span class="p">[</span><span class="n">r</span><span class="p">])</span>
+
+        <span class="k">for</span> <span class="n">e</span> <span class="ow">in</span> <span class="n">target_e</span><span class="p">:</span>
+
+            <span class="n">target_u</span><span class="o">.</span><span class="n">update</span><span class="p">(</span>
+                <span class="n">mapping</span><span class="o">.</span><span class="n">map_name</span><span class="p">(</span><span class="n">e</span><span class="p">,</span> <span class="s1">&#39;entrez&#39;</span><span class="p">,</span> <span class="s1">&#39;uniprot&#39;</span><span class="p">,</span> <span class="n">target</span><span class="p">)</span>
+            <span class="p">)</span>
+
+        <span class="k">for</span> <span class="n">r</span> <span class="ow">in</span> <span class="n">target_r</span><span class="p">:</span>
+
+            <span class="n">target_u</span><span class="o">.</span><span class="n">update</span><span class="p">(</span>
+                <span class="n">mapping</span><span class="o">.</span><span class="n">map_name</span><span class="p">(</span><span class="n">e</span><span class="p">,</span> <span class="s1">&#39;refseqp&#39;</span><span class="p">,</span> <span class="s1">&#39;uniprot&#39;</span><span class="p">,</span> <span class="n">target</span><span class="p">)</span>
+            <span class="p">)</span>
+
+
+        <span class="n">target_u</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="n">itertools</span><span class="o">.</span><span class="n">chain</span><span class="p">(</span>
+                <span class="o">*</span><span class="nb">map</span><span class="p">(</span>
+                    <span class="k">lambda</span> <span class="n">tu</span><span class="p">:</span>
+                        <span class="n">mapping</span><span class="o">.</span><span class="n">map_name</span><span class="p">(</span><span class="n">tu</span><span class="p">,</span> <span class="s1">&#39;uniprot&#39;</span><span class="p">,</span> <span class="s1">&#39;uniprot&#39;</span><span class="p">,</span> <span class="n">target</span><span class="p">),</span>
+                    <span class="n">target_u</span>
+                <span class="p">)</span>
+            <span class="p">)</span>
+        <span class="p">)</span>
+
+        <span class="n">result</span><span class="p">[</span><span class="n">u</span><span class="p">]</span> <span class="o">=</span> <span class="nb">sorted</span><span class="p">(</span><span class="nb">list</span><span class="p">(</span><span class="n">target_u</span><span class="p">))</span>
+
+    <span class="k">return</span> <span class="n">result</span></div>
+
+</pre></div>
+
+                </article>
+              
+              
+              
+              
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+                  
+  <h1>Source code for pypath.inputs.hpmr</h1><div class="highlight"><pre>
+<span></span><span class="ch">#!/usr/bin/env python</span>
+<span class="c1"># -*- coding: utf-8 -*-</span>
+
+<span class="c1">#</span>
+<span class="c1">#  This file is part of the `pypath` python module</span>
+<span class="c1">#</span>
+<span class="c1">#  Copyright 2014-2023</span>
+<span class="c1">#  EMBL, EMBL-EBI, Uniklinik RWTH Aachen, Heidelberg University</span>
+<span class="c1">#</span>
+<span class="c1">#  Authors: see the file `README.rst`</span>
+<span class="c1">#  Contact: Dénes Türei (turei.denes@gmail.com)</span>
+<span class="c1">#</span>
+<span class="c1">#  Distributed under the GPLv3 License.</span>
+<span class="c1">#  See accompanying file LICENSE.txt or copy at</span>
+<span class="c1">#      https://www.gnu.org/licenses/gpl-3.0.html</span>
+<span class="c1">#</span>
+<span class="c1">#  Website: https://pypath.omnipathdb.org/</span>
+<span class="c1">#</span>
+
+<span class="kn">from</span> <span class="nn">future.utils</span> <span class="kn">import</span> <span class="n">iteritems</span>
+
+<span class="kn">import</span> <span class="nn">os</span>
+<span class="kn">import</span> <span class="nn">re</span>
+<span class="kn">import</span> <span class="nn">collections</span>
+<span class="kn">import</span> <span class="nn">itertools</span>
+<span class="kn">import</span> <span class="nn">shutil</span>
+
+<span class="k">try</span><span class="p">:</span>
+    <span class="kn">import</span> <span class="nn">cPickle</span> <span class="k">as</span> <span class="nn">pickle</span>
+<span class="k">except</span><span class="p">:</span>
+    <span class="kn">import</span> <span class="nn">pickle</span>
+
+<span class="kn">import</span> <span class="nn">bs4</span>
+
+<span class="kn">import</span> <span class="nn">pypath.share.curl</span> <span class="k">as</span> <span class="nn">curl</span>
+<span class="kn">import</span> <span class="nn">pypath.share.common</span> <span class="k">as</span> <span class="nn">common</span>
+<span class="kn">import</span> <span class="nn">pypath.share.progress</span> <span class="k">as</span> <span class="nn">progress</span>
+<span class="kn">import</span> <span class="nn">pypath.share.cache</span> <span class="k">as</span> <span class="nn">cache</span>
+<span class="kn">import</span> <span class="nn">pypath.share.settings</span> <span class="k">as</span> <span class="nn">settings</span>
+<span class="kn">import</span> <span class="nn">pypath.share.session</span> <span class="k">as</span> <span class="nn">session_mod</span>
+<span class="kn">import</span> <span class="nn">pypath.resources.urls</span> <span class="k">as</span> <span class="nn">urls</span>
+<span class="kn">import</span> <span class="nn">pypath.internals.intera</span> <span class="k">as</span> <span class="nn">intera</span>
+<span class="kn">import</span> <span class="nn">pypath.utils.mapping</span> <span class="k">as</span> <span class="nn">mapping</span>
+
+<span class="n">_logger</span> <span class="o">=</span> <span class="n">session_mod</span><span class="o">.</span><span class="n">Logger</span><span class="p">(</span><span class="n">name</span> <span class="o">=</span> <span class="s1">&#39;hpmr_input&#39;</span><span class="p">)</span>
+<span class="n">_log</span> <span class="o">=</span> <span class="n">_logger</span><span class="o">.</span><span class="n">_log</span>
+
+
+<span class="n">HpmrInteraction</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">namedtuple</span><span class="p">(</span>
+    <span class="s1">&#39;HpmrInteraction&#39;</span><span class="p">,</span>
+    <span class="p">(</span>
+        <span class="s1">&#39;receptor&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;partner_role&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;partner&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;references&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;unambiguous&#39;</span><span class="p">,</span>
+    <span class="p">),</span>
+<span class="p">)</span>
+
+
+<div class="viewcode-block" id="get_hpmr">
+<a class="viewcode-back" href="../../../api/pypath.inputs.hpmr.get_hpmr.html#pypath.inputs.hpmr.get_hpmr">[docs]</a>
+<span class="k">def</span> <span class="nf">get_hpmr</span><span class="p">(</span><span class="n">use_cache</span> <span class="o">=</span> <span class="kc">None</span><span class="p">):</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Downloads ligand-receptor and receptor-receptor interactions from the</span>
+<span class="sd">    Human Plasma Membrane Receptome database.</span>
+
+<span class="sd">    Args</span>
+<span class="sd">        use_cache (bool): Use the intermediate cache (pickle file of</span>
+<span class="sd">            processed data).</span>
+
+<span class="sd">    Returns</span>
+<span class="sd">        (dict): Two elements: &quot;interactions&quot; and &quot;families&quot;.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="k">def</span> <span class="nf">get_partner</span><span class="p">(</span><span class="n">interactors</span><span class="p">,</span> <span class="n">typ</span><span class="p">,</span> <span class="n">recname</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span> <span class="n">references</span> <span class="o">=</span> <span class="kc">None</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        typ : str</span>
+<span class="sd">            `Receptor` or `Ligand`.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">components</span> <span class="o">=</span> <span class="p">[</span><span class="n">i</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="n">interactors</span> <span class="k">if</span> <span class="n">i</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">==</span> <span class="n">typ</span><span class="p">]</span>
+
+        <span class="k">if</span> <span class="n">typ</span> <span class="o">==</span> <span class="s1">&#39;Receptor&#39;</span> <span class="ow">and</span> <span class="n">recname</span><span class="p">:</span>
+
+            <span class="n">components</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">recname</span><span class="p">)</span>
+
+        <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">components</span><span class="p">)</span> <span class="o">==</span> <span class="mi">1</span><span class="p">:</span>
+
+            <span class="k">return</span> <span class="n">components</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span>
+
+        <span class="k">elif</span> <span class="nb">len</span><span class="p">(</span><span class="n">components</span><span class="p">)</span> <span class="o">&gt;</span> <span class="mi">1</span><span class="p">:</span>
+
+            <span class="k">return</span> <span class="n">intera</span><span class="o">.</span><span class="n">Complex</span><span class="p">(</span>
+                <span class="n">components</span> <span class="o">=</span> <span class="n">components</span><span class="p">,</span>
+                <span class="n">sources</span> <span class="o">=</span> <span class="s1">&#39;HPMR&#39;</span><span class="p">,</span>
+                <span class="n">references</span> <span class="o">=</span> <span class="n">references</span><span class="p">,</span>
+            <span class="p">)</span>
+
+
+    <span class="n">cachefile</span> <span class="o">=</span> <span class="n">cache</span><span class="o">.</span><span class="n">cache_item</span><span class="p">(</span><span class="s1">&#39;hpmr_preprocessed&#39;</span><span class="p">)</span>
+    <span class="n">use_cache</span> <span class="o">=</span> <span class="p">(</span>
+        <span class="n">use_cache</span>
+            <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">use_cache</span><span class="p">,</span> <span class="nb">bool</span><span class="p">)</span> <span class="k">else</span>
+        <span class="n">settings</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">&#39;use_intermediate_cache&#39;</span><span class="p">)</span>
+    <span class="p">)</span>
+
+    <span class="k">if</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">exists</span><span class="p">(</span><span class="n">cachefile</span><span class="p">)</span> <span class="ow">and</span> <span class="n">use_cache</span><span class="p">:</span>
+
+        <span class="n">_log</span><span class="p">(</span><span class="s1">&#39;Reading HPMR data from cache file `</span><span class="si">%s</span><span class="s1">`.&#39;</span> <span class="o">%</span> <span class="n">cachefile</span><span class="p">)</span>
+
+        <span class="k">return</span> <span class="n">pickle</span><span class="o">.</span><span class="n">load</span><span class="p">(</span><span class="nb">open</span><span class="p">(</span><span class="n">cachefile</span><span class="p">,</span> <span class="s1">&#39;rb&#39;</span><span class="p">))</span>
+
+    <span class="n">rerecname</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">compile</span><span class="p">(</span><span class="sa">r</span><span class="s1">&#39;Receptor ([A-z0-9]+) interacts with:&#39;</span><span class="p">)</span>
+    <span class="n">reint</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">compile</span><span class="p">(</span><span class="sa">r</span><span class="s1">&#39;(Receptor|Ligand) ([A-z0-9]+) -&#39;</span><span class="p">)</span>
+    <span class="n">rerefid</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">compile</span><span class="p">(</span><span class="sa">r</span><span class="s1">&#39;list_uids=([- \.:,0-9A-z]+)&#39;</span><span class="p">)</span>
+    <span class="n">refamid</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">compile</span><span class="p">(</span><span class="sa">r</span><span class="s1">&#39;.*FamId=([0-9\.]+)&#39;</span><span class="p">)</span>
+
+    <span class="n">a_family_title</span> <span class="o">=</span> <span class="s1">&#39;Open Family Page&#39;</span>
+    <span class="n">a_receptor_title</span> <span class="o">=</span> <span class="s1">&#39;Open Receptor Page&#39;</span>
+    <span class="n">a_titles</span> <span class="o">=</span> <span class="p">{</span><span class="n">a_family_title</span><span class="p">,</span> <span class="n">a_receptor_title</span><span class="p">}</span>
+
+    <span class="n">interactions</span> <span class="o">=</span> <span class="p">[]</span>
+    <span class="n">families</span> <span class="o">=</span> <span class="p">{}</span>
+    <span class="n">complexes</span> <span class="o">=</span> <span class="nb">set</span><span class="p">()</span>
+    <span class="n">recpages</span> <span class="o">=</span> <span class="p">[]</span>
+
+    <span class="n">c</span> <span class="o">=</span> <span class="n">curl</span><span class="o">.</span><span class="n">Curl</span><span class="p">(</span><span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;hpmri&#39;</span><span class="p">][</span><span class="s1">&#39;browse_rescued&#39;</span><span class="p">])</span>
+    <span class="n">soup</span> <span class="o">=</span> <span class="n">bs4</span><span class="o">.</span><span class="n">BeautifulSoup</span><span class="p">(</span><span class="n">c</span><span class="o">.</span><span class="n">result</span><span class="p">,</span> <span class="s1">&#39;html.parser&#39;</span><span class="p">)</span>
+
+    <span class="n">this_family</span> <span class="o">=</span> <span class="p">(</span><span class="s1">&#39;0&#39;</span><span class="p">,</span> <span class="kc">None</span><span class="p">)</span>
+    <span class="n">this_subfamily</span> <span class="o">=</span> <span class="p">(</span><span class="s1">&#39;0&#39;</span><span class="p">,</span> <span class="kc">None</span><span class="p">)</span>
+    <span class="n">this_subsubfamily</span> <span class="o">=</span> <span class="p">(</span><span class="s1">&#39;0&#39;</span><span class="p">,</span> <span class="kc">None</span><span class="p">)</span>
+
+    <span class="k">for</span> <span class="n">a</span> <span class="ow">in</span> <span class="n">soup</span><span class="o">.</span><span class="n">find_all</span><span class="p">(</span><span class="s1">&#39;a&#39;</span><span class="p">):</span>
+
+        <span class="n">a_title</span> <span class="o">=</span> <span class="n">a</span><span class="o">.</span><span class="n">attrs</span><span class="p">[</span><span class="s1">&#39;title&#39;</span><span class="p">]</span> <span class="k">if</span> <span class="s1">&#39;title&#39;</span> <span class="ow">in</span> <span class="n">a</span><span class="o">.</span><span class="n">attrs</span> <span class="k">else</span> <span class="kc">None</span>
+
+        <span class="k">if</span> <span class="n">a_title</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">a_titles</span><span class="p">:</span>
+
+            <span class="k">continue</span>
+
+        <span class="k">if</span> <span class="n">a_title</span> <span class="o">==</span> <span class="n">a_family_title</span><span class="p">:</span>
+
+            <span class="n">family_id</span> <span class="o">=</span> <span class="n">refamid</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="n">a</span><span class="o">.</span><span class="n">attrs</span><span class="p">[</span><span class="s1">&#39;href&#39;</span><span class="p">])</span><span class="o">.</span><span class="n">groups</span><span class="p">()[</span><span class="mi">0</span><span class="p">]</span>
+
+            <span class="k">if</span> <span class="n">family_id</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="n">this_subfamily</span><span class="p">[</span><span class="mi">0</span><span class="p">]):</span>
+
+                <span class="n">this_subsubfamily</span> <span class="o">=</span> <span class="p">(</span><span class="n">family_id</span><span class="p">,</span> <span class="n">a</span><span class="o">.</span><span class="n">text</span><span class="p">)</span>
+
+            <span class="k">elif</span> <span class="n">family_id</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="n">this_family</span><span class="p">[</span><span class="mi">0</span><span class="p">]):</span>
+
+                <span class="n">this_subfamily</span> <span class="o">=</span> <span class="p">(</span><span class="n">family_id</span><span class="p">,</span> <span class="n">a</span><span class="o">.</span><span class="n">text</span><span class="p">)</span>
+                <span class="n">this_subsubfamily</span> <span class="o">=</span> <span class="p">(</span><span class="s1">&#39;0&#39;</span><span class="p">,</span> <span class="kc">None</span><span class="p">)</span>
+
+            <span class="k">else</span><span class="p">:</span>
+
+                <span class="n">this_family</span> <span class="o">=</span> <span class="p">(</span><span class="n">family_id</span><span class="p">,</span> <span class="n">a</span><span class="o">.</span><span class="n">text</span><span class="p">)</span>
+                <span class="n">this_subfamily</span> <span class="o">=</span> <span class="p">(</span><span class="s1">&#39;0&#39;</span><span class="p">,</span> <span class="kc">None</span><span class="p">)</span>
+                <span class="n">this_subsubfamily</span> <span class="o">=</span> <span class="p">(</span><span class="s1">&#39;0&#39;</span><span class="p">,</span> <span class="kc">None</span><span class="p">)</span>
+
+        <span class="k">elif</span> <span class="n">a_title</span> <span class="o">==</span> <span class="n">a_receptor_title</span><span class="p">:</span>
+
+            <span class="n">recpages</span><span class="o">.</span><span class="n">append</span><span class="p">((</span>
+                <span class="n">a</span><span class="o">.</span><span class="n">attrs</span><span class="p">[</span><span class="s1">&#39;href&#39;</span><span class="p">],</span>
+                <span class="n">this_family</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span>
+                <span class="n">this_subfamily</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span>
+                <span class="n">this_subsubfamily</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span>
+            <span class="p">))</span>
+
+    <span class="n">prg</span> <span class="o">=</span> <span class="n">progress</span><span class="o">.</span><span class="n">Progress</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">recpages</span><span class="p">),</span> <span class="s1">&#39;Downloading HPMR data&#39;</span><span class="p">,</span> <span class="mi">1</span><span class="p">)</span>
+
+    <span class="n">i_complex</span> <span class="o">=</span> <span class="mi">0</span>
+
+    <span class="n">regene</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">compile</span><span class="p">(</span><span class="sa">r</span><span class="s1">&#39;Param=([^&amp;]+)&amp;ProtId=(\d+)&amp;ProtType=(\w+)&#39;</span><span class="p">)</span>
+
+    <span class="n">genes_curl</span> <span class="o">=</span> <span class="n">curl</span><span class="o">.</span><span class="n">Curl</span><span class="p">(</span>
+        <span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;hpmri&#39;</span><span class="p">][</span><span class="s1">&#39;genes_rescued&#39;</span><span class="p">],</span>
+        <span class="n">silent</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+        <span class="n">large</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
+    <span class="p">)</span>
+
+    <span class="k">for</span> <span class="n">url</span><span class="p">,</span> <span class="n">family</span><span class="p">,</span> <span class="n">subfamily</span><span class="p">,</span> <span class="n">subsubfamily</span> <span class="ow">in</span> <span class="n">recpages</span><span class="p">:</span>
+
+        <span class="n">protein</span><span class="p">,</span> <span class="n">prot_id</span><span class="p">,</span> <span class="n">prot_type</span> <span class="o">=</span> <span class="n">regene</span><span class="o">.</span><span class="n">search</span><span class="p">(</span><span class="n">url</span><span class="p">)</span><span class="o">.</span><span class="n">groups</span><span class="p">()</span>
+        <span class="n">fname</span> <span class="o">=</span> <span class="s1">&#39;gene_</span><span class="si">%s</span><span class="s1">-</span><span class="si">%s</span><span class="s1">-</span><span class="si">%s</span><span class="s1">.html&#39;</span> <span class="o">%</span> <span class="p">(</span><span class="n">protein</span><span class="p">,</span> <span class="n">prot_id</span><span class="p">,</span> <span class="n">prot_type</span><span class="p">)</span>
+        <span class="n">prg</span><span class="o">.</span><span class="n">step</span><span class="p">(</span><span class="n">status</span> <span class="o">=</span> <span class="s1">&#39;Processing `</span><span class="si">%s</span><span class="s1">`&#39;</span> <span class="o">%</span> <span class="n">fname</span><span class="p">)</span>
+
+        <span class="n">_log</span><span class="p">(</span>
+            <span class="s1">&#39;Accessing `</span><span class="si">%s</span><span class="s1">` from `</span><span class="si">%s</span><span class="s1">` (</span><span class="si">%s</span><span class="s1">).&#39;</span> <span class="o">%</span> <span class="p">(</span>
+                <span class="n">fname</span><span class="p">,</span>
+                <span class="n">genes_curl</span><span class="o">.</span><span class="n">cache_file_name</span><span class="p">,</span>
+                <span class="n">genes_curl</span><span class="o">.</span><span class="n">url</span><span class="p">,</span>
+            <span class="p">)</span>
+        <span class="p">)</span>
+
+        <span class="k">if</span> <span class="n">fname</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">genes_curl</span><span class="o">.</span><span class="n">result</span><span class="p">:</span>
+
+            <span class="n">_log</span><span class="p">(</span><span class="s1">&#39;File `</span><span class="si">%s</span><span class="s1">` not found in the archive.&#39;</span> <span class="o">%</span> <span class="n">fname</span><span class="p">)</span>
+            <span class="k">continue</span>
+
+        <span class="n">soup</span> <span class="o">=</span> <span class="n">bs4</span><span class="o">.</span><span class="n">BeautifulSoup</span><span class="p">(</span>
+            <span class="n">genes_curl</span><span class="o">.</span><span class="n">result</span><span class="p">[</span><span class="n">fname</span><span class="p">]</span><span class="o">.</span><span class="n">read</span><span class="p">(),</span>
+            <span class="s1">&#39;html.parser&#39;</span><span class="p">,</span>
+        <span class="p">)</span>
+        <span class="n">ints</span> <span class="o">=</span> <span class="n">soup</span><span class="o">.</span><span class="n">find</span><span class="p">(</span><span class="s1">&#39;div&#39;</span><span class="p">,</span> <span class="p">{</span><span class="s1">&#39;id&#39;</span><span class="p">:</span> <span class="s1">&#39;GeneInts&#39;</span><span class="p">})</span>
+
+        <span class="k">if</span> <span class="ow">not</span> <span class="n">ints</span><span class="p">:</span>
+
+            <span class="n">_log</span><span class="p">(</span><span class="s1">&#39;No interactions: `</span><span class="si">%s</span><span class="s1">`&#39;</span> <span class="o">%</span> <span class="n">url</span><span class="p">)</span>
+            <span class="k">continue</span>
+
+        <span class="n">recname</span> <span class="o">=</span> <span class="n">rerecname</span><span class="o">.</span><span class="n">search</span><span class="p">(</span>
+            <span class="n">ints</span><span class="o">.</span><span class="n">find_previous_sibling</span><span class="p">(</span><span class="s1">&#39;span&#39;</span><span class="p">)</span><span class="o">.</span><span class="n">text</span>
+        <span class="p">)</span>
+        <span class="n">recname</span> <span class="o">=</span> <span class="n">recname</span><span class="o">.</span><span class="n">groups</span><span class="p">()[</span><span class="mi">0</span><span class="p">]</span> <span class="k">if</span> <span class="n">recname</span> <span class="k">else</span> <span class="s1">&#39;Unknown&#39;</span>
+
+        <span class="k">if</span> <span class="n">recname</span> <span class="o">==</span> <span class="s1">&#39;Unknown&#39;</span><span class="p">:</span>
+
+            <span class="n">_log</span><span class="p">(</span><span class="s1">&#39;Could not find receptor name: `</span><span class="si">%s</span><span class="s1">`&#39;</span> <span class="o">%</span> <span class="n">url</span><span class="p">)</span>
+            <span class="k">continue</span>
+
+        <span class="n">recname_u</span> <span class="o">=</span> <span class="n">mapping</span><span class="o">.</span><span class="n">map_name0</span><span class="p">(</span><span class="n">recname</span><span class="p">,</span> <span class="s1">&#39;genesymbol&#39;</span><span class="p">,</span> <span class="s1">&#39;uniprot&#39;</span><span class="p">)</span>
+
+        <span class="k">if</span> <span class="ow">not</span> <span class="n">recname_u</span><span class="p">:</span>
+
+            <span class="k">continue</span>
+
+        <span class="n">families</span><span class="p">[</span><span class="n">recname_u</span><span class="p">]</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="n">family</span><span class="p">,</span>
+            <span class="n">subfamily</span><span class="p">,</span>
+            <span class="n">subsubfamily</span><span class="p">,</span>
+        <span class="p">)</span>
+
+        <span class="k">for</span> <span class="n">td</span> <span class="ow">in</span> <span class="n">ints</span><span class="o">.</span><span class="n">find_all</span><span class="p">(</span><span class="s1">&#39;td&#39;</span><span class="p">):</span>
+
+            <span class="n">interactors</span> <span class="o">=</span> <span class="p">[]</span>
+
+            <span class="k">for</span> <span class="n">span</span> <span class="ow">in</span> <span class="n">td</span><span class="o">.</span><span class="n">find_all</span><span class="p">(</span><span class="s1">&#39;span&#39;</span><span class="p">,</span> <span class="p">{</span><span class="s1">&#39;class&#39;</span><span class="p">:</span> <span class="s1">&#39;IntRow&#39;</span><span class="p">}):</span>
+
+                <span class="n">ints</span> <span class="o">=</span> <span class="n">reint</span><span class="o">.</span><span class="n">search</span><span class="p">(</span><span class="n">span</span><span class="o">.</span><span class="n">text</span><span class="p">)</span>
+
+                <span class="k">if</span> <span class="n">ints</span><span class="p">:</span>
+
+                    <span class="n">interactors</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">ints</span><span class="o">.</span><span class="n">groups</span><span class="p">())</span>
+
+            <span class="n">references</span> <span class="o">=</span> <span class="p">[]</span>
+
+            <span class="k">for</span> <span class="n">ref</span> <span class="ow">in</span> <span class="n">td</span><span class="o">.</span><span class="n">find_all</span><span class="p">(</span>
+                <span class="s1">&#39;a&#39;</span><span class="p">,</span> <span class="p">{</span><span class="s1">&#39;title&#39;</span><span class="p">:</span> <span class="s1">&#39;click to open reference in new window&#39;</span><span class="p">}</span>
+            <span class="p">):</span>
+
+                <span class="n">references</span><span class="o">.</span><span class="n">append</span><span class="p">(</span>
+                    <span class="n">rerefid</span><span class="o">.</span><span class="n">search</span><span class="p">(</span><span class="n">ref</span><span class="o">.</span><span class="n">attrs</span><span class="p">[</span><span class="s1">&#39;href&#39;</span><span class="p">])</span><span class="o">.</span><span class="n">groups</span><span class="p">()[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span>
+                <span class="p">)</span>
+
+            <span class="n">interactors_u</span> <span class="o">=</span> <span class="p">[]</span>
+
+            <span class="k">for</span> <span class="n">role</span><span class="p">,</span> <span class="n">genesymbol</span> <span class="ow">in</span> <span class="n">interactors</span><span class="p">:</span>
+
+                <span class="n">uniprot</span> <span class="o">=</span> <span class="p">(</span>
+                    <span class="n">mapping</span><span class="o">.</span><span class="n">map_name0</span><span class="p">(</span><span class="n">genesymbol</span><span class="p">,</span> <span class="s1">&#39;genesymbol&#39;</span><span class="p">,</span> <span class="s1">&#39;uniprot&#39;</span><span class="p">)</span>
+                <span class="p">)</span>
+
+                <span class="k">if</span> <span class="n">uniprot</span><span class="p">:</span>
+
+                    <span class="n">interactors_u</span><span class="o">.</span><span class="n">append</span><span class="p">((</span><span class="n">role</span><span class="p">,</span> <span class="n">uniprot</span><span class="p">))</span>
+
+            <span class="n">partner_role</span> <span class="o">=</span> <span class="p">(</span>
+                <span class="s1">&#39;receptor&#39;</span>
+                    <span class="k">if</span> <span class="nb">all</span><span class="p">(</span><span class="n">i</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">==</span> <span class="s1">&#39;Receptor&#39;</span> <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="n">interactors_u</span><span class="p">)</span> <span class="k">else</span>
+                <span class="s1">&#39;ligand&#39;</span>
+            <span class="p">)</span>
+
+            <span class="n">receptors</span> <span class="o">=</span> <span class="p">(</span>
+                <span class="n">recname_u</span>
+                    <span class="k">if</span> <span class="n">partner_role</span> <span class="o">==</span> <span class="s1">&#39;receptor&#39;</span> <span class="k">else</span>
+                <span class="n">get_partner</span><span class="p">(</span>
+                    <span class="n">interactors_u</span><span class="p">,</span>
+                    <span class="s1">&#39;Receptor&#39;</span><span class="p">,</span>
+                    <span class="n">recname</span> <span class="o">=</span> <span class="n">recname_u</span><span class="p">,</span>
+                    <span class="n">references</span> <span class="o">=</span> <span class="n">references</span><span class="p">,</span>
+                <span class="p">)</span>
+            <span class="p">)</span>
+
+            <span class="n">partners</span> <span class="o">=</span> <span class="p">(</span>
+                <span class="p">{</span><span class="n">u</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="k">for</span> <span class="n">u</span> <span class="ow">in</span> <span class="n">interactors_u</span><span class="p">}</span> <span class="o">-</span> <span class="p">{</span><span class="n">recname_u</span><span class="p">}</span>
+                    <span class="k">if</span> <span class="n">partner_role</span> <span class="o">==</span> <span class="s1">&#39;receptor&#39;</span> <span class="k">else</span>
+                <span class="n">get_partner</span><span class="p">(</span>
+                    <span class="n">interactors_u</span><span class="p">,</span>
+                    <span class="s1">&#39;Ligand&#39;</span><span class="p">,</span>
+                    <span class="n">references</span> <span class="o">=</span> <span class="n">references</span><span class="p">,</span>
+                <span class="p">)</span>
+            <span class="p">)</span>
+
+            <span class="n">receptors</span> <span class="o">=</span> <span class="n">common</span><span class="o">.</span><span class="n">to_list</span><span class="p">(</span><span class="n">receptors</span><span class="p">)</span>
+            <span class="n">partners</span> <span class="o">=</span> <span class="n">common</span><span class="o">.</span><span class="n">to_list</span><span class="p">(</span><span class="n">partners</span><span class="p">)</span>
+
+            <span class="n">unambiguous</span> <span class="o">=</span> <span class="p">(</span>
+                <span class="n">partner_role</span> <span class="o">==</span> <span class="s1">&#39;ligand&#39;</span> <span class="ow">or</span>
+                <span class="p">(</span>
+                    <span class="nb">len</span><span class="p">(</span><span class="n">receptors</span><span class="p">)</span> <span class="o">==</span> <span class="mi">1</span> <span class="ow">and</span>
+                    <span class="nb">len</span><span class="p">(</span><span class="n">partners</span><span class="p">)</span> <span class="o">==</span> <span class="mi">1</span>
+                <span class="p">)</span>
+            <span class="p">)</span>
+
+            <span class="k">for</span> <span class="n">receptor</span><span class="p">,</span> <span class="n">partner</span> <span class="ow">in</span> <span class="n">itertools</span><span class="o">.</span><span class="n">product</span><span class="p">(</span><span class="n">receptors</span><span class="p">,</span> <span class="n">partners</span><span class="p">):</span>
+
+                <span class="n">interactions</span><span class="o">.</span><span class="n">append</span><span class="p">(</span>
+                    <span class="n">HpmrInteraction</span><span class="p">(</span>
+                        <span class="n">receptor</span> <span class="o">=</span> <span class="n">receptor</span><span class="p">,</span>
+                        <span class="n">partner</span> <span class="o">=</span> <span class="n">partner</span><span class="p">,</span>
+                        <span class="n">partner_role</span> <span class="o">=</span> <span class="n">partner_role</span><span class="p">,</span>
+                        <span class="n">references</span> <span class="o">=</span> <span class="s1">&#39;;&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">references</span><span class="p">),</span>
+                        <span class="n">unambiguous</span> <span class="o">=</span> <span class="n">unambiguous</span><span class="p">,</span>
+                    <span class="p">)</span>
+                <span class="p">)</span>
+
+            <span class="k">for</span> <span class="n">entity</span> <span class="ow">in</span> <span class="n">itertools</span><span class="o">.</span><span class="n">chain</span><span class="p">(</span><span class="n">receptors</span><span class="p">,</span> <span class="n">partners</span><span class="p">):</span>
+
+                <span class="k">if</span> <span class="nb">hasattr</span><span class="p">(</span><span class="n">entity</span><span class="p">,</span> <span class="s1">&#39;components&#39;</span><span class="p">):</span>
+
+                    <span class="n">complexes</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">entity</span><span class="p">)</span>
+
+    <span class="n">prg</span><span class="o">.</span><span class="n">terminate</span><span class="p">()</span>
+
+    <span class="n">result</span> <span class="o">=</span> <span class="p">{</span>
+        <span class="s1">&#39;interactions&#39;</span><span class="p">:</span> <span class="n">interactions</span><span class="p">,</span>
+        <span class="s1">&#39;families&#39;</span><span class="p">:</span> <span class="n">families</span><span class="p">,</span>
+    <span class="p">}</span>
+
+    <span class="n">_log</span><span class="p">(</span><span class="s1">&#39;Saving HPMR data to cache file `</span><span class="si">%s</span><span class="s1">`.&#39;</span> <span class="o">%</span> <span class="n">cachefile</span><span class="p">)</span>
+    <span class="n">pickle</span><span class="o">.</span><span class="n">dump</span><span class="p">(</span><span class="n">result</span><span class="p">,</span> <span class="nb">open</span><span class="p">(</span><span class="n">cachefile</span><span class="p">,</span> <span class="s1">&#39;wb&#39;</span><span class="p">))</span>
+
+    <span class="k">return</span> <span class="n">result</span></div>
+
+
+
+<div class="viewcode-block" id="hpmr_complexes">
+<a class="viewcode-back" href="../../../api/pypath.inputs.hpmr.hpmr_complexes.html#pypath.inputs.hpmr.hpmr_complexes">[docs]</a>
+<span class="k">def</span> <span class="nf">hpmr_complexes</span><span class="p">(</span><span class="n">use_cache</span> <span class="o">=</span> <span class="kc">None</span><span class="p">):</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    HPMR does not contain unambiguous protein complex data, and considering</span>
+<span class="sd">    the resource is unmaintained, probably it never will. Hence this function</span>
+<span class="sd">    always returns an empty dict.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="n">hpmr_data</span> <span class="o">=</span> <span class="n">get_hpmr</span><span class="p">(</span><span class="n">use_cache</span> <span class="o">=</span> <span class="n">use_cache</span><span class="p">)</span>
+
+    <span class="n">complexes</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">(</span>
+        <span class="p">(</span>
+            <span class="n">cplex</span><span class="o">.</span><span class="fm">__str__</span><span class="p">(),</span>
+            <span class="n">cplex</span><span class="p">,</span>
+        <span class="p">)</span>
+        <span class="k">for</span> <span class="n">cplex</span> <span class="ow">in</span> <span class="n">hpmr_data</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">&#39;complexes&#39;</span><span class="p">,</span> <span class="p">())</span>
+    <span class="p">)</span>
+
+    <span class="k">return</span> <span class="n">complexes</span></div>
+
+
+
+<div class="viewcode-block" id="hpmr_interactions">
+<a class="viewcode-back" href="../../../api/pypath.inputs.hpmr.hpmr_interactions.html#pypath.inputs.hpmr.hpmr_interactions">[docs]</a>
+<span class="k">def</span> <span class="nf">hpmr_interactions</span><span class="p">(</span><span class="n">use_cache</span> <span class="o">=</span> <span class="kc">None</span><span class="p">):</span>
+
+    <span class="n">hpmr_data</span> <span class="o">=</span> <span class="n">get_hpmr</span><span class="p">(</span><span class="n">use_cache</span> <span class="o">=</span> <span class="n">use_cache</span><span class="p">)</span>
+
+    <span class="k">return</span> <span class="n">hpmr_data</span><span class="p">[</span><span class="s1">&#39;interactions&#39;</span><span class="p">]</span></div>
+
+
+
+<div class="viewcode-block" id="hpmr_annotations">
+<a class="viewcode-back" href="../../../api/pypath.inputs.hpmr.hpmr_annotations.html#pypath.inputs.hpmr.hpmr_annotations">[docs]</a>
+<span class="k">def</span> <span class="nf">hpmr_annotations</span><span class="p">(</span><span class="n">use_cache</span> <span class="o">=</span> <span class="kc">None</span><span class="p">):</span>
+
+    <span class="n">annot</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">defaultdict</span><span class="p">(</span><span class="nb">set</span><span class="p">)</span>
+
+    <span class="n">HPMRAnnotation</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">namedtuple</span><span class="p">(</span>
+        <span class="s1">&#39;HPMRAnnotation&#39;</span><span class="p">,</span>
+        <span class="p">(</span><span class="s1">&#39;role&#39;</span><span class="p">,</span> <span class="s1">&#39;mainclass&#39;</span><span class="p">,</span> <span class="s1">&#39;subclass&#39;</span><span class="p">,</span> <span class="s1">&#39;subsubclass&#39;</span><span class="p">),</span>
+    <span class="p">)</span>
+
+    <span class="n">hpmr_data</span> <span class="o">=</span> <span class="n">get_hpmr</span><span class="p">(</span><span class="n">use_cache</span> <span class="o">=</span> <span class="n">use_cache</span><span class="p">)</span>
+
+    <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="n">hpmr_data</span><span class="p">[</span><span class="s1">&#39;interactions&#39;</span><span class="p">]:</span>
+
+        <span class="c1"># first partner is always a receptor</span>
+        <span class="c1"># (because ligand pages simply don&#39;t work on HPMR webpage)</span>
+        <span class="n">args1</span> <span class="o">=</span> <span class="p">(</span><span class="s1">&#39;Receptor&#39;</span><span class="p">,)</span> <span class="o">+</span> <span class="p">(</span>
+            <span class="n">hpmr_data</span><span class="p">[</span><span class="s1">&#39;families&#39;</span><span class="p">][</span><span class="n">i</span><span class="p">[</span><span class="mi">0</span><span class="p">]]</span>
+                <span class="k">if</span> <span class="n">i</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="ow">in</span> <span class="n">hpmr_data</span><span class="p">[</span><span class="s1">&#39;families&#39;</span><span class="p">]</span> <span class="k">else</span>
+            <span class="p">(</span><span class="kc">None</span><span class="p">,</span> <span class="kc">None</span><span class="p">,</span> <span class="kc">None</span><span class="p">)</span>
+        <span class="p">)</span>
+
+        <span class="c1"># the second is either a ligand or another receptor</span>
+        <span class="n">args2</span> <span class="o">=</span> <span class="p">(</span><span class="n">i</span><span class="p">[</span><span class="mi">1</span><span class="p">],)</span> <span class="o">+</span> <span class="p">(</span>
+            <span class="n">hpmr_data</span><span class="p">[</span><span class="s1">&#39;families&#39;</span><span class="p">][</span><span class="n">i</span><span class="p">[</span><span class="mi">2</span><span class="p">]]</span>
+                <span class="k">if</span> <span class="n">i</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="ow">in</span> <span class="n">hpmr_data</span><span class="p">[</span><span class="s1">&#39;families&#39;</span><span class="p">]</span> <span class="k">else</span>
+            <span class="p">(</span><span class="kc">None</span><span class="p">,</span> <span class="kc">None</span><span class="p">,</span> <span class="kc">None</span><span class="p">)</span>
+        <span class="p">)</span>
+
+        <span class="n">annot</span><span class="p">[</span><span class="n">i</span><span class="p">[</span><span class="mi">0</span><span class="p">]]</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">HPMRAnnotation</span><span class="p">(</span><span class="o">*</span><span class="n">args1</span><span class="p">))</span>
+        <span class="n">annot</span><span class="p">[</span><span class="n">i</span><span class="p">[</span><span class="mi">2</span><span class="p">]]</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">HPMRAnnotation</span><span class="p">(</span><span class="o">*</span><span class="n">args2</span><span class="p">))</span>
+
+    <span class="k">for</span> <span class="n">uniprot</span><span class="p">,</span> <span class="n">classes</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="n">hpmr_data</span><span class="p">[</span><span class="s1">&#39;families&#39;</span><span class="p">]):</span>
+
+        <span class="n">args</span> <span class="o">=</span> <span class="p">(</span><span class="s1">&#39;Receptor&#39;</span><span class="p">,)</span> <span class="o">+</span> <span class="n">classes</span>
+
+        <span class="n">annot</span><span class="p">[</span><span class="n">uniprot</span><span class="p">]</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">HPMRAnnotation</span><span class="p">(</span><span class="o">*</span><span class="n">args</span><span class="p">))</span>
+
+    <span class="k">return</span> <span class="nb">dict</span><span class="p">(</span><span class="n">annot</span><span class="p">)</span></div>
+
+</pre></div>
+
+                </article>
+              
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diff --git a/_modules/pypath/inputs/hpo.html b/_modules/pypath/inputs/hpo.html
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@@ -0,0 +1,819 @@
+
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+
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+                  
+  <h1>Source code for pypath.inputs.hpo</h1><div class="highlight"><pre>
+<span></span><span class="ch">#!/usr/bin/env python</span>
+<span class="c1"># -*- coding: utf-8 -*-</span>
+
+<span class="c1">#</span>
+<span class="c1">#  This file is part of the `pypath` python module</span>
+<span class="c1">#</span>
+<span class="c1">#  Copyright 2014-2023</span>
+<span class="c1">#  EMBL, EMBL-EBI, Uniklinik RWTH Aachen, Heidelberg University</span>
+<span class="c1">#</span>
+<span class="c1">#  Authors: see the file `README.rst`</span>
+<span class="c1">#  Contact: Dénes Türei (turei.denes@gmail.com)</span>
+<span class="c1">#</span>
+<span class="c1">#  Distributed under the GPLv3 License.</span>
+<span class="c1">#  See accompanying file LICENSE.txt or copy at</span>
+<span class="c1">#      https://www.gnu.org/licenses/gpl-3.0.html</span>
+<span class="c1">#</span>
+<span class="c1">#  Website: https://pypath.omnipathdb.org/</span>
+<span class="c1">#</span>
+
+<span class="kn">from</span> <span class="nn">typing</span> <span class="kn">import</span> <span class="n">Union</span>
+
+<span class="kn">import</span> <span class="nn">re</span>
+<span class="kn">import</span> <span class="nn">collections</span>
+
+<span class="kn">import</span> <span class="nn">pypath.utils.mapping</span> <span class="k">as</span> <span class="nn">mapping</span>
+<span class="kn">import</span> <span class="nn">pypath.share.curl</span> <span class="k">as</span> <span class="nn">curl</span>
+<span class="kn">import</span> <span class="nn">pypath.resources.urls</span> <span class="k">as</span> <span class="nn">urls</span>
+<span class="kn">import</span> <span class="nn">pypath.formats.obo</span> <span class="k">as</span> <span class="nn">obo</span>
+
+
+<div class="viewcode-block" id="hpo_annotations">
+<a class="viewcode-back" href="../../../api/pypath.inputs.hpo.hpo_annotations.html#pypath.inputs.hpo.hpo_annotations">[docs]</a>
+<span class="k">def</span> <span class="nf">hpo_annotations</span><span class="p">()</span> <span class="o">-&gt;</span> <span class="nb">dict</span><span class="p">[</span><span class="nb">str</span><span class="p">,</span> <span class="nb">set</span><span class="p">[</span><span class="nb">tuple</span><span class="p">]]:</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Human Phenotype Ontology annotations.</span>
+
+<span class="sd">    Returns</span>
+<span class="sd">        Dict of proteins as keys and sets of HPO annotations as values.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="n">url</span> <span class="o">=</span> <span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;hpo&#39;</span><span class="p">][</span><span class="s1">&#39;gene&#39;</span><span class="p">]</span>
+    <span class="n">c</span> <span class="o">=</span> <span class="n">curl</span><span class="o">.</span><span class="n">Curl</span><span class="p">(</span><span class="n">url</span><span class="p">,</span> <span class="n">large</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span> <span class="n">silent</span> <span class="o">=</span> <span class="kc">False</span><span class="p">)</span>
+    <span class="n">_</span> <span class="o">=</span> <span class="nb">next</span><span class="p">(</span><span class="n">c</span><span class="o">.</span><span class="n">result</span><span class="p">)</span>
+
+    <span class="n">fields</span> <span class="o">=</span> <span class="p">(</span><span class="s1">&#39;entrez_gene_id&#39;</span><span class="p">,</span><span class="s1">&#39;entrez_gene_symbol&#39;</span><span class="p">,</span><span class="s1">&#39;hpo_id&#39;</span><span class="p">)</span>
+
+    <span class="n">HpoAnnotation</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">namedtuple</span><span class="p">(</span>
+        <span class="s1">&#39;HpoAnnotation&#39;</span><span class="p">,</span>
+        <span class="n">fields</span><span class="p">,</span><span class="n">defaults</span> <span class="o">=</span> <span class="p">(</span><span class="s2">&quot;&quot;</span><span class="p">,)</span> <span class="o">*</span> <span class="nb">len</span><span class="p">(</span><span class="n">fields</span><span class="p">)</span>
+    <span class="p">)</span>
+
+    <span class="n">result</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">defaultdict</span><span class="p">(</span><span class="nb">set</span><span class="p">)</span>
+
+    <span class="k">for</span> <span class="n">r</span> <span class="ow">in</span> <span class="n">c</span><span class="o">.</span><span class="n">result</span><span class="p">:</span>
+
+        <span class="n">r</span> <span class="o">=</span> <span class="n">r</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\t</span><span class="s1">&#39;</span><span class="p">)</span>
+
+        <span class="n">uniprots</span> <span class="o">=</span> <span class="n">mapping</span><span class="o">.</span><span class="n">map_name</span><span class="p">(</span><span class="n">r</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="s1">&#39;entrez&#39;</span><span class="p">,</span> <span class="s1">&#39;uniprot&#39;</span><span class="p">)</span>
+
+        <span class="k">for</span> <span class="n">uniprot</span> <span class="ow">in</span> <span class="n">uniprots</span><span class="p">:</span>
+
+            <span class="n">result</span><span class="p">[</span><span class="n">uniprot</span><span class="p">]</span><span class="o">.</span><span class="n">add</span><span class="p">(</span>
+                <span class="n">HpoAnnotation</span><span class="p">(</span>
+                    <span class="n">entrez_gene_id</span> <span class="o">=</span> <span class="n">r</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span>
+                    <span class="n">entrez_gene_symbol</span> <span class="o">=</span> <span class="n">r</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span>
+                    <span class="n">hpo_id</span> <span class="o">=</span> <span class="n">r</span><span class="p">[</span><span class="mi">2</span><span class="p">],</span>
+                <span class="p">)</span>
+            <span class="p">)</span>
+
+    <span class="k">return</span> <span class="nb">dict</span><span class="p">(</span><span class="n">result</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="hpo_terms">
+<a class="viewcode-back" href="../../../api/pypath.inputs.hpo.hpo_terms.html#pypath.inputs.hpo.hpo_terms">[docs]</a>
+<span class="k">def</span> <span class="nf">hpo_terms</span><span class="p">()</span> <span class="o">-&gt;</span> <span class="nb">dict</span><span class="p">[</span><span class="nb">str</span><span class="p">,</span> <span class="nb">str</span><span class="p">]:</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Human Phenotype Ontology accession to term mapping.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="k">return</span> <span class="n">hpo_ontology</span><span class="p">()[</span><span class="s1">&#39;terms&#39;</span><span class="p">]</span></div>
+
+
+
+<div class="viewcode-block" id="hpo_diseases">
+<a class="viewcode-back" href="../../../api/pypath.inputs.hpo.hpo_diseases.html#pypath.inputs.hpo.hpo_diseases">[docs]</a>
+<span class="k">def</span> <span class="nf">hpo_diseases</span><span class="p">()</span> <span class="o">-&gt;</span> <span class="nb">dict</span><span class="p">[</span><span class="nb">str</span><span class="p">,</span> <span class="nb">set</span><span class="p">[</span><span class="nb">tuple</span><span class="p">]]:</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    HPO term-disease relationships from Human Phenotype Ontology.</span>
+
+<span class="sd">    Returns</span>
+<span class="sd">        A set of disease records for each HPO term.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="n">url</span> <span class="o">=</span> <span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;hpo&#39;</span><span class="p">][</span><span class="s1">&#39;disease&#39;</span><span class="p">]</span>
+    <span class="n">c</span> <span class="o">=</span> <span class="n">curl</span><span class="o">.</span><span class="n">Curl</span><span class="p">(</span><span class="n">url</span><span class="p">,</span> <span class="n">large</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span> <span class="n">silent</span> <span class="o">=</span> <span class="kc">False</span><span class="p">)</span>
+
+    <span class="n">HpoDisease</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">namedtuple</span><span class="p">(</span>
+        <span class="s1">&#39;HpoDisease&#39;</span><span class="p">,</span>
+        <span class="p">(</span>
+            <span class="s1">&#39;omim&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;name&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;pmid&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;qualifier&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;evidence&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;onset&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;frequency&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;sex&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;modifier&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;aspect&#39;</span><span class="p">,</span>
+        <span class="p">),</span>
+    <span class="p">)</span>
+
+    <span class="n">result</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">defaultdict</span><span class="p">(</span><span class="nb">set</span><span class="p">)</span>
+
+    <span class="k">for</span> <span class="n">r</span> <span class="ow">in</span> <span class="n">c</span><span class="o">.</span><span class="n">result</span><span class="p">:</span>
+
+        <span class="k">if</span> <span class="n">r</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">==</span> <span class="s1">&#39;#&#39;</span><span class="p">:</span> <span class="k">continue</span>
+
+        <span class="n">r</span> <span class="o">=</span> <span class="n">r</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\t</span><span class="s1">&#39;</span><span class="p">)</span>
+
+        <span class="n">pmid</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">sub</span><span class="p">(</span><span class="s1">&#39;^PMID:&#39;</span><span class="p">,</span> <span class="s1">&#39;&#39;</span><span class="p">,</span> <span class="n">r</span><span class="p">[</span><span class="mi">4</span><span class="p">])</span> <span class="k">if</span> <span class="n">r</span><span class="p">[</span><span class="mi">4</span><span class="p">][:</span><span class="mi">4</span><span class="p">]</span> <span class="o">==</span> <span class="s1">&#39;PMID&#39;</span> <span class="k">else</span> <span class="kc">None</span>
+
+        <span class="n">result</span><span class="p">[</span><span class="n">r</span><span class="p">[</span><span class="mi">3</span><span class="p">]]</span><span class="o">.</span><span class="n">add</span><span class="p">(</span>
+            <span class="n">HpoDisease</span><span class="p">(</span>
+                <span class="n">omim</span> <span class="o">=</span> <span class="n">r</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span>
+                <span class="n">name</span> <span class="o">=</span> <span class="n">r</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span>
+                <span class="n">pmid</span> <span class="o">=</span> <span class="n">pmid</span><span class="p">,</span>
+                <span class="n">qualifier</span> <span class="o">=</span> <span class="n">r</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="ow">or</span> <span class="kc">None</span><span class="p">,</span>
+                <span class="n">evidence</span> <span class="o">=</span> <span class="n">r</span><span class="p">[</span><span class="mi">5</span><span class="p">]</span> <span class="ow">or</span> <span class="kc">None</span><span class="p">,</span>
+                <span class="n">onset</span> <span class="o">=</span> <span class="n">r</span><span class="p">[</span><span class="mi">6</span><span class="p">]</span> <span class="ow">or</span> <span class="kc">None</span><span class="p">,</span>
+                <span class="n">frequency</span> <span class="o">=</span> <span class="n">r</span><span class="p">[</span><span class="mi">7</span><span class="p">]</span> <span class="ow">or</span> <span class="kc">None</span><span class="p">,</span>
+                <span class="n">sex</span> <span class="o">=</span> <span class="n">r</span><span class="p">[</span><span class="mi">8</span><span class="p">]</span> <span class="ow">or</span> <span class="kc">None</span><span class="p">,</span>
+                <span class="n">modifier</span> <span class="o">=</span> <span class="n">r</span><span class="p">[</span><span class="mi">9</span><span class="p">]</span> <span class="ow">or</span> <span class="kc">None</span><span class="p">,</span>
+                <span class="n">aspect</span> <span class="o">=</span> <span class="n">r</span><span class="p">[</span><span class="mi">10</span><span class="p">],</span>
+            <span class="p">)</span>
+        <span class="p">)</span>
+
+    <span class="k">return</span> <span class="nb">dict</span><span class="p">(</span><span class="n">result</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="hpo_ontology">
+<a class="viewcode-back" href="../../../api/pypath.inputs.hpo.hpo_ontology.html#pypath.inputs.hpo.hpo_ontology">[docs]</a>
+<span class="k">def</span> <span class="nf">hpo_ontology</span><span class="p">()</span> <span class="o">-&gt;</span> <span class="nb">dict</span><span class="p">[</span><span class="nb">str</span><span class="p">,</span> <span class="nb">dict</span><span class="p">[</span><span class="nb">str</span><span class="p">,</span> <span class="n">Union</span><span class="p">[</span><span class="nb">str</span><span class="p">,</span> <span class="nb">set</span><span class="p">[</span><span class="nb">str</span><span class="p">]]]]:</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Ontology data from HPO.</span>
+
+<span class="sd">    Returns</span>
+<span class="sd">        Five dictionaries with term names, term definitions, parents in the</span>
+<span class="sd">        ontology tree, term synonyms and cross references to other databases.</span>
+<span class="sd">        The dicts &quot;terms&quot; and &quot;defs&quot; are one-to-one, while &quot;parents&quot;,</span>
+<span class="sd">        &quot;synonyms&quot; and &quot;xrefs&quot; are one-to-many mappings, the keys are always</span>
+<span class="sd">        HPO terms.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="n">url</span> <span class="o">=</span> <span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;hpo&#39;</span><span class="p">][</span><span class="s1">&#39;ontology&#39;</span><span class="p">]</span>
+    <span class="n">reader</span> <span class="o">=</span> <span class="n">obo</span><span class="o">.</span><span class="n">Obo</span><span class="p">(</span><span class="n">url</span><span class="p">)</span>
+
+    <span class="n">result</span> <span class="o">=</span> <span class="p">{</span>
+        <span class="s1">&#39;terms&#39;</span><span class="p">:</span> <span class="p">{},</span>
+        <span class="s1">&#39;defs&#39;</span><span class="p">:</span> <span class="p">{},</span>
+        <span class="s1">&#39;parents&#39;</span><span class="p">:</span> <span class="n">collections</span><span class="o">.</span><span class="n">defaultdict</span><span class="p">(</span><span class="nb">set</span><span class="p">),</span>
+        <span class="s1">&#39;synonyms&#39;</span><span class="p">:</span> <span class="n">collections</span><span class="o">.</span><span class="n">defaultdict</span><span class="p">(</span><span class="nb">set</span><span class="p">),</span>
+        <span class="s1">&#39;xrefs&#39;</span><span class="p">:</span> <span class="n">collections</span><span class="o">.</span><span class="n">defaultdict</span><span class="p">(</span><span class="nb">set</span><span class="p">),</span>
+    <span class="p">}</span>
+
+    <span class="k">for</span> <span class="n">r</span> <span class="ow">in</span> <span class="n">reader</span><span class="p">:</span>
+
+        <span class="k">if</span> <span class="n">r</span><span class="o">.</span><span class="n">stanza</span> <span class="o">!=</span> <span class="s1">&#39;Term&#39;</span><span class="p">:</span> <span class="k">continue</span>
+
+        <span class="k">if</span> <span class="p">(</span>
+            <span class="n">r</span><span class="o">.</span><span class="n">name</span> <span class="ow">is</span> <span class="kc">None</span> <span class="ow">or</span>
+            <span class="n">r</span><span class="o">.</span><span class="n">name</span><span class="o">.</span><span class="n">value</span> <span class="o">==</span> <span class="s1">&#39;obsolete&#39;</span> <span class="ow">or</span>
+            <span class="n">r</span><span class="o">.</span><span class="n">attrs</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">&#39;is_obsolete&#39;</span><span class="p">)</span>
+        <span class="p">):</span>
+            <span class="k">continue</span>
+
+        <span class="n">term</span> <span class="o">=</span> <span class="n">r</span><span class="o">.</span><span class="n">id</span><span class="o">.</span><span class="n">value</span>
+
+        <span class="n">name</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="p">(</span><span class="n">r</span><span class="o">.</span><span class="n">name</span><span class="o">.</span><span class="n">value</span><span class="p">,</span> <span class="n">r</span><span class="o">.</span><span class="n">name</span><span class="o">.</span><span class="n">modifiers</span><span class="p">)</span>
+                <span class="k">if</span> <span class="n">r</span><span class="o">.</span><span class="n">name</span><span class="o">.</span><span class="n">modifiers</span> <span class="k">else</span>
+            <span class="n">r</span><span class="o">.</span><span class="n">name</span><span class="o">.</span><span class="n">value</span>
+        <span class="p">)</span>
+
+        <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">name</span><span class="p">,</span> <span class="nb">tuple</span><span class="p">):</span> <span class="n">name</span> <span class="o">=</span> <span class="s1">&#39; &#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">n</span> <span class="k">for</span> <span class="n">n</span> <span class="ow">in</span> <span class="n">name</span> <span class="k">if</span> <span class="n">n</span><span class="p">)</span>
+
+        <span class="n">result</span><span class="p">[</span><span class="s1">&#39;terms&#39;</span><span class="p">][</span><span class="n">term</span><span class="p">]</span> <span class="o">=</span> <span class="n">name</span>
+
+        <span class="n">result</span><span class="p">[</span><span class="s1">&#39;defs&#39;</span><span class="p">][</span><span class="n">term</span><span class="p">]</span> <span class="o">=</span> <span class="n">r</span><span class="o">.</span><span class="n">definition</span><span class="o">.</span><span class="n">value</span> <span class="k">if</span> <span class="n">r</span><span class="o">.</span><span class="n">definition</span> <span class="k">else</span> <span class="kc">None</span>
+
+        <span class="k">for</span> <span class="n">key</span><span class="p">,</span> <span class="n">obokey</span> <span class="ow">in</span> <span class="p">(</span>
+            <span class="p">(</span><span class="s1">&#39;parents&#39;</span><span class="p">,</span> <span class="s1">&#39;is_a&#39;</span><span class="p">),</span>
+            <span class="p">(</span><span class="s1">&#39;synonyms&#39;</span><span class="p">,</span> <span class="s1">&#39;synonym&#39;</span><span class="p">),</span>
+            <span class="p">(</span><span class="s1">&#39;xrefs&#39;</span><span class="p">,</span> <span class="s1">&#39;xref&#39;</span><span class="p">),</span>
+        <span class="p">):</span>
+
+            <span class="n">proc</span> <span class="o">=</span> <span class="p">(</span>
+                <span class="k">lambda</span> <span class="n">x</span><span class="p">:</span> <span class="nb">tuple</span><span class="p">(</span><span class="n">x</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;:&#39;</span><span class="p">))</span>
+                    <span class="k">if</span> <span class="n">key</span> <span class="o">==</span> <span class="s1">&#39;xrefs&#39;</span> <span class="k">else</span>
+                <span class="k">lambda</span> <span class="n">x</span><span class="p">:</span> <span class="n">x</span>
+            <span class="p">)</span>
+
+            <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">r</span><span class="o">.</span><span class="n">attrs</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="n">obokey</span><span class="p">,</span> <span class="p">()):</span>
+                <span class="n">y</span> <span class="o">=</span> <span class="n">proc</span><span class="p">(</span><span class="n">x</span><span class="o">.</span><span class="n">value</span><span class="p">)</span>
+                <span class="n">result</span><span class="p">[</span><span class="n">key</span><span class="p">][</span><span class="n">term</span><span class="p">]</span><span class="o">.</span><span class="n">update</span><span class="p">(</span>
+                    <span class="p">{</span>
+                        <span class="n">y</span><span class="p">(</span><span class="n">x</span><span class="o">.</span><span class="n">value</span><span class="p">)</span>
+                        <span class="k">if</span> <span class="nb">type</span><span class="p">(</span><span class="n">y</span><span class="p">)</span> <span class="o">!=</span> <span class="nb">tuple</span> <span class="k">else</span>
+                        <span class="n">y</span>
+                    <span class="p">}</span>
+                <span class="p">)</span>
+
+    <span class="k">return</span> <span class="p">{</span><span class="n">k</span><span class="p">:</span> <span class="nb">dict</span><span class="p">(</span><span class="n">v</span><span class="p">)</span> <span class="k">for</span> <span class="n">k</span><span class="p">,</span> <span class="n">v</span> <span class="ow">in</span> <span class="n">result</span><span class="o">.</span><span class="n">items</span><span class="p">()}</span></div>
+
+</pre></div>
+
+                </article>
+              
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diff --git a/_modules/pypath/inputs/humancellmap.html b/_modules/pypath/inputs/humancellmap.html
new file mode 100644
index 000000000..cb08e6ab8
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@@ -0,0 +1,679 @@
+
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+                  
+  <h1>Source code for pypath.inputs.humancellmap</h1><div class="highlight"><pre>
+<span></span><span class="ch">#!/usr/bin/env python</span>
+<span class="c1"># -*- coding: utf-8 -*-</span>
+
+<span class="c1">#</span>
+<span class="c1">#  This file is part of the `pypath` python module</span>
+<span class="c1">#</span>
+<span class="c1">#  Copyright 2014-2023</span>
+<span class="c1">#  EMBL, EMBL-EBI, Uniklinik RWTH Aachen, Heidelberg University</span>
+<span class="c1">#</span>
+<span class="c1">#  Authors: see the file `README.rst`</span>
+<span class="c1">#  Contact: Dénes Türei (turei.denes@gmail.com)</span>
+<span class="c1">#</span>
+<span class="c1">#  Distributed under the GPLv3 License.</span>
+<span class="c1">#  See accompanying file LICENSE.txt or copy at</span>
+<span class="c1">#      https://www.gnu.org/licenses/gpl-3.0.html</span>
+<span class="c1">#</span>
+<span class="c1">#  Website: https://pypath.omnipathdb.org/</span>
+<span class="c1">#</span>
+
+<span class="kn">import</span> <span class="nn">collections</span>
+
+<span class="kn">import</span> <span class="nn">pypath.share.curl</span> <span class="k">as</span> <span class="nn">curl</span>
+<span class="kn">import</span> <span class="nn">pypath.resources.urls</span> <span class="k">as</span> <span class="nn">urls</span>
+<span class="kn">import</span> <span class="nn">pypath.utils.mapping</span> <span class="k">as</span> <span class="nn">mapping</span>
+
+
+<div class="viewcode-block" id="humancellmap_annotations">
+<a class="viewcode-back" href="../../../api/pypath.inputs.humancellmap.humancellmap_annotations.html#pypath.inputs.humancellmap.humancellmap_annotations">[docs]</a>
+<span class="k">def</span> <span class="nf">humancellmap_annotations</span><span class="p">():</span>
+
+    <span class="n">HumancellmapAnnotation</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">namedtuple</span><span class="p">(</span>
+        <span class="s1">&#39;HumancellmapAnnotation&#39;</span><span class="p">,</span>
+        <span class="p">[</span>
+            <span class="s1">&#39;localization&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;method&#39;</span><span class="p">,</span>
+        <span class="p">],</span>
+    <span class="p">)</span>
+
+    <span class="n">url</span> <span class="o">=</span> <span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;humancellmap&#39;</span><span class="p">][</span><span class="s1">&#39;preys_url&#39;</span><span class="p">]</span>
+
+    <span class="n">c</span> <span class="o">=</span> <span class="n">curl</span><span class="o">.</span><span class="n">Curl</span><span class="p">(</span><span class="n">url</span><span class="p">,</span> <span class="n">large</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span> <span class="n">silent</span> <span class="o">=</span> <span class="kc">False</span><span class="p">)</span>
+
+    <span class="n">result</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">defaultdict</span><span class="p">(</span><span class="nb">set</span><span class="p">)</span>
+
+    <span class="n">_</span> <span class="o">=</span> <span class="nb">next</span><span class="p">(</span><span class="n">c</span><span class="o">.</span><span class="n">result</span><span class="p">)</span>
+
+    <span class="k">for</span> <span class="n">l</span> <span class="ow">in</span> <span class="n">c</span><span class="o">.</span><span class="n">result</span><span class="p">:</span>
+
+        <span class="n">l</span> <span class="o">=</span> <span class="n">l</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\t</span><span class="s1">&#39;</span><span class="p">)</span>
+
+        <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">l</span><span class="p">)</span> <span class="o">&lt;</span> <span class="mi">10</span><span class="p">:</span>
+
+            <span class="k">continue</span>
+
+        <span class="k">for</span> <span class="n">method</span><span class="p">,</span> <span class="n">i_loc</span> <span class="ow">in</span> <span class="p">((</span><span class="s1">&#39;NMF&#39;</span><span class="p">,</span> <span class="mi">2</span><span class="p">),</span> <span class="p">(</span><span class="s1">&#39;SAFE&#39;</span><span class="p">,</span> <span class="mi">4</span><span class="p">)):</span>
+
+            <span class="k">for</span> <span class="n">localization</span> <span class="ow">in</span> <span class="n">l</span><span class="p">[</span><span class="n">i_loc</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;,&#39;</span><span class="p">):</span>
+
+                <span class="n">localization</span> <span class="o">=</span> <span class="n">localization</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span>
+
+                <span class="k">if</span> <span class="n">localization</span> <span class="ow">in</span> <span class="p">{</span><span class="s1">&#39;-&#39;</span><span class="p">,</span> <span class="s1">&#39;no prediction&#39;</span><span class="p">}:</span>
+
+                    <span class="k">continue</span>
+
+                <span class="k">for</span> <span class="n">uniprot</span> <span class="ow">in</span> <span class="n">mapping</span><span class="o">.</span><span class="n">map_name</span><span class="p">(</span><span class="n">l</span><span class="p">[</span><span class="mi">9</span><span class="p">],</span> <span class="s1">&#39;uniprot&#39;</span><span class="p">,</span> <span class="s1">&#39;uniprot&#39;</span><span class="p">):</span>
+
+                    <span class="n">result</span><span class="p">[</span><span class="n">uniprot</span><span class="p">]</span><span class="o">.</span><span class="n">add</span><span class="p">(</span>
+                        <span class="n">HumancellmapAnnotation</span><span class="p">(</span>
+                            <span class="n">localization</span> <span class="o">=</span> <span class="n">localization</span><span class="p">,</span>
+                            <span class="n">method</span> <span class="o">=</span> <span class="n">method</span><span class="p">,</span>
+                        <span class="p">)</span>
+                    <span class="p">)</span>
+
+    <span class="k">return</span> <span class="nb">dict</span><span class="p">(</span><span class="n">result</span><span class="p">)</span></div>
+
+
+</pre></div>
+
+                </article>
+              
+              
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diff --git a/_modules/pypath/inputs/humap.html b/_modules/pypath/inputs/humap.html
new file mode 100644
index 000000000..148c8e665
--- /dev/null
+++ b/_modules/pypath/inputs/humap.html
@@ -0,0 +1,699 @@
+
+<!DOCTYPE html>
+
+
+<html lang="en" data-content_root="../../../" >
+
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+    <meta charset="utf-8" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
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+  
+  
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+    document.documentElement.dataset.mode = localStorage.getItem("mode") || "";
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+  <h1>Source code for pypath.inputs.humap</h1><div class="highlight"><pre>
+<span></span><span class="ch">#!/usr/bin/env python</span>
+<span class="c1"># -*- coding: utf-8 -*-</span>
+
+<span class="c1">#</span>
+<span class="c1">#  This file is part of the `pypath` python module</span>
+<span class="c1">#</span>
+<span class="c1">#  Copyright 2014-2023</span>
+<span class="c1">#  EMBL, EMBL-EBI, Uniklinik RWTH Aachen, Heidelberg University</span>
+<span class="c1">#</span>
+<span class="c1">#  Authors: see the file `README.rst`</span>
+<span class="c1">#  Contact: Dénes Türei (turei.denes@gmail.com)</span>
+<span class="c1">#</span>
+<span class="c1">#  Distributed under the GPLv3 License.</span>
+<span class="c1">#  See accompanying file LICENSE.txt or copy at</span>
+<span class="c1">#      https://www.gnu.org/licenses/gpl-3.0.html</span>
+<span class="c1">#</span>
+<span class="c1">#  Website: https://pypath.omnipathdb.org/</span>
+<span class="c1">#</span>
+
+<span class="kn">import</span> <span class="nn">itertools</span>
+
+<span class="kn">import</span> <span class="nn">pypath.share.curl</span> <span class="k">as</span> <span class="nn">curl</span>
+<span class="kn">import</span> <span class="nn">pypath.resources.urls</span> <span class="k">as</span> <span class="nn">urls</span>
+<span class="kn">import</span> <span class="nn">pypath.utils.mapping</span> <span class="k">as</span> <span class="nn">mapping</span>
+<span class="kn">import</span> <span class="nn">pypath.internals.intera</span> <span class="k">as</span> <span class="nn">intera</span>
+
+
+<div class="viewcode-block" id="humap_complexes">
+<a class="viewcode-back" href="../../../api/pypath.inputs.humap.humap_complexes.html#pypath.inputs.humap.humap_complexes">[docs]</a>
+<span class="k">def</span> <span class="nf">humap_complexes</span><span class="p">():</span>
+
+    <span class="n">url</span> <span class="o">=</span> <span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;humap&#39;</span><span class="p">][</span><span class="s1">&#39;humap_url&#39;</span><span class="p">]</span>
+    <span class="n">c</span> <span class="o">=</span> <span class="n">curl</span><span class="o">.</span><span class="n">Curl</span><span class="p">(</span><span class="n">url</span><span class="p">,</span> <span class="n">large</span> <span class="o">=</span> <span class="kc">True</span><span class="p">)</span>
+
+    <span class="n">complexes</span> <span class="o">=</span> <span class="p">{}</span>
+
+    <span class="k">for</span> <span class="n">l</span> <span class="ow">in</span> <span class="n">c</span><span class="o">.</span><span class="n">result</span><span class="p">:</span>
+
+        <span class="n">l</span> <span class="o">=</span> <span class="n">l</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span><span class="o">.</span><span class="n">split</span><span class="p">()</span>
+
+        <span class="k">for</span> <span class="n">uniprots</span> <span class="ow">in</span> <span class="n">itertools</span><span class="o">.</span><span class="n">product</span><span class="p">(</span><span class="o">*</span><span class="p">(</span>
+            <span class="n">mapping</span><span class="o">.</span><span class="n">map_name</span><span class="p">(</span><span class="n">entrez</span><span class="p">,</span> <span class="s1">&#39;entrez&#39;</span><span class="p">,</span> <span class="s1">&#39;uniprot&#39;</span><span class="p">)</span>
+            <span class="k">for</span> <span class="n">entrez</span> <span class="ow">in</span> <span class="n">l</span>
+        <span class="p">)):</span>
+
+            <span class="n">cplex</span> <span class="o">=</span> <span class="n">intera</span><span class="o">.</span><span class="n">Complex</span><span class="p">(</span>
+                <span class="n">components</span> <span class="o">=</span> <span class="n">uniprots</span><span class="p">,</span>
+                <span class="n">sources</span> <span class="o">=</span> <span class="s1">&#39;hu.MAP&#39;</span><span class="p">,</span>
+            <span class="p">)</span>
+
+            <span class="n">complexes</span><span class="p">[</span><span class="n">cplex</span><span class="o">.</span><span class="fm">__str__</span><span class="p">()]</span> <span class="o">=</span> <span class="n">cplex</span>
+
+    <span class="k">return</span> <span class="n">complexes</span></div>
+
+
+
+<div class="viewcode-block" id="humap2_complexes">
+<a class="viewcode-back" href="../../../api/pypath.inputs.humap.humap2_complexes.html#pypath.inputs.humap.humap2_complexes">[docs]</a>
+<span class="k">def</span> <span class="nf">humap2_complexes</span><span class="p">(</span><span class="n">min_confidence</span> <span class="o">=</span> <span class="mi">0</span><span class="p">):</span>
+
+    <span class="n">url</span> <span class="o">=</span> <span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;humap&#39;</span><span class="p">][</span><span class="s1">&#39;humap2_url&#39;</span><span class="p">]</span>
+    <span class="n">c</span> <span class="o">=</span> <span class="n">curl</span><span class="o">.</span><span class="n">Curl</span><span class="p">(</span><span class="n">url</span><span class="p">,</span> <span class="n">large</span> <span class="o">=</span> <span class="kc">True</span><span class="p">)</span>
+
+    <span class="n">complexes</span> <span class="o">=</span> <span class="p">{}</span>
+
+    <span class="n">_</span> <span class="o">=</span> <span class="nb">next</span><span class="p">(</span><span class="n">c</span><span class="o">.</span><span class="n">result</span><span class="p">)</span>
+
+    <span class="k">for</span> <span class="n">l</span> <span class="ow">in</span> <span class="n">c</span><span class="o">.</span><span class="n">result</span><span class="p">:</span>
+
+        <span class="n">l</span> <span class="o">=</span> <span class="n">l</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;,&#39;</span><span class="p">)</span>
+
+        <span class="n">confidence</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">l</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span>
+
+        <span class="k">if</span> <span class="n">confidence</span> <span class="o">&lt;</span> <span class="n">min_confidence</span><span class="p">:</span>
+
+            <span class="k">continue</span>
+
+        <span class="k">for</span> <span class="n">uniprots</span> <span class="ow">in</span> <span class="n">itertools</span><span class="o">.</span><span class="n">product</span><span class="p">(</span><span class="o">*</span><span class="p">(</span>
+            <span class="n">mapping</span><span class="o">.</span><span class="n">map_name</span><span class="p">(</span><span class="n">uniprot</span><span class="p">,</span> <span class="s1">&#39;uniprot&#39;</span><span class="p">,</span> <span class="s1">&#39;uniprot&#39;</span><span class="p">)</span>
+            <span class="k">for</span> <span class="n">uniprot</span> <span class="ow">in</span> <span class="n">l</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">()</span>
+        <span class="p">)):</span>
+
+            <span class="k">if</span> <span class="ow">not</span> <span class="n">uniprots</span><span class="p">:</span>
+
+                <span class="k">continue</span>
+
+            <span class="n">cplex</span> <span class="o">=</span> <span class="n">intera</span><span class="o">.</span><span class="n">Complex</span><span class="p">(</span>
+                <span class="n">components</span> <span class="o">=</span> <span class="n">uniprots</span><span class="p">,</span>
+                <span class="n">sources</span> <span class="o">=</span> <span class="s1">&#39;hu.MAP2&#39;</span><span class="p">,</span>
+                <span class="n">attrs</span> <span class="o">=</span> <span class="p">{</span><span class="s1">&#39;humap2_confidence&#39;</span><span class="p">:</span> <span class="n">confidence</span><span class="p">},</span>
+            <span class="p">)</span>
+
+            <span class="n">complexes</span><span class="p">[</span><span class="n">cplex</span><span class="o">.</span><span class="fm">__str__</span><span class="p">()]</span> <span class="o">=</span> <span class="n">cplex</span>
+
+    <span class="k">return</span> <span class="n">complexes</span></div>
+
+</pre></div>
+
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+                  
+  <h1>Source code for pypath.inputs.huri</h1><div class="highlight"><pre>
+<span></span><span class="ch">#!/usr/bin/env python</span>
+<span class="c1"># -*- coding: utf-8 -*-</span>
+
+<span class="c1">#</span>
+<span class="c1">#  This file is part of the `pypath` python module</span>
+<span class="c1">#</span>
+<span class="c1">#  Copyright 2014-2023</span>
+<span class="c1">#  EMBL, EMBL-EBI, Uniklinik RWTH Aachen, Heidelberg University</span>
+<span class="c1">#</span>
+<span class="c1">#  Authors: see the file `README.rst`</span>
+<span class="c1">#  Contact: Dénes Türei (turei.denes@gmail.com)</span>
+<span class="c1">#</span>
+<span class="c1">#  Distributed under the GPLv3 License.</span>
+<span class="c1">#  See accompanying file LICENSE.txt or copy at</span>
+<span class="c1">#      https://www.gnu.org/licenses/gpl-3.0.html</span>
+<span class="c1">#</span>
+<span class="c1">#  Website: https://pypath.omnipathdb.org/</span>
+<span class="c1">#</span>
+
+<span class="kn">import</span> <span class="nn">re</span>
+<span class="kn">import</span> <span class="nn">collections</span>
+<span class="kn">import</span> <span class="nn">itertools</span>
+
+<span class="kn">import</span> <span class="nn">pypath.resources.urls</span> <span class="k">as</span> <span class="nn">urls</span>
+<span class="kn">import</span> <span class="nn">pypath.share.curl</span> <span class="k">as</span> <span class="nn">curl</span>
+<span class="kn">import</span> <span class="nn">pypath.utils.mapping</span> <span class="k">as</span> <span class="nn">mapping</span>
+<span class="kn">import</span> <span class="nn">pypath.inputs.common</span> <span class="k">as</span> <span class="nn">inputs_common</span>
+<span class="kn">import</span> <span class="nn">pypath.inputs.cell</span> <span class="k">as</span> <span class="nn">cell</span>
+
+
+<div class="viewcode-block" id="rolland_hi_ii_14">
+<a class="viewcode-back" href="../../../api/pypath.inputs.huri.rolland_hi_ii_14.html#pypath.inputs.huri.rolland_hi_ii_14">[docs]</a>
+<span class="k">def</span> <span class="nf">rolland_hi_ii_14</span><span class="p">():</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Loads the HI-II-14 unbiased interactome from the large scale screening</span>
+<span class="sd">    of from Rolland 2014.</span>
+<span class="sd">    Returns list of interactions.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="n">xlsname</span> <span class="o">=</span> <span class="n">cell</span><span class="o">.</span><span class="n">cell_supplementary</span><span class="p">(</span>
+        <span class="n">supp_url</span> <span class="o">=</span> <span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;hiii14&#39;</span><span class="p">][</span><span class="s1">&#39;url&#39;</span><span class="p">],</span>
+        <span class="n">article_url</span> <span class="o">=</span> <span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;hiii14&#39;</span><span class="p">][</span><span class="s1">&#39;article_url&#39;</span><span class="p">],</span>
+    <span class="p">)</span>
+    <span class="n">tbl</span> <span class="o">=</span> <span class="n">inputs_common</span><span class="o">.</span><span class="n">read_xls</span><span class="p">(</span><span class="n">xlsname</span><span class="p">,</span> <span class="n">sheet</span> <span class="o">=</span> <span class="s1">&#39;2G&#39;</span><span class="p">)</span>
+
+    <span class="k">for</span> <span class="n">row</span> <span class="ow">in</span> <span class="n">tbl</span><span class="p">[</span><span class="mi">1</span><span class="p">:]:</span>
+
+        <span class="k">yield</span> <span class="p">[</span><span class="n">c</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;.&#39;</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span> <span class="k">for</span> <span class="n">c</span> <span class="ow">in</span> <span class="n">row</span><span class="p">]</span></div>
+
+
+
+<div class="viewcode-block" id="vidal_hi_iii_old">
+<a class="viewcode-back" href="../../../api/pypath.inputs.huri.vidal_hi_iii_old.html#pypath.inputs.huri.vidal_hi_iii_old">[docs]</a>
+<span class="k">def</span> <span class="nf">vidal_hi_iii_old</span><span class="p">(</span><span class="n">fname</span><span class="p">):</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Loads the HI-III  unbiased interactome from preliminary data of</span>
+<span class="sd">    the next large scale screening of Vidal Lab.</span>
+
+<span class="sd">    The data is accessible here:</span>
+<span class="sd">        http://interactome.dfci.harvard.edu/H_sapiens/dload_trk.php</span>
+<span class="sd">    You need to register and accept the license terms.</span>
+
+<span class="sd">    Returns list of interactions.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="n">f</span> <span class="o">=</span> <span class="n">curl</span><span class="o">.</span><span class="n">FileOpener</span><span class="p">(</span><span class="n">fname</span><span class="p">)</span>
+
+    <span class="k">return</span> <span class="p">[</span><span class="n">l</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\t</span><span class="s1">&#39;</span><span class="p">)</span> <span class="k">for</span> <span class="n">l</span> <span class="ow">in</span> <span class="n">f</span><span class="o">.</span><span class="n">result</span><span class="p">][</span><span class="mi">1</span><span class="p">:]</span></div>
+
+
+
+<div class="viewcode-block" id="hi_iii_old">
+<a class="viewcode-back" href="../../../api/pypath.inputs.huri.hi_iii_old.html#pypath.inputs.huri.hi_iii_old">[docs]</a>
+<span class="k">def</span> <span class="nf">hi_iii_old</span><span class="p">():</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Loads the unbiased human interactome version III (HI-III).</span>
+<span class="sd">    This is an unpublished data and its use is limited.</span>
+<span class="sd">    Please check the conditions and licensing terms carefully at</span>
+<span class="sd">    http://interactome.baderlab.org.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="n">HiiiiInteraction</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">namedtuple</span><span class="p">(</span>
+        <span class="s1">&#39;HiiiiInteraction&#39;</span><span class="p">,</span>
+        <span class="p">[</span>
+            <span class="s1">&#39;id_a&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;id_b&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;isoform_a&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;isoform_b&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;screens&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;score&#39;</span><span class="p">,</span>
+        <span class="p">]</span>
+    <span class="p">)</span>
+
+
+    <span class="n">rescore</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">compile</span><span class="p">(</span><span class="sa">r</span><span class="s1">&#39;author score: ([\d\.]+)&#39;</span><span class="p">)</span>
+    <span class="n">rescreens</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">compile</span><span class="p">(</span><span class="sa">r</span><span class="s1">&#39;Found in screens ([\d,]+)&#39;</span><span class="p">)</span>
+
+    <span class="n">url</span> <span class="o">=</span> <span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;hid&#39;</span><span class="p">][</span><span class="s1">&#39;hi-iii&#39;</span><span class="p">]</span>
+    <span class="n">post_data</span> <span class="o">=</span> <span class="p">{</span>
+        <span class="s1">&#39;form[request_dataset]&#39;</span><span class="p">:</span> <span class="s1">&#39;2&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;form[request_file_format]&#39;</span><span class="p">:</span> <span class="s1">&#39;psi&#39;</span><span class="p">,</span>
+    <span class="p">}</span>
+
+    <span class="n">c</span> <span class="o">=</span> <span class="n">curl</span><span class="o">.</span><span class="n">Curl</span><span class="p">(</span>
+        <span class="n">url</span><span class="p">,</span>
+        <span class="n">silent</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+        <span class="n">large</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
+        <span class="n">post</span> <span class="o">=</span> <span class="n">post_data</span><span class="p">,</span>
+        <span class="n">slow</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
+    <span class="p">)</span>
+
+    <span class="k">for</span> <span class="n">row</span> <span class="ow">in</span> <span class="n">c</span><span class="o">.</span><span class="n">result</span><span class="p">:</span>
+
+        <span class="k">if</span> <span class="ow">not</span> <span class="n">row</span><span class="o">.</span><span class="n">strip</span><span class="p">():</span>
+
+            <span class="k">continue</span>
+
+        <span class="n">id_a</span><span class="p">,</span> <span class="n">id_b</span><span class="p">,</span> <span class="n">rest</span> <span class="o">=</span> <span class="n">row</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39; &#39;</span><span class="p">,</span> <span class="n">maxsplit</span> <span class="o">=</span> <span class="mi">2</span><span class="p">)</span>
+        <span class="n">id_a</span><span class="p">,</span> <span class="n">isoform_a</span> <span class="o">=</span> <span class="n">id_a</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;-&#39;</span><span class="p">)</span> <span class="k">if</span> <span class="s1">&#39;-&#39;</span> <span class="ow">in</span> <span class="n">id_a</span> <span class="k">else</span> <span class="p">(</span><span class="n">id_a</span><span class="p">,</span> <span class="mi">1</span><span class="p">)</span>
+        <span class="n">id_b</span><span class="p">,</span> <span class="n">isoform_b</span> <span class="o">=</span> <span class="n">id_b</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;-&#39;</span><span class="p">)</span> <span class="k">if</span> <span class="s1">&#39;-&#39;</span> <span class="ow">in</span> <span class="n">id_b</span> <span class="k">else</span> <span class="p">(</span><span class="n">id_b</span><span class="p">,</span> <span class="mi">1</span><span class="p">)</span>
+
+        <span class="n">sc</span> <span class="o">=</span> <span class="n">rescore</span><span class="o">.</span><span class="n">search</span><span class="p">(</span><span class="n">rest</span><span class="p">)</span>
+        <span class="n">score</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">sc</span><span class="o">.</span><span class="n">groups</span><span class="p">()[</span><span class="mi">0</span><span class="p">])</span> <span class="k">if</span> <span class="n">sc</span> <span class="k">else</span> <span class="kc">None</span>
+        <span class="n">screens</span> <span class="o">=</span> <span class="nb">tuple</span><span class="p">(</span>
+            <span class="nb">int</span><span class="p">(</span><span class="n">i</span><span class="p">)</span> <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="n">rescreens</span><span class="o">.</span><span class="n">search</span><span class="p">(</span><span class="n">rest</span><span class="p">)</span><span class="o">.</span><span class="n">groups</span><span class="p">()[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;,&#39;</span><span class="p">)</span>
+        <span class="p">)</span>
+
+        <span class="k">yield</span> <span class="n">HiiiiInteraction</span><span class="p">(</span>
+            <span class="n">id_a</span> <span class="o">=</span> <span class="n">id_a</span><span class="p">[</span><span class="mi">10</span><span class="p">:],</span>
+            <span class="n">id_b</span> <span class="o">=</span> <span class="n">id_b</span><span class="p">[</span><span class="mi">10</span><span class="p">:],</span>
+            <span class="n">isoform_a</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">isoform_a</span><span class="p">),</span>
+            <span class="n">isoform_b</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">isoform_b</span><span class="p">),</span>
+            <span class="n">screens</span> <span class="o">=</span> <span class="n">screens</span><span class="p">,</span>
+            <span class="n">score</span> <span class="o">=</span> <span class="n">score</span><span class="p">,</span>
+        <span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="lit_bm_13_interactions">
+<a class="viewcode-back" href="../../../api/pypath.inputs.huri.lit_bm_13_interactions.html#pypath.inputs.huri.lit_bm_13_interactions">[docs]</a>
+<span class="k">def</span> <span class="nf">lit_bm_13_interactions</span><span class="p">():</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Downloads and processes Lit-BM-13 dataset, the 2013 version of the</span>
+<span class="sd">    high confidence literature curated interactions from CCSB.</span>
+<span class="sd">    Returns list of interactions.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="n">LitBm13Interaction</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">namedtuple</span><span class="p">(</span>
+        <span class="s1">&#39;LitBm13Interaction&#39;</span><span class="p">,</span>
+        <span class="p">[</span>
+            <span class="s1">&#39;entrez_a&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;entrez_b&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;genesymbol_a&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;genesymbol_b&#39;</span><span class="p">,</span>
+        <span class="p">]</span>
+    <span class="p">)</span>
+
+    <span class="n">url</span> <span class="o">=</span> <span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;hid&#39;</span><span class="p">][</span><span class="s1">&#39;lit-bm-13&#39;</span><span class="p">]</span>
+    <span class="n">c</span> <span class="o">=</span> <span class="n">curl</span><span class="o">.</span><span class="n">Curl</span><span class="p">(</span><span class="n">url</span><span class="p">,</span> <span class="n">silent</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span> <span class="n">large</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span> <span class="n">slow</span> <span class="o">=</span> <span class="kc">True</span><span class="p">)</span>
+
+    <span class="n">_</span> <span class="o">=</span> <span class="nb">next</span><span class="p">(</span><span class="n">c</span><span class="o">.</span><span class="n">result</span><span class="p">)</span>
+
+    <span class="k">for</span> <span class="n">row</span> <span class="ow">in</span> <span class="n">c</span><span class="o">.</span><span class="n">result</span><span class="p">:</span>
+
+        <span class="n">row</span> <span class="o">=</span> <span class="n">row</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\t</span><span class="s1">&#39;</span><span class="p">)</span>
+
+        <span class="k">yield</span> <span class="n">LitBm13Interaction</span><span class="p">(</span>
+            <span class="n">entrez_a</span> <span class="o">=</span> <span class="n">row</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span>
+            <span class="n">entrez_b</span> <span class="o">=</span> <span class="n">row</span><span class="p">[</span><span class="mi">2</span><span class="p">],</span>
+            <span class="n">genesymbol_a</span> <span class="o">=</span> <span class="n">row</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span>
+            <span class="n">genesymbol_b</span> <span class="o">=</span> <span class="n">row</span><span class="p">[</span><span class="mi">3</span><span class="p">],</span>
+        <span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="lit_bm_17_interactions">
+<a class="viewcode-back" href="../../../api/pypath.inputs.huri.lit_bm_17_interactions.html#pypath.inputs.huri.lit_bm_17_interactions">[docs]</a>
+<span class="k">def</span> <span class="nf">lit_bm_17_interactions</span><span class="p">():</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Downloads and processes Lit-BM-13 dataset, the 2017 version of the</span>
+<span class="sd">    high confidence literature curated interactions from CCSB.</span>
+<span class="sd">    Returns list of interactions.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="n">LitBm17Interaction</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">namedtuple</span><span class="p">(</span>
+        <span class="s1">&#39;LitBm17Interaction&#39;</span><span class="p">,</span>
+        <span class="p">[</span>
+            <span class="s1">&#39;id_a&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;id_b&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;pubmed&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;score&#39;</span><span class="p">,</span>
+        <span class="p">]</span>
+    <span class="p">)</span>
+
+    <span class="n">url</span> <span class="o">=</span> <span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;hid&#39;</span><span class="p">][</span><span class="s1">&#39;lit-bm-17&#39;</span><span class="p">]</span>
+    <span class="n">c</span> <span class="o">=</span> <span class="n">curl</span><span class="o">.</span><span class="n">Curl</span><span class="p">(</span><span class="n">url</span><span class="p">,</span> <span class="n">silent</span> <span class="o">=</span> <span class="kc">False</span><span class="p">)</span>
+    <span class="n">data</span> <span class="o">=</span> <span class="n">c</span><span class="o">.</span><span class="n">result</span>
+
+    <span class="n">c</span> <span class="o">=</span> <span class="n">curl</span><span class="o">.</span><span class="n">Curl</span><span class="p">(</span><span class="n">url</span><span class="p">,</span> <span class="n">silent</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span> <span class="n">large</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span> <span class="n">slow</span> <span class="o">=</span> <span class="kc">True</span><span class="p">)</span>
+
+    <span class="n">_</span> <span class="o">=</span> <span class="nb">next</span><span class="p">(</span><span class="n">c</span><span class="o">.</span><span class="n">result</span><span class="p">)</span>
+
+    <span class="k">for</span> <span class="n">row</span> <span class="ow">in</span> <span class="n">c</span><span class="o">.</span><span class="n">result</span><span class="p">:</span>
+
+        <span class="n">row</span> <span class="o">=</span> <span class="n">row</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\t</span><span class="s1">&#39;</span><span class="p">)</span>
+
+        <span class="n">id_a</span> <span class="o">=</span> <span class="n">row</span><span class="p">[</span><span class="mi">0</span><span class="p">][</span><span class="mi">10</span><span class="p">:]</span>
+        <span class="n">id_b</span> <span class="o">=</span> <span class="n">row</span><span class="p">[</span><span class="mi">1</span><span class="p">][</span><span class="mi">10</span><span class="p">:]</span>
+
+        <span class="n">pubmed</span> <span class="o">=</span> <span class="n">row</span><span class="p">[</span><span class="mi">8</span><span class="p">][</span><span class="mi">7</span><span class="p">:]</span>
+        <span class="n">score</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">row</span><span class="p">[</span><span class="mi">14</span><span class="p">][</span><span class="mi">13</span><span class="p">:])</span>
+
+        <span class="k">yield</span> <span class="n">LitBm17Interaction</span><span class="p">(</span>
+            <span class="n">id_a</span> <span class="o">=</span> <span class="n">id_a</span><span class="p">,</span>
+            <span class="n">id_b</span> <span class="o">=</span> <span class="n">id_b</span><span class="p">,</span>
+            <span class="n">pubmed</span> <span class="o">=</span> <span class="n">pubmed</span><span class="p">,</span>
+            <span class="n">score</span> <span class="o">=</span> <span class="n">score</span><span class="p">,</span>
+        <span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="huri_interactions">
+<a class="viewcode-back" href="../../../api/pypath.inputs.huri.huri_interactions.html#pypath.inputs.huri.huri_interactions">[docs]</a>
+<span class="k">def</span> <span class="nf">huri_interactions</span><span class="p">():</span>
+
+    <span class="k">return</span> <span class="n">_huri_interactions</span><span class="p">(</span><span class="n">dataset</span> <span class="o">=</span> <span class="s1">&#39;huri&#39;</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="yu2011_interactions">
+<a class="viewcode-back" href="../../../api/pypath.inputs.huri.yu2011_interactions.html#pypath.inputs.huri.yu2011_interactions">[docs]</a>
+<span class="k">def</span> <span class="nf">yu2011_interactions</span><span class="p">():</span>
+
+    <span class="k">return</span> <span class="n">_huri_interactions</span><span class="p">(</span><span class="n">dataset</span> <span class="o">=</span> <span class="s1">&#39;yu-2011&#39;</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="hi_union_interactions">
+<a class="viewcode-back" href="../../../api/pypath.inputs.huri.hi_union_interactions.html#pypath.inputs.huri.hi_union_interactions">[docs]</a>
+<span class="k">def</span> <span class="nf">hi_union_interactions</span><span class="p">():</span>
+
+    <span class="k">return</span> <span class="n">_huri_interactions</span><span class="p">(</span><span class="n">dataset</span> <span class="o">=</span> <span class="s1">&#39;hi-union&#39;</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="yang2016_interactions">
+<a class="viewcode-back" href="../../../api/pypath.inputs.huri.yang2016_interactions.html#pypath.inputs.huri.yang2016_interactions">[docs]</a>
+<span class="k">def</span> <span class="nf">yang2016_interactions</span><span class="p">():</span>
+
+    <span class="k">return</span> <span class="n">_huri_interactions</span><span class="p">(</span><span class="n">dataset</span> <span class="o">=</span> <span class="s1">&#39;yang-2016&#39;</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="hi_ii_interactions">
+<a class="viewcode-back" href="../../../api/pypath.inputs.huri.hi_ii_interactions.html#pypath.inputs.huri.hi_ii_interactions">[docs]</a>
+<span class="k">def</span> <span class="nf">hi_ii_interactions</span><span class="p">():</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Interactions from Rolland 2014 https://pubmed.ncbi.nlm.nih.gov/25416956/.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="k">return</span> <span class="n">_huri_interactions</span><span class="p">(</span><span class="n">dataset</span> <span class="o">=</span> <span class="s1">&#39;hi-ii-14-pmi&#39;</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="hi_i_interactions">
+<a class="viewcode-back" href="../../../api/pypath.inputs.huri.hi_i_interactions.html#pypath.inputs.huri.hi_i_interactions">[docs]</a>
+<span class="k">def</span> <span class="nf">hi_i_interactions</span><span class="p">():</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Interactions from Rual 2005 https://pubmed.ncbi.nlm.nih.gov/16189514/.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="k">return</span> <span class="n">_huri_interactions</span><span class="p">(</span><span class="n">dataset</span> <span class="o">=</span> <span class="s1">&#39;hi-i-05-pmi&#39;</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="lit_bm_interactions">
+<a class="viewcode-back" href="../../../api/pypath.inputs.huri.lit_bm_interactions.html#pypath.inputs.huri.lit_bm_interactions">[docs]</a>
+<span class="k">def</span> <span class="nf">lit_bm_interactions</span><span class="p">():</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Literature collected interactions from Luck 2020.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="n">LitBmInteraction</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">namedtuple</span><span class="p">(</span>
+        <span class="s1">&#39;LitBmInteraction&#39;</span><span class="p">,</span>
+        <span class="p">[</span><span class="s1">&#39;uniprot_a&#39;</span><span class="p">,</span> <span class="s1">&#39;uniprot_b&#39;</span><span class="p">],</span>
+    <span class="p">)</span>
+
+    <span class="n">url</span> <span class="o">=</span> <span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;hid&#39;</span><span class="p">][</span><span class="s1">&#39;lit-bm&#39;</span><span class="p">]</span>
+    <span class="n">c</span> <span class="o">=</span> <span class="n">curl</span><span class="o">.</span><span class="n">Curl</span><span class="p">(</span><span class="n">url</span><span class="p">,</span> <span class="n">large</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span> <span class="n">silent</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span> <span class="n">slow</span> <span class="o">=</span> <span class="kc">True</span><span class="p">)</span>
+
+    <span class="k">for</span> <span class="n">row</span> <span class="ow">in</span> <span class="n">c</span><span class="o">.</span><span class="n">result</span><span class="p">:</span>
+
+        <span class="n">row</span> <span class="o">=</span> <span class="n">row</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\t</span><span class="s1">&#39;</span><span class="p">)</span>
+
+        <span class="n">uniprots_a</span> <span class="o">=</span> <span class="n">mapping</span><span class="o">.</span><span class="n">map_name</span><span class="p">(</span><span class="n">row</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="s1">&#39;ensembl&#39;</span><span class="p">,</span> <span class="s1">&#39;uniprot&#39;</span><span class="p">)</span>
+        <span class="n">uniprots_b</span> <span class="o">=</span> <span class="n">mapping</span><span class="o">.</span><span class="n">map_name</span><span class="p">(</span><span class="n">row</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span> <span class="s1">&#39;ensembl&#39;</span><span class="p">,</span> <span class="s1">&#39;uniprot&#39;</span><span class="p">)</span>
+
+        <span class="k">for</span> <span class="n">uniprot_a</span><span class="p">,</span> <span class="n">uniprot_b</span> <span class="ow">in</span> <span class="n">itertools</span><span class="o">.</span><span class="n">product</span><span class="p">(</span><span class="n">uniprots_a</span><span class="p">,</span> <span class="n">uniprots_b</span><span class="p">):</span>
+
+            <span class="k">yield</span> <span class="n">LitBmInteraction</span><span class="p">(</span>
+                <span class="n">uniprot_a</span> <span class="o">=</span> <span class="n">uniprot_a</span><span class="p">,</span>
+                <span class="n">uniprot_b</span> <span class="o">=</span> <span class="n">uniprot_b</span><span class="p">,</span>
+            <span class="p">)</span></div>
+
+
+
+<span class="k">def</span> <span class="nf">_huri_interactions</span><span class="p">(</span><span class="n">dataset</span><span class="p">):</span>
+
+    <span class="n">reuniprot</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">compile</span><span class="p">(</span><span class="sa">r</span><span class="s1">&#39;[a-z]+:([\w\.]+)(?:-?([0-9]?))?&#39;</span><span class="p">)</span>
+    <span class="n">rescore</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">compile</span><span class="p">(</span><span class="sa">r</span><span class="s1">&#39;author score: ([\.0-9]+)&#39;</span><span class="p">)</span>
+
+    <span class="n">HuriInteraction</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">namedtuple</span><span class="p">(</span>
+        <span class="s1">&#39;HuriInteraction&#39;</span><span class="p">,</span>
+        <span class="p">[</span>
+            <span class="s1">&#39;uniprot_a&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;uniprot_b&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;isoform_a&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;isoform_b&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;score&#39;</span><span class="p">,</span>
+        <span class="p">]</span>
+    <span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">_map_ids</span><span class="p">(</span><span class="n">_id</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="n">mapping</span><span class="o">.</span><span class="n">map_name</span><span class="p">(</span>
+            <span class="n">_id</span><span class="p">,</span>
+            <span class="n">_id</span><span class="p">[:</span><span class="mi">4</span><span class="p">]</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span> <span class="k">if</span> <span class="n">_id</span><span class="p">[:</span><span class="mi">4</span><span class="p">]</span> <span class="ow">in</span> <span class="p">{</span><span class="s1">&#39;ensp&#39;</span><span class="p">,</span> <span class="s1">&#39;enst&#39;</span><span class="p">}</span> <span class="k">else</span> <span class="s1">&#39;uniprot&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;uniprot&#39;</span><span class="p">,</span>
+        <span class="p">)</span>
+
+
+    <span class="n">url</span> <span class="o">=</span> <span class="n">dataset</span> <span class="k">if</span> <span class="n">dataset</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s1">&#39;http&#39;</span><span class="p">)</span> <span class="k">else</span> <span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;hid&#39;</span><span class="p">][</span><span class="n">dataset</span><span class="p">]</span>
+    <span class="n">c</span> <span class="o">=</span> <span class="n">curl</span><span class="o">.</span><span class="n">Curl</span><span class="p">(</span><span class="n">url</span><span class="p">,</span> <span class="n">large</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span> <span class="n">silent</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span> <span class="n">slow</span> <span class="o">=</span> <span class="kc">True</span><span class="p">)</span>
+    <span class="n">path</span> <span class="o">=</span> <span class="p">(</span>
+        <span class="n">c</span><span class="o">.</span><span class="n">fileobj</span><span class="o">.</span><span class="n">name</span>
+            <span class="k">if</span> <span class="nb">hasattr</span><span class="p">(</span><span class="n">c</span><span class="p">,</span> <span class="s1">&#39;fileobj&#39;</span><span class="p">)</span> <span class="k">else</span>
+        <span class="n">c</span><span class="o">.</span><span class="n">cache_file_name</span> <span class="ow">or</span> <span class="n">c</span><span class="o">.</span><span class="n">outfile</span>
+    <span class="p">)</span>
+    <span class="k">del</span> <span class="n">c</span>
+    <span class="n">c</span> <span class="o">=</span> <span class="n">curl</span><span class="o">.</span><span class="n">FileOpener</span><span class="p">(</span><span class="n">path</span><span class="p">)</span>
+
+    <span class="k">for</span> <span class="n">row</span> <span class="ow">in</span> <span class="n">c</span><span class="o">.</span><span class="n">result</span><span class="p">:</span>
+
+        <span class="n">score</span> <span class="o">=</span> <span class="n">rescore</span><span class="o">.</span><span class="n">search</span><span class="p">(</span><span class="n">row</span><span class="p">)</span>
+
+        <span class="k">if</span> <span class="n">score</span><span class="p">:</span>
+
+            <span class="n">score</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">score</span><span class="o">.</span><span class="n">groups</span><span class="p">()[</span><span class="mi">0</span><span class="p">])</span>
+
+        <span class="n">row</span> <span class="o">=</span> <span class="n">row</span><span class="o">.</span><span class="n">split</span><span class="p">()</span>
+
+        <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">row</span><span class="p">)</span> <span class="o">&lt;</span> <span class="mi">2</span><span class="p">:</span>
+
+            <span class="k">continue</span>
+
+        <span class="n">id_a</span><span class="p">,</span> <span class="n">isoform_a</span> <span class="o">=</span> <span class="n">reuniprot</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="n">row</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span><span class="o">.</span><span class="n">groups</span><span class="p">()</span>
+        <span class="n">id_b</span><span class="p">,</span> <span class="n">isoform_b</span> <span class="o">=</span> <span class="n">reuniprot</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="n">row</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span><span class="o">.</span><span class="n">groups</span><span class="p">()</span>
+
+        <span class="n">uniprots_a</span> <span class="o">=</span> <span class="n">_map_ids</span><span class="p">(</span><span class="n">id_a</span><span class="p">)</span>
+        <span class="n">uniprots_b</span> <span class="o">=</span> <span class="n">_map_ids</span><span class="p">(</span><span class="n">id_b</span><span class="p">)</span>
+
+        <span class="k">for</span> <span class="n">uniprot_a</span><span class="p">,</span> <span class="n">uniprot_b</span> <span class="ow">in</span> <span class="n">itertools</span><span class="o">.</span><span class="n">product</span><span class="p">(</span><span class="n">uniprots_a</span><span class="p">,</span> <span class="n">uniprots_b</span><span class="p">):</span>
+
+            <span class="c1">#pass</span>
+            <span class="k">yield</span> <span class="n">HuriInteraction</span><span class="p">(</span>
+                <span class="n">uniprot_a</span> <span class="o">=</span> <span class="n">uniprot_a</span><span class="p">,</span>
+                <span class="n">uniprot_b</span> <span class="o">=</span> <span class="n">uniprot_b</span><span class="p">,</span>
+                <span class="n">isoform_a</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">isoform_a</span><span class="p">)</span> <span class="k">if</span> <span class="n">isoform_a</span> <span class="k">else</span> <span class="mi">1</span><span class="p">,</span>
+                <span class="n">isoform_b</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">isoform_b</span><span class="p">)</span> <span class="k">if</span> <span class="n">isoform_b</span> <span class="k">else</span> <span class="mi">1</span><span class="p">,</span>
+                <span class="n">score</span> <span class="o">=</span> <span class="n">score</span><span class="p">,</span>
+            <span class="p">)</span>
+</pre></div>
+
+                </article>
+              
+              
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+  <h1>Source code for pypath.inputs.icellnet</h1><div class="highlight"><pre>
+<span></span><span class="ch">#!/usr/bin/env python</span>
+<span class="c1"># -*- coding: utf-8 -*-</span>
+
+<span class="c1">#</span>
+<span class="c1">#  This file is part of the `pypath` python module</span>
+<span class="c1">#</span>
+<span class="c1">#  Copyright 2014-2023</span>
+<span class="c1">#  EMBL, EMBL-EBI, Uniklinik RWTH Aachen, Heidelberg University</span>
+<span class="c1">#</span>
+<span class="c1">#  Authors: see the file `README.rst`</span>
+<span class="c1">#  Contact: Dénes Türei (turei.denes@gmail.com)</span>
+<span class="c1">#</span>
+<span class="c1">#  Distributed under the GPLv3 License.</span>
+<span class="c1">#  See accompanying file LICENSE.txt or copy at</span>
+<span class="c1">#      https://www.gnu.org/licenses/gpl-3.0.html</span>
+<span class="c1">#</span>
+<span class="c1">#  Website: https://pypath.omnipathdb.org/</span>
+<span class="c1">#</span>
+
+<span class="kn">from</span> <span class="nn">future.utils</span> <span class="kn">import</span> <span class="n">iteritems</span>
+
+<span class="kn">import</span> <span class="nn">re</span>
+<span class="kn">import</span> <span class="nn">collections</span>
+<span class="kn">import</span> <span class="nn">itertools</span>
+<span class="kn">import</span> <span class="nn">csv</span>
+
+<span class="kn">import</span> <span class="nn">pypath.resources.urls</span> <span class="k">as</span> <span class="nn">urls</span>
+<span class="kn">import</span> <span class="nn">pypath.share.curl</span> <span class="k">as</span> <span class="nn">curl</span>
+<span class="kn">import</span> <span class="nn">pypath.utils.mapping</span> <span class="k">as</span> <span class="nn">mapping</span>
+<span class="kn">import</span> <span class="nn">pypath.internals.intera</span> <span class="k">as</span> <span class="nn">intera</span>
+<span class="kn">import</span> <span class="nn">pypath.core.entity</span> <span class="k">as</span> <span class="nn">entity</span>
+<span class="kn">import</span> <span class="nn">pypath.inputs.pubmed</span> <span class="k">as</span> <span class="nn">pubmed_input</span>
+
+
+<span class="n">IcellnetRecord</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">namedtuple</span><span class="p">(</span>
+    <span class="s1">&#39;IcellnetRecord&#39;</span><span class="p">,</span>
+    <span class="p">[</span>
+        <span class="s1">&#39;ligand&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;receptor&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;family&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;subfamily&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;classification&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;resources&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;references&#39;</span><span class="p">,</span>
+    <span class="p">]</span>
+<span class="p">)</span>
+
+
+<div class="viewcode-block" id="icellnet_interactions">
+<a class="viewcode-back" href="../../../api/pypath.inputs.icellnet.icellnet_interactions.html#pypath.inputs.icellnet.icellnet_interactions">[docs]</a>
+<span class="k">def</span> <span class="nf">icellnet_interactions</span><span class="p">():</span>
+
+    <span class="n">url</span> <span class="o">=</span> <span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;icellnet&#39;</span><span class="p">][</span><span class="s1">&#39;url&#39;</span><span class="p">]</span>
+    <span class="n">c</span> <span class="o">=</span> <span class="n">curl</span><span class="o">.</span><span class="n">Curl</span><span class="p">(</span><span class="n">url</span><span class="p">,</span> <span class="n">silent</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span> <span class="n">large</span> <span class="o">=</span> <span class="kc">True</span><span class="p">)</span>
+
+    <span class="n">bom</span> <span class="o">=</span> <span class="n">c</span><span class="o">.</span><span class="n">fileobj</span><span class="o">.</span><span class="n">read</span><span class="p">(</span><span class="mi">1</span><span class="p">)</span> <span class="c1"># this file starts with an UTF8 BOM</span>
+
+    <span class="k">if</span> <span class="n">bom</span> <span class="o">!=</span> <span class="s1">&#39;</span><span class="se">\ufeff</span><span class="s1">&#39;</span><span class="p">:</span>
+
+        <span class="n">c</span><span class="o">.</span><span class="n">fileobj</span><span class="o">.</span><span class="n">seek</span><span class="p">(</span><span class="mi">0</span><span class="p">)</span>
+
+    <span class="n">tbl</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="n">csv</span><span class="o">.</span><span class="n">DictReader</span><span class="p">(</span><span class="n">c</span><span class="o">.</span><span class="n">result</span><span class="p">,</span> <span class="n">delimiter</span> <span class="o">=</span> <span class="s1">&#39;;&#39;</span><span class="p">))</span>
+
+    <span class="k">for</span> <span class="n">line</span> <span class="ow">in</span> <span class="n">tbl</span><span class="p">:</span>
+
+        <span class="n">references</span> <span class="o">=</span> <span class="n">_icellnet_get_references</span><span class="p">(</span><span class="n">line</span><span class="p">)</span>
+        <span class="n">resources</span> <span class="o">=</span> <span class="n">_icellnet_get_resources</span><span class="p">(</span><span class="n">line</span><span class="p">)</span>
+
+        <span class="k">if</span> <span class="n">resources</span><span class="p">:</span>
+
+            <span class="n">references</span><span class="o">.</span><span class="n">extend</span><span class="p">([</span><span class="n">r</span> <span class="k">for</span> <span class="n">r</span> <span class="ow">in</span> <span class="n">resources</span> <span class="k">if</span> <span class="n">r</span><span class="o">.</span><span class="n">isdigit</span><span class="p">()])</span>
+            <span class="n">resources</span> <span class="o">=</span> <span class="p">[</span><span class="n">r</span> <span class="k">for</span> <span class="n">r</span> <span class="ow">in</span> <span class="n">resources</span> <span class="k">if</span> <span class="ow">not</span> <span class="n">r</span><span class="o">.</span><span class="n">isdigit</span><span class="p">()]</span>
+
+        <span class="n">ligand_components</span> <span class="o">=</span> <span class="n">_icellnet_get_components</span><span class="p">(</span><span class="n">line</span><span class="p">,</span> <span class="s1">&#39;Ligand&#39;</span><span class="p">)</span>
+        <span class="n">receptor_components</span> <span class="o">=</span> <span class="n">_icellnet_get_components</span><span class="p">(</span><span class="n">line</span><span class="p">,</span> <span class="s1">&#39;Receptor&#39;</span><span class="p">)</span>
+
+        <span class="n">ligand</span> <span class="o">=</span> <span class="n">_icellnet_get_entity</span><span class="p">(</span><span class="n">ligand_components</span><span class="p">,</span> <span class="n">references</span><span class="p">)</span>
+        <span class="n">receptor</span> <span class="o">=</span> <span class="n">_icellnet_get_entity</span><span class="p">(</span><span class="n">receptor_components</span><span class="p">,</span> <span class="n">references</span><span class="p">)</span>
+
+        <span class="k">if</span> <span class="n">ligand</span> <span class="ow">and</span> <span class="n">receptor</span><span class="p">:</span>
+
+            <span class="k">yield</span> <span class="n">IcellnetRecord</span><span class="p">(</span>
+                <span class="n">ligand</span> <span class="o">=</span> <span class="n">ligand</span><span class="p">,</span>
+                <span class="n">receptor</span> <span class="o">=</span> <span class="n">receptor</span><span class="p">,</span>
+                <span class="n">family</span> <span class="o">=</span> <span class="n">line</span><span class="p">[</span><span class="s1">&#39;Family&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span> <span class="ow">or</span> <span class="kc">None</span><span class="p">,</span>
+                <span class="n">subfamily</span> <span class="o">=</span> <span class="n">line</span><span class="p">[</span><span class="s1">&#39;Subfamily&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span> <span class="ow">or</span> <span class="kc">None</span><span class="p">,</span>
+                <span class="n">classification</span> <span class="o">=</span> <span class="p">(</span>
+                    <span class="p">[</span>
+                        <span class="bp">cls</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s1">&#39;.&#39;</span><span class="p">,</span> <span class="s1">&#39;&#39;</span><span class="p">)</span><span class="o">.</span><span class="n">capitalize</span><span class="p">()</span>
+                        <span class="k">for</span> <span class="bp">cls</span> <span class="ow">in</span>
+                        <span class="n">line</span><span class="p">[</span><span class="s1">&#39;Classifications&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;/&#39;</span><span class="p">)</span>
+                    <span class="p">]</span>
+                        <span class="k">if</span> <span class="n">line</span><span class="p">[</span><span class="s1">&#39;Classifications&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span> <span class="k">else</span>
+                    <span class="kc">None</span>
+                <span class="p">),</span>
+                <span class="n">resources</span> <span class="o">=</span> <span class="n">resources</span><span class="p">,</span>
+                <span class="n">references</span> <span class="o">=</span> <span class="n">references</span><span class="p">,</span>
+            <span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="icellnet_complexes">
+<a class="viewcode-back" href="../../../api/pypath.inputs.icellnet.icellnet_complexes.html#pypath.inputs.icellnet.icellnet_complexes">[docs]</a>
+<span class="k">def</span> <span class="nf">icellnet_complexes</span><span class="p">():</span>
+
+    <span class="n">complexes</span> <span class="o">=</span> <span class="p">{}</span>
+
+    <span class="k">for</span> <span class="n">ia</span> <span class="ow">in</span> <span class="n">icellnet_interactions</span><span class="p">():</span>
+
+        <span class="k">for</span> <span class="n">attr</span> <span class="ow">in</span> <span class="p">(</span><span class="s1">&#39;ligand&#39;</span><span class="p">,</span> <span class="s1">&#39;receptor&#39;</span><span class="p">):</span>
+
+            <span class="k">if</span> <span class="nb">hasattr</span><span class="p">(</span><span class="nb">getattr</span><span class="p">(</span><span class="n">ia</span><span class="p">,</span> <span class="n">attr</span><span class="p">),</span> <span class="s1">&#39;components&#39;</span><span class="p">):</span>
+
+                <span class="n">cplex</span> <span class="o">=</span> <span class="nb">getattr</span><span class="p">(</span><span class="n">ia</span><span class="p">,</span> <span class="n">attr</span><span class="p">)</span>
+                <span class="n">cplex_str</span> <span class="o">=</span> <span class="n">cplex</span><span class="o">.</span><span class="fm">__str__</span><span class="p">()</span>
+
+                <span class="k">if</span> <span class="n">cplex_str</span> <span class="ow">in</span> <span class="n">complexes</span><span class="p">:</span>
+
+                    <span class="n">complexes</span><span class="p">[</span><span class="n">cplex_str</span><span class="p">]</span> <span class="o">+=</span> <span class="n">cplex</span>
+
+                <span class="k">else</span><span class="p">:</span>
+
+                    <span class="n">complexes</span><span class="p">[</span><span class="n">cplex_str</span><span class="p">]</span> <span class="o">=</span> <span class="n">cplex</span>
+
+    <span class="k">return</span> <span class="n">complexes</span></div>
+
+
+
+<div class="viewcode-block" id="icellnet_annotations">
+<a class="viewcode-back" href="../../../api/pypath.inputs.icellnet.icellnet_annotations.html#pypath.inputs.icellnet.icellnet_annotations">[docs]</a>
+<span class="k">def</span> <span class="nf">icellnet_annotations</span><span class="p">(</span><span class="n">complexes</span> <span class="o">=</span> <span class="kc">None</span><span class="p">):</span>
+
+    <span class="n">IcellnetAnnotation</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">namedtuple</span><span class="p">(</span>
+        <span class="s1">&#39;IcellnetAnnotation&#39;</span><span class="p">,</span>
+        <span class="p">[</span>
+            <span class="s1">&#39;role&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;family&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;subfamily&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;classification&#39;</span><span class="p">,</span>
+        <span class="p">]</span>
+    <span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">get_entities</span><span class="p">(</span><span class="n">ia</span><span class="p">,</span> <span class="n">entity_attr</span><span class="p">,</span> <span class="n">complexes</span><span class="p">):</span>
+
+        <span class="n">entities</span> <span class="o">=</span> <span class="nb">getattr</span><span class="p">(</span><span class="n">ia</span><span class="p">,</span> <span class="n">entity_attr</span><span class="p">)</span>
+
+        <span class="k">if</span> <span class="ow">not</span> <span class="n">entities</span><span class="p">:</span>
+
+            <span class="k">return</span> <span class="p">()</span>
+
+        <span class="n">complex_entities</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="p">(</span><span class="n">entities</span><span class="p">,)</span>
+                <span class="k">if</span> <span class="n">entity</span><span class="o">.</span><span class="n">Entity</span><span class="o">.</span><span class="n">_is_complex</span><span class="p">(</span><span class="n">entities</span><span class="p">)</span> <span class="k">else</span>
+            <span class="p">()</span>
+        <span class="p">)</span>
+        <span class="n">protein_entities</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="p">(</span><span class="n">entities</span><span class="p">,)</span>
+                <span class="k">if</span> <span class="n">entity</span><span class="o">.</span><span class="n">Entity</span><span class="o">.</span><span class="n">_is_protein</span><span class="p">(</span><span class="n">entities</span><span class="p">)</span> <span class="k">else</span>
+            <span class="nb">tuple</span><span class="p">(</span><span class="n">entities</span><span class="o">.</span><span class="n">components</span><span class="o">.</span><span class="n">keys</span><span class="p">())</span>
+        <span class="p">)</span>
+
+        <span class="k">return</span> <span class="p">(</span>
+            <span class="n">complex_entities</span>
+                <span class="k">if</span> <span class="n">complexes</span> <span class="o">==</span> <span class="kc">True</span> <span class="k">else</span>
+            <span class="n">protein_entities</span>
+                <span class="k">if</span> <span class="n">complexes</span> <span class="o">==</span> <span class="kc">False</span> <span class="k">else</span>
+            <span class="n">complex_entities</span> <span class="o">+</span> <span class="n">protein_entities</span>
+        <span class="p">)</span>
+
+
+    <span class="n">annotations</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">defaultdict</span><span class="p">(</span><span class="nb">set</span><span class="p">)</span>
+
+    <span class="k">for</span> <span class="n">ia</span> <span class="ow">in</span> <span class="n">icellnet_interactions</span><span class="p">():</span>
+
+        <span class="k">for</span> <span class="n">role</span> <span class="ow">in</span> <span class="p">(</span><span class="s1">&#39;ligand&#39;</span><span class="p">,</span> <span class="s1">&#39;receptor&#39;</span><span class="p">):</span>
+
+            <span class="k">for</span> <span class="n">en</span> <span class="ow">in</span> <span class="n">get_entities</span><span class="p">(</span><span class="n">ia</span><span class="p">,</span> <span class="n">role</span><span class="p">,</span> <span class="n">complexes</span><span class="p">):</span>
+
+                <span class="n">annotations</span><span class="p">[</span><span class="n">en</span><span class="p">]</span><span class="o">.</span><span class="n">add</span><span class="p">(</span>
+                    <span class="n">IcellnetAnnotation</span><span class="p">(</span>
+                        <span class="n">role</span> <span class="o">=</span> <span class="n">role</span><span class="p">,</span>
+                        <span class="n">family</span> <span class="o">=</span> <span class="n">ia</span><span class="o">.</span><span class="n">family</span><span class="p">,</span>
+                        <span class="n">subfamily</span> <span class="o">=</span> <span class="n">ia</span><span class="o">.</span><span class="n">subfamily</span><span class="p">,</span>
+                        <span class="n">classification</span> <span class="o">=</span> <span class="p">(</span>
+                            <span class="nb">tuple</span><span class="p">(</span><span class="nb">sorted</span><span class="p">(</span><span class="n">ia</span><span class="o">.</span><span class="n">classification</span><span class="p">))</span>
+                                <span class="k">if</span> <span class="n">ia</span><span class="o">.</span><span class="n">classification</span> <span class="k">else</span>
+                            <span class="kc">None</span>
+                        <span class="p">),</span>
+                    <span class="p">)</span>
+                <span class="p">)</span>
+
+    <span class="k">return</span> <span class="nb">dict</span><span class="p">(</span><span class="n">annotations</span><span class="p">)</span></div>
+
+
+
+<span class="k">def</span> <span class="nf">_icellnet_get_components</span><span class="p">(</span><span class="n">line</span><span class="p">,</span> <span class="n">prefix</span><span class="p">):</span>
+
+    <span class="n">genesymbols</span> <span class="o">=</span> <span class="p">[</span>
+        <span class="n">genesymbol</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span>
+        <span class="k">for</span> <span class="n">label</span><span class="p">,</span> <span class="n">genesymbol</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="n">line</span><span class="p">)</span>
+        <span class="k">if</span> <span class="n">label</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="n">prefix</span><span class="p">)</span> <span class="ow">and</span> <span class="n">genesymbol</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span>
+    <span class="p">]</span>
+
+    <span class="k">return</span> <span class="p">[</span>
+        <span class="n">uniprot</span>
+        <span class="k">for</span> <span class="n">uniprot</span> <span class="ow">in</span>
+        <span class="p">(</span>
+            <span class="n">mapping</span><span class="o">.</span><span class="n">map_name0</span><span class="p">(</span><span class="n">genesymbol</span><span class="p">,</span> <span class="s1">&#39;genesymbol&#39;</span><span class="p">,</span> <span class="s1">&#39;uniprot&#39;</span><span class="p">)</span>
+            <span class="k">for</span> <span class="n">genesymbol</span> <span class="ow">in</span> <span class="n">genesymbols</span>
+        <span class="p">)</span>
+        <span class="k">if</span> <span class="n">uniprot</span>
+    <span class="p">]</span>
+
+
+<span class="k">def</span> <span class="nf">_icellnet_get_entity</span><span class="p">(</span><span class="n">components</span><span class="p">,</span> <span class="n">references</span><span class="p">):</span>
+
+    <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">components</span><span class="p">)</span> <span class="o">&gt;</span> <span class="mi">1</span><span class="p">:</span>
+
+        <span class="k">return</span> <span class="n">intera</span><span class="o">.</span><span class="n">Complex</span><span class="p">(</span>
+            <span class="n">components</span> <span class="o">=</span> <span class="n">components</span><span class="p">,</span>
+            <span class="n">sources</span> <span class="o">=</span> <span class="s1">&#39;ICELLNET&#39;</span><span class="p">,</span>
+            <span class="n">references</span> <span class="o">=</span> <span class="n">references</span><span class="p">,</span>
+        <span class="p">)</span>
+
+    <span class="k">elif</span> <span class="nb">len</span><span class="p">(</span><span class="n">components</span><span class="p">)</span> <span class="o">==</span> <span class="mi">1</span><span class="p">:</span>
+
+        <span class="k">return</span> <span class="n">components</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span>
+
+
+<span class="k">def</span> <span class="nf">_icellnet_get_references</span><span class="p">(</span><span class="n">line</span><span class="p">):</span>
+
+    <span class="k">return</span> <span class="p">[</span>
+        <span class="nb">str</span><span class="p">(</span><span class="nb">int</span><span class="p">(</span><span class="nb">float</span><span class="p">(</span><span class="n">ref</span><span class="p">)))</span>
+        <span class="k">for</span> <span class="n">ref</span> <span class="ow">in</span>
+        <span class="n">pubmed_input</span><span class="o">.</span><span class="n">only_pmids</span><span class="p">(</span>
+            <span class="n">ref</span>
+            <span class="k">for</span> <span class="n">ref</span> <span class="ow">in</span>
+            <span class="p">(</span><span class="n">_ref</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span> <span class="k">for</span> <span class="n">_ref</span> <span class="ow">in</span> <span class="n">re</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="sa">r</span><span class="s1">&#39;[,;]&#39;</span><span class="p">,</span> <span class="n">line</span><span class="p">[</span><span class="s1">&#39;PubMed ID&#39;</span><span class="p">]))</span>
+            <span class="k">if</span> <span class="n">ref</span>
+        <span class="p">)</span>
+    <span class="p">]</span>
+
+
+<span class="k">def</span> <span class="nf">_icellnet_get_resources</span><span class="p">(</span><span class="n">line</span><span class="p">):</span>
+
+    <span class="c1"># the recent update of ICELLNET does not list the resources any more :(</span>
+    <span class="k">return</span> <span class="kc">None</span>
+
+    <span class="n">rerami</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">compile</span><span class="p">(</span><span class="sa">r</span><span class="s1">&#39;(Ramilowski)\d</span><span class="si">{4}</span><span class="s1">&#39;</span><span class="p">)</span>
+    <span class="n">resource_synonyms</span> <span class="o">=</span> <span class="p">{</span>
+        <span class="s1">&#39;Signor&#39;</span><span class="p">:</span> <span class="s1">&#39;SIGNOR&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;guidetopharmacology.org&#39;</span><span class="p">:</span> <span class="s1">&#39;Guide2Pharma&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;IUPHAR&#39;</span><span class="p">:</span> <span class="s1">&#39;Guide2Pharma&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;IUPHAR-DB&#39;</span><span class="p">:</span> <span class="s1">&#39;Guide2Pharma&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;GO_lig_rec&#39;</span><span class="p">:</span> <span class="s1">&#39;GO-lig-rec&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;CellPhone&#39;</span><span class="p">:</span> <span class="s1">&#39;CellPhoneDB&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;SignaLink&#39;</span><span class="p">:</span> <span class="s1">&#39;SignaLink3&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;Innate&#39;</span><span class="p">:</span> <span class="s1">&#39;InnateDB&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;Kegg&#39;</span><span class="p">:</span> <span class="s1">&#39;KEGG&#39;</span><span class="p">,</span>
+    <span class="p">}</span>
+
+    <span class="n">resources</span> <span class="o">=</span> <span class="n">line</span><span class="p">[</span><span class="s1">&#39;Source for interaction&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span>
+        <span class="s1">&#39;Dinarello et al.2013 (Immunity)&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;Dinarello2013&#39;</span>
+    <span class="p">)</span>
+    <span class="n">resources</span> <span class="o">=</span> <span class="p">{</span>
+        <span class="n">rerami</span><span class="o">.</span><span class="n">sub</span><span class="p">(</span>
+            <span class="sa">r</span><span class="s1">&#39;\g&lt;1&gt;2015&#39;</span><span class="p">,</span>
+            <span class="n">resource_synonyms</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="n">res</span><span class="p">,</span> <span class="n">res</span><span class="p">)</span>
+        <span class="p">)</span>
+        <span class="k">for</span> <span class="n">res</span> <span class="ow">in</span>
+        <span class="p">(</span><span class="n">_res</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span> <span class="k">for</span> <span class="n">_res</span> <span class="ow">in</span> <span class="n">re</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="sa">r</span><span class="s1">&#39;[/,; ]&#39;</span><span class="p">,</span> <span class="n">resources</span><span class="p">))</span>
+    <span class="p">}</span>
+
+    <span class="n">resources</span><span class="o">.</span><span class="n">discard</span><span class="p">(</span><span class="s1">&#39;&#39;</span><span class="p">)</span>
+    <span class="n">resources</span><span class="o">.</span><span class="n">discard</span><span class="p">(</span><span class="s1">&#39;DB&#39;</span><span class="p">)</span>
+
+    <span class="k">return</span> <span class="nb">sorted</span><span class="p">(</span><span class="n">resources</span><span class="p">)</span> <span class="ow">or</span> <span class="kc">None</span>
+</pre></div>
+
+                </article>
+              
+              
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diff --git a/_modules/pypath/inputs/integrins.html b/_modules/pypath/inputs/integrins.html
new file mode 100644
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+                        Webservice
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+                        Release history
+                      </a>
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+                
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+                      <a class="nav-link nav-internal" href="../../../reference.html">
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+                        The pypath book
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+
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+            <span class="sr-only">PyPI</span></a>
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+            <span class="sr-only">Saez Lab</span></a>
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+ `);
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+        
+          <div class="navbar-item">
+<nav class="navbar-nav">
+  <ul class="bd-navbar-elements navbar-nav">
+    
+                    <li class="nav-item">
+                      <a class="nav-link nav-internal" href="../../../index.html">
+                        Welcome to pypath!
+                      </a>
+                    </li>
+                
+
+                    <li class="nav-item">
+                      <a class="nav-link nav-internal" href="../../../webservice.html">
+                        Webservice
+                      </a>
+                    </li>
+                
+
+                    <li class="nav-item">
+                      <a class="nav-link nav-internal" href="../../../releasehistory.html">
+                        Release history
+                      </a>
+                    </li>
+                
+
+                    <li class="nav-item">
+                      <a class="nav-link nav-internal" href="../../../reference.html">
+                        Reference
+                      </a>
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+                
+
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+                        The pypath book
+                      </a>
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+                
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+    
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+document.write(`
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+    <span class="theme-switch nav-link" data-mode="light"><i class="fa-solid fa-sun fa-lg"></i></span>
+    <span class="theme-switch nav-link" data-mode="dark"><i class="fa-solid fa-moon fa-lg"></i></span>
+    <span class="theme-switch nav-link" data-mode="auto"><i class="fa-solid fa-circle-half-stroke fa-lg"></i></span>
+  </button>
+`);
+</script></div>
+        
+          <div class="navbar-item"><ul class="navbar-icon-links navbar-nav"
+    aria-label="Icon Links">
+        <li class="nav-item">
+          
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+          
+          <a href="https://github.com/saezlab/pypath" title="GitHub" class="nav-link" rel="noopener" target="_blank" data-bs-toggle="tooltip" data-bs-placement="bottom"><span><i class="fa-brands fa-square-github fa-lg" aria-hidden="true"></i></span>
+            <span class="sr-only">GitHub</span></a>
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+          
+          
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+          <a href="https://twitter.com/omnipathdb" title="Twitter" class="nav-link" rel="noopener" target="_blank" data-bs-toggle="tooltip" data-bs-placement="bottom"><span><i class="fa-brands fa-square-twitter fa-lg" aria-hidden="true"></i></span>
+            <span class="sr-only">Twitter</span></a>
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+        <li class="nav-item">
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+        <li class="nav-item">
+          
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+          
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+          
+          
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+          
+          <a href="https://omnipathdb.org/" title="OmniPath" class="nav-link" rel="noopener" target="_blank" data-bs-toggle="tooltip" data-bs-placement="bottom"><span><i class="fa-solid fa-university fa-lg" aria-hidden="true"></i></span>
+            <span class="sr-only">OmniPath</span></a>
+        </li>
+        <li class="nav-item">
+          
+          
+          
+          
+          
+          
+          
+          
+          <a href="https://saezlab.org/" title="Saez Lab" class="nav-link" rel="noopener" target="_blank" data-bs-toggle="tooltip" data-bs-placement="bottom"><span><i class="fa-solid fa-users fa-lg" aria-hidden="true"></i></span>
+            <span class="sr-only">Saez Lab</span></a>
+        </li>
+</ul></div>
+        
+      </div>
+    
+  </div>
+  
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+  <div class="sidebar-primary-items__end sidebar-primary__section">
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+  
+  <div id="rtd-footer-container"></div>
+
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+      
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+        
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+            <div class="bd-article-container">
+              
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+  <h1>Source code for pypath.inputs.integrins</h1><div class="highlight"><pre>
+<span></span><span class="ch">#!/usr/bin/env python</span>
+<span class="c1"># -*- coding: utf-8 -*-</span>
+
+<span class="c1">#</span>
+<span class="c1">#  This file is part of the `pypath` python module</span>
+<span class="c1">#</span>
+<span class="c1">#  Copyright 2014-2023</span>
+<span class="c1">#  EMBL, EMBL-EBI, Uniklinik RWTH Aachen, Heidelberg University</span>
+<span class="c1">#</span>
+<span class="c1">#  Authors: see the file `README.rst`</span>
+<span class="c1">#  Contact: Dénes Türei (turei.denes@gmail.com)</span>
+<span class="c1">#</span>
+<span class="c1">#  Distributed under the GPLv3 License.</span>
+<span class="c1">#  See accompanying file LICENSE.txt or copy at</span>
+<span class="c1">#      https://www.gnu.org/licenses/gpl-3.0.html</span>
+<span class="c1">#</span>
+<span class="c1">#  Website: https://pypath.omnipathdb.org/</span>
+<span class="c1">#</span>
+
+<span class="kn">import</span> <span class="nn">bs4</span>
+
+<span class="kn">import</span> <span class="nn">pypath.share.curl</span> <span class="k">as</span> <span class="nn">curl</span>
+<span class="kn">import</span> <span class="nn">pypath.resources.urls</span> <span class="k">as</span> <span class="nn">urls</span>
+<span class="kn">import</span> <span class="nn">pypath.utils.mapping</span> <span class="k">as</span> <span class="nn">mapping</span>
+
+
+<div class="viewcode-block" id="get_integrins">
+<a class="viewcode-back" href="../../../api/pypath.inputs.integrins.get_integrins.html#pypath.inputs.integrins.get_integrins">[docs]</a>
+<span class="k">def</span> <span class="nf">get_integrins</span><span class="p">():</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Returns a set of the UniProt IDs of the human integrins from</span>
+<span class="sd">    Table 1 of Takada et al 2007 (10.1186/gb-2007-8-5-215).</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="n">url</span> <span class="o">=</span> <span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;integrins&#39;</span><span class="p">][</span><span class="s1">&#39;url&#39;</span><span class="p">]</span>
+
+    <span class="n">req_headers</span> <span class="o">=</span> <span class="p">[</span>
+        <span class="s1">&#39;Host: www.ncbi.nlm.nih.gov&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;User-Agent: Mozilla/5.0 (X11; Linux x86_64; rv:67.0) &#39;</span>\
+            <span class="s1">&#39;Gecko/20100101 Firefox/67.0&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;Accept: text/html,application/xhtml+xml,&#39;</span>
+            <span class="s1">&#39;application/xml;q=0.9,*/*;q=0.8&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;Accept-Language: en-US,en;q=0.5&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;Connection: keep-alive&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;Upgrade-Insecure-Requests: 1&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;Pragma: no-cache&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;Cache-Control: no-cache&#39;</span><span class="p">,</span>
+    <span class="p">]</span>
+
+    <span class="n">c</span> <span class="o">=</span> <span class="n">curl</span><span class="o">.</span><span class="n">Curl</span><span class="p">(</span>
+        <span class="n">url</span><span class="p">,</span> <span class="n">silent</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span> <span class="n">req_headers</span> <span class="o">=</span> <span class="n">req_headers</span><span class="p">,</span> <span class="n">large</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
+    <span class="p">)</span>
+    <span class="n">soup</span> <span class="o">=</span> <span class="n">bs4</span><span class="o">.</span><span class="n">BeautifulSoup</span><span class="p">(</span><span class="n">c</span><span class="o">.</span><span class="n">fileobj</span><span class="o">.</span><span class="n">read</span><span class="p">(),</span> <span class="s1">&#39;lxml&#39;</span><span class="p">)</span>
+
+    <span class="n">integrins</span> <span class="o">=</span> <span class="p">[]</span>
+
+    <span class="n">rows</span> <span class="o">=</span> <span class="n">soup</span><span class="o">.</span><span class="n">find_all</span><span class="p">(</span><span class="s1">&#39;tr&#39;</span><span class="p">)</span>
+
+    <span class="k">for</span> <span class="n">tr</span> <span class="ow">in</span> <span class="n">rows</span><span class="p">[</span><span class="mi">1</span><span class="p">:]:</span>
+        <span class="n">cells</span> <span class="o">=</span> <span class="p">[</span><span class="n">td</span> <span class="k">for</span> <span class="n">td</span> <span class="ow">in</span> <span class="n">tr</span><span class="o">.</span><span class="n">find_all</span><span class="p">(</span><span class="s1">&#39;td&#39;</span><span class="p">)]</span>
+        <span class="n">integrins</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">cells</span><span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">text</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;}&#39;</span><span class="p">)[</span><span class="o">-</span><span class="mi">1</span><span class="p">])</span>
+
+    <span class="k">return</span> <span class="n">mapping</span><span class="o">.</span><span class="n">map_names</span><span class="p">(</span><span class="n">integrins</span><span class="p">,</span> <span class="s1">&#39;uniprot&#39;</span><span class="p">,</span> <span class="s1">&#39;uniprot&#39;</span><span class="p">)</span></div>
+
+</pre></div>
+
+                </article>
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diff --git a/_modules/pypath/inputs/intogen.html b/_modules/pypath/inputs/intogen.html
new file mode 100644
index 000000000..e2e72b4c7
--- /dev/null
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@@ -0,0 +1,708 @@
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+  <h1>Source code for pypath.inputs.intogen</h1><div class="highlight"><pre>
+<span></span><span class="ch">#!/usr/bin/env python</span>
+<span class="c1"># -*- coding: utf-8 -*-</span>
+
+<span class="c1">#</span>
+<span class="c1">#  This file is part of the `pypath` python module</span>
+<span class="c1">#</span>
+<span class="c1">#  Copyright 2014-2023</span>
+<span class="c1">#  EMBL, EMBL-EBI, Uniklinik RWTH Aachen, Heidelberg University</span>
+<span class="c1">#</span>
+<span class="c1">#  Authors: see the file `README.rst`</span>
+<span class="c1">#  Contact: Dénes Türei (turei.denes@gmail.com)</span>
+<span class="c1">#</span>
+<span class="c1">#  Distributed under the GPLv3 License.</span>
+<span class="c1">#  See accompanying file LICENSE.txt or copy at</span>
+<span class="c1">#      https://www.gnu.org/licenses/gpl-3.0.html</span>
+<span class="c1">#</span>
+<span class="c1">#  Website: https://pypath.omnipathdb.org/</span>
+<span class="c1">#</span>
+
+<span class="kn">from</span> <span class="nn">past.builtins</span> <span class="kn">import</span> <span class="n">xrange</span><span class="p">,</span> <span class="nb">range</span>
+
+<span class="kn">import</span> <span class="nn">csv</span>
+<span class="kn">import</span> <span class="nn">collections</span>
+
+<span class="kn">import</span> <span class="nn">pypath.resources.urls</span> <span class="k">as</span> <span class="nn">urls</span>
+<span class="kn">import</span> <span class="nn">pypath.share.curl</span> <span class="k">as</span> <span class="nn">curl</span>
+<span class="kn">import</span> <span class="nn">pypath.share.common</span> <span class="k">as</span> <span class="nn">common</span>
+<span class="kn">import</span> <span class="nn">pypath.share.settings</span> <span class="k">as</span> <span class="nn">settings</span>
+<span class="kn">import</span> <span class="nn">pypath.utils.mapping</span> <span class="k">as</span> <span class="nn">mapping</span>
+
+
+<div class="viewcode-block" id="intogen_annotations">
+<a class="viewcode-back" href="../../../api/pypath.inputs.intogen.intogen_annotations.html#pypath.inputs.intogen.intogen_annotations">[docs]</a>
+<span class="k">def</span> <span class="nf">intogen_annotations</span><span class="p">():</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Returns a list of cancer driver genes with their annotations,</span>
+<span class="sd">    according to the IntOGen database.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="n">IntogenAnnotation</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">namedtuple</span><span class="p">(</span>
+        <span class="s1">&#39;IntogenAnnotation&#39;</span><span class="p">,</span>
+        <span class="p">[</span>
+            <span class="s1">&#39;type&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;role&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;curated&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;oncodrive_role_prob&#39;</span><span class="p">,</span>
+        <span class="p">],</span>
+    <span class="p">)</span>
+
+
+    <span class="n">url</span> <span class="o">=</span> <span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;intogen&#39;</span><span class="p">][</span><span class="s1">&#39;db2014_2&#39;</span><span class="p">]</span>
+
+    <span class="k">with</span> <span class="n">settings</span><span class="o">.</span><span class="n">context</span><span class="p">(</span><span class="n">curl_connect_timeout</span> <span class="o">=</span> <span class="mi">100</span><span class="p">):</span>
+
+        <span class="n">c</span> <span class="o">=</span> <span class="n">curl</span><span class="o">.</span><span class="n">Curl</span><span class="p">(</span>
+            <span class="n">url</span><span class="p">,</span>
+            <span class="n">large</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
+            <span class="n">silent</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+            <span class="n">files_needed</span> <span class="o">=</span> <span class="p">[</span><span class="s1">&#39;Drivers_type_role.tsv&#39;</span><span class="p">],</span>
+            <span class="n">compr</span> <span class="o">=</span> <span class="s1">&#39;zip&#39;</span><span class="p">,</span>
+        <span class="p">)</span>
+
+    <span class="k">for</span> <span class="n">_</span> <span class="ow">in</span> <span class="n">xrange</span><span class="p">(</span><span class="mi">7</span><span class="p">):</span>
+
+        <span class="n">__</span> <span class="o">=</span> <span class="n">c</span><span class="o">.</span><span class="n">result</span><span class="p">[</span><span class="s1">&#39;Drivers_type_role.tsv&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">readline</span><span class="p">()</span>
+
+    <span class="n">data</span> <span class="o">=</span> <span class="n">csv</span><span class="o">.</span><span class="n">DictReader</span><span class="p">(</span>
+        <span class="n">c</span><span class="o">.</span><span class="n">result</span><span class="p">[</span><span class="s1">&#39;Drivers_type_role.tsv&#39;</span><span class="p">],</span>
+        <span class="n">delimiter</span> <span class="o">=</span> <span class="s1">&#39;</span><span class="se">\t</span><span class="s1">&#39;</span><span class="p">,</span>
+    <span class="p">)</span>
+    <span class="n">result</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">defaultdict</span><span class="p">(</span><span class="nb">set</span><span class="p">)</span>
+
+    <span class="k">for</span> <span class="n">rec</span> <span class="ow">in</span> <span class="n">data</span><span class="p">:</span>
+
+        <span class="n">uniprots</span> <span class="o">=</span> <span class="n">mapping</span><span class="o">.</span><span class="n">map_name</span><span class="p">(</span>
+            <span class="n">rec</span><span class="p">[</span><span class="s1">&#39;geneHGNCsymbol&#39;</span><span class="p">],</span>
+            <span class="s1">&#39;genesymbol&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;uniprot&#39;</span><span class="p">,</span>
+        <span class="p">)</span>
+
+        <span class="k">for</span> <span class="n">uniprot</span> <span class="ow">in</span> <span class="n">uniprots</span><span class="p">:</span>
+
+            <span class="n">role_prob</span><span class="p">,</span> <span class="n">curated</span> <span class="o">=</span> <span class="p">(</span>
+                <span class="p">(</span>
+                    <span class="mf">1.0</span><span class="p">,</span>
+                    <span class="kc">True</span><span class="p">,</span>
+                <span class="p">)</span>
+                <span class="k">if</span> <span class="n">rec</span><span class="p">[</span><span class="s1">&#39;OncodriveROLE_prob&#39;</span><span class="p">]</span> <span class="o">==</span> <span class="s1">&#39;Manually curated&#39;</span> <span class="k">else</span>
+                <span class="p">(</span>
+                    <span class="n">common</span><span class="o">.</span><span class="n">float_or_nan</span><span class="p">(</span><span class="n">rec</span><span class="p">[</span><span class="s1">&#39;OncodriveROLE_prob&#39;</span><span class="p">]),</span>
+                    <span class="kc">False</span><span class="p">,</span>
+                <span class="p">)</span>
+            <span class="p">)</span>
+
+            <span class="n">result</span><span class="p">[</span><span class="n">uniprot</span><span class="p">]</span><span class="o">.</span><span class="n">add</span><span class="p">(</span>
+                <span class="n">IntogenAnnotation</span><span class="p">(</span>
+                    <span class="nb">type</span> <span class="o">=</span> <span class="n">rec</span><span class="p">[</span><span class="s1">&#39;Driver_type&#39;</span><span class="p">],</span>
+                    <span class="n">role</span> <span class="o">=</span> <span class="n">rec</span><span class="p">[</span><span class="s1">&#39;Role&#39;</span><span class="p">],</span>
+                    <span class="n">curated</span> <span class="o">=</span> <span class="n">curated</span><span class="p">,</span>
+                    <span class="n">oncodrive_role_prob</span> <span class="o">=</span> <span class="n">role_prob</span><span class="p">,</span>
+                <span class="p">)</span>
+            <span class="p">)</span>
+
+    <span class="k">return</span> <span class="nb">dict</span><span class="p">(</span><span class="n">result</span><span class="p">)</span></div>
+
+</pre></div>
+
+                </article>
+              
+              
+              
+              
+              
+                <footer class="prev-next-footer">
+                  
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+              
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+            
+          </footer>
+        
+      </main>
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+  </div>
+  
+  <!-- Scripts loaded after <body> so the DOM is not blocked -->
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+  
+    <div class="footer-items__start">
+      
+        <div class="footer-item">
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+  <p class="copyright">
+    
+      © Copyright 2024, Denes Turei &lt;turei.denes@gmail.com&gt;, Nicolàs Palacio, Sebastian Lobentanzer, Olga Ivanova, Melih Darcan, Erva Ulusoy, Tennur Kilic, Omer Kaan Vural, Ahmet Rifaioglu, Charles Tapley Hoyt.
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+  
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+  
+    <div class="footer-items__end">
+      
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+</p></div>
+      
+    </div>
+  
+</div>
+
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+  </body>
+</html>
\ No newline at end of file
diff --git a/_modules/pypath/inputs/iptmnet.html b/_modules/pypath/inputs/iptmnet.html
new file mode 100644
index 000000000..97a45f779
--- /dev/null
+++ b/_modules/pypath/inputs/iptmnet.html
@@ -0,0 +1,760 @@
+
+<!DOCTYPE html>
+
+
+<html lang="en" data-content_root="../../../" >
+
+  <head>
+    <meta charset="utf-8" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+    <title>pypath.inputs.iptmnet &#8212; pypath 0.16.9 documentation</title>
+  
+  
+  
+  <script data-cfasync="false">
+    document.documentElement.dataset.mode = localStorage.getItem("mode") || "";
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+                  
+  <h1>Source code for pypath.inputs.iptmnet</h1><div class="highlight"><pre>
+<span></span><span class="ch">#!/usr/bin/env python</span>
+<span class="c1"># -*- coding: utf-8 -*-</span>
+
+<span class="c1">#</span>
+<span class="c1">#  This file is part of the `pypath` python module</span>
+<span class="c1">#</span>
+<span class="c1">#  Copyright 2014-2023</span>
+<span class="c1">#  EMBL, EMBL-EBI, Uniklinik RWTH Aachen, Heidelberg University</span>
+<span class="c1">#</span>
+<span class="c1">#  Authors: see the file `README.rst`</span>
+<span class="c1">#  Contact: Dénes Türei (turei.denes@gmail.com)</span>
+<span class="c1">#</span>
+<span class="c1">#  Distributed under the GPLv3 License.</span>
+<span class="c1">#  See accompanying file LICENSE.txt or copy at</span>
+<span class="c1">#      https://www.gnu.org/licenses/gpl-3.0.html</span>
+<span class="c1">#</span>
+<span class="c1">#  Website: https://pypath.omnipathdb.org/</span>
+<span class="c1">#</span>
+
+<span class="kn">import</span> <span class="nn">re</span>
+<span class="kn">import</span> <span class="nn">collections</span>
+
+<span class="kn">import</span> <span class="nn">pypath.resources.urls</span> <span class="k">as</span> <span class="nn">urls</span>
+<span class="kn">import</span> <span class="nn">pypath.share.curl</span> <span class="k">as</span> <span class="nn">curl</span>
+<span class="kn">import</span> <span class="nn">pypath_common._constants</span> <span class="k">as</span> <span class="nn">_const</span>
+<span class="kn">import</span> <span class="nn">pypath.utils.taxonomy</span> <span class="k">as</span> <span class="nn">taxonomy</span>
+<span class="kn">import</span> <span class="nn">pypath.utils.mapping</span> <span class="k">as</span> <span class="nn">mapping</span>
+<span class="kn">import</span> <span class="nn">pypath.inputs.common</span> <span class="k">as</span> <span class="nn">inputs_common</span>
+
+
+<span class="n">resite</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">compile</span><span class="p">(</span><span class="sa">r</span><span class="s1">&#39;([A-Z])(\d+)&#39;</span><span class="p">)</span>
+
+
+<span class="n">IptmnetInteraction</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">namedtuple</span><span class="p">(</span>
+    <span class="s1">&#39;IptmnetInteraction&#39;</span><span class="p">,</span>
+    <span class="p">[</span>
+        <span class="s1">&#39;enzyme&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;substrate&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;enzyme_isoform&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;substrate_isoform&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;ptm_type&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;resaa&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;resnum&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;score&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;references&#39;</span><span class="p">,</span>
+    <span class="p">]</span>
+<span class="p">)</span>
+
+
+<div class="viewcode-block" id="iptmnet_interactions">
+<a class="viewcode-back" href="../../../api/pypath.inputs.iptmnet.iptmnet_interactions.html#pypath.inputs.iptmnet.iptmnet_interactions">[docs]</a>
+<span class="k">def</span> <span class="nf">iptmnet_interactions</span><span class="p">(</span><span class="n">organism</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">):</span>
+
+    <span class="n">ptm_url</span> <span class="o">=</span> <span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;iptmnet&#39;</span><span class="p">][</span><span class="s1">&#39;ptms&#39;</span><span class="p">]</span>
+    <span class="n">score_url</span> <span class="o">=</span> <span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;iptmnet&#39;</span><span class="p">][</span><span class="s1">&#39;scores&#39;</span><span class="p">]</span>
+
+    <span class="n">c</span> <span class="o">=</span> <span class="n">curl</span><span class="o">.</span><span class="n">Curl</span><span class="p">(</span><span class="n">score_url</span><span class="p">,</span> <span class="n">large</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span> <span class="n">silent</span> <span class="o">=</span> <span class="kc">False</span><span class="p">)</span>
+
+    <span class="n">scores</span> <span class="o">=</span> <span class="p">{}</span>
+
+    <span class="k">for</span> <span class="n">line</span> <span class="ow">in</span> <span class="n">c</span><span class="o">.</span><span class="n">result</span><span class="p">:</span>
+
+        <span class="n">line</span> <span class="o">=</span> <span class="n">line</span><span class="o">.</span><span class="n">strip</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\n\r</span><span class="s1">&#39;</span><span class="p">)</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\t</span><span class="s1">&#39;</span><span class="p">)</span>
+
+        <span class="k">if</span> <span class="ow">not</span> <span class="n">line</span><span class="p">[</span><span class="mi">2</span><span class="p">]:</span>
+
+            <span class="k">continue</span>
+
+        <span class="n">site</span> <span class="o">=</span> <span class="n">resite</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="n">line</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span>
+
+        <span class="k">if</span> <span class="ow">not</span> <span class="n">site</span><span class="p">:</span>
+
+            <span class="k">continue</span>
+
+        <span class="n">resaa</span><span class="p">,</span> <span class="n">resnum</span> <span class="o">=</span> <span class="n">site</span><span class="o">.</span><span class="n">groups</span><span class="p">()</span>
+
+        <span class="n">resnum</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">resnum</span><span class="p">)</span>
+        <span class="n">score</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">line</span><span class="p">[</span><span class="mi">4</span><span class="p">])</span>
+        <span class="n">substrate</span><span class="p">,</span> <span class="n">isoform</span> <span class="o">=</span> <span class="n">inputs_common</span><span class="o">.</span><span class="n">_try_isoform</span><span class="p">(</span><span class="n">line</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span>
+        <span class="n">enzyme</span> <span class="o">=</span> <span class="n">line</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span>
+
+        <span class="n">key</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="n">enzyme</span><span class="p">,</span>
+            <span class="n">substrate</span><span class="p">,</span>
+            <span class="n">isoform</span><span class="p">,</span>
+            <span class="n">line</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span><span class="o">.</span><span class="n">lower</span><span class="p">(),</span> <span class="c1"># PTM type</span>
+            <span class="n">resaa</span><span class="p">,</span>
+            <span class="n">resnum</span><span class="p">,</span>
+        <span class="p">)</span>
+
+        <span class="n">scores</span><span class="p">[</span><span class="n">key</span><span class="p">]</span> <span class="o">=</span> <span class="n">score</span>
+
+    <span class="n">c</span> <span class="o">=</span> <span class="n">curl</span><span class="o">.</span><span class="n">Curl</span><span class="p">(</span><span class="n">ptm_url</span><span class="p">,</span> <span class="n">large</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span> <span class="n">silent</span> <span class="o">=</span> <span class="kc">False</span><span class="p">)</span>
+
+    <span class="k">for</span> <span class="n">line</span> <span class="ow">in</span> <span class="n">c</span><span class="o">.</span><span class="n">result</span><span class="p">:</span>
+
+        <span class="n">line</span> <span class="o">=</span> <span class="n">line</span><span class="o">.</span><span class="n">strip</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\n\r</span><span class="s1">&#39;</span><span class="p">)</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\t</span><span class="s1">&#39;</span><span class="p">)</span>
+
+        <span class="k">if</span> <span class="ow">not</span> <span class="n">line</span> <span class="ow">or</span> <span class="ow">not</span> <span class="n">line</span><span class="p">[</span><span class="mi">6</span><span class="p">]:</span>
+
+            <span class="k">continue</span>
+
+        <span class="n">organism_</span> <span class="o">=</span> <span class="n">line</span><span class="p">[</span><span class="mi">4</span><span class="p">]</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span>
+        <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="n">taxonomy</span><span class="o">.</span><span class="n">ensure_ncbi_tax_id</span><span class="p">(</span><span class="n">organism_</span><span class="p">)</span>
+                <span class="k">if</span> <span class="n">organism_</span> <span class="k">else</span>
+            <span class="n">_const</span><span class="o">.</span><span class="n">NOT_ORGANISM_SPECIFIC</span>
+        <span class="p">)</span>
+
+        <span class="k">if</span> <span class="n">organism</span> <span class="ow">and</span> <span class="n">ncbi_tax_id</span> <span class="o">!=</span> <span class="n">organism</span><span class="p">:</span>
+
+            <span class="k">continue</span>
+
+        <span class="n">substrate</span><span class="p">,</span> <span class="n">s_isoform</span> <span class="o">=</span> <span class="n">inputs_common</span><span class="o">.</span><span class="n">_try_isoform</span><span class="p">(</span><span class="n">line</span><span class="p">[</span><span class="mi">2</span><span class="p">])</span>
+        <span class="n">ptm_type</span> <span class="o">=</span> <span class="n">line</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span>
+
+        <span class="n">enzyme</span><span class="p">,</span> <span class="n">e_isoform</span> <span class="o">=</span> <span class="n">inputs_common</span><span class="o">.</span><span class="n">_try_isoform</span><span class="p">(</span><span class="n">line</span><span class="p">[</span><span class="mi">6</span><span class="p">])</span>
+
+        <span class="n">enzyme_ids</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="n">mapping</span><span class="o">.</span><span class="n">map_name</span><span class="p">(</span>
+                <span class="n">line</span><span class="p">[</span><span class="mi">6</span><span class="p">],</span>
+                <span class="s1">&#39;pro&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;uniprot&#39;</span><span class="p">,</span>
+                <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">organism</span><span class="p">,</span>
+            <span class="p">)</span>
+                <span class="k">if</span> <span class="n">line</span><span class="p">[</span><span class="mi">6</span><span class="p">]</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s1">&#39;PR:&#39;</span><span class="p">)</span> <span class="k">else</span>
+            <span class="p">(</span><span class="n">enzyme</span><span class="p">,)</span>
+        <span class="p">)</span>
+
+        <span class="n">refs</span> <span class="o">=</span> <span class="n">line</span><span class="p">[</span><span class="mi">9</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;,&#39;</span><span class="p">)</span>
+        <span class="n">resnum</span><span class="p">,</span> <span class="n">resaa</span> <span class="o">=</span> <span class="n">resite</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="n">line</span><span class="p">[</span><span class="mi">5</span><span class="p">])</span><span class="o">.</span><span class="n">groups</span><span class="p">()</span>
+
+        <span class="n">key</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="n">line</span><span class="p">[</span><span class="mi">6</span><span class="p">],</span>
+            <span class="n">substrate</span><span class="p">,</span>
+            <span class="n">isoform</span><span class="p">,</span>
+            <span class="n">ptm_type</span><span class="p">,</span>
+            <span class="n">resaa</span><span class="p">,</span>
+            <span class="n">resnum</span><span class="p">,</span>
+        <span class="p">)</span>
+
+        <span class="n">score</span> <span class="o">=</span> <span class="n">scores</span><span class="p">[</span><span class="n">key</span><span class="p">]</span> <span class="k">if</span> <span class="n">key</span> <span class="ow">in</span> <span class="n">scores</span> <span class="k">else</span> <span class="kc">None</span>
+
+        <span class="k">for</span> <span class="n">_enzyme</span> <span class="ow">in</span> <span class="n">enzyme_ids</span><span class="p">:</span>
+
+            <span class="k">yield</span> <span class="n">IptmnetInteraction</span><span class="p">(</span>
+                <span class="n">enzyme</span> <span class="o">=</span> <span class="n">_enzyme</span><span class="p">,</span>
+                <span class="n">substrate</span> <span class="o">=</span> <span class="n">substrate</span><span class="p">,</span>
+                <span class="n">enzyme_isoform</span> <span class="o">=</span> <span class="n">e_isoform</span><span class="p">,</span>
+                <span class="n">substrate_isoform</span> <span class="o">=</span> <span class="n">s_isoform</span><span class="p">,</span>
+                <span class="n">ptm_type</span> <span class="o">=</span> <span class="n">ptm_type</span><span class="p">,</span>
+                <span class="n">resaa</span> <span class="o">=</span> <span class="n">resaa</span><span class="p">,</span>
+                <span class="n">resnum</span> <span class="o">=</span> <span class="n">resnum</span><span class="p">,</span>
+                <span class="n">score</span> <span class="o">=</span> <span class="n">score</span><span class="p">,</span>
+                <span class="n">references</span> <span class="o">=</span> <span class="n">refs</span><span class="p">,</span>
+            <span class="p">)</span></div>
+
+</pre></div>
+
+                </article>
+              
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diff --git a/_modules/pypath/inputs/italk.html b/_modules/pypath/inputs/italk.html
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+
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+  <h1>Source code for pypath.inputs.italk</h1><div class="highlight"><pre>
+<span></span><span class="ch">#!/usr/bin/env python</span>
+<span class="c1"># -*- coding: utf-8 -*-</span>
+
+<span class="c1">#</span>
+<span class="c1">#  This file is part of the `pypath` python module</span>
+<span class="c1">#</span>
+<span class="c1">#  Copyright 2014-2023</span>
+<span class="c1">#  EMBL, EMBL-EBI, Uniklinik RWTH Aachen, Heidelberg University</span>
+<span class="c1">#</span>
+<span class="c1">#  Authors: see the file `README.rst`</span>
+<span class="c1">#  Contact: Dénes Türei (turei.denes@gmail.com)</span>
+<span class="c1">#</span>
+<span class="c1">#  Distributed under the GPLv3 License.</span>
+<span class="c1">#  See accompanying file LICENSE.txt or copy at</span>
+<span class="c1">#      https://www.gnu.org/licenses/gpl-3.0.html</span>
+<span class="c1">#</span>
+<span class="c1">#  Website: https://pypath.omnipathdb.org/</span>
+<span class="c1">#</span>
+
+<span class="kn">import</span> <span class="nn">itertools</span>
+<span class="kn">import</span> <span class="nn">collections</span>
+<span class="kn">import</span> <span class="nn">pyreadr</span>
+
+<span class="kn">import</span> <span class="nn">pypath.resources.urls</span> <span class="k">as</span> <span class="nn">urls</span>
+<span class="kn">import</span> <span class="nn">pypath.share.curl</span> <span class="k">as</span> <span class="nn">curl</span>
+<span class="kn">import</span> <span class="nn">pypath.utils.mapping</span> <span class="k">as</span> <span class="nn">mapping</span>
+<span class="kn">import</span> <span class="nn">pypath.share.common</span> <span class="k">as</span> <span class="nn">common</span>
+
+
+<div class="viewcode-block" id="italk_raw">
+<a class="viewcode-back" href="../../../api/pypath.inputs.italk.italk_raw.html#pypath.inputs.italk.italk_raw">[docs]</a>
+<span class="k">def</span> <span class="nf">italk_raw</span><span class="p">():</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Returns a ``pandas.DataFrame`` with the iTalk database contents.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+    
+    <span class="n">url</span> <span class="o">=</span> <span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;italk&#39;</span><span class="p">][</span><span class="s1">&#39;url&#39;</span><span class="p">]</span>
+    <span class="n">c</span> <span class="o">=</span> <span class="n">curl</span><span class="o">.</span><span class="n">Curl</span><span class="p">(</span><span class="n">url</span><span class="p">,</span> <span class="n">silent</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span> <span class="n">large</span> <span class="o">=</span> <span class="kc">True</span><span class="p">)</span>
+    <span class="n">rdata_path</span> <span class="o">=</span> <span class="n">c</span><span class="o">.</span><span class="n">fileobj</span><span class="o">.</span><span class="n">name</span>
+    <span class="n">c</span><span class="o">.</span><span class="n">fileobj</span><span class="o">.</span><span class="n">close</span><span class="p">()</span>
+    
+    <span class="n">rdata</span> <span class="o">=</span> <span class="n">pyreadr</span><span class="o">.</span><span class="n">read_r</span><span class="p">(</span><span class="n">rdata_path</span><span class="p">)[</span><span class="s1">&#39;database&#39;</span><span class="p">]</span>
+    
+    <span class="k">return</span> <span class="n">rdata</span></div>
+
+
+
+<div class="viewcode-block" id="italk_interactions">
+<a class="viewcode-back" href="../../../api/pypath.inputs.italk.italk_interactions.html#pypath.inputs.italk.italk_interactions">[docs]</a>
+<span class="k">def</span> <span class="nf">italk_interactions</span><span class="p">():</span>
+    
+    
+    <span class="n">ItalkInteraction</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">namedtuple</span><span class="p">(</span>
+        <span class="s1">&#39;ItalkInteraction&#39;</span><span class="p">,</span>
+        <span class="p">[</span>
+            <span class="s1">&#39;ligand&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;receptor&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;classification&#39;</span><span class="p">,</span>
+        <span class="p">]</span>
+    <span class="p">)</span>
+    
+    
+    <span class="n">rdata</span> <span class="o">=</span> <span class="n">italk_raw</span><span class="p">()</span>
+    <span class="n">result</span> <span class="o">=</span> <span class="p">[]</span>
+    
+    <span class="k">for</span> <span class="n">row</span> <span class="ow">in</span> <span class="n">rdata</span><span class="o">.</span><span class="n">itertuples</span><span class="p">():</span>
+        
+        <span class="k">if</span> <span class="p">(</span>
+            <span class="ow">not</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">row</span><span class="p">[</span><span class="mi">2</span><span class="p">],</span> <span class="nb">str</span><span class="p">)</span> <span class="ow">or</span>
+            <span class="ow">not</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">row</span><span class="p">[</span><span class="mi">4</span><span class="p">],</span> <span class="nb">str</span><span class="p">)</span>
+        <span class="p">):</span>
+            
+            <span class="k">continue</span>
+        
+        <span class="n">ligands</span> <span class="o">=</span> <span class="n">mapping</span><span class="o">.</span><span class="n">map_name</span><span class="p">(</span><span class="n">row</span><span class="p">[</span><span class="mi">2</span><span class="p">],</span> <span class="s1">&#39;genesymbol&#39;</span><span class="p">,</span> <span class="s1">&#39;uniprot&#39;</span><span class="p">)</span>
+        <span class="n">receptors</span> <span class="o">=</span> <span class="n">mapping</span><span class="o">.</span><span class="n">map_name</span><span class="p">(</span><span class="n">row</span><span class="p">[</span><span class="mi">4</span><span class="p">],</span> <span class="s1">&#39;genesymbol&#39;</span><span class="p">,</span> <span class="s1">&#39;uniprot&#39;</span><span class="p">)</span>
+        <span class="bp">cls</span> <span class="o">=</span> <span class="n">row</span><span class="p">[</span><span class="mi">6</span><span class="p">]</span>
+        
+        <span class="k">for</span> <span class="n">ligand</span><span class="p">,</span> <span class="n">receptor</span> <span class="ow">in</span> <span class="n">itertools</span><span class="o">.</span><span class="n">product</span><span class="p">(</span><span class="n">ligands</span><span class="p">,</span> <span class="n">receptors</span><span class="p">):</span>
+            
+            <span class="n">result</span><span class="o">.</span><span class="n">append</span><span class="p">(</span>
+                <span class="n">ItalkInteraction</span><span class="p">(</span>
+                    <span class="n">ligand</span> <span class="o">=</span> <span class="n">ligand</span><span class="p">,</span>
+                    <span class="n">receptor</span> <span class="o">=</span> <span class="n">receptor</span><span class="p">,</span>
+                    <span class="n">classification</span> <span class="o">=</span> <span class="bp">cls</span><span class="p">,</span>
+                <span class="p">)</span>
+            <span class="p">)</span>
+    
+    <span class="k">return</span> <span class="n">result</span></div>
+
+
+
+<div class="viewcode-block" id="italk_annotations">
+<a class="viewcode-back" href="../../../api/pypath.inputs.italk.italk_annotations.html#pypath.inputs.italk.italk_annotations">[docs]</a>
+<span class="k">def</span> <span class="nf">italk_annotations</span><span class="p">():</span>
+    
+    
+    <span class="n">ItalkAnnotation</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">namedtuple</span><span class="p">(</span>
+        <span class="s1">&#39;ItalkAnnotation&#39;</span><span class="p">,</span>
+        <span class="p">[</span>
+            <span class="s1">&#39;mainclass&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;subclass&#39;</span><span class="p">,</span>
+        <span class="p">]</span>
+    <span class="p">)</span>
+    
+    
+    <span class="n">rdata</span> <span class="o">=</span> <span class="n">italk_raw</span><span class="p">()</span>
+    <span class="n">result</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">defaultdict</span><span class="p">(</span><span class="nb">set</span><span class="p">)</span>
+    
+    <span class="k">for</span> <span class="n">row</span> <span class="ow">in</span> <span class="n">rdata</span><span class="o">.</span><span class="n">itertuples</span><span class="p">():</span>
+        
+        <span class="n">ligands</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="n">mapping</span><span class="o">.</span><span class="n">map_name</span><span class="p">(</span><span class="n">row</span><span class="p">[</span><span class="mi">2</span><span class="p">],</span> <span class="s1">&#39;genesymbol&#39;</span><span class="p">,</span> <span class="s1">&#39;uniprot&#39;</span><span class="p">)</span>
+                <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">row</span><span class="p">[</span><span class="mi">2</span><span class="p">],</span> <span class="nb">str</span><span class="p">)</span> <span class="k">else</span>
+            <span class="p">()</span>
+        <span class="p">)</span>
+        <span class="n">receptors</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="n">mapping</span><span class="o">.</span><span class="n">map_name</span><span class="p">(</span><span class="n">row</span><span class="p">[</span><span class="mi">4</span><span class="p">],</span> <span class="s1">&#39;genesymbol&#39;</span><span class="p">,</span> <span class="s1">&#39;uniprot&#39;</span><span class="p">)</span>
+                <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">row</span><span class="p">[</span><span class="mi">4</span><span class="p">],</span> <span class="nb">str</span><span class="p">)</span> <span class="k">else</span>
+            <span class="p">()</span>
+        <span class="p">)</span>
+        <span class="n">subclass</span> <span class="o">=</span> <span class="n">row</span><span class="p">[</span><span class="mi">6</span><span class="p">]</span>
+        
+        <span class="k">for</span> <span class="n">mainclass</span><span class="p">,</span> <span class="n">uniprot</span> <span class="ow">in</span> <span class="n">itertools</span><span class="o">.</span><span class="n">chain</span><span class="p">(</span>
+            <span class="n">itertools</span><span class="o">.</span><span class="n">zip_longest</span><span class="p">((),</span> <span class="n">ligands</span><span class="p">,</span> <span class="n">fillvalue</span> <span class="o">=</span> <span class="s1">&#39;ligand&#39;</span><span class="p">),</span>
+            <span class="n">itertools</span><span class="o">.</span><span class="n">zip_longest</span><span class="p">((),</span> <span class="n">receptors</span><span class="p">,</span> <span class="n">fillvalue</span> <span class="o">=</span> <span class="s1">&#39;receptor&#39;</span><span class="p">),</span>
+        <span class="p">):</span>
+            
+            <span class="n">result</span><span class="p">[</span><span class="n">uniprot</span><span class="p">]</span><span class="o">.</span><span class="n">add</span><span class="p">(</span>
+                <span class="n">ItalkAnnotation</span><span class="p">(</span>
+                    <span class="n">mainclass</span> <span class="o">=</span> <span class="n">mainclass</span><span class="p">,</span>
+                    <span class="n">subclass</span> <span class="o">=</span> <span class="n">subclass</span><span class="p">,</span>
+                <span class="p">)</span>
+            <span class="p">)</span>
+    
+    <span class="k">return</span> <span class="nb">dict</span><span class="p">(</span><span class="n">result</span><span class="p">)</span></div>
+
+</pre></div>
+
+                </article>
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+  <h1>Source code for pypath.inputs.kea</h1><div class="highlight"><pre>
+<span></span><span class="ch">#!/usr/bin/env python</span>
+<span class="c1"># -*- coding: utf-8 -*-</span>
+
+<span class="c1">#</span>
+<span class="c1">#  This file is part of the `pypath` python module</span>
+<span class="c1">#</span>
+<span class="c1">#  Copyright 2014-2023</span>
+<span class="c1">#  EMBL, EMBL-EBI, Uniklinik RWTH Aachen, Heidelberg University</span>
+<span class="c1">#</span>
+<span class="c1">#  Authors: see the file `README.rst`</span>
+<span class="c1">#  Contact: Dénes Türei (turei.denes@gmail.com)</span>
+<span class="c1">#</span>
+<span class="c1">#  Distributed under the GPLv3 License.</span>
+<span class="c1">#  See accompanying file LICENSE.txt or copy at</span>
+<span class="c1">#      https://www.gnu.org/licenses/gpl-3.0.html</span>
+<span class="c1">#</span>
+<span class="c1">#  Website: https://pypath.omnipathdb.org/</span>
+<span class="c1">#</span>
+
+<span class="kn">import</span> <span class="nn">re</span>
+<span class="kn">import</span> <span class="nn">collections</span>
+<span class="kn">import</span> <span class="nn">itertools</span>
+
+<span class="kn">import</span> <span class="nn">pypath.share.curl</span> <span class="k">as</span> <span class="nn">curl</span>
+<span class="kn">import</span> <span class="nn">pypath.resources.urls</span> <span class="k">as</span> <span class="nn">urls</span>
+<span class="kn">import</span> <span class="nn">pypath.utils.mapping</span> <span class="k">as</span> <span class="nn">mapping</span>
+
+
+<span class="n">_resources</span> <span class="o">=</span> <span class="p">{</span>
+    <span class="s1">&#39;phosphosite&#39;</span><span class="p">:</span> <span class="s1">&#39;PhosphoSite&#39;</span><span class="p">,</span>
+    <span class="s1">&#39;phosphopoint&#39;</span><span class="p">:</span> <span class="s1">&#39;PhosphoPoint&#39;</span><span class="p">,</span>
+    <span class="s1">&#39;hprd&#39;</span><span class="p">:</span> <span class="s1">&#39;HPRD&#39;</span><span class="p">,</span>
+    <span class="s1">&#39;networkin&#39;</span><span class="p">:</span> <span class="s1">&#39;NetworKIN&#39;</span><span class="p">,</span>
+    <span class="s1">&#39;kinexus&#39;</span><span class="p">:</span> <span class="s1">&#39;Kinexus&#39;</span><span class="p">,</span>
+    <span class="s1">&#39;phosphoelm&#39;</span><span class="p">:</span> <span class="s1">&#39;phosphoELM&#39;</span><span class="p">,</span>
+<span class="p">}</span>
+
+
+<div class="viewcode-block" id="kea_interactions">
+<a class="viewcode-back" href="../../../api/pypath.inputs.kea.kea_interactions.html#pypath.inputs.kea.kea_interactions">[docs]</a>
+<span class="k">def</span> <span class="nf">kea_interactions</span><span class="p">():</span>
+
+
+    <span class="n">KeaRecord</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">namedtuple</span><span class="p">(</span>
+        <span class="s1">&#39;KeaRecord&#39;</span><span class="p">,</span>
+        <span class="p">[</span>
+            <span class="s1">&#39;enzyme&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;substrate&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;residue_type&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;residue_offset&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;pmid&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;resource&#39;</span><span class="p">,</span>
+        <span class="p">]</span>
+    <span class="p">)</span>
+
+    <span class="n">resub</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">compile</span><span class="p">(</span><span class="sa">r</span><span class="s1">&#39;(\w+)_([A-Z])([0-9]+)&#39;</span><span class="p">)</span>
+
+    <span class="n">url</span> <span class="o">=</span> <span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;kea&#39;</span><span class="p">][</span><span class="s1">&#39;kinase_substrate&#39;</span><span class="p">]</span>
+
+    <span class="n">c</span> <span class="o">=</span> <span class="n">curl</span><span class="o">.</span><span class="n">Curl</span><span class="p">(</span><span class="n">url</span><span class="p">,</span> <span class="n">silent</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span> <span class="n">large</span> <span class="o">=</span> <span class="kc">True</span><span class="p">)</span>
+
+    <span class="n">result</span> <span class="o">=</span> <span class="p">[]</span>
+
+    <span class="k">for</span> <span class="n">rec</span> <span class="ow">in</span> <span class="n">c</span><span class="o">.</span><span class="n">result</span><span class="p">:</span>
+
+        <span class="n">rec</span> <span class="o">=</span> <span class="n">rec</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\t</span><span class="s1">&#39;</span><span class="p">)</span>
+
+        <span class="n">site</span> <span class="o">=</span> <span class="n">resub</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="n">rec</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">strip</span><span class="p">())</span>
+
+        <span class="k">if</span> <span class="ow">not</span> <span class="n">site</span><span class="p">:</span>
+
+            <span class="k">continue</span>
+
+        <span class="n">target</span><span class="p">,</span> <span class="n">resaa</span><span class="p">,</span> <span class="n">resnum</span> <span class="o">=</span> <span class="n">site</span><span class="o">.</span><span class="n">groups</span><span class="p">()</span>
+
+        <span class="n">e_uniprots</span> <span class="o">=</span> <span class="n">mapping</span><span class="o">.</span><span class="n">map_name</span><span class="p">(</span><span class="n">rec</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="s1">&#39;genesymbol&#39;</span><span class="p">,</span> <span class="s1">&#39;uniprot&#39;</span><span class="p">)</span>
+        <span class="n">s_uniprots</span> <span class="o">=</span> <span class="n">mapping</span><span class="o">.</span><span class="n">map_name</span><span class="p">(</span><span class="n">target</span><span class="p">,</span> <span class="s1">&#39;genesymbol&#39;</span><span class="p">,</span> <span class="s1">&#39;uniprot&#39;</span><span class="p">)</span>
+
+        <span class="k">for</span> <span class="n">enz</span><span class="p">,</span> <span class="n">sub</span> <span class="ow">in</span> <span class="n">itertools</span><span class="o">.</span><span class="n">product</span><span class="p">(</span><span class="n">e_uniprots</span><span class="p">,</span> <span class="n">s_uniprots</span><span class="p">):</span>
+
+            <span class="n">result</span><span class="o">.</span><span class="n">append</span><span class="p">(</span>
+                <span class="n">KeaRecord</span><span class="p">(</span>
+                    <span class="n">enzyme</span> <span class="o">=</span> <span class="n">enz</span><span class="p">,</span>
+                    <span class="n">substrate</span> <span class="o">=</span> <span class="n">sub</span><span class="p">,</span>
+                    <span class="n">residue_type</span> <span class="o">=</span> <span class="n">resaa</span><span class="p">,</span>
+                    <span class="n">residue_offset</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">resnum</span><span class="p">),</span>
+                    <span class="n">pmid</span> <span class="o">=</span> <span class="n">rec</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span><span class="o">.</span><span class="n">strip</span><span class="p">(),</span>
+                    <span class="n">resource</span> <span class="o">=</span> <span class="n">_resources</span><span class="p">[</span><span class="n">rec</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span><span class="o">.</span><span class="n">strip</span><span class="p">()]</span>
+                <span class="p">)</span>
+            <span class="p">)</span>
+
+    <span class="k">return</span> <span class="n">result</span></div>
+
+
+
+<div class="viewcode-block" id="kea_enzyme_substrate">
+<a class="viewcode-back" href="../../../api/pypath.inputs.kea.kea_enzyme_substrate.html#pypath.inputs.kea.kea_enzyme_substrate">[docs]</a>
+<span class="k">def</span> <span class="nf">kea_enzyme_substrate</span><span class="p">():</span>
+
+    <span class="k">return</span> <span class="p">[</span>
+        <span class="p">{</span>
+            <span class="s1">&#39;start&#39;</span><span class="p">:</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="s1">&#39;end&#39;</span><span class="p">:</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="s1">&#39;instance&#39;</span><span class="p">:</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="s1">&#39;substrate&#39;</span><span class="p">:</span> <span class="n">rec</span><span class="o">.</span><span class="n">substrate</span><span class="p">,</span>
+            <span class="s1">&#39;kinase&#39;</span><span class="p">:</span> <span class="n">rec</span><span class="o">.</span><span class="n">enzyme</span><span class="p">,</span>
+            <span class="s1">&#39;resaa&#39;</span><span class="p">:</span> <span class="n">rec</span><span class="o">.</span><span class="n">residue_type</span><span class="p">,</span>
+            <span class="s1">&#39;resnum&#39;</span><span class="p">:</span> <span class="n">rec</span><span class="o">.</span><span class="n">residue_offset</span><span class="p">,</span>
+            <span class="s1">&#39;references&#39;</span><span class="p">:</span> <span class="p">{</span><span class="n">rec</span><span class="o">.</span><span class="n">pmid</span><span class="p">},</span>
+            <span class="s1">&#39;typ&#39;</span><span class="p">:</span> <span class="s1">&#39;phosphorylation&#39;</span><span class="p">,</span>
+        <span class="p">}</span>
+        <span class="k">for</span> <span class="n">rec</span> <span class="ow">in</span> <span class="n">kea_interactions</span><span class="p">()</span>
+    <span class="p">]</span></div>
+
+</pre></div>
+
+                </article>
+              
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diff --git a/_modules/pypath/inputs/kegg.html b/_modules/pypath/inputs/kegg.html
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+                  
+  <h1>Source code for pypath.inputs.kegg</h1><div class="highlight"><pre>
+<span></span><span class="ch">#!/usr/bin/env python</span>
+<span class="c1"># -*- coding: utf-8 -*-</span>
+
+<span class="c1">#</span>
+<span class="c1">#  This file is part of the `pypath` python module</span>
+<span class="c1">#</span>
+<span class="c1">#  Copyright 2014-2023</span>
+<span class="c1">#  EMBL, EMBL-EBI, Uniklinik RWTH Aachen, Heidelberg University</span>
+<span class="c1">#</span>
+<span class="c1">#  Authors: see the file `README.rst`</span>
+<span class="c1">#  Contact: Dénes Türei (turei.denes@gmail.com)</span>
+<span class="c1">#</span>
+<span class="c1">#  Distributed under the GPLv3 License.</span>
+<span class="c1">#  See accompanying file LICENSE.txt or copy at</span>
+<span class="c1">#      https://www.gnu.org/licenses/gpl-3.0.html</span>
+<span class="c1">#</span>
+<span class="c1">#  Website: https://pypath.omnipathdb.org/</span>
+<span class="c1">#</span>
+
+<span class="kn">from</span> <span class="nn">future.utils</span> <span class="kn">import</span> <span class="n">iteritems</span>
+
+<span class="kn">import</span> <span class="nn">re</span>
+<span class="kn">import</span> <span class="nn">itertools</span>
+<span class="kn">import</span> <span class="nn">collections</span>
+<span class="kn">import</span> <span class="nn">bs4</span>
+<span class="kn">import</span> <span class="nn">warnings</span>
+
+<span class="kn">import</span> <span class="nn">pypath.share.curl</span> <span class="k">as</span> <span class="nn">curl</span>
+<span class="kn">import</span> <span class="nn">pypath.resources.urls</span> <span class="k">as</span> <span class="nn">urls</span>
+<span class="kn">import</span> <span class="nn">pypath.share.progress</span> <span class="k">as</span> <span class="nn">progress</span>
+<span class="kn">import</span> <span class="nn">pypath.share.common</span> <span class="k">as</span> <span class="nn">common</span>
+<span class="kn">import</span> <span class="nn">pypath.utils.mapping</span> <span class="k">as</span> <span class="nn">mapping</span>
+<span class="kn">import</span> <span class="nn">pypath.internals.intera</span> <span class="k">as</span> <span class="nn">intera</span>
+<span class="kn">import</span> <span class="nn">pypath.core.entity</span> <span class="k">as</span> <span class="nn">entity</span>
+
+
+<span class="n">KeggPathway</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">namedtuple</span><span class="p">(</span>
+    <span class="s1">&#39;KeggPathway&#39;</span><span class="p">,</span>
+    <span class="p">[</span><span class="s1">&#39;pathway&#39;</span><span class="p">],</span>
+<span class="p">)</span>
+
+
+<div class="viewcode-block" id="kegg_interactions">
+<a class="viewcode-back" href="../../../api/pypath.inputs.kegg.kegg_interactions.html#pypath.inputs.kegg.kegg_interactions">[docs]</a>
+<span class="k">def</span> <span class="nf">kegg_interactions</span><span class="p">():</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Downloads and processes KEGG Pathways.</span>
+<span class="sd">    Returns list of interactions.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="n">positive_terms</span> <span class="o">=</span> <span class="p">{</span><span class="s1">&#39;activation&#39;</span><span class="p">,</span> <span class="s1">&#39;expression&#39;</span><span class="p">}</span>
+    <span class="n">negative_terms</span> <span class="o">=</span> <span class="p">{</span><span class="s1">&#39;inhibition&#39;</span><span class="p">,</span> <span class="s1">&#39;repression&#39;</span><span class="p">}</span>
+    <span class="n">transc_terms</span> <span class="o">=</span> <span class="p">{</span><span class="s1">&#39;expression&#39;</span><span class="p">,</span> <span class="s1">&#39;repression&#39;</span><span class="p">}</span>
+    <span class="n">mechanism_terms</span> <span class="o">=</span> <span class="p">{</span>
+        <span class="s1">&#39;phosphorylation&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;binding/association&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;dissociation&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;ubiquitination&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;dephosphorylation&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;glycosylation&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;state change&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;methylation&#39;</span><span class="p">,</span>
+    <span class="p">}</span>
+    <span class="n">direct_terms</span> <span class="o">=</span> <span class="p">{</span><span class="s1">&#39;indirect effect&#39;</span><span class="p">}</span>
+
+    <span class="n">KeggInteraction</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">namedtuple</span><span class="p">(</span>
+        <span class="s1">&#39;KeggInteraction&#39;</span><span class="p">,</span>
+        <span class="p">[</span>
+            <span class="s1">&#39;id_a&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;id_b&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;effect&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;pathway&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;mechanism&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;is_direct&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;transcriptional&#39;</span><span class="p">,</span>
+        <span class="p">],</span>
+    <span class="p">)</span>
+
+    <span class="n">rehsa</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">compile</span><span class="p">(</span><span class="sa">r</span><span class="s1">&#39;.*(hsa[0-9]+).*&#39;</span><span class="p">)</span>
+    <span class="n">req_hdrs</span> <span class="o">=</span> <span class="p">[</span>
+        <span class="s1">&#39;Referer: http://www.genome.jp/kegg-bin/show_pathway&#39;</span>
+        <span class="s1">&#39;?map=hsa04710&amp;show_description=show&#39;</span>
+    <span class="p">]</span>
+    <span class="n">hsa_list</span> <span class="o">=</span> <span class="p">[]</span>
+    <span class="n">interactions</span> <span class="o">=</span> <span class="p">[]</span>
+
+    <span class="n">c</span> <span class="o">=</span> <span class="n">curl</span><span class="o">.</span><span class="n">Curl</span><span class="p">(</span><span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;kegg_pws&#39;</span><span class="p">][</span><span class="s1">&#39;list_url&#39;</span><span class="p">],</span> <span class="n">silent</span> <span class="o">=</span> <span class="kc">True</span><span class="p">)</span>
+    <span class="n">htmllst</span> <span class="o">=</span> <span class="n">c</span><span class="o">.</span><span class="n">result</span>
+    <span class="n">lstsoup</span> <span class="o">=</span> <span class="n">bs4</span><span class="o">.</span><span class="n">BeautifulSoup</span><span class="p">(</span><span class="n">htmllst</span><span class="p">,</span> <span class="s1">&#39;html.parser&#39;</span><span class="p">)</span>
+
+    <span class="k">for</span> <span class="n">a</span> <span class="ow">in</span> <span class="n">lstsoup</span><span class="o">.</span><span class="n">find_all</span><span class="p">(</span><span class="s1">&#39;a&#39;</span><span class="p">,</span> <span class="n">href</span> <span class="o">=</span> <span class="kc">True</span><span class="p">):</span>
+        <span class="n">m</span> <span class="o">=</span> <span class="n">rehsa</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="n">a</span><span class="p">[</span><span class="s1">&#39;href&#39;</span><span class="p">])</span>
+
+        <span class="k">if</span> <span class="n">m</span><span class="p">:</span>
+            <span class="n">hsa_list</span><span class="o">.</span><span class="n">append</span><span class="p">((</span><span class="n">m</span><span class="o">.</span><span class="n">groups</span><span class="p">(</span><span class="mi">0</span><span class="p">)[</span><span class="mi">0</span><span class="p">],</span> <span class="n">a</span><span class="o">.</span><span class="n">text</span><span class="p">))</span>
+
+    <span class="n">prg</span> <span class="o">=</span> <span class="n">progress</span><span class="o">.</span><span class="n">Progress</span><span class="p">(</span>
+        <span class="nb">len</span><span class="p">(</span><span class="n">hsa_list</span><span class="p">),</span> <span class="s1">&#39;Processing KEGG Pathways&#39;</span><span class="p">,</span> <span class="mi">1</span><span class="p">,</span> <span class="n">percent</span> <span class="o">=</span> <span class="kc">False</span>
+    <span class="p">)</span>
+
+    <span class="k">for</span> <span class="n">hsa</span><span class="p">,</span> <span class="n">pw</span> <span class="ow">in</span> <span class="n">hsa_list</span><span class="p">:</span>
+
+        <span class="n">prg</span><span class="o">.</span><span class="n">step</span><span class="p">()</span>
+        <span class="n">c</span> <span class="o">=</span> <span class="n">curl</span><span class="o">.</span><span class="n">Curl</span><span class="p">(</span>
+            <span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;kegg_pws&#39;</span><span class="p">][</span><span class="s1">&#39;kgml_url_2&#39;</span><span class="p">]</span> <span class="o">%</span> <span class="n">hsa</span><span class="p">,</span>
+            <span class="n">silent</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
+            <span class="n">req_headers</span> <span class="o">=</span> <span class="n">req_hdrs</span>
+        <span class="p">)</span>
+        <span class="n">kgml</span> <span class="o">=</span> <span class="n">c</span><span class="o">.</span><span class="n">result</span>
+
+        <span class="k">with</span> <span class="n">warnings</span><span class="o">.</span><span class="n">catch_warnings</span><span class="p">():</span>
+
+            <span class="n">warnings</span><span class="o">.</span><span class="n">simplefilter</span><span class="p">(</span><span class="s1">&#39;ignore&#39;</span><span class="p">)</span>
+            <span class="n">kgmlsoup</span> <span class="o">=</span> <span class="n">bs4</span><span class="o">.</span><span class="n">BeautifulSoup</span><span class="p">(</span><span class="n">kgml</span><span class="p">,</span> <span class="s1">&#39;html.parser&#39;</span><span class="p">)</span>
+
+        <span class="n">entries</span> <span class="o">=</span> <span class="p">{}</span>
+
+        <span class="k">for</span> <span class="n">ent</span> <span class="ow">in</span> <span class="n">kgmlsoup</span><span class="o">.</span><span class="n">find_all</span><span class="p">(</span><span class="s1">&#39;entry&#39;</span><span class="p">):</span>
+            <span class="n">gr</span> <span class="o">=</span> <span class="n">ent</span><span class="o">.</span><span class="n">find</span><span class="p">(</span><span class="s1">&#39;graphics&#39;</span><span class="p">)</span>
+
+            <span class="k">if</span> <span class="n">gr</span> <span class="ow">and</span> <span class="s1">&#39;name&#39;</span> <span class="ow">in</span> <span class="n">gr</span><span class="o">.</span><span class="n">attrs</span><span class="p">:</span>
+                <span class="n">entries</span><span class="p">[</span><span class="n">ent</span><span class="o">.</span><span class="n">attrs</span><span class="p">[</span><span class="s1">&#39;id&#39;</span><span class="p">]]</span> <span class="o">=</span> <span class="p">[</span>
+                    <span class="n">n</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span>
+                    <span class="k">for</span> <span class="n">n</span> <span class="ow">in</span> <span class="n">gr</span><span class="o">.</span><span class="n">attrs</span><span class="p">[</span><span class="s1">&#39;name&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s1">&#39;...&#39;</span><span class="p">,</span> <span class="s1">&#39;&#39;</span><span class="p">)</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;,&#39;</span><span class="p">)</span>
+                <span class="p">]</span>
+
+        <span class="n">uentries</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">([(</span><span class="n">eid</span><span class="p">,</span> <span class="n">common</span><span class="o">.</span><span class="n">unique_list</span><span class="p">(</span>
+            <span class="n">common</span><span class="o">.</span><span class="n">flat_list</span><span class="p">([</span>
+                <span class="n">mapping</span><span class="o">.</span><span class="n">map_name</span><span class="p">(</span>
+                    <span class="n">gn</span><span class="p">,</span> <span class="s1">&#39;genesymbol&#39;</span><span class="p">,</span> <span class="s1">&#39;uniprot&#39;</span><span class="p">,</span> <span class="n">strict</span> <span class="o">=</span> <span class="kc">True</span><span class="p">)</span> <span class="k">for</span> <span class="n">gn</span> <span class="ow">in</span> <span class="n">gns</span>
+            <span class="p">])))</span> <span class="k">for</span> <span class="n">eid</span><span class="p">,</span> <span class="n">gns</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="n">entries</span><span class="p">)])</span>
+
+        <span class="k">for</span> <span class="n">rel</span> <span class="ow">in</span> <span class="n">kgmlsoup</span><span class="o">.</span><span class="n">find_all</span><span class="p">(</span><span class="s1">&#39;relation&#39;</span><span class="p">):</span>
+
+            <span class="n">subtypes</span> <span class="o">=</span> <span class="p">{</span><span class="n">st</span><span class="o">.</span><span class="n">attrs</span><span class="p">[</span><span class="s1">&#39;name&#39;</span><span class="p">]</span> <span class="k">for</span> <span class="n">st</span> <span class="ow">in</span> <span class="n">rel</span><span class="o">.</span><span class="n">find_all</span><span class="p">(</span><span class="s1">&#39;subtype&#39;</span><span class="p">)}</span>
+
+            <span class="k">if</span> <span class="p">(</span>
+                <span class="n">rel</span><span class="o">.</span><span class="n">attrs</span><span class="p">[</span><span class="s1">&#39;entry1&#39;</span><span class="p">]</span> <span class="ow">in</span> <span class="n">uentries</span> <span class="ow">and</span>
+                <span class="n">rel</span><span class="o">.</span><span class="n">attrs</span><span class="p">[</span><span class="s1">&#39;entry2&#39;</span><span class="p">]</span> <span class="ow">in</span> <span class="n">uentries</span> <span class="ow">and</span>
+                <span class="n">subtypes</span>
+            <span class="p">):</span>
+
+                <span class="n">is_direct</span> <span class="o">=</span> <span class="s1">&#39;indirect effect&#39;</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">subtypes</span>
+                <span class="n">effect</span> <span class="o">=</span> <span class="p">(</span>
+                    <span class="s1">&#39;inhibition&#39;</span>
+                        <span class="k">if</span> <span class="n">negative_terms</span> <span class="o">&amp;</span> <span class="n">subtypes</span> <span class="k">else</span>
+                    <span class="s1">&#39;activation&#39;</span>
+                        <span class="k">if</span> <span class="n">positive_terms</span> <span class="o">&amp;</span> <span class="n">subtypes</span> <span class="k">else</span>
+                    <span class="s1">&#39;unknown&#39;</span>
+                <span class="p">)</span>
+                <span class="n">mechanism</span> <span class="o">=</span> <span class="s1">&#39;;&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">mechanism_terms</span> <span class="o">&amp;</span> <span class="n">subtypes</span><span class="p">)</span>
+                <span class="n">transcriptional</span> <span class="o">=</span> <span class="nb">bool</span><span class="p">(</span><span class="n">transc_terms</span> <span class="o">&amp;</span> <span class="n">subtypes</span><span class="p">)</span>
+
+                <span class="k">for</span> <span class="n">u1</span> <span class="ow">in</span> <span class="n">uentries</span><span class="p">[</span><span class="n">rel</span><span class="o">.</span><span class="n">attrs</span><span class="p">[</span><span class="s1">&#39;entry1&#39;</span><span class="p">]]:</span>
+
+                    <span class="k">for</span> <span class="n">u2</span> <span class="ow">in</span> <span class="n">uentries</span><span class="p">[</span><span class="n">rel</span><span class="o">.</span><span class="n">attrs</span><span class="p">[</span><span class="s1">&#39;entry2&#39;</span><span class="p">]]:</span>
+
+                        <span class="n">interactions</span><span class="o">.</span><span class="n">append</span><span class="p">(</span>
+                            <span class="n">KeggInteraction</span><span class="p">(</span>
+                                <span class="n">id_a</span> <span class="o">=</span> <span class="n">u1</span><span class="p">,</span>
+                                <span class="n">id_b</span> <span class="o">=</span> <span class="n">u2</span><span class="p">,</span>
+                                <span class="n">effect</span> <span class="o">=</span> <span class="n">effect</span><span class="p">,</span>
+                                <span class="n">pathway</span> <span class="o">=</span> <span class="n">pw</span><span class="p">,</span>
+                                <span class="n">mechanism</span> <span class="o">=</span> <span class="n">mechanism</span><span class="p">,</span>
+                                <span class="n">is_direct</span> <span class="o">=</span> <span class="n">is_direct</span><span class="p">,</span>
+                                <span class="n">transcriptional</span> <span class="o">=</span> <span class="n">transcriptional</span><span class="p">,</span>
+                            <span class="p">)</span>
+                        <span class="p">)</span>
+
+    <span class="n">prg</span><span class="o">.</span><span class="n">terminate</span><span class="p">()</span>
+
+    <span class="k">return</span> <span class="n">common</span><span class="o">.</span><span class="n">unique_list</span><span class="p">(</span><span class="n">interactions</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="kegg_pathways">
+<a class="viewcode-back" href="../../../api/pypath.inputs.kegg.kegg_pathways.html#pypath.inputs.kegg.kegg_pathways">[docs]</a>
+<span class="k">def</span> <span class="nf">kegg_pathways</span><span class="p">():</span>
+
+    <span class="n">data</span> <span class="o">=</span> <span class="n">kegg_interactions</span><span class="p">()</span>
+    <span class="n">pws</span> <span class="o">=</span> <span class="n">common</span><span class="o">.</span><span class="n">unique_list</span><span class="p">(</span><span class="nb">map</span><span class="p">(</span><span class="k">lambda</span> <span class="n">i</span><span class="p">:</span> <span class="n">i</span><span class="p">[</span><span class="mi">3</span><span class="p">],</span> <span class="n">data</span><span class="p">))</span>
+    <span class="n">proteins_pws</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">(</span><span class="nb">map</span><span class="p">(</span><span class="k">lambda</span> <span class="n">pw</span><span class="p">:</span> <span class="p">(</span><span class="n">pw</span><span class="p">,</span> <span class="nb">set</span><span class="p">([])),</span> <span class="n">pws</span><span class="p">))</span>
+    <span class="n">interactions_pws</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">(</span><span class="nb">map</span><span class="p">(</span><span class="k">lambda</span> <span class="n">pw</span><span class="p">:</span> <span class="p">(</span><span class="n">pw</span><span class="p">,</span> <span class="nb">set</span><span class="p">([])),</span> <span class="n">pws</span><span class="p">))</span>
+
+    <span class="k">for</span> <span class="n">rec</span> <span class="ow">in</span> <span class="n">data</span><span class="p">:</span>
+
+        <span class="n">u1</span><span class="p">,</span> <span class="n">u2</span><span class="p">,</span> <span class="n">eff</span><span class="p">,</span> <span class="n">pw</span> <span class="o">=</span> <span class="n">rec</span><span class="p">[:</span><span class="mi">4</span><span class="p">]</span>
+        <span class="n">proteins_pws</span><span class="p">[</span><span class="n">pw</span><span class="p">]</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">u1</span><span class="p">)</span>
+        <span class="n">proteins_pws</span><span class="p">[</span><span class="n">pw</span><span class="p">]</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">u2</span><span class="p">)</span>
+        <span class="n">interactions_pws</span><span class="p">[</span><span class="n">pw</span><span class="p">]</span><span class="o">.</span><span class="n">add</span><span class="p">((</span><span class="n">u1</span><span class="p">,</span> <span class="n">u2</span><span class="p">))</span>
+
+    <span class="k">return</span> <span class="n">proteins_pws</span><span class="p">,</span> <span class="n">interactions_pws</span></div>
+
+
+
+<div class="viewcode-block" id="kegg_pathway_annotations">
+<a class="viewcode-back" href="../../../api/pypath.inputs.kegg.kegg_pathway_annotations.html#pypath.inputs.kegg.kegg_pathway_annotations">[docs]</a>
+<span class="k">def</span> <span class="nf">kegg_pathway_annotations</span><span class="p">():</span>
+
+    <span class="n">result</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">defaultdict</span><span class="p">(</span><span class="nb">set</span><span class="p">)</span>
+
+    <span class="n">proteins</span><span class="p">,</span> <span class="n">interactions</span> <span class="o">=</span> <span class="n">kegg_pathways</span><span class="p">()</span>
+
+    <span class="k">for</span> <span class="n">pathway</span><span class="p">,</span> <span class="n">uniprots</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="n">proteins</span><span class="p">):</span>
+        <span class="n">record</span> <span class="o">=</span> <span class="n">KeggPathway</span><span class="p">(</span><span class="n">pathway</span> <span class="o">=</span> <span class="n">pathway</span><span class="p">)</span>
+
+        <span class="k">for</span> <span class="n">uniprot</span> <span class="ow">in</span> <span class="n">uniprots</span><span class="p">:</span>
+            <span class="n">result</span><span class="p">[</span><span class="n">uniprot</span><span class="p">]</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">record</span><span class="p">)</span>
+
+    <span class="k">return</span> <span class="nb">dict</span><span class="p">(</span><span class="n">result</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="kegg_pathway_annotations_pathwaycommons">
+<a class="viewcode-back" href="../../../api/pypath.inputs.kegg.kegg_pathway_annotations_pathwaycommons.html#pypath.inputs.kegg.kegg_pathway_annotations_pathwaycommons">[docs]</a>
+<span class="k">def</span> <span class="nf">kegg_pathway_annotations_pathwaycommons</span><span class="p">():</span>
+
+    <span class="n">result</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">defaultdict</span><span class="p">(</span><span class="nb">set</span><span class="p">)</span>
+
+    <span class="n">url</span> <span class="o">=</span> <span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;kegg_pws&#39;</span><span class="p">][</span><span class="s1">&#39;pw_annot&#39;</span><span class="p">]</span>
+    <span class="n">c</span> <span class="o">=</span> <span class="n">curl</span><span class="o">.</span><span class="n">Curl</span><span class="p">(</span><span class="n">url</span><span class="p">,</span> <span class="n">large</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span> <span class="n">silent</span> <span class="o">=</span> <span class="kc">False</span><span class="p">)</span>
+
+    <span class="k">for</span> <span class="n">row</span> <span class="ow">in</span> <span class="n">c</span><span class="o">.</span><span class="n">result</span><span class="p">:</span>
+
+        <span class="n">row</span> <span class="o">=</span> <span class="n">row</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\t</span><span class="s1">&#39;</span><span class="p">)</span>
+        <span class="n">name</span> <span class="o">=</span> <span class="n">row</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;;&#39;</span><span class="p">,</span> <span class="n">maxsplit</span> <span class="o">=</span> <span class="mi">1</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span>
+        <span class="n">name</span> <span class="o">=</span> <span class="n">name</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;:&#39;</span><span class="p">,</span> <span class="n">maxsplit</span> <span class="o">=</span> <span class="mi">1</span><span class="p">)[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span>
+        <span class="n">uniprots</span> <span class="o">=</span> <span class="n">row</span><span class="p">[</span><span class="mi">2</span><span class="p">:]</span>
+
+        <span class="n">annot</span> <span class="o">=</span> <span class="n">KeggPathway</span><span class="p">(</span><span class="n">pathway</span> <span class="o">=</span> <span class="n">name</span><span class="p">)</span>
+
+        <span class="k">for</span> <span class="n">uniprot</span> <span class="ow">in</span> <span class="n">uniprots</span><span class="p">:</span>
+
+            <span class="n">result</span><span class="p">[</span><span class="n">uniprot</span><span class="p">]</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">annot</span><span class="p">)</span>
+
+    <span class="k">return</span> <span class="nb">dict</span><span class="p">(</span><span class="n">result</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="kegg_medicus">
+<a class="viewcode-back" href="../../../api/pypath.inputs.kegg.kegg_medicus.html#pypath.inputs.kegg.kegg_medicus">[docs]</a>
+<span class="k">def</span> <span class="nf">kegg_medicus</span><span class="p">(</span><span class="n">max_entity_variations</span> <span class="o">=</span> <span class="mi">10</span><span class="p">):</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Retrieves and preprocesses the KEGG MEDICUS database. Returns a set of</span>
+<span class="sd">    raw interaction records (with the original identifiers and some further</span>
+<span class="sd">    attributes). Nested complexes and protein families are flattened which</span>
+<span class="sd">    means each interacting pair is either a single protein or a protein</span>
+<span class="sd">    complex. Then the combination of all variants of each interacting partner</span>
+<span class="sd">    yields a separate record. E.g. if a family of 3 proteins interacts with</span>
+<span class="sd">    a protein complex where one of the members can be 2 alternative proteins</span>
+<span class="sd">    then this interaction yields 6 records.</span>
+
+<span class="sd">    max_entity_variations : int</span>
+<span class="sd">        In KEGG MEDICUS many molecular entities are protein families or</span>
+<span class="sd">        families of often large and nested protein complexes. By this option</span>
+<span class="sd">        you can limit largest number of variants a single entity might yield,</span>
+<span class="sd">        so you won&#39;t end up with one complex yielding hundreds of</span>
+<span class="sd">        combinatiorial variants.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+
+    <span class="n">reentity</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">compile</span><span class="p">(</span><span class="sa">r</span><span class="s1">&#39;[,\+\(\)]|\w+&#39;</span><span class="p">)</span>
+    <span class="n">renminus2</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">compile</span><span class="p">(</span><span class="sa">r</span><span class="s1">&#39;\(n(?:-2)?\)&#39;</span><span class="p">)</span>
+    <span class="n">renetref</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">compile</span><span class="p">(</span><span class="sa">r</span><span class="s1">&#39;\[(N|nt)\d</span><span class="si">{5}</span><span class="s1">\]&#39;</span><span class="p">)</span>
+
+
+    <span class="n">KeggMedicusRawInteraction</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">namedtuple</span><span class="p">(</span>
+        <span class="s1">&#39;KeggMedicusRawInteraction&#39;</span><span class="p">,</span>
+        <span class="p">[</span>
+            <span class="s1">&#39;id_a&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;id_b&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;name_a&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;name_b&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;effect&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;itype&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;pw_type&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;type_a&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;type_b&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;network_id&#39;</span><span class="p">,</span>
+        <span class="p">],</span>
+    <span class="p">)</span>
+
+
+    <span class="n">i_code</span> <span class="o">=</span> <span class="p">{</span>
+        <span class="s1">&#39;-&gt;&#39;</span><span class="p">:</span> <span class="p">(</span><span class="s1">&#39;post_translational&#39;</span><span class="p">,</span> <span class="s1">&#39;stimulation&#39;</span><span class="p">),</span>
+        <span class="s1">&#39;=&gt;&#39;</span><span class="p">:</span> <span class="p">(</span><span class="s1">&#39;transcriptional&#39;</span><span class="p">,</span> <span class="s1">&#39;stimulation&#39;</span><span class="p">),</span>
+        <span class="s1">&#39;//&#39;</span><span class="p">:</span> <span class="p">(</span><span class="s1">&#39;post_translational&#39;</span><span class="p">,</span> <span class="s1">&#39;missing&#39;</span><span class="p">),</span>
+        <span class="s1">&#39;-|&#39;</span><span class="p">:</span> <span class="p">(</span><span class="s1">&#39;post_translational&#39;</span><span class="p">,</span> <span class="s1">&#39;inhibition&#39;</span><span class="p">),</span>
+        <span class="s1">&#39;=|&#39;</span><span class="p">:</span> <span class="p">(</span><span class="s1">&#39;transcriptional&#39;</span><span class="p">,</span> <span class="s1">&#39;inhibition&#39;</span><span class="p">),</span>
+        <span class="s1">&#39;--&#39;</span><span class="p">:</span> <span class="p">(</span><span class="s1">&#39;post_translational&#39;</span><span class="p">,</span> <span class="s1">&#39;undirected&#39;</span><span class="p">),</span>
+        <span class="s1">&#39;&gt;&gt;&#39;</span><span class="p">:</span> <span class="p">(</span><span class="s1">&#39;post_translational&#39;</span><span class="p">,</span> <span class="s1">&#39;enzyme_enzyme&#39;</span><span class="p">),</span>
+        <span class="s1">&#39;==&#39;</span><span class="p">:</span> <span class="p">(</span><span class="s1">&#39;post_translational&#39;</span><span class="p">,</span> <span class="s1">&#39;missing&#39;</span><span class="p">),</span>
+    <span class="p">}</span>
+
+
+    <span class="k">def</span> <span class="nf">process_entity</span><span class="p">(</span><span class="n">e</span><span class="p">):</span>
+
+        <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">e</span><span class="p">,</span> <span class="nb">str</span><span class="p">):</span>
+
+            <span class="n">e</span> <span class="o">=</span> <span class="n">renminus2</span><span class="o">.</span><span class="n">sub</span><span class="p">(</span><span class="s1">&#39;&#39;</span><span class="p">,</span> <span class="n">e</span><span class="p">)</span>
+            <span class="n">e</span> <span class="o">=</span> <span class="n">reentity</span><span class="o">.</span><span class="n">findall</span><span class="p">(</span><span class="n">e</span><span class="p">)</span>
+
+        <span class="n">sub</span> <span class="o">=</span> <span class="mi">0</span>
+        <span class="n">stack</span> <span class="o">=</span> <span class="p">[]</span>
+        <span class="n">cplex</span> <span class="o">=</span> <span class="kc">False</span>
+
+        <span class="k">for</span> <span class="n">it</span> <span class="ow">in</span> <span class="n">e</span><span class="p">:</span>
+
+            <span class="k">if</span> <span class="n">it</span> <span class="o">==</span> <span class="s1">&#39;,&#39;</span><span class="p">:</span>
+
+                <span class="k">continue</span>
+
+            <span class="k">elif</span> <span class="n">it</span> <span class="o">==</span> <span class="s1">&#39;)&#39;</span><span class="p">:</span>
+
+                <span class="n">sub</span> <span class="o">-=</span> <span class="mi">1</span>
+
+                <span class="k">if</span> <span class="ow">not</span> <span class="n">sub</span><span class="p">:</span>
+
+                    <span class="n">stack</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">process_entity</span><span class="p">(</span><span class="n">this_stack</span><span class="p">))</span>
+
+                <span class="k">else</span><span class="p">:</span>
+
+                    <span class="n">this_stack</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">it</span><span class="p">)</span>
+
+            <span class="k">elif</span> <span class="n">sub</span><span class="p">:</span>
+
+                <span class="n">this_stack</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">it</span><span class="p">)</span>
+
+                <span class="k">if</span> <span class="n">it</span> <span class="o">==</span> <span class="s1">&#39;(&#39;</span><span class="p">:</span>
+
+                    <span class="n">sub</span> <span class="o">+=</span> <span class="mi">1</span>
+
+            <span class="k">elif</span> <span class="n">it</span> <span class="o">==</span> <span class="s1">&#39;(&#39;</span><span class="p">:</span>
+
+                <span class="k">if</span> <span class="ow">not</span> <span class="n">sub</span><span class="p">:</span>
+
+                    <span class="n">this_stack</span> <span class="o">=</span> <span class="p">[]</span>
+
+                <span class="n">sub</span> <span class="o">+=</span> <span class="mi">1</span>
+
+            <span class="k">elif</span> <span class="n">it</span> <span class="o">==</span> <span class="s1">&#39;+&#39;</span><span class="p">:</span>
+
+                <span class="n">cplex</span> <span class="o">=</span> <span class="kc">True</span>
+
+            <span class="k">else</span><span class="p">:</span>
+
+                <span class="n">stack</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">it</span><span class="p">)</span>
+
+        <span class="k">if</span> <span class="n">cplex</span><span class="p">:</span>
+
+            <span class="n">stack</span> <span class="o">=</span> <span class="nb">tuple</span><span class="p">(</span><span class="n">stack</span><span class="p">)</span>
+
+        <span class="k">return</span> <span class="n">stack</span>
+
+
+    <span class="k">def</span> <span class="nf">flatten_entity</span><span class="p">(</span><span class="n">e</span><span class="p">):</span>
+
+        <span class="n">flat</span> <span class="o">=</span> <span class="p">[]</span>
+
+        <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">e</span><span class="p">,</span> <span class="nb">str</span><span class="p">):</span>
+
+            <span class="n">flat</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">e</span><span class="p">)</span>
+
+        <span class="k">elif</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">e</span><span class="p">,</span> <span class="nb">tuple</span><span class="p">):</span>
+
+            <span class="n">flat</span><span class="o">.</span><span class="n">extend</span><span class="p">(</span>
+                <span class="n">itertools</span><span class="o">.</span><span class="n">product</span><span class="p">(</span><span class="o">*</span><span class="p">(</span>
+                    <span class="p">(</span><span class="n">c</span><span class="p">,)</span>
+                        <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">c</span><span class="p">,</span> <span class="nb">str</span><span class="p">)</span> <span class="k">else</span>
+                    <span class="p">(</span><span class="n">flatten_entity</span><span class="p">(</span><span class="n">c</span><span class="p">),)</span>
+                        <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">c</span><span class="p">,</span> <span class="nb">tuple</span><span class="p">)</span> <span class="k">else</span>
+                    <span class="n">c</span>
+                    <span class="k">for</span> <span class="n">c</span> <span class="ow">in</span> <span class="n">e</span>
+                <span class="p">))</span>
+            <span class="p">)</span>
+
+        <span class="k">elif</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">e</span><span class="p">,</span> <span class="nb">list</span><span class="p">):</span>
+
+            <span class="n">flat</span><span class="o">.</span><span class="n">extend</span><span class="p">(</span><span class="n">itertools</span><span class="o">.</span><span class="n">chain</span><span class="p">(</span><span class="o">*</span><span class="p">(</span><span class="n">flatten_entity</span><span class="p">(</span><span class="n">c</span><span class="p">)</span> <span class="k">for</span> <span class="n">c</span> <span class="ow">in</span> <span class="n">e</span><span class="p">)))</span>
+
+        <span class="k">if</span> <span class="nb">any</span><span class="p">(</span>
+            <span class="nb">any</span><span class="p">(</span><span class="nb">isinstance</span><span class="p">(</span><span class="n">c</span><span class="p">,</span> <span class="nb">list</span><span class="p">)</span> <span class="k">for</span> <span class="n">c</span> <span class="ow">in</span> <span class="n">flate</span><span class="p">)</span>
+            <span class="k">for</span> <span class="n">flate</span> <span class="ow">in</span> <span class="n">flat</span>
+        <span class="p">):</span>
+
+            <span class="n">flat</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span>
+                <span class="n">itertools</span><span class="o">.</span><span class="n">chain</span><span class="p">(</span><span class="o">*</span><span class="p">(</span>
+                    <span class="n">flatten_entity</span><span class="p">(</span><span class="n">flate</span><span class="p">)</span> <span class="k">for</span> <span class="n">flate</span> <span class="ow">in</span> <span class="n">flat</span>
+                <span class="p">))</span>
+            <span class="p">)</span>
+
+        <span class="n">flat</span> <span class="o">=</span> <span class="p">[</span><span class="n">flatten_nested_complex</span><span class="p">(</span><span class="n">flate</span><span class="p">)</span> <span class="k">for</span> <span class="n">flate</span> <span class="ow">in</span> <span class="n">flat</span><span class="p">]</span>
+
+        <span class="k">return</span> <span class="n">flat</span>
+
+
+    <span class="k">def</span> <span class="nf">flatten_nested_complex</span><span class="p">(</span><span class="n">cplex</span><span class="p">):</span>
+
+        <span class="k">if</span> <span class="n">is_nested_complex</span><span class="p">(</span><span class="n">cplex</span><span class="p">):</span>
+
+            <span class="n">cplex</span> <span class="o">=</span> <span class="nb">tuple</span><span class="p">(</span>
+                <span class="n">member</span>
+                <span class="k">for</span> <span class="n">members</span> <span class="ow">in</span> <span class="n">cplex</span>
+                <span class="k">for</span> <span class="n">member</span> <span class="ow">in</span> <span class="p">(</span>
+                    <span class="n">members</span>
+                        <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">members</span><span class="p">,</span> <span class="nb">tuple</span><span class="p">)</span> <span class="k">else</span>
+                    <span class="p">(</span><span class="n">members</span><span class="p">,)</span>
+                <span class="p">)</span>
+            <span class="p">)</span>
+
+            <span class="k">if</span> <span class="n">is_nested_complex</span><span class="p">(</span><span class="n">cplex</span><span class="p">):</span>
+
+                <span class="n">cplex</span> <span class="o">=</span> <span class="n">flatten_nested_complex</span><span class="p">(</span><span class="n">cplex</span><span class="p">)</span>
+
+        <span class="k">return</span> <span class="n">cplex</span>
+
+
+    <span class="k">def</span> <span class="nf">is_nested_complex</span><span class="p">(</span><span class="n">cplex</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="p">(</span>
+            <span class="nb">isinstance</span><span class="p">(</span><span class="n">cplex</span><span class="p">,</span> <span class="nb">tuple</span><span class="p">)</span> <span class="ow">and</span>
+            <span class="nb">any</span><span class="p">(</span><span class="nb">isinstance</span><span class="p">(</span><span class="n">member</span><span class="p">,</span> <span class="nb">tuple</span><span class="p">)</span> <span class="k">for</span> <span class="n">member</span> <span class="ow">in</span> <span class="n">cplex</span><span class="p">)</span>
+        <span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">get_interactions</span><span class="p">(</span><span class="n">connections</span><span class="p">,</span> <span class="n">enames</span><span class="p">,</span> <span class="n">pw_type</span><span class="p">,</span> <span class="n">network_id</span><span class="p">):</span>
+
+        <span class="n">entities</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">(</span>
+            <span class="p">(</span>
+                <span class="n">i</span><span class="p">,</span>
+                <span class="n">flatten_entity</span><span class="p">(</span><span class="n">process_entity</span><span class="p">(</span><span class="n">connections</span><span class="p">[</span><span class="n">i</span><span class="p">]))</span>
+            <span class="p">)</span>
+            <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="nb">len</span><span class="p">(</span><span class="n">connections</span><span class="p">),</span> <span class="mi">2</span><span class="p">)</span>
+        <span class="p">)</span>
+
+        <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="nb">len</span><span class="p">(</span><span class="n">connections</span><span class="p">)</span> <span class="o">-</span> <span class="mi">1</span><span class="p">,</span> <span class="mi">2</span><span class="p">):</span>
+
+            <span class="n">itype</span><span class="p">,</span> <span class="n">effect</span> <span class="o">=</span> <span class="n">i_code</span><span class="p">[</span><span class="n">connections</span><span class="p">[</span><span class="n">i</span> <span class="o">+</span> <span class="mi">1</span><span class="p">]]</span>
+
+            <span class="k">if</span> <span class="p">(</span>
+                <span class="nb">len</span><span class="p">(</span><span class="n">entities</span><span class="p">[</span><span class="n">i</span><span class="p">])</span> <span class="o">&gt;</span> <span class="n">max_entity_variations</span> <span class="ow">or</span>
+                <span class="nb">len</span><span class="p">(</span><span class="n">entities</span><span class="p">[</span><span class="n">i</span> <span class="o">+</span> <span class="mi">2</span><span class="p">])</span> <span class="o">&gt;</span> <span class="n">max_entity_variations</span>
+            <span class="p">):</span>
+
+                <span class="k">continue</span>
+
+            <span class="k">for</span> <span class="n">id_a</span><span class="p">,</span> <span class="n">id_b</span> <span class="ow">in</span> <span class="n">itertools</span><span class="o">.</span><span class="n">product</span><span class="p">(</span><span class="n">entities</span><span class="p">[</span><span class="n">i</span><span class="p">],</span> <span class="n">entities</span><span class="p">[</span><span class="n">i</span> <span class="o">+</span> <span class="mi">2</span><span class="p">]):</span>
+
+                <span class="n">name_a</span><span class="p">,</span> <span class="n">type_a</span> <span class="o">=</span> <span class="n">get_name_type</span><span class="p">(</span><span class="n">id_a</span><span class="p">,</span> <span class="n">enames</span><span class="p">)</span>
+                <span class="n">name_b</span><span class="p">,</span> <span class="n">type_b</span> <span class="o">=</span> <span class="n">get_name_type</span><span class="p">(</span><span class="n">id_b</span><span class="p">,</span> <span class="n">enames</span><span class="p">)</span>
+
+                <span class="k">yield</span> <span class="n">KeggMedicusRawInteraction</span><span class="p">(</span>
+                    <span class="n">id_a</span> <span class="o">=</span> <span class="n">id_a</span><span class="p">,</span>
+                    <span class="n">id_b</span> <span class="o">=</span> <span class="n">id_b</span><span class="p">,</span>
+                    <span class="n">name_a</span> <span class="o">=</span> <span class="n">name_a</span><span class="p">,</span>
+                    <span class="n">name_b</span> <span class="o">=</span> <span class="n">name_b</span><span class="p">,</span>
+                    <span class="n">effect</span> <span class="o">=</span> <span class="n">effect</span><span class="p">,</span>
+                    <span class="n">itype</span> <span class="o">=</span> <span class="n">itype</span><span class="p">,</span>
+                    <span class="n">pw_type</span> <span class="o">=</span> <span class="n">pw_type</span><span class="p">,</span>
+                    <span class="n">type_a</span> <span class="o">=</span> <span class="n">type_a</span><span class="p">,</span>
+                    <span class="n">type_b</span> <span class="o">=</span> <span class="n">type_b</span><span class="p">,</span>
+                    <span class="n">network_id</span> <span class="o">=</span> <span class="n">network_id</span><span class="p">,</span>
+                <span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">get_name_type</span><span class="p">(</span><span class="n">_id</span><span class="p">,</span> <span class="n">enames</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="p">(</span>
+            <span class="nb">tuple</span><span class="p">(</span><span class="nb">zip</span><span class="p">(</span><span class="o">*</span><span class="p">(</span><span class="n">_get_name_type</span><span class="p">(</span><span class="n">i</span><span class="p">,</span> <span class="n">enames</span><span class="p">)</span> <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="n">_id</span><span class="p">)))</span>
+                <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">_id</span><span class="p">,</span> <span class="nb">tuple</span><span class="p">)</span> <span class="k">else</span>
+            <span class="n">_get_name_type</span><span class="p">(</span><span class="n">_id</span><span class="p">,</span> <span class="n">enames</span><span class="p">)</span>
+        <span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">_get_name_type</span><span class="p">(</span><span class="n">_id</span><span class="p">,</span> <span class="n">enames</span><span class="p">):</span>
+
+        <span class="k">if</span> <span class="n">_id</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">enames</span><span class="p">:</span>
+
+            <span class="n">dbget</span> <span class="o">=</span> <span class="n">kegg_dbget</span><span class="p">(</span><span class="n">_id</span><span class="p">)</span>
+
+            <span class="k">if</span> <span class="ow">not</span> <span class="n">dbget</span><span class="p">:</span>
+
+                <span class="n">name</span><span class="p">,</span> <span class="n">entity_type</span> <span class="o">=</span> <span class="p">(</span><span class="kc">None</span><span class="p">,</span> <span class="kc">None</span><span class="p">)</span>
+
+            <span class="k">else</span><span class="p">:</span>
+
+                <span class="n">name</span> <span class="o">=</span> <span class="p">(</span>
+                    <span class="n">dbget</span><span class="p">[</span><span class="s1">&#39;Name&#39;</span><span class="p">][</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span>
+                        <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">dbget</span><span class="p">[</span><span class="s1">&#39;Name&#39;</span><span class="p">],</span> <span class="nb">list</span><span class="p">)</span> <span class="k">else</span>
+                    <span class="n">dbget</span><span class="p">[</span><span class="s1">&#39;Name&#39;</span><span class="p">]</span>
+                <span class="p">)</span>
+                <span class="n">entity_type</span> <span class="o">=</span> <span class="n">dbget</span><span class="p">[</span><span class="s1">&#39;Type&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span>
+
+            <span class="n">enames</span><span class="p">[</span><span class="n">_id</span><span class="p">]</span> <span class="o">=</span> <span class="p">(</span><span class="n">name</span><span class="p">,</span> <span class="n">entity_type</span><span class="p">)</span>
+
+        <span class="k">return</span> <span class="n">enames</span><span class="p">[</span><span class="n">_id</span><span class="p">]</span>
+
+
+    <span class="n">recollect</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">compile</span><span class="p">(</span><span class="sa">r</span><span class="s1">&#39;^(GENE|PERTURBANT|VARIANT|METABOLITE)&#39;</span><span class="p">)</span>
+    <span class="n">recon</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">compile</span><span class="p">(</span><span class="sa">r</span><span class="s1">&#39;(-&gt;|--|//|-\||=&gt;|&gt;&gt;|=\||==)&#39;</span><span class="p">)</span>
+    <span class="n">rewrongspace</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">compile</span><span class="p">(</span><span class="sa">r</span><span class="s1">&#39;(\d+) (?=\d+)&#39;</span><span class="p">)</span>
+    <span class="n">result</span> <span class="o">=</span> <span class="nb">set</span><span class="p">()</span>
+    <span class="n">url</span> <span class="o">=</span> <span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;kegg_pws&#39;</span><span class="p">][</span><span class="s1">&#39;medicus&#39;</span><span class="p">]</span>
+    <span class="n">c</span> <span class="o">=</span> <span class="n">curl</span><span class="o">.</span><span class="n">Curl</span><span class="p">(</span><span class="n">url</span><span class="p">,</span> <span class="n">silent</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span> <span class="n">large</span> <span class="o">=</span> <span class="kc">True</span><span class="p">)</span>
+    <span class="n">enames</span> <span class="o">=</span> <span class="p">{}</span>
+    <span class="n">collecting</span> <span class="o">=</span> <span class="kc">None</span>
+
+    <span class="k">for</span> <span class="n">row</span> <span class="ow">in</span> <span class="n">c</span><span class="o">.</span><span class="n">result</span><span class="p">:</span>
+
+        <span class="n">begin_coll</span> <span class="o">=</span> <span class="n">recollect</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="n">row</span><span class="p">)</span>
+
+        <span class="k">if</span> <span class="n">begin_coll</span><span class="p">:</span>
+
+            <span class="n">collecting</span> <span class="o">=</span> <span class="n">begin_coll</span><span class="o">.</span><span class="n">group</span><span class="p">()</span>
+            <span class="n">row</span> <span class="o">=</span> <span class="n">row</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="n">maxsplit</span> <span class="o">=</span> <span class="mi">1</span><span class="p">)[</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span>
+
+        <span class="k">if</span> <span class="n">collecting</span><span class="p">:</span>
+
+            <span class="k">if</span> <span class="ow">not</span> <span class="n">begin_coll</span> <span class="ow">and</span> <span class="n">row</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">!=</span> <span class="s1">&#39; &#39;</span><span class="p">:</span>
+
+                <span class="n">collecting</span> <span class="o">=</span> <span class="kc">None</span>
+                <span class="k">continue</span>
+
+            <span class="k">if</span> <span class="n">collecting</span> <span class="o">==</span> <span class="s1">&#39;GENE&#39;</span><span class="p">:</span>
+
+                <span class="n">row</span> <span class="o">=</span> <span class="n">row</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;;&#39;</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span>
+
+            <span class="n">id_name</span> <span class="o">=</span> <span class="n">row</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="n">maxsplit</span> <span class="o">=</span> <span class="mi">1</span><span class="p">)</span>
+
+            <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">id_name</span><span class="p">)</span> <span class="o">==</span> <span class="mi">2</span><span class="p">:</span>
+
+                <span class="n">_id</span><span class="p">,</span> <span class="n">name</span> <span class="o">=</span> <span class="n">id_name</span>
+
+            <span class="k">else</span><span class="p">:</span>
+
+                <span class="n">_id</span> <span class="o">=</span> <span class="n">id_name</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span>
+                <span class="n">dbget</span> <span class="o">=</span> <span class="n">kegg_dbget</span><span class="p">(</span><span class="n">_id</span><span class="p">)</span>
+
+                <span class="n">name</span> <span class="o">=</span> <span class="p">(</span>
+                    <span class="n">dbget</span><span class="p">[</span><span class="s1">&#39;Name&#39;</span><span class="p">]</span>
+                        <span class="k">if</span> <span class="s1">&#39;Name&#39;</span> <span class="ow">in</span> <span class="n">dbget</span> <span class="k">else</span>
+                    <span class="n">dbget</span><span class="p">[</span><span class="s1">&#39;Composition&#39;</span><span class="p">]</span>
+                <span class="p">)</span>
+
+                <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">name</span><span class="p">,</span> <span class="nb">list</span><span class="p">):</span>
+
+                    <span class="n">name</span> <span class="o">=</span> <span class="n">name</span><span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span>
+
+            <span class="n">enames</span><span class="p">[</span><span class="n">_id</span><span class="p">]</span> <span class="o">=</span> <span class="p">(</span><span class="n">name</span><span class="o">.</span><span class="n">strip</span><span class="p">(),</span> <span class="n">collecting</span><span class="o">.</span><span class="n">lower</span><span class="p">())</span>
+
+    <span class="n">c</span><span class="o">.</span><span class="n">fileobj</span><span class="o">.</span><span class="n">seek</span><span class="p">(</span><span class="mi">0</span><span class="p">)</span>
+
+    <span class="k">for</span> <span class="n">row</span> <span class="ow">in</span> <span class="n">c</span><span class="o">.</span><span class="n">fileobj</span><span class="p">:</span>
+
+        <span class="k">if</span> <span class="n">row</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s1">&#39;ENTRY&#39;</span><span class="p">):</span>
+
+            <span class="n">pw_type</span> <span class="o">=</span> <span class="kc">None</span>
+            <span class="n">collecting</span> <span class="o">=</span> <span class="kc">None</span>
+            <span class="n">network_id</span> <span class="o">=</span> <span class="n">row</span><span class="o">.</span><span class="n">split</span><span class="p">()[</span><span class="mi">1</span><span class="p">]</span>
+
+        <span class="k">elif</span> <span class="n">row</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s1">&#39;TYPE&#39;</span><span class="p">):</span>
+
+            <span class="n">pw_type</span> <span class="o">=</span> <span class="n">row</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span><span class="o">.</span><span class="n">split</span><span class="p">()[</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span>
+
+        <span class="k">elif</span> <span class="n">row</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s1">&#39;  EXPANDED&#39;</span><span class="p">):</span>
+
+            <span class="n">connections</span> <span class="o">=</span> <span class="n">renetref</span><span class="o">.</span><span class="n">sub</span><span class="p">(</span><span class="s1">&#39;&#39;</span><span class="p">,</span> <span class="n">row</span><span class="p">)</span>
+            <span class="n">connections</span> <span class="o">=</span> <span class="n">recon</span><span class="o">.</span><span class="n">sub</span><span class="p">(</span><span class="s1">&#39; \g&lt;1&gt; &#39;</span><span class="p">,</span> <span class="n">connections</span><span class="p">)</span>
+            <span class="n">connections</span> <span class="o">=</span> <span class="n">rewrongspace</span><span class="o">.</span><span class="n">sub</span><span class="p">(</span><span class="s1">&#39;\g&lt;1&gt;,&#39;</span><span class="p">,</span> <span class="n">connections</span><span class="p">)</span>
+            <span class="n">connections</span> <span class="o">=</span> <span class="n">connections</span><span class="o">.</span><span class="n">split</span><span class="p">()[</span><span class="mi">1</span><span class="p">:]</span>
+
+        <span class="k">elif</span> <span class="n">row</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s1">&#39;///&#39;</span><span class="p">):</span>
+
+            <span class="n">result</span><span class="o">.</span><span class="n">update</span><span class="p">(</span>
+                <span class="nb">set</span><span class="p">(</span><span class="n">get_interactions</span><span class="p">(</span>
+                    <span class="n">connections</span><span class="p">,</span>
+                    <span class="n">enames</span><span class="p">,</span>
+                    <span class="n">pw_type</span><span class="p">,</span>
+                    <span class="n">network_id</span>
+                <span class="p">))</span>
+            <span class="p">)</span>
+
+    <span class="k">return</span> <span class="n">result</span></div>
+
+
+
+<div class="viewcode-block" id="kegg_medicus_interactions">
+<a class="viewcode-back" href="../../../api/pypath.inputs.kegg.kegg_medicus_interactions.html#pypath.inputs.kegg.kegg_medicus_interactions">[docs]</a>
+<span class="k">def</span> <span class="nf">kegg_medicus_interactions</span><span class="p">(</span><span class="n">max_entity_variations</span> <span class="o">=</span> <span class="mi">10</span><span class="p">,</span> <span class="n">complexes</span> <span class="o">=</span> <span class="kc">False</span><span class="p">):</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Retrieves and preprocesses human protein-protein and transcriptional</span>
+<span class="sd">    regulatory interactions from the KEGG MEDICUS database. Optionally</span>
+<span class="sd">    it returns protein complexes instead of interactions.</span>
+
+<span class="sd">    max_entity_variations : int</span>
+<span class="sd">        In KEGG MEDICUS many molecular entities are protein families or</span>
+<span class="sd">        families of often large and nested protein complexes. By this option</span>
+<span class="sd">        you can limit largest number of variants a single entity might yield,</span>
+<span class="sd">        so you won&#39;t end up with one complex yielding hundreds of</span>
+<span class="sd">        combinatiorial variants.</span>
+<span class="sd">    complexes : bool</span>
+<span class="sd">        Return a set of protein complexes instead of a list of molecular</span>
+<span class="sd">        interactions.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="n">KeggMedicusInteraction</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">namedtuple</span><span class="p">(</span>
+        <span class="s1">&#39;KeggMedicusInteraction&#39;</span><span class="p">,</span>
+        <span class="p">[</span>
+            <span class="s1">&#39;id_a&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;id_b&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;entity_type_a&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;entity_type_b&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;interaction_type&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;effect&#39;</span><span class="p">,</span>
+        <span class="p">]</span>
+    <span class="p">)</span>
+
+
+    <span class="n">result</span> <span class="o">=</span> <span class="p">[]</span>
+    <span class="n">cplexes</span> <span class="o">=</span> <span class="p">{}</span>
+
+
+    <span class="k">def</span> <span class="nf">process_complex</span><span class="p">(</span><span class="n">ids</span><span class="p">,</span> <span class="n">symbols</span><span class="p">,</span> <span class="n">types</span><span class="p">):</span>
+
+        <span class="k">if</span> <span class="n">ids</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">cplexes</span><span class="p">:</span>
+
+            <span class="k">if</span> <span class="ow">not</span> <span class="nb">all</span><span class="p">(</span><span class="n">t</span> <span class="o">==</span> <span class="s1">&#39;gene&#39;</span> <span class="k">for</span> <span class="n">t</span> <span class="ow">in</span> <span class="n">types</span><span class="p">):</span>
+
+                <span class="n">cplexes</span><span class="p">[</span><span class="n">ids</span><span class="p">]</span> <span class="o">=</span> <span class="nb">set</span><span class="p">()</span>
+
+            <span class="n">uniprots</span> <span class="o">=</span> <span class="p">[</span>
+                <span class="n">process_protein</span><span class="p">(</span><span class="n">id_</span><span class="p">,</span> <span class="n">symbol</span><span class="p">)</span>
+                <span class="k">for</span> <span class="n">id_</span><span class="p">,</span> <span class="n">symbol</span> <span class="ow">in</span> <span class="nb">zip</span><span class="p">(</span><span class="n">ids</span><span class="p">,</span> <span class="n">symbols</span><span class="p">)</span>
+            <span class="p">]</span>
+
+            <span class="n">this_cplexes</span> <span class="o">=</span> <span class="p">{</span>
+                <span class="n">intera</span><span class="o">.</span><span class="n">Complex</span><span class="p">(</span>
+                    <span class="n">components</span> <span class="o">=</span> <span class="n">components</span><span class="p">,</span>
+                    <span class="n">sources</span> <span class="o">=</span> <span class="s1">&#39;KEGG-MEDICUS&#39;</span><span class="p">,</span>
+                <span class="p">)</span>
+                <span class="k">for</span> <span class="n">components</span> <span class="ow">in</span> <span class="n">itertools</span><span class="o">.</span><span class="n">product</span><span class="p">(</span><span class="o">*</span><span class="n">uniprots</span><span class="p">)</span>
+            <span class="p">}</span>
+
+            <span class="n">cplexes</span><span class="p">[</span><span class="n">ids</span><span class="p">]</span> <span class="o">=</span> <span class="n">this_cplexes</span>
+
+        <span class="k">return</span> <span class="n">cplexes</span><span class="p">[</span><span class="n">ids</span><span class="p">]</span>
+
+
+    <span class="k">def</span> <span class="nf">process_protein</span><span class="p">(</span><span class="n">id_</span><span class="p">,</span> <span class="n">symbol</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="p">(</span>
+            <span class="n">mapping</span><span class="o">.</span><span class="n">map_name</span><span class="p">(</span><span class="n">id_</span><span class="p">,</span> <span class="s1">&#39;entrez&#39;</span><span class="p">,</span> <span class="s1">&#39;uniprot&#39;</span><span class="p">)</span> <span class="ow">or</span>
+            <span class="n">mapping</span><span class="o">.</span><span class="n">map_name</span><span class="p">(</span><span class="n">id_</span><span class="p">,</span> <span class="s1">&#39;genesymbol&#39;</span><span class="p">,</span> <span class="s1">&#39;uniprot&#39;</span><span class="p">)</span>
+        <span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">process_partner</span><span class="p">(</span><span class="n">ids</span><span class="p">,</span> <span class="n">symbols</span><span class="p">,</span> <span class="n">types</span> <span class="o">=</span> <span class="kc">None</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="p">(</span>
+            <span class="n">process_protein</span><span class="p">(</span><span class="n">ids</span><span class="p">,</span> <span class="n">symbols</span><span class="p">)</span>
+                <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">ids</span><span class="p">,</span> <span class="nb">str</span><span class="p">)</span> <span class="k">else</span>
+            <span class="n">process_complex</span><span class="p">(</span><span class="n">ids</span><span class="p">,</span> <span class="n">symbols</span><span class="p">,</span> <span class="n">types</span><span class="p">)</span>
+        <span class="p">)</span>
+
+
+    <span class="k">for</span> <span class="n">rec</span> <span class="ow">in</span> <span class="n">kegg_medicus</span><span class="p">(</span><span class="n">max_entity_variations</span> <span class="o">=</span> <span class="n">max_entity_variations</span><span class="p">):</span>
+
+        <span class="k">for</span> <span class="n">id_a</span><span class="p">,</span> <span class="n">id_b</span> <span class="ow">in</span> <span class="n">itertools</span><span class="o">.</span><span class="n">product</span><span class="p">(</span>
+            <span class="n">process_partner</span><span class="p">(</span><span class="n">rec</span><span class="o">.</span><span class="n">id_a</span><span class="p">,</span> <span class="n">rec</span><span class="o">.</span><span class="n">name_a</span><span class="p">,</span> <span class="n">rec</span><span class="o">.</span><span class="n">type_a</span><span class="p">),</span>
+            <span class="n">process_partner</span><span class="p">(</span><span class="n">rec</span><span class="o">.</span><span class="n">id_b</span><span class="p">,</span> <span class="n">rec</span><span class="o">.</span><span class="n">name_b</span><span class="p">,</span> <span class="n">rec</span><span class="o">.</span><span class="n">type_b</span><span class="p">),</span>
+        <span class="p">):</span>
+
+            <span class="k">if</span> <span class="ow">not</span> <span class="n">complexes</span><span class="p">:</span>
+
+                <span class="n">result</span><span class="o">.</span><span class="n">append</span><span class="p">(</span>
+                    <span class="n">KeggMedicusInteraction</span><span class="p">(</span>
+                        <span class="n">id_a</span> <span class="o">=</span> <span class="n">id_a</span><span class="p">,</span>
+                        <span class="n">id_b</span> <span class="o">=</span> <span class="n">id_b</span><span class="p">,</span>
+                        <span class="n">entity_type_a</span> <span class="o">=</span> <span class="n">entity</span><span class="o">.</span><span class="n">Entity</span><span class="o">.</span><span class="n">_get_entity_type</span><span class="p">(</span><span class="n">id_a</span><span class="p">),</span>
+                        <span class="n">entity_type_b</span> <span class="o">=</span> <span class="n">entity</span><span class="o">.</span><span class="n">Entity</span><span class="o">.</span><span class="n">_get_entity_type</span><span class="p">(</span><span class="n">id_b</span><span class="p">),</span>
+                        <span class="n">interaction_type</span> <span class="o">=</span> <span class="n">rec</span><span class="o">.</span><span class="n">itype</span><span class="p">,</span>
+                        <span class="n">effect</span> <span class="o">=</span> <span class="n">rec</span><span class="o">.</span><span class="n">effect</span><span class="p">,</span>
+                    <span class="p">)</span>
+                <span class="p">)</span>
+
+    <span class="k">return</span> <span class="nb">set</span><span class="o">.</span><span class="n">union</span><span class="p">(</span><span class="o">*</span><span class="n">cplexes</span><span class="o">.</span><span class="n">values</span><span class="p">())</span> <span class="k">if</span> <span class="n">complexes</span> <span class="k">else</span> <span class="n">result</span></div>
+
+
+
+
+<div class="viewcode-block" id="kegg_medicus_complexes">
+<a class="viewcode-back" href="../../../api/pypath.inputs.kegg.kegg_medicus_complexes.html#pypath.inputs.kegg.kegg_medicus_complexes">[docs]</a>
+<span class="k">def</span> <span class="nf">kegg_medicus_complexes</span><span class="p">(</span><span class="n">max_entity_variations</span> <span class="o">=</span> <span class="mi">10</span><span class="p">):</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Extracts a `dict` of protein complexes from the KEGG MEDICUS database.</span>
+
+<span class="sd">    max_entity_variations : int</span>
+<span class="sd">        In KEGG MEDICUS many molecular entities are protein families or</span>
+<span class="sd">        families of often large and nested protein complexes. By this option</span>
+<span class="sd">        you can limit largest number of variants a single entity might yield,</span>
+<span class="sd">        so you won&#39;t end up with one complex yielding hundreds of</span>
+<span class="sd">        combinatiorial variants.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="n">cplexes</span> <span class="o">=</span> <span class="n">kegg_medicus_interactions</span><span class="p">(</span>
+        <span class="n">max_entity_variations</span> <span class="o">=</span> <span class="n">max_entity_variations</span><span class="p">,</span>
+        <span class="n">complexes</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
+    <span class="p">)</span>
+
+    <span class="n">cplexes</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">((</span><span class="n">cplex</span><span class="o">.</span><span class="fm">__str__</span><span class="p">(),</span> <span class="n">cplex</span><span class="p">)</span> <span class="k">for</span> <span class="n">cplex</span> <span class="ow">in</span> <span class="n">cplexes</span><span class="p">)</span>
+
+    <span class="k">return</span> <span class="n">cplexes</span></div>
+
+
+
+
+
+<div class="viewcode-block" id="kegg_dbget">
+<a class="viewcode-back" href="../../../api/pypath.inputs.kegg.kegg_dbget.html#pypath.inputs.kegg.kegg_dbget">[docs]</a>
+<span class="k">def</span> <span class="nf">kegg_dbget</span><span class="p">(</span><span class="n">entry</span><span class="p">):</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Retrieves an entry (e.g. compounds, network modules) by the KEGG DBGET</span>
+<span class="sd">    interface (kegg.jp/dbget-bin/www_bget).</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="n">rexa</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">compile</span><span class="p">(</span><span class="sa">r</span><span class="s1">&#39;\xa0+&#39;</span><span class="p">)</span>
+    <span class="n">stripchars</span> <span class="o">=</span> <span class="s1">&#39;</span><span class="se">\r\n</span><span class="s1">; &#39;</span>
+    <span class="n">reffields</span> <span class="o">=</span> <span class="p">{</span><span class="s1">&#39;Authors&#39;</span><span class="p">,</span> <span class="s1">&#39;Title&#39;</span><span class="p">,</span> <span class="s1">&#39;Journal&#39;</span><span class="p">}</span>
+
+    <span class="n">result</span> <span class="o">=</span> <span class="p">{}</span>
+
+    <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">entry</span><span class="p">,</span> <span class="nb">int</span><span class="p">):</span>
+
+        <span class="n">entry</span> <span class="o">=</span> <span class="s1">&#39;hsa:</span><span class="si">%u</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="n">entry</span>
+
+    <span class="k">if</span> <span class="n">entry</span><span class="o">.</span><span class="n">isdigit</span><span class="p">():</span>
+
+        <span class="n">entry</span> <span class="o">=</span> <span class="s1">&#39;hsa:</span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="n">entry</span>
+
+    <span class="n">url</span> <span class="o">=</span> <span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;kegg_pws&#39;</span><span class="p">][</span><span class="s1">&#39;dbget&#39;</span><span class="p">]</span> <span class="o">%</span> <span class="n">entry</span>
+    <span class="n">c</span> <span class="o">=</span> <span class="n">curl</span><span class="o">.</span><span class="n">Curl</span><span class="p">(</span><span class="n">url</span><span class="p">,</span> <span class="n">silent</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span> <span class="n">large</span> <span class="o">=</span> <span class="kc">False</span><span class="p">)</span>
+    <span class="n">soup</span> <span class="o">=</span> <span class="n">bs4</span><span class="o">.</span><span class="n">BeautifulSoup</span><span class="p">(</span><span class="n">c</span><span class="o">.</span><span class="n">result</span><span class="p">,</span> <span class="s1">&#39;html.parser&#39;</span><span class="p">)</span>
+
+    <span class="n">tbl</span> <span class="o">=</span> <span class="n">soup</span><span class="o">.</span><span class="n">find_all</span><span class="p">(</span><span class="s1">&#39;table&#39;</span><span class="p">,</span> <span class="n">limit</span> <span class="o">=</span> <span class="mi">4</span><span class="p">)</span>
+
+    <span class="k">if</span> <span class="ow">not</span> <span class="n">tbl</span><span class="p">:</span>
+
+        <span class="k">return</span> <span class="kc">None</span>
+
+    <span class="n">tbl</span> <span class="o">=</span> <span class="n">tbl</span><span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span>
+
+    <span class="n">collecting_ref</span> <span class="o">=</span> <span class="kc">False</span>
+    <span class="n">last_ref</span> <span class="o">=</span> <span class="p">{}</span>
+
+    <span class="k">for</span> <span class="n">row</span> <span class="ow">in</span> <span class="n">tbl</span><span class="o">.</span><span class="n">findChildren</span><span class="p">(</span><span class="s1">&#39;tr&#39;</span><span class="p">,</span> <span class="n">recursive</span> <span class="o">=</span> <span class="kc">False</span><span class="p">):</span>
+
+        <span class="n">key</span> <span class="o">=</span> <span class="n">row</span><span class="o">.</span><span class="n">find</span><span class="p">(</span><span class="s1">&#39;th&#39;</span><span class="p">)</span><span class="o">.</span><span class="n">text</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span>
+        <span class="n">td</span> <span class="o">=</span> <span class="n">row</span><span class="o">.</span><span class="n">find</span><span class="p">(</span><span class="s1">&#39;td&#39;</span><span class="p">)</span>
+
+        <span class="k">if</span> <span class="n">collecting_ref</span><span class="p">:</span>
+
+            <span class="k">if</span> <span class="n">key</span> <span class="ow">in</span> <span class="n">reffields</span><span class="p">:</span>
+
+                <span class="n">last_ref</span><span class="p">[</span><span class="n">key</span><span class="p">]</span> <span class="o">=</span> <span class="n">td</span><span class="o">.</span><span class="n">text</span>
+                <span class="k">continue</span>
+
+            <span class="k">else</span><span class="p">:</span>
+
+                <span class="k">if</span> <span class="s1">&#39;References&#39;</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">result</span><span class="p">:</span>
+
+                    <span class="n">result</span><span class="p">[</span><span class="s1">&#39;References&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="p">[]</span>
+
+                <span class="n">result</span><span class="p">[</span><span class="s1">&#39;References&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">last_ref</span><span class="p">)</span>
+                <span class="n">last_ref</span> <span class="o">=</span> <span class="p">{}</span>
+                <span class="n">collecting_ref</span> <span class="o">=</span> <span class="kc">False</span>
+
+        <span class="k">if</span> <span class="n">key</span> <span class="o">==</span> <span class="s1">&#39;Reference&#39;</span><span class="p">:</span>
+
+            <span class="n">collecting_ref</span> <span class="o">=</span> <span class="kc">True</span>
+            <span class="n">last_ref</span><span class="p">[</span><span class="s1">&#39;PMID&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">findall</span><span class="p">(</span><span class="sa">r</span><span class="s1">&#39;\d+&#39;</span><span class="p">,</span> <span class="n">td</span><span class="o">.</span><span class="n">text</span><span class="p">)[</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span>
+            <span class="k">continue</span>
+
+        <span class="n">subtbl</span> <span class="o">=</span> <span class="n">td</span><span class="o">.</span><span class="n">find_all</span><span class="p">(</span><span class="s1">&#39;table&#39;</span><span class="p">)</span>
+
+        <span class="k">if</span> <span class="n">subtbl</span><span class="p">:</span>
+
+            <span class="n">value</span> <span class="o">=</span> <span class="p">{}</span>
+
+            <span class="k">for</span> <span class="n">st</span> <span class="ow">in</span> <span class="n">subtbl</span><span class="p">:</span>
+
+                <span class="k">for</span> <span class="n">subrow</span> <span class="ow">in</span> <span class="n">st</span><span class="o">.</span><span class="n">find_all</span><span class="p">(</span><span class="s1">&#39;tr&#39;</span><span class="p">):</span>
+
+                    <span class="n">subtd</span> <span class="o">=</span> <span class="n">subrow</span><span class="o">.</span><span class="n">find_all</span><span class="p">(</span><span class="s1">&#39;td&#39;</span><span class="p">)</span>
+
+                    <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">subtd</span><span class="p">)</span> <span class="o">&gt;</span> <span class="mi">1</span> <span class="ow">and</span> <span class="n">subtd</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">text</span><span class="p">:</span>
+
+                        <span class="n">value</span><span class="p">[</span><span class="n">rexa</span><span class="o">.</span><span class="n">sub</span><span class="p">(</span><span class="s1">&#39;&#39;</span><span class="p">,</span> <span class="n">subtd</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">text</span><span class="p">)]</span> <span class="o">=</span> <span class="p">(</span>
+                            <span class="n">subtd</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">text</span><span class="o">.</span><span class="n">strip</span><span class="p">(</span><span class="n">stripchars</span><span class="p">)</span>
+                        <span class="p">)</span>
+
+                    <span class="k">else</span><span class="p">:</span>
+
+                        <span class="n">subcontent</span> <span class="o">=</span> <span class="n">rexa</span><span class="o">.</span><span class="n">sub</span><span class="p">(</span><span class="s1">&#39; &#39;</span><span class="p">,</span> <span class="n">subtd</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">text</span><span class="p">)</span><span class="o">.</span><span class="n">split</span><span class="p">()</span>
+
+                        <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">subcontent</span><span class="p">)</span> <span class="o">&gt;</span> <span class="mi">1</span><span class="p">:</span>
+
+                            <span class="n">value</span><span class="p">[</span><span class="n">subcontent</span><span class="p">[</span><span class="mi">0</span><span class="p">]]</span> <span class="o">=</span> <span class="p">(</span>
+                                <span class="n">subcontent</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">strip</span><span class="p">(</span><span class="n">stripchars</span><span class="p">)</span>
+                            <span class="p">)</span>
+
+        <span class="k">else</span><span class="p">:</span>
+
+            <span class="n">value</span> <span class="o">=</span> <span class="n">rexa</span><span class="o">.</span><span class="n">sub</span><span class="p">(</span><span class="s1">&#39; &#39;</span><span class="p">,</span> <span class="n">td</span><span class="o">.</span><span class="n">text</span><span class="p">)</span><span class="o">.</span><span class="n">strip</span><span class="p">(</span><span class="n">stripchars</span><span class="p">)</span>
+
+            <span class="k">if</span> <span class="s1">&#39;</span><span class="se">\n</span><span class="s1">&#39;</span> <span class="ow">in</span> <span class="n">value</span><span class="p">:</span>
+
+                <span class="n">value</span> <span class="o">=</span> <span class="p">[</span>
+                    <span class="n">lval</span><span class="o">.</span><span class="n">strip</span><span class="p">(</span><span class="n">stripchars</span><span class="p">)</span>
+                    <span class="k">for</span> <span class="n">lval</span> <span class="ow">in</span> <span class="n">re</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="sa">r</span><span class="s1">&#39;\s*[\n\r]+\s*&#39;</span><span class="p">,</span> <span class="n">value</span><span class="p">)</span>
+                <span class="p">]</span>
+
+
+        <span class="k">if</span> <span class="n">key</span> <span class="o">==</span> <span class="s1">&#39;Entry&#39;</span><span class="p">:</span>
+
+            <span class="n">value</span><span class="p">,</span> <span class="n">result</span><span class="p">[</span><span class="s1">&#39;Type&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="nb">next</span><span class="p">(</span><span class="n">value</span><span class="o">.</span><span class="n">items</span><span class="p">()</span><span class="o">.</span><span class="fm">__iter__</span><span class="p">())</span>
+
+        <span class="n">result</span><span class="p">[</span><span class="n">key</span><span class="p">]</span> <span class="o">=</span> <span class="n">value</span>
+
+    <span class="k">return</span> <span class="n">result</span></div>
+
+</pre></div>
+
+                </article>
+              
+              
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+              
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diff --git a/_modules/pypath/inputs/kinasedotcom.html b/_modules/pypath/inputs/kinasedotcom.html
new file mode 100644
index 000000000..cdfb4ec90
--- /dev/null
+++ b/_modules/pypath/inputs/kinasedotcom.html
@@ -0,0 +1,679 @@
+
+<!DOCTYPE html>
+
+
+<html lang="en" data-content_root="../../../" >
+
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+    <meta charset="utf-8" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
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+  
+  
+  
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+
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+  <h1>Source code for pypath.inputs.kinasedotcom</h1><div class="highlight"><pre>
+<span></span><span class="ch">#!/usr/bin/env python</span>
+<span class="c1"># -*- coding: utf-8 -*-</span>
+
+<span class="c1">#</span>
+<span class="c1">#  This file is part of the `pypath` python module</span>
+<span class="c1">#</span>
+<span class="c1">#  Copyright 2014-2023</span>
+<span class="c1">#  EMBL, EMBL-EBI, Uniklinik RWTH Aachen, Heidelberg University</span>
+<span class="c1">#</span>
+<span class="c1">#  Authors: see the file `README.rst`</span>
+<span class="c1">#  Contact: Dénes Türei (turei.denes@gmail.com)</span>
+<span class="c1">#</span>
+<span class="c1">#  Distributed under the GPLv3 License.</span>
+<span class="c1">#  See accompanying file LICENSE.txt or copy at</span>
+<span class="c1">#      https://www.gnu.org/licenses/gpl-3.0.html</span>
+<span class="c1">#</span>
+<span class="c1">#  Website: https://pypath.omnipathdb.org/</span>
+<span class="c1">#</span>
+
+<span class="kn">import</span> <span class="nn">collections</span>
+
+<span class="kn">import</span> <span class="nn">pypath.share.curl</span> <span class="k">as</span> <span class="nn">curl</span>
+<span class="kn">import</span> <span class="nn">pypath.resources.urls</span> <span class="k">as</span> <span class="nn">urls</span>
+<span class="kn">import</span> <span class="nn">pypath.utils.mapping</span> <span class="k">as</span> <span class="nn">mapping</span>
+<span class="kn">import</span> <span class="nn">pypath.inputs.common</span> <span class="k">as</span> <span class="nn">inputs_common</span>
+
+
+<div class="viewcode-block" id="kinasedotcom_annotations">
+<a class="viewcode-back" href="../../../api/pypath.inputs.kinasedotcom.kinasedotcom_annotations.html#pypath.inputs.kinasedotcom.kinasedotcom_annotations">[docs]</a>
+<span class="k">def</span> <span class="nf">kinasedotcom_annotations</span><span class="p">():</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Downloads and processes kinase annotations from kinase.com.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="n">KinasedotcomAnnotation</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">namedtuple</span><span class="p">(</span>
+        <span class="s1">&#39;KinasedotcomAnnotation&#39;</span><span class="p">,</span>
+        <span class="p">[</span><span class="s1">&#39;group&#39;</span><span class="p">,</span> <span class="s1">&#39;family&#39;</span><span class="p">,</span> <span class="s1">&#39;subfamily&#39;</span><span class="p">]</span>
+    <span class="p">)</span>
+    <span class="n">KinasedotcomAnnotation</span><span class="o">.</span><span class="fm">__new__</span><span class="o">.</span><span class="vm">__defaults__</span> <span class="o">=</span> <span class="p">(</span><span class="kc">None</span><span class="p">,)</span>
+
+
+    <span class="k">def</span> <span class="nf">add_record</span><span class="p">(</span><span class="n">uniprot</span><span class="p">,</span> <span class="n">rec</span><span class="p">,</span> <span class="n">offset</span> <span class="o">=</span> <span class="mi">2</span><span class="p">):</span>
+
+        <span class="k">if</span> <span class="n">rec</span><span class="p">[</span><span class="n">offset</span><span class="p">]</span><span class="o">.</span><span class="n">strip</span><span class="p">():</span>
+            <span class="n">result</span><span class="p">[</span><span class="n">uniprot</span><span class="p">]</span><span class="o">.</span><span class="n">add</span><span class="p">(</span>
+                <span class="n">KinasedotcomAnnotation</span><span class="p">(</span>
+                    <span class="n">group</span> <span class="o">=</span> <span class="n">rec</span><span class="p">[</span><span class="n">offset</span><span class="p">]</span><span class="o">.</span><span class="n">strip</span><span class="p">(),</span>
+                    <span class="n">family</span> <span class="o">=</span> <span class="n">rec</span><span class="p">[</span><span class="n">offset</span> <span class="o">+</span> <span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">strip</span><span class="p">(),</span>
+                    <span class="n">subfamily</span> <span class="o">=</span> <span class="n">rec</span><span class="p">[</span><span class="n">offset</span> <span class="o">+</span> <span class="mi">2</span><span class="p">]</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span> <span class="ow">or</span> <span class="kc">None</span><span class="p">,</span>
+                <span class="p">)</span>
+            <span class="p">)</span>
+
+
+    <span class="n">url</span> <span class="o">=</span> <span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;kinome&#39;</span><span class="p">][</span><span class="s1">&#39;rescued&#39;</span><span class="p">]</span>
+    <span class="n">c</span> <span class="o">=</span> <span class="n">curl</span><span class="o">.</span><span class="n">Curl</span><span class="p">(</span><span class="n">url</span><span class="p">,</span> <span class="n">large</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span> <span class="n">silent</span> <span class="o">=</span> <span class="kc">False</span><span class="p">)</span>
+    <span class="n">xlsf</span> <span class="o">=</span> <span class="n">c</span><span class="o">.</span><span class="n">fileobj</span>
+    <span class="n">xlsname</span> <span class="o">=</span> <span class="n">xlsf</span><span class="o">.</span><span class="n">name</span>
+    <span class="n">xlsf</span><span class="o">.</span><span class="n">close</span><span class="p">()</span>
+    <span class="n">tbl</span> <span class="o">=</span> <span class="n">inputs_common</span><span class="o">.</span><span class="n">read_xls</span><span class="p">(</span><span class="n">xlsname</span><span class="p">)</span>
+
+    <span class="n">result</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">defaultdict</span><span class="p">(</span><span class="nb">set</span><span class="p">)</span>
+
+    <span class="k">for</span> <span class="n">rec</span> <span class="ow">in</span> <span class="n">tbl</span><span class="p">:</span>
+
+        <span class="n">uniprots</span> <span class="o">=</span> <span class="n">mapping</span><span class="o">.</span><span class="n">map_name</span><span class="p">(</span><span class="n">rec</span><span class="p">[</span><span class="mi">23</span><span class="p">]</span><span class="o">.</span><span class="n">strip</span><span class="p">(),</span> <span class="s1">&#39;genesymbol&#39;</span><span class="p">,</span> <span class="s1">&#39;uniprot&#39;</span><span class="p">)</span>
+
+        <span class="k">for</span> <span class="n">uniprot</span> <span class="ow">in</span> <span class="n">uniprots</span><span class="p">:</span>
+
+            <span class="n">add_record</span><span class="p">(</span><span class="n">uniprot</span><span class="p">,</span> <span class="n">rec</span><span class="p">)</span>
+
+            <span class="k">if</span> <span class="n">rec</span><span class="p">[</span><span class="mi">12</span><span class="p">]</span><span class="o">.</span><span class="n">strip</span><span class="p">():</span>
+
+                <span class="n">add_record</span><span class="p">(</span><span class="n">uniprot</span><span class="p">,</span> <span class="n">rec</span><span class="p">,</span> <span class="n">offset</span> <span class="o">=</span> <span class="mi">12</span><span class="p">)</span>
+
+    <span class="k">return</span> <span class="nb">dict</span><span class="p">(</span><span class="n">result</span><span class="p">)</span></div>
+
+</pre></div>
+
+                </article>
+              
+              
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diff --git a/_modules/pypath/inputs/lambert2018.html b/_modules/pypath/inputs/lambert2018.html
new file mode 100644
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+                  
+  <h1>Source code for pypath.inputs.lambert2018</h1><div class="highlight"><pre>
+<span></span><span class="ch">#!/usr/bin/env python</span>
+<span class="c1"># -*- coding: utf-8 -*-</span>
+
+<span class="c1">#</span>
+<span class="c1">#  This file is part of the `pypath` python module</span>
+<span class="c1">#</span>
+<span class="c1">#  Copyright 2014-2023</span>
+<span class="c1">#  EMBL, EMBL-EBI, Uniklinik RWTH Aachen, Heidelberg University</span>
+<span class="c1">#</span>
+<span class="c1">#  Authors: see the file `README.rst`</span>
+<span class="c1">#  Contact: Dénes Türei (turei.denes@gmail.com)</span>
+<span class="c1">#</span>
+<span class="c1">#  Distributed under the GPLv3 License.</span>
+<span class="c1">#  See accompanying file LICENSE.txt or copy at</span>
+<span class="c1">#      https://www.gnu.org/licenses/gpl-3.0.html</span>
+<span class="c1">#</span>
+<span class="c1">#  Website: https://pypath.omnipathdb.org/</span>
+<span class="c1">#</span>
+
+<span class="kn">import</span> <span class="nn">re</span>
+<span class="kn">import</span> <span class="nn">collections</span>
+
+<span class="kn">import</span> <span class="nn">pypath.inputs.common</span> <span class="k">as</span> <span class="nn">inputs_common</span>
+<span class="kn">import</span> <span class="nn">pypath.resources.urls</span> <span class="k">as</span> <span class="nn">urls</span>
+<span class="kn">import</span> <span class="nn">pypath.utils.mapping</span> <span class="k">as</span> <span class="nn">mapping</span>
+<span class="kn">import</span> <span class="nn">pypath.inputs.cell</span> <span class="k">as</span> <span class="nn">cell_input</span>
+<span class="kn">import</span> <span class="nn">pypath.share.common</span> <span class="k">as</span> <span class="nn">common</span>
+
+
+<div class="viewcode-block" id="lambert2018_s1_raw">
+<a class="viewcode-back" href="../../../api/pypath.inputs.lambert2018.lambert2018_s1_raw.html#pypath.inputs.lambert2018.lambert2018_s1_raw">[docs]</a>
+<span class="k">def</span> <span class="nf">lambert2018_s1_raw</span><span class="p">():</span>
+
+    <span class="k">def</span> <span class="nf">process_field</span><span class="p">(</span><span class="n">f</span><span class="p">):</span>
+
+        <span class="n">f</span> <span class="o">=</span> <span class="n">common</span><span class="o">.</span><span class="n">try_bool</span><span class="p">(</span><span class="n">common</span><span class="o">.</span><span class="n">try_float</span><span class="p">(</span><span class="n">f</span><span class="o">.</span><span class="n">strip</span><span class="p">()))</span>
+
+        <span class="k">return</span> <span class="kc">None</span> <span class="k">if</span> <span class="n">f</span> <span class="ow">in</span> <span class="p">{</span><span class="s1">&#39;&#39;</span><span class="p">,</span> <span class="s1">&#39;#N/A&#39;</span><span class="p">}</span> <span class="k">else</span> <span class="n">f</span>
+
+
+    <span class="n">path</span> <span class="o">=</span> <span class="n">cell_input</span><span class="o">.</span><span class="n">cell_supplementary</span><span class="p">(</span>
+        <span class="n">supp_url</span> <span class="o">=</span> <span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;lambert2018&#39;</span><span class="p">][</span><span class="s1">&#39;s1&#39;</span><span class="p">],</span>
+        <span class="n">article_url</span> <span class="o">=</span> <span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;lambert2018&#39;</span><span class="p">][</span><span class="s1">&#39;article&#39;</span><span class="p">],</span>
+    <span class="p">)</span>
+
+    <span class="n">content</span> <span class="o">=</span> <span class="n">inputs_common</span><span class="o">.</span><span class="n">read_xls</span><span class="p">(</span><span class="n">path</span><span class="p">,</span> <span class="n">sheet</span> <span class="o">=</span> <span class="mi">1</span><span class="p">)</span>
+
+    <span class="n">h0</span><span class="p">,</span> <span class="n">h1</span> <span class="o">=</span> <span class="n">content</span><span class="o">.</span><span class="n">pop</span><span class="p">(</span><span class="mi">0</span><span class="p">),</span> <span class="n">content</span><span class="o">.</span><span class="n">pop</span><span class="p">(</span><span class="mi">0</span><span class="p">)</span>
+    <span class="n">h1</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span> <span class="o">=</span> <span class="n">h0</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span>
+
+    <span class="n">names</span> <span class="o">=</span> <span class="p">[</span><span class="s1">&#39;</span><span class="si">%s</span><span class="s1">_</span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="n">n</span> <span class="k">for</span> <span class="n">n</span> <span class="ow">in</span> <span class="nb">zip</span><span class="p">()]</span>
+
+    <span class="n">record</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">namedtuple</span><span class="p">(</span>
+        <span class="s1">&#39;Lambert2018Raw&#39;</span><span class="p">,</span>
+        <span class="p">[</span>
+            <span class="n">nn</span> <span class="k">for</span> <span class="n">nn</span> <span class="ow">in</span> <span class="p">(</span>
+                <span class="n">re</span><span class="o">.</span><span class="n">sub</span><span class="p">(</span><span class="s1">&#39;[- ?;:]&#39;</span><span class="p">,</span> <span class="s1">&#39;_&#39;</span><span class="p">,</span> <span class="n">n</span><span class="p">)</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span><span class="o">.</span><span class="n">strip</span><span class="p">(</span><span class="s1">&#39;_ &#39;</span><span class="p">)</span>
+                <span class="k">for</span> <span class="n">n</span> <span class="ow">in</span> <span class="n">h1</span>
+            <span class="p">)</span>
+            <span class="k">if</span> <span class="n">nn</span>
+        <span class="p">]</span>
+    <span class="p">)</span>
+
+    <span class="n">nfields</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="n">record</span><span class="o">.</span><span class="n">_fields</span><span class="p">)</span>
+
+    <span class="k">return</span> <span class="p">[</span>
+        <span class="n">record</span><span class="p">(</span><span class="o">*</span><span class="p">(</span><span class="n">process_field</span><span class="p">(</span><span class="n">f</span><span class="p">)</span> <span class="k">for</span> <span class="n">f</span> <span class="ow">in</span> <span class="n">r</span><span class="p">[:</span><span class="n">nfields</span><span class="p">]))</span>
+        <span class="k">for</span> <span class="n">r</span> <span class="ow">in</span> <span class="n">content</span>
+    <span class="p">]</span></div>
+
+
+
+<div class="viewcode-block" id="lambert2018_annotations">
+<a class="viewcode-back" href="../../../api/pypath.inputs.lambert2018.lambert2018_annotations.html#pypath.inputs.lambert2018.lambert2018_annotations">[docs]</a>
+<span class="k">def</span> <span class="nf">lambert2018_annotations</span><span class="p">():</span>
+
+    <span class="n">Lambert2018Annotation</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">namedtuple</span><span class="p">(</span>
+        <span class="s1">&#39;Lambert2018Annotation&#39;</span><span class="p">,</span>
+        <span class="p">(</span>
+            <span class="s1">&#39;ensg&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;genesymbol&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;is_tf&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;tf_assessment&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;binding_mode&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;binding_domain&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;tf_disagree&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;binding_disagree&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;binding1&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;binding2&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;assessment1&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;assessment2&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;vaquerizas2009&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;cisbp&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;tfclass&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;tfcat_annot&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;tfcat_pmids&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;go&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;pdb&#39;</span><span class="p">,</span>
+        <span class="p">)</span>
+    <span class="p">)</span>
+
+    <span class="n">result</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">defaultdict</span><span class="p">(</span><span class="nb">set</span><span class="p">)</span>
+
+    <span class="k">for</span> <span class="n">r</span> <span class="ow">in</span> <span class="n">lambert2018_s1_raw</span><span class="p">():</span>
+
+        <span class="n">uniprots</span> <span class="o">=</span> <span class="n">mapping</span><span class="o">.</span><span class="n">map_name</span><span class="p">(</span><span class="n">r</span><span class="o">.</span><span class="n">name</span><span class="p">,</span> <span class="s1">&#39;genesymbol&#39;</span><span class="p">,</span> <span class="s1">&#39;uniprot&#39;</span><span class="p">)</span>
+        <span class="n">vaquerizas</span> <span class="o">=</span> <span class="n">r</span><span class="o">.</span><span class="n">vaquerizas_2009_tf_classification</span> <span class="ow">or</span> <span class="s1">&#39;no&#39;</span>
+
+        <span class="n">tfcat_annot</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="nb">tuple</span><span class="p">(</span><span class="n">common</span><span class="o">.</span><span class="n">del_empty</span><span class="p">(</span><span class="nb">sorted</span><span class="p">(</span>
+                <span class="n">a</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span> <span class="k">for</span> <span class="n">a</span> <span class="ow">in</span>
+                <span class="n">re</span><span class="o">.</span><span class="n">split</span><span class="p">(</span>
+                    <span class="s1">&#39;[_;]&#39;</span><span class="p">,</span>
+                    <span class="n">re</span><span class="o">.</span><span class="n">sub</span><span class="p">(</span>
+                        <span class="s1">&#39;PMIDS:[\d;]+&#39;</span><span class="p">,</span> <span class="s1">&#39;&#39;</span><span class="p">,</span>
+                        <span class="n">r</span><span class="o">.</span><span class="n">tf_cat_classification</span>
+                    <span class="p">)</span><span class="o">.</span>
+                    <span class="n">replace</span><span class="p">(</span><span class="s1">&#39;tf&#39;</span><span class="p">,</span> <span class="s1">&#39;TF&#39;</span><span class="p">)</span><span class="o">.</span>
+                    <span class="n">replace</span><span class="p">(</span><span class="s1">&#39;Transcription Factor&#39;</span><span class="p">,</span> <span class="s1">&#39;TF&#39;</span><span class="p">)</span>
+                <span class="p">)</span>
+            <span class="p">)))</span>
+                <span class="k">if</span> <span class="n">r</span><span class="o">.</span><span class="n">tf_cat_classification</span> <span class="k">else</span>
+            <span class="p">()</span>
+        <span class="p">)</span>
+
+        <span class="n">tfcat_pmids</span> <span class="o">=</span> <span class="n">common</span><span class="o">.</span><span class="n">re_safe_groups</span><span class="p">(</span>
+            <span class="s1">&#39;PMIDS:([\d;]+)&#39;</span><span class="p">,</span>
+            <span class="n">r</span><span class="o">.</span><span class="n">tf_cat_classification</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span>
+        <span class="p">)[</span><span class="mi">0</span><span class="p">]</span> <span class="k">if</span> <span class="n">r</span><span class="o">.</span><span class="n">tf_cat_classification</span> <span class="k">else</span> <span class="kc">None</span>
+
+        <span class="n">tfcat_pmids</span> <span class="o">=</span> <span class="kc">None</span> <span class="k">if</span> <span class="n">tfcat_pmids</span> <span class="o">==</span> <span class="s1">&#39;0&#39;</span> <span class="k">else</span> <span class="n">tfcat_pmids</span>
+
+        <span class="k">for</span> <span class="n">uniprot</span> <span class="ow">in</span> <span class="n">uniprots</span><span class="p">:</span>
+
+            <span class="n">result</span><span class="p">[</span><span class="n">uniprot</span><span class="p">]</span><span class="o">.</span><span class="n">add</span><span class="p">(</span>
+                <span class="n">Lambert2018Annotation</span><span class="p">(</span>
+                    <span class="n">ensg</span> <span class="o">=</span> <span class="n">r</span><span class="o">.</span><span class="n">id</span><span class="p">,</span>
+                    <span class="n">genesymbol</span> <span class="o">=</span> <span class="n">r</span><span class="o">.</span><span class="n">name</span><span class="p">,</span>
+                    <span class="n">is_tf</span> <span class="o">=</span> <span class="n">r</span><span class="o">.</span><span class="n">is_tf</span><span class="p">,</span>
+                    <span class="n">tf_assessment</span> <span class="o">=</span> <span class="n">r</span><span class="o">.</span><span class="n">tf_assessment</span><span class="p">,</span>
+                    <span class="n">binding_mode</span> <span class="o">=</span> <span class="n">r</span><span class="o">.</span><span class="n">binding_mode</span><span class="p">,</span>
+                    <span class="n">binding_domain</span> <span class="o">=</span> <span class="n">r</span><span class="o">.</span><span class="n">dbd</span><span class="p">,</span>
+                    <span class="n">tf_disagree</span> <span class="o">=</span> <span class="n">r</span><span class="o">.</span><span class="n">disagree_on_assessment</span> <span class="o">==</span> <span class="s1">&#39;Disagree&#39;</span><span class="p">,</span>
+                    <span class="n">binding_disagree</span> <span class="o">=</span> <span class="n">r</span><span class="o">.</span><span class="n">disagree_on_binding</span> <span class="o">==</span> <span class="s1">&#39;Disagree&#39;</span><span class="p">,</span>
+                    <span class="n">binding1</span> <span class="o">=</span> <span class="n">r</span><span class="o">.</span><span class="n">binding1</span><span class="p">,</span>
+                    <span class="n">binding2</span> <span class="o">=</span> <span class="n">r</span><span class="o">.</span><span class="n">binding2</span><span class="p">,</span>
+                    <span class="n">assessment1</span> <span class="o">=</span> <span class="n">r</span><span class="o">.</span><span class="n">assesment1</span><span class="p">,</span>
+                    <span class="n">assessment2</span> <span class="o">=</span> <span class="n">r</span><span class="o">.</span><span class="n">assesment2</span><span class="p">,</span>
+                    <span class="n">vaquerizas2009</span> <span class="o">=</span> <span class="n">vaquerizas</span><span class="p">,</span>
+                    <span class="n">cisbp</span> <span class="o">=</span> <span class="n">r</span><span class="o">.</span><span class="n">cisbp_considers_it_as_a_tf</span><span class="p">,</span>
+                    <span class="n">tfclass</span> <span class="o">=</span> <span class="n">r</span><span class="o">.</span><span class="n">tfclass_considers_it_as_a_tf</span><span class="p">,</span>
+                    <span class="n">tfcat_annot</span> <span class="o">=</span> <span class="n">tfcat_annot</span><span class="p">,</span>
+                    <span class="n">tfcat_pmids</span> <span class="o">=</span> <span class="n">tfcat_pmids</span><span class="p">,</span>
+                    <span class="n">go</span> <span class="o">=</span> <span class="n">r</span><span class="o">.</span><span class="n">is_a_go_tf</span><span class="p">,</span>
+                    <span class="n">pdb</span> <span class="o">=</span> <span class="n">r</span><span class="o">.</span><span class="n">pdb</span><span class="p">,</span>
+                <span class="p">)</span>
+            <span class="p">)</span>
+
+    <span class="k">return</span> <span class="nb">dict</span><span class="p">(</span><span class="n">result</span><span class="p">)</span></div>
+
+</pre></div>
+
+                </article>
+              
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diff --git a/_modules/pypath/inputs/li2012.html b/_modules/pypath/inputs/li2012.html
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+                  
+  <h1>Source code for pypath.inputs.li2012</h1><div class="highlight"><pre>
+<span></span><span class="ch">#!/usr/bin/env python</span>
+<span class="c1"># -*- coding: utf-8 -*-</span>
+
+<span class="c1">#</span>
+<span class="c1">#  This file is part of the `pypath` python module</span>
+<span class="c1">#</span>
+<span class="c1">#  Copyright 2014-2023</span>
+<span class="c1">#  EMBL, EMBL-EBI, Uniklinik RWTH Aachen, Heidelberg University</span>
+<span class="c1">#</span>
+<span class="c1">#  Authors: see the file `README.rst`</span>
+<span class="c1">#  Contact: Dénes Türei (turei.denes@gmail.com)</span>
+<span class="c1">#</span>
+<span class="c1">#  Distributed under the GPLv3 License.</span>
+<span class="c1">#  See accompanying file LICENSE.txt or copy at</span>
+<span class="c1">#      https://www.gnu.org/licenses/gpl-3.0.html</span>
+<span class="c1">#</span>
+<span class="c1">#  Website: https://pypath.omnipathdb.org/</span>
+<span class="c1">#</span>
+
+<span class="kn">from</span> <span class="nn">future.utils</span> <span class="kn">import</span> <span class="n">iteritems</span>
+
+<span class="kn">import</span> <span class="nn">pypath.share.curl</span> <span class="k">as</span> <span class="nn">curl</span>
+<span class="kn">import</span> <span class="nn">pypath.resources.urls</span> <span class="k">as</span> <span class="nn">urls</span>
+<span class="kn">import</span> <span class="nn">pypath.share.common</span> <span class="k">as</span> <span class="nn">common</span>
+<span class="kn">import</span> <span class="nn">pypath.inputs.common</span> <span class="k">as</span> <span class="nn">inputs_common</span>
+<span class="kn">import</span> <span class="nn">pypath.utils.mapping</span> <span class="k">as</span> <span class="nn">mapping</span>
+<span class="kn">import</span> <span class="nn">pypath.internals.intera</span> <span class="k">as</span> <span class="nn">intera</span>
+<span class="kn">import</span> <span class="nn">pypath.utils.seq</span> <span class="k">as</span> <span class="nn">seq</span>
+
+
+<div class="viewcode-block" id="get_li2012">
+<a class="viewcode-back" href="../../../api/pypath.inputs.li2012.get_li2012.html#pypath.inputs.li2012.get_li2012">[docs]</a>
+<span class="k">def</span> <span class="nf">get_li2012</span><span class="p">():</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Reads supplementary data of Li 2012 from local file.</span>
+<span class="sd">    Returns table (list of lists).</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="n">url</span> <span class="o">=</span> <span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;li2012&#39;</span><span class="p">][</span><span class="s1">&#39;url&#39;</span><span class="p">]</span>
+    <span class="n">c</span> <span class="o">=</span> <span class="n">curl</span><span class="o">.</span><span class="n">Curl</span><span class="p">(</span><span class="n">url</span><span class="p">,</span> <span class="n">silent</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span> <span class="n">large</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span> <span class="n">slow</span> <span class="o">=</span> <span class="kc">True</span><span class="p">)</span>
+    <span class="n">xls</span> <span class="o">=</span> <span class="n">c</span><span class="o">.</span><span class="n">fileobj</span>
+    <span class="n">xlsfile</span> <span class="o">=</span> <span class="n">xls</span><span class="o">.</span><span class="n">name</span>
+    <span class="n">xls</span><span class="o">.</span><span class="n">close</span><span class="p">()</span>
+    <span class="n">tbl</span> <span class="o">=</span> <span class="n">inputs_common</span><span class="o">.</span><span class="n">read_xls</span><span class="p">(</span><span class="n">xlsfile</span><span class="p">,</span> <span class="n">sheet</span> <span class="o">=</span> <span class="s1">&#39;File S1&#39;</span><span class="p">)</span>
+    <span class="k">return</span> <span class="nb">filter</span><span class="p">(</span><span class="k">lambda</span> <span class="n">l</span><span class="p">:</span> <span class="nb">len</span><span class="p">(</span><span class="n">l</span><span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">])</span> <span class="o">&gt;</span> <span class="mi">0</span><span class="p">,</span> <span class="nb">map</span><span class="p">(</span><span class="k">lambda</span> <span class="n">l</span><span class="p">:</span> <span class="n">l</span><span class="p">[:</span><span class="mi">7</span><span class="p">],</span> <span class="n">tbl</span><span class="p">[</span><span class="mi">2</span><span class="p">:]))</span></div>
+
+
+
+<div class="viewcode-block" id="li2012_interactions">
+<a class="viewcode-back" href="../../../api/pypath.inputs.li2012.li2012_interactions.html#pypath.inputs.li2012.li2012_interactions">[docs]</a>
+<span class="k">def</span> <span class="nf">li2012_interactions</span><span class="p">():</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Converts table read by ``pypath.inputs.li2012.get_li2012`` to</span>
+<span class="sd">    list of interactions.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="n">result</span> <span class="o">=</span> <span class="p">[]</span>
+    <span class="n">data</span> <span class="o">=</span> <span class="n">get_li2012</span><span class="p">()</span>
+
+    <span class="k">for</span> <span class="n">l</span> <span class="ow">in</span> <span class="n">data</span><span class="p">:</span>
+
+        <span class="n">subs_protein</span> <span class="o">=</span> <span class="n">l</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;/&#39;</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span>
+        <span class="n">tk_protein</span> <span class="o">=</span> <span class="n">l</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">()[</span><span class="mi">0</span><span class="p">]</span>
+        <span class="n">reader_protein</span> <span class="o">=</span> <span class="n">l</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">()[</span><span class="mi">0</span><span class="p">]</span>
+        <span class="n">route</span> <span class="o">=</span> <span class="n">l</span><span class="p">[</span><span class="mi">4</span><span class="p">]</span>
+        <span class="n">result</span><span class="o">.</span><span class="n">append</span><span class="p">((</span>
+            <span class="n">tk_protein</span><span class="p">,</span>
+            <span class="n">subs_protein</span><span class="p">,</span>
+            <span class="n">route</span><span class="p">,</span>
+            <span class="s1">&#39;phosphorylation&#39;</span>
+        <span class="p">))</span>
+        <span class="n">result</span><span class="o">.</span><span class="n">append</span><span class="p">((</span>
+            <span class="n">subs_protein</span><span class="p">,</span>
+            <span class="n">reader_protein</span><span class="p">,</span>
+            <span class="n">route</span><span class="p">,</span>
+            <span class="s1">&#39;phosphomotif_binding&#39;</span>
+        <span class="p">))</span>
+
+    <span class="k">return</span> <span class="p">[</span><span class="nb">list</span><span class="p">(</span><span class="n">l</span><span class="p">)</span> <span class="k">for</span> <span class="n">l</span> <span class="ow">in</span> <span class="n">common</span><span class="o">.</span><span class="n">unique_list</span><span class="p">(</span><span class="n">result</span><span class="p">)]</span></div>
+
+
+
+<div class="viewcode-block" id="li2012_enzyme_substrate">
+<a class="viewcode-back" href="../../../api/pypath.inputs.li2012.li2012_enzyme_substrate.html#pypath.inputs.li2012.li2012_enzyme_substrate">[docs]</a>
+<span class="k">def</span> <span class="nf">li2012_enzyme_substrate</span><span class="p">():</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Converts table read by ``pypath.inputs.li2012.get_li2012`` to</span>
+<span class="sd">    list of dicts of kinase-substrate interactions.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="n">result</span> <span class="o">=</span> <span class="p">[]</span>
+    <span class="n">data</span> <span class="o">=</span> <span class="n">get_li2012</span><span class="p">()</span>
+
+    <span class="k">for</span> <span class="n">l</span> <span class="ow">in</span> <span class="n">data</span><span class="p">:</span>
+
+        <span class="n">subs_protein</span> <span class="o">=</span> <span class="n">l</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;/&#39;</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span>
+        <span class="n">tk_protein</span> <span class="o">=</span> <span class="n">l</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">()[</span><span class="mi">0</span><span class="p">]</span>
+        <span class="n">subs_resnum</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">common</span><span class="o">.</span><span class="n">non_digit</span><span class="o">.</span><span class="n">sub</span><span class="p">(</span><span class="s1">&#39;&#39;</span><span class="p">,</span> <span class="n">l</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;/&#39;</span><span class="p">)[</span><span class="mi">1</span><span class="p">]))</span>
+        <span class="n">result</span><span class="o">.</span><span class="n">append</span><span class="p">(</span>
+            <span class="p">(</span>
+                <span class="n">subs_protein</span><span class="p">,</span> <span class="c1"># substrate</span>
+                <span class="n">tk_protein</span><span class="p">,</span> <span class="c1"># kinase</span>
+                <span class="kc">None</span><span class="p">,</span> <span class="c1"># instance</span>
+                <span class="kc">None</span><span class="p">,</span> <span class="c1"># start</span>
+                <span class="kc">None</span><span class="p">,</span> <span class="c1"># end</span>
+                <span class="s1">&#39;Y&#39;</span><span class="p">,</span>  <span class="c1"># residue letter</span>
+                <span class="n">subs_resnum</span><span class="p">,</span> <span class="c1"># residue offset</span>
+            <span class="p">)</span>
+        <span class="p">)</span>
+
+    <span class="n">result</span> <span class="o">=</span> <span class="p">[</span>
+        <span class="nb">dict</span><span class="p">(</span>
+            <span class="nb">zip</span><span class="p">(</span>
+                <span class="p">[</span>
+                    <span class="s1">&#39;substrate&#39;</span><span class="p">,</span> <span class="s1">&#39;kinase&#39;</span><span class="p">,</span> <span class="s1">&#39;instance&#39;</span><span class="p">,</span>
+                    <span class="s1">&#39;start&#39;</span><span class="p">,</span> <span class="s1">&#39;end&#39;</span><span class="p">,</span> <span class="s1">&#39;resaa&#39;</span><span class="p">,</span>
+                    <span class="s1">&#39;resnum&#39;</span><span class="p">,</span>
+                <span class="p">],</span>
+                <span class="nb">list</span><span class="p">(</span><span class="n">l</span><span class="p">)</span>
+            <span class="p">)</span>
+        <span class="p">)</span>
+        <span class="k">for</span> <span class="n">l</span> <span class="ow">in</span> <span class="n">common</span><span class="o">.</span><span class="n">unique_list</span><span class="p">(</span><span class="n">result</span><span class="p">)</span>
+    <span class="p">]</span>
+
+    <span class="k">return</span> <span class="n">result</span></div>
+
+
+
+<div class="viewcode-block" id="li2012_dmi">
+<a class="viewcode-back" href="../../../api/pypath.inputs.li2012.li2012_dmi.html#pypath.inputs.li2012.li2012_dmi">[docs]</a>
+<span class="k">def</span> <span class="nf">li2012_dmi</span><span class="p">():</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Converts table read by ``pypath.inputs.li2012.get_li2012`` to</span>
+<span class="sd">    list of ``pypath.internals.intera.DomainMotif`` objects.</span>
+<span class="sd">    Translates GeneSymbols to UniProt IDs.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="n">result</span> <span class="o">=</span> <span class="p">[]</span>
+    <span class="n">se</span> <span class="o">=</span> <span class="n">seq</span><span class="o">.</span><span class="n">swissprot_seq</span><span class="p">(</span><span class="n">isoforms</span> <span class="o">=</span> <span class="kc">True</span><span class="p">)</span>
+    <span class="n">data</span> <span class="o">=</span> <span class="n">get_li2012</span><span class="p">()</span>
+
+    <span class="k">for</span> <span class="n">l</span> <span class="ow">in</span> <span class="n">data</span><span class="p">:</span>
+
+        <span class="n">subs_protein</span> <span class="o">=</span> <span class="n">l</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;/&#39;</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span>
+        <span class="n">tk_protein</span> <span class="o">=</span> <span class="n">l</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">()[</span><span class="mi">0</span><span class="p">]</span>
+        <span class="n">reader_protein</span> <span class="o">=</span> <span class="n">l</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">()[</span><span class="mi">0</span><span class="p">]</span>
+        <span class="n">subs_uniprots</span> <span class="o">=</span> <span class="n">mapping</span><span class="o">.</span><span class="n">map_name</span><span class="p">(</span>
+            <span class="n">subs_protein</span><span class="p">,</span>
+            <span class="s1">&#39;genesymbol&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;uniprot&#39;</span><span class="p">,</span>
+        <span class="p">)</span>
+        <span class="n">tk_uniprots</span> <span class="o">=</span> <span class="n">mapping</span><span class="o">.</span><span class="n">map_name</span><span class="p">(</span><span class="n">tk_protein</span><span class="p">,</span> <span class="s1">&#39;genesymbol&#39;</span><span class="p">,</span> <span class="s1">&#39;uniprot&#39;</span><span class="p">)</span>
+        <span class="n">reader_uniprots</span> <span class="o">=</span> <span class="n">mapping</span><span class="o">.</span><span class="n">map_name</span><span class="p">(</span><span class="n">reader_protein</span><span class="p">,</span> <span class="s1">&#39;genesymbol&#39;</span><span class="p">,</span>
+                                          <span class="s1">&#39;uniprot&#39;</span><span class="p">)</span>
+        <span class="n">subs_resnum</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">common</span><span class="o">.</span><span class="n">non_digit</span><span class="o">.</span><span class="n">sub</span><span class="p">(</span><span class="s1">&#39;&#39;</span><span class="p">,</span> <span class="n">l</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;/&#39;</span><span class="p">)[</span><span class="mi">1</span><span class="p">]))</span>
+
+        <span class="k">for</span> <span class="n">su</span> <span class="ow">in</span> <span class="n">subs_uniprots</span><span class="p">:</span>
+
+            <span class="k">if</span> <span class="n">su</span> <span class="ow">in</span> <span class="n">se</span><span class="p">:</span>
+
+                <span class="n">subs_iso</span> <span class="o">=</span> <span class="kc">None</span>
+
+                <span class="k">for</span> <span class="n">iso</span><span class="p">,</span> <span class="n">s</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="n">se</span><span class="p">[</span><span class="n">su</span><span class="p">]</span><span class="o">.</span><span class="n">isof</span><span class="p">):</span>
+
+                    <span class="k">if</span> <span class="n">se</span><span class="p">[</span><span class="n">su</span><span class="p">]</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="n">subs_resnum</span><span class="p">,</span> <span class="n">isoform</span> <span class="o">=</span> <span class="n">iso</span><span class="p">)</span> <span class="o">==</span> <span class="s1">&#39;Y&#39;</span><span class="p">:</span>
+
+                        <span class="n">subs_iso</span> <span class="o">=</span> <span class="n">iso</span>
+                        <span class="k">break</span>
+
+                <span class="k">if</span> <span class="n">subs_iso</span><span class="p">:</span>
+
+                    <span class="n">start</span> <span class="o">=</span> <span class="nb">min</span><span class="p">(</span><span class="mi">1</span><span class="p">,</span> <span class="n">subs_resnum</span> <span class="o">-</span> <span class="mi">7</span><span class="p">)</span>
+                    <span class="n">end</span> <span class="o">=</span> <span class="nb">max</span><span class="p">(</span><span class="n">subs_resnum</span> <span class="o">+</span> <span class="mi">7</span><span class="p">,</span> <span class="nb">len</span><span class="p">(</span><span class="n">se</span><span class="p">[</span><span class="n">su</span><span class="p">]</span><span class="o">.</span><span class="n">isof</span><span class="p">[</span><span class="n">subs_iso</span><span class="p">]))</span>
+
+                    <span class="k">for</span> <span class="n">ku</span> <span class="ow">in</span> <span class="n">tk_uniprots</span><span class="p">:</span>
+
+                        <span class="n">res</span> <span class="o">=</span> <span class="n">intera</span><span class="o">.</span><span class="n">Residue</span><span class="p">(</span>
+                            <span class="n">subs_resnum</span><span class="p">,</span>
+                            <span class="s1">&#39;Y&#39;</span><span class="p">,</span>
+                            <span class="n">su</span><span class="p">,</span>
+                            <span class="n">isoform</span> <span class="o">=</span> <span class="n">subs_iso</span><span class="p">,</span>
+                        <span class="p">)</span>
+
+                        <span class="n">mot</span> <span class="o">=</span> <span class="n">intera</span><span class="o">.</span><span class="n">Motif</span><span class="p">(</span>
+                            <span class="n">su</span><span class="p">,</span>
+                            <span class="n">start</span><span class="p">,</span>
+                            <span class="n">end</span><span class="p">,</span>
+                            <span class="n">isoform</span> <span class="o">=</span> <span class="n">subs_iso</span><span class="p">,</span>
+                            <span class="n">instance</span> <span class="o">=</span> <span class="n">se</span><span class="p">[</span><span class="n">su</span><span class="p">]</span><span class="o">.</span><span class="n">get</span><span class="p">(</span>
+                                <span class="n">start</span><span class="p">,</span>
+                                <span class="n">end</span><span class="p">,</span>
+                                <span class="n">isoform</span> <span class="o">=</span> <span class="n">subs_iso</span>
+                            <span class="p">),</span>
+                        <span class="p">)</span>
+
+                        <span class="n">ptm</span> <span class="o">=</span> <span class="n">intera</span><span class="o">.</span><span class="n">Ptm</span><span class="p">(</span>
+                            <span class="n">su</span><span class="p">,</span>
+                            <span class="n">motif</span> <span class="o">=</span> <span class="n">mot</span><span class="p">,</span>
+                            <span class="n">residue</span> <span class="o">=</span> <span class="n">res</span><span class="p">,</span>
+                            <span class="n">isoform</span> <span class="o">=</span> <span class="n">subs_iso</span><span class="p">,</span>
+                            <span class="n">typ</span> <span class="o">=</span> <span class="s1">&#39;phosphorylation&#39;</span><span class="p">,</span>
+                            <span class="n">evidences</span> <span class="o">=</span> <span class="s1">&#39;Li2012&#39;</span>
+                        <span class="p">)</span>
+
+                        <span class="n">dom</span> <span class="o">=</span> <span class="n">intera</span><span class="o">.</span><span class="n">Domain</span><span class="p">(</span><span class="n">ku</span><span class="p">)</span>
+
+                        <span class="n">dommot</span> <span class="o">=</span> <span class="n">intera</span><span class="o">.</span><span class="n">DomainMotif</span><span class="p">(</span>
+                            <span class="n">domain</span> <span class="o">=</span> <span class="n">dom</span><span class="p">,</span>
+                            <span class="n">ptm</span> <span class="o">=</span> <span class="n">ptm</span><span class="p">,</span>
+                            <span class="n">evidences</span> <span class="o">=</span> <span class="s1">&#39;Li2012&#39;</span><span class="p">,</span>
+                        <span class="p">)</span>
+
+                        <span class="n">result</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">dommot</span><span class="p">)</span>
+
+    <span class="k">return</span> <span class="n">result</span></div>
+
+</pre></div>
+
+                </article>
+              
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+  <h1>Source code for pypath.inputs.lmpid</h1><div class="highlight"><pre>
+<span></span><span class="ch">#!/usr/bin/env python</span>
+<span class="c1"># -*- coding: utf-8 -*-</span>
+
+<span class="c1">#</span>
+<span class="c1">#  This file is part of the `pypath` python module</span>
+<span class="c1">#</span>
+<span class="c1">#  Copyright 2014-2023</span>
+<span class="c1">#  EMBL, EMBL-EBI, Uniklinik RWTH Aachen, Heidelberg University</span>
+<span class="c1">#</span>
+<span class="c1">#  Authors: see the file `README.rst`</span>
+<span class="c1">#  Contact: Dénes Türei (turei.denes@gmail.com)</span>
+<span class="c1">#</span>
+<span class="c1">#  Distributed under the GPLv3 License.</span>
+<span class="c1">#  See accompanying file LICENSE.txt or copy at</span>
+<span class="c1">#      https://www.gnu.org/licenses/gpl-3.0.html</span>
+<span class="c1">#</span>
+<span class="c1">#  Website: https://pypath.omnipathdb.org/</span>
+<span class="c1">#</span>
+
+<span class="kn">import</span> <span class="nn">bs4</span>
+
+<span class="kn">import</span> <span class="nn">pypath.share.curl</span> <span class="k">as</span> <span class="nn">curl</span>
+<span class="kn">import</span> <span class="nn">pypath.share.progress</span> <span class="k">as</span> <span class="nn">progress</span>
+<span class="kn">import</span> <span class="nn">pypath.resources.urls</span> <span class="k">as</span> <span class="nn">urls</span>
+<span class="kn">import</span> <span class="nn">pypath.utils.mapping</span> <span class="k">as</span> <span class="nn">mapping</span>
+<span class="kn">import</span> <span class="nn">pypath.inputs.uniprot_db</span> <span class="k">as</span> <span class="nn">uniprot_db</span>
+
+
+<div class="viewcode-block" id="load_lmpid">
+<a class="viewcode-back" href="../../../api/pypath.inputs.lmpid.load_lmpid.html#pypath.inputs.lmpid.load_lmpid">[docs]</a>
+<span class="k">def</span> <span class="nf">load_lmpid</span><span class="p">(</span><span class="n">organism</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">):</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Reads and processes LMPID data from local file</span>
+<span class="sd">    `pypath.data/LMPID_DATA_pubmed_ref.xml`.</span>
+<span class="sd">    The file was provided by LMPID authors and is now</span>
+<span class="sd">    redistributed with the module.</span>
+<span class="sd">    Returns list of domain-motif interactions.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="n">result</span> <span class="o">=</span> <span class="p">[]</span>
+
+    <span class="n">url</span> <span class="o">=</span> <span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;lmpid&#39;</span><span class="p">][</span><span class="s1">&#39;url&#39;</span><span class="p">]</span>
+    <span class="n">c</span> <span class="o">=</span> <span class="n">curl</span><span class="o">.</span><span class="n">Curl</span><span class="p">(</span><span class="n">url</span><span class="p">,</span> <span class="n">silent</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span> <span class="n">large</span> <span class="o">=</span> <span class="kc">False</span><span class="p">)</span>
+
+    <span class="n">soup</span> <span class="o">=</span> <span class="n">bs4</span><span class="o">.</span><span class="n">BeautifulSoup</span><span class="p">(</span><span class="n">c</span><span class="o">.</span><span class="n">result</span><span class="p">,</span> <span class="n">features</span> <span class="o">=</span> <span class="s1">&#39;xml&#39;</span><span class="p">)</span>
+    <span class="n">uniprots</span> <span class="o">=</span> <span class="n">uniprot_db</span><span class="o">.</span><span class="n">get_db</span><span class="p">(</span><span class="n">organism</span> <span class="o">=</span> <span class="n">organism</span><span class="p">,</span> <span class="n">swissprot</span> <span class="o">=</span> <span class="kc">None</span><span class="p">)</span>
+    <span class="n">prg</span> <span class="o">=</span> <span class="n">progress</span><span class="o">.</span><span class="n">Progress</span><span class="p">(</span>
+        <span class="nb">len</span><span class="p">(</span><span class="n">soup</span><span class="o">.</span><span class="n">find_all</span><span class="p">(</span><span class="s1">&#39;record&#39;</span><span class="p">)),</span>
+        <span class="s1">&#39;Processing data from LMPID&#39;</span><span class="p">,</span>
+        <span class="mi">21</span>
+    <span class="p">)</span>
+
+    <span class="k">for</span> <span class="n">rec</span> <span class="ow">in</span> <span class="n">soup</span><span class="o">.</span><span class="n">find_all</span><span class="p">(</span><span class="s1">&#39;record&#39;</span><span class="p">):</span>
+
+        <span class="n">prg</span><span class="o">.</span><span class="n">step</span><span class="p">()</span>
+        <span class="n">uniprot_bait</span> <span class="o">=</span> <span class="n">rec</span><span class="o">.</span><span class="n">bait_uniprot_id</span><span class="o">.</span><span class="n">text</span>
+        <span class="n">uniprot_prey</span> <span class="o">=</span> <span class="n">rec</span><span class="o">.</span><span class="n">prey_uniprot_id</span><span class="o">.</span><span class="n">text</span>
+
+        <span class="k">if</span> <span class="n">uniprot_bait</span> <span class="ow">in</span> <span class="n">uniprots</span> <span class="ow">and</span> <span class="n">uniprot_prey</span> <span class="ow">in</span> <span class="n">uniprots</span><span class="p">:</span>
+
+            <span class="n">result</span><span class="o">.</span><span class="n">append</span><span class="p">({</span>
+                <span class="s1">&#39;bait&#39;</span><span class="p">:</span> <span class="n">uniprot_bait</span><span class="p">,</span>
+                <span class="s1">&#39;prey&#39;</span><span class="p">:</span> <span class="n">uniprot_prey</span><span class="p">,</span>
+                <span class="s1">&#39;refs&#39;</span><span class="p">:</span> <span class="p">[</span><span class="n">x</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">rec</span><span class="o">.</span><span class="n">references</span><span class="o">.</span><span class="n">text</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;,&#39;</span><span class="p">)],</span>
+                <span class="s1">&#39;pos&#39;</span><span class="p">:</span>
+                <span class="p">[</span><span class="nb">int</span><span class="p">(</span><span class="n">x</span><span class="p">)</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">rec</span><span class="o">.</span><span class="n">sequence_position</span><span class="o">.</span><span class="n">text</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;-&#39;</span><span class="p">)],</span>
+                <span class="s1">&#39;inst&#39;</span><span class="p">:</span> <span class="n">rec</span><span class="o">.</span><span class="n">motif_instance</span><span class="o">.</span><span class="n">text</span><span class="p">,</span>
+                <span class="s1">&#39;dom&#39;</span><span class="p">:</span> <span class="n">rec</span><span class="o">.</span><span class="n">interacting_domain</span><span class="o">.</span><span class="n">text</span>
+            <span class="p">})</span>
+
+    <span class="n">prg</span><span class="o">.</span><span class="n">terminate</span><span class="p">()</span>
+
+    <span class="k">return</span> <span class="n">result</span></div>
+
+
+
+<div class="viewcode-block" id="lmpid_interactions">
+<a class="viewcode-back" href="../../../api/pypath.inputs.lmpid.lmpid_interactions.html#pypath.inputs.lmpid.lmpid_interactions">[docs]</a>
+<span class="k">def</span> <span class="nf">lmpid_interactions</span><span class="p">(</span><span class="n">organism</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">):</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Converts list of domain-motif interactions supplied by</span>
+<span class="sd">    ``pypath.inputs.lmpid.load_lmpid`` to list of interactions.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="n">data</span> <span class="o">=</span> <span class="n">load_lmpid</span><span class="p">(</span><span class="n">organism</span> <span class="o">=</span> <span class="n">organism</span><span class="p">)</span>
+
+    <span class="k">return</span> <span class="p">[[</span><span class="n">l</span><span class="p">[</span><span class="s1">&#39;prey&#39;</span><span class="p">],</span> <span class="n">l</span><span class="p">[</span><span class="s1">&#39;bait&#39;</span><span class="p">],</span> <span class="s1">&#39;;&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">l</span><span class="p">[</span><span class="s1">&#39;refs&#39;</span><span class="p">])]</span> <span class="k">for</span> <span class="n">l</span> <span class="ow">in</span> <span class="n">data</span><span class="p">]</span></div>
+
+
+
+<div class="viewcode-block" id="lmpid_dmi">
+<a class="viewcode-back" href="../../../api/pypath.inputs.lmpid.lmpid_dmi.html#pypath.inputs.lmpid.lmpid_dmi">[docs]</a>
+<span class="k">def</span> <span class="nf">lmpid_dmi</span><span class="p">(</span><span class="n">organism</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">):</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Converts list of domain-motif interactions supplied by</span>
+<span class="sd">    ``pypath.inputs.lmpid.load_lmpid`` to list of</span>
+<span class="sd">    ``pypath.intera.DomainMotif`` objects.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="n">data</span> <span class="o">=</span> <span class="n">load_lmpid</span><span class="p">(</span><span class="n">organism</span> <span class="o">=</span> <span class="n">organism</span><span class="p">)</span>
+
+    <span class="k">return</span> <span class="p">[{</span>
+        <span class="s1">&#39;motif_protein&#39;</span><span class="p">:</span> <span class="n">l</span><span class="p">[</span><span class="s1">&#39;bait&#39;</span><span class="p">],</span>
+        <span class="s1">&#39;domain_protein&#39;</span><span class="p">:</span> <span class="n">l</span><span class="p">[</span><span class="s1">&#39;prey&#39;</span><span class="p">],</span>
+        <span class="s1">&#39;instance&#39;</span><span class="p">:</span> <span class="n">l</span><span class="p">[</span><span class="s1">&#39;inst&#39;</span><span class="p">],</span>
+        <span class="s1">&#39;motif_start&#39;</span><span class="p">:</span> <span class="n">l</span><span class="p">[</span><span class="s1">&#39;pos&#39;</span><span class="p">][</span><span class="mi">0</span><span class="p">],</span>
+        <span class="s1">&#39;motif_end&#39;</span><span class="p">:</span> <span class="n">l</span><span class="p">[</span><span class="s1">&#39;pos&#39;</span><span class="p">][</span><span class="mi">1</span><span class="p">],</span>
+        <span class="s1">&#39;domain_name&#39;</span><span class="p">:</span> <span class="n">l</span><span class="p">[</span><span class="s1">&#39;dom&#39;</span><span class="p">],</span>
+        <span class="s1">&#39;domain_name_type&#39;</span><span class="p">:</span> <span class="s1">&#39;name&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;refs&#39;</span><span class="p">:</span> <span class="n">l</span><span class="p">[</span><span class="s1">&#39;refs&#39;</span><span class="p">]</span>
+    <span class="p">}</span> <span class="k">for</span> <span class="n">l</span> <span class="ow">in</span> <span class="n">data</span><span class="p">]</span></div>
+
+</pre></div>
+
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+  <h1>Source code for pypath.inputs.locate</h1><div class="highlight"><pre>
+<span></span><span class="ch">#!/usr/bin/env python</span>
+<span class="c1"># -*- coding: utf-8 -*-</span>
+
+<span class="c1">#</span>
+<span class="c1">#  This file is part of the `pypath` python module</span>
+<span class="c1">#</span>
+<span class="c1">#  Copyright 2014-2023</span>
+<span class="c1">#  EMBL, EMBL-EBI, Uniklinik RWTH Aachen, Heidelberg University</span>
+<span class="c1">#</span>
+<span class="c1">#  Authors: see the file `README.rst`</span>
+<span class="c1">#  Contact: Dénes Türei (turei.denes@gmail.com)</span>
+<span class="c1">#</span>
+<span class="c1">#  Distributed under the GPLv3 License.</span>
+<span class="c1">#  See accompanying file LICENSE.txt or copy at</span>
+<span class="c1">#      https://www.gnu.org/licenses/gpl-3.0.html</span>
+<span class="c1">#</span>
+<span class="c1">#  Website: https://pypath.omnipathdb.org/</span>
+<span class="c1">#</span>
+
+<span class="kn">from</span> <span class="nn">past.builtins</span> <span class="kn">import</span> <span class="n">xrange</span><span class="p">,</span> <span class="nb">range</span>
+
+<span class="kn">import</span> <span class="nn">collections</span>
+
+<span class="kn">from</span> <span class="nn">lxml</span> <span class="kn">import</span> <span class="n">etree</span>
+
+<span class="kn">import</span> <span class="nn">pypath.share.curl</span> <span class="k">as</span> <span class="nn">curl</span>
+<span class="kn">import</span> <span class="nn">pypath.resources.urls</span> <span class="k">as</span> <span class="nn">urls</span>
+<span class="kn">import</span> <span class="nn">pypath.inputs.uniprot_db</span> <span class="k">as</span> <span class="nn">uniprot_db</span>
+<span class="kn">import</span> <span class="nn">pypath.utils.taxonomy</span> <span class="k">as</span> <span class="nn">taxonomy</span>
+<span class="kn">import</span> <span class="nn">pypath.utils.mapping</span> <span class="k">as</span> <span class="nn">mapping</span>
+
+
+<div class="viewcode-block" id="locate_localizations">
+<a class="viewcode-back" href="../../../api/pypath.inputs.locate.locate_localizations.html#pypath.inputs.locate.locate_localizations">[docs]</a>
+<span class="k">def</span> <span class="nf">locate_localizations</span><span class="p">(</span>
+        <span class="n">organism</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">,</span>
+        <span class="n">literature</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
+        <span class="n">external</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
+        <span class="n">predictions</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+    <span class="p">):</span>
+
+    <span class="n">record</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">namedtuple</span><span class="p">(</span>
+        <span class="s1">&#39;LocateAnnotation&#39;</span><span class="p">,</span>
+        <span class="p">(</span><span class="s1">&#39;source&#39;</span><span class="p">,</span> <span class="s1">&#39;location&#39;</span><span class="p">,</span> <span class="s1">&#39;cls&#39;</span><span class="p">,</span> <span class="s1">&#39;pmid&#39;</span><span class="p">,</span> <span class="s1">&#39;score&#39;</span><span class="p">),</span>
+    <span class="p">)</span>
+    <span class="n">record</span><span class="o">.</span><span class="fm">__new__</span><span class="o">.</span><span class="vm">__defaults__</span> <span class="o">=</span> <span class="p">(</span><span class="kc">None</span><span class="p">,</span> <span class="kc">None</span><span class="p">,</span> <span class="kc">None</span><span class="p">)</span>
+
+    <span class="n">organism_uniprots</span> <span class="o">=</span> <span class="nb">set</span><span class="p">(</span>
+        <span class="n">uniprot_db</span><span class="o">.</span><span class="n">all_uniprots</span><span class="p">(</span><span class="n">organism</span> <span class="o">=</span> <span class="n">organism</span><span class="p">,</span> <span class="n">swissprot</span> <span class="o">=</span> <span class="kc">True</span><span class="p">)</span>
+    <span class="p">)</span>
+
+    <span class="n">organism_str</span> <span class="o">=</span> <span class="n">taxonomy</span><span class="o">.</span><span class="n">taxids</span><span class="p">[</span><span class="n">organism</span><span class="p">]</span>
+    <span class="n">url</span> <span class="o">=</span> <span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;locate&#39;</span><span class="p">][</span><span class="s1">&#39;url_rescued&#39;</span><span class="p">]</span> <span class="o">%</span> <span class="n">organism_str</span>
+    <span class="n">fname</span> <span class="o">=</span> <span class="n">url</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;/&#39;</span><span class="p">)[</span><span class="o">-</span><span class="mi">1</span><span class="p">][:</span><span class="o">-</span><span class="mi">4</span><span class="p">]</span>
+
+    <span class="n">c</span> <span class="o">=</span> <span class="n">curl</span><span class="o">.</span><span class="n">Curl</span><span class="p">(</span>
+        <span class="n">url</span><span class="p">,</span>
+        <span class="n">large</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
+        <span class="n">default_mode</span> <span class="o">=</span> <span class="s1">&#39;rb&#39;</span><span class="p">,</span>
+        <span class="n">silent</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+        <span class="n">files_needed</span> <span class="o">=</span> <span class="p">[</span><span class="n">fname</span><span class="p">],</span>
+    <span class="p">)</span>
+    <span class="n">c</span><span class="o">.</span><span class="n">result</span><span class="p">[</span><span class="n">fname</span><span class="p">]</span>
+
+    <span class="n">parser</span> <span class="o">=</span> <span class="n">etree</span><span class="o">.</span><span class="n">iterparse</span><span class="p">(</span><span class="n">c</span><span class="o">.</span><span class="n">result</span><span class="p">[</span><span class="n">fname</span><span class="p">],</span> <span class="n">events</span> <span class="o">=</span> <span class="p">(</span><span class="s1">&#39;start&#39;</span><span class="p">,</span> <span class="s1">&#39;end&#39;</span><span class="p">))</span>
+
+    <span class="n">result</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">defaultdict</span><span class="p">(</span><span class="nb">set</span><span class="p">)</span>
+    <span class="n">root</span> <span class="o">=</span> <span class="nb">next</span><span class="p">(</span><span class="n">parser</span><span class="p">)</span>
+    <span class="n">used_elements</span> <span class="o">=</span> <span class="p">[]</span>
+
+    <span class="k">for</span> <span class="n">ev</span><span class="p">,</span> <span class="n">elem</span> <span class="ow">in</span> <span class="n">parser</span><span class="p">:</span>
+
+        <span class="k">if</span> <span class="n">ev</span> <span class="o">==</span> <span class="s1">&#39;end&#39;</span> <span class="ow">and</span> <span class="n">elem</span><span class="o">.</span><span class="n">tag</span> <span class="o">==</span> <span class="s1">&#39;LOCATE_protein&#39;</span><span class="p">:</span>
+
+            <span class="n">tag_protein</span> <span class="o">=</span> <span class="n">elem</span><span class="o">.</span><span class="n">find</span><span class="p">(</span><span class="s1">&#39;protein&#39;</span><span class="p">)</span>
+            <span class="n">this_uniprot</span> <span class="o">=</span> <span class="kc">None</span>
+            <span class="n">this_uniprots</span> <span class="o">=</span> <span class="kc">None</span>
+            <span class="n">this_entrez</span>  <span class="o">=</span> <span class="kc">None</span>
+            <span class="n">this_organism</span> <span class="o">=</span> <span class="p">(</span>
+                <span class="n">tag_protein</span><span class="o">.</span><span class="n">find</span><span class="p">(</span><span class="s1">&#39;organism&#39;</span><span class="p">)</span><span class="o">.</span><span class="n">text</span>
+                    <span class="k">if</span> <span class="n">tag_protein</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span> <span class="k">else</span>
+                <span class="kc">None</span>
+            <span class="p">)</span>
+            <span class="n">this_class</span> <span class="o">=</span> <span class="p">(</span>
+                <span class="n">tag_protein</span><span class="o">.</span><span class="n">find</span><span class="p">(</span><span class="s1">&#39;class&#39;</span><span class="p">)</span><span class="o">.</span><span class="n">text</span>
+                    <span class="k">if</span> <span class="n">tag_protein</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span> <span class="k">else</span>
+                <span class="kc">None</span>
+            <span class="p">)</span>
+
+            <span class="n">xrefs</span> <span class="o">=</span> <span class="n">elem</span><span class="o">.</span><span class="n">find</span><span class="p">(</span><span class="s1">&#39;xrefs&#39;</span><span class="p">)</span>
+
+            <span class="k">if</span> <span class="n">xrefs</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
+                <span class="k">continue</span>
+
+            <span class="k">for</span> <span class="n">xref</span> <span class="ow">in</span> <span class="n">xrefs</span><span class="o">.</span><span class="n">findall</span><span class="p">(</span><span class="s1">&#39;xref&#39;</span><span class="p">):</span>
+                <span class="n">src</span> <span class="o">=</span> <span class="n">xref</span><span class="o">.</span><span class="n">find</span><span class="p">(</span><span class="s1">&#39;source&#39;</span><span class="p">)</span>
+                <span class="n">src_name</span> <span class="o">=</span> <span class="n">src</span><span class="o">.</span><span class="n">find</span><span class="p">(</span><span class="s1">&#39;source_name&#39;</span><span class="p">)</span><span class="o">.</span><span class="n">text</span>
+
+                <span class="k">if</span> <span class="n">src_name</span> <span class="o">==</span> <span class="s1">&#39;UniProtKB-SwissProt&#39;</span><span class="p">:</span>
+                    <span class="n">this_uniprot</span> <span class="o">=</span> <span class="n">src</span><span class="o">.</span><span class="n">find</span><span class="p">(</span><span class="s1">&#39;accn&#39;</span><span class="p">)</span><span class="o">.</span><span class="n">text</span>
+
+                <span class="k">if</span> <span class="n">src_name</span> <span class="o">==</span> <span class="s1">&#39;Entrez Gene&#39;</span><span class="p">:</span>
+                    <span class="n">this_entrez</span> <span class="o">=</span> <span class="n">src</span><span class="o">.</span><span class="n">find</span><span class="p">(</span><span class="s1">&#39;accn&#39;</span><span class="p">)</span><span class="o">.</span><span class="n">text</span>
+
+                <span class="k">if</span> <span class="n">src_name</span> <span class="o">==</span> <span class="s1">&#39;UniProt/SPTrEMBL&#39;</span> <span class="ow">and</span> <span class="n">this_uniprot</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
+                    <span class="n">this_uniprot</span> <span class="o">=</span> <span class="n">src</span><span class="o">.</span><span class="n">find</span><span class="p">(</span><span class="s1">&#39;accn&#39;</span><span class="p">)</span><span class="o">.</span><span class="n">text</span>
+
+            <span class="c1"># if we don&#39;t know what it is, does not make sense to proceed</span>
+            <span class="k">if</span> <span class="n">this_uniprot</span> <span class="ow">is</span> <span class="kc">None</span> <span class="ow">and</span> <span class="n">this_entrez</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
+                <span class="k">continue</span>
+
+            <span class="k">if</span> <span class="n">this_uniprot</span><span class="p">:</span>
+                <span class="n">this_uniprots</span> <span class="o">=</span> <span class="n">mapping</span><span class="o">.</span><span class="n">map_name</span><span class="p">(</span>
+                    <span class="n">this_uniprot</span><span class="p">,</span>
+                    <span class="s1">&#39;uniprot&#39;</span><span class="p">,</span>
+                    <span class="s1">&#39;uniprot&#39;</span><span class="p">,</span>
+                    <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">organism</span><span class="p">,</span>
+                <span class="p">)</span>
+
+            <span class="k">if</span> <span class="ow">not</span> <span class="n">this_uniprots</span> <span class="ow">and</span> <span class="n">this_entrez</span><span class="p">:</span>
+                <span class="n">this_uniprots</span> <span class="o">=</span> <span class="n">mapping</span><span class="o">.</span><span class="n">map_name</span><span class="p">(</span>
+                    <span class="n">this_entrez</span><span class="p">,</span>
+                    <span class="s1">&#39;entrez&#39;</span><span class="p">,</span>
+                    <span class="s1">&#39;uniprot&#39;</span><span class="p">,</span>
+                    <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">organism</span><span class="p">,</span>
+                <span class="p">)</span>
+
+            <span class="n">this_uniprots</span> <span class="o">=</span> <span class="nb">set</span><span class="p">(</span><span class="n">this_uniprots</span><span class="p">)</span> <span class="o">&amp;</span> <span class="n">organism_uniprots</span>
+
+            <span class="c1"># if we don&#39;t know what it is, does not make sense to proceed</span>
+            <span class="k">if</span> <span class="ow">not</span> <span class="n">this_uniprots</span><span class="p">:</span>
+                <span class="k">continue</span>
+
+            <span class="k">if</span> <span class="n">external</span><span class="p">:</span>
+                <span class="c1"># External database annotations</span>
+                <span class="n">extannot</span> <span class="o">=</span> <span class="n">elem</span><span class="o">.</span><span class="n">find</span><span class="p">(</span><span class="s1">&#39;externalannot&#39;</span><span class="p">)</span>
+
+                <span class="k">if</span> <span class="n">extannot</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
+                    <span class="k">for</span> <span class="n">extannotref</span> <span class="ow">in</span> <span class="n">extannot</span><span class="o">.</span><span class="n">findall</span><span class="p">(</span><span class="s1">&#39;reference&#39;</span><span class="p">):</span>
+                        <span class="n">sources</span> <span class="o">=</span> <span class="p">[]</span>
+
+                        <span class="k">for</span> <span class="n">src</span> <span class="ow">in</span> <span class="n">extannotref</span><span class="o">.</span><span class="n">findall</span><span class="p">(</span><span class="s1">&#39;source&#39;</span><span class="p">):</span>
+                            <span class="n">src_name</span> <span class="o">=</span> <span class="n">src</span><span class="o">.</span><span class="n">find</span><span class="p">(</span><span class="s1">&#39;source_name&#39;</span><span class="p">)</span>
+
+                            <span class="k">if</span> <span class="n">src_name</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
+                                <span class="n">sources</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">src_name</span><span class="o">.</span><span class="n">text</span><span class="p">)</span>
+
+                        <span class="n">sources</span> <span class="o">=</span> <span class="s1">&#39;;&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">sources</span><span class="p">)</span> <span class="k">if</span> <span class="n">sources</span> <span class="k">else</span> <span class="kc">None</span>
+                        <span class="n">locations</span> <span class="o">=</span>  <span class="n">extannotref</span><span class="o">.</span><span class="n">find</span><span class="p">(</span><span class="s1">&#39;locations&#39;</span><span class="p">)</span>
+
+                        <span class="k">if</span> <span class="n">locations</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
+                            <span class="k">for</span> <span class="n">location</span> <span class="ow">in</span> <span class="n">locations</span><span class="o">.</span><span class="n">findall</span><span class="p">(</span><span class="s1">&#39;location&#39;</span><span class="p">):</span>
+                                <span class="k">for</span> <span class="n">loc</span> <span class="ow">in</span> <span class="n">location</span><span class="o">.</span><span class="n">iterchildren</span><span class="p">():</span>
+                                    <span class="k">if</span> <span class="n">loc</span><span class="o">.</span><span class="n">tag</span><span class="p">[:</span><span class="mi">4</span><span class="p">]</span> <span class="o">==</span> <span class="s1">&#39;tier&#39;</span><span class="p">:</span>
+                                        <span class="n">this_loc</span> <span class="o">=</span> <span class="n">loc</span><span class="o">.</span><span class="n">text</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;,&#39;</span><span class="p">)</span>
+
+                                        <span class="k">for</span> <span class="n">uniprot</span> <span class="ow">in</span> <span class="n">this_uniprots</span><span class="p">:</span>
+                                            <span class="k">for</span> <span class="n">_loc</span> <span class="ow">in</span> <span class="n">this_loc</span><span class="p">:</span>
+                                                <span class="n">result</span><span class="p">[</span><span class="n">uniprot</span><span class="p">]</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">record</span><span class="p">(</span>
+                                                    <span class="n">source</span> <span class="o">=</span> <span class="n">sources</span><span class="p">,</span>
+                                                    <span class="n">location</span> <span class="o">=</span> <span class="n">_loc</span><span class="o">.</span><span class="n">strip</span><span class="p">(),</span>
+                                                    <span class="bp">cls</span> <span class="o">=</span> <span class="n">this_class</span><span class="p">,</span>
+                                                    <span class="n">score</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+                                                <span class="p">))</span>
+
+            <span class="k">if</span> <span class="n">predictions</span><span class="p">:</span>
+                <span class="c1"># Predictions</span>
+                <span class="n">sclpred</span> <span class="o">=</span> <span class="n">elem</span><span class="o">.</span><span class="n">find</span><span class="p">(</span><span class="s1">&#39;scl_prediction&#39;</span><span class="p">)</span>
+
+                <span class="k">if</span> <span class="n">sclpred</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
+                    <span class="k">for</span> <span class="n">sclpred_src</span> <span class="ow">in</span> <span class="n">sclpred</span><span class="o">.</span><span class="n">findall</span><span class="p">(</span><span class="s1">&#39;source&#39;</span><span class="p">):</span>
+                        <span class="n">score</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">sclpred_src</span><span class="o">.</span><span class="n">find</span><span class="p">(</span><span class="s1">&#39;evaluation&#39;</span><span class="p">)</span><span class="o">.</span><span class="n">text</span><span class="p">)</span>
+
+                        <span class="k">if</span> <span class="n">score</span> <span class="o">==</span> <span class="mf">0.0</span><span class="p">:</span>
+                            <span class="k">continue</span>
+
+                        <span class="n">this_src</span> <span class="o">=</span> <span class="n">sclpred_src</span><span class="o">.</span><span class="n">find</span><span class="p">(</span><span class="s1">&#39;method&#39;</span><span class="p">)</span><span class="o">.</span><span class="n">text</span>
+                        <span class="n">this_loc</span> <span class="o">=</span> <span class="n">sclpred_src</span><span class="o">.</span><span class="n">find</span><span class="p">(</span><span class="s1">&#39;location&#39;</span><span class="p">)</span><span class="o">.</span><span class="n">text</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span>
+
+                        <span class="k">if</span> <span class="n">this_loc</span> <span class="o">==</span> <span class="s1">&#39;no prediction&#39;</span><span class="p">:</span>
+                            <span class="k">continue</span>
+
+                        <span class="k">for</span> <span class="n">uniprot</span> <span class="ow">in</span> <span class="n">this_uniprots</span><span class="p">:</span>
+                            <span class="n">result</span><span class="p">[</span><span class="n">uniprot</span><span class="p">]</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">record</span><span class="p">(</span>
+                                <span class="n">source</span> <span class="o">=</span> <span class="n">this_src</span><span class="p">,</span>
+                                <span class="n">location</span> <span class="o">=</span> <span class="n">this_loc</span><span class="p">,</span>
+                                <span class="bp">cls</span> <span class="o">=</span> <span class="n">this_class</span><span class="p">,</span>
+                                <span class="n">score</span> <span class="o">=</span> <span class="n">score</span><span class="p">,</span>
+                            <span class="p">))</span>
+
+            <span class="k">if</span> <span class="n">literature</span><span class="p">:</span>
+                <span class="c1"># Literature curation</span>
+                <span class="n">lit</span> <span class="o">=</span> <span class="n">elem</span><span class="o">.</span><span class="n">find</span><span class="p">(</span><span class="s1">&#39;literature&#39;</span><span class="p">)</span>
+
+                <span class="k">if</span> <span class="n">lit</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
+
+                    <span class="k">for</span> <span class="n">litref</span> <span class="ow">in</span> <span class="n">lit</span><span class="o">.</span><span class="n">findall</span><span class="p">(</span><span class="s1">&#39;reference&#39;</span><span class="p">):</span>
+
+                        <span class="n">locs</span> <span class="o">=</span> <span class="nb">set</span><span class="p">()</span>
+
+                        <span class="k">for</span> <span class="n">lloc</span> <span class="ow">in</span> <span class="p">(</span>
+                            <span class="n">litref</span><span class="o">.</span><span class="n">find</span><span class="p">(</span><span class="s1">&#39;locations&#39;</span><span class="p">)</span><span class="o">.</span><span class="n">findall</span><span class="p">(</span><span class="s1">&#39;location&#39;</span><span class="p">)</span>
+                        <span class="p">):</span>
+
+                            <span class="k">for</span> <span class="n">loc</span> <span class="ow">in</span> <span class="n">lloc</span><span class="o">.</span><span class="n">iterchildren</span><span class="p">():</span>
+                                <span class="k">if</span> <span class="n">loc</span><span class="o">.</span><span class="n">tag</span><span class="p">[:</span><span class="mi">4</span><span class="p">]</span> <span class="o">==</span> <span class="s1">&#39;tier&#39;</span><span class="p">:</span>
+                                    <span class="n">locs</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">loc</span><span class="o">.</span><span class="n">text</span><span class="o">.</span><span class="n">lower</span><span class="p">())</span>
+
+                        <span class="n">pmid</span> <span class="o">=</span> <span class="n">litref</span><span class="o">.</span><span class="n">find</span><span class="p">(</span><span class="s1">&#39;source&#39;</span><span class="p">)</span>
+                        <span class="n">pmid</span> <span class="o">=</span> <span class="p">(</span>
+                            <span class="kc">None</span> <span class="k">if</span> <span class="n">pmid</span> <span class="ow">is</span> <span class="kc">None</span> <span class="k">else</span> <span class="n">pmid</span><span class="o">.</span><span class="n">find</span><span class="p">(</span><span class="s1">&#39;accn&#39;</span><span class="p">)</span><span class="o">.</span><span class="n">text</span>
+                        <span class="p">)</span>
+
+                        <span class="k">for</span> <span class="n">loc</span> <span class="ow">in</span> <span class="n">locs</span><span class="p">:</span>
+
+                            <span class="k">for</span> <span class="n">uniprot</span> <span class="ow">in</span> <span class="n">this_uniprots</span><span class="p">:</span>
+
+                                <span class="n">result</span><span class="p">[</span><span class="n">uniprot</span><span class="p">]</span><span class="o">.</span><span class="n">add</span><span class="p">(</span>
+                                    <span class="n">record</span><span class="p">(</span>
+                                        <span class="n">source</span> <span class="o">=</span> <span class="s1">&#39;literature&#39;</span><span class="p">,</span>
+                                        <span class="n">location</span> <span class="o">=</span> <span class="n">loc</span><span class="p">,</span>
+                                        <span class="n">pmid</span> <span class="o">=</span> <span class="n">pmid</span><span class="p">,</span>
+                                        <span class="bp">cls</span> <span class="o">=</span> <span class="n">this_class</span><span class="p">,</span>
+                                        <span class="n">score</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+                                    <span class="p">)</span>
+                                <span class="p">)</span>
+
+        <span class="n">used_elements</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">elem</span><span class="p">)</span>
+
+        <span class="c1"># removing used elements to keep memory low</span>
+        <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">used_elements</span><span class="p">)</span> <span class="o">&gt;</span> <span class="mi">1000</span><span class="p">:</span>
+            <span class="k">for</span> <span class="n">_</span> <span class="ow">in</span> <span class="n">xrange</span><span class="p">(</span><span class="mi">500</span><span class="p">):</span>
+                <span class="n">e</span> <span class="o">=</span> <span class="n">used_elements</span><span class="o">.</span><span class="n">pop</span><span class="p">(</span><span class="mi">0</span><span class="p">)</span>
+                <span class="n">e</span><span class="o">.</span><span class="n">clear</span><span class="p">()</span>
+
+    <span class="c1"># closing the XML</span>
+    <span class="n">c</span><span class="o">.</span><span class="n">fileobj</span><span class="o">.</span><span class="n">close</span><span class="p">()</span>
+    <span class="k">del</span> <span class="n">c</span>
+
+    <span class="k">return</span> <span class="nb">dict</span><span class="p">(</span><span class="n">result</span><span class="p">)</span></div>
+
+</pre></div>
+
+                </article>
+              
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+    <li class="breadcrumb-item active" aria-current="page">pypath.inputs.lrdb</li>
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+      
+    </div>
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+                <article class="bd-article">
+                  
+  <h1>Source code for pypath.inputs.lrdb</h1><div class="highlight"><pre>
+<span></span><span class="ch">#!/usr/bin/env python</span>
+<span class="c1"># -*- coding: utf-8 -*-</span>
+
+<span class="c1">#</span>
+<span class="c1">#  This file is part of the `pypath` python module</span>
+<span class="c1">#</span>
+<span class="c1">#  Copyright 2014-2023</span>
+<span class="c1">#  EMBL, EMBL-EBI, Uniklinik RWTH Aachen, Heidelberg University</span>
+<span class="c1">#</span>
+<span class="c1">#  Authors: see the file `README.rst`</span>
+<span class="c1">#  Contact: Dénes Türei (turei.denes@gmail.com)</span>
+<span class="c1">#</span>
+<span class="c1">#  Distributed under the GPLv3 License.</span>
+<span class="c1">#  See accompanying file LICENSE.txt or copy at</span>
+<span class="c1">#      https://www.gnu.org/licenses/gpl-3.0.html</span>
+<span class="c1">#</span>
+<span class="c1">#  Website: https://pypath.omnipathdb.org/</span>
+<span class="c1">#</span>
+
+<span class="kn">import</span> <span class="nn">csv</span>
+<span class="kn">import</span> <span class="nn">collections</span>
+
+<span class="kn">import</span> <span class="nn">pypath.share.curl</span> <span class="k">as</span> <span class="nn">curl</span>
+<span class="kn">import</span> <span class="nn">pypath.resources.urls</span> <span class="k">as</span> <span class="nn">urls</span>
+<span class="kn">import</span> <span class="nn">pypath.utils.mapping</span> <span class="k">as</span> <span class="nn">mapping</span>
+<span class="kn">import</span> <span class="nn">pypath.share.common</span> <span class="k">as</span> <span class="nn">common</span>
+
+
+<span class="n">LrdbAnnotation</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">namedtuple</span><span class="p">(</span>
+    <span class="s1">&#39;LrdbAnnotation&#39;</span><span class="p">,</span>
+    <span class="p">[</span>
+        <span class="s1">&#39;role&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;cell_type&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;sources&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;references&#39;</span><span class="p">,</span>
+    <span class="p">],</span>
+<span class="p">)</span>
+
+
+<div class="viewcode-block" id="lrdb_interactions">
+<a class="viewcode-back" href="../../../api/pypath.inputs.lrdb.lrdb_interactions.html#pypath.inputs.lrdb.lrdb_interactions">[docs]</a>
+<span class="k">def</span> <span class="nf">lrdb_interactions</span><span class="p">():</span>
+
+    <span class="n">resource_names</span> <span class="o">=</span> <span class="p">{</span>
+        <span class="s1">&#39;reactome&#39;</span><span class="p">:</span> <span class="s1">&#39;Reactome&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;fantom5&#39;</span><span class="p">:</span> <span class="s1">&#39;Fantom5&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;IUPHAR&#39;</span><span class="p">:</span> <span class="s1">&#39;Guide2Pharma&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;uniprot&#39;</span><span class="p">:</span> <span class="s1">&#39;UniProt&#39;</span><span class="p">,</span>
+    <span class="p">}</span>
+
+    <span class="k">def</span> <span class="nf">remove</span><span class="p">(</span><span class="n">lst</span><span class="p">,</span> <span class="n">to_remove</span><span class="p">):</span>
+        <span class="n">to_remove</span> <span class="o">=</span> <span class="n">common</span><span class="o">.</span><span class="n">to_set</span><span class="p">(</span><span class="n">to_remove</span><span class="p">)</span>
+
+        <span class="k">return</span> <span class="p">[</span>
+            <span class="n">it</span>
+            <span class="k">for</span> <span class="n">it</span> <span class="ow">in</span> <span class="n">lst</span>
+            <span class="k">if</span> <span class="n">it</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">to_remove</span>
+        <span class="p">]</span>
+
+    <span class="n">LrdbRecord</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">namedtuple</span><span class="p">(</span>
+        <span class="s1">&#39;LrdbRecord&#39;</span><span class="p">,</span>
+        <span class="p">[</span>
+            <span class="s1">&#39;ligand_genesymbol&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;receptor_genesymbol&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;sources&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;references&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;ligand_cells&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;receptor_cells&#39;</span><span class="p">,</span>
+        <span class="p">]</span>
+    <span class="p">)</span>
+
+    <span class="n">url</span> <span class="o">=</span> <span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;lrdb&#39;</span><span class="p">][</span><span class="s1">&#39;url&#39;</span><span class="p">]</span>
+
+    <span class="n">c</span> <span class="o">=</span> <span class="n">curl</span><span class="o">.</span><span class="n">Curl</span><span class="p">(</span><span class="n">url</span><span class="p">,</span> <span class="n">silent</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span> <span class="n">large</span> <span class="o">=</span> <span class="kc">True</span><span class="p">)</span>
+
+    <span class="n">reader</span> <span class="o">=</span> <span class="n">csv</span><span class="o">.</span><span class="n">DictReader</span><span class="p">(</span><span class="n">c</span><span class="o">.</span><span class="n">result</span><span class="p">,</span> <span class="n">delimiter</span> <span class="o">=</span> <span class="s1">&#39;</span><span class="se">\t</span><span class="s1">&#39;</span><span class="p">)</span>
+
+    <span class="n">result</span> <span class="o">=</span> <span class="p">[]</span>
+
+    <span class="k">for</span> <span class="n">rec</span> <span class="ow">in</span> <span class="n">reader</span><span class="p">:</span>
+
+        <span class="n">result</span><span class="o">.</span><span class="n">append</span><span class="p">(</span>
+            <span class="n">LrdbRecord</span><span class="p">(</span>
+                <span class="n">ligand_genesymbol</span> <span class="o">=</span> <span class="n">rec</span><span class="p">[</span><span class="s1">&#39;ligand&#39;</span><span class="p">],</span>
+                <span class="n">receptor_genesymbol</span> <span class="o">=</span> <span class="n">rec</span><span class="p">[</span><span class="s1">&#39;receptor&#39;</span><span class="p">],</span>
+                <span class="n">sources</span> <span class="o">=</span> <span class="p">[</span>
+                    <span class="n">resource_names</span><span class="p">[</span><span class="n">src</span><span class="p">]</span> <span class="k">if</span> <span class="n">src</span> <span class="ow">in</span> <span class="n">resource_names</span> <span class="k">else</span> <span class="n">src</span>
+                    <span class="k">for</span> <span class="n">src</span> <span class="ow">in</span>
+                    <span class="n">remove</span><span class="p">(</span>
+                        <span class="n">rec</span><span class="p">[</span><span class="s1">&#39;source&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;,&#39;</span><span class="p">),</span>
+                        <span class="p">{</span><span class="s1">&#39;literature&#39;</span><span class="p">,</span> <span class="s1">&#39;&#39;</span><span class="p">},</span>
+                    <span class="p">)</span>
+                <span class="p">],</span>
+                <span class="n">references</span> <span class="o">=</span> <span class="n">remove</span><span class="p">(</span><span class="n">rec</span><span class="p">[</span><span class="s1">&#39;PMIDs&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;,&#39;</span><span class="p">),</span> <span class="s1">&#39;&#39;</span><span class="p">),</span>
+                <span class="n">ligand_cells</span> <span class="o">=</span> <span class="n">remove</span><span class="p">(</span><span class="n">rec</span><span class="p">[</span><span class="s1">&#39;cells.L&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;,&#39;</span><span class="p">),</span> <span class="s1">&#39;&#39;</span><span class="p">),</span>
+                <span class="n">receptor_cells</span> <span class="o">=</span> <span class="n">remove</span><span class="p">(</span><span class="n">rec</span><span class="p">[</span><span class="s1">&#39;cells.R&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;,&#39;</span><span class="p">),</span> <span class="s1">&#39;&#39;</span><span class="p">),</span>
+            <span class="p">)</span>
+        <span class="p">)</span>
+
+    <span class="k">return</span> <span class="n">result</span></div>
+
+
+
+<div class="viewcode-block" id="lrdb_annotations">
+<a class="viewcode-back" href="../../../api/pypath.inputs.lrdb.lrdb_annotations.html#pypath.inputs.lrdb.lrdb_annotations">[docs]</a>
+<span class="k">def</span> <span class="nf">lrdb_annotations</span><span class="p">():</span>
+
+    <span class="n">result</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">defaultdict</span><span class="p">(</span><span class="nb">set</span><span class="p">)</span>
+
+    <span class="n">lrdb</span> <span class="o">=</span> <span class="n">lrdb_interactions</span><span class="p">()</span>
+
+    <span class="k">for</span> <span class="n">rec</span> <span class="ow">in</span> <span class="n">lrdb</span><span class="p">:</span>
+
+        <span class="k">for</span> <span class="n">role</span> <span class="ow">in</span> <span class="p">(</span><span class="s1">&#39;ligand&#39;</span><span class="p">,</span> <span class="s1">&#39;receptor&#39;</span><span class="p">):</span>
+
+            <span class="n">uniprots</span> <span class="o">=</span> <span class="n">mapping</span><span class="o">.</span><span class="n">map_name</span><span class="p">(</span>
+                <span class="nb">getattr</span><span class="p">(</span><span class="n">rec</span><span class="p">,</span> <span class="s1">&#39;</span><span class="si">%s</span><span class="s1">_genesymbol&#39;</span> <span class="o">%</span> <span class="n">role</span><span class="p">),</span>
+                <span class="s1">&#39;genesymbol&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;uniprot&#39;</span><span class="p">,</span>
+            <span class="p">)</span>
+
+            <span class="k">for</span> <span class="n">uniprot</span> <span class="ow">in</span> <span class="n">uniprots</span><span class="p">:</span>
+
+                <span class="n">cell_types</span> <span class="o">=</span> <span class="nb">getattr</span><span class="p">(</span><span class="n">rec</span><span class="p">,</span> <span class="s1">&#39;</span><span class="si">%s</span><span class="s1">_cells&#39;</span> <span class="o">%</span> <span class="n">role</span><span class="p">)</span> <span class="ow">or</span> <span class="p">(</span><span class="kc">None</span><span class="p">,)</span>
+
+                <span class="k">for</span> <span class="n">cell_type</span> <span class="ow">in</span> <span class="n">cell_types</span><span class="p">:</span>
+
+                    <span class="n">cell_type</span> <span class="o">=</span> <span class="p">(</span>
+                        <span class="s1">&#39;T lymphocyte&#39;</span>
+                            <span class="k">if</span> <span class="n">cell_type</span> <span class="o">==</span> <span class="s1">&#39;tymphocyte&#39;</span> <span class="k">else</span>
+                        <span class="n">cell_type</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s1">&#39;cells&#39;</span><span class="p">,</span> <span class="s1">&#39;cell&#39;</span><span class="p">)</span>
+                            <span class="k">if</span> <span class="n">cell_type</span> <span class="k">else</span>
+                        <span class="kc">None</span>
+                    <span class="p">)</span>
+
+                    <span class="n">result</span><span class="p">[</span><span class="n">uniprot</span><span class="p">]</span><span class="o">.</span><span class="n">add</span><span class="p">(</span>
+                        <span class="n">LrdbAnnotation</span><span class="p">(</span>
+                            <span class="n">role</span> <span class="o">=</span> <span class="n">role</span><span class="p">,</span>
+                            <span class="n">cell_type</span> <span class="o">=</span> <span class="n">cell_type</span><span class="p">,</span>
+                            <span class="n">sources</span> <span class="o">=</span> <span class="nb">tuple</span><span class="p">(</span><span class="nb">sorted</span><span class="p">(</span><span class="n">rec</span><span class="o">.</span><span class="n">sources</span><span class="p">)),</span>
+                            <span class="n">references</span> <span class="o">=</span> <span class="nb">tuple</span><span class="p">(</span><span class="nb">sorted</span><span class="p">(</span><span class="n">rec</span><span class="o">.</span><span class="n">references</span><span class="p">)),</span>
+                        <span class="p">)</span>
+                    <span class="p">)</span>
+
+    <span class="k">return</span> <span class="nb">dict</span><span class="p">(</span><span class="n">result</span><span class="p">)</span></div>
+
+</pre></div>
+
+                </article>
+              
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+        
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diff --git a/_modules/pypath/inputs/matrisome.html b/_modules/pypath/inputs/matrisome.html
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+                  
+  <h1>Source code for pypath.inputs.matrisome</h1><div class="highlight"><pre>
+<span></span><span class="ch">#!/usr/bin/env python</span>
+<span class="c1"># -*- coding: utf-8 -*-</span>
+
+<span class="c1">#</span>
+<span class="c1">#  This file is part of the `pypath` python module</span>
+<span class="c1">#</span>
+<span class="c1">#  Copyright 2014-2023</span>
+<span class="c1">#  EMBL, EMBL-EBI, Uniklinik RWTH Aachen, Heidelberg University</span>
+<span class="c1">#</span>
+<span class="c1">#  Authors: see the file `README.rst`</span>
+<span class="c1">#  Contact: Dénes Türei (turei.denes@gmail.com)</span>
+<span class="c1">#</span>
+<span class="c1">#  Distributed under the GPLv3 License.</span>
+<span class="c1">#  See accompanying file LICENSE.txt or copy at</span>
+<span class="c1">#      https://www.gnu.org/licenses/gpl-3.0.html</span>
+<span class="c1">#</span>
+<span class="c1">#  Website: https://pypath.omnipathdb.org/</span>
+<span class="c1">#</span>
+
+<span class="kn">import</span> <span class="nn">collections</span>
+
+<span class="kn">import</span> <span class="nn">pypath.share.curl</span> <span class="k">as</span> <span class="nn">curl</span>
+<span class="kn">import</span> <span class="nn">pypath.resources.urls</span> <span class="k">as</span> <span class="nn">urls</span>
+<span class="kn">import</span> <span class="nn">pypath.utils.mapping</span> <span class="k">as</span> <span class="nn">mapping</span>
+<span class="kn">import</span> <span class="nn">pypath.inputs.common</span> <span class="k">as</span> <span class="nn">inputs_common</span>
+
+
+<div class="viewcode-block" id="matrisome_annotations">
+<a class="viewcode-back" href="../../../api/pypath.inputs.matrisome.matrisome_annotations.html#pypath.inputs.matrisome.matrisome_annotations">[docs]</a>
+<span class="k">def</span> <span class="nf">matrisome_annotations</span><span class="p">(</span><span class="n">organism</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">):</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Downloads MatrisomeDB 2.0, a database of extracellular matrix proteins.</span>
+<span class="sd">    Returns dict where keys are UniProt IDs and values are tuples of</span>
+<span class="sd">    classes, subclasses and notes.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="n">MatrisomeAnnotation</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">namedtuple</span><span class="p">(</span>
+        <span class="s1">&#39;MatrisomeAnnotation&#39;</span><span class="p">,</span>
+        <span class="p">[</span><span class="s1">&#39;mainclass&#39;</span><span class="p">,</span> <span class="s1">&#39;subclass&#39;</span><span class="p">,</span> <span class="s1">&#39;subsubclass&#39;</span><span class="p">]</span>
+    <span class="p">)</span>
+
+
+    <span class="n">tax_names</span> <span class="o">=</span> <span class="p">{</span>
+        <span class="mi">10090</span><span class="p">:</span> <span class="p">(</span><span class="s1">&#39;Murine&#39;</span><span class="p">,</span> <span class="s1">&#39;mm&#39;</span><span class="p">),</span>
+        <span class="mi">9606</span><span class="p">:</span>  <span class="p">(</span><span class="s1">&#39;Human&#39;</span><span class="p">,</span>  <span class="s1">&#39;hs&#39;</span><span class="p">),</span>
+    <span class="p">}</span>
+
+    <span class="n">url</span> <span class="o">=</span> <span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;matrisome&#39;</span><span class="p">][</span><span class="s1">&#39;url_rescued&#39;</span><span class="p">]</span> <span class="o">%</span> <span class="n">tax_names</span><span class="p">[</span><span class="n">organism</span><span class="p">][</span><span class="mi">1</span><span class="p">]</span>
+    <span class="n">c</span> <span class="o">=</span> <span class="n">curl</span><span class="o">.</span><span class="n">Curl</span><span class="p">(</span><span class="n">url</span><span class="p">,</span> <span class="n">large</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span> <span class="n">silent</span> <span class="o">=</span> <span class="kc">False</span><span class="p">)</span>
+    <span class="n">xlsname</span> <span class="o">=</span> <span class="n">c</span><span class="o">.</span><span class="n">fname</span>
+    <span class="k">del</span><span class="p">(</span><span class="n">c</span><span class="p">)</span>
+    <span class="n">raw</span> <span class="o">=</span> <span class="n">inputs_common</span><span class="o">.</span><span class="n">read_xls</span><span class="p">(</span><span class="n">xlsname</span><span class="p">)[</span><span class="mi">1</span><span class="p">:]</span>
+
+    <span class="n">result</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">defaultdict</span><span class="p">(</span><span class="nb">set</span><span class="p">)</span>
+
+    <span class="k">for</span> <span class="n">r</span> <span class="ow">in</span> <span class="n">raw</span><span class="p">:</span>
+
+        <span class="n">uniprots</span> <span class="o">=</span> <span class="nb">set</span><span class="p">(</span><span class="n">r</span><span class="p">[</span><span class="mi">7</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;:&#39;</span><span class="p">))</span>
+        <span class="n">uniprots</span><span class="o">.</span><span class="n">discard</span><span class="p">(</span><span class="s1">&#39;&#39;</span><span class="p">)</span>
+
+        <span class="k">if</span> <span class="ow">not</span> <span class="n">uniprots</span><span class="p">:</span>
+            <span class="k">continue</span>
+
+        <span class="n">uniprots</span> <span class="o">=</span> <span class="n">mapping</span><span class="o">.</span><span class="n">map_names</span><span class="p">(</span><span class="n">uniprots</span><span class="p">,</span> <span class="s1">&#39;uniprot&#39;</span><span class="p">,</span> <span class="s1">&#39;uniprot&#39;</span><span class="p">)</span>
+
+        <span class="k">for</span> <span class="n">uniprot</span> <span class="ow">in</span> <span class="n">uniprots</span><span class="p">:</span>
+
+            <span class="n">result</span><span class="p">[</span><span class="n">uniprot</span><span class="p">]</span><span class="o">.</span><span class="n">add</span><span class="p">(</span>
+                <span class="n">MatrisomeAnnotation</span><span class="p">(</span>
+                    <span class="n">mainclass</span> <span class="o">=</span> <span class="n">r</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">strip</span><span class="p">(),</span>
+                    <span class="n">subclass</span> <span class="o">=</span> <span class="n">r</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">strip</span><span class="p">(),</span>
+                    <span class="n">subsubclass</span> <span class="o">=</span> <span class="n">r</span><span class="p">[</span><span class="mi">10</span><span class="p">]</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span> <span class="ow">or</span> <span class="kc">None</span><span class="p">,</span>
+                <span class="p">)</span>
+            <span class="p">)</span>
+
+    <span class="k">return</span> <span class="nb">dict</span><span class="p">(</span><span class="n">result</span><span class="p">)</span></div>
+
+
+
+<span class="k">def</span> <span class="nf">__matrisome_annotations_2</span><span class="p">():</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    This I made only to find out why certain proteins are missing from this</span>
+<span class="sd">    output. I will contact Matrisome people to ask why.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="n">url</span> <span class="o">=</span> <span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;matrisome&#39;</span><span class="p">][</span><span class="s1">&#39;url_dl&#39;</span><span class="p">]</span>
+    <span class="n">c</span> <span class="o">=</span> <span class="n">curl</span><span class="o">.</span><span class="n">Curl</span><span class="p">(</span><span class="n">url</span><span class="p">,</span> <span class="n">large</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span> <span class="n">silent</span> <span class="o">=</span> <span class="kc">False</span><span class="p">)</span>
+
+    <span class="n">_</span> <span class="o">=</span> <span class="nb">next</span><span class="p">(</span><span class="n">c</span><span class="o">.</span><span class="n">result</span><span class="p">)</span>
+
+    <span class="k">return</span> <span class="nb">set</span><span class="p">(</span><span class="n">r</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;,&#39;</span><span class="p">)[</span><span class="mi">1</span><span class="p">]</span> <span class="k">for</span> <span class="n">r</span> <span class="ow">in</span> <span class="n">c</span><span class="o">.</span><span class="n">result</span><span class="p">)</span>
+</pre></div>
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+  <h1>Source code for pypath.inputs.matrixdb</h1><div class="highlight"><pre>
+<span></span><span class="ch">#!/usr/bin/env python</span>
+<span class="c1"># -*- coding: utf-8 -*-</span>
+
+<span class="c1">#</span>
+<span class="c1">#  This file is part of the `pypath` python module</span>
+<span class="c1">#</span>
+<span class="c1">#  Copyright 2014-2023</span>
+<span class="c1">#  EMBL, EMBL-EBI, Uniklinik RWTH Aachen, Heidelberg University</span>
+<span class="c1">#</span>
+<span class="c1">#  Authors: see the file `README.rst`</span>
+<span class="c1">#  Contact: Dénes Türei (turei.denes@gmail.com)</span>
+<span class="c1">#</span>
+<span class="c1">#  Distributed under the GPLv3 License.</span>
+<span class="c1">#  See accompanying file LICENSE.txt or copy at</span>
+<span class="c1">#      https://www.gnu.org/licenses/gpl-3.0.html</span>
+<span class="c1">#</span>
+<span class="c1">#  Website: https://pypath.omnipathdb.org/</span>
+<span class="c1">#</span>
+
+<span class="kn">import</span> <span class="nn">collections</span>
+
+<span class="kn">import</span> <span class="nn">pypath.share.curl</span> <span class="k">as</span> <span class="nn">curl</span>
+<span class="kn">import</span> <span class="nn">pypath.resources.urls</span> <span class="k">as</span> <span class="nn">urls</span>
+<span class="kn">import</span> <span class="nn">pypath.utils.mapping</span> <span class="k">as</span> <span class="nn">mapping</span>
+<span class="kn">import</span> <span class="nn">pypath.inputs.uniprot_db</span> <span class="k">as</span> <span class="nn">uniprot_db</span>
+
+
+<div class="viewcode-block" id="matrixdb_interactions">
+<a class="viewcode-back" href="../../../api/pypath.inputs.matrixdb.matrixdb_interactions.html#pypath.inputs.matrixdb.matrixdb_interactions">[docs]</a>
+<span class="k">def</span> <span class="nf">matrixdb_interactions</span><span class="p">(</span><span class="n">organism</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">):</span>
+
+    <span class="n">url</span> <span class="o">=</span> <span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;matrixdb&#39;</span><span class="p">][</span><span class="s1">&#39;url&#39;</span><span class="p">]</span>
+    <span class="n">c</span> <span class="o">=</span> <span class="n">curl</span><span class="o">.</span><span class="n">Curl</span><span class="p">(</span><span class="n">url</span><span class="p">,</span> <span class="n">silent</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span> <span class="n">large</span> <span class="o">=</span> <span class="kc">True</span><span class="p">)</span>
+    <span class="n">f</span> <span class="o">=</span> <span class="n">c</span><span class="o">.</span><span class="n">result</span>
+    <span class="n">i</span> <span class="o">=</span> <span class="p">[]</span>
+    <span class="n">lnum</span> <span class="o">=</span> <span class="mi">0</span>
+
+    <span class="k">for</span> <span class="n">l</span> <span class="ow">in</span> <span class="n">f</span><span class="p">:</span>
+        <span class="k">if</span> <span class="n">lnum</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
+            <span class="n">lnum</span> <span class="o">+=</span> <span class="mi">1</span>
+
+            <span class="k">continue</span>
+
+        <span class="n">l</span> <span class="o">=</span> <span class="n">l</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\n</span><span class="s1">&#39;</span><span class="p">,</span> <span class="s1">&#39;&#39;</span><span class="p">)</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\r</span><span class="s1">&#39;</span><span class="p">,</span> <span class="s1">&#39;&#39;</span><span class="p">)</span>
+        <span class="n">l</span> <span class="o">=</span> <span class="n">l</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\t</span><span class="s1">&#39;</span><span class="p">)</span>
+        <span class="n">specA</span> <span class="o">=</span> <span class="mi">0</span> <span class="k">if</span> <span class="n">l</span><span class="p">[</span><span class="mi">9</span><span class="p">]</span> <span class="o">==</span> <span class="s1">&#39;-&#39;</span> <span class="k">else</span> <span class="nb">int</span><span class="p">(</span><span class="n">l</span><span class="p">[</span><span class="mi">9</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;:&#39;</span><span class="p">)[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;(&#39;</span><span class="p">)[</span><span class="mi">0</span><span class="p">])</span>
+        <span class="n">specB</span> <span class="o">=</span> <span class="mi">0</span> <span class="k">if</span> <span class="n">l</span><span class="p">[</span><span class="mi">10</span><span class="p">]</span> <span class="o">==</span> <span class="s1">&#39;-&#39;</span> <span class="k">else</span> <span class="nb">int</span><span class="p">(</span><span class="n">l</span><span class="p">[</span><span class="mi">10</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;:&#39;</span><span class="p">)[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;(&#39;</span><span class="p">)[</span><span class="mi">0</span><span class="p">])</span>
+
+        <span class="k">if</span> <span class="n">organism</span> <span class="ow">is</span> <span class="kc">None</span> <span class="ow">or</span> <span class="p">(</span><span class="n">specA</span> <span class="o">==</span> <span class="n">organism</span> <span class="ow">and</span> <span class="n">specB</span> <span class="o">==</span> <span class="n">organism</span><span class="p">):</span>
+            <span class="n">pm</span> <span class="o">=</span> <span class="p">[</span>
+                <span class="n">p</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s1">&#39;pubmed:&#39;</span><span class="p">,</span> <span class="s1">&#39;&#39;</span><span class="p">)</span> <span class="k">for</span> <span class="n">p</span> <span class="ow">in</span> <span class="n">l</span><span class="p">[</span><span class="mi">8</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;|&#39;</span><span class="p">)</span>
+                <span class="k">if</span> <span class="n">p</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s1">&#39;pubmed:&#39;</span><span class="p">)</span>
+            <span class="p">]</span>
+            <span class="n">met</span> <span class="o">=</span> <span class="p">[</span>
+                <span class="n">m</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;(&#39;</span><span class="p">)[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s1">&#39;)&#39;</span><span class="p">,</span> <span class="s1">&#39;&#39;</span><span class="p">)</span><span class="o">.</span><span class="n">strip</span><span class="p">(</span><span class="s1">&#39;&quot;&#39;</span><span class="p">)</span>
+                <span class="k">for</span> <span class="n">m</span> <span class="ow">in</span> <span class="n">l</span><span class="p">[</span><span class="mi">6</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;|&#39;</span><span class="p">)</span>
+                <span class="k">if</span> <span class="s1">&#39;(&#39;</span> <span class="ow">in</span> <span class="n">m</span>
+            <span class="p">]</span>
+            <span class="n">l</span> <span class="o">=</span> <span class="p">[</span><span class="n">l</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">l</span><span class="p">[</span><span class="mi">1</span><span class="p">]]</span>
+            <span class="n">interaction</span> <span class="o">=</span> <span class="p">()</span>
+
+            <span class="k">for</span> <span class="n">ll</span> <span class="ow">in</span> <span class="n">l</span><span class="p">:</span>
+                <span class="n">ll</span> <span class="o">=</span> <span class="n">ll</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;|&#39;</span><span class="p">)</span>
+                <span class="n">uniprot</span> <span class="o">=</span> <span class="s1">&#39;&#39;</span>
+
+                <span class="k">for</span> <span class="n">lll</span> <span class="ow">in</span> <span class="n">ll</span><span class="p">:</span>
+                    <span class="n">nm</span> <span class="o">=</span> <span class="n">lll</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;:&#39;</span><span class="p">)</span>
+
+                    <span class="k">if</span> <span class="n">nm</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">==</span> <span class="s1">&#39;uniprotkb&#39;</span> <span class="ow">and</span> <span class="nb">len</span><span class="p">(</span><span class="n">nm</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span> <span class="o">==</span> <span class="mi">6</span><span class="p">:</span>
+                        <span class="n">uniprot</span> <span class="o">=</span> <span class="n">nm</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span>
+
+                <span class="n">interaction</span> <span class="o">+=</span> <span class="p">(</span><span class="n">uniprot</span><span class="p">,</span> <span class="p">)</span>
+
+            <span class="n">interaction</span> <span class="o">+=</span> <span class="p">(</span><span class="s1">&#39;|&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">pm</span><span class="p">),</span> <span class="s1">&#39;|&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">met</span><span class="p">))</span>
+
+            <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">interaction</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span> <span class="o">&gt;</span> <span class="mi">5</span> <span class="ow">and</span> <span class="nb">len</span><span class="p">(</span><span class="n">interaction</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span> <span class="o">&gt;</span> <span class="mi">5</span><span class="p">:</span>
+                <span class="n">i</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="nb">list</span><span class="p">(</span><span class="n">interaction</span><span class="p">))</span>
+
+        <span class="n">lnum</span> <span class="o">+=</span> <span class="mi">1</span>
+
+    <span class="n">f</span><span class="o">.</span><span class="n">close</span><span class="p">()</span>
+
+    <span class="k">return</span> <span class="n">i</span></div>
+
+
+
+<span class="k">def</span> <span class="nf">_matrixdb_protein_list</span><span class="p">(</span><span class="n">category</span><span class="p">,</span> <span class="n">organism</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">):</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Returns a set of proteins annotated by MatrixDB.</span>
+
+<span class="sd">    :arg str category:</span>
+<span class="sd">        The protein annotation category. Possible values: `ecm`, `membrane`</span>
+<span class="sd">        or `secreted`.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="n">url</span> <span class="o">=</span> <span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;matrixdb&#39;</span><span class="p">][</span><span class="s1">&#39;</span><span class="si">%s</span><span class="s1">_proteins&#39;</span> <span class="o">%</span> <span class="n">category</span><span class="p">]</span>
+    <span class="n">c</span> <span class="o">=</span> <span class="n">curl</span><span class="o">.</span><span class="n">Curl</span><span class="p">(</span><span class="n">url</span><span class="p">,</span> <span class="n">silent</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span> <span class="n">large</span> <span class="o">=</span> <span class="kc">True</span><span class="p">)</span>
+
+    <span class="n">proteins</span> <span class="o">=</span> <span class="nb">set</span><span class="p">()</span>
+
+    <span class="c1"># header row</span>
+    <span class="n">_</span> <span class="o">=</span> <span class="nb">next</span><span class="p">(</span><span class="n">c</span><span class="o">.</span><span class="n">result</span><span class="p">)</span>
+
+    <span class="k">for</span> <span class="n">l</span> <span class="ow">in</span> <span class="n">c</span><span class="o">.</span><span class="n">result</span><span class="p">:</span>
+        <span class="k">if</span> <span class="ow">not</span> <span class="n">l</span><span class="p">:</span>
+            <span class="k">continue</span>
+
+        <span class="n">proteins</span><span class="o">.</span><span class="n">add</span><span class="p">(</span>
+            <span class="n">l</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s1">&#39;&quot;&#39;</span><span class="p">,</span> <span class="s1">&#39;&#39;</span><span class="p">)</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\t</span><span class="s1">&#39;</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span>
+        <span class="p">)</span>
+
+    <span class="n">proteins</span> <span class="o">=</span> <span class="n">mapping</span><span class="o">.</span><span class="n">map_names</span><span class="p">(</span><span class="n">proteins</span><span class="p">,</span> <span class="s1">&#39;uniprot&#39;</span><span class="p">,</span> <span class="s1">&#39;uniprot&#39;</span><span class="p">)</span>
+
+    <span class="k">if</span> <span class="n">organism</span><span class="p">:</span>
+
+        <span class="n">uniprots</span> <span class="o">=</span> <span class="n">uniprot_db</span><span class="o">.</span><span class="n">all_uniprots</span><span class="p">(</span>
+            <span class="n">organism</span> <span class="o">=</span> <span class="n">organism</span><span class="p">,</span>
+            <span class="n">swissprot</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
+        <span class="p">)</span>
+        <span class="n">proteins</span> <span class="o">=</span> <span class="n">proteins</span> <span class="o">&amp;</span> <span class="nb">set</span><span class="p">(</span><span class="n">uniprots</span><span class="p">)</span>
+
+    <span class="k">return</span> <span class="n">proteins</span>
+
+
+<div class="viewcode-block" id="matrixdb_membrane_proteins">
+<a class="viewcode-back" href="../../../api/pypath.inputs.matrixdb.matrixdb_membrane_proteins.html#pypath.inputs.matrixdb.matrixdb_membrane_proteins">[docs]</a>
+<span class="k">def</span> <span class="nf">matrixdb_membrane_proteins</span><span class="p">(</span><span class="n">organism</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">):</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Returns a set of membrane protein UniProt IDs retrieved from MatrixDB.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="k">return</span> <span class="n">_matrixdb_protein_list</span><span class="p">(</span><span class="s1">&#39;membrane&#39;</span><span class="p">,</span> <span class="n">organism</span> <span class="o">=</span> <span class="n">organism</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="matrixdb_secreted_proteins">
+<a class="viewcode-back" href="../../../api/pypath.inputs.matrixdb.matrixdb_secreted_proteins.html#pypath.inputs.matrixdb.matrixdb_secreted_proteins">[docs]</a>
+<span class="k">def</span> <span class="nf">matrixdb_secreted_proteins</span><span class="p">(</span><span class="n">organism</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">):</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Returns a set of secreted protein UniProt IDs retrieved from MatrixDB.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="k">return</span> <span class="n">_matrixdb_protein_list</span><span class="p">(</span><span class="s1">&#39;secreted&#39;</span><span class="p">,</span> <span class="n">organism</span> <span class="o">=</span> <span class="n">organism</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="matrixdb_ecm_proteins">
+<a class="viewcode-back" href="../../../api/pypath.inputs.matrixdb.matrixdb_ecm_proteins.html#pypath.inputs.matrixdb.matrixdb_ecm_proteins">[docs]</a>
+<span class="k">def</span> <span class="nf">matrixdb_ecm_proteins</span><span class="p">(</span><span class="n">organism</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">):</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Returns a set of ECM (extracellular matrix) protein UniProt IDs</span>
+<span class="sd">    retrieved from MatrixDB.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="k">return</span> <span class="n">_matrixdb_protein_list</span><span class="p">(</span><span class="s1">&#39;ecm&#39;</span><span class="p">,</span> <span class="n">organism</span> <span class="o">=</span> <span class="n">organism</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="matrixdb_annotations">
+<a class="viewcode-back" href="../../../api/pypath.inputs.matrixdb.matrixdb_annotations.html#pypath.inputs.matrixdb.matrixdb_annotations">[docs]</a>
+<span class="k">def</span> <span class="nf">matrixdb_annotations</span><span class="p">(</span><span class="n">organism</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">):</span>
+
+    <span class="n">MatrixdbAnnotation</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">namedtuple</span><span class="p">(</span>
+        <span class="s1">&#39;MatrixdbAnnotation&#39;</span><span class="p">,</span>
+        <span class="p">(</span><span class="s1">&#39;mainclass&#39;</span><span class="p">,),</span>
+    <span class="p">)</span>
+    <span class="n">annot</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">defaultdict</span><span class="p">(</span><span class="nb">set</span><span class="p">)</span>
+
+    <span class="k">for</span> <span class="bp">cls</span> <span class="ow">in</span> <span class="p">(</span><span class="s1">&#39;membrane&#39;</span><span class="p">,</span> <span class="s1">&#39;secreted&#39;</span><span class="p">,</span> <span class="s1">&#39;ecm&#39;</span><span class="p">):</span>
+        <span class="n">cls_annot</span> <span class="o">=</span> <span class="n">MatrixdbAnnotation</span><span class="p">(</span><span class="n">mainclass</span> <span class="o">=</span> <span class="bp">cls</span><span class="p">)</span>
+
+        <span class="n">method</span> <span class="o">=</span> <span class="nb">globals</span><span class="p">()[</span><span class="s1">&#39;matrixdb_</span><span class="si">%s</span><span class="s1">_proteins&#39;</span> <span class="o">%</span> <span class="bp">cls</span><span class="p">]</span>
+
+        <span class="k">for</span> <span class="n">uniprot</span> <span class="ow">in</span> <span class="n">method</span><span class="p">(</span><span class="n">organism</span> <span class="o">=</span> <span class="n">organism</span><span class="p">):</span>
+            <span class="n">annot</span><span class="p">[</span><span class="n">uniprot</span><span class="p">]</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">cls_annot</span><span class="p">)</span>
+
+    <span class="k">return</span> <span class="nb">dict</span><span class="p">(</span><span class="n">annot</span><span class="p">)</span></div>
+
+</pre></div>
+
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+  
+  
+</div>
+</div>
+              
+              
+              
+                
+<div id="searchbox"></div>
+                <article class="bd-article">
+                  
+  <h1>Source code for pypath.inputs.mcam</h1><div class="highlight"><pre>
+<span></span><span class="ch">#!/usr/bin/env python</span>
+<span class="c1"># -*- coding: utf-8 -*-</span>
+
+<span class="c1">#</span>
+<span class="c1">#  This file is part of the `pypath` python module</span>
+<span class="c1">#</span>
+<span class="c1">#  Copyright 2014-2023</span>
+<span class="c1">#  EMBL, EMBL-EBI, Uniklinik RWTH Aachen, Heidelberg University</span>
+<span class="c1">#</span>
+<span class="c1">#  Authors: see the file `README.rst`</span>
+<span class="c1">#  Contact: Dénes Türei (turei.denes@gmail.com)</span>
+<span class="c1">#</span>
+<span class="c1">#  Distributed under the GPLv3 License.</span>
+<span class="c1">#  See accompanying file LICENSE.txt or copy at</span>
+<span class="c1">#      https://www.gnu.org/licenses/gpl-3.0.html</span>
+<span class="c1">#</span>
+<span class="c1">#  Website: https://pypath.omnipathdb.org/</span>
+<span class="c1">#</span>
+
+<span class="kn">import</span> <span class="nn">pypath.resources.urls</span> <span class="k">as</span> <span class="nn">urls</span>
+<span class="kn">import</span> <span class="nn">pypath.share.curl</span> <span class="k">as</span> <span class="nn">curl</span>
+<span class="kn">import</span> <span class="nn">pypath.utils.mapping</span> <span class="k">as</span> <span class="nn">mapping</span>
+
+
+<div class="viewcode-block" id="mcam_cell_adhesion_molecules">
+<a class="viewcode-back" href="../../../api/pypath.inputs.mcam.mcam_cell_adhesion_molecules.html#pypath.inputs.mcam.mcam_cell_adhesion_molecules">[docs]</a>
+<span class="k">def</span> <span class="nf">mcam_cell_adhesion_molecules</span><span class="p">():</span>
+    
+    <span class="n">url</span> <span class="o">=</span> <span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;mcam&#39;</span><span class="p">][</span><span class="s1">&#39;url&#39;</span><span class="p">]</span>
+    
+    <span class="n">c</span> <span class="o">=</span> <span class="n">curl</span><span class="o">.</span><span class="n">Curl</span><span class="p">(</span><span class="n">url</span><span class="p">,</span> <span class="n">silent</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span> <span class="n">large</span> <span class="o">=</span> <span class="kc">True</span><span class="p">)</span>
+    
+    <span class="n">_</span> <span class="o">=</span> <span class="nb">next</span><span class="p">(</span><span class="n">c</span><span class="o">.</span><span class="n">result</span><span class="p">)</span>
+    
+    <span class="k">return</span> <span class="p">{</span>
+        <span class="n">uniprot</span>
+        <span class="k">for</span> <span class="n">line</span> <span class="ow">in</span> <span class="n">c</span><span class="o">.</span><span class="n">result</span>
+        <span class="k">for</span> <span class="n">_uniprot</span> <span class="ow">in</span> <span class="n">line</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\t</span><span class="s1">&#39;</span><span class="p">,</span> <span class="n">maxsplit</span> <span class="o">=</span> <span class="mi">1</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;;&#39;</span><span class="p">)</span>
+        <span class="k">for</span> <span class="n">uniprot</span> <span class="ow">in</span> <span class="n">mapping</span><span class="o">.</span><span class="n">map_name</span><span class="p">(</span>
+            <span class="n">_uniprot</span><span class="o">.</span><span class="n">strip</span><span class="p">(),</span>
+            <span class="s1">&#39;uniprot&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;uniprot&#39;</span><span class="p">,</span>
+        <span class="p">)</span>
+    <span class="p">}</span></div>
+
+</pre></div>
+
+                </article>
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diff --git a/_modules/pypath/inputs/membranome.html b/_modules/pypath/inputs/membranome.html
new file mode 100644
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+                  
+  <h1>Source code for pypath.inputs.membranome</h1><div class="highlight"><pre>
+<span></span><span class="ch">#!/usr/bin/env python</span>
+<span class="c1"># -*- coding: utf-8 -*-</span>
+
+<span class="c1">#</span>
+<span class="c1">#  This file is part of the `pypath` python module</span>
+<span class="c1">#</span>
+<span class="c1">#  Copyright 2014-2023</span>
+<span class="c1">#  EMBL, EMBL-EBI, Uniklinik RWTH Aachen, Heidelberg University</span>
+<span class="c1">#</span>
+<span class="c1">#  Authors: see the file `README.rst`</span>
+<span class="c1">#  Contact: Dénes Türei (turei.denes@gmail.com)</span>
+<span class="c1">#</span>
+<span class="c1">#  Distributed under the GPLv3 License.</span>
+<span class="c1">#  See accompanying file LICENSE.txt or copy at</span>
+<span class="c1">#      https://www.gnu.org/licenses/gpl-3.0.html</span>
+<span class="c1">#</span>
+<span class="c1">#  Website: https://pypath.omnipathdb.org/</span>
+<span class="c1">#</span>
+
+<span class="kn">import</span> <span class="nn">collections</span>
+<span class="kn">import</span> <span class="nn">json</span>
+
+<span class="kn">import</span> <span class="nn">pypath.share.curl</span> <span class="k">as</span> <span class="nn">curl</span>
+<span class="kn">import</span> <span class="nn">pypath.resources.urls</span> <span class="k">as</span> <span class="nn">urls</span>
+<span class="kn">import</span> <span class="nn">pypath.utils.mapping</span> <span class="k">as</span> <span class="nn">mapping</span>
+<span class="kn">import</span> <span class="nn">pypath.share.progress</span> <span class="k">as</span> <span class="nn">progress</span>
+
+
+<div class="viewcode-block" id="membranome_annotations">
+<a class="viewcode-back" href="../../../api/pypath.inputs.membranome.membranome_annotations.html#pypath.inputs.membranome.membranome_annotations">[docs]</a>
+<span class="k">def</span> <span class="nf">membranome_annotations</span><span class="p">():</span>
+
+    <span class="n">membr_url</span> <span class="o">=</span> <span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;membranome&#39;</span><span class="p">][</span><span class="s1">&#39;baseurl&#39;</span><span class="p">]</span> <span class="o">%</span> <span class="p">(</span><span class="s1">&#39;membranes&#39;</span><span class="p">,</span> <span class="s1">&#39;&#39;</span><span class="p">)</span>
+    <span class="n">c</span> <span class="o">=</span> <span class="n">curl</span><span class="o">.</span><span class="n">Curl</span><span class="p">(</span><span class="n">membr_url</span><span class="p">,</span> <span class="n">large</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span> <span class="n">silent</span> <span class="o">=</span> <span class="kc">False</span><span class="p">)</span>
+    <span class="n">membr_data</span> <span class="o">=</span> <span class="n">json</span><span class="o">.</span><span class="n">loads</span><span class="p">(</span><span class="n">c</span><span class="o">.</span><span class="n">fileobj</span><span class="o">.</span><span class="n">read</span><span class="p">())</span>
+    <span class="k">del</span> <span class="n">c</span>
+
+    <span class="n">membr</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">((</span><span class="n">m</span><span class="p">[</span><span class="s1">&#39;id&#39;</span><span class="p">],</span> <span class="n">m</span><span class="p">)</span> <span class="k">for</span> <span class="n">m</span> <span class="ow">in</span> <span class="n">membr_data</span><span class="p">[</span><span class="s1">&#39;objects&#39;</span><span class="p">])</span>
+
+    <span class="n">page</span> <span class="o">=</span> <span class="mi">1</span>
+    <span class="n">prot_all</span> <span class="o">=</span> <span class="p">[]</span>
+
+    <span class="n">prg</span> <span class="o">=</span> <span class="n">progress</span><span class="o">.</span><span class="n">Progress</span><span class="p">(</span><span class="mi">7</span><span class="p">,</span> <span class="s1">&#39;Downloading Membranome&#39;</span><span class="p">,</span> <span class="mi">1</span><span class="p">)</span>
+
+    <span class="k">while</span> <span class="kc">True</span><span class="p">:</span>
+
+        <span class="n">prg</span><span class="o">.</span><span class="n">step</span><span class="p">()</span>
+
+        <span class="n">prot_url</span> <span class="o">=</span> <span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;membranome&#39;</span><span class="p">][</span><span class="s1">&#39;baseurl&#39;</span><span class="p">]</span> <span class="o">%</span> <span class="p">(</span>
+            <span class="s1">&#39;proteins&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;?pageSize=1000&amp;pageNum=</span><span class="si">%u</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="n">page</span><span class="p">,</span>
+        <span class="p">)</span>
+        <span class="n">c</span> <span class="o">=</span> <span class="n">curl</span><span class="o">.</span><span class="n">Curl</span><span class="p">(</span><span class="n">prot_url</span><span class="p">,</span> <span class="n">large</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span> <span class="n">silent</span> <span class="o">=</span> <span class="kc">True</span><span class="p">)</span>
+        <span class="n">prot</span> <span class="o">=</span> <span class="n">json</span><span class="o">.</span><span class="n">loads</span><span class="p">(</span><span class="n">c</span><span class="o">.</span><span class="n">fileobj</span><span class="o">.</span><span class="n">read</span><span class="p">())</span>
+
+        <span class="n">prot_all</span><span class="o">.</span><span class="n">extend</span><span class="p">(</span><span class="n">prot</span><span class="p">[</span><span class="s1">&#39;objects&#39;</span><span class="p">])</span>
+
+        <span class="k">if</span> <span class="n">prot</span><span class="p">[</span><span class="s1">&#39;page_end&#39;</span><span class="p">]</span> <span class="o">&gt;=</span> <span class="n">prot</span><span class="p">[</span><span class="s1">&#39;total_objects&#39;</span><span class="p">]:</span>
+            <span class="k">break</span>
+
+        <span class="n">page</span> <span class="o">=</span> <span class="n">prot</span><span class="p">[</span><span class="s1">&#39;page_num&#39;</span><span class="p">]</span> <span class="o">+</span> <span class="mi">1</span>
+
+    <span class="n">prg</span><span class="o">.</span><span class="n">terminate</span><span class="p">()</span>
+
+    <span class="k">for</span> <span class="n">p</span> <span class="ow">in</span> <span class="n">prot_all</span><span class="p">:</span>
+
+        <span class="n">uniprots</span> <span class="o">=</span> <span class="n">mapping</span><span class="o">.</span><span class="n">map_name</span><span class="p">(</span><span class="n">p</span><span class="p">[</span><span class="s1">&#39;uniprotcode&#39;</span><span class="p">],</span> <span class="s1">&#39;uniprot&#39;</span><span class="p">,</span> <span class="s1">&#39;uniprot&#39;</span><span class="p">)</span>
+
+        <span class="k">for</span> <span class="n">uniprot</span> <span class="ow">in</span> <span class="n">uniprots</span><span class="p">:</span>
+
+            <span class="k">yield</span> <span class="p">(</span>
+                <span class="n">uniprot</span><span class="p">,</span>
+                <span class="n">membr</span><span class="p">[</span><span class="n">p</span><span class="p">[</span><span class="s1">&#39;membrane_id&#39;</span><span class="p">]][</span><span class="s1">&#39;name&#39;</span><span class="p">],</span>
+                <span class="n">membr</span><span class="p">[</span><span class="n">p</span><span class="p">[</span><span class="s1">&#39;membrane_id&#39;</span><span class="p">]][</span><span class="s1">&#39;topology_in&#39;</span><span class="p">]</span>
+                    <span class="k">if</span> <span class="n">p</span><span class="p">[</span><span class="s1">&#39;topology_show_in&#39;</span><span class="p">]</span> <span class="k">else</span>
+                <span class="n">membr</span><span class="p">[</span><span class="n">p</span><span class="p">[</span><span class="s1">&#39;membrane_id&#39;</span><span class="p">]][</span><span class="s1">&#39;topology_out&#39;</span><span class="p">],</span>
+            <span class="p">)</span></div>
+
+</pre></div>
+
+                </article>
+              
+              
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diff --git a/_modules/pypath/inputs/msigdb.html b/_modules/pypath/inputs/msigdb.html
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+
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+                  
+  <h1>Source code for pypath.inputs.msigdb</h1><div class="highlight"><pre>
+<span></span><span class="ch">#!/usr/bin/env python</span>
+<span class="c1"># -*- coding: utf-8 -*-</span>
+
+<span class="c1">#</span>
+<span class="c1">#  This file is part of the `pypath` python module</span>
+<span class="c1">#</span>
+<span class="c1">#  Copyright 2014-2023</span>
+<span class="c1">#  EMBL, EMBL-EBI, Uniklinik RWTH Aachen, Heidelberg University</span>
+<span class="c1">#</span>
+<span class="c1">#  Authors: see the file `README.rst`</span>
+<span class="c1">#  Contact: Dénes Türei (turei.denes@gmail.com)</span>
+<span class="c1">#</span>
+<span class="c1">#  Distributed under the GPLv3 License.</span>
+<span class="c1">#  See accompanying file LICENSE.txt or copy at</span>
+<span class="c1">#      https://www.gnu.org/licenses/gpl-3.0.html</span>
+<span class="c1">#</span>
+<span class="c1">#  Website: https://pypath.omnipathdb.org/</span>
+<span class="c1">#</span>
+
+<span class="kn">from</span> <span class="nn">future.utils</span> <span class="kn">import</span> <span class="n">iteritems</span>
+
+<span class="kn">import</span> <span class="nn">os</span>
+<span class="kn">import</span> <span class="nn">collections</span>
+
+<span class="kn">import</span> <span class="nn">pypath.share.curl</span> <span class="k">as</span> <span class="nn">curl</span>
+<span class="kn">import</span> <span class="nn">pypath.resources.urls</span> <span class="k">as</span> <span class="nn">urls</span>
+<span class="kn">import</span> <span class="nn">pypath.share.settings</span> <span class="k">as</span> <span class="nn">settings</span>
+<span class="kn">import</span> <span class="nn">pypath.share.session</span> <span class="k">as</span> <span class="nn">session</span>
+<span class="kn">import</span> <span class="nn">pypath.utils.mapping</span> <span class="k">as</span> <span class="nn">mapping</span>
+<span class="kn">import</span> <span class="nn">pypath.utils.taxonomy</span> <span class="k">as</span> <span class="nn">taxonomy</span>
+
+<span class="n">_logger</span> <span class="o">=</span> <span class="n">session</span><span class="o">.</span><span class="n">Logger</span><span class="p">(</span><span class="n">name</span> <span class="o">=</span> <span class="s1">&#39;msigdb_input&#39;</span><span class="p">)</span>
+<span class="n">_log</span> <span class="o">=</span> <span class="n">_logger</span><span class="o">.</span><span class="n">_log</span>
+
+
+<span class="n">ALL_COLLECTIONS</span> <span class="o">=</span> <span class="p">{</span>
+    <span class="s1">&#39;hallmark&#39;</span><span class="p">:</span> <span class="p">(</span><span class="s1">&#39;h.all&#39;</span><span class="p">,</span> <span class="s1">&#39;mh.all&#39;</span><span class="p">),</span>
+    <span class="s1">&#39;positional&#39;</span><span class="p">:</span> <span class="p">(</span><span class="s1">&#39;c1.all&#39;</span><span class="p">,</span> <span class="s1">&#39;m1.all&#39;</span><span class="p">),</span>
+    <span class="s1">&#39;chemical_and_genetic_perturbations&#39;</span><span class="p">:</span> <span class="p">(</span><span class="s1">&#39;c2.cgp&#39;</span><span class="p">,</span> <span class="s1">&#39;m2.cgp&#39;</span><span class="p">),</span>
+    <span class="s1">&#39;biocarta_pathways&#39;</span><span class="p">:</span> <span class="p">(</span><span class="s1">&#39;c2.cp.biocarta&#39;</span><span class="p">,</span> <span class="s1">&#39;m2.cp.biocarta&#39;</span><span class="p">),</span>
+    <span class="s1">&#39;kegg_pathways&#39;</span><span class="p">:</span> <span class="p">(</span><span class="s1">&#39;c2.cp.kegg&#39;</span><span class="p">,</span> <span class="kc">None</span><span class="p">),</span>
+    <span class="s1">&#39;pid_pathways&#39;</span><span class="p">:</span> <span class="p">(</span><span class="s1">&#39;c2.cp.pid&#39;</span><span class="p">,</span> <span class="kc">None</span><span class="p">),</span>
+    <span class="s1">&#39;reactome_pathways&#39;</span><span class="p">:</span> <span class="p">(</span><span class="s1">&#39;c2.cp.reactome&#39;</span><span class="p">,</span> <span class="s1">&#39;m2.cp.reactome&#39;</span><span class="p">),</span>
+    <span class="s1">&#39;wikipathways&#39;</span><span class="p">:</span> <span class="p">(</span><span class="s1">&#39;c2.cp.wikipathways&#39;</span><span class="p">,</span> <span class="s1">&#39;m2.cp.wikipathways&#39;</span><span class="p">),</span>
+    <span class="s1">&#39;mirna_targets_mirdb&#39;</span><span class="p">:</span> <span class="p">(</span><span class="s1">&#39;c3.mir.mirdb&#39;</span><span class="p">,</span> <span class="s1">&#39;m3.mirdb&#39;</span><span class="p">),</span>
+    <span class="s1">&#39;mirna_targets_legacy&#39;</span><span class="p">:</span> <span class="p">(</span><span class="s1">&#39;c3.mir.mir_legacy&#39;</span><span class="p">,</span> <span class="kc">None</span><span class="p">),</span>
+    <span class="s1">&#39;tf_targets_gtrf&#39;</span><span class="p">:</span> <span class="p">(</span><span class="s1">&#39;c3.tft.gtrd&#39;</span><span class="p">,</span> <span class="s1">&#39;m3.gtrd&#39;</span><span class="p">),</span>
+    <span class="s1">&#39;tf_targets_legacy&#39;</span><span class="p">:</span> <span class="p">(</span><span class="s1">&#39;c3.tft.tft_legacy&#39;</span><span class="p">,</span> <span class="kc">None</span><span class="p">),</span>
+    <span class="s1">&#39;cancer_gene_neighborhoods&#39;</span><span class="p">:</span> <span class="p">(</span><span class="s1">&#39;c4.cgn&#39;</span><span class="p">,</span> <span class="kc">None</span><span class="p">),</span>
+    <span class="s1">&#39;cancer_modules&#39;</span><span class="p">:</span> <span class="p">(</span><span class="s1">&#39;c4.cm&#39;</span><span class="p">,</span> <span class="kc">None</span><span class="p">),</span>
+    <span class="s1">&#39;go_biological_process&#39;</span><span class="p">:</span> <span class="p">(</span><span class="s1">&#39;c5.go.bp&#39;</span><span class="p">,</span> <span class="s1">&#39;m5.go.bp&#39;</span><span class="p">),</span>
+    <span class="s1">&#39;go_molecular_function&#39;</span><span class="p">:</span> <span class="p">(</span><span class="s1">&#39;c5.go.mf&#39;</span><span class="p">,</span> <span class="s1">&#39;m5.go.mf&#39;</span><span class="p">),</span>
+    <span class="s1">&#39;go_cellular_component&#39;</span><span class="p">:</span> <span class="p">(</span><span class="s1">&#39;c5.go.cc&#39;</span><span class="p">,</span> <span class="s1">&#39;m5.go.cc&#39;</span><span class="p">),</span>
+    <span class="s1">&#39;human_phenotype_ontology&#39;</span><span class="p">:</span> <span class="p">(</span><span class="s1">&#39;c5.hpo&#39;</span><span class="p">,</span> <span class="kc">None</span><span class="p">),</span>
+    <span class="s1">&#39;mouse_phenotype_ontology&#39;</span><span class="p">:</span> <span class="p">(</span><span class="kc">None</span><span class="p">,</span> <span class="s1">&#39;m5.mpt&#39;</span><span class="p">),</span>
+    <span class="s1">&#39;oncogenic_signatures&#39;</span><span class="p">:</span> <span class="p">(</span><span class="s1">&#39;c6.all&#39;</span><span class="p">,</span> <span class="kc">None</span><span class="p">),</span>
+    <span class="s1">&#39;immunesigdb&#39;</span><span class="p">:</span> <span class="p">(</span><span class="s1">&#39;c7.immunesigdb&#39;</span><span class="p">,</span> <span class="kc">None</span><span class="p">),</span>
+    <span class="s1">&#39;vaccine_response&#39;</span><span class="p">:</span> <span class="p">(</span><span class="s1">&#39;c7.vax&#39;</span><span class="p">,</span> <span class="kc">None</span><span class="p">),</span>
+    <span class="s1">&#39;cell_type_signatures&#39;</span><span class="p">:</span> <span class="p">(</span><span class="s1">&#39;c8.all&#39;</span><span class="p">,</span> <span class="s1">&#39;m8.all&#39;</span><span class="p">),</span>
+<span class="p">}</span>
+
+
+<div class="viewcode-block" id="msigdb_download">
+<a class="viewcode-back" href="../../../api/pypath.inputs.msigdb.msigdb_download.html#pypath.inputs.msigdb.msigdb_download">[docs]</a>
+<span class="k">def</span> <span class="nf">msigdb_download</span><span class="p">(</span>
+        <span class="n">registered_email</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+        <span class="n">collection</span> <span class="o">=</span> <span class="s1">&#39;msigdb&#39;</span><span class="p">,</span>
+        <span class="n">id_type</span> <span class="o">=</span> <span class="s1">&#39;symbols&#39;</span><span class="p">,</span>
+        <span class="n">force_download</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+        <span class="n">organism</span> <span class="o">=</span> <span class="s1">&#39;human&#39;</span><span class="p">,</span>
+        <span class="n">version</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+    <span class="p">):</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Downloads and preprocesses a collection of gmt format gene sets from</span>
+<span class="sd">    MSigDB. Returns dict of sets with gene set names as keys and molecular</span>
+<span class="sd">    identifiers as values.</span>
+
+<span class="sd">    :arg str,NoneType registered_email:</span>
+<span class="sd">        An email address registered at MSigDB. If `None` the `msigdb_email`</span>
+<span class="sd">        from ``pypath.settings`` will be used.</span>
+<span class="sd">    :arg str collection:</span>
+<span class="sd">        The name of the gene set collection. For available collections (e.g.</span>
+<span class="sd">        `h.all` or `c2.cpg`) refer to the MSigDB website:</span>
+<span class="sd">        http://software.broadinstitute.org/gsea/downloads.jsp#msigdb</span>
+<span class="sd">        The default value `msigdb` contains all the genesets however you</span>
+<span class="sd">        won&#39;t be able to distinguish which geneset comes from which</span>
+<span class="sd">        collection. For this you need to download the collections one by one.</span>
+<span class="sd">    :arg str id_type:</span>
+<span class="sd">        MSigDB provides Gene Symbols (`symbols`) and Entrez Gene IDs</span>
+<span class="sd">        (`entrez`).</span>
+<span class="sd">    :arg bool force_download:</span>
+<span class="sd">        Download even if cache content is available.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="n">registered_email</span> <span class="o">=</span> <span class="n">registered_email</span> <span class="ow">or</span> <span class="n">settings</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">&#39;msigdb_email&#39;</span><span class="p">)</span>
+
+    <span class="k">if</span> <span class="ow">not</span> <span class="n">registered_email</span><span class="p">:</span>
+
+        <span class="n">_log</span><span class="p">(</span>
+            <span class="s1">&#39;To download MSigDB you must provide an email address &#39;</span>
+            <span class="s1">&#39;you have previously registered at &#39;</span>
+            <span class="s1">&#39;`http://software.broadinstitute.org/gsea/register.jsp`. &#39;</span>
+            <span class="s1">&#39;Could not proceed, returning empty dict.&#39;</span>
+        <span class="p">)</span>
+
+        <span class="k">return</span> <span class="p">{}</span>
+
+    <span class="n">organisms</span> <span class="o">=</span> <span class="p">{</span><span class="mi">9606</span><span class="p">:</span> <span class="s1">&#39;Hs&#39;</span><span class="p">,</span> <span class="mi">10090</span><span class="p">:</span> <span class="s1">&#39;Mm&#39;</span><span class="p">}</span>
+    <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">taxonomy</span><span class="o">.</span><span class="n">ensure_ncbi_tax_id</span><span class="p">(</span><span class="n">organism</span><span class="p">)</span>
+    <span class="n">msigdb_org</span> <span class="o">=</span> <span class="n">organisms</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="n">ncbi_tax_id</span><span class="p">,</span> <span class="kc">None</span><span class="p">)</span>
+
+    <span class="k">if</span> <span class="ow">not</span> <span class="n">ncbi_tax_id</span><span class="p">:</span>
+
+        <span class="n">_log</span><span class="p">(</span><span class="sa">f</span><span class="s1">&#39;Could not recognize organism: `</span><span class="si">{</span><span class="n">organism</span><span class="si">}</span><span class="s1">`.&#39;</span><span class="p">)</span>
+
+        <span class="k">return</span> <span class="p">{}</span>
+
+    <span class="n">version</span> <span class="o">=</span> <span class="n">version</span> <span class="ow">or</span> <span class="n">settings</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">&#39;msigdb_version&#39;</span><span class="p">)</span>
+
+    <span class="c1">#http://www.gsea-msigdb.org/gsea/msigdb/download_file.jsp?filePath=/msigdb/release/2022.1.Mm/mh.all.v2022.1.Mm.symbols.gmt</span>
+    <span class="c1">#http://www.gsea-msigdb.org/gsea/msigdb/download_file.jsp?filePath=/msigdb/release/2022.1.Hs/h.all.v2022.1.Hs.symbols.gmt</span>
+
+    <span class="n">url</span> <span class="o">=</span> <span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;msigdb&#39;</span><span class="p">][</span><span class="s1">&#39;url&#39;</span><span class="p">]</span> <span class="o">%</span> <span class="p">(</span>
+        <span class="n">version</span><span class="p">,</span>
+        <span class="n">msigdb_org</span><span class="p">,</span>
+        <span class="n">collection</span><span class="p">,</span>
+        <span class="n">version</span><span class="p">,</span>
+        <span class="n">msigdb_org</span><span class="p">,</span>
+        <span class="n">id_type</span><span class="p">,</span>
+    <span class="p">)</span>
+
+    <span class="n">req_headers</span> <span class="o">=</span> <span class="p">[]</span>
+
+    <span class="c1"># we shouldn&#39;t need this cookie game any more as all files are available</span>
+    <span class="c1"># without any login or cookie from data.broadinstitute.org</span>
+    <span class="n">c_nocall</span> <span class="o">=</span> <span class="n">curl</span><span class="o">.</span><span class="n">Curl</span><span class="p">(</span>
+        <span class="n">url</span><span class="p">,</span>
+        <span class="n">call</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+        <span class="n">process</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+        <span class="n">bypass_url_encoding</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
+    <span class="p">)</span>
+
+    <span class="k">if</span> <span class="p">(</span>
+        <span class="ow">not</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">exists</span><span class="p">(</span><span class="n">c_nocall</span><span class="o">.</span><span class="n">cache_file_name</span><span class="p">)</span> <span class="ow">or</span>
+        <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">getsize</span><span class="p">(</span><span class="n">c_nocall</span><span class="o">.</span><span class="n">cache_file_name</span><span class="p">)</span> <span class="o">==</span> <span class="mi">0</span> <span class="ow">or</span>
+        <span class="n">force_download</span>
+    <span class="p">):</span>
+
+        <span class="n">c_login_1</span> <span class="o">=</span> <span class="n">curl</span><span class="o">.</span><span class="n">Curl</span><span class="p">(</span>
+            <span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;msigdb&#39;</span><span class="p">][</span><span class="s1">&#39;login1&#39;</span><span class="p">],</span>
+            <span class="n">cache</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+            <span class="n">write_cache</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+            <span class="n">process</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+            <span class="n">large</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
+            <span class="n">silent</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
+            <span class="n">post</span> <span class="o">=</span> <span class="p">{</span>
+                <span class="s1">&#39;username&#39;</span><span class="p">:</span> <span class="n">registered_email</span><span class="p">,</span>
+                <span class="s1">&#39;password&#39;</span><span class="p">:</span> <span class="s1">&#39;password&#39;</span><span class="p">,</span>
+            <span class="p">},</span>
+            <span class="n">empty_attempt_again</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+            <span class="n">follow</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+        <span class="p">)</span>
+
+        <span class="n">cookies</span> <span class="o">=</span> <span class="p">{}</span>
+
+        <span class="k">if</span> <span class="nb">hasattr</span><span class="p">(</span><span class="n">c_login_1</span><span class="p">,</span> <span class="s1">&#39;resp_headers&#39;</span><span class="p">):</span>
+
+            <span class="k">for</span> <span class="n">hdr</span> <span class="ow">in</span> <span class="n">c_login_1</span><span class="o">.</span><span class="n">resp_headers</span><span class="p">:</span>
+
+                <span class="k">if</span> <span class="n">hdr</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="sa">b</span><span class="s1">&#39;set-cookie&#39;</span><span class="p">):</span>
+
+                    <span class="n">cookie</span> <span class="o">=</span> <span class="n">hdr</span><span class="o">.</span><span class="n">decode</span><span class="p">(</span><span class="s1">&#39;ascii&#39;</span><span class="p">)</span>
+                    <span class="n">cookie</span> <span class="o">=</span> <span class="n">cookie</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;:&#39;</span><span class="p">,</span> <span class="n">maxsplit</span> <span class="o">=</span> <span class="mi">1</span><span class="p">)[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span>
+                    <span class="n">cookie</span> <span class="o">=</span> <span class="n">cookie</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;;&#39;</span><span class="p">,</span> <span class="n">maxsplit</span> <span class="o">=</span> <span class="mi">1</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span>
+                    <span class="n">cookie</span> <span class="o">=</span> <span class="nb">tuple</span><span class="p">(</span><span class="n">cookie</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;=&#39;</span><span class="p">,</span> <span class="n">maxsplit</span> <span class="o">=</span> <span class="mi">1</span><span class="p">))</span>
+                    <span class="n">_log</span><span class="p">(</span><span class="s1">&#39;msigdb cookie: `</span><span class="si">%s</span><span class="s1">=</span><span class="si">%s</span><span class="s1">`.&#39;</span> <span class="o">%</span> <span class="n">cookie</span><span class="p">)</span>
+                    <span class="n">cookies</span><span class="p">[</span><span class="n">cookie</span><span class="p">[</span><span class="mi">0</span><span class="p">]]</span> <span class="o">=</span> <span class="n">cookie</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span>
+
+        <span class="k">if</span> <span class="ow">not</span> <span class="n">cookies</span><span class="p">:</span>
+
+            <span class="n">_log</span><span class="p">(</span><span class="s1">&#39;msigdb: could not get cookie, returning empty list.&#39;</span><span class="p">)</span>
+
+            <span class="k">return</span> <span class="p">{}</span>
+
+        <span class="n">req_headers</span> <span class="o">=</span> <span class="p">[</span>
+            <span class="s1">&#39;Cookie: </span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="s1">&#39;;&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span>
+                <span class="s1">&#39;</span><span class="si">%s</span><span class="s1">=</span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="n">cookie</span>
+                <span class="k">for</span> <span class="n">cookie</span> <span class="ow">in</span> <span class="n">cookies</span><span class="o">.</span><span class="n">items</span><span class="p">()</span>
+            <span class="p">)</span>
+        <span class="p">]</span>
+
+        <span class="n">c_login_2</span> <span class="o">=</span> <span class="n">curl</span><span class="o">.</span><span class="n">Curl</span><span class="p">(</span>
+            <span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;msigdb&#39;</span><span class="p">][</span><span class="s1">&#39;login2&#39;</span><span class="p">],</span>
+            <span class="n">cache</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+            <span class="n">write_cache</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+            <span class="n">large</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+            <span class="n">silent</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
+            <span class="n">req_headers</span> <span class="o">=</span> <span class="n">req_headers</span><span class="p">,</span>
+            <span class="n">post</span> <span class="o">=</span> <span class="p">{</span>
+                <span class="s1">&#39;j_username&#39;</span><span class="p">:</span> <span class="n">registered_email</span><span class="p">,</span>
+                <span class="s1">&#39;j_password&#39;</span><span class="p">:</span> <span class="s1">&#39;password&#39;</span><span class="p">,</span>
+            <span class="p">},</span>
+            <span class="n">process</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+            <span class="n">empty_attempt_again</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+        <span class="p">)</span>
+
+        <span class="n">jsessionid_1</span> <span class="o">=</span> <span class="s1">&#39;&#39;</span>
+
+        <span class="k">if</span> <span class="nb">hasattr</span><span class="p">(</span><span class="n">c_login_2</span><span class="p">,</span> <span class="s1">&#39;resp_headers&#39;</span><span class="p">):</span>
+
+            <span class="k">for</span> <span class="n">hdr</span> <span class="ow">in</span> <span class="n">c_login_2</span><span class="o">.</span><span class="n">resp_headers</span><span class="p">:</span>
+
+                <span class="k">if</span> <span class="n">hdr</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="sa">b</span><span class="s1">&#39;set-cookie&#39;</span><span class="p">):</span>
+
+                    <span class="n">jsessionid_1</span> <span class="o">=</span> <span class="n">hdr</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="sa">b</span><span class="s1">&#39;:&#39;</span><span class="p">)[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="sa">b</span><span class="s1">&#39;;&#39;</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span>
+                    <span class="n">jsessionid_1</span> <span class="o">=</span> <span class="n">jsessionid_1</span><span class="o">.</span><span class="n">decode</span><span class="p">(</span><span class="s1">&#39;ascii&#39;</span><span class="p">)</span>
+
+            <span class="n">_log</span><span class="p">(</span>
+                <span class="s1">&#39;msigdb: logged in with email `</span><span class="si">%s</span><span class="s1">`, &#39;</span>
+                <span class="s1">&#39;new cookie obtained: `</span><span class="si">%s</span><span class="s1">`.&#39;</span> <span class="o">%</span> <span class="p">(</span>
+                    <span class="n">registered_email</span><span class="p">,</span>
+                    <span class="n">jsessionid_1</span>
+                <span class="p">)</span>
+            <span class="p">)</span>
+
+        <span class="n">_log</span><span class="p">(</span><span class="s1">&#39;msigdb cookies for upcoming request: </span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="n">req_headers</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span>
+
+    <span class="n">c</span> <span class="o">=</span> <span class="n">curl</span><span class="o">.</span><span class="n">Curl</span><span class="p">(</span>
+        <span class="n">url</span><span class="p">,</span>
+        <span class="n">req_headers</span> <span class="o">=</span> <span class="n">req_headers</span><span class="p">,</span>
+        <span class="n">silent</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+        <span class="n">large</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
+        <span class="n">bypass_url_encoding</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
+        <span class="n">cache</span> <span class="o">=</span> <span class="ow">not</span> <span class="n">force_download</span><span class="p">,</span>
+    <span class="p">)</span>
+
+    <span class="n">result</span> <span class="o">=</span> <span class="p">{}</span>
+
+    <span class="k">for</span> <span class="n">gset</span> <span class="ow">in</span> <span class="n">c</span><span class="o">.</span><span class="n">result</span><span class="p">:</span>
+
+        <span class="n">gset</span> <span class="o">=</span> <span class="n">gset</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\t</span><span class="s1">&#39;</span><span class="p">)</span>
+
+        <span class="n">result</span><span class="p">[</span><span class="n">gset</span><span class="p">[</span><span class="mi">0</span><span class="p">]]</span> <span class="o">=</span> <span class="nb">set</span><span class="p">(</span><span class="n">gset</span><span class="p">[</span><span class="mi">2</span><span class="p">:])</span>
+
+    <span class="k">return</span> <span class="n">result</span></div>
+
+
+
+<div class="viewcode-block" id="msigdb_download_collections">
+<a class="viewcode-back" href="../../../api/pypath.inputs.msigdb.msigdb_download_collections.html#pypath.inputs.msigdb.msigdb_download_collections">[docs]</a>
+<span class="k">def</span> <span class="nf">msigdb_download_collections</span><span class="p">(</span>
+        <span class="n">registered_email</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+        <span class="n">only_collections</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+        <span class="n">exclude</span> <span class="o">=</span> <span class="p">(</span><span class="s1">&#39;c5&#39;</span><span class="p">,</span> <span class="s1">&#39;m5&#39;</span><span class="p">),</span>
+        <span class="n">id_type</span> <span class="o">=</span> <span class="s1">&#39;symbols&#39;</span><span class="p">,</span>
+        <span class="n">organism</span> <span class="o">=</span> <span class="s1">&#39;human&#39;</span><span class="p">,</span>
+        <span class="n">version</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+    <span class="p">):</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Downloads all or some MSigDB gene set collections.</span>
+<span class="sd">    Returns a dict of dicts where upper level keys are collections while</span>
+<span class="sd">    lower level keys are geneset names and values are molecular identifiers.</span>
+
+<span class="sd">    :arg str,NoneType registered_email:</span>
+<span class="sd">        An email address registered at MSigDB. If `None` the `msigdb_email`</span>
+<span class="sd">        from ``pypath.settings`` will be used.</span>
+<span class="sd">    :arg set,NoneType only_collections:</span>
+<span class="sd">        Limit the annotations only to these collections. For available</span>
+<span class="sd">        collections e.g. ``{&#39;h.all&#39;, &#39;c2.cgp&#39;}`` refer to the MSigDB webpage:</span>
+<span class="sd">        http://software.broadinstitute.org/gsea/downloads.jsp#msigdb</span>
+<span class="sd">    :arg tuple exclude:</span>
+<span class="sd">        Exclude the collections having their name starting with any of the</span>
+<span class="sd">        strings in this tuple. By default `c5` and `m5` (Gene Ontology and</span>
+<span class="sd">        Human/Mouse Phenotype Ontology) is excluded.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="n">collection_data</span> <span class="o">=</span> <span class="p">{}</span>
+
+    <span class="n">organisms</span> <span class="o">=</span> <span class="p">{</span><span class="mi">9606</span><span class="p">:</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">10090</span><span class="p">:</span> <span class="mi">1</span><span class="p">}</span>
+    <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">taxonomy</span><span class="o">.</span><span class="n">ensure_ncbi_tax_id</span><span class="p">(</span><span class="n">organism</span><span class="p">)</span>
+    <span class="n">idx</span> <span class="o">=</span> <span class="n">organisms</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="n">ncbi_tax_id</span><span class="p">,</span> <span class="kc">None</span><span class="p">)</span>
+
+    <span class="k">for</span> <span class="n">collection</span><span class="p">,</span> <span class="n">labels</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="n">ALL_COLLECTIONS</span><span class="p">):</span>
+
+        <span class="n">label</span> <span class="o">=</span> <span class="n">labels</span><span class="p">[</span><span class="n">idx</span><span class="p">]</span>
+
+        <span class="k">if</span> <span class="p">(</span>
+            <span class="ow">not</span> <span class="n">label</span> <span class="ow">or</span>
+            <span class="p">(</span>
+                <span class="n">only_collections</span> <span class="ow">and</span>
+                <span class="n">label</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">only_collections</span>
+            <span class="p">)</span> <span class="ow">or</span>
+            <span class="nb">any</span><span class="p">(</span><span class="n">label</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="n">ex</span><span class="p">)</span> <span class="k">for</span> <span class="n">ex</span> <span class="ow">in</span> <span class="n">exclude</span><span class="p">)</span>
+        <span class="p">):</span>
+
+            <span class="k">continue</span>
+
+        <span class="n">_log</span><span class="p">(</span>
+            <span class="s1">&#39;MSigDB: downloading collection `</span><span class="si">%s</span><span class="s1">` (</span><span class="si">%s</span><span class="s1">).&#39;</span> <span class="o">%</span> <span class="p">(</span><span class="n">collection</span><span class="p">,</span> <span class="n">label</span><span class="p">)</span>
+        <span class="p">)</span>
+
+        <span class="n">collection_data</span><span class="p">[(</span><span class="n">collection</span><span class="p">,</span> <span class="n">label</span><span class="p">)]</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="n">msigdb_download</span><span class="p">(</span>
+                <span class="n">registered_email</span> <span class="o">=</span> <span class="n">registered_email</span><span class="p">,</span>
+                <span class="n">collection</span> <span class="o">=</span> <span class="n">label</span><span class="p">,</span>
+                <span class="n">id_type</span> <span class="o">=</span> <span class="n">id_type</span><span class="p">,</span>
+                <span class="n">organism</span> <span class="o">=</span> <span class="n">organism</span><span class="p">,</span>
+                <span class="n">version</span> <span class="o">=</span> <span class="n">version</span><span class="p">,</span>
+            <span class="p">)</span>
+        <span class="p">)</span>
+
+    <span class="k">return</span> <span class="n">collection_data</span></div>
+
+
+
+<div class="viewcode-block" id="msigdb_annotations">
+<a class="viewcode-back" href="../../../api/pypath.inputs.msigdb.msigdb_annotations.html#pypath.inputs.msigdb.msigdb_annotations">[docs]</a>
+<span class="k">def</span> <span class="nf">msigdb_annotations</span><span class="p">(</span>
+        <span class="n">registered_email</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+        <span class="n">only_collections</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+        <span class="n">exclude</span> <span class="o">=</span> <span class="p">(</span><span class="s1">&#39;c5&#39;</span><span class="p">,</span> <span class="s1">&#39;m5&#39;</span><span class="p">),</span>
+        <span class="n">organism</span> <span class="o">=</span> <span class="s1">&#39;human&#39;</span><span class="p">,</span>
+        <span class="n">version</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+    <span class="p">):</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Downloads all or some MSigDB gene set collections and processes them</span>
+<span class="sd">    to an annotation type dictionary.</span>
+
+<span class="sd">    :arg str,NoneType registered_email:</span>
+<span class="sd">        An email address registered at MSigDB. If `None` the `msigdb_email`</span>
+<span class="sd">        from ``pypath.settings`` will be used.</span>
+<span class="sd">    :arg set,NoneType only_collections:</span>
+<span class="sd">        Limit the annotations only to these collections. For available</span>
+<span class="sd">        collections e.g. ``{&#39;h.all&#39;, &#39;c2cgp&#39;}`` refer to the MSigDB webpage:</span>
+<span class="sd">        http://software.broadinstitute.org/gsea/downloads.jsp#msigdb</span>
+<span class="sd">    :arg tuple exclude:</span>
+<span class="sd">        Exclude the collections having their name starting with any of the</span>
+<span class="sd">        strings in this tuple. By default `c5` (Gene Ontology) is excluded.</span>
+
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="n">MsigdbAnnotation</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">namedtuple</span><span class="p">(</span>
+        <span class="s1">&#39;MsigdbAnnotation&#39;</span><span class="p">,</span>
+        <span class="p">[</span>
+            <span class="s1">&#39;collection&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;geneset&#39;</span><span class="p">,</span>
+        <span class="p">],</span>
+    <span class="p">)</span>
+
+
+    <span class="n">annotations</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">defaultdict</span><span class="p">(</span><span class="nb">set</span><span class="p">)</span>
+
+    <span class="n">collection_data</span> <span class="o">=</span> <span class="n">msigdb_download_collections</span><span class="p">(</span>
+        <span class="n">registered_email</span> <span class="o">=</span> <span class="n">registered_email</span><span class="p">,</span>
+        <span class="n">only_collections</span> <span class="o">=</span> <span class="n">only_collections</span><span class="p">,</span>
+        <span class="n">exclude</span> <span class="o">=</span> <span class="n">exclude</span><span class="p">,</span>
+        <span class="n">organism</span> <span class="o">=</span> <span class="n">organism</span><span class="p">,</span>
+        <span class="n">version</span> <span class="o">=</span> <span class="n">version</span><span class="p">,</span>
+    <span class="p">)</span>
+
+    <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">taxonomy</span><span class="o">.</span><span class="n">ensure_ncbi_tax_id</span><span class="p">(</span><span class="n">organism</span><span class="p">)</span>
+
+    <span class="k">for</span> <span class="p">(</span><span class="n">collection</span><span class="p">,</span> <span class="n">label</span><span class="p">),</span> <span class="n">genesets</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="n">collection_data</span><span class="p">):</span>
+
+        <span class="k">for</span> <span class="n">geneset</span><span class="p">,</span> <span class="n">genesymbols</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="n">genesets</span><span class="p">):</span>
+
+            <span class="n">this_annot</span> <span class="o">=</span> <span class="n">MsigdbAnnotation</span><span class="p">(</span>
+                <span class="n">collection</span> <span class="o">=</span> <span class="n">collection</span><span class="p">,</span>
+                <span class="n">geneset</span> <span class="o">=</span> <span class="n">geneset</span><span class="p">,</span>
+            <span class="p">)</span>
+
+            <span class="k">for</span> <span class="n">uniprot</span> <span class="ow">in</span> <span class="n">mapping</span><span class="o">.</span><span class="n">map_names</span><span class="p">(</span>
+                <span class="n">genesymbols</span><span class="p">,</span>
+                <span class="s1">&#39;genesymbol&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;uniprot&#39;</span><span class="p">,</span>
+                <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">,</span>
+            <span class="p">):</span>
+
+                <span class="n">annotations</span><span class="p">[</span><span class="n">uniprot</span><span class="p">]</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">this_annot</span><span class="p">)</span>
+
+    <span class="k">return</span> <span class="nb">dict</span><span class="p">(</span><span class="n">annotations</span><span class="p">)</span></div>
+
+</pre></div>
+
+                </article>
+              
+              
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+              
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diff --git a/_modules/pypath/inputs/netpath.html b/_modules/pypath/inputs/netpath.html
new file mode 100644
index 000000000..f37828f5a
--- /dev/null
+++ b/_modules/pypath/inputs/netpath.html
@@ -0,0 +1,835 @@
+
+<!DOCTYPE html>
+
+
+<html lang="en" data-content_root="../../../" >
+
+  <head>
+    <meta charset="utf-8" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
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+  
+  
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+  <script data-cfasync="false">
+    document.documentElement.dataset.mode = localStorage.getItem("mode") || "";
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+                  
+  <h1>Source code for pypath.inputs.netpath</h1><div class="highlight"><pre>
+<span></span><span class="ch">#!/usr/bin/env python</span>
+<span class="c1"># -*- coding: utf-8 -*-</span>
+
+<span class="c1">#</span>
+<span class="c1">#  This file is part of the `pypath` python module</span>
+<span class="c1">#</span>
+<span class="c1">#  Copyright 2014-2023</span>
+<span class="c1">#  EMBL, EMBL-EBI, Uniklinik RWTH Aachen, Heidelberg University</span>
+<span class="c1">#</span>
+<span class="c1">#  Authors: see the file `README.rst`</span>
+<span class="c1">#  Contact: Dénes Türei (turei.denes@gmail.com)</span>
+<span class="c1">#</span>
+<span class="c1">#  Distributed under the GPLv3 License.</span>
+<span class="c1">#  See accompanying file LICENSE.txt or copy at</span>
+<span class="c1">#      https://www.gnu.org/licenses/gpl-3.0.html</span>
+<span class="c1">#</span>
+<span class="c1">#  Website: https://pypath.omnipathdb.org/</span>
+<span class="c1">#</span>
+
+<span class="kn">from</span> <span class="nn">future.utils</span> <span class="kn">import</span> <span class="n">iteritems</span>
+
+<span class="kn">import</span> <span class="nn">re</span>
+<span class="kn">import</span> <span class="nn">collections</span>
+
+<span class="kn">import</span> <span class="nn">bs4</span>
+<span class="kn">import</span> <span class="nn">xml.etree.cElementTree</span> <span class="k">as</span> <span class="nn">ET</span>
+
+<span class="kn">import</span> <span class="nn">pypath.share.curl</span> <span class="k">as</span> <span class="nn">curl</span>
+<span class="kn">import</span> <span class="nn">pypath.resources.urls</span> <span class="k">as</span> <span class="nn">urls</span>
+<span class="kn">import</span> <span class="nn">pypath.utils.mapping</span> <span class="k">as</span> <span class="nn">mapping</span>
+
+
+<div class="viewcode-block" id="netpath_interactions">
+<a class="viewcode-back" href="../../../api/pypath.inputs.netpath.netpath_interactions.html#pypath.inputs.netpath.netpath_interactions">[docs]</a>
+<span class="k">def</span> <span class="nf">netpath_interactions</span><span class="p">():</span>
+
+    <span class="n">result</span> <span class="o">=</span> <span class="p">[]</span>
+    <span class="n">repwnum</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">compile</span><span class="p">(</span><span class="sa">r</span><span class="s1">&#39;NetPath_([0-9]+)_&#39;</span><span class="p">)</span>
+    <span class="n">mi</span> <span class="o">=</span> <span class="s1">&#39;{net:sf:psidev:mi}&#39;</span>
+    <span class="n">url</span> <span class="o">=</span> <span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;netpath_psimi&#39;</span><span class="p">][</span><span class="s1">&#39;url&#39;</span><span class="p">]</span>
+    <span class="n">c</span> <span class="o">=</span> <span class="n">curl</span><span class="o">.</span><span class="n">Curl</span><span class="p">(</span><span class="n">url</span><span class="p">,</span> <span class="n">silent</span> <span class="o">=</span> <span class="kc">False</span><span class="p">)</span>
+
+    <span class="n">data</span> <span class="o">=</span> <span class="n">c</span><span class="o">.</span><span class="n">result</span>
+    <span class="n">data</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">([(</span><span class="n">k</span><span class="p">,</span> <span class="n">v</span><span class="p">)</span> <span class="k">for</span> <span class="n">k</span><span class="p">,</span> <span class="n">v</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="n">data</span><span class="p">)</span> <span class="k">if</span> <span class="n">k</span><span class="o">.</span><span class="n">endswith</span><span class="p">(</span><span class="s1">&#39;xml&#39;</span><span class="p">)])</span>
+    <span class="n">pwnames</span> <span class="o">=</span> <span class="n">netpath_names</span><span class="p">()</span>
+
+    <span class="k">for</span> <span class="n">pwfile</span><span class="p">,</span> <span class="n">rawxml</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="n">data</span><span class="p">):</span>
+
+        <span class="k">try</span><span class="p">:</span>
+            <span class="n">pwnum</span> <span class="o">=</span> <span class="n">repwnum</span><span class="o">.</span><span class="n">findall</span><span class="p">(</span><span class="n">pwfile</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span>
+
+        <span class="k">except</span><span class="p">:</span>
+            <span class="n">sys</span><span class="o">.</span><span class="n">stdout</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s1">&#39;Error at processing file:</span><span class="se">\n</span><span class="s1">&#39;</span><span class="p">)</span>
+            <span class="n">sys</span><span class="o">.</span><span class="n">stdout</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="n">pwfile</span><span class="p">)</span>
+            <span class="n">sys</span><span class="o">.</span><span class="n">stdout</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\n</span><span class="s1">&#39;</span><span class="p">)</span>
+            <span class="n">sys</span><span class="o">.</span><span class="n">stdout</span><span class="o">.</span><span class="n">flush</span><span class="p">()</span>
+
+        <span class="n">pwname</span> <span class="o">=</span> <span class="n">pwnames</span><span class="p">[</span><span class="n">pwnum</span><span class="p">]</span>
+        <span class="n">root</span> <span class="o">=</span> <span class="n">ET</span><span class="o">.</span><span class="n">fromstring</span><span class="p">(</span><span class="n">rawxml</span><span class="p">)</span>
+
+        <span class="k">for</span> <span class="n">e</span> <span class="ow">in</span> <span class="n">root</span><span class="o">.</span><span class="n">findall</span><span class="p">(</span><span class="n">mi</span> <span class="o">+</span> <span class="s1">&#39;entry&#39;</span><span class="p">):</span>
+
+            <span class="n">thisInt</span> <span class="o">=</span> <span class="p">()</span>
+            <span class="n">db</span> <span class="o">=</span> <span class="p">[</span>
+                <span class="n">pr</span><span class="o">.</span><span class="n">find</span><span class="p">(</span><span class="n">mi</span> <span class="o">+</span> <span class="s1">&#39;primaryRef&#39;</span><span class="p">)</span><span class="o">.</span><span class="n">attrib</span><span class="p">[</span><span class="s1">&#39;db&#39;</span><span class="p">]</span>
+                <span class="k">for</span> <span class="n">pr</span> <span class="ow">in</span> <span class="n">e</span><span class="o">.</span><span class="n">find</span><span class="p">(</span><span class="n">mi</span> <span class="o">+</span> <span class="s1">&#39;source&#39;</span><span class="p">)</span><span class="o">.</span><span class="n">findall</span><span class="p">(</span><span class="n">mi</span> <span class="o">+</span> <span class="s1">&#39;xref&#39;</span><span class="p">)</span>
+            <span class="p">]</span>
+            <span class="n">refs</span> <span class="o">=</span> <span class="p">[]</span>
+            <span class="n">mets</span> <span class="o">=</span> <span class="p">[]</span>
+
+            <span class="k">for</span> <span class="n">ex</span> <span class="ow">in</span> <span class="n">e</span><span class="o">.</span><span class="n">find</span><span class="p">(</span><span class="n">mi</span> <span class="o">+</span> <span class="s1">&#39;experimentList&#39;</span><span class="p">)</span><span class="o">.</span><span class="n">findall</span><span class="p">(</span>
+                    <span class="n">mi</span> <span class="o">+</span> <span class="s1">&#39;experimentDescription&#39;</span><span class="p">):</span>
+                <span class="k">for</span> <span class="n">pm</span> <span class="ow">in</span> <span class="n">ex</span><span class="o">.</span><span class="n">find</span><span class="p">(</span><span class="n">mi</span> <span class="o">+</span> <span class="s1">&#39;bibref&#39;</span><span class="p">)</span><span class="o">.</span><span class="n">iter</span><span class="p">(</span><span class="n">mi</span> <span class="o">+</span> <span class="s1">&#39;primaryRef&#39;</span><span class="p">):</span>
+                    <span class="k">if</span> <span class="n">pm</span><span class="o">.</span><span class="n">attrib</span><span class="p">[</span><span class="s1">&#39;db&#39;</span><span class="p">]</span> <span class="o">==</span> <span class="s1">&#39;pubmed&#39;</span><span class="p">:</span>
+                        <span class="n">refs</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">pm</span><span class="o">.</span><span class="n">attrib</span><span class="p">[</span><span class="s1">&#39;id&#39;</span><span class="p">])</span>
+
+                <span class="k">for</span> <span class="n">me</span> <span class="ow">in</span> <span class="n">ex</span><span class="o">.</span><span class="n">find</span><span class="p">(</span><span class="n">mi</span> <span class="o">+</span> <span class="s1">&#39;interactionDetectionMethod&#39;</span><span class="p">)</span><span class="o">.</span>\
+                        <span class="nb">iter</span><span class="p">(</span><span class="n">mi</span> <span class="o">+</span> <span class="s1">&#39;shortLabel&#39;</span><span class="p">):</span>
+                    <span class="n">mets</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">me</span><span class="o">.</span><span class="n">text</span><span class="p">)</span>
+
+            <span class="n">mols</span> <span class="o">=</span> <span class="p">{}</span>
+
+            <span class="k">for</span> <span class="n">mo</span> <span class="ow">in</span> <span class="n">e</span><span class="o">.</span><span class="n">find</span><span class="p">(</span><span class="n">mi</span> <span class="o">+</span> <span class="s1">&#39;interactorList&#39;</span><span class="p">)</span><span class="o">.</span><span class="n">findall</span><span class="p">(</span><span class="n">mi</span> <span class="o">+</span> <span class="s1">&#39;interactor&#39;</span><span class="p">):</span>
+                <span class="n">iid</span> <span class="o">=</span> <span class="n">mo</span><span class="o">.</span><span class="n">attrib</span><span class="p">[</span><span class="s1">&#39;id&#39;</span><span class="p">]</span>
+                <span class="n">name</span> <span class="o">=</span> <span class="n">mo</span><span class="o">.</span><span class="n">find</span><span class="p">(</span><span class="n">mi</span> <span class="o">+</span> <span class="s1">&#39;names&#39;</span><span class="p">)</span><span class="o">.</span><span class="n">find</span><span class="p">(</span><span class="n">mi</span> <span class="o">+</span> <span class="s1">&#39;shortLabel&#39;</span><span class="p">)</span><span class="o">.</span><span class="n">text</span>
+                <span class="n">entrez</span> <span class="o">=</span> <span class="s1">&#39;&#39;</span>
+
+                <span class="k">if</span> <span class="n">mo</span><span class="o">.</span><span class="n">find</span><span class="p">(</span><span class="n">mi</span> <span class="o">+</span> <span class="s1">&#39;xref&#39;</span><span class="p">)</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
+                    <span class="n">entrez</span> <span class="o">=</span> <span class="s1">&#39;;&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">([</span>
+                        <span class="n">ac</span><span class="o">.</span><span class="n">attrib</span><span class="p">[</span><span class="s1">&#39;id&#39;</span><span class="p">]</span>
+                        <span class="k">for</span> <span class="n">ac</span> <span class="ow">in</span> <span class="n">mo</span><span class="o">.</span><span class="n">find</span><span class="p">(</span><span class="n">mi</span> <span class="o">+</span> <span class="s1">&#39;xref&#39;</span><span class="p">)</span>
+                        <span class="o">.</span><span class="n">findall</span><span class="p">(</span><span class="n">mi</span> <span class="o">+</span> <span class="s1">&#39;secondaryRef&#39;</span><span class="p">)</span>
+                        <span class="k">if</span> <span class="n">ac</span><span class="o">.</span><span class="n">attrib</span><span class="p">[</span><span class="s1">&#39;db&#39;</span><span class="p">]</span> <span class="o">==</span> <span class="s1">&#39;Entrez gene&#39;</span>
+                    <span class="p">])</span>
+
+                <span class="n">mols</span><span class="p">[</span><span class="n">iid</span><span class="p">]</span> <span class="o">=</span> <span class="p">(</span><span class="n">name</span><span class="p">,</span> <span class="n">entrez</span><span class="p">)</span>
+
+            <span class="n">theInt</span> <span class="o">=</span> <span class="n">e</span><span class="o">.</span><span class="n">find</span><span class="p">(</span><span class="n">mi</span> <span class="o">+</span> <span class="s1">&#39;interactionList&#39;</span><span class="p">)</span><span class="o">.</span><span class="n">find</span><span class="p">(</span><span class="n">mi</span> <span class="o">+</span> <span class="s1">&#39;interaction&#39;</span><span class="p">)</span>
+
+            <span class="k">for</span> <span class="n">p</span> <span class="ow">in</span> <span class="n">theInt</span><span class="o">.</span><span class="n">find</span><span class="p">(</span><span class="n">mi</span> <span class="o">+</span> <span class="s1">&#39;participantList&#39;</span><span class="p">)</span><span class="o">.</span><span class="n">findall</span><span class="p">(</span>
+                    <span class="n">mi</span> <span class="o">+</span> <span class="s1">&#39;participant&#39;</span><span class="p">):</span>
+                <span class="n">pid</span> <span class="o">=</span> <span class="n">p</span><span class="o">.</span><span class="n">find</span><span class="p">(</span><span class="n">mi</span> <span class="o">+</span> <span class="s1">&#39;interactorRef&#39;</span><span class="p">)</span><span class="o">.</span><span class="n">text</span>
+                <span class="n">roles</span> <span class="o">=</span> <span class="s1">&#39;&#39;</span>
+
+                <span class="k">if</span> <span class="n">p</span><span class="o">.</span><span class="n">find</span><span class="p">(</span><span class="n">mi</span> <span class="o">+</span> <span class="s1">&#39;experimentalRoleList&#39;</span><span class="p">)</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
+                    <span class="n">roles</span> <span class="o">=</span> <span class="s1">&#39;;&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">([</span>
+                        <span class="n">rl</span><span class="o">.</span><span class="n">find</span><span class="p">(</span><span class="n">mi</span> <span class="o">+</span> <span class="s1">&#39;names&#39;</span><span class="p">)</span><span class="o">.</span><span class="n">find</span><span class="p">(</span><span class="n">mi</span> <span class="o">+</span> <span class="s1">&#39;shortLabel&#39;</span><span class="p">)</span><span class="o">.</span><span class="n">text</span>
+                        <span class="k">for</span> <span class="n">rl</span> <span class="ow">in</span> <span class="n">p</span><span class="o">.</span><span class="n">find</span><span class="p">(</span><span class="n">mi</span> <span class="o">+</span> <span class="s1">&#39;experimentalRoleList&#39;</span><span class="p">)</span>
+                        <span class="o">.</span><span class="n">findall</span><span class="p">(</span><span class="n">mi</span> <span class="o">+</span> <span class="s1">&#39;experimentalRole&#39;</span><span class="p">)</span>
+                    <span class="p">])</span>
+
+                <span class="n">mols</span><span class="p">[</span><span class="n">pid</span><span class="p">]</span> <span class="o">+=</span> <span class="p">(</span><span class="n">roles</span><span class="p">,</span> <span class="p">)</span>
+
+            <span class="n">intTyp</span> <span class="o">=</span> <span class="p">(</span>
+                <span class="n">theInt</span><span class="o">.</span><span class="n">find</span><span class="p">(</span>
+                    <span class="n">mi</span> <span class="o">+</span> <span class="s1">&#39;interactionType&#39;</span>
+                <span class="p">)</span><span class="o">.</span><span class="n">find</span><span class="p">(</span>
+                    <span class="n">mi</span> <span class="o">+</span> <span class="s1">&#39;names&#39;</span>
+                <span class="p">)</span><span class="o">.</span><span class="n">find</span><span class="p">(</span>
+                    <span class="n">mi</span> <span class="o">+</span> <span class="s1">&#39;shortLabel&#39;</span>
+                <span class="p">)</span><span class="o">.</span><span class="n">text</span>
+            <span class="p">)</span>
+            <span class="n">molkeys</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="n">mols</span><span class="o">.</span><span class="n">keys</span><span class="p">())</span>
+
+            <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="nb">len</span><span class="p">(</span><span class="n">mols</span><span class="p">)</span> <span class="o">-</span> <span class="mi">1</span><span class="p">):</span>
+
+                <span class="k">for</span> <span class="n">j</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">i</span><span class="p">,</span> <span class="nb">len</span><span class="p">(</span><span class="n">mols</span><span class="p">)):</span>
+
+                    <span class="n">A</span> <span class="o">=</span> <span class="n">mols</span><span class="p">[</span><span class="n">molkeys</span><span class="p">[</span><span class="n">i</span><span class="p">]][</span><span class="mi">0</span><span class="p">:</span><span class="mi">2</span><span class="p">]</span>
+                    <span class="n">B</span> <span class="o">=</span> <span class="n">mols</span><span class="p">[</span><span class="n">molkeys</span><span class="p">[</span><span class="n">j</span><span class="p">]][</span><span class="mi">0</span><span class="p">:</span><span class="mi">2</span><span class="p">]</span>
+                    <span class="n">result</span><span class="o">.</span><span class="n">append</span><span class="p">(</span>
+                        <span class="nb">list</span><span class="p">(</span><span class="n">A</span><span class="p">)</span> <span class="o">+</span>
+                        <span class="nb">list</span><span class="p">(</span><span class="n">B</span><span class="p">)</span> <span class="o">+</span>
+                        <span class="p">[</span>
+                            <span class="s1">&#39;;&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">refs</span><span class="p">),</span>
+                            <span class="s1">&#39;;&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">mets</span><span class="p">),</span>
+                            <span class="n">intTyp</span><span class="p">,</span>
+                            <span class="n">pwname</span>
+                        <span class="p">]</span>
+                    <span class="p">)</span>
+
+    <span class="k">return</span> <span class="n">result</span></div>
+
+
+
+
+<div class="viewcode-block" id="netpath_names">
+<a class="viewcode-back" href="../../../api/pypath.inputs.netpath.netpath_names.html#pypath.inputs.netpath.netpath_names">[docs]</a>
+<span class="k">def</span> <span class="nf">netpath_names</span><span class="p">():</span>
+
+    <span class="n">repwnum</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">compile</span><span class="p">(</span><span class="sa">r</span><span class="s1">&#39;_([0-9]+)$&#39;</span><span class="p">)</span>
+    <span class="n">result</span> <span class="o">=</span> <span class="p">{}</span>
+    <span class="n">url</span> <span class="o">=</span> <span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;netpath_names&#39;</span><span class="p">][</span><span class="s1">&#39;url&#39;</span><span class="p">]</span>
+    <span class="n">c</span> <span class="o">=</span> <span class="n">curl</span><span class="o">.</span><span class="n">Curl</span><span class="p">(</span><span class="n">url</span><span class="p">,</span> <span class="n">silent</span> <span class="o">=</span> <span class="kc">False</span><span class="p">)</span>
+    <span class="n">html</span> <span class="o">=</span> <span class="n">c</span><span class="o">.</span><span class="n">result</span>
+    <span class="n">soup</span> <span class="o">=</span> <span class="n">bs4</span><span class="o">.</span><span class="n">BeautifulSoup</span><span class="p">(</span><span class="n">html</span><span class="p">,</span> <span class="s1">&#39;html.parser&#39;</span><span class="p">)</span>
+
+    <span class="k">for</span> <span class="n">a</span> <span class="ow">in</span> <span class="n">soup</span><span class="o">.</span><span class="n">find_all</span><span class="p">(</span><span class="s1">&#39;a&#39;</span><span class="p">):</span>
+
+        <span class="k">if</span> <span class="n">a</span><span class="o">.</span><span class="n">attrs</span><span class="p">[</span><span class="s1">&#39;href&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s1">&#39;pathways&#39;</span><span class="p">):</span>
+
+            <span class="n">num</span> <span class="o">=</span> <span class="n">repwnum</span><span class="o">.</span><span class="n">findall</span><span class="p">(</span><span class="n">a</span><span class="o">.</span><span class="n">attrs</span><span class="p">[</span><span class="s1">&#39;href&#39;</span><span class="p">])[</span><span class="mi">0</span><span class="p">]</span>
+            <span class="n">name</span> <span class="o">=</span> <span class="n">a</span><span class="o">.</span><span class="n">text</span>
+            <span class="n">result</span><span class="p">[</span><span class="n">num</span><span class="p">]</span> <span class="o">=</span> <span class="n">name</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span>
+
+    <span class="k">return</span> <span class="n">result</span></div>
+
+
+
+<div class="viewcode-block" id="netpath_pathway_annotations">
+<a class="viewcode-back" href="../../../api/pypath.inputs.netpath.netpath_pathway_annotations.html#pypath.inputs.netpath.netpath_pathway_annotations">[docs]</a>
+<span class="k">def</span> <span class="nf">netpath_pathway_annotations</span><span class="p">():</span>
+
+    <span class="n">NetpathPathway</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">namedtuple</span><span class="p">(</span>
+        <span class="s1">&#39;NetpathPathway&#39;</span><span class="p">,</span>
+        <span class="p">[</span><span class="s1">&#39;pathway&#39;</span><span class="p">],</span>
+    <span class="p">)</span>
+
+    <span class="n">result</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">defaultdict</span><span class="p">(</span><span class="nb">set</span><span class="p">)</span>
+
+    <span class="n">url_template</span> <span class="o">=</span> <span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;netpath_pw&#39;</span><span class="p">][</span><span class="s1">&#39;url&#39;</span><span class="p">]</span>
+
+    <span class="n">url_main</span> <span class="o">=</span> <span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;netpath_pw&#39;</span><span class="p">][</span><span class="s1">&#39;mainpage&#39;</span><span class="p">]</span>
+    <span class="n">c</span> <span class="o">=</span> <span class="n">curl</span><span class="o">.</span><span class="n">Curl</span><span class="p">(</span><span class="n">url_main</span><span class="p">,</span> <span class="n">cache</span> <span class="o">=</span> <span class="kc">False</span><span class="p">)</span>
+    <span class="n">cookie</span> <span class="o">=</span> <span class="p">[</span>
+        <span class="n">h</span><span class="o">.</span><span class="n">decode</span><span class="p">()</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;:&#39;</span><span class="p">)[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;;&#39;</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span>
+        <span class="k">for</span> <span class="n">h</span> <span class="ow">in</span> <span class="n">c</span><span class="o">.</span><span class="n">resp_headers</span>
+        <span class="k">if</span> <span class="n">h</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="sa">b</span><span class="s1">&#39;Set-Cookie&#39;</span><span class="p">)</span>
+    <span class="p">]</span>
+    <span class="n">cookie_hdr</span> <span class="o">=</span> <span class="p">[</span><span class="s1">&#39;Cookie: </span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="s1">&#39;; &#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">cookie</span><span class="p">)]</span>
+
+    <span class="n">pathway_ids</span> <span class="o">=</span> <span class="n">netpath_names</span><span class="p">()</span>
+
+    <span class="k">for</span> <span class="n">_id</span><span class="p">,</span> <span class="n">pathway</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="n">pathway_ids</span><span class="p">):</span>
+
+        <span class="n">url</span> <span class="o">=</span> <span class="n">url_template</span> <span class="o">%</span> <span class="nb">int</span><span class="p">(</span><span class="n">_id</span><span class="p">)</span>
+        <span class="n">c</span> <span class="o">=</span> <span class="n">curl</span><span class="o">.</span><span class="n">Curl</span><span class="p">(</span>
+            <span class="n">url</span><span class="p">,</span>
+            <span class="n">req_headers</span> <span class="o">=</span> <span class="n">cookie_hdr</span><span class="p">,</span>
+            <span class="n">silent</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+            <span class="n">encoding</span> <span class="o">=</span> <span class="s1">&#39;iso-8859-1&#39;</span><span class="p">,</span>
+        <span class="p">)</span>
+
+        <span class="n">soup</span> <span class="o">=</span> <span class="n">bs4</span><span class="o">.</span><span class="n">BeautifulSoup</span><span class="p">(</span><span class="n">c</span><span class="o">.</span><span class="n">result</span><span class="p">,</span> <span class="s1">&#39;html.parser&#39;</span><span class="p">)</span>
+
+        <span class="k">for</span> <span class="n">tbl</span> <span class="ow">in</span> <span class="n">soup</span><span class="o">.</span><span class="n">find_all</span><span class="p">(</span><span class="s1">&#39;table&#39;</span><span class="p">):</span>
+            <span class="n">hdr</span> <span class="o">=</span> <span class="n">tbl</span><span class="o">.</span><span class="n">find</span><span class="p">(</span><span class="s1">&#39;td&#39;</span><span class="p">,</span> <span class="p">{</span><span class="s1">&#39;class&#39;</span><span class="p">:</span> <span class="s1">&#39;barhead&#39;</span><span class="p">})</span>
+
+            <span class="k">if</span> <span class="ow">not</span> <span class="n">hdr</span> <span class="ow">or</span> <span class="ow">not</span> <span class="n">hdr</span><span class="o">.</span><span class="n">text</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s1">&#39;Molecules Invol&#39;</span><span class="p">):</span>
+                <span class="k">continue</span>
+
+            <span class="k">for</span> <span class="n">td</span> <span class="ow">in</span> <span class="n">tbl</span><span class="o">.</span><span class="n">find_all</span><span class="p">(</span><span class="s1">&#39;td&#39;</span><span class="p">):</span>
+                <span class="n">genesymbol</span> <span class="o">=</span> <span class="n">td</span><span class="o">.</span><span class="n">text</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span>
+
+                <span class="k">if</span> <span class="ow">not</span> <span class="n">genesymbol</span><span class="p">:</span>
+                    <span class="k">continue</span>
+
+                <span class="n">uniprots</span> <span class="o">=</span> <span class="n">mapping</span><span class="o">.</span><span class="n">map_name</span><span class="p">(</span>
+                    <span class="n">genesymbol</span><span class="p">,</span>
+                    <span class="s1">&#39;genesymbol&#39;</span><span class="p">,</span>
+                    <span class="s1">&#39;uniprot&#39;</span><span class="p">,</span>
+                <span class="p">)</span>
+
+                <span class="k">for</span> <span class="n">uniprot</span> <span class="ow">in</span> <span class="n">uniprots</span><span class="p">:</span>
+                    <span class="n">result</span><span class="p">[</span><span class="n">uniprot</span><span class="p">]</span><span class="o">.</span><span class="n">add</span><span class="p">(</span>
+                        <span class="n">NetpathPathway</span><span class="p">(</span>
+                            <span class="n">pathway</span> <span class="o">=</span> <span class="n">pathway</span>
+                        <span class="p">)</span>
+                    <span class="p">)</span>
+
+    <span class="k">return</span> <span class="nb">dict</span><span class="p">(</span><span class="n">result</span><span class="p">)</span></div>
+
+</pre></div>
+
+                </article>
+              
+              
+              
+              
+              
+                <footer class="prev-next-footer">
+                  
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+  <nav class="bd-toc-nav page-toc" aria-labelledby="pst-page-navigation-heading-2">
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diff --git a/_modules/pypath/inputs/oma.html b/_modules/pypath/inputs/oma.html
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@@ -0,0 +1,865 @@
+
+<!DOCTYPE html>
+
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+<html lang="en" data-content_root="../../../" >
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+  <h1>Source code for pypath.inputs.oma</h1><div class="highlight"><pre>
+<span></span><span class="ch">#!/usr/bin/env python</span>
+<span class="c1"># -*- coding: utf-8 -*-</span>
+
+<span class="c1">#</span>
+<span class="c1">#  This file is part of the `pypath` python module</span>
+<span class="c1">#</span>
+<span class="c1">#  Copyright 2014-2023</span>
+<span class="c1">#  EMBL, EMBL-EBI, Uniklinik RWTH Aachen, Heidelberg University</span>
+<span class="c1">#</span>
+<span class="c1">#  Authors: see the file `README.rst`</span>
+<span class="c1">#  Contact: Dénes Türei (turei.denes@gmail.com)</span>
+<span class="c1">#</span>
+<span class="c1">#  Distributed under the GPLv3 License.</span>
+<span class="c1">#  See accompanying file LICENSE.txt or copy at</span>
+<span class="c1">#      https://www.gnu.org/licenses/gpl-3.0.html</span>
+<span class="c1">#</span>
+<span class="c1">#  Website: https://pypath.omnipathdb.org/</span>
+<span class="c1">#</span>
+
+<span class="kn">from</span> <span class="nn">__future__</span> <span class="kn">import</span> <span class="n">annotations</span>
+
+<span class="kn">from</span> <span class="nn">typing</span> <span class="kn">import</span> <span class="n">Literal</span>
+<span class="kn">import</span> <span class="nn">collections</span>
+<span class="kn">import</span> <span class="nn">itertools</span>
+
+<span class="kn">import</span> <span class="nn">pandas</span> <span class="k">as</span> <span class="nn">pd</span>
+
+<span class="kn">import</span> <span class="nn">pypath.resources.urls</span> <span class="k">as</span> <span class="nn">urls</span>
+<span class="kn">import</span> <span class="nn">pypath.share.curl</span> <span class="k">as</span> <span class="nn">curl</span>
+<span class="kn">import</span> <span class="nn">pypath.share.common</span> <span class="k">as</span> <span class="nn">common</span>
+<span class="kn">import</span> <span class="nn">pypath.inputs.common</span> <span class="k">as</span> <span class="nn">inputs_common</span>
+<span class="kn">import</span> <span class="nn">pypath.utils.taxonomy</span> <span class="k">as</span> <span class="nn">taxonomy</span>
+<span class="kn">import</span> <span class="nn">pypath.utils.mapping</span> <span class="k">as</span> <span class="nn">mapping</span>
+
+
+<div class="viewcode-block" id="oma_orthologs">
+<a class="viewcode-back" href="../../../api/pypath.inputs.oma.oma_orthologs.html#pypath.inputs.oma.oma_orthologs">[docs]</a>
+<span class="k">def</span> <span class="nf">oma_orthologs</span><span class="p">(</span>
+        <span class="n">organism_a</span><span class="p">:</span> <span class="nb">str</span> <span class="o">|</span> <span class="nb">int</span> <span class="o">=</span> <span class="s1">&#39;human&#39;</span><span class="p">,</span>
+        <span class="n">organism_b</span><span class="p">:</span> <span class="nb">str</span> <span class="o">|</span> <span class="nb">int</span> <span class="o">=</span> <span class="s1">&#39;mouse&#39;</span><span class="p">,</span>
+        <span class="n">id_type</span><span class="p">:</span> <span class="nb">str</span> <span class="o">|</span> <span class="kc">None</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+        <span class="n">rel_type</span><span class="p">:</span> <span class="nb">set</span><span class="p">[</span><span class="n">Literal</span><span class="p">[</span><span class="s1">&#39;1:1&#39;</span><span class="p">,</span> <span class="s1">&#39;1:n&#39;</span><span class="p">,</span> <span class="s1">&#39;m:1&#39;</span><span class="p">,</span> <span class="s1">&#39;m:n&#39;</span><span class="p">]]</span> <span class="o">|</span> <span class="kc">None</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+        <span class="n">score</span><span class="p">:</span> <span class="nb">float</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+        <span class="n">return_df</span><span class="p">:</span> <span class="nb">bool</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+    <span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">list</span><span class="p">[</span><span class="nb">tuple</span><span class="p">]</span> <span class="o">|</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">:</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Retrieves pairwise relations between two genomes from the OMA</span>
+<span class="sd">    (Orthologous Matrix) database (https://omabrowser.org/oma/home/).</span>
+
+<span class="sd">    Args:</span>
+<span class="sd">        organism_a:</span>
+<span class="sd">            Name or NCBI Taxonomy ID of the first organism.</span>
+<span class="sd">        organism_b:</span>
+<span class="sd">            Name or NCBI Taxonomy ID of the second organism.</span>
+<span class="sd">        id_type:</span>
+<span class="sd">            OMA by default uses UniProt entry IDs and sometimes other</span>
+<span class="sd">            identifiers for genes. Set this parameter to control which</span>
+<span class="sd">            ID type all the identifiers are to be mapped to.</span>
+<span class="sd">        rel_type:</span>
+<span class="sd">            Restrict relations to certain types.</span>
+<span class="sd">        score:</span>
+<span class="sd">            Lower threshold for similarity metric.</span>
+<span class="sd">        return_df:</span>
+<span class="sd">            If True, returns a data frame instead of a list of tuples.</span>
+
+<span class="sd">    Returns:</span>
+<span class="sd">        A list with tuples of pairwise orthologous relationships or a data</span>
+<span class="sd">        frame with the same records.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="n">OmaGene</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">namedtuple</span><span class="p">(</span>
+        <span class="s1">&#39;OmaGene&#39;</span><span class="p">,</span>
+        <span class="p">(</span>
+            <span class="s1">&#39;id&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;oma_group&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;hog&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;taxon&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;chr&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;start&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;end&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;strand&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;main_isoform&#39;</span><span class="p">,</span>
+        <span class="p">)</span>
+    <span class="p">)</span>
+
+    <span class="n">OmaOrthology</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">namedtuple</span><span class="p">(</span>
+            <span class="s1">&#39;OmaOrthology&#39;</span><span class="p">,</span>
+            <span class="p">(</span>
+                <span class="s1">&#39;a&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;b&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;rel_type&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;dist&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;score&#39;</span><span class="p">,</span>
+            <span class="p">),</span>
+        <span class="p">)</span>
+
+    <span class="n">organism_a</span> <span class="o">=</span> <span class="n">taxonomy</span><span class="o">.</span><span class="n">ensure_ncbi_tax_id</span><span class="p">(</span><span class="n">organism_a</span><span class="p">)</span>
+    <span class="n">organism_b</span> <span class="o">=</span> <span class="n">taxonomy</span><span class="o">.</span><span class="n">ensure_ncbi_tax_id</span><span class="p">(</span><span class="n">organism_b</span><span class="p">)</span>
+    <span class="n">rel_type</span> <span class="o">=</span> <span class="n">common</span><span class="o">.</span><span class="n">to_set</span><span class="p">(</span><span class="n">rel_type</span><span class="p">)</span>
+    <span class="n">url</span> <span class="o">=</span> <span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;oma&#39;</span><span class="p">][</span><span class="s1">&#39;url&#39;</span><span class="p">]</span>
+    <span class="n">page</span> <span class="o">=</span> <span class="mi">1</span>
+    <span class="n">n_pages</span> <span class="o">=</span> <span class="mf">1e6</span>
+    <span class="c1"># first decleration is set to prevent recurrency.</span>
+    <span class="c1"># But at the end it will return as a list</span>
+    <span class="n">result</span> <span class="o">=</span> <span class="nb">set</span><span class="p">()</span>
+
+    <span class="k">while</span> <span class="kc">True</span><span class="p">:</span>
+
+        <span class="n">page_url</span> <span class="o">=</span> <span class="sa">f</span><span class="s1">&#39;</span><span class="si">{</span><span class="n">url</span><span class="si">}{</span><span class="n">organism_a</span><span class="si">}</span><span class="s1">/</span><span class="si">{</span><span class="n">organism_b</span><span class="si">}</span><span class="s1">/?page=</span><span class="si">{</span><span class="n">page</span><span class="si">}</span><span class="s1">&amp;per_page=1000&#39;</span>
+        <span class="n">c</span> <span class="o">=</span> <span class="n">curl</span><span class="o">.</span><span class="n">Curl</span><span class="p">(</span><span class="n">page_url</span><span class="p">,</span> <span class="n">silent</span> <span class="o">=</span> <span class="kc">False</span><span class="p">)</span>
+
+        <span class="k">if</span> <span class="ow">not</span> <span class="n">c</span><span class="o">.</span><span class="n">result</span><span class="p">:</span> <span class="k">break</span>
+
+        <span class="n">c</span><span class="o">.</span><span class="n">get_headers</span><span class="p">()</span>
+        <span class="n">n_pages</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">c</span><span class="o">.</span><span class="n">resp_headers_dict</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">&#39;x-total-count&#39;</span><span class="p">,</span> <span class="mf">1e8</span><span class="p">))</span> <span class="o">/</span> <span class="mi">100</span>
+        <span class="n">page</span> <span class="o">+=</span> <span class="mi">1</span>
+        <span class="n">data</span> <span class="o">=</span> <span class="n">inputs_common</span><span class="o">.</span><span class="n">json_read</span><span class="p">(</span><span class="n">c</span><span class="o">.</span><span class="n">result</span><span class="p">)</span>
+
+        <span class="k">for</span> <span class="n">rec</span> <span class="ow">in</span> <span class="n">data</span><span class="p">:</span>
+
+            <span class="k">if</span> <span class="p">(</span>
+                <span class="p">(</span><span class="n">score</span> <span class="ow">and</span> <span class="n">rec</span><span class="p">[</span><span class="s1">&#39;score&#39;</span><span class="p">]</span> <span class="o">&lt;</span> <span class="n">score</span><span class="p">)</span> <span class="ow">or</span>
+                <span class="p">(</span><span class="n">rel_type</span> <span class="ow">and</span> <span class="n">rec</span><span class="p">[</span><span class="s1">&#39;rel_type&#39;</span><span class="p">]</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">rel_type</span><span class="p">)</span>
+            <span class="p">):</span>
+                <span class="k">continue</span>
+
+            <span class="n">a</span><span class="p">,</span> <span class="n">b</span> <span class="o">=</span> <span class="p">(</span>
+                <span class="p">[</span>
+                    <span class="n">OmaGene</span><span class="p">(</span>
+                        <span class="nb">id</span> <span class="o">=</span> <span class="n">id_</span><span class="p">,</span>
+                        <span class="n">oma_group</span> <span class="o">=</span> <span class="n">e</span><span class="p">[</span><span class="s1">&#39;oma_group&#39;</span><span class="p">],</span>
+                        <span class="n">hog</span> <span class="o">=</span> <span class="n">e</span><span class="p">[</span><span class="s1">&#39;oma_hog_id&#39;</span><span class="p">],</span>
+                        <span class="n">taxon</span> <span class="o">=</span> <span class="n">e</span><span class="p">[</span><span class="s1">&#39;species&#39;</span><span class="p">][</span><span class="s1">&#39;taxon_id&#39;</span><span class="p">],</span>
+                        <span class="nb">chr</span> <span class="o">=</span> <span class="n">e</span><span class="p">[</span><span class="s1">&#39;chromosome&#39;</span><span class="p">],</span>
+                        <span class="n">start</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">e</span><span class="p">[</span><span class="s1">&#39;locus&#39;</span><span class="p">][</span><span class="s1">&#39;start&#39;</span><span class="p">]),</span>
+                        <span class="n">end</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">e</span><span class="p">[</span><span class="s1">&#39;locus&#39;</span><span class="p">][</span><span class="s1">&#39;end&#39;</span><span class="p">]),</span>
+                        <span class="n">strand</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">e</span><span class="p">[</span><span class="s1">&#39;locus&#39;</span><span class="p">][</span><span class="s1">&#39;strand&#39;</span><span class="p">]),</span>
+                        <span class="n">main_isoform</span> <span class="o">=</span> <span class="n">e</span><span class="p">[</span><span class="s1">&#39;is_main_isoform&#39;</span><span class="p">],</span>
+
+                    <span class="p">)</span>
+                    <span class="k">for</span> <span class="n">id_</span> <span class="ow">in</span> <span class="n">_id_translate</span><span class="p">(</span>
+                        <span class="n">id_</span> <span class="o">=</span> <span class="n">e</span><span class="p">[</span><span class="s1">&#39;canonicalid&#39;</span><span class="p">],</span>
+                        <span class="n">taxon</span> <span class="o">=</span> <span class="n">e</span><span class="p">[</span><span class="s1">&#39;species&#39;</span><span class="p">][</span><span class="s1">&#39;taxon_id&#39;</span><span class="p">],</span>
+                        <span class="n">id_type</span> <span class="o">=</span> <span class="n">id_type</span><span class="p">,</span>
+                    <span class="p">)</span>
+                <span class="p">]</span>
+                <span class="k">for</span> <span class="n">e</span> <span class="ow">in</span> <span class="p">(</span><span class="n">rec</span><span class="p">[</span><span class="sa">f</span><span class="s1">&#39;entry_</span><span class="si">{</span><span class="n">ei</span><span class="si">}</span><span class="s1">&#39;</span><span class="p">]</span> <span class="k">for</span> <span class="n">ei</span> <span class="ow">in</span> <span class="p">(</span><span class="mi">1</span><span class="p">,</span> <span class="mi">2</span><span class="p">))</span>
+            <span class="p">)</span>
+
+
+            <span class="n">result</span><span class="o">.</span><span class="n">update</span><span class="p">(</span>
+                <span class="p">{</span>
+                    <span class="n">OmaOrthology</span><span class="p">(</span>
+                        <span class="n">a</span> <span class="o">=</span> <span class="n">_a</span><span class="p">,</span>
+                        <span class="n">b</span> <span class="o">=</span> <span class="n">_b</span><span class="p">,</span>
+                        <span class="n">rel_type</span> <span class="o">=</span> <span class="n">rec</span><span class="p">[</span><span class="s1">&#39;rel_type&#39;</span><span class="p">],</span>
+                        <span class="n">dist</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">rec</span><span class="p">[</span><span class="s1">&#39;distance&#39;</span><span class="p">]),</span>
+                        <span class="n">score</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">rec</span><span class="p">[</span><span class="s1">&#39;score&#39;</span><span class="p">]),</span>
+                    <span class="p">)</span>
+                    <span class="k">for</span> <span class="n">_a</span><span class="p">,</span> <span class="n">_b</span> <span class="ow">in</span> <span class="n">itertools</span><span class="o">.</span><span class="n">product</span><span class="p">(</span><span class="n">a</span><span class="p">,</span> <span class="n">b</span><span class="p">)</span>
+                <span class="p">}</span>
+            <span class="p">)</span>
+
+        <span class="k">if</span> <span class="n">page</span> <span class="o">&gt;</span> <span class="n">n_pages</span><span class="p">:</span> <span class="k">break</span>
+
+    <span class="n">result</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="n">result</span><span class="p">)</span>
+
+    <span class="k">if</span> <span class="n">return_df</span><span class="p">:</span>
+
+        <span class="n">result</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">(</span><span class="n">result</span><span class="p">)</span>
+        <span class="n">result</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">concat</span><span class="p">(</span>
+            <span class="p">[</span>
+                <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">(</span><span class="n">result</span><span class="o">.</span><span class="n">a</span><span class="o">.</span><span class="n">tolist</span><span class="p">())</span><span class="o">.</span><span class="n">add_suffix</span><span class="p">(</span><span class="s1">&#39;_a&#39;</span><span class="p">,</span> <span class="n">axis</span> <span class="o">=</span> <span class="mi">1</span><span class="p">),</span>
+                <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">(</span><span class="n">result</span><span class="o">.</span><span class="n">b</span><span class="o">.</span><span class="n">tolist</span><span class="p">())</span><span class="o">.</span><span class="n">add_suffix</span><span class="p">(</span><span class="s1">&#39;_b&#39;</span><span class="p">,</span> <span class="n">axis</span> <span class="o">=</span> <span class="mi">1</span><span class="p">),</span>
+                <span class="n">result</span><span class="o">.</span><span class="n">drop</span><span class="p">([</span><span class="s1">&#39;a&#39;</span><span class="p">,</span> <span class="s1">&#39;b&#39;</span><span class="p">],</span> <span class="n">axis</span> <span class="o">=</span> <span class="mi">1</span><span class="p">),</span>
+            <span class="p">],</span>
+            <span class="n">axis</span> <span class="o">=</span> <span class="mi">1</span><span class="p">,</span>
+        <span class="p">)</span>
+
+    <span class="k">return</span> <span class="n">result</span></div>
+
+
+
+<div class="viewcode-block" id="oma_table">
+<a class="viewcode-back" href="../../../api/pypath.inputs.oma.oma_table.html#pypath.inputs.oma.oma_table">[docs]</a>
+<span class="k">def</span> <span class="nf">oma_table</span><span class="p">(</span>
+        <span class="n">organism_a</span><span class="p">:</span> <span class="nb">str</span> <span class="o">|</span> <span class="nb">int</span> <span class="o">=</span> <span class="s1">&#39;human&#39;</span><span class="p">,</span>
+        <span class="n">organism_b</span><span class="p">:</span> <span class="nb">str</span> <span class="o">|</span> <span class="nb">int</span> <span class="o">=</span> <span class="s1">&#39;mouse&#39;</span><span class="p">,</span>
+        <span class="n">id_type</span><span class="p">:</span> <span class="nb">str</span> <span class="o">|</span> <span class="kc">None</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+        <span class="n">rel_type</span><span class="p">:</span> <span class="nb">set</span><span class="p">[</span><span class="n">Literal</span><span class="p">[</span><span class="s1">&#39;1:1&#39;</span><span class="p">,</span> <span class="s1">&#39;1:n&#39;</span><span class="p">,</span> <span class="s1">&#39;m:1&#39;</span><span class="p">,</span> <span class="s1">&#39;m:n&#39;</span><span class="p">]]</span> <span class="o">|</span> <span class="kc">None</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+        <span class="n">score</span><span class="p">:</span> <span class="nb">float</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+        <span class="n">return_df</span><span class="p">:</span> <span class="nb">bool</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+    <span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">dict</span><span class="p">[</span><span class="nb">str</span><span class="p">[</span><span class="nb">set</span><span class="p">[</span><span class="nb">str</span><span class="p">]]]</span> <span class="o">|</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">:</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Translation table of orthologous gene pairs between two organisms from the</span>
+<span class="sd">    OMA (Orthologous Matrix) database (https://omabrowser.org/oma/home/).</span>
+
+<span class="sd">    Args:</span>
+<span class="sd">        organism_a:</span>
+<span class="sd">            Name or NCBI Taxonomy ID of the first organism.</span>
+<span class="sd">        organism_b:</span>
+<span class="sd">            Name or NCBI Taxonomy ID of the second organism.</span>
+<span class="sd">        id_type:</span>
+<span class="sd">            OMA by default uses UniProt entry IDs and sometimes other</span>
+<span class="sd">            identifiers for genes. Set this parameter to control which</span>
+<span class="sd">            ID type all the identifiers are to be mapped to.</span>
+<span class="sd">        rel_type:</span>
+<span class="sd">            Restrict relations to certain types.</span>
+<span class="sd">        score:</span>
+<span class="sd">            Lower threshold for similarity metric.</span>
+<span class="sd">        return_df:</span>
+<span class="sd">            If True, returns a data frame instead of a list of tuples.</span>
+
+<span class="sd">    Returns:</span>
+<span class="sd">        A dict with source organism identifiers as keys and sets of target</span>
+<span class="sd">        organism identifiers as values; or a two column data frame with</span>
+<span class="sd">        source organism-target organism identifier pairs.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="n">full</span> <span class="o">=</span> <span class="n">oma_orthologs</span><span class="p">(</span><span class="o">**</span><span class="nb">locals</span><span class="p">())</span>
+
+    <span class="k">if</span> <span class="n">return_df</span><span class="p">:</span>
+
+        <span class="n">result</span> <span class="o">=</span> <span class="n">full</span><span class="p">[[</span><span class="s1">&#39;id_a&#39;</span><span class="p">,</span> <span class="s1">&#39;id_b&#39;</span><span class="p">]]</span>
+
+    <span class="k">else</span><span class="p">:</span>
+
+        <span class="n">result</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">defaultdict</span><span class="p">(</span><span class="nb">set</span><span class="p">)</span>
+
+        <span class="k">for</span> <span class="n">o</span> <span class="ow">in</span> <span class="n">full</span><span class="p">:</span>
+
+            <span class="n">result</span><span class="p">[</span><span class="n">o</span><span class="o">.</span><span class="n">a</span><span class="o">.</span><span class="n">id</span><span class="p">]</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">o</span><span class="o">.</span><span class="n">b</span><span class="o">.</span><span class="n">id</span><span class="p">)</span>
+
+    <span class="k">return</span> <span class="n">result</span></div>
+
+
+
+<span class="k">def</span> <span class="nf">_id_translate</span><span class="p">(</span><span class="n">id_</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="n">taxon</span><span class="p">:</span> <span class="nb">int</span><span class="p">,</span> <span class="n">id_type</span><span class="p">:</span> <span class="nb">str</span> <span class="o">|</span> <span class="kc">None</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">set</span><span class="p">[</span><span class="nb">str</span><span class="p">]:</span>
+
+    <span class="k">if</span> <span class="ow">not</span> <span class="n">id_type</span><span class="p">:</span> <span class="k">return</span> <span class="p">{</span><span class="n">id_</span><span class="p">}</span>
+
+    <span class="n">s_id_type</span> <span class="o">=</span> <span class="p">(</span>
+        <span class="s1">&#39;ensg&#39;</span>
+            <span class="k">if</span> <span class="n">id_</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s1">&#39;ENS&#39;</span><span class="p">)</span> <span class="k">else</span>
+        <span class="s1">&#39;uniprot-entry&#39;</span>
+            <span class="k">if</span> <span class="s1">&#39;_&#39;</span> <span class="ow">in</span> <span class="n">id_</span> <span class="k">else</span>
+        <span class="s1">&#39;uniprot&#39;</span>
+    <span class="p">)</span>
+
+    <span class="n">uniprots</span> <span class="o">=</span> <span class="n">mapping</span><span class="o">.</span><span class="n">map_name</span><span class="p">(</span>
+        <span class="n">id_</span><span class="p">,</span>
+        <span class="n">s_id_type</span><span class="p">,</span>
+        <span class="s1">&#39;uniprot&#39;</span><span class="p">,</span>
+        <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">taxon</span><span class="p">,</span>
+    <span class="p">)</span>
+
+    <span class="k">return</span> <span class="n">mapping</span><span class="o">.</span><span class="n">map_names</span><span class="p">(</span>
+        <span class="n">uniprots</span><span class="p">,</span>
+        <span class="s1">&#39;uniprot&#39;</span><span class="p">,</span>
+        <span class="n">id_type</span><span class="p">,</span>
+        <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">taxon</span><span class="p">,</span>
+    <span class="p">)</span> <span class="k">if</span> <span class="n">uniprots</span> <span class="k">else</span> <span class="nb">set</span><span class="p">()</span>
+</pre></div>
+
+                </article>
+              
+              
+              
+              
+              
+                <footer class="prev-next-footer">
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+                  
+  <h1>Source code for pypath.inputs.opm</h1><div class="highlight"><pre>
+<span></span><span class="ch">#!/usr/bin/env python</span>
+<span class="c1"># -*- coding: utf-8 -*-</span>
+
+<span class="c1">#</span>
+<span class="c1">#  This file is part of the `pypath` python module</span>
+<span class="c1">#</span>
+<span class="c1">#  Copyright 2014-2023</span>
+<span class="c1">#  EMBL, EMBL-EBI, Uniklinik RWTH Aachen, Heidelberg University</span>
+<span class="c1">#</span>
+<span class="c1">#  Authors: see the file `README.rst`</span>
+<span class="c1">#  Contact: Dénes Türei (turei.denes@gmail.com)</span>
+<span class="c1">#</span>
+<span class="c1">#  Distributed under the GPLv3 License.</span>
+<span class="c1">#  See accompanying file LICENSE.txt or copy at</span>
+<span class="c1">#      https://www.gnu.org/licenses/gpl-3.0.html</span>
+<span class="c1">#</span>
+<span class="c1">#  Website: https://pypath.omnipathdb.org/</span>
+<span class="c1">#</span>
+
+<span class="kn">import</span> <span class="nn">re</span>
+<span class="kn">import</span> <span class="nn">csv</span>
+<span class="kn">import</span> <span class="nn">collections</span>
+
+<span class="kn">import</span> <span class="nn">pypath.share.curl</span> <span class="k">as</span> <span class="nn">curl</span>
+<span class="kn">import</span> <span class="nn">pypath.resources.urls</span> <span class="k">as</span> <span class="nn">urls</span>
+<span class="kn">import</span> <span class="nn">pypath.utils.mapping</span> <span class="k">as</span> <span class="nn">mapping</span>
+<span class="kn">import</span> <span class="nn">pypath.utils.taxonomy</span> <span class="k">as</span> <span class="nn">taxonomy</span>
+
+
+<div class="viewcode-block" id="opm_annotations">
+<a class="viewcode-back" href="../../../api/pypath.inputs.opm.opm_annotations.html#pypath.inputs.opm.opm_annotations">[docs]</a>
+<span class="k">def</span> <span class="nf">opm_annotations</span><span class="p">(</span><span class="n">organism</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">):</span>
+
+    <span class="n">reparentheses</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">compile</span><span class="p">(</span><span class="sa">r</span><span class="s1">&#39;\((.*)\)&#39;</span><span class="p">)</span>
+    <span class="n">regenesymbol</span>  <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">compile</span><span class="p">(</span><span class="sa">r</span><span class="s1">&#39; ([A-Z0-9]{3,}) &#39;</span><span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">get_dict</span><span class="p">(</span><span class="n">name</span><span class="p">):</span>
+
+        <span class="n">result</span> <span class="o">=</span> <span class="p">{}</span>
+        <span class="n">url</span> <span class="o">=</span> <span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;opm&#39;</span><span class="p">][</span><span class="n">name</span><span class="p">]</span>
+        <span class="n">c</span> <span class="o">=</span> <span class="n">curl</span><span class="o">.</span><span class="n">Curl</span><span class="p">(</span><span class="n">url</span><span class="p">,</span> <span class="n">large</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span> <span class="n">silent</span> <span class="o">=</span> <span class="kc">False</span><span class="p">)</span>
+        <span class="n">data</span> <span class="o">=</span> <span class="n">csv</span><span class="o">.</span><span class="n">DictReader</span><span class="p">(</span><span class="n">c</span><span class="o">.</span><span class="n">result</span><span class="p">,</span> <span class="n">delimiter</span> <span class="o">=</span> <span class="s1">&#39;,&#39;</span><span class="p">)</span>
+
+        <span class="k">for</span> <span class="n">rec</span> <span class="ow">in</span> <span class="n">data</span><span class="p">:</span>
+            <span class="n">result</span><span class="p">[</span><span class="n">rec</span><span class="p">[</span><span class="s1">&#39;id&#39;</span><span class="p">]]</span> <span class="o">=</span> <span class="n">rec</span><span class="p">[</span><span class="s1">&#39;name&#39;</span><span class="p">]</span>
+
+        <span class="k">return</span> <span class="n">result</span>
+
+
+    <span class="n">OpmAnnotation</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">namedtuple</span><span class="p">(</span>
+        <span class="s1">&#39;OpmAnnotation&#39;</span><span class="p">,</span>
+        <span class="p">[</span><span class="s1">&#39;membrane&#39;</span><span class="p">,</span> <span class="s1">&#39;family&#39;</span><span class="p">,</span> <span class="s1">&#39;transmembrane&#39;</span><span class="p">],</span>
+    <span class="p">)</span>
+
+
+    <span class="n">result</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">defaultdict</span><span class="p">(</span><span class="nb">set</span><span class="p">)</span>
+
+    <span class="n">organism_name</span> <span class="o">=</span> <span class="p">(</span>
+        <span class="n">taxonomy</span><span class="o">.</span><span class="n">phosphoelm_taxids</span><span class="p">[</span><span class="n">organism</span><span class="p">]</span>
+            <span class="k">if</span> <span class="n">organism</span> <span class="ow">in</span> <span class="n">taxonomy</span><span class="o">.</span><span class="n">phosphoelm_taxids</span> <span class="k">else</span>
+        <span class="kc">None</span>
+    <span class="p">)</span>
+
+    <span class="n">types</span> <span class="o">=</span> <span class="n">get_dict</span><span class="p">(</span><span class="s1">&#39;types&#39;</span><span class="p">)</span>
+    <span class="n">families</span> <span class="o">=</span> <span class="n">get_dict</span><span class="p">(</span><span class="s1">&#39;families&#39;</span><span class="p">)</span>
+
+    <span class="n">url</span> <span class="o">=</span> <span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;opm&#39;</span><span class="p">][</span><span class="s1">&#39;proteins&#39;</span><span class="p">]</span>
+    <span class="n">c</span> <span class="o">=</span> <span class="n">curl</span><span class="o">.</span><span class="n">Curl</span><span class="p">(</span><span class="n">url</span><span class="p">,</span> <span class="n">silent</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span> <span class="n">large</span> <span class="o">=</span> <span class="kc">True</span><span class="p">)</span>
+
+    <span class="n">data</span> <span class="o">=</span> <span class="n">csv</span><span class="o">.</span><span class="n">DictReader</span><span class="p">(</span><span class="n">c</span><span class="o">.</span><span class="n">result</span><span class="p">,</span> <span class="n">delimiter</span> <span class="o">=</span> <span class="s1">&#39;,&#39;</span><span class="p">)</span>
+
+    <span class="k">for</span> <span class="n">rec</span> <span class="ow">in</span> <span class="n">data</span><span class="p">:</span>
+
+        <span class="k">if</span> <span class="n">organism_name</span> <span class="ow">and</span> <span class="n">rec</span><span class="p">[</span><span class="s1">&#39;species_name_cache&#39;</span><span class="p">]</span> <span class="o">!=</span> <span class="n">organism_name</span><span class="p">:</span>
+
+            <span class="k">continue</span>
+
+        <span class="n">name</span> <span class="o">=</span> <span class="n">rec</span><span class="p">[</span><span class="s1">&#39;name&#39;</span><span class="p">]</span>
+
+        <span class="n">names</span> <span class="o">=</span> <span class="p">[</span>
+            <span class="n">name</span><span class="p">,</span>
+            <span class="n">name</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;(&#39;</span><span class="p">)[</span><span class="mi">0</span><span class="p">],</span>
+            <span class="n">name</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;,&#39;</span><span class="p">)[</span><span class="mi">0</span><span class="p">],</span>
+        <span class="p">]</span>
+
+        <span class="n">m</span> <span class="o">=</span> <span class="n">reparentheses</span><span class="o">.</span><span class="n">search</span><span class="p">(</span><span class="n">name</span><span class="p">)</span>
+
+        <span class="k">if</span> <span class="n">m</span><span class="p">:</span>
+            <span class="n">names</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">m</span><span class="o">.</span><span class="n">groups</span><span class="p">()[</span><span class="mi">0</span><span class="p">])</span>
+
+        <span class="n">genesymbols</span> <span class="o">=</span> <span class="n">regenesymbol</span><span class="o">.</span><span class="n">findall</span><span class="p">(</span><span class="n">name</span><span class="p">)</span>
+
+        <span class="k">for</span> <span class="n">this_name</span> <span class="ow">in</span> <span class="n">names</span><span class="p">:</span>
+            <span class="n">uniprot</span> <span class="o">=</span> <span class="n">mapping</span><span class="o">.</span><span class="n">map_name0</span><span class="p">(</span><span class="n">this_name</span><span class="p">,</span> <span class="s1">&#39;protein-name&#39;</span><span class="p">,</span> <span class="s1">&#39;uniprot&#39;</span><span class="p">)</span>
+
+            <span class="k">if</span> <span class="n">uniprot</span><span class="p">:</span>
+                <span class="k">break</span>
+
+        <span class="k">if</span> <span class="ow">not</span> <span class="n">uniprot</span><span class="p">:</span>
+            <span class="k">for</span> <span class="n">gs</span> <span class="ow">in</span> <span class="n">genesymbols</span><span class="p">:</span>
+                <span class="n">uniprot</span> <span class="o">=</span> <span class="p">(</span>
+                    <span class="n">mapping</span><span class="o">.</span><span class="n">map_name0</span><span class="p">(</span><span class="n">this_name</span><span class="p">,</span> <span class="s1">&#39;genesymbol&#39;</span><span class="p">,</span> <span class="s1">&#39;uniprot&#39;</span><span class="p">)</span>
+                <span class="p">)</span>
+
+                <span class="k">if</span> <span class="n">uniprot</span><span class="p">:</span>
+                    <span class="k">break</span>
+
+        <span class="k">if</span> <span class="ow">not</span> <span class="n">uniprot</span><span class="p">:</span>
+            <span class="k">continue</span>
+
+        <span class="n">result</span><span class="p">[</span><span class="n">uniprot</span><span class="p">]</span><span class="o">.</span><span class="n">add</span><span class="p">(</span>
+            <span class="n">OpmAnnotation</span><span class="p">(</span>
+                <span class="n">membrane</span> <span class="o">=</span> <span class="n">rec</span><span class="p">[</span><span class="s1">&#39;membrane_name_cache&#39;</span><span class="p">],</span>
+                <span class="n">family</span> <span class="o">=</span> <span class="n">rec</span><span class="p">[</span><span class="s1">&#39;family_name_cache&#39;</span><span class="p">],</span>
+                <span class="n">transmembrane</span> <span class="o">=</span> <span class="n">types</span><span class="p">[</span><span class="n">rec</span><span class="p">[</span><span class="s1">&#39;type_id&#39;</span><span class="p">]]</span> <span class="o">==</span> <span class="s1">&#39;Transmembrane&#39;</span><span class="p">,</span>
+            <span class="p">)</span>
+        <span class="p">)</span>
+
+    <span class="k">return</span> <span class="nb">dict</span><span class="p">(</span><span class="n">result</span><span class="p">)</span></div>
+
+</pre></div>
+
+                </article>
+              
+              
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+<div id="searchbox"></div>
+                <article class="bd-article">
+                  
+  <h1>Source code for pypath.inputs.panglaodb</h1><div class="highlight"><pre>
+<span></span><span class="ch">#!/usr/bin/env python</span>
+<span class="c1"># -*- coding: utf-8 -*-</span>
+
+<span class="c1">#</span>
+<span class="c1">#  This file is part of the `pypath` python module</span>
+<span class="c1">#</span>
+<span class="c1">#  Copyright 2014-2023</span>
+<span class="c1">#  EMBL, EMBL-EBI, Uniklinik RWTH Aachen, Heidelberg University</span>
+<span class="c1">#</span>
+<span class="c1">#  Authors: see the file `README.rst`</span>
+<span class="c1">#  Contact: Dénes Türei (turei.denes@gmail.com)</span>
+<span class="c1">#</span>
+<span class="c1">#  Distributed under the GPLv3 License.</span>
+<span class="c1">#  See accompanying file LICENSE.txt or copy at</span>
+<span class="c1">#      https://www.gnu.org/licenses/gpl-3.0.html</span>
+<span class="c1">#</span>
+<span class="c1">#  Website: https://pypath.omnipathdb.org/</span>
+<span class="c1">#</span>
+
+<span class="kn">import</span> <span class="nn">csv</span>
+<span class="kn">import</span> <span class="nn">collections</span>
+
+<span class="kn">import</span> <span class="nn">pypath.resources.urls</span> <span class="k">as</span> <span class="nn">urls</span>
+<span class="kn">import</span> <span class="nn">pypath.share.curl</span> <span class="k">as</span> <span class="nn">curl</span>
+<span class="kn">import</span> <span class="nn">pypath.share.settings</span> <span class="k">as</span> <span class="nn">settings</span>
+<span class="kn">import</span> <span class="nn">pypath.share.common</span> <span class="k">as</span> <span class="nn">common</span>
+<span class="kn">import</span> <span class="nn">pypath.utils.mapping</span> <span class="k">as</span> <span class="nn">mapping</span>
+
+
+<div class="viewcode-block" id="panglaodb_raw">
+<a class="viewcode-back" href="../../../api/pypath.inputs.panglaodb.panglaodb_raw.html#pypath.inputs.panglaodb.panglaodb_raw">[docs]</a>
+<span class="k">def</span> <span class="nf">panglaodb_raw</span><span class="p">():</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Cell type marker genes from PanglaoDB (https://panglaodb.se/index.html).</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="n">url</span> <span class="o">=</span> <span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;panglaodb&#39;</span><span class="p">][</span><span class="s1">&#39;url&#39;</span><span class="p">]</span>
+    <span class="n">headers</span> <span class="o">=</span> <span class="p">[</span><span class="n">settings</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">&#39;user_agent&#39;</span><span class="p">)]</span>
+    <span class="n">c</span> <span class="o">=</span> <span class="n">curl</span><span class="o">.</span><span class="n">Curl</span><span class="p">(</span><span class="n">url</span><span class="p">,</span> <span class="n">silent</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span> <span class="n">large</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span> <span class="n">req_headers</span> <span class="o">=</span> <span class="n">headers</span><span class="p">)</span>
+
+    <span class="n">result</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="n">csv</span><span class="o">.</span><span class="n">DictReader</span><span class="p">(</span><span class="n">c</span><span class="o">.</span><span class="n">result</span><span class="p">,</span> <span class="n">delimiter</span> <span class="o">=</span> <span class="s1">&#39;</span><span class="se">\t</span><span class="s1">&#39;</span><span class="p">))</span>
+
+    <span class="k">return</span> <span class="n">result</span></div>
+
+
+
+<div class="viewcode-block" id="panglaodb_annotations">
+<a class="viewcode-back" href="../../../api/pypath.inputs.panglaodb.panglaodb_annotations.html#pypath.inputs.panglaodb.panglaodb_annotations">[docs]</a>
+<span class="k">def</span> <span class="nf">panglaodb_annotations</span><span class="p">():</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Cell type marker genes from PanglaoDB (https://panglaodb.se/index.html).</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="n">to_float</span> <span class="o">=</span> <span class="n">common</span><span class="o">.</span><span class="n">float_or_nan</span>
+
+    <span class="n">record</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">namedtuple</span><span class="p">(</span>
+        <span class="s1">&#39;PanglaodbAnnotation&#39;</span><span class="p">,</span>
+        <span class="p">(</span>
+            <span class="s1">&#39;canonical_marker&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;cell_type&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;organ&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;germ_layer&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;entity_type&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;human&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;mouse&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;human_sensitivity&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;mouse_sensitivity&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;human_specificity&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;mouse_specificity&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;ubiquitiousness&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;ncbi_tax_id&#39;</span><span class="p">,</span>
+        <span class="p">)</span>
+    <span class="p">)</span>
+
+    <span class="n">result</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">defaultdict</span><span class="p">(</span><span class="nb">set</span><span class="p">)</span>
+
+    <span class="n">raw</span> <span class="o">=</span> <span class="n">panglaodb_raw</span><span class="p">()</span>
+
+    <span class="k">for</span> <span class="n">r</span> <span class="ow">in</span> <span class="n">raw</span><span class="p">:</span>
+
+        <span class="n">human</span> <span class="o">=</span> <span class="s1">&#39;Hs&#39;</span> <span class="ow">in</span> <span class="n">r</span><span class="p">[</span><span class="s1">&#39;species&#39;</span><span class="p">],</span>
+        <span class="n">mouse</span> <span class="o">=</span> <span class="s1">&#39;Mm&#39;</span> <span class="ow">in</span> <span class="n">r</span><span class="p">[</span><span class="s1">&#39;species&#39;</span><span class="p">],</span>
+
+        <span class="n">entity_type</span> <span class="o">=</span> <span class="s1">&#39;protein&#39;</span>
+        <span class="n">uniprots</span> <span class="o">=</span> <span class="n">mapping</span><span class="o">.</span><span class="n">map_name</span><span class="p">(</span>
+            <span class="n">r</span><span class="p">[</span><span class="s1">&#39;official gene symbol&#39;</span><span class="p">],</span>
+            <span class="s1">&#39;genesymbol&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;uniprot&#39;</span><span class="p">,</span>
+        <span class="p">)</span>
+        <span class="n">this_ncbi_tax_id</span> <span class="o">=</span> <span class="mi">9606</span>
+
+        <span class="k">if</span> <span class="ow">not</span> <span class="n">uniprots</span> <span class="ow">and</span> <span class="n">human</span><span class="p">:</span>
+
+            <span class="n">uniprots</span> <span class="o">=</span> <span class="n">mapping</span><span class="o">.</span><span class="n">map_name</span><span class="p">(</span>
+                <span class="n">r</span><span class="p">[</span><span class="s1">&#39;official gene symbol&#39;</span><span class="p">],</span>
+                <span class="s1">&#39;genesymbol&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;trembl&#39;</span><span class="p">,</span>
+            <span class="p">)</span>
+
+        <span class="k">if</span> <span class="ow">not</span> <span class="n">uniprots</span> <span class="ow">and</span> <span class="n">mouse</span><span class="p">:</span>
+
+            <span class="n">mouse_gs</span> <span class="o">=</span> <span class="s1">&#39;-&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span>
+                <span class="n">x</span><span class="o">.</span><span class="n">capitalize</span><span class="p">()</span>
+                <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">r</span><span class="p">[</span><span class="s1">&#39;official gene symbol&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;-&#39;</span><span class="p">)</span>
+            <span class="p">)</span>
+
+            <span class="n">uniprots</span> <span class="o">=</span> <span class="n">mapping</span><span class="o">.</span><span class="n">map_name</span><span class="p">(</span>
+                <span class="n">mouse_gs</span><span class="p">,</span>
+                <span class="s1">&#39;genesymbol&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;uniprot&#39;</span><span class="p">,</span>
+                <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="mi">10090</span><span class="p">,</span>
+            <span class="p">)</span>
+
+            <span class="k">if</span> <span class="ow">not</span> <span class="n">uniprots</span><span class="p">:</span>
+
+                <span class="n">uniprots</span> <span class="o">=</span> <span class="n">mapping</span><span class="o">.</span><span class="n">map_name</span><span class="p">(</span>
+                    <span class="n">mouse_gs</span><span class="p">,</span>
+                    <span class="s1">&#39;genesymbol&#39;</span><span class="p">,</span>
+                    <span class="s1">&#39;trembl&#39;</span><span class="p">,</span>
+                    <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="mi">10090</span><span class="p">,</span>
+                <span class="p">)</span>
+
+            <span class="n">this_ncbi_tax_id</span> <span class="o">=</span> <span class="mi">10090</span>
+
+        <span class="k">if</span> <span class="ow">not</span> <span class="n">uniprots</span> <span class="ow">and</span> <span class="n">r</span><span class="p">[</span><span class="s1">&#39;gene type&#39;</span><span class="p">]</span> <span class="o">==</span> <span class="s1">&#39;non-coding RNA&#39;</span><span class="p">:</span>
+
+            <span class="n">uniprots</span> <span class="o">=</span> <span class="p">(</span><span class="n">r</span><span class="p">[</span><span class="s1">&#39;official gene symbol&#39;</span><span class="p">],)</span>
+            <span class="n">entity_type</span> <span class="o">=</span> <span class="s1">&#39;lncrna&#39;</span>
+
+        <span class="k">for</span> <span class="n">u</span> <span class="ow">in</span> <span class="n">uniprots</span><span class="p">:</span>
+
+            <span class="n">result</span><span class="p">[</span><span class="n">u</span><span class="p">]</span><span class="o">.</span><span class="n">add</span><span class="p">(</span>
+                <span class="n">record</span><span class="p">(</span>
+                    <span class="n">canonical_marker</span> <span class="o">=</span> <span class="n">r</span><span class="p">[</span><span class="s1">&#39;canonical marker&#39;</span><span class="p">]</span> <span class="o">==</span> <span class="s1">&#39;1&#39;</span><span class="p">,</span>
+                    <span class="n">cell_type</span> <span class="o">=</span> <span class="n">r</span><span class="p">[</span><span class="s1">&#39;cell type&#39;</span><span class="p">],</span>
+                    <span class="n">organ</span> <span class="o">=</span> <span class="n">r</span><span class="p">[</span><span class="s1">&#39;organ&#39;</span><span class="p">],</span>
+                    <span class="n">germ_layer</span> <span class="o">=</span> <span class="n">r</span><span class="p">[</span><span class="s1">&#39;germ layer&#39;</span><span class="p">],</span>
+                    <span class="n">entity_type</span> <span class="o">=</span> <span class="n">entity_type</span><span class="p">,</span> <span class="c1"># TODO: handle all entity types</span>
+                    <span class="n">human</span> <span class="o">=</span> <span class="n">human</span><span class="p">,</span>
+                    <span class="n">mouse</span> <span class="o">=</span> <span class="n">mouse</span><span class="p">,</span>
+                    <span class="n">human_sensitivity</span> <span class="o">=</span> <span class="n">to_float</span><span class="p">(</span><span class="n">r</span><span class="p">[</span><span class="s1">&#39;sensitivity_human&#39;</span><span class="p">]),</span>
+                    <span class="n">mouse_sensitivity</span> <span class="o">=</span> <span class="n">to_float</span><span class="p">(</span><span class="n">r</span><span class="p">[</span><span class="s1">&#39;sensitivity_mouse&#39;</span><span class="p">]),</span>
+                    <span class="n">human_specificity</span> <span class="o">=</span> <span class="n">to_float</span><span class="p">(</span><span class="n">r</span><span class="p">[</span><span class="s1">&#39;specificity_human&#39;</span><span class="p">]),</span>
+                    <span class="n">mouse_specificity</span> <span class="o">=</span> <span class="n">to_float</span><span class="p">(</span><span class="n">r</span><span class="p">[</span><span class="s1">&#39;specificity_mouse&#39;</span><span class="p">]),</span>
+                    <span class="n">ubiquitiousness</span> <span class="o">=</span> <span class="n">to_float</span><span class="p">(</span><span class="n">r</span><span class="p">[</span><span class="s1">&#39;ubiquitousness index&#39;</span><span class="p">]),</span>
+                    <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">this_ncbi_tax_id</span><span class="p">,</span>
+                <span class="p">)</span>
+            <span class="p">)</span>
+
+    <span class="k">return</span> <span class="n">result</span></div>
+
+</pre></div>
+
+                </article>
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+  <h1>Source code for pypath.inputs.pdb</h1><div class="highlight"><pre>
+<span></span><span class="ch">#!/usr/bin/env python</span>
+<span class="c1"># -*- coding: utf-8 -*-</span>
+
+<span class="c1">#</span>
+<span class="c1">#  This file is part of the `pypath` python module</span>
+<span class="c1">#</span>
+<span class="c1">#  Copyright 2014-2023</span>
+<span class="c1">#  EMBL, EMBL-EBI, Uniklinik RWTH Aachen, Heidelberg University</span>
+<span class="c1">#</span>
+<span class="c1">#  Authors: see the file `README.rst`</span>
+<span class="c1">#  Contact: Dénes Türei (turei.denes@gmail.com)</span>
+<span class="c1">#</span>
+<span class="c1">#  Distributed under the GPLv3 License.</span>
+<span class="c1">#  See accompanying file LICENSE.txt or copy at</span>
+<span class="c1">#      https://www.gnu.org/licenses/gpl-3.0.html</span>
+<span class="c1">#</span>
+<span class="c1">#  Website: https://pypath.omnipathdb.org/</span>
+<span class="c1">#</span>
+
+<span class="kn">from</span> <span class="nn">future.utils</span> <span class="kn">import</span> <span class="n">iteritems</span>
+
+<span class="kn">import</span> <span class="nn">re</span>
+<span class="kn">import</span> <span class="nn">collections</span>
+
+<span class="kn">import</span> <span class="nn">pypath.resources.urls</span> <span class="k">as</span> <span class="nn">urls</span>
+<span class="kn">import</span> <span class="nn">pypath.share.curl</span> <span class="k">as</span> <span class="nn">curl</span>
+<span class="kn">import</span> <span class="nn">pypath.internals.intera</span> <span class="k">as</span> <span class="nn">intera</span>
+<span class="kn">import</span> <span class="nn">pypath.utils.reflists</span> <span class="k">as</span> <span class="nn">reflists</span>
+
+
+<div class="viewcode-block" id="pdb_uniprot">
+<a class="viewcode-back" href="../../../api/pypath.inputs.pdb.pdb_uniprot.html#pypath.inputs.pdb.pdb_uniprot">[docs]</a>
+<span class="k">def</span> <span class="nf">pdb_uniprot</span><span class="p">():</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Mapping between UniProt and PDB identifiers.</span>
+<span class="sd">    Returns two dictionaries:</span>
+<span class="sd">    * UniProt to PDB mapping: keys are UniProt IDs, values are sets of</span>
+<span class="sd">      tuples, each tuple with three values: the PDB structure ID, the</span>
+<span class="sd">      structure analysis method and the structure resolution</span>
+<span class="sd">    * PDB to UniProt mapping: keys are PDB IDs, values are sets of UniProt</span>
+<span class="sd">      IDs</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="n">c</span> <span class="o">=</span> <span class="n">curl</span><span class="o">.</span><span class="n">Curl</span><span class="p">(</span><span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;uniprot_pdb&#39;</span><span class="p">][</span><span class="s1">&#39;url&#39;</span><span class="p">],</span> <span class="n">silent</span> <span class="o">=</span> <span class="kc">False</span><span class="p">)</span>
+    <span class="n">data</span> <span class="o">=</span> <span class="n">c</span><span class="o">.</span><span class="n">result</span>
+
+    <span class="k">if</span> <span class="n">data</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
+        <span class="k">return</span> <span class="kc">None</span><span class="p">,</span> <span class="kc">None</span>
+
+    <span class="n">data</span> <span class="o">=</span> <span class="n">data</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\n</span><span class="s1">&#39;</span><span class="p">)</span>
+    <span class="n">u_pdb</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">defaultdict</span><span class="p">(</span><span class="nb">set</span><span class="p">)</span>
+    <span class="n">pdb_u</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">defaultdict</span><span class="p">(</span><span class="nb">set</span><span class="p">)</span>
+    <span class="n">pdb</span> <span class="o">=</span> <span class="kc">None</span>
+    <span class="n">pdb_re</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">compile</span><span class="p">(</span><span class="sa">r</span><span class="s1">&#39;[0-9A-Z]</span><span class="si">{4}</span><span class="s1">&#39;</span><span class="p">)</span>
+
+    <span class="k">for</span> <span class="n">l</span> <span class="ow">in</span> <span class="n">data</span><span class="p">:</span>
+
+        <span class="n">l</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">split</span><span class="p">(</span>
+            <span class="s1">&#39;[ ]{2,}&#39;</span><span class="p">,</span>
+            <span class="n">re</span><span class="o">.</span><span class="n">sub</span><span class="p">(</span>
+                <span class="s1">&#39;[ ]+,[ ]+&#39;</span><span class="p">,</span> <span class="s1">&#39;,&#39;</span><span class="p">,</span>
+                <span class="n">re</span><span class="o">.</span><span class="n">sub</span><span class="p">(</span>
+                    <span class="sa">r</span><span class="s1">&#39;[ ]*\(&#39;</span><span class="p">,</span> <span class="s1">&#39;(&#39;</span><span class="p">,</span>
+                    <span class="n">l</span>
+                <span class="p">)</span>
+            <span class="p">)</span>
+        <span class="p">)</span>
+
+        <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">l</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span> <span class="o">==</span> <span class="mi">4</span> <span class="ow">and</span> <span class="n">pdb_re</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="n">l</span><span class="p">[</span><span class="mi">0</span><span class="p">]):</span>
+
+            <span class="n">pdb</span> <span class="o">=</span> <span class="n">l</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span>
+            <span class="n">res</span> <span class="o">=</span> <span class="kc">None</span> <span class="k">if</span> <span class="n">l</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="o">==</span> <span class="s1">&#39;-&#39;</span> <span class="k">else</span> <span class="nb">float</span><span class="p">(</span><span class="n">l</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s1">&#39; A&#39;</span><span class="p">,</span> <span class="s1">&#39;&#39;</span><span class="p">))</span>
+            <span class="n">met</span> <span class="o">=</span> <span class="n">l</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span>
+
+        <span class="k">if</span> <span class="n">pdb</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span> <span class="ow">and</span> <span class="nb">len</span><span class="p">(</span><span class="n">l</span><span class="p">)</span> <span class="o">&gt;</span> <span class="mi">1</span><span class="p">:</span>
+
+            <span class="n">uniprots</span> <span class="o">=</span> <span class="n">l</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">l</span><span class="p">)</span> <span class="o">&lt;</span> <span class="mi">4</span> <span class="k">else</span> <span class="n">l</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span>
+            <span class="n">uniprots</span> <span class="o">=</span> <span class="p">{</span>
+                <span class="n">u</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;(&#39;</span><span class="p">)[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s1">&#39;)&#39;</span><span class="p">,</span> <span class="s1">&#39;&#39;</span><span class="p">)</span>
+                <span class="k">for</span> <span class="n">u</span> <span class="ow">in</span> <span class="n">uniprots</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;,&#39;</span><span class="p">)</span>
+                <span class="k">if</span> <span class="s1">&#39;(&#39;</span> <span class="ow">in</span> <span class="n">u</span>
+            <span class="p">}</span>
+            <span class="n">pdb_u</span><span class="p">[</span><span class="n">pdb</span><span class="p">]</span><span class="o">.</span><span class="n">update</span><span class="p">(</span><span class="n">uniprots</span><span class="p">)</span>
+
+            <span class="k">for</span> <span class="n">u</span> <span class="ow">in</span> <span class="n">uniprots</span><span class="p">:</span>
+
+                <span class="n">u_pdb</span><span class="p">[</span><span class="n">u</span><span class="p">]</span><span class="o">.</span><span class="n">add</span><span class="p">((</span><span class="n">pdb</span><span class="p">,</span> <span class="n">met</span><span class="p">,</span> <span class="n">res</span><span class="p">))</span>
+
+    <span class="k">return</span> <span class="nb">dict</span><span class="p">(</span><span class="n">u_pdb</span><span class="p">),</span> <span class="nb">dict</span><span class="p">(</span><span class="n">pdb_u</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="pdb_chains">
+<a class="viewcode-back" href="../../../api/pypath.inputs.pdb.pdb_chains.html#pypath.inputs.pdb.pdb_chains">[docs]</a>
+<span class="k">def</span> <span class="nf">pdb_chains</span><span class="p">():</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Amino acid chain level mapping between PDB and UniProt.</span>
+<span class="sd">    Returns two dictionaries:</span>
+<span class="sd">    * The first has UniProt IDs as keys and lists of dicts as values. Each</span>
+<span class="sd">      of these dicts defines a mapping between UniProt and PDB amino acid</span>
+<span class="sd">      chains with the chain identifier, PDB structure identifier and the</span>
+<span class="sd">      start and end of the chain in the UniProt sequence and the PDB</span>
+<span class="sd">      structure; the offset value is an integer if the PDB and the UniProt</span>
+<span class="sd">      chain are the same length, otherwise None.</span>
+<span class="sd">    * The second dict has PDB IDs as keys and dicts of chain mapping dicts</span>
+<span class="sd">      as values, which are similar to the ones in the previous point, but</span>
+<span class="sd">      here the chain identifiers are the keys.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="k">def</span> <span class="nf">to_int</span><span class="p">(</span><span class="n">i</span><span class="p">):</span>
+
+        <span class="k">if</span> <span class="n">i</span> <span class="o">==</span> <span class="s1">&#39;None&#39;</span><span class="p">:</span>
+
+            <span class="k">return</span> <span class="kc">None</span>
+
+        <span class="k">return</span> <span class="nb">int</span><span class="p">(</span><span class="n">non_digit</span><span class="o">.</span><span class="n">sub</span><span class="p">(</span><span class="s1">&#39;&#39;</span><span class="p">,</span> <span class="n">i</span><span class="p">))</span>
+
+
+    <span class="n">c</span> <span class="o">=</span> <span class="n">curl</span><span class="o">.</span><span class="n">Curl</span><span class="p">(</span><span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;pdb_chains&#39;</span><span class="p">][</span><span class="s1">&#39;url&#39;</span><span class="p">],</span> <span class="n">silent</span> <span class="o">=</span> <span class="kc">False</span><span class="p">)</span>
+    <span class="n">chains</span> <span class="o">=</span> <span class="n">c</span><span class="o">.</span><span class="n">result</span>
+
+    <span class="k">if</span> <span class="n">chains</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
+
+        <span class="k">return</span> <span class="kc">None</span><span class="p">,</span> <span class="kc">None</span>
+
+    <span class="n">chains</span> <span class="o">=</span> <span class="n">chains</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\r</span><span class="s1">&#39;</span><span class="p">,</span> <span class="s1">&#39;&#39;</span><span class="p">)</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\n</span><span class="s1">&#39;</span><span class="p">)</span>
+    <span class="k">del</span> <span class="n">chains</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span>
+    <span class="k">del</span> <span class="n">chains</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span>
+    <span class="n">pdb_u</span> <span class="o">=</span> <span class="p">{}</span>
+    <span class="n">u_pdb</span> <span class="o">=</span> <span class="p">{}</span>
+    <span class="n">non_digit</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">compile</span><span class="p">(</span><span class="sa">r</span><span class="s1">&#39;[^\d.-]+&#39;</span><span class="p">)</span>
+
+    <span class="k">for</span> <span class="n">l</span> <span class="ow">in</span> <span class="n">chains</span><span class="p">:</span>
+
+        <span class="n">l</span> <span class="o">=</span> <span class="n">l</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\t</span><span class="s1">&#39;</span><span class="p">)</span>
+
+        <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">l</span><span class="p">)</span> <span class="o">&gt;</span> <span class="mi">8</span><span class="p">:</span>
+
+            <span class="k">if</span> <span class="n">l</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">pdb_u</span><span class="p">:</span>
+
+                <span class="n">pdb_u</span><span class="p">[</span><span class="n">l</span><span class="p">[</span><span class="mi">0</span><span class="p">]]</span> <span class="o">=</span> <span class="p">{}</span>
+
+            <span class="n">pdb_u</span><span class="p">[</span><span class="n">l</span><span class="p">[</span><span class="mi">0</span><span class="p">]][</span><span class="n">l</span><span class="p">[</span><span class="mi">1</span><span class="p">]]</span> <span class="o">=</span> <span class="p">{</span>
+                <span class="s1">&#39;uniprot&#39;</span><span class="p">:</span> <span class="n">l</span><span class="p">[</span><span class="mi">2</span><span class="p">],</span>
+                <span class="s1">&#39;chain_beg&#39;</span><span class="p">:</span> <span class="n">to_int</span><span class="p">(</span><span class="n">l</span><span class="p">[</span><span class="mi">3</span><span class="p">]),</span>
+                <span class="s1">&#39;chain_end&#39;</span><span class="p">:</span> <span class="n">to_int</span><span class="p">(</span><span class="n">l</span><span class="p">[</span><span class="mi">4</span><span class="p">]),</span>
+                <span class="s1">&#39;pdb_beg&#39;</span><span class="p">:</span> <span class="n">to_int</span><span class="p">(</span><span class="n">l</span><span class="p">[</span><span class="mi">5</span><span class="p">]),</span>
+                <span class="s1">&#39;pdb_end&#39;</span><span class="p">:</span> <span class="n">to_int</span><span class="p">(</span><span class="n">l</span><span class="p">[</span><span class="mi">6</span><span class="p">]),</span>
+                <span class="s1">&#39;uniprot_beg&#39;</span><span class="p">:</span> <span class="n">to_int</span><span class="p">(</span><span class="n">l</span><span class="p">[</span><span class="mi">7</span><span class="p">]),</span>
+                <span class="s1">&#39;uniprot_end&#39;</span><span class="p">:</span> <span class="n">to_int</span><span class="p">(</span><span class="n">l</span><span class="p">[</span><span class="mi">8</span><span class="p">])</span>
+            <span class="p">}</span>
+
+            <span class="k">if</span> <span class="p">(</span>
+                <span class="n">pdb_u</span><span class="p">[</span><span class="n">l</span><span class="p">[</span><span class="mi">0</span><span class="p">]][</span><span class="n">l</span><span class="p">[</span><span class="mi">1</span><span class="p">]][</span><span class="s1">&#39;pdb_end&#39;</span><span class="p">]</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span> <span class="ow">and</span>
+                <span class="n">pdb_u</span><span class="p">[</span><span class="n">l</span><span class="p">[</span><span class="mi">0</span><span class="p">]][</span><span class="n">l</span><span class="p">[</span><span class="mi">1</span><span class="p">]][</span><span class="s1">&#39;pdb_beg&#39;</span><span class="p">]</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span> <span class="ow">and</span>
+                <span class="n">pdb_u</span><span class="p">[</span><span class="n">l</span><span class="p">[</span><span class="mi">0</span><span class="p">]][</span><span class="n">l</span><span class="p">[</span><span class="mi">1</span><span class="p">]][</span><span class="s1">&#39;uniprot_beg&#39;</span><span class="p">]</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span> <span class="ow">and</span>
+                <span class="n">pdb_u</span><span class="p">[</span><span class="n">l</span><span class="p">[</span><span class="mi">0</span><span class="p">]][</span><span class="n">l</span><span class="p">[</span><span class="mi">1</span><span class="p">]][</span><span class="s1">&#39;uniprot_end&#39;</span><span class="p">]</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span> <span class="ow">and</span>
+                <span class="p">(</span>
+                    <span class="n">pdb_u</span><span class="p">[</span><span class="n">l</span><span class="p">[</span><span class="mi">0</span><span class="p">]][</span><span class="n">l</span><span class="p">[</span><span class="mi">1</span><span class="p">]][</span><span class="s1">&#39;pdb_end&#39;</span><span class="p">]</span> <span class="o">-</span>
+                    <span class="n">pdb_u</span><span class="p">[</span><span class="n">l</span><span class="p">[</span><span class="mi">0</span><span class="p">]][</span><span class="n">l</span><span class="p">[</span><span class="mi">1</span><span class="p">]][</span><span class="s1">&#39;pdb_beg&#39;</span><span class="p">]</span> <span class="o">==</span>
+                    <span class="n">pdb_u</span><span class="p">[</span><span class="n">l</span><span class="p">[</span><span class="mi">0</span><span class="p">]][</span><span class="n">l</span><span class="p">[</span><span class="mi">1</span><span class="p">]][</span><span class="s1">&#39;uniprot_end&#39;</span><span class="p">]</span> <span class="o">-</span>
+                    <span class="n">pdb_u</span><span class="p">[</span><span class="n">l</span><span class="p">[</span><span class="mi">0</span><span class="p">]][</span><span class="n">l</span><span class="p">[</span><span class="mi">1</span><span class="p">]][</span><span class="s1">&#39;uniprot_beg&#39;</span><span class="p">]</span>
+                <span class="p">)</span>
+            <span class="p">):</span>
+
+                <span class="n">pdb_u</span><span class="p">[</span><span class="n">l</span><span class="p">[</span><span class="mi">0</span><span class="p">]][</span><span class="n">l</span><span class="p">[</span><span class="mi">1</span><span class="p">]][</span><span class="s1">&#39;offset&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="p">(</span>
+                    <span class="n">pdb_u</span><span class="p">[</span><span class="n">l</span><span class="p">[</span><span class="mi">0</span><span class="p">]][</span><span class="n">l</span><span class="p">[</span><span class="mi">1</span><span class="p">]][</span><span class="s1">&#39;uniprot_beg&#39;</span><span class="p">]</span> <span class="o">-</span>
+                    <span class="n">pdb_u</span><span class="p">[</span><span class="n">l</span><span class="p">[</span><span class="mi">0</span><span class="p">]][</span><span class="n">l</span><span class="p">[</span><span class="mi">1</span><span class="p">]][</span><span class="s1">&#39;pdb_beg&#39;</span><span class="p">]</span>
+                <span class="p">)</span>
+
+            <span class="k">else</span><span class="p">:</span>
+
+                <span class="n">pdb_u</span><span class="p">[</span><span class="n">l</span><span class="p">[</span><span class="mi">0</span><span class="p">]][</span><span class="n">l</span><span class="p">[</span><span class="mi">1</span><span class="p">]][</span><span class="s1">&#39;offset&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="kc">None</span>
+
+            <span class="k">if</span> <span class="n">l</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">u_pdb</span><span class="p">:</span>
+
+                <span class="n">u_pdb</span><span class="p">[</span><span class="n">l</span><span class="p">[</span><span class="mi">2</span><span class="p">]]</span> <span class="o">=</span> <span class="p">[]</span>
+
+            <span class="n">u_pdb</span><span class="p">[</span><span class="n">l</span><span class="p">[</span><span class="mi">2</span><span class="p">]]</span><span class="o">.</span><span class="n">append</span><span class="p">({</span>
+                <span class="s1">&#39;pdb&#39;</span><span class="p">:</span> <span class="n">l</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span>
+                <span class="s1">&#39;chain&#39;</span><span class="p">:</span> <span class="n">l</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span>
+                <span class="s1">&#39;chain_beg&#39;</span><span class="p">:</span> <span class="n">to_int</span><span class="p">(</span><span class="n">l</span><span class="p">[</span><span class="mi">3</span><span class="p">]),</span>
+                <span class="s1">&#39;chain_end&#39;</span><span class="p">:</span> <span class="n">to_int</span><span class="p">(</span><span class="n">l</span><span class="p">[</span><span class="mi">4</span><span class="p">]),</span>
+                <span class="s1">&#39;pdb_beg&#39;</span><span class="p">:</span> <span class="n">to_int</span><span class="p">(</span><span class="n">l</span><span class="p">[</span><span class="mi">5</span><span class="p">]),</span>
+                <span class="s1">&#39;pdb_end&#39;</span><span class="p">:</span> <span class="n">to_int</span><span class="p">(</span><span class="n">l</span><span class="p">[</span><span class="mi">6</span><span class="p">]),</span>
+                <span class="s1">&#39;uniprot_beg&#39;</span><span class="p">:</span> <span class="n">to_int</span><span class="p">(</span><span class="n">l</span><span class="p">[</span><span class="mi">7</span><span class="p">]),</span>
+                <span class="s1">&#39;uniprot_end&#39;</span><span class="p">:</span> <span class="n">to_int</span><span class="p">(</span><span class="n">l</span><span class="p">[</span><span class="mi">8</span><span class="p">]),</span>
+                <span class="s1">&#39;offset&#39;</span><span class="p">:</span> <span class="n">pdb_u</span><span class="p">[</span><span class="n">l</span><span class="p">[</span><span class="mi">0</span><span class="p">]][</span><span class="n">l</span><span class="p">[</span><span class="mi">1</span><span class="p">]][</span><span class="s1">&#39;offset&#39;</span><span class="p">]</span>
+            <span class="p">})</span>
+
+    <span class="k">return</span> <span class="n">u_pdb</span><span class="p">,</span> <span class="n">pdb_u</span></div>
+
+
+
+<div class="viewcode-block" id="pdb_complexes">
+<a class="viewcode-back" href="../../../api/pypath.inputs.pdb.pdb_complexes.html#pypath.inputs.pdb.pdb_complexes">[docs]</a>
+<span class="k">def</span> <span class="nf">pdb_complexes</span><span class="p">(</span><span class="n">organism</span> <span class="o">=</span> <span class="kc">None</span><span class="p">):</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Extracts protein complex data from PDB. The complexes are returned in</span>
+<span class="sd">    a dict with string keys and ``pypath.internals.intera.Complex``</span>
+<span class="sd">    objects as values. These latter carry their constitution, stoichiometry</span>
+<span class="sd">    and the PDB identifiers.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="n">complexes</span> <span class="o">=</span> <span class="p">{}</span>
+
+    <span class="n">uniprot_pdb</span><span class="p">,</span> <span class="n">pdb_uniprot</span> <span class="o">=</span> <span class="n">pdb_chains</span><span class="p">()</span>
+    <span class="k">del</span> <span class="n">uniprot_pdb</span>
+
+    <span class="k">for</span> <span class="n">pdb_id</span><span class="p">,</span> <span class="n">chains</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="n">pdb_uniprot</span><span class="p">):</span>
+
+        <span class="n">uniprots</span> <span class="o">=</span> <span class="nb">tuple</span><span class="p">(</span><span class="n">chain</span><span class="p">[</span><span class="s1">&#39;uniprot&#39;</span><span class="p">]</span> <span class="k">for</span> <span class="n">chain</span> <span class="ow">in</span> <span class="n">chains</span><span class="o">.</span><span class="n">values</span><span class="p">())</span>
+
+        <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">uniprots</span><span class="p">)</span> <span class="o">==</span> <span class="mi">1</span><span class="p">:</span>
+            <span class="k">continue</span>
+
+        <span class="c1"># if the organism set and any of the UniProt IDs does not</span>
+        <span class="c1"># belong to this organism we drop the complex</span>
+        <span class="k">if</span> <span class="n">organism</span> <span class="ow">and</span> <span class="n">reflists</span><span class="o">.</span><span class="n">is_not</span><span class="p">(</span><span class="n">uniprots</span><span class="p">,</span> <span class="s1">&#39;uniprot&#39;</span><span class="p">,</span> <span class="n">organism</span><span class="p">):</span>
+
+            <span class="k">continue</span>
+
+        <span class="n">cplex</span> <span class="o">=</span> <span class="n">intera</span><span class="o">.</span><span class="n">Complex</span><span class="p">(</span>
+            <span class="n">components</span> <span class="o">=</span> <span class="n">uniprots</span><span class="p">,</span>
+            <span class="n">sources</span> <span class="o">=</span> <span class="s1">&#39;PDB&#39;</span><span class="p">,</span>
+            <span class="n">ids</span> <span class="o">=</span> <span class="n">pdb_id</span><span class="p">,</span>
+        <span class="p">)</span>
+
+        <span class="k">if</span> <span class="n">cplex</span><span class="o">.</span><span class="fm">__str__</span><span class="p">()</span> <span class="ow">in</span> <span class="n">complexes</span><span class="p">:</span>
+
+            <span class="n">complexes</span><span class="p">[</span><span class="n">cplex</span><span class="o">.</span><span class="fm">__str__</span><span class="p">()]</span> <span class="o">+=</span> <span class="n">cplex</span>
+
+        <span class="k">else</span><span class="p">:</span>
+
+            <span class="n">complexes</span><span class="p">[</span><span class="n">cplex</span><span class="o">.</span><span class="fm">__str__</span><span class="p">()]</span> <span class="o">=</span> <span class="n">cplex</span>
+
+    <span class="k">return</span> <span class="n">complexes</span></div>
+
+</pre></div>
+
+                </article>
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diff --git a/_modules/pypath/inputs/phosphatome.html b/_modules/pypath/inputs/phosphatome.html
new file mode 100644
index 000000000..30ea5d3b0
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+                  
+  <h1>Source code for pypath.inputs.phosphatome</h1><div class="highlight"><pre>
+<span></span><span class="ch">#!/usr/bin/env python</span>
+<span class="c1"># -*- coding: utf-8 -*-</span>
+
+<span class="c1">#</span>
+<span class="c1">#  This file is part of the `pypath` python module</span>
+<span class="c1">#</span>
+<span class="c1">#  Copyright 2014-2023</span>
+<span class="c1">#  EMBL, EMBL-EBI, Uniklinik RWTH Aachen, Heidelberg University</span>
+<span class="c1">#</span>
+<span class="c1">#  Authors: see the file `README.rst`</span>
+<span class="c1">#  Contact: Dénes Türei (turei.denes@gmail.com)</span>
+<span class="c1">#</span>
+<span class="c1">#  Distributed under the GPLv3 License.</span>
+<span class="c1">#  See accompanying file LICENSE.txt or copy at</span>
+<span class="c1">#      https://www.gnu.org/licenses/gpl-3.0.html</span>
+<span class="c1">#</span>
+<span class="c1">#  Website: https://pypath.omnipathdb.org/</span>
+<span class="c1">#</span>
+
+<span class="kn">import</span> <span class="nn">collections</span>
+
+<span class="kn">import</span> <span class="nn">pypath.resources.urls</span> <span class="k">as</span> <span class="nn">urls</span>
+<span class="kn">import</span> <span class="nn">pypath.share.curl</span> <span class="k">as</span> <span class="nn">curl</span>
+<span class="kn">import</span> <span class="nn">pypath.utils.mapping</span> <span class="k">as</span> <span class="nn">mapping</span>
+<span class="kn">import</span> <span class="nn">pypath.inputs.common</span> <span class="k">as</span> <span class="nn">inputs_common</span>
+<span class="kn">import</span> <span class="nn">pypath.inputs.science</span> <span class="k">as</span> <span class="nn">science_input</span>
+
+
+<div class="viewcode-block" id="phosphatome_annotations">
+<a class="viewcode-back" href="../../../api/pypath.inputs.phosphatome.phosphatome_annotations.html#pypath.inputs.phosphatome.phosphatome_annotations">[docs]</a>
+<span class="k">def</span> <span class="nf">phosphatome_annotations</span><span class="p">():</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Downloads the list of phosphatases from Chen et al, Science Signaling</span>
+<span class="sd">    (2017) Table S1.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="n">PhosphatomeAnnotation</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">namedtuple</span><span class="p">(</span>
+        <span class="s1">&#39;PhosphatomeAnnotation&#39;</span><span class="p">,</span>
+        <span class="p">[</span>
+            <span class="s1">&#39;fold&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;family&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;subfamily&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;has_protein_substrates&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;has_non_protein_substrates&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;has_catalytic_activity&#39;</span><span class="p">,</span>
+        <span class="p">],</span>
+    <span class="p">)</span>
+
+    <span class="n">url</span> <span class="o">=</span> <span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;phosphatome&#39;</span><span class="p">][</span><span class="s1">&#39;url&#39;</span><span class="p">]</span>
+    <span class="n">path</span> <span class="o">=</span> <span class="n">science_input</span><span class="o">.</span><span class="n">science_download</span><span class="p">(</span><span class="n">url</span> <span class="o">=</span> <span class="n">url</span><span class="p">)</span>
+    <span class="n">c</span> <span class="o">=</span> <span class="n">curl</span><span class="o">.</span><span class="n">FileOpener</span><span class="p">(</span>
+        <span class="n">path</span><span class="p">,</span>
+        <span class="n">compr</span> <span class="o">=</span> <span class="s1">&#39;zip&#39;</span><span class="p">,</span>
+        <span class="n">files_needed</span> <span class="o">=</span> <span class="p">[</span><span class="s1">&#39;aag1796_Tables S1 to S23.xlsx&#39;</span><span class="p">],</span>
+        <span class="n">large</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
+        <span class="n">default_mode</span> <span class="o">=</span> <span class="s1">&#39;rb&#39;</span><span class="p">,</span>
+    <span class="p">)</span>
+    <span class="n">tbl</span> <span class="o">=</span> <span class="n">inputs_common</span><span class="o">.</span><span class="n">read_xls</span><span class="p">(</span><span class="n">c</span><span class="o">.</span><span class="n">result</span><span class="p">[</span><span class="s1">&#39;aag1796_Tables S1 to S23.xlsx&#39;</span><span class="p">])</span>
+    <span class="n">result</span> <span class="o">=</span> <span class="p">[]</span>
+
+    <span class="n">result</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">defaultdict</span><span class="p">(</span><span class="nb">set</span><span class="p">)</span>
+
+    <span class="k">for</span> <span class="n">rec</span> <span class="ow">in</span> <span class="n">tbl</span><span class="p">[</span><span class="mi">2</span><span class="p">:]:</span>
+
+        <span class="n">uniprots</span> <span class="o">=</span> <span class="n">mapping</span><span class="o">.</span><span class="n">map_name</span><span class="p">(</span><span class="n">rec</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="s1">&#39;genesymbol&#39;</span><span class="p">,</span> <span class="s1">&#39;uniprot&#39;</span><span class="p">)</span>
+
+        <span class="k">for</span> <span class="n">uniprot</span> <span class="ow">in</span> <span class="n">uniprots</span><span class="p">:</span>
+
+            <span class="n">result</span><span class="p">[</span><span class="n">uniprot</span><span class="p">]</span><span class="o">.</span><span class="n">add</span><span class="p">(</span>
+                <span class="n">PhosphatomeAnnotation</span><span class="p">(</span>
+                    <span class="n">fold</span> <span class="o">=</span> <span class="n">rec</span><span class="p">[</span><span class="mi">2</span><span class="p">],</span>
+                    <span class="n">family</span> <span class="o">=</span> <span class="n">rec</span><span class="p">[</span><span class="mi">3</span><span class="p">],</span>
+                    <span class="n">subfamily</span> <span class="o">=</span> <span class="n">rec</span><span class="p">[</span><span class="mi">4</span><span class="p">],</span>
+                    <span class="n">has_protein_substrates</span> <span class="o">=</span> <span class="n">rec</span><span class="p">[</span><span class="mi">21</span><span class="p">]</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span> <span class="o">==</span> <span class="s1">&#39;yes&#39;</span><span class="p">,</span>
+                    <span class="n">has_non_protein_substrates</span> <span class="o">=</span> <span class="p">(</span>
+                        <span class="n">rec</span><span class="p">[</span><span class="mi">22</span><span class="p">]</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span> <span class="o">==</span> <span class="s1">&#39;yes&#39;</span>
+                    <span class="p">),</span>
+                    <span class="n">has_catalytic_activity</span> <span class="o">=</span> <span class="n">rec</span><span class="p">[</span><span class="mi">23</span><span class="p">]</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span> <span class="o">==</span> <span class="s1">&#39;yes&#39;</span><span class="p">,</span>
+                <span class="p">)</span>
+            <span class="p">)</span>
+
+    <span class="k">return</span> <span class="nb">dict</span><span class="p">(</span><span class="n">result</span><span class="p">)</span></div>
+
+</pre></div>
+
+                </article>
+              
+              
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\ No newline at end of file
diff --git a/_modules/pypath/inputs/phosphosite.html b/_modules/pypath/inputs/phosphosite.html
new file mode 100644
index 000000000..1b7dbb1c4
--- /dev/null
+++ b/_modules/pypath/inputs/phosphosite.html
@@ -0,0 +1,1810 @@
+
+<!DOCTYPE html>
+
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+
+  <head>
+    <meta charset="utf-8" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+    <title>pypath.inputs.phosphosite &#8212; pypath 0.16.9 documentation</title>
+  
+  
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+  <script data-cfasync="false">
+    document.documentElement.dataset.mode = localStorage.getItem("mode") || "";
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+  <h1>Source code for pypath.inputs.phosphosite</h1><div class="highlight"><pre>
+<span></span><span class="ch">#!/usr/bin/env python</span>
+<span class="c1"># -*- coding: utf-8 -*-</span>
+
+<span class="c1">#</span>
+<span class="c1">#  This file is part of the `pypath` python module</span>
+<span class="c1">#</span>
+<span class="c1">#  Copyright 2014-2023</span>
+<span class="c1">#  EMBL, EMBL-EBI, Uniklinik RWTH Aachen, Heidelberg University</span>
+<span class="c1">#</span>
+<span class="c1">#  Authors: see the file `README.rst`</span>
+<span class="c1">#  Contact: Dénes Türei (turei.denes@gmail.com)</span>
+<span class="c1">#</span>
+<span class="c1">#  Distributed under the GPLv3 License.</span>
+<span class="c1">#  See accompanying file LICENSE.txt or copy at</span>
+<span class="c1">#      https://www.gnu.org/licenses/gpl-3.0.html</span>
+<span class="c1">#</span>
+<span class="c1">#  Website: https://pypath.omnipathdb.org/</span>
+<span class="c1">#</span>
+
+<span class="kn">from</span> <span class="nn">past.builtins</span> <span class="kn">import</span> <span class="n">xrange</span><span class="p">,</span> <span class="nb">range</span>
+<span class="kn">from</span> <span class="nn">future.utils</span> <span class="kn">import</span> <span class="n">iteritems</span>
+
+<span class="kn">import</span> <span class="nn">os</span>
+<span class="kn">import</span> <span class="nn">pickle</span>
+<span class="kn">import</span> <span class="nn">re</span>
+<span class="kn">import</span> <span class="nn">itertools</span>
+
+<span class="kn">import</span> <span class="nn">xml.etree.cElementTree</span> <span class="k">as</span> <span class="nn">ET</span>
+
+<span class="kn">import</span> <span class="nn">pypath.share.progress</span> <span class="k">as</span> <span class="nn">progress</span>
+<span class="kn">import</span> <span class="nn">pypath.utils.taxonomy</span> <span class="k">as</span> <span class="nn">taxonomy</span>
+<span class="kn">import</span> <span class="nn">pypath.internals.intera</span> <span class="k">as</span> <span class="nn">intera</span>
+<span class="kn">import</span> <span class="nn">pypath.share.curl</span> <span class="k">as</span> <span class="nn">curl</span>
+<span class="kn">import</span> <span class="nn">pypath.resources.urls</span> <span class="k">as</span> <span class="nn">urls</span>
+<span class="kn">import</span> <span class="nn">pypath.inputs.uniprot_db</span> <span class="k">as</span> <span class="nn">uniprot_db</span>
+<span class="kn">import</span> <span class="nn">pypath.inputs.common</span> <span class="k">as</span> <span class="nn">inputs_common</span>
+<span class="kn">import</span> <span class="nn">pypath.inputs.homologene</span> <span class="k">as</span> <span class="nn">homologene</span>
+<span class="kn">import</span> <span class="nn">pypath.utils.mapping</span> <span class="k">as</span> <span class="nn">mapping</span>
+<span class="kn">import</span> <span class="nn">pypath.share.common</span> <span class="k">as</span> <span class="nn">common</span>
+<span class="kn">import</span> <span class="nn">pypath.share.session</span> <span class="k">as</span> <span class="nn">session</span>
+
+<span class="n">_logger</span> <span class="o">=</span> <span class="n">session</span><span class="o">.</span><span class="n">Logger</span><span class="p">(</span><span class="n">name</span> <span class="o">=</span> <span class="s1">&#39;phosphosite_input&#39;</span><span class="p">)</span>
+
+
+<div class="viewcode-block" id="phosphosite_enzyme_substrate">
+<a class="viewcode-back" href="../../../api/pypath.inputs.phosphosite.phosphosite_enzyme_substrate.html#pypath.inputs.phosphosite.phosphosite_enzyme_substrate">[docs]</a>
+<span class="k">def</span> <span class="nf">phosphosite_enzyme_substrate</span><span class="p">(</span>
+        <span class="n">raw</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
+        <span class="n">organism</span> <span class="o">=</span> <span class="s1">&#39;human&#39;</span><span class="p">,</span>
+        <span class="n">strict</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
+    <span class="p">):</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Downloads and preprocesses phosphorylation site data from PhosphoSitePlus.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="n">url</span> <span class="o">=</span> <span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;psite_kin&#39;</span><span class="p">][</span><span class="s1">&#39;url&#39;</span><span class="p">]</span>
+    <span class="n">c</span> <span class="o">=</span> <span class="n">curl</span><span class="o">.</span><span class="n">Curl</span><span class="p">(</span>
+        <span class="n">url</span><span class="p">,</span>
+        <span class="n">silent</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+        <span class="n">compr</span> <span class="o">=</span> <span class="s1">&#39;gz&#39;</span><span class="p">,</span>
+        <span class="n">encoding</span> <span class="o">=</span> <span class="s1">&#39;iso-8859-1&#39;</span><span class="p">,</span>
+        <span class="n">large</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
+    <span class="p">)</span>
+    <span class="n">orto</span> <span class="o">=</span> <span class="p">{}</span>
+    <span class="n">data</span> <span class="o">=</span> <span class="n">c</span><span class="o">.</span><span class="n">result</span>
+    <span class="n">cols</span> <span class="o">=</span> <span class="p">{</span>
+        <span class="s1">&#39;kinase&#39;</span><span class="p">:</span> <span class="mi">2</span><span class="p">,</span>
+        <span class="s1">&#39;kinase_org&#39;</span><span class="p">:</span> <span class="mi">3</span><span class="p">,</span>
+        <span class="s1">&#39;substrate&#39;</span><span class="p">:</span> <span class="mi">6</span><span class="p">,</span>
+        <span class="s1">&#39;substrate_org&#39;</span><span class="p">:</span> <span class="mi">8</span><span class="p">,</span>
+        <span class="s1">&#39;residue&#39;</span><span class="p">:</span> <span class="mi">9</span><span class="p">,</span>
+        <span class="s1">&#39;motif&#39;</span><span class="p">:</span> <span class="mi">11</span>
+    <span class="p">}</span>
+    <span class="n">data</span> <span class="o">=</span> <span class="n">inputs_common</span><span class="o">.</span><span class="n">read_table</span><span class="p">(</span>
+        <span class="n">cols</span> <span class="o">=</span> <span class="n">cols</span><span class="p">,</span>
+        <span class="n">fileObject</span> <span class="o">=</span> <span class="n">data</span><span class="p">,</span>
+        <span class="n">sep</span> <span class="o">=</span> <span class="s1">&#39;</span><span class="se">\t</span><span class="s1">&#39;</span><span class="p">,</span>
+        <span class="n">hdr</span> <span class="o">=</span> <span class="mi">4</span><span class="p">,</span>
+    <span class="p">)</span>
+    <span class="n">result</span> <span class="o">=</span> <span class="p">[]</span>
+    <span class="n">non_digit</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">compile</span><span class="p">(</span><span class="sa">r</span><span class="s1">&#39;[^\d.-]+&#39;</span><span class="p">)</span>
+    <span class="n">motre</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">compile</span><span class="p">(</span><span class="sa">r</span><span class="s1">&#39;(_*)([A-Za-z]+)(_*)&#39;</span><span class="p">)</span>
+
+    <span class="k">for</span> <span class="n">r</span> <span class="ow">in</span> <span class="n">data</span><span class="p">:</span>
+
+        <span class="k">if</span> <span class="n">organism</span> <span class="ow">is</span> <span class="kc">None</span> <span class="ow">or</span> \
+            <span class="p">((</span><span class="n">r</span><span class="p">[</span><span class="s1">&#39;kinase_org&#39;</span><span class="p">]</span> <span class="o">==</span> <span class="n">organism</span> <span class="ow">or</span> <span class="ow">not</span> <span class="n">strict</span><span class="p">)</span> <span class="ow">and</span> \
+            <span class="n">r</span><span class="p">[</span><span class="s1">&#39;substrate_org&#39;</span><span class="p">]</span> <span class="o">==</span> <span class="n">organism</span><span class="p">):</span>
+
+            <span class="k">if</span> <span class="n">r</span><span class="p">[</span><span class="s1">&#39;kinase_org&#39;</span><span class="p">]</span> <span class="o">!=</span> <span class="n">organism</span><span class="p">:</span>
+                <span class="n">korg</span> <span class="o">=</span> <span class="n">r</span><span class="p">[</span><span class="s1">&#39;kinase_org&#39;</span><span class="p">]</span>
+                <span class="c1"># attempting to map by orthology:</span>
+                <span class="k">if</span> <span class="n">korg</span> <span class="ow">in</span> <span class="n">taxonomy</span><span class="o">.</span><span class="n">taxa</span> <span class="ow">and</span> <span class="n">organism</span> <span class="ow">in</span> <span class="n">taxonomy</span><span class="o">.</span><span class="n">taxa</span><span class="p">:</span>
+
+                    <span class="n">ktaxid</span> <span class="o">=</span> <span class="n">taxonomy</span><span class="o">.</span><span class="n">taxa</span><span class="p">[</span><span class="n">korg</span><span class="p">]</span>
+                    <span class="n">taxid</span> <span class="o">=</span> <span class="n">taxonomy</span><span class="o">.</span><span class="n">taxa</span><span class="p">[</span><span class="n">organism</span><span class="p">]</span>
+
+                    <span class="k">if</span> <span class="n">korg</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">orto</span><span class="p">:</span>
+
+                        <span class="n">orto</span><span class="p">[</span><span class="n">korg</span><span class="p">]</span> <span class="o">=</span> <span class="n">homologene</span><span class="o">.</span><span class="n">homologene_dict</span><span class="p">(</span>
+                            <span class="n">ktaxid</span><span class="p">,</span>
+                            <span class="n">taxid</span><span class="p">,</span>
+                            <span class="s1">&#39;refseqp&#39;</span><span class="p">,</span>
+                        <span class="p">)</span>
+
+                    <span class="n">korg_refseq</span> <span class="o">=</span> <span class="n">mapping</span><span class="o">.</span><span class="n">map_name</span><span class="p">(</span><span class="n">r</span><span class="p">[</span><span class="s1">&#39;kinase&#39;</span><span class="p">],</span>
+                                                    <span class="s1">&#39;uniprot&#39;</span><span class="p">,</span>
+                                                    <span class="s1">&#39;refseqp&#39;</span><span class="p">,</span>
+                                                    <span class="n">ktaxid</span><span class="p">)</span>
+
+                    <span class="n">kin_uniprot</span> <span class="o">=</span> \
+                        <span class="nb">list</span><span class="p">(</span>
+                            <span class="n">itertools</span><span class="o">.</span><span class="n">chain</span><span class="p">(</span>
+                                <span class="o">*</span><span class="nb">map</span><span class="p">(</span>
+                                    <span class="k">lambda</span> <span class="n">ors</span><span class="p">:</span>
+                                        <span class="n">mapping</span><span class="o">.</span><span class="n">map_name</span><span class="p">(</span><span class="n">ors</span><span class="p">,</span>
+                                                        <span class="s1">&#39;refseqp&#39;</span><span class="p">,</span>
+                                                        <span class="s1">&#39;uniprot&#39;</span><span class="p">,</span>
+                                                        <span class="n">taxid</span><span class="p">),</span>
+                                    <span class="n">itertools</span><span class="o">.</span><span class="n">chain</span><span class="p">(</span>
+                                        <span class="o">*</span><span class="nb">map</span><span class="p">(</span>
+                                            <span class="k">lambda</span> <span class="n">rs</span><span class="p">:</span>
+                                                <span class="n">orto</span><span class="p">[</span><span class="n">korg</span><span class="p">][</span><span class="n">rs</span><span class="p">],</span>
+                                            <span class="nb">filter</span><span class="p">(</span>
+                                                <span class="k">lambda</span> <span class="n">rs</span><span class="p">:</span>
+                                                    <span class="n">rs</span> <span class="ow">in</span> <span class="n">orto</span><span class="p">[</span><span class="n">korg</span><span class="p">],</span>
+                                                <span class="n">korg_refseq</span>
+                                            <span class="p">)</span>
+                                        <span class="p">)</span>
+                                    <span class="p">)</span>
+                                <span class="p">)</span>
+                            <span class="p">)</span>
+                        <span class="p">)</span>
+            <span class="k">else</span><span class="p">:</span>
+                <span class="n">kin_uniprot</span> <span class="o">=</span> <span class="p">[</span><span class="n">r</span><span class="p">[</span><span class="s1">&#39;kinase&#39;</span><span class="p">]]</span>
+
+            <span class="k">for</span> <span class="n">kinase</span> <span class="ow">in</span> <span class="n">kin_uniprot</span><span class="p">:</span>
+
+                <span class="n">r</span><span class="p">[</span><span class="s1">&#39;resaa&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">r</span><span class="p">[</span><span class="s1">&#39;residue&#39;</span><span class="p">][</span><span class="mi">0</span><span class="p">]</span>
+                <span class="n">r</span><span class="p">[</span><span class="s1">&#39;resnum&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">non_digit</span><span class="o">.</span><span class="n">sub</span><span class="p">(</span><span class="s1">&#39;&#39;</span><span class="p">,</span> <span class="n">r</span><span class="p">[</span><span class="s1">&#39;residue&#39;</span><span class="p">][</span><span class="mi">1</span><span class="p">:]))</span>
+                <span class="n">mot</span> <span class="o">=</span> <span class="n">motre</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="n">r</span><span class="p">[</span><span class="s1">&#39;motif&#39;</span><span class="p">])</span>
+
+                <span class="c1"># excluding e.g. Q12809_VAR_014388</span>
+                <span class="n">r</span><span class="p">[</span><span class="s1">&#39;substrate&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">r</span><span class="p">[</span><span class="s1">&#39;substrate&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;_&#39;</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span>
+                <span class="n">sisoform</span> <span class="o">=</span> <span class="mi">1</span> <span class="k">if</span> <span class="s1">&#39;-&#39;</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">r</span><span class="p">[</span><span class="s1">&#39;substrate&#39;</span><span class="p">]</span> <span class="k">else</span> \
+                    <span class="nb">int</span><span class="p">(</span><span class="n">r</span><span class="p">[</span><span class="s1">&#39;substrate&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;-&#39;</span><span class="p">)[</span><span class="mi">1</span><span class="p">])</span>
+                <span class="n">r</span><span class="p">[</span><span class="s1">&#39;substrate&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">r</span><span class="p">[</span><span class="s1">&#39;substrate&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;-&#39;</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span>
+
+                <span class="n">kisoform</span> <span class="o">=</span> <span class="p">(</span>
+                    <span class="mi">1</span> <span class="k">if</span> <span class="s1">&#39;-&#39;</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">kinase</span> <span class="k">else</span> <span class="nb">int</span><span class="p">(</span><span class="n">kinase</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;-&#39;</span><span class="p">)[</span><span class="mi">1</span><span class="p">])</span>
+                <span class="p">)</span>
+                <span class="n">kinase</span> <span class="o">=</span> <span class="n">kinase</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;-&#39;</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span>
+
+                <span class="n">r</span><span class="p">[</span><span class="s1">&#39;substrate&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">r</span><span class="p">[</span><span class="s1">&#39;substrate&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;-&#39;</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span>
+
+                <span class="k">if</span> <span class="n">mot</span><span class="p">:</span>
+                    <span class="n">r</span><span class="p">[</span><span class="s1">&#39;start&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">r</span><span class="p">[</span><span class="s1">&#39;resnum&#39;</span><span class="p">]</span> <span class="o">-</span> <span class="mi">7</span> <span class="o">+</span> <span class="nb">len</span><span class="p">(</span><span class="n">mot</span><span class="o">.</span><span class="n">groups</span><span class="p">()[</span><span class="mi">0</span><span class="p">])</span>
+                    <span class="n">r</span><span class="p">[</span><span class="s1">&#39;end&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">r</span><span class="p">[</span><span class="s1">&#39;resnum&#39;</span><span class="p">]</span> <span class="o">+</span> <span class="mi">7</span> <span class="o">-</span> <span class="nb">len</span><span class="p">(</span><span class="n">mot</span><span class="o">.</span><span class="n">groups</span><span class="p">()[</span><span class="mi">2</span><span class="p">])</span>
+                    <span class="n">r</span><span class="p">[</span><span class="s1">&#39;instance&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">r</span><span class="p">[</span><span class="s1">&#39;motif&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s1">&#39;_&#39;</span><span class="p">,</span> <span class="s1">&#39;&#39;</span><span class="p">)</span><span class="o">.</span><span class="n">upper</span><span class="p">()</span>
+                <span class="k">else</span><span class="p">:</span>
+                    <span class="n">r</span><span class="p">[</span><span class="s1">&#39;start&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="kc">None</span>
+                    <span class="n">r</span><span class="p">[</span><span class="s1">&#39;end&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="kc">None</span>
+                    <span class="n">r</span><span class="p">[</span><span class="s1">&#39;instance&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="kc">None</span>
+
+                <span class="k">if</span> <span class="n">raw</span><span class="p">:</span>
+                    <span class="n">r</span><span class="p">[</span><span class="s1">&#39;kinase&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">kinase</span>
+                    <span class="n">result</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">r</span><span class="p">)</span>
+                <span class="k">else</span><span class="p">:</span>
+                    <span class="n">res</span> <span class="o">=</span> <span class="n">intera</span><span class="o">.</span><span class="n">Residue</span><span class="p">(</span><span class="n">r</span><span class="p">[</span><span class="s1">&#39;resnum&#39;</span><span class="p">],</span> <span class="n">r</span><span class="p">[</span><span class="s1">&#39;resaa&#39;</span><span class="p">],</span>
+                                         <span class="n">r</span><span class="p">[</span><span class="s1">&#39;substrate&#39;</span><span class="p">],</span>
+                                         <span class="n">isoform</span> <span class="o">=</span> <span class="n">sisoform</span><span class="p">)</span>
+
+                    <span class="n">mot</span> <span class="o">=</span> <span class="n">intera</span><span class="o">.</span><span class="n">Motif</span><span class="p">(</span>
+                        <span class="n">r</span><span class="p">[</span><span class="s1">&#39;substrate&#39;</span><span class="p">],</span>
+                        <span class="n">r</span><span class="p">[</span><span class="s1">&#39;start&#39;</span><span class="p">],</span>
+                        <span class="n">r</span><span class="p">[</span><span class="s1">&#39;end&#39;</span><span class="p">],</span>
+                        <span class="n">instance</span> <span class="o">=</span> <span class="n">r</span><span class="p">[</span><span class="s1">&#39;instance&#39;</span><span class="p">],</span>
+                        <span class="n">isoform</span> <span class="o">=</span> <span class="n">sisoform</span><span class="p">)</span>
+
+                    <span class="n">ptm</span> <span class="o">=</span> <span class="n">intera</span><span class="o">.</span><span class="n">Ptm</span><span class="p">(</span><span class="n">protein</span> <span class="o">=</span> <span class="n">r</span><span class="p">[</span><span class="s1">&#39;substrate&#39;</span><span class="p">],</span>
+                                    <span class="n">residue</span> <span class="o">=</span> <span class="n">res</span><span class="p">,</span>
+                                    <span class="n">motif</span> <span class="o">=</span> <span class="n">mot</span><span class="p">,</span>
+                                    <span class="n">typ</span> <span class="o">=</span> <span class="s1">&#39;phosphorylation&#39;</span><span class="p">,</span>
+                                    <span class="n">source</span> <span class="o">=</span> <span class="s1">&#39;PhosphoSite&#39;</span><span class="p">,</span>
+                                    <span class="n">isoform</span> <span class="o">=</span> <span class="n">sisoform</span><span class="p">)</span>
+
+                    <span class="n">dom</span> <span class="o">=</span> <span class="n">intera</span><span class="o">.</span><span class="n">Domain</span><span class="p">(</span><span class="n">protein</span> <span class="o">=</span> <span class="n">kinase</span><span class="p">,</span> <span class="n">isoform</span> <span class="o">=</span> <span class="n">kisoform</span><span class="p">)</span>
+
+                    <span class="n">dommot</span> <span class="o">=</span> <span class="n">intera</span><span class="o">.</span><span class="n">DomainMotif</span><span class="p">(</span>
+                        <span class="n">domain</span> <span class="o">=</span> <span class="n">dom</span><span class="p">,</span> <span class="n">ptm</span> <span class="o">=</span> <span class="n">ptm</span><span class="p">,</span> <span class="n">sources</span> <span class="o">=</span> <span class="p">[</span><span class="s1">&#39;PhosphoSite&#39;</span><span class="p">])</span>
+
+                    <span class="n">result</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">dommot</span><span class="p">)</span>
+
+    <span class="k">return</span> <span class="n">result</span></div>
+
+
+
+<div class="viewcode-block" id="phosphosite_ptm_orthology">
+<a class="viewcode-back" href="../../../api/pypath.inputs.phosphosite.phosphosite_ptm_orthology.html#pypath.inputs.phosphosite.phosphosite_ptm_orthology">[docs]</a>
+<span class="k">def</span> <span class="nf">phosphosite_ptm_orthology</span><span class="p">():</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Returns an orthology translation dict of phosphosites</span>
+<span class="sd">    based on phosphorylation sites table from PhosphoSitePlus.</span>
+<span class="sd">    In the result all PTMs represented by a tuple of the following</span>
+<span class="sd">    6 elements: UniProt ID, isoform (int), residue one letter code,</span>
+<span class="sd">    residue number (int), NCBI Taxonomy ID (int), modification type.</span>
+
+<span class="sd">    :param int source: Source taxon (NCBI Taxonomy).</span>
+<span class="sd">    :param int target: Target taxon (NCBI Taxonomy).</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="n">result</span> <span class="o">=</span> <span class="p">{}</span>
+
+    <span class="n">nondigit</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">compile</span><span class="p">(</span><span class="sa">r</span><span class="s1">&#39;[^\d]+&#39;</span><span class="p">)</span>
+
+    <span class="n">unknown_taxa</span> <span class="o">=</span> <span class="nb">set</span><span class="p">([])</span>
+
+    <span class="k">for</span> <span class="n">typ</span> <span class="ow">in</span> <span class="n">common</span><span class="o">.</span><span class="n">psite_mod_types</span><span class="p">:</span>
+
+        <span class="n">groups</span> <span class="o">=</span> <span class="p">{}</span>
+
+        <span class="n">url</span> <span class="o">=</span> <span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;psite_</span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="n">typ</span><span class="p">[</span><span class="mi">0</span><span class="p">]][</span><span class="s1">&#39;url&#39;</span><span class="p">]</span>
+        <span class="n">c</span> <span class="o">=</span> <span class="n">curl</span><span class="o">.</span><span class="n">Curl</span><span class="p">(</span><span class="n">url</span><span class="p">,</span> <span class="n">silent</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span> <span class="n">large</span> <span class="o">=</span> <span class="kc">True</span><span class="p">)</span>
+
+        <span class="n">data</span> <span class="o">=</span> <span class="n">c</span><span class="o">.</span><span class="n">result</span>
+
+        <span class="k">for</span> <span class="n">_</span> <span class="ow">in</span> <span class="n">xrange</span><span class="p">(</span><span class="mi">4</span><span class="p">):</span>
+
+            <span class="n">__</span> <span class="o">=</span> <span class="nb">next</span><span class="p">(</span><span class="n">data</span><span class="p">)</span>
+
+        <span class="k">for</span> <span class="n">r</span> <span class="ow">in</span> <span class="n">data</span><span class="p">:</span>
+
+            <span class="n">r</span> <span class="o">=</span> <span class="n">common</span><span class="o">.</span><span class="n">decode</span><span class="p">(</span><span class="n">r</span><span class="p">,</span> <span class="s1">&#39;utf-8&#39;</span><span class="p">)</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\t</span><span class="s1">&#39;</span><span class="p">)</span>
+
+            <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">r</span><span class="p">)</span> <span class="o">&lt;</span> <span class="mi">10</span><span class="p">:</span>
+
+                <span class="k">continue</span>
+
+            <span class="n">uniprot</span> <span class="o">=</span> <span class="n">r</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span>
+            <span class="n">isoform</span> <span class="o">=</span> <span class="mi">1</span> <span class="k">if</span> <span class="s1">&#39;-&#39;</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">uniprot</span> <span class="k">else</span> <span class="nb">int</span><span class="p">(</span><span class="n">uniprot</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;-&#39;</span><span class="p">)[</span><span class="mi">1</span><span class="p">])</span>
+            <span class="n">uniprot</span> <span class="o">=</span> <span class="n">uniprot</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;-&#39;</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span>
+            <span class="n">aa</span> <span class="o">=</span> <span class="n">r</span><span class="p">[</span><span class="mi">4</span><span class="p">][</span><span class="mi">0</span><span class="p">]</span>
+            <span class="n">num</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">nondigit</span><span class="o">.</span><span class="n">sub</span><span class="p">(</span><span class="s1">&#39;&#39;</span><span class="p">,</span> <span class="n">r</span><span class="p">[</span><span class="mi">4</span><span class="p">]))</span>
+            <span class="k">if</span> <span class="n">r</span><span class="p">[</span><span class="mi">6</span><span class="p">]</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">taxonomy</span><span class="o">.</span><span class="n">taxa</span><span class="p">:</span>
+                <span class="n">unknown_taxa</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">r</span><span class="p">[</span><span class="mi">6</span><span class="p">])</span>
+                <span class="k">continue</span>
+
+            <span class="n">tax</span> <span class="o">=</span> <span class="n">taxonomy</span><span class="o">.</span><span class="n">taxa</span><span class="p">[</span><span class="n">r</span><span class="p">[</span><span class="mi">6</span><span class="p">]]</span>
+            <span class="n">group</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">r</span><span class="p">[</span><span class="mi">5</span><span class="p">])</span>
+
+            <span class="n">this_site</span> <span class="o">=</span> <span class="p">(</span><span class="n">uniprot</span><span class="p">,</span> <span class="n">isoform</span><span class="p">,</span> <span class="n">aa</span><span class="p">,</span> <span class="n">num</span><span class="p">,</span> <span class="n">tax</span><span class="p">,</span> <span class="n">typ</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span>
+
+            <span class="k">if</span> <span class="n">group</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">groups</span><span class="p">:</span>
+                <span class="n">groups</span><span class="p">[</span><span class="n">group</span><span class="p">]</span> <span class="o">=</span> <span class="nb">set</span><span class="p">([])</span>
+
+            <span class="n">groups</span><span class="p">[</span><span class="n">group</span><span class="p">]</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">this_site</span><span class="p">)</span>
+
+        <span class="k">for</span> <span class="n">group</span><span class="p">,</span> <span class="n">sites</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="n">groups</span><span class="p">):</span>
+
+            <span class="k">for</span> <span class="n">site1</span> <span class="ow">in</span> <span class="n">sites</span><span class="p">:</span>
+
+                <span class="k">for</span> <span class="n">site2</span> <span class="ow">in</span> <span class="n">sites</span><span class="p">:</span>
+
+                    <span class="k">if</span> <span class="n">site1</span><span class="p">[</span><span class="mi">4</span><span class="p">]</span> <span class="o">==</span> <span class="n">site2</span><span class="p">[</span><span class="mi">4</span><span class="p">]:</span>
+
+                        <span class="k">continue</span>
+
+                    <span class="k">if</span> <span class="n">site1</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">result</span><span class="p">:</span>
+
+                        <span class="n">result</span><span class="p">[</span><span class="n">site1</span><span class="p">]</span> <span class="o">=</span> <span class="p">{}</span>
+
+                    <span class="k">if</span> <span class="n">site2</span><span class="p">[</span><span class="mi">4</span><span class="p">]</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">result</span><span class="p">[</span><span class="n">site1</span><span class="p">]:</span>
+
+                        <span class="n">result</span><span class="p">[</span><span class="n">site1</span><span class="p">][</span><span class="n">site2</span><span class="p">[</span><span class="mi">4</span><span class="p">]]</span> <span class="o">=</span> <span class="nb">set</span><span class="p">([])</span>
+
+                    <span class="n">result</span><span class="p">[</span><span class="n">site1</span><span class="p">][</span><span class="n">site2</span><span class="p">[</span><span class="mi">4</span><span class="p">]]</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">site2</span><span class="p">)</span>
+
+    <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">unknown_taxa</span><span class="p">):</span>
+
+        <span class="n">_logger</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span>
+            <span class="s1">&#39;Unknown organisms encountered: </span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span>
+            <span class="s1">&#39;, &#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="nb">sorted</span><span class="p">(</span><span class="n">unknown_taxa</span><span class="p">))</span>
+        <span class="p">)</span>
+
+    <span class="k">return</span> <span class="n">result</span></div>
+
+
+
+<div class="viewcode-block" id="phosphosite_ptms">
+<a class="viewcode-back" href="../../../api/pypath.inputs.phosphosite.phosphosite_ptms.html#pypath.inputs.phosphosite.phosphosite_ptms">[docs]</a>
+<span class="k">def</span> <span class="nf">phosphosite_ptms</span><span class="p">(</span><span class="n">organism</span> <span class="o">=</span> <span class="s1">&#39;human&#39;</span><span class="p">):</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Downloads the phosphorylation site dataset from PhosphoSitePlus.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="n">result</span> <span class="o">=</span> <span class="p">[]</span>
+    <span class="n">url</span> <span class="o">=</span> <span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;psite_p&#39;</span><span class="p">][</span><span class="s1">&#39;url&#39;</span><span class="p">]</span>
+    <span class="n">nondigit</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">compile</span><span class="p">(</span><span class="sa">r</span><span class="s1">&#39;[^\d]+&#39;</span><span class="p">)</span>
+    <span class="n">remot</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">compile</span><span class="p">(</span><span class="sa">r</span><span class="s1">&#39;(_*)([A-Za-z]+)(_*)&#39;</span><span class="p">)</span>
+
+    <span class="n">c</span> <span class="o">=</span> <span class="n">curl</span><span class="o">.</span><span class="n">Curl</span><span class="p">(</span><span class="n">url</span><span class="p">,</span> <span class="n">silent</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span> <span class="n">large</span> <span class="o">=</span> <span class="kc">True</span><span class="p">)</span>
+    <span class="n">data</span> <span class="o">=</span> <span class="n">c</span><span class="o">.</span><span class="n">result</span>
+
+    <span class="k">for</span> <span class="n">_</span> <span class="ow">in</span> <span class="n">xrange</span><span class="p">(</span><span class="mi">4</span><span class="p">):</span>
+
+        <span class="n">_</span> <span class="o">=</span> <span class="nb">next</span><span class="p">(</span><span class="n">c</span><span class="o">.</span><span class="n">result</span><span class="p">)</span>
+
+    <span class="k">for</span> <span class="n">r</span> <span class="ow">in</span> <span class="n">data</span><span class="p">:</span>
+
+        <span class="n">r</span> <span class="o">=</span> <span class="n">r</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\t</span><span class="s1">&#39;</span><span class="p">)</span>
+
+        <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">r</span><span class="p">)</span> <span class="o">&gt;</span> <span class="mi">9</span> <span class="ow">and</span> <span class="p">(</span><span class="n">organism</span> <span class="ow">is</span> <span class="kc">None</span> <span class="ow">or</span> <span class="n">r</span><span class="p">[</span><span class="mi">6</span><span class="p">]</span> <span class="o">==</span> <span class="n">organism</span><span class="p">):</span>
+
+            <span class="n">uniprot</span> <span class="o">=</span> <span class="n">r</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span>
+            <span class="n">isoform</span> <span class="o">=</span> <span class="mi">1</span> <span class="k">if</span> <span class="s1">&#39;-&#39;</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">uniprot</span> <span class="k">else</span> <span class="nb">int</span><span class="p">(</span><span class="n">uniprot</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;-&#39;</span><span class="p">)[</span><span class="mi">1</span><span class="p">])</span>
+            <span class="n">uniprot</span> <span class="o">=</span> <span class="n">uniprot</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;-&#39;</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span>
+            <span class="n">typ</span> <span class="o">=</span> <span class="n">r</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span>
+
+            <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">typ</span><span class="p">)</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
+
+                <span class="n">typ</span> <span class="o">=</span> <span class="n">r</span><span class="p">[</span><span class="mi">4</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;-&#39;</span><span class="p">)[</span><span class="mi">1</span><span class="p">]</span> <span class="k">if</span> <span class="s1">&#39;-&#39;</span> <span class="ow">in</span> <span class="n">r</span><span class="p">[</span><span class="mi">4</span><span class="p">]</span> <span class="k">else</span> <span class="kc">None</span>
+
+            <span class="n">aa</span> <span class="o">=</span> <span class="n">r</span><span class="p">[</span><span class="mi">4</span><span class="p">][</span><span class="mi">0</span><span class="p">]</span>
+            <span class="n">num</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">nondigit</span><span class="o">.</span><span class="n">sub</span><span class="p">(</span><span class="s1">&#39;&#39;</span><span class="p">,</span> <span class="n">r</span><span class="p">[</span><span class="mi">4</span><span class="p">]))</span>
+            <span class="n">motif</span> <span class="o">=</span> <span class="n">remot</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="n">r</span><span class="p">[</span><span class="mi">9</span><span class="p">])</span>
+
+            <span class="k">if</span> <span class="n">motif</span><span class="p">:</span>
+
+                <span class="n">start</span> <span class="o">=</span> <span class="n">num</span> <span class="o">-</span> <span class="mi">7</span> <span class="o">+</span> <span class="nb">len</span><span class="p">(</span><span class="n">motif</span><span class="o">.</span><span class="n">groups</span><span class="p">()[</span><span class="mi">0</span><span class="p">])</span>
+                <span class="n">end</span> <span class="o">=</span> <span class="n">num</span> <span class="o">+</span> <span class="mi">7</span> <span class="o">-</span> <span class="nb">len</span><span class="p">(</span><span class="n">motif</span><span class="o">.</span><span class="n">groups</span><span class="p">()[</span><span class="mi">2</span><span class="p">])</span>
+                <span class="n">instance</span> <span class="o">=</span> <span class="n">r</span><span class="p">[</span><span class="mi">9</span><span class="p">]</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s1">&#39;_&#39;</span><span class="p">,</span> <span class="s1">&#39;&#39;</span><span class="p">)</span><span class="o">.</span><span class="n">upper</span><span class="p">()</span>
+
+            <span class="k">else</span><span class="p">:</span>
+
+                <span class="n">start</span> <span class="o">=</span> <span class="kc">None</span>
+                <span class="n">end</span> <span class="o">=</span> <span class="kc">None</span>
+                <span class="n">instance</span> <span class="o">=</span> <span class="kc">None</span>
+
+            <span class="n">res</span> <span class="o">=</span> <span class="n">intera</span><span class="o">.</span><span class="n">Residue</span><span class="p">(</span>
+                <span class="n">num</span><span class="p">,</span>
+                <span class="n">aa</span><span class="p">,</span>
+                <span class="n">uniprot</span><span class="p">,</span>
+                <span class="n">isoform</span> <span class="o">=</span> <span class="n">isoform</span><span class="p">,</span>
+            <span class="p">)</span>
+            <span class="n">mot</span> <span class="o">=</span> <span class="n">intera</span><span class="o">.</span><span class="n">Motif</span><span class="p">(</span>
+                <span class="n">uniprot</span><span class="p">,</span>
+                <span class="n">start</span><span class="p">,</span>
+                <span class="n">end</span><span class="p">,</span>
+                <span class="n">instance</span> <span class="o">=</span> <span class="n">instance</span><span class="p">,</span>
+                <span class="n">isoform</span> <span class="o">=</span> <span class="n">isoform</span><span class="p">,</span>
+            <span class="p">)</span>
+            <span class="n">ptm</span> <span class="o">=</span> <span class="n">intera</span><span class="o">.</span><span class="n">Ptm</span><span class="p">(</span>
+                <span class="n">uniprot</span><span class="p">,</span>
+                <span class="n">typ</span> <span class="o">=</span> <span class="n">typ</span><span class="p">,</span>
+                <span class="n">motif</span> <span class="o">=</span> <span class="n">mot</span><span class="p">,</span>
+                <span class="n">residue</span> <span class="o">=</span> <span class="n">res</span><span class="p">,</span>
+                <span class="n">evidences</span> <span class="o">=</span> <span class="s1">&#39;PhosphoSite&#39;</span><span class="p">,</span>
+                <span class="n">isoform</span> <span class="o">=</span> <span class="n">isoform</span><span class="p">,</span>
+            <span class="p">)</span>
+            <span class="n">result</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">ptm</span><span class="p">)</span>
+
+    <span class="k">return</span> <span class="n">result</span></div>
+
+
+
+<div class="viewcode-block" id="phosphosite_regsites">
+<a class="viewcode-back" href="../../../api/pypath.inputs.phosphosite.phosphosite_regsites.html#pypath.inputs.phosphosite.phosphosite_regsites">[docs]</a>
+<span class="k">def</span> <span class="nf">phosphosite_regsites</span><span class="p">():</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Downloads and preprocesses the regulatory sites dataset from</span>
+<span class="sd">    PhosphoSitePlus. This data provides information about which</span>
+<span class="sd">    proteins a PTM disrupts or induces the interaction with.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="n">kwds_pos</span> <span class="o">=</span> <span class="p">{</span>
+        <span class="s1">&#39;enzymatic activity, induced&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;activity, induced&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;protein stabilization&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;receptor inactivation, inhibited&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;receptor desensitization, inhibited&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;receptor internalization, inhibited&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;receptor recycling, induced&#39;</span>
+    <span class="p">}</span>
+
+    <span class="n">kwds_neg</span> <span class="o">=</span> <span class="p">{</span>
+        <span class="s1">&#39;enzymatic activity, inhibited&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;activity, inhibited&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;protein degradation&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;receptor inactivation, induced&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;receptor desensitization, induced&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;receptor internalization, induced&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;receptor recycling, inhibited&#39;</span>
+    <span class="p">}</span>
+
+    <span class="n">url</span> <span class="o">=</span> <span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;psite_reg&#39;</span><span class="p">][</span><span class="s1">&#39;url&#39;</span><span class="p">]</span>
+    <span class="n">c</span> <span class="o">=</span> <span class="n">curl</span><span class="o">.</span><span class="n">Curl</span><span class="p">(</span><span class="n">url</span><span class="p">,</span> <span class="n">silent</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span> <span class="n">compr</span> <span class="o">=</span> <span class="s1">&#39;gz&#39;</span><span class="p">,</span>
+                  <span class="n">encoding</span> <span class="o">=</span> <span class="s1">&#39;iso-8859-1&#39;</span><span class="p">,</span> <span class="n">large</span> <span class="o">=</span> <span class="kc">True</span><span class="p">)</span>
+    <span class="n">data</span> <span class="o">=</span> <span class="n">c</span><span class="o">.</span><span class="n">result</span>
+    <span class="n">cols</span> <span class="o">=</span> <span class="p">{</span>
+        <span class="s1">&#39;uniprot&#39;</span><span class="p">:</span> <span class="mi">3</span><span class="p">,</span>
+        <span class="s1">&#39;organism&#39;</span><span class="p">:</span> <span class="mi">6</span><span class="p">,</span>
+        <span class="s1">&#39;mod&#39;</span><span class="p">:</span> <span class="mi">7</span><span class="p">,</span>
+        <span class="s1">&#39;on_function&#39;</span><span class="p">:</span> <span class="mi">11</span><span class="p">,</span>
+        <span class="s1">&#39;on_process&#39;</span><span class="p">:</span> <span class="mi">12</span><span class="p">,</span>
+        <span class="s1">&#39;on_interact&#39;</span><span class="p">:</span> <span class="mi">13</span><span class="p">,</span>
+        <span class="s1">&#39;pmids&#39;</span><span class="p">:</span> <span class="mi">15</span><span class="p">,</span>
+        <span class="s1">&#39;comments&#39;</span><span class="p">:</span> <span class="mi">19</span>
+    <span class="p">}</span>
+
+    <span class="n">data</span> <span class="o">=</span> <span class="n">inputs_common</span><span class="o">.</span><span class="n">read_table</span><span class="p">(</span>
+        <span class="n">cols</span> <span class="o">=</span> <span class="n">cols</span><span class="p">,</span>
+        <span class="n">fileObject</span> <span class="o">=</span> <span class="n">data</span><span class="p">,</span>
+        <span class="n">sep</span> <span class="o">=</span> <span class="s1">&#39;</span><span class="se">\t</span><span class="s1">&#39;</span><span class="p">,</span>
+        <span class="n">hdr</span> <span class="o">=</span> <span class="mi">4</span><span class="p">,</span>
+    <span class="p">)</span>
+    <span class="n">regsites</span> <span class="o">=</span> <span class="p">{}</span>
+
+    <span class="k">for</span> <span class="n">r</span> <span class="ow">in</span> <span class="n">data</span><span class="p">:</span>
+
+        <span class="n">interact</span> <span class="o">=</span> <span class="p">[[</span><span class="n">y</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s1">&#39;)&#39;</span><span class="p">,</span> <span class="s1">&#39;&#39;</span><span class="p">)</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span> <span class="k">for</span> <span class="n">y</span> <span class="ow">in</span> <span class="n">x</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;(&#39;</span><span class="p">)]</span>
+                    <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">r</span><span class="p">[</span><span class="s1">&#39;on_interact&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;;&#39;</span><span class="p">)</span> <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">x</span><span class="p">)</span> <span class="o">&gt;</span> <span class="mi">0</span><span class="p">]</span>
+        <span class="n">induces</span> <span class="o">=</span> <span class="p">[</span><span class="n">x</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">interact</span> <span class="k">if</span> <span class="n">x</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="o">==</span> <span class="s1">&#39;INDUCES&#39;</span><span class="p">]</span>
+        <span class="n">disrupts</span> <span class="o">=</span> <span class="p">[</span><span class="n">x</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">interact</span> <span class="k">if</span> <span class="n">x</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="o">==</span> <span class="s1">&#39;DISRUPTS&#39;</span><span class="p">]</span>
+        <span class="n">mod</span> <span class="o">=</span> <span class="n">r</span><span class="p">[</span><span class="s1">&#39;mod&#39;</span><span class="p">]</span>
+        <span class="n">modt</span> <span class="o">=</span> <span class="n">r</span><span class="p">[</span><span class="s1">&#39;mod&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;-&#39;</span><span class="p">)</span>
+        <span class="n">mod</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="n">modt</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span>
+        <span class="n">aa</span> <span class="o">=</span> <span class="n">mod</span><span class="o">.</span><span class="n">pop</span><span class="p">(</span><span class="mi">0</span><span class="p">)</span>
+        <span class="n">modt</span> <span class="o">=</span> <span class="n">modt</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span>
+        <span class="n">res</span> <span class="o">=</span> <span class="s1">&#39;&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">mod</span><span class="p">)</span>
+        <span class="n">isoform</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="nb">int</span><span class="p">(</span><span class="n">r</span><span class="p">[</span><span class="s1">&#39;uniprot&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;-&#39;</span><span class="p">)[</span><span class="mi">1</span><span class="p">])</span>
+            <span class="k">if</span> <span class="s1">&#39;-&#39;</span> <span class="ow">in</span> <span class="n">r</span><span class="p">[</span><span class="s1">&#39;uniprot&#39;</span><span class="p">]</span>
+            <span class="k">else</span> <span class="mi">1</span>
+        <span class="p">)</span>
+        <span class="n">uniprot</span> <span class="o">=</span> <span class="n">r</span><span class="p">[</span><span class="s1">&#39;uniprot&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;-&#39;</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span>
+
+        <span class="k">if</span> <span class="n">uniprot</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">regsites</span><span class="p">:</span>
+            <span class="n">regsites</span><span class="p">[</span><span class="n">uniprot</span><span class="p">]</span> <span class="o">=</span> <span class="p">[]</span>
+
+        <span class="n">function</span> <span class="o">=</span> <span class="nb">set</span><span class="p">(</span><span class="nb">map</span><span class="p">(</span><span class="k">lambda</span> <span class="n">f</span><span class="p">:</span> <span class="n">f</span><span class="o">.</span><span class="n">strip</span><span class="p">(),</span>
+                           <span class="n">r</span><span class="p">[</span><span class="s1">&#39;on_function&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;;&#39;</span><span class="p">)))</span>
+
+        <span class="n">regsites</span><span class="p">[</span><span class="n">uniprot</span><span class="p">]</span><span class="o">.</span><span class="n">append</span><span class="p">({</span>
+            <span class="s1">&#39;aa&#39;</span><span class="p">:</span>       <span class="n">aa</span><span class="p">,</span>
+            <span class="s1">&#39;res&#39;</span><span class="p">:</span>      <span class="n">res</span><span class="p">,</span>
+            <span class="s1">&#39;modt&#39;</span><span class="p">:</span>     <span class="n">modt</span><span class="p">,</span>
+            <span class="s1">&#39;organism&#39;</span><span class="p">:</span> <span class="n">r</span><span class="p">[</span><span class="s1">&#39;organism&#39;</span><span class="p">],</span>
+            <span class="s1">&#39;pmids&#39;</span><span class="p">:</span>    <span class="nb">set</span><span class="p">(</span><span class="nb">map</span><span class="p">(</span><span class="k">lambda</span> <span class="n">f</span><span class="p">:</span> <span class="n">f</span><span class="o">.</span><span class="n">strip</span><span class="p">(),</span>
+                                <span class="n">r</span><span class="p">[</span><span class="s1">&#39;pmids&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;;&#39;</span><span class="p">))),</span>
+            <span class="s1">&#39;induces&#39;</span><span class="p">:</span>  <span class="n">induces</span><span class="p">,</span>
+            <span class="s1">&#39;disrupts&#39;</span><span class="p">:</span> <span class="n">disrupts</span><span class="p">,</span>
+            <span class="s1">&#39;isoform&#39;</span><span class="p">:</span>  <span class="n">isoform</span><span class="p">,</span>
+            <span class="s1">&#39;function&#39;</span><span class="p">:</span> <span class="n">function</span><span class="p">,</span>
+            <span class="s1">&#39;process&#39;</span><span class="p">:</span>  <span class="nb">set</span><span class="p">(</span><span class="nb">map</span><span class="p">(</span><span class="k">lambda</span> <span class="n">f</span><span class="p">:</span> <span class="n">f</span><span class="o">.</span><span class="n">strip</span><span class="p">(),</span>
+                                <span class="n">r</span><span class="p">[</span><span class="s1">&#39;on_process&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;;&#39;</span><span class="p">))),</span>
+            <span class="s1">&#39;comments&#39;</span><span class="p">:</span> <span class="n">r</span><span class="p">[</span><span class="s1">&#39;comments&#39;</span><span class="p">],</span>
+            <span class="s1">&#39;positive&#39;</span><span class="p">:</span> <span class="nb">bool</span><span class="p">(</span><span class="n">kwds_pos</span> <span class="o">&amp;</span> <span class="n">function</span><span class="p">),</span>
+            <span class="s1">&#39;negative&#39;</span><span class="p">:</span> <span class="nb">bool</span><span class="p">(</span><span class="n">kwds_neg</span> <span class="o">&amp;</span> <span class="n">function</span><span class="p">)</span>
+        <span class="p">})</span>
+
+    <span class="k">return</span> <span class="n">regsites</span></div>
+
+
+
+<div class="viewcode-block" id="phosphosite_regsites_one_organism">
+<a class="viewcode-back" href="../../../api/pypath.inputs.phosphosite.phosphosite_regsites_one_organism.html#pypath.inputs.phosphosite.phosphosite_regsites_one_organism">[docs]</a>
+<span class="k">def</span> <span class="nf">phosphosite_regsites_one_organism</span><span class="p">(</span><span class="n">organism</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">):</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Returns PhosphoSitePlus regulatory sites translated to</span>
+<span class="sd">    one organism by orthology. Residue numbers will be translated</span>
+<span class="sd">    where necessary, while gene symbols will be translated to</span>
+<span class="sd">    UniProt IDs of the given organism.</span>
+<span class="sd">    This works with human, mouse or rat.</span>
+
+<span class="sd">    :param int organism:</span>
+<span class="sd">        NCBI Taxonomy ID of the target organism. In this</span>
+<span class="sd">        method possible values are human, mouse or rat, as these species</span>
+<span class="sd">        provide the vast majority of the data, and are close enough to each</span>
+<span class="sd">        other that the sites can be safely translated between orthologous</span>
+<span class="sd">        proteins by sequence alignement.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="k">def</span> <span class="nf">genesymbols2uniprots</span><span class="p">(</span><span class="n">genesymbols</span><span class="p">,</span> <span class="n">tax</span><span class="p">):</span>
+        <span class="k">return</span> <span class="p">(</span>
+            <span class="nb">set</span><span class="p">(</span>
+                <span class="n">itertools</span><span class="o">.</span><span class="n">chain</span><span class="p">(</span>
+                    <span class="o">*</span><span class="nb">map</span><span class="p">(</span>
+                        <span class="k">lambda</span> <span class="n">gs</span><span class="p">:</span>
+                            <span class="n">mapping</span><span class="o">.</span><span class="n">map_name</span><span class="p">(</span>
+                                <span class="n">gs</span><span class="p">,</span>
+                                <span class="s1">&#39;genesymbol&#39;</span><span class="p">,</span>
+                                <span class="s1">&#39;uniprot&#39;</span><span class="p">,</span>
+                                <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">tax</span><span class="p">,</span>
+                            <span class="p">),</span>
+                        <span class="n">genesymbols</span>
+                    <span class="p">)</span>
+                <span class="p">)</span>
+            <span class="p">)</span>
+        <span class="p">)</span>
+
+    <span class="k">def</span> <span class="nf">translate_uniprots</span><span class="p">(</span><span class="n">uniprots</span><span class="p">,</span> <span class="n">homo</span><span class="p">):</span>
+        <span class="k">return</span> <span class="p">(</span>
+            <span class="nb">set</span><span class="p">(</span>
+                <span class="n">itertools</span><span class="o">.</span><span class="n">chain</span><span class="p">(</span>
+                    <span class="o">*</span><span class="nb">map</span><span class="p">(</span>
+                        <span class="k">lambda</span> <span class="n">usrc</span><span class="p">:</span>
+                            <span class="n">homo</span><span class="p">[</span><span class="n">usrc</span><span class="p">]</span> <span class="k">if</span> <span class="n">usrc</span> <span class="ow">in</span> <span class="n">homo</span> <span class="k">else</span> <span class="p">[],</span>
+                        <span class="n">uniprots</span>
+                    <span class="p">)</span>
+                <span class="p">)</span>
+            <span class="p">)</span>
+        <span class="p">)</span>
+
+    <span class="n">result</span> <span class="o">=</span> <span class="p">{}</span>
+
+    <span class="n">organisms</span> <span class="o">=</span> <span class="nb">set</span><span class="p">([</span><span class="mi">9606</span><span class="p">,</span> <span class="mi">10090</span><span class="p">,</span> <span class="mi">10116</span><span class="p">])</span>
+
+    <span class="n">mod_types</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">(</span><span class="n">common</span><span class="o">.</span><span class="n">psite_mod_types2</span><span class="p">)</span>
+
+    <span class="n">regsites</span> <span class="o">=</span> <span class="n">phosphosite_regsites</span><span class="p">()</span>
+
+    <span class="n">other_organisms</span> <span class="o">=</span> <span class="n">organisms</span> <span class="o">-</span> <span class="nb">set</span><span class="p">([</span><span class="n">organism</span><span class="p">])</span>
+
+    <span class="n">homology</span> <span class="o">=</span> <span class="p">(</span>
+        <span class="nb">dict</span><span class="p">(</span>
+            <span class="nb">map</span><span class="p">(</span>
+                <span class="k">lambda</span> <span class="n">other</span><span class="p">:</span>
+                    <span class="p">(</span>
+                        <span class="n">other</span><span class="p">,</span>
+                        <span class="n">homologene</span><span class="o">.</span><span class="n">homologene_uniprot_dict</span><span class="p">(</span>
+                            <span class="n">source</span> <span class="o">=</span> <span class="n">other</span><span class="p">,</span>
+                            <span class="n">target</span> <span class="o">=</span> <span class="n">organism</span><span class="p">,</span>
+                        <span class="p">)</span>
+                    <span class="p">),</span>
+                <span class="n">other_organisms</span>
+            <span class="p">)</span>
+        <span class="p">)</span>
+    <span class="p">)</span>
+
+    <span class="n">ptm_homology</span> <span class="o">=</span> <span class="n">phosphosite_ptm_orthology</span><span class="p">()</span>
+
+    <span class="n">proteome</span> <span class="o">=</span> <span class="n">uniprot_db</span><span class="o">.</span><span class="n">all_uniprots</span><span class="p">(</span>
+        <span class="n">organism</span> <span class="o">=</span> <span class="n">organism</span><span class="p">,</span>
+        <span class="n">swissprot</span> <span class="o">=</span> <span class="s1">&#39;YES&#39;</span><span class="p">,</span>
+    <span class="p">)</span>
+
+    <span class="k">for</span> <span class="n">substrate</span><span class="p">,</span> <span class="n">regs</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="n">regsites</span><span class="p">):</span>
+
+        <span class="n">subs</span> <span class="o">=</span> <span class="p">[]</span>
+
+        <span class="k">if</span> <span class="n">substrate</span> <span class="ow">in</span> <span class="n">proteome</span><span class="p">:</span>
+            <span class="n">subs</span> <span class="o">=</span> <span class="p">[</span><span class="n">substrate</span><span class="p">]</span>
+        <span class="k">else</span><span class="p">:</span>
+            <span class="k">for</span> <span class="n">other</span><span class="p">,</span> <span class="n">homo</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="n">homology</span><span class="p">):</span>
+                <span class="k">if</span> <span class="n">substrate</span> <span class="ow">in</span> <span class="n">homo</span><span class="p">:</span>
+                    <span class="n">subs</span> <span class="o">=</span> <span class="n">homo</span><span class="p">[</span><span class="n">substrate</span><span class="p">]</span>
+
+        <span class="k">for</span> <span class="n">sub</span> <span class="ow">in</span> <span class="n">subs</span><span class="p">:</span>
+
+            <span class="k">if</span> <span class="n">sub</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">result</span><span class="p">:</span>
+                <span class="n">result</span><span class="p">[</span><span class="n">sub</span><span class="p">]</span> <span class="o">=</span> <span class="p">{}</span>
+
+            <span class="k">for</span> <span class="n">reg</span> <span class="ow">in</span> <span class="n">regs</span><span class="p">:</span>
+
+                <span class="n">reg_organism</span> <span class="o">=</span> <span class="n">taxonomy</span><span class="o">.</span><span class="n">taxa</span><span class="p">[</span><span class="n">reg</span><span class="p">[</span><span class="s1">&#39;organism&#39;</span><span class="p">]]</span>
+
+                <span class="k">if</span> <span class="n">reg_organism</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">organisms</span><span class="p">:</span>
+                    <span class="k">continue</span>
+
+                <span class="k">if</span> <span class="n">reg</span><span class="p">[</span><span class="s1">&#39;modt&#39;</span><span class="p">]</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">mod_types</span><span class="p">:</span>
+
+                    <span class="n">_logger</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span>
+                        <span class="s1">&#39;Unknown PhosphoSite modification &#39;</span>
+                        <span class="s1">&#39;type code: </span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="n">reg</span><span class="p">[</span><span class="s1">&#39;modt&#39;</span><span class="p">]</span>
+                    <span class="p">)</span>
+                    <span class="k">continue</span>
+
+                <span class="n">mod_type</span> <span class="o">=</span> <span class="n">mod_types</span><span class="p">[</span><span class="n">reg</span><span class="p">[</span><span class="s1">&#39;modt&#39;</span><span class="p">]]</span>
+                <span class="n">resnum</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">reg</span><span class="p">[</span><span class="s1">&#39;res&#39;</span><span class="p">])</span>
+
+                <span class="n">psite_key</span> <span class="o">=</span> <span class="p">(</span>
+                    <span class="n">substrate</span><span class="p">,</span>
+                    <span class="n">reg</span><span class="p">[</span><span class="s1">&#39;isoform&#39;</span><span class="p">],</span>
+                    <span class="n">reg</span><span class="p">[</span><span class="s1">&#39;aa&#39;</span><span class="p">],</span>
+                    <span class="n">resnum</span><span class="p">,</span>
+                    <span class="n">reg_organism</span><span class="p">,</span>
+                    <span class="n">mod_type</span><span class="p">,</span>
+                <span class="p">)</span>
+
+                <span class="k">if</span> <span class="n">reg_organism</span> <span class="o">!=</span> <span class="n">organism</span><span class="p">:</span>
+
+                    <span class="n">regs_target</span> <span class="o">=</span> <span class="p">[]</span>
+                    <span class="n">disrupts</span>    <span class="o">=</span> <span class="p">[]</span>
+                    <span class="n">induces</span>     <span class="o">=</span> <span class="p">[]</span>
+
+                    <span class="k">if</span> <span class="n">psite_key</span> <span class="ow">in</span> <span class="n">ptm_homology</span><span class="p">:</span>
+
+                        <span class="k">if</span> <span class="n">organism</span> <span class="ow">in</span> <span class="n">ptm_homology</span><span class="p">[</span><span class="n">psite_key</span><span class="p">]:</span>
+
+                            <span class="n">regs_target</span> <span class="o">=</span> <span class="n">ptm_homology</span><span class="p">[</span><span class="n">psite_key</span><span class="p">][</span><span class="n">organism</span><span class="p">]</span>
+
+                    <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">regs_target</span><span class="p">):</span>
+
+                        <span class="n">disrupts</span> <span class="o">=</span> <span class="n">genesymbols2uniprots</span><span class="p">(</span>
+                            <span class="n">reg</span><span class="p">[</span><span class="s1">&#39;disrupts&#39;</span><span class="p">],</span>
+                            <span class="n">reg_organism</span><span class="p">,</span>
+                        <span class="p">)</span>
+                        <span class="n">disrupts</span> <span class="o">=</span> <span class="n">translate_uniprots</span><span class="p">(</span>
+                            <span class="n">disrupts</span><span class="p">,</span>
+                            <span class="n">homology</span><span class="p">[</span><span class="n">reg_organism</span><span class="p">],</span>
+                        <span class="p">)</span>
+                        <span class="n">induces</span>  <span class="o">=</span> <span class="n">genesymbols2uniprots</span><span class="p">(</span>
+                            <span class="n">reg</span><span class="p">[</span><span class="s1">&#39;induces&#39;</span><span class="p">],</span>
+                            <span class="n">reg_organism</span><span class="p">,</span>
+                        <span class="p">)</span>
+                        <span class="n">induces</span>  <span class="o">=</span> <span class="n">translate_uniprots</span><span class="p">(</span>
+                            <span class="n">induces</span><span class="p">,</span>
+                            <span class="n">homology</span><span class="p">[</span><span class="n">reg_organism</span><span class="p">],</span>
+                        <span class="p">)</span>
+
+                <span class="k">else</span><span class="p">:</span>
+
+                    <span class="n">regs_target</span> <span class="o">=</span> <span class="p">[</span><span class="n">psite_key</span><span class="p">]</span>
+
+                    <span class="n">disrupts</span> <span class="o">=</span> <span class="n">genesymbols2uniprots</span><span class="p">(</span><span class="n">reg</span><span class="p">[</span><span class="s1">&#39;disrupts&#39;</span><span class="p">],</span> <span class="n">organism</span><span class="p">)</span>
+                    <span class="n">induces</span>  <span class="o">=</span> <span class="n">genesymbols2uniprots</span><span class="p">(</span><span class="n">reg</span><span class="p">[</span><span class="s1">&#39;induces&#39;</span><span class="p">],</span> <span class="n">organism</span><span class="p">)</span>
+
+                <span class="k">for</span> <span class="n">regt</span> <span class="ow">in</span> <span class="n">regs_target</span><span class="p">:</span>
+
+                    <span class="n">modkey</span> <span class="o">=</span> <span class="p">(</span><span class="n">regt</span><span class="p">[</span><span class="mi">2</span><span class="p">],</span> <span class="n">regt</span><span class="p">[</span><span class="mi">3</span><span class="p">],</span> <span class="n">regt</span><span class="p">[</span><span class="mi">5</span><span class="p">])</span>
+
+                    <span class="k">if</span> <span class="n">modkey</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">result</span><span class="p">[</span><span class="n">sub</span><span class="p">]:</span>
+
+                        <span class="n">result</span><span class="p">[</span><span class="n">sub</span><span class="p">][</span><span class="n">modkey</span><span class="p">]</span> <span class="o">=</span> <span class="p">{</span>
+                            <span class="s1">&#39;induces&#39;</span><span class="p">:</span>  <span class="nb">set</span><span class="p">([]),</span>
+                            <span class="s1">&#39;disrupts&#39;</span><span class="p">:</span> <span class="nb">set</span><span class="p">([]),</span>
+                            <span class="s1">&#39;pmids&#39;</span><span class="p">:</span>    <span class="nb">set</span><span class="p">([]),</span>
+                            <span class="s1">&#39;isoforms&#39;</span><span class="p">:</span> <span class="nb">set</span><span class="p">([]),</span>
+                            <span class="s1">&#39;process&#39;</span><span class="p">:</span>  <span class="nb">set</span><span class="p">([]),</span>
+                            <span class="s1">&#39;function&#39;</span><span class="p">:</span> <span class="nb">set</span><span class="p">([]),</span>
+                            <span class="s1">&#39;positive&#39;</span><span class="p">:</span> <span class="kc">False</span><span class="p">,</span>
+                            <span class="s1">&#39;negative&#39;</span><span class="p">:</span> <span class="kc">False</span><span class="p">,</span>
+                            <span class="s1">&#39;comments&#39;</span><span class="p">:</span> <span class="p">[]</span>
+                        <span class="p">}</span>
+
+                    <span class="n">result</span><span class="p">[</span><span class="n">sub</span><span class="p">][</span><span class="n">modkey</span><span class="p">][</span><span class="s1">&#39;induces&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">update</span><span class="p">(</span><span class="n">induces</span><span class="p">)</span>
+                    <span class="n">result</span><span class="p">[</span><span class="n">sub</span><span class="p">][</span><span class="n">modkey</span><span class="p">][</span><span class="s1">&#39;disrupts&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">update</span><span class="p">(</span><span class="n">disrupts</span><span class="p">)</span>
+                    <span class="n">result</span><span class="p">[</span><span class="n">sub</span><span class="p">][</span><span class="n">modkey</span><span class="p">][</span><span class="s1">&#39;process&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">update</span><span class="p">(</span><span class="n">reg</span><span class="p">[</span><span class="s1">&#39;process&#39;</span><span class="p">])</span>
+                    <span class="n">result</span><span class="p">[</span><span class="n">sub</span><span class="p">][</span><span class="n">modkey</span><span class="p">][</span><span class="s1">&#39;function&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">update</span><span class="p">(</span><span class="n">reg</span><span class="p">[</span><span class="s1">&#39;function&#39;</span><span class="p">])</span>
+                    <span class="n">result</span><span class="p">[</span><span class="n">sub</span><span class="p">][</span><span class="n">modkey</span><span class="p">][</span><span class="s1">&#39;isoforms&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">update</span><span class="p">([</span><span class="n">regt</span><span class="p">[</span><span class="mi">1</span><span class="p">]])</span>
+                    <span class="n">result</span><span class="p">[</span><span class="n">sub</span><span class="p">][</span><span class="n">modkey</span><span class="p">][</span><span class="s1">&#39;pmids&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">update</span><span class="p">(</span><span class="n">reg</span><span class="p">[</span><span class="s1">&#39;pmids&#39;</span><span class="p">])</span>
+                    <span class="n">result</span><span class="p">[</span><span class="n">sub</span><span class="p">][</span><span class="n">modkey</span><span class="p">][</span><span class="s1">&#39;positive&#39;</span><span class="p">]</span> <span class="o">=</span> \
+                        <span class="n">result</span><span class="p">[</span><span class="n">sub</span><span class="p">][</span><span class="n">modkey</span><span class="p">][</span><span class="s1">&#39;positive&#39;</span><span class="p">]</span> <span class="ow">or</span> <span class="n">reg</span><span class="p">[</span><span class="s1">&#39;positive&#39;</span><span class="p">]</span>
+                    <span class="n">result</span><span class="p">[</span><span class="n">sub</span><span class="p">][</span><span class="n">modkey</span><span class="p">][</span><span class="s1">&#39;negative&#39;</span><span class="p">]</span> <span class="o">=</span> \
+                        <span class="n">result</span><span class="p">[</span><span class="n">sub</span><span class="p">][</span><span class="n">modkey</span><span class="p">][</span><span class="s1">&#39;negative&#39;</span><span class="p">]</span> <span class="ow">or</span> <span class="n">reg</span><span class="p">[</span><span class="s1">&#39;negative&#39;</span><span class="p">]</span>
+                    <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">reg</span><span class="p">[</span><span class="s1">&#39;comments&#39;</span><span class="p">]):</span>
+                        <span class="n">result</span><span class="p">[</span><span class="n">sub</span><span class="p">][</span><span class="n">modkey</span><span class="p">][</span><span class="s1">&#39;comments&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">reg</span><span class="p">[</span><span class="s1">&#39;comments&#39;</span><span class="p">])</span>
+
+
+    <span class="k">return</span> <span class="n">result</span></div>
+
+
+
+<div class="viewcode-block" id="regsites_tab">
+<a class="viewcode-back" href="../../../api/pypath.inputs.phosphosite.regsites_tab.html#pypath.inputs.phosphosite.regsites_tab">[docs]</a>
+<span class="k">def</span> <span class="nf">regsites_tab</span><span class="p">(</span><span class="n">regsites</span><span class="p">,</span> <span class="n">outfile</span> <span class="o">=</span> <span class="kc">None</span><span class="p">):</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Exports PhosphoSite regulatory sites as a tabular file, all</span>
+<span class="sd">    IDs translated to UniProt.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="n">header</span> <span class="o">=</span> <span class="p">[</span>
+        <span class="s1">&#39;uniprot_a&#39;</span><span class="p">,</span> <span class="s1">&#39;isoform_a&#39;</span><span class="p">,</span> <span class="s1">&#39;a_res_aa&#39;</span><span class="p">,</span> <span class="s1">&#39;a_res_num&#39;</span><span class="p">,</span> <span class="s1">&#39;a_mod_type&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;effect&#39;</span><span class="p">,</span> <span class="s1">&#39;uniprot_b&#39;</span><span class="p">,</span> <span class="s1">&#39;references&#39;</span>
+    <span class="p">]</span>
+    <span class="n">result</span> <span class="o">=</span> <span class="p">[]</span>
+    <span class="k">for</span> <span class="n">uniprot</span><span class="p">,</span> <span class="n">regsite</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="n">regsites</span><span class="p">):</span>
+        <span class="n">isoform</span> <span class="o">=</span> <span class="s1">&#39;1&#39;</span>
+        <span class="n">uniprot</span> <span class="o">=</span> <span class="n">uniprot</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;-&#39;</span><span class="p">)</span>
+        <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">uniprot</span><span class="p">)</span> <span class="o">&gt;</span> <span class="mi">1</span><span class="p">:</span>
+            <span class="n">isoform</span> <span class="o">=</span> <span class="n">uniprot</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span>
+        <span class="n">uniprot</span> <span class="o">=</span> <span class="n">uniprot</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span>
+        <span class="k">for</span> <span class="n">r</span> <span class="ow">in</span> <span class="n">regsite</span><span class="p">:</span>
+            <span class="k">if</span> <span class="n">r</span><span class="p">[</span><span class="s1">&#39;organism&#39;</span><span class="p">]</span> <span class="o">==</span> <span class="s1">&#39;human&#39;</span><span class="p">:</span>
+                <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="n">r</span><span class="p">[</span><span class="s1">&#39;induces&#39;</span><span class="p">]:</span>
+                    <span class="n">other</span> <span class="o">=</span> <span class="n">mapping</span><span class="o">.</span><span class="n">map_name</span><span class="p">(</span><span class="n">i</span><span class="p">,</span> <span class="s1">&#39;genesymbol&#39;</span><span class="p">,</span> <span class="s1">&#39;uniprot&#39;</span><span class="p">)</span>
+                    <span class="k">for</span> <span class="n">o</span> <span class="ow">in</span> <span class="n">other</span><span class="p">:</span>
+                        <span class="k">if</span> <span class="n">o</span> <span class="o">!=</span> <span class="s1">&#39;unmapped&#39;</span><span class="p">:</span>
+                            <span class="n">result</span><span class="o">.</span><span class="n">append</span><span class="p">([</span>
+                                <span class="n">uniprot</span><span class="p">,</span> <span class="n">isoform</span><span class="p">,</span> <span class="n">r</span><span class="p">[</span><span class="s1">&#39;aa&#39;</span><span class="p">],</span> <span class="n">r</span><span class="p">[</span><span class="s1">&#39;res&#39;</span><span class="p">],</span> <span class="n">r</span><span class="p">[</span><span class="s1">&#39;modt&#39;</span><span class="p">],</span>
+                                <span class="s1">&#39;+&#39;</span><span class="p">,</span> <span class="n">o</span>
+                            <span class="p">])</span>
+                <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="n">r</span><span class="p">[</span><span class="s1">&#39;disrupts&#39;</span><span class="p">]:</span>
+                    <span class="n">other</span> <span class="o">=</span> <span class="n">mapping</span><span class="o">.</span><span class="n">map_name</span><span class="p">(</span><span class="n">i</span><span class="p">,</span> <span class="s1">&#39;genesymbol&#39;</span><span class="p">,</span> <span class="s1">&#39;uniprot&#39;</span><span class="p">)</span>
+                    <span class="k">for</span> <span class="n">o</span> <span class="ow">in</span> <span class="n">other</span><span class="p">:</span>
+                        <span class="k">if</span> <span class="n">o</span> <span class="o">!=</span> <span class="s1">&#39;unmapped&#39;</span><span class="p">:</span>
+                            <span class="n">result</span><span class="o">.</span><span class="n">append</span><span class="p">([</span>
+                                <span class="n">uniprot</span><span class="p">,</span> <span class="n">isoform</span><span class="p">,</span> <span class="n">r</span><span class="p">[</span><span class="s1">&#39;aa&#39;</span><span class="p">],</span> <span class="n">r</span><span class="p">[</span><span class="s1">&#39;res&#39;</span><span class="p">],</span> <span class="n">r</span><span class="p">[</span><span class="s1">&#39;modt&#39;</span><span class="p">],</span>
+                                <span class="s1">&#39;-&#39;</span><span class="p">,</span> <span class="n">o</span><span class="p">,</span> <span class="s1">&#39;;&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">r</span><span class="p">[</span><span class="s1">&#39;pmids&#39;</span><span class="p">])</span>
+                            <span class="p">])</span>
+    <span class="k">if</span> <span class="n">outfile</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
+        <span class="n">out</span> <span class="o">=</span> <span class="s1">&#39;</span><span class="se">\t</span><span class="s1">&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">header</span><span class="p">)</span> <span class="o">+</span> <span class="s1">&#39;</span><span class="se">\n</span><span class="s1">&#39;</span>
+        <span class="k">for</span> <span class="n">r</span> <span class="ow">in</span> <span class="n">result</span><span class="p">:</span>
+            <span class="n">out</span> <span class="o">+=</span> <span class="s1">&#39;</span><span class="se">\t</span><span class="s1">&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">r</span><span class="p">)</span> <span class="o">+</span> <span class="s1">&#39;</span><span class="se">\n</span><span class="s1">&#39;</span>
+        <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">outfile</span><span class="p">,</span> <span class="s1">&#39;w&#39;</span><span class="p">)</span> <span class="k">as</span> <span class="n">f</span><span class="p">:</span>
+            <span class="n">f</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="n">out</span><span class="p">)</span>
+    <span class="k">return</span> <span class="n">result</span></div>
+
+
+
+
+<div class="viewcode-block" id="phosphosite_interactions">
+<a class="viewcode-back" href="../../../api/pypath.inputs.phosphosite.phosphosite_interactions.html#pypath.inputs.phosphosite.phosphosite_interactions">[docs]</a>
+<span class="k">def</span> <span class="nf">phosphosite_interactions</span><span class="p">(</span><span class="n">cache</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span> <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">):</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Downloads curated and HTP data from Phosphosite,</span>
+<span class="sd">    from preprocessed cache file if available.</span>
+<span class="sd">    Processes BioPAX format.</span>
+<span class="sd">    Returns list of interactions.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="n">curated_cache</span> <span class="o">=</span> <span class="n">urls</span><span class="o">.</span><span class="n">files</span><span class="p">[</span><span class="s1">&#39;phosphosite&#39;</span><span class="p">][</span><span class="s1">&#39;curated&#39;</span><span class="p">]</span>
+    <span class="n">noref_cache</span> <span class="o">=</span> <span class="n">urls</span><span class="o">.</span><span class="n">files</span><span class="p">[</span><span class="s1">&#39;phosphosite&#39;</span><span class="p">][</span><span class="s1">&#39;noref&#39;</span><span class="p">]</span>
+
+    <span class="k">if</span> <span class="n">cache</span> <span class="ow">and</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">exists</span><span class="p">(</span><span class="n">curated_cache</span><span class="p">)</span> <span class="ow">and</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">exists</span><span class="p">(</span><span class="n">noref_cache</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="p">(</span>
+            <span class="n">pickle</span><span class="o">.</span><span class="n">load</span><span class="p">(</span><span class="nb">open</span><span class="p">(</span><span class="n">curated_cache</span><span class="p">,</span> <span class="s1">&#39;rb&#39;</span><span class="p">)),</span>
+            <span class="n">pickle</span><span class="o">.</span><span class="n">load</span><span class="p">(</span><span class="nb">open</span><span class="p">(</span><span class="n">noref_cache</span><span class="p">,</span> <span class="s1">&#39;rb&#39;</span><span class="p">)),</span>
+        <span class="p">)</span>
+
+    <span class="n">result_curated</span> <span class="o">=</span> <span class="p">[]</span>
+    <span class="n">result_noref</span> <span class="o">=</span> <span class="p">[]</span>
+    <span class="n">url</span> <span class="o">=</span> <span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;psite_bp&#39;</span><span class="p">][</span><span class="s1">&#39;url&#39;</span><span class="p">]</span>
+    <span class="n">c</span> <span class="o">=</span> <span class="n">curl</span><span class="o">.</span><span class="n">Curl</span><span class="p">(</span><span class="n">url</span><span class="p">,</span> <span class="n">silent</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span> <span class="n">large</span> <span class="o">=</span> <span class="kc">True</span><span class="p">)</span>
+    <span class="n">bpax</span> <span class="o">=</span> <span class="n">c</span><span class="o">.</span><span class="n">gzfile</span>
+    <span class="n">xml</span> <span class="o">=</span> <span class="n">ET</span><span class="o">.</span><span class="n">parse</span><span class="p">(</span><span class="n">bpax</span><span class="p">)</span>
+    <span class="n">xmlroot</span> <span class="o">=</span> <span class="n">xml</span><span class="o">.</span><span class="n">getroot</span><span class="p">()</span>
+    <span class="n">bpprefix</span> <span class="o">=</span> <span class="s1">&#39;{http://www.biopax.org/release/biopax-level3.owl#}&#39;</span>
+    <span class="n">rdfprefix</span> <span class="o">=</span> <span class="s1">&#39;{http://www.w3.org/1999/02/22-rdf-syntax-ns#}&#39;</span>
+    <span class="n">proteins</span> <span class="o">=</span> <span class="p">{}</span>
+    <span class="k">for</span> <span class="n">p</span> <span class="ow">in</span> <span class="n">xmlroot</span><span class="o">.</span><span class="n">iter</span><span class="p">(</span><span class="n">bpprefix</span> <span class="o">+</span> <span class="s1">&#39;ProteinReference&#39;</span><span class="p">):</span>
+        <span class="n">psid</span> <span class="o">=</span> <span class="n">p</span><span class="o">.</span><span class="n">attrib</span><span class="p">[</span><span class="n">rdfprefix</span> <span class="o">+</span> <span class="s1">&#39;ID&#39;</span><span class="p">]</span>
+        <span class="n">db</span> <span class="o">=</span> <span class="n">p</span><span class="o">.</span><span class="n">find</span><span class="p">(</span><span class="n">bpprefix</span> <span class="o">+</span> <span class="s1">&#39;xref&#39;</span><span class="p">)</span><span class="o">.</span><span class="n">find</span><span class="p">(</span><span class="n">bpprefix</span> <span class="o">+</span> <span class="s1">&#39;UnificationXref&#39;</span><span class="p">)</span><span class="o">.</span><span class="n">find</span><span class="p">(</span>
+            <span class="n">bpprefix</span> <span class="o">+</span> <span class="s1">&#39;db&#39;</span><span class="p">)</span><span class="o">.</span><span class="n">text</span>
+        <span class="n">up</span> <span class="o">=</span> <span class="n">p</span><span class="o">.</span><span class="n">find</span><span class="p">(</span><span class="n">bpprefix</span> <span class="o">+</span> <span class="s1">&#39;xref&#39;</span><span class="p">)</span><span class="o">.</span><span class="n">find</span><span class="p">(</span><span class="n">bpprefix</span> <span class="o">+</span> <span class="s1">&#39;UnificationXref&#39;</span><span class="p">)</span><span class="o">.</span><span class="n">find</span><span class="p">(</span>
+            <span class="n">bpprefix</span> <span class="o">+</span> <span class="s1">&#39;id&#39;</span><span class="p">)</span><span class="o">.</span><span class="n">text</span>
+        <span class="n">tax</span> <span class="o">=</span> <span class="s1">&#39;&#39;</span>
+        <span class="k">if</span> <span class="n">p</span><span class="o">.</span><span class="n">find</span><span class="p">(</span><span class="n">bpprefix</span> <span class="o">+</span> <span class="s1">&#39;organism&#39;</span><span class="p">)</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
+            <span class="n">tmp</span> <span class="o">=</span> <span class="n">p</span><span class="o">.</span><span class="n">find</span><span class="p">(</span><span class="n">bpprefix</span> <span class="o">+</span> <span class="s1">&#39;organism&#39;</span><span class="p">)</span>
+            <span class="k">if</span> <span class="n">rdfprefix</span> <span class="o">+</span> <span class="s1">&#39;resource&#39;</span> <span class="ow">in</span> <span class="n">tmp</span><span class="o">.</span><span class="n">attrib</span><span class="p">:</span>
+                <span class="n">tax</span> <span class="o">=</span> <span class="n">tmp</span><span class="o">.</span><span class="n">attrib</span><span class="p">[</span><span class="n">rdfprefix</span> <span class="o">+</span> <span class="s1">&#39;resource&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;_&#39;</span><span class="p">)[</span><span class="mi">1</span><span class="p">]</span>
+        <span class="k">if</span> <span class="n">db</span> <span class="o">==</span> <span class="s1">&#39;UniProtKB&#39;</span><span class="p">:</span>
+            <span class="n">up</span> <span class="o">=</span> <span class="n">up</span><span class="p">[</span><span class="mi">0</span><span class="p">:</span><span class="mi">6</span><span class="p">]</span>
+        <span class="n">proteins</span><span class="p">[</span><span class="n">psid</span><span class="p">]</span> <span class="o">=</span> <span class="p">{</span><span class="s1">&#39;id&#39;</span><span class="p">:</span> <span class="n">up</span><span class="p">,</span> <span class="s1">&#39;db&#39;</span><span class="p">:</span> <span class="n">db</span><span class="p">,</span> <span class="s1">&#39;species&#39;</span><span class="p">:</span> <span class="n">tax</span><span class="p">,</span> <span class="s1">&#39;psid&#39;</span><span class="p">:</span> <span class="n">psid</span><span class="p">}</span>
+    <span class="n">evidences</span> <span class="o">=</span> <span class="p">{}</span>
+    <span class="k">for</span> <span class="n">p</span> <span class="ow">in</span> <span class="n">xmlroot</span><span class="o">.</span><span class="n">iter</span><span class="p">(</span><span class="n">bpprefix</span> <span class="o">+</span> <span class="s1">&#39;EvidenceCodeVocabulary&#39;</span><span class="p">):</span>
+        <span class="n">evid</span> <span class="o">=</span> <span class="n">p</span><span class="o">.</span><span class="n">attrib</span><span class="p">[</span><span class="n">rdfprefix</span> <span class="o">+</span> <span class="s1">&#39;ID&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;_&#39;</span><span class="p">)[</span><span class="mi">1</span><span class="p">]</span>
+        <span class="n">evname</span> <span class="o">=</span> <span class="n">p</span><span class="o">.</span><span class="n">find</span><span class="p">(</span><span class="n">bpprefix</span> <span class="o">+</span> <span class="s1">&#39;term&#39;</span><span class="p">)</span><span class="o">.</span><span class="n">text</span>
+        <span class="n">evidences</span><span class="p">[</span><span class="n">evid</span><span class="p">]</span> <span class="o">=</span> <span class="n">evname</span>
+    <span class="n">ev_short</span> <span class="o">=</span> <span class="p">{</span><span class="s1">&#39;0113&#39;</span><span class="p">:</span> <span class="s1">&#39;WB&#39;</span><span class="p">,</span> <span class="s1">&#39;0427&#39;</span><span class="p">:</span> <span class="s1">&#39;MS&#39;</span><span class="p">,</span> <span class="s1">&#39;0074&#39;</span><span class="p">:</span> <span class="s1">&#39;MA&#39;</span><span class="p">,</span> <span class="s1">&#39;0421&#39;</span><span class="p">:</span> <span class="s1">&#39;AB&#39;</span><span class="p">}</span>
+    <span class="n">nosrc</span> <span class="o">=</span> <span class="p">[]</span>
+    <span class="n">notgt</span> <span class="o">=</span> <span class="p">[]</span>
+    <span class="n">norefs</span> <span class="o">=</span> <span class="p">[]</span>
+    <span class="n">noev</span> <span class="o">=</span> <span class="p">[]</span>
+    <span class="n">noth</span> <span class="o">=</span> <span class="p">[]</span>
+    <span class="n">edges</span> <span class="o">=</span> <span class="p">[]</span>
+
+    <span class="k">for</span> <span class="n">c</span> <span class="ow">in</span> <span class="n">xmlroot</span><span class="o">.</span><span class="n">findall</span><span class="p">(</span><span class="n">bpprefix</span> <span class="o">+</span> <span class="s1">&#39;Catalysis&#39;</span><span class="p">):</span>
+        <span class="k">if</span> <span class="n">rdfprefix</span> <span class="o">+</span> <span class="s1">&#39;resource&#39;</span> <span class="ow">in</span> <span class="n">c</span><span class="o">.</span><span class="n">find</span><span class="p">(</span><span class="n">bpprefix</span> <span class="o">+</span> <span class="s1">&#39;controller&#39;</span><span class="p">)</span><span class="o">.</span><span class="n">attrib</span><span class="p">:</span>
+            <span class="n">src</span> <span class="o">=</span> <span class="s1">&#39;po_&#39;</span> <span class="o">+</span> \
+                <span class="n">c</span><span class="o">.</span><span class="n">find</span><span class="p">(</span>
+                    <span class="n">bpprefix</span> <span class="o">+</span> <span class="s1">&#39;controller&#39;</span><span class="p">)</span><span class="o">.</span><span class="n">attrib</span><span class="p">[</span><span class="n">rdfprefix</span> <span class="o">+</span> <span class="s1">&#39;resource&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;_&#39;</span><span class="p">)[</span><span class="mi">1</span><span class="p">]</span>
+        <span class="k">else</span><span class="p">:</span>
+            <span class="n">srcProt</span> <span class="o">=</span> <span class="n">c</span><span class="o">.</span><span class="n">find</span><span class="p">(</span><span class="n">bpprefix</span> <span class="o">+</span> <span class="s1">&#39;controller&#39;</span><span class="p">)</span><span class="o">.</span><span class="n">find</span><span class="p">(</span><span class="n">bpprefix</span> <span class="o">+</span>
+                                                           <span class="s1">&#39;Protein&#39;</span><span class="p">)</span>
+            <span class="k">if</span> <span class="n">srcProt</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
+                <span class="n">src</span> <span class="o">=</span> <span class="s1">&#39;po_&#39;</span> <span class="o">+</span> <span class="n">srcProt</span><span class="o">.</span><span class="n">attrib</span><span class="p">[</span><span class="n">rdfprefix</span> <span class="o">+</span> <span class="s1">&#39;ID&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;_&#39;</span><span class="p">)[</span><span class="mi">1</span><span class="p">]</span>
+            <span class="k">else</span><span class="p">:</span>
+                <span class="n">nosrc</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">c</span><span class="p">)</span>
+        <span class="n">tgtProt</span> <span class="o">=</span> <span class="n">c</span><span class="o">.</span><span class="n">find</span><span class="p">(</span><span class="n">bpprefix</span> <span class="o">+</span> <span class="s1">&#39;controlled&#39;</span><span class="p">)</span><span class="o">.</span><span class="n">iter</span><span class="p">(</span><span class="n">bpprefix</span> <span class="o">+</span>
+                                                       <span class="s1">&#39;ProteinReference&#39;</span><span class="p">)</span>
+        <span class="n">tgt</span> <span class="o">=</span> <span class="nb">next</span><span class="p">(</span><span class="n">tgtProt</span><span class="p">,</span> <span class="kc">None</span><span class="p">)</span>
+        <span class="k">if</span> <span class="n">tgt</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
+            <span class="n">tgt</span> <span class="o">=</span> <span class="n">tgt</span><span class="o">.</span><span class="n">attrib</span><span class="p">[</span><span class="n">rdfprefix</span> <span class="o">+</span> <span class="s1">&#39;ID&#39;</span><span class="p">]</span>
+        <span class="k">else</span><span class="p">:</span>
+            <span class="n">tgtProt</span> <span class="o">=</span> <span class="n">c</span><span class="o">.</span><span class="n">find</span><span class="p">(</span><span class="n">bpprefix</span> <span class="o">+</span> <span class="s1">&#39;controlled&#39;</span><span class="p">)</span><span class="o">.</span><span class="n">iter</span><span class="p">(</span><span class="n">bpprefix</span> <span class="o">+</span>
+                                                           <span class="s1">&#39;entityReference&#39;</span><span class="p">)</span>
+            <span class="n">tgt</span> <span class="o">=</span> <span class="nb">next</span><span class="p">(</span><span class="n">tgtProt</span><span class="p">,</span> <span class="kc">None</span><span class="p">)</span>
+            <span class="k">if</span> <span class="n">tgt</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
+                <span class="k">if</span> <span class="n">rdfprefix</span> <span class="o">+</span> <span class="s1">&#39;resource&#39;</span> <span class="ow">in</span> <span class="n">tgt</span><span class="o">.</span><span class="n">attrib</span><span class="p">:</span>
+                    <span class="n">tgt</span> <span class="o">=</span> <span class="n">tgt</span><span class="o">.</span><span class="n">attrib</span><span class="p">[</span><span class="n">rdfprefix</span> <span class="o">+</span> <span class="s1">&#39;resource&#39;</span><span class="p">][</span><span class="mi">1</span><span class="p">:]</span>
+            <span class="k">else</span><span class="p">:</span>
+                <span class="n">tgtProt</span> <span class="o">=</span> <span class="n">c</span><span class="o">.</span><span class="n">find</span><span class="p">(</span><span class="n">bpprefix</span> <span class="o">+</span> <span class="s1">&#39;controlled&#39;</span><span class="p">)</span><span class="o">.</span><span class="n">iter</span><span class="p">(</span><span class="n">bpprefix</span> <span class="o">+</span>
+                                                               <span class="s1">&#39;left&#39;</span><span class="p">)</span>
+                <span class="n">tgt</span> <span class="o">=</span> <span class="nb">next</span><span class="p">(</span><span class="n">tgtProt</span><span class="p">,</span> <span class="kc">None</span><span class="p">)</span>
+                <span class="k">if</span> <span class="n">tgt</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
+                    <span class="k">if</span> <span class="n">rdfprefix</span> <span class="o">+</span> <span class="s1">&#39;resource&#39;</span> <span class="ow">in</span> <span class="n">tgt</span><span class="o">.</span><span class="n">attrib</span><span class="p">:</span>
+                        <span class="n">tgt</span> <span class="o">=</span> <span class="s1">&#39;po_&#39;</span> <span class="o">+</span> \
+                            <span class="n">tgt</span><span class="o">.</span><span class="n">attrib</span><span class="p">[</span><span class="n">rdfprefix</span> <span class="o">+</span> <span class="s1">&#39;resource&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;_&#39;</span><span class="p">)[</span><span class="mi">1</span><span class="p">]</span>
+                <span class="k">else</span><span class="p">:</span>
+                    <span class="n">notgt</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">c</span><span class="p">)</span>
+        <span class="n">refs</span> <span class="o">=</span> <span class="n">c</span><span class="o">.</span><span class="n">iter</span><span class="p">(</span><span class="n">bpprefix</span> <span class="o">+</span> <span class="s1">&#39;PublicationXref&#39;</span><span class="p">)</span>
+        <span class="n">pmids</span> <span class="o">=</span> <span class="p">[]</span>
+        <span class="k">for</span> <span class="n">r</span> <span class="ow">in</span> <span class="n">refs</span><span class="p">:</span>
+            <span class="n">pm</span> <span class="o">=</span> <span class="n">r</span><span class="o">.</span><span class="n">attrib</span><span class="p">[</span><span class="n">rdfprefix</span> <span class="o">+</span> <span class="s1">&#39;ID&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;_&#39;</span><span class="p">)</span>
+            <span class="k">if</span> <span class="n">pm</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">==</span> <span class="s1">&#39;pmid&#39;</span><span class="p">:</span>
+                <span class="n">pmids</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">pm</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span>
+        <span class="n">refs</span> <span class="o">=</span> <span class="n">c</span><span class="o">.</span><span class="n">iter</span><span class="p">(</span><span class="n">bpprefix</span> <span class="o">+</span> <span class="s1">&#39;evidence&#39;</span><span class="p">)</span>
+        <span class="k">for</span> <span class="n">r</span> <span class="ow">in</span> <span class="n">refs</span><span class="p">:</span>
+            <span class="n">rrefs</span> <span class="o">=</span> <span class="n">r</span><span class="o">.</span><span class="n">iter</span><span class="p">(</span><span class="n">bpprefix</span> <span class="o">+</span> <span class="s1">&#39;xref&#39;</span><span class="p">)</span>
+            <span class="k">for</span> <span class="n">rr</span> <span class="ow">in</span> <span class="n">rrefs</span><span class="p">:</span>
+                <span class="k">if</span> <span class="n">rdfprefix</span> <span class="o">+</span> <span class="s1">&#39;resource&#39;</span> <span class="ow">in</span> <span class="n">rr</span><span class="o">.</span><span class="n">attrib</span><span class="p">:</span>
+                    <span class="n">pm</span> <span class="o">=</span> <span class="n">rr</span><span class="o">.</span><span class="n">attrib</span><span class="p">[</span><span class="n">rdfprefix</span> <span class="o">+</span> <span class="s1">&#39;resource&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;_&#39;</span><span class="p">)</span>
+                    <span class="k">if</span> <span class="n">pm</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">==</span> <span class="s1">&#39;pubmed&#39;</span><span class="p">:</span>
+                        <span class="n">pmids</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">pm</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span>
+        <span class="n">evs</span> <span class="o">=</span> <span class="p">[]</span>
+        <span class="k">for</span> <span class="n">e</span> <span class="ow">in</span> <span class="n">c</span><span class="o">.</span><span class="n">iter</span><span class="p">(</span><span class="n">bpprefix</span> <span class="o">+</span> <span class="s1">&#39;evidenceCode&#39;</span><span class="p">):</span>
+            <span class="k">if</span> <span class="n">rdfprefix</span> <span class="o">+</span> <span class="s1">&#39;resource&#39;</span> <span class="ow">in</span> <span class="n">e</span><span class="o">.</span><span class="n">attrib</span><span class="p">:</span>
+                <span class="n">evs</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">ev_short</span><span class="p">[</span><span class="n">e</span><span class="o">.</span><span class="n">attrib</span><span class="p">[</span><span class="n">rdfprefix</span> <span class="o">+</span> <span class="s1">&#39;resource&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;_&#39;</span><span class="p">)</span>
+                                    <span class="p">[</span><span class="mi">1</span><span class="p">]])</span>
+            <span class="k">else</span><span class="p">:</span>
+                <span class="n">ev</span> <span class="o">=</span> <span class="n">e</span><span class="o">.</span><span class="n">find</span><span class="p">(</span><span class="n">bpprefix</span> <span class="o">+</span> <span class="s1">&#39;EvidenceCodeVocabulary&#39;</span><span class="p">)</span>
+                <span class="n">evs</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">ev_short</span><span class="p">[</span><span class="n">ev</span><span class="o">.</span><span class="n">attrib</span><span class="p">[</span><span class="n">rdfprefix</span> <span class="o">+</span> <span class="s1">&#39;ID&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;_&#39;</span><span class="p">)[</span><span class="mi">1</span><span class="p">]])</span>
+        <span class="k">for</span> <span class="n">e</span> <span class="ow">in</span> <span class="n">c</span><span class="o">.</span><span class="n">iter</span><span class="p">(</span><span class="n">bpprefix</span> <span class="o">+</span> <span class="s1">&#39;evidence&#39;</span><span class="p">):</span>
+            <span class="k">if</span> <span class="n">rdfprefix</span> <span class="o">+</span> <span class="s1">&#39;resource&#39;</span> <span class="ow">in</span> <span class="n">e</span><span class="o">.</span><span class="n">attrib</span><span class="p">:</span>
+                <span class="n">ev</span> <span class="o">=</span> <span class="n">e</span><span class="o">.</span><span class="n">attrib</span><span class="p">[</span><span class="n">rdfprefix</span> <span class="o">+</span> <span class="s1">&#39;resource&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;_&#39;</span><span class="p">)</span>
+                <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">ev</span><span class="p">)</span> <span class="o">==</span> <span class="mi">4</span><span class="p">:</span>
+                    <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">ev</span><span class="p">[</span><span class="mi">3</span><span class="p">])</span> <span class="o">==</span> <span class="mi">4</span><span class="p">:</span>
+                        <span class="n">evs</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">ev_short</span><span class="p">[</span><span class="n">ev</span><span class="p">[</span><span class="mi">3</span><span class="p">]])</span>
+        <span class="k">if</span> <span class="p">(</span><span class="n">src</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span> <span class="ow">and</span> <span class="n">tgt</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span> <span class="ow">and</span> <span class="n">src</span> <span class="ow">in</span> <span class="n">proteins</span> <span class="ow">and</span>
+                <span class="n">tgt</span> <span class="ow">in</span> <span class="n">proteins</span> <span class="ow">and</span> <span class="n">proteins</span><span class="p">[</span><span class="n">src</span><span class="p">][</span><span class="s1">&#39;id&#39;</span><span class="p">]</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span> <span class="ow">and</span>
+                <span class="n">proteins</span><span class="p">[</span><span class="n">tgt</span><span class="p">][</span><span class="s1">&#39;id&#39;</span><span class="p">]</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">):</span>
+            <span class="n">edges</span><span class="o">.</span><span class="n">append</span><span class="p">({</span>
+                <span class="s1">&#39;src&#39;</span><span class="p">:</span> <span class="n">proteins</span><span class="p">[</span><span class="n">src</span><span class="p">],</span>
+                <span class="s1">&#39;tgt&#39;</span><span class="p">:</span> <span class="n">proteins</span><span class="p">[</span><span class="n">tgt</span><span class="p">],</span>
+                <span class="s1">&#39;pmids&#39;</span><span class="p">:</span> <span class="nb">list</span><span class="p">(</span><span class="nb">set</span><span class="p">(</span><span class="n">pmids</span><span class="p">)),</span>
+                <span class="s1">&#39;evs&#39;</span><span class="p">:</span> <span class="nb">list</span><span class="p">(</span><span class="nb">set</span><span class="p">(</span><span class="n">evs</span><span class="p">))</span>
+            <span class="p">})</span>
+            <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">evs</span><span class="p">)</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
+                <span class="n">noev</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">c</span><span class="p">)</span>
+            <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">pmids</span><span class="p">)</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
+                <span class="n">norefs</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">c</span><span class="p">)</span>
+            <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">evs</span><span class="p">)</span> <span class="o">==</span> <span class="mi">0</span> <span class="ow">and</span> <span class="nb">len</span><span class="p">(</span><span class="n">pmids</span><span class="p">)</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
+                <span class="n">noth</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">c</span><span class="p">)</span>
+
+    <span class="k">if</span> <span class="n">ncbi_tax_id</span><span class="p">:</span>
+
+        <span class="n">all_uniprots</span> <span class="o">=</span> <span class="n">uniprot_db</span><span class="o">.</span><span class="n">all_uniprots</span><span class="p">(</span><span class="n">organism</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">)</span>
+
+    <span class="k">for</span> <span class="n">e</span> <span class="ow">in</span> <span class="n">edges</span><span class="p">:</span>
+
+        <span class="k">if</span> <span class="p">(</span>
+            <span class="n">ncbi_tax_id</span> <span class="ow">and</span> <span class="p">(</span>
+                <span class="n">e</span><span class="p">[</span><span class="s1">&#39;src&#39;</span><span class="p">][</span><span class="s1">&#39;id&#39;</span><span class="p">]</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">all_uniprots</span> <span class="ow">or</span>
+                <span class="n">e</span><span class="p">[</span><span class="s1">&#39;tgt&#39;</span><span class="p">][</span><span class="s1">&#39;id&#39;</span><span class="p">]</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">all_uniprots</span>
+            <span class="p">)</span>
+        <span class="p">):</span>
+
+            <span class="k">continue</span>
+
+        <span class="n">this_iaction</span> <span class="o">=</span> <span class="p">[</span>
+            <span class="n">e</span><span class="p">[</span><span class="s1">&#39;src&#39;</span><span class="p">][</span><span class="s1">&#39;id&#39;</span><span class="p">],</span> <span class="n">e</span><span class="p">[</span><span class="s1">&#39;tgt&#39;</span><span class="p">][</span><span class="s1">&#39;id&#39;</span><span class="p">],</span> <span class="n">e</span><span class="p">[</span><span class="s1">&#39;src&#39;</span><span class="p">][</span><span class="s1">&#39;species&#39;</span><span class="p">],</span>
+            <span class="n">e</span><span class="p">[</span><span class="s1">&#39;tgt&#39;</span><span class="p">][</span><span class="s1">&#39;species&#39;</span><span class="p">],</span> <span class="s1">&#39;;&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">e</span><span class="p">[</span><span class="s1">&#39;evs&#39;</span><span class="p">]),</span> <span class="s1">&#39;;&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">e</span><span class="p">[</span><span class="s1">&#39;pmids&#39;</span><span class="p">])</span>
+        <span class="p">]</span>
+
+        <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">this_iaction</span><span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">])</span> <span class="o">&gt;</span> <span class="mi">0</span><span class="p">:</span>
+
+            <span class="n">result_curated</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">this_iaction</span><span class="p">)</span>
+
+        <span class="k">else</span><span class="p">:</span>
+
+            <span class="n">result_noref</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">this_iaction</span><span class="p">)</span>
+
+    <span class="n">pickle</span><span class="o">.</span><span class="n">dump</span><span class="p">(</span><span class="n">result_curated</span><span class="p">,</span> <span class="nb">open</span><span class="p">(</span><span class="n">curated_cache</span><span class="p">,</span> <span class="s1">&#39;wb&#39;</span><span class="p">))</span>
+    <span class="n">pickle</span><span class="o">.</span><span class="n">dump</span><span class="p">(</span><span class="n">result_noref</span><span class="p">,</span> <span class="nb">open</span><span class="p">(</span><span class="n">noref_cache</span><span class="p">,</span> <span class="s1">&#39;wb&#39;</span><span class="p">))</span>
+    <span class="k">return</span> <span class="n">result_curated</span><span class="p">,</span> <span class="n">result_noref</span></div>
+
+
+
+<div class="viewcode-block" id="phosphosite_interactions_new">
+<a class="viewcode-back" href="../../../api/pypath.inputs.phosphosite.phosphosite_interactions_new.html#pypath.inputs.phosphosite.phosphosite_interactions_new">[docs]</a>
+<span class="k">def</span> <span class="nf">phosphosite_interactions_new</span><span class="p">(</span><span class="n">cache</span> <span class="o">=</span> <span class="kc">True</span><span class="p">):</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Downloads curated and HTP data from Phosphosite,</span>
+<span class="sd">    from preprocessed cache file if available.</span>
+<span class="sd">    Processes BioPAX format.</span>
+<span class="sd">    Returns list of interactions.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="n">curated_cache</span> <span class="o">=</span> <span class="n">urls</span><span class="o">.</span><span class="n">files</span><span class="p">[</span><span class="s1">&#39;phosphosite&#39;</span><span class="p">][</span><span class="s1">&#39;curated&#39;</span><span class="p">]</span>
+    <span class="n">noref_cache</span> <span class="o">=</span> <span class="n">urls</span><span class="o">.</span><span class="n">files</span><span class="p">[</span><span class="s1">&#39;phosphosite&#39;</span><span class="p">][</span><span class="s1">&#39;noref&#39;</span><span class="p">]</span>
+
+    <span class="k">if</span> <span class="p">(</span>
+        <span class="n">cache</span> <span class="ow">and</span>
+        <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">exists</span><span class="p">(</span><span class="n">curated_cache</span><span class="p">)</span> <span class="ow">and</span>
+        <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">exists</span><span class="p">(</span><span class="n">noref_cache</span><span class="p">)</span>
+    <span class="p">):</span>
+
+        <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">curated_cache</span><span class="p">,</span> <span class="s1">&#39;rb&#39;</span><span class="p">)</span> <span class="k">as</span> <span class="n">fp</span><span class="p">:</span>
+
+            <span class="n">data_curated</span> <span class="o">=</span> <span class="n">pickle</span><span class="o">.</span><span class="n">load</span><span class="p">(</span><span class="n">fp</span><span class="p">)</span>
+
+        <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">noref_cache</span><span class="p">,</span> <span class="s1">&#39;rb&#39;</span><span class="p">)</span> <span class="k">as</span> <span class="n">fp</span><span class="p">:</span>
+
+            <span class="n">data_noref</span> <span class="o">=</span> <span class="n">pickle</span><span class="o">.</span><span class="n">load</span><span class="p">(</span><span class="n">fp</span><span class="p">)</span>
+
+        <span class="k">return</span> <span class="n">data_curated</span><span class="p">,</span> <span class="n">data_noref</span>
+
+
+    <span class="k">def</span> <span class="nf">collect_items</span><span class="p">(</span><span class="n">tagname</span><span class="p">,</span> <span class="n">process_method</span><span class="p">):</span>
+
+        <span class="n">result</span> <span class="o">=</span> <span class="p">{}</span>
+
+        <span class="k">for</span> <span class="n">p</span> <span class="ow">in</span> <span class="n">xmlroot</span><span class="o">.</span><span class="n">iter</span><span class="p">(</span><span class="n">tagname</span><span class="p">):</span>
+
+            <span class="n">key</span><span class="p">,</span> <span class="n">value</span> <span class="o">=</span> <span class="n">process_method</span><span class="p">(</span><span class="n">p</span><span class="p">)</span>
+            <span class="n">result</span><span class="p">[</span><span class="n">key</span><span class="p">]</span> <span class="o">=</span> <span class="n">value</span>
+
+        <span class="k">return</span> <span class="n">result</span>
+
+
+    <span class="k">def</span> <span class="nf">process_protein</span><span class="p">(</span><span class="n">protein</span><span class="p">):</span>
+
+        <span class="n">protein_id</span> <span class="o">=</span> <span class="n">protein</span><span class="o">.</span><span class="n">attrib</span><span class="p">[</span><span class="s1">&#39;</span><span class="si">%s</span><span class="s1">ID&#39;</span> <span class="o">%</span> <span class="n">rdfprefix</span><span class="p">]</span>
+        <span class="n">database</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="n">protein</span><span class="o">.</span><span class="n">find</span><span class="p">(</span>
+                <span class="s1">&#39;</span><span class="si">%s</span><span class="s1">xref&#39;</span> <span class="o">%</span> <span class="n">bpprefix</span>
+            <span class="p">)</span><span class="o">.</span><span class="n">find</span><span class="p">(</span>
+                <span class="s1">&#39;</span><span class="si">%s</span><span class="s1">UnificationXref&#39;</span> <span class="o">%</span> <span class="n">bpprefix</span>
+            <span class="p">)</span><span class="o">.</span><span class="n">find</span><span class="p">(</span>
+                <span class="s1">&#39;</span><span class="si">%s</span><span class="s1">db&#39;</span> <span class="o">%</span> <span class="n">bpprefix</span>
+            <span class="p">)</span><span class="o">.</span><span class="n">text</span>
+        <span class="p">)</span>
+        <span class="n">identifier</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="n">protein</span><span class="o">.</span><span class="n">find</span><span class="p">(</span>
+                <span class="s1">&#39;</span><span class="si">%s</span><span class="s1">xref&#39;</span> <span class="o">%</span> <span class="n">bpprefix</span>
+            <span class="p">)</span><span class="o">.</span><span class="n">find</span><span class="p">(</span>
+                <span class="s1">&#39;</span><span class="si">%s</span><span class="s1">UnificationXref&#39;</span> <span class="o">%</span> <span class="n">bpprefix</span>
+            <span class="p">)</span><span class="o">.</span><span class="n">find</span><span class="p">(</span>
+                <span class="s1">&#39;</span><span class="si">%s</span><span class="s1">id&#39;</span> <span class="o">%</span> <span class="n">bpprefix</span>
+            <span class="p">)</span><span class="o">.</span><span class="n">text</span>
+        <span class="p">)</span>
+
+        <span class="n">organism</span> <span class="o">=</span> <span class="kc">None</span>
+        <span class="n">e_organism</span> <span class="o">=</span> <span class="n">protein</span><span class="o">.</span><span class="n">find</span><span class="p">(</span><span class="s1">&#39;</span><span class="si">%s</span><span class="s1">organism&#39;</span> <span class="o">%</span> <span class="n">bpprefix</span><span class="p">)</span>
+        <span class="k">if</span> <span class="p">(</span>
+            <span class="n">e_organism</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span> <span class="ow">and</span>
+            <span class="s1">&#39;</span><span class="si">%s</span><span class="s1">resource&#39;</span> <span class="o">%</span> <span class="n">rdfprefix</span> <span class="ow">in</span> <span class="n">e_organism</span><span class="o">.</span><span class="n">attrib</span>
+        <span class="p">):</span>
+            <span class="n">organism</span> <span class="o">=</span> <span class="p">(</span>
+                <span class="n">e_organism</span><span class="o">.</span><span class="n">attrib</span><span class="p">[</span><span class="s1">&#39;</span><span class="si">%s</span><span class="s1">resource&#39;</span> <span class="o">%</span> <span class="n">rdfprefix</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;_&#39;</span><span class="p">)[</span><span class="mi">1</span><span class="p">]</span>
+            <span class="p">)</span>
+
+        <span class="k">return</span> <span class="n">protein_id</span><span class="p">,</span> <span class="p">(</span><span class="n">databas</span><span class="p">,</span> <span class="n">identifier</span><span class="p">,</span> <span class="n">organism</span><span class="p">)</span>
+
+    <span class="k">def</span> <span class="nf">process_site</span><span class="p">(</span><span class="n">site</span><span class="p">):</span>
+
+        <span class="n">site_id</span> <span class="o">=</span> <span class="n">site</span><span class="o">.</span><span class="n">attrib</span><span class="p">[</span><span class="s1">&#39;</span><span class="si">%s</span><span class="s1">ID&#39;</span> <span class="o">%</span> <span class="n">rdfprefix</span><span class="p">]</span>
+        <span class="n">site_offset</span> <span class="o">=</span> <span class="n">site</span><span class="o">.</span><span class="n">find</span><span class="p">(</span><span class="s1">&#39;</span><span class="si">%s</span><span class="s1">sequencePosition&#39;</span><span class="p">)</span><span class="o">.</span><span class="n">text</span>
+
+        <span class="k">return</span> <span class="n">site_id</span><span class="p">,</span> <span class="n">site_offset</span>
+
+
+    <span class="k">def</span> <span class="nf">process_modification</span><span class="p">(</span><span class="n">seqmodvoc</span><span class="p">):</span>
+
+        <span class="n">mod_id</span> <span class="o">=</span> <span class="n">seqmodvoc</span><span class="o">.</span><span class="n">attrib</span><span class="p">[</span><span class="s1">&#39;</span><span class="si">%s</span><span class="s1">ID&#39;</span> <span class="o">%</span> <span class="n">rdfprefix</span><span class="p">]</span>
+        <span class="n">residue</span><span class="p">,</span> <span class="n">mod</span> <span class="o">=</span> <span class="n">mod_id</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;_&#39;</span><span class="p">)</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;-&#39;</span><span class="p">)</span>
+
+        <span class="k">return</span> <span class="n">mod_id</span><span class="p">,</span> <span class="p">(</span><span class="n">residue</span><span class="p">,</span> <span class="n">mod</span><span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">get_resource</span><span class="p">(</span><span class="n">elem</span><span class="p">,</span> <span class="n">resource_tag</span><span class="p">):</span>
+
+        <span class="n">res_attr</span> <span class="o">=</span> <span class="s1">&#39;</span><span class="si">%s</span><span class="s1">resource&#39;</span> <span class="o">%</span> <span class="n">rdfprefix</span>
+
+        <span class="k">if</span> <span class="n">res_attr</span> <span class="ow">in</span> <span class="n">elem</span><span class="o">.</span><span class="n">attrib</span><span class="p">:</span>
+
+            <span class="k">return</span> <span class="n">elem</span><span class="o">.</span><span class="n">attrib</span><span class="p">[</span><span class="n">res_attr</span><span class="p">][</span><span class="mi">1</span><span class="p">:]</span>
+
+        <span class="k">else</span><span class="p">:</span>
+
+            <span class="k">return</span> <span class="n">elem</span><span class="o">.</span><span class="n">find</span><span class="p">(</span><span class="n">resource_tag</span><span class="p">)</span><span class="o">.</span><span class="n">attrib</span><span class="p">[</span><span class="s1">&#39;</span><span class="si">%s</span><span class="s1">ID&#39;</span> <span class="o">%</span> <span class="n">rdfprefix</span><span class="p">]</span>
+
+
+    <span class="k">def</span> <span class="nf">process_feature</span><span class="p">(</span><span class="n">feature</span><span class="p">):</span>
+
+        <span class="n">feature_id</span> <span class="o">=</span> <span class="n">feature</span><span class="o">.</span><span class="n">attrib</span><span class="p">[</span><span class="s1">&#39;</span><span class="si">%s</span><span class="s1">ID&#39;</span> <span class="o">%</span> <span class="n">rdfprefix</span><span class="p">]</span>
+        <span class="n">site</span> <span class="o">=</span> <span class="n">get_resource</span><span class="p">(</span>
+            <span class="n">feature</span><span class="o">.</span><span class="n">find</span><span class="p">(</span><span class="s1">&#39;</span><span class="si">%s</span><span class="s1">featureLocation&#39;</span> <span class="o">%</span> <span class="n">bpprefix</span><span class="p">),</span>
+            <span class="s1">&#39;</span><span class="si">%s</span><span class="s1">SequenceSite&#39;</span> <span class="o">%</span> <span class="n">bpprefix</span><span class="p">,</span>
+        <span class="p">)</span>
+        <span class="n">modification</span> <span class="o">=</span> <span class="n">get_resource</span><span class="p">(</span>
+            <span class="n">feature</span><span class="o">.</span><span class="n">find</span><span class="p">(</span><span class="s1">&#39;</span><span class="si">%s</span><span class="s1">modificationType&#39;</span> <span class="o">%</span> <span class="n">bpprefix</span><span class="p">),</span>
+            <span class="s1">&#39;</span><span class="si">%s</span><span class="s1">SequenceModificationVocabulary&#39;</span> <span class="o">%</span> <span class="n">bpprefix</span><span class="p">,</span>
+        <span class="p">)</span>
+
+        <span class="k">return</span> <span class="n">feature_id</span><span class="p">,</span> <span class="p">(</span><span class="n">site</span><span class="p">,</span> <span class="n">modification</span><span class="p">)</span>
+
+
+    <span class="n">result_curated</span> <span class="o">=</span> <span class="p">[]</span>
+    <span class="n">result_noref</span> <span class="o">=</span> <span class="p">[]</span>
+    <span class="n">bpprefix</span> <span class="o">=</span> <span class="s1">&#39;{http://www.biopax.org/release/biopax-level3.owl#}&#39;</span>
+    <span class="n">rdfprefix</span> <span class="o">=</span> <span class="s1">&#39;{http://www.w3.org/1999/02/22-rdf-syntax-ns#}&#39;</span>
+
+    <span class="n">url</span> <span class="o">=</span> <span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;psite_bp&#39;</span><span class="p">][</span><span class="s1">&#39;url&#39;</span><span class="p">]</span>
+    <span class="n">c</span> <span class="o">=</span> <span class="n">curl</span><span class="o">.</span><span class="n">Curl</span><span class="p">(</span><span class="n">url</span><span class="p">,</span> <span class="n">silent</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span> <span class="n">large</span> <span class="o">=</span> <span class="kc">True</span><span class="p">)</span>
+    <span class="n">bpax</span> <span class="o">=</span> <span class="n">c</span><span class="o">.</span><span class="n">gzfile</span>
+    <span class="n">xml</span> <span class="o">=</span> <span class="n">ET</span><span class="o">.</span><span class="n">parse</span><span class="p">(</span><span class="n">bpax</span><span class="p">)</span>
+    <span class="n">xmlroot</span> <span class="o">=</span> <span class="n">xml</span><span class="o">.</span><span class="n">getroot</span><span class="p">()</span>
+
+
+    <span class="n">proteins</span> <span class="o">=</span> <span class="n">collect_items</span><span class="p">(</span>
+        <span class="s1">&#39;</span><span class="si">%s</span><span class="s1">Protein&#39;</span> <span class="o">%</span> <span class="n">bpprefix</span><span class="p">,</span>
+        <span class="n">process_method</span> <span class="o">=</span> <span class="n">process_protein</span><span class="p">,</span>
+    <span class="p">)</span>
+    <span class="n">sites</span> <span class="o">=</span> <span class="n">collect_items</span><span class="p">(</span>
+        <span class="s1">&#39;</span><span class="si">%s</span><span class="s1">SequenceSite&#39;</span> <span class="o">%</span> <span class="n">bpprefix</span><span class="p">,</span>
+        <span class="n">process_method</span> <span class="o">=</span> <span class="n">process_site</span><span class="p">,</span>
+    <span class="p">)</span>
+    <span class="n">modifications</span> <span class="o">=</span> <span class="n">collect_items</span><span class="p">(</span>
+        <span class="s1">&#39;</span><span class="si">%s</span><span class="s1">SequenceModificationVocabulary&#39;</span> <span class="o">%</span> <span class="n">bpprefix</span><span class="p">,</span>
+        <span class="n">process_method</span> <span class="o">=</span> <span class="n">process_modification</span><span class="p">,</span>
+    <span class="p">)</span>
+    <span class="n">features</span> <span class="o">=</span> <span class="n">collect_items</span><span class="p">(</span>
+        <span class="s1">&#39;</span><span class="si">%s</span><span class="s1">ModificationFeature&#39;</span> <span class="o">%</span> <span class="n">bpprefix</span><span class="p">,</span>
+        <span class="n">process_method</span> <span class="o">=</span> <span class="n">process_feature</span><span class="p">,</span>
+    <span class="p">)</span>
+
+    <span class="n">evidences</span> <span class="o">=</span> <span class="p">{}</span>
+    <span class="k">for</span> <span class="n">p</span> <span class="ow">in</span> <span class="n">xmlroot</span><span class="o">.</span><span class="n">iter</span><span class="p">(</span><span class="n">bpprefix</span> <span class="o">+</span> <span class="s1">&#39;EvidenceCodeVocabulary&#39;</span><span class="p">):</span>
+        <span class="n">evid</span> <span class="o">=</span> <span class="n">p</span><span class="o">.</span><span class="n">attrib</span><span class="p">[</span><span class="n">rdfprefix</span> <span class="o">+</span> <span class="s1">&#39;ID&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;_&#39;</span><span class="p">)[</span><span class="mi">1</span><span class="p">]</span>
+        <span class="n">evname</span> <span class="o">=</span> <span class="n">p</span><span class="o">.</span><span class="n">find</span><span class="p">(</span><span class="n">bpprefix</span> <span class="o">+</span> <span class="s1">&#39;term&#39;</span><span class="p">)</span><span class="o">.</span><span class="n">text</span>
+        <span class="n">evidences</span><span class="p">[</span><span class="n">evid</span><span class="p">]</span> <span class="o">=</span> <span class="n">evname</span>
+    <span class="n">ev_short</span> <span class="o">=</span> <span class="p">{</span><span class="s1">&#39;0113&#39;</span><span class="p">:</span> <span class="s1">&#39;WB&#39;</span><span class="p">,</span> <span class="s1">&#39;0427&#39;</span><span class="p">:</span> <span class="s1">&#39;MS&#39;</span><span class="p">,</span> <span class="s1">&#39;0074&#39;</span><span class="p">:</span> <span class="s1">&#39;MA&#39;</span><span class="p">,</span> <span class="s1">&#39;0421&#39;</span><span class="p">:</span> <span class="s1">&#39;AB&#39;</span><span class="p">}</span>
+    <span class="n">nosrc</span> <span class="o">=</span> <span class="p">[]</span>
+    <span class="n">notgt</span> <span class="o">=</span> <span class="p">[]</span>
+    <span class="n">norefs</span> <span class="o">=</span> <span class="p">[]</span>
+    <span class="n">noev</span> <span class="o">=</span> <span class="p">[]</span>
+    <span class="n">noth</span> <span class="o">=</span> <span class="p">[]</span>
+    <span class="n">edges</span> <span class="o">=</span> <span class="p">[]</span>
+
+    <span class="k">for</span> <span class="n">c</span> <span class="ow">in</span> <span class="n">xmlroot</span><span class="o">.</span><span class="n">findall</span><span class="p">(</span><span class="n">bpprefix</span> <span class="o">+</span> <span class="s1">&#39;Catalysis&#39;</span><span class="p">):</span>
+        <span class="k">if</span> <span class="n">rdfprefix</span> <span class="o">+</span> <span class="s1">&#39;resource&#39;</span> <span class="ow">in</span> <span class="n">c</span><span class="o">.</span><span class="n">find</span><span class="p">(</span><span class="n">bpprefix</span> <span class="o">+</span> <span class="s1">&#39;controller&#39;</span><span class="p">)</span><span class="o">.</span><span class="n">attrib</span><span class="p">:</span>
+            <span class="n">src</span> <span class="o">=</span> <span class="s1">&#39;po_&#39;</span> <span class="o">+</span> \
+                <span class="n">c</span><span class="o">.</span><span class="n">find</span><span class="p">(</span>
+                    <span class="n">bpprefix</span> <span class="o">+</span> <span class="s1">&#39;controller&#39;</span><span class="p">)</span><span class="o">.</span><span class="n">attrib</span><span class="p">[</span><span class="n">rdfprefix</span> <span class="o">+</span> <span class="s1">&#39;resource&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;_&#39;</span><span class="p">)[</span><span class="mi">1</span><span class="p">]</span>
+        <span class="k">else</span><span class="p">:</span>
+            <span class="n">srcProt</span> <span class="o">=</span> <span class="n">c</span><span class="o">.</span><span class="n">find</span><span class="p">(</span><span class="n">bpprefix</span> <span class="o">+</span> <span class="s1">&#39;controller&#39;</span><span class="p">)</span><span class="o">.</span><span class="n">find</span><span class="p">(</span><span class="n">bpprefix</span> <span class="o">+</span>
+                                                           <span class="s1">&#39;Protein&#39;</span><span class="p">)</span>
+            <span class="k">if</span> <span class="n">srcProt</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
+                <span class="n">src</span> <span class="o">=</span> <span class="s1">&#39;po_&#39;</span> <span class="o">+</span> <span class="n">srcProt</span><span class="o">.</span><span class="n">attrib</span><span class="p">[</span><span class="n">rdfprefix</span> <span class="o">+</span> <span class="s1">&#39;ID&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;_&#39;</span><span class="p">)[</span><span class="mi">1</span><span class="p">]</span>
+            <span class="k">else</span><span class="p">:</span>
+                <span class="n">nosrc</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">c</span><span class="p">)</span>
+        <span class="n">tgtProt</span> <span class="o">=</span> <span class="n">c</span><span class="o">.</span><span class="n">find</span><span class="p">(</span><span class="n">bpprefix</span> <span class="o">+</span> <span class="s1">&#39;controlled&#39;</span><span class="p">)</span><span class="o">.</span><span class="n">iter</span><span class="p">(</span><span class="n">bpprefix</span> <span class="o">+</span>
+                                                       <span class="s1">&#39;ProteinReference&#39;</span><span class="p">)</span>
+        <span class="n">tgt</span> <span class="o">=</span> <span class="nb">next</span><span class="p">(</span><span class="n">tgtProt</span><span class="p">,</span> <span class="kc">None</span><span class="p">)</span>
+        <span class="k">if</span> <span class="n">tgt</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
+            <span class="n">tgt</span> <span class="o">=</span> <span class="n">tgt</span><span class="o">.</span><span class="n">attrib</span><span class="p">[</span><span class="n">rdfprefix</span> <span class="o">+</span> <span class="s1">&#39;ID&#39;</span><span class="p">]</span>
+        <span class="k">else</span><span class="p">:</span>
+            <span class="n">tgtProt</span> <span class="o">=</span> <span class="n">c</span><span class="o">.</span><span class="n">find</span><span class="p">(</span><span class="n">bpprefix</span> <span class="o">+</span> <span class="s1">&#39;controlled&#39;</span><span class="p">)</span><span class="o">.</span><span class="n">iter</span><span class="p">(</span><span class="n">bpprefix</span> <span class="o">+</span>
+                                                           <span class="s1">&#39;entityReference&#39;</span><span class="p">)</span>
+            <span class="n">tgt</span> <span class="o">=</span> <span class="nb">next</span><span class="p">(</span><span class="n">tgtProt</span><span class="p">,</span> <span class="kc">None</span><span class="p">)</span>
+            <span class="k">if</span> <span class="n">tgt</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
+                <span class="k">if</span> <span class="n">rdfprefix</span> <span class="o">+</span> <span class="s1">&#39;resource&#39;</span> <span class="ow">in</span> <span class="n">tgt</span><span class="o">.</span><span class="n">attrib</span><span class="p">:</span>
+                    <span class="n">tgt</span> <span class="o">=</span> <span class="n">tgt</span><span class="o">.</span><span class="n">attrib</span><span class="p">[</span><span class="n">rdfprefix</span> <span class="o">+</span> <span class="s1">&#39;resource&#39;</span><span class="p">][</span><span class="mi">1</span><span class="p">:]</span>
+            <span class="k">else</span><span class="p">:</span>
+                <span class="n">tgtProt</span> <span class="o">=</span> <span class="n">c</span><span class="o">.</span><span class="n">find</span><span class="p">(</span><span class="n">bpprefix</span> <span class="o">+</span> <span class="s1">&#39;controlled&#39;</span><span class="p">)</span><span class="o">.</span><span class="n">iter</span><span class="p">(</span><span class="n">bpprefix</span> <span class="o">+</span>
+                                                               <span class="s1">&#39;left&#39;</span><span class="p">)</span>
+                <span class="n">tgt</span> <span class="o">=</span> <span class="nb">next</span><span class="p">(</span><span class="n">tgtProt</span><span class="p">,</span> <span class="kc">None</span><span class="p">)</span>
+                <span class="k">if</span> <span class="n">tgt</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
+                    <span class="k">if</span> <span class="n">rdfprefix</span> <span class="o">+</span> <span class="s1">&#39;resource&#39;</span> <span class="ow">in</span> <span class="n">tgt</span><span class="o">.</span><span class="n">attrib</span><span class="p">:</span>
+                        <span class="n">tgt</span> <span class="o">=</span> <span class="s1">&#39;po_&#39;</span> <span class="o">+</span> \
+                            <span class="n">tgt</span><span class="o">.</span><span class="n">attrib</span><span class="p">[</span><span class="n">rdfprefix</span> <span class="o">+</span> <span class="s1">&#39;resource&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;_&#39;</span><span class="p">)[</span><span class="mi">1</span><span class="p">]</span>
+                <span class="k">else</span><span class="p">:</span>
+                    <span class="n">notgt</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">c</span><span class="p">)</span>
+        <span class="n">refs</span> <span class="o">=</span> <span class="n">c</span><span class="o">.</span><span class="n">iter</span><span class="p">(</span><span class="n">bpprefix</span> <span class="o">+</span> <span class="s1">&#39;PublicationXref&#39;</span><span class="p">)</span>
+        <span class="n">pmids</span> <span class="o">=</span> <span class="p">[]</span>
+        <span class="k">for</span> <span class="n">r</span> <span class="ow">in</span> <span class="n">refs</span><span class="p">:</span>
+            <span class="n">pm</span> <span class="o">=</span> <span class="n">r</span><span class="o">.</span><span class="n">attrib</span><span class="p">[</span><span class="n">rdfprefix</span> <span class="o">+</span> <span class="s1">&#39;ID&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;_&#39;</span><span class="p">)</span>
+            <span class="k">if</span> <span class="n">pm</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">==</span> <span class="s1">&#39;pmid&#39;</span><span class="p">:</span>
+                <span class="n">pmids</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">pm</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span>
+        <span class="n">refs</span> <span class="o">=</span> <span class="n">c</span><span class="o">.</span><span class="n">iter</span><span class="p">(</span><span class="n">bpprefix</span> <span class="o">+</span> <span class="s1">&#39;evidence&#39;</span><span class="p">)</span>
+        <span class="k">for</span> <span class="n">r</span> <span class="ow">in</span> <span class="n">refs</span><span class="p">:</span>
+            <span class="n">rrefs</span> <span class="o">=</span> <span class="n">r</span><span class="o">.</span><span class="n">iter</span><span class="p">(</span><span class="n">bpprefix</span> <span class="o">+</span> <span class="s1">&#39;xref&#39;</span><span class="p">)</span>
+            <span class="k">for</span> <span class="n">rr</span> <span class="ow">in</span> <span class="n">rrefs</span><span class="p">:</span>
+                <span class="k">if</span> <span class="n">rdfprefix</span> <span class="o">+</span> <span class="s1">&#39;resource&#39;</span> <span class="ow">in</span> <span class="n">rr</span><span class="o">.</span><span class="n">attrib</span><span class="p">:</span>
+                    <span class="n">pm</span> <span class="o">=</span> <span class="n">rr</span><span class="o">.</span><span class="n">attrib</span><span class="p">[</span><span class="n">rdfprefix</span> <span class="o">+</span> <span class="s1">&#39;resource&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;_&#39;</span><span class="p">)</span>
+                    <span class="k">if</span> <span class="n">pm</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">==</span> <span class="s1">&#39;pubmed&#39;</span><span class="p">:</span>
+                        <span class="n">pmids</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">pm</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span>
+        <span class="n">evs</span> <span class="o">=</span> <span class="p">[]</span>
+        <span class="k">for</span> <span class="n">e</span> <span class="ow">in</span> <span class="n">c</span><span class="o">.</span><span class="n">iter</span><span class="p">(</span><span class="n">bpprefix</span> <span class="o">+</span> <span class="s1">&#39;evidenceCode&#39;</span><span class="p">):</span>
+            <span class="k">if</span> <span class="n">rdfprefix</span> <span class="o">+</span> <span class="s1">&#39;resource&#39;</span> <span class="ow">in</span> <span class="n">e</span><span class="o">.</span><span class="n">attrib</span><span class="p">:</span>
+                <span class="n">evs</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">ev_short</span><span class="p">[</span><span class="n">e</span><span class="o">.</span><span class="n">attrib</span><span class="p">[</span><span class="n">rdfprefix</span> <span class="o">+</span> <span class="s1">&#39;resource&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;_&#39;</span><span class="p">)</span>
+                                    <span class="p">[</span><span class="mi">1</span><span class="p">]])</span>
+            <span class="k">else</span><span class="p">:</span>
+                <span class="n">ev</span> <span class="o">=</span> <span class="n">e</span><span class="o">.</span><span class="n">find</span><span class="p">(</span><span class="n">bpprefix</span> <span class="o">+</span> <span class="s1">&#39;EvidenceCodeVocabulary&#39;</span><span class="p">)</span>
+                <span class="n">evs</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">ev_short</span><span class="p">[</span><span class="n">ev</span><span class="o">.</span><span class="n">attrib</span><span class="p">[</span><span class="n">rdfprefix</span> <span class="o">+</span> <span class="s1">&#39;ID&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;_&#39;</span><span class="p">)[</span><span class="mi">1</span><span class="p">]])</span>
+        <span class="k">for</span> <span class="n">e</span> <span class="ow">in</span> <span class="n">c</span><span class="o">.</span><span class="n">iter</span><span class="p">(</span><span class="n">bpprefix</span> <span class="o">+</span> <span class="s1">&#39;evidence&#39;</span><span class="p">):</span>
+            <span class="k">if</span> <span class="n">rdfprefix</span> <span class="o">+</span> <span class="s1">&#39;resource&#39;</span> <span class="ow">in</span> <span class="n">e</span><span class="o">.</span><span class="n">attrib</span><span class="p">:</span>
+                <span class="n">ev</span> <span class="o">=</span> <span class="n">e</span><span class="o">.</span><span class="n">attrib</span><span class="p">[</span><span class="n">rdfprefix</span> <span class="o">+</span> <span class="s1">&#39;resource&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;_&#39;</span><span class="p">)</span>
+                <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">ev</span><span class="p">)</span> <span class="o">==</span> <span class="mi">4</span><span class="p">:</span>
+                    <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">ev</span><span class="p">[</span><span class="mi">3</span><span class="p">])</span> <span class="o">==</span> <span class="mi">4</span><span class="p">:</span>
+                        <span class="n">evs</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">ev_short</span><span class="p">[</span><span class="n">ev</span><span class="p">[</span><span class="mi">3</span><span class="p">]])</span>
+        <span class="k">if</span> <span class="p">(</span><span class="n">src</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span> <span class="ow">and</span> <span class="n">tgt</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span> <span class="ow">and</span> <span class="n">src</span> <span class="ow">in</span> <span class="n">proteins</span> <span class="ow">and</span>
+                <span class="n">tgt</span> <span class="ow">in</span> <span class="n">proteins</span> <span class="ow">and</span> <span class="n">proteins</span><span class="p">[</span><span class="n">src</span><span class="p">][</span><span class="s1">&#39;id&#39;</span><span class="p">]</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span> <span class="ow">and</span>
+                <span class="n">proteins</span><span class="p">[</span><span class="n">tgt</span><span class="p">][</span><span class="s1">&#39;id&#39;</span><span class="p">]</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">):</span>
+            <span class="n">edges</span><span class="o">.</span><span class="n">append</span><span class="p">({</span>
+                <span class="s1">&#39;src&#39;</span><span class="p">:</span> <span class="n">proteins</span><span class="p">[</span><span class="n">src</span><span class="p">],</span>
+                <span class="s1">&#39;tgt&#39;</span><span class="p">:</span> <span class="n">proteins</span><span class="p">[</span><span class="n">tgt</span><span class="p">],</span>
+                <span class="s1">&#39;pmids&#39;</span><span class="p">:</span> <span class="nb">list</span><span class="p">(</span><span class="nb">set</span><span class="p">(</span><span class="n">pmids</span><span class="p">)),</span>
+                <span class="s1">&#39;evs&#39;</span><span class="p">:</span> <span class="nb">list</span><span class="p">(</span><span class="nb">set</span><span class="p">(</span><span class="n">evs</span><span class="p">))</span>
+            <span class="p">})</span>
+            <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">evs</span><span class="p">)</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
+                <span class="n">noev</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">c</span><span class="p">)</span>
+            <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">pmids</span><span class="p">)</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
+                <span class="n">norefs</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">c</span><span class="p">)</span>
+            <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">evs</span><span class="p">)</span> <span class="o">==</span> <span class="mi">0</span> <span class="ow">and</span> <span class="nb">len</span><span class="p">(</span><span class="n">pmids</span><span class="p">)</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
+                <span class="n">noth</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">c</span><span class="p">)</span>
+    <span class="k">for</span> <span class="n">e</span> <span class="ow">in</span> <span class="n">edges</span><span class="p">:</span>
+        <span class="n">this_iaction</span> <span class="o">=</span> <span class="p">[</span>
+            <span class="n">e</span><span class="p">[</span><span class="s1">&#39;src&#39;</span><span class="p">][</span><span class="s1">&#39;id&#39;</span><span class="p">],</span> <span class="n">e</span><span class="p">[</span><span class="s1">&#39;tgt&#39;</span><span class="p">][</span><span class="s1">&#39;id&#39;</span><span class="p">],</span> <span class="n">e</span><span class="p">[</span><span class="s1">&#39;src&#39;</span><span class="p">][</span><span class="s1">&#39;species&#39;</span><span class="p">],</span>
+            <span class="n">e</span><span class="p">[</span><span class="s1">&#39;tgt&#39;</span><span class="p">][</span><span class="s1">&#39;species&#39;</span><span class="p">],</span> <span class="s1">&#39;;&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">e</span><span class="p">[</span><span class="s1">&#39;evs&#39;</span><span class="p">]),</span> <span class="s1">&#39;;&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">e</span><span class="p">[</span><span class="s1">&#39;pmids&#39;</span><span class="p">])</span>
+        <span class="p">]</span>
+        <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">this_iaction</span><span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">])</span> <span class="o">&gt;</span> <span class="mi">0</span><span class="p">:</span>
+            <span class="n">result_curated</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">this_iaction</span><span class="p">)</span>
+        <span class="k">else</span><span class="p">:</span>
+            <span class="n">result_noref</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">this_iaction</span><span class="p">)</span>
+    <span class="n">pickle</span><span class="o">.</span><span class="n">dump</span><span class="p">(</span><span class="n">result_curated</span><span class="p">,</span> <span class="nb">open</span><span class="p">(</span><span class="n">curated_cache</span><span class="p">,</span> <span class="s1">&#39;wb&#39;</span><span class="p">))</span>
+    <span class="n">pickle</span><span class="o">.</span><span class="n">dump</span><span class="p">(</span><span class="n">result_noref</span><span class="p">,</span> <span class="nb">open</span><span class="p">(</span><span class="n">noref_cache</span><span class="p">,</span> <span class="s1">&#39;wb&#39;</span><span class="p">))</span>
+    <span class="k">return</span> <span class="n">result_curated</span><span class="p">,</span> <span class="n">result_noref</span></div>
+
+
+
+<span class="k">def</span> <span class="nf">_phosphosite_filter_organism</span><span class="p">(</span><span class="n">psite_data</span><span class="p">,</span> <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">):</span>
+
+    <span class="n">all_uniprots</span> <span class="o">=</span> <span class="n">uniprot_db</span><span class="o">.</span><span class="n">all_uniprots</span><span class="p">(</span><span class="n">organism</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">)</span>
+
+    <span class="k">return</span> <span class="p">[</span>
+        <span class="n">rec</span>
+        <span class="k">for</span> <span class="n">rec</span> <span class="ow">in</span> <span class="n">psite_data</span>
+        <span class="k">if</span> <span class="n">rec</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="ow">in</span> <span class="n">all_uniprots</span> <span class="ow">and</span> <span class="n">rec</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="ow">in</span> <span class="n">all_uniprots</span>
+    <span class="p">]</span>
+
+
+<div class="viewcode-block" id="phosphosite_interactions_curated">
+<a class="viewcode-back" href="../../../api/pypath.inputs.phosphosite.phosphosite_interactions_curated.html#pypath.inputs.phosphosite.phosphosite_interactions_curated">[docs]</a>
+<span class="k">def</span> <span class="nf">phosphosite_interactions_curated</span><span class="p">(</span><span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">):</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Loads literature curated PhosphoSite data,</span>
+<span class="sd">    from preprocessed cache file if available.</span>
+<span class="sd">    Returns list of interactions.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="n">curated_cache</span> <span class="o">=</span> <span class="n">urls</span><span class="o">.</span><span class="n">files</span><span class="p">[</span><span class="s1">&#39;phosphosite&#39;</span><span class="p">][</span><span class="s1">&#39;curated&#39;</span><span class="p">]</span>
+    <span class="k">if</span> <span class="ow">not</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">exists</span><span class="p">(</span><span class="n">curated_cache</span><span class="p">):</span>
+        <span class="n">curated</span><span class="p">,</span> <span class="n">noref</span> <span class="o">=</span> <span class="n">phosphosite_interactions</span><span class="p">(</span><span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">)</span>
+        <span class="n">result</span> <span class="o">=</span> <span class="n">curated</span>
+    <span class="k">else</span><span class="p">:</span>
+        <span class="n">result</span> <span class="o">=</span> <span class="n">pickle</span><span class="o">.</span><span class="n">load</span><span class="p">(</span><span class="nb">open</span><span class="p">(</span><span class="n">curated_cache</span><span class="p">,</span> <span class="s1">&#39;rb&#39;</span><span class="p">))</span>
+
+    <span class="k">return</span> <span class="n">_phosphosite_filter_organism</span><span class="p">(</span><span class="n">result</span><span class="p">,</span> <span class="n">ncbi_tax_id</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="phosphosite_interactions_noref">
+<a class="viewcode-back" href="../../../api/pypath.inputs.phosphosite.phosphosite_interactions_noref.html#pypath.inputs.phosphosite.phosphosite_interactions_noref">[docs]</a>
+<span class="k">def</span> <span class="nf">phosphosite_interactions_noref</span><span class="p">(</span><span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">):</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Loads HTP PhosphoSite data,</span>
+<span class="sd">    from preprocessed cache file if available.</span>
+<span class="sd">    Returns list of interactions.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="n">noref_cache</span> <span class="o">=</span> <span class="n">urls</span><span class="o">.</span><span class="n">files</span><span class="p">[</span><span class="s1">&#39;phosphosite&#39;</span><span class="p">][</span><span class="s1">&#39;noref&#39;</span><span class="p">]</span>
+    <span class="k">if</span> <span class="ow">not</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">exists</span><span class="p">(</span><span class="n">noref_cache</span><span class="p">):</span>
+        <span class="n">curated</span><span class="p">,</span> <span class="n">noref</span> <span class="o">=</span> <span class="n">phosphosite_interactions</span><span class="p">(</span><span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">)</span>
+        <span class="n">result</span> <span class="o">=</span> <span class="n">noref</span>
+    <span class="k">else</span><span class="p">:</span>
+        <span class="n">result</span> <span class="o">=</span> <span class="n">pickle</span><span class="o">.</span><span class="n">load</span><span class="p">(</span><span class="nb">open</span><span class="p">(</span><span class="n">noref_cache</span><span class="p">,</span> <span class="s1">&#39;rb&#39;</span><span class="p">))</span>
+
+    <span class="k">return</span> <span class="n">_phosphosite_filter_organism</span><span class="p">(</span><span class="n">result</span><span class="p">,</span> <span class="n">ncbi_tax_id</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="phosphosite_directions">
+<a class="viewcode-back" href="../../../api/pypath.inputs.phosphosite.phosphosite_directions.html#pypath.inputs.phosphosite.phosphosite_directions">[docs]</a>
+<span class="k">def</span> <span class="nf">phosphosite_directions</span><span class="p">(</span><span class="n">organism</span> <span class="o">=</span> <span class="s1">&#39;human&#39;</span><span class="p">):</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    From curated and HTP PhosphoSite data generates a</span>
+<span class="sd">    list of directions.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="n">curated</span><span class="p">,</span> <span class="n">noref</span> <span class="o">=</span> <span class="n">phosphosite_interactions</span><span class="p">()</span>
+
+    <span class="k">return</span> <span class="p">[</span>
+        <span class="n">i</span><span class="p">[:</span><span class="mi">2</span><span class="p">]</span> <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="n">curated</span> <span class="o">+</span> <span class="n">noref</span> <span class="k">if</span> <span class="n">i</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="o">==</span> <span class="n">organism</span> <span class="ow">and</span> <span class="n">i</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span> <span class="o">==</span> <span class="n">organism</span>
+    <span class="p">]</span></div>
+
+
+
+<div class="viewcode-block" id="phosphosite_interactions_all">
+<a class="viewcode-back" href="../../../api/pypath.inputs.phosphosite.phosphosite_interactions_all.html#pypath.inputs.phosphosite.phosphosite_interactions_all">[docs]</a>
+<span class="k">def</span> <span class="nf">phosphosite_interactions_all</span><span class="p">():</span>
+
+    <span class="k">return</span> <span class="n">phosphosite_interactions_curated</span><span class="p">()</span> <span class="o">+</span> <span class="n">phosphosite_interactions_noref</span><span class="p">()</span></div>
+
+</pre></div>
+
+                </article>
+              
+              
+              
+              
+              
+                <footer class="prev-next-footer">
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diff --git a/_modules/pypath/inputs/pisa.html b/_modules/pypath/inputs/pisa.html
new file mode 100644
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@@ -0,0 +1,913 @@
+
+<!DOCTYPE html>
+
+
+<html lang="en" data-content_root="../../../" >
+
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+    <meta charset="utf-8" />
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+  
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+  <h1>Source code for pypath.inputs.pisa</h1><div class="highlight"><pre>
+<span></span><span class="ch">#!/usr/bin/env python</span>
+<span class="c1"># -*- coding: utf-8 -*-</span>
+
+<span class="c1">#</span>
+<span class="c1">#  This file is part of the `pypath` python module</span>
+<span class="c1">#</span>
+<span class="c1">#  Copyright 2014-2023</span>
+<span class="c1">#  EMBL, EMBL-EBI, Uniklinik RWTH Aachen, Heidelberg University</span>
+<span class="c1">#</span>
+<span class="c1">#  Authors: see the file `README.rst`</span>
+<span class="c1">#  Contact: Dénes Türei (turei.denes@gmail.com)</span>
+<span class="c1">#</span>
+<span class="c1">#  Distributed under the GPLv3 License.</span>
+<span class="c1">#  See accompanying file LICENSE.txt or copy at</span>
+<span class="c1">#      https://www.gnu.org/licenses/gpl-3.0.html</span>
+<span class="c1">#</span>
+<span class="c1">#  Website: https://pypath.omnipathdb.org/</span>
+<span class="c1">#</span>
+
+<span class="kn">from</span> <span class="nn">future.utils</span> <span class="kn">import</span> <span class="n">iteritems</span>
+<span class="kn">from</span> <span class="nn">past.builtins</span> <span class="kn">import</span> <span class="n">xrange</span><span class="p">,</span> <span class="nb">range</span>
+
+<span class="kn">import</span> <span class="nn">os</span>
+<span class="kn">import</span> <span class="nn">sys</span>
+<span class="kn">import</span> <span class="nn">re</span>
+<span class="kn">import</span> <span class="nn">collections</span>
+
+<span class="k">try</span><span class="p">:</span>
+    <span class="kn">import</span> <span class="nn">cPickle</span> <span class="k">as</span> <span class="nn">pickle</span>
+<span class="k">except</span><span class="p">:</span>
+    <span class="kn">import</span> <span class="nn">pickle</span>
+
+<span class="kn">import</span> <span class="nn">bs4</span>
+
+<span class="kn">import</span> <span class="nn">pypath.resources.urls</span> <span class="k">as</span> <span class="nn">urls</span>
+<span class="kn">import</span> <span class="nn">pypath.share.curl</span> <span class="k">as</span> <span class="nn">curl</span>
+<span class="kn">import</span> <span class="nn">pypath.share.common</span> <span class="k">as</span> <span class="nn">common</span>
+<span class="kn">import</span> <span class="nn">pypath.share.cache</span> <span class="k">as</span> <span class="nn">cache</span>
+<span class="kn">import</span> <span class="nn">pypath.share.progress</span> <span class="k">as</span> <span class="nn">progress</span>
+<span class="kn">import</span> <span class="nn">pypath.utils.pdb</span> <span class="k">as</span> <span class="nn">pdb_utils</span>
+<span class="kn">import</span> <span class="nn">pypath.inputs.pdb</span> <span class="k">as</span> <span class="nn">pdb_input</span>
+<span class="kn">import</span> <span class="nn">pypath.internals.intera</span> <span class="k">as</span> <span class="nn">intera</span>
+
+
+<span class="n">PisaBond</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">namedtuple</span><span class="p">(</span>
+    <span class="s1">&#39;PisaBond&#39;</span><span class="p">,</span>
+    <span class="p">(</span>
+        <span class="s1">&#39;uniprot_1&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;chain_1&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;residue_1&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;seqnum_1&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;uniprot_2&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;chain_2&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;residue_2&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;seqnum_2&#39;</span><span class="p">,</span>
+    <span class="p">),</span>
+<span class="p">)</span>
+
+
+<div class="viewcode-block" id="pisa_bonds">
+<a class="viewcode-back" href="../../../api/pypath.inputs.pisa.pisa_bonds.html#pypath.inputs.pisa.pisa_bonds">[docs]</a>
+<span class="k">def</span> <span class="nf">pisa_bonds</span><span class="p">(</span><span class="n">bonds</span><span class="p">,</span> <span class="n">chains</span><span class="p">):</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    To be refactored in the future. If you are interested in using this</span>
+<span class="sd">    function, please contact the authors.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="n">non_digit</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">compile</span><span class="p">(</span><span class="sa">r</span><span class="s1">&#39;[^\d.-]+&#39;</span><span class="p">)</span>
+    <span class="n">result</span> <span class="o">=</span> <span class="p">[]</span>
+
+    <span class="k">for</span> <span class="n">bond</span> <span class="ow">in</span> <span class="n">bonds</span><span class="o">.</span><span class="n">find_all</span><span class="p">(</span><span class="s1">&#39;bond&#39;</span><span class="p">):</span>
+
+        <span class="n">seqnum1</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">non_digit</span><span class="o">.</span><span class="n">sub</span><span class="p">(</span><span class="s1">&#39;&#39;</span><span class="p">,</span> <span class="n">bond</span><span class="o">.</span><span class="n">find</span><span class="p">(</span><span class="s1">&#39;seqnum-1&#39;</span><span class="p">)</span><span class="o">.</span><span class="n">text</span><span class="p">))</span>
+        <span class="n">seqnum2</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">non_digit</span><span class="o">.</span><span class="n">sub</span><span class="p">(</span><span class="s1">&#39;&#39;</span><span class="p">,</span> <span class="n">bond</span><span class="o">.</span><span class="n">find</span><span class="p">(</span><span class="s1">&#39;seqnum-2&#39;</span><span class="p">)</span><span class="o">.</span><span class="n">text</span><span class="p">))</span>
+        <span class="n">res1</span> <span class="o">=</span> <span class="n">bond</span><span class="o">.</span><span class="n">find</span><span class="p">(</span><span class="s1">&#39;res-1&#39;</span><span class="p">)</span><span class="o">.</span><span class="n">text</span>
+        <span class="n">res1</span> <span class="o">=</span> <span class="n">common</span><span class="o">.</span><span class="n">aaletters</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="n">res1</span><span class="p">,</span> <span class="n">res1</span><span class="p">)</span>
+        <span class="n">res2</span> <span class="o">=</span> <span class="n">bond</span><span class="o">.</span><span class="n">find</span><span class="p">(</span><span class="s1">&#39;res-2&#39;</span><span class="p">)</span><span class="o">.</span><span class="n">text</span>
+        <span class="n">res2</span> <span class="o">=</span> <span class="n">common</span><span class="o">.</span><span class="n">aaletters</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="n">res2</span><span class="p">,</span> <span class="n">res2</span><span class="p">)</span>
+        <span class="n">chain1</span> <span class="o">=</span> <span class="n">bond</span><span class="o">.</span><span class="n">find</span><span class="p">(</span><span class="s1">&#39;chain-1&#39;</span><span class="p">)</span><span class="o">.</span><span class="n">text</span>
+        <span class="n">chain2</span> <span class="o">=</span> <span class="n">bond</span><span class="o">.</span><span class="n">find</span><span class="p">(</span><span class="s1">&#39;chain-2&#39;</span><span class="p">)</span><span class="o">.</span><span class="n">text</span>
+        <span class="n">uniprot1</span> <span class="o">=</span> <span class="n">chains</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="n">chain1</span><span class="p">,</span> <span class="kc">None</span><span class="p">)</span>
+        <span class="n">uniprot2</span> <span class="o">=</span> <span class="n">chains</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="n">chain2</span><span class="p">,</span> <span class="kc">None</span><span class="p">)</span>
+
+        <span class="k">if</span> <span class="n">uniprot1</span> <span class="ow">and</span> <span class="n">uniprot2</span><span class="p">:</span>
+
+            <span class="n">result</span><span class="o">.</span><span class="n">append</span><span class="p">(</span>
+                <span class="n">PisaBond</span><span class="p">(</span>
+                    <span class="n">uniprot_1</span> <span class="o">=</span> <span class="n">uniprot1</span><span class="p">,</span>
+                    <span class="n">chain_1</span> <span class="o">=</span> <span class="n">chain1</span><span class="p">,</span>
+                    <span class="n">residue_1</span> <span class="o">=</span> <span class="n">res1</span><span class="p">,</span>
+                    <span class="n">seqnum_1</span> <span class="o">=</span> <span class="n">seqnum1</span><span class="p">,</span>
+                    <span class="n">uniprot_2</span> <span class="o">=</span> <span class="n">uniprot2</span><span class="p">,</span>
+                    <span class="n">chain_2</span> <span class="o">=</span> <span class="n">chain2</span><span class="p">,</span>
+                    <span class="n">residue_2</span> <span class="o">=</span> <span class="n">res2</span><span class="p">,</span>
+                    <span class="n">seqnum_2</span> <span class="o">=</span> <span class="n">seqnum2</span><span class="p">,</span>
+                <span class="p">)</span>
+            <span class="p">)</span>
+
+    <span class="k">return</span> <span class="n">result</span></div>
+
+
+
+<div class="viewcode-block" id="pisa_interfaces">
+<a class="viewcode-back" href="../../../api/pypath.inputs.pisa.pisa_interfaces.html#pypath.inputs.pisa.pisa_interfaces">[docs]</a>
+<span class="k">def</span> <span class="nf">pisa_interfaces</span><span class="p">(</span><span class="n">pdbs</span><span class="p">,</span> <span class="n">return_unmapped</span> <span class="o">=</span> <span class="kc">False</span><span class="p">):</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    To be refactored in the future. If you are interested in using this</span>
+<span class="sd">    function, please contact the authors.</span>
+
+<span class="sd">    Args</span>
+<span class="sd">        pdbs (set): A set of PDB IDs to query.</span>
+<span class="sd">        return_unmapped (bool): Return also a list of unmapped residues.</span>
+<span class="sd">        In this case, a tuple is returned, its first element is a dict of</span>
+<span class="sd">        interfaces, while its second element is a list of unmapped</span>
+<span class="sd">        residues (normally empty, if all residues could be mapped</span>
+<span class="sd">        between PDB and UniProt sequences).</span>
+
+<span class="sd">    Returns</span>
+<span class="sd">        A dict of dicts with interfaces. The upper level keys are PDB</span>
+<span class="sd">        structure IDs, the lower level keys are tuples of UniProt IDs,</span>
+<span class="sd">        the values are ``pypath.internals.intera.Interface`` objects.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="n">bond_types</span> <span class="o">=</span> <span class="p">{</span>
+        <span class="s1">&#39;hbonds&#39;</span><span class="p">:</span> <span class="s1">&#39;h-bonds&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;sbridges&#39;</span><span class="p">:</span> <span class="s1">&#39;salt-bridges&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;covbonds&#39;</span><span class="p">:</span> <span class="s1">&#39;cov-bonds&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;ssbonds&#39;</span><span class="p">:</span> <span class="s1">&#39;ss-bonds&#39;</span>
+    <span class="p">}</span>
+    <span class="n">interfaces</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">defaultdict</span><span class="p">(</span><span class="nb">dict</span><span class="p">)</span>
+    <span class="n">cachefile</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">cache</span><span class="o">.</span><span class="n">get_cachedir</span><span class="p">(),</span> <span class="s1">&#39;pisa.pickle&#39;</span><span class="p">)</span>
+    <span class="n">u_pdb</span><span class="p">,</span> <span class="n">pdb_u</span> <span class="o">=</span> <span class="n">pdb_input</span><span class="o">.</span><span class="n">pdb_chains</span><span class="p">()</span>
+
+    <span class="k">if</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">exists</span><span class="p">(</span><span class="n">cachefile</span><span class="p">):</span>
+
+        <span class="k">try</span><span class="p">:</span>
+            <span class="n">interfaces</span> <span class="o">=</span> <span class="n">pickle</span><span class="o">.</span><span class="n">load</span><span class="p">(</span><span class="nb">open</span><span class="p">(</span><span class="n">cachefile</span><span class="p">,</span> <span class="s1">&#39;rb&#39;</span><span class="p">))</span>
+
+        <span class="k">except</span><span class="p">:</span>
+            <span class="k">pass</span>
+
+    <span class="n">errors</span> <span class="o">=</span> <span class="p">[]</span>
+    <span class="n">unmapped_residues</span> <span class="o">=</span> <span class="p">[]</span>
+    <span class="n">p</span> <span class="o">=</span> <span class="mi">5</span>
+    <span class="n">pdbs</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="nb">set</span><span class="p">(</span><span class="n">pdbs</span><span class="p">)</span> <span class="o">-</span> <span class="nb">set</span><span class="p">(</span><span class="n">interfaces</span><span class="o">.</span><span class="n">keys</span><span class="p">()))</span>
+    <span class="n">prg</span> <span class="o">=</span> <span class="n">progress</span><span class="o">.</span><span class="n">Progress</span><span class="p">(</span>
+        <span class="nb">len</span><span class="p">(</span><span class="n">pdbs</span><span class="p">)</span> <span class="o">/</span> <span class="n">p</span><span class="p">,</span>
+        <span class="s1">&#39;Downloading data from PDBe PISA&#39;</span><span class="p">,</span>
+        <span class="mi">1</span><span class="p">,</span>
+    <span class="p">)</span>
+
+    <span class="n">pdbs</span> <span class="o">=</span> <span class="nb">sorted</span><span class="p">(</span><span class="n">common</span><span class="o">.</span><span class="n">to_set</span><span class="p">(</span><span class="n">pdbs</span><span class="p">))</span>
+
+    <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="n">xrange</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="nb">len</span><span class="p">(</span><span class="n">pdbs</span><span class="p">),</span> <span class="n">p</span><span class="p">):</span>
+
+        <span class="n">to</span> <span class="o">=</span> <span class="n">i</span> <span class="o">+</span> <span class="n">p</span>
+        <span class="n">thisPart</span> <span class="o">=</span> <span class="n">pdbs</span><span class="p">[</span><span class="n">i</span><span class="p">:</span><span class="n">to</span><span class="p">]</span>
+        <span class="n">url</span> <span class="o">=</span> <span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;pisa_interfaces&#39;</span><span class="p">][</span><span class="s1">&#39;url&#39;</span><span class="p">]</span> <span class="o">+</span> <span class="s1">&#39;,&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">thisPart</span><span class="p">)</span>
+        <span class="n">c</span> <span class="o">=</span> <span class="n">curl</span><span class="o">.</span><span class="n">Curl</span><span class="p">(</span><span class="n">url</span><span class="p">,</span> <span class="n">cache</span> <span class="o">=</span> <span class="kc">False</span><span class="p">)</span>
+        <span class="n">data</span> <span class="o">=</span> <span class="n">c</span><span class="o">.</span><span class="n">result</span>
+
+        <span class="k">if</span> <span class="ow">not</span> <span class="n">data</span><span class="p">:</span>
+
+            <span class="n">msg</span> <span class="o">=</span> <span class="s1">&#39;Could not download: </span><span class="se">\n\t\t</span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="n">url</span>
+            <span class="n">errors</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">msg</span><span class="p">)</span>
+
+            <span class="k">continue</span>
+
+        <span class="n">soup</span> <span class="o">=</span> <span class="n">bs4</span><span class="o">.</span><span class="n">BeautifulSoup</span><span class="p">(</span><span class="n">data</span><span class="p">,</span> <span class="s1">&#39;html.parser&#39;</span><span class="p">)</span>
+
+        <span class="k">for</span> <span class="n">pdb</span> <span class="ow">in</span> <span class="n">soup</span><span class="o">.</span><span class="n">find_all</span><span class="p">(</span><span class="s1">&#39;pdb_entry&#39;</span><span class="p">):</span>
+
+            <span class="n">pdb_id</span> <span class="o">=</span> <span class="n">pdb</span><span class="o">.</span><span class="n">find</span><span class="p">(</span><span class="s1">&#39;pdb_code&#39;</span><span class="p">)</span><span class="o">.</span><span class="n">text</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span>
+            <span class="n">interfaces</span><span class="p">[</span><span class="n">pdb_id</span><span class="p">]</span> <span class="o">=</span> <span class="p">{}</span>
+            <span class="n">chains</span> <span class="o">=</span> <span class="p">{}</span>
+            <span class="n">resconv</span> <span class="o">=</span> <span class="n">pdb_utils</span><span class="o">.</span><span class="n">ResidueMapper</span><span class="p">()</span>
+
+            <span class="k">if</span> <span class="n">pdb_id</span> <span class="ow">in</span> <span class="n">pdb_u</span><span class="p">:</span>
+
+                <span class="k">for</span> <span class="n">chain</span><span class="p">,</span> <span class="n">chain_data</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="n">pdb_u</span><span class="p">[</span><span class="n">pdb_id</span><span class="p">]):</span>
+
+                    <span class="n">chains</span><span class="p">[</span><span class="n">chain</span><span class="p">]</span> <span class="o">=</span> <span class="n">chain_data</span><span class="p">[</span><span class="s1">&#39;uniprot&#39;</span><span class="p">]</span>
+
+                <span class="k">for</span> <span class="n">interface</span> <span class="ow">in</span> <span class="n">pdb</span><span class="o">.</span><span class="n">find_all</span><span class="p">(</span><span class="s1">&#39;interface&#39;</span><span class="p">):</span>
+
+                    <span class="k">for</span> <span class="n">b</span><span class="p">,</span> <span class="n">t</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="n">bond_types</span><span class="p">):</span>
+
+                        <span class="n">bonds</span> <span class="o">=</span> <span class="n">interface</span><span class="o">.</span><span class="n">find</span><span class="p">(</span><span class="n">t</span><span class="p">)</span>
+
+                        <span class="k">if</span> <span class="n">bonds</span><span class="p">:</span>
+
+                            <span class="n">bonds</span> <span class="o">=</span> <span class="n">pisa_bonds</span><span class="p">(</span><span class="n">bonds</span><span class="p">,</span> <span class="n">chains</span><span class="p">)</span>
+
+                            <span class="k">for</span> <span class="n">bond</span> <span class="ow">in</span> <span class="n">bonds</span><span class="p">:</span>
+
+                                <span class="n">uniprots</span> <span class="o">=</span> <span class="p">(</span>
+                                    <span class="n">bond</span><span class="o">.</span><span class="n">uniprot_1</span><span class="p">,</span>
+                                    <span class="n">bond</span><span class="o">.</span><span class="n">uniprot_2</span><span class="p">,</span>
+                                <span class="p">)</span>
+
+                                <span class="k">if</span> <span class="n">uniprots</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">interfaces</span><span class="p">[</span><span class="n">pdb_id</span><span class="p">]:</span>
+
+                                    <span class="n">css</span> <span class="o">=</span> <span class="n">common</span><span class="o">.</span><span class="n">non_digit</span><span class="o">.</span><span class="n">sub</span><span class="p">(</span>
+                                        <span class="s1">&#39;&#39;</span><span class="p">,</span> <span class="n">interface</span><span class="o">.</span><span class="n">find</span><span class="p">(</span><span class="s1">&#39;css&#39;</span><span class="p">)</span><span class="o">.</span><span class="n">text</span><span class="p">)</span>
+                                    <span class="n">css</span> <span class="o">=</span> <span class="p">(</span>
+                                        <span class="kc">None</span> <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">css</span><span class="p">)</span> <span class="o">==</span> <span class="mi">0</span> <span class="k">else</span> <span class="nb">float</span><span class="p">(</span><span class="n">css</span><span class="p">)</span>
+                                    <span class="p">)</span>
+                                    <span class="n">area</span> <span class="o">=</span> <span class="n">common</span><span class="o">.</span><span class="n">non_digit</span><span class="o">.</span><span class="n">sub</span><span class="p">(</span>
+                                        <span class="s1">&#39;&#39;</span><span class="p">,</span> <span class="n">interface</span><span class="o">.</span><span class="n">find</span><span class="p">(</span><span class="s1">&#39;int_area&#39;</span><span class="p">)</span><span class="o">.</span><span class="n">text</span><span class="p">)</span>
+                                    <span class="n">area</span> <span class="o">=</span> <span class="kc">None</span> <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">area</span><span class="p">)</span> <span class="o">==</span> <span class="mi">0</span> <span class="k">else</span> <span class="nb">float</span><span class="p">(</span>
+                                        <span class="n">area</span><span class="p">)</span>
+                                    <span class="n">solv_en</span> <span class="o">=</span> <span class="n">common</span><span class="o">.</span><span class="n">non_digit</span><span class="o">.</span><span class="n">sub</span><span class="p">(</span>
+                                        <span class="s1">&#39;&#39;</span><span class="p">,</span>
+                                        <span class="n">interface</span><span class="o">.</span><span class="n">find</span><span class="p">(</span><span class="s1">&#39;int_solv_en&#39;</span><span class="p">)</span><span class="o">.</span><span class="n">text</span>
+                                    <span class="p">)</span>
+                                    <span class="n">solv_en</span> <span class="o">=</span> <span class="p">(</span>
+                                        <span class="kc">None</span>
+                                            <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">solv_en</span><span class="p">)</span> <span class="o">==</span> <span class="mi">0</span> <span class="k">else</span>
+                                        <span class="nb">float</span><span class="p">(</span><span class="n">solv_en</span><span class="p">)</span>
+                                    <span class="p">)</span>
+                                    <span class="n">stab_en</span> <span class="o">=</span> <span class="n">common</span><span class="o">.</span><span class="n">non_digit</span><span class="o">.</span><span class="n">sub</span><span class="p">(</span>
+                                        <span class="s1">&#39;&#39;</span><span class="p">,</span>
+                                        <span class="n">interface</span><span class="o">.</span><span class="n">find</span><span class="p">(</span><span class="s1">&#39;stab_en&#39;</span><span class="p">)</span><span class="o">.</span><span class="n">text</span>
+                                    <span class="p">)</span>
+                                    <span class="n">stab_en</span> <span class="o">=</span> <span class="p">(</span>
+                                        <span class="kc">None</span>
+                                            <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">stab_en</span><span class="p">)</span> <span class="o">==</span> <span class="mi">0</span> <span class="k">else</span>
+                                        <span class="nb">float</span><span class="p">(</span><span class="n">stab_en</span><span class="p">)</span>
+                                    <span class="p">)</span>
+                                    <span class="n">interfaces</span><span class="p">[</span><span class="n">pdb_id</span><span class="p">][</span><span class="n">uniprots</span><span class="p">]</span> <span class="o">=</span> <span class="p">(</span>
+                                        <span class="n">intera</span><span class="o">.</span><span class="n">Interface</span><span class="p">(</span>
+                                            <span class="n">uniprots</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span>
+                                            <span class="n">uniprots</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span>
+                                            <span class="n">source</span> <span class="o">=</span> <span class="s1">&#39;PISA&#39;</span><span class="p">,</span>
+                                            <span class="n">pdb</span> <span class="o">=</span> <span class="n">pdb_id</span><span class="p">,</span>
+                                            <span class="n">css</span> <span class="o">=</span> <span class="n">css</span><span class="p">,</span>
+                                            <span class="n">solv_en</span> <span class="o">=</span> <span class="n">solv_en</span><span class="p">,</span>
+                                            <span class="n">area</span> <span class="o">=</span> <span class="n">area</span><span class="p">,</span>
+                                            <span class="n">stab_en</span> <span class="o">=</span> <span class="n">stab_en</span><span class="p">,</span>
+                                        <span class="p">)</span>
+                                    <span class="p">)</span>
+
+                                <span class="n">res1</span> <span class="o">=</span> <span class="n">resconv</span><span class="o">.</span><span class="n">get_residue</span><span class="p">(</span>
+                                    <span class="n">pdb_id</span><span class="p">,</span>
+                                    <span class="n">bond</span><span class="o">.</span><span class="n">seqnum_1</span><span class="p">,</span>
+                                <span class="p">)</span>
+                                <span class="n">res2</span> <span class="o">=</span> <span class="n">resconv</span><span class="o">.</span><span class="n">get_residue</span><span class="p">(</span>
+                                    <span class="n">pdb_id</span><span class="p">,</span>
+                                    <span class="n">bond</span><span class="o">.</span><span class="n">seqnum_2</span><span class="p">,</span>
+                                <span class="p">)</span>
+
+                                <span class="k">if</span> <span class="p">(</span>
+                                    <span class="n">res1</span> <span class="ow">and</span>
+                                    <span class="n">res2</span> <span class="ow">and</span>
+                                    <span class="n">res1</span><span class="o">.</span><span class="n">uniprot</span> <span class="o">==</span> <span class="n">uniprots</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="ow">and</span>
+                                    <span class="n">res2</span><span class="o">.</span><span class="n">uniprot</span> <span class="o">==</span> <span class="n">uniprots</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span>
+                                <span class="p">):</span>
+
+                                    <span class="n">interfaces</span><span class="p">[</span><span class="n">pdb_id</span><span class="p">][</span><span class="n">uniprots</span><span class="p">]</span><span class="o">.</span><span class="n">add_residues</span><span class="p">(</span>
+                                        <span class="p">(</span>
+                                            <span class="n">res1</span><span class="o">.</span><span class="n">resnum</span><span class="p">,</span>
+                                            <span class="n">bond</span><span class="o">.</span><span class="n">residue_1</span><span class="p">,</span>
+                                            <span class="n">uniprots</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span>
+                                        <span class="p">),</span>
+                                        <span class="p">(</span>
+                                            <span class="n">res2</span><span class="o">.</span><span class="n">resnum</span><span class="p">,</span>
+                                            <span class="n">bond</span><span class="o">.</span><span class="n">residue_2</span><span class="p">,</span>
+                                            <span class="n">uniprots</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span>
+                                        <span class="p">),</span>
+                                        <span class="n">typ</span> <span class="o">=</span> <span class="n">b</span><span class="p">,</span>
+                                    <span class="p">)</span>
+
+                                <span class="k">else</span><span class="p">:</span>
+
+                                    <span class="n">unmapped_residues</span><span class="o">.</span><span class="n">append</span><span class="p">(</span>
+                                        <span class="p">(</span>
+                                            <span class="n">pdb_id</span><span class="p">,</span>
+                                            <span class="n">bond</span><span class="o">.</span><span class="n">seqnum_1</span><span class="p">,</span>
+                                            <span class="n">bond</span><span class="o">.</span><span class="n">seqnum_2</span><span class="p">,</span>
+                                            <span class="n">uniprots</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span>
+                                            <span class="n">uniprots</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span>
+                                        <span class="p">)</span>
+                                    <span class="p">)</span>
+
+        <span class="n">prg</span><span class="o">.</span><span class="n">step</span><span class="p">()</span>
+
+    <span class="n">prg</span><span class="o">.</span><span class="n">terminate</span><span class="p">()</span>
+    <span class="n">pickle</span><span class="o">.</span><span class="n">dump</span><span class="p">(</span><span class="n">interfaces</span><span class="p">,</span> <span class="nb">open</span><span class="p">(</span><span class="n">cachefile</span><span class="p">,</span> <span class="s1">&#39;wb&#39;</span><span class="p">),</span> <span class="mi">2</span><span class="p">)</span>
+    <span class="n">interfaces</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">(</span><span class="n">interfaces</span><span class="p">)</span>
+
+    <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">errors</span><span class="p">)</span> <span class="o">&gt;</span> <span class="mi">0</span><span class="p">:</span>
+
+        <span class="n">sys</span><span class="o">.</span><span class="n">stdout</span><span class="o">.</span><span class="n">write</span><span class="p">(</span>
+            <span class="s1">&#39;</span><span class="se">\t</span><span class="s1">:: Failed to download </span><span class="si">%u</span><span class="s1"> files of total </span><span class="si">%u</span><span class="s1">:</span><span class="se">\n\n</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="p">(</span>
+                <span class="nb">len</span><span class="p">(</span><span class="n">errors</span><span class="p">),</span>
+                <span class="nb">len</span><span class="p">(</span><span class="n">pdbs</span><span class="p">)(</span><span class="s1">&#39;P00968&#39;</span><span class="p">,</span> <span class="s1">&#39;P0A6F1&#39;</span><span class="p">)</span>
+            <span class="p">)</span>
+        <span class="p">)</span>
+
+        <span class="k">for</span> <span class="n">e</span> <span class="ow">in</span> <span class="n">errors</span><span class="p">:</span>
+
+            <span class="n">sys</span><span class="o">.</span><span class="n">stdout</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\t</span><span class="s1">&#39;</span> <span class="o">+</span> <span class="n">e</span> <span class="o">+</span> <span class="s1">&#39;</span><span class="se">\n</span><span class="s1">&#39;</span><span class="p">)</span>
+
+        <span class="n">sys</span><span class="o">.</span><span class="n">stdout</span><span class="o">.</span><span class="n">flush</span><span class="p">()</span>
+
+    <span class="k">if</span> <span class="n">return_unmapped</span><span class="p">:</span>
+        <span class="k">return</span> <span class="n">interfaces</span><span class="p">,</span> <span class="n">unmapped_residues</span>
+    <span class="k">else</span><span class="p">:</span>
+        <span class="k">return</span> <span class="n">interfaces</span></div>
+
+</pre></div>
+
+                </article>
+              
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diff --git a/_modules/pypath/inputs/progeny.html b/_modules/pypath/inputs/progeny.html
new file mode 100644
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+  <h1>Source code for pypath.inputs.progeny</h1><div class="highlight"><pre>
+<span></span><span class="ch">#!/usr/bin/env python</span>
+<span class="c1"># -*- coding: utf-8 -*-</span>
+
+<span class="c1">#</span>
+<span class="c1">#  This file is part of the `pypath` python module</span>
+<span class="c1">#</span>
+<span class="c1">#  Copyright 2014-2023</span>
+<span class="c1">#  EMBL, EMBL-EBI, Uniklinik RWTH Aachen, Heidelberg University</span>
+<span class="c1">#</span>
+<span class="c1">#  Authors: see the file `README.rst`</span>
+<span class="c1">#  Contact: Dénes Türei (turei.denes@gmail.com)</span>
+<span class="c1">#</span>
+<span class="c1">#  Distributed under the GPLv3 License.</span>
+<span class="c1">#  See accompanying file LICENSE.txt or copy at</span>
+<span class="c1">#      https://www.gnu.org/licenses/gpl-3.0.html</span>
+<span class="c1">#</span>
+<span class="c1">#  Website: https://pypath.omnipathdb.org/</span>
+<span class="c1">#</span>
+
+<span class="kn">import</span> <span class="nn">collections</span>
+
+<span class="kn">import</span> <span class="nn">pypath.share.session</span> <span class="k">as</span> <span class="nn">session</span>
+<span class="kn">import</span> <span class="nn">pypath.share.curl</span> <span class="k">as</span> <span class="nn">curl</span>
+<span class="kn">import</span> <span class="nn">pypath.resources.urls</span> <span class="k">as</span> <span class="nn">urls</span>
+<span class="kn">import</span> <span class="nn">pypath.utils.taxonomy</span> <span class="k">as</span> <span class="nn">taxonomy</span>
+<span class="kn">import</span> <span class="nn">pypath.utils.mapping</span> <span class="k">as</span> <span class="nn">mapping</span>
+<span class="kn">import</span> <span class="nn">pypath.inputs.rdata</span> <span class="k">as</span> <span class="nn">rdata</span>
+
+<span class="n">_logger</span> <span class="o">=</span> <span class="n">session</span><span class="o">.</span><span class="n">Logger</span><span class="p">(</span><span class="n">name</span> <span class="o">=</span> <span class="s1">&#39;progeny_input&#39;</span><span class="p">)</span>
+<span class="n">_log</span> <span class="o">=</span> <span class="n">_logger</span><span class="o">.</span><span class="n">_log</span>
+
+
+<div class="viewcode-block" id="progeny_raw">
+<a class="viewcode-back" href="../../../api/pypath.inputs.progeny.progeny_raw.html#pypath.inputs.progeny.progeny_raw">[docs]</a>
+<span class="k">def</span> <span class="nf">progeny_raw</span><span class="p">(</span><span class="n">organism</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">):</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Pathway responsive genes: signatures based on transcriptomics data</span>
+<span class="sd">    from PROGENy (https://github.com/saezlab/progeny).</span>
+
+<span class="sd">    Args</span>
+<span class="sd">        organism (int,str): Name or NCBI Taxonomy ID of the organism. Human</span>
+<span class="sd">            and mouse are supported.</span>
+
+<span class="sd">    Returns</span>
+<span class="sd">        (pandas.DataFrame): A data frame of genes, pathways, weights and</span>
+<span class="sd">            p-values for each association.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="n">_organism</span> <span class="o">=</span> <span class="n">taxonomy</span><span class="o">.</span><span class="n">ensure_common_name</span><span class="p">(</span><span class="n">organism</span><span class="p">)</span>
+
+    <span class="k">if</span> <span class="n">_organism</span> <span class="ow">not</span> <span class="ow">in</span> <span class="p">(</span><span class="s1">&#39;Human&#39;</span><span class="p">,</span> <span class="s1">&#39;Mouse&#39;</span><span class="p">):</span>
+
+        <span class="n">msg</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="s1">&#39;Wrong organism: `</span><span class="si">%s</span><span class="s1">`; &#39;</span>
+            <span class="s1">&#39;only human and mouse are available.&#39;</span> <span class="o">%</span> <span class="n">organism</span>
+        <span class="p">)</span>
+        <span class="n">_log</span><span class="p">(</span><span class="n">msg</span><span class="p">)</span>
+        <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="n">msg</span><span class="p">)</span>
+
+    <span class="n">_organism</span> <span class="o">=</span> <span class="n">_organism</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span>
+
+    <span class="n">url</span> <span class="o">=</span> <span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;progeny&#39;</span><span class="p">][</span><span class="s1">&#39;url&#39;</span><span class="p">]</span> <span class="o">%</span> <span class="n">_organism</span>
+    <span class="n">c</span> <span class="o">=</span> <span class="n">curl</span><span class="o">.</span><span class="n">Curl</span><span class="p">(</span><span class="n">url</span><span class="p">,</span> <span class="n">large</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span> <span class="n">silent</span> <span class="o">=</span> <span class="kc">False</span><span class="p">)</span>
+
+    <span class="n">rdata_path</span> <span class="o">=</span> <span class="n">c</span><span class="o">.</span><span class="n">fileobj</span><span class="o">.</span><span class="n">name</span>
+    <span class="n">c</span><span class="o">.</span><span class="n">fileobj</span><span class="o">.</span><span class="n">close</span><span class="p">()</span>
+
+    <span class="n">rdata_parsed</span> <span class="o">=</span> <span class="n">rdata</span><span class="o">.</span><span class="n">rdata</span><span class="o">.</span><span class="n">parser</span><span class="o">.</span><span class="n">parse_file</span><span class="p">(</span><span class="n">rdata_path</span><span class="p">)</span>
+    <span class="n">rdata_converted</span> <span class="o">=</span> <span class="n">rdata</span><span class="o">.</span><span class="n">rdata</span><span class="o">.</span><span class="n">conversion</span><span class="o">.</span><span class="n">convert</span><span class="p">(</span><span class="n">rdata_parsed</span><span class="p">)</span>
+
+    <span class="n">key</span> <span class="o">=</span> <span class="s1">&#39;model_</span><span class="si">%s</span><span class="s1">_full&#39;</span> <span class="o">%</span> <span class="n">_organism</span>
+
+    <span class="k">return</span> <span class="n">rdata_converted</span><span class="p">[</span><span class="n">key</span><span class="p">]</span></div>
+
+
+
+<div class="viewcode-block" id="progeny_annotations">
+<a class="viewcode-back" href="../../../api/pypath.inputs.progeny.progeny_annotations.html#pypath.inputs.progeny.progeny_annotations">[docs]</a>
+<span class="k">def</span> <span class="nf">progeny_annotations</span><span class="p">(</span><span class="n">organism</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">):</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Pathway responsive genes: signatures based on transcriptomics data</span>
+<span class="sd">    from PROGENy (https://github.com/saezlab/progeny).</span>
+
+<span class="sd">    Args</span>
+<span class="sd">        organism (int,str): Name or NCBI Taxonomy ID of the organism. Human</span>
+<span class="sd">            and mouse are supported.</span>
+
+<span class="sd">    Returns</span>
+<span class="sd">        (dict): Dict of sets, keys are UniProt IDs, values are pathway</span>
+<span class="sd">            association records, each with a weight and p-value.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="n">record</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">namedtuple</span><span class="p">(</span>
+        <span class="s1">&#39;ProgenyAnnotation&#39;</span><span class="p">,</span>
+        <span class="p">(</span>
+            <span class="s1">&#39;pathway&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;weight&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;p_value&#39;</span><span class="p">,</span>
+        <span class="p">)</span>
+    <span class="p">)</span>
+
+    <span class="n">raw</span> <span class="o">=</span> <span class="n">progeny_raw</span><span class="p">(</span><span class="n">organism</span> <span class="o">=</span> <span class="n">organism</span><span class="p">)</span>
+    <span class="n">result</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">defaultdict</span><span class="p">(</span><span class="nb">set</span><span class="p">)</span>
+
+    <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">taxonomy</span><span class="o">.</span><span class="n">ensure_ncbi_tax_id</span><span class="p">(</span><span class="n">organism</span><span class="p">)</span>
+
+    <span class="k">for</span> <span class="n">rec</span> <span class="ow">in</span> <span class="n">raw</span><span class="o">.</span><span class="n">itertuples</span><span class="p">():</span>
+
+        <span class="n">uniprots</span> <span class="o">=</span> <span class="n">mapping</span><span class="o">.</span><span class="n">map_name</span><span class="p">(</span>
+            <span class="n">rec</span><span class="o">.</span><span class="n">gene</span><span class="p">,</span>
+            <span class="s1">&#39;genesymbol&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;uniprot&#39;</span><span class="p">,</span>
+            <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">,</span>
+        <span class="p">)</span>
+
+        <span class="n">annot</span> <span class="o">=</span> <span class="n">record</span><span class="p">(</span>
+            <span class="n">pathway</span> <span class="o">=</span> <span class="n">rec</span><span class="o">.</span><span class="n">pathway</span><span class="p">,</span>
+            <span class="n">weight</span> <span class="o">=</span> <span class="n">rec</span><span class="o">.</span><span class="n">weight</span><span class="p">,</span>
+            <span class="n">p_value</span> <span class="o">=</span> <span class="n">rec</span><span class="p">[</span><span class="mi">4</span><span class="p">],</span> <span class="c1"># omg, stupid pandas</span>
+        <span class="p">)</span>
+
+        <span class="k">for</span> <span class="n">uniprot</span> <span class="ow">in</span> <span class="n">uniprots</span><span class="p">:</span>
+
+            <span class="n">result</span><span class="p">[</span><span class="n">uniprot</span><span class="p">]</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">annot</span><span class="p">)</span>
+
+    <span class="k">return</span> <span class="nb">dict</span><span class="p">(</span><span class="n">result</span><span class="p">)</span></div>
+
+</pre></div>
+
+                </article>
+              
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diff --git a/_modules/pypath/inputs/proteinatlas.html b/_modules/pypath/inputs/proteinatlas.html
new file mode 100644
index 000000000..f6a2e1e3d
--- /dev/null
+++ b/_modules/pypath/inputs/proteinatlas.html
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+
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+  <h1>Source code for pypath.inputs.proteinatlas</h1><div class="highlight"><pre>
+<span></span><span class="ch">#!/usr/bin/env python</span>
+<span class="c1"># -*- coding: utf-8 -*-</span>
+
+<span class="c1">#</span>
+<span class="c1">#  This file is part of the `pypath` python module</span>
+<span class="c1">#</span>
+<span class="c1">#  Copyright 2014-2023</span>
+<span class="c1">#  EMBL, EMBL-EBI, Uniklinik RWTH Aachen, Heidelberg University</span>
+<span class="c1">#</span>
+<span class="c1">#  Authors: see the file `README.rst`</span>
+<span class="c1">#  Contact: Dénes Türei (turei.denes@gmail.com)</span>
+<span class="c1">#</span>
+<span class="c1">#  Distributed under the GPLv3 License.</span>
+<span class="c1">#  See accompanying file LICENSE.txt or copy at</span>
+<span class="c1">#      https://www.gnu.org/licenses/gpl-3.0.html</span>
+<span class="c1">#</span>
+<span class="c1">#  Website: https://pypath.omnipathdb.org/</span>
+<span class="c1">#</span>
+
+<span class="kn">from</span> <span class="nn">future.utils</span> <span class="kn">import</span> <span class="n">iteritems</span>
+
+<span class="kn">import</span> <span class="nn">csv</span>
+<span class="kn">import</span> <span class="nn">collections</span>
+
+<span class="kn">import</span> <span class="nn">pypath.share.curl</span> <span class="k">as</span> <span class="nn">curl</span>
+<span class="kn">import</span> <span class="nn">pypath.resources.urls</span> <span class="k">as</span> <span class="nn">urls</span>
+<span class="kn">import</span> <span class="nn">pypath.utils.mapping</span> <span class="k">as</span> <span class="nn">mapping</span>
+<span class="kn">import</span> <span class="nn">pypath.inputs.common</span> <span class="k">as</span> <span class="nn">inputs_common</span>
+<span class="kn">import</span> <span class="nn">pypath.inputs.science</span> <span class="k">as</span> <span class="nn">science</span>
+
+
+<div class="viewcode-block" id="get_proteinatlas">
+<a class="viewcode-back" href="../../../api/pypath.inputs.proteinatlas.get_proteinatlas.html#pypath.inputs.proteinatlas.get_proteinatlas">[docs]</a>
+<span class="k">def</span> <span class="nf">get_proteinatlas</span><span class="p">(</span><span class="n">normal</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span> <span class="n">pathology</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span> <span class="n">cancer</span> <span class="o">=</span> <span class="kc">True</span><span class="p">):</span>
+
+    <span class="n">result</span> <span class="o">=</span> <span class="p">{</span>
+        <span class="s1">&#39;normal&#39;</span><span class="p">:</span>    <span class="n">collections</span><span class="o">.</span><span class="n">defaultdict</span><span class="p">(</span><span class="nb">dict</span><span class="p">),</span>
+        <span class="s1">&#39;pathology&#39;</span><span class="p">:</span> <span class="n">collections</span><span class="o">.</span><span class="n">defaultdict</span><span class="p">(</span><span class="nb">dict</span><span class="p">),</span>
+    <span class="p">}</span>
+
+
+    <span class="k">def</span> <span class="nf">line</span><span class="p">(</span><span class="n">l</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="n">l</span><span class="o">.</span><span class="n">strip</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\n\r</span><span class="s1">&#39;</span><span class="p">)</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\t</span><span class="s1">&#39;</span><span class="p">)</span>
+
+
+    <span class="k">if</span> <span class="n">normal</span><span class="p">:</span>
+
+        <span class="n">c</span> <span class="o">=</span> <span class="n">curl</span><span class="o">.</span><span class="n">Curl</span><span class="p">(</span><span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;proteinatlas&#39;</span><span class="p">][</span><span class="s1">&#39;normal&#39;</span><span class="p">],</span>
+                    <span class="n">silent</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span> <span class="n">large</span> <span class="o">=</span> <span class="kc">True</span><span class="p">)</span>
+        <span class="n">fp</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="n">c</span><span class="o">.</span><span class="n">result</span><span class="o">.</span><span class="n">values</span><span class="p">())[</span><span class="mi">0</span><span class="p">]</span>
+        <span class="n">hdr</span> <span class="o">=</span> <span class="n">line</span><span class="p">(</span><span class="n">fp</span><span class="o">.</span><span class="n">readline</span><span class="p">()</span><span class="o">.</span><span class="n">strip</span><span class="p">())</span>
+
+        <span class="k">for</span> <span class="n">l</span> <span class="ow">in</span> <span class="n">fp</span><span class="p">:</span>
+            <span class="n">l</span> <span class="o">=</span> <span class="n">line</span><span class="p">(</span><span class="n">l</span><span class="p">)</span>
+
+            <span class="n">uniprots</span> <span class="o">=</span> <span class="n">mapping</span><span class="o">.</span><span class="n">map_name</span><span class="p">(</span><span class="n">l</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span> <span class="s1">&#39;genesymbol&#39;</span><span class="p">,</span> <span class="s1">&#39;uniprot&#39;</span><span class="p">)</span>
+            <span class="n">tissue</span> <span class="o">=</span> <span class="s1">&#39;</span><span class="si">%s</span><span class="s1">:</span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="p">(</span><span class="n">l</span><span class="p">[</span><span class="mi">2</span><span class="p">],</span> <span class="n">l</span><span class="p">[</span><span class="mi">3</span><span class="p">])</span>
+
+            <span class="k">for</span> <span class="n">u</span> <span class="ow">in</span> <span class="n">uniprots</span><span class="p">:</span>
+                <span class="n">result</span><span class="p">[</span><span class="s1">&#39;normal&#39;</span><span class="p">][</span><span class="n">tissue</span><span class="p">][</span><span class="n">u</span><span class="p">]</span> <span class="o">=</span> <span class="p">(</span><span class="n">l</span><span class="p">[</span><span class="mi">4</span><span class="p">],</span> <span class="n">l</span><span class="p">[</span><span class="mi">5</span><span class="p">]</span><span class="o">.</span><span class="n">strip</span><span class="p">())</span>
+
+
+    <span class="k">if</span> <span class="n">cancer</span> <span class="ow">or</span> <span class="n">pathology</span><span class="p">:</span>
+
+        <span class="n">c</span> <span class="o">=</span> <span class="n">curl</span><span class="o">.</span><span class="n">Curl</span><span class="p">(</span><span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;proteinatlas&#39;</span><span class="p">][</span><span class="s1">&#39;pathology&#39;</span><span class="p">],</span>
+                    <span class="n">silent</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span> <span class="n">large</span> <span class="o">=</span> <span class="kc">True</span><span class="p">)</span>
+        <span class="n">fp</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="n">c</span><span class="o">.</span><span class="n">result</span><span class="o">.</span><span class="n">values</span><span class="p">())[</span><span class="mi">0</span><span class="p">]</span>
+        <span class="n">hdr</span> <span class="o">=</span> <span class="n">line</span><span class="p">(</span><span class="n">fp</span><span class="o">.</span><span class="n">readline</span><span class="p">())</span>
+
+        <span class="k">for</span> <span class="n">l</span> <span class="ow">in</span> <span class="n">fp</span><span class="p">:</span>
+
+            <span class="n">l</span> <span class="o">=</span> <span class="n">line</span><span class="p">(</span><span class="n">l</span><span class="p">)</span>
+            <span class="n">uniprots</span> <span class="o">=</span> <span class="n">mapping</span><span class="o">.</span><span class="n">map_name</span><span class="p">(</span><span class="n">l</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span> <span class="s1">&#39;genesymbol&#39;</span><span class="p">,</span> <span class="s1">&#39;uniprot&#39;</span><span class="p">)</span>
+            <span class="n">tissue</span>   <span class="o">=</span> <span class="n">l</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span>
+
+            <span class="n">values</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">(</span>
+                <span class="p">(</span><span class="n">h</span><span class="p">,</span> <span class="nb">float</span><span class="p">(</span><span class="n">l</span><span class="p">[</span><span class="n">i</span> <span class="o">+</span> <span class="mi">3</span><span class="p">])</span> <span class="k">if</span> <span class="s1">&#39;.&#39;</span> <span class="ow">in</span> <span class="n">l</span><span class="p">[</span><span class="n">i</span> <span class="o">+</span> <span class="mi">3</span><span class="p">]</span> <span class="k">else</span> <span class="nb">int</span><span class="p">(</span><span class="n">l</span><span class="p">[</span><span class="n">i</span> <span class="o">+</span> <span class="mi">3</span><span class="p">]))</span>
+                <span class="k">for</span> <span class="n">i</span><span class="p">,</span> <span class="n">h</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">hdr</span><span class="p">[</span><span class="mi">3</span><span class="p">:])</span>
+                <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">l</span><span class="p">)</span> <span class="ow">and</span> <span class="nb">len</span><span class="p">(</span><span class="n">l</span><span class="p">[</span><span class="n">i</span> <span class="o">+</span> <span class="mi">3</span><span class="p">]</span><span class="o">.</span><span class="n">strip</span><span class="p">())</span>
+            <span class="p">)</span>
+
+            <span class="k">for</span> <span class="n">u</span> <span class="ow">in</span> <span class="n">uniprots</span><span class="p">:</span>
+
+                <span class="n">result</span><span class="p">[</span><span class="s1">&#39;pathology&#39;</span><span class="p">][</span><span class="n">tissue</span><span class="p">][</span><span class="n">u</span><span class="p">]</span> <span class="o">=</span> <span class="n">values</span>
+
+    <span class="k">return</span> <span class="nb">dict</span><span class="p">((</span><span class="n">k</span><span class="p">,</span> <span class="nb">dict</span><span class="p">(</span><span class="n">v</span><span class="p">))</span> <span class="k">for</span> <span class="n">k</span><span class="p">,</span> <span class="n">v</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="n">result</span><span class="p">))</span></div>
+
+
+
+<div class="viewcode-block" id="proteinatlas_annotations">
+<a class="viewcode-back" href="../../../api/pypath.inputs.proteinatlas.proteinatlas_annotations.html#pypath.inputs.proteinatlas.proteinatlas_annotations">[docs]</a>
+<span class="k">def</span> <span class="nf">proteinatlas_annotations</span><span class="p">(</span><span class="n">normal</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span> <span class="n">pathology</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span> <span class="n">cancer</span> <span class="o">=</span> <span class="kc">True</span><span class="p">):</span>
+
+    <span class="n">LEVELS</span> <span class="o">=</span> <span class="p">(</span><span class="s1">&#39;Not detected&#39;</span><span class="p">,</span> <span class="s1">&#39;Low&#39;</span><span class="p">,</span> <span class="s1">&#39;Medium&#39;</span><span class="p">,</span> <span class="s1">&#39;High&#39;</span><span class="p">)</span>
+
+
+    <span class="n">ProteinatlasAnnotation</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">namedtuple</span><span class="p">(</span>
+        <span class="s1">&#39;ProtainatlasAnnotation&#39;</span><span class="p">,</span>
+        <span class="p">[</span>
+            <span class="s1">&#39;organ&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;tissue&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;level&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;status&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;n_not_detected&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;n_low&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;n_medium&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;n_high&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;prognostic&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;favourable&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;score&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;pathology&#39;</span><span class="p">,</span>
+        <span class="p">],</span>
+    <span class="p">)</span>
+    <span class="n">ProteinatlasAnnotation</span><span class="o">.</span><span class="fm">__new__</span><span class="o">.</span><span class="vm">__defaults__</span> <span class="o">=</span> <span class="p">(</span>
+        <span class="p">(</span><span class="kc">None</span><span class="p">,)</span> <span class="o">*</span> <span class="mi">4</span> <span class="o">+</span> <span class="p">(</span><span class="kc">False</span><span class="p">,</span> <span class="kc">False</span><span class="p">,</span> <span class="kc">None</span><span class="p">,</span> <span class="kc">False</span><span class="p">)</span>
+    <span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">n_or_none</span><span class="p">(</span><span class="n">ex</span><span class="p">,</span> <span class="n">key</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="n">ex</span><span class="p">[</span><span class="n">key</span><span class="p">]</span> <span class="k">if</span> <span class="n">key</span> <span class="ow">in</span> <span class="n">ex</span> <span class="k">else</span> <span class="kc">None</span>
+
+
+    <span class="n">data</span> <span class="o">=</span> <span class="n">get_proteinatlas</span><span class="p">(</span>
+        <span class="n">normal</span> <span class="o">=</span> <span class="n">normal</span><span class="p">,</span>
+        <span class="n">pathology</span> <span class="o">=</span> <span class="n">pathology</span><span class="p">,</span>
+        <span class="n">cancer</span> <span class="o">=</span> <span class="n">cancer</span><span class="p">,</span>
+    <span class="p">)</span>
+
+    <span class="n">result</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">defaultdict</span><span class="p">(</span><span class="nb">set</span><span class="p">)</span>
+
+    <span class="k">if</span> <span class="n">normal</span><span class="p">:</span>
+
+        <span class="k">for</span> <span class="n">tissue</span><span class="p">,</span> <span class="n">gex</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="n">data</span><span class="p">[</span><span class="s1">&#39;normal&#39;</span><span class="p">]):</span>
+
+            <span class="n">organ</span> <span class="o">=</span> <span class="n">tissue</span>
+
+            <span class="k">if</span> <span class="s1">&#39;:&#39;</span> <span class="ow">in</span> <span class="n">tissue</span><span class="p">:</span>
+                <span class="n">organ</span><span class="p">,</span> <span class="n">tissue</span> <span class="o">=</span> <span class="n">tissue</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;:&#39;</span><span class="p">)</span>
+
+            <span class="n">organ</span> <span class="o">=</span> <span class="n">organ</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span>
+            <span class="n">tissue</span> <span class="o">=</span> <span class="n">tissue</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span>
+
+            <span class="k">for</span> <span class="n">uniprot</span><span class="p">,</span> <span class="n">ex</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="n">gex</span><span class="p">):</span>
+                <span class="n">uniprots</span> <span class="o">=</span> <span class="n">mapping</span><span class="o">.</span><span class="n">map_name</span><span class="p">(</span><span class="n">uniprot</span><span class="p">,</span> <span class="s1">&#39;uniprot&#39;</span><span class="p">,</span> <span class="s1">&#39;uniprot&#39;</span><span class="p">)</span>
+
+                <span class="k">for</span> <span class="n">_uniprot</span> <span class="ow">in</span> <span class="n">uniprots</span><span class="p">:</span>
+                    <span class="n">result</span><span class="p">[</span><span class="n">_uniprot</span><span class="p">]</span><span class="o">.</span><span class="n">add</span><span class="p">(</span>
+                        <span class="n">ProteinatlasAnnotation</span><span class="p">(</span>
+                            <span class="n">organ</span> <span class="o">=</span> <span class="n">organ</span><span class="p">,</span>
+                            <span class="n">tissue</span> <span class="o">=</span> <span class="n">tissue</span><span class="p">,</span>
+                            <span class="n">level</span> <span class="o">=</span> <span class="n">ex</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span>
+                            <span class="n">status</span> <span class="o">=</span> <span class="n">ex</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span>
+                        <span class="p">)</span>
+                    <span class="p">)</span>
+
+    <span class="k">if</span> <span class="n">pathology</span> <span class="ow">or</span> <span class="n">cancer</span><span class="p">:</span>
+        <span class="k">for</span> <span class="n">condition</span><span class="p">,</span> <span class="n">gex</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="n">data</span><span class="p">[</span><span class="s1">&#39;pathology&#39;</span><span class="p">]):</span>
+            <span class="k">for</span> <span class="n">uniprot</span><span class="p">,</span> <span class="n">ex</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="n">gex</span><span class="p">):</span>
+                <span class="k">try</span><span class="p">:</span>
+                    <span class="n">effect</span><span class="p">,</span> <span class="n">score</span> <span class="o">=</span> <span class="nb">next</span><span class="p">(</span>
+                        <span class="n">i</span> <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="n">ex</span><span class="p">)</span> <span class="k">if</span> <span class="n">i</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">LEVELS</span>
+                    <span class="p">)</span>
+                    <span class="n">prognostic</span> <span class="o">=</span> <span class="ow">not</span> <span class="n">effect</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s1">&#39;unprognostic&#39;</span><span class="p">)</span>
+                    <span class="n">favourable</span> <span class="o">=</span> <span class="ow">not</span> <span class="n">effect</span><span class="o">.</span><span class="n">endswith</span><span class="p">(</span><span class="s1">&#39;unfavourable&#39;</span><span class="p">)</span>
+
+                <span class="k">except</span> <span class="ne">StopIteration</span><span class="p">:</span>
+                    <span class="n">prognostic</span><span class="p">,</span> <span class="n">favourable</span><span class="p">,</span> <span class="n">score</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span> <span class="kc">None</span><span class="p">,</span> <span class="kc">None</span>
+
+                <span class="n">uniprots</span> <span class="o">=</span> <span class="n">mapping</span><span class="o">.</span><span class="n">map_name</span><span class="p">(</span><span class="n">uniprot</span><span class="p">,</span> <span class="s1">&#39;uniprot&#39;</span><span class="p">,</span> <span class="s1">&#39;uniprot&#39;</span><span class="p">)</span>
+
+                <span class="k">for</span> <span class="n">_uniprot</span> <span class="ow">in</span> <span class="n">uniprots</span><span class="p">:</span>
+                    <span class="n">result</span><span class="p">[</span><span class="n">_uniprot</span><span class="p">]</span><span class="o">.</span><span class="n">add</span><span class="p">(</span>
+                        <span class="n">ProteinatlasAnnotation</span><span class="p">(</span>
+                            <span class="n">organ</span> <span class="o">=</span> <span class="n">condition</span><span class="p">,</span>
+                            <span class="n">tissue</span> <span class="o">=</span> <span class="n">condition</span><span class="p">,</span>
+                            <span class="n">level</span> <span class="o">=</span> <span class="nb">max</span><span class="p">(</span>
+                                <span class="p">(</span><span class="n">i</span> <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="n">ex</span><span class="p">)</span> <span class="k">if</span> <span class="n">i</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="ow">in</span> <span class="n">LEVELS</span><span class="p">),</span>
+                                <span class="n">key</span> <span class="o">=</span> <span class="k">lambda</span> <span class="n">i</span><span class="p">:</span> <span class="n">i</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span>
+                                <span class="n">default</span> <span class="o">=</span> <span class="p">(</span><span class="kc">None</span><span class="p">,),</span>
+                            <span class="p">)[</span><span class="mi">0</span><span class="p">],</span>
+                            <span class="n">status</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+                            <span class="n">n_not_detected</span> <span class="o">=</span> <span class="n">n_or_none</span><span class="p">(</span><span class="n">ex</span><span class="p">,</span> <span class="s1">&#39;Not detected&#39;</span><span class="p">),</span>
+                            <span class="n">n_low</span> <span class="o">=</span> <span class="n">n_or_none</span><span class="p">(</span><span class="n">ex</span><span class="p">,</span> <span class="s1">&#39;Low&#39;</span><span class="p">),</span>
+                            <span class="n">n_medium</span> <span class="o">=</span> <span class="n">n_or_none</span><span class="p">(</span><span class="n">ex</span><span class="p">,</span> <span class="s1">&#39;Medium&#39;</span><span class="p">),</span>
+                            <span class="n">n_high</span> <span class="o">=</span> <span class="n">n_or_none</span><span class="p">(</span><span class="n">ex</span><span class="p">,</span> <span class="s1">&#39;High&#39;</span><span class="p">),</span>
+                            <span class="n">prognostic</span> <span class="o">=</span> <span class="n">prognostic</span><span class="p">,</span>
+                            <span class="n">favourable</span> <span class="o">=</span> <span class="n">favourable</span><span class="p">,</span>
+                            <span class="n">score</span> <span class="o">=</span> <span class="n">score</span><span class="p">,</span>
+                            <span class="n">pathology</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
+                        <span class="p">)</span>
+                    <span class="p">)</span>
+
+    <span class="k">return</span> <span class="nb">dict</span><span class="p">(</span><span class="n">result</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="proteinatlas_subcellular_annotations">
+<a class="viewcode-back" href="../../../api/pypath.inputs.proteinatlas.proteinatlas_subcellular_annotations.html#pypath.inputs.proteinatlas.proteinatlas_subcellular_annotations">[docs]</a>
+<span class="k">def</span> <span class="nf">proteinatlas_subcellular_annotations</span><span class="p">():</span>
+
+    <span class="n">ProteinatlasSubcellularAnnotation</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">namedtuple</span><span class="p">(</span>
+        <span class="s1">&#39;ProteinatlasSubcellularAnnotation&#39;</span><span class="p">,</span>
+        <span class="p">[</span>
+            <span class="s1">&#39;location&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;status&#39;</span><span class="p">,</span>
+        <span class="p">],</span>
+    <span class="p">)</span>
+
+    <span class="n">url</span> <span class="o">=</span> <span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;proteinatlas&#39;</span><span class="p">][</span><span class="s1">&#39;subcell&#39;</span><span class="p">]</span>
+
+    <span class="n">c</span> <span class="o">=</span> <span class="n">curl</span><span class="o">.</span><span class="n">Curl</span><span class="p">(</span>
+        <span class="n">url</span><span class="p">,</span>
+        <span class="n">large</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
+        <span class="n">silent</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+        <span class="n">default_mode</span> <span class="o">=</span> <span class="s1">&#39;r&#39;</span><span class="p">,</span>
+    <span class="p">)</span>
+    <span class="n">reader</span> <span class="o">=</span> <span class="n">csv</span><span class="o">.</span><span class="n">DictReader</span><span class="p">(</span>
+        <span class="n">c</span><span class="o">.</span><span class="n">files_multipart</span><span class="p">[</span><span class="s1">&#39;subcellular_location.tsv&#39;</span><span class="p">],</span>
+        <span class="n">delimiter</span> <span class="o">=</span> <span class="s1">&#39;</span><span class="se">\t</span><span class="s1">&#39;</span><span class="p">,</span>
+    <span class="p">)</span>
+
+    <span class="n">result</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">defaultdict</span><span class="p">(</span><span class="nb">set</span><span class="p">)</span>
+
+    <span class="k">for</span> <span class="n">rec</span> <span class="ow">in</span> <span class="n">reader</span><span class="p">:</span>
+        <span class="n">uniprots</span> <span class="o">=</span> <span class="n">mapping</span><span class="o">.</span><span class="n">map_name</span><span class="p">(</span><span class="n">rec</span><span class="p">[</span><span class="s1">&#39;Gene name&#39;</span><span class="p">],</span> <span class="s1">&#39;genesymbol&#39;</span><span class="p">,</span> <span class="s1">&#39;uniprot&#39;</span><span class="p">)</span>
+
+        <span class="k">for</span> <span class="n">uniprot</span> <span class="ow">in</span> <span class="n">uniprots</span><span class="p">:</span>
+            <span class="k">for</span> <span class="n">status</span> <span class="ow">in</span> <span class="p">(</span><span class="s1">&#39;Enhanced&#39;</span><span class="p">,</span> <span class="s1">&#39;Supported&#39;</span><span class="p">,</span> <span class="s1">&#39;Uncertain&#39;</span><span class="p">):</span>
+                <span class="k">if</span> <span class="ow">not</span> <span class="n">rec</span><span class="p">[</span><span class="n">status</span><span class="p">]:</span>
+                    <span class="k">continue</span>
+
+                <span class="k">for</span> <span class="n">location</span> <span class="ow">in</span> <span class="n">rec</span><span class="p">[</span><span class="n">status</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;;&#39;</span><span class="p">):</span>
+                    <span class="n">result</span><span class="p">[</span><span class="n">uniprot</span><span class="p">]</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">ProteinatlasSubcellularAnnotation</span><span class="p">(</span>
+                        <span class="n">location</span> <span class="o">=</span> <span class="n">location</span><span class="p">,</span>
+                        <span class="n">status</span> <span class="o">=</span> <span class="n">status</span><span class="p">,</span>
+                    <span class="p">))</span>
+
+    <span class="k">return</span> <span class="nb">dict</span><span class="p">(</span><span class="n">result</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="proteinatlas_secretome_annotations">
+<a class="viewcode-back" href="../../../api/pypath.inputs.proteinatlas.proteinatlas_secretome_annotations.html#pypath.inputs.proteinatlas.proteinatlas_secretome_annotations">[docs]</a>
+<span class="k">def</span> <span class="nf">proteinatlas_secretome_annotations</span><span class="p">():</span>
+
+    <span class="n">ProteinatlasSecretomeAnnotation</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">namedtuple</span><span class="p">(</span>
+        <span class="s1">&#39;ProteinatlasSecretomeAnnotation&#39;</span><span class="p">,</span>
+        <span class="p">[</span>
+            <span class="s1">&#39;mainclass&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;secreted&#39;</span><span class="p">,</span>
+        <span class="p">],</span>
+    <span class="p">)</span>
+
+
+    <span class="n">url</span> <span class="o">=</span> <span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;proteinatlas&#39;</span><span class="p">][</span><span class="s1">&#39;secretome&#39;</span><span class="p">]</span>
+    <span class="n">path</span> <span class="o">=</span> <span class="n">science</span><span class="o">.</span><span class="n">science_download</span><span class="p">(</span><span class="n">url</span><span class="p">)</span>
+    <span class="n">reader</span> <span class="o">=</span> <span class="n">inputs_common</span><span class="o">.</span><span class="n">read_xls</span><span class="p">(</span><span class="n">path</span><span class="p">)[</span><span class="mi">1</span><span class="p">:]</span>
+    <span class="n">result</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">defaultdict</span><span class="p">(</span><span class="nb">set</span><span class="p">)</span>
+
+    <span class="k">for</span> <span class="n">rec</span> <span class="ow">in</span> <span class="n">reader</span><span class="p">:</span>
+
+        <span class="k">for</span> <span class="n">uniprot_original</span> <span class="ow">in</span> <span class="n">rec</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;,&#39;</span><span class="p">):</span>
+
+            <span class="n">uniprots</span> <span class="o">=</span> <span class="n">mapping</span><span class="o">.</span><span class="n">map_name</span><span class="p">(</span>
+                <span class="n">uniprot_original</span><span class="p">,</span>
+                <span class="s1">&#39;uniprot&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;uniprot&#39;</span><span class="p">,</span>
+            <span class="p">)</span>
+
+            <span class="k">for</span> <span class="n">uniprot</span> <span class="ow">in</span> <span class="n">uniprots</span><span class="p">:</span>
+                <span class="n">result</span><span class="p">[</span><span class="n">uniprot</span><span class="p">]</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">ProteinatlasSecretomeAnnotation</span><span class="p">(</span>
+                    <span class="n">mainclass</span> <span class="o">=</span> <span class="n">rec</span><span class="p">[</span><span class="mi">3</span><span class="p">],</span>
+                    <span class="n">secreted</span> <span class="o">=</span> <span class="s1">&#39;secreted&#39;</span> <span class="ow">in</span> <span class="n">rec</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span><span class="o">.</span><span class="n">lower</span><span class="p">(),</span>
+                <span class="p">))</span>
+
+    <span class="k">return</span> <span class="nb">dict</span><span class="p">(</span><span class="n">result</span><span class="p">)</span></div>
+
+</pre></div>
+
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diff --git a/_modules/pypath/inputs/ramilowski2015.html b/_modules/pypath/inputs/ramilowski2015.html
new file mode 100644
index 000000000..d19eb2eb9
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@@ -0,0 +1,778 @@
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+  <h1>Source code for pypath.inputs.ramilowski2015</h1><div class="highlight"><pre>
+<span></span><span class="ch">#!/usr/bin/env python</span>
+<span class="c1"># -*- coding: utf-8 -*-</span>
+
+<span class="c1">#</span>
+<span class="c1">#  This file is part of the `pypath` python module</span>
+<span class="c1">#</span>
+<span class="c1">#  Copyright 2014-2023</span>
+<span class="c1">#  EMBL, EMBL-EBI, Uniklinik RWTH Aachen, Heidelberg University</span>
+<span class="c1">#</span>
+<span class="c1">#  Authors: see the file `README.rst`</span>
+<span class="c1">#  Contact: Dénes Türei (turei.denes@gmail.com)</span>
+<span class="c1">#</span>
+<span class="c1">#  Distributed under the GPLv3 License.</span>
+<span class="c1">#  See accompanying file LICENSE.txt or copy at</span>
+<span class="c1">#      https://www.gnu.org/licenses/gpl-3.0.html</span>
+<span class="c1">#</span>
+<span class="c1">#  Website: https://pypath.omnipathdb.org/</span>
+<span class="c1">#</span>
+
+<span class="kn">import</span> <span class="nn">re</span>
+<span class="kn">import</span> <span class="nn">itertools</span>
+<span class="kn">import</span> <span class="nn">collections</span>
+
+<span class="kn">import</span> <span class="nn">pypath.share.curl</span> <span class="k">as</span> <span class="nn">curl</span>
+<span class="kn">import</span> <span class="nn">pypath.resources.urls</span> <span class="k">as</span> <span class="nn">urls</span>
+<span class="kn">import</span> <span class="nn">pypath.inputs.common</span> <span class="k">as</span> <span class="nn">inputs_common</span>
+<span class="kn">import</span> <span class="nn">pypath.utils.mapping</span> <span class="k">as</span> <span class="nn">mapping</span>
+
+
+<div class="viewcode-block" id="ramilowski_interactions">
+<a class="viewcode-back" href="../../../api/pypath.inputs.ramilowski2015.ramilowski_interactions.html#pypath.inputs.ramilowski2015.ramilowski_interactions">[docs]</a>
+<span class="k">def</span> <span class="nf">ramilowski_interactions</span><span class="p">(</span><span class="n">putative</span> <span class="o">=</span> <span class="kc">False</span><span class="p">):</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Downloads and processes ligand-receptor interactions from</span>
+<span class="sd">    Supplementary Table 2 of Ramilowski 2015.</span>
+
+<span class="sd">    Returns list of lists with ligand and receptor gene symbols, reference</span>
+<span class="sd">    and resources as elements.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="n">c</span> <span class="o">=</span> <span class="n">curl</span><span class="o">.</span><span class="n">Curl</span><span class="p">(</span><span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;rami&#39;</span><span class="p">][</span><span class="s1">&#39;url&#39;</span><span class="p">],</span> <span class="n">silent</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span> <span class="n">large</span> <span class="o">=</span> <span class="kc">True</span><span class="p">)</span>
+    <span class="n">xlsname</span> <span class="o">=</span> <span class="n">c</span><span class="o">.</span><span class="n">fname</span>
+    <span class="k">del</span><span class="p">(</span><span class="n">c</span><span class="p">)</span>
+    <span class="n">raw</span> <span class="o">=</span> <span class="n">inputs_common</span><span class="o">.</span><span class="n">read_xls</span><span class="p">(</span><span class="n">xlsname</span><span class="p">,</span> <span class="s1">&#39;All.Pairs&#39;</span><span class="p">)[</span><span class="mi">1</span><span class="p">:]</span>
+
+    <span class="n">Ramilowski2015Interaction</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">namedtuple</span><span class="p">(</span>
+        <span class="s1">&#39;Ramilowski2015Interaction&#39;</span><span class="p">,</span>
+        <span class="p">(</span>
+            <span class="s1">&#39;ligand&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;receptor&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;references&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;resources&#39;</span><span class="p">,</span>
+        <span class="p">),</span>
+    <span class="p">)</span>
+
+    <span class="k">return</span> <span class="p">[</span>
+        <span class="n">Ramilowski2015Interaction</span><span class="p">(</span>
+            <span class="n">ligand</span> <span class="o">=</span> <span class="n">r</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span>
+            <span class="n">receptor</span> <span class="o">=</span> <span class="n">r</span><span class="p">[</span><span class="mi">3</span><span class="p">],</span>
+            <span class="n">references</span> <span class="o">=</span> <span class="n">r</span><span class="p">[</span><span class="mi">13</span><span class="p">]</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s1">&#39; &#39;</span><span class="p">,</span> <span class="s1">&#39;&#39;</span><span class="p">),</span> <span class="c1"># references</span>
+            <span class="n">resources</span> <span class="o">=</span> <span class="s1">&#39;;&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span>
+                <span class="nb">filter</span><span class="p">(</span><span class="nb">len</span><span class="p">,</span> <span class="n">itertools</span><span class="o">.</span><span class="n">chain</span><span class="p">(</span><span class="n">r</span><span class="p">[</span><span class="mi">5</span><span class="p">:</span><span class="mi">11</span><span class="p">],</span> <span class="p">[</span><span class="n">r</span><span class="p">[</span><span class="mi">15</span><span class="p">]]))</span>
+            <span class="p">),</span>
+        <span class="p">)</span>
+        <span class="k">for</span> <span class="n">r</span> <span class="ow">in</span> <span class="n">raw</span>
+        <span class="k">if</span> <span class="ow">not</span> <span class="n">r</span><span class="p">[</span><span class="mi">15</span><span class="p">]</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s1">&#39;EXCLUDED&#39;</span><span class="p">)</span> <span class="ow">and</span> <span class="p">(</span>
+            <span class="n">putative</span> <span class="ow">or</span> <span class="n">r</span><span class="p">[</span><span class="mi">15</span><span class="p">]</span> <span class="o">!=</span> <span class="s1">&#39;putative&#39;</span>
+        <span class="p">)</span>
+    <span class="p">]</span>
+
+    <span class="k">return</span> <span class="n">raw</span></div>
+
+
+
+<div class="viewcode-block" id="ramilowski_locations">
+<a class="viewcode-back" href="../../../api/pypath.inputs.ramilowski2015.ramilowski_locations.html#pypath.inputs.ramilowski2015.ramilowski_locations">[docs]</a>
+<span class="k">def</span> <span class="nf">ramilowski_locations</span><span class="p">(</span><span class="n">long_notes</span> <span class="o">=</span> <span class="kc">False</span><span class="p">):</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Subcellular location annotations from Ramilowski 2015.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="n">reloc</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">compile</span><span class="p">(</span>
+        <span class="sa">r</span><span class="s1">&#39;([^\(]+[^\s^\(])&#39;</span>
+        <span class="sa">r</span><span class="s1">&#39;\s?\(&#39;</span>
+        <span class="sa">r</span><span class="s1">&#39;?(?:(.*[^\)])?)&#39;</span>
+        <span class="sa">r</span><span class="s1">&#39;\)?&#39;</span>
+    <span class="p">)</span>
+    <span class="n">resep</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">compile</span><span class="p">(</span><span class="sa">r</span><span class="s1">&#39;[\.;,]&#39;</span><span class="p">)</span>
+    <span class="n">renote</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">compile</span><span class="p">(</span><span class="sa">r</span><span class="s1">&#39;Note=([- \w\(\),\s\+\./%</span><span class="se">\&#39;</span><span class="s1">&quot;:;]*)&#39;</span><span class="p">)</span>
+
+    <span class="n">sources</span> <span class="o">=</span> <span class="p">(</span>
+        <span class="p">(</span><span class="mi">4</span><span class="p">,</span> <span class="s1">&#39;UniProt&#39;</span><span class="p">),</span>
+        <span class="p">(</span><span class="mi">5</span><span class="p">,</span> <span class="s1">&#39;HPRD&#39;</span><span class="p">),</span>
+        <span class="p">(</span><span class="mi">7</span><span class="p">,</span> <span class="s1">&#39;LocTree3&#39;</span><span class="p">),</span>
+        <span class="p">(</span><span class="mi">10</span><span class="p">,</span> <span class="s1">&#39;Consensus&#39;</span><span class="p">),</span>
+        <span class="p">(</span><span class="mi">11</span><span class="p">,</span> <span class="s1">&#39;Consensus6&#39;</span><span class="p">),</span>
+    <span class="p">)</span>
+
+    <span class="n">RamilowskiLocation</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">namedtuple</span><span class="p">(</span>
+        <span class="s1">&#39;RamilowskiLocation&#39;</span><span class="p">,</span>
+        <span class="p">[</span>
+            <span class="s1">&#39;location&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;source&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;tmh&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;note&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;long_note&#39;</span><span class="p">,</span>
+        <span class="p">],</span>
+    <span class="p">)</span>
+
+    <span class="n">url</span> <span class="o">=</span> <span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;rami&#39;</span><span class="p">][</span><span class="s1">&#39;loc&#39;</span><span class="p">]</span>
+    <span class="n">c</span> <span class="o">=</span> <span class="n">curl</span><span class="o">.</span><span class="n">Curl</span><span class="p">(</span><span class="n">url</span><span class="p">,</span> <span class="n">silent</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span> <span class="n">large</span> <span class="o">=</span> <span class="kc">True</span><span class="p">)</span>
+
+    <span class="n">_</span> <span class="o">=</span> <span class="nb">next</span><span class="p">(</span><span class="n">c</span><span class="o">.</span><span class="n">result</span><span class="p">)</span>
+
+    <span class="n">result</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">defaultdict</span><span class="p">(</span><span class="nb">set</span><span class="p">)</span>
+
+    <span class="k">for</span> <span class="n">l</span> <span class="ow">in</span> <span class="n">c</span><span class="o">.</span><span class="n">result</span><span class="p">:</span>
+        <span class="n">l</span> <span class="o">=</span> <span class="n">l</span><span class="o">.</span><span class="n">strip</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\n\r</span><span class="s1">&#39;</span><span class="p">)</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\t</span><span class="s1">&#39;</span><span class="p">)</span>
+
+        <span class="k">for</span> <span class="n">idx</span><span class="p">,</span> <span class="n">source</span> <span class="ow">in</span> <span class="n">sources</span><span class="p">:</span>
+            <span class="n">locs</span> <span class="o">=</span> <span class="n">l</span><span class="p">[</span><span class="n">idx</span><span class="p">]</span>
+
+            <span class="n">long_note</span> <span class="o">=</span> <span class="kc">None</span>
+            <span class="n">mnote</span> <span class="o">=</span> <span class="n">renote</span><span class="o">.</span><span class="n">search</span><span class="p">(</span><span class="n">locs</span><span class="p">)</span>
+
+            <span class="k">if</span> <span class="n">mnote</span><span class="p">:</span>
+                <span class="n">long_note</span> <span class="o">=</span> <span class="n">mnote</span><span class="o">.</span><span class="n">groups</span><span class="p">()[</span><span class="mi">0</span><span class="p">]</span>
+                <span class="n">locs</span> <span class="o">=</span> <span class="n">renote</span><span class="o">.</span><span class="n">sub</span><span class="p">(</span><span class="s1">&#39;&#39;</span><span class="p">,</span> <span class="n">locs</span><span class="p">)</span>
+
+            <span class="k">for</span> <span class="n">loc</span> <span class="ow">in</span> <span class="n">resep</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="n">locs</span><span class="p">):</span>
+
+                <span class="k">if</span> <span class="s1">&#39;:&#39;</span> <span class="ow">in</span> <span class="n">loc</span> <span class="ow">and</span> <span class="s1">&#39;GO:&#39;</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">loc</span><span class="p">:</span>
+
+                    <span class="n">loc</span> <span class="o">=</span> <span class="n">loc</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;:&#39;</span><span class="p">)[</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span>
+
+                <span class="n">loc</span> <span class="o">=</span> <span class="n">loc</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s1">&#39;- &#39;</span><span class="p">,</span> <span class="s1">&#39;-&#39;</span><span class="p">)</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span>
+
+                <span class="k">if</span> <span class="p">(</span>
+                    <span class="ow">not</span> <span class="n">loc</span> <span class="ow">or</span>
+                    <span class="nb">len</span><span class="p">(</span><span class="n">loc</span><span class="o">.</span><span class="n">split</span><span class="p">())</span> <span class="o">&gt;</span> <span class="mi">3</span> <span class="ow">or</span>
+                    <span class="n">re</span><span class="o">.</span><span class="n">search</span><span class="p">(</span><span class="sa">r</span><span class="s1">&#39;\d&#39;</span><span class="p">,</span> <span class="n">loc</span><span class="p">)</span> <span class="ow">or</span>
+                    <span class="n">loc</span> <span class="o">==</span> <span class="s1">&#39;n/a&#39;</span> <span class="ow">or</span>
+                    <span class="nb">any</span><span class="p">(</span>
+                        <span class="n">w</span> <span class="ow">in</span> <span class="n">loc</span> <span class="k">for</span> <span class="n">w</span> <span class="ow">in</span>
+                        <span class="p">(</span><span class="s1">&#39;tumor&#39;</span><span class="p">,)</span>
+                    <span class="p">)</span>
+                <span class="p">):</span>
+                    <span class="k">continue</span>
+
+                <span class="n">m</span> <span class="o">=</span> <span class="n">reloc</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="n">loc</span><span class="p">)</span>
+
+                <span class="k">if</span> <span class="ow">not</span> <span class="n">m</span><span class="p">:</span>
+                    <span class="k">continue</span>
+
+                <span class="n">location</span><span class="p">,</span> <span class="n">note</span> <span class="o">=</span> <span class="n">m</span><span class="o">.</span><span class="n">groups</span><span class="p">()</span>
+                <span class="n">tmh</span> <span class="o">=</span> <span class="n">l</span><span class="p">[</span><span class="mi">9</span><span class="p">]</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span>
+
+                <span class="n">uniprots</span> <span class="o">=</span> <span class="n">mapping</span><span class="o">.</span><span class="n">map_name</span><span class="p">(</span><span class="n">l</span><span class="p">[</span><span class="mi">3</span><span class="p">],</span> <span class="s1">&#39;uniprot&#39;</span><span class="p">,</span> <span class="s1">&#39;uniprot&#39;</span><span class="p">)</span>
+
+                <span class="k">for</span> <span class="n">uniprot</span> <span class="ow">in</span> <span class="n">uniprots</span><span class="p">:</span>
+
+                    <span class="n">result</span><span class="p">[</span><span class="n">uniprot</span><span class="p">]</span><span class="o">.</span><span class="n">add</span><span class="p">(</span>
+                        <span class="n">RamilowskiLocation</span><span class="p">(</span>
+                            <span class="n">location</span> <span class="o">=</span> <span class="p">(</span>
+                                <span class="n">location</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s1">&#39;=&#39;</span><span class="p">,</span> <span class="s1">&#39;&#39;</span><span class="p">)</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span>
+                            <span class="p">),</span>
+                            <span class="n">source</span> <span class="o">=</span> <span class="n">source</span><span class="p">,</span>
+                            <span class="n">tmh</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">tmh</span><span class="p">)</span> <span class="k">if</span> <span class="n">tmh</span><span class="o">.</span><span class="n">isdigit</span><span class="p">()</span> <span class="k">else</span> <span class="kc">None</span><span class="p">,</span>
+                            <span class="n">note</span> <span class="o">=</span> <span class="n">note</span><span class="p">,</span>
+                            <span class="n">long_note</span> <span class="o">=</span> <span class="n">long_note</span> <span class="k">if</span> <span class="n">long_notes</span> <span class="k">else</span> <span class="kc">None</span><span class="p">,</span>
+                        <span class="p">)</span>
+                    <span class="p">)</span>
+
+    <span class="k">return</span> <span class="nb">dict</span><span class="p">(</span><span class="n">result</span><span class="p">)</span></div>
+
+</pre></div>
+
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+                <article class="bd-article">
+                  
+  <h1>Source code for pypath.inputs.scconnect</h1><div class="highlight"><pre>
+<span></span><span class="ch">#!/usr/bin/env python</span>
+<span class="c1"># -*- coding: utf-8 -*-</span>
+
+<span class="c1">#</span>
+<span class="c1">#  This file is part of the `pypath` python module</span>
+<span class="c1">#</span>
+<span class="c1">#  Copyright 2014-2023</span>
+<span class="c1">#  EMBL, EMBL-EBI, Uniklinik RWTH Aachen, Heidelberg University</span>
+<span class="c1">#</span>
+<span class="c1">#  Authors: see the file `README.rst`</span>
+<span class="c1">#  Contact: Dénes Türei (turei.denes@gmail.com)</span>
+<span class="c1">#</span>
+<span class="c1">#  Distributed under the GPLv3 License.</span>
+<span class="c1">#  See accompanying file LICENSE.txt or copy at</span>
+<span class="c1">#      https://www.gnu.org/licenses/gpl-3.0.html</span>
+<span class="c1">#</span>
+<span class="c1">#  Website: https://pypath.omnipathdb.org/</span>
+<span class="c1">#</span>
+
+<span class="kn">import</span> <span class="nn">re</span>
+<span class="kn">import</span> <span class="nn">csv</span>
+<span class="kn">import</span> <span class="nn">collections</span>
+<span class="kn">import</span> <span class="nn">itertools</span>
+
+<span class="kn">import</span> <span class="nn">pypath.utils.mapping</span> <span class="k">as</span> <span class="nn">mapping</span>
+<span class="kn">import</span> <span class="nn">pypath.utils.taxonomy</span> <span class="k">as</span> <span class="nn">taxonomy</span>
+<span class="kn">import</span> <span class="nn">pypath.internals.intera</span> <span class="k">as</span> <span class="nn">intera</span>
+<span class="kn">import</span> <span class="nn">pypath.share.curl</span> <span class="k">as</span> <span class="nn">curl</span>
+<span class="kn">import</span> <span class="nn">pypath.resources.urls</span> <span class="k">as</span> <span class="nn">urls</span>
+<span class="kn">import</span> <span class="nn">pypath.share.common</span> <span class="k">as</span> <span class="nn">common</span>
+<span class="kn">import</span> <span class="nn">pypath_common._constants</span> <span class="k">as</span> <span class="nn">_const</span>
+<span class="kn">import</span> <span class="nn">pypath.share.session</span> <span class="k">as</span> <span class="nn">session</span>
+<span class="kn">import</span> <span class="nn">pypath.core.entity</span> <span class="k">as</span> <span class="nn">entity</span>
+
+<span class="n">_logger</span> <span class="o">=</span> <span class="n">session</span><span class="o">.</span><span class="n">Logger</span><span class="p">(</span><span class="n">name</span> <span class="o">=</span> <span class="s1">&#39;scconnect_input&#39;</span><span class="p">)</span>
+<span class="n">_log</span> <span class="o">=</span> <span class="n">_logger</span><span class="o">.</span><span class="n">_log</span>
+
+
+<div class="viewcode-block" id="scconnect_annotations">
+<a class="viewcode-back" href="../../../api/pypath.inputs.scconnect.scconnect_annotations.html#pypath.inputs.scconnect.scconnect_annotations">[docs]</a>
+<span class="k">def</span> <span class="nf">scconnect_annotations</span><span class="p">(</span><span class="n">organism</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">):</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Ligand and receptor annotations from scConnect</span>
+<span class="sd">    (https://github.com/JonETJakobsson/scConnect).</span>
+
+<span class="sd">    Args</span>
+<span class="sd">        organism (int,str): Name or identifier of the organism. Human, mouse,</span>
+<span class="sd">            fruitfly, zebrafish, chicken, C. elegans, Xenopus tropicalis,</span>
+<span class="sd">            yeast and Anolis carolinensis are available.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="n">_organism</span> <span class="o">=</span> <span class="n">taxonomy</span><span class="o">.</span><span class="n">ensure_ensembl_name</span><span class="p">(</span><span class="n">organism</span><span class="p">)</span>
+    <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">taxonomy</span><span class="o">.</span><span class="n">ensure_ncbi_tax_id</span><span class="p">(</span><span class="n">organism</span><span class="p">)</span>
+
+    <span class="k">if</span> <span class="ow">not</span> <span class="n">_organism</span><span class="p">:</span>
+
+        <span class="n">msg</span> <span class="o">=</span> <span class="s1">&#39;Could not recognize organism: `</span><span class="si">%s</span><span class="s1">`.&#39;</span> <span class="o">%</span> <span class="nb">str</span><span class="p">(</span><span class="n">organism</span><span class="p">)</span>
+        <span class="n">_log</span><span class="p">(</span><span class="n">msg</span><span class="p">)</span>
+        <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="n">msg</span><span class="p">)</span>
+
+    <span class="n">record</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">namedtuple</span><span class="p">(</span>
+        <span class="s1">&#39;ScconnectAnnotation&#39;</span><span class="p">,</span>
+        <span class="p">(</span>
+            <span class="s1">&#39;role&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;family&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;type&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;inferred_from&#39;</span><span class="p">,</span>
+        <span class="p">),</span>
+    <span class="p">)</span>
+
+    <span class="n">result</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">defaultdict</span><span class="p">(</span><span class="nb">set</span><span class="p">)</span>
+    <span class="n">reinf</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">compile</span><span class="p">(</span><span class="s1">&#39;inferred from (\w+)&#39;</span><span class="p">)</span>
+
+    <span class="k">for</span> <span class="n">role</span> <span class="ow">in</span> <span class="p">(</span><span class="s1">&#39;ligand&#39;</span><span class="p">,</span> <span class="s1">&#39;receptor&#39;</span><span class="p">):</span>
+
+        <span class="n">url</span> <span class="o">=</span> <span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;scconnect&#39;</span><span class="p">][</span><span class="s1">&#39;annot&#39;</span><span class="p">]</span> <span class="o">%</span> <span class="p">(</span><span class="n">_organism</span><span class="p">,</span> <span class="n">role</span><span class="p">)</span>
+        <span class="n">c</span> <span class="o">=</span> <span class="n">curl</span><span class="o">.</span><span class="n">Curl</span><span class="p">(</span><span class="n">url</span><span class="p">,</span> <span class="n">silent</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span> <span class="n">large</span> <span class="o">=</span> <span class="kc">True</span><span class="p">)</span>
+        <span class="n">tab</span> <span class="o">=</span> <span class="n">csv</span><span class="o">.</span><span class="n">DictReader</span><span class="p">(</span><span class="n">c</span><span class="o">.</span><span class="n">result</span><span class="p">)</span>
+
+        <span class="k">for</span> <span class="n">rec</span> <span class="ow">in</span> <span class="n">tab</span><span class="p">:</span>
+
+            <span class="n">typ</span> <span class="o">=</span> <span class="n">rec</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">&#39;type&#39;</span><span class="p">,</span> <span class="kc">None</span><span class="p">)</span>
+            <span class="n">family</span> <span class="o">=</span> <span class="n">rec</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">&#39;family&#39;</span><span class="p">,</span> <span class="kc">None</span><span class="p">)</span>
+            <span class="n">inferred_from</span> <span class="o">=</span> <span class="n">rec</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">&#39;comment&#39;</span><span class="p">,</span> <span class="kc">None</span><span class="p">)</span>
+
+            <span class="k">if</span> <span class="n">inferred_from</span><span class="p">:</span>
+
+                <span class="n">inferred_from</span> <span class="o">=</span> <span class="n">reinf</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="n">inferred_from</span><span class="p">)</span>
+
+                <span class="k">if</span> <span class="n">inferred_from</span><span class="p">:</span>
+
+                    <span class="n">inferred_from</span> <span class="o">=</span> <span class="n">inferred_from</span><span class="o">.</span><span class="n">groups</span><span class="p">()[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span>
+
+            <span class="n">annot</span> <span class="o">=</span> <span class="n">record</span><span class="p">(</span>
+                <span class="n">role</span> <span class="o">=</span> <span class="n">role</span><span class="p">,</span>
+                <span class="n">family</span> <span class="o">=</span> <span class="n">family</span><span class="p">,</span>
+                <span class="nb">type</span> <span class="o">=</span> <span class="n">typ</span><span class="p">,</span>
+                <span class="n">inferred_from</span> <span class="o">=</span> <span class="n">inferred_from</span><span class="p">,</span>
+            <span class="p">)</span>
+
+            <span class="n">genesymbols</span> <span class="o">=</span> <span class="p">(</span>
+                <span class="n">rec</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">&#39;gene&#39;</span><span class="p">,</span> <span class="n">rec</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">&#39;preprogene&#39;</span><span class="p">))</span><span class="o">.</span>
+                <span class="n">strip</span><span class="p">(</span><span class="s1">&#39;[</span><span class="se">\&#39;</span><span class="s1">]&#39;</span><span class="p">)</span><span class="o">.</span>
+                <span class="n">split</span><span class="p">(</span><span class="s1">&#39;,&#39;</span><span class="p">)</span>
+            <span class="p">)</span>
+
+            <span class="k">for</span> <span class="n">gs</span> <span class="ow">in</span> <span class="n">genesymbols</span><span class="p">:</span>
+
+                <span class="n">components</span> <span class="o">=</span> <span class="n">gs</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;|&#39;</span><span class="p">)</span>
+
+                <span class="n">uniprots</span> <span class="o">=</span> <span class="p">[</span>
+                    <span class="n">mapping</span><span class="o">.</span><span class="n">map_name</span><span class="p">(</span>
+                        <span class="n">gs_comp</span><span class="o">.</span><span class="n">strip</span><span class="p">(),</span>
+                        <span class="s1">&#39;genesymbol&#39;</span><span class="p">,</span>
+                        <span class="s1">&#39;uniprot&#39;</span><span class="p">,</span>
+                        <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">,</span>
+                    <span class="p">)</span>
+                    <span class="k">for</span> <span class="n">gs_comp</span> <span class="ow">in</span> <span class="n">components</span>
+                <span class="p">]</span>
+
+                <span class="k">for</span> <span class="n">ups</span> <span class="ow">in</span> <span class="n">itertools</span><span class="o">.</span><span class="n">product</span><span class="p">(</span><span class="o">*</span><span class="n">uniprots</span><span class="p">):</span>
+
+                    <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">ups</span><span class="p">)</span> <span class="o">&gt;</span> <span class="mi">1</span><span class="p">:</span>
+
+                        <span class="n">cplex</span> <span class="o">=</span> <span class="n">intera</span><span class="o">.</span><span class="n">Complex</span><span class="p">(</span>
+                            <span class="n">components</span> <span class="o">=</span> <span class="n">ups</span><span class="p">,</span>
+                            <span class="n">sources</span> <span class="o">=</span> <span class="s1">&#39;scConnect&#39;</span><span class="p">,</span>
+                        <span class="p">)</span>
+
+                        <span class="n">result</span><span class="p">[</span><span class="n">cplex</span><span class="p">]</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">annot</span><span class="p">)</span>
+
+                    <span class="k">else</span><span class="p">:</span>
+
+                        <span class="n">result</span><span class="p">[</span><span class="n">ups</span><span class="p">[</span><span class="mi">0</span><span class="p">]]</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">annot</span><span class="p">)</span>
+
+    <span class="k">return</span> <span class="nb">dict</span><span class="p">(</span><span class="n">result</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="scconnect_complexes">
+<a class="viewcode-back" href="../../../api/pypath.inputs.scconnect.scconnect_complexes.html#pypath.inputs.scconnect.scconnect_complexes">[docs]</a>
+<span class="k">def</span> <span class="nf">scconnect_complexes</span><span class="p">(</span><span class="n">organism</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">):</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Protein complexes from scConnect</span>
+<span class="sd">    (https://github.com/JonETJakobsson/scConnect).</span>
+
+<span class="sd">    Args</span>
+<span class="sd">        organism (int,str): Name or identifier of the organism. Human, mouse,</span>
+<span class="sd">            fruitfly, zebrafish, chicken, C. elegans, Xenopus tropicalis,</span>
+<span class="sd">            yeast and Anolis carolinensis are available.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="n">annot</span> <span class="o">=</span> <span class="n">scconnect_annotations</span><span class="p">(</span><span class="n">organism</span> <span class="o">=</span> <span class="n">organism</span><span class="p">)</span>
+
+    <span class="k">return</span> <span class="p">{</span>
+        <span class="n">cplex</span>
+        <span class="k">for</span> <span class="n">cplex</span> <span class="ow">in</span> <span class="n">annot</span><span class="o">.</span><span class="n">keys</span><span class="p">()</span>
+        <span class="k">if</span> <span class="n">entity</span><span class="o">.</span><span class="n">Entity</span><span class="o">.</span><span class="n">_is_complex</span><span class="p">(</span><span class="n">cplex</span><span class="p">)</span>
+    <span class="p">}</span></div>
+
+
+
+<div class="viewcode-block" id="scconnect_interactions">
+<a class="viewcode-back" href="../../../api/pypath.inputs.scconnect.scconnect_interactions.html#pypath.inputs.scconnect.scconnect_interactions">[docs]</a>
+<span class="k">def</span> <span class="nf">scconnect_interactions</span><span class="p">():</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Ligand-receptor interactions from scConnect</span>
+<span class="sd">    (https://github.com/JonETJakobsson/scConnect).</span>
+
+<span class="sd">    Returns</span>
+<span class="sd">        (list): List of interactions, each represented as a named tuple.</span>
+<span class="sd">            Proteins and protein complexes are translated to UniProt IDs,</span>
+<span class="sd">            small molecule IDs are left intact.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+
+    <span class="k">def</span> <span class="nf">process_partner</span><span class="p">(</span><span class="n">rec</span><span class="p">,</span> <span class="n">partner</span><span class="p">):</span>
+
+        <span class="n">organisms</span> <span class="o">=</span> <span class="p">[</span>
+            <span class="n">taxonomy</span><span class="o">.</span><span class="n">ensure_ncbi_tax_id</span><span class="p">(</span><span class="n">org</span><span class="p">)</span>
+                <span class="k">if</span> <span class="n">org</span> <span class="ow">not</span> <span class="ow">in</span> <span class="p">{</span><span class="s1">&#39;&#39;</span><span class="p">,</span> <span class="s1">&#39;None&#39;</span><span class="p">,</span> <span class="s1">&#39;Unknown&#39;</span><span class="p">}</span> <span class="k">else</span>
+            <span class="n">_const</span><span class="o">.</span><span class="n">NOT_ORGANISM_SPECIFIC</span>
+            <span class="k">for</span> <span class="n">org</span> <span class="ow">in</span> <span class="n">rec</span><span class="p">[</span><span class="s1">&#39;</span><span class="si">%s</span><span class="s1">_species&#39;</span> <span class="o">%</span> <span class="n">partner</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;|&#39;</span><span class="p">)</span>
+        <span class="p">]</span>
+        <span class="n">id_field</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="s1">&#39;target_uniprot&#39;</span>
+                <span class="k">if</span> <span class="n">partner</span> <span class="o">==</span> <span class="s1">&#39;target&#39;</span> <span class="k">else</span>
+            <span class="s1">&#39;ligand_gene_symbol&#39;</span>
+        <span class="p">)</span>
+        <span class="n">id_type</span> <span class="o">=</span> <span class="s1">&#39;uniprot&#39;</span> <span class="k">if</span> <span class="n">partner</span> <span class="o">==</span> <span class="s1">&#39;target&#39;</span> <span class="k">else</span> <span class="s1">&#39;genesymbol&#39;</span>
+
+        <span class="k">for</span> <span class="n">organism</span> <span class="ow">in</span> <span class="nb">set</span><span class="p">(</span><span class="n">organisms</span><span class="p">):</span>
+
+            <span class="n">ids_raw</span> <span class="o">=</span> <span class="p">[</span>
+                <span class="n">_id</span>
+                <span class="k">for</span> <span class="n">_id</span><span class="p">,</span> <span class="n">_org</span> <span class="ow">in</span>
+                <span class="nb">zip</span><span class="p">(</span>
+                    <span class="n">rec</span><span class="p">[</span><span class="n">id_field</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;|&#39;</span><span class="p">),</span>
+                    <span class="n">organisms</span>
+                <span class="p">)</span>
+                <span class="k">if</span> <span class="n">_org</span> <span class="o">==</span> <span class="n">organism</span> <span class="ow">or</span> <span class="n">organism</span> <span class="ow">is</span> <span class="kc">None</span>
+            <span class="p">]</span>
+
+            <span class="n">ids</span> <span class="o">=</span> <span class="p">(</span>
+                <span class="p">[</span>
+                    <span class="n">mapping</span><span class="o">.</span><span class="n">map_name</span><span class="p">(</span>
+                        <span class="n">_id</span><span class="p">,</span>
+                        <span class="n">id_type</span><span class="p">,</span>
+                        <span class="s1">&#39;uniprot&#39;</span><span class="p">,</span>
+                        <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">organism</span><span class="p">,</span>
+                    <span class="p">)</span>
+                    <span class="k">for</span> <span class="n">_id</span> <span class="ow">in</span> <span class="n">ids_raw</span>
+                <span class="p">]</span>
+                    <span class="k">if</span> <span class="n">organism</span> <span class="k">else</span>
+                <span class="p">[(</span><span class="n">rec</span><span class="p">[</span><span class="n">partner</span><span class="p">],)]</span>
+            <span class="p">)</span>
+
+            <span class="n">ids</span> <span class="o">=</span> <span class="p">[</span>
+                <span class="p">(</span>
+                    <span class="p">(</span>
+                        <span class="n">intera</span><span class="o">.</span><span class="n">Complex</span><span class="p">(</span>
+                            <span class="n">components</span> <span class="o">=</span> <span class="n">_ids</span><span class="p">,</span>
+                            <span class="n">sources</span> <span class="o">=</span> <span class="s1">&#39;scConnect&#39;</span><span class="p">,</span>
+                        <span class="p">),</span>
+                        <span class="s1">&#39;complex&#39;</span><span class="p">,</span>
+                    <span class="p">)</span>
+                        <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">_ids</span><span class="p">)</span> <span class="o">&gt;</span> <span class="mi">1</span> <span class="k">else</span>
+                    <span class="p">(</span>
+                        <span class="n">_ids</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span>
+                        <span class="s1">&#39;protein&#39;</span> <span class="k">if</span> <span class="n">organism</span> <span class="k">else</span> <span class="s1">&#39;small_molecule&#39;</span><span class="p">,</span>
+                    <span class="p">)</span>
+                <span class="p">)</span>
+                <span class="k">for</span> <span class="n">_ids</span> <span class="ow">in</span> <span class="n">itertools</span><span class="o">.</span><span class="n">product</span><span class="p">(</span><span class="o">*</span><span class="n">ids</span><span class="p">)</span>
+            <span class="p">]</span>
+
+            <span class="k">for</span> <span class="n">_id</span><span class="p">,</span> <span class="n">entity_type</span> <span class="ow">in</span> <span class="n">ids</span><span class="p">:</span>
+
+                <span class="k">yield</span> <span class="n">_id</span><span class="p">,</span> <span class="n">entity_type</span><span class="p">,</span> <span class="n">organism</span>
+
+
+    <span class="n">url</span> <span class="o">=</span> <span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;scconnect&#39;</span><span class="p">][</span><span class="s1">&#39;intera&#39;</span><span class="p">]</span>
+    <span class="n">c</span> <span class="o">=</span> <span class="n">curl</span><span class="o">.</span><span class="n">Curl</span><span class="p">(</span><span class="n">url</span><span class="p">,</span> <span class="n">silent</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span> <span class="n">large</span> <span class="o">=</span> <span class="kc">True</span><span class="p">)</span>
+    <span class="n">tab</span> <span class="o">=</span> <span class="n">csv</span><span class="o">.</span><span class="n">DictReader</span><span class="p">(</span><span class="n">c</span><span class="o">.</span><span class="n">result</span><span class="p">)</span>
+
+    <span class="n">record</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">namedtuple</span><span class="p">(</span>
+        <span class="s1">&#39;ScconnectInteraction&#39;</span><span class="p">,</span>
+        <span class="p">(</span>
+            <span class="s1">&#39;ligand_id&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;target_id&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;ligand_organism&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;target_organism&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;ligand_type&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;target_type&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;effect&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;references&#39;</span><span class="p">,</span>
+        <span class="p">),</span>
+    <span class="p">)</span>
+
+    <span class="n">result</span> <span class="o">=</span> <span class="p">[]</span>
+
+    <span class="k">for</span> <span class="n">rec</span> <span class="ow">in</span> <span class="n">tab</span><span class="p">:</span>
+
+        <span class="n">targets</span> <span class="o">=</span> <span class="n">process_partner</span><span class="p">(</span><span class="n">rec</span><span class="p">,</span> <span class="s1">&#39;target&#39;</span><span class="p">)</span>
+        <span class="n">ligands</span> <span class="o">=</span> <span class="n">process_partner</span><span class="p">(</span><span class="n">rec</span><span class="p">,</span> <span class="s1">&#39;ligand&#39;</span><span class="p">)</span>
+
+        <span class="k">for</span> <span class="n">ligand_target</span> <span class="ow">in</span> <span class="n">itertools</span><span class="o">.</span><span class="n">product</span><span class="p">(</span><span class="n">ligands</span><span class="p">,</span> <span class="n">targets</span><span class="p">):</span>
+
+            <span class="p">(</span>
+                <span class="p">(</span><span class="n">ligand</span><span class="p">,</span> <span class="n">ligand_type</span><span class="p">,</span> <span class="n">ligand_organism</span><span class="p">),</span>
+                <span class="p">(</span><span class="n">target</span><span class="p">,</span> <span class="n">target_type</span><span class="p">,</span> <span class="n">target_organism</span><span class="p">)</span>
+            <span class="p">)</span> <span class="o">=</span> <span class="n">ligand_target</span>
+
+            <span class="n">result</span><span class="o">.</span><span class="n">append</span><span class="p">(</span>
+                <span class="n">record</span><span class="p">(</span>
+                    <span class="n">ligand_id</span> <span class="o">=</span> <span class="n">ligand</span><span class="p">,</span>
+                    <span class="n">target_id</span> <span class="o">=</span> <span class="n">target</span><span class="p">,</span>
+                    <span class="n">ligand_organism</span> <span class="o">=</span> <span class="n">ligand_organism</span><span class="p">,</span>
+                    <span class="n">target_organism</span> <span class="o">=</span> <span class="n">target_organism</span><span class="p">,</span>
+                    <span class="n">ligand_type</span> <span class="o">=</span> <span class="n">ligand_type</span><span class="p">,</span>
+                    <span class="n">target_type</span> <span class="o">=</span> <span class="n">target_type</span><span class="p">,</span>
+                    <span class="n">effect</span> <span class="o">=</span> <span class="n">rec</span><span class="p">[</span><span class="s1">&#39;action&#39;</span><span class="p">],</span>
+                    <span class="n">references</span> <span class="o">=</span> <span class="n">rec</span><span class="p">[</span><span class="s1">&#39;pubmed_id&#39;</span><span class="p">],</span>
+                <span class="p">)</span>
+            <span class="p">)</span>
+
+    <span class="k">return</span> <span class="n">result</span></div>
+
+</pre></div>
+
+                </article>
+              
+              
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diff --git a/_modules/pypath/inputs/signalink.html b/_modules/pypath/inputs/signalink.html
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+                  
+  <h1>Source code for pypath.inputs.signalink</h1><div class="highlight"><pre>
+<span></span><span class="ch">#!/usr/bin/env python</span>
+<span class="c1"># -*- coding: utf-8 -*-</span>
+
+<span class="c1">#</span>
+<span class="c1">#  This file is part of the `pypath` python module</span>
+<span class="c1">#</span>
+<span class="c1">#  Copyright 2014-2023</span>
+<span class="c1">#  EMBL, EMBL-EBI, Uniklinik RWTH Aachen, Heidelberg University</span>
+<span class="c1">#</span>
+<span class="c1">#  Authors: see the file `README.rst`</span>
+<span class="c1">#  Contact: Dénes Türei (turei.denes@gmail.com)</span>
+<span class="c1">#</span>
+<span class="c1">#  Distributed under the GPLv3 License.</span>
+<span class="c1">#  See accompanying file LICENSE.txt or copy at</span>
+<span class="c1">#      https://www.gnu.org/licenses/gpl-3.0.html</span>
+<span class="c1">#</span>
+<span class="c1">#  Website: https://pypath.omnipathdb.org/</span>
+<span class="c1">#</span>
+
+<span class="kn">from</span> <span class="nn">future.utils</span> <span class="kn">import</span> <span class="n">iteritems</span>
+
+<span class="kn">import</span> <span class="nn">sys</span>
+<span class="kn">import</span> <span class="nn">re</span>
+<span class="kn">import</span> <span class="nn">collections</span>
+<span class="kn">import</span> <span class="nn">itertools</span>
+
+<span class="kn">import</span> <span class="nn">pypath.share.curl</span> <span class="k">as</span> <span class="nn">curl</span>
+<span class="kn">import</span> <span class="nn">pypath.resources.urls</span> <span class="k">as</span> <span class="nn">urls</span>
+<span class="kn">import</span> <span class="nn">pypath.share.common</span> <span class="k">as</span> <span class="nn">common</span>
+<span class="kn">import</span> <span class="nn">pypath.utils.mapping</span> <span class="k">as</span> <span class="nn">mapping</span>
+
+
+<div class="viewcode-block" id="signalink_interactions">
+<a class="viewcode-back" href="../../../api/pypath.inputs.signalink.signalink_interactions.html#pypath.inputs.signalink.signalink_interactions">[docs]</a>
+<span class="k">def</span> <span class="nf">signalink_interactions</span><span class="p">(</span><span class="n">organism</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">,</span> <span class="n">exclude_secondary</span> <span class="o">=</span> <span class="kc">True</span><span class="p">):</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Reads and processes SignaLink3 interactions from local file.</span>
+<span class="sd">    Returns list of interactions.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="n">SignalinkInteraction</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">namedtuple</span><span class="p">(</span>
+        <span class="s1">&#39;SignalinkInteraction&#39;</span><span class="p">,</span>
+        <span class="p">[</span>
+            <span class="s1">&#39;id_a&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;id_b&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;is_direct&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;is_directed&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;effect&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;pathways_a&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;pathways_b&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;functions_a&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;functions_b&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;references&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;resources&#39;</span><span class="p">,</span>
+        <span class="p">]</span>
+    <span class="p">)</span>
+
+    <span class="n">signalink_sources</span> <span class="o">=</span> <span class="p">{</span>
+        <span class="s1">&#39;SLKv2.0&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;SLKv2.1&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;SLKv3.0&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;SignaFish&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;TCRcuration&#39;</span><span class="p">,</span>
+    <span class="p">}</span>
+    <span class="n">repref</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">compile</span><span class="p">(</span><span class="sa">r</span><span class="s1">&#39;(?:.*:)?((?:[\w]+[^\s])?)\s?&#39;</span><span class="p">)</span>
+    <span class="n">nodes_pathways</span> <span class="o">=</span> <span class="p">{}</span>
+    <span class="n">nodes_organism</span> <span class="o">=</span> <span class="p">{}</span>
+    <span class="n">nodes_functions</span> <span class="o">=</span> <span class="p">{}</span>
+    <span class="n">interactions</span> <span class="o">=</span> <span class="p">[]</span>
+
+
+    <span class="k">def</span> <span class="nf">get_value</span><span class="p">(</span><span class="n">field</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="n">repref</span><span class="o">.</span><span class="n">sub</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\\</span><span class="s1">1&#39;</span><span class="p">,</span> <span class="n">field</span><span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">get_values</span><span class="p">(</span><span class="n">field</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="p">[</span><span class="n">get_value</span><span class="p">(</span><span class="n">f</span><span class="p">)</span> <span class="k">for</span> <span class="n">f</span> <span class="ow">in</span> <span class="n">field</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;|&#39;</span><span class="p">)]</span>
+
+
+    <span class="n">url_nodes</span> <span class="o">=</span> <span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;signalink&#39;</span><span class="p">][</span><span class="s1">&#39;nodes&#39;</span><span class="p">]</span>
+    <span class="n">c_nodes</span> <span class="o">=</span> <span class="n">curl</span><span class="o">.</span><span class="n">Curl</span><span class="p">(</span><span class="n">url_nodes</span><span class="p">,</span> <span class="n">silent</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span> <span class="n">large</span> <span class="o">=</span> <span class="kc">True</span><span class="p">)</span>
+    <span class="n">url_edges</span> <span class="o">=</span> <span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;signalink&#39;</span><span class="p">][</span><span class="s1">&#39;edges&#39;</span><span class="p">]</span>
+    <span class="n">c_edges</span> <span class="o">=</span> <span class="n">curl</span><span class="o">.</span><span class="n">Curl</span><span class="p">(</span><span class="n">url_edges</span><span class="p">,</span> <span class="n">silent</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span> <span class="n">large</span> <span class="o">=</span> <span class="kc">True</span><span class="p">)</span>
+
+    <span class="n">_</span> <span class="o">=</span> <span class="nb">next</span><span class="p">(</span><span class="n">c_nodes</span><span class="o">.</span><span class="n">result</span><span class="p">)</span>
+
+    <span class="k">for</span> <span class="n">l</span> <span class="ow">in</span> <span class="n">c_nodes</span><span class="o">.</span><span class="n">result</span><span class="p">:</span>
+
+        <span class="n">l</span> <span class="o">=</span> <span class="n">l</span><span class="o">.</span><span class="n">strip</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\n\r</span><span class="s1">&#39;</span><span class="p">)</span>
+
+        <span class="k">if</span> <span class="n">l</span><span class="p">:</span>
+
+            <span class="n">l</span> <span class="o">=</span> <span class="n">l</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\t</span><span class="s1">&#39;</span><span class="p">)</span>
+            <span class="n">_id</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">l</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span>
+            <span class="n">uniprot</span> <span class="o">=</span> <span class="n">get_value</span><span class="p">(</span><span class="n">l</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span>
+            <span class="n">pathways</span> <span class="o">=</span> <span class="p">(</span>
+                <span class="n">l</span><span class="p">[</span><span class="mi">4</span><span class="p">]</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s1">&#39;/Wingless&#39;</span><span class="p">,</span> <span class="s1">&#39;&#39;</span><span class="p">)</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;|&#39;</span><span class="p">)</span> <span class="k">if</span> <span class="n">l</span><span class="p">[</span><span class="mi">4</span><span class="p">]</span> <span class="k">else</span> <span class="p">[]</span>
+            <span class="p">)</span>
+            <span class="n">_organism</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">get_value</span><span class="p">(</span><span class="n">l</span><span class="p">[</span><span class="mi">3</span><span class="p">]))</span>
+            <span class="n">nodes_pathways</span><span class="p">[</span><span class="n">uniprot</span><span class="p">]</span> <span class="o">=</span> <span class="n">pathways</span>
+            <span class="n">nodes_organism</span><span class="p">[</span><span class="n">uniprot</span><span class="p">]</span> <span class="o">=</span> <span class="n">_organism</span>
+            <span class="n">nodes_functions</span><span class="p">[</span><span class="n">uniprot</span><span class="p">]</span> <span class="o">=</span> <span class="n">l</span><span class="p">[</span><span class="mi">6</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;|&#39;</span><span class="p">)</span> <span class="k">if</span> <span class="n">l</span><span class="p">[</span><span class="mi">6</span><span class="p">]</span> <span class="k">else</span> <span class="p">[]</span>
+
+    <span class="n">_</span> <span class="o">=</span> <span class="nb">next</span><span class="p">(</span><span class="n">c_edges</span><span class="o">.</span><span class="n">result</span><span class="p">)</span>
+
+    <span class="k">for</span> <span class="n">l</span> <span class="ow">in</span> <span class="n">c_edges</span><span class="o">.</span><span class="n">result</span><span class="p">:</span>
+
+        <span class="n">l</span> <span class="o">=</span> <span class="n">l</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\t</span><span class="s1">&#39;</span><span class="p">)</span>
+
+        <span class="k">if</span> <span class="n">exclude_secondary</span> <span class="ow">and</span> <span class="ow">not</span> <span class="nb">set</span><span class="p">(</span><span class="n">l</span><span class="p">[</span><span class="mi">6</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;|&#39;</span><span class="p">))</span> <span class="o">&amp;</span> <span class="n">signalink_sources</span><span class="p">:</span>
+
+            <span class="k">continue</span>
+
+        <span class="n">id_a</span> <span class="o">=</span> <span class="n">get_value</span><span class="p">(</span><span class="n">l</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span>
+        <span class="n">id_b</span> <span class="o">=</span> <span class="n">get_value</span><span class="p">(</span><span class="n">l</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span>
+
+        <span class="k">if</span> <span class="p">(</span>
+            <span class="n">nodes_organism</span><span class="p">[</span><span class="n">id_a</span><span class="p">]</span> <span class="o">!=</span> <span class="n">organism</span> <span class="ow">or</span>
+            <span class="n">nodes_organism</span><span class="p">[</span><span class="n">id_b</span><span class="p">]</span> <span class="o">!=</span> <span class="n">organism</span>
+        <span class="p">):</span>
+            <span class="k">continue</span>
+
+        <span class="n">resources</span> <span class="o">=</span> <span class="p">[</span>
+            <span class="n">res</span> <span class="k">for</span> <span class="n">res</span> <span class="ow">in</span> <span class="n">get_values</span><span class="p">(</span><span class="n">l</span><span class="p">[</span><span class="mi">6</span><span class="p">])</span>
+            <span class="k">if</span> <span class="ow">not</span> <span class="n">res</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s1">&#39;SLK&#39;</span><span class="p">)</span>
+        <span class="p">]</span>
+
+        <span class="n">interaction_attrs</span> <span class="o">=</span> <span class="p">{</span>
+            <span class="nb">tuple</span><span class="p">(</span><span class="n">iattr</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;:&#39;</span><span class="p">))</span>
+            <span class="k">for</span> <span class="n">iattr</span> <span class="ow">in</span> <span class="n">l</span><span class="p">[</span><span class="mi">5</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;|&#39;</span><span class="p">)</span>
+        <span class="p">}</span>
+
+        <span class="n">effects</span> <span class="o">=</span> <span class="p">[]</span>
+
+        <span class="k">if</span> <span class="p">(</span><span class="s1">&#39;MI&#39;</span><span class="p">,</span> <span class="s1">&#39;0624(stimulation)&#39;</span><span class="p">)</span> <span class="ow">in</span> <span class="n">interaction_attrs</span><span class="p">:</span>
+
+            <span class="n">effects</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="mi">1</span><span class="p">)</span>
+
+        <span class="k">if</span> <span class="p">(</span><span class="s1">&#39;MI&#39;</span><span class="p">,</span> <span class="s1">&#39;0623(inhibition)&#39;</span><span class="p">)</span> <span class="ow">in</span> <span class="n">interaction_attrs</span><span class="p">:</span>
+
+            <span class="n">effects</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="o">-</span><span class="mi">1</span><span class="p">)</span>
+
+        <span class="k">if</span> <span class="ow">not</span> <span class="n">effects</span><span class="p">:</span>
+
+            <span class="n">effects</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="mi">0</span><span class="p">)</span>
+
+        <span class="k">for</span> <span class="n">effect</span> <span class="ow">in</span> <span class="n">effects</span><span class="p">:</span>
+
+            <span class="n">interactions</span><span class="o">.</span><span class="n">append</span><span class="p">(</span>
+                <span class="n">SignalinkInteraction</span><span class="p">(</span>
+                    <span class="n">id_a</span> <span class="o">=</span> <span class="n">id_a</span><span class="p">,</span>
+                    <span class="n">id_b</span> <span class="o">=</span> <span class="n">id_b</span><span class="p">,</span>
+                    <span class="n">is_direct</span> <span class="o">=</span> <span class="p">(</span><span class="s1">&#39;is_direct&#39;</span><span class="p">,</span> <span class="s1">&#39;true&#39;</span><span class="p">)</span> <span class="ow">in</span> <span class="n">interaction_attrs</span><span class="p">,</span>
+                    <span class="n">is_directed</span> <span class="o">=</span> <span class="p">(</span><span class="s1">&#39;is_directed&#39;</span><span class="p">,</span> <span class="s1">&#39;true&#39;</span><span class="p">)</span> <span class="ow">in</span> <span class="n">interaction_attrs</span><span class="p">,</span>
+                    <span class="n">effect</span> <span class="o">=</span> <span class="n">effect</span><span class="p">,</span>
+                    <span class="n">pathways_a</span> <span class="o">=</span> <span class="n">nodes_pathways</span><span class="p">[</span><span class="n">id_a</span><span class="p">],</span>
+                    <span class="n">pathways_b</span> <span class="o">=</span> <span class="n">nodes_pathways</span><span class="p">[</span><span class="n">id_b</span><span class="p">],</span>
+                    <span class="n">functions_a</span> <span class="o">=</span> <span class="n">nodes_functions</span><span class="p">[</span><span class="n">id_a</span><span class="p">],</span>
+                    <span class="n">functions_b</span> <span class="o">=</span> <span class="n">nodes_functions</span><span class="p">[</span><span class="n">id_b</span><span class="p">],</span>
+                    <span class="n">references</span> <span class="o">=</span> <span class="n">get_values</span><span class="p">(</span><span class="n">l</span><span class="p">[</span><span class="mi">4</span><span class="p">]),</span>
+                    <span class="n">resources</span> <span class="o">=</span> <span class="n">resources</span><span class="p">,</span>
+                <span class="p">)</span>
+            <span class="p">)</span>
+
+    <span class="k">return</span> <span class="n">interactions</span></div>
+
+
+
+<div class="viewcode-block" id="signalink_annotations">
+<a class="viewcode-back" href="../../../api/pypath.inputs.signalink.signalink_annotations.html#pypath.inputs.signalink.signalink_annotations">[docs]</a>
+<span class="k">def</span> <span class="nf">signalink_annotations</span><span class="p">(</span><span class="n">organism</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">):</span>
+
+    <span class="n">SignalinkPathway</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">namedtuple</span><span class="p">(</span>
+        <span class="s1">&#39;SignalinkPathway&#39;</span><span class="p">,</span>
+        <span class="p">[</span>
+            <span class="s1">&#39;pathway&#39;</span><span class="p">,</span>
+        <span class="p">]</span>
+    <span class="p">)</span>
+
+    <span class="n">SignalinkFunction</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">namedtuple</span><span class="p">(</span>
+        <span class="s1">&#39;SignalinkFunction&#39;</span><span class="p">,</span>
+        <span class="p">[</span>
+            <span class="s1">&#39;function&#39;</span><span class="p">,</span>
+        <span class="p">]</span>
+    <span class="p">)</span>
+
+
+    <span class="n">result</span> <span class="o">=</span> <span class="p">{</span>
+        <span class="s1">&#39;pathway&#39;</span><span class="p">:</span> <span class="n">collections</span><span class="o">.</span><span class="n">defaultdict</span><span class="p">(</span><span class="nb">set</span><span class="p">),</span>
+        <span class="s1">&#39;function&#39;</span><span class="p">:</span> <span class="n">collections</span><span class="o">.</span><span class="n">defaultdict</span><span class="p">(</span><span class="nb">set</span><span class="p">),</span>
+    <span class="p">}</span>
+
+    <span class="n">interactions</span> <span class="o">=</span> <span class="n">signalink_interactions</span><span class="p">(</span><span class="n">organism</span> <span class="o">=</span> <span class="n">organism</span><span class="p">)</span>
+
+    <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="n">interactions</span><span class="p">:</span>
+
+        <span class="k">for</span> <span class="n">postfix</span> <span class="ow">in</span> <span class="p">(</span><span class="s1">&#39;_a&#39;</span><span class="p">,</span> <span class="s1">&#39;_b&#39;</span><span class="p">):</span>
+
+            <span class="n">_id</span> <span class="o">=</span> <span class="nb">getattr</span><span class="p">(</span><span class="n">i</span><span class="p">,</span> <span class="s1">&#39;id</span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="n">postfix</span><span class="p">)</span>
+
+            <span class="k">for</span> <span class="n">uniprot</span> <span class="ow">in</span> <span class="n">mapping</span><span class="o">.</span><span class="n">map_name</span><span class="p">(</span><span class="n">_id</span><span class="p">,</span> <span class="s1">&#39;uniprot&#39;</span><span class="p">,</span> <span class="s1">&#39;uniprot&#39;</span><span class="p">):</span>
+
+                <span class="k">for</span> <span class="n">attr</span><span class="p">,</span> <span class="n">record</span> <span class="ow">in</span> <span class="nb">zip</span><span class="p">(</span>
+                    <span class="p">(</span><span class="s1">&#39;pathway&#39;</span><span class="p">,</span> <span class="s1">&#39;function&#39;</span><span class="p">),</span>
+                    <span class="p">(</span><span class="n">SignalinkPathway</span><span class="p">,</span> <span class="n">SignalinkFunction</span><span class="p">),</span>
+                <span class="p">):</span>
+
+                    <span class="n">values</span> <span class="o">=</span> <span class="nb">getattr</span><span class="p">(</span><span class="n">i</span><span class="p">,</span> <span class="s1">&#39;</span><span class="si">%s</span><span class="s1">s</span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="p">(</span><span class="n">attr</span><span class="p">,</span> <span class="n">postfix</span><span class="p">))</span>
+
+                    <span class="k">for</span> <span class="n">value</span> <span class="ow">in</span> <span class="n">values</span><span class="p">:</span>
+
+                        <span class="n">result</span><span class="p">[</span><span class="n">attr</span><span class="p">][</span><span class="n">uniprot</span><span class="p">]</span><span class="o">.</span><span class="n">add</span><span class="p">(</span>
+                            <span class="n">record</span><span class="p">(</span><span class="n">value</span><span class="p">)</span>
+                        <span class="p">)</span>
+
+    <span class="k">return</span> <span class="nb">dict</span><span class="p">((</span><span class="n">k</span><span class="p">,</span> <span class="nb">dict</span><span class="p">(</span><span class="n">v</span><span class="p">))</span> <span class="k">for</span> <span class="n">k</span><span class="p">,</span> <span class="n">v</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="n">result</span><span class="p">))</span></div>
+
+
+
+<div class="viewcode-block" id="signalink_pathway_annotations">
+<a class="viewcode-back" href="../../../api/pypath.inputs.signalink.signalink_pathway_annotations.html#pypath.inputs.signalink.signalink_pathway_annotations">[docs]</a>
+<span class="k">def</span> <span class="nf">signalink_pathway_annotations</span><span class="p">(</span><span class="n">organism</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">):</span>
+
+    <span class="k">return</span> <span class="n">signalink_annotations</span><span class="p">(</span><span class="n">organism</span> <span class="o">=</span> <span class="n">organism</span><span class="p">)[</span><span class="s1">&#39;pathway&#39;</span><span class="p">]</span></div>
+
+
+
+<div class="viewcode-block" id="signalink_function_annotations">
+<a class="viewcode-back" href="../../../api/pypath.inputs.signalink.signalink_function_annotations.html#pypath.inputs.signalink.signalink_function_annotations">[docs]</a>
+<span class="k">def</span> <span class="nf">signalink_function_annotations</span><span class="p">(</span><span class="n">organism</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">):</span>
+
+    <span class="k">return</span> <span class="n">signalink_annotations</span><span class="p">(</span><span class="n">organism</span> <span class="o">=</span> <span class="n">organism</span><span class="p">)[</span><span class="s1">&#39;function&#39;</span><span class="p">]</span></div>
+
+</pre></div>
+
+                </article>
+              
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+                <article class="bd-article">
+                  
+  <h1>Source code for pypath.inputs.signor</h1><div class="highlight"><pre>
+<span></span><span class="ch">#!/usr/bin/env python</span>
+<span class="c1"># -*- coding: utf-8 -*-</span>
+
+<span class="c1">#</span>
+<span class="c1">#  This file is part of the `pypath` python module</span>
+<span class="c1">#</span>
+<span class="c1">#  Copyright 2014-2023</span>
+<span class="c1">#  EMBL, EMBL-EBI, Uniklinik RWTH Aachen, Heidelberg University</span>
+<span class="c1">#</span>
+<span class="c1">#  Authors: see the file `README.rst`</span>
+<span class="c1">#  Contact: Dénes Türei (turei.denes@gmail.com)</span>
+<span class="c1">#</span>
+<span class="c1">#  Distributed under the GPLv3 License.</span>
+<span class="c1">#  See accompanying file LICENSE.txt or copy at</span>
+<span class="c1">#      https://www.gnu.org/licenses/gpl-3.0.html</span>
+<span class="c1">#</span>
+<span class="c1">#  Website: https://pypath.omnipathdb.org/</span>
+<span class="c1">#</span>
+
+<span class="kn">from</span> <span class="nn">future.utils</span> <span class="kn">import</span> <span class="n">iteritems</span>
+
+<span class="kn">import</span> <span class="nn">sys</span>
+<span class="kn">import</span> <span class="nn">re</span>
+<span class="kn">import</span> <span class="nn">collections</span>
+<span class="kn">import</span> <span class="nn">itertools</span>
+<span class="kn">import</span> <span class="nn">bs4</span>
+<span class="kn">import</span> <span class="nn">csv</span>
+
+<span class="kn">import</span> <span class="nn">pypath.inputs.common</span> <span class="k">as</span> <span class="nn">inputs_common</span>
+<span class="kn">import</span> <span class="nn">pypath.share.progress</span> <span class="k">as</span> <span class="nn">progress</span>
+<span class="kn">import</span> <span class="nn">pypath.utils.taxonomy</span> <span class="k">as</span> <span class="nn">taxonomy</span>
+<span class="kn">import</span> <span class="nn">pypath.utils.mapping</span> <span class="k">as</span> <span class="nn">mapping</span>
+<span class="kn">import</span> <span class="nn">pypath.internals.intera</span> <span class="k">as</span> <span class="nn">intera</span>
+<span class="kn">import</span> <span class="nn">pypath.share.curl</span> <span class="k">as</span> <span class="nn">curl</span>
+<span class="kn">import</span> <span class="nn">pypath.resources.urls</span> <span class="k">as</span> <span class="nn">urls</span>
+<span class="kn">import</span> <span class="nn">pypath.share.common</span> <span class="k">as</span> <span class="nn">common</span>
+
+
+<div class="viewcode-block" id="signor_interactions">
+<a class="viewcode-back" href="../../../api/pypath.inputs.signor.signor_interactions.html#pypath.inputs.signor.signor_interactions">[docs]</a>
+<span class="k">def</span> <span class="nf">signor_interactions</span><span class="p">(</span>
+    <span class="n">organism</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">,</span>
+    <span class="n">raw_records</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+    <span class="n">expand_families</span> <span class="o">=</span> <span class="mi">0</span>
+<span class="p">):</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Downloads the full dataset from SIGNOR (https://signor.uniroma2.it/).</span>
+<span class="sd">    Returns the records with the most important fields.</span>
+<span class="sd">    If ``raw_records`` is `True` it returns the table split to list of</span>
+<span class="sd">    lists but unchanged content.</span>
+
+<span class="sd">    Args</span>
+<span class="sd">        organism (int, str): The NCBI Taxonomy ID or name of the organism.</span>
+<span class="sd">            Human (9606), mouse (10090) and rat (10116) are available.</span>
+<span class="sd">        raw_records (bool): Process the records or return them raw,</span>
+<span class="sd">            as they are.</span>
+<span class="sd">        expand_families (int): Expand protein families up to this size.</span>
+<span class="sd">            Zero or one means no expansion.</span>
+
+<span class="sd">    Return</span>
+<span class="sd">        list: A list with processed records as named tuples or dicts of</span>
+<span class="sd">            raw records if ``raw_records`` is True.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+
+    <span class="k">def</span> <span class="nf">process_name</span><span class="p">(</span><span class="n">name</span><span class="p">):</span>
+
+        <span class="n">isoform</span> <span class="o">=</span> <span class="kc">None</span>
+
+        <span class="k">if</span> <span class="n">name</span> <span class="ow">in</span> <span class="n">families</span><span class="p">:</span>
+
+            <span class="n">main</span> <span class="o">=</span> <span class="p">(</span>
+                <span class="n">families</span><span class="p">[</span><span class="n">name</span><span class="p">]</span>
+                    <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">families</span><span class="p">[</span><span class="n">name</span><span class="p">])</span> <span class="o">&lt;=</span> <span class="n">expand_families</span> <span class="k">else</span>
+                <span class="p">()</span>
+            <span class="p">)</span>
+
+        <span class="k">elif</span> <span class="n">name</span> <span class="ow">in</span> <span class="n">complexes_by_id</span><span class="p">:</span>
+
+            <span class="n">main</span> <span class="o">=</span> <span class="n">complexes_by_id</span><span class="p">[</span><span class="n">name</span><span class="p">]</span>
+
+        <span class="k">else</span><span class="p">:</span>
+
+            <span class="n">main</span><span class="p">,</span> <span class="n">isoform</span> <span class="o">=</span> <span class="n">inputs_common</span><span class="o">.</span><span class="n">_try_isoform</span><span class="p">(</span><span class="n">name</span><span class="p">)</span>
+            <span class="n">main</span> <span class="o">=</span> <span class="p">(</span><span class="n">main</span><span class="p">,)</span>
+
+        <span class="k">return</span> <span class="n">main</span><span class="p">,</span> <span class="n">isoform</span>
+
+
+    <span class="n">SignorInteraction</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">namedtuple</span><span class="p">(</span>
+        <span class="s1">&#39;SignorInteraction&#39;</span><span class="p">,</span>
+        <span class="p">(</span>
+            <span class="s1">&#39;source&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;target&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;source_isoform&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;target_isoform&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;source_type&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;target_type&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;effect&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;mechanism&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;ncbi_tax_id&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;pubmeds&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;direct&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;ptm_type&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;ptm_residue&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;ptm_motif&#39;</span><span class="p">,</span>
+        <span class="p">)</span>
+    <span class="p">)</span>
+
+    <span class="n">families</span> <span class="o">=</span> <span class="n">signor_protein_families</span><span class="p">(</span><span class="n">organism</span> <span class="o">=</span> <span class="n">organism</span><span class="p">)</span>
+    <span class="n">complexes</span> <span class="o">=</span> <span class="n">signor_complexes</span><span class="p">(</span><span class="n">organism</span> <span class="o">=</span> <span class="n">organism</span><span class="p">)</span>
+
+    <span class="n">complexes_by_id</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">defaultdict</span><span class="p">(</span><span class="nb">set</span><span class="p">)</span>
+
+    <span class="k">for</span> <span class="n">cplex</span> <span class="ow">in</span> <span class="n">complexes</span><span class="o">.</span><span class="n">values</span><span class="p">():</span>
+
+        <span class="k">for</span> <span class="n">cplex_id</span> <span class="ow">in</span> <span class="n">cplex</span><span class="o">.</span><span class="n">ids</span><span class="p">[</span><span class="s1">&#39;SIGNOR&#39;</span><span class="p">]:</span>
+
+            <span class="n">complexes_by_id</span><span class="p">[</span><span class="n">cplex_id</span><span class="p">]</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">cplex</span><span class="p">)</span>
+
+    <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">organism</span><span class="p">,</span> <span class="nb">int</span><span class="p">):</span>
+
+        <span class="k">if</span> <span class="n">organism</span> <span class="ow">in</span> <span class="n">taxonomy</span><span class="o">.</span><span class="n">taxids</span><span class="p">:</span>
+
+            <span class="n">_organism</span> <span class="o">=</span> <span class="n">taxonomy</span><span class="o">.</span><span class="n">taxids</span><span class="p">[</span><span class="n">organism</span><span class="p">]</span>
+
+        <span class="k">else</span><span class="p">:</span>
+
+            <span class="n">sys</span><span class="o">.</span><span class="n">stdout</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\t</span><span class="s1">:: Unknown organism: `</span><span class="si">%u</span><span class="s1">`.</span><span class="se">\n</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="n">organism</span><span class="p">)</span>
+            <span class="k">return</span> <span class="p">[]</span>
+
+    <span class="k">else</span><span class="p">:</span>
+
+        <span class="n">_organism</span> <span class="o">=</span> <span class="n">organism</span>
+
+    <span class="k">if</span> <span class="n">_organism</span> <span class="ow">not</span> <span class="ow">in</span> <span class="p">{</span><span class="s1">&#39;human&#39;</span><span class="p">,</span> <span class="s1">&#39;rat&#39;</span><span class="p">,</span> <span class="s1">&#39;mouse&#39;</span><span class="p">}:</span>
+
+        <span class="k">return</span> <span class="p">[]</span>
+
+    <span class="n">url</span> <span class="o">=</span> <span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;signor&#39;</span><span class="p">][</span><span class="s1">&#39;all_url_new&#39;</span><span class="p">]</span>
+    <span class="n">binary_data</span> <span class="o">=</span> <span class="p">[</span>
+        <span class="p">(</span><span class="sa">b</span><span class="s1">&#39;organism&#39;</span><span class="p">,</span> <span class="n">_organism</span><span class="o">.</span><span class="n">encode</span><span class="p">(</span><span class="s1">&#39;utf-8&#39;</span><span class="p">)),</span>
+        <span class="p">(</span><span class="sa">b</span><span class="s1">&#39;format&#39;</span><span class="p">,</span> <span class="sa">b</span><span class="s1">&#39;csv&#39;</span><span class="p">),</span>
+        <span class="p">(</span><span class="sa">b</span><span class="s1">&#39;submit&#39;</span><span class="p">,</span> <span class="sa">b</span><span class="s1">&#39;Download&#39;</span><span class="p">),</span>
+    <span class="p">]</span>
+
+    <span class="n">c</span> <span class="o">=</span> <span class="n">curl</span><span class="o">.</span><span class="n">Curl</span><span class="p">(</span>
+        <span class="n">url</span><span class="p">,</span>
+        <span class="n">silent</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+        <span class="n">large</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
+        <span class="n">follow</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
+        <span class="n">timeout</span> <span class="o">=</span> <span class="mi">180</span><span class="p">,</span>
+        <span class="n">binary_data</span> <span class="o">=</span> <span class="n">binary_data</span><span class="p">,</span>
+        <span class="n">return_headers</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
+    <span class="p">)</span>
+
+    <span class="n">reader</span> <span class="o">=</span> <span class="n">csv</span><span class="o">.</span><span class="n">DictReader</span><span class="p">(</span><span class="n">c</span><span class="o">.</span><span class="n">result</span><span class="p">,</span> <span class="n">delimiter</span> <span class="o">=</span> <span class="s1">&#39;</span><span class="se">\t</span><span class="s1">&#39;</span><span class="p">)</span>
+
+    <span class="k">if</span> <span class="n">raw_records</span><span class="p">:</span>
+
+        <span class="k">return</span> <span class="nb">list</span><span class="p">(</span><span class="n">reader</span><span class="p">)</span>
+
+    <span class="n">result</span> <span class="o">=</span> <span class="p">[]</span>
+
+    <span class="k">for</span> <span class="n">line</span> <span class="ow">in</span> <span class="n">reader</span><span class="p">:</span>
+
+        <span class="n">sources</span><span class="p">,</span> <span class="n">source_isoform</span> <span class="o">=</span> <span class="n">process_name</span><span class="p">(</span><span class="n">line</span><span class="p">[</span><span class="s1">&#39;IDA&#39;</span><span class="p">])</span>
+        <span class="n">targets</span><span class="p">,</span> <span class="n">target_isoform</span> <span class="o">=</span> <span class="n">process_name</span><span class="p">(</span><span class="n">line</span><span class="p">[</span><span class="s1">&#39;IDB&#39;</span><span class="p">])</span>
+
+        <span class="k">for</span> <span class="n">source</span><span class="p">,</span> <span class="n">target</span> <span class="ow">in</span> <span class="n">itertools</span><span class="o">.</span><span class="n">product</span><span class="p">(</span><span class="n">sources</span><span class="p">,</span> <span class="n">targets</span><span class="p">):</span>
+
+            <span class="n">this_record</span> <span class="o">=</span> <span class="n">SignorInteraction</span><span class="p">(</span>
+                <span class="n">source</span> <span class="o">=</span> <span class="n">source</span><span class="p">,</span>
+                <span class="n">target</span> <span class="o">=</span> <span class="n">target</span><span class="p">,</span>
+                <span class="n">source_isoform</span> <span class="o">=</span> <span class="n">source_isoform</span><span class="p">,</span>
+                <span class="n">target_isoform</span> <span class="o">=</span> <span class="n">target_isoform</span><span class="p">,</span>
+                <span class="n">source_type</span> <span class="o">=</span> <span class="n">line</span><span class="p">[</span><span class="s1">&#39;TYPEA&#39;</span><span class="p">],</span>
+                <span class="n">target_type</span> <span class="o">=</span> <span class="n">line</span><span class="p">[</span><span class="s1">&#39;TYPEB&#39;</span><span class="p">],</span>
+                <span class="n">effect</span> <span class="o">=</span> <span class="n">line</span><span class="p">[</span><span class="s1">&#39;EFFECT&#39;</span><span class="p">],</span>
+                <span class="n">mechanism</span> <span class="o">=</span> <span class="n">line</span><span class="p">[</span><span class="s1">&#39;MECHANISM&#39;</span><span class="p">],</span>
+                <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">line</span><span class="p">[</span><span class="s1">&#39;TAX_ID&#39;</span><span class="p">],</span>
+                <span class="n">pubmeds</span> <span class="o">=</span> <span class="n">line</span><span class="p">[</span><span class="s1">&#39;PMID&#39;</span><span class="p">],</span>
+                <span class="n">direct</span> <span class="o">=</span> <span class="n">line</span><span class="p">[</span><span class="s1">&#39;DIRECT&#39;</span><span class="p">]</span> <span class="o">==</span> <span class="s1">&#39;YES&#39;</span><span class="p">,</span>
+                <span class="n">ptm_type</span> <span class="o">=</span> <span class="n">line</span><span class="p">[</span><span class="s1">&#39;MECHANISM&#39;</span><span class="p">],</span>
+                <span class="n">ptm_residue</span> <span class="o">=</span> <span class="n">line</span><span class="p">[</span><span class="s1">&#39;RESIDUE&#39;</span><span class="p">],</span>
+                <span class="n">ptm_motif</span> <span class="o">=</span> <span class="n">line</span><span class="p">[</span><span class="s1">&#39;SEQUENCE&#39;</span><span class="p">],</span>
+            <span class="p">)</span>
+
+            <span class="n">result</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">this_record</span><span class="p">)</span>
+
+    <span class="k">return</span> <span class="n">result</span></div>
+
+
+
+<div class="viewcode-block" id="signor_enzyme_substrate">
+<a class="viewcode-back" href="../../../api/pypath.inputs.signor.signor_enzyme_substrate.html#pypath.inputs.signor.signor_enzyme_substrate">[docs]</a>
+<span class="k">def</span> <span class="nf">signor_enzyme_substrate</span><span class="p">(</span><span class="n">organism</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">):</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Loads and processes Signor PTMs.</span>
+<span class="sd">    Returns dict of dicts.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+    <span class="n">reres</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">compile</span><span class="p">(</span><span class="sa">r</span><span class="s1">&#39;([A-Za-z]</span><span class="si">{3}</span><span class="s1">)([0-9]+)&#39;</span><span class="p">)</span>
+    <span class="n">result</span> <span class="o">=</span> <span class="p">[]</span>
+    <span class="n">aalet</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">((</span><span class="n">k</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span><span class="o">.</span><span class="n">capitalize</span><span class="p">(),</span> <span class="n">v</span><span class="p">)</span>
+                 <span class="k">for</span> <span class="n">k</span><span class="p">,</span> <span class="n">v</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="n">common</span><span class="o">.</span><span class="n">aaletters</span><span class="p">))</span>
+
+    <span class="n">data</span> <span class="o">=</span> <span class="n">signor_interactions</span><span class="p">(</span><span class="n">organism</span> <span class="o">=</span> <span class="n">organism</span><span class="p">)</span>
+
+    <span class="k">for</span> <span class="n">d</span> <span class="ow">in</span> <span class="n">data</span><span class="p">:</span>
+
+        <span class="n">resm</span> <span class="o">=</span> <span class="n">reres</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="n">d</span><span class="o">.</span><span class="n">ptm_residue</span><span class="p">)</span>
+
+        <span class="k">if</span> <span class="n">resm</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
+            <span class="n">aa</span> <span class="o">=</span> <span class="n">aalet</span><span class="p">[</span><span class="n">resm</span><span class="o">.</span><span class="n">groups</span><span class="p">()[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">capitalize</span><span class="p">()]</span>
+            <span class="n">aanum</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">resm</span><span class="o">.</span><span class="n">groups</span><span class="p">()[</span><span class="mi">1</span><span class="p">])</span>
+            <span class="n">typ</span> <span class="o">=</span> <span class="n">d</span><span class="o">.</span><span class="n">ptm_type</span><span class="p">,</span>
+            <span class="n">inst</span> <span class="o">=</span> <span class="n">d</span><span class="o">.</span><span class="n">ptm_motif</span><span class="o">.</span><span class="n">upper</span><span class="p">()</span>
+            <span class="n">result</span><span class="o">.</span><span class="n">append</span><span class="p">({</span>
+                <span class="s1">&#39;typ&#39;</span><span class="p">:</span> <span class="n">d</span><span class="o">.</span><span class="n">ptm_type</span><span class="p">,</span>
+                <span class="s1">&#39;resnum&#39;</span><span class="p">:</span> <span class="n">aanum</span><span class="p">,</span>
+                <span class="s1">&#39;instance&#39;</span><span class="p">:</span> <span class="n">inst</span><span class="p">,</span>
+                <span class="s1">&#39;substrate&#39;</span><span class="p">:</span> <span class="n">d</span><span class="o">.</span><span class="n">target</span><span class="p">,</span>
+                <span class="s1">&#39;start&#39;</span><span class="p">:</span> <span class="n">aanum</span> <span class="o">-</span> <span class="mi">7</span><span class="p">,</span>
+                <span class="s1">&#39;end&#39;</span><span class="p">:</span> <span class="n">aanum</span> <span class="o">+</span> <span class="mi">7</span><span class="p">,</span>
+                <span class="s1">&#39;kinase&#39;</span><span class="p">:</span> <span class="n">d</span><span class="o">.</span><span class="n">source</span><span class="p">,</span>
+                <span class="s1">&#39;resaa&#39;</span><span class="p">:</span> <span class="n">aa</span><span class="p">,</span>
+                <span class="s1">&#39;motif&#39;</span><span class="p">:</span> <span class="n">inst</span><span class="p">,</span>
+                <span class="s1">&#39;enzyme_isoform&#39;</span><span class="p">:</span> <span class="n">d</span><span class="o">.</span><span class="n">source_isoform</span><span class="p">,</span>
+                <span class="s1">&#39;substrate_isoform&#39;</span><span class="p">:</span> <span class="n">d</span><span class="o">.</span><span class="n">target_isoform</span><span class="p">,</span>
+                <span class="s1">&#39;references&#39;</span><span class="p">:</span> <span class="p">{</span><span class="n">d</span><span class="o">.</span><span class="n">pubmeds</span><span class="p">}</span> <span class="k">if</span> <span class="n">d</span><span class="o">.</span><span class="n">pubmeds</span> <span class="o">!=</span> <span class="s1">&#39;Other&#39;</span> <span class="k">else</span> <span class="nb">set</span><span class="p">()</span>
+            <span class="p">})</span>
+
+    <span class="k">return</span> <span class="n">result</span></div>
+
+
+
+<div class="viewcode-block" id="signor_pathways">
+<a class="viewcode-back" href="../../../api/pypath.inputs.signor.signor_pathways.html#pypath.inputs.signor.signor_pathways">[docs]</a>
+<span class="k">def</span> <span class="nf">signor_pathways</span><span class="p">(</span><span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Obtains pathway annotations from Signor.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="n">url</span> <span class="o">=</span> <span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;signor&#39;</span><span class="p">][</span><span class="s1">&#39;list_url&#39;</span><span class="p">]</span>
+    <span class="n">baseurl</span> <span class="o">=</span> <span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;signor&#39;</span><span class="p">][</span><span class="s1">&#39;all_url_new&#39;</span><span class="p">]</span>
+
+    <span class="n">proteins_pathways</span> <span class="o">=</span> <span class="p">{}</span>
+    <span class="n">interactions_pathways</span> <span class="o">=</span> <span class="p">{}</span>
+
+    <span class="n">c</span> <span class="o">=</span> <span class="n">curl</span><span class="o">.</span><span class="n">Curl</span><span class="p">(</span><span class="n">url</span><span class="p">,</span> <span class="n">silent</span> <span class="o">=</span> <span class="kc">True</span><span class="p">)</span>
+
+    <span class="n">soup</span> <span class="o">=</span> <span class="n">bs4</span><span class="o">.</span><span class="n">BeautifulSoup</span><span class="p">(</span><span class="n">c</span><span class="o">.</span><span class="n">result</span><span class="p">,</span> <span class="s1">&#39;html.parser&#39;</span><span class="p">)</span>
+
+    <span class="n">pathway_names</span> <span class="o">=</span> <span class="p">[</span>
+        <span class="p">(</span><span class="n">opt</span><span class="p">[</span><span class="s1">&#39;value&#39;</span><span class="p">],</span> <span class="n">opt</span><span class="o">.</span><span class="n">text</span><span class="p">)</span>
+        <span class="k">for</span> <span class="n">opt</span> <span class="ow">in</span> <span class="n">soup</span><span class="o">.</span><span class="n">find</span><span class="p">(</span>
+            <span class="s1">&#39;select&#39;</span><span class="p">,</span> <span class="p">{</span><span class="s1">&#39;name&#39;</span><span class="p">:</span> <span class="s1">&#39;pathway_list&#39;</span><span class="p">}</span>
+        <span class="p">)</span><span class="o">.</span><span class="n">findAll</span><span class="p">(</span><span class="s1">&#39;option&#39;</span><span class="p">)</span>
+    <span class="p">]</span>
+
+    <span class="n">prg</span> <span class="o">=</span> <span class="n">progress</span><span class="o">.</span><span class="n">Progress</span><span class="p">(</span>
+        <span class="nb">len</span><span class="p">(</span><span class="n">pathway_names</span><span class="p">),</span>
+        <span class="s1">&#39;Downloading data from Signor&#39;</span><span class="p">,</span>
+        <span class="mi">1</span><span class="p">,</span>
+        <span class="n">percent</span> <span class="o">=</span> <span class="kc">False</span>
+    <span class="p">)</span>
+
+    <span class="k">for</span> <span class="n">short</span><span class="p">,</span> <span class="n">full</span> <span class="ow">in</span> <span class="n">pathway_names</span><span class="p">:</span>
+
+        <span class="n">prg</span><span class="o">.</span><span class="n">step</span><span class="p">()</span>
+
+        <span class="k">if</span> <span class="ow">not</span> <span class="n">short</span><span class="p">:</span>
+
+            <span class="k">continue</span>
+
+        <span class="n">binary_data</span> <span class="o">=</span> <span class="p">[</span>
+            <span class="p">(</span><span class="sa">b</span><span class="s1">&#39;pathway_list&#39;</span><span class="p">,</span> <span class="n">short</span><span class="o">.</span><span class="n">encode</span><span class="p">(</span><span class="s1">&#39;ascii&#39;</span><span class="p">)),</span>
+            <span class="p">(</span><span class="sa">b</span><span class="s1">&#39;submit&#39;</span><span class="p">,</span> <span class="sa">b</span><span class="s1">&#39;Download&#39;</span><span class="p">)</span>
+        <span class="p">]</span>
+
+        <span class="n">c_pw</span> <span class="o">=</span> <span class="n">curl</span><span class="o">.</span><span class="n">Curl</span><span class="p">(</span>
+            <span class="n">baseurl</span><span class="p">,</span>
+            <span class="n">silent</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
+            <span class="n">binary_data</span> <span class="o">=</span> <span class="n">binary_data</span><span class="p">,</span>
+            <span class="n">encoding</span> <span class="o">=</span> <span class="s1">&#39;utf-8&#39;</span><span class="p">,</span>
+        <span class="p">)</span>
+
+        <span class="c1">#csv.DictReader(c_pw.result)</span>
+
+        <span class="n">sep</span> <span class="o">=</span> <span class="s1">&#39;@#@#@&#39;</span>
+        <span class="n">lines</span> <span class="o">=</span> <span class="n">inputs_common</span><span class="o">.</span><span class="n">csv_sep_change</span><span class="p">(</span>
+            <span class="n">c_pw</span><span class="o">.</span><span class="n">result</span><span class="p">,</span>
+            <span class="s1">&#39;</span><span class="se">\t</span><span class="s1">&#39;</span><span class="p">,</span>
+            <span class="n">sep</span>
+        <span class="p">)</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\n</span><span class="s1">&#39;</span><span class="p">)[</span><span class="mi">1</span><span class="p">:]</span>
+
+        <span class="n">data</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span>
+            <span class="nb">filter</span><span class="p">(</span>
+                <span class="k">lambda</span> <span class="n">l</span><span class="p">:</span>
+                    <span class="nb">len</span><span class="p">(</span><span class="n">l</span><span class="p">)</span> <span class="o">&gt;</span> <span class="mi">6</span><span class="p">,</span>
+                <span class="nb">map</span><span class="p">(</span>
+                    <span class="k">lambda</span> <span class="n">l</span><span class="p">:</span>
+                        <span class="n">l</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="n">sep</span><span class="p">),</span>
+                    <span class="n">lines</span>
+                <span class="p">)</span>
+            <span class="p">)</span>
+        <span class="p">)</span>
+
+        <span class="n">proteins_pathways</span><span class="p">[</span><span class="n">full</span><span class="p">]</span> <span class="o">=</span> <span class="nb">set</span><span class="p">()</span>
+        <span class="n">interactions_pathways</span><span class="p">[</span><span class="n">full</span><span class="p">]</span> <span class="o">=</span> <span class="nb">set</span><span class="p">()</span>
+
+        <span class="k">for</span> <span class="n">row</span> <span class="ow">in</span> <span class="n">data</span><span class="p">:</span>
+
+            <span class="k">for</span> <span class="n">uniprot1</span><span class="p">,</span> <span class="n">uniprot2</span> <span class="ow">in</span> <span class="n">itertools</span><span class="o">.</span><span class="n">product</span><span class="p">(</span>
+                <span class="n">mapping</span><span class="o">.</span><span class="n">map_name</span><span class="p">(</span><span class="n">row</span><span class="p">[</span><span class="mi">4</span><span class="p">],</span> <span class="s1">&#39;uniprot&#39;</span><span class="p">,</span> <span class="s1">&#39;uniprot&#39;</span><span class="p">),</span>
+                <span class="n">mapping</span><span class="o">.</span><span class="n">map_name</span><span class="p">(</span><span class="n">row</span><span class="p">[</span><span class="mi">8</span><span class="p">],</span> <span class="s1">&#39;uniprot&#39;</span><span class="p">,</span> <span class="s1">&#39;uniprot&#39;</span><span class="p">),</span>
+            <span class="p">):</span>
+
+                <span class="n">proteins_pathways</span><span class="p">[</span><span class="n">full</span><span class="p">]</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">uniprot1</span><span class="p">)</span>
+                <span class="n">proteins_pathways</span><span class="p">[</span><span class="n">full</span><span class="p">]</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">uniprot2</span><span class="p">)</span>
+
+                <span class="n">interactions_pathways</span><span class="p">[</span><span class="n">full</span><span class="p">]</span><span class="o">.</span><span class="n">add</span><span class="p">((</span><span class="n">uniprot1</span><span class="p">,</span> <span class="n">uniprot2</span><span class="p">))</span>
+
+    <span class="n">prg</span><span class="o">.</span><span class="n">terminate</span><span class="p">()</span>
+
+    <span class="k">return</span> <span class="n">proteins_pathways</span><span class="p">,</span> <span class="n">interactions_pathways</span></div>
+
+
+
+<div class="viewcode-block" id="signor_pathway_annotations">
+<a class="viewcode-back" href="../../../api/pypath.inputs.signor.signor_pathway_annotations.html#pypath.inputs.signor.signor_pathway_annotations">[docs]</a>
+<span class="k">def</span> <span class="nf">signor_pathway_annotations</span><span class="p">():</span>
+
+    <span class="n">SignorPathway</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">namedtuple</span><span class="p">(</span>
+        <span class="s1">&#39;SignorPathway&#39;</span><span class="p">,</span> <span class="p">[</span><span class="s1">&#39;pathway&#39;</span><span class="p">]</span>
+    <span class="p">)</span>
+
+
+    <span class="n">result</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">defaultdict</span><span class="p">(</span><span class="nb">set</span><span class="p">)</span>
+
+    <span class="n">proteins</span><span class="p">,</span> <span class="n">interactions</span> <span class="o">=</span> <span class="n">signor_pathways</span><span class="p">()</span>
+
+    <span class="k">for</span> <span class="n">pathway</span><span class="p">,</span> <span class="n">uniprots</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="n">proteins</span><span class="p">):</span>
+
+        <span class="n">record</span> <span class="o">=</span> <span class="n">SignorPathway</span><span class="p">(</span><span class="n">pathway</span> <span class="o">=</span> <span class="n">pathway</span><span class="p">)</span>
+
+        <span class="k">for</span> <span class="n">uniprot</span> <span class="ow">in</span> <span class="n">uniprots</span><span class="p">:</span>
+
+            <span class="n">result</span><span class="p">[</span><span class="n">uniprot</span><span class="p">]</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">record</span><span class="p">)</span>
+
+    <span class="k">return</span> <span class="nb">dict</span><span class="p">(</span><span class="n">result</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="signor_protein_families">
+<a class="viewcode-back" href="../../../api/pypath.inputs.signor.signor_protein_families.html#pypath.inputs.signor.signor_protein_families">[docs]</a>
+<span class="k">def</span> <span class="nf">signor_protein_families</span><span class="p">(</span><span class="n">organism</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">):</span>
+    <span class="c1">#TODO: implement organism</span>
+
+    <span class="n">families</span> <span class="o">=</span> <span class="p">{}</span>
+
+    <span class="n">url</span> <span class="o">=</span> <span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;signor&#39;</span><span class="p">][</span><span class="s1">&#39;complexes&#39;</span><span class="p">]</span>
+    <span class="n">c</span> <span class="o">=</span> <span class="n">curl</span><span class="o">.</span><span class="n">Curl</span><span class="p">(</span>
+        <span class="n">url</span><span class="p">,</span>
+        <span class="n">binary_data</span> <span class="o">=</span> <span class="p">[(</span><span class="sa">b</span><span class="s1">&#39;submit&#39;</span><span class="p">,</span> <span class="sa">b</span><span class="s1">&#39;Download protein family data&#39;</span><span class="p">)],</span>
+        <span class="n">large</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
+    <span class="p">)</span>
+    <span class="n">_</span> <span class="o">=</span> <span class="nb">next</span><span class="p">(</span><span class="n">c</span><span class="o">.</span><span class="n">result</span><span class="p">)</span>
+
+    <span class="k">for</span> <span class="n">rec</span> <span class="ow">in</span> <span class="n">c</span><span class="o">.</span><span class="n">result</span><span class="p">:</span>
+
+        <span class="n">rec</span> <span class="o">=</span> <span class="n">rec</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;;&#39;</span><span class="p">)</span>
+        <span class="n">components</span> <span class="o">=</span> <span class="p">[</span><span class="n">u</span><span class="o">.</span><span class="n">strip</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\n\r</span><span class="s1">&quot; &#39;</span><span class="p">)</span> <span class="k">for</span> <span class="n">u</span> <span class="ow">in</span> <span class="n">rec</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;,&#39;</span><span class="p">)]</span>
+        <span class="n">families</span><span class="p">[</span><span class="n">rec</span><span class="p">[</span><span class="mi">0</span><span class="p">]]</span> <span class="o">=</span> <span class="n">components</span>
+
+    <span class="k">return</span> <span class="n">families</span></div>
+
+
+
+<div class="viewcode-block" id="signor_complexes">
+<a class="viewcode-back" href="../../../api/pypath.inputs.signor.signor_complexes.html#pypath.inputs.signor.signor_complexes">[docs]</a>
+<span class="k">def</span> <span class="nf">signor_complexes</span><span class="p">(</span><span class="n">organism</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">):</span>
+    <span class="c1">#TODO: implement organism</span>
+
+
+    <span class="k">def</span> <span class="nf">process_on_hold</span><span class="p">(</span><span class="n">on_hold</span><span class="p">,</span> <span class="n">complexes_by_id</span><span class="p">,</span> <span class="n">complexes</span><span class="p">):</span>
+
+        <span class="n">on_hold_next</span> <span class="o">=</span> <span class="p">[]</span>
+
+        <span class="k">for</span> <span class="n">name</span><span class="p">,</span> <span class="n">components</span><span class="p">,</span> <span class="n">id_</span> <span class="ow">in</span> <span class="n">on_hold</span><span class="p">:</span>
+
+            <span class="n">components</span> <span class="o">=</span> <span class="p">[</span>
+                <span class="p">[</span><span class="n">comp</span><span class="o">.</span><span class="n">components</span> <span class="k">for</span> <span class="n">comp</span> <span class="ow">in</span> <span class="n">complexes_by_id</span><span class="p">[</span><span class="n">comp_id</span><span class="p">]]</span>
+                    <span class="k">if</span> <span class="n">comp_id</span> <span class="ow">in</span> <span class="n">complexes_by_id</span> <span class="k">else</span>
+                <span class="p">((</span><span class="n">comp_id</span><span class="p">,),)</span>
+                <span class="k">for</span> <span class="n">comp_id</span> <span class="ow">in</span> <span class="n">components</span>
+            <span class="p">]</span>
+
+            <span class="k">for</span> <span class="n">components0</span> <span class="ow">in</span> <span class="n">itertools</span><span class="o">.</span><span class="n">product</span><span class="p">(</span><span class="o">*</span><span class="n">components</span><span class="p">):</span>
+
+                <span class="n">this_components</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="n">itertools</span><span class="o">.</span><span class="n">chain</span><span class="p">(</span><span class="o">*</span><span class="n">components0</span><span class="p">))</span>
+
+                <span class="k">if</span> <span class="nb">any</span><span class="p">(</span>
+                    <span class="n">comp</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s1">&#39;SIGNOR-C&#39;</span><span class="p">)</span> <span class="k">for</span> <span class="n">comp</span> <span class="ow">in</span> <span class="n">this_components</span>
+                <span class="p">):</span>
+
+                    <span class="n">on_hold_next</span><span class="o">.</span><span class="n">append</span><span class="p">((</span><span class="n">name</span><span class="p">,</span> <span class="n">this_components</span><span class="p">,</span> <span class="n">id_</span><span class="p">))</span>
+
+                <span class="k">else</span><span class="p">:</span>
+
+                    <span class="n">cplex</span> <span class="o">=</span> <span class="n">intera</span><span class="o">.</span><span class="n">Complex</span><span class="p">(</span>
+                        <span class="n">name</span> <span class="o">=</span> <span class="n">name</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s1">&#39;&quot;&#39;</span><span class="p">,</span> <span class="s1">&#39;&#39;</span><span class="p">)</span><span class="o">.</span><span class="n">strip</span><span class="p">(),</span>
+                        <span class="n">components</span> <span class="o">=</span> <span class="n">this_components</span><span class="p">,</span>
+                        <span class="n">sources</span> <span class="o">=</span> <span class="s1">&#39;SIGNOR&#39;</span><span class="p">,</span>
+                        <span class="n">ids</span> <span class="o">=</span> <span class="n">id_</span><span class="p">,</span>
+                    <span class="p">)</span>
+
+                    <span class="n">complexes</span><span class="p">[</span><span class="n">cplex</span><span class="o">.</span><span class="fm">__str__</span><span class="p">()]</span> <span class="o">=</span> <span class="n">cplex</span>
+                    <span class="n">complexes_by_id</span><span class="p">[</span><span class="n">id_</span><span class="p">]</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">cplex</span><span class="p">)</span>
+
+        <span class="k">return</span> <span class="n">on_hold_next</span><span class="p">,</span> <span class="n">complexes_by_id</span><span class="p">,</span> <span class="n">complexes</span>
+
+
+    <span class="n">complexes</span> <span class="o">=</span> <span class="p">{}</span>
+    <span class="n">on_hold</span> <span class="o">=</span> <span class="p">[]</span>
+
+    <span class="n">families</span> <span class="o">=</span> <span class="n">signor_protein_families</span><span class="p">(</span><span class="n">organism</span> <span class="o">=</span> <span class="n">organism</span><span class="p">)</span>
+
+    <span class="n">url</span> <span class="o">=</span> <span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;signor&#39;</span><span class="p">][</span><span class="s1">&#39;complexes&#39;</span><span class="p">]</span>
+    <span class="n">c</span> <span class="o">=</span> <span class="n">curl</span><span class="o">.</span><span class="n">Curl</span><span class="p">(</span>
+        <span class="n">url</span><span class="p">,</span>
+        <span class="n">binary_data</span> <span class="o">=</span> <span class="p">[(</span><span class="sa">b</span><span class="s1">&#39;submit&#39;</span><span class="p">,</span> <span class="sa">b</span><span class="s1">&#39;Download complex data&#39;</span><span class="p">)],</span>
+        <span class="n">large</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
+    <span class="p">)</span>
+    <span class="n">_</span> <span class="o">=</span> <span class="nb">next</span><span class="p">(</span><span class="n">c</span><span class="o">.</span><span class="n">result</span><span class="p">)</span>
+
+    <span class="n">complexes_by_id</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">defaultdict</span><span class="p">(</span><span class="nb">set</span><span class="p">)</span>
+
+    <span class="k">for</span> <span class="n">rec</span> <span class="ow">in</span> <span class="n">c</span><span class="o">.</span><span class="n">result</span><span class="p">:</span>
+
+        <span class="n">rec</span> <span class="o">=</span> <span class="n">rec</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;;&#39;</span><span class="p">)</span>
+        <span class="n">components</span> <span class="o">=</span> <span class="p">[</span><span class="n">u</span><span class="o">.</span><span class="n">strip</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\n\r</span><span class="s1">&quot; &#39;</span><span class="p">)</span> <span class="k">for</span> <span class="n">u</span> <span class="ow">in</span> <span class="n">rec</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;,&#39;</span><span class="p">)]</span>
+
+        <span class="n">components</span> <span class="o">=</span> <span class="p">[</span>
+            <span class="n">families</span><span class="p">[</span><span class="n">comp</span><span class="p">]</span> <span class="k">if</span> <span class="n">comp</span> <span class="ow">in</span> <span class="n">families</span> <span class="k">else</span> <span class="p">[</span><span class="n">comp</span><span class="p">]</span>
+            <span class="k">for</span> <span class="n">comp</span> <span class="ow">in</span> <span class="n">components</span>
+        <span class="p">]</span>
+
+        <span class="k">for</span> <span class="n">this_components</span> <span class="ow">in</span> <span class="n">itertools</span><span class="o">.</span><span class="n">product</span><span class="p">(</span><span class="o">*</span><span class="n">components</span><span class="p">):</span>
+
+            <span class="c1"># some complex contains other complexes</span>
+            <span class="k">if</span> <span class="nb">any</span><span class="p">(</span><span class="n">comp</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s1">&#39;SIGNOR-C&#39;</span><span class="p">)</span> <span class="k">for</span> <span class="n">comp</span> <span class="ow">in</span> <span class="n">this_components</span><span class="p">):</span>
+
+                <span class="n">on_hold</span><span class="o">.</span><span class="n">append</span><span class="p">((</span><span class="n">rec</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span> <span class="n">this_components</span><span class="p">,</span> <span class="n">rec</span><span class="p">[</span><span class="mi">0</span><span class="p">]))</span>
+
+            <span class="k">else</span><span class="p">:</span>
+
+                <span class="n">cplex</span> <span class="o">=</span> <span class="n">intera</span><span class="o">.</span><span class="n">Complex</span><span class="p">(</span>
+                    <span class="n">name</span> <span class="o">=</span> <span class="n">rec</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s1">&#39;&quot;&#39;</span><span class="p">,</span> <span class="s1">&#39;&#39;</span><span class="p">)</span><span class="o">.</span><span class="n">strip</span><span class="p">(),</span>
+                    <span class="n">components</span> <span class="o">=</span> <span class="n">this_components</span><span class="p">,</span>
+                    <span class="n">sources</span> <span class="o">=</span> <span class="s1">&#39;SIGNOR&#39;</span><span class="p">,</span>
+                    <span class="n">ids</span> <span class="o">=</span> <span class="n">rec</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span>
+                <span class="p">)</span>
+
+                <span class="n">complexes</span><span class="p">[</span><span class="n">cplex</span><span class="o">.</span><span class="fm">__str__</span><span class="p">()]</span> <span class="o">=</span> <span class="n">cplex</span>
+                <span class="n">complexes_by_id</span><span class="p">[</span><span class="n">rec</span><span class="p">[</span><span class="mi">0</span><span class="p">]]</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">cplex</span><span class="p">)</span>
+
+    <span class="k">while</span> <span class="kc">True</span><span class="p">:</span>
+
+        <span class="c1"># complexes are defined recursively</span>
+        <span class="n">count_on_hold</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="n">on_hold</span><span class="p">)</span>
+        <span class="n">on_hold</span><span class="p">,</span> <span class="n">complexes_by_id</span><span class="p">,</span> <span class="n">complexes</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="n">process_on_hold</span><span class="p">(</span><span class="n">on_hold</span><span class="p">,</span> <span class="n">complexes_by_id</span><span class="p">,</span> <span class="n">complexes</span><span class="p">)</span>
+        <span class="p">)</span>
+
+        <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">on_hold</span><span class="p">)</span> <span class="o">==</span> <span class="n">count_on_hold</span><span class="p">:</span>
+
+            <span class="k">break</span>
+
+    <span class="k">return</span> <span class="n">complexes</span></div>
+
+</pre></div>
+
+                </article>
+              
+              
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+  <h1>Source code for pypath.inputs.spike</h1><div class="highlight"><pre>
+<span></span><span class="ch">#!/usr/bin/env python</span>
+<span class="c1"># -*- coding: utf-8 -*-</span>
+
+<span class="c1">#</span>
+<span class="c1">#  This file is part of the `pypath` python module</span>
+<span class="c1">#</span>
+<span class="c1">#  Copyright 2014-2023</span>
+<span class="c1">#  EMBL, EMBL-EBI, Uniklinik RWTH Aachen, Heidelberg University</span>
+<span class="c1">#</span>
+<span class="c1">#  Authors: see the file `README.rst`</span>
+<span class="c1">#  Contact: Dénes Türei (turei.denes@gmail.com)</span>
+<span class="c1">#</span>
+<span class="c1">#  Distributed under the GPLv3 License.</span>
+<span class="c1">#  See accompanying file LICENSE.txt or copy at</span>
+<span class="c1">#      https://www.gnu.org/licenses/gpl-3.0.html</span>
+<span class="c1">#</span>
+<span class="c1">#  Website: https://pypath.omnipathdb.org/</span>
+<span class="c1">#</span>
+
+<span class="kn">import</span> <span class="nn">itertools</span>
+<span class="kn">import</span> <span class="nn">collections</span>
+
+<span class="kn">from</span> <span class="nn">typing</span> <span class="kn">import</span> <span class="n">Dict</span><span class="p">,</span> <span class="n">List</span>
+
+<span class="kn">import</span> <span class="nn">xml.etree.cElementTree</span> <span class="k">as</span> <span class="nn">ET</span>
+
+<span class="kn">import</span> <span class="nn">pypath.share.curl</span> <span class="k">as</span> <span class="nn">curl</span>
+<span class="kn">import</span> <span class="nn">pypath.resources.urls</span> <span class="k">as</span> <span class="nn">urls</span>
+<span class="kn">import</span> <span class="nn">pypath.utils.mapping</span> <span class="k">as</span> <span class="nn">mapping</span>
+<span class="kn">import</span> <span class="nn">pypath.internals.intera</span> <span class="k">as</span> <span class="nn">intera</span>
+
+
+<div class="viewcode-block" id="spike_interactions">
+<a class="viewcode-back" href="../../../api/pypath.inputs.spike.spike_interactions.html#pypath.inputs.spike.spike_interactions">[docs]</a>
+<span class="k">def</span> <span class="nf">spike_interactions</span><span class="p">(</span><span class="n">min_confidence</span><span class="p">:</span> <span class="nb">int</span> <span class="o">=</span> <span class="mi">2</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">List</span><span class="p">[</span><span class="nb">tuple</span><span class="p">]:</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Args</span>
+<span class="sd">        min_confidence:</span>
+<span class="sd">            Confidence (integrity) levels in SPIKE span from 1 to 4, 1</span>
+<span class="sd">            being the highest confidence.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="n">url</span> <span class="o">=</span> <span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;spike&#39;</span><span class="p">][</span><span class="s1">&#39;url&#39;</span><span class="p">]</span>
+    <span class="n">c</span> <span class="o">=</span> <span class="n">curl</span><span class="o">.</span><span class="n">Curl</span><span class="p">(</span>
+        <span class="n">url</span><span class="p">,</span>
+        <span class="n">silent</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+        <span class="n">large</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
+        <span class="n">files_needed</span> <span class="o">=</span> <span class="p">[</span><span class="s1">&#39;LatestSpikeDB.xml&#39;</span><span class="p">],</span>
+    <span class="p">)</span>
+    <span class="n">spikexml</span> <span class="o">=</span> <span class="n">c</span><span class="o">.</span><span class="n">result</span>
+
+    <span class="n">xml</span> <span class="o">=</span> <span class="n">ET</span><span class="o">.</span><span class="n">parse</span><span class="p">(</span><span class="n">spikexml</span><span class="p">[</span><span class="s1">&#39;LatestSpikeDB.xml&#39;</span><span class="p">])</span>
+
+    <span class="n">xmlroot</span> <span class="o">=</span> <span class="n">xml</span><span class="o">.</span><span class="n">getroot</span><span class="p">()</span>
+
+    <span class="c1"># iterating genes</span>
+
+    <span class="n">bblock</span> <span class="o">=</span> <span class="n">xmlroot</span><span class="o">.</span><span class="n">find</span><span class="p">(</span><span class="s1">&#39;BuildingBlock&#39;</span><span class="p">)</span>
+    <span class="n">rblock</span> <span class="o">=</span> <span class="n">xmlroot</span><span class="o">.</span><span class="n">find</span><span class="p">(</span><span class="s1">&#39;RegulationBlock&#39;</span><span class="p">)</span>
+    <span class="n">iblock</span> <span class="o">=</span> <span class="n">xmlroot</span><span class="o">.</span><span class="n">find</span><span class="p">(</span><span class="s1">&#39;InteractionBlock&#39;</span><span class="p">)</span>
+
+    <span class="n">genes</span> <span class="o">=</span> <span class="p">{}</span>
+    <span class="n">result</span> <span class="o">=</span> <span class="p">[]</span>
+
+    <span class="n">SpikeInteraction</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">namedtuple</span><span class="p">(</span>
+        <span class="s1">&#39;SpikeInteraction&#39;</span><span class="p">,</span>
+        <span class="p">(</span>
+            <span class="s1">&#39;entrez_a&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;genesymbol_a&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;entrez_b&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;genesymbol_b&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;directed&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;pmids&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;integrity&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;effect&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;assay&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;data_source&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;description&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;mechanism&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;regulation&#39;</span><span class="p">,</span>
+        <span class="p">)</span>
+    <span class="p">)</span>
+
+    <span class="n">Gene</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">namedtuple</span><span class="p">(</span><span class="s1">&#39;Gene&#39;</span><span class="p">,</span> <span class="p">(</span><span class="s1">&#39;entrez&#39;</span><span class="p">,</span> <span class="s1">&#39;genesymbol&#39;</span><span class="p">,</span> <span class="s1">&#39;type&#39;</span><span class="p">))</span>
+
+    <span class="k">for</span> <span class="n">gene</span> <span class="ow">in</span> <span class="n">bblock</span><span class="o">.</span><span class="n">findall</span><span class="p">(</span><span class="s1">&#39;Gene&#39;</span><span class="p">):</span>
+
+        <span class="n">sy</span> <span class="o">=</span> <span class="s1">&#39;&#39;</span> <span class="k">if</span> <span class="s1">&#39;name&#39;</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">gene</span><span class="o">.</span><span class="n">attrib</span> <span class="k">else</span> <span class="n">gene</span><span class="o">.</span><span class="n">attrib</span><span class="p">[</span><span class="s1">&#39;name&#39;</span><span class="p">]</span>
+        <span class="n">genes</span><span class="p">[</span><span class="n">gene</span><span class="o">.</span><span class="n">attrib</span><span class="p">[</span><span class="s1">&#39;id&#39;</span><span class="p">]]</span> <span class="o">=</span> <span class="p">[</span>
+            <span class="n">Gene</span><span class="p">(</span>
+                <span class="n">entrez</span> <span class="o">=</span> <span class="n">gene</span><span class="o">.</span><span class="n">find</span><span class="p">(</span><span class="s1">&#39;XRef&#39;</span><span class="p">)</span><span class="o">.</span><span class="n">attrib</span><span class="p">[</span><span class="s1">&#39;id&#39;</span><span class="p">],</span>
+                <span class="n">genesymbol</span> <span class="o">=</span> <span class="n">sy</span><span class="p">,</span>
+                <span class="nb">type</span> <span class="o">=</span> <span class="s1">&#39;gene&#39;</span><span class="p">,</span>
+            <span class="p">)</span>
+        <span class="p">]</span>
+
+    <span class="k">for</span> <span class="n">grp</span> <span class="ow">in</span> <span class="n">bblock</span><span class="o">.</span><span class="n">findall</span><span class="p">(</span><span class="s1">&#39;Group&#39;</span><span class="p">):</span>
+
+        <span class="k">if</span> <span class="n">grp</span><span class="o">.</span><span class="n">attrib</span><span class="p">[</span><span class="s1">&#39;type&#39;</span><span class="p">]</span> <span class="o">==</span> <span class="s1">&#39;Complex&#39;</span><span class="p">:</span>
+
+            <span class="n">members</span> <span class="o">=</span> <span class="p">[</span><span class="n">m</span><span class="o">.</span><span class="n">attrib</span><span class="p">[</span><span class="s1">&#39;ref&#39;</span><span class="p">]</span> <span class="k">for</span> <span class="n">m</span> <span class="ow">in</span> <span class="n">grp</span><span class="o">.</span><span class="n">findall</span><span class="p">(</span><span class="s1">&#39;Member&#39;</span><span class="p">)]</span>
+
+            <span class="k">if</span> <span class="nb">all</span><span class="p">(</span>
+                <span class="n">m</span> <span class="ow">in</span> <span class="n">genes</span> <span class="ow">and</span>
+                <span class="n">genes</span><span class="p">[</span><span class="n">m</span><span class="p">][</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">type</span> <span class="o">!=</span> <span class="s1">&#39;complex&#39;</span>
+                <span class="k">for</span> <span class="n">m</span> <span class="ow">in</span> <span class="n">members</span>
+            <span class="p">):</span>
+
+                <span class="n">uniprots</span> <span class="o">=</span> <span class="p">[</span>
+                    <span class="n">mapping</span><span class="o">.</span><span class="n">map_name</span><span class="p">(</span><span class="n">genes</span><span class="p">[</span><span class="n">m</span><span class="p">][</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">entrez</span><span class="p">,</span> <span class="s1">&#39;entrez&#39;</span><span class="p">,</span> <span class="s1">&#39;uniprot&#39;</span><span class="p">)</span>
+                    <span class="k">for</span> <span class="n">m</span> <span class="ow">in</span> <span class="n">members</span>
+                <span class="p">]</span>
+
+                <span class="n">genes</span><span class="p">[</span><span class="n">grp</span><span class="o">.</span><span class="n">attrib</span><span class="p">[</span><span class="s1">&#39;id&#39;</span><span class="p">]]</span> <span class="o">=</span> <span class="p">[</span>
+                    <span class="n">Gene</span><span class="p">(</span>
+                        <span class="n">entrez</span> <span class="o">=</span> <span class="n">cplex</span><span class="p">,</span>
+                        <span class="n">genesymbol</span> <span class="o">=</span> <span class="n">cplex</span><span class="p">,</span>
+                        <span class="nb">type</span> <span class="o">=</span> <span class="s1">&#39;complex&#39;</span><span class="p">,</span>
+                    <span class="p">)</span>
+                    <span class="k">for</span> <span class="n">cplex</span> <span class="ow">in</span>
+                    <span class="p">(</span>
+                        <span class="n">intera</span><span class="o">.</span><span class="n">Complex</span><span class="p">(</span>
+                            <span class="n">name</span> <span class="o">=</span> <span class="n">grp</span><span class="o">.</span><span class="n">attrib</span><span class="p">[</span><span class="s1">&#39;name&#39;</span><span class="p">],</span>
+                            <span class="n">components</span> <span class="o">=</span> <span class="n">ups</span><span class="p">,</span>
+                            <span class="n">sources</span> <span class="o">=</span> <span class="s1">&#39;SPIKE&#39;</span><span class="p">,</span>
+                        <span class="p">)</span>
+                        <span class="k">for</span> <span class="n">ups</span> <span class="ow">in</span> <span class="n">itertools</span><span class="o">.</span><span class="n">product</span><span class="p">(</span><span class="o">*</span><span class="n">uniprots</span><span class="p">)</span>
+                    <span class="p">)</span>
+                <span class="p">]</span>
+
+    <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="n">itertools</span><span class="o">.</span><span class="n">chain</span><span class="p">(</span>
+            <span class="n">rblock</span><span class="o">.</span><span class="n">findall</span><span class="p">(</span><span class="s1">&#39;Regulation&#39;</span><span class="p">),</span>
+            <span class="n">iblock</span><span class="o">.</span><span class="n">findall</span><span class="p">(</span><span class="s1">&#39;Interaction&#39;</span><span class="p">),</span>
+        <span class="p">):</span>
+
+        <span class="n">regulation</span> <span class="o">=</span> <span class="n">i</span><span class="o">.</span><span class="n">tag</span> <span class="o">==</span> <span class="s1">&#39;Regulation&#39;</span>
+        <span class="n">src_tag</span> <span class="o">=</span> <span class="s1">&#39;Source&#39;</span> <span class="k">if</span> <span class="n">regulation</span> <span class="k">else</span> <span class="s1">&#39;ProteinA&#39;</span>
+        <span class="n">tgt_tag</span> <span class="o">=</span> <span class="s1">&#39;PhysicalTarget&#39;</span> <span class="k">if</span> <span class="n">regulation</span> <span class="k">else</span> <span class="s1">&#39;ProteinB&#39;</span>
+
+        <span class="n">ds</span> <span class="o">=</span> <span class="n">i</span><span class="o">.</span><span class="n">attrib</span><span class="p">[</span><span class="s1">&#39;dataSource&#39;</span><span class="p">]</span>
+        <span class="n">itg</span> <span class="o">=</span> <span class="n">i</span><span class="o">.</span><span class="n">attrib</span><span class="p">[</span><span class="s1">&#39;integrity&#39;</span><span class="p">]</span>
+        <span class="n">eff</span> <span class="o">=</span> <span class="n">i</span><span class="o">.</span><span class="n">attrib</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">&#39;effect&#39;</span><span class="p">,</span> <span class="s1">&#39;&#39;</span><span class="p">)</span>
+        <span class="n">mec</span> <span class="o">=</span> <span class="n">i</span><span class="o">.</span><span class="n">attrib</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">&#39;mechanism&#39;</span><span class="p">,</span> <span class="s1">&#39;&#39;</span><span class="p">)</span>
+        <span class="n">src</span> <span class="o">=</span> <span class="n">i</span><span class="o">.</span><span class="n">find</span><span class="p">(</span><span class="n">src_tag</span><span class="p">)</span><span class="o">.</span><span class="n">attrib</span><span class="p">[</span><span class="s1">&#39;ref&#39;</span><span class="p">]</span>
+        <span class="n">tgt</span> <span class="o">=</span> <span class="n">i</span><span class="o">.</span><span class="n">find</span><span class="p">(</span><span class="n">tgt_tag</span><span class="p">)</span><span class="o">.</span><span class="n">attrib</span><span class="p">[</span><span class="s1">&#39;ref&#39;</span><span class="p">]</span>
+        <span class="n">dcd</span> <span class="o">=</span> <span class="nb">str</span><span class="p">(</span><span class="nb">int</span><span class="p">(</span><span class="n">regulation</span><span class="p">))</span>
+        <span class="n">dsc</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="s1">&#39;&#39;</span>
+                <span class="k">if</span> <span class="n">i</span><span class="o">.</span><span class="n">find</span><span class="p">(</span><span class="s1">&#39;Description&#39;</span><span class="p">)</span> <span class="ow">is</span> <span class="kc">None</span> <span class="k">else</span>
+            <span class="n">i</span><span class="o">.</span><span class="n">find</span><span class="p">(</span><span class="s1">&#39;Description&#39;</span><span class="p">)</span><span class="o">.</span><span class="n">text</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\n</span><span class="s1">&#39;</span><span class="p">,</span> <span class="s1">&#39; &#39;</span><span class="p">)</span>
+        <span class="p">)</span>
+        <span class="n">asy</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="s1">&#39;&#39;</span>
+                <span class="k">if</span> <span class="s1">&#39;biologicalAssay&#39;</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">i</span><span class="o">.</span><span class="n">attrib</span> <span class="k">else</span>
+            <span class="n">i</span><span class="o">.</span><span class="n">attrib</span><span class="p">[</span><span class="s1">&#39;biologicalAssay&#39;</span><span class="p">]</span>
+        <span class="p">)</span>
+        <span class="n">refs</span> <span class="o">=</span> <span class="n">i</span><span class="o">.</span><span class="n">findall</span><span class="p">(</span><span class="s1">&#39;Reference&#39;</span><span class="p">)</span>
+        <span class="n">pmids</span> <span class="o">=</span> <span class="p">[</span><span class="n">r</span><span class="o">.</span><span class="n">attrib</span><span class="p">[</span><span class="s1">&#39;pmid&#39;</span><span class="p">]</span> <span class="k">for</span> <span class="n">r</span> <span class="ow">in</span> <span class="n">refs</span><span class="p">]</span>
+
+        <span class="k">if</span> <span class="n">src</span> <span class="ow">in</span> <span class="n">genes</span> <span class="ow">and</span> <span class="n">tgt</span> <span class="ow">in</span> <span class="n">genes</span><span class="p">:</span>
+
+            <span class="k">if</span> <span class="nb">int</span><span class="p">(</span><span class="n">itg</span><span class="p">)</span> <span class="o">&lt;=</span> <span class="n">min_confidence</span><span class="p">:</span>
+
+                <span class="k">for</span> <span class="n">_src</span><span class="p">,</span> <span class="n">_tgt</span> <span class="ow">in</span> <span class="n">itertools</span><span class="o">.</span><span class="n">product</span><span class="p">(</span><span class="n">genes</span><span class="p">[</span><span class="n">src</span><span class="p">],</span> <span class="n">genes</span><span class="p">[</span><span class="n">tgt</span><span class="p">]):</span>
+
+                    <span class="n">result</span><span class="o">.</span><span class="n">append</span><span class="p">(</span>
+                        <span class="n">SpikeInteraction</span><span class="p">(</span>
+                            <span class="n">entrez_a</span> <span class="o">=</span> <span class="n">_src</span><span class="o">.</span><span class="n">entrez</span><span class="p">,</span>
+                            <span class="n">genesymbol_a</span> <span class="o">=</span> <span class="n">_src</span><span class="o">.</span><span class="n">genesymbol</span><span class="p">,</span>
+                            <span class="n">entrez_b</span> <span class="o">=</span> <span class="n">_tgt</span><span class="o">.</span><span class="n">entrez</span><span class="p">,</span>
+                            <span class="n">genesymbol_b</span> <span class="o">=</span> <span class="n">_tgt</span><span class="o">.</span><span class="n">genesymbol</span><span class="p">,</span>
+                            <span class="n">directed</span> <span class="o">=</span> <span class="n">dcd</span><span class="p">,</span>
+                            <span class="n">pmids</span> <span class="o">=</span> <span class="s1">&#39;;&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">pmids</span><span class="p">),</span>
+                            <span class="n">integrity</span> <span class="o">=</span> <span class="n">itg</span><span class="p">,</span>
+                            <span class="n">effect</span> <span class="o">=</span> <span class="n">eff</span><span class="p">,</span>
+                            <span class="n">assay</span> <span class="o">=</span> <span class="n">asy</span><span class="p">,</span>
+                            <span class="n">data_source</span> <span class="o">=</span> <span class="n">ds</span><span class="p">,</span>
+                            <span class="n">description</span> <span class="o">=</span> <span class="n">dsc</span><span class="p">,</span>
+                            <span class="n">mechanism</span> <span class="o">=</span> <span class="n">mec</span><span class="p">,</span>
+                            <span class="n">regulation</span> <span class="o">=</span> <span class="n">regulation</span><span class="p">,</span>
+                        <span class="p">)</span>
+                    <span class="p">)</span>
+
+    <span class="k">return</span> <span class="n">result</span></div>
+
+
+
+<div class="viewcode-block" id="spike_complexes">
+<a class="viewcode-back" href="../../../api/pypath.inputs.spike.spike_complexes.html#pypath.inputs.spike.spike_complexes">[docs]</a>
+<span class="k">def</span> <span class="nf">spike_complexes</span><span class="p">(</span><span class="n">min_confidence</span><span class="p">:</span> <span class="nb">int</span> <span class="o">=</span> <span class="mi">2</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">Dict</span><span class="p">[</span><span class="nb">str</span><span class="p">,</span> <span class="n">intera</span><span class="o">.</span><span class="n">Complex</span><span class="p">]:</span>
+
+    <span class="n">interactions</span> <span class="o">=</span> <span class="n">spike_interactions</span><span class="p">(</span><span class="n">min_confidence</span> <span class="o">=</span> <span class="n">min_confidence</span><span class="p">)</span>
+
+    <span class="n">complexes</span> <span class="o">=</span> <span class="p">[</span>
+        <span class="nb">getattr</span><span class="p">(</span><span class="n">i</span><span class="p">,</span> <span class="n">attr</span><span class="p">)</span>
+        <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="n">interactions</span>
+        <span class="k">for</span> <span class="n">attr</span> <span class="ow">in</span> <span class="p">(</span><span class="s1">&#39;entrez_a&#39;</span><span class="p">,</span> <span class="s1">&#39;entrez_b&#39;</span><span class="p">)</span>
+        <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="nb">getattr</span><span class="p">(</span><span class="n">i</span><span class="p">,</span> <span class="n">attr</span><span class="p">),</span> <span class="n">intera</span><span class="o">.</span><span class="n">Complex</span><span class="p">)</span>
+    <span class="p">]</span>
+
+    <span class="k">return</span> <span class="nb">dict</span><span class="p">((</span><span class="n">cplx</span><span class="o">.</span><span class="fm">__str__</span><span class="p">(),</span> <span class="n">cplx</span><span class="p">)</span> <span class="k">for</span> <span class="n">cplx</span> <span class="ow">in</span> <span class="n">complexes</span><span class="p">)</span></div>
+
+</pre></div>
+
+                </article>
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+  <h1>Source code for pypath.inputs.surfaceome</h1><div class="highlight"><pre>
+<span></span><span class="ch">#!/usr/bin/env python</span>
+<span class="c1"># -*- coding: utf-8 -*-</span>
+
+<span class="c1">#</span>
+<span class="c1">#  This file is part of the `pypath` python module</span>
+<span class="c1">#</span>
+<span class="c1">#  Copyright 2014-2023</span>
+<span class="c1">#  EMBL, EMBL-EBI, Uniklinik RWTH Aachen, Heidelberg University</span>
+<span class="c1">#</span>
+<span class="c1">#  Authors: see the file `README.rst`</span>
+<span class="c1">#  Contact: Dénes Türei (turei.denes@gmail.com)</span>
+<span class="c1">#</span>
+<span class="c1">#  Distributed under the GPLv3 License.</span>
+<span class="c1">#  See accompanying file LICENSE.txt or copy at</span>
+<span class="c1">#      https://www.gnu.org/licenses/gpl-3.0.html</span>
+<span class="c1">#</span>
+<span class="c1">#  Website: https://pypath.omnipathdb.org/</span>
+<span class="c1">#</span>
+
+<span class="kn">import</span> <span class="nn">pypath.share.curl</span> <span class="k">as</span> <span class="nn">curl</span>
+<span class="kn">import</span> <span class="nn">pypath.resources.urls</span> <span class="k">as</span> <span class="nn">urls</span>
+<span class="kn">import</span> <span class="nn">pypath.utils.mapping</span> <span class="k">as</span> <span class="nn">mapping</span>
+<span class="kn">import</span> <span class="nn">pypath.inputs.common</span> <span class="k">as</span> <span class="nn">inputs_common</span>
+
+
+<div class="viewcode-block" id="surfaceome_annotations">
+<a class="viewcode-back" href="../../../api/pypath.inputs.surfaceome.surfaceome_annotations.html#pypath.inputs.surfaceome.surfaceome_annotations">[docs]</a>
+<span class="k">def</span> <span class="nf">surfaceome_annotations</span><span class="p">():</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Downloads the &quot;In silico human surfaceome&quot;.</span>
+<span class="sd">    Dict with UniProt IDs as key and tuples of surface prediction score,</span>
+<span class="sd">    class and subclass as values (columns B, N, S and T of table S3).</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="n">url</span> <span class="o">=</span> <span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;surfaceome&#39;</span><span class="p">][</span><span class="s1">&#39;url&#39;</span><span class="p">]</span>
+    <span class="n">c</span> <span class="o">=</span> <span class="n">curl</span><span class="o">.</span><span class="n">Curl</span><span class="p">(</span><span class="n">url</span><span class="p">,</span> <span class="n">large</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span> <span class="n">silent</span> <span class="o">=</span> <span class="kc">False</span><span class="p">)</span>
+    <span class="n">xlsname</span> <span class="o">=</span> <span class="n">c</span><span class="o">.</span><span class="n">fname</span>
+    <span class="k">del</span><span class="p">(</span><span class="n">c</span><span class="p">)</span>
+    <span class="n">raw</span> <span class="o">=</span> <span class="n">inputs_common</span><span class="o">.</span><span class="n">read_xls</span><span class="p">(</span><span class="n">xlsname</span><span class="p">,</span> <span class="s1">&#39;in silico surfaceome only&#39;</span><span class="p">)[</span><span class="mi">2</span><span class="p">:]</span>
+
+    <span class="k">return</span> <span class="nb">dict</span><span class="p">(</span>
+        <span class="p">(</span>
+            <span class="n">uniprot</span><span class="p">,</span> <span class="c1"># uniprot</span>
+            <span class="p">(</span>
+                <span class="nb">float</span><span class="p">(</span><span class="n">r</span><span class="p">[</span><span class="mi">13</span><span class="p">]),</span> <span class="c1"># score</span>
+                <span class="n">r</span><span class="p">[</span><span class="mi">18</span><span class="p">]</span> <span class="k">if</span> <span class="n">r</span><span class="p">[</span><span class="mi">18</span><span class="p">]</span> <span class="k">else</span> <span class="kc">None</span><span class="p">,</span> <span class="c1"># class</span>
+                <span class="nb">set</span><span class="p">(</span><span class="n">r</span><span class="p">[</span><span class="mi">19</span><span class="p">]</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s1">&#39;KInase&#39;</span><span class="p">,</span> <span class="s1">&#39;Kinase&#39;</span><span class="p">)</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;;&#39;</span><span class="p">))</span>
+                    <span class="k">if</span> <span class="n">r</span><span class="p">[</span><span class="mi">19</span><span class="p">]</span> <span class="k">else</span>
+                <span class="nb">set</span><span class="p">(),</span> <span class="c1"># subclass</span>
+            <span class="p">)</span>
+        <span class="p">)</span>
+        <span class="k">for</span> <span class="n">r</span> <span class="ow">in</span> <span class="n">raw</span>
+        <span class="k">for</span> <span class="n">uniprot</span> <span class="ow">in</span> <span class="n">mapping</span><span class="o">.</span><span class="n">map_name</span><span class="p">(</span><span class="n">r</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span> <span class="s1">&#39;uniprot&#39;</span><span class="p">,</span> <span class="s1">&#39;uniprot&#39;</span><span class="p">)</span>
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+  <h1>Source code for pypath.inputs.talklr</h1><div class="highlight"><pre>
+<span></span><span class="ch">#!/usr/bin/env python</span>
+<span class="c1"># -*- coding: utf-8 -*-</span>
+
+<span class="c1">#</span>
+<span class="c1">#  This file is part of the `pypath` python module</span>
+<span class="c1">#</span>
+<span class="c1">#  Copyright 2014-2023</span>
+<span class="c1">#  EMBL, EMBL-EBI, Uniklinik RWTH Aachen, Heidelberg University</span>
+<span class="c1">#</span>
+<span class="c1">#  Authors: see the file `README.rst`</span>
+<span class="c1">#  Contact: Dénes Türei (turei.denes@gmail.com)</span>
+<span class="c1">#</span>
+<span class="c1">#  Distributed under the GPLv3 License.</span>
+<span class="c1">#  See accompanying file LICENSE.txt or copy at</span>
+<span class="c1">#      https://www.gnu.org/licenses/gpl-3.0.html</span>
+<span class="c1">#</span>
+<span class="c1">#  Website: https://pypath.omnipathdb.org/</span>
+<span class="c1">#</span>
+
+<span class="kn">import</span> <span class="nn">collections</span>
+
+<span class="kn">import</span> <span class="nn">pyreadr</span>
+
+<span class="kn">import</span> <span class="nn">pypath.share.curl</span> <span class="k">as</span> <span class="nn">curl</span>
+<span class="kn">import</span> <span class="nn">pypath.share.common</span> <span class="k">as</span> <span class="nn">common</span>
+<span class="kn">import</span> <span class="nn">pypath.resources.urls</span> <span class="k">as</span> <span class="nn">urls</span>
+<span class="kn">import</span> <span class="nn">pypath.utils.mapping</span> <span class="k">as</span> <span class="nn">mapping</span>
+
+
+<div class="viewcode-block" id="talklr_raw">
+<a class="viewcode-back" href="../../../api/pypath.inputs.talklr.talklr_raw.html#pypath.inputs.talklr.talklr_raw">[docs]</a>
+<span class="k">def</span> <span class="nf">talklr_raw</span><span class="p">(</span><span class="n">putative</span> <span class="o">=</span> <span class="kc">True</span><span class="p">):</span>
+
+    <span class="n">url</span> <span class="o">=</span> <span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;talklr&#39;</span><span class="p">][</span><span class="s1">&#39;url&#39;</span><span class="p">]</span>
+    <span class="n">c</span> <span class="o">=</span> <span class="n">curl</span><span class="o">.</span><span class="n">Curl</span><span class="p">(</span><span class="n">url</span><span class="p">,</span> <span class="n">large</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span> <span class="n">silent</span> <span class="o">=</span> <span class="kc">False</span><span class="p">)</span>
+    <span class="n">rdata_path</span> <span class="o">=</span> <span class="n">c</span><span class="o">.</span><span class="n">fileobj</span><span class="o">.</span><span class="n">name</span>
+    <span class="n">c</span><span class="o">.</span><span class="n">fileobj</span><span class="o">.</span><span class="n">close</span><span class="p">()</span>
+
+    <span class="n">rdata</span> <span class="o">=</span> <span class="n">pyreadr</span><span class="o">.</span><span class="n">read_r</span><span class="p">(</span><span class="n">rdata_path</span><span class="p">)[</span><span class="s1">&#39;receptor_ligand&#39;</span><span class="p">]</span>
+    <span class="n">rdata</span><span class="o">.</span><span class="n">columns</span> <span class="o">=</span> <span class="p">[</span><span class="n">col</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s1">&#39;.&#39;</span><span class="p">,</span> <span class="s1">&#39;_&#39;</span><span class="p">)</span> <span class="k">for</span> <span class="n">col</span> <span class="ow">in</span> <span class="n">rdata</span><span class="o">.</span><span class="n">columns</span><span class="p">]</span>
+
+    <span class="k">if</span> <span class="ow">not</span> <span class="n">putative</span><span class="p">:</span>
+
+        <span class="n">rdata</span> <span class="o">=</span> <span class="n">rdata</span><span class="p">[</span><span class="n">rdata</span><span class="o">.</span><span class="n">Pair_Evidence</span> <span class="o">!=</span> <span class="s1">&#39;putative&#39;</span><span class="p">]</span>
+
+    <span class="k">return</span> <span class="n">rdata</span></div>
+
+
+
+<div class="viewcode-block" id="talklr_interactions">
+<a class="viewcode-back" href="../../../api/pypath.inputs.talklr.talklr_interactions.html#pypath.inputs.talklr.talklr_interactions">[docs]</a>
+<span class="k">def</span> <span class="nf">talklr_interactions</span><span class="p">(</span><span class="n">putative</span> <span class="o">=</span> <span class="kc">True</span><span class="p">):</span>
+
+    <span class="n">TalklrInteraction</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">namedtuple</span><span class="p">(</span>
+        <span class="s1">&#39;TalklrInteraction&#39;</span><span class="p">,</span>
+        <span class="p">[</span><span class="s1">&#39;ligand&#39;</span><span class="p">,</span> <span class="s1">&#39;receptor&#39;</span><span class="p">,</span> <span class="s1">&#39;pmids&#39;</span><span class="p">,</span> <span class="s1">&#39;resources&#39;</span><span class="p">,</span> <span class="s1">&#39;putative&#39;</span><span class="p">],</span>
+    <span class="p">)</span>
+
+    <span class="n">resource_columns</span> <span class="o">=</span> <span class="p">{</span>
+        <span class="s1">&#39;DLRP&#39;</span><span class="p">:</span> <span class="p">(</span><span class="s1">&#39;DLRP&#39;</span><span class="p">,),</span>
+        <span class="s1">&#39;Guide2Pharma&#39;</span><span class="p">:</span> <span class="p">(</span><span class="s1">&#39;IUPHAR&#39;</span><span class="p">,),</span>
+        <span class="s1">&#39;HPRD&#39;</span><span class="p">:</span> <span class="p">(</span><span class="s1">&#39;HPRD&#39;</span><span class="p">,),</span>
+        <span class="s1">&#39;STRING&#39;</span><span class="p">:</span> <span class="p">(</span><span class="s1">&#39;STRING_binding&#39;</span><span class="p">,</span> <span class="s1">&#39;STRING_experiment&#39;</span><span class="p">),</span>
+        <span class="s1">&#39;HPMR&#39;</span><span class="p">:</span> <span class="p">(</span><span class="s1">&#39;HPMR&#39;</span><span class="p">,),</span>
+    <span class="p">}</span>
+
+    <span class="n">raw</span> <span class="o">=</span> <span class="n">talklr_raw</span><span class="p">(</span><span class="n">putative</span> <span class="o">=</span> <span class="n">putative</span><span class="p">)</span>
+
+    <span class="k">for</span> <span class="n">rec</span> <span class="ow">in</span> <span class="n">raw</span><span class="o">.</span><span class="n">itertuples</span><span class="p">():</span>
+
+        <span class="n">resources</span> <span class="o">=</span> <span class="nb">tuple</span><span class="p">(</span>
+            <span class="n">resource</span>
+            <span class="k">for</span> <span class="n">resource</span><span class="p">,</span> <span class="n">labels</span> <span class="ow">in</span> <span class="n">resource_columns</span><span class="o">.</span><span class="n">items</span><span class="p">()</span>
+            <span class="k">if</span> <span class="nb">any</span><span class="p">(</span>
+                <span class="n">common</span><span class="o">.</span><span class="n">is_str</span><span class="p">(</span><span class="nb">getattr</span><span class="p">(</span><span class="n">rec</span><span class="p">,</span> <span class="n">lab</span><span class="p">))</span>
+                <span class="k">for</span> <span class="n">lab</span> <span class="ow">in</span> <span class="n">labels</span>
+            <span class="p">)</span>
+        <span class="p">)</span>
+        <span class="n">pmids</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="nb">tuple</span><span class="p">(</span><span class="n">pmid</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span> <span class="k">for</span> <span class="n">pmid</span> <span class="ow">in</span> <span class="n">rec</span><span class="o">.</span><span class="n">PMID_Manual</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;,&#39;</span><span class="p">))</span>
+                <span class="k">if</span> <span class="n">common</span><span class="o">.</span><span class="n">is_str</span><span class="p">(</span><span class="n">rec</span><span class="o">.</span><span class="n">PMID_Manual</span><span class="p">)</span> <span class="k">else</span>
+            <span class="p">()</span>
+        <span class="p">)</span>
+
+        <span class="k">yield</span><span class="p">(</span>
+            <span class="n">TalklrInteraction</span><span class="p">(</span>
+                <span class="n">ligand</span> <span class="o">=</span> <span class="n">rec</span><span class="o">.</span><span class="n">Ligand_ApprovedSymbol</span><span class="p">,</span>
+                <span class="n">receptor</span> <span class="o">=</span> <span class="n">rec</span><span class="o">.</span><span class="n">Receptor_ApprovedSymbol</span><span class="p">,</span>
+                <span class="n">pmids</span> <span class="o">=</span> <span class="n">pmids</span><span class="p">,</span>
+                <span class="n">resources</span> <span class="o">=</span> <span class="n">resources</span><span class="p">,</span>
+                <span class="n">putative</span> <span class="o">=</span> <span class="n">rec</span><span class="o">.</span><span class="n">Pair_Evidence</span> <span class="o">==</span> <span class="s1">&#39;putative&#39;</span><span class="p">,</span>
+            <span class="p">)</span>
+        <span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="talklr_annotations">
+<a class="viewcode-back" href="../../../api/pypath.inputs.talklr.talklr_annotations.html#pypath.inputs.talklr.talklr_annotations">[docs]</a>
+<span class="k">def</span> <span class="nf">talklr_annotations</span><span class="p">(</span><span class="n">putative</span> <span class="o">=</span> <span class="kc">True</span><span class="p">):</span>
+
+    <span class="n">TalklrAnnotation</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">namedtuple</span><span class="p">(</span>
+        <span class="s1">&#39;TalklrAnnotation&#39;</span><span class="p">,</span>
+        <span class="p">[</span><span class="s1">&#39;role&#39;</span><span class="p">,</span> <span class="s1">&#39;pmid&#39;</span><span class="p">,</span> <span class="s1">&#39;putative&#39;</span><span class="p">]</span>
+    <span class="p">)</span>
+
+
+    <span class="n">result</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">defaultdict</span><span class="p">(</span><span class="nb">set</span><span class="p">)</span>
+
+    <span class="k">for</span> <span class="n">ia</span> <span class="ow">in</span> <span class="n">talklr_interactions</span><span class="p">(</span><span class="n">putative</span> <span class="o">=</span> <span class="n">putative</span><span class="p">):</span>
+
+        <span class="k">for</span> <span class="n">role</span> <span class="ow">in</span> <span class="p">(</span><span class="s1">&#39;ligand&#39;</span><span class="p">,</span> <span class="s1">&#39;receptor&#39;</span><span class="p">):</span>
+
+            <span class="n">uniprots</span> <span class="o">=</span> <span class="n">mapping</span><span class="o">.</span><span class="n">map_name</span><span class="p">(</span>
+                <span class="nb">getattr</span><span class="p">(</span><span class="n">ia</span><span class="p">,</span> <span class="n">role</span><span class="p">),</span>
+                <span class="s1">&#39;genesymbol&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;uniprot&#39;</span><span class="p">,</span>
+                <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">,</span>
+            <span class="p">)</span>
+
+            <span class="k">for</span> <span class="n">uniprot</span> <span class="ow">in</span> <span class="n">uniprots</span><span class="p">:</span>
+
+                <span class="k">for</span> <span class="n">pmid</span> <span class="ow">in</span> <span class="p">(</span><span class="n">ia</span><span class="o">.</span><span class="n">pmids</span> <span class="ow">or</span> <span class="p">(</span><span class="kc">None</span><span class="p">,)):</span>
+
+                    <span class="n">result</span><span class="p">[</span><span class="n">uniprot</span><span class="p">]</span><span class="o">.</span><span class="n">add</span><span class="p">(</span>
+                        <span class="n">TalklrAnnotation</span><span class="p">(</span>
+                            <span class="n">role</span> <span class="o">=</span> <span class="n">role</span><span class="p">,</span>
+                            <span class="n">pmid</span> <span class="o">=</span> <span class="n">pmid</span><span class="p">,</span>
+                            <span class="n">putative</span> <span class="o">=</span> <span class="n">ia</span><span class="o">.</span><span class="n">putative</span><span class="p">,</span>
+                        <span class="p">)</span>
+                    <span class="p">)</span>
+
+    <span class="k">return</span> <span class="nb">dict</span><span class="p">(</span><span class="n">result</span><span class="p">)</span></div>
+
+</pre></div>
+
+                </article>
+              
+              
+              
+              
+              
+                <footer class="prev-next-footer">
+                  
+<div class="prev-next-area">
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diff --git a/_modules/pypath/inputs/tcdb.html b/_modules/pypath/inputs/tcdb.html
new file mode 100644
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@@ -0,0 +1,729 @@
+
+<!DOCTYPE html>
+
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+<html lang="en" data-content_root="../../../" >
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+                  
+  <h1>Source code for pypath.inputs.tcdb</h1><div class="highlight"><pre>
+<span></span><span class="ch">#!/usr/bin/env python</span>
+<span class="c1"># -*- coding: utf-8 -*-</span>
+
+<span class="c1">#</span>
+<span class="c1">#  This file is part of the `pypath` python module</span>
+<span class="c1">#</span>
+<span class="c1">#  Copyright 2014-2023</span>
+<span class="c1">#  EMBL, EMBL-EBI, Uniklinik RWTH Aachen, Heidelberg University</span>
+<span class="c1">#</span>
+<span class="c1">#  Authors: see the file `README.rst`</span>
+<span class="c1">#  Contact: Dénes Türei (turei.denes@gmail.com)</span>
+<span class="c1">#</span>
+<span class="c1">#  Distributed under the GPLv3 License.</span>
+<span class="c1">#  See accompanying file LICENSE.txt or copy at</span>
+<span class="c1">#      https://www.gnu.org/licenses/gpl-3.0.html</span>
+<span class="c1">#</span>
+<span class="c1">#  Website: https://pypath.omnipathdb.org/</span>
+<span class="c1">#</span>
+
+<span class="kn">from</span> <span class="nn">future.utils</span> <span class="kn">import</span> <span class="n">iteritems</span>
+
+<span class="kn">import</span> <span class="nn">re</span>
+<span class="kn">import</span> <span class="nn">collections</span>
+<span class="kn">import</span> <span class="nn">bs4</span>
+
+<span class="kn">import</span> <span class="nn">pypath.resources.urls</span> <span class="k">as</span> <span class="nn">urls</span>
+<span class="kn">import</span> <span class="nn">pypath.share.curl</span> <span class="k">as</span> <span class="nn">curl</span>
+<span class="kn">import</span> <span class="nn">pypath.utils.mapping</span> <span class="k">as</span> <span class="nn">mapping</span>
+<span class="kn">import</span> <span class="nn">pypath.utils.reflists</span> <span class="k">as</span> <span class="nn">reflists</span>
+
+
+<div class="viewcode-block" id="tcdb_families">
+<a class="viewcode-back" href="../../../api/pypath.inputs.tcdb.tcdb_families.html#pypath.inputs.tcdb.tcdb_families">[docs]</a>
+<span class="k">def</span> <span class="nf">tcdb_families</span><span class="p">():</span>
+
+    <span class="n">retag</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">compile</span><span class="p">(</span><span class="sa">r</span><span class="s1">&#39;&lt;.*&gt;&#39;</span><span class="p">)</span>
+    <span class="n">rethe</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">compile</span><span class="p">(</span><span class="sa">r</span><span class="s1">&#39;^[tT]he (.*) (?:Super)?[Ff]amily&#39;</span><span class="p">)</span>
+
+    <span class="n">url</span> <span class="o">=</span> <span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;tcdb&#39;</span><span class="p">][</span><span class="s1">&#39;url_families&#39;</span><span class="p">]</span>
+
+    <span class="n">c</span> <span class="o">=</span> <span class="n">curl</span><span class="o">.</span><span class="n">Curl</span><span class="p">(</span><span class="n">url</span><span class="p">,</span> <span class="n">large</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span> <span class="n">silent</span> <span class="o">=</span> <span class="kc">False</span><span class="p">)</span>
+
+    <span class="n">lines</span> <span class="o">=</span> <span class="n">bs4</span><span class="o">.</span><span class="n">BeautifulSoup</span><span class="p">(</span><span class="n">c</span><span class="o">.</span><span class="n">result</span><span class="p">,</span> <span class="n">features</span> <span class="o">=</span> <span class="s1">&#39;lxml&#39;</span><span class="p">)</span><span class="o">.</span><span class="n">find</span><span class="p">(</span><span class="s1">&#39;p&#39;</span><span class="p">)</span><span class="o">.</span><span class="n">text</span>
+
+    <span class="k">return</span> <span class="nb">dict</span><span class="p">(</span>
+        <span class="p">(</span>
+            <span class="n">tcid</span><span class="p">,</span>
+            <span class="n">rethe</span><span class="o">.</span><span class="n">sub</span><span class="p">(</span><span class="sa">r</span><span class="s1">&#39;\g&lt;1&gt;&#39;</span><span class="p">,</span> <span class="n">family</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\t</span><span class="s1">&#39;</span><span class="p">,</span> <span class="s1">&#39; &#39;</span><span class="p">))</span>
+        <span class="p">)</span>
+        <span class="k">for</span> <span class="n">tcid</span><span class="p">,</span> <span class="n">family</span> <span class="ow">in</span>
+        <span class="p">(</span>
+            <span class="n">retag</span><span class="o">.</span><span class="n">sub</span><span class="p">(</span><span class="s1">&#39;&#39;</span><span class="p">,</span> <span class="n">line</span><span class="o">.</span><span class="n">strip</span><span class="p">())</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\t</span><span class="s1">&#39;</span><span class="p">,</span> <span class="n">maxsplit</span> <span class="o">=</span> <span class="mi">1</span><span class="p">)</span>
+            <span class="k">for</span> <span class="n">line</span> <span class="ow">in</span> <span class="n">lines</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\n</span><span class="s1">&#39;</span><span class="p">)</span>
+        <span class="p">)</span>
+    <span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="tcdb_classes">
+<a class="viewcode-back" href="../../../api/pypath.inputs.tcdb.tcdb_classes.html#pypath.inputs.tcdb.tcdb_classes">[docs]</a>
+<span class="k">def</span> <span class="nf">tcdb_classes</span><span class="p">():</span>
+
+    <span class="n">refam</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">compile</span><span class="p">(</span><span class="sa">r</span><span class="s1">&#39;(\d\.[A-Z]\.\d+)&#39;</span><span class="p">)</span>
+    <span class="n">retab</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">compile</span><span class="p">(</span><span class="sa">r</span><span class="s1">&#39;\t+&#39;</span><span class="p">)</span>
+
+    <span class="n">url</span> <span class="o">=</span> <span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;tcdb&#39;</span><span class="p">][</span><span class="s1">&#39;url_acc2tc&#39;</span><span class="p">]</span>
+
+    <span class="n">c</span> <span class="o">=</span> <span class="n">curl</span><span class="o">.</span><span class="n">Curl</span><span class="p">(</span><span class="n">url</span><span class="p">,</span> <span class="n">large</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span> <span class="n">silent</span> <span class="o">=</span> <span class="kc">False</span><span class="p">)</span>
+
+    <span class="n">result</span> <span class="o">=</span> <span class="p">{}</span>
+
+    <span class="k">for</span> <span class="n">line</span> <span class="ow">in</span> <span class="n">c</span><span class="o">.</span><span class="n">result</span><span class="p">:</span>
+
+        <span class="k">if</span> <span class="ow">not</span> <span class="n">line</span><span class="p">:</span>
+
+            <span class="k">continue</span>
+
+        <span class="n">ac</span><span class="p">,</span> <span class="n">tc</span> <span class="o">=</span> <span class="n">retab</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="n">line</span><span class="o">.</span><span class="n">rstrip</span><span class="p">())</span>
+        <span class="n">family</span> <span class="o">=</span> <span class="n">refam</span><span class="o">.</span><span class="n">search</span><span class="p">(</span><span class="n">tc</span><span class="p">)</span><span class="o">.</span><span class="n">groups</span><span class="p">()[</span><span class="mi">0</span><span class="p">]</span>
+
+        <span class="n">result</span><span class="p">[</span><span class="n">ac</span><span class="p">]</span> <span class="o">=</span> <span class="p">(</span><span class="n">tc</span><span class="p">,</span> <span class="n">family</span><span class="p">)</span>
+
+    <span class="k">return</span> <span class="n">result</span></div>
+
+
+
+<div class="viewcode-block" id="tcdb_annotations">
+<a class="viewcode-back" href="../../../api/pypath.inputs.tcdb.tcdb_annotations.html#pypath.inputs.tcdb.tcdb_annotations">[docs]</a>
+<span class="k">def</span> <span class="nf">tcdb_annotations</span><span class="p">(</span><span class="n">organism</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">):</span>
+
+
+    <span class="n">TcdbAnnotation</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">namedtuple</span><span class="p">(</span>
+        <span class="s1">&#39;TcdbAnnotation&#39;</span><span class="p">,</span>
+        <span class="p">[</span>
+            <span class="s1">&#39;family&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;tcid&#39;</span><span class="p">,</span>
+        <span class="p">]</span>
+    <span class="p">)</span>
+
+
+    <span class="n">families</span> <span class="o">=</span> <span class="n">tcdb_families</span><span class="p">()</span>
+    <span class="n">classes</span> <span class="o">=</span> <span class="n">tcdb_classes</span><span class="p">()</span>
+    <span class="n">result</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">defaultdict</span><span class="p">(</span><span class="nb">set</span><span class="p">)</span>
+
+    <span class="k">for</span> <span class="n">ac</span><span class="p">,</span> <span class="p">(</span><span class="n">tc</span><span class="p">,</span> <span class="n">family</span><span class="p">)</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="n">classes</span><span class="p">):</span>
+
+        <span class="n">uniprots</span> <span class="o">=</span> <span class="n">mapping</span><span class="o">.</span><span class="n">map_name</span><span class="p">(</span>
+            <span class="n">ac</span><span class="p">,</span>
+            <span class="s1">&#39;uniprot&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;uniprot&#39;</span><span class="p">,</span>
+            <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">organism</span><span class="p">,</span>
+        <span class="p">)</span>
+
+        <span class="k">for</span> <span class="n">uniprot</span> <span class="ow">in</span> <span class="n">uniprots</span><span class="p">:</span>
+
+            <span class="k">if</span> <span class="n">reflists</span><span class="o">.</span><span class="n">check</span><span class="p">(</span><span class="n">uniprot</span><span class="p">,</span> <span class="s1">&#39;uniprot&#39;</span><span class="p">,</span> <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">organism</span><span class="p">):</span>
+
+                <span class="n">result</span><span class="p">[</span><span class="n">uniprot</span><span class="p">]</span><span class="o">.</span><span class="n">add</span><span class="p">(</span>
+                    <span class="n">TcdbAnnotation</span><span class="p">(</span>
+                        <span class="n">family</span> <span class="o">=</span> <span class="n">families</span><span class="p">[</span><span class="n">family</span><span class="p">],</span>
+                        <span class="n">tcid</span> <span class="o">=</span> <span class="n">tc</span><span class="p">,</span>
+                    <span class="p">)</span>
+                <span class="p">)</span>
+
+    <span class="k">return</span> <span class="nb">dict</span><span class="p">(</span><span class="n">result</span><span class="p">)</span></div>
+
+</pre></div>
+
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+  <h1>Source code for pypath.inputs.tfcensus</h1><div class="highlight"><pre>
+<span></span><span class="ch">#!/usr/bin/env python</span>
+<span class="c1"># -*- coding: utf-8 -*-</span>
+
+<span class="c1">#</span>
+<span class="c1">#  This file is part of the `pypath` python module</span>
+<span class="c1">#</span>
+<span class="c1">#  Copyright 2014-2023</span>
+<span class="c1">#  EMBL, EMBL-EBI, Uniklinik RWTH Aachen, Heidelberg University</span>
+<span class="c1">#</span>
+<span class="c1">#  Authors: see the file `README.rst`</span>
+<span class="c1">#  Contact: Dénes Türei (turei.denes@gmail.com)</span>
+<span class="c1">#</span>
+<span class="c1">#  Distributed under the GPLv3 License.</span>
+<span class="c1">#  See accompanying file LICENSE.txt or copy at</span>
+<span class="c1">#      https://www.gnu.org/licenses/gpl-3.0.html</span>
+<span class="c1">#</span>
+<span class="c1">#  Website: https://pypath.omnipathdb.org/</span>
+<span class="c1">#</span>
+
+<span class="kn">import</span> <span class="nn">re</span>
+<span class="kn">import</span> <span class="nn">collections</span>
+
+<span class="kn">import</span> <span class="nn">pypath.share.curl</span> <span class="k">as</span> <span class="nn">curl</span>
+<span class="kn">import</span> <span class="nn">pypath.resources.urls</span> <span class="k">as</span> <span class="nn">urls</span>
+<span class="kn">import</span> <span class="nn">pypath.utils.mapping</span> <span class="k">as</span> <span class="nn">mapping</span>
+
+
+<div class="viewcode-block" id="tfcensus_annotations">
+<a class="viewcode-back" href="../../../api/pypath.inputs.tfcensus.tfcensus_annotations.html#pypath.inputs.tfcensus.tfcensus_annotations">[docs]</a>
+<span class="k">def</span> <span class="nf">tfcensus_annotations</span><span class="p">(</span><span class="n">only_classes</span> <span class="o">=</span> <span class="kc">None</span><span class="p">):</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Downloads and processes the list of all known transcription factors from</span>
+<span class="sd">    TF census (Vaquerizas 2009). This resource is human only.</span>
+<span class="sd">    Returns dict with UniProt IDs as keys and TF annotations as values.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="n">TfcensusAnnotation</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">namedtuple</span><span class="p">(</span>
+        <span class="s1">&#39;TfcensusAnnotation&#39;</span><span class="p">,</span>
+        <span class="p">[</span><span class="s1">&#39;tfcensus_class&#39;</span><span class="p">,</span> <span class="s1">&#39;tissue&#39;</span><span class="p">],</span>
+    <span class="p">)</span>
+
+
+    <span class="n">result</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">defaultdict</span><span class="p">(</span><span class="nb">set</span><span class="p">)</span>
+
+    <span class="n">reensg</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">compile</span><span class="p">(</span><span class="sa">r</span><span class="s1">&#39;ENSG[0-9]</span><span class="si">{11}</span><span class="s1">&#39;</span><span class="p">)</span>
+    <span class="n">url</span> <span class="o">=</span> <span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;vaquerizas2009&#39;</span><span class="p">][</span><span class="s1">&#39;url&#39;</span><span class="p">]</span>
+    <span class="n">c</span> <span class="o">=</span> <span class="n">curl</span><span class="o">.</span><span class="n">Curl</span><span class="p">(</span><span class="n">url</span><span class="p">,</span> <span class="n">silent</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span> <span class="n">large</span> <span class="o">=</span> <span class="kc">True</span><span class="p">)</span>
+
+    <span class="n">header</span> <span class="o">=</span> <span class="kc">True</span>
+
+    <span class="k">for</span> <span class="n">l</span> <span class="ow">in</span> <span class="n">c</span><span class="o">.</span><span class="n">result</span><span class="p">:</span>
+
+        <span class="n">l</span> <span class="o">=</span> <span class="n">l</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\t</span><span class="s1">&#39;</span><span class="p">)</span>
+
+        <span class="k">if</span> <span class="n">header</span><span class="p">:</span>
+
+            <span class="k">if</span> <span class="n">l</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">==</span> <span class="s1">&#39;Class&#39;</span><span class="p">:</span>
+
+                <span class="n">header</span> <span class="o">=</span> <span class="kc">False</span>
+
+            <span class="k">continue</span>
+
+        <span class="n">ensg</span> <span class="o">=</span> <span class="n">reensg</span><span class="o">.</span><span class="n">findall</span><span class="p">(</span><span class="n">l</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span>
+        <span class="n">hgnc</span> <span class="o">=</span> <span class="n">l</span><span class="p">[</span><span class="mi">5</span><span class="p">]</span>
+        <span class="n">tfcensus_class</span> <span class="o">=</span> <span class="n">l</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span>
+        <span class="n">tissues</span> <span class="o">=</span> <span class="n">l</span><span class="p">[</span><span class="mi">6</span><span class="p">]</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span> <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">l</span><span class="p">)</span> <span class="o">&gt;</span> <span class="mi">6</span> <span class="k">else</span> <span class="s1">&#39;&#39;</span>
+        <span class="n">tissues</span> <span class="o">=</span> <span class="n">tissues</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;;&#39;</span><span class="p">)</span> <span class="k">if</span> <span class="n">tissues</span> <span class="k">else</span> <span class="p">[</span><span class="kc">None</span><span class="p">]</span>
+
+        <span class="n">uniprots</span> <span class="o">=</span> <span class="n">mapping</span><span class="o">.</span><span class="n">map_names</span><span class="p">(</span><span class="n">ensg</span><span class="p">,</span> <span class="s1">&#39;ensembl&#39;</span><span class="p">,</span> <span class="s1">&#39;uniprot&#39;</span><span class="p">)</span>
+        <span class="n">uniprots</span><span class="o">.</span><span class="n">update</span><span class="p">(</span><span class="n">mapping</span><span class="o">.</span><span class="n">map_name</span><span class="p">(</span><span class="n">hgnc</span><span class="p">,</span> <span class="s1">&#39;genesymbol&#39;</span><span class="p">,</span> <span class="s1">&#39;uniprot&#39;</span><span class="p">))</span>
+
+        <span class="k">for</span> <span class="n">uniprot</span> <span class="ow">in</span> <span class="n">uniprots</span><span class="p">:</span>
+
+            <span class="k">for</span> <span class="n">tissue</span> <span class="ow">in</span> <span class="n">tissues</span><span class="p">:</span>
+
+                <span class="n">result</span><span class="p">[</span><span class="n">uniprot</span><span class="p">]</span><span class="o">.</span><span class="n">add</span><span class="p">(</span>
+                    <span class="n">TfcensusAnnotation</span><span class="p">(</span>
+                        <span class="n">tfcensus_class</span> <span class="o">=</span> <span class="n">tfcensus_class</span><span class="p">,</span>
+                        <span class="n">tissue</span> <span class="o">=</span> <span class="n">tissue</span><span class="p">,</span>
+                    <span class="p">)</span>
+                <span class="p">)</span>
+
+    <span class="k">return</span> <span class="nb">dict</span><span class="p">(</span><span class="n">result</span><span class="p">)</span></div>
+
+</pre></div>
+
+                </article>
+              
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+              
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+            
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+        
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+  <!-- Scripts loaded after <body> so the DOM is not blocked -->
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+      
+    </div>
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+</html>
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diff --git a/_modules/pypath/inputs/threedcomplex.html b/_modules/pypath/inputs/threedcomplex.html
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+                  
+  <h1>Source code for pypath.inputs.threedcomplex</h1><div class="highlight"><pre>
+<span></span><span class="ch">#!/usr/bin/env python</span>
+<span class="c1"># -*- coding: utf-8 -*-</span>
+
+<span class="c1">#</span>
+<span class="c1">#  This file is part of the `pypath` python module</span>
+<span class="c1">#</span>
+<span class="c1">#  Copyright 2014-2023</span>
+<span class="c1">#  EMBL, EMBL-EBI, Uniklinik RWTH Aachen, Heidelberg University</span>
+<span class="c1">#</span>
+<span class="c1">#  Authors: see the file `README.rst`</span>
+<span class="c1">#  Contact: Dénes Türei (turei.denes@gmail.com)</span>
+<span class="c1">#</span>
+<span class="c1">#  Distributed under the GPLv3 License.</span>
+<span class="c1">#  See accompanying file LICENSE.txt or copy at</span>
+<span class="c1">#      https://www.gnu.org/licenses/gpl-3.0.html</span>
+<span class="c1">#</span>
+<span class="c1">#  Website: https://pypath.omnipathdb.org/</span>
+<span class="c1">#</span>
+
+<span class="kn">from</span> <span class="nn">future.utils</span> <span class="kn">import</span> <span class="n">iteritems</span>
+
+<span class="kn">import</span> <span class="nn">itertools</span>
+<span class="kn">import</span> <span class="nn">collections</span>
+
+<span class="kn">import</span> <span class="nn">pypath.resources.urls</span> <span class="k">as</span> <span class="nn">urls</span>
+<span class="kn">import</span> <span class="nn">pypath.share.curl</span> <span class="k">as</span> <span class="nn">curl</span>
+<span class="kn">import</span> <span class="nn">pypath.share.progress</span> <span class="k">as</span> <span class="nn">progress</span>
+<span class="kn">import</span> <span class="nn">pypath.share.common</span> <span class="k">as</span> <span class="nn">common</span>
+<span class="kn">import</span> <span class="nn">pypath.inputs.pdb</span> <span class="k">as</span> <span class="nn">pdb_input</span>
+<span class="kn">import</span> <span class="nn">pypath.inputs.pfam</span> <span class="k">as</span> <span class="nn">pfam_input</span>
+<span class="kn">import</span> <span class="nn">pypath.internals.intera</span> <span class="k">as</span> <span class="nn">intera</span>
+
+
+<div class="viewcode-block" id="threedcomplex_complexes">
+<a class="viewcode-back" href="../../../api/pypath.inputs.threedcomplex.threedcomplex_complexes.html#pypath.inputs.threedcomplex.threedcomplex_complexes">[docs]</a>
+<span class="k">def</span> <span class="nf">threedcomplex_complexes</span><span class="p">():</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    To be implemented later. Should return dictionary of</span>
+<span class="sd">    pypath.internals.intera.Complex objects.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="k">raise</span> <span class="ne">NotImplementedError</span></div>
+
+
+
+<div class="viewcode-block" id="threedcomplex_ddi">
+<a class="viewcode-back" href="../../../api/pypath.inputs.threedcomplex.threedcomplex_ddi.html#pypath.inputs.threedcomplex.threedcomplex_ddi">[docs]</a>
+<span class="k">def</span> <span class="nf">threedcomplex_ddi</span><span class="p">(</span><span class="n">contacts</span> <span class="o">=</span> <span class="kc">None</span><span class="p">):</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Downloads and preprocesses data from the 3DComplex database</span>
+<span class="sd">    (http://shmoo.weizmann.ac.il/elevy/3dcomplexV6/Home.cgi).</span>
+
+<span class="sd">    Args</span>
+<span class="sd">        contacts (set): A map of 3D structure based contacts, as provided by</span>
+<span class="sd">            ``threedcomplex_contacts``. If None, it will be obtained</span>
+<span class="sd">            automatically.</span>
+
+<span class="sd">    Returns</span>
+<span class="sd">        A list of domain-domain interaction objects.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="n">contacts</span> <span class="o">=</span> <span class="n">contacts</span> <span class="ow">or</span> <span class="n">threedcomplex_contacts</span><span class="p">()</span>
+    <span class="n">uniprots</span> <span class="o">=</span> <span class="p">(</span>
+        <span class="n">common</span><span class="o">.</span><span class="n">values</span><span class="p">(</span><span class="n">contacts</span><span class="p">,</span> <span class="s1">&#39;uniprot_1&#39;</span><span class="p">)</span> <span class="o">|</span>
+        <span class="n">common</span><span class="o">.</span><span class="n">values</span><span class="p">(</span><span class="n">contacts</span><span class="p">,</span> <span class="s1">&#39;uniprot_2&#39;</span><span class="p">)</span>
+    <span class="p">)</span>
+    <span class="n">u_pfam</span> <span class="o">=</span> <span class="n">pfam_input</span><span class="o">.</span><span class="n">pfam_regions</span><span class="p">(</span><span class="n">uniprots</span><span class="p">,</span> <span class="n">value</span> <span class="o">=</span> <span class="s1">&#39;uniprot&#39;</span><span class="p">)</span>
+
+    <span class="n">ddi</span> <span class="o">=</span> <span class="p">[]</span>
+    <span class="n">prg</span> <span class="o">=</span> <span class="n">progress</span><span class="o">.</span><span class="n">Progress</span><span class="p">(</span>
+        <span class="nb">len</span><span class="p">(</span><span class="n">contacts</span><span class="p">),</span>
+        <span class="s1">&#39;Processing contact information&#39;</span><span class="p">,</span>
+        <span class="mi">9</span><span class="p">,</span>
+    <span class="p">)</span>
+
+    <span class="k">for</span> <span class="n">con</span> <span class="ow">in</span> <span class="n">contacts</span><span class="p">:</span>
+
+        <span class="n">prg</span><span class="o">.</span><span class="n">step</span><span class="p">()</span>
+
+        <span class="n">pdb</span> <span class="o">=</span> <span class="n">common</span><span class="o">.</span><span class="n">prefix</span><span class="p">(</span><span class="n">con</span><span class="o">.</span><span class="n">pdb</span><span class="p">,</span> <span class="s1">&#39;_&#39;</span><span class="p">)</span>
+        <span class="n">pfams1</span> <span class="o">=</span> <span class="p">{</span><span class="n">common</span><span class="o">.</span><span class="n">prefix</span><span class="p">(</span><span class="n">x</span><span class="p">,</span> <span class="s1">&#39;.&#39;</span><span class="p">)</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">con</span><span class="o">.</span><span class="n">domain_p1</span><span class="p">}</span>
+        <span class="n">pfams2</span> <span class="o">=</span> <span class="p">{</span><span class="n">common</span><span class="o">.</span><span class="n">prefix</span><span class="p">(</span><span class="n">x</span><span class="p">,</span> <span class="s1">&#39;.&#39;</span><span class="p">)</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">con</span><span class="o">.</span><span class="n">domain_p2</span><span class="p">}</span>
+
+        <span class="k">for</span> <span class="n">pfam1</span><span class="p">,</span> <span class="n">pfam2</span> <span class="ow">in</span> <span class="n">itertools</span><span class="o">.</span><span class="n">product</span><span class="p">(</span><span class="n">pfams1</span><span class="p">,</span> <span class="n">pfams2</span><span class="p">):</span>
+
+            <span class="n">pfam1_details</span> <span class="o">=</span> <span class="p">[{</span>
+                <span class="s1">&#39;start&#39;</span><span class="p">:</span> <span class="kc">None</span><span class="p">,</span>
+                <span class="s1">&#39;end&#39;</span><span class="p">:</span> <span class="kc">None</span><span class="p">,</span>
+                <span class="s1">&#39;isoform&#39;</span><span class="p">:</span> <span class="mi">1</span>
+            <span class="p">}]</span>
+            <span class="n">pfam2_details</span> <span class="o">=</span> <span class="p">[{</span>
+                <span class="s1">&#39;start&#39;</span><span class="p">:</span> <span class="kc">None</span><span class="p">,</span>
+                <span class="s1">&#39;end&#39;</span><span class="p">:</span> <span class="kc">None</span><span class="p">,</span>
+                <span class="s1">&#39;isoform&#39;</span><span class="p">:</span> <span class="mi">1</span>
+            <span class="p">}]</span>
+
+            <span class="k">if</span> <span class="n">con</span><span class="o">.</span><span class="n">uniprot_1</span> <span class="ow">in</span> <span class="n">u_pfam</span> <span class="ow">and</span> <span class="n">pfam1</span> <span class="ow">in</span> <span class="n">u_pfam</span><span class="p">[</span><span class="n">con</span><span class="o">.</span><span class="n">uniprot_1</span><span class="p">]:</span>
+
+                <span class="n">pfam1_details</span> <span class="o">=</span> <span class="n">u_pfam</span><span class="p">[</span><span class="n">con</span><span class="o">.</span><span class="n">uniprot_1</span><span class="p">][</span><span class="n">pfam1</span><span class="p">]</span>
+
+            <span class="k">if</span> <span class="n">con</span><span class="o">.</span><span class="n">uniprot_2</span> <span class="ow">in</span> <span class="n">u_pfam</span> <span class="ow">and</span> <span class="n">pfam2</span> <span class="ow">in</span> <span class="n">u_pfam</span><span class="p">[</span><span class="n">con</span><span class="o">.</span><span class="n">uniprot_2</span><span class="p">]:</span>
+
+                <span class="n">pfam2_details</span> <span class="o">=</span> <span class="n">u_pfam</span><span class="p">[</span><span class="n">con</span><span class="o">.</span><span class="n">uniprot_2</span><span class="p">][</span><span class="n">pfam2</span><span class="p">]</span>
+
+            <span class="k">for</span> <span class="n">pfam1_d</span><span class="p">,</span> <span class="n">pfam2_d</span> <span class="ow">in</span> <span class="n">itertools</span><span class="o">.</span><span class="n">product</span><span class="p">(</span>
+                <span class="n">pfam1_details</span><span class="p">,</span>
+                <span class="n">pfam2_details</span><span class="p">,</span>
+            <span class="p">):</span>
+
+                <span class="n">dom1</span> <span class="o">=</span> <span class="n">intera</span><span class="o">.</span><span class="n">Domain</span><span class="p">(</span>
+                    <span class="n">protein</span> <span class="o">=</span> <span class="n">con</span><span class="o">.</span><span class="n">uniprot_1</span><span class="p">,</span>
+                    <span class="n">domain</span> <span class="o">=</span> <span class="n">pfam1</span><span class="p">,</span>
+                    <span class="n">start</span> <span class="o">=</span> <span class="n">pfam1_d</span><span class="p">[</span><span class="s1">&#39;start&#39;</span><span class="p">],</span>
+                    <span class="n">end</span> <span class="o">=</span> <span class="n">pfam1_d</span><span class="p">[</span><span class="s1">&#39;end&#39;</span><span class="p">],</span>
+                    <span class="n">isoform</span> <span class="o">=</span> <span class="n">pfam1_d</span><span class="p">[</span><span class="s1">&#39;isoform&#39;</span><span class="p">],</span>
+                    <span class="n">chains</span> <span class="o">=</span> <span class="p">{</span><span class="n">pdb</span><span class="p">:</span> <span class="n">con</span><span class="o">.</span><span class="n">chain_1</span><span class="p">},</span>
+                <span class="p">)</span>
+                <span class="n">dom2</span> <span class="o">=</span> <span class="n">intera</span><span class="o">.</span><span class="n">Domain</span><span class="p">(</span>
+                    <span class="n">protein</span> <span class="o">=</span> <span class="n">con</span><span class="o">.</span><span class="n">uniprot_2</span><span class="p">,</span>
+                    <span class="n">domain</span> <span class="o">=</span> <span class="n">pfam2</span><span class="p">,</span>
+                    <span class="n">start</span> <span class="o">=</span> <span class="n">pfam2_d</span><span class="p">[</span><span class="s1">&#39;start&#39;</span><span class="p">],</span>
+                    <span class="n">end</span> <span class="o">=</span> <span class="n">pfam2_d</span><span class="p">[</span><span class="s1">&#39;end&#39;</span><span class="p">],</span>
+                    <span class="n">isoform</span> <span class="o">=</span> <span class="n">pfam2_d</span><span class="p">[</span><span class="s1">&#39;isoform&#39;</span><span class="p">],</span>
+                    <span class="n">chains</span> <span class="o">=</span> <span class="p">{</span><span class="n">pdb</span><span class="p">:</span> <span class="n">con</span><span class="o">.</span><span class="n">chain_2</span><span class="p">},</span>
+                <span class="p">)</span>
+                <span class="n">dd</span> <span class="o">=</span> <span class="n">intera</span><span class="o">.</span><span class="n">DomainDomain</span><span class="p">(</span>
+                    <span class="n">dom1</span><span class="p">,</span>
+                    <span class="n">dom2</span><span class="p">,</span>
+                    <span class="n">pdbs</span> <span class="o">=</span> <span class="n">pdb</span><span class="p">,</span>
+                    <span class="n">sources</span> <span class="o">=</span> <span class="s1">&#39;3DComplex&#39;</span><span class="p">,</span>
+                    <span class="n">contact_residues</span> <span class="o">=</span> <span class="n">con</span><span class="o">.</span><span class="n">n_residues</span><span class="p">,</span>
+                <span class="p">)</span>
+                <span class="n">ddi</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">dd</span><span class="p">)</span>
+
+    <span class="n">prg</span><span class="o">.</span><span class="n">terminate</span><span class="p">()</span>
+
+    <span class="k">return</span> <span class="n">ddi</span></div>
+
+
+
+<div class="viewcode-block" id="threedcomplex_chains">
+<a class="viewcode-back" href="../../../api/pypath.inputs.threedcomplex.threedcomplex_chains.html#pypath.inputs.threedcomplex.threedcomplex_chains">[docs]</a>
+<span class="k">def</span> <span class="nf">threedcomplex_chains</span><span class="p">():</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Returns the chain correspondancy map of the 3D Complex database.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="n">c</span> <span class="o">=</span> <span class="n">curl</span><span class="o">.</span><span class="n">Curl</span><span class="p">(</span>
+        <span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;3dcomplex_correspondancy&#39;</span><span class="p">][</span><span class="s1">&#39;url&#39;</span><span class="p">],</span>
+        <span class="n">silent</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+    <span class="p">)</span>
+    <span class="n">corresp</span> <span class="o">=</span> <span class="n">c</span><span class="o">.</span><span class="n">result</span>
+
+    <span class="n">corresp</span> <span class="o">=</span> <span class="n">corresp</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\n</span><span class="s1">&#39;</span><span class="p">)</span>
+    <span class="n">corr_dict</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">defaultdict</span><span class="p">(</span>
+        <span class="k">lambda</span><span class="p">:</span> <span class="n">collections</span><span class="o">.</span><span class="n">defaultdict</span><span class="p">(</span><span class="nb">dict</span><span class="p">)</span>
+    <span class="p">)</span>
+
+    <span class="c1"># chain correspondancy map in a dict</span>
+    <span class="k">for</span> <span class="n">l</span> <span class="ow">in</span> <span class="n">corresp</span><span class="p">:</span>
+
+        <span class="n">l</span> <span class="o">=</span> <span class="n">l</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\t</span><span class="s1">&#39;</span><span class="p">)</span>
+
+        <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">l</span><span class="p">)</span> <span class="o">&gt;</span> <span class="mi">2</span><span class="p">:</span>
+
+            <span class="n">pdb</span> <span class="o">=</span> <span class="n">common</span><span class="o">.</span><span class="n">prefix</span><span class="p">(</span><span class="n">l</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="s1">&#39;.&#39;</span><span class="p">)</span>
+            <span class="n">corr_dict</span><span class="p">[</span><span class="n">pdb</span><span class="p">][</span><span class="n">l</span><span class="p">[</span><span class="mi">1</span><span class="p">]]</span> <span class="o">=</span> <span class="n">l</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span>
+
+    <span class="k">return</span> <span class="nb">dict</span><span class="p">((</span><span class="n">k</span><span class="p">,</span> <span class="nb">dict</span><span class="p">(</span><span class="n">v</span><span class="p">))</span> <span class="k">for</span> <span class="n">k</span><span class="p">,</span> <span class="n">v</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="n">corr_dict</span><span class="p">))</span></div>
+
+
+
+<div class="viewcode-block" id="threedcomplex_contacts">
+<a class="viewcode-back" href="../../../api/pypath.inputs.threedcomplex.threedcomplex_contacts.html#pypath.inputs.threedcomplex.threedcomplex_contacts">[docs]</a>
+<span class="k">def</span> <span class="nf">threedcomplex_contacts</span><span class="p">(</span><span class="n">chains</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span> <span class="n">pdb_uniprot</span> <span class="o">=</span> <span class="kc">None</span><span class="p">):</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Returns the 3D structure based domain-domain contact map from the</span>
+<span class="sd">    3D Complex database.</span>
+
+<span class="sd">    Args</span>
+<span class="sd">        chains (dict): A dict of chain correspondancy map, as created by</span>
+<span class="sd">            ``threedcomplex_chains``. If None, it will be obtained</span>
+<span class="sd">            automatically.</span>
+<span class="sd">        pdb_uniprot (dict): A dict of PDB-UniProt mappings, as created by</span>
+<span class="sd">            ``pypath.inputs.pdb.pdb_chains``. If None, it will be obtained</span>
+<span class="sd">            automatically.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="n">ThreedcomplexContact</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">namedtuple</span><span class="p">(</span>
+        <span class="s1">&#39;ThreedcomplexContact&#39;</span><span class="p">,</span>
+        <span class="p">(</span>
+            <span class="s1">&#39;pdb&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;uniprot_1&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;uniprot_2&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;chain_1&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;chain_2&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;n_residues&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;length_1&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;length_2&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;domain_s1&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;domain_p1&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;domain_s2&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;domain_p2&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;ident&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;homo&#39;</span><span class="p">,</span>
+        <span class="p">),</span>
+    <span class="p">)</span>
+
+
+    <span class="n">chains</span> <span class="o">=</span> <span class="n">chains</span> <span class="ow">or</span> <span class="n">threedcomplex_chains</span><span class="p">()</span>
+    <span class="n">pdb_u</span> <span class="o">=</span> <span class="n">pdb_uniprot</span> <span class="ow">or</span> <span class="n">pdb_input</span><span class="o">.</span><span class="n">pdb_chains</span><span class="p">()[</span><span class="mi">1</span><span class="p">]</span>
+
+    <span class="n">c</span> <span class="o">=</span> <span class="n">curl</span><span class="o">.</span><span class="n">Curl</span><span class="p">(</span>
+        <span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;3dcomplex_contact&#39;</span><span class="p">][</span><span class="s1">&#39;url&#39;</span><span class="p">],</span>
+        <span class="n">silent</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+        <span class="n">slow</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
+    <span class="p">)</span>
+    <span class="n">contact</span> <span class="o">=</span> <span class="n">c</span><span class="o">.</span><span class="n">result</span>
+
+    <span class="n">result</span> <span class="o">=</span> <span class="nb">set</span><span class="p">()</span>
+
+    <span class="k">for</span> <span class="n">l</span> <span class="ow">in</span> <span class="n">contact</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\n</span><span class="s1">&#39;</span><span class="p">):</span>
+
+        <span class="n">l</span> <span class="o">=</span> <span class="n">l</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\t</span><span class="s1">&#39;</span><span class="p">)</span>
+
+        <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">l</span><span class="p">)</span> <span class="o">&gt;</span> <span class="mi">11</span><span class="p">:</span>
+
+            <span class="n">compl</span> <span class="o">=</span> <span class="n">l</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span>
+            <span class="n">pdb</span> <span class="o">=</span> <span class="n">common</span><span class="o">.</span><span class="n">prefix</span><span class="p">(</span><span class="n">compl</span><span class="p">,</span> <span class="s1">&#39;_&#39;</span><span class="p">)</span>
+
+            <span class="k">if</span> <span class="p">(</span>
+                <span class="n">compl</span> <span class="ow">in</span> <span class="n">chains</span> <span class="ow">and</span>
+                <span class="n">l</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="ow">in</span> <span class="n">chains</span><span class="p">[</span><span class="n">compl</span><span class="p">]</span> <span class="ow">and</span>
+                <span class="n">l</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="ow">in</span> <span class="n">chains</span><span class="p">[</span><span class="n">compl</span><span class="p">]</span>
+            <span class="p">):</span>
+
+                <span class="n">ch1</span> <span class="o">=</span> <span class="n">chains</span><span class="p">[</span><span class="n">compl</span><span class="p">][</span><span class="n">l</span><span class="p">[</span><span class="mi">1</span><span class="p">]]</span>
+                <span class="n">ch2</span> <span class="o">=</span> <span class="n">chains</span><span class="p">[</span><span class="n">compl</span><span class="p">][</span><span class="n">l</span><span class="p">[</span><span class="mi">2</span><span class="p">]]</span>
+
+                <span class="k">if</span> <span class="p">(</span>
+                    <span class="n">pdb</span> <span class="ow">in</span> <span class="n">pdb_u</span> <span class="ow">and</span>
+                    <span class="n">ch1</span> <span class="ow">in</span> <span class="n">pdb_u</span><span class="p">[</span><span class="n">pdb</span><span class="p">]</span> <span class="ow">and</span>
+                    <span class="n">ch2</span> <span class="ow">in</span> <span class="n">pdb_u</span><span class="p">[</span><span class="n">pdb</span><span class="p">]</span>
+                <span class="p">):</span>
+
+                    <span class="n">up1</span> <span class="o">=</span> <span class="n">pdb_u</span><span class="p">[</span><span class="n">pdb</span><span class="p">][</span><span class="n">ch1</span><span class="p">][</span><span class="s1">&#39;uniprot&#39;</span><span class="p">]</span>
+                    <span class="n">up2</span> <span class="o">=</span> <span class="n">pdb_u</span><span class="p">[</span><span class="n">pdb</span><span class="p">][</span><span class="n">ch2</span><span class="p">][</span><span class="s1">&#39;uniprot&#39;</span><span class="p">]</span>
+
+                    <span class="n">result</span><span class="o">.</span><span class="n">add</span><span class="p">(</span>
+                        <span class="n">ThreedcomplexContact</span><span class="p">(</span>
+                            <span class="n">pdb</span> <span class="o">=</span> <span class="n">compl</span><span class="p">,</span>
+                            <span class="n">uniprot_1</span> <span class="o">=</span> <span class="n">up1</span><span class="p">,</span>
+                            <span class="n">uniprot_2</span> <span class="o">=</span> <span class="n">up2</span><span class="p">,</span>
+                            <span class="n">chain_1</span> <span class="o">=</span> <span class="n">ch1</span><span class="p">,</span>
+                            <span class="n">chain_2</span> <span class="o">=</span> <span class="n">ch2</span><span class="p">,</span>
+                            <span class="n">n_residues</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">l</span><span class="p">[</span><span class="mi">3</span><span class="p">]),</span>
+                            <span class="n">length_1</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">l</span><span class="p">[</span><span class="mi">4</span><span class="p">]),</span>
+                            <span class="n">length_2</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">l</span><span class="p">[</span><span class="mi">5</span><span class="p">]),</span>
+                            <span class="n">domain_s1</span> <span class="o">=</span> <span class="nb">tuple</span><span class="p">(</span><span class="n">l</span><span class="p">[</span><span class="mi">6</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;;&#39;</span><span class="p">)),</span>
+                            <span class="n">domain_s2</span> <span class="o">=</span> <span class="nb">tuple</span><span class="p">(</span><span class="n">l</span><span class="p">[</span><span class="mi">8</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;;&#39;</span><span class="p">)),</span>
+                            <span class="n">domain_p1</span> <span class="o">=</span> <span class="nb">tuple</span><span class="p">(</span><span class="n">l</span><span class="p">[</span><span class="mi">7</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;;&#39;</span><span class="p">)),</span>
+                            <span class="n">domain_p2</span> <span class="o">=</span> <span class="nb">tuple</span><span class="p">(</span><span class="n">l</span><span class="p">[</span><span class="mi">9</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;;&#39;</span><span class="p">)),</span>
+                            <span class="n">ident</span> <span class="o">=</span> <span class="nb">bool</span><span class="p">(</span><span class="nb">int</span><span class="p">(</span><span class="n">l</span><span class="p">[</span><span class="mi">10</span><span class="p">])),</span>
+                            <span class="n">homo</span> <span class="o">=</span> <span class="nb">bool</span><span class="p">(</span><span class="nb">int</span><span class="p">(</span><span class="n">l</span><span class="p">[</span><span class="mi">11</span><span class="p">])),</span>
+                        <span class="p">)</span>
+                    <span class="p">)</span>
+
+    <span class="k">return</span> <span class="n">result</span></div>
+
+
+
+<div class="viewcode-block" id="threedcomplex_nresidues">
+<a class="viewcode-back" href="../../../api/pypath.inputs.threedcomplex.threedcomplex_nresidues.html#pypath.inputs.threedcomplex.threedcomplex_nresidues">[docs]</a>
+<span class="k">def</span> <span class="nf">threedcomplex_nresidues</span><span class="p">():</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Downloads and preprocesses data from the 3DComplex database</span>
+<span class="sd">    (http://shmoo.weizmann.ac.il/elevy/3dcomplexV6/Home.cgi).</span>
+
+<span class="sd">    Returns dict of dicts where top level keys are PDB IDs, second level</span>
+<span class="sd">    keys are pairs of tuples of UniProt IDs and values are list with the</span>
+<span class="sd">    number of amino acids in contact.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="n">nresidues</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">defaultdict</span><span class="p">(</span>
+        <span class="k">lambda</span><span class="p">:</span> <span class="n">collections</span><span class="o">.</span><span class="n">defaultdict</span><span class="p">(</span><span class="nb">list</span><span class="p">)</span>
+    <span class="p">)</span>
+
+    <span class="k">for</span> <span class="n">contact</span> <span class="ow">in</span> <span class="n">threedcomplex_contacts</span><span class="p">():</span>
+
+        <span class="n">uniprot_key</span> <span class="o">=</span> <span class="nb">tuple</span><span class="p">(</span><span class="nb">sorted</span><span class="p">((</span><span class="n">contact</span><span class="o">.</span><span class="n">uniprot_1</span><span class="p">,</span> <span class="n">contact</span><span class="o">.</span><span class="n">uniprot_2</span><span class="p">)))</span>
+        <span class="n">nresidues</span><span class="p">[</span><span class="n">contact</span><span class="o">.</span><span class="n">pdb</span><span class="p">][</span><span class="n">uniprot_key</span><span class="p">]</span> <span class="o">=</span> <span class="n">contact</span><span class="o">.</span><span class="n">n_residues</span>
+
+    <span class="k">return</span> <span class="nb">dict</span><span class="p">((</span><span class="n">k</span><span class="p">,</span> <span class="nb">dict</span><span class="p">(</span><span class="n">v</span><span class="p">))</span> <span class="k">for</span> <span class="n">k</span><span class="p">,</span> <span class="n">v</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="n">nresidues</span><span class="p">))</span></div>
+
+</pre></div>
+
+                </article>
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+  <h1>Source code for pypath.inputs.threedid</h1><div class="highlight"><pre>
+<span></span><span class="ch">#!/usr/bin/env python</span>
+<span class="c1"># -*- coding: utf-8 -*-</span>
+
+<span class="c1">#</span>
+<span class="c1">#  This file is part of the `pypath` python module</span>
+<span class="c1">#</span>
+<span class="c1">#  Copyright 2014-2023</span>
+<span class="c1">#  EMBL, EMBL-EBI, Uniklinik RWTH Aachen, Heidelberg University</span>
+<span class="c1">#</span>
+<span class="c1">#  Authors: see the file `README.rst`</span>
+<span class="c1">#  Contact: Dénes Türei (turei.denes@gmail.com)</span>
+<span class="c1">#</span>
+<span class="c1">#  Distributed under the GPLv3 License.</span>
+<span class="c1">#  See accompanying file LICENSE.txt or copy at</span>
+<span class="c1">#      https://www.gnu.org/licenses/gpl-3.0.html</span>
+<span class="c1">#</span>
+<span class="c1">#  Website: https://pypath.omnipathdb.org/</span>
+<span class="c1">#</span>
+
+<span class="kn">import</span> <span class="nn">os</span>
+<span class="kn">import</span> <span class="nn">pickle</span>
+
+<span class="kn">import</span> <span class="nn">pypath.resources.urls</span> <span class="k">as</span> <span class="nn">urls</span>
+<span class="kn">import</span> <span class="nn">pypath.share.curl</span> <span class="k">as</span> <span class="nn">curl</span>
+<span class="kn">import</span> <span class="nn">pypath.share.common</span> <span class="k">as</span> <span class="nn">common</span>
+<span class="kn">import</span> <span class="nn">pypath.inputs.pfam</span> <span class="k">as</span> <span class="nn">pfam_input</span>
+<span class="kn">import</span> <span class="nn">pypath.inputs.pdb</span> <span class="k">as</span> <span class="nn">pdb_input</span>
+<span class="kn">import</span> <span class="nn">pypath.inputs.uniprot_db</span> <span class="k">as</span> <span class="nn">uniprot_db</span>
+<span class="kn">import</span> <span class="nn">pypath.utils.pdb</span> <span class="k">as</span> <span class="nn">pdb_utils</span>
+<span class="kn">import</span> <span class="nn">pypath.share.cache</span> <span class="k">as</span> <span class="nn">cache</span>
+<span class="kn">import</span> <span class="nn">pypath.internals.intera</span> <span class="k">as</span> <span class="nn">intera</span>
+<span class="kn">import</span> <span class="nn">pypath.share.progress</span> <span class="k">as</span> <span class="nn">progress</span>
+
+
+<div class="viewcode-block" id="get_3did_ddi">
+<a class="viewcode-back" href="../../../api/pypath.inputs.threedid.get_3did_ddi.html#pypath.inputs.threedid.get_3did_ddi">[docs]</a>
+<span class="k">def</span> <span class="nf">get_3did_ddi</span><span class="p">(</span><span class="n">residues</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span> <span class="n">ddi_flat</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span> <span class="n">organism</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">):</span>
+
+    <span class="k">if</span> <span class="n">ddi_flat</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
+        <span class="n">c</span> <span class="o">=</span> <span class="n">curl</span><span class="o">.</span><span class="n">Curl</span><span class="p">(</span><span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;3did_ddi&#39;</span><span class="p">][</span><span class="s1">&#39;url&#39;</span><span class="p">],</span> <span class="n">silent</span> <span class="o">=</span> <span class="kc">False</span><span class="p">)</span>
+        <span class="n">data</span> <span class="o">=</span> <span class="n">c</span><span class="o">.</span><span class="n">result</span>
+        <span class="n">tmpfile</span> <span class="o">=</span> <span class="s1">&#39;3did_flat_tmp&#39;</span>
+
+        <span class="k">if</span> <span class="n">data</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
+            <span class="k">return</span> <span class="kc">None</span>
+
+        <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">tmpfile</span><span class="p">,</span> <span class="s1">&#39;w&#39;</span><span class="p">)</span> <span class="k">as</span> <span class="n">f</span><span class="p">:</span>
+            <span class="n">f</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="n">data</span><span class="p">)</span>
+
+        <span class="n">lnum</span> <span class="o">=</span> <span class="n">data</span><span class="o">.</span><span class="n">count</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\n</span><span class="s1">&#39;</span><span class="p">)</span>
+        <span class="k">del</span> <span class="n">data</span>
+
+    <span class="k">else</span><span class="p">:</span>
+        <span class="n">tmpfile</span> <span class="o">=</span> <span class="n">ddi_flat</span>
+
+    <span class="n">u_pfam</span><span class="p">,</span> <span class="n">pfam_u</span> <span class="o">=</span> <span class="n">pfam_input</span><span class="o">.</span><span class="n">pfam_uniprot</span><span class="p">(</span><span class="n">organism</span> <span class="o">=</span> <span class="n">organism</span><span class="p">)</span>
+    <span class="n">u_pdb</span><span class="p">,</span> <span class="n">pdb_u</span> <span class="o">=</span> <span class="n">pdb_input</span><span class="o">.</span><span class="n">pdb_chains</span><span class="p">()</span>
+
+    <span class="k">if</span> <span class="n">pfam_u</span> <span class="ow">is</span> <span class="kc">None</span> <span class="ow">or</span> <span class="n">pdb_u</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
+
+        <span class="k">return</span> <span class="kc">None</span>
+
+    <span class="n">ddi</span> <span class="o">=</span> <span class="p">{}</span>
+    <span class="n">interfaces</span> <span class="o">=</span> <span class="p">{}</span>
+    <span class="n">pdblist</span> <span class="o">=</span> <span class="p">{}</span>
+    <span class="n">ddi_collect</span> <span class="o">=</span> <span class="kc">False</span>
+    <span class="n">con_collect</span> <span class="o">=</span> <span class="kc">False</span>
+
+    <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">tmpfile</span><span class="p">,</span> <span class="s1">&#39;r&#39;</span><span class="p">)</span> <span class="k">as</span> <span class="n">f</span><span class="p">:</span>
+
+        <span class="n">prg</span> <span class="o">=</span> <span class="n">progress</span><span class="o">.</span><span class="n">Progress</span><span class="p">(</span><span class="n">lnum</span><span class="p">,</span> <span class="s1">&#39;Reading data&#39;</span><span class="p">,</span> <span class="mi">33</span><span class="p">)</span>
+
+        <span class="k">for</span> <span class="n">l</span> <span class="ow">in</span> <span class="n">f</span><span class="p">:</span>
+            <span class="n">prg</span><span class="o">.</span><span class="n">step</span><span class="p">()</span>
+
+            <span class="k">if</span> <span class="n">l</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s1">&#39;#=&#39;</span><span class="p">)</span> <span class="ow">and</span> <span class="n">con_collect</span><span class="p">:</span>
+
+                <span class="n">interfaces</span><span class="p">[(</span><span class="n">uniprot1</span><span class="p">,</span> <span class="n">uniprot2</span><span class="p">,</span> <span class="n">pdb</span><span class="p">)]</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">this_interface</span><span class="p">)</span>
+                <span class="n">con_collect</span> <span class="o">=</span> <span class="kc">False</span>
+
+            <span class="k">if</span> <span class="n">l</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s1">&#39;#=ID&#39;</span><span class="p">):</span>
+                <span class="c1"># new domain pair: attach previous to results:</span>
+                <span class="k">if</span> <span class="n">ddi_collect</span><span class="p">:</span>
+                    <span class="k">for</span> <span class="n">u1</span> <span class="ow">in</span> <span class="n">uniprots1</span><span class="p">:</span>
+                        <span class="k">for</span> <span class="n">u2</span> <span class="ow">in</span> <span class="n">uniprots2</span><span class="p">:</span>
+                            <span class="k">if</span> <span class="n">u1</span> <span class="o">!=</span> <span class="n">u2</span> <span class="ow">and</span> <span class="nb">len</span><span class="p">(</span><span class="n">pdblist</span><span class="p">)</span> <span class="o">&gt;</span> <span class="mi">0</span><span class="p">:</span>
+                                <span class="k">if</span> <span class="p">(</span><span class="n">u1</span><span class="p">,</span> <span class="n">u2</span><span class="p">)</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">ddi</span><span class="p">:</span>
+                                    <span class="n">ddi</span><span class="p">[(</span><span class="n">u1</span><span class="p">,</span> <span class="n">u2</span><span class="p">)]</span> <span class="o">=</span> <span class="p">{}</span>
+
+                                <span class="k">if</span> <span class="p">(</span><span class="n">pfam1</span><span class="p">,</span> <span class="n">pfam2</span><span class="p">)</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">ddi</span><span class="p">[(</span><span class="n">u1</span><span class="p">,</span> <span class="n">u2</span><span class="p">)]:</span>
+                                    <span class="n">ddi</span><span class="p">[(</span><span class="n">u1</span><span class="p">,</span> <span class="n">u2</span><span class="p">)][(</span><span class="n">pfam1</span><span class="p">,</span> <span class="n">pfam2</span><span class="p">)]</span> <span class="o">=</span> <span class="p">{</span>
+                                        <span class="s1">&#39;pdbs&#39;</span><span class="p">:</span> <span class="n">pdblist</span>
+                                    <span class="p">}</span>
+
+                    <span class="n">ddi_collect</span> <span class="o">=</span> <span class="kc">False</span>
+
+                <span class="n">pdblist</span> <span class="o">=</span> <span class="p">{}</span>
+                <span class="n">l</span> <span class="o">=</span> <span class="n">l</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\t</span><span class="s1">&#39;</span><span class="p">)</span>
+                <span class="n">pfam1</span> <span class="o">=</span> <span class="n">l</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;(&#39;</span><span class="p">)[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;.&#39;</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span>
+                <span class="n">pfam2</span> <span class="o">=</span> <span class="n">l</span><span class="p">[</span><span class="mi">4</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;.&#39;</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span>
+                <span class="n">uniprots1</span> <span class="o">=</span> <span class="p">[]</span> <span class="k">if</span> <span class="n">pfam1</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">pfam_u</span> <span class="k">else</span> <span class="n">pfam_u</span><span class="p">[</span><span class="n">pfam1</span><span class="p">]</span>
+                <span class="n">uniprots2</span> <span class="o">=</span> <span class="p">[]</span> <span class="k">if</span> <span class="n">pfam2</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">pfam_u</span> <span class="k">else</span> <span class="n">pfam_u</span><span class="p">[</span><span class="n">pfam2</span><span class="p">]</span>
+
+                <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="nb">set</span><span class="p">(</span><span class="n">uniprots1</span><span class="p">)</span> <span class="o">|</span> <span class="nb">set</span><span class="p">(</span><span class="n">uniprots2</span><span class="p">))</span> <span class="o">&gt;</span> <span class="mi">1</span><span class="p">:</span>
+
+                    <span class="n">ddi_collect</span> <span class="o">=</span> <span class="kc">True</span>
+
+            <span class="k">elif</span> <span class="n">l</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s1">&#39;#=3D&#39;</span><span class="p">):</span>
+
+                <span class="n">l</span> <span class="o">=</span> <span class="n">l</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\t</span><span class="s1">&#39;</span><span class="p">)</span>
+                <span class="n">pdb</span> <span class="o">=</span> <span class="n">l</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span>
+                <span class="n">chain1</span> <span class="o">=</span> <span class="n">l</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;:&#39;</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span>
+                <span class="n">chain2</span> <span class="o">=</span> <span class="n">l</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;:&#39;</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span>
+
+                <span class="k">if</span> <span class="p">(</span>
+                    <span class="n">pdb</span> <span class="ow">in</span> <span class="n">pdb_u</span> <span class="ow">and</span>
+                    <span class="n">chain1</span> <span class="ow">in</span> <span class="n">pdb_u</span><span class="p">[</span><span class="n">pdb</span><span class="p">]</span> <span class="ow">and</span>
+                    <span class="n">chain2</span> <span class="ow">in</span> <span class="n">pdb_u</span><span class="p">[</span><span class="n">pdb</span><span class="p">]</span>
+                <span class="p">):</span>
+
+                    <span class="n">uniprot1</span> <span class="o">=</span> <span class="n">pdb_u</span><span class="p">[</span><span class="n">pdb</span><span class="p">][</span><span class="n">chain1</span><span class="p">][</span><span class="s1">&#39;uniprot&#39;</span><span class="p">]</span>
+                    <span class="n">uniprot2</span> <span class="o">=</span> <span class="n">pdb_u</span><span class="p">[</span><span class="n">pdb</span><span class="p">][</span><span class="n">chain2</span><span class="p">][</span><span class="s1">&#39;uniprot&#39;</span><span class="p">]</span>
+
+                    <span class="k">if</span> <span class="n">uniprot1</span> <span class="o">!=</span> <span class="n">uniprot2</span><span class="p">:</span>
+
+                        <span class="k">if</span> <span class="n">pdb</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">pdblist</span><span class="p">:</span>
+
+                            <span class="n">pdblist</span><span class="p">[</span><span class="n">pdb</span><span class="p">]</span> <span class="o">=</span> <span class="p">[]</span>
+
+                        <span class="n">pdblist</span><span class="p">[</span><span class="n">pdb</span><span class="p">]</span> <span class="o">=</span> <span class="n">common</span><span class="o">.</span><span class="n">add_to_list</span><span class="p">(</span>
+                            <span class="n">pdblist</span><span class="p">[</span><span class="n">pdb</span><span class="p">],</span>
+                            <span class="p">(</span><span class="n">uniprot1</span><span class="p">,</span> <span class="n">uniprot2</span><span class="p">),</span>
+                        <span class="p">)</span>
+
+                    <span class="k">if</span> <span class="n">residues</span><span class="p">:</span>
+
+                        <span class="k">if</span> <span class="n">chain1</span> <span class="o">!=</span> <span class="n">chain2</span><span class="p">:</span>
+
+                            <span class="k">if</span> <span class="p">(</span>
+                                <span class="n">pdb_u</span><span class="p">[</span><span class="n">pdb</span><span class="p">][</span><span class="n">chain1</span><span class="p">][</span><span class="s1">&#39;offset&#39;</span><span class="p">]</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span> <span class="ow">and</span>
+                                <span class="n">pdb_u</span><span class="p">[</span><span class="n">pdb</span><span class="p">][</span><span class="n">chain2</span><span class="p">][</span><span class="s1">&#39;offset&#39;</span><span class="p">]</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span> <span class="ow">and</span>
+                                <span class="n">pdb_u</span><span class="p">[</span><span class="n">pdb</span><span class="p">][</span><span class="n">chain1</span><span class="p">][</span><span class="s1">&#39;uniprot&#39;</span><span class="p">]</span> <span class="o">!=</span>
+                                <span class="n">pdb_u</span><span class="p">[</span><span class="n">pdb</span><span class="p">][</span><span class="n">chain2</span><span class="p">][</span><span class="s1">&#39;uniprot&#39;</span><span class="p">]</span>
+                            <span class="p">):</span>
+
+                                <span class="n">con_collect</span> <span class="o">=</span> <span class="kc">True</span>
+                                <span class="n">offset1</span> <span class="o">=</span> <span class="n">pdb_u</span><span class="p">[</span><span class="n">pdb</span><span class="p">][</span><span class="n">chain1</span><span class="p">][</span><span class="s1">&#39;offset&#39;</span><span class="p">]</span>
+                                <span class="n">offset2</span> <span class="o">=</span> <span class="n">pdb_u</span><span class="p">[</span><span class="n">pdb</span><span class="p">][</span><span class="n">chain2</span><span class="p">][</span><span class="s1">&#39;offset&#39;</span><span class="p">]</span>
+
+                                <span class="n">this_interface</span> <span class="o">=</span> <span class="n">intera</span><span class="o">.</span><span class="n">Interface</span><span class="p">(</span>
+                                    <span class="n">uniprot1</span><span class="p">,</span>
+                                    <span class="n">uniprot2</span><span class="p">,</span>
+                                    <span class="n">source</span> <span class="o">=</span> <span class="s1">&#39;3DID&#39;</span><span class="p">,</span>
+                                    <span class="n">pdb</span> <span class="o">=</span> <span class="n">pdb</span><span class="p">,</span>
+                                <span class="p">)</span>
+
+                                <span class="n">key</span> <span class="o">=</span> <span class="p">(</span><span class="n">uniprot1</span><span class="p">,</span> <span class="n">uniprot2</span><span class="p">,</span> <span class="n">pdb</span><span class="p">)</span>
+
+                                <span class="k">if</span> <span class="n">key</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">interfaces</span><span class="p">:</span>
+
+                                    <span class="n">interfaces</span><span class="p">[</span><span class="n">key</span><span class="p">]</span> <span class="o">=</span> <span class="p">[]</span>
+
+                            <span class="k">else</span><span class="p">:</span>
+
+                                <span class="n">con_collect</span> <span class="o">=</span> <span class="kc">False</span>
+
+            <span class="k">elif</span> <span class="ow">not</span> <span class="n">residues</span> <span class="ow">or</span> <span class="ow">not</span> <span class="n">con_collect</span><span class="p">:</span>
+
+                <span class="k">continue</span>
+
+            <span class="k">else</span><span class="p">:</span>
+
+                <span class="n">l</span> <span class="o">=</span> <span class="n">l</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\t</span><span class="s1">&#39;</span><span class="p">)</span>
+
+                <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">l</span><span class="p">)</span> <span class="o">&gt;</span> <span class="mi">3</span><span class="p">:</span>
+
+                    <span class="n">rnum1</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">common</span><span class="o">.</span><span class="n">non_digit</span><span class="o">.</span><span class="n">sub</span><span class="p">(</span><span class="s1">&#39;&#39;</span><span class="p">,</span> <span class="n">l</span><span class="p">[</span><span class="mi">2</span><span class="p">]))</span> <span class="o">+</span> <span class="n">offset1</span>
+                    <span class="n">rnum2</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">common</span><span class="o">.</span><span class="n">non_digit</span><span class="o">.</span><span class="n">sub</span><span class="p">(</span><span class="s1">&#39;&#39;</span><span class="p">,</span> <span class="n">l</span><span class="p">[</span><span class="mi">3</span><span class="p">]))</span> <span class="o">+</span> <span class="n">offset2</span>
+
+                    <span class="n">this_interface</span><span class="o">.</span><span class="n">add_residues</span><span class="p">(</span>
+                        <span class="p">(</span><span class="n">rnum1</span><span class="p">,</span> <span class="n">l</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">uniprot1</span><span class="p">),</span>
+                        <span class="p">(</span><span class="n">rnum2</span><span class="p">,</span> <span class="n">l</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span> <span class="n">uniprot2</span><span class="p">),</span>
+                    <span class="p">)</span>
+
+        <span class="n">prg</span><span class="o">.</span><span class="n">terminate</span><span class="p">()</span>
+        <span class="n">prg</span> <span class="o">=</span> <span class="n">progress</span><span class="o">.</span><span class="n">Progress</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">ddi</span><span class="p">),</span> <span class="s1">&#39;Processing interfaces&#39;</span><span class="p">,</span> <span class="mi">99</span><span class="p">)</span>
+
+        <span class="k">if</span> <span class="n">residues</span><span class="p">:</span>
+
+            <span class="k">for</span> <span class="n">u</span><span class="p">,</span> <span class="n">v1</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="n">ddi</span><span class="p">):</span>
+
+                <span class="n">prg</span><span class="o">.</span><span class="n">step</span><span class="p">()</span>
+
+                <span class="k">for</span> <span class="n">d</span><span class="p">,</span> <span class="n">v2</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="n">v1</span><span class="p">):</span>
+                    <span class="k">for</span> <span class="n">p</span> <span class="ow">in</span> <span class="n">v2</span><span class="p">[</span><span class="s1">&#39;pdbs&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">keys</span><span class="p">():</span>
+
+                        <span class="n">key</span> <span class="o">=</span> <span class="p">(</span><span class="n">u</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">u</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span> <span class="n">p</span><span class="p">)</span>
+
+                        <span class="k">if</span> <span class="n">key</span> <span class="ow">in</span> <span class="n">interfaces</span><span class="p">:</span>
+
+                            <span class="n">ddi</span><span class="p">[</span><span class="n">u</span><span class="p">][</span><span class="n">d</span><span class="p">][</span><span class="s1">&#39;interfaces&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">interfaces</span><span class="p">[</span><span class="n">key</span><span class="p">]</span>
+
+        <span class="n">prg</span><span class="o">.</span><span class="n">terminate</span><span class="p">()</span>
+
+    <span class="k">if</span> <span class="n">ddi_flat</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
+
+        <span class="n">os</span><span class="o">.</span><span class="n">remove</span><span class="p">(</span><span class="n">tmpfile</span><span class="p">)</span>
+
+    <span class="k">if</span> <span class="n">residues</span><span class="p">:</span>
+
+        <span class="k">return</span> <span class="n">ddi</span><span class="p">,</span> <span class="n">interfaces</span>
+
+    <span class="k">else</span><span class="p">:</span>
+
+        <span class="k">return</span> <span class="n">ddi</span></div>
+
+
+
+<div class="viewcode-block" id="get_3did">
+<a class="viewcode-back" href="../../../api/pypath.inputs.threedid.get_3did.html#pypath.inputs.threedid.get_3did">[docs]</a>
+<span class="k">def</span> <span class="nf">get_3did</span><span class="p">(</span><span class="n">ddi_flat</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span> <span class="n">res</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span> <span class="n">organism</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">,</span> <span class="n">pickl</span> <span class="o">=</span> <span class="kc">True</span><span class="p">):</span>
+
+    <span class="n">resultfile</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">cache</span><span class="o">.</span><span class="n">get_cachedir</span><span class="p">(),</span> <span class="s1">&#39;3did_ddi.pickle&#39;</span><span class="p">)</span>
+
+    <span class="k">if</span> <span class="n">pickl</span> <span class="ow">and</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">exists</span><span class="p">(</span><span class="n">resultfile</span><span class="p">):</span>
+
+        <span class="n">result</span> <span class="o">=</span> <span class="n">pickle</span><span class="o">.</span><span class="n">load</span><span class="p">(</span><span class="nb">open</span><span class="p">(</span><span class="n">resultfile</span><span class="p">,</span> <span class="s1">&#39;rb&#39;</span><span class="p">))</span>
+
+        <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">result</span><span class="p">)</span> <span class="o">==</span> <span class="mi">1</span><span class="p">:</span>
+            <span class="k">return</span> <span class="n">result</span>
+
+        <span class="k">else</span><span class="p">:</span>
+            <span class="k">return</span> <span class="n">result</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">result</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span>
+
+    <span class="k">if</span> <span class="n">ddi_flat</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
+
+        <span class="n">c</span> <span class="o">=</span> <span class="n">curl</span><span class="o">.</span><span class="n">Curl</span><span class="p">(</span><span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;3did_ddi&#39;</span><span class="p">][</span><span class="s1">&#39;url&#39;</span><span class="p">],</span> <span class="n">silent</span> <span class="o">=</span> <span class="kc">False</span><span class="p">)</span>
+        <span class="n">data</span> <span class="o">=</span> <span class="n">c</span><span class="o">.</span><span class="n">result</span>
+        <span class="n">tmpfile</span> <span class="o">=</span> <span class="s1">&#39;3did_flat_tmp&#39;</span>
+
+        <span class="k">if</span> <span class="n">data</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
+
+            <span class="k">return</span> <span class="kc">None</span>
+
+        <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">tmpfile</span><span class="p">,</span> <span class="s1">&#39;w&#39;</span><span class="p">)</span> <span class="k">as</span> <span class="n">f</span><span class="p">:</span>
+
+            <span class="n">f</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="n">data</span><span class="p">)</span>
+
+        <span class="n">lnum</span> <span class="o">=</span> <span class="n">data</span><span class="o">.</span><span class="n">count</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\n</span><span class="s1">&#39;</span><span class="p">)</span>
+        <span class="k">del</span> <span class="n">data</span>
+
+    <span class="k">elif</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">exists</span><span class="p">(</span><span class="n">ddi_flat</span><span class="p">):</span>
+
+        <span class="n">tmpfile</span> <span class="o">=</span> <span class="n">ddi_flat</span>
+
+    <span class="k">else</span><span class="p">:</span>
+
+        <span class="k">return</span> <span class="kc">None</span>
+
+    <span class="n">u_pdb</span><span class="p">,</span> <span class="n">pdb_u</span> <span class="o">=</span> <span class="n">pdb_input</span><span class="o">.</span><span class="n">pdb_chains</span><span class="p">()</span>
+    <span class="n">all_unip</span> <span class="o">=</span> <span class="nb">set</span><span class="p">(</span><span class="n">uniprot_db</span><span class="o">.</span><span class="n">all_uniprots</span><span class="p">(</span><span class="n">organism</span> <span class="o">=</span> <span class="n">organism</span><span class="p">))</span>
+
+    <span class="k">if</span> <span class="n">all_unip</span> <span class="ow">is</span> <span class="kc">None</span> <span class="ow">or</span> <span class="n">pdb_u</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
+
+        <span class="k">return</span> <span class="kc">None</span>
+
+    <span class="n">ddi</span> <span class="o">=</span> <span class="p">[]</span>
+    <span class="n">interfaces</span> <span class="o">=</span> <span class="p">[]</span>
+    <span class="n">pdb</span> <span class="o">=</span> <span class="n">pdb_prev</span> <span class="o">=</span> <span class="n">intf</span> <span class="o">=</span> <span class="kc">None</span>
+    <span class="n">skip</span> <span class="o">=</span> <span class="kc">True</span>
+    <span class="n">rmap</span> <span class="o">=</span> <span class="n">pdb_utils</span><span class="o">.</span><span class="n">ResidueMapper</span><span class="p">()</span>
+
+    <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">tmpfile</span><span class="p">,</span> <span class="s1">&#39;r&#39;</span><span class="p">)</span> <span class="k">as</span> <span class="n">f</span><span class="p">:</span>
+
+        <span class="n">prg</span> <span class="o">=</span> <span class="n">progress</span><span class="o">.</span><span class="n">Progress</span><span class="p">(</span>
+            <span class="n">lnum</span><span class="p">,</span>
+            <span class="s1">&#39;Processing 3DID domain-domain interactions&#39;</span><span class="p">,</span>
+            <span class="mi">33</span><span class="p">,</span>
+        <span class="p">)</span>
+
+        <span class="k">for</span> <span class="n">l</span> <span class="ow">in</span> <span class="n">f</span><span class="p">:</span>
+
+            <span class="n">prg</span><span class="o">.</span><span class="n">step</span><span class="p">()</span>
+            <span class="n">l</span> <span class="o">=</span> <span class="n">l</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\t</span><span class="s1">&#39;</span><span class="p">)</span>
+
+            <span class="k">if</span> <span class="n">l</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s1">&#39;#=ID&#39;</span><span class="p">):</span>
+
+                <span class="n">pfam1</span> <span class="o">=</span> <span class="n">l</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;.&#39;</span><span class="p">)[</span><span class="mi">0</span><span class="p">][</span><span class="mi">2</span><span class="p">:]</span>
+                <span class="n">pfam2</span> <span class="o">=</span> <span class="n">l</span><span class="p">[</span><span class="mi">4</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;.&#39;</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span>
+
+            <span class="k">elif</span> <span class="n">l</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s1">&#39;#=3D&#39;</span><span class="p">):</span>
+
+                <span class="n">pdb_prev</span> <span class="o">=</span> <span class="n">pdb</span>
+                <span class="n">skip</span> <span class="o">=</span> <span class="kc">True</span>
+                <span class="n">pdb</span> <span class="o">=</span> <span class="n">l</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span>
+                <span class="n">chain1</span> <span class="o">=</span> <span class="n">l</span><span class="p">[</span><span class="mi">2</span><span class="p">][</span><span class="mi">0</span><span class="p">]</span>
+                <span class="n">chain2</span> <span class="o">=</span> <span class="n">l</span><span class="p">[</span><span class="mi">3</span><span class="p">][</span><span class="mi">0</span><span class="p">]</span>
+                <span class="n">uniprot1</span> <span class="o">=</span> <span class="n">uniprot2</span> <span class="o">=</span> <span class="kc">None</span>
+
+                <span class="k">if</span> <span class="n">pdb</span> <span class="o">!=</span> <span class="n">pdb_prev</span><span class="p">:</span>
+
+                    <span class="n">rmap</span><span class="o">.</span><span class="n">clean</span><span class="p">()</span>
+
+                <span class="k">if</span> <span class="n">pdb</span> <span class="ow">in</span> <span class="n">pdb_u</span><span class="p">:</span>
+
+                    <span class="k">if</span> <span class="n">chain1</span> <span class="ow">in</span> <span class="n">pdb_u</span><span class="p">[</span><span class="n">pdb</span><span class="p">]:</span>
+
+                        <span class="n">uniprot1</span> <span class="o">=</span> <span class="n">pdb_u</span><span class="p">[</span><span class="n">pdb</span><span class="p">][</span><span class="n">chain1</span><span class="p">][</span><span class="s1">&#39;uniprot&#39;</span><span class="p">]</span>
+
+                    <span class="k">if</span> <span class="n">chain2</span> <span class="ow">in</span> <span class="n">pdb_u</span><span class="p">[</span><span class="n">pdb</span><span class="p">]:</span>
+
+                        <span class="n">uniprot2</span> <span class="o">=</span> <span class="n">pdb_u</span><span class="p">[</span><span class="n">pdb</span><span class="p">][</span><span class="n">chain2</span><span class="p">][</span><span class="s1">&#39;uniprot&#39;</span><span class="p">]</span>
+
+                <span class="k">if</span> <span class="p">(</span>
+                    <span class="n">uniprot1</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span> <span class="ow">and</span>
+                    <span class="n">uniprot2</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span> <span class="ow">and</span>
+                    <span class="n">uniprot1</span> <span class="ow">in</span> <span class="n">all_unip</span> <span class="ow">and</span>
+                    <span class="n">uniprot2</span> <span class="ow">in</span> <span class="n">all_unip</span> <span class="ow">and</span>
+                    <span class="n">uniprot1</span> <span class="o">!=</span> <span class="n">uniprot2</span>
+                <span class="p">):</span>
+
+                    <span class="n">skip</span> <span class="o">=</span> <span class="kc">False</span>
+
+                    <span class="k">if</span> <span class="n">intf</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
+
+                        <span class="n">interfaces</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">intf</span><span class="p">)</span>
+
+                    <span class="n">intf</span> <span class="o">=</span> <span class="n">intera</span><span class="o">.</span><span class="n">Interface</span><span class="p">(</span><span class="n">uniprot1</span><span class="p">,</span> <span class="n">uniprot2</span><span class="p">,</span> <span class="s1">&#39;3DID&#39;</span><span class="p">,</span> <span class="n">pdb</span><span class="p">)</span>
+                    <span class="n">u1start</span> <span class="o">=</span> <span class="n">u1end</span> <span class="o">=</span> <span class="n">u2start</span> <span class="o">=</span> <span class="n">u2end</span> <span class="o">=</span> <span class="p">{}</span>
+
+                    <span class="k">if</span> <span class="n">l</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span><span class="o">.</span><span class="n">count</span><span class="p">(</span><span class="s1">&#39;-&#39;</span><span class="p">)</span> <span class="o">==</span> <span class="mi">1</span><span class="p">:</span>
+
+                        <span class="n">start1</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span>
+                            <span class="n">common</span><span class="o">.</span><span class="n">non_digit</span><span class="o">.</span><span class="n">sub</span><span class="p">(</span><span class="s1">&#39;&#39;</span><span class="p">,</span> <span class="n">l</span><span class="p">[</span><span class="mi">2</span><span class="p">][</span><span class="mi">2</span><span class="p">:]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;-&#39;</span><span class="p">)[</span><span class="mi">0</span><span class="p">])</span>
+                        <span class="p">)</span>
+                        <span class="n">end1</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span>
+                            <span class="n">common</span><span class="o">.</span><span class="n">non_digit</span><span class="o">.</span><span class="n">sub</span><span class="p">(</span><span class="s1">&#39;&#39;</span><span class="p">,</span> <span class="n">l</span><span class="p">[</span><span class="mi">2</span><span class="p">][</span><span class="mi">2</span><span class="p">:]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;-&#39;</span><span class="p">)[</span><span class="mi">1</span><span class="p">])</span>
+                        <span class="p">)</span>
+                        <span class="n">u1start</span> <span class="o">=</span> <span class="n">rmap</span><span class="o">.</span><span class="n">get_residue</span><span class="p">(</span>
+                            <span class="n">pdb</span><span class="p">,</span>
+                            <span class="n">start1</span><span class="p">,</span>
+                            <span class="n">chain</span> <span class="o">=</span> <span class="n">chain1</span><span class="p">,</span>
+                        <span class="p">)</span>
+                        <span class="n">u1end</span> <span class="o">=</span> <span class="n">rmap</span><span class="o">.</span><span class="n">get_residue</span><span class="p">(</span><span class="n">pdb</span><span class="p">,</span> <span class="n">end1</span><span class="p">,</span> <span class="n">chain</span> <span class="o">=</span> <span class="n">chain1</span><span class="p">)</span>
+
+                    <span class="k">if</span> <span class="n">l</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span><span class="o">.</span><span class="n">count</span><span class="p">(</span><span class="s1">&#39;-&#39;</span><span class="p">)</span> <span class="o">==</span> <span class="mi">1</span><span class="p">:</span>
+
+                        <span class="n">start2</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span>
+                            <span class="n">common</span><span class="o">.</span><span class="n">non_digit</span><span class="o">.</span><span class="n">sub</span><span class="p">(</span><span class="s1">&#39;&#39;</span><span class="p">,</span> <span class="n">l</span><span class="p">[</span><span class="mi">3</span><span class="p">][</span><span class="mi">2</span><span class="p">:]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;-&#39;</span><span class="p">)[</span><span class="mi">0</span><span class="p">])</span>
+                        <span class="p">)</span>
+                        <span class="n">end2</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span>
+                            <span class="n">common</span><span class="o">.</span><span class="n">non_digit</span><span class="o">.</span><span class="n">sub</span><span class="p">(</span><span class="s1">&#39;&#39;</span><span class="p">,</span> <span class="n">l</span><span class="p">[</span><span class="mi">3</span><span class="p">][</span><span class="mi">2</span><span class="p">:]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;-&#39;</span><span class="p">)[</span><span class="mi">1</span><span class="p">])</span>
+                        <span class="p">)</span>
+                        <span class="n">u2start</span> <span class="o">=</span> <span class="n">rmap</span><span class="o">.</span><span class="n">get_residue</span><span class="p">(</span>
+                            <span class="n">pdb</span><span class="p">,</span>
+                            <span class="n">start2</span><span class="p">,</span>
+                            <span class="n">chain</span> <span class="o">=</span> <span class="n">chain2</span><span class="p">,</span>
+                        <span class="p">)</span>
+                        <span class="n">u2end</span> <span class="o">=</span> <span class="n">rmap</span><span class="o">.</span><span class="n">get_residue</span><span class="p">(</span><span class="n">pdb</span><span class="p">,</span> <span class="n">end2</span><span class="p">,</span> <span class="n">chain</span> <span class="o">=</span> <span class="n">chain2</span><span class="p">)</span>
+
+                    <span class="n">u1start</span> <span class="o">=</span> <span class="n">u1start</span><span class="o">.</span><span class="n">resnum</span> <span class="k">if</span> <span class="n">u1start</span> <span class="k">else</span> <span class="kc">None</span>
+                    <span class="n">u1end</span> <span class="o">=</span> <span class="n">u1end</span><span class="o">.</span><span class="n">resnum</span> <span class="k">if</span> <span class="n">u1end</span> <span class="k">else</span> <span class="kc">None</span>
+                    <span class="n">u2start</span> <span class="o">=</span> <span class="n">u2start</span><span class="o">.</span><span class="n">resnum</span> <span class="k">if</span> <span class="n">u2start</span> <span class="k">else</span> <span class="kc">None</span>
+                    <span class="n">u2end</span> <span class="o">=</span> <span class="n">u2end</span><span class="o">.</span><span class="n">resnum</span> <span class="k">if</span> <span class="n">u2end</span> <span class="k">else</span> <span class="kc">None</span>
+
+                    <span class="n">dom1</span> <span class="o">=</span> <span class="n">intera</span><span class="o">.</span><span class="n">Domain</span><span class="p">(</span>
+                        <span class="n">uniprot1</span><span class="p">,</span>
+                        <span class="n">domain</span> <span class="o">=</span> <span class="n">pfam1</span><span class="p">,</span>
+                        <span class="n">start</span> <span class="o">=</span> <span class="n">u1start</span><span class="p">,</span>
+                        <span class="n">end</span> <span class="o">=</span> <span class="n">u1end</span><span class="p">,</span>
+                        <span class="n">isoform</span> <span class="o">=</span> <span class="mi">1</span><span class="p">,</span>
+                    <span class="p">)</span>
+
+                    <span class="n">dom2</span> <span class="o">=</span> <span class="n">intera</span><span class="o">.</span><span class="n">Domain</span><span class="p">(</span>
+                        <span class="n">uniprot2</span><span class="p">,</span>
+                        <span class="n">domain</span> <span class="o">=</span> <span class="n">pfam2</span><span class="p">,</span>
+                        <span class="n">start</span> <span class="o">=</span> <span class="n">u2start</span><span class="p">,</span>
+                        <span class="n">end</span> <span class="o">=</span> <span class="n">u2end</span><span class="p">,</span>
+                        <span class="n">isoform</span> <span class="o">=</span> <span class="mi">1</span><span class="p">,</span>
+                    <span class="p">)</span>
+
+                    <span class="n">dd</span> <span class="o">=</span> <span class="n">intera</span><span class="o">.</span><span class="n">DomainDomain</span><span class="p">(</span><span class="n">dom1</span><span class="p">,</span> <span class="n">dom2</span><span class="p">,</span> <span class="p">[</span><span class="n">pdb</span><span class="p">],</span> <span class="s1">&#39;3DID&#39;</span><span class="p">)</span>
+                    <span class="n">ddi</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">dd</span><span class="p">)</span>
+
+            <span class="k">elif</span> <span class="ow">not</span> <span class="n">skip</span> <span class="ow">and</span> <span class="n">res</span> <span class="ow">and</span> <span class="ow">not</span> <span class="n">l</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s1">&#39;//&#39;</span><span class="p">):</span>
+
+                <span class="n">conv1</span> <span class="o">=</span> <span class="n">rmap</span><span class="o">.</span><span class="n">get_residue</span><span class="p">(</span>
+                    <span class="n">pdb</span><span class="p">,</span>
+                    <span class="nb">int</span><span class="p">(</span><span class="n">common</span><span class="o">.</span><span class="n">non_digit</span><span class="o">.</span><span class="n">sub</span><span class="p">(</span><span class="s1">&#39;&#39;</span><span class="p">,</span> <span class="n">l</span><span class="p">[</span><span class="mi">2</span><span class="p">])),</span>
+                    <span class="n">chain</span> <span class="o">=</span> <span class="n">chain1</span><span class="p">,</span>
+                <span class="p">)</span>
+                <span class="n">conv2</span> <span class="o">=</span> <span class="n">rmap</span><span class="o">.</span><span class="n">get_residue</span><span class="p">(</span>
+                    <span class="n">pdb</span><span class="p">,</span>
+                    <span class="nb">int</span><span class="p">(</span><span class="n">common</span><span class="o">.</span><span class="n">non_digit</span><span class="o">.</span><span class="n">sub</span><span class="p">(</span><span class="s1">&#39;&#39;</span><span class="p">,</span> <span class="n">l</span><span class="p">[</span><span class="mi">3</span><span class="p">])),</span>
+                    <span class="n">chain</span> <span class="o">=</span> <span class="n">chain2</span><span class="p">,</span>
+                <span class="p">)</span>
+
+                <span class="k">if</span> <span class="n">conv1</span> <span class="ow">and</span> <span class="n">conv2</span><span class="p">:</span>
+
+                    <span class="n">intf</span><span class="o">.</span><span class="n">add_residues</span><span class="p">(</span>
+                        <span class="p">(</span><span class="n">conv1</span><span class="o">.</span><span class="n">resnum</span><span class="p">,</span> <span class="n">l</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">uniprot1</span><span class="p">),</span>
+                        <span class="p">(</span><span class="n">conv2</span><span class="o">.</span><span class="n">resnum</span><span class="p">,</span> <span class="n">l</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span> <span class="n">uniprot2</span><span class="p">),</span>
+                    <span class="p">)</span>
+
+        <span class="n">interfaces</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">intf</span><span class="p">)</span>
+        <span class="n">prg</span><span class="o">.</span><span class="n">terminate</span><span class="p">()</span>
+
+    <span class="k">if</span> <span class="n">ddi_flat</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
+
+        <span class="n">os</span><span class="o">.</span><span class="n">remove</span><span class="p">(</span><span class="n">tmpfile</span><span class="p">)</span>
+
+    <span class="k">if</span> <span class="n">res</span><span class="p">:</span>
+
+        <span class="n">pickle</span><span class="o">.</span><span class="n">dump</span><span class="p">([</span><span class="n">ddi</span><span class="p">,</span> <span class="n">interfaces</span><span class="p">],</span> <span class="nb">open</span><span class="p">(</span><span class="n">resultfile</span><span class="p">,</span> <span class="s1">&#39;wb&#39;</span><span class="p">))</span>
+
+        <span class="k">return</span> <span class="n">ddi</span><span class="p">,</span> <span class="n">interfaces</span>
+
+    <span class="k">else</span><span class="p">:</span>
+
+        <span class="n">pickle</span><span class="o">.</span><span class="n">dump</span><span class="p">([</span><span class="n">ddi</span><span class="p">],</span> <span class="nb">open</span><span class="p">(</span><span class="n">resultfile</span><span class="p">,</span> <span class="s1">&#39;wb&#39;</span><span class="p">))</span>
+
+        <span class="k">return</span> <span class="n">ddi</span></div>
+
+
+
+<div class="viewcode-block" id="get_3did_dmi">
+<a class="viewcode-back" href="../../../api/pypath.inputs.threedid.get_3did_dmi.html#pypath.inputs.threedid.get_3did_dmi">[docs]</a>
+<span class="k">def</span> <span class="nf">get_3did_dmi</span><span class="p">(</span><span class="n">dmi_flat</span> <span class="o">=</span> <span class="kc">None</span><span class="p">):</span>
+
+    <span class="n">resultfile</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">cache</span><span class="o">.</span><span class="n">get_cachedir</span><span class="p">(),</span> <span class="s1">&#39;3did_dmi.pickle&#39;</span><span class="p">)</span>
+
+    <span class="k">if</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">exists</span><span class="p">(</span><span class="n">resultfile</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="n">pickle</span><span class="o">.</span><span class="n">load</span><span class="p">(</span><span class="nb">open</span><span class="p">(</span><span class="n">resultfile</span><span class="p">,</span> <span class="s1">&#39;rb&#39;</span><span class="p">))</span>
+
+    <span class="k">if</span> <span class="n">dmi_flat</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
+
+        <span class="n">c</span> <span class="o">=</span> <span class="n">curl</span><span class="o">.</span><span class="n">Curl</span><span class="p">(</span><span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;3did_dmi&#39;</span><span class="p">][</span><span class="s1">&#39;url&#39;</span><span class="p">],</span> <span class="n">silent</span> <span class="o">=</span> <span class="kc">False</span><span class="p">)</span>
+        <span class="n">data</span> <span class="o">=</span> <span class="n">c</span><span class="o">.</span><span class="n">result</span>
+        <span class="n">tmpfile</span> <span class="o">=</span> <span class="s1">&#39;3did_dmi_flat_tmp&#39;</span>
+
+        <span class="k">if</span> <span class="n">data</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
+            <span class="k">return</span> <span class="kc">None</span>
+
+        <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">tmpfile</span><span class="p">,</span> <span class="s1">&#39;w&#39;</span><span class="p">)</span> <span class="k">as</span> <span class="n">f</span><span class="p">:</span>
+            <span class="n">f</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="n">data</span><span class="p">)</span>
+
+        <span class="n">lnum</span> <span class="o">=</span> <span class="n">data</span><span class="o">.</span><span class="n">count</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\n</span><span class="s1">&#39;</span><span class="p">)</span>
+        <span class="k">del</span> <span class="n">data</span>
+
+    <span class="k">elif</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">exists</span><span class="p">(</span><span class="n">dmi_flat</span><span class="p">):</span>
+
+        <span class="n">tmpfile</span> <span class="o">=</span> <span class="n">dmi_flat</span>
+
+    <span class="k">else</span><span class="p">:</span>
+
+        <span class="k">return</span> <span class="kc">None</span>
+
+    <span class="n">u_pdb</span><span class="p">,</span> <span class="n">pdb_u</span> <span class="o">=</span> <span class="n">pdb_input</span><span class="o">.</span><span class="n">pdb_chains</span><span class="p">()</span>
+
+    <span class="k">if</span> <span class="n">pdb_u</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
+
+        <span class="k">return</span> <span class="kc">None</span>
+
+    <span class="n">dmi</span> <span class="o">=</span> <span class="p">{}</span>
+    <span class="n">rmap</span> <span class="o">=</span> <span class="n">pdb_utils</span><span class="o">.</span><span class="n">ResidueMapper</span><span class="p">()</span>
+
+    <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">tmpfile</span><span class="p">,</span> <span class="s1">&#39;r&#39;</span><span class="p">)</span> <span class="k">as</span> <span class="n">f</span><span class="p">:</span>
+
+        <span class="n">prg</span> <span class="o">=</span> <span class="n">progress</span><span class="o">.</span><span class="n">Progress</span><span class="p">(</span>
+            <span class="n">lnum</span><span class="p">,</span>
+            <span class="s1">&#39;Processing 3DID domain-motif interactions&#39;</span><span class="p">,</span>
+            <span class="mi">1</span><span class="p">,</span>
+        <span class="p">)</span>
+
+        <span class="k">for</span> <span class="n">l</span> <span class="ow">in</span> <span class="n">f</span><span class="p">:</span>
+
+            <span class="n">prg</span><span class="o">.</span><span class="n">step</span><span class="p">()</span>
+
+            <span class="n">l</span> <span class="o">=</span> <span class="n">l</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span><span class="o">.</span><span class="n">split</span><span class="p">()</span>
+
+            <span class="k">if</span> <span class="n">l</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s1">&#39;#=ID&#39;</span><span class="p">):</span>
+
+                <span class="n">domain</span> <span class="o">=</span> <span class="n">l</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span>
+
+            <span class="k">if</span> <span class="n">l</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s1">&#39;#=PT&#39;</span><span class="p">):</span>
+
+                <span class="n">regex</span> <span class="o">=</span> <span class="n">l</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span>
+
+            <span class="k">if</span> <span class="n">l</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s1">&#39;#=3D&#39;</span><span class="p">):</span>
+
+                <span class="n">pdb</span> <span class="o">=</span> <span class="n">l</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span>
+                <span class="n">chain1</span> <span class="o">=</span> <span class="n">l</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;:&#39;</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span>
+                <span class="n">chain2</span> <span class="o">=</span> <span class="n">l</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;:&#39;</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span>
+
+                <span class="k">if</span> <span class="n">l</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span><span class="o">.</span><span class="n">count</span><span class="p">(</span><span class="s1">&#39;-&#39;</span><span class="p">)</span> <span class="o">==</span> <span class="mi">1</span> <span class="ow">and</span> <span class="n">l</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span><span class="o">.</span><span class="n">count</span><span class="p">(</span><span class="s1">&#39;-&#39;</span><span class="p">)</span> <span class="o">==</span> <span class="mi">1</span><span class="p">:</span>
+
+                    <span class="n">pdb_region1</span> <span class="o">=</span> <span class="p">[</span>
+                        <span class="nb">int</span><span class="p">(</span><span class="n">common</span><span class="o">.</span><span class="n">non_digit</span><span class="o">.</span><span class="n">sub</span><span class="p">(</span><span class="s1">&#39;&#39;</span><span class="p">,</span> <span class="n">x</span><span class="p">))</span>
+                        <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">l</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;:&#39;</span><span class="p">)[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;-&#39;</span><span class="p">)</span>
+                    <span class="p">]</span>
+                    <span class="n">pdb_region2</span> <span class="o">=</span> <span class="p">[</span>
+                        <span class="nb">int</span><span class="p">(</span><span class="n">common</span><span class="o">.</span><span class="n">non_digit</span><span class="o">.</span><span class="n">sub</span><span class="p">(</span><span class="s1">&#39;&#39;</span><span class="p">,</span> <span class="n">x</span><span class="p">))</span>
+                        <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">l</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;:&#39;</span><span class="p">)[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;-&#39;</span><span class="p">)</span>
+                    <span class="p">]</span>
+                    <span class="n">u1start</span> <span class="o">=</span> <span class="n">rmap</span><span class="o">.</span><span class="n">get_residue</span><span class="p">(</span>
+                        <span class="n">pdb</span><span class="p">,</span>
+                        <span class="n">pdb_region1</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span>
+                        <span class="n">chain</span> <span class="o">=</span> <span class="n">chain1</span><span class="p">,</span>
+                    <span class="p">)</span>
+                    <span class="n">u1end</span> <span class="o">=</span> <span class="n">rmap</span><span class="o">.</span><span class="n">get_residue</span><span class="p">(</span>
+                        <span class="n">pdb</span><span class="p">,</span>
+                        <span class="n">pdb_region1</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span>
+                        <span class="n">chain</span> <span class="o">=</span> <span class="n">chain1</span><span class="p">,</span>
+                    <span class="p">)</span>
+                    <span class="n">u2start</span> <span class="o">=</span> <span class="n">rmap</span><span class="o">.</span><span class="n">get_residue</span><span class="p">(</span>
+                        <span class="n">pdb</span><span class="p">,</span>
+                        <span class="n">pdb_region2</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span>
+                        <span class="n">chain</span> <span class="o">=</span> <span class="n">chain2</span><span class="p">,</span>
+                    <span class="p">)</span>
+                    <span class="n">u2end</span> <span class="o">=</span> <span class="n">rmap</span><span class="o">.</span><span class="n">get_residue</span><span class="p">(</span>
+                        <span class="n">pdb</span><span class="p">,</span>
+                        <span class="n">pdb_region2</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span>
+                        <span class="n">chain</span> <span class="o">=</span> <span class="n">chain2</span><span class="p">,</span>
+                    <span class="p">)</span>
+
+                    <span class="k">if</span> <span class="n">u1start</span> <span class="ow">and</span> <span class="n">u2start</span> <span class="ow">and</span> <span class="n">u1end</span> <span class="ow">and</span> <span class="n">u2end</span><span class="p">:</span>
+
+                        <span class="n">uniprot_key</span> <span class="o">=</span> <span class="p">(</span>
+                            <span class="n">u1start</span><span class="p">[</span><span class="n">chain1</span><span class="p">][</span><span class="s1">&#39;uniprot&#39;</span><span class="p">],</span>
+                            <span class="n">u2start</span><span class="p">[</span><span class="n">chain2</span><span class="p">][</span><span class="s1">&#39;uniprot&#39;</span><span class="p">],</span>
+                        <span class="p">)</span>
+
+                        <span class="n">residue_key</span> <span class="o">=</span> <span class="p">(</span>
+                            <span class="n">u1start</span><span class="p">[</span><span class="n">chain1</span><span class="p">][</span><span class="s1">&#39;resnum&#39;</span><span class="p">],</span>
+                            <span class="n">u1end</span><span class="p">[</span><span class="n">chain1</span><span class="p">][</span><span class="s1">&#39;resnum&#39;</span><span class="p">],</span>
+                            <span class="n">u2start</span><span class="p">[</span><span class="n">chain2</span><span class="p">][</span><span class="s1">&#39;resnum&#39;</span><span class="p">],</span>
+                            <span class="n">u2end</span><span class="p">[</span><span class="n">chain2</span><span class="p">][</span><span class="s1">&#39;resnum&#39;</span><span class="p">],</span>
+                        <span class="p">)</span>
+
+                        <span class="k">if</span> <span class="n">uniprot_key</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">dmi</span><span class="p">:</span>
+
+                            <span class="n">dmi</span><span class="p">[</span><span class="n">uniprot_key</span><span class="p">]</span> <span class="o">=</span> <span class="p">{}</span>
+
+                        <span class="k">if</span> <span class="n">residue_key</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">dmi</span><span class="p">[</span><span class="n">uniprot_key</span><span class="p">]:</span>
+
+                            <span class="n">dmi</span><span class="p">[</span><span class="n">uniprot_key</span><span class="p">][</span><span class="n">residue_key</span><span class="p">]</span> <span class="o">=</span> <span class="p">[]</span>
+
+                        <span class="n">dmi</span><span class="p">[</span><span class="n">uniprot_key</span><span class="p">][</span><span class="n">residue_key</span><span class="p">]</span><span class="o">.</span><span class="n">append</span><span class="p">({</span>
+                            <span class="s1">&#39;pdb&#39;</span><span class="p">:</span> <span class="n">pdb</span><span class="p">,</span>
+                            <span class="s1">&#39;regex&#39;</span><span class="p">:</span> <span class="n">regex</span><span class="p">,</span>
+                            <span class="s1">&#39;instance&#39;</span><span class="p">:</span> <span class="n">l</span><span class="p">[</span><span class="mi">4</span><span class="p">],</span>
+                            <span class="s1">&#39;domain&#39;</span><span class="p">:</span> <span class="n">domain</span><span class="p">,</span>
+                            <span class="s1">&#39;contacts&#39;</span><span class="p">:</span> <span class="nb">int</span><span class="p">(</span><span class="n">non_digit</span><span class="o">.</span><span class="n">sub</span><span class="p">(</span><span class="s1">&#39;&#39;</span><span class="p">,</span> <span class="n">l</span><span class="p">[</span><span class="mi">5</span><span class="p">])),</span>
+                            <span class="s1">&#39;topology&#39;</span><span class="p">:</span> <span class="nb">int</span><span class="p">(</span><span class="n">non_digit</span><span class="o">.</span><span class="n">sub</span><span class="p">(</span><span class="s1">&#39;&#39;</span><span class="p">,</span> <span class="n">l</span><span class="p">[</span><span class="mi">6</span><span class="p">])),</span>
+                        <span class="p">})</span>
+
+        <span class="n">prg</span><span class="o">.</span><span class="n">terminate</span><span class="p">()</span>
+
+    <span class="k">if</span> <span class="n">dmi_flat</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
+
+        <span class="n">os</span><span class="o">.</span><span class="n">remove</span><span class="p">(</span><span class="n">tmpfile</span><span class="p">)</span>
+
+    <span class="n">pickle</span><span class="o">.</span><span class="n">dump</span><span class="p">(</span><span class="n">dmi</span><span class="p">,</span> <span class="nb">open</span><span class="p">(</span><span class="n">resultfile</span><span class="p">,</span> <span class="s1">&#39;wb&#39;</span><span class="p">))</span>
+
+    <span class="k">return</span> <span class="n">dmi</span></div>
+
+
+
+<div class="viewcode-block" id="process_3did_dmi">
+<a class="viewcode-back" href="../../../api/pypath.inputs.threedid.process_3did_dmi.html#pypath.inputs.threedid.process_3did_dmi">[docs]</a>
+<span class="k">def</span> <span class="nf">process_3did_dmi</span><span class="p">():</span>
+
+    <span class="n">dmi</span> <span class="o">=</span> <span class="n">get_3did_dmi</span><span class="p">()</span>
+
+    <span class="k">if</span> <span class="n">dmi</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
+
+        <span class="k">return</span> <span class="kc">None</span>
+
+    <span class="n">dname_pfam</span><span class="p">,</span> <span class="n">pfam_dname</span> <span class="o">=</span> <span class="n">pfam_input</span><span class="o">.</span><span class="n">pfam_names</span><span class="p">()</span>
+    <span class="n">dname_re</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">compile</span><span class="p">(</span><span class="sa">r</span><span class="s1">&#39;(.*)(_[A-Z]</span><span class="si">{3}</span><span class="s1">_)(.*)&#39;</span><span class="p">)</span>
+    <span class="n">dmi2</span> <span class="o">=</span> <span class="p">{}</span>
+    <span class="n">prg</span> <span class="o">=</span> <span class="n">progress</span><span class="o">.</span><span class="n">Progress</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">dmi</span><span class="p">),</span> <span class="s1">&#39;Processing data&#39;</span><span class="p">,</span> <span class="mi">11</span><span class="p">)</span>
+
+    <span class="k">for</span> <span class="n">uniprots</span><span class="p">,</span> <span class="n">dmis</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="n">dmi</span><span class="p">):</span>
+        <span class="n">prg</span><span class="o">.</span><span class="n">step</span><span class="p">()</span>
+
+        <span class="k">if</span> <span class="n">uniprots</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">dmi2</span><span class="p">:</span>
+            <span class="n">dmi2</span><span class="p">[</span><span class="n">uniprots</span><span class="p">]</span> <span class="o">=</span> <span class="p">[]</span>
+
+        <span class="k">for</span> <span class="n">regions</span><span class="p">,</span> <span class="n">dmi_list</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="n">dmis</span><span class="p">):</span>
+            <span class="n">new</span> <span class="o">=</span> <span class="kc">True</span>
+
+            <span class="k">for</span> <span class="n">dm</span> <span class="ow">in</span> <span class="n">dmi_list</span><span class="p">:</span>
+                <span class="k">if</span> <span class="n">new</span><span class="p">:</span>
+                    <span class="n">pfam</span> <span class="o">=</span> <span class="kc">None</span>
+                    <span class="n">dname</span> <span class="o">=</span> <span class="kc">None</span>
+                    <span class="n">mname</span> <span class="o">=</span> <span class="kc">None</span>
+                    <span class="n">name_match</span> <span class="o">=</span> <span class="n">dname_re</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="n">dm</span><span class="p">[</span><span class="s1">&#39;domain&#39;</span><span class="p">])</span>
+
+                    <span class="k">if</span> <span class="n">name_match</span><span class="p">:</span>
+                        <span class="n">dname</span> <span class="o">=</span> <span class="n">name_match</span><span class="o">.</span><span class="n">groups</span><span class="p">(</span><span class="mi">0</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span>
+                        <span class="n">mname</span> <span class="o">=</span> <span class="s1">&#39;&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">name_match</span><span class="o">.</span><span class="n">groups</span><span class="p">(</span><span class="mi">0</span><span class="p">)[</span><span class="mi">1</span><span class="p">:])[</span><span class="mi">1</span><span class="p">:]</span>
+
+                    <span class="k">if</span> <span class="n">dname</span> <span class="ow">in</span> <span class="n">dname_pfam</span><span class="p">:</span>
+                        <span class="n">pfam</span> <span class="o">=</span> <span class="n">dname_pfam</span><span class="p">[</span><span class="n">dname</span><span class="p">][</span><span class="mi">0</span><span class="p">]</span>
+
+                    <span class="n">domain</span> <span class="o">=</span> <span class="n">pfam</span> <span class="k">if</span> <span class="n">pfam</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span> <span class="k">else</span> <span class="n">dname</span>
+                    <span class="n">domain_name</span> <span class="o">=</span> <span class="s1">&#39;pfam&#39;</span> <span class="k">if</span> <span class="n">pfam</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span> <span class="k">else</span> <span class="s1">&#39;domain_name&#39;</span>
+                    <span class="n">dom</span> <span class="o">=</span> <span class="n">intera</span><span class="o">.</span><span class="n">Domain</span><span class="p">(</span>
+                        <span class="n">uniprots</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span>
+                        <span class="n">domain</span> <span class="o">=</span> <span class="n">domain</span><span class="p">,</span>
+                        <span class="n">domain_id_type</span> <span class="o">=</span> <span class="n">domain_name</span><span class="p">,</span>
+                        <span class="n">start</span> <span class="o">=</span> <span class="n">regions</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span>
+                        <span class="n">end</span> <span class="o">=</span> <span class="n">regions</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span>
+                    <span class="n">mot</span> <span class="o">=</span> <span class="n">intera</span><span class="o">.</span><span class="n">Motif</span><span class="p">(</span>
+                        <span class="n">uniprots</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span>
+                        <span class="n">regions</span><span class="p">[</span><span class="mi">2</span><span class="p">],</span>
+                        <span class="n">regions</span><span class="p">[</span><span class="mi">3</span><span class="p">],</span>
+                        <span class="n">instance</span> <span class="o">=</span> <span class="n">dm</span><span class="p">[</span><span class="s1">&#39;instance&#39;</span><span class="p">],</span>
+                        <span class="n">regex</span> <span class="o">=</span> <span class="n">dm</span><span class="p">[</span><span class="s1">&#39;regex&#39;</span><span class="p">],</span>
+                        <span class="n">motif_name</span> <span class="o">=</span> <span class="n">mname</span><span class="p">)</span>
+                    <span class="n">ptm</span> <span class="o">=</span> <span class="n">intera</span><span class="o">.</span><span class="n">Ptm</span><span class="p">(</span><span class="n">uniprots</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span> <span class="n">motif</span> <span class="o">=</span> <span class="n">mot</span><span class="p">,</span> <span class="n">source</span> <span class="o">=</span> <span class="s1">&#39;3DID&#39;</span><span class="p">)</span>
+                    <span class="n">dommot</span> <span class="o">=</span> <span class="n">intera</span><span class="o">.</span><span class="n">DomainMotif</span><span class="p">(</span><span class="n">dom</span><span class="p">,</span> <span class="n">ptm</span><span class="p">,</span> <span class="n">sources</span> <span class="o">=</span> <span class="s1">&#39;3DID&#39;</span><span class="p">)</span>
+                    <span class="n">new</span> <span class="o">=</span> <span class="kc">False</span>
+
+                <span class="n">dommot</span><span class="o">.</span><span class="n">add_pdbs</span><span class="p">(</span><span class="n">dm</span><span class="p">[</span><span class="s1">&#39;pdb&#39;</span><span class="p">])</span>
+
+            <span class="n">dmi2</span><span class="p">[</span><span class="n">uniprots</span><span class="p">]</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">dommot</span><span class="p">)</span>
+
+    <span class="n">prg</span><span class="o">.</span><span class="n">terminate</span><span class="p">()</span>
+
+    <span class="k">return</span> <span class="n">dmi2</span></div>
+
+</pre></div>
+
+                </article>
+              
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diff --git a/_modules/pypath/inputs/topdb.html b/_modules/pypath/inputs/topdb.html
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+
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+                  
+  <h1>Source code for pypath.inputs.topdb</h1><div class="highlight"><pre>
+<span></span><span class="ch">#!/usr/bin/env python</span>
+<span class="c1"># -*- coding: utf-8 -*-</span>
+
+<span class="c1">#</span>
+<span class="c1">#  This file is part of the `pypath` python module</span>
+<span class="c1">#</span>
+<span class="c1">#  Copyright 2014-2023</span>
+<span class="c1">#  EMBL, EMBL-EBI, Uniklinik RWTH Aachen, Heidelberg University</span>
+<span class="c1">#</span>
+<span class="c1">#  Authors: see the file `README.rst`</span>
+<span class="c1">#  Contact: Dénes Türei (turei.denes@gmail.com)</span>
+<span class="c1">#</span>
+<span class="c1">#  Distributed under the GPLv3 License.</span>
+<span class="c1">#  See accompanying file LICENSE.txt or copy at</span>
+<span class="c1">#      https://www.gnu.org/licenses/gpl-3.0.html</span>
+<span class="c1">#</span>
+<span class="c1">#  Website: https://pypath.omnipathdb.org/</span>
+<span class="c1">#</span>
+
+<span class="kn">from</span> <span class="nn">past.builtins</span> <span class="kn">import</span> <span class="n">xrange</span><span class="p">,</span> <span class="nb">range</span>
+
+<span class="kn">import</span> <span class="nn">collections</span>
+<span class="kn">import</span> <span class="nn">itertools</span>
+
+<span class="kn">from</span> <span class="nn">lxml</span> <span class="kn">import</span> <span class="n">etree</span>
+
+<span class="kn">import</span> <span class="nn">pypath.share.curl</span> <span class="k">as</span> <span class="nn">curl</span>
+<span class="kn">import</span> <span class="nn">pypath.resources.urls</span> <span class="k">as</span> <span class="nn">urls</span>
+<span class="kn">import</span> <span class="nn">pypath.utils.mapping</span> <span class="k">as</span> <span class="nn">mapping</span>
+<span class="kn">import</span> <span class="nn">pypath.utils.taxonomy</span> <span class="k">as</span> <span class="nn">taxonomy</span>
+
+
+<div class="viewcode-block" id="topdb_annotations">
+<a class="viewcode-back" href="../../../api/pypath.inputs.topdb.topdb_annotations.html#pypath.inputs.topdb.topdb_annotations">[docs]</a>
+<span class="k">def</span> <span class="nf">topdb_annotations</span><span class="p">(</span><span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">):</span>
+
+    <span class="n">TopdbAnnotation</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">namedtuple</span><span class="p">(</span>
+        <span class="s1">&#39;TopdbAnnotation&#39;</span><span class="p">,</span>
+        <span class="p">[</span><span class="s1">&#39;membrane&#39;</span><span class="p">,</span> <span class="s1">&#39;topology&#39;</span><span class="p">,</span> <span class="s1">&#39;score&#39;</span><span class="p">,</span> <span class="s1">&#39;tmregions&#39;</span><span class="p">],</span>
+    <span class="p">)</span>
+
+    <span class="n">result</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">defaultdict</span><span class="p">(</span><span class="nb">set</span><span class="p">)</span>
+
+    <span class="n">url</span> <span class="o">=</span> <span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;topdb&#39;</span><span class="p">][</span><span class="s1">&#39;url&#39;</span><span class="p">]</span>
+    <span class="n">c</span> <span class="o">=</span> <span class="n">curl</span><span class="o">.</span><span class="n">Curl</span><span class="p">(</span>
+        <span class="n">url</span><span class="p">,</span>
+        <span class="n">large</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
+        <span class="n">default_mode</span> <span class="o">=</span> <span class="s1">&#39;rb&#39;</span><span class="p">,</span>
+        <span class="n">silent</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+    <span class="p">)</span>
+
+    <span class="n">parser</span> <span class="o">=</span> <span class="n">etree</span><span class="o">.</span><span class="n">iterparse</span><span class="p">(</span><span class="n">c</span><span class="o">.</span><span class="n">fileobj</span><span class="p">,</span> <span class="n">events</span> <span class="o">=</span> <span class="p">(</span><span class="s1">&#39;start&#39;</span><span class="p">,</span> <span class="s1">&#39;end&#39;</span><span class="p">))</span>
+
+    <span class="n">result</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">defaultdict</span><span class="p">(</span><span class="nb">set</span><span class="p">)</span>
+    <span class="n">root</span> <span class="o">=</span> <span class="nb">next</span><span class="p">(</span><span class="n">parser</span><span class="p">)</span>
+    <span class="n">used_elements</span> <span class="o">=</span> <span class="p">[]</span>
+
+    <span class="k">for</span> <span class="n">ev</span><span class="p">,</span> <span class="n">elem</span> <span class="ow">in</span> <span class="n">parser</span><span class="p">:</span>
+
+        <span class="k">if</span> <span class="n">ev</span> <span class="o">==</span> <span class="s1">&#39;end&#39;</span> <span class="ow">and</span> <span class="n">elem</span><span class="o">.</span><span class="n">tag</span> <span class="o">==</span> <span class="s1">&#39;TOPDB&#39;</span><span class="p">:</span>
+
+            <span class="n">used_elements</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">elem</span><span class="p">)</span>
+
+            <span class="n">organism</span> <span class="o">=</span> <span class="n">elem</span><span class="o">.</span><span class="n">find</span><span class="p">(</span><span class="s1">&#39;Organism&#39;</span><span class="p">)</span><span class="o">.</span><span class="n">text</span>
+            <span class="n">organism</span> <span class="o">=</span> <span class="n">taxonomy</span><span class="o">.</span><span class="n">ensure_ncbi_tax_id</span><span class="p">(</span><span class="n">organism</span><span class="p">)</span>
+
+            <span class="k">if</span> <span class="ow">not</span> <span class="n">organism</span><span class="p">:</span>
+
+                <span class="k">continue</span>
+
+            <span class="n">tag_uniprots</span> <span class="o">=</span> <span class="n">elem</span><span class="o">.</span><span class="n">find</span><span class="p">(</span><span class="s1">&#39;./CrossRef/UniProt&#39;</span><span class="p">)</span>
+
+            <span class="k">if</span> <span class="n">tag_uniprots</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
+                <span class="k">continue</span>
+
+            <span class="n">uniprots</span> <span class="o">=</span> <span class="p">[</span><span class="n">u</span><span class="o">.</span><span class="n">text</span> <span class="k">for</span> <span class="n">u</span> <span class="ow">in</span> <span class="n">tag_uniprots</span><span class="o">.</span><span class="n">findall</span><span class="p">(</span><span class="s1">&#39;AC&#39;</span><span class="p">)]</span>
+            <span class="n">uniprots</span> <span class="o">=</span> <span class="nb">set</span><span class="p">(</span>
+                <span class="n">mapping</span><span class="o">.</span><span class="n">map_name0</span><span class="p">(</span>
+                    <span class="n">u</span><span class="p">,</span>
+                    <span class="s1">&#39;uniprot&#39;</span><span class="p">,</span>
+                    <span class="s1">&#39;uniprot&#39;</span><span class="p">,</span>
+                    <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">,</span>
+                <span class="p">)</span>
+                <span class="k">for</span> <span class="n">u</span> <span class="ow">in</span> <span class="n">uniprots</span>
+            <span class="p">)</span>
+
+            <span class="k">if</span> <span class="ow">not</span> <span class="n">uniprots</span><span class="p">:</span>
+                <span class="k">continue</span>
+
+            <span class="n">membranes</span> <span class="o">=</span> <span class="nb">set</span><span class="p">(</span>
+                <span class="n">mem</span>
+                <span class="k">for</span> <span class="n">tag_mem</span> <span class="ow">in</span> <span class="n">elem</span><span class="o">.</span><span class="n">findall</span><span class="p">(</span><span class="s1">&#39;Membrane&#39;</span><span class="p">)</span>
+                <span class="k">for</span> <span class="n">mem</span> <span class="ow">in</span> <span class="n">tag_mem</span><span class="o">.</span><span class="n">text</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;;&#39;</span><span class="p">)</span>
+            <span class="p">)</span>
+
+            <span class="n">ntm</span> <span class="o">=</span> <span class="mi">0</span>
+            <span class="n">score</span> <span class="o">=</span> <span class="mi">0</span>
+            <span class="n">topologies</span> <span class="o">=</span> <span class="p">()</span>
+            <span class="n">tag_topo</span> <span class="o">=</span> <span class="n">elem</span><span class="o">.</span><span class="n">find</span><span class="p">(</span><span class="s1">&#39;Topology&#39;</span><span class="p">)</span>
+
+            <span class="k">if</span> <span class="n">tag_topo</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
+                <span class="n">ntm</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">tag_topo</span><span class="o">.</span><span class="n">find</span><span class="p">(</span><span class="s1">&#39;Numtm&#39;</span><span class="p">)</span><span class="o">.</span><span class="n">attrib</span><span class="p">[</span><span class="s1">&#39;Count&#39;</span><span class="p">])</span>
+                <span class="n">score</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">tag_topo</span><span class="o">.</span><span class="n">find</span><span class="p">(</span><span class="s1">&#39;Reliability&#39;</span><span class="p">)</span><span class="o">.</span><span class="n">text</span><span class="p">)</span>
+
+                <span class="n">topologies</span> <span class="o">=</span> <span class="nb">set</span><span class="p">(</span>
+                    <span class="n">tag_reg</span><span class="o">.</span><span class="n">attrib</span><span class="p">[</span><span class="s1">&#39;Loc&#39;</span><span class="p">]</span>
+                    <span class="k">for</span> <span class="n">tag_reg</span> <span class="ow">in</span> <span class="n">tag_topo</span><span class="o">.</span><span class="n">findall</span><span class="p">(</span><span class="s1">&#39;./Regions/Region&#39;</span><span class="p">)</span>
+                <span class="p">)</span>
+
+            <span class="k">if</span> <span class="ow">not</span> <span class="n">membranes</span><span class="p">:</span>
+                <span class="n">membranes</span> <span class="o">=</span> <span class="p">(</span><span class="kc">None</span><span class="p">,)</span>
+
+            <span class="k">if</span> <span class="ow">not</span> <span class="n">topologies</span><span class="p">:</span>
+                <span class="n">topologies</span> <span class="o">=</span> <span class="p">(</span><span class="kc">None</span><span class="p">,)</span>
+
+            <span class="k">for</span> <span class="n">topology</span><span class="p">,</span> <span class="n">membrane</span><span class="p">,</span> <span class="n">uniprot</span> <span class="ow">in</span> <span class="n">itertools</span><span class="o">.</span><span class="n">product</span><span class="p">(</span>
+                <span class="n">topologies</span><span class="p">,</span>
+                <span class="n">membranes</span><span class="p">,</span>
+                <span class="n">uniprots</span><span class="p">,</span>
+            <span class="p">):</span>
+
+                <span class="k">if</span> <span class="n">uniprot</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
+
+                    <span class="k">continue</span>
+
+                <span class="n">result</span><span class="p">[</span><span class="n">uniprot</span><span class="p">]</span><span class="o">.</span><span class="n">add</span><span class="p">(</span>
+                    <span class="n">TopdbAnnotation</span><span class="p">(</span>
+                        <span class="n">membrane</span> <span class="o">=</span> <span class="n">membrane</span><span class="p">,</span>
+                        <span class="n">topology</span> <span class="o">=</span> <span class="n">topology</span><span class="p">,</span>
+                        <span class="n">tmregions</span> <span class="o">=</span> <span class="n">ntm</span><span class="p">,</span>
+                        <span class="n">score</span> <span class="o">=</span> <span class="n">score</span><span class="p">,</span>
+                    <span class="p">)</span>
+                <span class="p">)</span>
+
+        <span class="c1"># removing used elements to keep memory low</span>
+        <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">used_elements</span><span class="p">)</span> <span class="o">&gt;</span> <span class="mi">2000</span><span class="p">:</span>
+            <span class="k">for</span> <span class="n">_</span> <span class="ow">in</span> <span class="n">xrange</span><span class="p">(</span><span class="mi">1000</span><span class="p">):</span>
+                <span class="n">e</span> <span class="o">=</span> <span class="n">used_elements</span><span class="o">.</span><span class="n">pop</span><span class="p">(</span><span class="mi">0</span><span class="p">)</span>
+                <span class="n">e</span><span class="o">.</span><span class="n">clear</span><span class="p">()</span>
+
+    <span class="c1"># closing the XML</span>
+    <span class="n">c</span><span class="o">.</span><span class="n">fileobj</span><span class="o">.</span><span class="n">close</span><span class="p">()</span>
+    <span class="k">del</span> <span class="n">c</span>
+
+    <span class="k">return</span> <span class="nb">dict</span><span class="p">(</span><span class="n">result</span><span class="p">)</span></div>
+
+</pre></div>
+
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diff --git a/_modules/pypath/inputs/wang.html b/_modules/pypath/inputs/wang.html
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+  <h1>Source code for pypath.inputs.wang</h1><div class="highlight"><pre>
+<span></span><span class="ch">#!/usr/bin/env python</span>
+<span class="c1"># -*- coding: utf-8 -*-</span>
+
+<span class="c1">#</span>
+<span class="c1">#  This file is part of the `pypath` python module</span>
+<span class="c1">#</span>
+<span class="c1">#  Copyright 2014-2023</span>
+<span class="c1">#  EMBL, EMBL-EBI, Uniklinik RWTH Aachen, Heidelberg University</span>
+<span class="c1">#</span>
+<span class="c1">#  Authors: see the file `README.rst`</span>
+<span class="c1">#  Contact: Dénes Türei (turei.denes@gmail.com)</span>
+<span class="c1">#</span>
+<span class="c1">#  Distributed under the GPLv3 License.</span>
+<span class="c1">#  See accompanying file LICENSE.txt or copy at</span>
+<span class="c1">#      https://www.gnu.org/licenses/gpl-3.0.html</span>
+<span class="c1">#</span>
+<span class="c1">#  Website: https://pypath.omnipathdb.org/</span>
+<span class="c1">#</span>
+
+<span class="kn">import</span> <span class="nn">collections</span>
+
+<span class="kn">from</span> <span class="nn">typing</span> <span class="kn">import</span> <span class="n">List</span><span class="p">,</span> <span class="n">Literal</span><span class="p">,</span> <span class="n">Union</span>
+
+<span class="kn">import</span> <span class="nn">pypath.resources.urls</span> <span class="k">as</span> <span class="nn">urls</span>
+<span class="kn">import</span> <span class="nn">pypath.share.curl</span> <span class="k">as</span> <span class="nn">curl</span>
+<span class="kn">import</span> <span class="nn">pypath.share.settings</span> <span class="k">as</span> <span class="nn">settings</span>
+<span class="kn">import</span> <span class="nn">pypath.inputs.embopress</span> <span class="k">as</span> <span class="nn">embo</span>
+<span class="kn">import</span> <span class="nn">pypath.inputs.ca1</span> <span class="k">as</span> <span class="nn">ca1</span>
+<span class="kn">import</span> <span class="nn">pypath.utils.mapping</span> <span class="k">as</span> <span class="nn">mapping</span>
+
+
+<span class="n">KEY</span> <span class="o">=</span> <span class="p">{</span>
+    <span class="s1">&#39;NA&#39;</span><span class="p">:</span> <span class="kc">None</span><span class="p">,</span>
+    <span class="s1">&#39;Neucleus&#39;</span><span class="p">:</span> <span class="s1">&#39;Nucleus&#39;</span><span class="p">,</span>
+    <span class="s1">&#39;Ribosomes&#39;</span><span class="p">:</span> <span class="s1">&#39;Ribosome&#39;</span><span class="p">,</span>
+    <span class="s1">&#39;Vesicles&#39;</span><span class="p">:</span> <span class="s1">&#39;Vesicle&#39;</span><span class="p">,</span>
+    <span class="s1">&#39;Endoplasmic reticulum&#39;</span><span class="p">:</span> <span class="s1">&#39;ER&#39;</span><span class="p">,</span>
+    <span class="s1">&#39;Not available&#39;</span><span class="p">:</span> <span class="kc">None</span><span class="p">,</span>
+    <span class="s1">&#39;Not Available&#39;</span><span class="p">:</span> <span class="kc">None</span><span class="p">,</span>
+    <span class="s1">&#39;Mitochondrial&#39;</span><span class="p">:</span> <span class="s1">&#39;Mitochondrion&#39;</span><span class="p">,</span>
+    <span class="s1">&#39;Mitochondria&#39;</span><span class="p">:</span> <span class="s1">&#39;Mitochondrion&#39;</span><span class="p">,</span>
+    <span class="s1">&#39;Anti-Apoptic&#39;</span><span class="p">:</span> <span class="s1">&#39;Anti-apoptotic&#39;</span><span class="p">,</span>
+<span class="p">}</span>
+
+
+<span class="n">ca1_interactions</span> <span class="o">=</span> <span class="n">ca1</span><span class="o">.</span><span class="n">ca1_interactions</span>
+
+
+<div class="viewcode-block" id="hsn_interactions">
+<a class="viewcode-back" href="../../../api/pypath.inputs.wang.hsn_interactions.html#pypath.inputs.wang.hsn_interactions">[docs]</a>
+<span class="k">def</span> <span class="nf">hsn_interactions</span><span class="p">(</span>
+        <span class="n">source</span><span class="p">:</span> <span class="n">Literal</span><span class="p">[</span><span class="s1">&#39;rescued&#39;</span><span class="p">,</span> <span class="s1">&#39;researchgate&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="s1">&#39;rescued&#39;</span><span class="p">,</span>
+    <span class="p">)</span> <span class="o">-&gt;</span> <span class="n">List</span><span class="p">[</span><span class="nb">tuple</span><span class="p">]:</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Downloads and processes HumanSignalingNetwork version 6</span>
+<span class="sd">    (published 2014 Jan by Edwin Wang).</span>
+
+<span class="sd">    Args</span>
+<span class="sd">        source: The same file is available from two domains: the OmniPath</span>
+<span class="sd">            rescued repository and Research Gate. These both are secondary</span>
+<span class="sd">            sources, the dataset is not available any more from its original</span>
+<span class="sd">            site of publication, which was the old webpage of the Wang Lab.</span>
+
+<span class="sd">    Details:</span>
+<span class="sd">        This dataset is identical to the one returned by `wang_interactions`,</span>
+<span class="sd">        but it does not contain function and localization details.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="n">effects</span> <span class="o">=</span> <span class="p">{</span>
+        <span class="s1">&#39;Pos&#39;</span><span class="p">:</span> <span class="s1">&#39;+&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;Neg&#39;</span><span class="p">:</span> <span class="s1">&#39;-&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;Phy&#39;</span><span class="p">:</span> <span class="s1">&#39;0&#39;</span><span class="p">,</span>
+    <span class="p">}</span>
+
+    <span class="k">class</span> <span class="nc">HsnInteraction</span><span class="p">(</span>
+            <span class="n">collections</span><span class="o">.</span><span class="n">namedtuple</span><span class="p">(</span>
+                <span class="s1">&#39;HsnInteractionBase&#39;</span><span class="p">,</span>
+                <span class="p">(</span>
+                    <span class="s1">&#39;genesymbol_source&#39;</span><span class="p">,</span>
+                    <span class="s1">&#39;genesymbol_target&#39;</span><span class="p">,</span>
+                    <span class="s1">&#39;entrez_source&#39;</span><span class="p">,</span>
+                    <span class="s1">&#39;entrez_target&#39;</span><span class="p">,</span>
+                    <span class="s1">&#39;effect&#39;</span><span class="p">,</span>
+                <span class="p">),</span>
+            <span class="p">),</span>
+        <span class="p">):</span>
+
+        <span class="k">def</span> <span class="fm">__new__</span><span class="p">(</span><span class="bp">cls</span><span class="p">,</span> <span class="o">*</span><span class="n">args</span><span class="p">):</span>
+
+            <span class="n">args</span> <span class="o">=</span> <span class="n">args</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">args</span><span class="p">)</span> <span class="o">==</span> <span class="mi">1</span> <span class="k">else</span> <span class="n">args</span>
+            <span class="n">identifiers</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">(</span><span class="nb">zip</span><span class="p">(</span>
+                <span class="p">(</span>
+                    <span class="s1">&#39;entrez_source&#39;</span><span class="p">,</span>
+                    <span class="s1">&#39;genesymbol_source&#39;</span><span class="p">,</span>
+                    <span class="s1">&#39;entrez_target&#39;</span><span class="p">,</span>
+                    <span class="s1">&#39;genesymbol_target&#39;</span><span class="p">,</span>
+                <span class="p">),</span>
+                <span class="n">args</span><span class="p">[:</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span>
+            <span class="p">))</span>
+
+            <span class="k">return</span> <span class="nb">super</span><span class="p">(</span><span class="n">HsnInteraction</span><span class="p">,</span> <span class="bp">cls</span><span class="p">)</span><span class="o">.</span><span class="fm">__new__</span><span class="p">(</span>
+                <span class="bp">cls</span><span class="p">,</span>
+                <span class="o">**</span><span class="n">identifiers</span><span class="p">,</span>
+                <span class="n">effect</span> <span class="o">=</span> <span class="n">effects</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="n">args</span><span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">],</span> <span class="n">args</span><span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">]),</span>
+            <span class="p">)</span>
+
+
+    <span class="n">url</span> <span class="o">=</span> <span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;hsn&#39;</span><span class="p">][</span><span class="n">source</span><span class="p">]</span>
+    <span class="n">c</span> <span class="o">=</span> <span class="n">curl</span><span class="o">.</span><span class="n">Curl</span><span class="p">(</span>
+        <span class="n">url</span><span class="p">,</span>
+        <span class="n">silent</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+        <span class="n">large</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
+        <span class="n">req_headers</span> <span class="o">=</span> <span class="p">[</span><span class="n">settings</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">&#39;user_agent&#39;</span><span class="p">)],</span>
+    <span class="p">)</span>
+    <span class="n">_</span> <span class="o">=</span> <span class="nb">next</span><span class="p">(</span><span class="n">c</span><span class="o">.</span><span class="n">result</span><span class="p">)</span>
+    <span class="n">result</span> <span class="o">=</span> <span class="p">[</span><span class="n">HsnInteraction</span><span class="p">(</span><span class="o">*</span><span class="n">r</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;,&#39;</span><span class="p">))</span> <span class="k">for</span> <span class="n">r</span> <span class="ow">in</span> <span class="n">c</span><span class="o">.</span><span class="n">result</span> <span class="k">if</span> <span class="n">r</span><span class="p">]</span>
+
+    <span class="k">return</span> <span class="n">result</span></div>
+
+
+
+<div class="viewcode-block" id="wang_interactions">
+<a class="viewcode-back" href="../../../api/pypath.inputs.wang.wang_interactions.html#pypath.inputs.wang.wang_interactions">[docs]</a>
+<span class="k">def</span> <span class="nf">wang_interactions</span><span class="p">()</span> <span class="o">-&gt;</span> <span class="n">List</span><span class="p">[</span><span class="nb">tuple</span><span class="p">]:</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Downloads and processes Wang Lab HumanSignalingNetwork.</span>
+<span class="sd">    Returns list of interactions as tuples of source, target and effect.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="n">url</span> <span class="o">=</span> <span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;wang&#39;</span><span class="p">][</span><span class="s1">&#39;rescued&#39;</span><span class="p">]</span>
+    <span class="n">c</span> <span class="o">=</span> <span class="n">curl</span><span class="o">.</span><span class="n">Curl</span><span class="p">(</span><span class="n">url</span><span class="p">,</span> <span class="n">silent</span> <span class="o">=</span> <span class="kc">False</span><span class="p">)</span>
+    <span class="n">data</span> <span class="o">=</span> <span class="n">c</span><span class="o">.</span><span class="n">result</span>
+    <span class="n">data</span> <span class="o">=</span> <span class="n">data</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\n</span><span class="s1">&#39;</span><span class="p">)</span>
+
+    <span class="k">return</span> <span class="n">_wang_process</span><span class="p">(</span><span class="n">data</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="cui_interactions">
+<a class="viewcode-back" href="../../../api/pypath.inputs.wang.cui_interactions.html#pypath.inputs.wang.cui_interactions">[docs]</a>
+<span class="k">def</span> <span class="nf">cui_interactions</span><span class="p">()</span> <span class="o">-&gt;</span> <span class="n">List</span><span class="p">[</span><span class="nb">tuple</span><span class="p">]:</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Interactions from Supplementary Table 9 of Cui et al. 2007</span>
+<span class="sd">    (https://www.embopress.org/doi/full/10.1038/msb4100200).</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="n">raw</span> <span class="o">=</span> <span class="n">embo</span><span class="o">.</span><span class="n">embopress_supplementary</span><span class="p">(</span>
+        <span class="n">url</span> <span class="o">=</span> <span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;wang&#39;</span><span class="p">][</span><span class="s1">&#39;cui&#39;</span><span class="p">],</span>
+        <span class="n">init_url</span> <span class="o">=</span> <span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;wang&#39;</span><span class="p">][</span><span class="s1">&#39;cui_init&#39;</span><span class="p">],</span>
+        <span class="n">sheet</span> <span class="o">=</span> <span class="s1">&#39;Supplementary Table 9&#39;</span><span class="p">,</span>
+    <span class="p">)</span>
+
+    <span class="k">return</span> <span class="n">_wang_process</span><span class="p">(</span><span class="n">raw</span><span class="p">)</span></div>
+
+
+
+<span class="k">def</span> <span class="nf">_wang_process</span><span class="p">(</span><span class="n">raw</span><span class="p">:</span> <span class="n">List</span><span class="p">[</span><span class="n">Union</span><span class="p">[</span><span class="n">List</span><span class="p">,</span> <span class="nb">str</span><span class="p">]])</span> <span class="o">-&gt;</span> <span class="n">List</span><span class="p">[</span><span class="nb">tuple</span><span class="p">]:</span>
+
+    <span class="n">Node</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">namedtuple</span><span class="p">(</span>
+        <span class="s1">&#39;Node&#39;</span><span class="p">,</span>
+        <span class="p">(</span>
+            <span class="s1">&#39;genesymbol&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;entrez&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;function&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;location&#39;</span><span class="p">,</span>
+        <span class="p">),</span>
+    <span class="p">)</span>
+
+    <span class="n">WangInteraction</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">namedtuple</span><span class="p">(</span>
+        <span class="s1">&#39;WangInteraction&#39;</span><span class="p">,</span>
+        <span class="p">(</span>
+            <span class="s1">&#39;genesymbol_source&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;genesymbol_target&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;entrez_source&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;entrez_target&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;effect&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;function_source&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;location_source&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;function_target&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;location_target&#39;</span><span class="p">,</span>
+        <span class="p">),</span>
+    <span class="p">)</span>
+
+    <span class="n">key</span> <span class="o">=</span> <span class="n">KEY</span><span class="o">.</span><span class="n">copy</span><span class="p">()</span>
+
+    <span class="n">result</span> <span class="o">=</span> <span class="p">[]</span>
+    <span class="n">nodes</span> <span class="o">=</span> <span class="p">{}</span>
+    <span class="n">reading_nodes</span> <span class="o">=</span> <span class="kc">False</span>
+    <span class="n">reading_edges</span> <span class="o">=</span> <span class="kc">False</span>
+    <span class="n">reading_key</span> <span class="o">=</span> <span class="kc">False</span>
+
+    <span class="n">_key</span> <span class="o">=</span> <span class="k">lambda</span> <span class="n">y</span><span class="p">:</span> <span class="p">(</span><span class="k">lambda</span> <span class="n">x</span><span class="p">:</span> <span class="n">key</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="n">x</span><span class="p">,</span> <span class="n">x</span><span class="p">))(</span><span class="n">key</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="n">y</span><span class="p">,</span> <span class="n">y</span><span class="p">))</span>
+
+    <span class="k">for</span> <span class="n">l</span> <span class="ow">in</span> <span class="n">raw</span><span class="p">:</span>
+
+        <span class="k">if</span> <span class="ow">not</span> <span class="n">l</span> <span class="ow">or</span> <span class="ow">not</span> <span class="n">l</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="ow">or</span> <span class="p">(</span><span class="nb">hasattr</span><span class="p">(</span><span class="n">l</span><span class="p">,</span> <span class="s1">&#39;strip&#39;</span><span class="p">)</span> <span class="ow">and</span> <span class="ow">not</span> <span class="n">l</span><span class="o">.</span><span class="n">strip</span><span class="p">()):</span>
+
+            <span class="n">reading_key</span> <span class="o">=</span> <span class="kc">False</span>
+            <span class="n">reading_nodes</span> <span class="o">=</span> <span class="kc">False</span>
+            <span class="n">reading_edges</span> <span class="o">=</span> <span class="kc">False</span>
+
+        <span class="n">l</span> <span class="o">=</span> <span class="n">l</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;,&#39;</span><span class="p">)</span> <span class="k">if</span> <span class="nb">hasattr</span><span class="p">(</span><span class="n">l</span><span class="p">,</span> <span class="s1">&#39;split&#39;</span><span class="p">)</span> <span class="k">else</span> <span class="n">l</span>
+
+        <span class="k">if</span> <span class="n">reading_key</span><span class="p">:</span>
+
+            <span class="n">key</span><span class="p">[</span><span class="n">l</span><span class="p">[</span><span class="mi">0</span><span class="p">]]</span> <span class="o">=</span> <span class="n">l</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span>
+
+        <span class="k">elif</span> <span class="n">reading_nodes</span><span class="p">:</span>
+
+            <span class="n">nodes</span><span class="p">[</span><span class="n">l</span><span class="p">[</span><span class="mi">0</span><span class="p">]]</span> <span class="o">=</span> <span class="n">Node</span><span class="p">(</span>
+                <span class="n">genesymbol</span> <span class="o">=</span> <span class="n">l</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span>
+                <span class="n">entrez</span> <span class="o">=</span> <span class="n">l</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;.&#39;</span><span class="p">)[</span><span class="mi">0</span><span class="p">],</span>
+                <span class="n">function</span> <span class="o">=</span> <span class="n">_key</span><span class="p">(</span><span class="n">l</span><span class="p">[</span><span class="mi">3</span><span class="p">]),</span>
+                <span class="n">location</span> <span class="o">=</span> <span class="n">_key</span><span class="p">(</span><span class="n">l</span><span class="p">[</span><span class="mi">4</span><span class="p">]),</span>
+            <span class="p">)</span>
+
+        <span class="k">elif</span> <span class="n">reading_edges</span><span class="p">:</span>
+
+            <span class="n">src</span> <span class="o">=</span> <span class="n">nodes</span><span class="p">[</span><span class="n">l</span><span class="p">[</span><span class="mi">0</span><span class="p">]]</span>
+            <span class="n">tgt</span> <span class="o">=</span> <span class="n">nodes</span><span class="p">[</span><span class="n">l</span><span class="p">[</span><span class="mi">1</span><span class="p">]]</span>
+
+            <span class="n">result</span><span class="o">.</span><span class="n">append</span><span class="p">(</span>
+                <span class="n">WangInteraction</span><span class="p">(</span>
+                    <span class="n">genesymbol_source</span> <span class="o">=</span> <span class="n">src</span><span class="o">.</span><span class="n">genesymbol</span><span class="p">,</span>
+                    <span class="n">genesymbol_target</span> <span class="o">=</span> <span class="n">tgt</span><span class="o">.</span><span class="n">genesymbol</span><span class="p">,</span>
+                    <span class="n">entrez_source</span> <span class="o">=</span> <span class="n">src</span><span class="o">.</span><span class="n">entrez</span><span class="p">,</span>
+                    <span class="n">entrez_target</span> <span class="o">=</span> <span class="n">tgt</span><span class="o">.</span><span class="n">entrez</span><span class="p">,</span>
+                    <span class="n">effect</span> <span class="o">=</span> <span class="n">l</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s1">&#39;_&#39;</span><span class="p">,</span> <span class="s1">&#39;-&#39;</span><span class="p">)</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;.&#39;</span><span class="p">)[</span><span class="mi">0</span><span class="p">],</span>
+                    <span class="n">function_source</span> <span class="o">=</span> <span class="n">src</span><span class="o">.</span><span class="n">function</span><span class="p">,</span>
+                    <span class="n">location_source</span> <span class="o">=</span> <span class="n">src</span><span class="o">.</span><span class="n">location</span><span class="p">,</span>
+                    <span class="n">function_target</span> <span class="o">=</span> <span class="n">tgt</span><span class="o">.</span><span class="n">function</span><span class="p">,</span>
+                    <span class="n">location_target</span> <span class="o">=</span> <span class="n">tgt</span><span class="o">.</span><span class="n">location</span><span class="p">,</span>
+                <span class="p">)</span>
+            <span class="p">)</span>
+
+        <span class="k">if</span> <span class="n">l</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s1">&#39;Node&#39;</span><span class="p">):</span>
+
+            <span class="n">reading_key</span> <span class="o">=</span> <span class="kc">False</span>
+            <span class="n">reading_nodes</span> <span class="o">=</span> <span class="kc">True</span>
+
+        <span class="k">if</span> <span class="n">l</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s1">&#39;From&#39;</span><span class="p">):</span>
+
+            <span class="n">reading_key</span> <span class="o">=</span> <span class="kc">False</span>
+            <span class="n">reading_nodes</span> <span class="o">=</span> <span class="kc">False</span>
+            <span class="n">reading_edges</span> <span class="o">=</span> <span class="kc">True</span>
+
+        <span class="k">if</span> <span class="n">l</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s1">&#39;Notes:&#39;</span><span class="p">):</span>
+
+            <span class="n">reading_key</span> <span class="o">=</span> <span class="kc">True</span>
+
+    <span class="k">return</span> <span class="n">result</span>
+
+
+<div class="viewcode-block" id="wang_annotations">
+<a class="viewcode-back" href="../../../api/pypath.inputs.wang.wang_annotations.html#pypath.inputs.wang.wang_annotations">[docs]</a>
+<span class="k">def</span> <span class="nf">wang_annotations</span><span class="p">():</span>
+
+    <span class="n">NA_VALUES</span> <span class="o">=</span> <span class="p">{</span><span class="kc">None</span><span class="p">,</span> <span class="s1">&#39;NA&#39;</span><span class="p">,</span> <span class="s1">&#39;Not available&#39;</span><span class="p">}</span>
+
+    <span class="n">record</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">namedtuple</span><span class="p">(</span>
+        <span class="s1">&#39;WangAnnotation&#39;</span><span class="p">,</span>
+        <span class="p">(</span>
+            <span class="s1">&#39;function&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;location&#39;</span><span class="p">,</span>
+        <span class="p">),</span>
+    <span class="p">)</span>
+
+    <span class="n">result</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">defaultdict</span><span class="p">(</span><span class="nb">set</span><span class="p">)</span>
+
+    <span class="k">for</span> <span class="n">dataset</span> <span class="ow">in</span> <span class="p">(</span><span class="s1">&#39;ca1&#39;</span><span class="p">,</span> <span class="s1">&#39;cui&#39;</span><span class="p">,</span> <span class="s1">&#39;wang&#39;</span><span class="p">):</span>
+
+        <span class="n">func</span> <span class="o">=</span> <span class="nb">globals</span><span class="p">()[</span><span class="s1">&#39;</span><span class="si">%s</span><span class="s1">_interactions&#39;</span> <span class="o">%</span> <span class="n">dataset</span><span class="p">]</span>
+        <span class="n">data</span> <span class="o">=</span> <span class="n">func</span><span class="p">()</span>
+
+        <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="n">data</span><span class="p">:</span>
+
+            <span class="k">for</span> <span class="n">side</span> <span class="ow">in</span> <span class="p">(</span><span class="s1">&#39;source&#39;</span><span class="p">,</span> <span class="s1">&#39;target&#39;</span><span class="p">):</span>
+
+                <span class="n">a_uniprot</span> <span class="o">=</span> <span class="s1">&#39;uniprot_</span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="n">side</span>
+                <span class="n">a_entrez</span> <span class="o">=</span> <span class="s1">&#39;entrez_</span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="n">side</span>
+                <span class="n">a_function</span> <span class="o">=</span> <span class="s1">&#39;function_</span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="n">side</span>
+                <span class="n">a_location</span> <span class="o">=</span> <span class="s1">&#39;location_</span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="n">side</span>
+
+                <span class="n">function</span> <span class="o">=</span> <span class="nb">getattr</span><span class="p">(</span><span class="n">i</span><span class="p">,</span> <span class="n">a_function</span><span class="p">)</span>
+                <span class="n">location</span> <span class="o">=</span> <span class="nb">getattr</span><span class="p">(</span><span class="n">i</span><span class="p">,</span> <span class="n">a_location</span><span class="p">)</span>
+
+                <span class="k">if</span> <span class="n">function</span> <span class="ow">in</span> <span class="n">NA_VALUES</span> <span class="ow">and</span> <span class="n">location</span> <span class="ow">in</span> <span class="n">NA_VALUES</span><span class="p">:</span>
+
+                    <span class="k">continue</span>
+
+                <span class="n">uniprots</span> <span class="o">=</span> <span class="p">(</span>
+                    <span class="p">(</span><span class="nb">getattr</span><span class="p">(</span><span class="n">i</span><span class="p">,</span> <span class="n">a_uniprot</span><span class="p">),)</span>
+                        <span class="k">if</span> <span class="nb">hasattr</span><span class="p">(</span><span class="n">i</span><span class="p">,</span> <span class="n">a_uniprot</span><span class="p">)</span> <span class="k">else</span>
+                    <span class="n">mapping</span><span class="o">.</span><span class="n">map_name</span><span class="p">(</span><span class="nb">getattr</span><span class="p">(</span><span class="n">i</span><span class="p">,</span> <span class="n">a_entrez</span><span class="p">),</span> <span class="s1">&#39;entrez&#39;</span><span class="p">,</span> <span class="s1">&#39;uniprot&#39;</span><span class="p">)</span>
+                <span class="p">)</span>
+
+                <span class="k">for</span> <span class="n">uniprot</span> <span class="ow">in</span> <span class="n">uniprots</span><span class="p">:</span>
+
+                    <span class="n">result</span><span class="p">[</span><span class="n">uniprot</span><span class="p">]</span><span class="o">.</span><span class="n">add</span><span class="p">(</span>
+                        <span class="n">record</span><span class="p">(</span>
+                            <span class="n">function</span> <span class="o">=</span> <span class="n">function</span><span class="p">,</span>
+                            <span class="n">location</span> <span class="o">=</span> <span class="n">location</span><span class="p">,</span>
+                        <span class="p">)</span>
+                    <span class="p">)</span>
+
+    <span class="k">return</span> <span class="nb">dict</span><span class="p">(</span><span class="n">result</span><span class="p">)</span></div>
+
+</pre></div>
+
+                </article>
+              
+              
+              
+              
+              
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+                  
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diff --git a/_modules/pypath/inputs/wojtowicz2020.html b/_modules/pypath/inputs/wojtowicz2020.html
new file mode 100644
index 000000000..e4fcb2905
--- /dev/null
+++ b/_modules/pypath/inputs/wojtowicz2020.html
@@ -0,0 +1,697 @@
+
+<!DOCTYPE html>
+
+
+<html lang="en" data-content_root="../../../" >
+
+  <head>
+    <meta charset="utf-8" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
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+  
+  
+  
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+  <h1>Source code for pypath.inputs.wojtowicz2020</h1><div class="highlight"><pre>
+<span></span><span class="ch">#!/usr/bin/env python</span>
+<span class="c1"># -*- coding: utf-8 -*-</span>
+
+<span class="c1">#</span>
+<span class="c1">#  This file is part of the `pypath` python module</span>
+<span class="c1">#</span>
+<span class="c1">#  Copyright 2014-2023</span>
+<span class="c1">#  EMBL, EMBL-EBI, Uniklinik RWTH Aachen, Heidelberg University</span>
+<span class="c1">#</span>
+<span class="c1">#  Authors: see the file `README.rst`</span>
+<span class="c1">#  Contact: Dénes Türei (turei.denes@gmail.com)</span>
+<span class="c1">#</span>
+<span class="c1">#  Distributed under the GPLv3 License.</span>
+<span class="c1">#  See accompanying file LICENSE.txt or copy at</span>
+<span class="c1">#      https://www.gnu.org/licenses/gpl-3.0.html</span>
+<span class="c1">#</span>
+<span class="c1">#  Website: https://pypath.omnipathdb.org/</span>
+<span class="c1">#</span>
+
+<span class="kn">import</span> <span class="nn">re</span>
+<span class="kn">import</span> <span class="nn">collections</span>
+<span class="kn">import</span> <span class="nn">itertools</span>
+
+<span class="kn">import</span> <span class="nn">pypath.inputs.common</span> <span class="k">as</span> <span class="nn">inputs_common</span>
+<span class="kn">import</span> <span class="nn">pypath.resources.urls</span> <span class="k">as</span> <span class="nn">urls</span>
+<span class="kn">import</span> <span class="nn">pypath.utils.mapping</span> <span class="k">as</span> <span class="nn">mapping</span>
+<span class="kn">import</span> <span class="nn">pypath.share.common</span> <span class="k">as</span> <span class="nn">common</span>
+<span class="kn">import</span> <span class="nn">pypath.inputs.cell</span> <span class="k">as</span> <span class="nn">cell_input</span>
+
+
+<div class="viewcode-block" id="wojtowicz2020_raw">
+<a class="viewcode-back" href="../../../api/pypath.inputs.wojtowicz2020.wojtowicz2020_raw.html#pypath.inputs.wojtowicz2020.wojtowicz2020_raw">[docs]</a>
+<span class="k">def</span> <span class="nf">wojtowicz2020_raw</span><span class="p">():</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Returns Supplementary Table S4 from 10.1016/j.cell.2020.07.025</span>
+<span class="sd">    (Wojtowicz et al. 2020) as a list of tuples.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="n">path</span> <span class="o">=</span> <span class="n">cell_input</span><span class="o">.</span><span class="n">cell_supplementary</span><span class="p">(</span>
+        <span class="n">supp_url</span> <span class="o">=</span> <span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;wojtowicz2020&#39;</span><span class="p">][</span><span class="s1">&#39;url&#39;</span><span class="p">],</span>
+        <span class="n">article_url</span> <span class="o">=</span> <span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;wojtowicz2020&#39;</span><span class="p">][</span><span class="s1">&#39;article&#39;</span><span class="p">],</span>
+    <span class="p">)</span>
+
+    <span class="n">content</span> <span class="o">=</span> <span class="n">inputs_common</span><span class="o">.</span><span class="n">read_xls</span><span class="p">(</span><span class="n">path</span><span class="p">)</span>
+
+    <span class="n">fields</span> <span class="o">=</span> <span class="n">content</span><span class="o">.</span><span class="n">pop</span><span class="p">(</span><span class="mi">0</span><span class="p">)</span>
+    <span class="n">fields</span> <span class="o">=</span> <span class="p">[</span><span class="n">re</span><span class="o">.</span><span class="n">sub</span><span class="p">(</span><span class="s1">&#39;[- ]&#39;</span><span class="p">,</span> <span class="s1">&#39;_&#39;</span><span class="p">,</span> <span class="n">f</span><span class="o">.</span><span class="n">lower</span><span class="p">())</span> <span class="k">for</span> <span class="n">f</span> <span class="ow">in</span> <span class="n">fields</span><span class="p">]</span>
+
+    <span class="n">Wojtowicz2020RawRecord</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">namedtuple</span><span class="p">(</span>
+        <span class="s1">&#39;Wojtowicz2020RawRecord&#39;</span><span class="p">,</span>
+        <span class="n">fields</span>
+    <span class="p">)</span>
+
+    <span class="k">return</span> <span class="p">[</span>
+        <span class="n">Wojtowicz2020RawRecord</span><span class="p">(</span>
+            <span class="o">*</span><span class="p">(</span>
+                <span class="nb">float</span><span class="p">(</span><span class="n">f</span><span class="p">)</span>
+                    <span class="k">if</span> <span class="mi">5</span> <span class="o">&lt;</span> <span class="n">i</span> <span class="o">&lt;</span> <span class="mi">17</span> <span class="k">else</span>
+                <span class="n">f</span>
+                <span class="k">for</span> <span class="n">i</span><span class="p">,</span> <span class="n">f</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">line</span><span class="p">)</span>
+            <span class="p">)</span>
+        <span class="p">)</span>
+        <span class="k">for</span> <span class="n">line</span> <span class="ow">in</span> <span class="n">content</span>
+    <span class="p">]</span></div>
+
+
+
+<span class="k">def</span> <span class="nf">_id_translate</span><span class="p">(</span><span class="n">name</span><span class="p">):</span>
+
+    <span class="k">return</span> <span class="n">mapping</span><span class="o">.</span><span class="n">map_name</span><span class="p">(</span><span class="n">name</span><span class="p">,</span> <span class="s1">&#39;genesymbol&#39;</span><span class="p">,</span> <span class="s1">&#39;uniprot&#39;</span><span class="p">)</span>
+
+
+<div class="viewcode-block" id="wojtowicz2020_interactions">
+<a class="viewcode-back" href="../../../api/pypath.inputs.wojtowicz2020.wojtowicz2020_interactions.html#pypath.inputs.wojtowicz2020.wojtowicz2020_interactions">[docs]</a>
+<span class="k">def</span> <span class="nf">wojtowicz2020_interactions</span><span class="p">():</span>
+
+    <span class="n">Wojtowicz2020Interaction</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">namedtuple</span><span class="p">(</span>
+        <span class="s1">&#39;Wojtowicz2020Interaction&#39;</span><span class="p">,</span>
+        <span class="p">[</span><span class="s1">&#39;id_a&#39;</span><span class="p">,</span> <span class="s1">&#39;id_b&#39;</span><span class="p">],</span>
+    <span class="p">)</span>
+
+    <span class="n">result</span> <span class="o">=</span> <span class="p">[]</span>
+
+    <span class="k">for</span> <span class="n">rec</span> <span class="ow">in</span> <span class="n">wojtowicz2020_raw</span><span class="p">():</span>
+
+        <span class="n">preys</span> <span class="o">=</span> <span class="n">_id_translate</span><span class="p">(</span><span class="n">rec</span><span class="o">.</span><span class="n">prey_gene_name</span><span class="p">)</span>
+        <span class="n">baits</span> <span class="o">=</span> <span class="n">_id_translate</span><span class="p">(</span><span class="n">rec</span><span class="o">.</span><span class="n">bait_gene_name</span><span class="p">)</span>
+
+        <span class="k">for</span> <span class="n">id_a</span><span class="p">,</span> <span class="n">id_b</span> <span class="ow">in</span> <span class="n">itertools</span><span class="o">.</span><span class="n">product</span><span class="p">(</span><span class="n">preys</span><span class="p">,</span> <span class="n">baits</span><span class="p">):</span>
+
+            <span class="n">result</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">Wojtowicz2020Interaction</span><span class="p">(</span><span class="n">id_a</span><span class="p">,</span> <span class="n">id_b</span><span class="p">))</span>
+
+    <span class="k">return</span> <span class="n">result</span></div>
+
+</pre></div>
+
+                </article>
+              
+              
+              
+              
+              
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diff --git a/_modules/pypath/inputs/zhong2015.html b/_modules/pypath/inputs/zhong2015.html
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+  <h1>Source code for pypath.inputs.zhong2015</h1><div class="highlight"><pre>
+<span></span><span class="ch">#!/usr/bin/env python</span>
+<span class="c1"># -*- coding: utf-8 -*-</span>
+
+<span class="c1">#</span>
+<span class="c1">#  This file is part of the `pypath` python module</span>
+<span class="c1">#</span>
+<span class="c1">#  Copyright 2014-2023</span>
+<span class="c1">#  EMBL, EMBL-EBI, Uniklinik RWTH Aachen, Heidelberg University</span>
+<span class="c1">#</span>
+<span class="c1">#  Authors: see the file `README.rst`</span>
+<span class="c1">#  Contact: Dénes Türei (turei.denes@gmail.com)</span>
+<span class="c1">#</span>
+<span class="c1">#  Distributed under the GPLv3 License.</span>
+<span class="c1">#  See accompanying file LICENSE.txt or copy at</span>
+<span class="c1">#      https://www.gnu.org/licenses/gpl-3.0.html</span>
+<span class="c1">#</span>
+<span class="c1">#  Website: https://pypath.omnipathdb.org/</span>
+<span class="c1">#</span>
+
+<span class="kn">import</span> <span class="nn">collections</span>
+
+<span class="kn">import</span> <span class="nn">pypath.share.curl</span> <span class="k">as</span> <span class="nn">curl</span>
+<span class="kn">import</span> <span class="nn">pypath.resources.urls</span> <span class="k">as</span> <span class="nn">urls</span>
+<span class="kn">import</span> <span class="nn">pypath.utils.mapping</span> <span class="k">as</span> <span class="nn">mapping</span>
+
+
+<div class="viewcode-block" id="zhong2015_annotations">
+<a class="viewcode-back" href="../../../api/pypath.inputs.zhong2015.zhong2015_annotations.html#pypath.inputs.zhong2015.zhong2015_annotations">[docs]</a>
+<span class="k">def</span> <span class="nf">zhong2015_annotations</span><span class="p">():</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    From 10.1111/nyas.12776 (PMID 25988664).</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="n">types</span> <span class="o">=</span> <span class="p">{</span>
+        <span class="s1">&#39;i&#39;</span><span class="p">:</span> <span class="s1">&#39;iCAM&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;m&#39;</span><span class="p">:</span> <span class="s1">&#39;matrix adhesion&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;ag&#39;</span><span class="p">:</span> <span class="s1">&#39;axonal guidance&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;aj&#39;</span><span class="p">:</span> <span class="s1">&#39;adherens junction&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;c&#39;</span><span class="p">:</span> <span class="s1">&#39;cell-cell adhesion&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;fa&#39;</span><span class="p">:</span> <span class="s1">&#39;focal adhesion&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;tj&#39;</span><span class="p">:</span> <span class="s1">&#39;tight junction&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;my&#39;</span><span class="p">:</span> <span class="s1">&#39;myelin interactions&#39;</span><span class="p">,</span>
+    <span class="p">}</span>
+
+    <span class="n">Zhong2015Annotation</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">namedtuple</span><span class="p">(</span>
+        <span class="s1">&#39;Zhong2015Annotation&#39;</span><span class="p">,</span>
+        <span class="p">[</span><span class="s1">&#39;type&#39;</span><span class="p">],</span>
+    <span class="p">)</span>
+    <span class="n">result</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">defaultdict</span><span class="p">(</span><span class="nb">set</span><span class="p">)</span>
+
+    <span class="n">url</span> <span class="o">=</span> <span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;zhong2015&#39;</span><span class="p">][</span><span class="s1">&#39;url&#39;</span><span class="p">]</span>
+    <span class="n">c</span> <span class="o">=</span> <span class="n">curl</span><span class="o">.</span><span class="n">Curl</span><span class="p">(</span><span class="n">url</span><span class="p">,</span> <span class="n">silent</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span> <span class="n">large</span> <span class="o">=</span> <span class="kc">True</span><span class="p">)</span>
+
+    <span class="n">_</span> <span class="o">=</span> <span class="nb">next</span><span class="p">(</span><span class="n">c</span><span class="o">.</span><span class="n">result</span><span class="p">)</span>
+
+    <span class="k">for</span> <span class="n">rec</span> <span class="ow">in</span> <span class="n">c</span><span class="o">.</span><span class="n">result</span><span class="p">:</span>
+        <span class="n">rec</span> <span class="o">=</span> <span class="n">rec</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\t</span><span class="s1">&#39;</span><span class="p">)</span>
+
+        <span class="n">uniprot</span> <span class="o">=</span> <span class="n">mapping</span><span class="o">.</span><span class="n">map_name0</span><span class="p">(</span><span class="n">rec</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="s1">&#39;genesymbol&#39;</span><span class="p">,</span> <span class="s1">&#39;uniprot&#39;</span><span class="p">)</span>
+
+        <span class="k">if</span> <span class="n">uniprot</span><span class="p">:</span>
+            <span class="n">result</span><span class="p">[</span><span class="n">uniprot</span><span class="p">]</span><span class="o">.</span><span class="n">add</span><span class="p">(</span>
+                <span class="n">Zhong2015Annotation</span><span class="p">(</span><span class="nb">type</span> <span class="o">=</span> <span class="n">types</span><span class="p">[</span><span class="n">rec</span><span class="p">[</span><span class="mi">2</span><span class="p">]])</span>
+            <span class="p">)</span>
+
+    <span class="k">return</span> <span class="nb">dict</span><span class="p">(</span><span class="n">result</span><span class="p">)</span></div>
+
+</pre></div>
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+                  
+  <h1>Source code for pypath.internals.annot_formats</h1><div class="highlight"><pre>
+<span></span><span class="ch">#!/usr/bin/env python</span>
+<span class="c1"># -*- coding: utf-8 -*-</span>
+
+<span class="c1">#</span>
+<span class="c1">#  This file is part of the `pypath` python module</span>
+<span class="c1">#</span>
+<span class="c1">#  Copyright 2014-2023</span>
+<span class="c1">#  EMBL, EMBL-EBI, Uniklinik RWTH Aachen, Heidelberg University</span>
+<span class="c1">#</span>
+<span class="c1">#  Authors: see the file `README.rst`</span>
+<span class="c1">#  Contact: Dénes Türei (turei.denes@gmail.com)</span>
+<span class="c1">#</span>
+<span class="c1">#  Distributed under the GPLv3 License.</span>
+<span class="c1">#  See accompanying file LICENSE.txt or copy at</span>
+<span class="c1">#      https://www.gnu.org/licenses/gpl-3.0.html</span>
+<span class="c1">#</span>
+<span class="c1">#  Website: https://pypath.omnipathdb.org/</span>
+<span class="c1">#</span>
+
+<span class="kn">import</span> <span class="nn">collections</span>
+
+<span class="k">try</span><span class="p">:</span>
+    <span class="kn">import</span> <span class="nn">collections.abc</span> <span class="k">as</span> <span class="nn">collections_abc</span>
+<span class="k">except</span><span class="p">:</span>
+    <span class="kn">import</span> <span class="nn">collections</span> <span class="k">as</span> <span class="nn">collections_abc</span>
+
+<span class="kn">import</span> <span class="nn">pypath.share.settings</span> <span class="k">as</span> <span class="nn">settings</span>
+<span class="kn">import</span> <span class="nn">pypath.share.common</span> <span class="k">as</span> <span class="nn">common</span>
+<span class="kn">import</span> <span class="nn">pypath.core.entity</span> <span class="k">as</span> <span class="nn">entity</span>
+
+
+<span class="n">AnnotDefKey</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">namedtuple</span><span class="p">(</span>
+    <span class="s1">&#39;AnnotDefKey&#39;</span><span class="p">,</span>
+    <span class="p">[</span>
+        <span class="s1">&#39;name&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;parent&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;resource&#39;</span><span class="p">,</span>
+    <span class="p">],</span>
+<span class="p">)</span>
+
+
+<div class="viewcode-block" id="AnnotDef">
+<a class="viewcode-back" href="../../../api/pypath.internals.annot_formats.AnnotDef.html#pypath.internals.annot_formats.AnnotDef">[docs]</a>
+<span class="k">class</span> <span class="nc">AnnotDef</span><span class="p">(</span>
+        <span class="n">collections</span><span class="o">.</span><span class="n">namedtuple</span><span class="p">(</span>
+            <span class="s1">&#39;AnnotDefBase&#39;</span><span class="p">,</span>
+            <span class="p">[</span>
+                <span class="s1">&#39;name&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;resource&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;parent&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;aspect&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;scope&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;source&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;args&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;exclude&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;transmitter&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;receiver&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;resource_name&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;limit&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;avoid&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;enabled&#39;</span><span class="p">,</span>
+            <span class="p">]</span>
+        <span class="p">)</span>
+    <span class="p">):</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Annotations are defined by a ``name``, a ``resource`` and an ``args``</span>
+<span class="sd">    parameter. If the former is a string it will be first looked up among the</span>
+<span class="sd">    annotation resources in ``pypath.annot.db``. Otherwise among the keys of</span>
+<span class="sd">    the classes in the ``CustomAnnotation`` object or in the dictionary of</span>
+<span class="sd">    the class_definitions. If ``source`` is a `set`, it will be used as a</span>
+<span class="sd">    category without further processing. If it is callable it will be called</span>
+<span class="sd">    and should return a `set`. If ``bool(args)`` is `False`, in case of</span>
+<span class="sd">    annotations in ``pypath.annot.db`` the ``to_set`` method will be called.</span>
+<span class="sd">    Otherwise ``args`` will be passed to the ``get_subset`` method.</span>
+<span class="sd">    If ``resource`` is callable, ``args`` will be passed if available.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+
+    <span class="k">def</span> <span class="fm">__new__</span><span class="p">(</span>
+            <span class="bp">cls</span><span class="p">,</span>
+            <span class="n">name</span><span class="p">,</span>
+            <span class="n">resource</span><span class="p">,</span>
+            <span class="n">parent</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">aspect</span>  <span class="o">=</span> <span class="s1">&#39;functional&#39;</span><span class="p">,</span>
+            <span class="n">scope</span> <span class="o">=</span> <span class="s1">&#39;specific&#39;</span><span class="p">,</span>
+            <span class="n">source</span> <span class="o">=</span> <span class="s1">&#39;resource_specific&#39;</span><span class="p">,</span>
+            <span class="n">args</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">exclude</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">transmitter</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">receiver</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">resource_name</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">limit</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">avoid</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">enabled</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
+        <span class="p">):</span>
+
+        <span class="n">resource_name</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="n">resource</span>
+                <span class="k">if</span> <span class="bp">cls</span><span class="o">.</span><span class="n">_is_resource_name</span><span class="p">(</span><span class="n">resource</span><span class="p">)</span> <span class="k">else</span>
+            <span class="p">(</span>
+                <span class="n">resource_name</span> <span class="ow">or</span>
+                <span class="n">settings</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">&#39;annot_composite_database_name&#39;</span><span class="p">)</span> <span class="ow">or</span>
+                <span class="s1">&#39;Unknown&#39;</span>
+            <span class="p">)</span>
+        <span class="p">)</span>
+
+        <span class="k">return</span> <span class="nb">super</span><span class="p">()</span><span class="o">.</span><span class="fm">__new__</span><span class="p">(</span>
+            <span class="bp">cls</span><span class="p">,</span>
+            <span class="n">name</span> <span class="o">=</span> <span class="n">name</span><span class="p">,</span>
+            <span class="n">resource</span> <span class="o">=</span> <span class="n">resource</span><span class="p">,</span>
+            <span class="n">parent</span> <span class="o">=</span> <span class="n">parent</span> <span class="ow">or</span> <span class="n">name</span><span class="p">,</span>
+            <span class="n">aspect</span> <span class="o">=</span> <span class="n">aspect</span><span class="p">,</span>
+            <span class="n">scope</span> <span class="o">=</span> <span class="n">scope</span><span class="p">,</span>
+            <span class="n">source</span> <span class="o">=</span> <span class="n">source</span><span class="p">,</span>
+            <span class="n">args</span> <span class="o">=</span> <span class="n">args</span><span class="p">,</span>
+            <span class="n">exclude</span> <span class="o">=</span> <span class="n">exclude</span><span class="p">,</span>
+            <span class="n">transmitter</span> <span class="o">=</span> <span class="n">transmitter</span><span class="p">,</span>
+            <span class="n">receiver</span> <span class="o">=</span> <span class="n">receiver</span><span class="p">,</span>
+            <span class="n">resource_name</span> <span class="o">=</span> <span class="n">resource_name</span><span class="p">,</span>
+            <span class="n">limit</span> <span class="o">=</span> <span class="bp">cls</span><span class="o">.</span><span class="n">_zero_one_or_more</span><span class="p">(</span><span class="n">limit</span><span class="p">),</span>
+            <span class="n">avoid</span> <span class="o">=</span> <span class="bp">cls</span><span class="o">.</span><span class="n">_zero_one_or_more</span><span class="p">(</span><span class="n">avoid</span><span class="p">),</span>
+            <span class="n">enabled</span> <span class="o">=</span> <span class="n">enabled</span><span class="p">,</span>
+        <span class="p">)</span>
+
+
+    <span class="nd">@property</span>
+    <span class="k">def</span> <span class="nf">key</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="n">AnnotDefKey</span><span class="p">(</span>
+            <span class="n">name</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">,</span>
+            <span class="n">parent</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">parent</span><span class="p">,</span>
+            <span class="n">resource</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">resource_name</span><span class="p">,</span>
+        <span class="p">)</span>
+
+
+    <span class="nd">@staticmethod</span>
+    <span class="k">def</span> <span class="nf">_is_resource_name</span><span class="p">(</span><span class="n">name</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="p">(</span>
+            <span class="nb">isinstance</span><span class="p">(</span><span class="n">name</span><span class="p">,</span> <span class="nb">str</span><span class="p">)</span> <span class="ow">and</span>
+            <span class="ow">not</span> <span class="p">(</span>
+                <span class="n">name</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s1">&#39;~&#39;</span><span class="p">)</span> <span class="ow">or</span>
+                <span class="n">name</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s1">&#39;#&#39;</span><span class="p">)</span>
+            <span class="p">)</span>
+        <span class="p">)</span>
+
+
+    <span class="nd">@staticmethod</span>
+    <span class="k">def</span> <span class="nf">_zero_one_or_more</span><span class="p">(</span><span class="n">arg</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="p">(</span>
+            <span class="p">()</span>
+                <span class="k">if</span> <span class="ow">not</span> <span class="n">arg</span> <span class="k">else</span>
+            <span class="p">(</span><span class="n">arg</span><span class="p">,)</span>
+                <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">arg</span><span class="p">,</span> <span class="p">(</span><span class="nb">str</span><span class="p">,</span> <span class="n">_annot_type</span><span class="p">))</span> <span class="k">else</span>
+            <span class="n">arg</span>
+        <span class="p">)</span></div>
+
+
+
+
+<div class="viewcode-block" id="AnnotOp">
+<a class="viewcode-back" href="../../../api/pypath.internals.annot_formats.AnnotOp.html#pypath.internals.annot_formats.AnnotOp">[docs]</a>
+<span class="k">class</span> <span class="nc">AnnotOp</span><span class="p">(</span>
+        <span class="n">collections</span><span class="o">.</span><span class="n">namedtuple</span><span class="p">(</span>
+            <span class="s1">&#39;AnnotOpBase&#39;</span><span class="p">,</span>
+            <span class="p">[</span><span class="s1">&#39;annots&#39;</span><span class="p">,</span> <span class="s1">&#39;op&#39;</span><span class="p">],</span>
+        <span class="p">)</span>
+    <span class="p">):</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Annotation operations consist of list of annotation definitions or names as</span>
+<span class="sd">    they can be looked up in the ``class_definitions`` of the</span>
+<span class="sd">    ``CustomAnnotation`` object and an operator to be called on the sets</span>
+<span class="sd">    (union, intersection or difference).</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="k">def</span> <span class="fm">__new__</span><span class="p">(</span><span class="bp">cls</span><span class="p">,</span> <span class="n">annots</span><span class="p">,</span> <span class="n">op</span> <span class="o">=</span> <span class="nb">set</span><span class="o">.</span><span class="n">union</span><span class="p">):</span>
+
+        <span class="k">if</span> <span class="n">op</span> <span class="ow">in</span> <span class="n">AnnotationGroup</span><span class="o">.</span><span class="n">_set_methods</span><span class="p">:</span>
+
+            <span class="n">op</span> <span class="o">=</span> <span class="nb">getattr</span><span class="p">(</span><span class="n">AnnotationGroup</span><span class="p">,</span> <span class="n">op</span><span class="o">.</span><span class="vm">__name__</span><span class="p">)</span>
+
+        <span class="k">return</span> <span class="nb">super</span><span class="p">()</span><span class="o">.</span><span class="fm">__new__</span><span class="p">(</span><span class="bp">cls</span><span class="p">,</span> <span class="n">annots</span><span class="p">,</span> <span class="n">op</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="AnnotationGroup">
+<a class="viewcode-back" href="../../../api/pypath.internals.annot_formats.AnnotationGroup.html#pypath.internals.annot_formats.AnnotationGroup">[docs]</a>
+<span class="k">class</span> <span class="nc">AnnotationGroup</span><span class="p">(</span><span class="n">collections_abc</span><span class="o">.</span><span class="n">Set</span><span class="p">):</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Represents a set of molecular entities sharing a custom defined</span>
+<span class="sd">    annotation. This class behaves like a ``set`` and set operations on it</span>
+<span class="sd">    result set objects. Normally this class is instantiated by</span>
+<span class="sd">    ``pypath.core.annot.CustomAnnotation`` in the process of populating</span>
+<span class="sd">    categories and the contents of the groups defined in</span>
+<span class="sd">    ``pypath.core.intercell_annot`` in case of annotations of the</span>
+<span class="sd">    intercellular communication roles.</span>
+<span class="sd">    For detailed definitions of the parameter values see the Supplementary</span>
+<span class="sd">    Table S10 in Turei et al. 2020 (in prep).</span>
+
+<span class="sd">    :param list,set,tuple members:</span>
+<span class="sd">        The identifiers of the entities in the category.</span>
+<span class="sd">    :param str name:</span>
+<span class="sd">        The name of the category.</span>
+<span class="sd">    :param str parent:</span>
+<span class="sd">        The name of the parent category; might be the same as ``name`` in</span>
+<span class="sd">        case of high level (generic) categories.</span>
+<span class="sd">    :param str aspect:</span>
+<span class="sd">        Either *functional* or *locational*.</span>
+<span class="sd">    :param str source:</span>
+<span class="sd">        Either *resource_specific* or *composite*.</span>
+<span class="sd">    :param str scope:</span>
+<span class="sd">        Either *specific* or *generic*.</span>
+<span class="sd">    :param str resource:</span>
+<span class="sd">        The resource (database) name; in case of composite categories it</span>
+<span class="sd">        should be the name of the database you are actually building, this</span>
+<span class="sd">        by default is `OmniPath` and you can change by the</span>
+<span class="sd">        ``pypath.share.settings`` module using the</span>
+<span class="sd">        ``annot_composite_database_name`` key.</span>
+<span class="sd">    :param bool transmitter:</span>
+<span class="sd">        Whether the category contains transmitters of signaling information</span>
+<span class="sd">        from the cell expressing the molecular entities in direction of other</span>
+<span class="sd">        cells.</span>
+<span class="sd">    :param bool receiver:</span>
+<span class="sd">        Whether the category contains receivers of signaling information</span>
+<span class="sd">        from other cells in direction of the cells expressing the molecular</span>
+<span class="sd">        entites in the category.</span>
+<span class="sd">    :param str,set limit:</span>
+<span class="sd">        Limit to this or these categories. E.g. if it&#39;s &#39;extracellular&#39;</span>
+<span class="sd">        the result will be the intersection of this category and</span>
+<span class="sd">        &#39;extracellular&#39; i.e. the category will be limited to extracellular</span>
+<span class="sd">        proteins.</span>
+<span class="sd">    :param str,set avoid:</span>
+<span class="sd">        Avoid elements of this or these categories. E.g. if it&#39;s</span>
+<span class="sd">        &#39;cell_surface&#39; then all cell_surface proteins will be removed from</span>
+<span class="sd">        this category.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+
+    <span class="n">_set_methods</span> <span class="o">=</span> <span class="p">{</span>
+        <span class="nb">set</span><span class="o">.</span><span class="n">union</span><span class="p">,</span>
+        <span class="nb">set</span><span class="o">.</span><span class="n">intersection</span><span class="p">,</span>
+        <span class="nb">set</span><span class="o">.</span><span class="n">difference</span><span class="p">,</span>
+        <span class="nb">set</span><span class="o">.</span><span class="n">symmetric_difference</span><span class="p">,</span>
+    <span class="p">}</span>
+
+
+<div class="viewcode-block" id="AnnotationGroup.__init__">
+<a class="viewcode-back" href="../../../api/pypath.internals.annot_formats.AnnotationGroup.html#pypath.internals.annot_formats.AnnotationGroup.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">members</span><span class="p">,</span>
+            <span class="n">name</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">parent</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">aspect</span> <span class="o">=</span> <span class="s1">&#39;functional&#39;</span><span class="p">,</span>
+            <span class="n">source</span> <span class="o">=</span> <span class="s1">&#39;resource_specific&#39;</span><span class="p">,</span>
+            <span class="n">scope</span> <span class="o">=</span> <span class="s1">&#39;specific&#39;</span><span class="p">,</span>
+            <span class="n">resource</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">transmitter</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">receiver</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">limit</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">avoid</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">enabled</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
+        <span class="p">):</span>
+
+        <span class="n">collections_abc</span><span class="o">.</span><span class="n">Set</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">members</span> <span class="o">=</span> <span class="nb">set</span><span class="p">(</span><span class="n">members</span><span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">name</span> <span class="o">=</span> <span class="n">name</span> <span class="ow">or</span> <span class="s1">&#39;unnamed&#39;</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">parent</span> <span class="o">=</span> <span class="n">parent</span> <span class="ow">or</span> <span class="bp">self</span><span class="o">.</span><span class="n">name</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">aspect</span> <span class="o">=</span> <span class="n">aspect</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">source</span> <span class="o">=</span> <span class="n">source</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">scope</span> <span class="o">=</span> <span class="n">scope</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">resource</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="n">resource</span> <span class="ow">or</span>
+            <span class="n">settings</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">&#39;annot_composite_database_name&#39;</span><span class="p">)</span> <span class="ow">or</span>
+            <span class="s1">&#39;Unknown&#39;</span>
+        <span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">transmitter</span> <span class="o">=</span> <span class="n">transmitter</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">receiver</span> <span class="o">=</span> <span class="n">receiver</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">limit</span> <span class="o">=</span> <span class="n">common</span><span class="o">.</span><span class="n">to_set</span><span class="p">(</span><span class="n">limit</span><span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">avoid</span> <span class="o">=</span> <span class="n">common</span><span class="o">.</span><span class="n">to_set</span><span class="p">(</span><span class="n">avoid</span><span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">enabled</span> <span class="o">=</span> <span class="n">enabled</span></div>
+
+
+
+    <span class="k">def</span> <span class="fm">__iter__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">members</span><span class="o">.</span><span class="fm">__iter__</span><span class="p">()</span>
+
+
+    <span class="k">def</span> <span class="fm">__contains__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">other</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="n">other</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">members</span>
+
+
+    <span class="k">def</span> <span class="fm">__len__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">members</span><span class="p">)</span>
+
+
+    <span class="nd">@classmethod</span>
+    <span class="k">def</span> <span class="nf">_from_iterable</span><span class="p">(</span><span class="bp">cls</span><span class="p">,</span> <span class="n">iterable</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="nb">set</span><span class="p">(</span><span class="n">iterable</span><span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="fm">__repr__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="s1">&#39;&lt;AnnotationGroup `</span><span class="si">%s</span><span class="s1">` from </span><span class="si">%s</span><span class="s1">, </span><span class="si">%u</span><span class="s1"> elements&gt;&#39;</span> <span class="o">%</span> <span class="p">(</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">,</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">resource</span><span class="p">,</span>
+            <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="p">),</span>
+        <span class="p">)</span>
+
+
+    <span class="nd">@property</span>
+    <span class="k">def</span> <span class="nf">label</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="s1">&#39;</span><span class="si">%s%s</span><span class="s1">@</span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="p">(</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">parent</span><span class="p">,</span>
+            <span class="s1">&#39;::</span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="bp">self</span><span class="o">.</span><span class="n">name</span> <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">name</span> <span class="o">!=</span> <span class="bp">self</span><span class="o">.</span><span class="n">parent</span> <span class="k">else</span> <span class="s1">&#39;&#39;</span><span class="p">,</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">resource</span>
+        <span class="p">)</span>
+
+
+    <span class="nd">@property</span>
+    <span class="k">def</span> <span class="nf">name_label</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="n">common</span><span class="o">.</span><span class="n">upper0</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">)</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s1">&#39;_&#39;</span><span class="p">,</span> <span class="s1">&#39; &#39;</span><span class="p">)</span>
+
+
+    <span class="nd">@property</span>
+    <span class="k">def</span> <span class="nf">key</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="n">AnnotDefKey</span><span class="p">(</span>
+            <span class="n">name</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">,</span>
+            <span class="n">parent</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">parent</span><span class="p">,</span>
+            <span class="n">resource</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">resource</span><span class="p">,</span>
+        <span class="p">)</span>
+
+
+<div class="viewcode-block" id="AnnotationGroup.filter_entity_type">
+<a class="viewcode-back" href="../../../api/pypath.internals.annot_formats.AnnotationGroup.html#pypath.internals.annot_formats.AnnotationGroup.filter_entity_type">[docs]</a>
+    <span class="k">def</span> <span class="nf">filter_entity_type</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">entity_type</span> <span class="o">=</span> <span class="kc">None</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Returns a copy of the group with only the selected entity types.</span>
+<span class="sd">        If ``entity_type`` is None returns the object itself.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">if</span> <span class="n">entity_type</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
+
+            <span class="k">return</span> <span class="bp">self</span>
+
+        <span class="k">else</span><span class="p">:</span>
+
+            <span class="n">members</span> <span class="o">=</span> <span class="n">entity</span><span class="o">.</span><span class="n">Entity</span><span class="o">.</span><span class="n">filter_entity_type</span><span class="p">(</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">members</span><span class="p">,</span>
+                <span class="n">entity_type</span> <span class="o">=</span> <span class="n">entity_type</span><span class="p">,</span>
+            <span class="p">)</span>
+
+            <span class="k">return</span> <span class="n">AnnotationGroup</span><span class="p">(</span>
+                <span class="n">members</span> <span class="o">=</span> <span class="n">members</span><span class="p">,</span>
+                <span class="n">name</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">,</span>
+                <span class="n">parent</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">parent</span><span class="p">,</span>
+                <span class="n">aspect</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">aspect</span><span class="p">,</span>
+                <span class="n">source</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">source</span><span class="p">,</span>
+                <span class="n">scope</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">scope</span><span class="p">,</span>
+                <span class="n">resource</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">resource</span><span class="p">,</span>
+                <span class="n">transmitter</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">transmitter</span><span class="p">,</span>
+                <span class="n">receiver</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">transmitter</span><span class="p">,</span>
+            <span class="p">)</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">count_entity_type</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">entity_type</span> <span class="o">=</span> <span class="kc">None</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="p">(</span>
+            <span class="n">entity</span><span class="o">.</span><span class="n">Entity</span><span class="o">.</span><span class="n">count_entity_type</span><span class="p">(</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">members</span><span class="p">,</span>
+                <span class="n">entity_type</span> <span class="o">=</span> <span class="n">entity_type</span><span class="p">,</span>
+            <span class="p">)</span>
+        <span class="p">)</span>
+
+
+    <span class="nd">@property</span>
+    <span class="k">def</span> <span class="nf">args</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="nb">dict</span><span class="p">(</span><span class="o">**</span><span class="bp">self</span><span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">keys</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="p">[</span><span class="s1">&#39;name&#39;</span><span class="p">,</span> <span class="s1">&#39;parent&#39;</span><span class="p">,</span> <span class="s1">&#39;source&#39;</span><span class="p">,</span> <span class="s1">&#39;scope&#39;</span><span class="p">,</span> <span class="s1">&#39;aspect&#39;</span><span class="p">]</span>
+
+
+    <span class="k">def</span> <span class="fm">__getitem__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">key</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="nb">getattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">key</span><span class="p">)</span>
+
+
+    <span class="nd">@property</span>
+    <span class="k">def</span> <span class="nf">n_proteins</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">count_entity_type</span><span class="p">(</span><span class="n">entity_type</span> <span class="o">=</span> <span class="s1">&#39;protein&#39;</span><span class="p">)</span>
+
+
+    <span class="nd">@property</span>
+    <span class="k">def</span> <span class="nf">n_mirnas</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">count_entity_type</span><span class="p">(</span><span class="n">entity_type</span> <span class="o">=</span> <span class="s1">&#39;mirna&#39;</span><span class="p">)</span>
+
+
+    <span class="nd">@property</span>
+    <span class="k">def</span> <span class="nf">n_complexes</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">count_entity_type</span><span class="p">(</span><span class="n">entity_type</span> <span class="o">=</span> <span class="s1">&#39;complex&#39;</span><span class="p">)</span>
+
+
+    <span class="nd">@property</span>
+    <span class="k">def</span> <span class="nf">proteins</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">filter_entity_type</span><span class="p">(</span><span class="n">entity_type</span> <span class="o">=</span> <span class="s1">&#39;protein&#39;</span><span class="p">)</span>
+
+
+    <span class="nd">@property</span>
+    <span class="k">def</span> <span class="nf">complexes</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">filter_entity_type</span><span class="p">(</span><span class="n">entity_type</span> <span class="o">=</span> <span class="s1">&#39;complex&#39;</span><span class="p">)</span>
+
+
+    <span class="nd">@property</span>
+    <span class="k">def</span> <span class="nf">mirnas</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">filter_entity_type</span><span class="p">(</span><span class="n">entity_type</span> <span class="o">=</span> <span class="s1">&#39;mirna&#39;</span><span class="p">)</span>
+
+
+    <span class="nd">@staticmethod</span>
+    <span class="k">def</span> <span class="nf">sets</span><span class="p">(</span><span class="o">*</span><span class="n">args</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="p">(</span>
+            <span class="p">(</span>
+                <span class="n">a</span>
+                    <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">a</span><span class="p">,</span> <span class="nb">set</span><span class="p">)</span> <span class="k">else</span>
+                <span class="n">a</span><span class="o">.</span><span class="n">members</span>
+                    <span class="k">if</span> <span class="nb">hasattr</span><span class="p">(</span><span class="n">a</span><span class="p">,</span> <span class="s1">&#39;members&#39;</span><span class="p">)</span> <span class="k">else</span>
+                <span class="n">common</span><span class="o">.</span><span class="n">to_set</span><span class="p">(</span><span class="n">a</span><span class="p">)</span>
+            <span class="p">)</span>
+            <span class="k">for</span> <span class="n">a</span> <span class="ow">in</span> <span class="n">args</span>
+        <span class="p">)</span>
+
+
+    <span class="nd">@classmethod</span>
+    <span class="k">def</span> <span class="nf">union</span><span class="p">(</span><span class="bp">cls</span><span class="p">,</span> <span class="o">*</span><span class="n">args</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="nb">set</span><span class="o">.</span><span class="n">union</span><span class="p">(</span><span class="o">*</span><span class="bp">cls</span><span class="o">.</span><span class="n">sets</span><span class="p">(</span><span class="o">*</span><span class="n">args</span><span class="p">))</span>
+
+
+    <span class="nd">@classmethod</span>
+    <span class="k">def</span> <span class="nf">intersection</span><span class="p">(</span><span class="bp">cls</span><span class="p">,</span> <span class="o">*</span><span class="n">args</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="nb">set</span><span class="o">.</span><span class="n">intersection</span><span class="p">(</span><span class="o">*</span><span class="bp">cls</span><span class="o">.</span><span class="n">sets</span><span class="p">(</span><span class="o">*</span><span class="n">args</span><span class="p">))</span>
+
+
+    <span class="nd">@classmethod</span>
+    <span class="k">def</span> <span class="nf">difference</span><span class="p">(</span><span class="bp">cls</span><span class="p">,</span> <span class="o">*</span><span class="n">args</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="nb">set</span><span class="o">.</span><span class="n">difference</span><span class="p">(</span><span class="o">*</span><span class="bp">cls</span><span class="o">.</span><span class="n">sets</span><span class="p">(</span><span class="o">*</span><span class="n">args</span><span class="p">))</span>
+
+
+    <span class="nd">@classmethod</span>
+    <span class="k">def</span> <span class="nf">symmetric_difference</span><span class="p">(</span><span class="bp">cls</span><span class="p">,</span> <span class="o">*</span><span class="n">args</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="nb">set</span><span class="o">.</span><span class="n">symmetric_difference</span><span class="p">(</span><span class="o">*</span><span class="bp">cls</span><span class="o">.</span><span class="n">sets</span><span class="p">(</span><span class="o">*</span><span class="n">args</span><span class="p">))</span>
+
+
+<div class="viewcode-block" id="AnnotationGroup.isdisjoint">
+<a class="viewcode-back" href="../../../api/pypath.internals.annot_formats.AnnotationGroup.html#pypath.internals.annot_formats.AnnotationGroup.isdisjoint">[docs]</a>
+    <span class="nd">@classmethod</span>
+    <span class="k">def</span> <span class="nf">isdisjoint</span><span class="p">(</span><span class="bp">cls</span><span class="p">,</span> <span class="o">*</span><span class="n">args</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="nb">set</span><span class="o">.</span><span class="n">isdisjoint</span><span class="p">(</span><span class="o">*</span><span class="bp">cls</span><span class="o">.</span><span class="n">sets</span><span class="p">(</span><span class="o">*</span><span class="n">args</span><span class="p">))</span></div>
+</div>
+
+
+
+<span class="n">_set_type</span> <span class="o">=</span> <span class="p">(</span><span class="nb">set</span><span class="p">,</span> <span class="n">AnnotationGroup</span><span class="p">)</span>
+<span class="n">_annot_type</span> <span class="o">=</span> <span class="n">_set_type</span> <span class="o">+</span> <span class="p">(</span><span class="n">AnnotDef</span><span class="p">,</span> <span class="n">AnnotOp</span><span class="p">)</span>
+</pre></div>
+
+                </article>
+              
+              
+              
+              
+              
+                <footer class="prev-next-footer">
+                  
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+  <h1>Source code for pypath.internals.intera</h1><div class="highlight"><pre>
+<span></span><span class="ch">#!/usr/bin/env python</span>
+<span class="c1"># -*- coding: utf-8 -*-</span>
+
+<span class="c1">#</span>
+<span class="c1">#  This file is part of the `pypath` python module</span>
+<span class="c1">#</span>
+<span class="c1">#  Copyright 2014-2023</span>
+<span class="c1">#  EMBL, EMBL-EBI, Uniklinik RWTH Aachen, Heidelberg University</span>
+<span class="c1">#</span>
+<span class="c1">#  Authors: see the file `README.rst`</span>
+<span class="c1">#  Contact: Dénes Türei (turei.denes@gmail.com)</span>
+<span class="c1">#</span>
+<span class="c1">#  Distributed under the GPLv3 License.</span>
+<span class="c1">#  See accompanying file LICENSE.txt or copy at</span>
+<span class="c1">#      https://www.gnu.org/licenses/gpl-3.0.html</span>
+<span class="c1">#</span>
+<span class="c1">#  Website: https://pypath.omnipathdb.org/</span>
+<span class="c1">#</span>
+
+<span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">This module provides classes to represent and handle</span>
+<span class="sd">structural details of protein interactions</span>
+<span class="sd">i.e. residues, post-translational modifications,</span>
+<span class="sd">short motifs, domains, domain-motifs and</span>
+<span class="sd">domain-motif interactions, binding interfaces.</span>
+<span class="sd">&quot;&quot;&quot;</span>
+
+<span class="kn">from</span> <span class="nn">future.utils</span> <span class="kn">import</span> <span class="n">iteritems</span>
+<span class="kn">from</span> <span class="nn">past.builtins</span> <span class="kn">import</span> <span class="n">xrange</span><span class="p">,</span> <span class="nb">range</span><span class="p">,</span> <span class="n">reduce</span>
+
+<span class="kn">import</span> <span class="nn">re</span>
+<span class="kn">import</span> <span class="nn">sys</span>
+<span class="kn">import</span> <span class="nn">importlib</span> <span class="k">as</span> <span class="nn">imp</span>
+<span class="kn">import</span> <span class="nn">collections</span>
+<span class="kn">import</span> <span class="nn">itertools</span>
+
+<span class="c1"># from pypath:</span>
+<span class="kn">import</span> <span class="nn">pypath.share.common</span> <span class="k">as</span> <span class="nn">common</span>
+<span class="kn">import</span> <span class="nn">pypath_common._constants</span> <span class="k">as</span> <span class="nn">_const</span>
+<span class="kn">import</span> <span class="nn">pypath.utils.mapping</span> <span class="k">as</span> <span class="nn">mapping</span>
+<span class="kn">import</span> <span class="nn">pypath.core.evidence</span> <span class="k">as</span> <span class="nn">evidence</span>
+<span class="kn">import</span> <span class="nn">pypath.core.entity</span> <span class="k">as</span> <span class="nn">entity</span>
+<span class="kn">import</span> <span class="nn">pypath.utils.taxonomy</span> <span class="k">as</span> <span class="nn">taxonomy</span>
+
+<span class="n">__all__</span> <span class="o">=</span> <span class="p">[</span>
+    <span class="s1">&#39;Residue&#39;</span><span class="p">,</span>
+    <span class="s1">&#39;Ptm&#39;</span><span class="p">,</span>
+    <span class="s1">&#39;Motif&#39;</span><span class="p">,</span>
+    <span class="s1">&#39;Domain&#39;</span><span class="p">,</span>
+    <span class="s1">&#39;DomainDomain&#39;</span><span class="p">,</span>
+    <span class="s1">&#39;DomainMotif&#39;</span><span class="p">,</span>
+    <span class="s1">&#39;Interface&#39;</span><span class="p">,</span>
+<span class="p">]</span>
+
+<span class="k">if</span> <span class="s1">&#39;unicode&#39;</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">__builtins__</span><span class="p">:</span>
+    <span class="n">unicode</span> <span class="o">=</span> <span class="nb">str</span>
+
+
+<span class="n">COMPLEX_SEP</span> <span class="o">=</span> <span class="s1">&#39;_&#39;</span>
+
+
+<div class="viewcode-block" id="Residue">
+<a class="viewcode-back" href="../../../api/pypath.internals.intera.Residue.html#pypath.internals.intera.Residue">[docs]</a>
+<span class="k">class</span> <span class="nc">Residue</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span>
+
+<div class="viewcode-block" id="Residue.__init__">
+<a class="viewcode-back" href="../../../api/pypath.internals.intera.Residue.html#pypath.internals.intera.Residue.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">number</span><span class="p">,</span>
+            <span class="n">name</span><span class="p">,</span>
+            <span class="n">protein</span><span class="p">,</span>
+            <span class="n">id_type</span> <span class="o">=</span> <span class="s1">&#39;uniprot&#39;</span><span class="p">,</span>
+            <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">,</span>
+            <span class="n">isoform</span> <span class="o">=</span> <span class="mi">1</span><span class="p">,</span>
+            <span class="n">mutated</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+            <span class="n">seq</span> <span class="o">=</span> <span class="kc">None</span>
+        <span class="p">):</span>
+
+        <span class="n">non_digit</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">compile</span><span class="p">(</span><span class="sa">r</span><span class="s1">&#39;[^\d.-]+&#39;</span><span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">name</span> <span class="o">=</span> <span class="n">name</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">number</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="n">number</span>
+                <span class="k">if</span> <span class="ow">not</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">number</span><span class="p">,</span> <span class="nb">str</span><span class="p">)</span> <span class="k">else</span>
+            <span class="nb">int</span><span class="p">(</span><span class="n">non_digit</span><span class="o">.</span><span class="n">sub</span><span class="p">(</span><span class="s1">&#39;&#39;</span><span class="p">,</span> <span class="n">number</span><span class="p">))</span>
+        <span class="p">)</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">protein</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="n">protein</span>
+                <span class="k">if</span> <span class="nb">hasattr</span><span class="p">(</span><span class="n">protein</span><span class="p">,</span> <span class="s1">&#39;identifier&#39;</span><span class="p">)</span> <span class="k">else</span>
+            <span class="n">entity</span><span class="o">.</span><span class="n">Entity</span><span class="p">(</span>
+                <span class="n">identifier</span> <span class="o">=</span> <span class="n">protein</span><span class="p">,</span>
+                <span class="n">id_type</span> <span class="o">=</span> <span class="n">id_type</span><span class="p">,</span>
+                <span class="n">taxon</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">,</span>
+            <span class="p">)</span>
+        <span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">mutated</span> <span class="o">=</span> <span class="n">mutated</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">seq</span> <span class="o">=</span> <span class="n">seq</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">isoform</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="n">isoform</span>
+                <span class="k">if</span> <span class="nb">type</span><span class="p">(</span><span class="n">isoform</span><span class="p">)</span> <span class="ow">is</span> <span class="nb">int</span> <span class="k">else</span>
+            <span class="nb">int</span><span class="p">(</span><span class="n">non_digit</span><span class="o">.</span><span class="n">sub</span><span class="p">(</span><span class="s1">&#39;&#39;</span><span class="p">,</span> <span class="n">isoform</span><span class="p">))</span>
+        <span class="p">)</span></div>
+
+
+
+    <span class="k">def</span> <span class="fm">__hash__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="nb">hash</span><span class="p">((</span><span class="bp">self</span><span class="o">.</span><span class="n">number</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">protein</span><span class="p">))</span>
+
+
+    <span class="k">def</span> <span class="fm">__eq__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">other</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="p">(</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">protein</span> <span class="o">==</span> <span class="n">other</span><span class="o">.</span><span class="n">protein</span> <span class="ow">and</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">number</span> <span class="o">==</span> <span class="n">other</span><span class="o">.</span><span class="n">number</span> <span class="ow">and</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">name</span> <span class="o">==</span> <span class="n">other</span><span class="o">.</span><span class="n">name</span>
+        <span class="p">)</span>
+
+    <span class="k">def</span> <span class="fm">__ne__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">other</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="fm">__eq__</span><span class="p">(</span><span class="n">other</span><span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="fm">__str__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="s1">&#39;Residue </span><span class="si">%s</span><span class="s1">-</span><span class="si">%u</span><span class="s1"> in protein </span><span class="si">%s</span><span class="s1">-</span><span class="si">%u%s</span><span class="se">\n</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="p">(</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">,</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">number</span><span class="p">,</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">protein</span><span class="o">.</span><span class="n">identifier</span><span class="p">,</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">isoform</span><span class="p">,</span>
+            <span class="s1">&#39; (mutated)&#39;</span> <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">mutated</span> <span class="k">else</span> <span class="s1">&#39;&#39;</span>
+        <span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="fm">__repr__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="s1">&#39;&lt;Residue </span><span class="si">%s</span><span class="s1">-</span><span class="si">%u</span><span class="s1">:</span><span class="si">%s%u</span><span class="s1">&gt;&#39;</span> <span class="o">%</span> <span class="p">(</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">protein</span><span class="o">.</span><span class="n">label</span><span class="p">,</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">isoform</span><span class="p">,</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">,</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">number</span><span class="p">,</span>
+        <span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">serialize</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="s1">&#39;</span><span class="si">%s%u</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">number</span><span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">in_isoform</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">isoform</span><span class="p">,</span> <span class="n">seq</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
+
+        <span class="n">seq</span> <span class="o">=</span> <span class="n">seq</span> <span class="ow">or</span> <span class="bp">self</span><span class="o">.</span><span class="n">seq</span>
+
+        <span class="k">if</span> <span class="n">seq</span> <span class="ow">and</span> <span class="n">seq</span><span class="o">.</span><span class="n">has_isoform</span><span class="p">(</span><span class="n">isoform</span><span class="p">):</span>
+
+            <span class="k">if</span> <span class="n">seq</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">number</span><span class="p">,</span> <span class="n">isoform</span><span class="o">=</span><span class="n">isoform</span><span class="p">)</span> <span class="o">==</span> <span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">:</span>
+
+                <span class="n">res</span> <span class="o">=</span> <span class="n">Residue</span><span class="p">(</span>
+                    <span class="n">number</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">number</span><span class="p">,</span>
+                    <span class="n">name</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">,</span>
+                    <span class="n">protein</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">protein</span><span class="p">,</span>
+                    <span class="n">id_type</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">id_type</span><span class="p">,</span>
+                    <span class="n">isoform</span> <span class="o">=</span> <span class="n">isoform</span><span class="p">,</span>
+                    <span class="n">mutated</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">mutated</span><span class="p">,</span>
+                <span class="p">)</span>
+                <span class="k">return</span> <span class="n">res</span>
+
+        <span class="k">return</span> <span class="kc">None</span></div>
+
+
+
+<div class="viewcode-block" id="Ptm">
+<a class="viewcode-back" href="../../../api/pypath.internals.intera.Ptm.html#pypath.internals.intera.Ptm">[docs]</a>
+<span class="k">class</span> <span class="nc">Ptm</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span>
+
+<div class="viewcode-block" id="Ptm.__init__">
+<a class="viewcode-back" href="../../../api/pypath.internals.intera.Ptm.html#pypath.internals.intera.Ptm.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">protein</span><span class="p">,</span>
+            <span class="n">id_type</span> <span class="o">=</span> <span class="s1">&#39;uniprot&#39;</span><span class="p">,</span>
+            <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">,</span>
+            <span class="n">typ</span> <span class="o">=</span> <span class="s1">&#39;unknown&#39;</span><span class="p">,</span>
+            <span class="n">motif</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">residue</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">isoform</span> <span class="o">=</span> <span class="mi">1</span><span class="p">,</span>
+            <span class="n">evidences</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">seq</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+        <span class="p">):</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">non_digit</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">compile</span><span class="p">(</span><span class="sa">r</span><span class="s1">&#39;[^\d.-]+&#39;</span><span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">protein</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="n">protein</span>
+                <span class="k">if</span> <span class="nb">hasattr</span><span class="p">(</span><span class="n">protein</span><span class="p">,</span> <span class="s1">&#39;identifier&#39;</span><span class="p">)</span> <span class="k">else</span>
+            <span class="n">entity</span><span class="o">.</span><span class="n">Entity</span><span class="p">(</span>
+                <span class="n">identifier</span> <span class="o">=</span> <span class="n">protein</span><span class="p">,</span>
+                <span class="n">id_type</span> <span class="o">=</span> <span class="n">id_type</span><span class="p">,</span>
+                <span class="n">taxon</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">,</span>
+            <span class="p">)</span>
+        <span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">id_type</span> <span class="o">=</span> <span class="n">id_type</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">typ</span> <span class="o">=</span> <span class="n">typ</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">seq</span> <span class="o">=</span> <span class="n">seq</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">motif</span> <span class="o">=</span> <span class="n">motif</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">residue</span> <span class="o">=</span> <span class="n">residue</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">isoform</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="n">isoform</span>
+                <span class="k">if</span> <span class="nb">type</span><span class="p">(</span><span class="n">isoform</span><span class="p">)</span> <span class="ow">is</span> <span class="nb">int</span> <span class="k">else</span>
+            <span class="nb">int</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">non_digit</span><span class="o">.</span><span class="n">sub</span><span class="p">(</span><span class="s1">&#39;&#39;</span><span class="p">,</span> <span class="n">isoform</span><span class="p">))</span>
+        <span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">isoforms</span> <span class="o">=</span> <span class="nb">set</span><span class="p">()</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">add_isoform</span><span class="p">(</span><span class="n">isoform</span><span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">evidences</span> <span class="o">=</span> <span class="n">evidence</span><span class="o">.</span><span class="n">Evidences</span><span class="p">()</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">add_evidences</span><span class="p">(</span><span class="n">evidences</span><span class="p">)</span></div>
+
+
+
+    <span class="k">def</span> <span class="fm">__hash__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="nb">hash</span><span class="p">((</span><span class="bp">self</span><span class="o">.</span><span class="n">residue</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">typ</span><span class="p">))</span>
+
+
+    <span class="k">def</span> <span class="fm">__str__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="p">(</span>
+            <span class="s1">&#39;</span><span class="si">%s</span><span class="s1"> in protein </span><span class="si">%s</span><span class="s1">-</span><span class="si">%u</span><span class="se">\n</span><span class="s1">    Motif: </span><span class="si">%s</span><span class="se">\n</span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="p">(</span>
+                <span class="p">(</span>
+                    <span class="s1">&#39;Domain-motif interaction&#39;</span>
+                        <span class="k">if</span> <span class="p">(</span>
+                            <span class="bp">self</span><span class="o">.</span><span class="n">typ</span> <span class="o">==</span> <span class="s1">&#39;unknown&#39;</span> <span class="ow">and</span>
+                            <span class="bp">self</span><span class="o">.</span><span class="n">residue</span> <span class="ow">is</span> <span class="kc">None</span>
+                        <span class="p">)</span> <span class="k">else</span>
+                    <span class="s1">&#39;PTM: </span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="bp">self</span><span class="o">.</span><span class="n">typ</span>
+                <span class="p">),</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">protein</span><span class="o">.</span><span class="n">label</span><span class="p">,</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">isoform</span><span class="p">,</span>
+                <span class="p">(</span>
+                    <span class="s1">&#39;unknown&#39;</span>
+                        <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">motif</span> <span class="ow">is</span> <span class="kc">None</span> <span class="k">else</span>
+                    <span class="bp">self</span><span class="o">.</span><span class="n">motif</span><span class="o">.</span><span class="fm">__str__</span><span class="p">()</span>
+                <span class="p">),</span>
+                <span class="p">(</span>
+                    <span class="s1">&#39;&#39;</span>
+                        <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">residue</span> <span class="ow">is</span> <span class="kc">None</span> <span class="k">else</span>
+                    <span class="s1">&#39;</span><span class="se">\n</span><span class="s1">    Residue: </span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="bp">self</span><span class="o">.</span><span class="n">residue</span><span class="o">.</span><span class="fm">__str__</span><span class="p">()</span>
+                <span class="p">),</span>
+            <span class="p">)</span>
+        <span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="fm">__repr__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="s1">&#39;&lt;PTM </span><span class="si">%s%s</span><span class="s1">&gt;&#39;</span> <span class="o">%</span> <span class="p">(</span>
+            <span class="p">(</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">residue</span><span class="o">.</span><span class="fm">__repr__</span><span class="p">()</span><span class="o">.</span><span class="n">strip</span><span class="p">(</span><span class="s1">&#39;&lt;&gt;&#39;</span><span class="p">)</span>
+                    <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">residue</span> <span class="k">else</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">protein</span><span class="o">.</span><span class="n">label</span>
+            <span class="p">),</span>
+            <span class="s1">&#39;:</span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="bp">self</span><span class="o">.</span><span class="n">typ</span> <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">residue</span> <span class="k">else</span> <span class="s1">&#39;&#39;</span><span class="p">,</span>
+        <span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="fm">__eq__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">other</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="p">(</span>
+            <span class="nb">isinstance</span><span class="p">(</span><span class="n">other</span><span class="p">,</span> <span class="n">Ptm</span><span class="p">)</span> <span class="ow">and</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">protein</span> <span class="o">==</span> <span class="n">other</span><span class="o">.</span><span class="n">protein</span> <span class="ow">and</span>
+            <span class="p">(</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">residue</span> <span class="o">==</span> <span class="n">other</span><span class="o">.</span><span class="n">residue</span> <span class="ow">or</span>
+                <span class="p">(</span>
+                    <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">residue</span> <span class="ow">is</span> <span class="kc">None</span> <span class="ow">or</span> <span class="n">other</span><span class="o">.</span><span class="n">residue</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">)</span> <span class="ow">and</span>
+                    <span class="bp">self</span><span class="o">.</span><span class="n">motif</span> <span class="o">==</span> <span class="n">other</span><span class="o">.</span><span class="n">motif</span>
+                <span class="p">)</span>
+            <span class="p">)</span> <span class="ow">and</span> <span class="p">(</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">typ</span> <span class="o">==</span> <span class="n">other</span><span class="o">.</span><span class="n">typ</span> <span class="ow">or</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">typ</span> <span class="ow">is</span> <span class="kc">None</span> <span class="ow">or</span> <span class="n">other</span><span class="o">.</span><span class="n">typ</span> <span class="ow">is</span> <span class="kc">None</span>
+            <span class="p">)</span>
+        <span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="fm">__ne__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">other</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="fm">__eq__</span><span class="p">(</span><span class="n">other</span><span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="fm">__contains__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">other</span><span class="p">):</span>
+
+        <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">other</span><span class="p">,</span> <span class="n">Residue</span><span class="p">):</span>
+
+            <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">residue</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
+
+                <span class="k">return</span> <span class="n">other</span> <span class="o">==</span> <span class="bp">self</span><span class="o">.</span><span class="n">residue</span>
+
+            <span class="k">elif</span> <span class="bp">self</span><span class="o">.</span><span class="n">motif</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
+
+                <span class="k">return</span> <span class="n">other</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">motif</span>
+
+            <span class="k">else</span><span class="p">:</span>
+
+                <span class="k">return</span> <span class="kc">False</span>
+
+        <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">other</span><span class="p">,</span> <span class="n">Motif</span><span class="p">):</span>
+
+            <span class="k">return</span> <span class="n">other</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">motif</span>
+
+        <span class="k">elif</span> <span class="n">other</span> <span class="o">==</span> <span class="bp">self</span><span class="o">.</span><span class="n">protein</span><span class="p">:</span>
+
+            <span class="k">return</span> <span class="kc">True</span>
+
+        <span class="k">elif</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">other</span><span class="p">,</span> <span class="n">Mutation</span><span class="p">):</span>
+
+            <span class="k">return</span> <span class="p">(</span>
+                <span class="n">other</span><span class="o">.</span><span class="n">original</span> <span class="o">==</span> <span class="bp">self</span><span class="o">.</span><span class="n">residue</span> <span class="ow">or</span>
+                <span class="n">other</span><span class="o">.</span><span class="n">original</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">motif</span>
+            <span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">__deepcopy__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">memo</span><span class="p">):</span>
+
+        <span class="n">new</span> <span class="o">=</span> <span class="nb">type</span><span class="p">(</span><span class="bp">self</span><span class="p">)(</span>
+            <span class="n">protein</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">protein</span><span class="p">,</span>
+            <span class="n">id_type</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">id_type</span><span class="p">,</span>
+            <span class="n">typ</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">typ</span><span class="p">,</span>
+            <span class="n">motif</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">motif</span><span class="p">,</span>
+            <span class="n">residue</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">residue</span><span class="p">,</span>
+            <span class="n">isoform</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">isoform</span><span class="p">,</span>
+        <span class="p">)</span>
+
+        <span class="n">new</span><span class="o">.</span><span class="n">add_isoform</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">isoforms</span><span class="p">)</span>
+
+        <span class="k">return</span> <span class="n">new</span>
+
+
+    <span class="k">def</span> <span class="nf">add_evidences</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">evidences</span><span class="p">):</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">evidences</span> <span class="o">+=</span> <span class="n">evidences</span>
+
+
+    <span class="k">def</span> <span class="nf">serialize</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="s1">&#39;</span><span class="si">%s</span><span class="s1">-</span><span class="si">%u</span><span class="s1">:</span><span class="si">%s</span><span class="s1">:</span><span class="si">%s</span><span class="s1">:</span><span class="si">%s</span><span class="s1">:</span><span class="si">%s</span><span class="s1">:</span><span class="si">%u</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="p">(</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">protein</span><span class="p">,</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">isoform</span><span class="p">,</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">typ</span><span class="p">,</span>
+            <span class="s1">&#39;,&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">sources</span><span class="p">),</span>
+            <span class="s1">&#39;:::0-0&#39;</span> <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">motif</span> <span class="ow">is</span> <span class="kc">None</span> <span class="k">else</span> <span class="bp">self</span><span class="o">.</span><span class="n">motif</span><span class="o">.</span><span class="n">serialize</span><span class="p">(),</span>
+            <span class="s1">&#39;&#39;</span> <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">residue</span> <span class="ow">is</span> <span class="kc">None</span> <span class="k">else</span> <span class="bp">self</span><span class="o">.</span><span class="n">residue</span><span class="o">.</span><span class="n">name</span><span class="p">,</span>
+            <span class="mi">0</span> <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">residue</span> <span class="ow">is</span> <span class="kc">None</span> <span class="k">else</span> <span class="bp">self</span><span class="o">.</span><span class="n">residue</span><span class="o">.</span><span class="n">number</span><span class="p">,</span>
+        <span class="p">)</span>
+
+    <span class="k">def</span> <span class="nf">print_residue</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="s1">&#39;</span><span class="si">%s</span><span class="s1">-</span><span class="si">%u</span><span class="s1">:</span><span class="si">%s</span><span class="s1">:</span><span class="si">%u</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="p">(</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">protein</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">isoform</span><span class="p">,</span>
+            <span class="s1">&#39;&#39;</span> <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">residue</span> <span class="ow">is</span> <span class="kc">None</span> <span class="k">else</span> <span class="bp">self</span><span class="o">.</span><span class="n">residue</span><span class="o">.</span><span class="n">name</span><span class="p">,</span>
+            <span class="mi">0</span> <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">residue</span> <span class="ow">is</span> <span class="kc">None</span> <span class="k">else</span> <span class="bp">self</span><span class="o">.</span><span class="n">residue</span><span class="o">.</span><span class="n">number</span><span class="p">,</span>
+        <span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">merge</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">other</span><span class="p">):</span>
+
+        <span class="k">if</span> <span class="bp">self</span> <span class="o">==</span> <span class="n">other</span><span class="p">:</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">add_evidences</span><span class="p">(</span><span class="n">other</span><span class="o">.</span><span class="n">evidences</span><span class="p">)</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">motif</span> <span class="o">=</span> <span class="p">(</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">motif</span>
+                    <span class="k">if</span> <span class="n">other</span><span class="o">.</span><span class="n">motif</span> <span class="ow">is</span> <span class="kc">None</span> <span class="k">else</span>
+                <span class="n">other</span><span class="o">.</span><span class="n">motif</span>
+                    <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">motif</span> <span class="ow">is</span> <span class="kc">None</span> <span class="k">else</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">motif</span><span class="o">.</span><span class="n">merge</span><span class="p">(</span><span class="n">other</span><span class="o">.</span><span class="n">motif</span><span class="p">)</span>
+            <span class="p">)</span>
+            <span class="k">if</span> <span class="p">(</span>
+                <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">typ</span> <span class="o">==</span> <span class="s1">&#39;unknown&#39;</span> <span class="ow">or</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">typ</span><span class="p">)</span> <span class="o">==</span> <span class="mi">3</span><span class="p">)</span> <span class="ow">and</span>
+                <span class="n">other</span><span class="o">.</span><span class="n">typ</span> <span class="o">!=</span> <span class="s1">&#39;unknown&#39;</span>
+            <span class="p">):</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">typ</span> <span class="o">=</span> <span class="n">other</span><span class="o">.</span><span class="n">typ</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">isoform</span> <span class="o">=</span> <span class="nb">min</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">isoform</span><span class="p">,</span> <span class="n">other</span><span class="o">.</span><span class="n">isoform</span><span class="p">)</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">isoforms</span> <span class="o">=</span> <span class="n">other</span><span class="o">.</span><span class="n">isoforms</span> <span class="o">|</span> <span class="bp">self</span><span class="o">.</span><span class="n">isoforms</span>
+
+
+    <span class="k">def</span> <span class="nf">add_isoform</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">isoform</span><span class="p">):</span>
+
+        <span class="n">isoform</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="nb">set</span><span class="p">([</span><span class="n">isoform</span><span class="p">])</span>
+                <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">isoform</span><span class="p">,</span> <span class="nb">int</span><span class="p">)</span> <span class="k">else</span>
+            <span class="n">isoform</span>
+                <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">isoform</span><span class="p">,</span> <span class="nb">set</span><span class="p">)</span> <span class="k">else</span>
+            <span class="p">{</span><span class="nb">int</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">non_digit</span><span class="o">.</span><span class="n">sub</span><span class="p">(</span><span class="s1">&#39;&#39;</span><span class="p">,</span> <span class="n">isoform</span><span class="p">))}</span>
+        <span class="p">)</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">isoforms</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">isoforms</span> <span class="o">|</span> <span class="n">isoform</span>
+
+
+    <span class="k">def</span> <span class="nf">get_isoforms</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">seq</span> <span class="o">=</span> <span class="kc">None</span><span class="p">):</span>
+
+        <span class="n">result</span> <span class="o">=</span> <span class="p">[]</span>
+        <span class="n">seq</span> <span class="o">=</span> <span class="n">seq</span> <span class="ow">or</span> <span class="bp">self</span><span class="o">.</span><span class="n">seq</span>
+
+        <span class="k">if</span> <span class="n">seq</span><span class="p">:</span>
+
+            <span class="k">for</span> <span class="n">isoform</span> <span class="ow">in</span> <span class="n">seq</span><span class="o">.</span><span class="n">get_isoforms</span><span class="p">():</span>
+
+                <span class="n">ptm</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">in_isoform</span><span class="p">(</span><span class="n">isoform</span><span class="p">,</span> <span class="n">seq</span><span class="p">)</span>
+
+                <span class="k">if</span> <span class="n">ptm</span><span class="p">:</span>
+
+                    <span class="n">result</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">ptm</span><span class="p">)</span>
+
+        <span class="k">return</span> <span class="n">result</span>
+
+
+    <span class="k">def</span> <span class="nf">in_isoform</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">isoform</span><span class="p">,</span> <span class="n">seq</span> <span class="o">=</span> <span class="kc">None</span><span class="p">):</span>
+
+        <span class="n">seq</span> <span class="o">=</span> <span class="n">seq</span> <span class="ow">or</span> <span class="bp">self</span><span class="o">.</span><span class="n">seq</span>
+
+        <span class="k">if</span> <span class="n">seq</span> <span class="ow">and</span> <span class="n">seq</span><span class="o">.</span><span class="n">has_isoform</span><span class="p">(</span><span class="n">isoform</span><span class="p">):</span>
+
+            <span class="k">if</span> <span class="p">(</span>
+                <span class="n">seq</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">residue</span><span class="o">.</span><span class="n">number</span><span class="p">,</span> <span class="n">isoform</span> <span class="o">=</span> <span class="n">isoform</span><span class="p">)</span> <span class="o">==</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">residue</span><span class="o">.</span><span class="n">name</span>
+            <span class="p">):</span>
+
+                <span class="n">res</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">residue</span><span class="o">.</span><span class="n">in_isoform</span><span class="p">(</span><span class="n">isoform</span><span class="p">,</span> <span class="n">seq</span> <span class="o">=</span> <span class="n">seq</span><span class="p">)</span>
+                <span class="n">mot</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">motif</span><span class="o">.</span><span class="n">in_isoform</span><span class="p">(</span><span class="n">isoform</span><span class="p">,</span> <span class="n">seq</span> <span class="o">=</span> <span class="n">seq</span><span class="p">)</span>
+
+                <span class="n">ptm</span> <span class="o">=</span> <span class="n">Ptm</span><span class="p">(</span>
+                    <span class="n">protein</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">protein</span><span class="p">,</span>
+                    <span class="n">id_type</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">id_type</span><span class="p">,</span>
+                    <span class="n">typ</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">typ</span><span class="p">,</span>
+                    <span class="n">motif</span> <span class="o">=</span> <span class="n">mot</span><span class="p">,</span>
+                    <span class="n">residue</span> <span class="o">=</span> <span class="n">res</span><span class="p">,</span>
+                    <span class="n">evidences</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">sources</span><span class="p">,</span>
+                    <span class="n">isoform</span> <span class="o">=</span> <span class="n">isoform</span><span class="p">,</span>
+                    <span class="n">seq</span> <span class="o">=</span> <span class="n">seq</span><span class="p">,</span>
+                <span class="p">)</span>
+
+                <span class="k">return</span> <span class="n">ptm</span></div>
+
+
+
+<div class="viewcode-block" id="Motif">
+<a class="viewcode-back" href="../../../api/pypath.internals.intera.Motif.html#pypath.internals.intera.Motif">[docs]</a>
+<span class="k">class</span> <span class="nc">Motif</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span>
+
+<div class="viewcode-block" id="Motif.__init__">
+<a class="viewcode-back" href="../../../api/pypath.internals.intera.Motif.html#pypath.internals.intera.Motif.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">protein</span><span class="p">,</span>
+            <span class="n">start</span><span class="p">,</span>
+            <span class="n">end</span><span class="p">,</span>
+            <span class="n">id_type</span> <span class="o">=</span> <span class="s1">&#39;uniprot&#39;</span><span class="p">,</span>
+            <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">,</span>
+            <span class="n">regex</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">instance</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">isoform</span> <span class="o">=</span> <span class="mi">1</span><span class="p">,</span>
+            <span class="n">motif_name</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">prob</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">elm</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">description</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">seq</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">evidences</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+        <span class="p">):</span>
+
+        <span class="n">non_digit</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">compile</span><span class="p">(</span><span class="sa">r</span><span class="s1">&#39;[^\d.-]+&#39;</span><span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">protein</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="n">protein</span>
+                <span class="k">if</span> <span class="nb">hasattr</span><span class="p">(</span><span class="n">protein</span><span class="p">,</span> <span class="s1">&#39;identifier&#39;</span><span class="p">)</span> <span class="k">else</span>
+            <span class="n">entity</span><span class="o">.</span><span class="n">Entity</span><span class="p">(</span>
+                <span class="n">protein</span><span class="p">,</span>
+                <span class="n">id_type</span> <span class="o">=</span> <span class="n">id_type</span><span class="p">,</span>
+                <span class="n">taxon</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">,</span>
+            <span class="p">)</span>
+        <span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">id_type</span> <span class="o">=</span> <span class="n">id_type</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">seq</span> <span class="o">=</span> <span class="n">seq</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">isoform</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="n">isoform</span>
+                <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">isoform</span><span class="p">,</span> <span class="nb">int</span><span class="p">)</span> <span class="k">else</span>
+            <span class="nb">int</span><span class="p">(</span><span class="n">non_digit</span><span class="o">.</span><span class="n">sub</span><span class="p">(</span><span class="s1">&#39;&#39;</span><span class="p">,</span> <span class="n">isoform</span><span class="p">))</span>
+        <span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">start</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="n">start</span>
+                <span class="k">if</span> <span class="ow">not</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">start</span><span class="p">,</span> <span class="nb">str</span><span class="p">)</span> <span class="k">else</span>
+            <span class="nb">int</span><span class="p">(</span><span class="n">non_digit</span><span class="o">.</span><span class="n">sub</span><span class="p">(</span><span class="s1">&#39;&#39;</span><span class="p">,</span> <span class="n">start</span><span class="p">))</span>
+        <span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">end</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="n">end</span>
+                <span class="k">if</span> <span class="ow">not</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">end</span><span class="p">,</span> <span class="nb">str</span><span class="p">)</span> <span class="k">else</span>
+            <span class="nb">int</span><span class="p">(</span><span class="n">non_digit</span><span class="o">.</span><span class="n">sub</span><span class="p">(</span><span class="s1">&#39;&#39;</span><span class="p">,</span> <span class="n">end</span><span class="p">))</span>
+        <span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">regex</span> <span class="o">=</span> <span class="kc">None</span> <span class="k">if</span> <span class="n">regex</span> <span class="ow">is</span> <span class="kc">None</span> <span class="k">else</span> <span class="n">re</span><span class="o">.</span><span class="n">compile</span><span class="p">(</span><span class="n">regex</span><span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">instance</span> <span class="o">=</span> <span class="n">instance</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">motif_name</span> <span class="o">=</span> <span class="n">motif_name</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">prob</span> <span class="o">=</span> <span class="n">prob</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">elm</span> <span class="o">=</span> <span class="n">elm</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">description</span> <span class="o">=</span> <span class="n">description</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">evidences</span> <span class="o">=</span> <span class="n">evidence</span><span class="o">.</span><span class="n">Evidences</span><span class="p">()</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">add_evidences</span><span class="p">(</span><span class="n">evidences</span><span class="p">)</span></div>
+
+
+
+    <span class="k">def</span> <span class="fm">__hash__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="nb">hash</span><span class="p">((</span><span class="bp">self</span><span class="o">.</span><span class="n">protein</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">start</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">end</span><span class="p">))</span>
+
+
+    <span class="k">def</span> <span class="fm">__eq__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">other</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="p">(</span>
+            <span class="n">other</span><span class="o">.</span><span class="n">protein</span> <span class="o">==</span> <span class="bp">self</span><span class="o">.</span><span class="n">protein</span> <span class="ow">and</span>
+            <span class="n">other</span><span class="o">.</span><span class="n">start</span> <span class="o">==</span> <span class="bp">self</span><span class="o">.</span><span class="n">start</span> <span class="ow">and</span>
+            <span class="n">other</span><span class="o">.</span><span class="n">end</span> <span class="o">==</span> <span class="bp">self</span><span class="o">.</span><span class="n">end</span>
+        <span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="fm">__contains__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">other</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="p">(</span>
+            <span class="p">(</span>
+                <span class="nb">isinstance</span><span class="p">(</span><span class="n">other</span><span class="p">,</span> <span class="n">Residue</span><span class="p">)</span> <span class="ow">and</span>
+                <span class="n">other</span><span class="o">.</span><span class="n">protein</span> <span class="o">==</span> <span class="bp">self</span><span class="o">.</span><span class="n">protein</span> <span class="ow">and</span>
+                <span class="n">other</span><span class="o">.</span><span class="n">number</span> <span class="o">&gt;=</span> <span class="bp">self</span><span class="o">.</span><span class="n">start</span> <span class="ow">and</span>
+                <span class="n">other</span><span class="o">.</span><span class="n">number</span> <span class="o">&lt;=</span> <span class="bp">self</span><span class="o">.</span><span class="n">end</span>
+            <span class="p">)</span> <span class="ow">or</span> <span class="p">(</span>
+                <span class="n">other</span> <span class="o">==</span> <span class="bp">self</span><span class="o">.</span><span class="n">protein</span> <span class="ow">or</span>
+                <span class="n">other</span> <span class="o">==</span> <span class="bp">self</span><span class="o">.</span><span class="n">instance</span> <span class="ow">or</span>
+                <span class="n">other</span> <span class="o">==</span> <span class="bp">self</span><span class="o">.</span><span class="n">motif_name</span>
+            <span class="p">)</span>
+        <span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">add_evidences</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">evidences</span><span class="p">):</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">evidences</span> <span class="o">+=</span> <span class="n">evidences</span>
+
+
+    <span class="k">def</span> <span class="nf">serialize</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="s1">&#39;</span><span class="si">%s</span><span class="s1">:</span><span class="si">%s</span><span class="s1">:</span><span class="si">%u</span><span class="s1">-</span><span class="si">%u</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="p">(</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">motif_name</span> <span class="ow">or</span> <span class="s1">&#39;unknown&#39;</span><span class="p">,</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">instance</span><span class="p">,</span>
+            <span class="mi">0</span> <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">start</span> <span class="ow">is</span> <span class="kc">None</span> <span class="k">else</span> <span class="bp">self</span><span class="o">.</span><span class="n">start</span><span class="p">,</span>
+            <span class="mi">0</span> <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">end</span> <span class="ow">is</span> <span class="kc">None</span> <span class="k">else</span> <span class="bp">self</span><span class="o">.</span><span class="n">end</span><span class="p">,</span>
+        <span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">print_residues</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="s1">&#39;</span><span class="si">%s</span><span class="s1">-</span><span class="si">%u</span><span class="s1">:</span><span class="si">%u</span><span class="s1">-</span><span class="si">%u</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="p">(</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">protein</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">isoform</span><span class="p">,</span>
+            <span class="mi">0</span> <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">start</span> <span class="ow">is</span> <span class="kc">None</span> <span class="k">else</span> <span class="bp">self</span><span class="o">.</span><span class="n">start</span><span class="p">,</span>
+            <span class="mi">0</span> <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">end</span> <span class="ow">is</span> <span class="kc">None</span> <span class="k">else</span> <span class="bp">self</span><span class="o">.</span><span class="n">end</span><span class="p">,</span>
+        <span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">merge</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">other</span><span class="p">):</span>
+
+        <span class="k">if</span> <span class="bp">self</span> <span class="o">==</span> <span class="n">other</span><span class="p">:</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">instance</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">instance</span> <span class="ow">or</span> <span class="n">other</span><span class="o">.</span><span class="n">instance</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">regex</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">regex</span> <span class="ow">or</span> <span class="n">other</span><span class="o">.</span><span class="n">regex</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">elm</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">elm</span> <span class="ow">or</span> <span class="n">other</span><span class="o">.</span><span class="n">elm</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">prob</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">prob</span> <span class="ow">or</span> <span class="n">other</span><span class="o">.</span><span class="n">prob</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">motif_name</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">motif_name</span> <span class="ow">or</span> <span class="n">other</span><span class="o">.</span><span class="n">motif_name</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">description</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">description</span> <span class="ow">or</span> <span class="n">other</span><span class="o">.</span><span class="n">description</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">evidences</span> <span class="o">+=</span> <span class="n">other</span><span class="o">.</span><span class="n">evidences</span>
+
+
+    <span class="k">def</span> <span class="fm">__str__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="p">(</span>
+            <span class="s1">&#39;Motif in protein </span><span class="si">%s</span><span class="s1">-</span><span class="si">%u</span><span class="s1">:</span><span class="se">\n</span><span class="s1">&#39;</span>
+            <span class="s1">&#39;</span><span class="se">\t</span><span class="s1">Name: </span><span class="si">%s</span><span class="se">\n</span><span class="s1">&#39;</span>
+            <span class="s1">&#39;</span><span class="se">\t</span><span class="s1">ELM: </span><span class="si">%s</span><span class="se">\n</span><span class="s1">&#39;</span>
+            <span class="s1">&#39;</span><span class="se">\t</span><span class="s1">Range: </span><span class="si">%u</span><span class="s1">-</span><span class="si">%u</span><span class="se">\n</span><span class="s1">&#39;</span>
+            <span class="s1">&#39;</span><span class="se">\t</span><span class="s1">Regex: </span><span class="si">%s</span><span class="se">\n</span><span class="s1">&#39;</span>
+            <span class="s1">&#39;</span><span class="se">\t</span><span class="s1">Instance: </span><span class="si">%s</span><span class="se">\n</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="p">(</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">protein</span><span class="o">.</span><span class="n">label</span><span class="p">,</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">isoform</span><span class="p">,</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">motif_name</span> <span class="ow">or</span> <span class="s1">&#39;unknown&#39;</span><span class="p">,</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">elm</span> <span class="ow">or</span> <span class="s1">&#39;unknown&#39;</span><span class="p">,</span>
+                <span class="mi">0</span> <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">start</span> <span class="ow">is</span> <span class="kc">None</span> <span class="k">else</span> <span class="bp">self</span><span class="o">.</span><span class="n">start</span><span class="p">,</span>
+                <span class="mi">0</span> <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">end</span> <span class="ow">is</span> <span class="kc">None</span> <span class="k">else</span> <span class="bp">self</span><span class="o">.</span><span class="n">end</span><span class="p">,</span>
+                <span class="s1">&#39;unknown&#39;</span> <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">regex</span> <span class="ow">is</span> <span class="kc">None</span> <span class="k">else</span> <span class="bp">self</span><span class="o">.</span><span class="n">regex</span><span class="o">.</span><span class="n">pattern</span><span class="p">,</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">instance</span> <span class="ow">or</span> <span class="s1">&#39;unknown&#39;</span><span class="p">,</span>
+            <span class="p">)</span>
+        <span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="fm">__repr__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="n">rng</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">range_str</span><span class="p">()</span>
+
+        <span class="k">return</span> <span class="s1">&#39;&lt;Motif </span><span class="si">%s</span><span class="s1">in </span><span class="si">%s</span><span class="s1">-</span><span class="si">%u%s</span><span class="s1">&gt;&#39;</span> <span class="o">%</span> <span class="p">(</span>
+            <span class="s1">&#39;</span><span class="si">%s</span><span class="s1"> &#39;</span> <span class="o">%</span> <span class="bp">self</span><span class="o">.</span><span class="n">motif_name</span> <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">motif_name</span> <span class="k">else</span> <span class="s1">&#39;&#39;</span><span class="p">,</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">protein</span><span class="o">.</span><span class="n">label</span><span class="p">,</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">isoform</span><span class="p">,</span>
+            <span class="s1">&#39; [</span><span class="si">%s</span><span class="s1">]&#39;</span> <span class="o">%</span> <span class="n">rng</span> <span class="k">if</span> <span class="n">rng</span> <span class="k">else</span> <span class="s1">&#39;&#39;</span><span class="p">,</span>
+        <span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">range</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="p">(</span>
+            <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">start</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">end</span><span class="p">)</span>
+                <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">start</span> <span class="ow">and</span> <span class="bp">self</span><span class="o">.</span><span class="n">end</span> <span class="k">else</span>
+            <span class="kc">None</span>
+        <span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">range_str</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="n">start_end</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">range</span><span class="p">()</span>
+
+        <span class="k">return</span> <span class="s1">&#39;</span><span class="si">%s</span><span class="s1">-</span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="n">start_end</span> <span class="k">if</span> <span class="n">start_end</span> <span class="k">else</span> <span class="s1">&#39;&#39;</span>
+
+
+    <span class="k">def</span> <span class="nf">in_isoform</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">isoform</span><span class="p">,</span> <span class="n">seq</span> <span class="o">=</span> <span class="kc">None</span><span class="p">):</span>
+
+        <span class="n">seq</span> <span class="o">=</span> <span class="n">seq</span> <span class="ow">or</span> <span class="bp">self</span><span class="o">.</span><span class="n">seq</span>
+
+        <span class="k">if</span> <span class="n">seq</span> <span class="ow">and</span> <span class="n">seq</span><span class="o">.</span><span class="n">has_isoform</span><span class="p">(</span><span class="n">isoform</span><span class="p">):</span>
+
+            <span class="n">start</span><span class="p">,</span> <span class="n">end</span><span class="p">,</span> <span class="n">reg</span> <span class="o">=</span> <span class="n">seq</span><span class="o">.</span><span class="n">get_region</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">start</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">start</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">end</span><span class="p">)</span>
+
+            <span class="n">mot</span> <span class="o">=</span> <span class="n">Motif</span><span class="p">(</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">protein</span><span class="p">,</span>
+                <span class="n">start</span><span class="p">,</span>
+                <span class="n">end</span><span class="p">,</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">id_type</span><span class="p">,</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">regex</span><span class="p">,</span>
+                <span class="n">reg</span><span class="p">,</span>
+                <span class="n">isoform</span><span class="p">,</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">motif_name</span><span class="p">,</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">prob</span><span class="p">,</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">elm</span><span class="p">,</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">description</span><span class="p">,</span>
+                <span class="n">seq</span><span class="p">,</span>
+            <span class="p">)</span>
+
+            <span class="k">return</span> <span class="n">mot</span>
+
+        <span class="k">return</span> <span class="kc">None</span></div>
+
+
+
+<div class="viewcode-block" id="Domain">
+<a class="viewcode-back" href="../../../api/pypath.internals.intera.Domain.html#pypath.internals.intera.Domain">[docs]</a>
+<span class="k">class</span> <span class="nc">Domain</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span>
+
+<div class="viewcode-block" id="Domain.__init__">
+<a class="viewcode-back" href="../../../api/pypath.internals.intera.Domain.html#pypath.internals.intera.Domain.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span>
+        <span class="bp">self</span><span class="p">,</span>
+        <span class="n">protein</span><span class="p">,</span>
+        <span class="n">id_type</span> <span class="o">=</span> <span class="s1">&#39;uniprot&#39;</span><span class="p">,</span>
+        <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">,</span>
+        <span class="n">domain</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+        <span class="n">domain_id_type</span> <span class="o">=</span> <span class="s1">&#39;pfam&#39;</span><span class="p">,</span>
+        <span class="n">start</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+        <span class="n">end</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+        <span class="n">isoform</span> <span class="o">=</span> <span class="mi">1</span><span class="p">,</span>
+        <span class="n">chains</span> <span class="o">=</span> <span class="p">{},</span>
+    <span class="p">):</span>
+
+        <span class="n">non_digit</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">compile</span><span class="p">(</span><span class="sa">r</span><span class="s1">&#39;[^\d.-]+&#39;</span><span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">protein</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="n">protein</span>
+                <span class="k">if</span> <span class="nb">hasattr</span><span class="p">(</span><span class="n">protein</span><span class="p">,</span> <span class="s1">&#39;identifier&#39;</span><span class="p">)</span> <span class="k">else</span>
+            <span class="n">entity</span><span class="o">.</span><span class="n">Entity</span><span class="p">(</span>
+                <span class="n">identifier</span> <span class="o">=</span> <span class="n">protein</span><span class="p">,</span>
+                <span class="n">id_type</span> <span class="o">=</span> <span class="n">id_type</span><span class="p">,</span>
+                <span class="n">taxon</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">,</span>
+            <span class="p">)</span>
+        <span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">id_type</span> <span class="o">=</span> <span class="n">id_type</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">domain</span> <span class="o">=</span> <span class="n">domain</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">domain_id_type</span> <span class="o">=</span> <span class="n">domain_id_type</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">start</span> <span class="o">=</span> <span class="n">start</span> <span class="k">if</span> <span class="nb">type</span><span class="p">(</span><span class="n">start</span><span class="p">)</span> <span class="ow">not</span> <span class="ow">in</span> <span class="p">[</span><span class="nb">str</span><span class="p">,</span> <span class="n">unicode</span><span class="p">]</span> \
+            <span class="k">else</span> <span class="nb">int</span><span class="p">(</span><span class="n">non_digit</span><span class="o">.</span><span class="n">sub</span><span class="p">(</span><span class="s1">&#39;&#39;</span><span class="p">,</span> <span class="n">start</span><span class="p">))</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">end</span> <span class="o">=</span> <span class="n">end</span> <span class="k">if</span> <span class="nb">type</span><span class="p">(</span><span class="n">end</span><span class="p">)</span> <span class="ow">not</span> <span class="ow">in</span> <span class="p">[</span><span class="nb">str</span><span class="p">,</span> <span class="n">unicode</span><span class="p">]</span> \
+            <span class="k">else</span> <span class="nb">int</span><span class="p">(</span><span class="n">non_digit</span><span class="o">.</span><span class="n">sub</span><span class="p">(</span><span class="s1">&#39;&#39;</span><span class="p">,</span> <span class="n">end</span><span class="p">))</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">isoform</span> <span class="o">=</span> <span class="n">isoform</span> <span class="k">if</span> <span class="nb">type</span><span class="p">(</span><span class="n">isoform</span><span class="p">)</span> <span class="ow">is</span> <span class="nb">int</span> \
+            <span class="k">else</span> <span class="nb">int</span><span class="p">(</span><span class="n">non_digit</span><span class="o">.</span><span class="n">sub</span><span class="p">(</span><span class="s1">&#39;&#39;</span><span class="p">,</span> <span class="n">isoform</span><span class="p">))</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">pdbs</span> <span class="o">=</span> <span class="p">{}</span>
+        <span class="k">for</span> <span class="n">pdb</span><span class="p">,</span> <span class="n">chain</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="n">chains</span><span class="p">):</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">add_chains</span><span class="p">(</span><span class="n">pdb</span><span class="p">,</span> <span class="n">chain</span><span class="p">)</span></div>
+
+
+
+    <span class="k">def</span> <span class="fm">__hash__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="nb">hash</span><span class="p">((</span><span class="bp">self</span><span class="o">.</span><span class="n">protein</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">domain</span><span class="p">))</span>
+
+
+    <span class="k">def</span> <span class="fm">__eq__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">other</span><span class="p">):</span>
+
+        <span class="k">if</span> <span class="nb">any</span><span class="p">(</span>
+            <span class="n">num</span> <span class="ow">is</span> <span class="kc">None</span>
+            <span class="k">for</span> <span class="n">num</span> <span class="ow">in</span> <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">start</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">end</span><span class="p">,</span> <span class="n">other</span><span class="o">.</span><span class="n">start</span><span class="p">,</span> <span class="n">other</span><span class="o">.</span><span class="n">end</span><span class="p">)</span>
+        <span class="p">):</span>
+
+            <span class="k">return</span> <span class="kc">False</span>
+
+        <span class="n">flk</span> <span class="o">=</span> <span class="nb">min</span><span class="p">(</span>
+            <span class="nb">max</span><span class="p">(</span>
+                <span class="nb">int</span><span class="p">(</span>
+                    <span class="nb">min</span><span class="p">(</span>
+                        <span class="bp">self</span><span class="o">.</span><span class="n">end</span> <span class="o">-</span> <span class="bp">self</span><span class="o">.</span><span class="n">start</span><span class="p">,</span>
+                        <span class="n">other</span><span class="o">.</span><span class="n">end</span> <span class="o">-</span> <span class="n">other</span><span class="o">.</span><span class="n">start</span>
+                    <span class="p">)</span> <span class="o">*</span> <span class="mf">0.1</span>
+                <span class="p">),</span>
+                <span class="mi">10</span>
+            <span class="p">),</span>
+            <span class="mi">30</span>
+        <span class="p">)</span>
+
+        <span class="k">return</span> <span class="p">(</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">protein</span> <span class="o">==</span> <span class="n">other</span><span class="o">.</span><span class="n">protein</span> <span class="ow">and</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">id_type</span> <span class="o">==</span> <span class="n">other</span><span class="o">.</span><span class="n">id_type</span> <span class="ow">and</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">start</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span> <span class="ow">and</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">end</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span> <span class="ow">and</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">start</span> <span class="o">&lt;</span> <span class="n">other</span><span class="o">.</span><span class="n">start</span> <span class="o">+</span> <span class="n">flk</span> <span class="ow">and</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">start</span> <span class="o">&gt;</span> <span class="n">other</span><span class="o">.</span><span class="n">start</span> <span class="o">-</span> <span class="n">flk</span> <span class="ow">and</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">end</span> <span class="o">&lt;</span> <span class="n">other</span><span class="o">.</span><span class="n">end</span> <span class="o">+</span> <span class="n">flk</span> <span class="ow">and</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">end</span> <span class="o">&gt;</span> <span class="n">other</span><span class="o">.</span><span class="n">end</span> <span class="o">-</span> <span class="n">flk</span>
+        <span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="fm">__ne__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">other</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="fm">__eq__</span><span class="p">(</span><span class="n">other</span><span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="fm">__contains__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">other</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="p">(</span>
+            <span class="p">(</span>
+                <span class="nb">isinstance</span><span class="p">(</span><span class="n">other</span><span class="p">,</span> <span class="n">Residue</span><span class="p">)</span> <span class="ow">and</span>
+                <span class="n">other</span><span class="o">.</span><span class="n">protein</span> <span class="o">==</span> <span class="bp">self</span><span class="o">.</span><span class="n">protein</span> <span class="ow">and</span>
+                <span class="n">other</span><span class="o">.</span><span class="n">number</span> <span class="o">&gt;=</span> <span class="bp">self</span><span class="o">.</span><span class="n">start</span> <span class="ow">and</span>
+                <span class="n">other</span><span class="o">.</span><span class="n">number</span> <span class="o">&lt;=</span> <span class="bp">self</span><span class="o">.</span><span class="n">end</span>
+            <span class="p">)</span> <span class="ow">or</span>
+            <span class="p">(</span>
+                <span class="nb">isinstance</span><span class="p">(</span><span class="n">other</span><span class="p">,</span> <span class="n">Motif</span><span class="p">)</span> <span class="ow">and</span>
+                <span class="n">other</span><span class="o">.</span><span class="n">protein</span> <span class="o">==</span> <span class="bp">self</span><span class="o">.</span><span class="n">protein</span> <span class="ow">and</span>
+                <span class="n">other</span><span class="o">.</span><span class="n">start</span> <span class="o">&lt;</span> <span class="bp">self</span><span class="o">.</span><span class="n">end</span> <span class="ow">and</span>
+                <span class="n">other</span><span class="o">.</span><span class="n">end</span> <span class="o">&lt;=</span> <span class="bp">self</span><span class="o">.</span><span class="n">start</span>
+            <span class="p">)</span> <span class="ow">or</span>
+            <span class="p">(</span>
+                <span class="nb">isinstance</span><span class="p">(</span><span class="n">other</span><span class="p">,</span> <span class="n">Ptm</span><span class="p">)</span> <span class="ow">and</span>
+                <span class="p">(</span>
+                    <span class="n">other</span><span class="o">.</span><span class="n">residue</span> <span class="ow">in</span> <span class="bp">self</span> <span class="ow">or</span>
+                    <span class="n">other</span><span class="o">.</span><span class="n">motif</span> <span class="ow">in</span> <span class="bp">self</span>
+                <span class="p">)</span>
+            <span class="p">)</span> <span class="ow">or</span>
+            <span class="p">(</span>
+                <span class="n">other</span> <span class="o">==</span> <span class="bp">self</span><span class="o">.</span><span class="n">protein</span> <span class="ow">or</span>
+                <span class="n">other</span> <span class="o">==</span> <span class="bp">self</span><span class="o">.</span><span class="n">instance</span> <span class="ow">or</span>
+                <span class="n">other</span> <span class="o">==</span> <span class="bp">self</span><span class="o">.</span><span class="n">motif_name</span>
+            <span class="p">)</span>
+        <span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">has_position</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="nb">bool</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">start</span> <span class="ow">and</span> <span class="bp">self</span><span class="o">.</span><span class="n">end</span><span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">get_position</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">start</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">end</span><span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">add_chains</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">pdb</span><span class="p">,</span> <span class="n">chain</span><span class="p">):</span>
+
+        <span class="k">if</span> <span class="n">pdb</span> <span class="ow">not</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">pdbs</span><span class="p">:</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">pdbs</span><span class="p">[</span><span class="n">pdb</span><span class="p">]</span> <span class="o">=</span> <span class="p">[]</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">pdbs</span><span class="p">[</span><span class="n">pdb</span><span class="p">]</span> <span class="o">=</span> <span class="n">common</span><span class="o">.</span><span class="n">add_to_list</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">pdbs</span><span class="p">[</span><span class="n">pdb</span><span class="p">],</span> <span class="n">chain</span><span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">serialize</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="s1">&#39;</span><span class="si">%s</span><span class="s1">-</span><span class="si">%u</span><span class="s1">:</span><span class="si">%s</span><span class="s1">:</span><span class="si">%u</span><span class="s1">-</span><span class="si">%u</span><span class="s1">:</span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="p">(</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">protein</span><span class="p">,</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">isoform</span><span class="p">,</span>
+            <span class="s1">&#39;unknown&#39;</span> <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">domain</span> <span class="ow">is</span> <span class="kc">None</span> <span class="k">else</span> <span class="bp">self</span><span class="o">.</span><span class="n">domain</span><span class="p">,</span>
+            <span class="mi">0</span> <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">start</span> <span class="ow">is</span> <span class="kc">None</span> <span class="k">else</span> <span class="bp">self</span><span class="o">.</span><span class="n">start</span><span class="p">,</span>
+            <span class="mi">0</span> <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">end</span> <span class="ow">is</span> <span class="kc">None</span> <span class="k">else</span> <span class="bp">self</span><span class="o">.</span><span class="n">end</span><span class="p">,</span>
+            <span class="s1">&#39;,&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span>
+                <span class="s1">&#39;</span><span class="si">%s</span><span class="s1">.</span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="p">(</span><span class="n">pdb</span><span class="p">,</span> <span class="s1">&#39;.&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">chains</span><span class="p">))</span>
+                <span class="k">for</span> <span class="n">pdb</span><span class="p">,</span> <span class="n">chains</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">pdbs</span><span class="p">)</span>
+            <span class="p">)</span>
+        <span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="fm">__str__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="p">(</span>
+            <span class="s1">&#39;Domain in protein </span><span class="si">%s</span><span class="s1">-</span><span class="si">%u</span><span class="s1">:</span><span class="se">\n</span><span class="s1">&#39;</span>
+            <span class="s1">&#39;</span><span class="se">\t</span><span class="s1">Name: </span><span class="si">%s</span><span class="se">\n</span><span class="s1">&#39;</span>
+            <span class="s1">&#39;</span><span class="se">\t</span><span class="s1">Range: </span><span class="si">%u</span><span class="s1">-</span><span class="si">%u</span><span class="se">\n</span><span class="s1">&#39;</span>
+            <span class="s1">&#39;</span><span class="se">\t</span><span class="s1">3D structures: </span><span class="si">%s</span><span class="se">\n</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="p">(</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">protein</span><span class="o">.</span><span class="n">label</span><span class="p">,</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">isoform</span><span class="p">,</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">domain</span> <span class="ow">or</span> <span class="s1">&#39;unknown&#39;</span><span class="p">,</span>
+                <span class="mi">0</span> <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">start</span> <span class="ow">is</span> <span class="kc">None</span> <span class="k">else</span> <span class="bp">self</span><span class="o">.</span><span class="n">start</span><span class="p">,</span>
+                <span class="mi">0</span> <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">end</span> <span class="ow">is</span> <span class="kc">None</span> <span class="k">else</span> <span class="bp">self</span><span class="o">.</span><span class="n">end</span><span class="p">,</span>
+                <span class="s1">&#39;, &#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span>
+                    <span class="s1">&#39;</span><span class="si">%s</span><span class="s1"> (chains </span><span class="si">%s</span><span class="s1">)&#39;</span> <span class="o">%</span> <span class="p">(</span><span class="n">pdb</span><span class="p">,</span> <span class="s1">&#39;, &#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">chains</span><span class="p">))</span>
+                    <span class="k">for</span> <span class="n">pdb</span><span class="p">,</span> <span class="n">chains</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">pdbs</span><span class="p">)</span>
+                <span class="p">)</span>
+            <span class="p">)</span>
+        <span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="fm">__repr__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="n">rng</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">range_str</span><span class="p">()</span>
+
+        <span class="k">return</span> <span class="s1">&#39;&lt;Domain </span><span class="si">%s</span><span class="s1">in </span><span class="si">%s</span><span class="s1">-</span><span class="si">%u%s</span><span class="s1">&gt;&#39;</span> <span class="o">%</span> <span class="p">(</span>
+            <span class="s1">&#39;</span><span class="si">%s</span><span class="s1"> &#39;</span> <span class="o">%</span> <span class="bp">self</span><span class="o">.</span><span class="n">domain</span> <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">domain</span> <span class="k">else</span> <span class="s1">&#39;&#39;</span><span class="p">,</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">protein</span><span class="o">.</span><span class="n">label</span><span class="p">,</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">isoform</span><span class="p">,</span>
+            <span class="s1">&#39; [</span><span class="si">%s</span><span class="s1">]&#39;</span> <span class="o">%</span> <span class="n">rng</span> <span class="k">if</span> <span class="n">rng</span> <span class="k">else</span> <span class="s1">&#39;&#39;</span><span class="p">,</span>
+        <span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">range</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="p">(</span>
+            <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">start</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">end</span><span class="p">)</span>
+                <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">start</span> <span class="ow">and</span> <span class="bp">self</span><span class="o">.</span><span class="n">end</span> <span class="k">else</span>
+            <span class="kc">None</span>
+        <span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">range_str</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="n">start_end</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">range</span><span class="p">()</span>
+
+        <span class="k">return</span> <span class="s1">&#39;</span><span class="si">%s</span><span class="s1">-</span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="n">start_end</span> <span class="k">if</span> <span class="n">start_end</span> <span class="k">else</span> <span class="s1">&#39;&#39;</span>
+
+    <span class="k">def</span> <span class="nf">merge</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">other</span><span class="p">):</span>
+
+        <span class="k">if</span> <span class="p">(</span>
+            <span class="bp">self</span> <span class="o">==</span> <span class="n">other</span> <span class="ow">or</span>
+            <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">start</span> <span class="ow">and</span> <span class="bp">self</span><span class="o">.</span><span class="n">end</span><span class="p">)</span> <span class="ow">is</span> <span class="kc">None</span> <span class="ow">or</span>
+            <span class="p">(</span><span class="n">other</span><span class="o">.</span><span class="n">start</span> <span class="ow">and</span> <span class="n">other</span><span class="o">.</span><span class="n">end</span><span class="p">)</span> <span class="ow">is</span> <span class="kc">None</span>
+        <span class="p">):</span>
+
+            <span class="k">for</span> <span class="n">pdb</span><span class="p">,</span> <span class="n">chain</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="n">other</span><span class="o">.</span><span class="n">pdbs</span><span class="p">):</span>
+
+                <span class="bp">self</span><span class="o">.</span><span class="n">add_chains</span><span class="p">(</span><span class="n">pdb</span><span class="p">,</span> <span class="n">chain</span><span class="p">)</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">domain_id_type</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">domain_id_type</span> <span class="ow">or</span> <span class="n">other</span><span class="o">.</span><span class="n">domain_id_type</span>
+
+            <span class="k">if</span> <span class="p">(</span>
+                <span class="p">(</span>
+                    <span class="bp">self</span><span class="o">.</span><span class="n">domain_id_type</span> <span class="o">!=</span> <span class="s1">&#39;pfam&#39;</span> <span class="ow">and</span>
+                    <span class="n">other</span><span class="o">.</span><span class="n">domain</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span>
+                <span class="p">)</span> <span class="ow">or</span>
+                <span class="p">(</span>
+                    <span class="bp">self</span><span class="o">.</span><span class="n">domain</span> <span class="ow">is</span> <span class="kc">None</span> <span class="ow">and</span>
+                    <span class="n">other</span><span class="o">.</span><span class="n">domain</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span>
+                <span class="p">)</span>
+            <span class="p">):</span>
+
+                <span class="bp">self</span><span class="o">.</span><span class="n">domain</span> <span class="o">=</span> <span class="n">other</span><span class="o">.</span><span class="n">domain</span></div>
+
+
+
+<div class="viewcode-block" id="DomainDomain">
+<a class="viewcode-back" href="../../../api/pypath.internals.intera.DomainDomain.html#pypath.internals.intera.DomainDomain">[docs]</a>
+<span class="k">class</span> <span class="nc">DomainDomain</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span>
+
+<div class="viewcode-block" id="DomainDomain.__init__">
+<a class="viewcode-back" href="../../../api/pypath.internals.intera.DomainDomain.html#pypath.internals.intera.DomainDomain.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">domain_a</span><span class="p">,</span>
+            <span class="n">domain_b</span><span class="p">,</span>
+            <span class="n">pdbs</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">sources</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">refs</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">contact_residues</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+        <span class="p">):</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">domains</span> <span class="o">=</span> <span class="p">[</span><span class="n">domain_a</span><span class="p">,</span> <span class="n">domain_b</span><span class="p">]</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">sources</span> <span class="o">=</span> <span class="nb">set</span><span class="p">([])</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">refs</span> <span class="o">=</span> <span class="nb">set</span><span class="p">([])</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">pdbs</span> <span class="o">=</span> <span class="nb">set</span><span class="p">([])</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">add_sources</span><span class="p">(</span><span class="n">sources</span><span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">add_refs</span><span class="p">(</span><span class="n">refs</span><span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">add_pdbs</span><span class="p">(</span><span class="n">pdbs</span><span class="p">)</span>
+<span class="w">        </span><span class="sd">&#39;&#39;&#39;This can be found from 3DComplexes; floating point</span>
+<span class="sd">        numbers show the number of residues in contact. Other</span>
+<span class="sd">        two numbers in the tuple are the length of domain sequences.&#39;&#39;&#39;</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">contact_residues</span> <span class="o">=</span> <span class="n">contact_residues</span></div>
+
+
+    <span class="k">def</span> <span class="fm">__hash__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+        <span class="k">return</span> <span class="nb">hash</span><span class="p">((</span><span class="bp">self</span><span class="o">.</span><span class="n">domain_a</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">domain_b</span><span class="p">))</span>
+
+    <span class="k">def</span> <span class="fm">__eq__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">other</span><span class="p">):</span>
+        <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="vm">__dict__</span> <span class="o">==</span> <span class="n">other</span><span class="o">.</span><span class="vm">__dict__</span><span class="p">:</span>
+            <span class="k">return</span> <span class="kc">True</span>
+        <span class="k">else</span><span class="p">:</span>
+            <span class="k">return</span> <span class="kc">False</span>
+
+    <span class="k">def</span> <span class="fm">__ne__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">other</span><span class="p">):</span>
+        <span class="k">return</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="fm">__eq__</span><span class="p">(</span><span class="n">other</span><span class="p">)</span>
+
+    <span class="k">def</span> <span class="fm">__contains__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">other</span><span class="p">):</span>
+        <span class="k">return</span> <span class="n">other</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">domains</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="ow">or</span> <span class="n">other</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">domains</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span>
+
+    <span class="k">def</span> <span class="nf">add_sources</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">source</span><span class="p">):</span>
+        <span class="k">if</span> <span class="n">source</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
+            <span class="k">return</span> <span class="kc">None</span>
+        <span class="k">elif</span> <span class="nb">type</span><span class="p">(</span><span class="n">source</span><span class="p">)</span> <span class="ow">in</span> <span class="n">_const</span><span class="o">.</span><span class="n">CHAR_TYPES</span><span class="p">:</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">_add_source</span><span class="p">(</span><span class="n">source</span><span class="p">)</span>
+        <span class="k">else</span><span class="p">:</span>
+            <span class="k">for</span> <span class="n">s</span> <span class="ow">in</span> <span class="n">source</span><span class="p">:</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">_add_source</span><span class="p">(</span><span class="n">s</span><span class="p">)</span>
+
+    <span class="k">def</span> <span class="nf">_add_source</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">source</span><span class="p">):</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">sources</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">source</span><span class="p">)</span>
+
+    <span class="k">def</span> <span class="nf">add_refs</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">refs</span><span class="p">):</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">refs</span> <span class="o">=</span> <span class="n">common</span><span class="o">.</span><span class="n">add_to_set</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">refs</span><span class="p">,</span> <span class="n">refs</span><span class="p">)</span>
+
+    <span class="k">def</span> <span class="nf">add_pdbs</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">pdbs</span><span class="p">):</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">pdbs</span> <span class="o">=</span> <span class="n">common</span><span class="o">.</span><span class="n">add_to_set</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">pdbs</span><span class="p">,</span> <span class="n">pdbs</span><span class="p">)</span>
+
+    <span class="k">def</span> <span class="nf">serialize</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+        <span class="k">return</span> <span class="s1">&#39;|&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">([</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">domains</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">serialize</span><span class="p">(),</span> <span class="bp">self</span><span class="o">.</span><span class="n">domains</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">serialize</span><span class="p">(),</span>
+            <span class="s1">&#39;,&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">sources</span><span class="p">),</span> <span class="s1">&#39;,&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">refs</span><span class="p">),</span> <span class="s1">&#39;,&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">pdbs</span><span class="p">)</span>
+        <span class="p">])</span>
+
+    <span class="c1"># domain1|domain2|sources|references|pdb</span>
+
+    <span class="k">def</span> <span class="fm">__str__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+        <span class="k">return</span> <span class="s1">&#39;Domain-domain interaction:</span><span class="se">\n</span><span class="s1">&#39;</span>\
+            <span class="s1">&#39; </span><span class="si">%s</span><span class="s1"> </span><span class="si">%s</span><span class="se">\n</span><span class="s1">&#39;</span>\
+            <span class="s1">&#39; Data sources: </span><span class="si">%s</span><span class="se">\n</span><span class="s1">&#39;</span>\
+            <span class="s1">&#39; References: </span><span class="si">%s</span><span class="se">\n</span><span class="s1">&#39;</span>\
+            <span class="s1">&#39; 3D structures: </span><span class="si">%s</span><span class="se">\n</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="p">(</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">domains</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="fm">__str__</span><span class="p">(),</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">domains</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="fm">__str__</span><span class="p">(),</span>
+                <span class="s1">&#39;, &#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">sources</span><span class="p">),</span>
+                <span class="s1">&#39;, &#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">refs</span><span class="p">),</span>
+                <span class="s1">&#39;,&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">pdbs</span><span class="p">)</span>
+            <span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="DomainMotif">
+<a class="viewcode-back" href="../../../api/pypath.internals.intera.DomainMotif.html#pypath.internals.intera.DomainMotif">[docs]</a>
+<span class="k">class</span> <span class="nc">DomainMotif</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span>
+
+
+<div class="viewcode-block" id="DomainMotif.__init__">
+<a class="viewcode-back" href="../../../api/pypath.internals.intera.DomainMotif.html#pypath.internals.intera.DomainMotif.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">domain</span><span class="p">,</span> <span class="n">ptm</span><span class="p">,</span> <span class="n">evidences</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span> <span class="n">pdbs</span> <span class="o">=</span> <span class="kc">None</span><span class="p">):</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">ptm</span> <span class="o">=</span> <span class="n">ptm</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">domain</span> <span class="o">=</span> <span class="n">domain</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">pdbs</span> <span class="o">=</span> <span class="nb">set</span><span class="p">()</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">pnetw_score</span> <span class="o">=</span> <span class="kc">None</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">add_pdbs</span><span class="p">(</span><span class="n">pdbs</span><span class="p">)</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">evidences</span> <span class="o">=</span> <span class="n">evidences</span> <span class="ow">or</span> <span class="n">evidence</span><span class="o">.</span><span class="n">Evidences</span><span class="p">()</span></div>
+
+
+
+    <span class="k">def</span> <span class="fm">__hash__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="nb">hash</span><span class="p">((</span><span class="bp">self</span><span class="o">.</span><span class="n">domain</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">ptm</span><span class="p">))</span>
+
+
+    <span class="k">def</span> <span class="fm">__str__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="p">(</span>
+            <span class="s1">&#39;Domain-motif interaction:</span><span class="se">\n</span><span class="s1">&#39;</span>
+            <span class="s1">&#39;  </span><span class="si">%s</span><span class="s1">  </span><span class="si">%s</span><span class="s1">&#39;</span>
+            <span class="s1">&#39;  Data sources: </span><span class="si">%s</span><span class="se">\n</span><span class="s1">&#39;</span>
+            <span class="s1">&#39;  References: </span><span class="si">%s</span><span class="se">\n</span><span class="s1">&#39;</span>
+            <span class="s1">&#39;  3D structures: </span><span class="se">\n</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="p">(</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">domain</span><span class="o">.</span><span class="fm">__str__</span><span class="p">(),</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">ptm</span><span class="o">.</span><span class="fm">__str__</span><span class="p">(),</span>
+                <span class="s1">&#39;, &#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">evidences</span><span class="o">.</span><span class="n">get_resource_names</span><span class="p">()),</span>
+                <span class="s1">&#39;, &#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="nb">str</span><span class="p">(</span><span class="n">r</span><span class="p">)</span> <span class="k">for</span> <span class="n">r</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">evidences</span><span class="o">.</span><span class="n">get_references</span><span class="p">()),</span>
+            <span class="p">)</span>
+        <span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="fm">__repr__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="s1">&#39;&lt;</span><span class="si">%s</span><span class="s1"> =&gt; </span><span class="si">%s</span><span class="s1"> [</span><span class="si">%s</span><span class="s1">]&gt;&#39;</span> <span class="o">%</span> <span class="p">(</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">domain</span><span class="o">.</span><span class="n">protein</span><span class="o">.</span><span class="n">label</span><span class="p">,</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">ptm</span><span class="o">.</span><span class="fm">__repr__</span><span class="p">()</span><span class="o">.</span><span class="n">strip</span><span class="p">(</span><span class="s1">&#39;&lt;&gt;&#39;</span><span class="p">)</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s1">&#39;PTM &#39;</span><span class="p">,</span> <span class="s1">&#39;&#39;</span><span class="p">),</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">evidences</span><span class="o">.</span><span class="fm">__repr__</span><span class="p">()</span><span class="o">.</span><span class="n">strip</span><span class="p">(</span><span class="s1">&#39;&lt;&gt;&#39;</span><span class="p">)</span>
+        <span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="fm">__eq__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">other</span><span class="p">):</span>
+
+        <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">other</span><span class="p">,</span> <span class="n">DomainMotif</span><span class="p">)</span> <span class="ow">and</span> \
+            <span class="bp">self</span><span class="o">.</span><span class="n">ptm</span> <span class="o">==</span> <span class="n">other</span><span class="o">.</span><span class="n">ptm</span> <span class="ow">and</span> \
+            <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">domain</span> <span class="o">==</span> <span class="n">other</span><span class="o">.</span><span class="n">domain</span> <span class="ow">or</span>
+             <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">domain</span><span class="o">.</span><span class="n">start</span> <span class="ow">and</span> <span class="bp">self</span><span class="o">.</span><span class="n">domain</span><span class="o">.</span><span class="n">end</span><span class="p">)</span> <span class="ow">is</span> <span class="kc">None</span> <span class="ow">or</span>
+             <span class="p">(</span><span class="n">other</span><span class="o">.</span><span class="n">domain</span><span class="o">.</span><span class="n">start</span> <span class="ow">and</span> <span class="n">other</span><span class="o">.</span><span class="n">domain</span><span class="o">.</span><span class="n">end</span><span class="p">)</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">):</span>
+            <span class="k">return</span> <span class="kc">True</span>
+        <span class="k">else</span><span class="p">:</span>
+            <span class="k">return</span> <span class="kc">False</span>
+
+
+    <span class="k">def</span> <span class="fm">__ne__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">other</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="fm">__eq__</span><span class="p">(</span><span class="n">other</span><span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="fm">__contains__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">other</span><span class="p">):</span>
+
+        <span class="k">if</span> <span class="n">other</span> <span class="o">==</span> <span class="bp">self</span><span class="o">.</span><span class="n">domain</span> <span class="ow">or</span> <span class="n">other</span> <span class="o">==</span> <span class="bp">self</span><span class="o">.</span><span class="n">ptm</span><span class="p">:</span>
+            <span class="k">return</span> <span class="kc">True</span>
+        <span class="k">elif</span> <span class="n">other</span> <span class="o">==</span> <span class="bp">self</span><span class="o">.</span><span class="n">domain</span><span class="o">.</span><span class="n">protein</span> <span class="ow">or</span> <span class="n">other</span> <span class="o">==</span> <span class="bp">self</span><span class="o">.</span><span class="n">ptm</span><span class="o">.</span><span class="n">protein</span><span class="p">:</span>
+            <span class="k">return</span> <span class="kc">True</span>
+        <span class="k">else</span><span class="p">:</span>
+            <span class="k">return</span> <span class="kc">False</span>
+
+
+<div class="viewcode-block" id="DomainMotif.key">
+<a class="viewcode-back" href="../../../api/pypath.internals.intera.DomainMotif.html#pypath.internals.intera.DomainMotif.key">[docs]</a>
+    <span class="k">def</span> <span class="nf">key</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Returns a unique key which is a tuple of the proteins, the residue</span>
+<span class="sd">        and the modification type.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">return</span> <span class="p">(</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">domain</span><span class="o">.</span><span class="n">protein</span><span class="p">,</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">ptm</span><span class="o">.</span><span class="n">protein</span><span class="p">,</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">ptm</span><span class="o">.</span><span class="n">residue</span><span class="o">.</span><span class="n">name</span><span class="p">,</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">ptm</span><span class="o">.</span><span class="n">residue</span><span class="o">.</span><span class="n">number</span><span class="p">,</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">ptm</span><span class="o">.</span><span class="n">typ</span><span class="p">,</span>
+        <span class="p">)</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">get_proteins</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">domain</span><span class="o">.</span><span class="n">protein</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">ptm</span><span class="o">.</span><span class="n">protein</span><span class="p">]</span>
+
+
+    <span class="k">def</span> <span class="nf">add_pdbs</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">pdbs</span><span class="p">):</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">pdbs</span> <span class="o">=</span> <span class="n">common</span><span class="o">.</span><span class="n">add_to_set</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">pdbs</span><span class="p">,</span> <span class="n">pdbs</span><span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">serialize</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="s1">&#39;|&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">([</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">domain</span><span class="o">.</span><span class="n">serialize</span><span class="p">(),</span> <span class="bp">self</span><span class="o">.</span><span class="n">ptm</span><span class="o">.</span><span class="n">serialize</span><span class="p">(),</span>
+            <span class="s1">&#39;,&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">sources</span><span class="p">),</span> <span class="s1">&#39;,&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">refs</span><span class="p">),</span> <span class="s1">&#39;,&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">pdbs</span><span class="p">)</span>
+        <span class="p">])</span>
+
+
+    <span class="k">def</span> <span class="nf">print_residues</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="s1">&#39;</span><span class="si">%s</span><span class="s1">-</span><span class="si">%u</span><span class="s1">:</span><span class="si">%s</span><span class="s1">:</span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="p">(</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">domain</span><span class="o">.</span><span class="n">protein</span><span class="p">,</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">domain</span><span class="o">.</span><span class="n">isoform</span><span class="p">,</span>
+            <span class="s1">&#39;</span><span class="si">%s</span><span class="s1">-</span><span class="si">%u</span><span class="s1">:&#39;</span> <span class="o">%</span> <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">ptm</span><span class="o">.</span><span class="n">protein</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">ptm</span><span class="o">.</span><span class="n">isoform</span><span class="p">)</span>
+                <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">ptm</span><span class="o">.</span><span class="n">motif</span> <span class="ow">is</span> <span class="kc">None</span> <span class="k">else</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">ptm</span><span class="o">.</span><span class="n">motif</span><span class="o">.</span><span class="n">print_residues</span><span class="p">(),</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">ptm</span><span class="o">.</span><span class="n">print_residue</span><span class="p">(),</span>
+        <span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">merge</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">other</span><span class="p">):</span>
+
+        <span class="k">if</span> <span class="bp">self</span> <span class="o">==</span> <span class="n">other</span><span class="p">:</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">domain</span><span class="o">.</span><span class="n">merge</span><span class="p">(</span><span class="n">other</span><span class="o">.</span><span class="n">domain</span><span class="p">)</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">ptm</span><span class="o">.</span><span class="n">merge</span><span class="p">(</span><span class="n">other</span><span class="o">.</span><span class="n">ptm</span><span class="p">)</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">add_evidences</span><span class="p">(</span><span class="n">other</span><span class="o">.</span><span class="n">evidences</span><span class="p">)</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">add_pdbs</span><span class="p">(</span><span class="n">other</span><span class="o">.</span><span class="n">pdbs</span><span class="p">)</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">pnetw_score</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">pnetw_score</span> <span class="ow">or</span> <span class="n">other</span><span class="o">.</span><span class="n">pnetw_score</span>
+
+
+    <span class="k">def</span> <span class="nf">resources</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">only_primary</span> <span class="o">=</span> <span class="kc">False</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="p">[</span>
+            <span class="s1">&#39;</span><span class="si">%s%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="p">(</span>
+                <span class="n">res</span><span class="p">,</span>
+                <span class="s1">&#39;_</span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="n">via</span> <span class="k">if</span> <span class="n">via</span> <span class="k">else</span> <span class="s1">&#39;&#39;</span><span class="p">,</span>
+            <span class="p">)</span>
+            <span class="k">for</span> <span class="n">res</span><span class="p">,</span> <span class="n">via</span> <span class="ow">in</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">evidences</span><span class="o">.</span><span class="n">get_resource_names_via</span><span class="p">(</span><span class="n">via</span> <span class="o">=</span> <span class="kc">None</span><span class="p">)</span>
+            <span class="k">if</span> <span class="ow">not</span> <span class="n">only_primary</span> <span class="ow">or</span> <span class="ow">not</span> <span class="n">via</span>
+        <span class="p">]</span>
+
+
+    <span class="k">def</span> <span class="nf">references</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">evidences</span><span class="o">.</span><span class="n">get_references</span><span class="p">()</span>
+
+
+    <span class="k">def</span> <span class="nf">references_by_resource</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">only_primary</span> <span class="o">=</span> <span class="kc">True</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="p">[</span>
+            <span class="p">(</span>
+                <span class="n">ev</span><span class="o">.</span><span class="n">resource</span><span class="o">.</span><span class="n">name</span><span class="p">,</span>
+                <span class="n">ev</span><span class="o">.</span><span class="n">resource</span><span class="o">.</span><span class="n">via</span><span class="p">,</span>
+                <span class="n">ref</span><span class="p">,</span>
+            <span class="p">)</span>
+            <span class="k">for</span> <span class="n">ev</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">evidences</span>
+            <span class="k">for</span> <span class="n">ref</span> <span class="ow">in</span> <span class="n">ev</span><span class="o">.</span><span class="n">references</span>
+            <span class="k">if</span> <span class="ow">not</span> <span class="n">only_primary</span> <span class="ow">or</span> <span class="ow">not</span> <span class="n">ev</span><span class="o">.</span><span class="n">resource</span><span class="o">.</span><span class="n">via</span>
+        <span class="p">]</span>
+
+
+    <span class="k">def</span> <span class="nf">references_by_resource_str</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">only_primary</span> <span class="o">=</span> <span class="kc">True</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="s1">&#39;;&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="nb">sorted</span><span class="p">(</span>
+            <span class="s1">&#39;</span><span class="si">%s%s</span><span class="s1">:</span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="p">(</span>
+                <span class="n">res</span><span class="p">,</span>
+                <span class="s1">&#39;_</span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="n">via</span> <span class="k">if</span> <span class="n">via</span> <span class="k">else</span> <span class="s1">&#39;&#39;</span><span class="p">,</span>
+                <span class="n">ref</span><span class="o">.</span><span class="n">pmid</span><span class="p">,</span>
+            <span class="p">)</span>
+            <span class="k">for</span> <span class="n">res</span><span class="p">,</span> <span class="n">via</span><span class="p">,</span> <span class="n">ref</span>
+            <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">references_by_resource</span><span class="p">(</span><span class="n">only_primary</span> <span class="o">=</span> <span class="n">only_primary</span><span class="p">)</span>
+        <span class="p">))</span>
+
+
+<div class="viewcode-block" id="DomainMotif.get_line">
+<a class="viewcode-back" href="../../../api/pypath.internals.intera.DomainMotif.html#pypath.internals.intera.DomainMotif.get_line">[docs]</a>
+    <span class="k">def</span> <span class="nf">get_line</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">resources_only_primary</span> <span class="o">=</span> <span class="kc">False</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Returns a list intended to be a row in a data frame of</span>
+<span class="sd">        enzyme-substrate relationships.</span>
+
+<span class="sd">        Elements of the list:</span>
+<span class="sd">            - enzyme</span>
+<span class="sd">            - enzyme_genesymbol</span>
+<span class="sd">            - substrate</span>
+<span class="sd">            - substrate_genesymbol</span>
+<span class="sd">            - isoforms</span>
+<span class="sd">            - residue_type</span>
+<span class="sd">            - residue_offset</span>
+<span class="sd">            - modification</span>
+<span class="sd">            - sources</span>
+<span class="sd">            - references</span>
+<span class="sd">            - curation_effort</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">return</span> <span class="p">[</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">domain</span><span class="o">.</span><span class="n">protein</span><span class="o">.</span><span class="n">identifier</span><span class="p">,</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">domain</span><span class="o">.</span><span class="n">protein</span><span class="o">.</span><span class="n">label</span><span class="p">,</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">ptm</span><span class="o">.</span><span class="n">protein</span><span class="o">.</span><span class="n">identifier</span><span class="p">,</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">ptm</span><span class="o">.</span><span class="n">protein</span><span class="o">.</span><span class="n">label</span><span class="p">,</span>
+            <span class="s1">&#39;;&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="nb">map</span><span class="p">(</span><span class="k">lambda</span> <span class="n">i</span><span class="p">:</span> <span class="s1">&#39;</span><span class="si">%u</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="n">i</span><span class="p">,</span> <span class="nb">sorted</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">ptm</span><span class="o">.</span><span class="n">isoforms</span><span class="p">))),</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">ptm</span><span class="o">.</span><span class="n">residue</span><span class="o">.</span><span class="n">name</span><span class="p">,</span>
+            <span class="s1">&#39;</span><span class="si">%u</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="bp">self</span><span class="o">.</span><span class="n">ptm</span><span class="o">.</span><span class="n">residue</span><span class="o">.</span><span class="n">number</span><span class="p">,</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">ptm</span><span class="o">.</span><span class="n">typ</span><span class="p">,</span>
+            <span class="s1">&#39;;&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="nb">sorted</span><span class="p">(</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">resources</span><span class="p">(</span><span class="n">only_primary</span> <span class="o">=</span> <span class="n">resources_only_primary</span><span class="p">)</span>
+            <span class="p">)),</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">references_by_resource_str</span><span class="p">(),</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">evidences</span><span class="o">.</span><span class="n">count_curation_effort</span><span class="p">(),</span>
+        <span class="p">]</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">add_evidences</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">evidences</span><span class="p">):</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">evidences</span> <span class="o">+=</span> <span class="n">evidences</span></div>
+
+
+
+<div class="viewcode-block" id="Regulation">
+<a class="viewcode-back" href="../../../api/pypath.internals.intera.Regulation.html#pypath.internals.intera.Regulation">[docs]</a>
+<span class="k">class</span> <span class="nc">Regulation</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span>
+
+<div class="viewcode-block" id="Regulation.__init__">
+<a class="viewcode-back" href="../../../api/pypath.internals.intera.Regulation.html#pypath.internals.intera.Regulation.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">ptm</span><span class="p">,</span> <span class="n">source</span><span class="p">,</span> <span class="n">target</span><span class="p">,</span> <span class="n">effect</span><span class="p">,</span> <span class="n">sources</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">refs</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">ptm</span> <span class="o">=</span> <span class="n">ptm</span> <span class="k">if</span> <span class="nb">type</span><span class="p">(</span><span class="n">ptm</span><span class="p">)</span> <span class="ow">is</span> <span class="nb">list</span> <span class="k">else</span> <span class="p">[</span><span class="n">ptm</span><span class="p">]</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">source</span> <span class="o">=</span> <span class="n">source</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">target</span> <span class="o">=</span> <span class="n">target</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">effect</span> <span class="o">=</span> <span class="n">effect</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">sources</span> <span class="o">=</span> <span class="nb">set</span><span class="p">([])</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">refs</span> <span class="o">=</span> <span class="nb">set</span><span class="p">([])</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">add_sources</span><span class="p">(</span><span class="n">sources</span><span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">add_refs</span><span class="p">(</span><span class="n">refs</span><span class="p">)</span></div>
+
+
+    <span class="k">def</span> <span class="fm">__hash__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+        <span class="k">return</span> <span class="nb">hash</span><span class="p">((</span><span class="bp">self</span><span class="o">.</span><span class="n">ptm</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">source</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">target</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">effect</span><span class="p">))</span>
+
+    <span class="k">def</span> <span class="fm">__eq__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">other</span><span class="p">):</span>
+        <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">other</span><span class="p">,</span> <span class="n">Regulation</span><span class="p">)</span> <span class="ow">and</span> \
+                <span class="bp">self</span><span class="o">.</span><span class="n">ptm</span> <span class="o">==</span> <span class="n">other</span><span class="o">.</span><span class="n">ptm</span> <span class="ow">and</span> \
+                <span class="bp">self</span><span class="o">.</span><span class="n">source</span> <span class="o">==</span> <span class="n">other</span><span class="o">.</span><span class="n">source</span> <span class="ow">and</span> \
+                <span class="bp">self</span><span class="o">.</span><span class="n">target</span> <span class="o">==</span> <span class="n">other</span><span class="o">.</span><span class="n">target</span> <span class="ow">and</span> \
+                <span class="bp">self</span><span class="o">.</span><span class="n">effect</span> <span class="o">==</span> <span class="n">other</span><span class="o">.</span><span class="n">effect</span><span class="p">:</span>
+            <span class="k">return</span> <span class="kc">True</span>
+        <span class="k">else</span><span class="p">:</span>
+            <span class="k">return</span> <span class="kc">False</span>
+
+    <span class="k">def</span> <span class="fm">__ne__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">other</span><span class="p">):</span>
+        <span class="k">return</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="fm">__eq__</span><span class="p">(</span><span class="n">other</span><span class="p">)</span>
+
+    <span class="k">def</span> <span class="nf">add_sources</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">source</span><span class="p">):</span>
+        <span class="k">if</span> <span class="n">source</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
+            <span class="k">return</span> <span class="kc">None</span>
+        <span class="k">elif</span> <span class="nb">type</span><span class="p">(</span><span class="n">source</span><span class="p">)</span> <span class="ow">in</span> <span class="n">_const</span><span class="o">.</span><span class="n">CHAR_TYPES</span><span class="p">:</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">_add_source</span><span class="p">(</span><span class="n">source</span><span class="p">)</span>
+        <span class="k">else</span><span class="p">:</span>
+            <span class="k">for</span> <span class="n">s</span> <span class="ow">in</span> <span class="n">source</span><span class="p">:</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">_add_source</span><span class="p">(</span><span class="n">s</span><span class="p">)</span>
+
+    <span class="k">def</span> <span class="nf">_add_source</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">source</span><span class="p">):</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">sources</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">source</span><span class="p">)</span>
+
+    <span class="k">def</span> <span class="nf">add_refs</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">refs</span><span class="p">):</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">refs</span> <span class="o">=</span> <span class="n">common</span><span class="o">.</span><span class="n">add_to_set</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">refs</span><span class="p">,</span> <span class="n">refs</span><span class="p">)</span>
+
+    <span class="k">def</span> <span class="nf">serialize</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+        <span class="k">return</span> <span class="s1">&#39;|&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">([</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">effect</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">ptm</span><span class="o">.</span><span class="n">serialize</span><span class="p">(),</span> <span class="bp">self</span><span class="o">.</span><span class="n">target</span><span class="p">,</span>
+            <span class="s1">&#39;,&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">sources</span><span class="p">),</span> <span class="s1">&#39;,&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">refs</span><span class="p">)</span>
+        <span class="p">])</span>
+
+    <span class="k">def</span> <span class="fm">__str__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+        <span class="k">return</span> <span class="s1">&#39;Regulation by PTM:</span><span class="se">\n</span><span class="s1">&#39;</span>\
+            <span class="s1">&#39; PTM on </span><span class="si">%s</span><span class="s1"> </span><span class="si">%s</span><span class="s1"> interaction with </span><span class="si">%s</span><span class="se">\n</span><span class="s1">&#39;</span>\
+            <span class="s1">&#39; </span><span class="si">%s</span><span class="s1"> </span><span class="se">\n</span><span class="s1">&#39;</span>\
+            <span class="s1">&#39; Data sources: </span><span class="si">%s</span><span class="se">\n</span><span class="s1">&#39;</span>\
+            <span class="s1">&#39; References: </span><span class="si">%s</span><span class="se">\n</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">source</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">target</span><span class="p">,</span>
+                                   <span class="bp">self</span><span class="o">.</span><span class="n">ptm</span><span class="o">.</span><span class="fm">__str__</span><span class="p">(),</span> <span class="s1">&#39;, &#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">sources</span><span class="p">),</span>
+                                   <span class="s1">&#39;, &#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">refs</span><span class="p">))</span>
+
+    <span class="k">def</span> <span class="nf">merge</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">other</span><span class="p">):</span>
+        <span class="k">if</span> <span class="bp">self</span> <span class="o">==</span> <span class="n">other</span><span class="p">:</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">ptm</span><span class="o">.</span><span class="n">merge</span><span class="p">(</span><span class="n">other</span><span class="o">.</span><span class="n">ptm</span><span class="p">)</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">add_sources</span><span class="p">(</span><span class="n">other</span><span class="o">.</span><span class="n">sources</span><span class="p">)</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">add_refs</span><span class="p">(</span><span class="n">other</span><span class="o">.</span><span class="n">refs</span><span class="p">)</span></div>
+
+
+
+<span class="c1">#TODO this class does not belong here, find a better place</span>
+<div class="viewcode-block" id="Complex">
+<a class="viewcode-back" href="../../../api/pypath.internals.intera.Complex.html#pypath.internals.intera.Complex">[docs]</a>
+<span class="k">class</span> <span class="nc">Complex</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span>
+
+    <span class="n">have_stoichiometry</span> <span class="o">=</span> <span class="p">{</span>
+        <span class="s1">&#39;PDB&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;Compleat&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;ComplexPortal&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;CellPhoneDB&#39;</span><span class="p">,</span>
+    <span class="p">}</span>
+
+
+<div class="viewcode-block" id="Complex.__init__">
+<a class="viewcode-back" href="../../../api/pypath.internals.intera.Complex.html#pypath.internals.intera.Complex.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">components</span><span class="p">,</span>
+            <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">,</span>
+            <span class="n">name</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">ids</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">sources</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">interactions</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">references</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">proteins</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">attrs</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+        <span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Represents a molecular complex.</span>
+
+<span class="sd">        components : list,dict</span>
+<span class="sd">            Either a list of identifiers or a dict with identifiers as keys</span>
+<span class="sd">            and stoichiometric coefficients as values. List of identifiers</span>
+<span class="sd">            also assumed to represent stoichiometry by repetition</span>
+<span class="sd">            of identifiers.</span>
+<span class="sd">        ncbi_tax_id : int</span>
+<span class="sd">            NCBI taxonomy identifier of the complex. It implies all members</span>
+<span class="sd">            of the complex belong to the same organism. Support for multi-</span>
+<span class="sd">            organism complexes will be implemented in the future.</span>
+<span class="sd">        name : str</span>
+<span class="sd">            A custom name or identifier of the complex.</span>
+<span class="sd">        ids : dict</span>
+<span class="sd">            Identifiers. If ``sources`` is a set, list or tuple it should be</span>
+<span class="sd">            a dict with database names as keys and set of identifiers as</span>
+<span class="sd">            values. If ``sources`` is a string, it can be a set of</span>
+<span class="sd">            identifiers or a single identifier.</span>
+<span class="sd">        sources : set,str</span>
+<span class="sd">            Database(s) the complex has been defined in.</span>
+<span class="sd">        interactions : list,dict</span>
+<span class="sd">            Interactions between the components of the complex. Either</span>
+<span class="sd">            a list of tuples of component IDs or a dict with tuples as</span>
+<span class="sd">            keys and custom interaction properties as values.</span>
+<span class="sd">        proteins : list,dict</span>
+<span class="sd">            Synonym for `components`, kept for compatibility.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">components</span> <span class="o">=</span> <span class="n">components</span> <span class="ow">or</span> <span class="n">proteins</span>
+
+        <span class="k">if</span> <span class="ow">not</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">components</span><span class="p">,</span> <span class="nb">dict</span><span class="p">):</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">components</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">(</span><span class="n">collections</span><span class="o">.</span><span class="n">Counter</span><span class="p">(</span><span class="n">components</span><span class="p">))</span>
+
+        <span class="k">else</span><span class="p">:</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">components</span> <span class="o">=</span> <span class="n">components</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">proteins</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">components</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">name</span> <span class="o">=</span> <span class="n">name</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">ids</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">defaultdict</span><span class="p">(</span><span class="nb">set</span><span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">add_ids</span><span class="p">(</span><span class="n">ids</span><span class="p">,</span> <span class="n">source</span> <span class="o">=</span> <span class="n">sources</span><span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">sources</span> <span class="o">=</span> <span class="n">common</span><span class="o">.</span><span class="n">to_set</span><span class="p">(</span><span class="n">sources</span><span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">references</span> <span class="o">=</span> <span class="n">common</span><span class="o">.</span><span class="n">to_set</span><span class="p">(</span><span class="n">references</span><span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">taxonomy</span><span class="o">.</span><span class="n">ensure_ncbi_tax_id</span><span class="p">(</span><span class="n">ncbi_tax_id</span><span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">attrs</span> <span class="o">=</span> <span class="p">{}</span>
+        <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">attrs</span><span class="p">,</span> <span class="nb">dict</span><span class="p">):</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">attrs</span><span class="o">.</span><span class="n">update</span><span class="p">(</span><span class="n">attrs</span><span class="p">)</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">interactions</span> <span class="o">=</span> <span class="n">interactions</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">reload</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="n">modname</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="vm">__class__</span><span class="o">.</span><span class="vm">__module__</span>
+        <span class="n">mod</span> <span class="o">=</span> <span class="nb">__import__</span><span class="p">(</span><span class="n">modname</span><span class="p">,</span> <span class="n">fromlist</span> <span class="o">=</span> <span class="p">[</span><span class="n">modname</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;.&#39;</span><span class="p">)[</span><span class="mi">0</span><span class="p">]])</span>
+        <span class="kn">import</span> <span class="nn">importlib</span> <span class="k">as</span> <span class="nn">imp</span>
+        <span class="n">imp</span><span class="o">.</span><span class="n">reload</span><span class="p">(</span><span class="n">mod</span><span class="p">)</span>
+        <span class="n">new</span> <span class="o">=</span> <span class="nb">getattr</span><span class="p">(</span><span class="n">mod</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="vm">__class__</span><span class="o">.</span><span class="vm">__name__</span><span class="p">)</span>
+        <span class="nb">setattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">&#39;__class__&#39;</span><span class="p">,</span> <span class="n">new</span><span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="fm">__str__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="s1">&#39;COMPLEX:</span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="p">(</span>
+            <span class="n">COMPLEX_SEP</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="nb">sorted</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">components</span><span class="o">.</span><span class="n">keys</span><span class="p">()))</span>
+        <span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="fm">__repr__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="s1">&#39;Complex</span><span class="si">%s</span><span class="s1">: </span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="p">(</span>
+            <span class="s1">&#39; </span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="bp">self</span><span class="o">.</span><span class="n">name</span> <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">name</span> <span class="k">else</span> <span class="s1">&#39;&#39;</span><span class="p">,</span>
+            <span class="bp">self</span><span class="o">.</span><span class="fm">__str__</span><span class="p">(),</span>
+        <span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="fm">__hash__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="nb">hash</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="fm">__str__</span><span class="p">())</span>
+
+
+    <span class="k">def</span> <span class="fm">__contains__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">other</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="n">other</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">components</span>
+
+
+    <span class="k">def</span> <span class="fm">__eq__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">other</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="fm">__hash__</span><span class="p">()</span> <span class="o">==</span> <span class="n">other</span><span class="o">.</span><span class="fm">__hash__</span><span class="p">()</span>
+
+
+    <span class="k">def</span> <span class="fm">__iadd__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">other</span><span class="p">):</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">merge</span><span class="p">(</span><span class="n">other</span><span class="p">)</span>
+
+        <span class="k">return</span> <span class="bp">self</span>
+
+
+    <span class="k">def</span> <span class="fm">__lt__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">other</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="fm">__str__</span><span class="p">()</span> <span class="o">&lt;</span> <span class="n">other</span>
+
+
+    <span class="k">def</span> <span class="fm">__gt__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">other</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="fm">__str__</span><span class="p">()</span> <span class="o">&gt;</span> <span class="n">other</span>
+
+
+    <span class="k">def</span> <span class="fm">__len__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">components</span><span class="p">)</span>
+
+
+<div class="viewcode-block" id="Complex.merge">
+<a class="viewcode-back" href="../../../api/pypath.internals.intera.Complex.html#pypath.internals.intera.Complex.merge">[docs]</a>
+    <span class="k">def</span> <span class="nf">merge</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">other</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Adds the annotations (sources, references, attrs) of the other</span>
+<span class="sd">        ``Complex`` instance to this one. If the other ``Complex`` has</span>
+<span class="sd">        different components it does nothing.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">if</span> <span class="bp">self</span> <span class="o">!=</span> <span class="n">other</span><span class="p">:</span>
+
+            <span class="k">return</span>
+
+        <span class="k">if</span> <span class="p">(</span>
+            <span class="nb">set</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">components</span><span class="o">.</span><span class="n">values</span><span class="p">())</span> <span class="o">==</span> <span class="p">{</span><span class="mi">1</span><span class="p">}</span> <span class="ow">and</span>
+            <span class="nb">set</span><span class="p">(</span><span class="n">other</span><span class="o">.</span><span class="n">components</span><span class="o">.</span><span class="n">values</span><span class="p">())</span> <span class="o">!=</span> <span class="p">{</span><span class="mi">1</span><span class="p">}</span>
+        <span class="p">):</span>
+            <span class="c1"># this complex has no stoichiometry information</span>
+            <span class="c1"># but the other has</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">components</span> <span class="o">=</span> <span class="n">other</span><span class="o">.</span><span class="n">components</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">sources</span><span class="o">.</span><span class="n">update</span><span class="p">(</span><span class="n">other</span><span class="o">.</span><span class="n">sources</span><span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">references</span><span class="o">.</span><span class="n">update</span><span class="p">(</span><span class="n">other</span><span class="o">.</span><span class="n">references</span><span class="p">)</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">add_ids</span><span class="p">(</span><span class="n">other</span><span class="o">.</span><span class="n">ids</span><span class="p">)</span>
+
+        <span class="k">for</span> <span class="n">k</span><span class="p">,</span> <span class="n">v</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="n">other</span><span class="o">.</span><span class="n">attrs</span><span class="p">):</span>
+
+            <span class="k">if</span> <span class="n">k</span> <span class="ow">not</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">attrs</span><span class="p">:</span>
+
+                <span class="bp">self</span><span class="o">.</span><span class="n">attrs</span><span class="p">[</span><span class="n">k</span><span class="p">]</span> <span class="o">=</span> <span class="n">v</span>
+
+            <span class="k">elif</span> <span class="nb">isinstance</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">attrs</span><span class="p">[</span><span class="n">k</span><span class="p">],</span> <span class="p">(</span><span class="nb">dict</span><span class="p">,</span> <span class="nb">set</span><span class="p">)):</span>
+
+                <span class="bp">self</span><span class="o">.</span><span class="n">attrs</span><span class="p">[</span><span class="n">k</span><span class="p">]</span><span class="o">.</span><span class="n">update</span><span class="p">(</span><span class="n">v</span><span class="p">)</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">add_ids</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">ids</span><span class="p">,</span> <span class="n">source</span> <span class="o">=</span> <span class="kc">None</span><span class="p">):</span>
+
+        <span class="k">if</span> <span class="ow">not</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">ids</span><span class="p">,</span> <span class="nb">dict</span><span class="p">):</span>
+
+            <span class="n">ids</span> <span class="o">=</span> <span class="n">common</span><span class="o">.</span><span class="n">to_set</span><span class="p">(</span><span class="n">ids</span><span class="p">)</span>
+
+        <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">ids</span><span class="p">,</span> <span class="nb">set</span><span class="p">)</span> <span class="ow">and</span> <span class="n">source</span><span class="p">:</span>
+
+            <span class="n">source</span> <span class="o">=</span> <span class="n">common</span><span class="o">.</span><span class="n">to_set</span><span class="p">(</span><span class="n">source</span><span class="p">)</span>
+
+            <span class="n">ids</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">((</span><span class="n">s</span><span class="p">,</span> <span class="n">ids</span><span class="p">)</span> <span class="k">for</span> <span class="n">s</span> <span class="ow">in</span> <span class="n">source</span><span class="p">)</span>
+
+        <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">ids</span><span class="p">,</span> <span class="nb">dict</span><span class="p">):</span>
+
+            <span class="k">for</span> <span class="n">this_source</span><span class="p">,</span> <span class="n">this_ids</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="n">ids</span><span class="p">):</span>
+
+                <span class="n">this_ids</span> <span class="o">=</span> <span class="n">common</span><span class="o">.</span><span class="n">to_set</span><span class="p">(</span><span class="n">this_ids</span><span class="p">)</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">ids</span><span class="p">[</span><span class="n">this_source</span><span class="p">]</span><span class="o">.</span><span class="n">update</span><span class="p">(</span><span class="n">this_ids</span><span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">get_interaction</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">component1</span><span class="p">,</span> <span class="n">component2</span><span class="p">):</span>
+
+        <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">has_interaction</span><span class="p">(</span><span class="n">component1</span><span class="p">,</span> <span class="n">component2</span><span class="p">):</span>
+
+            <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">interactions</span><span class="p">[(</span><span class="n">component1</span><span class="p">,</span> <span class="n">component2</span><span class="p">)]</span>
+
+
+    <span class="k">def</span> <span class="nf">set_interaction</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">component1</span><span class="p">,</span> <span class="n">component2</span><span class="p">,</span> <span class="n">interaction</span><span class="p">):</span>
+
+        <span class="n">key</span> <span class="o">=</span> <span class="p">(</span><span class="n">component1</span><span class="p">,</span> <span class="n">component2</span><span class="p">)</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">interactions</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">interactions</span> <span class="ow">or</span> <span class="p">{}</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">interactions</span><span class="p">[</span><span class="n">key</span><span class="p">]</span> <span class="o">=</span> <span class="n">interaction</span>
+
+
+    <span class="k">def</span> <span class="nf">has_interaction</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">component1</span><span class="p">,</span> <span class="n">component2</span><span class="p">):</span>
+
+        <span class="n">key</span> <span class="o">=</span> <span class="p">(</span><span class="n">component1</span><span class="p">,</span> <span class="n">component2</span><span class="p">)</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">interactions</span> <span class="ow">and</span> <span class="n">key</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">interactions</span>
+
+
+    <span class="k">def</span> <span class="nf">add_source</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">source</span><span class="p">):</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">sources</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">source</span><span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">iter_proteins</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">for</span> <span class="n">protein</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">proteins</span><span class="o">.</span><span class="n">keys</span><span class="p">():</span>
+
+            <span class="k">yield</span> <span class="n">protein</span>
+
+
+    <span class="fm">__iter__</span> <span class="o">=</span> <span class="n">iter_proteins</span>
+
+
+<div class="viewcode-block" id="Complex.add_attr">
+<a class="viewcode-back" href="../../../api/pypath.internals.intera.Complex.html#pypath.internals.intera.Complex.add_attr">[docs]</a>
+    <span class="k">def</span> <span class="nf">add_attr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">source</span><span class="p">,</span> <span class="n">attr</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Attributes can store annotations for complexes.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">attrs</span><span class="p">[</span><span class="n">source</span><span class="p">]</span> <span class="o">=</span> <span class="n">attr</span></div>
+
+
+
+    <span class="nd">@property</span>
+    <span class="k">def</span> <span class="nf">stoichiometry</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="s1">&#39;:&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span>
+            <span class="s1">&#39;</span><span class="si">%u</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="p">(</span>
+                <span class="n">cnt</span>
+                    <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">sources</span> <span class="o">&amp;</span> <span class="bp">self</span><span class="o">.</span><span class="n">have_stoichiometry</span> <span class="k">else</span>
+                <span class="mi">0</span>
+            <span class="p">)</span>
+            <span class="k">for</span> <span class="n">_id</span><span class="p">,</span> <span class="n">cnt</span> <span class="ow">in</span>
+            <span class="nb">sorted</span><span class="p">(</span>
+                <span class="n">iteritems</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">components</span><span class="p">),</span>
+                <span class="n">key</span> <span class="o">=</span> <span class="k">lambda</span> <span class="n">id_cnt</span><span class="p">:</span> <span class="n">id_cnt</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span>
+            <span class="p">)</span>
+        <span class="p">)</span>
+
+
+    <span class="nd">@property</span>
+    <span class="k">def</span> <span class="nf">stoichiometry_str</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="s1">&#39;;&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span>
+            <span class="n">itertools</span><span class="o">.</span><span class="n">chain</span><span class="p">(</span><span class="o">*</span><span class="p">(</span>
+                <span class="p">(</span><span class="n">comp</span><span class="p">,)</span> <span class="o">*</span> <span class="n">cnt</span>
+                <span class="k">for</span> <span class="n">comp</span><span class="p">,</span> <span class="n">cnt</span> <span class="ow">in</span>
+                <span class="nb">sorted</span><span class="p">(</span>
+                    <span class="n">iteritems</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">components</span><span class="p">),</span>
+                    <span class="n">key</span> <span class="o">=</span> <span class="k">lambda</span> <span class="n">comp_cnt</span><span class="p">:</span> <span class="n">comp_cnt</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span>
+                <span class="p">)</span>
+            <span class="p">))</span>
+        <span class="p">)</span>
+
+
+    <span class="nd">@property</span>
+    <span class="k">def</span> <span class="nf">stoichiometry_str_genesymbols</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="s1">&#39;;&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span>
+            <span class="n">itertools</span><span class="o">.</span><span class="n">chain</span><span class="p">(</span><span class="o">*</span><span class="p">(</span>
+                <span class="p">(</span>
+                    <span class="p">(</span>
+                        <span class="n">mapping</span><span class="o">.</span><span class="n">map_name0</span><span class="p">(</span>
+                            <span class="n">uniprot</span><span class="p">,</span>
+                            <span class="s1">&#39;uniprot&#39;</span><span class="p">,</span>
+                            <span class="s1">&#39;genesymbol&#39;</span><span class="p">,</span>
+                        <span class="p">)</span> <span class="ow">or</span>
+                        <span class="n">uniprot</span>
+                    <span class="p">),</span>
+                <span class="p">)</span> <span class="o">*</span> <span class="n">cnt</span>
+                <span class="k">for</span> <span class="n">uniprot</span><span class="p">,</span> <span class="n">cnt</span> <span class="ow">in</span>
+                <span class="nb">sorted</span><span class="p">(</span>
+                    <span class="n">iteritems</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">components</span><span class="p">),</span>
+                    <span class="n">key</span> <span class="o">=</span> <span class="k">lambda</span> <span class="n">comp_cnt</span><span class="p">:</span> <span class="n">comp_cnt</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span>
+                <span class="p">)</span>
+            <span class="p">))</span>
+        <span class="p">)</span>
+
+
+    <span class="nd">@property</span>
+    <span class="k">def</span> <span class="nf">genesymbols</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="nb">sorted</span><span class="p">(</span>
+            <span class="p">(</span>
+                <span class="n">mapping</span><span class="o">.</span><span class="n">map_name0</span><span class="p">(</span><span class="n">uniprot</span><span class="p">,</span> <span class="s1">&#39;uniprot&#39;</span><span class="p">,</span> <span class="s1">&#39;genesymbol&#39;</span><span class="p">)</span> <span class="ow">or</span>
+                <span class="n">uniprot</span>
+            <span class="p">)</span>
+            <span class="k">for</span> <span class="n">uniprot</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">components</span><span class="o">.</span><span class="n">keys</span><span class="p">()</span>
+        <span class="p">)</span>
+
+
+    <span class="nd">@property</span>
+    <span class="k">def</span> <span class="nf">genesymbol_str</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="n">COMPLEX_SEP</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">genesymbols</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="Interface">
+<a class="viewcode-back" href="../../../api/pypath.internals.intera.Interface.html#pypath.internals.intera.Interface">[docs]</a>
+<span class="k">class</span> <span class="nc">Interface</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span>
+
+
+<div class="viewcode-block" id="Interface.__init__">
+<a class="viewcode-back" href="../../../api/pypath.internals.intera.Interface.html#pypath.internals.intera.Interface.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span>
+                 <span class="n">id_a</span><span class="p">,</span>
+                 <span class="n">id_b</span><span class="p">,</span>
+                 <span class="n">source</span><span class="p">,</span>
+                 <span class="n">id_type</span><span class="o">=</span><span class="s1">&#39;uniprot&#39;</span><span class="p">,</span>
+                 <span class="n">pdb</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
+                 <span class="n">css</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
+                 <span class="n">stab_en</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
+                 <span class="n">solv_en</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
+                 <span class="n">area</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
+                 <span class="n">isoform_a</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span>
+                 <span class="n">isoform_b</span><span class="o">=</span><span class="mi">1</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&#39;&#39;&#39;</span>
+<span class="sd">        This class is to store residue level information of</span>
+<span class="sd">        protein-protein interfaces.</span>
+<span class="sd">        &#39;&#39;&#39;</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">source</span> <span class="o">=</span> <span class="n">source</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">isoform_a</span> <span class="o">=</span> <span class="n">isoform_a</span> <span class="k">if</span> <span class="nb">type</span><span class="p">(</span><span class="n">isoform_a</span><span class="p">)</span> <span class="ow">is</span> <span class="nb">int</span> \
+            <span class="k">else</span> <span class="nb">int</span><span class="p">(</span><span class="n">non_digit</span><span class="o">.</span><span class="n">sub</span><span class="p">(</span><span class="s1">&#39;&#39;</span><span class="p">,</span> <span class="n">isoform_a</span><span class="p">))</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">isoform_b</span> <span class="o">=</span> <span class="n">isoform_b</span> <span class="k">if</span> <span class="nb">type</span><span class="p">(</span><span class="n">isoform_b</span><span class="p">)</span> <span class="ow">is</span> <span class="nb">int</span> \
+            <span class="k">else</span> <span class="nb">int</span><span class="p">(</span><span class="n">non_digit</span><span class="o">.</span><span class="n">sub</span><span class="p">(</span><span class="s1">&#39;&#39;</span><span class="p">,</span> <span class="n">isoform_b</span><span class="p">))</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">pdb</span> <span class="o">=</span> <span class="n">pdb</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">id_a</span> <span class="o">=</span> <span class="n">id_a</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">id_b</span> <span class="o">=</span> <span class="n">id_b</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">id_type</span> <span class="o">=</span> <span class="n">id_type</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">types</span> <span class="o">=</span> <span class="p">[</span><span class="s1">&#39;undefined&#39;</span><span class="p">,</span> <span class="s1">&#39;hbonds&#39;</span><span class="p">,</span> <span class="s1">&#39;sbridges&#39;</span><span class="p">,</span> <span class="s1">&#39;ssbonds&#39;</span><span class="p">,</span> <span class="s1">&#39;covbonds&#39;</span><span class="p">]</span>
+        <span class="k">for</span> <span class="n">t</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">types</span><span class="p">:</span>
+            <span class="bp">self</span><span class="o">.</span><span class="vm">__dict__</span><span class="p">[</span><span class="n">t</span><span class="p">]</span> <span class="o">=</span> <span class="p">{</span><span class="n">id_a</span><span class="p">:</span> <span class="p">[],</span> <span class="n">id_b</span><span class="p">:</span> <span class="p">[]}</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">area</span> <span class="o">=</span> <span class="n">area</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">stab_en</span> <span class="o">=</span> <span class="n">stab_en</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">solv_en</span> <span class="o">=</span> <span class="n">solv_en</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">css</span> <span class="o">=</span> <span class="n">css</span></div>
+
+
+
+<div class="viewcode-block" id="Interface.add_residues">
+<a class="viewcode-back" href="../../../api/pypath.internals.intera.Interface.html#pypath.internals.intera.Interface.add_residues">[docs]</a>
+    <span class="k">def</span> <span class="nf">add_residues</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">res_a</span><span class="p">,</span> <span class="n">res_b</span><span class="p">,</span> <span class="n">typ</span><span class="o">=</span><span class="s1">&#39;undefined&#39;</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&#39;&#39;&#39;</span>
+<span class="sd">        Adds one pair of residues of type `typ`,</span>
+<span class="sd">        where `res_a` and `res_b` are tuples of</span>
+<span class="sd">        residue number in sequence and residue type,</span>
+<span class="sd">        e.g. (124, &#39;S&#39;) -- (means Serine #124)</span>
+<span class="sd">        `typ` can be undefined, hbonds, sbridges, ssbonds or covbonds</span>
+<span class="sd">        &#39;&#39;&#39;</span>
+        <span class="k">if</span> <span class="nb">type</span><span class="p">(</span><span class="n">res_a</span><span class="p">)</span> <span class="ow">is</span> <span class="ow">not</span> <span class="nb">tuple</span> <span class="ow">or</span> <span class="nb">type</span><span class="p">(</span><span class="n">res_b</span><span class="p">)</span> <span class="ow">is</span> <span class="ow">not</span> <span class="nb">tuple</span> \
+                <span class="ow">or</span> <span class="nb">type</span><span class="p">(</span><span class="n">res_a</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span> <span class="ow">is</span> <span class="ow">not</span> <span class="nb">int</span> <span class="ow">or</span> <span class="nb">type</span><span class="p">(</span><span class="n">res_b</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span> <span class="ow">is</span> <span class="ow">not</span> <span class="nb">int</span> \
+                <span class="ow">or</span> <span class="p">(</span><span class="nb">type</span><span class="p">(</span><span class="n">res_a</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span> <span class="ow">is</span> <span class="ow">not</span> <span class="n">unicode</span> <span class="ow">and</span> <span class="nb">type</span><span class="p">(</span><span class="n">res_a</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span> <span class="ow">is</span> <span class="ow">not</span> <span class="nb">str</span><span class="p">)</span> \
+                <span class="ow">or</span> <span class="p">(</span><span class="nb">type</span><span class="p">(</span><span class="n">res_b</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span> <span class="ow">is</span> <span class="ow">not</span> <span class="n">unicode</span> <span class="ow">and</span> <span class="nb">type</span><span class="p">(</span><span class="n">res_b</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span> <span class="ow">is</span> <span class="ow">not</span> <span class="nb">str</span><span class="p">)</span> \
+                <span class="ow">or</span> <span class="n">typ</span> <span class="ow">not</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="vm">__dict__</span><span class="p">:</span>
+            <span class="n">sys</span><span class="o">.</span><span class="n">stdout</span><span class="o">.</span><span class="n">write</span><span class="p">(</span>
+                <span class="s1">&#39;</span><span class="se">\t</span><span class="s1">Wrong parameters for Interface.add_residues()</span><span class="se">\n</span><span class="s1">&#39;</span><span class="p">)</span>
+        <span class="k">else</span><span class="p">:</span>
+            <span class="bp">self</span><span class="o">.</span><span class="vm">__dict__</span><span class="p">[</span><span class="n">typ</span><span class="p">][</span><span class="bp">self</span><span class="o">.</span><span class="n">id_a</span><span class="p">]</span><span class="o">.</span><span class="n">append</span><span class="p">(</span>
+                <span class="n">Residue</span><span class="p">(</span><span class="n">res_a</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">res_a</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span> <span class="n">res_a</span><span class="p">[</span><span class="mi">2</span><span class="p">],</span> <span class="bp">self</span><span class="o">.</span><span class="n">id_type</span><span class="p">))</span>
+            <span class="bp">self</span><span class="o">.</span><span class="vm">__dict__</span><span class="p">[</span><span class="n">typ</span><span class="p">][</span><span class="bp">self</span><span class="o">.</span><span class="n">id_b</span><span class="p">]</span><span class="o">.</span><span class="n">append</span><span class="p">(</span>
+                <span class="n">Residue</span><span class="p">(</span><span class="n">res_b</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">res_b</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span> <span class="n">res_b</span><span class="p">[</span><span class="mi">2</span><span class="p">],</span> <span class="bp">self</span><span class="o">.</span><span class="n">id_type</span><span class="p">))</span></div>
+
+
+
+<div class="viewcode-block" id="Interface.numof_residues">
+<a class="viewcode-back" href="../../../api/pypath.internals.intera.Interface.html#pypath.internals.intera.Interface.numof_residues">[docs]</a>
+    <span class="k">def</span> <span class="nf">numof_residues</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&#39;&#39;&#39;</span>
+<span class="sd">        Returns the number of residue pairs by bound type</span>
+<span class="sd">        &#39;&#39;&#39;</span>
+
+        <span class="n">nbonds</span> <span class="o">=</span> <span class="p">{}</span>
+
+        <span class="k">for</span> <span class="n">t</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">types</span><span class="p">:</span>
+
+            <span class="n">nbonds</span><span class="p">[</span><span class="n">t</span><span class="p">]</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="vm">__dict__</span><span class="p">[</span><span class="n">t</span><span class="p">][</span><span class="bp">self</span><span class="o">.</span><span class="n">id_a</span><span class="p">])</span>
+
+        <span class="k">return</span> <span class="n">nbonds</span></div>
+
+
+
+<div class="viewcode-block" id="Interface.bond_types">
+<a class="viewcode-back" href="../../../api/pypath.internals.intera.Interface.html#pypath.internals.intera.Interface.bond_types">[docs]</a>
+    <span class="k">def</span> <span class="nf">bond_types</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&#39;&#39;&#39;</span>
+<span class="sd">        Returns the bond types present in this interface</span>
+<span class="sd">        &#39;&#39;&#39;</span>
+        <span class="n">types</span> <span class="o">=</span> <span class="p">[]</span>
+
+        <span class="k">for</span> <span class="n">t</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">types</span><span class="p">:</span>
+
+            <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="vm">__dict__</span><span class="p">[</span><span class="n">t</span><span class="p">][</span><span class="bp">self</span><span class="o">.</span><span class="n">id_a</span><span class="p">])</span> <span class="o">&gt;</span> <span class="mi">0</span><span class="p">:</span>
+
+                <span class="n">types</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">t</span><span class="p">)</span>
+
+        <span class="k">return</span> <span class="n">types</span></div>
+
+
+
+<div class="viewcode-block" id="Interface.get_bonds">
+<a class="viewcode-back" href="../../../api/pypath.internals.intera.Interface.html#pypath.internals.intera.Interface.get_bonds">[docs]</a>
+    <span class="k">def</span> <span class="nf">get_bonds</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">typ</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">mode</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&#39;&#39;&#39;</span>
+<span class="sd">        Gives a generator to iterate throught bonds in</span>
+<span class="sd">        this interface. If no type given, bonds of all types</span>
+<span class="sd">        returned.</span>
+<span class="sd">        &#39;&#39;&#39;</span>
+
+        <span class="k">if</span> <span class="n">typ</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
+
+            <span class="n">typ</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">types</span>
+
+        <span class="k">if</span> <span class="nb">type</span><span class="p">(</span><span class="n">typ</span><span class="p">)</span> <span class="ow">is</span> <span class="nb">str</span><span class="p">:</span>
+
+            <span class="n">typ</span> <span class="o">=</span> <span class="p">[</span><span class="n">typ</span><span class="p">]</span>
+
+        <span class="k">for</span> <span class="n">t</span> <span class="ow">in</span> <span class="n">typ</span><span class="p">:</span>
+
+            <span class="k">if</span> <span class="n">t</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="vm">__dict__</span><span class="p">:</span>
+
+                <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="vm">__dict__</span><span class="p">[</span><span class="n">t</span><span class="p">][</span><span class="bp">self</span><span class="o">.</span><span class="n">id_a</span><span class="p">])):</span>
+
+                    <span class="k">if</span> <span class="n">mode</span> <span class="o">==</span> <span class="s1">&#39;dict&#39;</span><span class="p">:</span>
+
+                        <span class="k">yield</span> <span class="p">{</span>
+                            <span class="bp">self</span><span class="o">.</span><span class="n">id_a</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="vm">__dict__</span><span class="p">[</span><span class="n">t</span><span class="p">][</span><span class="bp">self</span><span class="o">.</span><span class="n">id_a</span><span class="p">][</span><span class="n">i</span><span class="p">],</span>
+                            <span class="bp">self</span><span class="o">.</span><span class="n">id_b</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="vm">__dict__</span><span class="p">[</span><span class="n">t</span><span class="p">][</span><span class="bp">self</span><span class="o">.</span><span class="n">id_b</span><span class="p">][</span><span class="n">i</span><span class="p">],</span>
+                            <span class="s1">&#39;type&#39;</span><span class="p">:</span> <span class="n">t</span><span class="p">,</span>
+                        <span class="p">}</span>
+
+                    <span class="k">else</span><span class="p">:</span>
+
+                        <span class="k">yield</span> <span class="p">(</span>
+                            <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">id_a</span><span class="p">,)</span> <span class="o">+</span>
+                            <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="vm">__dict__</span><span class="p">[</span><span class="n">t</span><span class="p">][</span><span class="bp">self</span><span class="o">.</span><span class="n">id_a</span><span class="p">][</span><span class="n">i</span><span class="p">]</span><span class="o">.</span><span class="n">serialize</span><span class="p">(),)</span> <span class="o">+</span>
+                            <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">id_b</span><span class="p">,)</span> <span class="o">+</span>
+                            <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="vm">__dict__</span><span class="p">[</span><span class="n">t</span><span class="p">][</span><span class="bp">self</span><span class="o">.</span><span class="n">id_b</span><span class="p">][</span><span class="n">i</span><span class="p">]</span><span class="o">.</span><span class="n">serialize</span><span class="p">(),)</span> <span class="o">+</span>
+                            <span class="p">(</span><span class="n">t</span><span class="p">,)</span>
+                        <span class="p">)</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">serialize</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="n">res</span> <span class="o">=</span> <span class="p">[]</span>
+        <span class="k">for</span> <span class="n">t</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">types</span><span class="p">:</span>
+
+            <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="vm">__dict__</span><span class="p">[</span><span class="n">t</span><span class="p">][</span><span class="bp">self</span><span class="o">.</span><span class="n">id_a</span><span class="p">]</span> <span class="ow">and</span> <span class="bp">self</span><span class="o">.</span><span class="vm">__dict__</span><span class="p">[</span><span class="n">t</span><span class="p">][</span><span class="bp">self</span><span class="o">.</span><span class="n">id_b</span><span class="p">]:</span>
+
+                <span class="n">res</span><span class="o">.</span><span class="n">append</span><span class="p">(</span>
+                    <span class="s1">&#39;</span><span class="si">%s</span><span class="s1">:</span><span class="si">%s</span><span class="s1">+</span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="p">(</span>
+                        <span class="n">t</span><span class="p">,</span>
+                        <span class="s1">&#39;,&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="vm">__dict__</span><span class="p">[</span><span class="n">t</span><span class="p">][</span><span class="bp">self</span><span class="o">.</span><span class="n">id_a</span><span class="p">]</span><span class="o">.</span><span class="n">serialize</span><span class="p">()),</span>
+                        <span class="s1">&#39;,&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="vm">__dict__</span><span class="p">[</span><span class="n">t</span><span class="p">][</span><span class="bp">self</span><span class="o">.</span><span class="n">id_b</span><span class="p">]</span><span class="o">.</span><span class="n">serialize</span><span class="p">()),</span>
+                    <span class="p">)</span>
+                <span class="p">)</span>
+
+        <span class="k">return</span> <span class="p">(</span>
+            <span class="s1">&#39;</span><span class="si">%s</span><span class="s1">-</span><span class="si">%u</span><span class="s1">:</span><span class="si">%s</span><span class="s1">-</span><span class="si">%u</span><span class="s1">:</span><span class="si">%s</span><span class="s1">:</span><span class="si">%s</span><span class="s1">:</span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="p">(</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">id_a</span><span class="p">,</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">isoform_a</span><span class="p">,</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">id_b</span><span class="p">,</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">isoform_b</span><span class="p">,</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">source</span><span class="p">,</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">pdb</span><span class="p">,</span>
+                <span class="s1">&#39;:&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">res</span><span class="p">),</span>
+            <span class="p">)</span>
+        <span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="fm">__str__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="n">nbonds</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">numof_residues</span><span class="p">()</span>
+
+        <span class="k">return</span> <span class="p">(</span>
+            <span class="s1">&#39;Molecular interface between </span><span class="si">%s</span><span class="s1"> and </span><span class="si">%s</span><span class="s1">,</span><span class="se">\n</span><span class="s1">&#39;</span>
+            <span class="s1">&#39;as observed in PDB structure </span><span class="si">%s</span><span class="se">\n\n</span><span class="s1">&#39;</span>
+            <span class="s1">&#39; Data source: </span><span class="si">%s</span><span class="se">\n</span><span class="s1">&#39;</span>
+            <span class="s1">&#39; Number of residues in contact: </span><span class="si">%u</span><span class="se">\n</span><span class="s1">&#39;</span>
+            <span class="s1">&#39; Hydrogene bonds: </span><span class="si">%u</span><span class="se">\n</span><span class="s1">&#39;</span>
+            <span class="s1">&#39; Covalent bonds: </span><span class="si">%u</span><span class="se">\n</span><span class="s1">&#39;</span>
+            <span class="s1">&#39; Saltbridges: </span><span class="si">%u</span><span class="se">\n</span><span class="s1">&#39;</span>
+            <span class="s1">&#39; S-S bonds: </span><span class="si">%u</span><span class="se">\n</span><span class="s1">&#39;</span>
+            <span class="s1">&#39; Stable energy: </span><span class="si">%s</span><span class="se">\n</span><span class="s1">&#39;</span>
+            <span class="s1">&#39; Solvation energy: </span><span class="si">%s</span><span class="se">\n</span><span class="s1">&#39;</span>
+            <span class="s1">&#39; Surface area: </span><span class="si">%s</span><span class="se">\n</span><span class="s1">&#39;</span>
+            <span class="s1">&#39; Complexation significance score: </span><span class="si">%s</span><span class="se">\n</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="p">(</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">id_a</span><span class="p">,</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">id_b</span><span class="p">,</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">pdb</span><span class="p">,</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">source</span><span class="p">,</span>
+                <span class="nb">sum</span><span class="p">(</span><span class="n">nbonds</span><span class="o">.</span><span class="n">values</span><span class="p">()),</span>
+                <span class="n">nbonds</span><span class="p">[</span><span class="s1">&#39;hbonds&#39;</span><span class="p">],</span>
+                <span class="n">nbonds</span><span class="p">[</span><span class="s1">&#39;covbonds&#39;</span><span class="p">],</span>
+                <span class="n">nbonds</span><span class="p">[</span><span class="s1">&#39;sbridges&#39;</span><span class="p">],</span>
+                <span class="n">nbonds</span><span class="p">[</span><span class="s1">&#39;ssbonds&#39;</span><span class="p">],</span>
+                <span class="s1">&#39;n/a&#39;</span> <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">stab_en</span> <span class="ow">is</span> <span class="kc">None</span> <span class="k">else</span> <span class="nb">str</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">stab_en</span><span class="p">),</span>
+                <span class="s1">&#39;n/a&#39;</span> <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">solv_en</span> <span class="ow">is</span> <span class="kc">None</span> <span class="k">else</span> <span class="nb">str</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">solv_en</span><span class="p">),</span>
+                <span class="s1">&#39;n/a&#39;</span> <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">area</span> <span class="ow">is</span> <span class="kc">None</span> <span class="k">else</span> <span class="nb">str</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">area</span><span class="p">),</span>
+                <span class="s1">&#39;n/a&#39;</span> <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">css</span> <span class="ow">is</span> <span class="kc">None</span> <span class="k">else</span> <span class="nb">str</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">css</span><span class="p">),</span>
+            <span class="p">)</span>
+        <span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="fm">__repr__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="n">nbonds</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">numof_residues</span><span class="p">()</span>
+
+        <span class="k">return</span> <span class="p">(</span>
+            <span class="s1">&#39;Interface [</span><span class="si">%s</span><span class="s1">-</span><span class="si">%s</span><span class="s1">, </span><span class="si">%u</span><span class="s1"> bonds]&#39;</span> <span class="o">%</span> <span class="p">(</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">id_a</span><span class="p">,</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">id_b</span><span class="p">,</span>
+                <span class="nb">sum</span><span class="p">(</span><span class="n">nbonds</span><span class="o">.</span><span class="n">values</span><span class="p">()),</span>
+            <span class="p">)</span>
+        <span class="p">)</span></div>
+
+</pre></div>
+
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+                  
+  <h1>Source code for pypath.omnipath</h1><div class="highlight"><pre>
+<span></span><span class="ch">#!/usr/bin/env python</span>
+<span class="c1"># -*- coding: utf-8 -*-</span>
+
+<span class="c1">#</span>
+<span class="c1">#  This file is part of the `pypath` python module</span>
+<span class="c1">#</span>
+<span class="c1">#  Copyright 2014-2023</span>
+<span class="c1">#  EMBL, EMBL-EBI, Uniklinik RWTH Aachen, Heidelberg University</span>
+<span class="c1">#</span>
+<span class="c1">#  Authors: see the file `README.rst`</span>
+<span class="c1">#  Contact: Dénes Türei (turei.denes@gmail.com)</span>
+<span class="c1">#</span>
+<span class="c1">#  Distributed under the GPLv3 License.</span>
+<span class="c1">#  See accompanying file LICENSE.txt or copy at</span>
+<span class="c1">#      https://www.gnu.org/licenses/gpl-3.0.html</span>
+<span class="c1">#</span>
+<span class="c1">#  Website: https://pypath.omnipathdb.org/</span>
+<span class="c1">#</span>
+
+<span class="kn">import</span> <span class="nn">os</span>
+<span class="kn">import</span> <span class="nn">copy</span>
+
+<span class="kn">from</span> <span class="nn">pypath.share</span> <span class="kn">import</span> <span class="n">session</span> <span class="k">as</span> <span class="n">_session_mod</span>
+<span class="kn">from</span> <span class="nn">pypath.share</span> <span class="kn">import</span> <span class="n">settings</span> <span class="k">as</span> <span class="n">_settings_mod</span>
+<span class="kn">from</span> <span class="nn">pypath.omnipath</span> <span class="kn">import</span> <span class="n">app</span> <span class="k">as</span> <span class="n">_app_mod</span>
+
+
+<span class="n">_logger</span> <span class="o">=</span> <span class="n">_session_mod</span><span class="o">.</span><span class="n">Logger</span><span class="p">(</span><span class="n">name</span> <span class="o">=</span> <span class="s1">&#39;omnipath.init&#39;</span><span class="p">)</span>
+<span class="n">_log</span> <span class="o">=</span> <span class="n">_logger</span><span class="o">.</span><span class="n">_log</span>
+
+
+<span class="n">_log</span><span class="p">(</span><span class="s1">&#39;Welcome to the OmniPath database manager app.&#39;</span><span class="p">)</span>
+
+
+<div class="viewcode-block" id="init">
+<a class="viewcode-back" href="../../api/pypath.omnipath.init.html#pypath.omnipath.init">[docs]</a>
+<span class="k">def</span> <span class="nf">init</span><span class="p">(</span><span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+
+    <span class="n">param</span> <span class="o">=</span> <span class="p">(</span>
+        <span class="n">copy</span><span class="o">.</span><span class="n">deepcopy</span><span class="p">(</span><span class="nb">globals</span><span class="p">()[</span><span class="s1">&#39;OP_DB_ARGS&#39;</span><span class="p">])</span>
+            <span class="k">if</span> <span class="s1">&#39;OP_DB_ARGS&#39;</span> <span class="ow">in</span> <span class="nb">globals</span><span class="p">()</span> <span class="k">else</span>
+        <span class="p">{}</span>
+    <span class="p">)</span>
+
+    <span class="n">_log</span><span class="p">(</span>
+        <span class="s1">&#39;You can customize the database building process by &#39;</span>
+        <span class="s1">&#39;setting parameters in the `OP_DB_ARGS` global variable &#39;</span>
+        <span class="s1">&#39;or by calling `init` again with keyword arguments or after &#39;</span>
+        <span class="s1">&#39;setting values in the `pypath.share.settings` module.&#39;</span>
+        <span class="s1">&#39;You can define your own databases following the examples in &#39;</span>
+        <span class="s1">&#39;`pypath/omnipath/databases/builtins.json`. &#39;</span>
+        <span class="s1">&#39;See more details in `pypath/omnipath/databases/db_template.json` &#39;</span>
+        <span class="s1">&#39;and the code of method &#39;</span>
+        <span class="s1">&#39;`pypath.omnipath.app.DatabaseManager.load_dataset`.&#39;</span>
+    <span class="p">)</span>
+
+    <span class="n">param</span><span class="o">.</span><span class="n">update</span><span class="p">(</span><span class="n">kwargs</span><span class="p">)</span>
+
+    <span class="nb">globals</span><span class="p">()[</span><span class="s1">&#39;db&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">_app_mod</span><span class="o">.</span><span class="n">DatabaseManager</span><span class="p">(</span><span class="o">**</span><span class="n">param</span><span class="p">)</span></div>
+
+
+
+<span class="n">init</span><span class="p">()</span>
+</pre></div>
+
+                </article>
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diff --git a/_modules/pypath/omnipath/app.html b/_modules/pypath/omnipath/app.html
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+  
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+                      </a>
+                    </li>
+                
+
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+                      <a class="nav-link nav-internal" href="../../../webservice.html">
+                        Webservice
+                      </a>
+                    </li>
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+                      <a class="nav-link nav-internal" href="../../../releasehistory.html">
+                        Release history
+                      </a>
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+                        Reference
+                      </a>
+                    </li>
+                
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+                    <li class="nav-item">
+                      <a class="nav-link nav-internal" href="../../../notebooks/manual.html">
+                        The pypath book
+                      </a>
+                    </li>
+                
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+</nav></div>
+      
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+    
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+          
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+          
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+    
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+                      </a>
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+                      <a class="nav-link nav-internal" href="../../../webservice.html">
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+  </button>
+`);
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+    aria-label="Icon Links">
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+            <span class="sr-only">GitHub</span></a>
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+    <li class="breadcrumb-item"><a href="../omnipath.html" class="nav-link">pypath.omnipath</a></li>
+    
+    <li class="breadcrumb-item active" aria-current="page">pypath.omnipath.app</li>
+  </ul>
+</nav>
+</div>
+      
+    </div>
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+</div>
+</div>
+              
+              
+              
+                
+<div id="searchbox"></div>
+                <article class="bd-article">
+                  
+  <h1>Source code for pypath.omnipath.app</h1><div class="highlight"><pre>
+<span></span><span class="ch">#!/usr/bin/env python</span>
+<span class="c1"># -*- coding: utf-8 -*-</span>
+
+<span class="c1">#</span>
+<span class="c1">#  This file is part of the `pypath` python module</span>
+<span class="c1">#</span>
+<span class="c1">#  Copyright 2014-2023</span>
+<span class="c1">#  EMBL, EMBL-EBI, Uniklinik RWTH Aachen, Heidelberg University</span>
+<span class="c1">#</span>
+<span class="c1">#  Authors: see the file `README.rst`</span>
+<span class="c1">#  Contact: Dénes Türei (turei.denes@gmail.com)</span>
+<span class="c1">#</span>
+<span class="c1">#  Distributed under the GPLv3 License.</span>
+<span class="c1">#  See accompanying file LICENSE.txt or copy at</span>
+<span class="c1">#      https://www.gnu.org/licenses/gpl-3.0.html</span>
+<span class="c1">#</span>
+<span class="c1">#  Website: https://pypath.omnipathdb.org/</span>
+<span class="c1">#</span>
+
+<span class="kn">from</span> <span class="nn">__future__</span> <span class="kn">import</span> <span class="n">annotations</span>
+
+<span class="kn">from</span> <span class="nn">typing</span> <span class="kn">import</span> <span class="n">Literal</span>
+
+<span class="kn">import</span> <span class="nn">os</span>
+<span class="kn">import</span> <span class="nn">sys</span>
+<span class="kn">import</span> <span class="nn">shutil</span>
+<span class="kn">import</span> <span class="nn">importlib</span> <span class="k">as</span> <span class="nn">imp</span>
+<span class="kn">import</span> <span class="nn">time</span>
+<span class="kn">import</span> <span class="nn">pprint</span>
+<span class="kn">import</span> <span class="nn">copy</span>
+<span class="kn">import</span> <span class="nn">collections</span>
+<span class="kn">import</span> <span class="nn">itertools</span>
+
+<span class="kn">import</span> <span class="nn">pypath.resources.network</span> <span class="k">as</span> <span class="nn">netres</span>
+<span class="kn">from</span> <span class="nn">pypath.core</span> <span class="kn">import</span> <span class="n">annot</span>
+<span class="kn">from</span> <span class="nn">pypath.core</span> <span class="kn">import</span> <span class="n">intercell</span>
+<span class="kn">from</span> <span class="nn">pypath.core</span> <span class="kn">import</span> <span class="nb">complex</span>
+<span class="kn">from</span> <span class="nn">pypath.core</span> <span class="kn">import</span> <span class="n">enz_sub</span>
+<span class="kn">from</span> <span class="nn">pypath.core</span> <span class="kn">import</span> <span class="n">network</span>
+<span class="kn">from</span> <span class="nn">pypath.share</span> <span class="kn">import</span> <span class="n">session</span> <span class="k">as</span> <span class="n">session_mod</span>
+
+<span class="kn">import</span> <span class="nn">pypath.share.settings</span> <span class="k">as</span> <span class="nn">settings</span>
+<span class="kn">import</span> <span class="nn">pypath.share.common</span> <span class="k">as</span> <span class="nn">common</span>
+
+
+<div class="viewcode-block" id="DatabaseManager">
+<a class="viewcode-back" href="../../../api/pypath.omnipath.app.DatabaseManager.html#pypath.omnipath.app.DatabaseManager">[docs]</a>
+<span class="k">class</span> <span class="nc">DatabaseManager</span><span class="p">(</span><span class="n">session_mod</span><span class="o">.</span><span class="n">Logger</span><span class="p">):</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Builds and serves the databases in OmniPath such as various networks,</span>
+<span class="sd">    enzyme-substrate interactions, protein complexes, annotations and</span>
+<span class="sd">    inter-cellular communication roles. Saves the databases to and loads</span>
+<span class="sd">    them from pickle dumps on demand.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+
+<div class="viewcode-block" id="DatabaseManager.__init__">
+<a class="viewcode-back" href="../../../api/pypath.omnipath.app.DatabaseManager.html#pypath.omnipath.app.DatabaseManager.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">rebuild</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+
+        <span class="n">session_mod</span><span class="o">.</span><span class="n">Logger</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">name</span> <span class="o">=</span> <span class="s1">&#39;omnipath.dbmanager&#39;</span><span class="p">)</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">timestamp</span> <span class="o">=</span> <span class="n">time</span><span class="o">.</span><span class="n">strftime</span><span class="p">(</span><span class="n">settings</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">&#39;timestamp_format&#39;</span><span class="p">))</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">param</span> <span class="o">=</span> <span class="n">kwargs</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">rebuild</span> <span class="o">=</span> <span class="n">rebuild</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">datasets</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">get_param</span><span class="p">(</span><span class="s1">&#39;datasets&#39;</span><span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">ensure_dirs</span><span class="p">()</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">network_dfs</span> <span class="o">=</span> <span class="p">{}</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span><span class="s1">&#39;The OmniPath database manager has been initialized.&#39;</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="DatabaseManager.reload">
+<a class="viewcode-back" href="../../../api/pypath.omnipath.app.DatabaseManager.html#pypath.omnipath.app.DatabaseManager.reload">[docs]</a>
+    <span class="k">def</span> <span class="nf">reload</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Reloads the object from the module level.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">modname</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="vm">__class__</span><span class="o">.</span><span class="vm">__module__</span>
+        <span class="n">mod</span> <span class="o">=</span> <span class="nb">__import__</span><span class="p">(</span><span class="n">modname</span><span class="p">,</span> <span class="n">fromlist</span> <span class="o">=</span> <span class="p">[</span><span class="n">modname</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;.&#39;</span><span class="p">)[</span><span class="mi">0</span><span class="p">]])</span>
+        <span class="n">imp</span><span class="o">.</span><span class="n">reload</span><span class="p">(</span><span class="n">mod</span><span class="p">)</span>
+        <span class="n">new</span> <span class="o">=</span> <span class="nb">getattr</span><span class="p">(</span><span class="n">mod</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="vm">__class__</span><span class="o">.</span><span class="vm">__name__</span><span class="p">)</span>
+        <span class="nb">setattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">&#39;__class__&#39;</span><span class="p">,</span> <span class="n">new</span><span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">foreach_dataset</span><span class="p">(</span><span class="n">method</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">reload_module</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="DatabaseManager.build">
+<a class="viewcode-back" href="../../../api/pypath.omnipath.app.DatabaseManager.html#pypath.omnipath.app.DatabaseManager.build">[docs]</a>
+    <span class="k">def</span> <span class="nf">build</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Builds all built-in datasets.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span>
+            <span class="s1">&#39;Building databases. Rebuild forced: </span><span class="si">%s</span><span class="s1">.&#39;</span> <span class="o">%</span> <span class="nb">str</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">rebuild</span><span class="p">)</span>
+        <span class="p">)</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">foreach_dataset</span><span class="p">(</span><span class="n">method</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">ensure_dataset</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="DatabaseManager.ensure_dataset">
+<a class="viewcode-back" href="../../../api/pypath.omnipath.app.DatabaseManager.html#pypath.omnipath.app.DatabaseManager.ensure_dataset">[docs]</a>
+    <span class="k">def</span> <span class="nf">ensure_dataset</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">dataset</span><span class="p">,</span>
+            <span class="n">force_reload</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+            <span class="n">force_rebuild</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+            <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">,</span>
+        <span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Makes sure a dataset is loaded. It loads only if it&#39;s not loaded</span>
+<span class="sd">        yet or :py:arg:`force_reload` is ``True``. It only builds if it&#39;s</span>
+<span class="sd">        not availabe as a pickle dump or :py:arg:`force_rebuild` is ``True``.</span>
+
+<span class="sd">        :arg str dataset:</span>
+<span class="sd">            The name of the dataset.</span>
+<span class="sd">        :arg int ncbi_tax_id:</span>
+<span class="sd">            NCBI Taxonomy ID of the organism. Considered only if the dataset</span>
+<span class="sd">            builds for one organism and saved to organism specific pickle</span>
+<span class="sd">            files.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">for</span> <span class="n">dep_dataset</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">dataset_dependencies</span><span class="p">(</span><span class="n">dataset</span><span class="p">):</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">ensure_dataset</span><span class="p">(</span><span class="n">dep_dataset</span><span class="p">)</span>
+
+        <span class="n">rebuild_dataset</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">get_param</span><span class="p">(</span><span class="s1">&#39;rebuild_</span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="n">dataset</span><span class="p">)</span>
+
+        <span class="n">_dataset</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_dataset_taxid</span><span class="p">(</span><span class="n">dataset</span><span class="p">,</span> <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">)</span>
+
+        <span class="k">if</span> <span class="p">(</span>
+            <span class="n">force_reload</span> <span class="ow">or</span>
+            <span class="n">force_rebuild</span> <span class="ow">or</span>
+            <span class="ow">not</span> <span class="nb">hasattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">_dataset</span><span class="p">)</span>
+        <span class="p">):</span>
+
+            <span class="k">if</span> <span class="p">(</span>
+                <span class="n">force_rebuild</span> <span class="ow">or</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">rebuild</span> <span class="ow">or</span>
+                <span class="n">rebuild_dataset</span> <span class="ow">or</span>
+                <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">pickle_exists</span><span class="p">(</span><span class="n">dataset</span><span class="p">,</span> <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">)</span>
+            <span class="p">):</span>
+
+                <span class="bp">self</span><span class="o">.</span><span class="n">remove_db</span><span class="p">(</span><span class="n">dataset</span><span class="p">,</span> <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">)</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">build_dataset</span><span class="p">(</span><span class="n">dataset</span><span class="p">,</span> <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">)</span>
+
+            <span class="k">elif</span> <span class="p">(</span>
+                <span class="ow">not</span> <span class="nb">hasattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">_dataset</span><span class="p">)</span> <span class="ow">or</span>
+                <span class="n">force_reload</span>
+            <span class="p">):</span>
+
+                <span class="bp">self</span><span class="o">.</span><span class="n">load_dataset</span><span class="p">(</span><span class="n">dataset</span><span class="p">,</span> <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="DatabaseManager.dataset_dependencies">
+<a class="viewcode-back" href="../../../api/pypath.omnipath.app.DatabaseManager.html#pypath.omnipath.app.DatabaseManager.dataset_dependencies">[docs]</a>
+    <span class="k">def</span> <span class="nf">dataset_dependencies</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">dataset</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Returns the dependencies of a dataset. E.g. to build `annotations`</span>
+<span class="sd">        `complexes` must be loaded hence the former is dependent on the</span>
+<span class="sd">        latter.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">deps</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">get_param</span><span class="p">(</span><span class="s1">&#39;dependencies&#39;</span><span class="p">)</span>
+
+        <span class="k">return</span> <span class="n">deps</span><span class="p">[</span><span class="n">dataset</span><span class="p">]</span> <span class="k">if</span> <span class="n">dataset</span> <span class="ow">in</span> <span class="n">deps</span> <span class="k">else</span> <span class="p">()</span></div>
+
+
+
+<div class="viewcode-block" id="DatabaseManager.ensure_dirs">
+<a class="viewcode-back" href="../../../api/pypath.omnipath.app.DatabaseManager.html#pypath.omnipath.app.DatabaseManager.ensure_dirs">[docs]</a>
+    <span class="k">def</span> <span class="nf">ensure_dirs</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Checks if the directories for tables, figures and pickles exist and</span>
+<span class="sd">        creates them if necessary.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">get_param</span><span class="p">(</span><span class="s1">&#39;timestamp_dirs&#39;</span><span class="p">):</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">tables_dir</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">get_param</span><span class="p">(</span><span class="s1">&#39;tables_dir&#39;</span><span class="p">),</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">timestamp</span>
+            <span class="p">)</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">figures_dir</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">get_param</span><span class="p">(</span><span class="s1">&#39;figures_dir&#39;</span><span class="p">),</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">timestamp</span><span class="p">,</span>
+            <span class="p">)</span>
+            <span class="n">settings</span><span class="o">.</span><span class="n">setup</span><span class="p">(</span>
+                <span class="n">tables_dir</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">tables_dir</span><span class="p">,</span>
+                <span class="n">figures_dir</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">figures_dir</span><span class="p">,</span>
+            <span class="p">)</span>
+
+        <span class="n">os</span><span class="o">.</span><span class="n">makedirs</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">get_param</span><span class="p">(</span><span class="s1">&#39;pickle_dir&#39;</span><span class="p">),</span> <span class="n">exist_ok</span> <span class="o">=</span> <span class="kc">True</span><span class="p">)</span>
+
+        <span class="k">for</span> <span class="n">_dir</span> <span class="ow">in</span> <span class="p">(</span><span class="s1">&#39;pickle&#39;</span><span class="p">,</span> <span class="s1">&#39;tables&#39;</span><span class="p">,</span> <span class="s1">&#39;figures&#39;</span><span class="p">):</span>
+
+            <span class="n">path</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">get_param</span><span class="p">(</span><span class="s1">&#39;</span><span class="si">%s</span><span class="s1">_dir&#39;</span> <span class="o">%</span> <span class="n">_dir</span><span class="p">)</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span>
+                <span class="s1">&#39;</span><span class="si">%s</span><span class="s1"> directory: `</span><span class="si">%s</span><span class="s1">` (exists: </span><span class="si">%s</span><span class="s1">).&#39;</span> <span class="o">%</span> <span class="p">(</span>
+                    <span class="n">_dir</span><span class="o">.</span><span class="n">capitalize</span><span class="p">(),</span>
+                    <span class="n">path</span><span class="p">,</span>
+                    <span class="s1">&#39;yes&#39;</span> <span class="k">if</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">exists</span><span class="p">(</span><span class="n">path</span><span class="p">)</span> <span class="k">else</span> <span class="s1">&#39;no&#39;</span><span class="p">,</span>
+                <span class="p">)</span>
+            <span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="DatabaseManager.pickle_path">
+<a class="viewcode-back" href="../../../api/pypath.omnipath.app.DatabaseManager.html#pypath.omnipath.app.DatabaseManager.pickle_path">[docs]</a>
+    <span class="k">def</span> <span class="nf">pickle_path</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">dataset</span><span class="p">,</span> <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Returns the path of the pickle dump for a dataset according to</span>
+<span class="sd">        the current settings.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">pickle_fname</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">get_param</span><span class="p">(</span><span class="s1">&#39;</span><span class="si">%s</span><span class="s1">_pickle&#39;</span> <span class="o">%</span> <span class="n">dataset</span><span class="p">)</span> <span class="ow">or</span>
+            <span class="s1">&#39;</span><span class="si">%s</span><span class="s1">.pickle&#39;</span> <span class="o">%</span> <span class="n">dataset</span>
+        <span class="p">)</span>
+
+        <span class="k">if</span> <span class="n">dataset</span> <span class="o">==</span> <span class="s1">&#39;enz_sub&#39;</span><span class="p">:</span>
+
+            <span class="n">pickle_fname</span> <span class="o">=</span> <span class="n">pickle_fname</span> <span class="o">%</span> <span class="n">ncbi_tax_id</span>
+
+        <span class="k">return</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">get_param</span><span class="p">(</span><span class="s1">&#39;pickle_dir&#39;</span><span class="p">),</span>
+            <span class="n">pickle_fname</span><span class="p">,</span>
+        <span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="DatabaseManager.pickle_exists">
+<a class="viewcode-back" href="../../../api/pypath.omnipath.app.DatabaseManager.html#pypath.omnipath.app.DatabaseManager.pickle_exists">[docs]</a>
+    <span class="k">def</span> <span class="nf">pickle_exists</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">dataset</span><span class="p">,</span> <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Tells if a pickle dump of a particular dataset exists.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">return</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">exists</span><span class="p">(</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">pickle_path</span><span class="p">(</span><span class="n">dataset</span><span class="p">,</span> <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">)</span>
+        <span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="DatabaseManager.table_path">
+<a class="viewcode-back" href="../../../api/pypath.omnipath.app.DatabaseManager.html#pypath.omnipath.app.DatabaseManager.table_path">[docs]</a>
+    <span class="k">def</span> <span class="nf">table_path</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">dataset</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Returns the full path for a table (to be exported or imported).</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">return</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">get_param</span><span class="p">(</span><span class="s1">&#39;tables_dir&#39;</span><span class="p">),</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">get_param</span><span class="p">(</span><span class="s1">&#39;</span><span class="si">%s</span><span class="s1">_tsv&#39;</span> <span class="o">%</span> <span class="n">dataset</span><span class="p">),</span>
+        <span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="DatabaseManager.build_dataset">
+<a class="viewcode-back" href="../../../api/pypath.omnipath.app.DatabaseManager.html#pypath.omnipath.app.DatabaseManager.build_dataset">[docs]</a>
+    <span class="k">def</span> <span class="nf">build_dataset</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">dataset</span><span class="p">,</span> <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Builds a dataset.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span><span class="s1">&#39;Building dataset `</span><span class="si">%s</span><span class="s1">`.&#39;</span> <span class="o">%</span> <span class="n">dataset</span><span class="p">)</span>
+
+        <span class="n">args</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">get_build_args</span><span class="p">(</span><span class="n">dataset</span><span class="p">)</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span><span class="s1">&#39;Build param: [</span><span class="si">%s</span><span class="s1">].&#39;</span> <span class="o">%</span> <span class="n">common</span><span class="o">.</span><span class="n">dict_str</span><span class="p">(</span><span class="n">args</span><span class="p">))</span>
+
+        <span class="n">mod</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">ensure_module</span><span class="p">(</span><span class="n">dataset</span><span class="p">)</span>
+
+        <span class="k">if</span> <span class="n">dataset</span> <span class="o">==</span> <span class="s1">&#39;enz_sub&#39;</span><span class="p">:</span>
+
+            <span class="n">args</span><span class="p">[</span><span class="s1">&#39;ncbi_tax_id&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span>
+
+        <span class="k">if</span> <span class="nb">hasattr</span><span class="p">(</span><span class="n">mod</span><span class="p">,</span> <span class="s1">&#39;db&#39;</span><span class="p">):</span>
+
+            <span class="nb">delattr</span><span class="p">(</span><span class="n">mod</span><span class="p">,</span> <span class="s1">&#39;db&#39;</span><span class="p">)</span>
+
+        <span class="n">db</span> <span class="o">=</span> <span class="n">mod</span><span class="o">.</span><span class="n">get_db</span><span class="p">(</span><span class="o">**</span><span class="n">args</span><span class="p">)</span>
+
+        <span class="n">pickle_path</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">pickle_path</span><span class="p">(</span><span class="n">dataset</span><span class="p">,</span> <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">)</span>
+
+        <span class="n">old_pickle_path</span> <span class="o">=</span> <span class="s1">&#39;</span><span class="si">%s</span><span class="s1">.old&#39;</span> <span class="o">%</span> <span class="n">pickle_path</span>
+
+        <span class="k">if</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">exists</span><span class="p">(</span><span class="n">pickle_path</span><span class="p">):</span>
+
+            <span class="n">shutil</span><span class="o">.</span><span class="n">move</span><span class="p">(</span><span class="n">pickle_path</span><span class="p">,</span> <span class="n">old_pickle_path</span><span class="p">)</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span><span class="s1">&#39;Saving dataset `</span><span class="si">%s</span><span class="s1">` to `</span><span class="si">%s</span><span class="s1">`.&#39;</span> <span class="o">%</span> <span class="p">(</span><span class="n">dataset</span><span class="p">,</span> <span class="n">pickle_path</span><span class="p">))</span>
+
+        <span class="k">try</span><span class="p">:</span>
+            <span class="n">db</span><span class="o">.</span><span class="n">save_to_pickle</span><span class="p">(</span><span class="n">pickle_file</span> <span class="o">=</span> <span class="n">pickle_path</span><span class="p">)</span>
+
+            <span class="k">if</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">exists</span><span class="p">(</span><span class="n">old_pickle_path</span><span class="p">):</span>
+
+                <span class="n">os</span><span class="o">.</span><span class="n">remove</span><span class="p">(</span><span class="n">old_pickle_path</span><span class="p">)</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span>
+                <span class="s1">&#39;Saved dataset `</span><span class="si">%s</span><span class="s1">` to `</span><span class="si">%s</span><span class="s1">`.&#39;</span> <span class="o">%</span> <span class="p">(</span>
+                    <span class="n">dataset</span><span class="p">,</span>
+                    <span class="n">pickle_path</span>
+                <span class="p">)</span>
+            <span class="p">)</span>
+
+        <span class="k">except</span> <span class="ne">Exception</span> <span class="k">as</span> <span class="n">e</span><span class="p">:</span>
+
+            <span class="n">exc</span> <span class="o">=</span> <span class="n">sys</span><span class="o">.</span><span class="n">exc_info</span><span class="p">()</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">_log_traceback</span><span class="p">()</span>
+            <span class="n">os</span><span class="o">.</span><span class="n">remove</span><span class="p">(</span><span class="n">pickle_path</span><span class="p">)</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span>
+                <span class="s1">&#39;Failed to save dataset `</span><span class="si">%s</span><span class="s1">` to `</span><span class="si">%s</span><span class="s1">`. &#39;</span>
+                <span class="s1">&#39;The dataset is currently loaded. &#39;</span>
+                <span class="s1">&#39;Try restart Python and re-build the dataset. &#39;</span>
+                <span class="s1">&#39;If the issue persists please report it.&#39;</span> <span class="o">%</span> <span class="p">(</span>
+                    <span class="n">dataset</span><span class="p">,</span>
+                    <span class="n">pickle_path</span><span class="p">,</span>
+                <span class="p">)</span>
+            <span class="p">)</span>
+
+            <span class="k">if</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">exists</span><span class="p">(</span><span class="n">old_pickle_path</span><span class="p">):</span>
+
+                <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span><span class="s1">&#39;Restoring the old version of `</span><span class="si">%s</span><span class="s1">`.&#39;</span> <span class="o">%</span> <span class="n">pickle_path</span><span class="p">)</span>
+                <span class="n">shutil</span><span class="o">.</span><span class="n">move</span><span class="p">(</span><span class="n">old_pickle_path</span><span class="p">,</span> <span class="n">pickle_path</span><span class="p">)</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span><span class="s1">&#39;Successfully built dataset `</span><span class="si">%s</span><span class="s1">`.&#39;</span> <span class="o">%</span> <span class="n">dataset</span><span class="p">)</span>
+
+        <span class="n">_dataset</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_dataset_taxid</span><span class="p">(</span><span class="n">dataset</span><span class="p">,</span> <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">)</span>
+
+        <span class="nb">setattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">_dataset</span><span class="p">,</span> <span class="n">db</span><span class="p">)</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_add_network_df</span><span class="p">(</span><span class="n">dataset</span><span class="p">,</span> <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="DatabaseManager.ensure_module">
+<a class="viewcode-back" href="../../../api/pypath.omnipath.app.DatabaseManager.html#pypath.omnipath.app.DatabaseManager.ensure_module">[docs]</a>
+    <span class="k">def</span> <span class="nf">ensure_module</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">dataset</span><span class="p">,</span> <span class="n">reset</span> <span class="o">=</span> <span class="kc">True</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Makes sure the module providing a particular dataset is available</span>
+<span class="sd">        and has no default database loaded yet (:py:attr:`db` attribute</span>
+<span class="sd">        of the module).</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">mod_str</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">get_param</span><span class="p">(</span><span class="s1">&#39;</span><span class="si">%s</span><span class="s1">_mod&#39;</span> <span class="o">%</span> <span class="n">dataset</span><span class="p">)</span>
+        <span class="n">mod</span> <span class="o">=</span> <span class="n">sys</span><span class="o">.</span><span class="n">modules</span><span class="p">[</span><span class="s1">&#39;pypath.core.</span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="n">mod_str</span><span class="p">]</span>
+
+        <span class="k">if</span> <span class="n">reset</span> <span class="ow">and</span> <span class="nb">hasattr</span><span class="p">(</span><span class="n">mod</span><span class="p">,</span> <span class="s1">&#39;db&#39;</span><span class="p">):</span>
+
+            <span class="nb">delattr</span><span class="p">(</span><span class="n">mod</span><span class="p">,</span> <span class="s1">&#39;db&#39;</span><span class="p">)</span>
+
+        <span class="k">return</span> <span class="n">mod</span></div>
+
+
+
+<div class="viewcode-block" id="DatabaseManager.reload_module">
+<a class="viewcode-back" href="../../../api/pypath.omnipath.app.DatabaseManager.html#pypath.omnipath.app.DatabaseManager.reload_module">[docs]</a>
+    <span class="k">def</span> <span class="nf">reload_module</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">dataset</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Reloads the module of the database object of a particular dataset.</span>
+<span class="sd">        E.g. in case of network datasets the ``pypath.network`` module</span>
+<span class="sd">        will be reloaded.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">mod</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">ensure_module</span><span class="p">(</span><span class="n">dataset</span><span class="p">,</span> <span class="n">reset</span> <span class="o">=</span> <span class="kc">False</span><span class="p">)</span>
+        <span class="n">imp</span><span class="o">.</span><span class="n">reload</span><span class="p">(</span><span class="n">mod</span><span class="p">)</span>
+
+        <span class="k">if</span> <span class="nb">hasattr</span><span class="p">(</span><span class="n">mod</span><span class="p">,</span> <span class="s1">&#39;db&#39;</span><span class="p">):</span>
+
+            <span class="n">mod</span><span class="o">.</span><span class="n">db</span><span class="o">.</span><span class="n">reload</span><span class="p">()</span></div>
+
+
+
+<div class="viewcode-block" id="DatabaseManager.get_build_args">
+<a class="viewcode-back" href="../../../api/pypath.omnipath.app.DatabaseManager.html#pypath.omnipath.app.DatabaseManager.get_build_args">[docs]</a>
+    <span class="k">def</span> <span class="nf">get_build_args</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">dataset</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Retrieves the default database build parameters for a dataset.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">args</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">get_param</span><span class="p">(</span><span class="s1">&#39;</span><span class="si">%s</span><span class="s1">_args&#39;</span> <span class="o">%</span> <span class="n">dataset</span><span class="p">)</span> <span class="ow">or</span> <span class="p">{}</span>
+
+        <span class="k">if</span> <span class="nb">hasattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">&#39;get_args_</span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="n">dataset</span><span class="p">):</span>
+
+            <span class="n">args</span><span class="o">.</span><span class="n">update</span><span class="p">(</span><span class="nb">getattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">&#39;get_args_</span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="n">dataset</span><span class="p">)())</span>
+
+        <span class="k">return</span> <span class="n">args</span></div>
+
+
+
+<div class="viewcode-block" id="DatabaseManager.load_dataset">
+<a class="viewcode-back" href="../../../api/pypath.omnipath.app.DatabaseManager.html#pypath.omnipath.app.DatabaseManager.load_dataset">[docs]</a>
+    <span class="k">def</span> <span class="nf">load_dataset</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">dataset</span><span class="p">,</span> <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Loads a dataset, builds it if no pickle dump is available.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">pickle_path</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">pickle_path</span><span class="p">(</span><span class="n">dataset</span><span class="p">,</span> <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">)</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span><span class="s1">&#39;Loading dataset `</span><span class="si">%s</span><span class="s1">` from `</span><span class="si">%s</span><span class="s1">`.&#39;</span> <span class="o">%</span> <span class="p">(</span><span class="n">dataset</span><span class="p">,</span> <span class="n">pickle_path</span><span class="p">))</span>
+
+        <span class="n">mod</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">ensure_module</span><span class="p">(</span><span class="n">dataset</span><span class="p">)</span>
+
+        <span class="n">_dataset</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_dataset_taxid</span><span class="p">(</span><span class="n">dataset</span><span class="p">,</span> <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">)</span>
+
+        <span class="nb">setattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">_dataset</span><span class="p">,</span> <span class="n">mod</span><span class="o">.</span><span class="n">get_db</span><span class="p">(</span><span class="n">pickle_file</span> <span class="o">=</span> <span class="n">pickle_path</span><span class="p">))</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span><span class="s1">&#39;Loaded dataset `</span><span class="si">%s</span><span class="s1">` from `</span><span class="si">%s</span><span class="s1">`.&#39;</span> <span class="o">%</span> <span class="p">(</span><span class="n">dataset</span><span class="p">,</span> <span class="n">pickle_path</span><span class="p">))</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_add_network_df</span><span class="p">(</span><span class="n">dataset</span><span class="p">,</span> <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">)</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">_dataset_taxid</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">dataset</span><span class="p">,</span> <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="s1">&#39;</span><span class="si">%s%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="p">(</span>
+            <span class="n">dataset</span><span class="p">,</span>
+            <span class="s1">&#39;_</span><span class="si">%u</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="n">ncbi_tax_id</span> <span class="k">if</span> <span class="n">dataset</span> <span class="o">==</span> <span class="s1">&#39;enz_sub&#39;</span> <span class="k">else</span> <span class="s1">&#39;&#39;</span><span class="p">,</span>
+        <span class="p">)</span>
+
+
+    <span class="c1"># TODO</span>
+    <span class="c1"># the get_args_* methods below will be replaced by the</span>
+    <span class="c1"># pypath.omnipath.databases module</span>
+
+<div class="viewcode-block" id="DatabaseManager.get_args_curated">
+<a class="viewcode-back" href="../../../api/pypath.omnipath.app.DatabaseManager.html#pypath.omnipath.app.DatabaseManager.get_args_curated">[docs]</a>
+    <span class="k">def</span> <span class="nf">get_args_curated</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Returns the arguments for building the curated PPI network dataset.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">resources</span> <span class="o">=</span> <span class="n">copy</span><span class="o">.</span><span class="n">deepcopy</span><span class="p">(</span><span class="n">netres</span><span class="o">.</span><span class="n">pathway</span><span class="p">)</span>
+        <span class="n">resources</span><span class="o">.</span><span class="n">update</span><span class="p">(</span><span class="n">copy</span><span class="o">.</span><span class="n">deepcopy</span><span class="p">(</span><span class="n">netres</span><span class="o">.</span><span class="n">enzyme_substrate</span><span class="p">))</span>
+
+        <span class="k">return</span> <span class="p">{</span><span class="s1">&#39;resources&#39;</span><span class="p">:</span> <span class="n">resources</span><span class="p">}</span></div>
+
+
+
+<div class="viewcode-block" id="DatabaseManager.get_args_tf_target">
+<a class="viewcode-back" href="../../../api/pypath.omnipath.app.DatabaseManager.html#pypath.omnipath.app.DatabaseManager.get_args_tf_target">[docs]</a>
+    <span class="k">def</span> <span class="nf">get_args_tf_target</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Returns the arguments for building the TF-target network dataset.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">transcription</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="n">netres</span><span class="o">.</span><span class="n">dorothea_expand_levels</span><span class="p">(</span>
+                <span class="n">resources</span> <span class="o">=</span> <span class="n">netres</span><span class="o">.</span><span class="n">transcription</span><span class="p">,</span>
+                <span class="n">levels</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">get_param</span><span class="p">(</span><span class="s1">&#39;tfregulons_levels&#39;</span><span class="p">),</span>
+            <span class="p">)</span>
+                <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">get_param</span><span class="p">(</span><span class="s1">&#39;dorothea_expand_levels&#39;</span><span class="p">)</span> <span class="k">else</span>
+            <span class="n">netres</span><span class="o">.</span><span class="n">transcription</span>
+        <span class="p">)</span>
+
+        <span class="k">return</span> <span class="p">{</span><span class="s1">&#39;resources&#39;</span><span class="p">:</span> <span class="n">transcription</span><span class="p">}</span></div>
+
+
+
+<div class="viewcode-block" id="DatabaseManager.get_args_tf_mirna">
+<a class="viewcode-back" href="../../../api/pypath.omnipath.app.DatabaseManager.html#pypath.omnipath.app.DatabaseManager.get_args_tf_mirna">[docs]</a>
+    <span class="k">def</span> <span class="nf">get_args_tf_mirna</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Returns the arguments for building the TF-miRNA network dataset.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">return</span> <span class="p">{</span><span class="s1">&#39;resources&#39;</span><span class="p">:</span> <span class="n">netres</span><span class="o">.</span><span class="n">tf_mirna</span><span class="p">}</span></div>
+
+
+
+<div class="viewcode-block" id="DatabaseManager.get_args_mirna_mrna">
+<a class="viewcode-back" href="../../../api/pypath.omnipath.app.DatabaseManager.html#pypath.omnipath.app.DatabaseManager.get_args_mirna_mrna">[docs]</a>
+    <span class="k">def</span> <span class="nf">get_args_mirna_mrna</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Returns the arguments for building the miRNA-mRNA network dataset.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">return</span> <span class="p">{</span><span class="s1">&#39;resources&#39;</span><span class="p">:</span> <span class="n">netres</span><span class="o">.</span><span class="n">mirnatarget</span><span class="p">}</span></div>
+
+
+
+<div class="viewcode-block" id="DatabaseManager.get_args_lncrna_mrna">
+<a class="viewcode-back" href="../../../api/pypath.omnipath.app.DatabaseManager.html#pypath.omnipath.app.DatabaseManager.get_args_lncrna_mrna">[docs]</a>
+    <span class="k">def</span> <span class="nf">get_args_lncrna_mrna</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Returns the arguments for building the lncRNA-mRNA network dataset.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">return</span> <span class="p">{</span><span class="s1">&#39;resources&#39;</span><span class="p">:</span> <span class="n">netres</span><span class="o">.</span><span class="n">lncrna_mrna</span><span class="p">}</span></div>
+
+
+
+<div class="viewcode-block" id="DatabaseManager.get_args_small_molecule">
+<a class="viewcode-back" href="../../../api/pypath.omnipath.app.DatabaseManager.html#pypath.omnipath.app.DatabaseManager.get_args_small_molecule">[docs]</a>
+    <span class="k">def</span> <span class="nf">get_args_small_molecule</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Returns the arguments for building the small molecule-protein</span>
+<span class="sd">        network dataset.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">return</span> <span class="p">{</span><span class="s1">&#39;resources&#39;</span><span class="p">:</span> <span class="n">netres</span><span class="o">.</span><span class="n">small_molecule</span><span class="p">}</span></div>
+
+
+
+<div class="viewcode-block" id="DatabaseManager.compile_tables">
+<a class="viewcode-back" href="../../../api/pypath.omnipath.app.DatabaseManager.html#pypath.omnipath.app.DatabaseManager.compile_tables">[docs]</a>
+    <span class="k">def</span> <span class="nf">compile_tables</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Compiles the `summaries` table for all datasets. These tables contain</span>
+<span class="sd">        various quantitative descriptions of the data contents.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">foreach_dataset</span><span class="p">(</span><span class="n">method</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">compile_table</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="DatabaseManager.compile_table">
+<a class="viewcode-back" href="../../../api/pypath.omnipath.app.DatabaseManager.html#pypath.omnipath.app.DatabaseManager.compile_table">[docs]</a>
+    <span class="k">def</span> <span class="nf">compile_table</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">dataset</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Compiles the `summaries` table for a dataset. These tables contain</span>
+<span class="sd">        various quantitative descriptions of the data contents.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">table_path</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">table_path</span><span class="p">(</span><span class="n">dataset</span><span class="p">)</span>
+        <span class="n">db</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">get_db</span><span class="p">(</span><span class="n">dataset</span><span class="p">)</span>
+        <span class="n">db</span><span class="o">.</span><span class="n">update_summaries</span><span class="p">()</span>
+        <span class="n">db</span><span class="o">.</span><span class="n">summaries_tab</span><span class="p">(</span><span class="n">outfile</span> <span class="o">=</span> <span class="n">table_path</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="DatabaseManager.foreach_dataset">
+<a class="viewcode-back" href="../../../api/pypath.omnipath.app.DatabaseManager.html#pypath.omnipath.app.DatabaseManager.foreach_dataset">[docs]</a>
+    <span class="k">def</span> <span class="nf">foreach_dataset</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">method</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Applies a method for each dataset.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">for</span> <span class="n">dataset</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">datasets</span><span class="p">:</span>
+
+            <span class="n">_</span> <span class="o">=</span> <span class="n">method</span><span class="p">(</span><span class="n">dataset</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="DatabaseManager.get_db">
+<a class="viewcode-back" href="../../../api/pypath.omnipath.app.DatabaseManager.html#pypath.omnipath.app.DatabaseManager.get_db">[docs]</a>
+    <span class="k">def</span> <span class="nf">get_db</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">dataset</span><span class="p">,</span> <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Returns a dataset object. Loads and builds the dataset if necessary.</span>
+
+<span class="sd">        :arg int ncbi_tax_id:</span>
+<span class="sd">            NCBI Taxonomy ID of the organism. Considered only if the dataset</span>
+<span class="sd">            builds for one organism and saved to organism specific pickle</span>
+<span class="sd">            files.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">ensure_dataset</span><span class="p">(</span><span class="n">dataset</span><span class="p">,</span> <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">)</span>
+
+        <span class="n">_dataset</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_dataset_taxid</span><span class="p">(</span><span class="n">dataset</span><span class="p">,</span> <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">)</span>
+
+        <span class="k">return</span> <span class="nb">getattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">_dataset</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="DatabaseManager.remove_db">
+<a class="viewcode-back" href="../../../api/pypath.omnipath.app.DatabaseManager.html#pypath.omnipath.app.DatabaseManager.remove_db">[docs]</a>
+    <span class="k">def</span> <span class="nf">remove_db</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">dataset</span><span class="p">,</span> <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Removes a dataset. Deletes the references to the object</span>
+<span class="sd">        in the module, however if you have references elsewhere in your</span>
+<span class="sd">        code it remains in the memory.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">_dataset</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_dataset_taxid</span><span class="p">(</span><span class="n">dataset</span><span class="p">,</span> <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">)</span>
+
+        <span class="k">if</span> <span class="nb">hasattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">_dataset</span><span class="p">):</span>
+
+            <span class="nb">delattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">_dataset</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="DatabaseManager.remove_all">
+<a class="viewcode-back" href="../../../api/pypath.omnipath.app.DatabaseManager.html#pypath.omnipath.app.DatabaseManager.remove_all">[docs]</a>
+    <span class="k">def</span> <span class="nf">remove_all</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Removes all loaded datasets. Deletes the references to the objects</span>
+<span class="sd">        in the module, however if you have references elsewhere in your</span>
+<span class="sd">        code they remain in the memory.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">foreach_dataset</span><span class="p">(</span><span class="n">method</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">ensure_module</span><span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">foreach_dataset</span><span class="p">(</span><span class="n">method</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">remove_db</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="DatabaseManager.get_param">
+<a class="viewcode-back" href="../../../api/pypath.omnipath.app.DatabaseManager.html#pypath.omnipath.app.DatabaseManager.get_param">[docs]</a>
+    <span class="k">def</span> <span class="nf">get_param</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">key</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Retrieves a parameter from the :py:attr:`param` dict of the current</span>
+<span class="sd">        object or from the module settings.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">param</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="n">key</span><span class="p">,</span> <span class="n">settings</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="n">key</span><span class="p">))</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">_create_network_df</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">dataset</span> <span class="o">=</span> <span class="s1">&#39;omnipath&#39;</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+
+        <span class="n">graph</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">get_db</span><span class="p">(</span><span class="n">dataset</span><span class="p">)</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_network_df</span><span class="p">(</span><span class="n">graph</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
+
+
+<div class="viewcode-block" id="DatabaseManager.network_df">
+<a class="viewcode-back" href="../../../api/pypath.omnipath.app.DatabaseManager.html#pypath.omnipath.app.DatabaseManager.network_df">[docs]</a>
+    <span class="k">def</span> <span class="nf">network_df</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">dataset</span><span class="p">,</span> <span class="n">by_source</span> <span class="o">=</span> <span class="kc">False</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Creates a data frame of a network dataset where rows aggregate</span>
+<span class="sd">        information from all resources describing an interaction.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">ensure_dataset</span><span class="p">(</span><span class="n">dataset</span><span class="p">)</span>
+
+        <span class="n">by_source_str</span> <span class="o">=</span> <span class="s1">&#39;by_source&#39;</span> <span class="k">if</span> <span class="n">by_source</span> <span class="k">else</span> <span class="s1">&#39;plain&#39;</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">network_dfs</span><span class="p">[</span><span class="n">dataset</span><span class="p">][</span><span class="n">by_source_str</span><span class="p">]</span></div>
+
+
+
+<div class="viewcode-block" id="DatabaseManager.network_df_by_source">
+<a class="viewcode-back" href="../../../api/pypath.omnipath.app.DatabaseManager.html#pypath.omnipath.app.DatabaseManager.network_df_by_source">[docs]</a>
+    <span class="k">def</span> <span class="nf">network_df_by_source</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">dataset</span> <span class="o">=</span> <span class="s1">&#39;omnipath&#39;</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Creates a data frame of a network dataset where each row contains</span>
+<span class="sd">        information from one resource.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">ensure_dataset</span><span class="p">(</span><span class="n">dataset</span><span class="p">)</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">network_dfs</span><span class="p">[</span><span class="n">dataset</span><span class="p">][</span><span class="s1">&#39;by_source&#39;</span><span class="p">]</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">_network_df</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">obj</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+
+        <span class="k">if</span> <span class="ow">not</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">obj</span><span class="p">,</span> <span class="n">network</span><span class="o">.</span><span class="n">Network</span><span class="p">):</span>
+
+            <span class="n">obj</span> <span class="o">=</span> <span class="n">network</span><span class="o">.</span><span class="n">Network</span><span class="o">.</span><span class="n">from_igraph</span><span class="p">(</span><span class="n">obj</span><span class="p">)</span>
+
+        <span class="n">obj</span><span class="o">.</span><span class="n">make_df</span><span class="p">(</span><span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
+
+        <span class="k">return</span> <span class="n">obj</span><span class="o">.</span><span class="n">df</span>
+
+
+    <span class="k">def</span> <span class="nf">_add_network_df</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">dataset</span><span class="p">,</span> <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">):</span>
+
+        <span class="n">_dataset</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_dataset_taxid</span><span class="p">(</span><span class="n">dataset</span><span class="p">,</span> <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">)</span>
+
+        <span class="n">obj</span> <span class="o">=</span> <span class="nb">getattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">_dataset</span><span class="p">)</span>
+
+        <span class="k">if</span> <span class="p">(</span>
+            <span class="p">(</span>
+                <span class="nb">hasattr</span><span class="p">(</span><span class="n">obj</span><span class="p">,</span> <span class="s1">&#39;graph&#39;</span><span class="p">)</span> <span class="ow">and</span>
+                <span class="nb">hasattr</span><span class="p">(</span><span class="n">obj</span><span class="o">.</span><span class="n">graph</span><span class="p">,</span> <span class="s1">&#39;es&#39;</span><span class="p">)</span>
+            <span class="p">)</span> <span class="ow">or</span>
+            <span class="nb">isinstance</span><span class="p">(</span><span class="n">obj</span><span class="p">,</span> <span class="n">network</span><span class="o">.</span><span class="n">Network</span><span class="p">)</span>
+        <span class="p">):</span>
+
+            <span class="n">network_df</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_network_df</span><span class="p">(</span><span class="n">obj</span><span class="p">,</span> <span class="n">by_source</span> <span class="o">=</span> <span class="kc">False</span><span class="p">)</span>
+            <span class="n">network_df_by_source</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_network_df</span><span class="p">(</span><span class="n">obj</span><span class="p">,</span> <span class="n">by_source</span> <span class="o">=</span> <span class="kc">True</span><span class="p">)</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">network_dfs</span><span class="p">[</span><span class="n">dataset</span><span class="p">]</span> <span class="o">=</span> <span class="p">{}</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">network_dfs</span><span class="p">[</span><span class="n">dataset</span><span class="p">][</span><span class="s1">&#39;plain&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">network_df</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">network_dfs</span><span class="p">[</span><span class="n">dataset</span><span class="p">][</span><span class="s1">&#39;by_source&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">network_df_by_source</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span><span class="s1">&#39;Created network data frames for `</span><span class="si">%s</span><span class="s1">`.&#39;</span> <span class="o">%</span> <span class="n">dataset</span><span class="p">)</span>
+
+
+<div class="viewcode-block" id="DatabaseManager.set_network">
+<a class="viewcode-back" href="../../../api/pypath.omnipath.app.DatabaseManager.html#pypath.omnipath.app.DatabaseManager.set_network">[docs]</a>
+    <span class="k">def</span> <span class="nf">set_network</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">dataset</span><span class="p">,</span> <span class="n">by_source</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Sets dataset as the default</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">network_df</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">network_df</span><span class="p">(</span><span class="n">dataset</span><span class="p">,</span> <span class="n">by_source</span> <span class="o">=</span> <span class="n">by_source</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">ensure_dataset</span><span class="p">(</span><span class="s1">&#39;intercell&#39;</span><span class="p">)</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">intercell</span><span class="o">.</span><span class="n">register_network</span><span class="p">(</span><span class="n">network_df</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="DatabaseManager.define_dataset">
+<a class="viewcode-back" href="../../../api/pypath.omnipath.app.DatabaseManager.html#pypath.omnipath.app.DatabaseManager.define_dataset">[docs]</a>
+    <span class="k">def</span> <span class="nf">define_dataset</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">name</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
+            <span class="n">module</span><span class="p">:</span> <span class="n">Literal</span><span class="p">[</span>
+                <span class="s1">&#39;annot&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;complex&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;enz_sub&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;intercell&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;network&#39;</span><span class="p">,</span>
+            <span class="p">],</span>
+            <span class="n">args</span><span class="p">:</span> <span class="nb">dict</span> <span class="o">|</span> <span class="kc">None</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">pickle</span><span class="p">:</span> <span class="nb">str</span> <span class="o">|</span> <span class="kc">None</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="o">**</span><span class="n">param</span><span class="p">,</span>
+        <span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Add a new dataset definition.</span>
+
+<span class="sd">        Args</span>
+<span class="sd">            name:</span>
+<span class="sd">                Arbitrary name for the dataset.</span>
+<span class="sd">            module:</span>
+<span class="sd">                A database builder module: this determines the type of the</span>
+<span class="sd">                dataset.</span>
+<span class="sd">            args:</span>
+<span class="sd">                Arguments for the database provider method (typically</span>
+<span class="sd">                called ``get_db``) of the above module.</span>
+<span class="sd">            pickle:</span>
+<span class="sd">                A name for the pickle file, if not provided it will be</span>
+<span class="sd">                named as &quot;&lt;name&gt;_&lt;module&gt;.pickle&quot;.</span>
+<span class="sd">            param:</span>
+<span class="sd">                Further parameters, saved directly into the :attr:``param``</span>
+<span class="sd">                dict of this object, however the three arguments above</span>
+<span class="sd">                override values provided this way.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">settings</span><span class="o">.</span><span class="n">setup</span><span class="p">(</span><span class="n">datasets</span> <span class="o">=</span> <span class="n">setting</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">&#39;datasets&#39;</span><span class="p">)</span> <span class="o">+</span> <span class="p">[</span><span class="n">name</span><span class="p">])</span>
+
+        <span class="n">param</span><span class="p">[</span><span class="sa">f</span><span class="s1">&#39;</span><span class="si">{</span><span class="n">name</span><span class="si">}</span><span class="s1">_pickle&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">pickle</span> <span class="ow">or</span> <span class="sa">f</span><span class="s1">&#39;</span><span class="si">{</span><span class="n">name</span><span class="si">}</span><span class="s1">_</span><span class="si">{</span><span class="n">module</span><span class="si">}</span><span class="s1">.pickle&#39;</span>
+        <span class="n">param</span><span class="p">[</span><span class="sa">f</span><span class="s1">&#39;</span><span class="si">{</span><span class="n">name</span><span class="si">}</span><span class="s1">_mod&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">module</span>
+        <span class="n">param</span><span class="p">[</span><span class="sa">f</span><span class="s1">&#39;</span><span class="si">{</span><span class="n">name</span><span class="si">}</span><span class="s1">_args&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">args</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">param</span><span class="o">.</span><span class="n">update</span><span class="p">(</span><span class="n">param</span><span class="p">)</span></div>
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+<div class="header-article-items header-article__inner">
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+                  
+  <h1>Source code for pypath.omnipath.databases</h1><div class="highlight"><pre>
+<span></span><span class="ch">#!/usr/bin/env python</span>
+<span class="c1"># -*- coding: utf-8 -*-</span>
+
+<span class="c1">#</span>
+<span class="c1">#  This file is part of the `pypath` python module</span>
+<span class="c1">#</span>
+<span class="c1">#  Copyright 2014-2023</span>
+<span class="c1">#  EMBL, EMBL-EBI, Uniklinik RWTH Aachen, Heidelberg University</span>
+<span class="c1">#</span>
+<span class="c1">#  Authors: see the file `README.rst`</span>
+<span class="c1">#  Contact: Dénes Türei (turei.denes@gmail.com)</span>
+<span class="c1">#</span>
+<span class="c1">#  Distributed under the GPLv3 License.</span>
+<span class="c1">#  See accompanying file LICENSE.txt or copy at</span>
+<span class="c1">#      https://www.gnu.org/licenses/gpl-3.0.html</span>
+<span class="c1">#</span>
+<span class="c1">#  Website: https://pypath.omnipathdb.org/</span>
+<span class="c1">#</span>
+
+<span class="kn">import</span> <span class="nn">pypath.omnipath.databases.define</span> <span class="k">as</span> <span class="nn">define</span>
+
+
+<div class="viewcode-block" id="class_and_param">
+<a class="viewcode-back" href="../../../api/pypath.omnipath.databases.class_and_param.html#pypath.omnipath.databases.class_and_param">[docs]</a>
+<span class="k">def</span> <span class="nf">class_and_param</span><span class="p">(</span><span class="n">label</span><span class="p">):</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Retrieves the database definition of a built in database.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+    
+    <span class="n">manager</span> <span class="o">=</span> <span class="n">get_manager</span><span class="p">()</span>
+    
+    <span class="k">return</span> <span class="n">manager</span><span class="o">.</span><span class="n">class_and_param</span><span class="p">(</span><span class="n">label</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="build">
+<a class="viewcode-back" href="../../../api/pypath.omnipath.databases.build.html#pypath.omnipath.databases.build">[docs]</a>
+<span class="k">def</span> <span class="nf">build</span><span class="p">(</span><span class="n">label</span><span class="p">):</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Builds a built in database and returns the instance.</span>
+<span class="sd">    This is not the preferred method to get a database instance.</span>
+<span class="sd">    Unless there is a strong reason, both built in and user defined databases</span>
+<span class="sd">    should be managed by the ``pypath.omnipath.app`` module.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+    
+    <span class="n">manager</span> <span class="o">=</span> <span class="n">get_manager</span><span class="p">()</span>
+    
+    <span class="k">return</span> <span class="n">manager</span><span class="o">.</span><span class="n">build</span><span class="p">(</span><span class="n">label</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="get_manager">
+<a class="viewcode-back" href="../../../api/pypath.omnipath.databases.get_manager.html#pypath.omnipath.databases.get_manager">[docs]</a>
+<span class="k">def</span> <span class="nf">get_manager</span><span class="p">():</span>
+    
+    <span class="k">if</span> <span class="s1">&#39;manager&#39;</span> <span class="ow">not</span> <span class="ow">in</span> <span class="nb">globals</span><span class="p">():</span>
+        
+        <span class="n">init_manager</span><span class="p">()</span>
+    
+    <span class="k">return</span> <span class="nb">globals</span><span class="p">()[</span><span class="s1">&#39;manager&#39;</span><span class="p">]</span></div>
+
+
+
+<div class="viewcode-block" id="init_manager">
+<a class="viewcode-back" href="../../../api/pypath.omnipath.databases.init_manager.html#pypath.omnipath.databases.init_manager">[docs]</a>
+<span class="k">def</span> <span class="nf">init_manager</span><span class="p">():</span>
+    
+    <span class="nb">globals</span><span class="p">()[</span><span class="s1">&#39;manager&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">define</span><span class="o">.</span><span class="n">DatabaseDefinitionManager</span><span class="p">()</span></div>
+
+</pre></div>
+
+                </article>
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diff --git a/_modules/pypath/omnipath/databases/define.html b/_modules/pypath/omnipath/databases/define.html
new file mode 100644
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+    <li class="breadcrumb-item"><a href="../databases.html" class="nav-link">pypath.omnipath.databases</a></li>
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+                <article class="bd-article">
+                  
+  <h1>Source code for pypath.omnipath.databases.define</h1><div class="highlight"><pre>
+<span></span><span class="ch">#!/usr/bin/env python</span>
+<span class="c1"># -*- coding: utf-8 -*-</span>
+
+<span class="c1">#</span>
+<span class="c1">#  This file is part of the `pypath` python module</span>
+<span class="c1">#</span>
+<span class="c1">#  Copyright 2014-2023</span>
+<span class="c1">#  EMBL, EMBL-EBI, Uniklinik RWTH Aachen, Heidelberg University</span>
+<span class="c1">#</span>
+<span class="c1">#  Authors: see the file `README.rst`</span>
+<span class="c1">#  Contact: Dénes Türei (turei.denes@gmail.com)</span>
+<span class="c1">#</span>
+<span class="c1">#  Distributed under the GPLv3 License.</span>
+<span class="c1">#  See accompanying file LICENSE.txt or copy at</span>
+<span class="c1">#      https://www.gnu.org/licenses/gpl-3.0.html</span>
+<span class="c1">#</span>
+<span class="c1">#  Website: https://pypath.omnipathdb.org/</span>
+<span class="c1">#</span>
+
+<span class="kn">from</span> <span class="nn">future.utils</span> <span class="kn">import</span> <span class="n">iteritems</span>
+
+<span class="kn">import</span> <span class="nn">importlib</span>
+<span class="kn">import</span> <span class="nn">os</span>
+<span class="kn">import</span> <span class="nn">itertools</span>
+<span class="kn">import</span> <span class="nn">json</span>
+
+<span class="kn">import</span> <span class="nn">pypath.share.session</span> <span class="k">as</span> <span class="nn">session</span>
+<span class="kn">import</span> <span class="nn">pypath.omnipath.databases.build</span> <span class="k">as</span> <span class="nn">build</span>
+
+<span class="n">_logger</span> <span class="o">=</span> <span class="n">session</span><span class="o">.</span><span class="n">Logger</span><span class="p">(</span><span class="n">name</span> <span class="o">=</span> <span class="s1">&#39;db_define&#39;</span><span class="p">)</span>
+<span class="n">_log</span> <span class="o">=</span> <span class="n">_logger</span><span class="o">.</span><span class="n">_log</span>
+<span class="n">_console</span> <span class="o">=</span> <span class="n">_logger</span><span class="o">.</span><span class="n">_console</span>
+
+
+<div class="viewcode-block" id="DatabaseDefinition">
+<a class="viewcode-back" href="../../../../api/pypath.omnipath.databases.define.DatabaseDefinition.html#pypath.omnipath.databases.define.DatabaseDefinition">[docs]</a>
+<span class="k">class</span> <span class="nc">DatabaseDefinition</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span>
+
+
+<div class="viewcode-block" id="DatabaseDefinition.__init__">
+<a class="viewcode-back" href="../../../../api/pypath.omnipath.databases.define.DatabaseDefinition.html#pypath.omnipath.databases.define.DatabaseDefinition.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">label</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">label</span> <span class="o">=</span> <span class="n">label</span>
+
+        <span class="n">_def</span> <span class="o">=</span> <span class="n">kwargs</span><span class="o">.</span><span class="n">pop</span><span class="p">(</span><span class="s1">&#39;def&#39;</span><span class="p">,</span> <span class="p">{})</span>
+
+        <span class="k">for</span> <span class="n">k</span><span class="p">,</span> <span class="n">v</span> <span class="ow">in</span> <span class="n">itertools</span><span class="o">.</span><span class="n">chain</span><span class="p">(</span>
+            <span class="n">iteritems</span><span class="p">(</span><span class="n">kwargs</span><span class="p">),</span>
+            <span class="n">iteritems</span><span class="p">(</span><span class="n">_def</span><span class="p">),</span>
+        <span class="p">):</span>
+
+            <span class="nb">setattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">k</span><span class="p">,</span> <span class="n">v</span><span class="p">)</span></div>
+
+
+
+    <span class="k">def</span> <span class="fm">__repr__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="s1">&#39;&lt;</span><span class="si">%s</span><span class="s1"> database: </span><span class="si">%s</span><span class="s1">&gt;&#39;</span> <span class="o">%</span> <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">dbclass</span><span class="o">.</span><span class="n">capitalize</span><span class="p">(),</span> <span class="bp">self</span><span class="o">.</span><span class="n">label</span><span class="p">)</span>
+
+
+<div class="viewcode-block" id="DatabaseDefinition.from_json">
+<a class="viewcode-back" href="../../../../api/pypath.omnipath.databases.define.DatabaseDefinition.html#pypath.omnipath.databases.define.DatabaseDefinition.from_json">[docs]</a>
+    <span class="nd">@classmethod</span>
+    <span class="k">def</span> <span class="nf">from_json</span><span class="p">(</span><span class="bp">cls</span><span class="p">,</span> <span class="n">path</span><span class="p">,</span> <span class="n">label</span> <span class="o">=</span> <span class="kc">None</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        :param str path:</span>
+<span class="sd">            Path to JSON file with database definition.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">data</span> <span class="o">=</span> <span class="bp">cls</span><span class="o">.</span><span class="n">_parse_json</span><span class="p">(</span><span class="n">path</span> <span class="o">=</span> <span class="n">path</span><span class="p">,</span> <span class="n">label</span> <span class="o">=</span> <span class="n">label</span><span class="p">)</span>
+
+        <span class="k">return</span> <span class="bp">cls</span><span class="p">(</span><span class="o">**</span><span class="n">data</span><span class="p">)</span></div>
+
+
+
+    <span class="nd">@staticmethod</span>
+    <span class="k">def</span> <span class="nf">_parse_json</span><span class="p">(</span><span class="n">path</span><span class="p">,</span> <span class="n">label</span> <span class="o">=</span> <span class="kc">None</span><span class="p">):</span>
+
+        <span class="n">data</span> <span class="o">=</span> <span class="n">DatabaseDefinition</span><span class="o">.</span><span class="n">_read_json</span><span class="p">(</span><span class="n">path</span><span class="p">)</span> <span class="ow">or</span> <span class="p">{}</span>
+
+        <span class="k">if</span> <span class="n">label</span><span class="p">:</span>
+
+            <span class="k">if</span> <span class="n">label</span> <span class="ow">in</span> <span class="n">data</span><span class="p">:</span>
+
+                <span class="n">data</span> <span class="o">=</span> <span class="n">data</span><span class="p">[</span><span class="n">label</span><span class="p">]</span>
+                <span class="n">data</span><span class="p">[</span><span class="s1">&#39;label&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">label</span>
+
+            <span class="k">else</span><span class="p">:</span>
+
+                <span class="n">_console</span><span class="p">(</span>
+                    <span class="s1">&#39;Entry `</span><span class="si">%s</span><span class="s1">` not available in file `</span><span class="si">%s</span><span class="s1">`.&#39;</span> <span class="o">%</span> <span class="p">(</span>
+                        <span class="n">label</span><span class="p">,</span>
+                        <span class="n">path</span><span class="p">,</span>
+                    <span class="p">)</span>
+                <span class="p">)</span>
+
+        <span class="k">return</span> <span class="n">data</span>
+
+
+    <span class="nd">@staticmethod</span>
+    <span class="k">def</span> <span class="nf">_read_json</span><span class="p">(</span><span class="n">path</span><span class="p">):</span>
+
+        <span class="k">if</span> <span class="ow">not</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">exists</span><span class="p">(</span><span class="n">path</span><span class="p">):</span>
+
+            <span class="n">_console</span><span class="p">(</span><span class="s1">&#39;No such file: `</span><span class="si">%s</span><span class="s1">`.&#39;</span> <span class="o">%</span> <span class="n">path</span><span class="p">)</span>
+
+        <span class="k">else</span><span class="p">:</span>
+
+            <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">path</span><span class="p">)</span> <span class="k">as</span> <span class="n">json_file</span><span class="p">:</span>
+
+                <span class="k">return</span> <span class="n">json</span><span class="o">.</span><span class="n">load</span><span class="p">(</span><span class="n">json_file</span><span class="p">)</span>
+
+
+<div class="viewcode-block" id="DatabaseDefinition.from_dict">
+<a class="viewcode-back" href="../../../../api/pypath.omnipath.databases.define.DatabaseDefinition.html#pypath.omnipath.databases.define.DatabaseDefinition.from_dict">[docs]</a>
+    <span class="nd">@classmethod</span>
+    <span class="k">def</span> <span class="nf">from_dict</span><span class="p">(</span><span class="bp">cls</span><span class="p">,</span> <span class="n">dct</span><span class="p">,</span> <span class="n">label</span> <span class="o">=</span> <span class="kc">None</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        :param dict dct:</span>
+<span class="sd">            Dictionary containing the parameters for the database definition.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">if</span> <span class="n">label</span><span class="p">:</span>
+
+            <span class="n">dct</span><span class="p">[</span><span class="s1">&#39;label&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">label</span>
+
+        <span class="k">return</span> <span class="bp">cls</span><span class="p">(</span><span class="o">**</span><span class="n">dct</span><span class="p">)</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">get</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">attr</span><span class="p">):</span>
+
+        <span class="k">if</span> <span class="nb">hasattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">attr</span><span class="p">):</span>
+
+            <span class="k">return</span> <span class="nb">getattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">attr</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="DatabaseClass">
+<a class="viewcode-back" href="../../../../api/pypath.omnipath.databases.define.DatabaseClass.html#pypath.omnipath.databases.define.DatabaseClass">[docs]</a>
+<span class="k">class</span> <span class="nc">DatabaseClass</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Describes a class of databases which can be filled with different data</span>
+<span class="sd">    but here the module and the class implementing the database are defined.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+<div class="viewcode-block" id="DatabaseClass.__init__">
+<a class="viewcode-back" href="../../../../api/pypath.omnipath.databases.define.DatabaseClass.html#pypath.omnipath.databases.define.DatabaseClass.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">module</span><span class="p">,</span> <span class="n">method</span><span class="p">,</span> <span class="n">label</span> <span class="o">=</span> <span class="kc">None</span><span class="p">):</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">label</span> <span class="o">=</span> <span class="n">label</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">module</span> <span class="o">=</span> <span class="n">module</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">method</span> <span class="o">=</span> <span class="n">method</span></div>
+
+
+
+    <span class="k">def</span> <span class="fm">__repr__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="p">(</span>
+            <span class="s1">&#39;&lt;Database class `</span><span class="si">%s</span><span class="s1">`, module: `</span><span class="si">%s</span><span class="s1">`, class or method: `</span><span class="si">%s</span><span class="s1">`&gt;&#39;</span> <span class="o">%</span> <span class="p">(</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">label</span><span class="p">,</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">module</span><span class="p">,</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">method</span><span class="o">.</span><span class="vm">__name__</span>
+                    <span class="k">if</span> <span class="nb">hasattr</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">method</span><span class="p">,</span> <span class="s1">&#39;__name__&#39;</span><span class="p">)</span> <span class="k">else</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">method</span><span class="p">,</span>
+            <span class="p">)</span>
+        <span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">get_class</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">if</span> <span class="nb">callable</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">method</span><span class="p">):</span>
+
+            <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">method</span>
+
+        <span class="k">else</span><span class="p">:</span>
+
+            <span class="k">try</span><span class="p">:</span>
+
+                <span class="n">mod</span> <span class="o">=</span> <span class="n">importlib</span><span class="o">.</span><span class="n">import_module</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">module</span><span class="p">)</span>
+
+                <span class="k">if</span> <span class="nb">hasattr</span><span class="p">(</span><span class="n">mod</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">method</span><span class="p">):</span>
+
+                    <span class="k">return</span> <span class="nb">getattr</span><span class="p">(</span><span class="n">mod</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">method</span><span class="p">)</span>
+
+                <span class="k">else</span><span class="p">:</span>
+
+                    <span class="n">_console</span><span class="p">(</span>
+                        <span class="s1">&#39;Module `</span><span class="si">%s</span><span class="s1">` has no class or method `</span><span class="si">%s</span><span class="s1">`.&#39;</span> <span class="o">%</span> <span class="p">(</span>
+                            <span class="bp">self</span><span class="o">.</span><span class="n">module</span><span class="p">,</span>
+                            <span class="bp">self</span><span class="o">.</span><span class="n">method</span><span class="p">,</span>
+                        <span class="p">)</span>
+                    <span class="p">)</span>
+
+            <span class="k">except</span> <span class="ne">ImportError</span><span class="p">:</span>
+
+                <span class="n">_console</span><span class="p">(</span><span class="s1">&#39;Failed to import `</span><span class="si">%s</span><span class="s1">`.&#39;</span> <span class="o">%</span> <span class="bp">self</span><span class="o">.</span><span class="n">module</span><span class="p">)</span>
+
+
+    <span class="nd">@classmethod</span>
+    <span class="k">def</span> <span class="nf">from_json</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">path</span><span class="p">,</span> <span class="n">label</span> <span class="o">=</span> <span class="kc">None</span><span class="p">):</span>
+
+        <span class="n">data</span> <span class="o">=</span> <span class="n">DatabaseDefinition</span><span class="o">.</span><span class="n">_parse_json</span><span class="p">(</span><span class="n">path</span> <span class="o">=</span> <span class="n">path</span><span class="p">,</span> <span class="n">label</span> <span class="o">=</span> <span class="n">label</span><span class="p">)</span>
+
+        <span class="k">return</span> <span class="bp">cls</span><span class="p">(</span><span class="o">**</span><span class="n">data</span><span class="p">)</span>
+
+
+    <span class="nd">@classmethod</span>
+    <span class="k">def</span> <span class="nf">from_dict</span><span class="p">(</span><span class="bp">cls</span><span class="p">,</span> <span class="n">dct</span><span class="p">,</span> <span class="n">label</span> <span class="o">=</span> <span class="kc">None</span><span class="p">):</span>
+
+        <span class="k">if</span> <span class="n">label</span><span class="p">:</span>
+
+            <span class="n">dct</span><span class="p">[</span><span class="s1">&#39;label&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">label</span>
+
+        <span class="k">return</span> <span class="bp">cls</span><span class="p">(</span><span class="o">**</span><span class="n">dct</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="DatabaseDefinitionManager">
+<a class="viewcode-back" href="../../../../api/pypath.omnipath.databases.define.DatabaseDefinitionManager.html#pypath.omnipath.databases.define.DatabaseDefinitionManager">[docs]</a>
+<span class="k">class</span> <span class="nc">DatabaseDefinitionManager</span><span class="p">(</span><span class="n">session</span><span class="o">.</span><span class="n">Logger</span><span class="p">):</span>
+
+
+<div class="viewcode-block" id="DatabaseDefinitionManager.__init__">
+<a class="viewcode-back" href="../../../../api/pypath.omnipath.databases.define.DatabaseDefinitionManager.html#pypath.omnipath.databases.define.DatabaseDefinitionManager.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">classes</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span> <span class="n">databases</span> <span class="o">=</span> <span class="kc">None</span><span class="p">):</span>
+
+        <span class="n">session</span><span class="o">.</span><span class="n">Logger</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">name</span> <span class="o">=</span> <span class="s1">&#39;db_define&#39;</span><span class="p">)</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_classes</span> <span class="o">=</span> <span class="n">classes</span> <span class="ow">or</span> <span class="bp">self</span><span class="o">.</span><span class="n">_default_json</span><span class="p">(</span><span class="s1">&#39;classes&#39;</span><span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">_databases</span> <span class="o">=</span> <span class="n">databases</span> <span class="ow">or</span> <span class="bp">self</span><span class="o">.</span><span class="n">_default_json</span><span class="p">(</span><span class="s1">&#39;builtins&#39;</span><span class="p">)</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">load</span><span class="p">()</span></div>
+
+
+
+    <span class="k">def</span> <span class="fm">__repr__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="s1">&#39;&lt;Database definitions: </span><span class="si">%u</span><span class="s1"> classes and </span><span class="si">%u</span><span class="s1"> definitions&gt;&#39;</span> <span class="o">%</span> <span class="p">(</span>
+            <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">classes</span><span class="p">),</span>
+            <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">databases</span><span class="p">),</span>
+        <span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">load</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_classes</span><span class="p">,</span> <span class="nb">str</span><span class="p">):</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span><span class="s1">&#39;Reading database classes from `</span><span class="si">%s</span><span class="s1">`&#39;</span> <span class="o">%</span> <span class="bp">self</span><span class="o">.</span><span class="n">_classes</span><span class="p">)</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">_classes</span> <span class="o">=</span> <span class="n">DatabaseDefinition</span><span class="o">.</span><span class="n">_read_json</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_classes</span><span class="p">)</span>
+
+        <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_databases</span><span class="p">,</span> <span class="nb">str</span><span class="p">):</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span>
+                <span class="s1">&#39;Reading database definitions from `</span><span class="si">%s</span><span class="s1">`&#39;</span> <span class="o">%</span> <span class="bp">self</span><span class="o">.</span><span class="n">_databases</span>
+            <span class="p">)</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">_databases</span> <span class="o">=</span> <span class="n">DatabaseDefinition</span><span class="o">.</span><span class="n">_read_json</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_databases</span><span class="p">)</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">classes</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">(</span>
+            <span class="p">(</span>
+                <span class="n">label</span><span class="p">,</span>
+                <span class="n">DatabaseClass</span><span class="o">.</span><span class="n">from_dict</span><span class="p">(</span><span class="n">label</span> <span class="o">=</span> <span class="n">label</span><span class="p">,</span> <span class="n">dct</span> <span class="o">=</span> <span class="n">param</span><span class="p">)</span>
+            <span class="p">)</span>
+            <span class="k">for</span> <span class="n">label</span><span class="p">,</span> <span class="n">param</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_classes</span><span class="p">)</span>
+        <span class="p">)</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">databases</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">(</span>
+            <span class="p">(</span>
+                <span class="n">label</span><span class="p">,</span>
+                <span class="n">DatabaseDefinition</span><span class="o">.</span><span class="n">from_dict</span><span class="p">(</span><span class="n">label</span> <span class="o">=</span> <span class="n">label</span><span class="p">,</span> <span class="n">dct</span> <span class="o">=</span> <span class="n">param</span><span class="p">)</span>
+            <span class="p">)</span>
+            <span class="k">for</span> <span class="n">label</span><span class="p">,</span> <span class="n">param</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_databases</span><span class="p">)</span>
+        <span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">get_db_class</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">label</span><span class="p">):</span>
+
+        <span class="k">if</span> <span class="n">label</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">classes</span><span class="p">:</span>
+
+            <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">classes</span><span class="p">[</span><span class="n">label</span><span class="p">]</span>
+
+        <span class="k">else</span><span class="p">:</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span><span class="s1">&#39;No such database class: `</span><span class="si">%s</span><span class="s1">`.&#39;</span> <span class="o">%</span> <span class="n">label</span><span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">get_db_definition</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">label</span><span class="p">):</span>
+
+        <span class="k">if</span> <span class="n">label</span> <span class="ow">not</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">databases</span><span class="p">:</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span>
+                <span class="s1">&#39;Warning: no parameters for label `</span><span class="si">%s</span><span class="s1">`, &#39;</span>
+                <span class="s1">&#39;returning empty dict.&#39;</span> <span class="o">%</span> <span class="n">label</span>
+            <span class="p">)</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">databases</span><span class="p">[</span><span class="n">label</span><span class="p">]</span> <span class="k">if</span> <span class="n">label</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">databases</span> <span class="k">else</span> <span class="p">{}</span>
+
+
+    <span class="k">def</span> <span class="nf">get_class</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">label</span><span class="p">):</span>
+
+        <span class="n">dbclass</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">get_db_class</span><span class="p">(</span><span class="n">label</span><span class="p">)</span>
+
+        <span class="k">if</span> <span class="n">dbclass</span><span class="p">:</span>
+
+            <span class="k">return</span> <span class="n">dbclass</span><span class="o">.</span><span class="n">get_class</span><span class="p">()</span>
+
+
+<div class="viewcode-block" id="DatabaseDefinitionManager.class_and_param">
+<a class="viewcode-back" href="../../../../api/pypath.omnipath.databases.define.DatabaseDefinitionManager.html#pypath.omnipath.databases.define.DatabaseDefinitionManager.class_and_param">[docs]</a>
+    <span class="k">def</span> <span class="nf">class_and_param</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">label</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        For a database definition label returns the class or method and its</span>
+<span class="sd">        arguments which are necessary to build the database according to</span>
+<span class="sd">        the definition.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">db_def</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">get_db_definition</span><span class="p">(</span><span class="n">label</span><span class="p">)</span>
+
+        <span class="k">if</span> <span class="n">db_def</span><span class="p">:</span>
+
+            <span class="n">db_class</span> <span class="o">=</span> <span class="n">db_def</span><span class="o">.</span><span class="n">dbclass</span>
+
+            <span class="k">if</span> <span class="ow">not</span> <span class="nb">callable</span><span class="p">(</span><span class="n">db_class</span><span class="p">):</span>
+
+                <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">db_class</span><span class="p">,</span> <span class="nb">dict</span><span class="p">):</span>
+
+                    <span class="n">db_class</span> <span class="o">=</span> <span class="n">DatabaseClass</span><span class="p">(</span><span class="o">**</span><span class="n">db_class</span><span class="p">)</span>
+
+                <span class="k">elif</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">db_class</span><span class="p">,</span> <span class="nb">str</span><span class="p">):</span>
+
+                    <span class="n">db_class</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">get_db_class</span><span class="p">(</span><span class="n">db_class</span><span class="p">)</span>
+
+        <span class="k">return</span> <span class="n">db_class</span><span class="p">,</span> <span class="n">db_def</span></div>
+
+
+
+<div class="viewcode-block" id="DatabaseDefinitionManager.build">
+<a class="viewcode-back" href="../../../../api/pypath.omnipath.databases.define.DatabaseDefinitionManager.html#pypath.omnipath.databases.define.DatabaseDefinitionManager.build">[docs]</a>
+    <span class="k">def</span> <span class="nf">build</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">label</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        For a database definition label returns an instance of the database:</span>
+<span class="sd">        creates an instance of the class or calls the method with the</span>
+<span class="sd">        arguments in the database definition. Returns the database instance.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">db_class</span><span class="p">,</span> <span class="n">db_def</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">class_and_param</span><span class="p">(</span><span class="n">label</span><span class="p">)</span>
+
+        <span class="k">if</span> <span class="n">db_class</span><span class="p">:</span>
+
+            <span class="k">return</span> <span class="n">build</span><span class="o">.</span><span class="n">build</span><span class="p">(</span><span class="n">db_class</span><span class="p">,</span> <span class="n">db_def</span><span class="p">)</span></div>
+
+
+
+    <span class="nd">@staticmethod</span>
+    <span class="k">def</span> <span class="nf">_default_json</span><span class="p">(</span><span class="n">name</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span>
+            <span class="n">session</span><span class="o">.</span><span class="n">session</span><span class="p">()</span><span class="o">.</span><span class="n">module_root</span><span class="p">,</span>
+            <span class="s1">&#39;omnipath&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;databases&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;</span><span class="si">%s</span><span class="s1">.json&#39;</span> <span class="o">%</span> <span class="n">name</span><span class="p">,</span>
+        <span class="p">)</span></div>
+
+</pre></div>
+
+                </article>
+              
+              
+              
+              
+              
+                <footer class="prev-next-footer">
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@@ -0,0 +1,1651 @@
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+        <li class="nav-item">
+          
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+          
+          <a href="https://twitter.com/omnipathdb" title="Twitter" class="nav-link" rel="noopener" target="_blank" data-bs-toggle="tooltip" data-bs-placement="bottom"><span><i class="fa-brands fa-square-twitter fa-lg" aria-hidden="true"></i></span>
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+        <li class="nav-item">
+          
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+                <article class="bd-article">
+                  
+  <h1>Source code for pypath.omnipath.export</h1><div class="highlight"><pre>
+<span></span><span class="ch">#!/usr/bin/env python</span>
+<span class="c1"># -*- coding: utf-8 -*-</span>
+
+<span class="c1">#</span>
+<span class="c1">#  This file is part of the `pypath` python module</span>
+<span class="c1">#</span>
+<span class="c1">#  Copyright 2014-2023</span>
+<span class="c1">#  EMBL, EMBL-EBI, Uniklinik RWTH Aachen, Heidelberg University</span>
+<span class="c1">#</span>
+<span class="c1">#  Authors: see the file `README.rst`</span>
+<span class="c1">#  Contact: Dénes Türei (turei.denes@gmail.com)</span>
+<span class="c1">#</span>
+<span class="c1">#  Distributed under the GPLv3 License.</span>
+<span class="c1">#  See accompanying file LICENSE.txt or copy at</span>
+<span class="c1">#      https://www.gnu.org/licenses/gpl-3.0.html</span>
+<span class="c1">#</span>
+<span class="c1">#  Website: https://pypath.omnipathdb.org/</span>
+<span class="c1">#</span>
+
+<span class="kn">from</span> <span class="nn">future.utils</span> <span class="kn">import</span> <span class="n">iteritems</span>
+<span class="kn">from</span> <span class="nn">past.builtins</span> <span class="kn">import</span> <span class="n">xrange</span><span class="p">,</span> <span class="nb">range</span>
+
+<span class="kn">import</span> <span class="nn">os</span>
+<span class="kn">import</span> <span class="nn">sys</span>
+<span class="kn">import</span> <span class="nn">importlib</span> <span class="k">as</span> <span class="nn">imp</span>
+<span class="kn">import</span> <span class="nn">re</span>
+<span class="kn">import</span> <span class="nn">json</span>
+<span class="kn">import</span> <span class="nn">copy</span>
+<span class="kn">import</span> <span class="nn">itertools</span>
+<span class="kn">import</span> <span class="nn">collections</span>
+
+<span class="kn">import</span> <span class="nn">pandas</span> <span class="k">as</span> <span class="nn">pd</span>
+
+<span class="kn">import</span> <span class="nn">pypath.share.progress</span> <span class="k">as</span> <span class="nn">progress</span>
+<span class="kn">import</span> <span class="nn">pypath.resources.urls</span> <span class="k">as</span> <span class="nn">urls</span>
+<span class="kn">import</span> <span class="nn">pypath.resources.data_formats</span> <span class="k">as</span> <span class="nn">data_formats</span>
+<span class="kn">import</span> <span class="nn">pypath.share.settings</span> <span class="k">as</span> <span class="nn">settings</span>
+<span class="kn">import</span> <span class="nn">pypath.core.entity</span> <span class="k">as</span> <span class="nn">entity</span>
+<span class="kn">import</span> <span class="nn">pypath.share.session</span> <span class="k">as</span> <span class="nn">session</span>
+<span class="kn">import</span> <span class="nn">pypath.resources.network</span> <span class="k">as</span> <span class="nn">netres</span>
+<span class="kn">import</span> <span class="nn">pypath.share.common</span> <span class="k">as</span> <span class="nn">common</span>
+
+<span class="n">strip_json</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">compile</span><span class="p">(</span><span class="sa">r</span><span class="s1">&#39;[\[\]</span><span class="si">{}</span><span class="s1">\&quot;]&#39;</span><span class="p">)</span>
+<span class="n">simple_types</span> <span class="o">=</span> <span class="p">{</span><span class="nb">bool</span><span class="p">,</span> <span class="nb">int</span><span class="p">,</span> <span class="nb">float</span><span class="p">,</span> <span class="nb">type</span><span class="p">(</span><span class="kc">None</span><span class="p">)}</span>
+
+
+<div class="viewcode-block" id="Export">
+<a class="viewcode-back" href="../../../api/pypath.omnipath.export.Export.html#pypath.omnipath.export.Export">[docs]</a>
+<span class="k">class</span> <span class="nc">Export</span><span class="p">(</span><span class="n">session</span><span class="o">.</span><span class="n">Logger</span><span class="p">):</span>
+
+    <span class="n">default_header_uniquepairs</span> <span class="o">=</span> <span class="p">[</span>
+        <span class="s1">&#39;UniProt_A&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;GeneSymbol_A&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;UniProt_B&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;GeneSymbol_B&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;Databases&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;PubMed_IDs&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;Undirected&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;Direction_A-B&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;Direction_B-A&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;Stimulatory_A-B&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;Inhibitory_A-B&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;Stimulatory_B-A&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;Inhibitory_B-A&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;Category&#39;</span><span class="p">,</span>
+    <span class="p">]</span>
+
+    <span class="n">default_dtypes_uniquepairs</span> <span class="o">=</span> <span class="p">{</span>
+        <span class="s1">&#39;UniProt_A&#39;</span><span class="p">:</span> <span class="s1">&#39;category&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;GeneSymbol_A&#39;</span><span class="p">:</span> <span class="s1">&#39;category&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;UniProt_B&#39;</span><span class="p">:</span> <span class="s1">&#39;category&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;GeneSymbol_B&#39;</span><span class="p">:</span> <span class="s1">&#39;category&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;Undirected&#39;</span><span class="p">:</span> <span class="s1">&#39;category&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;Direction_A-B&#39;</span><span class="p">:</span> <span class="s1">&#39;category&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;Direction_B-A&#39;</span><span class="p">:</span> <span class="s1">&#39;category&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;Stimulatory_A-B&#39;</span><span class="p">:</span> <span class="s1">&#39;category&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;Inhibitory_A-B&#39;</span><span class="p">:</span> <span class="s1">&#39;category&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;Stimulatory_B-A&#39;</span><span class="p">:</span> <span class="s1">&#39;category&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;Inhibitory_B-A&#39;</span><span class="p">:</span> <span class="s1">&#39;category&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;Category&#39;</span><span class="p">:</span> <span class="s1">&#39;category&#39;</span><span class="p">,</span>
+    <span class="p">}</span>
+
+    <span class="n">default_header_bydirs</span> <span class="o">=</span> <span class="p">[</span>
+        <span class="s1">&#39;source&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;target&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;source_genesymbol&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;target_genesymbol&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;is_directed&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;is_stimulation&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;is_inhibition&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;consensus_direction&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;consensus_stimulation&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;consensus_inhibition&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;sources&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;references&#39;</span><span class="p">,</span>
+    <span class="p">]</span>
+
+    <span class="n">default_dtypes_bydirs</span> <span class="o">=</span> <span class="p">{</span>
+        <span class="s1">&#39;source&#39;</span><span class="p">:</span> <span class="s1">&#39;category&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;target&#39;</span><span class="p">:</span> <span class="s1">&#39;category&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;source_genesymbol&#39;</span><span class="p">:</span> <span class="s1">&#39;category&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;target_genesymbol&#39;</span><span class="p">:</span> <span class="s1">&#39;category&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;is_directed&#39;</span><span class="p">:</span> <span class="s1">&#39;int8&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;is_stimulation&#39;</span><span class="p">:</span> <span class="s1">&#39;int8&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;is_inhibition&#39;</span><span class="p">:</span> <span class="s1">&#39;int8&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;consensus_direction&#39;</span><span class="p">:</span> <span class="s1">&#39;int8&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;consensus_stimulation&#39;</span><span class="p">:</span> <span class="s1">&#39;int8&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;consensus_inhibition&#39;</span><span class="p">:</span> <span class="s1">&#39;int8&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;sources&#39;</span><span class="p">:</span> <span class="s1">&#39;category&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;references&#39;</span><span class="p">:</span> <span class="s1">&#39;category&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;curation_effort&#39;</span><span class="p">:</span> <span class="s1">&#39;int16&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;extra_attrs&#39;</span><span class="p">:</span> <span class="s1">&#39;category&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;evidences&#39;</span><span class="p">:</span> <span class="s1">&#39;category&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;entity_type_source&#39;</span><span class="p">:</span> <span class="s1">&#39;category&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;entity_type_target&#39;</span><span class="p">:</span> <span class="s1">&#39;category&#39;</span><span class="p">,</span>
+    <span class="p">}</span>
+
+<div class="viewcode-block" id="Export.__init__">
+<a class="viewcode-back" href="../../../api/pypath.omnipath.export.Export.html#pypath.omnipath.export.Export.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">network</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">only_sources</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">extra_node_attrs</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">extra_edge_attrs</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">outfile</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">default_vertex_attr_processor</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">default_edge_attr_processor</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">pa</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+        <span class="p">):</span>
+
+        <span class="n">session</span><span class="o">.</span><span class="n">Logger</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">name</span> <span class="o">=</span> <span class="s1">&#39;export&#39;</span><span class="p">)</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span><span class="s1">&#39;Export object created for network.&#39;</span><span class="p">)</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">extra_node_attrs</span> <span class="o">=</span> <span class="n">extra_node_attrs</span> <span class="ow">or</span> <span class="p">{}</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">extra_edge_attrs</span> <span class="o">=</span> <span class="n">extra_edge_attrs</span> <span class="ow">or</span> <span class="p">{}</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">outfile</span> <span class="o">=</span> <span class="n">outfile</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">network</span> <span class="o">=</span> <span class="n">network</span> <span class="ow">or</span> <span class="n">pa</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">pa</span>      <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">network</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">_set_graph</span><span class="p">()</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">only_sources</span> <span class="o">=</span> <span class="n">only_sources</span>
+
+        <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">only_sources</span><span class="p">,</span> <span class="nb">list</span><span class="p">):</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">only_sources</span> <span class="o">=</span> <span class="nb">set</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">only_sources</span><span class="p">)</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">default_vertex_attr_processor</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="n">default_vertex_attr_processor</span> <span class="ow">or</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">default_vertex_attr_processor</span>
+        <span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">default_edge_attr_processor</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="n">default_edge_attr_processor</span> <span class="ow">or</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">default_edge_attr_processor</span>
+        <span class="p">)</span></div>
+
+
+    <span class="k">def</span> <span class="nf">reload</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="n">modname</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="vm">__class__</span><span class="o">.</span><span class="vm">__module__</span>
+        <span class="n">mod</span> <span class="o">=</span> <span class="nb">__import__</span><span class="p">(</span><span class="n">modname</span><span class="p">,</span> <span class="n">fromlist</span> <span class="o">=</span> <span class="p">[</span><span class="n">modname</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;.&#39;</span><span class="p">)[</span><span class="mi">0</span><span class="p">]])</span>
+        <span class="n">imp</span><span class="o">.</span><span class="n">reload</span><span class="p">(</span><span class="n">mod</span><span class="p">)</span>
+        <span class="n">new</span> <span class="o">=</span> <span class="nb">getattr</span><span class="p">(</span><span class="n">mod</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="vm">__class__</span><span class="o">.</span><span class="vm">__name__</span><span class="p">)</span>
+        <span class="nb">setattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">&#39;__class__&#39;</span><span class="p">,</span> <span class="n">new</span><span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">_set_graph</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">graph</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">pa</span><span class="o">.</span><span class="n">_get_undirected</span><span class="p">()</span>
+                <span class="k">if</span> <span class="nb">hasattr</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">pa</span><span class="p">,</span> <span class="s1">&#39;_get_undirected&#39;</span><span class="p">)</span> <span class="k">else</span>
+            <span class="kc">None</span>
+        <span class="p">)</span>
+
+
+<div class="viewcode-block" id="Export.make_df">
+<a class="viewcode-back" href="../../../api/pypath.omnipath.export.Export.html#pypath.omnipath.export.Export.make_df">[docs]</a>
+    <span class="k">def</span> <span class="nf">make_df</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">unique_pairs</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
+            <span class="n">extra_node_attrs</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">extra_edge_attrs</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+        <span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Creates a data frame from the network.</span>
+
+<span class="sd">        By default UniProt IDs, Gene Symbols, source databases, literature</span>
+<span class="sd">        references, directionality and sign information and interaction type</span>
+<span class="sd">        are included.</span>
+
+<span class="sd">        Args</span>
+<span class="sd">        -----</span>
+<span class="sd">        :param bool unique_pairs:</span>
+<span class="sd">            If `True` each line corresponds to a unique pair of molecules,</span>
+<span class="sd">            all directionality and sign information are covered in other</span>
+<span class="sd">            columns. If `False`, order of `A` and `B` IDs corresponds to</span>
+<span class="sd">            the direction while sign covered in further columns.</span>
+<span class="sd">        :param dict extra_node_attrs:</span>
+<span class="sd">            Additional node attributes to be included in the exported table.</span>
+<span class="sd">            Keys are column names used in the header while values are names</span>
+<span class="sd">            of vertex attributes. Values also might be methods which then</span>
+<span class="sd">            will be called then on each vertex. These should return strings</span>
+<span class="sd">            or their result will be converted to string.</span>
+<span class="sd">            In the header `_A` and `_B` suffixes will be appended to the</span>
+<span class="sd">            column names so the values can be assigned to A and B side</span>
+<span class="sd">            interaction partners.</span>
+<span class="sd">        :param dict extra_edge_attrs:</span>
+<span class="sd">            Additional edge attributes to be included in the exported table.</span>
+<span class="sd">            Keys are column names used in the header while values are names</span>
+<span class="sd">            of edge attributes or callables accepting an edge as single</span>
+<span class="sd">            argument.</span>
+<span class="sd">        :param str outfile:</span>
+<span class="sd">            Name of the output file. If `None` a file name</span>
+<span class="sd">            &quot;netrowk-&lt;session id&gt;.tab&quot; is used.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span><span class="s1">&#39;Creating data frame of type `</span><span class="si">%s</span><span class="s1">`.&#39;</span> <span class="o">%</span> <span class="p">(</span>
+            <span class="s1">&#39;unique pairs&#39;</span> <span class="k">if</span> <span class="n">unique_pairs</span> <span class="k">else</span> <span class="s1">&#39;by direction&#39;</span>
+        <span class="p">))</span>
+
+        <span class="n">kwargs</span> <span class="o">=</span> <span class="nb">locals</span><span class="p">()</span>
+        <span class="n">_</span> <span class="o">=</span> <span class="n">kwargs</span><span class="o">.</span><span class="n">pop</span><span class="p">(</span><span class="s1">&#39;self&#39;</span><span class="p">)</span>
+
+        <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">graph</span><span class="p">:</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">_make_df_igraph</span><span class="p">(</span><span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
+
+        <span class="k">else</span><span class="p">:</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">_make_df_network</span><span class="p">(</span><span class="o">**</span><span class="n">kwargs</span><span class="p">)</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">_make_df_network</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">unique_pairs</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
+            <span class="n">extra_node_attrs</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">extra_edge_attrs</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+        <span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        See docs at method ``make_df``.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span><span class="s1">&#39;Creating data frame from `core.network.Network` object.&#39;</span><span class="p">)</span>
+
+        <span class="k">if</span> <span class="n">unique_pairs</span><span class="p">:</span>
+
+            <span class="n">msg</span> <span class="o">=</span> <span class="p">(</span>
+                <span class="s1">&#39;Data frame with unique pairs from `core.network.Network` &#39;</span>
+                <span class="s1">&#39;is not implemented yet, only possible to create it from &#39;</span>
+                <span class="s1">&#39;`legacy.main.PyPath` object.&#39;</span>
+            <span class="p">)</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span><span class="n">msg</span><span class="p">)</span>
+            <span class="k">raise</span> <span class="ne">NotImplementedError</span><span class="p">(</span><span class="n">msg</span><span class="p">)</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">extra_node_attrs</span> <span class="o">=</span> <span class="n">extra_node_attrs</span> <span class="ow">or</span> <span class="bp">self</span><span class="o">.</span><span class="n">extra_node_attrs</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">extra_edge_attrs</span> <span class="o">=</span> <span class="n">extra_edge_attrs</span> <span class="ow">or</span> <span class="bp">self</span><span class="o">.</span><span class="n">extra_edge_attrs</span>
+
+        <span class="n">header</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">get_header</span><span class="p">(</span><span class="n">unique_pairs</span> <span class="o">=</span> <span class="n">unique_pairs</span><span class="p">)</span>
+
+        <span class="n">dtypes</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">default_dtypes_uniquepairs</span>
+                <span class="k">if</span> <span class="n">unique_pairs</span> <span class="k">else</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">default_dtypes_bydirs</span>
+        <span class="p">)</span>
+        <span class="n">dtypes</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">(</span><span class="n">i</span> <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="n">dtypes</span><span class="o">.</span><span class="n">items</span><span class="p">()</span> <span class="k">if</span> <span class="n">i</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="ow">in</span> <span class="n">header</span><span class="p">)</span>
+
+        <span class="n">result</span> <span class="o">=</span> <span class="p">[]</span>
+
+        <span class="k">for</span> <span class="n">ia</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">network</span><span class="p">:</span>
+
+            <span class="n">result</span><span class="o">.</span><span class="n">extend</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">process_interaction</span><span class="p">(</span><span class="n">ia</span><span class="p">))</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">df</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">(</span><span class="n">result</span><span class="p">,</span> <span class="n">columns</span> <span class="o">=</span> <span class="n">header</span><span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">df</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">df</span><span class="o">.</span><span class="n">astype</span><span class="p">(</span><span class="n">dtypes</span><span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">process_interaction</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">ia</span><span class="p">):</span>
+
+        <span class="n">result</span> <span class="o">=</span> <span class="p">[]</span>
+
+        <span class="n">consensus</span> <span class="o">=</span> <span class="n">ia</span><span class="o">.</span><span class="n">consensus</span><span class="p">()</span>
+
+        <span class="k">for</span> <span class="n">_dir</span> <span class="ow">in</span> <span class="p">(</span><span class="s1">&#39;a_b&#39;</span><span class="p">,</span> <span class="s1">&#39;b_a&#39;</span><span class="p">):</span>
+
+            <span class="n">nodes</span> <span class="o">=</span> <span class="nb">getattr</span><span class="p">(</span><span class="n">ia</span><span class="p">,</span> <span class="n">_dir</span><span class="p">)</span>
+            <span class="n">directed</span> <span class="o">=</span> <span class="nb">bool</span><span class="p">(</span><span class="n">ia</span><span class="o">.</span><span class="n">direction</span><span class="p">[</span><span class="n">nodes</span><span class="p">])</span>
+            <span class="n">directed_rev</span> <span class="o">=</span> <span class="nb">bool</span><span class="p">(</span><span class="n">ia</span><span class="o">.</span><span class="n">direction</span><span class="p">[</span><span class="nb">tuple</span><span class="p">(</span><span class="nb">reversed</span><span class="p">(</span><span class="n">nodes</span><span class="p">))])</span>
+
+            <span class="k">if</span> <span class="p">(</span>
+                <span class="p">(</span>
+                    <span class="ow">not</span> <span class="n">directed</span> <span class="ow">and</span>
+                    <span class="p">(</span><span class="n">_dir</span> <span class="o">==</span> <span class="s1">&#39;b_a&#39;</span> <span class="ow">or</span> <span class="n">directed_rev</span><span class="p">)</span>
+                <span class="p">)</span> <span class="ow">or</span> <span class="p">(</span>
+                    <span class="n">ia</span><span class="o">.</span><span class="n">is_loop</span><span class="p">()</span> <span class="ow">and</span>
+                    <span class="n">_dir</span> <span class="o">==</span> <span class="s1">&#39;b_a&#39;</span>
+                <span class="p">)</span>
+            <span class="p">):</span>
+
+                <span class="k">continue</span>
+
+            <span class="n">positive</span> <span class="o">=</span> <span class="nb">getattr</span><span class="p">(</span><span class="n">ia</span><span class="p">,</span> <span class="s1">&#39;positive_</span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="n">_dir</span><span class="p">)()</span>
+            <span class="n">negative</span> <span class="o">=</span> <span class="nb">getattr</span><span class="p">(</span><span class="n">ia</span><span class="p">,</span> <span class="s1">&#39;negative_</span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="n">_dir</span><span class="p">)()</span>
+
+            <span class="n">resources</span> <span class="o">=</span> <span class="s1">&#39;;&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span>
+                <span class="nb">sorted</span><span class="p">(</span><span class="nb">set</span><span class="p">(</span>
+                    <span class="s1">&#39;</span><span class="si">%s%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="p">(</span>
+                        <span class="n">res</span><span class="p">,</span>
+                        <span class="p">(</span><span class="s1">&#39;_</span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="n">via</span><span class="p">)</span> <span class="k">if</span> <span class="n">via</span> <span class="k">else</span> <span class="s1">&#39;&#39;</span><span class="p">,</span>
+                    <span class="p">)</span>
+                    <span class="k">for</span> <span class="n">res</span><span class="p">,</span> <span class="n">via</span> <span class="ow">in</span>
+                    <span class="n">itertools</span><span class="o">.</span><span class="n">chain</span><span class="p">(</span>
+                        <span class="n">ia</span><span class="o">.</span><span class="n">get_resource_names_via</span><span class="p">(</span>
+                            <span class="n">direction</span> <span class="o">=</span> <span class="s1">&#39;undirected&#39;</span><span class="p">,</span>
+                            <span class="n">via</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+                        <span class="p">),</span>
+                        <span class="n">ia</span><span class="o">.</span><span class="n">get_resource_names_via</span><span class="p">(</span>
+                            <span class="n">direction</span> <span class="o">=</span> <span class="n">nodes</span><span class="p">,</span>
+                            <span class="n">via</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+                        <span class="p">),</span>
+                    <span class="p">)</span>
+                <span class="p">))</span>
+            <span class="p">)</span>
+
+            <span class="n">references</span> <span class="o">=</span> <span class="s1">&#39;;&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span>
+                <span class="nb">sorted</span><span class="p">(</span><span class="nb">set</span><span class="p">(</span>
+                    <span class="s1">&#39;</span><span class="si">%s</span><span class="s1">:</span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="p">(</span>
+                        <span class="n">ev</span><span class="o">.</span><span class="n">resource</span><span class="o">.</span><span class="n">via</span> <span class="ow">or</span> <span class="n">ev</span><span class="o">.</span><span class="n">resource</span><span class="o">.</span><span class="n">name</span><span class="p">,</span>
+                        <span class="n">ref</span><span class="o">.</span><span class="n">pmid</span>
+                    <span class="p">)</span>
+                    <span class="k">for</span> <span class="n">ev</span> <span class="ow">in</span> <span class="n">itertools</span><span class="o">.</span><span class="n">chain</span><span class="p">(</span>
+                        <span class="n">ia</span><span class="o">.</span><span class="n">get_evidences</span><span class="p">(</span><span class="n">direction</span> <span class="o">=</span> <span class="s1">&#39;undirected&#39;</span><span class="p">),</span>
+                        <span class="n">ia</span><span class="o">.</span><span class="n">get_evidences</span><span class="p">(</span><span class="n">direction</span> <span class="o">=</span> <span class="n">nodes</span><span class="p">),</span>
+                    <span class="p">)</span>
+                    <span class="k">for</span> <span class="n">ref</span> <span class="ow">in</span> <span class="n">ev</span><span class="o">.</span><span class="n">references</span>
+                    <span class="k">if</span> <span class="ow">not</span> <span class="n">ev</span><span class="o">.</span><span class="n">resource</span><span class="o">.</span><span class="n">via</span>
+                <span class="p">))</span>
+            <span class="p">)</span>
+
+            <span class="n">this_row</span> <span class="o">=</span> <span class="p">[</span>
+                <span class="n">nodes</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">identifier</span><span class="p">,</span>
+                <span class="n">nodes</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">identifier</span><span class="p">,</span>
+                <span class="n">nodes</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">label</span><span class="p">,</span>
+                <span class="n">nodes</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">label</span><span class="p">,</span>
+                <span class="nb">int</span><span class="p">(</span><span class="n">directed</span><span class="p">),</span>
+                <span class="nb">int</span><span class="p">(</span><span class="n">positive</span><span class="p">),</span>
+                <span class="nb">int</span><span class="p">(</span><span class="n">negative</span><span class="p">),</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">match_consensus</span><span class="p">(</span>
+                    <span class="n">consensus</span><span class="p">,</span>
+                    <span class="n">nodes</span><span class="p">,</span>
+                <span class="p">),</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">match_consensus</span><span class="p">(</span>
+                    <span class="n">consensus</span><span class="p">,</span>
+                    <span class="n">nodes</span><span class="p">,</span>
+                    <span class="s1">&#39;positive&#39;</span><span class="p">,</span>
+                <span class="p">),</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">match_consensus</span><span class="p">(</span>
+                    <span class="n">consensus</span><span class="p">,</span>
+                    <span class="n">nodes</span><span class="p">,</span>
+                    <span class="s1">&#39;negative&#39;</span><span class="p">,</span>
+                <span class="p">),</span>
+                <span class="n">resources</span><span class="p">,</span>
+                <span class="n">references</span><span class="p">,</span>
+            <span class="p">]</span>
+
+            <span class="n">this_row</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">add_extra_fields</span><span class="p">(</span><span class="n">ia</span><span class="p">,</span> <span class="n">this_row</span><span class="p">,</span> <span class="n">nodes</span><span class="p">)</span>
+
+            <span class="n">result</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">this_row</span><span class="p">)</span>
+
+        <span class="k">return</span> <span class="n">result</span>
+
+
+    <span class="nd">@staticmethod</span>
+    <span class="k">def</span> <span class="nf">match_consensus</span><span class="p">(</span><span class="n">consensus</span><span class="p">,</span> <span class="n">nodes</span><span class="p">,</span> <span class="n">effect</span> <span class="o">=</span> <span class="kc">None</span><span class="p">):</span>
+
+        <span class="n">param</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="n">nodes</span><span class="p">)</span> <span class="o">+</span> <span class="p">[</span><span class="s1">&#39;directed&#39;</span><span class="p">]</span>
+
+        <span class="k">if</span> <span class="n">effect</span><span class="p">:</span>
+
+            <span class="n">param</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">effect</span><span class="p">)</span>
+
+        <span class="k">return</span> <span class="nb">int</span><span class="p">(</span>
+            <span class="nb">any</span><span class="p">(</span>
+                <span class="n">co</span><span class="p">[:</span><span class="nb">len</span><span class="p">(</span><span class="n">param</span><span class="p">)]</span> <span class="o">==</span> <span class="n">param</span>
+                <span class="k">for</span> <span class="n">co</span> <span class="ow">in</span> <span class="n">consensus</span>
+            <span class="p">)</span>
+        <span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">_make_df_igraph</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">unique_pairs</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
+            <span class="n">extra_node_attrs</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">extra_edge_attrs</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+        <span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        See docs at method ``make_df``.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span><span class="s1">&#39;Creating data frame from `legacy.main.PyPath` object.&#39;</span><span class="p">)</span>
+
+        <span class="n">result</span> <span class="o">=</span> <span class="p">[]</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">pa</span><span class="o">.</span><span class="n">genesymbol_labels</span><span class="p">()</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">extra_node_attrs</span> <span class="o">=</span> <span class="n">extra_node_attrs</span> <span class="ow">or</span> <span class="bp">self</span><span class="o">.</span><span class="n">extra_node_attrs</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">extra_edge_attrs</span> <span class="o">=</span> <span class="n">extra_edge_attrs</span> <span class="ow">or</span> <span class="bp">self</span><span class="o">.</span><span class="n">extra_edge_attrs</span>
+
+        <span class="n">dtypes</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">default_dtypes_uniquepairs</span>
+                <span class="k">if</span> <span class="n">unique_pairs</span> <span class="k">else</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">default_dtypes_bydirs</span>
+        <span class="p">)</span>
+
+        <span class="n">header</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">get_header</span><span class="p">(</span><span class="n">unique_pairs</span> <span class="o">=</span> <span class="n">unique_pairs</span><span class="p">)</span>
+
+        <span class="n">prg</span> <span class="o">=</span> <span class="n">progress</span><span class="o">.</span><span class="n">Progress</span><span class="p">(</span>
+            <span class="n">total</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">graph</span><span class="o">.</span><span class="n">ecount</span><span class="p">(),</span>
+            <span class="n">name</span> <span class="o">=</span> <span class="s1">&#39;Creating table&#39;</span><span class="p">,</span>
+            <span class="n">interval</span> <span class="o">=</span> <span class="mi">31</span>
+        <span class="p">)</span>
+
+        <span class="k">for</span> <span class="n">e</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">graph</span><span class="o">.</span><span class="n">es</span><span class="p">:</span>
+
+            <span class="c1"># adding default fields</span>
+            <span class="n">lines</span> <span class="o">=</span> <span class="p">(</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">_process_edge_uniquepairs_igraph</span><span class="p">(</span><span class="n">e</span><span class="p">)</span>
+                    <span class="k">if</span> <span class="n">unique_pairs</span> <span class="k">else</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">_process_edge_bydirection_igraph</span><span class="p">(</span><span class="n">e</span><span class="p">)</span>
+            <span class="p">)</span>
+
+            <span class="n">result</span><span class="o">.</span><span class="n">extend</span><span class="p">(</span><span class="n">lines</span><span class="p">)</span>
+
+            <span class="n">prg</span><span class="o">.</span><span class="n">step</span><span class="p">()</span>
+
+        <span class="n">prg</span><span class="o">.</span><span class="n">terminate</span><span class="p">()</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">df</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">(</span><span class="n">result</span><span class="p">,</span> <span class="n">columns</span> <span class="o">=</span> <span class="n">header</span><span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">df</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">df</span><span class="o">.</span><span class="n">astype</span><span class="p">(</span><span class="n">dtypes</span><span class="p">)</span>
+
+
+<div class="viewcode-block" id="Export.get_header">
+<a class="viewcode-back" href="../../../api/pypath.omnipath.export.Export.html#pypath.omnipath.export.Export.get_header">[docs]</a>
+    <span class="k">def</span> <span class="nf">get_header</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">unique_pairs</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
+        <span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Creates a data frame header (list of field names) according to the</span>
+<span class="sd">        data frame type and the extra fields.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">suffix_a</span> <span class="o">=</span> <span class="s1">&#39;A&#39;</span> <span class="k">if</span> <span class="n">unique_pairs</span> <span class="k">else</span> <span class="s1">&#39;source&#39;</span>
+        <span class="n">suffix_b</span> <span class="o">=</span> <span class="s1">&#39;B&#39;</span> <span class="k">if</span> <span class="n">unique_pairs</span> <span class="k">else</span> <span class="s1">&#39;target&#39;</span>
+
+        <span class="n">header</span> <span class="o">=</span> <span class="n">copy</span><span class="o">.</span><span class="n">copy</span><span class="p">(</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">default_header_uniquepairs</span>
+            <span class="k">if</span> <span class="n">unique_pairs</span> <span class="k">else</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">default_header_bydirs</span>
+        <span class="p">)</span>
+        <span class="n">header</span> <span class="o">+=</span> <span class="bp">self</span><span class="o">.</span><span class="n">extra_edge_attrs</span><span class="o">.</span><span class="n">keys</span><span class="p">()</span>
+        <span class="n">header</span> <span class="o">+=</span> <span class="p">[</span>
+            <span class="s1">&#39;</span><span class="si">%s</span><span class="s1">_</span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="p">(</span><span class="n">x</span><span class="p">,</span> <span class="n">suffix_a</span><span class="p">)</span>
+            <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">extra_node_attrs</span><span class="o">.</span><span class="n">keys</span><span class="p">()</span>
+        <span class="p">]</span>
+        <span class="n">header</span> <span class="o">+=</span> <span class="p">[</span>
+            <span class="s1">&#39;</span><span class="si">%s</span><span class="s1">_</span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="p">(</span><span class="n">x</span><span class="p">,</span> <span class="n">suffix_b</span><span class="p">)</span>
+            <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">extra_node_attrs</span><span class="o">.</span><span class="n">keys</span><span class="p">()</span>
+        <span class="p">]</span>
+
+        <span class="k">return</span> <span class="n">header</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">_process_edge_uniquepairs_igraph</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">e</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Returns a table row representing a network edge with covering all</span>
+<span class="sd">        annotations in a single row: directionality represented by fields</span>
+<span class="sd">        like `Direction_A-B` and `Direction_B-A` effect sign a similar way.</span>
+
+<span class="sd">        Args</span>
+<span class="sd">        -----</span>
+<span class="sd">        :param igraph.Edge e:</span>
+<span class="sd">            An edge from a pypath igraph object.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">only_sources</span> <span class="ow">and</span> <span class="ow">not</span> <span class="n">e</span><span class="p">[</span><span class="s1">&#39;sources&#39;</span><span class="p">]</span> <span class="o">&amp;</span> <span class="bp">self</span><span class="o">.</span><span class="n">only_sources</span><span class="p">:</span>
+
+            <span class="k">return</span> <span class="p">[]</span>
+
+        <span class="n">vertex_a</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">graph</span><span class="o">.</span><span class="n">vs</span><span class="p">[</span><span class="n">e</span><span class="o">.</span><span class="n">source</span><span class="p">]</span>
+        <span class="n">vertex_b</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">graph</span><span class="o">.</span><span class="n">vs</span><span class="p">[</span><span class="n">e</span><span class="o">.</span><span class="n">target</span><span class="p">]</span>
+
+        <span class="n">name_a</span><span class="p">,</span> <span class="n">label_a</span> <span class="o">=</span> <span class="n">entity</span><span class="o">.</span><span class="n">Entity</span><span class="o">.</span><span class="n">igraph_vertex_name_label</span><span class="p">(</span><span class="n">vertex_a</span><span class="p">)</span>
+        <span class="n">name_b</span><span class="p">,</span> <span class="n">label_b</span> <span class="o">=</span> <span class="n">entity</span><span class="o">.</span><span class="n">Entity</span><span class="o">.</span><span class="n">igraph_vertex_name_label</span><span class="p">(</span><span class="n">vertex_b</span><span class="p">)</span>
+
+        <span class="k">return</span> <span class="p">[</span>
+            <span class="nb">list</span><span class="p">(</span><span class="n">itertools</span><span class="o">.</span><span class="n">chain</span><span class="p">(</span>
+                <span class="p">(</span>
+                    <span class="c1"># uniprots, genesymbols</span>
+                        <span class="n">name_a</span><span class="p">,</span>
+                        <span class="n">label_a</span><span class="p">,</span>
+                        <span class="n">name_b</span><span class="p">,</span>
+                        <span class="n">label_b</span><span class="p">,</span>
+                    <span class="c1"># sources, references</span>
+                        <span class="s1">&#39;;&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="nb">list</span><span class="p">(</span><span class="n">e</span><span class="p">[</span><span class="s1">&#39;sources&#39;</span><span class="p">])),</span>
+                        <span class="s1">&#39;;&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span>
+                            <span class="nb">sorted</span><span class="p">(</span>
+                                <span class="nb">set</span><span class="p">(</span><span class="n">r</span><span class="o">.</span><span class="n">pmid</span> <span class="k">for</span> <span class="n">r</span> <span class="ow">in</span> <span class="n">e</span><span class="p">[</span><span class="s1">&#39;references&#39;</span><span class="p">]),</span>
+                                <span class="n">key</span> <span class="o">=</span> <span class="nb">int</span>
+                            <span class="p">)</span>
+                        <span class="p">),</span>
+                    <span class="c1"># directions</span>
+                        <span class="s1">&#39;;&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">e</span><span class="p">[</span><span class="s1">&#39;dirs&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">get_dir</span><span class="p">(</span>
+                            <span class="s1">&#39;undirected&#39;</span><span class="p">,</span> <span class="n">sources</span><span class="o">=</span><span class="kc">True</span><span class="p">)),</span>
+                        <span class="s1">&#39;;&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">e</span><span class="p">[</span><span class="s1">&#39;dirs&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">get_dir</span><span class="p">(</span>
+                            <span class="p">(</span><span class="n">name_a</span><span class="p">,</span> <span class="n">name_b</span><span class="p">),</span> <span class="n">sources</span><span class="o">=</span><span class="kc">True</span><span class="p">)),</span>
+                        <span class="s1">&#39;;&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">e</span><span class="p">[</span><span class="s1">&#39;dirs&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">get_dir</span><span class="p">(</span>
+                            <span class="p">(</span><span class="n">name_b</span><span class="p">,</span> <span class="n">name_a</span><span class="p">),</span> <span class="n">sources</span><span class="o">=</span><span class="kc">True</span><span class="p">))</span>
+                <span class="p">),</span>
+                <span class="p">(</span>
+                    <span class="c1"># signs</span>
+                    <span class="s1">&#39;;&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">a</span><span class="p">)</span> <span class="k">for</span> <span class="n">a</span> <span class="ow">in</span>
+                    <span class="n">itertools</span><span class="o">.</span><span class="n">chain</span><span class="p">(</span>
+                        <span class="n">e</span><span class="p">[</span><span class="s1">&#39;dirs&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">get_sign</span><span class="p">((</span><span class="n">name_a</span><span class="p">,</span> <span class="n">name_b</span><span class="p">),</span> <span class="n">sources</span><span class="o">=</span><span class="kc">True</span><span class="p">),</span>
+                        <span class="n">e</span><span class="p">[</span><span class="s1">&#39;dirs&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">get_sign</span><span class="p">((</span><span class="n">name_b</span><span class="p">,</span> <span class="n">name_a</span><span class="p">),</span> <span class="n">sources</span><span class="o">=</span><span class="kc">True</span><span class="p">),</span>
+                    <span class="p">)</span>
+                <span class="p">),</span>
+                <span class="p">(</span>
+                    <span class="c1"># category</span>
+                    <span class="s1">&#39;;&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">e</span><span class="p">[</span><span class="s1">&#39;type&#39;</span><span class="p">]),</span>
+                <span class="p">)</span>
+            <span class="p">))</span>
+        <span class="p">]</span>
+
+    <span class="k">def</span> <span class="nf">_process_edge_bydirection_igraph</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">e</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Returns one or more table rows representing a network edge a way</span>
+<span class="sd">        that opposite direction connections contained in separate rows.</span>
+<span class="sd">        Directionality and sign information covered in 3 columns:</span>
+<span class="sd">        `is_directed`, `is_inhibition` and `is_stimulation`.</span>
+<span class="sd">        This is the row format used in the webservice.</span>
+
+<span class="sd">        Args</span>
+<span class="sd">        -----</span>
+<span class="sd">        :param igraph.Edge e:</span>
+<span class="sd">            An edge from a pypath igraph object.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">lines</span> <span class="o">=</span> <span class="p">[]</span>
+
+        <span class="n">consensus_edges</span> <span class="o">=</span> <span class="nb">set</span><span class="p">(</span><span class="nb">map</span><span class="p">(</span><span class="nb">tuple</span><span class="p">,</span> <span class="n">e</span><span class="p">[</span><span class="s1">&#39;dirs&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">consensus_edges</span><span class="p">()))</span>
+        <span class="n">consensus_dir</span> <span class="o">=</span> <span class="nb">set</span><span class="p">(</span><span class="n">c</span><span class="p">[:</span><span class="mi">3</span><span class="p">]</span> <span class="k">for</span> <span class="n">c</span> <span class="ow">in</span> <span class="n">consensus_edges</span><span class="p">)</span>
+
+        <span class="k">for</span> <span class="n">d</span> <span class="ow">in</span> <span class="p">[</span><span class="s1">&#39;straight&#39;</span><span class="p">,</span> <span class="s1">&#39;reverse&#39;</span><span class="p">]:</span>
+
+            <span class="n">uniprots</span> <span class="o">=</span> <span class="nb">getattr</span><span class="p">(</span><span class="n">e</span><span class="p">[</span><span class="s1">&#39;dirs&#39;</span><span class="p">],</span> <span class="n">d</span><span class="p">)</span>
+
+            <span class="k">if</span> <span class="n">e</span><span class="p">[</span><span class="s1">&#39;dirs&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">dirs</span><span class="p">[</span><span class="n">uniprots</span><span class="p">]:</span>
+
+                <span class="n">is_stimulation</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">e</span><span class="p">[</span><span class="s1">&#39;dirs&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">is_stimulation</span><span class="p">(</span><span class="n">uniprots</span><span class="p">))</span>
+                <span class="n">is_inhibition</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">e</span><span class="p">[</span><span class="s1">&#39;dirs&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">is_inhibition</span><span class="p">(</span><span class="n">uniprots</span><span class="p">))</span>
+
+                <span class="n">this_edge</span> <span class="o">=</span> <span class="p">[</span>
+                    <span class="n">entity</span><span class="o">.</span><span class="n">Entity</span><span class="o">.</span><span class="n">entity_name_str</span><span class="p">(</span><span class="n">uniprots</span><span class="p">[</span><span class="mi">0</span><span class="p">]),</span>
+                    <span class="n">entity</span><span class="o">.</span><span class="n">Entity</span><span class="o">.</span><span class="n">entity_name_str</span><span class="p">(</span><span class="n">uniprots</span><span class="p">[</span><span class="mi">1</span><span class="p">]),</span>
+                    <span class="bp">self</span><span class="o">.</span><span class="n">pa</span><span class="o">.</span><span class="n">name_to_label</span><span class="p">(</span><span class="n">uniprots</span><span class="p">[</span><span class="mi">0</span><span class="p">]),</span>
+                    <span class="bp">self</span><span class="o">.</span><span class="n">pa</span><span class="o">.</span><span class="n">name_to_label</span><span class="p">(</span><span class="n">uniprots</span><span class="p">[</span><span class="mi">1</span><span class="p">]),</span>
+                    <span class="mi">1</span><span class="p">,</span> <span class="c1"># is_directed</span>
+                    <span class="n">is_stimulation</span><span class="p">,</span>
+                    <span class="n">is_inhibition</span><span class="p">,</span>
+                    <span class="nb">int</span><span class="p">(</span>
+                        <span class="p">(</span><span class="n">uniprots</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">uniprots</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span> <span class="s1">&#39;directed&#39;</span><span class="p">)</span>
+                        <span class="ow">in</span> <span class="n">consensus_dir</span>
+                    <span class="p">),</span>
+                    <span class="nb">int</span><span class="p">(</span>
+                        <span class="p">(</span><span class="n">uniprots</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">uniprots</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span> <span class="s1">&#39;directed&#39;</span><span class="p">,</span> <span class="s1">&#39;positive&#39;</span><span class="p">)</span>
+                        <span class="ow">in</span> <span class="n">consensus_edges</span>
+                    <span class="p">),</span>
+                    <span class="nb">int</span><span class="p">(</span>
+                        <span class="p">(</span><span class="n">uniprots</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">uniprots</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span> <span class="s1">&#39;directed&#39;</span><span class="p">,</span> <span class="s1">&#39;negative&#39;</span><span class="p">)</span>
+                        <span class="ow">in</span> <span class="n">consensus_edges</span>
+                    <span class="p">),</span>
+                <span class="p">]</span>
+
+                <span class="n">dsources</span> <span class="o">=</span> <span class="p">(</span>
+                    <span class="n">e</span><span class="p">[</span><span class="s1">&#39;dirs&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">get_dir</span><span class="p">(</span><span class="n">uniprots</span><span class="p">,</span> <span class="n">sources</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span> <span class="o">|</span>
+                    <span class="n">e</span><span class="p">[</span><span class="s1">&#39;dirs&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">get_dir</span><span class="p">(</span><span class="s1">&#39;undirected&#39;</span><span class="p">,</span> <span class="n">sources</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
+                <span class="p">)</span>
+
+                <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">only_sources</span> <span class="ow">and</span> <span class="ow">not</span> <span class="n">dsources</span> <span class="o">&amp;</span> <span class="bp">self</span><span class="o">.</span><span class="n">only_sources</span><span class="p">:</span>
+
+                    <span class="k">continue</span>
+
+                <span class="n">this_edge</span><span class="o">.</span><span class="n">extend</span><span class="p">([</span>
+                    <span class="s1">&#39;;&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="nb">sorted</span><span class="p">(</span><span class="n">dsources</span><span class="p">)),</span>
+                    <span class="s1">&#39;;&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span>
+                        <span class="n">r</span><span class="o">.</span><span class="n">pmid</span>
+                        <span class="k">for</span> <span class="n">r</span> <span class="ow">in</span> <span class="n">itertools</span><span class="o">.</span><span class="n">chain</span><span class="p">(</span><span class="o">*</span><span class="p">(</span>
+                            <span class="n">rs</span> <span class="k">for</span> <span class="n">s</span><span class="p">,</span> <span class="n">rs</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="n">e</span><span class="p">[</span><span class="s1">&#39;refs_by_source&#39;</span><span class="p">])</span>
+                            <span class="k">if</span> <span class="n">s</span> <span class="ow">in</span> <span class="n">dsources</span>
+                        <span class="p">))</span>
+                    <span class="p">)</span>
+                <span class="p">])</span>
+
+                <span class="n">this_edge</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">add_extra_fields</span><span class="p">(</span><span class="n">e</span><span class="p">,</span> <span class="n">this_edge</span><span class="p">,</span> <span class="n">uniprots</span><span class="p">)</span>
+
+                <span class="n">lines</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">this_edge</span><span class="p">)</span>
+
+        <span class="k">if</span> <span class="ow">not</span> <span class="n">e</span><span class="p">[</span><span class="s1">&#39;dirs&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">is_directed</span><span class="p">():</span>
+
+            <span class="n">this_edge</span> <span class="o">=</span> <span class="p">[</span>
+                <span class="n">entity</span><span class="o">.</span><span class="n">Entity</span><span class="o">.</span><span class="n">entity_name_str</span><span class="p">(</span><span class="n">e</span><span class="p">[</span><span class="s1">&#39;dirs&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">nodes</span><span class="p">[</span><span class="mi">0</span><span class="p">]),</span>
+                <span class="n">entity</span><span class="o">.</span><span class="n">Entity</span><span class="o">.</span><span class="n">entity_name_str</span><span class="p">(</span><span class="n">e</span><span class="p">[</span><span class="s1">&#39;dirs&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">nodes</span><span class="p">[</span><span class="mi">1</span><span class="p">]),</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">pa</span><span class="o">.</span><span class="n">name_to_label</span><span class="p">(</span><span class="n">e</span><span class="p">[</span><span class="s1">&#39;dirs&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">nodes</span><span class="p">[</span><span class="mi">0</span><span class="p">]),</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">pa</span><span class="o">.</span><span class="n">name_to_label</span><span class="p">(</span><span class="n">e</span><span class="p">[</span><span class="s1">&#39;dirs&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">nodes</span><span class="p">[</span><span class="mi">1</span><span class="p">]),</span>
+                <span class="mi">0</span><span class="p">,</span>
+                <span class="mi">0</span><span class="p">,</span>
+                <span class="mi">0</span><span class="p">,</span>
+                <span class="mi">0</span><span class="p">,</span>
+                <span class="mi">0</span><span class="p">,</span>
+                <span class="mi">0</span><span class="p">,</span>
+                <span class="s1">&#39;;&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="nb">sorted</span><span class="p">(</span><span class="n">e</span><span class="p">[</span><span class="s1">&#39;sources&#39;</span><span class="p">])),</span>
+                <span class="s1">&#39;;&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">([</span><span class="n">r</span><span class="o">.</span><span class="n">pmid</span> <span class="k">for</span> <span class="n">r</span> <span class="ow">in</span> <span class="n">e</span><span class="p">[</span><span class="s1">&#39;references&#39;</span><span class="p">]]),</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">_dip_urls</span><span class="p">(</span><span class="n">e</span><span class="p">),</span>
+            <span class="p">]</span>
+
+            <span class="n">this_edge</span> <span class="o">=</span> <span class="p">(</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">add_extra_fields_igraph</span><span class="p">(</span><span class="n">e</span><span class="p">,</span> <span class="n">this_edge</span><span class="p">,</span> <span class="s1">&#39;undirected&#39;</span><span class="p">)</span>
+            <span class="p">)</span>
+
+            <span class="n">lines</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">this_edge</span><span class="p">)</span>
+
+        <span class="k">return</span> <span class="n">lines</span>
+
+
+<div class="viewcode-block" id="Export.add_extra_fields">
+<a class="viewcode-back" href="../../../api/pypath.omnipath.export.Export.html#pypath.omnipath.export.Export.add_extra_fields">[docs]</a>
+    <span class="k">def</span> <span class="nf">add_extra_fields</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">e</span><span class="p">,</span> <span class="n">line</span><span class="p">,</span> <span class="n">dr</span> <span class="o">=</span> <span class="kc">None</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Takes one table row and using the `igraph.Edge` object and the</span>
+<span class="sd">        direction provided adds the extra node and edge attribute fields</span>
+<span class="sd">        as they are defined in `extra_node_attrs` and `extra_edge_attrs`.</span>
+
+<span class="sd">        Returns the row with extra fields added.</span>
+
+<span class="sd">        Args</span>
+<span class="sd">        -----</span>
+<span class="sd">        :param igraph.Edge e:</span>
+<span class="sd">            One edge.</span>
+<span class="sd">        :param list line:</span>
+<span class="sd">            A table row.</span>
+<span class="sd">        :param tuple,str dr:</span>
+<span class="sd">            Direction key. A tuple of names (most often UniProt IDs) or</span>
+<span class="sd">            `undirected`.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="c1"># extra edge attributes on demand of the user</span>
+        <span class="k">for</span> <span class="n">k</span><span class="p">,</span> <span class="n">v</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">extra_edge_attrs</span><span class="p">):</span>
+
+            <span class="n">line</span><span class="o">.</span><span class="n">append</span><span class="p">(</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">generic_attr_processor</span><span class="p">(</span><span class="n">v</span><span class="p">,</span> <span class="n">e</span><span class="p">,</span> <span class="n">dr</span><span class="p">)</span>
+                    <span class="k">if</span> <span class="nb">hasattr</span><span class="p">(</span><span class="n">v</span><span class="p">,</span> <span class="s1">&#39;__call__&#39;</span><span class="p">)</span> <span class="k">else</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">default_edge_attr_processor</span><span class="p">(</span>
+                    <span class="n">e</span><span class="p">[</span><span class="n">v</span><span class="p">]</span>
+                        <span class="k">if</span> <span class="p">(</span>
+                            <span class="bp">self</span><span class="o">.</span><span class="n">graph</span> <span class="ow">and</span>
+                            <span class="n">v</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">graph</span><span class="o">.</span><span class="n">es</span><span class="o">.</span><span class="n">attributes</span><span class="p">()</span>
+                        <span class="p">)</span> <span class="k">else</span>
+                    <span class="nb">getattr</span><span class="p">(</span><span class="n">e</span><span class="p">,</span> <span class="n">v</span><span class="p">)</span>
+                        <span class="k">if</span> <span class="nb">hasattr</span><span class="p">(</span><span class="n">e</span><span class="p">,</span> <span class="n">v</span><span class="p">)</span> <span class="k">else</span>
+                    <span class="n">e</span><span class="o">.</span><span class="n">attrs</span><span class="p">[</span><span class="n">v</span><span class="p">]</span>
+                        <span class="k">if</span> <span class="n">v</span> <span class="ow">in</span> <span class="n">e</span><span class="o">.</span><span class="n">attrs</span> <span class="k">else</span>
+                    <span class="kc">None</span>
+                <span class="p">)</span>
+            <span class="p">)</span>
+
+        <span class="c1"># extra vertex attributes</span>
+
+        <span class="n">nodes</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">graph</span><span class="o">.</span><span class="n">vs</span><span class="p">[</span><span class="n">e</span><span class="o">.</span><span class="n">source</span><span class="p">],</span> <span class="bp">self</span><span class="o">.</span><span class="n">graph</span><span class="o">.</span><span class="n">vs</span><span class="p">[</span><span class="n">e</span><span class="o">.</span><span class="n">target</span><span class="p">])</span>
+                <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">graph</span> <span class="k">else</span>
+            <span class="n">dr</span>
+        <span class="p">)</span>
+
+        <span class="k">for</span> <span class="n">vertex</span> <span class="ow">in</span> <span class="n">nodes</span><span class="p">:</span>
+
+            <span class="k">for</span> <span class="n">k</span><span class="p">,</span> <span class="n">v</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">extra_node_attrs</span><span class="p">):</span>
+
+                <span class="n">line</span><span class="o">.</span><span class="n">append</span><span class="p">(</span>
+                    <span class="bp">self</span><span class="o">.</span><span class="n">generic_attr_processor</span><span class="p">(</span><span class="n">v</span><span class="p">,</span> <span class="n">vertex</span><span class="p">,</span> <span class="n">dr</span><span class="p">)</span>
+                    <span class="k">if</span> <span class="nb">hasattr</span><span class="p">(</span><span class="n">v</span><span class="p">,</span> <span class="s1">&#39;__call__&#39;</span><span class="p">)</span> <span class="k">else</span>
+                    <span class="bp">self</span><span class="o">.</span><span class="n">default_vertex_attr_processor</span><span class="p">(</span>
+                        <span class="n">vertex</span><span class="p">[</span><span class="n">v</span><span class="p">]</span>
+                            <span class="k">if</span> <span class="p">(</span>
+                                <span class="bp">self</span><span class="o">.</span><span class="n">graph</span> <span class="ow">and</span>
+                                <span class="n">v</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">graph</span><span class="o">.</span><span class="n">vs</span><span class="o">.</span><span class="n">attributes</span><span class="p">()</span>
+                            <span class="p">)</span> <span class="k">else</span>
+                        <span class="nb">getattr</span><span class="p">(</span><span class="n">vertex</span><span class="p">,</span> <span class="n">v</span><span class="p">)</span>
+                            <span class="k">if</span> <span class="nb">hasattr</span><span class="p">(</span><span class="n">vertex</span><span class="p">,</span> <span class="n">v</span><span class="p">)</span> <span class="k">else</span>
+                        <span class="n">vertex</span><span class="o">.</span><span class="n">attrs</span><span class="p">[</span><span class="n">v</span><span class="p">]</span>
+                            <span class="k">if</span> <span class="n">v</span> <span class="ow">in</span> <span class="n">vertex</span><span class="o">.</span><span class="n">attrs</span> <span class="k">else</span>
+                        <span class="kc">None</span>
+                    <span class="p">)</span>
+                <span class="p">)</span>
+
+        <span class="k">return</span> <span class="n">line</span></div>
+
+
+
+    <span class="nd">@staticmethod</span>
+    <span class="k">def</span> <span class="nf">default_vertex_attr_processor</span><span class="p">(</span><span class="n">vattr</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="p">(</span>
+            <span class="n">vattr</span> <span class="k">if</span> <span class="nb">type</span><span class="p">(</span><span class="n">vattr</span><span class="p">)</span> <span class="ow">in</span> <span class="n">simple_types</span> <span class="k">else</span>
+            <span class="s1">&#39;;&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">([</span>
+                <span class="n">x</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span>
+                <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">strip_json</span><span class="o">.</span><span class="n">sub</span><span class="p">(</span><span class="s1">&#39;&#39;</span><span class="p">,</span>
+                    <span class="n">json</span><span class="o">.</span><span class="n">dumps</span><span class="p">(</span>
+                        <span class="n">common</span><span class="o">.</span><span class="n">sets_to_sorted_lists</span><span class="p">(</span><span class="n">vattr</span><span class="p">)</span>
+                    <span class="p">))</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;,&#39;</span><span class="p">)</span>
+            <span class="p">])</span>
+        <span class="p">)</span>
+
+    <span class="nd">@staticmethod</span>
+    <span class="k">def</span> <span class="nf">default_edge_attr_processor</span><span class="p">(</span><span class="n">eattr</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="p">(</span>
+            <span class="n">eattr</span> <span class="k">if</span> <span class="nb">type</span><span class="p">(</span><span class="n">eattr</span><span class="p">)</span> <span class="ow">in</span> <span class="n">simple_types</span> <span class="k">else</span>
+            <span class="s1">&#39;;&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">([</span>
+                <span class="n">x</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span>
+                <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span>
+                <span class="n">strip_json</span><span class="o">.</span><span class="n">sub</span><span class="p">(</span>
+                    <span class="s1">&#39;&#39;</span><span class="p">,</span>
+                    <span class="n">json</span><span class="o">.</span><span class="n">dumps</span><span class="p">(</span>
+                        <span class="n">common</span><span class="o">.</span><span class="n">sets_to_sorted_lists</span><span class="p">(</span><span class="n">eattr</span><span class="p">)</span>
+                    <span class="p">)</span>
+                <span class="p">)</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;,&#39;</span><span class="p">)</span>
+            <span class="p">])</span>
+        <span class="p">)</span>
+
+<div class="viewcode-block" id="Export.generic_attr_processor">
+<a class="viewcode-back" href="../../../api/pypath.omnipath.export.Export.html#pypath.omnipath.export.Export.generic_attr_processor">[docs]</a>
+    <span class="nd">@staticmethod</span>
+    <span class="k">def</span> <span class="nf">generic_attr_processor</span><span class="p">(</span><span class="n">proc</span><span class="p">,</span> <span class="n">obj</span><span class="p">,</span> <span class="n">dr</span> <span class="o">=</span> <span class="kc">None</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Wraps the attribute processor to handle unknown number of arguments.</span>
+
+<span class="sd">        Not knowing if the attribute processor expects one or two arguments,</span>
+<span class="sd">        have no better way than try: if calling with 2 arguments fails with</span>
+<span class="sd">        `TypeError` we call with one argument.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">dr</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="s1">&#39;undirected&#39;</span>
+                <span class="k">if</span> <span class="p">(</span>
+                    <span class="n">dr</span> <span class="ow">and</span>
+                    <span class="nb">hasattr</span><span class="p">(</span><span class="n">obj</span><span class="p">,</span> <span class="s1">&#39;is_directed&#39;</span><span class="p">)</span> <span class="ow">and</span>
+                    <span class="ow">not</span> <span class="n">obj</span><span class="o">.</span><span class="n">is_directed</span><span class="p">()</span>
+                <span class="p">)</span> <span class="k">else</span>
+            <span class="n">dr</span>
+        <span class="p">)</span>
+
+        <span class="k">try</span><span class="p">:</span>
+
+            <span class="k">return</span> <span class="n">proc</span><span class="p">(</span><span class="n">obj</span><span class="p">,</span> <span class="n">dr</span><span class="p">)</span>
+
+        <span class="k">except</span> <span class="ne">TypeError</span> <span class="k">as</span> <span class="n">e</span><span class="p">:</span>
+
+            <span class="k">try</span><span class="p">:</span>
+
+                <span class="k">return</span> <span class="n">proc</span><span class="p">(</span><span class="n">obj</span><span class="p">)</span>
+
+            <span class="k">except</span> <span class="ne">TypeError</span><span class="p">:</span>
+
+                <span class="k">raise</span> <span class="n">e</span></div>
+
+
+
+<div class="viewcode-block" id="Export.write_tab">
+<a class="viewcode-back" href="../../../api/pypath.omnipath.export.Export.html#pypath.omnipath.export.Export.write_tab">[docs]</a>
+    <span class="k">def</span> <span class="nf">write_tab</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">outfile</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Writes the data frame into a tab separated file.</span>
+
+<span class="sd">        Args</span>
+<span class="sd">        -----</span>
+<span class="sd">        :param **kwargs:</span>
+<span class="sd">            Forwarded to `make_df()`.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">if</span> <span class="ow">not</span> <span class="nb">hasattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">&#39;df&#39;</span><span class="p">):</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">make_df</span><span class="p">(</span><span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="n">outfile</span> <span class="o">=</span> <span class="n">outfile</span><span class="p">)</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">write</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">outfile</span> <span class="o">=</span> <span class="kc">None</span><span class="p">):</span>
+
+        <span class="n">outfile</span> <span class="o">=</span> <span class="n">outfile</span> <span class="ow">or</span> <span class="bp">self</span><span class="o">.</span><span class="n">outfile</span> <span class="ow">or</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">pa</span><span class="o">.</span><span class="n">outdir</span><span class="p">,</span> <span class="s1">&#39;network-</span><span class="si">%s</span><span class="s1">.tab&#39;</span> <span class="o">%</span> <span class="bp">self</span><span class="o">.</span><span class="n">pa</span><span class="o">.</span><span class="n">session</span>
+        <span class="p">)</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">df</span><span class="o">.</span><span class="n">to_csv</span><span class="p">(</span><span class="n">outfile</span><span class="p">,</span> <span class="n">sep</span> <span class="o">=</span> <span class="s1">&#39;</span><span class="se">\t</span><span class="s1">&#39;</span><span class="p">,</span> <span class="n">index</span> <span class="o">=</span> <span class="kc">False</span><span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">webservice_interactions_df</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="n">datasets</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="s1">&#39;omnipath&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;kinaseextra&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;ligrecextra&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;pathwayextra&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;mirnatarget&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;dorothea&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;collectri&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;tf_target&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;lncrna_mrna&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;tf_mirna&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;small_molecule&#39;</span><span class="p">,</span>
+        <span class="p">)</span>
+
+        <span class="k">def</span> <span class="nf">get_dataset_callback</span><span class="p">(</span><span class="n">dataset</span><span class="p">:</span> <span class="nb">str</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">callable</span><span class="p">:</span>
+
+            <span class="k">def</span> <span class="nf">has_dataset</span><span class="p">(</span><span class="n">e</span><span class="p">,</span> <span class="n">d</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">bool</span><span class="p">:</span>
+
+                <span class="k">return</span> <span class="n">e</span><span class="o">.</span><span class="n">has_dataset</span><span class="p">(</span><span class="n">dataset</span><span class="p">,</span> <span class="n">direction</span> <span class="o">=</span> <span class="n">d</span><span class="p">)</span>
+
+            <span class="k">return</span> <span class="n">has_dataset</span>
+
+
+        <span class="n">dataset_args</span> <span class="o">=</span> <span class="p">{</span>
+            <span class="n">dataset</span><span class="p">:</span> <span class="n">get_dataset_callback</span><span class="p">(</span><span class="n">dataset</span><span class="p">)</span>
+            <span class="k">for</span> <span class="n">dataset</span> <span class="ow">in</span> <span class="n">datasets</span>
+        <span class="p">}</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">make_df</span><span class="p">(</span>
+            <span class="n">unique_pairs</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+            <span class="n">extra_node_attrs</span> <span class="o">=</span> <span class="p">{</span>
+                <span class="s1">&#39;ncbi_tax_id&#39;</span><span class="p">:</span> <span class="s1">&#39;taxon&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;entity_type&#39;</span><span class="p">:</span> <span class="s1">&#39;entity_type&#39;</span><span class="p">,</span>
+            <span class="p">},</span>
+            <span class="n">extra_edge_attrs</span> <span class="o">=</span> <span class="p">{</span>
+                <span class="o">**</span><span class="n">dataset_args</span><span class="p">,</span>
+                <span class="o">**</span><span class="p">{</span>
+                    <span class="s1">&#39;dorothea_curated&#39;</span><span class="p">:</span> <span class="k">lambda</span> <span class="n">e</span><span class="p">,</span> <span class="n">d</span><span class="p">:</span> <span class="p">(</span>
+                        <span class="n">e</span><span class="o">.</span><span class="n">_get_attr</span><span class="p">(</span><span class="s1">&#39;DoRothEA&#39;</span><span class="p">,</span> <span class="s1">&#39;curated&#39;</span><span class="p">,</span> <span class="n">d</span><span class="p">)</span>
+                    <span class="p">),</span>
+                    <span class="s1">&#39;dorothea_chipseq&#39;</span><span class="p">:</span> <span class="k">lambda</span> <span class="n">e</span><span class="p">,</span> <span class="n">d</span><span class="p">:</span> <span class="p">(</span>
+                        <span class="n">e</span><span class="o">.</span><span class="n">_get_attr</span><span class="p">(</span><span class="s1">&#39;DoRothEA&#39;</span><span class="p">,</span> <span class="s1">&#39;chipseq&#39;</span><span class="p">,</span> <span class="n">d</span><span class="p">)</span>
+                    <span class="p">),</span>
+                    <span class="s1">&#39;dorothea_tfbs&#39;</span><span class="p">:</span> <span class="k">lambda</span> <span class="n">e</span><span class="p">,</span> <span class="n">d</span><span class="p">:</span> <span class="p">(</span>
+                        <span class="n">e</span><span class="o">.</span><span class="n">_get_attr</span><span class="p">(</span><span class="s1">&#39;DoRothEA&#39;</span><span class="p">,</span> <span class="s1">&#39;tfbs&#39;</span><span class="p">,</span> <span class="n">d</span><span class="p">)</span>
+                    <span class="p">),</span>
+                    <span class="s1">&#39;dorothea_coexp&#39;</span><span class="p">:</span> <span class="k">lambda</span> <span class="n">e</span><span class="p">,</span> <span class="n">d</span><span class="p">:</span> <span class="p">(</span>
+                        <span class="n">e</span><span class="o">.</span><span class="n">_get_attr</span><span class="p">(</span><span class="s1">&#39;DoRothEA&#39;</span><span class="p">,</span> <span class="s1">&#39;coexp&#39;</span><span class="p">,</span> <span class="n">d</span><span class="p">)</span>
+                    <span class="p">),</span>
+                    <span class="s1">&#39;dorothea_level&#39;</span><span class="p">:</span> <span class="k">lambda</span> <span class="n">e</span><span class="p">,</span> <span class="n">d</span><span class="p">:</span> <span class="p">(</span>
+                        <span class="s1">&#39;;&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">e</span><span class="o">.</span><span class="n">dorothea_levels</span><span class="p">(</span><span class="n">d</span><span class="p">))</span>
+                    <span class="p">),</span>
+                    <span class="s1">&#39;type&#39;</span><span class="p">:</span> <span class="k">lambda</span> <span class="n">e</span><span class="p">,</span> <span class="n">d</span><span class="p">:</span> <span class="p">(</span>
+                        <span class="nb">list</span><span class="p">(</span><span class="n">e</span><span class="o">.</span><span class="n">get_interaction_types</span><span class="p">(</span><span class="n">direction</span> <span class="o">=</span> <span class="n">d</span><span class="p">))[</span><span class="mi">0</span><span class="p">]</span>
+                    <span class="p">),</span>
+                    <span class="s1">&#39;curation_effort&#39;</span><span class="p">:</span> <span class="k">lambda</span> <span class="n">e</span><span class="p">,</span> <span class="n">d</span><span class="p">:</span> <span class="p">(</span>
+                        <span class="n">e</span><span class="o">.</span><span class="n">count_curation_effort</span><span class="p">(</span><span class="n">direction</span> <span class="o">=</span> <span class="n">d</span><span class="p">)</span> <span class="o">+</span> <span class="p">(</span>
+                            <span class="n">e</span><span class="o">.</span><span class="n">count_curation_effort</span><span class="p">(</span><span class="n">direction</span> <span class="o">=</span> <span class="s1">&#39;undirected&#39;</span><span class="p">)</span>
+                                <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">d</span><span class="p">,</span> <span class="nb">tuple</span><span class="p">)</span> <span class="k">else</span>
+                            <span class="mi">0</span>
+                        <span class="p">)</span>
+                    <span class="p">),</span>
+                    <span class="s1">&#39;extra_attrs&#39;</span><span class="p">:</span> <span class="k">lambda</span> <span class="n">e</span><span class="p">,</span> <span class="n">d</span><span class="p">:</span> <span class="n">e</span><span class="o">.</span><span class="n">serialize_attrs</span><span class="p">(</span><span class="n">d</span><span class="p">),</span>
+                    <span class="s1">&#39;evidences&#39;</span><span class="p">:</span> <span class="k">lambda</span> <span class="n">e</span><span class="p">,</span> <span class="n">d</span><span class="p">:</span> <span class="n">e</span><span class="o">.</span><span class="n">serialize_evidences</span><span class="p">(</span><span class="n">d</span><span class="p">),</span>
+                <span class="p">},</span>
+            <span class="p">},</span>
+        <span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">webservice_interactions_df_legacy</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="n">sources_omnipath</span> <span class="o">=</span> <span class="nb">set</span><span class="p">(</span>
+            <span class="n">f</span><span class="o">.</span><span class="n">name</span> <span class="k">for</span> <span class="n">f</span> <span class="ow">in</span> <span class="n">data_formats</span><span class="o">.</span><span class="n">omnipath</span><span class="o">.</span><span class="n">values</span><span class="p">()</span>
+        <span class="p">)</span>
+        <span class="n">sources_extra_directions</span> <span class="o">=</span> <span class="n">settings</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">&#39;network_extra_directions&#39;</span><span class="p">)</span>
+        <span class="n">sources_kinase_extra</span> <span class="o">=</span> <span class="nb">set</span><span class="p">(</span>
+            <span class="n">f</span><span class="o">.</span><span class="n">name</span> <span class="k">for</span> <span class="n">f</span> <span class="ow">in</span> <span class="n">data_formats</span><span class="o">.</span><span class="n">ptm_misc</span><span class="o">.</span><span class="n">values</span><span class="p">()</span>
+        <span class="p">)</span>
+        <span class="n">sources_ligrec_extra</span> <span class="o">=</span> <span class="nb">set</span><span class="p">(</span>
+            <span class="n">f</span><span class="o">.</span><span class="n">name</span> <span class="k">for</span> <span class="n">f</span> <span class="ow">in</span> <span class="n">data_formats</span><span class="o">.</span><span class="n">ligand_receptor</span><span class="o">.</span><span class="n">values</span><span class="p">()</span>
+        <span class="p">)</span>
+        <span class="n">sources_pathway_extra</span> <span class="o">=</span> <span class="nb">set</span><span class="p">(</span>
+            <span class="n">f</span><span class="o">.</span><span class="n">name</span> <span class="k">for</span> <span class="n">f</span> <span class="ow">in</span> <span class="n">data_formats</span><span class="o">.</span><span class="n">pathway_noref</span><span class="o">.</span><span class="n">values</span><span class="p">()</span>
+        <span class="p">)</span>
+        <span class="n">sources_mirna</span> <span class="o">=</span> <span class="nb">set</span><span class="p">(</span>
+            <span class="n">f</span><span class="o">.</span><span class="n">name</span> <span class="k">for</span> <span class="n">f</span> <span class="ow">in</span> <span class="n">data_formats</span><span class="o">.</span><span class="n">mirna_target</span><span class="o">.</span><span class="n">values</span><span class="p">()</span>
+        <span class="p">)</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">make_df</span><span class="p">(</span>
+            <span class="n">unique_pairs</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+            <span class="n">extra_node_attrs</span> <span class="o">=</span> <span class="p">{</span>
+                <span class="s1">&#39;ncbi_tax_id&#39;</span><span class="p">:</span> <span class="s1">&#39;ncbi_tax_id&#39;</span>
+            <span class="p">},</span>
+            <span class="n">extra_edge_attrs</span> <span class="o">=</span> <span class="p">{</span>
+                <span class="s1">&#39;omnipath&#39;</span><span class="p">:</span> <span class="k">lambda</span> <span class="n">e</span><span class="p">,</span> <span class="n">d</span><span class="p">:</span> <span class="p">(</span>
+                    <span class="p">(</span>
+                        <span class="nb">bool</span><span class="p">(</span><span class="n">e</span><span class="p">[</span><span class="s1">&#39;dirs&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">sources</span><span class="p">[</span><span class="n">d</span><span class="p">]</span> <span class="o">&amp;</span> <span class="n">sources_omnipath</span><span class="p">)</span> <span class="ow">or</span>
+                        <span class="p">(</span>
+                            <span class="nb">bool</span><span class="p">(</span>
+                                <span class="n">e</span><span class="p">[</span><span class="s1">&#39;dirs&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">sources</span><span class="p">[</span><span class="s1">&#39;undirected&#39;</span><span class="p">]</span> <span class="o">&amp;</span>
+                                <span class="n">sources_omnipath</span>
+                            <span class="p">)</span> <span class="ow">and</span>
+                            <span class="nb">bool</span><span class="p">(</span>
+                                <span class="n">e</span><span class="p">[</span><span class="s1">&#39;dirs&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">sources</span><span class="p">[</span><span class="n">d</span><span class="p">]</span> <span class="o">&amp;</span>
+                                <span class="n">sources_extra_directions</span>
+                            <span class="p">)</span>
+                        <span class="p">)</span>
+                    <span class="p">)</span> <span class="ow">and</span>
+                    <span class="s1">&#39;PPI&#39;</span> <span class="ow">in</span> <span class="n">e</span><span class="p">[</span><span class="s1">&#39;type&#39;</span><span class="p">]</span>
+                <span class="p">),</span>
+                <span class="s1">&#39;kinaseextra&#39;</span><span class="p">:</span> <span class="k">lambda</span> <span class="n">e</span><span class="p">,</span> <span class="n">d</span><span class="p">:</span> <span class="p">(</span>
+                    <span class="nb">bool</span><span class="p">(</span><span class="n">e</span><span class="p">[</span><span class="s1">&#39;dirs&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">sources</span><span class="p">[</span><span class="n">d</span><span class="p">]</span> <span class="o">&amp;</span> <span class="n">sources_kinase_extra</span><span class="p">)</span> <span class="ow">and</span>
+                    <span class="s1">&#39;PPI&#39;</span> <span class="ow">in</span> <span class="n">e</span><span class="p">[</span><span class="s1">&#39;type&#39;</span><span class="p">]</span>
+                <span class="p">),</span>
+                <span class="s1">&#39;ligrecextra&#39;</span><span class="p">:</span> <span class="k">lambda</span> <span class="n">e</span><span class="p">,</span> <span class="n">d</span><span class="p">:</span> <span class="p">(</span>
+                    <span class="nb">bool</span><span class="p">(</span><span class="n">e</span><span class="p">[</span><span class="s1">&#39;dirs&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">sources</span><span class="p">[</span><span class="n">d</span><span class="p">]</span> <span class="o">&amp;</span> <span class="n">sources_ligrec_extra</span><span class="p">)</span> <span class="ow">and</span>
+                    <span class="s1">&#39;PPI&#39;</span> <span class="ow">in</span> <span class="n">e</span><span class="p">[</span><span class="s1">&#39;type&#39;</span><span class="p">]</span>
+                <span class="p">),</span>
+                <span class="s1">&#39;pathwayextra&#39;</span><span class="p">:</span> <span class="k">lambda</span> <span class="n">e</span><span class="p">,</span> <span class="n">d</span><span class="p">:</span> <span class="p">(</span>
+                    <span class="nb">bool</span><span class="p">(</span><span class="n">e</span><span class="p">[</span><span class="s1">&#39;dirs&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">sources</span><span class="p">[</span><span class="n">d</span><span class="p">]</span> <span class="o">&amp;</span> <span class="n">sources_pathway_extra</span><span class="p">)</span> <span class="ow">and</span>
+                    <span class="s1">&#39;TF&#39;</span> <span class="ow">in</span> <span class="n">e</span><span class="p">[</span><span class="s1">&#39;type&#39;</span><span class="p">]</span>
+                <span class="p">),</span>
+                <span class="s1">&#39;mirnatarget&#39;</span><span class="p">:</span> <span class="k">lambda</span> <span class="n">e</span><span class="p">,</span> <span class="n">d</span><span class="p">:</span> <span class="p">(</span>
+                    <span class="nb">bool</span><span class="p">(</span><span class="n">e</span><span class="p">[</span><span class="s1">&#39;dirs&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">sources</span><span class="p">[</span><span class="n">d</span><span class="p">]</span> <span class="o">&amp;</span> <span class="n">sources_mirna</span><span class="p">)</span> <span class="ow">and</span>
+                    <span class="s1">&#39;MTI&#39;</span> <span class="ow">in</span> <span class="n">e</span><span class="p">[</span><span class="s1">&#39;type&#39;</span><span class="p">]</span>
+                <span class="p">),</span>
+                <span class="s1">&#39;dorothea&#39;</span><span class="p">:</span> <span class="k">lambda</span> <span class="n">e</span><span class="p">,</span> <span class="n">d</span><span class="p">:</span> <span class="p">(</span>
+                    <span class="s1">&#39;TF&#39;</span> <span class="ow">in</span> <span class="n">e</span><span class="p">[</span><span class="s1">&#39;sources_by_type&#39;</span><span class="p">]</span> <span class="ow">and</span> <span class="nb">bool</span><span class="p">(</span>
+                        <span class="n">e</span><span class="p">[</span><span class="s1">&#39;sources_by_type&#39;</span><span class="p">][</span><span class="s1">&#39;TF&#39;</span><span class="p">]</span> <span class="o">&amp;</span>
+                        <span class="n">e</span><span class="p">[</span><span class="s1">&#39;dirs&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">sources</span><span class="p">[</span><span class="n">d</span><span class="p">]</span>
+                    <span class="p">)</span>
+                <span class="p">),</span>
+                <span class="s1">&#39;dorothea_curated&#39;</span><span class="p">:</span> <span class="s1">&#39;dorothea_curated&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;dorothea_chipseq&#39;</span><span class="p">:</span> <span class="s1">&#39;dorothea_chipseq&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;dorothea_tfbs&#39;</span><span class="p">:</span>    <span class="s1">&#39;dorothea_tfbs&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;dorothea_coexp&#39;</span><span class="p">:</span>   <span class="s1">&#39;dorothea_coexp&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;dorothea_level&#39;</span><span class="p">:</span> <span class="k">lambda</span> <span class="n">e</span><span class="p">,</span> <span class="n">d</span><span class="p">:</span> <span class="p">(</span>
+                    <span class="s1">&#39;;&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="nb">sorted</span><span class="p">(</span><span class="n">e</span><span class="p">[</span><span class="s1">&#39;dorothea_level&#39;</span><span class="p">]))</span> <span class="k">if</span>
+                    <span class="s1">&#39;dorothea_level&#39;</span> <span class="ow">in</span> <span class="n">e</span><span class="o">.</span><span class="n">attributes</span><span class="p">()</span> <span class="ow">and</span>
+                    <span class="s1">&#39;TF&#39;</span> <span class="ow">in</span> <span class="n">e</span><span class="p">[</span><span class="s1">&#39;sources_by_type&#39;</span><span class="p">]</span> <span class="ow">and</span> <span class="nb">bool</span><span class="p">(</span>
+                        <span class="n">e</span><span class="p">[</span><span class="s1">&#39;sources_by_type&#39;</span><span class="p">][</span><span class="s1">&#39;TF&#39;</span><span class="p">]</span> <span class="o">&amp;</span>
+                        <span class="n">e</span><span class="p">[</span><span class="s1">&#39;dirs&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">sources</span><span class="p">[</span><span class="n">d</span><span class="p">]</span>
+                    <span class="p">)</span> <span class="k">else</span> <span class="s1">&#39;&#39;</span><span class="p">),</span>
+                <span class="c1"># quite wrong (taking only the first one):</span>
+                <span class="s1">&#39;type&#39;</span><span class="p">:</span> <span class="k">lambda</span> <span class="n">e</span><span class="p">:</span> <span class="n">e</span><span class="p">[</span><span class="s1">&#39;type&#39;</span><span class="p">][</span><span class="mi">0</span><span class="p">],</span>
+                <span class="s1">&#39;curation_effort&#39;</span><span class="p">:</span> <span class="k">lambda</span> <span class="n">e</span><span class="p">,</span> <span class="n">d</span><span class="p">:</span> <span class="p">(</span>
+                    <span class="n">e</span><span class="o">.</span><span class="n">count_curation_effort</span><span class="p">(</span><span class="n">direction</span> <span class="o">=</span> <span class="n">d</span><span class="p">)</span> <span class="o">+</span> <span class="p">(</span>
+                        <span class="n">e</span><span class="o">.</span><span class="n">count_curation_effort</span><span class="p">(</span><span class="n">direction</span> <span class="o">=</span> <span class="s1">&#39;undirected&#39;</span><span class="p">)</span>
+                            <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">d</span><span class="p">,</span> <span class="nb">tuple</span><span class="p">)</span> <span class="k">else</span>
+                        <span class="mi">0</span>
+                    <span class="p">)</span>
+                <span class="p">),</span>
+            <span class="p">}</span>
+        <span class="p">)</span>
+
+<div class="viewcode-block" id="Export.sources_table">
+<a class="viewcode-back" href="../../../api/pypath.omnipath.export.Export.html#pypath.omnipath.export.Export.sources_table">[docs]</a>
+    <span class="nd">@classmethod</span>
+    <span class="k">def</span> <span class="nf">sources_table</span><span class="p">(</span>
+            <span class="bp">cls</span><span class="p">,</span>
+            <span class="n">pa</span><span class="p">,</span>
+            <span class="n">only_sources</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">unique_pairs</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
+            <span class="n">extra_edge_attrs</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">extra_node_attrs</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">outfile</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">default_vertex_attr_processor</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">default_edge_attr_processor</span>   <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+        <span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Creates a data frame which contains a column for each source database</span>
+<span class="sd">        with binary values showing presence-absence of interactions across</span>
+<span class="sd">        resources.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">new</span> <span class="o">=</span> <span class="bp">cls</span><span class="p">(</span>
+            <span class="n">pa</span> <span class="o">=</span> <span class="n">pa</span><span class="p">,</span>
+            <span class="n">only_sources</span> <span class="o">=</span> <span class="n">only_sources</span><span class="p">,</span>
+            <span class="n">extra_edge_attrs</span> <span class="o">=</span> <span class="n">extra_edge_attrs</span> <span class="ow">or</span> <span class="p">{},</span>
+            <span class="n">extra_node_attrs</span> <span class="o">=</span> <span class="n">extra_node_attrs</span> <span class="ow">or</span> <span class="p">{},</span>
+            <span class="n">outfile</span> <span class="o">=</span> <span class="n">outfile</span><span class="p">,</span>
+            <span class="n">default_vertex_attr_processor</span> <span class="o">=</span> <span class="n">default_vertex_attr_processor</span><span class="p">,</span>
+            <span class="n">default_edge_attr_processor</span>   <span class="o">=</span> <span class="n">default_edge_attr_processor</span><span class="p">,</span>
+        <span class="p">)</span>
+
+        <span class="n">new</span><span class="o">.</span><span class="n">make_df</span><span class="p">(</span><span class="n">unique_pairs</span> <span class="o">=</span> <span class="n">unique_pairs</span><span class="p">)</span>
+
+        <span class="n">src_attr</span> <span class="o">=</span> <span class="s1">&#39;Databases&#39;</span> <span class="k">if</span> <span class="n">unique_pairs</span> <span class="k">else</span> <span class="s1">&#39;sources&#39;</span>
+
+        <span class="n">src_all</span> <span class="o">=</span> <span class="nb">sorted</span><span class="p">(</span><span class="n">only_sources</span> <span class="ow">or</span> <span class="n">pa</span><span class="o">.</span><span class="n">sources</span><span class="p">)</span>
+
+        <span class="n">src_cols</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">((</span><span class="n">src</span><span class="p">,</span> <span class="p">[])</span> <span class="k">for</span> <span class="n">src</span> <span class="ow">in</span> <span class="n">src_all</span><span class="p">)</span>
+
+        <span class="k">for</span> <span class="n">i</span><span class="p">,</span> <span class="n">row</span> <span class="ow">in</span> <span class="n">new</span><span class="o">.</span><span class="n">df</span><span class="o">.</span><span class="n">iterrows</span><span class="p">():</span>
+
+            <span class="n">this_row_src</span> <span class="o">=</span> <span class="nb">set</span><span class="p">(</span><span class="n">row</span><span class="p">[</span><span class="n">src_attr</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;;&#39;</span><span class="p">))</span>
+
+            <span class="k">for</span> <span class="n">src</span> <span class="ow">in</span> <span class="n">src_all</span><span class="p">:</span>
+
+                <span class="n">src_cols</span><span class="p">[</span><span class="n">src</span><span class="p">]</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="nb">int</span><span class="p">(</span><span class="n">src</span> <span class="ow">in</span> <span class="n">this_row_src</span><span class="p">))</span>
+
+        <span class="k">for</span> <span class="n">src</span> <span class="ow">in</span> <span class="n">src_all</span><span class="p">:</span>
+
+            <span class="n">new</span><span class="o">.</span><span class="n">df</span><span class="o">.</span><span class="n">insert</span><span class="p">(</span>
+                <span class="n">loc</span> <span class="o">=</span> <span class="n">new</span><span class="o">.</span><span class="n">df</span><span class="o">.</span><span class="n">columns</span><span class="o">.</span><span class="n">get_loc</span><span class="p">(</span><span class="n">src_attr</span><span class="p">),</span>
+                <span class="n">column</span> <span class="o">=</span> <span class="n">src</span><span class="p">,</span>
+                <span class="n">value</span> <span class="o">=</span> <span class="n">src_cols</span><span class="p">[</span><span class="n">src</span><span class="p">]</span>
+            <span class="p">)</span>
+
+        <span class="k">return</span> <span class="n">new</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">_dip_urls</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">e</span><span class="p">):</span>
+
+        <span class="n">attrs</span> <span class="o">=</span> <span class="n">e</span><span class="o">.</span><span class="n">attrs</span> <span class="k">if</span> <span class="nb">hasattr</span><span class="p">(</span><span class="n">e</span><span class="p">,</span> <span class="s1">&#39;attrs&#39;</span><span class="p">)</span> <span class="k">else</span> <span class="n">e</span><span class="o">.</span><span class="n">attributes</span>
+
+        <span class="n">result</span> <span class="o">=</span> <span class="p">[]</span>
+
+        <span class="k">if</span> <span class="s1">&#39;dip_id&#39;</span> <span class="ow">in</span> <span class="n">attrs</span><span class="p">:</span>
+
+            <span class="n">dip_ids</span> <span class="o">=</span> <span class="nb">sorted</span><span class="p">(</span><span class="n">common</span><span class="o">.</span><span class="n">to_set</span><span class="p">(</span><span class="n">attrs</span><span class="p">[</span><span class="s1">&#39;dip_id&#39;</span><span class="p">]))</span>
+
+            <span class="k">for</span> <span class="n">dip_id</span> <span class="ow">in</span> <span class="n">dip_ids</span><span class="p">:</span>
+
+                <span class="k">try</span><span class="p">:</span>
+                    <span class="n">result</span><span class="o">.</span><span class="n">append</span><span class="p">(</span>
+                        <span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;dip&#39;</span><span class="p">][</span><span class="s1">&#39;ik&#39;</span><span class="p">]</span> <span class="o">%</span> <span class="p">(</span>
+                            <span class="nb">int</span><span class="p">(</span><span class="n">dip_id</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;-&#39;</span><span class="p">)[</span><span class="mi">1</span><span class="p">][:</span><span class="o">-</span><span class="mi">1</span><span class="p">])</span>
+                        <span class="p">)</span>
+                    <span class="p">)</span>
+                <span class="k">except</span><span class="p">:</span>
+
+                    <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span><span class="s1">&#39;Could not find DIP ID: </span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="n">dip_id</span><span class="p">)</span>
+
+        <span class="k">return</span> <span class="s1">&#39;;&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">result</span><span class="p">)</span></div>
+
+</pre></div>
+
+                </article>
+              
+              
+              
+              
+              
+                <footer class="prev-next-footer">
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+                </footer>
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+  <h1>Source code for pypath.omnipath.param</h1><div class="highlight"><pre>
+<span></span><span class="ch">#!/usr/bin/env python</span>
+<span class="c1"># -*- coding: utf-8 -*-</span>
+
+<span class="c1">#</span>
+<span class="c1">#  This file is part of the `pypath` python module</span>
+<span class="c1">#</span>
+<span class="c1">#  Copyright 2014-2023</span>
+<span class="c1">#  EMBL, EMBL-EBI, Uniklinik RWTH Aachen, Heidelberg University</span>
+<span class="c1">#</span>
+<span class="c1">#  Authors: see the file `README.rst`</span>
+<span class="c1">#  Contact: Dénes Türei (turei.denes@gmail.com)</span>
+<span class="c1">#</span>
+<span class="c1">#  Distributed under the GPLv3 License.</span>
+<span class="c1">#  See accompanying file LICENSE.txt or copy at</span>
+<span class="c1">#      https://www.gnu.org/licenses/gpl-3.0.html</span>
+<span class="c1">#</span>
+<span class="c1">#  Website: https://pypath.omnipathdb.org/</span>
+<span class="c1">#</span>
+
+<span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">Contains auxiliary functions for preparation of arguments for building built</span>
+<span class="sd">in databases. When users define custom, non built in databases, they can use</span>
+<span class="sd">the functions from here or define and provide their own functions from their</span>
+<span class="sd">own code.</span>
+<span class="sd">&quot;&quot;&quot;</span>
+
+<span class="kn">import</span> <span class="nn">copy</span>
+
+<span class="kn">import</span> <span class="nn">pypath.share.settings</span> <span class="k">as</span> <span class="nn">settings</span>
+<span class="kn">import</span> <span class="nn">pypath.resources.network</span> <span class="k">as</span> <span class="nn">netres</span>
+
+
+<div class="viewcode-block" id="curated_ppi_resources">
+<a class="viewcode-back" href="../../../api/pypath.omnipath.param.curated_ppi_resources.html#pypath.omnipath.param.curated_ppi_resources">[docs]</a>
+<span class="k">def</span> <span class="nf">curated_ppi_resources</span><span class="p">():</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Returns a resource set which more or less corresponds to the literature</span>
+<span class="sd">    curated activity flow resources. It is an union of the literature curated</span>
+<span class="sd">    activity flow and enzyme-substrate resources.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="n">resources</span> <span class="o">=</span> <span class="n">copy</span><span class="o">.</span><span class="n">deepcopy</span><span class="p">(</span><span class="n">netres</span><span class="o">.</span><span class="n">pathway</span><span class="p">)</span>
+    <span class="n">resources</span><span class="o">.</span><span class="n">update</span><span class="p">(</span><span class="n">copy</span><span class="o">.</span><span class="n">deepcopy</span><span class="p">(</span><span class="n">netres</span><span class="o">.</span><span class="n">enzyme_substrate</span><span class="p">))</span>
+
+    <span class="k">return</span> <span class="n">resources</span></div>
+
+
+
+<div class="viewcode-block" id="tf_target_resources">
+<a class="viewcode-back" href="../../../api/pypath.omnipath.param.tf_target_resources.html#pypath.omnipath.param.tf_target_resources">[docs]</a>
+<span class="k">def</span> <span class="nf">tf_target_resources</span><span class="p">():</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Returns the resource set for building the TF-target network dataset.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="n">transcription</span> <span class="o">=</span> <span class="p">(</span>
+        <span class="n">netres</span><span class="o">.</span><span class="n">dorothea_expand_levels</span><span class="p">(</span>
+            <span class="n">resources</span> <span class="o">=</span> <span class="n">netres</span><span class="o">.</span><span class="n">transcription</span><span class="p">,</span>
+            <span class="n">levels</span> <span class="o">=</span> <span class="n">settings</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">&#39;tfregulons_levels&#39;</span><span class="p">),</span>
+        <span class="p">)</span>
+            <span class="k">if</span> <span class="n">settings</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">&#39;dorothea_expand_levels&#39;</span><span class="p">)</span> <span class="k">else</span>
+        <span class="n">netres</span><span class="o">.</span><span class="n">transcription</span>
+    <span class="p">)</span>
+
+    <span class="k">return</span> <span class="n">transcription</span></div>
+
+</pre></div>
+
+                </article>
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+                <article class="bd-article">
+                  
+  <h1>Source code for pypath.omnipath.server.build</h1><div class="highlight"><pre>
+<span></span><span class="ch">#!/usr/bin/env python</span>
+<span class="c1"># -*- coding: utf-8 -*-</span>
+
+<span class="c1">#</span>
+<span class="c1">#  This file is part of the `pypath` python module</span>
+<span class="c1">#</span>
+<span class="c1">#  Copyright 2014-2023</span>
+<span class="c1">#  EMBL, EMBL-EBI, Uniklinik RWTH Aachen, Heidelberg University</span>
+<span class="c1">#</span>
+<span class="c1">#  Authors: see the file `README.rst`</span>
+<span class="c1">#  Contact: Dénes Türei (turei.denes@gmail.com)</span>
+<span class="c1">#</span>
+<span class="c1">#  Distributed under the GPLv3 License.</span>
+<span class="c1">#  See accompanying file LICENSE.txt or copy at</span>
+<span class="c1">#      https://www.gnu.org/licenses/gpl-3.0.html</span>
+<span class="c1">#</span>
+<span class="c1">#  Website: https://pypath.omnipathdb.org/</span>
+<span class="c1">#</span>
+
+<span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">This is a standalone module with the only purpose of</span>
+<span class="sd">building the tables for the webservice.</span>
+<span class="sd">&quot;&quot;&quot;</span>
+
+<span class="kn">from</span> <span class="nn">future.utils</span> <span class="kn">import</span> <span class="n">iteritems</span>
+
+<span class="kn">import</span> <span class="nn">os</span>
+<span class="kn">import</span> <span class="nn">importlib</span> <span class="k">as</span> <span class="nn">imp</span>
+<span class="kn">import</span> <span class="nn">copy</span>
+
+<span class="kn">import</span> <span class="nn">pandas</span> <span class="k">as</span> <span class="nn">pd</span>
+
+<span class="kn">import</span> <span class="nn">pypath.core.enz_sub</span> <span class="k">as</span> <span class="nn">enz_sub</span>
+<span class="kn">import</span> <span class="nn">pypath.core.complex</span> <span class="k">as</span> <span class="nn">complex</span>
+<span class="kn">import</span> <span class="nn">pypath.core.annot</span> <span class="k">as</span> <span class="nn">annot</span>
+<span class="kn">import</span> <span class="nn">pypath.core.intercell</span> <span class="k">as</span> <span class="nn">intercell</span>
+<span class="kn">import</span> <span class="nn">pypath.omnipath.export</span> <span class="k">as</span> <span class="nn">export</span>
+<span class="kn">import</span> <span class="nn">pypath.resources.data_formats</span> <span class="k">as</span> <span class="nn">data_formats</span>
+<span class="kn">import</span> <span class="nn">pypath.share.session</span> <span class="k">as</span> <span class="nn">session_mod</span>
+<span class="kn">import</span> <span class="nn">pypath.omnipath</span> <span class="k">as</span> <span class="nn">omnipath</span>
+
+
+<span class="n">NO_HOMOLOGY_TRANSLATION</span> <span class="o">=</span> <span class="p">{</span>
+    <span class="s1">&#39;mirna_mrna&#39;</span><span class="p">,</span>
+    <span class="s1">&#39;lncrna_mrna&#39;</span><span class="p">,</span>
+    <span class="s1">&#39;tf_mirna&#39;</span><span class="p">,</span>
+    <span class="s1">&#39;small_molecule&#39;</span><span class="p">,</span>
+<span class="p">}</span>
+
+
+<div class="viewcode-block" id="WebserviceTables">
+<a class="viewcode-back" href="../../../../api/pypath.omnipath.server.build.WebserviceTables.html#pypath.omnipath.server.build.WebserviceTables">[docs]</a>
+<span class="k">class</span> <span class="nc">WebserviceTables</span><span class="p">(</span><span class="n">session_mod</span><span class="o">.</span><span class="n">Logger</span><span class="p">):</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Creates the data frames which the web service uses to serve the data from.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+
+<div class="viewcode-block" id="WebserviceTables.__init__">
+<a class="viewcode-back" href="../../../../api/pypath.omnipath.server.build.WebserviceTables.html#pypath.omnipath.server.build.WebserviceTables.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">only_human</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+            <span class="n">build_dir</span> <span class="o">=</span> <span class="s1">&#39;.&#39;</span><span class="p">,</span>
+            <span class="n">outfile_interactions</span> <span class="o">=</span> <span class="s1">&#39;omnipath_webservice_interactions.tsv&#39;</span><span class="p">,</span>
+            <span class="n">outfile_enz_sub</span> <span class="o">=</span> <span class="s1">&#39;omnipath_webservice_enz_sub.tsv&#39;</span><span class="p">,</span>
+            <span class="n">outfile_complexes</span> <span class="o">=</span> <span class="s1">&#39;omnipath_webservice_complexes.tsv&#39;</span><span class="p">,</span>
+            <span class="n">outfile_annotations</span> <span class="o">=</span> <span class="s1">&#39;omnipath_webservice_annotations.tsv&#39;</span><span class="p">,</span>
+            <span class="n">outfile_intercell</span> <span class="o">=</span> <span class="s1">&#39;omnipath_webservice_intercell.tsv&#39;</span><span class="p">,</span>
+            <span class="n">network_datasets</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+        <span class="p">):</span>
+
+        <span class="n">session_mod</span><span class="o">.</span><span class="n">Logger</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">name</span> <span class="o">=</span> <span class="s1">&#39;websrvtab&#39;</span><span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span><span class="s1">&#39;WebserviceTables initialized.&#39;</span><span class="p">)</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">only_human</span> <span class="o">=</span> <span class="n">only_human</span>
+
+        <span class="n">databases</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="s1">&#39;interactions&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;complexes&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;enz_sub&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;annotations&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;intercell&#39;</span><span class="p">,</span>
+        <span class="p">)</span>
+
+        <span class="k">for</span> <span class="n">db</span> <span class="ow">in</span> <span class="n">databases</span><span class="p">:</span>
+
+            <span class="n">attr</span> <span class="o">=</span> <span class="s1">&#39;outfile_</span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="n">db</span>
+
+            <span class="nb">setattr</span><span class="p">(</span>
+                <span class="bp">self</span><span class="p">,</span>
+                <span class="n">attr</span><span class="p">,</span>
+                <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span>
+                    <span class="n">build_dir</span><span class="p">,</span>
+                    <span class="nb">locals</span><span class="p">()[</span><span class="n">attr</span><span class="p">]</span>
+                <span class="p">)</span>
+            <span class="p">)</span>
+
+        <span class="n">os</span><span class="o">.</span><span class="n">makedirs</span><span class="p">(</span><span class="n">build_dir</span><span class="p">,</span> <span class="n">exist_ok</span> <span class="o">=</span> <span class="kc">True</span><span class="p">)</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">network_datasets</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="n">network_datasets</span> <span class="ow">or</span>
+            <span class="p">(</span>
+                <span class="s1">&#39;omnipath&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;tf_target&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;mirna_mrna&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;tf_mirna&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;lncrna_mrna&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;small_molecule&#39;</span><span class="p">,</span>
+            <span class="p">)</span>
+        <span class="p">)</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">reload</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="n">modname</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="vm">__class__</span><span class="o">.</span><span class="vm">__module__</span>
+        <span class="n">mod</span> <span class="o">=</span> <span class="nb">__import__</span><span class="p">(</span><span class="n">modname</span><span class="p">,</span> <span class="n">fromlist</span><span class="o">=</span><span class="p">[</span><span class="n">modname</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;.&#39;</span><span class="p">)[</span><span class="mi">0</span><span class="p">]])</span>
+        <span class="n">imp</span><span class="o">.</span><span class="n">reload</span><span class="p">(</span><span class="n">mod</span><span class="p">)</span>
+        <span class="n">new</span> <span class="o">=</span> <span class="nb">getattr</span><span class="p">(</span><span class="n">mod</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="vm">__class__</span><span class="o">.</span><span class="vm">__name__</span><span class="p">)</span>
+        <span class="nb">setattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">&#39;__class__&#39;</span><span class="p">,</span> <span class="n">new</span><span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">main</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">interactions</span><span class="p">()</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">enz_sub</span><span class="p">()</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">complexes</span><span class="p">()</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">annotations</span><span class="p">()</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">intercell</span><span class="p">()</span>
+
+
+    <span class="k">def</span> <span class="nf">interactions</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span><span class="s1">&#39;Building `interactions` data frame.&#39;</span><span class="p">)</span>
+        <span class="n">dataframes</span> <span class="o">=</span> <span class="p">[]</span>
+
+        <span class="k">for</span> <span class="n">dataset</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">network_datasets</span><span class="p">:</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span><span class="s1">&#39;Building `</span><span class="si">%s</span><span class="s1">` interactions.&#39;</span> <span class="o">%</span> <span class="n">dataset</span><span class="p">)</span>
+
+            <span class="n">netw</span> <span class="o">=</span> <span class="n">omnipath</span><span class="o">.</span><span class="n">db</span><span class="o">.</span><span class="n">get_db</span><span class="p">(</span><span class="n">dataset</span><span class="p">)</span>
+
+            <span class="n">exp</span> <span class="o">=</span> <span class="n">export</span><span class="o">.</span><span class="n">Export</span><span class="p">(</span><span class="n">netw</span><span class="p">)</span>
+            <span class="n">exp</span><span class="o">.</span><span class="n">webservice_interactions_df</span><span class="p">()</span>
+            <span class="n">dataframes</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">exp</span><span class="o">.</span><span class="n">df</span><span class="p">)</span>
+
+            <span class="k">if</span> <span class="n">dataset</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">NO_HOMOLOGY_TRANSLATION</span><span class="p">:</span>
+
+                <span class="k">for</span> <span class="n">rodent</span> <span class="ow">in</span> <span class="p">(</span><span class="mi">10090</span><span class="p">,</span> <span class="mi">10116</span><span class="p">):</span>
+
+                    <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span>
+                        <span class="s1">&#39;Translating `</span><span class="si">%s</span><span class="s1">` interactions to organism `</span><span class="si">%u</span><span class="s1">`&#39;</span> <span class="o">%</span> <span class="p">(</span>
+                            <span class="n">dataset</span><span class="p">,</span>
+                            <span class="n">rodent</span><span class="p">,</span>
+                        <span class="p">)</span>
+                    <span class="p">)</span>
+
+                    <span class="n">rodent_netw</span> <span class="o">=</span> <span class="n">netw</span><span class="o">.</span><span class="n">homology_translate</span><span class="p">(</span><span class="n">rodent</span><span class="p">)</span>
+                    <span class="n">exp</span> <span class="o">=</span> <span class="n">export</span><span class="o">.</span><span class="n">Export</span><span class="p">(</span><span class="n">rodent_netw</span><span class="p">)</span>
+                    <span class="n">exp</span><span class="o">.</span><span class="n">webservice_interactions_df</span><span class="p">()</span>
+                    <span class="n">dataframes</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">exp</span><span class="o">.</span><span class="n">df</span><span class="p">)</span>
+
+                    <span class="k">del</span> <span class="n">rodent_netw</span>
+
+            <span class="k">del</span> <span class="n">exp</span>
+            <span class="k">del</span> <span class="n">netw</span>
+            <span class="n">omnipath</span><span class="o">.</span><span class="n">db</span><span class="o">.</span><span class="n">remove_db</span><span class="p">(</span><span class="n">dataset</span><span class="p">)</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">df_interactions</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">concat</span><span class="p">(</span><span class="n">dataframes</span><span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">df_interactions</span><span class="o">.</span><span class="n">to_csv</span><span class="p">(</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">outfile_interactions</span><span class="p">,</span>
+            <span class="n">sep</span> <span class="o">=</span> <span class="s1">&#39;</span><span class="se">\t</span><span class="s1">&#39;</span><span class="p">,</span>
+            <span class="n">index</span> <span class="o">=</span> <span class="kc">False</span>
+        <span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span><span class="s1">&#39;Data frame `interactions` has been exported to `</span><span class="si">%s</span><span class="s1">`.&#39;</span> <span class="o">%</span> <span class="p">(</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">outfile_interactions</span><span class="p">,</span>
+        <span class="p">))</span>
+
+
+    <span class="k">def</span> <span class="nf">interactions_legacy</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span>
+            <span class="s1">&#39;Building `interactions` data frame from &#39;</span>
+            <span class="s1">&#39;`legacy.main.PyPath` object.&#39;</span>
+        <span class="p">)</span>
+
+        <span class="kn">import</span> <span class="nn">pypath.legacy.main</span> <span class="k">as</span> <span class="nn">main</span>
+
+        <span class="n">dataframes</span> <span class="o">=</span> <span class="p">[]</span>
+
+        <span class="n">tf_target</span> <span class="o">=</span> <span class="n">copy</span><span class="o">.</span><span class="n">deepcopy</span><span class="p">(</span><span class="n">data_formats</span><span class="o">.</span><span class="n">transcription</span><span class="p">)</span>
+        <span class="n">tf_target</span><span class="p">[</span><span class="s1">&#39;dorothea&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">input_args</span><span class="p">[</span><span class="s1">&#39;levels&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="p">{</span>
+            <span class="s1">&#39;A&#39;</span><span class="p">,</span> <span class="s1">&#39;B&#39;</span><span class="p">,</span> <span class="s1">&#39;C&#39;</span><span class="p">,</span> <span class="s1">&#39;D&#39;</span><span class="p">,</span>
+        <span class="p">}</span>
+        <span class="n">tf_target</span><span class="p">[</span><span class="s1">&#39;dorothea&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">must_have_references</span> <span class="o">=</span> <span class="kc">False</span>
+
+        <span class="n">param</span> <span class="o">=</span> <span class="p">{</span>
+            <span class="s1">&#39;PPI&#39;</span><span class="p">:</span> <span class="p">(</span>
+                <span class="s1">&#39;load_omnipath&#39;</span><span class="p">,</span>
+                <span class="p">{</span>
+                    <span class="s1">&#39;kinase_substrate_extra&#39;</span><span class="p">:</span> <span class="kc">True</span><span class="p">,</span>
+                    <span class="s1">&#39;ligand_receptor_extra&#39;</span><span class="p">:</span> <span class="kc">True</span><span class="p">,</span>
+                    <span class="s1">&#39;pathway_extra&#39;</span><span class="p">:</span> <span class="kc">True</span><span class="p">,</span>
+                <span class="p">},</span>
+            <span class="p">),</span>
+            <span class="s1">&#39;TF-target&#39;</span><span class="p">:</span> <span class="p">(</span>
+                <span class="s1">&#39;init_network&#39;</span><span class="p">,</span>
+                <span class="p">{</span><span class="s1">&#39;lst&#39;</span><span class="p">:</span> <span class="n">tf_target</span><span class="p">},</span>
+            <span class="p">),</span>
+            <span class="s1">&#39;miRNA-target&#39;</span><span class="p">:</span> <span class="p">(</span>
+                <span class="s1">&#39;init_network&#39;</span><span class="p">,</span>
+                <span class="p">{</span><span class="s1">&#39;lst&#39;</span><span class="p">:</span> <span class="n">data_formats</span><span class="o">.</span><span class="n">mirna_target</span><span class="p">},</span>
+            <span class="p">),</span>
+            <span class="s1">&#39;lncRNA-target&#39;</span><span class="p">:</span> <span class="p">(</span>
+                <span class="s1">&#39;init_network&#39;</span><span class="p">,</span>
+                <span class="p">{</span><span class="s1">&#39;lst&#39;</span><span class="p">:</span> <span class="n">data_formats</span><span class="o">.</span><span class="n">lncrna_target</span><span class="p">},</span>
+            <span class="p">)</span>
+        <span class="p">}</span>
+
+        <span class="k">for</span> <span class="n">name</span><span class="p">,</span> <span class="p">(</span><span class="n">to_call</span><span class="p">,</span> <span class="n">kwargs</span><span class="p">)</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="n">param</span><span class="p">):</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span><span class="s1">&#39;Building </span><span class="si">%s</span><span class="s1"> interactions.&#39;</span> <span class="o">%</span> <span class="n">name</span><span class="p">)</span>
+
+            <span class="n">pa</span> <span class="o">=</span> <span class="n">main</span><span class="o">.</span><span class="n">PyPath</span><span class="p">()</span>
+            <span class="nb">getattr</span><span class="p">(</span><span class="n">pa</span><span class="p">,</span> <span class="n">to_call</span><span class="p">)(</span><span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
+
+            <span class="n">e</span> <span class="o">=</span> <span class="n">export</span><span class="o">.</span><span class="n">Export</span><span class="p">(</span><span class="n">pa</span><span class="p">)</span>
+            <span class="n">e</span><span class="o">.</span><span class="n">webservice_interactions_df</span><span class="p">()</span>
+            <span class="n">dataframes</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">e</span><span class="o">.</span><span class="n">df</span><span class="p">)</span>
+
+            <span class="k">if</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">only_human</span> <span class="ow">and</span> <span class="n">name</span> <span class="o">!=</span> <span class="s1">&#39;lncRNA-target&#39;</span><span class="p">:</span>
+
+                <span class="n">graph_human</span> <span class="o">=</span> <span class="kc">None</span>
+
+                <span class="k">for</span> <span class="n">rodent</span> <span class="ow">in</span> <span class="p">(</span><span class="mi">10090</span><span class="p">,</span> <span class="mi">10116</span><span class="p">):</span>
+
+                    <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span>
+                        <span class="s1">&#39;Translating </span><span class="si">%s</span><span class="s1"> interactions to organism `</span><span class="si">%u</span><span class="s1">`&#39;</span> <span class="o">%</span> <span class="p">(</span>
+                            <span class="n">name</span><span class="p">,</span>
+                            <span class="n">rodent</span><span class="p">,</span>
+                        <span class="p">)</span>
+                    <span class="p">)</span>
+
+                    <span class="k">if</span> <span class="n">pa</span><span class="o">.</span><span class="n">ncbi_tax_id</span> <span class="o">==</span> <span class="mi">9606</span><span class="p">:</span>
+
+                        <span class="k">if</span> <span class="n">pa</span><span class="o">.</span><span class="n">graph</span><span class="o">.</span><span class="n">ecount</span><span class="p">()</span> <span class="o">&lt;</span> <span class="mi">100000</span><span class="p">:</span>
+
+                            <span class="n">graph_human</span> <span class="o">=</span> <span class="n">copy</span><span class="o">.</span><span class="n">deepcopy</span><span class="p">(</span><span class="n">pa</span><span class="o">.</span><span class="n">graph</span><span class="p">)</span>
+
+                    <span class="k">else</span><span class="p">:</span>
+
+                        <span class="k">if</span> <span class="n">graph_human</span><span class="p">:</span>
+
+                            <span class="n">pa</span><span class="o">.</span><span class="n">graph</span> <span class="o">=</span> <span class="n">graph_human</span>
+                            <span class="n">pa</span><span class="o">.</span><span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="mi">9606</span>
+                            <span class="n">pa</span><span class="o">.</span><span class="n">genesymbol_labels</span><span class="p">(</span><span class="n">remap_all</span> <span class="o">=</span> <span class="kc">True</span><span class="p">)</span>
+                            <span class="n">pa</span><span class="o">.</span><span class="n">update_vname</span><span class="p">()</span>
+
+                        <span class="k">else</span><span class="p">:</span>
+
+                            <span class="k">del</span> <span class="n">e</span>
+                            <span class="k">del</span> <span class="n">pa</span>
+                            <span class="n">pa</span> <span class="o">=</span> <span class="n">main</span><span class="o">.</span><span class="n">PyPath</span><span class="p">()</span>
+                            <span class="nb">getattr</span><span class="p">(</span><span class="n">pa</span><span class="p">,</span> <span class="n">to_call</span><span class="p">)(</span><span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
+
+                    <span class="n">pa</span><span class="o">.</span><span class="n">orthology_translation</span><span class="p">(</span><span class="n">rodent</span><span class="p">)</span>
+                    <span class="n">e</span> <span class="o">=</span> <span class="n">export</span><span class="o">.</span><span class="n">Export</span><span class="p">(</span><span class="n">pa</span><span class="p">)</span>
+                    <span class="n">e</span><span class="o">.</span><span class="n">webservice_interactions_df</span><span class="p">()</span>
+                    <span class="n">dataframes</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">e</span><span class="o">.</span><span class="n">df</span><span class="p">)</span>
+
+        <span class="k">del</span> <span class="n">e</span>
+        <span class="k">del</span> <span class="n">pa</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">df_interactions</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">concat</span><span class="p">(</span><span class="n">dataframes</span><span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">df_interactions</span><span class="o">.</span><span class="n">to_csv</span><span class="p">(</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">outfile_interactions</span><span class="p">,</span>
+            <span class="n">sep</span> <span class="o">=</span> <span class="s1">&#39;</span><span class="se">\t</span><span class="s1">&#39;</span><span class="p">,</span>
+            <span class="n">index</span> <span class="o">=</span> <span class="kc">False</span>
+        <span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span><span class="s1">&#39;Data frame `interactions` has been exported to `</span><span class="si">%s</span><span class="s1">`.&#39;</span> <span class="o">%</span> <span class="p">(</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">outfile_interactions</span><span class="p">,</span>
+        <span class="p">))</span>
+
+
+    <span class="k">def</span> <span class="nf">enz_sub</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span><span class="s1">&#39;Building `enz_sub` data frame.&#39;</span><span class="p">)</span>
+
+        <span class="n">dataframes</span> <span class="o">=</span> <span class="p">[]</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span><span class="s1">&#39;Building `enz_sub` data frame for organism `9606`.&#39;</span><span class="p">)</span>
+        <span class="n">enz_sub_a</span> <span class="o">=</span> <span class="n">omnipath</span><span class="o">.</span><span class="n">db</span><span class="o">.</span><span class="n">get_db</span><span class="p">(</span><span class="s1">&#39;enz_sub&#39;</span><span class="p">)</span>
+        <span class="n">enz_sub_a</span><span class="o">.</span><span class="n">make_df</span><span class="p">(</span><span class="n">tax_id</span> <span class="o">=</span> <span class="kc">True</span><span class="p">)</span>
+        <span class="n">dataframes</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">enz_sub_a</span><span class="o">.</span><span class="n">df</span><span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span>
+            <span class="s1">&#39;Finished building `enz_sub` data frame for organism `9606`.&#39;</span>
+        <span class="p">)</span>
+        <span class="n">omnipath</span><span class="o">.</span><span class="n">db</span><span class="o">.</span><span class="n">remove_db</span><span class="p">(</span><span class="s1">&#39;enz_sub&#39;</span><span class="p">,</span> <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">)</span>
+
+        <span class="k">if</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">only_human</span><span class="p">:</span>
+
+            <span class="k">for</span> <span class="n">rodent</span> <span class="ow">in</span> <span class="p">(</span><span class="mi">10090</span><span class="p">,</span> <span class="mi">10116</span><span class="p">):</span>
+
+                <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span>
+                    <span class="s1">&#39;Building `enz_sub` data frame for &#39;</span>
+                    <span class="s1">&#39;organism `</span><span class="si">%s</span><span class="s1">`.&#39;</span> <span class="o">%</span> <span class="n">rodent</span>
+                <span class="p">)</span>
+
+                <span class="n">enz_sub_a</span> <span class="o">=</span> <span class="n">omnipath</span><span class="o">.</span><span class="n">db</span><span class="o">.</span><span class="n">get_db</span><span class="p">(</span>
+                    <span class="s1">&#39;enz_sub&#39;</span><span class="p">,</span>
+                    <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">rodent</span><span class="p">,</span>
+                <span class="p">)</span>
+                <span class="n">enz_sub_a</span><span class="o">.</span><span class="n">make_df</span><span class="p">(</span><span class="n">tax_id</span> <span class="o">=</span> <span class="kc">True</span><span class="p">)</span>
+                <span class="n">dataframes</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">enz_sub_a</span><span class="o">.</span><span class="n">df</span><span class="p">)</span>
+
+                <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span>
+                    <span class="s1">&#39;Finished building `enz_sub` data frame for &#39;</span>
+                    <span class="s1">&#39;organism `</span><span class="si">%s</span><span class="s1">`.&#39;</span> <span class="o">%</span> <span class="n">rodent</span>
+                <span class="p">)</span>
+
+                <span class="n">omnipath</span><span class="o">.</span><span class="n">db</span><span class="o">.</span><span class="n">remove_db</span><span class="p">(</span><span class="s1">&#39;enz_sub&#39;</span><span class="p">,</span> <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">rodent</span><span class="p">)</span>
+                <span class="k">del</span> <span class="n">enz_sub_a</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">df_enz_sub</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">concat</span><span class="p">(</span><span class="n">dataframes</span><span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">df_enz_sub</span><span class="o">.</span><span class="n">to_csv</span><span class="p">(</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">outfile_enz_sub</span><span class="p">,</span>
+            <span class="n">sep</span> <span class="o">=</span> <span class="s1">&#39;</span><span class="se">\t</span><span class="s1">&#39;</span><span class="p">,</span>
+            <span class="n">index</span> <span class="o">=</span> <span class="kc">False</span>
+        <span class="p">)</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span><span class="s1">&#39;Data frame `enz_sub` has been exported to `</span><span class="si">%s</span><span class="s1">`.&#39;</span> <span class="o">%</span> <span class="p">(</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">outfile_enz_sub</span><span class="p">,</span>
+        <span class="p">))</span>
+
+
+    <span class="k">def</span> <span class="nf">complexes</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span><span class="s1">&#39;Building `complexes` data frame.&#39;</span><span class="p">)</span>
+
+        <span class="n">co</span> <span class="o">=</span> <span class="n">omnipath</span><span class="o">.</span><span class="n">db</span><span class="o">.</span><span class="n">get_db</span><span class="p">(</span><span class="s1">&#39;complex&#39;</span><span class="p">)</span>
+
+        <span class="n">co</span><span class="o">.</span><span class="n">make_df</span><span class="p">()</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">df_complexes</span> <span class="o">=</span> <span class="n">co</span><span class="o">.</span><span class="n">df</span>
+
+        <span class="k">del</span> <span class="n">co</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">df_complexes</span><span class="o">.</span><span class="n">to_csv</span><span class="p">(</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">outfile_complexes</span><span class="p">,</span>
+            <span class="n">sep</span> <span class="o">=</span> <span class="s1">&#39;</span><span class="se">\t</span><span class="s1">&#39;</span><span class="p">,</span>
+            <span class="n">index</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+        <span class="p">)</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span><span class="s1">&#39;Data frame `complexes` has been exported to `</span><span class="si">%s</span><span class="s1">`.&#39;</span> <span class="o">%</span> <span class="p">(</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">outfile_complexes</span><span class="p">,</span>
+        <span class="p">))</span>
+
+
+    <span class="k">def</span> <span class="nf">annotations</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span><span class="s1">&#39;Building `annotations` data frame.&#39;</span><span class="p">)</span>
+
+        <span class="n">an</span> <span class="o">=</span> <span class="n">omnipath</span><span class="o">.</span><span class="n">db</span><span class="o">.</span><span class="n">get_db</span><span class="p">(</span><span class="s1">&#39;annotations&#39;</span><span class="p">)</span>
+
+        <span class="n">an</span><span class="o">.</span><span class="n">make_narrow_df</span><span class="p">()</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">df_annotations</span> <span class="o">=</span> <span class="n">an</span><span class="o">.</span><span class="n">narrow_df</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">df_annotations</span><span class="o">.</span><span class="n">to_csv</span><span class="p">(</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">outfile_annotations</span><span class="p">,</span>
+            <span class="n">sep</span> <span class="o">=</span> <span class="s1">&#39;</span><span class="se">\t</span><span class="s1">&#39;</span><span class="p">,</span>
+            <span class="n">index</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+        <span class="p">)</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span><span class="s1">&#39;Data frame `annotations` has been exported to `</span><span class="si">%s</span><span class="s1">`.&#39;</span> <span class="o">%</span> <span class="p">(</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">outfile_annotations</span><span class="p">,</span>
+        <span class="p">))</span>
+
+
+    <span class="k">def</span> <span class="nf">intercell</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span><span class="s1">&#39;Building `intercell` data frame.&#39;</span><span class="p">)</span>
+
+        <span class="n">i</span> <span class="o">=</span> <span class="n">omnipath</span><span class="o">.</span><span class="n">db</span><span class="o">.</span><span class="n">get_db</span><span class="p">(</span><span class="s1">&#39;intercell&#39;</span><span class="p">)</span>
+
+        <span class="n">i</span><span class="o">.</span><span class="n">make_df</span><span class="p">()</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">df_intercell</span> <span class="o">=</span> <span class="n">i</span><span class="o">.</span><span class="n">df</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">df_intercell</span><span class="o">.</span><span class="n">to_csv</span><span class="p">(</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">outfile_intercell</span><span class="p">,</span>
+            <span class="n">sep</span> <span class="o">=</span> <span class="s1">&#39;</span><span class="se">\t</span><span class="s1">&#39;</span><span class="p">,</span>
+            <span class="n">index</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+        <span class="p">)</span>
+
+        <span class="k">del</span> <span class="n">i</span>
+        <span class="n">omnipath</span><span class="o">.</span><span class="n">db</span><span class="o">.</span><span class="n">remove_db</span><span class="p">(</span><span class="s1">&#39;intercell&#39;</span><span class="p">)</span>
+        <span class="n">omnipath</span><span class="o">.</span><span class="n">db</span><span class="o">.</span><span class="n">remove_db</span><span class="p">(</span><span class="s1">&#39;complex&#39;</span><span class="p">)</span>
+        <span class="n">omnipath</span><span class="o">.</span><span class="n">db</span><span class="o">.</span><span class="n">remove_db</span><span class="p">(</span><span class="s1">&#39;annotations&#39;</span><span class="p">)</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span><span class="s1">&#39;Data frame `intercell` has been exported to `</span><span class="si">%s</span><span class="s1">`.&#39;</span> <span class="o">%</span> <span class="p">(</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">outfile_intercell</span><span class="p">,</span>
+        <span class="p">))</span></div>
+
+</pre></div>
+
+                </article>
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+                  
+  <h1>Source code for pypath.omnipath.server.generate_about_page</h1><div class="highlight"><pre>
+<span></span><span class="ch">#!/usr/bin/env python</span>
+<span class="c1"># -*- coding: utf-8 -*-</span>
+
+<span class="c1">#</span>
+<span class="c1">#  This file is part of the `pypath` python module</span>
+<span class="c1">#</span>
+<span class="c1">#  Copyright 2014-2023</span>
+<span class="c1">#  EMBL, EMBL-EBI, Uniklinik RWTH Aachen, Heidelberg University</span>
+<span class="c1">#</span>
+<span class="c1">#  Authors: see the file `README.rst`</span>
+<span class="c1">#  Contact: Dénes Türei (turei.denes@gmail.com)</span>
+<span class="c1">#</span>
+<span class="c1">#  Distributed under the GPLv3 License.</span>
+<span class="c1">#  See accompanying file LICENSE.txt or copy at</span>
+<span class="c1">#      https://www.gnu.org/licenses/gpl-3.0.html</span>
+<span class="c1">#</span>
+<span class="c1">#  Website: https://pypath.omnipathdb.org/</span>
+<span class="c1">#</span>
+
+<span class="kn">from</span> <span class="nn">future.utils</span> <span class="kn">import</span> <span class="n">iteritems</span>
+
+<span class="kn">import</span> <span class="nn">pypath.omnipath.server._html</span> <span class="k">as</span> <span class="nn">_html</span>
+<span class="kn">import</span> <span class="nn">pypath.resources.urls</span> <span class="k">as</span> <span class="nn">urls</span>
+
+<span class="kn">import</span> <span class="nn">pypath.share.common</span> <span class="k">as</span> <span class="nn">common</span>
+<span class="kn">import</span> <span class="nn">pypath.share.session</span> <span class="k">as</span> <span class="nn">session_mod</span>
+<span class="n">_logger</span> <span class="o">=</span> <span class="n">session_mod</span><span class="o">.</span><span class="n">Logger</span><span class="p">(</span><span class="n">name</span> <span class="o">=</span> <span class="s1">&#39;generate_about_page&#39;</span><span class="p">)</span>
+<span class="n">_log</span> <span class="o">=</span> <span class="n">_logger</span><span class="o">.</span><span class="n">_log</span>
+
+<span class="n">__all__</span> <span class="o">=</span> <span class="p">[</span><span class="s1">&#39;generate_about_html&#39;</span><span class="p">,</span> <span class="s1">&#39;write_html&#39;</span><span class="p">]</span>
+
+<span class="k">if</span> <span class="s1">&#39;long&#39;</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">__builtins__</span><span class="p">:</span>
+    <span class="n">long</span> <span class="o">=</span> <span class="nb">int</span>
+
+<span class="k">if</span> <span class="s1">&#39;unicode&#39;</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">__builtins__</span><span class="p">:</span>
+    <span class="n">unicode</span> <span class="o">=</span> <span class="nb">str</span>
+
+<span class="n">pypath_methods</span> <span class="o">=</span> <span class="p">{</span>
+    <span class="s1">&#39;data&#39;</span><span class="p">:</span> <span class="s1">&#39;Data source (URLs and files)&#39;</span><span class="p">,</span>
+    <span class="s1">&#39;format&#39;</span><span class="p">:</span> <span class="s1">&#39;Data format definition&#39;</span><span class="p">,</span>
+    <span class="s1">&#39;intr&#39;</span><span class="p">:</span> <span class="s1">&#39;Interactions&#39;</span><span class="p">,</span>
+    <span class="s1">&#39;input&#39;</span><span class="p">:</span> <span class="s1">&#39;Data input methods&#39;</span><span class="p">,</span>
+    <span class="s1">&#39;ptm&#39;</span><span class="p">:</span> <span class="s1">&#39;Enzyme-substrate relationships and PTMs&#39;</span><span class="p">,</span>
+    <span class="s1">&#39;dmi&#39;</span><span class="p">:</span> <span class="s1">&#39;Domain-motif interactions&#39;</span><span class="p">,</span>
+    <span class="s1">&#39;ddi&#39;</span><span class="p">:</span> <span class="s1">&#39;Domain-domain interactions&#39;</span><span class="p">,</span>
+    <span class="s1">&#39;misc&#39;</span><span class="p">:</span> <span class="s1">&#39;Miscellaneous&#39;</span><span class="p">,</span>
+<span class="p">}</span>
+
+
+<div class="viewcode-block" id="generate_about_html">
+<a class="viewcode-back" href="../../../../api/pypath.omnipath.server.generate_about_page.generate_about_html.html#pypath.omnipath.server.generate_about_page.generate_about_html">[docs]</a>
+<span class="k">def</span> <span class="nf">generate_about_html</span><span class="p">(</span><span class="n">descriptions</span><span class="p">,</span> <span class="nb">format</span> <span class="o">=</span> <span class="s1">&#39;b&#39;</span><span class="p">):</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Generates a HTML page from the `descriptions` array.</span>
+<span class="sd">    This HTML is provided by the webservice under `/info`,</span>
+<span class="sd">    or can be saved locally with `write_html()`.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+    <span class="c1"># Header</span>
+    <span class="n">title</span> <span class="o">=</span> <span class="s1">&#39;Metadata about resources in OmniPath and pypath&#39;</span>
+    <span class="n">doc</span> <span class="o">=</span> <span class="p">(</span>
+        <span class="s1">&#39;&lt;div class=&quot;yellowbox box&quot;&gt;</span><span class="se">\n</span><span class="s1">&#39;</span>
+        <span class="s1">&#39;&lt;p&gt;</span><span class="se">\n</span><span class="s1">&#39;</span>
+            <span class="s1">&#39;&lt;em&gt;</span><span class="se">\n</span><span class="s1">&#39;</span>
+            <span class="s1">&#39;We created this webpage in Nov 2016.</span><span class="se">\n</span><span class="s1">&#39;</span>
+            <span class="s1">&#39;Since the end of 2019 we have been gradually updating and </span><span class="se">\n</span><span class="s1">&#39;</span>
+            <span class="s1">&#39;extending the information. As of July 2020 we updated the URLs</span><span class="se">\n</span><span class="s1">&#39;</span>
+            <span class="s1">&#39;and licensing terms of most of the resources.</span><span class="se">\n</span><span class="s1">&#39;</span>
+            <span class="s1">&#39;Most of the &quot;pypath methods&quot; and the</span><span class="se">\n</span><span class="s1">&#39;</span>
+            <span class="s1">&#39;years of releases are out of date.</span><span class="se">\n</span><span class="s1">&#39;</span>
+            <span class="s1">&#39;We will keep updating these, if you find any wrong information</span><span class="se">\n</span><span class="s1">&#39;</span>
+            <span class="s1">&#39;please notify us at omnipathdb@gmail.com.</span><span class="se">\n</span><span class="s1">&#39;</span>
+            <span class="s1">&#39;About updates of the OmniPath database content please refer to</span><span class="se">\n</span><span class="s1">&#39;</span>
+            <span class="s1">&#39;&lt;a href=&quot;http://archive.omnipathdb.org/README.txt&quot;&gt;</span><span class="se">\n</span><span class="s1">&#39;</span>
+                <span class="s1">&#39;our archive.</span><span class="se">\n</span><span class="s1">&#39;</span>
+            <span class="s1">&#39;&lt;/a&gt;</span><span class="se">\n</span><span class="s1">&#39;</span>
+            <span class="s1">&#39;&lt;/em&gt;</span><span class="se">\n</span><span class="s1">&#39;</span>
+        <span class="s1">&#39;&lt;/p&gt;</span><span class="se">\n</span><span class="s1">&#39;</span>
+        <span class="s1">&#39;&lt;/div&gt;</span><span class="se">\n</span><span class="s1">&#39;</span>
+        <span class="s1">&#39;&lt;p&gt;This collection is a byproduct of the development of</span><span class="se">\n</span><span class="s1">&#39;</span>
+        <span class="s1">&#39;OmniPath, a database built from above 100 resources.</span><span class="se">\n</span><span class="s1">&#39;</span>
+        <span class="s1">&#39;Initially OmniPath focused on the literature curatied activity</span><span class="se">\n</span><span class="s1">&#39;</span>
+        <span class="s1">&#39;flow networks. Today it covers a much broader range of molecular</span><span class="se">\n</span><span class="s1">&#39;</span>
+        <span class="s1">&#39;interaction data, and besides its network database OmniPath</span><span class="se">\n</span><span class="s1">&#39;</span>
+        <span class="s1">&#39;has four other databases: enzyme-PTM relationships, protein</span><span class="se">\n</span><span class="s1">&#39;</span>
+        <span class="s1">&#39;complexes, molecular annotations (function, localization,</span><span class="se">\n</span><span class="s1">&#39;</span>
+        <span class="s1">&#39;structure, etc) and intercellular communication roles.</span><span class="se">\n</span><span class="s1">&#39;</span>
+        <span class="s1">&#39;The &quot;omnipath&quot; dataset of the network database follows the</span><span class="se">\n</span><span class="s1">&#39;</span>
+        <span class="s1">&#39;principles of the initial release of OmniPath, focusing on </span><span class="se">\n</span><span class="s1">&#39;</span>
+        <span class="s1">&#39;high quality, manually curated signaling pathways. The &#39;</span>
+        <span class="s1">&#39;descriptions here cite the relevant sentences &#39;</span>
+        <span class="s1">&#39;about the curation protocols from the original articles and</span><span class="se">\n</span><span class="s1">&#39;</span>
+        <span class="s1">&#39;webpages. URLs pointing to the articles and the webpages, and some</span><span class="se">\n</span><span class="s1">&#39;</span>
+        <span class="s1">&#39;additional metadata are provided where available.</span><span class="se">\n</span><span class="s1">&#39;</span>
+        <span class="s1">&#39;The resources with green title are included by default in</span><span class="se">\n</span><span class="s1">&#39;</span>
+        <span class="s1">&#39;OmniPath. &lt;span class=&quot;code&quot;&gt;pypath&lt;/span&gt; methods are listed</span><span class="se">\n</span><span class="s1">&#39;</span>
+        <span class="s1">&#39; where available, to know more please look at</span><span class="se">\n</span><span class="s1">&lt;a &#39;</span>
+        <span class="s1">&#39;target=&quot;_blank&quot; href=&quot;https://pypath.omnipathdb.org/&quot;&gt;&#39;</span>
+        <span class="s1">&#39;pypath documentation.&lt;/a&gt;</span><span class="se">\n</span><span class="s1">&#39;</span>
+        <span class="s1">&#39;&lt;p class=&quot;small&quot;&gt;</span><span class="se">\n</span><span class="s1">&#39;</span>
+        <span class="s1">&#39;&lt;strong&gt;How we collected the license information?&lt;/strong&gt;</span><span class="se">\n</span><span class="s1">&#39;</span>
+        <span class="s1">&#39;We searched for license information</span><span class="se">\n</span><span class="s1">&#39;</span>
+        <span class="s1">&#39;in the main, About, Download and FAQ sections of the webpages,</span><span class="se">\n</span><span class="s1">&#39;</span>
+        <span class="s1">&#39;and run Google searches for the database name and license.</span><span class="se">\n</span><span class="s1">&#39;</span>
+        <span class="s1">&#39;Where we could not find anything about licensing, we assumed</span><span class="se">\n</span><span class="s1">&#39;</span>
+        <span class="s1">&#39;no license. Unfortunately due to todays restrictive copyright</span><span class="se">\n</span><span class="s1">&#39;</span>
+        <span class="s1">&#39;legislations, users don</span><span class="se">\&#39;</span><span class="s1">t have the freedom to use, modify and</span><span class="se">\n</span><span class="s1">&#39;</span>
+        <span class="s1">&#39;redistribute the data without a license explicitely granting</span><span class="se">\n</span><span class="s1">&#39;</span>
+        <span class="s1">&#39;these to them. Despite the clear intention from the authors to</span><span class="se">\n</span><span class="s1">&#39;</span>
+        <span class="s1">&#39;make their data public, and statements on the webpage like</span><span class="se">\n</span><span class="s1">&#39;</span>
+        <span class="s1">&#39;&quot;free to use&quot; or &quot;available for download&quot;. In these cases</span><span class="se">\n</span><span class="s1">&#39;</span>
+        <span class="s1">&#39;we contacted the authors for permission to redistribute their</span><span class="se">\n</span><span class="s1">&#39;</span>
+        <span class="s1">&#39;data.&lt;/p&gt;</span><span class="se">\n</span><span class="s1">&#39;</span>
+    <span class="p">)</span>
+    <span class="n">doc</span> <span class="o">+=</span> <span class="s1">&#39;</span><span class="se">\t</span><span class="s1">&lt;h2&gt;Contents&lt;/h2&gt;</span><span class="se">\n</span><span class="s1">&#39;</span>
+    <span class="n">doc</span> <span class="o">+=</span> <span class="s1">&#39;</span><span class="se">\t</span><span class="s1">&lt;ul&gt;</span><span class="se">\n</span><span class="s1">&#39;</span>
+
+    <span class="c1"># Table of Content</span>
+    <span class="k">for</span> <span class="n">k</span><span class="p">,</span> <span class="n">v</span> <span class="ow">in</span> <span class="nb">sorted</span><span class="p">(</span><span class="n">descriptions</span><span class="o">.</span><span class="n">items</span><span class="p">(),</span> <span class="n">key</span><span class="o">=</span><span class="k">lambda</span> <span class="n">x</span><span class="p">:</span> <span class="n">x</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">lower</span><span class="p">()):</span>
+        <span class="n">doc</span> <span class="o">+=</span> <span class="s1">&#39;</span><span class="se">\t\t\t</span><span class="s1">&lt;li&gt;&lt;a href=&quot;#</span><span class="si">%s</span><span class="s1">&quot; class=&quot;</span><span class="si">%s</span><span class="s1">&quot;&gt;</span><span class="si">%s%s</span><span class="s1">&lt;/a&gt;&lt;/li&gt;</span><span class="se">\n</span><span class="s1">&#39;</span> <span class="o">%</span> \
+            <span class="p">(</span>
+                <span class="n">k</span><span class="p">,</span>
+                <span class="s1">&#39;omnipath&#39;</span>
+                    <span class="k">if</span> <span class="s1">&#39;omnipath&#39;</span> <span class="ow">in</span> <span class="n">v</span> <span class="ow">and</span> <span class="n">v</span><span class="p">[</span><span class="s1">&#39;omnipath&#39;</span><span class="p">]</span> <span class="k">else</span> <span class="s1">&#39;base&#39;</span><span class="p">,</span>
+                <span class="n">v</span><span class="p">[</span><span class="s1">&#39;label&#39;</span><span class="p">]</span> <span class="k">if</span> <span class="s1">&#39;label&#39;</span> <span class="ow">in</span> <span class="n">v</span> <span class="k">else</span> <span class="n">k</span><span class="p">,</span>
+                <span class="p">(</span><span class="s1">&#39; – </span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="n">v</span><span class="p">[</span><span class="s1">&#39;full_name&#39;</span><span class="p">])</span> <span class="k">if</span> <span class="s1">&#39;full_name&#39;</span> <span class="ow">in</span> <span class="n">v</span> <span class="k">else</span> <span class="s1">&#39;&#39;</span>
+            <span class="p">)</span>
+    <span class="n">doc</span> <span class="o">+=</span> <span class="s1">&#39;</span><span class="se">\t</span><span class="s1">&lt;/ul&gt;</span><span class="se">\n</span><span class="s1">&#39;</span>
+
+    <span class="c1"># Sections</span>
+    <span class="k">for</span> <span class="n">k</span><span class="p">,</span> <span class="n">v</span> <span class="ow">in</span> <span class="nb">sorted</span><span class="p">(</span><span class="n">descriptions</span><span class="o">.</span><span class="n">items</span><span class="p">(),</span> <span class="n">key</span><span class="o">=</span><span class="k">lambda</span> <span class="n">x</span><span class="p">:</span> <span class="n">x</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">lower</span><span class="p">()):</span>
+
+        <span class="n">resource_type</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="n">common</span><span class="o">.</span><span class="n">to_list</span><span class="p">(</span><span class="n">v</span><span class="p">[</span><span class="s1">&#39;type&#39;</span><span class="p">])</span> <span class="k">if</span> <span class="s1">&#39;type&#39;</span> <span class="ow">in</span> <span class="n">v</span> <span class="k">else</span> <span class="p">[</span><span class="s1">&#39;Undefined&#39;</span><span class="p">]</span>
+        <span class="p">)</span>
+        <span class="n">resource_subtype</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="n">common</span><span class="o">.</span><span class="n">to_list</span><span class="p">(</span><span class="n">v</span><span class="p">[</span><span class="s1">&#39;subtype&#39;</span><span class="p">])</span> <span class="k">if</span> <span class="s1">&#39;subtype&#39;</span> <span class="ow">in</span> <span class="n">v</span> <span class="k">else</span> <span class="p">[</span><span class="s1">&#39;Undefined&#39;</span><span class="p">]</span>
+        <span class="p">)</span>
+        <span class="n">resource_type</span> <span class="o">=</span> <span class="s1">&#39;, &#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">t</span><span class="o">.</span><span class="n">capitalize</span><span class="p">()</span> <span class="k">for</span> <span class="n">t</span> <span class="ow">in</span> <span class="n">resource_type</span><span class="p">)</span>
+        <span class="n">resource_subtype</span> <span class="o">=</span> <span class="s1">&#39;, &#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">t</span><span class="o">.</span><span class="n">capitalize</span><span class="p">()</span> <span class="k">for</span> <span class="n">t</span> <span class="ow">in</span> <span class="n">resource_subtype</span><span class="p">)</span>
+
+        <span class="n">doc</span> <span class="o">+=</span> <span class="sa">u</span><span class="s1">&#39;</span><span class="se">\t\t</span><span class="s1">&lt;br&gt;</span><span class="se">\n\t\t</span><span class="s1">&lt;h2 id=&quot;</span><span class="si">%s</span><span class="s1">&quot; class=&quot;</span><span class="si">%s</span><span class="s1">&quot;&gt;</span><span class="si">%s%s</span><span class="s1">&lt;/h2&gt;</span><span class="se">\n</span><span class="s1">&#39;</span> <span class="o">%</span> \
+            <span class="p">(</span><span class="n">k</span><span class="p">,</span> <span class="s1">&#39;omnipath&#39;</span> <span class="k">if</span> <span class="s1">&#39;omnipath&#39;</span> <span class="ow">in</span> <span class="n">v</span> <span class="ow">and</span> <span class="n">v</span><span class="p">[</span><span class="s1">&#39;omnipath&#39;</span><span class="p">]</span> <span class="k">else</span> <span class="s1">&#39;base&#39;</span><span class="p">,</span>
+             <span class="n">v</span><span class="p">[</span><span class="s1">&#39;label&#39;</span><span class="p">]</span> <span class="k">if</span> <span class="s1">&#39;label&#39;</span> <span class="ow">in</span> <span class="n">v</span> <span class="k">else</span> <span class="n">k</span><span class="p">,</span>
+             <span class="p">(</span><span class="sa">u</span><span class="s1">&#39; – </span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="p">(</span><span class="n">v</span><span class="p">[</span><span class="s1">&#39;full_name&#39;</span><span class="p">],))</span> <span class="k">if</span> <span class="s1">&#39;full_name&#39;</span> <span class="ow">in</span> <span class="n">v</span> <span class="k">else</span> <span class="s1">&#39;&#39;</span><span class="p">)</span>
+        <span class="n">doc</span> <span class="o">+=</span> <span class="s1">&#39;</span><span class="se">\t\t\t</span><span class="s1">&lt;p&gt;&lt;b&gt;Category || Subcategory &amp;gt;&amp;gt;&amp;gt;&lt;/b&gt; </span><span class="si">%s</span><span class="s1"> || </span><span class="si">%s</span><span class="s1">&lt;/p&gt;</span><span class="se">\n</span><span class="s1">&#39;</span> <span class="o">%</span> \
+            <span class="p">(</span><span class="n">resource_type</span><span class="p">,</span> <span class="n">resource_subtype</span><span class="p">)</span>
+        <span class="k">if</span> <span class="s1">&#39;year&#39;</span> <span class="ow">in</span> <span class="n">v</span><span class="p">:</span>
+            <span class="n">doc</span> <span class="o">+=</span> <span class="s1">&#39;</span><span class="se">\t\t\t</span><span class="s1">&lt;h3&gt;Last released: </span><span class="si">%u</span><span class="s1">&lt;\h3&gt;</span><span class="se">\n</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="n">v</span><span class="p">[</span><span class="s1">&#39;year&#39;</span><span class="p">]</span>
+        <span class="k">if</span> <span class="s1">&#39;releases&#39;</span> <span class="ow">in</span> <span class="n">v</span><span class="p">:</span>
+            <span class="n">doc</span> <span class="o">+=</span> <span class="s1">&#39;</span><span class="se">\t\t\t</span><span class="s1">&lt;p&gt;&lt;b&gt;Released in years: &lt;/b&gt;</span><span class="si">%s</span><span class="s1">&lt;/p&gt;</span><span class="se">\n</span><span class="s1">&#39;</span> <span class="o">%</span> \
+                <span class="s1">&#39;, &#39;</span><span class="o">.</span><span class="n">join</span><span class="p">([</span><span class="s1">&#39;</span><span class="si">%u</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="n">y</span> <span class="k">for</span> <span class="n">y</span> <span class="ow">in</span> <span class="n">v</span><span class="p">[</span><span class="s1">&#39;releases&#39;</span><span class="p">]])</span>
+        <span class="k">if</span> <span class="s1">&#39;authors&#39;</span> <span class="ow">in</span> <span class="n">v</span> <span class="ow">and</span> <span class="n">v</span><span class="p">[</span><span class="s1">&#39;authors&#39;</span><span class="p">]</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
+            <span class="n">doc</span> <span class="o">+=</span> <span class="s1">&#39;</span><span class="se">\t\t\t</span><span class="s1">&lt;p&gt;&lt;b&gt;Created by &lt;/b&gt;</span><span class="si">%s</span><span class="s1">&lt;/p&gt;</span><span class="se">\n</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="s1">&#39;, &#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">v</span><span class="p">[</span>
+                <span class="s1">&#39;authors&#39;</span><span class="p">])</span>
+        <span class="k">if</span> <span class="s1">&#39;emails&#39;</span> <span class="ow">in</span> <span class="n">v</span> <span class="ow">and</span> <span class="n">v</span><span class="p">[</span><span class="s1">&#39;emails&#39;</span><span class="p">]</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
+            <span class="n">doc</span> <span class="o">+=</span> <span class="s1">&#39;</span><span class="se">\t\t\t</span><span class="s1">&lt;p&gt;&lt;b&gt;Contact: &lt;/b&gt;&lt;/p&gt;</span><span class="se">\n\n\t\t\t\t</span><span class="s1">&lt;ul&gt;</span><span class="se">\n</span><span class="si">%s</span><span class="se">\n</span><span class="s1">&#39;</span> <span class="o">%</span> \
+                <span class="s1">&#39;&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">([</span><span class="s1">&#39;</span><span class="se">\t\t\t\t</span><span class="s1">&lt;li&gt;&lt;a href=&quot;mailto:</span><span class="si">%s</span><span class="s1">&quot;&gt;</span><span class="si">%s</span><span class="s1"> &amp;lt;</span><span class="si">%s</span><span class="s1">&amp;gt;&lt;/li&gt;</span><span class="se">\n</span><span class="s1">&#39;</span> <span class="o">%</span>
+                         <span class="p">(</span><span class="n">email</span><span class="p">,</span> <span class="n">contact_name</span><span class="p">,</span> <span class="n">email</span><span class="p">)</span> <span class="k">for</span> <span class="n">email</span><span class="p">,</span> <span class="n">contact_name</span> <span class="ow">in</span>
+                         <span class="nb">zip</span><span class="p">(</span><span class="n">v</span><span class="p">[</span><span class="s1">&#39;emails&#39;</span><span class="p">][::</span><span class="mi">2</span><span class="p">],</span> <span class="n">v</span><span class="p">[</span><span class="s1">&#39;emails&#39;</span><span class="p">][</span><span class="mi">1</span><span class="p">::</span><span class="mi">2</span><span class="p">])])</span>
+            <span class="n">doc</span> <span class="o">+=</span> <span class="s1">&#39;</span><span class="se">\t\t\t\t</span><span class="s1">&lt;/ul&gt;</span><span class="se">\n</span><span class="s1">&#39;</span>
+
+            <span class="n">emails</span> <span class="o">=</span> <span class="p">(</span>
+                <span class="s2">&quot;, &quot;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="s2">&quot;</span><span class="si">%s</span><span class="s2"> &lt;</span><span class="si">%s</span><span class="s2">&gt;&quot;</span> <span class="o">%</span> <span class="p">(</span><span class="n">contact_name</span><span class="p">,</span> <span class="n">email</span><span class="p">)</span>
+                          <span class="k">for</span> <span class="n">email</span><span class="p">,</span> <span class="n">contact_name</span> <span class="ow">in</span>
+                          <span class="nb">zip</span><span class="p">(</span><span class="n">v</span><span class="p">[</span><span class="s1">&#39;emails&#39;</span><span class="p">][::</span><span class="mi">2</span><span class="p">],</span> <span class="n">v</span><span class="p">[</span><span class="s1">&#39;emails&#39;</span><span class="p">][</span><span class="mi">1</span><span class="p">::</span><span class="mi">2</span><span class="p">]))</span>  <span class="c1"># zip makes (0,1),(2,3) ...</span>
+                <span class="k">if</span> <span class="s1">&#39;emails&#39;</span> <span class="ow">in</span> <span class="n">v</span> <span class="k">else</span> <span class="s1">&#39;&#39;</span>
+            <span class="p">)</span>
+        <span class="k">if</span> <span class="s1">&#39;license&#39;</span> <span class="ow">in</span> <span class="n">v</span><span class="p">:</span>
+            <span class="k">try</span><span class="p">:</span>
+                <span class="n">license</span> <span class="o">=</span> <span class="n">v</span><span class="p">[</span><span class="s1">&#39;license&#39;</span><span class="p">]</span>
+
+                <span class="n">doc</span> <span class="o">+=</span> <span class="p">(</span>
+                    <span class="s1">&#39;</span><span class="se">\t\t\t</span><span class="s1">&lt;p&gt;&lt;b&gt;License:&lt;/b&gt; &#39;</span>
+                    <span class="s1">&#39;&lt;a href=&quot;</span><span class="si">%s</span><span class="s1">&quot; target=&quot;_blank&quot;&gt;</span><span class="si">%s%s</span><span class="s1">&lt;/a&gt;</span><span class="si">%s</span><span class="s1">&lt;/p&gt;</span><span class="se">\n</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="p">(</span>
+                        <span class="n">license</span><span class="o">.</span><span class="n">url</span><span class="p">,</span>
+                        <span class="n">license</span><span class="o">.</span><span class="n">full_name</span><span class="p">,</span>
+                        <span class="p">(</span><span class="s1">&#39; (</span><span class="si">%s</span><span class="s1">)&#39;</span> <span class="o">%</span> <span class="n">license</span><span class="o">.</span><span class="n">name</span><span class="p">)</span> <span class="k">if</span> <span class="n">license</span><span class="o">.</span><span class="n">name</span> <span class="o">!=</span> <span class="n">k</span> <span class="k">else</span> <span class="s1">&#39;&#39;</span><span class="p">,</span>
+                        <span class="p">(</span><span class="s1">&#39;&lt;/p&gt;</span><span class="se">\n\t\t\t</span><span class="s1">&lt;p&gt;&lt;em&gt;&quot;</span><span class="si">%s</span><span class="s1">&quot;&lt;/em&gt;&#39;</span> <span class="o">%</span> <span class="n">license</span><span class="o">.</span><span class="n">note</span><span class="p">)</span>
+                            <span class="k">if</span> <span class="nb">hasattr</span><span class="p">(</span><span class="n">license</span><span class="p">,</span> <span class="s1">&#39;note&#39;</span><span class="p">)</span> <span class="k">else</span>
+                        <span class="s1">&#39;&#39;</span>
+                    <span class="p">)</span>
+                <span class="p">)</span>
+
+            <span class="k">except</span> <span class="ne">KeyError</span><span class="p">:</span>
+
+                <span class="n">_log</span><span class="p">(</span>
+                    <span class="s1">&#39;Wrong license format or incomplete &#39;</span>
+                    <span class="s1">&#39;information for `</span><span class="si">%s</span><span class="s1">`.&#39;</span> <span class="o">%</span> <span class="n">k</span>
+                <span class="p">)</span>
+
+        <span class="k">if</span> <span class="s1">&#39;urls&#39;</span> <span class="ow">in</span> <span class="n">v</span><span class="p">:</span>
+            <span class="k">for</span> <span class="n">uk</span><span class="p">,</span> <span class="n">uv</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="n">v</span><span class="p">[</span><span class="s1">&#39;urls&#39;</span><span class="p">]):</span>
+                <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">uv</span><span class="p">)</span> <span class="o">&gt;</span> <span class="mi">0</span> <span class="ow">and</span> <span class="n">uk</span> <span class="o">!=</span> <span class="s1">&#39;omictools&#39;</span><span class="p">:</span>
+                    <span class="k">try</span><span class="p">:</span>
+                        <span class="n">doc</span> <span class="o">+=</span> <span class="s1">&#39;</span><span class="se">\t\t\t</span><span class="s1">&lt;h3&gt;</span><span class="si">%s</span><span class="s1">&lt;/h3&gt;</span><span class="se">\n</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="p">(</span><span class="n">uk</span><span class="o">.</span><span class="n">capitalize</span><span class="p">())</span>
+                        <span class="n">doc</span> <span class="o">+=</span> <span class="s1">&#39;</span><span class="se">\t\t\t</span><span class="s1">&lt;ul&gt;</span><span class="se">\n</span><span class="s1">&#39;</span>
+                        <span class="k">for</span> <span class="n">a</span> <span class="ow">in</span> <span class="n">uv</span><span class="p">:</span>
+                            <span class="n">doc</span> <span class="o">+=</span> <span class="p">(</span>
+                                    <span class="s1">&#39;</span><span class="se">\t\t\t\t</span><span class="s1">&lt;li&gt;&lt;a href=&quot;</span><span class="si">%s</span><span class="s1">&quot; &#39;</span>
+                                    <span class="s1">&#39;target=&quot;_blank&quot;&gt;</span><span class="si">%s</span><span class="s1">&lt;/a&gt;&lt;/li&gt;</span><span class="se">\n</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="p">(</span>
+                                        <span class="n">a</span><span class="p">,</span> <span class="n">a</span>
+                                    <span class="p">)</span>
+                            <span class="p">)</span>
+                        <span class="n">doc</span> <span class="o">+=</span> <span class="s1">&#39;</span><span class="se">\t\t\t</span><span class="s1">&lt;/ul&gt;</span><span class="se">\n</span><span class="s1">&#39;</span>
+                    <span class="k">except</span> <span class="ne">UnicodeDecodeError</span><span class="p">:</span>
+                        <span class="n">_log</span><span class="p">(</span><span class="s1">&#39;UnicodeDecodeError at </span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="n">k</span><span class="p">)</span>
+
+        <span class="k">if</span> <span class="s1">&#39;pubmeds&#39;</span> <span class="ow">in</span> <span class="n">v</span><span class="p">:</span>
+            <span class="n">doc</span> <span class="o">+=</span> <span class="s1">&#39;</span><span class="se">\t\t\t</span><span class="s1">&lt;h3&gt;PubMed&lt;/h3&gt;</span><span class="se">\n</span><span class="s1">&#39;</span>
+            <span class="n">doc</span> <span class="o">+=</span> <span class="s1">&#39;</span><span class="se">\t\t\t</span><span class="s1">&lt;ul&gt;</span><span class="se">\n</span><span class="s1">&#39;</span>
+            <span class="k">for</span> <span class="n">pmid</span> <span class="ow">in</span> <span class="n">v</span><span class="p">[</span><span class="s1">&#39;pubmeds&#39;</span><span class="p">]:</span>
+                <span class="n">doc</span> <span class="o">+=</span> <span class="s1">&#39;</span><span class="se">\t\t\t\t</span><span class="s1">&lt;li&gt;&lt;a href=&quot;</span><span class="si">%s</span><span class="s1">&quot; &#39;</span>\
+                    <span class="s1">&#39;target=&quot;_blank&quot;&gt;</span><span class="si">%s</span><span class="s1">&lt;/a&gt;&lt;/li&gt;</span><span class="se">\n</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="p">(</span>
+                        <span class="s1">&#39;http://www.ncbi.nlm.nih.gov/pubmed/</span><span class="si">%u</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="n">pmid</span><span class="p">,</span>
+                        <span class="s1">&#39;http://www.ncbi.nlm.nih.gov/pubmed/</span><span class="si">%u</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="n">pmid</span>
+                    <span class="p">)</span>
+            <span class="n">doc</span> <span class="o">+=</span> <span class="s1">&#39;</span><span class="se">\t\t\t</span><span class="s1">&lt;/ul&gt;</span><span class="se">\n</span><span class="s1">&#39;</span>
+        <span class="k">if</span> <span class="s1">&#39;urls&#39;</span> <span class="ow">in</span> <span class="n">v</span> <span class="ow">and</span> <span class="s1">&#39;omictools&#39;</span> <span class="ow">in</span> <span class="n">v</span><span class="p">[</span><span class="s1">&#39;urls&#39;</span><span class="p">]</span> <span class="ow">or</span> <span class="s1">&#39;pathguide&#39;</span> <span class="ow">in</span> <span class="n">v</span><span class="p">:</span>
+            <span class="n">doc</span> <span class="o">+=</span> <span class="s1">&#39;</span><span class="se">\t\t\t</span><span class="s1">&lt;h3&gt;Collections&lt;/h3&gt;</span><span class="se">\n\t\t\t</span><span class="s1">&lt;ul&gt;&#39;</span>
+            <span class="k">if</span> <span class="s1">&#39;omictools&#39;</span> <span class="ow">in</span> <span class="n">v</span><span class="p">[</span><span class="s1">&#39;urls&#39;</span><span class="p">]:</span>
+                <span class="n">doc</span> <span class="o">+=</span> <span class="s1">&#39;</span><span class="se">\t\t\t</span><span class="s1">&lt;li&gt;&lt;a href=&quot;</span><span class="si">%s</span><span class="s1">&quot; target=&quot;_blank&quot;&gt;OmicTools&lt;/a&gt;&lt;/li&gt;</span><span class="se">\n</span><span class="s1">&#39;</span> <span class="o">%</span> \
+                    <span class="n">v</span><span class="p">[</span><span class="s1">&#39;urls&#39;</span><span class="p">][</span><span class="s1">&#39;omictools&#39;</span><span class="p">][</span><span class="mi">0</span><span class="p">]</span>
+            <span class="k">if</span> <span class="s1">&#39;pathguide&#39;</span> <span class="ow">in</span> <span class="n">v</span><span class="p">:</span>
+                <span class="n">doc</span> <span class="o">+=</span> <span class="s1">&#39;</span><span class="se">\t\t\t</span><span class="s1">&lt;li&gt;&lt;a href=&quot;</span><span class="si">%s</span><span class="s1">&quot; target=&quot;_blank&quot;&gt;PathGuide&lt;/a&gt;&lt;/li&gt;</span><span class="se">\n</span><span class="s1">&#39;</span> <span class="o">%</span> \
+                    <span class="p">(</span><span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;pathguide&#39;</span><span class="p">][</span><span class="s1">&#39;url&#39;</span><span class="p">]</span> <span class="o">%</span> <span class="n">v</span><span class="p">[</span><span class="s1">&#39;pathguide&#39;</span><span class="p">])</span>
+            <span class="n">doc</span> <span class="o">+=</span> <span class="s1">&#39;</span><span class="se">\t\t\t</span><span class="s1">&lt;/ul&gt;</span><span class="se">\n</span><span class="s1">&#39;</span>
+        <span class="k">if</span> <span class="s1">&#39;taxons&#39;</span> <span class="ow">in</span> <span class="n">v</span><span class="p">:</span>
+            <span class="n">doc</span> <span class="o">+=</span> <span class="s1">&#39;&lt;p&gt;&lt;b&gt;Taxons: &lt;/b&gt;&lt;em&gt;</span><span class="si">%s</span><span class="s1">&lt;/em&gt;&lt;/p&gt;&#39;</span> <span class="o">%</span> \
+                <span class="s1">&#39;, &#39;</span><span class="o">.</span><span class="n">join</span><span class="p">([</span><span class="s1">&#39;</span><span class="si">%s%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="p">(</span><span class="n">t</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">upper</span><span class="p">(),</span> <span class="n">t</span><span class="p">[</span><span class="mi">1</span><span class="p">:])</span>
+                           <span class="k">for</span> <span class="n">t</span> <span class="ow">in</span> <span class="n">v</span><span class="p">[</span><span class="s1">&#39;taxons&#39;</span><span class="p">]])</span>
+        <span class="k">if</span> <span class="s1">&#39;size&#39;</span> <span class="ow">in</span> <span class="n">v</span> <span class="ow">and</span> <span class="nb">type</span><span class="p">(</span><span class="n">v</span><span class="p">[</span><span class="s1">&#39;size&#39;</span><span class="p">])</span> <span class="ow">is</span> <span class="nb">dict</span> <span class="ow">and</span> \
+                <span class="n">v</span><span class="p">[</span><span class="s1">&#39;size&#39;</span><span class="p">][</span><span class="s1">&#39;nodes&#39;</span><span class="p">]</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span> <span class="ow">and</span> <span class="n">v</span><span class="p">[</span><span class="s1">&#39;size&#39;</span><span class="p">][</span><span class="s1">&#39;edges&#39;</span><span class="p">]</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
+            <span class="n">doc</span> <span class="o">+=</span> <span class="s1">&#39;&lt;p&gt;&lt;b&gt;Nodes: &lt;/b&gt;</span><span class="si">%s</span><span class="s1">, &lt;b&gt;Edges:&lt;/b&gt;</span><span class="si">%s</span><span class="s1">&lt;/p&gt;&#39;</span> <span class="o">%</span> <span class="p">(</span>
+                <span class="n">v</span><span class="p">[</span><span class="s1">&#39;size&#39;</span><span class="p">][</span><span class="s1">&#39;nodes&#39;</span><span class="p">],</span> <span class="n">v</span><span class="p">[</span><span class="s1">&#39;size&#39;</span><span class="p">][</span><span class="s1">&#39;edges&#39;</span><span class="p">])</span>
+        <span class="k">if</span> <span class="s1">&#39;data_import&#39;</span> <span class="ow">in</span> <span class="n">v</span><span class="p">:</span>
+            <span class="n">doc</span> <span class="o">+=</span> <span class="s1">&#39;</span><span class="se">\t\t\t</span><span class="s1">&lt;p&gt;&lt;b&gt;Direct data import from: &lt;/b&gt;</span><span class="si">%s</span><span class="s1">&lt;/p&gt;</span><span class="se">\n</span><span class="s1">&#39;</span> <span class="o">%</span> \
+                <span class="s1">&#39;, &#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">v</span><span class="p">[</span><span class="s1">&#39;data_import&#39;</span><span class="p">])</span>
+        <span class="k">if</span> <span class="s1">&#39;includes&#39;</span> <span class="ow">in</span> <span class="n">v</span><span class="p">:</span>
+            <span class="n">doc</span> <span class="o">+=</span> <span class="s1">&#39;</span><span class="se">\t\t\t</span><span class="s1">&lt;p&gt;&lt;b&gt;Includes data from: &lt;/b&gt;</span><span class="si">%s</span><span class="s1">&lt;/p&gt;</span><span class="se">\n</span><span class="s1">&#39;</span> <span class="o">%</span> \
+                <span class="s1">&#39;, &#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">v</span><span class="p">[</span><span class="s1">&#39;includes&#39;</span><span class="p">])</span>
+        <span class="k">if</span> <span class="s1">&#39;descriptions&#39;</span> <span class="ow">in</span> <span class="n">v</span> <span class="ow">or</span> <span class="s1">&#39;notes&#39;</span> <span class="ow">in</span> <span class="n">v</span><span class="p">:</span>
+            <span class="n">doc</span> <span class="o">+=</span> <span class="s1">&#39;</span><span class="se">\t\t\t</span><span class="s1">&lt;h3&gt;Quotes&lt;/h3&gt;</span><span class="se">\n</span><span class="s1">&#39;</span>
+            <span class="k">if</span> <span class="s1">&#39;descriptions&#39;</span> <span class="ow">in</span> <span class="n">v</span><span class="p">:</span>
+                <span class="n">doc</span> <span class="o">+=</span> <span class="s1">&#39;</span><span class="se">\t\t\t\t</span><span class="s1">&lt;div class=&quot;quotebox box&quot;&gt;</span><span class="se">\n</span><span class="s1">&#39;</span>
+                <span class="n">description_full</span> <span class="o">=</span> <span class="s2">&quot; &quot;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">v</span><span class="p">[</span><span class="s1">&#39;descriptions&#39;</span><span class="p">])</span>
+                <span class="n">pars</span> <span class="o">=</span> <span class="n">description_full</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\n</span><span class="s1">&#39;</span><span class="p">)</span>
+                <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">pars</span><span class="p">)</span> <span class="o">&gt;</span> <span class="mi">0</span><span class="p">:</span>
+                    <span class="n">doc</span> <span class="o">+=</span> <span class="s1">&#39;</span><span class="se">\t\t\t\t</span><span class="s1">&lt;p&gt;</span><span class="si">%s</span><span class="s1">&lt;/p&gt;</span><span class="se">\n</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="n">pars</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span>
+                <span class="c1"># for p in pars:</span>
+                <span class="c1">#     p = p.strip()</span>
+                <span class="c1">#     if len(p) &gt; 0:</span>
+                <span class="c1">#         doc += &#39;\t\t\t\t&lt;p&gt;%s&lt;/p&gt;\n&#39; % p</span>
+                <span class="n">doc</span> <span class="o">+=</span> <span class="s1">&#39;</span><span class="se">\t\t\t\t</span><span class="s1">&lt;/div&gt;</span><span class="se">\n</span><span class="s1">&#39;</span>
+            <span class="k">if</span> <span class="s1">&#39;notes&#39;</span> <span class="ow">in</span> <span class="n">v</span><span class="p">:</span>
+                <span class="n">doc</span> <span class="o">+=</span> <span class="s1">&#39;</span><span class="se">\t\t\t</span><span class="s1">&lt;h3&gt;Notes&lt;/h3&gt;</span><span class="se">\n</span><span class="s1">&#39;</span>
+                <span class="n">doc</span> <span class="o">+=</span> <span class="s1">&#39;</span><span class="se">\t\t\t\t</span><span class="s1">&lt;div class=&quot;quotebox box&quot;&gt;</span><span class="se">\n</span><span class="s1">&#39;</span>
+                <span class="n">notes_full</span> <span class="o">=</span> <span class="s2">&quot; &quot;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">v</span><span class="p">[</span><span class="s1">&#39;notes&#39;</span><span class="p">])</span>
+                <span class="n">pars</span> <span class="o">=</span> <span class="n">notes_full</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\n</span><span class="s1">&#39;</span><span class="p">)</span>
+                <span class="k">for</span> <span class="n">p</span> <span class="ow">in</span> <span class="n">pars</span><span class="p">:</span>
+                    <span class="n">p</span> <span class="o">=</span> <span class="n">p</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span>
+                    <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">p</span><span class="p">)</span> <span class="o">&gt;</span> <span class="mi">0</span><span class="p">:</span>
+                        <span class="n">doc</span> <span class="o">+=</span> <span class="s1">&#39;</span><span class="se">\t\t\t\t</span><span class="s1">&lt;p&gt;</span><span class="si">%s</span><span class="s1">&lt;/p&gt;</span><span class="se">\n</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="n">p</span>
+                <span class="n">doc</span> <span class="o">+=</span> <span class="s1">&#39;</span><span class="se">\t\t\t\t</span><span class="s1">&lt;/div&gt;</span><span class="se">\n</span><span class="s1">&#39;</span>
+        <span class="k">if</span> <span class="s1">&#39;data_integration&#39;</span> <span class="ow">in</span> <span class="n">v</span><span class="p">:</span>
+            <span class="n">doc</span> <span class="o">+=</span> <span class="s1">&#39;</span><span class="se">\t\t\t</span><span class="s1">&lt;p&gt;&lt;b&gt;Data integration in &#39;</span>\
+                <span class="s1">&#39;&lt;span class=&quot;code&quot;&gt;pypath:&lt;/span&gt;&lt;/b&gt; </span><span class="si">%s</span><span class="s1">&lt;/p&gt;&#39;</span> <span class="o">%</span> \
+                <span class="n">v</span><span class="p">[</span><span class="s1">&#39;data_integration&#39;</span><span class="p">]</span>
+        <span class="c1"># turned off temporarily, until we update this information</span>
+        <span class="c1">#if &#39;pypath&#39; in v:</span>
+        <span class="k">if</span> <span class="kc">False</span><span class="p">:</span>
+            <span class="n">doc</span> <span class="o">+=</span> <span class="s1">&#39;</span><span class="se">\t\t\t</span><span class="s1">&lt;h3&gt;Methods in &lt;span class=&quot;code&quot;&gt;pypath&#39;</span>\
+                <span class="s1">&#39;&lt;/span&gt;&lt;/h3&gt;</span><span class="se">\n</span><span class="s1">&#39;</span>
+            <span class="n">doc</span> <span class="o">+=</span> <span class="s1">&#39;</span><span class="se">\t\t\t\t</span><span class="s1">&lt;div class=&quot;codebox box&quot;&gt;</span><span class="se">\n</span><span class="s1">&#39;</span>
+            <span class="k">for</span> <span class="n">cat</span> <span class="ow">in</span> <span class="nb">sorted</span><span class="p">(</span><span class="n">pypath_methods</span><span class="o">.</span><span class="n">keys</span><span class="p">()):</span>
+                <span class="n">name</span> <span class="o">=</span> <span class="n">pypath_methods</span><span class="p">[</span><span class="n">cat</span><span class="p">]</span>
+                <span class="k">if</span> <span class="n">cat</span> <span class="ow">in</span> <span class="n">v</span><span class="p">[</span><span class="s1">&#39;pypath&#39;</span><span class="p">]:</span>
+                    <span class="n">doc</span> <span class="o">+=</span> <span class="s1">&#39;</span><span class="se">\t\t\t\t\t</span><span class="s1">&lt;p&gt;</span><span class="si">%s</span><span class="s1">&lt;/p&gt;</span><span class="se">\n\t\t\t\t\t</span><span class="s1">&lt;ul&gt;</span><span class="se">\n</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="n">name</span>
+                    <span class="k">for</span> <span class="n">met</span> <span class="ow">in</span> <span class="n">v</span><span class="p">[</span><span class="s1">&#39;pypath&#39;</span><span class="p">][</span><span class="n">cat</span><span class="p">]:</span>
+                        <span class="n">doc</span> <span class="o">+=</span> <span class="s1">&#39;</span><span class="se">\t\t\t\t\t\t</span><span class="s1">&lt;li&gt;&lt;span class=&quot;code&quot;&gt;</span><span class="si">%s</span><span class="s1">&#39;</span>\
+                            <span class="s1">&#39;&lt;/span&gt;&lt;/li&gt;</span><span class="se">\n</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="n">met</span>
+                    <span class="n">doc</span> <span class="o">+=</span> <span class="s1">&#39;</span><span class="se">\t\t\t\t\t</span><span class="s1">&lt;/ul&gt;</span><span class="se">\n</span><span class="s1">&#39;</span>
+            <span class="n">doc</span> <span class="o">+=</span> <span class="s1">&#39;</span><span class="se">\t\t\t\t</span><span class="s1">&lt;/div&gt;</span><span class="se">\n</span><span class="s1">&#39;</span>
+
+    <span class="k">if</span> <span class="nb">format</span> <span class="o">==</span> <span class="s1">&#39;b&#39;</span><span class="p">:</span>
+        <span class="k">return</span> <span class="n">_html</span><span class="o">.</span><span class="n">default_template</span><span class="p">(</span><span class="n">doc</span><span class="p">,</span> <span class="n">title</span><span class="p">,</span> <span class="n">title</span><span class="p">)</span>
+    <span class="k">return</span> <span class="n">_html</span><span class="o">.</span><span class="n">default_template</span><span class="p">(</span><span class="n">doc</span><span class="p">,</span> <span class="n">title</span><span class="p">,</span> <span class="n">title</span><span class="p">,</span> <span class="nb">format</span><span class="o">=</span><span class="s1">&#39;str&#39;</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="write_html">
+<a class="viewcode-back" href="../../../../api/pypath.omnipath.server.generate_about_page.write_html.html#pypath.omnipath.server.generate_about_page.write_html">[docs]</a>
+<span class="k">def</span> <span class="nf">write_html</span><span class="p">(</span><span class="n">descriptions</span><span class="p">,</span> <span class="n">filename</span><span class="o">=</span><span class="s1">&#39;resources.html&#39;</span><span class="p">):</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Saves the HTML descriptions to custom local file.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+    <span class="k">if</span> <span class="ow">not</span> <span class="n">descriptions</span><span class="p">:</span>
+        <span class="n">_logger</span><span class="o">.</span><span class="n">_console</span><span class="p">(</span><span class="s2">&quot;Empty description was provided. Cannot write html.&quot;</span><span class="p">)</span>
+        <span class="k">return</span> <span class="kc">None</span>
+
+    <span class="n">html</span> <span class="o">=</span> <span class="n">generate_about_html</span><span class="p">(</span><span class="n">descriptions</span><span class="p">,</span> <span class="nb">format</span><span class="o">=</span><span class="s2">&quot;str&quot;</span><span class="p">)</span>
+    <span class="c1">#with codecs.open(filename, encoding=&#39;utf-8&#39;, mode=&#39;w&#39;) as f:</span>
+    <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">filename</span><span class="p">,</span> <span class="s1">&#39;w&#39;</span><span class="p">)</span> <span class="k">as</span> <span class="n">f</span><span class="p">:</span>
+        <span class="n">f</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="n">html</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="resource_list_latex">
+<a class="viewcode-back" href="../../../../api/pypath.omnipath.server.generate_about_page.resource_list_latex.html#pypath.omnipath.server.generate_about_page.resource_list_latex">[docs]</a>
+<span class="k">def</span> <span class="nf">resource_list_latex</span><span class="p">(</span><span class="n">descriptions</span><span class="p">,</span>
+                        <span class="n">filename</span><span class="o">=</span><span class="s1">&#39;resource-list.tex&#39;</span><span class="p">,</span>
+                        <span class="n">latex_hdr</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span>
+                        <span class="n">fontsize</span><span class="o">=</span><span class="mi">8</span><span class="p">,</span>
+                        <span class="n">font</span><span class="o">=</span><span class="s1">&#39;HelveticaNeueLTStd-LtCn&#39;</span><span class="p">):</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Generates Supplementary Table 3 (The list of the 52 resources considered) for the article.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+    <span class="k">if</span> <span class="ow">not</span> <span class="n">descriptions</span><span class="p">:</span>
+        <span class="n">_logger</span><span class="o">.</span><span class="n">_console</span><span class="p">(</span><span class="s2">&quot;Empty description was provided. Cannot generate table.&quot;</span><span class="p">)</span>
+        <span class="k">return</span> <span class="kc">None</span>
+
+    <span class="n">_latex_hdr</span> <span class="o">=</span> <span class="sa">r</span><span class="s1">&#39;&#39;&#39;\documentclass[a4paper,</span><span class="si">%u</span><span class="s1">pt]</span><span class="si">{extarticle}</span>
+<span class="s1">        \usepackage</span><span class="si">{fontspec}</span>
+<span class="s1">        \usepackage</span><span class="si">{xunicode}</span>
+<span class="s1">        \usepackage</span><span class="si">{polyglossia}</span>
+<span class="s1">        \setdefaultlanguage</span><span class="si">{english}</span>
+<span class="s1">        \usepackage</span><span class="si">{xltxtra}</span>
+<span class="s1">        \usepackage</span><span class="si">{microtype}</span>
+<span class="s1">        \usepackage[margin=5pt,portrait,paperwidth=15cm,paperheight=18cm]</span><span class="si">{geometry}</span>
+<span class="s1">        \usepackage</span><span class="si">{amsmath}</span>
+<span class="s1">        \usepackage</span><span class="si">{amssymb}</span>
+<span class="s1">        \usepackage</span><span class="si">{textcomp}</span>
+<span class="s1">        \usepackage[usenames,dvipsnames,svgnames,table]</span><span class="si">{xcolor}</span>
+<span class="s1">        \usepackage</span><span class="si">{color}</span>
+<span class="s1">        \usepackage</span><span class="si">{booktabs}</span>
+<span class="s1">        \usepackage</span><span class="si">{tabularx}</span>
+<span class="s1">        \setmainfont{</span><span class="si">%s</span><span class="s1">}</span>
+<span class="s1">        \definecolor</span><span class="si">{grey875}{gray}{0.125}</span>
+<span class="s1">        \begin</span><span class="si">{document}</span>
+<span class="s1">        \color</span><span class="si">{grey875}</span>
+<span class="s1">        \thispagestyle</span><span class="si">{empty}</span>
+<span class="s1">        \vfill</span>
+<span class="s1">    &#39;&#39;&#39;</span> <span class="o">%</span> <span class="p">(</span><span class="n">fontsize</span><span class="p">,</span> <span class="n">font</span><span class="p">)</span> <span class="k">if</span> <span class="n">latex_hdr</span> <span class="k">else</span> <span class="s1">&#39;&#39;</span>
+    <span class="n">_latex_end</span> <span class="o">=</span> <span class="sa">r</span><span class="s1">&#39;&#39;&#39;</span>
+<span class="s1">            \end</span><span class="si">{document}</span>
+<span class="s1">        &#39;&#39;&#39;</span> <span class="k">if</span> <span class="n">latex_hdr</span> <span class="k">else</span> <span class="s1">&#39;&#39;</span>
+    <span class="n">tex</span> <span class="o">=</span> <span class="sa">r</span><span class="s1">&#39;&#39;&#39;\begin</span><span class="si">{tabularx}</span><span class="s1">{0.94\textwidth}{&gt;{\raggedright\scriptsize\arraybackslash\hsize=.15\hsize}X&gt;{\raggedright\scriptsize\arraybackslash\hsize=.35\hsize}X&gt;{\raggedright\scriptsize\arraybackslash\hsize=.15\hsize}X&gt;{\raggedright\scriptsize\arraybackslash\hsize=.15\hsize}X}</span>
+<span class="s1">    \toprule</span>
+<span class="s1">    Resource name &amp; Class, subclass &amp; Resource name &amp; Class, subclass \\</span>
+<span class="s1">    \midrule</span>
+<span class="s1">    &#39;&#39;&#39;</span>
+    <span class="n">res</span> <span class="o">=</span> <span class="nb">sorted</span><span class="p">(</span>
+        <span class="p">[(</span><span class="n">v</span><span class="p">[</span><span class="s1">&#39;label&#39;</span><span class="p">]</span> <span class="k">if</span> <span class="s1">&#39;label&#39;</span> <span class="ow">in</span> <span class="n">v</span> <span class="k">else</span> <span class="n">k</span><span class="p">,</span>
+          <span class="s1">&#39;</span><span class="si">%s</span><span class="s1">, </span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="p">(</span><span class="n">v</span><span class="p">[</span><span class="s1">&#39;type&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">capitalize</span><span class="p">(),</span> <span class="n">v</span><span class="p">[</span><span class="s1">&#39;subtype&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">capitalize</span><span class="p">())</span>
+          <span class="k">if</span> <span class="s1">&#39;type&#39;</span> <span class="ow">in</span> <span class="n">v</span> <span class="ow">and</span> <span class="s1">&#39;subtype&#39;</span> <span class="ow">in</span> <span class="n">v</span> <span class="k">else</span> <span class="s1">&#39;&#39;</span><span class="p">)</span>
+         <span class="k">for</span> <span class="n">k</span><span class="p">,</span> <span class="n">v</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="n">descriptions</span><span class="p">)],</span>
+        <span class="n">key</span><span class="o">=</span><span class="k">lambda</span> <span class="n">x</span><span class="p">:</span> <span class="n">x</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">lower</span><span class="p">())</span>
+    <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">res</span><span class="p">)</span> <span class="o">%</span> <span class="mi">2</span> <span class="o">!=</span> <span class="mi">0</span><span class="p">:</span>
+        <span class="n">res</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="s1">&#39;&#39;</span><span class="p">)</span>
+    <span class="n">res2</span> <span class="o">=</span> <span class="nb">zip</span><span class="p">(</span><span class="n">res</span><span class="p">[:</span><span class="nb">int</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">res</span><span class="p">)</span> <span class="o">/</span> <span class="mi">2</span><span class="p">)],</span> <span class="n">res</span><span class="p">[</span><span class="nb">int</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">res</span><span class="p">)</span> <span class="o">/</span> <span class="mi">2</span><span class="p">):])</span>
+    <span class="k">for</span> <span class="n">r</span> <span class="ow">in</span> <span class="n">res2</span><span class="p">:</span>
+        <span class="n">tex</span> <span class="o">+=</span> <span class="sa">r</span><span class="s1">&#39;</span><span class="si">%s</span><span class="s1"> &amp; </span><span class="si">%s</span><span class="s1"> &amp; </span><span class="si">%s</span><span class="s1"> &amp; </span><span class="si">%s</span><span class="s1"> </span><span class="se">\\</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="p">(</span>
+            <span class="n">r</span><span class="p">[</span><span class="mi">0</span><span class="p">][</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s1">&#39;&amp;&#39;</span><span class="p">,</span> <span class="s1">&#39;\&amp;&#39;</span><span class="p">),</span>
+            <span class="n">r</span><span class="p">[</span><span class="mi">0</span><span class="p">][</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s1">&#39;&amp;&#39;</span><span class="p">,</span> <span class="s1">&#39;\&amp;&#39;</span><span class="p">),</span>
+            <span class="p">(</span><span class="n">r</span><span class="p">[</span><span class="mi">1</span><span class="p">][</span><span class="mi">0</span><span class="p">]</span> <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">r</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span> <span class="k">else</span> <span class="s1">&#39;&#39;</span><span class="p">)</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s1">&#39;&amp;&#39;</span><span class="p">,</span> <span class="s1">&#39;\&amp;&#39;</span><span class="p">),</span>
+            <span class="p">(</span><span class="n">r</span><span class="p">[</span><span class="mi">1</span><span class="p">][</span><span class="mi">1</span><span class="p">]</span> <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">r</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span> <span class="k">else</span> <span class="s1">&#39;&#39;</span><span class="p">)</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s1">&#39;&amp;&#39;</span><span class="p">,</span> <span class="s1">&#39;\&amp;&#39;</span><span class="p">),</span>
+        <span class="p">)</span> <span class="o">+</span> <span class="s1">&#39;</span><span class="se">\n</span><span class="s1">&#39;</span>
+    <span class="n">tex</span> <span class="o">+=</span> <span class="sa">r</span><span class="s1">&#39;\bottomrule&#39;</span> <span class="o">+</span> <span class="s1">&#39;</span><span class="se">\n</span><span class="s1">&#39;</span>
+    <span class="n">tex</span> <span class="o">+=</span> <span class="sa">r</span><span class="s1">&#39;\end</span><span class="si">{tabularx}</span><span class="s1">&#39;</span> <span class="o">+</span> <span class="s1">&#39;</span><span class="se">\n</span><span class="s1">&#39;</span>
+    <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">filename</span><span class="p">,</span> <span class="s1">&#39;w&#39;</span><span class="p">)</span> <span class="k">as</span> <span class="n">f</span><span class="p">:</span>
+        <span class="n">f</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s1">&#39;</span><span class="si">%s%s%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="p">(</span><span class="n">_latex_hdr</span> <span class="k">if</span> <span class="n">latex_hdr</span> <span class="k">else</span> <span class="s1">&#39;&#39;</span><span class="p">,</span> <span class="n">tex</span><span class="p">,</span> <span class="n">_latex_end</span>
+                            <span class="k">if</span> <span class="n">latex_hdr</span> <span class="k">else</span> <span class="s1">&#39;&#39;</span><span class="p">))</span></div>
+
+
+
+<div class="viewcode-block" id="export_licenses">
+<a class="viewcode-back" href="../../../../api/pypath.omnipath.server.generate_about_page.export_licenses.html#pypath.omnipath.server.generate_about_page.export_licenses">[docs]</a>
+<span class="k">def</span> <span class="nf">export_licenses</span><span class="p">(</span><span class="n">descriptions</span><span class="p">,</span> <span class="n">outfile</span><span class="o">=</span><span class="s1">&#39;licenses.tsv&#39;</span><span class="p">):</span>
+
+    <span class="k">if</span> <span class="ow">not</span> <span class="n">descriptions</span><span class="p">:</span>
+        <span class="n">_logger</span><span class="o">.</span><span class="n">_console</span><span class="p">(</span>
+            <span class="s1">&#39;Empty description was provided. Cannot export licenses.&#39;</span>
+        <span class="p">)</span>
+        <span class="k">return</span> <span class="kc">None</span>
+
+    <span class="n">hdr</span> <span class="o">=</span> <span class="p">[</span>
+        <span class="s1">&#39;Name&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;License&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;License URL&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;Contact&#39;</span><span class="p">,</span>
+    <span class="p">]</span>
+    <span class="n">rows</span> <span class="o">=</span> <span class="p">[]</span>
+
+    <span class="k">for</span> <span class="n">k</span><span class="p">,</span> <span class="n">v</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="n">descriptions</span><span class="p">):</span>
+        <span class="n">name</span> <span class="o">=</span> <span class="n">v</span><span class="p">[</span><span class="s1">&#39;label&#39;</span><span class="p">]</span> <span class="k">if</span> <span class="s1">&#39;label&#39;</span> <span class="ow">in</span> <span class="n">v</span> <span class="k">else</span> <span class="n">k</span>
+        <span class="n">license_name</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="n">v</span><span class="p">[</span><span class="s1">&#39;license&#39;</span><span class="p">][</span><span class="s1">&#39;name&#39;</span><span class="p">]</span>
+                <span class="k">if</span> <span class="s1">&#39;license&#39;</span> <span class="ow">in</span> <span class="n">v</span> <span class="ow">and</span> <span class="s1">&#39;name&#39;</span> <span class="ow">in</span> <span class="n">v</span><span class="p">[</span><span class="s1">&#39;license&#39;</span><span class="p">]</span> <span class="k">else</span>
+            <span class="s1">&#39;&#39;</span>
+        <span class="p">)</span>
+        <span class="n">license_comment</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="s2">&quot;&quot;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">v</span><span class="p">[</span><span class="s1">&#39;license&#39;</span><span class="p">][</span><span class="s1">&#39;comment&#39;</span><span class="p">])</span>
+            <span class="k">if</span> <span class="s1">&#39;license&#39;</span> <span class="ow">in</span> <span class="n">v</span> <span class="ow">and</span> <span class="s1">&#39;comment&#39;</span> <span class="ow">in</span> <span class="n">v</span><span class="p">[</span><span class="s1">&#39;license&#39;</span><span class="p">]</span> <span class="k">else</span> <span class="s1">&#39;&#39;</span>
+        <span class="p">)</span>
+        <span class="n">license_url</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="n">v</span><span class="p">[</span><span class="s1">&#39;license&#39;</span><span class="p">][</span><span class="s1">&#39;url&#39;</span><span class="p">]</span>
+                <span class="k">if</span> <span class="s1">&#39;license&#39;</span> <span class="ow">in</span> <span class="n">v</span> <span class="ow">and</span> <span class="s1">&#39;url&#39;</span> <span class="ow">in</span> <span class="n">v</span><span class="p">[</span><span class="s1">&#39;license&#39;</span><span class="p">]</span> <span class="k">else</span>
+            <span class="s1">&#39;&#39;</span>
+        <span class="p">)</span>
+        <span class="n">emails</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="s2">&quot;, &quot;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="s2">&quot;</span><span class="si">%s</span><span class="s2"> &lt;</span><span class="si">%s</span><span class="s2">&gt;&quot;</span> <span class="o">%</span> <span class="p">(</span><span class="n">contact_name</span><span class="p">,</span> <span class="n">email</span><span class="p">)</span>
+                <span class="k">for</span> <span class="n">email</span><span class="p">,</span> <span class="n">contact_name</span>
+                <span class="c1"># zip makes (0,1),(2,3) ...</span>
+                <span class="ow">in</span> <span class="nb">zip</span><span class="p">(</span><span class="n">v</span><span class="p">[</span><span class="s1">&#39;emails&#39;</span><span class="p">][::</span><span class="mi">2</span><span class="p">],</span> <span class="n">v</span><span class="p">[</span><span class="s1">&#39;emails&#39;</span><span class="p">][</span><span class="mi">1</span><span class="p">::</span><span class="mi">2</span><span class="p">]))</span>
+            <span class="k">if</span> <span class="s1">&#39;emails&#39;</span> <span class="ow">in</span> <span class="n">v</span> <span class="k">else</span> <span class="s1">&#39;&#39;</span>
+        <span class="p">)</span>
+
+        <span class="n">rows</span><span class="o">.</span><span class="n">append</span><span class="p">([</span>
+            <span class="n">name</span><span class="p">,</span>
+            <span class="n">license_name</span><span class="p">,</span>
+            <span class="n">license_url</span><span class="p">,</span>
+            <span class="n">emails</span><span class="p">,</span>
+            <span class="n">license_comment</span>
+        <span class="p">])</span>
+
+    <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">outfile</span><span class="p">,</span> <span class="s1">&#39;w&#39;</span><span class="p">)</span> <span class="k">as</span> <span class="n">fp</span><span class="p">:</span>
+
+        <span class="n">_</span> <span class="o">=</span> <span class="n">fp</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\t</span><span class="s1">&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">hdr</span><span class="p">)</span> <span class="o">+</span> <span class="s1">&#39;</span><span class="se">\n</span><span class="s1">&#39;</span><span class="p">)</span>
+        <span class="p">[</span><span class="nb">print</span><span class="p">(</span><span class="n">row</span><span class="p">)</span> <span class="k">for</span> <span class="n">row</span> <span class="ow">in</span> <span class="n">rows</span><span class="p">]</span>
+        <span class="n">_</span> <span class="o">=</span> <span class="n">fp</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\n</span><span class="s1">&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span>
+            <span class="s1">&#39;</span><span class="se">\t</span><span class="s1">&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">row</span><span class="p">)</span> <span class="k">for</span> <span class="n">row</span> <span class="ow">in</span> <span class="n">rows</span>
+        <span class="p">))</span></div>
+
+</pre></div>
+
+                </article>
+              
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diff --git a/_modules/pypath/omnipath/server/legacy.html b/_modules/pypath/omnipath/server/legacy.html
new file mode 100644
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@@ -0,0 +1,919 @@
+
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+          
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+          
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+          
+          
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+          
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+            <span class="sr-only">OmniPath</span></a>
+        </li>
+        <li class="nav-item">
+          
+          
+          
+          
+          
+          
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+          <a href="https://saezlab.org/" title="Saez Lab" class="nav-link" rel="noopener" target="_blank" data-bs-toggle="tooltip" data-bs-placement="bottom"><span><i class="fa-solid fa-users fa-lg" aria-hidden="true"></i></span>
+            <span class="sr-only">Saez Lab</span></a>
+        </li>
+</ul></div>
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+                  
+  <h1>Source code for pypath.omnipath.server.legacy</h1><div class="highlight"><pre>
+<span></span><span class="ch">#!/usr/bin/env python</span>
+<span class="c1"># -*- coding: utf-8 -*-</span>
+
+<span class="c1">#</span>
+<span class="c1">#  This file is part of the `pypath` python module</span>
+<span class="c1">#</span>
+<span class="c1">#  Copyright 2014-2023</span>
+<span class="c1">#  EMBL, EMBL-EBI, Uniklinik RWTH Aachen, Heidelberg University</span>
+<span class="c1">#</span>
+<span class="c1">#  Authors: see the file `README.rst`</span>
+<span class="c1">#  Contact: Dénes Türei (turei.denes@gmail.com)</span>
+<span class="c1">#</span>
+<span class="c1">#  Distributed under the GPLv3 License.</span>
+<span class="c1">#  See accompanying file LICENSE.txt or copy at</span>
+<span class="c1">#      https://www.gnu.org/licenses/gpl-3.0.html</span>
+<span class="c1">#</span>
+<span class="c1">#  Website: https://pypath.omnipathdb.org/</span>
+<span class="c1">#</span>
+
+<span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">Old server class working from a ``pypath.legacy.main.PyPath`` object.</span>
+<span class="sd">&quot;&quot;&quot;</span>
+
+<span class="kn">import</span> <span class="nn">json</span>
+
+<span class="kn">import</span> <span class="nn">pypath.omnipath.server.run</span> <span class="k">as</span> <span class="nn">server</span>
+
+
+<div class="viewcode-block" id="PypathServer">
+<a class="viewcode-back" href="../../../../api/pypath.omnipath.server.legacy.PypathServer.html#pypath.omnipath.server.legacy.PypathServer">[docs]</a>
+<span class="k">class</span> <span class="nc">PypathServer</span><span class="p">(</span><span class="n">server</span><span class="o">.</span><span class="n">BaseServer</span><span class="p">):</span>
+    
+    
+<div class="viewcode-block" id="PypathServer.__init__">
+<a class="viewcode-back" href="../../../../api/pypath.omnipath.server.legacy.PypathServer.html#pypath.omnipath.server.legacy.PypathServer.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">pypath</span><span class="p">):</span>
+        
+        <span class="bp">self</span><span class="o">.</span><span class="n">p</span> <span class="o">=</span> <span class="n">pypath</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">g</span> <span class="o">=</span> <span class="n">pypath</span><span class="o">.</span><span class="n">graph</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">isLeaf</span> <span class="o">=</span> <span class="kc">True</span>
+        
+        <span class="n">server</span><span class="o">.</span><span class="n">BaseServer</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span></div>
+
+    
+    
+    <span class="k">def</span> <span class="nf">network</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">req</span><span class="p">):</span>
+        
+        <span class="n">hdr</span> <span class="o">=</span> <span class="p">[</span><span class="s1">&#39;nodes&#39;</span><span class="p">,</span> <span class="s1">&#39;edges&#39;</span><span class="p">,</span> <span class="s1">&#39;is_directed&#39;</span><span class="p">,</span> <span class="s1">&#39;sources&#39;</span><span class="p">]</span>
+        <span class="n">val</span> <span class="o">=</span> <span class="p">[</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">g</span><span class="o">.</span><span class="n">vcount</span><span class="p">(),</span> <span class="bp">self</span><span class="o">.</span><span class="n">g</span><span class="o">.</span><span class="n">ecount</span><span class="p">(),</span> <span class="nb">int</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">g</span><span class="o">.</span><span class="n">is_directed</span><span class="p">()),</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">p</span><span class="o">.</span><span class="n">sources</span>
+        <span class="p">]</span>
+        <span class="k">if</span> <span class="sa">b</span><span class="s1">&#39;format&#39;</span> <span class="ow">in</span> <span class="n">req</span><span class="o">.</span><span class="n">args</span> <span class="ow">and</span> <span class="n">req</span><span class="o">.</span><span class="n">args</span><span class="p">[</span><span class="sa">b</span><span class="s1">&#39;format&#39;</span><span class="p">]</span> <span class="o">==</span> <span class="sa">b</span><span class="s1">&#39;json&#39;</span><span class="p">:</span>
+            <span class="k">return</span> <span class="n">json</span><span class="o">.</span><span class="n">dumps</span><span class="p">(</span><span class="nb">dict</span><span class="p">(</span><span class="nb">zip</span><span class="p">(</span><span class="n">hdr</span><span class="p">,</span> <span class="n">val</span><span class="p">)))</span>
+        <span class="k">else</span><span class="p">:</span>
+            <span class="k">return</span> <span class="s1">&#39;</span><span class="si">%s</span><span class="se">\n</span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="p">(</span><span class="s1">&#39;</span><span class="se">\t</span><span class="s1">&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">hdr</span><span class="p">),</span> <span class="s1">&#39;</span><span class="se">\t</span><span class="s1">&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span>
+                <span class="p">[</span><span class="nb">str</span><span class="p">(</span><span class="n">v</span><span class="p">)</span> <span class="k">if</span> <span class="nb">type</span><span class="p">(</span><span class="n">v</span><span class="p">)</span> <span class="ow">is</span> <span class="ow">not</span> <span class="nb">list</span> <span class="k">else</span> <span class="s1">&#39;;&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">v</span><span class="p">)</span> <span class="k">for</span> <span class="n">v</span> <span class="ow">in</span> <span class="n">val</span><span class="p">]))</span>
+
+
+    <span class="k">def</span> <span class="nf">interactions</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">req</span><span class="p">):</span>
+        
+        <span class="n">fields</span> <span class="o">=</span> <span class="p">[</span><span class="sa">b</span><span class="s1">&#39;sources&#39;</span><span class="p">,</span> <span class="sa">b</span><span class="s1">&#39;references&#39;</span><span class="p">]</span>
+        <span class="n">result</span> <span class="o">=</span> <span class="p">[]</span>
+        <span class="n">elist</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_get_eids</span><span class="p">(</span><span class="n">req</span><span class="p">)</span>
+        <span class="n">res</span> <span class="o">=</span> <span class="p">[]</span>
+        <span class="n">hdr</span> <span class="o">=</span> <span class="p">[</span>
+            <span class="s1">&#39;source&#39;</span><span class="p">,</span> <span class="s1">&#39;target&#39;</span><span class="p">,</span> <span class="s1">&#39;is_directed&#39;</span><span class="p">,</span> <span class="s1">&#39;is_stimulation&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;is_inhibition&#39;</span>
+        <span class="p">]</span>
+        
+        <span class="k">if</span> <span class="sa">b</span><span class="s1">&#39;fields&#39;</span> <span class="ow">in</span> <span class="n">req</span><span class="o">.</span><span class="n">args</span><span class="p">:</span>
+            
+            <span class="n">hdr</span> <span class="o">+=</span> <span class="p">[</span>
+                <span class="n">f</span><span class="o">.</span><span class="n">decode</span><span class="p">(</span><span class="s1">&#39;utf-8&#39;</span><span class="p">)</span>
+                <span class="k">for</span> <span class="n">f</span> <span class="ow">in</span> <span class="n">fields</span>
+                <span class="k">if</span> <span class="n">f</span> <span class="ow">in</span> <span class="sa">b</span><span class="s1">&#39;,&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">req</span><span class="o">.</span><span class="n">args</span><span class="p">[</span><span class="sa">b</span><span class="s1">&#39;fields&#39;</span><span class="p">])</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="sa">b</span><span class="s1">&#39;,&#39;</span><span class="p">)</span>
+            <span class="p">]</span>
+        
+        <span class="k">if</span> <span class="p">(</span>
+            <span class="sa">b</span><span class="s1">&#39;genesymbols&#39;</span> <span class="ow">in</span> <span class="n">req</span><span class="o">.</span><span class="n">args</span> <span class="ow">and</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">_parse_arg</span><span class="p">(</span><span class="n">req</span><span class="o">.</span><span class="n">args</span><span class="p">[</span><span class="sa">b</span><span class="s1">&#39;genesymbols&#39;</span><span class="p">])</span>
+        <span class="p">):</span>
+            <span class="n">genesymbols</span> <span class="o">=</span> <span class="kc">True</span>
+            <span class="n">hdr</span><span class="o">.</span><span class="n">insert</span><span class="p">(</span><span class="mi">2</span><span class="p">,</span> <span class="s1">&#39;source_genesymbol&#39;</span><span class="p">)</span>
+            <span class="n">hdr</span><span class="o">.</span><span class="n">insert</span><span class="p">(</span><span class="mi">3</span><span class="p">,</span> <span class="s1">&#39;target_genesymbol&#39;</span><span class="p">)</span>
+        <span class="k">else</span><span class="p">:</span>
+            <span class="n">genesymbols</span> <span class="o">=</span> <span class="kc">False</span>
+        
+        <span class="n">all_sources</span> <span class="o">=</span> <span class="nb">set</span><span class="p">([])</span>
+        <span class="k">for</span> <span class="n">eid</span> <span class="ow">in</span> <span class="n">elist</span><span class="p">:</span>
+            <span class="n">e</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">g</span><span class="o">.</span><span class="n">es</span><span class="p">[</span><span class="n">eid</span><span class="p">]</span>
+            <span class="n">all_sources</span> <span class="o">=</span> <span class="n">all_sources</span> <span class="o">|</span> <span class="n">e</span><span class="p">[</span><span class="s1">&#39;sources&#39;</span><span class="p">]</span>
+            <span class="k">for</span> <span class="n">d</span> <span class="ow">in</span> <span class="p">[</span><span class="s1">&#39;straight&#39;</span><span class="p">,</span> <span class="s1">&#39;reverse&#39;</span><span class="p">]:</span>
+                <span class="n">uniprots</span> <span class="o">=</span> <span class="nb">getattr</span><span class="p">(</span><span class="n">e</span><span class="p">[</span><span class="s1">&#39;dirs&#39;</span><span class="p">],</span> <span class="n">d</span><span class="p">)</span>
+                
+                <span class="k">if</span> <span class="n">e</span><span class="p">[</span><span class="s1">&#39;dirs&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">dirs</span><span class="p">[</span><span class="n">uniprots</span><span class="p">]:</span>
+                    
+                    <span class="n">thisEdge</span> <span class="o">=</span> <span class="p">[</span>
+                        <span class="n">uniprots</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">uniprots</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span>
+                    <span class="p">]</span>
+                    
+                    <span class="k">if</span> <span class="n">genesymbols</span><span class="p">:</span>
+                        
+                        <span class="n">thisEdge</span><span class="o">.</span><span class="n">extend</span><span class="p">([</span>
+                            <span class="bp">self</span><span class="o">.</span><span class="n">g</span><span class="o">.</span><span class="n">vs</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">p</span><span class="o">.</span><span class="n">nodDct</span><span class="p">[</span><span class="n">uniprots</span><span class="p">[</span><span class="mi">0</span><span class="p">]]][</span><span class="s1">&#39;label&#39;</span><span class="p">],</span>
+                            <span class="bp">self</span><span class="o">.</span><span class="n">g</span><span class="o">.</span><span class="n">vs</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">p</span><span class="o">.</span><span class="n">nodDct</span><span class="p">[</span><span class="n">uniprots</span><span class="p">[</span><span class="mi">1</span><span class="p">]]][</span><span class="s1">&#39;label&#39;</span><span class="p">]</span>
+                        <span class="p">])</span>
+                    
+                    <span class="n">thisEdge</span><span class="o">.</span><span class="n">extend</span><span class="p">([</span>
+                        <span class="mi">1</span><span class="p">,</span>
+                        <span class="nb">int</span><span class="p">(</span><span class="n">e</span><span class="p">[</span><span class="s1">&#39;dirs&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">is_stimulation</span><span class="p">(</span><span class="n">uniprots</span><span class="p">)),</span>
+                        <span class="nb">int</span><span class="p">(</span><span class="n">e</span><span class="p">[</span><span class="s1">&#39;dirs&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">is_inhibition</span><span class="p">(</span><span class="n">uniprots</span><span class="p">))</span>
+                    <span class="p">])</span>
+                    <span class="n">dsources</span> <span class="o">=</span> <span class="n">e</span><span class="p">[</span><span class="s1">&#39;dirs&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">get_dir</span><span class="p">(</span><span class="n">uniprots</span><span class="p">,</span> <span class="n">sources</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
+                    <span class="n">dsources</span> <span class="o">=</span> <span class="n">dsources</span> <span class="o">|</span> <span class="n">e</span><span class="p">[</span><span class="s1">&#39;dirs&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">get_dir</span><span class="p">(</span>
+                        <span class="s1">&#39;undirected&#39;</span><span class="p">,</span> <span class="n">sources</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
+                    <span class="k">if</span> <span class="s1">&#39;sources&#39;</span> <span class="ow">in</span> <span class="n">hdr</span><span class="p">:</span>
+                        <span class="n">thisEdge</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="nb">list</span><span class="p">(</span><span class="n">dsources</span><span class="p">))</span>
+                    <span class="k">if</span> <span class="s1">&#39;references&#39;</span> <span class="ow">in</span> <span class="n">hdr</span><span class="p">:</span>
+                        <span class="n">thisEdge</span><span class="o">.</span><span class="n">append</span><span class="p">([</span>
+                            <span class="n">r</span><span class="o">.</span><span class="n">pmid</span>
+                            <span class="k">for</span> <span class="n">r</span> <span class="ow">in</span> <span class="n">flat_list</span><span class="p">([</span>
+                                <span class="n">rs</span> <span class="k">for</span> <span class="n">s</span><span class="p">,</span> <span class="n">rs</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="n">e</span><span class="p">[</span><span class="s1">&#39;refs_by_source&#39;</span><span class="p">])</span>
+                                <span class="k">if</span> <span class="n">s</span> <span class="ow">in</span> <span class="n">dsources</span>
+                            <span class="p">])</span>
+                        <span class="p">])</span>
+                    <span class="n">thisEdge</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_dip_urls</span><span class="p">(</span><span class="n">e</span><span class="p">))</span>
+                    <span class="n">res</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">thisEdge</span><span class="p">)</span>
+            
+            <span class="k">if</span> <span class="ow">not</span> <span class="n">e</span><span class="p">[</span><span class="s1">&#39;dirs&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">is_directed</span><span class="p">():</span>
+                
+                <span class="n">thisEdge</span> <span class="o">=</span> <span class="p">[</span><span class="n">e</span><span class="p">[</span><span class="s1">&#39;dirs&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">nodes</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">e</span><span class="p">[</span><span class="s1">&#39;dirs&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">nodes</span><span class="p">[</span><span class="mi">1</span><span class="p">]]</span>
+                <span class="k">if</span> <span class="n">genesymbols</span><span class="p">:</span>
+                    
+                    <span class="n">thisEdge</span><span class="o">.</span><span class="n">extend</span><span class="p">([</span>
+                        <span class="bp">self</span><span class="o">.</span><span class="n">g</span><span class="o">.</span><span class="n">vs</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">p</span><span class="o">.</span><span class="n">nodDct</span><span class="p">[</span><span class="n">e</span><span class="p">[</span><span class="s1">&#39;dirs&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">nodes</span><span class="p">[</span><span class="mi">0</span><span class="p">]]][</span><span class="s1">&#39;label&#39;</span><span class="p">],</span>
+                        <span class="bp">self</span><span class="o">.</span><span class="n">g</span><span class="o">.</span><span class="n">vs</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">p</span><span class="o">.</span><span class="n">nodDct</span><span class="p">[</span><span class="n">e</span><span class="p">[</span><span class="s1">&#39;dirs&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">nodes</span><span class="p">[</span><span class="mi">1</span><span class="p">]]][</span><span class="s1">&#39;label&#39;</span><span class="p">]</span>
+                    <span class="p">])</span>
+                
+                <span class="n">thisEdge</span><span class="o">.</span><span class="n">extend</span><span class="p">([</span><span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">])</span>
+                <span class="k">if</span> <span class="s1">&#39;sources&#39;</span> <span class="ow">in</span> <span class="n">hdr</span><span class="p">:</span>
+                    <span class="n">thisEdge</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="nb">list</span><span class="p">(</span><span class="n">e</span><span class="p">[</span><span class="s1">&#39;sources&#39;</span><span class="p">]))</span>
+                <span class="k">if</span> <span class="s1">&#39;references&#39;</span> <span class="ow">in</span> <span class="n">hdr</span><span class="p">:</span>
+                    <span class="n">thisEdge</span><span class="o">.</span><span class="n">append</span><span class="p">([</span><span class="n">r</span><span class="o">.</span><span class="n">pmid</span> <span class="k">for</span> <span class="n">r</span> <span class="ow">in</span> <span class="n">e</span><span class="p">[</span><span class="s1">&#39;references&#39;</span><span class="p">]])</span>
+                <span class="n">thisEdge</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_dip_urls</span><span class="p">(</span><span class="n">e</span><span class="p">))</span>
+                <span class="n">res</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">thisEdge</span><span class="p">)</span>
+        
+        <span class="k">if</span> <span class="s1">&#39;DIP&#39;</span> <span class="ow">in</span> <span class="n">all_sources</span><span class="p">:</span>
+            <span class="n">hdr</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="s1">&#39;dip_url&#39;</span><span class="p">)</span>
+        <span class="k">else</span><span class="p">:</span>
+            <span class="n">res</span> <span class="o">=</span> <span class="nb">map</span><span class="p">(</span><span class="k">lambda</span> <span class="n">r</span><span class="p">:</span> <span class="n">r</span><span class="p">[:</span><span class="o">-</span><span class="mi">1</span><span class="p">],</span> <span class="n">res</span><span class="p">)</span>
+        <span class="k">if</span> <span class="sa">b</span><span class="s1">&#39;format&#39;</span> <span class="ow">in</span> <span class="n">req</span><span class="o">.</span><span class="n">args</span> <span class="ow">and</span> <span class="n">req</span><span class="o">.</span><span class="n">args</span><span class="p">[</span><span class="sa">b</span><span class="s1">&#39;format&#39;</span><span class="p">]</span> <span class="o">==</span> <span class="sa">b</span><span class="s1">&#39;json&#39;</span><span class="p">:</span>
+            <span class="k">return</span> <span class="n">json</span><span class="o">.</span><span class="n">dumps</span><span class="p">([</span><span class="nb">dict</span><span class="p">(</span><span class="nb">zip</span><span class="p">(</span><span class="n">hdr</span><span class="p">,</span> <span class="n">r</span><span class="p">))</span> <span class="k">for</span> <span class="n">r</span> <span class="ow">in</span> <span class="n">res</span><span class="p">])</span>
+        <span class="k">else</span><span class="p">:</span>
+            <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_table_output</span><span class="p">(</span><span class="n">res</span><span class="p">,</span> <span class="n">hdr</span><span class="p">,</span> <span class="n">req</span><span class="p">)</span>
+    
+    
+    
+    <span class="k">def</span> <span class="nf">_table_output</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">res</span><span class="p">,</span> <span class="n">hdr</span><span class="p">,</span> <span class="n">req</span><span class="p">):</span>
+        
+        <span class="k">return</span> <span class="s1">&#39;</span><span class="si">%s%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="p">(</span><span class="s1">&#39;&#39;</span> <span class="k">if</span> <span class="ow">not</span> <span class="nb">bool</span><span class="p">(</span><span class="n">req</span><span class="o">.</span><span class="n">args</span><span class="p">[</span><span class="sa">b</span><span class="s1">&#39;header&#39;</span><span class="p">])</span> <span class="k">else</span>
+                         <span class="s1">&#39;</span><span class="si">%s</span><span class="se">\n</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="s1">&#39;</span><span class="se">\t</span><span class="s1">&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">hdr</span><span class="p">),</span> <span class="s1">&#39;</span><span class="se">\n</span><span class="s1">&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">([</span>
+                             <span class="s1">&#39;</span><span class="se">\t</span><span class="s1">&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">([</span>
+                                 <span class="s1">&#39;;&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">f</span><span class="p">)</span> <span class="k">if</span> <span class="nb">type</span><span class="p">(</span><span class="n">f</span><span class="p">)</span> <span class="ow">is</span> <span class="nb">list</span> <span class="ow">or</span>
+                                 <span class="nb">type</span><span class="p">(</span><span class="n">f</span><span class="p">)</span> <span class="ow">is</span> <span class="nb">set</span> <span class="k">else</span> <span class="nb">str</span><span class="p">(</span><span class="n">f</span><span class="p">)</span> <span class="k">for</span> <span class="n">f</span> <span class="ow">in</span> <span class="n">r</span>
+                             <span class="p">])</span> <span class="k">for</span> <span class="n">r</span> <span class="ow">in</span> <span class="n">res</span>
+                         <span class="p">]))</span>
+    
+    
+    
+    <span class="k">def</span> <span class="nf">_get_eids</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">req</span><span class="p">):</span>
+        
+        <span class="n">names</span> <span class="o">=</span> <span class="kc">None</span> <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">req</span><span class="o">.</span><span class="n">postpath</span><span class="p">)</span> <span class="o">&lt;=</span> <span class="mi">1</span> <span class="k">else</span> <span class="n">req</span><span class="o">.</span><span class="n">postpath</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;,&#39;</span><span class="p">)</span>
+        <span class="n">ids</span> <span class="o">=</span> <span class="nb">range</span><span class="p">(</span>
+            <span class="mi">0</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">g</span><span class="o">.</span><span class="n">vcount</span><span class="p">())</span> <span class="k">if</span> <span class="n">names</span> <span class="ow">is</span> <span class="kc">None</span> <span class="k">else</span> <span class="bp">self</span><span class="o">.</span><span class="n">p</span><span class="o">.</span><span class="n">names2vids</span><span class="p">(</span><span class="n">names</span><span class="p">)</span>
+        <span class="n">ids</span> <span class="o">=</span> <span class="nb">set</span><span class="p">(</span><span class="n">ids</span><span class="p">)</span>
+        <span class="n">elist</span> <span class="o">=</span> <span class="nb">set</span><span class="p">(</span><span class="nb">range</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">g</span><span class="o">.</span><span class="n">ecount</span><span class="p">()))</span> <span class="k">if</span> <span class="n">names</span> <span class="ow">is</span> <span class="kc">None</span> <span class="k">else</span> <span class="nb">set</span><span class="p">([])</span>
+        <span class="k">if</span> <span class="n">names</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
+            <span class="n">alist</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">(</span><span class="nb">zip</span><span class="p">(</span><span class="n">ids</span><span class="p">,</span> <span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">g</span><span class="o">.</span><span class="n">neighbors</span><span class="p">(</span><span class="n">i</span><span class="p">)</span> <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="n">ids</span><span class="p">]))</span>
+            <span class="k">for</span> <span class="n">one</span><span class="p">,</span> <span class="n">others</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="n">alist</span><span class="p">):</span>
+                <span class="k">for</span> <span class="n">two</span> <span class="ow">in</span> <span class="n">others</span><span class="p">:</span>
+                    <span class="n">e</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">g</span><span class="o">.</span><span class="n">get_eid</span><span class="p">(</span><span class="n">one</span><span class="p">,</span> <span class="n">two</span><span class="p">,</span> <span class="n">directed</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">error</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span>
+                    <span class="k">if</span> <span class="n">e</span> <span class="o">!=</span> <span class="o">-</span><span class="mi">1</span><span class="p">:</span>
+                        <span class="n">elist</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">e</span><span class="p">)</span>
+                    <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">g</span><span class="o">.</span><span class="n">is_directed</span><span class="p">():</span>
+                        <span class="n">e</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">g</span><span class="o">.</span><span class="n">get_eid</span><span class="p">(</span>
+                            <span class="n">two</span><span class="p">,</span> <span class="n">one</span><span class="p">,</span> <span class="n">directed</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">error</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span>
+                        <span class="k">if</span> <span class="n">e</span> <span class="o">!=</span> <span class="o">-</span><span class="mi">1</span><span class="p">:</span>
+                            <span class="n">elist</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">e</span><span class="p">)</span>
+        <span class="k">return</span> <span class="n">elist</span>
+    
+    
+    <span class="k">def</span> <span class="nf">ptms</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">req</span><span class="p">):</span>
+        <span class="n">fields</span> <span class="o">=</span> <span class="p">[</span>
+            <span class="sa">b</span><span class="s1">&#39;is_stimulation&#39;</span><span class="p">,</span> <span class="sa">b</span><span class="s1">&#39;is_inhibition&#39;</span><span class="p">,</span> <span class="sa">b</span><span class="s1">&#39;sources&#39;</span><span class="p">,</span> <span class="sa">b</span><span class="s1">&#39;references&#39;</span>
+        <span class="p">]</span>
+        <span class="n">result</span> <span class="o">=</span> <span class="p">[]</span>
+        <span class="n">elist</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_get_eids</span><span class="p">(</span><span class="n">req</span><span class="p">)</span>
+        <span class="n">res</span> <span class="o">=</span> <span class="p">[]</span>
+        <span class="n">hdr</span> <span class="o">=</span> <span class="p">[</span>
+            <span class="s1">&#39;enzyme&#39;</span><span class="p">,</span> <span class="s1">&#39;substrate&#39;</span><span class="p">,</span> <span class="s1">&#39;residue_type&#39;</span><span class="p">,</span> <span class="s1">&#39;residue_offset&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;modification&#39;</span>
+        <span class="p">]</span>
+        
+        <span class="k">if</span> <span class="p">(</span>
+            <span class="sa">b</span><span class="s1">&#39;genesymbols&#39;</span> <span class="ow">in</span> <span class="n">req</span><span class="o">.</span><span class="n">args</span> <span class="ow">and</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">_parse_arg</span><span class="p">(</span><span class="n">req</span><span class="o">.</span><span class="n">args</span><span class="p">[</span><span class="sa">b</span><span class="s1">&#39;genesymbols&#39;</span><span class="p">])</span>
+        <span class="p">):</span>
+            <span class="n">genesymbols</span> <span class="o">=</span> <span class="kc">True</span>
+            <span class="n">hdr</span><span class="o">.</span><span class="n">insert</span><span class="p">(</span><span class="mi">2</span><span class="p">,</span> <span class="s1">&#39;enzyme_genesymbol&#39;</span><span class="p">)</span>
+            <span class="n">hdr</span><span class="o">.</span><span class="n">insert</span><span class="p">(</span><span class="mi">3</span><span class="p">,</span> <span class="s1">&#39;substrate_genesymbol&#39;</span><span class="p">)</span>
+        <span class="k">else</span><span class="p">:</span>
+            <span class="n">genesymbols</span> <span class="o">=</span> <span class="kc">False</span>
+        
+        <span class="k">if</span> <span class="sa">b</span><span class="s1">&#39;fields&#39;</span> <span class="ow">in</span> <span class="n">req</span><span class="o">.</span><span class="n">args</span><span class="p">:</span>
+            
+            <span class="n">hdr</span> <span class="o">+=</span> <span class="p">[</span>
+                <span class="n">f</span><span class="o">.</span><span class="n">decode</span><span class="p">(</span><span class="s1">&#39;utf-8&#39;</span><span class="p">)</span>
+                <span class="k">for</span> <span class="n">f</span> <span class="ow">in</span> <span class="n">fields</span>
+                <span class="k">if</span> <span class="n">f</span> <span class="ow">in</span> <span class="sa">b</span><span class="s1">&#39;,&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">req</span><span class="o">.</span><span class="n">args</span><span class="p">[</span><span class="sa">b</span><span class="s1">&#39;fields&#39;</span><span class="p">])</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="sa">b</span><span class="s1">&#39;,&#39;</span><span class="p">)</span>
+            <span class="p">]</span>
+        
+        <span class="k">if</span> <span class="s1">&#39;ptm&#39;</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">g</span><span class="o">.</span><span class="n">es</span><span class="o">.</span><span class="n">attributes</span><span class="p">():</span>
+            <span class="k">for</span> <span class="n">eid</span> <span class="ow">in</span> <span class="n">elist</span><span class="p">:</span>
+                <span class="n">e</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">g</span><span class="o">.</span><span class="n">es</span><span class="p">[</span><span class="n">eid</span><span class="p">]</span>
+                <span class="k">for</span> <span class="n">ptm</span> <span class="ow">in</span> <span class="n">e</span><span class="p">[</span><span class="s1">&#39;ptm&#39;</span><span class="p">]:</span>
+                    <span class="k">if</span> <span class="s1">&#39;ptmtype&#39;</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">req</span><span class="o">.</span><span class="n">args</span> <span class="ow">or</span> <span class="n">ptm</span><span class="o">.</span><span class="n">ptm</span><span class="o">.</span><span class="n">typ</span> <span class="ow">in</span> <span class="n">req</span><span class="o">.</span><span class="n">args</span><span class="p">[</span>
+                            <span class="s1">&#39;ptmtype&#39;</span><span class="p">]:</span>
+                        <span class="n">thisPtm</span> <span class="o">=</span> <span class="p">[</span>
+                            <span class="n">ptm</span><span class="o">.</span><span class="n">domain</span><span class="o">.</span><span class="n">protein</span><span class="p">,</span> <span class="n">ptm</span><span class="o">.</span><span class="n">ptm</span><span class="o">.</span><span class="n">protein</span>
+                        <span class="p">]</span>
+                        
+                        <span class="k">if</span> <span class="n">genesymbols</span><span class="p">:</span>
+                            
+                            <span class="n">thisPtm</span><span class="o">.</span><span class="n">extend</span><span class="p">([</span>
+                                <span class="bp">self</span><span class="o">.</span><span class="n">g</span><span class="o">.</span><span class="n">vs</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">p</span><span class="o">.</span><span class="n">nodDct</span><span class="p">[</span>
+                                    <span class="n">ptm</span><span class="o">.</span><span class="n">domain</span><span class="o">.</span><span class="n">protein</span><span class="p">]][</span><span class="s1">&#39;label&#39;</span><span class="p">],</span>
+                                <span class="bp">self</span><span class="o">.</span><span class="n">g</span><span class="o">.</span><span class="n">vs</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">p</span><span class="o">.</span><span class="n">nodDct</span><span class="p">[</span>
+                                    <span class="n">ptm</span><span class="o">.</span><span class="n">ptm</span><span class="o">.</span><span class="n">protein</span><span class="p">]][</span><span class="s1">&#39;label&#39;</span><span class="p">]</span>
+                            <span class="p">])</span>
+                        
+                        <span class="n">thisPtm</span><span class="o">.</span><span class="n">extend</span><span class="p">([</span>
+                            <span class="n">ptm</span><span class="o">.</span><span class="n">ptm</span><span class="o">.</span><span class="n">residue</span><span class="o">.</span><span class="n">name</span><span class="p">,</span> <span class="n">ptm</span><span class="o">.</span><span class="n">ptm</span><span class="o">.</span><span class="n">residue</span><span class="o">.</span><span class="n">number</span><span class="p">,</span>
+                            <span class="n">ptm</span><span class="o">.</span><span class="n">ptm</span><span class="o">.</span><span class="n">typ</span>
+                        <span class="p">])</span>
+                        
+                        <span class="k">if</span> <span class="s1">&#39;is_stimulation&#39;</span> <span class="ow">in</span> <span class="n">hdr</span><span class="p">:</span>
+                            <span class="n">thisPtm</span><span class="o">.</span><span class="n">append</span><span class="p">(</span>
+                                <span class="nb">int</span><span class="p">(</span><span class="n">e</span><span class="p">[</span><span class="s1">&#39;dirs&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">is_stimulation</span><span class="p">((</span>
+                                    <span class="n">ptm</span><span class="o">.</span><span class="n">domain</span><span class="o">.</span><span class="n">protein</span><span class="p">,</span> <span class="n">ptm</span><span class="o">.</span><span class="n">ptm</span><span class="o">.</span><span class="n">protein</span><span class="p">))))</span>
+                        
+                        <span class="k">if</span> <span class="s1">&#39;is_inhibition&#39;</span> <span class="ow">in</span> <span class="n">hdr</span><span class="p">:</span>
+                            <span class="n">thisPtm</span><span class="o">.</span><span class="n">append</span><span class="p">(</span>
+                                <span class="nb">int</span><span class="p">(</span><span class="n">e</span><span class="p">[</span><span class="s1">&#39;dirs&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">is_inhibition</span><span class="p">((</span>
+                                    <span class="n">ptm</span><span class="o">.</span><span class="n">domain</span><span class="o">.</span><span class="n">protein</span><span class="p">,</span> <span class="n">ptm</span><span class="o">.</span><span class="n">ptm</span><span class="o">.</span><span class="n">protein</span><span class="p">))))</span>
+                        
+                        <span class="k">if</span> <span class="s1">&#39;sources&#39;</span> <span class="ow">in</span> <span class="n">hdr</span><span class="p">:</span>
+                            <span class="n">thisPtm</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="nb">list</span><span class="p">(</span><span class="n">ptm</span><span class="o">.</span><span class="n">ptm</span><span class="o">.</span><span class="n">sources</span><span class="p">))</span>
+                        
+                        <span class="k">if</span> <span class="s1">&#39;references&#39;</span> <span class="ow">in</span> <span class="n">hdr</span><span class="p">:</span>
+                            <span class="n">thisPtm</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="nb">list</span><span class="p">(</span><span class="n">ptm</span><span class="o">.</span><span class="n">refs</span><span class="p">))</span>
+                        <span class="n">res</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">thisPtm</span><span class="p">)</span>
+        
+        <span class="k">if</span> <span class="sa">b</span><span class="s1">&#39;format&#39;</span> <span class="ow">in</span> <span class="n">req</span><span class="o">.</span><span class="n">args</span> <span class="ow">and</span> <span class="n">req</span><span class="o">.</span><span class="n">args</span><span class="p">[</span><span class="sa">b</span><span class="s1">&#39;format&#39;</span><span class="p">]</span> <span class="o">==</span> <span class="sa">b</span><span class="s1">&#39;json&#39;</span><span class="p">:</span>
+            <span class="k">return</span> <span class="n">json</span><span class="o">.</span><span class="n">dumps</span><span class="p">([</span><span class="nb">dict</span><span class="p">(</span><span class="nb">zip</span><span class="p">(</span><span class="n">hdr</span><span class="p">,</span> <span class="n">r</span><span class="p">))</span> <span class="k">for</span> <span class="n">r</span> <span class="ow">in</span> <span class="n">res</span><span class="p">])</span>
+        <span class="k">else</span><span class="p">:</span>
+            <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_table_output</span><span class="p">(</span><span class="n">res</span><span class="p">,</span> <span class="n">hdr</span><span class="p">,</span> <span class="n">req</span><span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">resources</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">req</span><span class="p">):</span>
+        
+        <span class="n">hdr</span> <span class="o">=</span> <span class="p">[</span>
+            <span class="s1">&#39;database&#39;</span><span class="p">,</span> <span class="s1">&#39;proteins&#39;</span><span class="p">,</span> <span class="s1">&#39;interactions&#39;</span><span class="p">,</span> <span class="s1">&#39;directions&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;stimulations&#39;</span><span class="p">,</span> <span class="s1">&#39;inhibitions&#39;</span><span class="p">,</span> <span class="s1">&#39;signs&#39;</span>
+        <span class="p">]</span>
+        <span class="n">res</span> <span class="o">=</span> <span class="p">[[</span>
+            <span class="c1"># database name</span>
+            <span class="n">s</span><span class="p">,</span>
+            <span class="c1"># number of proteins</span>
+            <span class="nb">len</span><span class="p">([</span><span class="mi">1</span> <span class="k">for</span> <span class="n">v</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">g</span><span class="o">.</span><span class="n">vs</span> <span class="k">if</span> <span class="n">s</span> <span class="ow">in</span> <span class="n">v</span><span class="p">[</span><span class="s1">&#39;sources&#39;</span><span class="p">]]),</span>
+            <span class="c1"># number of interacting pairs</span>
+            <span class="nb">len</span><span class="p">([</span><span class="mi">1</span> <span class="k">for</span> <span class="n">e</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">g</span><span class="o">.</span><span class="n">es</span> <span class="k">if</span> <span class="n">s</span> <span class="ow">in</span> <span class="n">e</span><span class="p">[</span><span class="s1">&#39;sources&#39;</span><span class="p">]]),</span>
+            <span class="c1"># number of directions</span>
+            <span class="nb">sum</span><span class="p">([</span><span class="n">s</span> <span class="ow">in</span> <span class="n">e</span><span class="p">[</span><span class="s1">&#39;dirs&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">sources</span><span class="p">[</span><span class="n">d</span><span class="p">]</span> \
+                 <span class="k">for</span> <span class="n">e</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">g</span><span class="o">.</span><span class="n">es</span> <span class="k">for</span> <span class="n">d</span> <span class="ow">in</span> <span class="n">e</span><span class="p">[</span><span class="s1">&#39;dirs&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">which_dirs</span><span class="p">()]),</span>
+            <span class="c1"># number of stimulations</span>
+            <span class="nb">sum</span><span class="p">([</span><span class="n">s</span> <span class="ow">in</span> <span class="n">e</span><span class="p">[</span><span class="s1">&#39;dirs&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">positive_sources</span><span class="p">[</span><span class="n">d</span><span class="p">]</span> \
+                 <span class="k">for</span> <span class="n">e</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">g</span><span class="o">.</span><span class="n">es</span> <span class="k">for</span> <span class="n">d</span> <span class="ow">in</span> <span class="n">e</span><span class="p">[</span><span class="s1">&#39;dirs&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">which_dirs</span><span class="p">()]),</span>
+            <span class="c1"># number of inhibitions</span>
+            <span class="nb">sum</span><span class="p">([</span><span class="n">s</span> <span class="ow">in</span> <span class="n">e</span><span class="p">[</span><span class="s1">&#39;dirs&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">negative_sources</span><span class="p">[</span><span class="n">d</span><span class="p">]</span> \
+                 <span class="k">for</span> <span class="n">e</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">g</span><span class="o">.</span><span class="n">es</span> <span class="k">for</span> <span class="n">d</span> <span class="ow">in</span> <span class="n">e</span><span class="p">[</span><span class="s1">&#39;dirs&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">which_dirs</span><span class="p">()]),</span>
+            <span class="c1"># number of signs</span>
+            <span class="nb">sum</span><span class="p">([</span><span class="n">s</span> <span class="ow">in</span> <span class="n">sg</span> <span class="k">for</span> <span class="n">e</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">g</span><span class="o">.</span><span class="n">es</span> <span class="k">for</span> <span class="n">d</span> <span class="ow">in</span> <span class="n">e</span><span class="p">[</span><span class="s1">&#39;dirs&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">which_dirs</span><span class="p">()</span> \
+                 <span class="k">for</span> <span class="n">sg</span> <span class="ow">in</span> <span class="p">[</span><span class="n">e</span><span class="p">[</span><span class="s1">&#39;dirs&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">positive_sources</span><span class="p">[</span><span class="n">d</span><span class="p">],</span>
+                            <span class="n">e</span><span class="p">[</span><span class="s1">&#39;dirs&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">negative_sources</span><span class="p">[</span><span class="n">d</span><span class="p">]]]),</span>
+        <span class="p">]</span>
+            <span class="k">for</span> <span class="n">s</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">p</span><span class="o">.</span><span class="n">sources</span><span class="p">]</span>
+        <span class="k">if</span> <span class="sa">b</span><span class="s1">&#39;format&#39;</span> <span class="ow">in</span> <span class="n">req</span><span class="o">.</span><span class="n">args</span> <span class="ow">and</span> <span class="n">req</span><span class="o">.</span><span class="n">args</span><span class="p">[</span><span class="sa">b</span><span class="s1">&#39;format&#39;</span><span class="p">]</span> <span class="o">==</span> <span class="sa">b</span><span class="s1">&#39;json&#39;</span><span class="p">:</span>
+            <span class="k">return</span> <span class="n">json</span><span class="o">.</span><span class="n">dumps</span><span class="p">([</span><span class="nb">dict</span><span class="p">(</span><span class="nb">zip</span><span class="p">(</span><span class="n">hdr</span><span class="p">,</span> <span class="n">r</span><span class="p">))</span> <span class="k">for</span> <span class="n">r</span> <span class="ow">in</span> <span class="n">res</span><span class="p">])</span>
+        <span class="k">else</span><span class="p">:</span>
+            <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_table_output</span><span class="p">(</span><span class="n">res</span><span class="p">,</span> <span class="n">hdr</span><span class="p">,</span> <span class="n">req</span><span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">_dip_urls</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">e</span><span class="p">):</span>
+        <span class="n">result</span> <span class="o">=</span> <span class="p">[]</span>
+        <span class="k">if</span> <span class="s1">&#39;dip_id&#39;</span> <span class="ow">in</span> <span class="n">e</span><span class="o">.</span><span class="n">attributes</span><span class="p">():</span>
+            <span class="k">for</span> <span class="n">dip_id</span> <span class="ow">in</span> <span class="n">e</span><span class="p">[</span><span class="s1">&#39;dip_id&#39;</span><span class="p">]:</span>
+                <span class="k">try</span><span class="p">:</span>
+                    <span class="n">result</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;dip&#39;</span><span class="p">][</span><span class="s1">&#39;ik&#39;</span><span class="p">]</span> <span class="o">%</span>
+                                <span class="nb">int</span><span class="p">(</span><span class="n">dip_id</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;-&#39;</span><span class="p">)[</span><span class="mi">1</span><span class="p">][:</span><span class="o">-</span><span class="mi">1</span><span class="p">]))</span>
+                <span class="k">except</span><span class="p">:</span>
+                    
+                    <span class="nb">print</span><span class="p">(</span><span class="n">dip_id</span><span class="p">)</span>
+                
+        <span class="k">return</span> <span class="s1">&#39;;&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">result</span><span class="p">)</span></div>
+
+</pre></div>
+
+                </article>
+              
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new file mode 100644
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+                      </a>
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+            <span class="sr-only">GitHub</span></a>
+        </li>
+        <li class="nav-item">
+          
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+          
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+          
+          
+          <a href="https://twitter.com/omnipathdb" title="Twitter" class="nav-link" rel="noopener" target="_blank" data-bs-toggle="tooltip" data-bs-placement="bottom"><span><i class="fa-brands fa-square-twitter fa-lg" aria-hidden="true"></i></span>
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+          
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+            <span class="sr-only">PyPI</span></a>
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+          
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+            <span class="sr-only">Saez Lab</span></a>
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+    
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+                      </a>
+                    </li>
+                
+
+                    <li class="nav-item">
+                      <a class="nav-link nav-internal" href="../../../../webservice.html">
+                        Webservice
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+                      <a class="nav-link nav-internal" href="../../../../notebooks/manual.html">
+                        The pypath book
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+    <span class="theme-switch nav-link" data-mode="dark"><i class="fa-solid fa-moon fa-lg"></i></span>
+    <span class="theme-switch nav-link" data-mode="auto"><i class="fa-solid fa-circle-half-stroke fa-lg"></i></span>
+  </button>
+`);
+</script></div>
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+    aria-label="Icon Links">
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+<div id="searchbox"></div>
+                <article class="bd-article">
+                  
+  <h1>Source code for pypath.omnipath.server.run</h1><div class="highlight"><pre>
+<span></span><span class="ch">#!/usr/bin/env python</span>
+<span class="c1"># -*- coding: utf-8 -*-</span>
+
+<span class="c1">#</span>
+<span class="c1">#  This file is part of the `pypath` python module</span>
+<span class="c1">#</span>
+<span class="c1">#  Copyright 2014-2023</span>
+<span class="c1">#  EMBL, EMBL-EBI, Uniklinik RWTH Aachen, Heidelberg University</span>
+<span class="c1">#</span>
+<span class="c1">#  Authors: see the file `README.rst`</span>
+<span class="c1">#  Contact: Dénes Türei (turei.denes@gmail.com)</span>
+<span class="c1">#</span>
+<span class="c1">#  Distributed under the GPLv3 License.</span>
+<span class="c1">#  See accompanying file LICENSE.txt or copy at</span>
+<span class="c1">#      https://www.gnu.org/licenses/gpl-3.0.html</span>
+<span class="c1">#</span>
+<span class="c1">#  Website: https://pypath.omnipathdb.org/</span>
+<span class="c1">#</span>
+
+<span class="kn">from</span> <span class="nn">future.utils</span> <span class="kn">import</span> <span class="n">iteritems</span>
+
+<span class="kn">import</span> <span class="nn">sys</span>
+<span class="kn">import</span> <span class="nn">os</span>
+<span class="kn">import</span> <span class="nn">re</span>
+<span class="kn">import</span> <span class="nn">copy</span>
+<span class="kn">import</span> <span class="nn">collections</span>
+<span class="kn">import</span> <span class="nn">itertools</span>
+<span class="kn">import</span> <span class="nn">hashlib</span>
+<span class="kn">import</span> <span class="nn">warnings</span>
+<span class="kn">import</span> <span class="nn">contextlib</span>
+
+<span class="kn">from</span> <span class="nn">pypath.share</span> <span class="kn">import</span> <span class="n">session</span> <span class="k">as</span> <span class="n">session_mod</span>
+
+<span class="n">_logger</span> <span class="o">=</span> <span class="n">session_mod</span><span class="o">.</span><span class="n">Logger</span><span class="p">(</span><span class="n">name</span> <span class="o">=</span> <span class="s1">&#39;server&#39;</span><span class="p">)</span>
+<span class="n">_log</span> <span class="o">=</span> <span class="n">_logger</span><span class="o">.</span><span class="n">_log</span>
+
+<span class="k">try</span><span class="p">:</span>
+    <span class="kn">import</span> <span class="nn">twisted.web.resource</span>
+    <span class="kn">import</span> <span class="nn">twisted.web.server</span>
+    <span class="kn">import</span> <span class="nn">twisted.internet.reactor</span>
+    <span class="n">TwistedWebResource</span> <span class="o">=</span> <span class="n">twisted</span><span class="o">.</span><span class="n">web</span><span class="o">.</span><span class="n">resource</span><span class="o">.</span><span class="n">Resource</span>
+    <span class="n">TwistedWebSite</span> <span class="o">=</span> <span class="n">twisted</span><span class="o">.</span><span class="n">web</span><span class="o">.</span><span class="n">server</span><span class="o">.</span><span class="n">Site</span>
+    <span class="n">TWISTED_NOT_DONE_YET</span> <span class="o">=</span> <span class="n">twisted</span><span class="o">.</span><span class="n">web</span><span class="o">.</span><span class="n">server</span><span class="o">.</span><span class="n">NOT_DONE_YET</span>
+    <span class="n">twisted_listen_tcp</span> <span class="o">=</span> <span class="n">twisted</span><span class="o">.</span><span class="n">internet</span><span class="o">.</span><span class="n">reactor</span><span class="o">.</span><span class="n">listenTCP</span>
+    <span class="n">twisted_run</span> <span class="o">=</span> <span class="n">twisted</span><span class="o">.</span><span class="n">internet</span><span class="o">.</span><span class="n">reactor</span><span class="o">.</span><span class="n">run</span>
+<span class="k">except</span><span class="p">:</span>
+    <span class="n">_log</span><span class="p">(</span><span class="s1">&#39;No module `twisted` available. Necessary to run HTTP server.&#39;</span><span class="p">,</span> <span class="o">-</span><span class="mi">1</span><span class="p">)</span>
+<div class="viewcode-block" id="TwistedWebResource">
+<a class="viewcode-back" href="../../../../api/pypath.omnipath.server.run.TwistedWebResource.html#pypath.omnipath.server.run.TwistedWebResource">[docs]</a>
+    <span class="k">class</span> <span class="nc">TwistedWebResource</span><span class="p">:</span> <span class="k">pass</span></div>
+
+<div class="viewcode-block" id="TwistedWebSite">
+<a class="viewcode-back" href="../../../../api/pypath.omnipath.server.run.TwistedWebSite.html#pypath.omnipath.server.run.TwistedWebSite">[docs]</a>
+    <span class="k">class</span> <span class="nc">TwistedWebSite</span><span class="p">:</span> <span class="k">pass</span></div>
+
+    <span class="n">TWISTED_NOT_DONE_YET</span> <span class="o">=</span> <span class="kc">None</span>
+    <span class="n">twisted_listen_tcp</span> <span class="o">=</span> <span class="k">lambda</span><span class="p">:</span> <span class="kc">None</span>
+    <span class="n">twisted_run</span> <span class="o">=</span> <span class="k">lambda</span><span class="p">:</span> <span class="kc">None</span>
+
+<span class="kn">import</span> <span class="nn">urllib</span>
+<span class="kn">import</span> <span class="nn">json</span>
+<span class="kn">import</span> <span class="nn">mimetypes</span>
+
+<span class="kn">import</span> <span class="nn">pandas</span> <span class="k">as</span> <span class="nn">pd</span>
+<span class="kn">import</span> <span class="nn">numpy</span> <span class="k">as</span> <span class="nn">np</span>
+
+<span class="kn">import</span> <span class="nn">pypath.resources</span> <span class="k">as</span> <span class="nn">resources</span>
+<span class="kn">from</span> <span class="nn">pypath.omnipath.server</span> <span class="kn">import</span> <span class="n">generate_about_page</span>
+<span class="kn">import</span> <span class="nn">pypath.omnipath.server._html</span> <span class="k">as</span> <span class="nn">_html</span>
+<span class="kn">import</span> <span class="nn">pypath.resources.urls</span> <span class="k">as</span> <span class="nn">urls</span>
+<span class="kn">import</span> <span class="nn">pypath.resources</span> <span class="k">as</span> <span class="nn">resources_mod</span>
+<span class="kn">import</span> <span class="nn">pypath.share.common</span> <span class="k">as</span> <span class="nn">common</span>
+<span class="kn">import</span> <span class="nn">pypath_common._constants</span> <span class="k">as</span> <span class="nn">_const</span>
+<span class="kn">import</span> <span class="nn">pypath.core.intercell_annot</span> <span class="k">as</span> <span class="nn">intercell_annot</span>
+<span class="kn">import</span> <span class="nn">pypath.share.settings</span> <span class="k">as</span> <span class="nn">settings</span>
+<span class="kn">from</span> <span class="nn">pypath.share.common</span> <span class="kn">import</span> <span class="n">flat_list</span>
+<span class="kn">from</span> <span class="nn">pypath._metadata</span> <span class="kn">import</span> <span class="n">__version__</span>
+
+<span class="k">if</span> <span class="s1">&#39;unicode&#39;</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">__builtins__</span><span class="p">:</span>
+    <span class="n">unicode</span> <span class="o">=</span> <span class="nb">str</span>
+
+
+<span class="n">LICENSE_IGNORE</span> <span class="o">=</span> <span class="s1">&#39;ignore&#39;</span>
+
+
+<div class="viewcode-block" id="stop_server">
+<a class="viewcode-back" href="../../../../api/pypath.omnipath.server.run.stop_server.html#pypath.omnipath.server.run.stop_server">[docs]</a>
+<span class="k">def</span> <span class="nf">stop_server</span><span class="p">():</span>
+
+    <span class="n">reactor</span><span class="o">.</span><span class="n">removeAll</span><span class="p">()</span></div>
+
+
+
+<div class="viewcode-block" id="ignore_pandas_copywarn">
+<a class="viewcode-back" href="../../../../api/pypath.omnipath.server.run.ignore_pandas_copywarn.html#pypath.omnipath.server.run.ignore_pandas_copywarn">[docs]</a>
+<span class="nd">@contextlib</span><span class="o">.</span><span class="n">contextmanager</span>
+<span class="k">def</span> <span class="nf">ignore_pandas_copywarn</span><span class="p">():</span>
+
+    <span class="k">try</span><span class="p">:</span>
+
+        <span class="k">with</span> <span class="n">warnings</span><span class="o">.</span><span class="n">catch_warnings</span><span class="p">():</span>
+
+            <span class="n">warnings</span><span class="o">.</span><span class="n">simplefilter</span><span class="p">(</span><span class="s1">&#39;ignore&#39;</span><span class="p">,</span> <span class="n">pd</span><span class="o">.</span><span class="n">errors</span><span class="o">.</span><span class="n">SettingWithCopyWarning</span><span class="p">)</span>
+
+            <span class="k">yield</span>
+
+    <span class="k">finally</span><span class="p">:</span>
+
+        <span class="k">pass</span></div>
+
+
+
+<div class="viewcode-block" id="BaseServer">
+<a class="viewcode-back" href="../../../../api/pypath.omnipath.server.run.BaseServer.html#pypath.omnipath.server.run.BaseServer">[docs]</a>
+<span class="k">class</span> <span class="nc">BaseServer</span><span class="p">(</span><span class="n">TwistedWebResource</span><span class="p">,</span> <span class="n">session_mod</span><span class="o">.</span><span class="n">Logger</span><span class="p">):</span>
+
+
+    <span class="n">recomment</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">compile</span><span class="p">(</span><span class="sa">b</span><span class="s1">&#39;&lt;!--\s*Title:(.*?)--&gt;&#39;</span><span class="p">)</span>
+
+
+<div class="viewcode-block" id="BaseServer.__init__">
+<a class="viewcode-back" href="../../../../api/pypath.omnipath.server.run.BaseServer.html#pypath.omnipath.server.run.BaseServer.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">if</span> <span class="ow">not</span> <span class="nb">hasattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">&#39;_log_name&#39;</span><span class="p">):</span>
+
+            <span class="n">session_mod</span><span class="o">.</span><span class="n">Logger</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="n">name</span> <span class="o">=</span> <span class="s1">&#39;server&#39;</span><span class="p">)</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span><span class="s1">&#39;Initializing BaseServer.&#39;</span><span class="p">)</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">htmls</span> <span class="o">=</span> <span class="p">[</span><span class="s1">&#39;info&#39;</span><span class="p">,</span> <span class="s1">&#39;error_page.html&#39;</span><span class="p">]</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">welcome_message</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="s1">&#39;Hello, this is the REST service of pypath </span><span class="si">%s</span><span class="s1">. Welcome!</span><span class="se">\n</span><span class="s1">&#39;</span>
+            <span class="s1">&#39;For the descriptions of pathway resources go to `/info`.</span><span class="se">\n</span><span class="s1">&#39;</span>
+            <span class="s1">&#39;Available query types: interactions, enz_sub, complexes, </span><span class="se">\n</span><span class="s1">&#39;</span>
+            <span class="s1">&#39;annotations, intercell&#39;</span>
+        <span class="p">)</span> <span class="o">%</span> <span class="n">__version__</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">isLeaf</span> <span class="o">=</span> <span class="kc">True</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">_set_www_root</span><span class="p">()</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">_read_license_secret</span><span class="p">()</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">_res_ctrl</span> <span class="o">=</span> <span class="n">resources_mod</span><span class="o">.</span><span class="n">get_controller</span><span class="p">()</span>
+
+        <span class="n">TwistedWebResource</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span><span class="s1">&#39;Twisted resource initialized.&#39;</span><span class="p">)</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">render_GET</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">request</span><span class="p">):</span>
+
+        <span class="n">response</span> <span class="o">=</span> <span class="p">[]</span>
+
+        <span class="n">request</span><span class="o">.</span><span class="n">postpath</span> <span class="o">=</span> <span class="p">[</span><span class="n">i</span><span class="o">.</span><span class="n">decode</span><span class="p">(</span><span class="s1">&#39;utf-8&#39;</span><span class="p">)</span> <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="n">request</span><span class="o">.</span><span class="n">postpath</span> <span class="k">if</span> <span class="n">i</span><span class="p">]</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span>
+            <span class="s1">&#39;Processing request: `</span><span class="si">%s</span><span class="s1">` from `</span><span class="si">%s</span><span class="s1">`; headers: [</span><span class="si">%s</span><span class="s1">].&#39;</span> <span class="o">%</span> <span class="p">(</span>
+                <span class="n">request</span><span class="o">.</span><span class="n">uri</span><span class="o">.</span><span class="n">decode</span><span class="p">(</span><span class="s1">&#39;utf-8&#39;</span><span class="p">),</span>
+                <span class="nb">str</span><span class="p">(</span><span class="n">request</span><span class="o">.</span><span class="n">getClientAddress</span><span class="p">()),</span>
+                <span class="n">common</span><span class="o">.</span><span class="n">dict_str</span><span class="p">(</span><span class="n">request</span><span class="o">.</span><span class="n">getAllHeaders</span><span class="p">()),</span>
+            <span class="p">)</span>
+        <span class="p">)</span>
+
+        <span class="k">if</span> <span class="ow">not</span> <span class="n">request</span><span class="o">.</span><span class="n">postpath</span><span class="p">:</span>
+
+            <span class="n">request</span><span class="o">.</span><span class="n">postpath</span> <span class="o">=</span> <span class="p">[</span><span class="s1">&#39;index.html&#39;</span><span class="p">]</span>
+
+        <span class="n">request</span><span class="o">.</span><span class="n">postpath</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_query_type</span><span class="p">(</span><span class="n">request</span><span class="o">.</span><span class="n">postpath</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_set_headers</span><span class="p">(</span><span class="n">request</span><span class="p">)</span>
+
+        <span class="k">if</span> <span class="p">(</span>
+            <span class="n">request</span><span class="o">.</span><span class="n">postpath</span> <span class="ow">and</span>
+            <span class="p">(</span>
+                <span class="nb">hasattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">request</span><span class="o">.</span><span class="n">postpath</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span> <span class="ow">or</span>
+                <span class="n">request</span><span class="o">.</span><span class="n">postpath</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">==</span> <span class="s1">&#39;error_page.html&#39;</span>
+            <span class="p">)</span> <span class="ow">and</span>
+            <span class="n">request</span><span class="o">.</span><span class="n">postpath</span><span class="p">[</span><span class="mi">0</span><span class="p">][</span><span class="mi">0</span><span class="p">]</span> <span class="o">!=</span> <span class="s1">&#39;_&#39;</span>
+        <span class="p">):</span>
+
+            <span class="k">if</span> <span class="n">request</span><span class="o">.</span><span class="n">postpath</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">==</span> <span class="s1">&#39;error_page.html&#39;</span><span class="p">:</span>
+
+                <span class="n">toCall</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_error_page</span>
+
+            <span class="k">else</span><span class="p">:</span>
+
+                <span class="bp">self</span><span class="o">.</span><span class="n">_process_postpath</span><span class="p">(</span><span class="n">request</span><span class="p">)</span>
+                <span class="n">toCall</span> <span class="o">=</span> <span class="nb">getattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">request</span><span class="o">.</span><span class="n">postpath</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span>
+
+            <span class="k">if</span> <span class="nb">hasattr</span><span class="p">(</span><span class="n">toCall</span><span class="p">,</span> <span class="s1">&#39;__call__&#39;</span><span class="p">):</span>
+
+                <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span>
+                    <span class="s1">&#39;Query type: `</span><span class="si">%s</span><span class="s1">`; Arguments: [</span><span class="si">%s</span><span class="s1">].&#39;</span> <span class="o">%</span> <span class="p">(</span>
+                        <span class="n">request</span><span class="o">.</span><span class="n">postpath</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span>
+                        <span class="n">common</span><span class="o">.</span><span class="n">dict_str</span><span class="p">(</span><span class="n">request</span><span class="o">.</span><span class="n">args</span><span class="p">),</span>
+                    <span class="p">)</span>
+                <span class="p">)</span>
+
+                <span class="k">try</span><span class="p">:</span>
+
+                    <span class="n">response</span> <span class="o">=</span> <span class="n">toCall</span><span class="p">(</span><span class="n">request</span><span class="p">)</span>
+                    <span class="n">response</span> <span class="o">=</span> <span class="p">(</span>
+                        <span class="n">response</span><span class="o">.</span><span class="n">encode</span><span class="p">(</span><span class="s1">&#39;utf-8&#39;</span><span class="p">)</span>
+                        <span class="k">if</span> <span class="nb">hasattr</span><span class="p">(</span><span class="n">response</span><span class="p">,</span> <span class="s1">&#39;encode&#39;</span><span class="p">)</span> <span class="k">else</span>
+                        <span class="n">response</span>
+                    <span class="p">)</span>
+                    <span class="n">response</span> <span class="o">=</span> <span class="p">[</span><span class="n">response</span><span class="p">]</span>
+
+                <span class="k">except</span><span class="p">:</span>
+
+                    <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span>
+                        <span class="s1">&#39;Error while rendering `</span><span class="si">%s</span><span class="s1">`:&#39;</span> <span class="o">%</span>
+                        <span class="n">request</span><span class="o">.</span><span class="n">uri</span><span class="o">.</span><span class="n">decode</span><span class="p">(</span><span class="s1">&#39;utf-8&#39;</span><span class="p">)</span>
+                    <span class="p">)</span>
+                    <span class="bp">self</span><span class="o">.</span><span class="n">_log_traceback</span><span class="p">()</span>
+                    <span class="k">raise</span>
+
+        <span class="k">else</span><span class="p">:</span>
+
+            <span class="n">local_path</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_local_path</span><span class="p">(</span><span class="n">request</span><span class="p">)</span>
+
+            <span class="k">if</span> <span class="n">local_path</span><span class="p">:</span>
+
+                <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">local_path</span><span class="p">,</span> <span class="s1">&#39;rb&#39;</span><span class="p">)</span> <span class="k">as</span> <span class="n">fp</span><span class="p">:</span>
+
+                    <span class="n">response</span> <span class="o">=</span> <span class="p">[</span><span class="n">fp</span><span class="o">.</span><span class="n">read</span><span class="p">()]</span>
+
+                <span class="n">response</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_add_html_header</span><span class="p">(</span><span class="n">local_path</span><span class="p">,</span> <span class="n">response</span><span class="p">)</span>
+
+        <span class="k">if</span> <span class="ow">not</span> <span class="n">response</span><span class="p">:</span>
+
+            <span class="n">response</span> <span class="o">=</span> <span class="p">[</span>
+                <span class="p">(</span>
+                    <span class="s2">&quot;Not found: </span><span class="si">%s%s</span><span class="s2">&quot;</span> <span class="o">%</span> <span class="p">(</span>
+                        <span class="s1">&#39;/&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">request</span><span class="o">.</span><span class="n">postpath</span><span class="p">),</span>
+                        <span class="s1">&#39;&#39;</span>
+                        <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">request</span><span class="o">.</span><span class="n">args</span><span class="p">)</span> <span class="o">==</span> <span class="mi">0</span> <span class="k">else</span>
+                        <span class="s1">&#39;?</span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span>
+                            <span class="s1">&#39;&amp;&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">([</span>
+                                <span class="s1">&#39;</span><span class="si">%s</span><span class="s1">=</span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="p">(</span>
+                                    <span class="n">k</span><span class="o">.</span><span class="n">decode</span><span class="p">(</span><span class="s1">&#39;utf-8&#39;</span><span class="p">),</span>
+                                    <span class="n">v</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">decode</span><span class="p">(</span><span class="s1">&#39;utf-8&#39;</span><span class="p">)</span>
+                                <span class="p">)</span>
+                                <span class="k">for</span> <span class="n">k</span><span class="p">,</span> <span class="n">v</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="n">request</span><span class="o">.</span><span class="n">args</span><span class="p">)</span>
+                                <span class="k">if</span> <span class="n">v</span>
+                            <span class="p">])</span>
+                    <span class="p">)</span>
+                <span class="p">)</span><span class="o">.</span><span class="n">encode</span><span class="p">(</span><span class="s1">&#39;utf-8&#39;</span><span class="p">)</span>
+            <span class="p">]</span>
+
+        <span class="n">request</span><span class="o">.</span><span class="n">setHeader</span><span class="p">(</span><span class="s1">&#39;Content-Length&#39;</span><span class="p">,</span>  <span class="nb">str</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">response</span><span class="p">[</span><span class="mi">0</span><span class="p">])))</span>
+        <span class="n">request</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="n">response</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span>
+            <span class="s1">&#39;Finished serving request: `</span><span class="si">%s</span><span class="s1">`.&#39;</span> <span class="o">%</span> <span class="n">request</span><span class="o">.</span><span class="n">uri</span><span class="o">.</span><span class="n">decode</span><span class="p">(</span><span class="s1">&#39;utf-8&#39;</span><span class="p">)</span>
+        <span class="p">)</span>
+
+        <span class="n">request</span><span class="o">.</span><span class="n">finish</span><span class="p">()</span>
+
+        <span class="k">return</span> <span class="n">TWISTED_NOT_DONE_YET</span>
+
+
+    <span class="k">def</span> <span class="nf">render_POST</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">request</span><span class="p">):</span>
+
+        <span class="k">if</span> <span class="p">(</span>
+            <span class="n">request</span><span class="o">.</span><span class="n">getHeader</span><span class="p">(</span><span class="sa">b</span><span class="s1">&#39;content-type&#39;</span><span class="p">)</span> <span class="ow">and</span>
+            <span class="n">request</span><span class="o">.</span><span class="n">getHeader</span><span class="p">(</span><span class="sa">b</span><span class="s1">&#39;content-type&#39;</span><span class="p">)</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="sa">b</span><span class="s1">&#39;application/json&#39;</span><span class="p">)</span>
+        <span class="p">):</span>
+
+            <span class="n">post_content</span> <span class="o">=</span> <span class="n">request</span><span class="o">.</span><span class="n">content</span><span class="o">.</span><span class="n">getvalue</span><span class="p">()</span>
+
+            <span class="k">if</span> <span class="n">post_content</span> <span class="ow">and</span> <span class="n">post_content</span><span class="o">.</span><span class="n">strip</span><span class="p">():</span>
+
+                <span class="n">args_raw</span> <span class="o">=</span> <span class="n">json</span><span class="o">.</span><span class="n">loads</span><span class="p">(</span><span class="n">post_content</span><span class="p">)</span>
+                <span class="n">request</span><span class="o">.</span><span class="n">args</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">(</span>
+                    <span class="p">(</span>
+                        <span class="n">k</span><span class="o">.</span><span class="n">encode</span><span class="p">(</span><span class="s1">&#39;utf-8&#39;</span><span class="p">),</span>
+                        <span class="p">[</span><span class="n">v</span><span class="o">.</span><span class="n">encode</span><span class="p">(</span><span class="s1">&#39;utf-8&#39;</span><span class="p">)]</span>
+                        <span class="k">if</span> <span class="nb">type</span><span class="p">(</span><span class="n">v</span><span class="p">)</span> <span class="ow">is</span> <span class="ow">not</span> <span class="nb">list</span> <span class="k">else</span>
+                        <span class="p">[</span><span class="s1">&#39;,&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">v</span><span class="p">)</span><span class="o">.</span><span class="n">encode</span><span class="p">(</span><span class="s1">&#39;utf-8&#39;</span><span class="p">)]</span>
+                    <span class="p">)</span>
+                    <span class="k">for</span> <span class="n">k</span><span class="p">,</span> <span class="n">v</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="n">args_raw</span><span class="p">)</span>
+                <span class="p">)</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">render_GET</span><span class="p">(</span><span class="n">request</span><span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">_set_www_root</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">wwwbuiltin</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span>
+            <span class="n">session_mod</span><span class="o">.</span><span class="n">session</span><span class="p">()</span><span class="o">.</span><span class="n">module_root</span><span class="p">,</span>
+            <span class="s1">&#39;data&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;www&#39;</span><span class="p">,</span>
+        <span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">wwwroot</span> <span class="o">=</span> <span class="n">settings</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">&#39;www_root&#39;</span><span class="p">)</span>
+
+        <span class="k">if</span> <span class="ow">not</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">exists</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">wwwroot</span><span class="p">):</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">wwwroot</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">wwwbuiltin</span>
+
+
+    <span class="k">def</span> <span class="nf">_local_path</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">request</span><span class="p">):</span>
+
+        <span class="k">if</span> <span class="n">request</span><span class="o">.</span><span class="n">postpath</span> <span class="ow">and</span> <span class="n">request</span><span class="o">.</span><span class="n">postpath</span><span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">][</span><span class="mi">0</span><span class="p">]</span> <span class="ow">in</span> <span class="p">(</span><span class="s1">&#39;_&#39;</span><span class="p">,</span> <span class="s1">&#39;.&#39;</span><span class="p">):</span>
+
+            <span class="k">return</span>
+
+        <span class="k">for</span> <span class="n">wwwroot</span> <span class="ow">in</span> <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">wwwroot</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">wwwbuiltin</span><span class="p">):</span>
+
+            <span class="n">path</span> <span class="o">=</span>  <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">wwwroot</span><span class="p">,</span> <span class="o">*</span><span class="n">request</span><span class="o">.</span><span class="n">postpath</span><span class="p">)</span>
+
+            <span class="k">if</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">isfile</span><span class="p">(</span><span class="n">path</span><span class="p">):</span>
+
+                <span class="k">return</span> <span class="n">path</span>
+
+
+    <span class="k">def</span> <span class="nf">_set_headers</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">request</span><span class="p">):</span>
+
+        <span class="k">for</span> <span class="n">k</span><span class="p">,</span> <span class="n">v</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="n">request</span><span class="o">.</span><span class="n">args</span><span class="p">):</span>
+
+            <span class="n">request</span><span class="o">.</span><span class="n">args</span><span class="p">[</span><span class="n">k</span><span class="p">]</span> <span class="o">=</span> <span class="p">[</span><span class="sa">b</span><span class="s1">&#39;,&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">v</span><span class="p">)]</span>
+
+        <span class="n">request</span><span class="o">.</span><span class="n">setHeader</span><span class="p">(</span><span class="s1">&#39;Cache-Control&#39;</span><span class="p">,</span> <span class="s1">&#39;Public&#39;</span><span class="p">)</span>
+        <span class="n">request</span><span class="o">.</span><span class="n">setHeader</span><span class="p">(</span><span class="s1">&#39;Access-Control-Allow-Origin&#39;</span><span class="p">,</span> <span class="s1">&#39;*&#39;</span><span class="p">)</span>
+
+        <span class="k">if</span> <span class="s1">&#39;&#39;</span> <span class="ow">in</span> <span class="n">request</span><span class="o">.</span><span class="n">postpath</span><span class="p">:</span>
+
+            <span class="n">request</span><span class="o">.</span><span class="n">postpath</span><span class="o">.</span><span class="n">remove</span><span class="p">(</span><span class="s1">&#39;&#39;</span><span class="p">)</span>
+
+        <span class="k">if</span> <span class="ow">not</span> <span class="n">request</span><span class="o">.</span><span class="n">postpath</span><span class="p">:</span>
+
+            <span class="n">request</span><span class="o">.</span><span class="n">postpath</span> <span class="o">=</span> <span class="p">[</span><span class="s1">&#39;index.html&#39;</span><span class="p">]</span>
+
+        <span class="k">if</span> <span class="n">request</span><span class="o">.</span><span class="n">postpath</span> <span class="ow">and</span> <span class="n">request</span><span class="o">.</span><span class="n">postpath</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">==</span> <span class="s1">&#39;resources&#39;</span><span class="p">:</span>
+
+            <span class="n">request</span><span class="o">.</span><span class="n">args</span><span class="p">[</span><span class="sa">b</span><span class="s1">&#39;format&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="p">[</span><span class="sa">b</span><span class="s1">&#39;json&#39;</span><span class="p">]</span>
+
+        <span class="n">local_path</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_local_path</span><span class="p">(</span><span class="n">request</span><span class="p">)</span>
+
+        <span class="k">if</span> <span class="n">local_path</span><span class="p">:</span>
+
+            <span class="n">format_</span> <span class="o">=</span> <span class="n">mimetypes</span><span class="o">.</span><span class="n">guess_type</span><span class="p">(</span><span class="n">local_path</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span>
+            <span class="n">format_</span> <span class="o">=</span> <span class="p">(</span>
+                <span class="nb">tuple</span><span class="p">(</span><span class="n">format_</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;/&#39;</span><span class="p">))</span>
+                    <span class="k">if</span> <span class="n">format_</span> <span class="k">else</span>
+                <span class="p">(</span><span class="s1">&#39;text&#39;</span><span class="p">,</span> <span class="s1">&#39;plain&#39;</span><span class="p">)</span>
+            <span class="p">)</span>
+
+        <span class="k">elif</span> <span class="p">(</span>
+            <span class="ow">not</span> <span class="n">request</span><span class="o">.</span><span class="n">postpath</span> <span class="ow">or</span>
+            <span class="n">request</span><span class="o">.</span><span class="n">postpath</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">htmls</span> <span class="ow">or</span>
+            <span class="n">request</span><span class="o">.</span><span class="n">postpath</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">==</span> <span class="s1">&#39;error_page.html&#39;</span>
+        <span class="p">):</span>
+
+            <span class="n">format_</span> <span class="o">=</span> <span class="p">(</span><span class="s1">&#39;text&#39;</span><span class="p">,</span> <span class="s1">&#39;html&#39;</span><span class="p">)</span>
+
+        <span class="k">elif</span> <span class="p">(</span>
+            <span class="sa">b</span><span class="s1">&#39;format&#39;</span> <span class="ow">in</span> <span class="n">request</span><span class="o">.</span><span class="n">args</span> <span class="ow">and</span>
+            <span class="n">request</span><span class="o">.</span><span class="n">args</span><span class="p">[</span><span class="sa">b</span><span class="s1">&#39;format&#39;</span><span class="p">][</span><span class="mi">0</span><span class="p">]</span> <span class="o">==</span> <span class="sa">b</span><span class="s1">&#39;json&#39;</span>
+        <span class="p">):</span>
+
+            <span class="n">format_</span> <span class="o">=</span> <span class="p">(</span><span class="s1">&#39;application&#39;</span><span class="p">,</span> <span class="s1">&#39;json&#39;</span><span class="p">)</span>
+
+        <span class="k">elif</span> <span class="n">request</span><span class="o">.</span><span class="n">postpath</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">==</span> <span class="s1">&#39;favicon.ico&#39;</span><span class="p">:</span>
+
+            <span class="n">format_</span> <span class="o">=</span> <span class="p">(</span><span class="s1">&#39;image&#39;</span><span class="p">,</span> <span class="s1">&#39;vnd.microsoft.icon&#39;</span><span class="p">)</span>
+
+        <span class="k">else</span><span class="p">:</span>
+
+            <span class="n">request</span><span class="o">.</span><span class="n">args</span><span class="p">[</span><span class="sa">b</span><span class="s1">&#39;format&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="p">[</span><span class="sa">b</span><span class="s1">&#39;text&#39;</span><span class="p">]</span>
+            <span class="n">format_</span> <span class="o">=</span> <span class="p">(</span><span class="s1">&#39;text&#39;</span><span class="p">,</span> <span class="s1">&#39;plain&#39;</span><span class="p">)</span>
+
+        <span class="n">request</span><span class="o">.</span><span class="n">setHeader</span><span class="p">(</span>
+            <span class="s1">&#39;Content-Type&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;</span><span class="si">%s</span><span class="s1">/</span><span class="si">%s%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="p">(</span>
+                <span class="n">format_</span> <span class="o">+</span> <span class="p">(</span>
+                    <span class="s1">&#39;; charset=utf-8&#39;</span> <span class="k">if</span> <span class="n">format_</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">==</span> <span class="s1">&#39;text&#39;</span> <span class="k">else</span> <span class="s1">&#39;&#39;</span><span class="p">,</span>
+                <span class="p">)</span>
+            <span class="p">)</span>
+        <span class="p">)</span>
+
+        <span class="n">request</span><span class="o">.</span><span class="n">args</span><span class="p">[</span><span class="sa">b</span><span class="s1">&#39;header&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="p">[</span><span class="sa">b</span><span class="s1">&#39;1&#39;</span><span class="p">]</span>
+                <span class="k">if</span> <span class="sa">b</span><span class="s1">&#39;header&#39;</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">request</span><span class="o">.</span><span class="n">args</span> <span class="k">else</span>
+            <span class="n">request</span><span class="o">.</span><span class="n">args</span><span class="p">[</span><span class="sa">b</span><span class="s1">&#39;header&#39;</span><span class="p">]</span>
+        <span class="p">)</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_set_fields</span><span class="p">(</span><span class="n">request</span><span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">_set_license</span><span class="p">(</span><span class="n">request</span><span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">_set_fields</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">req</span><span class="p">):</span>
+
+        <span class="n">synonyms</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">field_synonyms</span>
+                <span class="k">if</span> <span class="nb">hasattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">&#39;field_synonyms&#39;</span><span class="p">)</span> <span class="k">else</span>
+            <span class="p">{}</span>
+        <span class="p">)</span>
+
+        <span class="k">if</span> <span class="sa">b</span><span class="s1">&#39;fields&#39;</span> <span class="ow">in</span> <span class="n">req</span><span class="o">.</span><span class="n">args</span><span class="p">:</span>
+
+            <span class="n">used</span> <span class="o">=</span> <span class="nb">set</span><span class="p">()</span>
+
+            <span class="n">fields_checked</span> <span class="o">=</span> <span class="p">[]</span>
+
+            <span class="k">for</span> <span class="n">field</span> <span class="ow">in</span> <span class="n">req</span><span class="o">.</span><span class="n">args</span><span class="p">[</span><span class="sa">b</span><span class="s1">&#39;fields&#39;</span><span class="p">][</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">decode</span><span class="p">(</span><span class="s1">&#39;utf-8&#39;</span><span class="p">)</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;,&#39;</span><span class="p">):</span>
+
+                <span class="n">field</span> <span class="o">=</span> <span class="n">synonyms</span><span class="p">[</span><span class="n">field</span><span class="p">]</span> <span class="k">if</span> <span class="n">field</span> <span class="ow">in</span> <span class="n">synonyms</span> <span class="k">else</span> <span class="n">field</span>
+
+                <span class="k">if</span> <span class="n">field</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">used</span><span class="p">:</span>
+
+                    <span class="n">fields_checked</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">field</span><span class="p">)</span>
+                    <span class="n">used</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">field</span><span class="p">)</span>
+
+            <span class="n">req</span><span class="o">.</span><span class="n">args</span><span class="p">[</span><span class="sa">b</span><span class="s1">&#39;fields&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="p">[</span><span class="s1">&#39;,&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">fields_checked</span><span class="p">)</span><span class="o">.</span><span class="n">encode</span><span class="p">(</span><span class="s1">&#39;utf-8&#39;</span><span class="p">)]</span>
+
+        <span class="k">else</span><span class="p">:</span>
+
+            <span class="n">req</span><span class="o">.</span><span class="n">args</span><span class="p">[</span><span class="sa">b</span><span class="s1">&#39;fields&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="p">[]</span>
+
+
+    <span class="k">def</span> <span class="nf">_set_license</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">req</span><span class="p">):</span>
+
+        <span class="n">query_type</span> <span class="o">=</span> <span class="n">req</span><span class="o">.</span><span class="n">postpath</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="k">if</span> <span class="n">req</span><span class="o">.</span><span class="n">postpath</span> <span class="k">else</span> <span class="kc">None</span>
+        <span class="n">query_type</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_query_type</span><span class="p">(</span><span class="n">query_type</span><span class="p">)</span>
+
+        <span class="k">if</span> <span class="p">(</span>
+            <span class="ow">not</span> <span class="nb">hasattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">&#39;args_reference&#39;</span><span class="p">)</span> <span class="ow">or</span>
+            <span class="ow">not</span> <span class="n">query_type</span> <span class="ow">or</span>
+            <span class="n">query_type</span> <span class="ow">not</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">args_reference</span> <span class="ow">or</span>
+            <span class="s1">&#39;license&#39;</span> <span class="ow">not</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">args_reference</span><span class="p">[</span><span class="n">query_type</span><span class="p">]</span>
+        <span class="p">):</span>
+
+            <span class="k">return</span>
+
+        <span class="n">auth</span> <span class="o">=</span> <span class="kc">False</span>
+
+        <span class="k">if</span> <span class="sa">b</span><span class="s1">&#39;password&#39;</span> <span class="ow">in</span> <span class="n">req</span><span class="o">.</span><span class="n">args</span><span class="p">:</span>
+
+            <span class="n">req_secret</span> <span class="o">=</span> <span class="n">hashlib</span><span class="o">.</span><span class="n">md5</span><span class="p">(</span><span class="n">req</span><span class="o">.</span><span class="n">args</span><span class="p">[</span><span class="sa">b</span><span class="s1">&#39;password&#39;</span><span class="p">][</span><span class="mi">0</span><span class="p">])</span><span class="o">.</span><span class="n">hexdigest</span><span class="p">()</span>
+
+            <span class="n">auth</span> <span class="o">=</span> <span class="p">(</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">_license_secret</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span> <span class="ow">and</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">_license_secret</span> <span class="o">==</span> <span class="n">req_secret</span>
+            <span class="p">)</span>
+
+            <span class="c1"># if someone sent a good password</span>
+            <span class="c1"># why not to ignore the licenses</span>
+            <span class="k">if</span> <span class="n">auth</span><span class="p">:</span>
+
+                <span class="n">req</span><span class="o">.</span><span class="n">args</span><span class="p">[</span><span class="sa">b</span><span class="s1">&#39;license&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="p">[</span><span class="sa">b</span><span class="s1">&#39;ignore&#39;</span><span class="p">]</span>
+
+        <span class="c1"># if the license level is not set</span>
+        <span class="c1"># or set to `ignore` but no successfull authentication</span>
+        <span class="c1"># we fall back to the default license level</span>
+        <span class="k">if</span> <span class="p">(</span>
+            <span class="sa">b</span><span class="s1">&#39;license&#39;</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">req</span><span class="o">.</span><span class="n">args</span> <span class="ow">or</span> <span class="p">(</span>
+                <span class="ow">not</span> <span class="n">auth</span> <span class="ow">and</span>
+                <span class="n">req</span><span class="o">.</span><span class="n">args</span><span class="p">[</span><span class="sa">b</span><span class="s1">&#39;license&#39;</span><span class="p">][</span><span class="mi">0</span><span class="p">]</span> <span class="o">==</span> <span class="sa">b</span><span class="s1">&#39;ignore&#39;</span>
+            <span class="p">)</span>
+        <span class="p">):</span>
+
+            <span class="n">req</span><span class="o">.</span><span class="n">args</span><span class="p">[</span><span class="sa">b</span><span class="s1">&#39;license&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_default_license</span>
+
+
+    <span class="k">def</span> <span class="nf">_process_postpath</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">req</span><span class="p">):</span>
+
+        <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">req</span><span class="o">.</span><span class="n">postpath</span><span class="p">)</span> <span class="o">&gt;</span> <span class="mi">1</span><span class="p">:</span>
+
+            <span class="n">ids_left</span> <span class="o">=</span> <span class="p">[</span><span class="n">req</span><span class="o">.</span><span class="n">postpath</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">encode</span><span class="p">(</span><span class="s1">&#39;utf-8&#39;</span><span class="p">)]</span>
+
+            <span class="n">ids_right</span> <span class="o">=</span> <span class="p">(</span>
+                <span class="p">[</span><span class="n">req</span><span class="o">.</span><span class="n">postpath</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span><span class="o">.</span><span class="n">encode</span><span class="p">(</span><span class="s1">&#39;utf-8&#39;</span><span class="p">)]</span>
+                <span class="k">if</span> <span class="p">(</span>
+                    <span class="nb">len</span><span class="p">(</span><span class="n">req</span><span class="o">.</span><span class="n">postpath</span><span class="p">)</span> <span class="o">&gt;</span> <span class="mi">2</span> <span class="ow">and</span>
+                    <span class="n">req</span><span class="o">.</span><span class="n">postpath</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span> <span class="ow">not</span> <span class="ow">in</span> <span class="p">{</span><span class="s1">&#39;and&#39;</span><span class="p">,</span> <span class="s1">&#39;or&#39;</span><span class="p">}</span>
+                <span class="p">)</span> <span class="k">else</span>
+                <span class="kc">None</span>
+            <span class="p">)</span>
+
+            <span class="n">left_right</span> <span class="o">=</span> <span class="p">(</span>
+                <span class="p">[</span><span class="sa">b</span><span class="s1">&#39;OR&#39;</span><span class="p">]</span>
+                <span class="k">if</span> <span class="n">req</span><span class="o">.</span><span class="n">postpath</span><span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span> <span class="ow">not</span> <span class="ow">in</span> <span class="p">{</span><span class="s1">&#39;and&#39;</span><span class="p">,</span> <span class="s1">&#39;or&#39;</span><span class="p">}</span> <span class="k">else</span>
+                <span class="p">[</span><span class="n">req</span><span class="o">.</span><span class="n">postpath</span><span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">encode</span><span class="p">(</span><span class="s1">&#39;utf-8&#39;</span><span class="p">)]</span>
+            <span class="p">)</span>
+
+            <span class="k">if</span> <span class="n">ids_right</span><span class="p">:</span>
+
+                <span class="k">if</span> <span class="n">req</span><span class="o">.</span><span class="n">postpath</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">==</span> <span class="s1">&#39;enzsub&#39;</span><span class="p">:</span>
+
+                    <span class="n">req</span><span class="o">.</span><span class="n">args</span><span class="p">[</span><span class="sa">b</span><span class="s1">&#39;enzymes&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">ids_left</span>
+                    <span class="n">req</span><span class="o">.</span><span class="n">args</span><span class="p">[</span><span class="sa">b</span><span class="s1">&#39;substrates&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">ids_right</span>
+
+                <span class="k">else</span><span class="p">:</span>
+                    <span class="n">req</span><span class="o">.</span><span class="n">args</span><span class="p">[</span><span class="sa">b</span><span class="s1">&#39;sources&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">ids_left</span>
+                    <span class="n">req</span><span class="o">.</span><span class="n">args</span><span class="p">[</span><span class="sa">b</span><span class="s1">&#39;targets&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">ids_right</span>
+
+            <span class="k">else</span><span class="p">:</span>
+                <span class="n">req</span><span class="o">.</span><span class="n">args</span><span class="p">[</span><span class="sa">b</span><span class="s1">&#39;partners&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">ids_left</span>
+
+            <span class="k">if</span> <span class="n">req</span><span class="o">.</span><span class="n">postpath</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">==</span> <span class="s1">&#39;enzsub&#39;</span><span class="p">:</span>
+                <span class="n">req</span><span class="o">.</span><span class="n">args</span><span class="p">[</span><span class="sa">b</span><span class="s1">&#39;enzyme_substrate&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">left_right</span>
+            <span class="k">else</span><span class="p">:</span>
+                <span class="n">req</span><span class="o">.</span><span class="n">args</span><span class="p">[</span><span class="sa">b</span><span class="s1">&#39;source_target&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">left_right</span>
+
+
+    <span class="k">def</span> <span class="nf">_query_type</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">query_type</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="p">(</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">query_type_synonyms</span><span class="p">[</span><span class="n">query_type</span><span class="p">]</span>
+                <span class="k">if</span> <span class="p">(</span>
+                    <span class="nb">hasattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">&#39;query_type_synonyms&#39;</span><span class="p">)</span> <span class="ow">and</span>
+                    <span class="n">query_type</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">query_type_synonyms</span>
+                <span class="p">)</span> <span class="k">else</span>
+            <span class="n">query_type</span>
+        <span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">_add_html_header</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">local_path</span><span class="p">,</span> <span class="n">response</span><span class="p">):</span>
+
+        <span class="k">if</span> <span class="p">(</span>
+            <span class="n">local_path</span><span class="o">.</span><span class="n">endswith</span><span class="p">(</span><span class="s1">&#39;html&#39;</span><span class="p">)</span> <span class="ow">or</span>
+            <span class="n">local_path</span><span class="o">.</span><span class="n">endswith</span><span class="p">(</span><span class="s1">&#39;htm&#39;</span><span class="p">)</span>
+        <span class="p">)</span> <span class="ow">and</span> <span class="ow">not</span> <span class="n">response</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="sa">b</span><span class="s1">&#39;&lt;!DOCTYPE html&gt;&#39;</span><span class="p">):</span>
+
+            <span class="n">head_foot</span> <span class="o">=</span> <span class="p">[</span>
+                <span class="p">(</span>
+                    <span class="sa">b</span><span class="s1">&#39;&lt;!DOCTYPE html&gt;</span><span class="se">\n</span><span class="s1">&lt;html lang=&quot;en&quot;&gt;</span><span class="se">\n</span><span class="s1">&#39;</span>
+                    <span class="sa">b</span><span class="s1">&#39;&lt;head&gt;&lt;title&gt;</span><span class="si">%s</span><span class="s1">&lt;/title&gt;&lt;/head&gt;</span><span class="se">\n</span><span class="s1">&lt;body&gt;</span><span class="se">\n</span><span class="s1">&#39;</span>
+                <span class="p">),</span>
+                <span class="sa">b</span><span class="s1">&#39;&lt;/body&gt;</span><span class="se">\n</span><span class="s1">&lt;/html&gt;&#39;</span><span class="p">,</span>
+            <span class="p">]</span>
+
+            <span class="k">for</span> <span class="n">wwwroot</span> <span class="ow">in</span> <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">wwwroot</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">wwwbuiltin</span><span class="p">):</span>
+
+                <span class="k">for</span> <span class="n">i</span><span class="p">,</span> <span class="n">part</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">((</span><span class="s1">&#39;header&#39;</span><span class="p">,</span> <span class="s1">&#39;footer&#39;</span><span class="p">)):</span>
+
+                    <span class="n">path</span> <span class="o">=</span>  <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">wwwroot</span><span class="p">,</span> <span class="s1">&#39;_</span><span class="si">%s</span><span class="s1">.html&#39;</span> <span class="o">%</span> <span class="n">part</span><span class="p">)</span>
+
+                    <span class="k">if</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">exists</span><span class="p">(</span><span class="n">path</span><span class="p">):</span>
+
+                        <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">path</span><span class="p">,</span> <span class="s1">&#39;rb&#39;</span><span class="p">)</span> <span class="k">as</span> <span class="n">fp</span><span class="p">:</span>
+
+                            <span class="n">head_foot</span><span class="p">[</span><span class="n">i</span><span class="p">]</span> <span class="o">=</span> <span class="n">fp</span><span class="o">.</span><span class="n">read</span><span class="p">()</span>
+
+            <span class="k">if</span> <span class="sa">b</span><span class="s1">&#39;</span><span class="si">%s</span><span class="s1">&#39;</span> <span class="ow">in</span> <span class="n">head_foot</span><span class="p">[</span><span class="mi">0</span><span class="p">]:</span>
+
+                <span class="n">title</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">recomment</span><span class="o">.</span><span class="n">search</span><span class="p">(</span><span class="n">response</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span>
+                <span class="n">title</span> <span class="o">=</span> <span class="n">title</span><span class="o">.</span><span class="n">groups</span><span class="p">()[</span><span class="mi">0</span><span class="p">]</span> <span class="k">if</span> <span class="n">title</span> <span class="k">else</span> <span class="sa">b</span><span class="s1">&#39;pypath server&#39;</span>
+                <span class="n">head_foot</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">=</span> <span class="n">head_foot</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">%</span> <span class="n">title</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span>
+
+            <span class="n">response</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">=</span> <span class="n">head_foot</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">+</span> <span class="n">response</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">+</span> <span class="n">head_foot</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span>
+
+        <span class="k">return</span> <span class="n">response</span>
+
+
+    <span class="k">def</span> <span class="nf">about</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">req</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">welcome_message</span>
+
+
+    <span class="k">def</span> <span class="nf">info</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">req</span><span class="p">):</span>
+
+        <span class="k">if</span> <span class="p">(</span>
+            <span class="sa">b</span><span class="s1">&#39;format&#39;</span> <span class="ow">in</span> <span class="n">req</span><span class="o">.</span><span class="n">args</span> <span class="ow">and</span>
+            <span class="n">req</span><span class="o">.</span><span class="n">args</span><span class="p">[</span><span class="sa">b</span><span class="s1">&#39;format&#39;</span><span class="p">][</span><span class="mi">0</span><span class="p">]</span> <span class="o">==</span> <span class="sa">b</span><span class="s1">&#39;json&#39;</span> <span class="ow">and</span>
+            <span class="nb">hasattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">&#39;resources&#39;</span><span class="p">)</span>
+        <span class="p">):</span>
+
+            <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">resources</span><span class="p">(</span><span class="n">req</span><span class="p">)</span>
+
+        <span class="n">rc</span> <span class="o">=</span> <span class="n">resources</span><span class="o">.</span><span class="n">get_controller</span><span class="p">()</span>
+        <span class="n">rc</span><span class="o">.</span><span class="n">update</span><span class="p">()</span>
+
+        <span class="k">return</span> <span class="n">generate_about_page</span><span class="o">.</span><span class="n">generate_about_html</span><span class="p">(</span><span class="n">rc</span><span class="o">.</span><span class="n">data</span><span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">_root</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">req</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="n">_html</span><span class="o">.</span><span class="n">main_page</span><span class="p">()</span>
+
+
+    <span class="k">def</span> <span class="nf">_parse_arg</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">arg</span><span class="p">):</span>
+
+        <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">arg</span><span class="p">,</span> <span class="nb">list</span><span class="p">)</span> <span class="ow">and</span> <span class="n">arg</span><span class="p">:</span>
+            <span class="n">arg</span> <span class="o">=</span> <span class="n">arg</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span>
+        <span class="k">if</span> <span class="nb">hasattr</span><span class="p">(</span><span class="n">arg</span><span class="p">,</span> <span class="s1">&#39;decode&#39;</span><span class="p">):</span>
+            <span class="n">arg</span> <span class="o">=</span> <span class="n">arg</span><span class="o">.</span><span class="n">decode</span><span class="p">(</span><span class="s1">&#39;utf-8&#39;</span><span class="p">)</span>
+        <span class="k">if</span> <span class="nb">hasattr</span><span class="p">(</span><span class="n">arg</span><span class="p">,</span> <span class="s1">&#39;lower&#39;</span><span class="p">):</span>
+            <span class="n">arg</span> <span class="o">=</span> <span class="n">arg</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span>
+        <span class="k">if</span> <span class="nb">hasattr</span><span class="p">(</span><span class="n">arg</span><span class="p">,</span> <span class="s1">&#39;isdigit&#39;</span><span class="p">)</span> <span class="ow">and</span> <span class="n">arg</span><span class="o">.</span><span class="n">isdigit</span><span class="p">():</span>
+            <span class="n">arg</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">arg</span><span class="p">)</span>
+        <span class="k">if</span> <span class="n">arg</span> <span class="ow">in</span> <span class="n">_const</span><span class="o">.</span><span class="n">BOOLEAN_FALSE</span><span class="p">:</span>
+            <span class="n">arg</span> <span class="o">=</span> <span class="kc">False</span>
+        <span class="k">if</span> <span class="n">arg</span> <span class="ow">in</span> <span class="n">_const</span><span class="o">.</span><span class="n">BOOLEAN_TRUE</span><span class="p">:</span>
+            <span class="n">arg</span> <span class="o">=</span> <span class="kc">True</span>
+
+        <span class="k">return</span> <span class="nb">bool</span><span class="p">(</span><span class="n">arg</span><span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">_read_license_secret</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_license_secret</span> <span class="o">=</span> <span class="kc">None</span>
+
+        <span class="n">path</span> <span class="o">=</span> <span class="n">settings</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">&#39;license_secret&#39;</span><span class="p">)</span>
+
+        <span class="k">if</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">exists</span><span class="p">(</span><span class="n">path</span><span class="p">):</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span><span class="s1">&#39;Reading license unlocking secret from `</span><span class="si">%s</span><span class="s1">`.&#39;</span> <span class="o">%</span> <span class="n">path</span><span class="p">)</span>
+
+            <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">path</span><span class="p">,</span> <span class="s1">&#39;r&#39;</span><span class="p">)</span> <span class="k">as</span> <span class="n">fp</span><span class="p">:</span>
+
+                <span class="bp">self</span><span class="o">.</span><span class="n">_license_secret</span> <span class="o">=</span> <span class="n">fp</span><span class="o">.</span><span class="n">read</span><span class="p">()</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_default_license</span> <span class="o">=</span> <span class="p">[</span>
+            <span class="n">settings</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">&#39;server_default_license&#39;</span><span class="p">)</span><span class="o">.</span><span class="n">encode</span><span class="p">(</span><span class="s1">&#39;ascii&#39;</span><span class="p">)</span>
+        <span class="p">]</span>
+
+
+    <span class="k">def</span> <span class="nf">_error_page</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">req</span><span class="p">):</span>
+
+        <span class="n">req</span><span class="o">.</span><span class="n">setResponseCode</span><span class="p">(</span><span class="mi">500</span><span class="p">)</span>
+
+        <span class="k">return</span> <span class="n">_html</span><span class="o">.</span><span class="n">http_500</span><span class="p">()</span></div>
+
+
+
+<div class="viewcode-block" id="TableServer">
+<a class="viewcode-back" href="../../../../api/pypath.omnipath.server.run.TableServer.html#pypath.omnipath.server.run.TableServer">[docs]</a>
+<span class="k">class</span> <span class="nc">TableServer</span><span class="p">(</span><span class="n">BaseServer</span><span class="p">):</span>
+
+    <span class="n">query_types</span> <span class="o">=</span> <span class="p">{</span>
+        <span class="s1">&#39;annotations&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;intercell&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;interactions&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;enz_sub&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;enzsub&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;ptms&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;complexes&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;about&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;info&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;queries&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;annotations_summary&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;intercell_summary&#39;</span><span class="p">,</span>
+    <span class="p">}</span>
+    <span class="n">data_query_types</span> <span class="o">=</span> <span class="p">{</span>
+        <span class="s1">&#39;annotations&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;intercell&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;interactions&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;enzsub&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;complexes&#39;</span><span class="p">,</span>
+    <span class="p">}</span>
+    <span class="n">list_fields</span> <span class="o">=</span> <span class="p">{</span>
+        <span class="s1">&#39;sources&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;references&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;isoforms&#39;</span><span class="p">,</span>
+    <span class="p">}</span>
+
+    <span class="n">int_list_fields</span> <span class="o">=</span> <span class="p">{</span>
+        <span class="s1">&#39;references&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;isoforms&#39;</span><span class="p">,</span>
+    <span class="p">}</span>
+
+    <span class="n">field_synonyms</span> <span class="o">=</span> <span class="p">{</span>
+        <span class="s1">&#39;organism&#39;</span><span class="p">:</span> <span class="s1">&#39;ncbi_tax_id&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;tfregulons_level&#39;</span><span class="p">:</span> <span class="s1">&#39;dorothea_level&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;tfregulons_curated&#39;</span><span class="p">:</span> <span class="s1">&#39;dorothea_curated&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;tfregulons_chipseq&#39;</span><span class="p">:</span> <span class="s1">&#39;dorothea_chipseq&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;tfregulons_tfbs&#39;</span><span class="p">:</span> <span class="s1">&#39;dorothea_tfbs&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;tfregulons_coexp&#39;</span><span class="p">:</span> <span class="s1">&#39;dorothea_coexp&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;sources&#39;</span><span class="p">:</span> <span class="s1">&#39;resources&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;databases&#39;</span><span class="p">:</span> <span class="s1">&#39;resources&#39;</span><span class="p">,</span>
+    <span class="p">}</span>
+
+    <span class="n">args_reference</span> <span class="o">=</span> <span class="p">{</span>
+        <span class="s1">&#39;interactions&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;header&#39;</span><span class="p">:</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="s1">&#39;format&#39;</span><span class="p">:</span> <span class="p">{</span>
+                <span class="s1">&#39;json&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;tab&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;text&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;tsv&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;table&#39;</span>
+            <span class="p">},</span>
+            <span class="s1">&#39;license&#39;</span><span class="p">:</span> <span class="p">{</span>
+                <span class="s1">&#39;ignore&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;academic&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;non_profit&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;nonprofit&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;for_profit&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;forprofit&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;commercial&#39;</span><span class="p">,</span>
+            <span class="p">},</span>
+            <span class="s1">&#39;password&#39;</span><span class="p">:</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="s1">&#39;limit&#39;</span><span class="p">:</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="s1">&#39;datasets&#39;</span><span class="p">:</span> <span class="p">{</span>
+                <span class="s1">&#39;omnipath&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;tfregulons&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;dorothea&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;collectri&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;tf_target&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;tf_mirna&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;lncrna_mrna&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;kinaseextra&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;ligrecextra&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;pathwayextra&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;mirnatarget&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;small_molecule&#39;</span><span class="p">,</span>
+            <span class="p">},</span>
+            <span class="s1">&#39;types&#39;</span><span class="p">:</span> <span class="p">{</span>
+                <span class="s1">&#39;post_translational&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;transcriptional&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;post_transcriptional&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;mirna_transcriptional&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;lncrna_post_transcriptional&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;small_molecule_protein&#39;</span><span class="p">,</span>
+            <span class="p">},</span>
+            <span class="s1">&#39;sources&#39;</span><span class="p">:</span>  <span class="kc">None</span><span class="p">,</span>
+            <span class="s1">&#39;resources&#39;</span><span class="p">:</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="s1">&#39;databases&#39;</span><span class="p">:</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="s1">&#39;targets&#39;</span><span class="p">:</span>  <span class="kc">None</span><span class="p">,</span>
+            <span class="s1">&#39;partners&#39;</span><span class="p">:</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="s1">&#39;genesymbols&#39;</span><span class="p">:</span> <span class="n">_const</span><span class="o">.</span><span class="n">BOOLEAN_VALUES</span><span class="p">,</span>
+            <span class="s1">&#39;evidences&#39;</span><span class="p">:</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="s1">&#39;extra_attrs&#39;</span><span class="p">:</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="s1">&#39;fields&#39;</span><span class="p">:</span> <span class="p">{</span>
+                <span class="s1">&#39;entity_type&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;references&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;sources&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;tfregulons_level&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;tfregulons_curated&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;tfregulons_chipseq&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;tfregulons_tfbs&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;tfregulons_coexp&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;dorothea_level&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;dorothea_curated&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;dorothea_chipseq&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;dorothea_tfbs&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;dorothea_coexp&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;type&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;ncbi_tax_id&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;databases&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;resources&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;organism&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;curation_effort&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;datasets&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;extra_attrs&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;evidences&#39;</span><span class="p">,</span>
+            <span class="p">},</span>
+            <span class="s1">&#39;tfregulons_levels&#39;</span><span class="p">:</span>  <span class="p">{</span><span class="s1">&#39;A&#39;</span><span class="p">,</span> <span class="s1">&#39;B&#39;</span><span class="p">,</span> <span class="s1">&#39;C&#39;</span><span class="p">,</span> <span class="s1">&#39;D&#39;</span><span class="p">,</span> <span class="s1">&#39;E&#39;</span><span class="p">},</span>
+            <span class="s1">&#39;tfregulons_methods&#39;</span><span class="p">:</span> <span class="p">{</span>
+                <span class="s1">&#39;curated&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;chipseq&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;coexp&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;tfbs&#39;</span><span class="p">,</span>
+            <span class="p">},</span>
+            <span class="s1">&#39;dorothea_levels&#39;</span><span class="p">:</span>  <span class="p">{</span><span class="s1">&#39;A&#39;</span><span class="p">,</span> <span class="s1">&#39;B&#39;</span><span class="p">,</span> <span class="s1">&#39;C&#39;</span><span class="p">,</span> <span class="s1">&#39;D&#39;</span><span class="p">,</span> <span class="s1">&#39;E&#39;</span><span class="p">},</span>
+            <span class="s1">&#39;dorothea_methods&#39;</span><span class="p">:</span> <span class="p">{</span>
+                <span class="s1">&#39;curated&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;chipseq&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;coexp&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;tfbs&#39;</span><span class="p">,</span>
+            <span class="p">},</span>
+            <span class="s1">&#39;organisms&#39;</span><span class="p">:</span> <span class="p">{</span>
+                <span class="s1">&#39;9606&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;10090&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;10116&#39;</span><span class="p">,</span>
+            <span class="p">},</span>
+            <span class="s1">&#39;source_target&#39;</span><span class="p">:</span> <span class="p">{</span>
+                <span class="s1">&#39;AND&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;OR&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;and&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;or&#39;</span><span class="p">,</span>
+            <span class="p">},</span>
+            <span class="s1">&#39;directed&#39;</span><span class="p">:</span> <span class="n">_const</span><span class="o">.</span><span class="n">BOOLEAN_VALUES</span><span class="p">,</span>
+            <span class="s1">&#39;signed&#39;</span><span class="p">:</span> <span class="n">_const</span><span class="o">.</span><span class="n">BOOLEAN_VALUES</span><span class="p">,</span>
+            <span class="s1">&#39;loops&#39;</span><span class="p">:</span> <span class="n">_const</span><span class="o">.</span><span class="n">BOOLEAN_VALUES</span><span class="p">,</span>
+            <span class="s1">&#39;entity_types&#39;</span><span class="p">:</span> <span class="p">{</span>
+                <span class="s1">&#39;protein&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;complex&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;mirna&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;lncrna&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;small_molecule&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;drug&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;metabolite&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;lipid&#39;</span><span class="p">,</span>
+            <span class="p">},</span>
+        <span class="p">},</span>
+        <span class="s1">&#39;enzsub&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;header&#39;</span><span class="p">:</span>      <span class="kc">None</span><span class="p">,</span>
+            <span class="s1">&#39;format&#39;</span><span class="p">:</span> <span class="p">{</span>
+                <span class="s1">&#39;json&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;tab&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;text&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;tsv&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;table&#39;</span><span class="p">,</span>
+            <span class="p">},</span>
+            <span class="s1">&#39;license&#39;</span><span class="p">:</span> <span class="p">{</span>
+                <span class="s1">&#39;ignore&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;academic&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;non_profit&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;nonprofit&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;for_profit&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;forprofit&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;commercial&#39;</span><span class="p">,</span>
+            <span class="p">},</span>
+            <span class="s1">&#39;password&#39;</span><span class="p">:</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="s1">&#39;limit&#39;</span><span class="p">:</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="s1">&#39;enzymes&#39;</span><span class="p">:</span>     <span class="kc">None</span><span class="p">,</span>
+            <span class="s1">&#39;substrates&#39;</span><span class="p">:</span>  <span class="kc">None</span><span class="p">,</span>
+            <span class="s1">&#39;partners&#39;</span><span class="p">:</span>    <span class="kc">None</span><span class="p">,</span>
+            <span class="s1">&#39;genesymbols&#39;</span><span class="p">:</span> <span class="n">_const</span><span class="o">.</span><span class="n">BOOLEAN_VALUES</span><span class="p">,</span>
+            <span class="s1">&#39;organisms&#39;</span><span class="p">:</span> <span class="p">{</span>
+                <span class="s1">&#39;9606&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;10090&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;10116&#39;</span><span class="p">,</span>
+            <span class="p">},</span>
+            <span class="s1">&#39;databases&#39;</span><span class="p">:</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="s1">&#39;resources&#39;</span><span class="p">:</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="s1">&#39;residues&#39;</span><span class="p">:</span>  <span class="kc">None</span><span class="p">,</span>
+            <span class="s1">&#39;modification&#39;</span><span class="p">:</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="s1">&#39;types&#39;</span><span class="p">:</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="s1">&#39;fields&#39;</span><span class="p">:</span> <span class="p">{</span>
+                <span class="s1">&#39;sources&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;references&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;ncbi_tax_id&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;organism&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;databases&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;resources&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;isoforms&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;curation_effort&#39;</span><span class="p">,</span>
+            <span class="p">},</span>
+            <span class="s1">&#39;enzyme_substrate&#39;</span><span class="p">:</span> <span class="p">{</span>
+                <span class="s1">&#39;AND&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;OR&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;and&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;or&#39;</span><span class="p">,</span>
+            <span class="p">}</span>
+        <span class="p">},</span>
+        <span class="s1">&#39;annotations&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;header&#39;</span><span class="p">:</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="s1">&#39;format&#39;</span><span class="p">:</span> <span class="p">{</span>
+                <span class="s1">&#39;json&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;tab&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;text&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;tsv&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;table&#39;</span><span class="p">,</span>
+            <span class="p">},</span>
+            <span class="s1">&#39;license&#39;</span><span class="p">:</span> <span class="p">{</span>
+                <span class="s1">&#39;ignore&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;academic&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;non_profit&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;nonprofit&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;for_profit&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;forprofit&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;commercial&#39;</span><span class="p">,</span>
+            <span class="p">},</span>
+            <span class="s1">&#39;password&#39;</span><span class="p">:</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="s1">&#39;limit&#39;</span><span class="p">:</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="s1">&#39;databases&#39;</span><span class="p">:</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="s1">&#39;resources&#39;</span><span class="p">:</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="s1">&#39;proteins&#39;</span><span class="p">:</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="s1">&#39;fields&#39;</span><span class="p">:</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="s1">&#39;genesymbols&#39;</span><span class="p">:</span> <span class="n">_const</span><span class="o">.</span><span class="n">BOOLEAN_VALUES</span><span class="p">,</span>
+            <span class="s1">&#39;entity_types&#39;</span><span class="p">:</span> <span class="p">{</span>
+                <span class="s1">&#39;protein&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;complex&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;mirna&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;lncrna&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;small_molecule&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;drug&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;metabolite&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;lipid&#39;</span><span class="p">,</span>
+            <span class="p">},</span>
+        <span class="p">},</span>
+        <span class="s1">&#39;annotations_summary&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;header&#39;</span><span class="p">:</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="s1">&#39;format&#39;</span><span class="p">:</span> <span class="p">{</span>
+                <span class="s1">&#39;json&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;tab&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;text&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;tsv&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;table&#39;</span><span class="p">,</span>
+            <span class="p">},</span>
+            <span class="s1">&#39;databases&#39;</span><span class="p">:</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="s1">&#39;resources&#39;</span><span class="p">:</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="s1">&#39;fields&#39;</span><span class="p">:</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="s1">&#39;cytoscape&#39;</span><span class="p">:</span> <span class="n">_const</span><span class="o">.</span><span class="n">BOOLEAN_VALUES</span><span class="p">,</span>
+        <span class="p">},</span>
+        <span class="s1">&#39;intercell&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;header&#39;</span><span class="p">:</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="s1">&#39;format&#39;</span><span class="p">:</span> <span class="p">{</span>
+                <span class="s1">&#39;json&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;tab&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;text&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;tsv&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;table&#39;</span><span class="p">,</span>
+            <span class="p">},</span>
+            <span class="s1">&#39;license&#39;</span><span class="p">:</span> <span class="p">{</span>
+                <span class="s1">&#39;ignore&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;academic&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;non_profit&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;nonprofit&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;for_profit&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;forprofit&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;commercial&#39;</span><span class="p">,</span>
+            <span class="p">},</span>
+            <span class="s1">&#39;password&#39;</span><span class="p">:</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="s1">&#39;limit&#39;</span><span class="p">:</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="s1">&#39;scope&#39;</span><span class="p">:</span> <span class="p">{</span>
+                <span class="s1">&#39;specific&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;generic&#39;</span><span class="p">,</span>
+            <span class="p">},</span>
+            <span class="s1">&#39;aspect&#39;</span><span class="p">:</span> <span class="p">{</span>
+                <span class="s1">&#39;functional&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;locational&#39;</span><span class="p">,</span>
+            <span class="p">},</span>
+            <span class="s1">&#39;source&#39;</span><span class="p">:</span> <span class="p">{</span>
+                <span class="s1">&#39;resource_specific&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;composite&#39;</span><span class="p">,</span>
+            <span class="p">},</span>
+            <span class="s1">&#39;categories&#39;</span><span class="p">:</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="s1">&#39;databases&#39;</span><span class="p">:</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="s1">&#39;resources&#39;</span><span class="p">:</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="s1">&#39;parent&#39;</span><span class="p">:</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="s1">&#39;proteins&#39;</span><span class="p">:</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="s1">&#39;fields&#39;</span><span class="p">:</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="s1">&#39;entity_types&#39;</span><span class="p">:</span> <span class="p">{</span>
+                <span class="s1">&#39;protein&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;complex&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;mirna&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;lncrna&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;small_molecule&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;drug&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;metabolite&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;lipid&#39;</span><span class="p">,</span>
+            <span class="p">},</span>
+            <span class="s1">&#39;transmitter&#39;</span><span class="p">:</span> <span class="n">_const</span><span class="o">.</span><span class="n">BOOLEAN_VALUES</span><span class="p">,</span>
+            <span class="s1">&#39;receiver&#39;</span><span class="p">:</span> <span class="n">_const</span><span class="o">.</span><span class="n">BOOLEAN_VALUES</span><span class="p">,</span>
+            <span class="s1">&#39;trans&#39;</span><span class="p">:</span> <span class="n">_const</span><span class="o">.</span><span class="n">BOOLEAN_VALUES</span><span class="p">,</span>
+            <span class="s1">&#39;rec&#39;</span><span class="p">:</span> <span class="n">_const</span><span class="o">.</span><span class="n">BOOLEAN_VALUES</span><span class="p">,</span>
+            <span class="s1">&#39;secreted&#39;</span><span class="p">:</span> <span class="n">_const</span><span class="o">.</span><span class="n">BOOLEAN_VALUES</span><span class="p">,</span>
+            <span class="s1">&#39;plasma_membrane_peripheral&#39;</span><span class="p">:</span> <span class="n">_const</span><span class="o">.</span><span class="n">BOOLEAN_VALUES</span><span class="p">,</span>
+            <span class="s1">&#39;plasma_membrane_transmembrane&#39;</span><span class="p">:</span> <span class="n">_const</span><span class="o">.</span><span class="n">BOOLEAN_VALUES</span><span class="p">,</span>
+            <span class="s1">&#39;sec&#39;</span><span class="p">:</span> <span class="n">_const</span><span class="o">.</span><span class="n">BOOLEAN_VALUES</span><span class="p">,</span>
+            <span class="s1">&#39;pmp&#39;</span><span class="p">:</span> <span class="n">_const</span><span class="o">.</span><span class="n">BOOLEAN_VALUES</span><span class="p">,</span>
+            <span class="s1">&#39;pmtm&#39;</span><span class="p">:</span> <span class="n">_const</span><span class="o">.</span><span class="n">BOOLEAN_VALUES</span><span class="p">,</span>
+            <span class="s1">&#39;causality&#39;</span><span class="p">:</span> <span class="p">{</span>
+                <span class="s1">&#39;transmitter&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;trans&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;receiver&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;rec&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;both&#39;</span>
+            <span class="p">},</span>
+            <span class="s1">&#39;topology&#39;</span><span class="p">:</span> <span class="p">{</span>
+                <span class="s1">&#39;secreted&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;sec&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;plasma_membrane_peripheral&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;pmp&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;plasma_membrane_transmembrane&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;pmtm&#39;</span><span class="p">,</span>
+            <span class="p">},</span>
+        <span class="p">},</span>
+        <span class="s1">&#39;intercell_summary&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;header&#39;</span><span class="p">:</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="s1">&#39;format&#39;</span><span class="p">:</span> <span class="p">{</span>
+                <span class="s1">&#39;json&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;tab&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;text&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;tsv&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;table&#39;</span><span class="p">,</span>
+            <span class="p">},</span>
+            <span class="s1">&#39;scope&#39;</span><span class="p">:</span> <span class="p">{</span>
+                <span class="s1">&#39;specific&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;generic&#39;</span><span class="p">,</span>
+            <span class="p">},</span>
+            <span class="s1">&#39;aspect&#39;</span><span class="p">:</span> <span class="p">{</span>
+                <span class="s1">&#39;functional&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;locational&#39;</span><span class="p">,</span>
+            <span class="p">},</span>
+            <span class="s1">&#39;source&#39;</span><span class="p">:</span> <span class="p">{</span>
+                <span class="s1">&#39;resource_specific&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;generic&#39;</span><span class="p">,</span>
+            <span class="p">},</span>
+            <span class="s1">&#39;categories&#39;</span><span class="p">:</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="s1">&#39;resources&#39;</span><span class="p">:</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="s1">&#39;databases&#39;</span><span class="p">:</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="s1">&#39;parent&#39;</span><span class="p">:</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="s1">&#39;fields&#39;</span><span class="p">:</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="s1">&#39;transmitter&#39;</span><span class="p">:</span> <span class="n">_const</span><span class="o">.</span><span class="n">BOOLEAN_VALUES</span><span class="p">,</span>
+            <span class="s1">&#39;receiver&#39;</span><span class="p">:</span> <span class="n">_const</span><span class="o">.</span><span class="n">BOOLEAN_VALUES</span><span class="p">,</span>
+            <span class="s1">&#39;trans&#39;</span><span class="p">:</span> <span class="n">_const</span><span class="o">.</span><span class="n">BOOLEAN_VALUES</span><span class="p">,</span>
+            <span class="s1">&#39;rec&#39;</span><span class="p">:</span> <span class="n">_const</span><span class="o">.</span><span class="n">BOOLEAN_VALUES</span><span class="p">,</span>
+            <span class="s1">&#39;secreted&#39;</span><span class="p">:</span> <span class="n">_const</span><span class="o">.</span><span class="n">BOOLEAN_VALUES</span><span class="p">,</span>
+            <span class="s1">&#39;plasma_membrane_peripheral&#39;</span><span class="p">:</span> <span class="n">_const</span><span class="o">.</span><span class="n">BOOLEAN_VALUES</span><span class="p">,</span>
+            <span class="s1">&#39;plasma_membrane_transmembrane&#39;</span><span class="p">:</span> <span class="n">_const</span><span class="o">.</span><span class="n">BOOLEAN_VALUES</span><span class="p">,</span>
+            <span class="s1">&#39;sec&#39;</span><span class="p">:</span> <span class="n">_const</span><span class="o">.</span><span class="n">BOOLEAN_VALUES</span><span class="p">,</span>
+            <span class="s1">&#39;pmp&#39;</span><span class="p">:</span> <span class="n">_const</span><span class="o">.</span><span class="n">BOOLEAN_VALUES</span><span class="p">,</span>
+            <span class="s1">&#39;pmtm&#39;</span><span class="p">:</span> <span class="n">_const</span><span class="o">.</span><span class="n">BOOLEAN_VALUES</span><span class="p">,</span>
+        <span class="p">},</span>
+        <span class="s1">&#39;complexes&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;header&#39;</span><span class="p">:</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="s1">&#39;format&#39;</span><span class="p">:</span> <span class="p">{</span>
+                <span class="s1">&#39;json&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;tab&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;text&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;tsv&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;table&#39;</span><span class="p">,</span>
+            <span class="p">},</span>
+            <span class="s1">&#39;license&#39;</span><span class="p">:</span> <span class="p">{</span>
+                <span class="s1">&#39;ignore&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;academic&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;non_profit&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;nonprofit&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;for_profit&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;forprofit&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;commercial&#39;</span><span class="p">,</span>
+            <span class="p">},</span>
+            <span class="s1">&#39;password&#39;</span><span class="p">:</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="s1">&#39;limit&#39;</span><span class="p">:</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="s1">&#39;databases&#39;</span><span class="p">:</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="s1">&#39;resources&#39;</span><span class="p">:</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="s1">&#39;proteins&#39;</span><span class="p">:</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="s1">&#39;fields&#39;</span><span class="p">:</span> <span class="kc">None</span><span class="p">,</span>
+        <span class="p">},</span>
+        <span class="s1">&#39;resources&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;license&#39;</span><span class="p">:</span> <span class="p">{</span>
+                <span class="s1">&#39;ignore&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;academic&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;non_profit&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;nonprofit&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;for_profit&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;forprofit&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;commercial&#39;</span><span class="p">,</span>
+            <span class="p">},</span>
+            <span class="s1">&#39;format&#39;</span><span class="p">:</span> <span class="p">{</span>
+                <span class="s1">&#39;json&#39;</span><span class="p">,</span>
+            <span class="p">},</span>
+            <span class="s1">&#39;datasets&#39;</span><span class="p">:</span> <span class="p">{</span>
+                <span class="s1">&#39;interactions&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;interaction&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;network&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;enzsub&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;enz_sub&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;enzyme-substrate&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;annotations&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;annotation&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;annot&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;intercell&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;complex&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;complexes&#39;</span><span class="p">,</span>
+            <span class="p">},</span>
+            <span class="s1">&#39;subtypes&#39;</span><span class="p">:</span> <span class="kc">None</span><span class="p">,</span>
+        <span class="p">},</span>
+        <span class="s1">&#39;queries&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;format&#39;</span><span class="p">:</span> <span class="p">{</span>
+                <span class="s1">&#39;tab&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;text&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;tsv&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;table&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;json&#39;</span><span class="p">,</span>
+            <span class="p">},</span>
+        <span class="p">},</span>
+    <span class="p">}</span>
+
+
+    <span class="n">query_type_synonyms</span> <span class="o">=</span> <span class="p">{</span>
+        <span class="s1">&#39;interactions&#39;</span><span class="p">:</span> <span class="s1">&#39;interactions&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;interaction&#39;</span><span class="p">:</span> <span class="s1">&#39;interactions&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;network&#39;</span><span class="p">:</span> <span class="s1">&#39;interactions&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;enz_sub&#39;</span><span class="p">:</span> <span class="s1">&#39;enzsub&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;enz-sub&#39;</span><span class="p">:</span> <span class="s1">&#39;enzsub&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;ptms&#39;</span><span class="p">:</span> <span class="s1">&#39;enzsub&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;ptm&#39;</span><span class="p">:</span> <span class="s1">&#39;enzsub&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;enzyme-substrate&#39;</span><span class="p">:</span> <span class="s1">&#39;enzsub&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;enzyme_substrate&#39;</span><span class="p">:</span> <span class="s1">&#39;enzsub&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;annotations&#39;</span><span class="p">:</span> <span class="s1">&#39;annotations&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;annotation&#39;</span><span class="p">:</span> <span class="s1">&#39;annotations&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;annot&#39;</span><span class="p">:</span> <span class="s1">&#39;annotations&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;intercell&#39;</span><span class="p">:</span> <span class="s1">&#39;intercell&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;intercellular&#39;</span><span class="p">:</span> <span class="s1">&#39;intercell&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;inter_cell&#39;</span><span class="p">:</span> <span class="s1">&#39;intercell&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;inter-cell&#39;</span><span class="p">:</span> <span class="s1">&#39;intercell&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;complex&#39;</span><span class="p">:</span> <span class="s1">&#39;complexes&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;complexes&#39;</span><span class="p">:</span> <span class="s1">&#39;complexes&#39;</span><span class="p">,</span>
+    <span class="p">}</span>
+    <span class="n">datasets_</span> <span class="o">=</span> <span class="p">{</span>
+        <span class="s1">&#39;omnipath&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;tfregulons&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;dorothea&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;collectri&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;tf_target&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;kinaseextra&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;ligrecextra&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;pathwayextra&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;mirnatarget&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;tf_mirna&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;lncrna_mrna&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;small_molecule&#39;</span><span class="p">,</span>
+    <span class="p">}</span>
+    <span class="n">dorothea_methods</span> <span class="o">=</span> <span class="p">{</span><span class="s1">&#39;curated&#39;</span><span class="p">,</span> <span class="s1">&#39;coexp&#39;</span><span class="p">,</span> <span class="s1">&#39;chipseq&#39;</span><span class="p">,</span> <span class="s1">&#39;tfbs&#39;</span><span class="p">}</span>
+    <span class="n">dataset2type</span> <span class="o">=</span> <span class="p">{</span>
+        <span class="s1">&#39;omnipath&#39;</span><span class="p">:</span> <span class="s1">&#39;post_translational&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;tfregulons&#39;</span><span class="p">:</span> <span class="s1">&#39;transcriptional&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;dorothea&#39;</span><span class="p">:</span> <span class="s1">&#39;transcriptional&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;collectri&#39;</span><span class="p">:</span> <span class="s1">&#39;transcriptional&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;tf_target&#39;</span><span class="p">:</span> <span class="s1">&#39;transcriptional&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;kinaseextra&#39;</span><span class="p">:</span> <span class="s1">&#39;post_translational&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;ligrecextra&#39;</span><span class="p">:</span> <span class="s1">&#39;post_translational&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;pathwayextra&#39;</span><span class="p">:</span> <span class="s1">&#39;post_translational&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;mirnatarget&#39;</span><span class="p">:</span> <span class="s1">&#39;post_transcriptional&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;tf_mirna&#39;</span><span class="p">:</span> <span class="s1">&#39;mirna_transcriptional&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;lncrna_mrna&#39;</span><span class="p">:</span> <span class="s1">&#39;lncrna_post_transcriptional&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;small_molecule&#39;</span><span class="p">:</span> <span class="s1">&#39;small_molecule_protein&#39;</span><span class="p">,</span>
+    <span class="p">}</span>
+    <span class="n">interaction_fields</span> <span class="o">=</span> <span class="p">{</span>
+        <span class="s1">&#39;references&#39;</span><span class="p">,</span> <span class="s1">&#39;sources&#39;</span><span class="p">,</span> <span class="s1">&#39;dorothea_level&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;dorothea_curated&#39;</span><span class="p">,</span> <span class="s1">&#39;dorothea_chipseq&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;dorothea_tfbs&#39;</span><span class="p">,</span> <span class="s1">&#39;dorothea_coexp&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;tfregulons_level&#39;</span><span class="p">,</span> <span class="s1">&#39;tfregulons_curated&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;tfregulons_chipseq&#39;</span><span class="p">,</span> <span class="s1">&#39;tfregulons_tfbs&#39;</span><span class="p">,</span> <span class="s1">&#39;tfregulons_coexp&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;type&#39;</span><span class="p">,</span> <span class="s1">&#39;ncbi_tax_id&#39;</span><span class="p">,</span> <span class="s1">&#39;databases&#39;</span><span class="p">,</span> <span class="s1">&#39;organism&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;curation_effort&#39;</span><span class="p">,</span> <span class="s1">&#39;resources&#39;</span><span class="p">,</span> <span class="s1">&#39;entity_type&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;datasets&#39;</span><span class="p">,</span> <span class="s1">&#39;extra_attrs&#39;</span><span class="p">,</span> <span class="s1">&#39;evidences&#39;</span><span class="p">,</span>
+    <span class="p">}</span>
+    <span class="n">enzsub_fields</span> <span class="o">=</span> <span class="p">{</span>
+        <span class="s1">&#39;references&#39;</span><span class="p">,</span> <span class="s1">&#39;sources&#39;</span><span class="p">,</span> <span class="s1">&#39;databases&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;isoforms&#39;</span><span class="p">,</span> <span class="s1">&#39;organism&#39;</span><span class="p">,</span> <span class="s1">&#39;ncbi_tax_id&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;curation_effort&#39;</span><span class="p">,</span> <span class="s1">&#39;resources&#39;</span><span class="p">,</span>
+    <span class="p">}</span>
+    <span class="n">default_input_files</span> <span class="o">=</span> <span class="p">{</span>
+        <span class="s1">&#39;interactions&#39;</span><span class="p">:</span> <span class="s1">&#39;omnipath_webservice_interactions.tsv&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;enzsub&#39;</span><span class="p">:</span> <span class="s1">&#39;omnipath_webservice_enz_sub.tsv&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;annotations&#39;</span><span class="p">:</span> <span class="s1">&#39;omnipath_webservice_annotations.tsv&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;complexes&#39;</span><span class="p">:</span> <span class="s1">&#39;omnipath_webservice_complexes.tsv&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;intercell&#39;</span><span class="p">:</span> <span class="s1">&#39;omnipath_webservice_intercell.tsv&#39;</span><span class="p">,</span>
+    <span class="p">}</span>
+    <span class="n">default_dtypes</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">defaultdict</span><span class="p">(</span>
+        <span class="nb">dict</span><span class="p">,</span>
+        <span class="n">interactions</span> <span class="o">=</span> <span class="p">{</span>
+            <span class="s1">&#39;source&#39;</span><span class="p">:</span> <span class="s1">&#39;category&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;target&#39;</span><span class="p">:</span> <span class="s1">&#39;category&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;source_genesymbol&#39;</span><span class="p">:</span> <span class="s1">&#39;category&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;target_genesymbol&#39;</span><span class="p">:</span> <span class="s1">&#39;category&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;is_directed&#39;</span><span class="p">:</span> <span class="s1">&#39;int8&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;is_stimulation&#39;</span><span class="p">:</span> <span class="s1">&#39;int8&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;is_inhibition&#39;</span><span class="p">:</span> <span class="s1">&#39;int8&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;consensus_direction&#39;</span><span class="p">:</span> <span class="s1">&#39;int8&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;consensus_stimulation&#39;</span><span class="p">:</span> <span class="s1">&#39;int8&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;consensus_inhibition&#39;</span><span class="p">:</span> <span class="s1">&#39;int8&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;sources&#39;</span><span class="p">:</span> <span class="s1">&#39;category&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;references&#39;</span><span class="p">:</span> <span class="s1">&#39;category&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;dorothea_curated&#39;</span><span class="p">:</span> <span class="s1">&#39;category&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;dorothea_chipseq&#39;</span><span class="p">:</span> <span class="s1">&#39;category&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;dorothea_tfbs&#39;</span><span class="p">:</span> <span class="s1">&#39;category&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;dorothea_coexp&#39;</span><span class="p">:</span> <span class="s1">&#39;category&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;dorothea_level&#39;</span><span class="p">:</span> <span class="s1">&#39;category&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;type&#39;</span><span class="p">:</span> <span class="s1">&#39;category&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;ncbi_tax_id_source&#39;</span><span class="p">:</span> <span class="s1">&#39;int16&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;ncbi_tax_id_target&#39;</span><span class="p">:</span> <span class="s1">&#39;int16&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;entity_type_source&#39;</span><span class="p">:</span> <span class="s1">&#39;category&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;entity_type_target&#39;</span><span class="p">:</span> <span class="s1">&#39;category&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;curation_effort&#39;</span><span class="p">:</span> <span class="s1">&#39;int16&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;extra_attrs&#39;</span><span class="p">:</span> <span class="s1">&#39;category&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;evidences&#39;</span><span class="p">:</span> <span class="s1">&#39;category&#39;</span><span class="p">,</span>
+        <span class="p">},</span>
+        <span class="n">annotations</span> <span class="o">=</span> <span class="p">{</span>
+            <span class="s1">&#39;uniprot&#39;</span><span class="p">:</span> <span class="s1">&#39;category&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;genesymbol&#39;</span><span class="p">:</span> <span class="s1">&#39;category&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;entity_type&#39;</span><span class="p">:</span> <span class="s1">&#39;category&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;source&#39;</span><span class="p">:</span> <span class="s1">&#39;category&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;label&#39;</span><span class="p">:</span> <span class="s1">&#39;category&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;value&#39;</span><span class="p">:</span> <span class="s1">&#39;category&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;record_id&#39;</span><span class="p">:</span> <span class="s1">&#39;uint32&#39;</span><span class="p">,</span>
+        <span class="p">},</span>
+        <span class="n">enzsub</span> <span class="o">=</span> <span class="p">{</span>
+            <span class="s1">&#39;enzyme&#39;</span><span class="p">:</span> <span class="s1">&#39;category&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;substrate&#39;</span><span class="p">:</span> <span class="s1">&#39;category&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;enzyme_genesymbol&#39;</span><span class="p">:</span> <span class="s1">&#39;category&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;substrate_genesymbol&#39;</span><span class="p">:</span> <span class="s1">&#39;category&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;isoforms&#39;</span><span class="p">:</span> <span class="s1">&#39;category&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;residue_type&#39;</span><span class="p">:</span> <span class="s1">&#39;category&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;residue_offset&#39;</span><span class="p">:</span> <span class="s1">&#39;uint16&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;modification&#39;</span><span class="p">:</span> <span class="s1">&#39;category&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;sources&#39;</span><span class="p">:</span> <span class="s1">&#39;category&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;references&#39;</span><span class="p">:</span> <span class="s1">&#39;category&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;ncbi_tax_id&#39;</span><span class="p">:</span> <span class="s1">&#39;int16&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;curation_effort&#39;</span><span class="p">:</span> <span class="s1">&#39;int32&#39;</span><span class="p">,</span>
+        <span class="p">},</span>
+        <span class="n">complexes</span> <span class="o">=</span> <span class="p">{</span>
+            <span class="s1">&#39;name&#39;</span><span class="p">:</span> <span class="s1">&#39;category&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;stoichiometry&#39;</span><span class="p">:</span> <span class="s1">&#39;category&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;sources&#39;</span><span class="p">:</span> <span class="s1">&#39;category&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;references&#39;</span><span class="p">:</span> <span class="s1">&#39;category&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;identifiers&#39;</span><span class="p">:</span> <span class="s1">&#39;category&#39;</span><span class="p">,</span>
+        <span class="p">},</span>
+        <span class="n">intercell</span> <span class="o">=</span> <span class="p">{</span>
+            <span class="s1">&#39;category&#39;</span><span class="p">:</span> <span class="s1">&#39;category&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;database&#39;</span><span class="p">:</span> <span class="s1">&#39;category&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;uniprot&#39;</span><span class="p">:</span> <span class="s1">&#39;category&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;genesymbol&#39;</span><span class="p">:</span> <span class="s1">&#39;category&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;parent&#39;</span><span class="p">:</span> <span class="s1">&#39;category&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;aspect&#39;</span><span class="p">:</span> <span class="s1">&#39;category&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;scope&#39;</span><span class="p">:</span> <span class="s1">&#39;category&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;source&#39;</span><span class="p">:</span> <span class="s1">&#39;category&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;entity_type&#39;</span><span class="p">:</span> <span class="s1">&#39;category&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;consensus_score&#39;</span><span class="p">:</span> <span class="s1">&#39;uint16&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;transmitter&#39;</span><span class="p">:</span> <span class="s1">&#39;bool&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;receiver&#39;</span><span class="p">:</span> <span class="s1">&#39;bool&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;secreted&#39;</span><span class="p">:</span> <span class="s1">&#39;bool&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;plasma_membrane_transmembrane&#39;</span><span class="p">:</span> <span class="s1">&#39;bool&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;plasma_membrane_peripheral&#39;</span><span class="p">:</span> <span class="s1">&#39;bool&#39;</span><span class="p">,</span>
+        <span class="p">}</span>
+    <span class="p">)</span>
+
+    <span class="c1"># the annotation attributes served for the cytoscape app</span>
+    <span class="n">cytoscape_attributes</span> <span class="o">=</span> <span class="p">{</span>
+        <span class="p">(</span><span class="s1">&#39;Zhong2015&#39;</span><span class="p">,</span> <span class="s1">&#39;type&#39;</span><span class="p">),</span>
+        <span class="p">(</span><span class="s1">&#39;MatrixDB&#39;</span><span class="p">,</span> <span class="s1">&#39;mainclass&#39;</span><span class="p">),</span>
+        <span class="p">(</span><span class="s1">&#39;Matrisome&#39;</span><span class="p">,</span> <span class="p">(</span><span class="s1">&#39;mainclass&#39;</span><span class="p">,</span> <span class="s1">&#39;subclass&#39;</span><span class="p">,</span> <span class="s1">&#39;subsubclass&#39;</span><span class="p">)),</span>
+        <span class="c1"># (&#39;TFcensus&#39;, &#39;in TFcensus&#39;),</span>
+        <span class="p">(</span><span class="s1">&#39;Locate&#39;</span><span class="p">,</span> <span class="p">(</span><span class="s1">&#39;location&#39;</span><span class="p">,</span> <span class="s1">&#39;cls&#39;</span><span class="p">)),</span>
+        <span class="p">(</span>
+            <span class="s1">&#39;Phosphatome&#39;</span><span class="p">,</span>
+            <span class="p">(</span>
+                <span class="s1">&#39;family&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;subfamily&#39;</span><span class="p">,</span>
+                <span class="c1">#&#39;has_protein_substrates&#39;,</span>
+            <span class="p">)</span>
+        <span class="p">),</span>
+        <span class="p">(</span><span class="s1">&#39;CancerSEA&#39;</span><span class="p">,</span> <span class="s1">&#39;state&#39;</span><span class="p">),</span>
+        <span class="p">(</span><span class="s1">&#39;GO_Intercell&#39;</span><span class="p">,</span> <span class="s1">&#39;mainclass&#39;</span><span class="p">),</span>
+        <span class="p">(</span><span class="s1">&#39;Adhesome&#39;</span><span class="p">,</span> <span class="s1">&#39;mainclass&#39;</span><span class="p">),</span>
+        <span class="p">(</span><span class="s1">&#39;SignaLink3&#39;</span><span class="p">,</span> <span class="s1">&#39;pathway&#39;</span><span class="p">),</span>
+        <span class="p">(</span>
+            <span class="s1">&#39;HPA_secretome&#39;</span><span class="p">,</span>
+            <span class="p">(</span>
+                <span class="s1">&#39;mainclass&#39;</span><span class="p">,</span>
+                <span class="c1">#&#39;secreted&#39;,</span>
+            <span class="p">)</span>
+        <span class="p">),</span>
+        <span class="p">(</span>
+            <span class="s1">&#39;OPM&#39;</span><span class="p">,</span>
+            <span class="p">(</span>
+                <span class="s1">&#39;membrane&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;family&#39;</span><span class="p">,</span>
+                <span class="c1">#&#39;transmembrane&#39;,</span>
+            <span class="p">)</span>
+        <span class="p">),</span>
+        <span class="p">(</span><span class="s1">&#39;KEGG&#39;</span><span class="p">,</span> <span class="s1">&#39;pathway&#39;</span><span class="p">),</span>
+        <span class="c1">#(</span>
+            <span class="c1">#&#39;CellPhoneDB&#39;,</span>
+            <span class="c1">#(</span>
+                <span class="c1">## &#39;receptor&#39;,</span>
+                <span class="c1">## &#39;peripheral&#39;,</span>
+                <span class="c1">## &#39;secreted&#39;,</span>
+                <span class="c1">## &#39;transmembrane&#39;,</span>
+                <span class="c1">## &#39;receptor_class&#39;,</span>
+                <span class="c1">## &#39;secreted_class&#39;,</span>
+            <span class="c1">#)</span>
+        <span class="c1">#),</span>
+        <span class="p">(</span><span class="s1">&#39;kinase.com&#39;</span><span class="p">,</span> <span class="p">(</span><span class="s1">&#39;group&#39;</span><span class="p">,</span> <span class="s1">&#39;family&#39;</span><span class="p">,</span> <span class="s1">&#39;subfamily&#39;</span><span class="p">)),</span>
+        <span class="p">(</span><span class="s1">&#39;Membranome&#39;</span><span class="p">,</span> <span class="p">(</span><span class="s1">&#39;membrane&#39;</span><span class="p">,)),</span>
+        <span class="c1">#(&#39;CSPA&#39;, &#39;in CSPA&#39;),</span>
+        <span class="c1">#(&#39;MSigDB&#39;, &#39;geneset&#39;),</span>
+        <span class="c1">#(&#39;Integrins&#39;, &#39;in Integrins&#39;),</span>
+        <span class="p">(</span><span class="s1">&#39;HGNC&#39;</span><span class="p">,</span> <span class="s1">&#39;mainclass&#39;</span><span class="p">),</span>
+        <span class="p">(</span><span class="s1">&#39;CPAD&#39;</span><span class="p">,</span> <span class="p">(</span><span class="s1">&#39;pathway&#39;</span><span class="p">,</span> <span class="s1">&#39;effect_on_cancer&#39;</span><span class="p">,</span> <span class="s1">&#39;cancer&#39;</span><span class="p">,</span> <span class="p">)),</span>
+        <span class="p">(</span><span class="s1">&#39;Signor&#39;</span><span class="p">,</span> <span class="s1">&#39;pathway&#39;</span><span class="p">),</span>
+        <span class="p">(</span><span class="s1">&#39;Ramilowski2015&#39;</span><span class="p">,</span> <span class="s1">&#39;mainclass&#39;</span><span class="p">),</span>
+        <span class="p">(</span><span class="s1">&#39;HPA_subcellular&#39;</span><span class="p">,</span> <span class="s1">&#39;location&#39;</span><span class="p">),</span>
+        <span class="c1">#(&#39;DisGeNet&#39;, &#39;disease&#39;),</span>
+        <span class="p">(</span><span class="s1">&#39;Surfaceome&#39;</span><span class="p">,</span> <span class="p">(</span><span class="s1">&#39;mainclass&#39;</span><span class="p">,</span> <span class="s1">&#39;subclasses&#39;</span><span class="p">)),</span>
+        <span class="p">(</span><span class="s1">&#39;IntOGen&#39;</span><span class="p">,</span> <span class="s1">&#39;role&#39;</span><span class="p">),</span>
+        <span class="p">(</span><span class="s1">&#39;HPMR&#39;</span><span class="p">,</span> <span class="p">(</span><span class="s1">&#39;role&#39;</span><span class="p">,</span> <span class="s1">&#39;mainclass&#39;</span><span class="p">,</span> <span class="s1">&#39;subclass&#39;</span><span class="p">,</span> <span class="s1">&#39;subsubclass&#39;</span><span class="p">)),</span>
+        <span class="c1">#(&#39;CancerGeneCensus&#39;,</span>
+            <span class="c1">#(</span>
+                <span class="c1">##&#39;hallmark&#39;,</span>
+                <span class="c1">##&#39;somatic&#39;,</span>
+                <span class="c1">##&#39;germline&#39;,</span>
+                <span class="c1">#&#39;tumour_types_somatic&#39;,</span>
+                <span class="c1">#&#39;tumour_types_germline&#39;,</span>
+            <span class="c1">#)</span>
+        <span class="c1">#),</span>
+        <span class="c1">#(&#39;DGIdb&#39;, &#39;category&#39;),</span>
+        <span class="p">(</span><span class="s1">&#39;ComPPI&#39;</span><span class="p">,</span> <span class="s1">&#39;location&#39;</span><span class="p">),</span>
+        <span class="p">(</span><span class="s1">&#39;Exocarta&#39;</span><span class="p">,</span> <span class="s1">&#39;vesicle&#39;</span><span class="p">),</span>
+        <span class="p">(</span><span class="s1">&#39;Vesiclepedia&#39;</span><span class="p">,</span> <span class="s1">&#39;vesicle&#39;</span><span class="p">),</span>
+        <span class="p">(</span><span class="s1">&#39;Ramilowski_location&#39;</span><span class="p">,</span> <span class="s1">&#39;location&#39;</span><span class="p">),</span>
+        <span class="p">(</span><span class="s1">&#39;LRdb&#39;</span><span class="p">,</span> <span class="p">(</span><span class="s1">&#39;role&#39;</span><span class="p">,</span> <span class="s1">&#39;cell_type&#39;</span><span class="p">)),</span>
+    <span class="p">}</span>
+
+<div class="viewcode-block" id="TableServer.__init__">
+<a class="viewcode-back" href="../../../../api/pypath.omnipath.server.run.TableServer.html#pypath.omnipath.server.run.TableServer.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">input_files</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">only_tables</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">exclude_tables</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+        <span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Server based on ``pandas`` data frames.</span>
+
+<span class="sd">        :param dict input_files:</span>
+<span class="sd">            Paths to tables exported by the ``pypath.websrvtab`` module.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">session_mod</span><span class="o">.</span><span class="n">Logger</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">name</span> <span class="o">=</span> <span class="s1">&#39;server&#39;</span><span class="p">)</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span><span class="s1">&#39;TableServer starting up.&#39;</span><span class="p">)</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">input_files</span> <span class="o">=</span> <span class="n">copy</span><span class="o">.</span><span class="n">deepcopy</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">default_input_files</span><span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">input_files</span><span class="o">.</span><span class="n">update</span><span class="p">(</span><span class="n">input_files</span> <span class="ow">or</span> <span class="p">{})</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">data</span> <span class="o">=</span> <span class="p">{}</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">to_load</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">data_query_types</span> <span class="o">-</span> <span class="n">common</span><span class="o">.</span><span class="n">to_set</span><span class="p">(</span><span class="n">exclude_tables</span><span class="p">)</span>
+                <span class="k">if</span> <span class="n">only_tables</span> <span class="ow">is</span> <span class="kc">None</span> <span class="k">else</span>
+            <span class="n">common</span><span class="o">.</span><span class="n">to_set</span><span class="p">(</span><span class="n">only_tables</span><span class="p">)</span>
+        <span class="p">)</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span><span class="s1">&#39;Datasets to load: </span><span class="si">%s</span><span class="s1">.&#39;</span> <span class="o">%</span> <span class="p">(</span><span class="s1">&#39;, &#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="nb">sorted</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">to_load</span><span class="p">))))</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_read_tables</span><span class="p">()</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_preprocess_interactions</span><span class="p">()</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">_preprocess_enzsub</span><span class="p">()</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">_preprocess_annotations</span><span class="p">()</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">_preprocess_complexes</span><span class="p">()</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">_preprocess_intercell</span><span class="p">()</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">_update_resources</span><span class="p">()</span>
+
+        <span class="n">BaseServer</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span><span class="s1">&#39;TableServer startup ready.&#39;</span><span class="p">)</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">_read_tables</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span><span class="s1">&#39;Loading data tables.&#39;</span><span class="p">)</span>
+
+        <span class="k">for</span> <span class="n">name</span><span class="p">,</span> <span class="n">fname</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">input_files</span><span class="p">):</span>
+
+            <span class="k">if</span> <span class="n">name</span> <span class="ow">not</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">to_load</span><span class="p">:</span>
+
+                <span class="k">continue</span>
+
+            <span class="n">fname_gz</span> <span class="o">=</span> <span class="sa">f</span><span class="s1">&#39;</span><span class="si">{</span><span class="n">fname</span><span class="si">}</span><span class="s1">.gz&#39;</span>
+            <span class="n">fname</span> <span class="o">=</span> <span class="n">fname_gz</span> <span class="k">if</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">exists</span><span class="p">(</span><span class="n">fname_gz</span><span class="p">)</span> <span class="k">else</span> <span class="n">fname</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span><span class="s1">&#39;Loading dataset `</span><span class="si">%s</span><span class="s1">` from file `</span><span class="si">%s</span><span class="s1">`.&#39;</span> <span class="o">%</span> <span class="p">(</span><span class="n">name</span><span class="p">,</span> <span class="n">fname</span><span class="p">))</span>
+
+            <span class="k">if</span> <span class="ow">not</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">exists</span><span class="p">(</span><span class="n">fname</span><span class="p">):</span>
+
+                <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span>
+                    <span class="s1">&#39;Missing table: `</span><span class="si">%s</span><span class="s1">`.&#39;</span> <span class="o">%</span> <span class="n">fname</span>
+                <span class="p">)</span>
+                <span class="k">continue</span>
+
+            <span class="n">dtype</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">default_dtypes</span><span class="p">[</span><span class="n">name</span><span class="p">]</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">data</span><span class="p">[</span><span class="n">name</span><span class="p">]</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">read_csv</span><span class="p">(</span>
+                <span class="n">fname</span><span class="p">,</span>
+                <span class="n">sep</span> <span class="o">=</span> <span class="s1">&#39;</span><span class="se">\t</span><span class="s1">&#39;</span><span class="p">,</span>
+                <span class="n">index_col</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+                <span class="n">dtype</span> <span class="o">=</span> <span class="n">dtype</span><span class="p">,</span>
+            <span class="p">)</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span>
+                <span class="s1">&#39;Table `</span><span class="si">%s</span><span class="s1">` loaded from file `</span><span class="si">%s</span><span class="s1">`.&#39;</span> <span class="o">%</span> <span class="p">(</span><span class="n">name</span><span class="p">,</span> <span class="n">fname</span><span class="p">)</span>
+            <span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">_network</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">req</span><span class="p">):</span>
+
+        <span class="n">hdr</span> <span class="o">=</span> <span class="p">[</span><span class="s1">&#39;nodes&#39;</span><span class="p">,</span> <span class="s1">&#39;edges&#39;</span><span class="p">,</span> <span class="s1">&#39;is_directed&#39;</span><span class="p">,</span> <span class="s1">&#39;sources&#39;</span><span class="p">]</span>
+        <span class="n">tbl</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span><span class="p">[</span><span class="s1">&#39;network&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">field</span>
+        <span class="n">val</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">(</span><span class="nb">zip</span><span class="p">(</span><span class="n">tbl</span><span class="o">.</span><span class="n">field</span><span class="p">,</span> <span class="n">tbl</span><span class="o">.</span><span class="n">value</span><span class="p">))</span>
+
+        <span class="k">if</span> <span class="sa">b</span><span class="s1">&#39;format&#39;</span> <span class="ow">in</span> <span class="n">req</span><span class="o">.</span><span class="n">args</span> <span class="ow">and</span> <span class="n">req</span><span class="o">.</span><span class="n">args</span><span class="p">[</span><span class="sa">b</span><span class="s1">&#39;format&#39;</span><span class="p">]</span> <span class="o">==</span> <span class="sa">b</span><span class="s1">&#39;json&#39;</span><span class="p">:</span>
+            <span class="k">return</span> <span class="n">json</span><span class="o">.</span><span class="n">dumps</span><span class="p">(</span><span class="n">val</span><span class="p">)</span>
+        <span class="k">else</span><span class="p">:</span>
+            <span class="k">return</span> <span class="s1">&#39;</span><span class="si">%s</span><span class="se">\n</span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="p">(</span><span class="s1">&#39;</span><span class="se">\t</span><span class="s1">&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">hdr</span><span class="p">),</span> <span class="s1">&#39;</span><span class="se">\t</span><span class="s1">&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span>
+                <span class="p">[</span><span class="nb">str</span><span class="p">(</span><span class="n">val</span><span class="p">[</span><span class="n">h</span><span class="p">])</span> <span class="k">for</span> <span class="n">h</span> <span class="ow">in</span> <span class="n">hdr</span><span class="p">]))</span>
+
+
+    <span class="k">def</span> <span class="nf">_preprocess_interactions</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">if</span> <span class="s1">&#39;interactions&#39;</span> <span class="ow">not</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span><span class="p">:</span>
+
+            <span class="k">return</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span><span class="s1">&#39;Preprocessing interactions.&#39;</span><span class="p">)</span>
+        <span class="n">tbl</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span><span class="p">[</span><span class="s1">&#39;interactions&#39;</span><span class="p">]</span>
+        <span class="n">tbl</span><span class="p">[</span><span class="s1">&#39;set_sources&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">Series</span><span class="p">(</span>
+            <span class="p">[</span><span class="nb">set</span><span class="p">(</span><span class="n">s</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;;&#39;</span><span class="p">))</span> <span class="k">for</span> <span class="n">s</span> <span class="ow">in</span> <span class="n">tbl</span><span class="o">.</span><span class="n">sources</span><span class="p">]</span>
+        <span class="p">)</span>
+        <span class="n">tbl</span><span class="p">[</span><span class="s1">&#39;set_dorothea_level&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">Series</span><span class="p">(</span>
+            <span class="p">[</span>
+                <span class="nb">set</span><span class="p">(</span><span class="n">s</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;;&#39;</span><span class="p">))</span>
+                <span class="k">if</span> <span class="ow">not</span> <span class="n">pd</span><span class="o">.</span><span class="n">isnull</span><span class="p">(</span><span class="n">s</span><span class="p">)</span> <span class="k">else</span>
+                <span class="nb">set</span><span class="p">([])</span>
+                <span class="k">for</span> <span class="n">s</span> <span class="ow">in</span> <span class="n">tbl</span><span class="o">.</span><span class="n">dorothea_level</span>
+            <span class="p">]</span>
+        <span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">_preprocess_enzsub</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">if</span> <span class="s1">&#39;enzsub&#39;</span> <span class="ow">not</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span><span class="p">:</span>
+
+            <span class="k">return</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span><span class="s1">&#39;Preprocessing enzyme-substrate relationships.&#39;</span><span class="p">)</span>
+        <span class="n">tbl</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span><span class="p">[</span><span class="s1">&#39;enzsub&#39;</span><span class="p">]</span>
+        <span class="n">tbl</span><span class="p">[</span><span class="s1">&#39;set_sources&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">Series</span><span class="p">(</span>
+            <span class="p">[</span><span class="nb">set</span><span class="p">(</span><span class="n">s</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;;&#39;</span><span class="p">))</span> <span class="k">for</span> <span class="n">s</span> <span class="ow">in</span> <span class="n">tbl</span><span class="o">.</span><span class="n">sources</span><span class="p">]</span>
+        <span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">_preprocess_complexes</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">if</span> <span class="s1">&#39;complexes&#39;</span> <span class="ow">not</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span><span class="p">:</span>
+
+            <span class="k">return</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span><span class="s1">&#39;Preprocessing complexes.&#39;</span><span class="p">)</span>
+        <span class="n">tbl</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span><span class="p">[</span><span class="s1">&#39;complexes&#39;</span><span class="p">]</span>
+
+        <span class="n">tbl</span> <span class="o">=</span> <span class="n">tbl</span><span class="p">[</span><span class="o">~</span><span class="n">tbl</span><span class="o">.</span><span class="n">components</span><span class="o">.</span><span class="n">isna</span><span class="p">()]</span>
+
+        <span class="k">with</span> <span class="n">ignore_pandas_copywarn</span><span class="p">():</span>
+
+            <span class="n">tbl</span><span class="p">[</span><span class="s1">&#39;set_sources&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="p">[</span><span class="nb">set</span><span class="p">(</span><span class="n">s</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;;&#39;</span><span class="p">))</span> <span class="k">for</span> <span class="n">s</span> <span class="ow">in</span> <span class="n">tbl</span><span class="o">.</span><span class="n">sources</span><span class="p">]</span>
+            <span class="n">tbl</span><span class="p">[</span><span class="s1">&#39;set_proteins&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="p">[</span><span class="nb">set</span><span class="p">(</span><span class="n">c</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;_&#39;</span><span class="p">))</span> <span class="k">for</span> <span class="n">c</span> <span class="ow">in</span> <span class="n">tbl</span><span class="o">.</span><span class="n">components</span><span class="p">]</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">data</span><span class="p">[</span><span class="s1">&#39;complexes&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">tbl</span>
+
+
+    <span class="k">def</span> <span class="nf">_preprocess_annotations_old</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">if</span> <span class="s1">&#39;annotations&#39;</span> <span class="ow">not</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span><span class="p">:</span>
+
+            <span class="k">return</span>
+
+        <span class="n">renum</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">compile</span><span class="p">(</span><span class="sa">r</span><span class="s1">&#39;[-\d\.]+&#39;</span><span class="p">)</span>
+
+
+        <span class="k">def</span> <span class="nf">_agg_values</span><span class="p">(</span><span class="n">vals</span><span class="p">):</span>
+
+            <span class="n">result</span> <span class="o">=</span> <span class="p">(</span>
+                <span class="s1">&#39;#&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="nb">sorted</span><span class="p">(</span><span class="nb">set</span><span class="p">(</span><span class="nb">str</span><span class="p">(</span><span class="n">ii</span><span class="p">)</span> <span class="k">for</span> <span class="n">ii</span> <span class="ow">in</span> <span class="n">vals</span><span class="p">)))</span>
+                <span class="k">if</span> <span class="ow">not</span> <span class="nb">all</span><span class="p">(</span>
+                    <span class="nb">isinstance</span><span class="p">(</span><span class="n">i</span><span class="p">,</span> <span class="p">(</span><span class="nb">int</span><span class="p">,</span> <span class="nb">float</span><span class="p">))</span> <span class="ow">or</span> <span class="p">(</span>
+                        <span class="nb">isinstance</span><span class="p">(</span><span class="n">i</span><span class="p">,</span> <span class="nb">str</span><span class="p">)</span> <span class="ow">and</span>
+                        <span class="n">i</span> <span class="ow">and</span> <span class="p">(</span>
+                            <span class="n">i</span> <span class="ow">is</span> <span class="kc">None</span> <span class="ow">or</span>
+                            <span class="n">renum</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="n">i</span><span class="p">)</span>
+                        <span class="p">)</span>
+                    <span class="p">)</span>
+                    <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="n">vals</span>
+                <span class="p">)</span> <span class="k">else</span>
+                <span class="s1">&#39;&lt;numeric&gt;&#39;</span>
+            <span class="p">)</span>
+
+            <span class="k">return</span> <span class="n">result</span>
+
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span><span class="s1">&#39;Preprocessing annotations.&#39;</span><span class="p">)</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">data</span><span class="p">[</span><span class="s1">&#39;annotations_summary&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span><span class="p">[</span><span class="s1">&#39;annotations&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">groupby</span><span class="p">(</span>
+            <span class="p">[</span><span class="s1">&#39;source&#39;</span><span class="p">,</span> <span class="s1">&#39;label&#39;</span><span class="p">],</span>
+        <span class="p">)</span><span class="o">.</span><span class="n">agg</span><span class="p">({</span><span class="s1">&#39;value&#39;</span><span class="p">:</span> <span class="n">_agg_values</span><span class="p">})</span><span class="o">.</span><span class="n">reset_index</span><span class="p">(</span><span class="n">drop</span> <span class="o">=</span> <span class="kc">False</span><span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">_preprocess_annotations</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">if</span> <span class="s1">&#39;annotations&#39;</span> <span class="ow">not</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span><span class="p">:</span>
+
+            <span class="k">return</span>
+
+        <span class="n">renum</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">compile</span><span class="p">(</span><span class="sa">r</span><span class="s1">&#39;[-\d\.]+&#39;</span><span class="p">)</span>
+
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span><span class="s1">&#39;Preprocessing annotations.&#39;</span><span class="p">)</span>
+
+        <span class="n">values_by_key</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">defaultdict</span><span class="p">(</span><span class="nb">set</span><span class="p">)</span>
+
+        <span class="c1"># we need to do it this way as we are memory limited on the server</span>
+        <span class="c1"># and pandas groupby is very memory intensive</span>
+        <span class="k">for</span> <span class="n">row</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span><span class="p">[</span><span class="s1">&#39;annotations&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">itertuples</span><span class="p">():</span>
+
+            <span class="n">value</span> <span class="o">=</span> <span class="p">(</span>
+                <span class="s1">&#39;&lt;numeric&gt;&#39;</span>
+                <span class="k">if</span> <span class="p">(</span>
+                    <span class="p">(</span>
+                        <span class="ow">not</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">row</span><span class="o">.</span><span class="n">value</span><span class="p">,</span> <span class="nb">bool</span><span class="p">)</span> <span class="ow">and</span>
+                        <span class="nb">isinstance</span><span class="p">(</span><span class="n">row</span><span class="o">.</span><span class="n">value</span><span class="p">,</span> <span class="p">(</span><span class="nb">int</span><span class="p">,</span> <span class="nb">float</span><span class="p">))</span>
+                    <span class="p">)</span> <span class="ow">or</span>
+                    <span class="n">renum</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="n">row</span><span class="o">.</span><span class="n">value</span><span class="p">)</span>
+                <span class="p">)</span> <span class="k">else</span>
+                <span class="nb">str</span><span class="p">(</span><span class="n">row</span><span class="o">.</span><span class="n">value</span><span class="p">)</span>
+            <span class="p">)</span>
+
+            <span class="n">values_by_key</span><span class="p">[(</span><span class="n">row</span><span class="o">.</span><span class="n">source</span><span class="p">,</span> <span class="n">row</span><span class="o">.</span><span class="n">label</span><span class="p">)]</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">value</span><span class="p">)</span>
+
+        <span class="k">for</span> <span class="n">vals</span> <span class="ow">in</span> <span class="n">values_by_key</span><span class="o">.</span><span class="n">values</span><span class="p">():</span>
+
+            <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">vals</span><span class="p">)</span> <span class="o">&gt;</span> <span class="mi">1</span><span class="p">:</span>
+
+                <span class="n">vals</span><span class="o">.</span><span class="n">discard</span><span class="p">(</span><span class="s1">&#39;&lt;numeric&gt;&#39;</span><span class="p">)</span>
+
+            <span class="n">vals</span><span class="o">.</span><span class="n">discard</span><span class="p">(</span><span class="s1">&#39;&#39;</span><span class="p">)</span>
+            <span class="n">vals</span><span class="o">.</span><span class="n">discard</span><span class="p">(</span><span class="s1">&#39;nan&#39;</span><span class="p">)</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">data</span><span class="p">[</span><span class="s1">&#39;annotations_summary&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">(</span>
+            <span class="nb">list</span><span class="p">(</span>
+                <span class="p">(</span><span class="n">source</span><span class="p">,</span> <span class="n">label</span><span class="p">,</span> <span class="s1">&#39;#&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="nb">sorted</span><span class="p">(</span><span class="n">values</span><span class="p">)))</span>
+                <span class="k">for</span> <span class="p">(</span><span class="n">source</span><span class="p">,</span> <span class="n">label</span><span class="p">),</span> <span class="n">values</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="n">values_by_key</span><span class="p">)</span>
+            <span class="p">),</span>
+            <span class="n">columns</span> <span class="o">=</span> <span class="p">[</span><span class="s1">&#39;source&#39;</span><span class="p">,</span> <span class="s1">&#39;label&#39;</span><span class="p">,</span> <span class="s1">&#39;value&#39;</span><span class="p">],</span>
+        <span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">_preprocess_intercell</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">if</span> <span class="s1">&#39;intercell&#39;</span> <span class="ow">not</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span><span class="p">:</span>
+
+            <span class="k">return</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span><span class="s1">&#39;Preprocessing intercell data.&#39;</span><span class="p">)</span>
+        <span class="n">tbl</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span><span class="p">[</span><span class="s1">&#39;intercell&#39;</span><span class="p">]</span>
+        <span class="n">tbl</span><span class="o">.</span><span class="n">drop</span><span class="p">(</span><span class="s1">&#39;full_name&#39;</span><span class="p">,</span> <span class="n">axis</span> <span class="o">=</span> <span class="mi">1</span><span class="p">,</span> <span class="n">inplace</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span> <span class="n">errors</span> <span class="o">=</span> <span class="s1">&#39;ignore&#39;</span><span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">data</span><span class="p">[</span><span class="s1">&#39;intercell_summary&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">tbl</span><span class="o">.</span><span class="n">filter</span><span class="p">(</span>
+            <span class="p">[</span><span class="s1">&#39;category&#39;</span><span class="p">,</span> <span class="s1">&#39;parent&#39;</span><span class="p">,</span> <span class="s1">&#39;database&#39;</span><span class="p">],</span>
+        <span class="p">)</span><span class="o">.</span><span class="n">drop_duplicates</span><span class="p">()</span>
+
+
+    <span class="k">def</span> <span class="nf">_update_resources</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span><span class="s1">&#39;Updating resource information.&#39;</span><span class="p">)</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_resources_dict</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">defaultdict</span><span class="p">(</span><span class="nb">dict</span><span class="p">)</span>
+
+        <span class="n">res_ctrl</span> <span class="o">=</span> <span class="n">resources_mod</span><span class="o">.</span><span class="n">get_controller</span><span class="p">()</span>
+
+        <span class="k">for</span> <span class="n">query_type</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">data_query_types</span><span class="p">:</span>
+
+            <span class="k">if</span> <span class="n">query_type</span> <span class="ow">not</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span><span class="p">:</span>
+
+                <span class="k">continue</span>
+
+            <span class="n">tbl</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span><span class="p">[</span><span class="n">query_type</span><span class="p">]</span>
+
+            <span class="c1"># finding out what is the name of the column with the resources</span>
+            <span class="c1"># as this is different across the tables</span>
+            <span class="k">for</span> <span class="n">colname</span><span class="p">,</span> <span class="n">argname</span> <span class="ow">in</span> <span class="p">(</span>
+                <span class="p">(</span><span class="s1">&#39;database&#39;</span><span class="p">,</span> <span class="s1">&#39;databases&#39;</span><span class="p">),</span>
+                <span class="p">(</span><span class="s1">&#39;sources&#39;</span><span class="p">,</span> <span class="s1">&#39;databases&#39;</span><span class="p">),</span>
+                <span class="p">(</span><span class="s1">&#39;source&#39;</span><span class="p">,</span> <span class="s1">&#39;databases&#39;</span><span class="p">),</span>
+                <span class="p">(</span><span class="s1">&#39;category&#39;</span><span class="p">,</span> <span class="s1">&#39;categories&#39;</span><span class="p">)</span>
+            <span class="p">):</span>
+
+                <span class="k">if</span> <span class="n">colname</span> <span class="ow">in</span> <span class="n">tbl</span><span class="o">.</span><span class="n">columns</span><span class="p">:</span>
+
+                    <span class="k">break</span>
+
+            <span class="c1"># collecting all resource names</span>
+            <span class="n">values</span> <span class="o">=</span> <span class="nb">sorted</span><span class="p">(</span><span class="nb">set</span><span class="p">(</span>
+                <span class="n">itertools</span><span class="o">.</span><span class="n">chain</span><span class="p">(</span><span class="o">*</span><span class="p">(</span>
+                    <span class="n">val</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;;&#39;</span><span class="p">)</span> <span class="k">for</span> <span class="n">val</span> <span class="ow">in</span> <span class="nb">getattr</span><span class="p">(</span><span class="n">tbl</span><span class="p">,</span> <span class="n">colname</span><span class="p">)</span>
+                <span class="p">))</span>
+            <span class="p">))</span>
+
+            <span class="k">for</span> <span class="n">db</span> <span class="ow">in</span> <span class="n">values</span><span class="p">:</span>
+
+                <span class="k">if</span> <span class="s1">&#39;license&#39;</span> <span class="ow">not</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">_resources_dict</span><span class="p">[</span><span class="n">db</span><span class="p">]:</span>
+
+                    <span class="n">license</span> <span class="o">=</span> <span class="n">res_ctrl</span><span class="o">.</span><span class="n">license</span><span class="p">(</span><span class="n">db</span><span class="p">)</span>
+
+                    <span class="k">if</span> <span class="n">license</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
+
+                        <span class="n">msg</span> <span class="o">=</span> <span class="s1">&#39;No license for resource `</span><span class="si">%s</span><span class="s1">`.&#39;</span> <span class="o">%</span> <span class="nb">str</span><span class="p">(</span><span class="n">db</span><span class="p">)</span>
+                        <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span><span class="n">msg</span><span class="p">)</span>
+                        <span class="k">raise</span> <span class="ne">RuntimeError</span><span class="p">(</span><span class="n">msg</span><span class="p">)</span>
+
+                    <span class="n">license_data</span> <span class="o">=</span> <span class="n">license</span><span class="o">.</span><span class="n">features</span>
+                    <span class="n">license_data</span><span class="p">[</span><span class="s1">&#39;name&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">license</span><span class="o">.</span><span class="n">name</span>
+                    <span class="n">license_data</span><span class="p">[</span><span class="s1">&#39;full_name&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">license</span><span class="o">.</span><span class="n">full_name</span>
+                    <span class="bp">self</span><span class="o">.</span><span class="n">_resources_dict</span><span class="p">[</span><span class="n">db</span><span class="p">][</span><span class="s1">&#39;license&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">license_data</span>
+
+                <span class="k">if</span> <span class="s1">&#39;queries&#39;</span> <span class="ow">not</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">_resources_dict</span><span class="p">[</span><span class="n">db</span><span class="p">]:</span>
+
+                    <span class="bp">self</span><span class="o">.</span><span class="n">_resources_dict</span><span class="p">[</span><span class="n">db</span><span class="p">][</span><span class="s1">&#39;queries&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="p">{}</span>
+
+                <span class="k">if</span> <span class="n">query_type</span> <span class="ow">not</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">_resources_dict</span><span class="p">[</span><span class="n">db</span><span class="p">][</span><span class="s1">&#39;queries&#39;</span><span class="p">]:</span>
+
+                    <span class="k">if</span> <span class="n">query_type</span> <span class="o">==</span> <span class="s1">&#39;interactions&#39;</span><span class="p">:</span>
+
+                        <span class="n">datasets</span> <span class="o">=</span> <span class="nb">set</span><span class="p">()</span>
+
+                        <span class="k">for</span> <span class="n">dataset</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">datasets_</span><span class="p">:</span>
+
+                            <span class="k">if</span> <span class="n">dataset</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">tbl</span><span class="o">.</span><span class="n">columns</span><span class="p">:</span>
+
+                                <span class="k">continue</span>
+
+                            <span class="k">for</span> <span class="n">in_dataset</span><span class="p">,</span> <span class="n">resources</span> <span class="ow">in</span> <span class="nb">zip</span><span class="p">(</span>
+                                <span class="nb">getattr</span><span class="p">(</span><span class="n">tbl</span><span class="p">,</span> <span class="n">dataset</span><span class="p">),</span>
+                                <span class="n">tbl</span><span class="o">.</span><span class="n">set_sources</span><span class="p">,</span>
+                            <span class="p">):</span>
+
+                                <span class="k">if</span> <span class="n">in_dataset</span> <span class="ow">and</span> <span class="n">db</span> <span class="ow">in</span> <span class="n">resources</span><span class="p">:</span>
+
+                                    <span class="n">datasets</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">dataset</span><span class="p">)</span>
+                                    <span class="k">break</span>
+
+                        <span class="bp">self</span><span class="o">.</span><span class="n">_resources_dict</span><span class="p">[</span><span class="n">db</span><span class="p">][</span><span class="s1">&#39;queries&#39;</span><span class="p">][</span><span class="n">query_type</span><span class="p">]</span> <span class="o">=</span> <span class="p">{</span>
+                            <span class="s1">&#39;datasets&#39;</span><span class="p">:</span> <span class="nb">sorted</span><span class="p">(</span><span class="n">datasets</span><span class="p">),</span>
+                        <span class="p">}</span>
+
+                    <span class="k">elif</span> <span class="n">query_type</span> <span class="o">==</span> <span class="s1">&#39;intercell&#39;</span><span class="p">:</span>
+
+                        <span class="n">tbl_db</span> <span class="o">=</span> <span class="n">tbl</span><span class="p">[</span>
+                            <span class="p">(</span><span class="n">tbl</span><span class="o">.</span><span class="n">database</span> <span class="o">==</span> <span class="n">db</span><span class="p">)</span> <span class="o">&amp;</span>
+                            <span class="p">(</span><span class="n">tbl</span><span class="o">.</span><span class="n">scope</span> <span class="o">==</span> <span class="s1">&#39;generic&#39;</span><span class="p">)</span>
+                        <span class="p">]</span>
+
+                        <span class="bp">self</span><span class="o">.</span><span class="n">_resources_dict</span><span class="p">[</span><span class="n">db</span><span class="p">][</span><span class="s1">&#39;queries&#39;</span><span class="p">][</span><span class="n">query_type</span><span class="p">]</span> <span class="o">=</span> <span class="p">{</span>
+                            <span class="s1">&#39;generic_categories&#39;</span><span class="p">:</span> <span class="nb">sorted</span><span class="p">(</span>
+                                <span class="nb">set</span><span class="p">(</span><span class="n">tbl_db</span><span class="o">.</span><span class="n">category</span><span class="p">)</span>
+                            <span class="p">),</span>
+                        <span class="p">}</span>
+
+                    <span class="k">else</span><span class="p">:</span>
+
+                        <span class="bp">self</span><span class="o">.</span><span class="n">_resources_dict</span><span class="p">[</span><span class="n">db</span><span class="p">][</span><span class="s1">&#39;queries&#39;</span><span class="p">][</span><span class="n">query_type</span><span class="p">]</span> <span class="o">=</span> <span class="p">{}</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">args_reference</span><span class="p">[</span><span class="n">query_type</span><span class="p">][</span><span class="n">argname</span><span class="p">]</span> <span class="o">=</span> <span class="n">values</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_resources_dict</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_resources_dict</span><span class="p">)</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span><span class="s1">&#39;Finished updating resource information.&#39;</span><span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">_check_args</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">req</span><span class="p">):</span>
+
+        <span class="n">result</span> <span class="o">=</span> <span class="p">[]</span>
+        <span class="n">argname</span> <span class="o">=</span> <span class="n">req</span><span class="o">.</span><span class="n">postpath</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span>
+        <span class="n">ref</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">args_reference</span><span class="p">[</span><span class="s1">&#39;resources&#39;</span><span class="p">]</span>
+                <span class="k">if</span> <span class="n">argname</span> <span class="o">==</span> <span class="s1">&#39;databases&#39;</span> <span class="k">else</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">args_reference</span><span class="p">[</span><span class="n">argname</span><span class="p">]</span>
+        <span class="p">)</span>
+
+        <span class="k">for</span> <span class="n">arg</span><span class="p">,</span> <span class="n">val</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="n">req</span><span class="o">.</span><span class="n">args</span><span class="p">):</span>
+
+            <span class="n">arg</span> <span class="o">=</span> <span class="n">arg</span><span class="o">.</span><span class="n">decode</span><span class="p">(</span><span class="s1">&#39;utf-8&#39;</span><span class="p">)</span>
+
+            <span class="k">if</span> <span class="n">arg</span> <span class="ow">in</span> <span class="n">ref</span><span class="p">:</span>
+
+                <span class="k">if</span> <span class="ow">not</span> <span class="n">ref</span><span class="p">[</span><span class="n">arg</span><span class="p">]</span> <span class="ow">or</span> <span class="ow">not</span> <span class="n">val</span><span class="p">:</span>
+
+                    <span class="k">continue</span>
+
+                <span class="n">val</span> <span class="o">=</span> <span class="p">(</span>
+                    <span class="p">{</span><span class="n">val</span><span class="p">[</span><span class="mi">0</span><span class="p">]}</span>
+                    <span class="k">if</span> <span class="nb">type</span><span class="p">(</span><span class="n">val</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span> <span class="ow">is</span> <span class="nb">int</span> <span class="k">else</span>
+                    <span class="nb">set</span><span class="p">(</span><span class="n">val</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">decode</span><span class="p">(</span><span class="s1">&#39;utf-8&#39;</span><span class="p">)</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;,&#39;</span><span class="p">))</span>
+                <span class="p">)</span>
+
+                <span class="n">unknowns</span> <span class="o">=</span> <span class="n">val</span> <span class="o">-</span> <span class="nb">set</span><span class="p">(</span><span class="n">ref</span><span class="p">[</span><span class="n">arg</span><span class="p">])</span>
+
+                <span class="k">if</span> <span class="n">unknowns</span><span class="p">:</span>
+
+                    <span class="n">result</span><span class="o">.</span><span class="n">append</span><span class="p">(</span>
+                        <span class="s1">&#39; ==&gt; Unknown values for argument `</span><span class="si">%s</span><span class="s1">`: `</span><span class="si">%s</span><span class="s1">`&#39;</span> <span class="o">%</span> <span class="p">(</span>
+                            <span class="n">arg</span><span class="p">,</span>
+                            <span class="s1">&#39;, &#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="nb">str</span><span class="p">(</span><span class="n">u</span><span class="p">)</span> <span class="k">for</span> <span class="n">u</span> <span class="ow">in</span> <span class="n">unknowns</span><span class="p">)</span>
+                        <span class="p">)</span>
+                    <span class="p">)</span>
+
+            <span class="k">else</span><span class="p">:</span>
+
+                <span class="n">result</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="s1">&#39; ==&gt; Unknown argument: `</span><span class="si">%s</span><span class="s1">`&#39;</span> <span class="o">%</span> <span class="n">arg</span><span class="p">)</span>
+
+        <span class="n">req</span><span class="o">.</span><span class="n">args</span><span class="p">[</span><span class="sa">b</span><span class="s1">&#39;header&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_parse_arg</span><span class="p">(</span><span class="n">req</span><span class="o">.</span><span class="n">args</span><span class="p">[</span><span class="sa">b</span><span class="s1">&#39;header&#39;</span><span class="p">])</span>
+
+        <span class="k">if</span> <span class="n">result</span><span class="p">:</span>
+
+            <span class="k">return</span> <span class="p">(</span>
+                <span class="s1">&#39;Something is not entirely good:</span><span class="se">\n</span><span class="si">%s</span><span class="se">\n\n</span><span class="s1">&#39;</span>
+                <span class="s1">&#39;Please check the examples at</span><span class="se">\n</span><span class="s1">&#39;</span>
+                <span class="s1">&#39;https://github.com/saezlab/pypath</span><span class="se">\n</span><span class="s1">&#39;</span>
+                <span class="s1">&#39;and</span><span class="se">\n</span><span class="s1">&#39;</span>
+                <span class="s1">&#39;https://github.com/saezlab/DoRothEA</span><span class="se">\n</span><span class="s1">&#39;</span>
+                <span class="s1">&#39;If you still experiencing issues contact us at</span><span class="se">\n</span><span class="s1">&#39;</span>
+                <span class="s1">&#39;https://github.com/saezlab/pypath/issues&#39;</span>
+                <span class="s1">&#39;&#39;</span> <span class="o">%</span> <span class="s1">&#39;</span><span class="se">\n</span><span class="s1">&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">result</span><span class="p">)</span>
+            <span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">queries</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">req</span><span class="p">):</span>
+
+        <span class="n">query_type</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="n">req</span><span class="o">.</span><span class="n">postpath</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span>
+                <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">req</span><span class="o">.</span><span class="n">postpath</span><span class="p">)</span> <span class="o">&gt;</span> <span class="mi">1</span> <span class="k">else</span>
+            <span class="s1">&#39;interactions&#39;</span>
+        <span class="p">)</span>
+
+        <span class="n">query_type</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_query_type</span><span class="p">(</span><span class="n">query_type</span><span class="p">)</span>
+
+        <span class="n">query_param</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="n">req</span><span class="o">.</span><span class="n">postpath</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span>
+                <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">req</span><span class="o">.</span><span class="n">postpath</span><span class="p">)</span> <span class="o">&gt;</span> <span class="mi">2</span> <span class="k">else</span>
+            <span class="kc">None</span>
+        <span class="p">)</span>
+
+        <span class="k">if</span> <span class="n">query_type</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">args_reference</span><span class="p">:</span>
+
+            <span class="n">result</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">(</span>
+                <span class="p">(</span>
+                    <span class="n">k</span><span class="p">,</span>
+                    <span class="nb">sorted</span><span class="p">(</span><span class="n">v</span><span class="p">)</span> <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">v</span><span class="p">,</span> <span class="n">_const</span><span class="o">.</span><span class="n">LIST_LIKE</span><span class="p">)</span> <span class="k">else</span> <span class="n">v</span>
+                <span class="p">)</span>
+                <span class="k">for</span> <span class="n">k</span><span class="p">,</span> <span class="n">v</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">args_reference</span><span class="p">[</span><span class="n">query_type</span><span class="p">]</span><span class="o">.</span><span class="n">items</span><span class="p">()</span>
+            <span class="p">)</span>
+
+            <span class="k">if</span> <span class="n">query_param</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span> <span class="ow">and</span> <span class="n">query_param</span> <span class="ow">in</span> <span class="n">result</span><span class="p">:</span>
+
+                <span class="n">result</span> <span class="o">=</span> <span class="p">{</span><span class="n">query_param</span><span class="p">:</span> <span class="n">result</span><span class="p">[</span><span class="n">query_param</span><span class="p">]}</span>
+
+        <span class="k">else</span><span class="p">:</span>
+
+            <span class="n">result</span> <span class="o">=</span> <span class="p">{}</span>
+            <span class="n">result</span><span class="p">[</span><span class="n">query_type</span><span class="p">]</span> <span class="o">=</span> <span class="p">(</span>
+                <span class="s1">&#39;No possible arguments defined for&#39;</span>
+                <span class="s1">&#39;query `</span><span class="si">%s</span><span class="s1">` or no such query available.&#39;</span> <span class="o">%</span> <span class="n">query_type</span>
+            <span class="p">)</span>
+
+        <span class="n">result</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_dict_set_to_list</span><span class="p">(</span><span class="n">result</span><span class="p">)</span>
+
+        <span class="k">if</span> <span class="sa">b</span><span class="s1">&#39;format&#39;</span> <span class="ow">in</span> <span class="n">req</span><span class="o">.</span><span class="n">args</span> <span class="ow">and</span> <span class="n">req</span><span class="o">.</span><span class="n">args</span><span class="p">[</span><span class="sa">b</span><span class="s1">&#39;format&#39;</span><span class="p">][</span><span class="mi">0</span><span class="p">]</span> <span class="o">==</span> <span class="sa">b</span><span class="s1">&#39;json&#39;</span><span class="p">:</span>
+
+            <span class="k">return</span> <span class="n">json</span><span class="o">.</span><span class="n">dumps</span><span class="p">(</span><span class="n">result</span><span class="p">)</span>
+
+        <span class="k">else</span><span class="p">:</span>
+
+            <span class="k">return</span> <span class="s1">&#39;argument</span><span class="se">\t</span><span class="s1">values</span><span class="se">\n</span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="s1">&#39;</span><span class="se">\n</span><span class="s1">&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span>
+                <span class="s1">&#39;</span><span class="si">%s</span><span class="se">\t</span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="p">(</span>
+                    <span class="n">k</span><span class="p">,</span>
+                    <span class="s1">&#39;;&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">v</span><span class="p">)</span>
+                        <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">v</span><span class="p">,</span> <span class="p">(</span><span class="nb">list</span><span class="p">,</span> <span class="nb">set</span><span class="p">,</span> <span class="nb">tuple</span><span class="p">))</span> <span class="k">else</span>
+                    <span class="nb">str</span><span class="p">(</span><span class="n">v</span><span class="p">)</span>
+                <span class="p">)</span>
+                <span class="k">for</span> <span class="n">k</span><span class="p">,</span> <span class="n">v</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="n">result</span><span class="p">)</span>
+            <span class="p">)</span>
+
+
+    <span class="nd">@classmethod</span>
+    <span class="k">def</span> <span class="nf">_dict_set_to_list</span><span class="p">(</span><span class="bp">cls</span><span class="p">,</span> <span class="n">dct</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="nb">dict</span><span class="p">(</span>
+            <span class="p">(</span>
+                <span class="n">key</span><span class="p">,</span>
+                <span class="p">(</span>
+                    <span class="nb">sorted</span><span class="p">(</span><span class="n">val</span><span class="p">)</span>
+                        <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">val</span><span class="p">,</span> <span class="n">_const</span><span class="o">.</span><span class="n">LIST_LIKE</span><span class="p">)</span> <span class="k">else</span>
+                    <span class="bp">cls</span><span class="o">.</span><span class="n">_dict_set_to_list</span><span class="p">(</span><span class="n">val</span><span class="p">)</span>
+                        <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">val</span><span class="p">,</span> <span class="nb">dict</span><span class="p">)</span> <span class="k">else</span>
+                    <span class="n">val</span>
+                <span class="p">)</span>
+            <span class="p">)</span>
+            <span class="k">for</span> <span class="n">key</span><span class="p">,</span> <span class="n">val</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="n">dct</span><span class="p">)</span>
+        <span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">databases</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">req</span><span class="p">):</span>
+
+        <span class="n">query_type</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="n">req</span><span class="o">.</span><span class="n">postpath</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span>
+                <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">req</span><span class="o">.</span><span class="n">postpath</span><span class="p">)</span> <span class="o">&gt;</span> <span class="mi">1</span> <span class="k">else</span>
+            <span class="s1">&#39;interactions&#39;</span>
+        <span class="p">)</span>
+
+        <span class="n">query_type</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_query_type</span><span class="p">(</span><span class="n">query_type</span><span class="p">)</span>
+
+        <span class="n">datasets</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="nb">set</span><span class="p">(</span><span class="n">req</span><span class="o">.</span><span class="n">postpath</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;,&#39;</span><span class="p">))</span>
+                <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">req</span><span class="o">.</span><span class="n">postpath</span><span class="p">)</span> <span class="o">&gt;</span> <span class="mi">2</span> <span class="k">else</span>
+            <span class="kc">None</span>
+        <span class="p">)</span>
+
+        <span class="n">tbl</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">data</span><span class="p">[</span><span class="n">query_type</span><span class="p">]</span>
+                <span class="k">if</span> <span class="n">query_type</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span> <span class="k">else</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">data</span><span class="p">[</span><span class="s1">&#39;interactions&#39;</span><span class="p">]</span>
+        <span class="p">)</span>
+
+        <span class="c1"># filter for datasets</span>
+        <span class="k">if</span> <span class="n">query_type</span> <span class="o">==</span> <span class="s1">&#39;interactions&#39;</span><span class="p">:</span>
+
+            <span class="k">if</span> <span class="n">datasets</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
+
+                <span class="n">tbl</span> <span class="o">=</span> <span class="n">tbl</span><span class="o">.</span><span class="n">loc</span><span class="p">[</span><span class="n">tbl</span><span class="o">.</span><span class="n">type</span><span class="o">.</span><span class="n">isin</span><span class="p">(</span><span class="n">datasets</span><span class="p">)]</span>
+
+            <span class="k">else</span><span class="p">:</span>
+
+                <span class="n">datasets</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_get_datasets</span><span class="p">()</span>
+
+            <span class="n">result</span> <span class="o">=</span> <span class="p">{}</span>
+
+            <span class="k">for</span> <span class="n">dataset</span> <span class="ow">in</span> <span class="n">datasets</span><span class="p">:</span>
+
+                <span class="n">result</span><span class="p">[</span><span class="n">dataset</span><span class="p">]</span> <span class="o">=</span> <span class="nb">sorted</span><span class="p">(</span><span class="nb">set</span><span class="o">.</span><span class="n">union</span><span class="p">(</span>
+                    <span class="o">*</span><span class="n">tbl</span><span class="p">[</span><span class="n">tbl</span><span class="o">.</span><span class="n">type</span> <span class="o">==</span> <span class="n">dataset</span><span class="p">]</span><span class="o">.</span><span class="n">set_sources</span><span class="p">)</span>
+                <span class="p">)</span>
+
+        <span class="k">else</span><span class="p">:</span>
+
+            <span class="n">result</span> <span class="o">=</span> <span class="p">{}</span>
+            <span class="n">result</span><span class="p">[</span><span class="s1">&#39;*&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="nb">sorted</span><span class="p">(</span><span class="nb">set</span><span class="o">.</span><span class="n">union</span><span class="p">(</span><span class="o">*</span><span class="n">tbl</span><span class="o">.</span><span class="n">set_sources</span><span class="p">))</span>
+
+        <span class="k">if</span> <span class="sa">b</span><span class="s1">&#39;format&#39;</span> <span class="ow">in</span> <span class="n">req</span><span class="o">.</span><span class="n">args</span> <span class="ow">and</span> <span class="n">req</span><span class="o">.</span><span class="n">args</span><span class="p">[</span><span class="sa">b</span><span class="s1">&#39;format&#39;</span><span class="p">][</span><span class="mi">0</span><span class="p">]</span> <span class="o">==</span> <span class="sa">b</span><span class="s1">&#39;json&#39;</span><span class="p">:</span>
+
+            <span class="k">return</span> <span class="n">json</span><span class="o">.</span><span class="n">dumps</span><span class="p">(</span><span class="n">result</span><span class="p">)</span>
+
+        <span class="k">else</span><span class="p">:</span>
+
+            <span class="k">return</span> <span class="s1">&#39;dataset</span><span class="se">\t</span><span class="s1">resources</span><span class="se">\n</span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="s1">&#39;</span><span class="se">\n</span><span class="s1">&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span>
+                <span class="s1">&#39;</span><span class="si">%s</span><span class="se">\t</span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="p">(</span><span class="n">k</span><span class="p">,</span> <span class="s1">&#39;;&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">v</span><span class="p">))</span> <span class="k">for</span> <span class="n">k</span><span class="p">,</span> <span class="n">v</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="n">result</span><span class="p">)</span>
+            <span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">_get_datasets</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="nb">list</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">data</span><span class="p">[</span><span class="s1">&#39;interactions&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">type</span><span class="o">.</span><span class="n">unique</span><span class="p">())</span>
+
+
+    <span class="k">def</span> <span class="nf">datasets</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">req</span><span class="p">):</span>
+
+        <span class="n">query_type</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="n">req</span><span class="o">.</span><span class="n">postpath</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span>
+                <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">req</span><span class="o">.</span><span class="n">postpath</span><span class="p">)</span> <span class="o">&gt;</span> <span class="mi">1</span> <span class="k">else</span>
+            <span class="s1">&#39;interactions&#39;</span>
+        <span class="p">)</span>
+
+        <span class="k">if</span> <span class="n">query_type</span> <span class="o">==</span> <span class="s1">&#39;interactions&#39;</span><span class="p">:</span>
+
+            <span class="n">result</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_get_datasets</span><span class="p">()</span>
+
+        <span class="k">else</span><span class="p">:</span>
+
+            <span class="n">result</span> <span class="o">=</span> <span class="p">[]</span>
+
+        <span class="k">if</span> <span class="sa">b</span><span class="s1">&#39;format&#39;</span> <span class="ow">in</span> <span class="n">req</span><span class="o">.</span><span class="n">args</span> <span class="ow">and</span> <span class="n">req</span><span class="o">.</span><span class="n">args</span><span class="p">[</span><span class="sa">b</span><span class="s1">&#39;format&#39;</span><span class="p">][</span><span class="mi">0</span><span class="p">]</span> <span class="o">==</span> <span class="sa">b</span><span class="s1">&#39;json&#39;</span><span class="p">:</span>
+
+            <span class="k">return</span> <span class="n">json</span><span class="o">.</span><span class="n">dumps</span><span class="p">(</span><span class="n">result</span><span class="p">)</span>
+
+        <span class="k">else</span><span class="p">:</span>
+
+            <span class="k">return</span> <span class="s1">&#39;;&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">result</span><span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">interactions</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">req</span><span class="p">,</span>
+            <span class="n">datasets</span>  <span class="o">=</span> <span class="p">{</span><span class="s1">&#39;omnipath&#39;</span><span class="p">},</span>
+            <span class="n">databases</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">dorothea_levels</span> <span class="o">=</span> <span class="p">{</span><span class="s1">&#39;A&#39;</span><span class="p">,</span> <span class="s1">&#39;B&#39;</span><span class="p">},</span>
+            <span class="n">organisms</span> <span class="o">=</span> <span class="p">{</span><span class="mi">9606</span><span class="p">},</span>
+            <span class="n">source_target</span> <span class="o">=</span> <span class="s1">&#39;OR&#39;</span><span class="p">,</span>
+        <span class="p">):</span>
+
+        <span class="n">bad_req</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_check_args</span><span class="p">(</span><span class="n">req</span><span class="p">)</span>
+
+        <span class="k">if</span> <span class="n">bad_req</span><span class="p">:</span>
+
+            <span class="k">return</span> <span class="n">bad_req</span>
+
+        <span class="n">hdr</span> <span class="o">=</span> <span class="p">[</span>
+            <span class="s1">&#39;source&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;target&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;is_directed&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;is_stimulation&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;is_inhibition&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;consensus_direction&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;consensus_stimulation&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;consensus_inhibition&#39;</span><span class="p">,</span>
+        <span class="p">]</span>
+
+        <span class="k">if</span> <span class="sa">b</span><span class="s1">&#39;source_target&#39;</span> <span class="ow">in</span> <span class="n">req</span><span class="o">.</span><span class="n">args</span><span class="p">:</span>
+
+            <span class="n">source_target</span> <span class="o">=</span> <span class="p">(</span>
+                <span class="n">req</span><span class="o">.</span><span class="n">args</span><span class="p">[</span><span class="sa">b</span><span class="s1">&#39;source_target&#39;</span><span class="p">][</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">decode</span><span class="p">(</span><span class="s1">&#39;utf-8&#39;</span><span class="p">)</span><span class="o">.</span><span class="n">upper</span><span class="p">()</span>
+            <span class="p">)</span>
+
+        <span class="c1"># changes the old, &quot;tfregulons&quot; names to new &quot;dorothea&quot;</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">_tfregulons_dorothea</span><span class="p">(</span><span class="n">req</span><span class="p">)</span>
+
+        <span class="k">if</span> <span class="sa">b</span><span class="s1">&#39;databases&#39;</span> <span class="ow">in</span> <span class="n">req</span><span class="o">.</span><span class="n">args</span><span class="p">:</span>
+
+            <span class="n">req</span><span class="o">.</span><span class="n">args</span><span class="p">[</span><span class="sa">b</span><span class="s1">&#39;resources&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">req</span><span class="o">.</span><span class="n">args</span><span class="p">[</span><span class="sa">b</span><span class="s1">&#39;databases&#39;</span><span class="p">]</span>
+
+        <span class="n">args</span> <span class="o">=</span> <span class="p">{}</span>
+
+        <span class="k">for</span> <span class="n">arg</span> <span class="ow">in</span> <span class="p">(</span>
+            <span class="s1">&#39;datasets&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;types&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;sources&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;targets&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;partners&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;resources&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;organisms&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;dorothea_levels&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;dorothea_methods&#39;</span><span class="p">,</span>
+        <span class="p">):</span>
+
+            <span class="n">args</span><span class="p">[</span><span class="n">arg</span><span class="p">]</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_args_set</span><span class="p">(</span><span class="n">req</span><span class="p">,</span> <span class="n">arg</span><span class="p">)</span>
+
+        <span class="c1"># here adjust on the defaults otherwise we serve empty</span>
+        <span class="c1"># response by default</span>
+        <span class="k">if</span> <span class="ow">not</span> <span class="n">args</span><span class="p">[</span><span class="s1">&#39;types&#39;</span><span class="p">]:</span>
+
+            <span class="n">args</span><span class="p">[</span><span class="s1">&#39;datasets&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">args</span><span class="p">[</span><span class="s1">&#39;datasets&#39;</span><span class="p">]</span> <span class="ow">or</span> <span class="n">datasets</span>
+
+        <span class="c1"># keep only valid dataset names</span>
+        <span class="n">args</span><span class="p">[</span><span class="s1">&#39;datasets&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">args</span><span class="p">[</span><span class="s1">&#39;datasets&#39;</span><span class="p">]</span> <span class="o">&amp;</span> <span class="bp">self</span><span class="o">.</span><span class="n">datasets_</span>
+
+        <span class="n">args</span><span class="p">[</span><span class="s1">&#39;organisms&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="nb">set</span><span class="p">(</span>
+            <span class="nb">int</span><span class="p">(</span><span class="n">t</span><span class="p">)</span> <span class="k">for</span> <span class="n">t</span> <span class="ow">in</span> <span class="n">args</span><span class="p">[</span><span class="s1">&#39;organisms&#39;</span><span class="p">]</span> <span class="k">if</span> <span class="n">t</span><span class="o">.</span><span class="n">isdigit</span><span class="p">()</span>
+        <span class="p">)</span>
+        <span class="n">args</span><span class="p">[</span><span class="s1">&#39;organisms&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">args</span><span class="p">[</span><span class="s1">&#39;organisms&#39;</span><span class="p">]</span> <span class="ow">or</span> <span class="n">organisms</span>
+
+        <span class="c1"># do not allow impossible values</span>
+        <span class="c1"># those would result KeyError later</span>
+        <span class="n">args</span><span class="p">[</span><span class="s1">&#39;dorothea_levels&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="n">args</span><span class="p">[</span><span class="s1">&#39;dorothea_levels&#39;</span><span class="p">]</span> <span class="ow">or</span>
+            <span class="n">dorothea_levels</span>
+        <span class="p">)</span>
+        <span class="n">args</span><span class="p">[</span><span class="s1">&#39;dorothea_methods&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="n">args</span><span class="p">[</span><span class="s1">&#39;dorothea_methods&#39;</span><span class="p">]</span> <span class="o">&amp;</span> <span class="bp">self</span><span class="o">.</span><span class="n">dorothea_methods</span>
+        <span class="p">)</span>
+
+        <span class="c1"># provide genesymbols: yes or no</span>
+        <span class="k">if</span> <span class="p">(</span>
+            <span class="sa">b</span><span class="s1">&#39;genesymbols&#39;</span> <span class="ow">in</span> <span class="n">req</span><span class="o">.</span><span class="n">args</span> <span class="ow">and</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">_parse_arg</span><span class="p">(</span><span class="n">req</span><span class="o">.</span><span class="n">args</span><span class="p">[</span><span class="sa">b</span><span class="s1">&#39;genesymbols&#39;</span><span class="p">])</span>
+        <span class="p">):</span>
+            <span class="n">genesymbols</span> <span class="o">=</span> <span class="kc">True</span>
+            <span class="n">hdr</span><span class="o">.</span><span class="n">insert</span><span class="p">(</span><span class="mi">2</span><span class="p">,</span> <span class="s1">&#39;source_genesymbol&#39;</span><span class="p">)</span>
+            <span class="n">hdr</span><span class="o">.</span><span class="n">insert</span><span class="p">(</span><span class="mi">3</span><span class="p">,</span> <span class="s1">&#39;target_genesymbol&#39;</span><span class="p">)</span>
+        <span class="k">else</span><span class="p">:</span>
+            <span class="n">genesymbols</span> <span class="o">=</span> <span class="kc">False</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span><span class="s1">&#39;Processed arguments: [</span><span class="si">%s</span><span class="s1">].&#39;</span> <span class="o">%</span> <span class="n">common</span><span class="o">.</span><span class="n">dict_str</span><span class="p">(</span><span class="n">args</span><span class="p">))</span>
+
+        <span class="c1"># starting from the entire dataset</span>
+        <span class="n">tbl</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span><span class="p">[</span><span class="s1">&#39;interactions&#39;</span><span class="p">]</span>
+
+        <span class="c1"># filter by type</span>
+        <span class="k">if</span> <span class="n">args</span><span class="p">[</span><span class="s1">&#39;types&#39;</span><span class="p">]:</span>
+
+            <span class="n">tbl</span> <span class="o">=</span> <span class="n">tbl</span><span class="o">.</span><span class="n">loc</span><span class="p">[</span><span class="n">tbl</span><span class="o">.</span><span class="n">type</span><span class="o">.</span><span class="n">isin</span><span class="p">(</span><span class="n">args</span><span class="p">[</span><span class="s1">&#39;types&#39;</span><span class="p">])]</span>
+
+        <span class="c1"># if partners provided those will overwrite</span>
+        <span class="c1"># sources and targets</span>
+        <span class="n">args</span><span class="p">[</span><span class="s1">&#39;sources&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">args</span><span class="p">[</span><span class="s1">&#39;sources&#39;</span><span class="p">]</span> <span class="ow">or</span> <span class="n">args</span><span class="p">[</span><span class="s1">&#39;partners&#39;</span><span class="p">]</span>
+        <span class="n">args</span><span class="p">[</span><span class="s1">&#39;targets&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">args</span><span class="p">[</span><span class="s1">&#39;targets&#39;</span><span class="p">]</span> <span class="ow">or</span> <span class="n">args</span><span class="p">[</span><span class="s1">&#39;partners&#39;</span><span class="p">]</span>
+
+        <span class="c1"># then we filter by source and target</span>
+        <span class="c1"># which matched against both standard names</span>
+        <span class="c1"># and gene symbols</span>
+        <span class="k">if</span> <span class="n">args</span><span class="p">[</span><span class="s1">&#39;sources&#39;</span><span class="p">]</span> <span class="ow">and</span> <span class="n">args</span><span class="p">[</span><span class="s1">&#39;targets&#39;</span><span class="p">]</span> <span class="ow">and</span> <span class="n">source_target</span> <span class="o">==</span> <span class="s1">&#39;OR&#39;</span><span class="p">:</span>
+
+            <span class="n">tbl</span> <span class="o">=</span> <span class="n">tbl</span><span class="o">.</span><span class="n">loc</span><span class="p">[</span>
+                <span class="n">tbl</span><span class="o">.</span><span class="n">target</span><span class="o">.</span><span class="n">isin</span><span class="p">(</span><span class="n">args</span><span class="p">[</span><span class="s1">&#39;targets&#39;</span><span class="p">])</span> <span class="o">|</span>
+                <span class="n">tbl</span><span class="o">.</span><span class="n">target_genesymbol</span><span class="o">.</span><span class="n">isin</span><span class="p">(</span><span class="n">args</span><span class="p">[</span><span class="s1">&#39;targets&#39;</span><span class="p">])</span> <span class="o">|</span>
+                <span class="n">tbl</span><span class="o">.</span><span class="n">source</span><span class="o">.</span><span class="n">isin</span><span class="p">(</span><span class="n">args</span><span class="p">[</span><span class="s1">&#39;sources&#39;</span><span class="p">])</span> <span class="o">|</span>
+                <span class="n">tbl</span><span class="o">.</span><span class="n">source_genesymbol</span><span class="o">.</span><span class="n">isin</span><span class="p">(</span><span class="n">args</span><span class="p">[</span><span class="s1">&#39;sources&#39;</span><span class="p">])</span>
+            <span class="p">]</span>
+
+        <span class="k">else</span><span class="p">:</span>
+
+            <span class="k">if</span> <span class="n">args</span><span class="p">[</span><span class="s1">&#39;sources&#39;</span><span class="p">]:</span>
+                <span class="n">tbl</span> <span class="o">=</span> <span class="n">tbl</span><span class="o">.</span><span class="n">loc</span><span class="p">[</span>
+                    <span class="n">tbl</span><span class="o">.</span><span class="n">source</span><span class="o">.</span><span class="n">isin</span><span class="p">(</span><span class="n">args</span><span class="p">[</span><span class="s1">&#39;sources&#39;</span><span class="p">])</span> <span class="o">|</span>
+                    <span class="n">tbl</span><span class="o">.</span><span class="n">source_genesymbol</span><span class="o">.</span><span class="n">isin</span><span class="p">(</span><span class="n">args</span><span class="p">[</span><span class="s1">&#39;sources&#39;</span><span class="p">])</span>
+                <span class="p">]</span>
+
+            <span class="k">if</span> <span class="n">args</span><span class="p">[</span><span class="s1">&#39;targets&#39;</span><span class="p">]:</span>
+                <span class="n">tbl</span> <span class="o">=</span> <span class="n">tbl</span><span class="o">.</span><span class="n">loc</span><span class="p">[</span>
+                    <span class="n">tbl</span><span class="o">.</span><span class="n">target</span><span class="o">.</span><span class="n">isin</span><span class="p">(</span><span class="n">args</span><span class="p">[</span><span class="s1">&#39;targets&#39;</span><span class="p">])</span> <span class="o">|</span>
+                    <span class="n">tbl</span><span class="o">.</span><span class="n">target_genesymbol</span><span class="o">.</span><span class="n">isin</span><span class="p">(</span><span class="n">args</span><span class="p">[</span><span class="s1">&#39;targets&#39;</span><span class="p">])</span>
+                <span class="p">]</span>
+
+        <span class="c1"># filter by datasets</span>
+        <span class="k">if</span> <span class="n">args</span><span class="p">[</span><span class="s1">&#39;datasets&#39;</span><span class="p">]:</span>
+
+            <span class="n">tbl</span> <span class="o">=</span> <span class="n">tbl</span><span class="o">.</span><span class="n">query</span><span class="p">(</span><span class="s1">&#39; or &#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">args</span><span class="p">[</span><span class="s1">&#39;datasets&#39;</span><span class="p">]))</span>
+
+        <span class="c1"># filter by organism</span>
+        <span class="n">tbl</span> <span class="o">=</span> <span class="n">tbl</span><span class="o">.</span><span class="n">loc</span><span class="p">[</span>
+            <span class="n">tbl</span><span class="o">.</span><span class="n">ncbi_tax_id_source</span><span class="o">.</span><span class="n">isin</span><span class="p">(</span><span class="n">args</span><span class="p">[</span><span class="s1">&#39;organisms&#39;</span><span class="p">])</span> <span class="o">|</span>
+            <span class="n">tbl</span><span class="o">.</span><span class="n">ncbi_tax_id_target</span><span class="o">.</span><span class="n">isin</span><span class="p">(</span><span class="n">args</span><span class="p">[</span><span class="s1">&#39;organisms&#39;</span><span class="p">])</span>
+        <span class="p">]</span>
+
+        <span class="n">dorothea_included</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="s1">&#39;dorothea&#39;</span> <span class="ow">in</span> <span class="n">args</span><span class="p">[</span><span class="s1">&#39;datasets&#39;</span><span class="p">]</span> <span class="ow">or</span>
+            <span class="nb">any</span><span class="p">(</span><span class="n">res</span><span class="o">.</span><span class="n">endswith</span><span class="p">(</span><span class="s1">&#39;DoRothEA&#39;</span><span class="p">)</span> <span class="k">for</span> <span class="n">res</span> <span class="ow">in</span> <span class="n">args</span><span class="p">[</span><span class="s1">&#39;resources&#39;</span><span class="p">])</span> <span class="ow">or</span>
+            <span class="p">(</span>
+                <span class="s1">&#39;transcriptional&#39;</span> <span class="ow">in</span> <span class="n">args</span><span class="p">[</span><span class="s1">&#39;types&#39;</span><span class="p">]</span> <span class="ow">and</span>
+                <span class="ow">not</span> <span class="n">args</span><span class="p">[</span><span class="s1">&#39;datasets&#39;</span><span class="p">]</span>
+            <span class="p">)</span>
+        <span class="p">)</span>
+
+        <span class="c1"># filter by DoRothEA confidence levels</span>
+        <span class="k">if</span> <span class="n">dorothea_included</span> <span class="ow">and</span> <span class="n">args</span><span class="p">[</span><span class="s1">&#39;dorothea_levels&#39;</span><span class="p">]:</span>
+
+            <span class="n">tbl</span> <span class="o">=</span> <span class="n">tbl</span><span class="o">.</span><span class="n">loc</span><span class="p">[</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">_dorothea_dataset_filter</span><span class="p">(</span><span class="n">tbl</span><span class="p">,</span> <span class="n">args</span><span class="p">)</span> <span class="o">|</span>
+                <span class="p">[</span>
+                    <span class="nb">bool</span><span class="p">(</span><span class="n">levels</span> <span class="o">&amp;</span> <span class="n">args</span><span class="p">[</span><span class="s1">&#39;dorothea_levels&#39;</span><span class="p">])</span>
+                    <span class="k">for</span> <span class="n">levels</span> <span class="ow">in</span> <span class="n">tbl</span><span class="o">.</span><span class="n">set_dorothea_level</span>
+                <span class="p">]</span>
+            <span class="p">]</span>
+
+        <span class="c1"># filter by databases</span>
+        <span class="k">if</span> <span class="n">args</span><span class="p">[</span><span class="s1">&#39;resources&#39;</span><span class="p">]:</span>
+
+            <span class="n">tbl</span> <span class="o">=</span> <span class="n">tbl</span><span class="o">.</span><span class="n">loc</span><span class="p">[</span>
+                <span class="p">[</span>
+                    <span class="nb">bool</span><span class="p">(</span><span class="n">sources</span> <span class="o">&amp;</span> <span class="n">args</span><span class="p">[</span><span class="s1">&#39;resources&#39;</span><span class="p">])</span>
+                    <span class="k">for</span> <span class="n">sources</span> <span class="ow">in</span> <span class="n">tbl</span><span class="o">.</span><span class="n">set_sources</span>
+                <span class="p">]</span>
+            <span class="p">]</span>
+
+         <span class="c1"># filtering for entity types</span>
+        <span class="k">if</span> <span class="sa">b</span><span class="s1">&#39;entity_types&#39;</span> <span class="ow">in</span> <span class="n">req</span><span class="o">.</span><span class="n">args</span><span class="p">:</span>
+
+            <span class="n">entity_types</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_args_set</span><span class="p">(</span><span class="n">req</span><span class="p">,</span> <span class="s1">&#39;entity_types&#39;</span><span class="p">)</span>
+
+            <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">entity_types</span><span class="p">)</span> <span class="o">==</span> <span class="mi">1</span> <span class="ow">and</span> <span class="s1">&#39;protein&#39;</span> <span class="ow">in</span> <span class="n">entity_types</span><span class="p">:</span>
+
+                <span class="c1"># pandas is awful:</span>
+                <span class="n">tbl</span> <span class="o">=</span> <span class="n">tbl</span><span class="o">.</span><span class="n">loc</span><span class="p">[</span>
+                    <span class="n">np</span><span class="o">.</span><span class="n">logical_and</span><span class="p">(</span>
+                        <span class="n">tbl</span><span class="o">.</span><span class="n">entity_type_source</span><span class="o">.</span><span class="n">astype</span><span class="p">(</span><span class="s1">&#39;string&#39;</span><span class="p">)</span> <span class="o">==</span> <span class="s1">&#39;protein&#39;</span><span class="p">,</span>
+                        <span class="n">tbl</span><span class="o">.</span><span class="n">entity_type_target</span><span class="o">.</span><span class="n">astype</span><span class="p">(</span><span class="s1">&#39;string&#39;</span><span class="p">)</span> <span class="o">==</span> <span class="s1">&#39;protein&#39;</span><span class="p">,</span>
+                    <span class="p">)</span>
+                <span class="p">]</span>
+
+            <span class="k">else</span><span class="p">:</span>
+
+                <span class="n">tbl</span> <span class="o">=</span> <span class="n">tbl</span><span class="o">.</span><span class="n">loc</span><span class="p">[</span>
+                    <span class="n">tbl</span><span class="o">.</span><span class="n">entity_type_source</span><span class="o">.</span><span class="n">isin</span><span class="p">(</span><span class="n">entity_types</span><span class="p">)</span> <span class="o">|</span>
+                    <span class="n">tbl</span><span class="o">.</span><span class="n">entity_type_target</span><span class="o">.</span><span class="n">isin</span><span class="p">(</span><span class="n">entity_types</span><span class="p">)</span>
+                <span class="p">]</span>
+
+        <span class="c1"># filtering by DoRothEA methods</span>
+        <span class="k">if</span> <span class="n">dorothea_included</span> <span class="ow">and</span> <span class="n">args</span><span class="p">[</span><span class="s1">&#39;dorothea_methods&#39;</span><span class="p">]:</span>
+
+            <span class="n">q</span> <span class="o">=</span> <span class="p">[</span><span class="s1">&#39;dorothea_</span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="n">m</span> <span class="k">for</span> <span class="n">m</span> <span class="ow">in</span> <span class="n">args</span><span class="p">[</span><span class="s1">&#39;dorothea_methods&#39;</span><span class="p">]]</span>
+
+            <span class="n">tbl</span> <span class="o">=</span> <span class="n">tbl</span><span class="o">.</span><span class="n">loc</span><span class="p">[</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">_dorothea_dataset_filter</span><span class="p">(</span><span class="n">tbl</span><span class="p">,</span> <span class="n">args</span><span class="p">)</span> <span class="o">|</span>
+                <span class="n">tbl</span><span class="p">[</span><span class="n">q</span><span class="p">]</span><span class="o">.</span><span class="n">any</span><span class="p">(</span><span class="mi">1</span><span class="p">)</span>
+            <span class="p">]</span>
+
+        <span class="c1"># filter directed &amp; signed</span>
+        <span class="k">if</span> <span class="p">(</span>
+            <span class="sa">b</span><span class="s1">&#39;directed&#39;</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">req</span><span class="o">.</span><span class="n">args</span> <span class="ow">or</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">_parse_arg</span><span class="p">(</span><span class="n">req</span><span class="o">.</span><span class="n">args</span><span class="p">[</span><span class="sa">b</span><span class="s1">&#39;directed&#39;</span><span class="p">])</span>
+        <span class="p">):</span>
+
+            <span class="n">tbl</span> <span class="o">=</span> <span class="n">tbl</span><span class="o">.</span><span class="n">loc</span><span class="p">[</span><span class="n">tbl</span><span class="o">.</span><span class="n">is_directed</span> <span class="o">==</span> <span class="mi">1</span><span class="p">]</span>
+
+        <span class="k">if</span> <span class="p">(</span>
+            <span class="sa">b</span><span class="s1">&#39;signed&#39;</span> <span class="ow">in</span> <span class="n">req</span><span class="o">.</span><span class="n">args</span> <span class="ow">and</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">_parse_arg</span><span class="p">(</span><span class="n">req</span><span class="o">.</span><span class="n">args</span><span class="p">[</span><span class="sa">b</span><span class="s1">&#39;signed&#39;</span><span class="p">])</span>
+        <span class="p">):</span>
+
+            <span class="n">tbl</span> <span class="o">=</span> <span class="n">tbl</span><span class="o">.</span><span class="n">loc</span><span class="p">[</span><span class="n">np</span><span class="o">.</span><span class="n">logical_or</span><span class="p">(</span>
+                <span class="n">tbl</span><span class="o">.</span><span class="n">is_stimulation</span> <span class="o">==</span> <span class="mi">1</span><span class="p">,</span>
+                <span class="n">tbl</span><span class="o">.</span><span class="n">is_inhibition</span> <span class="o">==</span> <span class="mi">1</span>
+            <span class="p">)]</span>
+
+        <span class="c1"># loops: remove by default</span>
+        <span class="k">if</span> <span class="p">(</span>
+            <span class="sa">b</span><span class="s1">&#39;loops&#39;</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">req</span><span class="o">.</span><span class="n">args</span> <span class="ow">or</span>
+            <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">_parse_arg</span><span class="p">(</span><span class="n">req</span><span class="o">.</span><span class="n">args</span><span class="p">[</span><span class="sa">b</span><span class="s1">&#39;loops&#39;</span><span class="p">])</span>
+        <span class="p">):</span>
+
+            <span class="c1"># pandas is a disaster:</span>
+            <span class="n">tbl</span> <span class="o">=</span> <span class="n">tbl</span><span class="o">.</span><span class="n">loc</span><span class="p">[</span>
+                <span class="n">tbl</span><span class="o">.</span><span class="n">source</span><span class="o">.</span><span class="n">astype</span><span class="p">(</span><span class="s1">&#39;string&#39;</span><span class="p">)</span> <span class="o">!=</span>
+                <span class="n">tbl</span><span class="o">.</span><span class="n">target</span><span class="o">.</span><span class="n">astype</span><span class="p">(</span><span class="s1">&#39;string&#39;</span><span class="p">)</span>
+            <span class="p">]</span>
+
+        <span class="n">req</span><span class="o">.</span><span class="n">args</span><span class="p">[</span><span class="sa">b</span><span class="s1">&#39;fields&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">req</span><span class="o">.</span><span class="n">args</span><span class="p">[</span><span class="sa">b</span><span class="s1">&#39;fields&#39;</span><span class="p">]</span> <span class="ow">or</span> <span class="p">[</span><span class="sa">b</span><span class="s1">&#39;&#39;</span><span class="p">]</span>
+
+        <span class="n">_fields</span> <span class="o">=</span> <span class="p">[</span>
+            <span class="n">f</span> <span class="k">for</span> <span class="n">f</span> <span class="ow">in</span>
+            <span class="n">req</span><span class="o">.</span><span class="n">args</span><span class="p">[</span><span class="sa">b</span><span class="s1">&#39;fields&#39;</span><span class="p">][</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">decode</span><span class="p">(</span><span class="s1">&#39;utf-8&#39;</span><span class="p">)</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;,&#39;</span><span class="p">)</span>
+            <span class="k">if</span> <span class="n">f</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">interaction_fields</span>
+        <span class="p">]</span>
+
+        <span class="k">for</span> <span class="n">f</span> <span class="ow">in</span> <span class="p">(</span><span class="sa">b</span><span class="s1">&#39;evidences&#39;</span><span class="p">,</span> <span class="sa">b</span><span class="s1">&#39;extra_attrs&#39;</span><span class="p">):</span>
+
+            <span class="k">if</span> <span class="n">f</span> <span class="ow">in</span> <span class="n">req</span><span class="o">.</span><span class="n">uri</span> <span class="ow">and</span> <span class="n">f</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">req</span><span class="o">.</span><span class="n">args</span><span class="p">[</span><span class="sa">b</span><span class="s1">&#39;fields&#39;</span><span class="p">][</span><span class="mi">0</span><span class="p">]:</span>
+
+                <span class="n">_fields</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">f</span><span class="o">.</span><span class="n">decode</span><span class="p">(</span><span class="s1">&#39;utf-8&#39;</span><span class="p">))</span>
+
+        <span class="k">for</span> <span class="n">f</span> <span class="ow">in</span> <span class="n">_fields</span><span class="p">:</span>
+
+            <span class="k">if</span> <span class="n">f</span> <span class="o">==</span> <span class="s1">&#39;ncbi_tax_id&#39;</span> <span class="ow">or</span> <span class="n">f</span> <span class="o">==</span> <span class="s1">&#39;organism&#39;</span><span class="p">:</span>
+
+                <span class="n">hdr</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="s1">&#39;ncbi_tax_id_source&#39;</span><span class="p">)</span>
+                <span class="n">hdr</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="s1">&#39;ncbi_tax_id_target&#39;</span><span class="p">)</span>
+
+            <span class="k">elif</span> <span class="n">f</span> <span class="o">==</span> <span class="s1">&#39;entity_type&#39;</span><span class="p">:</span>
+
+                <span class="n">hdr</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="s1">&#39;entity_type_source&#39;</span><span class="p">)</span>
+                <span class="n">hdr</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="s1">&#39;entity_type_target&#39;</span><span class="p">)</span>
+
+            <span class="k">elif</span> <span class="n">f</span> <span class="ow">in</span> <span class="p">{</span><span class="s1">&#39;databases&#39;</span><span class="p">,</span> <span class="s1">&#39;resources&#39;</span><span class="p">}:</span>
+
+                <span class="n">hdr</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="s1">&#39;sources&#39;</span><span class="p">)</span>
+
+            <span class="k">elif</span> <span class="n">f</span> <span class="o">==</span> <span class="s1">&#39;datasets&#39;</span><span class="p">:</span>
+
+                <span class="n">hdr</span><span class="o">.</span><span class="n">extend</span><span class="p">(</span>
+                    <span class="nb">set</span><span class="p">(</span><span class="n">tbl</span><span class="o">.</span><span class="n">columns</span><span class="p">)</span> <span class="o">&amp;</span>
+                    <span class="bp">self</span><span class="o">.</span><span class="n">args_reference</span><span class="p">[</span><span class="s1">&#39;interactions&#39;</span><span class="p">][</span><span class="s1">&#39;datasets&#39;</span><span class="p">]</span> <span class="o">&amp;</span>
+                    <span class="n">args</span><span class="p">[</span><span class="s1">&#39;datasets&#39;</span><span class="p">]</span>
+                <span class="p">)</span>
+
+            <span class="k">else</span><span class="p">:</span>
+
+                <span class="n">hdr</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">f</span><span class="p">)</span>
+
+        <span class="n">license</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_get_license</span><span class="p">(</span><span class="n">req</span><span class="p">)</span>
+
+        <span class="n">tbl</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_filter_by_license_interactions</span><span class="p">(</span><span class="n">tbl</span><span class="p">,</span> <span class="n">license</span><span class="p">)</span>
+
+        <span class="n">tbl</span> <span class="o">=</span> <span class="n">tbl</span><span class="o">.</span><span class="n">loc</span><span class="p">[:,</span><span class="n">hdr</span><span class="p">]</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_serve_dataframe</span><span class="p">(</span><span class="n">tbl</span><span class="p">,</span> <span class="n">req</span><span class="p">)</span>
+
+
+    <span class="nd">@classmethod</span>
+    <span class="k">def</span> <span class="nf">_dataset_included</span><span class="p">(</span><span class="bp">cls</span><span class="p">,</span> <span class="n">dataset</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="n">args</span><span class="p">:</span> <span class="nb">dict</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">bool</span><span class="p">:</span>
+
+        <span class="k">return</span> <span class="p">(</span>
+            <span class="n">dataset</span> <span class="ow">in</span> <span class="n">args</span><span class="p">[</span><span class="s1">&#39;datasets&#39;</span><span class="p">]</span> <span class="ow">or</span>
+            <span class="p">(</span>
+                <span class="ow">not</span> <span class="n">args</span><span class="p">[</span><span class="s1">&#39;datasets&#39;</span><span class="p">]</span> <span class="ow">and</span>
+                <span class="bp">cls</span><span class="o">.</span><span class="n">dataset2type</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="n">dataset</span><span class="p">,</span> <span class="kc">None</span><span class="p">)</span> <span class="ow">in</span> <span class="n">args</span><span class="p">[</span><span class="s1">&#39;types&#39;</span><span class="p">]</span>
+            <span class="p">)</span>
+        <span class="p">)</span>
+
+
+    <span class="nd">@classmethod</span>
+    <span class="k">def</span> <span class="nf">_dorothea_dataset_filter</span><span class="p">(</span><span class="bp">cls</span><span class="p">,</span> <span class="n">tbl</span><span class="p">:</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">,</span> <span class="n">args</span><span class="p">:</span> <span class="nb">dict</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="p">(</span>
+            <span class="p">(</span>
+                <span class="c1"># if the tf_target dataset is requested</span>
+                <span class="c1"># we need to serve it including the parts which</span>
+                <span class="c1"># don&#39;t fit the filters below</span>
+                <span class="bp">cls</span><span class="o">.</span><span class="n">_dataset_included</span><span class="p">(</span><span class="s1">&#39;tf_target&#39;</span><span class="p">,</span> <span class="n">args</span><span class="p">)</span> <span class="o">&amp;</span>
+                <span class="n">tbl</span><span class="o">.</span><span class="n">tf_target</span>
+            <span class="p">)</span> <span class="o">|</span>
+            <span class="p">(</span>
+                <span class="bp">cls</span><span class="o">.</span><span class="n">_dataset_included</span><span class="p">(</span><span class="s1">&#39;collectri&#39;</span><span class="p">,</span> <span class="n">args</span><span class="p">)</span> <span class="o">&amp;</span>
+                <span class="n">tbl</span><span class="o">.</span><span class="n">collectri</span>
+            <span class="p">)</span> <span class="o">|</span>
+            <span class="p">(</span><span class="n">tbl</span><span class="o">.</span><span class="n">type</span> <span class="o">!=</span> <span class="s1">&#39;transcriptional&#39;</span><span class="p">)</span>
+        <span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">_tfregulons_dorothea</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">req</span><span class="p">):</span>
+
+        <span class="k">for</span> <span class="n">arg</span> <span class="ow">in</span> <span class="p">(</span><span class="sa">b</span><span class="s1">&#39;datasets&#39;</span><span class="p">,</span> <span class="sa">b</span><span class="s1">&#39;fields&#39;</span><span class="p">):</span>
+
+            <span class="k">if</span> <span class="n">arg</span> <span class="ow">in</span> <span class="n">req</span><span class="o">.</span><span class="n">args</span><span class="p">:</span>
+
+                <span class="n">req</span><span class="o">.</span><span class="n">args</span><span class="p">[</span><span class="n">arg</span><span class="p">]</span> <span class="o">=</span> <span class="p">[</span>
+                    <span class="n">it</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="sa">b</span><span class="s1">&#39;tfregulons&#39;</span><span class="p">,</span> <span class="sa">b</span><span class="s1">&#39;dorothea&#39;</span><span class="p">)</span>
+                    <span class="k">for</span> <span class="n">it</span> <span class="ow">in</span> <span class="n">req</span><span class="o">.</span><span class="n">args</span><span class="p">[</span><span class="n">arg</span><span class="p">]</span>
+                <span class="p">]</span>
+
+        <span class="k">for</span> <span class="n">postfix</span> <span class="ow">in</span> <span class="p">(</span><span class="sa">b</span><span class="s1">&#39;levels&#39;</span><span class="p">,</span> <span class="sa">b</span><span class="s1">&#39;methods&#39;</span><span class="p">):</span>
+
+            <span class="n">key</span> <span class="o">=</span> <span class="sa">b</span><span class="s1">&#39;tfregulons_</span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="n">postfix</span>
+            <span class="n">new_key</span> <span class="o">=</span> <span class="sa">b</span><span class="s1">&#39;dorothea_</span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="n">postfix</span>
+
+            <span class="k">if</span> <span class="n">key</span> <span class="ow">in</span> <span class="n">req</span><span class="o">.</span><span class="n">args</span> <span class="ow">and</span> <span class="n">new_key</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">req</span><span class="o">.</span><span class="n">args</span><span class="p">:</span>
+
+                <span class="n">req</span><span class="o">.</span><span class="n">args</span><span class="p">[</span><span class="n">new_key</span><span class="p">]</span> <span class="o">=</span> <span class="n">req</span><span class="o">.</span><span class="n">args</span><span class="p">[</span><span class="n">key</span><span class="p">]</span>
+                <span class="n">_</span> <span class="o">=</span> <span class="n">req</span><span class="o">.</span><span class="n">args</span><span class="o">.</span><span class="n">pop</span><span class="p">(</span><span class="n">key</span><span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">enzsub</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">req</span><span class="p">,</span>
+            <span class="n">organisms</span> <span class="o">=</span> <span class="p">{</span><span class="mi">9606</span><span class="p">},</span>
+            <span class="n">enzyme_substrate</span> <span class="o">=</span> <span class="s1">&#39;OR&#39;</span>
+        <span class="p">):</span>
+
+        <span class="n">bad_req</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_check_args</span><span class="p">(</span><span class="n">req</span><span class="p">)</span>
+
+        <span class="k">if</span> <span class="n">bad_req</span><span class="p">:</span>
+
+            <span class="k">return</span> <span class="n">bad_req</span>
+
+        <span class="n">hdr</span> <span class="o">=</span> <span class="p">[</span>
+            <span class="s1">&#39;enzyme&#39;</span><span class="p">,</span> <span class="s1">&#39;substrate&#39;</span><span class="p">,</span> <span class="s1">&#39;residue_type&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;residue_offset&#39;</span><span class="p">,</span> <span class="s1">&#39;modification&#39;</span>
+        <span class="p">]</span>
+
+        <span class="k">if</span> <span class="sa">b</span><span class="s1">&#39;enzyme_substrate&#39;</span> <span class="ow">in</span> <span class="n">req</span><span class="o">.</span><span class="n">args</span><span class="p">:</span>
+
+            <span class="n">enzyme_substrate</span> <span class="o">=</span> <span class="p">(</span>
+                <span class="n">req</span><span class="o">.</span><span class="n">args</span><span class="p">[</span><span class="sa">b</span><span class="s1">&#39;enzyme_substrate&#39;</span><span class="p">][</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">decode</span><span class="p">(</span><span class="s1">&#39;utf-8&#39;</span><span class="p">)</span><span class="o">.</span><span class="n">upper</span><span class="p">()</span>
+            <span class="p">)</span>
+
+        <span class="k">if</span> <span class="sa">b</span><span class="s1">&#39;databases&#39;</span> <span class="ow">in</span> <span class="n">req</span><span class="o">.</span><span class="n">args</span><span class="p">:</span>
+
+            <span class="n">req</span><span class="o">.</span><span class="n">args</span><span class="p">[</span><span class="sa">b</span><span class="s1">&#39;resources&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">req</span><span class="o">.</span><span class="n">args</span><span class="p">[</span><span class="sa">b</span><span class="s1">&#39;databases&#39;</span><span class="p">]</span>
+
+        <span class="n">args</span> <span class="o">=</span> <span class="p">{}</span>
+
+        <span class="k">for</span> <span class="n">arg</span> <span class="ow">in</span> <span class="p">(</span>
+            <span class="s1">&#39;enzymes&#39;</span><span class="p">,</span> <span class="s1">&#39;substrates&#39;</span><span class="p">,</span> <span class="s1">&#39;partners&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;resources&#39;</span><span class="p">,</span> <span class="s1">&#39;organisms&#39;</span><span class="p">,</span> <span class="s1">&#39;types&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;residues&#39;</span>
+        <span class="p">):</span>
+
+            <span class="n">args</span><span class="p">[</span><span class="n">arg</span><span class="p">]</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_args_set</span><span class="p">(</span><span class="n">req</span><span class="p">,</span> <span class="n">arg</span><span class="p">)</span>
+
+        <span class="n">args</span><span class="p">[</span><span class="s1">&#39;organisms&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="nb">set</span><span class="p">(</span>
+            <span class="nb">int</span><span class="p">(</span><span class="n">t</span><span class="p">)</span> <span class="k">for</span> <span class="n">t</span> <span class="ow">in</span> <span class="n">args</span><span class="p">[</span><span class="s1">&#39;organisms&#39;</span><span class="p">]</span> <span class="k">if</span> <span class="n">t</span><span class="o">.</span><span class="n">isdigit</span><span class="p">()</span>
+        <span class="p">)</span>
+        <span class="n">args</span><span class="p">[</span><span class="s1">&#39;organisms&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">args</span><span class="p">[</span><span class="s1">&#39;organisms&#39;</span><span class="p">]</span> <span class="ow">or</span> <span class="n">organisms</span>
+
+        <span class="c1"># provide genesymbols: yes or no</span>
+        <span class="k">if</span> <span class="p">(</span>
+            <span class="sa">b</span><span class="s1">&#39;genesymbols&#39;</span> <span class="ow">in</span> <span class="n">req</span><span class="o">.</span><span class="n">args</span> <span class="ow">and</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">_parse_arg</span><span class="p">(</span><span class="n">req</span><span class="o">.</span><span class="n">args</span><span class="p">[</span><span class="sa">b</span><span class="s1">&#39;genesymbols&#39;</span><span class="p">])</span>
+        <span class="p">):</span>
+            <span class="n">genesymbols</span> <span class="o">=</span> <span class="kc">True</span>
+            <span class="n">hdr</span><span class="o">.</span><span class="n">insert</span><span class="p">(</span><span class="mi">2</span><span class="p">,</span> <span class="s1">&#39;enzyme_genesymbol&#39;</span><span class="p">)</span>
+            <span class="n">hdr</span><span class="o">.</span><span class="n">insert</span><span class="p">(</span><span class="mi">3</span><span class="p">,</span> <span class="s1">&#39;substrate_genesymbol&#39;</span><span class="p">)</span>
+        <span class="k">else</span><span class="p">:</span>
+            <span class="n">genesymbols</span> <span class="o">=</span> <span class="kc">False</span>
+
+        <span class="c1"># starting from the entire dataset</span>
+        <span class="n">tbl</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span><span class="p">[</span><span class="s1">&#39;enzsub&#39;</span><span class="p">]</span>
+
+        <span class="c1"># filter by type</span>
+        <span class="k">if</span> <span class="n">args</span><span class="p">[</span><span class="s1">&#39;types&#39;</span><span class="p">]:</span>
+            <span class="n">tbl</span> <span class="o">=</span> <span class="n">tbl</span><span class="o">.</span><span class="n">loc</span><span class="p">[</span><span class="n">tbl</span><span class="o">.</span><span class="n">modification</span><span class="o">.</span><span class="n">isin</span><span class="p">(</span><span class="n">args</span><span class="p">[</span><span class="s1">&#39;types&#39;</span><span class="p">])]</span>
+
+        <span class="c1"># if partners provided those will overwrite</span>
+        <span class="c1"># enzymes and substrates</span>
+        <span class="n">args</span><span class="p">[</span><span class="s1">&#39;enzymes&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">args</span><span class="p">[</span><span class="s1">&#39;enzymes&#39;</span><span class="p">]</span> <span class="ow">or</span> <span class="n">args</span><span class="p">[</span><span class="s1">&#39;partners&#39;</span><span class="p">]</span>
+        <span class="n">args</span><span class="p">[</span><span class="s1">&#39;substrates&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">args</span><span class="p">[</span><span class="s1">&#39;substrates&#39;</span><span class="p">]</span> <span class="ow">or</span> <span class="n">args</span><span class="p">[</span><span class="s1">&#39;partners&#39;</span><span class="p">]</span>
+
+        <span class="c1"># then we filter by enzyme and substrate</span>
+        <span class="c1"># which matched against both standard names</span>
+        <span class="c1"># and gene symbols</span>
+        <span class="k">if</span> <span class="p">(</span>
+            <span class="n">args</span><span class="p">[</span><span class="s1">&#39;enzymes&#39;</span><span class="p">]</span> <span class="ow">and</span>
+            <span class="n">args</span><span class="p">[</span><span class="s1">&#39;substrates&#39;</span><span class="p">]</span> <span class="ow">and</span>
+            <span class="n">enzyme_substrate</span> <span class="o">==</span> <span class="s1">&#39;OR&#39;</span>
+        <span class="p">):</span>
+
+            <span class="n">tbl</span> <span class="o">=</span> <span class="n">tbl</span><span class="o">.</span><span class="n">loc</span><span class="p">[</span>
+                <span class="n">tbl</span><span class="o">.</span><span class="n">substrate</span><span class="o">.</span><span class="n">isin</span><span class="p">(</span><span class="n">args</span><span class="p">[</span><span class="s1">&#39;substrates&#39;</span><span class="p">])</span> <span class="o">|</span>
+                <span class="n">tbl</span><span class="o">.</span><span class="n">substrate_genesymbol</span><span class="o">.</span><span class="n">isin</span><span class="p">(</span><span class="n">args</span><span class="p">[</span><span class="s1">&#39;substrates&#39;</span><span class="p">])</span> <span class="o">|</span>
+                <span class="n">tbl</span><span class="o">.</span><span class="n">enzyme</span><span class="o">.</span><span class="n">isin</span><span class="p">(</span><span class="n">args</span><span class="p">[</span><span class="s1">&#39;enzymes&#39;</span><span class="p">])</span> <span class="o">|</span>
+                <span class="n">tbl</span><span class="o">.</span><span class="n">enzyme_genesymbol</span><span class="o">.</span><span class="n">isin</span><span class="p">(</span><span class="n">args</span><span class="p">[</span><span class="s1">&#39;enzymes&#39;</span><span class="p">])</span>
+            <span class="p">]</span>
+
+        <span class="k">else</span><span class="p">:</span>
+
+            <span class="k">if</span> <span class="n">args</span><span class="p">[</span><span class="s1">&#39;enzymes&#39;</span><span class="p">]:</span>
+                <span class="n">tbl</span> <span class="o">=</span> <span class="n">tbl</span><span class="o">.</span><span class="n">loc</span><span class="p">[</span>
+                    <span class="n">tbl</span><span class="o">.</span><span class="n">enzyme</span><span class="o">.</span><span class="n">isin</span><span class="p">(</span><span class="n">args</span><span class="p">[</span><span class="s1">&#39;enzymes&#39;</span><span class="p">])</span> <span class="o">|</span>
+                    <span class="n">tbl</span><span class="o">.</span><span class="n">enzyme_genesymbol</span><span class="o">.</span><span class="n">isin</span><span class="p">(</span><span class="n">args</span><span class="p">[</span><span class="s1">&#39;enzymes&#39;</span><span class="p">])</span>
+                <span class="p">]</span>
+
+            <span class="k">if</span> <span class="n">args</span><span class="p">[</span><span class="s1">&#39;substrates&#39;</span><span class="p">]:</span>
+                <span class="n">tbl</span> <span class="o">=</span> <span class="n">tbl</span><span class="o">.</span><span class="n">loc</span><span class="p">[</span>
+                    <span class="n">tbl</span><span class="o">.</span><span class="n">substrate</span><span class="o">.</span><span class="n">isin</span><span class="p">(</span><span class="n">args</span><span class="p">[</span><span class="s1">&#39;substrates&#39;</span><span class="p">])</span> <span class="o">|</span>
+                    <span class="n">tbl</span><span class="o">.</span><span class="n">substrate_genesymbol</span><span class="o">.</span><span class="n">isin</span><span class="p">(</span><span class="n">args</span><span class="p">[</span><span class="s1">&#39;substrates&#39;</span><span class="p">])</span>
+                <span class="p">]</span>
+
+        <span class="c1"># filter by organism</span>
+        <span class="n">tbl</span> <span class="o">=</span> <span class="n">tbl</span><span class="o">.</span><span class="n">loc</span><span class="p">[</span><span class="n">tbl</span><span class="o">.</span><span class="n">ncbi_tax_id</span><span class="o">.</span><span class="n">isin</span><span class="p">(</span><span class="n">args</span><span class="p">[</span><span class="s1">&#39;organisms&#39;</span><span class="p">])]</span>
+
+        <span class="c1"># filter by databases</span>
+        <span class="k">if</span> <span class="n">args</span><span class="p">[</span><span class="s1">&#39;resources&#39;</span><span class="p">]:</span>
+
+            <span class="n">tbl</span> <span class="o">=</span> <span class="n">tbl</span><span class="o">.</span><span class="n">loc</span><span class="p">[</span>
+                <span class="p">[</span>
+                    <span class="nb">bool</span><span class="p">(</span><span class="n">args</span><span class="p">[</span><span class="s1">&#39;resources&#39;</span><span class="p">]</span> <span class="o">&amp;</span> <span class="n">sources</span><span class="p">)</span>
+                    <span class="k">for</span> <span class="n">sources</span> <span class="ow">in</span> <span class="n">tbl</span><span class="o">.</span><span class="n">set_sources</span>
+                <span class="p">]</span>
+            <span class="p">]</span>
+
+        <span class="k">if</span> <span class="n">req</span><span class="o">.</span><span class="n">args</span><span class="p">[</span><span class="sa">b</span><span class="s1">&#39;fields&#39;</span><span class="p">]:</span>
+
+            <span class="n">_fields</span> <span class="o">=</span> <span class="p">[</span>
+                <span class="n">f</span> <span class="k">for</span> <span class="n">f</span> <span class="ow">in</span>
+                <span class="n">req</span><span class="o">.</span><span class="n">args</span><span class="p">[</span><span class="sa">b</span><span class="s1">&#39;fields&#39;</span><span class="p">][</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">decode</span><span class="p">(</span><span class="s1">&#39;utf-8&#39;</span><span class="p">)</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;,&#39;</span><span class="p">)</span>
+                <span class="k">if</span> <span class="n">f</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">enzsub_fields</span>
+            <span class="p">]</span>
+
+            <span class="k">for</span> <span class="n">f</span> <span class="ow">in</span> <span class="n">_fields</span><span class="p">:</span>
+
+                <span class="k">if</span> <span class="n">f</span> <span class="o">==</span> <span class="s1">&#39;ncbi_tax_id&#39;</span> <span class="ow">or</span> <span class="n">f</span> <span class="o">==</span> <span class="s1">&#39;organism&#39;</span><span class="p">:</span>
+
+                    <span class="n">hdr</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="s1">&#39;ncbi_tax_id&#39;</span><span class="p">)</span>
+
+                <span class="k">elif</span> <span class="n">f</span> <span class="ow">in</span> <span class="p">{</span><span class="s1">&#39;databases&#39;</span><span class="p">,</span> <span class="s1">&#39;resources&#39;</span><span class="p">}:</span>
+
+                    <span class="n">hdr</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="s1">&#39;sources&#39;</span><span class="p">)</span>
+
+                <span class="k">else</span><span class="p">:</span>
+
+                    <span class="n">hdr</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">f</span><span class="p">)</span>
+
+        <span class="n">license</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_get_license</span><span class="p">(</span><span class="n">req</span><span class="p">)</span>
+
+        <span class="n">tbl</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_filter_by_license_interactions</span><span class="p">(</span><span class="n">tbl</span><span class="p">,</span> <span class="n">license</span><span class="p">)</span>
+
+        <span class="n">tbl</span> <span class="o">=</span> <span class="n">tbl</span><span class="o">.</span><span class="n">loc</span><span class="p">[:,</span><span class="n">hdr</span><span class="p">]</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_serve_dataframe</span><span class="p">(</span><span class="n">tbl</span><span class="p">,</span> <span class="n">req</span><span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">ptms</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">req</span><span class="p">):</span>
+
+        <span class="n">req</span><span class="o">.</span><span class="n">postpath</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">=</span> <span class="s1">&#39;enzsub&#39;</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">enzsub</span><span class="p">(</span><span class="n">req</span><span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">enz_sub</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">req</span><span class="p">):</span>
+
+        <span class="n">req</span><span class="o">.</span><span class="n">postpath</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">=</span> <span class="s1">&#39;enzsub&#39;</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">enzsub</span><span class="p">(</span><span class="n">req</span><span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">annotations</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">req</span><span class="p">):</span>
+
+        <span class="n">bad_req</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_check_args</span><span class="p">(</span><span class="n">req</span><span class="p">)</span>
+
+        <span class="k">if</span> <span class="n">bad_req</span><span class="p">:</span>
+
+            <span class="k">return</span> <span class="n">bad_req</span>
+
+        <span class="k">if</span> <span class="sa">b</span><span class="s1">&#39;databases&#39;</span> <span class="ow">in</span> <span class="n">req</span><span class="o">.</span><span class="n">args</span><span class="p">:</span>
+
+            <span class="n">req</span><span class="o">.</span><span class="n">args</span><span class="p">[</span><span class="sa">b</span><span class="s1">&#39;resources&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">req</span><span class="o">.</span><span class="n">args</span><span class="p">[</span><span class="sa">b</span><span class="s1">&#39;databases&#39;</span><span class="p">]</span>
+
+        <span class="k">if</span> <span class="p">(</span>
+            <span class="ow">not</span> <span class="n">settings</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">&#39;server_annotations_full_download&#39;</span><span class="p">)</span> <span class="ow">and</span>
+            <span class="ow">not</span> <span class="sa">b</span><span class="s1">&#39;resources&#39;</span> <span class="ow">in</span> <span class="n">req</span><span class="o">.</span><span class="n">args</span> <span class="ow">and</span>
+            <span class="ow">not</span> <span class="sa">b</span><span class="s1">&#39;proteins&#39;</span> <span class="ow">in</span> <span class="n">req</span><span class="o">.</span><span class="n">args</span>
+        <span class="p">):</span>
+
+            <span class="k">return</span> <span class="p">(</span>
+                <span class="s1">&#39;Downloading the entire annotations database by the REST &#39;</span>
+                <span class="s1">&#39;API is not allowed because of its huge size (&gt;1GB). &#39;</span>
+                <span class="s1">&#39;We recommend to query a set of proteins or a few &#39;</span>
+                <span class="s1">&#39;resources, depending on your interest. &#39;</span>
+                <span class="s1">&#39;You can always download the full database from &#39;</span>
+                <span class="s1">&#39;https://archive.omnipathdb.org/&#39;</span>
+                <span class="s1">&#39;omnipath_webservice_annotations__recent.tsv&#39;</span>
+            <span class="p">)</span>
+
+        <span class="c1"># starting from the entire dataset</span>
+        <span class="n">tbl</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span><span class="p">[</span><span class="s1">&#39;annotations&#39;</span><span class="p">]</span>
+
+        <span class="n">hdr</span> <span class="o">=</span> <span class="n">tbl</span><span class="o">.</span><span class="n">columns</span>
+
+        <span class="c1"># filtering for resources</span>
+        <span class="k">if</span> <span class="sa">b</span><span class="s1">&#39;resources&#39;</span> <span class="ow">in</span> <span class="n">req</span><span class="o">.</span><span class="n">args</span><span class="p">:</span>
+
+            <span class="n">resources</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_args_set</span><span class="p">(</span><span class="n">req</span><span class="p">,</span> <span class="s1">&#39;resources&#39;</span><span class="p">)</span>
+
+            <span class="n">tbl</span> <span class="o">=</span> <span class="n">tbl</span><span class="o">.</span><span class="n">loc</span><span class="p">[</span><span class="n">tbl</span><span class="o">.</span><span class="n">source</span><span class="o">.</span><span class="n">isin</span><span class="p">(</span><span class="n">resources</span><span class="p">)]</span>
+
+        <span class="c1"># filtering for entity types</span>
+        <span class="k">if</span> <span class="sa">b</span><span class="s1">&#39;entity_types&#39;</span> <span class="ow">in</span> <span class="n">req</span><span class="o">.</span><span class="n">args</span><span class="p">:</span>
+
+            <span class="n">entity_types</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_args_set</span><span class="p">(</span><span class="n">req</span><span class="p">,</span> <span class="s1">&#39;entity_types&#39;</span><span class="p">)</span>
+
+            <span class="n">tbl</span> <span class="o">=</span> <span class="n">tbl</span><span class="o">.</span><span class="n">loc</span><span class="p">[</span><span class="n">tbl</span><span class="o">.</span><span class="n">entity_type</span><span class="o">.</span><span class="n">isin</span><span class="p">(</span><span class="n">entity_types</span><span class="p">)]</span>
+
+        <span class="c1"># filtering for proteins</span>
+        <span class="k">if</span> <span class="sa">b</span><span class="s1">&#39;proteins&#39;</span> <span class="ow">in</span> <span class="n">req</span><span class="o">.</span><span class="n">args</span><span class="p">:</span>
+
+            <span class="n">proteins</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_args_set</span><span class="p">(</span><span class="n">req</span><span class="p">,</span> <span class="s1">&#39;proteins&#39;</span><span class="p">)</span>
+
+            <span class="n">tbl</span> <span class="o">=</span> <span class="n">tbl</span><span class="o">.</span><span class="n">loc</span><span class="p">[</span>
+                <span class="n">tbl</span><span class="o">.</span><span class="n">uniprot</span><span class="o">.</span><span class="n">isin</span><span class="p">(</span><span class="n">proteins</span><span class="p">)</span> <span class="o">|</span>
+                <span class="n">tbl</span><span class="o">.</span><span class="n">genesymbol</span><span class="o">.</span><span class="n">isin</span><span class="p">(</span><span class="n">proteins</span><span class="p">)</span>
+            <span class="p">]</span>
+
+        <span class="c1"># provide genesymbols: yes or no</span>
+        <span class="k">if</span> <span class="p">(</span>
+            <span class="sa">b</span><span class="s1">&#39;genesymbols&#39;</span> <span class="ow">in</span> <span class="n">req</span><span class="o">.</span><span class="n">args</span> <span class="ow">and</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">_parse_arg</span><span class="p">(</span><span class="n">req</span><span class="o">.</span><span class="n">args</span><span class="p">[</span><span class="sa">b</span><span class="s1">&#39;genesymbols&#39;</span><span class="p">])</span>
+        <span class="p">):</span>
+            <span class="n">genesymbols</span> <span class="o">=</span> <span class="kc">True</span>
+            <span class="n">hdr</span><span class="o">.</span><span class="n">insert</span><span class="p">(</span><span class="mi">1</span><span class="p">,</span> <span class="s1">&#39;genesymbol&#39;</span><span class="p">)</span>
+        <span class="k">else</span><span class="p">:</span>
+            <span class="n">genesymbols</span> <span class="o">=</span> <span class="kc">False</span>
+
+        <span class="n">license</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_get_license</span><span class="p">(</span><span class="n">req</span><span class="p">)</span>
+
+        <span class="n">tbl</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_filter_by_license_annotations</span><span class="p">(</span><span class="n">tbl</span><span class="p">,</span> <span class="n">license</span><span class="p">)</span>
+
+        <span class="n">tbl</span> <span class="o">=</span> <span class="n">tbl</span><span class="o">.</span><span class="n">loc</span><span class="p">[:,</span><span class="n">hdr</span><span class="p">]</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_serve_dataframe</span><span class="p">(</span><span class="n">tbl</span><span class="p">,</span> <span class="n">req</span><span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">annotations_summary</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">req</span><span class="p">):</span>
+
+        <span class="n">bad_req</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_check_args</span><span class="p">(</span><span class="n">req</span><span class="p">)</span>
+
+        <span class="k">if</span> <span class="n">bad_req</span><span class="p">:</span>
+
+            <span class="k">return</span> <span class="n">bad_req</span>
+
+        <span class="k">if</span> <span class="sa">b</span><span class="s1">&#39;databases&#39;</span> <span class="ow">in</span> <span class="n">req</span><span class="o">.</span><span class="n">args</span><span class="p">:</span>
+
+            <span class="n">req</span><span class="o">.</span><span class="n">args</span><span class="p">[</span><span class="sa">b</span><span class="s1">&#39;resources&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">req</span><span class="o">.</span><span class="n">args</span><span class="p">[</span><span class="sa">b</span><span class="s1">&#39;databases&#39;</span><span class="p">]</span>
+
+        <span class="c1"># starting from the entire dataset</span>
+        <span class="n">tbl</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span><span class="p">[</span><span class="s1">&#39;annotations_summary&#39;</span><span class="p">]</span>
+
+        <span class="n">hdr</span> <span class="o">=</span> <span class="n">tbl</span><span class="o">.</span><span class="n">columns</span>
+
+        <span class="c1"># filtering for resources</span>
+        <span class="k">if</span> <span class="sa">b</span><span class="s1">&#39;resources&#39;</span> <span class="ow">in</span> <span class="n">req</span><span class="o">.</span><span class="n">args</span><span class="p">:</span>
+
+            <span class="n">resources</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_args_set</span><span class="p">(</span><span class="n">req</span><span class="p">,</span> <span class="s1">&#39;resources&#39;</span><span class="p">)</span>
+
+            <span class="n">tbl</span> <span class="o">=</span> <span class="n">tbl</span><span class="o">.</span><span class="n">loc</span><span class="p">[</span><span class="n">tbl</span><span class="o">.</span><span class="n">source</span><span class="o">.</span><span class="n">isin</span><span class="p">(</span><span class="n">resources</span><span class="p">)]</span>
+
+        <span class="k">if</span> <span class="p">(</span>
+            <span class="sa">b</span><span class="s1">&#39;cytoscape&#39;</span> <span class="ow">in</span> <span class="n">req</span><span class="o">.</span><span class="n">args</span> <span class="ow">and</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">_parse_arg</span><span class="p">(</span><span class="n">req</span><span class="o">.</span><span class="n">args</span><span class="p">[</span><span class="sa">b</span><span class="s1">&#39;cytoscape&#39;</span><span class="p">])</span>
+        <span class="p">):</span>
+
+            <span class="n">cytoscape</span> <span class="o">=</span> <span class="kc">True</span>
+
+        <span class="k">else</span><span class="p">:</span>
+
+            <span class="n">cytoscape</span> <span class="o">=</span> <span class="kc">False</span>
+
+        <span class="n">tbl</span> <span class="o">=</span> <span class="n">tbl</span><span class="o">.</span><span class="n">loc</span><span class="p">[:,</span><span class="n">hdr</span><span class="p">]</span>
+
+        <span class="k">if</span> <span class="n">cytoscape</span><span class="p">:</span>
+
+            <span class="n">tbl</span> <span class="o">=</span> <span class="n">tbl</span><span class="o">.</span><span class="n">set_index</span><span class="p">([</span><span class="s1">&#39;source&#39;</span><span class="p">,</span> <span class="s1">&#39;label&#39;</span><span class="p">],</span> <span class="n">drop</span> <span class="o">=</span> <span class="kc">False</span><span class="p">)</span>
+
+            <span class="n">cytoscape_keys</span> <span class="o">=</span> <span class="p">{</span>
+                <span class="p">(</span><span class="n">source</span><span class="p">,</span> <span class="n">label</span><span class="p">)</span>
+                <span class="k">for</span> <span class="n">source</span><span class="p">,</span> <span class="n">labels</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">cytoscape_attributes</span>
+                <span class="k">for</span> <span class="n">label</span> <span class="ow">in</span> <span class="p">(</span>
+                    <span class="n">labels</span> <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">labels</span><span class="p">,</span> <span class="nb">tuple</span><span class="p">)</span> <span class="k">else</span> <span class="p">(</span><span class="n">labels</span><span class="p">,)</span>
+                <span class="p">)</span>
+            <span class="p">}</span> <span class="o">&amp;</span> <span class="nb">set</span><span class="p">(</span><span class="n">tbl</span><span class="o">.</span><span class="n">index</span><span class="p">)</span>
+
+            <span class="n">tbl</span> <span class="o">=</span> <span class="n">tbl</span><span class="o">.</span><span class="n">loc</span><span class="p">[</span><span class="nb">list</span><span class="p">(</span><span class="n">cytoscape_keys</span><span class="p">)]</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_serve_dataframe</span><span class="p">(</span><span class="n">tbl</span><span class="p">,</span> <span class="n">req</span><span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">intercell</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">req</span><span class="p">):</span>
+
+        <span class="n">bad_req</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_check_args</span><span class="p">(</span><span class="n">req</span><span class="p">)</span>
+
+        <span class="k">if</span> <span class="n">bad_req</span><span class="p">:</span>
+
+            <span class="k">return</span> <span class="n">bad_req</span>
+
+        <span class="k">if</span> <span class="sa">b</span><span class="s1">&#39;databases&#39;</span> <span class="ow">in</span> <span class="n">req</span><span class="o">.</span><span class="n">args</span><span class="p">:</span>
+
+            <span class="n">req</span><span class="o">.</span><span class="n">args</span><span class="p">[</span><span class="sa">b</span><span class="s1">&#39;resources&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">req</span><span class="o">.</span><span class="n">args</span><span class="p">[</span><span class="sa">b</span><span class="s1">&#39;databases&#39;</span><span class="p">]</span>
+
+
+        <span class="c1"># starting from the entire dataset</span>
+        <span class="n">tbl</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span><span class="p">[</span><span class="s1">&#39;intercell&#39;</span><span class="p">]</span>
+
+        <span class="n">hdr</span> <span class="o">=</span> <span class="n">tbl</span><span class="o">.</span><span class="n">columns</span>
+
+        <span class="c1"># filtering for category types</span>
+        <span class="k">for</span> <span class="n">var</span> <span class="ow">in</span> <span class="p">(</span>
+            <span class="s1">&#39;aspect&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;source&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;scope&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;transmitter&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;receiver&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;parent&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;resources&#39;</span><span class="p">,</span>
+        <span class="p">):</span>
+
+            <span class="k">if</span> <span class="n">var</span><span class="o">.</span><span class="n">encode</span><span class="p">(</span><span class="s1">&#39;ascii&#39;</span><span class="p">)</span> <span class="ow">in</span> <span class="n">req</span><span class="o">.</span><span class="n">args</span><span class="p">:</span>
+
+                <span class="n">values</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_args_set</span><span class="p">(</span><span class="n">req</span><span class="p">,</span> <span class="n">var</span><span class="p">)</span>
+
+                <span class="k">if</span> <span class="n">var</span> <span class="ow">in</span> <span class="p">{</span><span class="s1">&#39;resources&#39;</span><span class="p">,</span> <span class="s1">&#39;databases&#39;</span><span class="p">}:</span>
+
+                    <span class="n">var</span> <span class="o">=</span> <span class="s1">&#39;database&#39;</span>
+
+                <span class="n">tbl</span> <span class="o">=</span> <span class="n">tbl</span><span class="o">.</span><span class="n">loc</span><span class="p">[</span><span class="nb">getattr</span><span class="p">(</span><span class="n">tbl</span><span class="p">,</span> <span class="n">var</span><span class="p">)</span><span class="o">.</span><span class="n">isin</span><span class="p">(</span><span class="n">values</span><span class="p">)]</span>
+
+        <span class="k">for</span> <span class="p">(</span><span class="n">_long</span><span class="p">,</span> <span class="n">short</span><span class="p">)</span> <span class="ow">in</span> <span class="p">(</span>
+            <span class="p">(</span><span class="s1">&#39;transmitter&#39;</span><span class="p">,</span> <span class="s1">&#39;trans&#39;</span><span class="p">),</span>
+            <span class="p">(</span><span class="s1">&#39;receiver&#39;</span><span class="p">,</span> <span class="s1">&#39;rec&#39;</span><span class="p">),</span>
+            <span class="p">(</span><span class="s1">&#39;secreted&#39;</span><span class="p">,</span> <span class="s1">&#39;sec&#39;</span><span class="p">),</span>
+            <span class="p">(</span><span class="s1">&#39;plasma_membrane_peripheral&#39;</span><span class="p">,</span> <span class="s1">&#39;pmp&#39;</span><span class="p">),</span>
+            <span class="p">(</span><span class="s1">&#39;plasma_membrane_transmembrane&#39;</span><span class="p">,</span> <span class="s1">&#39;pmtm&#39;</span><span class="p">),</span>
+        <span class="p">):</span>
+
+            <span class="n">this_arg</span> <span class="o">=</span> <span class="kc">None</span>
+            <span class="n">_long_b</span> <span class="o">=</span> <span class="n">_long</span><span class="o">.</span><span class="n">encode</span><span class="p">(</span><span class="s1">&#39;ascii&#39;</span><span class="p">)</span>
+            <span class="n">short_b</span> <span class="o">=</span> <span class="n">short</span><span class="o">.</span><span class="n">encode</span><span class="p">(</span><span class="s1">&#39;ascii&#39;</span><span class="p">)</span>
+
+            <span class="k">if</span> <span class="n">_long_b</span> <span class="ow">in</span> <span class="n">req</span><span class="o">.</span><span class="n">args</span><span class="p">:</span>
+
+                <span class="n">this_arg</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_parse_arg</span><span class="p">(</span><span class="n">req</span><span class="o">.</span><span class="n">args</span><span class="p">[</span><span class="n">_long_b</span><span class="p">])</span>
+
+            <span class="k">elif</span> <span class="n">short_b</span> <span class="ow">in</span> <span class="n">req</span><span class="o">.</span><span class="n">args</span><span class="p">:</span>
+
+                <span class="n">this_arg</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_parse_arg</span><span class="p">(</span><span class="n">req</span><span class="o">.</span><span class="n">args</span><span class="p">[</span><span class="n">short_b</span><span class="p">])</span>
+
+            <span class="k">if</span> <span class="n">this_arg</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
+
+                <span class="n">tbl</span> <span class="o">=</span> <span class="n">tbl</span><span class="o">.</span><span class="n">loc</span><span class="p">[</span><span class="nb">getattr</span><span class="p">(</span><span class="n">tbl</span><span class="p">,</span> <span class="n">_long</span><span class="p">)</span> <span class="o">==</span> <span class="n">this_arg</span><span class="p">]</span>
+
+        <span class="k">if</span> <span class="sa">b</span><span class="s1">&#39;causality&#39;</span> <span class="ow">in</span> <span class="n">req</span><span class="o">.</span><span class="n">args</span><span class="p">:</span>
+
+            <span class="n">causality</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_args_set</span><span class="p">(</span><span class="n">req</span><span class="p">,</span> <span class="s1">&#39;causality&#39;</span><span class="p">)</span>
+
+            <span class="n">trans</span> <span class="o">=</span> <span class="n">causality</span> <span class="o">&amp;</span> <span class="p">{</span><span class="s1">&#39;transmitter&#39;</span><span class="p">,</span> <span class="s1">&#39;trans&#39;</span><span class="p">,</span> <span class="s1">&#39;both&#39;</span><span class="p">}</span>
+            <span class="n">rec</span> <span class="o">=</span> <span class="n">causality</span> <span class="o">&amp;</span> <span class="p">{</span><span class="s1">&#39;receiver&#39;</span><span class="p">,</span> <span class="s1">&#39;rec&#39;</span><span class="p">,</span> <span class="s1">&#39;both&#39;</span><span class="p">}</span>
+            <span class="n">tbl</span> <span class="o">=</span> <span class="p">(</span>
+                <span class="n">tbl</span><span class="o">.</span><span class="n">loc</span><span class="p">[</span><span class="n">tbl</span><span class="o">.</span><span class="n">transmitter</span> <span class="o">|</span> <span class="n">tbl</span><span class="o">.</span><span class="n">receiver</span><span class="p">]</span>
+                    <span class="k">if</span> <span class="n">trans</span> <span class="ow">and</span> <span class="n">rec</span> <span class="k">else</span>
+                <span class="n">tbl</span><span class="o">.</span><span class="n">loc</span><span class="p">[</span><span class="n">tbl</span><span class="o">.</span><span class="n">transmitter</span><span class="p">]</span>
+                    <span class="k">if</span> <span class="n">trans</span> <span class="k">else</span>
+                <span class="n">tbl</span><span class="o">.</span><span class="n">loc</span><span class="p">[</span><span class="n">tbl</span><span class="o">.</span><span class="n">receiver</span><span class="p">]</span>
+                    <span class="k">if</span> <span class="n">rec</span> <span class="k">else</span>
+                <span class="n">tbl</span>
+            <span class="p">)</span>
+
+        <span class="k">if</span> <span class="sa">b</span><span class="s1">&#39;topology&#39;</span> <span class="ow">in</span> <span class="n">req</span><span class="o">.</span><span class="n">args</span><span class="p">:</span>
+
+            <span class="n">topology</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_args_set</span><span class="p">(</span><span class="n">req</span><span class="p">,</span> <span class="s1">&#39;topology&#39;</span><span class="p">)</span>
+            <span class="n">query</span> <span class="o">=</span> <span class="s1">&#39; or &#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span>
+                <span class="n">colname</span>
+                <span class="k">for</span> <span class="n">enabled</span><span class="p">,</span> <span class="n">colname</span> <span class="ow">in</span>
+                <span class="p">(</span>
+                    <span class="p">(</span><span class="n">topology</span> <span class="o">&amp;</span> <span class="p">{</span><span class="s1">&#39;secreted&#39;</span><span class="p">,</span> <span class="s1">&#39;sec&#39;</span><span class="p">},</span> <span class="s1">&#39;secreted&#39;</span><span class="p">),</span>
+                    <span class="p">(</span>
+                        <span class="n">topology</span> <span class="o">&amp;</span> <span class="p">{</span><span class="s1">&#39;plasma_membrane_peripheral&#39;</span><span class="p">,</span> <span class="s1">&#39;pmp&#39;</span><span class="p">},</span>
+                        <span class="s1">&#39;plasma_membrane_peripheral&#39;</span>
+                    <span class="p">),</span>
+                    <span class="p">(</span>
+                        <span class="n">topology</span> <span class="o">&amp;</span> <span class="p">{</span><span class="s1">&#39;plasma_membrane_transmembrane&#39;</span><span class="p">,</span> <span class="s1">&#39;pmtm&#39;</span><span class="p">},</span>
+                        <span class="s1">&#39;plasma_membrane_transmembrane&#39;</span>
+                    <span class="p">)</span>
+                <span class="p">)</span>
+                <span class="k">if</span> <span class="n">enabled</span>
+            <span class="p">)</span>
+
+            <span class="k">if</span> <span class="n">query</span><span class="p">:</span>
+
+                <span class="n">tbl</span> <span class="o">=</span> <span class="n">tbl</span><span class="o">.</span><span class="n">query</span><span class="p">(</span><span class="n">query</span><span class="p">)</span>
+
+        <span class="c1"># filtering for categories</span>
+        <span class="k">if</span> <span class="sa">b</span><span class="s1">&#39;categories&#39;</span> <span class="ow">in</span> <span class="n">req</span><span class="o">.</span><span class="n">args</span><span class="p">:</span>
+
+            <span class="n">categories</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_args_set</span><span class="p">(</span><span class="n">req</span><span class="p">,</span> <span class="s1">&#39;categories&#39;</span><span class="p">)</span>
+
+            <span class="n">tbl</span> <span class="o">=</span> <span class="n">tbl</span><span class="o">.</span><span class="n">loc</span><span class="p">[</span><span class="n">tbl</span><span class="o">.</span><span class="n">category</span><span class="o">.</span><span class="n">isin</span><span class="p">(</span><span class="n">categories</span><span class="p">)]</span>
+
+        <span class="c1"># filtering for entity types</span>
+        <span class="k">if</span> <span class="sa">b</span><span class="s1">&#39;entity_types&#39;</span> <span class="ow">in</span> <span class="n">req</span><span class="o">.</span><span class="n">args</span><span class="p">:</span>
+
+            <span class="n">entity_types</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_args_set</span><span class="p">(</span><span class="n">req</span><span class="p">,</span> <span class="s1">&#39;entity_types&#39;</span><span class="p">)</span>
+
+            <span class="n">tbl</span> <span class="o">=</span> <span class="n">tbl</span><span class="o">.</span><span class="n">loc</span><span class="p">[</span><span class="n">tbl</span><span class="o">.</span><span class="n">entity_type</span><span class="o">.</span><span class="n">isin</span><span class="p">(</span><span class="n">entity_types</span><span class="p">)]</span>
+
+        <span class="c1"># filtering for proteins</span>
+        <span class="k">if</span> <span class="sa">b</span><span class="s1">&#39;proteins&#39;</span> <span class="ow">in</span> <span class="n">req</span><span class="o">.</span><span class="n">args</span><span class="p">:</span>
+
+            <span class="n">proteins</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_args_set</span><span class="p">(</span><span class="n">req</span><span class="p">,</span> <span class="s1">&#39;proteins&#39;</span><span class="p">)</span>
+
+            <span class="n">tbl</span> <span class="o">=</span> <span class="n">tbl</span><span class="o">.</span><span class="n">loc</span><span class="p">[</span>
+                <span class="n">np</span><span class="o">.</span><span class="n">logical_or</span><span class="p">(</span>
+                    <span class="n">tbl</span><span class="o">.</span><span class="n">uniprot</span><span class="o">.</span><span class="n">isin</span><span class="p">(</span><span class="n">proteins</span><span class="p">),</span>
+                    <span class="n">tbl</span><span class="o">.</span><span class="n">genesymbol</span><span class="o">.</span><span class="n">isin</span><span class="p">(</span><span class="n">proteins</span><span class="p">),</span>
+                <span class="p">)</span>
+            <span class="p">]</span>
+
+        <span class="n">license</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_get_license</span><span class="p">(</span><span class="n">req</span><span class="p">)</span>
+
+        <span class="n">tbl</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_filter_by_license_intercell</span><span class="p">(</span><span class="n">tbl</span><span class="p">,</span> <span class="n">license</span><span class="p">)</span>
+
+        <span class="n">tbl</span> <span class="o">=</span> <span class="n">tbl</span><span class="o">.</span><span class="n">loc</span><span class="p">[:,</span><span class="n">hdr</span><span class="p">]</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_serve_dataframe</span><span class="p">(</span><span class="n">tbl</span><span class="p">,</span> <span class="n">req</span><span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">intercell_summary</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">req</span><span class="p">):</span>
+
+        <span class="n">bad_req</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_check_args</span><span class="p">(</span><span class="n">req</span><span class="p">)</span>
+
+        <span class="k">if</span> <span class="n">bad_req</span><span class="p">:</span>
+
+            <span class="k">return</span> <span class="n">bad_req</span>
+
+        <span class="k">if</span> <span class="sa">b</span><span class="s1">&#39;databases&#39;</span> <span class="ow">in</span> <span class="n">req</span><span class="o">.</span><span class="n">args</span><span class="p">:</span>
+
+            <span class="n">req</span><span class="o">.</span><span class="n">args</span><span class="p">[</span><span class="sa">b</span><span class="s1">&#39;resources&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">req</span><span class="o">.</span><span class="n">args</span><span class="p">[</span><span class="sa">b</span><span class="s1">&#39;databases&#39;</span><span class="p">]</span>
+
+        <span class="c1"># starting from the entire dataset</span>
+        <span class="n">tbl</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span><span class="p">[</span><span class="s1">&#39;intercell_summary&#39;</span><span class="p">]</span>
+
+        <span class="n">hdr</span> <span class="o">=</span> <span class="n">tbl</span><span class="o">.</span><span class="n">columns</span>
+
+        <span class="c1"># filtering for category types</span>
+        <span class="k">for</span> <span class="n">var</span> <span class="ow">in</span> <span class="p">(</span>
+            <span class="s1">&#39;aspect&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;source&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;scope&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;transmitter&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;receiver&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;parent&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;resources&#39;</span><span class="p">,</span>
+        <span class="p">):</span>
+
+            <span class="k">if</span> <span class="n">var</span><span class="o">.</span><span class="n">encode</span><span class="p">(</span><span class="s1">&#39;ascii&#39;</span><span class="p">)</span> <span class="ow">in</span> <span class="n">req</span><span class="o">.</span><span class="n">args</span><span class="p">:</span>
+
+                <span class="n">values</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_args_set</span><span class="p">(</span><span class="n">req</span><span class="p">,</span> <span class="n">var</span><span class="p">)</span>
+
+                <span class="n">tbl</span> <span class="o">=</span> <span class="n">tbl</span><span class="o">.</span><span class="n">loc</span><span class="p">[</span><span class="nb">getattr</span><span class="p">(</span><span class="n">tbl</span><span class="p">,</span> <span class="n">var</span><span class="p">)</span><span class="o">.</span><span class="n">isin</span><span class="p">(</span><span class="n">values</span><span class="p">)]</span>
+
+        <span class="c1"># filtering for categories</span>
+        <span class="k">if</span> <span class="sa">b</span><span class="s1">&#39;categories&#39;</span> <span class="ow">in</span> <span class="n">req</span><span class="o">.</span><span class="n">args</span><span class="p">:</span>
+
+            <span class="n">categories</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_args_set</span><span class="p">(</span><span class="n">req</span><span class="p">,</span> <span class="s1">&#39;categories&#39;</span><span class="p">)</span>
+
+            <span class="n">tbl</span> <span class="o">=</span> <span class="n">tbl</span><span class="o">.</span><span class="n">loc</span><span class="p">[</span><span class="n">tbl</span><span class="o">.</span><span class="n">category</span><span class="o">.</span><span class="n">isin</span><span class="p">(</span><span class="n">categories</span><span class="p">)]</span>
+
+        <span class="n">tbl</span> <span class="o">=</span> <span class="n">tbl</span><span class="o">.</span><span class="n">loc</span><span class="p">[:,</span><span class="n">hdr</span><span class="p">]</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_serve_dataframe</span><span class="p">(</span><span class="n">tbl</span><span class="p">,</span> <span class="n">req</span><span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">complexes</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">req</span><span class="p">):</span>
+
+        <span class="n">bad_req</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_check_args</span><span class="p">(</span><span class="n">req</span><span class="p">)</span>
+
+        <span class="k">if</span> <span class="n">bad_req</span><span class="p">:</span>
+
+            <span class="k">return</span> <span class="n">bad_req</span>
+
+        <span class="k">if</span> <span class="sa">b</span><span class="s1">&#39;databases&#39;</span> <span class="ow">in</span> <span class="n">req</span><span class="o">.</span><span class="n">args</span><span class="p">:</span>
+
+            <span class="n">req</span><span class="o">.</span><span class="n">args</span><span class="p">[</span><span class="sa">b</span><span class="s1">&#39;resources&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">req</span><span class="o">.</span><span class="n">args</span><span class="p">[</span><span class="sa">b</span><span class="s1">&#39;databases&#39;</span><span class="p">]</span>
+
+        <span class="c1"># starting from the entire dataset</span>
+        <span class="n">tbl</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span><span class="p">[</span><span class="s1">&#39;complexes&#39;</span><span class="p">]</span>
+
+        <span class="n">hdr</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="n">tbl</span><span class="o">.</span><span class="n">columns</span><span class="p">)</span>
+        <span class="n">hdr</span><span class="o">.</span><span class="n">remove</span><span class="p">(</span><span class="s1">&#39;set_sources&#39;</span><span class="p">)</span>
+        <span class="n">hdr</span><span class="o">.</span><span class="n">remove</span><span class="p">(</span><span class="s1">&#39;set_proteins&#39;</span><span class="p">)</span>
+
+        <span class="c1"># filtering for resources</span>
+        <span class="k">if</span> <span class="sa">b</span><span class="s1">&#39;resources&#39;</span> <span class="ow">in</span> <span class="n">req</span><span class="o">.</span><span class="n">args</span><span class="p">:</span>
+
+            <span class="n">resources</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_args_set</span><span class="p">(</span><span class="n">req</span><span class="p">,</span> <span class="s1">&#39;resources&#39;</span><span class="p">)</span>
+
+            <span class="n">tbl</span> <span class="o">=</span> <span class="n">tbl</span><span class="o">.</span><span class="n">loc</span><span class="p">[</span>
+                <span class="p">[</span>
+                    <span class="nb">bool</span><span class="p">(</span><span class="n">sources</span> <span class="o">&amp;</span> <span class="n">resources</span><span class="p">)</span>
+                    <span class="k">for</span> <span class="n">sources</span> <span class="ow">in</span> <span class="n">tbl</span><span class="o">.</span><span class="n">set_sources</span>
+                <span class="p">]</span>
+            <span class="p">]</span>
+
+        <span class="c1"># filtering for proteins</span>
+        <span class="k">if</span> <span class="sa">b</span><span class="s1">&#39;proteins&#39;</span> <span class="ow">in</span> <span class="n">req</span><span class="o">.</span><span class="n">args</span><span class="p">:</span>
+
+            <span class="n">proteins</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_args_set</span><span class="p">(</span><span class="n">req</span><span class="p">,</span> <span class="s1">&#39;proteins&#39;</span><span class="p">)</span>
+
+            <span class="n">tbl</span> <span class="o">=</span> <span class="n">tbl</span><span class="o">.</span><span class="n">loc</span><span class="p">[</span>
+                <span class="p">[</span>
+                    <span class="nb">bool</span><span class="p">(</span><span class="n">this_proteins</span> <span class="o">&amp;</span> <span class="n">proteins</span><span class="p">)</span>
+                    <span class="k">for</span> <span class="n">this_proteins</span> <span class="ow">in</span> <span class="n">tbl</span><span class="o">.</span><span class="n">set_proteins</span>
+                <span class="p">]</span>
+            <span class="p">]</span>
+
+        <span class="n">license</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_get_license</span><span class="p">(</span><span class="n">req</span><span class="p">)</span>
+
+        <span class="n">tbl</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_filter_by_license_complexes</span><span class="p">(</span><span class="n">tbl</span><span class="p">,</span> <span class="n">license</span><span class="p">)</span>
+
+        <span class="n">tbl</span> <span class="o">=</span> <span class="n">tbl</span><span class="o">.</span><span class="n">loc</span><span class="p">[:,</span><span class="n">hdr</span><span class="p">]</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_serve_dataframe</span><span class="p">(</span><span class="n">tbl</span><span class="p">,</span> <span class="n">req</span><span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">resources</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">req</span><span class="p">):</span>
+
+        <span class="n">datasets</span> <span class="o">=</span> <span class="p">(</span>
+
+            <span class="p">{</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">_query_type</span><span class="p">(</span><span class="n">dataset</span><span class="o">.</span><span class="n">decode</span><span class="p">(</span><span class="s1">&#39;ascii&#39;</span><span class="p">))</span>
+                <span class="k">for</span> <span class="n">dataset</span> <span class="ow">in</span> <span class="n">req</span><span class="o">.</span><span class="n">args</span><span class="p">[</span><span class="sa">b</span><span class="s1">&#39;datasets&#39;</span><span class="p">]</span>
+            <span class="p">}</span>
+
+            <span class="k">if</span> <span class="sa">b</span><span class="s1">&#39;datasets&#39;</span> <span class="ow">in</span> <span class="n">req</span><span class="o">.</span><span class="n">args</span> <span class="k">else</span>
+
+            <span class="kc">None</span>
+
+        <span class="p">)</span>
+
+        <span class="n">res_ctrl</span> <span class="o">=</span> <span class="n">resources_mod</span><span class="o">.</span><span class="n">get_controller</span><span class="p">()</span>
+        <span class="n">license</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_get_license</span><span class="p">(</span><span class="n">req</span><span class="p">)</span>
+
+        <span class="k">return</span> <span class="n">json</span><span class="o">.</span><span class="n">dumps</span><span class="p">(</span>
+            <span class="nb">dict</span><span class="p">(</span>
+                <span class="p">(</span><span class="n">k</span><span class="p">,</span> <span class="n">v</span><span class="p">)</span>
+                <span class="k">for</span> <span class="n">k</span><span class="p">,</span> <span class="n">v</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_resources_dict</span><span class="p">)</span>
+                <span class="k">if</span> <span class="p">(</span>
+                    <span class="n">res_ctrl</span><span class="o">.</span><span class="n">license</span><span class="p">(</span><span class="n">k</span><span class="p">)</span><span class="o">.</span><span class="n">enables</span><span class="p">(</span><span class="n">license</span><span class="p">)</span> <span class="ow">and</span>
+                    <span class="p">(</span>
+                        <span class="ow">not</span> <span class="n">datasets</span> <span class="ow">or</span>
+                        <span class="n">datasets</span> <span class="o">&amp;</span> <span class="nb">set</span><span class="p">(</span><span class="n">v</span><span class="p">[</span><span class="s1">&#39;datasets&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">keys</span><span class="p">())</span>
+                    <span class="p">)</span>
+                <span class="p">)</span>
+            <span class="p">)</span>
+        <span class="p">)</span>
+
+
+
+    <span class="nd">@staticmethod</span>
+    <span class="k">def</span> <span class="nf">_get_license</span><span class="p">(</span><span class="n">req</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="n">req</span><span class="o">.</span><span class="n">args</span><span class="p">[</span><span class="sa">b</span><span class="s1">&#39;license&#39;</span><span class="p">][</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">decode</span><span class="p">(</span><span class="s1">&#39;utf-8&#39;</span><span class="p">)</span>
+
+
+    <span class="nd">@classmethod</span>
+    <span class="k">def</span> <span class="nf">_filter_by_license_complexes</span><span class="p">(</span><span class="bp">cls</span><span class="p">,</span> <span class="n">tbl</span><span class="p">,</span> <span class="n">license</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="bp">cls</span><span class="o">.</span><span class="n">_filter_by_license</span><span class="p">(</span>
+            <span class="n">tbl</span> <span class="o">=</span> <span class="n">tbl</span><span class="p">,</span>
+            <span class="n">license</span> <span class="o">=</span> <span class="n">license</span><span class="p">,</span>
+            <span class="n">res_col</span> <span class="o">=</span> <span class="s1">&#39;sources&#39;</span><span class="p">,</span>
+            <span class="n">simple</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+            <span class="n">prefix_col</span> <span class="o">=</span> <span class="s1">&#39;identifiers&#39;</span><span class="p">,</span>
+        <span class="p">)</span>
+
+
+    <span class="nd">@classmethod</span>
+    <span class="k">def</span> <span class="nf">_filter_by_license_interactions</span><span class="p">(</span><span class="bp">cls</span><span class="p">,</span> <span class="n">tbl</span><span class="p">,</span> <span class="n">license</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="bp">cls</span><span class="o">.</span><span class="n">_filter_by_license</span><span class="p">(</span>
+            <span class="n">tbl</span> <span class="o">=</span> <span class="n">tbl</span><span class="p">,</span>
+            <span class="n">license</span> <span class="o">=</span> <span class="n">license</span><span class="p">,</span>
+            <span class="n">res_col</span> <span class="o">=</span> <span class="s1">&#39;sources&#39;</span><span class="p">,</span>
+            <span class="n">simple</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+            <span class="n">prefix_col</span> <span class="o">=</span> <span class="s1">&#39;references&#39;</span><span class="p">,</span>
+        <span class="p">)</span>
+
+
+    <span class="nd">@classmethod</span>
+    <span class="k">def</span> <span class="nf">_filter_by_license_annotations</span><span class="p">(</span><span class="bp">cls</span><span class="p">,</span> <span class="n">tbl</span><span class="p">,</span> <span class="n">license</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="bp">cls</span><span class="o">.</span><span class="n">_filter_by_license</span><span class="p">(</span>
+            <span class="n">tbl</span> <span class="o">=</span> <span class="n">tbl</span><span class="p">,</span>
+            <span class="n">license</span> <span class="o">=</span> <span class="n">license</span><span class="p">,</span>
+            <span class="n">res_col</span> <span class="o">=</span> <span class="s1">&#39;source&#39;</span><span class="p">,</span>
+            <span class="n">simple</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
+        <span class="p">)</span>
+
+
+    <span class="nd">@classmethod</span>
+    <span class="k">def</span> <span class="nf">_filter_by_license_intercell</span><span class="p">(</span><span class="bp">cls</span><span class="p">,</span> <span class="n">tbl</span><span class="p">,</span> <span class="n">license</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="bp">cls</span><span class="o">.</span><span class="n">_filter_by_license</span><span class="p">(</span>
+            <span class="n">tbl</span> <span class="o">=</span> <span class="n">tbl</span><span class="p">,</span>
+            <span class="n">license</span> <span class="o">=</span> <span class="n">license</span><span class="p">,</span>
+            <span class="n">res_col</span> <span class="o">=</span> <span class="s1">&#39;database&#39;</span><span class="p">,</span>
+            <span class="n">simple</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
+        <span class="p">)</span>
+
+
+    <span class="nd">@staticmethod</span>
+    <span class="k">def</span> <span class="nf">_filter_by_license</span><span class="p">(</span>
+            <span class="n">tbl</span><span class="p">,</span>
+            <span class="n">license</span><span class="p">,</span>
+            <span class="n">res_col</span><span class="p">,</span>
+            <span class="n">simple</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+            <span class="n">prefix_col</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+        <span class="p">):</span>
+
+        <span class="k">def</span> <span class="nf">filter_resources</span><span class="p">(</span><span class="n">res</span><span class="p">):</span>
+
+            <span class="n">res</span> <span class="o">=</span> <span class="p">{</span>
+                <span class="n">r</span> <span class="k">for</span> <span class="n">r</span> <span class="ow">in</span> <span class="n">res</span>
+                <span class="k">if</span> <span class="n">res_ctrl</span><span class="o">.</span><span class="n">license</span><span class="p">(</span><span class="n">r</span><span class="p">)</span><span class="o">.</span><span class="n">enables</span><span class="p">(</span><span class="n">license</span><span class="p">)</span>
+            <span class="p">}</span>
+
+            <span class="n">composite</span> <span class="o">=</span> <span class="p">[</span>
+                <span class="n">r</span> <span class="k">for</span> <span class="n">r</span> <span class="ow">in</span> <span class="n">res</span>
+                <span class="k">if</span> <span class="n">res_ctrl</span><span class="o">.</span><span class="n">license</span><span class="p">(</span><span class="n">r</span><span class="p">)</span><span class="o">.</span><span class="n">name</span> <span class="o">==</span> <span class="s1">&#39;Composite&#39;</span>
+            <span class="p">]</span>
+
+            <span class="k">if</span> <span class="n">composite</span><span class="p">:</span>
+
+                <span class="n">composite_to_remove</span> <span class="o">=</span> <span class="p">{</span>
+                    <span class="n">comp_res</span>
+                    <span class="k">for</span> <span class="n">comp_res</span> <span class="ow">in</span> <span class="n">composite</span>
+                    <span class="k">if</span> <span class="ow">not</span> <span class="n">res_ctrl</span><span class="o">.</span><span class="n">secondary_resources</span><span class="p">(</span><span class="n">comp_res</span><span class="p">,</span> <span class="kc">True</span><span class="p">)</span> <span class="o">&amp;</span> <span class="n">res</span>
+                <span class="p">}</span>
+
+                <span class="n">res</span> <span class="o">=</span> <span class="n">res</span> <span class="o">-</span> <span class="n">composite_to_remove</span>
+
+            <span class="k">return</span> <span class="n">res</span>
+
+
+        <span class="k">if</span> <span class="n">license</span> <span class="o">==</span> <span class="n">LICENSE_IGNORE</span> <span class="ow">or</span> <span class="n">tbl</span><span class="o">.</span><span class="n">shape</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
+
+            <span class="k">return</span> <span class="n">tbl</span>
+
+        <span class="n">res_ctrl</span> <span class="o">=</span> <span class="n">resources_mod</span><span class="o">.</span><span class="n">get_controller</span><span class="p">()</span>
+
+        <span class="n">_res_col</span> <span class="o">=</span> <span class="nb">getattr</span><span class="p">(</span><span class="n">tbl</span><span class="p">,</span> <span class="n">res_col</span><span class="p">)</span>
+
+        <span class="k">if</span> <span class="n">simple</span><span class="p">:</span>
+
+            <span class="n">bool_idx</span> <span class="o">=</span> <span class="p">[</span>
+                <span class="n">res_ctrl</span><span class="o">.</span><span class="n">license</span><span class="p">(</span><span class="n">res</span><span class="p">)</span><span class="o">.</span><span class="n">enables</span><span class="p">(</span><span class="n">license</span><span class="p">)</span>
+                <span class="k">for</span> <span class="n">res</span> <span class="ow">in</span> <span class="n">_res_col</span>
+            <span class="p">]</span>
+
+        <span class="k">else</span><span class="p">:</span>
+
+            <span class="n">_set_res_col</span> <span class="o">=</span> <span class="n">tbl</span><span class="o">.</span><span class="n">set_sources</span>
+
+            <span class="n">_res_to_keep</span> <span class="o">=</span> <span class="p">[</span>
+                <span class="n">filter_resources</span><span class="p">(</span><span class="n">ress</span><span class="p">)</span>
+                <span class="k">for</span> <span class="n">ress</span> <span class="ow">in</span> <span class="n">_set_res_col</span>
+            <span class="p">]</span>
+
+            <span class="k">with</span> <span class="n">ignore_pandas_copywarn</span><span class="p">():</span>
+
+                <span class="n">tbl</span><span class="p">[</span><span class="n">res_col</span><span class="p">]</span> <span class="o">=</span> <span class="p">[</span>
+                    <span class="s1">&#39;;&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="nb">sorted</span><span class="p">(</span><span class="n">ress</span><span class="p">))</span>
+                    <span class="k">for</span> <span class="n">ress</span> <span class="ow">in</span> <span class="n">_res_to_keep</span>
+                <span class="p">]</span>
+
+            <span class="k">if</span> <span class="n">prefix_col</span><span class="p">:</span>
+
+                <span class="n">_prefix_col</span> <span class="o">=</span> <span class="nb">getattr</span><span class="p">(</span><span class="n">tbl</span><span class="p">,</span> <span class="n">prefix_col</span><span class="p">)</span>
+
+                <span class="n">_new_prefix_col</span> <span class="o">=</span> <span class="p">[</span>
+
+                    <span class="s1">&#39;;&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="nb">sorted</span><span class="p">(</span>
+                        <span class="n">pref_res</span>
+                        <span class="k">for</span> <span class="n">pref_res</span> <span class="ow">in</span> <span class="n">pref_ress</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;;&#39;</span><span class="p">)</span>
+                        <span class="k">if</span> <span class="p">(</span>
+                            <span class="n">pref_res</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;:&#39;</span><span class="p">,</span> <span class="n">maxsplit</span> <span class="o">=</span> <span class="mi">1</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span> <span class="ow">in</span>
+                            <span class="n">_res_to_keep</span><span class="p">[</span><span class="n">i</span><span class="p">]</span>
+                        <span class="p">)</span>
+                    <span class="p">))</span>
+
+                        <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">pref_ress</span><span class="p">,</span> <span class="nb">str</span><span class="p">)</span> <span class="k">else</span>
+
+                    <span class="n">pref_ress</span>
+
+                    <span class="k">for</span> <span class="n">i</span><span class="p">,</span> <span class="n">pref_ress</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">_prefix_col</span><span class="p">)</span>
+                <span class="p">]</span>
+
+                <span class="k">with</span> <span class="n">ignore_pandas_copywarn</span><span class="p">():</span>
+
+                    <span class="n">tbl</span><span class="p">[</span><span class="n">prefix_col</span><span class="p">]</span> <span class="o">=</span> <span class="n">_new_prefix_col</span>
+
+            <span class="n">bool_idx</span> <span class="o">=</span> <span class="p">[</span><span class="nb">bool</span><span class="p">(</span><span class="n">res</span><span class="p">)</span> <span class="k">for</span> <span class="n">res</span> <span class="ow">in</span> <span class="n">tbl</span><span class="p">[</span><span class="n">res_col</span><span class="p">]]</span>
+
+        <span class="n">tbl</span> <span class="o">=</span> <span class="n">tbl</span><span class="o">.</span><span class="n">loc</span><span class="p">[</span><span class="n">bool_idx</span><span class="p">]</span>
+
+        <span class="k">return</span> <span class="n">tbl</span>
+
+
+    <span class="nd">@classmethod</span>
+    <span class="k">def</span> <span class="nf">_serve_dataframe</span><span class="p">(</span><span class="bp">cls</span><span class="p">,</span> <span class="n">tbl</span><span class="p">,</span> <span class="n">req</span><span class="p">):</span>
+
+        <span class="k">if</span> <span class="sa">b</span><span class="s1">&#39;limit&#39;</span> <span class="ow">in</span> <span class="n">req</span><span class="o">.</span><span class="n">args</span><span class="p">:</span>
+
+            <span class="n">limit</span> <span class="o">=</span> <span class="n">req</span><span class="o">.</span><span class="n">args</span><span class="p">[</span><span class="sa">b</span><span class="s1">&#39;limit&#39;</span><span class="p">][</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">decode</span><span class="p">(</span><span class="s1">&#39;utf-8&#39;</span><span class="p">)</span>
+
+            <span class="k">if</span> <span class="n">limit</span><span class="o">.</span><span class="n">isdigit</span><span class="p">():</span>
+
+                <span class="n">limit</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">limit</span><span class="p">)</span>
+                <span class="n">tbl</span> <span class="o">=</span> <span class="n">tbl</span><span class="o">.</span><span class="n">head</span><span class="p">(</span><span class="n">limit</span><span class="p">)</span>
+
+        <span class="k">if</span> <span class="sa">b</span><span class="s1">&#39;format&#39;</span> <span class="ow">in</span> <span class="n">req</span><span class="o">.</span><span class="n">args</span> <span class="ow">and</span> <span class="n">req</span><span class="o">.</span><span class="n">args</span><span class="p">[</span><span class="sa">b</span><span class="s1">&#39;format&#39;</span><span class="p">][</span><span class="mi">0</span><span class="p">]</span> <span class="o">==</span> <span class="sa">b</span><span class="s1">&#39;json&#39;</span><span class="p">:</span>
+
+            <span class="n">data_json</span> <span class="o">=</span> <span class="n">tbl</span><span class="o">.</span><span class="n">to_json</span><span class="p">(</span><span class="n">orient</span> <span class="o">=</span> <span class="s1">&#39;records&#39;</span><span class="p">)</span>
+            <span class="c1"># this is necessary because in the data frame we keep lists</span>
+            <span class="c1"># as `;` separated strings but in json is nicer to serve</span>
+            <span class="c1"># them as lists</span>
+            <span class="n">data_json</span> <span class="o">=</span> <span class="n">json</span><span class="o">.</span><span class="n">loads</span><span class="p">(</span><span class="n">data_json</span><span class="p">)</span>
+
+            <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="n">data_json</span><span class="p">:</span>
+
+                <span class="k">for</span> <span class="n">k</span><span class="p">,</span> <span class="n">v</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="n">i</span><span class="p">):</span>
+
+                    <span class="k">if</span> <span class="n">k</span> <span class="ow">in</span> <span class="bp">cls</span><span class="o">.</span><span class="n">list_fields</span><span class="p">:</span>
+
+                        <span class="n">i</span><span class="p">[</span><span class="n">k</span><span class="p">]</span> <span class="o">=</span> <span class="p">(</span>
+                            <span class="p">[</span>
+                                <span class="p">(</span>
+                                    <span class="nb">int</span><span class="p">(</span><span class="n">f</span><span class="p">)</span>
+                                    <span class="k">if</span> <span class="p">(</span>
+                                        <span class="n">k</span> <span class="ow">in</span> <span class="bp">cls</span><span class="o">.</span><span class="n">int_list_fields</span> <span class="ow">and</span>
+                                        <span class="n">f</span><span class="o">.</span><span class="n">isdigit</span><span class="p">()</span>
+                                    <span class="p">)</span> <span class="k">else</span>
+                                    <span class="n">f</span>
+                                <span class="p">)</span>
+                                <span class="k">for</span> <span class="n">f</span> <span class="ow">in</span> <span class="n">v</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;;&#39;</span><span class="p">)</span>
+                            <span class="p">]</span>
+                            <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">v</span><span class="p">,</span> <span class="nb">str</span><span class="p">)</span> <span class="k">else</span>
+                            <span class="p">[]</span>
+                        <span class="p">)</span>
+
+            <span class="k">return</span> <span class="n">json</span><span class="o">.</span><span class="n">dumps</span><span class="p">(</span><span class="n">data_json</span><span class="p">)</span>
+
+        <span class="k">else</span><span class="p">:</span>
+
+            <span class="k">return</span> <span class="n">tbl</span><span class="o">.</span><span class="n">to_csv</span><span class="p">(</span>
+                <span class="n">sep</span> <span class="o">=</span> <span class="s1">&#39;</span><span class="se">\t</span><span class="s1">&#39;</span><span class="p">,</span>
+                <span class="n">index</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+                <span class="n">header</span> <span class="o">=</span> <span class="nb">bool</span><span class="p">(</span><span class="n">req</span><span class="o">.</span><span class="n">args</span><span class="p">[</span><span class="sa">b</span><span class="s1">&#39;header&#39;</span><span class="p">]),</span>
+                <span class="n">chunksize</span> <span class="o">=</span> <span class="mf">2e5</span><span class="p">,</span>
+            <span class="p">)</span>
+
+
+    <span class="nd">@staticmethod</span>
+    <span class="k">def</span> <span class="nf">_args_set</span><span class="p">(</span><span class="n">req</span><span class="p">,</span> <span class="n">arg</span><span class="p">):</span>
+
+        <span class="n">arg</span> <span class="o">=</span> <span class="n">arg</span><span class="o">.</span><span class="n">encode</span><span class="p">(</span><span class="s1">&#39;utf-8&#39;</span><span class="p">)</span>
+
+        <span class="k">return</span> <span class="p">(</span>
+            <span class="nb">set</span><span class="p">(</span><span class="n">req</span><span class="o">.</span><span class="n">args</span><span class="p">[</span><span class="n">arg</span><span class="p">][</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">decode</span><span class="p">(</span><span class="s1">&#39;utf-8&#39;</span><span class="p">)</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;,&#39;</span><span class="p">))</span>
+            <span class="k">if</span> <span class="n">arg</span> <span class="ow">in</span> <span class="n">req</span><span class="o">.</span><span class="n">args</span>
+            <span class="k">else</span> <span class="nb">set</span><span class="p">()</span>
+        <span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="Rest">
+<a class="viewcode-back" href="../../../../api/pypath.omnipath.server.run.Rest.html#pypath.omnipath.server.run.Rest">[docs]</a>
+<span class="k">class</span> <span class="nc">Rest</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span>
+
+<div class="viewcode-block" id="Rest.__init__">
+<a class="viewcode-back" href="../../../../api/pypath.omnipath.server.run.Rest.html#pypath.omnipath.server.run.Rest.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">port</span><span class="p">,</span>
+            <span class="n">serverclass</span> <span class="o">=</span> <span class="n">TableServer</span><span class="p">,</span>
+            <span class="n">start</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
+            <span class="o">**</span><span class="n">kwargs</span>
+        <span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Runs a webserver serving a `PyPath` instance listening</span>
+<span class="sd">        to a custom port.</span>
+
+<span class="sd">        Args</span>
+<span class="sd">        -----</span>
+<span class="sd">        :param int port:</span>
+<span class="sd">            The port to listen to.</span>
+<span class="sd">        :param str serverclass&#39;</span>
+<span class="sd">            The class implementing the server.</span>
+<span class="sd">        :param **kwargs:</span>
+<span class="sd">            Arguments for initialization of the server class.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">port</span> <span class="o">=</span> <span class="n">port</span>
+        <span class="n">_log</span><span class="p">(</span><span class="s1">&#39;Creating the server class.&#39;</span><span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">server</span> <span class="o">=</span> <span class="n">serverclass</span><span class="p">(</span><span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
+        <span class="n">_log</span><span class="p">(</span><span class="s1">&#39;Server class ready.&#39;</span><span class="p">)</span>
+
+        <span class="k">if</span> <span class="n">start</span><span class="p">:</span>
+
+            <span class="n">_log</span><span class="p">(</span><span class="s1">&#39;Starting the twisted server.&#39;</span><span class="p">)</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">start</span><span class="p">()</span></div>
+
+
+    <span class="k">def</span> <span class="nf">start</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">site</span> <span class="o">=</span> <span class="n">TwistedWebSite</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">server</span><span class="p">)</span>
+        <span class="n">_log</span><span class="p">(</span><span class="s1">&#39;Site created.&#39;</span><span class="p">)</span>
+        <span class="n">twisted_listen_tcp</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">port</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">site</span><span class="p">)</span>
+        <span class="n">_log</span><span class="p">(</span><span class="s1">&#39;Server going to listen on port </span><span class="si">%u</span><span class="s1"> from now.&#39;</span> <span class="o">%</span> <span class="bp">self</span><span class="o">.</span><span class="n">port</span><span class="p">)</span>
+        <span class="n">twisted_run</span><span class="p">()</span></div>
+
+</pre></div>
+
+                </article>
+              
+              
+              
+              
+              
+                <footer class="prev-next-footer">
+                  
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diff --git a/_modules/pypath/resources/descriptions.html b/_modules/pypath/resources/descriptions.html
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@@ -0,0 +1,3958 @@
+
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+
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+<html lang="en" data-content_root="../../../" >
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+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
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+  
+  
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+    document.documentElement.dataset.mode = localStorage.getItem("mode") || "";
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+    <script>DOCUMENTATION_OPTIONS.pagename = '_modules/pypath/resources/descriptions';</script>
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+  
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+                      </a>
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+                      <a class="nav-link nav-internal" href="../../../webservice.html">
+                        Webservice
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+                        Release history
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+            <span class="sr-only">Saez Lab</span></a>
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+</ul></div>
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+    <li class="breadcrumb-item"><a href="../../index.html" class="nav-link">Module code</a></li>
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+    <li class="breadcrumb-item"><a href="../resources.html" class="nav-link">pypath.resources</a></li>
+    
+    <li class="breadcrumb-item active" aria-current="page">pypath.resou...</li>
+  </ul>
+</nav>
+</div>
+      
+    </div>
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+</div>
+</div>
+              
+              
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+                
+<div id="searchbox"></div>
+                <article class="bd-article">
+                  
+  <h1>Source code for pypath.resources.descriptions</h1><div class="highlight"><pre>
+<span></span><span class="ch">#!/usr/bin/env python</span>
+<span class="c1"># -*- coding: utf-8 -*-</span>
+
+<span class="c1">#</span>
+<span class="c1">#  This file is part of the `pypath` python module</span>
+<span class="c1">#</span>
+<span class="c1">#  Copyright 2014-2023</span>
+<span class="c1">#  EMBL, EMBL-EBI, Uniklinik RWTH Aachen, Heidelberg University</span>
+<span class="c1">#</span>
+<span class="c1">#  Authors: see the file `README.rst`</span>
+<span class="c1">#  Contact: Dénes Türei (turei.denes@gmail.com)</span>
+<span class="c1">#</span>
+<span class="c1">#  Distributed under the GPLv3 License.</span>
+<span class="c1">#  See accompanying file LICENSE.txt or copy at</span>
+<span class="c1">#      https://www.gnu.org/licenses/gpl-3.0.html</span>
+<span class="c1">#</span>
+<span class="c1">#  Website: https://pypath.omnipathdb.org/</span>
+<span class="c1">#</span>
+
+<span class="kn">import</span> <span class="nn">sys</span>
+<span class="kn">from</span> <span class="nn">future.utils</span> <span class="kn">import</span> <span class="n">iteritems</span>
+
+<span class="kn">import</span> <span class="nn">codecs</span>
+<span class="kn">import</span> <span class="nn">bs4</span>
+<span class="kn">import</span> <span class="nn">textwrap</span>
+
+<span class="kn">import</span> <span class="nn">pypath.omnipath.server._html</span> <span class="k">as</span> <span class="nn">_html</span>
+<span class="kn">import</span> <span class="nn">pypath.resources.data_formats</span> <span class="k">as</span> <span class="nn">data_formats</span>
+<span class="kn">import</span> <span class="nn">pypath.resources.urls</span> <span class="k">as</span> <span class="nn">urls</span>
+<span class="kn">import</span> <span class="nn">pypath.share.session</span> <span class="k">as</span> <span class="nn">session_mod</span>
+
+<span class="n">__all__</span> <span class="o">=</span> <span class="p">[</span><span class="s1">&#39;descriptions&#39;</span><span class="p">,</span> <span class="s1">&#39;gen_html&#39;</span><span class="p">,</span> <span class="s1">&#39;write_html&#39;</span><span class="p">]</span>
+
+<span class="k">if</span> <span class="s1">&#39;long&#39;</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">__builtins__</span><span class="p">:</span>
+    <span class="n">long</span> <span class="o">=</span> <span class="nb">int</span>
+
+<span class="k">if</span> <span class="s1">&#39;unicode&#39;</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">__builtins__</span><span class="p">:</span>
+    <span class="n">unicode</span> <span class="o">=</span> <span class="nb">str</span>
+
+
+<span class="n">_logger</span> <span class="o">=</span> <span class="n">session_mod</span><span class="o">.</span><span class="n">Logger</span><span class="p">(</span><span class="n">name</span> <span class="o">=</span> <span class="s1">&#39;descriptions&#39;</span><span class="p">)</span>
+<span class="n">_log</span> <span class="o">=</span> <span class="n">_logger</span><span class="o">.</span><span class="n">_log</span>
+
+
+<span class="n">descriptions</span> <span class="o">=</span> <span class="p">{</span>
+    <span class="s1">&#39;HuRI&#39;</span><span class="p">:</span> <span class="p">{</span>
+        <span class="s1">&#39;year&#39;</span><span class="p">:</span> <span class="mi">2016</span><span class="p">,</span>
+        <span class="s1">&#39;releases&#39;</span><span class="p">:</span> <span class="p">[</span><span class="mi">2012</span><span class="p">,</span> <span class="mi">2014</span><span class="p">,</span> <span class="mi">2016</span><span class="p">],</span>
+        <span class="s1">&#39;recommend&#39;</span><span class="p">:</span>
+        <span class="s1">&#39;very large, quality controlled, unbiased yeast-2-hybrid screening&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;label&#39;</span><span class="p">:</span> <span class="s1">&#39;HuRI HI-III&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;full_name&#39;</span><span class="p">:</span> <span class="s1">&#39;Human Reference Interactome&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;urls&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;articles&#39;</span><span class="p">:</span>
+            <span class="p">[</span><span class="s1">&#39;http://www.cell.com/cell/abstract/S0092-8674(14)01422-6&#39;</span><span class="p">],</span>
+            <span class="s1">&#39;webpages&#39;</span><span class="p">:</span> <span class="p">[</span>
+                <span class="s1">&#39;http://interactome.dfci.harvard.edu/H_sapiens/&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;http://www.interactome-atlas.org/&#39;</span><span class="p">,</span>
+            <span class="p">],</span>
+        <span class="p">},</span>
+        <span class="s1">&#39;pubmeds&#39;</span><span class="p">:</span> <span class="p">[</span><span class="mi">25416956</span><span class="p">],</span>
+        <span class="s1">&#39;emails&#39;</span><span class="p">:</span>
+        <span class="p">[(</span><span class="s1">&#39;Michael_Calderwood@dfci.harvard.edu&#39;</span><span class="p">,</span> <span class="s1">&#39;Michael Calderwood&#39;</span><span class="p">)],</span>
+        <span class="s1">&#39;type&#39;</span><span class="p">:</span> <span class="s1">&#39;high-throughput&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;subtype&#39;</span><span class="p">:</span> <span class="s1">&#39;yeast 2 hybrid&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;omnipath&#39;</span><span class="p">:</span> <span class="kc">False</span><span class="p">,</span>
+        <span class="s1">&#39;license&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;name&#39;</span><span class="p">:</span>
+            <span class="s1">&#39;No license. &quot;This dataset is freely available to the research community through the search engine or via download.&quot;&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;url&#39;</span><span class="p">:</span> <span class="s1">&#39;http://www.gnu.org/licenses/license-list.html#NoLicense&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;commercial_use&#39;</span><span class="p">:</span> <span class="kc">False</span>
+        <span class="p">}</span>
+    <span class="p">},</span>
+    <span class="s1">&#39;HuRI Lit-BM&#39;</span><span class="p">:</span> <span class="p">{</span>
+        <span class="s1">&#39;year&#39;</span><span class="p">:</span> <span class="mi">2017</span><span class="p">,</span>
+        <span class="s1">&#39;releases&#39;</span><span class="p">:</span> <span class="p">[</span><span class="mi">2013</span><span class="p">,</span> <span class="mi">2017</span><span class="p">],</span>
+        <span class="s1">&#39;label&#39;</span><span class="p">:</span> <span class="s1">&#39;HuRI Lit-BM-17&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;full_name&#39;</span><span class="p">:</span> <span class="s1">&#39;Human Reference Interactome Literature Benchmark&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;urls&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;articles&#39;</span><span class="p">:</span>
+            <span class="p">[</span><span class="s1">&#39;http://www.cell.com/cell/abstract/S0092-8674(14)01422-6&#39;</span><span class="p">],</span>
+            <span class="s1">&#39;webpages&#39;</span><span class="p">:</span> <span class="p">[</span>
+                <span class="s1">&#39;http://interactome.dfci.harvard.edu/H_sapiens/&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;http://www.interactome-atlas.org/&#39;</span><span class="p">,</span>
+            <span class="p">],</span>
+        <span class="p">},</span>
+        <span class="s1">&#39;authors&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;CCSB&#39;</span><span class="p">],</span>
+        <span class="s1">&#39;pubmeds&#39;</span><span class="p">:</span> <span class="p">[</span><span class="mi">25416956</span><span class="p">],</span>
+        <span class="s1">&#39;descriptions&#39;</span><span class="p">:</span> <span class="p">[</span>
+<span class="w">            </span><span class="sa">u</span><span class="sd">&#39;&#39;&#39;</span>
+<span class="sd">            High-quality non-systematic Literature dataset. In 2013, we extracted interaction data from BIND, BioGRID, DIP, HPRD, MINT, IntAct, and PDB to generate a high-quality binary literature dataset comprising ~11,000 protein-protein interactions that are binary and supported by at least two traceable pieces of evidence (publications and/or methods) (Rolland et al Cell 2014). Although this dataset does not result from a systematic investigation of the interactome search space and should thus be used with caution for any network topology analyses, it represents valuable interactions for targeted studies and is freely available to the research community through the search engine or via download.</span>
+<span class="sd">            &#39;&#39;&#39;</span>
+        <span class="p">],</span>
+        <span class="s1">&#39;emails&#39;</span><span class="p">:</span>
+        <span class="p">[(</span><span class="s1">&#39;Michael_Calderwood@dfci.harvard.edu&#39;</span><span class="p">,</span> <span class="s1">&#39;Michael Calderwood&#39;</span><span class="p">)],</span>
+        <span class="s1">&#39;type&#39;</span><span class="p">:</span> <span class="s1">&#39;high-throughput&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;subtype&#39;</span><span class="p">:</span> <span class="s1">&#39;yeast 2 hybrid&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;omnipath&#39;</span><span class="p">:</span> <span class="kc">False</span><span class="p">,</span>
+        <span class="s1">&#39;pypath&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;get&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;pypath.dataio.get_lit_bm_13()&#39;</span><span class="p">],</span>
+            <span class="s1">&#39;data&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;pypath.urls.urls[</span><span class="se">\&#39;</span><span class="s1">hid</span><span class="se">\&#39;</span><span class="s1">][</span><span class="se">\&#39;</span><span class="s1">lit-bm-13</span><span class="se">\&#39;</span><span class="s1">]&#39;</span><span class="p">],</span>
+            <span class="s1">&#39;input&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;pypath.data_formats.interaction_misc[</span><span class="se">\&#39;</span><span class="s1">lit13</span><span class="se">\&#39;</span><span class="s1">]&#39;</span><span class="p">]</span>
+        <span class="p">},</span>
+        <span class="s1">&#39;license&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;name&#39;</span><span class="p">:</span>
+            <span class="s1">&#39;No license. &quot;This dataset is freely available to the research community through the search engine or via download.&quot;&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;url&#39;</span><span class="p">:</span> <span class="s1">&#39;http://www.gnu.org/licenses/license-list.html#NoLicense&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;commercial_use&#39;</span><span class="p">:</span> <span class="kc">False</span>
+        <span class="p">}</span>
+    <span class="p">},</span>
+    <span class="s1">&#39;ELM&#39;</span><span class="p">:</span> <span class="p">{</span>
+        <span class="s1">&#39;year&#39;</span><span class="p">:</span> <span class="mi">2014</span><span class="p">,</span>
+        <span class="s1">&#39;releases&#39;</span><span class="p">:</span> <span class="p">[</span><span class="mi">2003</span><span class="p">,</span> <span class="mi">2008</span><span class="p">,</span> <span class="mi">2009</span><span class="p">,</span> <span class="mi">2012</span><span class="p">,</span> <span class="mi">2013</span><span class="p">,</span> <span class="mi">2014</span><span class="p">,</span> <span class="mi">2016</span><span class="p">],</span>
+        <span class="s1">&#39;size&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;nodes&#39;</span><span class="p">:</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="s1">&#39;edges&#39;</span><span class="p">:</span> <span class="kc">None</span>
+        <span class="p">},</span>
+        <span class="s1">&#39;authors&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;ELM Consortium&#39;</span><span class="p">],</span>
+        <span class="s1">&#39;label&#39;</span><span class="p">:</span> <span class="s1">&#39;ELM&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;color&#39;</span><span class="p">:</span> <span class="s1">&#39;&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;urls&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;webpages&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;http://elm.eu.org/&#39;</span><span class="p">],</span>
+            <span class="s1">&#39;articles&#39;</span><span class="p">:</span> <span class="p">[</span>
+                <span class="s1">&#39;http://nar.oxfordjournals.org/content/40/D1/D242.long&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;http://nar.oxfordjournals.org/content/42/D1/D259.long&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;http://nar.oxfordjournals.org/content/44/D1/D294.long&#39;</span>
+            <span class="p">],</span>
+            <span class="s1">&#39;omictools&#39;</span><span class="p">:</span>
+            <span class="p">[</span><span class="s1">&#39;http://omictools.com/eukaryotic-linear-motif-resource-tool&#39;</span><span class="p">]</span>
+        <span class="p">},</span>
+        <span class="s1">&#39;annot&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;domain&#39;</span><span class="p">,</span> <span class="s1">&#39;residue&#39;</span><span class="p">],</span>
+        <span class="s1">&#39;recommend&#39;</span><span class="p">:</span>
+        <span class="s1">&#39;structural details: domain-motif relationships; very high confidence&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;pubmeds&#39;</span><span class="p">:</span> <span class="p">[</span><span class="mi">22110040</span><span class="p">,</span> <span class="mi">24214962</span><span class="p">,</span> <span class="mi">26615199</span><span class="p">],</span>
+        <span class="s1">&#39;emails&#39;</span><span class="p">:</span> <span class="p">[(</span><span class="s1">&#39;feedback@elm.eu.org&#39;</span><span class="p">,</span> <span class="s1">&#39;ELM Team&#39;</span><span class="p">),</span> <span class="p">(</span><span class="s1">&#39;gibson@embl.de&#39;</span><span class="p">,</span>
+                                                         <span class="s1">&#39;Toby Gibson&#39;</span><span class="p">)],</span>
+        <span class="s1">&#39;type&#39;</span><span class="p">:</span> <span class="s1">&#39;literature curated&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;subtype&#39;</span><span class="p">:</span> <span class="s1">&#39;post-translational modifications&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;data_integration&#39;</span><span class="p">:</span> <span class="s1">&#39;dynamic&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;descritpions&#39;</span><span class="p">:</span> <span class="p">[</span>
+<span class="w">            </span><span class="sa">u</span><span class="sd">&#39;&#39;&#39;</span>
+<span class="sd">            Ideally, each motif class has multiple example instances of this motif annotated, whereby an instance is described as a match to the regular expression pattern of the ELM motif class in a protein sequence. For each instance entry, ideally, multiple sources of experimental evidence are recorded (identifying participant, detecting motif presence and detecting interaction), and, following annotation best practices, a reliability score is given by the annotator.</span>
+<span class="sd">            &#39;&#39;&#39;</span>
+        <span class="p">],</span>
+        <span class="s1">&#39;omnipath&#39;</span><span class="p">:</span> <span class="kc">True</span><span class="p">,</span>
+        <span class="s1">&#39;license&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;name&#39;</span><span class="p">:</span> <span class="s1">&#39;ELM Software License Agreement, non-free&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;url&#39;</span><span class="p">:</span> <span class="s1">&#39;http://elm.eu.org/media/Elm_academic_license.pdf&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;commercial_use&#39;</span><span class="p">:</span> <span class="kc">False</span>
+        <span class="p">},</span>
+        <span class="s1">&#39;pypath&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;data&#39;</span><span class="p">:</span> <span class="p">[</span>
+                <span class="s1">&#39;pypath.urls.urls[</span><span class="se">\&#39;</span><span class="s1">ielm_domains</span><span class="se">\&#39;</span><span class="s1">][</span><span class="se">\&#39;</span><span class="s1">url</span><span class="se">\&#39;</span><span class="s1">]&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;pypath.urls.urls[</span><span class="se">\&#39;</span><span class="s1">elm_class</span><span class="se">\&#39;</span><span class="s1">][</span><span class="se">\&#39;</span><span class="s1">url</span><span class="se">\&#39;</span><span class="s1">]&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;pypath.urls.urls[</span><span class="se">\&#39;</span><span class="s1">elm_inst</span><span class="se">\&#39;</span><span class="s1">][</span><span class="se">\&#39;</span><span class="s1">url</span><span class="se">\&#39;</span><span class="s1">]&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;urls.urls[</span><span class="se">\&#39;</span><span class="s1">elm_int</span><span class="se">\&#39;</span><span class="s1">][</span><span class="se">\&#39;</span><span class="s1">url</span><span class="se">\&#39;</span><span class="s1">]&#39;</span>
+            <span class="p">],</span>
+            <span class="s1">&#39;format&#39;</span><span class="p">:</span> <span class="p">[</span>
+                <span class="s1">&#39;pypath.data_formats.ptm[</span><span class="se">\&#39;</span><span class="s1">elm</span><span class="se">\&#39;</span><span class="s1">]&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;pypath.data_formats.omnipath[</span><span class="se">\&#39;</span><span class="s1">elm</span><span class="se">\&#39;</span><span class="s1">]&#39;</span>
+            <span class="p">],</span>
+            <span class="s1">&#39;input&#39;</span><span class="p">:</span> <span class="p">[</span>
+                <span class="s1">&#39;pypath.dataio.get_elm_domains()&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;pypath.dataio.get_elm_classes()&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;pypath.dataio.get_elm_instances()&#39;</span>
+            <span class="p">],</span>
+            <span class="s1">&#39;intr&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;pypath.dataio.get_elm_interactions()&#39;</span><span class="p">],</span>
+            <span class="s1">&#39;dmi&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;pypath.pypath.PyPath.load_elm()&#39;</span><span class="p">]</span>
+        <span class="p">}</span>
+    <span class="p">},</span>
+    <span class="s1">&#39;LMPID&#39;</span><span class="p">:</span> <span class="p">{</span>
+        <span class="s1">&#39;year&#39;</span><span class="p">:</span> <span class="mi">2015</span><span class="p">,</span>
+        <span class="s1">&#39;releases&#39;</span><span class="p">:</span> <span class="p">[</span><span class="mi">2015</span><span class="p">],</span>
+        <span class="s1">&#39;size&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;nodes&#39;</span><span class="p">:</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="s1">&#39;edges&#39;</span><span class="p">:</span> <span class="kc">None</span>
+        <span class="p">},</span>
+        <span class="s1">&#39;authors&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;Bose Institute&#39;</span><span class="p">],</span>
+        <span class="s1">&#39;label&#39;</span><span class="p">:</span> <span class="s1">&#39;LMPID&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;color&#39;</span><span class="p">:</span> <span class="s1">&#39;&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;urls&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;webpages&#39;</span><span class="p">:</span>
+            <span class="p">[</span><span class="s1">&#39;http://bicresources.jcbose.ac.in/ssaha4/lmpid/index.php&#39;</span><span class="p">],</span>
+            <span class="s1">&#39;articles&#39;</span><span class="p">:</span>
+            <span class="p">[</span><span class="s1">&#39;http://database.oxfordjournals.org/content/2015/bav014.long&#39;</span><span class="p">],</span>
+            <span class="s1">&#39;omictools&#39;</span><span class="p">:</span> <span class="p">[</span>
+                <span class="s1">&#39;http://omictools.com/linear-motif-mediated-protein-interaction-database-tool&#39;</span>
+            <span class="p">]</span>
+        <span class="p">},</span>
+        <span class="s1">&#39;pubmeds&#39;</span><span class="p">:</span> <span class="p">[</span><span class="mi">25776024</span><span class="p">],</span>
+        <span class="s1">&#39;emails&#39;</span><span class="p">:</span> <span class="p">[(</span><span class="s1">&#39;ssaha4@jcbose.ac.in&#39;</span><span class="p">,</span> <span class="s1">&#39;Sudipto Saha&#39;</span><span class="p">)],</span>
+        <span class="s1">&#39;type&#39;</span><span class="p">:</span> <span class="s1">&#39;literature curated&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;subtype&#39;</span><span class="p">:</span> <span class="s1">&#39;post-translational modifications&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;recommend&#39;</span><span class="p">:</span>
+        <span class="s1">&#39;structural details: domain-motif relationships; similar to ELM, but more recent and larger&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;annot&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;domain&#39;</span><span class="p">,</span> <span class="s1">&#39;mechanism&#39;</span><span class="p">],</span>
+        <span class="s1">&#39;descriptions&#39;</span><span class="p">:</span> <span class="p">[</span>
+<span class="w">            </span><span class="sa">u</span><span class="sd">&#39;&#39;&#39;</span>
+<span class="sd">            LMPID (Linear Motif mediated Protein Interaction Database) is a manually curated database which provides comprehensive experimentally validated information about the LMs mediating PPIs from all organisms on a single platform. About 2200 entries have been compiled by detailed manual curation of PubMed abstracts, of which about 1000 LM entries were being annotated for the first time, as compared with the Eukaryotic LM resource.</span>
+<span class="sd">            &#39;&#39;&#39;</span>
+        <span class="p">],</span>
+        <span class="s1">&#39;omnipath&#39;</span><span class="p">:</span> <span class="kc">True</span><span class="p">,</span>
+        <span class="s1">&#39;pypath&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;input&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;pypath.dataio.load_lmpid()&#39;</span><span class="p">],</span>
+            <span class="s1">&#39;intr&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;pypath.dataio.lmpid_interactions()&#39;</span><span class="p">],</span>
+            <span class="s1">&#39;data&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;pypath.data/LMPID_DATA_pubmed_ref.xml&#39;</span><span class="p">],</span>
+            <span class="s1">&#39;format&#39;</span><span class="p">:</span> <span class="p">[</span>
+                <span class="s1">&#39;pypath.data_formats.ptm[</span><span class="se">\&#39;</span><span class="s1">lmpid</span><span class="se">\&#39;</span><span class="s1">]&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;pypath.data_formats.omnipath[</span><span class="se">\&#39;</span><span class="s1">lmpid</span><span class="se">\&#39;</span><span class="s1">]&#39;</span>
+            <span class="p">],</span>
+            <span class="s1">&#39;dmi&#39;</span><span class="p">:</span> <span class="p">[</span>
+                <span class="s1">&#39;pypath.dataio.lmpid_dmi()&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;pypath.pypath.PyPath().process_dmi(source = </span><span class="se">\&#39;</span><span class="s1">LMPID</span><span class="se">\&#39;</span><span class="s1">)&#39;</span>
+            <span class="p">]</span>
+        <span class="p">},</span>
+        <span class="s1">&#39;license&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;name&#39;</span><span class="p">:</span>
+            <span class="s1">&#39;No license. If you are using this database please cite Sarkar 2015.&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;url&#39;</span><span class="p">:</span> <span class="s1">&#39;http://www.gnu.org/licenses/license-list.html#NoLicense&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;commercial_use&#39;</span><span class="p">:</span> <span class="kc">False</span>
+        <span class="p">}</span>
+    <span class="p">},</span>
+    <span class="s1">&#39;PDZBase&#39;</span><span class="p">:</span> <span class="p">{</span>
+        <span class="s1">&#39;year&#39;</span><span class="p">:</span> <span class="mi">2004</span><span class="p">,</span>
+        <span class="s1">&#39;releases&#39;</span><span class="p">:</span> <span class="p">[</span><span class="mi">2004</span><span class="p">],</span>
+        <span class="s1">&#39;authors&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;Weinstein Group&#39;</span><span class="p">],</span>
+        <span class="s1">&#39;urls&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;webpages&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;http://abc.med.cornell.edu/pdzbase&#39;</span><span class="p">],</span>
+            <span class="s1">&#39;articles&#39;</span><span class="p">:</span> <span class="p">[</span>
+                <span class="s1">&#39;http://bioinformatics.oxfordjournals.org/content/21/6/827.long&#39;</span>
+            <span class="p">],</span>
+            <span class="s1">&#39;omictools&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;http://omictools.com/pdzbase-tool&#39;</span><span class="p">]</span>
+        <span class="p">},</span>
+        <span class="s1">&#39;pubmeds&#39;</span><span class="p">:</span> <span class="p">[</span><span class="mi">15513994</span><span class="p">],</span>
+        <span class="s1">&#39;taxons&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;human&#39;</span><span class="p">],</span>
+        <span class="s1">&#39;color&#39;</span><span class="p">:</span> <span class="kc">None</span><span class="p">,</span>
+        <span class="s1">&#39;label&#39;</span><span class="p">:</span> <span class="s1">&#39;PDZBase&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;annot&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;domain&#39;</span><span class="p">],</span>
+        <span class="s1">&#39;recommend&#39;</span><span class="p">:</span>
+        <span class="s1">&#39;a handful specific interactions for proteins with PDZ domain&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;descriptions&#39;</span><span class="p">:</span> <span class="p">[</span>
+<span class="w">            </span><span class="sa">u</span><span class="sd">&#39;&#39;&#39;</span>
+<span class="sd">            PDZBase is a database that aims to contain all known PDZ-domain-mediated protein-protein interactions. Currently, PDZBase contains approximately 300 such interactions, which have been manually extracted from &amp;gt;200 articles.</span>
+<span class="sd">            PDZBase currently contains ∼300 interactions, all of which have been manually extracted from the literature, and have been independently verified by two curators. The extracted information comes from in vivo (co-immunoprecipitation) or in vitro experiments (GST-fusion or related pull-down experiments). Interactions identified solely from high throughput methods (e.g. yeast two-hybrid or mass spectrometry) were not included in PDZBase. Other prerequisites for inclusion in the database are: that knowledge of the binding sites on both interacting proteins must be available (for instance through a truncation or mutagenesis experiment); that interactions must be mediated directly by the PDZ-domain, and not by any other possible domain within the protein.</span>
+<span class="sd">            &#39;&#39;&#39;</span>
+        <span class="p">],</span>
+        <span class="s1">&#39;emails&#39;</span><span class="p">:</span> <span class="p">[(</span><span class="s1">&#39;haw2002@med.cornell.edu&#39;</span><span class="p">,</span> <span class="s1">&#39;Harel Weinstein&#39;</span><span class="p">),</span>
+                   <span class="p">(</span><span class="s1">&#39;pdzbase@med.cornell.edu&#39;</span><span class="p">,</span> <span class="s1">&#39;PDZBase Team&#39;</span><span class="p">)],</span>
+        <span class="s1">&#39;type&#39;</span><span class="p">:</span> <span class="s1">&#39;literature curated&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;subtype&#39;</span><span class="p">:</span> <span class="s1">&#39;activity flow&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;omnipath&#39;</span><span class="p">:</span> <span class="kc">True</span><span class="p">,</span>
+        <span class="s1">&#39;pypath&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;intr&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;pypath.dataio.get_pdzbase()&#39;</span><span class="p">],</span>
+            <span class="s1">&#39;data&#39;</span><span class="p">:</span> <span class="p">[</span>
+                <span class="s1">&#39;pypath.urls.urls[</span><span class="se">\&#39;</span><span class="s1">pdzbase</span><span class="se">\&#39;</span><span class="s1">]&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;pypath.urls.urls[</span><span class="se">\&#39;</span><span class="s1">pdz_details</span><span class="se">\&#39;</span><span class="s1">]&#39;</span>
+            <span class="p">],</span>
+            <span class="s1">&#39;format&#39;</span><span class="p">:</span> <span class="p">[</span>
+                <span class="s1">&#39;pypath.data_formats.pathway[</span><span class="se">\&#39;</span><span class="s1">pdz</span><span class="se">\&#39;</span><span class="s1">]&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;pypath.data_formats.omnipath[</span><span class="se">\&#39;</span><span class="s1">pdz</span><span class="se">\&#39;</span><span class="s1">]&#39;</span>
+            <span class="p">]</span>
+        <span class="p">},</span>
+        <span class="s1">&#39;license&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;name&#39;</span><span class="p">:</span> <span class="s1">&#39;No license.&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;url&#39;</span><span class="p">:</span> <span class="s1">&#39;http://www.gnu.org/licenses/license-list.html#NoLicense&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;commercial_use&#39;</span><span class="p">:</span> <span class="kc">False</span>
+        <span class="p">},</span>
+        <span class="s1">&#39;pathguide&#39;</span><span class="p">:</span> <span class="mi">160</span>
+    <span class="p">},</span>
+    <span class="s1">&#39;Guide2Pharma&#39;</span><span class="p">:</span> <span class="p">{</span>
+        <span class="s1">&#39;year&#39;</span><span class="p">:</span> <span class="mi">2015</span><span class="p">,</span>
+        <span class="s1">&#39;releases&#39;</span><span class="p">:</span> <span class="p">[</span><span class="mi">2007</span><span class="p">,</span> <span class="mi">2008</span><span class="p">,</span> <span class="mi">2009</span><span class="p">,</span> <span class="mi">2011</span><span class="p">,</span> <span class="mi">2013</span><span class="p">,</span> <span class="mi">2014</span><span class="p">,</span> <span class="mi">2015</span><span class="p">,</span> <span class="mi">2016</span><span class="p">],</span>
+        <span class="s1">&#39;size&#39;</span><span class="p">:</span> <span class="kc">None</span><span class="p">,</span>
+        <span class="s1">&#39;authors&#39;</span><span class="p">:</span> <span class="kc">None</span><span class="p">,</span>
+        <span class="s1">&#39;label&#39;</span><span class="p">:</span> <span class="s1">&#39;Guide to Pharmacology&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;full_name&#39;</span><span class="p">:</span> <span class="s1">&#39;Guide to Pharmacology&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;color&#39;</span><span class="p">:</span> <span class="kc">None</span><span class="p">,</span>
+        <span class="s1">&#39;pubmeds&#39;</span><span class="p">:</span> <span class="p">[</span><span class="mi">24234439</span><span class="p">],</span>
+        <span class="s1">&#39;urls&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;webpages&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;http://www.guidetopharmacology.org/&#39;</span><span class="p">],</span>
+            <span class="s1">&#39;articles&#39;</span><span class="p">:</span> <span class="p">[</span>
+                <span class="s1">&#39;http://nar.oxfordjournals.org/content/42/D1/D1098.long&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;http://onlinelibrary.wiley.com/doi/10.1111/j.1476-5381.2011.01649_1.x/full&#39;</span>
+            <span class="p">],</span>
+            <span class="s1">&#39;omictools&#39;</span><span class="p">:</span> <span class="p">[</span>
+                <span class="s1">&#39;http://omictools.com/international-union-of-basic-and-clinical-pharmacology-british-pharmacological-society-guide-to-pharmacology-tool&#39;</span>
+            <span class="p">]</span>
+        <span class="p">},</span>
+        <span class="s1">&#39;recommend&#39;</span><span class="p">:</span>
+        <span class="s1">&#39;one of the strongest in ligand-receptor interactions; still does not contain everything, therefore worth to combine with larger activity flow resources like Signor&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;descriptions&#39;</span><span class="p">:</span> <span class="p">[</span>
+<span class="w">            </span><span class="sa">u</span><span class="sd">&#39;&#39;&#39;</span>
+<span class="sd">            Presently, the resource describes the interactions between target proteins and 6064 distinct ligand entities (Table 1). Ligands are listed against targets by their action (e.g. activator, inhibitor), and also classified according to substance types and their status as approved drugs. Classes include metabolites (a general category for all biogenic, non-peptide, organic molecules including lipids, hormones and neurotransmitters), synthetic organic chemicals (e.g. small molecule drugs), natural products, mammalian endogenous peptides, synthetic and other peptides including toxins from non-mammalian organisms, antibodies, inorganic substances and other, not readily classifiable compounds.</span>
+<span class="sd">            The new database was constructed by integrating data from IUPHAR-DB and the published GRAC compendium. An overview of the curation process is depicted as an organizational flow chart in Figure 2. New information was added to the existing relational database behind IUPHAR-DB and new webpages were created to display the integrated information. For each new target, information on human, mouse and rat genes and proteins, including gene symbol, full name, location, gene ID, UniProt and Ensembl IDs was manually curated from HGNC, the Mouse Genome Database (MGD) at Mouse Genome Informatics (MGI), the Rat Genome Database (RGD), UniProt and Ensembl, respectively. In addition, ‘Other names’, target-specific fields such as ‘Principal transduction’, text from the ‘Overview’ and ‘Comments’ sections and reference citations (downloaded from PubMed; http://www.ncbi.nlm.nih.gov/pubmed) were captured from GRAC and uploaded into the database against a unique Object ID.</span>
+<span class="sd">            &#39;&#39;&#39;</span>
+        <span class="p">],</span>
+        <span class="s1">&#39;emails&#39;</span><span class="p">:</span>
+        <span class="p">[(</span><span class="s1">&#39;enquiries@guidetopharmacology.org&#39;</span><span class="p">,</span> <span class="s1">&#39;Guide to Pharmacology Team&#39;</span><span class="p">),</span>
+         <span class="p">(</span><span class="s1">&#39;cdsouthan@hotmail.com&#39;</span><span class="p">,</span> <span class="s1">&#39;Cristopher Southan&#39;</span><span class="p">)],</span>
+        <span class="s1">&#39;type&#39;</span><span class="p">:</span> <span class="s1">&#39;literature curated&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;subtype&#39;</span><span class="p">:</span> <span class="s1">&#39;activity flow&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;omnipath&#39;</span><span class="p">:</span> <span class="kc">True</span><span class="p">,</span>
+        <span class="s1">&#39;license&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;name&#39;</span><span class="p">:</span> <span class="s1">&#39;CC-Attribution-ShareAlike-3.0&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;url&#39;</span><span class="p">:</span> <span class="s1">&#39;http://creativecommons.org/licenses/by-sa/3.0/&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;commercial_use&#39;</span><span class="p">:</span> <span class="kc">True</span>
+        <span class="p">},</span>
+        <span class="s1">&#39;pypath&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;data&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;pypath.data_formats&#39;</span><span class="p">],</span>
+            <span class="s1">&#39;format&#39;</span><span class="p">:</span> <span class="p">[</span>
+                <span class="s1">&#39;pypath.data_formats.pathway[</span><span class="se">\&#39;</span><span class="s1">guide2pharma</span><span class="se">\&#39;</span><span class="s1">]&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;pypath.data_formats.omnipath[</span><span class="se">\&#39;</span><span class="s1">guide2pharma</span><span class="se">\&#39;</span><span class="s1">]&#39;</span>
+            <span class="p">]</span>
+        <span class="p">},</span>
+        <span class="s1">&#39;pathguide&#39;</span><span class="p">:</span> <span class="mi">345</span>
+    <span class="p">},</span>
+    <span class="s1">&#39;phosphoELM&#39;</span><span class="p">:</span> <span class="p">{</span>
+        <span class="s1">&#39;year&#39;</span><span class="p">:</span> <span class="mi">2010</span><span class="p">,</span>
+        <span class="s1">&#39;releases&#39;</span><span class="p">:</span> <span class="p">[</span><span class="mi">2004</span><span class="p">,</span> <span class="mi">2007</span><span class="p">,</span> <span class="mi">2010</span><span class="p">],</span>
+        <span class="s1">&#39;urls&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;webpages&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;http://phospho.elm.eu.org/&#39;</span><span class="p">],</span>
+            <span class="s1">&#39;articles&#39;</span><span class="p">:</span> <span class="p">[</span>
+                <span class="s1">&#39;http://www.biomedcentral.com/1471-2105/5/79&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;http://nar.oxfordjournals.org/content/36/suppl_1/D240.full&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;http://nar.oxfordjournals.org/content/39/suppl_1/D261&#39;</span>
+            <span class="p">],</span>
+            <span class="s1">&#39;omictools&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;http://omictools.com/phospho-elm-tool&#39;</span><span class="p">]</span>
+        <span class="p">},</span>
+        <span class="s1">&#39;pubmeds&#39;</span><span class="p">:</span> <span class="p">[</span><span class="mi">15212693</span><span class="p">,</span> <span class="mi">17962309</span><span class="p">,</span> <span class="mi">21062810</span><span class="p">],</span>
+        <span class="s1">&#39;annot&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;mechanism&#39;</span><span class="p">,</span> <span class="s1">&#39;residue&#39;</span><span class="p">],</span>
+        <span class="s1">&#39;recommend&#39;</span><span class="p">:</span>
+        <span class="s1">&#39;one of the largest kinase-substrate databases; substantial number of specific proteins and interactions, with more receptors than PhosphoSite&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;descriptions&#39;</span><span class="p">:</span> <span class="p">[</span>
+<span class="w">            </span><span class="sa">u</span><span class="sd">&#39;&#39;&#39;</span>
+<span class="sd">            Phospho.ELM http://phospho.elm.eu.org is a new resource containing experimentally verified phosphorylation sites manually curated from the literature and is developed as part of the ELM (Eukaryotic Linear Motif) resource. Phospho.ELM constitutes the largest searchable collection of phosphorylation sites available to the research community. The Phospho.ELM entries store information about substrate proteins with the exact positions of residues known to be phosphorylated by cellular kinases. Additional annotation includes literature references, subcellular compartment, tissue distribution, and information about the signaling pathways involved as well as links to the molecular interaction database MINT. Phospho.ELM version 2.0 contains 1,703 phosphorylation site instances for 556 phosphorylated proteins. (Diella 2004)</span>
+<span class="sd">            &#39;&#39;&#39;</span><span class="p">,</span> <span class="sa">u</span><span class="s1">&#39;&#39;&#39;</span>
+<span class="s1">            Phospho.ELM is a manually curated database of eukaryotic phosphorylation sites. The resource includes data collected from published literature as well as high-throughput data sets. The current release of the Phospho.ELM data set (version 7.0, July 2007) contains 4078 phospho-protein sequences covering 12,025 phospho-serine, 2,362 phospho-threonine and 2,083 phospho-tyrosine sites with a total of 16,470 sites.</span>
+<span class="s1">            For each phospho-site we report if the phosphorylation evidence has been identified by small-scale analysis (low throughput; LTP) that typically focus on one or a few proteins at a time or by large-scale experiments (high throughput; HTP), which mainly apply MS techniques. It is noteworthy that in our data set there is a small overlap between instances identified by LTP and HTP experiments. (Diella 2007)</span>
+<span class="s1">            &#39;&#39;&#39;</span><span class="p">,</span> <span class="sa">u</span><span class="s1">&#39;&#39;&#39;</span>
+<span class="s1">            The current release of the Phospho.ELM data set (version 9.0) contains more than 42,500 non-redundant instances of phosphorylated residues in more than 11,000 different protein sequences (3370 tyrosine, 31 754 serine and 7449 threonine residues). For each phosphosite we report whether the phosphorylation evidence has been identified by small-scale analyses (low-throughput, LTP) and/or by large-scale experiments (high-throughput, HTP), which mainly apply MS techniques. The majority of the protein instances from Phospho. ELM are vertebrate (mostly Homo sapiens (62%) and Mus musculus (16%)) though 22</span><span class="si">% a</span><span class="s1">re from other species, mainly Drosophila melanogaster (13%) and Caenorhabditis elegans (7%). In total, more than 300 different kinases have been annotated and a document providing additional information about all kinases annotated in Phospho.ELM can be found at http://phospho.elm.eu.org/kinases.html. (Dinkel 2010)</span>
+<span class="s1">            &#39;&#39;&#39;</span>
+        <span class="p">],</span>
+        <span class="s1">&#39;emails&#39;</span><span class="p">:</span> <span class="p">[(</span><span class="s1">&#39;toby.gibson@embl.de&#39;</span><span class="p">,</span> <span class="s1">&#39;Toby Gibson&#39;</span><span class="p">)],</span>
+        <span class="s1">&#39;type&#39;</span><span class="p">:</span> <span class="s1">&#39;Literature curated&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;data_integration&#39;</span><span class="p">:</span> <span class="s1">&#39;dynamic&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;subtype&#39;</span><span class="p">:</span> <span class="s1">&#39;PTM&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;label&#39;</span><span class="p">:</span> <span class="s1">&#39;phospho.ELM&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;omnipath&#39;</span><span class="p">:</span> <span class="kc">True</span><span class="p">,</span>
+        <span class="s1">&#39;license&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;name&#39;</span><span class="p">:</span> <span class="s1">&#39;phospho.ELM Academic License, non-free&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;url&#39;</span><span class="p">:</span>
+            <span class="s1">&#39;http://phospho.elm.eu.org/dumps/Phospho.Elm_AcademicLicense.pdf&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;commercial_use&#39;</span><span class="p">:</span> <span class="kc">False</span>
+        <span class="p">},</span>
+        <span class="s1">&#39;pypath&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;format&#39;</span><span class="p">:</span> <span class="p">[</span>
+                <span class="s1">&#39;pypath.data_formats.ptm[</span><span class="se">\&#39;</span><span class="s1">phelm</span><span class="se">\&#39;</span><span class="s1">]&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;pypath.data_formats.omnipath[</span><span class="se">\&#39;</span><span class="s1">phelm</span><span class="se">\&#39;</span><span class="s1">]&#39;</span>
+            <span class="p">],</span>
+            <span class="s1">&#39;data&#39;</span><span class="p">:</span> <span class="p">[</span>
+                <span class="s1">&#39;pypath.urls.urls[</span><span class="se">\&#39;</span><span class="s1">p_elm</span><span class="se">\&#39;</span><span class="s1">][</span><span class="se">\&#39;</span><span class="s1">psites</span><span class="se">\&#39;</span><span class="s1">]&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;urls.urls[</span><span class="se">\&#39;</span><span class="s1">p_elm_kin</span><span class="se">\&#39;</span><span class="s1">][</span><span class="se">\&#39;</span><span class="s1">url</span><span class="se">\&#39;</span><span class="s1">]&#39;</span>
+            <span class="p">],</span>
+            <span class="s1">&#39;intr&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;pypath.dataio.phelm_interactions()&#39;</span><span class="p">],</span>
+            <span class="s1">&#39;input&#39;</span><span class="p">:</span> <span class="p">[</span>
+                <span class="s1">&#39;pypath.dataio.get_phosphoelm()&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;pypath.dataio.get_phelm_kinases()&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;pypath.dataio.phelm_psites()&#39;</span>
+            <span class="p">],</span>
+            <span class="s1">&#39;ptm&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;pypath.pypath.PyPath().load_phosphoelm()&#39;</span><span class="p">]</span>
+        <span class="p">},</span>
+        <span class="s1">&#39;pathguide&#39;</span><span class="p">:</span> <span class="mi">138</span>
+    <span class="p">},</span>
+    <span class="s1">&#39;DOMINO&#39;</span><span class="p">:</span> <span class="p">{</span>
+        <span class="s1">&#39;year&#39;</span><span class="p">:</span> <span class="mi">2006</span><span class="p">,</span>
+        <span class="s1">&#39;releases&#39;</span><span class="p">:</span> <span class="p">[</span><span class="mi">2006</span><span class="p">],</span>
+        <span class="s1">&#39;authors&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;Cesareni Group&#39;</span><span class="p">],</span>
+        <span class="s1">&#39;urls&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;webpages&#39;</span><span class="p">:</span>
+            <span class="p">[</span><span class="s1">&#39;http://mint.bio.uniroma2.it/domino/search/searchWelcome.do&#39;</span><span class="p">],</span>
+            <span class="s1">&#39;articles&#39;</span><span class="p">:</span>
+            <span class="p">[</span><span class="s1">&#39;http://nar.oxfordjournals.org/content/35/suppl_1/D557.long&#39;</span><span class="p">],</span>
+            <span class="s1">&#39;omictools&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;http://omictools.com/domino-tool&#39;</span><span class="p">]</span>
+        <span class="p">},</span>
+        <span class="s1">&#39;pubmeds&#39;</span><span class="p">:</span> <span class="p">[</span><span class="mi">17135199</span><span class="p">],</span>
+        <span class="s1">&#39;taxons&#39;</span><span class="p">:</span> <span class="p">[</span>
+            <span class="s1">&#39;human&#39;</span><span class="p">,</span> <span class="s1">&#39;yeast&#39;</span><span class="p">,</span> <span class="s1">&#39;C. elegans&#39;</span><span class="p">,</span> <span class="s1">&#39;mouse&#39;</span><span class="p">,</span> <span class="s1">&#39;rat&#39;</span><span class="p">,</span> <span class="s1">&#39;HIV&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;D. melanogaster&#39;</span><span class="p">,</span> <span class="s1">&#39;A. thaliana&#39;</span><span class="p">,</span> <span class="s1">&#39;X. laevis&#39;</span><span class="p">,</span> <span class="s1">&#39;B. taurus&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;G. gallus&#39;</span><span class="p">,</span> <span class="s1">&#39;O. cuniculus&#39;</span><span class="p">,</span> <span class="s1">&#39;Plasmodium falciparum&#39;</span>
+        <span class="p">],</span>
+        <span class="s1">&#39;annot&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;experiment&#39;</span><span class="p">],</span>
+        <span class="s1">&#39;recommend&#39;</span><span class="p">:</span>
+        <span class="s1">&#39;rich details and many specific information; discontinued, Signor from the same lab is larger and newer, and contains most of its data&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;descriptions&#39;</span><span class="p">:</span> <span class="p">[</span>
+<span class="w">            </span><span class="sa">u</span><span class="sd">&#39;&#39;&#39;</span>
+<span class="sd">            DOMINO aims at annotating all the available information about domain-peptide and domain–domain interactions. The core of DOMINO, of July 24, 2006 consists of more than 3900 interactions extracted from peer-reviewed articles and annotated by expert biologists. A total of 717 manuscripts have been processed, thus covering a large fraction of the published information about domain–peptide interactions. The curation effort has focused on the following domains: SH3, SH2, 14-3-3, PDZ, PTB, WW, EVH, VHS, FHA, EH, FF, BRCT, Bromo, Chromo and GYF. However, interactions mediated by as many as 150 different domain families are stored in DOMINO.</span>
+<span class="sd">            &#39;&#39;&#39;</span><span class="p">,</span> <span class="sa">u</span><span class="s1">&#39;&#39;&#39;</span>
+<span class="s1">            DOMINO is an open-access database comprising more than 3900 annotated experiments describing interactions mediated by protein-interaction domains. The curation effort aims at covering the interactions mediated by the following domains (SH3, SH2, 14-3-3, PDZ, PTB, WW, EVH, VHS, FHA, EH, FF, BRCT, Bromo, Chromo, GYF). However, interactions mediated by as many as 150 different domain families are stored in DOMINO.</span>
+<span class="s1">            &#39;&#39;&#39;</span><span class="p">,</span> <span class="sa">u</span><span class="s1">&#39;&#39;&#39;</span>
+<span class="s1">            The curation process follows the PSI-MI 2.5 standard but with special emphasis on the mapping of the interaction to specific protein domains of both participating proteins. This is achieved by paying special attention to the shortest protein fragment that was experimentally verified as sufficient for the interaction. Whenever the authors report only the name of the domain mediating the interaction (i.e. SH3, SH2 ...), without stating the coordinates of the experimental binding range, the curator may choose to enter the coordinates of the Pfam domain match in the protein sequence. Finally whenever the information is available, any mutation or posttranslational modification affecting the interaction affinity is noted in the database.</span>
+<span class="s1">            &#39;&#39;&#39;</span>
+        <span class="p">],</span>
+        <span class="s1">&#39;emails&#39;</span><span class="p">:</span> <span class="p">[(</span><span class="s1">&#39;giovanni.cesareni@uniroma2.it&#39;</span><span class="p">,</span> <span class="s1">&#39;Gianni Cesareni&#39;</span><span class="p">)],</span>
+        <span class="s1">&#39;type&#39;</span><span class="p">:</span> <span class="s1">&#39;Literature curated&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;subtype&#39;</span><span class="p">:</span> <span class="s1">&#39;PTM&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;omnipath&#39;</span><span class="p">:</span> <span class="kc">True</span><span class="p">,</span>
+        <span class="s1">&#39;license&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;name&#39;</span><span class="p">:</span> <span class="s1">&#39;CC-Attribution-2.5&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;url&#39;</span><span class="p">:</span> <span class="s1">&#39;http://creativecommons.org/licenses/by/2.5&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;commercial_use&#39;</span><span class="p">:</span> <span class="kc">True</span>
+        <span class="p">},</span>
+        <span class="s1">&#39;pypath&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;data&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;pypath.urls.urls[</span><span class="se">\&#39;</span><span class="s1">domino</span><span class="se">\&#39;</span><span class="s1">][</span><span class="se">\&#39;</span><span class="s1">url</span><span class="se">\&#39;</span><span class="s1">]&#39;</span><span class="p">],</span>
+            <span class="s1">&#39;input&#39;</span><span class="p">:</span>
+            <span class="p">[</span><span class="s1">&#39;pypath.dataio.get_domino()&#39;</span><span class="p">,</span> <span class="s1">&#39;pypath.dataio.get_domino_ddi()&#39;</span><span class="p">],</span>
+            <span class="s1">&#39;format&#39;</span><span class="p">:</span> <span class="p">[</span>
+                <span class="s1">&#39;pypath.data_formats.ptm[</span><span class="se">\&#39;</span><span class="s1">domino</span><span class="se">\&#39;</span><span class="s1">]&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;pypath.data_formats.omnipath[</span><span class="se">\&#39;</span><span class="s1">domino</span><span class="se">\&#39;</span><span class="s1">]&#39;</span>
+            <span class="p">],</span>
+            <span class="s1">&#39;intr&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;pypath.dataio.domino_interactions()&#39;</span><span class="p">],</span>
+            <span class="s1">&#39;ptm&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;pypath.dataio.get_domino_ptms()&#39;</span><span class="p">],</span>
+            <span class="s1">&#39;dmi&#39;</span><span class="p">:</span> <span class="p">[</span>
+                <span class="s1">&#39;pypath.dataio.get_domino_dmi()&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;pypath.pypath.PyPath().load_domino_dmi()&#39;</span>
+            <span class="p">],</span>
+            <span class="s1">&#39;ddi&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;pypath.dataio.get_domino_ddi()&#39;</span><span class="p">]</span>
+        <span class="p">},</span>
+        <span class="s1">&#39;pathguide&#39;</span><span class="p">:</span> <span class="mi">239</span>
+    <span class="p">},</span>
+    <span class="s1">&#39;dbPTM&#39;</span><span class="p">:</span> <span class="p">{</span>
+        <span class="s1">&#39;year&#39;</span><span class="p">:</span> <span class="mi">2015</span><span class="p">,</span>
+        <span class="s1">&#39;releases&#39;</span><span class="p">:</span> <span class="p">[</span><span class="mi">2005</span><span class="p">,</span> <span class="mi">2009</span><span class="p">,</span> <span class="mi">2012</span><span class="p">,</span> <span class="mi">2015</span><span class="p">],</span>
+        <span class="s1">&#39;authors&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;ISBLab&#39;</span><span class="p">],</span>
+        <span class="s1">&#39;urls&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;webpages&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;http://dbptm.mbc.nctu.edu.tw/&#39;</span><span class="p">],</span>
+            <span class="s1">&#39;articles&#39;</span><span class="p">:</span> <span class="p">[</span>
+                <span class="s1">&#39;http://nar.oxfordjournals.org/content/41/D1/D295.long&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;http://www.biomedcentral.com/1756-0500/2/111&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;http://nar.oxfordjournals.org/content/34/suppl_1/D622.long&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;http://nar.oxfordjournals.org/content/44/D1/D435.long&#39;</span>
+            <span class="p">],</span>
+            <span class="s1">&#39;omictools&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;http://omictools.com/dbptm-tool&#39;</span><span class="p">]</span>
+        <span class="p">},</span>
+        <span class="s1">&#39;pubmeds&#39;</span><span class="p">:</span> <span class="p">[</span><span class="mi">16381945</span><span class="p">,</span> <span class="mi">19549291</span><span class="p">,</span> <span class="mi">23193290</span><span class="p">,</span> <span class="mi">26578568</span><span class="p">],</span>
+        <span class="s1">&#39;taxons&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;human&#39;</span><span class="p">,</span> <span class="s1">&#39;Metazoa&#39;</span><span class="p">,</span> <span class="s1">&#39;Bacteria&#39;</span><span class="p">,</span> <span class="s1">&#39;plants&#39;</span><span class="p">,</span> <span class="s1">&#39;yeast&#39;</span><span class="p">],</span>
+        <span class="s1">&#39;annot&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;mechanism&#39;</span><span class="p">,</span> <span class="s1">&#39;residue&#39;</span><span class="p">],</span>
+        <span class="s1">&#39;recommend&#39;</span><span class="p">:</span>
+        <span class="s1">&#39;integrates many small efforts; beside phosphorylations provides all types of PTMs and enzyme-substrate relationships&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;descriptions&#39;</span><span class="p">:</span> <span class="p">[</span>
+<span class="w">            </span><span class="sa">u</span><span class="sd">&#39;&#39;&#39;</span>
+<span class="sd">            Due to the inaccessibility of database contents in several online PTM resources, a total 11 biological databases related to PTMs are integrated in dbPTM, including UniProtKB/SwissProt, version 9.0 of Phospho.ELM, PhosphoSitePlus, PHOSIDA, version 6.0 of O-GLYCBASE, dbOGAP, dbSNO, version 1.0 of UbiProt, PupDB, version 1.1 of SysPTM and release 9.0 of HPRD.</span>
+<span class="sd">            With the high throughput of MS-based methods in post-translational proteomics, this update also includes manually curated MS/MS-identified peptides associated with PTMs from research articles through a literature survey. First, a table list of PTM-related keywords is constructed by referring to the UniProtKB/SwissProt PTM list (http://www.uniprot.org/docs/ptmlist.txt) and the annotations of RESID (28). Then, all fields in the PubMed database are searched based on the keywords of the constructed table list. This is then followed by downloading the full text of the research articles. For the various experiments of proteomic identification, a text-mining system is developed to survey full-text literature that potentially describes the site-specific identification of modified sites. Approximately 800 original and review articles associated with MS/MS proteomics and protein modifications are retrieved from PubMed (July 2012). Next, the full-length articles are manually reviewed for precisely extracting the MS/MS peptides along with the modified sites. Furthermore, in order to determine the locations of PTMs on a full-length protein sequence, the experimentally verified MS/MS peptides are then mapped to UniProtKB protein entries based on its database identifier (ID) and sequence identity. In the process of data mapping, MS/MS peptides that cannot align exactly to a protein sequence are discarded. Finally, each mapped PTM site is attributed with a corresponding literature (PubMed ID).</span>
+<span class="sd">            &#39;&#39;&#39;</span><span class="p">,</span> <span class="sa">u</span><span class="s1">&#39;&#39;&#39;</span>
+<span class="s1">            dbPTM was developed as a comprehensive database of experimentally verified PTMs from several databases with annotations of potential PTMs for all UniProtKB protein entries. For this tenth anniversary of dbPTM, the updated resource includes not only a comprehensive dataset of experimentally verified PTMs, supported by the literature, but also an integrative interface for accessing all available databases and tools that are associated with PTM analysis. As well as collecting experimental PTM data from 14 public databases, this update manually curates over 12,000 modified peptides, including the emerging S-nitrosylation, S-glutathionylation and succinylation, from approximately 500 research articles, which were retrieved by text mining.</span>
+<span class="s1">            &#39;&#39;&#39;</span>
+        <span class="p">],</span>
+        <span class="s1">&#39;emails&#39;</span><span class="p">:</span> <span class="p">[(</span><span class="s1">&#39;francis@saturn.yzu.edu.tw&#39;</span><span class="p">,</span> <span class="s1">&#39;Hsien-Da Huang&#39;</span><span class="p">),</span>
+                   <span class="p">(</span><span class="s1">&#39;bryan@mail.nctu.edu.tw&#39;</span><span class="p">,</span> <span class="s1">&#39;Hsien-Da Huang&#39;</span><span class="p">)],</span>
+        <span class="s1">&#39;type&#39;</span><span class="p">:</span> <span class="s1">&#39;Literature curated&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;subtype&#39;</span><span class="p">:</span> <span class="s1">&#39;PTM&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;omnipath&#39;</span><span class="p">:</span> <span class="kc">True</span><span class="p">,</span>
+        <span class="s1">&#39;data_integration&#39;</span><span class="p">:</span> <span class="s1">&#39;dynamic&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;license&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;name&#39;</span><span class="p">:</span> <span class="s1">&#39;No license&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;url&#39;</span><span class="p">:</span> <span class="s1">&#39;http://www.gnu.org/licenses/license-list.html#NoLicense&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;commercial_use&#39;</span><span class="p">:</span> <span class="kc">False</span>
+        <span class="p">},</span>
+        <span class="s1">&#39;pypath&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;format&#39;</span><span class="p">:</span> <span class="p">[</span>
+                <span class="s1">&#39;pypath.data_formats.ptm[</span><span class="se">\&#39;</span><span class="s1">dbptm</span><span class="se">\&#39;</span><span class="s1">]&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;pypath.data_formats.omnipath[</span><span class="se">\&#39;</span><span class="s1">dbptm</span><span class="se">\&#39;</span><span class="s1">]&#39;</span>
+            <span class="p">],</span>
+            <span class="s1">&#39;data&#39;</span><span class="p">:</span> <span class="p">[</span>
+                <span class="s1">&#39;pypath.urls.urls[</span><span class="se">\&#39;</span><span class="s1">dbptm_benchmark</span><span class="se">\&#39;</span><span class="s1">][</span><span class="se">\&#39;</span><span class="s1">urls</span><span class="se">\&#39;</span><span class="s1">]&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;pypath.urls.urls[</span><span class="se">\&#39;</span><span class="s1">dbptm</span><span class="se">\&#39;</span><span class="s1">][</span><span class="se">\&#39;</span><span class="s1">urls</span><span class="se">\&#39;</span><span class="s1">]&#39;</span>
+            <span class="p">],</span>
+            <span class="s1">&#39;input&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;pypath.dataio.get_dbptm()&#39;</span><span class="p">],</span>
+            <span class="s1">&#39;intr&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;pypath.dataio.dbptm_interactions()&#39;</span><span class="p">],</span>
+            <span class="s1">&#39;ptm&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;pypath.pypath.PyPath().load_dbptm()&#39;</span><span class="p">]</span>
+        <span class="p">}</span>
+    <span class="p">},</span>
+    <span class="s1">&#39;SIGNOR&#39;</span><span class="p">:</span> <span class="p">{</span>
+        <span class="s1">&#39;year&#39;</span><span class="p">:</span> <span class="mi">2015</span><span class="p">,</span>
+        <span class="s1">&#39;releases&#39;</span><span class="p">:</span> <span class="p">[</span><span class="mi">2015</span><span class="p">,</span><span class="mi">2019</span><span class="p">],</span>
+        <span class="s1">&#39;urls&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;webpages&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;http://signor.uniroma2.it/&#39;</span><span class="p">],</span>
+            <span class="s1">&#39;articles&#39;</span><span class="p">:</span> <span class="p">[</span>
+                <span class="s1">&#39;http://nar.oxfordjournals.org/content/44/D1/D548&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;http://f1000research.com/posters/1098359&#39;</span>
+            <span class="p">],</span>
+            <span class="s1">&#39;omictools&#39;</span><span class="p">:</span>
+            <span class="p">[</span><span class="s1">&#39;http://omictools.com/signaling-network-open-resource-tool&#39;</span><span class="p">]</span>
+        <span class="p">},</span>
+        <span class="s1">&#39;full_name&#39;</span><span class="p">:</span> <span class="s1">&#39;Signaling Network Open Resource&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;pubmeds&#39;</span><span class="p">:</span> <span class="p">[</span><span class="mi">26467481</span><span class="p">],</span>
+        <span class="s1">&#39;annot&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;mechanism&#39;</span><span class="p">,</span> <span class="s1">&#39;pathway&#39;</span><span class="p">],</span>
+        <span class="s1">&#39;recommend&#39;</span><span class="p">:</span>
+        <span class="s1">&#39;provides effect sign for an unprecedented number of interactions; large and recent curation effort; many specific entities; PTMs with enzymes&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;descriptions&#39;</span><span class="p">:</span> <span class="p">[</span>
+<span class="w">            </span><span class="sa">u</span><span class="sd">&#39;&#39;&#39;</span>
+<span class="sd">            SIGNOR, the SIGnaling Network Open Resource, organizes and stores in a structured format signaling information published in the scientific literature. The captured information is stored as binary causative relationships between biological entities and can be represented graphically as activity flow. The entire network can be freely downloaded and used to support logic modeling or to interpret high content datasets. The core of this project is a collection of more than 11000 manually-annotated causal relationships between proteins that participate in signal transduction. Each relationship is linked to the literature reporting the experimental evidence. In addition each node is annotated with the chemical inhibitors that modulate its activity. The signaling information is mapped to the human proteome even if the experimental evidence is based on experiments on mammalian model organisms.</span>
+<span class="sd">            &#39;&#39;&#39;</span>
+        <span class="p">],</span>
+        <span class="s1">&#39;authors&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;Cesareni Group&#39;</span><span class="p">],</span>
+        <span class="s1">&#39;label&#39;</span><span class="p">:</span> <span class="s1">&#39;SIGNOR&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;color&#39;</span><span class="p">:</span> <span class="s1">&#39;&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;data_import&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;SignaLink3&#39;</span><span class="p">,</span> <span class="s1">&#39;PhosphoSite&#39;</span><span class="p">],</span>
+        <span class="s1">&#39;type&#39;</span><span class="p">:</span> <span class="s1">&#39;literature curated&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;subtype&#39;</span><span class="p">:</span> <span class="s1">&#39;activity flow&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;omnipath&#39;</span><span class="p">:</span> <span class="kc">True</span><span class="p">,</span>
+        <span class="s1">&#39;emails&#39;</span><span class="p">:</span> <span class="p">[(</span><span class="s1">&#39;perfetto@live.it&#39;</span><span class="p">,</span> <span class="s1">&#39;Livia Perfetto&#39;</span><span class="p">)],</span>
+        <span class="s1">&#39;license&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;name&#39;</span><span class="p">:</span> <span class="s1">&#39;CC-Attribution-ShareAlike 4.0&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;url&#39;</span><span class="p">:</span> <span class="s1">&#39;https://creativecommons.org/licenses/by-sa/4.0/&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;commercial_use&#39;</span><span class="p">:</span> <span class="kc">True</span>
+        <span class="p">},</span>
+        <span class="s1">&#39;pypath&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;data&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;pypath.urls.urls[</span><span class="se">\&#39;</span><span class="s1">signor</span><span class="se">\&#39;</span><span class="s1">][</span><span class="se">\&#39;</span><span class="s1">all_url</span><span class="se">\&#39;</span><span class="s1">]&#39;</span><span class="p">],</span>
+            <span class="s1">&#39;format&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;pypath.data_formats.pathway[</span><span class="se">\&#39;</span><span class="s1">signor</span><span class="se">\&#39;</span><span class="s1">]&#39;</span><span class="p">],</span>
+            <span class="s1">&#39;intr&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;pypath.dataio.signor_interactions()&#39;</span><span class="p">],</span>
+            <span class="s1">&#39;ptm&#39;</span><span class="p">:</span> <span class="p">[</span>
+                <span class="s1">&#39;pypath.dataio.load_signor_ptms()&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;pypath.pypath.PyPath().load_signor_ptms()&#39;</span>
+            <span class="p">]</span>
+        <span class="p">}</span>
+    <span class="p">},</span>
+    <span class="s1">&#39;HuPho&#39;</span><span class="p">:</span> <span class="p">{</span>
+        <span class="s1">&#39;year&#39;</span><span class="p">:</span> <span class="mi">2015</span><span class="p">,</span>
+        <span class="s1">&#39;releases&#39;</span><span class="p">:</span> <span class="p">[</span><span class="mi">2012</span><span class="p">,</span> <span class="mi">2015</span><span class="p">],</span>
+        <span class="s1">&#39;urls&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;webpages&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;http://hupho.uniroma2.it/&#39;</span><span class="p">],</span>
+            <span class="s1">&#39;articles&#39;</span><span class="p">:</span> <span class="p">[</span>
+                <span class="s1">&#39;http://onlinelibrary.wiley.com/doi/10.1111/j.1742-4658.2012.08712.x/full&#39;</span>
+            <span class="p">],</span>
+            <span class="s1">&#39;omictools&#39;</span><span class="p">:</span>
+            <span class="p">[</span><span class="s1">&#39;http://omictools.com/human-phosphatase-portal-tool&#39;</span><span class="p">]</span>
+        <span class="p">},</span>
+        <span class="s1">&#39;pubmeds&#39;</span><span class="p">:</span> <span class="p">[</span><span class="mi">22804825</span><span class="p">],</span>
+        <span class="s1">&#39;descriptions&#39;</span><span class="p">:</span> <span class="p">[</span>
+<span class="w">            </span><span class="sa">u</span><span class="sd">&#39;&#39;&#39;</span>
+<span class="sd">            In order to offer a proteome-wide perspective of the phosphatase interactome, we have embarked on an extensive text-mining-assisted literature curation effort to extend phosphatase interaction information that was not yet covered by protein–protein interaction (PPI) databases. Interaction evidence captured by expert curators was annotated in the protein interaction database MINT according to the rapid curation standard. This data set was next integrated with protein interaction information from three additional major PPI databases, IntAct, BioGRID and DIP. These databases are part of the PSIMEx consortium and adopt a common data model and common controlled vocabularies, thus facilitating data integration. Duplicated entries were merged and redundant interactions have been removed.</span>
+<span class="sd">            As a result, from the HuPho website it is possible to explore experimental evidence from 718 scientific articles reporting 4600 experiments supporting protein interactions where at least one of the partners is a phosphatase. Since some interactions are supported by more than one piece of evidence, the actual number of non-redundant interactions is smaller, 2500 at the time of writing this paper. Moreover, 199 phosphatases have at least one reported ligand, while 53 have none. Interaction evidence is fairly evenly distributed in the four PSIMEx resources suggesting a substantial lack of overlap among the data curated by each database.</span>
+<span class="sd">            &#39;&#39;&#39;</span>
+        <span class="p">],</span>
+        <span class="s1">&#39;notes&#39;</span><span class="p">:</span> <span class="p">[</span>
+<span class="w">            </span><span class="sa">u</span><span class="sd">&#39;&#39;&#39;</span>
+<span class="sd">            The database is dynamically updated, so is up to date at any given time. That&#39;s why it is marked as up to date in 2015, despite it has no new release after 2012.</span>
+<span class="sd">            &#39;&#39;&#39;</span>
+        <span class="p">],</span>
+        <span class="s1">&#39;authors&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;Cesareni Group&#39;</span><span class="p">],</span>
+        <span class="s1">&#39;label&#39;</span><span class="p">:</span> <span class="s1">&#39;HuPho&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;full_name&#39;</span><span class="p">:</span> <span class="s1">&#39;Human Phosphatase Portal&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;color&#39;</span><span class="p">:</span> <span class="s1">&#39;&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;type&#39;</span><span class="p">:</span> <span class="s1">&#39;high throughput and literature curated&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;subtype&#39;</span><span class="p">:</span> <span class="s1">&#39;post-translational modification&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;omnipath&#39;</span><span class="p">:</span> <span class="kc">False</span><span class="p">,</span>
+        <span class="s1">&#39;emails&#39;</span><span class="p">:</span> <span class="p">[(</span><span class="s1">&#39;perfetto@live.it&#39;</span><span class="p">,</span> <span class="s1">&#39;Livia Perfetto&#39;</span><span class="p">)],</span>
+        <span class="s1">&#39;license&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;name&#39;</span><span class="p">:</span> <span class="s1">&#39;No license&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;url&#39;</span><span class="p">:</span> <span class="s1">&#39;http://www.gnu.org/licenses/license-list.html#NoLicense&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;commercial_use&#39;</span><span class="p">:</span> <span class="kc">False</span>
+        <span class="p">}</span>
+    <span class="p">},</span>
+    <span class="s1">&#39;SignaLink3&#39;</span><span class="p">:</span> <span class="p">{</span>
+        <span class="s1">&#39;year&#39;</span><span class="p">:</span> <span class="mi">2015</span><span class="p">,</span>
+        <span class="s1">&#39;releases&#39;</span><span class="p">:</span> <span class="p">[</span><span class="mi">2010</span><span class="p">,</span> <span class="mi">2012</span><span class="p">,</span> <span class="mi">2016</span><span class="p">],</span>
+        <span class="s1">&#39;size&#39;</span><span class="p">:</span> <span class="mi">0</span><span class="p">,</span>
+        <span class="s1">&#39;authors&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;NetBiol Group&#39;</span><span class="p">],</span>
+        <span class="s1">&#39;label&#39;</span><span class="p">:</span> <span class="s1">&#39;SignaLink&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;color&#39;</span><span class="p">:</span> <span class="s1">&#39;&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;pubmeds&#39;</span><span class="p">:</span> <span class="p">[</span><span class="mi">20542890</span><span class="p">,</span> <span class="mi">23331499</span><span class="p">],</span>
+        <span class="s1">&#39;urls&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;webpages&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;http://signalink.org/&#39;</span><span class="p">],</span>
+            <span class="s1">&#39;articles&#39;</span><span class="p">:</span> <span class="p">[</span>
+                <span class="s1">&#39;http://bioinformatics.oxfordjournals.org/content/26/16/2042.long&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;http://www.biomedcentral.com/1752-0509/7/7&#39;</span>
+            <span class="p">],</span>
+            <span class="s1">&#39;omictools&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;http://omictools.com/signalink-tool&#39;</span><span class="p">]</span>
+        <span class="p">},</span>
+        <span class="s1">&#39;taxons&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;human&#39;</span><span class="p">,</span> <span class="s1">&#39;D. melanogaster&#39;</span><span class="p">,</span> <span class="s1">&#39;C. elegans&#39;</span><span class="p">],</span>
+        <span class="s1">&#39;annot&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;pathway&#39;</span><span class="p">],</span>
+        <span class="s1">&#39;recommend&#39;</span><span class="p">:</span>
+        <span class="s1">&#39;one of the largest resources with effect sign; due to its specific, biochemically defined pathways suitable for cross-talk analysis&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;descriptions&#39;</span><span class="p">:</span> <span class="p">[</span>
+<span class="w">            </span><span class="sa">u</span><span class="sd">&#39;&#39;&#39;</span>
+<span class="sd">            In each of the three organisms, we first listed signaling proteins and interactions from reviews (and from WormBook in C.elegans) and then added further signaling interactions of the listed proteins. To identify additional interactions in C.elegans, we examined all interactions (except for transcription regulation) of the signaling proteins listed in WormBase and added only those to SignaLink that we could manually identify in the literature as an experimentally verified signaling interaction. For D.melanogaster, we added to SignaLink those genetic interactions from FlyBase that were also reported in at least one yeast-2-hybrid experiment. For humans, we manually checked the reliability and directions for the PPIs found with the search engines iHop and Chilibot.</span>
+<span class="sd">            SignaLink assigns proteins to signaling pathways using the full texts of pathway reviews (written by pathway experts). While most signaling resources consider 5–15 reviews per pathway, SignaLink uses a total of 170 review papers, i.e. more than 20 per pathway on average. Interactions were curated from a total of 941 articles (PubMed IDs are available at the website). We added a small number of proteins based on InParanoid ortholog clusters. For curation, we used a self-developed graphical tool and Perl/Python scripts. The current version of SignaLink was completed in May 2008 based on WormBase (version 191), FlyBase (2008.6), Ensembl, UniProt and the publications listed on the website.</span>
+<span class="sd">            The curation protocol of SignaLink (Fig. 1A) contains several steps aimed specifically at reducing data and curation errors. We used reviews as a starting point, manually looked up interactions three times, and manually searched for interactions of known signaling proteins with no signaling interactions so far in the database.</span>
+<span class="sd">            &#39;&#39;&#39;</span>
+        <span class="p">],</span>
+        <span class="s1">&#39;notes&#39;</span><span class="p">:</span> <span class="p">[</span>
+<span class="w">            </span><span class="sa">u</span><span class="sd">&#39;&#39;&#39;</span>
+<span class="sd">            For OmniPath we used the literature curated part of version 3 of SignaLink, which is unpublished yet. Version 2 is publicly available, and format definitions in pypath exist to load the version 2 alternatively.</span>
+<span class="sd">            &#39;&#39;&#39;</span>
+        <span class="p">],</span>
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+        <span class="s1">&#39;license&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;name&#39;</span><span class="p">:</span> <span class="s1">&#39;CC-Attribution 4.0&#39;</span><span class="p">,</span>
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+            <span class="s1">&#39;commercial_use&#39;</span><span class="p">:</span> <span class="kc">True</span>
+
+        <span class="p">},</span>
+        <span class="s1">&#39;pypath&#39;</span><span class="p">:</span> <span class="p">{</span>
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+    <span class="p">},</span>
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+        <span class="s1">&#39;year&#39;</span><span class="p">:</span> <span class="mi">2012</span><span class="p">,</span>
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+            <span class="s1">&#39;edges&#39;</span><span class="p">:</span> <span class="kc">None</span>
+        <span class="p">},</span>
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+        <span class="s1">&#39;label&#39;</span><span class="p">:</span> <span class="s1">&#39;DeathDomain&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;color&#39;</span><span class="p">:</span> <span class="s1">&#39;&#39;</span><span class="p">,</span>
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+        <span class="s1">&#39;urls&#39;</span><span class="p">:</span> <span class="p">{</span>
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+        <span class="p">},</span>
+        <span class="s1">&#39;license&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;name&#39;</span><span class="p">:</span>
+            <span class="s1">&#39;No license. Please cite the following paper when you use Death Domain database in your publications, which is very important to sustain our service: Kwon et al. 2012&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;url&#39;</span><span class="p">:</span> <span class="s1">&#39;http://www.gnu.org/licenses/license-list.html#NoLicense&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;commercial_use&#39;</span><span class="p">:</span> <span class="kc">False</span>
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+        <span class="s1">&#39;taxons&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;human&#39;</span><span class="p">],</span>
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+        <span class="s1">&#39;recommend&#39;</span><span class="p">:</span>
+        <span class="s1">&#39;focused deep curation effort on death domain superfamily proteins; many specific relationships&#39;</span><span class="p">,</span>
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+<span class="w">            </span><span class="sa">u</span><span class="sd">&#39;&#39;&#39;</span>
+<span class="sd">            The PubMed database was used as the primary source for collecting information and constructing the DD database. After finding synonyms for each of the 99 DD superfamily proteins using UniProtKB and Entrez Gene, we obtained a list of articles using each name of the proteins and its synonyms on a PubMed search, and we selected the articles that contained evidence for physical binding among the proteins denoted. We also manually screened information that was in other databases, such as DIP, IntAct, MINT, STRING and Entrez Gene. All of the 295 articles used for database construction are listed on our database website.</span>
+<span class="sd">            &#39;&#39;&#39;</span>
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+        <span class="s1">&#39;notes&#39;</span><span class="p">:</span> <span class="p">[</span>
+<span class="w">            </span><span class="sa">u</span><span class="sd">&#39;&#39;&#39;</span>
+<span class="sd">            Detailful dataset with many references. Sadly the data can be extracted only by parsing HTML. It doesn&#39;t mean more difficulty than parsing XML formats, just these are not intended to use for this purpose.</span>
+<span class="sd">            &#39;&#39;&#39;</span>
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+        <span class="s1">&#39;type&#39;</span><span class="p">:</span> <span class="s1">&#39;literature curated&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;subtype&#39;</span><span class="p">:</span> <span class="s1">&#39;activity flow&#39;</span><span class="p">,</span>
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+        <span class="s1">&#39;pypath&#39;</span><span class="p">:</span> <span class="p">{</span>
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+        <span class="s1">&#39;releases&#39;</span><span class="p">:</span> <span class="p">[</span><span class="mi">2010</span><span class="p">,</span> <span class="mi">2012</span><span class="p">],</span>
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+            <span class="p">],</span>
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+            <span class="p">]</span>
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+        <span class="s1">&#39;identifiers&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;GeneSymbol&#39;</span><span class="p">],</span>
+        <span class="s1">&#39;recommend&#39;</span><span class="p">:</span>
+        <span class="s1">&#39;high number of specific interactions; focused on TRP channels&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;descriptions&#39;</span><span class="p">:</span> <span class="p">[</span>
+<span class="w">            </span><span class="sa">u</span><span class="sd">&#39;&#39;&#39;</span>
+<span class="sd">            The literature on TRP channel PPIs found in the PubMed database serve as the primary information source for constructing the TRIP Database. First, a list of synonyms for the term ‘TRP channels’ was constructed from UniprotKB, Entrez Gene, membrane protein databases (Supplementary Table S2) and published review papers for nomenclature. Second, using these synonyms, a list of articles was obtained through a PubMed search. Third, salient articles were collected through a survey of PubMed abstracts and subsequently by search of full-text papers. Finally, we selected articles that contain evidence for physical binding among the proteins denoted. To prevent omission of relevant papers, we manually screened information in other databases, such as DIP, IntAct, MINT, STRING, BioGRID, Entrez Gene, IUPHAR-DB and ISI Web of Knowledge (from Thomson Reuters). All 277 articles used for database construction are listed in our database website.</span>
+<span class="sd">            &#39;&#39;&#39;</span>
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+        <span class="s1">&#39;notes&#39;</span><span class="p">:</span> <span class="p">[</span>
+<span class="w">            </span><span class="sa">u</span><span class="sd">&#39;&#39;&#39;</span>
+<span class="sd">            Good manually curated dataset focusing on TRP channel proteins, with ~800 binary interactions. The provided formats are not well suitable for bioinformatics use because of the non standard protein names, with greek letters and only human understandable formulas. Using HTML processing from 5-6 different tables, with couple hundreds lines of code, one have a chance to compile a usable table.</span>
+<span class="sd">            &#39;&#39;&#39;</span>
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+        <span class="s1">&#39;type&#39;</span><span class="p">:</span> <span class="s1">&#39;literature curated&#39;</span><span class="p">,</span>
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+        <span class="s1">&#39;omnipath&#39;</span><span class="p">:</span> <span class="kc">True</span><span class="p">,</span>
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+            <span class="s1">&#39;format&#39;</span><span class="p">:</span> <span class="p">[</span>
+                <span class="s1">&#39;pypath.data_formats.pathway[</span><span class="se">\&#39;</span><span class="s1">trip</span><span class="se">\&#39;</span><span class="s1">]&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;pypath.data_formats.omnipath[</span><span class="se">\&#39;</span><span class="s1">trip</span><span class="se">\&#39;</span><span class="s1">]&#39;</span>
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+        <span class="p">},</span>
+        <span class="s1">&#39;license&#39;</span><span class="p">:</span> <span class="p">{</span>
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+    <span class="p">},</span>
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+        <span class="s1">&#39;label&#39;</span><span class="p">:</span> <span class="s1">&#39;Awan 2007&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;color&#39;</span><span class="p">:</span> <span class="s1">&#39;&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;data_import&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;BioCarta&#39;</span><span class="p">,</span> <span class="s1">&#39;CA1&#39;</span><span class="p">],</span>
+        <span class="s1">&#39;contains&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;BioCarta&#39;</span><span class="p">,</span> <span class="s1">&#39;CA1&#39;</span><span class="p">],</span>
+        <span class="s1">&#39;urls&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;articles&#39;</span><span class="p">:</span>
+            <span class="p">[</span><span class="s1">&#39;http://www.cancer-systemsbiology.org/Papers/iet-sb2007.pdf&#39;</span><span class="p">]</span>
+        <span class="p">},</span>
+        <span class="s1">&#39;emails&#39;</span><span class="p">:</span> <span class="p">[(</span><span class="s1">&#39;Edwin.Wang@cnrc-nrc.gc.ca&#39;</span><span class="p">,</span> <span class="s1">&#39;Edwin Wang&#39;</span><span class="p">)],</span>
+        <span class="s1">&#39;pubmeds&#39;</span><span class="p">:</span> <span class="p">[</span><span class="mi">17907678</span><span class="p">],</span>
+        <span class="s1">&#39;descriptions&#39;</span><span class="p">:</span> <span class="p">[</span>
+<span class="w">            </span><span class="sa">u</span><span class="sd">&#39;&#39;&#39;</span>
+<span class="sd">            To construct the human cellular signalling network, we manually curated signalling pathways from literature. The signalling data source for our pathways is the BioCarta database (http://www.biocarta.com/genes/allpathways.asp), which, so far, is the most comprehensive database for human cellular signalling pathways. Our curated pathway database recorded gene names and functions, cellular locations of each gene and relationships between genes such as activation, inhibition, translocation, enzyme digestion, gene transcription and translation, signal stimulation and so on. To ensure the accuracy and the consistency of the database, each referenced pathway was cross-checked by different researchers and finally all the documented pathways were checked by one researcher. In total, 164 signalling pathways were documented (supplementary Table 2). Furthermore, we merged the curated data with another literature-mined human cellular signalling network. As a result, the merged network contains nearly 1100 proteins (SupplementaryNetworkFile). To construct a signalling network, we considered relationships of proteins as links (activation or inactivation as directed links and physical interactions in protein complexes as neutral links) and proteins as nodes.</span>
+<span class="sd">            &#39;&#39;&#39;</span>
+        <span class="p">],</span>
+        <span class="s1">&#39;type&#39;</span><span class="p">:</span> <span class="s1">&#39;literature curated&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;subtype&#39;</span><span class="p">:</span> <span class="s1">&#39;activity flow&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;omnipath&#39;</span><span class="p">:</span> <span class="kc">False</span><span class="p">,</span>
+        <span class="s1">&#39;license&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;name&#39;</span><span class="p">:</span> <span class="s1">&#39;No license&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;url&#39;</span><span class="p">:</span> <span class="s1">&#39;http://www.gnu.org/licenses/license-list.html#NoLicense&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;commercial_use&#39;</span><span class="p">:</span> <span class="kc">False</span>
+        <span class="p">}</span>
+    <span class="p">},</span>
+    <span class="s1">&#39;Cui2007&#39;</span><span class="p">:</span> <span class="p">{</span>
+        <span class="s1">&#39;year&#39;</span><span class="p">:</span> <span class="mi">2007</span><span class="p">,</span>
+        <span class="s1">&#39;authors&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;Wang Group&#39;</span><span class="p">],</span>
+        <span class="s1">&#39;label&#39;</span><span class="p">:</span> <span class="s1">&#39;Cui 2007&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;color&#39;</span><span class="p">:</span> <span class="s1">&#39;&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;data_import&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;Awan2007&#39;</span><span class="p">,</span> <span class="s1">&#39;CancerCellMap&#39;</span><span class="p">],</span>
+        <span class="s1">&#39;pubmeds&#39;</span><span class="p">:</span> <span class="p">[</span><span class="mi">18091723</span><span class="p">],</span>
+        <span class="s1">&#39;contains&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;Awan2007&#39;</span><span class="p">,</span> <span class="s1">&#39;CancerCellMap&#39;</span><span class="p">,</span> <span class="s1">&#39;CA1&#39;</span><span class="p">,</span> <span class="s1">&#39;BioCarta&#39;</span><span class="p">],</span>
+        <span class="s1">&#39;urls&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;articles&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;http://msb.embopress.org/content/3/1/152&#39;</span><span class="p">],</span>
+            <span class="s1">&#39;webpages&#39;</span><span class="p">:</span> <span class="p">[]</span>
+        <span class="p">},</span>
+        <span class="s1">&#39;emails&#39;</span><span class="p">:</span> <span class="p">[(</span><span class="s1">&#39;Edwin.Wang@cnrc-nrc.gc.ca&#39;</span><span class="p">,</span> <span class="s1">&#39;Edwin Wang&#39;</span><span class="p">)],</span>
+        <span class="s1">&#39;files&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;articles&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;Cui2007.pdf&#39;</span><span class="p">],</span>
+            <span class="s1">&#39;data&#39;</span><span class="p">:</span> <span class="p">{</span>
+                <span class="s1">&#39;raw&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;cui-network.xls&#39;</span><span class="p">,</span> <span class="p">],</span>
+                <span class="s1">&#39;processed&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;cui.sif&#39;</span><span class="p">]</span>
+            <span class="p">}</span>
+        <span class="p">},</span>
+        <span class="s1">&#39;identifiers&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;EntrezGene&#39;</span><span class="p">],</span>
+        <span class="s1">&#39;size&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;edges&#39;</span><span class="p">:</span> <span class="mi">4249</span><span class="p">,</span>
+            <span class="s1">&#39;nodes&#39;</span><span class="p">:</span> <span class="mi">1528</span>
+        <span class="p">},</span>
+        <span class="s1">&#39;taxons&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;human&#39;</span><span class="p">],</span>
+        <span class="s1">&#39;descriptions&#39;</span><span class="p">:</span> <span class="p">[</span>
+<span class="w">            </span><span class="sa">u</span><span class="sd">&#39;&#39;&#39;</span>
+<span class="sd">            To build up the human signaling network, we manually curated the signaling molecules (most of them are proteins) and the interactions between these molecules from the most comprehensive signaling pathway database, BioCarta (http://www.biocarta.com/). The pathways in the database are illustrated as diagrams. We manually recorded the names, functions, cellular locations, biochemical classifications and the regulatory (including activating and inhibitory) and interaction relations of the signaling molecules for each signaling pathway. To ensure the accuracy of the curation, all the data have been crosschecked four times by different researchers. After combining the curated information with another literature‐mined signaling network that contains ∼500 signaling molecules (Ma&#39;ayan et al, 2005)[this is the CA1], we obtained a signaling network containing ∼1100 proteins (Awan et al, 2007). We further extended this network by extracting and adding the signaling molecules and their relations from the Cancer Cell Map (http://cancer.cellmap.org/cellmap/), a database that contains 10 manually curated signaling pathways for cancer. As a result, the network contains 1634 nodes and 5089 links that include 2403 activation links (positive links), 741 inhibitory links (negative links), 1915 physical links (neutral links) and 30 links whose types are unknown (Supplementary Table 9). To our knowledge, this network is the biggest cellular signaling network at present.</span>
+<span class="sd">            &#39;&#39;&#39;</span><span class="p">,</span> <span class="sa">u</span><span class="s1">&#39;&#39;&#39;</span>
+<span class="s1">            From Awan 2007: To construct the human cellular signalling network, we manually curated signalling pathways from literature. The signalling data source for our pathways is the BioCarta database (http://www.biocarta.com/genes/allpathways.asp), which, so far, is the most comprehensive database for human cellular signalling pathways. Our curated pathway database recorded gene names and functions, cellular locations of each gene and relationships between genes such as activation, inhibition, translocation, enzyme digestion, gene transcription and translation, signal stimulation and so on. To ensure the accuracy and the consistency of the database, each referenced pathway was cross-checked by different researchers and finally all the documented pathways were checked by one researcher.</span>
+<span class="s1">            &#39;&#39;&#39;</span>
+        <span class="p">],</span>
+        <span class="s1">&#39;notes&#39;</span><span class="p">:</span> <span class="p">[</span>
+<span class="w">            </span><span class="sa">u</span><span class="sd">&#39;&#39;&#39;</span>
+<span class="sd">            Excellent signaling network with good topology for all those who doesn&#39;t mind to use data of unknown origin. Supposedly a manually curated network, but data files doesn&#39;t include article references. Merging CA1 network with CancerCellMap and BioCarta (also without references) makes the origin of the data untraceable.</span>
+<span class="sd">            &#39;&#39;&#39;</span>
+        <span class="p">],</span>
+        <span class="s1">&#39;type&#39;</span><span class="p">:</span> <span class="s1">&#39;literature curated&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;subtype&#39;</span><span class="p">:</span> <span class="s1">&#39;activity flow&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;omnipath&#39;</span><span class="p">:</span> <span class="kc">False</span><span class="p">,</span>
+        <span class="s1">&#39;license&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;name&#39;</span><span class="p">:</span> <span class="s1">&#39;No license&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;url&#39;</span><span class="p">:</span> <span class="s1">&#39;http://www.gnu.org/licenses/license-list.html#NoLicense&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;commercial_use&#39;</span><span class="p">:</span> <span class="kc">False</span>
+        <span class="p">}</span>
+    <span class="p">},</span>
+    <span class="s1">&#39;BioCarta&#39;</span><span class="p">:</span> <span class="p">{</span>
+        <span class="s1">&#39;year&#39;</span><span class="p">:</span> <span class="mi">2006</span><span class="p">,</span>
+        <span class="s1">&#39;releases&#39;</span><span class="p">:</span> <span class="p">[</span><span class="mi">2006</span><span class="p">],</span>
+        <span class="s1">&#39;size&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;nodes&#39;</span><span class="p">:</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="s1">&#39;edges&#39;</span><span class="p">:</span> <span class="kc">None</span>
+        <span class="p">},</span>
+        <span class="s1">&#39;authors&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;Community&#39;</span><span class="p">],</span>
+        <span class="s1">&#39;label&#39;</span><span class="p">:</span> <span class="s1">&#39;BioCarta&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;color&#39;</span><span class="p">:</span> <span class="s1">&#39;&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;urls&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;webpages&#39;</span><span class="p">:</span> <span class="p">[</span>
+                <span class="s1">&#39;http://www.biocarta.com/&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;http://cgap.nci.nih.gov/Pathways/BioCarta_Pathways&#39;</span>
+            <span class="p">],</span>
+            <span class="s1">&#39;articles&#39;</span><span class="p">:</span> <span class="p">[]</span>
+        <span class="p">},</span>
+        <span class="s1">&#39;emails&#39;</span><span class="p">:</span>
+        <span class="p">[(</span><span class="s1">&#39;info@biocarta.com&#39;</span><span class="p">,</span> <span class="s1">&#39;BioCarta Scientific Advisory Board&#39;</span><span class="p">)],</span>
+        <span class="s1">&#39;taxons&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;human&#39;</span><span class="p">],</span>
+        <span class="s1">&#39;descriptions&#39;</span><span class="p">:</span> <span class="p">[</span>
+<span class="w">            </span><span class="sa">u</span><span class="sd">&#39;&#39;&#39;</span>
+<span class="sd">            Community built pathway database based on expert curation.</span>
+<span class="sd">            &#39;&#39;&#39;</span>
+        <span class="p">],</span>
+        <span class="s1">&#39;notes&#39;</span><span class="p">:</span> <span class="p">[</span>
+<span class="w">            </span><span class="sa">u</span><span class="sd">&#39;&#39;&#39;</span>
+<span class="sd">            This resource includes a huge number of pathways, each curated by experts from a few reviews. The data is not available for download from the original webpage, only from second hand, for example from NCI-PID, in NCI-XML format. However, these files doesn&#39;t contain any references, which makes problematic the use of the BioCarta dataset. Also, some pathways are reviewed long time ago, possibly outdated.</span>
+<span class="sd">            &#39;&#39;&#39;</span><span class="p">,</span> <span class="s1">&#39;&#39;&#39;</span>
+<span class="s1">            The Company and the website looks like was abandoned around 2003-2006.</span>
+<span class="s1">            &#39;&#39;&#39;</span>
+        <span class="p">],</span>
+        <span class="s1">&#39;type&#39;</span><span class="p">:</span> <span class="s1">&#39;literature curated&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;subtype&#39;</span><span class="p">:</span> <span class="s1">&#39;activity flow&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;omnipath&#39;</span><span class="p">:</span> <span class="kc">False</span><span class="p">,</span>
+        <span class="s1">&#39;license&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;name&#39;</span><span class="p">:</span>
+            <span class="s1">&#39;BioCarta webpage Terms and Conditions of Use (pathways are not owned by BioCarta and are free to use)&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;url&#39;</span><span class="p">:</span>
+            <span class="s1">&#39;http://web.archive.org/web/20150207091158/http://biocarta.com/legal/terms.asp&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;commercial_use&#39;</span><span class="p">:</span> <span class="kc">False</span>
+        <span class="p">}</span>
+    <span class="p">},</span>
+    <span class="s1">&#39;TLR&#39;</span><span class="p">:</span> <span class="p">{</span>
+        <span class="s1">&#39;urls&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;articles&#39;</span><span class="p">:</span>
+            <span class="p">[</span><span class="s1">&#39;https://www.embopress.org/doi/10.1038/msb4100057&#39;</span><span class="p">]</span>
+        <span class="p">},</span>
+        <span class="s1">&#39;type&#39;</span><span class="p">:</span> <span class="s1">&#39;literature curated&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;subtype&#39;</span><span class="p">:</span> <span class="s1">&#39;model&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;omnipath&#39;</span><span class="p">:</span> <span class="kc">False</span><span class="p">,</span>
+        <span class="s1">&#39;license&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;name&#39;</span><span class="p">:</span> <span class="s1">&#39;No license&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;url&#39;</span><span class="p">:</span> <span class="s1">&#39;http://www.gnu.org/licenses/license-list.html#NoLicense&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;commercial_use&#39;</span><span class="p">:</span> <span class="kc">False</span>
+        <span class="p">}</span>
+    <span class="p">},</span>
+    <span class="s1">&#39;CA1&#39;</span><span class="p">:</span> <span class="p">{</span>
+        <span class="s1">&#39;year&#39;</span><span class="p">:</span> <span class="mi">2005</span><span class="p">,</span>
+        <span class="s1">&#39;releases&#39;</span><span class="p">:</span> <span class="p">[</span><span class="mi">2005</span><span class="p">],</span>
+        <span class="s1">&#39;size&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;nodes&#39;</span><span class="p">:</span> <span class="mi">545</span><span class="p">,</span>
+            <span class="s1">&#39;edges&#39;</span><span class="p">:</span> <span class="mi">1259</span>
+        <span class="p">},</span>
+        <span class="s1">&#39;authors&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;Iyengar Lab&#39;</span><span class="p">],</span>
+        <span class="s1">&#39;label&#39;</span><span class="p">:</span> <span class="s1">&#39;Ma</span><span class="se">\&#39;</span><span class="s1">ayan 2005&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;full_name&#39;</span><span class="p">:</span> <span class="s1">&#39;Human Hippocampal CA1 Region Neurons Signaling Network&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;color&#39;</span><span class="p">:</span> <span class="s1">&#39;&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;pubmeds&#39;</span><span class="p">:</span> <span class="p">[</span><span class="mi">16099987</span><span class="p">],</span>
+        <span class="s1">&#39;urls&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;articles&#39;</span><span class="p">:</span>
+            <span class="p">[</span><span class="s1">&#39;http://www.sciencemag.org/content/309/5737/1078.full&#39;</span><span class="p">],</span>
+            <span class="s1">&#39;webpages&#39;</span><span class="p">:</span> <span class="p">[]</span>
+        <span class="p">},</span>
+        <span class="s1">&#39;emails&#39;</span><span class="p">:</span> <span class="p">[(</span><span class="s1">&#39;ravi.iyengar@mssm.edu&#39;</span><span class="p">,</span> <span class="s1">&#39;Ravi Iyengar&#39;</span><span class="p">)],</span>
+        <span class="s1">&#39;taxons&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;human&#39;</span><span class="p">,</span> <span class="s1">&#39;mouse&#39;</span><span class="p">],</span>
+        <span class="s1">&#39;annot&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;localization&#39;</span><span class="p">,</span> <span class="s1">&#39;mechanism&#39;</span><span class="p">],</span>
+        <span class="s1">&#39;recommend&#39;</span><span class="p">:</span>
+        <span class="s1">&#39;among the largest resources providing effect signs; more than a decade old dataset, used in many studies&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;descriptions&#39;</span><span class="p">:</span> <span class="p">[</span>
+<span class="w">            </span><span class="sa">u</span><span class="sd">&#39;&#39;&#39;</span>
+<span class="sd">            We used published research literature to identify the key components of signaling pathways and cellular machines, and their binary interactions. Most components (~80%) have been described in hippocampal neurons or related neuronal cells. Other components are from other cells, but are included because they are key components in processes known to occur in hippocampal neurons, such as translation. We then established that these interactions were both direct and functionally relevant. All of the connections were individually verified by at least one of the authors of this paper by reading the relevant primary paper(s). We developed a system made of 545 components (nodes) and 1259 links (connections). We used arbitrary but consistent rules to sort components into various groups. For instance, transcription factors are considered a as part of the transcriptional machinery, although it may also be equally valid to consider them as the most downstream component of the central signaling network. Similarly the AMPA receptor-channel (AMPAR) is considered part of the ion channels in the electrical response system since its activity is essential to defining the postsynaptic response, although it binds to and is activated by glutamate, and hence can be also considered a ligand gated receptor-channel in the plasma membrane. The links were specified by two criteria: function and biochemical mechanism. Three types of functional links were specified. This follows the rules used for representation of pathways in Science’s STKE (S1). Links may be activating, inhibitory or neutral. Neutral links do not specify directionality between components, and are mostly used to represent scaffolding and anchoring undirected or bidirectional interactions. The biochemical specification includes defining the reactions as non-covalent binding interactions or enzymatic reactions. Within the enzymatic category, reactions were further specified as phosphorylation, dephosphorylation, hydrolysis, etc. These two criteria for specification are independent and were defined for all interactions. For the analyses in this study we only used the functional criteria: activating, inhibitory or neutral specifications. We chose papers that demonstrated direct interactions that were supported by either biochemical or physiological effects of the interactions. From these papers we identified the components and interactions that make up the system we analyzed. During this specification process we did not consider whether these interactions would come together to form higher order organizational units. Each component and interaction was validated by a reference from the primary literature (1202 papers were used). A list of authors who read the papers to validate the components and interactions is provided under authors contributions.</span>
+<span class="sd">            &#39;&#39;&#39;</span>
+        <span class="p">],</span>
+        <span class="s1">&#39;notes&#39;</span><span class="p">:</span> <span class="p">[</span>
+<span class="w">            </span><span class="sa">u</span><span class="sd">&#39;&#39;&#39;</span>
+<span class="sd">            One of the earliest manually curated networks, available in easily accessible tabular format, including UniProt IDs and PubMed references.</span>
+<span class="sd">            &#39;&#39;&#39;</span>
+        <span class="p">],</span>
+        <span class="s1">&#39;type&#39;</span><span class="p">:</span> <span class="s1">&#39;literature curated&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;subtype&#39;</span><span class="p">:</span> <span class="s1">&#39;activity flow&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;omnipath&#39;</span><span class="p">:</span> <span class="kc">True</span><span class="p">,</span>
+        <span class="s1">&#39;data_integration&#39;</span><span class="p">:</span> <span class="s1">&#39;dynamic&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;pypath&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;intr&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;pypath.urls.urls[</span><span class="se">\&#39;</span><span class="s1">ca1</span><span class="se">\&#39;</span><span class="s1">][</span><span class="se">\&#39;</span><span class="s1">url</span><span class="se">\&#39;</span><span class="s1">]&#39;</span><span class="p">],</span>
+            <span class="s1">&#39;data&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;pypath.dataio.get_ca1()&#39;</span><span class="p">],</span>
+            <span class="s1">&#39;format&#39;</span><span class="p">:</span> <span class="p">[</span>
+                <span class="s1">&#39;pypath.data_formats.pathway[</span><span class="se">\&#39;</span><span class="s1">ca1</span><span class="se">\&#39;</span><span class="s1">]&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;pypath.data_formats.omnipath[</span><span class="se">\&#39;</span><span class="s1">ca1</span><span class="se">\&#39;</span><span class="s1">]&#39;</span>
+            <span class="p">]</span>
+        <span class="p">},</span>
+        <span class="s1">&#39;license&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;name&#39;</span><span class="p">:</span> <span class="s1">&#39;No license&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;url&#39;</span><span class="p">:</span> <span class="s1">&#39;http://www.gnu.org/licenses/license-list.html#NoLicense&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;commercial_use&#39;</span><span class="p">:</span> <span class="kc">False</span>
+        <span class="p">}</span>
+    <span class="p">},</span>
+    <span class="s1">&#39;CancerCellMap&#39;</span><span class="p">:</span> <span class="p">{</span>
+        <span class="s1">&#39;year&#39;</span><span class="p">:</span> <span class="mi">2006</span><span class="p">,</span>
+        <span class="s1">&#39;relases&#39;</span><span class="p">:</span> <span class="p">[</span><span class="mi">2004</span><span class="p">,</span> <span class="mi">2006</span><span class="p">],</span>
+        <span class="s1">&#39;urls&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;articles&#39;</span><span class="p">:</span> <span class="p">[],</span>
+            <span class="s1">&#39;webpages&#39;</span><span class="p">:</span> <span class="p">[</span>
+                <span class="s1">&#39;http://www.pathwaycommons.org/archives/PC1/last_release-2011/tab_delim_network/by_source/&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;http://web.archive.org/web/20130729025707/http://cancer.cellmap.org/cellmap/home.do&#39;</span>
+            <span class="p">]</span>
+        <span class="p">},</span>
+        <span class="s1">&#39;authors&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;Bader Lab&#39;</span><span class="p">],</span>
+        <span class="s1">&#39;emails&#39;</span><span class="p">:</span> <span class="p">[(</span><span class="s1">&#39;gary.bader@utoronto.ca&#39;</span><span class="p">,</span> <span class="s1">&#39;Gary Bader&#39;</span><span class="p">)],</span>
+        <span class="s1">&#39;descriptions&#39;</span><span class="p">:</span> <span class="p">[</span>
+<span class="w">            </span><span class="sa">u</span><span class="sd">&#39;&#39;&#39;</span>
+<span class="sd">            Manually curated data, unpublished. A team of M.Sc. and Ph.D. biologists at the Institute of Bioinformatics in Bangalore, India read original research papers and hand-entered the pathway data into our database. The quality of the Cancer Cell Map pathways is very high. Half of the pathways were reviewed by experts at Memorial Sloan-Kettering Cancer Center and were found to contain only a few errors, which were subsequently fixed. A pathway is a collection of all genes/proteins that have been described as pathway members in any publication and all the interactions between them that can be found described in the literature.</span>
+<span class="sd">            &#39;&#39;&#39;</span>
+        <span class="p">],</span>
+        <span class="s1">&#39;notes&#39;</span><span class="p">:</span> <span class="p">[</span>
+<span class="w">            </span><span class="sa">u</span><span class="sd">&#39;&#39;&#39;</span>
+<span class="sd">            One of the earliest manually curated datasets, now only available from second hand, e.g. from PathwayCommons. Included in many other resources. Contains binary interactions with PubMed references.</span>
+<span class="sd">            &#39;&#39;&#39;</span>
+        <span class="p">],</span>
+        <span class="s1">&#39;taxons&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;human&#39;</span><span class="p">,</span> <span class="s1">&#39;mouse&#39;</span><span class="p">,</span> <span class="s1">&#39;rat&#39;</span><span class="p">],</span>
+        <span class="s1">&#39;annot&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;localization&#39;</span><span class="p">],</span>
+        <span class="s1">&#39;recommend&#39;</span><span class="p">:</span>
+        <span class="s1">&#39;old literature curated resource; effect signs for some interactions&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;type&#39;</span><span class="p">:</span> <span class="s1">&#39;literature curated&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;subtype&#39;</span><span class="p">:</span> <span class="s1">&#39;interaction&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;omnipath&#39;</span><span class="p">:</span> <span class="kc">True</span><span class="p">,</span>
+        <span class="s1">&#39;pypath&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;intr&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;pypath.dataio.get_ccmap()&#39;</span><span class="p">],</span>
+            <span class="s1">&#39;data&#39;</span><span class="p">:</span> <span class="p">[</span>
+                <span class="s1">&#39;pypath.urls.urls[</span><span class="se">\&#39;</span><span class="s1">ccmap</span><span class="se">\&#39;</span><span class="s1">][</span><span class="se">\&#39;</span><span class="s1">nodes</span><span class="se">\&#39;</span><span class="s1">]&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;pypath.urls.urls[</span><span class="se">\&#39;</span><span class="s1">ccmap</span><span class="se">\&#39;</span><span class="s1">][</span><span class="se">\&#39;</span><span class="s1">edges</span><span class="se">\&#39;</span><span class="s1">]&#39;</span>
+            <span class="p">],</span>
+            <span class="s1">&#39;format&#39;</span><span class="p">:</span> <span class="p">[</span>
+                <span class="s1">&#39;pypath.data_formats.interaction[</span><span class="se">\&#39;</span><span class="s1">ccmap</span><span class="se">\&#39;</span><span class="s1">]&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;pypath.data_formats.omnipath[</span><span class="se">\&#39;</span><span class="s1">ccmap</span><span class="se">\&#39;</span><span class="s1">]&#39;</span>
+            <span class="p">]</span>
+        <span class="p">},</span>
+        <span class="s1">&#39;data_integration&#39;</span><span class="p">:</span> <span class="s1">&#39;dynamic&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;license&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;name&#39;</span><span class="p">:</span> <span class="s1">&#39;CC-Attribution-2.5&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;url&#39;</span><span class="p">:</span> <span class="s1">&#39;http://creativecommons.org/licenses/by/2.5/&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;commercial_use&#39;</span><span class="p">:</span> <span class="kc">True</span>
+        <span class="p">},</span>
+        <span class="s1">&#39;pathguide&#39;</span><span class="p">:</span> <span class="mi">223</span>
+    <span class="p">},</span>
+    <span class="s1">&#39;CARFMAP&#39;</span><span class="p">:</span> <span class="p">{</span>
+        <span class="s1">&#39;year&#39;</span><span class="p">:</span> <span class="mi">2015</span><span class="p">,</span>
+        <span class="s1">&#39;urls&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;articles&#39;</span><span class="p">:</span> <span class="p">[</span>
+                <span class="s1">&#39;http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0143274&#39;</span>
+            <span class="p">],</span>
+            <span class="s1">&#39;webpages&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;http://visionet.erc.monash.edu.au/CARFMAP/&#39;</span><span class="p">]</span>
+        <span class="p">},</span>
+        <span class="s1">&#39;pubmeds&#39;</span><span class="p">:</span> <span class="p">[</span><span class="mi">26673252</span><span class="p">],</span>
+        <span class="s1">&#39;emails&#39;</span><span class="p">:</span> <span class="p">[(</span><span class="s1">&#39;hieu.nim@monash.edu&#39;</span><span class="p">,</span> <span class="s1">&#39;Hieu T Nim&#39;</span><span class="p">),</span>
+                   <span class="p">(</span><span class="s1">&#39;sarah.boyd@monash.edu&#39;</span><span class="p">,</span> <span class="s1">&#39;Sarah E Boyd&#39;</span><span class="p">)],</span>
+        <span class="s1">&#39;license&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;name&#39;</span><span class="p">:</span> <span class="s1">&#39;CC-Attribution-4.0&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;url&#39;</span><span class="p">:</span> <span class="s1">&#39;http://creativecommons.org/licenses/by/4.0/&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;commercial_use&#39;</span><span class="p">:</span> <span class="kc">True</span>
+        <span class="p">},</span>
+        <span class="s1">&#39;omnipath&#39;</span><span class="p">:</span> <span class="kc">False</span><span class="p">,</span>
+        <span class="s1">&#39;type&#39;</span><span class="p">:</span> <span class="s1">&#39;Literature curated&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;subtype&#39;</span><span class="p">:</span> <span class="s1">&#39;Pathway&#39;</span>
+    <span class="p">},</span>
+    <span class="s1">&#39;HSN&#39;</span><span class="p">:</span> <span class="p">{</span>
+        <span class="s1">&#39;year&#39;</span><span class="p">:</span> <span class="mi">2014</span><span class="p">,</span>
+        <span class="s1">&#39;releases&#39;</span><span class="p">:</span> <span class="p">[</span><span class="mi">2009</span><span class="p">,</span> <span class="mi">2010</span><span class="p">,</span> <span class="mi">2011</span><span class="p">,</span> <span class="mi">2012</span><span class="p">,</span> <span class="mi">2013</span><span class="p">,</span> <span class="mi">2014</span><span class="p">],</span>
+        <span class="s1">&#39;nodes&#39;</span><span class="p">:</span> <span class="mi">6300</span><span class="p">,</span>
+        <span class="s1">&#39;edges&#39;</span><span class="p">:</span> <span class="mi">63000</span><span class="p">,</span>
+        <span class="s1">&#39;authors&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;Wang Group&#39;</span><span class="p">],</span>
+        <span class="s1">&#39;full_name&#39;</span><span class="p">:</span> <span class="s1">&#39;Human Signaling Network version 6&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;label&#39;</span><span class="p">:</span> <span class="s1">&#39;HumanSignalingNetwork&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;color&#39;</span><span class="p">:</span> <span class="s1">&#39;&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;data_import&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;Cui2007&#39;</span><span class="p">,</span> <span class="s1">&#39;BioCarta&#39;</span><span class="p">,</span> <span class="s1">&#39;CST&#39;</span><span class="p">,</span> <span class="s1">&#39;NCI-PID&#39;</span><span class="p">,</span> <span class="s1">&#39;iHOP&#39;</span><span class="p">],</span>
+        <span class="s1">&#39;urls&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;webpages&#39;</span><span class="p">:</span> <span class="p">[</span>
+                <span class="s1">&#39;http://www.cancer-systemsbiology.org/dataandsoftware.htm&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;http://www.bri.nrc.ca/wang/&#39;</span>
+            <span class="p">],</span>
+            <span class="s1">&#39;articles&#39;</span><span class="p">:</span> <span class="p">[]</span>
+        <span class="p">},</span>
+        <span class="s1">&#39;emails&#39;</span><span class="p">:</span> <span class="p">[(</span><span class="s1">&#39;Edwin.Wang@cnrc-nrc.gc.ca&#39;</span><span class="p">,</span> <span class="s1">&#39;Edwin Wang&#39;</span><span class="p">)],</span>
+        <span class="s1">&#39;taxons&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;human&#39;</span><span class="p">,</span> <span class="s1">&#39;mouse&#39;</span><span class="p">,</span> <span class="s1">&#39;rat&#39;</span><span class="p">],</span>
+        <span class="s1">&#39;contains&#39;</span><span class="p">:</span> <span class="p">[</span>
+            <span class="s1">&#39;Cui2007&#39;</span><span class="p">,</span> <span class="s1">&#39;CancerCellMap&#39;</span><span class="p">,</span> <span class="s1">&#39;Awan2007&#39;</span><span class="p">,</span> <span class="s1">&#39;NetPath&#39;</span><span class="p">,</span> <span class="s1">&#39;CA1&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;NCI-PID&#39;</span><span class="p">,</span> <span class="s1">&#39;BioCarta&#39;</span><span class="p">,</span> <span class="s1">&#39;CST&#39;</span><span class="p">,</span> <span class="s1">&#39;iHOP&#39;</span>
+        <span class="p">],</span>
+        <span class="s1">&#39;descriptions&#39;</span><span class="p">:</span> <span class="p">[</span>
+<span class="w">            </span><span class="sa">u</span><span class="sd">&#39;&#39;&#39;</span>
+<span class="sd">            Composed from multiple manually curated datasets, and contains own manual cuartion effort. Methods are unclear, and the dataset has not been published in reviewed paper. Based on the Cui et al 2007.</span>
+<span class="sd">            Wang Lab has manually curated human signaling data from literature since 2005. The data sources include BioCarta, CST Signaling pathways, NCI Pathway Interaction Database, iHOP, and many review papers. The contents are updated every year.</span>
+<span class="sd">            iHOP is not literature curated, but is a literature mining platform.</span>
+<span class="sd">            &#39;&#39;&#39;</span>
+        <span class="p">],</span>
+        <span class="s1">&#39;notes&#39;</span><span class="p">:</span> <span class="p">[</span>
+<span class="w">            </span><span class="sa">u</span><span class="sd">&#39;&#39;&#39;</span>
+<span class="sd">            This network aims to merge multiple manually curated networks. Unfortunately a precise description of the sources and methods is missing. Also, the dataset does not include the references. Moreover, the data file misses header and key, so users can only guess about the meaning of columns and values.</span>
+<span class="sd">            &#39;&#39;&#39;</span>
+        <span class="p">],</span>
+        <span class="s1">&#39;type&#39;</span><span class="p">:</span> <span class="s1">&#39;literature curated&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;data_integration&#39;</span><span class="p">:</span> <span class="s1">&#39;dynamic&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;subtype&#39;</span><span class="p">:</span> <span class="s1">&#39;activity flow&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;omnipath&#39;</span><span class="p">:</span> <span class="kc">False</span><span class="p">,</span>
+        <span class="s1">&#39;license&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;name&#39;</span><span class="p">:</span> <span class="s1">&#39;No license&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;url&#39;</span><span class="p">:</span> <span class="s1">&#39;http://www.gnu.org/licenses/license-list.html#NoLicense&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;commercial_use&#39;</span><span class="p">:</span> <span class="kc">False</span>
+        <span class="p">},</span>
+        <span class="s1">&#39;pypath&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;data&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;pypath.urls.urls[</span><span class="se">\&#39;</span><span class="s1">hsn</span><span class="se">\&#39;</span><span class="s1">]&#39;</span><span class="p">],</span>
+            <span class="s1">&#39;format&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;pypath.data_formats.interaction_misc[</span><span class="se">\&#39;</span><span class="s1">hsn</span><span class="se">\&#39;</span><span class="s1">]&#39;</span><span class="p">],</span>
+            <span class="s1">&#39;intr&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;pypath.dataio.get_hsn()&#39;</span><span class="p">]</span>
+        <span class="p">}</span>
+    <span class="p">},</span>
+    <span class="s1">&#39;Ataxia&#39;</span><span class="p">:</span> <span class="p">{</span>
+        <span class="s1">&#39;year&#39;</span><span class="p">:</span> <span class="mi">2010</span><span class="p">,</span>
+        <span class="s1">&#39;urls&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;webpages&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;http://franklin.imgen.bcm.tmc.edu/ppi/tables.html&#39;</span><span class="p">],</span>
+            <span class="s1">&#39;articles&#39;</span><span class="p">:</span>
+            <span class="p">[</span><span class="s1">&#39;http://hmg.oxfordjournals.org/content/20/3/510.long&#39;</span><span class="p">]</span>
+        <span class="p">},</span>
+        <span class="s1">&#39;taxons&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;human&#39;</span><span class="p">],</span>
+        <span class="s1">&#39;authors&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;Shaw Lab&#39;</span><span class="p">],</span>
+        <span class="s1">&#39;descriptions&#39;</span><span class="p">:</span> <span class="p">[</span>
+<span class="w">            </span><span class="sa">u</span><span class="sd">&#39;&#39;&#39;</span>
+<span class="sd">            In order to expand the interaction dataset, we added relevant direct protein–protein interactions from currently available human protein–protein interaction networks (Rual et al., 2005; Stelzl et al., 2005). We also searched public databases, including BIND (Bader et al., 2003), DIP (Xenarios et al., 2002), HPRD (Peri et al., 2003), MINT (Zanzoni et al., 2002), and MIPS (Pagel et al., 2005), to identify literature-based binary interactions involving the 54 ataxia-associated baits and the 561 interacting prey proteins. We identified 4796 binary protein–protein interactions for our Y2H baits and prey proteins (Table S4) and incorporated them in the Y2H protein–protein interaction map (Figures 4A–4C).</span>
+<span class="sd">            &#39;&#39;&#39;</span>
+        <span class="p">],</span>
+        <span class="s1">&#39;notes&#39;</span><span class="p">:</span> <span class="p">[</span>
+<span class="w">            </span><span class="sa">u</span><span class="sd">&#39;&#39;&#39;</span>
+<span class="sd">            The Ataxia network doesn&#39;t contain original manual curation effort. The integrated data are very old.</span>
+<span class="sd">            &#39;&#39;&#39;</span>
+        <span class="p">],</span>
+        <span class="s1">&#39;type&#39;</span><span class="p">:</span> <span class="s1">&#39;high-throughput&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;subtype&#39;</span><span class="p">:</span> <span class="s1">&#39;interaction&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;omnipath&#39;</span><span class="p">:</span> <span class="kc">False</span><span class="p">,</span>
+        <span class="s1">&#39;emails&#39;</span><span class="p">:</span> <span class="p">[(</span><span class="s1">&#39;Tong_Hao@dfci.harvard.edu&#39;</span><span class="p">,</span> <span class="s1">&#39;Tong Hao&#39;</span><span class="p">),</span>
+                   <span class="p">(</span><span class="s1">&#39;barabasi@gmail.com&#39;</span><span class="p">,</span> <span class="s1">&#39;Albert-Laszlo Barabasi&#39;</span><span class="p">)],</span>
+        <span class="s1">&#39;license&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;url&#39;</span><span class="p">:</span> <span class="s1">&#39;http://creativecommons.org/licenses/by-nc/2.5&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;name&#39;</span><span class="p">:</span> <span class="s1">&#39;CC-Attribution-2.5&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;commercial_use&#39;</span><span class="p">:</span> <span class="kc">True</span>
+        <span class="p">}</span>
+    <span class="p">},</span>
+    <span class="s1">&#39;Reactome&#39;</span><span class="p">:</span> <span class="p">{</span>
+        <span class="s1">&#39;year&#39;</span><span class="p">:</span> <span class="mi">2016</span><span class="p">,</span>
+        <span class="s1">&#39;releases&#39;</span><span class="p">:</span> <span class="p">[</span><span class="mi">2004</span><span class="p">,</span> <span class="mi">2008</span><span class="p">,</span> <span class="mi">2010</span><span class="p">,</span> <span class="mi">2012</span><span class="p">,</span> <span class="mi">2014</span><span class="p">,</span> <span class="mi">2015</span><span class="p">,</span> <span class="mi">2016</span><span class="p">],</span>
+        <span class="s1">&#39;urls&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;webpages&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;http://reactome.org/&#39;</span><span class="p">],</span>
+            <span class="s1">&#39;articles&#39;</span><span class="p">:</span> <span class="p">[</span>
+                <span class="s1">&#39;http://nar.oxfordjournals.org/content/33/suppl_1/D428.long&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;http://nar.oxfordjournals.org/content/37/suppl_1/D619.long&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;http://onlinelibrary.wiley.com/doi/10.1002/pmic.201100066/abstract&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;http://nar.oxfordjournals.org/content/39/suppl_1/D691.long&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;http://genomebiology.com/content/8/3/R39&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;http://nar.oxfordjournals.org/content/42/D1/D472.long&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;http://www.mdpi.com/2072-6694/4/4/1180/htm&#39;</span>
+            <span class="p">],</span>
+            <span class="s1">&#39;omictools&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;http://omictools.com/reactome-tool&#39;</span><span class="p">]</span>
+        <span class="p">},</span>
+        <span class="s1">&#39;pubmeds&#39;</span><span class="p">:</span>
+        <span class="p">[</span><span class="mi">15608231</span><span class="p">,</span> <span class="mi">18981052</span><span class="p">,</span> <span class="mi">21751369</span><span class="p">,</span> <span class="mi">21067998</span><span class="p">,</span> <span class="mi">24213504</span><span class="p">,</span> <span class="mi">24243840</span><span class="p">],</span>
+        <span class="s1">&#39;annot&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;localization&#39;</span><span class="p">,</span> <span class="s1">&#39;mechanism&#39;</span><span class="p">,</span> <span class="s1">&#39;pathway&#39;</span><span class="p">],</span>
+        <span class="s1">&#39;recommend&#39;</span><span class="p">:</span>
+        <span class="s1">&#39;the largest process description resource; peerless coverage; both signaling and metabolism&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;descriptions&#39;</span><span class="p">:</span> <span class="p">[</span>
+<span class="w">            </span><span class="sa">u</span><span class="sd">&#39;&#39;&#39;</span>
+<span class="sd">            Once the content of the module is approved by the author and curation staff, it is peer-reviewed on the development web-site, by one or more bench biologists selected by the curator in consultation with the author. The peer review is open and the reviewers are acknowledged in the database by name. Any issues raised in the review are resolved, and the new module is scheduled for release.</span>
+<span class="sd">            &#39;&#39;&#39;</span>
+        <span class="p">],</span>
+        <span class="s1">&#39;notes&#39;</span><span class="p">:</span> <span class="p">[</span>
+<span class="w">            </span><span class="sa">u</span><span class="sd">&#39;&#39;&#39;</span>
+<span class="sd">            No binary interactions can be exported programmatically from any format of the Reactome dataset. Reactome&#39;s curation method doesn&#39;t cover binary interactions, the inferred lists on the webpage are based on automatic expansion of complexes and reactions, and thus are unreliable. In lack of information, references cannot be assigned to interactions.</span>
+<span class="sd">            &#39;&#39;&#39;</span>
+        <span class="p">],</span>
+        <span class="s1">&#39;type&#39;</span><span class="p">:</span> <span class="s1">&#39;literature curated&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;subtype&#39;</span><span class="p">:</span> <span class="s1">&#39;process description&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;data_integration&#39;</span><span class="p">:</span> <span class="s1">&#39;dynamic&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;omnipath&#39;</span><span class="p">:</span> <span class="kc">False</span><span class="p">,</span>
+        <span class="s1">&#39;emails&#39;</span><span class="p">:</span> <span class="p">[(</span><span class="s1">&#39;help@reactome.org&#39;</span><span class="p">,</span> <span class="s1">&#39;Reactome Team&#39;</span><span class="p">),</span>
+                   <span class="p">(</span><span class="s1">&#39;hhe@ebi.ac.uk&#39;</span><span class="p">,</span> <span class="s1">&#39;Henning Hermjakob&#39;</span><span class="p">)],</span>
+        <span class="s1">&#39;license&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;name&#39;</span><span class="p">:</span> <span class="s1">&#39;CC-Attribution-4.0&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;url&#39;</span><span class="p">:</span> <span class="s1">&#39;http://creativecommons.org/licenses/by/4.0/&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;commercial_use&#39;</span><span class="p">:</span> <span class="kc">True</span>
+        <span class="p">},</span>
+        <span class="s1">&#39;pypath&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;data&#39;</span><span class="p">:</span> <span class="p">[</span>
+                <span class="s1">&#39;pypath.urls.urls[</span><span class="se">\&#39;</span><span class="s1">reactome</span><span class="se">\&#39;</span><span class="s1">][</span><span class="se">\&#39;</span><span class="s1">sbml</span><span class="se">\&#39;</span><span class="s1">]&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;pypath.urls.urls[</span><span class="se">\&#39;</span><span class="s1">reactome</span><span class="se">\&#39;</span><span class="s1">][</span><span class="se">\&#39;</span><span class="s1">biopax_l2</span><span class="se">\&#39;</span><span class="s1">]&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;pypath.urls.urls[</span><span class="se">\&#39;</span><span class="s1">reactome</span><span class="se">\&#39;</span><span class="s1">][</span><span class="se">\&#39;</span><span class="s1">biopax_l3</span><span class="se">\&#39;</span><span class="s1">]&#39;</span>
+            <span class="p">],</span>
+            <span class="s1">&#39;format&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;pypath.data_formats.reaction_misc[</span><span class="se">\&#39;</span><span class="s1">reactome</span><span class="se">\&#39;</span><span class="s1">]&#39;</span><span class="p">],</span>
+            <span class="s1">&#39;intr&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;pypath.dataio.reactome_interactions()&#39;</span><span class="p">],</span>
+            <span class="s1">&#39;input&#39;</span><span class="p">:</span> <span class="p">[</span>
+                <span class="s1">&#39;pypath.dataio.reactome_sbml()&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;pypath.dataio.reactome_biopax()&#39;</span>
+            <span class="p">]</span>
+        <span class="p">},</span>
+        <span class="s1">&#39;pathguide&#39;</span><span class="p">:</span> <span class="mi">103</span>
+    <span class="p">},</span>
+    <span class="s1">&#39;Li2012&#39;</span><span class="p">:</span> <span class="p">{</span>
+        <span class="s1">&#39;year&#39;</span><span class="p">:</span> <span class="mi">2012</span><span class="p">,</span>
+        <span class="s1">&#39;urls&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;articles&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;http://genome.cshlp.org/content/22/7/1222&#39;</span><span class="p">]</span>
+        <span class="p">},</span>
+        <span class="s1">&#39;pubmeds&#39;</span><span class="p">:</span> <span class="p">[</span><span class="mi">22194470</span><span class="p">],</span>
+        <span class="s1">&#39;label&#39;</span><span class="p">:</span> <span class="s1">&#39;Li 2012&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;authors&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;Wang Lab&#39;</span><span class="p">],</span>
+        <span class="s1">&#39;emails&#39;</span><span class="p">:</span> <span class="p">[(</span><span class="s1">&#39;edwin.wang@cnrc-nrc.gc.ca&#39;</span><span class="p">,</span> <span class="s1">&#39;Edwin Wang&#39;</span><span class="p">)],</span>
+        <span class="s1">&#39;taxons&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;human&#39;</span><span class="p">],</span>
+        <span class="s1">&#39;descriptions&#39;</span><span class="p">:</span> <span class="p">[</span>
+<span class="w">            </span><span class="sa">u</span><span class="sd">&#39;&#39;&#39;</span>
+<span class="sd">            Human phosphotyrosine signaling network.</span>
+<span class="sd">            We manually collected the experimentally determined human TK–substrate interactions and substrate–SH2/PTB domain interactions from the literature (see Supplemental Materials), as well as the Phospho.ELM and PhosphoSitePlus databases. [71 references, 585 circuits]</span>
+<span class="sd">            &#39;&#39;&#39;</span>
+        <span class="p">],</span>
+        <span class="s1">&#39;type&#39;</span><span class="p">:</span> <span class="s1">&#39;high-throughput&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;data_integration&#39;</span><span class="p">:</span> <span class="s1">&#39;static&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;subtype&#39;</span><span class="p">:</span> <span class="s1">&#39;yeast 2 hybrid&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;omnipath&#39;</span><span class="p">:</span> <span class="kc">False</span><span class="p">,</span>
+        <span class="s1">&#39;pypath&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;input&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;pypath.dataio.get_li2012()&#39;</span><span class="p">],</span>
+            <span class="s1">&#39;data&#39;</span><span class="p">:</span> <span class="p">[</span>
+                <span class="s1">&#39;pypath.urls.urls[</span><span class="se">\&#39;</span><span class="s1">li2012</span><span class="se">\&#39;</span><span class="s1">][</span><span class="se">\&#39;</span><span class="s1">file</span><span class="se">\&#39;</span><span class="s1">]&#39;</span>
+                <span class="s1">&#39;pypath.data/li2012.csv&#39;</span>
+            <span class="p">],</span>
+            <span class="s1">&#39;intr&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;pypath.dataio.li2012_interactions()&#39;</span><span class="p">],</span>
+            <span class="s1">&#39;dmi&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;pypath.dataio.li2012_dmi()&#39;</span><span class="p">],</span>
+            <span class="s1">&#39;ptm&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;pypath.dataio.li2012_phospho()&#39;</span><span class="p">],</span>
+            <span class="s1">&#39;format&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;pypath.data_formats.ptm_misc[</span><span class="se">\&#39;</span><span class="s1">li2012</span><span class="se">\&#39;</span><span class="s1">]&#39;</span><span class="p">]</span>
+        <span class="p">},</span>
+        <span class="s1">&#39;license&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;name&#39;</span><span class="p">:</span> <span class="s1">&#39;No license.&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;url&#39;</span><span class="p">:</span> <span class="s1">&#39;http://www.gnu.org/licenses/license-list.html#NoLicense&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;commercial_use&#39;</span><span class="p">:</span> <span class="kc">False</span>
+        <span class="p">}</span>
+    <span class="p">},</span>
+    <span class="s1">&#39;Zaman2013&#39;</span><span class="p">:</span> <span class="p">{</span>
+        <span class="s1">&#39;year&#39;</span><span class="p">:</span> <span class="mi">2013</span><span class="p">,</span>
+        <span class="s1">&#39;urls&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;articles&#39;</span><span class="p">:</span> <span class="p">[</span>
+                <span class="s1">&#39;http://www.sciencedirect.com/science/article/pii/S2211124713004695&#39;</span>
+            <span class="p">],</span>
+            <span class="s1">&#39;webpages&#39;</span><span class="p">:</span> <span class="p">[]</span>
+        <span class="p">},</span>
+        <span class="s1">&#39;pubmeds&#39;</span><span class="p">:</span> <span class="p">[</span><span class="mi">24075989</span><span class="p">],</span>
+        <span class="s1">&#39;label&#39;</span><span class="p">:</span> <span class="s1">&#39;Zaman 2013&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;authors&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;Wang Lab&#39;</span><span class="p">],</span>
+        <span class="s1">&#39;emails&#39;</span><span class="p">:</span> <span class="p">[(</span><span class="s1">&#39;edwin.wang@cnrc-nrc.gc.ca&#39;</span><span class="p">,</span> <span class="s1">&#39;Edwin Wang&#39;</span><span class="p">)],</span>
+        <span class="s1">&#39;contains&#39;</span><span class="p">:</span> <span class="p">[</span>
+            <span class="s1">&#39;HumanSignalingNetwork&#39;</span><span class="p">,</span> <span class="s1">&#39;Cui2007&#39;</span><span class="p">,</span> <span class="s1">&#39;CA1&#39;</span><span class="p">,</span> <span class="s1">&#39;BioCarta&#39;</span><span class="p">,</span> <span class="s1">&#39;Awan2007&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;Li2012&#39;</span><span class="p">,</span> <span class="s1">&#39;NCI-PID&#39;</span>
+        <span class="p">],</span>
+        <span class="s1">&#39;descriptions&#39;</span><span class="p">:</span> <span class="p">[</span>
+<span class="w">            </span><span class="sa">u</span><span class="sd">&#39;&#39;&#39;</span>
+<span class="sd">            The human signaling network (Version 4, containing more than 6,000 genes and more than 50,000 relations) includes our previous data obtained from manually curated signaling networks (Awan et al., 2007; Cui et al., 2007; Li et al., 2012) and by PID (http://pid.nci.nih.gov/) and our recent manual curations using the iHOP database (http://www.ihop-net.org/UniPub/iHOP/).</span>
+<span class="sd">            &#39;&#39;&#39;</span>
+        <span class="p">],</span>
+        <span class="s1">&#39;type&#39;</span><span class="p">:</span> <span class="s1">&#39;literature curated&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;subtype&#39;</span><span class="p">:</span> <span class="s1">&#39;activity flow&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;omnipath&#39;</span><span class="p">:</span> <span class="kc">False</span><span class="p">,</span>
+        <span class="s1">&#39;license&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;name&#39;</span><span class="p">:</span> <span class="s1">&#39;No license.&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;url&#39;</span><span class="p">:</span> <span class="s1">&#39;http://www.gnu.org/licenses/license-list.html#NoLicense&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;commercial_use&#39;</span><span class="p">:</span> <span class="kc">False</span>
+        <span class="p">}</span>
+    <span class="p">},</span>
+    <span class="s1">&#39;AlzPathway&#39;</span><span class="p">:</span> <span class="p">{</span>
+        <span class="s1">&#39;year&#39;</span><span class="p">:</span> <span class="mi">2015</span><span class="p">,</span>
+        <span class="s1">&#39;releases&#39;</span><span class="p">:</span> <span class="p">[</span><span class="mi">2012</span><span class="p">,</span> <span class="mi">2015</span><span class="p">],</span>
+        <span class="s1">&#39;size&#39;</span><span class="p">:</span> <span class="mi">0</span><span class="p">,</span>
+        <span class="s1">&#39;authors&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;Tokyo Bioinf&#39;</span><span class="p">],</span>
+        <span class="s1">&#39;label&#39;</span><span class="p">:</span> <span class="s1">&#39;AlzPathway&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;color&#39;</span><span class="p">:</span> <span class="s1">&#39;&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;urls&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;articles&#39;</span><span class="p">:</span> <span class="p">[</span>
+                <span class="s1">&#39;http://www.biomedcentral.com/1752-0509/6/52&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;http://onlinelibrary.wiley.com/doi/10.1038/clpt.2013.37/epdf&#39;</span><span class="p">,</span>
+                <span class="sa">r</span><span class="s1">&#39;http://link.springer.com/protocol/10.1007</span><span class="si">%2F</span><span class="s1">978-1-4939-2627-5_25&#39;</span>
+            <span class="p">],</span>
+            <span class="s1">&#39;webpages&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;http://alzpathway.org/AlzPathway.html&#39;</span><span class="p">]</span>
+        <span class="p">},</span>
+        <span class="s1">&#39;pubmeds&#39;</span><span class="p">:</span> <span class="p">[</span><span class="mi">23511713</span><span class="p">,</span> <span class="mi">22647208</span><span class="p">],</span>
+        <span class="s1">&#39;emails&#39;</span><span class="p">:</span> <span class="p">[(</span><span class="s1">&#39;ogishima@sysmedbio.org&#39;</span><span class="p">,</span> <span class="s1">&#39;Soichi Ogishima&#39;</span><span class="p">),</span>
+                   <span class="p">(</span><span class="s1">&#39;info@alzpathway.org&#39;</span><span class="p">,</span> <span class="s1">&#39;Soichi Ogishima&#39;</span><span class="p">)],</span>
+        <span class="s1">&#39;license&#39;</span><span class="p">:</span>
+<span class="w">        </span><span class="sa">u</span><span class="sd">&#39;&#39;&#39;Licensed under a Creative Commons Attribution 3.0 Unported License. Cite Mizuno et al&#39;&#39;&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;descriptions&#39;</span><span class="p">:</span> <span class="p">[</span>
+<span class="w">            </span><span class="sa">u</span><span class="sd">&#39;&#39;&#39;</span>
+<span class="sd">            We collected 123 review articles related to AD accessible from PubMed. We then manually curated these review articles, and have built an AD pathway map by using CellDesigner. Molecules are distinguished by the following types: proteins, complexes, simple molecules, genes, RNAs, ions, degraded products, and phenotypes. Gene symbols are pursuant to the HGNC symbols. Reactions are also distinguished by the following categories: state transition, transcription, translation, heterodimer association, dissociation, transport, unknown transition, and omitted transition. All the reactions have evidences to the references in PubMed ID using the MIRIAM scheme. All the references used for constructing the AlzPathway are listed in the ‘References for AlzPathway’. Cellular types are distinguished by the followings: neuron, astrocyte, and microglial cells. Cellular compartments are also distinguished by the followings: brain blood barrier, presynaptic, postsynaptic, and their inner cellular localizations.</span>
+<span class="sd">            &#39;&#39;&#39;</span>
+        <span class="p">],</span>
+        <span class="s1">&#39;notes&#39;</span><span class="p">:</span> <span class="p">[</span>
+<span class="w">            </span><span class="sa">u</span><span class="sd">&#39;&#39;&#39;</span>
+<span class="sd">            References can be fetched only from XML formats, not from the SIF file. Among approx. 150 protein-protein interactions, also contains interactions of many small molecules, denoted by pubchem IDs.</span>
+<span class="sd">            &#39;&#39;&#39;</span>
+        <span class="p">],</span>
+        <span class="s1">&#39;type&#39;</span><span class="p">:</span> <span class="s1">&#39;literature curated&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;data_integration&#39;</span><span class="p">:</span> <span class="s1">&#39;static&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;subtype&#39;</span><span class="p">:</span> <span class="s1">&#39;activity flow&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;omnipath&#39;</span><span class="p">:</span> <span class="kc">False</span><span class="p">,</span>
+        <span class="s1">&#39;pypath&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;data&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;pypath.data/alzpw-ppi.csv&#39;</span><span class="p">],</span>
+            <span class="s1">&#39;format&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;pypath.data_formats.interaction[</span><span class="se">\&#39;</span><span class="s1">alz</span><span class="se">\&#39;</span><span class="s1">]&#39;</span><span class="p">]</span>
+        <span class="p">},</span>
+        <span class="s1">&#39;license&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;name&#39;</span><span class="p">:</span> <span class="s1">&#39;CC-Attribution-3.0&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;url&#39;</span><span class="p">:</span> <span class="s1">&#39;http://creativecommons.org/licenses/by/3.0/&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;commercial_use&#39;</span><span class="p">:</span> <span class="kc">True</span>
+        <span class="p">}</span>
+    <span class="p">},</span>
+    <span class="s1">&#39;MPPI&#39;</span><span class="p">:</span> <span class="p">{</span>
+        <span class="s1">&#39;year&#39;</span><span class="p">:</span> <span class="mi">2005</span><span class="p">,</span>
+        <span class="s1">&#39;releases&#39;</span><span class="p">:</span> <span class="p">[</span><span class="mi">2000</span><span class="p">,</span> <span class="mi">2005</span><span class="p">],</span>
+        <span class="s1">&#39;size&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;nodes&#39;</span><span class="p">:</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="s1">&#39;edges&#39;</span><span class="p">:</span> <span class="kc">None</span>
+        <span class="p">},</span>
+        <span class="s1">&#39;authors&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;MIPS Munich&#39;</span><span class="p">],</span>
+        <span class="s1">&#39;license&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;name&#39;</span><span class="p">:</span>
+            <span class="s1">&#39;No license. &quot;You are free to use the database as you please including full download of&#39;</span>
+            <span class="s1">&#39; the dataset for your own analyses as long as you cite the source properly (Pagel et al. 2005).&quot;&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;url&#39;</span><span class="p">:</span> <span class="s1">&#39;http://www.gnu.org/licenses/license-list.html#NoLicense&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;commercial_use&#39;</span><span class="p">:</span> <span class="kc">False</span> <span class="c1"># To be clarified</span>
+        <span class="p">},</span>
+        <span class="s1">&#39;label&#39;</span><span class="p">:</span> <span class="s1">&#39;MPPI&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;full_name&#39;</span><span class="p">:</span> <span class="s1">&#39;The MIPS Mammalian Protein-Protein Interaction Database&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;urls&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;articles&#39;</span><span class="p">:</span>
+            <span class="p">[</span><span class="s1">&#39;http://bioinformatics.oxfordjournals.org/content/21/6/832&#39;</span><span class="p">],</span>
+            <span class="s1">&#39;webpages&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;http://mips.helmholtz-muenchen.de/proj/ppi/&#39;</span><span class="p">],</span>
+            <span class="s1">&#39;omictools&#39;</span><span class="p">:</span> <span class="p">[</span>
+                <span class="s1">&#39;http://omictools.com/mips-mammalian-protein-protein-interaction-database-tool&#39;</span>
+            <span class="p">]</span>
+        <span class="p">},</span>
+        <span class="s1">&#39;emails&#39;</span><span class="p">:</span> <span class="p">[(</span><span class="s1">&#39;p.pagel@wzw.tum.de&#39;</span><span class="p">,</span> <span class="s1">&#39;Philipp Pagel&#39;</span><span class="p">),</span>
+                   <span class="p">(</span><span class="s1">&#39;d.frishman@helmholtz-muenchen.de&#39;</span><span class="p">,</span> <span class="s1">&#39;Dmitrij Frishman&#39;</span><span class="p">)],</span>
+        <span class="s1">&#39;pubmeds&#39;</span><span class="p">:</span> <span class="p">[</span><span class="mi">15531608</span><span class="p">],</span>
+        <span class="s1">&#39;taxons&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;human&#39;</span><span class="p">,</span> <span class="s1">&#39;mammalia&#39;</span><span class="p">],</span>
+        <span class="s1">&#39;data_integration&#39;</span><span class="p">:</span> <span class="s1">&#39;static&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;recommend&#39;</span><span class="p">:</span>
+        <span class="s1">&#39;small, literature curated interaction dataset; complements well activity flow resources&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;descriptions&#39;</span><span class="p">:</span> <span class="p">[</span>
+<span class="w">            </span><span class="sa">u</span><span class="sd">&#39;&#39;&#39;</span>
+<span class="sd">            The first and foremost principle of our MPPI database is to favor quality over completeness. Therefore, we decided to include only published experimental evidence derived from individual experiments as opposed to large-scale surveys. High-throughput data may be integrated later, but will be marked to distinguish it from evidence derived from individual experiments.</span>
+<span class="sd">            &#39;&#39;&#39;</span>
+        <span class="p">],</span>
+        <span class="s1">&#39;notes&#39;</span><span class="p">:</span> <span class="p">[</span>
+<span class="w">            </span><span class="sa">u</span><span class="sd">&#39;&#39;&#39;</span>
+<span class="sd">            This database contains hundreds of interactions curated manually from original papers. The format is perfect, with UniProt IDs, and PubMed references.</span>
+<span class="sd">            &#39;&#39;&#39;</span>
+        <span class="p">],</span>
+        <span class="s1">&#39;type&#39;</span><span class="p">:</span> <span class="s1">&#39;literature curated&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;subtype&#39;</span><span class="p">:</span> <span class="s1">&#39;interaction&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;omnipath&#39;</span><span class="p">:</span> <span class="kc">True</span><span class="p">,</span>
+        <span class="s1">&#39;pypath&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;data&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;pypath.data/mppi_human_rep.csv&#39;</span><span class="p">],</span>
+            <span class="s1">&#39;format&#39;</span><span class="p">:</span> <span class="p">[</span>
+                <span class="s1">&#39;pypath.data_formats.interaction[</span><span class="se">\&#39;</span><span class="s1">mppi</span><span class="se">\&#39;</span><span class="s1">]&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;pypath.data_formats.omnipath[</span><span class="se">\&#39;</span><span class="s1">mppi</span><span class="se">\&#39;</span><span class="s1">]&#39;</span>
+            <span class="p">]</span>
+        <span class="p">},</span>
+        <span class="s1">&#39;pathguide&#39;</span><span class="p">:</span> <span class="mi">319</span>
+    <span class="p">},</span>
+    <span class="s1">&#39;Negatome&#39;</span><span class="p">:</span> <span class="p">{</span>
+        <span class="s1">&#39;year&#39;</span><span class="p">:</span> <span class="mi">2013</span><span class="p">,</span>
+        <span class="s1">&#39;relases&#39;</span><span class="p">:</span> <span class="p">[</span><span class="mi">2009</span><span class="p">],</span>
+        <span class="s1">&#39;urls&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;articles&#39;</span><span class="p">:</span> <span class="p">[</span>
+                <span class="s1">&#39;http://nar.oxfordjournals.org/content/38/suppl_1/D540.long&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;http://nar.oxfordjournals.org/content/42/D1/D396.long&#39;</span>
+            <span class="p">],</span>
+            <span class="s1">&#39;webpages&#39;</span><span class="p">:</span>
+            <span class="p">[</span><span class="s1">&#39;http://mips.helmholtz-muenchen.de/proj/ppi/negatome/&#39;</span><span class="p">],</span>
+            <span class="s1">&#39;omictools&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;http://omictools.com/negatome-tool&#39;</span><span class="p">]</span>
+        <span class="p">},</span>
+        <span class="s1">&#39;pubmeds&#39;</span><span class="p">:</span> <span class="p">[</span><span class="mi">24214996</span><span class="p">,</span> <span class="mi">19920129</span><span class="p">],</span>
+        <span class="s1">&#39;emails&#39;</span><span class="p">:</span> <span class="p">[(</span><span class="s1">&#39;d.frishman@helmholtz-muenchen.de&#39;</span><span class="p">,</span> <span class="s1">&#39;Dmitrij Frishman&#39;</span><span class="p">)],</span>
+        <span class="s1">&#39;descriptions&#39;</span><span class="p">:</span> <span class="p">[</span>
+<span class="w">            </span><span class="sa">u</span><span class="sd">&#39;&#39;&#39;</span>
+<span class="sd">            Annotation of the manual dataset was performed analogous to the annotation of protein–protein interactions and protein complexes in previous projects published by our group. Information about NIPs was extracted from scientific literature using only data from individual experiments but not from high-throughput experiments. Only mammalian proteins were considered. Data from high-throughput experiments were omitted in order to maintain the highest possible standard of reliability.</span>
+<span class="sd">            &#39;&#39;&#39;</span>
+        <span class="p">],</span>
+        <span class="s1">&#39;type&#39;</span><span class="p">:</span> <span class="s1">&#39;literature curated&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;data_integration&#39;</span><span class="p">:</span> <span class="s1">&#39;static&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;subtype&#39;</span><span class="p">:</span> <span class="s1">&#39;negative&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;omnipath&#39;</span><span class="p">:</span> <span class="kc">True</span><span class="p">,</span>
+        <span class="s1">&#39;license&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;name&#39;</span><span class="p">:</span> <span class="s1">&#39;No license&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;url&#39;</span><span class="p">:</span> <span class="s1">&#39;http://www.gnu.org/licenses/license-list.html#NoLicense&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;commercial_use&#39;</span><span class="p">:</span> <span class="kc">False</span>
+        <span class="p">},</span>
+        <span class="s1">&#39;pypath&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;data&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;pypath.data/negatome_manual.csv&#39;</span><span class="p">],</span>
+            <span class="s1">&#39;format&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;pypath.data_formats.negative[</span><span class="se">\&#39;</span><span class="s1">negatome</span><span class="se">\&#39;</span><span class="s1">]&#39;</span><span class="p">],</span>
+            <span class="s1">&#39;misc&#39;</span><span class="p">:</span> <span class="p">[</span>
+                <span class="s1">&#39;pypath.pypath.PyPath().negative_report()&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;pypath.pypath.PyPath().apply_negative()&#39;</span>
+            <span class="p">]</span>
+        <span class="p">},</span>
+        <span class="s1">&#39;pathguide&#39;</span><span class="p">:</span> <span class="mi">444</span>
+    <span class="p">},</span>
+    <span class="s1">&#39;Macrophage&#39;</span><span class="p">:</span> <span class="p">{</span>
+        <span class="s1">&#39;year&#39;</span><span class="p">:</span> <span class="mi">2010</span><span class="p">,</span>
+        <span class="s1">&#39;urls&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;articles&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;http://www.biomedcentral.com/1752-0509/4/63&#39;</span><span class="p">],</span>
+            <span class="s1">&#39;webpages&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;http://www.macrophages.com/macrophage-pathways&#39;</span><span class="p">],</span>
+            <span class="s1">&#39;omictools&#39;</span><span class="p">:</span>
+            <span class="p">[</span><span class="s1">&#39;http://omictools.com/macrophage-pathway-knowledgebase-tool&#39;</span><span class="p">]</span>
+        <span class="p">},</span>
+        <span class="s1">&#39;emails&#39;</span><span class="p">:</span> <span class="p">[(</span><span class="s1">&#39;tom.freeman@roslin.ed.ac.uk&#39;</span><span class="p">,</span> <span class="s1">&#39;Tom Freeman&#39;</span><span class="p">)],</span>
+        <span class="s1">&#39;pubmeds&#39;</span><span class="p">:</span> <span class="p">[</span><span class="mi">20470404</span><span class="p">],</span>
+        <span class="s1">&#39;annot&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;localization&#39;</span><span class="p">,</span> <span class="s1">&#39;mechanism&#39;</span><span class="p">],</span>
+        <span class="s1">&#39;recommend&#39;</span><span class="p">:</span>
+        <span class="s1">&#39;medium size resource with effect signs; high ratio of specific interactions; interactions confirmed in macrophages&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;descriptions&#39;</span><span class="p">:</span> <span class="p">[</span>
+<span class="w">            </span><span class="sa">u</span><span class="sd">&#39;&#39;&#39;</span>
+<span class="sd">            Ongoing analysis of macrophage-related datasets and an interest in consolidating our knowledge of a number of signalling pathways directed our choice of pathways to be mapped (see Figure 1). Public and propriety databases were initially used as resources for data mining, but ultimately all molecular interaction data was sourced from published literature. Manual curation of the literature was performed to firstly evaluate the quality of the evidence supporting an interaction and secondly, to extract the necessary and additional pieces of information required to &#39;understand&#39; the pathway and construct an interaction diagram. We have drawn pathways based on our desire to model pathways active in a human macrophage and therefore all components have been depicted using standard human gene nomenclature (HGNC). However, our understanding of the pathway components and the interactions between them, have been drawn largely from a consensus view of literature knowledge. As such the pathways presented here are based on data derived from a range of different cellular systems and mammalian species (human and mouse).</span>
+<span class="sd">            &#39;&#39;&#39;</span>
+        <span class="p">],</span>
+        <span class="s1">&#39;type&#39;</span><span class="p">:</span> <span class="s1">&#39;literature curated&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;subtype&#39;</span><span class="p">:</span> <span class="s1">&#39;activity flow&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;omnipath&#39;</span><span class="p">:</span> <span class="kc">True</span><span class="p">,</span>
+        <span class="s1">&#39;license&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;name&#39;</span><span class="p">:</span> <span class="s1">&#39;CC-Attribution 4.0&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;url&#39;</span><span class="p">:</span> <span class="s1">&#39;https://creativecommons.org/licenses/by/4.0/legalcode&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;commercial_use&#39;</span><span class="p">:</span> <span class="kc">True</span>
+        <span class="p">},</span>
+        <span class="s1">&#39;data_integration&#39;</span><span class="p">:</span> <span class="s1">&#39;static&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;pypath&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;data&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;pypath.data/macrophage_strict.csv&#39;</span><span class="p">],</span>
+            <span class="s1">&#39;format&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;pypath.data_formats.pathway[</span><span class="se">\&#39;</span><span class="s1">macrophage</span><span class="se">\&#39;</span><span class="s1">]&#39;</span><span class="p">]</span>
+        <span class="p">}</span>
+    <span class="p">},</span>
+    <span class="s1">&#39;NetPath&#39;</span><span class="p">:</span> <span class="p">{</span>
+        <span class="s1">&#39;year&#39;</span><span class="p">:</span> <span class="mi">2015</span><span class="p">,</span>
+        <span class="s1">&#39;releases&#39;</span><span class="p">:</span> <span class="p">[</span><span class="mi">2010</span><span class="p">,</span> <span class="mi">2011</span><span class="p">,</span> <span class="mi">2012</span><span class="p">,</span> <span class="mi">2013</span><span class="p">,</span> <span class="mi">2014</span><span class="p">,</span> <span class="mi">2015</span><span class="p">],</span>
+        <span class="s1">&#39;size&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;nodes&#39;</span><span class="p">:</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="s1">&#39;edges&#39;</span><span class="p">:</span> <span class="kc">None</span>
+        <span class="p">},</span>
+        <span class="s1">&#39;authors&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;Pandey Lab&#39;</span><span class="p">,</span> <span class="s1">&#39;IOB Bangalore&#39;</span><span class="p">],</span>
+        <span class="s1">&#39;emails&#39;</span><span class="p">:</span> <span class="p">[(</span><span class="s1">&#39;pandey@jhmi.edu&#39;</span><span class="p">,</span> <span class="s1">&#39;Akhilesh Pandey&#39;</span><span class="p">)],</span>
+        <span class="s1">&#39;license&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;name&#39;</span><span class="p">:</span> <span class="s1">&#39;CC-Attribution 2.5&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;url&#39;</span><span class="p">:</span> <span class="s1">&#39;http://creativecommons.org/licenses/by/2.5/&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;commercial_use&#39;</span><span class="p">:</span> <span class="kc">True</span>
+            <span class="p">},</span>
+        <span class="s1">&#39;label&#39;</span><span class="p">:</span> <span class="s1">&#39;NetPath&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;color&#39;</span><span class="p">:</span> <span class="s1">&#39;&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;data_import&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;CancerCellMap&#39;</span><span class="p">],</span>
+        <span class="s1">&#39;includes&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;CancerCellMap&#39;</span><span class="p">],</span>
+        <span class="s1">&#39;annot&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;experiment&#39;</span><span class="p">,</span> <span class="s1">&#39;mechanism&#39;</span><span class="p">,</span> <span class="s1">&#39;pathway&#39;</span><span class="p">],</span>
+        <span class="s1">&#39;urls&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;articles&#39;</span><span class="p">:</span> <span class="p">[</span>
+                <span class="s1">&#39;http://genomebiology.com/content/11/1/R3&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;http://database.oxfordjournals.org/content/2011/bar032.long&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;http://database.oxfordjournals.org/content/2011/bar021.long&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;http://www.omicsonline.com/0974-276X/JPB-04-184.php&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;http://www.biomedcentral.com/1756-0500/4/408&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3830942/&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;http://link.springer.com/article/10.1007/s12079-012-0168-0&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;http://www.hindawi.com/journals/jst/2012/376470/&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;http://link.springer.com/article/10.1007/s12079-012-0186-y&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;http://link.springer.com/article/10.1007/s12079-012-0181-3&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;http://link.springer.com/article/10.1007/s12079-013-0197-3&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;http://www.tandfonline.com/doi/full/10.3109/15419061.2013.791683&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;http://link.springer.com/article/10.1007/s12079-013-0200-z&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;http://database.oxfordjournals.org/content/2014/bau007.long&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;http://link.springer.com/article/10.1007/s12079-014-0224-z&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;http://www.hindawi.com/journals/jst/2014/962962/&#39;</span>
+            <span class="p">],</span>
+            <span class="s1">&#39;webpages&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;http://netpath.org/&#39;</span><span class="p">]</span>
+        <span class="p">},</span>
+        <span class="s1">&#39;pubmeds&#39;</span><span class="p">:</span> <span class="p">[</span>
+            <span class="mi">20067622</span><span class="p">,</span> <span class="mi">21959865</span><span class="p">,</span> <span class="mi">21742767</span><span class="p">,</span> <span class="mi">21996254</span><span class="p">,</span> <span class="mi">24255551</span><span class="p">,</span> <span class="mi">22684822</span><span class="p">,</span>
+            <span class="mi">22649723</span><span class="p">,</span> <span class="mi">23255051</span><span class="p">,</span> <span class="mi">23161412</span><span class="p">,</span> <span class="mi">23504413</span><span class="p">,</span> <span class="mi">23631681</span><span class="p">,</span> <span class="mi">23606317</span><span class="p">,</span>
+            <span class="mi">24573880</span><span class="p">,</span> <span class="mi">24584707</span><span class="p">,</span> <span class="mi">24829797</span>
+        <span class="p">],</span>
+        <span class="s1">&#39;recommend&#39;</span><span class="p">:</span>
+        <span class="s1">&#39;the smallest process description resource, but represents a high quality literature curation effort; provides pathway annotations&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;descriptions&#39;</span><span class="p">:</span> <span class="p">[</span>
+<span class="w">            </span><span class="sa">u</span><span class="sd">&#39;&#39;&#39;</span>
+<span class="sd">            The initial annotation process of any signaling pathway involves gathering and reading of review articles to achieve a brief overview of the pathway. This process is followed by listing all the molecules that arereported to be involved in the pathway under annotation. Information regarding potential pathway authorities are also gathered at this initial stage. Pathway experts are involved in initial screening of the molecules listed to check for any obvious omissions. In the second phase, annotators manually perform extensive literature searches using search keys, which include all the alter native names of the molecules involved, the name of the pathway, the names of reactions, and so on. In addition, the iHOP resource is also used to perform advanced PubMed-based literature searches to collect the reactions that were reported to be implicated in a given pathway. The collected reactions are manually entered using the PathBuilder annotation interface, which is subjected to an internal review process involving PhD level scientists with expertise in the areas of molecular biology, immunology and biochemistry. However, there are instances where a molecule has been implicated in a pathway in a published report but the associated experimental evidence is either weak or differs from experiments carried out by other groups. For this purpose, we recruit several investigators as pathway authorities based on their expertise in individual signaling pathways. The review by pathway authorities occasionally leads to correction of errors or, more commonly, to inclusion of additional information. Finally, the pathway authorities help in assessing whether the work of all major laboratories has been incorporated for the given signaling pathway.</span>
+<span class="sd">            &#39;&#39;&#39;</span>
+        <span class="p">],</span>
+        <span class="s1">&#39;notes&#39;</span><span class="p">:</span> <span class="p">[</span>
+<span class="w">            </span><span class="sa">u</span><span class="sd">&#39;&#39;&#39;</span>
+<span class="sd">            Formats are unclear. The tab delimited format contains the pathway memberships of genes, PubMed references, but not the interaction partners! The Excel file is very weird, in fact it is not an excel table, and contains only a few rows from the tab file. The PSI-MI XML is much better. By writing a simple parser, a lot of details can be extracted.</span>
+<span class="sd">            &#39;&#39;&#39;</span>
+        <span class="p">],</span>
+        <span class="s1">&#39;type&#39;</span><span class="p">:</span> <span class="s1">&#39;literature curated&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;subtype&#39;</span><span class="p">:</span> <span class="s1">&#39;process description&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;data_integration&#39;</span><span class="p">:</span> <span class="s1">&#39;dynamic&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;omnipath&#39;</span><span class="p">:</span> <span class="kc">False</span><span class="p">,</span>
+        <span class="s1">&#39;license&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;name&#39;</span><span class="p">:</span> <span class="s1">&#39;CC-Attribution-2.5&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;url&#39;</span><span class="p">:</span> <span class="s1">&#39;http://creativecommons.org/licenses/by/2.5/&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;commercial_use&#39;</span><span class="p">:</span> <span class="kc">True</span>
+        <span class="p">},</span>
+        <span class="s1">&#39;pypath&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;input&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;pypath.dataio.netpath_names()&#39;</span><span class="p">],</span>
+            <span class="s1">&#39;intr&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;pypath.dataio.netpath()&#39;</span><span class="p">],</span>
+            <span class="s1">&#39;data&#39;</span><span class="p">:</span> <span class="p">[</span>
+                <span class="s1">&#39;pypath.urls.urls[</span><span class="se">\&#39;</span><span class="s1">netpath_psimi</span><span class="se">\&#39;</span><span class="s1">]&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;pypath.urls.urls[</span><span class="se">\&#39;</span><span class="s1">netpath_names</span><span class="se">\&#39;</span><span class="s1">]&#39;</span>
+            <span class="p">],</span>
+            <span class="s1">&#39;format&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;pypath.data_formats.interaction[</span><span class="se">\&#39;</span><span class="s1">netpath</span><span class="se">\&#39;</span><span class="s1">]&#39;</span><span class="p">]</span>
+        <span class="p">},</span>
+        <span class="s1">&#39;pathguide&#39;</span><span class="p">:</span> <span class="mi">315</span>
+    <span class="p">},</span>
+    <span class="s1">&#39;InnateDB&#39;</span><span class="p">:</span> <span class="p">{</span>
+        <span class="s1">&#39;year&#39;</span><span class="p">:</span> <span class="mi">2015</span><span class="p">,</span>
+        <span class="s1">&#39;urls&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;articles&#39;</span><span class="p">:</span> <span class="p">[</span>
+                <span class="s1">&#39;http://msb.embopress.org/content/4/1/218.long&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;http://www.biomedcentral.com/1752-0509/4/117&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;http://nar.oxfordjournals.org/content/41/D1/D1228.long&#39;</span>
+            <span class="p">],</span>
+            <span class="s1">&#39;webpages&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;http://www.innatedb.com/&#39;</span><span class="p">],</span>
+            <span class="s1">&#39;omictools&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;http://omictools.com/innatedb-tool&#39;</span><span class="p">]</span>
+        <span class="p">},</span>
+        <span class="s1">&#39;authors&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;Brinkman Lab&#39;</span><span class="p">,</span> <span class="s1">&#39;Hancock Lab&#39;</span><span class="p">,</span> <span class="s1">&#39;Lynn Group&#39;</span><span class="p">],</span>
+        <span class="s1">&#39;emails&#39;</span><span class="p">:</span> <span class="p">[(</span><span class="s1">&#39;innatedb-mail@sfu.ca&#39;</span><span class="p">,</span> <span class="s1">&#39;InnateDB Team&#39;</span><span class="p">),</span>
+                   <span class="p">(</span><span class="s1">&#39;david.lynn@sahmri.com&#39;</span><span class="p">,</span> <span class="s1">&#39;David Lynn&#39;</span><span class="p">)],</span>
+        <span class="s1">&#39;pubmeds&#39;</span><span class="p">:</span> <span class="p">[</span><span class="mi">20727158</span><span class="p">,</span> <span class="mi">23180781</span><span class="p">,</span> <span class="mi">18766178</span><span class="p">],</span>
+        <span class="s1">&#39;releases&#39;</span><span class="p">:</span> <span class="p">[</span><span class="mi">2008</span><span class="p">,</span> <span class="mi">2010</span><span class="p">,</span> <span class="mi">2013</span><span class="p">,</span> <span class="mi">2014</span><span class="p">,</span> <span class="mi">2015</span><span class="p">],</span>
+        <span class="s1">&#39;annot&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;experiment&#39;</span><span class="p">,</span> <span class="s1">&#39;mechanism&#39;</span><span class="p">],</span>
+        <span class="s1">&#39;recommend&#39;</span><span class="p">:</span>
+        <span class="s1">&#39;middle size interaction resource; special focus on immune pathways&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;descriptions&#39;</span><span class="p">:</span> <span class="p">[</span>
+<span class="w">            </span><span class="sa">u</span><span class="sd">&#39;&#39;&#39;</span>
+<span class="sd">            InnateDB (www.innatedb.com) is a database and integrated analysis platform specifically designed to facilitate systems-level analyses of the mammalian innate immune response (Lynn et al. 2008; 2010, 2013). To enrich our knowledge of innate immunity networks and pathways, the InnateDB curation team has contextually annotated &gt;25,000 human and mouse innate immunity-relevant molecular interactions through the review of &gt;5,000 biomedical articles. Curation adheres to the MIMIx guidelines and new interactions are added weekly. Importantly, interactions are curated between molecules with a documented role in an innate immunity relevant biological process or pathway and all other interactors regardless of whether the interacting molecule has any known role in innate immunity. This approach captures interactions between the innate immune system and other systems.</span>
+
+<span class="sd">            InnateDB is not limited to data on the innate immune system. It is a comprehensive database of human, mouse and bovine molecular interactions and pathways, consisting of more than 300,000 molecular interactions and 3,000+ pathways, integrated from major public molecular interaction and pathway databases. InnateDB is also an analysis platform offering user-friendly bioinformatics tools, including pathway and ontology analysis, network visualization and analysis and the ability to upload and analyze user-supplied gene expression or other quantitative data in a network and/or pathway context. The platform has a global profile and is utilised by &gt;10,000 users per annum and is widely cited. A mirror of the site hosted in Australia is also available at innatedb.sahmri.com.</span>
+
+<span class="sd">            Note that new interactions and gene annotations are added to InnateDB on an almost weekly database so the data is being continuously updated.</span>
+<span class="sd">            &#39;&#39;&#39;</span>
+        <span class="p">],</span>
+        <span class="s1">&#39;notes&#39;</span><span class="p">:</span> <span class="p">[</span>
+<span class="w">            </span><span class="sa">u</span><span class="sd">&#39;&#39;&#39;</span>
+<span class="sd">            Probably the largest manually curated binary protein interaction dataset, developed by a dedicated full time team of curators. Formats are clear and accessible, comprising UniProt IDs, PubMed references, experimental evidences and mechanisms.</span>
+<span class="sd">            &#39;&#39;&#39;</span>
+        <span class="p">],</span>
+        <span class="s1">&#39;type&#39;</span><span class="p">:</span> <span class="s1">&#39;literature curated&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;data_integration&#39;</span><span class="p">:</span> <span class="s1">&#39;static&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;subtype&#39;</span><span class="p">:</span> <span class="s1">&#39;interaction&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;omnipath&#39;</span><span class="p">:</span> <span class="kc">True</span><span class="p">,</span>
+        <span class="s1">&#39;license&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;name&#39;</span><span class="p">:</span> <span class="s1">&#39;Design Science License&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;url&#39;</span><span class="p">:</span> <span class="s1">&#39;http://www.innatedb.com/license.jsp&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;commercial_use&#39;</span><span class="p">:</span> <span class="kc">True</span>
+        <span class="p">},</span>
+        <span class="s1">&#39;pypath&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;format&#39;</span><span class="p">:</span> <span class="p">[</span>
+                <span class="s1">&#39;pypath.data_formats.interaction[</span><span class="se">\&#39;</span><span class="s1">innatedb</span><span class="se">\&#39;</span><span class="s1">]&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;pypath.data_formats.omnipath[</span><span class="se">\&#39;</span><span class="s1">innatedb</span><span class="se">\&#39;</span><span class="s1">]&#39;</span>
+            <span class="p">],</span>
+            <span class="s1">&#39;data&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;pypath.data/innatedb.csv&#39;</span><span class="p">]</span>
+        <span class="p">},</span>
+        <span class="s1">&#39;pathguide&#39;</span><span class="p">:</span> <span class="mi">264</span>
+    <span class="p">},</span>
+    <span class="s1">&#39;CORUM&#39;</span><span class="p">:</span> <span class="p">{</span>
+        <span class="s1">&#39;year&#39;</span><span class="p">:</span> <span class="mi">2012</span><span class="p">,</span>
+        <span class="s1">&#39;releases&#39;</span><span class="p">:</span> <span class="p">[</span><span class="mi">2007</span><span class="p">,</span> <span class="mi">2009</span><span class="p">],</span>
+        <span class="s1">&#39;urls&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;articles&#39;</span><span class="p">:</span> <span class="p">[</span>
+                <span class="s1">&#39;http://nar.oxfordjournals.org/content/36/suppl_1/D646.long&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;http://nar.oxfordjournals.org/content/38/suppl_1/D497.long&#39;</span>
+            <span class="p">],</span>
+            <span class="s1">&#39;webpages&#39;</span><span class="p">:</span>
+            <span class="p">[</span><span class="s1">&#39;http://mips.helmholtz-muenchen.de/genre/proj/corum&#39;</span><span class="p">],</span>
+            <span class="s1">&#39;omictools&#39;</span><span class="p">:</span> <span class="p">[</span>
+                <span class="s1">&#39;http://omictools.com/comprehensive-resource-of-mammalian-protein-complexes-tool&#39;</span>
+            <span class="p">]</span>
+        <span class="p">},</span>
+        <span class="s1">&#39;full_name&#39;</span><span class="p">:</span> <span class="s1">&#39;Comprehensive Resource of Mammalian protein complexes&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;emails&#39;</span><span class="p">:</span> <span class="p">[(</span><span class="s1">&#39;andreas.ruepp@helmholtz-muenchen.de&#39;</span><span class="p">,</span> <span class="s1">&#39;Andreas Ruepp&#39;</span><span class="p">)],</span>
+        <span class="s1">&#39;pubmeds&#39;</span><span class="p">:</span> <span class="p">[</span><span class="mi">19884131</span><span class="p">,</span> <span class="mi">17965090</span><span class="p">],</span>
+        <span class="s1">&#39;taxons&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;human&#39;</span><span class="p">,</span> <span class="s1">&#39;mouse&#39;</span><span class="p">,</span> <span class="s1">&#39;rat&#39;</span><span class="p">],</span>
+        <span class="s1">&#39;descriptions&#39;</span><span class="p">:</span> <span class="p">[</span>
+<span class="w">            </span><span class="sa">u</span><span class="sd">&#39;&#39;&#39;</span>
+<span class="sd">            The CORUM database is a collection of experimentally verified mammalian protein complexes. Information is manually derived by critical reading of the scientific literature from expert annotators. Information about protein complexes includes protein complex names, subunits, literature references as well as the function of the complexes.</span>
+<span class="sd">            In order to provide a high-quality dataset of mammalian protein complexes, all entries are manually created. Only protein complexes which have been isolated and characterized by reliable experimental evidence are included in CORUM. To be considered for CORUM, a protein complex has to be isolated as one molecule and must not be a construct derived from several experiments. Also, artificial constructs of subcomplexes are not taken into account. Since information from high-throughput experi ments contains a significant fraction of false-positive results, this type of data is excluded. References for relevant articles were mainly found in general review articles, cross-references to related protein complexes within analysed literature and comments on referenced articles in UniProt.</span>
+<span class="sd">            &#39;&#39;&#39;</span>
+        <span class="p">],</span>
+        <span class="s1">&#39;notes&#39;</span><span class="p">:</span> <span class="p">[</span>
+<span class="w">            </span><span class="sa">u</span><span class="sd">&#39;&#39;&#39;</span>
+<span class="sd">            CORUM is not part of the OmniPath pathways network, because we did not applied any complex expansion. But it has an interface built in the pypath module.</span>
+<span class="sd">            &#39;&#39;&#39;</span>
+        <span class="p">],</span>
+        <span class="s1">&#39;type&#39;</span><span class="p">:</span> <span class="s1">&#39;literature curated&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;data_integration&#39;</span><span class="p">:</span> <span class="s1">&#39;dynamic&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;subtype&#39;</span><span class="p">:</span> <span class="s1">&#39;complexes&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;omnipath&#39;</span><span class="p">:</span> <span class="kc">False</span><span class="p">,</span>
+        <span class="s1">&#39;license&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;name&#39;</span><span class="p">:</span> <span class="s1">&#39;No license.&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;url&#39;</span><span class="p">:</span> <span class="s1">&#39;http://www.gnu.org/licenses/license-list.html#NoLicense&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;commercial_use&#39;</span><span class="p">:</span> <span class="kc">False</span>
+        <span class="p">},</span>
+        <span class="s1">&#39;pypath&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;data&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;pypath.urls.urls[</span><span class="se">\&#39;</span><span class="s1">corum</span><span class="se">\&#39;</span><span class="s1">][</span><span class="se">\&#39;</span><span class="s1">url</span><span class="se">\&#39;</span><span class="s1">]&#39;</span><span class="p">],</span>
+            <span class="s1">&#39;input&#39;</span><span class="p">:</span> <span class="p">[</span>
+                <span class="s1">&#39;pypath.dataio.get_corum()&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;pypath.pypath.PyPath().load_corum()&#39;</span>
+            <span class="p">]</span>
+        <span class="p">},</span>
+        <span class="s1">&#39;pathguide&#39;</span><span class="p">:</span> <span class="mi">322</span>
+    <span class="p">},</span>
+    <span class="s1">&#39;CST&#39;</span><span class="p">:</span> <span class="p">{</span>
+        <span class="s1">&#39;year&#39;</span><span class="p">:</span> <span class="mi">2015</span><span class="p">,</span>
+        <span class="s1">&#39;releases&#39;</span><span class="p">:</span> <span class="p">[</span><span class="mi">2005</span><span class="p">,</span> <span class="mi">2015</span><span class="p">],</span>
+        <span class="s1">&#39;nodes&#39;</span><span class="p">:</span> <span class="kc">None</span><span class="p">,</span>
+        <span class="s1">&#39;edges&#39;</span><span class="p">:</span> <span class="kc">None</span><span class="p">,</span>
+        <span class="s1">&#39;authors&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;CST&#39;</span><span class="p">],</span>
+        <span class="s1">&#39;label&#39;</span><span class="p">:</span> <span class="s1">&#39;CST Pathways&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;color&#39;</span><span class="p">:</span> <span class="s1">&#39;&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;full_name&#39;</span><span class="p">:</span> <span class="s1">&#39;Cell Signaling Technology Pathways&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;urls&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;articles&#39;</span><span class="p">:</span> <span class="p">[],</span>
+            <span class="s1">&#39;webpages&#39;</span><span class="p">:</span> <span class="p">[</span>
+                <span class="s1">&#39;http://www.cellsignal.com/common/content/content.jsp?id=science-pathways&#39;</span>
+            <span class="p">]</span>
+        <span class="p">},</span>
+        <span class="s1">&#39;emails&#39;</span><span class="p">:</span> <span class="p">[(</span><span class="s1">&#39;info@cellsignal.com&#39;</span><span class="p">,</span> <span class="s1">&#39;Cell Signaling Technology&#39;</span><span class="p">)],</span>
+        <span class="s1">&#39;descriptions&#39;</span><span class="p">:</span> <span class="p">[</span>
+<span class="w">            </span><span class="sa">u</span><span class="sd">&#39;&#39;&#39;</span>
+<span class="sd">            On these resource pages you can find signaling pathway diagrams, research overviews, relevant antibody products, publications, and other research resources organized by topic. The pathway diagrams associated with these topics have been assembled by CST scientists and outside experts to provide succinct and current overviews of selected signaling pathways.</span>
+<span class="sd">            &#39;&#39;&#39;</span>
+        <span class="p">],</span>
+        <span class="s1">&#39;notes&#39;</span><span class="p">:</span> <span class="p">[</span>
+<span class="w">            </span><span class="sa">u</span><span class="sd">&#39;&#39;&#39;</span>
+<span class="sd">            The pathway diagrams are based on good quality, manually curated data, probably from review articles. However, those are available only in graphical (PDF and InDesign) formats. There is no programmatic way to obtain the interactions and references, as it was confirmed by the authors, who I contacted by mail. Wang&#39;s HumanSignalingNetwork includes the data from this resource, which probably has been entered manually, but Wang&#39;s data doesn&#39;t have source annotations, despite it&#39;s compiled from multiple sources. The date of the beginning of this project is estimated using the Internet wayback machine.</span>
+<span class="sd">            &#39;&#39;&#39;</span>
+        <span class="p">],</span>
+        <span class="s1">&#39;type&#39;</span><span class="p">:</span> <span class="s1">&#39;literature curated&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;subtype&#39;</span><span class="p">:</span> <span class="s1">&#39;activity flow&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;omnipath&#39;</span><span class="p">:</span> <span class="kc">False</span><span class="p">,</span>
+        <span class="s1">&#39;license&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;name&#39;</span><span class="p">:</span> <span class="s1">&#39;No license.&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;url&#39;</span><span class="p">:</span> <span class="s1">&#39;http://www.gnu.org/licenses/license-list.html#NoLicense&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;commercial_use&#39;</span><span class="p">:</span> <span class="kc">False</span>
+        <span class="p">},</span>
+    <span class="p">},</span>
+    <span class="s1">&#39;DIP&#39;</span><span class="p">:</span> <span class="p">{</span>
+        <span class="s1">&#39;year&#39;</span><span class="p">:</span> <span class="mi">2016</span><span class="p">,</span>
+        <span class="s1">&#39;releases&#39;</span><span class="p">:</span> <span class="p">[</span>
+            <span class="mi">2000</span><span class="p">,</span> <span class="mi">2001</span><span class="p">,</span> <span class="mi">2002</span><span class="p">,</span> <span class="mi">2003</span><span class="p">,</span> <span class="mi">2004</span><span class="p">,</span> <span class="mi">2005</span><span class="p">,</span> <span class="mi">2006</span><span class="p">,</span> <span class="mi">2007</span><span class="p">,</span> <span class="mi">2008</span><span class="p">,</span> <span class="mi">2009</span><span class="p">,</span> <span class="mi">2010</span><span class="p">,</span>
+            <span class="mi">2011</span><span class="p">,</span> <span class="mi">2012</span><span class="p">,</span> <span class="mi">2013</span><span class="p">,</span> <span class="mi">2014</span><span class="p">,</span> <span class="mi">2015</span><span class="p">,</span> <span class="mi">2016</span>
+        <span class="p">],</span>
+        <span class="s1">&#39;size&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;nodes&#39;</span><span class="p">:</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="s1">&#39;edges&#39;</span><span class="p">:</span> <span class="kc">None</span>
+        <span class="p">},</span>
+        <span class="s1">&#39;authors&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;UCLA&#39;</span><span class="p">,</span> <span class="s1">&#39;Eisenberg Group&#39;</span><span class="p">],</span>
+        <span class="s1">&#39;label&#39;</span><span class="p">:</span> <span class="s1">&#39;DIP&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;full_name&#39;</span><span class="p">:</span> <span class="s1">&#39;Database of Interacting Proteins&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;color&#39;</span><span class="p">:</span> <span class="s1">&#39;&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;urls&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;articles&#39;</span><span class="p">:</span> <span class="p">[</span>
+                <span class="s1">&#39;http://nar.oxfordjournals.org/content/28/1/289.long&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;http://nar.oxfordjournals.org/content/29/1/239.long&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;http://nar.oxfordjournals.org/content/30/1/303.long&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;http://nar.oxfordjournals.org/content/32/suppl_1/D449.full&#39;</span>
+            <span class="p">],</span>
+            <span class="s1">&#39;webpages&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;http://dip.doe-mbi.ucla.edu/dip/Main.cgi&#39;</span><span class="p">],</span>
+            <span class="s1">&#39;omictools&#39;</span><span class="p">:</span>
+            <span class="p">[</span><span class="s1">&#39;http://omictools.com/database-of-interacting-proteins-tool&#39;</span><span class="p">]</span>
+        <span class="p">},</span>
+        <span class="s1">&#39;pubmeds&#39;</span><span class="p">:</span> <span class="p">[</span><span class="mi">10592249</span><span class="p">,</span> <span class="mi">11125102</span><span class="p">,</span> <span class="mi">11752321</span><span class="p">,</span> <span class="mi">14681454</span><span class="p">],</span>
+        <span class="s1">&#39;annot&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;mechanism&#39;</span><span class="p">,</span> <span class="s1">&#39;experiment&#39;</span><span class="p">],</span>
+        <span class="s1">&#39;recommend&#39;</span><span class="p">:</span>
+        <span class="s1">&#39;one of the earliest interaction databases; remarkable literature curation effort&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;descriptions&#39;</span><span class="p">:</span> <span class="p">[</span>
+<span class="w">            </span><span class="sa">u</span><span class="sd">&#39;&#39;&#39;</span>
+<span class="sd">            In the beginning (near 2000), it was a entirely manually curated database:</span>
+<span class="sd">            Currently protein–protein interactions are entered into the DIP only following publication in peer-reviewed journals. Entry is done manually by the curator, followed by automated tests that show the proteins and citations exist. Interactions are double-checked by a second curator and flagged accordingly in the database.</span>
+<span class="sd">            From 2001, it contains high-throughput interactions:</span>
+<span class="sd">            Because the reliability of experimental evidence varies widely, methods of quality assessment have been developed and utilized to identify the most reliable subset of the interactions. This CORE set can be used as a reference when evaluating the reliability of high-throughput protein-protein interaction data sets, for development of prediction methods, as well as in the studies of the properties of protein interaction networks.</span>
+<span class="sd">            &#39;&#39;&#39;</span>
+        <span class="p">],</span>
+        <span class="s1">&#39;notes&#39;</span><span class="p">:</span> <span class="p">[</span>
+<span class="w">            </span><span class="sa">u</span><span class="sd">&#39;&#39;&#39;</span>
+<span class="sd">            The &#39;core&#39; dataset contains manually curated interactions from small-scale studies. Interactions are well annotated with PubMed IDs, evidences, and mechanism (binding, chemical reaction, etc). The format is esily accessible (MITAB).</span>
+<span class="sd">            &#39;&#39;&#39;</span>
+        <span class="p">],</span>
+        <span class="s1">&#39;type&#39;</span><span class="p">:</span> <span class="s1">&#39;literature curated&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;subtype&#39;</span><span class="p">:</span> <span class="s1">&#39;interaction&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;data_integration&#39;</span><span class="p">:</span> <span class="s1">&#39;static&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;omnipath&#39;</span><span class="p">:</span> <span class="kc">True</span><span class="p">,</span>
+        <span class="s1">&#39;emails&#39;</span><span class="p">:</span> <span class="p">[(</span><span class="s1">&#39;david@mbi.ucla.edu&#39;</span><span class="p">,</span> <span class="s1">&#39;David Eisenberg&#39;</span><span class="p">)],</span>
+        <span class="s1">&#39;license&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;name&#39;</span><span class="p">:</span> <span class="s1">&#39;CC-Attribution-NoDerivs-3.0&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;url&#39;</span><span class="p">:</span> <span class="s1">&#39;http://creativecommons.org/licenses/by-nd/3.0/&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;commercial_use&#39;</span><span class="p">:</span> <span class="kc">True</span>
+        <span class="p">},</span>
+        <span class="s1">&#39;pypath&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;format&#39;</span><span class="p">:</span> <span class="p">[</span>
+                <span class="s1">&#39;pypath.data_formats.interaction[</span><span class="se">\&#39;</span><span class="s1">dip</span><span class="se">\&#39;</span><span class="s1">]&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;pypath.data_formats.interaction[</span><span class="se">\&#39;</span><span class="s1">omnipath</span><span class="se">\&#39;</span><span class="s1">]&#39;</span>
+            <span class="p">],</span>
+            <span class="s1">&#39;data&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;pypath.data/dip_human_core_processed.csv&#39;</span><span class="p">]</span>
+        <span class="p">},</span>
+        <span class="s1">&#39;pathguide&#39;</span><span class="p">:</span> <span class="mi">3</span>
+    <span class="p">},</span>
+    <span class="s1">&#39;DEPOD&#39;</span><span class="p">:</span> <span class="p">{</span>
+        <span class="s1">&#39;year&#39;</span><span class="p">:</span> <span class="mi">2016</span><span class="p">,</span>
+        <span class="s1">&#39;releases&#39;</span><span class="p">:</span> <span class="p">[</span><span class="mi">2013</span><span class="p">,</span> <span class="mi">2014</span><span class="p">,</span> <span class="mi">2016</span><span class="p">],</span>
+        <span class="s1">&#39;size&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;nodes&#39;</span><span class="p">:</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="s1">&#39;edges&#39;</span><span class="p">:</span> <span class="kc">None</span>
+        <span class="p">},</span>
+        <span class="s1">&#39;authors&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;EMBL &amp; EMBL-EBI&#39;</span><span class="p">],</span>
+        <span class="s1">&#39;label&#39;</span><span class="p">:</span> <span class="s1">&#39;DEPOD&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;full_name&#39;</span><span class="p">:</span> <span class="s1">&#39;Human Dephosphorylation Database&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;urls&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;articles&#39;</span><span class="p">:</span> <span class="p">[</span>
+                <span class="s1">&#39;http://stke.sciencemag.org/content/6/275/rs10.long&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;http://nar.oxfordjournals.org/content/43/D1/D531.long&#39;</span>
+            <span class="p">],</span>
+            <span class="s1">&#39;webpages&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;http://www.koehn.embl.de/depod/index.php&#39;</span><span class="p">],</span>
+            <span class="s1">&#39;omictools&#39;</span><span class="p">:</span>
+            <span class="p">[</span><span class="s1">&#39;http://omictools.com/dephosphorylation-database-tool&#39;</span><span class="p">]</span>
+        <span class="p">},</span>
+        <span class="s1">&#39;pubmeds&#39;</span><span class="p">:</span> <span class="p">[</span><span class="mi">23674824</span><span class="p">,</span> <span class="mi">25332398</span><span class="p">],</span>
+        <span class="s1">&#39;taxons&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;human&#39;</span><span class="p">],</span>
+        <span class="s1">&#39;annot&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;residue&#39;</span><span class="p">,</span> <span class="s1">&#39;experiment&#39;</span><span class="p">],</span>
+        <span class="s1">&#39;recommend&#39;</span><span class="p">:</span>
+        <span class="s1">&#39;the only resource focusing on dephosphorylation interactions; most of these can not be found anywhere else&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;descriptions&#39;</span><span class="p">:</span> <span class="p">[</span>
+<span class="w">            </span><span class="sa">u</span><span class="sd">&#39;&#39;&#39;</span>
+<span class="sd">            DEPOD the human DEPhOsphorylation Database (version 1.0) is a manually curated database collecting human active phosphatases, their experimentally verified protein and non-protein substrates and dephosphorylation site information, and pathways in which they are involved. It also provides links to popular kinase databases and protein-protein interaction databases for these phosphatases and substrates. DEPOD aims to be a valuable resource for studying human phosphatases and their substrate specificities and molecular mechanisms; phosphatase-targeted drug discovery and development; connecting phosphatases with kinases through their common substrates; completing the human phosphorylation/dephosphorylation network.</span>
+<span class="sd">            &#39;&#39;&#39;</span>
+        <span class="p">],</span>
+        <span class="s1">&#39;notes&#39;</span><span class="p">:</span> <span class="p">[</span>
+<span class="w">            </span><span class="sa">u</span><span class="sd">&#39;&#39;&#39;</span>
+<span class="sd">            Nice manually curated dataset with PubMed references, in easily accessible MITAB format with UniProt IDs, comprises 832 dephosphorylation reactions on protein substrates, and few hundreds on small molecules.</span>
+<span class="sd">            &#39;&#39;&#39;</span>
+        <span class="p">],</span>
+        <span class="s1">&#39;type&#39;</span><span class="p">:</span> <span class="s1">&#39;literature curated&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;subtype&#39;</span><span class="p">:</span> <span class="s1">&#39;post-translational modification&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;omnipath&#39;</span><span class="p">:</span> <span class="kc">True</span><span class="p">,</span>
+        <span class="s1">&#39;emails&#39;</span><span class="p">:</span> <span class="p">[(</span><span class="s1">&#39;koehn@embl.de&#39;</span><span class="p">,</span> <span class="s1">&#39;Maja Kohn&#39;</span><span class="p">)],</span>
+        <span class="s1">&#39;license&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;name&#39;</span><span class="p">:</span> <span class="s1">&#39;CC-Attribution-NonCommercial 4.0&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;url&#39;</span><span class="p">:</span> <span class="s1">&#39;https://creativecommons.org/licenses/by-nc/4.0/&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;commercial_use&#39;</span><span class="p">:</span> <span class="kc">False</span>
+        <span class="p">},</span>
+        <span class="s1">&#39;pypath&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;format&#39;</span><span class="p">:</span> <span class="p">[</span>
+                <span class="s1">&#39;pypath.data_formats.ptm[</span><span class="se">\&#39;</span><span class="s1">depod</span><span class="se">\&#39;</span><span class="s1">]&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;pypath.data_formats.omnipath[</span><span class="se">\&#39;</span><span class="s1">depod</span><span class="se">\&#39;</span><span class="s1">]&#39;</span>
+            <span class="p">],</span>
+            <span class="s1">&#39;data&#39;</span><span class="p">:</span> <span class="p">[</span>
+                <span class="s1">&#39;pypath.data/depod-refs.csv&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;pypath.urls.urls[</span><span class="se">\&#39;</span><span class="s1">depod</span><span class="se">\&#39;</span><span class="s1">][</span><span class="se">\&#39;</span><span class="s1">url</span><span class="se">\&#39;</span><span class="s1">]&#39;</span>
+            <span class="p">],</span>
+            <span class="s1">&#39;input&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;pypath.dataio.get_depod()&#39;</span><span class="p">],</span>
+            <span class="s1">&#39;ptm&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;pypath.pypath.PyPath().load_depod_dmi()&#39;</span><span class="p">]</span>
+        <span class="p">}</span>
+    <span class="p">},</span>
+    <span class="s1">&#39;PhosphoPoint&#39;</span><span class="p">:</span> <span class="p">{</span>
+        <span class="s1">&#39;year&#39;</span><span class="p">:</span> <span class="mi">2008</span><span class="p">,</span>
+        <span class="s1">&#39;urls&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;articles&#39;</span><span class="p">:</span> <span class="p">[</span>
+                <span class="s1">&#39;http://bioinformatics.oxfordjournals.org/content/24/16/i14.long&#39;</span>
+            <span class="p">],</span>
+            <span class="s1">&#39;webpages&#39;</span><span class="p">:</span> <span class="p">[</span>
+                <span class="s1">&#39;http://kinase.bioinformatics.tw/&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;http://web.archive.org/web/20140530070613/http://kinase.bioinformatics.tw/&#39;</span>
+            <span class="p">],</span>
+            <span class="s1">&#39;omictools&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;http://omictools.com/phosphopoint-tool&#39;</span><span class="p">]</span>
+        <span class="p">},</span>
+        <span class="s1">&#39;taxons&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;human&#39;</span><span class="p">],</span>
+        <span class="s1">&#39;pubmeds&#39;</span><span class="p">:</span> <span class="p">[</span><span class="mi">18689816</span><span class="p">],</span>
+        <span class="s1">&#39;descriptions&#39;</span><span class="p">:</span> <span class="p">[</span>
+<span class="w">            </span><span class="sa">u</span><span class="sd">&#39;&#39;&#39;</span>
+<span class="sd">            We have integrated three existing databases, including Phospho.ELM (release 6.0, total 9236 phosphorylation sites), HPRD (release 6, total 8992 phosphorylation sites), SwissProt (release 51.5, total 6529 phosphorylation sites), and our manually curated 400 kinase–substrate pairs, which are primarily from review articles.</span>
+<span class="sd">            Among these phosphorylation sites, 7843 (6152+995+696) are from high-throughput (HTP) screening, 6329 (3828+1152+1349) are from low-throughput (LTP) analysis, and only 679 (420+97+162) are both from HTP and LTP screening. One special note is that there are 887 phosphorylation sites, which do not have annotation from literature in the SwissProt database and it is not possible distinguish whether these are from HTP or LTP.</span>
+<span class="sd">            &#39;&#39;&#39;</span>
+        <span class="p">],</span>
+        <span class="s1">&#39;notes&#39;</span><span class="p">:</span> <span class="p">[</span>
+<span class="w">            </span><span class="sa">u</span><span class="sd">&#39;&#39;&#39;</span>
+<span class="sd">            It contains 400 manually curated interactions and much more from HTP methods. The manually curated set can not be distinguished in the data formats offered.</span>
+<span class="sd">            &#39;&#39;&#39;</span>
+        <span class="p">],</span>
+        <span class="s1">&#39;type&#39;</span><span class="p">:</span> <span class="s1">&#39;literature curated and prediction&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;subtype&#39;</span><span class="p">:</span> <span class="s1">&#39;post-translational modification&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;data_integration&#39;</span><span class="p">:</span> <span class="s1">&#39;static&#39;</span><span class="p">,</span>
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+            <span class="s1">&#39;name&#39;</span><span class="p">:</span> <span class="s1">&#39;CC-Attribution-ShareAlike 4.0&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;url&#39;</span><span class="p">:</span> <span class="s1">&#39;https://creativecommons.org/licenses/by-sa/4.0/&#39;</span><span class="p">,</span>
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+        <span class="p">},</span>
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+        <span class="s1">&#39;pathguide&#39;</span><span class="p">:</span> <span class="mi">164</span><span class="p">,</span>
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+        <span class="s1">&#39;recommend&#39;</span><span class="p">:</span>
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+        <span class="s1">&#39;full_name&#39;</span><span class="p">:</span> <span class="s1">&#39;Signaling Pathway Integrated Knowledge Engine&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;annot&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;experiment&#39;</span><span class="p">,</span> <span class="s1">&#39;mechanism&#39;</span><span class="p">],</span>
+        <span class="s1">&#39;recommend&#39;</span><span class="p">:</span>
+        <span class="s1">&#39;one of the 3 large resources providing effect signs; combined with Signor and SignaLink gives the major part of the literature curated activity flow network&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;descriptions&#39;</span><span class="p">:</span> <span class="p">[</span>
+<span class="w">            </span><span class="sa">u</span><span class="sd">&#39;&#39;&#39;</span>
+<span class="sd">            SPIKE’s data on relationships between entities come from three sources: (i) Highly curated data submitted directly to SPIKE database by SPIKE curators and experts in various biomedical domains. (ii) Data imported from external signaling pathway databaes. At present, SPIKE database imports such data from Reactome, KEGG, NetPath and The Transcription Factor Encyclopedia (http://www.cisreg.ca/cgi-bin/tfe/home.pl). (iii) Data on protein–protein interactions (PPIs) imported either directly from wide-scale studies that recorded such interactions [to date,PPI data were imported from Stelzl et al., Rual et al. and Lim et al.] or from external PPI databases [IntAct and MINT]. Relationship data coming from these different sources vary greatly in their quality and this is reflected by a quality level attribute, which is attached to each relationship in SPIKE database (Supplementary Data). Each relationship in SPIKE is linked to at least one PubMed reference that supports it.</span>
+<span class="sd">            As of August 2010, the SPIKE database contains 20 412 genes/proteins, 542 complexes (327 of high quality), 320 protein families (167 of high quality) and 39 small molecules. These entities are linked by 34 338 interactions (of which 2400 are of high quality) and 6074 regulations (4420 of high quality). These are associated with 5873 journal references in total.</span>
+<span class="sd">            Each of the maps is constructed by a domain expert; typically the same expert will also be responsible later for keeping it up-to-date. The expert reads the relevant literature and identifies those interactions and regulations that are pertinent to the pathway.</span>
+<span class="sd">            The regulations and interactions in the database are assigned quality values ranging from 1 to 4. In general, relationships (regulations and interactions) derived from highly focused biochemical studies are assigned high quality (2 or 1) while those derived from high-throughput experiments are assigned lower quality (4 or 3). The curator uses best judgment to assign a quality level. For example, relationships mentioned in two independent research reports, or cited repeatedly in reviews written by leading authorities will get quality 1. Relationships with cited concrete references and those imported en masse from external curated signaling DBs are initially assigned quality 2 but later can be changed to the highest quality after the curator has read and was convinced by the cited papers. Data imported from protein-protein interaction DBs and datasets are assigned quality 3 or 4, depending on the experimental technique.</span>
+<span class="sd">            &#39;&#39;&#39;</span>
+        <span class="p">],</span>
+        <span class="s1">&#39;type&#39;</span><span class="p">:</span> <span class="s1">&#39;literature curated&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;subtype&#39;</span><span class="p">:</span> <span class="s1">&#39;activity flow&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;data_integration&#39;</span><span class="p">:</span> <span class="s1">&#39;static&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;omnipath&#39;</span><span class="p">:</span> <span class="kc">True</span><span class="p">,</span>
+        <span class="s1">&#39;emails&#39;</span><span class="p">:</span> <span class="p">[(</span><span class="s1">&#39;rshamir@tau.ac.il&#39;</span><span class="p">,</span> <span class="s1">&#39;Ron Shamir&#39;</span><span class="p">)],</span>
+        <span class="s1">&#39;license&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;name&#39;</span><span class="p">:</span> <span class="s1">&#39;CC-Attribution 4.0&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;url&#39;</span><span class="p">:</span> <span class="s1">&#39;https://creativecommons.org/licenses/by/4.0/&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;commercial_use&#39;</span><span class="p">:</span> <span class="kc">True</span>
+        <span class="p">},</span>
+        <span class="s1">&#39;pypath&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;format&#39;</span><span class="p">:</span> <span class="p">[</span>
+                <span class="s1">&#39;pypath.data_formats.pathway[</span><span class="se">\&#39;</span><span class="s1">spike</span><span class="se">\&#39;</span><span class="s1">]&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;pypath.data_formats.omnipath[</span><span class="se">\&#39;</span><span class="s1">spike</span><span class="se">\&#39;</span><span class="s1">]&#39;</span>
+            <span class="p">],</span>
+            <span class="s1">&#39;data&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;pypath.data/spike_hc.csv&#39;</span><span class="p">]</span>
+        <span class="p">},</span>
+        <span class="s1">&#39;pathguide&#39;</span><span class="p">:</span> <span class="mi">317</span>
+    <span class="p">},</span>
+    <span class="s1">&#39;NCI-PID&#39;</span><span class="p">:</span> <span class="p">{</span>
+        <span class="s1">&#39;year&#39;</span><span class="p">:</span> <span class="mi">2012</span><span class="p">,</span>
+        <span class="s1">&#39;releases&#39;</span><span class="p">:</span> <span class="p">[</span><span class="mi">2008</span><span class="p">,</span> <span class="mi">2012</span><span class="p">],</span>
+        <span class="s1">&#39;size&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;nodes&#39;</span><span class="p">:</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="s1">&#39;edges&#39;</span><span class="p">:</span> <span class="kc">None</span>
+        <span class="p">},</span>
+        <span class="s1">&#39;authors&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;NCI&#39;</span><span class="p">],</span>
+        <span class="s1">&#39;label&#39;</span><span class="p">:</span> <span class="s1">&#39;NCI-PID&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;full_name&#39;</span><span class="p">:</span> <span class="s1">&#39;NCI-Nature Pathway Interaction Database&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;color&#39;</span><span class="p">:</span> <span class="s1">&#39;&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;urls&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;webpages&#39;</span><span class="p">:</span> <span class="p">[</span>
+                <span class="s1">&#39;http://pid.nci.nih.gov/index.shtml&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;http://www.ndexbio.org/&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;http://web.archive.org/web/20150908030438/http://pid.nci.nih.gov/index.shtml&#39;</span>
+            <span class="p">],</span>
+            <span class="s1">&#39;articles&#39;</span><span class="p">:</span>
+            <span class="p">[</span><span class="s1">&#39;http://nar.oxfordjournals.org/content/37/suppl_1/D674.long&#39;</span><span class="p">]</span>
+        <span class="p">},</span>
+        <span class="s1">&#39;pubmeds&#39;</span><span class="p">:</span> <span class="p">[</span><span class="mi">18832364</span><span class="p">],</span>
+        <span class="s1">&#39;data_import&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;BioCarta&#39;</span><span class="p">,</span> <span class="s1">&#39;Reactome&#39;</span><span class="p">],</span>
+        <span class="s1">&#39;contains&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;BioCarta&#39;</span><span class="p">,</span> <span class="s1">&#39;Reactome&#39;</span><span class="p">],</span>
+        <span class="s1">&#39;taxons&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;human&#39;</span><span class="p">],</span>
+        <span class="s1">&#39;annot&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;experiment&#39;</span><span class="p">,</span> <span class="s1">&#39;localization&#39;</span><span class="p">,</span> <span class="s1">&#39;mechanism&#39;</span><span class="p">,</span> <span class="s1">&#39;pathway&#39;</span><span class="p">],</span>
+        <span class="s1">&#39;recommend&#39;</span><span class="p">:</span>
+        <span class="s1">&#39;one of the largest process description resources; represents remarkable curation effort; discontinued&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;descriptions&#39;</span><span class="p">:</span> <span class="p">[</span>
+<span class="w">            </span><span class="sa">u</span><span class="sd">&#39;&#39;&#39;</span>
+<span class="sd">            In curating, editors synthesize meaningful networks of events into defined pathways and adhere to the PID data model for consistency in data representation: molecules and biological processes are annotated with standardized names and unambiguous identifiers; and signaling and regulatory events are annotated with evidence codes and references. To ensure accurate data representation, editors assemble pathways from data that is principally derived from primary research publications. The majority of data in PID is human; however, if a finding discovered in another mammal is also deemed to occur in humans, editors may decide to include this finding, but will also record that the evidence was inferred from another species. Prior to publication, all pathways are reviewed by one or more experts in a field for accuracy and completeness.</span>
+<span class="sd">            &#39;&#39;&#39;</span>
+        <span class="p">],</span>
+        <span class="s1">&#39;notes&#39;</span><span class="p">:</span> <span class="p">[</span>
+<span class="w">            </span><span class="sa">u</span><span class="sd">&#39;&#39;&#39;</span>
+<span class="sd">            From the NCI-XML interactions with references, directions and signs can be extracted. Complexes are ommited.</span>
+<span class="sd">            &#39;&#39;&#39;</span><span class="p">,</span> <span class="sa">u</span><span class="s1">&#39;&#39;&#39;</span>
+<span class="s1">            From the end of 2015, the original NCI-PID webpage is not accessible anymore, and the data is available through the NDEx webserver and API.</span>
+<span class="s1">            &#39;&#39;&#39;</span>
+        <span class="p">],</span>
+        <span class="s1">&#39;type&#39;</span><span class="p">:</span> <span class="s1">&#39;literature curated&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;subtype&#39;</span><span class="p">:</span> <span class="s1">&#39;process description&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;omnipath&#39;</span><span class="p">:</span> <span class="kc">False</span><span class="p">,</span>
+        <span class="s1">&#39;emails&#39;</span><span class="p">:</span> <span class="p">[(</span><span class="s1">&#39;yanch@mail.nih.gov&#39;</span><span class="p">,</span> <span class="s1">&#39;Chunhua Yan&#39;</span><span class="p">)],</span>
+        <span class="s1">&#39;license&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;name&#39;</span><span class="p">:</span> <span class="s1">&#39;No license&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;url&#39;</span><span class="p">:</span> <span class="s1">&#39;http://www.gnu.org/licenses/license-list.html#NoLicense&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;commercial_use&#39;</span><span class="p">:</span> <span class="kc">False</span>
+        <span class="p">},</span>
+        <span class="s1">&#39;pypath&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;data&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;pypath.urls.urls[</span><span class="se">\&#39;</span><span class="s1">nci-pid</span><span class="se">\&#39;</span><span class="s1">][</span><span class="se">\&#39;</span><span class="s1">biopax_l3</span><span class="se">\&#39;</span><span class="s1">]&#39;</span><span class="p">],</span>
+            <span class="s1">&#39;format&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;pypath.data_formats.reaction_misc[</span><span class="se">\&#39;</span><span class="s1">nci_pid</span><span class="se">\&#39;</span><span class="s1">]&#39;</span><span class="p">],</span>
+            <span class="s1">&#39;input&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;pypath.dataio.pid_biopax()&#39;</span><span class="p">],</span>
+            <span class="s1">&#39;intr&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;pypath.dataio.pid_interactions()&#39;</span><span class="p">]</span>
+        <span class="p">},</span>
+        <span class="s1">&#39;pathguide&#39;</span><span class="p">:</span> <span class="mi">119</span>
+    <span class="p">},</span>
+    <span class="s1">&#39;WikiPathways&#39;</span><span class="p">:</span> <span class="p">{</span>
+        <span class="s1">&#39;year&#39;</span><span class="p">:</span> <span class="mi">2016</span><span class="p">,</span>
+        <span class="s1">&#39;releases&#39;</span><span class="p">:</span> <span class="p">[</span><span class="mi">2009</span><span class="p">,</span> <span class="mi">2010</span><span class="p">,</span> <span class="mi">2011</span><span class="p">,</span> <span class="mi">2012</span><span class="p">,</span> <span class="mi">2013</span><span class="p">,</span> <span class="mi">2014</span><span class="p">,</span> <span class="mi">2015</span><span class="p">,</span> <span class="mi">2016</span><span class="p">],</span>
+        <span class="s1">&#39;urls&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;webpages&#39;</span><span class="p">:</span>
+            <span class="p">[</span><span class="s1">&#39;http://www.wikipathways.org/index.php/WikiPathways&#39;</span><span class="p">],</span>
+            <span class="s1">&#39;articles&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;http://nar.oxfordjournals.org/content/40/D1/D1301&#39;</span><span class="p">],</span>
+            <span class="s1">&#39;omictools&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;http://omictools.com/wikipathways-tool&#39;</span><span class="p">]</span>
+        <span class="p">},</span>
+        <span class="s1">&#39;recommend&#39;</span><span class="p">:</span>
+        <span class="s1">&#39;process description resource developed in a community effort; high proportion of specific proteins&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;descriptions&#39;</span><span class="p">:</span> <span class="p">[</span>
+<span class="w">            </span><span class="sa">u</span><span class="sd">&#39;&#39;&#39;</span>
+<span class="sd">            The goal of WikiPathways is to capture knowledge about biological pathways (the elements, their interactions and layout) in a form that is both human readable and amenable to computational analysis.</span>
+<span class="sd">            &#39;&#39;&#39;</span>
+        <span class="p">],</span>
+        <span class="s1">&#39;notes&#39;</span><span class="p">:</span> <span class="p">[</span>
+<span class="w">            </span><span class="sa">u</span><span class="sd">&#39;&#39;&#39;</span>
+<span class="sd">            The data is not accessible. Interactions are available in BioPAX format, but without references.</span>
+<span class="sd">            &#39;&#39;&#39;</span>
+        <span class="p">],</span>
+        <span class="s1">&#39;type&#39;</span><span class="p">:</span> <span class="s1">&#39;literature curated&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;subtype&#39;</span><span class="p">:</span> <span class="s1">&#39;process description&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;omnipath&#39;</span><span class="p">:</span> <span class="kc">False</span><span class="p">,</span>
+        <span class="s1">&#39;emails&#39;</span><span class="p">:</span> <span class="p">[(</span><span class="s1">&#39;thomaskelder@gmail.com&#39;</span><span class="p">,</span> <span class="s1">&#39;Thomas Kelder&#39;</span><span class="p">),</span>
+                   <span class="p">(</span><span class="s1">&#39;apico@gladstone.ucsf.edu&#39;</span><span class="p">,</span> <span class="s1">&#39;Alex Pico&#39;</span><span class="p">)],</span>
+        <span class="s1">&#39;license&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;name&#39;</span><span class="p">:</span> <span class="s1">&#39;CC-Attribution-3.0&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;url&#39;</span><span class="p">:</span> <span class="s1">&#39;http://creativecommons.org/licenses/by/3.0/&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;commercial_use&#39;</span><span class="p">:</span> <span class="kc">True</span>
+        <span class="p">},</span>
+        <span class="s1">&#39;pathguide&#39;</span><span class="p">:</span> <span class="mi">237</span>
+    <span class="p">},</span>
+    <span class="s1">&#39;ConsensusPathDB&#39;</span><span class="p">:</span> <span class="p">{</span>
+        <span class="s1">&#39;year&#39;</span><span class="p">:</span> <span class="mi">2015</span><span class="p">,</span>
+        <span class="s1">&#39;releases&#39;</span><span class="p">:</span> <span class="p">[</span><span class="mi">2007</span><span class="p">,</span> <span class="mi">2008</span><span class="p">,</span> <span class="mi">2009</span><span class="p">,</span> <span class="mi">2010</span><span class="p">,</span> <span class="mi">2011</span><span class="p">,</span> <span class="mi">2012</span><span class="p">,</span> <span class="mi">2013</span><span class="p">,</span> <span class="mi">2014</span><span class="p">,</span> <span class="mi">2015</span><span class="p">],</span>
+        <span class="s1">&#39;urls&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;webpages&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;http://cpdb.molgen.mpg.de/CPDB&#39;</span><span class="p">],</span>
+            <span class="s1">&#39;articles&#39;</span><span class="p">:</span> <span class="p">[</span>
+                <span class="s1">&#39;http://nar.oxfordjournals.org/content/37/suppl_1/D623.long&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;http://nar.oxfordjournals.org/content/39/suppl_1/D712.long&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;http://nar.oxfordjournals.org/content/41/D1/D793.long&#39;</span>
+            <span class="p">],</span>
+            <span class="s1">&#39;omictools&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;http://omictools.com/consensuspathdb-tool&#39;</span><span class="p">]</span>
+        <span class="p">},</span>
+        <span class="s1">&#39;taxons&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;human&#39;</span><span class="p">,</span> <span class="s1">&#39;mouse&#39;</span><span class="p">,</span> <span class="s1">&#39;yeast&#39;</span><span class="p">],</span>
+        <span class="s1">&#39;pubmeds&#39;</span><span class="p">:</span> <span class="p">[</span><span class="mi">18940869</span><span class="p">,</span> <span class="mi">23143270</span><span class="p">,</span> <span class="mi">21071422</span><span class="p">],</span>
+        <span class="s1">&#39;descriptions&#39;</span><span class="p">:</span> <span class="p">[</span>
+<span class="w">            </span><span class="sd">&#39;&#39;&#39;</span>
+<span class="sd">            Interaction data in ConsensusPathDB currently originates from 12 interaction databases and comprises physical interactions, biochemical reactions and gene regulations. Importantly, the source of physical entities and interactions is always recorded, which allows linking to the original data in the source database.</span>
+<span class="sd">            In order to assess the content overlap of the source databases and to reduce redundancy, we have applied a method to merge identical physical entities and identify similar interactions. The method is straightforward and efficient for the integration of networks from any single species. Simple physical entities of the same type (genes, proteins, transcripts, metabolites) are compared on the basis of common database identifiers like UniProt, Ensembl, Entrez, ChEBI, etc. Since different databases tend to annotate physical entities with different identifier types (e.g. some databases annotate proteins with UniProt identifiers, others with Ensembl identifiers), we first translated the annotations to a uniform identifier type, which is a UniProt entry name in case of proteins, Ensembl gene ID in case of genes and transcripts, and KEGG/ChEBI ID in case of metabolites. Protein complexes are compared according to their individual protein composition. Simple physical entities with the same identifier, and complexes with the same composition, are merged in ConsensusPathDB. Information provided by the according source databases for the merged entities is stored in a complementary manner.</span>
+<span class="sd">            Functional interactions of physical entities are also compared with each other. Here, we distinguish between primary and secondary interaction participants. Primary participants are substrates and products in case of biochemical reactions, interactors in case of physical interactions and target genes in case of gene regulation. All other participants, e.g. enzymes and interaction modifiers, are secondary participants. If the primary participants of two or more interactions match, these interactions are considered similar. Two similar interactions may have different stoichiometry, modification and/or localization of the participants. To allow for flexibility, similar interactions are marked as such in the database, but the decision whether they should be considered identical despite mismatching details is left to the user and depends on his specific problem. Moreover, ConsensusPathDB does not provide any additional quality control filters. All interactions provided by the different database sources are treated in the same way.</span>
+<span class="sd">            &#39;&#39;&#39;</span>
+        <span class="p">],</span>
+        <span class="s1">&#39;notes&#39;</span><span class="p">:</span> <span class="p">[</span>
+<span class="w">            </span><span class="sa">u</span><span class="sd">&#39;&#39;&#39;</span>
+<span class="sd">            ConsensusPathDB comprises data from 32 resources. The format is easy to use, tab delimited text file, with UniProtKB names and PubMed IDs. However, the dataset is extremely huge, and several databases containing HTP data is included.</span>
+<span class="sd">            &#39;&#39;&#39;</span>
+        <span class="p">],</span>
+        <span class="s1">&#39;type&#39;</span><span class="p">:</span> <span class="s1">&#39;literature curated&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;subtype&#39;</span><span class="p">:</span> <span class="s1">&#39;activity flow&#39;</span><span class="p">,</span>
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+        <span class="s1">&#39;year&#39;</span><span class="p">:</span> <span class="mi">2016</span><span class="p">,</span>
+        <span class="s1">&#39;releases&#39;</span><span class="p">:</span>
+        <span class="p">[</span><span class="mi">2003</span><span class="p">,</span> <span class="mi">2006</span><span class="p">,</span> <span class="mi">2008</span><span class="p">,</span> <span class="mi">2009</span><span class="p">,</span> <span class="mi">2010</span><span class="p">,</span> <span class="mi">2011</span><span class="p">,</span> <span class="mi">2012</span><span class="p">,</span> <span class="mi">2013</span><span class="p">,</span> <span class="mi">2014</span><span class="p">,</span> <span class="mi">2015</span><span class="p">,</span> <span class="mi">2016</span><span class="p">],</span>
+        <span class="s1">&#39;size&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;nodes&#39;</span><span class="p">:</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="s1">&#39;edges&#39;</span><span class="p">:</span> <span class="kc">None</span>
+        <span class="p">},</span>
+        <span class="s1">&#39;authors&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;EBI&#39;</span><span class="p">],</span>
+        <span class="s1">&#39;label&#39;</span><span class="p">:</span> <span class="s1">&#39;IntAct&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;full_name&#39;</span><span class="p">:</span> <span class="s1">&#39;IntAct Molecular Interaction Database&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;data_import&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;InnateDB&#39;</span><span class="p">,</span> <span class="s1">&#39;MINT&#39;</span><span class="p">],</span>
+        <span class="s1">&#39;urls&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;articles&#39;</span><span class="p">:</span> <span class="p">[</span>
+                <span class="s1">&#39;http://nar.oxfordjournals.org/content/42/D1/D358.long&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;http://nar.oxfordjournals.org/content/40/D1/D841.long&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;http://nar.oxfordjournals.org/content/38/suppl_1/D525.long&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;http://nar.oxfordjournals.org/content/35/suppl_1/D561.long&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;http://nar.oxfordjournals.org/content/32/suppl_1/D452.long&#39;</span>
+            <span class="p">],</span>
+            <span class="s1">&#39;webpages&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;http://www.ebi.ac.uk/intact/&#39;</span><span class="p">],</span>
+            <span class="s1">&#39;omictools&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;http://omictools.com/intact-tool&#39;</span><span class="p">]</span>
+        <span class="p">},</span>
+        <span class="s1">&#39;pubmeds&#39;</span><span class="p">:</span> <span class="p">[</span><span class="mi">14681455</span><span class="p">,</span> <span class="mi">17145710</span><span class="p">,</span> <span class="mi">19850723</span><span class="p">,</span> <span class="mi">22121220</span><span class="p">,</span> <span class="mi">24234451</span><span class="p">],</span>
+        <span class="s1">&#39;annot&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;experiment&#39;</span><span class="p">,</span> <span class="s1">&#39;mechanism&#39;</span><span class="p">],</span>
+        <span class="s1">&#39;recommend&#39;</span><span class="p">:</span>
+        <span class="s1">&#39;the largest interaction resource; highest coverage on the human proteome; miscore confidence score&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;descriptions&#39;</span><span class="p">:</span> <span class="p">[</span>
+<span class="w">            </span><span class="sa">u</span><span class="sd">&#39;&#39;&#39;</span>
+<span class="sd">            The information within the IntAct database primarily consists of protein–protein interaction (PPI) data. The majority of the PPI data within the database is annotated to IMEx standards, as agreed by the IMEx consortium. All such records contain a full description of the experimental conditions in which the interaction was observed. This includes full details of the constructs used in each experiment, such as the presence and position of tags, the minimal binding region defined by deletion mutants and the effect of any point mutations, referenced to UniProtKB, the underlying protein sequence database. Protein interactions can be described down to the isoform level, or indeed to the post-translationally cleaved mature peptide level if such information is available in the publication, using the appropriate UniProtKB identifiers.</span>
+<span class="sd">            Each entry in IntAct is peer reviewed by a senior curator, and not released until accepted by that curator. Additional rule-based checks are run at the database level, and manually fixed when necessary. Finally, on release of the data, the original author of each publication is contacted and asked to comment on the representation of their data; again manual updates are made to the entry should the author highlight any errors.</span>
+<span class="sd">            All binary interactions evidences in the IntAct database, including those generated by Spoke expansion of co-complex data, are clustered to produce a non-redundant set of protein pairs (R. C. Jimenez et al., manuscript in preparation). Each binary pair is then scored, using a simple addition of the cumulated value of a weighted score for the interaction detection method and the interaction type for each interaction evidence associated with that binary pair, as described using the PSI-MI CV terms. The scores are given in Table 1, all children of each given parent receives that score. Only experimental data is scored, inferred interactions, for example, would be excluded. Any low confidence data or data manually tagged by a curator for exclusion from the process, would not be scored. Isoforms and post-processed protein chains are regarded as distinct proteins for scoring purposes.</span>
+<span class="sd">            &#39;&#39;&#39;</span>
+        <span class="p">],</span>
+        <span class="s1">&#39;notes&#39;</span><span class="p">:</span> <span class="p">[</span>
+<span class="w">            </span><span class="sa">u</span><span class="sd">&#39;&#39;&#39;</span>
+<span class="sd">            We can not draw a sharp distinction between low and high throughput methods, and I can agree, that this is not the only and best measure of quality considering experimental data. I see that IntAct came up with a good solution to estimate the confidence of interactions. The mi-score system gives a comprehensive way to synthetize information from multiple experiments, and weight interactions according to experimental methods, interaction type, and number of evidences.</span>
+<span class="sd">            &#39;&#39;&#39;</span>
+        <span class="p">],</span>
+        <span class="s1">&#39;type&#39;</span><span class="p">:</span> <span class="s1">&#39;literature curated and high-throughput&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;subtype&#39;</span><span class="p">:</span> <span class="s1">&#39;interaction&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;omnipath&#39;</span><span class="p">:</span> <span class="kc">True</span><span class="p">,</span>
+        <span class="s1">&#39;emails&#39;</span><span class="p">:</span> <span class="p">[(</span><span class="s1">&#39;orchard@ebi.ac.uk&#39;</span><span class="p">,</span> <span class="s1">&#39;Sandra Orchard&#39;</span><span class="p">),</span>
+                   <span class="p">(</span><span class="s1">&#39;hhe@ebi.ac.uk&#39;</span><span class="p">,</span> <span class="s1">&#39;Henning Hermjakob&#39;</span><span class="p">)],</span>
+        <span class="s1">&#39;license&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;name&#39;</span><span class="p">:</span> <span class="s1">&#39;CC-Attribution 4.0&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;url&#39;</span><span class="p">:</span> <span class="s1">&#39;https://creativecommons.org/licenses/by/4.0/&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;commercial_use&#39;</span><span class="p">:</span> <span class="kc">True</span>
+        <span class="p">},</span>
+        <span class="s1">&#39;pathguide&#39;</span><span class="p">:</span> <span class="mi">111</span><span class="p">,</span>
+        <span class="s1">&#39;pypath&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;data&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;pypath.data/intact_filtered.csv&#39;</span><span class="p">],</span>
+            <span class="s1">&#39;format&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;pypath.data_formats.interaction_misc[</span><span class="se">\&#39;</span><span class="s1">intact</span><span class="se">\&#39;</span><span class="s1">]&#39;</span><span class="p">]</span>
+        <span class="p">}</span>
+    <span class="p">},</span>
+    <span class="s1">&#39;MatrixDB&#39;</span><span class="p">:</span> <span class="p">{</span>
+        <span class="s1">&#39;year&#39;</span><span class="p">:</span> <span class="mi">2015</span><span class="p">,</span>
+        <span class="s1">&#39;releases&#39;</span><span class="p">:</span> <span class="p">[</span><span class="mi">2009</span><span class="p">,</span> <span class="mi">2011</span><span class="p">,</span> <span class="mi">2015</span><span class="p">],</span>
+        <span class="s1">&#39;urls&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;articles&#39;</span><span class="p">:</span> <span class="p">[</span>
+                <span class="s1">&#39;http://bioinformatics.oxfordjournals.org/content/25/5/690.long&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;http://nar.oxfordjournals.org/content/43/D1/D321.long&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;http://nar.oxfordjournals.org/content/39/suppl_1/D235.long&#39;</span>
+            <span class="p">],</span>
+            <span class="s1">&#39;webpages&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;http://matrixdb.univ-lyon1.fr/&#39;</span><span class="p">],</span>
+            <span class="s1">&#39;omictools&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;http://omictools.com/matrixdb-tool&#39;</span><span class="p">]</span>
+        <span class="p">},</span>
+        <span class="s1">&#39;pubmeds&#39;</span><span class="p">:</span> <span class="p">[</span><span class="mi">19147664</span><span class="p">,</span> <span class="mi">20852260</span><span class="p">,</span> <span class="mi">25378329</span><span class="p">],</span>
+        <span class="s1">&#39;taxons&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;mammalia&#39;</span><span class="p">],</span>
+        <span class="s1">&#39;annot&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;experiment&#39;</span><span class="p">],</span>
+        <span class="s1">&#39;recommend&#39;</span><span class="p">:</span>
+        <span class="s1">&#39;small, literature curated interaction resource; many interactions for receptors and extracellular proteins&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;descriptions&#39;</span><span class="p">:</span> <span class="p">[</span>
+<span class="w">            </span><span class="sa">u</span><span class="sd">&#39;&#39;&#39;</span>
+<span class="sd">            Protein data were imported from the UniProtKB/Swiss-Prot database (Bairoch et al., 2005) and identified by UniProtKB/SwissProt accession numbers. In order to list all the partners of a protein, interactions are associated by default to the accession number of the human protein. The actual source species used in experiments is indicated in the page reporting interaction data. Intracellular and membrane proteins were included to obtain a comprehensive network of the partners of extracellular molecules. Indeed, ECM proteins and GAGs bind to a number of membrane proteins or cell-associated proteoglycans and some of them interact with intracellular partners upon internalization (Dixelius et al., 2000). ECM proteins were identified by the UniProtKB/Swiss-Prot keyword ‘extracellular matrix’ and by the GO terms ‘extracellular matrix’, ‘proteinaceous extracellular matrix’ and their child terms. The proteins annotated with the GO terms ‘extracellular region’ and ‘extracellular space’, which are used for proteins found in biological fluids, were not included because circulating molecules do not directly contribute to the extracellular scaffold. Additionally, 96 proteins were manually (re-)annotated through literature curation. MatrixDB integrates 1378 interactions from the Human Protein Reference Database (HPRD, Prasad et al., 2009), 211 interactions from the Molecular INTeraction database (MINT, Chatr-Aryamontri et al., 2007), 46 interactions from the Database of Interacting Proteins (DIP, Salwinski et al., 2004), 232 interactions from IntAct (Kerrien et al., 2007a) and 839 from BioGRID (Breitkreutz et al., 2008) involving at least one extracellular biomolecule of mammalian origin. We added 283 interactions from manual literature curation and 65 interactions from protein and GAG array experiments.</span>
+<span class="sd">            &#39;&#39;&#39;</span><span class="p">,</span> <span class="sa">u</span><span class="s1">&#39;&#39;&#39;</span>
+<span class="s1">            Interaction data stored in MatrixDB are (i) experimentally determined in the laboratory using surface plasmon resonance (SPR) binding assays, including protein and glycosaminoglycan arrays probed by SPR imaging, (ii) extracted from the literature by manual curation and (iii) imported from other interaction databases belonging to the IMEx consortium [IntAct, DIP, MINT, BioGRID], as well as from the Human Protein Reference Database. Imported data are restricted to interactions involving at least one extracellular protein.</span>
+<span class="s1">            &#39;&#39;&#39;</span><span class="p">,</span> <span class="sa">u</span><span class="s1">&#39;&#39;&#39;</span>
+<span class="s1">            The content of MatrixDB has been updated with new interaction data manually curated by the MatrixDB team, and by importing interaction data from four interaction databases of the IMEx consortium via The Proteomics Standard Initiative Common QUery InterfaCe (PSICQUIC), a community standard for computational access to molecular-interaction data resources.  In the current release MatrixDB contains 904 interactions supported by 1244 experiments, which have been manually curated from 237 publications, compared to 490 interactions supported by 847 experiments in the previous version of the database. This is the MatrixDB ‘core’ data set.</span>
+<span class="s1">            &#39;&#39;&#39;</span>
+        <span class="p">],</span>
+        <span class="s1">&#39;notes&#39;</span><span class="p">:</span> <span class="p">[</span>
+<span class="w">            </span><span class="sa">u</span><span class="sd">&#39;&#39;&#39;</span>
+<span class="sd">            Very nice! Note: The interactions imported from IMEX databases or any other database, are collected separately, in the PSICQUIC-extended dataset. The MatrixDB-core dataset is curated manually by the MatrixDB team.</span>
+<span class="sd">            &#39;&#39;&#39;</span>
+        <span class="p">],</span>
+        <span class="s1">&#39;type&#39;</span><span class="p">:</span> <span class="s1">&#39;literature curated&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;subtype&#39;</span><span class="p">:</span> <span class="s1">&#39;interaction&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;data_integration&#39;</span><span class="p">:</span> <span class="s1">&#39;static&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;omnipath&#39;</span><span class="p">:</span> <span class="kc">True</span><span class="p">,</span>
+        <span class="s1">&#39;emails&#39;</span><span class="p">:</span> <span class="p">[(</span><span class="s1">&#39;matrixdb@ibcp.fr&#39;</span><span class="p">,</span> <span class="s1">&#39;MatrixDB Team&#39;</span><span class="p">),</span>
+                   <span class="p">(</span><span class="s1">&#39;sylvie.ricard-blum@ibcp.fr&#39;</span><span class="p">,</span> <span class="s1">&#39;Sylvie Ricard-Blum&#39;</span><span class="p">)],</span>
+        <span class="s1">&#39;license&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;name&#39;</span><span class="p">:</span> <span class="s1">&#39;CC BY 4.0&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;url&#39;</span><span class="p">:</span> <span class="s1">&#39;https://creativecommons.org/licenses/by/4.0/&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;commercial_use&#39;</span><span class="p">:</span> <span class="kc">True</span>
+        <span class="p">},</span>
+        <span class="s1">&#39;pypath&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;format&#39;</span><span class="p">:</span> <span class="p">[</span>
+                <span class="s1">&#39;pypath.data_formats.interaction[</span><span class="se">\&#39;</span><span class="s1">matrixdb</span><span class="se">\&#39;</span><span class="s1">]&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;pypath.data_formats.omnipath[</span><span class="se">\&#39;</span><span class="s1">matrixdb</span><span class="se">\&#39;</span><span class="s1">]&#39;</span>
+            <span class="p">],</span>
+            <span class="s1">&#39;data&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;pypath.data/matrixdb_core.csv&#39;</span><span class="p">]</span>
+        <span class="p">},</span>
+        <span class="s1">&#39;pathguide&#39;</span><span class="p">:</span> <span class="mi">298</span>
+    <span class="p">},</span>
+    <span class="s1">&#39;PathwayCommons&#39;</span><span class="p">:</span> <span class="p">{</span>
+        <span class="s1">&#39;year&#39;</span><span class="p">:</span> <span class="mi">2016</span><span class="p">,</span>
+        <span class="s1">&#39;releases&#39;</span><span class="p">:</span> <span class="p">[</span><span class="mi">2010</span><span class="p">,</span> <span class="mi">2011</span><span class="p">,</span> <span class="mi">2012</span><span class="p">,</span> <span class="mi">2013</span><span class="p">,</span> <span class="mi">2014</span><span class="p">,</span> <span class="mi">2015</span><span class="p">,</span> <span class="mi">2016</span><span class="p">],</span>
+        <span class="s1">&#39;urls&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;webpages&#39;</span><span class="p">:</span> <span class="p">[</span>
+                <span class="s1">&#39;http://www.pathwaycommons.org/pc2/&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;http://www.pathwaycommons.org/about/&#39;</span>
+            <span class="p">],</span>
+            <span class="s1">&#39;articles&#39;</span><span class="p">:</span>
+            <span class="p">[</span><span class="s1">&#39;http://nar.oxfordjournals.org/content/39/suppl_1/D685.long&#39;</span><span class="p">],</span>
+            <span class="s1">&#39;omictools&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;http://omictools.com/pathway-commons-tool&#39;</span><span class="p">]</span>
+        <span class="p">},</span>
+        <span class="s1">&#39;label&#39;</span><span class="p">:</span> <span class="s1">&#39;PathwayCommons&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;authors&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;Bader Lab&#39;</span><span class="p">,</span> <span class="s1">&#39;MSKCC cBio&#39;</span><span class="p">],</span>
+        <span class="s1">&#39;notes&#39;</span><span class="p">:</span> <span class="p">[</span>
+<span class="w">            </span><span class="sa">u</span><span class="sd">&#39;&#39;&#39;</span>
+<span class="sd">            Pathway Commons is a collection of publicly available pathway information from multiple organisms. It provides researchers with convenient access to a comprehensive collection of biological pathways from multiple sources represented in a common language for gene and metabolic pathway analysis.</span>
+<span class="sd">            &#39;&#39;&#39;</span><span class="p">,</span> <span class="sa">u</span><span class="s1">&#39;&#39;&#39;</span>
+<span class="s1">            Pathway Commons integrates a number of pathway and molecular interaction databases supporting BioPAX and PSI-MI formats into one large BioPAX model, which can be queried using our web API (documented below). This API can be used by computational biologists to download custom subsets of Pathway Commons for analysis, or can be used to incorporate powerful biological pathway and network information retrieval and query functionality into websites, scripts and software. For computational biologists looking for comprehensive biological pathway data for analysis, we also make available batch downloads of the data in several formats.</span>
+<span class="s1">            &#39;&#39;&#39;</span><span class="p">,</span> <span class="sa">u</span><span class="s1">&#39;&#39;&#39;</span>
+<span class="s1">            Warehouse data (canonical molecules, ontologies) are converted to BioPAX utility classes, such as EntityReference, ControlledVocabulary, EntityFeature sub-classes, and saved as the initial BioPAX model, which forms the foundation for integrating pathway data and for id-mapping.</span>
+<span class="s1">            Pathway and binary interaction data (interactions, participants) are normalized next and merged into the database. Original reference molecules are replaced with the corresponding BioPAX warehouse objects.</span>
+<span class="s1">            &#39;&#39;&#39;</span>
+        <span class="p">],</span>
+        <span class="s1">&#39;data_import&#39;</span><span class="p">:</span> <span class="p">[</span>
+            <span class="s1">&#39;Reactome&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;NCI-PID&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;CancerCellMap&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;BioCarta&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;HPRD&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;PhosphoSite&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;PANTHER&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;DIP&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;IntAct&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;BioGRID&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;BIND&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;CORUM&#39;</span><span class="p">,</span>
+        <span class="p">],</span>
+        <span class="s1">&#39;license&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;name&#39;</span><span class="p">:</span> <span class="s1">&#39;Constituting databases carry their own licenses.&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;url&#39;</span><span class="p">:</span> <span class="s1">&#39;https://www.pathwaycommons.org/pc2/datasources&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;commercial_use&#39;</span><span class="p">:</span> <span class="kc">False</span> <span class="c1"># Partially</span>
+        <span class="p">},</span>
+        <span class="s1">&#39;type&#39;</span><span class="p">:</span> <span class="s1">&#39;combined&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;subtype&#39;</span><span class="p">:</span> <span class="s1">&#39;interaction&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;pubmeds&#39;</span><span class="p">:</span> <span class="p">[</span><span class="mi">21071392</span><span class="p">],</span>
+        <span class="s1">&#39;omnipath&#39;</span><span class="p">:</span> <span class="kc">False</span><span class="p">,</span>
+        <span class="s1">&#39;emails&#39;</span><span class="p">:</span> <span class="p">[(</span><span class="s1">&#39;gary.bader@utoronto.ca&#39;</span><span class="p">,</span> <span class="s1">&#39;Gary Bader&#39;</span><span class="p">)],</span>
+        <span class="s1">&#39;pathguide&#39;</span><span class="p">:</span> <span class="mi">293</span>
+    <span class="p">},</span>
+    <span class="s1">&#39;Laudanna&#39;</span><span class="p">:</span> <span class="p">{</span>
+        <span class="s1">&#39;year&#39;</span><span class="p">:</span> <span class="mi">2014</span><span class="p">,</span>
+        <span class="s1">&#39;releases&#39;</span><span class="p">:</span> <span class="p">[</span><span class="mi">2014</span><span class="p">],</span>
+        <span class="s1">&#39;urls&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;webpages&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;http://dp.univr.it/~laudanna/LCTST/downloads/&#39;</span><span class="p">]</span>
+        <span class="p">},</span>
+        <span class="s1">&#39;full_name&#39;</span><span class="p">:</span>
+        <span class="s1">&#39;Compiled Datasets for Network Analysis from Laudanna Lab&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;authors&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;Laudanna Lab&#39;</span><span class="p">],</span>
+        <span class="s1">&#39;type&#39;</span><span class="p">:</span> <span class="s1">&#39;combined&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;subtype&#39;</span><span class="p">:</span> <span class="s1">&#39;mixed&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;notes&#39;</span><span class="p">:</span> <span class="p">[</span>
+<span class="w">            </span><span class="sd">&#39;&#39;&#39;</span>
+<span class="sd">            Data sets are compiled from public data-bases and from literature and manually curated for accuracy. They are intended for network reconstruction, topological and multidimensional analysis in cell biology.</span>
+<span class="sd">            &#39;&#39;&#39;</span>
+        <span class="p">],</span>
+        <span class="s1">&#39;omnipath&#39;</span><span class="p">:</span> <span class="kc">False</span><span class="p">,</span>
+        <span class="s1">&#39;data_import&#39;</span><span class="p">:</span> <span class="p">[</span>
+            <span class="s1">&#39;BioGRID&#39;</span><span class="p">,</span> <span class="s1">&#39;ConsensusPathDB&#39;</span><span class="p">,</span> <span class="s1">&#39;dbPTM&#39;</span><span class="p">,</span> <span class="s1">&#39;DIP&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;HumanSignalingNetwork&#39;</span><span class="p">,</span> <span class="s1">&#39;IntAct&#39;</span><span class="p">,</span> <span class="s1">&#39;MINT&#39;</span><span class="p">,</span> <span class="s1">&#39;MPPI&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;PathwayCommons&#39;</span><span class="p">,</span> <span class="s1">&#39;phospho.ELM&#39;</span><span class="p">,</span> <span class="s1">&#39;PhosphoPoint&#39;</span><span class="p">,</span> <span class="s1">&#39;PhosphoSite&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;SignaLink&#39;</span>
+        <span class="p">],</span>
+        <span class="s1">&#39;emails&#39;</span><span class="p">:</span> <span class="p">[(</span><span class="s1">&#39;giovanni.scardoni@gmail.com&#39;</span><span class="p">,</span> <span class="s1">&#39;Giovanni Scardoni&#39;</span><span class="p">)],</span>
+        <span class="s1">&#39;license&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;name&#39;</span><span class="p">:</span> <span class="s1">&#39;CC-Attribution-NonCommercial 4.0&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;url&#39;</span><span class="p">:</span> <span class="s1">&#39;https://creativecommons.org/licenses/by-nc/4.0/&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;commercial_use&#39;</span><span class="p">:</span> <span class="kc">False</span>
+        <span class="p">},</span>
+        <span class="s1">&#39;pypath&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;data&#39;</span><span class="p">:</span> <span class="p">[</span>
+                <span class="s1">&#39;pypath.urls.urls[</span><span class="se">\&#39;</span><span class="s1">sigflow</span><span class="se">\&#39;</span><span class="s1">]&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;pypath.urls.urls[</span><span class="se">\&#39;</span><span class="s1">sigdir</span><span class="se">\&#39;</span><span class="s1">]&#39;</span>
+            <span class="p">],</span>
+            <span class="s1">&#39;input&#39;</span><span class="p">:</span> <span class="p">[</span>
+                <span class="s1">&#39;pypath.dataio.get_laudanna_directions()&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;pypath.dataio.get_laudanna_effects()&#39;</span>
+            <span class="p">],</span>
+            <span class="s1">&#39;misc&#39;</span><span class="p">:</span> <span class="p">[</span>
+                <span class="s1">&#39;pypath.pypath.PyPath().laudanna_directions()&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;pypath.pypath.PyPath().laudanna_effects()&#39;</span>
+            <span class="p">]</span>
+        <span class="p">}</span>
+    <span class="p">},</span>
+    <span class="s1">&#39;ORegAnno&#39;</span><span class="p">:</span> <span class="p">{</span>
+        <span class="s1">&#39;year&#39;</span><span class="p">:</span> <span class="mi">2016</span><span class="p">,</span>
+        <span class="s1">&#39;urls&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;articles&#39;</span><span class="p">:</span> <span class="p">[</span>
+                <span class="s1">&#39;https://academic.oup.com/nar/article/44/D1/D126/2502683&#39;</span><span class="p">,</span>
+            <span class="p">],</span>
+            <span class="s1">&#39;webpages&#39;</span><span class="p">:</span> <span class="p">[</span>
+                <span class="s1">&#39;http://www.oreganno.org/&#39;</span><span class="p">,</span>
+            <span class="p">]</span>
+        <span class="p">},</span>
+        <span class="s1">&#39;emails&#39;</span><span class="p">:</span> <span class="p">[(</span><span class="s1">&#39;ogriffit@genome.wustl.edu&#39;</span><span class="p">,</span> <span class="s1">&#39;Obi L. Griffith&#39;</span><span class="p">)],</span>
+        <span class="s1">&#39;type&#39;</span><span class="p">:</span> <span class="s1">&#39;literature curated &amp; high throughput&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;subtype&#39;</span><span class="p">:</span> <span class="s1">&#39;transcription regulation&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;full_name&#39;</span><span class="p">:</span> <span class="s1">&#39;Open Regulatory Annotation&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;omnipath&#39;</span><span class="p">:</span> <span class="kc">False</span><span class="p">,</span>
+        <span class="s1">&#39;dorothea&#39;</span><span class="p">:</span> <span class="kc">True</span><span class="p">,</span>
+        <span class="s1">&#39;pubmeds&#39;</span><span class="p">:</span> <span class="p">[</span><span class="mi">26578589</span><span class="p">],</span>
+        <span class="s1">&#39;license&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;name&#39;</span><span class="p">:</span> <span class="s1">&#39;GNU LGPLv3&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;url&#39;</span><span class="p">:</span> <span class="s1">&#39;http://www.gnu.org/licenses/license-list.html#LGPLv3&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;commercial_use&#39;</span><span class="p">:</span> <span class="kc">True</span>
+        <span class="p">},</span>
+        <span class="s1">&#39;notes&#39;</span><span class="p">:</span> <span class="p">[</span>
+<span class="w">            </span><span class="sd">&#39;&#39;&#39;</span>
+<span class="sd">            One of the largest TF-target databases. Covers at least 18</span>
+<span class="sd">            organisms and contains data from literature curation and many</span>
+<span class="sd">            screening technologies and in silico prediction.</span>
+<span class="sd">            &#39;&#39;&#39;</span>
+        <span class="p">],</span>
+        <span class="s1">&#39;pypath&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;data&#39;</span><span class="p">:</span> <span class="p">[</span>
+                <span class="s1">&#39;pypath.urls.urls[</span><span class="se">\&#39;</span><span class="s1">oreganno</span><span class="se">\&#39;</span><span class="s1">]&#39;</span><span class="p">,</span>
+            <span class="p">],</span>
+            <span class="s1">&#39;input&#39;</span><span class="p">:</span> <span class="p">[</span>
+                <span class="s1">&#39;pypath.dataio.get_oreganno()&#39;</span><span class="p">,</span>
+            <span class="p">],</span>
+        <span class="p">},</span>
+        <span class="s1">&#39;omictools&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;https://omictools.com/oreganno-tool&#39;</span><span class="p">],</span>
+    <span class="p">},</span>
+    <span class="s1">&#39;PAZAR&#39;</span><span class="p">:</span> <span class="p">{</span>
+        <span class="s1">&#39;year&#39;</span><span class="p">:</span> <span class="mi">2009</span><span class="p">,</span>
+        <span class="s1">&#39;releases&#39;</span><span class="p">:</span> <span class="p">[</span><span class="mi">2007</span><span class="p">],</span>
+        <span class="s1">&#39;urls&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;articles&#39;</span><span class="p">:</span> <span class="p">[</span>
+                <span class="p">(</span>
+                    <span class="s1">&#39;https://genomebiology.biomedcentral.com/&#39;</span>
+                    <span class="s1">&#39;articles/10.1186/gb-2007-8-10-r207&#39;</span>
+                <span class="p">),</span>
+                <span class="s1">&#39;https://academic.oup.com/nar/article/37/suppl_1/D54/1010368&#39;</span><span class="p">,</span>
+            <span class="p">],</span>
+            <span class="s1">&#39;webpages&#39;</span><span class="p">:</span> <span class="p">[</span>
+                <span class="s1">&#39;http://www.pazar.info/&#39;</span><span class="p">,</span>
+            <span class="p">],</span>
+        <span class="p">},</span>
+        <span class="s1">&#39;emails&#39;</span><span class="p">:</span> <span class="p">[(</span><span class="s1">&#39;wyeth@cmmt.ubc.ca&#39;</span><span class="p">,</span> <span class="s1">&#39;Wyeth Wasserman&#39;</span><span class="p">)],</span>
+        <span class="s1">&#39;authors&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;Wasserman Lab&#39;</span><span class="p">],</span>
+        <span class="s1">&#39;type&#39;</span><span class="p">:</span> <span class="s1">&#39;literature curated &amp; high throughput&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;subtype&#39;</span><span class="p">:</span> <span class="s1">&#39;transcription regulation&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;full_name&#39;</span><span class="p">:</span> <span class="p">(</span>
+            <span class="s1">&#39;A Public Database of Transcription Factor &#39;</span>
+            <span class="s1">&#39;and Regulatory Sequence Annotation&#39;</span>
+        <span class="p">),</span>
+        <span class="s1">&#39;omnipath&#39;</span><span class="p">:</span> <span class="kc">False</span><span class="p">,</span>
+        <span class="s1">&#39;dorothea&#39;</span><span class="p">:</span> <span class="kc">True</span><span class="p">,</span>
+        <span class="s1">&#39;pubmeds&#39;</span><span class="p">:</span> <span class="p">[</span><span class="mi">18971253</span><span class="p">,</span> <span class="mi">17916232</span><span class="p">],</span>
+        <span class="s1">&#39;license&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;name&#39;</span><span class="p">:</span> <span class="s1">&#39;GNU LGPLv3&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;url&#39;</span><span class="p">:</span> <span class="s1">&#39;http://www.gnu.org/licenses/license-list.html#LGPLv3&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;commercial_use&#39;</span><span class="p">:</span> <span class="kc">True</span>
+        <span class="p">},</span>
+        <span class="s1">&#39;notes&#39;</span><span class="p">:</span> <span class="p">[</span>
+<span class="w">            </span><span class="sd">&#39;&#39;&#39;</span>
+<span class="sd">            One of the oldest and largest TF-target databases. From the</span>
+<span class="sd">            Wasserman Lab, who also developed JASPAR and many other tools.</span>
+<span class="sd">            Unfortunately the website is down at the moment (April 2019).</span>
+<span class="sd">            Which was, by the way, in that time (2007) a super nice and</span>
+<span class="sd">            innovative design for a molecular database webpage.</span>
+<span class="sd">            &#39;&#39;&#39;</span>
+        <span class="p">],</span>
+        <span class="s1">&#39;pypath&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;data&#39;</span><span class="p">:</span> <span class="p">[</span>
+                <span class="s1">&#39;pypath.urls.urls[</span><span class="se">\&#39;</span><span class="s1">pazar</span><span class="se">\&#39;</span><span class="s1">]&#39;</span><span class="p">,</span>
+            <span class="p">],</span>
+            <span class="s1">&#39;input&#39;</span><span class="p">:</span> <span class="p">[</span>
+                <span class="s1">&#39;pypath.dataio.get_pazar()&#39;</span><span class="p">,</span>
+            <span class="p">],</span>
+        <span class="p">},</span>
+        <span class="s1">&#39;omictools&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;http://omictools.com/pazar-tool&#39;</span><span class="p">],</span>
+    <span class="p">},</span>
+<span class="c1"># From here on, only license info</span>
+    <span class="s1">&#39;TRRUST&#39;</span><span class="p">:</span> <span class="p">{</span>
+        <span class="s1">&#39;license&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;name&#39;</span><span class="p">:</span> <span class="s1">&#39;CC-Attribution-ShareAlike 4.0&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;url&#39;</span><span class="p">:</span> <span class="s1">&#39;http://creativecommons.org/licenses/by-nc-sa/4.0/&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;commercial_use&#39;</span><span class="p">:</span> <span class="kc">True</span>
+        <span class="p">}</span>
+    <span class="p">},</span>
+    <span class="s1">&#39;HTRIdb&#39;</span><span class="p">:</span> <span class="p">{</span>
+        <span class="s1">&#39;license&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;name&#39;</span><span class="p">:</span> <span class="s1">&#39;GNU LGPLv3&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;url&#39;</span><span class="p">:</span> <span class="s1">&#39;http://www.gnu.org/licenses/license-list.html#LGPLv3&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;commercial_use&#39;</span><span class="p">:</span> <span class="kc">True</span>
+        <span class="p">}</span>
+    <span class="p">},</span>
+    <span class="s1">&#39;NFIRegulomeDB&#39;</span><span class="p">:</span> <span class="p">{</span>
+        <span class="s1">&#39;license&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;name&#39;</span><span class="p">:</span> <span class="s1">&#39;GNU LGPLv3&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;url&#39;</span><span class="p">:</span> <span class="s1">&#39;http://www.gnu.org/licenses/license-list.html#LGPLv3&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;commercial_use&#39;</span><span class="p">:</span> <span class="kc">True</span>
+        <span class="p">}</span>
+    <span class="p">},</span>
+    <span class="s1">&#39;TFe&#39;</span><span class="p">:</span> <span class="p">{</span>
+        <span class="s1">&#39;license&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;name&#39;</span><span class="p">:</span> <span class="s1">&#39;CC-Attribution-ShareAlike 3.0&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;url&#39;</span><span class="p">:</span> <span class="s1">&#39;https://creativecommons.org/licenses/by-sa/3.0/&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;commercial_use&#39;</span><span class="p">:</span> <span class="kc">True</span>
+        <span class="p">}</span>
+    <span class="p">},</span>
+    <span class="s1">&#39;TRRD&#39;</span><span class="p">:</span> <span class="p">{</span>
+        <span class="s1">&#39;license&#39;</span><span class="p">:</span> <span class="p">{</span><span class="c1"># Via TfactS</span>
+            <span class="s1">&#39;name&#39;</span><span class="p">:</span> <span class="s1">&#39;CC-Attribution 4.0&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;url&#39;</span><span class="p">:</span> <span class="s1">&#39;https://creativecommons.org/licenses/by/4.0/&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;commercial_use&#39;</span><span class="p">:</span> <span class="kc">True</span> <span class="c1"># Again, via TfactS</span>
+        <span class="p">}</span>
+    <span class="p">},</span>
+    <span class="s1">&#39;TRED&#39;</span><span class="p">:</span> <span class="p">{</span><span class="c1"># PENDING</span>
+        <span class="c1">#&#39;license&#39;: {</span>
+        <span class="c1">#    &#39;name&#39;: &#39;&#39;,</span>
+        <span class="c1">#    &#39;url&#39;: &#39;&#39;,</span>
+        <span class="c1">#    &#39;commercial_use&#39;: False</span>
+        <span class="c1">#}</span>
+    <span class="p">},</span>
+    <span class="s1">&#39;Fantom4&#39;</span><span class="p">:</span> <span class="p">{</span>
+        <span class="s1">&#39;license&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;name&#39;</span><span class="p">:</span> <span class="s1">&#39;CC-Attribution 4.0&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;url&#39;</span><span class="p">:</span> <span class="s1">&#39;http://creativecommons.org/licenses/by/4.0/&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;commercial_use&#39;</span><span class="p">:</span> <span class="kc">True</span>
+        <span class="p">}</span>
+    <span class="p">},</span>
+    <span class="s1">&#39;RegNetwork&#39;</span><span class="p">:</span> <span class="p">{</span><span class="c1"># PENDING</span>
+        <span class="c1">#&#39;license&#39;: {</span>
+        <span class="c1">#    &#39;name&#39;: &#39;&#39;,</span>
+        <span class="c1">#    &#39;url&#39;: &#39;&#39;,</span>
+        <span class="c1">#    &#39;commercial_use&#39;: False</span>
+        <span class="c1">#}</span>
+    <span class="p">},</span>
+    <span class="s1">&#39;TfactS&#39;</span><span class="p">:</span> <span class="p">{</span>
+        <span class="s1">&#39;license&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;name&#39;</span><span class="p">:</span> <span class="s1">&#39;CC-Attribution 4.0&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;url&#39;</span><span class="p">:</span> <span class="s1">&#39;https://creativecommons.org/licenses/by/4.0/&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;commercial_use&#39;</span><span class="p">:</span> <span class="kc">True</span>
+        <span class="p">}</span>
+    <span class="p">},</span>
+    <span class="s1">&#39;GeneOntology&#39;</span><span class="p">:</span> <span class="p">{</span>
+        <span class="s1">&#39;license&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;name&#39;</span><span class="p">:</span> <span class="s1">&#39;CC-Attribution 4.0&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;url&#39;</span><span class="p">:</span> <span class="s1">&#39;https://creativecommons.org/licenses/by/4.0/&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;commercial_use&#39;</span><span class="p">:</span> <span class="kc">True</span>
+        <span class="p">}</span>
+    <span class="p">},</span>
+    <span class="s1">&#39;Membranome&#39;</span><span class="p">:</span> <span class="p">{</span>
+        <span class="s1">&#39;license&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;name&#39;</span><span class="p">:</span> <span class="s1">&#39;Apache 2.0&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;url&#39;</span><span class="p">:</span> <span class="s1">&#39;http://www.apache.org/licenses/LICENSE-2.0.html&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;commercial_use&#39;</span><span class="p">:</span> <span class="kc">True</span>
+        <span class="p">}</span>
+    <span class="p">},</span>
+    <span class="s1">&#39;Exocarta&#39;</span><span class="p">:</span> <span class="p">{</span><span class="c1"># PENDING</span>
+        <span class="c1">#&#39;license&#39;: {</span>
+        <span class="c1">#    &#39;name&#39;: &#39;&#39;,</span>
+        <span class="c1">#    &#39;url&#39;: &#39;&#39;,</span>
+        <span class="c1">#    &#39;commercial_use&#39;: False</span>
+        <span class="c1">#}</span>
+    <span class="p">},</span>
+    <span class="s1">&#39;Vesiclepedia&#39;</span><span class="p">:</span> <span class="p">{</span><span class="c1"># PENDING</span>
+        <span class="c1">#&#39;license&#39;: {</span>
+        <span class="c1">#    &#39;name&#39;: &#39;&#39;,</span>
+        <span class="c1">#    &#39;url&#39;: &#39;&#39;,</span>
+        <span class="c1">#    &#39;commercial_use&#39;: False</span>
+        <span class="c1">#}</span>
+    <span class="p">},</span>
+    <span class="s1">&#39;Matrisome&#39;</span><span class="p">:</span> <span class="p">{</span><span class="c1"># PENDING</span>
+        <span class="c1">#&#39;license&#39;: {</span>
+        <span class="c1">#    &#39;name&#39;: &#39;&#39;,</span>
+        <span class="c1">#    &#39;url&#39;: &#39;&#39;,</span>
+        <span class="c1">#    &#39;commercial_use&#39;: False</span>
+        <span class="c1">#}</span>
+    <span class="p">},</span>
+    <span class="s1">&#39;CSPA&#39;</span><span class="p">:</span> <span class="p">{</span><span class="c1"># PENDING</span>
+        <span class="c1">#&#39;license&#39;: {</span>
+        <span class="c1">#    &#39;name&#39;: &#39;&#39;,</span>
+        <span class="c1">#    &#39;url&#39;: &#39;&#39;,</span>
+        <span class="c1">#    &#39;commercial_use&#39;: False</span>
+        <span class="c1">#}</span>
+    <span class="p">},</span>
+    <span class="s1">&#39;HPMR&#39;</span><span class="p">:</span> <span class="p">{</span>
+        <span class="s1">&#39;license&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;name&#39;</span><span class="p">:</span> <span class="s1">&#39;CC-Attribution-NonCommercial 4.0&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;url&#39;</span><span class="p">:</span> <span class="s1">&#39;https://creativecommons.org/licenses/by-nc/4.0/&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;commercial_use&#39;</span><span class="p">:</span> <span class="kc">False</span>
+        <span class="p">}</span>
+    <span class="p">},</span>
+    <span class="s1">&#39;LOCATE&#39;</span><span class="p">:</span> <span class="p">{</span><span class="c1"># PENDING</span>
+        <span class="c1">#&#39;license&#39;: {</span>
+        <span class="c1">#    &#39;name&#39;: &#39;&#39;,</span>
+        <span class="c1">#    &#39;url&#39;: &#39;&#39;,</span>
+        <span class="c1">#    &#39;commercial_use&#39;: False</span>
+        <span class="c1">#}</span>
+    <span class="p">},</span>
+    <span class="s1">&#39;CellPhoneDB&#39;</span><span class="p">:</span> <span class="p">{</span>
+        <span class="s1">&#39;license&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;name&#39;</span><span class="p">:</span> <span class="s1">&#39;MIT License&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;url&#39;</span><span class="p">:</span> <span class="s1">&#39;https://github.com/Teichlab/cellphonedb/blob/master/LICENSE&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;commercial_use&#39;</span><span class="p">:</span> <span class="kc">True</span>
+        <span class="p">}</span>
+    <span class="p">},</span>
+    <span class="s1">&#39;ComPPI&#39;</span><span class="p">:</span> <span class="p">{</span>
+        <span class="s1">&#39;license&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;name&#39;</span><span class="p">:</span> <span class="s1">&#39;CC-Attribution-ShareAlike 4.0&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;url&#39;</span><span class="p">:</span> <span class="s1">&#39;https://creativecommons.org/licenses/by-sa/4.0/&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;commercial_use&#39;</span><span class="p">:</span> <span class="kc">True</span>
+        <span class="p">}</span>
+    <span class="p">},</span>
+    <span class="s1">&#39;Kirouac2010&#39;</span><span class="p">:</span> <span class="p">{</span>
+        <span class="s1">&#39;license&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;name&#39;</span><span class="p">:</span> <span class="s1">&#39;CC-Attribution-NonCommercial-NoDerivs 3.0&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;url&#39;</span><span class="p">:</span> <span class="s1">&#39;https://creativecommons.org/licenses/by-nc-nd/3.0/&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;commercial_use&#39;</span><span class="p">:</span> <span class="kc">False</span>
+        <span class="p">}</span>
+    <span class="p">},</span>
+    <span class="s1">&#39;Ramilowski2015&#39;</span><span class="p">:</span> <span class="p">{</span>
+        <span class="s1">&#39;license&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;name&#39;</span><span class="p">:</span> <span class="s1">&#39;CC-Attribution 4.0&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;url&#39;</span><span class="p">:</span> <span class="s1">&#39;http://creativecommons.org/licenses/by/4.0/&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;commercial_use&#39;</span><span class="p">:</span> <span class="kc">True</span>
+        <span class="p">}</span>
+    <span class="p">},</span>
+    <span class="s1">&#39;Adhesome&#39;</span><span class="p">:</span> <span class="p">{</span><span class="c1"># PENDING</span>
+        <span class="c1">#&#39;license&#39;: {</span>
+        <span class="c1">#    &#39;name&#39;: &#39;&#39;,</span>
+        <span class="c1">#    &#39;url&#39;: &#39;&#39;,</span>
+        <span class="c1">#    &#39;commercial_use&#39;: False</span>
+        <span class="c1">#}</span>
+    <span class="p">},</span>
+    <span class="s1">&#39;Integrins&#39;</span><span class="p">:</span> <span class="p">{</span><span class="c1"># PENDING</span>
+        <span class="c1">#&#39;license&#39;: {</span>
+        <span class="c1">#    &#39;name&#39;: &#39;&#39;,</span>
+        <span class="c1">#    &#39;url&#39;: &#39;&#39;,</span>
+        <span class="c1">#    &#39;commercial_use&#39;: False</span>
+        <span class="c1">#}</span>
+    <span class="p">},</span>
+    <span class="s1">&#39;Zhong2015&#39;</span><span class="p">:</span> <span class="p">{</span><span class="c1"># PENDING</span>
+        <span class="c1">#&#39;license&#39;: {</span>
+        <span class="c1">#    &#39;name&#39;: &#39;&#39;,</span>
+        <span class="c1">#    &#39;url&#39;: &#39;&#39;,</span>
+        <span class="c1">#    &#39;commercial_use&#39;: False</span>
+        <span class="c1">#}</span>
+    <span class="p">},</span>
+    <span class="s1">&#39;HGNC&#39;</span><span class="p">:</span> <span class="p">{</span>
+        <span class="s1">&#39;license&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;name&#39;</span><span class="p">:</span> <span class="s1">&#39;Custom license&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;url&#39;</span><span class="p">:</span> <span class="s1">&#39;https://www.genenames.org/about/&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;commercial_use&#39;</span><span class="p">:</span> <span class="kc">True</span>
+        <span class="p">}</span>
+    <span class="p">},</span>
+    <span class="s1">&#39;TopDB&#39;</span><span class="p">:</span> <span class="p">{</span>
+        <span class="s1">&#39;license&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;name&#39;</span><span class="p">:</span> <span class="s1">&#39;CC-Attribution-NonCommercial 4.0&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;url&#39;</span><span class="p">:</span> <span class="s1">&#39;https://creativecommons.org/licenses/by-nc/4.0/&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;commercial_use&#39;</span><span class="p">:</span> <span class="kc">False</span>
+        <span class="p">}</span>
+    <span class="p">},</span>
+    <span class="s1">&#39;OPM&#39;</span><span class="p">:</span> <span class="p">{</span>
+        <span class="s1">&#39;license&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;name&#39;</span><span class="p">:</span> <span class="s1">&#39;Apache 2.0&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;url&#39;</span><span class="p">:</span> <span class="s1">&#39;http://www.apache.org/licenses/LICENSE-2.0.html&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;commercial_use&#39;</span><span class="p">:</span> <span class="kc">True</span>
+        <span class="p">}</span>
+    <span class="p">},</span>
+    <span class="s1">&#39;Havugimana&#39;</span><span class="p">:</span> <span class="p">{</span>
+        <span class="s1">&#39;license&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;name&#39;</span><span class="p">:</span> <span class="s1">&#39;CC-Attribution-ShareAlike 4.0&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;url&#39;</span><span class="p">:</span> <span class="s1">&#39;https://creativecommons.org/licenses/by-sa/4.0/&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;commercial_use&#39;</span><span class="p">:</span> <span class="kc">True</span>
+        <span class="p">}</span>
+    <span class="p">},</span>
+    <span class="s1">&#39;Compleat&#39;</span><span class="p">:</span> <span class="p">{</span>
+        <span class="s1">&#39;license&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;name&#39;</span><span class="p">:</span> <span class="s1">&#39;CC-Attribution-NonCommercial 4.0&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;url&#39;</span><span class="p">:</span> <span class="s1">&#39;https://creativecommons.org/licenses/by-nc/4.0/&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;commercial_use&#39;</span><span class="p">:</span> <span class="kc">False</span>
+        <span class="p">}</span>
+    <span class="p">},</span>
+    <span class="s1">&#39;ComplexPortal&#39;</span><span class="p">:</span> <span class="p">{</span>
+        <span class="s1">&#39;license&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;name&#39;</span><span class="p">:</span> <span class="s1">&#39;CC-Attribution 4.0&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;url&#39;</span><span class="p">:</span> <span class="s1">&#39;https://creativecommons.org/licenses/by/4.0/&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;commercial_use&#39;</span><span class="p">:</span> <span class="kc">True</span>
+        <span class="p">}</span>
+    <span class="p">},</span>
+    <span class="s1">&#39;HPA&#39;</span><span class="p">:</span> <span class="p">{</span>
+        <span class="s1">&#39;license&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;name&#39;</span><span class="p">:</span> <span class="s1">&#39;CC-Attribution-ShareAlike 3.0&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;url&#39;</span><span class="p">:</span> <span class="s1">&#39;https://creativecommons.org/licenses/by-sa/3.0/&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;commercial_use&#39;</span><span class="p">:</span> <span class="kc">True</span>
+        <span class="p">}</span>
+    <span class="p">},</span>
+    <span class="s1">&#39;PDB&#39;</span><span class="p">:</span> <span class="p">{</span>
+        <span class="s1">&#39;license&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;name&#39;</span><span class="p">:</span> <span class="s1">&#39;Custom license&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;url&#39;</span><span class="p">:</span> <span class="s1">&#39;https://www.wwpdb.org/about/privacy&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;commercial_use&#39;</span><span class="p">:</span> <span class="kc">True</span>
+        <span class="p">}</span>
+    <span class="p">},</span>
+    <span class="s1">&#39;Humap&#39;</span><span class="p">:</span> <span class="p">{</span>
+        <span class="s1">&#39;license&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;name&#39;</span><span class="p">:</span> <span class="s1">&#39;CC0-Attribution&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;url&#39;</span><span class="p">:</span> <span class="s1">&#39;https://creativecommons.org/share-your-work/public-domain/cc0/&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;commercial_use&#39;</span><span class="p">:</span> <span class="kc">True</span>
+        <span class="p">}</span>
+    <span class="p">},</span>
+    <span class="s1">&#39;PhosphoNetworks&#39;</span><span class="p">:</span> <span class="p">{</span>
+        <span class="s1">&#39;license&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;name&#39;</span><span class="p">:</span> <span class="s1">&#39;Custom license&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;url&#39;</span><span class="p">:</span> <span class="s1">&#39;https://phosphonetworks.org/about.html&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;commercial_use&#39;</span><span class="p">:</span> <span class="kc">False</span>
+        <span class="p">}</span>
+    <span class="p">},</span>
+    <span class="s1">&#39;MIMP&#39;</span><span class="p">:</span> <span class="p">{</span><span class="c1"># PENDING</span>
+        <span class="c1">#&#39;license&#39;: {</span>
+        <span class="c1">#    &#39;name&#39;: &#39;&#39;,</span>
+        <span class="c1">#    &#39;url&#39;: &#39;&#39;,</span>
+        <span class="c1">#    &#39;commercial_use&#39;: False</span>
+        <span class="c1">#}</span>
+    <span class="p">},</span>
+    <span class="s1">&#39;Li2012&#39;</span><span class="p">:</span> <span class="p">{</span>
+        <span class="s1">&#39;license&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;name&#39;</span><span class="p">:</span> <span class="s1">&#39;CC-Attribution-NonCommercial 3.0&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;url&#39;</span><span class="p">:</span> <span class="s1">&#39;https://creativecommons.org/licenses/by-nc/3.0/&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;commercial_use&#39;</span><span class="p">:</span> <span class="kc">False</span>
+        <span class="p">}</span>
+    <span class="p">},</span>
+    <span class="s1">&#39;UniProt&#39;</span><span class="p">:</span> <span class="p">{</span>
+        <span class="s1">&#39;license&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;name&#39;</span><span class="p">:</span> <span class="s1">&#39;CC-Attribution 4.0&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;url&#39;</span><span class="p">:</span> <span class="s1">&#39;http://creativecommons.org/licenses/by/4.0/&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;commercial_use&#39;</span><span class="p">:</span> <span class="kc">True</span>
+        <span class="p">}</span>
+    <span class="p">},</span>
+    <span class="s1">&#39;miRBase&#39;</span><span class="p">:</span> <span class="p">{</span>
+        <span class="s1">&#39;license&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;name&#39;</span><span class="p">:</span> <span class="s1">&#39;CC0&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;url&#39;</span><span class="p">:</span> <span class="s1">&#39;https://creativecommons.org/share-your-work/public-domain/cc0/&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;commercial_use&#39;</span><span class="p">:</span> <span class="kc">True</span>
+        <span class="p">}</span>
+    <span class="p">},</span>
+    <span class="s1">&#39;mir2Disease&#39;</span><span class="p">:</span> <span class="p">{</span><span class="c1"># PENDING</span>
+        <span class="c1">#&#39;license&#39;: {</span>
+        <span class="c1">#    &#39;name&#39;: &#39;&#39;,</span>
+        <span class="c1">#    &#39;url&#39;: &#39;&#39;,</span>
+        <span class="c1">#    &#39;commercial_use&#39;: False</span>
+        <span class="c1">#}</span>
+    <span class="p">},</span>
+    <span class="s1">&#39;miRDeatdhDB&#39;</span><span class="p">:</span> <span class="p">{</span><span class="c1"># PENDING</span>
+        <span class="c1">#&#39;license&#39;: {</span>
+        <span class="c1">#    &#39;name&#39;: &#39;&#39;,</span>
+        <span class="c1">#    &#39;url&#39;: &#39;&#39;,</span>
+        <span class="c1">#    &#39;commercial_use&#39;: False</span>
+        <span class="c1">#}</span>
+    <span class="p">},</span>
+    <span class="s1">&#39;TransmiR&#39;</span><span class="p">:</span> <span class="p">{</span>
+        <span class="s1">&#39;license&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;name&#39;</span><span class="p">:</span> <span class="s1">&#39;CC-Attribution-NonCommercial 4.0&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;url&#39;</span><span class="p">:</span> <span class="s1">&#39;https://creativecommons.org/licenses/by-nc/4.0/&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;commercial_use&#39;</span><span class="p">:</span> <span class="kc">False</span>
+        <span class="p">}</span>
+    <span class="p">},</span>
+    <span class="s1">&#39;ENCODE&#39;</span><span class="p">:</span> <span class="p">{</span>
+        <span class="s1">&#39;license&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;name&#39;</span><span class="p">:</span> <span class="s1">&#39;CC-Attribution 4.0&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;url&#39;</span><span class="p">:</span> <span class="s1">&#39;https://creativecommons.org/licenses/by/4.0/&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;commercial_use&#39;</span><span class="p">:</span> <span class="kc">True</span>
+        <span class="p">}</span>
+    <span class="p">},</span>
+    <span class="s1">&#39;lncRNADisease&#39;</span><span class="p">:</span> <span class="p">{</span><span class="c1"># PENDING</span>
+        <span class="c1">#&#39;license&#39;: {</span>
+        <span class="c1">#    &#39;name&#39;: &#39;&#39;,</span>
+        <span class="c1">#    &#39;url&#39;: &#39;&#39;,</span>
+        <span class="c1">#    &#39;commercial_use&#39;: False</span>
+        <span class="c1">#}</span>
+    <span class="p">},</span>
+    <span class="s1">&#39;lncrnadb&#39;</span><span class="p">:</span> <span class="p">{</span><span class="c1"># PENDING</span>
+        <span class="c1">#&#39;license&#39;: {</span>
+        <span class="c1">#    &#39;name&#39;: &#39;&#39;,</span>
+        <span class="c1">#    &#39;url&#39;: &#39;&#39;,</span>
+        <span class="c1">#    &#39;commercial_use&#39;: False</span>
+        <span class="c1">#}</span>
+    <span class="p">},</span>
+    <span class="s1">&#39;miRecords&#39;</span><span class="p">:</span> <span class="p">{</span>
+        <span class="s1">&#39;license&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;name&#39;</span><span class="p">:</span> <span class="s1">&#39;Custom license&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;url&#39;</span><span class="p">:</span> <span class="s1">&#39;http://c1.accurascience.com/miRecords/copyright.php&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;commercial_use&#39;</span><span class="p">:</span> <span class="kc">False</span>
+        <span class="p">}</span>
+    <span class="p">},</span>
+    <span class="s1">&#39;miRTarBase&#39;</span><span class="p">:</span> <span class="p">{</span>
+        <span class="s1">&#39;license&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;name&#39;</span><span class="p">:</span> <span class="s1">&#39;Custom license&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;url&#39;</span><span class="p">:</span> <span class="s1">&#39;http://mirtarbase.mbc.nctu.edu.tw/cache/download/LICENSE&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;commercial_use&#39;</span><span class="p">:</span> <span class="kc">False</span>
+        <span class="p">}</span>
+    <span class="p">},</span>
+    <span class="s1">&#39;HIPPIE&#39;</span><span class="p">:</span> <span class="p">{</span>
+        <span class="s1">&#39;license&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;name&#39;</span><span class="p">:</span> <span class="s1">&#39;CC-Attribution 4.0&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;url&#39;</span><span class="p">:</span> <span class="s1">&#39;https://creativecommons.org/licenses/by/4.0/&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;commercial_use&#39;</span><span class="p">:</span> <span class="kc">True</span>
+        <span class="p">}</span>
+    <span class="p">},</span>
+    <span class="s1">&#39;CPAD&#39;</span><span class="p">:</span> <span class="p">{</span>
+        <span class="s1">&#39;license&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;name&#39;</span><span class="p">:</span> <span class="s1">&#39;Custom license&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;url&#39;</span><span class="p">:</span> <span class="s1">&#39;https://www.iitm.ac.in/bioinfo/CPAD/&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;commercial_use&#39;</span><span class="p">:</span> <span class="kc">False</span>
+        <span class="p">}</span>
+    <span class="p">},</span>
+    <span class="s1">&#39;IntOGen&#39;</span><span class="p">:</span> <span class="p">{</span>
+        <span class="s1">&#39;license&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;name&#39;</span><span class="p">:</span> <span class="s1">&#39;CC-Attribution-NonCommercial 4.0&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;url&#39;</span><span class="p">:</span> <span class="s1">&#39;http://creativecommons.org/licenses/by-nc/4.0/&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;commercial_use&#39;</span><span class="p">:</span> <span class="kc">False</span>
+        <span class="p">}</span>
+    <span class="p">},</span>
+    <span class="s1">&#39;COSMIC&#39;</span><span class="p">:</span> <span class="p">{</span>
+        <span class="s1">&#39;license&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;name&#39;</span><span class="p">:</span> <span class="s1">&#39;Custom license&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;url&#39;</span><span class="p">:</span> <span class="s1">&#39;https://cancer.sanger.ac.uk/cosmic/license&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;commercial_use&#39;</span><span class="p">:</span> <span class="kc">False</span>
+        <span class="p">}</span>
+    <span class="p">},</span>
+    <span class="s1">&#39;DGIdb&#39;</span><span class="p">:</span> <span class="p">{</span>
+        <span class="s1">&#39;license&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;name&#39;</span><span class="p">:</span> <span class="s1">&#39;MIT license&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;url&#39;</span><span class="p">:</span> <span class="s1">&#39;https://github.com/griffithlab/dgi-db/blob/master/LICENSE&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;commercial_use&#39;</span><span class="p">:</span> <span class="kc">True</span>
+        <span class="p">}</span>
+    <span class="p">},</span>
+    <span class="s1">&#39;DisGeNet&#39;</span><span class="p">:</span> <span class="p">{</span>
+        <span class="s1">&#39;license&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;name&#39;</span><span class="p">:</span> <span class="s1">&#39;CC-Attribution-ShareAlike-NonCommercial 4.0&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;url&#39;</span><span class="p">:</span> <span class="s1">&#39;https://creativecommons.org/licenses/by-nc-sa/4.0/&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;commercial_use&#39;</span><span class="p">:</span> <span class="kc">False</span>
+        <span class="p">}</span>
+    <span class="p">},</span>
+    <span class="s1">&#39;kinase.com&#39;</span><span class="p">:</span> <span class="p">{</span>
+        <span class="s1">&#39;license&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;name&#39;</span><span class="p">:</span> <span class="s1">&#39;Custom license&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;url&#39;</span><span class="p">:</span> <span class="s1">&#39;http://kinase.com/about/Disclaimer.html&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;commercial_use&#39;</span><span class="p">:</span> <span class="kc">False</span>
+        <span class="p">}</span>
+    <span class="p">},</span>
+    <span class="s1">&#39;phosphatome&#39;</span><span class="p">:</span> <span class="p">{</span><span class="c1"># PENDING</span>
+        <span class="c1">#&#39;license&#39;: {</span>
+        <span class="c1">#    &#39;name&#39;: &#39;&#39;,</span>
+        <span class="c1">#    &#39;url&#39;: &#39;&#39;,</span>
+        <span class="c1">#    &#39;commercial_use&#39;: False</span>
+        <span class="c1">#}</span>
+    <span class="p">},</span>
+    <span class="s1">&#39;Vaquerizas2009&#39;</span><span class="p">:</span> <span class="p">{</span><span class="c1"># PENDING</span>
+        <span class="c1">#&#39;license&#39;: {</span>
+        <span class="c1">#    &#39;name&#39;: &#39;&#39;,</span>
+        <span class="c1">#    &#39;url&#39;: &#39;&#39;,</span>
+        <span class="c1">#    &#39;commercial_use&#39;: False</span>
+        <span class="c1">#}</span>
+    <span class="p">},</span>
+    <span class="s1">&#39;ProtMapper&#39;</span><span class="p">:</span> <span class="p">{</span>
+        <span class="s1">&#39;license&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;name&#39;</span><span class="p">:</span> <span class="s1">&#39;CC-Attribution-ShareAlike-NonCommercial 4.0&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;url&#39;</span><span class="p">:</span> <span class="s1">&#39;https://creativecommons.org/licenses/by-nc-sa/4.0/&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;commercial_use&#39;</span><span class="p">:</span> <span class="kc">False</span>
+        <span class="p">}</span>
+    <span class="p">},</span>
+    <span class="s1">&#39;ABS&#39;</span><span class="p">:</span> <span class="p">{</span>
+        <span class="s1">&#39;license&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;name&#39;</span><span class="p">:</span> <span class="s1">&#39;GNU-GPLv2&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;url&#39;</span><span class="p">:</span> <span class="s1">&#39;http://genome.crg.es/main/GNU-GPL.html&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;commercial_use&#39;</span><span class="p">:</span> <span class="kc">True</span>
+        <span class="p">}</span>
+    <span class="p">},</span>
+    <span class="s1">&#39;LRdb&#39;</span><span class="p">:</span> <span class="p">{</span>
+        <span class="s1">&#39;license&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;name&#39;</span><span class="p">:</span> <span class="s1">&#39;No license&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;url&#39;</span><span class="p">:</span> <span class="s1">&#39;http://www.gnu.org/licenses/license-list.html#NoLicense&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;commercial_use&#39;</span><span class="p">:</span> <span class="kc">False</span><span class="p">,</span>
+        <span class="p">},</span>
+        <span class="s1">&#39;emails&#39;</span><span class="p">:</span> <span class="p">[(</span><span class="s1">&#39;jacques.colinge@inserm.fr&#39;</span><span class="p">,</span> <span class="s1">&#39;Jacques Colinge&#39;</span><span class="p">),],</span>
+    <span class="p">},</span>
+    <span class="s1">&#39;MSigDB&#39;</span><span class="p">:</span> <span class="p">{</span>
+        <span class="s1">&#39;license&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;name&#39;</span><span class="p">:</span> <span class="s1">&#39;CC-Attribution 4.0&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;url&#39;</span><span class="p">:</span> <span class="s1">&#39;http://creativecommons.org/licenses/by/4.0/&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;commercial_use&#39;</span><span class="p">:</span> <span class="kc">True</span><span class="p">,</span>
+        <span class="p">},</span>
+        <span class="s1">&#39;emails&#39;</span><span class="p">:</span> <span class="p">[(</span><span class="s1">&#39;gsea-team@broadinstitute.org&#39;</span><span class="p">,</span> <span class="s1">&#39;GSEA Team&#39;</span><span class="p">),],</span>
+    <span class="p">},</span>
+    <span class="s1">&#39;Baccin2019&#39;</span><span class="p">:</span> <span class="p">{</span>
+        <span class="s1">&#39;license&#39;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;name&#39;</span><span class="p">:</span> <span class="s1">&#39;No license&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;url&#39;</span><span class="p">:</span> <span class="s1">&#39;http://www.gnu.org/licenses/license-list.html#NoLicense&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;commercial_use&#39;</span><span class="p">:</span> <span class="kc">False</span><span class="p">,</span>
+        <span class="p">},</span>
+        <span class="s1">&#39;emails&#39;</span><span class="p">:</span> <span class="p">[</span>
+            <span class="p">(</span><span class="s1">&#39;lars.velten@embl.de&#39;</span><span class="p">,</span> <span class="s1">&#39;Lars Velten&#39;</span><span class="p">),</span>
+            <span class="p">(</span><span class="s1">&#39;a.trumpp@dkfz-heidelberg.de&#39;</span><span class="p">,</span> <span class="s1">&#39;Andreas Trumpp&#39;</span><span class="p">),</span>
+            <span class="p">(</span><span class="s1">&#39;s.haas@dkfz-heidelberg.de&#39;</span><span class="p">,</span> <span class="s1">&#39;Simon Haas&#39;</span><span class="p">),</span>
+        <span class="p">],</span>
+    <span class="p">},</span>
+<span class="p">}</span>
+
+<span class="n">pypath_methods</span> <span class="o">=</span> <span class="p">{</span>
+    <span class="s1">&#39;data&#39;</span><span class="p">:</span> <span class="s1">&#39;Data source (URLs and files)&#39;</span><span class="p">,</span>
+    <span class="s1">&#39;format&#39;</span><span class="p">:</span> <span class="s1">&#39;Data format definition&#39;</span><span class="p">,</span>
+    <span class="s1">&#39;intr&#39;</span><span class="p">:</span> <span class="s1">&#39;Interactions&#39;</span><span class="p">,</span>
+    <span class="s1">&#39;input&#39;</span><span class="p">:</span> <span class="s1">&#39;Data input methods&#39;</span><span class="p">,</span>
+    <span class="s1">&#39;ptm&#39;</span><span class="p">:</span> <span class="s1">&#39;Enzyme-substrate relationships and PTMs&#39;</span><span class="p">,</span>
+    <span class="s1">&#39;dmi&#39;</span><span class="p">:</span> <span class="s1">&#39;Domain-motif interactions&#39;</span><span class="p">,</span>
+    <span class="s1">&#39;ddi&#39;</span><span class="p">:</span> <span class="s1">&#39;Domain-domain interactions&#39;</span><span class="p">,</span>
+    <span class="s1">&#39;misc&#39;</span><span class="p">:</span> <span class="s1">&#39;Miscellaneous&#39;</span>
+<span class="p">}</span>
+
+
+<div class="viewcode-block" id="gen_html">
+<a class="viewcode-back" href="../../../api/pypath.resources.descriptions.gen_html.html#pypath.resources.descriptions.gen_html">[docs]</a>
+<span class="k">def</span> <span class="nf">gen_html</span><span class="p">():</span>
+<span class="w">    </span><span class="sd">&#39;&#39;&#39;</span>
+<span class="sd">    Generates a HTML page from the `descriptions` array.</span>
+<span class="sd">    This HTML is provided by the webservice under `/info`,</span>
+<span class="sd">    or can be saved locally with `write_html()`.</span>
+<span class="sd">    &#39;&#39;&#39;</span>
+    <span class="c1"># Header</span>
+    <span class="n">title</span> <span class="o">=</span> <span class="s1">&#39;Metadata about signaling pathway resources&#39;</span>
+    <span class="n">doc</span> <span class="o">=</span> <span class="p">(</span>
+        <span class="s1">&#39;&lt;div class=&quot;yellowbox box&quot;&gt;</span><span class="se">\n</span><span class="s1">&#39;</span>
+        <span class="s1">&#39;&lt;p&gt;</span><span class="se">\n</span><span class="s1">&#39;</span>
+            <span class="s1">&#39;&lt;em&gt;</span><span class="se">\n</span><span class="s1">&#39;</span>
+            <span class="s1">&#39;Information on this page has been last revised in Nov 2016.</span><span class="se">\n</span><span class="s1">&#39;</span>
+            <span class="s1">&#39;As of Oct 2019 we are working on updating and extending this</span><span class="se">\n</span><span class="s1">&#39;</span>
+            <span class="s1">&#39;page and will publish the new version soon.</span><span class="se">\n</span><span class="s1">&#39;</span>
+            <span class="s1">&#39;About updates of the OmniPath database content please refer to</span><span class="se">\n</span><span class="s1">&#39;</span>
+            <span class="s1">&#39;&lt;a href=&quot;http://archive.omnipathdb.org/README.txt&quot;&gt;</span><span class="se">\n</span><span class="s1">&#39;</span>
+                <span class="s1">&#39;our archive.</span><span class="se">\n</span><span class="s1">&#39;</span>
+            <span class="s1">&#39;&lt;/a&gt;</span><span class="se">\n</span><span class="s1">&#39;</span>
+            <span class="s1">&#39;&lt;/em&gt;</span><span class="se">\n</span><span class="s1">&#39;</span>
+        <span class="s1">&#39;&lt;/p&gt;</span><span class="se">\n</span><span class="s1">&#39;</span>
+        <span class="s1">&#39;&lt;/div&gt;</span><span class="se">\n</span><span class="s1">&#39;</span>
+        <span class="s1">&#39;&lt;p&gt;This collection was created during the construction &#39;</span>
+        <span class="s1">&#39;of OmniPath when we considered more than 50 resources and &#39;</span>
+        <span class="s1">&#39;selected the ones containing literature curation effort. &#39;</span>
+        <span class="s1">&#39;OmniPath is a network &#39;</span>
+        <span class="s1">&#39;of signaling pathways intending to &#39;</span>
+        <span class="s1">&#39;combine all high quality, manually curated efforts. The &#39;</span>
+        <span class="s1">&#39;descriptions here cite the relevant sentences &#39;</span>
+        <span class="s1">&#39;about the curation protocols from the original articles and webpages. &#39;</span>
+        <span class="s1">&#39;URLs pointing to the articles and the webpages, and some &#39;</span>
+        <span class="s1">&#39;additional metadata are provided where available. &#39;</span>
+        <span class="s1">&#39;The resources with green title are included by default in &#39;</span>
+        <span class="s1">&#39;OmniPath. &lt;span class=&quot;code&quot;&gt;pypath&lt;/span&gt; methods are listed &#39;</span>
+        <span class="s1">&#39; where available, to know more please look at &lt;a &#39;</span>
+        <span class="s1">&#39;target=&quot;_blank&quot; href=&quot;http://pypath.omnipathdb.org/&quot;&gt;&#39;</span>
+        <span class="s1">&#39;pypath documentation.&lt;/a&gt; This list is only about network &#39;</span>
+        <span class="s1">&#39;resources. &lt;span class=&quot;code&quot;&gt;pypath&lt;/span&gt; is able to &#39;</span>
+        <span class="s1">&#39;process and integrate many other resources, please see &#39;</span>
+        <span class="s1">&#39;the paper and the documentation to know more.&lt;/p&gt;&#39;</span>
+        <span class="s1">&#39;&lt;p class=&quot;small&quot;&gt;We searched for license information &#39;</span>
+        <span class="s1">&#39;in the main, About, Download and FAQ sections of the webpages, &#39;</span>
+        <span class="s1">&#39;and run Google searches for the database name and license. &#39;</span>
+        <span class="s1">&#39;Where we could not find anything about licensing, we assumed &#39;</span>
+        <span class="s1">&#39;no license. Unfortunately due to todays restrictive copyright &#39;</span>
+        <span class="s1">&#39;legislations, users don</span><span class="se">\&#39;</span><span class="s1">t have the freedom to use, modify and &#39;</span>
+        <span class="s1">&#39;redistribute the data without a license explicitely granting &#39;</span>
+        <span class="s1">&#39;these to them. Despite the clear intention from the authors to &#39;</span>
+        <span class="s1">&#39;make their data public, and statements on the webpage like &#39;</span>
+        <span class="s1">&#39;&quot;free to use&quot; or &quot;available for download&quot;.&lt;/p&gt;</span><span class="se">\n</span><span class="s1">&#39;</span>
+    <span class="p">)</span>
+    <span class="n">doc</span> <span class="o">+=</span> <span class="s1">&#39;</span><span class="se">\t</span><span class="s1">&lt;h2&gt;Contents&lt;/h2&gt;</span><span class="se">\n</span><span class="s1">&#39;</span>
+    <span class="n">doc</span> <span class="o">+=</span> <span class="s1">&#39;</span><span class="se">\t</span><span class="s1">&lt;ul&gt;</span><span class="se">\n</span><span class="s1">&#39;</span>
+    <span class="c1"># Table of Content</span>
+    <span class="k">for</span> <span class="n">k</span><span class="p">,</span> <span class="n">v</span> <span class="ow">in</span> <span class="nb">sorted</span><span class="p">(</span><span class="n">descriptions</span><span class="o">.</span><span class="n">items</span><span class="p">(),</span> <span class="n">key</span><span class="o">=</span><span class="k">lambda</span> <span class="n">x</span><span class="p">:</span> <span class="n">x</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">lower</span><span class="p">()):</span>
+        <span class="n">doc</span> <span class="o">+=</span> <span class="s1">&#39;</span><span class="se">\t\t\t</span><span class="s1">&lt;li&gt;&lt;a href=&quot;#</span><span class="si">%s</span><span class="s1">&quot; class=&quot;</span><span class="si">%s</span><span class="s1">&quot;&gt;</span><span class="si">%s</span><span class="s1">&lt;/a&gt;&lt;/li&gt;</span><span class="se">\n</span><span class="s1">&#39;</span> <span class="o">%</span> \
+            <span class="p">(</span><span class="n">k</span><span class="p">,</span> <span class="s1">&#39;omnipath&#39;</span> <span class="k">if</span> <span class="s1">&#39;omnipath&#39;</span> <span class="ow">in</span> <span class="n">v</span> <span class="ow">and</span> <span class="n">v</span><span class="p">[</span><span class="s1">&#39;omnipath&#39;</span><span class="p">]</span> <span class="k">else</span> <span class="s1">&#39;base&#39;</span><span class="p">,</span>
+             <span class="n">v</span><span class="p">[</span><span class="s1">&#39;label&#39;</span><span class="p">]</span> <span class="k">if</span> <span class="s1">&#39;label&#39;</span> <span class="ow">in</span> <span class="n">v</span> <span class="k">else</span> <span class="n">k</span><span class="p">)</span>
+    <span class="n">doc</span> <span class="o">+=</span> <span class="s1">&#39;</span><span class="se">\t</span><span class="s1">&lt;/ul&gt;</span><span class="se">\n</span><span class="s1">&#39;</span>
+    <span class="c1"># Sections</span>
+    <span class="k">for</span> <span class="n">k</span><span class="p">,</span> <span class="n">v</span> <span class="ow">in</span> <span class="nb">sorted</span><span class="p">(</span><span class="n">descriptions</span><span class="o">.</span><span class="n">items</span><span class="p">(),</span> <span class="n">key</span><span class="o">=</span><span class="k">lambda</span> <span class="n">x</span><span class="p">:</span> <span class="n">x</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">lower</span><span class="p">()):</span>
+        <span class="n">doc</span> <span class="o">+=</span> <span class="sa">u</span><span class="s1">&#39;</span><span class="se">\t\t</span><span class="s1">&lt;br&gt;</span><span class="se">\n\t\t</span><span class="s1">&lt;h2 id=&quot;</span><span class="si">%s</span><span class="s1">&quot; class=&quot;</span><span class="si">%s</span><span class="s1">&quot;&gt;</span><span class="si">%s%s</span><span class="s1">&lt;/h2&gt;</span><span class="se">\n</span><span class="s1">&#39;</span> <span class="o">%</span> \
+            <span class="p">(</span><span class="n">k</span><span class="p">,</span> <span class="s1">&#39;omnipath&#39;</span> <span class="k">if</span> <span class="s1">&#39;omnipath&#39;</span> <span class="ow">in</span> <span class="n">v</span> <span class="ow">and</span> <span class="n">v</span><span class="p">[</span><span class="s1">&#39;omnipath&#39;</span><span class="p">]</span> <span class="k">else</span> <span class="s1">&#39;base&#39;</span><span class="p">,</span>
+             <span class="n">v</span><span class="p">[</span><span class="s1">&#39;label&#39;</span><span class="p">]</span> <span class="k">if</span> <span class="s1">&#39;label&#39;</span> <span class="ow">in</span> <span class="n">v</span> <span class="k">else</span> <span class="n">k</span><span class="p">,</span>
+             <span class="p">(</span><span class="sa">u</span><span class="s1">&#39; – </span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="p">(</span><span class="n">v</span><span class="p">[</span><span class="s1">&#39;full_name&#39;</span><span class="p">],))</span> <span class="k">if</span> <span class="s1">&#39;full_name&#39;</span> <span class="ow">in</span> <span class="n">v</span> <span class="k">else</span> <span class="s1">&#39;&#39;</span><span class="p">)</span>
+        <span class="n">doc</span> <span class="o">+=</span> <span class="s1">&#39;</span><span class="se">\t\t\t</span><span class="s1">&lt;p&gt;&lt;b&gt;Category || Subcategory &amp;gt;&amp;gt;&amp;gt;&lt;/b&gt; </span><span class="si">%s</span><span class="s1"> || </span><span class="si">%s</span><span class="s1">&lt;/p&gt;</span><span class="se">\n</span><span class="s1">&#39;</span> <span class="o">%</span> \
+            <span class="p">(</span><span class="n">v</span><span class="p">[</span><span class="s1">&#39;type&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">capitalize</span><span class="p">()</span> <span class="k">if</span> <span class="s1">&#39;type&#39;</span> <span class="ow">in</span> <span class="n">v</span> <span class="k">else</span> <span class="s1">&#39;Undefined&#39;</span><span class="p">,</span>
+                <span class="n">v</span><span class="p">[</span><span class="s1">&#39;subtype&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">capitalize</span><span class="p">()</span> <span class="k">if</span> <span class="s1">&#39;subtype&#39;</span> <span class="ow">in</span> <span class="n">v</span> <span class="k">else</span> <span class="s1">&#39;Undefined&#39;</span><span class="p">)</span>
+        <span class="k">if</span> <span class="s1">&#39;year&#39;</span> <span class="ow">in</span> <span class="n">v</span><span class="p">:</span>
+            <span class="n">doc</span> <span class="o">+=</span> <span class="s1">&#39;</span><span class="se">\t\t\t</span><span class="s1">&lt;h3&gt;Last released: </span><span class="si">%u</span><span class="s1">&lt;\h3&gt;</span><span class="se">\n</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="n">v</span><span class="p">[</span><span class="s1">&#39;year&#39;</span><span class="p">]</span>
+        <span class="k">if</span> <span class="s1">&#39;releases&#39;</span> <span class="ow">in</span> <span class="n">v</span><span class="p">:</span>
+            <span class="n">doc</span> <span class="o">+=</span> <span class="s1">&#39;</span><span class="se">\t\t\t</span><span class="s1">&lt;p&gt;&lt;b&gt;Released in years: &lt;/b&gt;</span><span class="si">%s</span><span class="s1">&lt;/p&gt;</span><span class="se">\n</span><span class="s1">&#39;</span> <span class="o">%</span> \
+                <span class="s1">&#39;, &#39;</span><span class="o">.</span><span class="n">join</span><span class="p">([</span><span class="s1">&#39;</span><span class="si">%u</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="n">y</span> <span class="k">for</span> <span class="n">y</span> <span class="ow">in</span> <span class="n">v</span><span class="p">[</span><span class="s1">&#39;releases&#39;</span><span class="p">]])</span>
+        <span class="k">if</span> <span class="s1">&#39;authors&#39;</span> <span class="ow">in</span> <span class="n">v</span> <span class="ow">and</span> <span class="n">v</span><span class="p">[</span><span class="s1">&#39;authors&#39;</span><span class="p">]</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
+            <span class="n">doc</span> <span class="o">+=</span> <span class="s1">&#39;</span><span class="se">\t\t\t</span><span class="s1">&lt;p&gt;&lt;b&gt;Created by &lt;/b&gt;</span><span class="si">%s</span><span class="s1">&lt;/p&gt;</span><span class="se">\n</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="s1">&#39;, &#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">v</span><span class="p">[</span>
+                <span class="s1">&#39;authors&#39;</span><span class="p">])</span>
+        <span class="k">if</span> <span class="s1">&#39;emails&#39;</span> <span class="ow">in</span> <span class="n">v</span> <span class="ow">and</span> <span class="n">v</span><span class="p">[</span><span class="s1">&#39;emails&#39;</span><span class="p">]</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
+            <span class="n">doc</span> <span class="o">+=</span> <span class="s1">&#39;</span><span class="se">\t\t\t</span><span class="s1">&lt;p&gt;&lt;b&gt;Contact: &lt;/b&gt;&lt;/p&gt;</span><span class="se">\n\n\t\t\t\t</span><span class="s1">&lt;ul&gt;</span><span class="se">\n</span><span class="si">%s</span><span class="se">\n</span><span class="s1">&#39;</span> <span class="o">%</span> \
+                <span class="s1">&#39;&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">([</span><span class="s1">&#39;</span><span class="se">\t\t\t\t</span><span class="s1">&lt;li&gt;&lt;a href=&quot;mailto:</span><span class="si">%s</span><span class="s1">&quot;&gt;</span><span class="si">%s</span><span class="s1"> &amp;lt;</span><span class="si">%s</span><span class="s1">&amp;gt;&lt;/li&gt;</span><span class="se">\n</span><span class="s1">&#39;</span> <span class="o">%</span>
+                         <span class="p">(</span><span class="n">em</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">em</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span> <span class="n">em</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span> <span class="k">for</span> <span class="n">em</span> <span class="ow">in</span> <span class="n">v</span><span class="p">[</span><span class="s1">&#39;emails&#39;</span><span class="p">]])</span>
+            <span class="n">doc</span> <span class="o">+=</span> <span class="s1">&#39;</span><span class="se">\t\t\t\t</span><span class="s1">&lt;/ul&gt;</span><span class="se">\n</span><span class="s1">&#39;</span>
+        <span class="k">if</span> <span class="s1">&#39;license&#39;</span> <span class="ow">in</span> <span class="n">v</span><span class="p">:</span>
+            <span class="k">try</span><span class="p">:</span>
+                <span class="n">doc</span> <span class="o">+=</span> <span class="s1">&#39;</span><span class="se">\t\t\t</span><span class="s1">&lt;p&gt;&lt;b&gt;License:&lt;/b&gt; </span><span class="si">%s%s%s</span><span class="s1">&lt;/p&gt;</span><span class="se">\n</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="p">(</span>
+                    <span class="p">(</span><span class="s1">&#39;&lt;a href=&quot;</span><span class="si">%s</span><span class="s1">&quot; target=&quot;_blank&quot;&gt;&#39;</span> <span class="o">%</span> <span class="n">v</span><span class="p">[</span><span class="s1">&#39;license&#39;</span><span class="p">][</span><span class="s1">&#39;url&#39;</span><span class="p">])</span> <span class="k">if</span>
+                    <span class="s1">&#39;url&#39;</span> <span class="ow">in</span> <span class="n">v</span><span class="p">[</span><span class="s1">&#39;license&#39;</span><span class="p">]</span> <span class="k">else</span> <span class="s1">&#39;&#39;</span><span class="p">,</span> <span class="n">v</span><span class="p">[</span><span class="s1">&#39;license&#39;</span><span class="p">][</span><span class="s1">&#39;name&#39;</span><span class="p">],</span> <span class="s1">&#39;&lt;/a&gt;&#39;</span>
+                    <span class="k">if</span> <span class="s1">&#39;url&#39;</span> <span class="ow">in</span> <span class="n">v</span><span class="p">[</span><span class="s1">&#39;license&#39;</span><span class="p">]</span> <span class="k">else</span> <span class="s1">&#39;&#39;</span><span class="p">)</span>
+            <span class="k">except</span> <span class="ne">KeyError</span><span class="p">:</span>
+                <span class="n">_log</span><span class="p">(</span><span class="s1">&#39;Wrong license format for `</span><span class="si">%s</span><span class="s1">`.&#39;</span> <span class="o">%</span> <span class="n">k</span><span class="p">)</span>
+        <span class="k">if</span> <span class="s1">&#39;urls&#39;</span> <span class="ow">in</span> <span class="n">v</span><span class="p">:</span>
+            <span class="k">for</span> <span class="n">uk</span><span class="p">,</span> <span class="n">uv</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="n">v</span><span class="p">[</span><span class="s1">&#39;urls&#39;</span><span class="p">]):</span>
+                <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">uv</span><span class="p">)</span> <span class="o">&gt;</span> <span class="mi">0</span> <span class="ow">and</span> <span class="n">uk</span> <span class="o">!=</span> <span class="s1">&#39;omictools&#39;</span><span class="p">:</span>
+                    <span class="k">try</span><span class="p">:</span>
+                        <span class="n">doc</span> <span class="o">+=</span> <span class="s1">&#39;</span><span class="se">\t\t\t</span><span class="s1">&lt;h3&gt;</span><span class="si">%s</span><span class="s1">&lt;/h3&gt;</span><span class="se">\n</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="p">(</span><span class="n">uk</span><span class="o">.</span><span class="n">capitalize</span><span class="p">())</span>
+                        <span class="n">doc</span> <span class="o">+=</span> <span class="s1">&#39;</span><span class="se">\t\t\t</span><span class="s1">&lt;ul&gt;</span><span class="se">\n</span><span class="s1">&#39;</span>
+                        <span class="k">for</span> <span class="n">a</span> <span class="ow">in</span> <span class="n">uv</span><span class="p">:</span>
+                            <span class="n">doc</span> <span class="o">+=</span> <span class="p">(</span>
+                                <span class="s1">&#39;</span><span class="se">\t\t\t\t</span><span class="s1">&lt;li&gt;&lt;a href=&quot;</span><span class="si">%s</span><span class="s1">&quot; &#39;</span>
+                                <span class="s1">&#39;target=&quot;_blank&quot;&gt;</span><span class="si">%s</span><span class="s1">&lt;/a&gt;&lt;/li&gt;</span><span class="se">\n</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="p">(</span>
+                                    <span class="n">a</span><span class="p">,</span> <span class="n">a</span>
+                                <span class="p">)</span>
+                            <span class="p">)</span>
+                        <span class="n">doc</span> <span class="o">+=</span> <span class="s1">&#39;</span><span class="se">\t\t\t</span><span class="s1">&lt;/ul&gt;</span><span class="se">\n</span><span class="s1">&#39;</span>
+                    <span class="k">except</span> <span class="ne">UnicodeDecodeError</span><span class="p">:</span>
+                        <span class="n">sys</span><span class="o">.</span><span class="n">stdout</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s1">&#39;UnicdeDecodeError at </span><span class="si">%s</span><span class="se">\n</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="n">k</span><span class="p">)</span>
+                        <span class="n">sys</span><span class="o">.</span><span class="n">stdout</span><span class="o">.</span><span class="n">flush</span><span class="p">()</span>
+        <span class="k">if</span> <span class="s1">&#39;pubmeds&#39;</span> <span class="ow">in</span> <span class="n">v</span><span class="p">:</span>
+            <span class="n">doc</span> <span class="o">+=</span> <span class="s1">&#39;</span><span class="se">\t\t\t</span><span class="s1">&lt;h3&gt;PubMed&lt;/h3&gt;</span><span class="se">\n</span><span class="s1">&#39;</span>
+            <span class="n">doc</span> <span class="o">+=</span> <span class="s1">&#39;</span><span class="se">\t\t\t</span><span class="s1">&lt;ul&gt;</span><span class="se">\n</span><span class="s1">&#39;</span>
+            <span class="k">for</span> <span class="n">pmid</span> <span class="ow">in</span> <span class="n">v</span><span class="p">[</span><span class="s1">&#39;pubmeds&#39;</span><span class="p">]:</span>
+                <span class="n">doc</span> <span class="o">+=</span> <span class="s1">&#39;</span><span class="se">\t\t\t\t</span><span class="s1">&lt;li&gt;&lt;a href=&quot;</span><span class="si">%s</span><span class="s1">&quot; &#39;</span>\
+                    <span class="s1">&#39;target=&quot;_blank&quot;&gt;</span><span class="si">%s</span><span class="s1">&lt;/a&gt;&lt;/li&gt;</span><span class="se">\n</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="p">(</span>
+                        <span class="s1">&#39;http://www.ncbi.nlm.nih.gov/pubmed/</span><span class="si">%u</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="n">pmid</span><span class="p">,</span>
+                        <span class="s1">&#39;http://www.ncbi.nlm.nih.gov/pubmed/</span><span class="si">%u</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="n">pmid</span>
+                    <span class="p">)</span>
+            <span class="n">doc</span> <span class="o">+=</span> <span class="s1">&#39;</span><span class="se">\t\t\t</span><span class="s1">&lt;/ul&gt;</span><span class="se">\n</span><span class="s1">&#39;</span>
+        <span class="k">if</span> <span class="p">(</span><span class="s1">&#39;urls&#39;</span> <span class="ow">in</span> <span class="n">v</span> <span class="ow">and</span> <span class="s1">&#39;omictools&#39;</span> <span class="ow">in</span> <span class="n">v</span><span class="p">[</span><span class="s1">&#39;urls&#39;</span><span class="p">])</span> <span class="ow">or</span> <span class="s1">&#39;pathguide&#39;</span> <span class="ow">in</span> <span class="n">v</span><span class="p">:</span>
+            <span class="n">doc</span> <span class="o">+=</span> <span class="s1">&#39;</span><span class="se">\t\t\t</span><span class="s1">&lt;h3&gt;Collections&lt;/h3&gt;</span><span class="se">\n\t\t\t</span><span class="s1">&lt;ul&gt;&#39;</span>
+            <span class="k">if</span> <span class="s1">&#39;omictools&#39;</span> <span class="ow">in</span> <span class="n">v</span><span class="p">[</span><span class="s1">&#39;urls&#39;</span><span class="p">]:</span>
+                <span class="n">doc</span> <span class="o">+=</span> <span class="s1">&#39;</span><span class="se">\t\t\t</span><span class="s1">&lt;li&gt;&lt;a href=&quot;</span><span class="si">%s</span><span class="s1">&quot; target=&quot;_blank&quot;&gt;OmicTools&lt;/a&gt;&lt;/li&gt;</span><span class="se">\n</span><span class="s1">&#39;</span> <span class="o">%</span> \
+                    <span class="n">v</span><span class="p">[</span><span class="s1">&#39;urls&#39;</span><span class="p">][</span><span class="s1">&#39;omictools&#39;</span><span class="p">][</span><span class="mi">0</span><span class="p">]</span>
+            <span class="k">if</span> <span class="s1">&#39;pathguide&#39;</span> <span class="ow">in</span> <span class="n">v</span><span class="p">:</span>
+                <span class="n">doc</span> <span class="o">+=</span> <span class="s1">&#39;</span><span class="se">\t\t\t</span><span class="s1">&lt;li&gt;&lt;a href=&quot;</span><span class="si">%s</span><span class="s1">&quot; target=&quot;_blank&quot;&gt;PathGuide&lt;/a&gt;&lt;/li&gt;</span><span class="se">\n</span><span class="s1">&#39;</span> <span class="o">%</span> \
+                    <span class="p">(</span><span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;pathguide&#39;</span><span class="p">][</span><span class="s1">&#39;url&#39;</span><span class="p">]</span> <span class="o">%</span> <span class="n">v</span><span class="p">[</span><span class="s1">&#39;pathguide&#39;</span><span class="p">])</span>
+            <span class="n">doc</span> <span class="o">+=</span> <span class="s1">&#39;</span><span class="se">\t\t\t</span><span class="s1">&lt;/ul&gt;</span><span class="se">\n</span><span class="s1">&#39;</span>
+        <span class="k">if</span> <span class="s1">&#39;taxons&#39;</span> <span class="ow">in</span> <span class="n">v</span><span class="p">:</span>
+            <span class="n">doc</span> <span class="o">+=</span> <span class="s1">&#39;&lt;p&gt;&lt;b&gt;Taxons: &lt;/b&gt;&lt;em&gt;</span><span class="si">%s</span><span class="s1">&lt;/em&gt;&lt;/p&gt;&#39;</span> <span class="o">%</span> \
+                <span class="s1">&#39;, &#39;</span><span class="o">.</span><span class="n">join</span><span class="p">([</span><span class="s1">&#39;</span><span class="si">%s%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="p">(</span><span class="n">t</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">upper</span><span class="p">(),</span> <span class="n">t</span><span class="p">[</span><span class="mi">1</span><span class="p">:])</span>
+                           <span class="k">for</span> <span class="n">t</span> <span class="ow">in</span> <span class="n">v</span><span class="p">[</span><span class="s1">&#39;taxons&#39;</span><span class="p">]])</span>
+        <span class="k">if</span> <span class="s1">&#39;size&#39;</span> <span class="ow">in</span> <span class="n">v</span> <span class="ow">and</span> <span class="nb">type</span><span class="p">(</span><span class="n">v</span><span class="p">[</span><span class="s1">&#39;size&#39;</span><span class="p">])</span> <span class="ow">is</span> <span class="nb">dict</span> <span class="ow">and</span> \
+                <span class="n">v</span><span class="p">[</span><span class="s1">&#39;size&#39;</span><span class="p">][</span><span class="s1">&#39;nodes&#39;</span><span class="p">]</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span> <span class="ow">and</span> <span class="n">v</span><span class="p">[</span><span class="s1">&#39;size&#39;</span><span class="p">][</span><span class="s1">&#39;edges&#39;</span><span class="p">]</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
+            <span class="n">doc</span> <span class="o">+=</span> <span class="s1">&#39;&lt;p&gt;&lt;b&gt;Nodes: &lt;/b&gt;</span><span class="si">%s</span><span class="s1">, &lt;b&gt;Edges:&lt;/b&gt;</span><span class="si">%s</span><span class="s1">&lt;/p&gt;&#39;</span> <span class="o">%</span> <span class="p">(</span>
+                <span class="n">v</span><span class="p">[</span><span class="s1">&#39;size&#39;</span><span class="p">][</span><span class="s1">&#39;nodes&#39;</span><span class="p">],</span> <span class="n">v</span><span class="p">[</span><span class="s1">&#39;size&#39;</span><span class="p">][</span><span class="s1">&#39;edges&#39;</span><span class="p">])</span>
+        <span class="k">if</span> <span class="s1">&#39;data_import&#39;</span> <span class="ow">in</span> <span class="n">v</span><span class="p">:</span>
+            <span class="n">doc</span> <span class="o">+=</span> <span class="s1">&#39;</span><span class="se">\t\t\t</span><span class="s1">&lt;p&gt;&lt;b&gt;Direct data import from: &lt;/b&gt;</span><span class="si">%s</span><span class="s1">&lt;/p&gt;</span><span class="se">\n</span><span class="s1">&#39;</span> <span class="o">%</span> \
+                <span class="s1">&#39;, &#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">v</span><span class="p">[</span><span class="s1">&#39;data_import&#39;</span><span class="p">])</span>
+        <span class="k">if</span> <span class="s1">&#39;includes&#39;</span> <span class="ow">in</span> <span class="n">v</span><span class="p">:</span>
+            <span class="n">doc</span> <span class="o">+=</span> <span class="s1">&#39;</span><span class="se">\t\t\t</span><span class="s1">&lt;p&gt;&lt;b&gt;Includes data from: &lt;/b&gt;</span><span class="si">%s</span><span class="s1">&lt;/p&gt;</span><span class="se">\n</span><span class="s1">&#39;</span> <span class="o">%</span> \
+                <span class="s1">&#39;, &#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">v</span><span class="p">[</span><span class="s1">&#39;includes&#39;</span><span class="p">])</span>
+        <span class="k">if</span> <span class="s1">&#39;descriptions&#39;</span> <span class="ow">in</span> <span class="n">v</span> <span class="ow">or</span> <span class="s1">&#39;notes&#39;</span> <span class="ow">in</span> <span class="n">v</span><span class="p">:</span>
+            <span class="n">doc</span> <span class="o">+=</span> <span class="s1">&#39;</span><span class="se">\t\t\t</span><span class="s1">&lt;h3&gt;Quotes&lt;/h3&gt;</span><span class="se">\n</span><span class="s1">&#39;</span>
+            <span class="k">if</span> <span class="s1">&#39;descriptions&#39;</span> <span class="ow">in</span> <span class="n">v</span><span class="p">:</span>
+                <span class="n">doc</span> <span class="o">+=</span> <span class="s1">&#39;</span><span class="se">\t\t\t\t</span><span class="s1">&lt;div class=&quot;quotebox box&quot;&gt;</span><span class="se">\n</span><span class="s1">&#39;</span>
+                <span class="n">pars</span> <span class="o">=</span> <span class="n">v</span><span class="p">[</span><span class="s1">&#39;descriptions&#39;</span><span class="p">][</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\n</span><span class="s1">&#39;</span><span class="p">)</span>
+                <span class="k">for</span> <span class="n">p</span> <span class="ow">in</span> <span class="n">pars</span><span class="p">:</span>
+                    <span class="n">p</span> <span class="o">=</span> <span class="n">p</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span>
+                    <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">p</span><span class="p">)</span> <span class="o">&gt;</span> <span class="mi">0</span><span class="p">:</span>
+                        <span class="n">doc</span> <span class="o">+=</span> <span class="s1">&#39;</span><span class="se">\t\t\t\t</span><span class="s1">&lt;p&gt;</span><span class="si">%s</span><span class="s1">&lt;/p&gt;</span><span class="se">\n</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="n">p</span>
+                <span class="n">doc</span> <span class="o">+=</span> <span class="s1">&#39;</span><span class="se">\t\t\t\t</span><span class="s1">&lt;/div&gt;</span><span class="se">\n</span><span class="s1">&#39;</span>
+            <span class="k">if</span> <span class="s1">&#39;notes&#39;</span> <span class="ow">in</span> <span class="n">v</span><span class="p">:</span>
+                <span class="n">doc</span> <span class="o">+=</span> <span class="s1">&#39;</span><span class="se">\t\t\t\t</span><span class="s1">&lt;div class=&quot;quotebox box&quot;&gt;</span><span class="se">\n</span><span class="s1">&#39;</span>
+                <span class="n">pars</span> <span class="o">=</span> <span class="n">v</span><span class="p">[</span><span class="s1">&#39;notes&#39;</span><span class="p">][</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\n</span><span class="s1">&#39;</span><span class="p">)</span>
+                <span class="k">for</span> <span class="n">p</span> <span class="ow">in</span> <span class="n">pars</span><span class="p">:</span>
+                    <span class="n">p</span> <span class="o">=</span> <span class="n">p</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span>
+                    <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">p</span><span class="p">)</span> <span class="o">&gt;</span> <span class="mi">0</span><span class="p">:</span>
+                        <span class="n">doc</span> <span class="o">+=</span> <span class="s1">&#39;</span><span class="se">\t\t\t\t</span><span class="s1">&lt;p&gt;</span><span class="si">%s</span><span class="s1">&lt;/p&gt;</span><span class="se">\n</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="n">p</span>
+                <span class="n">doc</span> <span class="o">+=</span> <span class="s1">&#39;</span><span class="se">\t\t\t\t</span><span class="s1">&lt;/div&gt;</span><span class="se">\n</span><span class="s1">&#39;</span>
+        <span class="k">if</span> <span class="s1">&#39;data_integration&#39;</span> <span class="ow">in</span> <span class="n">v</span><span class="p">:</span>
+            <span class="n">doc</span> <span class="o">+=</span> <span class="s1">&#39;</span><span class="se">\t\t\t</span><span class="s1">&lt;p&gt;&lt;b&gt;Data integration in &#39;</span>\
+                <span class="s1">&#39;&lt;span class=&quot;code&quot;&gt;pypath:&lt;/span&gt;&lt;/b&gt; </span><span class="si">%s</span><span class="s1">&lt;/p&gt;&#39;</span> <span class="o">%</span> \
+                <span class="n">v</span><span class="p">[</span><span class="s1">&#39;data_integration&#39;</span><span class="p">]</span>
+        <span class="k">if</span> <span class="s1">&#39;pypath&#39;</span> <span class="ow">in</span> <span class="n">v</span><span class="p">:</span>
+            <span class="n">doc</span> <span class="o">+=</span> <span class="s1">&#39;</span><span class="se">\t\t\t</span><span class="s1">&lt;h3&gt;Methods in &lt;span class=&quot;code&quot;&gt;pypath&#39;</span>\
+                <span class="s1">&#39;&lt;/span&gt;&lt;/h3&gt;</span><span class="se">\n</span><span class="s1">&#39;</span>
+            <span class="n">doc</span> <span class="o">+=</span> <span class="s1">&#39;</span><span class="se">\t\t\t\t</span><span class="s1">&lt;div class=&quot;codebox box&quot;&gt;</span><span class="se">\n</span><span class="s1">&#39;</span>
+            <span class="k">for</span> <span class="n">cat</span> <span class="ow">in</span> <span class="nb">sorted</span><span class="p">(</span><span class="n">pypath_methods</span><span class="o">.</span><span class="n">keys</span><span class="p">()):</span>
+                <span class="n">name</span> <span class="o">=</span> <span class="n">pypath_methods</span><span class="p">[</span><span class="n">cat</span><span class="p">]</span>
+                <span class="k">if</span> <span class="n">cat</span> <span class="ow">in</span> <span class="n">v</span><span class="p">[</span><span class="s1">&#39;pypath&#39;</span><span class="p">]:</span>
+                    <span class="n">doc</span> <span class="o">+=</span> <span class="s1">&#39;</span><span class="se">\t\t\t\t\t</span><span class="s1">&lt;p&gt;</span><span class="si">%s</span><span class="s1">&lt;/p&gt;</span><span class="se">\n\t\t\t\t\t</span><span class="s1">&lt;ul&gt;</span><span class="se">\n</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="n">name</span>
+                    <span class="k">for</span> <span class="n">met</span> <span class="ow">in</span> <span class="n">v</span><span class="p">[</span><span class="s1">&#39;pypath&#39;</span><span class="p">][</span><span class="n">cat</span><span class="p">]:</span>
+                        <span class="n">doc</span> <span class="o">+=</span> <span class="s1">&#39;</span><span class="se">\t\t\t\t\t\t</span><span class="s1">&lt;li&gt;&lt;span class=&quot;code&quot;&gt;</span><span class="si">%s</span><span class="s1">&#39;</span>\
+                            <span class="s1">&#39;&lt;/span&gt;&lt;/li&gt;</span><span class="se">\n</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="n">met</span>
+                    <span class="n">doc</span> <span class="o">+=</span> <span class="s1">&#39;</span><span class="se">\t\t\t\t\t</span><span class="s1">&lt;/ul&gt;</span><span class="se">\n</span><span class="s1">&#39;</span>
+            <span class="n">doc</span> <span class="o">+=</span> <span class="s1">&#39;</span><span class="se">\t\t\t\t</span><span class="s1">&lt;/div&gt;</span><span class="se">\n</span><span class="s1">&#39;</span>
+
+    <span class="k">return</span> <span class="n">_html</span><span class="o">.</span><span class="n">default_template</span><span class="p">(</span><span class="n">doc</span><span class="p">,</span> <span class="n">title</span><span class="p">,</span> <span class="n">title</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="write_html">
+<a class="viewcode-back" href="../../../api/pypath.resources.descriptions.write_html.html#pypath.resources.descriptions.write_html">[docs]</a>
+<span class="k">def</span> <span class="nf">write_html</span><span class="p">(</span><span class="n">filename</span><span class="o">=</span><span class="s1">&#39;resources.html&#39;</span><span class="p">):</span>
+<span class="w">    </span><span class="sd">&#39;&#39;&#39;</span>
+<span class="sd">    Saves the HTML descriptions to custom local file.</span>
+<span class="sd">    &#39;&#39;&#39;</span>
+    <span class="n">html</span> <span class="o">=</span> <span class="n">gen_html</span><span class="p">()</span>
+    <span class="c1"># with codecs.open(filename, encoding = &#39;utf-8&#39;, mode = &#39;w&#39;) as f:</span>
+    <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">filename</span><span class="p">,</span> <span class="s1">&#39;w&#39;</span><span class="p">)</span> <span class="k">as</span> <span class="n">f</span><span class="p">:</span>
+        <span class="n">f</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="n">html</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="resource_list_latex">
+<a class="viewcode-back" href="../../../api/pypath.resources.descriptions.resource_list_latex.html#pypath.resources.descriptions.resource_list_latex">[docs]</a>
+<span class="k">def</span> <span class="nf">resource_list_latex</span><span class="p">(</span><span class="n">filename</span><span class="o">=</span><span class="s1">&#39;resource-list.tex&#39;</span><span class="p">,</span>
+                        <span class="n">latex_hdr</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span>
+                        <span class="n">fontsize</span><span class="o">=</span><span class="mi">8</span><span class="p">,</span>
+                        <span class="n">font</span><span class="o">=</span><span class="s1">&#39;HelveticaNeueLTStd-LtCn&#39;</span><span class="p">):</span>
+<span class="w">    </span><span class="sd">&#39;&#39;&#39;</span>
+<span class="sd">    Generates Supplementary Table 3 (The list of the 52 resources considered) for the article.</span>
+<span class="sd">    &#39;&#39;&#39;</span>
+    <span class="n">_latex_hdr</span> <span class="o">=</span> <span class="sa">r</span><span class="s1">&#39;&#39;&#39;\documentclass[a4paper,</span><span class="si">%u</span><span class="s1">pt]</span><span class="si">{extarticle}</span>
+<span class="s1">        \usepackage</span><span class="si">{fontspec}</span>
+<span class="s1">        \usepackage</span><span class="si">{xunicode}</span>
+<span class="s1">        \usepackage</span><span class="si">{polyglossia}</span>
+<span class="s1">        \setdefaultlanguage</span><span class="si">{english}</span>
+<span class="s1">        \usepackage</span><span class="si">{xltxtra}</span>
+<span class="s1">        \usepackage</span><span class="si">{microtype}</span>
+<span class="s1">        \usepackage[margin=5pt,portrait,paperwidth=15cm,paperheight=18cm]</span><span class="si">{geometry}</span>
+<span class="s1">        \usepackage</span><span class="si">{amsmath}</span>
+<span class="s1">        \usepackage</span><span class="si">{amssymb}</span>
+<span class="s1">        \usepackage</span><span class="si">{textcomp}</span>
+<span class="s1">        \usepackage[usenames,dvipsnames,svgnames,table]</span><span class="si">{xcolor}</span>
+<span class="s1">        \usepackage</span><span class="si">{color}</span>
+<span class="s1">        \usepackage</span><span class="si">{booktabs}</span>
+<span class="s1">        \usepackage</span><span class="si">{tabularx}</span>
+<span class="s1">        \setmainfont{</span><span class="si">%s</span><span class="s1">}</span>
+<span class="s1">        \definecolor</span><span class="si">{grey875}{gray}{0.125}</span>
+<span class="s1">        \begin</span><span class="si">{document}</span>
+<span class="s1">        \color</span><span class="si">{grey875}</span>
+<span class="s1">        \thispagestyle</span><span class="si">{empty}</span>
+<span class="s1">        \vfill</span>
+<span class="s1">    &#39;&#39;&#39;</span> <span class="o">%</span> <span class="p">(</span><span class="n">fontsize</span><span class="p">,</span> <span class="n">font</span><span class="p">)</span> <span class="k">if</span> <span class="n">latex_hdr</span> <span class="k">else</span> <span class="s1">&#39;&#39;</span>
+    <span class="n">_latex_end</span> <span class="o">=</span> <span class="sa">r</span><span class="s1">&#39;&#39;&#39;</span>
+<span class="s1">            \end</span><span class="si">{document}</span>
+<span class="s1">        &#39;&#39;&#39;</span> <span class="k">if</span> <span class="n">latex_hdr</span> <span class="k">else</span> <span class="s1">&#39;&#39;</span>
+    <span class="n">tex</span> <span class="o">=</span> <span class="sa">r</span><span class="s1">&#39;&#39;&#39;\begin</span><span class="si">{tabularx}</span><span class="s1">{0.94\textwidth}{&gt;{\raggedright\scriptsize\arraybackslash\hsize=.15\hsize}X&gt;{\raggedright\scriptsize\arraybackslash\hsize=.35\hsize}X&gt;{\raggedright\scriptsize\arraybackslash\hsize=.15\hsize}X&gt;{\raggedright\scriptsize\arraybackslash\hsize=.15\hsize}X}</span>
+<span class="s1">    \toprule</span>
+<span class="s1">    Resource name &amp; Class, subclass &amp; Resource name &amp; Class, subclass \\</span>
+<span class="s1">    \midrule</span>
+<span class="s1">    &#39;&#39;&#39;</span>
+    <span class="n">res</span> <span class="o">=</span> <span class="nb">sorted</span><span class="p">(</span>
+        <span class="p">[(</span><span class="n">v</span><span class="p">[</span><span class="s1">&#39;label&#39;</span><span class="p">]</span> <span class="k">if</span> <span class="s1">&#39;label&#39;</span> <span class="ow">in</span> <span class="n">v</span> <span class="k">else</span> <span class="n">k</span><span class="p">,</span>
+          <span class="s1">&#39;</span><span class="si">%s</span><span class="s1">, </span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="p">(</span><span class="n">v</span><span class="p">[</span><span class="s1">&#39;type&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">capitalize</span><span class="p">(),</span> <span class="n">v</span><span class="p">[</span><span class="s1">&#39;subtype&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">capitalize</span><span class="p">())</span>
+          <span class="k">if</span> <span class="s1">&#39;type&#39;</span> <span class="ow">in</span> <span class="n">v</span> <span class="ow">and</span> <span class="s1">&#39;subtype&#39;</span> <span class="ow">in</span> <span class="n">v</span> <span class="k">else</span> <span class="s1">&#39;&#39;</span><span class="p">)</span>
+         <span class="k">for</span> <span class="n">k</span><span class="p">,</span> <span class="n">v</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="n">descriptions</span><span class="p">)],</span>
+        <span class="n">key</span><span class="o">=</span><span class="k">lambda</span> <span class="n">x</span><span class="p">:</span> <span class="n">x</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">lower</span><span class="p">())</span>
+    <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">res</span><span class="p">)</span> <span class="o">%</span> <span class="mi">2</span> <span class="o">!=</span> <span class="mi">0</span><span class="p">:</span>
+        <span class="n">res</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="s1">&#39;&#39;</span><span class="p">)</span>
+    <span class="n">res2</span> <span class="o">=</span> <span class="nb">zip</span><span class="p">(</span><span class="n">res</span><span class="p">[:</span><span class="nb">int</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">res</span><span class="p">)</span> <span class="o">/</span> <span class="mi">2</span><span class="p">)],</span> <span class="n">res</span><span class="p">[</span><span class="nb">int</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">res</span><span class="p">)</span> <span class="o">/</span> <span class="mi">2</span><span class="p">):])</span>
+    <span class="k">for</span> <span class="n">r</span> <span class="ow">in</span> <span class="n">res2</span><span class="p">:</span>
+        <span class="n">tex</span> <span class="o">+=</span> <span class="sa">r</span><span class="s1">&#39;</span><span class="si">%s</span><span class="s1"> &amp; </span><span class="si">%s</span><span class="s1"> &amp; </span><span class="si">%s</span><span class="s1"> &amp; </span><span class="si">%s</span><span class="s1"> </span><span class="se">\\</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="p">(</span>
+            <span class="n">r</span><span class="p">[</span><span class="mi">0</span><span class="p">][</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s1">&#39;&amp;&#39;</span><span class="p">,</span> <span class="s1">&#39;\&amp;&#39;</span><span class="p">),</span>
+            <span class="n">r</span><span class="p">[</span><span class="mi">0</span><span class="p">][</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s1">&#39;&amp;&#39;</span><span class="p">,</span> <span class="s1">&#39;\&amp;&#39;</span><span class="p">),</span>
+            <span class="p">(</span><span class="n">r</span><span class="p">[</span><span class="mi">1</span><span class="p">][</span><span class="mi">0</span><span class="p">]</span> <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">r</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span> <span class="k">else</span> <span class="s1">&#39;&#39;</span><span class="p">)</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s1">&#39;&amp;&#39;</span><span class="p">,</span> <span class="s1">&#39;\&amp;&#39;</span><span class="p">),</span>
+            <span class="p">(</span><span class="n">r</span><span class="p">[</span><span class="mi">1</span><span class="p">][</span><span class="mi">1</span><span class="p">]</span> <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">r</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span> <span class="k">else</span> <span class="s1">&#39;&#39;</span><span class="p">)</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s1">&#39;&amp;&#39;</span><span class="p">,</span> <span class="s1">&#39;\&amp;&#39;</span><span class="p">),</span>
+        <span class="p">)</span> <span class="o">+</span> <span class="s1">&#39;</span><span class="se">\n</span><span class="s1">&#39;</span>
+    <span class="n">tex</span> <span class="o">+=</span> <span class="sa">r</span><span class="s1">&#39;\bottomrule&#39;</span> <span class="o">+</span> <span class="s1">&#39;</span><span class="se">\n</span><span class="s1">&#39;</span>
+    <span class="n">tex</span> <span class="o">+=</span> <span class="sa">r</span><span class="s1">&#39;\end</span><span class="si">{tabularx}</span><span class="s1">&#39;</span> <span class="o">+</span> <span class="s1">&#39;</span><span class="se">\n</span><span class="s1">&#39;</span>
+    <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">filename</span><span class="p">,</span> <span class="s1">&#39;w&#39;</span><span class="p">)</span> <span class="k">as</span> <span class="n">f</span><span class="p">:</span>
+        <span class="n">f</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s1">&#39;</span><span class="si">%s%s%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="p">(</span><span class="n">_latex_hdr</span> <span class="k">if</span> <span class="n">latex_hdr</span> <span class="k">else</span> <span class="s1">&#39;&#39;</span><span class="p">,</span> <span class="n">tex</span><span class="p">,</span> <span class="n">_latex_end</span>
+                            <span class="k">if</span> <span class="n">latex_hdr</span> <span class="k">else</span> <span class="s1">&#39;&#39;</span><span class="p">))</span></div>
+
+
+
+<div class="viewcode-block" id="export_licenses">
+<a class="viewcode-back" href="../../../api/pypath.resources.descriptions.export_licenses.html#pypath.resources.descriptions.export_licenses">[docs]</a>
+<span class="k">def</span> <span class="nf">export_licenses</span><span class="p">(</span><span class="n">outfile</span> <span class="o">=</span> <span class="s1">&#39;licenses.tsv&#39;</span><span class="p">):</span>
+
+    <span class="n">hdr</span> <span class="o">=</span> <span class="p">[</span>
+        <span class="s1">&#39;Name&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;License&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;License URL&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;Contact&#39;</span><span class="p">,</span>
+    <span class="p">]</span>
+    <span class="n">rows</span> <span class="o">=</span> <span class="p">[]</span>
+
+    <span class="k">for</span> <span class="n">k</span><span class="p">,</span> <span class="n">v</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="n">descriptions</span><span class="p">):</span>
+
+        <span class="n">name</span> <span class="o">=</span> <span class="n">v</span><span class="p">[</span><span class="s1">&#39;label&#39;</span><span class="p">]</span> <span class="k">if</span> <span class="s1">&#39;label&#39;</span> <span class="ow">in</span> <span class="n">v</span> <span class="k">else</span> <span class="n">k</span>
+        <span class="n">license_name</span> <span class="o">=</span> <span class="n">v</span><span class="p">[</span><span class="s1">&#39;license&#39;</span><span class="p">][</span><span class="s1">&#39;name&#39;</span><span class="p">]</span> <span class="k">if</span> <span class="s1">&#39;license&#39;</span> <span class="ow">in</span> <span class="n">v</span> <span class="k">else</span> <span class="s1">&#39;&#39;</span>
+        <span class="n">license_url</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="n">v</span><span class="p">[</span><span class="s1">&#39;license&#39;</span><span class="p">][</span><span class="s1">&#39;url&#39;</span><span class="p">]</span>
+                <span class="k">if</span> <span class="s1">&#39;license&#39;</span> <span class="ow">in</span> <span class="n">v</span> <span class="ow">and</span> <span class="s1">&#39;url&#39;</span> <span class="ow">in</span> <span class="n">v</span><span class="p">[</span><span class="s1">&#39;license&#39;</span><span class="p">]</span> <span class="k">else</span>
+            <span class="s1">&#39;&#39;</span>
+        <span class="p">)</span>
+        <span class="n">emails</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="s1">&#39;,&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="s1">&#39;</span><span class="si">%s</span><span class="s1"> &lt;</span><span class="si">%s</span><span class="s1">&gt;&#39;</span> <span class="o">%</span> <span class="nb">tuple</span><span class="p">(</span><span class="nb">reversed</span><span class="p">(</span><span class="n">e</span><span class="p">))</span> <span class="k">for</span> <span class="n">e</span> <span class="ow">in</span> <span class="n">v</span><span class="p">[</span><span class="s1">&#39;emails&#39;</span><span class="p">])</span>
+            <span class="k">if</span> <span class="s1">&#39;emails&#39;</span> <span class="ow">in</span> <span class="n">v</span> <span class="k">else</span> <span class="s1">&#39;&#39;</span>
+        <span class="p">)</span>
+
+        <span class="n">rows</span><span class="o">.</span><span class="n">append</span><span class="p">([</span>
+            <span class="n">name</span><span class="p">,</span>
+            <span class="n">license_name</span><span class="p">,</span>
+            <span class="n">license_url</span><span class="p">,</span>
+            <span class="n">emails</span><span class="p">,</span>
+        <span class="p">])</span>
+
+    <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">outfile</span><span class="p">,</span> <span class="s1">&#39;w&#39;</span><span class="p">)</span> <span class="k">as</span> <span class="n">fp</span><span class="p">:</span>
+
+        <span class="n">_</span> <span class="o">=</span> <span class="n">fp</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\t</span><span class="s1">&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">hdr</span><span class="p">)</span> <span class="o">+</span> <span class="s1">&#39;</span><span class="se">\n</span><span class="s1">&#39;</span><span class="p">)</span>
+        <span class="n">_</span> <span class="o">=</span> <span class="n">fp</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\n</span><span class="s1">&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span>
+            <span class="s1">&#39;</span><span class="se">\t</span><span class="s1">&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">row</span><span class="p">)</span> <span class="k">for</span> <span class="n">row</span> <span class="ow">in</span> <span class="n">rows</span>
+        <span class="p">))</span></div>
+
+</pre></div>
+
+                </article>
+              
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diff --git a/_modules/pypath/utils/mapping.html b/_modules/pypath/utils/mapping.html
new file mode 100644
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@@ -0,0 +1,4567 @@
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+                <article class="bd-article">
+                  
+  <h1>Source code for pypath.utils.mapping</h1><div class="highlight"><pre>
+<span></span><span class="ch">#!/usr/bin/env python</span>
+<span class="c1"># -*- coding: utf-8 -*-</span>
+
+<span class="c1">#</span>
+<span class="c1">#  This file is part of the `pypath` python module</span>
+<span class="c1">#</span>
+<span class="c1">#  Copyright 2014-2023</span>
+<span class="c1">#  EMBL, EMBL-EBI, Uniklinik RWTH Aachen, Heidelberg University</span>
+<span class="c1">#</span>
+<span class="c1">#  Authors: see the file `README.rst`</span>
+<span class="c1">#  Contact: Dénes Türei (turei.denes@gmail.com)</span>
+<span class="c1">#</span>
+<span class="c1">#  Distributed under the GPLv3 License.</span>
+<span class="c1">#  See accompanying file LICENSE.txt or copy at</span>
+<span class="c1">#      https://www.gnu.org/licenses/gpl-3.0.html</span>
+<span class="c1">#</span>
+<span class="c1">#  Website: https://pypath.omnipathdb.org/</span>
+<span class="c1">#</span>
+
+<span class="kn">from</span> <span class="nn">__future__</span> <span class="kn">import</span> <span class="n">annotations</span>
+
+<span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">Performs mapping between IDs of different consensus systems for</span>
+<span class="sd">proteins and genes, miRNAs, and chemical compounds.</span>
+
+<span class="sd">&quot;&quot;&quot;</span>
+
+<span class="kn">from</span> <span class="nn">future.utils</span> <span class="kn">import</span> <span class="n">iteritems</span>
+<span class="kn">from</span> <span class="nn">past.builtins</span> <span class="kn">import</span> <span class="n">xrange</span><span class="p">,</span> <span class="nb">range</span>
+
+<span class="kn">import</span> <span class="nn">os</span>
+<span class="kn">import</span> <span class="nn">sys</span>
+<span class="kn">import</span> <span class="nn">math</span>
+<span class="kn">import</span> <span class="nn">re</span>
+<span class="kn">import</span> <span class="nn">importlib</span> <span class="k">as</span> <span class="nn">imp</span>
+<span class="kn">import</span> <span class="nn">collections</span>
+<span class="kn">import</span> <span class="nn">functools</span>
+<span class="kn">import</span> <span class="nn">datetime</span>
+<span class="kn">import</span> <span class="nn">time</span>
+
+<span class="kn">import</span> <span class="nn">urllib</span>
+
+<span class="k">if</span> <span class="ow">not</span> <span class="nb">hasattr</span><span class="p">(</span><span class="n">urllib</span><span class="p">,</span> <span class="s1">&#39;urlencode&#39;</span><span class="p">):</span>
+
+    <span class="kn">import</span> <span class="nn">urllib.parse</span>
+    <span class="n">_urllib</span> <span class="o">=</span> <span class="n">urllib</span>
+    <span class="n">urllib</span> <span class="o">=</span> <span class="n">_urllib</span><span class="o">.</span><span class="n">parse</span>
+
+<span class="kn">import</span> <span class="nn">json</span>
+<span class="k">try</span><span class="p">:</span>
+    <span class="kn">import</span> <span class="nn">cPickle</span> <span class="k">as</span> <span class="nn">pickle</span>
+<span class="k">except</span><span class="p">:</span>
+    <span class="kn">import</span> <span class="nn">pickle</span>
+
+<span class="kn">from</span> <span class="nn">typing</span> <span class="kn">import</span> <span class="n">Iterable</span><span class="p">,</span> <span class="n">List</span><span class="p">,</span> <span class="n">Literal</span><span class="p">,</span> <span class="n">Optional</span><span class="p">,</span> <span class="n">Set</span><span class="p">,</span> <span class="n">Union</span>
+
+<span class="kn">import</span> <span class="nn">pandas</span> <span class="k">as</span> <span class="nn">pd</span>
+<span class="kn">import</span> <span class="nn">timeloop</span>
+
+<span class="c1"># from pypath:</span>
+<span class="kn">import</span> <span class="nn">pypath.share.progress</span> <span class="k">as</span> <span class="nn">progress</span>
+<span class="kn">import</span> <span class="nn">pypath.share.common</span> <span class="k">as</span> <span class="nn">common</span>
+<span class="kn">import</span> <span class="nn">pypath_common._constants</span> <span class="k">as</span> <span class="nn">_const</span>
+<span class="kn">import</span> <span class="nn">pypath.share.cache</span> <span class="k">as</span> <span class="nn">cache_mod</span>
+<span class="kn">import</span> <span class="nn">pypath.internals.maps</span> <span class="k">as</span> <span class="nn">maps</span>
+<span class="kn">import</span> <span class="nn">pypath.resources.urls</span> <span class="k">as</span> <span class="nn">urls</span>
+<span class="kn">import</span> <span class="nn">pypath.share.curl</span> <span class="k">as</span> <span class="nn">curl</span>
+<span class="kn">import</span> <span class="nn">pypath.inputs</span> <span class="k">as</span> <span class="nn">inputs</span>
+<span class="kn">import</span> <span class="nn">pypath.inputs.uniprot</span> <span class="k">as</span> <span class="nn">uniprot_input</span>
+<span class="kn">import</span> <span class="nn">pypath.inputs.uniprot_db</span> <span class="k">as</span> <span class="nn">uniprot_db</span>
+<span class="kn">import</span> <span class="nn">pypath.inputs.pro</span> <span class="k">as</span> <span class="nn">pro_input</span>
+<span class="kn">import</span> <span class="nn">pypath.inputs.biomart</span> <span class="k">as</span> <span class="nn">biomart_input</span>
+<span class="kn">import</span> <span class="nn">pypath.inputs.unichem</span> <span class="k">as</span> <span class="nn">unichem_input</span>
+<span class="kn">import</span> <span class="nn">pypath.inputs.ramp</span> <span class="k">as</span> <span class="nn">ramp_input</span>
+<span class="kn">import</span> <span class="nn">pypath.inputs.hmdb</span> <span class="k">as</span> <span class="nn">hmdb_input</span>
+<span class="kn">import</span> <span class="nn">pypath.internals.input_formats</span> <span class="k">as</span> <span class="nn">input_formats</span>
+<span class="kn">import</span> <span class="nn">pypath.utils.reflists</span> <span class="k">as</span> <span class="nn">reflists</span>
+<span class="kn">import</span> <span class="nn">pypath.utils.taxonomy</span> <span class="k">as</span> <span class="nn">taxonomy</span>
+<span class="kn">import</span> <span class="nn">pypath.share.settings</span> <span class="k">as</span> <span class="nn">settings</span>
+<span class="kn">import</span> <span class="nn">pypath.share.session</span> <span class="k">as</span> <span class="nn">session_mod</span>
+<span class="n">_logger</span> <span class="o">=</span> <span class="n">session_mod</span><span class="o">.</span><span class="n">log</span><span class="p">()</span>
+
+
+<span class="n">__all__</span> <span class="o">=</span> <span class="p">[</span><span class="s1">&#39;MapReader&#39;</span><span class="p">,</span> <span class="s1">&#39;MappingTable&#39;</span><span class="p">,</span> <span class="s1">&#39;Mapper&#39;</span><span class="p">]</span>
+
+<span class="n">_logger</span> <span class="o">=</span> <span class="n">session_mod</span><span class="o">.</span><span class="n">Logger</span><span class="p">(</span><span class="n">name</span> <span class="o">=</span> <span class="s1">&#39;mapping&#39;</span><span class="p">)</span>
+<span class="n">_log</span> <span class="o">=</span> <span class="n">_logger</span><span class="o">.</span><span class="n">_log</span>
+
+<span class="k">try</span><span class="p">:</span>
+    <span class="n">UNICHEM_NAME_TYPES</span> <span class="o">=</span> <span class="nb">set</span><span class="p">(</span><span class="n">unichem_input</span><span class="o">.</span><span class="n">unichem_sources</span><span class="p">()</span><span class="o">.</span><span class="n">values</span><span class="p">())</span>
+<span class="k">except</span> <span class="ne">Exception</span> <span class="k">as</span> <span class="n">e</span><span class="p">:</span>
+    <span class="n">exc</span> <span class="o">=</span> <span class="n">sys</span><span class="o">.</span><span class="n">exc_info</span><span class="p">()</span>
+    <span class="n">_log</span><span class="p">(</span><span class="s1">&#39;Failed to retrieve UniChem ID types:&#39;</span><span class="p">)</span>
+    <span class="n">_logger</span><span class="o">.</span><span class="n">_log_traceback</span><span class="p">()</span>
+    <span class="n">UNICHEM_NAME_TYPES</span> <span class="o">=</span> <span class="p">()</span>
+
+<span class="n">RESOURCES_EXPLICIT</span> <span class="o">=</span> <span class="p">(</span><span class="s1">&#39;uniprot&#39;</span><span class="p">,</span> <span class="s1">&#39;basic&#39;</span><span class="p">,</span> <span class="s1">&#39;mirbase&#39;</span><span class="p">,</span> <span class="s1">&#39;ipi&#39;</span><span class="p">)</span>
+
+<span class="n">RESOURCES_IMPLICIT</span> <span class="o">=</span> <span class="p">(</span>
+    <span class="p">(</span>
+        <span class="n">input_formats</span><span class="o">.</span><span class="n">AC_MAPPING</span><span class="p">,</span>
+        <span class="s1">&#39;uniprot&#39;</span><span class="p">,</span>
+        <span class="n">input_formats</span><span class="o">.</span><span class="n">UniprotListMapping</span><span class="p">,</span>
+    <span class="p">),</span>
+    <span class="p">(</span>
+        <span class="n">input_formats</span><span class="o">.</span><span class="n">PRO_MAPPING</span><span class="p">,</span>
+        <span class="s1">&#39;pro&#39;</span><span class="p">,</span>
+        <span class="n">input_formats</span><span class="o">.</span><span class="n">ProMapping</span><span class="p">,</span>
+    <span class="p">),</span>
+    <span class="p">(</span>
+        <span class="n">input_formats</span><span class="o">.</span><span class="n">BIOMART_MAPPING</span><span class="p">,</span>
+        <span class="s1">&#39;biomart&#39;</span><span class="p">,</span>
+        <span class="n">input_formats</span><span class="o">.</span><span class="n">BiomartMapping</span><span class="p">,</span>
+    <span class="p">),</span>
+    <span class="p">(</span>
+        <span class="n">input_formats</span><span class="o">.</span><span class="n">ARRAY_MAPPING</span><span class="p">,</span>
+        <span class="s1">&#39;array&#39;</span><span class="p">,</span>
+        <span class="n">input_formats</span><span class="o">.</span><span class="n">ArrayMapping</span><span class="p">,</span>
+    <span class="p">),</span>
+    <span class="p">(</span>
+        <span class="p">{</span><span class="n">n</span><span class="p">:</span> <span class="n">n</span> <span class="k">for</span> <span class="n">n</span> <span class="ow">in</span> <span class="n">UNICHEM_NAME_TYPES</span><span class="p">},</span>
+        <span class="s1">&#39;unichem&#39;</span><span class="p">,</span>
+        <span class="n">input_formats</span><span class="o">.</span><span class="n">UnichemMapping</span><span class="p">,</span>
+    <span class="p">),</span>
+    <span class="p">(</span>
+        <span class="nb">dict</span><span class="p">(</span>
+            <span class="o">**</span><span class="p">{</span>
+                <span class="n">it</span><span class="p">:</span> <span class="n">it</span>
+                <span class="k">for</span> <span class="n">it</span> <span class="ow">in</span> <span class="n">ramp_input</span><span class="o">.</span><span class="n">ramp_id_types_2</span><span class="p">(</span><span class="s1">&#39;compound&#39;</span><span class="p">)</span>
+            <span class="p">},</span>
+            <span class="o">**</span><span class="n">input_formats</span><span class="o">.</span><span class="n">RAMP_MAPPING</span><span class="p">,</span>
+        <span class="p">),</span>
+        <span class="s1">&#39;ramp&#39;</span><span class="p">,</span>
+        <span class="n">input_formats</span><span class="o">.</span><span class="n">RampMapping</span><span class="p">,</span>
+    <span class="p">),</span>
+    <span class="p">(</span>
+        <span class="nb">dict</span><span class="p">(</span>
+            <span class="o">**</span><span class="p">{</span>
+                <span class="n">it</span><span class="p">:</span> <span class="n">it</span>
+                <span class="k">for</span> <span class="n">it</span> <span class="ow">in</span> <span class="n">hmdb_input</span><span class="o">.</span><span class="n">ID_FIELDS</span>
+            <span class="p">},</span>
+            <span class="o">**</span><span class="n">input_formats</span><span class="o">.</span><span class="n">HMDB_MAPPING</span><span class="p">,</span>
+        <span class="p">),</span>
+        <span class="s1">&#39;hmdb&#39;</span><span class="p">,</span>
+        <span class="n">input_formats</span><span class="o">.</span><span class="n">HmdbMapping</span><span class="p">,</span>
+    <span class="p">),</span>
+<span class="p">)</span>
+
+<span class="n">UNIPROT_ID_TYPES</span> <span class="o">=</span> <span class="p">{</span>
+    <span class="s1">&#39;uniprot&#39;</span><span class="p">,</span>
+    <span class="s1">&#39;trembl&#39;</span><span class="p">,</span>
+    <span class="s1">&#39;swissprot&#39;</span><span class="p">,</span>
+    <span class="s1">&#39;uniprot-pri&#39;</span><span class="p">,</span>
+    <span class="s1">&#39;uniprot-sec&#39;</span><span class="p">,</span>
+<span class="p">}</span>
+
+<span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">Classes for reading and use serving ID mapping data from custom file,</span>
+<span class="sd">function, UniProt, UniProt ID Mapping, Ensembl BioMart,</span>
+<span class="sd">PRO (Protein Ontology), miRBase or pickle file.</span>
+<span class="sd">&quot;&quot;&quot;</span>
+
+<span class="n">MappingTableKey</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">namedtuple</span><span class="p">(</span>
+    <span class="s1">&#39;MappingTableKey&#39;</span><span class="p">,</span>
+    <span class="p">[</span>
+        <span class="s1">&#39;id_type&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;target_id_type&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;ncbi_tax_id&#39;</span><span class="p">,</span>
+    <span class="p">],</span>
+<span class="p">)</span>
+<span class="n">MappingTableKey</span><span class="o">.</span><span class="fm">__new__</span><span class="o">.</span><span class="vm">__defaults__</span> <span class="o">=</span> <span class="p">(</span><span class="s1">&#39;protein&#39;</span><span class="p">,</span> <span class="mi">9606</span><span class="p">)</span>
+
+
+<div class="viewcode-block" id="MapReader">
+<a class="viewcode-back" href="../../../api/pypath.utils.mapping.MapReader.html#pypath.utils.mapping.MapReader">[docs]</a>
+<span class="k">class</span> <span class="nc">MapReader</span><span class="p">(</span><span class="n">session_mod</span><span class="o">.</span><span class="n">Logger</span><span class="p">):</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Reads ID translation data and creates ``MappingTable`` instances.</span>
+<span class="sd">    When initializing ID conversion tables for the first time</span>
+<span class="sd">    data is downloaded from UniProt and read into dictionaries.</span>
+<span class="sd">    It takes a couple of seconds. Data is saved to pickle</span>
+<span class="sd">    dumps, this way later the tables load much faster.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+<div class="viewcode-block" id="MapReader.__init__">
+<a class="viewcode-back" href="../../../api/pypath.utils.mapping.MapReader.html#pypath.utils.mapping.MapReader.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">param</span><span class="p">,</span>
+            <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">entity_type</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">load_a_to_b</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
+            <span class="n">load_b_to_a</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+            <span class="n">uniprots</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">lifetime</span> <span class="o">=</span> <span class="mi">300</span><span class="p">,</span>
+            <span class="n">resource_id_types</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+        <span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Args</span>
+<span class="sd">            param (MappingInput): A mapping table definition, any child of</span>
+<span class="sd">                the `internals.input_formats.MappingInput` class.</span>
+<span class="sd">            ncbi_tax_id (int): NCBI Taxonomy identifier of the organism.</span>
+<span class="sd">            entity_type (str): An optional, custom string showing the type of</span>
+<span class="sd">                the entities,  e.g. `protein`. This is not mandatory for the</span>
+<span class="sd">                identification of mapping tables, hence the same name types</span>
+<span class="sd">                can&#39;t be used for different entities. E.g. if both proteins</span>
+<span class="sd">                and miRNAs have Entrez gene IDs then these should be</span>
+<span class="sd">                different ID types (e.g. `entrez_protein` and `entrez_mirna`)</span>
+<span class="sd">                or both protein and miRNA IDs can be loaded into one mapping</span>
+<span class="sd">                table and simply called `entrez`.</span>
+<span class="sd">            load_a_to_b (bool): Load the mapping table for translation from</span>
+<span class="sd">                `id_type` to `target_id_type`.</span>
+<span class="sd">            load_b_to_a (bool): Load the mapping table for translation from</span>
+<span class="sd">                `target_id_type` to `id_type`.</span>
+<span class="sd">            uniprots (set): UniProt IDs to query in case the source of the</span>
+<span class="sd">                mapping table is the UniProt web service.</span>
+<span class="sd">            lifetime (int): If this table has not been used for longer than</span>
+<span class="sd">                this preiod it is to be removed at next cleanup. Time in</span>
+<span class="sd">                seconds. Passed to ``MappingTable``.</span>
+<span class="sd">            resource_id_types: Additional mappings between pypath and resource</span>
+<span class="sd">                specific identifier type labels.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">session_mod</span><span class="o">.</span><span class="n">Logger</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">name</span> <span class="o">=</span> <span class="s1">&#39;mapping&#39;</span><span class="p">)</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="n">ncbi_tax_id</span> <span class="ow">or</span>
+            <span class="n">param</span><span class="o">.</span><span class="n">ncbi_tax_id</span> <span class="ow">or</span>
+            <span class="n">settings</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">&#39;default_organism&#39;</span><span class="p">)</span>
+        <span class="p">)</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span>
+            <span class="s1">&#39;Reader created for ID translation table, parameters: &#39;</span>
+            <span class="s1">&#39;`ncbi_tax_id=</span><span class="si">%u</span><span class="s1">, id_a=</span><span class="si">%s</span><span class="s1">, id_b=</span><span class="si">%s</span><span class="s1">, &#39;</span>
+            <span class="s1">&#39;load_a_to_b=</span><span class="si">%u</span><span class="s1">, load_b_to_a=</span><span class="si">%u</span><span class="s1">, &#39;</span>
+            <span class="s1">&#39;input_type=</span><span class="si">%s</span><span class="s1"> (</span><span class="si">%s</span><span class="s1">)`.&#39;</span> <span class="o">%</span> <span class="p">(</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">ncbi_tax_id</span><span class="p">,</span>
+                <span class="n">param</span><span class="o">.</span><span class="n">id_type_a</span><span class="p">,</span>
+                <span class="n">param</span><span class="o">.</span><span class="n">id_type_b</span><span class="p">,</span>
+                <span class="n">load_a_to_b</span><span class="p">,</span>
+                <span class="n">load_b_to_a</span><span class="p">,</span>
+                <span class="n">param</span><span class="o">.</span><span class="n">type</span><span class="p">,</span>
+                <span class="n">param</span><span class="o">.</span><span class="vm">__class__</span><span class="o">.</span><span class="vm">__name__</span><span class="p">,</span>
+            <span class="p">)</span>
+        <span class="p">)</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">cachedir</span> <span class="o">=</span> <span class="n">cache_mod</span><span class="o">.</span><span class="n">get_cachedir</span><span class="p">()</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">id_type_a</span> <span class="o">=</span> <span class="n">param</span><span class="o">.</span><span class="n">id_type_a</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">id_type_b</span> <span class="o">=</span> <span class="n">param</span><span class="o">.</span><span class="n">id_type_b</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">load_a_to_b</span> <span class="o">=</span> <span class="n">load_a_to_b</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">load_b_to_a</span> <span class="o">=</span> <span class="n">load_b_to_a</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">entity_type</span> <span class="o">=</span> <span class="n">entity_type</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">source_type</span> <span class="o">=</span> <span class="n">param</span><span class="o">.</span><span class="n">type</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">param</span> <span class="o">=</span> <span class="n">param</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">lifetime</span> <span class="o">=</span> <span class="n">lifetime</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">a_to_b</span> <span class="o">=</span> <span class="kc">None</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">b_to_a</span> <span class="o">=</span> <span class="kc">None</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">uniprots</span> <span class="o">=</span> <span class="n">uniprots</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">_resource_id_types</span> <span class="o">=</span> <span class="n">resource_id_types</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">load</span><span class="p">()</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">reload</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="n">modname</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="vm">__class__</span><span class="o">.</span><span class="vm">__module__</span>
+        <span class="n">mod</span> <span class="o">=</span> <span class="nb">__import__</span><span class="p">(</span><span class="n">modname</span><span class="p">,</span> <span class="n">fromlist</span> <span class="o">=</span> <span class="p">[</span><span class="n">modname</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;.&#39;</span><span class="p">)[</span><span class="mi">0</span><span class="p">]])</span>
+        <span class="n">imp</span><span class="o">.</span><span class="n">reload</span><span class="p">(</span><span class="n">mod</span><span class="p">)</span>
+        <span class="n">new</span> <span class="o">=</span> <span class="nb">getattr</span><span class="p">(</span><span class="n">mod</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="vm">__class__</span><span class="o">.</span><span class="vm">__name__</span><span class="p">)</span>
+        <span class="nb">setattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">&#39;__class__&#39;</span><span class="p">,</span> <span class="n">new</span><span class="p">)</span>
+
+
+<div class="viewcode-block" id="MapReader.load">
+<a class="viewcode-back" href="../../../api/pypath.utils.mapping.MapReader.html#pypath.utils.mapping.MapReader.load">[docs]</a>
+    <span class="k">def</span> <span class="nf">load</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        The complete process of loading mapping tables. First sets up the</span>
+<span class="sd">        paths of the cache files, then loads the tables from the cache files</span>
+<span class="sd">        or the original sources if necessary. Upon successful loading from an</span>
+<span class="sd">        original source writes the results to cache files.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">use_cache</span> <span class="o">=</span> <span class="n">settings</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">&#39;mapping_use_cache&#39;</span><span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">setup_cache</span><span class="p">()</span>
+
+        <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">use_cache</span><span class="p">:</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">read_cache</span><span class="p">()</span>
+
+        <span class="k">if</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">tables_loaded</span><span class="p">():</span>
+
+            <span class="c1"># read from the original source</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">read</span><span class="p">()</span>
+
+            <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">tables_loaded</span><span class="p">():</span>
+
+                <span class="c1"># write cache only at successful loading</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">write_cache</span><span class="p">()</span></div>
+
+
+
+    <span class="nd">@property</span>
+    <span class="k">def</span> <span class="nf">mapping_table_a_to_b</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Returns a ``MappingTable`` instance created from the already</span>
+<span class="sd">        loaded data.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_get_mapping_table</span><span class="p">(</span><span class="s1">&#39;a&#39;</span><span class="p">,</span> <span class="s1">&#39;b&#39;</span><span class="p">)</span>
+
+
+    <span class="nd">@property</span>
+    <span class="k">def</span> <span class="nf">mapping_table_b_to_a</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Returns a ``MappingTable`` instance created from the already</span>
+<span class="sd">        loaded data.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_get_mapping_table</span><span class="p">(</span><span class="s1">&#39;b&#39;</span><span class="p">,</span> <span class="s1">&#39;a&#39;</span><span class="p">)</span>
+
+
+<div class="viewcode-block" id="MapReader.id_type_side">
+<a class="viewcode-back" href="../../../api/pypath.utils.mapping.MapReader.html#pypath.utils.mapping.MapReader.id_type_side">[docs]</a>
+    <span class="k">def</span> <span class="nf">id_type_side</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">id_type</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Tells if an ID type is on the &quot;a&quot; or &quot;b&quot; (source or target) side</span>
+<span class="sd">        in the current mapping table definition.</span>
+
+<span class="sd">        Args</span>
+<span class="sd">            id_type (str): An ID type label.</span>
+
+<span class="sd">        Returns</span>
+<span class="sd">            Returns the string &quot;a&quot; if `id_type` is on the source side in</span>
+<span class="sd">            the mapping table definition, &quot;b&quot; if it is on the target side,</span>
+<span class="sd">            None if the `id_type` is not in the definition.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">return</span> <span class="p">(</span>
+            <span class="s1">&#39;a&#39;</span>
+                <span class="k">if</span> <span class="n">id_type</span> <span class="o">==</span> <span class="bp">self</span><span class="o">.</span><span class="n">id_type_a</span> <span class="k">else</span>
+            <span class="s1">&#39;b&#39;</span>
+                <span class="k">if</span> <span class="n">id_type</span> <span class="o">==</span> <span class="bp">self</span><span class="o">.</span><span class="n">id_type_b</span> <span class="k">else</span>
+            <span class="kc">None</span>
+        <span class="p">)</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">_get_mapping_table</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">*</span><span class="n">args</span><span class="p">):</span>
+
+        <span class="n">data</span> <span class="o">=</span> <span class="nb">getattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">&#39;</span><span class="si">%s</span><span class="s1">_to_</span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="n">args</span><span class="p">)</span>
+        <span class="n">id_type</span> <span class="o">=</span> <span class="nb">getattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">&#39;id_type_</span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="n">args</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span>
+        <span class="n">target_id_type</span> <span class="o">=</span> <span class="nb">getattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">&#39;id_type_</span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="n">args</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span>
+
+        <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">data</span><span class="p">,</span> <span class="nb">dict</span><span class="p">):</span>
+
+            <span class="k">return</span> <span class="n">MappingTable</span><span class="p">(</span>
+                <span class="n">data</span> <span class="o">=</span> <span class="n">data</span><span class="p">,</span>
+                <span class="n">id_type</span> <span class="o">=</span> <span class="n">id_type</span><span class="p">,</span>
+                <span class="n">target_id_type</span> <span class="o">=</span> <span class="n">target_id_type</span><span class="p">,</span>
+                <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">ncbi_tax_id</span><span class="p">,</span>
+                <span class="n">lifetime</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">lifetime</span><span class="p">,</span>
+            <span class="p">)</span>
+
+
+<div class="viewcode-block" id="MapReader.tables_loaded">
+<a class="viewcode-back" href="../../../api/pypath.utils.mapping.MapReader.html#pypath.utils.mapping.MapReader.tables_loaded">[docs]</a>
+    <span class="k">def</span> <span class="nf">tables_loaded</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Tells if the requested tables have been created.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">return</span> <span class="p">(</span>
+            <span class="p">(</span><span class="nb">bool</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">a_to_b</span><span class="p">)</span> <span class="ow">or</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">load_a_to_b</span><span class="p">)</span> <span class="ow">and</span>
+            <span class="p">(</span><span class="nb">bool</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">b_to_a</span><span class="p">)</span> <span class="ow">or</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">load_b_to_a</span><span class="p">)</span>
+        <span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="MapReader.write_cache">
+<a class="viewcode-back" href="../../../api/pypath.utils.mapping.MapReader.html#pypath.utils.mapping.MapReader.write_cache">[docs]</a>
+    <span class="k">def</span> <span class="nf">write_cache</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Exports the ID translation data into pickle files.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_write_cache</span><span class="p">(</span><span class="s1">&#39;a&#39;</span><span class="p">,</span> <span class="s1">&#39;b&#39;</span><span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">_write_cache</span><span class="p">(</span><span class="s1">&#39;b&#39;</span><span class="p">,</span> <span class="s1">&#39;a&#39;</span><span class="p">)</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">_write_cache</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">*</span><span class="n">args</span><span class="p">):</span>
+
+        <span class="n">data</span> <span class="o">=</span> <span class="nb">getattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">&#39;</span><span class="si">%s</span><span class="s1">_to_</span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="n">args</span><span class="p">)</span>
+
+        <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">_to_be_loaded</span><span class="p">(</span><span class="o">*</span><span class="n">args</span><span class="p">)</span> <span class="ow">and</span> <span class="n">data</span><span class="p">:</span>
+
+            <span class="n">cachefile</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_attr</span><span class="p">(</span><span class="s1">&#39;cachefile&#39;</span><span class="p">,</span> <span class="o">*</span><span class="n">args</span><span class="p">)</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">_remove_cache_file</span><span class="p">(</span><span class="o">*</span><span class="n">args</span><span class="p">)</span>
+
+            <span class="n">pickle</span><span class="o">.</span><span class="n">dump</span><span class="p">(</span><span class="n">data</span><span class="p">,</span> <span class="nb">open</span><span class="p">(</span><span class="n">cachefile</span><span class="p">,</span> <span class="s1">&#39;wb&#39;</span><span class="p">))</span>
+
+
+<div class="viewcode-block" id="MapReader.read_cache">
+<a class="viewcode-back" href="../../../api/pypath.utils.mapping.MapReader.html#pypath.utils.mapping.MapReader.read_cache">[docs]</a>
+    <span class="k">def</span> <span class="nf">read_cache</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Reads the ID translation data from a previously saved pickle file.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_read_cache</span><span class="p">(</span><span class="s1">&#39;a&#39;</span><span class="p">,</span> <span class="s1">&#39;b&#39;</span><span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">_read_cache</span><span class="p">(</span><span class="s1">&#39;b&#39;</span><span class="p">,</span> <span class="s1">&#39;a&#39;</span><span class="p">)</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">_read_cache</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">*</span><span class="n">args</span><span class="p">):</span>
+
+        <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">_to_be_loaded</span><span class="p">(</span><span class="o">*</span><span class="n">args</span><span class="p">):</span>
+
+            <span class="n">cachefile</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_attr</span><span class="p">(</span><span class="s1">&#39;cachefile&#39;</span><span class="p">,</span> <span class="o">*</span><span class="n">args</span><span class="p">)</span>
+
+            <span class="k">if</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">exists</span><span class="p">(</span><span class="n">cachefile</span><span class="p">):</span>
+
+                <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">cachefile</span><span class="p">,</span> <span class="s1">&#39;rb&#39;</span><span class="p">)</span> <span class="k">as</span> <span class="n">fp</span><span class="p">:</span>
+
+                    <span class="n">from_cache</span> <span class="o">=</span> <span class="n">pickle</span><span class="o">.</span><span class="n">load</span><span class="p">(</span><span class="n">fp</span><span class="p">)</span>
+
+                <span class="nb">setattr</span><span class="p">(</span>
+                    <span class="bp">self</span><span class="p">,</span>
+                    <span class="s1">&#39;</span><span class="si">%s</span><span class="s1">_to_</span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="n">args</span><span class="p">,</span>
+                    <span class="n">from_cache</span><span class="p">,</span>
+                <span class="p">)</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span>
+                    <span class="s1">&#39;Loading `</span><span class="si">%s</span><span class="s1">` to `</span><span class="si">%s</span><span class="s1">` mapping table &#39;</span>
+                    <span class="s1">&#39;from pickle file `</span><span class="si">%s</span><span class="s1">`.&#39;</span> <span class="o">%</span> <span class="p">(</span>
+                        <span class="bp">self</span><span class="o">.</span><span class="n">param</span><span class="o">.</span><span class="n">id_type_a</span><span class="p">,</span>
+                        <span class="bp">self</span><span class="o">.</span><span class="n">param</span><span class="o">.</span><span class="n">id_type_b</span><span class="p">,</span>
+                        <span class="n">cachefile</span><span class="p">,</span>
+                    <span class="p">)</span>
+                <span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">_to_be_loaded</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">*</span><span class="n">args</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_attr</span><span class="p">(</span><span class="s1">&#39;load&#39;</span><span class="p">,</span> <span class="o">*</span><span class="n">args</span><span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">_attr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">attr</span><span class="p">,</span> <span class="o">*</span><span class="n">args</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="nb">getattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">_attr_name</span><span class="p">(</span><span class="n">attr</span><span class="p">,</span> <span class="o">*</span><span class="n">args</span><span class="p">))</span>
+
+
+    <span class="nd">@staticmethod</span>
+    <span class="k">def</span> <span class="nf">_attr_name</span><span class="p">(</span><span class="n">attr</span><span class="p">,</span> <span class="o">*</span><span class="n">args</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="s1">&#39;</span><span class="si">%s</span><span class="s1">_</span><span class="si">%s</span><span class="s1">_to_</span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="p">((</span><span class="n">attr</span><span class="p">,)</span> <span class="o">+</span> <span class="n">args</span><span class="p">)</span>
+
+
+<div class="viewcode-block" id="MapReader.read">
+<a class="viewcode-back" href="../../../api/pypath.utils.mapping.MapReader.html#pypath.utils.mapping.MapReader.read">[docs]</a>
+    <span class="k">def</span> <span class="nf">read</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Reads the ID translation data from the original source.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">method</span> <span class="o">=</span> <span class="s1">&#39;read_mapping_</span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="bp">self</span><span class="o">.</span><span class="n">source_type</span>
+
+        <span class="k">if</span> <span class="nb">hasattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">method</span><span class="p">):</span>
+
+            <span class="nb">getattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">method</span><span class="p">)()</span></div>
+
+
+
+<div class="viewcode-block" id="MapReader.setup_cache">
+<a class="viewcode-back" href="../../../api/pypath.utils.mapping.MapReader.html#pypath.utils.mapping.MapReader.setup_cache">[docs]</a>
+    <span class="k">def</span> <span class="nf">setup_cache</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Constructs the cache file path as md5 hash of the parameters.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_setup_cache</span><span class="p">(</span><span class="s1">&#39;a&#39;</span><span class="p">,</span> <span class="s1">&#39;b&#39;</span><span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">_setup_cache</span><span class="p">(</span><span class="s1">&#39;b&#39;</span><span class="p">,</span> <span class="s1">&#39;a&#39;</span><span class="p">)</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">_setup_cache</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">*</span><span class="n">args</span><span class="p">):</span>
+
+        <span class="n">mapping_id_attr</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_attr_name</span><span class="p">(</span><span class="s1">&#39;mapping_id&#39;</span><span class="p">,</span> <span class="o">*</span><span class="n">args</span><span class="p">)</span>
+        <span class="n">cachefile_attr</span>  <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_attr_name</span><span class="p">(</span><span class="s1">&#39;cachefile&#39;</span><span class="p">,</span> <span class="o">*</span><span class="n">args</span><span class="p">)</span>
+
+        <span class="nb">setattr</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">mapping_id_attr</span><span class="p">,</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">_get_mapping_id</span><span class="p">(</span><span class="o">*</span><span class="n">args</span><span class="p">),</span>
+        <span class="p">)</span>
+
+        <span class="nb">setattr</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">cachefile_attr</span><span class="p">,</span>
+            <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">cachedir</span><span class="p">,</span> <span class="nb">getattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">mapping_id_attr</span><span class="p">)),</span>
+        <span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">_get_mapping_id</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">*</span><span class="n">args</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Returns an md5 checksum unambigously identifying the mapping table</span>
+<span class="sd">        by the identifiers, the direction of translation, the organism</span>
+<span class="sd">        and other parameters like, for example, the source URL.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">return</span> <span class="n">common</span><span class="o">.</span><span class="n">md5</span><span class="p">(</span>
+            <span class="n">json</span><span class="o">.</span><span class="n">dumps</span><span class="p">(</span>
+                <span class="p">(</span>
+                    <span class="nb">getattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">&#39;id_type_</span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="n">args</span><span class="p">[</span><span class="mi">0</span><span class="p">]),</span>
+                    <span class="nb">getattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">&#39;id_type_</span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="n">args</span><span class="p">[</span><span class="mi">1</span><span class="p">]),</span>
+                    <span class="bp">self</span><span class="o">.</span><span class="n">ncbi_tax_id</span><span class="p">,</span>
+                    <span class="nb">sorted</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">param</span><span class="o">.</span><span class="vm">__dict__</span><span class="o">.</span><span class="n">items</span><span class="p">())</span>
+                <span class="p">)</span>
+            <span class="p">)</span>
+        <span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">_cache_files_exist</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Checks if both cache files are either not necessary or exist.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">return</span> <span class="p">(</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">cache_file_exists</span><span class="p">(</span><span class="s1">&#39;a&#39;</span><span class="p">,</span> <span class="s1">&#39;b&#39;</span><span class="p">)</span> <span class="ow">and</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">cache_file_exists</span><span class="p">(</span><span class="s1">&#39;b&#39;</span><span class="p">,</span> <span class="s1">&#39;a&#39;</span><span class="p">)</span>
+        <span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">_cache_file_exists</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">*</span><span class="n">args</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Checks if a cache file is either not necessary or exists.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">return</span> <span class="p">(</span>
+            <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">_attr</span><span class="p">(</span><span class="s1">&#39;load&#39;</span><span class="p">,</span> <span class="o">*</span><span class="n">args</span><span class="p">)</span> <span class="ow">or</span>
+            <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">isfile</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_attr</span><span class="p">(</span><span class="s1">&#39;cachefile&#39;</span><span class="p">,</span> <span class="o">*</span><span class="n">args</span><span class="p">))</span>
+        <span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">_remove_cache_file</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">*</span><span class="n">args</span><span class="p">):</span>
+
+        <span class="n">cachefile</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_attr</span><span class="p">(</span><span class="s1">&#39;cachefile&#39;</span><span class="p">,</span> <span class="o">*</span><span class="n">args</span><span class="p">)</span>
+
+        <span class="k">if</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">exists</span><span class="p">(</span><span class="n">cachefile</span><span class="p">):</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span><span class="s1">&#39;Removing mapping table cache file `</span><span class="si">%s</span><span class="s1">`.&#39;</span> <span class="o">%</span> <span class="n">cachefile</span><span class="p">)</span>
+            <span class="n">os</span><span class="o">.</span><span class="n">remove</span><span class="p">(</span><span class="n">cachefile</span><span class="p">)</span>
+
+
+<div class="viewcode-block" id="MapReader.read_mapping_file">
+<a class="viewcode-back" href="../../../api/pypath.utils.mapping.MapReader.html#pypath.utils.mapping.MapReader.read_mapping_file">[docs]</a>
+    <span class="k">def</span> <span class="nf">read_mapping_file</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Reads a mapping table from a local file or a function.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">if</span> <span class="ow">not</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">exists</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">param</span><span class="o">.</span><span class="n">input</span><span class="p">):</span>
+
+            <span class="n">method</span> <span class="o">=</span> <span class="n">inputs</span><span class="o">.</span><span class="n">get_method</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">param</span><span class="o">.</span><span class="n">input</span><span class="p">)</span>
+
+            <span class="k">if</span> <span class="ow">not</span> <span class="n">method</span><span class="p">:</span>
+
+                <span class="k">return</span> <span class="p">{}</span>
+
+            <span class="k">else</span><span class="p">:</span>
+
+                <span class="n">input_args</span> <span class="o">=</span> <span class="p">(</span>
+                    <span class="bp">self</span><span class="o">.</span><span class="n">param</span><span class="o">.</span><span class="n">input_args</span>
+                        <span class="k">if</span> <span class="nb">hasattr</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">param</span><span class="p">,</span> <span class="s1">&#39;input_args&#39;</span><span class="p">)</span> <span class="k">else</span>
+                    <span class="p">{}</span>
+                <span class="p">)</span>
+                <span class="n">infile</span> <span class="o">=</span> <span class="n">method</span><span class="p">(</span><span class="o">**</span><span class="n">input_args</span><span class="p">)</span>
+
+        <span class="k">else</span><span class="p">:</span>
+
+            <span class="n">infile</span> <span class="o">=</span> <span class="nb">open</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">param</span><span class="o">.</span><span class="n">input</span><span class="p">,</span> <span class="n">encoding</span> <span class="o">=</span> <span class="s1">&#39;utf-8&#39;</span><span class="p">,</span> <span class="n">mode</span> <span class="o">=</span> <span class="s1">&#39;r&#39;</span><span class="p">)</span>
+            <span class="n">total</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">getsize</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">param</span><span class="o">.</span><span class="n">input</span><span class="p">)</span>
+
+        <span class="n">a_to_b</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">defaultdict</span><span class="p">(</span><span class="nb">set</span><span class="p">)</span>
+        <span class="n">b_to_a</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">defaultdict</span><span class="p">(</span><span class="nb">set</span><span class="p">)</span>
+
+        <span class="k">for</span> <span class="n">i</span><span class="p">,</span> <span class="n">line</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">infile</span><span class="p">):</span>
+
+            <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">param</span><span class="o">.</span><span class="n">header</span> <span class="ow">and</span> <span class="n">i</span> <span class="o">&lt;</span> <span class="bp">self</span><span class="o">.</span><span class="n">param</span><span class="o">.</span><span class="n">header</span><span class="p">:</span>
+
+                <span class="k">continue</span>
+
+            <span class="k">if</span> <span class="nb">hasattr</span><span class="p">(</span><span class="n">line</span><span class="p">,</span> <span class="s1">&#39;decode&#39;</span><span class="p">):</span>
+
+                <span class="n">line</span> <span class="o">=</span> <span class="n">line</span><span class="o">.</span><span class="n">decode</span><span class="p">(</span><span class="s1">&#39;utf-8&#39;</span><span class="p">)</span>
+
+            <span class="k">if</span> <span class="nb">hasattr</span><span class="p">(</span><span class="n">line</span><span class="p">,</span> <span class="s1">&#39;rstrip&#39;</span><span class="p">):</span>
+
+                <span class="n">line</span> <span class="o">=</span> <span class="n">line</span><span class="o">.</span><span class="n">rstrip</span><span class="p">()</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">param</span><span class="o">.</span><span class="n">separator</span><span class="p">)</span>
+
+            <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">line</span><span class="p">)</span> <span class="o">&lt;</span> <span class="nb">max</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">param</span><span class="o">.</span><span class="n">col_a</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">param</span><span class="o">.</span><span class="n">col_b</span><span class="p">):</span>
+
+                <span class="k">continue</span>
+
+            <span class="n">id_a</span> <span class="o">=</span> <span class="n">line</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">param</span><span class="o">.</span><span class="n">col_a</span><span class="p">]</span>
+            <span class="n">id_b</span> <span class="o">=</span> <span class="n">line</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">param</span><span class="o">.</span><span class="n">col_b</span><span class="p">]</span>
+
+            <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">load_a_to_b</span><span class="p">:</span>
+
+                <span class="n">a_to_b</span><span class="p">[</span><span class="n">id_a</span><span class="p">]</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">id_b</span><span class="p">)</span>
+
+            <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">load_b_to_a</span><span class="p">:</span>
+
+                <span class="n">b_to_a</span><span class="p">[</span><span class="n">id_b</span><span class="p">]</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">id_a</span><span class="p">)</span>
+
+        <span class="k">if</span> <span class="nb">hasattr</span><span class="p">(</span><span class="n">infile</span><span class="p">,</span> <span class="s1">&#39;close&#39;</span><span class="p">):</span>
+
+            <span class="n">infile</span><span class="o">.</span><span class="n">close</span><span class="p">()</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">a_to_b</span> <span class="o">=</span> <span class="n">a_to_b</span> <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">load_a_to_b</span> <span class="k">else</span> <span class="kc">None</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">b_to_a</span> <span class="o">=</span> <span class="n">b_to_a</span> <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">load_b_to_a</span> <span class="k">else</span> <span class="kc">None</span></div>
+
+
+
+    <span class="nd">@staticmethod</span>
+    <span class="k">def</span> <span class="nf">_uniprotkb_id_type</span><span class="p">(</span><span class="n">id_type</span><span class="p">:</span> <span class="nb">str</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">bool</span><span class="p">:</span>
+
+        <span class="k">return</span> <span class="n">input_formats</span><span class="o">.</span><span class="n">UniprotListMapping</span><span class="o">.</span><span class="n">_uniprotkb_id_type</span><span class="p">(</span>
+            <span class="n">id_type</span><span class="p">,</span>
+        <span class="p">)</span>
+
+
+<div class="viewcode-block" id="MapReader.read_mapping_uniprot_list">
+<a class="viewcode-back" href="../../../api/pypath.utils.mapping.MapReader.html#pypath.utils.mapping.MapReader.read_mapping_uniprot_list">[docs]</a>
+    <span class="k">def</span> <span class="nf">read_mapping_uniprot_list</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Builds a mapping table by downloading data from UniProt&#39;s</span>
+<span class="sd">        upload lists service.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">a_to_b</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">defaultdict</span><span class="p">(</span><span class="nb">set</span><span class="p">)</span>
+        <span class="n">b_to_a</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">defaultdict</span><span class="p">(</span><span class="nb">set</span><span class="p">)</span>
+        <span class="n">swap</span> <span class="o">=</span> <span class="kc">False</span>
+
+        <span class="k">if</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">uniprots</span><span class="p">:</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">set_uniprot_space</span><span class="p">()</span>
+
+        <span class="c1"># We need a list to query this service, and we have method only for</span>
+        <span class="c1"># getting a proteome wide list of UniProt IDs. If the translated</span>
+        <span class="c1"># ID type is not UniProt, then first we need to translate the</span>
+        <span class="c1"># proteome wide reference list from UniProt to the target ID type.</span>
+        <span class="k">if</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">_uniprotkb_id_type</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">param</span><span class="o">.</span><span class="n">id_type_a</span><span class="p">):</span>
+
+            <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">_uniprotkb_id_type</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">param</span><span class="o">.</span><span class="n">id_type_b</span><span class="p">):</span>
+
+                <span class="n">swap</span> <span class="o">=</span> <span class="kc">True</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">param</span><span class="o">.</span><span class="n">swap_sides</span><span class="p">()</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">load_a_to_b</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">load_b_to_a</span> <span class="o">=</span> <span class="p">(</span>
+                    <span class="bp">self</span><span class="o">.</span><span class="n">load_b_to_a</span><span class="p">,</span>
+                    <span class="bp">self</span><span class="o">.</span><span class="n">load_a_to_b</span><span class="p">,</span>
+                <span class="p">)</span>
+                <span class="n">upload_ac_list</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">uniprots</span>
+
+            <span class="k">else</span><span class="p">:</span>
+
+                <span class="n">u_target</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_read_mapping_uniprot_list</span><span class="p">(</span>
+                    <span class="n">uniprot_id_type_a</span> <span class="o">=</span> <span class="s1">&#39;UniProtKB_AC-ID&#39;</span><span class="p">,</span>
+                    <span class="n">uniprot_id_type_b</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">param</span><span class="o">.</span><span class="n">uniprot_id_type_a</span><span class="p">,</span>
+                <span class="p">)</span>
+
+                <span class="n">upload_ac_list</span> <span class="o">=</span> <span class="p">[</span><span class="n">l</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\t</span><span class="s1">&#39;</span><span class="p">)[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span> <span class="k">for</span> <span class="n">l</span> <span class="ow">in</span> <span class="n">u_target</span><span class="p">]</span>
+
+        <span class="k">else</span><span class="p">:</span>
+
+            <span class="n">upload_ac_list</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">uniprots</span>
+
+        <span class="n">uniprot_data</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_read_mapping_uniprot_list</span><span class="p">(</span>
+            <span class="n">upload_ac_list</span> <span class="o">=</span> <span class="n">upload_ac_list</span><span class="p">,</span>
+        <span class="p">)</span>
+        <span class="n">ens</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">param</span><span class="o">.</span><span class="n">id_type_a</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s1">&#39;ens&#39;</span><span class="p">)</span> <span class="ow">or</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">param</span><span class="o">.</span><span class="n">id_type_b</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s1">&#39;ens&#39;</span><span class="p">)</span> <span class="ow">or</span>
+            <span class="s1">&#39;ensembl&#39;</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">param</span><span class="o">.</span><span class="n">id_type_a</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span> <span class="ow">or</span>
+            <span class="s1">&#39;ensembl&#39;</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">param</span><span class="o">.</span><span class="n">id_type_b</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span>
+        <span class="p">)</span>
+        <span class="n">reens</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">compile</span><span class="p">(</span><span class="sa">r</span><span class="s1">&#39;(ENS[A-Z]+\d+)\.\d+&#39;</span><span class="p">)</span>
+
+        <span class="k">for</span> <span class="n">l</span> <span class="ow">in</span> <span class="n">uniprot_data</span><span class="p">:</span>
+
+            <span class="k">if</span> <span class="ow">not</span> <span class="n">l</span><span class="p">:</span>
+
+                <span class="k">continue</span>
+
+            <span class="k">if</span> <span class="n">ens</span><span class="p">:</span>
+
+                <span class="n">l</span> <span class="o">=</span> <span class="n">reens</span><span class="o">.</span><span class="n">sub</span><span class="p">(</span><span class="sa">r</span><span class="s1">&#39;\1&#39;</span><span class="p">,</span> <span class="n">l</span><span class="p">)</span>
+
+            <span class="n">l</span> <span class="o">=</span> <span class="n">l</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\t</span><span class="s1">&#39;</span><span class="p">)</span>
+
+            <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">load_a_to_b</span><span class="p">:</span>
+
+                <span class="n">a_to_b</span><span class="p">[</span><span class="n">l</span><span class="p">[</span><span class="mi">0</span><span class="p">]]</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">l</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span>
+
+            <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">load_b_to_a</span><span class="p">:</span>
+
+                <span class="n">b_to_a</span><span class="p">[</span><span class="n">l</span><span class="p">[</span><span class="mi">1</span><span class="p">]]</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">l</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span>
+
+        <span class="k">if</span> <span class="n">swap</span><span class="p">:</span>
+
+            <span class="n">a_to_b</span><span class="p">,</span> <span class="n">b_to_a</span> <span class="o">=</span> <span class="n">b_to_a</span><span class="p">,</span> <span class="n">a_to_b</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">load_a_to_b</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">load_b_to_a</span> <span class="o">=</span> <span class="p">(</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">load_b_to_a</span><span class="p">,</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">load_a_to_b</span><span class="p">,</span>
+            <span class="p">)</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">param</span><span class="o">.</span><span class="n">swap_sides</span><span class="p">()</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">a_to_b</span> <span class="o">=</span> <span class="n">a_to_b</span> <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">load_a_to_b</span> <span class="k">else</span> <span class="kc">None</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">b_to_a</span> <span class="o">=</span> <span class="n">b_to_a</span> <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">load_b_to_a</span> <span class="k">else</span> <span class="kc">None</span></div>
+
+
+
+<div class="viewcode-block" id="MapReader.set_uniprot_space">
+<a class="viewcode-back" href="../../../api/pypath.utils.mapping.MapReader.html#pypath.utils.mapping.MapReader.set_uniprot_space">[docs]</a>
+    <span class="k">def</span> <span class="nf">set_uniprot_space</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">swissprot</span> <span class="o">=</span> <span class="kc">None</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Sets up a search space of UniProt IDs.</span>
+
+<span class="sd">        Args</span>
+<span class="sd">            swissprot (bool): Use only SwissProt IDs, not TrEMBL. True</span>
+<span class="sd">                loads only SwissProt IDs, False only TrEMBL IDs, None</span>
+<span class="sd">                loads both.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">swissprot</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">param</span><span class="o">.</span><span class="n">swissprot</span> <span class="k">if</span> <span class="n">swissprot</span> <span class="ow">is</span> <span class="kc">None</span> <span class="k">else</span> <span class="n">swissprot</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">uniprots</span> <span class="o">=</span> <span class="n">uniprot_db</span><span class="o">.</span><span class="n">all_uniprots</span><span class="p">(</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">ncbi_tax_id</span><span class="p">,</span>
+            <span class="n">swissprot</span> <span class="o">=</span> <span class="n">swissprot</span><span class="p">,</span>
+        <span class="p">)</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">_read_mapping_uniprot_list</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">uniprot_id_type_a</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">uniprot_id_type_b</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">upload_ac_list</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">chunk_size</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+        <span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Reads a mapping table from UniProt &quot;upload lists&quot; service.</span>
+
+<span class="sd">        Args</span>
+<span class="sd">            uniprot_id_type_a (str): Source ID type label as used in UniProt.</span>
+<span class="sd">            uniprot_id_type_b (str): Target ID type label as used in UniProt.</span>
+<span class="sd">            upload_ac_list (list): The identifiers to use in the query to</span>
+<span class="sd">                the ID Mapping service. By default the list of all UniProt</span>
+<span class="sd">                IDs for the organism is used.</span>
+<span class="sd">            chunk_size (int): Number of IDs in one query. Too large queries</span>
+<span class="sd">                might fail, by default we include 100,000 IDs in one query.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">chunk_size</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="n">chunk_size</span> <span class="ow">or</span>
+            <span class="n">settings</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">&#39;uniprot_uploadlists_chunk_size&#39;</span><span class="p">)</span>
+        <span class="p">)</span>
+        <span class="n">uniprot_id_type_a</span> <span class="o">=</span> <span class="n">uniprot_id_type_a</span> <span class="ow">or</span> <span class="bp">self</span><span class="o">.</span><span class="n">param</span><span class="o">.</span><span class="n">uniprot_id_type_a</span>
+        <span class="n">uniprot_id_type_b</span> <span class="o">=</span> <span class="n">uniprot_id_type_b</span> <span class="ow">or</span> <span class="bp">self</span><span class="o">.</span><span class="n">param</span><span class="o">.</span><span class="n">uniprot_id_type_b</span>
+
+        <span class="k">if</span> <span class="ow">not</span> <span class="n">upload_ac_list</span><span class="p">:</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span>
+                <span class="s1">&#39;No identifiers provided, &#39;</span>
+                <span class="s1">&#39;using all UniProt IDs of the organism.&#39;</span>
+            <span class="p">)</span>
+            <span class="n">upload_ac_list</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">uniprots</span>
+
+        <span class="n">upload_ac_list</span> <span class="o">=</span> <span class="nb">sorted</span><span class="p">(</span><span class="n">upload_ac_list</span><span class="p">)</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span>
+            <span class="s1">&#39;Querying the UniProt ID Mapping service for ID translation &#39;</span>
+            <span class="s1">&#39;data. Querying a list of </span><span class="si">%u</span><span class="s1"> IDs.&#39;</span> <span class="o">%</span> <span class="nb">len</span><span class="p">(</span><span class="n">upload_ac_list</span><span class="p">)</span>
+        <span class="p">)</span>
+
+        <span class="n">run_url</span> <span class="o">=</span> <span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;uniprot_idmapping&#39;</span><span class="p">][</span><span class="s1">&#39;run&#39;</span><span class="p">]</span>
+        <span class="n">poll_result</span> <span class="o">=</span> <span class="p">{}</span>
+        <span class="n">result</span> <span class="o">=</span> <span class="p">[]</span>
+
+        <span class="c1"># loading data in chunks of 10,000 by default</span>
+        <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">math</span><span class="o">.</span><span class="n">ceil</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">upload_ac_list</span><span class="p">)</span> <span class="o">/</span> <span class="n">chunk_size</span><span class="p">)):</span>
+
+            <span class="n">this_chunk</span> <span class="o">=</span> <span class="n">upload_ac_list</span><span class="p">[</span><span class="n">i</span> <span class="o">*</span> <span class="n">chunk_size</span><span class="p">:(</span><span class="n">i</span> <span class="o">+</span> <span class="mi">1</span><span class="p">)</span> <span class="o">*</span> <span class="n">chunk_size</span><span class="p">]</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span>
+                <span class="s1">&#39;Request to UniProt ID Mapping, chunk #</span><span class="si">%u</span><span class="s1"> with </span><span class="si">%u</span><span class="s1"> IDs.&#39;</span> <span class="o">%</span> <span class="p">(</span>
+                    <span class="n">i</span><span class="p">,</span>
+                    <span class="nb">len</span><span class="p">(</span><span class="n">this_chunk</span><span class="p">),</span>
+                <span class="p">)</span>
+            <span class="p">)</span>
+
+            <span class="n">post</span> <span class="o">=</span> <span class="p">{</span>
+                <span class="s1">&#39;from&#39;</span><span class="p">:</span> <span class="n">uniprot_id_type_a</span><span class="p">,</span>
+                <span class="s1">&#39;to&#39;</span><span class="p">:</span> <span class="n">uniprot_id_type_b</span><span class="p">,</span>
+                <span class="s1">&#39;ids&#39;</span><span class="p">:</span> <span class="s1">&#39; &#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="nb">sorted</span><span class="p">(</span><span class="n">this_chunk</span><span class="p">)),</span>
+            <span class="p">}</span>
+            <span class="n">accept_json</span> <span class="o">=</span> <span class="p">{</span><span class="s1">&#39;req_headers&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;Accept: application/json&#39;</span><span class="p">]}</span>
+
+            <span class="n">run_args</span> <span class="o">=</span> <span class="p">{</span><span class="s1">&#39;url&#39;</span><span class="p">:</span> <span class="n">run_url</span><span class="p">,</span> <span class="s1">&#39;post&#39;</span><span class="p">:</span> <span class="n">post</span><span class="p">}</span>
+            <span class="n">nocache</span> <span class="o">=</span> <span class="p">{</span><span class="s1">&#39;cache&#39;</span><span class="p">:</span> <span class="kc">False</span><span class="p">,</span> <span class="s1">&#39;large&#39;</span><span class="p">:</span> <span class="kc">False</span><span class="p">}</span>
+            <span class="n">large</span> <span class="o">=</span> <span class="p">{</span><span class="s1">&#39;silent&#39;</span><span class="p">:</span> <span class="kc">False</span><span class="p">,</span> <span class="s1">&#39;large&#39;</span><span class="p">:</span> <span class="kc">True</span><span class="p">}</span>
+
+            <span class="n">cache_path</span> <span class="o">=</span> <span class="n">curl</span><span class="o">.</span><span class="n">Curl</span><span class="o">.</span><span class="n">cache_path</span><span class="p">(</span><span class="o">**</span><span class="n">run_args</span><span class="p">)</span>
+
+            <span class="k">if</span> <span class="ow">not</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">exists</span><span class="p">(</span><span class="n">cache_path</span><span class="p">):</span>
+
+                <span class="n">run_c</span> <span class="o">=</span> <span class="n">curl</span><span class="o">.</span><span class="n">Curl</span><span class="p">(</span> <span class="o">**</span><span class="n">run_args</span><span class="p">,</span> <span class="o">**</span><span class="n">nocache</span><span class="p">,</span> <span class="o">**</span><span class="n">accept_json</span><span class="p">)</span>
+
+                <span class="k">if</span> <span class="n">run_c</span><span class="o">.</span><span class="n">status</span> <span class="o">!=</span> <span class="mi">200</span><span class="p">:</span>
+
+                    <span class="k">raise</span> <span class="ne">RuntimeError</span><span class="p">(</span>
+                        <span class="s1">&#39;Failed to submit job to UniProt ID Mapping. &#39;</span>
+                        <span class="s1">&#39;See details in the log.&#39;</span>
+                    <span class="p">)</span>
+
+                <span class="n">jobid</span> <span class="o">=</span> <span class="n">json</span><span class="o">.</span><span class="n">loads</span><span class="p">(</span><span class="n">run_c</span><span class="o">.</span><span class="n">result</span><span class="p">)[</span><span class="s1">&#39;jobId&#39;</span><span class="p">]</span>
+
+                <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span>
+                    <span class="sa">f</span><span class="s1">&#39;Submitted job to UniProt ID Mapping, job ID: `</span><span class="si">{</span><span class="n">jobid</span><span class="si">}</span><span class="s1">`.&#39;</span>
+                <span class="p">)</span>
+
+                <span class="n">timeout</span> <span class="o">=</span> <span class="n">settings</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">&#39;uniprot_idmapping_timeout&#39;</span><span class="p">)</span>
+                <span class="n">interval</span> <span class="o">=</span> <span class="n">settings</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">&#39;uniprot_idmapping_poll_interval&#39;</span><span class="p">)</span>
+                <span class="n">max_polls</span> <span class="o">=</span> <span class="n">math</span><span class="o">.</span><span class="n">ceil</span><span class="p">(</span><span class="n">timeout</span> <span class="o">/</span> <span class="n">interval</span><span class="p">)</span>
+                <span class="n">poll_url</span> <span class="o">=</span> <span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;uniprot_idmapping&#39;</span><span class="p">][</span><span class="s1">&#39;poll&#39;</span><span class="p">]</span> <span class="o">%</span> <span class="n">jobid</span>
+                <span class="n">poll_args</span> <span class="o">=</span> <span class="p">{</span><span class="s1">&#39;url&#39;</span><span class="p">:</span> <span class="n">poll_url</span><span class="p">}</span> <span class="o">|</span> <span class="n">nocache</span> <span class="o">|</span> <span class="n">accept_json</span>
+
+                <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">max_polls</span><span class="p">):</span>
+
+                    <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span>
+                        <span class="sa">f</span><span class="s1">&#39;Polling job UniProt ID Mapping job `</span><span class="si">{</span><span class="n">jobid</span><span class="si">}</span><span class="s1">`, &#39;</span>
+                        <span class="sa">f</span><span class="s1">&#39;poll </span><span class="si">{</span><span class="n">i</span><span class="w"> </span><span class="o">+</span><span class="w"> </span><span class="mi">1</span><span class="si">}</span><span class="s1"> of </span><span class="si">{</span><span class="n">max_polls</span><span class="si">}</span><span class="s1">.&#39;</span>
+                    <span class="p">)</span>
+
+                    <span class="n">poll_c</span> <span class="o">=</span> <span class="n">curl</span><span class="o">.</span><span class="n">Curl</span><span class="p">(</span><span class="o">**</span><span class="n">poll_args</span><span class="p">)</span>
+
+                    <span class="k">if</span> <span class="n">poll_c</span><span class="o">.</span><span class="n">status</span> <span class="o">!=</span> <span class="mi">200</span><span class="p">:</span>
+
+                        <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span><span class="sa">f</span><span class="s1">&#39;Poll failed with HTTP </span><span class="si">{</span><span class="n">poll_c</span><span class="o">.</span><span class="n">status</span><span class="si">}</span><span class="s1">.&#39;</span><span class="p">)</span>
+                        <span class="k">continue</span>
+
+                    <span class="n">poll_result</span> <span class="o">=</span> <span class="n">json</span><span class="o">.</span><span class="n">loads</span><span class="p">(</span><span class="n">poll_c</span><span class="o">.</span><span class="n">result</span><span class="p">)</span>
+
+                    <span class="k">if</span> <span class="s1">&#39;status&#39;</span> <span class="ow">in</span> <span class="n">poll_result</span> <span class="ow">or</span> <span class="s1">&#39;failedIds&#39;</span> <span class="ow">in</span> <span class="n">poll_result</span><span class="p">:</span>
+
+                        <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span>
+                            <span class="sa">f</span><span class="s1">&#39;UniProt ID Mapping job `</span><span class="si">{</span><span class="n">jobid</span><span class="si">}</span><span class="s1">` &#39;</span>
+                            <span class="s1">&#39;successfully completed.&#39;</span>
+                        <span class="p">)</span>
+                        <span class="k">break</span>
+
+                    <span class="k">elif</span> <span class="s1">&#39;messages&#39;</span> <span class="ow">in</span> <span class="n">poll_result</span><span class="p">:</span>
+
+                        <span class="n">msg</span> <span class="o">=</span> <span class="p">(</span>
+                            <span class="s1">&#39;UniProt ID Mapping job failed: &#39;</span> <span class="o">+</span>
+                            <span class="s1">&#39; &#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">common</span><span class="o">.</span><span class="n">to_list</span><span class="p">(</span><span class="n">poll_result</span><span class="p">[</span><span class="s1">&#39;messages&#39;</span><span class="p">]))</span>
+                        <span class="p">)</span>
+
+                        <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span><span class="n">msg</span><span class="p">)</span>
+
+                        <span class="k">raise</span> <span class="ne">RuntimeError</span><span class="p">(</span><span class="n">msg</span><span class="p">)</span>
+
+                    <span class="n">time</span><span class="o">.</span><span class="n">sleep</span><span class="p">(</span><span class="n">interval</span><span class="p">)</span>
+
+                <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span>
+                    <span class="s1">&#39;Getting UniProt ID Mapping results URL &#39;</span>
+                    <span class="s1">&#39;for job `</span><span class="si">{jobid}</span><span class="s1">`.&#39;</span>
+                <span class="p">)</span>
+                <span class="n">det_url</span> <span class="o">=</span> <span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;uniprot_idmapping&#39;</span><span class="p">][</span><span class="s1">&#39;details&#39;</span><span class="p">]</span> <span class="o">%</span> <span class="n">jobid</span>
+                <span class="n">det_c</span> <span class="o">=</span> <span class="n">curl</span><span class="o">.</span><span class="n">Curl</span><span class="p">(</span><span class="n">url</span> <span class="o">=</span> <span class="n">det_url</span><span class="p">,</span> <span class="o">**</span><span class="n">nocache</span><span class="p">,</span> <span class="o">**</span><span class="n">accept_json</span><span class="p">)</span>
+                <span class="n">result_url</span> <span class="o">=</span> <span class="p">(</span>
+                    <span class="n">json</span><span class="o">.</span><span class="n">loads</span><span class="p">(</span><span class="n">det_c</span><span class="o">.</span><span class="n">result</span><span class="p">)[</span><span class="s1">&#39;redirectURL&#39;</span><span class="p">]</span><span class="o">.</span>
+                    <span class="n">replace</span><span class="p">(</span><span class="s1">&#39;/idmapping/results/&#39;</span><span class="p">,</span> <span class="s1">&#39;/idmapping/stream/&#39;</span><span class="p">)</span><span class="o">.</span>
+                    <span class="n">replace</span><span class="p">(</span><span class="s1">&#39;/results/&#39;</span><span class="p">,</span> <span class="s1">&#39;/results/stream/&#39;</span><span class="p">)</span><span class="o">.</span>
+                    <span class="fm">__add__</span><span class="p">(</span><span class="s1">&#39;?format=tsv&#39;</span><span class="p">)</span>
+                <span class="p">)</span>
+
+                <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span>
+                    <span class="s1">&#39;Retrieving UniProt ID Mapping results &#39;</span>
+                    <span class="sa">f</span><span class="s1">&#39;from `</span><span class="si">{</span><span class="n">result_url</span><span class="si">}</span><span class="s1">`.&#39;</span>
+                <span class="p">)</span>
+
+                <span class="k">with</span> <span class="n">curl</span><span class="o">.</span><span class="n">cache_delete_on</span><span class="p">():</span>
+
+                    <span class="n">res_c</span> <span class="o">=</span> <span class="n">curl</span><span class="o">.</span><span class="n">Curl</span><span class="p">(</span>
+                        <span class="n">url</span> <span class="o">=</span> <span class="n">result_url</span><span class="p">,</span>
+                        <span class="n">cache</span> <span class="o">=</span> <span class="n">cache_path</span><span class="p">,</span>
+                        <span class="o">**</span><span class="n">large</span>
+                    <span class="p">)</span>
+
+            <span class="k">else</span><span class="p">:</span>
+
+                <span class="n">res_c</span> <span class="o">=</span> <span class="n">curl</span><span class="o">.</span><span class="n">Curl</span><span class="p">(</span><span class="o">**</span><span class="n">run_args</span><span class="p">,</span> <span class="o">**</span><span class="n">large</span><span class="p">)</span>
+
+            <span class="n">result</span><span class="o">.</span><span class="n">extend</span><span class="p">(</span><span class="nb">list</span><span class="p">(</span><span class="n">res_c</span><span class="o">.</span><span class="n">fileobj</span><span class="p">)[</span><span class="mi">1</span><span class="p">:])</span>
+
+        <span class="k">return</span> <span class="n">result</span>
+
+
+<div class="viewcode-block" id="MapReader.read_mapping_uniprot">
+<a class="viewcode-back" href="../../../api/pypath.utils.mapping.MapReader.html#pypath.utils.mapping.MapReader.read_mapping_uniprot">[docs]</a>
+    <span class="k">def</span> <span class="nf">read_mapping_uniprot</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Downloads ID mappings directly from UniProt.</span>
+<span class="sd">        See the names of possible identifiers here:</span>
+<span class="sd">        http://www.uniprot.org/help/programmatic_access</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">query</span> <span class="o">=</span> <span class="n">uniprot_input</span><span class="o">.</span><span class="n">UniprotQuery</span><span class="p">(</span>
+            <span class="n">reviewed</span> <span class="o">=</span> <span class="kc">True</span> <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">param</span><span class="o">.</span><span class="n">swissprot</span> <span class="k">else</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">organism</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">ncbi_tax_id</span><span class="p">,</span>
+            <span class="n">fields</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">param</span><span class="o">.</span><span class="n">_resource_id_type_a</span><span class="p">,</span>
+        <span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span><span class="sa">f</span><span class="s1">&#39;UniProt REST API call: `</span><span class="si">{</span><span class="n">query</span><span class="o">.</span><span class="n">url_plain</span><span class="si">}</span><span class="s1">`.&#39;</span><span class="p">)</span>
+        <span class="n">trembl</span> <span class="o">=</span> <span class="s1">&#39;trembl&#39;</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">param</span>
+        <span class="n">protein_name</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">param</span><span class="o">.</span><span class="n">field</span> <span class="o">==</span> <span class="s1">&#39;protein names&#39;</span>
+        <span class="n">query</span><span class="o">.</span><span class="n">name_process</span> <span class="o">=</span> <span class="ow">not</span> <span class="n">protein_name</span> <span class="ow">and</span> <span class="ow">not</span> <span class="n">trembl</span>
+        <span class="n">data</span> <span class="o">=</span> <span class="n">query</span><span class="o">.</span><span class="n">perform</span><span class="p">()</span>
+
+        <span class="k">if</span> <span class="ow">not</span> <span class="n">query</span><span class="o">.</span><span class="n">name_process</span><span class="p">:</span>
+
+            <span class="k">def</span> <span class="nf">maybe_split</span><span class="p">(</span><span class="n">v</span><span class="p">):</span>
+
+                <span class="k">if</span> <span class="n">trembl</span> <span class="ow">and</span> <span class="ow">not</span> <span class="nb">any</span><span class="p">(</span><span class="n">ch</span><span class="o">.</span><span class="n">islower</span><span class="p">()</span> <span class="k">for</span> <span class="n">ch</span> <span class="ow">in</span> <span class="n">v</span><span class="p">):</span>
+                    <span class="n">v</span> <span class="o">=</span> <span class="n">common</span><span class="o">.</span><span class="n">del_empty</span><span class="p">(</span><span class="n">query</span><span class="o">.</span><span class="n">_FIELDSEP</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="n">v</span><span class="p">))</span>
+                <span class="k">elif</span> <span class="n">protein_name</span><span class="p">:</span>
+                    <span class="n">v</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_process_protein_name</span><span class="p">(</span><span class="n">v</span><span class="p">)</span>
+
+                <span class="k">return</span> <span class="n">v</span>
+
+
+            <span class="n">data</span> <span class="o">=</span> <span class="p">{</span><span class="n">k</span><span class="p">:</span> <span class="n">maybe_split</span><span class="p">(</span><span class="n">v</span><span class="p">)</span> <span class="k">for</span> <span class="n">k</span><span class="p">,</span> <span class="n">v</span> <span class="ow">in</span> <span class="n">data</span><span class="o">.</span><span class="n">items</span><span class="p">()}</span>
+
+        <span class="n">data</span> <span class="o">=</span> <span class="p">{</span><span class="n">k</span><span class="p">:</span> <span class="n">common</span><span class="o">.</span><span class="n">to_set</span><span class="p">(</span><span class="n">v</span><span class="p">)</span> <span class="k">for</span> <span class="n">k</span><span class="p">,</span> <span class="n">v</span> <span class="ow">in</span> <span class="n">data</span><span class="o">.</span><span class="n">items</span><span class="p">()}</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">a_to_b</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="n">common</span><span class="o">.</span><span class="n">swap_dict</span><span class="p">(</span><span class="n">data</span><span class="p">,</span> <span class="n">force_sets</span> <span class="o">=</span> <span class="kc">True</span><span class="p">)</span>
+                <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">load_a_to_b</span> <span class="k">else</span>
+            <span class="kc">None</span>
+        <span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">b_to_a</span> <span class="o">=</span> <span class="n">data</span> <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">load_b_to_a</span> <span class="k">else</span> <span class="kc">None</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">read_mapping_pro</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="n">pro_data</span> <span class="o">=</span> <span class="n">pro_input</span><span class="o">.</span><span class="n">pro_mapping</span><span class="p">(</span><span class="n">target_id_type</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">param</span><span class="o">.</span><span class="n">id_type</span><span class="p">)</span>
+
+        <span class="n">pro_to_other</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">defaultdict</span><span class="p">(</span><span class="nb">set</span><span class="p">)</span>
+
+        <span class="k">for</span> <span class="n">pro</span><span class="p">,</span> <span class="n">other</span> <span class="ow">in</span> <span class="n">pro_data</span><span class="p">:</span>
+
+            <span class="n">pro_to_other</span><span class="p">[</span><span class="n">pro</span><span class="p">]</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">other</span><span class="p">)</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">a_to_b</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="kc">None</span>
+                <span class="k">if</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">load_a_to_b</span> <span class="k">else</span>
+            <span class="n">common</span><span class="o">.</span><span class="n">swap_dict</span><span class="p">(</span><span class="n">pro_to_other</span><span class="p">,</span> <span class="n">force_sets</span> <span class="o">=</span> <span class="kc">True</span><span class="p">)</span>
+                <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">param</span><span class="o">.</span><span class="n">to_pro</span> <span class="k">else</span>
+            <span class="nb">dict</span><span class="p">(</span><span class="n">pro_to_other</span><span class="p">)</span>
+        <span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">b_to_a</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="kc">None</span>
+                <span class="k">if</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">load_b_to_a</span> <span class="k">else</span>
+            <span class="nb">dict</span><span class="p">(</span><span class="n">pro_to_other</span><span class="p">)</span>
+                <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">param</span><span class="o">.</span><span class="n">to_pro</span> <span class="k">else</span>
+            <span class="n">common</span><span class="o">.</span><span class="n">swap_dict</span><span class="p">(</span><span class="n">pro_to_other</span><span class="p">,</span> <span class="n">force_sets</span> <span class="o">=</span> <span class="kc">True</span><span class="p">)</span>
+        <span class="p">)</span>
+
+
+<div class="viewcode-block" id="MapReader.read_mapping_biomart">
+<a class="viewcode-back" href="../../../api/pypath.utils.mapping.MapReader.html#pypath.utils.mapping.MapReader.read_mapping_biomart">[docs]</a>
+    <span class="k">def</span> <span class="nf">read_mapping_biomart</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Loads a mapping table using BioMart data.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">ens_organism</span> <span class="o">=</span> <span class="n">taxonomy</span><span class="o">.</span><span class="n">ensure_ensembl_name</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">param</span><span class="o">.</span><span class="n">ncbi_tax_id</span><span class="p">)</span>
+
+        <span class="k">if</span> <span class="ow">not</span> <span class="n">ens_organism</span><span class="p">:</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span>
+                <span class="s1">&#39;Organism not available in Ensembl: `</span><span class="si">%u</span><span class="s1">`.&#39;</span> <span class="o">%</span> <span class="p">(</span>
+                    <span class="bp">self</span><span class="o">.</span><span class="n">param</span><span class="o">.</span><span class="n">ncbi_tax_id</span>
+                <span class="p">)</span>
+            <span class="p">)</span>
+            <span class="k">return</span>
+
+        <span class="n">dataset</span> <span class="o">=</span> <span class="s1">&#39;</span><span class="si">%s</span><span class="s1">_gene_ensembl&#39;</span> <span class="o">%</span> <span class="n">ens_organism</span>
+        <span class="n">biomart_data</span> <span class="o">=</span> <span class="n">biomart_input</span><span class="o">.</span><span class="n">biomart_query</span><span class="p">(</span>
+            <span class="n">attrs</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">param</span><span class="o">.</span><span class="n">attrs</span><span class="p">,</span>
+            <span class="n">dataset</span> <span class="o">=</span> <span class="n">dataset</span><span class="p">,</span>
+        <span class="p">)</span>
+
+        <span class="n">a_to_b</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">defaultdict</span><span class="p">(</span><span class="nb">set</span><span class="p">)</span>
+        <span class="n">b_to_a</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">defaultdict</span><span class="p">(</span><span class="nb">set</span><span class="p">)</span>
+
+        <span class="k">for</span> <span class="n">rec</span> <span class="ow">in</span> <span class="n">biomart_data</span><span class="p">:</span>
+
+            <span class="n">id_a</span> <span class="o">=</span> <span class="nb">getattr</span><span class="p">(</span><span class="n">rec</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">param</span><span class="o">.</span><span class="n">biomart_id_type_a</span><span class="p">)</span>
+            <span class="n">id_b</span> <span class="o">=</span> <span class="nb">getattr</span><span class="p">(</span><span class="n">rec</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">param</span><span class="o">.</span><span class="n">biomart_id_type_b</span><span class="p">)</span>
+
+            <span class="k">if</span> <span class="n">id_a</span> <span class="ow">and</span> <span class="n">id_b</span><span class="p">:</span>
+
+                <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">load_a_to_b</span><span class="p">:</span>
+
+                    <span class="n">a_to_b</span><span class="p">[</span><span class="n">id_a</span><span class="p">]</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">id_b</span><span class="p">)</span>
+
+                <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">load_b_to_a</span><span class="p">:</span>
+
+                    <span class="n">b_to_a</span><span class="p">[</span><span class="n">id_b</span><span class="p">]</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">id_a</span><span class="p">)</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">a_to_b</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">(</span><span class="n">a_to_b</span><span class="p">)</span> <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">load_a_to_b</span> <span class="k">else</span> <span class="kc">None</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">b_to_a</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">(</span><span class="n">b_to_a</span><span class="p">)</span> <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">load_b_to_a</span> <span class="k">else</span> <span class="kc">None</span></div>
+
+
+
+<div class="viewcode-block" id="MapReader.read_mapping_array">
+<a class="viewcode-back" href="../../../api/pypath.utils.mapping.MapReader.html#pypath.utils.mapping.MapReader.read_mapping_array">[docs]</a>
+    <span class="k">def</span> <span class="nf">read_mapping_array</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Loads mapping table between microarray probe IDs and genes.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">probe_mapping</span> <span class="o">=</span> <span class="n">biomart_input</span><span class="o">.</span><span class="n">biomart_microarrays</span><span class="p">(</span>
+            <span class="n">organism</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">param</span><span class="o">.</span><span class="n">ncbi_tax_id</span><span class="p">,</span>
+            <span class="n">vendor</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">param</span><span class="o">.</span><span class="n">array_id</span><span class="p">,</span>
+            <span class="n">gene</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">param</span><span class="o">.</span><span class="n">ensembl_id</span> <span class="o">==</span> <span class="s1">&#39;ensg&#39;</span><span class="p">,</span>
+            <span class="n">transcript</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">param</span><span class="o">.</span><span class="n">ensembl_id</span> <span class="o">==</span> <span class="s1">&#39;enst&#39;</span><span class="p">,</span>
+            <span class="n">peptide</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">param</span><span class="o">.</span><span class="n">ensembl_id</span> <span class="o">==</span> <span class="s1">&#39;ensp&#39;</span><span class="p">,</span>
+        <span class="p">)</span>
+
+        <span class="n">a_to_b__probe_to_gene</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">param</span><span class="o">.</span><span class="n">id_type_a</span> <span class="o">==</span> <span class="bp">self</span><span class="o">.</span><span class="n">param</span><span class="o">.</span><span class="n">array_id</span>
+
+        <span class="k">if</span> <span class="p">(</span>
+            <span class="p">(</span>
+                <span class="n">a_to_b__probe_to_gene</span> <span class="ow">and</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">load_a_to_b</span>
+            <span class="p">)</span> <span class="ow">or</span> <span class="p">(</span>
+                <span class="ow">not</span> <span class="n">a_to_b__probe_to_gene</span> <span class="ow">and</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">load_b_to_a</span>
+            <span class="p">)</span>
+        <span class="p">):</span>
+
+            <span class="n">probe_to_gene</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">defaultdict</span><span class="p">(</span><span class="nb">set</span><span class="p">)</span>
+
+            <span class="k">for</span> <span class="n">ensembl_id</span><span class="p">,</span> <span class="n">probes</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="n">probe_mapping</span><span class="p">):</span>
+
+                <span class="k">for</span> <span class="n">probe</span> <span class="ow">in</span> <span class="n">probes</span><span class="p">:</span>
+
+                    <span class="n">probe_to_gene</span><span class="p">[</span><span class="n">probe</span><span class="o">.</span><span class="n">probe</span><span class="p">]</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">ensembl_id</span><span class="p">)</span>
+
+            <span class="nb">setattr</span><span class="p">(</span>
+                <span class="bp">self</span><span class="p">,</span>
+                <span class="s1">&#39;a_to_b&#39;</span> <span class="k">if</span> <span class="n">a_to_b__probe_to_gene</span> <span class="k">else</span> <span class="s1">&#39;b_to_a&#39;</span><span class="p">,</span>
+                <span class="nb">dict</span><span class="p">(</span><span class="n">probe_to_gene</span><span class="p">),</span>
+            <span class="p">)</span>
+
+        <span class="k">if</span> <span class="p">(</span>
+            <span class="p">(</span>
+                <span class="n">a_to_b__probe_to_gene</span> <span class="ow">and</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">load_b_to_a</span>
+            <span class="p">)</span> <span class="ow">or</span> <span class="p">(</span>
+                <span class="ow">not</span> <span class="n">a_to_b__probe_to_gene</span> <span class="ow">and</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">load_a_to_b</span>
+            <span class="p">)</span>
+        <span class="p">):</span>
+
+            <span class="n">gene_to_probe</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">(</span>
+                <span class="p">(</span>
+                    <span class="n">ensembl_id</span><span class="p">,</span>
+                    <span class="p">{</span><span class="n">p</span><span class="o">.</span><span class="n">probe</span> <span class="k">for</span> <span class="n">p</span> <span class="ow">in</span> <span class="n">probe_ids</span><span class="p">}</span>
+                <span class="p">)</span>
+                <span class="k">for</span> <span class="n">ensembl_id</span><span class="p">,</span> <span class="n">probe_ids</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="n">probe_mapping</span><span class="p">)</span>
+            <span class="p">)</span>
+
+            <span class="nb">setattr</span><span class="p">(</span>
+                <span class="bp">self</span><span class="p">,</span>
+                <span class="s1">&#39;b_to_a&#39;</span> <span class="k">if</span> <span class="n">a_to_b__probe_to_gene</span> <span class="k">else</span> <span class="s1">&#39;a_to_b&#39;</span><span class="p">,</span>
+                <span class="n">gene_to_probe</span><span class="p">,</span>
+            <span class="p">)</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">_read_mapping_smallmolecule</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Loads a small molecule ID translation table.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">param</span><span class="o">.</span><span class="n">input_method</span><span class="p">:</span>
+
+            <span class="n">method</span> <span class="o">=</span> <span class="n">inputs</span><span class="o">.</span><span class="n">get_method</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">param</span><span class="o">.</span><span class="n">input_method</span><span class="p">)</span>
+
+        <span class="k">else</span><span class="p">:</span>
+
+            <span class="n">mod</span> <span class="o">=</span> <span class="nb">globals</span><span class="p">()[</span><span class="sa">f</span><span class="s1">&#39;</span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">source_type</span><span class="si">}</span><span class="s1">_input&#39;</span><span class="p">]</span>
+            <span class="n">method</span> <span class="o">=</span> <span class="nb">getattr</span><span class="p">(</span><span class="n">mod</span><span class="p">,</span> <span class="sa">f</span><span class="s1">&#39;</span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">source_type</span><span class="si">}</span><span class="s1">_mapping&#39;</span><span class="p">)</span>
+
+        <span class="n">data</span> <span class="o">=</span> <span class="n">method</span><span class="p">(</span>
+            <span class="n">id_type_a</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">resource_id_type_a</span><span class="p">,</span>
+            <span class="n">id_type_b</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">resource_id_type_b</span><span class="p">,</span>
+        <span class="p">)</span>
+
+        <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">load_a_to_b</span><span class="p">:</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">a_to_b</span> <span class="o">=</span> <span class="n">data</span>
+
+        <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">load_b_to_a</span><span class="p">:</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">b_to_a</span> <span class="o">=</span> <span class="n">common</span><span class="o">.</span><span class="n">swap_dict</span><span class="p">(</span><span class="n">data</span><span class="p">,</span> <span class="n">force_sets</span> <span class="o">=</span> <span class="kc">True</span><span class="p">)</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">_const</span><span class="o">.</span><span class="n">NOT_ORGANISM_SPECIFIC</span>
+
+
+<div class="viewcode-block" id="MapReader.read_mapping_ramp">
+<a class="viewcode-back" href="../../../api/pypath.utils.mapping.MapReader.html#pypath.utils.mapping.MapReader.read_mapping_ramp">[docs]</a>
+    <span class="k">def</span> <span class="nf">read_mapping_ramp</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Loads an ID translation table from RaMP.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_read_mapping_smallmolecule</span><span class="p">()</span></div>
+
+
+
+<div class="viewcode-block" id="MapReader.read_mapping_unichem">
+<a class="viewcode-back" href="../../../api/pypath.utils.mapping.MapReader.html#pypath.utils.mapping.MapReader.read_mapping_unichem">[docs]</a>
+    <span class="k">def</span> <span class="nf">read_mapping_unichem</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Loads an ID translation table from UniChem.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_read_mapping_smallmolecule</span><span class="p">()</span></div>
+
+
+
+<div class="viewcode-block" id="MapReader.read_mapping_hmdb">
+<a class="viewcode-back" href="../../../api/pypath.utils.mapping.MapReader.html#pypath.utils.mapping.MapReader.read_mapping_hmdb">[docs]</a>
+    <span class="k">def</span> <span class="nf">read_mapping_hmdb</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Loads an ID translation table from th Human Metabolome Database.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_read_mapping_smallmolecule</span><span class="p">()</span></div>
+
+
+
+    <span class="nd">@staticmethod</span>
+    <span class="k">def</span> <span class="nf">_process_protein_name</span><span class="p">(</span><span class="n">name</span><span class="p">):</span>
+
+        <span class="n">rebr</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">compile</span><span class="p">(</span><span class="sa">r</span><span class="s1">&#39;\(([^\)]{3,})\)&#39;</span><span class="p">)</span>
+        <span class="n">resq</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">compile</span><span class="p">(</span><span class="sa">r</span><span class="s1">&#39;\[([^\]]{3,})\]&#39;</span><span class="p">)</span>
+
+        <span class="n">names</span> <span class="o">=</span> <span class="p">[</span><span class="n">name</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;(&#39;</span><span class="p">)[</span><span class="mi">0</span><span class="p">]]</span>
+        <span class="n">names</span> <span class="o">+=</span> <span class="n">rebr</span><span class="o">.</span><span class="n">findall</span><span class="p">(</span><span class="n">name</span><span class="p">)</span>
+        <span class="n">others</span> <span class="o">=</span> <span class="n">common</span><span class="o">.</span><span class="n">flat_list</span><span class="p">([</span><span class="n">x</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;;&#39;</span><span class="p">)</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">resq</span><span class="o">.</span><span class="n">findall</span><span class="p">(</span><span class="n">name</span><span class="p">)])</span>
+        <span class="n">others</span> <span class="o">=</span> <span class="p">[</span><span class="n">x</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;:&#39;</span><span class="p">)[</span><span class="mi">1</span><span class="p">]</span> <span class="k">if</span> <span class="s1">&#39;:&#39;</span> <span class="ow">in</span> <span class="n">x</span> <span class="k">else</span> <span class="n">x</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">others</span><span class="p">]</span>
+        <span class="n">others</span> <span class="o">=</span> <span class="p">[</span><span class="n">x</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;(&#39;</span><span class="p">)[</span><span class="mi">1</span><span class="p">]</span> <span class="k">if</span> <span class="s1">&#39;(&#39;</span> <span class="ow">in</span> <span class="n">x</span> <span class="k">else</span> <span class="n">x</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">others</span><span class="p">]</span>
+        <span class="n">names</span> <span class="o">+=</span> <span class="n">others</span>
+
+        <span class="k">return</span> <span class="p">{</span><span class="n">x</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">names</span><span class="p">}</span>
+
+
+<div class="viewcode-block" id="MapReader.resource_id_type">
+<a class="viewcode-back" href="../../../api/pypath.utils.mapping.MapReader.html#pypath.utils.mapping.MapReader.resource_id_type">[docs]</a>
+    <span class="k">def</span> <span class="nf">resource_id_type</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">side</span> <span class="o">=</span> <span class="n">Literal</span><span class="p">[</span><span class="s1">&#39;a&#39;</span><span class="p">,</span> <span class="s1">&#39;b&#39;</span><span class="p">])</span> <span class="o">-&gt;</span> <span class="nb">str</span> <span class="o">|</span> <span class="kc">None</span><span class="p">:</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Resource specific identifier type.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">return</span> <span class="p">(</span>
+            <span class="nb">getattr</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">param</span><span class="p">,</span> <span class="sa">f</span><span class="s1">&#39;resource_id_type_</span><span class="si">{</span><span class="n">side</span><span class="si">}</span><span class="s1">&#39;</span><span class="p">)</span> <span class="ow">or</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">_resource_id_types</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="nb">getattr</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">param</span><span class="p">,</span> <span class="sa">f</span><span class="s1">&#39;id_type_</span><span class="si">{</span><span class="n">side</span><span class="si">}</span><span class="s1">&#39;</span><span class="p">))</span>
+        <span class="p">)</span></div>
+
+
+
+    <span class="nd">@property</span>
+    <span class="k">def</span> <span class="nf">resource_id_type_a</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">str</span> <span class="o">|</span> <span class="kc">None</span><span class="p">:</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">resource_id_type</span><span class="p">(</span><span class="s1">&#39;a&#39;</span><span class="p">)</span>
+
+
+    <span class="nd">@property</span>
+    <span class="k">def</span> <span class="nf">resource_id_type_b</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">str</span> <span class="o">|</span> <span class="kc">None</span><span class="p">:</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">resource_id_type</span><span class="p">(</span><span class="s1">&#39;b&#39;</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="MappingTable">
+<a class="viewcode-back" href="../../../api/pypath.utils.mapping.MappingTable.html#pypath.utils.mapping.MappingTable">[docs]</a>
+<span class="k">class</span> <span class="nc">MappingTable</span><span class="p">(</span><span class="n">session_mod</span><span class="o">.</span><span class="n">Logger</span><span class="p">):</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    This is the class directly handling ID translation data.</span>
+<span class="sd">    It does not care about loading it or what kind of IDs these</span>
+<span class="sd">    only accepts the translation dictionary.</span>
+
+<span class="sd">    lifetime : int</span>
+<span class="sd">        If this table has not been used for longer than this preiod it is</span>
+<span class="sd">        to be removed at next cleanup. Time in seconds.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+<div class="viewcode-block" id="MappingTable.__init__">
+<a class="viewcode-back" href="../../../api/pypath.utils.mapping.MappingTable.html#pypath.utils.mapping.MappingTable.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">data</span><span class="p">,</span>
+            <span class="n">id_type</span><span class="p">,</span>
+            <span class="n">target_id_type</span><span class="p">,</span>
+            <span class="n">ncbi_tax_id</span><span class="p">,</span>
+            <span class="n">lifetime</span> <span class="o">=</span> <span class="mi">300</span><span class="p">,</span>
+        <span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Wrapper around a dictionary of identifier mapping. The dictionary</span>
+<span class="sd">        is located in the `data` attribute, keys are the source identifiers,</span>
+<span class="sd">        values are sets of target identifiers. Most often the mapping is</span>
+<span class="sd">        unambigous, which means one target identifier for each source</span>
+<span class="sd">        identifier.</span>
+
+<span class="sd">        Args</span>
+<span class="sd">            data (dict): The identifier translation dictionary.</span>
+<span class="sd">            id_type (str): The source ID type.</span>
+<span class="sd">            target_id_type (str): The target ID type.</span>
+<span class="sd">            ncbi_tax_id (int): NCBI Taxonomy identifier of the organism.</span>
+<span class="sd">            lifetime (int): Time in seconds to keep the table loaded in</span>
+<span class="sd">                the memory. If not used, the table will be unloaded after</span>
+<span class="sd">                this time. Each usage resets the expiry time.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">session_mod</span><span class="o">.</span><span class="n">Logger</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">name</span> <span class="o">=</span> <span class="s1">&#39;mapping&#39;</span><span class="p">)</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">id_type</span> <span class="o">=</span> <span class="n">id_type</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">target_id_type</span> <span class="o">=</span> <span class="n">target_id_type</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">data</span> <span class="o">=</span> <span class="n">data</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">lifetime</span> <span class="o">=</span> <span class="n">lifetime</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">_used</span><span class="p">()</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">reload</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="n">modname</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="vm">__class__</span><span class="o">.</span><span class="vm">__module__</span>
+        <span class="n">mod</span> <span class="o">=</span> <span class="nb">__import__</span><span class="p">(</span><span class="n">modname</span><span class="p">,</span> <span class="n">fromlist</span> <span class="o">=</span> <span class="p">[</span><span class="n">modname</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;.&#39;</span><span class="p">)[</span><span class="mi">0</span><span class="p">]])</span>
+        <span class="n">imp</span><span class="o">.</span><span class="n">reload</span><span class="p">(</span><span class="n">mod</span><span class="p">)</span>
+        <span class="n">new</span> <span class="o">=</span> <span class="nb">getattr</span><span class="p">(</span><span class="n">mod</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="vm">__class__</span><span class="o">.</span><span class="vm">__name__</span><span class="p">)</span>
+        <span class="nb">setattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">&#39;__class__&#39;</span><span class="p">,</span> <span class="n">new</span><span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="fm">__getitem__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">key</span><span class="p">):</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_used</span><span class="p">()</span>
+
+        <span class="k">if</span> <span class="n">key</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span><span class="p">:</span>
+
+            <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span><span class="p">[</span><span class="n">key</span><span class="p">]</span>
+
+        <span class="k">return</span> <span class="nb">set</span><span class="p">()</span>
+
+
+    <span class="k">def</span> <span class="fm">__contains__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">key</span><span class="p">):</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_used</span><span class="p">()</span>
+
+        <span class="k">return</span> <span class="n">key</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span>
+
+
+    <span class="k">def</span> <span class="fm">__len__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">data</span><span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">_used</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_last_used</span> <span class="o">=</span> <span class="n">time</span><span class="o">.</span><span class="n">time</span><span class="p">()</span>
+
+
+    <span class="k">def</span> <span class="nf">_expired</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="n">time</span><span class="o">.</span><span class="n">time</span><span class="p">()</span> <span class="o">-</span> <span class="bp">self</span><span class="o">.</span><span class="n">_last_used</span> <span class="o">&gt;</span> <span class="bp">self</span><span class="o">.</span><span class="n">lifetime</span>
+
+
+<div class="viewcode-block" id="MappingTable.get_key">
+<a class="viewcode-back" href="../../../api/pypath.utils.mapping.MappingTable.html#pypath.utils.mapping.MappingTable.get_key">[docs]</a>
+    <span class="k">def</span> <span class="nf">get_key</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Creates a mapping table key, a tuple with all the defining properties</span>
+<span class="sd">        of the mapping table.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">return</span> <span class="n">MappingTableKey</span><span class="p">(</span>
+            <span class="n">id_type</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">id_type</span><span class="p">,</span>
+            <span class="n">target_id_type</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">target_id_type</span><span class="p">,</span>
+            <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">ncbi_tax_id</span><span class="p">,</span>
+        <span class="p">)</span></div>
+
+
+
+    <span class="nd">@property</span>
+    <span class="k">def</span> <span class="nf">key</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="n">MappingTableKey</span><span class="p">(</span>
+            <span class="n">id_type</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">id_type</span><span class="p">,</span>
+            <span class="n">target_id_type</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">target_id_type</span><span class="p">,</span>
+            <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">ncbi_tax_id</span><span class="p">,</span>
+        <span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="fm">__repr__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="s1">&#39;&lt;MappingTable from=</span><span class="si">%s</span><span class="s1">, to=</span><span class="si">%s</span><span class="s1">, taxon=</span><span class="si">%u</span><span class="s1"> (</span><span class="si">%u</span><span class="s1"> IDs)&gt;&#39;</span> <span class="o">%</span> <span class="p">(</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">key</span> <span class="o">+</span> <span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="p">),)</span>
+        <span class="p">)</span>
+
+
+    <span class="nd">@property</span>
+    <span class="k">def</span> <span class="nf">items</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span><span class="o">.</span><span class="n">items</span>
+
+
+    <span class="nd">@property</span>
+    <span class="k">def</span> <span class="nf">keys</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span><span class="o">.</span><span class="n">keys</span>
+
+
+    <span class="nd">@property</span>
+    <span class="k">def</span> <span class="nf">values</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span><span class="o">.</span><span class="n">values</span></div>
+
+
+
+<div class="viewcode-block" id="Mapper">
+<a class="viewcode-back" href="../../../api/pypath.utils.mapping.Mapper.html#pypath.utils.mapping.Mapper">[docs]</a>
+<span class="k">class</span> <span class="nc">Mapper</span><span class="p">(</span><span class="n">session_mod</span><span class="o">.</span><span class="n">Logger</span><span class="p">):</span>
+
+    <span class="n">default_name_types</span> <span class="o">=</span> <span class="n">settings</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">&#39;default_name_types&#39;</span><span class="p">)</span>
+    <span class="n">default_label_types</span> <span class="o">=</span> <span class="n">settings</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">&#39;default_label_types&#39;</span><span class="p">)</span>
+
+    <span class="k">def</span> <span class="nf">_get_label_type_to_id_type</span><span class="p">(</span><span class="n">default_name_types</span><span class="p">):</span>
+
+        <span class="n">label_type_to_id_type</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">(</span>
+            <span class="p">(</span>
+                <span class="n">label_type</span><span class="p">,</span>
+                <span class="n">default_name_types</span><span class="p">[</span><span class="n">entity_type</span><span class="p">],</span>
+            <span class="p">)</span>
+            <span class="k">for</span> <span class="n">entity_type</span><span class="p">,</span> <span class="n">label_type</span> <span class="ow">in</span>
+            <span class="n">iteritems</span><span class="p">(</span><span class="n">settings</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">&#39;default_label_types&#39;</span><span class="p">))</span>
+        <span class="p">)</span>
+        <span class="c1">#TODO: some nicer solution</span>
+        <span class="n">label_type_to_id_type</span><span class="p">[</span><span class="s1">&#39;mir-name&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="s1">&#39;mir-pre&#39;</span>
+
+        <span class="k">return</span> <span class="n">label_type_to_id_type</span>
+
+    <span class="n">label_type_to_id_type</span> <span class="o">=</span> <span class="n">_get_label_type_to_id_type</span><span class="p">(</span><span class="n">default_name_types</span><span class="p">)</span>
+
+
+<div class="viewcode-block" id="Mapper.__init__">
+<a class="viewcode-back" href="../../../api/pypath.utils.mapping.Mapper.html#pypath.utils.mapping.Mapper.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">cleanup_period</span> <span class="o">=</span> <span class="mi">10</span><span class="p">,</span>
+            <span class="n">lifetime</span> <span class="o">=</span> <span class="mi">300</span><span class="p">,</span>
+            <span class="n">translate_deleted_uniprot</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">keep_invalid_uniprot</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">trembl_swissprot_by_genesymbol</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+        <span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        cleanup_period : int</span>
+<span class="sd">            Periodically check and remove unused mapping data.</span>
+<span class="sd">            Time in seconds. If `None` tables kept forever.</span>
+<span class="sd">        lifetime : int</span>
+<span class="sd">            If a table has not been used for longer than this preiod it is</span>
+<span class="sd">            to be removed at next cleanup.</span>
+<span class="sd">        translate_deleted_uniprot : bool</span>
+<span class="sd">            Do an extra attempt to translate deleted or obsolete UniProt IDs</span>
+<span class="sd">            by retrieving their archived datasheet and use the gene symbol</span>
+<span class="sd">            to find the corresponding valid UniProt ID?</span>
+<span class="sd">        keep_invalid_uniprot : bool</span>
+<span class="sd">            If the target ID is UniProt, keep the results if they fit the</span>
+<span class="sd">            format for UniProt IDs (we won&#39;t check if they are deleted or</span>
+<span class="sd">            from a different taxon). The alternative is to keep only those</span>
+<span class="sd">            which are in the list of all UniProt IDs for the given organism.</span>
+<span class="sd">        trembl_swissprot_by_genesymbol : bool</span>
+<span class="sd">            Attempt to translate TrEMBL IDs to SwissProt by translating to</span>
+<span class="sd">            gene symbols and then to SwissProt.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">session_mod</span><span class="o">.</span><span class="n">Logger</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">name</span> <span class="o">=</span> <span class="s1">&#39;mapping&#39;</span><span class="p">)</span>
+
+        <span class="n">cleanup_period</span> <span class="o">=</span> <span class="n">settings</span><span class="o">.</span><span class="n">get</span><span class="p">(</span>
+            <span class="s1">&#39;mapper_cleanup_interval&#39;</span><span class="p">,</span>
+            <span class="n">cleanup_period</span>
+        <span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">_translate_deleted_uniprot</span> <span class="o">=</span> <span class="n">settings</span><span class="o">.</span><span class="n">get</span><span class="p">(</span>
+            <span class="s1">&#39;mapper_translate_deleted_uniprot&#39;</span><span class="p">,</span>
+            <span class="n">translate_deleted_uniprot</span><span class="p">,</span>
+        <span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">_keep_invalid_uniprot</span> <span class="o">=</span> <span class="n">settings</span><span class="o">.</span><span class="n">get</span><span class="p">(</span>
+            <span class="s1">&#39;mapper_keep_invalid_uniprot&#39;</span><span class="p">,</span>
+            <span class="n">keep_invalid_uniprot</span><span class="p">,</span>
+        <span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">_trembl_swissprot_by_genesymbol</span> <span class="o">=</span> <span class="n">settings</span><span class="o">.</span><span class="n">get</span><span class="p">(</span>
+            <span class="s1">&#39;mapper_trembl_swissprot_by_genesymbol&#39;</span><span class="p">,</span>
+            <span class="n">trembl_swissprot_by_genesymbol</span><span class="p">,</span>
+        <span class="p">)</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_mapper_cleanup_timeloop</span> <span class="o">=</span> <span class="n">timeloop</span><span class="o">.</span><span class="n">Timeloop</span><span class="p">()</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">_mapper_cleanup_timeloop</span><span class="o">.</span><span class="n">logger</span><span class="o">.</span><span class="n">setLevel</span><span class="p">(</span><span class="mi">9999</span><span class="p">)</span>
+
+        <span class="k">for</span> <span class="n">job</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">_mapper_cleanup_timeloop</span><span class="o">.</span><span class="n">jobs</span><span class="p">:</span>
+
+            <span class="k">if</span> <span class="n">job</span><span class="o">.</span><span class="n">is_alive</span><span class="p">():</span>
+
+                <span class="n">job</span><span class="o">.</span><span class="n">stop</span><span class="p">()</span>
+                <span class="n">job</span><span class="o">.</span><span class="n">stopped</span><span class="o">.</span><span class="n">set</span><span class="p">()</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_mapper_cleanup_timeloop</span><span class="o">.</span><span class="n">jobs</span> <span class="o">=</span> <span class="p">[]</span>
+
+
+        <span class="nd">@self</span><span class="o">.</span><span class="n">_mapper_cleanup_timeloop</span><span class="o">.</span><span class="n">job</span><span class="p">(</span>
+            <span class="n">interval</span> <span class="o">=</span> <span class="n">datetime</span><span class="o">.</span><span class="n">timedelta</span><span class="p">(</span>
+                <span class="n">seconds</span> <span class="o">=</span> <span class="n">cleanup_period</span>
+            <span class="p">)</span>
+        <span class="p">)</span>
+        <span class="k">def</span> <span class="nf">_cleanup</span><span class="p">():</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">remove_expired</span><span class="p">()</span>
+
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_mapper_cleanup_timeloop</span><span class="o">.</span><span class="n">start</span><span class="p">(</span><span class="n">block</span> <span class="o">=</span> <span class="kc">False</span><span class="p">)</span>
+
+        <span class="c1"># regex for matching UniProt AC format</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">reuniprot</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">compile</span><span class="p">(</span><span class="sa">r</span><span class="s1">&#39;^(?:</span><span class="si">%s</span><span class="s1">)$&#39;</span> <span class="o">%</span> <span class="n">uniprot_input</span><span class="o">.</span><span class="n">reac</span><span class="o">.</span><span class="n">pattern</span><span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">remipreac</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">compile</span><span class="p">(</span><span class="sa">r</span><span class="s1">&#39;^MI\d</span><span class="si">{7}</span><span class="s1">$&#39;</span><span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">remimatac</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">compile</span><span class="p">(</span><span class="sa">r</span><span class="s1">&#39;^MIMAT\d</span><span class="si">{7}</span><span class="s1">$&#39;</span><span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">remipreid</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">compile</span><span class="p">(</span>
+            <span class="sa">r</span><span class="s1">&#39;^[a-z]</span><span class="si">{3}</span><span class="s1">-&#39;</span>
+            <span class="sa">r</span><span class="s1">&#39;(?:mir|MIR|let|lsy|lin)-?&#39;</span>
+            <span class="sa">r</span><span class="s1">&#39;\d+-?[A-z\*]*(?:-((?!p)[\w\*\.-])+)?$&#39;</span>
+        <span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">remimatid</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">compile</span><span class="p">(</span>
+            <span class="sa">r</span><span class="s1">&#39;^[a-z]</span><span class="si">{3}</span><span class="s1">-&#39;</span>
+            <span class="sa">r</span><span class="s1">&#39;(?:miR|let|lsy|lin)-?&#39;</span>
+            <span class="sa">r</span><span class="s1">&#39;\d+[a-z\*]*(?:-((?!p)[\w\*])+)?(?:-(3|5)p)?$&#39;</span>
+        <span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">cachedir</span> <span class="o">=</span> <span class="n">cache_mod</span><span class="o">.</span><span class="n">get_cachedir</span><span class="p">()</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span> <span class="ow">or</span> <span class="n">settings</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">&#39;default_organism&#39;</span><span class="p">)</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">unmapped</span> <span class="o">=</span> <span class="p">[]</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">tables</span> <span class="o">=</span> <span class="p">{}</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">uniprot_mapped</span> <span class="o">=</span> <span class="p">[]</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">trace</span> <span class="o">=</span> <span class="p">[]</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">uniprot_static_names</span> <span class="o">=</span> <span class="p">{</span>
+            <span class="s1">&#39;uniprot_id&#39;</span><span class="p">:</span> <span class="s1">&#39;UniProtKB-ID&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;embl&#39;</span><span class="p">:</span> <span class="s1">&#39;EMBL-CDS&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;embl_id&#39;</span><span class="p">:</span> <span class="s1">&#39;EMBL&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;entrez&#39;</span><span class="p">:</span> <span class="s1">&#39;GeneID&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;gi&#39;</span><span class="p">:</span> <span class="s1">&#39;GI&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;refseqp&#39;</span><span class="p">:</span> <span class="s1">&#39;RefSeq&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;refseqn&#39;</span><span class="p">:</span> <span class="s1">&#39;RefSeq_NT&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;ensembl&#39;</span><span class="p">:</span> <span class="s1">&#39;Ensembl&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;ensg&#39;</span><span class="p">:</span> <span class="s1">&#39;ENSEMBL&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;ensp&#39;</span><span class="p">:</span> <span class="s1">&#39;ENSEMBL_PRO_ID&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;enst&#39;</span><span class="p">:</span> <span class="s1">&#39;ENSEMBL_TRS&#39;</span><span class="p">,</span>
+            <span class="s1">&#39;hgnc&#39;</span><span class="p">:</span> <span class="s1">&#39;HGNC&#39;</span><span class="p">,</span>
+        <span class="p">}</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">names_uniprot_static</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="n">common</span><span class="o">.</span><span class="n">swap_dict_simple</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">uniprot_static_names</span><span class="p">)</span>
+        <span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="Mapper.reload">
+<a class="viewcode-back" href="../../../api/pypath.utils.mapping.Mapper.html#pypath.utils.mapping.Mapper.reload">[docs]</a>
+    <span class="k">def</span> <span class="nf">reload</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Reload the class from the module level.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">modname</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="vm">__class__</span><span class="o">.</span><span class="vm">__module__</span>
+        <span class="n">mod</span> <span class="o">=</span> <span class="nb">__import__</span><span class="p">(</span><span class="n">modname</span><span class="p">,</span> <span class="n">fromlist</span> <span class="o">=</span> <span class="p">[</span><span class="n">modname</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;.&#39;</span><span class="p">)[</span><span class="mi">0</span><span class="p">]])</span>
+        <span class="n">imp</span><span class="o">.</span><span class="n">reload</span><span class="p">(</span><span class="n">mod</span><span class="p">)</span>
+        <span class="n">new</span> <span class="o">=</span> <span class="nb">getattr</span><span class="p">(</span><span class="n">mod</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="vm">__class__</span><span class="o">.</span><span class="vm">__name__</span><span class="p">)</span>
+        <span class="nb">setattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">&#39;__class__&#39;</span><span class="p">,</span> <span class="n">new</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="Mapper.get_table_key">
+<a class="viewcode-back" href="../../../api/pypath.utils.mapping.Mapper.html#pypath.utils.mapping.Mapper.get_table_key">[docs]</a>
+    <span class="k">def</span> <span class="nf">get_table_key</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">id_type</span><span class="p">,</span>
+            <span class="n">target_id_type</span><span class="p">,</span>
+            <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+        <span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Returns a tuple unambigously identifying a mapping table.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span> <span class="ow">or</span> <span class="bp">self</span><span class="o">.</span><span class="n">ncbi_tax_id</span>
+
+        <span class="k">return</span> <span class="n">MappingTableKey</span><span class="p">(</span>
+            <span class="n">id_type</span> <span class="o">=</span> <span class="n">id_type</span><span class="p">,</span>
+            <span class="n">target_id_type</span> <span class="o">=</span> <span class="n">target_id_type</span><span class="p">,</span>
+            <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">,</span>
+        <span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="Mapper.which_table">
+<a class="viewcode-back" href="../../../api/pypath.utils.mapping.Mapper.html#pypath.utils.mapping.Mapper.which_table">[docs]</a>
+    <span class="k">def</span> <span class="nf">which_table</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">id_type</span><span class="p">,</span>
+            <span class="n">target_id_type</span><span class="p">,</span>
+            <span class="n">load</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
+            <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+        <span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Returns the table which is suitable to convert an ID of</span>
+<span class="sd">        id_type to target_id_type. If no such table have been loaded</span>
+<span class="sd">        yet, it attempts to load from UniProt. If all attempts failed</span>
+<span class="sd">        returns `None`.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">tbl</span> <span class="o">=</span> <span class="kc">None</span>
+        <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span> <span class="ow">or</span> <span class="bp">self</span><span class="o">.</span><span class="n">ncbi_tax_id</span>
+
+
+        <span class="k">def</span> <span class="nf">check_loaded</span><span class="p">():</span>
+
+            <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">which_table</span><span class="p">(</span>
+                <span class="n">id_type</span> <span class="o">=</span> <span class="n">id_type</span><span class="p">,</span>
+                <span class="n">target_id_type</span> <span class="o">=</span> <span class="n">target_id_type</span><span class="p">,</span>
+                <span class="n">load</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+                <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">,</span>
+            <span class="p">)</span>
+
+
+        <span class="n">tbl_key</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">get_table_key</span><span class="p">(</span>
+            <span class="n">id_type</span> <span class="o">=</span> <span class="n">id_type</span><span class="p">,</span>
+            <span class="n">target_id_type</span> <span class="o">=</span> <span class="n">target_id_type</span><span class="p">,</span>
+            <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">,</span>
+        <span class="p">)</span>
+        <span class="n">tbl_key_noorganism</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">get_table_key</span><span class="p">(</span>
+            <span class="o">*</span><span class="n">tbl_key</span><span class="p">[:</span><span class="o">-</span><span class="mi">1</span><span class="p">],</span>
+            <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">_const</span><span class="o">.</span><span class="n">NOT_ORGANISM_SPECIFIC</span><span class="p">,</span>
+        <span class="p">)</span>
+
+        <span class="n">tbl_key_rev</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">get_table_key</span><span class="p">(</span>
+            <span class="n">id_type</span> <span class="o">=</span> <span class="n">target_id_type</span><span class="p">,</span>
+            <span class="n">target_id_type</span> <span class="o">=</span> <span class="n">id_type</span><span class="p">,</span>
+            <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">,</span>
+        <span class="p">)</span>
+        <span class="n">tbl_key_rev_noorganism</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">get_table_key</span><span class="p">(</span>
+            <span class="o">*</span><span class="n">tbl_key_rev</span><span class="p">[:</span><span class="o">-</span><span class="mi">1</span><span class="p">],</span>
+            <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">_const</span><span class="o">.</span><span class="n">NOT_ORGANISM_SPECIFIC</span><span class="p">,</span>
+        <span class="p">)</span>
+
+        <span class="k">if</span> <span class="n">tbl_key</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">tables</span><span class="p">:</span>
+
+            <span class="n">tbl</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">tables</span><span class="p">[</span><span class="n">tbl_key</span><span class="p">]</span>
+
+        <span class="k">elif</span> <span class="n">tbl_key_noorganism</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">tables</span><span class="p">:</span>
+
+            <span class="n">tbl</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">tables</span><span class="p">[</span><span class="n">tbl_key_noorganism</span><span class="p">]</span>
+
+        <span class="k">elif</span> <span class="n">tbl_key_rev</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">tables</span><span class="p">:</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">create_reverse</span><span class="p">(</span><span class="n">tbl_key_rev</span><span class="p">)</span>
+            <span class="n">tbl</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">tables</span><span class="p">[</span><span class="n">tbl_key_rev</span><span class="p">]</span>
+
+        <span class="k">elif</span> <span class="n">tbl_key_rev_noorganism</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">tables</span><span class="p">:</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">create_reverse</span><span class="p">(</span><span class="n">tbl_key_rev_noorganism</span><span class="p">)</span>
+            <span class="n">tbl</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">tables</span><span class="p">[</span><span class="n">tbl_key_rev_noorganism</span><span class="p">]</span>
+
+        <span class="k">elif</span> <span class="n">load</span><span class="p">:</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span>
+                <span class="s1">&#39;Requested to load ID translation table from &#39;</span>
+                <span class="s1">&#39;`</span><span class="si">%s</span><span class="s1">` to `</span><span class="si">%s</span><span class="s1">`, organism: </span><span class="si">%u</span><span class="s1">.&#39;</span> <span class="o">%</span> <span class="p">(</span>
+                    <span class="n">id_type</span><span class="p">,</span>
+                    <span class="n">target_id_type</span><span class="p">,</span>
+                    <span class="n">ncbi_tax_id</span><span class="p">,</span>
+                <span class="p">)</span>
+            <span class="p">)</span>
+
+            <span class="k">if</span> <span class="n">id_type</span> <span class="o">==</span> <span class="s1">&#39;complex&#39;</span> <span class="ow">or</span> <span class="n">target_id_type</span> <span class="o">==</span> <span class="s1">&#39;complex&#39;</span><span class="p">:</span>
+
+                <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s1">&#39;Can not translate protein complexes.&#39;</span><span class="p">)</span>
+
+            <span class="n">id_types</span> <span class="o">=</span> <span class="p">(</span><span class="n">id_type</span><span class="p">,</span> <span class="n">target_id_type</span><span class="p">)</span>
+            <span class="n">id_types_rev</span> <span class="o">=</span> <span class="nb">tuple</span><span class="p">(</span><span class="nb">reversed</span><span class="p">(</span><span class="n">id_types</span><span class="p">))</span>
+            <span class="n">resource</span> <span class="o">=</span> <span class="kc">None</span>
+
+            <span class="k">for</span> <span class="n">resource_attr</span> <span class="ow">in</span> <span class="n">RESOURCES_EXPLICIT</span><span class="p">:</span>
+
+                <span class="n">resources</span> <span class="o">=</span> <span class="nb">getattr</span><span class="p">(</span><span class="n">maps</span><span class="p">,</span> <span class="n">resource_attr</span><span class="p">)</span>
+
+                <span class="k">if</span> <span class="n">id_types</span> <span class="ow">in</span> <span class="n">resources</span><span class="p">:</span>
+
+                    <span class="n">resource</span> <span class="o">=</span> <span class="n">resources</span><span class="p">[</span><span class="n">id_types</span><span class="p">]</span>
+                    <span class="n">load_a_to_b</span> <span class="o">=</span> <span class="kc">True</span>
+                    <span class="n">load_b_to_a</span> <span class="o">=</span> <span class="kc">False</span>
+
+                <span class="k">elif</span> <span class="n">id_types_rev</span> <span class="ow">in</span> <span class="n">resources</span><span class="p">:</span>
+
+                    <span class="n">resource</span> <span class="o">=</span> <span class="n">resources</span><span class="p">[</span><span class="n">id_types_rev</span><span class="p">]</span>
+                    <span class="n">load_a_to_b</span> <span class="o">=</span> <span class="kc">False</span>
+                    <span class="n">load_b_to_a</span> <span class="o">=</span> <span class="kc">True</span>
+
+                <span class="k">if</span> <span class="n">resource</span><span class="p">:</span>
+
+                    <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span>
+                        <span class="s1">&#39;Chosen built-in defined ID translation table: &#39;</span>
+                        <span class="s1">&#39;resource=</span><span class="si">%s</span><span class="s1">, id_type_a=</span><span class="si">%s</span><span class="s1">, id_type_b=</span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="p">(</span>
+                            <span class="n">resource_attr</span><span class="p">,</span>
+                            <span class="n">resource</span><span class="o">.</span><span class="n">id_type_a</span><span class="p">,</span>
+                            <span class="n">resource</span><span class="o">.</span><span class="n">id_type_b</span><span class="p">,</span>
+                        <span class="p">)</span>
+                    <span class="p">)</span>
+
+                    <span class="bp">self</span><span class="o">.</span><span class="n">load_mapping</span><span class="p">(</span>
+                        <span class="n">resource</span> <span class="o">=</span> <span class="n">resource</span><span class="p">,</span>
+                        <span class="n">load_a_to_b</span> <span class="o">=</span> <span class="n">load_a_to_b</span><span class="p">,</span>
+                        <span class="n">load_b_to_a</span> <span class="o">=</span> <span class="n">load_b_to_a</span><span class="p">,</span>
+                        <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">,</span>
+                    <span class="p">)</span>
+
+                    <span class="n">tbl</span> <span class="o">=</span> <span class="n">check_loaded</span><span class="p">()</span>
+
+                    <span class="k">break</span>
+
+                <span class="k">if</span> <span class="n">tbl</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
+
+                    <span class="k">break</span>
+
+            <span class="k">if</span> <span class="n">tbl</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
+
+                <span class="n">basic_services</span> <span class="o">=</span> <span class="p">{</span><span class="s1">&#39;hmdb&#39;</span><span class="p">,</span> <span class="s1">&#39;ramp&#39;</span><span class="p">,</span> <span class="s1">&#39;uniprot&#39;</span><span class="p">,</span> <span class="s1">&#39;unichem&#39;</span><span class="p">}</span>
+
+                <span class="k">for</span> <span class="p">(</span><span class="n">service_ids</span><span class="p">,</span> <span class="n">service_id_type</span><span class="p">,</span> <span class="n">input_cls</span><span class="p">)</span> <span class="ow">in</span> <span class="p">(</span>
+                    <span class="n">RESOURCES_IMPLICIT</span>
+                <span class="p">):</span>
+
+                    <span class="k">if</span> <span class="p">(</span>
+                        <span class="p">(</span>
+                            <span class="n">input_cls</span><span class="o">.</span><span class="n">possible</span><span class="p">(</span>
+                                <span class="n">id_type</span><span class="p">,</span>
+                                <span class="n">target_id_type</span><span class="p">,</span>
+                                <span class="n">ncbi_tax_id</span><span class="p">,</span>
+                            <span class="p">)</span> <span class="ow">and</span>
+                            <span class="n">id_type</span> <span class="o">!=</span> <span class="n">target_id_type</span>
+                        <span class="p">)</span> <span class="ow">or</span> <span class="p">(</span>
+                            <span class="n">service_id_type</span> <span class="o">==</span> <span class="s1">&#39;pro&#39;</span> <span class="ow">and</span> <span class="p">(</span>
+                                <span class="p">(</span>
+                                    <span class="n">id_type</span> <span class="ow">in</span> <span class="n">service_ids</span> <span class="ow">or</span>
+                                    <span class="n">target_id_type</span> <span class="ow">in</span> <span class="n">service_ids</span>
+                                <span class="p">)</span> <span class="ow">and</span>
+                                <span class="p">(</span>
+                                    <span class="n">id_type</span> <span class="o">==</span> <span class="n">service_id_type</span> <span class="ow">or</span>
+                                    <span class="n">target_id_type</span> <span class="o">==</span> <span class="n">service_id_type</span>
+                                <span class="p">)</span>
+                            <span class="p">)</span>
+                        <span class="p">)</span> <span class="ow">or</span> <span class="p">(</span>
+                            <span class="n">service_id_type</span> <span class="o">==</span> <span class="s1">&#39;biomart&#39;</span> <span class="ow">and</span> <span class="p">(</span>
+                                <span class="p">(</span>
+                                    <span class="n">id_type</span> <span class="ow">in</span> <span class="n">service_ids</span> <span class="ow">and</span>
+                                    <span class="n">target_id_type</span> <span class="ow">in</span> <span class="n">service_ids</span>
+                                <span class="p">)</span>
+                            <span class="p">)</span>
+                        <span class="p">)</span> <span class="ow">or</span> <span class="p">(</span>
+                            <span class="n">service_id_type</span> <span class="o">==</span> <span class="s1">&#39;array&#39;</span> <span class="ow">and</span> <span class="p">(</span>
+                                <span class="p">(</span>
+                                    <span class="n">id_type</span> <span class="ow">in</span> <span class="n">service_ids</span> <span class="ow">and</span>
+                                    <span class="n">target_id_type</span> <span class="ow">in</span> <span class="p">{</span><span class="s1">&#39;ensg&#39;</span><span class="p">,</span> <span class="s1">&#39;enst&#39;</span><span class="p">,</span> <span class="s1">&#39;ensp&#39;</span><span class="p">}</span>
+                                <span class="p">)</span> <span class="ow">or</span>
+                                <span class="p">(</span>
+                                    <span class="n">target_id_type</span> <span class="ow">in</span> <span class="n">service_ids</span> <span class="ow">and</span>
+                                    <span class="n">id_type</span> <span class="ow">in</span> <span class="p">{</span><span class="s1">&#39;ensg&#39;</span><span class="p">,</span> <span class="s1">&#39;enst&#39;</span><span class="p">,</span> <span class="s1">&#39;ensp&#39;</span><span class="p">}</span>
+                                <span class="p">)</span>
+                            <span class="p">)</span>
+                        <span class="p">)</span>
+                    <span class="p">):</span>
+
+                        <span class="k">if</span> <span class="n">target_id_type</span> <span class="o">==</span> <span class="n">service_id_type</span><span class="p">:</span>
+
+                            <span class="n">_id_type</span><span class="p">,</span> <span class="n">_target_id_type</span> <span class="o">=</span> <span class="p">(</span>
+                                <span class="n">target_id_type</span><span class="p">,</span>
+                                <span class="n">id_type</span><span class="p">,</span>
+                            <span class="p">)</span>
+                            <span class="n">load_a_to_b</span> <span class="o">=</span> <span class="kc">False</span>
+                            <span class="n">load_b_to_a</span> <span class="o">=</span> <span class="kc">True</span>
+
+                        <span class="k">else</span><span class="p">:</span>
+
+                            <span class="n">_id_type</span><span class="p">,</span> <span class="n">_target_id_type</span> <span class="o">=</span> <span class="p">(</span>
+                                <span class="n">id_type</span><span class="p">,</span>
+                                <span class="n">target_id_type</span><span class="p">,</span>
+                            <span class="p">)</span>
+                            <span class="n">load_a_to_b</span> <span class="o">=</span> <span class="kc">True</span>
+                            <span class="n">load_b_to_a</span> <span class="o">=</span> <span class="kc">False</span>
+
+                        <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span>
+                            <span class="s1">&#39;Chosen ID translation table from service: &#39;</span>
+                            <span class="s1">&#39;service=</span><span class="si">%s</span><span class="s1">, id_type_a=</span><span class="si">%s</span><span class="s1">, id_type_b=</span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="p">(</span>
+                                <span class="n">service_id_type</span><span class="p">,</span>
+                                <span class="n">_id_type</span><span class="p">,</span>
+                                <span class="n">_target_id_type</span><span class="p">,</span>
+                            <span class="p">)</span>
+                        <span class="p">)</span>
+
+                        <span class="k">if</span> <span class="n">service_id_type</span> <span class="ow">in</span> <span class="p">{</span><span class="s1">&#39;hmdb&#39;</span><span class="p">,</span> <span class="s1">&#39;ramp&#39;</span><span class="p">,</span> <span class="s1">&#39;unichem&#39;</span><span class="p">}:</span>
+
+                            <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">_const</span><span class="o">.</span><span class="n">NOT_ORGANISM_SPECIFIC</span>
+                            <span class="n">tbl_key</span> <span class="o">=</span> <span class="n">tbl_key_noorganism</span>
+                            <span class="n">tbl_key_rev</span> <span class="o">=</span> <span class="n">tbl_key_rev_noorganism</span>
+
+                        <span class="c1"># for uniprot/idmapping or PRO or array</span>
+                        <span class="c1"># we create here the mapping params</span>
+                        <span class="n">this_param</span> <span class="o">=</span> <span class="n">input_cls</span><span class="p">(</span>
+                            <span class="n">id_type_a</span> <span class="o">=</span> <span class="n">_id_type</span><span class="p">,</span>
+                            <span class="n">id_type_b</span> <span class="o">=</span> <span class="n">_target_id_type</span><span class="p">,</span>
+                            <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">,</span>
+                        <span class="p">)</span>
+
+                        <span class="n">reader</span> <span class="o">=</span> <span class="n">MapReader</span><span class="p">(</span>
+                            <span class="n">param</span> <span class="o">=</span> <span class="n">this_param</span><span class="p">,</span>
+                            <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">,</span>
+                            <span class="n">load_a_to_b</span> <span class="o">=</span> <span class="n">load_a_to_b</span><span class="p">,</span>
+                            <span class="n">load_b_to_a</span> <span class="o">=</span> <span class="n">load_b_to_a</span><span class="p">,</span>
+                            <span class="n">uniprots</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+                            <span class="n">lifetime</span> <span class="o">=</span> <span class="mi">300</span><span class="p">,</span>
+                            <span class="n">resource_id_types</span> <span class="o">=</span> <span class="n">service_ids</span><span class="p">,</span>
+                        <span class="p">)</span>
+
+                        <span class="bp">self</span><span class="o">.</span><span class="n">tables</span><span class="p">[</span><span class="n">tbl_key</span><span class="p">]</span> <span class="o">=</span> <span class="nb">getattr</span><span class="p">(</span>
+                            <span class="n">reader</span><span class="p">,</span>
+                            <span class="s1">&#39;mapping_table_</span><span class="si">%s</span><span class="s1">_to_</span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="p">(</span>
+                                <span class="n">reader</span><span class="o">.</span><span class="n">id_type_side</span><span class="p">(</span><span class="n">tbl_key</span><span class="o">.</span><span class="n">id_type</span><span class="p">),</span>
+                                <span class="n">reader</span><span class="o">.</span><span class="n">id_type_side</span><span class="p">(</span><span class="n">tbl_key</span><span class="o">.</span><span class="n">target_id_type</span><span class="p">),</span>
+                            <span class="p">)</span>
+                        <span class="p">)</span>
+
+                    <span class="n">tbl</span> <span class="o">=</span> <span class="n">check_loaded</span><span class="p">()</span>
+
+                    <span class="k">if</span> <span class="n">tbl</span><span class="p">:</span>
+
+                        <span class="k">break</span>
+
+            <span class="k">if</span> <span class="n">tbl</span> <span class="ow">is</span> <span class="kc">None</span> <span class="ow">and</span> <span class="n">id_type</span> <span class="o">==</span> <span class="s1">&#39;genesymbol5&#39;</span><span class="p">:</span>
+
+                <span class="bp">self</span><span class="o">.</span><span class="n">load_genesymbol5</span><span class="p">(</span><span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">)</span>
+
+                <span class="n">tbl</span> <span class="o">=</span> <span class="n">check_loaded</span><span class="p">()</span>
+
+            <span class="k">if</span> <span class="n">tbl</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
+
+                <span class="k">if</span> <span class="p">(</span>
+                    <span class="n">settings</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">&#39;mapping_uniprot_static&#39;</span><span class="p">)</span> <span class="ow">and</span>
+                    <span class="n">id_type</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">uniprot_static_names</span> <span class="ow">and</span>
+                    <span class="n">target_id_type</span> <span class="o">==</span> <span class="s1">&#39;uniprot&#39;</span>
+                <span class="p">):</span>
+
+                    <span class="bp">self</span><span class="o">.</span><span class="n">load_uniprot_static</span><span class="p">([</span><span class="n">id_type</span><span class="p">])</span>
+
+                    <span class="n">tbl</span> <span class="o">=</span> <span class="n">check_loaded</span><span class="p">()</span>
+
+        <span class="k">if</span> <span class="n">tbl</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span>
+                <span class="s1">&#39;Could not find suitable ID translation table &#39;</span>
+                <span class="sa">f</span><span class="s1">&#39;between id types `</span><span class="si">{</span><span class="n">id_type</span><span class="si">}</span><span class="s1">` and `</span><span class="si">{</span><span class="n">target_id_type</span><span class="si">}</span><span class="s1">` &#39;</span>
+                <span class="sa">f</span><span class="s1">&#39;for organism `</span><span class="si">{</span><span class="n">ncbi_tax_id</span><span class="si">}</span><span class="s1">`.&#39;</span>
+            <span class="p">)</span>
+
+        <span class="k">if</span> <span class="nb">hasattr</span><span class="p">(</span><span class="n">tbl</span><span class="p">,</span> <span class="s1">&#39;_used&#39;</span><span class="p">):</span>
+
+            <span class="n">tbl</span><span class="o">.</span><span class="n">_used</span><span class="p">()</span>
+
+        <span class="k">return</span> <span class="n">tbl</span></div>
+
+
+
+<div class="viewcode-block" id="Mapper.reverse_mapping">
+<a class="viewcode-back" href="../../../api/pypath.utils.mapping.Mapper.html#pypath.utils.mapping.Mapper.reverse_mapping">[docs]</a>
+    <span class="nd">@staticmethod</span>
+    <span class="k">def</span> <span class="nf">reverse_mapping</span><span class="p">(</span><span class="n">mapping_table</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Creates an opposite direction `MappingTable` by swapping the</span>
+<span class="sd">        dictionary inside an existing `MappingTable` object.</span>
+
+<span class="sd">        Args</span>
+<span class="sd">            mapping_table (MappingTable): A `MappingTable` object.</span>
+
+<span class="sd">        Returns</span>
+<span class="sd">            A new `MappingTable` object.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">rev_data</span> <span class="o">=</span> <span class="n">common</span><span class="o">.</span><span class="n">swap_dict</span><span class="p">(</span><span class="n">mapping_table</span><span class="o">.</span><span class="n">data</span><span class="p">)</span>
+
+        <span class="k">return</span> <span class="n">MappingTable</span><span class="p">(</span>
+            <span class="n">data</span> <span class="o">=</span> <span class="n">rev_data</span><span class="p">,</span>
+            <span class="n">id_type</span> <span class="o">=</span> <span class="n">mapping_table</span><span class="o">.</span><span class="n">target_id_type</span><span class="p">,</span>
+            <span class="n">target_id_type</span> <span class="o">=</span> <span class="n">mapping_table</span><span class="o">.</span><span class="n">id_type</span><span class="p">,</span>
+            <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">mapping_table</span><span class="o">.</span><span class="n">ncbi_tax_id</span><span class="p">,</span>
+            <span class="n">lifetime</span> <span class="o">=</span> <span class="n">mapping_table</span><span class="o">.</span><span class="n">lifetime</span><span class="p">,</span>
+        <span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="Mapper.reverse_key">
+<a class="viewcode-back" href="../../../api/pypath.utils.mapping.Mapper.html#pypath.utils.mapping.Mapper.reverse_key">[docs]</a>
+    <span class="k">def</span> <span class="nf">reverse_key</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">key</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        For a mapping table key returns a new key with the identifiers</span>
+<span class="sd">        reversed.</span>
+
+<span class="sd">        Args</span>
+<span class="sd">            key (tuple): A mapping table key.</span>
+
+<span class="sd">        Returns</span>
+<span class="sd">            A tuple representing a mapping table key, identifiers swapped.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">return</span> <span class="p">(</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">get_table_key</span><span class="p">(</span>
+                <span class="n">id_type</span> <span class="o">=</span> <span class="n">key</span><span class="o">.</span><span class="n">target_id_type</span><span class="p">,</span>
+                <span class="n">target_id_type</span> <span class="o">=</span> <span class="n">key</span><span class="o">.</span><span class="n">id_type</span><span class="p">,</span>
+                <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">key</span><span class="o">.</span><span class="n">ncbi_tax_id</span><span class="p">,</span>
+            <span class="p">)</span>
+        <span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="Mapper.create_reverse">
+<a class="viewcode-back" href="../../../api/pypath.utils.mapping.Mapper.html#pypath.utils.mapping.Mapper.create_reverse">[docs]</a>
+    <span class="k">def</span> <span class="nf">create_reverse</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">key</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Creates a mapping table with ``id_type`` and ``target_id_type``</span>
+<span class="sd">        (i.e. direction of the ID translation) swapped.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">table</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">tables</span><span class="p">[</span><span class="n">key</span><span class="p">]</span>
+        <span class="n">rev_key</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">reverse_key</span><span class="p">(</span><span class="n">key</span><span class="p">)</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">tables</span><span class="p">[</span><span class="n">rev_key</span><span class="p">]</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">reverse_mapping</span><span class="p">(</span><span class="n">table</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="Mapper.map_name0">
+<a class="viewcode-back" href="../../../api/pypath.utils.mapping.Mapper.html#pypath.utils.mapping.Mapper.map_name0">[docs]</a>
+    <span class="k">def</span> <span class="nf">map_name0</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">name</span><span class="p">,</span>
+            <span class="n">id_type</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">target_id_type</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">strict</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+            <span class="n">expand_complexes</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">uniprot_cleanup</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+        <span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Translates the name and returns only one of the resulted IDs. It</span>
+<span class="sd">        means in case of ambiguous ID translation, a random one of them</span>
+<span class="sd">        will be picked and returned. Recommended to use only if the</span>
+<span class="sd">        translation between the given ID types is mostly unambigous and</span>
+<span class="sd">        the loss of information can be ignored. See more details at</span>
+<span class="sd">        `map_name`.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">names</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">map_name</span><span class="p">(</span>
+            <span class="n">name</span> <span class="o">=</span> <span class="n">name</span><span class="p">,</span>
+            <span class="n">id_type</span> <span class="o">=</span> <span class="n">id_type</span><span class="p">,</span>
+            <span class="n">target_id_type</span> <span class="o">=</span> <span class="n">target_id_type</span><span class="p">,</span>
+            <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">,</span>
+            <span class="n">strict</span> <span class="o">=</span> <span class="n">strict</span><span class="p">,</span>
+            <span class="n">expand_complexes</span> <span class="o">=</span> <span class="n">expand_complexes</span><span class="p">,</span>
+            <span class="n">uniprot_cleanup</span> <span class="o">=</span> <span class="n">uniprot_cleanup</span><span class="p">,</span>
+        <span class="p">)</span>
+
+        <span class="k">return</span> <span class="nb">list</span><span class="p">(</span><span class="n">names</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span> <span class="k">if</span> <span class="n">names</span> <span class="k">else</span> <span class="kc">None</span></div>
+
+
+
+<div class="viewcode-block" id="Mapper.map_name">
+<a class="viewcode-back" href="../../../api/pypath.utils.mapping.Mapper.html#pypath.utils.mapping.Mapper.map_name">[docs]</a>
+    <span class="nd">@common</span><span class="o">.</span><span class="n">ignore_unhashable</span>
+    <span class="nd">@functools</span><span class="o">.</span><span class="n">lru_cache</span><span class="p">(</span><span class="n">maxsize</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="mf">1e5</span><span class="p">))</span>
+    <span class="k">def</span> <span class="nf">map_name</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">name</span><span class="p">,</span>
+            <span class="n">id_type</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">target_id_type</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">strict</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+            <span class="n">expand_complexes</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
+            <span class="n">uniprot_cleanup</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
+        <span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Translates one instance of one ID type to a different one.</span>
+<span class="sd">        Returns set of the target ID type.</span>
+
+<span class="sd">        This function should be used to convert individual IDs.</span>
+<span class="sd">        It takes care about everything and ideally you don&#39;t need to</span>
+<span class="sd">        think on the details.</span>
+
+<span class="sd">        How does it work: looks up dictionaries between the original</span>
+<span class="sd">        and target ID type, if doesn&#39;t find, attempts to load from the</span>
+<span class="sd">        predefined inputs.</span>
+<span class="sd">        If the original name is genesymbol, first it looks up among the</span>
+<span class="sd">        preferred gene names from UniProt, if not found, it takes an</span>
+<span class="sd">        attempt with the alternative gene names. If the gene symbol</span>
+<span class="sd">        still couldn&#39;t be found, and strict = False, the last attempt</span>
+<span class="sd">        only the first 5 characters of the gene symbol matched. If the</span>
+<span class="sd">        target name type is uniprot, then it converts all the ACs to</span>
+<span class="sd">        primary. Then, for the Trembl IDs it looks up the preferred gene</span>
+<span class="sd">        names, and find Swissprot IDs with the same preferred gene name.</span>
+
+<span class="sd">        Args</span>
+<span class="sd">            name (str): The original name to be converted.</span>
+<span class="sd">            id_type (str): The type of the name. Available by default:</span>
+<span class="sd">                - genesymbol (gene name)</span>
+<span class="sd">                - entrez (Entrez Gene ID \[#\])</span>
+<span class="sd">                - refseqp (NCBI RefSeq Protein ID \[NP\_\*|XP\_\*\])</span>
+<span class="sd">                - ensp (Ensembl protein ID \[ENSP\*\])</span>
+<span class="sd">                - enst (Ensembl transcript ID \[ENST\*\])</span>
+<span class="sd">                - ensg (Ensembl genomic DNA ID \[ENSG\*\])</span>
+<span class="sd">                - hgnc (HGNC ID \[HGNC:#\])</span>
+<span class="sd">                - gi (GI number \[#\])</span>
+<span class="sd">                - embl (DDBJ/EMBL/GeneBank CDS accession)</span>
+<span class="sd">                - embl_id (DDBJ/EMBL/GeneBank accession)</span>
+<span class="sd">                And many more, see the code of</span>
+<span class="sd">                ``pypath.internals.input_formats``</span>
+<span class="sd">            target_id_type (str): The name type to translate to, more or</span>
+<span class="sd">                less the same values are available as for ``id_type``.</span>
+<span class="sd">            ncbi_tax_id (int): NCBI Taxonomy ID of the organism.</span>
+<span class="sd">            strict (bool): In case a Gene Symbol can not be translated,</span>
+<span class="sd">                try to add number &quot;1&quot; to the end, or try to match only</span>
+<span class="sd">                its first five characters. This option is rarely used,</span>
+<span class="sd">                but it makes possible to translate some non-standard</span>
+<span class="sd">                gene names typically found in old, unmaintained resources.</span>
+<span class="sd">            expand_complexes (bool): When encountering complexes,</span>
+<span class="sd">                translated the IDs of its components and return a set</span>
+<span class="sd">                of IDs. The alternative behaviour is to return the</span>
+<span class="sd">                `Complex` objects.</span>
+<span class="sd">            uniprot_cleanup (bool): When the `target_id_type` is UniProt</span>
+<span class="sd">                ID, call the `uniprot_cleanup` function at the end.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">if</span> <span class="ow">not</span> <span class="n">name</span><span class="p">:</span>
+
+            <span class="k">return</span> <span class="nb">set</span><span class="p">()</span>
+
+        <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span> <span class="ow">or</span> <span class="bp">self</span><span class="o">.</span><span class="n">ncbi_tax_id</span>
+
+        <span class="c1"># we support translating from more name types</span>
+        <span class="c1"># at the same time</span>
+        <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">id_type</span><span class="p">,</span> <span class="p">(</span><span class="nb">list</span><span class="p">,</span> <span class="nb">set</span><span class="p">,</span> <span class="nb">tuple</span><span class="p">)):</span>
+
+            <span class="k">return</span> <span class="nb">set</span><span class="o">.</span><span class="n">union</span><span class="p">(</span>
+                <span class="o">*</span><span class="p">(</span>
+                    <span class="bp">self</span><span class="o">.</span><span class="n">map_name</span><span class="p">(</span>
+                        <span class="n">name</span> <span class="o">=</span> <span class="n">name</span><span class="p">,</span>
+                        <span class="n">id_type</span> <span class="o">=</span> <span class="n">this_id_type</span><span class="p">,</span>
+                        <span class="n">target_id_type</span> <span class="o">=</span> <span class="n">target_id_type</span><span class="p">,</span>
+                        <span class="n">strict</span> <span class="o">=</span> <span class="n">strict</span><span class="p">,</span>
+                        <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">,</span>
+                    <span class="p">)</span>
+                    <span class="k">for</span> <span class="n">this_id_type</span> <span class="ow">in</span> <span class="n">id_type</span>
+                <span class="p">)</span>
+            <span class="p">)</span>
+
+        <span class="c1"># complexes</span>
+        <span class="k">if</span> <span class="nb">hasattr</span><span class="p">(</span><span class="n">name</span><span class="p">,</span> <span class="s1">&#39;components&#39;</span><span class="p">):</span>
+
+            <span class="k">if</span> <span class="n">expand_complexes</span><span class="p">:</span>
+
+               <span class="k">return</span> <span class="nb">set</span><span class="p">(</span><span class="n">name</span><span class="o">.</span><span class="n">components</span><span class="o">.</span><span class="n">keys</span><span class="p">())</span>
+
+            <span class="k">else</span><span class="p">:</span>
+
+                <span class="k">return</span> <span class="p">{</span><span class="n">name</span><span class="p">}</span>
+
+        <span class="c1"># translating from an ID type to the same ID type?</span>
+        <span class="k">elif</span> <span class="n">id_type</span> <span class="o">==</span> <span class="n">target_id_type</span><span class="p">:</span>
+
+            <span class="k">if</span> <span class="n">target_id_type</span> <span class="o">!=</span> <span class="s1">&#39;uniprot&#39;</span> <span class="ow">or</span> <span class="ow">not</span> <span class="n">uniprot_cleanup</span><span class="p">:</span>
+
+                <span class="c1"># no need for translation</span>
+                <span class="k">return</span> <span class="p">{</span><span class="n">name</span><span class="p">}</span>
+
+            <span class="k">else</span><span class="p">:</span>
+
+                <span class="c1"># we still try to search the primary UniProt</span>
+                <span class="n">mapped_names</span> <span class="o">=</span> <span class="p">{</span><span class="n">name</span><span class="p">}</span>
+
+        <span class="c1"># actual translation comes here</span>
+        <span class="k">elif</span> <span class="n">id_type</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s1">&#39;refseq&#39;</span><span class="p">):</span>
+
+            <span class="c1"># RefSeq is special</span>
+            <span class="n">mapped_names</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_map_refseq</span><span class="p">(</span>
+                <span class="n">refseq</span> <span class="o">=</span> <span class="n">name</span><span class="p">,</span>
+                <span class="n">id_type</span> <span class="o">=</span> <span class="n">id_type</span><span class="p">,</span>
+                <span class="n">target_id_type</span> <span class="o">=</span> <span class="n">target_id_type</span><span class="p">,</span>
+                <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">,</span>
+                <span class="n">strict</span> <span class="o">=</span> <span class="n">strict</span><span class="p">,</span>
+            <span class="p">)</span>
+
+        <span class="k">elif</span> <span class="n">id_type</span> <span class="o">==</span> <span class="s1">&#39;ensp&#39;</span><span class="p">:</span>
+
+            <span class="n">mapped_names</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_map_ensp</span><span class="p">(</span>
+                <span class="n">ensp</span> <span class="o">=</span> <span class="n">name</span><span class="p">,</span>
+                <span class="n">target_id_type</span> <span class="o">=</span> <span class="n">target_id_type</span><span class="p">,</span>
+                <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">,</span>
+            <span class="p">)</span>
+
+        <span class="k">elif</span> <span class="n">target_id_type</span> <span class="o">==</span> <span class="s1">&#39;ensp&#39;</span><span class="p">:</span>
+
+            <span class="n">mapped_names</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_map_to_ensp</span><span class="p">(</span>
+                <span class="n">name</span> <span class="o">=</span> <span class="n">name</span><span class="p">,</span>
+                <span class="n">id_type</span> <span class="o">=</span> <span class="n">id_type</span><span class="p">,</span>
+                <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">,</span>
+            <span class="p">)</span>
+
+        <span class="k">elif</span> <span class="p">(</span>
+            <span class="p">(</span>
+                <span class="n">id_type</span> <span class="ow">in</span> <span class="n">input_formats</span><span class="o">.</span><span class="n">ARRAY_MAPPING</span> <span class="ow">and</span>
+                <span class="ow">not</span> <span class="n">target_id_type</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s1">&#39;ens&#39;</span><span class="p">)</span>
+            <span class="p">)</span> <span class="ow">or</span> <span class="p">(</span>
+                <span class="n">target_id_type</span> <span class="ow">in</span> <span class="n">input_formats</span><span class="o">.</span><span class="n">ARRAY_MAPPING</span> <span class="ow">and</span>
+                <span class="ow">not</span> <span class="n">id_type</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s1">&#39;ens&#39;</span><span class="p">)</span>
+            <span class="p">)</span>
+        <span class="p">):</span>
+
+            <span class="c1"># microarray probe IDs we are able to directly translate</span>
+            <span class="c1"># only to and from Ensembl gene, transcript and protein IDs</span>
+            <span class="c1"># if the other ID is different (such as uniprot), we translate</span>
+            <span class="c1"># in two steps, via Ensembl peptide ID:</span>
+            <span class="n">mapped_names</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">chain_map</span><span class="p">(</span>
+                <span class="n">name</span> <span class="o">=</span> <span class="n">name</span><span class="p">,</span>
+                <span class="n">id_type</span> <span class="o">=</span> <span class="n">id_type</span><span class="p">,</span>
+                <span class="n">by_id_type</span> <span class="o">=</span> <span class="s1">&#39;ensp&#39;</span><span class="p">,</span>
+                <span class="n">target_id_type</span> <span class="o">=</span> <span class="n">target_id_type</span><span class="p">,</span>
+                <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">,</span>
+                <span class="n">strict</span> <span class="o">=</span> <span class="n">strict</span><span class="p">,</span>
+                <span class="n">expand_complexes</span> <span class="o">=</span> <span class="n">expand_complexes</span><span class="p">,</span>
+                <span class="n">uniprot_cleanup</span> <span class="o">=</span> <span class="n">uniprot_cleanup</span><span class="p">,</span>
+            <span class="p">)</span>
+
+        <span class="k">else</span><span class="p">:</span>
+
+            <span class="c1"># all the other ID types</span>
+            <span class="n">mapped_names</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_map_name</span><span class="p">(</span>
+                <span class="n">name</span> <span class="o">=</span> <span class="n">name</span><span class="p">,</span>
+                <span class="n">id_type</span> <span class="o">=</span> <span class="n">id_type</span><span class="p">,</span>
+                <span class="n">target_id_type</span> <span class="o">=</span> <span class="n">target_id_type</span><span class="p">,</span>
+                <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">,</span>
+            <span class="p">)</span>
+
+        <span class="c1"># as ID translation tables for PRO IDs are not organism specific</span>
+        <span class="c1"># we need an extra step to limit the results to the target organism</span>
+        <span class="k">if</span> <span class="n">id_type</span> <span class="o">==</span> <span class="s1">&#39;pro&#39;</span> <span class="ow">and</span> <span class="n">target_id_type</span> <span class="o">==</span> <span class="s1">&#39;uniprot&#39;</span><span class="p">:</span>
+
+            <span class="n">mapped_names</span> <span class="o">=</span> <span class="p">(</span>
+                <span class="n">mapped_names</span> <span class="o">&amp;</span>
+                <span class="n">reflists</span><span class="o">.</span><span class="n">get_reflist</span><span class="p">(</span>
+                    <span class="n">id_type</span> <span class="o">=</span> <span class="s1">&#39;uniprot&#39;</span><span class="p">,</span>
+                    <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">,</span>
+                <span class="p">)</span>
+            <span class="p">)</span>
+
+        <span class="c1"># by default the uniprot-genesymbol tables contain only SwissProt</span>
+        <span class="k">if</span> <span class="n">id_type</span> <span class="o">==</span> <span class="s1">&#39;uniprot&#39;</span> <span class="ow">and</span> <span class="n">target_id_type</span> <span class="o">==</span> <span class="s1">&#39;genesymbol&#39;</span><span class="p">:</span>
+
+            <span class="n">mapped_names</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_map_name</span><span class="p">(</span>
+                <span class="n">name</span> <span class="o">=</span> <span class="n">name</span><span class="p">,</span>
+                <span class="n">id_type</span> <span class="o">=</span> <span class="s1">&#39;trembl&#39;</span><span class="p">,</span>
+                <span class="n">target_id_type</span> <span class="o">=</span> <span class="s1">&#39;genesymbol&#39;</span><span class="p">,</span>
+                <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">,</span>
+            <span class="p">)</span>
+
+            <span class="k">if</span> <span class="ow">not</span> <span class="n">mapped_names</span><span class="p">:</span>
+
+                <span class="n">uniprots</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_map_name</span><span class="p">(</span>
+                    <span class="n">name</span> <span class="o">=</span> <span class="n">name</span><span class="p">,</span>
+                    <span class="n">id_type</span> <span class="o">=</span> <span class="s1">&#39;uniprot-sec&#39;</span><span class="p">,</span>
+                    <span class="n">target_id_type</span> <span class="o">=</span> <span class="s1">&#39;uniprot-pri&#39;</span><span class="p">,</span>
+                    <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">,</span>
+                <span class="p">)</span>
+
+                <span class="k">if</span> <span class="n">uniprots</span><span class="p">:</span>
+
+                    <span class="n">mapped_names</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">map_names</span><span class="p">(</span>
+                        <span class="n">names</span> <span class="o">=</span> <span class="n">uniprots</span><span class="p">,</span>
+                        <span class="n">id_type</span> <span class="o">=</span> <span class="s1">&#39;uniprot&#39;</span><span class="p">,</span>
+                        <span class="n">target_id_type</span> <span class="o">=</span> <span class="s1">&#39;genesymbol&#39;</span><span class="p">,</span>
+                        <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">,</span>
+                    <span class="p">)</span>
+
+        <span class="c1"># further attempts to set it right if</span>
+        <span class="c1"># first attempt was not successful</span>
+
+        <span class="c1"># for miRNAs if the translation from mature miRNA name failed</span>
+        <span class="c1"># we still try if maybe it is a hairpin name</span>
+        <span class="c1"># or the other way around</span>
+        <span class="k">if</span> <span class="ow">not</span> <span class="n">mapped_names</span> <span class="ow">and</span> <span class="n">id_type</span> <span class="ow">in</span> <span class="p">{</span><span class="s1">&#39;mir-mat-name&#39;</span><span class="p">,</span> <span class="s1">&#39;mir-name&#39;</span><span class="p">}:</span>
+
+            <span class="k">for</span> <span class="n">id_type0</span><span class="p">,</span> <span class="n">id_type1</span><span class="p">,</span> <span class="n">target_id_type0</span><span class="p">,</span> <span class="n">target_id_type1</span> <span class="ow">in</span> <span class="p">(</span>
+                <span class="p">(</span><span class="s1">&#39;mir-name&#39;</span><span class="p">,</span> <span class="s1">&#39;mir-mat-name&#39;</span><span class="p">,</span> <span class="s1">&#39;mir-pre&#39;</span><span class="p">,</span> <span class="s1">&#39;mirbase&#39;</span><span class="p">),</span>
+                <span class="p">(</span><span class="s1">&#39;mir-mat-name&#39;</span><span class="p">,</span> <span class="s1">&#39;mir-name&#39;</span><span class="p">,</span> <span class="s1">&#39;mirbase&#39;</span><span class="p">,</span> <span class="s1">&#39;mir-pre&#39;</span><span class="p">),</span>
+            <span class="p">):</span>
+
+                <span class="k">if</span> <span class="n">id_type</span> <span class="o">==</span> <span class="n">id_type0</span><span class="p">:</span>
+
+                    <span class="n">mapped_names</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_map_name</span><span class="p">(</span>
+                        <span class="n">name</span> <span class="o">=</span> <span class="n">name</span><span class="p">,</span>
+                        <span class="n">id_type</span> <span class="o">=</span> <span class="n">id_type1</span><span class="p">,</span>
+                        <span class="n">target_id_type</span> <span class="o">=</span> <span class="n">target_id_type1</span><span class="p">,</span>
+                        <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">,</span>
+                    <span class="p">)</span>
+
+                    <span class="k">if</span> <span class="n">mapped_names</span> <span class="ow">and</span> <span class="n">target_id_type</span> <span class="o">==</span> <span class="n">target_id_type0</span><span class="p">:</span>
+
+                        <span class="n">mapped_names</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">map_names</span><span class="p">(</span>
+                            <span class="n">names</span> <span class="o">=</span> <span class="n">mapped_names</span><span class="p">,</span>
+                            <span class="n">id_type</span> <span class="o">=</span> <span class="n">target_id_type1</span><span class="p">,</span>
+                            <span class="n">target_id_type</span> <span class="o">=</span> <span class="n">target_id_type0</span><span class="p">,</span>
+                            <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">,</span>
+                        <span class="p">)</span>
+
+                    <span class="k">if</span> <span class="n">mapped_names</span><span class="p">:</span>
+
+                        <span class="k">break</span>
+
+        <span class="c1"># for genesymbol, we automatically try 2 steps mapping via uniprot</span>
+        <span class="k">if</span> <span class="p">(</span>
+            <span class="ow">not</span> <span class="n">mapped_names</span> <span class="ow">and</span> <span class="p">(</span>
+                <span class="n">id_type</span> <span class="o">==</span> <span class="s1">&#39;genesymbol&#39;</span> <span class="ow">or</span>
+                <span class="n">target_id_type</span> <span class="o">==</span> <span class="s1">&#39;genesymbol&#39;</span>
+            <span class="p">)</span> <span class="ow">and</span>
+            <span class="n">id_type</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">UNIPROT_ID_TYPES</span> <span class="ow">and</span>
+            <span class="n">target_id_type</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">UNIPROT_ID_TYPES</span>
+        <span class="p">):</span>
+
+            <span class="n">mapped_names</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">chain_map</span><span class="p">(</span>
+                <span class="n">name</span> <span class="o">=</span> <span class="n">name</span><span class="p">,</span>
+                <span class="n">id_type</span> <span class="o">=</span> <span class="n">id_type</span><span class="p">,</span>
+                <span class="n">by_id_type</span> <span class="o">=</span> <span class="s1">&#39;uniprot&#39;</span><span class="p">,</span>
+                <span class="n">target_id_type</span> <span class="o">=</span> <span class="n">target_id_type</span><span class="p">,</span>
+                <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">,</span>
+            <span class="p">)</span>
+
+        <span class="k">if</span> <span class="ow">not</span> <span class="n">mapped_names</span><span class="p">:</span>
+
+            <span class="c1"># maybe it should be all uppercase (e.g. human gene symbols)?</span>
+            <span class="n">mapped_names</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_map_name</span><span class="p">(</span>
+                <span class="n">name</span> <span class="o">=</span> <span class="n">name</span><span class="o">.</span><span class="n">upper</span><span class="p">(),</span>
+                <span class="n">id_type</span> <span class="o">=</span> <span class="n">id_type</span><span class="p">,</span>
+                <span class="n">target_id_type</span> <span class="o">=</span> <span class="n">target_id_type</span><span class="p">,</span>
+                <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">,</span>
+            <span class="p">)</span>
+
+        <span class="k">if</span> <span class="p">(</span>
+            <span class="ow">not</span> <span class="n">mapped_names</span> <span class="ow">and</span>
+            <span class="n">id_type</span> <span class="ow">not</span> <span class="ow">in</span> <span class="p">{</span><span class="s1">&#39;uniprot&#39;</span><span class="p">,</span> <span class="s1">&#39;trembl&#39;</span><span class="p">,</span> <span class="s1">&#39;uniprot-sec&#39;</span><span class="p">}</span>
+        <span class="p">):</span>
+
+            <span class="c1"># maybe should be capitalized (e.g. rodent gene symbols)?</span>
+            <span class="n">mapped_names</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_map_name</span><span class="p">(</span>
+                <span class="n">name</span> <span class="o">=</span> <span class="n">name</span><span class="o">.</span><span class="n">capitalize</span><span class="p">(),</span>
+                <span class="n">id_type</span> <span class="o">=</span> <span class="n">id_type</span><span class="p">,</span>
+                <span class="n">target_id_type</span> <span class="o">=</span> <span class="n">target_id_type</span><span class="p">,</span>
+                <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">,</span>
+            <span class="p">)</span>
+
+        <span class="k">if</span> <span class="p">(</span>
+            <span class="ow">not</span> <span class="n">mapped_names</span> <span class="ow">and</span>
+            <span class="n">id_type</span> <span class="ow">not</span> <span class="ow">in</span> <span class="p">{</span><span class="s1">&#39;uniprot&#39;</span><span class="p">,</span> <span class="s1">&#39;trembl&#39;</span><span class="p">,</span> <span class="s1">&#39;uniprot-sec&#39;</span><span class="p">}</span>
+        <span class="p">):</span>
+
+            <span class="c1"># maybe it should be all lowercase?</span>
+            <span class="n">mapped_names</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_map_name</span><span class="p">(</span>
+                <span class="n">name</span> <span class="o">=</span> <span class="n">name</span><span class="o">.</span><span class="n">lower</span><span class="p">(),</span>
+                <span class="n">id_type</span> <span class="o">=</span> <span class="n">id_type</span><span class="p">,</span>
+                <span class="n">target_id_type</span> <span class="o">=</span> <span class="n">target_id_type</span><span class="p">,</span>
+                <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">,</span>
+            <span class="p">)</span>
+
+        <span class="k">if</span> <span class="p">(</span>
+            <span class="ow">not</span> <span class="n">mapped_names</span> <span class="ow">and</span>
+            <span class="n">id_type</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s1">&#39;ens&#39;</span><span class="p">)</span> <span class="ow">and</span>
+            <span class="s1">&#39;.&#39;</span> <span class="ow">in</span> <span class="n">name</span>
+        <span class="p">):</span>
+
+            <span class="c1"># trying to split the part after the dot:</span>
+            <span class="n">mapped_names</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_map_name</span><span class="p">(</span>
+                <span class="n">name</span> <span class="o">=</span> <span class="n">name</span><span class="o">.</span><span class="n">upper</span><span class="p">()</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;.&#39;</span><span class="p">)[</span><span class="mi">0</span><span class="p">],</span>
+                <span class="n">id_type</span> <span class="o">=</span> <span class="n">id_type</span><span class="p">,</span>
+                <span class="n">target_id_type</span> <span class="o">=</span> <span class="n">target_id_type</span><span class="p">,</span>
+                <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">,</span>
+            <span class="p">)</span>
+
+        <span class="k">if</span> <span class="p">(</span>
+            <span class="ow">not</span> <span class="n">mapped_names</span> <span class="ow">and</span>
+            <span class="s1">&#39;:&#39;</span> <span class="ow">in</span> <span class="n">name</span>
+        <span class="p">):</span>
+
+            <span class="c1"># trying to remove the prefix which sometimes</span>
+            <span class="c1"># shows the ID type, e.g. CHEBI:4956 should become 4956</span>
+            <span class="n">mapped_names</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_map_name</span><span class="p">(</span>
+                <span class="n">name</span> <span class="o">=</span> <span class="n">common</span><span class="o">.</span><span class="n">remove_prefix</span><span class="p">(</span><span class="n">name</span><span class="p">,</span> <span class="s1">&#39;:&#39;</span><span class="p">),</span>
+                <span class="n">id_type</span> <span class="o">=</span> <span class="n">id_type</span><span class="p">,</span>
+                <span class="n">target_id_type</span> <span class="o">=</span> <span class="n">target_id_type</span><span class="p">,</span>
+                <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">,</span>
+            <span class="p">)</span>
+
+        <span class="c1"># if a gene symbol could not be translated by the default</span>
+        <span class="c1"># conversion table, containing only the primary gene symbols</span>
+        <span class="c1"># in next step we try the secondary (synonym) gene symbols</span>
+        <span class="k">if</span> <span class="p">(</span>
+            <span class="ow">not</span> <span class="n">mapped_names</span> <span class="ow">and</span>
+            <span class="n">id_type</span> <span class="o">==</span> <span class="s1">&#39;genesymbol&#39;</span>
+        <span class="p">):</span>
+
+            <span class="n">mapped_names</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_map_name</span><span class="p">(</span>
+                <span class="n">name</span> <span class="o">=</span> <span class="n">name</span><span class="p">,</span>
+                <span class="n">id_type</span> <span class="o">=</span> <span class="s1">&#39;genesymbol-syn&#39;</span><span class="p">,</span>
+                <span class="n">target_id_type</span> <span class="o">=</span> <span class="n">target_id_type</span><span class="p">,</span>
+                <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">,</span>
+            <span class="p">)</span>
+
+            <span class="c1"># for gene symbols we might try one more thing,</span>
+            <span class="c1"># sometimes the source gene symbol missing some isoform</span>
+            <span class="c1"># information or number because it refers to the first</span>
+            <span class="c1"># or all isoforms or subtypes; or the opposite: the</span>
+            <span class="c1"># original resource contains a gene symbol with a number</span>
+            <span class="c1"># appended which is not part of the official primary</span>
+            <span class="c1"># gene symbol</span>
+            <span class="c1">#</span>
+            <span class="c1"># here we try to translate by adding a number `1` or</span>
+            <span class="c1"># by matching only the first few letters;</span>
+            <span class="c1"># obviously we can not exclude mistranslation here</span>
+            <span class="c1">#</span>
+            <span class="c1"># by setting `strict = True` this step is disabled</span>
+            <span class="k">if</span> <span class="ow">not</span> <span class="n">strict</span> <span class="ow">and</span> <span class="ow">not</span> <span class="n">mapped_names</span><span class="p">:</span>
+
+                <span class="n">mapped_names</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_map_name</span><span class="p">(</span>
+                    <span class="n">name</span> <span class="o">=</span> <span class="s1">&#39;</span><span class="si">%s</span><span class="s1">1&#39;</span> <span class="o">%</span> <span class="n">name</span><span class="p">,</span>
+                    <span class="n">id_type</span> <span class="o">=</span> <span class="s1">&#39;genesymbol&#39;</span><span class="p">,</span>
+                    <span class="n">target_id_type</span> <span class="o">=</span> <span class="n">target_id_type</span><span class="p">,</span>
+                    <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">,</span>
+                <span class="p">)</span>
+
+                <span class="k">if</span> <span class="ow">not</span> <span class="n">mapped_names</span> <span class="ow">and</span> <span class="n">target_id_type</span> <span class="o">==</span> <span class="s1">&#39;uniprot&#39;</span><span class="p">:</span>
+
+                    <span class="n">mapped_names</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_map_name</span><span class="p">(</span>
+                        <span class="n">name</span> <span class="o">=</span> <span class="n">name</span><span class="p">,</span>
+                        <span class="n">id_type</span> <span class="o">=</span> <span class="s1">&#39;genesymbol5&#39;</span><span class="p">,</span>
+                        <span class="n">target_id_type</span> <span class="o">=</span> <span class="n">target_id_type</span><span class="p">,</span>
+                        <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">,</span>
+                    <span class="p">)</span>
+
+
+        <span class="c1"># for UniProt IDs we do a few more steps to</span>
+        <span class="c1"># try to find out the primary SwissProt ID</span>
+        <span class="k">if</span> <span class="n">uniprot_cleanup</span> <span class="ow">and</span> <span class="n">target_id_type</span> <span class="o">==</span> <span class="s1">&#39;uniprot&#39;</span><span class="p">:</span>
+
+            <span class="n">mapped_names</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">uniprot_cleanup</span><span class="p">(</span>
+                <span class="n">uniprots</span> <span class="o">=</span> <span class="n">mapped_names</span><span class="p">,</span>
+                <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">,</span>
+            <span class="p">)</span>
+
+        <span class="k">return</span> <span class="n">mapped_names</span></div>
+
+
+
+<div class="viewcode-block" id="Mapper.uniprot_cleanup">
+<a class="viewcode-back" href="../../../api/pypath.utils.mapping.Mapper.html#pypath.utils.mapping.Mapper.uniprot_cleanup">[docs]</a>
+    <span class="k">def</span> <span class="nf">uniprot_cleanup</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">uniprots</span><span class="p">,</span> <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="kc">None</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        We use this function as a standard callback when the target ID</span>
+<span class="sd">        type is UniProt. It checks if the format of the IDs are correct,</span>
+<span class="sd">        if they are part of the organism proteome, attempts to translate</span>
+<span class="sd">        secondary and deleted IDs to their primary, recent counterparts.</span>
+
+<span class="sd">        Args</span>
+<span class="sd">            uniprots (str,set): One or more UniProt IDs.</span>
+<span class="sd">            ncbi_tax_id (int): The NCBI Taxonomy identifier of the organism.</span>
+
+<span class="sd">        Returns</span>
+<span class="sd">            Set of checked and potentially translated UniProt iDs. Elements</span>
+<span class="sd">            which do not fit the criteria will be discarded.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span> <span class="ow">or</span> <span class="bp">self</span><span class="o">.</span><span class="n">ncbi_tax_id</span>
+
+        <span class="n">uniprots</span> <span class="o">=</span> <span class="n">common</span><span class="o">.</span><span class="n">to_set</span><span class="p">(</span><span class="n">uniprots</span><span class="p">)</span>
+
+        <span class="c1"># step 1: translate secondary IDs to primary</span>
+        <span class="n">uniprots</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">primary_uniprot</span><span class="p">(</span><span class="n">uniprots</span><span class="p">)</span>
+
+        <span class="c1"># step 2: translate TrEMBL to SwissProt by gene symbols</span>
+        <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">_trembl_swissprot_by_genesymbol</span><span class="p">:</span>
+
+            <span class="n">uniprots</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">trembl_swissprot</span><span class="p">(</span>
+                <span class="n">uniprots</span><span class="p">,</span>
+                <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">,</span>
+            <span class="p">)</span>
+
+        <span class="c1"># step 3: translate deleted IDs by gene symbols</span>
+        <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">_translate_deleted_uniprot</span><span class="p">:</span>
+
+            <span class="n">uniprots</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">translate_deleted_uniprots_by_genesymbol</span><span class="p">(</span>
+                <span class="n">uniprots</span>
+            <span class="p">)</span>
+
+        <span class="c1"># step 4: check if the IDs exist in the proteome of the organism</span>
+        <span class="k">if</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">_keep_invalid_uniprot</span><span class="p">:</span>
+
+            <span class="n">uniprots</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">only_valid_uniprots</span><span class="p">(</span>
+                <span class="n">uniprots</span><span class="p">,</span>
+                <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">,</span>
+            <span class="p">)</span>
+
+        <span class="c1"># step 5: ensure the format validity</span>
+        <span class="n">uniprots</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">only_uniprot_ac</span><span class="p">(</span><span class="n">uniprots</span><span class="p">)</span>
+
+        <span class="k">return</span> <span class="n">uniprots</span></div>
+
+
+
+<div class="viewcode-block" id="Mapper.map_names">
+<a class="viewcode-back" href="../../../api/pypath.utils.mapping.Mapper.html#pypath.utils.mapping.Mapper.map_names">[docs]</a>
+    <span class="k">def</span> <span class="nf">map_names</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">names</span><span class="p">,</span>
+            <span class="n">id_type</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">target_id_type</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">strict</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+            <span class="n">expand_complexes</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
+            <span class="n">uniprot_cleanup</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
+        <span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Same as ``map_name`` but translates multiple IDs at once. These two</span>
+<span class="sd">        functions could be seamlessly implemented as one, still I created</span>
+<span class="sd">        separate functions to always make it explicit if a set of translated</span>
+<span class="sd">        IDs come from multiple original IDs.</span>
+
+<span class="sd">        Args</span>
+<span class="sd">            name (str): The original name to be converted.</span>
+<span class="sd">            id_type (str): The type of the name. Available by default:</span>
+<span class="sd">                - genesymbol (gene name)</span>
+<span class="sd">                - entrez (Entrez Gene ID \[#\])</span>
+<span class="sd">                - refseqp (NCBI RefSeq Protein ID \[NP\_\*|XP\_\*\])</span>
+<span class="sd">                - ensp (Ensembl protein ID \[ENSP\*\])</span>
+<span class="sd">                - enst (Ensembl transcript ID \[ENST\*\])</span>
+<span class="sd">                - ensg (Ensembl genomic DNA ID \[ENSG\*\])</span>
+<span class="sd">                - hgnc (HGNC ID \[HGNC:#\])</span>
+<span class="sd">                - gi (GI number \[#\])</span>
+<span class="sd">                - embl (DDBJ/EMBL/GeneBank CDS accession)</span>
+<span class="sd">                - embl_id (DDBJ/EMBL/GeneBank accession)</span>
+<span class="sd">                And many more, see the code of</span>
+<span class="sd">                ``pypath.internals.input_formats``</span>
+<span class="sd">            target_id_type (str): The name type to translate to, more or</span>
+<span class="sd">                less the same values are available as for ``id_type``.</span>
+<span class="sd">            ncbi_tax_id (int): NCBI Taxonomy ID of the organism.</span>
+<span class="sd">            strict (bool): In case a Gene Symbol can not be translated,</span>
+<span class="sd">                try to add number &quot;1&quot; to the end, or try to match only</span>
+<span class="sd">                its first five characters. This option is rarely used,</span>
+<span class="sd">                but it makes possible to translate some non-standard</span>
+<span class="sd">                gene names typically found in old, unmaintained resources.</span>
+<span class="sd">            expand_complexes (bool): When encountering complexes,</span>
+<span class="sd">                translated the IDs of its components and return a set</span>
+<span class="sd">                of IDs. The alternative behaviour is to return the</span>
+<span class="sd">                `Complex` objects.</span>
+<span class="sd">            uniprot_cleanup (bool): When the `target_id_type` is UniProt</span>
+<span class="sd">                ID, call the `uniprot_cleanup` function at the end.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">return</span> <span class="nb">set</span><span class="o">.</span><span class="n">union</span><span class="p">(</span>
+            <span class="o">*</span><span class="p">(</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">map_name</span><span class="p">(</span>
+                    <span class="n">name</span> <span class="o">=</span> <span class="n">name</span><span class="p">,</span>
+                    <span class="n">id_type</span> <span class="o">=</span> <span class="n">id_type</span><span class="p">,</span>
+                    <span class="n">target_id_type</span> <span class="o">=</span> <span class="n">target_id_type</span><span class="p">,</span>
+                    <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">,</span>
+                    <span class="n">strict</span> <span class="o">=</span> <span class="n">strict</span><span class="p">,</span>
+                <span class="p">)</span>
+                <span class="k">for</span> <span class="n">name</span> <span class="ow">in</span> <span class="n">names</span>
+            <span class="p">)</span>
+        <span class="p">)</span> <span class="k">if</span> <span class="n">names</span> <span class="k">else</span> <span class="nb">set</span><span class="p">()</span></div>
+
+
+
+<div class="viewcode-block" id="Mapper.chain_map">
+<a class="viewcode-back" href="../../../api/pypath.utils.mapping.Mapper.html#pypath.utils.mapping.Mapper.chain_map">[docs]</a>
+    <span class="k">def</span> <span class="nf">chain_map</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">name</span><span class="p">,</span>
+            <span class="n">id_type</span><span class="p">,</span>
+            <span class="n">by_id_type</span><span class="p">,</span>
+            <span class="n">target_id_type</span><span class="p">,</span>
+            <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="o">**</span><span class="n">kwargs</span>
+        <span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Translate IDs which can not be directly translated in two steps:</span>
+<span class="sd">        from `id_type` to `via_id_type` and from there to `target_id_type`.</span>
+
+<span class="sd">        Args</span>
+<span class="sd">            name (str): The original name to be converted.</span>
+<span class="sd">            id_type (str): The type of the name.</span>
+<span class="sd">            by_id_type (str): The intermediate name type.</span>
+<span class="sd">            target_id_type (str): The name type to translate to, more or</span>
+<span class="sd">                less the same values are available as for ``id_type``.</span>
+<span class="sd">            ncbi_tax_id (int): The NCBI Taxonomy identifier of the organism.</span>
+<span class="sd">            kwargs: Passed to `map_name`.</span>
+
+<span class="sd">        Returns</span>
+<span class="sd">            Set of IDs of type `target_id_type`.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span> <span class="ow">or</span> <span class="bp">self</span><span class="o">.</span><span class="n">ncbi_tax_id</span>
+
+        <span class="n">mapped_names</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">map_names</span><span class="p">(</span>
+            <span class="n">names</span> <span class="o">=</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">map_name</span><span class="p">(</span>
+                    <span class="n">name</span> <span class="o">=</span> <span class="n">name</span><span class="p">,</span>
+                    <span class="n">id_type</span> <span class="o">=</span> <span class="n">id_type</span><span class="p">,</span>
+                    <span class="n">target_id_type</span> <span class="o">=</span> <span class="n">by_id_type</span><span class="p">,</span>
+                    <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">,</span>
+                    <span class="o">**</span><span class="n">kwargs</span>
+                <span class="p">),</span>
+            <span class="n">id_type</span> <span class="o">=</span> <span class="n">by_id_type</span><span class="p">,</span>
+            <span class="n">target_id_type</span> <span class="o">=</span> <span class="n">target_id_type</span><span class="p">,</span>
+            <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">,</span>
+            <span class="o">**</span><span class="n">kwargs</span>
+        <span class="p">)</span>
+
+        <span class="k">return</span> <span class="n">mapped_names</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">_map_refseq</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">refseq</span><span class="p">,</span>
+            <span class="n">id_type</span><span class="p">,</span>
+            <span class="n">target_id_type</span><span class="p">,</span>
+            <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">strict</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+        <span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        ID translation adapted to the specialities of RefSeq IDs.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">mapped_names</span> <span class="o">=</span> <span class="nb">set</span><span class="p">()</span>
+        <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span> <span class="ow">or</span> <span class="bp">self</span><span class="o">.</span><span class="n">ncbi_tax_id</span>
+
+        <span class="c1"># try first as it is</span>
+        <span class="n">mapped_names</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_map_name</span><span class="p">(</span>
+            <span class="n">name</span> <span class="o">=</span> <span class="n">refseq</span><span class="p">,</span>
+            <span class="n">id_type</span> <span class="o">=</span> <span class="n">id_type</span><span class="p">,</span>
+            <span class="n">target_id_type</span> <span class="o">=</span> <span class="n">target_id_type</span><span class="p">,</span>
+            <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">,</span>
+        <span class="p">)</span>
+
+        <span class="c1"># then with the number at the end removed</span>
+        <span class="c1"># this is disabled if `strict = True`</span>
+        <span class="k">if</span> <span class="ow">not</span> <span class="n">mapped_names</span> <span class="ow">and</span> <span class="ow">not</span> <span class="n">strict</span><span class="p">:</span>
+
+            <span class="n">mapped_names</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_map_name</span><span class="p">(</span>
+                <span class="n">name</span> <span class="o">=</span> <span class="n">refseq</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;.&#39;</span><span class="p">)[</span><span class="mi">0</span><span class="p">],</span>
+                <span class="n">id_type</span> <span class="o">=</span> <span class="n">id_type</span><span class="p">,</span>
+                <span class="n">target_id_type</span> <span class="o">=</span> <span class="n">target_id_type</span><span class="p">,</span>
+                <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">,</span>
+            <span class="p">)</span>
+
+        <span class="k">if</span> <span class="ow">not</span> <span class="n">mapped_names</span> <span class="ow">and</span> <span class="ow">not</span> <span class="n">strict</span><span class="p">:</span>
+
+            <span class="n">rstem</span> <span class="o">=</span> <span class="n">refseq</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;.&#39;</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span>
+
+            <span class="c1"># try some other numbers</span>
+            <span class="c1"># this risky and is disabled if `strict = True`</span>
+            <span class="k">for</span> <span class="n">n</span> <span class="ow">in</span> <span class="n">xrange</span><span class="p">(</span><span class="mi">49</span><span class="p">):</span>
+
+                <span class="n">mapped_names</span><span class="o">.</span><span class="n">update</span><span class="p">(</span>
+                    <span class="bp">self</span><span class="o">.</span><span class="n">_map_name</span><span class="p">(</span>
+                        <span class="n">name</span> <span class="o">=</span> <span class="s1">&#39;</span><span class="si">%s</span><span class="s1">.</span><span class="si">%u</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="p">(</span><span class="n">rstem</span><span class="p">,</span> <span class="n">n</span><span class="p">),</span>
+                        <span class="n">id_type</span> <span class="o">=</span> <span class="n">id_type</span><span class="p">,</span>
+                        <span class="n">target_id_type</span> <span class="o">=</span> <span class="n">target_id_type</span><span class="p">,</span>
+                        <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">,</span>
+                    <span class="p">)</span>
+                <span class="p">)</span>
+
+        <span class="k">return</span> <span class="n">mapped_names</span>
+
+
+    <span class="k">def</span> <span class="nf">_map_ensp</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">ensp</span><span class="p">,</span>
+            <span class="n">target_id_type</span><span class="p">,</span>
+            <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+        <span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Special ID translation from ENSP (Ensembl peptide IDs).</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">mapped_names</span> <span class="o">=</span> <span class="nb">set</span><span class="p">()</span>
+        <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span> <span class="ow">or</span> <span class="bp">self</span><span class="o">.</span><span class="n">ncbi_tax_id</span>
+
+        <span class="c1"># try first UniProt ID Mapping</span>
+        <span class="c1"># then Ensembl BioMart</span>
+        <span class="k">for</span> <span class="n">id_type</span> <span class="ow">in</span> <span class="p">(</span><span class="s1">&#39;ensp&#39;</span><span class="p">,</span> <span class="s1">&#39;ensp_biomart&#39;</span><span class="p">):</span>
+
+            <span class="k">if</span> <span class="ow">not</span> <span class="n">mapped_names</span><span class="p">:</span>
+
+                <span class="n">mapped_names</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_map_name</span><span class="p">(</span>
+                    <span class="n">name</span> <span class="o">=</span> <span class="n">ensp</span><span class="p">,</span>
+                    <span class="n">id_type</span> <span class="o">=</span> <span class="n">id_type</span><span class="p">,</span>
+                    <span class="n">target_id_type</span> <span class="o">=</span> <span class="n">target_id_type</span><span class="p">,</span>
+                    <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">,</span>
+                <span class="p">)</span>
+
+        <span class="k">if</span> <span class="ow">not</span> <span class="n">mapped_names</span><span class="p">:</span>
+
+            <span class="n">tax_ensp</span> <span class="o">=</span> <span class="s1">&#39;</span><span class="si">%u</span><span class="s1">.</span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="p">(</span><span class="n">ncbi_tax_id</span><span class="p">,</span> <span class="n">ensp</span><span class="p">)</span>
+
+            <span class="c1"># this uses UniProt ID Mapping with STRING ID type</span>
+            <span class="n">mapped_names</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_map_name</span><span class="p">(</span>
+                <span class="n">name</span> <span class="o">=</span> <span class="n">tax_ensp</span><span class="p">,</span>
+                <span class="n">id_type</span> <span class="o">=</span> <span class="s1">&#39;ensp_string&#39;</span><span class="p">,</span>
+                <span class="n">target_id_type</span> <span class="o">=</span> <span class="n">target_id_type</span><span class="p">,</span>
+                <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">,</span>
+            <span class="p">)</span>
+
+        <span class="k">return</span> <span class="n">mapped_names</span>
+
+
+    <span class="k">def</span> <span class="nf">_map_to_ensp</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">name</span><span class="p">,</span>
+            <span class="n">id_type</span><span class="p">,</span>
+            <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+        <span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Special ID translation to ENSP (Ensembl peptide IDs).</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">mapped_names</span> <span class="o">=</span> <span class="nb">set</span><span class="p">()</span>
+        <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span> <span class="ow">or</span> <span class="bp">self</span><span class="o">.</span><span class="n">ncbi_tax_id</span>
+
+        <span class="c1"># try first UniProt ID Mapping</span>
+        <span class="c1"># then Ensembl BioMart</span>
+        <span class="k">for</span> <span class="n">target_id_type</span> <span class="ow">in</span> <span class="p">(</span><span class="s1">&#39;ensp&#39;</span><span class="p">,</span> <span class="s1">&#39;ensp_biomart&#39;</span><span class="p">):</span>
+
+            <span class="k">if</span> <span class="ow">not</span> <span class="n">mapped_names</span><span class="p">:</span>
+
+                <span class="n">mapped_names</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_map_name</span><span class="p">(</span>
+                    <span class="n">name</span> <span class="o">=</span> <span class="n">name</span><span class="p">,</span>
+                    <span class="n">id_type</span> <span class="o">=</span> <span class="n">id_type</span><span class="p">,</span>
+                    <span class="n">target_id_type</span> <span class="o">=</span> <span class="n">target_id_type</span><span class="p">,</span>
+                    <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">,</span>
+                <span class="p">)</span>
+
+        <span class="k">if</span> <span class="ow">not</span> <span class="n">mapped_names</span><span class="p">:</span>
+
+            <span class="c1"># this uses UniProt ID Mapping with STRING type</span>
+            <span class="n">mapped_names</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_map_name</span><span class="p">(</span>
+                <span class="n">name</span> <span class="o">=</span> <span class="n">name</span><span class="p">,</span>
+                <span class="n">id_type</span> <span class="o">=</span> <span class="n">id_type</span><span class="p">,</span>
+                <span class="n">target_id_type</span> <span class="o">=</span> <span class="s1">&#39;ensp_string&#39;</span><span class="p">,</span>
+                <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">,</span>
+            <span class="p">)</span>
+
+            <span class="n">mapped_names</span> <span class="o">=</span> <span class="p">{</span><span class="n">n</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;.&#39;</span><span class="p">)[</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span> <span class="k">for</span> <span class="n">n</span> <span class="ow">in</span> <span class="n">mapped_names</span><span class="p">}</span>
+
+        <span class="k">return</span> <span class="n">mapped_names</span>
+
+
+    <span class="k">def</span> <span class="nf">_map_name</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">name</span><span class="p">,</span>
+            <span class="n">id_type</span><span class="p">,</span>
+            <span class="n">target_id_type</span><span class="p">,</span>
+            <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+        <span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Once we have defined the name type and the target name type,</span>
+<span class="sd">        this function looks it up in the most suitable dictionary.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span> <span class="ow">or</span> <span class="bp">self</span><span class="o">.</span><span class="n">ncbi_tax_id</span>
+
+        <span class="n">tbl</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">which_table</span><span class="p">(</span>
+            <span class="n">id_type</span><span class="p">,</span>
+            <span class="n">target_id_type</span><span class="p">,</span>
+            <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">,</span>
+        <span class="p">)</span>
+
+        <span class="k">return</span> <span class="n">tbl</span><span class="p">[</span><span class="n">name</span><span class="p">]</span> <span class="k">if</span> <span class="n">tbl</span> <span class="k">else</span> <span class="nb">set</span><span class="p">()</span>
+
+
+<div class="viewcode-block" id="Mapper.translation_dict">
+<a class="viewcode-back" href="../../../api/pypath.utils.mapping.Mapper.html#pypath.utils.mapping.Mapper.translation_dict">[docs]</a>
+    <span class="k">def</span> <span class="nf">translation_dict</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">id_type</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
+            <span class="n">target_id_type</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
+            <span class="n">ncbi_tax_id</span><span class="p">:</span> <span class="nb">int</span> <span class="o">|</span> <span class="kc">None</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+        <span class="p">)</span> <span class="o">-&gt;</span> <span class="n">MappingTable</span> <span class="o">|</span> <span class="kc">None</span><span class="p">:</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Translation table as a dict.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">which_table</span><span class="p">(</span>
+            <span class="n">id_type</span><span class="p">,</span>
+            <span class="n">target_id_type</span><span class="p">,</span>
+            <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span> <span class="ow">or</span> <span class="bp">self</span><span class="o">.</span><span class="n">ncbi_tax_id</span><span class="p">,</span>
+        <span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="Mapper.translation_df">
+<a class="viewcode-back" href="../../../api/pypath.utils.mapping.Mapper.html#pypath.utils.mapping.Mapper.translation_df">[docs]</a>
+    <span class="k">def</span> <span class="nf">translation_df</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">id_type</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
+            <span class="n">target_id_type</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
+            <span class="n">ncbi_tax_id</span><span class="p">:</span> <span class="nb">int</span> <span class="o">|</span> <span class="kc">None</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+        <span class="p">)</span> <span class="o">-&gt;</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span> <span class="o">|</span> <span class="kc">None</span><span class="p">:</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Translation table as a data frame.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">tbl</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">translation_dict</span><span class="p">(</span><span class="n">id_type</span><span class="p">,</span> <span class="n">target_id_type</span><span class="p">,</span> <span class="n">ncbi_tax_id</span><span class="p">)</span>
+
+        <span class="k">if</span> <span class="n">tbl</span><span class="p">:</span>
+
+            <span class="k">return</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">(</span>
+                <span class="p">(</span>
+                    <span class="p">(</span><span class="n">source_id</span><span class="p">,</span> <span class="n">target_id</span><span class="p">)</span>
+                    <span class="k">for</span> <span class="n">source_id</span><span class="p">,</span> <span class="n">target_ids</span> <span class="ow">in</span> <span class="n">tbl</span><span class="o">.</span><span class="n">data</span><span class="o">.</span><span class="n">items</span><span class="p">()</span> <span class="k">for</span>
+                    <span class="n">target_id</span> <span class="ow">in</span> <span class="n">target_ids</span>
+                <span class="p">),</span>
+                <span class="n">columns</span> <span class="o">=</span> <span class="p">[</span><span class="n">id_type</span><span class="p">,</span> <span class="n">target_id_type</span><span class="p">],</span>
+            <span class="p">)</span></div>
+
+
+
+    <span class="c1">#</span>
+    <span class="c1"># ID specific translation methods</span>
+    <span class="c1">#</span>
+
+
+<div class="viewcode-block" id="Mapper.label">
+<a class="viewcode-back" href="../../../api/pypath.utils.mapping.Mapper.html#pypath.utils.mapping.Mapper.label">[docs]</a>
+    <span class="k">def</span> <span class="nf">label</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">name</span><span class="p">,</span>
+            <span class="n">entity_type</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">id_type</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+        <span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        For any kind of entity, either protein, miRNA or protein complex,</span>
+<span class="sd">        returns the preferred human readable label. For proteins this means</span>
+<span class="sd">        Gene Symbols, for miRNAs miRNA names, for complexes a series of</span>
+<span class="sd">        Gene Symbols.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">name</span><span class="p">,</span> <span class="n">_const</span><span class="o">.</span><span class="n">LIST_LIKE</span><span class="p">):</span>
+
+            <span class="k">return</span> <span class="p">[</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">label</span><span class="p">(</span>
+                    <span class="n">_name</span><span class="p">,</span>
+                    <span class="n">entity_type</span> <span class="o">=</span> <span class="n">entity_type</span><span class="p">,</span>
+                    <span class="n">id_type</span> <span class="o">=</span> <span class="n">id_type</span><span class="p">,</span>
+                    <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">,</span>
+                <span class="p">)</span>
+                <span class="k">for</span> <span class="n">_name</span> <span class="ow">in</span> <span class="n">name</span>
+            <span class="p">]</span>
+
+        <span class="k">elif</span> <span class="nb">hasattr</span><span class="p">(</span><span class="n">name</span><span class="p">,</span> <span class="s1">&#39;genesymbol_str&#39;</span><span class="p">):</span>
+
+            <span class="k">return</span> <span class="n">name</span><span class="o">.</span><span class="n">genesymbol_str</span>
+
+        <span class="k">elif</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">name</span><span class="p">,</span> <span class="nb">str</span><span class="p">):</span>
+
+            <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span> <span class="ow">or</span> <span class="bp">self</span><span class="o">.</span><span class="n">ncbi_tax_id</span>
+
+            <span class="n">entity_type</span> <span class="o">=</span> <span class="p">(</span>
+                <span class="n">entity_type</span> <span class="ow">or</span>
+                <span class="p">(</span>
+                    <span class="s1">&#39;small_molecule&#39;</span>
+                        <span class="k">if</span> <span class="n">ncbi_tax_id</span> <span class="o">==</span> <span class="n">_const</span><span class="o">.</span><span class="n">NOT_ORGANISM_SPECIFIC</span> <span class="k">else</span>
+                    <span class="s1">&#39;protein&#39;</span>
+                <span class="p">)</span>
+            <span class="p">)</span>
+
+            <span class="k">if</span> <span class="n">name</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s1">&#39;MIMAT&#39;</span><span class="p">):</span>
+
+                <span class="k">return</span> <span class="n">map_name0</span><span class="p">(</span>
+                    <span class="n">name</span><span class="p">,</span>
+                    <span class="n">id_type</span> <span class="ow">or</span> <span class="s1">&#39;mirbase&#39;</span><span class="p">,</span>
+                    <span class="s1">&#39;mir-mat-name&#39;</span><span class="p">,</span>
+                    <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">,</span>
+                <span class="p">)</span> <span class="ow">or</span> <span class="n">name</span>
+
+            <span class="k">elif</span> <span class="n">name</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s1">&#39;MI&#39;</span><span class="p">):</span>
+
+                <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">map_name0</span><span class="p">(</span>
+                    <span class="n">name</span><span class="p">,</span>
+                    <span class="n">id_type</span> <span class="ow">or</span> <span class="s1">&#39;mir-pre&#39;</span><span class="p">,</span>
+                    <span class="s1">&#39;mir-name&#39;</span><span class="p">,</span>
+                    <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">,</span>
+                <span class="p">)</span> <span class="ow">or</span> <span class="n">name</span>
+
+            <span class="k">elif</span> <span class="n">entity_type</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">default_label_types</span><span class="p">:</span>
+
+                <span class="n">id_type</span> <span class="o">=</span> <span class="n">id_type</span> <span class="ow">or</span> <span class="bp">self</span><span class="o">.</span><span class="n">default_name_types</span><span class="p">[</span><span class="n">entity_type</span><span class="p">]</span>
+                <span class="n">target_id_type</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">default_label_types</span><span class="p">[</span><span class="n">entity_type</span><span class="p">]</span>
+
+                <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">map_name0</span><span class="p">(</span>
+                    <span class="n">name</span><span class="p">,</span>
+                    <span class="n">id_type</span> <span class="o">=</span> <span class="n">id_type</span><span class="p">,</span>
+                    <span class="n">target_id_type</span> <span class="o">=</span> <span class="n">target_id_type</span><span class="p">,</span>
+                    <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">,</span>
+                <span class="p">)</span> <span class="ow">or</span> <span class="n">name</span>
+
+            <span class="k">else</span><span class="p">:</span>
+
+                <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">map_name0</span><span class="p">(</span>
+                    <span class="n">name</span><span class="p">,</span>
+                    <span class="n">id_type</span> <span class="ow">or</span> <span class="s1">&#39;uniprot&#39;</span><span class="p">,</span>
+                    <span class="s1">&#39;genesymbol&#39;</span><span class="p">,</span>
+                    <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">,</span>
+                <span class="p">)</span> <span class="ow">or</span> <span class="n">name</span>
+
+        <span class="k">else</span><span class="p">:</span>
+
+            <span class="k">return</span> <span class="nb">str</span><span class="p">(</span><span class="n">name</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="Mapper.identifier">
+<a class="viewcode-back" href="../../../api/pypath.utils.mapping.Mapper.html#pypath.utils.mapping.Mapper.identifier">[docs]</a>
+    <span class="k">def</span> <span class="nf">identifier</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">label</span><span class="p">:</span> <span class="n">Union</span><span class="p">[</span><span class="nb">str</span><span class="p">,</span> <span class="n">Iterable</span><span class="p">[</span><span class="nb">str</span><span class="p">]],</span>
+            <span class="n">ncbi_tax_id</span><span class="p">:</span> <span class="n">Optional</span><span class="p">[</span><span class="nb">int</span><span class="p">]</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">id_type</span><span class="p">:</span> <span class="n">Optional</span><span class="p">[</span><span class="nb">str</span><span class="p">]</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">entity_type</span><span class="p">:</span>
+                <span class="n">Optional</span><span class="p">[</span>
+                    <span class="n">Literal</span><span class="p">[</span>
+                        <span class="s1">&#39;drug&#39;</span><span class="p">,</span>
+                        <span class="s1">&#39;lncrna&#39;</span><span class="p">,</span>
+                        <span class="s1">&#39;mirna&#39;</span><span class="p">,</span>
+                        <span class="s1">&#39;protein&#39;</span><span class="p">,</span>
+                        <span class="s1">&#39;small_molecule&#39;</span><span class="p">,</span>
+                    <span class="p">]</span>
+                <span class="p">]</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+        <span class="p">)</span> <span class="o">-&gt;</span> <span class="n">Union</span><span class="p">[</span><span class="n">Set</span><span class="p">[</span><span class="nb">str</span><span class="p">],</span> <span class="n">List</span><span class="p">[</span><span class="n">Set</span><span class="p">[</span><span class="nb">str</span><span class="p">]]]:</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        For a label returns the corresponding primary identifier. The type</span>
+<span class="sd">        of default identifiers is determined by the settings module. Note,</span>
+<span class="sd">        this kind of translation is not always unambigous, one gene symbol</span>
+<span class="sd">        might correspond to multiple UniProt IDs.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">if</span> <span class="ow">not</span> <span class="n">common</span><span class="o">.</span><span class="n">is_str</span><span class="p">(</span><span class="n">label</span><span class="p">):</span>
+
+            <span class="k">return</span> <span class="p">[</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">identifier</span><span class="p">(</span>
+                    <span class="n">_label</span><span class="p">,</span>
+                    <span class="n">entity_type</span> <span class="o">=</span> <span class="n">entity_type</span><span class="p">,</span>
+                    <span class="n">id_type</span> <span class="o">=</span> <span class="n">id_type</span><span class="p">,</span>
+                    <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">,</span>
+                <span class="p">)</span>
+                <span class="k">for</span> <span class="n">_label</span> <span class="ow">in</span> <span class="n">label</span>
+            <span class="p">]</span>
+
+        <span class="k">elif</span> <span class="nb">hasattr</span><span class="p">(</span><span class="n">label</span><span class="p">,</span> <span class="s1">&#39;components&#39;</span><span class="p">):</span>
+
+            <span class="k">return</span> <span class="n">label</span><span class="o">.</span><span class="fm">__str__</span><span class="p">()</span>
+
+        <span class="k">elif</span> <span class="n">common</span><span class="o">.</span><span class="n">is_str</span><span class="p">(</span><span class="n">label</span><span class="p">):</span>
+
+            <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span> <span class="ow">or</span> <span class="bp">self</span><span class="o">.</span><span class="n">ncbi_tax_id</span>
+
+            <span class="n">entity_type</span> <span class="o">=</span> <span class="p">(</span>
+                <span class="n">entity_type</span> <span class="ow">or</span>
+                <span class="p">(</span>
+                    <span class="s1">&#39;small_molecule&#39;</span>
+                        <span class="k">if</span> <span class="n">ncbi_tax_id</span> <span class="o">==</span> <span class="n">_const</span><span class="o">.</span><span class="n">NOT_ORGANISM_SPECIFIC</span> <span class="k">else</span>
+                    <span class="s1">&#39;protein&#39;</span>
+                <span class="p">)</span>
+            <span class="p">)</span>
+
+            <span class="n">id_type</span> <span class="o">=</span> <span class="p">(</span>
+                <span class="n">id_type</span> <span class="ow">or</span>
+                <span class="n">settings</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">&#39;default_label_types&#39;</span><span class="p">)[</span><span class="n">entity_type</span><span class="p">]</span>
+            <span class="p">)</span>
+
+            <span class="n">target_id_type</span> <span class="o">=</span> <span class="n">settings</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">&#39;default_name_types&#39;</span><span class="p">)[</span><span class="n">entity_type</span><span class="p">]</span>
+
+            <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">map_name</span><span class="p">(</span>
+                <span class="n">label</span><span class="p">,</span>
+                <span class="n">id_type</span> <span class="o">=</span> <span class="n">id_type</span><span class="p">,</span>
+                <span class="n">target_id_type</span> <span class="o">=</span> <span class="n">target_id_type</span><span class="p">,</span>
+                <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">,</span>
+            <span class="p">)</span>
+
+        <span class="k">else</span><span class="p">:</span>
+
+            <span class="k">return</span> <span class="nb">str</span><span class="p">(</span><span class="n">name</span><span class="p">)</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">identifier0</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">label</span><span class="p">:</span> <span class="n">Union</span><span class="p">[</span><span class="nb">str</span><span class="p">,</span> <span class="n">Iterable</span><span class="p">[</span><span class="nb">str</span><span class="p">]],</span>
+            <span class="n">ncbi_tax_id</span><span class="p">:</span> <span class="n">Optional</span><span class="p">[</span><span class="nb">int</span><span class="p">]</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">id_type</span><span class="p">:</span> <span class="n">Optional</span><span class="p">[</span><span class="nb">str</span><span class="p">]</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">entity_type</span><span class="p">:</span>
+                <span class="n">Optional</span><span class="p">[</span>
+                    <span class="n">Literal</span><span class="p">[</span>
+                        <span class="s1">&#39;drug&#39;</span><span class="p">,</span>
+                        <span class="s1">&#39;lncrna&#39;</span><span class="p">,</span>
+                        <span class="s1">&#39;mirna&#39;</span><span class="p">,</span>
+                        <span class="s1">&#39;protein&#39;</span><span class="p">,</span>
+                        <span class="s1">&#39;small_molecule&#39;</span><span class="p">,</span>
+                    <span class="p">]</span>
+                <span class="p">]</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+        <span class="p">)</span> <span class="o">-&gt;</span> <span class="n">Union</span><span class="p">[</span><span class="nb">str</span><span class="p">,</span> <span class="n">List</span><span class="p">[</span><span class="nb">str</span><span class="p">]]:</span>
+
+        <span class="n">args</span> <span class="o">=</span> <span class="nb">locals</span><span class="p">()</span>
+        <span class="n">_</span> <span class="o">=</span> <span class="n">args</span><span class="o">.</span><span class="n">pop</span><span class="p">(</span><span class="s1">&#39;self&#39;</span><span class="p">)</span>
+        <span class="n">ids</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">identifier</span><span class="p">(</span><span class="o">**</span><span class="n">args</span><span class="p">)</span>
+
+        <span class="k">return</span> <span class="p">(</span>
+            <span class="n">common</span><span class="o">.</span><span class="n">first</span><span class="p">(</span><span class="n">ids</span><span class="p">)</span>
+                <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">label</span><span class="p">,</span> <span class="nb">str</span><span class="p">)</span> <span class="k">else</span>
+            <span class="nb">list</span><span class="p">(</span><span class="nb">map</span><span class="p">(</span><span class="n">common</span><span class="o">.</span><span class="n">first</span><span class="p">,</span> <span class="n">ids</span><span class="p">))</span>
+        <span class="p">)</span>
+
+
+<div class="viewcode-block" id="Mapper.guess_type">
+<a class="viewcode-back" href="../../../api/pypath.utils.mapping.Mapper.html#pypath.utils.mapping.Mapper.guess_type">[docs]</a>
+    <span class="k">def</span> <span class="nf">guess_type</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">name</span><span class="p">,</span> <span class="n">entity_type</span> <span class="o">=</span> <span class="kc">None</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        From a string, tries to guess the ID type and optionally the entity</span>
+<span class="sd">        type. Returns a tuple of strings: ID type and entity type.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">if</span> <span class="p">(</span>
+            <span class="p">(</span>
+                <span class="ow">not</span> <span class="n">entity_type</span> <span class="ow">or</span>
+                <span class="n">entity_type</span> <span class="o">==</span> <span class="s1">&#39;protein&#39;</span>
+            <span class="p">)</span> <span class="ow">and</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">reuniprot</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="n">name</span><span class="p">)</span>
+        <span class="p">):</span>
+
+            <span class="k">return</span> <span class="s1">&#39;uniprot&#39;</span><span class="p">,</span> <span class="s1">&#39;protein&#39;</span>
+
+        <span class="k">if</span> <span class="ow">not</span> <span class="n">entity_type</span> <span class="ow">or</span> <span class="n">entity_type</span> <span class="o">==</span> <span class="s1">&#39;mirna&#39;</span><span class="p">:</span>
+
+            <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">remipreac</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="n">name</span><span class="p">):</span>
+
+                <span class="k">return</span> <span class="s1">&#39;mir-pre&#39;</span><span class="p">,</span> <span class="s1">&#39;mirna&#39;</span>
+
+            <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">remimatac</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="n">name</span><span class="p">):</span>
+
+                <span class="k">return</span> <span class="s1">&#39;mirbase&#39;</span><span class="p">,</span> <span class="s1">&#39;mirna&#39;</span>
+
+            <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">remimatid</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="n">name</span><span class="p">):</span>
+
+                <span class="k">return</span> <span class="s1">&#39;mir-mat-name&#39;</span><span class="p">,</span> <span class="s1">&#39;mirna&#39;</span>
+
+            <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">remipreid</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="n">name</span><span class="p">):</span>
+
+                <span class="k">return</span> <span class="s1">&#39;mir-name&#39;</span><span class="p">,</span> <span class="s1">&#39;mirna&#39;</span>
+
+        <span class="k">return</span> <span class="kc">None</span><span class="p">,</span> <span class="n">entity_type</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">id_from_label</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">label</span><span class="p">,</span>
+            <span class="n">label_id_type</span> <span class="o">=</span> <span class="s1">&#39;genesymbol&#39;</span><span class="p">,</span>
+            <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+        <span class="p">):</span>
+
+        <span class="k">if</span> <span class="n">label_id_type</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">label_type_to_id_type</span><span class="p">:</span>
+
+            <span class="n">ids</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">map_name</span><span class="p">(</span>
+                <span class="n">label</span><span class="p">,</span>
+                <span class="n">label_id_type</span><span class="p">,</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">label_type_to_id_type</span><span class="p">[</span><span class="n">label_id_type</span><span class="p">],</span>
+                <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">,</span>
+            <span class="p">)</span>
+
+        <span class="k">return</span> <span class="n">ids</span> <span class="ow">or</span> <span class="p">{</span><span class="n">label</span><span class="p">}</span>
+
+    <span class="k">def</span> <span class="nf">id_from_label0</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">label</span><span class="p">,</span>
+            <span class="n">label_id_type</span> <span class="o">=</span> <span class="s1">&#39;genesymbol&#39;</span><span class="p">,</span>
+            <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+        <span class="p">):</span>
+
+        <span class="k">return</span> <span class="nb">next</span><span class="p">(</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">id_from_label</span><span class="p">(</span>
+                <span class="n">label</span> <span class="o">=</span> <span class="n">label</span><span class="p">,</span>
+                <span class="n">label_id_type</span> <span class="o">=</span> <span class="n">label_id_type</span><span class="p">,</span>
+                <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span>
+            <span class="p">)</span><span class="o">.</span><span class="fm">__iter__</span><span class="p">()</span>
+        <span class="p">)</span>
+
+
+<div class="viewcode-block" id="Mapper.primary_uniprot">
+<a class="viewcode-back" href="../../../api/pypath.utils.mapping.Mapper.html#pypath.utils.mapping.Mapper.primary_uniprot">[docs]</a>
+    <span class="k">def</span> <span class="nf">primary_uniprot</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">uniprots</span><span class="p">,</span> <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="kc">None</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        For an iterable of UniProt IDs returns a set with the secondary IDs</span>
+<span class="sd">        changed to the corresponding primary IDs. Anything what is not a</span>
+<span class="sd">        secondary UniProt ID left intact.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">primaries</span> <span class="o">=</span> <span class="nb">set</span><span class="p">()</span>
+        <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span> <span class="ow">or</span> <span class="bp">self</span><span class="o">.</span><span class="n">ncbi_tax_id</span>
+
+        <span class="k">for</span> <span class="n">uniprot</span> <span class="ow">in</span> <span class="n">uniprots</span><span class="p">:</span>
+
+            <span class="n">primary</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">map_name</span><span class="p">(</span>
+                <span class="n">name</span> <span class="o">=</span> <span class="n">uniprot</span><span class="p">,</span>
+                <span class="n">id_type</span> <span class="o">=</span> <span class="s1">&#39;uniprot-sec&#39;</span><span class="p">,</span>
+                <span class="n">target_id_type</span> <span class="o">=</span> <span class="s1">&#39;uniprot-pri&#39;</span><span class="p">,</span>
+                <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">,</span>
+            <span class="p">)</span>
+
+            <span class="k">if</span> <span class="n">primary</span><span class="p">:</span>
+
+                <span class="n">primaries</span><span class="o">.</span><span class="n">update</span><span class="p">(</span><span class="n">primary</span><span class="p">)</span>
+
+            <span class="k">else</span><span class="p">:</span>
+
+                <span class="c1"># most probably this UniProt is already primary</span>
+                <span class="n">primaries</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">uniprot</span><span class="p">)</span>
+
+        <span class="k">return</span> <span class="n">primaries</span></div>
+
+
+
+<div class="viewcode-block" id="Mapper.trembl_swissprot">
+<a class="viewcode-back" href="../../../api/pypath.utils.mapping.Mapper.html#pypath.utils.mapping.Mapper.trembl_swissprot">[docs]</a>
+    <span class="k">def</span> <span class="nf">trembl_swissprot</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">uniprots</span><span class="p">,</span> <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="kc">None</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        For an iterable of TrEMBL and SwissProt IDs, returns a set with</span>
+<span class="sd">        only SwissProt, mapping from TrEMBL to gene symbols, and</span>
+<span class="sd">        then back to SwissProt. If this kind of translation is not successful</span>
+<span class="sd">        for any of the IDs it will be kept in the result, no matter if it&#39;s</span>
+<span class="sd">        not a SwissProt ID. If the</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span> <span class="ow">or</span> <span class="bp">self</span><span class="o">.</span><span class="n">ncbi_tax_id</span>
+        <span class="n">swissprots</span> <span class="o">=</span> <span class="nb">set</span><span class="p">()</span>
+
+        <span class="k">for</span> <span class="n">uniprot</span> <span class="ow">in</span> <span class="n">uniprots</span><span class="p">:</span>
+
+            <span class="n">swissprot</span> <span class="o">=</span> <span class="kc">None</span>
+            <span class="n">genesymbols</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">map_name</span><span class="p">(</span>
+                <span class="n">name</span> <span class="o">=</span> <span class="n">uniprot</span><span class="p">,</span>
+                <span class="n">id_type</span> <span class="o">=</span> <span class="s1">&#39;trembl&#39;</span><span class="p">,</span>
+                <span class="n">target_id_type</span> <span class="o">=</span> <span class="s1">&#39;genesymbol&#39;</span><span class="p">,</span>
+                <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">,</span>
+            <span class="p">)</span>
+
+            <span class="n">this_swissprots</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">map_names</span><span class="p">(</span>
+                <span class="n">names</span> <span class="o">=</span> <span class="n">genesymbols</span><span class="p">,</span>
+                <span class="n">id_type</span> <span class="o">=</span> <span class="s1">&#39;genesymbol&#39;</span><span class="p">,</span>
+                <span class="n">target_id_type</span> <span class="o">=</span> <span class="s1">&#39;swissprot&#39;</span><span class="p">,</span>
+                <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">,</span>
+            <span class="p">)</span>
+
+            <span class="k">if</span> <span class="ow">not</span> <span class="n">this_swissprots</span><span class="p">:</span>
+
+                <span class="n">swissprots</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">uniprot</span><span class="p">)</span>
+
+            <span class="k">else</span><span class="p">:</span>
+
+                <span class="n">swissprots</span><span class="o">.</span><span class="n">update</span><span class="p">(</span><span class="n">this_swissprots</span><span class="p">)</span>
+
+        <span class="k">return</span> <span class="n">swissprots</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">translate_deleted_uniprots_by_genesymbol</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">uniprots</span><span class="p">,</span>
+            <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+        <span class="p">):</span>
+
+        <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">uniprots</span><span class="p">,</span> <span class="nb">str</span><span class="p">):</span>
+
+            <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">translate_deleted_uniprot_by_genesymbol</span><span class="p">(</span>
+                <span class="n">uniprots</span><span class="p">,</span>
+                <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">,</span>
+            <span class="p">)</span>
+
+        <span class="k">else</span><span class="p">:</span>
+
+            <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span> <span class="ow">or</span> <span class="bp">self</span><span class="o">.</span><span class="n">ncbi_tax_id</span>
+
+            <span class="k">return</span> <span class="nb">set</span><span class="o">.</span><span class="n">union</span><span class="p">(</span><span class="o">*</span><span class="p">(</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">translate_deleted_uniprot_by_genesymbol</span><span class="p">(</span>
+                    <span class="n">uniprot</span><span class="p">,</span>
+                    <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">,</span>
+                <span class="p">)</span>
+                <span class="k">for</span> <span class="n">uniprot</span> <span class="ow">in</span> <span class="n">uniprots</span>
+            <span class="p">))</span> <span class="k">if</span> <span class="n">uniprots</span> <span class="k">else</span> <span class="nb">set</span><span class="p">()</span>
+
+
+<div class="viewcode-block" id="Mapper.translate_deleted_uniprot_by_genesymbol">
+<a class="viewcode-back" href="../../../api/pypath.utils.mapping.Mapper.html#pypath.utils.mapping.Mapper.translate_deleted_uniprot_by_genesymbol">[docs]</a>
+    <span class="k">def</span> <span class="nf">translate_deleted_uniprot_by_genesymbol</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">uniprot</span><span class="p">,</span>
+            <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+        <span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Due to potentially ambiguous translation always returns set.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span> <span class="ow">or</span> <span class="bp">self</span><span class="o">.</span><span class="n">ncbi_tax_id</span>
+
+        <span class="k">if</span> <span class="n">uniprot_db</span><span class="o">.</span><span class="n">is_uniprot</span><span class="p">(</span><span class="n">uniprot</span><span class="p">,</span> <span class="n">organism</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">):</span>
+
+            <span class="k">return</span> <span class="p">{</span><span class="n">uniprot</span><span class="p">}</span>
+
+        <span class="k">elif</span> <span class="bp">self</span><span class="o">.</span><span class="n">other_organism_uniprot</span><span class="p">(</span><span class="n">uniprot</span><span class="p">,</span> <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">):</span>
+
+            <span class="k">return</span> <span class="nb">set</span><span class="p">()</span>
+
+        <span class="k">else</span><span class="p">:</span>
+
+            <span class="n">genesymbol</span><span class="p">,</span> <span class="n">taxid</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">deleted_uniprot_genesymbol</span><span class="p">(</span><span class="n">uniprot</span><span class="p">)</span>
+
+            <span class="k">if</span> <span class="n">genesymbol</span> <span class="ow">and</span> <span class="n">taxid</span> <span class="o">==</span> <span class="n">ncbi_tax_id</span><span class="p">:</span>
+
+                <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">map_name</span><span class="p">(</span>
+                    <span class="n">genesymbol</span><span class="p">,</span>
+                    <span class="s1">&#39;genesymbol&#39;</span><span class="p">,</span>
+                    <span class="s1">&#39;uniprot&#39;</span><span class="p">,</span>
+                    <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">,</span>
+                    <span class="n">uniprot_cleanup</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+                <span class="p">)</span>
+
+        <span class="k">return</span> <span class="p">{</span><span class="n">uniprot</span><span class="p">}</span></div>
+
+
+
+<div class="viewcode-block" id="Mapper.other_organism_uniprot">
+<a class="viewcode-back" href="../../../api/pypath.utils.mapping.Mapper.html#pypath.utils.mapping.Mapper.other_organism_uniprot">[docs]</a>
+    <span class="k">def</span> <span class="nf">other_organism_uniprot</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">uniprot</span><span class="p">,</span> <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="kc">None</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Tells if ``uniprot`` is an UniProt ID from some other organism than</span>
+<span class="sd">        ``ncbi_tax_id``.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span> <span class="ow">or</span> <span class="bp">self</span><span class="o">.</span><span class="n">ncbi_tax_id</span>
+
+        <span class="n">uniprot_taxid</span> <span class="o">=</span> <span class="n">taxonomy</span><span class="o">.</span><span class="n">uniprot_taxid</span><span class="p">(</span><span class="n">uniprot</span><span class="p">)</span>
+
+        <span class="k">return</span> <span class="n">uniprot_taxid</span> <span class="ow">and</span> <span class="n">uniprot_taxid</span> <span class="o">!=</span> <span class="n">ncbi_tax_id</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">deleted_uniprot_genesymbol</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">uniprot</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="n">uniprot_input</span><span class="o">.</span><span class="n">deleted_uniprot_genesymbol</span><span class="p">(</span><span class="n">uniprot</span><span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">only_valid_uniprots</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">uniprots</span><span class="p">,</span> <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="kc">None</span><span class="p">):</span>
+
+        <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span> <span class="ow">or</span> <span class="bp">self</span><span class="o">.</span><span class="n">ncbi_tax_id</span>
+
+        <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">uniprots</span><span class="p">,</span> <span class="nb">str</span><span class="p">):</span>
+
+            <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">valid_uniprot</span><span class="p">(</span><span class="n">uniprots</span><span class="p">,</span> <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">)</span>
+
+        <span class="k">else</span><span class="p">:</span>
+
+            <span class="k">return</span> <span class="p">{</span>
+                <span class="n">uniprot</span>
+                <span class="k">for</span> <span class="n">uniprot</span> <span class="ow">in</span> <span class="n">uniprots</span>
+                <span class="k">if</span> <span class="n">uniprot_db</span><span class="o">.</span><span class="n">is_uniprot</span><span class="p">(</span><span class="n">uniprot</span><span class="p">,</span> <span class="n">organism</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">)</span>
+            <span class="p">}</span>
+
+
+<div class="viewcode-block" id="Mapper.valid_uniprot">
+<a class="viewcode-back" href="../../../api/pypath.utils.mapping.Mapper.html#pypath.utils.mapping.Mapper.valid_uniprot">[docs]</a>
+    <span class="k">def</span> <span class="nf">valid_uniprot</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">uniprot</span><span class="p">,</span> <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="kc">None</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        If the UniProt ID ``uniprot`` exist in the proteome of the organism</span>
+<span class="sd">        ``ncbi_tax_id`` returns the ID, otherwise returns None.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span> <span class="ow">or</span> <span class="bp">self</span><span class="o">.</span><span class="n">ncbi_tax_id</span>
+
+        <span class="k">if</span> <span class="n">uniprot_db</span><span class="o">.</span><span class="n">is_uniprot</span><span class="p">(</span><span class="n">uniprot</span><span class="p">,</span> <span class="n">organism</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">):</span>
+
+            <span class="k">return</span> <span class="n">uniprot</span></div>
+
+
+
+<div class="viewcode-block" id="Mapper.only_uniprot_ac">
+<a class="viewcode-back" href="../../../api/pypath.utils.mapping.Mapper.html#pypath.utils.mapping.Mapper.only_uniprot_ac">[docs]</a>
+    <span class="k">def</span> <span class="nf">only_uniprot_ac</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">uniprots</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        For one or more strings returns only those which match the format</span>
+<span class="sd">        of UniProt accession numbers.</span>
+<span class="sd">        The format is defined here:</span>
+<span class="sd">        https://www.uniprot.org/help/accession_numbers</span>
+
+<span class="sd">        If string provided, returns string or None.</span>
+<span class="sd">        If iterable provided, returns set (potentially empty if none of the</span>
+<span class="sd">        strings are valid).</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">uniprots</span><span class="p">,</span> <span class="nb">str</span><span class="p">):</span>
+
+            <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_only_uniprot_ac</span><span class="p">(</span><span class="n">uniprots</span><span class="p">)</span>
+
+        <span class="k">else</span><span class="p">:</span>
+
+            <span class="k">return</span> <span class="p">{</span>
+                <span class="n">validated</span>
+                <span class="k">for</span> <span class="n">validated</span> <span class="ow">in</span>
+                <span class="p">(</span>
+                    <span class="bp">self</span><span class="o">.</span><span class="n">_only_uniprot_ac</span><span class="p">(</span><span class="n">uniprot</span><span class="p">)</span>
+                    <span class="k">for</span> <span class="n">uniprot</span> <span class="ow">in</span> <span class="n">uniprots</span>
+                <span class="p">)</span>
+                <span class="k">if</span> <span class="n">validated</span>
+            <span class="p">}</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">_only_uniprot_ac</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">uniprot</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="n">uniprot</span> <span class="k">if</span> <span class="n">uniprot_input</span><span class="o">.</span><span class="n">valid_uniprot</span><span class="p">(</span><span class="n">uniprot</span><span class="p">)</span> <span class="k">else</span> <span class="kc">None</span>
+
+    <span class="c1">#</span>
+    <span class="c1"># Mapping table management methods</span>
+    <span class="c1">#</span>
+
+<div class="viewcode-block" id="Mapper.mapping_tables">
+<a class="viewcode-back" href="../../../api/pypath.utils.mapping.Mapper.html#pypath.utils.mapping.Mapper.mapping_tables">[docs]</a>
+    <span class="nd">@staticmethod</span>
+    <span class="k">def</span> <span class="nf">mapping_tables</span><span class="p">():</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        List of mapping tables available to load.</span>
+
+<span class="sd">        Returns</span>
+<span class="sd">            (list): A list of tuples, each representing an ID translation</span>
+<span class="sd">                table, with the ID types, the data source and the loader</span>
+<span class="sd">                class.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">MappingTableDefinition</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">namedtuple</span><span class="p">(</span>
+            <span class="s1">&#39;MappingTableDefinition&#39;</span><span class="p">,</span>
+            <span class="p">(</span>
+                <span class="s1">&#39;id_type_a&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;id_type_b&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;resource&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;input_class&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;resource_id_type_a&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;resource_id_type_b&#39;</span><span class="p">,</span>
+            <span class="p">),</span>
+        <span class="p">)</span>
+
+        <span class="n">MappingTableDefinition</span><span class="o">.</span><span class="fm">__new__</span><span class="o">.</span><span class="vm">__defaults__</span> <span class="o">=</span> <span class="p">(</span><span class="kc">None</span><span class="p">,</span> <span class="kc">None</span><span class="p">)</span>
+
+        <span class="n">result</span> <span class="o">=</span> <span class="p">[]</span>
+
+        <span class="k">for</span> <span class="n">resource_attr</span> <span class="ow">in</span> <span class="n">RESOURCES_EXPLICIT</span><span class="p">:</span>
+
+            <span class="n">resources</span> <span class="o">=</span> <span class="nb">getattr</span><span class="p">(</span><span class="n">maps</span><span class="p">,</span> <span class="n">resource_attr</span><span class="p">)</span>
+
+            <span class="k">for</span> <span class="p">(</span><span class="n">id_type_a</span><span class="p">,</span> <span class="n">id_type_b</span><span class="p">),</span> <span class="n">inputdef</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="n">resources</span><span class="p">):</span>
+
+                <span class="n">result</span><span class="o">.</span><span class="n">append</span><span class="p">(</span>
+                    <span class="n">MappingTableDefinition</span><span class="p">(</span>
+                        <span class="n">id_type_a</span> <span class="o">=</span> <span class="n">id_type_a</span><span class="p">,</span>
+                        <span class="n">id_type_b</span> <span class="o">=</span> <span class="n">id_type_b</span><span class="p">,</span>
+                        <span class="n">resource</span> <span class="o">=</span> <span class="n">resource_attr</span><span class="p">,</span>
+                        <span class="n">input_class</span> <span class="o">=</span> <span class="n">inputdef</span><span class="o">.</span><span class="vm">__class__</span><span class="o">.</span><span class="vm">__name__</span><span class="p">,</span>
+                        <span class="n">resource_id_type_a</span> <span class="o">=</span> <span class="n">inputdef</span><span class="o">.</span><span class="n">_resource_id_type_a</span><span class="p">,</span>
+                        <span class="n">resource_id_type_b</span> <span class="o">=</span> <span class="n">inputdef</span><span class="o">.</span><span class="n">_resource_id_type_b</span><span class="p">,</span>
+                    <span class="p">)</span>
+                <span class="p">)</span>
+
+        <span class="k">for</span> <span class="n">service_ids</span><span class="p">,</span> <span class="n">service_id_type</span><span class="p">,</span> <span class="n">input_cls</span> <span class="ow">in</span> <span class="n">RESOURCES_IMPLICIT</span><span class="p">:</span>
+
+            <span class="n">service_ids</span> <span class="o">=</span> <span class="p">(</span>
+                <span class="n">iteritems</span><span class="p">(</span><span class="n">service_ids</span><span class="p">)</span>
+                    <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">service_ids</span><span class="p">,</span> <span class="nb">dict</span><span class="p">)</span> <span class="k">else</span>
+                <span class="nb">zip</span><span class="p">(</span><span class="o">*</span><span class="p">(</span><span class="n">service_ids</span><span class="p">,)</span> <span class="o">*</span> <span class="mi">2</span><span class="p">)</span>
+            <span class="p">)</span>
+
+            <span class="k">for</span> <span class="n">id_type</span><span class="p">,</span> <span class="n">resource_id_type</span> <span class="ow">in</span> <span class="n">service_ids</span><span class="p">:</span>
+
+                <span class="n">id_type_b</span> <span class="o">=</span> <span class="s1">&#39;pro&#39;</span> <span class="k">if</span> <span class="n">service_id_type</span> <span class="o">==</span> <span class="s1">&#39;pro&#39;</span> <span class="k">else</span> <span class="kc">None</span>
+
+                <span class="n">result</span><span class="o">.</span><span class="n">append</span><span class="p">(</span>
+                    <span class="n">MappingTableDefinition</span><span class="p">(</span>
+                        <span class="n">id_type_a</span> <span class="o">=</span> <span class="n">id_type</span><span class="p">,</span>
+                        <span class="n">id_type_b</span> <span class="o">=</span> <span class="n">id_type_b</span><span class="p">,</span>
+                        <span class="n">resource</span> <span class="o">=</span> <span class="n">service_id_type</span><span class="p">,</span>
+                        <span class="n">input_class</span> <span class="o">=</span> <span class="n">input_cls</span><span class="o">.</span><span class="vm">__name__</span><span class="p">,</span>
+                        <span class="n">resource_id_type_a</span> <span class="o">=</span> <span class="n">resource_id_type</span><span class="p">,</span>
+                        <span class="n">resource_id_type_b</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+                    <span class="p">)</span>
+                <span class="p">)</span>
+
+        <span class="k">return</span> <span class="n">result</span></div>
+
+
+
+<div class="viewcode-block" id="Mapper.id_types">
+<a class="viewcode-back" href="../../../api/pypath.utils.mapping.Mapper.html#pypath.utils.mapping.Mapper.id_types">[docs]</a>
+    <span class="nd">@classmethod</span>
+    <span class="k">def</span> <span class="nf">id_types</span><span class="p">(</span><span class="bp">cls</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        A list of all identifier types that can be handled by any of the</span>
+<span class="sd">        resources.</span>
+
+<span class="sd">        Returns</span>
+<span class="sd">            (list): A list of tuples with the identifier type labels used</span>
+<span class="sd">                in pypath and in the original resource. If the latter is</span>
+<span class="sd">                None, typically the ID type has no name in the original</span>
+<span class="sd">                resource.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">IdType</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">namedtuple</span><span class="p">(</span>
+            <span class="s1">&#39;IdType&#39;</span><span class="p">,</span>
+            <span class="p">(</span>
+                <span class="s1">&#39;pypath&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;original&#39;</span><span class="p">,</span>
+            <span class="p">),</span>
+        <span class="p">)</span>
+
+        <span class="k">return</span> <span class="p">{</span>
+            <span class="n">IdType</span><span class="p">(</span>
+                <span class="n">pypath</span> <span class="o">=</span> <span class="nb">getattr</span><span class="p">(</span><span class="n">mapdef</span><span class="p">,</span> <span class="s1">&#39;id_type_</span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="n">side</span><span class="p">),</span>
+                <span class="n">original</span> <span class="o">=</span> <span class="nb">getattr</span><span class="p">(</span><span class="n">mapdef</span><span class="p">,</span> <span class="s1">&#39;resource_id_type_</span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="n">side</span><span class="p">),</span>
+            <span class="p">)</span>
+            <span class="k">for</span> <span class="n">mapdef</span> <span class="ow">in</span> <span class="bp">cls</span><span class="o">.</span><span class="n">mapping_tables</span><span class="p">()</span>
+            <span class="k">for</span> <span class="n">side</span> <span class="ow">in</span> <span class="p">(</span><span class="s1">&#39;a&#39;</span><span class="p">,</span> <span class="s1">&#39;b&#39;</span><span class="p">)</span>
+            <span class="k">if</span> <span class="nb">getattr</span><span class="p">(</span><span class="n">mapdef</span><span class="p">,</span> <span class="s1">&#39;id_type_</span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="n">side</span><span class="p">)</span>
+        <span class="p">}</span></div>
+
+
+
+<div class="viewcode-block" id="Mapper.has_mapping_table">
+<a class="viewcode-back" href="../../../api/pypath.utils.mapping.Mapper.html#pypath.utils.mapping.Mapper.has_mapping_table">[docs]</a>
+    <span class="k">def</span> <span class="nf">has_mapping_table</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">id_type</span><span class="p">,</span>
+            <span class="n">target_id_type</span><span class="p">,</span>
+            <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+        <span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Tells if a mapping table is loaded. If it&#39;s loaded, it resets the</span>
+<span class="sd">        expiry timer so the table remains loaded.</span>
+
+<span class="sd">        Returns</span>
+<span class="sd">            (bool): True if the mapping table is loaded.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span> <span class="ow">or</span> <span class="bp">self</span><span class="o">.</span><span class="n">ncbi_tax_id</span>
+
+        <span class="n">key</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">get_table_key</span><span class="p">(</span>
+            <span class="n">id_type</span> <span class="o">=</span> <span class="n">id_type</span><span class="p">,</span>
+            <span class="n">target_id_type</span> <span class="o">=</span> <span class="n">target_id_type</span><span class="p">,</span>
+            <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">,</span>
+        <span class="p">)</span>
+
+        <span class="k">if</span> <span class="n">key</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">tables</span><span class="p">:</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">tables</span><span class="p">[</span><span class="n">key</span><span class="p">]</span><span class="o">.</span><span class="n">_used</span><span class="p">()</span>
+
+        <span class="k">return</span> <span class="n">key</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">tables</span></div>
+
+
+
+<div class="viewcode-block" id="Mapper.load_mapping">
+<a class="viewcode-back" href="../../../api/pypath.utils.mapping.Mapper.html#pypath.utils.mapping.Mapper.load_mapping">[docs]</a>
+    <span class="k">def</span> <span class="nf">load_mapping</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">resource</span><span class="p">,</span>
+            <span class="o">**</span><span class="n">kwargs</span>
+        <span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Loads a single mapping table based on input definition in</span>
+<span class="sd">        ``resource``. ``**kwargs`` passed to ``MapReader``.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">if</span> <span class="p">(</span>
+            <span class="n">resource</span><span class="o">.</span><span class="n">type</span> <span class="ow">in</span> <span class="p">{</span><span class="s1">&#39;file&#39;</span><span class="p">,</span> <span class="s1">&#39;pickle&#39;</span><span class="p">}</span> <span class="ow">and</span>
+            <span class="ow">not</span> <span class="p">(</span>
+                <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">exists</span><span class="p">(</span><span class="n">resource</span><span class="o">.</span><span class="n">input</span><span class="p">)</span> <span class="ow">or</span>
+                <span class="n">inputs</span><span class="o">.</span><span class="n">get_method</span><span class="p">(</span><span class="n">resource</span><span class="o">.</span><span class="n">input</span><span class="p">)</span>
+            <span class="p">)</span>
+        <span class="p">):</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span>
+                <span class="s1">&#39;Could not load mapping: no such &#39;</span>
+                <span class="s1">&#39;file or function: `</span><span class="si">%s</span><span class="s1">`.&#39;</span> <span class="o">%</span> <span class="n">resource</span><span class="o">.</span><span class="n">input</span>
+            <span class="p">)</span>
+            <span class="k">return</span>
+
+        <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">kwargs</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">&#39;ncbi_tax_id&#39;</span><span class="p">,</span> <span class="n">resource</span><span class="o">.</span><span class="n">ncbi_tax_id</span><span class="p">)</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span>
+            <span class="s1">&#39;Loading mapping table for organism `</span><span class="si">%s</span><span class="s1">` &#39;</span>
+            <span class="s1">&#39;with identifiers `</span><span class="si">%s</span><span class="s1">` and `</span><span class="si">%s</span><span class="s1">`, &#39;</span>
+            <span class="s1">&#39;input type `</span><span class="si">%s</span><span class="s1">`&#39;</span> <span class="o">%</span> <span class="p">(</span>
+                <span class="n">ncbi_tax_id</span><span class="p">,</span>
+                <span class="n">resource</span><span class="o">.</span><span class="n">id_type_a</span><span class="p">,</span>
+                <span class="n">resource</span><span class="o">.</span><span class="n">id_type_b</span><span class="p">,</span>
+                <span class="n">resource</span><span class="o">.</span><span class="n">type</span><span class="p">,</span>
+            <span class="p">)</span>
+        <span class="p">)</span>
+
+        <span class="n">reader</span> <span class="o">=</span> <span class="n">MapReader</span><span class="p">(</span><span class="n">param</span> <span class="o">=</span> <span class="n">resource</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
+
+        <span class="n">a_to_b</span> <span class="o">=</span> <span class="n">reader</span><span class="o">.</span><span class="n">mapping_table_a_to_b</span>
+        <span class="n">b_to_a</span> <span class="o">=</span> <span class="n">reader</span><span class="o">.</span><span class="n">mapping_table_b_to_a</span>
+
+        <span class="k">for</span> <span class="n">sides</span> <span class="ow">in</span> <span class="p">((</span><span class="s1">&#39;a&#39;</span><span class="p">,</span> <span class="s1">&#39;b&#39;</span><span class="p">),</span> <span class="p">(</span><span class="s1">&#39;b&#39;</span><span class="p">,</span> <span class="s1">&#39;a&#39;</span><span class="p">)):</span>
+
+            <span class="n">table</span> <span class="o">=</span> <span class="nb">locals</span><span class="p">()[</span><span class="s1">&#39;</span><span class="si">%s</span><span class="s1">_to_</span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="n">sides</span><span class="p">]</span>
+
+            <span class="k">if</span> <span class="n">table</span><span class="p">:</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span>
+                    <span class="s1">&#39;Sucessfully loaded mapping table for organism `</span><span class="si">%s</span><span class="s1">` &#39;</span>
+                    <span class="s1">&#39;with identifiers `</span><span class="si">%s</span><span class="s1">` to `</span><span class="si">%s</span><span class="s1">`.&#39;</span> <span class="o">%</span> <span class="p">(</span>
+                        <span class="nb">str</span><span class="p">(</span><span class="n">ncbi_tax_id</span><span class="p">),</span>
+                        <span class="nb">getattr</span><span class="p">(</span><span class="n">resource</span><span class="p">,</span> <span class="sa">f</span><span class="s1">&#39;id_type_</span><span class="si">{</span><span class="n">sides</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="si">}</span><span class="s1">&#39;</span><span class="p">),</span>
+                        <span class="nb">getattr</span><span class="p">(</span><span class="n">resource</span><span class="p">,</span> <span class="sa">f</span><span class="s1">&#39;id_type_</span><span class="si">{</span><span class="n">sides</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="si">}</span><span class="s1">&#39;</span><span class="p">),</span>
+                    <span class="p">)</span>
+                <span class="p">)</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">tables</span><span class="p">[</span><span class="n">table</span><span class="o">.</span><span class="n">get_key</span><span class="p">()]</span> <span class="o">=</span> <span class="n">table</span></div>
+
+
+
+<div class="viewcode-block" id="Mapper.swissprots">
+<a class="viewcode-back" href="../../../api/pypath.utils.mapping.Mapper.html#pypath.utils.mapping.Mapper.swissprots">[docs]</a>
+    <span class="k">def</span> <span class="nf">swissprots</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">uniprots</span><span class="p">,</span> <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="kc">None</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Creates a dict translating a set of potentially secondary and</span>
+<span class="sd">        non-reviewed UniProt IDs to primary SwissProt IDs (whenever</span>
+<span class="sd">        is possible).</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">swissprots</span> <span class="o">=</span> <span class="p">{}</span>
+
+        <span class="k">for</span> <span class="n">uniprot</span> <span class="ow">in</span> <span class="n">uniprots</span><span class="p">:</span>
+
+            <span class="n">swissprots</span><span class="p">[</span><span class="n">uniprot</span><span class="p">]</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">map_name</span><span class="p">(</span>
+                <span class="n">name</span> <span class="o">=</span> <span class="n">uniprot</span><span class="p">,</span>
+                <span class="n">id_type</span> <span class="o">=</span> <span class="s1">&#39;uniprot&#39;</span><span class="p">,</span>
+                <span class="n">target_id_type</span> <span class="o">=</span> <span class="s1">&#39;uniprot&#39;</span><span class="p">,</span>
+                <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">,</span>
+            <span class="p">)</span>
+
+        <span class="k">return</span> <span class="n">swissprots</span></div>
+
+
+
+<div class="viewcode-block" id="Mapper.load_genesymbol5">
+<a class="viewcode-back" href="../../../api/pypath.utils.mapping.Mapper.html#pypath.utils.mapping.Mapper.load_genesymbol5">[docs]</a>
+    <span class="k">def</span> <span class="nf">load_genesymbol5</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="kc">None</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Creates a Gene Symbol to UniProt mapping table with the first</span>
+<span class="sd">        5 characters of each Gene Symbol.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span> <span class="ow">or</span> <span class="bp">self</span><span class="o">.</span><span class="n">ncbi_tax_id</span>
+
+        <span class="n">genesymbol_table</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">which_table</span><span class="p">(</span>
+            <span class="n">id_type</span> <span class="o">=</span> <span class="s1">&#39;genesymbol&#39;</span><span class="p">,</span>
+            <span class="n">target_id_type</span> <span class="o">=</span> <span class="s1">&#39;uniprot&#39;</span><span class="p">,</span>
+            <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">,</span>
+        <span class="p">)</span>
+        <span class="n">genesymbol_syn_table</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">which_table</span><span class="p">(</span>
+            <span class="n">id_type</span> <span class="o">=</span> <span class="s1">&#39;genesymbol-syn&#39;</span><span class="p">,</span>
+            <span class="n">target_id_type</span> <span class="o">=</span> <span class="s1">&#39;uniprot&#39;</span><span class="p">,</span>
+            <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">,</span>
+        <span class="p">)</span>
+
+        <span class="n">genesymbol5_data</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">defaultdict</span><span class="p">(</span><span class="nb">set</span><span class="p">)</span>
+
+        <span class="k">for</span> <span class="n">table</span> <span class="ow">in</span> <span class="p">(</span><span class="n">genesymbol_table</span><span class="p">,</span> <span class="n">genesymbol_syn_table</span><span class="p">):</span>
+
+            <span class="k">for</span> <span class="n">genesymbol</span><span class="p">,</span> <span class="n">uniprots</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="n">table</span><span class="o">.</span><span class="n">data</span><span class="p">):</span>
+
+                <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">genesymbol</span><span class="p">)</span> <span class="o">&gt;=</span> <span class="mi">5</span><span class="p">:</span>
+
+                    <span class="n">genesymbol5</span> <span class="o">=</span> <span class="n">genesymbol</span><span class="p">[:</span><span class="mi">5</span><span class="p">]</span>
+
+                    <span class="n">genesymbol5_data</span><span class="p">[</span><span class="n">genesymbol5</span><span class="p">]</span><span class="o">.</span><span class="n">update</span><span class="p">(</span><span class="n">uniprots</span><span class="p">)</span>
+
+        <span class="n">mapping_table</span> <span class="o">=</span> <span class="n">MappingTable</span><span class="p">(</span>
+            <span class="n">data</span> <span class="o">=</span> <span class="n">genesymbol5_data</span><span class="p">,</span>
+            <span class="n">id_type</span> <span class="o">=</span> <span class="s1">&#39;genesymbol5&#39;</span><span class="p">,</span>
+            <span class="n">target_id_type</span> <span class="o">=</span> <span class="s1">&#39;uniprot&#39;</span><span class="p">,</span>
+            <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">,</span>
+        <span class="p">)</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">tables</span><span class="p">[</span><span class="n">mapping_table</span><span class="o">.</span><span class="n">get_key</span><span class="p">()]</span> <span class="o">=</span> <span class="n">mapping_table</span></div>
+
+
+
+<div class="viewcode-block" id="Mapper.load_uniprot_static">
+<a class="viewcode-back" href="../../../api/pypath.utils.mapping.Mapper.html#pypath.utils.mapping.Mapper.load_uniprot_static">[docs]</a>
+    <span class="k">def</span> <span class="nf">load_uniprot_static</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">keys</span><span class="p">,</span>
+            <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+        <span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Loads mapping tables from the huge static mapping file from UniProt.</span>
+<span class="sd">        Takes long to download and process, also requires more memory. This</span>
+<span class="sd">        is the last thing we try if everything else failed.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">cachedir</span> <span class="o">=</span> <span class="n">cache_mod</span><span class="o">.</span><span class="n">get_cachedir</span><span class="p">()</span>
+        <span class="n">data</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">((</span><span class="n">key</span><span class="p">,</span> <span class="n">collections</span><span class="o">.</span><span class="n">defaultdict</span><span class="p">(</span><span class="nb">set</span><span class="p">))</span> <span class="k">for</span> <span class="n">key</span> <span class="ow">in</span> <span class="n">keys</span><span class="p">)</span>
+        <span class="n">cache_files</span> <span class="o">=</span> <span class="p">{}</span>
+        <span class="n">to_load</span> <span class="o">=</span> <span class="nb">set</span><span class="p">()</span>
+        <span class="n">id_type_b</span> <span class="o">=</span> <span class="s1">&#39;uniprot&#39;</span>
+
+        <span class="c1"># attempting to load them from Pickle</span>
+        <span class="k">for</span> <span class="n">key</span> <span class="ow">in</span> <span class="n">keys</span><span class="p">:</span>
+
+            <span class="n">mapping_id</span> <span class="o">=</span> <span class="n">common</span><span class="o">.</span><span class="n">md5</span><span class="p">(</span>
+                <span class="n">json</span><span class="o">.</span><span class="n">dumps</span><span class="p">(</span>
+                    <span class="p">(</span>
+                        <span class="n">key</span><span class="p">,</span>
+                        <span class="s1">&#39;uniprot_static&#39;</span><span class="p">,</span>
+                    <span class="p">)</span>
+                <span class="p">)</span>
+            <span class="p">)</span>
+
+            <span class="n">cachefile</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">cachedir</span><span class="p">,</span> <span class="n">mapping_id</span><span class="p">)</span>
+            <span class="n">cache_files</span><span class="p">[</span><span class="n">key</span><span class="p">]</span> <span class="o">=</span> <span class="n">cachefile</span>
+
+            <span class="k">if</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">exists</span><span class="p">(</span><span class="n">cachefile</span><span class="p">):</span>
+
+                <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">cachefile</span><span class="p">,</span> <span class="s1">&#39;rb&#39;</span><span class="p">)</span> <span class="k">as</span> <span class="n">fp</span><span class="p">:</span>
+
+                    <span class="n">data</span><span class="p">[</span><span class="n">key</span><span class="p">]</span> <span class="o">=</span> <span class="n">pickle</span><span class="o">.</span><span class="n">load</span><span class="p">(</span><span class="n">fp</span><span class="p">)</span>
+
+            <span class="k">else</span><span class="p">:</span>
+
+                <span class="n">to_load</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">key</span><span class="p">)</span>
+
+        <span class="c1"># loading the remaining from the big UniProt mapping file:</span>
+        <span class="k">if</span> <span class="n">to_load</span><span class="p">:</span>
+
+            <span class="n">url</span> <span class="o">=</span> <span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;uniprot_idmap_ftp&#39;</span><span class="p">][</span><span class="s1">&#39;url&#39;</span><span class="p">]</span>
+            <span class="n">c</span> <span class="o">=</span> <span class="n">curl</span><span class="o">.</span><span class="n">Curl</span><span class="p">(</span><span class="n">url</span><span class="p">,</span> <span class="n">silent</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span> <span class="n">large</span> <span class="o">=</span> <span class="kc">True</span><span class="p">)</span>
+
+            <span class="n">prg</span> <span class="o">=</span> <span class="n">progress</span><span class="o">.</span><span class="n">Progress</span><span class="p">(</span>
+                <span class="n">c</span><span class="o">.</span><span class="n">size</span><span class="p">,</span>
+                <span class="s1">&#39;Processing ID conversion list&#39;</span><span class="p">,</span>
+                <span class="mi">99</span><span class="p">,</span>
+            <span class="p">)</span>
+
+            <span class="k">for</span> <span class="n">line</span> <span class="ow">in</span> <span class="n">c</span><span class="o">.</span><span class="n">result</span><span class="p">:</span>
+
+                <span class="n">prg</span><span class="o">.</span><span class="n">step</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">line</span><span class="p">))</span>
+
+                <span class="n">line</span> <span class="o">=</span> <span class="n">common</span><span class="o">.</span><span class="n">decode</span><span class="p">(</span><span class="n">line</span><span class="p">,</span> <span class="s1">&#39;ascii&#39;</span><span class="p">)</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\t</span><span class="s1">&#39;</span><span class="p">)</span>
+
+                <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">line</span><span class="p">)</span> <span class="o">&gt;</span> <span class="mi">2</span> <span class="ow">and</span> <span class="n">line</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">names_uniprot_static</span><span class="p">:</span>
+
+                    <span class="n">id_type_a</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">names_uniprot_static</span><span class="p">[</span><span class="n">line</span><span class="p">[</span><span class="mi">1</span><span class="p">]]</span>
+
+                    <span class="n">key_a_to_b</span> <span class="o">=</span> <span class="n">MappingTableKey</span><span class="p">(</span>
+                        <span class="n">id_type</span> <span class="o">=</span> <span class="n">id_type_a</span><span class="p">,</span>
+                        <span class="n">target_id_type</span> <span class="o">=</span> <span class="n">id_type_b</span><span class="p">,</span>
+                        <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">,</span>
+                    <span class="p">)</span>
+                    <span class="n">key_b_to_a</span> <span class="o">=</span> <span class="n">MappingTableKey</span><span class="p">(</span>
+                        <span class="n">id_type</span> <span class="o">=</span> <span class="n">id_type_b</span><span class="p">,</span>
+                        <span class="n">target_id_type</span> <span class="o">=</span> <span class="n">id_type_a</span><span class="p">,</span>
+                        <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">,</span>
+                    <span class="p">)</span>
+
+                    <span class="n">this_uniprot</span> <span class="o">=</span> <span class="n">line</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;-&#39;</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span>
+
+                    <span class="k">if</span> <span class="n">key_a_to_b</span> <span class="ow">in</span> <span class="n">to_load</span><span class="p">:</span>
+
+                        <span class="n">data</span><span class="p">[</span><span class="n">key_a_to_b</span><span class="p">][</span><span class="n">line</span><span class="p">[</span><span class="mi">2</span><span class="p">]]</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">this_uniprot</span><span class="p">)</span>
+
+                    <span class="k">if</span> <span class="n">key_b_to_a</span> <span class="ow">in</span> <span class="n">to_load</span><span class="p">:</span>
+
+                        <span class="n">data</span><span class="p">[</span><span class="n">key_b_to_a</span><span class="p">][</span><span class="n">this_uniprot</span><span class="p">]</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">line</span><span class="p">[</span><span class="mi">2</span><span class="p">])</span>
+
+            <span class="n">prg</span><span class="o">.</span><span class="n">terminate</span><span class="p">()</span>
+
+            <span class="k">for</span> <span class="n">key</span><span class="p">,</span> <span class="n">this_data</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="n">data</span><span class="p">):</span>
+
+                <span class="n">pickle</span><span class="o">.</span><span class="n">dump</span><span class="p">(</span><span class="n">this_data</span><span class="p">,</span> <span class="nb">open</span><span class="p">(</span><span class="n">cache_files</span><span class="p">[</span><span class="n">key</span><span class="p">],</span> <span class="s1">&#39;wb&#39;</span><span class="p">))</span>
+
+        <span class="k">for</span> <span class="n">key</span><span class="p">,</span> <span class="n">this_data</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="n">data</span><span class="p">):</span>
+
+            <span class="n">table</span> <span class="o">=</span> <span class="n">MappingTable</span><span class="p">(</span>
+                <span class="n">data</span> <span class="o">=</span> <span class="n">this_data</span><span class="p">,</span>
+                <span class="n">id_type</span> <span class="o">=</span> <span class="n">key</span><span class="p">,</span>
+                <span class="n">target_id_type</span> <span class="o">=</span> <span class="n">id_type_b</span><span class="p">,</span>
+                <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">,</span>
+                <span class="n">lifetime</span> <span class="o">=</span> <span class="mi">600</span><span class="p">,</span>
+            <span class="p">)</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">tables</span><span class="p">[</span><span class="n">key</span><span class="p">]</span> <span class="o">=</span> <span class="n">table</span></div>
+
+
+
+<div class="viewcode-block" id="Mapper.remove_table">
+<a class="viewcode-back" href="../../../api/pypath.utils.mapping.Mapper.html#pypath.utils.mapping.Mapper.remove_table">[docs]</a>
+    <span class="k">def</span> <span class="nf">remove_table</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">id_type</span><span class="p">,</span> <span class="n">target_id_type</span><span class="p">,</span> <span class="n">ncbi_tax_id</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Removes the table defined by the ID types and organism.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">key</span> <span class="o">=</span> <span class="n">MappingTableKey</span><span class="p">(</span>
+            <span class="n">id_type</span> <span class="o">=</span> <span class="n">id_type</span><span class="p">,</span>
+            <span class="n">target_id_type</span> <span class="o">=</span> <span class="n">target_id_type</span><span class="p">,</span>
+            <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">,</span>
+        <span class="p">)</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">remove_key</span><span class="p">(</span><span class="n">key</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="Mapper.remove_key">
+<a class="viewcode-back" href="../../../api/pypath.utils.mapping.Mapper.html#pypath.utils.mapping.Mapper.remove_key">[docs]</a>
+    <span class="k">def</span> <span class="nf">remove_key</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">key</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Removes the table with key ``key`` if exists.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">if</span> <span class="n">key</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">tables</span><span class="p">:</span>
+
+            <span class="k">if</span> <span class="n">key</span> <span class="ow">and</span> <span class="nb">len</span><span class="p">(</span><span class="n">key</span><span class="p">)</span> <span class="o">==</span> <span class="mi">3</span><span class="p">:</span>
+
+                <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span>
+                    <span class="s1">&#39;Removing mapping table `</span><span class="si">%s</span><span class="s1">` &#39;</span>
+                    <span class="s1">&#39;to `</span><span class="si">%s</span><span class="s1">` for organism `</span><span class="si">%u</span><span class="s1">`.&#39;</span> <span class="o">%</span> <span class="n">key</span>
+                <span class="p">)</span>
+
+            <span class="k">del</span> <span class="bp">self</span><span class="o">.</span><span class="n">tables</span><span class="p">[</span><span class="n">key</span><span class="p">]</span></div>
+
+
+
+<div class="viewcode-block" id="Mapper.remove_expired">
+<a class="viewcode-back" href="../../../api/pypath.utils.mapping.Mapper.html#pypath.utils.mapping.Mapper.remove_expired">[docs]</a>
+    <span class="k">def</span> <span class="nf">remove_expired</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Removes tables last used a longer time ago than their lifetime.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">to_remove</span> <span class="o">=</span> <span class="nb">set</span><span class="p">()</span>
+
+        <span class="k">for</span> <span class="n">key</span><span class="p">,</span> <span class="n">table</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">tables</span><span class="p">):</span>
+
+            <span class="k">if</span> <span class="ow">not</span> <span class="n">table</span> <span class="ow">or</span> <span class="n">table</span><span class="o">.</span><span class="n">_expired</span><span class="p">():</span>
+
+                <span class="n">to_remove</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">key</span><span class="p">)</span>
+
+        <span class="k">for</span> <span class="n">key</span> <span class="ow">in</span> <span class="n">to_remove</span><span class="p">:</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">remove_key</span><span class="p">(</span><span class="n">key</span><span class="p">)</span></div>
+
+
+
+    <span class="k">def</span> <span class="fm">__del__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">if</span> <span class="nb">hasattr</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_mapper_cleanup_timeloop</span><span class="p">,</span> <span class="s1">&#39;stop&#39;</span><span class="p">):</span>
+
+            <span class="k">for</span> <span class="n">job</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">_mapper_cleanup_timeloop</span><span class="o">.</span><span class="n">jobs</span><span class="p">:</span>
+
+                <span class="k">if</span> <span class="n">job</span><span class="o">.</span><span class="n">is_alive</span><span class="p">():</span>
+
+                    <span class="n">job</span><span class="o">.</span><span class="n">stop</span><span class="p">()</span>
+                    <span class="n">job</span><span class="o">.</span><span class="n">stopped</span><span class="o">.</span><span class="n">set</span><span class="p">()</span></div>
+
+
+
+<div class="viewcode-block" id="init">
+<a class="viewcode-back" href="../../../api/pypath.utils.mapping.init.html#pypath.utils.mapping.init">[docs]</a>
+<span class="k">def</span> <span class="nf">init</span><span class="p">(</span><span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Create a new `Mapper` instance under the `mapper` attribute of this</span>
+<span class="sd">    module.</span>
+
+<span class="sd">    Returns</span>
+<span class="sd">        None.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="k">if</span> <span class="s1">&#39;mapper&#39;</span> <span class="ow">in</span> <span class="nb">globals</span><span class="p">():</span>
+
+        <span class="nb">globals</span><span class="p">()[</span><span class="s1">&#39;mapper&#39;</span><span class="p">]</span><span class="o">.</span><span class="fm">__del__</span><span class="p">()</span>
+
+    <span class="nb">globals</span><span class="p">()[</span><span class="s1">&#39;mapper&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">Mapper</span><span class="p">(</span><span class="o">**</span><span class="n">kwargs</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="get_mapper">
+<a class="viewcode-back" href="../../../api/pypath.utils.mapping.get_mapper.html#pypath.utils.mapping.get_mapper">[docs]</a>
+<span class="k">def</span> <span class="nf">get_mapper</span><span class="p">(</span><span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    The module under its `mapper` attribute has an instance of the `Mapper`</span>
+<span class="sd">    object, which manages the ID translations. This function creates the</span>
+<span class="sd">    instance if does not exist and returns it.</span>
+
+<span class="sd">    Returns</span>
+<span class="sd">        A Mapper object.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="k">if</span> <span class="s1">&#39;mapper&#39;</span> <span class="ow">not</span> <span class="ow">in</span> <span class="nb">globals</span><span class="p">():</span>
+
+        <span class="n">init</span><span class="p">(</span><span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
+
+    <span class="k">return</span> <span class="nb">globals</span><span class="p">()[</span><span class="s1">&#39;mapper&#39;</span><span class="p">]</span></div>
+
+
+
+<div class="viewcode-block" id="map_name">
+<a class="viewcode-back" href="../../../api/pypath.utils.mapping.map_name.html#pypath.utils.mapping.map_name">[docs]</a>
+<span class="k">def</span> <span class="nf">map_name</span><span class="p">(</span>
+        <span class="n">name</span><span class="p">,</span>
+        <span class="n">id_type</span><span class="p">,</span>
+        <span class="n">target_id_type</span><span class="p">,</span>
+        <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+        <span class="n">strict</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+        <span class="n">expand_complexes</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
+        <span class="n">uniprot_cleanup</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
+    <span class="p">):</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Translates one instance of one ID type to a different one.</span>
+<span class="sd">    Returns set of the target ID type.</span>
+
+<span class="sd">    This function should be used to convert individual IDs.</span>
+<span class="sd">    It takes care about everything and ideally you don&#39;t need to</span>
+<span class="sd">    think on the details.</span>
+
+<span class="sd">    How does it work: looks up dictionaries between the original</span>
+<span class="sd">    and target ID type, if doesn&#39;t find, attempts to load from the</span>
+<span class="sd">    predefined inputs.</span>
+<span class="sd">    If the original name is genesymbol, first it looks up among the</span>
+<span class="sd">    preferred gene names from UniProt, if not found, it takes an</span>
+<span class="sd">    attempt with the alternative gene names. If the gene symbol</span>
+<span class="sd">    still couldn&#39;t be found, and strict = False, the last attempt</span>
+<span class="sd">    only the first 5 characters of the gene symbol matched. If the</span>
+<span class="sd">    target name type is uniprot, then it converts all the ACs to</span>
+<span class="sd">    primary. Then, for the Trembl IDs it looks up the preferred gene</span>
+<span class="sd">    names, and find Swissprot IDs with the same preferred gene name.</span>
+
+<span class="sd">    Args</span>
+<span class="sd">        name (str): The original name to be converted.</span>
+<span class="sd">        id_type (str): The type of the name. Available by default:</span>
+<span class="sd">            - genesymbol (gene name)</span>
+<span class="sd">            - entrez (Entrez Gene ID \[#\])</span>
+<span class="sd">            - refseqp (NCBI RefSeq Protein ID \[NP\_\*|XP\_\*\])</span>
+<span class="sd">            - ensp (Ensembl protein ID \[ENSP\*\])</span>
+<span class="sd">            - enst (Ensembl transcript ID \[ENST\*\])</span>
+<span class="sd">            - ensg (Ensembl genomic DNA ID \[ENSG\*\])</span>
+<span class="sd">            - hgnc (HGNC ID \[HGNC:#\])</span>
+<span class="sd">            - gi (GI number \[#\])</span>
+<span class="sd">            - embl (DDBJ/EMBL/GeneBank CDS accession)</span>
+<span class="sd">            - embl_id (DDBJ/EMBL/GeneBank accession)</span>
+<span class="sd">            And many more, see the code of</span>
+<span class="sd">            ``pypath.internals.input_formats``</span>
+<span class="sd">        target_id_type (str): The name type to translate to, more or</span>
+<span class="sd">            less the same values are available as for ``id_type``.</span>
+<span class="sd">        ncbi_tax_id (int): NCBI Taxonomy ID of the organism.</span>
+<span class="sd">        strict (bool): In case a Gene Symbol can not be translated,</span>
+<span class="sd">            try to add number &quot;1&quot; to the end, or try to match only</span>
+<span class="sd">            its first five characters. This option is rarely used,</span>
+<span class="sd">            but it makes possible to translate some non-standard</span>
+<span class="sd">            gene names typically found in old, unmaintained resources.</span>
+<span class="sd">        expand_complexes (bool): When encountering complexes,</span>
+<span class="sd">            translated the IDs of its components and return a set</span>
+<span class="sd">            of IDs. The alternative behaviour is to return the</span>
+<span class="sd">            `Complex` objects.</span>
+<span class="sd">        uniprot_cleanup (bool): When the `target_id_type` is UniProt</span>
+<span class="sd">            ID, call the `uniprot_cleanup` function at the end.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="n">mapper</span> <span class="o">=</span> <span class="n">get_mapper</span><span class="p">()</span>
+
+    <span class="k">return</span> <span class="n">mapper</span><span class="o">.</span><span class="n">map_name</span><span class="p">(</span>
+        <span class="n">name</span> <span class="o">=</span> <span class="n">name</span><span class="p">,</span>
+        <span class="n">id_type</span> <span class="o">=</span> <span class="n">id_type</span><span class="p">,</span>
+        <span class="n">target_id_type</span> <span class="o">=</span> <span class="n">target_id_type</span><span class="p">,</span>
+        <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">,</span>
+        <span class="n">strict</span> <span class="o">=</span> <span class="n">strict</span><span class="p">,</span>
+        <span class="n">expand_complexes</span> <span class="o">=</span> <span class="n">expand_complexes</span><span class="p">,</span>
+        <span class="n">uniprot_cleanup</span> <span class="o">=</span> <span class="n">uniprot_cleanup</span><span class="p">,</span>
+    <span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="map_name0">
+<a class="viewcode-back" href="../../../api/pypath.utils.mapping.map_name0.html#pypath.utils.mapping.map_name0">[docs]</a>
+<span class="k">def</span> <span class="nf">map_name0</span><span class="p">(</span>
+        <span class="n">name</span><span class="p">,</span>
+        <span class="n">id_type</span><span class="p">,</span>
+        <span class="n">target_id_type</span><span class="p">,</span>
+        <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+        <span class="n">strict</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+        <span class="n">expand_complexes</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
+        <span class="n">uniprot_cleanup</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
+    <span class="p">):</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Translates the name and returns only one of the resulted IDs. It</span>
+<span class="sd">    means in case of ambiguous ID translation, a random one of them</span>
+<span class="sd">    will be picked and returned. Recommended to use only if the</span>
+<span class="sd">    translation between the given ID types is mostly unambigous and</span>
+<span class="sd">    the loss of information can be ignored. See more details at</span>
+<span class="sd">    `map_name`.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="n">mapper</span> <span class="o">=</span> <span class="n">get_mapper</span><span class="p">()</span>
+
+    <span class="k">return</span> <span class="n">mapper</span><span class="o">.</span><span class="n">map_name0</span><span class="p">(</span>
+        <span class="n">name</span> <span class="o">=</span> <span class="n">name</span><span class="p">,</span>
+        <span class="n">id_type</span> <span class="o">=</span> <span class="n">id_type</span><span class="p">,</span>
+        <span class="n">target_id_type</span> <span class="o">=</span> <span class="n">target_id_type</span><span class="p">,</span>
+        <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">,</span>
+        <span class="n">strict</span> <span class="o">=</span> <span class="n">strict</span><span class="p">,</span>
+        <span class="n">expand_complexes</span> <span class="o">=</span> <span class="n">expand_complexes</span><span class="p">,</span>
+        <span class="n">uniprot_cleanup</span> <span class="o">=</span> <span class="n">uniprot_cleanup</span><span class="p">,</span>
+    <span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="map_names">
+<a class="viewcode-back" href="../../../api/pypath.utils.mapping.map_names.html#pypath.utils.mapping.map_names">[docs]</a>
+<span class="k">def</span> <span class="nf">map_names</span><span class="p">(</span>
+        <span class="n">names</span><span class="p">,</span>
+        <span class="n">id_type</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+        <span class="n">target_id_type</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+        <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+        <span class="n">strict</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+        <span class="n">expand_complexes</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
+        <span class="n">uniprot_cleanup</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
+    <span class="p">):</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Same as ``map_name`` but translates multiple IDs at once. These two</span>
+<span class="sd">    functions could be seamlessly implemented as one, still I created</span>
+<span class="sd">    separate functions to always make it explicit if a set of translated</span>
+<span class="sd">    IDs come from multiple original IDs.</span>
+
+<span class="sd">    Args</span>
+<span class="sd">        name (str): The original name to be converted.</span>
+<span class="sd">        id_type (str): The type of the name. Available by default:</span>
+<span class="sd">            - genesymbol (gene name)</span>
+<span class="sd">            - entrez (Entrez Gene ID \[#\])</span>
+<span class="sd">            - refseqp (NCBI RefSeq Protein ID \[NP\_\*|XP\_\*\])</span>
+<span class="sd">            - ensp (Ensembl protein ID \[ENSP\*\])</span>
+<span class="sd">            - enst (Ensembl transcript ID \[ENST\*\])</span>
+<span class="sd">            - ensg (Ensembl genomic DNA ID \[ENSG\*\])</span>
+<span class="sd">            - hgnc (HGNC ID \[HGNC:#\])</span>
+<span class="sd">            - gi (GI number \[#\])</span>
+<span class="sd">            - embl (DDBJ/EMBL/GeneBank CDS accession)</span>
+<span class="sd">            - embl_id (DDBJ/EMBL/GeneBank accession)</span>
+<span class="sd">            And many more, see the code of</span>
+<span class="sd">            ``pypath.internals.input_formats``</span>
+<span class="sd">        target_id_type (str): The name type to translate to, more or</span>
+<span class="sd">            less the same values are available as for ``id_type``.</span>
+<span class="sd">        ncbi_tax_id (int): NCBI Taxonomy ID of the organism.</span>
+<span class="sd">        strict (bool): In case a Gene Symbol can not be translated,</span>
+<span class="sd">            try to add number &quot;1&quot; to the end, or try to match only</span>
+<span class="sd">            its first five characters. This option is rarely used,</span>
+<span class="sd">            but it makes possible to translate some non-standard</span>
+<span class="sd">            gene names typically found in old, unmaintained resources.</span>
+<span class="sd">        expand_complexes (bool): When encountering complexes,</span>
+<span class="sd">            translated the IDs of its components and return a set</span>
+<span class="sd">            of IDs. The alternative behaviour is to return the</span>
+<span class="sd">            `Complex` objects.</span>
+<span class="sd">        uniprot_cleanup (bool): When the `target_id_type` is UniProt</span>
+<span class="sd">            ID, call the `Mapper.uniprot_cleanup` function at the end.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="n">mapper</span> <span class="o">=</span> <span class="n">get_mapper</span><span class="p">()</span>
+
+    <span class="k">return</span> <span class="n">mapper</span><span class="o">.</span><span class="n">map_names</span><span class="p">(</span>
+        <span class="n">names</span> <span class="o">=</span> <span class="n">names</span><span class="p">,</span>
+        <span class="n">id_type</span> <span class="o">=</span> <span class="n">id_type</span><span class="p">,</span>
+        <span class="n">target_id_type</span> <span class="o">=</span> <span class="n">target_id_type</span><span class="p">,</span>
+        <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">,</span>
+        <span class="n">strict</span> <span class="o">=</span> <span class="n">strict</span><span class="p">,</span>
+        <span class="n">expand_complexes</span> <span class="o">=</span> <span class="n">expand_complexes</span><span class="p">,</span>
+        <span class="n">uniprot_cleanup</span> <span class="o">=</span> <span class="n">uniprot_cleanup</span><span class="p">,</span>
+    <span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="label">
+<a class="viewcode-back" href="../../../api/pypath.utils.mapping.label.html#pypath.utils.mapping.label">[docs]</a>
+<span class="k">def</span> <span class="nf">label</span><span class="p">(</span><span class="n">name</span><span class="p">,</span> <span class="n">id_type</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span> <span class="n">entity_type</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span> <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">):</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    For any kind of entity, either protein, miRNA or protein complex,</span>
+<span class="sd">    returns the preferred human readable label. For proteins this means</span>
+<span class="sd">    Gene Symbols, for miRNAs miRNA names, for complexes a series of</span>
+<span class="sd">    Gene Symbols.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="n">mapper</span> <span class="o">=</span> <span class="n">get_mapper</span><span class="p">()</span>
+
+    <span class="k">return</span> <span class="n">mapper</span><span class="o">.</span><span class="n">label</span><span class="p">(</span>
+        <span class="n">name</span> <span class="o">=</span> <span class="n">name</span><span class="p">,</span>
+        <span class="n">id_type</span> <span class="o">=</span> <span class="n">id_type</span><span class="p">,</span>
+        <span class="n">entity_type</span> <span class="o">=</span> <span class="n">entity_type</span><span class="p">,</span>
+        <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">,</span>
+    <span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="guess_type">
+<a class="viewcode-back" href="../../../api/pypath.utils.mapping.guess_type.html#pypath.utils.mapping.guess_type">[docs]</a>
+<span class="k">def</span> <span class="nf">guess_type</span><span class="p">(</span><span class="n">name</span><span class="p">,</span> <span class="n">entity_type</span> <span class="o">=</span> <span class="kc">None</span><span class="p">):</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    From a string, tries to guess the ID type and optionally the entity</span>
+<span class="sd">    type. Returns a tuple of strings: ID type and entity type.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="n">mapper</span> <span class="o">=</span> <span class="n">get_mapper</span><span class="p">()</span>
+
+    <span class="k">return</span> <span class="n">mapper</span><span class="o">.</span><span class="n">guess_type</span><span class="p">(</span><span class="n">name</span> <span class="o">=</span> <span class="n">name</span><span class="p">,</span> <span class="n">entity_type</span> <span class="o">=</span> <span class="n">entity_type</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="id_from_label">
+<a class="viewcode-back" href="../../../api/pypath.utils.mapping.id_from_label.html#pypath.utils.mapping.id_from_label">[docs]</a>
+<span class="k">def</span> <span class="nf">id_from_label</span><span class="p">(</span><span class="n">label</span><span class="p">,</span> <span class="n">label_id_type</span> <span class="o">=</span> <span class="s1">&#39;genesymbol&#39;</span><span class="p">,</span> <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="kc">None</span><span class="p">):</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    For a label (e.g. Gene Symbol) returns the corresponding IDs (e.g.</span>
+<span class="sd">    UniProt IDs).</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="n">mapper</span> <span class="o">=</span> <span class="n">get_mapper</span><span class="p">()</span>
+
+    <span class="k">return</span> <span class="n">mapper</span><span class="o">.</span><span class="n">id_from_label</span><span class="p">(</span>
+        <span class="n">label</span> <span class="o">=</span> <span class="n">label</span><span class="p">,</span>
+        <span class="n">label_id_type</span> <span class="o">=</span> <span class="n">label_id_type</span><span class="p">,</span>
+        <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">,</span>
+    <span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="id_from_label0">
+<a class="viewcode-back" href="../../../api/pypath.utils.mapping.id_from_label0.html#pypath.utils.mapping.id_from_label0">[docs]</a>
+<span class="k">def</span> <span class="nf">id_from_label0</span><span class="p">(</span><span class="n">label</span><span class="p">,</span> <span class="n">label_id_type</span> <span class="o">=</span> <span class="s1">&#39;genesymbol&#39;</span><span class="p">,</span> <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="kc">None</span><span class="p">):</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    For a label (e.g. Gene Symbol) returns a single ID (e.g. UniProt IDs).</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="n">mapper</span> <span class="o">=</span> <span class="n">get_mapper</span><span class="p">()</span>
+
+    <span class="k">return</span> <span class="n">mapper</span><span class="o">.</span><span class="n">id_from_label0</span><span class="p">(</span>
+        <span class="n">label</span> <span class="o">=</span> <span class="n">label</span><span class="p">,</span>
+        <span class="n">label_id_type</span> <span class="o">=</span> <span class="n">label_id_type</span><span class="p">,</span>
+        <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">,</span>
+    <span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="translation_dict">
+<a class="viewcode-back" href="../../../api/pypath.utils.mapping.translation_dict.html#pypath.utils.mapping.translation_dict">[docs]</a>
+<span class="k">def</span> <span class="nf">translation_dict</span><span class="p">(</span>
+        <span class="n">id_type</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
+        <span class="n">target_id_type</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
+        <span class="n">ncbi_tax_id</span><span class="p">:</span> <span class="nb">int</span> <span class="o">|</span> <span class="kc">None</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+    <span class="p">)</span> <span class="o">-&gt;</span> <span class="n">MappingTable</span> <span class="o">|</span> <span class="kc">None</span><span class="p">:</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Identifier translation table as a dict of sets.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="n">mapper</span> <span class="o">=</span> <span class="n">get_mapper</span><span class="p">()</span>
+
+    <span class="k">return</span> <span class="n">mapper</span><span class="o">.</span><span class="n">translation_dict</span><span class="p">(</span>
+        <span class="n">id_type</span> <span class="o">=</span> <span class="n">id_type</span><span class="p">,</span>
+        <span class="n">target_id_type</span> <span class="o">=</span> <span class="n">target_id_type</span><span class="p">,</span>
+        <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">,</span>
+    <span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="translation_df">
+<a class="viewcode-back" href="../../../api/pypath.utils.mapping.translation_df.html#pypath.utils.mapping.translation_df">[docs]</a>
+<span class="k">def</span> <span class="nf">translation_df</span><span class="p">(</span>
+        <span class="n">id_type</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
+        <span class="n">target_id_type</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
+        <span class="n">ncbi_tax_id</span><span class="p">:</span> <span class="nb">int</span> <span class="o">|</span> <span class="kc">None</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+    <span class="p">)</span> <span class="o">-&gt;</span> <span class="n">MappingTable</span> <span class="o">|</span> <span class="kc">None</span><span class="p">:</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Identifier translation table as a `pandas.DataFrame`.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="n">mapper</span> <span class="o">=</span> <span class="n">get_mapper</span><span class="p">()</span>
+
+    <span class="k">return</span> <span class="n">mapper</span><span class="o">.</span><span class="n">translation_df</span><span class="p">(</span>
+        <span class="n">id_type</span> <span class="o">=</span> <span class="n">id_type</span><span class="p">,</span>
+        <span class="n">target_id_type</span> <span class="o">=</span> <span class="n">target_id_type</span><span class="p">,</span>
+        <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">,</span>
+    <span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="mapping_tables">
+<a class="viewcode-back" href="../../../api/pypath.utils.mapping.mapping_tables.html#pypath.utils.mapping.mapping_tables">[docs]</a>
+<span class="k">def</span> <span class="nf">mapping_tables</span><span class="p">()</span> <span class="o">-&gt;</span> <span class="nb">list</span><span class="p">[</span><span class="n">MappingTableDefinition</span><span class="p">]:</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    A list of built-in mapping tables.</span>
+
+<span class="sd">    If `id_type_b` is `None`, that means translation to all other ID types</span>
+<span class="sd">    provided by the same resource is possible.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="k">return</span> <span class="n">get_mapper</span><span class="p">()</span><span class="o">.</span><span class="n">mapping_tables</span><span class="p">()</span></div>
+
+
+
+<div class="viewcode-block" id="id_types">
+<a class="viewcode-back" href="../../../api/pypath.utils.mapping.id_types.html#pypath.utils.mapping.id_types">[docs]</a>
+<span class="k">def</span> <span class="nf">id_types</span><span class="p">()</span> <span class="o">-&gt;</span> <span class="nb">list</span><span class="p">[</span><span class="n">IdType</span><span class="p">]:</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Identifier types with their labels.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="k">return</span> <span class="n">get_mapper</span><span class="p">()</span><span class="o">.</span><span class="n">id_types</span><span class="p">()</span></div>
+
+</pre></div>
+
+                </article>
+              
+              
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+              
+              
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diff --git a/_modules/pypath/utils/orthology.html b/_modules/pypath/utils/orthology.html
new file mode 100644
index 000000000..509c6db0e
--- /dev/null
+++ b/_modules/pypath/utils/orthology.html
@@ -0,0 +1,2980 @@
+
+<!DOCTYPE html>
+
+
+<html lang="en" data-content_root="../../../" >
+
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+    <meta charset="utf-8" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+    <title>pypath.utils.orthology &#8212; pypath 0.16.9 documentation</title>
+  
+  
+  
+  <script data-cfasync="false">
+    document.documentElement.dataset.mode = localStorage.getItem("mode") || "";
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+                  
+  <h1>Source code for pypath.utils.orthology</h1><div class="highlight"><pre>
+<span></span><span class="ch">#!/usr/bin/env python</span>
+<span class="c1"># -*- coding: utf-8 -*-</span>
+
+<span class="c1">#</span>
+<span class="c1">#  This file is part of the `pypath` python module</span>
+<span class="c1">#</span>
+<span class="c1">#  Copyright 2014-2023</span>
+<span class="c1">#  EMBL, EMBL-EBI, Uniklinik RWTH Aachen, Heidelberg University</span>
+<span class="c1">#</span>
+<span class="c1">#  Authors: see the file `README.rst`</span>
+<span class="c1">#  Contact: Dénes Türei (turei.denes@gmail.com)</span>
+<span class="c1">#</span>
+<span class="c1">#  Distributed under the GPLv3 License.</span>
+<span class="c1">#  See accompanying file LICENSE.txt or copy at</span>
+<span class="c1">#      https://www.gnu.org/licenses/gpl-3.0.html</span>
+<span class="c1">#</span>
+<span class="c1">#  Website: https://pypath.omnipathdb.org/</span>
+<span class="c1">#</span>
+
+<span class="kn">from</span> <span class="nn">__future__</span> <span class="kn">import</span> <span class="n">annotations</span>
+
+<span class="kn">from</span> <span class="nn">future.utils</span> <span class="kn">import</span> <span class="n">iteritems</span>
+<span class="kn">from</span> <span class="nn">past.builtins</span> <span class="kn">import</span> <span class="n">xrange</span><span class="p">,</span> <span class="nb">range</span>
+<span class="kn">from</span> <span class="nn">typing</span> <span class="kn">import</span> <span class="n">Literal</span>
+
+<span class="kn">import</span> <span class="nn">os</span>
+<span class="kn">import</span> <span class="nn">sys</span>
+<span class="kn">import</span> <span class="nn">itertools</span>
+<span class="kn">import</span> <span class="nn">functools</span>
+<span class="kn">import</span> <span class="nn">collections</span>
+<span class="kn">import</span> <span class="nn">importlib</span> <span class="k">as</span> <span class="nn">imp</span>
+<span class="kn">import</span> <span class="nn">re</span>
+<span class="kn">import</span> <span class="nn">time</span>
+<span class="kn">import</span> <span class="nn">datetime</span>
+<span class="kn">import</span> <span class="nn">json</span>
+<span class="kn">import</span> <span class="nn">pickle</span>
+<span class="kn">import</span> <span class="nn">copy</span>
+<span class="kn">import</span> <span class="nn">abc</span>
+<span class="kn">import</span> <span class="nn">inspect</span>
+<span class="kn">import</span> <span class="nn">types</span> <span class="k">as</span> <span class="nn">_types</span>
+
+<span class="kn">import</span> <span class="nn">timeloop</span>
+<span class="kn">import</span> <span class="nn">pandas</span> <span class="k">as</span> <span class="nn">pd</span>
+
+<span class="kn">import</span> <span class="nn">pypath.utils.mapping</span> <span class="k">as</span> <span class="nn">mapping</span>
+<span class="kn">import</span> <span class="nn">pypath.share.common</span> <span class="k">as</span> <span class="nn">common</span>
+<span class="kn">import</span> <span class="nn">pypath_common._constants</span> <span class="k">as</span> <span class="nn">_const</span>
+<span class="kn">import</span> <span class="nn">pypath.internals.intera</span> <span class="k">as</span> <span class="nn">intera</span>
+<span class="kn">import</span> <span class="nn">pypath.resources.urls</span> <span class="k">as</span> <span class="nn">urls</span>
+<span class="kn">import</span> <span class="nn">pypath.share.curl</span> <span class="k">as</span> <span class="nn">curl</span>
+<span class="kn">import</span> <span class="nn">pypath.inputs.uniprot</span> <span class="k">as</span> <span class="nn">uniprot_input</span>
+<span class="kn">import</span> <span class="nn">pypath.inputs.uniprot_db</span> <span class="k">as</span> <span class="nn">uniprot_db</span>
+<span class="kn">import</span> <span class="nn">pypath.inputs.homologene</span> <span class="k">as</span> <span class="nn">homologene_input</span>
+<span class="kn">import</span> <span class="nn">pypath.inputs.oma</span> <span class="k">as</span> <span class="nn">oma_input</span>
+<span class="kn">import</span> <span class="nn">pypath.inputs.biomart</span> <span class="k">as</span> <span class="nn">biomart</span>
+<span class="kn">import</span> <span class="nn">pypath.utils.seq</span> <span class="k">as</span> <span class="nn">_se</span>
+<span class="kn">import</span> <span class="nn">pypath.share.session</span> <span class="k">as</span> <span class="nn">session</span>
+<span class="kn">import</span> <span class="nn">pypath.share.settings</span> <span class="k">as</span> <span class="nn">settings</span>
+<span class="kn">import</span> <span class="nn">pypath.utils.taxonomy</span> <span class="k">as</span> <span class="nn">taxonomy</span>
+<span class="kn">import</span> <span class="nn">pypath.share.cache</span> <span class="k">as</span> <span class="nn">cache_mod</span>
+
+<span class="n">_orthology_cleanup_timeloop</span> <span class="o">=</span> <span class="n">timeloop</span><span class="o">.</span><span class="n">Timeloop</span><span class="p">()</span>
+<span class="n">_orthology_cleanup_timeloop</span><span class="o">.</span><span class="n">logger</span><span class="o">.</span><span class="n">setLevel</span><span class="p">(</span><span class="mi">9999</span><span class="p">)</span>
+
+<span class="n">_logger</span> <span class="o">=</span> <span class="n">session</span><span class="o">.</span><span class="n">Logger</span><span class="p">(</span><span class="n">name</span> <span class="o">=</span> <span class="s1">&#39;orthology&#39;</span><span class="p">)</span>
+<span class="n">_log</span> <span class="o">=</span> <span class="n">_logger</span><span class="o">.</span><span class="n">_log</span>
+
+
+<div class="viewcode-block" id="OrthologMeta">
+<a class="viewcode-back" href="../../../api/pypath.utils.orthology.OrthologMeta.html#pypath.utils.orthology.OrthologMeta">[docs]</a>
+<span class="k">class</span> <span class="nc">OrthologMeta</span><span class="p">(</span><span class="n">abc</span><span class="o">.</span><span class="n">ABCMeta</span><span class="p">):</span>
+
+
+    <span class="k">def</span> <span class="fm">__new__</span><span class="p">(</span>
+            <span class="bp">cls</span><span class="p">,</span>
+            <span class="n">name</span><span class="p">,</span>
+            <span class="n">supercls</span><span class="p">,</span>
+            <span class="n">attrs</span><span class="p">,</span>
+            <span class="n">resource</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
+            <span class="n">fields</span><span class="p">:</span> <span class="nb">tuple</span><span class="p">[</span><span class="nb">str</span><span class="p">]</span> <span class="o">=</span> <span class="p">(</span><span class="s1">&#39;id&#39;</span><span class="p">,),</span>
+        <span class="p">):</span>
+
+        <span class="n">Base</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">namedtuple</span><span class="p">(</span><span class="sa">f</span><span class="s1">&#39;</span><span class="si">{</span><span class="n">name</span><span class="si">}</span><span class="s1">Base&#39;</span><span class="p">,</span> <span class="n">fields</span><span class="p">)</span>
+
+        <span class="k">def</span> <span class="nf">new_method</span><span class="p">(</span><span class="bp">cls</span><span class="p">,</span> <span class="o">*</span><span class="n">args</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+
+            <span class="k">return</span> <span class="n">Base</span><span class="o">.</span><span class="fm">__new__</span><span class="p">(</span><span class="bp">cls</span><span class="p">,</span> <span class="o">*</span><span class="n">args</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
+
+        <span class="n">sig</span> <span class="o">=</span> <span class="n">inspect</span><span class="o">.</span><span class="n">signature</span><span class="p">(</span><span class="n">new_method</span><span class="p">)</span>
+        <span class="n">new_params</span> <span class="o">=</span> <span class="p">[</span>
+            <span class="n">inspect</span><span class="o">.</span><span class="n">Parameter</span><span class="p">(</span><span class="n">arg</span><span class="p">,</span> <span class="n">inspect</span><span class="o">.</span><span class="n">Parameter</span><span class="o">.</span><span class="n">POSITIONAL_OR_KEYWORD</span><span class="p">)</span>
+            <span class="k">for</span> <span class="n">arg</span> <span class="ow">in</span> <span class="n">fields</span>
+        <span class="p">]</span>
+        <span class="n">new_method</span><span class="o">.</span><span class="n">__signature__</span> <span class="o">=</span> <span class="n">sig</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span>
+            <span class="n">parameters</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="n">itertools</span><span class="o">.</span><span class="n">chain</span><span class="p">(</span>
+                <span class="p">(</span><span class="n">sig</span><span class="o">.</span><span class="n">parameters</span><span class="p">[</span><span class="s1">&#39;cls&#39;</span><span class="p">],),</span>
+                <span class="n">new_params</span><span class="p">,</span>
+            <span class="p">))</span>
+        <span class="p">)</span>
+
+        <span class="n">clazz</span> <span class="o">=</span> <span class="n">_types</span><span class="o">.</span><span class="n">new_class</span><span class="p">(</span><span class="n">name</span><span class="p">,</span> <span class="p">(</span><span class="n">Base</span><span class="p">,))</span>
+        <span class="nb">setattr</span><span class="p">(</span><span class="n">clazz</span><span class="p">,</span> <span class="s1">&#39;__new__&#39;</span><span class="p">,</span> <span class="n">new_method</span><span class="p">)</span>
+        <span class="nb">setattr</span><span class="p">(</span><span class="n">clazz</span><span class="p">,</span> <span class="s1">&#39;_resource&#39;</span><span class="p">,</span> <span class="n">resource</span><span class="p">)</span>
+        <span class="n">clazz</span><span class="o">.</span><span class="vm">__module__</span> <span class="o">=</span> <span class="vm">__name__</span>
+
+        <span class="k">return</span> <span class="n">clazz</span></div>
+
+
+
+<div class="viewcode-block" id="OrthologBase">
+<a class="viewcode-back" href="../../../api/pypath.utils.orthology.OrthologBase.html#pypath.utils.orthology.OrthologBase">[docs]</a>
+<span class="k">class</span> <span class="nc">OrthologBase</span><span class="p">:</span>
+
+
+    <span class="k">def</span> <span class="fm">__str__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">id</span>
+
+
+    <span class="k">def</span> <span class="fm">__repr__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="sa">f</span><span class="s1">&#39;&lt;Ortholog </span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">id</span><span class="si">}</span><span class="s1"> (</span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">_resource</span><span class="si">}</span><span class="s1">)&gt;&#39;</span>
+
+
+    <span class="k">def</span> <span class="fm">__eq__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">other</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="fm">__str__</span><span class="p">()</span> <span class="o">==</span> <span class="n">other</span><span class="o">.</span><span class="fm">__str__</span><span class="p">()</span>
+
+
+    <span class="k">def</span> <span class="fm">__hash__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">id</span><span class="o">.</span><span class="fm">__hash__</span><span class="p">()</span></div>
+
+
+
+<div class="viewcode-block" id="OmaOrtholog">
+<a class="viewcode-back" href="../../../api/pypath.utils.orthology.OmaOrtholog.html#pypath.utils.orthology.OmaOrtholog">[docs]</a>
+<span class="k">class</span> <span class="nc">OmaOrtholog</span><span class="p">(</span></div>
+
+        <span class="n">OrthologBase</span><span class="p">,</span>
+        <span class="n">metaclass</span> <span class="o">=</span> <span class="n">OrthologMeta</span><span class="p">,</span>
+        <span class="n">resource</span> <span class="o">=</span> <span class="s1">&#39;OMA&#39;</span><span class="p">,</span>
+        <span class="n">fields</span> <span class="o">=</span> <span class="p">(</span><span class="s1">&#39;id&#39;</span><span class="p">,</span> <span class="s1">&#39;rel_type&#39;</span><span class="p">,</span> <span class="s1">&#39;score&#39;</span><span class="p">),</span>
+    <span class="p">):</span> <span class="k">pass</span>
+
+
+
+<div class="viewcode-block" id="EnsemblOrtholog">
+<a class="viewcode-back" href="../../../api/pypath.utils.orthology.EnsemblOrtholog.html#pypath.utils.orthology.EnsemblOrtholog">[docs]</a>
+<span class="k">class</span> <span class="nc">EnsemblOrtholog</span><span class="p">(</span></div>
+
+        <span class="n">OrthologBase</span><span class="p">,</span>
+        <span class="n">metaclass</span> <span class="o">=</span> <span class="n">OrthologMeta</span><span class="p">,</span>
+        <span class="n">resource</span> <span class="o">=</span> <span class="s1">&#39;Ensembl&#39;</span><span class="p">,</span>
+        <span class="n">fields</span> <span class="o">=</span> <span class="p">(</span><span class="s1">&#39;id&#39;</span><span class="p">,</span> <span class="s1">&#39;types&#39;</span><span class="p">,</span> <span class="s1">&#39;hc&#39;</span><span class="p">),</span>
+    <span class="p">):</span> <span class="k">pass</span>
+
+
+<div class="viewcode-block" id="HomologeneOrtholog">
+<a class="viewcode-back" href="../../../api/pypath.utils.orthology.HomologeneOrtholog.html#pypath.utils.orthology.HomologeneOrtholog">[docs]</a>
+<span class="k">class</span> <span class="nc">HomologeneOrtholog</span><span class="p">(</span></div>
+
+        <span class="n">OrthologBase</span><span class="p">,</span>
+        <span class="n">metaclass</span> <span class="o">=</span> <span class="n">OrthologMeta</span><span class="p">,</span>
+        <span class="n">resource</span> <span class="o">=</span> <span class="s1">&#39;HomoloGene&#39;</span><span class="p">,</span>
+    <span class="p">):</span> <span class="k">pass</span>
+
+
+<span class="n">OrthologyTableKey</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">namedtuple</span><span class="p">(</span>
+    <span class="s1">&#39;OrthologyTableKey&#39;</span><span class="p">,</span>
+    <span class="p">(</span><span class="s1">&#39;source&#39;</span><span class="p">,</span> <span class="s1">&#39;target&#39;</span><span class="p">,</span> <span class="s1">&#39;only_swissprot&#39;</span><span class="p">,</span> <span class="s1">&#39;resource&#39;</span><span class="p">,</span> <span class="s1">&#39;id_type&#39;</span><span class="p">),</span>
+<span class="p">)</span>
+
+<div class="viewcode-block" id="OrthologyManager">
+<a class="viewcode-back" href="../../../api/pypath.utils.orthology.OrthologyManager.html#pypath.utils.orthology.OrthologyManager">[docs]</a>
+<span class="k">class</span> <span class="nc">OrthologyManager</span><span class="p">(</span><span class="n">session</span><span class="o">.</span><span class="n">Logger</span><span class="p">):</span>
+
+    <span class="n">TRANSLATION_PARAM</span> <span class="o">=</span> <span class="p">(</span>
+        <span class="s1">&#39;oma&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;homologene&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;oma_rel_type&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;oma_score&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;ensembl&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;ensembl_hc&#39;</span><span class="p">,</span>
+        <span class="s1">&#39;ensembl_types&#39;</span><span class="p">,</span>
+    <span class="p">)</span>
+    <span class="n">RESOURCE_PARAM</span> <span class="o">=</span> <span class="p">{</span>
+        <span class="s1">&#39;oma&#39;</span><span class="p">:</span> <span class="p">(</span><span class="s1">&#39;rel_type&#39;</span><span class="p">,</span> <span class="s1">&#39;score&#39;</span><span class="p">),</span>
+        <span class="s1">&#39;ensembl&#39;</span><span class="p">:</span> <span class="p">(</span><span class="s1">&#39;hc&#39;</span><span class="p">,</span> <span class="s1">&#39;types&#39;</span><span class="p">),</span>
+        <span class="s1">&#39;homologene&#39;</span><span class="p">:</span> <span class="p">(),</span>
+    <span class="p">}</span>
+
+<div class="viewcode-block" id="OrthologyManager.__init__">
+<a class="viewcode-back" href="../../../api/pypath.utils.orthology.OrthologyManager.html#pypath.utils.orthology.OrthologyManager.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">cleanup_period</span><span class="p">:</span> <span class="nb">int</span> <span class="o">=</span> <span class="mi">10</span><span class="p">,</span>
+            <span class="n">lifetime</span><span class="p">:</span> <span class="nb">int</span> <span class="o">=</span> <span class="mi">300</span><span class="p">,</span>
+            <span class="o">**</span><span class="n">kwargs</span>
+        <span class="p">):</span>
+
+        <span class="n">session</span><span class="o">.</span><span class="n">Logger</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">name</span> <span class="o">=</span> <span class="s1">&#39;orthology&#39;</span><span class="p">)</span>
+
+
+        <span class="nd">@_orthology_cleanup_timeloop</span><span class="o">.</span><span class="n">job</span><span class="p">(</span>
+            <span class="n">interval</span> <span class="o">=</span> <span class="n">datetime</span><span class="o">.</span><span class="n">timedelta</span><span class="p">(</span>
+                <span class="n">seconds</span> <span class="o">=</span> <span class="n">cleanup_period</span>
+            <span class="p">)</span>
+        <span class="p">)</span>
+        <span class="k">def</span> <span class="nf">_cleanup</span><span class="p">():</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">_remove_expired</span><span class="p">()</span>
+
+
+        <span class="n">_orthology_cleanup_timeloop</span><span class="o">.</span><span class="n">start</span><span class="p">(</span><span class="n">block</span> <span class="o">=</span> <span class="kc">False</span><span class="p">)</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">lifetime</span> <span class="o">=</span> <span class="n">lifetime</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">tables</span> <span class="o">=</span> <span class="p">{}</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">expiry</span> <span class="o">=</span> <span class="p">{}</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">_param</span> <span class="o">=</span> <span class="p">{</span><span class="n">k</span><span class="p">:</span> <span class="n">kwargs</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="n">k</span><span class="p">,</span> <span class="kc">None</span><span class="p">)</span> <span class="k">for</span> <span class="n">k</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">TRANSLATION_PARAM</span><span class="p">}</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span><span class="s1">&#39;OrthologyManager has been created.&#39;</span><span class="p">)</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">reload</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="n">modname</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="vm">__class__</span><span class="o">.</span><span class="vm">__module__</span>
+        <span class="n">mod</span> <span class="o">=</span> <span class="nb">__import__</span><span class="p">(</span><span class="n">modname</span><span class="p">,</span> <span class="n">fromlist</span><span class="o">=</span><span class="p">[</span><span class="n">modname</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;.&#39;</span><span class="p">)[</span><span class="mi">0</span><span class="p">]])</span>
+        <span class="n">imp</span><span class="o">.</span><span class="n">reload</span><span class="p">(</span><span class="n">mod</span><span class="p">)</span>
+        <span class="n">new</span> <span class="o">=</span> <span class="nb">getattr</span><span class="p">(</span><span class="n">mod</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="vm">__class__</span><span class="o">.</span><span class="vm">__name__</span><span class="p">)</span>
+        <span class="nb">setattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">&#39;__class__&#39;</span><span class="p">,</span> <span class="n">new</span><span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">which_table</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">target</span><span class="p">:</span> <span class="nb">str</span> <span class="o">|</span> <span class="nb">int</span><span class="p">,</span>
+            <span class="n">source</span><span class="p">:</span> <span class="nb">str</span> <span class="o">|</span> <span class="nb">int</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">,</span>
+            <span class="n">only_swissprot</span><span class="p">:</span> <span class="nb">bool</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
+            <span class="n">resource</span><span class="p">:</span> <span class="n">Literal</span><span class="p">[</span><span class="s1">&#39;oma&#39;</span><span class="p">,</span> <span class="s1">&#39;homologene&#39;</span><span class="p">,</span> <span class="s1">&#39;ensembl&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="s1">&#39;oma&#39;</span><span class="p">,</span>
+            <span class="n">id_type</span><span class="p">:</span> <span class="nb">str</span> <span class="o">=</span> <span class="s1">&#39;uniprot&#39;</span><span class="p">,</span>
+        <span class="p">):</span>
+
+        <span class="n">loc</span> <span class="o">=</span> <span class="nb">locals</span><span class="p">()</span>
+        <span class="n">key</span> <span class="o">=</span> <span class="n">OrthologyTableKey</span><span class="p">(</span><span class="o">**</span><span class="p">{</span>
+            <span class="n">f</span><span class="p">:</span> <span class="n">loc</span><span class="p">[</span><span class="n">f</span><span class="p">]</span>
+            <span class="k">for</span> <span class="n">f</span> <span class="ow">in</span> <span class="n">OrthologyTableKey</span><span class="o">.</span><span class="n">_fields</span>
+        <span class="p">})</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">expiry</span><span class="p">[</span><span class="n">key</span><span class="p">]</span> <span class="o">=</span> <span class="n">time</span><span class="o">.</span><span class="n">time</span><span class="p">()</span>
+
+        <span class="k">if</span> <span class="n">key</span> <span class="ow">not</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">tables</span><span class="p">:</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">load</span><span class="p">(</span><span class="n">key</span><span class="p">)</span>
+
+        <span class="k">if</span> <span class="n">key</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">tables</span><span class="p">:</span>
+
+            <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">tables</span><span class="p">[</span><span class="n">key</span><span class="p">]</span>
+
+
+    <span class="k">def</span> <span class="nf">load</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">key</span><span class="p">):</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">tables</span><span class="p">[</span><span class="n">key</span><span class="p">]</span> <span class="o">=</span> <span class="nb">globals</span><span class="p">()[</span><span class="sa">f</span><span class="s1">&#39;</span><span class="si">{</span><span class="n">key</span><span class="o">.</span><span class="n">resource</span><span class="o">.</span><span class="n">capitalize</span><span class="p">()</span><span class="si">}</span><span class="s1">Orthology&#39;</span><span class="p">](</span>
+            <span class="n">target</span> <span class="o">=</span> <span class="n">key</span><span class="o">.</span><span class="n">target</span><span class="p">,</span>
+            <span class="n">source</span> <span class="o">=</span> <span class="n">key</span><span class="o">.</span><span class="n">source</span><span class="p">,</span>
+            <span class="n">only_swissprot</span> <span class="o">=</span> <span class="n">key</span><span class="o">.</span><span class="n">only_swissprot</span><span class="p">,</span>
+            <span class="n">id_type</span> <span class="o">=</span> <span class="n">key</span><span class="o">.</span><span class="n">id_type</span><span class="p">,</span>
+        <span class="p">)</span>
+
+
+<div class="viewcode-block" id="OrthologyManager.translate">
+<a class="viewcode-back" href="../../../api/pypath.utils.orthology.OrthologyManager.html#pypath.utils.orthology.OrthologyManager.translate">[docs]</a>
+    <span class="nd">@common</span><span class="o">.</span><span class="n">ignore_unhashable</span>
+    <span class="nd">@functools</span><span class="o">.</span><span class="n">lru_cache</span><span class="p">(</span><span class="n">maxsize</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="mf">1e5</span><span class="p">))</span>
+    <span class="k">def</span> <span class="nf">translate</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">identifiers</span><span class="p">:</span> <span class="nb">str</span> <span class="o">|</span> <span class="n">Iterable</span><span class="p">[</span><span class="nb">str</span><span class="p">],</span>
+            <span class="n">target</span><span class="p">:</span> <span class="nb">str</span> <span class="o">|</span> <span class="nb">int</span><span class="p">,</span>
+            <span class="n">source</span><span class="p">:</span> <span class="nb">str</span> <span class="o">|</span> <span class="nb">int</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">,</span>
+            <span class="n">id_type</span><span class="p">:</span> <span class="nb">str</span> <span class="o">=</span> <span class="s1">&#39;uniprot&#39;</span><span class="p">,</span>
+            <span class="n">only_swissprot</span><span class="p">:</span> <span class="nb">bool</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
+            <span class="n">oma</span><span class="p">:</span> <span class="nb">bool</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">homologene</span><span class="p">:</span> <span class="nb">bool</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">ensembl</span><span class="p">:</span> <span class="nb">bool</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">oma_rel_type</span><span class="p">:</span> <span class="p">(</span>
+                <span class="nb">set</span><span class="p">[</span><span class="n">Literal</span><span class="p">[</span><span class="s1">&#39;1:1&#39;</span><span class="p">,</span> <span class="s1">&#39;1:n&#39;</span><span class="p">,</span> <span class="s1">&#39;m:1&#39;</span><span class="p">,</span> <span class="s1">&#39;m:n&#39;</span><span class="p">]]</span> <span class="o">|</span>
+                <span class="kc">None</span>
+            <span class="p">)</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">oma_score</span><span class="p">:</span> <span class="nb">float</span> <span class="o">|</span> <span class="kc">None</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">ensembl_hc</span><span class="p">:</span> <span class="nb">bool</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
+            <span class="n">ensembl_types</span><span class="p">:</span> <span class="p">(</span>
+                <span class="nb">list</span><span class="p">[</span><span class="n">Literal</span><span class="p">[</span><span class="s1">&#39;one2one&#39;</span><span class="p">,</span> <span class="s1">&#39;one2many&#39;</span><span class="p">,</span> <span class="s1">&#39;many2many&#39;</span><span class="p">]]</span> <span class="o">|</span>
+                <span class="kc">None</span>
+            <span class="p">)</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">full_records</span><span class="p">:</span> <span class="nb">bool</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+        <span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Translate one or more identifiers by orthologous gene pairs.</span>
+
+<span class="sd">        Args:</span>
+<span class="sd">            identifiers:</span>
+<span class="sd">                One or more identifers of the source organism, of ID type</span>
+<span class="sd">                `id_type`.</span>
+<span class="sd">            target:</span>
+<span class="sd">                Name or NCBI Taxonomy ID of the target organism.</span>
+<span class="sd">            source:</span>
+<span class="sd">                Name or NCBI Taxonomy ID of the source organism.</span>
+<span class="sd">            id_type:</span>
+<span class="sd">                The identifier type to use.</span>
+<span class="sd">            only_swissprot:</span>
+<span class="sd">                Use only SwissProt IDs.</span>
+<span class="sd">            oma</span>
+<span class="sd">                Use orthology information from the Orthologous Matrix (OMA).</span>
+<span class="sd">                Currently this is the recommended source for orthology data.</span>
+<span class="sd">            homologene:</span>
+<span class="sd">                Use orthology information from NCBI HomoloGene.</span>
+<span class="sd">            ensembl:</span>
+<span class="sd">                Use orthology information from Ensembl.</span>
+<span class="sd">            oma_rel_type:</span>
+<span class="sd">                Restrict relations to certain types.</span>
+<span class="sd">            oma_score:</span>
+<span class="sd">                Lower threshold for similarity metric.</span>
+<span class="sd">            ensembl_hc:</span>
+<span class="sd">                Use only the high confidence orthology relations from Ensembl.</span>
+<span class="sd">            ensembl_types:</span>
+<span class="sd">                Ensembl orthology relation types to use. Possible values are</span>
+<span class="sd">                `one2one`, `one2many` and `many2many`. By default only</span>
+<span class="sd">                `one2one` is used.</span>
+<span class="sd">            full_records:</span>
+<span class="sd">                Include not only the identifiers, but also some properties of</span>
+<span class="sd">                the orthology relationships.</span>
+
+<span class="sd">        Returns:</span>
+<span class="sd">            Set of identifiers of orthologous genes or proteins in the</span>
+<span class="sd">            target taxon.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">target</span> <span class="o">=</span> <span class="n">taxonomy</span><span class="o">.</span><span class="n">ensure_ncbi_tax_id</span><span class="p">(</span><span class="n">target</span><span class="p">)</span>
+        <span class="n">source</span> <span class="o">=</span> <span class="n">taxonomy</span><span class="o">.</span><span class="n">ensure_ncbi_tax_id</span><span class="p">(</span><span class="n">source</span><span class="p">)</span>
+        <span class="n">param</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_translation_param</span><span class="p">(</span><span class="nb">locals</span><span class="p">())</span>
+        <span class="n">proc</span> <span class="o">=</span> <span class="p">(</span><span class="k">lambda</span> <span class="n">x</span><span class="p">:</span> <span class="n">x</span><span class="p">)</span> <span class="k">if</span> <span class="n">full_records</span> <span class="k">else</span> <span class="p">(</span><span class="k">lambda</span> <span class="n">x</span><span class="p">:</span> <span class="n">x</span><span class="o">.</span><span class="n">id</span><span class="p">)</span>
+
+        <span class="n">result</span> <span class="o">=</span> <span class="nb">set</span><span class="p">()</span>
+
+        <span class="k">for</span> <span class="n">resource</span><span class="p">,</span> <span class="n">keys</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">RESOURCE_PARAM</span><span class="o">.</span><span class="n">items</span><span class="p">():</span>
+
+            <span class="k">if</span> <span class="ow">not</span> <span class="n">param</span><span class="p">[</span><span class="n">resource</span><span class="p">]:</span>
+
+                <span class="k">continue</span>
+
+            <span class="n">table</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">which_table</span><span class="p">(</span>
+                <span class="n">target</span> <span class="o">=</span> <span class="n">target</span><span class="p">,</span>
+                <span class="n">source</span> <span class="o">=</span> <span class="n">source</span><span class="p">,</span>
+                <span class="n">only_swissprot</span> <span class="o">=</span> <span class="n">only_swissprot</span><span class="p">,</span>
+                <span class="n">id_type</span> <span class="o">=</span> <span class="n">id_type</span><span class="p">,</span>
+                <span class="n">resource</span> <span class="o">=</span> <span class="n">resource</span><span class="p">,</span>
+            <span class="p">)</span>
+
+            <span class="n">result</span><span class="o">.</span><span class="n">update</span><span class="p">(</span>
+                <span class="n">table</span><span class="o">.</span><span class="n">translate</span><span class="p">(</span>
+                    <span class="n">identifiers</span><span class="p">,</span>
+                    <span class="n">full_records</span> <span class="o">=</span> <span class="n">full_records</span><span class="p">,</span>
+                    <span class="o">**</span><span class="p">{</span><span class="n">k</span><span class="p">:</span> <span class="n">v</span> <span class="k">for</span> <span class="n">k</span><span class="p">,</span> <span class="n">v</span> <span class="ow">in</span> <span class="n">param</span><span class="o">.</span><span class="n">items</span><span class="p">()</span> <span class="k">if</span> <span class="n">k</span> <span class="ow">in</span> <span class="n">keys</span><span class="p">},</span>
+                <span class="p">)</span>
+            <span class="p">)</span>
+
+        <span class="k">return</span> <span class="n">result</span></div>
+
+
+
+<div class="viewcode-block" id="OrthologyManager.get_dict">
+<a class="viewcode-back" href="../../../api/pypath.utils.orthology.OrthologyManager.html#pypath.utils.orthology.OrthologyManager.get_dict">[docs]</a>
+    <span class="k">def</span> <span class="nf">get_dict</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">target</span><span class="p">:</span> <span class="nb">str</span> <span class="o">|</span> <span class="nb">int</span><span class="p">,</span>
+            <span class="n">source</span><span class="p">:</span> <span class="nb">str</span> <span class="o">|</span> <span class="nb">int</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">,</span>
+            <span class="n">id_type</span><span class="p">:</span> <span class="nb">str</span> <span class="o">=</span> <span class="s1">&#39;uniprot&#39;</span><span class="p">,</span>
+            <span class="n">only_swissprot</span><span class="p">:</span> <span class="nb">bool</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
+            <span class="n">oma</span><span class="p">:</span> <span class="nb">bool</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">homologene</span><span class="p">:</span> <span class="nb">bool</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">ensembl</span><span class="p">:</span> <span class="nb">bool</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">oma_rel_type</span><span class="p">:</span> <span class="p">(</span>
+                <span class="nb">set</span><span class="p">[</span><span class="n">Literal</span><span class="p">[</span><span class="s1">&#39;1:1&#39;</span><span class="p">,</span> <span class="s1">&#39;1:n&#39;</span><span class="p">,</span> <span class="s1">&#39;m:1&#39;</span><span class="p">,</span> <span class="s1">&#39;m:n&#39;</span><span class="p">]]</span> <span class="o">|</span>
+                <span class="kc">None</span>
+            <span class="p">)</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">oma_score</span><span class="p">:</span> <span class="nb">float</span> <span class="o">|</span> <span class="kc">None</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">ensembl_hc</span><span class="p">:</span> <span class="nb">bool</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
+            <span class="n">ensembl_types</span><span class="p">:</span> <span class="p">(</span>
+                <span class="nb">list</span><span class="p">[</span><span class="n">Literal</span><span class="p">[</span><span class="s1">&#39;one2one&#39;</span><span class="p">,</span> <span class="s1">&#39;one2many&#39;</span><span class="p">,</span> <span class="s1">&#39;many2many&#39;</span><span class="p">]]</span> <span class="o">|</span>
+                <span class="kc">None</span>
+            <span class="p">)</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">full_records</span><span class="p">:</span> <span class="nb">bool</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+        <span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">dict</span><span class="p">[</span><span class="nb">str</span><span class="p">,</span> <span class="nb">set</span><span class="p">[</span><span class="n">OrthologBase</span><span class="p">]]:</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Create a dictionary for one source organism and ID type.</span>
+
+<span class="sd">        Args:</span>
+<span class="sd">            target:</span>
+<span class="sd">                Name or NCBI Taxonomy ID of the target organism.</span>
+<span class="sd">            source:</span>
+<span class="sd">                Name or NCBI Taxonomy ID of the source organism.</span>
+<span class="sd">            id_type:</span>
+<span class="sd">                The identifier type to use.</span>
+<span class="sd">            only_swissprot:</span>
+<span class="sd">                Use only SwissProt IDs.</span>
+<span class="sd">            oma</span>
+<span class="sd">                Use orthology information from the Orthologous Matrix (OMA).</span>
+<span class="sd">                Currently this is the recommended source for orthology data.</span>
+<span class="sd">            homologene:</span>
+<span class="sd">                Use orthology information from NCBI HomoloGene.</span>
+<span class="sd">            ensembl:</span>
+<span class="sd">                Use orthology information from Ensembl.</span>
+<span class="sd">            oma_rel_type:</span>
+<span class="sd">                Restrict relations to certain types.</span>
+<span class="sd">            oma_score:</span>
+<span class="sd">                Lower threshold for similarity metric.</span>
+<span class="sd">            ensembl_hc:</span>
+<span class="sd">                Use only the high confidence orthology relations from Ensembl.</span>
+<span class="sd">            ensembl_types:</span>
+<span class="sd">                Ensembl orthology relation types to use. Possible values are</span>
+<span class="sd">                `one2one`, `one2many` and `many2many`. By default only</span>
+<span class="sd">                `one2one` is used.</span>
+<span class="sd">            full_records:</span>
+<span class="sd">                Include not only the identifiers, but also some properties of</span>
+<span class="sd">                the orthology relationships.</span>
+
+<span class="sd">        Returns:</span>
+<span class="sd">            A dict with identifiers of the source organism as keys, and</span>
+<span class="sd">            sets of their orthologs as values.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">target</span> <span class="o">=</span> <span class="n">taxonomy</span><span class="o">.</span><span class="n">ensure_ncbi_tax_id</span><span class="p">(</span><span class="n">target</span><span class="p">)</span>
+        <span class="n">source</span> <span class="o">=</span> <span class="n">taxonomy</span><span class="o">.</span><span class="n">ensure_ncbi_tax_id</span><span class="p">(</span><span class="n">source</span><span class="p">)</span>
+        <span class="n">param</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_translation_param</span><span class="p">(</span><span class="nb">locals</span><span class="p">())</span>
+
+        <span class="n">result</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">defaultdict</span><span class="p">(</span><span class="nb">set</span><span class="p">)</span>
+
+        <span class="k">for</span> <span class="n">resource</span><span class="p">,</span> <span class="n">keys</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">RESOURCE_PARAM</span><span class="o">.</span><span class="n">items</span><span class="p">():</span>
+
+            <span class="k">if</span> <span class="ow">not</span> <span class="n">param</span><span class="p">[</span><span class="n">resource</span><span class="p">]:</span>
+
+                <span class="k">continue</span>
+
+            <span class="n">table</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">which_table</span><span class="p">(</span>
+                <span class="n">target</span> <span class="o">=</span> <span class="n">target</span><span class="p">,</span>
+                <span class="n">source</span> <span class="o">=</span> <span class="n">source</span><span class="p">,</span>
+                <span class="n">only_swissprot</span> <span class="o">=</span> <span class="n">only_swissprot</span><span class="p">,</span>
+                <span class="n">id_type</span> <span class="o">=</span> <span class="n">id_type</span><span class="p">,</span>
+                <span class="n">resource</span> <span class="o">=</span> <span class="n">resource</span><span class="p">,</span>
+            <span class="p">)</span>
+            <span class="n">dct</span> <span class="o">=</span> <span class="n">table</span><span class="o">.</span><span class="n">asdict</span><span class="p">(</span>
+                <span class="n">full_records</span> <span class="o">=</span> <span class="n">full_records</span><span class="p">,</span>
+                <span class="o">**</span><span class="p">{</span>
+                    <span class="n">p</span><span class="p">:</span> <span class="n">v</span>
+                    <span class="k">for</span> <span class="n">p</span><span class="p">,</span> <span class="n">v</span> <span class="ow">in</span> <span class="n">param</span><span class="o">.</span><span class="n">items</span><span class="p">()</span>
+                    <span class="k">if</span> <span class="n">p</span> <span class="ow">in</span> <span class="n">keys</span>
+                <span class="p">}</span>
+            <span class="p">)</span>
+
+            <span class="k">for</span> <span class="n">s</span><span class="p">,</span> <span class="n">o</span> <span class="ow">in</span> <span class="n">dct</span><span class="o">.</span><span class="n">items</span><span class="p">():</span>
+
+                <span class="n">result</span><span class="p">[</span><span class="n">s</span><span class="p">]</span><span class="o">.</span><span class="n">update</span><span class="p">(</span><span class="n">o</span><span class="p">)</span>
+
+        <span class="k">return</span> <span class="nb">dict</span><span class="p">(</span><span class="n">result</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="OrthologyManager.get_df">
+<a class="viewcode-back" href="../../../api/pypath.utils.orthology.OrthologyManager.html#pypath.utils.orthology.OrthologyManager.get_df">[docs]</a>
+    <span class="k">def</span> <span class="nf">get_df</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">target</span><span class="p">:</span> <span class="nb">str</span> <span class="o">|</span> <span class="nb">int</span><span class="p">,</span>
+            <span class="n">source</span><span class="p">:</span> <span class="nb">str</span> <span class="o">|</span> <span class="nb">int</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">,</span>
+            <span class="n">id_type</span><span class="p">:</span> <span class="nb">str</span> <span class="o">=</span> <span class="s1">&#39;uniprot&#39;</span><span class="p">,</span>
+            <span class="n">only_swissprot</span><span class="p">:</span> <span class="nb">bool</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
+            <span class="n">oma</span><span class="p">:</span> <span class="nb">bool</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">homologene</span><span class="p">:</span> <span class="nb">bool</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">ensembl</span><span class="p">:</span> <span class="nb">bool</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">oma_rel_type</span><span class="p">:</span> <span class="p">(</span>
+                <span class="nb">set</span><span class="p">[</span><span class="n">Literal</span><span class="p">[</span><span class="s1">&#39;1:1&#39;</span><span class="p">,</span> <span class="s1">&#39;1:n&#39;</span><span class="p">,</span> <span class="s1">&#39;m:1&#39;</span><span class="p">,</span> <span class="s1">&#39;m:n&#39;</span><span class="p">]]</span> <span class="o">|</span>
+                <span class="kc">None</span>
+            <span class="p">)</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">oma_score</span><span class="p">:</span> <span class="nb">float</span> <span class="o">|</span> <span class="kc">None</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">ensembl_hc</span><span class="p">:</span> <span class="nb">bool</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
+            <span class="n">ensembl_types</span><span class="p">:</span> <span class="p">(</span>
+                <span class="nb">list</span><span class="p">[</span><span class="n">Literal</span><span class="p">[</span><span class="s1">&#39;one2one&#39;</span><span class="p">,</span> <span class="s1">&#39;one2many&#39;</span><span class="p">,</span> <span class="s1">&#39;many2many&#39;</span><span class="p">]]</span> <span class="o">|</span>
+                <span class="kc">None</span>
+            <span class="p">)</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">full_records</span><span class="p">:</span> <span class="nb">bool</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+            <span class="o">**</span><span class="n">kwargs</span>
+        <span class="p">)</span> <span class="o">-&gt;</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">:</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Create a data frame for one source organism and ID type.</span>
+
+<span class="sd">        Args:</span>
+<span class="sd">            target:</span>
+<span class="sd">                Name or NCBI Taxonomy ID of the target organism.</span>
+<span class="sd">            source:</span>
+<span class="sd">                Name or NCBI Taxonomy ID of the source organism.</span>
+<span class="sd">            id_type:</span>
+<span class="sd">                The identifier type to use.</span>
+<span class="sd">            only_swissprot:</span>
+<span class="sd">                Use only SwissProt IDs.</span>
+<span class="sd">            oma</span>
+<span class="sd">                Use orthology information from the Orthologous Matrix (OMA).</span>
+<span class="sd">                Currently this is the recommended source for orthology data.</span>
+<span class="sd">            homologene:</span>
+<span class="sd">                Use orthology information from NCBI HomoloGene.</span>
+<span class="sd">            ensembl:</span>
+<span class="sd">                Use orthology information from Ensembl.</span>
+<span class="sd">            oma_rel_type:</span>
+<span class="sd">                Restrict relations to certain types.</span>
+<span class="sd">            oma_score:</span>
+<span class="sd">                Lower threshold for similarity metric.</span>
+<span class="sd">            ensembl_hc:</span>
+<span class="sd">                Use only the high confidence orthology relations from Ensembl.</span>
+<span class="sd">            ensembl_types:</span>
+<span class="sd">                Ensembl orthology relation types to use. Possible values are</span>
+<span class="sd">                `one2one`, `one2many` and `many2many`. By default only</span>
+<span class="sd">                `one2one` is used.</span>
+<span class="sd">            full_records:</span>
+<span class="sd">                Include not only the identifiers, but also some properties of</span>
+<span class="sd">                the orthology relationships.</span>
+<span class="sd">            kwargs:</span>
+<span class="sd">                Ignored.</span>
+
+<span class="sd">        Returns:</span>
+<span class="sd">            A data frame with pairs of orthologous identifiers,</span>
+<span class="sd">            in two columns: &quot;source&quot; and &quot;target&quot;.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">target</span> <span class="o">=</span> <span class="n">taxonomy</span><span class="o">.</span><span class="n">ensure_ncbi_tax_id</span><span class="p">(</span><span class="n">target</span><span class="p">)</span>
+        <span class="n">source</span> <span class="o">=</span> <span class="n">taxonomy</span><span class="o">.</span><span class="n">ensure_ncbi_tax_id</span><span class="p">(</span><span class="n">source</span><span class="p">)</span>
+        <span class="n">param</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_translation_param</span><span class="p">(</span><span class="nb">locals</span><span class="p">())</span>
+
+        <span class="n">result</span> <span class="o">=</span> <span class="p">[]</span>
+
+        <span class="k">for</span> <span class="n">resource</span><span class="p">,</span> <span class="n">keys</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">RESOURCE_PARAM</span><span class="o">.</span><span class="n">items</span><span class="p">():</span>
+
+            <span class="k">if</span> <span class="ow">not</span> <span class="n">param</span><span class="p">[</span><span class="n">resource</span><span class="p">]:</span>
+
+                <span class="k">continue</span>
+
+            <span class="n">table</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">which_table</span><span class="p">(</span>
+                <span class="n">target</span> <span class="o">=</span> <span class="n">target</span><span class="p">,</span>
+                <span class="n">source</span> <span class="o">=</span> <span class="n">source</span><span class="p">,</span>
+                <span class="n">only_swissprot</span> <span class="o">=</span> <span class="n">only_swissprot</span><span class="p">,</span>
+                <span class="n">id_type</span> <span class="o">=</span> <span class="n">id_type</span><span class="p">,</span>
+                <span class="n">resource</span> <span class="o">=</span> <span class="n">resource</span><span class="p">,</span>
+            <span class="p">)</span>
+
+            <span class="n">result</span><span class="o">.</span><span class="n">append</span><span class="p">(</span>
+                <span class="n">table</span><span class="o">.</span><span class="n">df</span><span class="p">(</span>
+                    <span class="n">full_records</span> <span class="o">=</span> <span class="n">full_records</span><span class="p">,</span>
+                    <span class="o">**</span><span class="p">{</span>
+                        <span class="n">p</span><span class="p">:</span> <span class="n">v</span>
+                        <span class="k">for</span> <span class="n">p</span><span class="p">,</span> <span class="n">v</span> <span class="ow">in</span> <span class="n">param</span><span class="o">.</span><span class="n">items</span><span class="p">()</span>
+                        <span class="k">if</span> <span class="n">p</span> <span class="ow">in</span> <span class="n">keys</span>
+                    <span class="p">}</span>
+                <span class="p">)</span>
+            <span class="p">)</span>
+
+        <span class="k">return</span> <span class="n">pd</span><span class="o">.</span><span class="n">concat</span><span class="p">(</span><span class="n">result</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="OrthologyManager.translate_df">
+<a class="viewcode-back" href="../../../api/pypath.utils.orthology.OrthologyManager.html#pypath.utils.orthology.OrthologyManager.translate_df">[docs]</a>
+    <span class="k">def</span> <span class="nf">translate_df</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">df</span><span class="p">:</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">,</span>
+            <span class="n">target</span><span class="p">:</span> <span class="nb">str</span> <span class="o">|</span> <span class="nb">int</span><span class="p">,</span>
+            <span class="n">source</span><span class="p">:</span> <span class="nb">str</span> <span class="o">|</span> <span class="nb">int</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">,</span>
+            <span class="n">cols</span><span class="p">:</span> <span class="nb">str</span> <span class="o">|</span> <span class="nb">list</span><span class="p">[</span><span class="nb">str</span><span class="p">]</span> <span class="o">|</span> <span class="nb">dict</span><span class="p">[</span><span class="nb">str</span><span class="p">,</span> <span class="nb">str</span><span class="p">]</span> <span class="o">|</span> <span class="kc">None</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">id_type</span><span class="p">:</span> <span class="nb">str</span> <span class="o">=</span> <span class="s1">&#39;uniprot&#39;</span><span class="p">,</span>
+            <span class="n">only_swissprot</span><span class="p">:</span> <span class="nb">bool</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
+            <span class="n">oma</span><span class="p">:</span> <span class="nb">bool</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">homologene</span><span class="p">:</span> <span class="nb">bool</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">ensembl</span><span class="p">:</span> <span class="nb">bool</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">oma_rel_type</span><span class="p">:</span> <span class="p">(</span>
+                <span class="nb">set</span><span class="p">[</span><span class="n">Literal</span><span class="p">[</span><span class="s1">&#39;1:1&#39;</span><span class="p">,</span> <span class="s1">&#39;1:n&#39;</span><span class="p">,</span> <span class="s1">&#39;m:1&#39;</span><span class="p">,</span> <span class="s1">&#39;m:n&#39;</span><span class="p">]]</span> <span class="o">|</span>
+                <span class="kc">None</span>
+            <span class="p">)</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">oma_score</span><span class="p">:</span> <span class="nb">float</span> <span class="o">|</span> <span class="kc">None</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">ensembl_hc</span><span class="p">:</span> <span class="nb">bool</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
+            <span class="n">ensembl_types</span><span class="p">:</span> <span class="p">(</span>
+                <span class="nb">list</span><span class="p">[</span><span class="n">Literal</span><span class="p">[</span><span class="s1">&#39;one2one&#39;</span><span class="p">,</span> <span class="s1">&#39;one2many&#39;</span><span class="p">,</span> <span class="s1">&#39;many2many&#39;</span><span class="p">]]</span> <span class="o">|</span>
+                <span class="kc">None</span>
+            <span class="p">)</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="o">**</span><span class="n">kwargs</span><span class="p">:</span> <span class="nb">str</span> <span class="o">|</span> <span class="nb">tuple</span><span class="p">[</span><span class="nb">str</span><span class="p">,</span> <span class="nb">str</span><span class="p">]</span>
+        <span class="p">)</span> <span class="o">-&gt;</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">:</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Translate columns in a data frame.</span>
+
+<span class="sd">        Args:</span>
+<span class="sd">            df:</span>
+<span class="sd">                A data frame.</span>
+<span class="sd">            cols:</span>
+<span class="sd">                One or more columns to be translated. It can be a single</span>
+<span class="sd">                column name, an iterable of column names or a dict where</span>
+<span class="sd">                keys are column names and values are ID types. Except this</span>
+<span class="sd">                last case, identifiers are assumed to be `id_type`.</span>
+<span class="sd">            target:</span>
+<span class="sd">                Name or NCBI Taxonomy ID of the target organism.</span>
+<span class="sd">            source:</span>
+<span class="sd">                Name or NCBI Taxonomy ID of the source organism.</span>
+<span class="sd">            id_type:</span>
+<span class="sd">                The default identifier type to use, will be used for all</span>
+<span class="sd">                columns where ID type is not specified.</span>
+<span class="sd">            only_swissprot:</span>
+<span class="sd">                Use only SwissProt IDs.</span>
+<span class="sd">            oma</span>
+<span class="sd">                Use orthology information from the Orthologous Matrix (OMA).</span>
+<span class="sd">                Currently this is the recommended source for orthology data.</span>
+<span class="sd">            homologene:</span>
+<span class="sd">                Use orthology information from NCBI HomoloGene.</span>
+<span class="sd">            ensembl:</span>
+<span class="sd">                Use orthology information from Ensembl.</span>
+<span class="sd">            oma_rel_type:</span>
+<span class="sd">                Restrict relations to certain types.</span>
+<span class="sd">            oma_score:</span>
+<span class="sd">                Lower threshold for similarity metric.</span>
+<span class="sd">            ensembl_hc:</span>
+<span class="sd">                Use only the high confidence orthology relations from Ensembl.</span>
+<span class="sd">            ensembl_types:</span>
+<span class="sd">                Ensembl orthology relation types to use. Possible values are</span>
+<span class="sd">                `one2one`, `one2many` and `many2many`. By default only</span>
+<span class="sd">                `one2one` is used.</span>
+<span class="sd">            kwargs:</span>
+<span class="sd">                Same as providing a dict to ``cols``, but beware, keys</span>
+<span class="sd">                (column names) can not match existing argument names of</span>
+<span class="sd">                this function.</span>
+
+<span class="sd">        Returns:</span>
+<span class="sd">            A data frame with the same column layout as the input, and the</span>
+<span class="sd">            identifiers translated as demanded. Rows that could not be</span>
+<span class="sd">            translated are omitted.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">if</span> <span class="ow">not</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">cols</span><span class="p">,</span> <span class="nb">dict</span><span class="p">):</span>
+
+            <span class="n">cols</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">((</span><span class="n">col</span><span class="p">,</span> <span class="n">id_type</span><span class="p">)</span> <span class="k">for</span> <span class="n">col</span> <span class="ow">in</span> <span class="n">common</span><span class="o">.</span><span class="n">to_list</span><span class="p">(</span><span class="n">cols</span><span class="p">))</span>
+
+        <span class="n">kwargs</span><span class="o">.</span><span class="n">update</span><span class="p">(</span><span class="n">cols</span><span class="p">)</span>
+        <span class="n">id_types</span> <span class="o">=</span> <span class="nb">set</span><span class="p">(</span><span class="n">kwargs</span><span class="o">.</span><span class="n">values</span><span class="p">())</span>
+
+        <span class="k">for</span> <span class="n">_id_type</span> <span class="ow">in</span> <span class="nb">set</span><span class="p">(</span><span class="n">cols</span><span class="o">.</span><span class="n">values</span><span class="p">()):</span>
+
+            <span class="n">args</span> <span class="o">=</span> <span class="nb">locals</span><span class="p">()</span><span class="o">.</span><span class="n">copy</span><span class="p">()</span>
+            <span class="n">args</span><span class="o">.</span><span class="n">pop</span><span class="p">(</span><span class="s1">&#39;self&#39;</span><span class="p">)</span>
+            <span class="n">args</span><span class="p">[</span><span class="s1">&#39;id_type&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">_id_type</span>
+            <span class="n">ortho_df</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">get_df</span><span class="p">(</span><span class="o">**</span><span class="n">args</span><span class="p">)</span>
+
+            <span class="n">table</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">which_table</span><span class="p">(</span>
+                <span class="n">target</span> <span class="o">=</span> <span class="n">target</span><span class="p">,</span>
+                <span class="n">source</span> <span class="o">=</span> <span class="n">source</span><span class="p">,</span>
+                <span class="n">only_swissprot</span> <span class="o">=</span> <span class="n">only_swissprot</span><span class="p">,</span>
+                <span class="n">id_type</span> <span class="o">=</span> <span class="n">_id_type</span><span class="p">,</span>
+                <span class="n">resource</span> <span class="o">=</span> <span class="s1">&#39;oma&#39;</span><span class="p">,</span>
+            <span class="p">)</span>
+
+            <span class="n">df</span> <span class="o">=</span> <span class="n">table</span><span class="o">.</span><span class="n">translate_df</span><span class="p">(</span>
+                <span class="n">df</span> <span class="o">=</span> <span class="n">df</span><span class="p">,</span>
+                <span class="n">cols</span> <span class="o">=</span> <span class="p">[</span><span class="n">c</span> <span class="k">for</span> <span class="n">c</span><span class="p">,</span> <span class="n">i</span> <span class="ow">in</span> <span class="n">cols</span><span class="o">.</span><span class="n">items</span><span class="p">()</span> <span class="k">if</span> <span class="n">i</span> <span class="o">==</span> <span class="n">_id_type</span><span class="p">],</span>
+                <span class="n">ortho_df</span> <span class="o">=</span> <span class="n">ortho_df</span><span class="p">,</span>
+            <span class="p">)</span>
+
+        <span class="k">return</span> <span class="n">df</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">_translation_param</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">loc</span><span class="p">:</span> <span class="nb">dict</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">dict</span><span class="p">:</span>
+
+        <span class="n">param</span> <span class="o">=</span> <span class="p">{}</span>
+
+        <span class="k">for</span> <span class="n">resource</span><span class="p">,</span> <span class="n">keys</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">RESOURCE_PARAM</span><span class="o">.</span><span class="n">items</span><span class="p">():</span>
+
+            <span class="n">enabled</span> <span class="o">=</span> <span class="n">common</span><span class="o">.</span><span class="n">first_value</span><span class="p">(</span>
+                <span class="n">loc</span><span class="p">[</span><span class="n">resource</span><span class="p">],</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">_param</span><span class="p">[</span><span class="n">resource</span><span class="p">],</span>
+                <span class="n">settings</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="sa">f</span><span class="s1">&#39;orthology_</span><span class="si">{</span><span class="n">resource</span><span class="si">}</span><span class="s1">&#39;</span><span class="p">),</span>
+            <span class="p">)</span>
+            <span class="n">param</span><span class="p">[</span><span class="n">resource</span><span class="p">]</span> <span class="o">=</span> <span class="n">enabled</span>
+
+            <span class="k">if</span> <span class="n">enabled</span><span class="p">:</span>
+
+                <span class="k">for</span> <span class="n">key</span> <span class="ow">in</span> <span class="n">keys</span><span class="p">:</span>
+
+                    <span class="n">param</span><span class="p">[</span><span class="n">key</span><span class="p">]</span> <span class="o">=</span> <span class="n">common</span><span class="o">.</span><span class="n">first_value</span><span class="p">(</span>
+                        <span class="n">loc</span><span class="p">[</span><span class="sa">f</span><span class="s1">&#39;</span><span class="si">{</span><span class="n">resource</span><span class="si">}</span><span class="s1">_</span><span class="si">{</span><span class="n">key</span><span class="si">}</span><span class="s1">&#39;</span><span class="p">],</span>
+                        <span class="bp">self</span><span class="o">.</span><span class="n">_param</span><span class="p">[</span><span class="sa">f</span><span class="s1">&#39;</span><span class="si">{</span><span class="n">resource</span><span class="si">}</span><span class="s1">_</span><span class="si">{</span><span class="n">key</span><span class="si">}</span><span class="s1">&#39;</span><span class="p">],</span>
+                        <span class="n">settings</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="sa">f</span><span class="s1">&#39;orthology_</span><span class="si">{</span><span class="n">resource</span><span class="si">}</span><span class="s1">_</span><span class="si">{</span><span class="n">key</span><span class="si">}</span><span class="s1">&#39;</span><span class="p">),</span>
+                    <span class="p">)</span>
+
+        <span class="k">return</span> <span class="n">param</span>
+
+
+    <span class="k">def</span> <span class="nf">_remove_expired</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">for</span> <span class="n">key</span><span class="p">,</span> <span class="n">last_used</span> <span class="ow">in</span> <span class="nb">list</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">expiry</span><span class="o">.</span><span class="n">items</span><span class="p">()):</span>
+
+            <span class="k">if</span> <span class="n">time</span><span class="o">.</span><span class="n">time</span><span class="p">()</span> <span class="o">-</span> <span class="n">last_used</span> <span class="o">&gt;</span> <span class="bp">self</span><span class="o">.</span><span class="n">lifetime</span> <span class="ow">and</span> <span class="n">key</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">tables</span><span class="p">:</span>
+
+                <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span>
+                    <span class="s1">&#39;Removing orthology table from taxon </span><span class="si">%u</span><span class="s1"> to </span><span class="si">%u</span><span class="s1"> &#39;</span>
+                    <span class="s1">&#39;(only SwissProt: </span><span class="si">%s</span><span class="s1">; resource: </span><span class="si">%s</span><span class="s1">; ID type: </span><span class="si">%s</span><span class="s1">)&#39;</span> <span class="o">%</span> <span class="n">key</span>
+                <span class="p">)</span>
+
+                <span class="k">del</span> <span class="bp">self</span><span class="o">.</span><span class="n">tables</span><span class="p">[</span><span class="n">key</span><span class="p">]</span>
+                <span class="k">del</span> <span class="bp">self</span><span class="o">.</span><span class="n">expiry</span><span class="p">[</span><span class="n">key</span><span class="p">]</span>
+
+
+    <span class="k">def</span> <span class="fm">__del__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">if</span> <span class="nb">hasattr</span><span class="p">(</span><span class="n">_orthology_cleanup_timeloop</span><span class="p">,</span> <span class="s1">&#39;stop&#39;</span><span class="p">):</span>
+
+            <span class="n">_orthology_cleanup_timeloop</span><span class="o">.</span><span class="n">stop</span><span class="p">()</span></div>
+
+
+
+<div class="viewcode-block" id="SequenceContainer">
+<a class="viewcode-back" href="../../../api/pypath.utils.orthology.SequenceContainer.html#pypath.utils.orthology.SequenceContainer">[docs]</a>
+<span class="k">class</span> <span class="nc">SequenceContainer</span><span class="p">(</span><span class="n">session</span><span class="o">.</span><span class="n">Logger</span><span class="p">):</span>
+
+
+<div class="viewcode-block" id="SequenceContainer.__init__">
+<a class="viewcode-back" href="../../../api/pypath.utils.orthology.SequenceContainer.html#pypath.utils.orthology.SequenceContainer.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">preload_seq</span> <span class="o">=</span> <span class="p">[],</span> <span class="n">isoforms</span> <span class="o">=</span> <span class="kc">True</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        This is an object to store sequences of multiple</span>
+<span class="sd">        organisms and select the appropriate one.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">if</span> <span class="ow">not</span> <span class="nb">hasattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">&#39;_logger&#39;</span><span class="p">):</span>
+
+            <span class="n">session</span><span class="o">.</span><span class="n">Logger</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">name</span> <span class="o">=</span> <span class="s1">&#39;orthology&#39;</span><span class="p">)</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">seq_isoforms</span> <span class="o">=</span> <span class="n">isoforms</span>
+
+        <span class="k">for</span> <span class="n">taxon</span> <span class="ow">in</span> <span class="n">preload_seq</span><span class="p">:</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">load_seq</span><span class="p">(</span><span class="n">taxon</span><span class="p">)</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">load_seq</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">taxon</span><span class="p">):</span>
+
+        <span class="k">if</span> <span class="ow">not</span> <span class="nb">hasattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">&#39;seq&#39;</span><span class="p">):</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">seq</span> <span class="o">=</span> <span class="p">{}</span>
+
+        <span class="n">taxon</span> <span class="o">=</span> <span class="n">taxon</span> <span class="ow">or</span> <span class="bp">self</span><span class="o">.</span><span class="n">ncbi_tax_id</span>
+
+        <span class="k">if</span> <span class="n">taxon</span> <span class="ow">not</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">seq</span><span class="p">:</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">seq</span><span class="p">[</span><span class="n">taxon</span><span class="p">]</span> <span class="o">=</span> <span class="n">_se</span><span class="o">.</span><span class="n">swissprot_seq</span><span class="p">(</span>
+                <span class="n">organism</span> <span class="o">=</span> <span class="n">taxon</span><span class="p">,</span>
+                <span class="n">isoforms</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">seq_isoforms</span>
+            <span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">get_seq</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">protein</span><span class="p">,</span> <span class="n">taxon</span> <span class="o">=</span> <span class="kc">None</span><span class="p">):</span>
+
+        <span class="k">if</span> <span class="n">taxon</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
+
+            <span class="k">if</span> <span class="n">taxon</span> <span class="ow">not</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">seq</span><span class="p">:</span>
+
+                <span class="bp">self</span><span class="o">.</span><span class="n">load_seq</span><span class="p">(</span><span class="n">taxon</span><span class="p">)</span>
+
+            <span class="k">if</span> <span class="n">protein</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">seq</span><span class="p">[</span><span class="n">taxon</span><span class="p">]:</span>
+
+                <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">seq</span><span class="p">[</span><span class="n">taxon</span><span class="p">][</span><span class="n">protein</span><span class="p">]</span>
+
+        <span class="k">else</span><span class="p">:</span>
+
+            <span class="k">for</span> <span class="n">taxon</span><span class="p">,</span> <span class="n">seq</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">seq</span><span class="p">):</span>
+
+                <span class="k">if</span> <span class="n">protein</span> <span class="ow">in</span> <span class="n">seq</span><span class="p">:</span>
+
+                    <span class="k">return</span> <span class="n">seq</span><span class="p">[</span><span class="n">protein</span><span class="p">]</span></div>
+
+
+
+<div class="viewcode-block" id="Proteomes">
+<a class="viewcode-back" href="../../../api/pypath.utils.orthology.Proteomes.html#pypath.utils.orthology.Proteomes">[docs]</a>
+<span class="k">class</span> <span class="nc">Proteomes</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span>
+
+
+<div class="viewcode-block" id="Proteomes.__init__">
+<a class="viewcode-back" href="../../../api/pypath.utils.orthology.Proteomes.html#pypath.utils.orthology.Proteomes.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">preload_prot</span><span class="p">:</span> <span class="nb">list</span><span class="p">[</span><span class="nb">int</span><span class="p">]</span> <span class="o">|</span> <span class="kc">None</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">only_swissprot</span><span class="p">:</span> <span class="nb">bool</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
+        <span class="p">):</span>
+
+        <span class="k">if</span> <span class="ow">not</span> <span class="nb">hasattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">&#39;_taxonomy&#39;</span><span class="p">):</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">_taxonomy</span> <span class="o">=</span> <span class="p">{}</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">_up_taxonomy</span> <span class="o">=</span> <span class="p">{}</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">_proteomes</span> <span class="o">=</span> <span class="p">{}</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">only_swissprot</span> <span class="o">=</span> <span class="n">only_swissprot</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">load_taxonomy</span><span class="p">()</span>
+
+        <span class="k">for</span> <span class="n">taxon</span> <span class="ow">in</span> <span class="p">(</span><span class="n">preload_prot</span> <span class="ow">or</span> <span class="p">()):</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">load_proteome</span><span class="p">(</span><span class="n">taxon</span><span class="p">)</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">load_proteome</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">taxon</span><span class="p">:</span> <span class="nb">int</span><span class="p">,</span> <span class="n">only_swissprot</span><span class="p">:</span> <span class="nb">bool</span> <span class="o">|</span> <span class="kc">None</span> <span class="o">=</span> <span class="kc">None</span><span class="p">):</span>
+
+        <span class="n">only_swissprot</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">only_swissprot</span>
+                <span class="k">if</span> <span class="n">only_swissprot</span> <span class="ow">is</span> <span class="kc">None</span> <span class="k">else</span>
+            <span class="n">only_swissprot</span>
+        <span class="p">)</span>
+
+        <span class="n">key</span> <span class="o">=</span> <span class="p">(</span><span class="n">taxon</span><span class="p">,</span> <span class="n">only_swissprot</span><span class="p">)</span>
+
+        <span class="k">if</span> <span class="n">key</span> <span class="ow">not</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">_proteomes</span><span class="p">:</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">_proteomes</span><span class="p">[</span><span class="n">key</span><span class="p">]</span> <span class="o">=</span> <span class="p">(</span>
+                <span class="nb">set</span><span class="p">(</span><span class="n">uniprot_db</span><span class="o">.</span><span class="n">all_uniprots</span><span class="p">(</span><span class="o">*</span><span class="n">key</span><span class="p">))</span>
+            <span class="p">)</span>
+
+            <span class="k">for</span> <span class="n">protein</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">_proteomes</span><span class="p">[</span><span class="n">key</span><span class="p">]:</span>
+
+                <span class="bp">self</span><span class="o">.</span><span class="n">_taxonomy</span><span class="p">[</span><span class="n">protein</span><span class="p">]</span> <span class="o">=</span> <span class="n">key</span>
+
+            <span class="k">if</span> <span class="ow">not</span> <span class="n">only_swissprot</span><span class="p">:</span>
+
+                <span class="bp">self</span><span class="o">.</span><span class="n">load_proteome</span><span class="p">(</span><span class="n">taxon</span><span class="p">,</span> <span class="kc">True</span><span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">get_taxon</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">protein</span><span class="p">,</span> <span class="n">only_swissprot</span> <span class="o">=</span> <span class="kc">True</span><span class="p">):</span>
+
+        <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">get_taxon_trembl</span><span class="p">(</span><span class="n">protein</span><span class="p">)</span>
+
+        <span class="k">if</span> <span class="p">(</span>
+            <span class="n">only_swissprot</span> <span class="ow">and</span>
+            <span class="n">ncbi_tax_id</span> <span class="ow">and</span>
+            <span class="ow">not</span> <span class="n">uniprot_db</span><span class="o">.</span><span class="n">is_swissprot</span><span class="p">(</span><span class="n">protein</span><span class="p">,</span> <span class="n">organism</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span><span class="p">)</span>
+        <span class="p">):</span>
+
+            <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="kc">None</span>
+
+        <span class="k">return</span> <span class="n">ncbi_tax_id</span>
+
+
+    <span class="k">def</span> <span class="nf">get_taxon_trembl</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">protein</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_up_taxonomy</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="n">protein</span><span class="p">,</span> <span class="kc">None</span><span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">has_protein</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">protein</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="n">protein</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">_taxonomy</span>
+
+
+    <span class="k">def</span> <span class="nf">is_swissprot</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">protein</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="nb">bool</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">get_taxon</span><span class="p">(</span><span class="n">protein</span><span class="p">,</span> <span class="n">only_swissprot</span> <span class="o">=</span> <span class="kc">True</span><span class="p">))</span>
+
+
+    <span class="k">def</span> <span class="nf">load_taxonomy</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_up_taxonomy</span> <span class="o">=</span> <span class="n">uniprot_input</span><span class="o">.</span><span class="n">uniprot_taxonomy</span><span class="p">(</span><span class="n">ncbi_tax_ids</span> <span class="o">=</span> <span class="kc">True</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="ProteinOrthology">
+<a class="viewcode-back" href="../../../api/pypath.utils.orthology.ProteinOrthology.html#pypath.utils.orthology.ProteinOrthology">[docs]</a>
+<span class="k">class</span> <span class="nc">ProteinOrthology</span><span class="p">(</span><span class="n">Proteomes</span><span class="p">):</span>
+
+    <span class="n">_param</span> <span class="o">=</span> <span class="p">(</span><span class="s1">&#39;id&#39;</span><span class="p">,)</span>
+
+
+<div class="viewcode-block" id="ProteinOrthology.__init__">
+<a class="viewcode-back" href="../../../api/pypath.utils.orthology.ProteinOrthology.html#pypath.utils.orthology.ProteinOrthology.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">target</span><span class="p">:</span> <span class="nb">str</span> <span class="o">|</span> <span class="nb">int</span><span class="p">,</span>
+            <span class="n">source</span><span class="p">:</span> <span class="nb">str</span> <span class="o">|</span> <span class="nb">int</span> <span class="o">|</span> <span class="kc">None</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">,</span>
+            <span class="n">id_type</span><span class="p">:</span> <span class="nb">str</span> <span class="o">=</span> <span class="s1">&#39;uniprot&#39;</span><span class="p">,</span>
+            <span class="n">only_swissprot</span><span class="p">:</span> <span class="nb">bool</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
+            <span class="o">**</span><span class="n">kwargs</span>
+        <span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        This class translates between homologous UniProt IDs of two organisms</span>
+<span class="sd">        based on NCBI HomoloGene and Ensembl data. In case of HomoloGene,</span>
+<span class="sd">        the UniProt-UniProt translation table is created by translating the</span>
+<span class="sd">        source organism UniProts to RefSeq and Entrez IDs, finding the</span>
+<span class="sd">        homologues (orthologues) for these IDs, and then translating them</span>
+<span class="sd">        to the target organism UniProt IDs. In case of Ensembl, we obtain</span>
+<span class="sd">        data with Ensembl protein identifiers and translate those to UniProt.</span>
+
+<span class="sd">        Args</span>
+<span class="sd">            target:</span>
+<span class="sd">                Name or NCBI Taxonomy ID of the target organism.</span>
+<span class="sd">            source:</span>
+<span class="sd">                Name or NCBI Taxonomy ID of the source organism.</span>
+<span class="sd">            id_type:</span>
+<span class="sd">                The identifier type to use.</span>
+<span class="sd">            only_swissprot:</span>
+<span class="sd">                Use only SwissProt IDs.</span>
+<span class="sd">            kwargs:</span>
+<span class="sd">                Resource specific parameters.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">data</span> <span class="o">=</span> <span class="p">{}</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">target</span> <span class="o">=</span> <span class="n">taxonomy</span><span class="o">.</span><span class="n">ensure_ncbi_tax_id</span><span class="p">(</span><span class="n">target</span><span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">source</span> <span class="o">=</span> <span class="n">taxonomy</span><span class="o">.</span><span class="n">ensure_ncbi_tax_id</span><span class="p">(</span><span class="n">source</span><span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">id_type</span> <span class="o">=</span> <span class="n">id_type</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">_resource_l</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">resource</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span>
+        <span class="n">Proteomes</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">only_swissprot</span> <span class="o">=</span> <span class="n">only_swissprot</span><span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">load_proteome</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">source</span><span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">_set_param</span><span class="p">(</span><span class="n">kwargs</span><span class="p">,</span> <span class="o">*</span><span class="bp">self</span><span class="o">.</span><span class="n">_param</span><span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">load</span><span class="p">()</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">reload</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="n">modname</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="vm">__class__</span><span class="o">.</span><span class="vm">__module__</span>
+        <span class="n">mod</span> <span class="o">=</span> <span class="nb">__import__</span><span class="p">(</span><span class="n">modname</span><span class="p">,</span> <span class="n">fromlist</span><span class="o">=</span><span class="p">[</span><span class="n">modname</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;.&#39;</span><span class="p">)[</span><span class="mi">0</span><span class="p">]])</span>
+        <span class="n">imp</span><span class="o">.</span><span class="n">reload</span><span class="p">(</span><span class="n">mod</span><span class="p">)</span>
+        <span class="n">new</span> <span class="o">=</span> <span class="nb">getattr</span><span class="p">(</span><span class="n">mod</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="vm">__class__</span><span class="o">.</span><span class="vm">__name__</span><span class="p">)</span>
+        <span class="nb">setattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">&#39;__class__&#39;</span><span class="p">,</span> <span class="n">new</span><span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">load</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">source</span> <span class="o">=</span> <span class="kc">None</span><span class="p">):</span>
+
+        <span class="k">pass</span>
+
+
+<div class="viewcode-block" id="ProteinOrthology.translate">
+<a class="viewcode-back" href="../../../api/pypath.utils.orthology.ProteinOrthology.html#pypath.utils.orthology.ProteinOrthology.translate">[docs]</a>
+    <span class="k">def</span> <span class="nf">translate</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">identifier</span><span class="p">:</span> <span class="nb">str</span> <span class="o">|</span> <span class="n">Iterable</span><span class="p">[</span><span class="nb">str</span><span class="p">],</span>
+            <span class="n">full_records</span><span class="p">:</span> <span class="nb">bool</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+            <span class="o">**</span><span class="n">kwargs</span>
+        <span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">set</span><span class="p">[</span><span class="nb">str</span><span class="p">]:</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        For one UniProt ID of the source organism returns all orthologues</span>
+<span class="sd">        from the target organism.</span>
+
+<span class="sd">        Args:</span>
+<span class="sd">            identifier:</span>
+<span class="sd">                An identifier corresponding to the ID type and source organism</span>
+<span class="sd">                of the instance.</span>
+<span class="sd">            full_records:</span>
+<span class="sd">                Include not only the identifiers, but also some properties of</span>
+<span class="sd">                the orthology relationships.</span>
+<span class="sd">            kwargs:</span>
+<span class="sd">                Resource specific translation parameters.</span>
+
+<span class="sd">        Returns:</span>
+<span class="sd">            A set of identifiers of orthologues in the target taxon.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">identifier</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="p">(</span><span class="n">identifier</span><span class="p">,)</span>
+                <span class="k">if</span> <span class="nb">hasattr</span><span class="p">(</span><span class="n">identifier</span><span class="p">,</span> <span class="s1">&#39;components&#39;</span><span class="p">)</span> <span class="k">else</span>
+            <span class="n">common</span><span class="o">.</span><span class="n">to_list</span><span class="p">(</span><span class="n">identifier</span><span class="p">)</span>
+        <span class="p">)</span>
+
+        <span class="n">result</span> <span class="o">=</span> <span class="nb">set</span><span class="o">.</span><span class="n">union</span><span class="p">(</span><span class="o">*</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">data</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="n">i</span><span class="p">,</span> <span class="nb">set</span><span class="p">())</span> <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="n">identifier</span><span class="p">))</span>
+
+        <span class="k">if</span> <span class="ow">not</span> <span class="n">full_records</span><span class="p">:</span>
+
+            <span class="n">result</span> <span class="o">=</span> <span class="p">{</span><span class="n">o</span><span class="o">.</span><span class="n">id</span> <span class="k">for</span> <span class="n">o</span> <span class="ow">in</span> <span class="n">result</span><span class="p">}</span>
+
+        <span class="k">return</span> <span class="n">result</span></div>
+
+
+
+<div class="viewcode-block" id="ProteinOrthology.asdict">
+<a class="viewcode-back" href="../../../api/pypath.utils.orthology.ProteinOrthology.html#pypath.utils.orthology.ProteinOrthology.asdict">[docs]</a>
+    <span class="k">def</span> <span class="nf">asdict</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">full_records</span><span class="p">:</span> <span class="nb">bool</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+            <span class="o">**</span><span class="n">kwargs</span>
+        <span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">dict</span><span class="p">[</span><span class="nb">str</span><span class="p">,</span> <span class="nb">set</span><span class="p">[</span><span class="n">OrthologBase</span><span class="p">]]:</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Create a dictionary from the translation table.</span>
+
+<span class="sd">        Args:</span>
+<span class="sd">            full_records:</span>
+<span class="sd">                Include not only the identifiers, but also some properties of</span>
+<span class="sd">                the orthology relationships.</span>
+<span class="sd">            kwargs:</span>
+<span class="sd">                Resource specific filtering criteria.</span>
+
+<span class="sd">        Returns:</span>
+<span class="sd">            A dict with identifiers of the source organism as keys, and</span>
+<span class="sd">            sets of their orthologs as values.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">proc</span> <span class="o">=</span> <span class="p">(</span><span class="k">lambda</span> <span class="n">x</span><span class="p">:</span> <span class="n">x</span><span class="p">)</span> <span class="k">if</span> <span class="n">full_records</span> <span class="k">else</span> <span class="p">(</span><span class="k">lambda</span> <span class="n">x</span><span class="p">:</span> <span class="n">x</span><span class="o">.</span><span class="n">id</span><span class="p">)</span>
+
+        <span class="k">return</span> <span class="p">{</span>
+            <span class="n">s</span><span class="p">:</span> <span class="p">{</span><span class="n">proc</span><span class="p">(</span><span class="n">o</span><span class="p">)</span> <span class="k">for</span> <span class="n">o</span> <span class="ow">in</span> <span class="n">orthologs</span> <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="n">o</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">)}</span>
+            <span class="k">for</span> <span class="n">s</span><span class="p">,</span> <span class="n">orthologs</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span><span class="o">.</span><span class="n">items</span><span class="p">()</span>
+        <span class="p">}</span></div>
+
+
+
+<div class="viewcode-block" id="ProteinOrthology.df">
+<a class="viewcode-back" href="../../../api/pypath.utils.orthology.ProteinOrthology.html#pypath.utils.orthology.ProteinOrthology.df">[docs]</a>
+    <span class="k">def</span> <span class="nf">df</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">full_records</span><span class="p">:</span> <span class="nb">bool</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">:</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Orthologous pairs as data frame.</span>
+
+<span class="sd">        Args:</span>
+<span class="sd">            full_records:</span>
+<span class="sd">                Include not only the identifiers, but also some properties of</span>
+<span class="sd">                the orthology relationships.</span>
+<span class="sd">            kwargs:</span>
+<span class="sd">                Resource specific filtering criteria.</span>
+
+<span class="sd">        Returns:</span>
+<span class="sd">            A data frame with pairs of orthologous identifiers,</span>
+<span class="sd">            in two columns: &quot;source&quot; and &quot;target&quot;.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">_log</span><span class="p">(</span>
+            <span class="s1">&#39;Creating translation data frame between &#39;</span>
+            <span class="sa">f</span><span class="s1">&#39;organisms `</span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">source</span><span class="si">}</span><span class="s1">` and `</span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">target</span><span class="si">}</span><span class="s1">`, &#39;</span>
+            <span class="sa">f</span><span class="s1">&#39;ID type `</span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">id_type</span><span class="si">}</span><span class="s1">`.&#39;</span>
+        <span class="p">)</span>
+
+        <span class="n">df</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">(</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">asdict</span><span class="p">(</span><span class="n">full_records</span> <span class="o">=</span> <span class="n">full_records</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">)</span><span class="o">.</span><span class="n">items</span><span class="p">(),</span>
+                <span class="n">columns</span> <span class="o">=</span> <span class="p">[</span><span class="s1">&#39;source&#39;</span><span class="p">,</span> <span class="s1">&#39;target&#39;</span><span class="p">],</span>
+            <span class="p">)</span><span class="o">.</span>
+            <span class="n">explode</span><span class="p">(</span><span class="s1">&#39;target&#39;</span><span class="p">,</span> <span class="n">ignore_index</span> <span class="o">=</span> <span class="kc">True</span><span class="p">)</span><span class="o">.</span>
+            <span class="n">dropna</span><span class="p">()</span><span class="o">.</span>
+            <span class="n">reset_index</span><span class="p">(</span><span class="n">drop</span> <span class="o">=</span> <span class="kc">True</span><span class="p">)</span>
+        <span class="p">)</span>
+
+        <span class="k">if</span> <span class="n">full_records</span><span class="p">:</span>
+
+            <span class="c1"># some beautiful pandas code again</span>
+            <span class="n">df</span> <span class="o">=</span> <span class="p">(</span>
+                <span class="n">pd</span><span class="o">.</span><span class="n">concat</span><span class="p">(</span>
+                    <span class="p">[</span>
+                        <span class="n">df</span><span class="o">.</span><span class="n">source</span><span class="p">,</span>
+                        <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">(</span><span class="n">df</span><span class="o">.</span><span class="n">target</span><span class="o">.</span><span class="n">tolist</span><span class="p">()),</span>
+                    <span class="p">],</span>
+                    <span class="n">axis</span> <span class="o">=</span> <span class="mi">1</span><span class="p">,</span>
+                <span class="p">)</span><span class="o">.</span>
+                <span class="n">rename</span><span class="p">(</span><span class="n">columns</span> <span class="o">=</span> <span class="p">{</span><span class="s1">&#39;id&#39;</span><span class="p">:</span> <span class="s1">&#39;target&#39;</span><span class="p">})</span>
+            <span class="p">)</span>
+
+        <span class="k">return</span> <span class="n">df</span></div>
+
+
+
+<div class="viewcode-block" id="ProteinOrthology.translate_df">
+<a class="viewcode-back" href="../../../api/pypath.utils.orthology.ProteinOrthology.html#pypath.utils.orthology.ProteinOrthology.translate_df">[docs]</a>
+    <span class="k">def</span> <span class="nf">translate_df</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">df</span><span class="p">:</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">,</span>
+            <span class="n">cols</span><span class="p">:</span> <span class="nb">str</span> <span class="o">|</span> <span class="nb">list</span><span class="p">[</span><span class="nb">str</span><span class="p">]</span> <span class="o">|</span> <span class="kc">None</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">ortho_df</span><span class="p">:</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span> <span class="o">|</span> <span class="kc">None</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="o">**</span><span class="n">kwargs</span>
+        <span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Translate columns in a data frame.</span>
+
+<span class="sd">        Args:</span>
+<span class="sd">            df:</span>
+<span class="sd">                A data frame.</span>
+<span class="sd">            cols:</span>
+<span class="sd">                One or more columns to be translated. It can be a single</span>
+<span class="sd">                column name, an iterable of column names or a dict where</span>
+<span class="sd">                keys are column names and values are ID types. Except this</span>
+<span class="sd">                last case, identifiers are assumed to be UniProt.</span>
+<span class="sd">            ortho_df:</span>
+<span class="sd">                Override the translation data frame. If provided, the</span>
+<span class="sd">                parameters in `kwargs` won&#39;t have an effect. Must have</span>
+<span class="sd">                columns &quot;source&quot; and &quot;target&quot;.</span>
+<span class="sd">            kwargs:</span>
+<span class="sd">                Resource specific translation parameters.</span>
+
+<span class="sd">        Returns:</span>
+<span class="sd">            A data frame with the same column layout as the input, and the</span>
+<span class="sd">            identifiers translated as demanded. Rows that could not be</span>
+<span class="sd">            translated are omitted.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">_log</span><span class="p">(</span>
+            <span class="sa">f</span><span class="s1">&#39;Translating data frame column(s) from &#39;</span>
+            <span class="sa">f</span><span class="s1">&#39;organism `</span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">source</span><span class="si">}</span><span class="s1">` to `</span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">target</span><span class="si">}</span><span class="s1">`.&#39;</span>
+        <span class="p">)</span>
+
+        <span class="n">ortho_df</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">df</span><span class="p">(</span><span class="o">**</span><span class="n">kwargs</span><span class="p">)</span> <span class="k">if</span> <span class="n">ortho_df</span> <span class="ow">is</span> <span class="kc">None</span> <span class="k">else</span> <span class="n">ortho_df</span><span class="p">)</span><span class="o">.</span>
+            <span class="n">rename</span><span class="p">(</span>
+                <span class="p">{</span>
+                    <span class="s1">&#39;source&#39;</span><span class="p">:</span> <span class="s1">&#39;pypath_internal_source&#39;</span><span class="p">,</span>
+                    <span class="s1">&#39;target&#39;</span><span class="p">:</span> <span class="s1">&#39;pypath_internal_target&#39;</span><span class="p">,</span>
+                <span class="p">},</span>
+                <span class="n">axis</span> <span class="o">=</span> <span class="mi">1</span><span class="p">,</span>
+            <span class="p">)</span>
+        <span class="p">)</span>
+
+        <span class="n">col_order</span> <span class="o">=</span> <span class="n">df</span><span class="o">.</span><span class="n">columns</span>
+        <span class="n">cols</span> <span class="o">=</span> <span class="n">common</span><span class="o">.</span><span class="n">to_list</span><span class="p">(</span><span class="n">cols</span><span class="p">)</span>
+
+        <span class="k">for</span> <span class="n">col</span> <span class="ow">in</span> <span class="n">cols</span><span class="p">:</span>
+
+            <span class="n">_log</span><span class="p">(</span>
+                <span class="sa">f</span><span class="s1">&#39;Translating `</span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">id_type</span><span class="si">}</span><span class="s1">` IDs of organism `</span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">source</span><span class="si">}</span><span class="s1">` &#39;</span>
+                <span class="sa">f</span><span class="s1">&#39;in column `</span><span class="si">{</span><span class="n">col</span><span class="si">}</span><span class="s1">` to organism `</span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">target</span><span class="si">}</span><span class="s1">`.&#39;</span>
+            <span class="p">)</span>
+
+            <span class="n">df</span> <span class="o">=</span> <span class="p">(</span>
+                <span class="n">df</span><span class="o">.</span><span class="n">merge</span><span class="p">(</span>
+                    <span class="n">ortho_df</span><span class="o">.</span><span class="n">rename</span><span class="p">({</span><span class="s1">&#39;pypath_internal_source&#39;</span><span class="p">:</span> <span class="n">col</span><span class="p">},</span> <span class="n">axis</span> <span class="o">=</span> <span class="mi">1</span><span class="p">),</span>
+                    <span class="n">on</span> <span class="o">=</span> <span class="n">col</span><span class="p">,</span>
+                    <span class="n">how</span> <span class="o">=</span> <span class="s1">&#39;inner&#39;</span><span class="p">,</span>
+                <span class="p">)</span><span class="o">.</span>
+                <span class="n">drop</span><span class="p">(</span><span class="n">col</span><span class="p">,</span> <span class="n">axis</span> <span class="o">=</span> <span class="mi">1</span><span class="p">)</span><span class="o">.</span>
+                <span class="n">rename</span><span class="p">({</span><span class="s1">&#39;pypath_internal_target&#39;</span><span class="p">:</span> <span class="n">col</span><span class="p">},</span> <span class="n">axis</span> <span class="o">=</span> <span class="mi">1</span><span class="p">)</span>
+            <span class="p">)</span>
+
+        <span class="k">return</span> <span class="n">df</span><span class="p">[</span><span class="n">col_order</span><span class="p">]</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">_translation_param</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">loc</span><span class="p">:</span> <span class="nb">dict</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">dict</span><span class="p">:</span>
+
+        <span class="k">return</span> <span class="nb">dict</span><span class="p">(</span>
+            <span class="p">(</span><span class="n">p</span><span class="p">,</span> <span class="n">loc</span><span class="p">[</span><span class="n">p</span><span class="p">])</span>
+            <span class="k">for</span> <span class="n">p</span> <span class="ow">in</span> <span class="n">OrthologyManager</span><span class="o">.</span><span class="n">TRANSLATION_PARAM</span>
+        <span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">_set_param</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">loc</span><span class="p">:</span> <span class="nb">dict</span><span class="p">,</span> <span class="o">*</span><span class="n">params</span><span class="p">:</span> <span class="nb">str</span><span class="p">):</span>
+
+        <span class="k">for</span> <span class="n">param</span> <span class="ow">in</span> <span class="n">params</span><span class="p">:</span>
+
+            <span class="n">key</span> <span class="o">=</span> <span class="sa">f</span><span class="s1">&#39;orthology_</span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">_resource_l</span><span class="si">}</span><span class="s1">_</span><span class="si">{</span><span class="n">param</span><span class="si">}</span><span class="s1">&#39;</span>
+            <span class="nb">setattr</span><span class="p">(</span>
+                <span class="bp">self</span><span class="p">,</span>
+                <span class="n">param</span><span class="p">,</span>
+                <span class="n">common</span><span class="o">.</span><span class="n">first_value</span><span class="p">(</span><span class="n">loc</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="n">param</span><span class="p">,</span> <span class="kc">None</span><span class="p">),</span> <span class="n">settings</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="n">key</span><span class="p">)),</span>
+            <span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">match</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">ortholog</span><span class="p">:</span> <span class="n">OrthologBase</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">bool</span><span class="p">:</span>
+
+        <span class="k">return</span> <span class="kc">True</span>
+
+
+    <span class="k">def</span> <span class="nf">_from_pickle</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">bool</span><span class="p">:</span>
+
+        <span class="k">if</span> <span class="p">(</span>
+            <span class="n">settings</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">&#39;orthology_cache&#39;</span><span class="p">)</span> <span class="ow">and</span>
+            <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">exists</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">pickle_path</span><span class="p">)</span>
+        <span class="p">):</span>
+
+            <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">pickle_path</span><span class="p">,</span> <span class="s1">&#39;rb&#39;</span><span class="p">)</span> <span class="k">as</span> <span class="n">fp</span><span class="p">:</span>
+
+                <span class="bp">self</span><span class="o">.</span><span class="n">data</span> <span class="o">=</span> <span class="n">pickle</span><span class="o">.</span><span class="n">load</span><span class="p">(</span><span class="n">fp</span><span class="p">)</span>
+                <span class="n">_log</span><span class="p">(</span>
+                    <span class="s1">&#39;Orthology table from taxon </span><span class="si">%u</span><span class="s1"> to </span><span class="si">%u</span><span class="s1"> (only SwissProt: </span><span class="si">%s</span><span class="s1">; &#39;</span>
+                    <span class="s1">&#39;resource: </span><span class="si">%s</span><span class="s1">; ID type: </span><span class="si">%s</span><span class="s1">) has been loaded from `</span><span class="si">%s</span><span class="s1">`.&#39;</span> <span class="o">%</span> <span class="p">(</span>
+                        <span class="bp">self</span><span class="o">.</span><span class="n">key</span> <span class="o">+</span> <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">pickle_path</span><span class="p">,)</span>
+                    <span class="p">)</span>
+                <span class="p">)</span>
+                <span class="k">return</span> <span class="kc">True</span>
+
+        <span class="k">return</span> <span class="kc">False</span>
+
+
+    <span class="k">def</span> <span class="nf">_to_pickle</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">pickle_path</span><span class="p">,</span> <span class="s1">&#39;wb&#39;</span><span class="p">)</span> <span class="k">as</span> <span class="n">fp</span><span class="p">:</span>
+
+            <span class="n">pickle</span><span class="o">.</span><span class="n">dump</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">data</span><span class="p">,</span> <span class="n">fp</span><span class="p">)</span>
+            <span class="n">_log</span><span class="p">(</span>
+                <span class="s1">&#39;Orthology table from taxon </span><span class="si">%u</span><span class="s1"> to </span><span class="si">%u</span><span class="s1"> (only SwissProt: </span><span class="si">%s</span><span class="s1">; &#39;</span>
+                <span class="s1">&#39;resource: </span><span class="si">%s</span><span class="s1">; ID type: </span><span class="si">%s</span><span class="s1">) has been saved to `</span><span class="si">%s</span><span class="s1">`.&#39;</span> <span class="o">%</span> <span class="p">(</span>
+                    <span class="bp">self</span><span class="o">.</span><span class="n">key</span> <span class="o">+</span> <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">pickle_path</span><span class="p">,)</span>
+                <span class="p">)</span>
+            <span class="p">)</span>
+
+
+    <span class="nd">@property</span>
+    <span class="k">def</span> <span class="nf">key</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="n">OrthologyTableKey</span><span class="p">(</span>
+            <span class="n">source</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">source</span><span class="p">,</span>
+            <span class="n">target</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">target</span><span class="p">,</span>
+            <span class="n">only_swissprot</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">only_swissprot</span><span class="p">,</span>
+            <span class="n">resource</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_resource_l</span><span class="p">,</span>
+            <span class="n">id_type</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">id_type</span><span class="p">,</span>
+        <span class="p">)</span>
+
+
+    <span class="nd">@property</span>
+    <span class="k">def</span> <span class="nf">pickle_path</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span>
+            <span class="n">cache_mod</span><span class="o">.</span><span class="n">get_cachedir</span><span class="p">(),</span>
+            <span class="sa">f</span><span class="s1">&#39;</span><span class="si">{</span><span class="n">common</span><span class="o">.</span><span class="n">md5</span><span class="p">(</span><span class="n">json</span><span class="o">.</span><span class="n">dumps</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">key</span><span class="p">))</span><span class="si">}</span><span class="s1">.pickle&#39;</span><span class="p">,</span>
+        <span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="fm">__len__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="nb">sum</span><span class="p">(</span><span class="nb">map</span><span class="p">(</span><span class="nb">len</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span><span class="o">.</span><span class="n">values</span><span class="p">()))</span>
+
+
+    <span class="k">def</span> <span class="fm">__repr__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="p">(</span>
+            <span class="sa">f</span><span class="s1">&#39;&lt;</span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">resource</span><span class="si">}</span><span class="s1"> Orthology table from </span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">source</span><span class="si">}</span><span class="s1"> to &#39;</span>
+            <span class="sa">f</span><span class="s1">&#39;</span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">target</span><span class="si">}</span><span class="s1">: </span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">id_type</span><span class="si">}</span><span class="s1"> IDs, </span><span class="si">{</span><span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span><span class="si">}</span><span class="s1"> relationships&gt;&#39;</span>
+        <span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="HomologeneOrthology">
+<a class="viewcode-back" href="../../../api/pypath.utils.orthology.HomologeneOrthology.html#pypath.utils.orthology.HomologeneOrthology">[docs]</a>
+<span class="k">class</span> <span class="nc">HomologeneOrthology</span><span class="p">(</span><span class="n">ProteinOrthology</span><span class="p">):</span>
+
+    <span class="n">resource</span> <span class="o">=</span> <span class="s1">&#39;HomoloGene&#39;</span>
+
+
+<div class="viewcode-block" id="HomologeneOrthology.load">
+<a class="viewcode-back" href="../../../api/pypath.utils.orthology.HomologeneOrthology.html#pypath.utils.orthology.HomologeneOrthology.load">[docs]</a>
+    <span class="k">def</span> <span class="nf">load</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Load orthology data from NCBI HomoloGene.</span>
+
+<span class="sd">        Builds orthology translation table as dict based on NCBI HomoloGene</span>
+<span class="sd">        data. If the `id_type` is supported by HomoloGene (Gene Symbol, RefSeq,</span>
+<span class="sd">        Entrez, GI), the data will be simply loaded. For other ID types it</span>
+<span class="sd">        translates HomoloGene Gene Symbol, RefSeq and Entrez tables to UniProt</span>
+<span class="sd">        and then translates the orthologous UniProt pairs to the desired</span>
+<span class="sd">        ID type.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">_from_pickle</span><span class="p">():</span>
+
+            <span class="k">return</span>
+
+        <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">id_type</span> <span class="ow">in</span> <span class="p">(</span><span class="s1">&#39;genesymbol&#39;</span><span class="p">,</span> <span class="s1">&#39;refseq&#39;</span><span class="p">,</span> <span class="s1">&#39;refseqp&#39;</span><span class="p">,</span> <span class="s1">&#39;entrez&#39;</span><span class="p">,</span> <span class="s1">&#39;gi&#39;</span><span class="p">):</span>
+
+            <span class="n">data</span> <span class="o">=</span> <span class="n">homologene_input</span><span class="o">.</span><span class="n">homologene_dict</span><span class="p">(</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">source</span><span class="p">,</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">target</span><span class="p">,</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">id_type</span><span class="p">,</span>
+            <span class="p">)</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">data</span> <span class="o">=</span> <span class="p">{</span>
+                <span class="n">s</span><span class="p">:</span> <span class="p">{</span><span class="n">HomologeneOrtholog</span><span class="p">(</span><span class="n">t</span><span class="p">)</span> <span class="k">for</span> <span class="n">t</span> <span class="ow">in</span> <span class="n">target_ids</span><span class="p">}</span>
+                <span class="k">for</span> <span class="n">s</span><span class="p">,</span> <span class="n">target_ids</span> <span class="ow">in</span> <span class="n">data</span><span class="o">.</span><span class="n">items</span><span class="p">()</span>
+            <span class="p">}</span>
+            <span class="k">return</span>
+
+        <span class="n">hg</span> <span class="o">=</span> <span class="p">{</span>
+            <span class="n">id_type</span><span class="p">:</span> <span class="n">homologene_input</span><span class="o">.</span><span class="n">homologene_dict</span><span class="p">(</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">source</span><span class="p">,</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">target</span><span class="p">,</span>
+                <span class="n">id_type</span><span class="p">,</span>
+            <span class="p">)</span>
+            <span class="k">for</span> <span class="n">id_type</span> <span class="ow">in</span> <span class="p">(</span><span class="s1">&#39;genesymbol&#39;</span><span class="p">,</span> <span class="s1">&#39;refseq&#39;</span><span class="p">,</span> <span class="s1">&#39;entrez&#39;</span><span class="p">)</span>
+        <span class="p">}</span>
+
+        <span class="n">_log</span><span class="p">(</span>
+            <span class="s1">&#39;Loading orthology data from NCBI HomoloGene &#39;</span>
+            <span class="sa">f</span><span class="s1">&#39;between organisms `</span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">source</span><span class="si">}</span><span class="s1">` and `</span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">target</span><span class="si">}</span><span class="s1">`.&#39;</span>
+        <span class="p">)</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">data</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">defaultdict</span><span class="p">(</span><span class="nb">set</span><span class="p">)</span>
+
+        <span class="k">for</span> <span class="n">u</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">_proteomes</span><span class="p">[(</span><span class="bp">self</span><span class="o">.</span><span class="n">source</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">only_swissprot</span><span class="p">)]:</span>
+
+            <span class="n">target_uniprots</span> <span class="o">=</span> <span class="nb">set</span><span class="p">()</span>
+
+            <span class="k">for</span> <span class="n">id_type</span><span class="p">,</span> <span class="n">hgdata</span> <span class="ow">in</span> <span class="n">hg</span><span class="o">.</span><span class="n">items</span><span class="p">():</span>
+
+                <span class="n">hg_source_ids</span> <span class="o">=</span> <span class="n">mapping</span><span class="o">.</span><span class="n">map_name</span><span class="p">(</span>
+                    <span class="n">u</span><span class="p">,</span>
+                    <span class="s1">&#39;uniprot&#39;</span><span class="p">,</span>
+                    <span class="n">id_type</span><span class="p">,</span>
+                    <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">source</span><span class="p">,</span>
+                <span class="p">)</span>
+
+                <span class="k">if</span> <span class="ow">not</span> <span class="n">hg_source_ids</span><span class="p">:</span> <span class="k">continue</span>
+
+                <span class="n">hg_target_ids</span> <span class="o">=</span> <span class="nb">set</span><span class="o">.</span><span class="n">union</span><span class="p">(</span><span class="o">*</span><span class="p">(</span>
+                    <span class="n">hgdata</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="n">s</span><span class="p">,</span> <span class="nb">set</span><span class="p">())</span>
+                    <span class="k">for</span> <span class="n">s</span> <span class="ow">in</span> <span class="n">hg_source_ids</span><span class="p">)</span>
+                <span class="p">)</span>
+
+                <span class="k">if</span> <span class="ow">not</span> <span class="n">hg_target_ids</span><span class="p">:</span> <span class="k">continue</span>
+
+                <span class="n">target_uniprots</span><span class="o">.</span><span class="n">update</span><span class="p">(</span>
+                    <span class="n">mapping</span><span class="o">.</span><span class="n">map_names</span><span class="p">(</span>
+                        <span class="n">hg_target_ids</span><span class="p">,</span>
+                        <span class="n">id_type</span><span class="p">,</span>
+                        <span class="s1">&#39;uniprot&#39;</span><span class="p">,</span>
+                        <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">target</span><span class="p">,</span>
+                    <span class="p">)</span>
+                <span class="p">)</span>
+
+            <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">id_type</span> <span class="o">==</span> <span class="s1">&#39;uniprot&#39;</span><span class="p">:</span>
+
+                <span class="n">source_ids</span> <span class="o">=</span> <span class="p">(</span><span class="n">u</span><span class="p">,)</span>
+                <span class="n">target_ids</span> <span class="o">=</span> <span class="n">target_uniprots</span>
+
+            <span class="k">else</span><span class="p">:</span>
+
+                <span class="n">source_ids</span> <span class="o">=</span> <span class="n">mapping</span><span class="o">.</span><span class="n">map_name</span><span class="p">(</span>
+                    <span class="n">u</span><span class="p">,</span>
+                    <span class="s1">&#39;uniprot&#39;</span><span class="p">,</span>
+                    <span class="bp">self</span><span class="o">.</span><span class="n">id_type</span><span class="p">,</span>
+                    <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">source</span><span class="p">,</span>
+                <span class="p">)</span>
+                <span class="n">target_ids</span> <span class="o">=</span> <span class="n">mapping</span><span class="o">.</span><span class="n">map_names</span><span class="p">(</span>
+                    <span class="n">target_uniprots</span><span class="p">,</span>
+                    <span class="s1">&#39;uniprot&#39;</span><span class="p">,</span>
+                    <span class="bp">self</span><span class="o">.</span><span class="n">id_type</span><span class="p">,</span>
+                    <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">target</span><span class="p">,</span>
+                <span class="p">)</span>
+
+            <span class="k">for</span> <span class="n">s</span> <span class="ow">in</span> <span class="n">source_ids</span><span class="p">:</span>
+
+                <span class="bp">self</span><span class="o">.</span><span class="n">data</span><span class="p">[</span><span class="n">s</span><span class="p">]</span><span class="o">.</span><span class="n">update</span><span class="p">(</span>
+                    <span class="p">{</span>
+                        <span class="n">HomologeneOrtholog</span><span class="p">(</span><span class="n">t</span><span class="p">)</span>
+                        <span class="k">for</span> <span class="n">t</span> <span class="ow">in</span> <span class="n">target_ids</span>
+                    <span class="p">}</span>
+                <span class="p">)</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">data</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">data</span><span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">_to_pickle</span><span class="p">()</span></div>
+</div>
+
+
+
+<div class="viewcode-block" id="EnsemblOrthology">
+<a class="viewcode-back" href="../../../api/pypath.utils.orthology.EnsemblOrthology.html#pypath.utils.orthology.EnsemblOrthology">[docs]</a>
+<span class="k">class</span> <span class="nc">EnsemblOrthology</span><span class="p">(</span><span class="n">ProteinOrthology</span><span class="p">):</span>
+
+    <span class="n">_param</span> <span class="o">=</span> <span class="p">(</span><span class="s1">&#39;hc&#39;</span><span class="p">,</span> <span class="s1">&#39;types&#39;</span><span class="p">)</span>
+    <span class="n">resource</span> <span class="o">=</span> <span class="s1">&#39;Ensembl&#39;</span>
+
+<div class="viewcode-block" id="EnsemblOrthology.__init__">
+<a class="viewcode-back" href="../../../api/pypath.utils.orthology.EnsemblOrthology.html#pypath.utils.orthology.EnsemblOrthology.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">target</span><span class="p">:</span> <span class="nb">int</span> <span class="o">|</span> <span class="nb">str</span><span class="p">,</span>
+            <span class="n">source</span><span class="p">:</span> <span class="nb">int</span> <span class="o">|</span> <span class="nb">str</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">,</span>
+            <span class="n">id_type</span><span class="p">:</span> <span class="nb">str</span> <span class="o">=</span> <span class="s1">&#39;uniprot&#39;</span><span class="p">,</span>
+            <span class="n">only_swissprot</span><span class="p">:</span> <span class="nb">bool</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">hc</span><span class="p">:</span> <span class="nb">bool</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">types</span><span class="p">:</span> <span class="nb">list</span><span class="p">[</span><span class="n">Literal</span><span class="p">[</span>
+                <span class="s1">&#39;one2one&#39;</span><span class="p">,</span> <span class="s1">&#39;one2many&#39;</span><span class="p">,</span> <span class="s1">&#39;many2many&#39;</span>
+            <span class="p">]]</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+        <span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Orthology translation with Ensembl data.</span>
+
+<span class="sd">        Args</span>
+<span class="sd">            target:</span>
+<span class="sd">                Name or NCBI Taxonomy ID of the target organism.</span>
+<span class="sd">            source:</span>
+<span class="sd">                Name or NCBI Taxonomy ID of the source organism.</span>
+<span class="sd">            id_type:</span>
+<span class="sd">                The identifier type to use.</span>
+<span class="sd">            only_swissprot:</span>
+<span class="sd">                Use only SwissProt IDs.</span>
+<span class="sd">            hc:</span>
+<span class="sd">                Use only high confidence orthology relations</span>
+<span class="sd">                from Ensembl. By default it is True. You can also set it</span>
+<span class="sd">                by the `ensembl_hc` attribute.</span>
+<span class="sd">            types:</span>
+<span class="sd">                The Ensembl orthology relationship types</span>
+<span class="sd">                to use. Possible values are `one2one`, `one2many` and</span>
+<span class="sd">                `many2many`. By default only `one2one` is used. You can</span>
+<span class="sd">                also set this parameter by the `ensembl_types` attribute.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">ProteinOrthology</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="o">**</span><span class="nb">locals</span><span class="p">())</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">load</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="n">target_organism</span> <span class="o">=</span> <span class="n">taxonomy</span><span class="o">.</span><span class="n">ensure_ensembl_name</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">target</span><span class="p">)</span>
+        <span class="n">source_organism</span> <span class="o">=</span> <span class="n">taxonomy</span><span class="o">.</span><span class="n">ensure_ensembl_name</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">source</span><span class="p">)</span>
+
+        <span class="n">_log</span><span class="p">(</span>
+            <span class="s1">&#39;Loading orthology data from Ensembl &#39;</span>
+            <span class="sa">f</span><span class="s1">&#39;between organisms `</span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">source</span><span class="si">}</span><span class="s1">` and `</span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">target</span><span class="si">}</span><span class="s1">`.&#39;</span>
+        <span class="p">)</span>
+
+        <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">_from_pickle</span><span class="p">():</span>
+
+            <span class="k">return</span>
+
+        <span class="k">if</span> <span class="ow">not</span> <span class="n">target_organism</span> <span class="ow">or</span> <span class="ow">not</span> <span class="n">source_organism</span><span class="p">:</span>
+
+            <span class="n">_log</span><span class="p">(</span>
+                <span class="s1">&#39;No Ensembl orthology data available between &#39;</span>
+                <span class="sa">f</span><span class="s1">&#39;organisms `</span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">source</span><span class="si">}</span><span class="s1">` and `</span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">target</span><span class="si">}</span><span class="s1">`.&#39;</span>
+            <span class="p">)</span>
+            <span class="k">return</span>
+
+        <span class="n">target_prefix</span> <span class="o">=</span> <span class="sa">f</span><span class="s1">&#39;</span><span class="si">{</span><span class="n">target_organism</span><span class="si">}</span><span class="s1">_homolog_&#39;</span>
+
+        <span class="n">attr_target_ensp</span> <span class="o">=</span> <span class="sa">f</span><span class="s1">&#39;</span><span class="si">{</span><span class="n">target_prefix</span><span class="si">}</span><span class="s1">ensembl_peptide&#39;</span>
+        <span class="n">attr_conf</span> <span class="o">=</span> <span class="sa">f</span><span class="s1">&#39;</span><span class="si">{</span><span class="n">target_prefix</span><span class="si">}</span><span class="s1">orthology_confidence&#39;</span>
+        <span class="n">attr_type</span> <span class="o">=</span> <span class="sa">f</span><span class="s1">&#39;</span><span class="si">{</span><span class="n">target_prefix</span><span class="si">}</span><span class="s1">orthology_type&#39;</span>
+
+        <span class="n">ensembl_data</span> <span class="o">=</span> <span class="n">biomart</span><span class="o">.</span><span class="n">biomart_homology</span><span class="p">(</span>
+            <span class="n">source_organism</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">source</span><span class="p">,</span>
+            <span class="n">target_organism</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">target</span><span class="p">,</span>
+        <span class="p">)</span>
+
+        <span class="n">_id_types</span> <span class="o">=</span> <span class="p">{</span>
+            <span class="s1">&#39;target&#39;</span><span class="p">:</span> <span class="p">{</span>
+                <span class="s1">&#39;genesymbol&#39;</span><span class="p">:</span> <span class="sa">f</span><span class="s1">&#39;</span><span class="si">{</span><span class="n">target_prefix</span><span class="si">}</span><span class="s1">associated_gene_name&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;ensp&#39;</span><span class="p">:</span> <span class="sa">f</span><span class="s1">&#39;</span><span class="si">{</span><span class="n">target_prefix</span><span class="si">}</span><span class="s1">ensembl_peptide&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;ensg&#39;</span><span class="p">:</span> <span class="sa">f</span><span class="s1">&#39;</span><span class="si">{</span><span class="n">target_prefix</span><span class="si">}</span><span class="s1">ensembl_gene&#39;</span><span class="p">,</span>
+            <span class="p">},</span>
+            <span class="s1">&#39;source&#39;</span><span class="p">:</span> <span class="p">{</span>
+                <span class="s1">&#39;genesymbol&#39;</span><span class="p">:</span> <span class="s1">&#39;external_gene_name&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;ensp&#39;</span><span class="p">:</span> <span class="s1">&#39;ensembl_peptide_id&#39;</span><span class="p">,</span>
+                <span class="s1">&#39;ensg&#39;</span><span class="p">:</span> <span class="s1">&#39;ensembl_gene_id&#39;</span><span class="p">,</span>
+            <span class="p">},</span>
+        <span class="p">}</span>
+        <span class="n">attr_tgt_id</span> <span class="o">=</span> <span class="n">_id_types</span><span class="p">[</span><span class="s1">&#39;target&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">get</span><span class="p">(</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">id_type</span><span class="p">,</span>
+            <span class="sa">f</span><span class="s1">&#39;</span><span class="si">{</span><span class="n">target_prefix</span><span class="si">}</span><span class="s1">ensembl_peptide&#39;</span><span class="p">,</span>
+        <span class="p">)</span>
+        <span class="n">attr_src_id</span> <span class="o">=</span> <span class="n">_id_types</span><span class="p">[</span><span class="s1">&#39;source&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">get</span><span class="p">(</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">id_type</span><span class="p">,</span>
+            <span class="s1">&#39;ensembl_peptide_id&#39;</span><span class="p">,</span>
+        <span class="p">)</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">data</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">defaultdict</span><span class="p">(</span><span class="nb">set</span><span class="p">)</span>
+
+        <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">id_type</span> <span class="ow">in</span> <span class="n">_id_types</span><span class="p">[</span><span class="s1">&#39;target&#39;</span><span class="p">]:</span>
+
+            <span class="k">for</span> <span class="n">r</span> <span class="ow">in</span> <span class="n">ensembl_data</span><span class="p">:</span>
+
+                <span class="bp">self</span><span class="o">.</span><span class="n">data</span><span class="p">[</span><span class="nb">getattr</span><span class="p">(</span><span class="n">r</span><span class="p">,</span> <span class="n">attr_src_id</span><span class="p">)]</span><span class="o">.</span><span class="n">add</span><span class="p">(</span>
+                    <span class="n">EnsemblOrtholog</span><span class="p">(</span>
+                        <span class="nb">id</span> <span class="o">=</span> <span class="nb">getattr</span><span class="p">(</span><span class="n">r</span><span class="p">,</span> <span class="n">attr_tgt_id</span><span class="p">),</span>
+                        <span class="n">hc</span> <span class="o">=</span> <span class="nb">getattr</span><span class="p">(</span><span class="n">r</span><span class="p">,</span> <span class="n">attr_conf</span><span class="p">)</span> <span class="o">==</span> <span class="s1">&#39;1&#39;</span><span class="p">,</span>
+                        <span class="n">types</span> <span class="o">=</span> <span class="nb">getattr</span><span class="p">(</span><span class="n">r</span><span class="p">,</span> <span class="n">attr_type</span><span class="p">)</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;_&#39;</span><span class="p">)[</span><span class="o">-</span><span class="mi">1</span><span class="p">],</span>
+                    <span class="p">)</span>
+                <span class="p">)</span>
+
+        <span class="k">for</span> <span class="n">r</span> <span class="ow">in</span> <span class="n">ensembl_data</span><span class="p">:</span>
+
+            <span class="n">ids</span> <span class="o">=</span> <span class="p">{}</span>
+
+            <span class="k">for</span> <span class="n">side</span><span class="p">,</span> <span class="n">attr_id</span> <span class="ow">in</span> <span class="p">(</span>
+                    <span class="p">(</span><span class="s1">&#39;source&#39;</span><span class="p">,</span> <span class="n">attr_src_id</span><span class="p">),</span>
+                    <span class="p">(</span><span class="s1">&#39;target&#39;</span><span class="p">,</span> <span class="n">attr_tgt_id</span><span class="p">)</span>
+                <span class="p">):</span>
+
+                <span class="n">uniprots</span> <span class="o">=</span> <span class="n">mapping</span><span class="o">.</span><span class="n">map_name</span><span class="p">(</span>
+                    <span class="nb">getattr</span><span class="p">(</span><span class="n">r</span><span class="p">,</span> <span class="n">attr_id</span><span class="p">),</span>
+                    <span class="s1">&#39;ensp&#39;</span><span class="p">,</span>
+                    <span class="s1">&#39;uniprot&#39;</span><span class="p">,</span>
+                    <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="nb">getattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">side</span><span class="p">),</span>
+                <span class="p">)</span>
+                <span class="n">ids</span><span class="p">[</span><span class="n">side</span><span class="p">]</span> <span class="o">=</span> <span class="n">mapping</span><span class="o">.</span><span class="n">map_names</span><span class="p">(</span>
+                    <span class="n">uniprots</span><span class="p">,</span>
+                    <span class="s1">&#39;uniprot&#39;</span><span class="p">,</span>
+                    <span class="bp">self</span><span class="o">.</span><span class="n">id_type</span><span class="p">,</span>
+                    <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="nb">getattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">side</span><span class="p">),</span>
+                    <span class="n">uniprot_cleanup</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+                <span class="p">)</span>
+
+                <span class="k">if</span> <span class="ow">not</span> <span class="n">ids</span><span class="p">[</span><span class="n">side</span><span class="p">]:</span>
+
+                    <span class="k">continue</span>
+
+            <span class="k">for</span> <span class="n">s</span> <span class="ow">in</span> <span class="n">ids</span><span class="p">[</span><span class="s1">&#39;source&#39;</span><span class="p">]:</span>
+
+                <span class="bp">self</span><span class="o">.</span><span class="n">data</span><span class="p">[</span><span class="n">s</span><span class="p">]</span><span class="o">.</span><span class="n">update</span><span class="p">(</span>
+                    <span class="p">{</span>
+                        <span class="n">EnsemblOrtholog</span><span class="p">(</span>
+                            <span class="nb">id</span> <span class="o">=</span> <span class="n">t</span><span class="p">,</span>
+                            <span class="n">hc</span> <span class="o">=</span> <span class="nb">getattr</span><span class="p">(</span><span class="n">r</span><span class="p">,</span> <span class="n">attr_conf</span><span class="p">)</span> <span class="o">==</span> <span class="s1">&#39;1&#39;</span><span class="p">,</span>
+                            <span class="n">types</span> <span class="o">=</span> <span class="nb">getattr</span><span class="p">(</span><span class="n">r</span><span class="p">,</span> <span class="n">attr_type</span><span class="p">)</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;_&#39;</span><span class="p">)[</span><span class="o">-</span><span class="mi">1</span><span class="p">],</span>
+                        <span class="p">)</span>
+                        <span class="k">for</span> <span class="n">t</span> <span class="ow">in</span> <span class="n">ids</span><span class="p">[</span><span class="s1">&#39;target&#39;</span><span class="p">]</span>
+                    <span class="p">}</span>
+                <span class="p">)</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">data</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">data</span><span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">_to_pickle</span><span class="p">()</span>
+
+
+<div class="viewcode-block" id="EnsemblOrthology.match">
+<a class="viewcode-back" href="../../../api/pypath.utils.orthology.EnsemblOrthology.html#pypath.utils.orthology.EnsemblOrthology.match">[docs]</a>
+    <span class="k">def</span> <span class="nf">match</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">ortholog</span><span class="p">:</span> <span class="n">OrthologBase</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">bool</span><span class="p">:</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Check an ortholog against filtering criteria.</span>
+
+<span class="sd">        Args:</span>
+<span class="sd">            ortholog:</span>
+<span class="sd">                An ortholog record.</span>
+<span class="sd">            kwargs:</span>
+<span class="sd">                Override default filtering parameters.</span>
+
+<span class="sd">        Returns:</span>
+<span class="sd">            True if the ortholog meets the criteria.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">kwargs</span> <span class="o">=</span> <span class="p">{</span><span class="n">k</span><span class="p">:</span> <span class="n">v</span> <span class="k">for</span> <span class="n">k</span><span class="p">,</span> <span class="n">v</span> <span class="ow">in</span> <span class="n">kwargs</span><span class="o">.</span><span class="n">items</span><span class="p">()</span> <span class="k">if</span> <span class="n">v</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">}</span>
+        <span class="n">hc</span> <span class="o">=</span> <span class="n">kwargs</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">&#39;hc&#39;</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">hc</span><span class="p">)</span>
+        <span class="n">types</span> <span class="o">=</span> <span class="n">kwargs</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">&#39;types&#39;</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">types</span><span class="p">)</span>
+
+        <span class="k">return</span> <span class="p">(</span>
+            <span class="p">(</span><span class="ow">not</span> <span class="n">hc</span> <span class="ow">or</span> <span class="n">ortholog</span><span class="o">.</span><span class="n">hc</span><span class="p">)</span> <span class="ow">and</span>
+            <span class="p">(</span><span class="ow">not</span> <span class="n">types</span> <span class="ow">or</span> <span class="n">ortholog</span><span class="o">.</span><span class="n">types</span> <span class="ow">in</span> <span class="n">types</span><span class="p">)</span>
+        <span class="p">)</span></div>
+</div>
+
+
+
+<div class="viewcode-block" id="OmaOrthology">
+<a class="viewcode-back" href="../../../api/pypath.utils.orthology.OmaOrthology.html#pypath.utils.orthology.OmaOrthology">[docs]</a>
+<span class="k">class</span> <span class="nc">OmaOrthology</span><span class="p">(</span><span class="n">ProteinOrthology</span><span class="p">):</span>
+
+    <span class="n">_param</span> <span class="o">=</span> <span class="p">(</span><span class="s1">&#39;rel_type&#39;</span><span class="p">,</span> <span class="s1">&#39;score&#39;</span><span class="p">)</span>
+    <span class="n">resource</span> <span class="o">=</span> <span class="s1">&#39;OMA&#39;</span>
+
+<div class="viewcode-block" id="OmaOrthology.__init__">
+<a class="viewcode-back" href="../../../api/pypath.utils.orthology.OmaOrthology.html#pypath.utils.orthology.OmaOrthology.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">target</span><span class="p">:</span> <span class="nb">int</span> <span class="o">|</span> <span class="nb">str</span><span class="p">,</span>
+            <span class="n">source</span><span class="p">:</span> <span class="nb">int</span> <span class="o">|</span> <span class="nb">str</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">,</span>
+            <span class="n">id_type</span><span class="p">:</span> <span class="nb">str</span> <span class="o">=</span> <span class="s1">&#39;uniprot&#39;</span><span class="p">,</span>
+            <span class="n">only_swissprot</span><span class="p">:</span> <span class="nb">bool</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">rel_type</span><span class="p">:</span> <span class="p">(</span>
+                <span class="nb">set</span><span class="p">[</span><span class="n">Literal</span><span class="p">[</span><span class="s1">&#39;1:1&#39;</span><span class="p">,</span> <span class="s1">&#39;1:n&#39;</span><span class="p">,</span> <span class="s1">&#39;m:1&#39;</span><span class="p">,</span> <span class="s1">&#39;m:n&#39;</span><span class="p">]]</span> <span class="o">|</span>
+                <span class="kc">None</span>
+             <span class="p">)</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">score</span><span class="p">:</span> <span class="nb">float</span> <span class="o">|</span> <span class="kc">None</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+        <span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Orthology translation with Ensembl data.</span>
+
+<span class="sd">        Args</span>
+<span class="sd">            target:</span>
+<span class="sd">                Name or NCBI Taxonomy ID of the target organism.</span>
+<span class="sd">            source:</span>
+<span class="sd">                Name or NCBI Taxonomy ID of the source organism.</span>
+<span class="sd">            id_type:</span>
+<span class="sd">                The identifier type to use.</span>
+<span class="sd">            only_swissprot:</span>
+<span class="sd">                Use only SwissProt IDs.</span>
+<span class="sd">            rel_type:</span>
+<span class="sd">                Restrict relations to certain types.</span>
+<span class="sd">            score:</span>
+<span class="sd">                Lower threshold for similarity metric.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">ProteinOrthology</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="o">**</span><span class="nb">locals</span><span class="p">())</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">load</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="n">_log</span><span class="p">(</span>
+            <span class="s1">&#39;Loading orthology data from OMA &#39;</span>
+            <span class="sa">f</span><span class="s1">&#39;between organisms `</span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">source</span><span class="si">}</span><span class="s1">` and `</span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">target</span><span class="si">}</span><span class="s1">`.&#39;</span>
+        <span class="p">)</span>
+
+        <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">_from_pickle</span><span class="p">():</span>
+
+            <span class="k">return</span>
+
+        <span class="n">oma_data</span> <span class="o">=</span> <span class="n">oma_input</span><span class="o">.</span><span class="n">oma_orthologs</span><span class="p">(</span>
+            <span class="n">organism_a</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">source</span><span class="p">,</span>
+            <span class="n">organism_b</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">target</span><span class="p">,</span>
+            <span class="n">id_type</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">id_type</span><span class="p">,</span>
+        <span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">data</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">defaultdict</span><span class="p">(</span><span class="nb">set</span><span class="p">)</span>
+
+        <span class="k">for</span> <span class="n">rec</span> <span class="ow">in</span> <span class="n">oma_data</span><span class="p">:</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">data</span><span class="p">[</span><span class="n">rec</span><span class="o">.</span><span class="n">a</span><span class="o">.</span><span class="n">id</span><span class="p">]</span><span class="o">.</span><span class="n">add</span><span class="p">(</span>
+                <span class="n">OmaOrtholog</span><span class="p">(</span>
+                    <span class="nb">id</span> <span class="o">=</span> <span class="n">rec</span><span class="o">.</span><span class="n">b</span><span class="o">.</span><span class="n">id</span><span class="p">,</span>
+                    <span class="n">score</span> <span class="o">=</span> <span class="n">rec</span><span class="o">.</span><span class="n">score</span><span class="p">,</span>
+                    <span class="n">rel_type</span> <span class="o">=</span> <span class="n">rec</span><span class="o">.</span><span class="n">rel_type</span><span class="p">,</span>
+                <span class="p">)</span>
+            <span class="p">)</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">data</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">data</span><span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">_to_pickle</span><span class="p">()</span>
+
+
+<div class="viewcode-block" id="OmaOrthology.match">
+<a class="viewcode-back" href="../../../api/pypath.utils.orthology.OmaOrthology.html#pypath.utils.orthology.OmaOrthology.match">[docs]</a>
+    <span class="k">def</span> <span class="nf">match</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">ortholog</span><span class="p">:</span> <span class="n">OrthologBase</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">bool</span><span class="p">:</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Check an ortholog against filtering criteria.</span>
+
+<span class="sd">        Args:</span>
+<span class="sd">            ortholog:</span>
+<span class="sd">                An ortholog record.</span>
+<span class="sd">            kwargs:</span>
+<span class="sd">                Override default filtering parameters.</span>
+
+<span class="sd">        Returns:</span>
+<span class="sd">            True if the ortholog meets the criteria.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">kwargs</span> <span class="o">=</span> <span class="p">{</span><span class="n">k</span><span class="p">:</span> <span class="n">v</span> <span class="k">for</span> <span class="n">k</span><span class="p">,</span> <span class="n">v</span> <span class="ow">in</span> <span class="n">kwargs</span><span class="o">.</span><span class="n">items</span><span class="p">()</span> <span class="k">if</span> <span class="n">v</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">}</span>
+        <span class="n">score</span> <span class="o">=</span> <span class="n">kwargs</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">&#39;score&#39;</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">score</span><span class="p">)</span>
+        <span class="n">rel_type</span> <span class="o">=</span> <span class="n">kwargs</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">&#39;rel_type&#39;</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">rel_type</span><span class="p">)</span>
+
+        <span class="k">return</span> <span class="p">(</span>
+            <span class="p">(</span><span class="n">score</span> <span class="ow">is</span> <span class="kc">None</span> <span class="ow">or</span> <span class="n">ortholog</span><span class="o">.</span><span class="n">score</span> <span class="o">&gt;=</span> <span class="n">score</span><span class="p">)</span> <span class="ow">and</span>
+            <span class="p">(</span><span class="ow">not</span> <span class="n">rel_type</span> <span class="ow">or</span> <span class="n">ortholog</span><span class="o">.</span><span class="n">rel_type</span> <span class="ow">in</span> <span class="n">rel_type</span><span class="p">)</span>
+        <span class="p">)</span></div>
+</div>
+
+
+
+<div class="viewcode-block" id="PtmOrthology">
+<a class="viewcode-back" href="../../../api/pypath.utils.orthology.PtmOrthology.html#pypath.utils.orthology.PtmOrthology">[docs]</a>
+<span class="k">class</span> <span class="nc">PtmOrthology</span><span class="p">(</span><span class="n">Proteomes</span><span class="p">,</span> <span class="n">SequenceContainer</span><span class="p">):</span>
+
+
+<div class="viewcode-block" id="PtmOrthology.__init__">
+<a class="viewcode-back" href="../../../api/pypath.utils.orthology.PtmOrthology.html#pypath.utils.orthology.PtmOrthology.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">target</span><span class="p">:</span> <span class="nb">str</span> <span class="o">|</span> <span class="nb">int</span><span class="p">,</span>
+            <span class="n">source</span><span class="p">:</span> <span class="nb">str</span> <span class="o">|</span> <span class="nb">int</span> <span class="o">|</span> <span class="kc">None</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="n">only_swissprot</span><span class="p">:</span> <span class="nb">bool</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
+            <span class="n">strict</span><span class="p">:</span> <span class="nb">bool</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
+            <span class="n">orthology_args</span><span class="p">:</span> <span class="nb">dict</span> <span class="o">|</span> <span class="kc">None</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+        <span class="p">):</span>
+
+        <span class="k">if</span> <span class="ow">not</span> <span class="nb">hasattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">&#39;_logger&#39;</span><span class="p">):</span>
+
+            <span class="n">session</span><span class="o">.</span><span class="n">Logger</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">name</span> <span class="o">=</span> <span class="s1">&#39;orthology&#39;</span><span class="p">)</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">manager</span> <span class="o">=</span> <span class="n">get_manager</span><span class="p">()</span>
+        <span class="n">SequenceContainer</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span>
+        <span class="n">Proteomes</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">only_swissprot</span> <span class="o">=</span> <span class="n">only_swissprot</span><span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">source</span> <span class="o">=</span> <span class="n">taxonomy</span><span class="o">.</span><span class="n">ensure_ncbi_tax_id</span><span class="p">(</span><span class="n">source</span><span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">target</span> <span class="o">=</span> <span class="n">taxonomy</span><span class="o">.</span><span class="n">ensure_ncbi_tax_id</span><span class="p">(</span><span class="n">target</span><span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">load_seq</span><span class="p">(</span><span class="n">taxon</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">target</span><span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">reptm</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">compile</span><span class="p">(</span><span class="sa">r</span><span class="s1">&#39;([A-Z\d]{6,10})_([A-Z])(\d*)&#39;</span><span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">strict</span> <span class="o">=</span> <span class="n">strict</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">orthology_args</span> <span class="o">=</span> <span class="n">orthology_args</span> <span class="ow">or</span> <span class="p">{}</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">id_type</span> <span class="o">=</span> <span class="s1">&#39;uniprot&#39;</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">ptm_orthology</span><span class="p">()</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">reload</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="n">modname</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="vm">__class__</span><span class="o">.</span><span class="vm">__module__</span>
+        <span class="n">mod</span> <span class="o">=</span> <span class="nb">__import__</span><span class="p">(</span><span class="n">modname</span><span class="p">,</span> <span class="n">fromlist</span><span class="o">=</span><span class="p">[</span><span class="n">modname</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;.&#39;</span><span class="p">)[</span><span class="mi">0</span><span class="p">]])</span>
+        <span class="n">imp</span><span class="o">.</span><span class="n">reload</span><span class="p">(</span><span class="n">mod</span><span class="p">)</span>
+        <span class="n">new</span> <span class="o">=</span> <span class="nb">getattr</span><span class="p">(</span><span class="n">mod</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="vm">__class__</span><span class="o">.</span><span class="vm">__name__</span><span class="p">)</span>
+        <span class="nb">setattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">&#39;__class__&#39;</span><span class="p">,</span> <span class="n">new</span><span class="p">)</span>
+
+
+<div class="viewcode-block" id="PtmOrthology.translate_site">
+<a class="viewcode-back" href="../../../api/pypath.utils.orthology.PtmOrthology.html#pypath.utils.orthology.PtmOrthology.translate_site">[docs]</a>
+    <span class="k">def</span> <span class="nf">translate_site</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">protein</span><span class="p">:</span> <span class="nb">str</span> <span class="o">|</span> <span class="n">intera</span><span class="o">.</span><span class="n">Protein</span><span class="p">,</span>
+            <span class="n">res</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
+            <span class="n">offset</span><span class="p">:</span> <span class="nb">int</span><span class="p">,</span>
+            <span class="n">isoform</span><span class="p">:</span> <span class="nb">int</span> <span class="o">=</span> <span class="mi">1</span><span class="p">,</span>
+            <span class="n">typ</span><span class="p">:</span> <span class="nb">str</span> <span class="o">=</span> <span class="s1">&#39;phosphorylation&#39;</span><span class="p">,</span>
+            <span class="n">source_organism</span><span class="p">:</span> <span class="nb">str</span> <span class="o">|</span> <span class="nb">int</span> <span class="o">|</span> <span class="kc">None</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+        <span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">set</span><span class="p">[</span><span class="nb">tuple</span><span class="p">]:</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Translates one PTM site.</span>
+
+<span class="sd">        Args:</span>
+<span class="sd">            protein:</span>
+<span class="sd">                A protein identifier or an intera.Protein object.</span>
+<span class="sd">            res:</span>
+<span class="sd">                Single letter code of the residue.</span>
+<span class="sd">            offset:</span>
+<span class="sd">                Sequence offset of the site.</span>
+<span class="sd">            isoform:</span>
+<span class="sd">                Sequence isoform.</span>
+<span class="sd">            typ:</span>
+<span class="sd">                Modification type.</span>
+<span class="sd">            source_organism:</span>
+<span class="sd">                Name or NCBI Taxonomy ID of the source organism.</span>
+
+<span class="sd">        Returns:</span>
+<span class="sd">            A list of tuples with the identifier, isoform, residue, offset,</span>
+<span class="sd">            taxon and modification type of the orthologous PTM sites.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">result</span> <span class="o">=</span> <span class="nb">set</span><span class="p">()</span>
+        <span class="n">source</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_get_source</span><span class="p">(</span><span class="n">source_organism</span><span class="p">)</span>
+        <span class="n">protein_id</span> <span class="o">=</span> <span class="nb">getattr</span><span class="p">(</span><span class="n">protein</span><span class="p">,</span> <span class="s1">&#39;identifier&#39;</span><span class="p">,</span> <span class="n">protein</span><span class="p">)</span>
+        <span class="n">sourceptm</span> <span class="o">=</span> <span class="p">(</span><span class="n">protein_id</span><span class="p">,</span> <span class="n">isoform</span><span class="p">,</span> <span class="n">res</span><span class="p">,</span> <span class="n">offset</span><span class="p">,</span> <span class="n">source</span><span class="p">,</span> <span class="n">typ</span><span class="p">)</span>
+
+        <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">get_taxon</span><span class="p">(</span><span class="n">protein_id</span><span class="p">)</span> <span class="o">==</span> <span class="bp">self</span><span class="o">.</span><span class="n">target</span><span class="p">:</span>
+            <span class="n">result</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">sourceptm</span><span class="p">)</span>
+            <span class="k">return</span> <span class="n">result</span>
+
+        <span class="k">if</span> <span class="n">sourceptm</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">ptmortho</span><span class="p">:</span>
+
+            <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">target</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">ptmortho</span><span class="p">[</span><span class="n">sourceptm</span><span class="p">]:</span>
+
+                <span class="n">result</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">ptmortho</span><span class="p">[</span><span class="n">sourceptm</span><span class="p">]</span>
+
+        <span class="k">if</span> <span class="ow">not</span> <span class="n">result</span> <span class="ow">and</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">strict</span><span class="p">:</span>
+
+            <span class="n">tsubs</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">manager</span><span class="o">.</span><span class="n">translate</span><span class="p">(</span>
+                <span class="n">identifiers</span> <span class="o">=</span> <span class="n">protein_id</span><span class="p">,</span>
+                <span class="n">target</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">target</span><span class="p">,</span>
+                <span class="n">source</span> <span class="o">=</span> <span class="n">source</span><span class="p">,</span>
+                <span class="n">only_swissprot</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">only_swissprot</span><span class="p">,</span>
+                <span class="n">id_type</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">id_type</span><span class="p">,</span>
+                <span class="o">**</span><span class="bp">self</span><span class="o">.</span><span class="n">orthology_args</span>
+            <span class="p">)</span>
+
+            <span class="k">for</span> <span class="n">tsub</span> <span class="ow">in</span> <span class="n">tsubs</span><span class="p">:</span>
+
+                <span class="n">se</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">get_seq</span><span class="p">(</span><span class="n">tsub</span><span class="p">,</span> <span class="n">taxon</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">target</span><span class="p">)</span>
+
+                <span class="k">if</span> <span class="n">se</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
+                    <span class="k">continue</span>
+
+                <span class="k">for</span> <span class="n">toffset</span> <span class="ow">in</span> <span class="n">xrange</span><span class="p">(</span><span class="n">offset</span><span class="p">,</span> <span class="n">offset</span> <span class="o">+</span> <span class="mi">3</span><span class="p">):</span>
+
+                    <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="n">se</span><span class="o">.</span><span class="n">isoforms</span><span class="p">():</span>
+
+                        <span class="n">tres</span> <span class="o">=</span> <span class="n">se</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="n">toffset</span><span class="p">,</span> <span class="n">isoform</span> <span class="o">=</span> <span class="n">i</span><span class="p">)</span>
+
+                        <span class="k">if</span> <span class="n">tres</span> <span class="o">==</span> <span class="n">res</span><span class="p">:</span>
+
+                            <span class="n">result</span><span class="o">.</span><span class="n">add</span><span class="p">((</span>
+                                <span class="n">tsub</span><span class="p">,</span>
+                                <span class="n">i</span><span class="p">,</span>
+                                <span class="n">tres</span><span class="p">,</span>
+                                <span class="n">toffset</span><span class="p">,</span>
+                                <span class="bp">self</span><span class="o">.</span><span class="n">target</span><span class="p">,</span>
+                                <span class="n">typ</span><span class="p">,</span>
+                            <span class="p">))</span>
+
+                    <span class="k">if</span> <span class="n">result</span><span class="p">:</span>
+                        <span class="k">break</span>
+
+        <span class="k">return</span> <span class="n">result</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">translate_domain</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">domain</span><span class="p">:</span> <span class="n">intera</span><span class="o">.</span><span class="n">Domain</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">list</span><span class="p">[</span><span class="n">intera</span><span class="o">.</span><span class="n">Domain</span><span class="p">]:</span>
+
+        <span class="k">return</span> <span class="p">[</span>
+            <span class="n">intera</span><span class="o">.</span><span class="n">Domain</span><span class="p">(</span>
+                <span class="n">protein</span> <span class="o">=</span> <span class="n">target_id</span><span class="p">,</span>
+                <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">target</span><span class="p">,</span>
+            <span class="p">)</span>
+            <span class="k">for</span> <span class="n">target_id</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">manager</span><span class="o">.</span><span class="n">translate</span><span class="p">(</span>
+                <span class="n">identifiers</span> <span class="o">=</span> <span class="n">domain</span><span class="o">.</span><span class="n">protein</span><span class="o">.</span><span class="n">identifier</span><span class="p">,</span>
+                <span class="n">target</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">target</span><span class="p">,</span>
+                <span class="n">id_type</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">id_type</span><span class="p">,</span>
+                <span class="n">source</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">get_source</span><span class="p">(</span><span class="n">domain</span><span class="o">.</span><span class="n">ncbi_tax_id</span><span class="p">),</span>
+                <span class="n">only_swissprot</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">only_swissprot</span><span class="p">,</span>
+                <span class="o">**</span><span class="bp">self</span><span class="o">.</span><span class="n">orthology_args</span>
+            <span class="p">)</span>
+        <span class="p">]</span>
+
+
+    <span class="k">def</span> <span class="nf">translate_ptm</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">ptm</span><span class="p">:</span> <span class="n">intera</span><span class="o">.</span><span class="n">Ptm</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">list</span><span class="p">[</span><span class="n">intera</span><span class="o">.</span><span class="n">Ptm</span><span class="p">]:</span>
+
+        <span class="n">tptms</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">translate_site</span><span class="p">(</span>
+            <span class="n">ptm</span><span class="o">.</span><span class="n">protein</span><span class="p">,</span>
+            <span class="n">ptm</span><span class="o">.</span><span class="n">residue</span><span class="o">.</span><span class="n">name</span><span class="p">,</span>
+            <span class="n">ptm</span><span class="o">.</span><span class="n">residue</span><span class="o">.</span><span class="n">number</span><span class="p">,</span>
+            <span class="n">ptm</span><span class="o">.</span><span class="n">residue</span><span class="o">.</span><span class="n">isoform</span><span class="p">,</span>
+            <span class="n">ptm</span><span class="o">.</span><span class="n">typ</span><span class="p">,</span>
+        <span class="p">)</span>
+
+        <span class="n">result</span> <span class="o">=</span> <span class="p">[]</span>
+
+        <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">tptms</span><span class="p">:</span>
+
+            <span class="n">se</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">get_seq</span><span class="p">(</span><span class="n">x</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">taxon</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">target</span><span class="p">)</span>
+
+            <span class="k">if</span> <span class="p">(</span><span class="n">se</span> <span class="ow">is</span> <span class="kc">None</span> <span class="ow">or</span> <span class="n">x</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">se</span><span class="o">.</span><span class="n">isof</span><span class="p">)</span> <span class="ow">and</span> <span class="bp">self</span><span class="o">.</span><span class="n">strict</span><span class="p">:</span>
+                <span class="k">continue</span>
+
+            <span class="n">res</span> <span class="o">=</span> <span class="n">intera</span><span class="o">.</span><span class="n">Residue</span><span class="p">(</span>
+                <span class="n">number</span> <span class="o">=</span> <span class="n">x</span><span class="p">[</span><span class="mi">3</span><span class="p">],</span>
+                <span class="n">name</span> <span class="o">=</span> <span class="n">x</span><span class="p">[</span><span class="mi">2</span><span class="p">],</span>
+                <span class="n">protein</span> <span class="o">=</span> <span class="n">x</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span>
+                <span class="n">isoform</span> <span class="o">=</span> <span class="n">x</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span>
+                <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">target</span><span class="p">,</span>
+            <span class="p">)</span>
+            <span class="n">start</span><span class="p">,</span> <span class="n">end</span><span class="p">,</span> <span class="n">region</span> <span class="o">=</span> <span class="p">(</span>
+                <span class="n">se</span><span class="o">.</span><span class="n">get_region</span><span class="p">(</span><span class="n">x</span><span class="p">[</span><span class="mi">3</span><span class="p">],</span> <span class="n">isoform</span> <span class="o">=</span> <span class="n">x</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span>
+                <span class="k">if</span> <span class="n">se</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span> <span class="ow">and</span> <span class="n">x</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="ow">in</span> <span class="n">se</span><span class="o">.</span><span class="n">isof</span>
+                <span class="k">else</span> <span class="p">(</span><span class="kc">None</span><span class="p">,</span> <span class="kc">None</span><span class="p">,</span> <span class="kc">None</span><span class="p">)</span>
+            <span class="p">)</span>
+            <span class="n">mot</span> <span class="o">=</span> <span class="n">intera</span><span class="o">.</span><span class="n">Motif</span><span class="p">(</span>
+                <span class="n">protein</span> <span class="o">=</span> <span class="n">x</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span>
+                <span class="n">start</span> <span class="o">=</span> <span class="n">start</span><span class="p">,</span>
+                <span class="n">end</span> <span class="o">=</span> <span class="n">end</span><span class="p">,</span>
+                <span class="n">instance</span> <span class="o">=</span> <span class="n">region</span><span class="p">,</span>
+                <span class="n">isoform</span> <span class="o">=</span> <span class="n">x</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span>
+                <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">target</span><span class="p">,</span>
+            <span class="p">)</span>
+
+            <span class="n">ptm</span> <span class="o">=</span> <span class="n">intera</span><span class="o">.</span><span class="n">Ptm</span><span class="p">(</span>
+                <span class="n">protein</span> <span class="o">=</span> <span class="n">x</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span>
+                <span class="n">motif</span> <span class="o">=</span> <span class="n">mot</span><span class="p">,</span>
+                <span class="n">residue</span> <span class="o">=</span> <span class="n">res</span><span class="p">,</span>
+                <span class="n">typ</span> <span class="o">=</span> <span class="n">x</span><span class="p">[</span><span class="mi">5</span><span class="p">],</span>
+                <span class="n">isoform</span> <span class="o">=</span> <span class="n">x</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span>
+                <span class="n">evidences</span> <span class="o">=</span> <span class="n">ptm</span><span class="o">.</span><span class="n">evidences</span><span class="p">,</span>
+                <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">target</span><span class="p">,</span>
+            <span class="p">)</span>
+
+            <span class="n">result</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">ptm</span><span class="p">)</span>
+
+        <span class="k">return</span> <span class="n">result</span>
+
+
+    <span class="k">def</span> <span class="nf">translate_domain_motif</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">dmotif</span><span class="p">:</span> <span class="n">intera</span><span class="o">.</span><span class="n">DomainMotif</span><span class="p">,</span>
+        <span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">list</span><span class="p">[</span><span class="n">intera</span><span class="o">.</span><span class="n">DomainMotif</span><span class="p">]:</span>
+
+        <span class="n">ds</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">translate_domain</span><span class="p">(</span><span class="n">dmotif</span><span class="o">.</span><span class="n">domain</span><span class="p">)</span>
+        <span class="n">ps</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">translate_ptm</span><span class="p">(</span><span class="n">dmotif</span><span class="o">.</span><span class="n">ptm</span><span class="p">)</span>
+
+        <span class="k">return</span> <span class="p">[</span>
+            <span class="n">intera</span><span class="o">.</span><span class="n">DomainMotif</span><span class="p">(</span>
+                <span class="n">x</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span>
+                <span class="n">x</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span>
+                <span class="n">evidences</span> <span class="o">=</span> <span class="n">dmotif</span><span class="o">.</span><span class="n">evidences</span><span class="p">,</span>
+            <span class="p">)</span>
+            <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">itertools</span><span class="o">.</span><span class="n">product</span><span class="p">(</span><span class="n">ds</span><span class="p">,</span> <span class="n">ps</span><span class="p">)</span>
+        <span class="p">]</span>
+
+
+    <span class="k">def</span> <span class="nf">translate_residue</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">residue</span><span class="p">:</span> <span class="n">intera</span><span class="o">.</span><span class="n">Residue</span><span class="p">,</span>
+        <span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">list</span><span class="p">[</span><span class="n">intera</span><span class="o">.</span><span class="n">Residue</span><span class="p">]:</span>
+
+        <span class="k">return</span> <span class="p">[</span>
+            <span class="n">intera</span><span class="o">.</span><span class="n">Residue</span><span class="p">(</span><span class="n">r</span><span class="p">[</span><span class="mi">3</span><span class="p">],</span> <span class="n">r</span><span class="p">[</span><span class="mi">2</span><span class="p">],</span> <span class="n">r</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">isoform</span> <span class="o">=</span> <span class="n">r</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span>
+            <span class="k">for</span> <span class="n">r</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">translate_site</span><span class="p">(</span>
+                <span class="n">residue</span><span class="o">.</span><span class="n">protein</span><span class="p">,</span>
+                <span class="n">residue</span><span class="o">.</span><span class="n">name</span><span class="p">,</span>
+                <span class="n">residue</span><span class="o">.</span><span class="n">number</span><span class="p">,</span>
+                <span class="n">residue</span><span class="o">.</span><span class="n">isoform</span><span class="p">,</span>
+            <span class="p">)</span>
+        <span class="p">]</span>
+
+
+<div class="viewcode-block" id="PtmOrthology.translate">
+<a class="viewcode-back" href="../../../api/pypath.utils.orthology.PtmOrthology.html#pypath.utils.orthology.PtmOrthology.translate">[docs]</a>
+    <span class="k">def</span> <span class="nf">translate</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">x</span><span class="p">,</span> <span class="n">return_strings</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Translates anything: string notation, intera objects, tuples.</span>
+
+<span class="sd">        - one PTM provided as tuple of (UniProt, amino acid, offest)</span>
+<span class="sd">        - one PTM provided as string (e.g. `P00533_S231`)</span>
+<span class="sd">        - instance from pypath.intera: DomainMotif, Domain or Ptm</span>
+
+<span class="sd">        Additional arguments can be isoform and typ (modification type).</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">result</span> <span class="o">=</span> <span class="p">[]</span>
+
+        <span class="k">if</span> <span class="nb">type</span><span class="p">(</span><span class="n">x</span><span class="p">)</span> <span class="ow">is</span> <span class="nb">tuple</span><span class="p">:</span>
+
+            <span class="n">result</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">translate_site</span><span class="p">(</span><span class="o">*</span><span class="n">x</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
+
+        <span class="k">elif</span> <span class="nb">type</span><span class="p">(</span><span class="n">x</span><span class="p">)</span> <span class="ow">in</span> <span class="n">_const</span><span class="o">.</span><span class="n">CHAR_TYPES</span><span class="p">:</span>
+
+            <span class="n">ptm</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">reptm</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="n">x</span><span class="p">)</span>
+
+            <span class="k">if</span> <span class="n">ptm</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
+
+                <span class="n">result</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">translate_site</span><span class="p">(</span>
+                    <span class="n">ptm</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span>
+                    <span class="n">ptm</span><span class="p">[</span><span class="mi">2</span><span class="p">],</span>
+                    <span class="nb">int</span><span class="p">(</span><span class="n">ptm</span><span class="p">[</span><span class="mi">3</span><span class="p">]),</span>
+                    <span class="o">**</span><span class="n">kwargs</span>
+                <span class="p">)</span>
+
+        <span class="k">if</span> <span class="n">return_strings</span><span class="p">:</span>
+
+            <span class="n">result</span> <span class="o">=</span> <span class="p">[</span><span class="s1">&#39;</span><span class="si">%s</span><span class="s1">_</span><span class="si">%s%u</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="p">(</span><span class="n">r</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">r</span><span class="p">[</span><span class="mi">2</span><span class="p">],</span> <span class="n">r</span><span class="p">[</span><span class="mi">3</span><span class="p">])</span> <span class="k">for</span> <span class="n">r</span> <span class="ow">in</span> <span class="n">result</span><span class="p">]</span>
+
+        <span class="k">elif</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">x</span><span class="p">,</span> <span class="n">intera</span><span class="o">.</span><span class="n">Ptm</span><span class="p">):</span>
+
+            <span class="n">result</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">translate_ptm</span><span class="p">(</span><span class="n">x</span><span class="p">)</span>
+
+        <span class="k">elif</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">x</span><span class="p">,</span> <span class="n">intera</span><span class="o">.</span><span class="n">Domain</span><span class="p">):</span>
+
+            <span class="n">result</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">translate_domain</span><span class="p">(</span><span class="n">x</span><span class="p">)</span>
+
+        <span class="k">elif</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">x</span><span class="p">,</span> <span class="n">intera</span><span class="o">.</span><span class="n">DomainMotif</span><span class="p">):</span>
+
+            <span class="n">result</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">translate_domain_motif</span><span class="p">(</span><span class="n">x</span><span class="p">)</span>
+
+        <span class="k">return</span> <span class="n">result</span></div>
+
+
+
+<div class="viewcode-block" id="PtmOrthology.ptm_orthology">
+<a class="viewcode-back" href="../../../api/pypath.utils.orthology.PtmOrthology.html#pypath.utils.orthology.PtmOrthology.ptm_orthology">[docs]</a>
+    <span class="k">def</span> <span class="nf">ptm_orthology</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Load PTM orthology data from PhosphoSite.</span>
+
+<span class="sd">        Creates an orthology translation dict of phosphosites</span>
+<span class="sd">        based on phosphorylation sites table from PhosphoSitePlus.</span>
+<span class="sd">        In the result all PTMs represented by a tuple of the following</span>
+<span class="sd">        6 elements: UniProt ID, isoform (int), residue one letter code,</span>
+<span class="sd">        residue number (int), NCBI Taxonomy ID (int), modification type.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">ptmortho</span> <span class="o">=</span> <span class="p">{}</span>
+
+        <span class="n">nondigit</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">compile</span><span class="p">(</span><span class="sa">r</span><span class="s1">&#39;[^\d]+&#39;</span><span class="p">)</span>
+
+        <span class="n">unknown_taxa</span> <span class="o">=</span> <span class="nb">set</span><span class="p">()</span>
+
+        <span class="k">for</span> <span class="n">typ</span> <span class="ow">in</span> <span class="n">common</span><span class="o">.</span><span class="n">psite_mod_types</span><span class="p">:</span>
+
+            <span class="n">groups</span> <span class="o">=</span> <span class="p">{}</span>
+
+            <span class="n">url</span> <span class="o">=</span> <span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;psite_</span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="n">typ</span><span class="p">[</span><span class="mi">0</span><span class="p">]][</span><span class="s1">&#39;url&#39;</span><span class="p">]</span>
+            <span class="n">c</span> <span class="o">=</span> <span class="n">curl</span><span class="o">.</span><span class="n">Curl</span><span class="p">(</span><span class="n">url</span><span class="p">,</span> <span class="n">silent</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span> <span class="n">large</span> <span class="o">=</span> <span class="kc">True</span><span class="p">)</span>
+
+            <span class="n">data</span> <span class="o">=</span> <span class="n">c</span><span class="o">.</span><span class="n">result</span>
+
+            <span class="k">for</span> <span class="n">_</span> <span class="ow">in</span> <span class="n">xrange</span><span class="p">(</span><span class="mi">4</span><span class="p">):</span>
+                <span class="n">null</span> <span class="o">=</span> <span class="nb">next</span><span class="p">(</span><span class="n">data</span><span class="p">)</span>
+
+            <span class="k">for</span> <span class="n">r</span> <span class="ow">in</span> <span class="n">data</span><span class="p">:</span>
+
+                <span class="n">r</span> <span class="o">=</span> <span class="n">r</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\t</span><span class="s1">&#39;</span><span class="p">)</span>
+
+                <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">r</span><span class="p">)</span> <span class="o">&lt;</span> <span class="mi">10</span><span class="p">:</span>
+
+                    <span class="k">continue</span>
+
+                <span class="n">uniprot</span> <span class="o">=</span> <span class="n">r</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span>
+                <span class="n">isoform</span> <span class="o">=</span> <span class="p">(</span>
+                    <span class="mi">1</span>
+                        <span class="k">if</span> <span class="s1">&#39;-&#39;</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">uniprot</span> <span class="k">else</span>
+                    <span class="nb">int</span><span class="p">(</span><span class="n">uniprot</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;-&#39;</span><span class="p">)[</span><span class="mi">1</span><span class="p">])</span>
+                <span class="p">)</span>
+                <span class="n">uniprot</span> <span class="o">=</span> <span class="n">uniprot</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;-&#39;</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span>
+                <span class="n">aa</span> <span class="o">=</span> <span class="n">r</span><span class="p">[</span><span class="mi">4</span><span class="p">][</span><span class="mi">0</span><span class="p">]</span>
+                <span class="n">num</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">nondigit</span><span class="o">.</span><span class="n">sub</span><span class="p">(</span><span class="s1">&#39;&#39;</span><span class="p">,</span> <span class="n">r</span><span class="p">[</span><span class="mi">4</span><span class="p">]))</span>
+
+                <span class="k">if</span> <span class="n">r</span><span class="p">[</span><span class="mi">6</span><span class="p">]</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">taxonomy</span><span class="o">.</span><span class="n">taxa</span><span class="p">:</span>
+
+                    <span class="n">unknown_taxa</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">r</span><span class="p">[</span><span class="mi">6</span><span class="p">])</span>
+                    <span class="k">continue</span>
+
+                <span class="n">tax</span> <span class="o">=</span> <span class="n">taxonomy</span><span class="o">.</span><span class="n">taxa</span><span class="p">[</span><span class="n">r</span><span class="p">[</span><span class="mi">6</span><span class="p">]]</span>
+                <span class="n">group</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">r</span><span class="p">[</span><span class="mi">5</span><span class="p">])</span>
+
+                <span class="n">this_site</span> <span class="o">=</span> <span class="p">(</span><span class="n">uniprot</span><span class="p">,</span> <span class="n">isoform</span><span class="p">,</span> <span class="n">aa</span><span class="p">,</span> <span class="n">num</span><span class="p">,</span> <span class="n">tax</span><span class="p">,</span> <span class="n">typ</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span>
+
+                <span class="k">if</span> <span class="n">group</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">groups</span><span class="p">:</span>
+                    <span class="n">groups</span><span class="p">[</span><span class="n">group</span><span class="p">]</span> <span class="o">=</span> <span class="nb">set</span><span class="p">([])</span>
+
+                <span class="n">groups</span><span class="p">[</span><span class="n">group</span><span class="p">]</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">this_site</span><span class="p">)</span>
+
+            <span class="k">for</span> <span class="n">group</span><span class="p">,</span> <span class="n">sites</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="n">groups</span><span class="p">):</span>
+
+                <span class="k">for</span> <span class="n">site1</span> <span class="ow">in</span> <span class="n">sites</span><span class="p">:</span>
+
+                    <span class="k">for</span> <span class="n">site2</span> <span class="ow">in</span> <span class="n">sites</span><span class="p">:</span>
+
+                        <span class="k">if</span> <span class="n">site1</span><span class="p">[</span><span class="mi">4</span><span class="p">]</span> <span class="o">==</span> <span class="n">site2</span><span class="p">[</span><span class="mi">4</span><span class="p">]:</span>
+
+                            <span class="k">continue</span>
+
+                        <span class="k">if</span> <span class="n">site1</span> <span class="ow">not</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">ptmortho</span><span class="p">:</span>
+
+                            <span class="bp">self</span><span class="o">.</span><span class="n">ptmortho</span><span class="p">[</span><span class="n">site1</span><span class="p">]</span> <span class="o">=</span> <span class="p">{}</span>
+
+                        <span class="k">if</span> <span class="n">site2</span><span class="p">[</span><span class="mi">4</span><span class="p">]</span> <span class="ow">not</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">ptmortho</span><span class="p">[</span><span class="n">site1</span><span class="p">]:</span>
+
+                            <span class="bp">self</span><span class="o">.</span><span class="n">ptmortho</span><span class="p">[</span><span class="n">site1</span><span class="p">][</span><span class="n">site2</span><span class="p">[</span><span class="mi">4</span><span class="p">]]</span> <span class="o">=</span> <span class="nb">set</span><span class="p">([])</span>
+
+                        <span class="bp">self</span><span class="o">.</span><span class="n">ptmortho</span><span class="p">[</span><span class="n">site1</span><span class="p">][</span><span class="n">site2</span><span class="p">[</span><span class="mi">4</span><span class="p">]]</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">site2</span><span class="p">)</span>
+
+        <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">unknown_taxa</span><span class="p">):</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span>
+                <span class="s1">&#39;Unknown taxa encountered: </span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="p">(</span>
+                    <span class="s1">&#39;, &#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="nb">sorted</span><span class="p">(</span><span class="n">unknown_taxa</span><span class="p">))</span>
+                <span class="p">)</span>
+            <span class="p">)</span></div>
+
+
+    <span class="k">def</span> <span class="nf">_get_source</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">source</span><span class="p">:</span> <span class="nb">str</span> <span class="o">|</span> <span class="nb">int</span> <span class="o">|</span> <span class="kc">None</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">int</span><span class="p">:</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Returns the NCBI Taxonomy ID of the source taxon.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">taxonomy</span><span class="o">.</span><span class="n">ensure_ncbi_tax_id</span><span class="p">(</span><span class="n">source</span><span class="p">)</span> <span class="ow">or</span> <span class="bp">self</span><span class="o">.</span><span class="n">source</span>
+
+        <span class="k">if</span> <span class="ow">not</span> <span class="n">ncbi_tax_id</span><span class="p">:</span>
+
+            <span class="n">msg</span> <span class="o">=</span> <span class="p">(</span>
+                <span class="sa">f</span><span class="s1">&#39;No source taxon provided (argument: `</span><span class="si">{</span><span class="n">source</span><span class="si">}</span><span class="s1">`, &#39;</span>
+                <span class="sa">f</span><span class="s1">&#39;instance: `</span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">source</span><span class="si">}</span><span class="s1">`)&#39;</span>
+            <span class="p">)</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span><span class="n">msg</span><span class="p">)</span>
+            <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="n">msg</span><span class="p">)</span>
+
+        <span class="k">return</span> <span class="n">ncbi_tax_id</span>
+
+
+    <span class="k">def</span> <span class="fm">__len__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="nb">len</span><span class="p">(</span><span class="nb">getattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">&#39;ptmortho&#39;</span><span class="p">,</span> <span class="p">()))</span>
+
+
+    <span class="k">def</span> <span class="fm">__repr__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="sa">f</span><span class="s1">&#39;&lt;PTM Orthology: </span><span class="si">{</span><span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span><span class="si">}</span><span class="s1"> sites&gt;&#39;</span></div>
+
+
+
+<div class="viewcode-block" id="init">
+<a class="viewcode-back" href="../../../api/pypath.utils.orthology.init.html#pypath.utils.orthology.init">[docs]</a>
+<span class="k">def</span> <span class="nf">init</span><span class="p">():</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Initialize the orthology manager.</span>
+
+<span class="sd">    Creates an instance of the orthology manager. Stores it in the module</span>
+<span class="sd">    namespace.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="nb">globals</span><span class="p">()[</span><span class="s1">&#39;manager&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">OrthologyManager</span><span class="p">()</span></div>
+
+
+
+<div class="viewcode-block" id="get_manager">
+<a class="viewcode-back" href="../../../api/pypath.utils.orthology.get_manager.html#pypath.utils.orthology.get_manager">[docs]</a>
+<span class="k">def</span> <span class="nf">get_manager</span><span class="p">():</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Access the orthology manager.</span>
+
+<span class="sd">    Returns the orthology manager, an object which loads and unloads the</span>
+<span class="sd">    orthology lookup tables as necessary, and provides the interface for</span>
+<span class="sd">    querying the orthology data. Normally an instance of the manager</span>
+<span class="sd">    belongs to the module, and if it does not exist yet, will be created</span>
+<span class="sd">    automatically.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="k">if</span> <span class="s1">&#39;manager&#39;</span> <span class="ow">not</span> <span class="ow">in</span> <span class="nb">globals</span><span class="p">():</span>
+
+        <span class="n">init</span><span class="p">()</span>
+
+    <span class="k">return</span> <span class="nb">globals</span><span class="p">()[</span><span class="s1">&#39;manager&#39;</span><span class="p">]</span></div>
+
+
+
+<div class="viewcode-block" id="translate">
+<a class="viewcode-back" href="../../../api/pypath.utils.orthology.translate.html#pypath.utils.orthology.translate">[docs]</a>
+<span class="k">def</span> <span class="nf">translate</span><span class="p">(</span>
+        <span class="n">identifiers</span><span class="p">:</span> <span class="nb">str</span> <span class="o">|</span> <span class="n">Iterable</span><span class="p">[</span><span class="nb">str</span><span class="p">],</span>
+        <span class="n">target</span><span class="p">:</span> <span class="nb">str</span> <span class="o">|</span> <span class="nb">int</span><span class="p">,</span>
+        <span class="n">source</span><span class="p">:</span> <span class="nb">str</span> <span class="o">|</span> <span class="nb">int</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">,</span>
+        <span class="n">id_type</span><span class="p">:</span> <span class="nb">str</span> <span class="o">=</span> <span class="s1">&#39;uniprot&#39;</span><span class="p">,</span>
+        <span class="n">only_swissprot</span><span class="p">:</span> <span class="nb">bool</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
+        <span class="n">oma</span><span class="p">:</span> <span class="nb">bool</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+        <span class="n">homologene</span><span class="p">:</span> <span class="nb">bool</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+        <span class="n">ensembl</span><span class="p">:</span> <span class="nb">bool</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+        <span class="n">oma_rel_type</span><span class="p">:</span> <span class="p">(</span>
+            <span class="nb">set</span><span class="p">[</span><span class="n">Literal</span><span class="p">[</span><span class="s1">&#39;1:1&#39;</span><span class="p">,</span> <span class="s1">&#39;1:n&#39;</span><span class="p">,</span> <span class="s1">&#39;m:1&#39;</span><span class="p">,</span> <span class="s1">&#39;m:n&#39;</span><span class="p">]]</span> <span class="o">|</span>
+            <span class="kc">None</span>
+        <span class="p">)</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+        <span class="n">oma_score</span><span class="p">:</span> <span class="nb">float</span> <span class="o">|</span> <span class="kc">None</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+        <span class="n">ensembl_hc</span><span class="p">:</span> <span class="nb">bool</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
+        <span class="n">ensembl_types</span><span class="p">:</span> <span class="p">(</span>
+            <span class="nb">list</span><span class="p">[</span><span class="n">Literal</span><span class="p">[</span><span class="s1">&#39;one2one&#39;</span><span class="p">,</span> <span class="s1">&#39;one2many&#39;</span><span class="p">,</span> <span class="s1">&#39;many2many&#39;</span><span class="p">]]</span> <span class="o">|</span>
+            <span class="kc">None</span>
+        <span class="p">)</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+        <span class="n">full_records</span><span class="p">:</span> <span class="nb">bool</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+    <span class="p">):</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Translate one or more identifiers by orthologous gene pairs.</span>
+
+<span class="sd">    Args:</span>
+<span class="sd">        identifiers:</span>
+<span class="sd">            One or more identifers of the source organism, of ID type</span>
+<span class="sd">            `id_type`.</span>
+<span class="sd">        target:</span>
+<span class="sd">            Name or NCBI Taxonomy ID of the target organism.</span>
+<span class="sd">        source:</span>
+<span class="sd">            Name or NCBI Taxonomy ID of the source organism.</span>
+<span class="sd">        id_type:</span>
+<span class="sd">            The identifier type to use.</span>
+<span class="sd">        only_swissprot:</span>
+<span class="sd">            Use only SwissProt IDs.</span>
+<span class="sd">        oma</span>
+<span class="sd">            Use orthology information from the Orthologous Matrix (OMA).</span>
+<span class="sd">            Currently this is the recommended source for orthology data.</span>
+<span class="sd">        homologene:</span>
+<span class="sd">            Use orthology information from NCBI HomoloGene.</span>
+<span class="sd">        ensembl:</span>
+<span class="sd">            Use orthology information from Ensembl.</span>
+<span class="sd">        oma_rel_type:</span>
+<span class="sd">            Restrict relations to certain types.</span>
+<span class="sd">        oma_score:</span>
+<span class="sd">            Lower threshold for similarity metric.</span>
+<span class="sd">        ensembl_hc:</span>
+<span class="sd">            Use only the high confidence orthology relations from Ensembl.</span>
+<span class="sd">        ensembl_types:</span>
+<span class="sd">            Ensembl orthology relation types to use. Possible values are</span>
+<span class="sd">            `one2one`, `one2many` and `many2many`. By default only</span>
+<span class="sd">            `one2one` is used.</span>
+<span class="sd">        full_records:</span>
+<span class="sd">            Include not only the identifiers, but also some properties of</span>
+<span class="sd">            the orthology relationships.</span>
+
+<span class="sd">    Returns:</span>
+<span class="sd">        Set of identifiers of orthologous genes or proteins in the</span>
+<span class="sd">        target taxon.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="n">manager</span> <span class="o">=</span> <span class="n">get_manager</span><span class="p">()</span>
+
+    <span class="n">args</span> <span class="o">=</span> <span class="nb">locals</span><span class="p">()</span><span class="o">.</span><span class="n">copy</span><span class="p">()</span>
+    <span class="n">args</span><span class="o">.</span><span class="n">pop</span><span class="p">(</span><span class="s1">&#39;manager&#39;</span><span class="p">)</span>
+
+    <span class="k">return</span> <span class="n">manager</span><span class="o">.</span><span class="n">translate</span><span class="p">(</span><span class="o">**</span><span class="n">args</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="get_dict">
+<a class="viewcode-back" href="../../../api/pypath.utils.orthology.get_dict.html#pypath.utils.orthology.get_dict">[docs]</a>
+<span class="k">def</span> <span class="nf">get_dict</span><span class="p">(</span>
+        <span class="n">target</span><span class="p">:</span> <span class="nb">str</span> <span class="o">|</span> <span class="nb">int</span><span class="p">,</span>
+        <span class="n">source</span><span class="p">:</span> <span class="nb">str</span> <span class="o">|</span> <span class="nb">int</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">,</span>
+        <span class="n">id_type</span><span class="p">:</span> <span class="nb">str</span> <span class="o">=</span> <span class="s1">&#39;uniprot&#39;</span><span class="p">,</span>
+        <span class="n">only_swissprot</span><span class="p">:</span> <span class="nb">bool</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
+        <span class="n">oma</span><span class="p">:</span> <span class="nb">bool</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+        <span class="n">homologene</span><span class="p">:</span> <span class="nb">bool</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+        <span class="n">ensembl</span><span class="p">:</span> <span class="nb">bool</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+        <span class="n">oma_rel_type</span><span class="p">:</span> <span class="p">(</span>
+            <span class="nb">set</span><span class="p">[</span><span class="n">Literal</span><span class="p">[</span><span class="s1">&#39;1:1&#39;</span><span class="p">,</span> <span class="s1">&#39;1:n&#39;</span><span class="p">,</span> <span class="s1">&#39;m:1&#39;</span><span class="p">,</span> <span class="s1">&#39;m:n&#39;</span><span class="p">]]</span> <span class="o">|</span>
+            <span class="kc">None</span>
+        <span class="p">)</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+        <span class="n">oma_score</span><span class="p">:</span> <span class="nb">float</span> <span class="o">|</span> <span class="kc">None</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+        <span class="n">ensembl_hc</span><span class="p">:</span> <span class="nb">bool</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
+        <span class="n">ensembl_types</span><span class="p">:</span> <span class="p">(</span>
+            <span class="nb">list</span><span class="p">[</span><span class="n">Literal</span><span class="p">[</span><span class="s1">&#39;one2one&#39;</span><span class="p">,</span> <span class="s1">&#39;one2many&#39;</span><span class="p">,</span> <span class="s1">&#39;many2many&#39;</span><span class="p">]]</span> <span class="o">|</span>
+            <span class="kc">None</span>
+        <span class="p">)</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+        <span class="n">full_records</span><span class="p">:</span> <span class="nb">bool</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+    <span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">dict</span><span class="p">[</span><span class="nb">str</span><span class="p">,</span> <span class="nb">set</span><span class="p">[</span><span class="n">OrthologBase</span><span class="p">]]:</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Create a dictionary for one source organism and ID type.</span>
+
+<span class="sd">    Args:</span>
+<span class="sd">        target:</span>
+<span class="sd">            Name or NCBI Taxonomy ID of the target organism.</span>
+<span class="sd">        source:</span>
+<span class="sd">            Name or NCBI Taxonomy ID of the source organism.</span>
+<span class="sd">        id_type:</span>
+<span class="sd">            The identifier type to use.</span>
+<span class="sd">        only_swissprot:</span>
+<span class="sd">            Use only SwissProt IDs.</span>
+<span class="sd">        oma</span>
+<span class="sd">            Use orthology information from the Orthologous Matrix (OMA).</span>
+<span class="sd">            Currently this is the recommended source for orthology data.</span>
+<span class="sd">        homologene:</span>
+<span class="sd">            Use orthology information from NCBI HomoloGene.</span>
+<span class="sd">        ensembl:</span>
+<span class="sd">            Use orthology information from Ensembl.</span>
+<span class="sd">        oma_rel_type:</span>
+<span class="sd">            Restrict relations to certain types.</span>
+<span class="sd">        oma_score:</span>
+<span class="sd">            Lower threshold for similarity metric.</span>
+<span class="sd">        ensembl_hc:</span>
+<span class="sd">            Use only the high confidence orthology relations from Ensembl.</span>
+<span class="sd">        ensembl_types:</span>
+<span class="sd">            Ensembl orthology relation types to use. Possible values are</span>
+<span class="sd">            `one2one`, `one2many` and `many2many`. By default only</span>
+<span class="sd">            `one2one` is used.</span>
+<span class="sd">        full_records:</span>
+<span class="sd">            Include not only the identifiers, but also some properties of</span>
+<span class="sd">            the orthology relationships.</span>
+
+<span class="sd">    Returns:</span>
+<span class="sd">        A dict with identifiers of the source organism as keys, and</span>
+<span class="sd">        sets of their orthologs as values.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="n">manager</span> <span class="o">=</span> <span class="n">get_manager</span><span class="p">()</span>
+
+    <span class="n">args</span> <span class="o">=</span> <span class="nb">locals</span><span class="p">()</span><span class="o">.</span><span class="n">copy</span><span class="p">()</span>
+    <span class="n">args</span><span class="o">.</span><span class="n">pop</span><span class="p">(</span><span class="s1">&#39;manager&#39;</span><span class="p">)</span>
+
+    <span class="k">return</span> <span class="n">manager</span><span class="o">.</span><span class="n">get_dict</span><span class="p">(</span><span class="o">**</span><span class="n">args</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="get_df">
+<a class="viewcode-back" href="../../../api/pypath.utils.orthology.get_df.html#pypath.utils.orthology.get_df">[docs]</a>
+<span class="k">def</span> <span class="nf">get_df</span><span class="p">(</span>
+        <span class="n">target</span><span class="p">:</span> <span class="nb">str</span> <span class="o">|</span> <span class="nb">int</span><span class="p">,</span>
+        <span class="n">source</span><span class="p">:</span> <span class="nb">str</span> <span class="o">|</span> <span class="nb">int</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">,</span>
+        <span class="n">id_type</span><span class="p">:</span> <span class="nb">str</span> <span class="o">=</span> <span class="s1">&#39;uniprot&#39;</span><span class="p">,</span>
+        <span class="n">only_swissprot</span><span class="p">:</span> <span class="nb">bool</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
+        <span class="n">oma</span><span class="p">:</span> <span class="nb">bool</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+        <span class="n">homologene</span><span class="p">:</span> <span class="nb">bool</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+        <span class="n">ensembl</span><span class="p">:</span> <span class="nb">bool</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+        <span class="n">oma_rel_type</span><span class="p">:</span> <span class="p">(</span>
+            <span class="nb">set</span><span class="p">[</span><span class="n">Literal</span><span class="p">[</span><span class="s1">&#39;1:1&#39;</span><span class="p">,</span> <span class="s1">&#39;1:n&#39;</span><span class="p">,</span> <span class="s1">&#39;m:1&#39;</span><span class="p">,</span> <span class="s1">&#39;m:n&#39;</span><span class="p">]]</span> <span class="o">|</span>
+            <span class="kc">None</span>
+        <span class="p">)</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+        <span class="n">oma_score</span><span class="p">:</span> <span class="nb">float</span> <span class="o">|</span> <span class="kc">None</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+        <span class="n">ensembl_hc</span><span class="p">:</span> <span class="nb">bool</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
+        <span class="n">ensembl_types</span><span class="p">:</span> <span class="p">(</span>
+            <span class="nb">list</span><span class="p">[</span><span class="n">Literal</span><span class="p">[</span><span class="s1">&#39;one2one&#39;</span><span class="p">,</span> <span class="s1">&#39;one2many&#39;</span><span class="p">,</span> <span class="s1">&#39;many2many&#39;</span><span class="p">]]</span> <span class="o">|</span>
+            <span class="kc">None</span>
+        <span class="p">)</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+        <span class="n">full_records</span><span class="p">:</span> <span class="nb">bool</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+        <span class="o">**</span><span class="n">kwargs</span>
+    <span class="p">)</span> <span class="o">-&gt;</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">:</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Create a data frame for one source organism and ID type.</span>
+
+<span class="sd">    Args:</span>
+<span class="sd">        target:</span>
+<span class="sd">            Name or NCBI Taxonomy ID of the target organism.</span>
+<span class="sd">        source:</span>
+<span class="sd">            Name or NCBI Taxonomy ID of the source organism.</span>
+<span class="sd">        id_type:</span>
+<span class="sd">            The identifier type to use.</span>
+<span class="sd">        only_swissprot:</span>
+<span class="sd">            Use only SwissProt IDs.</span>
+<span class="sd">        oma</span>
+<span class="sd">            Use orthology information from the Orthologous Matrix (OMA).</span>
+<span class="sd">            Currently this is the recommended source for orthology data.</span>
+<span class="sd">        homologene:</span>
+<span class="sd">            Use orthology information from NCBI HomoloGene.</span>
+<span class="sd">        ensembl:</span>
+<span class="sd">            Use orthology information from Ensembl.</span>
+<span class="sd">        oma_rel_type:</span>
+<span class="sd">            Restrict relations to certain types.</span>
+<span class="sd">        oma_score:</span>
+<span class="sd">            Lower threshold for similarity metric.</span>
+<span class="sd">        ensembl_hc:</span>
+<span class="sd">            Use only the high confidence orthology relations from Ensembl.</span>
+<span class="sd">        ensembl_types:</span>
+<span class="sd">            Ensembl orthology relation types to use. Possible values are</span>
+<span class="sd">            `one2one`, `one2many` and `many2many`. By default only</span>
+<span class="sd">            `one2one` is used.</span>
+<span class="sd">        full_records:</span>
+<span class="sd">            Include not only the identifiers, but also some properties of</span>
+<span class="sd">            the orthology relationships.</span>
+<span class="sd">        kwargs:</span>
+<span class="sd">            Ignored.</span>
+
+<span class="sd">    Returns:</span>
+<span class="sd">        A data frame with pairs of orthologous identifiers,</span>
+<span class="sd">        in two columns: &quot;source&quot; and &quot;target&quot;.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="n">manager</span> <span class="o">=</span> <span class="n">get_manager</span><span class="p">()</span>
+
+    <span class="n">args</span> <span class="o">=</span> <span class="nb">locals</span><span class="p">()</span><span class="o">.</span><span class="n">copy</span><span class="p">()</span>
+    <span class="n">args</span><span class="o">.</span><span class="n">pop</span><span class="p">(</span><span class="s1">&#39;manager&#39;</span><span class="p">)</span>
+    <span class="n">args</span><span class="o">.</span><span class="n">pop</span><span class="p">(</span><span class="s1">&#39;kwargs&#39;</span><span class="p">)</span>
+
+    <span class="k">return</span> <span class="n">manager</span><span class="o">.</span><span class="n">get_df</span><span class="p">(</span><span class="o">**</span><span class="n">args</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="translate_df">
+<a class="viewcode-back" href="../../../api/pypath.utils.orthology.translate_df.html#pypath.utils.orthology.translate_df">[docs]</a>
+<span class="k">def</span> <span class="nf">translate_df</span><span class="p">(</span>
+        <span class="n">df</span><span class="p">:</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">,</span>
+        <span class="n">target</span><span class="p">:</span> <span class="nb">str</span> <span class="o">|</span> <span class="nb">int</span><span class="p">,</span>
+        <span class="n">source</span><span class="p">:</span> <span class="nb">str</span> <span class="o">|</span> <span class="nb">int</span> <span class="o">=</span> <span class="mi">9606</span><span class="p">,</span>
+        <span class="n">cols</span><span class="p">:</span> <span class="nb">str</span> <span class="o">|</span> <span class="nb">list</span><span class="p">[</span><span class="nb">str</span><span class="p">]</span> <span class="o">|</span> <span class="nb">dict</span><span class="p">[</span><span class="nb">str</span><span class="p">,</span> <span class="nb">str</span><span class="p">]</span> <span class="o">|</span> <span class="kc">None</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+        <span class="n">id_type</span><span class="p">:</span> <span class="nb">str</span> <span class="o">=</span> <span class="s1">&#39;uniprot&#39;</span><span class="p">,</span>
+        <span class="n">only_swissprot</span><span class="p">:</span> <span class="nb">bool</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
+        <span class="n">oma</span><span class="p">:</span> <span class="nb">bool</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+        <span class="n">homologene</span><span class="p">:</span> <span class="nb">bool</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+        <span class="n">ensembl</span><span class="p">:</span> <span class="nb">bool</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+        <span class="n">oma_rel_type</span><span class="p">:</span> <span class="p">(</span>
+            <span class="nb">set</span><span class="p">[</span><span class="n">Literal</span><span class="p">[</span><span class="s1">&#39;1:1&#39;</span><span class="p">,</span> <span class="s1">&#39;1:n&#39;</span><span class="p">,</span> <span class="s1">&#39;m:1&#39;</span><span class="p">,</span> <span class="s1">&#39;m:n&#39;</span><span class="p">]]</span> <span class="o">|</span>
+            <span class="kc">None</span>
+        <span class="p">)</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+        <span class="n">oma_score</span><span class="p">:</span> <span class="nb">float</span> <span class="o">|</span> <span class="kc">None</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+        <span class="n">ensembl_hc</span><span class="p">:</span> <span class="nb">bool</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
+        <span class="n">ensembl_types</span><span class="p">:</span> <span class="p">(</span>
+            <span class="nb">list</span><span class="p">[</span><span class="n">Literal</span><span class="p">[</span><span class="s1">&#39;one2one&#39;</span><span class="p">,</span> <span class="s1">&#39;one2many&#39;</span><span class="p">,</span> <span class="s1">&#39;many2many&#39;</span><span class="p">]]</span> <span class="o">|</span>
+            <span class="kc">None</span>
+        <span class="p">)</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+        <span class="o">**</span><span class="n">kwargs</span><span class="p">:</span> <span class="nb">str</span> <span class="o">|</span> <span class="nb">tuple</span><span class="p">[</span><span class="nb">str</span><span class="p">,</span> <span class="nb">str</span><span class="p">]</span>
+    <span class="p">)</span> <span class="o">-&gt;</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">:</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Translate columns in a data frame.</span>
+
+<span class="sd">    Args:</span>
+<span class="sd">        df:</span>
+<span class="sd">            A data frame.</span>
+<span class="sd">        target:</span>
+<span class="sd">            Name or NCBI Taxonomy ID of the target organism.</span>
+<span class="sd">        source:</span>
+<span class="sd">            Name or NCBI Taxonomy ID of the source organism.</span>
+<span class="sd">        cols:</span>
+<span class="sd">            One or more columns to be translated. It can be a single</span>
+<span class="sd">            column name, an iterable of column names or a dict where</span>
+<span class="sd">            keys are column names and values are ID types. Except this</span>
+<span class="sd">            last case, identifiers are assumed to be `id_type`.</span>
+<span class="sd">        id_type:</span>
+<span class="sd">            The default identifier type to use, will be used for all</span>
+<span class="sd">            columns where ID type is not specified.</span>
+<span class="sd">        only_swissprot:</span>
+<span class="sd">            Use only SwissProt IDs.</span>
+<span class="sd">        oma</span>
+<span class="sd">            Use orthology information from the Orthologous Matrix (OMA).</span>
+<span class="sd">            Currently this is the recommended source for orthology data.</span>
+<span class="sd">        homologene:</span>
+<span class="sd">            Use orthology information from NCBI HomoloGene.</span>
+<span class="sd">        ensembl:</span>
+<span class="sd">            Use orthology information from Ensembl.</span>
+<span class="sd">        oma_rel_type:</span>
+<span class="sd">            Restrict relations to certain types.</span>
+<span class="sd">        oma_score:</span>
+<span class="sd">            Lower threshold for similarity metric.</span>
+<span class="sd">        ensembl_hc:</span>
+<span class="sd">            Use only the high confidence orthology relations from Ensembl.</span>
+<span class="sd">        ensembl_types:</span>
+<span class="sd">            Ensembl orthology relation types to use. Possible values are</span>
+<span class="sd">            `one2one`, `one2many` and `many2many`. By default only</span>
+<span class="sd">            `one2one` is used.</span>
+<span class="sd">        kwargs:</span>
+<span class="sd">            Same as providing a dict to ``cols``, but beware, keys</span>
+<span class="sd">            (column names) can not match existing argument names of</span>
+<span class="sd">            this function.</span>
+
+<span class="sd">    Returns:</span>
+<span class="sd">        A data frame with the same column layout as the input, and the</span>
+<span class="sd">        identifiers translated as demanded. Rows that could not be</span>
+<span class="sd">        translated are omitted.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="n">manager</span> <span class="o">=</span> <span class="n">get_manager</span><span class="p">()</span>
+
+    <span class="n">args</span> <span class="o">=</span> <span class="nb">locals</span><span class="p">()</span><span class="o">.</span><span class="n">copy</span><span class="p">()</span>
+    <span class="n">args</span><span class="o">.</span><span class="n">pop</span><span class="p">(</span><span class="s1">&#39;manager&#39;</span><span class="p">)</span>
+    <span class="n">args</span><span class="o">.</span><span class="n">pop</span><span class="p">(</span><span class="s1">&#39;kwargs&#39;</span><span class="p">)</span>
+
+    <span class="k">return</span> <span class="n">manager</span><span class="o">.</span><span class="n">translate_df</span><span class="p">(</span><span class="o">**</span><span class="n">args</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">)</span></div>
+
+</pre></div>
+
+                </article>
+              
+              
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+              
+              
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+                  
+  <h1>Source code for pypath.utils.pyreact</h1><div class="highlight"><pre>
+<span></span><span class="ch">#!/usr/bin/env python</span>
+<span class="c1"># -*- coding: utf-8 -*-</span>
+
+<span class="c1">#</span>
+<span class="c1">#  This file is part of the `pypath` python module</span>
+<span class="c1">#</span>
+<span class="c1">#  Copyright 2014-2023</span>
+<span class="c1">#  EMBL, EMBL-EBI, Uniklinik RWTH Aachen, Heidelberg University</span>
+<span class="c1">#</span>
+<span class="c1">#  Authors: see the file `README.rst`</span>
+<span class="c1">#  Contact: Dénes Türei (turei.denes@gmail.com)</span>
+<span class="c1">#</span>
+<span class="c1">#  Distributed under the GPLv3 License.</span>
+<span class="c1">#  See accompanying file LICENSE.txt or copy at</span>
+<span class="c1">#      https://www.gnu.org/licenses/gpl-3.0.html</span>
+<span class="c1">#</span>
+<span class="c1">#  Website: https://pypath.omnipathdb.org/</span>
+<span class="c1">#</span>
+
+<span class="kn">from</span> <span class="nn">__future__</span> <span class="kn">import</span> <span class="n">print_function</span>
+<span class="kn">from</span> <span class="nn">future.utils</span> <span class="kn">import</span> <span class="n">iteritems</span>
+<span class="kn">from</span> <span class="nn">past.builtins</span> <span class="kn">import</span> <span class="n">xrange</span><span class="p">,</span> <span class="nb">range</span><span class="p">,</span> <span class="n">reduce</span>
+
+<span class="kn">import</span> <span class="nn">os</span>
+<span class="kn">import</span> <span class="nn">sys</span>
+<span class="kn">import</span> <span class="nn">importlib</span> <span class="k">as</span> <span class="nn">imp</span>
+<span class="kn">import</span> <span class="nn">re</span>
+<span class="kn">import</span> <span class="nn">gzip</span>
+<span class="kn">import</span> <span class="nn">tarfile</span>
+<span class="kn">import</span> <span class="nn">zipfile</span>
+<span class="kn">import</span> <span class="nn">struct</span>
+<span class="kn">import</span> <span class="nn">itertools</span>
+<span class="kn">import</span> <span class="nn">bs4</span>
+<span class="kn">import</span> <span class="nn">time</span>
+<span class="kn">from</span> <span class="nn">lxml</span> <span class="kn">import</span> <span class="n">etree</span>
+<span class="k">try</span><span class="p">:</span>
+    <span class="kn">import</span> <span class="nn">cPickle</span> <span class="k">as</span> <span class="nn">pickle</span>
+<span class="k">except</span><span class="p">:</span>
+    <span class="kn">import</span> <span class="nn">pickle</span>
+
+<span class="kn">import</span> <span class="nn">pypath.utils.mapping</span> <span class="k">as</span> <span class="nn">mapping</span>
+<span class="kn">import</span> <span class="nn">pypath.utils.reflists</span> <span class="k">as</span> <span class="nn">reflists</span>
+<span class="kn">import</span> <span class="nn">pypath.share.common</span> <span class="k">as</span> <span class="nn">common</span>
+<span class="kn">import</span> <span class="nn">pypath_common._constants</span> <span class="k">as</span> <span class="nn">_const</span>
+<span class="kn">import</span> <span class="nn">pypath.share.progress</span> <span class="k">as</span> <span class="nn">progress</span>
+<span class="kn">import</span> <span class="nn">pypath.share.curl</span> <span class="k">as</span> <span class="nn">curl</span>
+<span class="kn">import</span> <span class="nn">pypath.internals.intera</span> <span class="k">as</span> <span class="nn">intera</span>
+<span class="kn">import</span> <span class="nn">pypath.internals.refs</span> <span class="k">as</span> <span class="nn">refs</span>
+<span class="kn">import</span> <span class="nn">pypath.inputs.uniprot</span> <span class="k">as</span> <span class="nn">uniprot_input</span>
+<span class="kn">import</span> <span class="nn">pypath.resources.urls</span> <span class="k">as</span> <span class="nn">urls</span>
+<span class="kn">import</span> <span class="nn">pypath.utils.seq</span> <span class="k">as</span> <span class="nn">seq</span>
+<span class="kn">import</span> <span class="nn">pypath.share.session</span> <span class="k">as</span> <span class="nn">session_mod</span>
+<span class="kn">import</span> <span class="nn">pypath.share.cache</span> <span class="k">as</span> <span class="nn">cache</span>
+
+
+<div class="viewcode-block" id="BioPaxReader">
+<a class="viewcode-back" href="../../../api/pypath.utils.pyreact.BioPaxReader.html#pypath.utils.pyreact.BioPaxReader">[docs]</a>
+<span class="k">class</span> <span class="nc">BioPaxReader</span><span class="p">(</span><span class="n">session_mod</span><span class="o">.</span><span class="n">Logger</span><span class="p">):</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    This class parses a BioPAX file and exposes its content easily accessible</span>
+<span class="sd">    for further processing. First it opens the file, if necessary it extracts</span>
+<span class="sd">    from the archive. Then an `lxml.etree.iterparse` object is created, so the</span>
+<span class="sd">    iteration is efficient and memory requirements are minimal. The iterparse</span>
+<span class="sd">    object is iterated then, and for each tag included in the</span>
+<span class="sd">    `BioPaxReader.methods` dict, the appropriate method is called. These me-</span>
+<span class="sd">    thods extract information from the BioPAX entity, and store it in arbit-</span>
+<span class="sd">    rary data structures: strings, lists or dicts. These are stored in dicts</span>
+<span class="sd">    where keys are the original IDs of the tags, prefixed with the unique ID</span>
+<span class="sd">    of the parser object. This is necessary to give a way to merge later the</span>
+<span class="sd">    result of parsing more BioPAX files. For example, `id42` may identify</span>
+<span class="sd">    EGFR in one file, but AKT1 in the other. Then, the parser of the first</span>
+<span class="sd">    file has a unique ID of a 5 letter random string, the second parser a</span>
+<span class="sd">    different one, and the molecules with the same ID can be distinguished</span>
+<span class="sd">    at merging, e.g. EGFR will be `ffjh2@id42` and AKT1 will be `tr9gy@id42`.</span>
+<span class="sd">    The methods and the resulted dicts are named after the BioPAX elements,</span>
+<span class="sd">    sometimes abbreviated. For example, `BioPaxReader.protein()` processes</span>
+<span class="sd">    the `&lt;bp:Protein&gt;` elements, and stores the results in</span>
+<span class="sd">    `BioPaxReader.proteins`.</span>
+
+<span class="sd">    In its current state, this class does not parse every information and</span>
+<span class="sd">    all BioPax entities. For example, nucleic acid related entities and</span>
+<span class="sd">    interactions are omitted. But these easily can be added with minor mo-</span>
+<span class="sd">    difications.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+<div class="viewcode-block" id="BioPaxReader.__init__">
+<a class="viewcode-back" href="../../../api/pypath.utils.pyreact.BioPaxReader.html#pypath.utils.pyreact.BioPaxReader.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span>
+            <span class="bp">self</span><span class="p">,</span>
+            <span class="n">biopax</span><span class="p">,</span>
+            <span class="n">source</span><span class="p">,</span>
+            <span class="n">cleanup_period</span><span class="o">=</span><span class="mi">800</span><span class="p">,</span>
+            <span class="n">file_from_archive</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
+            <span class="n">silent</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span>
+        <span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        :param str,FileOpener biopax: either a filename, or a FileOpener</span>
+<span class="sd">        object; if string is supplied, the FileOpener will be created in-</span>
+<span class="sd">        ternally</span>
+
+<span class="sd">        :param str source: the name of the data source, e.g. *Reactome*</span>
+
+<span class="sd">        :param int cleanup_period: the number of last elements stored</span>
+<span class="sd">        during the iteration of lxml.etree.iterparse; lower number</span>
+<span class="sd">        results lower memory usage, but might risk that an element is</span>
+<span class="sd">        deleted before it has been processed. Default is 800, which is</span>
+<span class="sd">        a safe option.</span>
+
+<span class="sd">        :param str file_from_archive: in case of processing an archive</span>
+<span class="sd">        which may contain multiple files (tar.gz or zip), the path of</span>
+<span class="sd">        the file to be processed needs to be supplied.</span>
+<span class="sd">        E.g. *BioPax/Homo_sapiens.owl*.</span>
+
+<span class="sd">        :param bool silent: whether print status messages and progress</span>
+<span class="sd">        bars during processing. If you process large number of small</span>
+<span class="sd">        files, better to set False, in case of one large file, True.</span>
+<span class="sd">        The default is *False*.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">session_mod</span><span class="o">.</span><span class="n">Logger</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">name</span> <span class="o">=</span> <span class="s1">&#39;biopax&#39;</span><span class="p">)</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">biopax</span> <span class="o">=</span> <span class="n">biopax</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">source</span> <span class="o">=</span> <span class="n">source</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">file_from_archive</span> <span class="o">=</span> <span class="n">file_from_archive</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">cleanup_period</span> <span class="o">=</span> <span class="n">cleanup_period</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">biopax_tmp_file</span> <span class="o">=</span> <span class="kc">None</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">cachedir</span> <span class="o">=</span> <span class="n">cache</span><span class="o">.</span><span class="n">get_cachedir</span><span class="p">()</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">parser_id</span> <span class="o">=</span> <span class="n">common</span><span class="o">.</span><span class="n">random_string</span><span class="p">()</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">silent</span> <span class="o">=</span> <span class="n">silent</span>
+
+        <span class="c1"># string constants</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">bppref</span> <span class="o">=</span> <span class="s1">&#39;{http://www.biopax.org/release/biopax-level3.owl#}&#39;</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">rdfpref</span> <span class="o">=</span> <span class="s1">&#39;{http://www.w3.org/1999/02/22-rdf-syntax-ns#}&#39;</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">rdfid</span> <span class="o">=</span> <span class="s1">&#39;</span><span class="si">%s</span><span class="s1">ID&#39;</span> <span class="o">%</span> <span class="bp">self</span><span class="o">.</span><span class="n">rdfpref</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">rdfab</span> <span class="o">=</span> <span class="s1">&#39;</span><span class="si">%s</span><span class="s1">about&#39;</span> <span class="o">%</span> <span class="bp">self</span><span class="o">.</span><span class="n">rdfpref</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">rdfres</span> <span class="o">=</span> <span class="s1">&#39;</span><span class="si">%s</span><span class="s1">resource&#39;</span> <span class="o">%</span> <span class="bp">self</span><span class="o">.</span><span class="n">rdfpref</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">bpprot</span> <span class="o">=</span> <span class="s1">&#39;</span><span class="si">%s</span><span class="s1">Protein&#39;</span> <span class="o">%</span> <span class="bp">self</span><span class="o">.</span><span class="n">bppref</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">bpcplx</span> <span class="o">=</span> <span class="s1">&#39;</span><span class="si">%s</span><span class="s1">Complex&#39;</span> <span class="o">%</span> <span class="bp">self</span><span class="o">.</span><span class="n">bppref</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">bpprre</span> <span class="o">=</span> <span class="s1">&#39;</span><span class="si">%s</span><span class="s1">ProteinReference&#39;</span> <span class="o">%</span> <span class="bp">self</span><span class="o">.</span><span class="n">bppref</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">bpreac</span> <span class="o">=</span> <span class="s1">&#39;</span><span class="si">%s</span><span class="s1">BiochemicalReaction&#39;</span> <span class="o">%</span> <span class="bp">self</span><span class="o">.</span><span class="n">bppref</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">bpcata</span> <span class="o">=</span> <span class="s1">&#39;</span><span class="si">%s</span><span class="s1">Catalysis&#39;</span> <span class="o">%</span> <span class="bp">self</span><span class="o">.</span><span class="n">bppref</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">bpctrl</span> <span class="o">=</span> <span class="s1">&#39;</span><span class="si">%s</span><span class="s1">Control&#39;</span> <span class="o">%</span> <span class="bp">self</span><span class="o">.</span><span class="n">bppref</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">bpmodu</span> <span class="o">=</span> <span class="s1">&#39;</span><span class="si">%s</span><span class="s1">Modulation&#39;</span> <span class="o">%</span> <span class="bp">self</span><span class="o">.</span><span class="n">bppref</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">bpcoma</span> <span class="o">=</span> <span class="s1">&#39;</span><span class="si">%s</span><span class="s1">ComplexAssembly&#39;</span> <span class="o">%</span> <span class="bp">self</span><span class="o">.</span><span class="n">bppref</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">bptran</span> <span class="o">=</span> <span class="s1">&#39;</span><span class="si">%s</span><span class="s1">Transport&#39;</span> <span class="o">%</span> <span class="bp">self</span><span class="o">.</span><span class="n">bppref</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">bptrbr</span> <span class="o">=</span> <span class="s1">&#39;</span><span class="si">%s</span><span class="s1">TransportWithBiochemicalReaction&#39;</span> <span class="o">%</span> <span class="bp">self</span><span class="o">.</span><span class="n">bppref</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">bpmoli</span> <span class="o">=</span> <span class="s1">&#39;</span><span class="si">%s</span><span class="s1">MolecularInteraction&#39;</span> <span class="o">%</span> <span class="bp">self</span><span class="o">.</span><span class="n">bppref</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">bppstp</span> <span class="o">=</span> <span class="s1">&#39;</span><span class="si">%s</span><span class="s1">PathwayStep&#39;</span> <span class="o">%</span> <span class="bp">self</span><span class="o">.</span><span class="n">bppref</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">bpuxrf</span> <span class="o">=</span> <span class="s1">&#39;</span><span class="si">%s</span><span class="s1">UnificationXref&#39;</span> <span class="o">%</span> <span class="bp">self</span><span class="o">.</span><span class="n">bppref</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">bpstoi</span> <span class="o">=</span> <span class="s1">&#39;</span><span class="si">%s</span><span class="s1">Stoichiometry&#39;</span> <span class="o">%</span> <span class="bp">self</span><span class="o">.</span><span class="n">bppref</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">bppubr</span> <span class="o">=</span> <span class="s1">&#39;</span><span class="si">%s</span><span class="s1">PublicationXref&#39;</span> <span class="o">%</span> <span class="bp">self</span><span class="o">.</span><span class="n">bppref</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">bppath</span> <span class="o">=</span> <span class="s1">&#39;</span><span class="si">%s</span><span class="s1">Pathway&#39;</span> <span class="o">%</span> <span class="bp">self</span><span class="o">.</span><span class="n">bppref</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">bpfrfe</span> <span class="o">=</span> <span class="s1">&#39;</span><span class="si">%s</span><span class="s1">FragmentFeature&#39;</span> <span class="o">%</span> <span class="bp">self</span><span class="o">.</span><span class="n">bppref</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">bpseqi</span> <span class="o">=</span> <span class="s1">&#39;</span><span class="si">%s</span><span class="s1">SequenceInterval&#39;</span> <span class="o">%</span> <span class="bp">self</span><span class="o">.</span><span class="n">bppref</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">bpseqs</span> <span class="o">=</span> <span class="s1">&#39;</span><span class="si">%s</span><span class="s1">SequenceSite&#39;</span> <span class="o">%</span> <span class="bp">self</span><span class="o">.</span><span class="n">bppref</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">bpmodf</span> <span class="o">=</span> <span class="s1">&#39;</span><span class="si">%s</span><span class="s1">ModificationFeature&#39;</span> <span class="o">%</span> <span class="bp">self</span><span class="o">.</span><span class="n">bppref</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">bpmodv</span> <span class="o">=</span> <span class="s1">&#39;</span><span class="si">%s</span><span class="s1">SequenceModificationVocabulary&#39;</span> <span class="o">%</span> <span class="bp">self</span><span class="o">.</span><span class="n">bppref</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">bpmphe</span> <span class="o">=</span> <span class="s1">&#39;</span><span class="si">%s</span><span class="s1">memberPhysicalEntity&#39;</span> <span class="o">%</span> <span class="bp">self</span><span class="o">.</span><span class="n">bppref</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">bpmerf</span> <span class="o">=</span> <span class="s1">&#39;</span><span class="si">%s</span><span class="s1">memberEntityReference&#39;</span> <span class="o">%</span> <span class="bp">self</span><span class="o">.</span><span class="n">bppref</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">bperef</span> <span class="o">=</span> <span class="s1">&#39;</span><span class="si">%s</span><span class="s1">entityReference&#39;</span> <span class="o">%</span> <span class="bp">self</span><span class="o">.</span><span class="n">bppref</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">bpxref</span> <span class="o">=</span> <span class="s1">&#39;</span><span class="si">%s</span><span class="s1">xref&#39;</span> <span class="o">%</span> <span class="bp">self</span><span class="o">.</span><span class="n">bppref</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">bpdinm</span> <span class="o">=</span> <span class="s1">&#39;</span><span class="si">%s</span><span class="s1">displayName&#39;</span> <span class="o">%</span> <span class="bp">self</span><span class="o">.</span><span class="n">bppref</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">bprelr</span> <span class="o">=</span> <span class="s1">&#39;</span><span class="si">%s</span><span class="s1">RelationshipXref&#39;</span> <span class="o">%</span> <span class="bp">self</span><span class="o">.</span><span class="n">bppref</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">bpcsto</span> <span class="o">=</span> <span class="s1">&#39;</span><span class="si">%s</span><span class="s1">componentStoichiometry&#39;</span> <span class="o">%</span> <span class="bp">self</span><span class="o">.</span><span class="n">bppref</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">bpcomp</span> <span class="o">=</span> <span class="s1">&#39;</span><span class="si">%s</span><span class="s1">component&#39;</span> <span class="o">%</span> <span class="bp">self</span><span class="o">.</span><span class="n">bppref</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">bpstoc</span> <span class="o">=</span> <span class="s1">&#39;</span><span class="si">%s</span><span class="s1">stoichiometricCoefficient&#39;</span> <span class="o">%</span> <span class="bp">self</span><span class="o">.</span><span class="n">bppref</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">bpphye</span> <span class="o">=</span> <span class="s1">&#39;</span><span class="si">%s</span><span class="s1">physicalEntity&#39;</span> <span class="o">%</span> <span class="bp">self</span><span class="o">.</span><span class="n">bppref</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">bpcted</span> <span class="o">=</span> <span class="s1">&#39;</span><span class="si">%s</span><span class="s1">controlled&#39;</span> <span class="o">%</span> <span class="bp">self</span><span class="o">.</span><span class="n">bppref</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">bpcter</span> <span class="o">=</span> <span class="s1">&#39;</span><span class="si">%s</span><span class="s1">controller&#39;</span> <span class="o">%</span> <span class="bp">self</span><span class="o">.</span><span class="n">bppref</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">bpctyp</span> <span class="o">=</span> <span class="s1">&#39;</span><span class="si">%s</span><span class="s1">controlType&#39;</span> <span class="o">%</span> <span class="bp">self</span><span class="o">.</span><span class="n">bppref</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">bppart</span> <span class="o">=</span> <span class="s1">&#39;</span><span class="si">%s</span><span class="s1">participant&#39;</span> <span class="o">%</span> <span class="bp">self</span><span class="o">.</span><span class="n">bppref</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">bpleft</span> <span class="o">=</span> <span class="s1">&#39;</span><span class="si">%s</span><span class="s1">left&#39;</span> <span class="o">%</span> <span class="bp">self</span><span class="o">.</span><span class="n">bppref</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">bprgth</span> <span class="o">=</span> <span class="s1">&#39;</span><span class="si">%s</span><span class="s1">right&#39;</span> <span class="o">%</span> <span class="bp">self</span><span class="o">.</span><span class="n">bppref</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">bpsprc</span> <span class="o">=</span> <span class="s1">&#39;</span><span class="si">%s</span><span class="s1">stepProcess&#39;</span> <span class="o">%</span> <span class="bp">self</span><span class="o">.</span><span class="n">bppref</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">bpfeat</span> <span class="o">=</span> <span class="s1">&#39;</span><span class="si">%s</span><span class="s1">feature&#39;</span> <span class="o">%</span> <span class="bp">self</span><span class="o">.</span><span class="n">bppref</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">bpfelo</span> <span class="o">=</span> <span class="s1">&#39;</span><span class="si">%s</span><span class="s1">featureLocation&#39;</span> <span class="o">%</span> <span class="bp">self</span><span class="o">.</span><span class="n">bppref</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">bpibeg</span> <span class="o">=</span> <span class="s1">&#39;</span><span class="si">%s</span><span class="s1">sequenceIntervalBegin&#39;</span> <span class="o">%</span> <span class="bp">self</span><span class="o">.</span><span class="n">bppref</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">bpiend</span> <span class="o">=</span> <span class="s1">&#39;</span><span class="si">%s</span><span class="s1">sequenceIntervalEnd&#39;</span> <span class="o">%</span> <span class="bp">self</span><span class="o">.</span><span class="n">bppref</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">bpseqp</span> <span class="o">=</span> <span class="s1">&#39;</span><span class="si">%s</span><span class="s1">sequencePosition&#39;</span> <span class="o">%</span> <span class="bp">self</span><span class="o">.</span><span class="n">bppref</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">bpmoty</span> <span class="o">=</span> <span class="s1">&#39;</span><span class="si">%s</span><span class="s1">modificationType&#39;</span> <span class="o">%</span> <span class="bp">self</span><span class="o">.</span><span class="n">bppref</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">bppcom</span> <span class="o">=</span> <span class="s1">&#39;</span><span class="si">%s</span><span class="s1">pathwayComponent&#39;</span> <span class="o">%</span> <span class="bp">self</span><span class="o">.</span><span class="n">bppref</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">bpterm</span> <span class="o">=</span> <span class="s1">&#39;</span><span class="si">%s</span><span class="s1">term&#39;</span> <span class="o">%</span> <span class="bp">self</span><span class="o">.</span><span class="n">bppref</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">bpdb</span> <span class="o">=</span> <span class="s1">&#39;</span><span class="si">%s</span><span class="s1">db&#39;</span> <span class="o">%</span> <span class="bp">self</span><span class="o">.</span><span class="n">bppref</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">bpid</span> <span class="o">=</span> <span class="s1">&#39;</span><span class="si">%s</span><span class="s1">id&#39;</span> <span class="o">%</span> <span class="bp">self</span><span class="o">.</span><span class="n">bppref</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">upStr</span> <span class="o">=</span> <span class="s1">&#39;UniProt&#39;</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">proteins</span> <span class="o">=</span> <span class="p">{}</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">pfamilies</span> <span class="o">=</span> <span class="p">{}</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">complexes</span> <span class="o">=</span> <span class="p">{}</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">cvariations</span> <span class="o">=</span> <span class="p">{}</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">prefs</span> <span class="o">=</span> <span class="p">{}</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">ids</span> <span class="o">=</span> <span class="p">{}</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">reactions</span> <span class="o">=</span> <span class="p">{}</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">cassemblies</span> <span class="o">=</span> <span class="p">{}</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">interactions</span> <span class="o">=</span> <span class="p">{}</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">transports</span> <span class="o">=</span> <span class="p">{}</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">transwreas</span> <span class="o">=</span> <span class="p">{}</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">stoichiometries</span> <span class="o">=</span> <span class="p">{}</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">catalyses</span> <span class="o">=</span> <span class="p">{}</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">controls</span> <span class="o">=</span> <span class="p">{}</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">pwsteps</span> <span class="o">=</span> <span class="p">{}</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">pubrefs</span> <span class="o">=</span> <span class="p">{}</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">fragfeas</span> <span class="o">=</span> <span class="p">{}</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">seqints</span> <span class="o">=</span> <span class="p">{}</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">seqsites</span> <span class="o">=</span> <span class="p">{}</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">modfeas</span> <span class="o">=</span> <span class="p">{}</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">seqmodvocs</span> <span class="o">=</span> <span class="p">{}</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">pathways</span> <span class="o">=</span> <span class="p">{}</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">interactions_not2</span> <span class="o">=</span> <span class="p">{}</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">methods</span> <span class="o">=</span> <span class="p">{</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">bpprot</span><span class="p">:</span> <span class="s1">&#39;protein&#39;</span><span class="p">,</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">bpcplx</span><span class="p">:</span> <span class="s1">&#39;cplex&#39;</span><span class="p">,</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">bpprre</span><span class="p">:</span> <span class="s1">&#39;pref&#39;</span><span class="p">,</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">bpuxrf</span><span class="p">:</span> <span class="s1">&#39;uxref&#39;</span><span class="p">,</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">bprelr</span><span class="p">:</span> <span class="s1">&#39;rxref&#39;</span><span class="p">,</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">bpstoi</span><span class="p">:</span> <span class="s1">&#39;stoichiometry&#39;</span><span class="p">,</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">bpreac</span><span class="p">:</span> <span class="s1">&#39;reaction&#39;</span><span class="p">,</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">bpcoma</span><span class="p">:</span> <span class="s1">&#39;cassembly&#39;</span><span class="p">,</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">bptrbr</span><span class="p">:</span> <span class="s1">&#39;reaction&#39;</span><span class="p">,</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">bptran</span><span class="p">:</span> <span class="s1">&#39;reaction&#39;</span><span class="p">,</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">bpmoli</span><span class="p">:</span> <span class="s1">&#39;interaction&#39;</span><span class="p">,</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">bpcata</span><span class="p">:</span> <span class="s1">&#39;catalysis&#39;</span><span class="p">,</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">bpmodu</span><span class="p">:</span> <span class="s1">&#39;catalysis&#39;</span><span class="p">,</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">bpctrl</span><span class="p">:</span> <span class="s1">&#39;control&#39;</span><span class="p">,</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">bppstp</span><span class="p">:</span> <span class="s1">&#39;pwstep&#39;</span><span class="p">,</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">bppubr</span><span class="p">:</span> <span class="s1">&#39;pubref&#39;</span><span class="p">,</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">bpfrfe</span><span class="p">:</span> <span class="s1">&#39;fragfea&#39;</span><span class="p">,</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">bpseqi</span><span class="p">:</span> <span class="s1">&#39;seqint&#39;</span><span class="p">,</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">bpseqs</span><span class="p">:</span> <span class="s1">&#39;seqsite&#39;</span><span class="p">,</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">bpmodf</span><span class="p">:</span> <span class="s1">&#39;modfea&#39;</span><span class="p">,</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">bpmodv</span><span class="p">:</span> <span class="s1">&#39;seqmodvoc&#39;</span><span class="p">,</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">bppath</span><span class="p">:</span> <span class="s1">&#39;pathway&#39;</span>
+        <span class="p">}</span></div>
+
+
+    <span class="k">def</span> <span class="nf">reload</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="n">modname</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="vm">__class__</span><span class="o">.</span><span class="vm">__module__</span>
+        <span class="n">mod</span> <span class="o">=</span> <span class="nb">__import__</span><span class="p">(</span><span class="n">modname</span><span class="p">,</span> <span class="n">fromlist</span><span class="o">=</span><span class="p">[</span><span class="n">modname</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;.&#39;</span><span class="p">)[</span><span class="mi">0</span><span class="p">]])</span>
+        <span class="n">imp</span><span class="o">.</span><span class="n">reload</span><span class="p">(</span><span class="n">mod</span><span class="p">)</span>
+        <span class="n">new</span> <span class="o">=</span> <span class="nb">getattr</span><span class="p">(</span><span class="n">mod</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="vm">__class__</span><span class="o">.</span><span class="vm">__name__</span><span class="p">)</span>
+        <span class="nb">setattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">&#39;__class__&#39;</span><span class="p">,</span> <span class="n">new</span><span class="p">)</span>
+
+<div class="viewcode-block" id="BioPaxReader.process">
+<a class="viewcode-back" href="../../../api/pypath.utils.pyreact.BioPaxReader.html#pypath.utils.pyreact.BioPaxReader.process">[docs]</a>
+    <span class="k">def</span> <span class="nf">process</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">silent</span><span class="o">=</span><span class="kc">False</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        This method executes the total workflow of BioPax processing.</span>
+
+<span class="sd">        :param bool silent: whether to print status messages and progress bars.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">silent</span> <span class="o">=</span> <span class="n">silent</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">open_biopax</span><span class="p">()</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">biopax_size</span><span class="p">()</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">extract</span><span class="p">()</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">set_progress</span><span class="p">()</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">init_etree</span><span class="p">()</span>
+        <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">bp</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">iterate</span><span class="p">()</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">close_biopax</span><span class="p">()</span>
+
+            <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">interactions_not2</span><span class="p">):</span>
+
+                <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span>
+                    <span class="s1">&#39;</span><span class="si">%u</span><span class="s1"> interactions have not exactly 2 &#39;</span>
+                    <span class="s1">&#39;participants (</span><span class="si">%s</span><span class="s1">).&#39;</span> <span class="o">%</span> <span class="p">(</span>
+                        <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">interactions_not2</span><span class="p">),</span>
+                        <span class="bp">self</span><span class="o">.</span><span class="n">source</span><span class="p">,</span>
+                    <span class="p">)</span>
+                <span class="p">)</span>
+
+        <span class="k">else</span><span class="p">:</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span>
+                <span class="s1">&#39;XML syntax error or empty file encountered. &#39;</span>
+                <span class="s1">&#39;Skipping to next file or resource.&#39;</span>
+            <span class="p">)</span></div>
+
+
+<div class="viewcode-block" id="BioPaxReader.open_biopax">
+<a class="viewcode-back" href="../../../api/pypath.utils.pyreact.BioPaxReader.html#pypath.utils.pyreact.BioPaxReader.open_biopax">[docs]</a>
+    <span class="k">def</span> <span class="nf">open_biopax</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Opens the BioPax file. This method should not be called directly,</span>
+<span class="sd">        ``BioPaxReader.process()`` calls it.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+        <span class="n">opener_args</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="p">{</span>
+                <span class="s1">&#39;default_mode&#39;</span><span class="p">:</span> <span class="s1">&#39;rb&#39;</span><span class="p">,</span>
+            <span class="p">}</span>
+            <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">file_from_archive</span> <span class="ow">is</span> <span class="kc">None</span> <span class="k">else</span>
+            <span class="p">{</span>
+                <span class="s1">&#39;files_needed&#39;</span><span class="p">:</span> <span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">file_from_archive</span><span class="p">],</span>
+            <span class="p">}</span>
+        <span class="p">)</span>
+        <span class="k">if</span> <span class="nb">type</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">biopax</span><span class="p">)</span> <span class="ow">is</span> <span class="n">curl</span><span class="o">.</span><span class="n">FileOpener</span><span class="p">:</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">opener</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">biopax</span>
+        <span class="k">else</span><span class="p">:</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">opener</span> <span class="o">=</span> <span class="n">curl</span><span class="o">.</span><span class="n">FileOpener</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">biopax</span><span class="p">,</span> <span class="o">**</span><span class="n">opener_args</span><span class="p">)</span>
+        <span class="k">if</span> <span class="nb">type</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">opener</span><span class="o">.</span><span class="n">result</span><span class="p">)</span> <span class="ow">is</span> <span class="nb">dict</span><span class="p">:</span>
+            <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">file_from_archive</span> <span class="ow">is</span> <span class="kc">None</span> <span class="ow">or</span> \
+                    <span class="bp">self</span><span class="o">.</span><span class="n">file_from_archive</span> <span class="ow">not</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">opener</span><span class="o">.</span><span class="n">result</span><span class="p">:</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">file_from_archive</span> <span class="o">=</span> \
+                    <span class="nb">sorted</span><span class="p">(</span><span class="nb">list</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">opener</span><span class="o">.</span><span class="n">result</span><span class="o">.</span><span class="n">keys</span><span class="p">()))[</span><span class="mi">0</span><span class="p">]</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">_biopax</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">opener</span><span class="o">.</span><span class="n">result</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">file_from_archive</span><span class="p">]</span>
+        <span class="k">elif</span> <span class="bp">self</span><span class="o">.</span><span class="n">opener</span><span class="o">.</span><span class="n">type</span> <span class="o">==</span> <span class="s1">&#39;gz&#39;</span><span class="p">:</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">_biopax</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">opener</span><span class="o">.</span><span class="n">gzfile</span>
+        <span class="k">else</span><span class="p">:</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">_biopax</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">opener</span><span class="o">.</span><span class="n">fileobj</span></div>
+
+
+<div class="viewcode-block" id="BioPaxReader.biopax_size">
+<a class="viewcode-back" href="../../../api/pypath.utils.pyreact.BioPaxReader.html#pypath.utils.pyreact.BioPaxReader.biopax_size">[docs]</a>
+    <span class="k">def</span> <span class="nf">biopax_size</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Gets the uncompressed size of the BioPax XML. This is needed in</span>
+<span class="sd">        order to have a progress bar. This method should not be called</span>
+<span class="sd">        directly, ``BioPaxReader.process()`` calls it.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">bp_filesize</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">opener</span><span class="o">.</span><span class="n">sizes</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">file_from_archive</span><span class="p">]</span> \
+            <span class="k">if</span> <span class="nb">hasattr</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">opener</span><span class="p">,</span> <span class="s1">&#39;sizes&#39;</span><span class="p">)</span> <span class="k">else</span> <span class="bp">self</span><span class="o">.</span><span class="n">opener</span><span class="o">.</span><span class="n">size</span></div>
+
+
+<div class="viewcode-block" id="BioPaxReader.extract">
+<a class="viewcode-back" href="../../../api/pypath.utils.pyreact.BioPaxReader.html#pypath.utils.pyreact.BioPaxReader.extract">[docs]</a>
+    <span class="k">def</span> <span class="nf">extract</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Extracts the BioPax file from compressed archive. Creates a</span>
+<span class="sd">        temporary file. This is needed to trace the progress of</span>
+<span class="sd">        processing, which is useful in case of large files.</span>
+<span class="sd">        This method should not be called directly,</span>
+<span class="sd">        ``BioPaxReader.process()`` calls it.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">opener</span><span class="o">.</span><span class="n">type</span> <span class="o">!=</span> <span class="s1">&#39;plain&#39;</span><span class="p">:</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">biopax_tmp_file</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">cachedir</span><span class="p">,</span>
+                <span class="s1">&#39;biopax.processing.tmp.owl&#39;</span><span class="p">,</span>
+            <span class="p">)</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span>
+                <span class="s1">&#39;Extracting </span><span class="si">%s</span><span class="s1"> from </span><span class="si">%s</span><span class="s1"> compressed file.&#39;</span> <span class="o">%</span> <span class="p">(</span>
+                    <span class="bp">self</span><span class="o">.</span><span class="n">file_from_archive</span><span class="p">,</span>
+                    <span class="bp">self</span><span class="o">.</span><span class="n">opener</span><span class="o">.</span><span class="n">type</span>
+                <span class="p">)</span>
+            <span class="p">)</span>
+
+            <span class="k">if</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">silent</span><span class="p">:</span>
+                <span class="n">prg</span> <span class="o">=</span> <span class="n">progress</span><span class="o">.</span><span class="n">Progress</span><span class="p">(</span>
+                    <span class="bp">self</span><span class="o">.</span><span class="n">bp_filesize</span><span class="p">,</span> <span class="s1">&#39;Extracting </span><span class="si">%s</span><span class="s1"> from </span><span class="si">%s</span><span class="s1"> compressed file&#39;</span> <span class="o">%</span>
+                    <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">file_from_archive</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">opener</span><span class="o">.</span><span class="n">type</span><span class="p">),</span> <span class="mi">1000000</span><span class="p">)</span>
+
+            <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">biopax_tmp_file</span><span class="p">,</span> <span class="s1">&#39;wb&#39;</span><span class="p">)</span> <span class="k">as</span> <span class="n">tmpf</span><span class="p">:</span>
+
+                <span class="k">while</span> <span class="kc">True</span><span class="p">:</span>
+
+                    <span class="n">chunk</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_biopax</span><span class="o">.</span><span class="n">read</span><span class="p">(</span><span class="mi">100000</span><span class="p">)</span>
+                    <span class="k">if</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">silent</span><span class="p">:</span>
+                        <span class="n">prg</span><span class="o">.</span><span class="n">step</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">chunk</span><span class="p">))</span>
+                    <span class="k">if</span> <span class="ow">not</span> <span class="nb">len</span><span class="p">(</span><span class="n">chunk</span><span class="p">):</span>
+                        <span class="k">break</span>
+                    <span class="k">if</span> <span class="nb">hasattr</span><span class="p">(</span><span class="n">chunk</span><span class="p">,</span> <span class="s1">&#39;encode&#39;</span><span class="p">):</span>
+                        <span class="n">chunk</span> <span class="o">=</span> <span class="n">chunk</span><span class="o">.</span><span class="n">encode</span><span class="p">(</span><span class="s1">&#39;utf8&#39;</span><span class="p">)</span>
+                    <span class="n">tmpf</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="n">chunk</span><span class="p">)</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">_biopax</span> <span class="o">=</span> <span class="nb">open</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">biopax_tmp_file</span><span class="p">,</span> <span class="s1">&#39;rb&#39;</span><span class="p">)</span>
+
+            <span class="k">if</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">silent</span><span class="p">:</span>
+                <span class="n">prg</span><span class="o">.</span><span class="n">terminate</span><span class="p">()</span></div>
+
+
+<div class="viewcode-block" id="BioPaxReader.init_etree">
+<a class="viewcode-back" href="../../../api/pypath.utils.pyreact.BioPaxReader.html#pypath.utils.pyreact.BioPaxReader.init_etree">[docs]</a>
+    <span class="k">def</span> <span class="nf">init_etree</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Creates the ``lxml.etree.iterparse`` object.</span>
+<span class="sd">        This method should not be called directly,</span>
+<span class="sd">        ``BioPaxReader.process()`` calls it.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+        <span class="k">try</span><span class="p">:</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">bp</span> <span class="o">=</span> <span class="n">etree</span><span class="o">.</span><span class="n">iterparse</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_biopax</span><span class="p">,</span> <span class="n">events</span><span class="o">=</span><span class="p">(</span><span class="s1">&#39;start&#39;</span><span class="p">,</span> <span class="s1">&#39;end&#39;</span><span class="p">))</span>
+            <span class="n">_</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">root</span> <span class="o">=</span> <span class="nb">next</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">bp</span><span class="p">)</span>
+
+        <span class="k">except</span> <span class="n">etree</span><span class="o">.</span><span class="n">XMLSyntaxError</span><span class="p">:</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">bp</span> <span class="o">=</span> <span class="kc">None</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">used_elements</span> <span class="o">=</span> <span class="p">[]</span></div>
+
+
+<div class="viewcode-block" id="BioPaxReader.set_progress">
+<a class="viewcode-back" href="../../../api/pypath.utils.pyreact.BioPaxReader.html#pypath.utils.pyreact.BioPaxReader.set_progress">[docs]</a>
+    <span class="k">def</span> <span class="nf">set_progress</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Initializes a progress bar.</span>
+<span class="sd">        This method should not be called directly,</span>
+<span class="sd">        ``BioPaxReader.process()`` calls it.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+        <span class="k">if</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">silent</span><span class="p">:</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">prg</span> <span class="o">=</span> <span class="n">progress</span><span class="o">.</span><span class="n">Progress</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">bp_filesize</span><span class="p">,</span>
+                                         <span class="s1">&#39;Processing </span><span class="si">%s</span><span class="s1"> from BioPAX XML&#39;</span> <span class="o">%</span>
+                                         <span class="bp">self</span><span class="o">.</span><span class="n">source</span><span class="p">,</span> <span class="mi">33</span><span class="p">)</span></div>
+
+
+<div class="viewcode-block" id="BioPaxReader.iterate">
+<a class="viewcode-back" href="../../../api/pypath.utils.pyreact.BioPaxReader.html#pypath.utils.pyreact.BioPaxReader.iterate">[docs]</a>
+    <span class="k">def</span> <span class="nf">iterate</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Iterates the BioPax XML and calls the appropriate methods</span>
+<span class="sd">        for each element.</span>
+<span class="sd">        This method should not be called directly,</span>
+<span class="sd">        ``BioPaxReader.process()`` calls it.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">fpos</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_biopax</span><span class="o">.</span><span class="n">tell</span><span class="p">()</span>
+        <span class="k">try</span><span class="p">:</span>
+            <span class="k">for</span> <span class="n">ev</span><span class="p">,</span> <span class="n">elem</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">bp</span><span class="p">:</span>
+                <span class="c1"># step the progressbar:</span>
+                <span class="n">new_fpos</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_biopax</span><span class="o">.</span><span class="n">tell</span><span class="p">()</span>
+                <span class="k">if</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">silent</span><span class="p">:</span>
+                    <span class="bp">self</span><span class="o">.</span><span class="n">prg</span><span class="o">.</span><span class="n">step</span><span class="p">(</span><span class="n">new_fpos</span> <span class="o">-</span> <span class="bp">self</span><span class="o">.</span><span class="n">fpos</span><span class="p">)</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">fpos</span> <span class="o">=</span> <span class="n">new_fpos</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">next_elem</span> <span class="o">=</span> <span class="n">elem</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">next_event</span> <span class="o">=</span> <span class="n">ev</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">next_id</span> <span class="o">=</span> <span class="s1">&#39;</span><span class="si">%s</span><span class="s1">@</span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> \
+                    <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">parser_id</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">next_elem</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">rdfid</span><span class="p">))</span> \
+                    <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">rdfid</span> <span class="ow">in</span> <span class="n">elem</span><span class="o">.</span><span class="n">attrib</span> \
+                    <span class="k">else</span> <span class="s1">&#39;</span><span class="si">%s</span><span class="s1">@</span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> \
+                    <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">parser_id</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">next_elem</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">rdfab</span><span class="p">))</span>
+                <span class="k">if</span> <span class="n">ev</span> <span class="o">==</span> <span class="s1">&#39;end&#39;</span> <span class="ow">and</span> <span class="bp">self</span><span class="o">.</span><span class="n">next_elem</span><span class="o">.</span><span class="n">tag</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">methods</span><span class="p">:</span>
+                    <span class="n">method</span> <span class="o">=</span> <span class="nb">getattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">methods</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">next_elem</span><span class="o">.</span><span class="n">tag</span><span class="p">])</span>
+                    <span class="n">method</span><span class="p">()</span>
+                    <span class="bp">self</span><span class="o">.</span><span class="n">root</span><span class="o">.</span><span class="n">clear</span><span class="p">()</span>
+                <span class="c1"># self.used_elements.append(self.next_elem)</span>
+                <span class="c1"># self.cleanup_hook()</span>
+        <span class="k">except</span> <span class="n">etree</span><span class="o">.</span><span class="n">XMLSyntaxError</span> <span class="k">as</span> <span class="n">e</span><span class="p">:</span>
+            <span class="k">if</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">silent</span><span class="p">:</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">prg</span><span class="o">.</span><span class="n">terminate</span><span class="p">(</span><span class="n">status</span><span class="o">=</span><span class="s1">&#39;failed&#39;</span><span class="p">)</span>
+            <span class="n">sys</span><span class="o">.</span><span class="n">stdout</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\n\t</span><span class="s1">:: Syntax error in BioPAX:</span><span class="se">\n\t\t</span><span class="si">%s</span><span class="se">\n</span><span class="s1">&#39;</span> <span class="o">%</span>
+                             <span class="nb">str</span><span class="p">(</span><span class="n">e</span><span class="p">))</span>
+            <span class="n">sys</span><span class="o">.</span><span class="n">stdout</span><span class="o">.</span><span class="n">flush</span><span class="p">()</span>
+        <span class="k">if</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">silent</span><span class="p">:</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">prg</span><span class="o">.</span><span class="n">terminate</span><span class="p">()</span></div>
+
+
+<div class="viewcode-block" id="BioPaxReader.cleanup_hook">
+<a class="viewcode-back" href="../../../api/pypath.utils.pyreact.BioPaxReader.html#pypath.utils.pyreact.BioPaxReader.cleanup_hook">[docs]</a>
+    <span class="k">def</span> <span class="nf">cleanup_hook</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Removes the used elements to free up memory.</span>
+<span class="sd">        This method should not be called directly,</span>
+<span class="sd">        ``BioPaxReader.iterate()`` calls it.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+        <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">used_elements</span><span class="p">)</span> <span class="o">&gt;</span> <span class="bp">self</span><span class="o">.</span><span class="n">cleanup_period</span><span class="p">:</span>
+            <span class="k">for</span> <span class="n">_</span> <span class="ow">in</span> <span class="n">xrange</span><span class="p">(</span><span class="nb">int</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">cleanup_period</span> <span class="o">/</span> <span class="mi">2</span><span class="p">)):</span>
+                <span class="n">e</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">used_elements</span><span class="o">.</span><span class="n">pop</span><span class="p">()</span>
+                <span class="n">e</span><span class="o">.</span><span class="n">clear</span><span class="p">()</span></div>
+
+
+<div class="viewcode-block" id="BioPaxReader.close_biopax">
+<a class="viewcode-back" href="../../../api/pypath.utils.pyreact.BioPaxReader.html#pypath.utils.pyreact.BioPaxReader.close_biopax">[docs]</a>
+    <span class="k">def</span> <span class="nf">close_biopax</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Deletes the iterator and closes the file object.</span>
+<span class="sd">        This method should not be called directly,</span>
+<span class="sd">        ``BioPaxReader.process()`` calls it.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+        <span class="k">del</span> <span class="bp">self</span><span class="o">.</span><span class="n">bp</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">_biopax</span><span class="o">.</span><span class="n">close</span><span class="p">()</span></div>
+
+
+    <span class="k">def</span> <span class="nf">protein</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+        <span class="n">entref</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">next_elem</span><span class="o">.</span><span class="n">find</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">bperef</span><span class="p">)</span>
+        <span class="k">if</span> <span class="n">entref</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
+            <span class="n">protein</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">get_none</span><span class="p">(</span><span class="n">entref</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">rdfres</span><span class="p">))</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s1">&#39;#&#39;</span><span class="p">,</span> <span class="s1">&#39;&#39;</span><span class="p">)</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">proteins</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">next_id</span><span class="p">]</span> <span class="o">=</span> <span class="p">{</span>
+                <span class="s1">&#39;protein&#39;</span><span class="p">:</span> <span class="s1">&#39;</span><span class="si">%s</span><span class="s1">@</span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">parser_id</span><span class="p">,</span> <span class="n">protein</span><span class="p">),</span>
+                <span class="s1">&#39;seqfeatures&#39;</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">_bp_collect_resources</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">bpfeat</span><span class="p">),</span>
+                <span class="s1">&#39;modfeatures&#39;</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">_bp_collect_resources</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">bpfeat</span><span class="p">)</span>
+            <span class="p">}</span>
+        <span class="k">else</span><span class="p">:</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">pfamilies</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">next_id</span><span class="p">]</span> <span class="o">=</span> \
+                <span class="bp">self</span><span class="o">.</span><span class="n">_bp_collect_resources</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">bpmphe</span><span class="p">)</span>
+
+    <span class="k">def</span> <span class="nf">pref</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">prefs</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">next_id</span><span class="p">]</span> <span class="o">=</span> <span class="p">{}</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">prefs</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">next_id</span><span class="p">][</span><span class="s1">&#39;uxrefs&#39;</span><span class="p">]</span> <span class="o">=</span> \
+            <span class="bp">self</span><span class="o">.</span><span class="n">_bp_collect_resources</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">bpxref</span><span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">prefs</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">next_id</span><span class="p">][</span><span class="s1">&#39;prefs&#39;</span><span class="p">]</span> <span class="o">=</span> \
+            <span class="bp">self</span><span class="o">.</span><span class="n">_bp_collect_resources</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">bpmerf</span><span class="p">)</span>
+
+    <span class="k">def</span> <span class="nf">uxref</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+        <span class="n">db</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">next_elem</span><span class="o">.</span><span class="n">find</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">bpdb</span><span class="p">)</span>
+        <span class="n">id_type</span> <span class="o">=</span> <span class="n">db</span><span class="o">.</span><span class="n">text</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span>
+        <span class="n">i</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">next_elem</span><span class="o">.</span><span class="n">find</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">bpid</span><span class="p">)</span>
+        <span class="k">if</span> <span class="n">i</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">ids</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">next_id</span><span class="p">]</span> <span class="o">=</span> <span class="p">(</span><span class="n">id_type</span><span class="p">,</span> <span class="n">i</span><span class="o">.</span><span class="n">text</span><span class="p">)</span>
+
+    <span class="k">def</span> <span class="nf">rxref</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+        <span class="n">db</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">next_elem</span><span class="o">.</span><span class="n">find</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">bpdb</span><span class="p">)</span>
+        <span class="k">if</span> <span class="n">db</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
+            <span class="n">id_type</span> <span class="o">=</span> <span class="n">db</span><span class="o">.</span><span class="n">text</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span>
+            <span class="n">i</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">next_elem</span><span class="o">.</span><span class="n">find</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">bpid</span><span class="p">)</span>
+            <span class="k">if</span> <span class="n">i</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">ids</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">next_id</span><span class="p">]</span> <span class="o">=</span> <span class="p">(</span><span class="n">id_type</span><span class="p">,</span> <span class="n">i</span><span class="o">.</span><span class="n">text</span><span class="p">)</span>
+
+    <span class="k">def</span> <span class="nf">cplex</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+        <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">next_elem</span><span class="o">.</span><span class="n">find</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">bpcsto</span><span class="p">)</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">complexes</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">next_id</span><span class="p">]</span> <span class="o">=</span> \
+                <span class="bp">self</span><span class="o">.</span><span class="n">_bp_collect_resources</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">bpcsto</span><span class="p">)</span>
+        <span class="k">elif</span> <span class="bp">self</span><span class="o">.</span><span class="n">next_elem</span><span class="o">.</span><span class="n">find</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">bpmphe</span><span class="p">)</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">cvariations</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">next_id</span><span class="p">]</span> <span class="o">=</span> \
+                <span class="bp">self</span><span class="o">.</span><span class="n">_bp_collect_resources</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">bpmphe</span><span class="p">)</span>
+        <span class="k">elif</span> <span class="bp">self</span><span class="o">.</span><span class="n">next_elem</span><span class="o">.</span><span class="n">find</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">bpcomp</span><span class="p">)</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">complexes</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">next_id</span><span class="p">]</span> <span class="o">=</span> \
+                <span class="bp">self</span><span class="o">.</span><span class="n">_bp_collect_resources</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">bpcomp</span><span class="p">)</span>
+
+    <span class="k">def</span> <span class="nf">stoichiometry</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+        <span class="n">snum</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">next_elem</span><span class="o">.</span><span class="n">find</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">bpstoc</span><span class="p">)</span><span class="o">.</span><span class="n">text</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">stoichiometries</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">next_id</span><span class="p">]</span> <span class="o">=</span> <span class="p">(</span><span class="s1">&#39;</span><span class="si">%s</span><span class="s1">@</span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="p">(</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">parser_id</span><span class="p">,</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">next_elem</span><span class="o">.</span><span class="n">find</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">bpphye</span><span class="p">)</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">rdfres</span><span class="p">)</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span>
+                <span class="s1">&#39;#&#39;</span><span class="p">,</span> <span class="s1">&#39;&#39;</span><span class="p">)),</span> <span class="nb">int</span><span class="p">(</span><span class="nb">float</span><span class="p">(</span><span class="n">snum</span><span class="p">)))</span>
+
+    <span class="k">def</span> <span class="nf">interaction</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+        <span class="n">part</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_bp_collect_resources</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">bpleft</span><span class="p">)</span>
+        <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">part</span><span class="p">)</span> <span class="o">==</span> <span class="mi">2</span><span class="p">:</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">interactions</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">next_id</span><span class="p">]</span> <span class="o">=</span> <span class="p">{</span>
+                <span class="s1">&#39;refs&#39;</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">_bp_collect_resources</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">bpxref</span><span class="p">),</span>
+                <span class="s1">&#39;left&#39;</span><span class="p">:</span> <span class="p">[</span><span class="n">part</span><span class="p">[</span><span class="mi">0</span><span class="p">]],</span>
+                <span class="s1">&#39;right&#39;</span><span class="p">:</span> <span class="p">[</span><span class="n">part</span><span class="p">[</span><span class="mi">1</span><span class="p">]],</span>
+                <span class="s1">&#39;type&#39;</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">next_elem</span><span class="o">.</span><span class="n">tag</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;}&#39;</span><span class="p">)[</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span>
+            <span class="p">}</span>
+        <span class="k">else</span><span class="p">:</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">interactions_not2</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">next_id</span><span class="p">]</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="n">part</span><span class="p">)</span>
+
+    <span class="k">def</span> <span class="nf">reaction</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">reactions</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">next_id</span><span class="p">]</span> <span class="o">=</span> <span class="p">{</span>
+            <span class="s1">&#39;refs&#39;</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">_bp_collect_resources</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">bpxref</span><span class="p">),</span>
+            <span class="s1">&#39;left&#39;</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">_bp_collect_resources</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">bpleft</span><span class="p">),</span>
+            <span class="s1">&#39;right&#39;</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">_bp_collect_resources</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">bprgth</span><span class="p">),</span>
+            <span class="s1">&#39;type&#39;</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">next_elem</span><span class="o">.</span><span class="n">tag</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;}&#39;</span><span class="p">)[</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span>
+        <span class="p">}</span>
+
+    <span class="k">def</span> <span class="nf">cassembly</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">cassemblies</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">next_id</span><span class="p">]</span> <span class="o">=</span> <span class="p">{</span>
+            <span class="s1">&#39;refs&#39;</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">_bp_collect_resources</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">bpxref</span><span class="p">),</span>
+            <span class="s1">&#39;left&#39;</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">_bp_collect_resources</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">bpleft</span><span class="p">),</span>
+            <span class="s1">&#39;right&#39;</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">_bp_collect_resources</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">bprgth</span><span class="p">),</span>
+            <span class="s1">&#39;type&#39;</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">next_elem</span><span class="o">.</span><span class="n">tag</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;}&#39;</span><span class="p">)[</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span>
+        <span class="p">}</span>
+
+    <span class="k">def</span> <span class="nf">catalysis</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+        <span class="n">cter</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">next_elem</span><span class="o">.</span><span class="n">find</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">bpcter</span><span class="p">)</span>
+        <span class="n">cted</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">next_elem</span><span class="o">.</span><span class="n">find</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">bpcted</span><span class="p">)</span>
+        <span class="k">if</span> <span class="n">cter</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span> <span class="ow">and</span> <span class="n">cted</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
+            <span class="n">typ</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">next_elem</span><span class="o">.</span><span class="n">find</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">bpctyp</span><span class="p">)</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">catalyses</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">next_id</span><span class="p">]</span> <span class="o">=</span> <span class="p">{</span>
+                <span class="s1">&#39;controller&#39;</span><span class="p">:</span> <span class="s1">&#39;</span><span class="si">%s</span><span class="s1">@</span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span>
+                <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">parser_id</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">get_none</span><span class="p">(</span><span class="n">cter</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">rdfres</span><span class="p">))),</span>
+                <span class="s1">&#39;controlled&#39;</span><span class="p">:</span> <span class="s1">&#39;</span><span class="si">%s</span><span class="s1">@</span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span>
+                <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">parser_id</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">get_none</span><span class="p">(</span><span class="n">cted</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">rdfres</span><span class="p">))),</span>
+                <span class="s1">&#39;type&#39;</span><span class="p">:</span> <span class="s1">&#39;&#39;</span> <span class="k">if</span> <span class="n">typ</span> <span class="ow">is</span> <span class="kc">None</span> <span class="k">else</span> <span class="n">typ</span><span class="o">.</span><span class="n">text</span>
+            <span class="p">}</span>
+
+    <span class="k">def</span> <span class="nf">control</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+        <span class="n">cter</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">next_elem</span><span class="o">.</span><span class="n">find</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">bpcter</span><span class="p">)</span>
+        <span class="n">cted</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">next_elem</span><span class="o">.</span><span class="n">find</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">bpcted</span><span class="p">)</span>
+        <span class="k">if</span> <span class="n">cter</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span> <span class="ow">and</span> <span class="n">cted</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
+            <span class="n">typ</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">next_elem</span><span class="o">.</span><span class="n">find</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">bpctyp</span><span class="p">)</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">controls</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">next_id</span><span class="p">]</span> <span class="o">=</span> <span class="p">{</span>
+                <span class="s1">&#39;refs&#39;</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">_bp_collect_resources</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">bpxref</span><span class="p">),</span>
+                <span class="s1">&#39;controller&#39;</span><span class="p">:</span> <span class="s1">&#39;</span><span class="si">%s</span><span class="s1">@</span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span>
+                <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">parser_id</span><span class="p">,</span> <span class="n">cter</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">rdfres</span><span class="p">)</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s1">&#39;#&#39;</span><span class="p">,</span> <span class="s1">&#39;&#39;</span><span class="p">)),</span>
+                <span class="s1">&#39;controlled&#39;</span><span class="p">:</span> <span class="s1">&#39;</span><span class="si">%s</span><span class="s1">@</span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span>
+                <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">parser_id</span><span class="p">,</span> <span class="n">cted</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">rdfres</span><span class="p">)</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s1">&#39;#&#39;</span><span class="p">,</span> <span class="s1">&#39;&#39;</span><span class="p">)),</span>
+                <span class="s1">&#39;type&#39;</span><span class="p">:</span> <span class="s1">&#39;&#39;</span> <span class="k">if</span> <span class="n">typ</span> <span class="ow">is</span> <span class="kc">None</span> <span class="k">else</span> <span class="n">typ</span><span class="o">.</span><span class="n">text</span>
+            <span class="p">}</span>
+
+    <span class="k">def</span> <span class="nf">pwstep</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">pwsteps</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">next_id</span><span class="p">]</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_bp_collect_resources</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">bppstp</span><span class="p">)</span>
+
+    <span class="k">def</span> <span class="nf">pubref</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+        <span class="n">pmid</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">next_elem</span><span class="o">.</span><span class="n">find</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">bpid</span><span class="p">)</span>
+        <span class="k">if</span> <span class="n">pmid</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">pubrefs</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">next_id</span><span class="p">]</span> <span class="o">=</span> <span class="n">pmid</span><span class="o">.</span><span class="n">text</span>
+
+    <span class="k">def</span> <span class="nf">fragfea</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+        <span class="n">felo</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">next_elem</span><span class="o">.</span><span class="n">find</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">bpfelo</span><span class="p">)</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">rdfres</span><span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">fragfeas</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">next_id</span><span class="p">]</span> <span class="o">=</span> <span class="s1">&#39;</span><span class="si">%s</span><span class="s1">@</span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> \
+            <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">parser_id</span><span class="p">,</span> <span class="n">felo</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s1">&#39;#&#39;</span><span class="p">,</span> <span class="s1">&#39;&#39;</span><span class="p">))</span>
+
+    <span class="k">def</span> <span class="nf">seqint</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+        <span class="n">beg</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">next_elem</span><span class="o">.</span><span class="n">find</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">bpibeg</span><span class="p">)</span>
+        <span class="n">end</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">next_elem</span><span class="o">.</span><span class="n">find</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">bpiend</span><span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">seqints</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">next_id</span><span class="p">]</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="s1">&#39;</span><span class="si">%s</span><span class="s1">@</span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">parser_id</span><span class="p">,</span> <span class="n">beg</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">rdfres</span><span class="p">)</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s1">&#39;#&#39;</span><span class="p">,</span> <span class="s1">&#39;&#39;</span><span class="p">))</span>
+            <span class="k">if</span> <span class="n">beg</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span> <span class="k">else</span> <span class="kc">None</span><span class="p">,</span>
+            <span class="s1">&#39;</span><span class="si">%s</span><span class="s1">@</span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">parser_id</span><span class="p">,</span> <span class="n">end</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">rdfres</span><span class="p">)</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s1">&#39;#&#39;</span><span class="p">,</span> <span class="s1">&#39;&#39;</span><span class="p">))</span>
+            <span class="k">if</span> <span class="n">end</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span> <span class="k">else</span> <span class="kc">None</span><span class="p">)</span>
+
+    <span class="k">def</span> <span class="nf">seqsite</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+        <span class="n">seqp</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">next_elem</span><span class="o">.</span><span class="n">find</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">bpseqp</span><span class="p">)</span>
+        <span class="k">if</span> <span class="n">seqp</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span> <span class="ow">and</span> <span class="n">seqp</span><span class="o">.</span><span class="n">text</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">seqsites</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">next_id</span><span class="p">]</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">seqp</span><span class="o">.</span><span class="n">text</span><span class="p">)</span>
+
+    <span class="k">def</span> <span class="nf">modfea</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+        <span class="n">felo</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">next_elem</span><span class="o">.</span><span class="n">find</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">bpfelo</span><span class="p">)</span>
+        <span class="n">moty</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">next_elem</span><span class="o">.</span><span class="n">find</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">bpmoty</span><span class="p">)</span>
+        <span class="k">if</span> <span class="n">felo</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span> <span class="ow">and</span> <span class="n">moty</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">modfeas</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">next_id</span><span class="p">]</span> <span class="o">=</span> <span class="p">(</span>
+                <span class="s1">&#39;</span><span class="si">%s</span><span class="s1">@</span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="p">(</span>
+                    <span class="bp">self</span><span class="o">.</span><span class="n">parser_id</span><span class="p">,</span>
+                    <span class="bp">self</span><span class="o">.</span><span class="n">next_elem</span><span class="o">.</span><span class="n">find</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">bpfelo</span><span class="p">)</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">rdfres</span><span class="p">)</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span>
+                        <span class="s1">&#39;#&#39;</span><span class="p">,</span> <span class="s1">&#39;&#39;</span><span class="p">)),</span> <span class="s1">&#39;</span><span class="si">%s</span><span class="s1">@</span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span>
+                <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">parser_id</span><span class="p">,</span>
+                 <span class="bp">self</span><span class="o">.</span><span class="n">next_elem</span><span class="o">.</span><span class="n">find</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">bpmoty</span><span class="p">)</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">rdfres</span><span class="p">)</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span>
+                     <span class="s1">&#39;#&#39;</span><span class="p">,</span> <span class="s1">&#39;&#39;</span><span class="p">)))</span>
+
+    <span class="k">def</span> <span class="nf">seqmodvoc</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+        <span class="n">term</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">next_elem</span><span class="o">.</span><span class="n">find</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">bpterm</span><span class="p">)</span>
+        <span class="k">if</span> <span class="n">term</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">seqmodvocs</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">next_id</span><span class="p">]</span> <span class="o">=</span> <span class="n">term</span><span class="o">.</span><span class="n">text</span>
+
+    <span class="k">def</span> <span class="nf">pathway</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+        <span class="n">name</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">next_elem</span><span class="o">.</span><span class="n">find</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">bpdinm</span><span class="p">)</span>
+        <span class="k">if</span> <span class="n">name</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
+            <span class="n">name</span> <span class="o">=</span> <span class="n">name</span><span class="o">.</span><span class="n">text</span>
+        <span class="k">try</span><span class="p">:</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">pathways</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">next_id</span><span class="p">]</span> <span class="o">=</span> <span class="p">{</span>
+                <span class="s1">&#39;components&#39;</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">_bp_collect_resources</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">bppcom</span><span class="p">),</span>
+                <span class="s1">&#39;name&#39;</span><span class="p">:</span> <span class="n">name</span>
+            <span class="p">}</span>
+        <span class="k">except</span> <span class="ne">TypeError</span><span class="p">:</span>
+            <span class="n">sys</span><span class="o">.</span><span class="n">stdout</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s1">&#39;Wrong type at element:</span><span class="se">\n</span><span class="s1">&#39;</span><span class="p">)</span>
+            <span class="n">sys</span><span class="o">.</span><span class="n">stdout</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s1">&#39;</span><span class="si">%s</span><span class="s1"> </span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span>
+                             <span class="p">(</span><span class="nb">str</span><span class="p">(</span><span class="n">etree</span><span class="o">.</span><span class="n">tostring</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">next_elem</span><span class="p">))[:</span><span class="mi">76</span><span class="p">],</span> <span class="s1">&#39;...&#39;</span><span class="p">))</span>
+            <span class="n">sys</span><span class="o">.</span><span class="n">stdout</span><span class="o">.</span><span class="n">flush</span><span class="p">()</span>
+
+    <span class="k">def</span> <span class="nf">get_none</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">something</span><span class="p">):</span>
+        <span class="k">if</span> <span class="n">something</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
+            <span class="k">return</span> <span class="n">something</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s1">&#39;#&#39;</span><span class="p">,</span> <span class="s1">&#39;&#39;</span><span class="p">)</span>
+        <span class="k">return</span> <span class="n">something</span>
+
+    <span class="k">def</span> <span class="nf">_bp_collect_resources</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">tag</span><span class="p">,</span> <span class="n">restype</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
+        <span class="k">return</span> \
+            <span class="nb">list</span><span class="p">(</span>
+                <span class="nb">map</span><span class="p">(</span>
+                    <span class="k">lambda</span> <span class="n">e</span><span class="p">:</span>
+                    <span class="s1">&#39;</span><span class="si">%s</span><span class="s1">@</span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span>
+                    <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">parser_id</span><span class="p">,</span> <span class="n">e</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">rdfres</span><span class="p">)</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s1">&#39;#&#39;</span><span class="p">,</span> <span class="s1">&#39;&#39;</span><span class="p">)),</span>
+                    <span class="nb">filter</span><span class="p">(</span>
+                        <span class="k">lambda</span> <span class="n">e</span><span class="p">:</span>
+                        <span class="bp">self</span><span class="o">.</span><span class="n">rdfres</span> <span class="ow">in</span> <span class="n">e</span><span class="o">.</span><span class="n">attrib</span> <span class="ow">and</span> <span class="p">(</span>
+                            <span class="n">restype</span> <span class="ow">is</span> <span class="kc">None</span> <span class="ow">or</span>
+                            <span class="n">e</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">rdfres</span><span class="p">)</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s1">&#39;#&#39;</span><span class="p">,</span> <span class="s1">&#39;&#39;</span><span class="p">)</span>
+                            <span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="n">restype</span><span class="p">)</span>
+                        <span class="p">),</span>
+                        <span class="bp">self</span><span class="o">.</span><span class="n">next_elem</span><span class="o">.</span><span class="n">iterfind</span><span class="p">(</span><span class="n">tag</span><span class="p">)</span>
+                    <span class="p">)</span>
+                <span class="p">)</span>
+            <span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="AttributeHandler">
+<a class="viewcode-back" href="../../../api/pypath.utils.pyreact.AttributeHandler.html#pypath.utils.pyreact.AttributeHandler">[docs]</a>
+<span class="k">class</span> <span class="nc">AttributeHandler</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span>
+<div class="viewcode-block" id="AttributeHandler.__init__">
+<a class="viewcode-back" href="../../../api/pypath.utils.pyreact.AttributeHandler.html#pypath.utils.pyreact.AttributeHandler.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+        <span class="k">pass</span></div>
+
+
+    <span class="k">def</span> <span class="nf">add_source</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">source</span><span class="p">):</span>
+        <span class="k">if</span> <span class="nb">type</span><span class="p">(</span><span class="n">source</span><span class="p">)</span> <span class="ow">in</span> <span class="n">_const</span><span class="o">.</span><span class="n">CHAR_TYPES</span><span class="p">:</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">_add_source</span><span class="p">(</span><span class="n">source</span><span class="p">)</span>
+        <span class="k">else</span><span class="p">:</span>
+            <span class="k">for</span> <span class="n">s</span> <span class="ow">in</span> <span class="n">source</span><span class="p">:</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">_add_source</span><span class="p">(</span><span class="n">s</span><span class="p">)</span>
+
+    <span class="k">def</span> <span class="nf">_add_source</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">source</span><span class="p">):</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">sources</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">source</span><span class="p">)</span>
+        <span class="k">if</span> <span class="n">source</span> <span class="ow">not</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">attrs</span><span class="p">:</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">attrs</span><span class="p">[</span><span class="n">source</span><span class="p">]</span> <span class="o">=</span> <span class="p">{}</span>
+
+    <span class="k">def</span> <span class="nf">merge_attrs</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">attrs</span><span class="p">):</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">attrs</span> <span class="o">=</span> <span class="n">common</span><span class="o">.</span><span class="n">merge_dicts</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">attrs</span><span class="p">,</span> <span class="n">attrs</span><span class="p">)</span>
+
+    <span class="k">def</span> <span class="nf">update_attr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">attr</span><span class="p">):</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">attrs</span> <span class="o">=</span> <span class="n">common</span><span class="o">.</span><span class="n">dict_set_path</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">attrs</span><span class="p">,</span> <span class="n">attr</span><span class="p">)</span>
+
+    <span class="k">def</span> <span class="fm">__iadd__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">other</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&#39;&#39;&#39;</span>
+<span class="sd">        Members or ids of entities should never change, as</span>
+<span class="sd">        these are their unique, hashable and comparable</span>
+<span class="sd">        attributes.</span>
+
+<span class="sd">        __iadd__ operator is for merging entities with</span>
+<span class="sd">        identical members or ids.</span>
+<span class="sd">        &#39;&#39;&#39;</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">sources</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">sources</span> <span class="o">|</span> <span class="n">other</span><span class="o">.</span><span class="n">sources</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">merge_attrs</span><span class="p">(</span><span class="n">other</span><span class="o">.</span><span class="n">attrs</span><span class="p">)</span>
+        <span class="k">return</span> <span class="bp">self</span></div>
+
+
+
+<div class="viewcode-block" id="Entity">
+<a class="viewcode-back" href="../../../api/pypath.utils.pyreact.Entity.html#pypath.utils.pyreact.Entity">[docs]</a>
+<span class="k">class</span> <span class="nc">Entity</span><span class="p">(</span><span class="n">AttributeHandler</span><span class="p">):</span>
+<div class="viewcode-block" id="Entity.__init__">
+<a class="viewcode-back" href="../../../api/pypath.utils.pyreact.Entity.html#pypath.utils.pyreact.Entity.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">identifier</span><span class="p">,</span> <span class="n">id_type</span><span class="p">,</span> <span class="n">sources</span><span class="o">=</span><span class="p">[],</span> <span class="n">attrs</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
+        <span class="nb">super</span><span class="p">(</span><span class="n">Entity</span><span class="p">,</span> <span class="bp">self</span><span class="p">)</span><span class="o">.</span><span class="fm">__init__</span><span class="p">()</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">id</span> <span class="o">=</span> <span class="n">identifier</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">id_type</span> <span class="o">=</span> <span class="n">id_type</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">sources</span> <span class="o">=</span> <span class="nb">set</span><span class="p">([])</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">attrs</span> <span class="o">=</span> <span class="p">{}</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">add_source</span><span class="p">(</span><span class="n">sources</span><span class="p">)</span>
+        <span class="k">if</span> <span class="n">attrs</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">merge_attrs</span><span class="p">(</span><span class="n">attrs</span><span class="p">)</span></div>
+
+
+    <span class="k">def</span> <span class="fm">__str__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+        <span class="k">return</span> <span class="s1">&#39;</span><span class="si">%s</span><span class="s1"> (</span><span class="si">%s</span><span class="s1">)&#39;</span> <span class="o">%</span> <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">id</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">id_type</span><span class="p">)</span>
+
+    <span class="k">def</span> <span class="fm">__hash__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+        <span class="k">return</span> <span class="nb">hash</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="fm">__str__</span><span class="p">())</span>
+
+    <span class="k">def</span> <span class="fm">__eq__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">other</span><span class="p">):</span>
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="fm">__str__</span><span class="p">()</span> <span class="o">==</span> <span class="n">other</span><span class="o">.</span><span class="fm">__str__</span><span class="p">()</span>
+
+    <span class="k">def</span> <span class="fm">__gt__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">other</span><span class="p">):</span>
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="fm">__str__</span><span class="p">()</span> <span class="o">&gt;</span> <span class="n">other</span><span class="o">.</span><span class="fm">__str__</span><span class="p">()</span>
+
+    <span class="k">def</span> <span class="fm">__lt__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">other</span><span class="p">):</span>
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="fm">__str__</span><span class="p">()</span> <span class="o">&lt;</span> <span class="n">other</span><span class="o">.</span><span class="fm">__str__</span><span class="p">()</span>
+
+    <span class="k">def</span> <span class="fm">__repr__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+        <span class="k">return</span> <span class="s1">&#39;</span><span class="si">%s</span><span class="s1"> (</span><span class="si">%s</span><span class="s1">)&#39;</span> <span class="o">%</span> <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">id</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">id_type</span><span class="p">)</span>
+
+    <span class="k">def</span> <span class="fm">__iter__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        With this method it is possible to iterate ``Entity`` objects</span>
+<span class="sd">        just like ``EntitySet`` objects.</span>
+
+<span class="sd">        Yields the object.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+        <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="p">[</span><span class="bp">self</span><span class="p">]:</span>
+            <span class="k">yield</span> <span class="n">i</span>
+
+<div class="viewcode-block" id="Entity.expand">
+<a class="viewcode-back" href="../../../api/pypath.utils.pyreact.Entity.html#pypath.utils.pyreact.Entity.expand">[docs]</a>
+    <span class="k">def</span> <span class="nf">expand</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        With this method it is possible to iterate ``Entity`` objects</span>
+<span class="sd">        just like ``EntitySet`` objects.</span>
+
+<span class="sd">        Yields string.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+        <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">id</span><span class="p">]:</span>
+            <span class="k">yield</span> <span class="n">i</span></div>
+
+
+    <span class="k">def</span> <span class="nf">itermembers</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+        <span class="k">for</span> <span class="n">m</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="fm">__iter__</span><span class="p">():</span>
+            <span class="k">yield</span> <span class="p">(</span><span class="n">m</span><span class="p">,</span> <span class="p">{})</span></div>
+
+
+
+<div class="viewcode-block" id="Protein">
+<a class="viewcode-back" href="../../../api/pypath.utils.pyreact.Protein.html#pypath.utils.pyreact.Protein">[docs]</a>
+<span class="k">class</span> <span class="nc">Protein</span><span class="p">(</span><span class="n">Entity</span><span class="p">):</span>
+<div class="viewcode-block" id="Protein.__init__">
+<a class="viewcode-back" href="../../../api/pypath.utils.pyreact.Protein.html#pypath.utils.pyreact.Protein.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">protein_id</span><span class="p">,</span> <span class="n">id_type</span><span class="o">=</span><span class="s1">&#39;uniprot&#39;</span><span class="p">,</span> <span class="n">sources</span><span class="o">=</span><span class="p">[],</span> <span class="n">attrs</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
+        <span class="nb">super</span><span class="p">(</span><span class="n">Protein</span><span class="p">,</span> <span class="bp">self</span><span class="p">)</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span>
+            <span class="n">protein_id</span><span class="p">,</span> <span class="n">id_type</span><span class="p">,</span> <span class="n">sources</span><span class="o">=</span><span class="n">sources</span><span class="p">,</span> <span class="n">attrs</span><span class="o">=</span><span class="n">attrs</span><span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">type</span> <span class="o">=</span> <span class="s1">&#39;protein&#39;</span></div>
+
+
+    <span class="k">def</span> <span class="nf">reload</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+        <span class="n">modname</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="vm">__class__</span><span class="o">.</span><span class="vm">__module__</span>
+        <span class="n">mod</span> <span class="o">=</span> <span class="nb">__import__</span><span class="p">(</span><span class="n">modname</span><span class="p">,</span> <span class="n">fromlist</span><span class="o">=</span><span class="p">[</span><span class="n">modname</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;.&#39;</span><span class="p">)[</span><span class="mi">0</span><span class="p">]])</span>
+        <span class="n">imp</span><span class="o">.</span><span class="n">reload</span><span class="p">(</span><span class="n">mod</span><span class="p">)</span>
+        <span class="n">new</span> <span class="o">=</span> <span class="nb">getattr</span><span class="p">(</span><span class="n">mod</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="vm">__class__</span><span class="o">.</span><span class="vm">__name__</span><span class="p">)</span>
+        <span class="nb">setattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">&#39;__class__&#39;</span><span class="p">,</span> <span class="n">new</span><span class="p">)</span>
+
+    <span class="k">def</span> <span class="nf">key</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">id</span>
+
+    <span class="k">def</span> <span class="nf">proteins</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+        <span class="k">return</span> <span class="nb">set</span><span class="p">([</span><span class="bp">self</span><span class="o">.</span><span class="n">id</span><span class="p">])</span>
+
+    <span class="k">def</span> <span class="fm">__ror__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">other</span><span class="p">):</span>
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">proteins</span><span class="p">()</span> <span class="o">|</span> <span class="n">other</span>
+
+    <span class="k">def</span> <span class="fm">__rand__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">other</span><span class="p">):</span>
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">proteins</span><span class="p">()</span> <span class="o">&amp;</span> <span class="n">other</span>
+
+    <span class="k">def</span> <span class="fm">__rsub__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">other</span><span class="p">):</span>
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">proteins</span><span class="p">()</span> <span class="o">-</span> <span class="n">other</span></div>
+
+
+
+<div class="viewcode-block" id="Reference">
+<a class="viewcode-back" href="../../../api/pypath.utils.pyreact.Reference.html#pypath.utils.pyreact.Reference">[docs]</a>
+<span class="k">class</span> <span class="nc">Reference</span><span class="p">(</span><span class="n">Entity</span><span class="p">):</span>
+<div class="viewcode-block" id="Reference.__init__">
+<a class="viewcode-back" href="../../../api/pypath.utils.pyreact.Reference.html#pypath.utils.pyreact.Reference.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">ref_id</span><span class="p">,</span> <span class="n">id_type</span><span class="o">=</span><span class="s1">&#39;pubmed&#39;</span><span class="p">,</span> <span class="n">sources</span><span class="o">=</span><span class="p">[]):</span>
+        <span class="nb">super</span><span class="p">(</span><span class="n">Reference</span><span class="p">,</span> <span class="bp">self</span><span class="p">)</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="n">ref_id</span><span class="p">,</span> <span class="n">id_type</span><span class="p">,</span> <span class="n">sources</span><span class="o">=</span><span class="n">sources</span><span class="p">)</span></div>
+
+
+    <span class="k">def</span> <span class="nf">get_ref</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+        <span class="k">return</span> <span class="n">refs</span><span class="o">.</span><span class="n">Reference</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">ref_id</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="EntitySet">
+<a class="viewcode-back" href="../../../api/pypath.utils.pyreact.EntitySet.html#pypath.utils.pyreact.EntitySet">[docs]</a>
+<span class="k">class</span> <span class="nc">EntitySet</span><span class="p">(</span><span class="n">AttributeHandler</span><span class="p">):</span>
+<div class="viewcode-block" id="EntitySet.__init__">
+<a class="viewcode-back" href="../../../api/pypath.utils.pyreact.EntitySet.html#pypath.utils.pyreact.EntitySet.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">members</span><span class="p">,</span> <span class="n">sources</span><span class="o">=</span><span class="p">[],</span> <span class="n">sep</span><span class="o">=</span><span class="s1">&#39;;&#39;</span><span class="p">,</span> <span class="n">parent</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
+        <span class="nb">super</span><span class="p">(</span><span class="n">EntitySet</span><span class="p">,</span> <span class="bp">self</span><span class="p">)</span><span class="o">.</span><span class="fm">__init__</span><span class="p">()</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">parent</span> <span class="o">=</span> <span class="n">parent</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">members</span> <span class="o">=</span> <span class="nb">sorted</span><span class="p">(</span><span class="n">common</span><span class="o">.</span><span class="n">unique_list</span><span class="p">(</span><span class="n">members</span><span class="p">))</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">set</span> <span class="o">=</span> <span class="nb">set</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">members</span><span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">sources</span> <span class="o">=</span> <span class="nb">set</span><span class="p">([])</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">attrs</span> <span class="o">=</span> <span class="p">{}</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">add_source</span><span class="p">(</span><span class="n">sources</span><span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">originals</span> <span class="o">=</span> <span class="p">{}</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">type</span> <span class="o">=</span> <span class="kc">None</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">sep</span> <span class="o">=</span> <span class="n">sep</span></div>
+
+
+    <span class="k">def</span> <span class="fm">__str__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">sep</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="nb">sorted</span><span class="p">(</span><span class="nb">map</span><span class="p">(</span><span class="k">lambda</span> <span class="n">x</span><span class="p">:</span> <span class="nb">str</span><span class="p">(</span><span class="n">x</span><span class="p">),</span> <span class="nb">list</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">members</span><span class="p">))))</span>
+
+    <span class="k">def</span> <span class="fm">__repr__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+        <span class="k">return</span> <span class="s1">&#39;</span><span class="si">%s</span><span class="s1">: </span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="vm">__class__</span><span class="o">.</span><span class="vm">__name__</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="fm">__str__</span><span class="p">())</span>
+
+    <span class="k">def</span> <span class="fm">__hash__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+        <span class="k">return</span> <span class="nb">hash</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="fm">__str__</span><span class="p">())</span>
+
+    <span class="k">def</span> <span class="fm">__eq__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">other</span><span class="p">):</span>
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="fm">__str__</span><span class="p">()</span> <span class="o">==</span> <span class="n">other</span><span class="o">.</span><span class="fm">__str__</span><span class="p">()</span>
+
+    <span class="k">def</span> <span class="fm">__gt__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">other</span><span class="p">):</span>
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="fm">__str__</span><span class="p">()</span> <span class="o">&gt;</span> <span class="n">other</span><span class="o">.</span><span class="fm">__str__</span><span class="p">()</span>
+
+    <span class="k">def</span> <span class="fm">__lt__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">other</span><span class="p">):</span>
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="fm">__str__</span><span class="p">()</span> <span class="o">&lt;</span> <span class="n">other</span><span class="o">.</span><span class="fm">__str__</span><span class="p">()</span>
+
+    <span class="k">def</span> <span class="fm">__iter__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+        <span class="k">for</span> <span class="n">m</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">members</span><span class="p">:</span>
+            <span class="k">yield</span> <span class="n">m</span>
+
+    <span class="k">def</span> <span class="nf">add_source</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">source</span><span class="p">):</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">sources</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">source</span><span class="p">)</span>
+        <span class="k">if</span> <span class="n">source</span> <span class="ow">not</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">attrs</span><span class="p">:</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">attrs</span><span class="p">[</span><span class="n">source</span><span class="p">]</span> <span class="o">=</span> <span class="p">{}</span></div>
+
+
+
+<div class="viewcode-block" id="Intersecting">
+<a class="viewcode-back" href="../../../api/pypath.utils.pyreact.Intersecting.html#pypath.utils.pyreact.Intersecting">[docs]</a>
+<span class="k">class</span> <span class="nc">Intersecting</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span>
+<div class="viewcode-block" id="Intersecting.__init__">
+<a class="viewcode-back" href="../../../api/pypath.utils.pyreact.Intersecting.html#pypath.utils.pyreact.Intersecting.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+        <span class="k">pass</span></div>
+
+
+    <span class="k">def</span> <span class="fm">__eq__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">other</span><span class="p">):</span>
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">type</span> <span class="o">==</span> <span class="n">other</span><span class="o">.</span><span class="n">type</span> <span class="ow">and</span> \
+            <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">set</span><span class="o">.</span><span class="n">isdisjoint</span><span class="p">(</span><span class="n">other</span><span class="o">.</span><span class="n">set</span><span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="Complex">
+<a class="viewcode-back" href="../../../api/pypath.utils.pyreact.Complex.html#pypath.utils.pyreact.Complex">[docs]</a>
+<span class="k">class</span> <span class="nc">Complex</span><span class="p">(</span><span class="n">EntitySet</span><span class="p">):</span>
+<div class="viewcode-block" id="Complex.__init__">
+<a class="viewcode-back" href="../../../api/pypath.utils.pyreact.Complex.html#pypath.utils.pyreact.Complex.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">members</span><span class="p">,</span> <span class="n">source</span><span class="p">,</span> <span class="n">parent</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
+        <span class="nb">super</span><span class="p">(</span><span class="n">Complex</span><span class="p">,</span> <span class="bp">self</span><span class="p">)</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="n">members</span><span class="p">,</span> <span class="n">source</span><span class="p">,</span> <span class="n">parent</span><span class="o">=</span><span class="n">parent</span><span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">type</span> <span class="o">=</span> <span class="s1">&#39;complex&#39;</span></div>
+
+
+    <span class="k">def</span> <span class="fm">__str__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+        <span class="k">return</span> <span class="s1">&#39;&lt;</span><span class="si">%s</span><span class="s1">&gt;&#39;</span> <span class="o">%</span> <span class="n">EntitySet</span><span class="o">.</span><span class="fm">__str__</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span>
+
+    <span class="k">def</span> <span class="nf">reload</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+        <span class="n">modname</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="vm">__class__</span><span class="o">.</span><span class="vm">__module__</span>
+        <span class="n">mod</span> <span class="o">=</span> <span class="nb">__import__</span><span class="p">(</span><span class="n">modname</span><span class="p">,</span> <span class="n">fromlist</span><span class="o">=</span><span class="p">[</span><span class="n">modname</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;.&#39;</span><span class="p">)[</span><span class="mi">0</span><span class="p">]])</span>
+        <span class="n">imp</span><span class="o">.</span><span class="n">reload</span><span class="p">(</span><span class="n">mod</span><span class="p">)</span>
+        <span class="n">new</span> <span class="o">=</span> <span class="nb">getattr</span><span class="p">(</span><span class="n">mod</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="vm">__class__</span><span class="o">.</span><span class="vm">__name__</span><span class="p">)</span>
+        <span class="nb">setattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">&#39;__class__&#39;</span><span class="p">,</span> <span class="n">new</span><span class="p">)</span>
+
+    <span class="k">def</span> <span class="nf">get_stoichiometries</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">source</span><span class="p">,</span> <span class="n">cid</span><span class="p">,</span> <span class="n">with_pids</span><span class="o">=</span><span class="kc">False</span><span class="p">):</span>
+        <span class="k">if</span> <span class="n">source</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">sources</span> <span class="ow">and</span> <span class="n">cid</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">attrs</span><span class="p">[</span><span class="n">source</span><span class="p">]:</span>
+            <span class="k">return</span> \
+                <span class="nb">list</span><span class="p">(</span>
+                    <span class="nb">map</span><span class="p">(</span>
+                        <span class="k">lambda</span> <span class="n">memb</span><span class="p">:</span>
+                            <span class="p">(</span><span class="n">memb</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">memb</span><span class="p">[</span><span class="mi">1</span><span class="p">][</span><span class="s1">&#39;stoi&#39;</span><span class="p">],</span> <span class="n">memb</span><span class="p">[</span><span class="mi">1</span><span class="p">][</span><span class="s1">&#39;pid&#39;</span><span class="p">])</span>
+                        <span class="k">if</span> <span class="n">with_pids</span> <span class="k">else</span> <span class="p">(</span><span class="n">memb</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">memb</span><span class="p">[</span><span class="mi">1</span><span class="p">][</span><span class="s1">&#39;stoi&#39;</span><span class="p">]),</span>
+                        <span class="nb">filter</span><span class="p">(</span>
+                            <span class="k">lambda</span> <span class="n">memb</span><span class="p">:</span>
+                                <span class="nb">type</span><span class="p">(</span><span class="n">memb</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span> <span class="ow">is</span> <span class="nb">dict</span>
+                                <span class="ow">and</span> <span class="s1">&#39;stoi&#39;</span> <span class="ow">in</span> <span class="n">memb</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span>
+                                <span class="ow">and</span> <span class="s1">&#39;pid&#39;</span> <span class="ow">in</span> <span class="n">memb</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span>
+                            <span class="n">iteritems</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">attrs</span><span class="p">[</span><span class="n">source</span><span class="p">][</span><span class="n">cid</span><span class="p">])</span>
+                        <span class="p">)</span>
+                    <span class="p">)</span>
+                <span class="p">)</span>
+
+    <span class="k">def</span> <span class="nf">expand</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+        <span class="k">for</span> <span class="n">i</span><span class="p">,</span> <span class="n">m1</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">members</span><span class="p">):</span>
+            <span class="k">for</span> <span class="n">m2</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">members</span><span class="p">[</span><span class="n">i</span> <span class="o">+</span> <span class="mi">1</span><span class="p">:]:</span>
+                <span class="k">yield</span> <span class="n">m1</span><span class="p">,</span> <span class="n">m2</span>
+
+    <span class="k">def</span> <span class="nf">itermembers</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+        <span class="k">for</span> <span class="n">m</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">members</span><span class="p">:</span>
+            <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">parent</span><span class="o">.</span><span class="n">proteins</span><span class="p">[</span><span class="n">m</span><span class="p">]</span>
+
+    <span class="k">def</span> <span class="nf">key</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+        <span class="k">return</span> <span class="nb">tuple</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">members</span><span class="p">)</span>
+
+    <span class="k">def</span> <span class="nf">proteins</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+        <span class="k">return</span> <span class="nb">set</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">members</span><span class="p">)</span>
+
+    <span class="k">def</span> <span class="fm">__ror__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">other</span><span class="p">):</span>
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">proteins</span><span class="p">()</span> <span class="o">|</span> <span class="n">other</span>
+
+    <span class="k">def</span> <span class="fm">__rand__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">other</span><span class="p">):</span>
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">proteins</span><span class="p">()</span> <span class="o">&amp;</span> <span class="n">other</span>
+
+    <span class="k">def</span> <span class="fm">__rsub__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">other</span><span class="p">):</span>
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">proteins</span><span class="p">()</span> <span class="o">-</span> <span class="n">other</span></div>
+
+
+
+<div class="viewcode-block" id="ProteinFamily">
+<a class="viewcode-back" href="../../../api/pypath.utils.pyreact.ProteinFamily.html#pypath.utils.pyreact.ProteinFamily">[docs]</a>
+<span class="k">class</span> <span class="nc">ProteinFamily</span><span class="p">(</span><span class="n">Intersecting</span><span class="p">,</span> <span class="n">EntitySet</span><span class="p">):</span>
+<div class="viewcode-block" id="ProteinFamily.__init__">
+<a class="viewcode-back" href="../../../api/pypath.utils.pyreact.ProteinFamily.html#pypath.utils.pyreact.ProteinFamily.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">members</span><span class="p">,</span> <span class="n">source</span><span class="p">,</span> <span class="n">parent</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
+        <span class="n">EntitySet</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">members</span><span class="p">,</span> <span class="n">source</span><span class="p">,</span> <span class="n">parent</span><span class="o">=</span><span class="n">parent</span><span class="p">)</span>
+        <span class="n">Intersecting</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">type</span> <span class="o">=</span> <span class="s1">&#39;pfamily&#39;</span></div>
+
+
+    <span class="k">def</span> <span class="fm">__str__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+        <span class="k">return</span> <span class="s1">&#39;|</span><span class="si">%s</span><span class="s1">|&#39;</span> <span class="o">%</span> <span class="n">EntitySet</span><span class="o">.</span><span class="fm">__str__</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span>
+
+    <span class="k">def</span> <span class="nf">reload</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+        <span class="n">modname</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="vm">__class__</span><span class="o">.</span><span class="vm">__module__</span>
+        <span class="n">mod</span> <span class="o">=</span> <span class="nb">__import__</span><span class="p">(</span><span class="n">modname</span><span class="p">,</span> <span class="n">fromlist</span><span class="o">=</span><span class="p">[</span><span class="n">modname</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;.&#39;</span><span class="p">)[</span><span class="mi">0</span><span class="p">]])</span>
+        <span class="n">imp</span><span class="o">.</span><span class="n">reload</span><span class="p">(</span><span class="n">mod</span><span class="p">)</span>
+        <span class="n">new</span> <span class="o">=</span> <span class="nb">getattr</span><span class="p">(</span><span class="n">mod</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="vm">__class__</span><span class="o">.</span><span class="vm">__name__</span><span class="p">)</span>
+        <span class="nb">setattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">&#39;__class__&#39;</span><span class="p">,</span> <span class="n">new</span><span class="p">)</span>
+
+    <span class="k">def</span> <span class="nf">_itermembers1</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Iterates protein family, yields proteins.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+        <span class="k">for</span> <span class="n">m</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">members</span><span class="p">:</span>
+            <span class="k">if</span> <span class="n">m</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">parent</span><span class="o">.</span><span class="n">proteins</span><span class="p">:</span>
+                <span class="k">yield</span> <span class="bp">self</span><span class="o">.</span><span class="n">parent</span><span class="o">.</span><span class="n">proteins</span><span class="p">[</span><span class="n">m</span><span class="p">]</span>
+            <span class="k">else</span><span class="p">:</span>
+                <span class="n">this_attrs</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">(</span><span class="nb">map</span><span class="p">(</span><span class="k">lambda</span> <span class="n">s</span><span class="p">:</span>
+                                      <span class="p">(</span><span class="n">s</span><span class="p">,</span> <span class="p">{</span><span class="s1">&#39;pids&#39;</span><span class="p">:</span> <span class="p">{},</span>
+                                           <span class="s1">&#39;prefs&#39;</span><span class="p">:</span> <span class="p">{},</span>
+                                           <span class="s1">&#39;originals&#39;</span><span class="p">:</span> <span class="p">{}}),</span>
+                                      <span class="bp">self</span><span class="o">.</span><span class="n">source</span><span class="p">))</span>
+                <span class="k">for</span> <span class="n">s</span><span class="p">,</span> <span class="n">a</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">attrs</span><span class="p">):</span>
+                    <span class="k">for</span> <span class="n">pfid</span><span class="p">,</span> <span class="n">aa</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="n">a</span><span class="p">):</span>
+                        <span class="n">this_attrs</span><span class="p">[</span><span class="n">s</span><span class="p">][</span><span class="s1">&#39;pids&#39;</span><span class="p">][</span><span class="n">pfid</span><span class="p">]</span> <span class="o">=</span> <span class="p">{}</span>
+                <span class="k">yield</span> <span class="n">Protein</span><span class="p">(</span><span class="n">m</span><span class="p">,</span> <span class="n">sources</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">sources</span><span class="p">,</span> <span class="n">attrs</span><span class="o">=</span><span class="n">this_attrs</span><span class="p">)</span>
+
+    <span class="k">def</span> <span class="nf">expand</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+        <span class="k">for</span> <span class="n">pkey</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="fm">__iter__</span><span class="p">():</span>
+            <span class="k">yield</span> <span class="bp">self</span><span class="o">.</span><span class="n">parent</span><span class="o">.</span><span class="n">proteins</span><span class="p">[</span><span class="n">pkey</span><span class="p">]</span>
+
+    <span class="k">def</span> <span class="nf">itermembers</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+        <span class="k">for</span> <span class="n">m</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">expand</span><span class="p">():</span>
+            <span class="n">attrs</span> <span class="o">=</span> \
+                <span class="nb">dict</span><span class="p">(</span>
+                    <span class="nb">map</span><span class="p">(</span>
+                        <span class="k">lambda</span> <span class="n">s</span><span class="p">:</span>
+                            <span class="p">(</span>
+                                <span class="n">s</span><span class="p">,</span>
+                                <span class="nb">dict</span><span class="p">(</span>
+                                    <span class="nb">map</span><span class="p">(</span>
+                                        <span class="k">lambda</span> <span class="n">pf</span><span class="p">:</span>
+                                            <span class="p">(</span><span class="n">pf</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">pf</span><span class="p">[</span><span class="mi">1</span><span class="p">][</span><span class="n">m</span><span class="o">.</span><span class="n">id</span><span class="p">][</span><span class="s1">&#39;pid&#39;</span><span class="p">]),</span>
+                                        <span class="n">iteritems</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">attrs</span><span class="p">[</span><span class="n">s</span><span class="p">])</span>
+                                    <span class="p">)</span>
+                                <span class="p">)</span>
+                            <span class="p">),</span>
+                        <span class="bp">self</span><span class="o">.</span><span class="n">sources</span>
+                    <span class="p">)</span>
+                <span class="p">)</span>
+            <span class="k">yield</span> <span class="p">(</span><span class="n">m</span><span class="p">,</span> <span class="n">attrs</span><span class="p">)</span>
+
+    <span class="k">def</span> <span class="nf">key</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+        <span class="k">return</span> <span class="nb">tuple</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">members</span><span class="p">)</span>
+
+    <span class="k">def</span> <span class="nf">proteins</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+        <span class="k">return</span> <span class="nb">set</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">members</span><span class="p">)</span>
+
+    <span class="k">def</span> <span class="fm">__ror__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">other</span><span class="p">):</span>
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">proteins</span><span class="p">()</span> <span class="o">|</span> <span class="n">other</span>
+
+    <span class="k">def</span> <span class="fm">__rand__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">other</span><span class="p">):</span>
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">proteins</span><span class="p">()</span> <span class="o">&amp;</span> <span class="n">other</span>
+
+    <span class="k">def</span> <span class="fm">__rsub__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">other</span><span class="p">):</span>
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">proteins</span><span class="p">()</span> <span class="o">-</span> <span class="n">other</span></div>
+
+
+
+<div class="viewcode-block" id="ComplexVariations">
+<a class="viewcode-back" href="../../../api/pypath.utils.pyreact.ComplexVariations.html#pypath.utils.pyreact.ComplexVariations">[docs]</a>
+<span class="k">class</span> <span class="nc">ComplexVariations</span><span class="p">(</span><span class="n">Intersecting</span><span class="p">,</span> <span class="n">EntitySet</span><span class="p">):</span>
+<div class="viewcode-block" id="ComplexVariations.__init__">
+<a class="viewcode-back" href="../../../api/pypath.utils.pyreact.ComplexVariations.html#pypath.utils.pyreact.ComplexVariations.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">members</span><span class="p">,</span> <span class="n">source</span><span class="p">,</span> <span class="n">parent</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
+        <span class="n">EntitySet</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">members</span><span class="p">,</span> <span class="n">source</span><span class="p">,</span> <span class="n">sep</span><span class="o">=</span><span class="s1">&#39;|&#39;</span><span class="p">,</span> <span class="n">parent</span><span class="o">=</span><span class="n">parent</span><span class="p">)</span>
+        <span class="n">Intersecting</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">type</span> <span class="o">=</span> <span class="s1">&#39;cvariations&#39;</span></div>
+
+
+    <span class="k">def</span> <span class="fm">__str__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+        <span class="k">return</span> <span class="s1">&#39;&lt;</span><span class="si">%s</span><span class="s1">&gt;&#39;</span> <span class="o">%</span> <span class="n">EntitySet</span><span class="o">.</span><span class="fm">__str__</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span>
+
+    <span class="k">def</span> <span class="nf">reload</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+        <span class="n">modname</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="vm">__class__</span><span class="o">.</span><span class="vm">__module__</span>
+        <span class="n">mod</span> <span class="o">=</span> <span class="nb">__import__</span><span class="p">(</span><span class="n">modname</span><span class="p">,</span> <span class="n">fromlist</span><span class="o">=</span><span class="p">[</span><span class="n">modname</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;.&#39;</span><span class="p">)[</span><span class="mi">0</span><span class="p">]])</span>
+        <span class="n">imp</span><span class="o">.</span><span class="n">reload</span><span class="p">(</span><span class="n">mod</span><span class="p">)</span>
+        <span class="n">new</span> <span class="o">=</span> <span class="nb">getattr</span><span class="p">(</span><span class="n">mod</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="vm">__class__</span><span class="o">.</span><span class="vm">__name__</span><span class="p">)</span>
+        <span class="nb">setattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">&#39;__class__&#39;</span><span class="p">,</span> <span class="n">new</span><span class="p">)</span>
+
+    <span class="k">def</span> <span class="nf">expand</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+        <span class="k">for</span> <span class="n">m</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">members</span><span class="p">:</span>
+            <span class="k">for</span> <span class="n">m1</span><span class="p">,</span> <span class="n">m2</span> <span class="ow">in</span> <span class="n">m</span><span class="o">.</span><span class="n">expand</span><span class="p">():</span>
+                <span class="k">yield</span> <span class="n">m1</span><span class="p">,</span> <span class="n">m2</span>
+
+<div class="viewcode-block" id="ComplexVariations.itermembers">
+<a class="viewcode-back" href="../../../api/pypath.utils.pyreact.ComplexVariations.html#pypath.utils.pyreact.ComplexVariations.itermembers">[docs]</a>
+    <span class="k">def</span> <span class="nf">itermembers</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        This is a convenient iterator for the expand methods</span>
+<span class="sd">        of higher classes like ``ReactionSide`` or ``Control``.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+        <span class="k">for</span> <span class="n">m</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="fm">__iter__</span><span class="p">():</span>
+            <span class="n">attrs</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">(</span>
+                <span class="nb">map</span><span class="p">(</span>
+                    <span class="k">lambda</span> <span class="n">s</span><span class="p">:</span>
+                        <span class="p">(</span>
+                            <span class="n">s</span><span class="p">,</span>
+                            <span class="n">reduce</span><span class="p">(</span>
+                                <span class="k">lambda</span> <span class="n">c1</span><span class="p">,</span> <span class="n">c2</span><span class="p">:</span>
+                                    <span class="n">c1</span> <span class="o">|</span> <span class="n">c2</span><span class="p">,</span>
+                                <span class="nb">map</span><span class="p">(</span>
+                                    <span class="k">lambda</span> <span class="n">cid</span><span class="p">:</span>
+                                        <span class="n">m</span><span class="o">.</span><span class="n">attrs</span><span class="p">[</span><span class="n">s</span><span class="p">][</span><span class="n">cid</span><span class="p">][</span><span class="s1">&#39;children&#39;</span><span class="p">]</span>
+                                    <span class="k">if</span>
+                                        <span class="s1">&#39;children&#39;</span> <span class="ow">in</span> <span class="n">m</span><span class="o">.</span><span class="n">attrs</span><span class="p">[</span><span class="n">s</span><span class="p">][</span><span class="n">cid</span><span class="p">]</span>
+                                    <span class="k">else</span>
+                                        <span class="nb">set</span><span class="p">([</span><span class="n">cid</span><span class="p">]),</span>
+                                    <span class="nb">filter</span><span class="p">(</span>
+                                        <span class="k">lambda</span> <span class="n">cid</span><span class="p">:</span>
+                                            <span class="n">cid</span> <span class="ow">in</span> <span class="n">m</span><span class="o">.</span><span class="n">attrs</span><span class="p">[</span><span class="n">s</span><span class="p">],</span>
+                                        <span class="bp">self</span><span class="o">.</span><span class="n">attrs</span><span class="p">[</span><span class="n">s</span><span class="p">][</span><span class="s1">&#39;cids&#39;</span><span class="p">]</span>
+                                    <span class="p">)</span>
+                                <span class="p">)</span>
+                            <span class="p">)</span>
+                        <span class="p">),</span>
+                    <span class="bp">self</span><span class="o">.</span><span class="n">sources</span>
+                <span class="p">)</span>
+            <span class="p">)</span>
+            <span class="k">yield</span> <span class="p">(</span><span class="n">m</span><span class="p">,</span> <span class="n">attrs</span><span class="p">)</span></div>
+
+
+    <span class="k">def</span> <span class="nf">key</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="fm">__str__</span><span class="p">()</span>
+
+    <span class="k">def</span> <span class="nf">proteins</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+        <span class="k">return</span> \
+            <span class="n">reduce</span><span class="p">(</span>
+                <span class="k">lambda</span> <span class="n">m1</span><span class="p">,</span> <span class="n">m2</span><span class="p">:</span>
+                    <span class="n">m1</span> <span class="o">|</span> <span class="n">m2</span><span class="p">,</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">members</span><span class="p">,</span>
+                <span class="nb">set</span><span class="p">([])</span>
+            <span class="p">)</span>
+
+    <span class="k">def</span> <span class="fm">__ror__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">other</span><span class="p">):</span>
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">proteins</span><span class="p">()</span> <span class="o">|</span> <span class="n">other</span>
+
+    <span class="k">def</span> <span class="fm">__rand__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">other</span><span class="p">):</span>
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">proteins</span><span class="p">()</span> <span class="o">&amp;</span> <span class="n">other</span>
+
+    <span class="k">def</span> <span class="fm">__rsub__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">other</span><span class="p">):</span>
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">proteins</span><span class="p">()</span> <span class="o">-</span> <span class="n">other</span></div>
+
+
+
+<div class="viewcode-block" id="PyReact">
+<a class="viewcode-back" href="../../../api/pypath.utils.pyreact.PyReact.html#pypath.utils.pyreact.PyReact">[docs]</a>
+<span class="k">class</span> <span class="nc">PyReact</span><span class="p">(</span><span class="n">session_mod</span><span class="o">.</span><span class="n">Logger</span><span class="p">):</span>
+
+<div class="viewcode-block" id="PyReact.__init__">
+<a class="viewcode-back" href="../../../api/pypath.utils.pyreact.PyReact.html#pypath.utils.pyreact.PyReact.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span>
+        <span class="bp">self</span><span class="p">,</span>
+        <span class="n">ncbi_tax_id</span><span class="o">=</span><span class="mi">9606</span><span class="p">,</span>
+        <span class="n">default_id_types</span><span class="o">=</span><span class="p">{},</span>
+        <span class="n">modifications</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span>
+        <span class="n">seq</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
+        <span class="n">silent</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span>
+        <span class="n">max_complex_combinations</span><span class="o">=</span><span class="mi">100</span><span class="p">,</span>
+        <span class="n">max_reaction_combinations</span><span class="o">=</span><span class="mi">100</span><span class="p">,</span>
+    <span class="p">):</span>
+
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">cachedir</span> <span class="o">=</span> <span class="n">cache</span><span class="o">.</span><span class="n">get_cachedir</span><span class="p">()</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">ncbi_tax_id</span> <span class="o">=</span> <span class="n">ncbi_tax_id</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">modifications</span> <span class="o">=</span> <span class="n">modifications</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">parsers</span> <span class="o">=</span> <span class="p">{}</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">sources</span> <span class="o">=</span> <span class="nb">set</span><span class="p">([])</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">seq</span> <span class="o">=</span> <span class="n">seq</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">mapper</span> <span class="o">=</span> <span class="n">mapping</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">silent</span> <span class="o">=</span> <span class="n">silent</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">max_complex_combinations</span> <span class="o">=</span> <span class="n">max_complex_combinations</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">max_reaction_combinations</span> <span class="o">=</span> <span class="n">max_reaction_combinations</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">slow_complexes</span> <span class="o">=</span> <span class="p">{}</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">huge_complexes</span> <span class="o">=</span> <span class="p">{}</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">huge_reactions</span> <span class="o">=</span> <span class="p">{}</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">refs</span> <span class="o">=</span> <span class="p">{}</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">species</span> <span class="o">=</span> <span class="p">{}</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">proteins</span> <span class="o">=</span> <span class="p">{}</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">pfamilies</span> <span class="o">=</span> <span class="p">{}</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">complexes</span> <span class="o">=</span> <span class="p">{}</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">cvariations</span> <span class="o">=</span> <span class="p">{}</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">reactions</span> <span class="o">=</span> <span class="p">{}</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">controls</span> <span class="o">=</span> <span class="p">{}</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">mods</span> <span class="o">=</span> <span class="p">{}</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">frags</span> <span class="o">=</span> <span class="p">{}</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">rrefs</span> <span class="o">=</span> <span class="p">{}</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">rproteins</span> <span class="o">=</span> <span class="p">{}</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">rpfamilies</span> <span class="o">=</span> <span class="p">{}</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">rcomplexes</span> <span class="o">=</span> <span class="p">{}</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">rcvariations</span> <span class="o">=</span> <span class="p">{}</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">rreactions</span> <span class="o">=</span> <span class="p">{}</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">rcontrols</span> <span class="o">=</span> <span class="p">{}</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">references</span> <span class="o">=</span> <span class="p">{}</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">id_types</span> <span class="o">=</span> <span class="p">{}</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">default_id_types</span> <span class="o">=</span> <span class="p">{</span><span class="s1">&#39;protein&#39;</span><span class="p">:</span> <span class="s1">&#39;uniprot&#39;</span><span class="p">}</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">default_id_types</span><span class="o">.</span><span class="n">update</span><span class="p">(</span><span class="n">default_id_types</span><span class="p">)</span>
+
+        <span class="n">session_mod</span><span class="o">.</span><span class="n">Logger</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">name</span> <span class="o">=</span> <span class="s1">&#39;pyreact&#39;</span><span class="p">)</span></div>
+
+
+    <span class="k">def</span> <span class="nf">reload</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+        <span class="n">modname</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="vm">__class__</span><span class="o">.</span><span class="vm">__module__</span>
+        <span class="n">mod</span> <span class="o">=</span> <span class="nb">__import__</span><span class="p">(</span><span class="n">modname</span><span class="p">,</span> <span class="n">fromlist</span><span class="o">=</span><span class="p">[</span><span class="n">modname</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;.&#39;</span><span class="p">)[</span><span class="mi">0</span><span class="p">]])</span>
+        <span class="n">imp</span><span class="o">.</span><span class="n">reload</span><span class="p">(</span><span class="n">mod</span><span class="p">)</span>
+        <span class="n">new</span> <span class="o">=</span> <span class="nb">getattr</span><span class="p">(</span><span class="n">mod</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="vm">__class__</span><span class="o">.</span><span class="vm">__name__</span><span class="p">)</span>
+        <span class="nb">setattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">&#39;__class__&#39;</span><span class="p">,</span> <span class="n">new</span><span class="p">)</span>
+
+    <span class="k">def</span> <span class="nf">load_reactome</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span><span class="s1">&#39;Loading Reactome.&#39;</span><span class="p">)</span>
+
+        <span class="k">def</span> <span class="nf">reactome_id_proc</span><span class="p">(</span><span class="n">_id</span><span class="p">):</span>
+            <span class="n">_id</span> <span class="o">=</span> <span class="n">_id</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;-&#39;</span><span class="p">)</span>
+            <span class="k">return</span> <span class="p">{</span>
+                <span class="s1">&#39;id&#39;</span><span class="p">:</span> <span class="n">_id</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span>
+                <span class="s1">&#39;isoform&#39;</span><span class="p">:</span> <span class="nb">int</span><span class="p">(</span><span class="n">_id</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span> <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">_id</span><span class="p">)</span> <span class="o">&gt;</span> <span class="mi">1</span> <span class="k">else</span> <span class="mi">1</span>
+            <span class="p">}</span>
+
+        <span class="n">biopax</span> <span class="o">=</span> <span class="n">curl</span><span class="o">.</span><span class="n">Curl</span><span class="p">(</span>
+            <span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;reactome&#39;</span><span class="p">][</span><span class="s1">&#39;biopax_l3&#39;</span><span class="p">],</span>
+            <span class="n">large</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span>
+            <span class="n">silent</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">silent</span><span class="p">,</span>
+        <span class="p">)</span>
+        <span class="n">parser</span> <span class="o">=</span> <span class="n">BioPaxReader</span><span class="p">(</span>
+            <span class="n">biopax</span><span class="o">.</span><span class="n">outfile</span><span class="p">,</span> <span class="s1">&#39;Reactome&#39;</span><span class="p">,</span>
+            <span class="n">file_from_archive</span><span class="o">=</span><span class="s1">&#39;Homo_sapiens.owl&#39;</span>
+        <span class="p">)</span>
+        <span class="n">parser</span><span class="o">.</span><span class="n">process</span><span class="p">()</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">add_dataset</span><span class="p">(</span>
+            <span class="n">parser</span><span class="p">,</span>
+            <span class="n">id_types</span><span class="o">=</span><span class="p">{</span><span class="s1">&#39;uniprot isoform&#39;</span><span class="p">:</span> <span class="s1">&#39;uniprot&#39;</span><span class="p">},</span>
+            <span class="n">process_id</span><span class="o">=</span><span class="n">reactome_id_proc</span><span class="p">)</span>
+
+    <span class="k">def</span> <span class="nf">load_acsn</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span><span class="s1">&#39;Loading ACSN.&#39;</span><span class="p">)</span>
+
+        <span class="n">biopax</span> <span class="o">=</span> <span class="n">curl</span><span class="o">.</span><span class="n">Curl</span><span class="p">(</span>
+            <span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;acsn&#39;</span><span class="p">][</span><span class="s1">&#39;biopax_l3&#39;</span><span class="p">],</span>
+            <span class="n">large</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span>
+            <span class="n">silent</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">silent</span><span class="p">,</span>
+            <span class="n">default_mode</span> <span class="o">=</span> <span class="s1">&#39;rb&#39;</span><span class="p">,</span>
+        <span class="p">)</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">parser</span> <span class="o">=</span> <span class="n">BioPaxReader</span><span class="p">(</span><span class="n">biopax</span><span class="o">.</span><span class="n">outfile</span><span class="p">,</span> <span class="s1">&#39;ACSN&#39;</span><span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">parser</span><span class="o">.</span><span class="n">process</span><span class="p">()</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">add_dataset</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">parser</span><span class="p">,</span> <span class="n">id_types</span><span class="o">=</span><span class="p">{</span><span class="s1">&#39;hgnc&#39;</span><span class="p">:</span> <span class="s1">&#39;genesymbol&#39;</span><span class="p">})</span>
+        <span class="k">del</span> <span class="bp">self</span><span class="o">.</span><span class="n">parser</span>
+
+    <span class="k">def</span> <span class="nf">load_kegg</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span><span class="s1">&#39;Loading KEGG.&#39;</span><span class="p">)</span>
+
+        <span class="n">biopax</span> <span class="o">=</span> <span class="n">curl</span><span class="o">.</span><span class="n">Curl</span><span class="p">(</span>
+            <span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;kegg_pws&#39;</span><span class="p">][</span><span class="s1">&#39;biopax_l3&#39;</span><span class="p">],</span>
+            <span class="n">large</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span>
+            <span class="n">silent</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">silent</span><span class="p">,</span>
+        <span class="p">)</span>
+
+        <span class="n">parser</span> <span class="o">=</span> <span class="n">BioPaxReader</span><span class="p">(</span><span class="n">biopax</span><span class="o">.</span><span class="n">outfile</span><span class="p">,</span> <span class="s1">&#39;KEGG&#39;</span><span class="p">)</span>
+        <span class="n">parser</span><span class="o">.</span><span class="n">process</span><span class="p">()</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">add_dataset</span><span class="p">(</span><span class="n">parser</span><span class="p">,</span> <span class="p">{</span><span class="s1">&#39;uniprot knowledgebase&#39;</span><span class="p">:</span> <span class="s1">&#39;uniprot&#39;</span><span class="p">})</span>
+
+    <span class="k">def</span> <span class="nf">load_pid</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span><span class="s1">&#39;Loading NCI-PID.&#39;</span><span class="p">)</span>
+
+        <span class="n">biopax</span> <span class="o">=</span> <span class="n">curl</span><span class="o">.</span><span class="n">Curl</span><span class="p">(</span>
+            <span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;nci-pid&#39;</span><span class="p">][</span><span class="s1">&#39;biopax_l3&#39;</span><span class="p">],</span>
+            <span class="n">large</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span>
+            <span class="n">silent</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">silent</span><span class="p">,</span>
+        <span class="p">)</span>
+
+        <span class="n">parser</span> <span class="o">=</span> <span class="n">BioPaxReader</span><span class="p">(</span><span class="n">biopax</span><span class="o">.</span><span class="n">outfile</span><span class="p">,</span> <span class="s1">&#39;NCI-PID&#39;</span><span class="p">)</span>
+        <span class="n">parser</span><span class="o">.</span><span class="n">process</span><span class="p">()</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">add_dataset</span><span class="p">(</span><span class="n">parser</span><span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">load_wikipathways</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span><span class="s1">&#39;Loading WikiPathways.&#39;</span><span class="p">)</span>
+
+        <span class="n">biopaxes</span> <span class="o">=</span> <span class="n">curl</span><span class="o">.</span><span class="n">Curl</span><span class="p">(</span>
+            <span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;wikipw&#39;</span><span class="p">][</span><span class="s1">&#39;biopax_l3&#39;</span><span class="p">],</span>
+            <span class="n">large</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span>
+            <span class="n">silent</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">silent</span>
+        <span class="p">)</span>
+
+        <span class="k">if</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">silent</span><span class="p">:</span>
+            <span class="n">prg</span> <span class="o">=</span> <span class="n">progress</span><span class="o">.</span><span class="n">Progress</span><span class="p">(</span>
+                <span class="nb">len</span><span class="p">(</span><span class="n">biopaxes</span><span class="o">.</span><span class="n">result</span><span class="p">),</span>
+                <span class="s1">&#39;Processing multiple BioPAX files&#39;</span><span class="p">,</span>
+                <span class="mi">1</span><span class="p">,</span>
+                <span class="n">percent</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span>
+            <span class="p">)</span>
+
+        <span class="n">silent_default</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">silent</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">silent</span> <span class="o">=</span> <span class="kc">True</span>
+
+        <span class="k">for</span> <span class="n">fname</span> <span class="ow">in</span> <span class="n">biopaxes</span><span class="o">.</span><span class="n">files_multipart</span><span class="o">.</span><span class="n">keys</span><span class="p">():</span>
+
+            <span class="k">if</span> <span class="ow">not</span> <span class="n">silent_default</span><span class="p">:</span>
+                <span class="n">prg</span><span class="o">.</span><span class="n">step</span><span class="p">()</span>
+            <span class="n">parser</span> <span class="o">=</span> <span class="n">BioPaxReader</span><span class="p">(</span>
+                <span class="n">biopaxes</span><span class="o">.</span><span class="n">outfile</span><span class="p">,</span> <span class="s1">&#39;WikiPathways&#39;</span><span class="p">,</span> <span class="n">file_from_archive</span><span class="o">=</span><span class="n">fname</span><span class="p">)</span>
+            <span class="n">parser</span><span class="o">.</span><span class="n">process</span><span class="p">(</span><span class="n">silent</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">add_dataset</span><span class="p">(</span>
+                <span class="n">parser</span><span class="p">,</span>
+                <span class="n">id_types</span><span class="o">=</span><span class="p">{</span>
+                    <span class="s1">&#39;ensembl&#39;</span><span class="p">:</span> <span class="s1">&#39;ensg&#39;</span><span class="p">,</span>
+                    <span class="s1">&#39;entrez gene&#39;</span><span class="p">:</span> <span class="s1">&#39;entrez&#39;</span><span class="p">,</span>
+                    <span class="s1">&#39;hgnc&#39;</span><span class="p">:</span> <span class="s1">&#39;genesymbol&#39;</span>
+                <span class="p">})</span>
+
+        <span class="k">if</span> <span class="ow">not</span> <span class="n">silent_default</span><span class="p">:</span>
+            <span class="n">prg</span><span class="o">.</span><span class="n">terminate</span><span class="p">()</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">silent</span> <span class="o">=</span> <span class="n">silent_default</span>
+
+
+    <span class="k">def</span> <span class="nf">load_panther</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span><span class="s1">&#39;Loading PANTHER.&#39;</span><span class="p">)</span>
+
+        <span class="n">biopaxes</span> <span class="o">=</span> <span class="n">curl</span><span class="o">.</span><span class="n">Curl</span><span class="p">(</span>
+            <span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;panther&#39;</span><span class="p">][</span><span class="s1">&#39;biopax_l3&#39;</span><span class="p">],</span> <span class="n">large</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">silent</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">silent</span><span class="p">)</span>
+        <span class="k">if</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">silent</span><span class="p">:</span>
+            <span class="n">prg</span> <span class="o">=</span> <span class="n">progress</span><span class="o">.</span><span class="n">Progress</span><span class="p">(</span>
+                <span class="nb">len</span><span class="p">(</span><span class="n">biopaxes</span><span class="o">.</span><span class="n">files_multipart</span><span class="p">),</span>
+                <span class="s1">&#39;Processing multiple BioPAX files&#39;</span><span class="p">,</span>
+                <span class="mi">1</span><span class="p">,</span>
+                <span class="n">percent</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span>
+
+        <span class="n">silent_default</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">silent</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">silent</span> <span class="o">=</span> <span class="kc">True</span>
+
+        <span class="k">for</span> <span class="n">fname</span> <span class="ow">in</span> <span class="n">biopaxes</span><span class="o">.</span><span class="n">files_multipart</span><span class="o">.</span><span class="n">keys</span><span class="p">():</span>
+
+            <span class="k">if</span> <span class="ow">not</span> <span class="n">silent_default</span><span class="p">:</span>
+                <span class="n">prg</span><span class="o">.</span><span class="n">step</span><span class="p">()</span>
+            <span class="n">parser</span> <span class="o">=</span> <span class="n">BioPaxReader</span><span class="p">(</span>
+                <span class="n">biopaxes</span><span class="o">.</span><span class="n">outfile</span><span class="p">,</span> <span class="s1">&#39;PANTHER&#39;</span><span class="p">,</span> <span class="n">file_from_archive</span><span class="o">=</span><span class="n">fname</span><span class="p">)</span>
+            <span class="n">parser</span><span class="o">.</span><span class="n">process</span><span class="p">(</span><span class="n">silent</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">add_dataset</span><span class="p">(</span>
+                <span class="n">parser</span><span class="p">,</span>
+                <span class="n">id_types</span><span class="o">=</span><span class="p">{</span>
+                    <span class="s1">&#39;ensembl&#39;</span><span class="p">:</span> <span class="s1">&#39;ensg&#39;</span><span class="p">,</span>
+                    <span class="s1">&#39;entrez gene&#39;</span><span class="p">:</span> <span class="s1">&#39;entrez&#39;</span><span class="p">,</span>
+                    <span class="s1">&#39;hgnc&#39;</span><span class="p">:</span> <span class="s1">&#39;genesymbol&#39;</span>
+                <span class="p">})</span>
+
+        <span class="k">if</span> <span class="ow">not</span> <span class="n">silent_default</span><span class="p">:</span>
+            <span class="n">prg</span><span class="o">.</span><span class="n">terminate</span><span class="p">()</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">silent</span> <span class="o">=</span> <span class="n">silent_default</span>
+
+
+    <span class="k">def</span> <span class="nf">load_netpath</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span><span class="s1">&#39;Loading NetPath.&#39;</span><span class="p">)</span>
+
+        <span class="n">names</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">netpath_names</span><span class="p">()</span>
+
+        <span class="k">if</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">silent</span><span class="p">:</span>
+            <span class="n">prg</span> <span class="o">=</span> <span class="n">progress</span><span class="o">.</span><span class="n">Progress</span><span class="p">(</span>
+                <span class="nb">len</span><span class="p">(</span><span class="n">names</span><span class="p">),</span>
+                <span class="s1">&#39;Processing multiple BioPAX files&#39;</span><span class="p">,</span>
+                <span class="mi">1</span><span class="p">,</span>
+                <span class="n">percent</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span>
+
+        <span class="n">silent_default</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">silent</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">silent</span> <span class="o">=</span> <span class="kc">True</span>
+
+        <span class="k">for</span> <span class="n">pwnum</span> <span class="ow">in</span> <span class="n">names</span><span class="o">.</span><span class="n">keys</span><span class="p">():</span>
+
+            <span class="k">if</span> <span class="ow">not</span> <span class="n">silent_default</span><span class="p">:</span>
+                <span class="n">prg</span><span class="o">.</span><span class="n">step</span><span class="p">()</span>
+            <span class="n">biopax</span> <span class="o">=</span> <span class="n">curl</span><span class="o">.</span><span class="n">Curl</span><span class="p">(</span>
+                <span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;netpath_bp&#39;</span><span class="p">][</span><span class="s1">&#39;biopax_l3&#39;</span><span class="p">]</span> <span class="o">%</span> <span class="nb">int</span><span class="p">(</span><span class="n">pwnum</span><span class="p">),</span> <span class="n">silent</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
+            <span class="n">parser</span> <span class="o">=</span> <span class="n">BioPaxReader</span><span class="p">(</span><span class="n">biopax</span><span class="o">.</span><span class="n">outfile</span><span class="p">,</span> <span class="s1">&#39;NetPath&#39;</span><span class="p">)</span>
+            <span class="n">parser</span><span class="o">.</span><span class="n">process</span><span class="p">(</span><span class="n">silent</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">add_dataset</span><span class="p">(</span>
+                <span class="n">parser</span><span class="p">,</span>
+                <span class="n">id_types</span><span class="o">=</span><span class="p">{</span>
+                    <span class="s1">&#39;ensembl&#39;</span><span class="p">:</span> <span class="s1">&#39;ensg&#39;</span><span class="p">,</span>
+                    <span class="s1">&#39;entrez gene&#39;</span><span class="p">:</span> <span class="s1">&#39;entrez&#39;</span><span class="p">,</span>
+                    <span class="s1">&#39;hgnc&#39;</span><span class="p">:</span> <span class="s1">&#39;genesymbol&#39;</span>
+                <span class="p">})</span>
+
+        <span class="k">if</span> <span class="ow">not</span> <span class="n">silent_default</span><span class="p">:</span>
+            <span class="n">prg</span><span class="o">.</span><span class="n">terminate</span><span class="p">()</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">silent</span> <span class="o">=</span> <span class="n">silent_default</span>
+
+
+    <span class="k">def</span> <span class="nf">netpath_names</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="n">repwnum</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">compile</span><span class="p">(</span><span class="sa">r</span><span class="s1">&#39;_([0-9]+)$&#39;</span><span class="p">)</span>
+        <span class="n">result</span> <span class="o">=</span> <span class="p">{}</span>
+        <span class="n">url</span> <span class="o">=</span> <span class="n">urls</span><span class="o">.</span><span class="n">urls</span><span class="p">[</span><span class="s1">&#39;netpath_names&#39;</span><span class="p">][</span><span class="s1">&#39;url&#39;</span><span class="p">]</span>
+        <span class="n">c</span> <span class="o">=</span> <span class="n">curl</span><span class="o">.</span><span class="n">Curl</span><span class="p">(</span><span class="n">url</span><span class="p">)</span>
+        <span class="n">html</span> <span class="o">=</span> <span class="n">c</span><span class="o">.</span><span class="n">result</span>
+        <span class="n">soup</span> <span class="o">=</span> <span class="n">bs4</span><span class="o">.</span><span class="n">BeautifulSoup</span><span class="p">(</span><span class="n">html</span><span class="p">,</span> <span class="s1">&#39;html.parser&#39;</span><span class="p">)</span>
+        <span class="k">for</span> <span class="n">a</span> <span class="ow">in</span> <span class="n">soup</span><span class="o">.</span><span class="n">find_all</span><span class="p">(</span><span class="s1">&#39;a&#39;</span><span class="p">):</span>
+            <span class="k">if</span> <span class="n">a</span><span class="o">.</span><span class="n">attrs</span><span class="p">[</span><span class="s1">&#39;href&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s1">&#39;pathways&#39;</span><span class="p">):</span>
+                <span class="n">num</span> <span class="o">=</span> <span class="n">repwnum</span><span class="o">.</span><span class="n">findall</span><span class="p">(</span><span class="n">a</span><span class="o">.</span><span class="n">attrs</span><span class="p">[</span><span class="s1">&#39;href&#39;</span><span class="p">])[</span><span class="mi">0</span><span class="p">]</span>
+                <span class="n">name</span> <span class="o">=</span> <span class="n">a</span><span class="o">.</span><span class="n">text</span>
+                <span class="n">result</span><span class="p">[</span><span class="n">num</span><span class="p">]</span> <span class="o">=</span> <span class="n">name</span>
+        <span class="k">return</span> <span class="n">result</span>
+
+
+    <span class="k">def</span> <span class="nf">load_all</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_log</span><span class="p">(</span><span class="s1">&#39;Loading all databases.&#39;</span><span class="p">)</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">load_wikipathways</span><span class="p">()</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">load_netpath</span><span class="p">()</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">load_panther</span><span class="p">()</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">load_acsn</span><span class="p">()</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">load_pid</span><span class="p">()</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">load_reactome</span><span class="p">()</span>
+
+
+    <span class="k">def</span> <span class="nf">add_dataset</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">parser</span><span class="p">,</span> <span class="n">id_types</span><span class="o">=</span><span class="p">{},</span> <span class="n">process_id</span><span class="o">=</span><span class="k">lambda</span> <span class="n">x</span><span class="p">:</span> <span class="p">{</span><span class="s1">&#39;id&#39;</span><span class="p">:</span> <span class="n">x</span><span class="p">}):</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">id_types</span><span class="o">.</span><span class="n">update</span><span class="p">(</span><span class="n">id_types</span><span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">source</span> <span class="o">=</span> <span class="n">parser</span><span class="o">.</span><span class="n">source</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">parser</span> <span class="o">=</span> <span class="n">parser</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">id_processor</span> <span class="o">=</span> <span class="n">process_id</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">merge</span><span class="p">()</span>
+
+
+    <span class="k">def</span> <span class="nf">merge</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">source</span> <span class="ow">not</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">huge_complexes</span><span class="p">:</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">huge_complexes</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">source</span><span class="p">]</span> <span class="o">=</span> <span class="p">{}</span>
+        <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">source</span> <span class="ow">not</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">slow_complexes</span><span class="p">:</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">slow_complexes</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">source</span><span class="p">]</span> <span class="o">=</span> <span class="p">{}</span>
+        <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">source</span> <span class="ow">not</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">huge_reactions</span><span class="p">:</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">huge_reactions</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">source</span><span class="p">]</span> <span class="o">=</span> <span class="p">{}</span>
+
+        <span class="k">if</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">silent</span><span class="p">:</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">prg</span> <span class="o">=</span> <span class="n">progress</span><span class="o">.</span><span class="n">Progress</span><span class="p">(</span>
+                <span class="mi">12</span><span class="p">,</span> <span class="s1">&#39;Processing </span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="bp">self</span><span class="o">.</span><span class="n">source</span><span class="p">,</span> <span class="mi">1</span><span class="p">,</span> <span class="n">percent</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">sources</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">source</span><span class="p">)</span>
+        <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">source</span> <span class="ow">not</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">parsers</span><span class="p">:</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">parsers</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">source</span><span class="p">]</span> <span class="o">=</span> <span class="p">{}</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">parsers</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">source</span><span class="p">][</span><span class="bp">self</span><span class="o">.</span><span class="n">parser</span><span class="o">.</span><span class="n">parser_id</span><span class="p">]</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">parser</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">set_corrections</span><span class="p">()</span>
+
+        <span class="k">if</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">silent</span><span class="p">:</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">prg</span><span class="o">.</span><span class="n">step</span><span class="p">(</span><span class="n">status</span><span class="o">=</span><span class="s1">&#39;processing references&#39;</span><span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">merge_refs</span><span class="p">()</span>
+
+        <span class="k">if</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">silent</span><span class="p">:</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">prg</span><span class="o">.</span><span class="n">step</span><span class="p">(</span><span class="n">status</span><span class="o">=</span><span class="s1">&#39;processing proteins&#39;</span><span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">merge_proteins</span><span class="p">()</span>
+
+        <span class="k">if</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">silent</span><span class="p">:</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">prg</span><span class="o">.</span><span class="n">step</span><span class="p">(</span><span class="n">status</span><span class="o">=</span><span class="s1">&#39;processing protein families&#39;</span><span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">merge_pfamilies</span><span class="p">()</span>
+
+        <span class="k">if</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">silent</span><span class="p">:</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">prg</span><span class="o">.</span><span class="n">step</span><span class="p">(</span><span class="n">status</span><span class="o">=</span><span class="s1">&#39;processing protein modifications&#39;</span><span class="p">)</span>
+        <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">modifications</span><span class="p">:</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">merge_modifications</span><span class="p">()</span>
+
+        <span class="k">if</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">silent</span><span class="p">:</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">prg</span><span class="o">.</span><span class="n">step</span><span class="p">(</span><span class="n">status</span><span class="o">=</span><span class="s1">&#39;processing complexes&#39;</span><span class="p">)</span>
+        <span class="n">remaining</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">merge_complexes</span><span class="p">()</span>
+
+        <span class="k">if</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">silent</span><span class="p">:</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">prg</span><span class="o">.</span><span class="n">step</span><span class="p">(</span><span class="n">status</span><span class="o">=</span><span class="s1">&#39;processing complex variations&#39;</span><span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">merge_cvariations</span><span class="p">()</span>
+
+        <span class="k">if</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">silent</span><span class="p">:</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">prg</span><span class="o">.</span><span class="n">step</span><span class="p">(</span><span class="n">status</span><span class="o">=</span><span class="s1">&#39;processing complexes 2&#39;</span><span class="p">)</span>
+        <span class="n">remaining</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">merge_complexes</span><span class="p">(</span><span class="n">this_round</span><span class="o">=</span><span class="n">remaining</span><span class="p">)</span>
+
+        <span class="k">if</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">silent</span><span class="p">:</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">prg</span><span class="o">.</span><span class="n">step</span><span class="p">(</span><span class="n">status</span><span class="o">=</span><span class="s1">&#39;generating complex variations&#39;</span><span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">gen_cvariations</span><span class="p">()</span>
+
+        <span class="k">if</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">silent</span><span class="p">:</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">prg</span><span class="o">.</span><span class="n">step</span><span class="p">(</span><span class="n">status</span><span class="o">=</span><span class="s1">&#39;processing reactions&#39;</span><span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">merge_reactions</span><span class="p">()</span>
+
+        <span class="k">if</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">silent</span><span class="p">:</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">prg</span><span class="o">.</span><span class="n">step</span><span class="p">(</span><span class="n">status</span><span class="o">=</span><span class="s1">&#39;processing complex asseblies&#39;</span><span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">merge_cassemblies</span><span class="p">()</span>
+
+        <span class="k">if</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">silent</span><span class="p">:</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">prg</span><span class="o">.</span><span class="n">step</span><span class="p">(</span><span class="n">status</span><span class="o">=</span><span class="s1">&#39;processing controls&#39;</span><span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">merge_controls</span><span class="p">()</span>
+
+        <span class="k">if</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">silent</span><span class="p">:</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">prg</span><span class="o">.</span><span class="n">step</span><span class="p">(</span><span class="n">status</span><span class="o">=</span><span class="s1">&#39;processing catalyses&#39;</span><span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">merge_catalyses</span><span class="p">()</span>
+
+        <span class="k">if</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">silent</span><span class="p">:</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">prg</span><span class="o">.</span><span class="n">terminate</span><span class="p">()</span>
+
+            <span class="n">sys</span><span class="o">.</span><span class="n">stdout</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\t</span><span class="s1">:: </span><span class="si">%u</span><span class="s1"> proteins, </span><span class="si">%u</span><span class="s1"> complexes&#39;</span>
+                             <span class="s1">&#39;, </span><span class="si">%u</span><span class="s1"> reactions and </span><span class="si">%u</span><span class="s1">&#39;</span>
+                             <span class="s1">&#39; controls have been added.</span><span class="se">\n</span><span class="s1">&#39;</span> <span class="o">%</span>
+                             <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">proteins_added</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">complexes_added</span><span class="p">,</span>
+                              <span class="bp">self</span><span class="o">.</span><span class="n">reactions_added</span> <span class="o">+</span> <span class="bp">self</span><span class="o">.</span><span class="n">cassemblies_added</span><span class="p">,</span>
+                              <span class="bp">self</span><span class="o">.</span><span class="n">controls_added</span> <span class="o">+</span> <span class="bp">self</span><span class="o">.</span><span class="n">catalyses_added</span><span class="p">))</span>
+            <span class="n">sys</span><span class="o">.</span><span class="n">stdout</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\t</span><span class="s1">:: </span><span class="si">%u</span><span class="s1"> complexes have not been expanded &#39;</span>
+                             <span class="s1">&#39;because number of combinations larger than </span><span class="si">%u</span><span class="s1">.</span><span class="se">\n</span><span class="s1">&#39;</span>
+                             <span class="o">%</span> <span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">huge_complexes</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">source</span><span class="p">]),</span>
+                                <span class="bp">self</span><span class="o">.</span><span class="n">max_complex_combinations</span><span class="p">))</span>
+            <span class="n">sys</span><span class="o">.</span><span class="n">stdout</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\t</span><span class="s1">:: </span><span class="si">%u</span><span class="s1"> complexes took longer &#39;</span>
+                             <span class="s1">&#39;to process than 5 seconds.</span><span class="se">\n</span><span class="s1">&#39;</span> <span class="o">%</span>
+                             <span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">slow_complexes</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">source</span><span class="p">])))</span>
+            <span class="n">sys</span><span class="o">.</span><span class="n">stdout</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\t</span><span class="s1">:: </span><span class="si">%u</span><span class="s1"> reactions have not been expanded &#39;</span>
+                             <span class="s1">&#39;because number of combinations larger than </span><span class="si">%u</span><span class="s1">.</span><span class="se">\n</span><span class="s1">&#39;</span>
+                             <span class="o">%</span> <span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">huge_reactions</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">source</span><span class="p">]),</span>
+                                <span class="bp">self</span><span class="o">.</span><span class="n">max_reaction_combinations</span><span class="p">))</span>
+            <span class="n">sys</span><span class="o">.</span><span class="n">stdout</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\t</span><span class="s1">:: Access them in `huge_complexes`, &#39;</span>
+                             <span class="s1">&#39;`slow_complexes` and `huge_reactions`.</span><span class="se">\n</span><span class="s1">&#39;</span><span class="p">)</span>
+            <span class="n">sys</span><span class="o">.</span><span class="n">stdout</span><span class="o">.</span><span class="n">flush</span><span class="p">()</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">remove_defaults</span><span class="p">()</span>
+
+    <span class="k">def</span> <span class="nf">remove_defaults</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">parser</span> <span class="o">=</span> <span class="kc">None</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">source</span> <span class="o">=</span> <span class="kc">None</span>
+
+    <span class="k">def</span> <span class="nf">set_corrections</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+        <span class="c1"># because not all can follow the standards...</span>
+        <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">source</span> <span class="o">==</span> <span class="s1">&#39;ACSN&#39;</span><span class="p">:</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">pref_correction</span> <span class="o">=</span> <span class="k">lambda</span> <span class="n">l</span><span class="p">:</span> <span class="nb">filter</span><span class="p">(</span><span class="k">lambda</span> <span class="n">e</span><span class="p">:</span> <span class="n">e</span><span class="p">[</span><span class="mi">6</span><span class="p">:</span><span class="mi">10</span><span class="p">]</span> <span class="o">==</span> <span class="s1">&#39;HUGO&#39;</span><span class="p">,</span> <span class="n">l</span><span class="p">)</span>
+        <span class="k">else</span><span class="p">:</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">pref_correction</span> <span class="o">=</span> <span class="k">lambda</span> <span class="n">l</span><span class="p">:</span> <span class="n">l</span>
+        <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">source</span> <span class="o">==</span> <span class="s1">&#39;ACSN&#39;</span><span class="p">:</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">pref_refs</span> <span class="o">=</span> <span class="k">lambda</span> <span class="n">l</span><span class="p">:</span> <span class="nb">filter</span><span class="p">(</span><span class="k">lambda</span> <span class="n">e</span><span class="p">:</span> <span class="n">e</span><span class="p">[</span><span class="mi">6</span><span class="p">:</span><span class="mi">12</span><span class="p">]</span> <span class="o">==</span> <span class="s1">&#39;PubMed&#39;</span><span class="p">,</span> <span class="n">l</span><span class="p">)</span>
+        <span class="k">else</span><span class="p">:</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">pref_refs</span> <span class="o">=</span> <span class="k">lambda</span> <span class="n">l</span><span class="p">:</span> <span class="p">[]</span>
+        <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">source</span> <span class="ow">in</span> <span class="p">[</span>
+                <span class="s1">&#39;ACSN&#39;</span><span class="p">,</span> <span class="s1">&#39;WikiPathways&#39;</span><span class="p">,</span> <span class="s1">&#39;NetPath&#39;</span><span class="p">,</span> <span class="s1">&#39;PANTHER&#39;</span><span class="p">,</span> <span class="s1">&#39;NCI-PID&#39;</span><span class="p">,</span> <span class="s1">&#39;KEGG&#39;</span>
+        <span class="p">]:</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">ambiguous_ids_permitted</span> <span class="o">=</span> <span class="kc">True</span>
+        <span class="k">else</span><span class="p">:</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">ambiguous_ids_permitted</span> <span class="o">=</span> <span class="kc">False</span>
+
+    <span class="k">def</span> <span class="nf">merge_refs</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">refs_added</span> <span class="o">=</span> <span class="mi">0</span>
+
+        <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">source</span> <span class="ow">not</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">rrefs</span><span class="p">:</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">rrefs</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">source</span><span class="p">]</span> <span class="o">=</span> <span class="p">{}</span>
+
+        <span class="k">for</span> <span class="n">refid</span><span class="p">,</span> <span class="n">pubmed</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">parser</span><span class="o">.</span><span class="n">pubrefs</span><span class="p">):</span>
+
+            <span class="n">ref</span> <span class="o">=</span> <span class="n">Reference</span><span class="p">(</span><span class="n">pubmed</span><span class="p">,</span> <span class="n">sources</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">source</span><span class="p">)</span>
+            <span class="n">ref</span><span class="o">.</span><span class="n">attrs</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">source</span><span class="p">][</span><span class="s1">&#39;refid&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="nb">set</span><span class="p">([])</span>
+            <span class="n">ref</span><span class="o">.</span><span class="n">attrs</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">source</span><span class="p">][</span><span class="s1">&#39;refid&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">refid</span><span class="p">)</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">refs_added</span> <span class="o">+=</span> <span class="mi">1</span>
+
+            <span class="k">if</span> <span class="n">pubmed</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">refs</span><span class="p">:</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">refs</span><span class="p">[</span><span class="n">pubmed</span><span class="p">]</span> <span class="o">+=</span> <span class="n">ref</span>
+            <span class="k">else</span><span class="p">:</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">refs</span><span class="p">[</span><span class="n">pubmed</span><span class="p">]</span> <span class="o">=</span> <span class="n">ref</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">rrefs</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">source</span><span class="p">][</span><span class="n">refid</span><span class="p">]</span> <span class="o">=</span> <span class="n">pubmed</span>
+
+    <span class="k">def</span> <span class="nf">merge_proteins</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+        <span class="k">def</span> <span class="nf">get_protein_ids</span><span class="p">(</span><span class="n">pref</span><span class="p">):</span>
+
+            <span class="n">pids</span> <span class="o">=</span> <span class="p">[]</span>
+            <span class="n">refs</span> <span class="o">=</span> <span class="p">[]</span>
+            <span class="k">if</span> <span class="n">pref</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">parser</span><span class="o">.</span><span class="n">prefs</span><span class="p">:</span>
+                <span class="n">uxrefs</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">pref_correction</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">parser</span><span class="o">.</span><span class="n">prefs</span><span class="p">[</span><span class="n">pref</span><span class="p">][</span>
+                    <span class="s1">&#39;uxrefs&#39;</span><span class="p">])</span>
+                <span class="n">pids</span> <span class="o">=</span> \
+                    <span class="n">common</span><span class="o">.</span><span class="n">unique_list</span><span class="p">(</span>
+                        <span class="nb">map</span><span class="p">(</span>
+                            <span class="k">lambda</span> <span class="n">uxref</span><span class="p">:</span>
+                                <span class="bp">self</span><span class="o">.</span><span class="n">parser</span><span class="o">.</span><span class="n">ids</span><span class="p">[</span><span class="n">uxref</span><span class="p">],</span>
+                            <span class="nb">filter</span><span class="p">(</span>
+                                <span class="k">lambda</span> <span class="n">uxref</span><span class="p">:</span>
+                                    <span class="n">uxref</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">parser</span><span class="o">.</span><span class="n">ids</span><span class="p">,</span>
+                                <span class="n">uxrefs</span>
+                            <span class="p">)</span>
+                        <span class="p">)</span>
+                    <span class="p">)</span>
+                <span class="n">refids</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">pref_refs</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">parser</span><span class="o">.</span><span class="n">prefs</span><span class="p">[</span><span class="n">pref</span><span class="p">][</span><span class="s1">&#39;uxrefs&#39;</span><span class="p">])</span>
+                <span class="n">refs</span> <span class="o">=</span> \
+                    <span class="n">common</span><span class="o">.</span><span class="n">unique_list</span><span class="p">(</span>
+                        <span class="nb">map</span><span class="p">(</span>
+                            <span class="k">lambda</span> <span class="n">refid</span><span class="p">:</span>
+                                <span class="bp">self</span><span class="o">.</span><span class="n">parser</span><span class="o">.</span><span class="n">ids</span><span class="p">[</span><span class="n">refid</span><span class="p">],</span>
+                            <span class="nb">filter</span><span class="p">(</span>
+                                <span class="k">lambda</span> <span class="n">refid</span><span class="p">:</span>
+                                    <span class="n">refid</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">parser</span><span class="o">.</span><span class="n">ids</span><span class="p">,</span>
+                                <span class="n">refids</span>
+                            <span class="p">)</span>
+                        <span class="p">)</span>
+                    <span class="p">)</span>
+                <span class="c1"># in panther proteinreferences are children of</span>
+                <span class="c1"># other proteinreferences...</span>
+                <span class="k">for</span> <span class="n">subpref</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">parser</span><span class="o">.</span><span class="n">prefs</span><span class="p">[</span><span class="n">pref</span><span class="p">][</span><span class="s1">&#39;prefs&#39;</span><span class="p">]:</span>
+                    <span class="n">subpids</span><span class="p">,</span> <span class="n">subrefs</span> <span class="o">=</span> <span class="n">get_protein_ids</span><span class="p">(</span><span class="n">subpref</span><span class="p">)</span>
+                    <span class="n">pids</span><span class="o">.</span><span class="n">extend</span><span class="p">(</span><span class="n">subpids</span><span class="p">)</span>
+                    <span class="n">refs</span><span class="o">.</span><span class="n">extend</span><span class="p">(</span><span class="n">subrefs</span><span class="p">)</span>
+            <span class="k">return</span> <span class="n">pids</span><span class="p">,</span> <span class="n">refs</span>
+
+        <span class="k">def</span> <span class="nf">map_protein_ids</span><span class="p">(</span><span class="n">ids</span><span class="p">):</span>
+            <span class="n">target_ids</span> <span class="o">=</span> <span class="p">[]</span>
+            <span class="n">id_attrs</span> <span class="o">=</span> <span class="p">{}</span>
+            <span class="k">for</span> <span class="n">id_type</span><span class="p">,</span> <span class="n">_id</span> <span class="ow">in</span> <span class="n">ids</span><span class="p">:</span>
+                <span class="k">if</span> <span class="n">id_type</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">id_types</span><span class="p">:</span>
+                    <span class="n">std_id_type</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">id_types</span><span class="p">[</span><span class="n">id_type</span><span class="p">]</span>
+                <span class="k">else</span><span class="p">:</span>
+                    <span class="n">std_id_type</span> <span class="o">=</span> <span class="n">id_type</span>
+                <span class="n">id_a</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">id_processor</span><span class="p">(</span><span class="n">_id</span><span class="p">)</span>
+                <span class="n">id_attrs</span><span class="p">[</span><span class="n">id_a</span><span class="p">[</span><span class="s1">&#39;id&#39;</span><span class="p">]]</span> <span class="o">=</span> <span class="n">id_a</span>
+                <span class="k">if</span> <span class="n">id_a</span><span class="p">[</span><span class="s1">&#39;id&#39;</span><span class="p">]</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
+                    <span class="n">target_ids</span><span class="o">.</span><span class="n">extend</span><span class="p">(</span>
+                        <span class="bp">self</span><span class="o">.</span><span class="n">mapper</span><span class="o">.</span><span class="n">map_name</span><span class="p">(</span><span class="n">id_a</span><span class="p">[</span><span class="s1">&#39;id&#39;</span><span class="p">],</span> <span class="n">std_id_type</span><span class="p">,</span>
+                                             <span class="bp">self</span><span class="o">.</span><span class="n">default_id_types</span><span class="p">[</span><span class="s1">&#39;protein&#39;</span><span class="p">]))</span>
+            <span class="n">target_ids</span> <span class="o">=</span> <span class="nb">filter</span><span class="p">(</span>
+                <span class="k">lambda</span> <span class="n">p</span><span class="p">:</span> <span class="n">reflists</span><span class="o">.</span><span class="n">check</span><span class="p">(</span>
+                    <span class="n">p</span><span class="p">,</span>
+                    <span class="bp">self</span><span class="o">.</span><span class="n">default_id_types</span><span class="p">[</span><span class="s1">&#39;protein&#39;</span><span class="p">],</span>
+                    <span class="bp">self</span><span class="o">.</span><span class="n">ncbi_tax_id</span>
+                <span class="p">),</span>
+                <span class="n">target_ids</span><span class="p">)</span>
+            <span class="n">target_ids</span> <span class="o">=</span> <span class="n">common</span><span class="o">.</span><span class="n">unique_list</span><span class="p">(</span><span class="n">target_ids</span><span class="p">)</span>
+            <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">target_ids</span><span class="p">)</span> <span class="o">&gt;</span> <span class="mi">1</span><span class="p">:</span>
+                <span class="k">if</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">ambiguous_ids_permitted</span><span class="p">:</span>
+                    <span class="n">sys</span><span class="o">.</span><span class="n">stdout</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\t</span><span class="s1">:: Ambiguous ID &#39;</span>
+                                     <span class="s1">&#39;translation: from </span><span class="si">%s</span><span class="s1"> to </span><span class="si">%s</span><span class="se">\n</span><span class="s1">&#39;</span> <span class="o">%</span>
+                                     <span class="p">(</span><span class="n">ids</span><span class="p">,</span> <span class="n">target_ids</span><span class="p">))</span>
+            <span class="k">elif</span> <span class="nb">len</span><span class="p">(</span><span class="n">target_ids</span><span class="p">)</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
+                <span class="n">target_ids</span> <span class="o">=</span> <span class="kc">None</span>
+            <span class="k">else</span><span class="p">:</span>
+                <span class="n">target_ids</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="n">target_ids</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span>
+            <span class="k">return</span> <span class="n">target_ids</span><span class="p">,</span> <span class="n">id_attrs</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">rproteins</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">source</span><span class="p">]</span> <span class="o">=</span> <span class="p">{}</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">proteins_added</span> <span class="o">=</span> <span class="mi">0</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">pfamilies_added</span> <span class="o">=</span> <span class="mi">0</span>
+
+        <span class="k">for</span> <span class="n">pid</span><span class="p">,</span> <span class="n">p</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">parser</span><span class="o">.</span><span class="n">proteins</span><span class="p">):</span>
+            <span class="n">ids</span><span class="p">,</span> <span class="n">pubmeds</span> <span class="o">=</span> <span class="n">get_protein_ids</span><span class="p">(</span><span class="n">p</span><span class="p">[</span><span class="s1">&#39;protein&#39;</span><span class="p">])</span>
+            <span class="n">target_id</span><span class="p">,</span> <span class="n">id_attrs</span> <span class="o">=</span> <span class="n">map_protein_ids</span><span class="p">(</span><span class="n">ids</span><span class="p">)</span>
+            <span class="k">if</span> <span class="n">target_id</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
+                <span class="k">continue</span>
+            <span class="k">if</span> <span class="nb">type</span><span class="p">(</span><span class="n">target_id</span><span class="p">)</span> <span class="ow">is</span> <span class="nb">list</span><span class="p">:</span>
+                <span class="c1"># go for a protein family:</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">add_pfamily</span><span class="p">(</span><span class="nb">list</span><span class="p">(</span><span class="nb">map</span><span class="p">(</span><span class="k">lambda</span> <span class="n">t</span><span class="p">:</span> <span class="p">(</span><span class="n">t</span><span class="p">,</span> <span class="n">pid</span><span class="p">),</span> <span class="n">target_id</span><span class="p">)),</span> <span class="n">pid</span><span class="p">)</span>
+                <span class="k">continue</span>
+            <span class="n">attrs</span> <span class="o">=</span> <span class="p">{</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">source</span><span class="p">:</span> <span class="p">{</span>
+                    <span class="s1">&#39;prefs&#39;</span><span class="p">:</span> <span class="nb">set</span><span class="p">([</span><span class="n">p</span><span class="p">[</span><span class="s1">&#39;protein&#39;</span><span class="p">]]),</span>
+                    <span class="s1">&#39;pids&#39;</span><span class="p">:</span> <span class="p">{</span>
+                        <span class="n">pid</span><span class="p">:</span> <span class="p">{}</span>
+                    <span class="p">},</span>
+                    <span class="s1">&#39;refs&#39;</span><span class="p">:</span> <span class="nb">set</span><span class="p">(</span><span class="n">pubmeds</span><span class="p">),</span>
+                    <span class="s1">&#39;originals&#39;</span><span class="p">:</span> <span class="nb">set</span><span class="p">([])</span>
+                <span class="p">}</span>
+            <span class="p">}</span>
+            <span class="k">for</span> <span class="n">original_id</span><span class="p">,</span> <span class="n">id_a</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="n">id_attrs</span><span class="p">):</span>
+                <span class="n">attrs</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">source</span><span class="p">][</span><span class="s1">&#39;originals&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">original_id</span><span class="p">)</span>
+                <span class="k">for</span> <span class="n">k</span><span class="p">,</span> <span class="n">v</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="n">id_a</span><span class="p">):</span>
+                    <span class="k">if</span> <span class="n">k</span> <span class="o">!=</span> <span class="s1">&#39;id&#39;</span><span class="p">:</span>
+                        <span class="n">attrs</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">source</span><span class="p">][</span><span class="s1">&#39;pids&#39;</span><span class="p">][</span><span class="n">pid</span><span class="p">][</span><span class="n">k</span><span class="p">]</span> <span class="o">=</span> <span class="nb">set</span><span class="p">([])</span>
+                        <span class="n">attrs</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">source</span><span class="p">][</span><span class="s1">&#39;pids&#39;</span><span class="p">][</span><span class="n">pid</span><span class="p">][</span><span class="n">k</span><span class="p">]</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">v</span><span class="p">)</span>
+            <span class="n">protein</span> <span class="o">=</span> <span class="n">Protein</span><span class="p">(</span>
+                <span class="n">target_id</span><span class="p">,</span> <span class="n">sources</span><span class="o">=</span><span class="nb">set</span><span class="p">([</span><span class="bp">self</span><span class="o">.</span><span class="n">source</span><span class="p">]),</span> <span class="n">attrs</span><span class="o">=</span><span class="n">attrs</span><span class="p">)</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">proteins_added</span> <span class="o">+=</span> <span class="mi">1</span>
+            <span class="k">if</span> <span class="n">target_id</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">proteins</span><span class="p">:</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">proteins</span><span class="p">[</span><span class="n">target_id</span><span class="p">]</span> <span class="o">+=</span> <span class="n">protein</span>
+            <span class="k">else</span><span class="p">:</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">proteins</span><span class="p">[</span><span class="n">target_id</span><span class="p">]</span> <span class="o">=</span> <span class="n">protein</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">rproteins</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">source</span><span class="p">][</span><span class="n">pid</span><span class="p">]</span> <span class="o">=</span> <span class="n">target_id</span>
+
+    <span class="k">def</span> <span class="nf">preprocess_seqmodvoc</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">seqmod_dict</span> <span class="o">=</span> <span class="p">{}</span>
+        <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">source</span> <span class="ow">in</span> <span class="n">common</span><span class="o">.</span><span class="n">mod_keywords</span><span class="p">:</span>
+            <span class="n">kws</span> <span class="o">=</span> <span class="n">common</span><span class="o">.</span><span class="n">mod_keywords</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">source</span><span class="p">]</span>
+            <span class="n">aas</span> <span class="o">=</span> <span class="n">common</span><span class="o">.</span><span class="n">aanames</span>
+            <span class="k">for</span> <span class="n">modkey</span><span class="p">,</span> <span class="n">modname</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">parser</span><span class="o">.</span><span class="n">seqmodvocs</span><span class="p">):</span>
+                <span class="k">for</span> <span class="n">mod_std_name</span><span class="p">,</span> <span class="n">kwlist</span> <span class="ow">in</span> <span class="n">kws</span><span class="p">:</span>
+                    <span class="k">if</span> <span class="nb">all</span><span class="p">(</span><span class="nb">map</span><span class="p">(</span><span class="k">lambda</span> <span class="n">kw</span><span class="p">:</span> <span class="n">kw</span> <span class="ow">in</span> <span class="n">modname</span><span class="p">,</span> <span class="n">kwlist</span><span class="p">)):</span>
+                        <span class="n">this_aa</span> <span class="o">=</span> <span class="kc">None</span>
+                        <span class="k">for</span> <span class="n">aan</span><span class="p">,</span> <span class="n">aa</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="n">aas</span><span class="p">):</span>
+                            <span class="k">if</span> <span class="n">aan</span> <span class="ow">in</span> <span class="n">modname</span><span class="p">:</span>
+                                <span class="n">this_aa</span> <span class="o">=</span> <span class="n">aa</span>
+                                <span class="k">break</span>
+                        <span class="bp">self</span><span class="o">.</span><span class="n">seqmod_dict</span><span class="p">[</span><span class="n">modkey</span><span class="p">]</span> <span class="o">=</span> <span class="p">(</span><span class="n">mod_std_name</span><span class="p">,</span> <span class="n">this_aa</span><span class="p">)</span>
+
+    <span class="k">def</span> <span class="nf">merge_modifications</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">load_sequences</span><span class="p">()</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">preprocess_seqmodvoc</span><span class="p">()</span>
+
+        <span class="k">def</span> <span class="nf">get_protein</span><span class="p">(</span><span class="n">pid</span><span class="p">):</span>
+            <span class="n">proteins</span> <span class="o">=</span> <span class="p">[]</span>
+            <span class="k">if</span> <span class="n">pid</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">rproteins</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">source</span><span class="p">]:</span>
+                <span class="n">_id</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">rproteins</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">source</span><span class="p">][</span><span class="n">pid</span><span class="p">]</span>
+                <span class="k">if</span> <span class="s1">&#39;isoform&#39;</span> <span class="ow">in</span> \
+                        <span class="bp">self</span><span class="o">.</span><span class="n">proteins</span><span class="p">[</span><span class="n">_id</span><span class="p">]</span><span class="o">.</span><span class="n">attrs</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">source</span><span class="p">][</span><span class="s1">&#39;pids&#39;</span><span class="p">][</span><span class="n">pid</span><span class="p">]:</span>
+                    <span class="k">for</span> <span class="n">isof</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">proteins</span><span class="p">[</span><span class="n">_id</span><span class="p">]</span><span class="o">.</span><span class="n">attrs</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">source</span><span class="p">]</span>\
+                            <span class="p">[</span><span class="s1">&#39;pids&#39;</span><span class="p">][</span><span class="n">pid</span><span class="p">][</span><span class="s1">&#39;isoform&#39;</span><span class="p">]:</span>
+                        <span class="n">proteins</span><span class="o">.</span><span class="n">append</span><span class="p">((</span><span class="n">_id</span><span class="p">,</span> <span class="n">isof</span><span class="p">))</span>
+                <span class="k">else</span><span class="p">:</span>
+                    <span class="n">proteins</span><span class="o">.</span><span class="n">append</span><span class="p">((</span><span class="n">_id</span><span class="p">,</span> <span class="kc">None</span><span class="p">))</span>
+            <span class="k">return</span> <span class="n">proteins</span>
+
+        <span class="k">def</span> <span class="nf">get_seqsite</span><span class="p">(</span><span class="n">seqsite</span><span class="p">):</span>
+            <span class="k">if</span> <span class="n">seqsite</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">parser</span><span class="o">.</span><span class="n">seqsites</span><span class="p">:</span>
+                <span class="k">return</span> <span class="nb">int</span><span class="p">(</span><span class="nb">float</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">parser</span><span class="o">.</span><span class="n">seqsites</span><span class="p">[</span><span class="n">seqsite</span><span class="p">]))</span>
+
+        <span class="k">def</span> <span class="nf">get_residue</span><span class="p">(</span><span class="n">protein</span><span class="p">,</span> <span class="n">isof</span><span class="p">,</span> <span class="n">resnum</span><span class="p">,</span> <span class="n">resname</span><span class="p">):</span>
+            <span class="k">if</span> <span class="n">protein</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">seq</span><span class="p">:</span>
+                <span class="k">if</span> <span class="n">isof</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span> <span class="ow">and</span> <span class="n">isof</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">seq</span><span class="p">[</span><span class="n">protein</span><span class="p">]</span><span class="o">.</span><span class="n">isof</span><span class="p">:</span>
+                    <span class="n">sresname</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">seq</span><span class="p">[</span><span class="n">protein</span><span class="p">]</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="n">resnum</span><span class="p">,</span> <span class="n">isoform</span><span class="o">=</span><span class="n">isof</span><span class="p">)</span>
+                    <span class="k">if</span> <span class="n">sresname</span> <span class="o">==</span> <span class="n">resname</span> <span class="ow">or</span> <span class="n">resname</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
+                        <span class="k">return</span> <span class="n">sresname</span><span class="p">,</span> <span class="n">isof</span>
+                <span class="k">for</span> <span class="n">isof</span> <span class="ow">in</span> <span class="nb">sorted</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">seq</span><span class="p">[</span><span class="n">protein</span><span class="p">]</span><span class="o">.</span><span class="n">isoforms</span><span class="p">()):</span>
+                    <span class="n">sresname</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">seq</span><span class="p">[</span><span class="n">protein</span><span class="p">]</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="n">resnum</span><span class="p">,</span> <span class="n">isoform</span><span class="o">=</span><span class="n">isof</span><span class="p">)</span>
+                    <span class="k">if</span> <span class="n">sresname</span> <span class="o">==</span> <span class="n">resname</span> <span class="ow">or</span> <span class="n">resname</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
+                        <span class="k">return</span> <span class="n">sresname</span><span class="p">,</span> <span class="n">isof</span>
+            <span class="k">return</span> <span class="n">resname</span><span class="p">,</span> <span class="n">isof</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">fragfeatures_added</span> <span class="o">=</span> <span class="mi">0</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">modfeatures_added</span> <span class="o">=</span> <span class="mi">0</span>
+
+        <span class="k">for</span> <span class="n">pid</span><span class="p">,</span> <span class="n">p</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">parser</span><span class="o">.</span><span class="n">proteins</span><span class="p">):</span>
+            <span class="n">proteins</span> <span class="o">=</span> <span class="n">get_protein</span><span class="p">(</span><span class="n">pid</span><span class="p">)</span>
+
+            <span class="k">for</span> <span class="n">modfea</span> <span class="ow">in</span> <span class="n">p</span><span class="p">[</span><span class="s1">&#39;modfeatures&#39;</span><span class="p">]:</span>
+
+                <span class="k">if</span> <span class="n">modfea</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">parser</span><span class="o">.</span><span class="n">fragfeas</span><span class="p">:</span>
+                    <span class="n">seqint</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">parser</span><span class="o">.</span><span class="n">fragfeas</span><span class="p">[</span><span class="n">modfea</span><span class="p">]</span>
+                    <span class="k">if</span> <span class="n">seqint</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">parser</span><span class="o">.</span><span class="n">seqints</span><span class="p">:</span>
+                        <span class="n">start</span> <span class="o">=</span> <span class="n">get_seqsite</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">parser</span><span class="o">.</span><span class="n">seqints</span><span class="p">[</span><span class="n">seqint</span><span class="p">][</span><span class="mi">0</span><span class="p">])</span>
+                        <span class="n">end</span> <span class="o">=</span> <span class="n">get_seqsite</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">parser</span><span class="o">.</span><span class="n">seqints</span><span class="p">[</span><span class="n">seqint</span><span class="p">][</span><span class="mi">1</span><span class="p">])</span>
+                        <span class="k">if</span> <span class="n">start</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span> <span class="ow">and</span> <span class="n">end</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
+                            <span class="k">for</span> <span class="n">protein</span><span class="p">,</span> <span class="n">isof</span> <span class="ow">in</span> <span class="n">proteins</span><span class="p">:</span>
+                                <span class="k">if</span> <span class="n">protein</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">seq</span><span class="p">:</span>
+                                    <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">seq</span><span class="p">[</span><span class="n">protein</span><span class="p">]</span><span class="o">.</span><span class="n">has_isoform</span><span class="p">(</span><span class="n">isof</span><span class="p">):</span>
+                                        <span class="n">frag</span> <span class="o">=</span> <span class="p">(</span><span class="n">protein</span><span class="p">,</span> <span class="n">isof</span><span class="p">,</span> <span class="n">start</span><span class="p">,</span> <span class="n">end</span><span class="p">)</span>
+                                        <span class="k">if</span> <span class="n">frag</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">frags</span><span class="p">:</span>
+                                            <span class="bp">self</span><span class="o">.</span><span class="n">frags</span><span class="p">[</span><span class="n">frag</span><span class="p">]</span><span class="o">.</span><span class="n">add_evidences</span><span class="p">(</span>
+                                                <span class="bp">self</span><span class="o">.</span><span class="n">source</span>
+                                            <span class="p">)</span>
+                                        <span class="k">else</span><span class="p">:</span>
+                                            <span class="n">instance</span> <span class="o">=</span> \
+                                                <span class="bp">self</span><span class="o">.</span><span class="n">seq</span><span class="p">[</span><span class="n">protein</span><span class="p">]</span><span class="o">.</span><span class="n">get</span><span class="p">(</span>
+                                                    <span class="n">start</span><span class="p">,</span> <span class="n">end</span><span class="p">,</span> <span class="n">isof</span><span class="p">)</span>
+                                            <span class="n">mot</span> <span class="o">=</span> <span class="n">intera</span><span class="o">.</span><span class="n">Motif</span><span class="p">(</span>
+                                                <span class="n">protein</span><span class="p">,</span>
+                                                <span class="n">start</span><span class="p">,</span>
+                                                <span class="n">end</span><span class="p">,</span>
+                                                <span class="n">isoform</span><span class="o">=</span><span class="n">isof</span><span class="p">,</span>
+                                                <span class="n">instance</span><span class="o">=</span><span class="n">instance</span><span class="p">,</span>
+                                                <span class="n">evidences</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">source</span><span class="p">,</span>
+                                            <span class="p">)</span>
+                                            <span class="bp">self</span><span class="o">.</span><span class="n">frags</span><span class="p">[</span><span class="n">frag</span><span class="p">]</span> <span class="o">=</span> <span class="n">mot</span>
+                                        <span class="bp">self</span><span class="o">.</span><span class="n">proteins</span><span class="p">[</span><span class="n">protein</span><span class="p">]</span><span class="o">.</span><span class="n">update_attr</span><span class="p">([</span>
+                                            <span class="bp">self</span><span class="o">.</span><span class="n">source</span><span class="p">,</span> <span class="s1">&#39;pids&#39;</span><span class="p">,</span> <span class="n">pid</span><span class="p">,</span> <span class="s1">&#39;frags&#39;</span><span class="p">,</span>
+                                            <span class="p">{</span><span class="n">frag</span><span class="p">}</span>
+                                        <span class="p">])</span>
+                                        <span class="bp">self</span><span class="o">.</span><span class="n">fragfeatures_added</span> <span class="o">+=</span> <span class="mi">1</span>
+
+                <span class="k">if</span> <span class="n">modfea</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">parser</span><span class="o">.</span><span class="n">modfeas</span><span class="p">:</span>
+                    <span class="n">resnum</span> <span class="o">=</span> <span class="n">get_seqsite</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">parser</span><span class="o">.</span><span class="n">modfeas</span><span class="p">[</span><span class="n">modfea</span><span class="p">][</span><span class="mi">0</span><span class="p">])</span>
+                    <span class="n">seqmodvoc</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">parser</span><span class="o">.</span><span class="n">modfeas</span><span class="p">[</span><span class="n">modfea</span><span class="p">][</span><span class="mi">1</span><span class="p">]</span>
+                    <span class="k">if</span> <span class="n">seqmodvoc</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">seqmod_dict</span><span class="p">:</span>
+                        <span class="n">typ</span><span class="p">,</span> <span class="n">resname</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">seqmod_dict</span><span class="p">[</span><span class="n">seqmodvoc</span><span class="p">]</span>
+                        <span class="k">for</span> <span class="n">protein</span><span class="p">,</span> <span class="n">isof</span> <span class="ow">in</span> <span class="n">proteins</span><span class="p">:</span>
+                            <span class="k">if</span> <span class="n">protein</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">seq</span> <span class="ow">and</span> <span class="n">resnum</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
+                                <span class="n">resname</span><span class="p">,</span> <span class="n">isof</span> <span class="o">=</span> \
+                                    <span class="n">get_residue</span><span class="p">(</span><span class="n">protein</span><span class="p">,</span> <span class="n">isof</span><span class="p">,</span> <span class="n">resnum</span><span class="p">,</span> <span class="n">resname</span><span class="p">)</span>
+                                <span class="n">mod</span> <span class="o">=</span> <span class="p">(</span><span class="n">protein</span><span class="p">,</span> <span class="n">isof</span><span class="p">,</span> <span class="n">resnum</span><span class="p">,</span> <span class="n">resname</span><span class="p">,</span> <span class="n">typ</span><span class="p">)</span>
+                                <span class="k">if</span> <span class="n">mod</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">mods</span><span class="p">:</span>
+                                    <span class="bp">self</span><span class="o">.</span><span class="n">mods</span><span class="p">[</span><span class="n">mod</span><span class="p">]</span><span class="o">.</span><span class="n">add_evidences</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">source</span><span class="p">)</span>
+                                <span class="k">else</span><span class="p">:</span>
+                                    <span class="n">res</span> <span class="o">=</span> <span class="n">intera</span><span class="o">.</span><span class="n">Residue</span><span class="p">(</span>
+                                        <span class="n">resnum</span><span class="p">,</span> <span class="n">resname</span><span class="p">,</span> <span class="n">protein</span><span class="p">,</span> <span class="n">isoform</span><span class="o">=</span><span class="n">isof</span><span class="p">)</span>
+                                    <span class="n">start</span><span class="p">,</span> <span class="n">end</span><span class="p">,</span> <span class="n">instance</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">seq</span><span class="p">[</span>
+                                        <span class="n">protein</span><span class="p">]</span><span class="o">.</span><span class="n">get_region</span><span class="p">(</span>
+                                            <span class="n">resnum</span><span class="p">,</span> <span class="n">isoform</span><span class="o">=</span><span class="n">isof</span><span class="p">)</span>
+                                    <span class="n">mot</span> <span class="o">=</span> <span class="n">intera</span><span class="o">.</span><span class="n">Motif</span><span class="p">(</span>
+                                        <span class="n">protein</span><span class="p">,</span>
+                                        <span class="n">start</span><span class="p">,</span>
+                                        <span class="n">end</span><span class="p">,</span>
+                                        <span class="n">isoform</span><span class="o">=</span><span class="n">isof</span><span class="p">,</span>
+                                        <span class="n">instance</span><span class="o">=</span><span class="n">instance</span><span class="p">)</span>
+                                    <span class="n">ptm</span> <span class="o">=</span> <span class="n">intera</span><span class="o">.</span><span class="n">Ptm</span><span class="p">(</span>
+                                        <span class="n">protein</span><span class="p">,</span>
+                                        <span class="n">motif</span><span class="o">=</span><span class="n">mot</span><span class="p">,</span>
+                                        <span class="n">residue</span><span class="o">=</span><span class="n">res</span><span class="p">,</span>
+                                        <span class="n">evidences</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">source</span><span class="p">,</span>
+                                        <span class="n">isoform</span><span class="o">=</span><span class="n">isof</span><span class="p">,</span>
+                                        <span class="n">typ</span><span class="o">=</span><span class="n">typ</span><span class="p">,</span>
+                                    <span class="p">)</span>
+                                    <span class="bp">self</span><span class="o">.</span><span class="n">mods</span><span class="p">[</span><span class="n">mod</span><span class="p">]</span> <span class="o">=</span> <span class="n">ptm</span>
+                                <span class="k">try</span><span class="p">:</span>
+                                    <span class="bp">self</span><span class="o">.</span><span class="n">proteins</span><span class="p">[</span><span class="n">protein</span><span class="p">]</span><span class="o">.</span><span class="n">update_attr</span><span class="p">([</span>
+                                        <span class="bp">self</span><span class="o">.</span><span class="n">source</span><span class="p">,</span> <span class="s1">&#39;pids&#39;</span><span class="p">,</span> <span class="n">pid</span><span class="p">,</span> <span class="s1">&#39;mods&#39;</span><span class="p">,</span>
+                                        <span class="nb">set</span><span class="p">([</span><span class="n">mod</span><span class="p">])</span>
+                                    <span class="p">])</span>
+                                <span class="k">except</span><span class="p">:</span>
+                                    <span class="nb">print</span><span class="p">(</span><span class="n">protein</span><span class="p">,</span> <span class="n">pid</span><span class="p">)</span>
+                                <span class="bp">self</span><span class="o">.</span><span class="n">modfeatures_added</span> <span class="o">+=</span> <span class="mi">1</span>
+
+    <span class="k">def</span> <span class="nf">merge_pfamilies</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">source</span> <span class="ow">not</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">rpfamilies</span><span class="p">:</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">rpfamilies</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">source</span><span class="p">]</span> <span class="o">=</span> <span class="p">{}</span>
+
+        <span class="n">this_round</span> <span class="o">=</span> <span class="nb">set</span><span class="p">(</span><span class="nb">list</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">parser</span><span class="o">.</span><span class="n">pfamilies</span><span class="o">.</span><span class="n">keys</span><span class="p">()))</span>
+        <span class="n">next_round</span> <span class="o">=</span> <span class="p">[]</span>
+        <span class="n">prev_round</span> <span class="o">=</span> <span class="o">-</span><span class="mi">1</span>
+        <span class="k">while</span> <span class="nb">len</span><span class="p">(</span><span class="n">this_round</span><span class="p">)</span> <span class="o">-</span> <span class="n">prev_round</span> <span class="o">!=</span> <span class="mi">0</span><span class="p">:</span>
+            <span class="n">prev_round</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="n">this_round</span><span class="p">)</span>
+            <span class="k">for</span> <span class="n">pfid</span> <span class="ow">in</span> <span class="n">this_round</span><span class="p">:</span>
+                <span class="n">pids</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">parser</span><span class="o">.</span><span class="n">pfamilies</span><span class="p">[</span><span class="n">pfid</span><span class="p">]</span>
+                <span class="n">subpf_unproc</span> <span class="o">=</span> \
+                    <span class="nb">any</span><span class="p">(</span><span class="nb">map</span><span class="p">(</span><span class="k">lambda</span> <span class="n">pid</span><span class="p">:</span> <span class="n">pid</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">parser</span><span class="o">.</span><span class="n">pfamilies</span><span class="p">,</span> <span class="n">pids</span><span class="p">))</span>
+                <span class="k">if</span> <span class="n">subpf_unproc</span><span class="p">:</span>
+                    <span class="n">next_round</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">pfid</span><span class="p">)</span>
+                    <span class="k">continue</span>
+                <span class="n">proteins</span> <span class="o">=</span> \
+                    <span class="nb">list</span><span class="p">(</span>
+                        <span class="nb">map</span><span class="p">(</span>
+                            <span class="k">lambda</span> <span class="n">pid</span><span class="p">:</span>
+                                <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">rproteins</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">source</span><span class="p">][</span><span class="n">pid</span><span class="p">],</span> <span class="n">pid</span><span class="p">),</span>
+                            <span class="nb">filter</span><span class="p">(</span>
+                                <span class="k">lambda</span> <span class="n">pid</span><span class="p">:</span>
+                                    <span class="n">pid</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">rproteins</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">source</span><span class="p">],</span>
+                                <span class="n">pids</span>
+                            <span class="p">)</span>
+                        <span class="p">)</span>
+                    <span class="p">)</span>
+                <span class="n">subpfs</span> <span class="o">=</span> \
+                    <span class="nb">list</span><span class="p">(</span>
+                        <span class="nb">map</span><span class="p">(</span>
+                            <span class="k">lambda</span> <span class="n">pid</span><span class="p">:</span>
+                                <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">rpfamilies</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">source</span><span class="p">][</span><span class="n">pid</span><span class="p">],</span> <span class="n">pid</span><span class="p">),</span>
+                            <span class="nb">filter</span><span class="p">(</span>
+                                <span class="k">lambda</span> <span class="n">pid</span><span class="p">:</span>
+                                    <span class="n">pid</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">rpfamilies</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">source</span><span class="p">],</span>
+                                <span class="n">pids</span>
+                            <span class="p">)</span>
+                        <span class="p">)</span>
+                    <span class="p">)</span>
+                <span class="k">for</span> <span class="n">spf</span><span class="p">,</span> <span class="n">spfid</span> <span class="ow">in</span> <span class="n">subpfs</span><span class="p">:</span>
+                    <span class="n">spfmembs</span> <span class="o">=</span> \
+                        <span class="nb">list</span><span class="p">(</span>
+                            <span class="nb">map</span><span class="p">(</span>
+                                <span class="k">lambda</span> <span class="n">p</span><span class="p">:</span>
+                                    <span class="p">(</span><span class="n">p</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">p</span><span class="p">[</span><span class="mi">1</span><span class="p">][</span><span class="s1">&#39;pid&#39;</span><span class="p">]),</span>
+                                <span class="n">iteritems</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">pfamilies</span><span class="p">[</span><span class="n">spf</span><span class="p">]</span><span class="o">.</span><span class="n">attrs</span><span class="p">[</span>
+                                          <span class="bp">self</span><span class="o">.</span><span class="n">source</span><span class="p">][</span><span class="n">spfid</span><span class="p">])</span>
+                            <span class="p">)</span>
+                        <span class="p">)</span>
+                    <span class="n">proteins</span><span class="o">.</span><span class="n">extend</span><span class="p">(</span><span class="n">spfmembs</span><span class="p">)</span>
+
+                <span class="bp">self</span><span class="o">.</span><span class="n">add_pfamily</span><span class="p">(</span><span class="n">proteins</span><span class="p">,</span> <span class="n">pfid</span><span class="p">)</span>
+
+            <span class="n">this_round</span> <span class="o">=</span> <span class="n">next_round</span>
+            <span class="n">next_round</span> <span class="o">=</span> <span class="p">[]</span>
+
+    <span class="k">def</span> <span class="nf">add_pfamily</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">proteins</span><span class="p">,</span> <span class="n">pfid</span><span class="p">):</span>
+        <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">source</span> <span class="ow">not</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">rpfamilies</span><span class="p">:</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">rpfamilies</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">source</span><span class="p">]</span> <span class="o">=</span> <span class="p">{}</span>
+
+        <span class="n">members</span> <span class="o">=</span> <span class="nb">sorted</span><span class="p">(</span><span class="n">common</span><span class="o">.</span><span class="n">unique_list</span><span class="p">(</span><span class="nb">map</span><span class="p">(</span><span class="k">lambda</span> <span class="n">p</span><span class="p">:</span> <span class="n">p</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">proteins</span><span class="p">)))</span>
+
+        <span class="c1"># this necessary if we add protein family because of</span>
+        <span class="c1"># ambiguous id mapping; we want to make sure protein</span>
+        <span class="c1"># exists for each member of the family.</span>
+        <span class="k">for</span> <span class="n">m</span> <span class="ow">in</span> <span class="n">members</span><span class="p">:</span>
+            <span class="k">if</span> <span class="n">m</span> <span class="ow">not</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">proteins</span><span class="p">:</span>
+                <span class="n">p</span> <span class="o">=</span> <span class="n">Protein</span><span class="p">(</span><span class="n">m</span><span class="p">,</span> <span class="n">sources</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">source</span><span class="p">)</span>
+                <span class="n">p</span><span class="o">.</span><span class="n">attrs</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">source</span><span class="p">][</span><span class="s1">&#39;pids&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="p">{}</span>
+                <span class="n">p</span><span class="o">.</span><span class="n">attrs</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">source</span><span class="p">][</span><span class="s1">&#39;pids&#39;</span><span class="p">][</span><span class="n">pfid</span><span class="p">]</span> <span class="o">=</span> <span class="p">{}</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">proteins</span><span class="p">[</span><span class="n">m</span><span class="p">]</span> <span class="o">=</span> <span class="n">p</span>
+        <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">members</span><span class="p">):</span>
+            <span class="n">pf</span> <span class="o">=</span> <span class="n">ProteinFamily</span><span class="p">(</span><span class="n">members</span><span class="p">,</span> <span class="n">source</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">source</span><span class="p">,</span> <span class="n">parent</span><span class="o">=</span><span class="bp">self</span><span class="p">)</span>
+            <span class="n">members</span> <span class="o">=</span> <span class="nb">tuple</span><span class="p">(</span><span class="n">members</span><span class="p">)</span>
+            <span class="n">pf</span><span class="o">.</span><span class="n">attrs</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">source</span><span class="p">][</span><span class="n">pfid</span><span class="p">]</span> <span class="o">=</span> <span class="p">{}</span>
+            <span class="k">for</span> <span class="n">protein</span><span class="p">,</span> <span class="n">pid</span> <span class="ow">in</span> <span class="n">proteins</span><span class="p">:</span>
+                <span class="n">pf</span><span class="o">.</span><span class="n">attrs</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">source</span><span class="p">][</span><span class="n">pfid</span><span class="p">][</span><span class="n">protein</span><span class="p">]</span> <span class="o">=</span> <span class="p">{}</span>
+                <span class="n">pf</span><span class="o">.</span><span class="n">attrs</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">source</span><span class="p">][</span><span class="n">pfid</span><span class="p">][</span><span class="n">protein</span><span class="p">][</span><span class="s1">&#39;pid&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">pid</span>
+            <span class="k">if</span> <span class="n">members</span> <span class="ow">not</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">pfamilies</span><span class="p">:</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">pfamilies</span><span class="p">[</span><span class="n">members</span><span class="p">]</span> <span class="o">=</span> <span class="n">pf</span>
+            <span class="k">else</span><span class="p">:</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">pfamilies</span><span class="p">[</span><span class="n">members</span><span class="p">]</span> <span class="o">+=</span> <span class="n">pf</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">rpfamilies</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">source</span><span class="p">][</span><span class="n">pfid</span><span class="p">]</span> <span class="o">=</span> <span class="n">members</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">pfamilies_added</span> <span class="o">+=</span> <span class="mi">1</span>
+
+<div class="viewcode-block" id="PyReact.merge_complexes">
+<a class="viewcode-back" href="../../../api/pypath.utils.pyreact.PyReact.html#pypath.utils.pyreact.PyReact.merge_complexes">[docs]</a>
+    <span class="k">def</span> <span class="nf">merge_complexes</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">this_round</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Merges complexes from the active ``BioPaxReader`` object.</span>
+<span class="sd">        Protein families and subcomplexes are expanded, and all combinations</span>
+<span class="sd">        are created as separate complexes. The complexes from the same ID</span>
+<span class="sd">        are added to sets in the ``rcomplexes`` dict.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">complexes_added</span> <span class="o">=</span> <span class="mi">0</span>
+        <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">source</span> <span class="ow">not</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">rcomplexes</span><span class="p">:</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">rcomplexes</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">source</span><span class="p">]</span> <span class="o">=</span> <span class="p">{}</span>
+
+        <span class="n">no_protein</span> <span class="o">=</span> <span class="nb">set</span><span class="p">([])</span>
+        <span class="n">this_round</span> <span class="o">=</span> <span class="nb">set</span><span class="p">(</span><span class="nb">list</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">parser</span><span class="o">.</span><span class="n">complexes</span><span class="o">.</span><span class="n">keys</span><span class="p">()))</span> \
+            <span class="k">if</span> <span class="n">this_round</span> <span class="ow">is</span> <span class="kc">None</span> <span class="k">else</span> <span class="n">this_round</span>
+        <span class="n">next_round</span> <span class="o">=</span> <span class="p">[]</span>
+        <span class="n">prev_round</span> <span class="o">=</span> <span class="o">-</span><span class="mi">1</span>
+
+        <span class="k">while</span> <span class="nb">len</span><span class="p">(</span><span class="n">this_round</span><span class="p">)</span> <span class="o">-</span> <span class="n">prev_round</span> <span class="o">!=</span> <span class="mi">0</span><span class="p">:</span>
+            <span class="n">prev_round</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="n">this_round</span><span class="p">)</span>
+            <span class="k">for</span> <span class="n">cid</span> <span class="ow">in</span> <span class="n">this_round</span><span class="p">:</span>
+                <span class="n">start_time</span> <span class="o">=</span> <span class="n">time</span><span class="o">.</span><span class="n">time</span><span class="p">()</span>
+                <span class="n">stois</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">parser</span><span class="o">.</span><span class="n">complexes</span><span class="p">[</span><span class="n">cid</span><span class="p">]</span>
+
+                <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">parser</span><span class="o">.</span><span class="n">stoichiometries</span><span class="p">):</span>
+                    <span class="n">pids</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span>
+                        <span class="nb">map</span><span class="p">(</span><span class="k">lambda</span> <span class="n">stoi</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">parser</span><span class="o">.</span><span class="n">stoichiometries</span><span class="p">[</span><span class="n">stoi</span><span class="p">],</span>
+                            <span class="n">stois</span><span class="p">))</span>
+                <span class="k">else</span><span class="p">:</span>
+                    <span class="n">pids</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="nb">map</span><span class="p">(</span><span class="k">lambda</span> <span class="n">comp</span><span class="p">:</span> <span class="p">(</span><span class="n">comp</span><span class="p">,</span> <span class="mi">1</span><span class="p">),</span> <span class="n">stois</span><span class="p">))</span>
+
+                <span class="n">subc_unproc</span> <span class="o">=</span> \
+                    <span class="nb">any</span><span class="p">(</span>
+                        <span class="nb">map</span><span class="p">(</span>
+                            <span class="k">lambda</span> <span class="n">pid</span><span class="p">:</span>
+                                <span class="p">(</span><span class="n">pid</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">parser</span><span class="o">.</span><span class="n">complexes</span> <span class="ow">or</span>
+                                    <span class="n">pid</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">parser</span><span class="o">.</span><span class="n">cvariations</span><span class="p">)</span>
+                            <span class="ow">and</span> <span class="n">pid</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="ow">not</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">rcomplexes</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">source</span><span class="p">]</span>
+                            <span class="ow">and</span> <span class="n">pid</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">no_protein</span><span class="p">,</span>
+                            <span class="n">pids</span>
+                        <span class="p">)</span>
+                    <span class="p">)</span>
+                <span class="k">if</span> <span class="n">subc_unproc</span><span class="p">:</span>
+                    <span class="n">next_round</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">cid</span><span class="p">)</span>
+                    <span class="k">continue</span>
+
+                <span class="n">proteins</span> <span class="o">=</span> \
+                    <span class="nb">list</span><span class="p">(</span>
+                        <span class="nb">map</span><span class="p">(</span>
+                            <span class="k">lambda</span> <span class="n">pid</span><span class="p">:</span>
+                                <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">rproteins</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">source</span><span class="p">][</span><span class="n">pid</span><span class="p">[</span><span class="mi">0</span><span class="p">]],</span>
+                                    <span class="n">pid</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span> <span class="n">pid</span><span class="p">[</span><span class="mi">0</span><span class="p">]),</span>
+                            <span class="nb">filter</span><span class="p">(</span>
+                                <span class="k">lambda</span> <span class="n">pid</span><span class="p">:</span>
+                                    <span class="n">pid</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">rproteins</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">source</span><span class="p">],</span>
+                                <span class="n">pids</span>
+                            <span class="p">)</span>
+                        <span class="p">)</span>
+                    <span class="p">)</span>
+                <span class="n">pfamilies</span> <span class="o">=</span> \
+                    <span class="nb">list</span><span class="p">(</span>
+                        <span class="nb">map</span><span class="p">(</span>
+                            <span class="k">lambda</span> <span class="n">pfid</span><span class="p">:</span>
+                                <span class="nb">list</span><span class="p">(</span>
+                                    <span class="nb">map</span><span class="p">(</span>
+                                        <span class="k">lambda</span> <span class="n">memb</span><span class="p">:</span>
+                                            <span class="p">(</span><span class="n">memb</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">pfid</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span> <span class="n">memb</span><span class="p">[</span><span class="mi">1</span><span class="p">][</span><span class="s1">&#39;pid&#39;</span><span class="p">]),</span>
+                                        <span class="n">iteritems</span><span class="p">(</span>
+                                            <span class="bp">self</span><span class="o">.</span><span class="n">pfamilies</span><span class="p">[</span>
+                                                <span class="bp">self</span><span class="o">.</span><span class="n">rpfamilies</span>
+                                                <span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">source</span><span class="p">][</span><span class="n">pfid</span><span class="p">[</span><span class="mi">0</span><span class="p">]]]</span>
+                                                <span class="o">.</span><span class="n">attrs</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">source</span><span class="p">][</span><span class="n">pfid</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span>
+                                                                    <span class="p">]</span>
+                                        <span class="p">)</span>
+                                    <span class="p">)</span>
+                                <span class="p">),</span>
+                            <span class="nb">filter</span><span class="p">(</span>
+                                <span class="k">lambda</span> <span class="n">pfid</span><span class="p">:</span>
+                                    <span class="n">pfid</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">rpfamilies</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">source</span><span class="p">],</span>
+                                <span class="n">pids</span>
+                            <span class="p">)</span>
+                        <span class="p">)</span>
+                    <span class="p">)</span>
+
+                <span class="n">pfnum</span> <span class="o">=</span> <span class="mi">0</span>
+                <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">pfamilies</span><span class="p">):</span>
+                    <span class="n">pfnum</span> <span class="o">=</span> <span class="n">reduce</span><span class="p">(</span><span class="k">lambda</span> <span class="n">pf1l</span><span class="p">,</span> <span class="n">pf2l</span><span class="p">:</span> <span class="n">pf1l</span> <span class="o">*</span> <span class="n">pf2l</span><span class="p">,</span>
+                                   <span class="nb">map</span><span class="p">(</span><span class="k">lambda</span> <span class="n">pf</span><span class="p">:</span> <span class="nb">len</span><span class="p">(</span><span class="n">pf</span><span class="p">),</span> <span class="n">pfamilies</span><span class="p">))</span>
+
+                <span class="k">if</span> <span class="n">pfnum</span> <span class="o">&gt;</span> <span class="bp">self</span><span class="o">.</span><span class="n">max_complex_combinations</span><span class="p">:</span>
+                    <span class="bp">self</span><span class="o">.</span><span class="n">huge_complexes</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">source</span><span class="p">][</span><span class="n">cid</span><span class="p">]</span> <span class="o">=</span> <span class="n">pfnum</span>
+                    <span class="k">continue</span>
+
+                <span class="n">subcplexs</span> <span class="o">=</span> \
+                    <span class="nb">list</span><span class="p">(</span>
+                        <span class="nb">map</span><span class="p">(</span>
+                            <span class="k">lambda</span> <span class="n">scid</span><span class="p">:</span>
+                                <span class="nb">map</span><span class="p">(</span>
+                                    <span class="k">lambda</span> <span class="n">memb</span><span class="p">:</span>
+                                        <span class="p">(</span><span class="n">memb</span><span class="p">,</span> <span class="n">scid</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span> <span class="n">scid</span><span class="p">[</span><span class="mi">0</span><span class="p">]),</span>
+                                    <span class="bp">self</span><span class="o">.</span><span class="n">rcomplexes</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">source</span><span class="p">][</span><span class="n">scid</span><span class="p">[</span><span class="mi">0</span><span class="p">]]</span>
+                                <span class="p">),</span>
+                            <span class="nb">filter</span><span class="p">(</span>
+                                <span class="k">lambda</span> <span class="n">scid</span><span class="p">:</span>
+                                    <span class="n">scid</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">rcomplexes</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">source</span><span class="p">],</span>
+                                <span class="n">pids</span>
+                            <span class="p">)</span>
+                        <span class="p">)</span>
+                    <span class="p">)</span>
+
+                <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">subcplexs</span><span class="p">):</span>
+
+                    <span class="n">subcplexs</span> <span class="o">=</span> <span class="n">itertools</span><span class="o">.</span><span class="n">product</span><span class="p">(</span><span class="o">*</span><span class="n">subcplexs</span><span class="p">)</span>
+                    <span class="n">subcmembs</span> <span class="o">=</span> <span class="p">[]</span>
+
+                    <span class="k">for</span> <span class="n">this_subcplex</span> <span class="ow">in</span> <span class="n">subcplexs</span><span class="p">:</span>
+                        <span class="k">for</span> <span class="n">sckey</span><span class="p">,</span> <span class="n">scstoi</span><span class="p">,</span> <span class="n">scid</span> <span class="ow">in</span> <span class="n">this_subcplex</span><span class="p">:</span>
+                            <span class="k">if</span> <span class="n">scid</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">no_protein</span><span class="p">:</span>
+                                <span class="n">sc</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">complexes</span><span class="p">[</span><span class="n">sckey</span><span class="p">]</span>
+                                <span class="n">scmembs</span> <span class="o">=</span> <span class="n">sc</span><span class="o">.</span><span class="n">get_stoichiometries</span><span class="p">(</span>
+                                    <span class="bp">self</span><span class="o">.</span><span class="n">source</span><span class="p">,</span> <span class="n">scid</span><span class="p">,</span> <span class="n">with_pids</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
+                                <span class="n">scmembs</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span>
+                                    <span class="nb">map</span><span class="p">(</span><span class="k">lambda</span> <span class="n">p</span><span class="p">:</span> <span class="p">(</span><span class="n">p</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">p</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="o">*</span> <span class="n">scstoi</span><span class="p">,</span> <span class="n">p</span><span class="p">[</span><span class="mi">2</span><span class="p">]),</span>
+                                        <span class="n">scmembs</span><span class="p">))</span>
+                                <span class="n">subcmembs</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">scmembs</span><span class="p">)</span>
+
+                <span class="k">else</span><span class="p">:</span>
+                    <span class="n">subcmembs</span> <span class="o">=</span> <span class="p">[[]]</span>
+
+                <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">subcmembs</span><span class="p">)</span> <span class="o">*</span> <span class="n">pfnum</span> <span class="o">&gt;</span> <span class="bp">self</span><span class="o">.</span><span class="n">max_complex_combinations</span><span class="p">:</span>
+                    <span class="bp">self</span><span class="o">.</span><span class="n">huge_complexes</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">source</span><span class="p">][</span><span class="n">cid</span><span class="p">]</span> <span class="o">=</span> \
+                        <span class="nb">len</span><span class="p">(</span><span class="n">subcmembs</span><span class="p">)</span> <span class="o">*</span> <span class="n">pfnum</span>
+                    <span class="k">continue</span>
+
+                <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">proteins</span><span class="p">)</span> <span class="ow">or</span> <span class="nb">len</span><span class="p">(</span><span class="n">pfamilies</span><span class="p">)</span> <span class="ow">or</span> \
+                        <span class="nb">type</span><span class="p">(</span><span class="n">subcplexs</span><span class="p">)</span> <span class="ow">is</span> <span class="ow">not</span> <span class="nb">list</span><span class="p">:</span>
+
+                    <span class="k">if</span> <span class="ow">not</span> <span class="nb">len</span><span class="p">(</span><span class="n">pfamilies</span><span class="p">):</span>
+                        <span class="n">pfamilies</span> <span class="o">=</span> <span class="p">[[]]</span>
+                    <span class="k">else</span><span class="p">:</span>
+                        <span class="n">pfamilies</span> <span class="o">=</span> <span class="n">itertools</span><span class="o">.</span><span class="n">product</span><span class="p">(</span><span class="o">*</span><span class="n">pfamilies</span><span class="p">)</span>
+
+                    <span class="k">for</span> <span class="n">pfamily</span> <span class="ow">in</span> <span class="n">pfamilies</span><span class="p">:</span>
+
+                        <span class="k">for</span> <span class="n">subc</span> <span class="ow">in</span> <span class="n">subcmembs</span><span class="p">:</span>
+
+                            <span class="n">this_proteins</span> <span class="o">=</span> \
+                                <span class="n">proteins</span> <span class="o">+</span> <span class="nb">list</span><span class="p">(</span><span class="n">pfamily</span><span class="p">)</span> <span class="o">+</span> <span class="nb">list</span><span class="p">(</span><span class="n">subc</span><span class="p">)</span>
+
+                            <span class="n">members</span> <span class="o">=</span> <span class="nb">sorted</span><span class="p">(</span>
+                                <span class="n">common</span><span class="o">.</span><span class="n">unique_list</span><span class="p">(</span>
+                                    <span class="nb">map</span><span class="p">(</span><span class="k">lambda</span> <span class="n">p</span><span class="p">:</span> <span class="n">p</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">this_proteins</span><span class="p">)))</span>
+                            <span class="k">if</span> <span class="ow">not</span> <span class="nb">len</span><span class="p">(</span><span class="n">members</span><span class="p">):</span>
+                                <span class="k">continue</span>
+                            <span class="n">cplex</span> <span class="o">=</span> <span class="n">Complex</span><span class="p">(</span>
+                                <span class="n">members</span><span class="p">,</span> <span class="n">source</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">source</span><span class="p">,</span> <span class="n">parent</span><span class="o">=</span><span class="bp">self</span><span class="p">)</span>
+
+                            <span class="n">members</span> <span class="o">=</span> <span class="nb">tuple</span><span class="p">(</span><span class="n">members</span><span class="p">)</span>
+                            <span class="n">cplex</span><span class="o">.</span><span class="n">attrs</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">source</span><span class="p">][</span><span class="n">cid</span><span class="p">]</span> <span class="o">=</span> <span class="p">{}</span>
+                            <span class="k">for</span> <span class="n">protein</span><span class="p">,</span> <span class="n">stoi</span><span class="p">,</span> <span class="n">pid</span> <span class="ow">in</span> <span class="n">this_proteins</span><span class="p">:</span>
+                                <span class="n">cplex</span><span class="o">.</span><span class="n">attrs</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">source</span><span class="p">][</span><span class="n">cid</span><span class="p">][</span><span class="n">protein</span><span class="p">]</span> <span class="o">=</span> <span class="p">{}</span>
+                                <span class="n">cplex</span><span class="o">.</span><span class="n">attrs</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">source</span><span class="p">][</span><span class="n">cid</span><span class="p">][</span><span class="n">protein</span><span class="p">][</span>
+                                    <span class="s1">&#39;pid&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">pid</span>
+                                <span class="n">cplex</span><span class="o">.</span><span class="n">attrs</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">source</span><span class="p">][</span><span class="n">cid</span><span class="p">][</span><span class="n">protein</span><span class="p">][</span>
+                                    <span class="s1">&#39;stoi&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">stoi</span>
+                            <span class="k">if</span> <span class="n">members</span> <span class="ow">not</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">complexes</span><span class="p">:</span>
+                                <span class="bp">self</span><span class="o">.</span><span class="n">complexes</span><span class="p">[</span><span class="n">members</span><span class="p">]</span> <span class="o">=</span> <span class="n">cplex</span>
+                            <span class="k">else</span><span class="p">:</span>
+                                <span class="bp">self</span><span class="o">.</span><span class="n">complexes</span><span class="p">[</span><span class="n">members</span><span class="p">]</span> <span class="o">+=</span> <span class="n">cplex</span>
+                            <span class="bp">self</span><span class="o">.</span><span class="n">complexes_added</span> <span class="o">+=</span> <span class="mi">1</span>
+                            <span class="k">if</span> <span class="n">cid</span> <span class="ow">not</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">rcomplexes</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">source</span><span class="p">]:</span>
+                                <span class="bp">self</span><span class="o">.</span><span class="n">rcomplexes</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">source</span><span class="p">][</span><span class="n">cid</span><span class="p">]</span> <span class="o">=</span> <span class="nb">set</span><span class="p">([])</span>
+                            <span class="bp">self</span><span class="o">.</span><span class="n">rcomplexes</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">source</span><span class="p">][</span><span class="n">cid</span><span class="p">]</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">members</span><span class="p">)</span>
+
+                <span class="k">else</span><span class="p">:</span>
+                    <span class="n">no_protein</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">cid</span><span class="p">)</span>
+
+                <span class="n">elapsed</span> <span class="o">=</span> <span class="n">time</span><span class="o">.</span><span class="n">time</span><span class="p">()</span> <span class="o">-</span> <span class="n">start_time</span>
+
+                <span class="k">if</span> <span class="n">elapsed</span> <span class="o">&gt;</span> <span class="mi">5</span><span class="p">:</span>
+                    <span class="bp">self</span><span class="o">.</span><span class="n">slow_complexes</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">source</span><span class="p">][</span><span class="n">cid</span><span class="p">]</span> <span class="o">=</span> <span class="n">elapsed</span>
+
+            <span class="n">this_round</span> <span class="o">=</span> <span class="n">next_round</span>
+            <span class="n">next_round</span> <span class="o">=</span> <span class="p">[]</span>
+
+        <span class="k">return</span> <span class="n">this_round</span></div>
+
+
+<div class="viewcode-block" id="PyReact.merge_cvariations">
+<a class="viewcode-back" href="../../../api/pypath.utils.pyreact.PyReact.html#pypath.utils.pyreact.PyReact.merge_cvariations">[docs]</a>
+    <span class="k">def</span> <span class="nf">merge_cvariations</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        This processes those complexes which are in fact a set of complex variations.</span>
+<span class="sd">        As simple complexes also are always extended to complex variations because</span>
+<span class="sd">        they might have not only simple proteins but protein families as members,</span>
+<span class="sd">        here we only add new records to the attributes of already existing complexes.</span>
+<span class="sd">        After ``merge_complexes`` will be called again, to process those simple</span>
+<span class="sd">        complexes which have any of the complex variations processed here among their</span>
+<span class="sd">        subcomplexes.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">cvariations_added</span> <span class="o">=</span> <span class="mi">0</span>
+        <span class="k">for</span> <span class="n">cvid</span><span class="p">,</span> <span class="n">cv</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">parser</span><span class="o">.</span><span class="n">cvariations</span><span class="p">):</span>
+
+            <span class="n">cplexes</span> <span class="o">=</span> \
+                <span class="nb">dict</span><span class="p">(</span>
+                    <span class="nb">map</span><span class="p">(</span>
+                        <span class="k">lambda</span> <span class="n">cid</span><span class="p">:</span>
+                            <span class="p">(</span><span class="n">cid</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">rcomplexes</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">source</span><span class="p">][</span><span class="n">cid</span><span class="p">]),</span>
+                        <span class="nb">filter</span><span class="p">(</span>
+                            <span class="k">lambda</span> <span class="n">cid</span><span class="p">:</span>
+                                <span class="n">cid</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">rcomplexes</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">source</span><span class="p">],</span>
+                            <span class="n">cv</span>
+                        <span class="p">)</span>
+                    <span class="p">)</span>
+                <span class="p">)</span>
+
+            <span class="k">for</span> <span class="n">cid</span><span class="p">,</span> <span class="n">ckeys</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="n">cplexes</span><span class="p">):</span>
+                <span class="k">for</span> <span class="n">ckey</span> <span class="ow">in</span> <span class="n">ckeys</span><span class="p">:</span>
+                    <span class="n">c</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">complexes</span><span class="p">[</span><span class="n">ckey</span><span class="p">]</span>
+                    <span class="k">if</span> <span class="n">cvid</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">c</span><span class="o">.</span><span class="n">attrs</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">source</span><span class="p">]</span> <span class="ow">and</span> <span class="n">cid</span> <span class="ow">in</span> <span class="n">c</span><span class="o">.</span><span class="n">attrs</span><span class="p">[</span>
+                            <span class="bp">self</span><span class="o">.</span><span class="n">source</span><span class="p">]:</span>
+                        <span class="n">c</span><span class="o">.</span><span class="n">attrs</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">source</span><span class="p">][</span><span class="n">cvid</span><span class="p">]</span> <span class="o">=</span> <span class="p">{</span><span class="s1">&#39;children&#39;</span><span class="p">:</span> <span class="nb">set</span><span class="p">([])}</span>
+                    <span class="k">if</span> <span class="n">cid</span> <span class="ow">in</span> <span class="n">c</span><span class="o">.</span><span class="n">attrs</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">source</span><span class="p">]:</span>
+                        <span class="n">c</span><span class="o">.</span><span class="n">attrs</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">source</span><span class="p">][</span><span class="n">cvid</span><span class="p">][</span><span class="s1">&#39;children&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">cid</span><span class="p">)</span>
+                        <span class="n">c</span><span class="o">.</span><span class="n">attrs</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">source</span><span class="p">][</span><span class="n">cvid</span><span class="p">]</span><span class="o">.</span><span class="n">update</span><span class="p">(</span><span class="n">c</span><span class="o">.</span><span class="n">attrs</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">source</span><span class="p">][</span>
+                            <span class="n">cid</span><span class="p">])</span>
+
+            <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">cplexes</span><span class="p">):</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">rcomplexes</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">source</span><span class="p">][</span><span class="n">cvid</span><span class="p">]</span> <span class="o">=</span> \
+                    <span class="n">reduce</span><span class="p">(</span>
+                        <span class="k">lambda</span> <span class="n">c1</span><span class="p">,</span> <span class="n">c2</span><span class="p">:</span>
+                            <span class="n">c1</span> <span class="o">|</span> <span class="n">c2</span><span class="p">,</span>
+                        <span class="n">cplexes</span><span class="o">.</span><span class="n">values</span><span class="p">()</span>
+                <span class="p">)</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">cvariations_added</span> <span class="o">+=</span> <span class="mi">1</span></div>
+
+
+<div class="viewcode-block" id="PyReact.gen_cvariations">
+<a class="viewcode-back" href="../../../api/pypath.utils.pyreact.PyReact.html#pypath.utils.pyreact.PyReact.gen_cvariations">[docs]</a>
+    <span class="k">def</span> <span class="nf">gen_cvariations</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Because one key from the BioPax file might represent more complexes,</span>
+<span class="sd">        *complexvariations* are created to give a way to represent sets of</span>
+<span class="sd">        combinations. These are created for all complexes, even with only</span>
+<span class="sd">        one unambiguous constitution. The keys are the constitutions of</span>
+<span class="sd">        all the combinations listed in alphabetic order, separated by ``|``.</span>
+<span class="sd">        For example, ``A,B,C|A,B,D|A,B,E``.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">rcvariations</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">source</span><span class="p">]</span> <span class="o">=</span> <span class="p">{}</span>
+
+        <span class="k">for</span> <span class="n">cid</span><span class="p">,</span> <span class="n">keys</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">rcomplexes</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">source</span><span class="p">]):</span>
+
+            <span class="n">membs</span> <span class="o">=</span> <span class="nb">map</span><span class="p">(</span><span class="k">lambda</span> <span class="n">key</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">complexes</span><span class="p">[</span><span class="n">key</span><span class="p">],</span> <span class="n">keys</span><span class="p">)</span>
+
+            <span class="n">cvar</span> <span class="o">=</span> <span class="n">ComplexVariations</span><span class="p">(</span><span class="n">membs</span><span class="p">,</span> <span class="n">source</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">source</span><span class="p">,</span> <span class="n">parent</span><span class="o">=</span><span class="bp">self</span><span class="p">)</span>
+            <span class="n">cvar</span><span class="o">.</span><span class="n">attrs</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">source</span><span class="p">][</span><span class="s1">&#39;cids&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="nb">set</span><span class="p">([</span><span class="n">cid</span><span class="p">])</span>
+
+            <span class="n">key</span> <span class="o">=</span> <span class="n">cvar</span><span class="o">.</span><span class="fm">__str__</span><span class="p">()</span>
+            <span class="k">if</span> <span class="n">key</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">cvariations</span><span class="p">:</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">cvariations</span><span class="p">[</span><span class="n">key</span><span class="p">]</span> <span class="o">+=</span> <span class="n">cvar</span>
+            <span class="k">else</span><span class="p">:</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">cvariations</span><span class="p">[</span><span class="n">key</span><span class="p">]</span> <span class="o">=</span> <span class="n">cvar</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">rcvariations</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">source</span><span class="p">][</span><span class="n">cid</span><span class="p">]</span> <span class="o">=</span> <span class="n">key</span></div>
+
+
+    <span class="k">def</span> <span class="nf">merge_reactions</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">reactions_added</span> <span class="o">=</span> <span class="mi">0</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">_merge_reactions</span><span class="p">((</span><span class="s1">&#39;reactions&#39;</span><span class="p">,</span> <span class="s1">&#39;reaction&#39;</span><span class="p">))</span>
+
+    <span class="k">def</span> <span class="nf">merge_cassemblies</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">cassemblies_added</span> <span class="o">=</span> <span class="mi">0</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">_merge_reactions</span><span class="p">((</span><span class="s1">&#39;cassemblies&#39;</span><span class="p">,</span> <span class="s1">&#39;cassembly&#39;</span><span class="p">))</span>
+
+    <span class="k">def</span> <span class="nf">_merge_reactions</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">rclass</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Merges reaction type entities from the active parser.</span>
+<span class="sd">        Here protein families and complex variations are not expanded.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">source</span> <span class="ow">not</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">rreactions</span><span class="p">:</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">rreactions</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">source</span><span class="p">]</span> <span class="o">=</span> <span class="p">{}</span>
+
+        <span class="k">def</span> <span class="nf">get_side</span><span class="p">(</span><span class="n">ids</span><span class="p">):</span>
+            <span class="n">members</span> <span class="o">=</span> <span class="p">[]</span>
+            <span class="n">memb_ids</span> <span class="o">=</span> <span class="p">{}</span>
+            <span class="k">for</span> <span class="n">_id</span> <span class="ow">in</span> <span class="n">ids</span><span class="p">:</span>
+                <span class="k">for</span> <span class="bp">cls</span> <span class="ow">in</span> <span class="p">(</span><span class="s1">&#39;proteins&#39;</span><span class="p">,</span> <span class="s1">&#39;pfamilies&#39;</span><span class="p">,</span> <span class="s1">&#39;cvariations&#39;</span><span class="p">):</span>
+                    <span class="n">r</span> <span class="o">=</span> <span class="nb">getattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">&#39;r</span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="bp">cls</span><span class="p">)[</span><span class="bp">self</span><span class="o">.</span><span class="n">source</span><span class="p">]</span>
+                    <span class="k">if</span> <span class="n">_id</span> <span class="ow">in</span> <span class="n">r</span><span class="p">:</span>
+                        <span class="n">e</span> <span class="o">=</span> <span class="nb">getattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="bp">cls</span><span class="p">)[</span><span class="n">r</span><span class="p">[</span><span class="n">_id</span><span class="p">]]</span>
+                        <span class="n">members</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">e</span><span class="p">)</span>
+                        <span class="n">memb_ids</span><span class="p">[</span><span class="n">e</span><span class="o">.</span><span class="n">key</span><span class="p">()]</span> <span class="o">=</span> <span class="p">{</span><span class="s1">&#39;id&#39;</span><span class="p">:</span> <span class="n">_id</span><span class="p">,</span> <span class="s1">&#39;type&#39;</span><span class="p">:</span> <span class="bp">cls</span><span class="p">}</span>
+            <span class="k">return</span> <span class="n">members</span><span class="p">,</span> <span class="n">memb_ids</span>
+
+        <span class="k">for</span> <span class="n">rid</span><span class="p">,</span> <span class="n">reac</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="nb">getattr</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">parser</span><span class="p">,</span> <span class="n">rclass</span><span class="p">[</span><span class="mi">0</span><span class="p">])):</span>
+
+            <span class="n">left</span><span class="p">,</span> <span class="n">l_ids</span> <span class="o">=</span> <span class="n">get_side</span><span class="p">(</span><span class="n">reac</span><span class="p">[</span><span class="s1">&#39;left&#39;</span><span class="p">])</span>
+            <span class="n">right</span><span class="p">,</span> <span class="n">r_ids</span> <span class="o">=</span> <span class="n">get_side</span><span class="p">(</span><span class="n">reac</span><span class="p">[</span><span class="s1">&#39;right&#39;</span><span class="p">])</span>
+            <span class="n">left_attrs</span> <span class="o">=</span> <span class="p">{</span><span class="bp">self</span><span class="o">.</span><span class="n">source</span><span class="p">:</span> <span class="p">{</span><span class="n">rid</span><span class="p">:</span> <span class="n">l_ids</span><span class="p">}}</span>
+            <span class="n">right_attrs</span> <span class="o">=</span> <span class="p">{</span><span class="bp">self</span><span class="o">.</span><span class="n">source</span><span class="p">:</span> <span class="p">{</span><span class="n">rid</span><span class="p">:</span> <span class="n">r_ids</span><span class="p">}}</span>
+
+            <span class="n">nleft</span> <span class="o">=</span> \
+                <span class="n">reduce</span><span class="p">(</span>
+                    <span class="k">lambda</span> <span class="n">m1</span><span class="p">,</span> <span class="n">m2</span><span class="p">:</span>
+                        <span class="n">m1</span> <span class="o">*</span> <span class="n">m2</span><span class="p">,</span>
+                    <span class="nb">map</span><span class="p">(</span>
+                        <span class="k">lambda</span> <span class="n">m</span><span class="p">:</span>
+                            <span class="nb">len</span><span class="p">(</span><span class="n">m</span><span class="o">.</span><span class="n">members</span><span class="p">)</span> <span class="k">if</span> <span class="nb">hasattr</span><span class="p">(</span><span class="n">m</span><span class="p">,</span> <span class="s1">&#39;members&#39;</span><span class="p">)</span> <span class="k">else</span> <span class="mi">1</span><span class="p">,</span>
+                        <span class="n">left</span>
+                    <span class="p">),</span>
+                    <span class="mi">1</span>
+                <span class="p">)</span>
+            <span class="n">nright</span> <span class="o">=</span> \
+                <span class="n">reduce</span><span class="p">(</span>
+                    <span class="k">lambda</span> <span class="n">m1</span><span class="p">,</span> <span class="n">m2</span><span class="p">:</span>
+                        <span class="n">m1</span> <span class="o">*</span> <span class="n">m2</span><span class="p">,</span>
+                    <span class="nb">map</span><span class="p">(</span>
+                        <span class="k">lambda</span> <span class="n">m</span><span class="p">:</span>
+                            <span class="nb">len</span><span class="p">(</span><span class="n">m</span><span class="o">.</span><span class="n">members</span><span class="p">)</span> <span class="k">if</span> <span class="nb">hasattr</span><span class="p">(</span><span class="n">m</span><span class="p">,</span> <span class="s1">&#39;members&#39;</span><span class="p">)</span> <span class="k">else</span> <span class="mi">1</span><span class="p">,</span>
+                        <span class="n">right</span>
+                    <span class="p">),</span>
+                    <span class="mi">1</span>
+                <span class="p">)</span>
+
+            <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">left</span><span class="p">)</span> <span class="ow">or</span> <span class="nb">len</span><span class="p">(</span><span class="n">right</span><span class="p">):</span>
+                <span class="k">if</span> <span class="n">nleft</span> <span class="o">&lt;=</span> <span class="bp">self</span><span class="o">.</span><span class="n">max_reaction_combinations</span> <span class="ow">and</span> \
+                        <span class="n">nright</span> <span class="o">&lt;=</span> <span class="bp">self</span><span class="o">.</span><span class="n">max_reaction_combinations</span><span class="p">:</span>
+
+                    <span class="n">reaction</span> <span class="o">=</span> <span class="n">Reaction</span><span class="p">(</span>
+                        <span class="n">left</span><span class="p">,</span>
+                        <span class="n">right</span><span class="p">,</span>
+                        <span class="n">left_attrs</span><span class="p">,</span>
+                        <span class="n">right_attrs</span><span class="p">,</span>
+                        <span class="n">source</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">source</span><span class="p">,</span>
+                        <span class="n">parent</span><span class="o">=</span><span class="bp">self</span><span class="p">)</span>
+                    <span class="n">reaction</span><span class="o">.</span><span class="n">attrs</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">source</span><span class="p">][</span><span class="n">rid</span><span class="p">]</span> <span class="o">=</span> <span class="p">{}</span>
+
+                    <span class="n">this_refs</span> <span class="o">=</span> \
+                        <span class="nb">set</span><span class="p">(</span>
+                            <span class="nb">list</span><span class="p">(</span>
+                                <span class="nb">map</span><span class="p">(</span>
+                                    <span class="k">lambda</span> <span class="n">r</span><span class="p">:</span>
+                                        <span class="bp">self</span><span class="o">.</span><span class="n">rrefs</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">source</span><span class="p">][</span><span class="n">r</span><span class="p">],</span>
+                                    <span class="nb">filter</span><span class="p">(</span>
+                                        <span class="k">lambda</span> <span class="n">r</span><span class="p">:</span>
+                                            <span class="n">r</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">parser</span><span class="o">.</span><span class="n">pubrefs</span><span class="p">,</span>
+                                        <span class="n">reac</span><span class="p">[</span><span class="s1">&#39;refs&#39;</span><span class="p">]</span>
+                                    <span class="p">)</span>
+                                <span class="p">)</span>
+                            <span class="p">)</span>
+                        <span class="p">)</span>
+
+                    <span class="n">reaction</span><span class="o">.</span><span class="n">attrs</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">source</span><span class="p">][</span><span class="n">rid</span><span class="p">][</span><span class="s1">&#39;refs&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">this_refs</span>
+                    <span class="n">reaction</span><span class="o">.</span><span class="n">attrs</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">source</span><span class="p">][</span><span class="n">rid</span><span class="p">][</span><span class="s1">&#39;type&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">rclass</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span>
+
+                    <span class="n">key</span> <span class="o">=</span> <span class="n">reaction</span><span class="o">.</span><span class="fm">__str__</span><span class="p">()</span>
+
+                    <span class="k">if</span> <span class="n">key</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">reactions</span><span class="p">:</span>
+                        <span class="c1"># print(key, type(self.reactions[key]), self.reactions[key].__str__(), type(reaction), reaction.__str__())</span>
+                        <span class="bp">self</span><span class="o">.</span><span class="n">reactions</span><span class="p">[</span><span class="n">key</span><span class="p">]</span> <span class="o">+=</span> <span class="n">reaction</span>
+                    <span class="k">else</span><span class="p">:</span>
+                        <span class="bp">self</span><span class="o">.</span><span class="n">reactions</span><span class="p">[</span><span class="n">key</span><span class="p">]</span> <span class="o">=</span> <span class="n">reaction</span>
+
+                    <span class="nb">setattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">&#39;</span><span class="si">%s</span><span class="s1">_added&#39;</span> <span class="o">%</span> <span class="n">rclass</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span>
+                            <span class="nb">getattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">&#39;</span><span class="si">%s</span><span class="s1">_added&#39;</span> <span class="o">%</span> <span class="n">rclass</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span> <span class="o">+</span> <span class="mi">1</span><span class="p">)</span>
+
+                    <span class="bp">self</span><span class="o">.</span><span class="n">rreactions</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">source</span><span class="p">][</span><span class="n">rid</span><span class="p">]</span> <span class="o">=</span> <span class="n">key</span>
+
+                <span class="k">else</span><span class="p">:</span>
+                    <span class="bp">self</span><span class="o">.</span><span class="n">huge_reactions</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">source</span><span class="p">][</span><span class="n">rid</span><span class="p">]</span> <span class="o">=</span> <span class="nb">max</span><span class="p">(</span><span class="n">nleft</span><span class="p">,</span> <span class="n">nright</span><span class="p">)</span>
+
+    <span class="k">def</span> <span class="nf">merge_controls</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">controls_added</span> <span class="o">=</span> <span class="mi">0</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">_merge_controls</span><span class="p">((</span><span class="s1">&#39;controls&#39;</span><span class="p">,</span> <span class="s1">&#39;control&#39;</span><span class="p">))</span>
+
+    <span class="k">def</span> <span class="nf">merge_catalyses</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">catalyses_added</span> <span class="o">=</span> <span class="mi">0</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">_merge_controls</span><span class="p">((</span><span class="s1">&#39;catalyses&#39;</span><span class="p">,</span> <span class="s1">&#39;catalysis&#39;</span><span class="p">))</span>
+
+    <span class="k">def</span> <span class="nf">_merge_controls</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">cclass</span><span class="p">):</span>
+
+        <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">source</span> <span class="ow">not</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">rcontrols</span><span class="p">:</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">rcontrols</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">source</span><span class="p">]</span> <span class="o">=</span> <span class="p">{}</span>
+
+        <span class="k">def</span> <span class="nf">get_party</span><span class="p">(</span><span class="n">_id</span><span class="p">):</span>
+            <span class="k">for</span> <span class="bp">cls</span> <span class="ow">in</span> <span class="p">[</span><span class="s1">&#39;proteins&#39;</span><span class="p">,</span> <span class="s1">&#39;pfamilies&#39;</span><span class="p">,</span> <span class="s1">&#39;cvariations&#39;</span><span class="p">,</span> <span class="s1">&#39;reactions&#39;</span><span class="p">]:</span>
+                <span class="k">if</span> <span class="n">_id</span> <span class="ow">in</span> <span class="nb">getattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">&#39;r</span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="bp">cls</span><span class="p">)[</span><span class="bp">self</span><span class="o">.</span><span class="n">source</span><span class="p">]:</span>
+                    <span class="n">key</span> <span class="o">=</span> <span class="nb">getattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">&#39;r</span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="bp">cls</span><span class="p">)[</span><span class="bp">self</span><span class="o">.</span><span class="n">source</span><span class="p">][</span><span class="n">_id</span><span class="p">]</span>
+                    <span class="n">entity</span> <span class="o">=</span> <span class="nb">getattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="bp">cls</span><span class="p">)[</span><span class="n">key</span><span class="p">]</span>
+                    <span class="k">return</span> <span class="p">(</span><span class="bp">cls</span><span class="p">,</span> <span class="n">key</span><span class="p">,</span> <span class="n">entity</span><span class="p">)</span>
+            <span class="k">return</span> <span class="kc">None</span><span class="p">,</span> <span class="kc">None</span><span class="p">,</span> <span class="kc">None</span>
+
+        <span class="k">for</span> <span class="n">cid</span><span class="p">,</span> <span class="n">ctrl</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="nb">getattr</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">parser</span><span class="p">,</span> <span class="n">cclass</span><span class="p">[</span><span class="mi">0</span><span class="p">])):</span>
+
+            <span class="n">erclass</span><span class="p">,</span> <span class="n">erkey</span><span class="p">,</span> <span class="n">erent</span> <span class="o">=</span> <span class="n">get_party</span><span class="p">(</span><span class="n">ctrl</span><span class="p">[</span><span class="s1">&#39;controller&#39;</span><span class="p">])</span>
+            <span class="n">edclass</span><span class="p">,</span> <span class="n">edkey</span><span class="p">,</span> <span class="n">edent</span> <span class="o">=</span> <span class="n">get_party</span><span class="p">(</span><span class="n">ctrl</span><span class="p">[</span><span class="s1">&#39;controlled&#39;</span><span class="p">])</span>
+
+            <span class="c1"># print(&#39;n = %u, erclass: %s, edclass: %s, er: %s, ed: %s&#39; % (n, erclass, edclass, ctrl[&#39;controller&#39;], ctrl[&#39;controlled&#39;]))</span>
+
+            <span class="k">if</span> <span class="n">erent</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span> <span class="ow">and</span> <span class="n">edent</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
+
+                <span class="n">this_refs</span> <span class="o">=</span> \
+                    <span class="nb">set</span><span class="p">(</span>
+                        <span class="nb">list</span><span class="p">(</span>
+                            <span class="nb">map</span><span class="p">(</span>
+                                <span class="k">lambda</span> <span class="n">r</span><span class="p">:</span>
+                                    <span class="bp">self</span><span class="o">.</span><span class="n">rrefs</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">source</span><span class="p">][</span><span class="n">r</span><span class="p">],</span>
+                                <span class="nb">filter</span><span class="p">(</span>
+                                    <span class="k">lambda</span> <span class="n">r</span><span class="p">:</span>
+                                        <span class="n">r</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">parser</span><span class="o">.</span><span class="n">pubrefs</span><span class="p">,</span>
+                                    <span class="n">ctrl</span><span class="p">[</span><span class="s1">&#39;refs&#39;</span><span class="p">]</span>
+                                <span class="p">)</span>
+                            <span class="p">)</span>
+                        <span class="p">)</span>
+                    <span class="p">)</span> \
+                    <span class="k">if</span> <span class="s1">&#39;refs&#39;</span> <span class="ow">in</span> <span class="n">ctrl</span> <span class="k">else</span> <span class="nb">set</span><span class="p">([])</span>
+
+                <span class="n">control</span> <span class="o">=</span> <span class="n">Control</span><span class="p">(</span>
+                    <span class="n">erent</span><span class="p">,</span> <span class="n">edent</span><span class="p">,</span> <span class="n">source</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">source</span><span class="p">,</span> <span class="n">parent</span><span class="o">=</span><span class="bp">self</span><span class="p">)</span>
+                <span class="n">control</span><span class="o">.</span><span class="n">attrs</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">source</span><span class="p">][</span><span class="n">cid</span><span class="p">]</span> <span class="o">=</span> <span class="p">{}</span>
+                <span class="n">control</span><span class="o">.</span><span class="n">attrs</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">source</span><span class="p">][</span><span class="n">cid</span><span class="p">][</span><span class="s1">&#39;refs&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">this_refs</span>
+                <span class="n">control</span><span class="o">.</span><span class="n">attrs</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">source</span><span class="p">][</span><span class="n">cid</span><span class="p">][</span><span class="s1">&#39;class&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">cclass</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span>
+                <span class="n">control</span><span class="o">.</span><span class="n">attrs</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">source</span><span class="p">][</span><span class="n">cid</span><span class="p">][</span><span class="s1">&#39;type&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">ctrl</span><span class="p">[</span><span class="s1">&#39;type&#39;</span><span class="p">]</span>
+
+                <span class="n">key</span> <span class="o">=</span> <span class="n">control</span><span class="o">.</span><span class="fm">__str__</span><span class="p">()</span>
+
+                <span class="k">if</span> <span class="n">key</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">controls</span><span class="p">:</span>
+                    <span class="bp">self</span><span class="o">.</span><span class="n">controls</span><span class="p">[</span><span class="n">key</span><span class="p">]</span> <span class="o">+=</span> <span class="n">control</span>
+                <span class="k">else</span><span class="p">:</span>
+                    <span class="bp">self</span><span class="o">.</span><span class="n">controls</span><span class="p">[</span><span class="n">key</span><span class="p">]</span> <span class="o">=</span> <span class="n">control</span>
+                <span class="nb">setattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">&#39;</span><span class="si">%s</span><span class="s1">_added&#39;</span> <span class="o">%</span> <span class="n">cclass</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span>
+                        <span class="nb">getattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">&#39;</span><span class="si">%s</span><span class="s1">_added&#39;</span> <span class="o">%</span> <span class="n">cclass</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span> <span class="o">+</span> <span class="mi">1</span><span class="p">)</span>
+
+                <span class="bp">self</span><span class="o">.</span><span class="n">rcontrols</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">source</span><span class="p">][</span><span class="n">cid</span><span class="p">]</span> <span class="o">=</span> <span class="n">key</span>
+
+    <span class="k">def</span> <span class="nf">basic_stats</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">exclude_empty</span><span class="o">=</span><span class="kc">False</span><span class="p">):</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">stats</span> <span class="o">=</span> <span class="p">{</span>
+            <span class="s1">&#39;proteins&#39;</span><span class="p">:</span> <span class="p">{},</span>
+            <span class="s1">&#39;complexes&#39;</span><span class="p">:</span> <span class="p">{},</span>
+            <span class="s1">&#39;mods&#39;</span><span class="p">:</span> <span class="p">{},</span>
+            <span class="s1">&#39;reactions&#39;</span><span class="p">:</span> <span class="p">{},</span>
+            <span class="s1">&#39;controls&#39;</span><span class="p">:</span> <span class="p">{},</span>
+            <span class="s1">&#39;refs&#39;</span><span class="p">:</span> <span class="p">{}</span>
+        <span class="p">}</span>
+        <span class="n">comb</span> <span class="o">=</span> <span class="p">[]</span>
+        <span class="k">for</span> <span class="n">n</span> <span class="ow">in</span> <span class="n">xrange</span><span class="p">(</span><span class="mi">1</span><span class="p">,</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">sources</span><span class="p">)</span> <span class="o">+</span> <span class="mi">1</span><span class="p">):</span>
+            <span class="n">comb</span><span class="o">.</span><span class="n">extend</span><span class="p">(</span><span class="nb">list</span><span class="p">(</span><span class="n">itertools</span><span class="o">.</span><span class="n">combinations</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">sources</span><span class="p">,</span> <span class="n">n</span><span class="p">)))</span>
+        <span class="n">comb</span> <span class="o">=</span> \
+            <span class="nb">list</span><span class="p">(</span>
+                <span class="nb">map</span><span class="p">(</span>
+                    <span class="k">lambda</span> <span class="n">s</span><span class="p">:</span>
+                        <span class="p">(</span><span class="nb">tuple</span><span class="p">(</span><span class="nb">sorted</span><span class="p">(</span><span class="n">s</span><span class="p">)),</span> <span class="nb">set</span><span class="p">(</span><span class="n">s</span><span class="p">)),</span>
+                    <span class="n">comb</span>
+                <span class="p">)</span>
+            <span class="p">)</span>
+        <span class="k">for</span> <span class="n">etyp</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">stats</span><span class="o">.</span><span class="n">keys</span><span class="p">():</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">stats</span><span class="p">[</span><span class="n">etyp</span><span class="p">]</span> <span class="o">=</span> \
+                <span class="nb">dict</span><span class="p">(</span>
+                <span class="nb">map</span><span class="p">(</span>
+                    <span class="k">lambda</span> <span class="n">s</span><span class="p">:</span>
+                        <span class="p">(</span><span class="n">s</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="mi">0</span><span class="p">),</span>
+                    <span class="n">comb</span>
+                <span class="p">)</span>
+            <span class="p">)</span>
+            <span class="k">for</span> <span class="n">e</span> <span class="ow">in</span> <span class="nb">getattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">etyp</span><span class="p">)</span><span class="o">.</span><span class="n">values</span><span class="p">():</span>
+                <span class="k">for</span> <span class="n">c</span> <span class="ow">in</span> <span class="n">comb</span><span class="p">:</span>
+                    <span class="n">_sources</span> <span class="o">=</span> <span class="p">(</span>
+                        <span class="n">e</span><span class="o">.</span><span class="n">evidences</span><span class="o">.</span><span class="n">get_resource_names</span><span class="p">()</span>
+                            <span class="k">if</span> <span class="nb">hasattr</span><span class="p">(</span><span class="n">e</span><span class="p">,</span> <span class="s1">&#39;evidences&#39;</span><span class="p">)</span> <span class="k">else</span>
+                        <span class="n">common</span><span class="o">.</span><span class="n">to_set</span><span class="p">(</span><span class="n">e</span><span class="o">.</span><span class="n">sources</span><span class="p">)</span>
+                    <span class="p">)</span>
+                    <span class="k">if</span> <span class="n">c</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="o">&lt;=</span> <span class="n">_sources</span><span class="p">:</span>
+                        <span class="k">if</span> \
+                            <span class="ow">not</span> <span class="n">exclude_empty</span> \
+                                <span class="ow">or</span> <span class="p">(</span>
+                                    <span class="n">etyp</span> <span class="ow">not</span> <span class="ow">in</span>
+                                    <span class="p">[</span><span class="s1">&#39;complexes&#39;</span><span class="p">,</span> <span class="s1">&#39;reactions&#39;</span><span class="p">,</span> <span class="s1">&#39;controls&#39;</span><span class="p">]</span>
+                                <span class="p">)</span> <span class="ow">or</span> <span class="p">(</span>
+                                    <span class="n">etyp</span> <span class="o">==</span> <span class="s1">&#39;complexes&#39;</span>
+                                    <span class="ow">and</span>
+                                    <span class="nb">len</span><span class="p">(</span><span class="n">e</span><span class="o">.</span><span class="n">members</span><span class="p">)</span> <span class="o">&gt;</span> <span class="mi">1</span>
+                                <span class="p">)</span> <span class="ow">or</span> <span class="p">(</span>
+                                    <span class="n">etyp</span> <span class="o">==</span> <span class="s1">&#39;reactions&#39;</span>
+                                    <span class="ow">and</span>
+                                    <span class="nb">len</span><span class="p">(</span><span class="n">e</span><span class="o">.</span><span class="n">left</span><span class="o">.</span><span class="n">members</span><span class="p">)</span>
+                                    <span class="ow">and</span>
+                                    <span class="nb">len</span><span class="p">(</span><span class="n">e</span><span class="o">.</span><span class="n">right</span><span class="o">.</span><span class="n">members</span><span class="p">)</span>
+                                <span class="p">)</span> <span class="ow">or</span> <span class="p">(</span>
+                                    <span class="n">etyp</span> <span class="o">==</span> <span class="s1">&#39;controls&#39;</span>
+                                    <span class="ow">and</span> <span class="p">(</span>
+                                        <span class="p">(</span>
+                                            <span class="p">(</span>
+                                                <span class="n">e</span><span class="o">.</span><span class="n">controller</span><span class="o">.</span><span class="vm">__class__</span><span class="o">.</span><span class="vm">__name__</span> <span class="o">==</span> <span class="s1">&#39;Complex&#39;</span>
+                                                <span class="ow">or</span>
+                                                <span class="n">e</span><span class="o">.</span><span class="n">controller</span><span class="o">.</span><span class="vm">__class__</span><span class="o">.</span><span class="vm">__name__</span> <span class="o">==</span> <span class="s1">&#39;ProteinFamily&#39;</span>
+                                            <span class="p">)</span> <span class="ow">and</span>
+                                            <span class="nb">len</span><span class="p">(</span><span class="n">e</span><span class="o">.</span><span class="n">controller</span><span class="o">.</span><span class="n">members</span><span class="p">)</span>
+                                        <span class="p">)</span> <span class="ow">or</span> <span class="p">(</span>
+                                            <span class="n">e</span><span class="o">.</span><span class="n">controller</span><span class="o">.</span><span class="vm">__class__</span><span class="o">.</span><span class="vm">__name__</span> <span class="o">==</span>
+                                <span class="s1">&#39;ComplexVariations&#39;</span>
+                                            <span class="ow">and</span>
+                                            <span class="nb">any</span><span class="p">(</span><span class="nb">map</span><span class="p">(</span><span class="k">lambda</span> <span class="n">m</span><span class="p">:</span> <span class="nb">bool</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">m</span><span class="o">.</span><span class="n">members</span><span class="p">)),</span>
+                                                    <span class="n">e</span><span class="o">.</span><span class="n">controller</span><span class="o">.</span><span class="n">members</span><span class="p">))</span>
+                                        <span class="p">)</span>
+                                    <span class="p">)</span> <span class="ow">and</span> <span class="p">(</span>
+                                        <span class="nb">len</span><span class="p">(</span><span class="n">e</span><span class="o">.</span><span class="n">controlled</span><span class="o">.</span><span class="n">left</span><span class="o">.</span><span class="n">members</span><span class="p">)</span>
+                                        <span class="ow">and</span>
+                                        <span class="nb">len</span><span class="p">(</span><span class="n">e</span><span class="o">.</span><span class="n">controlled</span><span class="o">.</span><span class="n">right</span><span class="o">.</span><span class="n">members</span><span class="p">)</span>
+                                    <span class="p">)</span>
+                                <span class="p">):</span>
+
+                            <span class="bp">self</span><span class="o">.</span><span class="n">stats</span><span class="p">[</span><span class="n">etyp</span><span class="p">][</span><span class="n">c</span><span class="p">[</span><span class="mi">0</span><span class="p">]]</span> <span class="o">+=</span> <span class="mi">1</span>
+
+    <span class="k">def</span> <span class="nf">simpson_stats</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+        <span class="k">if</span> <span class="ow">not</span> <span class="nb">hasattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">&#39;stats&#39;</span><span class="p">):</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">basic_stats</span><span class="p">()</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">simpson_sim</span> <span class="o">=</span> <span class="p">{</span>
+            <span class="s1">&#39;proteins&#39;</span><span class="p">:</span> <span class="p">{},</span>
+            <span class="s1">&#39;complexes&#39;</span><span class="p">:</span> <span class="p">{},</span>
+            <span class="s1">&#39;mods&#39;</span><span class="p">:</span> <span class="p">{},</span>
+            <span class="s1">&#39;reactions&#39;</span><span class="p">:</span> <span class="p">{},</span>
+            <span class="s1">&#39;controls&#39;</span><span class="p">:</span> <span class="p">{},</span>
+            <span class="s1">&#39;refs&#39;</span><span class="p">:</span> <span class="p">{}</span>
+        <span class="p">}</span>
+        <span class="k">for</span> <span class="n">etyp</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">simpson_sim</span><span class="o">.</span><span class="n">keys</span><span class="p">():</span>
+            <span class="k">for</span> <span class="n">s1</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">sources</span><span class="p">:</span>
+                <span class="k">for</span> <span class="n">s2</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">sources</span><span class="p">:</span>
+                    <span class="k">if</span> <span class="n">s1</span> <span class="o">!=</span> <span class="n">s2</span><span class="p">:</span>
+                        <span class="bp">self</span><span class="o">.</span><span class="n">simpson_sim</span><span class="p">[</span><span class="n">etyp</span><span class="p">][(</span><span class="n">s1</span><span class="p">,</span> <span class="n">s2</span><span class="p">)]</span> <span class="o">=</span> \
+                            <span class="n">common</span><span class="o">.</span><span class="n">simpson_index_counts</span><span class="p">(</span>
+                                <span class="bp">self</span><span class="o">.</span><span class="n">stats</span><span class="p">[</span><span class="n">etyp</span><span class="p">][</span><span class="nb">tuple</span><span class="p">([</span><span class="n">s1</span><span class="p">])],</span>
+                                <span class="bp">self</span><span class="o">.</span><span class="n">stats</span><span class="p">[</span><span class="n">etyp</span><span class="p">][</span><span class="nb">tuple</span><span class="p">([</span><span class="n">s2</span><span class="p">])],</span>
+                                <span class="bp">self</span><span class="o">.</span><span class="n">stats</span><span class="p">[</span><span class="n">etyp</span><span class="p">][</span><span class="nb">tuple</span><span class="p">(</span><span class="nb">sorted</span><span class="p">([</span><span class="n">s1</span><span class="p">,</span> <span class="n">s2</span><span class="p">]))]</span>
+                        <span class="p">)</span>
+
+    <span class="k">def</span> <span class="nf">resource_graph_edges</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">etyp</span><span class="p">):</span>
+        <span class="k">if</span> <span class="ow">not</span> <span class="nb">hasattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">&#39;simpson_sim&#39;</span><span class="p">):</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">simpson_stats</span><span class="p">()</span>
+        <span class="n">stats</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">stats</span><span class="p">[</span><span class="n">etyp</span><span class="p">]</span>
+        <span class="n">sim</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">simpson_sim</span><span class="p">[</span><span class="n">etyp</span><span class="p">]</span>
+        <span class="n">edges</span> <span class="o">=</span> <span class="p">[]</span>
+        <span class="n">nodes</span> <span class="o">=</span> <span class="p">{}</span>
+        <span class="k">for</span> <span class="n">s1</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">sources</span><span class="p">:</span>
+            <span class="n">nodes</span><span class="p">[</span><span class="n">s1</span><span class="p">]</span> <span class="o">=</span> <span class="n">stats</span><span class="p">[(</span><span class="n">s1</span><span class="p">,</span> <span class="p">)]</span>
+            <span class="k">for</span> <span class="n">s2</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">sources</span><span class="p">:</span>
+                <span class="k">if</span> <span class="n">s1</span> <span class="o">!=</span> <span class="n">s2</span> <span class="ow">and</span> <span class="n">sim</span><span class="p">[(</span><span class="n">s1</span><span class="p">,</span> <span class="n">s2</span><span class="p">)]</span> <span class="o">&gt;</span> <span class="mf">0.0</span><span class="p">:</span>
+                    <span class="n">edges</span><span class="o">.</span><span class="n">append</span><span class="p">([</span><span class="n">s1</span><span class="p">,</span> <span class="n">s2</span><span class="p">,</span> <span class="n">sim</span><span class="p">[(</span><span class="n">s1</span><span class="p">,</span> <span class="n">s2</span><span class="p">)]])</span>
+        <span class="k">return</span> <span class="n">edges</span><span class="p">,</span> <span class="n">nodes</span>
+
+    <span class="k">def</span> <span class="nf">iterate_reactions</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+        <span class="k">pass</span>
+
+    <span class="k">def</span> <span class="nf">load_sequences</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+        <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">seq</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">seq</span> <span class="o">=</span> <span class="n">seq</span><span class="o">.</span><span class="n">swissprot_seq</span><span class="p">(</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">ncbi_tax_id</span><span class="p">,</span> <span class="n">isoforms</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
+
+    <span class="c1"># interaction iterators from here</span>
+
+    <span class="k">def</span> <span class="nf">expand</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">def</span> <span class="nf">add_interactions</span><span class="p">(</span><span class="n">gen</span><span class="p">):</span>
+            <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="n">gen</span><span class="p">:</span>
+                <span class="n">key</span> <span class="o">=</span> <span class="p">(</span><span class="n">i</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">i</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span>
+                <span class="k">if</span> <span class="n">key</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">aggregate</span><span class="p">:</span>
+                    <span class="n">aggregate</span><span class="p">[</span><span class="n">key</span><span class="p">]</span> <span class="o">=</span> <span class="n">i</span>
+                    <span class="n">aggregate</span><span class="p">[</span><span class="n">key</span><span class="p">][</span><span class="mi">2</span><span class="p">]</span> <span class="o">=</span> <span class="nb">set</span><span class="p">([</span><span class="n">i</span><span class="p">[</span><span class="mi">2</span><span class="p">]])</span>
+                <span class="k">else</span><span class="p">:</span>
+                    <span class="n">aggregate</span><span class="p">[</span><span class="n">key</span><span class="p">][</span><span class="mi">4</span><span class="p">]</span><span class="o">.</span><span class="n">update</span><span class="p">(</span><span class="n">i</span><span class="p">[</span><span class="mi">4</span><span class="p">])</span>
+                    <span class="n">aggregate</span><span class="p">[</span><span class="n">key</span><span class="p">][</span><span class="mi">5</span><span class="p">]</span><span class="o">.</span><span class="n">update</span><span class="p">(</span><span class="n">i</span><span class="p">[</span><span class="mi">5</span><span class="p">])</span>
+                    <span class="n">aggregate</span><span class="p">[</span><span class="n">key</span><span class="p">][</span><span class="mi">2</span><span class="p">]</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">i</span><span class="p">[</span><span class="mi">2</span><span class="p">])</span>
+                    <span class="n">aggregate</span><span class="p">[</span><span class="n">key</span><span class="p">][</span><span class="mi">3</span><span class="p">]</span> <span class="o">=</span> <span class="n">aggregate</span><span class="p">[</span><span class="n">key</span><span class="p">][</span><span class="mi">3</span><span class="p">]</span> <span class="ow">or</span> <span class="n">i</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span>
+
+        <span class="n">aggregate</span> <span class="o">=</span> <span class="p">{}</span>
+        <span class="n">add_interactions</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">in_same_component</span><span class="p">())</span>
+        <span class="n">add_interactions</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">co_control</span><span class="p">())</span>
+        <span class="n">add_interactions</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">interacts_with</span><span class="p">())</span>
+        <span class="n">add_interactions</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">state_change</span><span class="p">())</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">interactions</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="n">aggregate</span><span class="o">.</span><span class="n">values</span><span class="p">())</span>
+
+    <span class="k">def</span> <span class="nf">expand_by_source</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">def</span> <span class="nf">add_interactions</span><span class="p">(</span><span class="n">gen</span><span class="p">):</span>
+            <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="n">gen</span><span class="p">:</span>
+                <span class="n">key</span> <span class="o">=</span> <span class="p">(</span><span class="n">i</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">i</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span> <span class="n">i</span><span class="p">[</span><span class="mi">4</span><span class="p">])</span>
+                <span class="k">if</span> <span class="n">key</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">aggregate</span><span class="p">:</span>
+                    <span class="n">aggregate</span><span class="p">[</span><span class="n">key</span><span class="p">]</span> <span class="o">=</span> <span class="n">i</span>
+                    <span class="n">aggregate</span><span class="p">[</span><span class="n">key</span><span class="p">][</span><span class="mi">2</span><span class="p">]</span> <span class="o">=</span> <span class="nb">set</span><span class="p">([</span><span class="n">i</span><span class="p">[</span><span class="mi">2</span><span class="p">]])</span>
+                <span class="k">else</span><span class="p">:</span>
+                    <span class="n">aggregate</span><span class="p">[</span><span class="n">key</span><span class="p">][</span><span class="mi">5</span><span class="p">]</span><span class="o">.</span><span class="n">update</span><span class="p">(</span><span class="n">i</span><span class="p">[</span><span class="mi">5</span><span class="p">])</span>
+                    <span class="n">aggregate</span><span class="p">[</span><span class="n">key</span><span class="p">][</span><span class="mi">2</span><span class="p">]</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">i</span><span class="p">[</span><span class="mi">2</span><span class="p">])</span>
+                    <span class="n">aggregate</span><span class="p">[</span><span class="n">key</span><span class="p">][</span><span class="mi">3</span><span class="p">]</span> <span class="o">=</span> <span class="n">aggregate</span><span class="p">[</span><span class="n">key</span><span class="p">][</span><span class="mi">3</span><span class="p">]</span> <span class="ow">or</span> <span class="n">i</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span>
+
+        <span class="n">aggregate</span> <span class="o">=</span> <span class="p">{}</span>
+        <span class="n">add_interactions</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">in_same_component</span><span class="p">(</span><span class="n">by_source</span><span class="o">=</span><span class="kc">True</span><span class="p">))</span>
+        <span class="n">add_interactions</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">co_control</span><span class="p">(</span><span class="n">by_source</span><span class="o">=</span><span class="kc">True</span><span class="p">))</span>
+        <span class="n">add_interactions</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">interacts_with</span><span class="p">(</span><span class="n">by_source</span><span class="o">=</span><span class="kc">True</span><span class="p">))</span>
+        <span class="n">add_interactions</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">state_change</span><span class="p">(</span><span class="n">by_source</span><span class="o">=</span><span class="kc">True</span><span class="p">))</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">interactions_by_source</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="n">aggregate</span><span class="o">.</span><span class="n">values</span><span class="p">())</span>
+        <span class="n">pickle</span><span class="o">.</span><span class="n">dump</span><span class="p">(</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">interactions_by_source</span><span class="p">,</span>
+            <span class="nb">open</span><span class="p">(</span>
+                <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span>
+                    <span class="bp">self</span><span class="o">.</span><span class="n">cachedir</span><span class="p">,</span>
+                    <span class="s1">&#39;reaction_interactions_by_source.pickle&#39;</span><span class="p">,</span>
+                <span class="p">),</span>
+                <span class="s1">&#39;wb&#39;</span>
+            <span class="p">)</span>
+        <span class="p">)</span>
+
+<div class="viewcode-block" id="PyReact.in_same_component">
+<a class="viewcode-back" href="../../../api/pypath.utils.pyreact.PyReact.html#pypath.utils.pyreact.PyReact.in_same_component">[docs]</a>
+    <span class="k">def</span> <span class="nf">in_same_component</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">by_source</span><span class="o">=</span><span class="kc">False</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        For all complexes connects all members of the complex with each other.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">prg</span> <span class="o">=</span> <span class="n">progress</span><span class="o">.</span><span class="n">Progress</span><span class="p">(</span>
+            <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">complexes</span><span class="p">),</span> <span class="s1">&#39;Expanding `in same component` interactions&#39;</span><span class="p">,</span>
+            <span class="mi">1</span><span class="p">)</span>
+        <span class="n">aggregate_src</span> <span class="o">=</span> <span class="p">{}</span>
+        <span class="k">for</span> <span class="n">c</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">complexes</span><span class="o">.</span><span class="n">values</span><span class="p">():</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">prg</span><span class="o">.</span><span class="n">step</span><span class="p">()</span>
+            <span class="k">for</span> <span class="n">i</span><span class="p">,</span> <span class="n">p1</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">c</span><span class="p">):</span>
+                <span class="k">for</span> <span class="n">p2</span> <span class="ow">in</span> <span class="nb">list</span><span class="p">(</span><span class="n">c</span><span class="p">)[</span><span class="n">i</span> <span class="o">+</span> <span class="mi">1</span><span class="p">:]:</span>
+                    <span class="n">key</span> <span class="o">=</span> <span class="p">(</span><span class="n">p1</span><span class="p">,</span> <span class="n">p2</span><span class="p">)</span>
+                    <span class="k">if</span> <span class="n">key</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">aggregate_src</span><span class="p">:</span>
+                        <span class="n">aggregate_src</span><span class="p">[</span><span class="n">key</span><span class="p">]</span> <span class="o">=</span> <span class="nb">set</span><span class="p">([])</span>
+                    <span class="n">aggregate_src</span><span class="p">[</span><span class="n">key</span><span class="p">]</span><span class="o">.</span><span class="n">update</span><span class="p">(</span><span class="n">c</span><span class="o">.</span><span class="n">sources</span><span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">prg</span><span class="o">.</span><span class="n">terminate</span><span class="p">()</span>
+        <span class="k">for</span> <span class="p">(</span><span class="n">p1</span><span class="p">,</span> <span class="n">p2</span><span class="p">),</span> <span class="n">s</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="n">aggregate_src</span><span class="p">):</span>
+            <span class="k">if</span> <span class="n">by_source</span><span class="p">:</span>
+                <span class="k">for</span> <span class="n">ss</span> <span class="ow">in</span> <span class="n">s</span><span class="p">:</span>
+                    <span class="k">yield</span> <span class="p">[</span><span class="n">p1</span><span class="p">,</span> <span class="n">p2</span><span class="p">,</span> <span class="s1">&#39;IN_SAME_COMPONENT&#39;</span><span class="p">,</span> <span class="kc">False</span><span class="p">,</span> <span class="n">ss</span><span class="p">,</span> <span class="nb">set</span><span class="p">([])]</span>
+            <span class="k">else</span><span class="p">:</span>
+                <span class="k">yield</span> <span class="p">[</span><span class="n">p1</span><span class="p">,</span> <span class="n">p2</span><span class="p">,</span> <span class="s1">&#39;IN_SAME_COMPONENT&#39;</span><span class="p">,</span> <span class="kc">False</span><span class="p">,</span> <span class="n">s</span><span class="p">,</span> <span class="nb">set</span><span class="p">([])]</span></div>
+
+
+    <span class="k">def</span> <span class="nf">protein_get_refs</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">source</span><span class="p">,</span> <span class="n">protein_elem</span><span class="p">):</span>
+        <span class="k">if</span> <span class="n">protein_elem</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">rproteins</span><span class="p">[</span><span class="n">source</span><span class="p">]:</span>
+            <span class="n">protein</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">proteins</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">rproteins</span><span class="p">[</span><span class="n">source</span><span class="p">][</span><span class="n">protein_elem</span><span class="p">]]</span>
+            <span class="n">elem</span> <span class="o">=</span> <span class="n">protein</span><span class="o">.</span><span class="n">attrs</span><span class="p">[</span><span class="n">source</span><span class="p">][</span><span class="s1">&#39;pids&#39;</span><span class="p">][</span><span class="n">protein_elem</span><span class="p">]</span>
+            <span class="k">if</span> <span class="s1">&#39;refs&#39;</span> <span class="ow">in</span> <span class="n">elem</span><span class="p">:</span>
+                <span class="k">return</span> <span class="n">elem</span><span class="p">[</span><span class="s1">&#39;refs&#39;</span><span class="p">]</span>
+        <span class="k">return</span> <span class="nb">set</span><span class="p">([])</span>
+
+    <span class="k">def</span> <span class="nf">complex_get_refs</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">source</span><span class="p">,</span> <span class="n">cplex_elem</span><span class="p">):</span>
+        <span class="n">refs</span> <span class="o">=</span> <span class="nb">set</span><span class="p">([])</span>
+        <span class="k">for</span> <span class="n">cplex_key</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">rcomplexes</span><span class="p">[</span><span class="n">source</span><span class="p">][</span><span class="n">cplex_elem</span><span class="p">]:</span>
+            <span class="n">cplex</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">complexes</span><span class="p">[</span><span class="n">cplex_key</span><span class="p">]</span>
+            <span class="k">if</span> <span class="n">cplex_elem</span> <span class="ow">in</span> <span class="n">cplex</span><span class="o">.</span><span class="n">attrs</span><span class="p">[</span><span class="n">source</span><span class="p">]:</span>
+                <span class="n">elem</span> <span class="o">=</span> <span class="n">cplex</span><span class="o">.</span><span class="n">attrs</span><span class="p">[</span><span class="n">source</span><span class="p">][</span><span class="n">cplex_elem</span><span class="p">]</span>
+                <span class="k">for</span> <span class="n">protein</span><span class="p">,</span> <span class="n">pdata</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="n">elem</span><span class="p">):</span>
+                    <span class="k">if</span> <span class="n">protein</span> <span class="o">!=</span> <span class="s1">&#39;children&#39;</span><span class="p">:</span>
+                        <span class="n">refs</span><span class="o">.</span><span class="n">update</span><span class="p">(</span>
+                            <span class="bp">self</span><span class="o">.</span><span class="n">protein_get_refs</span><span class="p">(</span><span class="n">source</span><span class="p">,</span> <span class="n">elem</span><span class="p">[</span><span class="n">protein</span><span class="p">][</span>
+                                <span class="s1">&#39;pid&#39;</span><span class="p">]))</span>
+        <span class="k">return</span> <span class="n">refs</span>
+
+    <span class="k">def</span> <span class="nf">co_control</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">by_source</span><span class="o">=</span><span class="kc">False</span><span class="p">):</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">prg</span> <span class="o">=</span> <span class="n">progress</span><span class="o">.</span><span class="n">Progress</span><span class="p">(</span>
+            <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">controls</span><span class="p">),</span> <span class="s1">&#39;Expanding `co-control` interactions&#39;</span><span class="p">,</span> <span class="mi">1</span><span class="p">)</span>
+        <span class="n">aggregate_src</span> <span class="o">=</span> <span class="p">{}</span>
+        <span class="n">aggregate_ref</span> <span class="o">=</span> <span class="p">{}</span>
+        <span class="k">for</span> <span class="n">co</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">controls</span><span class="o">.</span><span class="n">values</span><span class="p">():</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">prg</span><span class="o">.</span><span class="n">step</span><span class="p">()</span>
+            <span class="k">if</span> <span class="n">co</span><span class="o">.</span><span class="n">controller</span><span class="o">.</span><span class="n">type</span> <span class="o">!=</span> <span class="s1">&#39;pfamily&#39;</span><span class="p">:</span>
+                <span class="n">proteins</span> <span class="o">=</span> <span class="nb">sorted</span><span class="p">(</span><span class="nb">list</span><span class="p">(</span><span class="n">co</span><span class="o">.</span><span class="n">controller</span><span class="o">.</span><span class="n">proteins</span><span class="p">()))</span>
+                <span class="k">for</span> <span class="n">i</span><span class="p">,</span> <span class="n">p1</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">proteins</span><span class="p">):</span>
+                    <span class="k">for</span> <span class="n">p2</span> <span class="ow">in</span> <span class="n">proteins</span><span class="p">[</span><span class="n">i</span> <span class="o">+</span> <span class="mi">1</span><span class="p">:]:</span>
+                        <span class="n">key</span> <span class="o">=</span> <span class="p">(</span><span class="n">p1</span><span class="p">,</span> <span class="n">p2</span><span class="p">)</span>
+                        <span class="k">if</span> <span class="n">key</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">aggregate_src</span><span class="p">:</span>
+                            <span class="n">aggregate_src</span><span class="p">[</span><span class="n">key</span><span class="p">]</span> <span class="o">=</span> <span class="nb">set</span><span class="p">([])</span>
+                        <span class="n">aggregate_src</span><span class="p">[</span><span class="n">key</span><span class="p">]</span><span class="o">.</span><span class="n">update</span><span class="p">(</span><span class="n">co</span><span class="o">.</span><span class="n">sources</span><span class="p">)</span>
+                        <span class="k">for</span> <span class="n">s</span><span class="p">,</span> <span class="n">codata</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="n">co</span><span class="o">.</span><span class="n">attrs</span><span class="p">):</span>
+                            <span class="k">for</span> <span class="n">coid</span><span class="p">,</span> <span class="n">d</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="n">codata</span><span class="p">):</span>
+                                <span class="k">if</span> <span class="n">by_source</span><span class="p">:</span>
+                                    <span class="k">if</span> <span class="n">s</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">aggregate_ref</span><span class="p">:</span>
+                                        <span class="n">aggregate_ref</span><span class="p">[</span><span class="n">s</span><span class="p">]</span> <span class="o">=</span> <span class="p">{}</span>
+                                    <span class="k">if</span> <span class="n">key</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">aggregate_ref</span><span class="p">[</span><span class="n">s</span><span class="p">]:</span>
+                                        <span class="n">aggregate_ref</span><span class="p">[</span><span class="n">s</span><span class="p">][</span><span class="n">key</span><span class="p">]</span> <span class="o">=</span> <span class="nb">set</span><span class="p">([])</span>
+                                    <span class="n">aggregate_ref</span><span class="p">[</span><span class="n">s</span><span class="p">][</span><span class="n">key</span><span class="p">]</span><span class="o">.</span><span class="n">update</span><span class="p">(</span><span class="n">d</span><span class="p">[</span><span class="s1">&#39;refs&#39;</span><span class="p">])</span>
+                                <span class="k">else</span><span class="p">:</span>
+                                    <span class="k">if</span> <span class="n">key</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">aggregate_ref</span><span class="p">:</span>
+                                        <span class="n">aggregate_ref</span><span class="p">[</span><span class="n">key</span><span class="p">]</span> <span class="o">=</span> <span class="nb">set</span><span class="p">([])</span>
+                                    <span class="n">aggregate_ref</span><span class="p">[</span><span class="n">key</span><span class="p">]</span><span class="o">.</span><span class="n">update</span><span class="p">(</span><span class="n">d</span><span class="p">[</span><span class="s1">&#39;refs&#39;</span><span class="p">])</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">prg</span><span class="o">.</span><span class="n">terminate</span><span class="p">()</span>
+        <span class="k">for</span> <span class="p">(</span><span class="n">p1</span><span class="p">,</span> <span class="n">p2</span><span class="p">),</span> <span class="n">s</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="n">aggregate_src</span><span class="p">):</span>
+            <span class="k">if</span> <span class="n">by_source</span><span class="p">:</span>
+                <span class="k">for</span> <span class="n">ss</span> <span class="ow">in</span> <span class="n">s</span><span class="p">:</span>
+                    <span class="k">yield</span> <span class="p">[</span>
+                        <span class="n">p1</span><span class="p">,</span> <span class="n">p2</span><span class="p">,</span> <span class="s1">&#39;CO_CONTROL&#39;</span><span class="p">,</span> <span class="kc">False</span><span class="p">,</span> <span class="n">ss</span><span class="p">,</span> <span class="n">aggregate_ref</span><span class="p">[</span><span class="n">ss</span><span class="p">][(</span>
+                            <span class="n">p1</span><span class="p">,</span> <span class="n">p2</span><span class="p">)]</span>
+                    <span class="p">]</span>
+            <span class="k">else</span><span class="p">:</span>
+                <span class="k">yield</span> <span class="p">[</span><span class="n">p1</span><span class="p">,</span> <span class="n">p2</span><span class="p">,</span> <span class="s1">&#39;CO_CONTROL&#39;</span><span class="p">,</span> <span class="kc">False</span><span class="p">,</span> <span class="n">s</span><span class="p">,</span> <span class="n">aggregate_ref</span><span class="p">[(</span><span class="n">p1</span><span class="p">,</span> <span class="n">p2</span><span class="p">)]]</span>
+
+    <span class="k">def</span> <span class="nf">interacts_with</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">by_source</span><span class="o">=</span><span class="kc">False</span><span class="p">):</span>
+        <span class="n">aggregate_src</span> <span class="o">=</span> <span class="p">{}</span>
+        <span class="n">aggregate_ref</span> <span class="o">=</span> <span class="p">{}</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">prg</span> <span class="o">=</span> <span class="n">progress</span><span class="o">.</span><span class="n">Progress</span><span class="p">(</span>
+            <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">reactions</span><span class="p">),</span> <span class="s1">&#39;Expanding `interacts with` interactions&#39;</span><span class="p">,</span> <span class="mi">1</span><span class="p">)</span>
+        <span class="k">for</span> <span class="n">rs</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">reactions</span><span class="o">.</span><span class="n">values</span><span class="p">():</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">prg</span><span class="o">.</span><span class="n">step</span><span class="p">()</span>
+            <span class="n">isrc</span> <span class="o">=</span> \
+                <span class="nb">set</span><span class="p">(</span><span class="nb">list</span><span class="p">(</span>
+                    <span class="nb">map</span><span class="p">(</span>
+                        <span class="k">lambda</span> <span class="n">s</span><span class="p">:</span>
+                            <span class="n">s</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span>
+                        <span class="nb">filter</span><span class="p">(</span>
+                            <span class="k">lambda</span> <span class="n">s</span><span class="p">:</span>
+                                <span class="nb">len</span><span class="p">(</span>
+                                    <span class="nb">list</span><span class="p">(</span>
+                                        <span class="nb">filter</span><span class="p">(</span>
+                                            <span class="k">lambda</span> <span class="n">rr</span><span class="p">:</span>
+                                                <span class="n">rr</span><span class="p">[</span><span class="s1">&#39;type&#39;</span><span class="p">]</span> <span class="o">==</span> <span class="s1">&#39;interaction&#39;</span><span class="p">,</span>
+                                            <span class="n">s</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">values</span><span class="p">()</span>
+                                        <span class="p">)</span>
+                                    <span class="p">)</span>
+                                <span class="p">),</span>
+                            <span class="n">iteritems</span><span class="p">(</span><span class="n">rs</span><span class="o">.</span><span class="n">attrs</span><span class="p">)</span>
+                        <span class="p">)</span>
+                    <span class="p">)</span>
+                <span class="p">))</span>
+            <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">isrc</span><span class="p">):</span>
+                <span class="k">for</span> <span class="n">r</span> <span class="ow">in</span> <span class="n">rs</span><span class="o">.</span><span class="n">expand</span><span class="p">():</span>
+                    <span class="k">for</span> <span class="n">i</span><span class="p">,</span> <span class="n">p1</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">r</span><span class="o">.</span><span class="n">left</span><span class="o">.</span><span class="n">proteins</span><span class="p">()):</span>
+                        <span class="k">for</span> <span class="n">p2</span> <span class="ow">in</span> <span class="nb">list</span><span class="p">(</span><span class="n">r</span><span class="o">.</span><span class="n">right</span><span class="o">.</span><span class="n">proteins</span><span class="p">())[</span><span class="n">i</span> <span class="o">+</span> <span class="mi">1</span><span class="p">:]:</span>
+                            <span class="n">key</span> <span class="o">=</span> <span class="nb">tuple</span><span class="p">(</span><span class="nb">sorted</span><span class="p">([</span><span class="n">p1</span><span class="p">,</span> <span class="n">p2</span><span class="p">]))</span>
+                            <span class="k">if</span> <span class="n">key</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">aggregate_src</span><span class="p">:</span>
+                                <span class="n">aggregate_src</span><span class="p">[</span><span class="n">key</span><span class="p">]</span> <span class="o">=</span> <span class="nb">set</span><span class="p">([])</span>
+                            <span class="n">aggregate_src</span><span class="p">[</span><span class="n">key</span><span class="p">]</span><span class="o">.</span><span class="n">update</span><span class="p">(</span><span class="n">isrc</span><span class="p">)</span>
+                            <span class="k">for</span> <span class="n">s</span> <span class="ow">in</span> <span class="n">isrc</span><span class="p">:</span>
+                                <span class="k">if</span> <span class="n">by_source</span><span class="p">:</span>
+                                    <span class="k">if</span> <span class="n">s</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">aggregate_ref</span><span class="p">:</span>
+                                        <span class="n">aggregate_ref</span><span class="p">[</span><span class="n">s</span><span class="p">]</span> <span class="o">=</span> <span class="p">{}</span>
+                                    <span class="k">if</span> <span class="n">key</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">aggregate_ref</span><span class="p">[</span><span class="n">s</span><span class="p">]:</span>
+                                        <span class="n">aggregate_ref</span><span class="p">[</span><span class="n">s</span><span class="p">][</span><span class="n">key</span><span class="p">]</span> <span class="o">=</span> <span class="nb">set</span><span class="p">([])</span>
+                                    <span class="k">for</span> <span class="n">rid</span><span class="p">,</span> <span class="n">rdata</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="n">r</span><span class="o">.</span><span class="n">attrs</span><span class="p">[</span><span class="n">s</span><span class="p">]):</span>
+                                        <span class="k">if</span> <span class="n">rdata</span><span class="p">[</span><span class="s1">&#39;type&#39;</span><span class="p">]</span> <span class="o">==</span> <span class="s1">&#39;interaction&#39;</span><span class="p">:</span>
+                                            <span class="n">aggregate_ref</span><span class="p">[</span><span class="n">s</span><span class="p">][</span><span class="n">key</span><span class="p">]</span><span class="o">.</span><span class="n">update</span><span class="p">(</span><span class="n">rdata</span><span class="p">[</span>
+                                                <span class="s1">&#39;refs&#39;</span><span class="p">])</span>
+                                <span class="k">else</span><span class="p">:</span>
+                                    <span class="k">if</span> <span class="n">key</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">aggregate_ref</span><span class="p">:</span>
+                                        <span class="n">aggregate_ref</span><span class="p">[</span><span class="n">key</span><span class="p">]</span> <span class="o">=</span> <span class="nb">set</span><span class="p">([])</span>
+                                    <span class="k">for</span> <span class="n">rid</span><span class="p">,</span> <span class="n">rdata</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="n">r</span><span class="o">.</span><span class="n">attrs</span><span class="p">[</span><span class="n">s</span><span class="p">]):</span>
+                                        <span class="k">if</span> <span class="n">rdata</span><span class="p">[</span><span class="s1">&#39;type&#39;</span><span class="p">]</span> <span class="o">==</span> <span class="s1">&#39;interaction&#39;</span><span class="p">:</span>
+                                            <span class="n">aggregate_ref</span><span class="p">[</span><span class="n">key</span><span class="p">]</span><span class="o">.</span><span class="n">update</span><span class="p">(</span><span class="n">rdata</span><span class="p">[</span>
+                                                <span class="s1">&#39;refs&#39;</span><span class="p">])</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">prg</span><span class="o">.</span><span class="n">terminate</span><span class="p">()</span>
+        <span class="k">for</span> <span class="p">(</span><span class="n">p1</span><span class="p">,</span> <span class="n">p2</span><span class="p">),</span> <span class="n">s</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="n">aggregate_src</span><span class="p">):</span>
+            <span class="k">if</span> <span class="n">by_source</span><span class="p">:</span>
+                <span class="k">for</span> <span class="n">ss</span> <span class="ow">in</span> <span class="n">s</span><span class="p">:</span>
+                    <span class="k">yield</span> <span class="p">[</span>
+                        <span class="n">p1</span><span class="p">,</span> <span class="n">p2</span><span class="p">,</span> <span class="s1">&#39;INTERACTS_WITH&#39;</span><span class="p">,</span> <span class="kc">False</span><span class="p">,</span> <span class="n">ss</span><span class="p">,</span> <span class="n">aggregate_ref</span><span class="p">[</span><span class="n">ss</span><span class="p">][</span>
+                            <span class="p">(</span><span class="n">p1</span><span class="p">,</span> <span class="n">p2</span><span class="p">)]</span>
+                    <span class="p">]</span>
+            <span class="k">else</span><span class="p">:</span>
+                <span class="k">yield</span> <span class="p">[</span>
+                    <span class="n">p1</span><span class="p">,</span> <span class="n">p2</span><span class="p">,</span> <span class="s1">&#39;INTERACTS_WITH&#39;</span><span class="p">,</span> <span class="kc">False</span><span class="p">,</span> <span class="n">s</span><span class="p">,</span> <span class="n">aggregate_ref</span><span class="p">[(</span><span class="n">p1</span><span class="p">,</span> <span class="n">p2</span><span class="p">)]</span>
+                <span class="p">]</span>
+
+    <span class="k">def</span> <span class="nf">state_change</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">by_source</span><span class="o">=</span><span class="kc">False</span><span class="p">):</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">prg</span> <span class="o">=</span> <span class="n">progress</span><span class="o">.</span><span class="n">Progress</span><span class="p">(</span>
+            <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">controls</span><span class="p">),</span> <span class="s1">&#39;Expanding `state change` interactions&#39;</span><span class="p">,</span> <span class="mi">1</span><span class="p">)</span>
+        <span class="n">aggregate_src</span> <span class="o">=</span> <span class="p">{}</span>
+        <span class="n">aggregate_ref</span> <span class="o">=</span> <span class="p">{}</span>
+        <span class="k">for</span> <span class="n">cos</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">controls</span><span class="o">.</span><span class="n">values</span><span class="p">():</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">prg</span><span class="o">.</span><span class="n">step</span><span class="p">()</span>
+            <span class="k">for</span> <span class="n">co</span> <span class="ow">in</span> <span class="n">cos</span><span class="o">.</span><span class="n">expand</span><span class="p">():</span>
+                <span class="n">er_proteins</span> <span class="o">=</span> <span class="n">co</span><span class="o">.</span><span class="n">controller</span><span class="o">.</span><span class="n">proteins</span><span class="p">()</span>
+                <span class="k">for</span> <span class="n">s</span> <span class="ow">in</span> <span class="n">co</span><span class="o">.</span><span class="n">sources</span><span class="p">:</span>
+                    <span class="n">ldiff</span><span class="p">,</span> <span class="n">rdiff</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">reaction_mod_diff</span><span class="p">(</span><span class="n">s</span><span class="p">,</span> <span class="n">co</span><span class="o">.</span><span class="n">controlled</span><span class="p">)</span>
+                    <span class="k">for</span> <span class="n">p2</span> <span class="ow">in</span> <span class="n">ldiff</span><span class="o">.</span><span class="n">keys</span><span class="p">():</span>
+                        <span class="k">if</span> <span class="n">ldiff</span><span class="p">[</span><span class="n">p2</span><span class="p">]</span> <span class="o">!=</span> <span class="n">rdiff</span><span class="p">[</span><span class="n">p2</span><span class="p">]:</span>
+                            <span class="k">for</span> <span class="n">p1</span> <span class="ow">in</span> <span class="n">er_proteins</span><span class="p">:</span>
+                                <span class="n">key</span> <span class="o">=</span> <span class="p">(</span><span class="n">p1</span><span class="p">,</span> <span class="n">p2</span><span class="p">)</span>
+                                <span class="k">if</span> <span class="n">key</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">aggregate_src</span><span class="p">:</span>
+                                    <span class="n">aggregate_src</span><span class="p">[</span><span class="n">key</span><span class="p">]</span> <span class="o">=</span> <span class="nb">set</span><span class="p">([])</span>
+                                <span class="n">aggregate_src</span><span class="p">[</span><span class="n">key</span><span class="p">]</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">s</span><span class="p">)</span>
+                                <span class="n">refs</span> <span class="o">=</span> <span class="nb">set</span><span class="p">([])</span>
+                                <span class="k">for</span> <span class="n">rid</span><span class="p">,</span> <span class="n">rdata</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span>
+                                        <span class="n">co</span><span class="o">.</span><span class="n">controlled</span><span class="o">.</span><span class="n">attrs</span><span class="p">[</span><span class="n">s</span><span class="p">]):</span>
+                                    <span class="n">refs</span><span class="o">.</span><span class="n">update</span><span class="p">(</span><span class="n">rdata</span><span class="p">[</span><span class="s1">&#39;refs&#39;</span><span class="p">])</span>
+                                <span class="k">if</span> <span class="n">by_source</span><span class="p">:</span>
+                                    <span class="k">if</span> <span class="n">s</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">aggregate_ref</span><span class="p">:</span>
+                                        <span class="n">aggregate_ref</span><span class="p">[</span><span class="n">s</span><span class="p">]</span> <span class="o">=</span> <span class="p">{}</span>
+                                    <span class="k">if</span> <span class="n">key</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">aggregate_ref</span><span class="p">[</span><span class="n">s</span><span class="p">]:</span>
+                                        <span class="n">aggregate_ref</span><span class="p">[</span><span class="n">s</span><span class="p">][</span><span class="n">key</span><span class="p">]</span> <span class="o">=</span> <span class="nb">set</span><span class="p">([])</span>
+                                    <span class="n">aggregate_ref</span><span class="p">[</span><span class="n">s</span><span class="p">][</span><span class="n">key</span><span class="p">]</span><span class="o">.</span><span class="n">update</span><span class="p">(</span><span class="n">refs</span><span class="p">)</span>
+                                <span class="k">else</span><span class="p">:</span>
+                                    <span class="k">if</span> <span class="n">key</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">aggregate_ref</span><span class="p">:</span>
+                                        <span class="n">aggregate_ref</span><span class="p">[</span><span class="n">key</span><span class="p">]</span> <span class="o">=</span> <span class="nb">set</span><span class="p">([])</span>
+                                    <span class="n">aggregate_ref</span><span class="p">[</span><span class="n">key</span><span class="p">]</span><span class="o">.</span><span class="n">update</span><span class="p">(</span><span class="n">refs</span><span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">prg</span><span class="o">.</span><span class="n">terminate</span><span class="p">()</span>
+        <span class="k">for</span> <span class="p">(</span><span class="n">p1</span><span class="p">,</span> <span class="n">p2</span><span class="p">),</span> <span class="n">s</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="n">aggregate_src</span><span class="p">):</span>
+            <span class="k">if</span> <span class="n">by_source</span><span class="p">:</span>
+                <span class="k">for</span> <span class="n">ss</span> <span class="ow">in</span> <span class="n">s</span><span class="p">:</span>
+                    <span class="k">yield</span> <span class="p">[</span>
+                        <span class="n">p1</span><span class="p">,</span> <span class="n">p2</span><span class="p">,</span> <span class="s1">&#39;STATE_CHANGE&#39;</span><span class="p">,</span> <span class="kc">True</span><span class="p">,</span> <span class="n">ss</span><span class="p">,</span> <span class="n">aggregate_ref</span><span class="p">[</span><span class="n">ss</span><span class="p">][(</span>
+                            <span class="n">p1</span><span class="p">,</span> <span class="n">p2</span><span class="p">)]</span>
+                    <span class="p">]</span>
+            <span class="k">else</span><span class="p">:</span>
+                <span class="k">yield</span> <span class="p">[</span>
+                    <span class="n">p1</span><span class="p">,</span> <span class="n">p2</span><span class="p">,</span> <span class="s1">&#39;STATE_CHANGE&#39;</span><span class="p">,</span> <span class="kc">True</span><span class="p">,</span> <span class="n">s</span><span class="p">,</span> <span class="n">aggregate_ref</span><span class="p">[(</span><span class="n">p1</span><span class="p">,</span> <span class="n">p2</span><span class="p">)]</span>
+                <span class="p">]</span>
+
+    <span class="k">def</span> <span class="nf">reaction_mod_diff</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">source</span><span class="p">,</span> <span class="n">reaction</span><span class="p">,</span> <span class="n">by_rid</span><span class="o">=</span><span class="kc">False</span><span class="p">):</span>
+        <span class="n">left</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">reaction_side_get_mods</span><span class="p">(</span><span class="n">source</span><span class="p">,</span> <span class="n">reaction</span><span class="o">.</span><span class="n">left</span><span class="p">,</span> <span class="n">by_rid</span><span class="p">)</span>
+        <span class="n">right</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">reaction_side_get_mods</span><span class="p">(</span><span class="n">source</span><span class="p">,</span> <span class="n">reaction</span><span class="o">.</span><span class="n">right</span><span class="p">,</span> <span class="n">by_rid</span><span class="p">)</span>
+        <span class="k">return</span> <span class="n">common</span><span class="o">.</span><span class="n">dict_diff</span><span class="p">(</span><span class="n">left</span><span class="p">,</span> <span class="n">right</span><span class="p">)</span>
+
+    <span class="k">def</span> <span class="nf">reaction_side_get_mods</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">source</span><span class="p">,</span> <span class="n">rside</span><span class="p">,</span> <span class="n">by_rid</span><span class="o">=</span><span class="kc">False</span><span class="p">):</span>
+        <span class="n">mods</span> <span class="o">=</span> <span class="p">{}</span>
+        <span class="k">for</span> <span class="n">rid</span><span class="p">,</span> <span class="n">rd</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="n">rside</span><span class="o">.</span><span class="n">attrs</span><span class="p">[</span><span class="n">source</span><span class="p">]):</span>
+            <span class="k">for</span> <span class="n">ent_key</span><span class="p">,</span> <span class="n">data</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="n">rd</span><span class="p">):</span>
+                <span class="k">if</span> <span class="n">data</span><span class="p">[</span><span class="s1">&#39;type&#39;</span><span class="p">]</span> <span class="o">==</span> <span class="s1">&#39;proteins&#39;</span><span class="p">:</span>
+                    <span class="n">next_mods</span> <span class="o">=</span> <span class="p">{</span>
+                        <span class="n">ent_key</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">protein_get_mods</span><span class="p">(</span><span class="n">source</span><span class="p">,</span> <span class="n">data</span><span class="p">[</span><span class="s1">&#39;id&#39;</span><span class="p">])</span>
+                    <span class="p">}</span>
+                <span class="k">elif</span> <span class="n">data</span><span class="p">[</span><span class="s1">&#39;type&#39;</span><span class="p">]</span> <span class="o">==</span> <span class="s1">&#39;complexes&#39;</span><span class="p">:</span>
+                    <span class="n">next_mods</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">complex_get_mods</span><span class="p">(</span><span class="n">source</span><span class="p">,</span> <span class="n">data</span><span class="p">[</span><span class="s1">&#39;id&#39;</span><span class="p">])</span>
+                <span class="k">if</span> <span class="n">by_rid</span><span class="p">:</span>
+                    <span class="k">if</span> <span class="n">rid</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">mods</span><span class="p">:</span>
+                        <span class="n">mods</span><span class="p">[</span><span class="n">rid</span><span class="p">]</span> <span class="o">=</span> <span class="p">{}</span>
+                    <span class="n">common</span><span class="o">.</span><span class="n">merge_dicts</span><span class="p">(</span><span class="n">mods</span><span class="p">[</span><span class="n">rid</span><span class="p">],</span> <span class="p">{</span><span class="n">rid</span><span class="p">:</span> <span class="n">next_mods</span><span class="p">})</span>
+                <span class="k">else</span><span class="p">:</span>
+                    <span class="n">common</span><span class="o">.</span><span class="n">merge_dicts</span><span class="p">(</span><span class="n">mods</span><span class="p">,</span> <span class="n">next_mods</span><span class="p">)</span>
+        <span class="k">return</span> <span class="n">mods</span>
+
+    <span class="k">def</span> <span class="nf">protein_get_mods</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">source</span><span class="p">,</span> <span class="n">protein_elem</span><span class="p">):</span>
+        <span class="k">if</span> <span class="n">protein_elem</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">rproteins</span><span class="p">[</span><span class="n">source</span><span class="p">]:</span>
+            <span class="n">protein</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">proteins</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">rproteins</span><span class="p">[</span><span class="n">source</span><span class="p">][</span><span class="n">protein_elem</span><span class="p">]]</span>
+            <span class="n">elem</span> <span class="o">=</span> <span class="n">protein</span><span class="o">.</span><span class="n">attrs</span><span class="p">[</span><span class="n">source</span><span class="p">][</span><span class="s1">&#39;pids&#39;</span><span class="p">][</span><span class="n">protein_elem</span><span class="p">]</span>
+            <span class="k">if</span> <span class="s1">&#39;mods&#39;</span> <span class="ow">in</span> <span class="n">elem</span><span class="p">:</span>
+                <span class="k">return</span> <span class="n">elem</span><span class="p">[</span><span class="s1">&#39;mods&#39;</span><span class="p">]</span>
+        <span class="k">return</span> <span class="nb">set</span><span class="p">([])</span>
+
+    <span class="k">def</span> <span class="nf">complex_get_mods</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">source</span><span class="p">,</span> <span class="n">complex_elem</span><span class="p">):</span>
+        <span class="n">mods</span> <span class="o">=</span> <span class="p">{}</span>
+        <span class="k">for</span> <span class="n">cplex_key</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">rcomplexes</span><span class="p">[</span><span class="n">source</span><span class="p">][</span><span class="n">complex_elem</span><span class="p">]:</span>
+            <span class="n">cplex</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">complexes</span><span class="p">[</span><span class="n">cplex_key</span><span class="p">]</span>
+            <span class="k">if</span> <span class="n">complex_elem</span> <span class="ow">in</span> <span class="n">cplex</span><span class="o">.</span><span class="n">attrs</span><span class="p">[</span><span class="n">source</span><span class="p">]:</span>
+                <span class="n">elem</span> <span class="o">=</span> <span class="n">cplex</span><span class="o">.</span><span class="n">attrs</span><span class="p">[</span><span class="n">source</span><span class="p">][</span><span class="n">complex_elem</span><span class="p">]</span>
+                <span class="k">for</span> <span class="n">protein</span><span class="p">,</span> <span class="n">pdata</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="n">elem</span><span class="p">):</span>
+                    <span class="k">if</span> <span class="n">protein</span> <span class="o">!=</span> <span class="s1">&#39;children&#39;</span><span class="p">:</span>
+                        <span class="n">mods</span><span class="p">[</span><span class="n">protein</span><span class="p">]</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">protein_get_mods</span><span class="p">(</span>
+                            <span class="n">source</span><span class="p">,</span> <span class="n">elem</span><span class="p">[</span><span class="n">protein</span><span class="p">][</span><span class="s1">&#39;pid&#39;</span><span class="p">])</span>
+        <span class="k">return</span> <span class="n">mods</span></div>
+
+
+<span class="c1"># ## ## ## ## ## ##</span>
+
+
+<div class="viewcode-block" id="ReactionSide">
+<a class="viewcode-back" href="../../../api/pypath.utils.pyreact.ReactionSide.html#pypath.utils.pyreact.ReactionSide">[docs]</a>
+<span class="k">class</span> <span class="nc">ReactionSide</span><span class="p">(</span><span class="n">AttributeHandler</span><span class="p">):</span>
+<div class="viewcode-block" id="ReactionSide.__init__">
+<a class="viewcode-back" href="../../../api/pypath.utils.pyreact.ReactionSide.html#pypath.utils.pyreact.ReactionSide.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">members</span><span class="p">,</span> <span class="n">source</span><span class="o">=</span><span class="p">[],</span> <span class="n">parent</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
+        <span class="nb">super</span><span class="p">(</span><span class="n">ReactionSide</span><span class="p">,</span> <span class="bp">self</span><span class="p">)</span><span class="o">.</span><span class="fm">__init__</span><span class="p">()</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">members</span> <span class="o">=</span> <span class="nb">sorted</span><span class="p">(</span><span class="n">members</span><span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">sources</span> <span class="o">=</span> <span class="nb">set</span><span class="p">([])</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">attrs</span> <span class="o">=</span> <span class="p">{}</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">add_source</span><span class="p">(</span><span class="n">source</span><span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">parent</span> <span class="o">=</span> <span class="n">parent</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">is_expanded</span> <span class="o">=</span> <span class="kc">False</span></div>
+
+
+    <span class="k">def</span> <span class="nf">reload</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+        <span class="n">modname</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="vm">__class__</span><span class="o">.</span><span class="vm">__module__</span>
+        <span class="n">mod</span> <span class="o">=</span> <span class="nb">__import__</span><span class="p">(</span><span class="n">modname</span><span class="p">,</span> <span class="n">fromlist</span><span class="o">=</span><span class="p">[</span><span class="n">modname</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;.&#39;</span><span class="p">)[</span><span class="mi">0</span><span class="p">]])</span>
+        <span class="n">imp</span><span class="o">.</span><span class="n">reload</span><span class="p">(</span><span class="n">mod</span><span class="p">)</span>
+        <span class="n">new</span> <span class="o">=</span> <span class="nb">getattr</span><span class="p">(</span><span class="n">mod</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="vm">__class__</span><span class="o">.</span><span class="vm">__name__</span><span class="p">)</span>
+        <span class="nb">setattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">&#39;__class__&#39;</span><span class="p">,</span> <span class="n">new</span><span class="p">)</span>
+        <span class="nb">map</span><span class="p">(</span><span class="k">lambda</span> <span class="n">m</span><span class="p">:</span> <span class="n">m</span><span class="o">.</span><span class="n">reload</span><span class="p">(),</span> <span class="bp">self</span><span class="o">.</span><span class="n">members</span><span class="p">)</span>
+
+    <span class="k">def</span> <span class="fm">__hash__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+        <span class="k">return</span> <span class="nb">hash</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="fm">__str__</span><span class="p">())</span>
+
+    <span class="k">def</span> <span class="fm">__repr__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="fm">__str__</span><span class="p">()</span>
+
+    <span class="k">def</span> <span class="fm">__str__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+        <span class="k">return</span> <span class="s1">&#39;ReactionSide: (</span><span class="si">%s</span><span class="s1">)&#39;</span> <span class="o">%</span> \
+            <span class="p">(</span><span class="s1">&#39;+&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="nb">map</span><span class="p">(</span><span class="k">lambda</span> <span class="n">m</span><span class="p">:</span> <span class="n">m</span><span class="o">.</span><span class="fm">__str__</span><span class="p">(),</span> <span class="bp">self</span><span class="o">.</span><span class="n">members</span><span class="p">)))</span>
+
+    <span class="k">def</span> <span class="nf">equality</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">one</span><span class="p">,</span> <span class="n">two</span><span class="p">):</span>
+        <span class="k">return</span> \
+            <span class="nb">all</span><span class="p">(</span>
+                <span class="nb">map</span><span class="p">(</span>
+                    <span class="k">lambda</span> <span class="n">m1</span><span class="p">:</span>
+                    <span class="nb">any</span><span class="p">(</span>
+                        <span class="nb">map</span><span class="p">(</span>
+                            <span class="k">lambda</span> <span class="n">m2</span><span class="p">:</span>
+                                <span class="ow">not</span> <span class="n">m1</span><span class="o">.</span><span class="n">set</span><span class="o">.</span><span class="n">isdisjoint</span><span class="p">(</span><span class="n">m2</span><span class="o">.</span><span class="n">set</span><span class="p">),</span>
+                            <span class="nb">filter</span><span class="p">(</span>
+                                <span class="k">lambda</span> <span class="n">m2</span><span class="p">:</span>
+                                    <span class="n">m2</span><span class="o">.</span><span class="n">type</span> <span class="o">==</span> <span class="n">m1</span><span class="o">.</span><span class="n">type</span><span class="p">,</span>
+                                <span class="n">two</span><span class="o">.</span><span class="n">members</span>
+                            <span class="p">)</span>
+                        <span class="p">)</span>
+                    <span class="p">),</span>
+                    <span class="nb">filter</span><span class="p">(</span>
+                        <span class="k">lambda</span> <span class="n">m1</span><span class="p">:</span>
+                        <span class="n">m1</span><span class="o">.</span><span class="n">type</span> <span class="o">==</span> <span class="s1">&#39;cvariations&#39;</span> <span class="ow">or</span> <span class="n">m1</span><span class="o">.</span><span class="n">type</span> <span class="o">==</span> <span class="s1">&#39;pfamily&#39;</span><span class="p">,</span>
+                        <span class="n">one</span><span class="o">.</span><span class="n">members</span>
+                    <span class="p">)</span>
+                <span class="p">)</span>
+            <span class="p">)</span> <span class="ow">and</span> \
+            <span class="nb">all</span><span class="p">(</span>
+                <span class="nb">map</span><span class="p">(</span>
+                    <span class="k">lambda</span> <span class="n">m1</span><span class="p">:</span>
+                    <span class="n">m1</span> <span class="ow">in</span> <span class="n">two</span><span class="o">.</span><span class="n">set</span><span class="p">,</span>
+                    <span class="nb">filter</span><span class="p">(</span>
+                        <span class="k">lambda</span> <span class="n">m1</span><span class="p">:</span>
+                        <span class="n">m1</span><span class="o">.</span><span class="n">type</span> <span class="o">==</span> <span class="s1">&#39;protein&#39;</span><span class="p">,</span>
+                        <span class="n">one</span><span class="o">.</span><span class="n">members</span>
+                    <span class="p">)</span>
+                <span class="p">)</span>
+            <span class="p">)</span>
+
+    <span class="k">def</span> <span class="fm">__eq__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">other</span><span class="p">):</span>
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">equality</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">other</span><span class="p">)</span> <span class="ow">and</span> <span class="bp">self</span><span class="o">.</span><span class="n">equality</span><span class="p">(</span><span class="n">other</span><span class="p">,</span> <span class="bp">self</span><span class="p">)</span>
+
+    <span class="k">def</span> <span class="fm">__iter__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+        <span class="k">for</span> <span class="n">m</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">members</span><span class="p">:</span>
+            <span class="k">yield</span> <span class="n">m</span>
+
+<div class="viewcode-block" id="ReactionSide.expand">
+<a class="viewcode-back" href="../../../api/pypath.utils.pyreact.ReactionSide.html#pypath.utils.pyreact.ReactionSide.expand">[docs]</a>
+    <span class="k">def</span> <span class="nf">expand</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Expands the ``ReactionSide`` by iterating over all combinations</span>
+<span class="sd">        of all ``ComplexVariation`` and ``ProteinFamily`` members, so</span>
+<span class="sd">        yields ``ReactionSide`` objects with only ``Protein`` and ``Complex``</span>
+<span class="sd">        members. Yields tuple, because ``ReactionSide`` is initialized in</span>
+<span class="sd">        ``Reaction``, the tuple is suitable to serve as ``members`` and</span>
+<span class="sd">        ``attrs``.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+        <span class="c1"># collecting protein attributes</span>
+        <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">is_expanded</span><span class="p">:</span>
+            <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="p">[</span><span class="mi">1</span><span class="p">]:</span>
+                <span class="k">yield</span> <span class="bp">self</span><span class="o">.</span><span class="n">members</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">attrs</span>
+        <span class="k">else</span><span class="p">:</span>
+            <span class="k">try</span><span class="p">:</span>
+                <span class="n">pattrs</span> <span class="o">=</span> \
+                    <span class="nb">dict</span><span class="p">(</span>
+                        <span class="nb">map</span><span class="p">(</span>
+                            <span class="k">lambda</span> <span class="n">m</span><span class="p">:</span>
+                                <span class="p">(</span>
+                                    <span class="n">m</span><span class="o">.</span><span class="n">id</span><span class="p">,</span>
+                                    <span class="nb">dict</span><span class="p">(</span>
+                                        <span class="nb">map</span><span class="p">(</span>
+                                            <span class="k">lambda</span> <span class="n">d1</span><span class="p">:</span>
+                                                <span class="p">(</span>
+                                                    <span class="n">d1</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span>
+                                                    <span class="nb">dict</span><span class="p">(</span>
+                                                        <span class="nb">map</span><span class="p">(</span>
+                                                            <span class="k">lambda</span> <span class="n">d2</span><span class="p">:</span>
+                                                                <span class="p">(</span><span class="n">d2</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">d2</span><span class="p">[</span>
+                                                                 <span class="mi">1</span><span class="p">][</span><span class="n">m</span><span class="o">.</span><span class="n">id</span><span class="p">]),</span>
+                                                            <span class="n">iteritems</span><span class="p">(</span><span class="n">d1</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span>
+                                                        <span class="p">)</span>
+                                                    <span class="p">)</span>
+                                                <span class="p">),</span>
+                                            <span class="n">iteritems</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">attrs</span><span class="p">)</span>
+                                        <span class="p">)</span>
+                                    <span class="p">)</span>
+                                <span class="p">),</span>
+                            <span class="nb">filter</span><span class="p">(</span>
+                                <span class="k">lambda</span> <span class="n">m</span><span class="p">:</span>
+                                    <span class="n">m</span><span class="o">.</span><span class="n">type</span> <span class="o">==</span> <span class="s1">&#39;protein&#39;</span><span class="p">,</span>
+                                <span class="bp">self</span><span class="o">.</span><span class="n">members</span>
+                            <span class="p">)</span>
+                        <span class="p">)</span>
+                    <span class="p">)</span>
+            <span class="k">except</span><span class="p">:</span>
+                <span class="nb">print</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">attrs</span><span class="p">)</span>
+            <span class="k">for</span> <span class="n">c</span> <span class="ow">in</span> \
+                    <span class="n">itertools</span><span class="o">.</span><span class="n">product</span><span class="p">(</span>
+                        <span class="o">*</span><span class="nb">list</span><span class="p">(</span>
+                            <span class="nb">map</span><span class="p">(</span>
+                                <span class="k">lambda</span> <span class="n">m</span><span class="p">:</span>
+                                    <span class="nb">list</span><span class="p">(</span>
+                                        <span class="nb">zip</span><span class="p">(</span>
+                                            <span class="n">m</span><span class="o">.</span><span class="n">itermembers</span><span class="p">(),</span>
+                                            <span class="p">[</span><span class="n">m</span><span class="o">.</span><span class="n">key</span><span class="p">()]</span> <span class="o">*</span> <span class="p">(</span>
+                                                <span class="nb">len</span><span class="p">(</span><span class="n">m</span><span class="o">.</span><span class="n">members</span><span class="p">)</span>
+                                                <span class="k">if</span> <span class="nb">hasattr</span><span class="p">(</span><span class="n">m</span><span class="p">,</span> <span class="s1">&#39;members&#39;</span><span class="p">)</span>
+                                                <span class="k">else</span> <span class="mi">1</span><span class="p">)</span>
+                                        <span class="p">)</span>
+                                    <span class="p">),</span>
+                                <span class="bp">self</span><span class="o">.</span><span class="n">members</span>
+                            <span class="p">)</span>
+                        <span class="p">)</span>
+                    <span class="p">):</span>
+
+                <span class="n">attrs</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">(</span><span class="nb">map</span><span class="p">(</span><span class="k">lambda</span> <span class="n">s</span><span class="p">:</span> <span class="p">(</span><span class="n">s</span><span class="p">,</span>
+                                            <span class="nb">dict</span><span class="p">(</span><span class="nb">map</span><span class="p">(</span><span class="k">lambda</span> <span class="n">rid</span><span class="p">:</span> <span class="p">(</span><span class="n">rid</span><span class="p">,</span> <span class="p">{}),</span>
+                                                     <span class="bp">self</span><span class="o">.</span><span class="n">attrs</span><span class="p">[</span><span class="n">s</span><span class="p">]</span><span class="o">.</span><span class="n">keys</span><span class="p">()))),</span> <span class="bp">self</span><span class="o">.</span><span class="n">sources</span><span class="p">))</span>
+                <span class="n">members</span> <span class="o">=</span> <span class="p">[]</span>
+                <span class="k">for</span> <span class="p">((</span><span class="n">m</span><span class="p">,</span> <span class="n">a</span><span class="p">),</span> <span class="n">k</span><span class="p">)</span> <span class="ow">in</span> <span class="n">c</span><span class="p">:</span>
+                    <span class="n">members</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">m</span><span class="p">)</span>
+                    <span class="k">if</span> <span class="n">m</span><span class="o">.</span><span class="n">type</span> <span class="o">==</span> <span class="s1">&#39;protein&#39;</span><span class="p">:</span>
+                        <span class="c1"># if it was a protein, we just copy</span>
+                        <span class="k">if</span> <span class="n">m</span><span class="o">.</span><span class="n">id</span> <span class="ow">in</span> <span class="n">pattrs</span><span class="p">:</span>
+                            <span class="k">for</span> <span class="n">s</span><span class="p">,</span> <span class="n">d1</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="n">pattrs</span><span class="p">[</span><span class="n">m</span><span class="o">.</span><span class="n">id</span><span class="p">]):</span>
+                                <span class="k">for</span> <span class="n">rid</span><span class="p">,</span> <span class="n">d2</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="n">d1</span><span class="p">):</span>
+                                    <span class="n">attrs</span><span class="p">[</span><span class="n">s</span><span class="p">][</span><span class="n">rid</span><span class="p">][</span><span class="n">m</span><span class="o">.</span><span class="n">id</span><span class="p">]</span> <span class="o">=</span> <span class="n">d2</span>
+                        <span class="c1"># if it is from a protein family</span>
+                        <span class="k">else</span><span class="p">:</span>
+                            <span class="c1"># for each resource</span>
+                            <span class="k">for</span> <span class="n">s</span><span class="p">,</span> <span class="n">r</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="n">attrs</span><span class="p">):</span>
+                                <span class="c1"># for each original reaction id</span>
+                                <span class="k">for</span> <span class="n">rid</span><span class="p">,</span> <span class="n">d</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">attrs</span><span class="p">[</span><span class="n">s</span><span class="p">]):</span>
+                                    <span class="c1"># the key of the new entity (here: str,</span>
+                                    <span class="c1"># uniprot id)</span>
+                                    <span class="k">if</span> <span class="n">k</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">attrs</span><span class="p">[</span><span class="n">s</span><span class="p">][</span><span class="n">rid</span><span class="p">]:</span>
+                                        <span class="n">attrs</span><span class="p">[</span><span class="n">s</span><span class="p">][</span><span class="n">rid</span><span class="p">][</span><span class="n">m</span><span class="o">.</span><span class="n">key</span><span class="p">()]</span> <span class="o">=</span> <span class="p">(</span>
+                                            <span class="c1"># the type is obvious, the id is from the `a` dict supplied</span>
+                                            <span class="c1"># by the ProteinFamily object, and we look up the id belonging</span>
+                                            <span class="c1"># to the key of the original entity</span>
+                                            <span class="p">{</span>
+                                                <span class="s1">&#39;type&#39;</span><span class="p">:</span> <span class="s1">&#39;proteins&#39;</span><span class="p">,</span>
+                                                <span class="s1">&#39;id&#39;</span><span class="p">:</span> <span class="n">a</span><span class="p">[</span><span class="n">s</span><span class="p">][</span><span class="bp">self</span><span class="o">.</span><span class="n">attrs</span><span class="p">[</span><span class="n">s</span><span class="p">][</span><span class="n">rid</span><span class="p">][</span>
+                                                    <span class="n">k</span><span class="p">][</span><span class="s1">&#39;id&#39;</span><span class="p">]]</span>
+                                            <span class="p">})</span>
+                    <span class="c1"># if it is a complex from a complex variations</span>
+                    <span class="k">elif</span> <span class="n">m</span><span class="o">.</span><span class="n">type</span> <span class="o">==</span> <span class="s1">&#39;complex&#39;</span><span class="p">:</span>
+                        <span class="k">for</span> <span class="n">s</span><span class="p">,</span> <span class="n">r</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="n">attrs</span><span class="p">):</span>
+                            <span class="k">for</span> <span class="n">rid</span><span class="p">,</span> <span class="n">d</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="n">r</span><span class="p">):</span>
+                                <span class="k">if</span> <span class="n">k</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">attrs</span><span class="p">[</span><span class="n">s</span><span class="p">][</span><span class="n">rid</span><span class="p">]:</span>
+                                    <span class="n">cid</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">attrs</span><span class="p">[</span><span class="n">s</span><span class="p">][</span><span class="n">rid</span><span class="p">][</span><span class="n">k</span><span class="p">][</span><span class="s1">&#39;id&#39;</span><span class="p">]</span>
+                                    <span class="n">attrs</span><span class="p">[</span><span class="n">s</span><span class="p">][</span><span class="n">rid</span><span class="p">][</span><span class="n">m</span><span class="o">.</span><span class="n">key</span><span class="p">()]</span> <span class="o">=</span> \
+                                        <span class="p">{</span><span class="s1">&#39;type&#39;</span><span class="p">:</span> <span class="s1">&#39;complexes&#39;</span><span class="p">,</span> <span class="s1">&#39;id&#39;</span><span class="p">:</span> <span class="n">cid</span><span class="p">}</span>
+                <span class="k">yield</span> <span class="n">members</span><span class="p">,</span> <span class="n">attrs</span></div>
+
+
+    <span class="k">def</span> <span class="nf">proteins</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+        <span class="k">return</span> \
+            <span class="n">reduce</span><span class="p">(</span>
+                <span class="k">lambda</span> <span class="n">m1</span><span class="p">,</span> <span class="n">m2</span><span class="p">:</span>
+                    <span class="n">m1</span> <span class="o">|</span> <span class="n">m2</span><span class="o">.</span><span class="n">proteins</span><span class="p">(),</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">members</span><span class="p">,</span>
+                <span class="nb">set</span><span class="p">([])</span>
+            <span class="p">)</span>
+
+    <span class="k">def</span> <span class="fm">__ror__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">other</span><span class="p">):</span>
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">proteins</span><span class="p">()</span> <span class="o">|</span> <span class="n">other</span>
+
+    <span class="k">def</span> <span class="fm">__rand__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">other</span><span class="p">):</span>
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">proteins</span><span class="p">()</span> <span class="o">&amp;</span> <span class="n">other</span>
+
+    <span class="k">def</span> <span class="fm">__rsub__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">other</span><span class="p">):</span>
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">proteins</span><span class="p">()</span> <span class="o">-</span> <span class="n">other</span></div>
+
+
+
+<div class="viewcode-block" id="Reaction">
+<a class="viewcode-back" href="../../../api/pypath.utils.pyreact.Reaction.html#pypath.utils.pyreact.Reaction">[docs]</a>
+<span class="k">class</span> <span class="nc">Reaction</span><span class="p">(</span><span class="n">AttributeHandler</span><span class="p">):</span>
+<div class="viewcode-block" id="Reaction.__init__">
+<a class="viewcode-back" href="../../../api/pypath.utils.pyreact.Reaction.html#pypath.utils.pyreact.Reaction.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span>
+                 <span class="n">left</span><span class="p">,</span>
+                 <span class="n">right</span><span class="p">,</span>
+                 <span class="n">left_attrs</span><span class="p">,</span>
+                 <span class="n">right_attrs</span><span class="p">,</span>
+                 <span class="n">source</span><span class="o">=</span><span class="p">[],</span>
+                 <span class="n">parent</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
+        <span class="nb">super</span><span class="p">(</span><span class="n">Reaction</span><span class="p">,</span> <span class="bp">self</span><span class="p">)</span><span class="o">.</span><span class="fm">__init__</span><span class="p">()</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">parent</span> <span class="o">=</span> <span class="n">parent</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">left</span> <span class="o">=</span> <span class="n">ReactionSide</span><span class="p">(</span><span class="n">left</span><span class="p">,</span> <span class="n">source</span><span class="p">,</span> <span class="n">parent</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">parent</span><span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">right</span> <span class="o">=</span> <span class="n">ReactionSide</span><span class="p">(</span><span class="n">right</span><span class="p">,</span> <span class="n">source</span><span class="p">,</span> <span class="n">parent</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">parent</span><span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">left</span><span class="o">.</span><span class="n">merge_attrs</span><span class="p">(</span><span class="n">left_attrs</span><span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">right</span><span class="o">.</span><span class="n">merge_attrs</span><span class="p">(</span><span class="n">right_attrs</span><span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">attrs</span> <span class="o">=</span> <span class="p">{}</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">sources</span> <span class="o">=</span> <span class="nb">set</span><span class="p">([])</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">add_source</span><span class="p">(</span><span class="n">source</span><span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">is_expanded</span> <span class="o">=</span> <span class="kc">False</span></div>
+
+
+    <span class="k">def</span> <span class="nf">reload</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+        <span class="n">modname</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="vm">__class__</span><span class="o">.</span><span class="vm">__module__</span>
+        <span class="n">mod</span> <span class="o">=</span> <span class="nb">__import__</span><span class="p">(</span><span class="n">modname</span><span class="p">,</span> <span class="n">fromlist</span><span class="o">=</span><span class="p">[</span><span class="n">modname</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;.&#39;</span><span class="p">)[</span><span class="mi">0</span><span class="p">]])</span>
+        <span class="n">imp</span><span class="o">.</span><span class="n">reload</span><span class="p">(</span><span class="n">mod</span><span class="p">)</span>
+        <span class="n">new</span> <span class="o">=</span> <span class="nb">getattr</span><span class="p">(</span><span class="n">mod</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="vm">__class__</span><span class="o">.</span><span class="vm">__name__</span><span class="p">)</span>
+        <span class="nb">setattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">&#39;__class__&#39;</span><span class="p">,</span> <span class="n">new</span><span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">left</span><span class="o">.</span><span class="n">reload</span><span class="p">()</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">right</span><span class="o">.</span><span class="n">reload</span><span class="p">()</span>
+
+    <span class="k">def</span> <span class="fm">__repr__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="fm">__str__</span><span class="p">()</span>
+
+    <span class="k">def</span> <span class="fm">__str__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+        <span class="k">return</span> <span class="s1">&#39;Reaction: LEFT(</span><span class="si">%s</span><span class="s1">) --&gt; RIGHT(</span><span class="si">%s</span><span class="s1">)&#39;</span> <span class="o">%</span> \
+            <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">left</span><span class="o">.</span><span class="fm">__str__</span><span class="p">(),</span> <span class="bp">self</span><span class="o">.</span><span class="n">right</span><span class="o">.</span><span class="fm">__str__</span><span class="p">())</span>
+
+    <span class="k">def</span> <span class="fm">__hash__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+        <span class="k">return</span> <span class="nb">hash</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="fm">__str__</span><span class="p">())</span>
+
+    <span class="k">def</span> <span class="fm">__eq__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">other</span><span class="p">):</span>
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">left</span> <span class="o">==</span> <span class="n">other</span><span class="o">.</span><span class="n">left</span> <span class="ow">and</span> <span class="bp">self</span><span class="o">.</span><span class="n">right</span> <span class="o">==</span> <span class="n">other</span><span class="o">.</span><span class="n">right</span>
+
+    <span class="k">def</span> <span class="fm">__iadd__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">other</span><span class="p">):</span>
+        <span class="bp">self</span> <span class="o">=</span> <span class="n">AttributeHandler</span><span class="o">.</span><span class="fm">__iadd__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">other</span><span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">left</span> <span class="o">+=</span> <span class="n">other</span><span class="o">.</span><span class="n">left</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">right</span> <span class="o">+=</span> <span class="n">other</span><span class="o">.</span><span class="n">right</span>
+        <span class="k">return</span> <span class="bp">self</span>
+
+    <span class="k">def</span> <span class="nf">expand</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+        <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">is_expanded</span><span class="p">:</span>
+            <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="p">[</span><span class="mi">1</span><span class="p">]:</span>
+                <span class="k">yield</span> <span class="bp">self</span>
+        <span class="k">else</span><span class="p">:</span>
+            <span class="n">expanded</span> <span class="o">=</span> <span class="p">[]</span>
+
+            <span class="n">lAllProteins</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">left</span><span class="o">.</span><span class="n">proteins</span><span class="p">()</span>
+            <span class="n">rAllProteins</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">right</span><span class="o">.</span><span class="n">proteins</span><span class="p">()</span>
+            <span class="n">diffAllProteins</span> <span class="o">=</span> <span class="n">rAllProteins</span> <span class="o">^</span> <span class="n">lAllProteins</span>
+
+            <span class="n">lefts</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">left</span><span class="o">.</span><span class="n">expand</span><span class="p">())</span>
+            <span class="n">rights</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">right</span><span class="o">.</span><span class="n">expand</span><span class="p">())</span>
+
+            <span class="n">diffs</span> <span class="o">=</span> <span class="nb">set</span><span class="p">([])</span>
+            <span class="k">for</span> <span class="n">t</span> <span class="ow">in</span> <span class="n">xrange</span><span class="p">(</span><span class="mi">2</span><span class="p">):</span>
+                <span class="k">if</span> <span class="n">t</span> <span class="o">==</span> <span class="mi">1</span><span class="p">:</span>
+                    <span class="k">try</span><span class="p">:</span>
+                        <span class="n">minDiff</span> <span class="o">=</span> <span class="nb">min</span><span class="p">(</span><span class="n">diffs</span><span class="p">)</span>
+                    <span class="k">except</span> <span class="ne">ValueError</span><span class="p">:</span>
+                        <span class="nb">print</span><span class="p">(</span><span class="s1">&#39;Empty sequence error: </span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="bp">self</span><span class="o">.</span><span class="fm">__str__</span><span class="p">())</span>
+                <span class="k">for</span> <span class="n">left</span> <span class="ow">in</span> <span class="n">lefts</span><span class="p">:</span>
+                    <span class="k">for</span> <span class="n">right</span> <span class="ow">in</span> <span class="n">rights</span><span class="p">:</span>
+                        <span class="n">r</span> <span class="o">=</span> <span class="n">Reaction</span><span class="p">(</span>
+                            <span class="n">left</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span>
+                            <span class="n">right</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span>
+                            <span class="n">left</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span>
+                            <span class="n">right</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span>
+                            <span class="n">source</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">sources</span><span class="p">,</span>
+                            <span class="n">parent</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">parent</span><span class="p">)</span>
+                        <span class="n">lProteins</span> <span class="o">=</span> <span class="n">r</span><span class="o">.</span><span class="n">left</span><span class="o">.</span><span class="n">proteins</span><span class="p">()</span>
+                        <span class="n">rProteins</span> <span class="o">=</span> <span class="n">r</span><span class="o">.</span><span class="n">right</span><span class="o">.</span><span class="n">proteins</span><span class="p">()</span>
+                        <span class="n">diffProteins</span> <span class="o">=</span> <span class="n">lProteins</span> <span class="o">^</span> <span class="n">rProteins</span>
+
+                        <span class="n">diff</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="n">diffProteins</span><span class="p">)</span>
+                        <span class="n">diffs</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">diff</span><span class="p">)</span>
+                        <span class="k">if</span> <span class="n">t</span> <span class="o">==</span> <span class="mi">1</span> <span class="ow">and</span> <span class="n">diff</span> <span class="o">==</span> <span class="n">minDiff</span><span class="p">:</span>
+                            <span class="n">r</span><span class="o">.</span><span class="n">left</span><span class="o">.</span><span class="n">is_expanded</span> <span class="o">=</span> <span class="kc">True</span>
+                            <span class="n">r</span><span class="o">.</span><span class="n">right</span><span class="o">.</span><span class="n">is_expanded</span> <span class="o">=</span> <span class="kc">True</span>
+                            <span class="n">r</span><span class="o">.</span><span class="n">is_expanded</span> <span class="o">=</span> <span class="kc">True</span>
+                            <span class="n">r</span><span class="o">.</span><span class="n">attrs</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">attrs</span>
+
+                            <span class="k">yield</span> <span class="n">r</span>
+
+                        <span class="k">else</span><span class="p">:</span>
+                            <span class="k">del</span> <span class="n">r</span></div>
+
+            <span class="c1">#</span>
+            <span class="c1">#minDiff = min(map(lambda e: e[1], expanded))</span>
+
+            <span class="c1"># for r, d in expanded:</span>
+            <span class="c1"># if d == minDiff:</span>
+            <span class="c1"># yield r</span>
+
+
+<div class="viewcode-block" id="Control">
+<a class="viewcode-back" href="../../../api/pypath.utils.pyreact.Control.html#pypath.utils.pyreact.Control">[docs]</a>
+<span class="k">class</span> <span class="nc">Control</span><span class="p">(</span><span class="n">AttributeHandler</span><span class="p">):</span>
+<div class="viewcode-block" id="Control.__init__">
+<a class="viewcode-back" href="../../../api/pypath.utils.pyreact.Control.html#pypath.utils.pyreact.Control.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">er</span><span class="p">,</span> <span class="n">ed</span><span class="p">,</span> <span class="n">source</span><span class="o">=</span><span class="p">[],</span> <span class="n">parent</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
+        <span class="nb">super</span><span class="p">(</span><span class="n">Control</span><span class="p">,</span> <span class="bp">self</span><span class="p">)</span><span class="o">.</span><span class="fm">__init__</span><span class="p">()</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">controller</span> <span class="o">=</span> <span class="n">er</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">controlled</span> <span class="o">=</span> <span class="n">ed</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">attrs</span> <span class="o">=</span> <span class="p">{}</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">sources</span> <span class="o">=</span> <span class="nb">set</span><span class="p">([])</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">add_source</span><span class="p">(</span><span class="n">source</span><span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">parent</span> <span class="o">=</span> <span class="n">parent</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">is_expanded</span> <span class="o">=</span> <span class="kc">False</span></div>
+
+
+    <span class="k">def</span> <span class="nf">reload</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+        <span class="n">modname</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="vm">__class__</span><span class="o">.</span><span class="vm">__module__</span>
+        <span class="n">mod</span> <span class="o">=</span> <span class="nb">__import__</span><span class="p">(</span><span class="n">modname</span><span class="p">,</span> <span class="n">fromlist</span><span class="o">=</span><span class="p">[</span><span class="n">modname</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;.&#39;</span><span class="p">)[</span><span class="mi">0</span><span class="p">]])</span>
+        <span class="n">imp</span><span class="o">.</span><span class="n">reload</span><span class="p">(</span><span class="n">mod</span><span class="p">)</span>
+        <span class="n">new</span> <span class="o">=</span> <span class="nb">getattr</span><span class="p">(</span><span class="n">mod</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="vm">__class__</span><span class="o">.</span><span class="vm">__name__</span><span class="p">)</span>
+        <span class="nb">setattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">&#39;__class__&#39;</span><span class="p">,</span> <span class="n">new</span><span class="p">)</span>
+
+    <span class="k">def</span> <span class="fm">__str__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+        <span class="k">return</span> <span class="s1">&#39;Control: C.ER(</span><span class="si">%s</span><span class="s1">) --&gt; C.ED(</span><span class="si">%s</span><span class="s1">)&#39;</span> <span class="o">%</span> \
+            <span class="p">(</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">controller</span><span class="o">.</span><span class="fm">__str__</span><span class="p">(),</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">controlled</span><span class="o">.</span><span class="fm">__str__</span><span class="p">()</span>
+            <span class="p">)</span>
+
+    <span class="k">def</span> <span class="fm">__repr__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="fm">__str__</span><span class="p">()</span>
+
+    <span class="k">def</span> <span class="fm">__hash__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+        <span class="k">return</span> <span class="nb">hash</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="fm">__str__</span><span class="p">())</span>
+
+    <span class="k">def</span> <span class="fm">__eq__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">other</span><span class="p">):</span>
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">controller</span> <span class="o">==</span> <span class="n">other</span><span class="o">.</span><span class="n">controller</span> \
+            <span class="ow">and</span> <span class="bp">self</span><span class="o">.</span><span class="n">controlled</span> <span class="o">==</span> <span class="n">other</span><span class="o">.</span><span class="n">controlled</span>
+
+    <span class="k">def</span> <span class="nf">expand</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+        <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">is_expanded</span><span class="p">:</span>
+            <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="p">[</span><span class="bp">self</span><span class="p">]:</span>
+                <span class="k">yield</span> <span class="bp">self</span>
+        <span class="k">else</span><span class="p">:</span>
+            <span class="k">for</span> <span class="n">ed</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">controlled</span><span class="o">.</span><span class="n">expand</span><span class="p">():</span>
+                <span class="k">for</span> <span class="n">er</span><span class="p">,</span> <span class="n">erattrs</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">controller</span><span class="o">.</span><span class="n">itermembers</span><span class="p">():</span>
+                    <span class="n">c</span> <span class="o">=</span> <span class="n">Control</span><span class="p">(</span>
+                        <span class="n">er</span><span class="p">,</span> <span class="n">ed</span><span class="p">,</span> <span class="n">source</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">sources</span><span class="p">,</span> <span class="n">parent</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">parent</span><span class="p">)</span>
+                    <span class="n">c</span><span class="o">.</span><span class="n">attrs</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">attrs</span>
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+  <h1>Source code for pypath.utils.uniprot</h1><div class="highlight"><pre>
+<span></span><span class="ch">#!/usr/bin/env python</span>
+<span class="c1"># -*- coding: utf-8 -*-</span>
+
+<span class="c1">#</span>
+<span class="c1">#  This file is part of the `pypath` python module</span>
+<span class="c1">#</span>
+<span class="c1">#  Copyright 2014-2023</span>
+<span class="c1">#  EMBL, EMBL-EBI, Uniklinik RWTH Aachen, Heidelberg University</span>
+<span class="c1">#</span>
+<span class="c1">#  Authors: see the file `README.rst`</span>
+<span class="c1">#  Contact: Dénes Türei (turei.denes@gmail.com)</span>
+<span class="c1">#</span>
+<span class="c1">#  Distributed under the GPLv3 License.</span>
+<span class="c1">#  See accompanying file LICENSE.txt or copy at</span>
+<span class="c1">#      https://www.gnu.org/licenses/gpl-3.0.html</span>
+<span class="c1">#</span>
+<span class="c1">#  Website: https://pypath.omnipathdb.org/</span>
+<span class="c1">#</span>
+
+<span class="kn">from</span> <span class="nn">__future__</span> <span class="kn">import</span> <span class="n">annotations</span>
+
+<span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">Interface to UniProt protein datasheets.</span>
+<span class="sd">&quot;&quot;&quot;</span>
+
+<span class="kn">from</span> <span class="nn">future.utils</span> <span class="kn">import</span> <span class="n">iteritems</span>
+
+<span class="kn">import</span> <span class="nn">os</span>
+<span class="kn">import</span> <span class="nn">sys</span>
+<span class="kn">import</span> <span class="nn">re</span>
+<span class="kn">import</span> <span class="nn">shutil</span>
+<span class="kn">import</span> <span class="nn">importlib</span> <span class="k">as</span> <span class="nn">imp</span>
+<span class="kn">import</span> <span class="nn">collections</span>
+<span class="kn">import</span> <span class="nn">itertools</span>
+
+<span class="kn">import</span> <span class="nn">pypath.inputs.uniprot</span> <span class="k">as</span> <span class="nn">uniprot_input</span>
+<span class="kn">import</span> <span class="nn">pypath.inputs.genecards</span> <span class="k">as</span> <span class="nn">genecards_input</span>
+<span class="kn">import</span> <span class="nn">pypath.share.common</span> <span class="k">as</span> <span class="nn">common</span>
+<span class="kn">import</span> <span class="nn">pypath_common._constants</span> <span class="k">as</span> <span class="nn">_const</span>
+<span class="kn">import</span> <span class="nn">pypath.share.settings</span> <span class="k">as</span> <span class="nn">settings</span>
+<span class="kn">import</span> <span class="nn">pypath.core.entity</span> <span class="k">as</span> <span class="nn">entity</span>
+
+
+<div class="viewcode-block" id="UniprotProtein">
+<a class="viewcode-back" href="../../../api/pypath.utils.uniprot.UniprotProtein.html#pypath.utils.uniprot.UniprotProtein">[docs]</a>
+<span class="k">class</span> <span class="nc">UniprotProtein</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span>
+
+    <span class="n">_relength</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">compile</span><span class="p">(</span><span class="sa">r</span><span class="s1">&#39;([0-9]+) AA&#39;</span><span class="p">)</span>
+    <span class="n">_rename</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">compile</span><span class="p">(</span><span class="sa">r</span><span class="s1">&#39;Name=([\w\(\)-]+)\W&#39;</span><span class="p">)</span>
+    <span class="n">_rerecname</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">compile</span><span class="p">(</span><span class="sa">r</span><span class="s1">&#39;(?:Rec|Sub)Name: Full=([^;\{]+)(?: \{.*\})?;&#39;</span><span class="p">)</span>
+    <span class="n">_recc</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">compile</span><span class="p">(</span><span class="sa">r</span><span class="s1">&#39;-!- ([A-Z ]+):\s?(.*)&#39;</span><span class="p">)</span>
+    <span class="n">_remw</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">compile</span><span class="p">(</span><span class="sa">r</span><span class="s1">&#39;([0-9]+) MW&#39;</span><span class="p">)</span>
+    <span class="n">_redb</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">compile</span><span class="p">(</span><span class="sa">r</span><span class="s1">&#39;([^;]+);\s?(.*)\s?\.\s?(?:\[(.*)\])?&#39;</span><span class="p">)</span>
+    <span class="n">_redbsep</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">compile</span><span class="p">(</span><span class="sa">r</span><span class="s1">&#39;\s?;\s?&#39;</span><span class="p">)</span>
+    <span class="n">_retaxid</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">compile</span><span class="p">(</span><span class="sa">r</span><span class="s1">&#39;=(\d+)[^\d]&#39;</span><span class="p">)</span>
+    <span class="n">_rexref</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">compile</span><span class="p">(</span><span class="sa">r</span><span class="s1">&#39;[\.,]?\s?\{[^\}]+\}&#39;</span><span class="p">)</span>
+    <span class="n">_reec</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">compile</span><span class="p">(</span><span class="sa">r</span><span class="s1">&#39;EC=(\d+(?:\.[-\d]+)+)&#39;</span><span class="p">)</span>
+
+<div class="viewcode-block" id="UniprotProtein.__init__">
+<a class="viewcode-back" href="../../../api/pypath.utils.uniprot.UniprotProtein.html#pypath.utils.uniprot.UniprotProtein.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">uniprot_id</span><span class="p">):</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">uniprot_id</span> <span class="o">=</span> <span class="n">uniprot_id</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">load</span><span class="p">()</span></div>
+
+
+
+    <span class="k">def</span> <span class="nf">reload</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="n">modname</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="vm">__class__</span><span class="o">.</span><span class="vm">__module__</span>
+        <span class="n">mod</span> <span class="o">=</span> <span class="nb">__import__</span><span class="p">(</span><span class="n">modname</span><span class="p">,</span> <span class="n">fromlist</span> <span class="o">=</span> <span class="p">[</span><span class="n">modname</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;.&#39;</span><span class="p">)[</span><span class="mi">0</span><span class="p">]])</span>
+        <span class="n">imp</span><span class="o">.</span><span class="n">reload</span><span class="p">(</span><span class="n">mod</span><span class="p">)</span>
+        <span class="n">new</span> <span class="o">=</span> <span class="nb">getattr</span><span class="p">(</span><span class="n">mod</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="vm">__class__</span><span class="o">.</span><span class="vm">__name__</span><span class="p">)</span>
+        <span class="nb">setattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">&#39;__class__&#39;</span><span class="p">,</span> <span class="n">new</span><span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="nf">load</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">raw</span> <span class="o">=</span> <span class="n">uniprot_input</span><span class="o">.</span><span class="n">protein_datasheet</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">uniprot_id</span><span class="p">)</span>
+
+
+    <span class="nd">@property</span>
+    <span class="k">def</span> <span class="nf">is_reviewed</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="s1">&#39;Reviewed&#39;</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">raw</span><span class="p">[</span><span class="mi">0</span><span class="p">][</span><span class="mi">1</span><span class="p">]</span>
+
+
+    <span class="nd">@property</span>
+    <span class="k">def</span> <span class="nf">id</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">raw</span><span class="p">[</span><span class="mi">0</span><span class="p">][</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">()[</span><span class="mi">0</span><span class="p">]</span>
+
+
+    <span class="nd">@property</span>
+    <span class="k">def</span> <span class="nf">ac</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="nb">next</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">itertag</span><span class="p">(</span><span class="s1">&#39;AC&#39;</span><span class="p">))</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;;&#39;</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span>
+
+
+    <span class="nd">@property</span>
+    <span class="k">def</span> <span class="nf">length</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Returns the length (number of residues) of the canonical sequence.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">return</span> <span class="nb">int</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_relength</span><span class="o">.</span><span class="n">search</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">raw</span><span class="p">[</span><span class="mi">0</span><span class="p">][</span><span class="mi">1</span><span class="p">])</span><span class="o">.</span><span class="n">groups</span><span class="p">()[</span><span class="mi">0</span><span class="p">])</span>
+
+
+    <span class="nd">@property</span>
+    <span class="k">def</span> <span class="nf">organism</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="nb">int</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_retaxid</span><span class="o">.</span><span class="n">search</span><span class="p">(</span><span class="nb">next</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">itertag</span><span class="p">(</span><span class="s1">&#39;OX&#39;</span><span class="p">)))</span><span class="o">.</span><span class="n">groups</span><span class="p">()[</span><span class="mi">0</span><span class="p">])</span>
+
+
+    <span class="nd">@property</span>
+    <span class="k">def</span> <span class="nf">full_name</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_rerecname</span><span class="o">.</span><span class="n">search</span><span class="p">(</span><span class="nb">next</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">itertag</span><span class="p">(</span><span class="s1">&#39;DE&#39;</span><span class="p">)))</span><span class="o">.</span><span class="n">groups</span><span class="p">()[</span><span class="mi">0</span><span class="p">]</span>
+
+
+    <span class="nd">@property</span>
+    <span class="k">def</span> <span class="nf">ec</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="nb">set</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_reec</span><span class="o">.</span><span class="n">findall</span><span class="p">(</span><span class="s1">&#39;&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">itertag</span><span class="p">(</span><span class="s1">&#39;DE&#39;</span><span class="p">))))</span>
+
+
+    <span class="nd">@property</span>
+    <span class="k">def</span> <span class="nf">info</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">if</span> <span class="ow">not</span> <span class="nb">hasattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">&#39;_info&#39;</span><span class="p">):</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">update_info</span><span class="p">()</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_info</span>
+
+
+    <span class="k">def</span> <span class="nf">update_info</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="n">result</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">defaultdict</span><span class="p">(</span><span class="nb">list</span><span class="p">)</span>
+        <span class="n">title</span> <span class="o">=</span> <span class="kc">None</span>
+
+        <span class="k">for</span> <span class="n">cc</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">itertag</span><span class="p">(</span><span class="s1">&#39;CC&#39;</span><span class="p">):</span>
+
+            <span class="k">if</span> <span class="n">cc</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s1">&#39;---&#39;</span><span class="p">):</span>
+
+                <span class="k">break</span>
+
+            <span class="n">m</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_recc</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="n">cc</span><span class="p">)</span>
+
+            <span class="k">if</span> <span class="n">m</span><span class="p">:</span>
+
+                <span class="n">title</span><span class="p">,</span> <span class="n">cc</span> <span class="o">=</span> <span class="n">m</span><span class="o">.</span><span class="n">groups</span><span class="p">()</span>
+
+            <span class="n">line</span> <span class="o">=</span> <span class="n">cc</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span>
+
+            <span class="k">if</span> <span class="n">line</span><span class="p">:</span>
+
+                <span class="n">result</span><span class="p">[</span><span class="n">title</span><span class="p">]</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">line</span><span class="p">)</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_info</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">(</span>
+            <span class="p">(</span>
+                <span class="n">title</span><span class="p">,</span>
+                <span class="s1">&#39; &#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">line</span><span class="p">)</span>
+            <span class="p">)</span>
+            <span class="k">for</span> <span class="n">title</span><span class="p">,</span> <span class="n">line</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="n">result</span><span class="p">)</span>
+        <span class="p">)</span>
+
+
+    <span class="nd">@property</span>
+    <span class="k">def</span> <span class="nf">function_genecards</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="n">summaries</span> <span class="o">=</span> <span class="n">genecards_input</span><span class="o">.</span><span class="n">genecards_summaries</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">genesymbol</span><span class="p">)</span>
+
+        <span class="k">return</span> <span class="s1">&#39; &#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span>
+            <span class="s1">&#39;</span><span class="si">%s</span><span class="s1">: </span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="p">(</span><span class="n">resource</span><span class="p">,</span> <span class="n">summary</span><span class="p">)</span>
+            <span class="k">for</span> <span class="n">resource</span><span class="p">,</span> <span class="n">summary</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="n">summaries</span><span class="p">)</span>
+        <span class="p">)</span>
+
+
+    <span class="nd">@property</span>
+    <span class="k">def</span> <span class="nf">function_with_xrefs</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">info_section</span><span class="p">(</span><span class="s1">&#39;FUNCTION&#39;</span><span class="p">)</span>
+
+
+    <span class="nd">@property</span>
+    <span class="k">def</span> <span class="nf">function</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">remove_xrefs</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">function_with_xrefs</span><span class="p">)</span>
+
+
+    <span class="nd">@property</span>
+    <span class="k">def</span> <span class="nf">function_with_genecards</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="s1">&#39;</span><span class="si">%s</span><span class="s1"> </span><span class="si">%s</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="p">(</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">function</span><span class="p">,</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">function_genecards</span><span class="p">,</span>
+        <span class="p">)</span>
+
+
+    <span class="nd">@property</span>
+    <span class="k">def</span> <span class="nf">function_or_genecards</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">function</span> <span class="ow">or</span> <span class="bp">self</span><span class="o">.</span><span class="n">function_genecards</span>
+
+
+    <span class="nd">@property</span>
+    <span class="k">def</span> <span class="nf">subcellular_location</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">remove_xrefs</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">subcellular_location_with_xrefs</span><span class="p">)</span>
+
+
+    <span class="nd">@property</span>
+    <span class="k">def</span> <span class="nf">tissue_specificity</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">remove_xrefs</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">tissue_specificity_with_xrefs</span><span class="p">)</span>
+
+
+    <span class="nd">@property</span>
+    <span class="k">def</span> <span class="nf">subunit</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">remove_xrefs</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">subunit_with_xrefs</span><span class="p">)</span>
+
+
+    <span class="nd">@property</span>
+    <span class="k">def</span> <span class="nf">interaction</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">remove_xrefs</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">interaction_with_xrefs</span><span class="p">)</span>
+
+
+    <span class="nd">@property</span>
+    <span class="k">def</span> <span class="nf">sequence_caution</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">remove_xrefs</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">sequence_caution_with_xrefs</span><span class="p">)</span>
+
+
+    <span class="nd">@property</span>
+    <span class="k">def</span> <span class="nf">catalytic_activity</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">remove_xrefs</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">catalytic_activity_with_xrefs</span><span class="p">)</span>
+
+
+    <span class="nd">@property</span>
+    <span class="k">def</span> <span class="nf">activity_regulation</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">remove_xrefs</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">activity_regulation_with_xrefs</span><span class="p">)</span>
+
+
+    <span class="nd">@property</span>
+    <span class="k">def</span> <span class="nf">alternative_products</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">remove_xrefs</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">alternative_products_with_xrefs</span><span class="p">)</span>
+
+
+    <span class="nd">@property</span>
+    <span class="k">def</span> <span class="nf">ptm</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">remove_xrefs</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">ptm_with_xrefs</span><span class="p">)</span>
+
+
+    <span class="nd">@property</span>
+    <span class="k">def</span> <span class="nf">disease</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">remove_xrefs</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">disease_with_xrefs</span><span class="p">)</span>
+
+
+    <span class="nd">@property</span>
+    <span class="k">def</span> <span class="nf">similarity</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">remove_xrefs</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">similarity_with_xrefs</span><span class="p">)</span>
+
+
+    <span class="nd">@property</span>
+    <span class="k">def</span> <span class="nf">web_resource</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">remove_xrefs</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">web_resource_with_xrefs</span><span class="p">)</span>
+
+
+    <span class="nd">@property</span>
+    <span class="k">def</span> <span class="nf">subcellular_location_with_xrefs</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">info_section</span><span class="p">(</span><span class="s1">&#39;SUBCELLULAR LOCATION&#39;</span><span class="p">)</span>
+
+
+    <span class="nd">@property</span>
+    <span class="k">def</span> <span class="nf">tissue_specificity_with_xrefs</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">info_section</span><span class="p">(</span><span class="s1">&#39;TISSUE SPECIFICITY&#39;</span><span class="p">)</span>
+
+
+    <span class="nd">@property</span>
+    <span class="k">def</span> <span class="nf">subunit_with_xrefs</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">info_section</span><span class="p">(</span><span class="s1">&#39;SUBUNIT&#39;</span><span class="p">)</span>
+
+
+    <span class="nd">@property</span>
+    <span class="k">def</span> <span class="nf">interaction_with_xrefs</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">info_section</span><span class="p">(</span><span class="s1">&#39;INTERACTION&#39;</span><span class="p">)</span>
+
+
+    <span class="nd">@property</span>
+    <span class="k">def</span> <span class="nf">sequence_caution_with_xrefs</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">info_section</span><span class="p">(</span><span class="s1">&#39;SEQUENCE CAUTION&#39;</span><span class="p">)</span>
+
+
+    <span class="nd">@property</span>
+    <span class="k">def</span> <span class="nf">catalytic_activity_with_xrefs</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">info_section</span><span class="p">(</span><span class="s1">&#39;CATALYTIC ACTIVITY&#39;</span><span class="p">)</span>
+
+
+    <span class="nd">@property</span>
+    <span class="k">def</span> <span class="nf">activity_regulation_with_xrefs</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">info_section</span><span class="p">(</span><span class="s1">&#39;ACTIVITY REGULATION&#39;</span><span class="p">)</span>
+
+
+    <span class="nd">@property</span>
+    <span class="k">def</span> <span class="nf">alternative_products_with_xrefs</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">info_section</span><span class="p">(</span><span class="s1">&#39;ALTERNATIVE PRODUCTS&#39;</span><span class="p">)</span>
+
+
+    <span class="nd">@property</span>
+    <span class="k">def</span> <span class="nf">ptm_with_xrefs</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">info_section</span><span class="p">(</span><span class="s1">&#39;PTM&#39;</span><span class="p">)</span>
+
+
+    <span class="nd">@property</span>
+    <span class="k">def</span> <span class="nf">disease_with_xrefs</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">info_section</span><span class="p">(</span><span class="s1">&#39;DISEASE&#39;</span><span class="p">)</span>
+
+
+    <span class="nd">@property</span>
+    <span class="k">def</span> <span class="nf">similarity_with_xrefs</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">info_section</span><span class="p">(</span><span class="s1">&#39;SIMILARITY&#39;</span><span class="p">)</span>
+
+
+    <span class="nd">@property</span>
+    <span class="k">def</span> <span class="nf">web_resource_with_xrefs</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">info_section</span><span class="p">(</span><span class="s1">&#39;WEB RESOURCE&#39;</span><span class="p">)</span>
+
+
+    <span class="nd">@property</span>
+    <span class="k">def</span> <span class="nf">lengths</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Returns the length of all isoforms as a list.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">return</span> <span class="p">[</span>
+            <span class="nb">int</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_relength</span><span class="o">.</span><span class="n">search</span><span class="p">(</span><span class="n">sq</span><span class="p">)</span><span class="o">.</span><span class="n">groups</span><span class="p">()[</span><span class="mi">0</span><span class="p">])</span>
+            <span class="k">for</span> <span class="n">sq</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">itertag</span><span class="p">(</span><span class="s1">&#39;SQ&#39;</span><span class="p">)</span>
+        <span class="p">]</span>
+
+
+    <span class="nd">@property</span>
+    <span class="k">def</span> <span class="nf">weight</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Returns the molecular weight of the canonical isoform in Daltons.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">try</span><span class="p">:</span>
+
+            <span class="k">return</span> <span class="nb">int</span><span class="p">(</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">_remw</span><span class="o">.</span><span class="n">search</span><span class="p">(</span><span class="nb">next</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">itertag</span><span class="p">(</span><span class="s1">&#39;SQ&#39;</span><span class="p">)))</span><span class="o">.</span><span class="n">groups</span><span class="p">()[</span><span class="mi">0</span><span class="p">]</span>
+            <span class="p">)</span>
+
+        <span class="k">except</span> <span class="ne">StopIteration</span><span class="p">:</span>
+
+            <span class="k">return</span> <span class="kc">None</span>
+
+
+    <span class="nd">@property</span>
+    <span class="k">def</span> <span class="nf">weights</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Returns the molecular weights of all isoforms as a list.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">return</span> <span class="p">[</span>
+            <span class="nb">int</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_remw</span><span class="o">.</span><span class="n">search</span><span class="p">(</span><span class="n">sq</span><span class="p">)</span><span class="o">.</span><span class="n">groups</span><span class="p">()[</span><span class="mi">0</span><span class="p">])</span>
+            <span class="k">for</span> <span class="n">sq</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">itertag</span><span class="p">(</span><span class="s1">&#39;SQ&#39;</span><span class="p">)</span>
+        <span class="p">]</span>
+
+
+    <span class="nd">@property</span>
+    <span class="k">def</span> <span class="nf">databases</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Returns the database identifiers (cross-references) as a dict of</span>
+<span class="sd">        database names and identifiers.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">if</span> <span class="ow">not</span> <span class="nb">hasattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">&#39;_databases&#39;</span><span class="p">):</span>
+
+            <span class="bp">self</span><span class="o">.</span><span class="n">update_databases</span><span class="p">()</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_databases</span>
+
+
+    <span class="k">def</span> <span class="nf">update_databases</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="n">result</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">defaultdict</span><span class="p">(</span><span class="nb">set</span><span class="p">)</span>
+
+        <span class="k">for</span> <span class="n">db</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">itertag</span><span class="p">(</span><span class="s1">&#39;DR&#39;</span><span class="p">):</span>
+
+            <span class="n">m</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_redb</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="n">db</span><span class="p">)</span>
+
+            <span class="k">if</span> <span class="n">m</span><span class="p">:</span>
+
+                <span class="n">dbname</span><span class="p">,</span> <span class="n">ids</span><span class="p">,</span> <span class="n">subtype</span> <span class="o">=</span> <span class="n">m</span><span class="o">.</span><span class="n">groups</span><span class="p">()</span>
+                <span class="n">ids</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_redbsep</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="n">ids</span><span class="p">)</span>
+                <span class="n">ids</span> <span class="o">=</span> <span class="nb">tuple</span><span class="p">(</span><span class="n">_id</span> <span class="k">for</span> <span class="n">_id</span> <span class="ow">in</span> <span class="n">ids</span> <span class="k">if</span> <span class="n">_id</span> <span class="o">!=</span> <span class="s1">&#39;-&#39;</span><span class="p">)</span>
+
+                <span class="k">if</span> <span class="n">subtype</span><span class="p">:</span>
+
+                    <span class="n">ids</span> <span class="o">+=</span> <span class="p">(</span><span class="n">subtype</span><span class="p">,)</span>
+
+                <span class="n">ids</span> <span class="o">=</span> <span class="n">ids</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">ids</span><span class="p">)</span> <span class="o">==</span> <span class="mi">1</span> <span class="k">else</span> <span class="n">ids</span>
+                <span class="n">result</span><span class="p">[</span><span class="n">dbname</span><span class="p">]</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">ids</span><span class="p">)</span>
+
+        <span class="bp">self</span><span class="o">.</span><span class="n">_databases</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">(</span><span class="n">result</span><span class="p">)</span>
+
+
+<div class="viewcode-block" id="UniprotProtein.info_section">
+<a class="viewcode-back" href="../../../api/pypath.utils.uniprot.UniprotProtein.html#pypath.utils.uniprot.UniprotProtein.info_section">[docs]</a>
+    <span class="k">def</span> <span class="nf">info_section</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">title</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Retrieves a section from the description. If the section is not</span>
+<span class="sd">        availeble, returns ``None``.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">info</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">info</span>
+
+        <span class="k">if</span> <span class="n">title</span> <span class="ow">in</span> <span class="n">info</span><span class="p">:</span>
+
+            <span class="k">return</span> <span class="n">info</span><span class="p">[</span><span class="n">title</span><span class="p">]</span></div>
+
+
+    <span class="nd">@property</span>
+    <span class="k">def</span> <span class="nf">genesymbol</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">try</span><span class="p">:</span>
+
+            <span class="n">m</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_rename</span><span class="o">.</span><span class="n">search</span><span class="p">(</span><span class="nb">next</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">itertag</span><span class="p">(</span><span class="s1">&#39;GN&#39;</span><span class="p">)))</span>
+
+            <span class="k">return</span> <span class="n">m</span><span class="o">.</span><span class="n">groups</span><span class="p">()[</span><span class="mi">0</span><span class="p">]</span> <span class="k">if</span> <span class="n">m</span> <span class="k">else</span> <span class="bp">self</span><span class="o">.</span><span class="n">ac</span>
+
+        <span class="k">except</span> <span class="ne">StopIteration</span><span class="p">:</span>
+
+            <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">ac</span>
+
+
+    <span class="nd">@property</span>
+    <span class="k">def</span> <span class="nf">keywords_with_xrefs</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Returns the keywords as a list with keeping the cross-references.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">return</span> <span class="p">[</span>
+            <span class="n">kw</span> <span class="k">for</span> <span class="n">kw</span> <span class="ow">in</span>
+            <span class="n">itertools</span><span class="o">.</span><span class="n">chain</span><span class="p">(</span>
+                <span class="o">*</span><span class="p">(</span>
+                    <span class="bp">self</span><span class="o">.</span><span class="n">_redbsep</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="n">kw</span><span class="o">.</span><span class="n">strip</span><span class="p">(</span><span class="s1">&#39;.&#39;</span><span class="p">))</span>
+                    <span class="k">for</span> <span class="n">kw</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">itertag</span><span class="p">(</span><span class="s1">&#39;KW&#39;</span><span class="p">)</span>
+                <span class="p">)</span>
+            <span class="p">)</span>
+            <span class="k">if</span> <span class="n">kw</span>
+        <span class="p">]</span>
+
+
+    <span class="nd">@property</span>
+    <span class="k">def</span> <span class="nf">keywords</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Returns the keywords as a list.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">return</span> <span class="p">(</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">remove_xrefs</span><span class="p">(</span>
+                <span class="s1">&#39;</span><span class="se">\t</span><span class="s1">&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">keywords_with_xrefs</span><span class="p">)</span>
+            <span class="p">)</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\t</span><span class="s1">&#39;</span><span class="p">)</span>
+        <span class="p">)</span>
+
+
+    <span class="nd">@classmethod</span>
+    <span class="k">def</span> <span class="nf">remove_xrefs</span><span class="p">(</span><span class="bp">cls</span><span class="p">,</span> <span class="n">value</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="bp">cls</span><span class="o">.</span><span class="n">_rexref</span><span class="o">.</span><span class="n">sub</span><span class="p">(</span><span class="s1">&#39;&#39;</span><span class="p">,</span> <span class="n">value</span><span class="p">)</span> <span class="k">if</span> <span class="n">value</span> <span class="k">else</span> <span class="n">value</span>
+
+
+    <span class="nd">@property</span>
+    <span class="k">def</span> <span class="nf">sequence</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Returns the canonical sequence (the first one) as a string of</span>
+<span class="sd">        standard capital letter residue symbols.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="n">result</span> <span class="o">=</span> <span class="p">[]</span>
+        <span class="n">collect</span> <span class="o">=</span> <span class="kc">False</span>
+
+        <span class="k">for</span> <span class="n">tag</span><span class="p">,</span> <span class="n">line</span> <span class="ow">in</span> <span class="bp">self</span><span class="p">:</span>
+
+            <span class="k">if</span> <span class="ow">not</span> <span class="n">collect</span> <span class="ow">and</span> <span class="n">tag</span> <span class="o">==</span> <span class="s1">&#39;SQ&#39;</span><span class="p">:</span>
+
+                <span class="n">collect</span> <span class="o">=</span> <span class="kc">True</span>
+
+            <span class="k">elif</span> <span class="n">collect</span><span class="p">:</span>
+
+                <span class="k">if</span> <span class="n">tag</span> <span class="o">==</span> <span class="s1">&#39;  &#39;</span><span class="p">:</span>
+
+                    <span class="n">result</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">line</span><span class="p">)</span>
+
+                <span class="k">else</span><span class="p">:</span>
+
+                    <span class="k">break</span>
+
+        <span class="k">return</span> <span class="s1">&#39;&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">x</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s1">&#39; &#39;</span><span class="p">,</span> <span class="s1">&#39;&#39;</span><span class="p">)</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">result</span><span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="fm">__iter__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">raw</span><span class="o">.</span><span class="fm">__iter__</span><span class="p">()</span>
+
+
+    <span class="k">def</span> <span class="nf">itertag</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">tag</span><span class="p">):</span>
+
+        <span class="k">for</span> <span class="n">_tag</span><span class="p">,</span> <span class="n">line</span> <span class="ow">in</span> <span class="bp">self</span><span class="p">:</span>
+
+            <span class="k">if</span> <span class="n">_tag</span> <span class="o">==</span> <span class="n">tag</span><span class="p">:</span>
+
+                <span class="k">yield</span> <span class="n">line</span>
+
+
+    <span class="k">def</span> <span class="nf">has_tag</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">tag</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="nb">any</span><span class="p">(</span><span class="n">line</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">==</span> <span class="n">tag</span> <span class="k">for</span> <span class="n">line</span> <span class="ow">in</span> <span class="bp">self</span><span class="p">)</span>
+
+
+    <span class="k">def</span> <span class="fm">__repr__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+
+        <span class="k">return</span> <span class="s1">&#39;&lt;UniProt datasheet </span><span class="si">%s</span><span class="s1"> (</span><span class="si">%s</span><span class="s1">)&gt;&#39;</span> <span class="o">%</span> <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">ac</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">genesymbol</span><span class="p">)</span></div>
+
+
+
+<span class="k">def</span> <span class="nf">_update_methods</span><span class="p">():</span>
+
+    <span class="k">for</span> <span class="n">method_name</span> <span class="ow">in</span> <span class="n">UniprotProtein</span><span class="o">.</span><span class="vm">__dict__</span><span class="o">.</span><span class="n">keys</span><span class="p">():</span>
+
+        <span class="k">if</span> <span class="n">method_name</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s1">&#39;_&#39;</span><span class="p">):</span>
+
+            <span class="k">continue</span>
+
+        <span class="k">def</span> <span class="nf">create_method</span><span class="p">(</span><span class="n">method_name</span><span class="p">):</span>
+
+            <span class="k">def</span> <span class="nf">method</span><span class="p">(</span><span class="n">uniprot_id</span><span class="p">,</span> <span class="o">*</span><span class="n">args</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+
+                <span class="n">bound_m</span> <span class="o">=</span> <span class="nb">getattr</span><span class="p">(</span><span class="n">UniprotProtein</span><span class="p">(</span><span class="n">uniprot_id</span><span class="p">),</span> <span class="n">method_name</span><span class="p">)</span>
+
+                <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="nb">getattr</span><span class="p">(</span><span class="n">UniprotProtein</span><span class="p">,</span> <span class="n">method_name</span><span class="p">),</span> <span class="nb">property</span><span class="p">):</span>
+
+                    <span class="k">return</span> <span class="n">bound_m</span>
+
+                <span class="k">else</span><span class="p">:</span>
+
+                    <span class="k">return</span> <span class="n">bound_m</span><span class="p">(</span><span class="o">*</span><span class="n">args</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
+
+            <span class="k">return</span> <span class="n">method</span>
+
+        <span class="n">_method</span> <span class="o">=</span> <span class="n">create_method</span><span class="p">(</span><span class="n">method_name</span><span class="p">)</span>
+
+        <span class="n">common</span><span class="o">.</span><span class="n">add_method</span><span class="p">(</span>
+            <span class="bp">cls</span> <span class="o">=</span> <span class="n">sys</span><span class="o">.</span><span class="n">modules</span><span class="p">[</span><span class="vm">__name__</span><span class="p">],</span>
+            <span class="n">method_name</span> <span class="o">=</span> <span class="n">method_name</span><span class="p">,</span>
+            <span class="n">method</span> <span class="o">=</span> <span class="n">_method</span><span class="p">,</span>
+            <span class="n">doc</span> <span class="o">=</span> <span class="nb">getattr</span><span class="p">(</span><span class="n">UniprotProtein</span><span class="p">,</span> <span class="n">method_name</span><span class="p">)</span><span class="o">.</span><span class="vm">__doc__</span><span class="p">,</span>
+        <span class="p">)</span>
+
+
+<span class="n">_update_methods</span><span class="p">()</span>
+
+
+<div class="viewcode-block" id="query">
+<a class="viewcode-back" href="../../../api/pypath.utils.uniprot.query.html#pypath.utils.uniprot.query">[docs]</a>
+<span class="k">def</span> <span class="nf">query</span><span class="p">(</span><span class="o">*</span><span class="n">uniprot_ids</span><span class="p">):</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Queries the datasheet of one or more UniProt IDs.</span>
+<span class="sd">    Returns a single ``UniprotProtein`` object or a list of those objects.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="k">if</span> <span class="p">(</span>
+        <span class="nb">len</span><span class="p">(</span><span class="n">uniprot_ids</span><span class="p">)</span> <span class="o">&gt;</span> <span class="mi">0</span> <span class="ow">and</span>
+        <span class="nb">isinstance</span><span class="p">(</span><span class="n">uniprot_ids</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">_const</span><span class="o">.</span><span class="n">LIST_LIKE</span><span class="p">)</span>
+    <span class="p">):</span>
+
+        <span class="n">uniprot_ids</span> <span class="o">=</span> <span class="n">uniprot_ids</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span>
+
+    <span class="n">uniprot_ids</span> <span class="o">=</span> <span class="n">common</span><span class="o">.</span><span class="n">to_list</span><span class="p">(</span><span class="n">uniprot_ids</span><span class="p">)</span>
+    <span class="n">uniprot_ids</span> <span class="o">=</span> <span class="n">entity</span><span class="o">.</span><span class="n">Entity</span><span class="o">.</span><span class="n">only_proteins</span><span class="p">(</span><span class="n">uniprot_ids</span><span class="p">)</span>
+
+    <span class="n">single_id</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="n">uniprot_ids</span><span class="p">)</span> <span class="o">==</span> <span class="mi">1</span>
+
+    <span class="n">result</span> <span class="o">=</span> <span class="p">[</span>
+        <span class="n">UniprotProtein</span><span class="p">(</span><span class="n">uniprot_id</span><span class="p">)</span>
+        <span class="k">for</span> <span class="n">uniprot_id</span> <span class="ow">in</span> <span class="n">uniprot_ids</span>
+    <span class="p">]</span>
+    <span class="n">result</span> <span class="o">=</span> <span class="p">[</span><span class="n">u</span> <span class="k">for</span> <span class="n">u</span> <span class="ow">in</span> <span class="n">result</span> <span class="k">if</span> <span class="n">u</span><span class="o">.</span><span class="n">raw</span><span class="p">]</span>
+
+    <span class="k">return</span> <span class="n">common</span><span class="o">.</span><span class="n">first</span><span class="p">(</span><span class="n">result</span><span class="p">)</span> <span class="k">if</span> <span class="n">single_id</span> <span class="k">else</span> <span class="n">result</span></div>
+
+
+
+<div class="viewcode-block" id="collect">
+<a class="viewcode-back" href="../../../api/pypath.utils.uniprot.collect.html#pypath.utils.uniprot.collect">[docs]</a>
+<span class="k">def</span> <span class="nf">collect</span><span class="p">(</span><span class="n">uniprot_ids</span><span class="p">,</span> <span class="o">*</span><span class="n">features</span><span class="p">):</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Collects data about one or more UniProt IDs.</span>
+
+<span class="sd">    :param str,list uniprot_ids:</span>
+<span class="sd">        One or more UniProt IDs.</span>
+<span class="sd">    :param *str,list features:</span>
+<span class="sd">        Features to query: these must be method (property) names of the</span>
+<span class="sd">        ``UniprotProtein`` class. E.g. ``[&#39;ac&#39;, &#39;genesymbol&#39;, &#39;function&#39;]``.</span>
+
+<span class="sd">    :return:</span>
+<span class="sd">        A ``collections.OrderedDict`` object with feature names as keys and</span>
+<span class="sd">        list of values for each UniProt ID as values.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="n">uniprot_ids</span> <span class="o">=</span> <span class="n">entity</span><span class="o">.</span><span class="n">Entity</span><span class="o">.</span><span class="n">only_proteins</span><span class="p">(</span><span class="n">uniprot_ids</span><span class="p">)</span>
+
+    <span class="n">resources</span> <span class="o">=</span> <span class="p">[</span>
+        <span class="n">UniprotProtein</span><span class="p">(</span><span class="n">uniprot_id</span><span class="p">)</span>
+        <span class="k">for</span> <span class="n">uniprot_id</span> <span class="ow">in</span> <span class="n">uniprot_ids</span>
+    <span class="p">]</span>
+    <span class="c1"># this is mainly for removal of obsolate records</span>
+    <span class="c1"># where the response from the server is empty</span>
+    <span class="c1"># most of the times it removes nothing</span>
+    <span class="n">resources</span> <span class="o">=</span> <span class="p">[</span><span class="n">u</span> <span class="k">for</span> <span class="n">u</span> <span class="ow">in</span> <span class="n">resources</span> <span class="k">if</span> <span class="n">u</span><span class="o">.</span><span class="n">raw</span><span class="p">]</span>
+
+    <span class="n">features</span> <span class="o">=</span> <span class="n">features</span> <span class="ow">or</span> <span class="n">default_features</span>
+
+    <span class="k">if</span> <span class="s1">&#39;ac&#39;</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">features</span><span class="p">:</span>
+
+        <span class="n">features</span> <span class="o">=</span> <span class="p">[</span><span class="s1">&#39;ac&#39;</span><span class="p">]</span> <span class="o">+</span> <span class="nb">list</span><span class="p">(</span><span class="n">features</span><span class="p">)</span>
+
+    <span class="n">table</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">OrderedDict</span><span class="p">(</span>
+        <span class="p">(</span>
+            <span class="n">feature_name</span><span class="p">,</span>
+            <span class="p">[</span>
+                <span class="nb">getattr</span><span class="p">(</span><span class="n">resource</span><span class="p">,</span> <span class="n">feature_name</span><span class="p">)</span>
+                <span class="k">for</span> <span class="n">resource</span> <span class="ow">in</span> <span class="n">resources</span>
+            <span class="p">]</span>
+        <span class="p">)</span>
+        <span class="k">for</span> <span class="n">feature_name</span> <span class="ow">in</span> <span class="n">features</span>
+    <span class="p">)</span>
+
+    <span class="k">return</span> <span class="n">table</span></div>
+
+
+
+<div class="viewcode-block" id="features_table">
+<a class="viewcode-back" href="../../../api/pypath.utils.uniprot.features_table.html#pypath.utils.uniprot.features_table">[docs]</a>
+<span class="k">def</span> <span class="nf">features_table</span><span class="p">(</span>
+        <span class="n">uniprot_ids</span><span class="p">,</span>
+        <span class="o">*</span><span class="n">features</span><span class="p">,</span>
+        <span class="n">width</span> <span class="o">=</span> <span class="mi">40</span><span class="p">,</span>
+        <span class="n">maxlen</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+        <span class="n">tablefmt</span> <span class="o">=</span> <span class="s1">&#39;fancy_grid&#39;</span><span class="p">,</span>
+        <span class="o">**</span><span class="n">kwargs</span>
+    <span class="p">):</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Returns a table with the requested features of a list of UniProt IDs.</span>
+<span class="sd">    The underlying table formatting module is ``tabulate``, a versatile</span>
+<span class="sd">    module to export various ascii tables as well as HTML or LaTeX --</span>
+<span class="sd">    check the docs for formatting options:</span>
+<span class="sd">    https://github.com/astanin/python-tabulate</span>
+
+<span class="sd">    Args</span>
+<span class="sd">        kwargs:</span>
+<span class="sd">            Passed to ``tabulate.tabulate``.</span>
+
+<span class="sd">    Returns</span>
+<span class="sd">        The table as a string.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="n">maxlen</span> <span class="o">=</span> <span class="n">maxlen</span> <span class="ow">or</span> <span class="n">settings</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">&#39;uniprot_info_maxlen&#39;</span><span class="p">)</span>
+
+    <span class="n">features</span> <span class="o">=</span> <span class="n">features</span> <span class="ow">or</span> <span class="n">default_features</span>
+
+    <span class="n">tbl</span> <span class="o">=</span> <span class="n">collect</span><span class="p">(</span><span class="n">uniprot_ids</span><span class="p">,</span> <span class="o">*</span><span class="n">features</span><span class="p">)</span>
+
+    <span class="k">return</span> <span class="n">common</span><span class="o">.</span><span class="n">table_format</span><span class="p">(</span>
+        <span class="n">tbl</span><span class="p">,</span>
+        <span class="n">width</span> <span class="o">=</span> <span class="n">width</span><span class="p">,</span>
+        <span class="n">maxlen</span> <span class="o">=</span> <span class="n">maxlen</span><span class="p">,</span>
+        <span class="n">tablefmt</span> <span class="o">=</span> <span class="n">tablefmt</span><span class="p">,</span>
+        <span class="o">**</span><span class="n">kwargs</span>
+    <span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="print_features">
+<a class="viewcode-back" href="../../../api/pypath.utils.uniprot.print_features.html#pypath.utils.uniprot.print_features">[docs]</a>
+<span class="k">def</span> <span class="nf">print_features</span><span class="p">(</span>
+        <span class="n">uniprot_ids</span><span class="p">,</span>
+        <span class="o">*</span><span class="n">features</span><span class="p">,</span>
+        <span class="n">fileobj</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+        <span class="n">width</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+        <span class="n">maxlen</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+        <span class="n">tablefmt</span> <span class="o">=</span> <span class="s1">&#39;fancy_grid&#39;</span><span class="p">,</span>
+        <span class="o">**</span><span class="n">kwargs</span>
+    <span class="p">):</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Prints a table with the requested features of a list of UniProt IDs.</span>
+<span class="sd">    The underlying table formatting module is ``tabulate``, a versatile</span>
+<span class="sd">    module to export various ascii tables as well as HTML or LaTeX --</span>
+<span class="sd">    check the docs for formatting options:</span>
+<span class="sd">    https://github.com/astanin/python-tabulate</span>
+
+<span class="sd">    Args</span>
+<span class="sd">        kwargs:</span>
+<span class="sd">            Passed to ``tabulate.tabulate``.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="n">maxlen</span> <span class="o">=</span> <span class="n">maxlen</span> <span class="ow">or</span> <span class="n">settings</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">&#39;uniprot_info_maxlen&#39;</span><span class="p">)</span>
+    <span class="n">features</span> <span class="o">=</span> <span class="n">features</span> <span class="ow">or</span> <span class="n">default_features</span>
+    <span class="n">term_width</span> <span class="o">=</span> <span class="p">(</span><span class="n">shutil</span><span class="o">.</span><span class="n">get_terminal_size</span><span class="p">()</span><span class="o">.</span><span class="n">columns</span> <span class="o">-</span> <span class="mi">60</span><span class="p">)</span> <span class="o">*</span> <span class="mi">2</span> <span class="o">+</span> <span class="mi">40</span>
+    <span class="n">width</span> <span class="o">=</span> <span class="n">width</span> <span class="ow">or</span> <span class="nb">int</span><span class="p">(</span><span class="n">term_width</span> <span class="o">/</span> <span class="nb">len</span><span class="p">(</span><span class="n">features</span><span class="p">))</span> <span class="k">if</span> <span class="n">term_width</span> <span class="k">else</span> <span class="mi">40</span>
+    <span class="n">fileobj</span> <span class="o">=</span> <span class="n">fileobj</span> <span class="ow">or</span> <span class="n">sys</span><span class="o">.</span><span class="n">stdout</span>
+
+    <span class="n">fileobj</span><span class="o">.</span><span class="n">write</span><span class="p">(</span>
+        <span class="n">features_table</span><span class="p">(</span>
+            <span class="n">uniprot_ids</span><span class="p">,</span>
+            <span class="o">*</span><span class="n">features</span><span class="p">,</span>
+            <span class="n">width</span> <span class="o">=</span> <span class="n">width</span><span class="p">,</span>
+            <span class="n">maxlen</span> <span class="o">=</span> <span class="n">maxlen</span><span class="p">,</span>
+            <span class="n">tablefmt</span> <span class="o">=</span> <span class="n">tablefmt</span><span class="p">,</span>
+            <span class="o">**</span><span class="n">kwargs</span>
+        <span class="p">)</span>
+    <span class="p">)</span>
+    <span class="n">fileobj</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">linesep</span><span class="p">)</span>
+    <span class="n">fileobj</span><span class="o">.</span><span class="n">flush</span><span class="p">()</span></div>
+
+
+
+<div class="viewcode-block" id="info">
+<a class="viewcode-back" href="../../../api/pypath.utils.uniprot.info.html#pypath.utils.uniprot.info">[docs]</a>
+<span class="k">def</span> <span class="nf">info</span><span class="p">(</span>
+        <span class="o">*</span><span class="n">uniprot_ids</span><span class="p">,</span>
+        <span class="n">features</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+        <span class="n">fileobj</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+        <span class="n">header</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+        <span class="o">**</span><span class="n">kwargs</span>
+    <span class="p">):</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Prints a table with the most important (or the requested) features of a</span>
+<span class="sd">    list of UniProt IDs.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="k">if</span> <span class="p">(</span>
+        <span class="nb">len</span><span class="p">(</span><span class="n">uniprot_ids</span><span class="p">)</span> <span class="o">==</span> <span class="mi">1</span> <span class="ow">and</span>
+        <span class="nb">isinstance</span><span class="p">(</span><span class="n">uniprot_ids</span><span class="p">,</span> <span class="n">_const</span><span class="o">.</span><span class="n">LIST_LIKE</span><span class="p">)</span>
+    <span class="p">):</span>
+
+        <span class="n">uniprot_ids</span> <span class="o">=</span> <span class="n">uniprot_ids</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span>
+
+    <span class="n">features</span> <span class="o">=</span> <span class="n">features</span> <span class="ow">or</span> <span class="n">default_features</span>
+
+    <span class="n">fileobj</span> <span class="o">=</span> <span class="n">fileobj</span> <span class="ow">or</span> <span class="n">sys</span><span class="o">.</span><span class="n">stdout</span>
+
+    <span class="n">header</span> <span class="o">=</span> <span class="p">(</span>
+        <span class="n">header</span> <span class="ow">or</span>
+        <span class="s1">&#39;=====&gt; [</span><span class="si">%u</span><span class="s1"> proteins] &lt;=====</span><span class="se">\n</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="nb">len</span><span class="p">(</span>
+            <span class="nb">list</span><span class="p">(</span>
+                <span class="n">entity</span><span class="o">.</span><span class="n">Entity</span><span class="o">.</span><span class="n">filter_entity_type</span><span class="p">(</span>
+                    <span class="n">common</span><span class="o">.</span><span class="n">to_list</span><span class="p">(</span><span class="n">uniprot_ids</span><span class="p">),</span>
+                    <span class="n">entity_type</span> <span class="o">=</span> <span class="s1">&#39;protein&#39;</span><span class="p">,</span>
+                <span class="p">)</span>
+            <span class="p">)</span>
+        <span class="p">)</span>
+    <span class="p">)</span>
+
+    <span class="n">fileobj</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="n">header</span><span class="p">)</span>
+
+    <span class="n">print_features</span><span class="p">(</span>
+        <span class="n">common</span><span class="o">.</span><span class="n">to_list</span><span class="p">(</span><span class="n">uniprot_ids</span><span class="p">),</span>
+        <span class="o">*</span><span class="n">features</span><span class="p">,</span>
+        <span class="n">fileobj</span> <span class="o">=</span> <span class="n">fileobj</span><span class="p">,</span>
+        <span class="o">**</span><span class="n">kwargs</span>
+    <span class="p">)</span></div>
+
+
+
+<div class="viewcode-block" id="browse">
+<a class="viewcode-back" href="../../../api/pypath.utils.uniprot.browse.html#pypath.utils.uniprot.browse">[docs]</a>
+<span class="k">def</span> <span class="nf">browse</span><span class="p">(</span><span class="n">groups</span><span class="p">,</span> <span class="n">start</span> <span class="o">=</span> <span class="mi">0</span><span class="p">,</span> <span class="n">fileobj</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Browses through a series of protein groups, printing an information table</span>
+<span class="sd">    for each group. ``kwargs`` passed to ``info`` and then to print_features``.</span>
+<span class="sd">    Parameters for ``common.table_format`` can be provided.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="n">labels</span> <span class="o">=</span> <span class="nb">sorted</span><span class="p">(</span><span class="n">groups</span><span class="o">.</span><span class="n">keys</span><span class="p">())</span>
+    <span class="n">n_groups</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="n">labels</span><span class="p">)</span>
+    <span class="n">stop</span> <span class="o">=</span> <span class="kc">False</span>
+    <span class="n">maxlen_default</span> <span class="o">=</span> <span class="n">kwargs</span><span class="p">[</span><span class="s1">&#39;maxlen&#39;</span><span class="p">]</span> <span class="k">if</span> <span class="s1">&#39;maxlen&#39;</span> <span class="ow">in</span> <span class="n">kwargs</span> <span class="k">else</span> <span class="mi">500</span>
+    <span class="n">fileobj</span> <span class="o">=</span> <span class="n">fileobj</span> <span class="ow">or</span> <span class="n">sys</span><span class="o">.</span><span class="n">stdout</span>
+
+    <span class="k">for</span> <span class="n">n</span><span class="p">,</span> <span class="n">label</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">labels</span><span class="p">):</span>
+
+        <span class="k">if</span> <span class="n">start</span> <span class="o">&gt;</span> <span class="n">n</span> <span class="o">+</span> <span class="mi">1</span><span class="p">:</span>
+
+            <span class="k">continue</span>
+
+        <span class="k">if</span> <span class="n">stop</span><span class="p">:</span>
+
+            <span class="k">break</span>
+
+        <span class="n">kwargs</span><span class="p">[</span><span class="s1">&#39;maxlen&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">maxlen_default</span>
+
+        <span class="k">while</span> <span class="kc">True</span><span class="p">:</span>
+
+            <span class="n">uniprots</span> <span class="o">=</span> <span class="n">groups</span><span class="p">[</span><span class="n">label</span><span class="p">]</span>
+            <span class="n">uniprots</span> <span class="o">=</span> <span class="p">(</span>
+                <span class="n">uniprots</span><span class="o">.</span><span class="n">members</span>
+                    <span class="k">if</span> <span class="nb">hasattr</span><span class="p">(</span><span class="n">uniprots</span><span class="p">,</span> <span class="s1">&#39;members&#39;</span><span class="p">)</span> <span class="k">else</span>
+                <span class="n">uniprots</span>
+            <span class="p">)</span>
+
+            <span class="n">header</span> <span class="o">=</span> <span class="p">(</span>
+                <span class="s1">&#39;[</span><span class="si">%u</span><span class="s1">/</span><span class="si">%u</span><span class="s1">] =====&gt; </span><span class="si">%s</span><span class="s1"> &lt;===== [</span><span class="si">%u</span><span class="s1"> proteins]</span><span class="se">\n</span><span class="s1">&#39;</span> <span class="o">%</span> <span class="p">(</span>
+                    <span class="n">n</span> <span class="o">+</span> <span class="mi">1</span><span class="p">,</span>
+                    <span class="n">n_groups</span><span class="p">,</span>
+                    <span class="n">label</span><span class="p">,</span>
+                    <span class="nb">len</span><span class="p">(</span><span class="n">uniprots</span><span class="p">)</span>
+                <span class="p">)</span>
+            <span class="p">)</span>
+
+            <span class="n">info</span><span class="p">(</span><span class="n">uniprots</span><span class="p">,</span> <span class="n">fileobj</span> <span class="o">=</span> <span class="n">fileobj</span><span class="p">,</span> <span class="n">header</span> <span class="o">=</span> <span class="n">header</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
+
+            <span class="n">inp</span> <span class="o">=</span> <span class="nb">input</span><span class="p">()</span>
+
+            <span class="k">if</span> <span class="n">inp</span> <span class="o">==</span> <span class="s1">&#39;q&#39;</span><span class="p">:</span>
+
+                <span class="n">stop</span> <span class="o">=</span> <span class="kc">True</span>
+                <span class="k">break</span>
+
+            <span class="k">elif</span> <span class="n">inp</span><span class="o">.</span><span class="n">isdigit</span><span class="p">():</span>
+
+                <span class="n">kwargs</span><span class="p">[</span><span class="s1">&#39;maxlen&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">inp</span><span class="p">)</span>
+
+            <span class="k">else</span><span class="p">:</span>
+
+                <span class="n">fileobj</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">linesep</span> <span class="o">*</span> <span class="mi">2</span><span class="p">)</span>
+                <span class="k">break</span>
+
+    <span class="n">sys</span><span class="o">.</span><span class="n">stdout</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">linesep</span><span class="p">)</span>
+    <span class="n">sys</span><span class="o">.</span><span class="n">stdout</span><span class="o">.</span><span class="n">flush</span><span class="p">()</span></div>
+
+
+
+<span class="n">default_features</span> <span class="o">=</span> <span class="p">(</span>
+    <span class="s1">&#39;ac&#39;</span><span class="p">,</span>
+    <span class="s1">&#39;genesymbol&#39;</span><span class="p">,</span>
+    <span class="s1">&#39;length&#39;</span><span class="p">,</span>
+    <span class="s1">&#39;weight&#39;</span><span class="p">,</span>
+    <span class="s1">&#39;full_name&#39;</span><span class="p">,</span>
+    <span class="s1">&#39;function_or_genecards&#39;</span><span class="p">,</span>
+    <span class="s1">&#39;keywords&#39;</span><span class="p">,</span>
+    <span class="s1">&#39;subcellular_location&#39;</span><span class="p">,</span>
+<span class="p">)</span>
+</pre></div>
+
+                </article>
+              
+              
+              
+              
+              
+                <footer class="prev-next-footer">
+                  
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+
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+  <section id="pypath-core-annot-adhesome">
+<h1>pypath.core.annot.Adhesome<a class="headerlink" href="#pypath-core-annot-adhesome" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.core.annot.Adhesome">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.core.annot.</span></span><span class="sig-name descname"><span class="pre">Adhesome</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#Adhesome"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.Adhesome" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <a class="reference internal" href="pypath.core.annot.AnnotationBase.html#pypath.core.annot.AnnotationBase" title="pypath.core.annot.AnnotationBase"><code class="xref py py-class docutils literal notranslate"><span class="pre">AnnotationBase</span></code></a></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Adhesome.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#Adhesome.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.Adhesome.__init__" title="Link to this definition">§</a></dt>
+<dd><p>Represents annotations for a set of proteins.
+Loads the data from the original resource and provides methods
+to query the annotations.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>name</strong> (<em>str</em>) – A custom name for the annotation resource.</p></li>
+<li><p><strong>ncbi_tax_id</strong> (<em>int</em>) – NCBI Taxonomy identifier.</p></li>
+<li><p><strong>input_method</strong> (<em>callable</em><em>,</em><em>str</em>) – Either a callable or the name of a method in any submodules of
+the <code class="docutils literal notranslate"><span class="pre">pypath.inputs</span></code>  module. Should return a dict with
+UniProt IDs as keys or an object suitable for <code class="docutils literal notranslate"><span class="pre">process_method</span></code>.</p></li>
+<li><p><strong>input_args</strong> (<em>dict</em>) – Arguments for the <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Adhesome.__init__" title="pypath.core.annot.Adhesome.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>(**kwargs)</p></td>
+<td><p>Represents annotations for a set of proteins.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Adhesome.add_complexes_by_inference" title="pypath.core.annot.Adhesome.add_complexes_by_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">add_complexes_by_inference</span></code></a>([complexes])</p></td>
+<td><p>Creates complex annotations by in silico inference and adds them to this annotation set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Adhesome.all_complexes" title="pypath.core.annot.Adhesome.all_complexes"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_complexes</span></code></a>()</p></td>
+<td><p>All protein complexes annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Adhesome.all_entities" title="pypath.core.annot.Adhesome.all_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_entities</span></code></a>([entity_types])</p></td>
+<td><p>All entities annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Adhesome.all_mirnas" title="pypath.core.annot.Adhesome.all_mirnas"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_mirnas</span></code></a>()</p></td>
+<td><p>All miRNAs annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Adhesome.all_proteins" title="pypath.core.annot.Adhesome.all_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_proteins</span></code></a>()</p></td>
+<td><p>All UniProt IDs annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Adhesome.all_refs" title="pypath.core.annot.Adhesome.all_refs"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_refs</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Adhesome.annotate_complex" title="pypath.core.annot.Adhesome.annotate_complex"><code class="xref py py-obj docutils literal notranslate"><span class="pre">annotate_complex</span></code></a>(cplex)</p></td>
+<td><p>Infers annotations for a single complex.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Adhesome.browse" title="pypath.core.annot.Adhesome.browse"><code class="xref py py-obj docutils literal notranslate"><span class="pre">browse</span></code></a>([field, start])</p></td>
+<td><p>Print gene information as a table.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Adhesome.complex_inference" title="pypath.core.annot.Adhesome.complex_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">complex_inference</span></code></a>([complexes])</p></td>
+<td><p>Annotates all complexes in <cite>complexes</cite>, by default in the default complex database (existing in the <cite>complex</cite> module or generated on demand according to the module's current settings).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Adhesome.coverage" title="pypath.core.annot.Adhesome.coverage"><code class="xref py py-obj docutils literal notranslate"><span class="pre">coverage</span></code></a>(other)</p></td>
+<td><p>Calculates the coverage of the annotation i.e. the proportion of entities having at least one record in this annotation resource for an arbitrary set of entities.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Adhesome.curation_effort" title="pypath.core.annot.Adhesome.curation_effort"><code class="xref py py-obj docutils literal notranslate"><span class="pre">curation_effort</span></code></a>()</p></td>
+<td><p>Counts the reference-record pairs.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">from_dump</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_entity_type</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Adhesome.get_names" title="pypath.core.annot.Adhesome.get_names"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_names</span></code></a>()</p></td>
+<td><p>Returns the list of field names in the records.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Adhesome.get_reference_set" title="pypath.core.annot.Adhesome.get_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_reference_set</span></code></a>([proteins, complexes, ...])</p></td>
+<td><p>Retrieves the reference set i.e. the set of all entities which potentially have annotation in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Adhesome.get_subset" title="pypath.core.annot.Adhesome.get_subset"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Adhesome.get_subset_bool_array" title="pypath.core.annot.Adhesome.get_subset_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset_bool_array</span></code></a>([reference_set])</p></td>
+<td><p>Returns a boolean vector with True and False values for each entity in the reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Adhesome.get_values" title="pypath.core.annot.Adhesome.get_values"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_values</span></code></a>(name[, exclude_none])</p></td>
+<td><p>Returns the set of all possible values of a field.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_complex</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_mirna</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_protein</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Adhesome.labels" title="pypath.core.annot.Adhesome.labels"><code class="xref py py-obj docutils literal notranslate"><span class="pre">labels</span></code></a>([method])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Adhesome.load" title="pypath.core.annot.Adhesome.load"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load</span></code></a>()</p></td>
+<td><p>Loads the annotation data by calling the input method.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Adhesome.load_data" title="pypath.core.annot.Adhesome.load_data"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_data</span></code></a>()</p></td>
+<td><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Adhesome.load_proteins" title="pypath.core.annot.Adhesome.load_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_proteins</span></code></a>()</p></td>
+<td><p>Retrieves a set of all UniProt IDs to have a base set of the entire proteome.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Adhesome.make_df" title="pypath.core.annot.Adhesome.make_df"><code class="xref py py-obj docutils literal notranslate"><span class="pre">make_df</span></code></a>([rebuild])</p></td>
+<td><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complex_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Adhesome.numof_entities" title="pypath.core.annot.Adhesome.numof_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_entities</span></code></a>()</p></td>
+<td><p>The number of annotated entities in the resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirna_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirnas</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_protein_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_proteins</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Adhesome.numof_records" title="pypath.core.annot.Adhesome.numof_records"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_records</span></code></a>([entity_types])</p></td>
+<td><p>The total number of annotation records.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Adhesome.numof_references" title="pypath.core.annot.Adhesome.numof_references"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_references</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Adhesome.process" title="pypath.core.annot.Adhesome.process"><code class="xref py py-obj docutils literal notranslate"><span class="pre">process</span></code></a>()</p></td>
+<td><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">proportion</span></code>(other)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Adhesome.reload" title="pypath.core.annot.Adhesome.reload"><code class="xref py py-obj docutils literal notranslate"><span class="pre">reload</span></code></a>()</p></td>
+<td><p>Reloads the object from the module level.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">save_to_pickle</span></code>(pickle_file)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Adhesome.select" title="pypath.core.annot.Adhesome.select"><code class="xref py py-obj docutils literal notranslate"><span class="pre">select</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Adhesome.set_method" title="pypath.core.annot.Adhesome.set_method"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_method</span></code></a>()</p></td>
+<td><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if necessary.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Adhesome.set_reference_set" title="pypath.core.annot.Adhesome.set_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_reference_set</span></code></a>()</p></td>
+<td><p>Assigns the reference set to the :py:attr``reference_set`` attribute.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Adhesome.show" title="pypath.core.annot.Adhesome.show"><code class="xref py py-obj docutils literal notranslate"><span class="pre">show</span></code></a>([method, table_param])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic information from the UniProt datasheets.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Adhesome.subset_intersection" title="pypath.core.annot.Adhesome.subset_intersection"><code class="xref py py-obj docutils literal notranslate"><span class="pre">subset_intersection</span></code></a>(universe, **kwargs)</p></td>
+<td><p>Calculates the proportion of entities in a subset occuring in the set <code class="docutils literal notranslate"><span class="pre">universe</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Adhesome.to_array" title="pypath.core.annot.Adhesome.to_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_array</span></code></a>([reference_set, use_fields])</p></td>
+<td><p>Returns an entity vs feature array.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Adhesome.to_bool_array" title="pypath.core.annot.Adhesome.to_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_bool_array</span></code></a>(reference_set)</p></td>
+<td><p>Returns a presence/absence boolean array for a reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Adhesome.to_set" title="pypath.core.annot.Adhesome.to_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_set</span></code></a>()</p></td>
+<td><p>Returns the entities present in this annotation resource as a set.</p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Attributes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_fields</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">summary</span></code></p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Adhesome.add_complexes_by_inference">
+<span class="sig-name descname"><span class="pre">add_complexes_by_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Adhesome.add_complexes_by_inference" title="Link to this definition">§</a></dt>
+<dd><p>Creates complex annotations by in silico inference and adds them
+to this annotation set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Adhesome.all_complexes">
+<span class="sig-name descname"><span class="pre">all_complexes</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Adhesome.all_complexes" title="Link to this definition">§</a></dt>
+<dd><p>All protein complexes annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Adhesome.all_entities">
+<span class="sig-name descname"><span class="pre">all_entities</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Adhesome.all_entities" title="Link to this definition">§</a></dt>
+<dd><p>All entities annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Adhesome.all_mirnas">
+<span class="sig-name descname"><span class="pre">all_mirnas</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Adhesome.all_mirnas" title="Link to this definition">§</a></dt>
+<dd><p>All miRNAs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Adhesome.all_proteins">
+<span class="sig-name descname"><span class="pre">all_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Adhesome.all_proteins" title="Link to this definition">§</a></dt>
+<dd><p>All UniProt IDs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Adhesome.all_refs">
+<span class="sig-name descname"><span class="pre">all_refs</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Adhesome.all_refs" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects the references
+across all records. Returns <em>list</em>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Adhesome.annotate_complex">
+<span class="sig-name descname"><span class="pre">annotate_complex</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cplex</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Adhesome.annotate_complex" title="Link to this definition">§</a></dt>
+<dd><p>Infers annotations for a single complex.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Adhesome.browse">
+<span class="sig-name descname"><span class="pre">browse</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">field</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">start</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Adhesome.browse" title="Link to this definition">§</a></dt>
+<dd><p>Print gene information as a table.</p>
+<p>Presents information about annotation categories as ascii tables
+printed in the terminal. If one category provided, prints one table.
+If multiple categories provided, prints a table for each of them one
+by one proceeding to the next one once you hit return. If no categories
+provided goes through all levels of the primary category.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>field:</dt><dd><p>The field to browse categories by.</p>
+<ul class="simple">
+<li><p>If None the primary field will be selected.
+If this annotation resource doesn’t have fields, all proteins
+will be presented as one single category.</p></li>
+<li><p>If a string it will be considered a field name and it will
+browse through all levels of this field.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">list</span></code>, set or tuple, it will be considered either a
+<code class="docutils literal notranslate"><span class="pre">list</span></code> of field names or a list of values from the primary
+field. In the former case all combinations of the values of
+the fields will be presented, in the latter case the browsing
+will be limited to the levels of the primary field contained
+in <code class="docutils literal notranslate"><span class="pre">field</span></code>.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">dict</span></code>, keys are supposed to be field names and values
+as list of levels. If any of the values are None, all levels
+from that field will be used.</p></li>
+</ul>
+</dd>
+<dt>start:</dt><dd><p>Start browsing from this category. E.g. if there are 500
+categories and start is 250 it will skip everything before the
+250th.</p>
+</dd>
+<dt>kwargs:</dt><dd><p>Passed to <code class="docutils literal notranslate"><span class="pre">pypath.utils.uniprot.info</span></code>.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Adhesome.complex_inference">
+<span class="sig-name descname"><span class="pre">complex_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Adhesome.complex_inference" title="Link to this definition">§</a></dt>
+<dd><p>Annotates all complexes in <cite>complexes</cite>, by default in the default
+complex database (existing in the <cite>complex</cite> module or generated
+on demand according to the module’s current settings).</p>
+<dl class="field-list simple">
+<dt class="field-odd">Returns<span class="colon">:</span></dt>
+<dd class="field-odd"><p><ul class="simple">
+<li><p><em>Dict with complexes as keys and sets of annotations as values.</em></p></li>
+<li><p><em>Complexes with no valid information in this annotation resource</em></p></li>
+<li><p><em>won’t be in the dict.</em></p></li>
+</ul>
+</p>
+</dd>
+<dt class="field-even">Parameters<span class="colon">:</span></dt>
+<dd class="field-even"><p><strong>complexes</strong> (<em>iterable</em>) – Iterable yielding complexes.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Adhesome.coverage">
+<span class="sig-name descname"><span class="pre">coverage</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">other</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Adhesome.coverage" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the coverage of the annotation i.e. the proportion of
+entities having at least one record in this annotation resource
+for an arbitrary set of entities.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Adhesome.curation_effort">
+<span class="sig-name descname"><span class="pre">curation_effort</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Adhesome.curation_effort" title="Link to this definition">§</a></dt>
+<dd><p>Counts the reference-record pairs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Adhesome.get_names">
+<span class="sig-name descname"><span class="pre">get_names</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Adhesome.get_names" title="Link to this definition">§</a></dt>
+<dd><p>Returns the list of field names in the records. The annotation
+consists of uniform records and each entity might be annotated
+with one or more records. Each record is a tuple of fields, for
+example <code class="docutils literal notranslate"><span class="pre">('cell_type',</span> <span class="pre">'expression_level',</span> <span class="pre">'score')</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Adhesome.get_reference_set">
+<em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">get_reference_set</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">proteins</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">swissprot_only</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Adhesome.get_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the reference set i.e. the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Adhesome.get_subset">
+<span class="sig-name descname"><span class="pre">get_subset</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Adhesome.get_subset" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Adhesome.get_subset_bool_array">
+<span class="sig-name descname"><span class="pre">get_subset_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Adhesome.get_subset_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a boolean vector with True and False values for each entity
+in the reference set. The values represent presence absence data
+in the simplest case, but by providing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> any kind of matching
+and filtering is possible. <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> are passed to the <code class="docutils literal notranslate"><span class="pre">select</span></code>
+method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Adhesome.get_values">
+<span class="sig-name descname"><span class="pre">get_values</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">exclude_none</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Adhesome.get_values" title="Link to this definition">§</a></dt>
+<dd><p>Returns the set of all possible values of a field. E.g. if the
+records of this annotation have a field <code class="docutils literal notranslate"><span class="pre">cell_type</span></code> then calling
+this method can tell you that across all records the values of
+this field might be <code class="docutils literal notranslate"><span class="pre">{'macrophage',</span> <span class="pre">'epithelial_cell',</span> <span class="pre">...}</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Adhesome.labels">
+<span class="sig-name descname"><span class="pre">labels</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Adhesome.labels" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Adhesome.load">
+<span class="sig-name descname"><span class="pre">load</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Adhesome.load" title="Link to this definition">§</a></dt>
+<dd><p>Loads the annotation data by calling the input method.
+Infers annotations for complexes in the complex database if
+py:attr:<code class="docutils literal notranslate"><span class="pre">infer_complexes</span></code> is True.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Adhesome.load_data">
+<span class="sig-name descname"><span class="pre">load_data</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Adhesome.load_data" title="Link to this definition">§</a></dt>
+<dd><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Adhesome.load_proteins">
+<span class="sig-name descname"><span class="pre">load_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Adhesome.load_proteins" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a set of all UniProt IDs to have a base set of the entire
+proteome.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Adhesome.make_df">
+<span class="sig-name descname"><span class="pre">make_df</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">rebuild</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Adhesome.make_df" title="Link to this definition">§</a></dt>
+<dd><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.
+The data frame will be assigned to :py:attr``df``.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Adhesome.numof_entities">
+<span class="sig-name descname"><span class="pre">numof_entities</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Adhesome.numof_entities" title="Link to this definition">§</a></dt>
+<dd><p>The number of annotated entities in the resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Adhesome.numof_records">
+<span class="sig-name descname"><span class="pre">numof_records</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Adhesome.numof_records" title="Link to this definition">§</a></dt>
+<dd><p>The total number of annotation records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Adhesome.numof_references">
+<span class="sig-name descname"><span class="pre">numof_references</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Adhesome.numof_references" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects and counts the
+references across all records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Adhesome.process">
+<span class="sig-name descname"><span class="pre">process</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Adhesome.process" title="Link to this definition">§</a></dt>
+<dd><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Adhesome.reload">
+<span class="sig-name descname"><span class="pre">reload</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Adhesome.reload" title="Link to this definition">§</a></dt>
+<dd><p>Reloads the object from the module level.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Adhesome.select">
+<span class="sig-name descname"><span class="pre">select</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Adhesome.select" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Adhesome.set_method">
+<span class="sig-name descname"><span class="pre">set_method</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Adhesome.set_method" title="Link to this definition">§</a></dt>
+<dd><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if
+necessary.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Adhesome.set_reference_set">
+<span class="sig-name descname"><span class="pre">set_reference_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Adhesome.set_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Assigns the reference set to the :py:attr``reference_set`` attribute.
+The reference set is the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Adhesome.show">
+<span class="sig-name descname"><span class="pre">show</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">table_param</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Adhesome.show" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic
+information from the UniProt datasheets.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Adhesome.subset_intersection">
+<span class="sig-name descname"><span class="pre">subset_intersection</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">universe</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Adhesome.subset_intersection" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the proportion of entities in a subset occuring in the
+set <code class="docutils literal notranslate"><span class="pre">universe</span></code>. The subset is selected by passing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> to the
+<code class="docutils literal notranslate"><span class="pre">select</span></code> method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Adhesome.to_array">
+<span class="sig-name descname"><span class="pre">to_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_fields</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Adhesome.to_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns an entity vs feature array. In case of more complex
+annotations this might be huge.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Adhesome.to_bool_array">
+<span class="sig-name descname"><span class="pre">to_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Adhesome.to_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a presence/absence boolean array for a reference set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Adhesome.to_set">
+<span class="sig-name descname"><span class="pre">to_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Adhesome.to_set" title="Link to this definition">§</a></dt>
+<dd><p>Returns the entities present in this annotation resource as a set.</p>
+</dd></dl>
+
+</dd></dl>
+
+</section>
+
+
+                </article>
+              
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+  <section id="pypath-core-annot-almen2009">
+<h1>pypath.core.annot.Almen2009<a class="headerlink" href="#pypath-core-annot-almen2009" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.core.annot.Almen2009">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.core.annot.</span></span><span class="sig-name descname"><span class="pre">Almen2009</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#Almen2009"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.Almen2009" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <a class="reference internal" href="pypath.core.annot.AnnotationBase.html#pypath.core.annot.AnnotationBase" title="pypath.core.annot.AnnotationBase"><code class="xref py py-class docutils literal notranslate"><span class="pre">AnnotationBase</span></code></a></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Almen2009.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#Almen2009.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.Almen2009.__init__" title="Link to this definition">§</a></dt>
+<dd><p>Represents annotations for a set of proteins.
+Loads the data from the original resource and provides methods
+to query the annotations.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>name</strong> (<em>str</em>) – A custom name for the annotation resource.</p></li>
+<li><p><strong>ncbi_tax_id</strong> (<em>int</em>) – NCBI Taxonomy identifier.</p></li>
+<li><p><strong>input_method</strong> (<em>callable</em><em>,</em><em>str</em>) – Either a callable or the name of a method in any submodules of
+the <code class="docutils literal notranslate"><span class="pre">pypath.inputs</span></code>  module. Should return a dict with
+UniProt IDs as keys or an object suitable for <code class="docutils literal notranslate"><span class="pre">process_method</span></code>.</p></li>
+<li><p><strong>input_args</strong> (<em>dict</em>) – Arguments for the <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Almen2009.__init__" title="pypath.core.annot.Almen2009.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>([ncbi_tax_id])</p></td>
+<td><p>Represents annotations for a set of proteins.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Almen2009.add_complexes_by_inference" title="pypath.core.annot.Almen2009.add_complexes_by_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">add_complexes_by_inference</span></code></a>([complexes])</p></td>
+<td><p>Creates complex annotations by in silico inference and adds them to this annotation set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Almen2009.all_complexes" title="pypath.core.annot.Almen2009.all_complexes"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_complexes</span></code></a>()</p></td>
+<td><p>All protein complexes annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Almen2009.all_entities" title="pypath.core.annot.Almen2009.all_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_entities</span></code></a>([entity_types])</p></td>
+<td><p>All entities annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Almen2009.all_mirnas" title="pypath.core.annot.Almen2009.all_mirnas"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_mirnas</span></code></a>()</p></td>
+<td><p>All miRNAs annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Almen2009.all_proteins" title="pypath.core.annot.Almen2009.all_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_proteins</span></code></a>()</p></td>
+<td><p>All UniProt IDs annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Almen2009.all_refs" title="pypath.core.annot.Almen2009.all_refs"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_refs</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Almen2009.annotate_complex" title="pypath.core.annot.Almen2009.annotate_complex"><code class="xref py py-obj docutils literal notranslate"><span class="pre">annotate_complex</span></code></a>(cplex)</p></td>
+<td><p>Infers annotations for a single complex.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Almen2009.browse" title="pypath.core.annot.Almen2009.browse"><code class="xref py py-obj docutils literal notranslate"><span class="pre">browse</span></code></a>([field, start])</p></td>
+<td><p>Print gene information as a table.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Almen2009.complex_inference" title="pypath.core.annot.Almen2009.complex_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">complex_inference</span></code></a>([complexes])</p></td>
+<td><p>Annotates all complexes in <cite>complexes</cite>, by default in the default complex database (existing in the <cite>complex</cite> module or generated on demand according to the module's current settings).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Almen2009.coverage" title="pypath.core.annot.Almen2009.coverage"><code class="xref py py-obj docutils literal notranslate"><span class="pre">coverage</span></code></a>(other)</p></td>
+<td><p>Calculates the coverage of the annotation i.e. the proportion of entities having at least one record in this annotation resource for an arbitrary set of entities.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Almen2009.curation_effort" title="pypath.core.annot.Almen2009.curation_effort"><code class="xref py py-obj docutils literal notranslate"><span class="pre">curation_effort</span></code></a>()</p></td>
+<td><p>Counts the reference-record pairs.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">from_dump</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_entity_type</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Almen2009.get_names" title="pypath.core.annot.Almen2009.get_names"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_names</span></code></a>()</p></td>
+<td><p>Returns the list of field names in the records.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Almen2009.get_reference_set" title="pypath.core.annot.Almen2009.get_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_reference_set</span></code></a>([proteins, complexes, ...])</p></td>
+<td><p>Retrieves the reference set i.e. the set of all entities which potentially have annotation in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Almen2009.get_subset" title="pypath.core.annot.Almen2009.get_subset"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Almen2009.get_subset_bool_array" title="pypath.core.annot.Almen2009.get_subset_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset_bool_array</span></code></a>([reference_set])</p></td>
+<td><p>Returns a boolean vector with True and False values for each entity in the reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Almen2009.get_values" title="pypath.core.annot.Almen2009.get_values"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_values</span></code></a>(name[, exclude_none])</p></td>
+<td><p>Returns the set of all possible values of a field.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_complex</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_mirna</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_protein</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Almen2009.labels" title="pypath.core.annot.Almen2009.labels"><code class="xref py py-obj docutils literal notranslate"><span class="pre">labels</span></code></a>([method])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Almen2009.load" title="pypath.core.annot.Almen2009.load"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load</span></code></a>()</p></td>
+<td><p>Loads the annotation data by calling the input method.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Almen2009.load_data" title="pypath.core.annot.Almen2009.load_data"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_data</span></code></a>()</p></td>
+<td><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Almen2009.load_proteins" title="pypath.core.annot.Almen2009.load_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_proteins</span></code></a>()</p></td>
+<td><p>Retrieves a set of all UniProt IDs to have a base set of the entire proteome.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Almen2009.make_df" title="pypath.core.annot.Almen2009.make_df"><code class="xref py py-obj docutils literal notranslate"><span class="pre">make_df</span></code></a>([rebuild])</p></td>
+<td><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complex_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Almen2009.numof_entities" title="pypath.core.annot.Almen2009.numof_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_entities</span></code></a>()</p></td>
+<td><p>The number of annotated entities in the resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirna_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirnas</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_protein_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_proteins</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Almen2009.numof_records" title="pypath.core.annot.Almen2009.numof_records"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_records</span></code></a>([entity_types])</p></td>
+<td><p>The total number of annotation records.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Almen2009.numof_references" title="pypath.core.annot.Almen2009.numof_references"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_references</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Almen2009.process" title="pypath.core.annot.Almen2009.process"><code class="xref py py-obj docutils literal notranslate"><span class="pre">process</span></code></a>()</p></td>
+<td><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">proportion</span></code>(other)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Almen2009.reload" title="pypath.core.annot.Almen2009.reload"><code class="xref py py-obj docutils literal notranslate"><span class="pre">reload</span></code></a>()</p></td>
+<td><p>Reloads the object from the module level.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">save_to_pickle</span></code>(pickle_file)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Almen2009.select" title="pypath.core.annot.Almen2009.select"><code class="xref py py-obj docutils literal notranslate"><span class="pre">select</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Almen2009.set_method" title="pypath.core.annot.Almen2009.set_method"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_method</span></code></a>()</p></td>
+<td><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if necessary.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Almen2009.set_reference_set" title="pypath.core.annot.Almen2009.set_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_reference_set</span></code></a>()</p></td>
+<td><p>Assigns the reference set to the :py:attr``reference_set`` attribute.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Almen2009.show" title="pypath.core.annot.Almen2009.show"><code class="xref py py-obj docutils literal notranslate"><span class="pre">show</span></code></a>([method, table_param])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic information from the UniProt datasheets.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Almen2009.subset_intersection" title="pypath.core.annot.Almen2009.subset_intersection"><code class="xref py py-obj docutils literal notranslate"><span class="pre">subset_intersection</span></code></a>(universe, **kwargs)</p></td>
+<td><p>Calculates the proportion of entities in a subset occuring in the set <code class="docutils literal notranslate"><span class="pre">universe</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Almen2009.to_array" title="pypath.core.annot.Almen2009.to_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_array</span></code></a>([reference_set, use_fields])</p></td>
+<td><p>Returns an entity vs feature array.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Almen2009.to_bool_array" title="pypath.core.annot.Almen2009.to_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_bool_array</span></code></a>(reference_set)</p></td>
+<td><p>Returns a presence/absence boolean array for a reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Almen2009.to_set" title="pypath.core.annot.Almen2009.to_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_set</span></code></a>()</p></td>
+<td><p>Returns the entities present in this annotation resource as a set.</p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Attributes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_fields</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">summary</span></code></p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Almen2009.add_complexes_by_inference">
+<span class="sig-name descname"><span class="pre">add_complexes_by_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Almen2009.add_complexes_by_inference" title="Link to this definition">§</a></dt>
+<dd><p>Creates complex annotations by in silico inference and adds them
+to this annotation set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Almen2009.all_complexes">
+<span class="sig-name descname"><span class="pre">all_complexes</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Almen2009.all_complexes" title="Link to this definition">§</a></dt>
+<dd><p>All protein complexes annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Almen2009.all_entities">
+<span class="sig-name descname"><span class="pre">all_entities</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Almen2009.all_entities" title="Link to this definition">§</a></dt>
+<dd><p>All entities annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Almen2009.all_mirnas">
+<span class="sig-name descname"><span class="pre">all_mirnas</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Almen2009.all_mirnas" title="Link to this definition">§</a></dt>
+<dd><p>All miRNAs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Almen2009.all_proteins">
+<span class="sig-name descname"><span class="pre">all_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Almen2009.all_proteins" title="Link to this definition">§</a></dt>
+<dd><p>All UniProt IDs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Almen2009.all_refs">
+<span class="sig-name descname"><span class="pre">all_refs</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Almen2009.all_refs" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects the references
+across all records. Returns <em>list</em>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Almen2009.annotate_complex">
+<span class="sig-name descname"><span class="pre">annotate_complex</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cplex</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Almen2009.annotate_complex" title="Link to this definition">§</a></dt>
+<dd><p>Infers annotations for a single complex.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Almen2009.browse">
+<span class="sig-name descname"><span class="pre">browse</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">field</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">start</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Almen2009.browse" title="Link to this definition">§</a></dt>
+<dd><p>Print gene information as a table.</p>
+<p>Presents information about annotation categories as ascii tables
+printed in the terminal. If one category provided, prints one table.
+If multiple categories provided, prints a table for each of them one
+by one proceeding to the next one once you hit return. If no categories
+provided goes through all levels of the primary category.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>field:</dt><dd><p>The field to browse categories by.</p>
+<ul class="simple">
+<li><p>If None the primary field will be selected.
+If this annotation resource doesn’t have fields, all proteins
+will be presented as one single category.</p></li>
+<li><p>If a string it will be considered a field name and it will
+browse through all levels of this field.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">list</span></code>, set or tuple, it will be considered either a
+<code class="docutils literal notranslate"><span class="pre">list</span></code> of field names or a list of values from the primary
+field. In the former case all combinations of the values of
+the fields will be presented, in the latter case the browsing
+will be limited to the levels of the primary field contained
+in <code class="docutils literal notranslate"><span class="pre">field</span></code>.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">dict</span></code>, keys are supposed to be field names and values
+as list of levels. If any of the values are None, all levels
+from that field will be used.</p></li>
+</ul>
+</dd>
+<dt>start:</dt><dd><p>Start browsing from this category. E.g. if there are 500
+categories and start is 250 it will skip everything before the
+250th.</p>
+</dd>
+<dt>kwargs:</dt><dd><p>Passed to <code class="docutils literal notranslate"><span class="pre">pypath.utils.uniprot.info</span></code>.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Almen2009.complex_inference">
+<span class="sig-name descname"><span class="pre">complex_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Almen2009.complex_inference" title="Link to this definition">§</a></dt>
+<dd><p>Annotates all complexes in <cite>complexes</cite>, by default in the default
+complex database (existing in the <cite>complex</cite> module or generated
+on demand according to the module’s current settings).</p>
+<dl class="field-list simple">
+<dt class="field-odd">Returns<span class="colon">:</span></dt>
+<dd class="field-odd"><p><ul class="simple">
+<li><p><em>Dict with complexes as keys and sets of annotations as values.</em></p></li>
+<li><p><em>Complexes with no valid information in this annotation resource</em></p></li>
+<li><p><em>won’t be in the dict.</em></p></li>
+</ul>
+</p>
+</dd>
+<dt class="field-even">Parameters<span class="colon">:</span></dt>
+<dd class="field-even"><p><strong>complexes</strong> (<em>iterable</em>) – Iterable yielding complexes.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Almen2009.coverage">
+<span class="sig-name descname"><span class="pre">coverage</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">other</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Almen2009.coverage" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the coverage of the annotation i.e. the proportion of
+entities having at least one record in this annotation resource
+for an arbitrary set of entities.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Almen2009.curation_effort">
+<span class="sig-name descname"><span class="pre">curation_effort</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Almen2009.curation_effort" title="Link to this definition">§</a></dt>
+<dd><p>Counts the reference-record pairs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Almen2009.get_names">
+<span class="sig-name descname"><span class="pre">get_names</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Almen2009.get_names" title="Link to this definition">§</a></dt>
+<dd><p>Returns the list of field names in the records. The annotation
+consists of uniform records and each entity might be annotated
+with one or more records. Each record is a tuple of fields, for
+example <code class="docutils literal notranslate"><span class="pre">('cell_type',</span> <span class="pre">'expression_level',</span> <span class="pre">'score')</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Almen2009.get_reference_set">
+<em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">get_reference_set</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">proteins</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">swissprot_only</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Almen2009.get_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the reference set i.e. the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Almen2009.get_subset">
+<span class="sig-name descname"><span class="pre">get_subset</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Almen2009.get_subset" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Almen2009.get_subset_bool_array">
+<span class="sig-name descname"><span class="pre">get_subset_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Almen2009.get_subset_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a boolean vector with True and False values for each entity
+in the reference set. The values represent presence absence data
+in the simplest case, but by providing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> any kind of matching
+and filtering is possible. <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> are passed to the <code class="docutils literal notranslate"><span class="pre">select</span></code>
+method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Almen2009.get_values">
+<span class="sig-name descname"><span class="pre">get_values</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">exclude_none</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Almen2009.get_values" title="Link to this definition">§</a></dt>
+<dd><p>Returns the set of all possible values of a field. E.g. if the
+records of this annotation have a field <code class="docutils literal notranslate"><span class="pre">cell_type</span></code> then calling
+this method can tell you that across all records the values of
+this field might be <code class="docutils literal notranslate"><span class="pre">{'macrophage',</span> <span class="pre">'epithelial_cell',</span> <span class="pre">...}</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Almen2009.labels">
+<span class="sig-name descname"><span class="pre">labels</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Almen2009.labels" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Almen2009.load">
+<span class="sig-name descname"><span class="pre">load</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Almen2009.load" title="Link to this definition">§</a></dt>
+<dd><p>Loads the annotation data by calling the input method.
+Infers annotations for complexes in the complex database if
+py:attr:<code class="docutils literal notranslate"><span class="pre">infer_complexes</span></code> is True.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Almen2009.load_data">
+<span class="sig-name descname"><span class="pre">load_data</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Almen2009.load_data" title="Link to this definition">§</a></dt>
+<dd><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Almen2009.load_proteins">
+<span class="sig-name descname"><span class="pre">load_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Almen2009.load_proteins" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a set of all UniProt IDs to have a base set of the entire
+proteome.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Almen2009.make_df">
+<span class="sig-name descname"><span class="pre">make_df</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">rebuild</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Almen2009.make_df" title="Link to this definition">§</a></dt>
+<dd><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.
+The data frame will be assigned to :py:attr``df``.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Almen2009.numof_entities">
+<span class="sig-name descname"><span class="pre">numof_entities</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Almen2009.numof_entities" title="Link to this definition">§</a></dt>
+<dd><p>The number of annotated entities in the resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Almen2009.numof_records">
+<span class="sig-name descname"><span class="pre">numof_records</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Almen2009.numof_records" title="Link to this definition">§</a></dt>
+<dd><p>The total number of annotation records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Almen2009.numof_references">
+<span class="sig-name descname"><span class="pre">numof_references</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Almen2009.numof_references" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects and counts the
+references across all records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Almen2009.process">
+<span class="sig-name descname"><span class="pre">process</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Almen2009.process" title="Link to this definition">§</a></dt>
+<dd><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Almen2009.reload">
+<span class="sig-name descname"><span class="pre">reload</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Almen2009.reload" title="Link to this definition">§</a></dt>
+<dd><p>Reloads the object from the module level.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Almen2009.select">
+<span class="sig-name descname"><span class="pre">select</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Almen2009.select" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Almen2009.set_method">
+<span class="sig-name descname"><span class="pre">set_method</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Almen2009.set_method" title="Link to this definition">§</a></dt>
+<dd><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if
+necessary.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Almen2009.set_reference_set">
+<span class="sig-name descname"><span class="pre">set_reference_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Almen2009.set_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Assigns the reference set to the :py:attr``reference_set`` attribute.
+The reference set is the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Almen2009.show">
+<span class="sig-name descname"><span class="pre">show</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">table_param</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Almen2009.show" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic
+information from the UniProt datasheets.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Almen2009.subset_intersection">
+<span class="sig-name descname"><span class="pre">subset_intersection</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">universe</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Almen2009.subset_intersection" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the proportion of entities in a subset occuring in the
+set <code class="docutils literal notranslate"><span class="pre">universe</span></code>. The subset is selected by passing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> to the
+<code class="docutils literal notranslate"><span class="pre">select</span></code> method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Almen2009.to_array">
+<span class="sig-name descname"><span class="pre">to_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_fields</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Almen2009.to_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns an entity vs feature array. In case of more complex
+annotations this might be huge.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Almen2009.to_bool_array">
+<span class="sig-name descname"><span class="pre">to_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Almen2009.to_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a presence/absence boolean array for a reference set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Almen2009.to_set">
+<span class="sig-name descname"><span class="pre">to_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Almen2009.to_set" title="Link to this definition">§</a></dt>
+<dd><p>Returns the entities present in this annotation resource as a set.</p>
+</dd></dl>
+
+</dd></dl>
+
+</section>
+
+
+                </article>
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+  <section id="pypath-core-annot-annotationbase">
+<h1>pypath.core.annot.AnnotationBase<a class="headerlink" href="#pypath-core-annot-annotationbase" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.core.annot.AnnotationBase">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.core.annot.</span></span><span class="sig-name descname"><span class="pre">AnnotationBase</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">input_method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">input_args</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'protein'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">swissprot_only</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">proteins</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">infer_complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">dump</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">primary_field</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">check_ids</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#AnnotationBase"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.AnnotationBase" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <a class="reference internal" href="pypath.internals.resource.AbstractResource.html#pypath.internals.resource.AbstractResource" title="pypath.internals.resource.AbstractResource"><code class="xref py py-class docutils literal notranslate"><span class="pre">AbstractResource</span></code></a></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.AnnotationBase.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">input_method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">input_args</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'protein'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">swissprot_only</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">proteins</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">infer_complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">dump</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">primary_field</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">check_ids</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#AnnotationBase.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.AnnotationBase.__init__" title="Link to this definition">§</a></dt>
+<dd><p>Represents annotations for a set of proteins.
+Loads the data from the original resource and provides methods
+to query the annotations.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>name</strong> (<em>str</em>) – A custom name for the annotation resource.</p></li>
+<li><p><strong>ncbi_tax_id</strong> (<em>int</em>) – NCBI Taxonomy identifier.</p></li>
+<li><p><strong>input_method</strong> (<em>callable</em><em>,</em><em>str</em>) – Either a callable or the name of a method in any submodules of
+the <code class="docutils literal notranslate"><span class="pre">pypath.inputs</span></code>  module. Should return a dict with
+UniProt IDs as keys or an object suitable for <code class="docutils literal notranslate"><span class="pre">process_method</span></code>.</p></li>
+<li><p><strong>input_args</strong> (<em>dict</em>) – Arguments for the <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.AnnotationBase.__init__" title="pypath.core.annot.AnnotationBase.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>(name[, ncbi_tax_id, input_method, ...])</p></td>
+<td><p>Represents annotations for a set of proteins.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.AnnotationBase.add_complexes_by_inference" title="pypath.core.annot.AnnotationBase.add_complexes_by_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">add_complexes_by_inference</span></code></a>([complexes])</p></td>
+<td><p>Creates complex annotations by in silico inference and adds them to this annotation set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.AnnotationBase.all_complexes" title="pypath.core.annot.AnnotationBase.all_complexes"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_complexes</span></code></a>()</p></td>
+<td><p>All protein complexes annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.AnnotationBase.all_entities" title="pypath.core.annot.AnnotationBase.all_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_entities</span></code></a>([entity_types])</p></td>
+<td><p>All entities annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.AnnotationBase.all_mirnas" title="pypath.core.annot.AnnotationBase.all_mirnas"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_mirnas</span></code></a>()</p></td>
+<td><p>All miRNAs annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.AnnotationBase.all_proteins" title="pypath.core.annot.AnnotationBase.all_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_proteins</span></code></a>()</p></td>
+<td><p>All UniProt IDs annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.AnnotationBase.all_refs" title="pypath.core.annot.AnnotationBase.all_refs"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_refs</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.AnnotationBase.annotate_complex" title="pypath.core.annot.AnnotationBase.annotate_complex"><code class="xref py py-obj docutils literal notranslate"><span class="pre">annotate_complex</span></code></a>(cplex)</p></td>
+<td><p>Infers annotations for a single complex.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.AnnotationBase.browse" title="pypath.core.annot.AnnotationBase.browse"><code class="xref py py-obj docutils literal notranslate"><span class="pre">browse</span></code></a>([field, start])</p></td>
+<td><p>Print gene information as a table.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.AnnotationBase.complex_inference" title="pypath.core.annot.AnnotationBase.complex_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">complex_inference</span></code></a>([complexes])</p></td>
+<td><p>Annotates all complexes in <cite>complexes</cite>, by default in the default complex database (existing in the <cite>complex</cite> module or generated on demand according to the module's current settings).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.AnnotationBase.coverage" title="pypath.core.annot.AnnotationBase.coverage"><code class="xref py py-obj docutils literal notranslate"><span class="pre">coverage</span></code></a>(other)</p></td>
+<td><p>Calculates the coverage of the annotation i.e. the proportion of entities having at least one record in this annotation resource for an arbitrary set of entities.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.AnnotationBase.curation_effort" title="pypath.core.annot.AnnotationBase.curation_effort"><code class="xref py py-obj docutils literal notranslate"><span class="pre">curation_effort</span></code></a>()</p></td>
+<td><p>Counts the reference-record pairs.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">from_dump</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_entity_type</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.AnnotationBase.get_names" title="pypath.core.annot.AnnotationBase.get_names"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_names</span></code></a>()</p></td>
+<td><p>Returns the list of field names in the records.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.AnnotationBase.get_reference_set" title="pypath.core.annot.AnnotationBase.get_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_reference_set</span></code></a>([proteins, complexes, ...])</p></td>
+<td><p>Retrieves the reference set i.e. the set of all entities which potentially have annotation in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.AnnotationBase.get_subset" title="pypath.core.annot.AnnotationBase.get_subset"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.AnnotationBase.get_subset_bool_array" title="pypath.core.annot.AnnotationBase.get_subset_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset_bool_array</span></code></a>([reference_set])</p></td>
+<td><p>Returns a boolean vector with True and False values for each entity in the reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.AnnotationBase.get_values" title="pypath.core.annot.AnnotationBase.get_values"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_values</span></code></a>(name[, exclude_none])</p></td>
+<td><p>Returns the set of all possible values of a field.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_complex</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_mirna</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_protein</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.AnnotationBase.labels" title="pypath.core.annot.AnnotationBase.labels"><code class="xref py py-obj docutils literal notranslate"><span class="pre">labels</span></code></a>([method])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.AnnotationBase.load" title="pypath.core.annot.AnnotationBase.load"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load</span></code></a>()</p></td>
+<td><p>Loads the annotation data by calling the input method.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.AnnotationBase.load_data" title="pypath.core.annot.AnnotationBase.load_data"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_data</span></code></a>()</p></td>
+<td><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.AnnotationBase.load_proteins" title="pypath.core.annot.AnnotationBase.load_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_proteins</span></code></a>()</p></td>
+<td><p>Retrieves a set of all UniProt IDs to have a base set of the entire proteome.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.AnnotationBase.make_df" title="pypath.core.annot.AnnotationBase.make_df"><code class="xref py py-obj docutils literal notranslate"><span class="pre">make_df</span></code></a>([rebuild])</p></td>
+<td><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complex_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.AnnotationBase.numof_entities" title="pypath.core.annot.AnnotationBase.numof_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_entities</span></code></a>()</p></td>
+<td><p>The number of annotated entities in the resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirna_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirnas</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_protein_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_proteins</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.AnnotationBase.numof_records" title="pypath.core.annot.AnnotationBase.numof_records"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_records</span></code></a>([entity_types])</p></td>
+<td><p>The total number of annotation records.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.AnnotationBase.numof_references" title="pypath.core.annot.AnnotationBase.numof_references"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_references</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.AnnotationBase.process" title="pypath.core.annot.AnnotationBase.process"><code class="xref py py-obj docutils literal notranslate"><span class="pre">process</span></code></a>()</p></td>
+<td><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">proportion</span></code>(other)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.AnnotationBase.reload" title="pypath.core.annot.AnnotationBase.reload"><code class="xref py py-obj docutils literal notranslate"><span class="pre">reload</span></code></a>()</p></td>
+<td><p>Reloads the object from the module level.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">save_to_pickle</span></code>(pickle_file)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.AnnotationBase.select" title="pypath.core.annot.AnnotationBase.select"><code class="xref py py-obj docutils literal notranslate"><span class="pre">select</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.AnnotationBase.set_method" title="pypath.core.annot.AnnotationBase.set_method"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_method</span></code></a>()</p></td>
+<td><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if necessary.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.AnnotationBase.set_reference_set" title="pypath.core.annot.AnnotationBase.set_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_reference_set</span></code></a>()</p></td>
+<td><p>Assigns the reference set to the :py:attr``reference_set`` attribute.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.AnnotationBase.show" title="pypath.core.annot.AnnotationBase.show"><code class="xref py py-obj docutils literal notranslate"><span class="pre">show</span></code></a>([method, table_param])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic information from the UniProt datasheets.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.AnnotationBase.subset_intersection" title="pypath.core.annot.AnnotationBase.subset_intersection"><code class="xref py py-obj docutils literal notranslate"><span class="pre">subset_intersection</span></code></a>(universe, **kwargs)</p></td>
+<td><p>Calculates the proportion of entities in a subset occuring in the set <code class="docutils literal notranslate"><span class="pre">universe</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.AnnotationBase.to_array" title="pypath.core.annot.AnnotationBase.to_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_array</span></code></a>([reference_set, use_fields])</p></td>
+<td><p>Returns an entity vs feature array.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.AnnotationBase.to_bool_array" title="pypath.core.annot.AnnotationBase.to_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_bool_array</span></code></a>(reference_set)</p></td>
+<td><p>Returns a presence/absence boolean array for a reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.AnnotationBase.to_set" title="pypath.core.annot.AnnotationBase.to_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_set</span></code></a>()</p></td>
+<td><p>Returns the entities present in this annotation resource as a set.</p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Attributes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_fields</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">summary</span></code></p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.AnnotationBase.add_complexes_by_inference">
+<span class="sig-name descname"><span class="pre">add_complexes_by_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#AnnotationBase.add_complexes_by_inference"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.AnnotationBase.add_complexes_by_inference" title="Link to this definition">§</a></dt>
+<dd><p>Creates complex annotations by in silico inference and adds them
+to this annotation set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.AnnotationBase.all_complexes">
+<span class="sig-name descname"><span class="pre">all_complexes</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#AnnotationBase.all_complexes"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.AnnotationBase.all_complexes" title="Link to this definition">§</a></dt>
+<dd><p>All protein complexes annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.AnnotationBase.all_entities">
+<span class="sig-name descname"><span class="pre">all_entities</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#AnnotationBase.all_entities"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.AnnotationBase.all_entities" title="Link to this definition">§</a></dt>
+<dd><p>All entities annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.AnnotationBase.all_mirnas">
+<span class="sig-name descname"><span class="pre">all_mirnas</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#AnnotationBase.all_mirnas"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.AnnotationBase.all_mirnas" title="Link to this definition">§</a></dt>
+<dd><p>All miRNAs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.AnnotationBase.all_proteins">
+<span class="sig-name descname"><span class="pre">all_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#AnnotationBase.all_proteins"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.AnnotationBase.all_proteins" title="Link to this definition">§</a></dt>
+<dd><p>All UniProt IDs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.AnnotationBase.all_refs">
+<span class="sig-name descname"><span class="pre">all_refs</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#AnnotationBase.all_refs"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.AnnotationBase.all_refs" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects the references
+across all records. Returns <em>list</em>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.AnnotationBase.annotate_complex">
+<span class="sig-name descname"><span class="pre">annotate_complex</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cplex</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#AnnotationBase.annotate_complex"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.AnnotationBase.annotate_complex" title="Link to this definition">§</a></dt>
+<dd><p>Infers annotations for a single complex.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.AnnotationBase.browse">
+<span class="sig-name descname"><span class="pre">browse</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">field</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">start</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#AnnotationBase.browse"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.AnnotationBase.browse" title="Link to this definition">§</a></dt>
+<dd><p>Print gene information as a table.</p>
+<p>Presents information about annotation categories as ascii tables
+printed in the terminal. If one category provided, prints one table.
+If multiple categories provided, prints a table for each of them one
+by one proceeding to the next one once you hit return. If no categories
+provided goes through all levels of the primary category.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>field:</dt><dd><p>The field to browse categories by.</p>
+<ul class="simple">
+<li><p>If None the primary field will be selected.
+If this annotation resource doesn’t have fields, all proteins
+will be presented as one single category.</p></li>
+<li><p>If a string it will be considered a field name and it will
+browse through all levels of this field.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">list</span></code>, set or tuple, it will be considered either a
+<code class="docutils literal notranslate"><span class="pre">list</span></code> of field names or a list of values from the primary
+field. In the former case all combinations of the values of
+the fields will be presented, in the latter case the browsing
+will be limited to the levels of the primary field contained
+in <code class="docutils literal notranslate"><span class="pre">field</span></code>.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">dict</span></code>, keys are supposed to be field names and values
+as list of levels. If any of the values are None, all levels
+from that field will be used.</p></li>
+</ul>
+</dd>
+<dt>start:</dt><dd><p>Start browsing from this category. E.g. if there are 500
+categories and start is 250 it will skip everything before the
+250th.</p>
+</dd>
+<dt>kwargs:</dt><dd><p>Passed to <code class="docutils literal notranslate"><span class="pre">pypath.utils.uniprot.info</span></code>.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.AnnotationBase.complex_inference">
+<span class="sig-name descname"><span class="pre">complex_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#AnnotationBase.complex_inference"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.AnnotationBase.complex_inference" title="Link to this definition">§</a></dt>
+<dd><p>Annotates all complexes in <cite>complexes</cite>, by default in the default
+complex database (existing in the <cite>complex</cite> module or generated
+on demand according to the module’s current settings).</p>
+<dl class="field-list simple">
+<dt class="field-odd">Returns<span class="colon">:</span></dt>
+<dd class="field-odd"><p><ul class="simple">
+<li><p><em>Dict with complexes as keys and sets of annotations as values.</em></p></li>
+<li><p><em>Complexes with no valid information in this annotation resource</em></p></li>
+<li><p><em>won’t be in the dict.</em></p></li>
+</ul>
+</p>
+</dd>
+<dt class="field-even">Parameters<span class="colon">:</span></dt>
+<dd class="field-even"><p><strong>complexes</strong> (<em>iterable</em>) – Iterable yielding complexes.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.AnnotationBase.coverage">
+<span class="sig-name descname"><span class="pre">coverage</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">other</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#AnnotationBase.coverage"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.AnnotationBase.coverage" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the coverage of the annotation i.e. the proportion of
+entities having at least one record in this annotation resource
+for an arbitrary set of entities.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.AnnotationBase.curation_effort">
+<span class="sig-name descname"><span class="pre">curation_effort</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#AnnotationBase.curation_effort"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.AnnotationBase.curation_effort" title="Link to this definition">§</a></dt>
+<dd><p>Counts the reference-record pairs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.AnnotationBase.get_names">
+<span class="sig-name descname"><span class="pre">get_names</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#AnnotationBase.get_names"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.AnnotationBase.get_names" title="Link to this definition">§</a></dt>
+<dd><p>Returns the list of field names in the records. The annotation
+consists of uniform records and each entity might be annotated
+with one or more records. Each record is a tuple of fields, for
+example <code class="docutils literal notranslate"><span class="pre">('cell_type',</span> <span class="pre">'expression_level',</span> <span class="pre">'score')</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.AnnotationBase.get_reference_set">
+<em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">get_reference_set</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">proteins</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">swissprot_only</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#AnnotationBase.get_reference_set"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.AnnotationBase.get_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the reference set i.e. the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.AnnotationBase.get_subset">
+<span class="sig-name descname"><span class="pre">get_subset</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.AnnotationBase.get_subset" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.AnnotationBase.get_subset_bool_array">
+<span class="sig-name descname"><span class="pre">get_subset_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#AnnotationBase.get_subset_bool_array"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.AnnotationBase.get_subset_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a boolean vector with True and False values for each entity
+in the reference set. The values represent presence absence data
+in the simplest case, but by providing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> any kind of matching
+and filtering is possible. <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> are passed to the <code class="docutils literal notranslate"><span class="pre">select</span></code>
+method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.AnnotationBase.get_values">
+<span class="sig-name descname"><span class="pre">get_values</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">exclude_none</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#AnnotationBase.get_values"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.AnnotationBase.get_values" title="Link to this definition">§</a></dt>
+<dd><p>Returns the set of all possible values of a field. E.g. if the
+records of this annotation have a field <code class="docutils literal notranslate"><span class="pre">cell_type</span></code> then calling
+this method can tell you that across all records the values of
+this field might be <code class="docutils literal notranslate"><span class="pre">{'macrophage',</span> <span class="pre">'epithelial_cell',</span> <span class="pre">...}</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.AnnotationBase.labels">
+<span class="sig-name descname"><span class="pre">labels</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#AnnotationBase.labels"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.AnnotationBase.labels" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.AnnotationBase.load">
+<span class="sig-name descname"><span class="pre">load</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#AnnotationBase.load"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.AnnotationBase.load" title="Link to this definition">§</a></dt>
+<dd><p>Loads the annotation data by calling the input method.
+Infers annotations for complexes in the complex database if
+py:attr:<code class="docutils literal notranslate"><span class="pre">infer_complexes</span></code> is True.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.AnnotationBase.load_data">
+<span class="sig-name descname"><span class="pre">load_data</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.AnnotationBase.load_data" title="Link to this definition">§</a></dt>
+<dd><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.AnnotationBase.load_proteins">
+<span class="sig-name descname"><span class="pre">load_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#AnnotationBase.load_proteins"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.AnnotationBase.load_proteins" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a set of all UniProt IDs to have a base set of the entire
+proteome.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.AnnotationBase.make_df">
+<span class="sig-name descname"><span class="pre">make_df</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">rebuild</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#AnnotationBase.make_df"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.AnnotationBase.make_df" title="Link to this definition">§</a></dt>
+<dd><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.
+The data frame will be assigned to :py:attr``df``.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.AnnotationBase.numof_entities">
+<span class="sig-name descname"><span class="pre">numof_entities</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#AnnotationBase.numof_entities"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.AnnotationBase.numof_entities" title="Link to this definition">§</a></dt>
+<dd><p>The number of annotated entities in the resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.AnnotationBase.numof_records">
+<span class="sig-name descname"><span class="pre">numof_records</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#AnnotationBase.numof_records"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.AnnotationBase.numof_records" title="Link to this definition">§</a></dt>
+<dd><p>The total number of annotation records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.AnnotationBase.numof_references">
+<span class="sig-name descname"><span class="pre">numof_references</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#AnnotationBase.numof_references"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.AnnotationBase.numof_references" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects and counts the
+references across all records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.AnnotationBase.process">
+<span class="sig-name descname"><span class="pre">process</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.AnnotationBase.process" title="Link to this definition">§</a></dt>
+<dd><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.AnnotationBase.reload">
+<span class="sig-name descname"><span class="pre">reload</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#AnnotationBase.reload"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.AnnotationBase.reload" title="Link to this definition">§</a></dt>
+<dd><p>Reloads the object from the module level.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.AnnotationBase.select">
+<span class="sig-name descname"><span class="pre">select</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#AnnotationBase.select"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.AnnotationBase.select" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.AnnotationBase.set_method">
+<span class="sig-name descname"><span class="pre">set_method</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.AnnotationBase.set_method" title="Link to this definition">§</a></dt>
+<dd><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if
+necessary.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.AnnotationBase.set_reference_set">
+<span class="sig-name descname"><span class="pre">set_reference_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#AnnotationBase.set_reference_set"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.AnnotationBase.set_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Assigns the reference set to the :py:attr``reference_set`` attribute.
+The reference set is the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.AnnotationBase.show">
+<span class="sig-name descname"><span class="pre">show</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">table_param</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#AnnotationBase.show"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.AnnotationBase.show" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic
+information from the UniProt datasheets.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.AnnotationBase.subset_intersection">
+<span class="sig-name descname"><span class="pre">subset_intersection</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">universe</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#AnnotationBase.subset_intersection"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.AnnotationBase.subset_intersection" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the proportion of entities in a subset occuring in the
+set <code class="docutils literal notranslate"><span class="pre">universe</span></code>. The subset is selected by passing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> to the
+<code class="docutils literal notranslate"><span class="pre">select</span></code> method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.AnnotationBase.to_array">
+<span class="sig-name descname"><span class="pre">to_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_fields</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#AnnotationBase.to_array"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.AnnotationBase.to_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns an entity vs feature array. In case of more complex
+annotations this might be huge.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.AnnotationBase.to_bool_array">
+<span class="sig-name descname"><span class="pre">to_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#AnnotationBase.to_bool_array"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.AnnotationBase.to_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a presence/absence boolean array for a reference set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.AnnotationBase.to_set">
+<span class="sig-name descname"><span class="pre">to_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#AnnotationBase.to_set"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.AnnotationBase.to_set" title="Link to this definition">§</a></dt>
+<dd><p>Returns the entities present in this annotation resource as a set.</p>
+</dd></dl>
+
+</dd></dl>
+
+</section>
+
+
+                </article>
+              
+              
+              
+              
+              
+                <footer class="prev-next-footer">
+                  
+<div class="prev-next-area">
+    <a class="left-prev"
+       href="pypath.core.annot.Almen2009.html"
+       title="previous page">
+      <i class="fa-solid fa-angle-left"></i>
+      <div class="prev-next-info">
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+  <section id="pypath-core-annot-annotationtable">
+<h1>pypath.core.annot.AnnotationTable<a class="headerlink" href="#pypath-core-annot-annotationtable" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.core.annot.AnnotationTable">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.core.annot.</span></span><span class="sig-name descname"><span class="pre">AnnotationTable</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">proteins</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">protein_sources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">complex_sources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_fields</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">swissprot_only</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">keep_annotators</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">create_dataframe</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">load</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">pickle_file</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#AnnotationTable"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.AnnotationTable" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">Logger</span></code></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.AnnotationTable.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">proteins</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">protein_sources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">complex_sources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_fields</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">swissprot_only</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">keep_annotators</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">create_dataframe</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">load</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">pickle_file</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#AnnotationTable.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.AnnotationTable.__init__" title="Link to this definition">§</a></dt>
+<dd><p>Manages a custom set of annotation resources. Loads data and
+accepts queries, provides methods for converting the data to
+data frame.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>proteins</strong> (<em>set</em>) – A reference set of proteins (UniProt IDs).</p></li>
+<li><p><strong>complexes</strong> (<em>set</em>) – A reference set of complexes.</p></li>
+<li><p><strong>protein_sources</strong> (<em>set</em>) – Class names providing the protein annotations. If not provided
+the module’s <code class="docutils literal notranslate"><span class="pre">protein_sources_default</span></code> attribute will be used.</p></li>
+<li><p><strong>complex_sources</strong> (<em>set</em>) – Class names providing the complex annotations. If not provided
+the module’s <code class="docutils literal notranslate"><span class="pre">complex_sources_default</span></code> attribute will be used.</p></li>
+<li><p><strong>use_fields</strong> (<em>dict</em>) – A dict with resource names as keys and tuple of field labels as
+values. If provided for any resource only these fields will be
+used for constructing the data frame. If <cite>None</cite>, the module’s
+<code class="docutils literal notranslate"><span class="pre">default_fields</span></code> settings will be used.</p></li>
+<li><p><strong>use_complexes</strong> (<em>bool</em>) – Whether to include complexes in the annotations.</p></li>
+<li><p><strong>create_dataframe</strong> (<em>bool</em>) – Whether to create a boolean data frame of annotations, apart
+from having the annotator objects.</p></li>
+<li><p><strong>load</strong> (<em>bool</em>) – Load the data upon initialization. If <cite>False</cite>, you will have a
+chance to call the <code class="docutils literal notranslate"><span class="pre">load</span></code> method later.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.AnnotationTable.__init__" title="pypath.core.annot.AnnotationTable.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>([proteins, complexes, ...])</p></td>
+<td><p>Manages a custom set of annotation resources.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.AnnotationTable.all_annotations" title="pypath.core.annot.AnnotationTable.all_annotations"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_annotations</span></code></a>(entity)</p></td>
+<td><p>Returns all annotation records for one protein in a single list.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.AnnotationTable.all_annotations_str" title="pypath.core.annot.AnnotationTable.all_annotations_str"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_annotations_str</span></code></a>(protein)</p></td>
+<td><p>Returns all annotation records for one protein serialized.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">annotate_network</span></code>(pa)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">ensure_array</span></code>([reference_set, rebuild])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">export_network_stats</span></code>(pa)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_entities</span></code>([entity_type])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_mirnas</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_proteins</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">keep</span></code>(keep)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">load</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_complex_resources</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_from_pickle</span></code>(pickle_file)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_protein_resources</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">make_array</span></code>([reference_set])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">make_dataframe</span></code>([reference_set])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">make_narrow_df</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">make_sets</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">network_stats</span></code>(pa)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_entities</span></code>([entity_type])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirnas</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_proteins</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_records</span></code>([entity_type])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_resources</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.AnnotationTable.reload" title="pypath.core.annot.AnnotationTable.reload"><code class="xref py py-obj docutils literal notranslate"><span class="pre">reload</span></code></a>()</p></td>
+<td><p>Reloads the object from the module level.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">save_to_pickle</span></code>(pickle_file)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.AnnotationTable.search" title="pypath.core.annot.AnnotationTable.search"><code class="xref py py-obj docutils literal notranslate"><span class="pre">search</span></code></a>(protein)</p></td>
+<td><p>Returns a dictionary with all annotations of a protein.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_cols</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_reference_set</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">summaries_tab</span></code>([outfile, return_table])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_array</span></code>([reference_set])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_dataframe</span></code>([reference_set])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">update_summaries</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.AnnotationTable.all_annotations">
+<span class="sig-name descname"><span class="pre">all_annotations</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#AnnotationTable.all_annotations"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.AnnotationTable.all_annotations" title="Link to this definition">§</a></dt>
+<dd><p>Returns all annotation records for one protein in a single list.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.AnnotationTable.all_annotations_str">
+<span class="sig-name descname"><span class="pre">all_annotations_str</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">protein</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#AnnotationTable.all_annotations_str"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.AnnotationTable.all_annotations_str" title="Link to this definition">§</a></dt>
+<dd><p>Returns all annotation records for one protein serialized.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.AnnotationTable.reload">
+<span class="sig-name descname"><span class="pre">reload</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#AnnotationTable.reload"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.AnnotationTable.reload" title="Link to this definition">§</a></dt>
+<dd><p>Reloads the object from the module level.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.AnnotationTable.search">
+<span class="sig-name descname"><span class="pre">search</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">protein</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#AnnotationTable.search"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.AnnotationTable.search" title="Link to this definition">§</a></dt>
+<dd><p>Returns a dictionary with all annotations of a protein. Keys are the
+resource names.</p>
+</dd></dl>
+
+</dd></dl>
+
+</section>
+
+
+                </article>
+              
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+  <section id="pypath-core-annot-baccin2019">
+<h1>pypath.core.annot.Baccin2019<a class="headerlink" href="#pypath-core-annot-baccin2019" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.core.annot.Baccin2019">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.core.annot.</span></span><span class="sig-name descname"><span class="pre">Baccin2019</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#Baccin2019"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.Baccin2019" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <a class="reference internal" href="pypath.core.annot.AnnotationBase.html#pypath.core.annot.AnnotationBase" title="pypath.core.annot.AnnotationBase"><code class="xref py py-class docutils literal notranslate"><span class="pre">AnnotationBase</span></code></a></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Baccin2019.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#Baccin2019.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.Baccin2019.__init__" title="Link to this definition">§</a></dt>
+<dd><p>Represents annotations for a set of proteins.
+Loads the data from the original resource and provides methods
+to query the annotations.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>name</strong> (<em>str</em>) – A custom name for the annotation resource.</p></li>
+<li><p><strong>ncbi_tax_id</strong> (<em>int</em>) – NCBI Taxonomy identifier.</p></li>
+<li><p><strong>input_method</strong> (<em>callable</em><em>,</em><em>str</em>) – Either a callable or the name of a method in any submodules of
+the <code class="docutils literal notranslate"><span class="pre">pypath.inputs</span></code>  module. Should return a dict with
+UniProt IDs as keys or an object suitable for <code class="docutils literal notranslate"><span class="pre">process_method</span></code>.</p></li>
+<li><p><strong>input_args</strong> (<em>dict</em>) – Arguments for the <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Baccin2019.__init__" title="pypath.core.annot.Baccin2019.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>([ncbi_tax_id])</p></td>
+<td><p>Represents annotations for a set of proteins.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Baccin2019.add_complexes_by_inference" title="pypath.core.annot.Baccin2019.add_complexes_by_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">add_complexes_by_inference</span></code></a>([complexes])</p></td>
+<td><p>Creates complex annotations by in silico inference and adds them to this annotation set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Baccin2019.all_complexes" title="pypath.core.annot.Baccin2019.all_complexes"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_complexes</span></code></a>()</p></td>
+<td><p>All protein complexes annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Baccin2019.all_entities" title="pypath.core.annot.Baccin2019.all_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_entities</span></code></a>([entity_types])</p></td>
+<td><p>All entities annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Baccin2019.all_mirnas" title="pypath.core.annot.Baccin2019.all_mirnas"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_mirnas</span></code></a>()</p></td>
+<td><p>All miRNAs annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Baccin2019.all_proteins" title="pypath.core.annot.Baccin2019.all_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_proteins</span></code></a>()</p></td>
+<td><p>All UniProt IDs annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Baccin2019.all_refs" title="pypath.core.annot.Baccin2019.all_refs"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_refs</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Baccin2019.annotate_complex" title="pypath.core.annot.Baccin2019.annotate_complex"><code class="xref py py-obj docutils literal notranslate"><span class="pre">annotate_complex</span></code></a>(cplex)</p></td>
+<td><p>Infers annotations for a single complex.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Baccin2019.browse" title="pypath.core.annot.Baccin2019.browse"><code class="xref py py-obj docutils literal notranslate"><span class="pre">browse</span></code></a>([field, start])</p></td>
+<td><p>Print gene information as a table.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Baccin2019.complex_inference" title="pypath.core.annot.Baccin2019.complex_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">complex_inference</span></code></a>([complexes])</p></td>
+<td><p>Annotates all complexes in <cite>complexes</cite>, by default in the default complex database (existing in the <cite>complex</cite> module or generated on demand according to the module's current settings).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Baccin2019.coverage" title="pypath.core.annot.Baccin2019.coverage"><code class="xref py py-obj docutils literal notranslate"><span class="pre">coverage</span></code></a>(other)</p></td>
+<td><p>Calculates the coverage of the annotation i.e. the proportion of entities having at least one record in this annotation resource for an arbitrary set of entities.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Baccin2019.curation_effort" title="pypath.core.annot.Baccin2019.curation_effort"><code class="xref py py-obj docutils literal notranslate"><span class="pre">curation_effort</span></code></a>()</p></td>
+<td><p>Counts the reference-record pairs.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">from_dump</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_entity_type</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Baccin2019.get_names" title="pypath.core.annot.Baccin2019.get_names"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_names</span></code></a>()</p></td>
+<td><p>Returns the list of field names in the records.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Baccin2019.get_reference_set" title="pypath.core.annot.Baccin2019.get_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_reference_set</span></code></a>([proteins, complexes, ...])</p></td>
+<td><p>Retrieves the reference set i.e. the set of all entities which potentially have annotation in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Baccin2019.get_subset" title="pypath.core.annot.Baccin2019.get_subset"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Baccin2019.get_subset_bool_array" title="pypath.core.annot.Baccin2019.get_subset_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset_bool_array</span></code></a>([reference_set])</p></td>
+<td><p>Returns a boolean vector with True and False values for each entity in the reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Baccin2019.get_values" title="pypath.core.annot.Baccin2019.get_values"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_values</span></code></a>(name[, exclude_none])</p></td>
+<td><p>Returns the set of all possible values of a field.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_complex</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_mirna</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_protein</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Baccin2019.labels" title="pypath.core.annot.Baccin2019.labels"><code class="xref py py-obj docutils literal notranslate"><span class="pre">labels</span></code></a>([method])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Baccin2019.load" title="pypath.core.annot.Baccin2019.load"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load</span></code></a>()</p></td>
+<td><p>Loads the annotation data by calling the input method.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Baccin2019.load_data" title="pypath.core.annot.Baccin2019.load_data"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_data</span></code></a>()</p></td>
+<td><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Baccin2019.load_proteins" title="pypath.core.annot.Baccin2019.load_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_proteins</span></code></a>()</p></td>
+<td><p>Retrieves a set of all UniProt IDs to have a base set of the entire proteome.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Baccin2019.make_df" title="pypath.core.annot.Baccin2019.make_df"><code class="xref py py-obj docutils literal notranslate"><span class="pre">make_df</span></code></a>([rebuild])</p></td>
+<td><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complex_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Baccin2019.numof_entities" title="pypath.core.annot.Baccin2019.numof_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_entities</span></code></a>()</p></td>
+<td><p>The number of annotated entities in the resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirna_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirnas</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_protein_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_proteins</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Baccin2019.numof_records" title="pypath.core.annot.Baccin2019.numof_records"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_records</span></code></a>([entity_types])</p></td>
+<td><p>The total number of annotation records.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Baccin2019.numof_references" title="pypath.core.annot.Baccin2019.numof_references"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_references</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Baccin2019.process" title="pypath.core.annot.Baccin2019.process"><code class="xref py py-obj docutils literal notranslate"><span class="pre">process</span></code></a>()</p></td>
+<td><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">proportion</span></code>(other)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Baccin2019.reload" title="pypath.core.annot.Baccin2019.reload"><code class="xref py py-obj docutils literal notranslate"><span class="pre">reload</span></code></a>()</p></td>
+<td><p>Reloads the object from the module level.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">save_to_pickle</span></code>(pickle_file)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Baccin2019.select" title="pypath.core.annot.Baccin2019.select"><code class="xref py py-obj docutils literal notranslate"><span class="pre">select</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Baccin2019.set_method" title="pypath.core.annot.Baccin2019.set_method"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_method</span></code></a>()</p></td>
+<td><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if necessary.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Baccin2019.set_reference_set" title="pypath.core.annot.Baccin2019.set_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_reference_set</span></code></a>()</p></td>
+<td><p>Assigns the reference set to the :py:attr``reference_set`` attribute.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Baccin2019.show" title="pypath.core.annot.Baccin2019.show"><code class="xref py py-obj docutils literal notranslate"><span class="pre">show</span></code></a>([method, table_param])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic information from the UniProt datasheets.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Baccin2019.subset_intersection" title="pypath.core.annot.Baccin2019.subset_intersection"><code class="xref py py-obj docutils literal notranslate"><span class="pre">subset_intersection</span></code></a>(universe, **kwargs)</p></td>
+<td><p>Calculates the proportion of entities in a subset occuring in the set <code class="docutils literal notranslate"><span class="pre">universe</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Baccin2019.to_array" title="pypath.core.annot.Baccin2019.to_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_array</span></code></a>([reference_set, use_fields])</p></td>
+<td><p>Returns an entity vs feature array.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Baccin2019.to_bool_array" title="pypath.core.annot.Baccin2019.to_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_bool_array</span></code></a>(reference_set)</p></td>
+<td><p>Returns a presence/absence boolean array for a reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Baccin2019.to_set" title="pypath.core.annot.Baccin2019.to_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_set</span></code></a>()</p></td>
+<td><p>Returns the entities present in this annotation resource as a set.</p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Attributes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_fields</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">summary</span></code></p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Baccin2019.add_complexes_by_inference">
+<span class="sig-name descname"><span class="pre">add_complexes_by_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Baccin2019.add_complexes_by_inference" title="Link to this definition">§</a></dt>
+<dd><p>Creates complex annotations by in silico inference and adds them
+to this annotation set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Baccin2019.all_complexes">
+<span class="sig-name descname"><span class="pre">all_complexes</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Baccin2019.all_complexes" title="Link to this definition">§</a></dt>
+<dd><p>All protein complexes annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Baccin2019.all_entities">
+<span class="sig-name descname"><span class="pre">all_entities</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Baccin2019.all_entities" title="Link to this definition">§</a></dt>
+<dd><p>All entities annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Baccin2019.all_mirnas">
+<span class="sig-name descname"><span class="pre">all_mirnas</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Baccin2019.all_mirnas" title="Link to this definition">§</a></dt>
+<dd><p>All miRNAs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Baccin2019.all_proteins">
+<span class="sig-name descname"><span class="pre">all_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Baccin2019.all_proteins" title="Link to this definition">§</a></dt>
+<dd><p>All UniProt IDs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Baccin2019.all_refs">
+<span class="sig-name descname"><span class="pre">all_refs</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Baccin2019.all_refs" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects the references
+across all records. Returns <em>list</em>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Baccin2019.annotate_complex">
+<span class="sig-name descname"><span class="pre">annotate_complex</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cplex</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Baccin2019.annotate_complex" title="Link to this definition">§</a></dt>
+<dd><p>Infers annotations for a single complex.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Baccin2019.browse">
+<span class="sig-name descname"><span class="pre">browse</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">field</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">start</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Baccin2019.browse" title="Link to this definition">§</a></dt>
+<dd><p>Print gene information as a table.</p>
+<p>Presents information about annotation categories as ascii tables
+printed in the terminal. If one category provided, prints one table.
+If multiple categories provided, prints a table for each of them one
+by one proceeding to the next one once you hit return. If no categories
+provided goes through all levels of the primary category.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>field:</dt><dd><p>The field to browse categories by.</p>
+<ul class="simple">
+<li><p>If None the primary field will be selected.
+If this annotation resource doesn’t have fields, all proteins
+will be presented as one single category.</p></li>
+<li><p>If a string it will be considered a field name and it will
+browse through all levels of this field.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">list</span></code>, set or tuple, it will be considered either a
+<code class="docutils literal notranslate"><span class="pre">list</span></code> of field names or a list of values from the primary
+field. In the former case all combinations of the values of
+the fields will be presented, in the latter case the browsing
+will be limited to the levels of the primary field contained
+in <code class="docutils literal notranslate"><span class="pre">field</span></code>.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">dict</span></code>, keys are supposed to be field names and values
+as list of levels. If any of the values are None, all levels
+from that field will be used.</p></li>
+</ul>
+</dd>
+<dt>start:</dt><dd><p>Start browsing from this category. E.g. if there are 500
+categories and start is 250 it will skip everything before the
+250th.</p>
+</dd>
+<dt>kwargs:</dt><dd><p>Passed to <code class="docutils literal notranslate"><span class="pre">pypath.utils.uniprot.info</span></code>.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Baccin2019.complex_inference">
+<span class="sig-name descname"><span class="pre">complex_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Baccin2019.complex_inference" title="Link to this definition">§</a></dt>
+<dd><p>Annotates all complexes in <cite>complexes</cite>, by default in the default
+complex database (existing in the <cite>complex</cite> module or generated
+on demand according to the module’s current settings).</p>
+<dl class="field-list simple">
+<dt class="field-odd">Returns<span class="colon">:</span></dt>
+<dd class="field-odd"><p><ul class="simple">
+<li><p><em>Dict with complexes as keys and sets of annotations as values.</em></p></li>
+<li><p><em>Complexes with no valid information in this annotation resource</em></p></li>
+<li><p><em>won’t be in the dict.</em></p></li>
+</ul>
+</p>
+</dd>
+<dt class="field-even">Parameters<span class="colon">:</span></dt>
+<dd class="field-even"><p><strong>complexes</strong> (<em>iterable</em>) – Iterable yielding complexes.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Baccin2019.coverage">
+<span class="sig-name descname"><span class="pre">coverage</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">other</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Baccin2019.coverage" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the coverage of the annotation i.e. the proportion of
+entities having at least one record in this annotation resource
+for an arbitrary set of entities.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Baccin2019.curation_effort">
+<span class="sig-name descname"><span class="pre">curation_effort</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Baccin2019.curation_effort" title="Link to this definition">§</a></dt>
+<dd><p>Counts the reference-record pairs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Baccin2019.get_names">
+<span class="sig-name descname"><span class="pre">get_names</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Baccin2019.get_names" title="Link to this definition">§</a></dt>
+<dd><p>Returns the list of field names in the records. The annotation
+consists of uniform records and each entity might be annotated
+with one or more records. Each record is a tuple of fields, for
+example <code class="docutils literal notranslate"><span class="pre">('cell_type',</span> <span class="pre">'expression_level',</span> <span class="pre">'score')</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Baccin2019.get_reference_set">
+<em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">get_reference_set</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">proteins</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">swissprot_only</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Baccin2019.get_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the reference set i.e. the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Baccin2019.get_subset">
+<span class="sig-name descname"><span class="pre">get_subset</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Baccin2019.get_subset" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Baccin2019.get_subset_bool_array">
+<span class="sig-name descname"><span class="pre">get_subset_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Baccin2019.get_subset_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a boolean vector with True and False values for each entity
+in the reference set. The values represent presence absence data
+in the simplest case, but by providing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> any kind of matching
+and filtering is possible. <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> are passed to the <code class="docutils literal notranslate"><span class="pre">select</span></code>
+method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Baccin2019.get_values">
+<span class="sig-name descname"><span class="pre">get_values</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">exclude_none</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Baccin2019.get_values" title="Link to this definition">§</a></dt>
+<dd><p>Returns the set of all possible values of a field. E.g. if the
+records of this annotation have a field <code class="docutils literal notranslate"><span class="pre">cell_type</span></code> then calling
+this method can tell you that across all records the values of
+this field might be <code class="docutils literal notranslate"><span class="pre">{'macrophage',</span> <span class="pre">'epithelial_cell',</span> <span class="pre">...}</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Baccin2019.labels">
+<span class="sig-name descname"><span class="pre">labels</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Baccin2019.labels" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Baccin2019.load">
+<span class="sig-name descname"><span class="pre">load</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Baccin2019.load" title="Link to this definition">§</a></dt>
+<dd><p>Loads the annotation data by calling the input method.
+Infers annotations for complexes in the complex database if
+py:attr:<code class="docutils literal notranslate"><span class="pre">infer_complexes</span></code> is True.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Baccin2019.load_data">
+<span class="sig-name descname"><span class="pre">load_data</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Baccin2019.load_data" title="Link to this definition">§</a></dt>
+<dd><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Baccin2019.load_proteins">
+<span class="sig-name descname"><span class="pre">load_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Baccin2019.load_proteins" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a set of all UniProt IDs to have a base set of the entire
+proteome.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Baccin2019.make_df">
+<span class="sig-name descname"><span class="pre">make_df</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">rebuild</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Baccin2019.make_df" title="Link to this definition">§</a></dt>
+<dd><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.
+The data frame will be assigned to :py:attr``df``.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Baccin2019.numof_entities">
+<span class="sig-name descname"><span class="pre">numof_entities</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Baccin2019.numof_entities" title="Link to this definition">§</a></dt>
+<dd><p>The number of annotated entities in the resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Baccin2019.numof_records">
+<span class="sig-name descname"><span class="pre">numof_records</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Baccin2019.numof_records" title="Link to this definition">§</a></dt>
+<dd><p>The total number of annotation records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Baccin2019.numof_references">
+<span class="sig-name descname"><span class="pre">numof_references</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Baccin2019.numof_references" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects and counts the
+references across all records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Baccin2019.process">
+<span class="sig-name descname"><span class="pre">process</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Baccin2019.process" title="Link to this definition">§</a></dt>
+<dd><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Baccin2019.reload">
+<span class="sig-name descname"><span class="pre">reload</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Baccin2019.reload" title="Link to this definition">§</a></dt>
+<dd><p>Reloads the object from the module level.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Baccin2019.select">
+<span class="sig-name descname"><span class="pre">select</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Baccin2019.select" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Baccin2019.set_method">
+<span class="sig-name descname"><span class="pre">set_method</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Baccin2019.set_method" title="Link to this definition">§</a></dt>
+<dd><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if
+necessary.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Baccin2019.set_reference_set">
+<span class="sig-name descname"><span class="pre">set_reference_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Baccin2019.set_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Assigns the reference set to the :py:attr``reference_set`` attribute.
+The reference set is the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Baccin2019.show">
+<span class="sig-name descname"><span class="pre">show</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">table_param</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Baccin2019.show" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic
+information from the UniProt datasheets.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Baccin2019.subset_intersection">
+<span class="sig-name descname"><span class="pre">subset_intersection</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">universe</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Baccin2019.subset_intersection" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the proportion of entities in a subset occuring in the
+set <code class="docutils literal notranslate"><span class="pre">universe</span></code>. The subset is selected by passing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> to the
+<code class="docutils literal notranslate"><span class="pre">select</span></code> method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Baccin2019.to_array">
+<span class="sig-name descname"><span class="pre">to_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_fields</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Baccin2019.to_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns an entity vs feature array. In case of more complex
+annotations this might be huge.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Baccin2019.to_bool_array">
+<span class="sig-name descname"><span class="pre">to_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Baccin2019.to_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a presence/absence boolean array for a reference set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Baccin2019.to_set">
+<span class="sig-name descname"><span class="pre">to_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Baccin2019.to_set" title="Link to this definition">§</a></dt>
+<dd><p>Returns the entities present in this annotation resource as a set.</p>
+</dd></dl>
+
+</dd></dl>
+
+</section>
+
+
+                </article>
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+  <section id="pypath-core-annot-biogps">
+<h1>pypath.core.annot.Biogps<a class="headerlink" href="#pypath-core-annot-biogps" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.core.annot.Biogps">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.core.annot.</span></span><span class="sig-name descname"><span class="pre">Biogps</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#Biogps"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.Biogps" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <a class="reference internal" href="pypath.core.annot.AnnotationBase.html#pypath.core.annot.AnnotationBase" title="pypath.core.annot.AnnotationBase"><code class="xref py py-class docutils literal notranslate"><span class="pre">AnnotationBase</span></code></a></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Biogps.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#Biogps.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.Biogps.__init__" title="Link to this definition">§</a></dt>
+<dd><p>Represents annotations for a set of proteins.
+Loads the data from the original resource and provides methods
+to query the annotations.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>name</strong> (<em>str</em>) – A custom name for the annotation resource.</p></li>
+<li><p><strong>ncbi_tax_id</strong> (<em>int</em>) – NCBI Taxonomy identifier.</p></li>
+<li><p><strong>input_method</strong> (<em>callable</em><em>,</em><em>str</em>) – Either a callable or the name of a method in any submodules of
+the <code class="docutils literal notranslate"><span class="pre">pypath.inputs</span></code>  module. Should return a dict with
+UniProt IDs as keys or an object suitable for <code class="docutils literal notranslate"><span class="pre">process_method</span></code>.</p></li>
+<li><p><strong>input_args</strong> (<em>dict</em>) – Arguments for the <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Biogps.__init__" title="pypath.core.annot.Biogps.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>([ncbi_tax_id])</p></td>
+<td><p>Represents annotations for a set of proteins.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Biogps.add_complexes_by_inference" title="pypath.core.annot.Biogps.add_complexes_by_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">add_complexes_by_inference</span></code></a>([complexes])</p></td>
+<td><p>Creates complex annotations by in silico inference and adds them to this annotation set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Biogps.all_complexes" title="pypath.core.annot.Biogps.all_complexes"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_complexes</span></code></a>()</p></td>
+<td><p>All protein complexes annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Biogps.all_entities" title="pypath.core.annot.Biogps.all_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_entities</span></code></a>([entity_types])</p></td>
+<td><p>All entities annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Biogps.all_mirnas" title="pypath.core.annot.Biogps.all_mirnas"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_mirnas</span></code></a>()</p></td>
+<td><p>All miRNAs annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Biogps.all_proteins" title="pypath.core.annot.Biogps.all_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_proteins</span></code></a>()</p></td>
+<td><p>All UniProt IDs annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Biogps.all_refs" title="pypath.core.annot.Biogps.all_refs"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_refs</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Biogps.annotate_complex" title="pypath.core.annot.Biogps.annotate_complex"><code class="xref py py-obj docutils literal notranslate"><span class="pre">annotate_complex</span></code></a>(cplex)</p></td>
+<td><p>Infers annotations for a single complex.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Biogps.browse" title="pypath.core.annot.Biogps.browse"><code class="xref py py-obj docutils literal notranslate"><span class="pre">browse</span></code></a>([field, start])</p></td>
+<td><p>Print gene information as a table.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Biogps.complex_inference" title="pypath.core.annot.Biogps.complex_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">complex_inference</span></code></a>([complexes])</p></td>
+<td><p>Annotates all complexes in <cite>complexes</cite>, by default in the default complex database (existing in the <cite>complex</cite> module or generated on demand according to the module's current settings).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Biogps.coverage" title="pypath.core.annot.Biogps.coverage"><code class="xref py py-obj docutils literal notranslate"><span class="pre">coverage</span></code></a>(other)</p></td>
+<td><p>Calculates the coverage of the annotation i.e. the proportion of entities having at least one record in this annotation resource for an arbitrary set of entities.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Biogps.curation_effort" title="pypath.core.annot.Biogps.curation_effort"><code class="xref py py-obj docutils literal notranslate"><span class="pre">curation_effort</span></code></a>()</p></td>
+<td><p>Counts the reference-record pairs.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">from_dump</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_entity_type</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Biogps.get_names" title="pypath.core.annot.Biogps.get_names"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_names</span></code></a>()</p></td>
+<td><p>Returns the list of field names in the records.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Biogps.get_reference_set" title="pypath.core.annot.Biogps.get_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_reference_set</span></code></a>([proteins, complexes, ...])</p></td>
+<td><p>Retrieves the reference set i.e. the set of all entities which potentially have annotation in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Biogps.get_subset" title="pypath.core.annot.Biogps.get_subset"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Biogps.get_subset_bool_array" title="pypath.core.annot.Biogps.get_subset_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset_bool_array</span></code></a>([reference_set])</p></td>
+<td><p>Returns a boolean vector with True and False values for each entity in the reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Biogps.get_values" title="pypath.core.annot.Biogps.get_values"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_values</span></code></a>(name[, exclude_none])</p></td>
+<td><p>Returns the set of all possible values of a field.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_complex</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_mirna</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_protein</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Biogps.labels" title="pypath.core.annot.Biogps.labels"><code class="xref py py-obj docutils literal notranslate"><span class="pre">labels</span></code></a>([method])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Biogps.load" title="pypath.core.annot.Biogps.load"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load</span></code></a>()</p></td>
+<td><p>Loads the annotation data by calling the input method.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Biogps.load_data" title="pypath.core.annot.Biogps.load_data"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_data</span></code></a>()</p></td>
+<td><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Biogps.load_proteins" title="pypath.core.annot.Biogps.load_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_proteins</span></code></a>()</p></td>
+<td><p>Retrieves a set of all UniProt IDs to have a base set of the entire proteome.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Biogps.make_df" title="pypath.core.annot.Biogps.make_df"><code class="xref py py-obj docutils literal notranslate"><span class="pre">make_df</span></code></a>([rebuild])</p></td>
+<td><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complex_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Biogps.numof_entities" title="pypath.core.annot.Biogps.numof_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_entities</span></code></a>()</p></td>
+<td><p>The number of annotated entities in the resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirna_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirnas</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_protein_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_proteins</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Biogps.numof_records" title="pypath.core.annot.Biogps.numof_records"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_records</span></code></a>([entity_types])</p></td>
+<td><p>The total number of annotation records.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Biogps.numof_references" title="pypath.core.annot.Biogps.numof_references"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_references</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Biogps.process" title="pypath.core.annot.Biogps.process"><code class="xref py py-obj docutils literal notranslate"><span class="pre">process</span></code></a>()</p></td>
+<td><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">proportion</span></code>(other)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Biogps.reload" title="pypath.core.annot.Biogps.reload"><code class="xref py py-obj docutils literal notranslate"><span class="pre">reload</span></code></a>()</p></td>
+<td><p>Reloads the object from the module level.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">save_to_pickle</span></code>(pickle_file)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Biogps.select" title="pypath.core.annot.Biogps.select"><code class="xref py py-obj docutils literal notranslate"><span class="pre">select</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Biogps.set_method" title="pypath.core.annot.Biogps.set_method"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_method</span></code></a>()</p></td>
+<td><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if necessary.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Biogps.set_reference_set" title="pypath.core.annot.Biogps.set_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_reference_set</span></code></a>()</p></td>
+<td><p>Assigns the reference set to the :py:attr``reference_set`` attribute.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Biogps.show" title="pypath.core.annot.Biogps.show"><code class="xref py py-obj docutils literal notranslate"><span class="pre">show</span></code></a>([method, table_param])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic information from the UniProt datasheets.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Biogps.subset_intersection" title="pypath.core.annot.Biogps.subset_intersection"><code class="xref py py-obj docutils literal notranslate"><span class="pre">subset_intersection</span></code></a>(universe, **kwargs)</p></td>
+<td><p>Calculates the proportion of entities in a subset occuring in the set <code class="docutils literal notranslate"><span class="pre">universe</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Biogps.to_array" title="pypath.core.annot.Biogps.to_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_array</span></code></a>([reference_set, use_fields])</p></td>
+<td><p>Returns an entity vs feature array.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Biogps.to_bool_array" title="pypath.core.annot.Biogps.to_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_bool_array</span></code></a>(reference_set)</p></td>
+<td><p>Returns a presence/absence boolean array for a reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Biogps.to_set" title="pypath.core.annot.Biogps.to_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_set</span></code></a>()</p></td>
+<td><p>Returns the entities present in this annotation resource as a set.</p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Attributes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_fields</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">summary</span></code></p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Biogps.add_complexes_by_inference">
+<span class="sig-name descname"><span class="pre">add_complexes_by_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Biogps.add_complexes_by_inference" title="Link to this definition">§</a></dt>
+<dd><p>Creates complex annotations by in silico inference and adds them
+to this annotation set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Biogps.all_complexes">
+<span class="sig-name descname"><span class="pre">all_complexes</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Biogps.all_complexes" title="Link to this definition">§</a></dt>
+<dd><p>All protein complexes annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Biogps.all_entities">
+<span class="sig-name descname"><span class="pre">all_entities</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Biogps.all_entities" title="Link to this definition">§</a></dt>
+<dd><p>All entities annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Biogps.all_mirnas">
+<span class="sig-name descname"><span class="pre">all_mirnas</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Biogps.all_mirnas" title="Link to this definition">§</a></dt>
+<dd><p>All miRNAs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Biogps.all_proteins">
+<span class="sig-name descname"><span class="pre">all_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Biogps.all_proteins" title="Link to this definition">§</a></dt>
+<dd><p>All UniProt IDs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Biogps.all_refs">
+<span class="sig-name descname"><span class="pre">all_refs</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Biogps.all_refs" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects the references
+across all records. Returns <em>list</em>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Biogps.annotate_complex">
+<span class="sig-name descname"><span class="pre">annotate_complex</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cplex</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Biogps.annotate_complex" title="Link to this definition">§</a></dt>
+<dd><p>Infers annotations for a single complex.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Biogps.browse">
+<span class="sig-name descname"><span class="pre">browse</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">field</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">start</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Biogps.browse" title="Link to this definition">§</a></dt>
+<dd><p>Print gene information as a table.</p>
+<p>Presents information about annotation categories as ascii tables
+printed in the terminal. If one category provided, prints one table.
+If multiple categories provided, prints a table for each of them one
+by one proceeding to the next one once you hit return. If no categories
+provided goes through all levels of the primary category.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>field:</dt><dd><p>The field to browse categories by.</p>
+<ul class="simple">
+<li><p>If None the primary field will be selected.
+If this annotation resource doesn’t have fields, all proteins
+will be presented as one single category.</p></li>
+<li><p>If a string it will be considered a field name and it will
+browse through all levels of this field.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">list</span></code>, set or tuple, it will be considered either a
+<code class="docutils literal notranslate"><span class="pre">list</span></code> of field names or a list of values from the primary
+field. In the former case all combinations of the values of
+the fields will be presented, in the latter case the browsing
+will be limited to the levels of the primary field contained
+in <code class="docutils literal notranslate"><span class="pre">field</span></code>.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">dict</span></code>, keys are supposed to be field names and values
+as list of levels. If any of the values are None, all levels
+from that field will be used.</p></li>
+</ul>
+</dd>
+<dt>start:</dt><dd><p>Start browsing from this category. E.g. if there are 500
+categories and start is 250 it will skip everything before the
+250th.</p>
+</dd>
+<dt>kwargs:</dt><dd><p>Passed to <code class="docutils literal notranslate"><span class="pre">pypath.utils.uniprot.info</span></code>.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Biogps.complex_inference">
+<span class="sig-name descname"><span class="pre">complex_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Biogps.complex_inference" title="Link to this definition">§</a></dt>
+<dd><p>Annotates all complexes in <cite>complexes</cite>, by default in the default
+complex database (existing in the <cite>complex</cite> module or generated
+on demand according to the module’s current settings).</p>
+<dl class="field-list simple">
+<dt class="field-odd">Returns<span class="colon">:</span></dt>
+<dd class="field-odd"><p><ul class="simple">
+<li><p><em>Dict with complexes as keys and sets of annotations as values.</em></p></li>
+<li><p><em>Complexes with no valid information in this annotation resource</em></p></li>
+<li><p><em>won’t be in the dict.</em></p></li>
+</ul>
+</p>
+</dd>
+<dt class="field-even">Parameters<span class="colon">:</span></dt>
+<dd class="field-even"><p><strong>complexes</strong> (<em>iterable</em>) – Iterable yielding complexes.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Biogps.coverage">
+<span class="sig-name descname"><span class="pre">coverage</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">other</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Biogps.coverage" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the coverage of the annotation i.e. the proportion of
+entities having at least one record in this annotation resource
+for an arbitrary set of entities.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Biogps.curation_effort">
+<span class="sig-name descname"><span class="pre">curation_effort</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Biogps.curation_effort" title="Link to this definition">§</a></dt>
+<dd><p>Counts the reference-record pairs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Biogps.get_names">
+<span class="sig-name descname"><span class="pre">get_names</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Biogps.get_names" title="Link to this definition">§</a></dt>
+<dd><p>Returns the list of field names in the records. The annotation
+consists of uniform records and each entity might be annotated
+with one or more records. Each record is a tuple of fields, for
+example <code class="docutils literal notranslate"><span class="pre">('cell_type',</span> <span class="pre">'expression_level',</span> <span class="pre">'score')</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Biogps.get_reference_set">
+<em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">get_reference_set</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">proteins</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">swissprot_only</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Biogps.get_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the reference set i.e. the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Biogps.get_subset">
+<span class="sig-name descname"><span class="pre">get_subset</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Biogps.get_subset" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Biogps.get_subset_bool_array">
+<span class="sig-name descname"><span class="pre">get_subset_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Biogps.get_subset_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a boolean vector with True and False values for each entity
+in the reference set. The values represent presence absence data
+in the simplest case, but by providing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> any kind of matching
+and filtering is possible. <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> are passed to the <code class="docutils literal notranslate"><span class="pre">select</span></code>
+method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Biogps.get_values">
+<span class="sig-name descname"><span class="pre">get_values</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">exclude_none</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Biogps.get_values" title="Link to this definition">§</a></dt>
+<dd><p>Returns the set of all possible values of a field. E.g. if the
+records of this annotation have a field <code class="docutils literal notranslate"><span class="pre">cell_type</span></code> then calling
+this method can tell you that across all records the values of
+this field might be <code class="docutils literal notranslate"><span class="pre">{'macrophage',</span> <span class="pre">'epithelial_cell',</span> <span class="pre">...}</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Biogps.labels">
+<span class="sig-name descname"><span class="pre">labels</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Biogps.labels" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Biogps.load">
+<span class="sig-name descname"><span class="pre">load</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Biogps.load" title="Link to this definition">§</a></dt>
+<dd><p>Loads the annotation data by calling the input method.
+Infers annotations for complexes in the complex database if
+py:attr:<code class="docutils literal notranslate"><span class="pre">infer_complexes</span></code> is True.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Biogps.load_data">
+<span class="sig-name descname"><span class="pre">load_data</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Biogps.load_data" title="Link to this definition">§</a></dt>
+<dd><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Biogps.load_proteins">
+<span class="sig-name descname"><span class="pre">load_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Biogps.load_proteins" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a set of all UniProt IDs to have a base set of the entire
+proteome.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Biogps.make_df">
+<span class="sig-name descname"><span class="pre">make_df</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">rebuild</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Biogps.make_df" title="Link to this definition">§</a></dt>
+<dd><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.
+The data frame will be assigned to :py:attr``df``.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Biogps.numof_entities">
+<span class="sig-name descname"><span class="pre">numof_entities</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Biogps.numof_entities" title="Link to this definition">§</a></dt>
+<dd><p>The number of annotated entities in the resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Biogps.numof_records">
+<span class="sig-name descname"><span class="pre">numof_records</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Biogps.numof_records" title="Link to this definition">§</a></dt>
+<dd><p>The total number of annotation records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Biogps.numof_references">
+<span class="sig-name descname"><span class="pre">numof_references</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Biogps.numof_references" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects and counts the
+references across all records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Biogps.process">
+<span class="sig-name descname"><span class="pre">process</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Biogps.process" title="Link to this definition">§</a></dt>
+<dd><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Biogps.reload">
+<span class="sig-name descname"><span class="pre">reload</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Biogps.reload" title="Link to this definition">§</a></dt>
+<dd><p>Reloads the object from the module level.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Biogps.select">
+<span class="sig-name descname"><span class="pre">select</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Biogps.select" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Biogps.set_method">
+<span class="sig-name descname"><span class="pre">set_method</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Biogps.set_method" title="Link to this definition">§</a></dt>
+<dd><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if
+necessary.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Biogps.set_reference_set">
+<span class="sig-name descname"><span class="pre">set_reference_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Biogps.set_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Assigns the reference set to the :py:attr``reference_set`` attribute.
+The reference set is the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Biogps.show">
+<span class="sig-name descname"><span class="pre">show</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">table_param</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Biogps.show" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic
+information from the UniProt datasheets.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Biogps.subset_intersection">
+<span class="sig-name descname"><span class="pre">subset_intersection</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">universe</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Biogps.subset_intersection" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the proportion of entities in a subset occuring in the
+set <code class="docutils literal notranslate"><span class="pre">universe</span></code>. The subset is selected by passing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> to the
+<code class="docutils literal notranslate"><span class="pre">select</span></code> method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Biogps.to_array">
+<span class="sig-name descname"><span class="pre">to_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_fields</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Biogps.to_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns an entity vs feature array. In case of more complex
+annotations this might be huge.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Biogps.to_bool_array">
+<span class="sig-name descname"><span class="pre">to_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Biogps.to_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a presence/absence boolean array for a reference set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Biogps.to_set">
+<span class="sig-name descname"><span class="pre">to_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Biogps.to_set" title="Link to this definition">§</a></dt>
+<dd><p>Returns the entities present in this annotation resource as a set.</p>
+</dd></dl>
+
+</dd></dl>
+
+</section>
+
+
+                </article>
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+  <section id="pypath-core-annot-cancergenecensus">
+<h1>pypath.core.annot.CancerGeneCensus<a class="headerlink" href="#pypath-core-annot-cancergenecensus" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.core.annot.CancerGeneCensus">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.core.annot.</span></span><span class="sig-name descname"><span class="pre">CancerGeneCensus</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#CancerGeneCensus"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.CancerGeneCensus" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <a class="reference internal" href="pypath.core.annot.AnnotationBase.html#pypath.core.annot.AnnotationBase" title="pypath.core.annot.AnnotationBase"><code class="xref py py-class docutils literal notranslate"><span class="pre">AnnotationBase</span></code></a></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CancerGeneCensus.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#CancerGeneCensus.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.CancerGeneCensus.__init__" title="Link to this definition">§</a></dt>
+<dd><p>Represents annotations for a set of proteins.
+Loads the data from the original resource and provides methods
+to query the annotations.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>name</strong> (<em>str</em>) – A custom name for the annotation resource.</p></li>
+<li><p><strong>ncbi_tax_id</strong> (<em>int</em>) – NCBI Taxonomy identifier.</p></li>
+<li><p><strong>input_method</strong> (<em>callable</em><em>,</em><em>str</em>) – Either a callable or the name of a method in any submodules of
+the <code class="docutils literal notranslate"><span class="pre">pypath.inputs</span></code>  module. Should return a dict with
+UniProt IDs as keys or an object suitable for <code class="docutils literal notranslate"><span class="pre">process_method</span></code>.</p></li>
+<li><p><strong>input_args</strong> (<em>dict</em>) – Arguments for the <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CancerGeneCensus.__init__" title="pypath.core.annot.CancerGeneCensus.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>(**kwargs)</p></td>
+<td><p>Represents annotations for a set of proteins.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CancerGeneCensus.add_complexes_by_inference" title="pypath.core.annot.CancerGeneCensus.add_complexes_by_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">add_complexes_by_inference</span></code></a>([complexes])</p></td>
+<td><p>Creates complex annotations by in silico inference and adds them to this annotation set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CancerGeneCensus.all_complexes" title="pypath.core.annot.CancerGeneCensus.all_complexes"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_complexes</span></code></a>()</p></td>
+<td><p>All protein complexes annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CancerGeneCensus.all_entities" title="pypath.core.annot.CancerGeneCensus.all_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_entities</span></code></a>([entity_types])</p></td>
+<td><p>All entities annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CancerGeneCensus.all_mirnas" title="pypath.core.annot.CancerGeneCensus.all_mirnas"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_mirnas</span></code></a>()</p></td>
+<td><p>All miRNAs annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CancerGeneCensus.all_proteins" title="pypath.core.annot.CancerGeneCensus.all_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_proteins</span></code></a>()</p></td>
+<td><p>All UniProt IDs annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CancerGeneCensus.all_refs" title="pypath.core.annot.CancerGeneCensus.all_refs"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_refs</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CancerGeneCensus.annotate_complex" title="pypath.core.annot.CancerGeneCensus.annotate_complex"><code class="xref py py-obj docutils literal notranslate"><span class="pre">annotate_complex</span></code></a>(cplex)</p></td>
+<td><p>Infers annotations for a single complex.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CancerGeneCensus.browse" title="pypath.core.annot.CancerGeneCensus.browse"><code class="xref py py-obj docutils literal notranslate"><span class="pre">browse</span></code></a>([field, start])</p></td>
+<td><p>Print gene information as a table.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CancerGeneCensus.complex_inference" title="pypath.core.annot.CancerGeneCensus.complex_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">complex_inference</span></code></a>([complexes])</p></td>
+<td><p>Annotates all complexes in <cite>complexes</cite>, by default in the default complex database (existing in the <cite>complex</cite> module or generated on demand according to the module's current settings).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CancerGeneCensus.coverage" title="pypath.core.annot.CancerGeneCensus.coverage"><code class="xref py py-obj docutils literal notranslate"><span class="pre">coverage</span></code></a>(other)</p></td>
+<td><p>Calculates the coverage of the annotation i.e. the proportion of entities having at least one record in this annotation resource for an arbitrary set of entities.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CancerGeneCensus.curation_effort" title="pypath.core.annot.CancerGeneCensus.curation_effort"><code class="xref py py-obj docutils literal notranslate"><span class="pre">curation_effort</span></code></a>()</p></td>
+<td><p>Counts the reference-record pairs.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">from_dump</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_entity_type</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CancerGeneCensus.get_names" title="pypath.core.annot.CancerGeneCensus.get_names"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_names</span></code></a>()</p></td>
+<td><p>Returns the list of field names in the records.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CancerGeneCensus.get_reference_set" title="pypath.core.annot.CancerGeneCensus.get_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_reference_set</span></code></a>([proteins, complexes, ...])</p></td>
+<td><p>Retrieves the reference set i.e. the set of all entities which potentially have annotation in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CancerGeneCensus.get_subset" title="pypath.core.annot.CancerGeneCensus.get_subset"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CancerGeneCensus.get_subset_bool_array" title="pypath.core.annot.CancerGeneCensus.get_subset_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset_bool_array</span></code></a>([reference_set])</p></td>
+<td><p>Returns a boolean vector with True and False values for each entity in the reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CancerGeneCensus.get_values" title="pypath.core.annot.CancerGeneCensus.get_values"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_values</span></code></a>(name[, exclude_none])</p></td>
+<td><p>Returns the set of all possible values of a field.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_complex</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_mirna</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_protein</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CancerGeneCensus.labels" title="pypath.core.annot.CancerGeneCensus.labels"><code class="xref py py-obj docutils literal notranslate"><span class="pre">labels</span></code></a>([method])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CancerGeneCensus.load" title="pypath.core.annot.CancerGeneCensus.load"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load</span></code></a>()</p></td>
+<td><p>Loads the annotation data by calling the input method.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CancerGeneCensus.load_data" title="pypath.core.annot.CancerGeneCensus.load_data"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_data</span></code></a>()</p></td>
+<td><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CancerGeneCensus.load_proteins" title="pypath.core.annot.CancerGeneCensus.load_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_proteins</span></code></a>()</p></td>
+<td><p>Retrieves a set of all UniProt IDs to have a base set of the entire proteome.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CancerGeneCensus.make_df" title="pypath.core.annot.CancerGeneCensus.make_df"><code class="xref py py-obj docutils literal notranslate"><span class="pre">make_df</span></code></a>([rebuild])</p></td>
+<td><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complex_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CancerGeneCensus.numof_entities" title="pypath.core.annot.CancerGeneCensus.numof_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_entities</span></code></a>()</p></td>
+<td><p>The number of annotated entities in the resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirna_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirnas</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_protein_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_proteins</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CancerGeneCensus.numof_records" title="pypath.core.annot.CancerGeneCensus.numof_records"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_records</span></code></a>([entity_types])</p></td>
+<td><p>The total number of annotation records.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CancerGeneCensus.numof_references" title="pypath.core.annot.CancerGeneCensus.numof_references"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_references</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CancerGeneCensus.process" title="pypath.core.annot.CancerGeneCensus.process"><code class="xref py py-obj docutils literal notranslate"><span class="pre">process</span></code></a>()</p></td>
+<td><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">proportion</span></code>(other)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CancerGeneCensus.reload" title="pypath.core.annot.CancerGeneCensus.reload"><code class="xref py py-obj docutils literal notranslate"><span class="pre">reload</span></code></a>()</p></td>
+<td><p>Reloads the object from the module level.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">save_to_pickle</span></code>(pickle_file)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CancerGeneCensus.select" title="pypath.core.annot.CancerGeneCensus.select"><code class="xref py py-obj docutils literal notranslate"><span class="pre">select</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CancerGeneCensus.set_method" title="pypath.core.annot.CancerGeneCensus.set_method"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_method</span></code></a>()</p></td>
+<td><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if necessary.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CancerGeneCensus.set_reference_set" title="pypath.core.annot.CancerGeneCensus.set_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_reference_set</span></code></a>()</p></td>
+<td><p>Assigns the reference set to the :py:attr``reference_set`` attribute.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CancerGeneCensus.show" title="pypath.core.annot.CancerGeneCensus.show"><code class="xref py py-obj docutils literal notranslate"><span class="pre">show</span></code></a>([method, table_param])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic information from the UniProt datasheets.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CancerGeneCensus.subset_intersection" title="pypath.core.annot.CancerGeneCensus.subset_intersection"><code class="xref py py-obj docutils literal notranslate"><span class="pre">subset_intersection</span></code></a>(universe, **kwargs)</p></td>
+<td><p>Calculates the proportion of entities in a subset occuring in the set <code class="docutils literal notranslate"><span class="pre">universe</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CancerGeneCensus.to_array" title="pypath.core.annot.CancerGeneCensus.to_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_array</span></code></a>([reference_set, use_fields])</p></td>
+<td><p>Returns an entity vs feature array.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CancerGeneCensus.to_bool_array" title="pypath.core.annot.CancerGeneCensus.to_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_bool_array</span></code></a>(reference_set)</p></td>
+<td><p>Returns a presence/absence boolean array for a reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CancerGeneCensus.to_set" title="pypath.core.annot.CancerGeneCensus.to_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_set</span></code></a>()</p></td>
+<td><p>Returns the entities present in this annotation resource as a set.</p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Attributes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_fields</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">summary</span></code></p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CancerGeneCensus.add_complexes_by_inference">
+<span class="sig-name descname"><span class="pre">add_complexes_by_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CancerGeneCensus.add_complexes_by_inference" title="Link to this definition">§</a></dt>
+<dd><p>Creates complex annotations by in silico inference and adds them
+to this annotation set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CancerGeneCensus.all_complexes">
+<span class="sig-name descname"><span class="pre">all_complexes</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CancerGeneCensus.all_complexes" title="Link to this definition">§</a></dt>
+<dd><p>All protein complexes annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CancerGeneCensus.all_entities">
+<span class="sig-name descname"><span class="pre">all_entities</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CancerGeneCensus.all_entities" title="Link to this definition">§</a></dt>
+<dd><p>All entities annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CancerGeneCensus.all_mirnas">
+<span class="sig-name descname"><span class="pre">all_mirnas</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CancerGeneCensus.all_mirnas" title="Link to this definition">§</a></dt>
+<dd><p>All miRNAs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CancerGeneCensus.all_proteins">
+<span class="sig-name descname"><span class="pre">all_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CancerGeneCensus.all_proteins" title="Link to this definition">§</a></dt>
+<dd><p>All UniProt IDs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CancerGeneCensus.all_refs">
+<span class="sig-name descname"><span class="pre">all_refs</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CancerGeneCensus.all_refs" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects the references
+across all records. Returns <em>list</em>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CancerGeneCensus.annotate_complex">
+<span class="sig-name descname"><span class="pre">annotate_complex</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cplex</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CancerGeneCensus.annotate_complex" title="Link to this definition">§</a></dt>
+<dd><p>Infers annotations for a single complex.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CancerGeneCensus.browse">
+<span class="sig-name descname"><span class="pre">browse</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">field</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">start</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CancerGeneCensus.browse" title="Link to this definition">§</a></dt>
+<dd><p>Print gene information as a table.</p>
+<p>Presents information about annotation categories as ascii tables
+printed in the terminal. If one category provided, prints one table.
+If multiple categories provided, prints a table for each of them one
+by one proceeding to the next one once you hit return. If no categories
+provided goes through all levels of the primary category.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>field:</dt><dd><p>The field to browse categories by.</p>
+<ul class="simple">
+<li><p>If None the primary field will be selected.
+If this annotation resource doesn’t have fields, all proteins
+will be presented as one single category.</p></li>
+<li><p>If a string it will be considered a field name and it will
+browse through all levels of this field.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">list</span></code>, set or tuple, it will be considered either a
+<code class="docutils literal notranslate"><span class="pre">list</span></code> of field names or a list of values from the primary
+field. In the former case all combinations of the values of
+the fields will be presented, in the latter case the browsing
+will be limited to the levels of the primary field contained
+in <code class="docutils literal notranslate"><span class="pre">field</span></code>.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">dict</span></code>, keys are supposed to be field names and values
+as list of levels. If any of the values are None, all levels
+from that field will be used.</p></li>
+</ul>
+</dd>
+<dt>start:</dt><dd><p>Start browsing from this category. E.g. if there are 500
+categories and start is 250 it will skip everything before the
+250th.</p>
+</dd>
+<dt>kwargs:</dt><dd><p>Passed to <code class="docutils literal notranslate"><span class="pre">pypath.utils.uniprot.info</span></code>.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CancerGeneCensus.complex_inference">
+<span class="sig-name descname"><span class="pre">complex_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CancerGeneCensus.complex_inference" title="Link to this definition">§</a></dt>
+<dd><p>Annotates all complexes in <cite>complexes</cite>, by default in the default
+complex database (existing in the <cite>complex</cite> module or generated
+on demand according to the module’s current settings).</p>
+<dl class="field-list simple">
+<dt class="field-odd">Returns<span class="colon">:</span></dt>
+<dd class="field-odd"><p><ul class="simple">
+<li><p><em>Dict with complexes as keys and sets of annotations as values.</em></p></li>
+<li><p><em>Complexes with no valid information in this annotation resource</em></p></li>
+<li><p><em>won’t be in the dict.</em></p></li>
+</ul>
+</p>
+</dd>
+<dt class="field-even">Parameters<span class="colon">:</span></dt>
+<dd class="field-even"><p><strong>complexes</strong> (<em>iterable</em>) – Iterable yielding complexes.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CancerGeneCensus.coverage">
+<span class="sig-name descname"><span class="pre">coverage</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">other</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CancerGeneCensus.coverage" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the coverage of the annotation i.e. the proportion of
+entities having at least one record in this annotation resource
+for an arbitrary set of entities.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CancerGeneCensus.curation_effort">
+<span class="sig-name descname"><span class="pre">curation_effort</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CancerGeneCensus.curation_effort" title="Link to this definition">§</a></dt>
+<dd><p>Counts the reference-record pairs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CancerGeneCensus.get_names">
+<span class="sig-name descname"><span class="pre">get_names</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CancerGeneCensus.get_names" title="Link to this definition">§</a></dt>
+<dd><p>Returns the list of field names in the records. The annotation
+consists of uniform records and each entity might be annotated
+with one or more records. Each record is a tuple of fields, for
+example <code class="docutils literal notranslate"><span class="pre">('cell_type',</span> <span class="pre">'expression_level',</span> <span class="pre">'score')</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CancerGeneCensus.get_reference_set">
+<em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">get_reference_set</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">proteins</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">swissprot_only</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CancerGeneCensus.get_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the reference set i.e. the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CancerGeneCensus.get_subset">
+<span class="sig-name descname"><span class="pre">get_subset</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CancerGeneCensus.get_subset" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CancerGeneCensus.get_subset_bool_array">
+<span class="sig-name descname"><span class="pre">get_subset_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CancerGeneCensus.get_subset_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a boolean vector with True and False values for each entity
+in the reference set. The values represent presence absence data
+in the simplest case, but by providing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> any kind of matching
+and filtering is possible. <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> are passed to the <code class="docutils literal notranslate"><span class="pre">select</span></code>
+method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CancerGeneCensus.get_values">
+<span class="sig-name descname"><span class="pre">get_values</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">exclude_none</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CancerGeneCensus.get_values" title="Link to this definition">§</a></dt>
+<dd><p>Returns the set of all possible values of a field. E.g. if the
+records of this annotation have a field <code class="docutils literal notranslate"><span class="pre">cell_type</span></code> then calling
+this method can tell you that across all records the values of
+this field might be <code class="docutils literal notranslate"><span class="pre">{'macrophage',</span> <span class="pre">'epithelial_cell',</span> <span class="pre">...}</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CancerGeneCensus.labels">
+<span class="sig-name descname"><span class="pre">labels</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CancerGeneCensus.labels" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CancerGeneCensus.load">
+<span class="sig-name descname"><span class="pre">load</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CancerGeneCensus.load" title="Link to this definition">§</a></dt>
+<dd><p>Loads the annotation data by calling the input method.
+Infers annotations for complexes in the complex database if
+py:attr:<code class="docutils literal notranslate"><span class="pre">infer_complexes</span></code> is True.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CancerGeneCensus.load_data">
+<span class="sig-name descname"><span class="pre">load_data</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CancerGeneCensus.load_data" title="Link to this definition">§</a></dt>
+<dd><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CancerGeneCensus.load_proteins">
+<span class="sig-name descname"><span class="pre">load_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CancerGeneCensus.load_proteins" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a set of all UniProt IDs to have a base set of the entire
+proteome.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CancerGeneCensus.make_df">
+<span class="sig-name descname"><span class="pre">make_df</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">rebuild</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CancerGeneCensus.make_df" title="Link to this definition">§</a></dt>
+<dd><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.
+The data frame will be assigned to :py:attr``df``.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CancerGeneCensus.numof_entities">
+<span class="sig-name descname"><span class="pre">numof_entities</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CancerGeneCensus.numof_entities" title="Link to this definition">§</a></dt>
+<dd><p>The number of annotated entities in the resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CancerGeneCensus.numof_records">
+<span class="sig-name descname"><span class="pre">numof_records</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CancerGeneCensus.numof_records" title="Link to this definition">§</a></dt>
+<dd><p>The total number of annotation records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CancerGeneCensus.numof_references">
+<span class="sig-name descname"><span class="pre">numof_references</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CancerGeneCensus.numof_references" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects and counts the
+references across all records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CancerGeneCensus.process">
+<span class="sig-name descname"><span class="pre">process</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CancerGeneCensus.process" title="Link to this definition">§</a></dt>
+<dd><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CancerGeneCensus.reload">
+<span class="sig-name descname"><span class="pre">reload</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CancerGeneCensus.reload" title="Link to this definition">§</a></dt>
+<dd><p>Reloads the object from the module level.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CancerGeneCensus.select">
+<span class="sig-name descname"><span class="pre">select</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CancerGeneCensus.select" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CancerGeneCensus.set_method">
+<span class="sig-name descname"><span class="pre">set_method</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CancerGeneCensus.set_method" title="Link to this definition">§</a></dt>
+<dd><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if
+necessary.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CancerGeneCensus.set_reference_set">
+<span class="sig-name descname"><span class="pre">set_reference_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CancerGeneCensus.set_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Assigns the reference set to the :py:attr``reference_set`` attribute.
+The reference set is the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CancerGeneCensus.show">
+<span class="sig-name descname"><span class="pre">show</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">table_param</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CancerGeneCensus.show" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic
+information from the UniProt datasheets.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CancerGeneCensus.subset_intersection">
+<span class="sig-name descname"><span class="pre">subset_intersection</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">universe</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CancerGeneCensus.subset_intersection" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the proportion of entities in a subset occuring in the
+set <code class="docutils literal notranslate"><span class="pre">universe</span></code>. The subset is selected by passing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> to the
+<code class="docutils literal notranslate"><span class="pre">select</span></code> method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CancerGeneCensus.to_array">
+<span class="sig-name descname"><span class="pre">to_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_fields</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CancerGeneCensus.to_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns an entity vs feature array. In case of more complex
+annotations this might be huge.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CancerGeneCensus.to_bool_array">
+<span class="sig-name descname"><span class="pre">to_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CancerGeneCensus.to_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a presence/absence boolean array for a reference set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CancerGeneCensus.to_set">
+<span class="sig-name descname"><span class="pre">to_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CancerGeneCensus.to_set" title="Link to this definition">§</a></dt>
+<dd><p>Returns the entities present in this annotation resource as a set.</p>
+</dd></dl>
+
+</dd></dl>
+
+</section>
+
+
+                </article>
+              
+              
+              
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+  <section id="pypath-core-annot-cancerdrugsdb">
+<h1>pypath.core.annot.Cancerdrugsdb<a class="headerlink" href="#pypath-core-annot-cancerdrugsdb" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.core.annot.Cancerdrugsdb">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.core.annot.</span></span><span class="sig-name descname"><span class="pre">Cancerdrugsdb</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#Cancerdrugsdb"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.Cancerdrugsdb" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <a class="reference internal" href="pypath.core.annot.AnnotationBase.html#pypath.core.annot.AnnotationBase" title="pypath.core.annot.AnnotationBase"><code class="xref py py-class docutils literal notranslate"><span class="pre">AnnotationBase</span></code></a></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cancerdrugsdb.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#Cancerdrugsdb.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.Cancerdrugsdb.__init__" title="Link to this definition">§</a></dt>
+<dd><p>Approved cancer drugs from the Cancer Drugs Database
+(<a class="reference external" href="https://www.anticancerfund.org/en/cancerdrugs-db">https://www.anticancerfund.org/en/cancerdrugs-db</a>).</p>
+</dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Cancerdrugsdb.__init__" title="pypath.core.annot.Cancerdrugsdb.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>(**kwargs)</p></td>
+<td><p>Approved cancer drugs from the Cancer Drugs Database (<a class="reference external" href="https://www.anticancerfund.org/en/cancerdrugs-db">https://www.anticancerfund.org/en/cancerdrugs-db</a>).</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Cancerdrugsdb.add_complexes_by_inference" title="pypath.core.annot.Cancerdrugsdb.add_complexes_by_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">add_complexes_by_inference</span></code></a>([complexes])</p></td>
+<td><p>Creates complex annotations by in silico inference and adds them to this annotation set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Cancerdrugsdb.all_complexes" title="pypath.core.annot.Cancerdrugsdb.all_complexes"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_complexes</span></code></a>()</p></td>
+<td><p>All protein complexes annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Cancerdrugsdb.all_entities" title="pypath.core.annot.Cancerdrugsdb.all_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_entities</span></code></a>([entity_types])</p></td>
+<td><p>All entities annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Cancerdrugsdb.all_mirnas" title="pypath.core.annot.Cancerdrugsdb.all_mirnas"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_mirnas</span></code></a>()</p></td>
+<td><p>All miRNAs annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Cancerdrugsdb.all_proteins" title="pypath.core.annot.Cancerdrugsdb.all_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_proteins</span></code></a>()</p></td>
+<td><p>All UniProt IDs annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Cancerdrugsdb.all_refs" title="pypath.core.annot.Cancerdrugsdb.all_refs"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_refs</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Cancerdrugsdb.annotate_complex" title="pypath.core.annot.Cancerdrugsdb.annotate_complex"><code class="xref py py-obj docutils literal notranslate"><span class="pre">annotate_complex</span></code></a>(cplex)</p></td>
+<td><p>Infers annotations for a single complex.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Cancerdrugsdb.browse" title="pypath.core.annot.Cancerdrugsdb.browse"><code class="xref py py-obj docutils literal notranslate"><span class="pre">browse</span></code></a>([field, start])</p></td>
+<td><p>Print gene information as a table.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Cancerdrugsdb.complex_inference" title="pypath.core.annot.Cancerdrugsdb.complex_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">complex_inference</span></code></a>([complexes])</p></td>
+<td><p>Annotates all complexes in <cite>complexes</cite>, by default in the default complex database (existing in the <cite>complex</cite> module or generated on demand according to the module's current settings).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Cancerdrugsdb.coverage" title="pypath.core.annot.Cancerdrugsdb.coverage"><code class="xref py py-obj docutils literal notranslate"><span class="pre">coverage</span></code></a>(other)</p></td>
+<td><p>Calculates the coverage of the annotation i.e. the proportion of entities having at least one record in this annotation resource for an arbitrary set of entities.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Cancerdrugsdb.curation_effort" title="pypath.core.annot.Cancerdrugsdb.curation_effort"><code class="xref py py-obj docutils literal notranslate"><span class="pre">curation_effort</span></code></a>()</p></td>
+<td><p>Counts the reference-record pairs.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">from_dump</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_entity_type</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Cancerdrugsdb.get_names" title="pypath.core.annot.Cancerdrugsdb.get_names"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_names</span></code></a>()</p></td>
+<td><p>Returns the list of field names in the records.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Cancerdrugsdb.get_reference_set" title="pypath.core.annot.Cancerdrugsdb.get_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_reference_set</span></code></a>([proteins, complexes, ...])</p></td>
+<td><p>Retrieves the reference set i.e. the set of all entities which potentially have annotation in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Cancerdrugsdb.get_subset" title="pypath.core.annot.Cancerdrugsdb.get_subset"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Cancerdrugsdb.get_subset_bool_array" title="pypath.core.annot.Cancerdrugsdb.get_subset_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset_bool_array</span></code></a>([reference_set])</p></td>
+<td><p>Returns a boolean vector with True and False values for each entity in the reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Cancerdrugsdb.get_values" title="pypath.core.annot.Cancerdrugsdb.get_values"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_values</span></code></a>(name[, exclude_none])</p></td>
+<td><p>Returns the set of all possible values of a field.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_complex</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_mirna</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_protein</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Cancerdrugsdb.labels" title="pypath.core.annot.Cancerdrugsdb.labels"><code class="xref py py-obj docutils literal notranslate"><span class="pre">labels</span></code></a>([method])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Cancerdrugsdb.load" title="pypath.core.annot.Cancerdrugsdb.load"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load</span></code></a>()</p></td>
+<td><p>Loads the annotation data by calling the input method.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Cancerdrugsdb.load_data" title="pypath.core.annot.Cancerdrugsdb.load_data"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_data</span></code></a>()</p></td>
+<td><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Cancerdrugsdb.load_proteins" title="pypath.core.annot.Cancerdrugsdb.load_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_proteins</span></code></a>()</p></td>
+<td><p>Retrieves a set of all UniProt IDs to have a base set of the entire proteome.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Cancerdrugsdb.make_df" title="pypath.core.annot.Cancerdrugsdb.make_df"><code class="xref py py-obj docutils literal notranslate"><span class="pre">make_df</span></code></a>([rebuild])</p></td>
+<td><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complex_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Cancerdrugsdb.numof_entities" title="pypath.core.annot.Cancerdrugsdb.numof_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_entities</span></code></a>()</p></td>
+<td><p>The number of annotated entities in the resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirna_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirnas</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_protein_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_proteins</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Cancerdrugsdb.numof_records" title="pypath.core.annot.Cancerdrugsdb.numof_records"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_records</span></code></a>([entity_types])</p></td>
+<td><p>The total number of annotation records.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Cancerdrugsdb.numof_references" title="pypath.core.annot.Cancerdrugsdb.numof_references"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_references</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Cancerdrugsdb.process" title="pypath.core.annot.Cancerdrugsdb.process"><code class="xref py py-obj docutils literal notranslate"><span class="pre">process</span></code></a>()</p></td>
+<td><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">proportion</span></code>(other)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Cancerdrugsdb.reload" title="pypath.core.annot.Cancerdrugsdb.reload"><code class="xref py py-obj docutils literal notranslate"><span class="pre">reload</span></code></a>()</p></td>
+<td><p>Reloads the object from the module level.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">save_to_pickle</span></code>(pickle_file)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Cancerdrugsdb.select" title="pypath.core.annot.Cancerdrugsdb.select"><code class="xref py py-obj docutils literal notranslate"><span class="pre">select</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Cancerdrugsdb.set_method" title="pypath.core.annot.Cancerdrugsdb.set_method"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_method</span></code></a>()</p></td>
+<td><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if necessary.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Cancerdrugsdb.set_reference_set" title="pypath.core.annot.Cancerdrugsdb.set_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_reference_set</span></code></a>()</p></td>
+<td><p>Assigns the reference set to the :py:attr``reference_set`` attribute.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Cancerdrugsdb.show" title="pypath.core.annot.Cancerdrugsdb.show"><code class="xref py py-obj docutils literal notranslate"><span class="pre">show</span></code></a>([method, table_param])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic information from the UniProt datasheets.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Cancerdrugsdb.subset_intersection" title="pypath.core.annot.Cancerdrugsdb.subset_intersection"><code class="xref py py-obj docutils literal notranslate"><span class="pre">subset_intersection</span></code></a>(universe, **kwargs)</p></td>
+<td><p>Calculates the proportion of entities in a subset occuring in the set <code class="docutils literal notranslate"><span class="pre">universe</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Cancerdrugsdb.to_array" title="pypath.core.annot.Cancerdrugsdb.to_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_array</span></code></a>([reference_set, use_fields])</p></td>
+<td><p>Returns an entity vs feature array.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Cancerdrugsdb.to_bool_array" title="pypath.core.annot.Cancerdrugsdb.to_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_bool_array</span></code></a>(reference_set)</p></td>
+<td><p>Returns a presence/absence boolean array for a reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Cancerdrugsdb.to_set" title="pypath.core.annot.Cancerdrugsdb.to_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_set</span></code></a>()</p></td>
+<td><p>Returns the entities present in this annotation resource as a set.</p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Attributes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_fields</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">summary</span></code></p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cancerdrugsdb.add_complexes_by_inference">
+<span class="sig-name descname"><span class="pre">add_complexes_by_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cancerdrugsdb.add_complexes_by_inference" title="Link to this definition">§</a></dt>
+<dd><p>Creates complex annotations by in silico inference and adds them
+to this annotation set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cancerdrugsdb.all_complexes">
+<span class="sig-name descname"><span class="pre">all_complexes</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cancerdrugsdb.all_complexes" title="Link to this definition">§</a></dt>
+<dd><p>All protein complexes annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cancerdrugsdb.all_entities">
+<span class="sig-name descname"><span class="pre">all_entities</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cancerdrugsdb.all_entities" title="Link to this definition">§</a></dt>
+<dd><p>All entities annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cancerdrugsdb.all_mirnas">
+<span class="sig-name descname"><span class="pre">all_mirnas</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cancerdrugsdb.all_mirnas" title="Link to this definition">§</a></dt>
+<dd><p>All miRNAs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cancerdrugsdb.all_proteins">
+<span class="sig-name descname"><span class="pre">all_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cancerdrugsdb.all_proteins" title="Link to this definition">§</a></dt>
+<dd><p>All UniProt IDs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cancerdrugsdb.all_refs">
+<span class="sig-name descname"><span class="pre">all_refs</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cancerdrugsdb.all_refs" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects the references
+across all records. Returns <em>list</em>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cancerdrugsdb.annotate_complex">
+<span class="sig-name descname"><span class="pre">annotate_complex</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cplex</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cancerdrugsdb.annotate_complex" title="Link to this definition">§</a></dt>
+<dd><p>Infers annotations for a single complex.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cancerdrugsdb.browse">
+<span class="sig-name descname"><span class="pre">browse</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">field</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">start</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cancerdrugsdb.browse" title="Link to this definition">§</a></dt>
+<dd><p>Print gene information as a table.</p>
+<p>Presents information about annotation categories as ascii tables
+printed in the terminal. If one category provided, prints one table.
+If multiple categories provided, prints a table for each of them one
+by one proceeding to the next one once you hit return. If no categories
+provided goes through all levels of the primary category.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>field:</dt><dd><p>The field to browse categories by.</p>
+<ul class="simple">
+<li><p>If None the primary field will be selected.
+If this annotation resource doesn’t have fields, all proteins
+will be presented as one single category.</p></li>
+<li><p>If a string it will be considered a field name and it will
+browse through all levels of this field.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">list</span></code>, set or tuple, it will be considered either a
+<code class="docutils literal notranslate"><span class="pre">list</span></code> of field names or a list of values from the primary
+field. In the former case all combinations of the values of
+the fields will be presented, in the latter case the browsing
+will be limited to the levels of the primary field contained
+in <code class="docutils literal notranslate"><span class="pre">field</span></code>.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">dict</span></code>, keys are supposed to be field names and values
+as list of levels. If any of the values are None, all levels
+from that field will be used.</p></li>
+</ul>
+</dd>
+<dt>start:</dt><dd><p>Start browsing from this category. E.g. if there are 500
+categories and start is 250 it will skip everything before the
+250th.</p>
+</dd>
+<dt>kwargs:</dt><dd><p>Passed to <code class="docutils literal notranslate"><span class="pre">pypath.utils.uniprot.info</span></code>.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cancerdrugsdb.complex_inference">
+<span class="sig-name descname"><span class="pre">complex_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cancerdrugsdb.complex_inference" title="Link to this definition">§</a></dt>
+<dd><p>Annotates all complexes in <cite>complexes</cite>, by default in the default
+complex database (existing in the <cite>complex</cite> module or generated
+on demand according to the module’s current settings).</p>
+<dl class="field-list simple">
+<dt class="field-odd">Returns<span class="colon">:</span></dt>
+<dd class="field-odd"><p><ul class="simple">
+<li><p><em>Dict with complexes as keys and sets of annotations as values.</em></p></li>
+<li><p><em>Complexes with no valid information in this annotation resource</em></p></li>
+<li><p><em>won’t be in the dict.</em></p></li>
+</ul>
+</p>
+</dd>
+<dt class="field-even">Parameters<span class="colon">:</span></dt>
+<dd class="field-even"><p><strong>complexes</strong> (<em>iterable</em>) – Iterable yielding complexes.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cancerdrugsdb.coverage">
+<span class="sig-name descname"><span class="pre">coverage</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">other</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cancerdrugsdb.coverage" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the coverage of the annotation i.e. the proportion of
+entities having at least one record in this annotation resource
+for an arbitrary set of entities.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cancerdrugsdb.curation_effort">
+<span class="sig-name descname"><span class="pre">curation_effort</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cancerdrugsdb.curation_effort" title="Link to this definition">§</a></dt>
+<dd><p>Counts the reference-record pairs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cancerdrugsdb.get_names">
+<span class="sig-name descname"><span class="pre">get_names</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cancerdrugsdb.get_names" title="Link to this definition">§</a></dt>
+<dd><p>Returns the list of field names in the records. The annotation
+consists of uniform records and each entity might be annotated
+with one or more records. Each record is a tuple of fields, for
+example <code class="docutils literal notranslate"><span class="pre">('cell_type',</span> <span class="pre">'expression_level',</span> <span class="pre">'score')</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cancerdrugsdb.get_reference_set">
+<em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">get_reference_set</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">proteins</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">swissprot_only</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cancerdrugsdb.get_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the reference set i.e. the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cancerdrugsdb.get_subset">
+<span class="sig-name descname"><span class="pre">get_subset</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cancerdrugsdb.get_subset" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cancerdrugsdb.get_subset_bool_array">
+<span class="sig-name descname"><span class="pre">get_subset_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cancerdrugsdb.get_subset_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a boolean vector with True and False values for each entity
+in the reference set. The values represent presence absence data
+in the simplest case, but by providing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> any kind of matching
+and filtering is possible. <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> are passed to the <code class="docutils literal notranslate"><span class="pre">select</span></code>
+method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cancerdrugsdb.get_values">
+<span class="sig-name descname"><span class="pre">get_values</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">exclude_none</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cancerdrugsdb.get_values" title="Link to this definition">§</a></dt>
+<dd><p>Returns the set of all possible values of a field. E.g. if the
+records of this annotation have a field <code class="docutils literal notranslate"><span class="pre">cell_type</span></code> then calling
+this method can tell you that across all records the values of
+this field might be <code class="docutils literal notranslate"><span class="pre">{'macrophage',</span> <span class="pre">'epithelial_cell',</span> <span class="pre">...}</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cancerdrugsdb.labels">
+<span class="sig-name descname"><span class="pre">labels</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cancerdrugsdb.labels" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cancerdrugsdb.load">
+<span class="sig-name descname"><span class="pre">load</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cancerdrugsdb.load" title="Link to this definition">§</a></dt>
+<dd><p>Loads the annotation data by calling the input method.
+Infers annotations for complexes in the complex database if
+py:attr:<code class="docutils literal notranslate"><span class="pre">infer_complexes</span></code> is True.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cancerdrugsdb.load_data">
+<span class="sig-name descname"><span class="pre">load_data</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cancerdrugsdb.load_data" title="Link to this definition">§</a></dt>
+<dd><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cancerdrugsdb.load_proteins">
+<span class="sig-name descname"><span class="pre">load_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cancerdrugsdb.load_proteins" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a set of all UniProt IDs to have a base set of the entire
+proteome.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cancerdrugsdb.make_df">
+<span class="sig-name descname"><span class="pre">make_df</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">rebuild</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cancerdrugsdb.make_df" title="Link to this definition">§</a></dt>
+<dd><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.
+The data frame will be assigned to :py:attr``df``.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cancerdrugsdb.numof_entities">
+<span class="sig-name descname"><span class="pre">numof_entities</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cancerdrugsdb.numof_entities" title="Link to this definition">§</a></dt>
+<dd><p>The number of annotated entities in the resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cancerdrugsdb.numof_records">
+<span class="sig-name descname"><span class="pre">numof_records</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cancerdrugsdb.numof_records" title="Link to this definition">§</a></dt>
+<dd><p>The total number of annotation records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cancerdrugsdb.numof_references">
+<span class="sig-name descname"><span class="pre">numof_references</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cancerdrugsdb.numof_references" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects and counts the
+references across all records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cancerdrugsdb.process">
+<span class="sig-name descname"><span class="pre">process</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cancerdrugsdb.process" title="Link to this definition">§</a></dt>
+<dd><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cancerdrugsdb.reload">
+<span class="sig-name descname"><span class="pre">reload</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cancerdrugsdb.reload" title="Link to this definition">§</a></dt>
+<dd><p>Reloads the object from the module level.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cancerdrugsdb.select">
+<span class="sig-name descname"><span class="pre">select</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cancerdrugsdb.select" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cancerdrugsdb.set_method">
+<span class="sig-name descname"><span class="pre">set_method</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cancerdrugsdb.set_method" title="Link to this definition">§</a></dt>
+<dd><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if
+necessary.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cancerdrugsdb.set_reference_set">
+<span class="sig-name descname"><span class="pre">set_reference_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cancerdrugsdb.set_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Assigns the reference set to the :py:attr``reference_set`` attribute.
+The reference set is the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cancerdrugsdb.show">
+<span class="sig-name descname"><span class="pre">show</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">table_param</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cancerdrugsdb.show" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic
+information from the UniProt datasheets.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cancerdrugsdb.subset_intersection">
+<span class="sig-name descname"><span class="pre">subset_intersection</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">universe</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cancerdrugsdb.subset_intersection" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the proportion of entities in a subset occuring in the
+set <code class="docutils literal notranslate"><span class="pre">universe</span></code>. The subset is selected by passing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> to the
+<code class="docutils literal notranslate"><span class="pre">select</span></code> method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cancerdrugsdb.to_array">
+<span class="sig-name descname"><span class="pre">to_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_fields</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cancerdrugsdb.to_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns an entity vs feature array. In case of more complex
+annotations this might be huge.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cancerdrugsdb.to_bool_array">
+<span class="sig-name descname"><span class="pre">to_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cancerdrugsdb.to_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a presence/absence boolean array for a reference set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cancerdrugsdb.to_set">
+<span class="sig-name descname"><span class="pre">to_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cancerdrugsdb.to_set" title="Link to this definition">§</a></dt>
+<dd><p>Returns the entities present in this annotation resource as a set.</p>
+</dd></dl>
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+                  
+  <section id="pypath-core-annot-cancersea">
+<h1>pypath.core.annot.Cancersea<a class="headerlink" href="#pypath-core-annot-cancersea" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.core.annot.Cancersea">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.core.annot.</span></span><span class="sig-name descname"><span class="pre">Cancersea</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#Cancersea"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.Cancersea" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <a class="reference internal" href="pypath.core.annot.AnnotationBase.html#pypath.core.annot.AnnotationBase" title="pypath.core.annot.AnnotationBase"><code class="xref py py-class docutils literal notranslate"><span class="pre">AnnotationBase</span></code></a></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cancersea.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#Cancersea.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.Cancersea.__init__" title="Link to this definition">§</a></dt>
+<dd><p>Represents annotations for a set of proteins.
+Loads the data from the original resource and provides methods
+to query the annotations.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>name</strong> (<em>str</em>) – A custom name for the annotation resource.</p></li>
+<li><p><strong>ncbi_tax_id</strong> (<em>int</em>) – NCBI Taxonomy identifier.</p></li>
+<li><p><strong>input_method</strong> (<em>callable</em><em>,</em><em>str</em>) – Either a callable or the name of a method in any submodules of
+the <code class="docutils literal notranslate"><span class="pre">pypath.inputs</span></code>  module. Should return a dict with
+UniProt IDs as keys or an object suitable for <code class="docutils literal notranslate"><span class="pre">process_method</span></code>.</p></li>
+<li><p><strong>input_args</strong> (<em>dict</em>) – Arguments for the <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Cancersea.__init__" title="pypath.core.annot.Cancersea.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>(**kwargs)</p></td>
+<td><p>Represents annotations for a set of proteins.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Cancersea.add_complexes_by_inference" title="pypath.core.annot.Cancersea.add_complexes_by_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">add_complexes_by_inference</span></code></a>([complexes])</p></td>
+<td><p>Creates complex annotations by in silico inference and adds them to this annotation set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Cancersea.all_complexes" title="pypath.core.annot.Cancersea.all_complexes"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_complexes</span></code></a>()</p></td>
+<td><p>All protein complexes annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Cancersea.all_entities" title="pypath.core.annot.Cancersea.all_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_entities</span></code></a>([entity_types])</p></td>
+<td><p>All entities annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Cancersea.all_mirnas" title="pypath.core.annot.Cancersea.all_mirnas"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_mirnas</span></code></a>()</p></td>
+<td><p>All miRNAs annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Cancersea.all_proteins" title="pypath.core.annot.Cancersea.all_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_proteins</span></code></a>()</p></td>
+<td><p>All UniProt IDs annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Cancersea.all_refs" title="pypath.core.annot.Cancersea.all_refs"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_refs</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Cancersea.annotate_complex" title="pypath.core.annot.Cancersea.annotate_complex"><code class="xref py py-obj docutils literal notranslate"><span class="pre">annotate_complex</span></code></a>(cplex)</p></td>
+<td><p>Infers annotations for a single complex.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Cancersea.browse" title="pypath.core.annot.Cancersea.browse"><code class="xref py py-obj docutils literal notranslate"><span class="pre">browse</span></code></a>([field, start])</p></td>
+<td><p>Print gene information as a table.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Cancersea.complex_inference" title="pypath.core.annot.Cancersea.complex_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">complex_inference</span></code></a>([complexes])</p></td>
+<td><p>Annotates all complexes in <cite>complexes</cite>, by default in the default complex database (existing in the <cite>complex</cite> module or generated on demand according to the module's current settings).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Cancersea.coverage" title="pypath.core.annot.Cancersea.coverage"><code class="xref py py-obj docutils literal notranslate"><span class="pre">coverage</span></code></a>(other)</p></td>
+<td><p>Calculates the coverage of the annotation i.e. the proportion of entities having at least one record in this annotation resource for an arbitrary set of entities.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Cancersea.curation_effort" title="pypath.core.annot.Cancersea.curation_effort"><code class="xref py py-obj docutils literal notranslate"><span class="pre">curation_effort</span></code></a>()</p></td>
+<td><p>Counts the reference-record pairs.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">from_dump</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_entity_type</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Cancersea.get_names" title="pypath.core.annot.Cancersea.get_names"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_names</span></code></a>()</p></td>
+<td><p>Returns the list of field names in the records.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Cancersea.get_reference_set" title="pypath.core.annot.Cancersea.get_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_reference_set</span></code></a>([proteins, complexes, ...])</p></td>
+<td><p>Retrieves the reference set i.e. the set of all entities which potentially have annotation in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Cancersea.get_subset" title="pypath.core.annot.Cancersea.get_subset"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Cancersea.get_subset_bool_array" title="pypath.core.annot.Cancersea.get_subset_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset_bool_array</span></code></a>([reference_set])</p></td>
+<td><p>Returns a boolean vector with True and False values for each entity in the reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Cancersea.get_values" title="pypath.core.annot.Cancersea.get_values"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_values</span></code></a>(name[, exclude_none])</p></td>
+<td><p>Returns the set of all possible values of a field.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_complex</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_mirna</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_protein</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Cancersea.labels" title="pypath.core.annot.Cancersea.labels"><code class="xref py py-obj docutils literal notranslate"><span class="pre">labels</span></code></a>([method])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Cancersea.load" title="pypath.core.annot.Cancersea.load"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load</span></code></a>()</p></td>
+<td><p>Loads the annotation data by calling the input method.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Cancersea.load_data" title="pypath.core.annot.Cancersea.load_data"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_data</span></code></a>()</p></td>
+<td><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Cancersea.load_proteins" title="pypath.core.annot.Cancersea.load_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_proteins</span></code></a>()</p></td>
+<td><p>Retrieves a set of all UniProt IDs to have a base set of the entire proteome.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Cancersea.make_df" title="pypath.core.annot.Cancersea.make_df"><code class="xref py py-obj docutils literal notranslate"><span class="pre">make_df</span></code></a>([rebuild])</p></td>
+<td><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complex_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Cancersea.numof_entities" title="pypath.core.annot.Cancersea.numof_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_entities</span></code></a>()</p></td>
+<td><p>The number of annotated entities in the resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirna_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirnas</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_protein_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_proteins</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Cancersea.numof_records" title="pypath.core.annot.Cancersea.numof_records"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_records</span></code></a>([entity_types])</p></td>
+<td><p>The total number of annotation records.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Cancersea.numof_references" title="pypath.core.annot.Cancersea.numof_references"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_references</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Cancersea.process" title="pypath.core.annot.Cancersea.process"><code class="xref py py-obj docutils literal notranslate"><span class="pre">process</span></code></a>()</p></td>
+<td><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">proportion</span></code>(other)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Cancersea.reload" title="pypath.core.annot.Cancersea.reload"><code class="xref py py-obj docutils literal notranslate"><span class="pre">reload</span></code></a>()</p></td>
+<td><p>Reloads the object from the module level.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">save_to_pickle</span></code>(pickle_file)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Cancersea.select" title="pypath.core.annot.Cancersea.select"><code class="xref py py-obj docutils literal notranslate"><span class="pre">select</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Cancersea.set_method" title="pypath.core.annot.Cancersea.set_method"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_method</span></code></a>()</p></td>
+<td><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if necessary.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Cancersea.set_reference_set" title="pypath.core.annot.Cancersea.set_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_reference_set</span></code></a>()</p></td>
+<td><p>Assigns the reference set to the :py:attr``reference_set`` attribute.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Cancersea.show" title="pypath.core.annot.Cancersea.show"><code class="xref py py-obj docutils literal notranslate"><span class="pre">show</span></code></a>([method, table_param])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic information from the UniProt datasheets.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Cancersea.subset_intersection" title="pypath.core.annot.Cancersea.subset_intersection"><code class="xref py py-obj docutils literal notranslate"><span class="pre">subset_intersection</span></code></a>(universe, **kwargs)</p></td>
+<td><p>Calculates the proportion of entities in a subset occuring in the set <code class="docutils literal notranslate"><span class="pre">universe</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Cancersea.to_array" title="pypath.core.annot.Cancersea.to_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_array</span></code></a>([reference_set, use_fields])</p></td>
+<td><p>Returns an entity vs feature array.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Cancersea.to_bool_array" title="pypath.core.annot.Cancersea.to_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_bool_array</span></code></a>(reference_set)</p></td>
+<td><p>Returns a presence/absence boolean array for a reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Cancersea.to_set" title="pypath.core.annot.Cancersea.to_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_set</span></code></a>()</p></td>
+<td><p>Returns the entities present in this annotation resource as a set.</p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Attributes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_fields</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">summary</span></code></p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cancersea.add_complexes_by_inference">
+<span class="sig-name descname"><span class="pre">add_complexes_by_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cancersea.add_complexes_by_inference" title="Link to this definition">§</a></dt>
+<dd><p>Creates complex annotations by in silico inference and adds them
+to this annotation set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cancersea.all_complexes">
+<span class="sig-name descname"><span class="pre">all_complexes</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cancersea.all_complexes" title="Link to this definition">§</a></dt>
+<dd><p>All protein complexes annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cancersea.all_entities">
+<span class="sig-name descname"><span class="pre">all_entities</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cancersea.all_entities" title="Link to this definition">§</a></dt>
+<dd><p>All entities annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cancersea.all_mirnas">
+<span class="sig-name descname"><span class="pre">all_mirnas</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cancersea.all_mirnas" title="Link to this definition">§</a></dt>
+<dd><p>All miRNAs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cancersea.all_proteins">
+<span class="sig-name descname"><span class="pre">all_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cancersea.all_proteins" title="Link to this definition">§</a></dt>
+<dd><p>All UniProt IDs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cancersea.all_refs">
+<span class="sig-name descname"><span class="pre">all_refs</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cancersea.all_refs" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects the references
+across all records. Returns <em>list</em>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cancersea.annotate_complex">
+<span class="sig-name descname"><span class="pre">annotate_complex</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cplex</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cancersea.annotate_complex" title="Link to this definition">§</a></dt>
+<dd><p>Infers annotations for a single complex.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cancersea.browse">
+<span class="sig-name descname"><span class="pre">browse</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">field</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">start</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cancersea.browse" title="Link to this definition">§</a></dt>
+<dd><p>Print gene information as a table.</p>
+<p>Presents information about annotation categories as ascii tables
+printed in the terminal. If one category provided, prints one table.
+If multiple categories provided, prints a table for each of them one
+by one proceeding to the next one once you hit return. If no categories
+provided goes through all levels of the primary category.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>field:</dt><dd><p>The field to browse categories by.</p>
+<ul class="simple">
+<li><p>If None the primary field will be selected.
+If this annotation resource doesn’t have fields, all proteins
+will be presented as one single category.</p></li>
+<li><p>If a string it will be considered a field name and it will
+browse through all levels of this field.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">list</span></code>, set or tuple, it will be considered either a
+<code class="docutils literal notranslate"><span class="pre">list</span></code> of field names or a list of values from the primary
+field. In the former case all combinations of the values of
+the fields will be presented, in the latter case the browsing
+will be limited to the levels of the primary field contained
+in <code class="docutils literal notranslate"><span class="pre">field</span></code>.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">dict</span></code>, keys are supposed to be field names and values
+as list of levels. If any of the values are None, all levels
+from that field will be used.</p></li>
+</ul>
+</dd>
+<dt>start:</dt><dd><p>Start browsing from this category. E.g. if there are 500
+categories and start is 250 it will skip everything before the
+250th.</p>
+</dd>
+<dt>kwargs:</dt><dd><p>Passed to <code class="docutils literal notranslate"><span class="pre">pypath.utils.uniprot.info</span></code>.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cancersea.complex_inference">
+<span class="sig-name descname"><span class="pre">complex_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cancersea.complex_inference" title="Link to this definition">§</a></dt>
+<dd><p>Annotates all complexes in <cite>complexes</cite>, by default in the default
+complex database (existing in the <cite>complex</cite> module or generated
+on demand according to the module’s current settings).</p>
+<dl class="field-list simple">
+<dt class="field-odd">Returns<span class="colon">:</span></dt>
+<dd class="field-odd"><p><ul class="simple">
+<li><p><em>Dict with complexes as keys and sets of annotations as values.</em></p></li>
+<li><p><em>Complexes with no valid information in this annotation resource</em></p></li>
+<li><p><em>won’t be in the dict.</em></p></li>
+</ul>
+</p>
+</dd>
+<dt class="field-even">Parameters<span class="colon">:</span></dt>
+<dd class="field-even"><p><strong>complexes</strong> (<em>iterable</em>) – Iterable yielding complexes.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cancersea.coverage">
+<span class="sig-name descname"><span class="pre">coverage</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">other</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cancersea.coverage" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the coverage of the annotation i.e. the proportion of
+entities having at least one record in this annotation resource
+for an arbitrary set of entities.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cancersea.curation_effort">
+<span class="sig-name descname"><span class="pre">curation_effort</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cancersea.curation_effort" title="Link to this definition">§</a></dt>
+<dd><p>Counts the reference-record pairs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cancersea.get_names">
+<span class="sig-name descname"><span class="pre">get_names</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cancersea.get_names" title="Link to this definition">§</a></dt>
+<dd><p>Returns the list of field names in the records. The annotation
+consists of uniform records and each entity might be annotated
+with one or more records. Each record is a tuple of fields, for
+example <code class="docutils literal notranslate"><span class="pre">('cell_type',</span> <span class="pre">'expression_level',</span> <span class="pre">'score')</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cancersea.get_reference_set">
+<em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">get_reference_set</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">proteins</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">swissprot_only</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cancersea.get_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the reference set i.e. the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cancersea.get_subset">
+<span class="sig-name descname"><span class="pre">get_subset</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cancersea.get_subset" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cancersea.get_subset_bool_array">
+<span class="sig-name descname"><span class="pre">get_subset_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cancersea.get_subset_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a boolean vector with True and False values for each entity
+in the reference set. The values represent presence absence data
+in the simplest case, but by providing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> any kind of matching
+and filtering is possible. <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> are passed to the <code class="docutils literal notranslate"><span class="pre">select</span></code>
+method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cancersea.get_values">
+<span class="sig-name descname"><span class="pre">get_values</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">exclude_none</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cancersea.get_values" title="Link to this definition">§</a></dt>
+<dd><p>Returns the set of all possible values of a field. E.g. if the
+records of this annotation have a field <code class="docutils literal notranslate"><span class="pre">cell_type</span></code> then calling
+this method can tell you that across all records the values of
+this field might be <code class="docutils literal notranslate"><span class="pre">{'macrophage',</span> <span class="pre">'epithelial_cell',</span> <span class="pre">...}</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cancersea.labels">
+<span class="sig-name descname"><span class="pre">labels</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cancersea.labels" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cancersea.load">
+<span class="sig-name descname"><span class="pre">load</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cancersea.load" title="Link to this definition">§</a></dt>
+<dd><p>Loads the annotation data by calling the input method.
+Infers annotations for complexes in the complex database if
+py:attr:<code class="docutils literal notranslate"><span class="pre">infer_complexes</span></code> is True.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cancersea.load_data">
+<span class="sig-name descname"><span class="pre">load_data</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cancersea.load_data" title="Link to this definition">§</a></dt>
+<dd><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cancersea.load_proteins">
+<span class="sig-name descname"><span class="pre">load_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cancersea.load_proteins" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a set of all UniProt IDs to have a base set of the entire
+proteome.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cancersea.make_df">
+<span class="sig-name descname"><span class="pre">make_df</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">rebuild</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cancersea.make_df" title="Link to this definition">§</a></dt>
+<dd><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.
+The data frame will be assigned to :py:attr``df``.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cancersea.numof_entities">
+<span class="sig-name descname"><span class="pre">numof_entities</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cancersea.numof_entities" title="Link to this definition">§</a></dt>
+<dd><p>The number of annotated entities in the resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cancersea.numof_records">
+<span class="sig-name descname"><span class="pre">numof_records</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cancersea.numof_records" title="Link to this definition">§</a></dt>
+<dd><p>The total number of annotation records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cancersea.numof_references">
+<span class="sig-name descname"><span class="pre">numof_references</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cancersea.numof_references" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects and counts the
+references across all records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cancersea.process">
+<span class="sig-name descname"><span class="pre">process</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cancersea.process" title="Link to this definition">§</a></dt>
+<dd><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cancersea.reload">
+<span class="sig-name descname"><span class="pre">reload</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cancersea.reload" title="Link to this definition">§</a></dt>
+<dd><p>Reloads the object from the module level.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cancersea.select">
+<span class="sig-name descname"><span class="pre">select</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cancersea.select" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cancersea.set_method">
+<span class="sig-name descname"><span class="pre">set_method</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cancersea.set_method" title="Link to this definition">§</a></dt>
+<dd><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if
+necessary.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cancersea.set_reference_set">
+<span class="sig-name descname"><span class="pre">set_reference_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cancersea.set_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Assigns the reference set to the :py:attr``reference_set`` attribute.
+The reference set is the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cancersea.show">
+<span class="sig-name descname"><span class="pre">show</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">table_param</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cancersea.show" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic
+information from the UniProt datasheets.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cancersea.subset_intersection">
+<span class="sig-name descname"><span class="pre">subset_intersection</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">universe</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cancersea.subset_intersection" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the proportion of entities in a subset occuring in the
+set <code class="docutils literal notranslate"><span class="pre">universe</span></code>. The subset is selected by passing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> to the
+<code class="docutils literal notranslate"><span class="pre">select</span></code> method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cancersea.to_array">
+<span class="sig-name descname"><span class="pre">to_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_fields</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cancersea.to_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns an entity vs feature array. In case of more complex
+annotations this might be huge.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cancersea.to_bool_array">
+<span class="sig-name descname"><span class="pre">to_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cancersea.to_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a presence/absence boolean array for a reference set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cancersea.to_set">
+<span class="sig-name descname"><span class="pre">to_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cancersea.to_set" title="Link to this definition">§</a></dt>
+<dd><p>Returns the entities present in this annotation resource as a set.</p>
+</dd></dl>
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+  <section id="pypath-core-annot-cellphonedb">
+<h1>pypath.core.annot.CellPhoneDB<a class="headerlink" href="#pypath-core-annot-cellphonedb" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.core.annot.CellPhoneDB">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.core.annot.</span></span><span class="sig-name descname"><span class="pre">CellPhoneDB</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#CellPhoneDB"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.CellPhoneDB" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <a class="reference internal" href="pypath.core.annot.AnnotationBase.html#pypath.core.annot.AnnotationBase" title="pypath.core.annot.AnnotationBase"><code class="xref py py-class docutils literal notranslate"><span class="pre">AnnotationBase</span></code></a></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellPhoneDB.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#CellPhoneDB.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.CellPhoneDB.__init__" title="Link to this definition">§</a></dt>
+<dd><p>Represents annotations for a set of proteins.
+Loads the data from the original resource and provides methods
+to query the annotations.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>name</strong> (<em>str</em>) – A custom name for the annotation resource.</p></li>
+<li><p><strong>ncbi_tax_id</strong> (<em>int</em>) – NCBI Taxonomy identifier.</p></li>
+<li><p><strong>input_method</strong> (<em>callable</em><em>,</em><em>str</em>) – Either a callable or the name of a method in any submodules of
+the <code class="docutils literal notranslate"><span class="pre">pypath.inputs</span></code>  module. Should return a dict with
+UniProt IDs as keys or an object suitable for <code class="docutils literal notranslate"><span class="pre">process_method</span></code>.</p></li>
+<li><p><strong>input_args</strong> (<em>dict</em>) – Arguments for the <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CellPhoneDB.__init__" title="pypath.core.annot.CellPhoneDB.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>(**kwargs)</p></td>
+<td><p>Represents annotations for a set of proteins.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CellPhoneDB.add_complexes_by_inference" title="pypath.core.annot.CellPhoneDB.add_complexes_by_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">add_complexes_by_inference</span></code></a>([complexes])</p></td>
+<td><p>Creates complex annotations by in silico inference and adds them to this annotation set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CellPhoneDB.all_complexes" title="pypath.core.annot.CellPhoneDB.all_complexes"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_complexes</span></code></a>()</p></td>
+<td><p>All protein complexes annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CellPhoneDB.all_entities" title="pypath.core.annot.CellPhoneDB.all_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_entities</span></code></a>([entity_types])</p></td>
+<td><p>All entities annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CellPhoneDB.all_mirnas" title="pypath.core.annot.CellPhoneDB.all_mirnas"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_mirnas</span></code></a>()</p></td>
+<td><p>All miRNAs annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CellPhoneDB.all_proteins" title="pypath.core.annot.CellPhoneDB.all_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_proteins</span></code></a>()</p></td>
+<td><p>All UniProt IDs annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CellPhoneDB.all_refs" title="pypath.core.annot.CellPhoneDB.all_refs"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_refs</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CellPhoneDB.annotate_complex" title="pypath.core.annot.CellPhoneDB.annotate_complex"><code class="xref py py-obj docutils literal notranslate"><span class="pre">annotate_complex</span></code></a>(cplex)</p></td>
+<td><p>Infers annotations for a single complex.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CellPhoneDB.browse" title="pypath.core.annot.CellPhoneDB.browse"><code class="xref py py-obj docutils literal notranslate"><span class="pre">browse</span></code></a>([field, start])</p></td>
+<td><p>Print gene information as a table.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CellPhoneDB.complex_inference" title="pypath.core.annot.CellPhoneDB.complex_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">complex_inference</span></code></a>([complexes])</p></td>
+<td><p>Annotates all complexes in <cite>complexes</cite>, by default in the default complex database (existing in the <cite>complex</cite> module or generated on demand according to the module's current settings).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CellPhoneDB.coverage" title="pypath.core.annot.CellPhoneDB.coverage"><code class="xref py py-obj docutils literal notranslate"><span class="pre">coverage</span></code></a>(other)</p></td>
+<td><p>Calculates the coverage of the annotation i.e. the proportion of entities having at least one record in this annotation resource for an arbitrary set of entities.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CellPhoneDB.curation_effort" title="pypath.core.annot.CellPhoneDB.curation_effort"><code class="xref py py-obj docutils literal notranslate"><span class="pre">curation_effort</span></code></a>()</p></td>
+<td><p>Counts the reference-record pairs.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">from_dump</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_entity_type</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CellPhoneDB.get_names" title="pypath.core.annot.CellPhoneDB.get_names"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_names</span></code></a>()</p></td>
+<td><p>Returns the list of field names in the records.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CellPhoneDB.get_reference_set" title="pypath.core.annot.CellPhoneDB.get_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_reference_set</span></code></a>([proteins, complexes, ...])</p></td>
+<td><p>Retrieves the reference set i.e. the set of all entities which potentially have annotation in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CellPhoneDB.get_subset" title="pypath.core.annot.CellPhoneDB.get_subset"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CellPhoneDB.get_subset_bool_array" title="pypath.core.annot.CellPhoneDB.get_subset_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset_bool_array</span></code></a>([reference_set])</p></td>
+<td><p>Returns a boolean vector with True and False values for each entity in the reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CellPhoneDB.get_values" title="pypath.core.annot.CellPhoneDB.get_values"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_values</span></code></a>(name[, exclude_none])</p></td>
+<td><p>Returns the set of all possible values of a field.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_complex</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_mirna</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_protein</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CellPhoneDB.labels" title="pypath.core.annot.CellPhoneDB.labels"><code class="xref py py-obj docutils literal notranslate"><span class="pre">labels</span></code></a>([method])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CellPhoneDB.load" title="pypath.core.annot.CellPhoneDB.load"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load</span></code></a>()</p></td>
+<td><p>Loads the annotation data by calling the input method.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CellPhoneDB.load_data" title="pypath.core.annot.CellPhoneDB.load_data"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_data</span></code></a>()</p></td>
+<td><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CellPhoneDB.load_proteins" title="pypath.core.annot.CellPhoneDB.load_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_proteins</span></code></a>()</p></td>
+<td><p>Retrieves a set of all UniProt IDs to have a base set of the entire proteome.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CellPhoneDB.make_df" title="pypath.core.annot.CellPhoneDB.make_df"><code class="xref py py-obj docutils literal notranslate"><span class="pre">make_df</span></code></a>([rebuild])</p></td>
+<td><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complex_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CellPhoneDB.numof_entities" title="pypath.core.annot.CellPhoneDB.numof_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_entities</span></code></a>()</p></td>
+<td><p>The number of annotated entities in the resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirna_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirnas</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_protein_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_proteins</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CellPhoneDB.numof_records" title="pypath.core.annot.CellPhoneDB.numof_records"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_records</span></code></a>([entity_types])</p></td>
+<td><p>The total number of annotation records.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CellPhoneDB.numof_references" title="pypath.core.annot.CellPhoneDB.numof_references"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_references</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CellPhoneDB.process" title="pypath.core.annot.CellPhoneDB.process"><code class="xref py py-obj docutils literal notranslate"><span class="pre">process</span></code></a>()</p></td>
+<td><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">proportion</span></code>(other)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CellPhoneDB.reload" title="pypath.core.annot.CellPhoneDB.reload"><code class="xref py py-obj docutils literal notranslate"><span class="pre">reload</span></code></a>()</p></td>
+<td><p>Reloads the object from the module level.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">save_to_pickle</span></code>(pickle_file)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CellPhoneDB.select" title="pypath.core.annot.CellPhoneDB.select"><code class="xref py py-obj docutils literal notranslate"><span class="pre">select</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CellPhoneDB.set_method" title="pypath.core.annot.CellPhoneDB.set_method"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_method</span></code></a>()</p></td>
+<td><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if necessary.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CellPhoneDB.set_reference_set" title="pypath.core.annot.CellPhoneDB.set_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_reference_set</span></code></a>()</p></td>
+<td><p>Assigns the reference set to the :py:attr``reference_set`` attribute.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CellPhoneDB.show" title="pypath.core.annot.CellPhoneDB.show"><code class="xref py py-obj docutils literal notranslate"><span class="pre">show</span></code></a>([method, table_param])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic information from the UniProt datasheets.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CellPhoneDB.subset_intersection" title="pypath.core.annot.CellPhoneDB.subset_intersection"><code class="xref py py-obj docutils literal notranslate"><span class="pre">subset_intersection</span></code></a>(universe, **kwargs)</p></td>
+<td><p>Calculates the proportion of entities in a subset occuring in the set <code class="docutils literal notranslate"><span class="pre">universe</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CellPhoneDB.to_array" title="pypath.core.annot.CellPhoneDB.to_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_array</span></code></a>([reference_set, use_fields])</p></td>
+<td><p>Returns an entity vs feature array.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CellPhoneDB.to_bool_array" title="pypath.core.annot.CellPhoneDB.to_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_bool_array</span></code></a>(reference_set)</p></td>
+<td><p>Returns a presence/absence boolean array for a reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CellPhoneDB.to_set" title="pypath.core.annot.CellPhoneDB.to_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_set</span></code></a>()</p></td>
+<td><p>Returns the entities present in this annotation resource as a set.</p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Attributes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_fields</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">summary</span></code></p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellPhoneDB.add_complexes_by_inference">
+<span class="sig-name descname"><span class="pre">add_complexes_by_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellPhoneDB.add_complexes_by_inference" title="Link to this definition">§</a></dt>
+<dd><p>Creates complex annotations by in silico inference and adds them
+to this annotation set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellPhoneDB.all_complexes">
+<span class="sig-name descname"><span class="pre">all_complexes</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellPhoneDB.all_complexes" title="Link to this definition">§</a></dt>
+<dd><p>All protein complexes annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellPhoneDB.all_entities">
+<span class="sig-name descname"><span class="pre">all_entities</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellPhoneDB.all_entities" title="Link to this definition">§</a></dt>
+<dd><p>All entities annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellPhoneDB.all_mirnas">
+<span class="sig-name descname"><span class="pre">all_mirnas</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellPhoneDB.all_mirnas" title="Link to this definition">§</a></dt>
+<dd><p>All miRNAs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellPhoneDB.all_proteins">
+<span class="sig-name descname"><span class="pre">all_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellPhoneDB.all_proteins" title="Link to this definition">§</a></dt>
+<dd><p>All UniProt IDs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellPhoneDB.all_refs">
+<span class="sig-name descname"><span class="pre">all_refs</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellPhoneDB.all_refs" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects the references
+across all records. Returns <em>list</em>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellPhoneDB.annotate_complex">
+<span class="sig-name descname"><span class="pre">annotate_complex</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cplex</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellPhoneDB.annotate_complex" title="Link to this definition">§</a></dt>
+<dd><p>Infers annotations for a single complex.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellPhoneDB.browse">
+<span class="sig-name descname"><span class="pre">browse</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">field</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">start</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellPhoneDB.browse" title="Link to this definition">§</a></dt>
+<dd><p>Print gene information as a table.</p>
+<p>Presents information about annotation categories as ascii tables
+printed in the terminal. If one category provided, prints one table.
+If multiple categories provided, prints a table for each of them one
+by one proceeding to the next one once you hit return. If no categories
+provided goes through all levels of the primary category.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>field:</dt><dd><p>The field to browse categories by.</p>
+<ul class="simple">
+<li><p>If None the primary field will be selected.
+If this annotation resource doesn’t have fields, all proteins
+will be presented as one single category.</p></li>
+<li><p>If a string it will be considered a field name and it will
+browse through all levels of this field.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">list</span></code>, set or tuple, it will be considered either a
+<code class="docutils literal notranslate"><span class="pre">list</span></code> of field names or a list of values from the primary
+field. In the former case all combinations of the values of
+the fields will be presented, in the latter case the browsing
+will be limited to the levels of the primary field contained
+in <code class="docutils literal notranslate"><span class="pre">field</span></code>.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">dict</span></code>, keys are supposed to be field names and values
+as list of levels. If any of the values are None, all levels
+from that field will be used.</p></li>
+</ul>
+</dd>
+<dt>start:</dt><dd><p>Start browsing from this category. E.g. if there are 500
+categories and start is 250 it will skip everything before the
+250th.</p>
+</dd>
+<dt>kwargs:</dt><dd><p>Passed to <code class="docutils literal notranslate"><span class="pre">pypath.utils.uniprot.info</span></code>.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellPhoneDB.complex_inference">
+<span class="sig-name descname"><span class="pre">complex_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellPhoneDB.complex_inference" title="Link to this definition">§</a></dt>
+<dd><p>Annotates all complexes in <cite>complexes</cite>, by default in the default
+complex database (existing in the <cite>complex</cite> module or generated
+on demand according to the module’s current settings).</p>
+<dl class="field-list simple">
+<dt class="field-odd">Returns<span class="colon">:</span></dt>
+<dd class="field-odd"><p><ul class="simple">
+<li><p><em>Dict with complexes as keys and sets of annotations as values.</em></p></li>
+<li><p><em>Complexes with no valid information in this annotation resource</em></p></li>
+<li><p><em>won’t be in the dict.</em></p></li>
+</ul>
+</p>
+</dd>
+<dt class="field-even">Parameters<span class="colon">:</span></dt>
+<dd class="field-even"><p><strong>complexes</strong> (<em>iterable</em>) – Iterable yielding complexes.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellPhoneDB.coverage">
+<span class="sig-name descname"><span class="pre">coverage</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">other</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellPhoneDB.coverage" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the coverage of the annotation i.e. the proportion of
+entities having at least one record in this annotation resource
+for an arbitrary set of entities.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellPhoneDB.curation_effort">
+<span class="sig-name descname"><span class="pre">curation_effort</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellPhoneDB.curation_effort" title="Link to this definition">§</a></dt>
+<dd><p>Counts the reference-record pairs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellPhoneDB.get_names">
+<span class="sig-name descname"><span class="pre">get_names</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellPhoneDB.get_names" title="Link to this definition">§</a></dt>
+<dd><p>Returns the list of field names in the records. The annotation
+consists of uniform records and each entity might be annotated
+with one or more records. Each record is a tuple of fields, for
+example <code class="docutils literal notranslate"><span class="pre">('cell_type',</span> <span class="pre">'expression_level',</span> <span class="pre">'score')</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellPhoneDB.get_reference_set">
+<em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">get_reference_set</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">proteins</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">swissprot_only</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellPhoneDB.get_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the reference set i.e. the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellPhoneDB.get_subset">
+<span class="sig-name descname"><span class="pre">get_subset</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellPhoneDB.get_subset" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellPhoneDB.get_subset_bool_array">
+<span class="sig-name descname"><span class="pre">get_subset_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellPhoneDB.get_subset_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a boolean vector with True and False values for each entity
+in the reference set. The values represent presence absence data
+in the simplest case, but by providing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> any kind of matching
+and filtering is possible. <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> are passed to the <code class="docutils literal notranslate"><span class="pre">select</span></code>
+method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellPhoneDB.get_values">
+<span class="sig-name descname"><span class="pre">get_values</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">exclude_none</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellPhoneDB.get_values" title="Link to this definition">§</a></dt>
+<dd><p>Returns the set of all possible values of a field. E.g. if the
+records of this annotation have a field <code class="docutils literal notranslate"><span class="pre">cell_type</span></code> then calling
+this method can tell you that across all records the values of
+this field might be <code class="docutils literal notranslate"><span class="pre">{'macrophage',</span> <span class="pre">'epithelial_cell',</span> <span class="pre">...}</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellPhoneDB.labels">
+<span class="sig-name descname"><span class="pre">labels</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellPhoneDB.labels" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellPhoneDB.load">
+<span class="sig-name descname"><span class="pre">load</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellPhoneDB.load" title="Link to this definition">§</a></dt>
+<dd><p>Loads the annotation data by calling the input method.
+Infers annotations for complexes in the complex database if
+py:attr:<code class="docutils literal notranslate"><span class="pre">infer_complexes</span></code> is True.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellPhoneDB.load_data">
+<span class="sig-name descname"><span class="pre">load_data</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellPhoneDB.load_data" title="Link to this definition">§</a></dt>
+<dd><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellPhoneDB.load_proteins">
+<span class="sig-name descname"><span class="pre">load_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellPhoneDB.load_proteins" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a set of all UniProt IDs to have a base set of the entire
+proteome.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellPhoneDB.make_df">
+<span class="sig-name descname"><span class="pre">make_df</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">rebuild</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellPhoneDB.make_df" title="Link to this definition">§</a></dt>
+<dd><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.
+The data frame will be assigned to :py:attr``df``.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellPhoneDB.numof_entities">
+<span class="sig-name descname"><span class="pre">numof_entities</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellPhoneDB.numof_entities" title="Link to this definition">§</a></dt>
+<dd><p>The number of annotated entities in the resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellPhoneDB.numof_records">
+<span class="sig-name descname"><span class="pre">numof_records</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellPhoneDB.numof_records" title="Link to this definition">§</a></dt>
+<dd><p>The total number of annotation records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellPhoneDB.numof_references">
+<span class="sig-name descname"><span class="pre">numof_references</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellPhoneDB.numof_references" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects and counts the
+references across all records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellPhoneDB.process">
+<span class="sig-name descname"><span class="pre">process</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellPhoneDB.process" title="Link to this definition">§</a></dt>
+<dd><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellPhoneDB.reload">
+<span class="sig-name descname"><span class="pre">reload</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellPhoneDB.reload" title="Link to this definition">§</a></dt>
+<dd><p>Reloads the object from the module level.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellPhoneDB.select">
+<span class="sig-name descname"><span class="pre">select</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellPhoneDB.select" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellPhoneDB.set_method">
+<span class="sig-name descname"><span class="pre">set_method</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellPhoneDB.set_method" title="Link to this definition">§</a></dt>
+<dd><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if
+necessary.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellPhoneDB.set_reference_set">
+<span class="sig-name descname"><span class="pre">set_reference_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellPhoneDB.set_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Assigns the reference set to the :py:attr``reference_set`` attribute.
+The reference set is the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellPhoneDB.show">
+<span class="sig-name descname"><span class="pre">show</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">table_param</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellPhoneDB.show" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic
+information from the UniProt datasheets.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellPhoneDB.subset_intersection">
+<span class="sig-name descname"><span class="pre">subset_intersection</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">universe</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellPhoneDB.subset_intersection" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the proportion of entities in a subset occuring in the
+set <code class="docutils literal notranslate"><span class="pre">universe</span></code>. The subset is selected by passing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> to the
+<code class="docutils literal notranslate"><span class="pre">select</span></code> method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellPhoneDB.to_array">
+<span class="sig-name descname"><span class="pre">to_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_fields</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellPhoneDB.to_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns an entity vs feature array. In case of more complex
+annotations this might be huge.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellPhoneDB.to_bool_array">
+<span class="sig-name descname"><span class="pre">to_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellPhoneDB.to_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a presence/absence boolean array for a reference set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellPhoneDB.to_set">
+<span class="sig-name descname"><span class="pre">to_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellPhoneDB.to_set" title="Link to this definition">§</a></dt>
+<dd><p>Returns the entities present in this annotation resource as a set.</p>
+</dd></dl>
+
+</dd></dl>
+
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+  <section id="pypath-core-annot-cellphonedbcomplex">
+<h1>pypath.core.annot.CellPhoneDBComplex<a class="headerlink" href="#pypath-core-annot-cellphonedbcomplex" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.core.annot.CellPhoneDBComplex">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.core.annot.</span></span><span class="sig-name descname"><span class="pre">CellPhoneDBComplex</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#CellPhoneDBComplex"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.CellPhoneDBComplex" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <a class="reference internal" href="pypath.core.annot.CellPhoneDB.html#pypath.core.annot.CellPhoneDB" title="pypath.core.annot.CellPhoneDB"><code class="xref py py-class docutils literal notranslate"><span class="pre">CellPhoneDB</span></code></a></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellPhoneDBComplex.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#CellPhoneDBComplex.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.CellPhoneDBComplex.__init__" title="Link to this definition">§</a></dt>
+<dd><p>Represents annotations for a set of proteins.
+Loads the data from the original resource and provides methods
+to query the annotations.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>name</strong> (<em>str</em>) – A custom name for the annotation resource.</p></li>
+<li><p><strong>ncbi_tax_id</strong> (<em>int</em>) – NCBI Taxonomy identifier.</p></li>
+<li><p><strong>input_method</strong> (<em>callable</em><em>,</em><em>str</em>) – Either a callable or the name of a method in any submodules of
+the <code class="docutils literal notranslate"><span class="pre">pypath.inputs</span></code>  module. Should return a dict with
+UniProt IDs as keys or an object suitable for <code class="docutils literal notranslate"><span class="pre">process_method</span></code>.</p></li>
+<li><p><strong>input_args</strong> (<em>dict</em>) – Arguments for the <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CellPhoneDBComplex.__init__" title="pypath.core.annot.CellPhoneDBComplex.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>(**kwargs)</p></td>
+<td><p>Represents annotations for a set of proteins.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CellPhoneDBComplex.add_complexes_by_inference" title="pypath.core.annot.CellPhoneDBComplex.add_complexes_by_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">add_complexes_by_inference</span></code></a>([complexes])</p></td>
+<td><p>Creates complex annotations by in silico inference and adds them to this annotation set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CellPhoneDBComplex.all_complexes" title="pypath.core.annot.CellPhoneDBComplex.all_complexes"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_complexes</span></code></a>()</p></td>
+<td><p>All protein complexes annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CellPhoneDBComplex.all_entities" title="pypath.core.annot.CellPhoneDBComplex.all_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_entities</span></code></a>([entity_types])</p></td>
+<td><p>All entities annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CellPhoneDBComplex.all_mirnas" title="pypath.core.annot.CellPhoneDBComplex.all_mirnas"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_mirnas</span></code></a>()</p></td>
+<td><p>All miRNAs annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CellPhoneDBComplex.all_proteins" title="pypath.core.annot.CellPhoneDBComplex.all_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_proteins</span></code></a>()</p></td>
+<td><p>All UniProt IDs annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CellPhoneDBComplex.all_refs" title="pypath.core.annot.CellPhoneDBComplex.all_refs"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_refs</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CellPhoneDBComplex.annotate_complex" title="pypath.core.annot.CellPhoneDBComplex.annotate_complex"><code class="xref py py-obj docutils literal notranslate"><span class="pre">annotate_complex</span></code></a>(cplex)</p></td>
+<td><p>Infers annotations for a single complex.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CellPhoneDBComplex.browse" title="pypath.core.annot.CellPhoneDBComplex.browse"><code class="xref py py-obj docutils literal notranslate"><span class="pre">browse</span></code></a>([field, start])</p></td>
+<td><p>Print gene information as a table.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CellPhoneDBComplex.complex_inference" title="pypath.core.annot.CellPhoneDBComplex.complex_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">complex_inference</span></code></a>([complexes])</p></td>
+<td><p>Annotates all complexes in <cite>complexes</cite>, by default in the default complex database (existing in the <cite>complex</cite> module or generated on demand according to the module's current settings).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CellPhoneDBComplex.coverage" title="pypath.core.annot.CellPhoneDBComplex.coverage"><code class="xref py py-obj docutils literal notranslate"><span class="pre">coverage</span></code></a>(other)</p></td>
+<td><p>Calculates the coverage of the annotation i.e. the proportion of entities having at least one record in this annotation resource for an arbitrary set of entities.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CellPhoneDBComplex.curation_effort" title="pypath.core.annot.CellPhoneDBComplex.curation_effort"><code class="xref py py-obj docutils literal notranslate"><span class="pre">curation_effort</span></code></a>()</p></td>
+<td><p>Counts the reference-record pairs.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">from_dump</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_entity_type</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CellPhoneDBComplex.get_names" title="pypath.core.annot.CellPhoneDBComplex.get_names"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_names</span></code></a>()</p></td>
+<td><p>Returns the list of field names in the records.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CellPhoneDBComplex.get_reference_set" title="pypath.core.annot.CellPhoneDBComplex.get_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_reference_set</span></code></a>([proteins, complexes, ...])</p></td>
+<td><p>Retrieves the reference set i.e. the set of all entities which potentially have annotation in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CellPhoneDBComplex.get_subset" title="pypath.core.annot.CellPhoneDBComplex.get_subset"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CellPhoneDBComplex.get_subset_bool_array" title="pypath.core.annot.CellPhoneDBComplex.get_subset_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset_bool_array</span></code></a>([reference_set])</p></td>
+<td><p>Returns a boolean vector with True and False values for each entity in the reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CellPhoneDBComplex.get_values" title="pypath.core.annot.CellPhoneDBComplex.get_values"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_values</span></code></a>(name[, exclude_none])</p></td>
+<td><p>Returns the set of all possible values of a field.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_complex</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_mirna</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_protein</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CellPhoneDBComplex.labels" title="pypath.core.annot.CellPhoneDBComplex.labels"><code class="xref py py-obj docutils literal notranslate"><span class="pre">labels</span></code></a>([method])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CellPhoneDBComplex.load" title="pypath.core.annot.CellPhoneDBComplex.load"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load</span></code></a>()</p></td>
+<td><p>Loads the annotation data by calling the input method.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CellPhoneDBComplex.load_data" title="pypath.core.annot.CellPhoneDBComplex.load_data"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_data</span></code></a>()</p></td>
+<td><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CellPhoneDBComplex.load_proteins" title="pypath.core.annot.CellPhoneDBComplex.load_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_proteins</span></code></a>()</p></td>
+<td><p>Retrieves a set of all UniProt IDs to have a base set of the entire proteome.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CellPhoneDBComplex.make_df" title="pypath.core.annot.CellPhoneDBComplex.make_df"><code class="xref py py-obj docutils literal notranslate"><span class="pre">make_df</span></code></a>([rebuild])</p></td>
+<td><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complex_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CellPhoneDBComplex.numof_entities" title="pypath.core.annot.CellPhoneDBComplex.numof_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_entities</span></code></a>()</p></td>
+<td><p>The number of annotated entities in the resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirna_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirnas</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_protein_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_proteins</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CellPhoneDBComplex.numof_records" title="pypath.core.annot.CellPhoneDBComplex.numof_records"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_records</span></code></a>([entity_types])</p></td>
+<td><p>The total number of annotation records.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CellPhoneDBComplex.numof_references" title="pypath.core.annot.CellPhoneDBComplex.numof_references"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_references</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CellPhoneDBComplex.process" title="pypath.core.annot.CellPhoneDBComplex.process"><code class="xref py py-obj docutils literal notranslate"><span class="pre">process</span></code></a>()</p></td>
+<td><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">proportion</span></code>(other)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CellPhoneDBComplex.reload" title="pypath.core.annot.CellPhoneDBComplex.reload"><code class="xref py py-obj docutils literal notranslate"><span class="pre">reload</span></code></a>()</p></td>
+<td><p>Reloads the object from the module level.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">save_to_pickle</span></code>(pickle_file)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CellPhoneDBComplex.select" title="pypath.core.annot.CellPhoneDBComplex.select"><code class="xref py py-obj docutils literal notranslate"><span class="pre">select</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CellPhoneDBComplex.set_method" title="pypath.core.annot.CellPhoneDBComplex.set_method"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_method</span></code></a>()</p></td>
+<td><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if necessary.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CellPhoneDBComplex.set_reference_set" title="pypath.core.annot.CellPhoneDBComplex.set_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_reference_set</span></code></a>()</p></td>
+<td><p>Assigns the reference set to the :py:attr``reference_set`` attribute.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CellPhoneDBComplex.show" title="pypath.core.annot.CellPhoneDBComplex.show"><code class="xref py py-obj docutils literal notranslate"><span class="pre">show</span></code></a>([method, table_param])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic information from the UniProt datasheets.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CellPhoneDBComplex.subset_intersection" title="pypath.core.annot.CellPhoneDBComplex.subset_intersection"><code class="xref py py-obj docutils literal notranslate"><span class="pre">subset_intersection</span></code></a>(universe, **kwargs)</p></td>
+<td><p>Calculates the proportion of entities in a subset occuring in the set <code class="docutils literal notranslate"><span class="pre">universe</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CellPhoneDBComplex.to_array" title="pypath.core.annot.CellPhoneDBComplex.to_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_array</span></code></a>([reference_set, use_fields])</p></td>
+<td><p>Returns an entity vs feature array.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CellPhoneDBComplex.to_bool_array" title="pypath.core.annot.CellPhoneDBComplex.to_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_bool_array</span></code></a>(reference_set)</p></td>
+<td><p>Returns a presence/absence boolean array for a reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CellPhoneDBComplex.to_set" title="pypath.core.annot.CellPhoneDBComplex.to_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_set</span></code></a>()</p></td>
+<td><p>Returns the entities present in this annotation resource as a set.</p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Attributes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_fields</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">summary</span></code></p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellPhoneDBComplex.add_complexes_by_inference">
+<span class="sig-name descname"><span class="pre">add_complexes_by_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellPhoneDBComplex.add_complexes_by_inference" title="Link to this definition">§</a></dt>
+<dd><p>Creates complex annotations by in silico inference and adds them
+to this annotation set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellPhoneDBComplex.all_complexes">
+<span class="sig-name descname"><span class="pre">all_complexes</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellPhoneDBComplex.all_complexes" title="Link to this definition">§</a></dt>
+<dd><p>All protein complexes annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellPhoneDBComplex.all_entities">
+<span class="sig-name descname"><span class="pre">all_entities</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellPhoneDBComplex.all_entities" title="Link to this definition">§</a></dt>
+<dd><p>All entities annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellPhoneDBComplex.all_mirnas">
+<span class="sig-name descname"><span class="pre">all_mirnas</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellPhoneDBComplex.all_mirnas" title="Link to this definition">§</a></dt>
+<dd><p>All miRNAs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellPhoneDBComplex.all_proteins">
+<span class="sig-name descname"><span class="pre">all_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellPhoneDBComplex.all_proteins" title="Link to this definition">§</a></dt>
+<dd><p>All UniProt IDs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellPhoneDBComplex.all_refs">
+<span class="sig-name descname"><span class="pre">all_refs</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellPhoneDBComplex.all_refs" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects the references
+across all records. Returns <em>list</em>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellPhoneDBComplex.annotate_complex">
+<span class="sig-name descname"><span class="pre">annotate_complex</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cplex</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellPhoneDBComplex.annotate_complex" title="Link to this definition">§</a></dt>
+<dd><p>Infers annotations for a single complex.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellPhoneDBComplex.browse">
+<span class="sig-name descname"><span class="pre">browse</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">field</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">start</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellPhoneDBComplex.browse" title="Link to this definition">§</a></dt>
+<dd><p>Print gene information as a table.</p>
+<p>Presents information about annotation categories as ascii tables
+printed in the terminal. If one category provided, prints one table.
+If multiple categories provided, prints a table for each of them one
+by one proceeding to the next one once you hit return. If no categories
+provided goes through all levels of the primary category.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>field:</dt><dd><p>The field to browse categories by.</p>
+<ul class="simple">
+<li><p>If None the primary field will be selected.
+If this annotation resource doesn’t have fields, all proteins
+will be presented as one single category.</p></li>
+<li><p>If a string it will be considered a field name and it will
+browse through all levels of this field.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">list</span></code>, set or tuple, it will be considered either a
+<code class="docutils literal notranslate"><span class="pre">list</span></code> of field names or a list of values from the primary
+field. In the former case all combinations of the values of
+the fields will be presented, in the latter case the browsing
+will be limited to the levels of the primary field contained
+in <code class="docutils literal notranslate"><span class="pre">field</span></code>.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">dict</span></code>, keys are supposed to be field names and values
+as list of levels. If any of the values are None, all levels
+from that field will be used.</p></li>
+</ul>
+</dd>
+<dt>start:</dt><dd><p>Start browsing from this category. E.g. if there are 500
+categories and start is 250 it will skip everything before the
+250th.</p>
+</dd>
+<dt>kwargs:</dt><dd><p>Passed to <code class="docutils literal notranslate"><span class="pre">pypath.utils.uniprot.info</span></code>.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellPhoneDBComplex.complex_inference">
+<span class="sig-name descname"><span class="pre">complex_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellPhoneDBComplex.complex_inference" title="Link to this definition">§</a></dt>
+<dd><p>Annotates all complexes in <cite>complexes</cite>, by default in the default
+complex database (existing in the <cite>complex</cite> module or generated
+on demand according to the module’s current settings).</p>
+<dl class="field-list simple">
+<dt class="field-odd">Returns<span class="colon">:</span></dt>
+<dd class="field-odd"><p><ul class="simple">
+<li><p><em>Dict with complexes as keys and sets of annotations as values.</em></p></li>
+<li><p><em>Complexes with no valid information in this annotation resource</em></p></li>
+<li><p><em>won’t be in the dict.</em></p></li>
+</ul>
+</p>
+</dd>
+<dt class="field-even">Parameters<span class="colon">:</span></dt>
+<dd class="field-even"><p><strong>complexes</strong> (<em>iterable</em>) – Iterable yielding complexes.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellPhoneDBComplex.coverage">
+<span class="sig-name descname"><span class="pre">coverage</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">other</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellPhoneDBComplex.coverage" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the coverage of the annotation i.e. the proportion of
+entities having at least one record in this annotation resource
+for an arbitrary set of entities.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellPhoneDBComplex.curation_effort">
+<span class="sig-name descname"><span class="pre">curation_effort</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellPhoneDBComplex.curation_effort" title="Link to this definition">§</a></dt>
+<dd><p>Counts the reference-record pairs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellPhoneDBComplex.get_names">
+<span class="sig-name descname"><span class="pre">get_names</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellPhoneDBComplex.get_names" title="Link to this definition">§</a></dt>
+<dd><p>Returns the list of field names in the records. The annotation
+consists of uniform records and each entity might be annotated
+with one or more records. Each record is a tuple of fields, for
+example <code class="docutils literal notranslate"><span class="pre">('cell_type',</span> <span class="pre">'expression_level',</span> <span class="pre">'score')</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellPhoneDBComplex.get_reference_set">
+<em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">get_reference_set</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">proteins</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">swissprot_only</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellPhoneDBComplex.get_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the reference set i.e. the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellPhoneDBComplex.get_subset">
+<span class="sig-name descname"><span class="pre">get_subset</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellPhoneDBComplex.get_subset" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellPhoneDBComplex.get_subset_bool_array">
+<span class="sig-name descname"><span class="pre">get_subset_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellPhoneDBComplex.get_subset_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a boolean vector with True and False values for each entity
+in the reference set. The values represent presence absence data
+in the simplest case, but by providing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> any kind of matching
+and filtering is possible. <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> are passed to the <code class="docutils literal notranslate"><span class="pre">select</span></code>
+method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellPhoneDBComplex.get_values">
+<span class="sig-name descname"><span class="pre">get_values</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">exclude_none</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellPhoneDBComplex.get_values" title="Link to this definition">§</a></dt>
+<dd><p>Returns the set of all possible values of a field. E.g. if the
+records of this annotation have a field <code class="docutils literal notranslate"><span class="pre">cell_type</span></code> then calling
+this method can tell you that across all records the values of
+this field might be <code class="docutils literal notranslate"><span class="pre">{'macrophage',</span> <span class="pre">'epithelial_cell',</span> <span class="pre">...}</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellPhoneDBComplex.labels">
+<span class="sig-name descname"><span class="pre">labels</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellPhoneDBComplex.labels" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellPhoneDBComplex.load">
+<span class="sig-name descname"><span class="pre">load</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellPhoneDBComplex.load" title="Link to this definition">§</a></dt>
+<dd><p>Loads the annotation data by calling the input method.
+Infers annotations for complexes in the complex database if
+py:attr:<code class="docutils literal notranslate"><span class="pre">infer_complexes</span></code> is True.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellPhoneDBComplex.load_data">
+<span class="sig-name descname"><span class="pre">load_data</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellPhoneDBComplex.load_data" title="Link to this definition">§</a></dt>
+<dd><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellPhoneDBComplex.load_proteins">
+<span class="sig-name descname"><span class="pre">load_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellPhoneDBComplex.load_proteins" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a set of all UniProt IDs to have a base set of the entire
+proteome.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellPhoneDBComplex.make_df">
+<span class="sig-name descname"><span class="pre">make_df</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">rebuild</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellPhoneDBComplex.make_df" title="Link to this definition">§</a></dt>
+<dd><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.
+The data frame will be assigned to :py:attr``df``.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellPhoneDBComplex.numof_entities">
+<span class="sig-name descname"><span class="pre">numof_entities</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellPhoneDBComplex.numof_entities" title="Link to this definition">§</a></dt>
+<dd><p>The number of annotated entities in the resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellPhoneDBComplex.numof_records">
+<span class="sig-name descname"><span class="pre">numof_records</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellPhoneDBComplex.numof_records" title="Link to this definition">§</a></dt>
+<dd><p>The total number of annotation records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellPhoneDBComplex.numof_references">
+<span class="sig-name descname"><span class="pre">numof_references</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellPhoneDBComplex.numof_references" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects and counts the
+references across all records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellPhoneDBComplex.process">
+<span class="sig-name descname"><span class="pre">process</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellPhoneDBComplex.process" title="Link to this definition">§</a></dt>
+<dd><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellPhoneDBComplex.reload">
+<span class="sig-name descname"><span class="pre">reload</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellPhoneDBComplex.reload" title="Link to this definition">§</a></dt>
+<dd><p>Reloads the object from the module level.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellPhoneDBComplex.select">
+<span class="sig-name descname"><span class="pre">select</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellPhoneDBComplex.select" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellPhoneDBComplex.set_method">
+<span class="sig-name descname"><span class="pre">set_method</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellPhoneDBComplex.set_method" title="Link to this definition">§</a></dt>
+<dd><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if
+necessary.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellPhoneDBComplex.set_reference_set">
+<span class="sig-name descname"><span class="pre">set_reference_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellPhoneDBComplex.set_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Assigns the reference set to the :py:attr``reference_set`` attribute.
+The reference set is the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellPhoneDBComplex.show">
+<span class="sig-name descname"><span class="pre">show</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">table_param</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellPhoneDBComplex.show" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic
+information from the UniProt datasheets.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellPhoneDBComplex.subset_intersection">
+<span class="sig-name descname"><span class="pre">subset_intersection</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">universe</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellPhoneDBComplex.subset_intersection" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the proportion of entities in a subset occuring in the
+set <code class="docutils literal notranslate"><span class="pre">universe</span></code>. The subset is selected by passing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> to the
+<code class="docutils literal notranslate"><span class="pre">select</span></code> method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellPhoneDBComplex.to_array">
+<span class="sig-name descname"><span class="pre">to_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_fields</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellPhoneDBComplex.to_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns an entity vs feature array. In case of more complex
+annotations this might be huge.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellPhoneDBComplex.to_bool_array">
+<span class="sig-name descname"><span class="pre">to_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellPhoneDBComplex.to_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a presence/absence boolean array for a reference set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellPhoneDBComplex.to_set">
+<span class="sig-name descname"><span class="pre">to_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellPhoneDBComplex.to_set" title="Link to this definition">§</a></dt>
+<dd><p>Returns the entities present in this annotation resource as a set.</p>
+</dd></dl>
+
+</dd></dl>
+
+</section>
+
+
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+  <section id="pypath-core-annot-cellsurfaceproteinatlas">
+<h1>pypath.core.annot.CellSurfaceProteinAtlas<a class="headerlink" href="#pypath-core-annot-cellsurfaceproteinatlas" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.core.annot.CellSurfaceProteinAtlas">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.core.annot.</span></span><span class="sig-name descname"><span class="pre">CellSurfaceProteinAtlas</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#CellSurfaceProteinAtlas"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.CellSurfaceProteinAtlas" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <a class="reference internal" href="pypath.core.annot.AnnotationBase.html#pypath.core.annot.AnnotationBase" title="pypath.core.annot.AnnotationBase"><code class="xref py py-class docutils literal notranslate"><span class="pre">AnnotationBase</span></code></a></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellSurfaceProteinAtlas.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#CellSurfaceProteinAtlas.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.CellSurfaceProteinAtlas.__init__" title="Link to this definition">§</a></dt>
+<dd><p>The name of this resource abbreviated as <cite>CSPA</cite>.</p>
+</dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CellSurfaceProteinAtlas.__init__" title="pypath.core.annot.CellSurfaceProteinAtlas.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>([ncbi_tax_id])</p></td>
+<td><p>The name of this resource abbreviated as <cite>CSPA</cite>.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CellSurfaceProteinAtlas.add_complexes_by_inference" title="pypath.core.annot.CellSurfaceProteinAtlas.add_complexes_by_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">add_complexes_by_inference</span></code></a>([complexes])</p></td>
+<td><p>Creates complex annotations by in silico inference and adds them to this annotation set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CellSurfaceProteinAtlas.all_complexes" title="pypath.core.annot.CellSurfaceProteinAtlas.all_complexes"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_complexes</span></code></a>()</p></td>
+<td><p>All protein complexes annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CellSurfaceProteinAtlas.all_entities" title="pypath.core.annot.CellSurfaceProteinAtlas.all_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_entities</span></code></a>([entity_types])</p></td>
+<td><p>All entities annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CellSurfaceProteinAtlas.all_mirnas" title="pypath.core.annot.CellSurfaceProteinAtlas.all_mirnas"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_mirnas</span></code></a>()</p></td>
+<td><p>All miRNAs annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CellSurfaceProteinAtlas.all_proteins" title="pypath.core.annot.CellSurfaceProteinAtlas.all_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_proteins</span></code></a>()</p></td>
+<td><p>All UniProt IDs annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CellSurfaceProteinAtlas.all_refs" title="pypath.core.annot.CellSurfaceProteinAtlas.all_refs"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_refs</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CellSurfaceProteinAtlas.annotate_complex" title="pypath.core.annot.CellSurfaceProteinAtlas.annotate_complex"><code class="xref py py-obj docutils literal notranslate"><span class="pre">annotate_complex</span></code></a>(cplex)</p></td>
+<td><p>Infers annotations for a single complex.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CellSurfaceProteinAtlas.browse" title="pypath.core.annot.CellSurfaceProteinAtlas.browse"><code class="xref py py-obj docutils literal notranslate"><span class="pre">browse</span></code></a>([field, start])</p></td>
+<td><p>Print gene information as a table.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CellSurfaceProteinAtlas.complex_inference" title="pypath.core.annot.CellSurfaceProteinAtlas.complex_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">complex_inference</span></code></a>([complexes])</p></td>
+<td><p>Annotates all complexes in <cite>complexes</cite>, by default in the default complex database (existing in the <cite>complex</cite> module or generated on demand according to the module's current settings).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CellSurfaceProteinAtlas.coverage" title="pypath.core.annot.CellSurfaceProteinAtlas.coverage"><code class="xref py py-obj docutils literal notranslate"><span class="pre">coverage</span></code></a>(other)</p></td>
+<td><p>Calculates the coverage of the annotation i.e. the proportion of entities having at least one record in this annotation resource for an arbitrary set of entities.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CellSurfaceProteinAtlas.curation_effort" title="pypath.core.annot.CellSurfaceProteinAtlas.curation_effort"><code class="xref py py-obj docutils literal notranslate"><span class="pre">curation_effort</span></code></a>()</p></td>
+<td><p>Counts the reference-record pairs.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">from_dump</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_entity_type</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CellSurfaceProteinAtlas.get_names" title="pypath.core.annot.CellSurfaceProteinAtlas.get_names"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_names</span></code></a>()</p></td>
+<td><p>Returns the list of field names in the records.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CellSurfaceProteinAtlas.get_reference_set" title="pypath.core.annot.CellSurfaceProteinAtlas.get_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_reference_set</span></code></a>([proteins, complexes, ...])</p></td>
+<td><p>Retrieves the reference set i.e. the set of all entities which potentially have annotation in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CellSurfaceProteinAtlas.get_subset" title="pypath.core.annot.CellSurfaceProteinAtlas.get_subset"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CellSurfaceProteinAtlas.get_subset_bool_array" title="pypath.core.annot.CellSurfaceProteinAtlas.get_subset_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset_bool_array</span></code></a>([reference_set])</p></td>
+<td><p>Returns a boolean vector with True and False values for each entity in the reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CellSurfaceProteinAtlas.get_values" title="pypath.core.annot.CellSurfaceProteinAtlas.get_values"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_values</span></code></a>(name[, exclude_none])</p></td>
+<td><p>Returns the set of all possible values of a field.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_complex</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_mirna</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_protein</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CellSurfaceProteinAtlas.labels" title="pypath.core.annot.CellSurfaceProteinAtlas.labels"><code class="xref py py-obj docutils literal notranslate"><span class="pre">labels</span></code></a>([method])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CellSurfaceProteinAtlas.load" title="pypath.core.annot.CellSurfaceProteinAtlas.load"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load</span></code></a>()</p></td>
+<td><p>Loads the annotation data by calling the input method.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CellSurfaceProteinAtlas.load_data" title="pypath.core.annot.CellSurfaceProteinAtlas.load_data"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_data</span></code></a>()</p></td>
+<td><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CellSurfaceProteinAtlas.load_proteins" title="pypath.core.annot.CellSurfaceProteinAtlas.load_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_proteins</span></code></a>()</p></td>
+<td><p>Retrieves a set of all UniProt IDs to have a base set of the entire proteome.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CellSurfaceProteinAtlas.make_df" title="pypath.core.annot.CellSurfaceProteinAtlas.make_df"><code class="xref py py-obj docutils literal notranslate"><span class="pre">make_df</span></code></a>([rebuild])</p></td>
+<td><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complex_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CellSurfaceProteinAtlas.numof_entities" title="pypath.core.annot.CellSurfaceProteinAtlas.numof_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_entities</span></code></a>()</p></td>
+<td><p>The number of annotated entities in the resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirna_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirnas</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_protein_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_proteins</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CellSurfaceProteinAtlas.numof_records" title="pypath.core.annot.CellSurfaceProteinAtlas.numof_records"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_records</span></code></a>([entity_types])</p></td>
+<td><p>The total number of annotation records.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CellSurfaceProteinAtlas.numof_references" title="pypath.core.annot.CellSurfaceProteinAtlas.numof_references"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_references</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CellSurfaceProteinAtlas.process" title="pypath.core.annot.CellSurfaceProteinAtlas.process"><code class="xref py py-obj docutils literal notranslate"><span class="pre">process</span></code></a>()</p></td>
+<td><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">proportion</span></code>(other)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CellSurfaceProteinAtlas.reload" title="pypath.core.annot.CellSurfaceProteinAtlas.reload"><code class="xref py py-obj docutils literal notranslate"><span class="pre">reload</span></code></a>()</p></td>
+<td><p>Reloads the object from the module level.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">save_to_pickle</span></code>(pickle_file)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CellSurfaceProteinAtlas.select" title="pypath.core.annot.CellSurfaceProteinAtlas.select"><code class="xref py py-obj docutils literal notranslate"><span class="pre">select</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CellSurfaceProteinAtlas.set_method" title="pypath.core.annot.CellSurfaceProteinAtlas.set_method"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_method</span></code></a>()</p></td>
+<td><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if necessary.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CellSurfaceProteinAtlas.set_reference_set" title="pypath.core.annot.CellSurfaceProteinAtlas.set_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_reference_set</span></code></a>()</p></td>
+<td><p>Assigns the reference set to the :py:attr``reference_set`` attribute.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CellSurfaceProteinAtlas.show" title="pypath.core.annot.CellSurfaceProteinAtlas.show"><code class="xref py py-obj docutils literal notranslate"><span class="pre">show</span></code></a>([method, table_param])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic information from the UniProt datasheets.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CellSurfaceProteinAtlas.subset_intersection" title="pypath.core.annot.CellSurfaceProteinAtlas.subset_intersection"><code class="xref py py-obj docutils literal notranslate"><span class="pre">subset_intersection</span></code></a>(universe, **kwargs)</p></td>
+<td><p>Calculates the proportion of entities in a subset occuring in the set <code class="docutils literal notranslate"><span class="pre">universe</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CellSurfaceProteinAtlas.to_array" title="pypath.core.annot.CellSurfaceProteinAtlas.to_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_array</span></code></a>([reference_set, use_fields])</p></td>
+<td><p>Returns an entity vs feature array.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CellSurfaceProteinAtlas.to_bool_array" title="pypath.core.annot.CellSurfaceProteinAtlas.to_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_bool_array</span></code></a>(reference_set)</p></td>
+<td><p>Returns a presence/absence boolean array for a reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CellSurfaceProteinAtlas.to_set" title="pypath.core.annot.CellSurfaceProteinAtlas.to_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_set</span></code></a>()</p></td>
+<td><p>Returns the entities present in this annotation resource as a set.</p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Attributes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_fields</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">summary</span></code></p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellSurfaceProteinAtlas.add_complexes_by_inference">
+<span class="sig-name descname"><span class="pre">add_complexes_by_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellSurfaceProteinAtlas.add_complexes_by_inference" title="Link to this definition">§</a></dt>
+<dd><p>Creates complex annotations by in silico inference and adds them
+to this annotation set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellSurfaceProteinAtlas.all_complexes">
+<span class="sig-name descname"><span class="pre">all_complexes</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellSurfaceProteinAtlas.all_complexes" title="Link to this definition">§</a></dt>
+<dd><p>All protein complexes annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellSurfaceProteinAtlas.all_entities">
+<span class="sig-name descname"><span class="pre">all_entities</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellSurfaceProteinAtlas.all_entities" title="Link to this definition">§</a></dt>
+<dd><p>All entities annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellSurfaceProteinAtlas.all_mirnas">
+<span class="sig-name descname"><span class="pre">all_mirnas</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellSurfaceProteinAtlas.all_mirnas" title="Link to this definition">§</a></dt>
+<dd><p>All miRNAs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellSurfaceProteinAtlas.all_proteins">
+<span class="sig-name descname"><span class="pre">all_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellSurfaceProteinAtlas.all_proteins" title="Link to this definition">§</a></dt>
+<dd><p>All UniProt IDs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellSurfaceProteinAtlas.all_refs">
+<span class="sig-name descname"><span class="pre">all_refs</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellSurfaceProteinAtlas.all_refs" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects the references
+across all records. Returns <em>list</em>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellSurfaceProteinAtlas.annotate_complex">
+<span class="sig-name descname"><span class="pre">annotate_complex</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cplex</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellSurfaceProteinAtlas.annotate_complex" title="Link to this definition">§</a></dt>
+<dd><p>Infers annotations for a single complex.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellSurfaceProteinAtlas.browse">
+<span class="sig-name descname"><span class="pre">browse</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">field</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">start</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellSurfaceProteinAtlas.browse" title="Link to this definition">§</a></dt>
+<dd><p>Print gene information as a table.</p>
+<p>Presents information about annotation categories as ascii tables
+printed in the terminal. If one category provided, prints one table.
+If multiple categories provided, prints a table for each of them one
+by one proceeding to the next one once you hit return. If no categories
+provided goes through all levels of the primary category.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>field:</dt><dd><p>The field to browse categories by.</p>
+<ul class="simple">
+<li><p>If None the primary field will be selected.
+If this annotation resource doesn’t have fields, all proteins
+will be presented as one single category.</p></li>
+<li><p>If a string it will be considered a field name and it will
+browse through all levels of this field.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">list</span></code>, set or tuple, it will be considered either a
+<code class="docutils literal notranslate"><span class="pre">list</span></code> of field names or a list of values from the primary
+field. In the former case all combinations of the values of
+the fields will be presented, in the latter case the browsing
+will be limited to the levels of the primary field contained
+in <code class="docutils literal notranslate"><span class="pre">field</span></code>.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">dict</span></code>, keys are supposed to be field names and values
+as list of levels. If any of the values are None, all levels
+from that field will be used.</p></li>
+</ul>
+</dd>
+<dt>start:</dt><dd><p>Start browsing from this category. E.g. if there are 500
+categories and start is 250 it will skip everything before the
+250th.</p>
+</dd>
+<dt>kwargs:</dt><dd><p>Passed to <code class="docutils literal notranslate"><span class="pre">pypath.utils.uniprot.info</span></code>.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellSurfaceProteinAtlas.complex_inference">
+<span class="sig-name descname"><span class="pre">complex_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellSurfaceProteinAtlas.complex_inference" title="Link to this definition">§</a></dt>
+<dd><p>Annotates all complexes in <cite>complexes</cite>, by default in the default
+complex database (existing in the <cite>complex</cite> module or generated
+on demand according to the module’s current settings).</p>
+<dl class="field-list simple">
+<dt class="field-odd">Returns<span class="colon">:</span></dt>
+<dd class="field-odd"><p><ul class="simple">
+<li><p><em>Dict with complexes as keys and sets of annotations as values.</em></p></li>
+<li><p><em>Complexes with no valid information in this annotation resource</em></p></li>
+<li><p><em>won’t be in the dict.</em></p></li>
+</ul>
+</p>
+</dd>
+<dt class="field-even">Parameters<span class="colon">:</span></dt>
+<dd class="field-even"><p><strong>complexes</strong> (<em>iterable</em>) – Iterable yielding complexes.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellSurfaceProteinAtlas.coverage">
+<span class="sig-name descname"><span class="pre">coverage</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">other</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellSurfaceProteinAtlas.coverage" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the coverage of the annotation i.e. the proportion of
+entities having at least one record in this annotation resource
+for an arbitrary set of entities.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellSurfaceProteinAtlas.curation_effort">
+<span class="sig-name descname"><span class="pre">curation_effort</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellSurfaceProteinAtlas.curation_effort" title="Link to this definition">§</a></dt>
+<dd><p>Counts the reference-record pairs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellSurfaceProteinAtlas.get_names">
+<span class="sig-name descname"><span class="pre">get_names</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellSurfaceProteinAtlas.get_names" title="Link to this definition">§</a></dt>
+<dd><p>Returns the list of field names in the records. The annotation
+consists of uniform records and each entity might be annotated
+with one or more records. Each record is a tuple of fields, for
+example <code class="docutils literal notranslate"><span class="pre">('cell_type',</span> <span class="pre">'expression_level',</span> <span class="pre">'score')</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellSurfaceProteinAtlas.get_reference_set">
+<em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">get_reference_set</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">proteins</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">swissprot_only</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellSurfaceProteinAtlas.get_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the reference set i.e. the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellSurfaceProteinAtlas.get_subset">
+<span class="sig-name descname"><span class="pre">get_subset</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellSurfaceProteinAtlas.get_subset" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellSurfaceProteinAtlas.get_subset_bool_array">
+<span class="sig-name descname"><span class="pre">get_subset_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellSurfaceProteinAtlas.get_subset_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a boolean vector with True and False values for each entity
+in the reference set. The values represent presence absence data
+in the simplest case, but by providing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> any kind of matching
+and filtering is possible. <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> are passed to the <code class="docutils literal notranslate"><span class="pre">select</span></code>
+method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellSurfaceProteinAtlas.get_values">
+<span class="sig-name descname"><span class="pre">get_values</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">exclude_none</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellSurfaceProteinAtlas.get_values" title="Link to this definition">§</a></dt>
+<dd><p>Returns the set of all possible values of a field. E.g. if the
+records of this annotation have a field <code class="docutils literal notranslate"><span class="pre">cell_type</span></code> then calling
+this method can tell you that across all records the values of
+this field might be <code class="docutils literal notranslate"><span class="pre">{'macrophage',</span> <span class="pre">'epithelial_cell',</span> <span class="pre">...}</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellSurfaceProteinAtlas.labels">
+<span class="sig-name descname"><span class="pre">labels</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellSurfaceProteinAtlas.labels" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellSurfaceProteinAtlas.load">
+<span class="sig-name descname"><span class="pre">load</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellSurfaceProteinAtlas.load" title="Link to this definition">§</a></dt>
+<dd><p>Loads the annotation data by calling the input method.
+Infers annotations for complexes in the complex database if
+py:attr:<code class="docutils literal notranslate"><span class="pre">infer_complexes</span></code> is True.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellSurfaceProteinAtlas.load_data">
+<span class="sig-name descname"><span class="pre">load_data</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellSurfaceProteinAtlas.load_data" title="Link to this definition">§</a></dt>
+<dd><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellSurfaceProteinAtlas.load_proteins">
+<span class="sig-name descname"><span class="pre">load_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellSurfaceProteinAtlas.load_proteins" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a set of all UniProt IDs to have a base set of the entire
+proteome.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellSurfaceProteinAtlas.make_df">
+<span class="sig-name descname"><span class="pre">make_df</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">rebuild</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellSurfaceProteinAtlas.make_df" title="Link to this definition">§</a></dt>
+<dd><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.
+The data frame will be assigned to :py:attr``df``.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellSurfaceProteinAtlas.numof_entities">
+<span class="sig-name descname"><span class="pre">numof_entities</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellSurfaceProteinAtlas.numof_entities" title="Link to this definition">§</a></dt>
+<dd><p>The number of annotated entities in the resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellSurfaceProteinAtlas.numof_records">
+<span class="sig-name descname"><span class="pre">numof_records</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellSurfaceProteinAtlas.numof_records" title="Link to this definition">§</a></dt>
+<dd><p>The total number of annotation records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellSurfaceProteinAtlas.numof_references">
+<span class="sig-name descname"><span class="pre">numof_references</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellSurfaceProteinAtlas.numof_references" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects and counts the
+references across all records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellSurfaceProteinAtlas.process">
+<span class="sig-name descname"><span class="pre">process</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellSurfaceProteinAtlas.process" title="Link to this definition">§</a></dt>
+<dd><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellSurfaceProteinAtlas.reload">
+<span class="sig-name descname"><span class="pre">reload</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellSurfaceProteinAtlas.reload" title="Link to this definition">§</a></dt>
+<dd><p>Reloads the object from the module level.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellSurfaceProteinAtlas.select">
+<span class="sig-name descname"><span class="pre">select</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellSurfaceProteinAtlas.select" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellSurfaceProteinAtlas.set_method">
+<span class="sig-name descname"><span class="pre">set_method</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellSurfaceProteinAtlas.set_method" title="Link to this definition">§</a></dt>
+<dd><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if
+necessary.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellSurfaceProteinAtlas.set_reference_set">
+<span class="sig-name descname"><span class="pre">set_reference_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellSurfaceProteinAtlas.set_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Assigns the reference set to the :py:attr``reference_set`` attribute.
+The reference set is the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellSurfaceProteinAtlas.show">
+<span class="sig-name descname"><span class="pre">show</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">table_param</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellSurfaceProteinAtlas.show" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic
+information from the UniProt datasheets.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellSurfaceProteinAtlas.subset_intersection">
+<span class="sig-name descname"><span class="pre">subset_intersection</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">universe</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellSurfaceProteinAtlas.subset_intersection" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the proportion of entities in a subset occuring in the
+set <code class="docutils literal notranslate"><span class="pre">universe</span></code>. The subset is selected by passing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> to the
+<code class="docutils literal notranslate"><span class="pre">select</span></code> method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellSurfaceProteinAtlas.to_array">
+<span class="sig-name descname"><span class="pre">to_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_fields</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellSurfaceProteinAtlas.to_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns an entity vs feature array. In case of more complex
+annotations this might be huge.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellSurfaceProteinAtlas.to_bool_array">
+<span class="sig-name descname"><span class="pre">to_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellSurfaceProteinAtlas.to_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a presence/absence boolean array for a reference set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellSurfaceProteinAtlas.to_set">
+<span class="sig-name descname"><span class="pre">to_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellSurfaceProteinAtlas.to_set" title="Link to this definition">§</a></dt>
+<dd><p>Returns the entities present in this annotation resource as a set.</p>
+</dd></dl>
+
+</dd></dl>
+
+</section>
+
+
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diff --git a/api/pypath.core.annot.CellSurfaceProteinAtlasCellType.html b/api/pypath.core.annot.CellSurfaceProteinAtlasCellType.html
new file mode 100644
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+  <section id="pypath-core-annot-cellsurfaceproteinatlascelltype">
+<h1>pypath.core.annot.CellSurfaceProteinAtlasCellType<a class="headerlink" href="#pypath-core-annot-cellsurfaceproteinatlascelltype" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.core.annot.CellSurfaceProteinAtlasCellType">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.core.annot.</span></span><span class="sig-name descname"><span class="pre">CellSurfaceProteinAtlasCellType</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#CellSurfaceProteinAtlasCellType"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.CellSurfaceProteinAtlasCellType" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <a class="reference internal" href="pypath.core.annot.AnnotationBase.html#pypath.core.annot.AnnotationBase" title="pypath.core.annot.AnnotationBase"><code class="xref py py-class docutils literal notranslate"><span class="pre">AnnotationBase</span></code></a></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellSurfaceProteinAtlasCellType.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#CellSurfaceProteinAtlasCellType.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.CellSurfaceProteinAtlasCellType.__init__" title="Link to this definition">§</a></dt>
+<dd><p>The name of this resource abbreviated as <cite>CSPA</cite>.</p>
+</dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CellSurfaceProteinAtlasCellType.__init__" title="pypath.core.annot.CellSurfaceProteinAtlasCellType.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>([ncbi_tax_id])</p></td>
+<td><p>The name of this resource abbreviated as <cite>CSPA</cite>.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CellSurfaceProteinAtlasCellType.add_complexes_by_inference" title="pypath.core.annot.CellSurfaceProteinAtlasCellType.add_complexes_by_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">add_complexes_by_inference</span></code></a>([complexes])</p></td>
+<td><p>Creates complex annotations by in silico inference and adds them to this annotation set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CellSurfaceProteinAtlasCellType.all_complexes" title="pypath.core.annot.CellSurfaceProteinAtlasCellType.all_complexes"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_complexes</span></code></a>()</p></td>
+<td><p>All protein complexes annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CellSurfaceProteinAtlasCellType.all_entities" title="pypath.core.annot.CellSurfaceProteinAtlasCellType.all_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_entities</span></code></a>([entity_types])</p></td>
+<td><p>All entities annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CellSurfaceProteinAtlasCellType.all_mirnas" title="pypath.core.annot.CellSurfaceProteinAtlasCellType.all_mirnas"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_mirnas</span></code></a>()</p></td>
+<td><p>All miRNAs annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CellSurfaceProteinAtlasCellType.all_proteins" title="pypath.core.annot.CellSurfaceProteinAtlasCellType.all_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_proteins</span></code></a>()</p></td>
+<td><p>All UniProt IDs annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CellSurfaceProteinAtlasCellType.all_refs" title="pypath.core.annot.CellSurfaceProteinAtlasCellType.all_refs"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_refs</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CellSurfaceProteinAtlasCellType.annotate_complex" title="pypath.core.annot.CellSurfaceProteinAtlasCellType.annotate_complex"><code class="xref py py-obj docutils literal notranslate"><span class="pre">annotate_complex</span></code></a>(cplex)</p></td>
+<td><p>Infers annotations for a single complex.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CellSurfaceProteinAtlasCellType.browse" title="pypath.core.annot.CellSurfaceProteinAtlasCellType.browse"><code class="xref py py-obj docutils literal notranslate"><span class="pre">browse</span></code></a>([field, start])</p></td>
+<td><p>Print gene information as a table.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CellSurfaceProteinAtlasCellType.complex_inference" title="pypath.core.annot.CellSurfaceProteinAtlasCellType.complex_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">complex_inference</span></code></a>([complexes])</p></td>
+<td><p>Annotates all complexes in <cite>complexes</cite>, by default in the default complex database (existing in the <cite>complex</cite> module or generated on demand according to the module's current settings).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CellSurfaceProteinAtlasCellType.coverage" title="pypath.core.annot.CellSurfaceProteinAtlasCellType.coverage"><code class="xref py py-obj docutils literal notranslate"><span class="pre">coverage</span></code></a>(other)</p></td>
+<td><p>Calculates the coverage of the annotation i.e. the proportion of entities having at least one record in this annotation resource for an arbitrary set of entities.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CellSurfaceProteinAtlasCellType.curation_effort" title="pypath.core.annot.CellSurfaceProteinAtlasCellType.curation_effort"><code class="xref py py-obj docutils literal notranslate"><span class="pre">curation_effort</span></code></a>()</p></td>
+<td><p>Counts the reference-record pairs.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">from_dump</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_entity_type</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CellSurfaceProteinAtlasCellType.get_names" title="pypath.core.annot.CellSurfaceProteinAtlasCellType.get_names"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_names</span></code></a>()</p></td>
+<td><p>Returns the list of field names in the records.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CellSurfaceProteinAtlasCellType.get_reference_set" title="pypath.core.annot.CellSurfaceProteinAtlasCellType.get_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_reference_set</span></code></a>([proteins, complexes, ...])</p></td>
+<td><p>Retrieves the reference set i.e. the set of all entities which potentially have annotation in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CellSurfaceProteinAtlasCellType.get_subset" title="pypath.core.annot.CellSurfaceProteinAtlasCellType.get_subset"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CellSurfaceProteinAtlasCellType.get_subset_bool_array" title="pypath.core.annot.CellSurfaceProteinAtlasCellType.get_subset_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset_bool_array</span></code></a>([reference_set])</p></td>
+<td><p>Returns a boolean vector with True and False values for each entity in the reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CellSurfaceProteinAtlasCellType.get_values" title="pypath.core.annot.CellSurfaceProteinAtlasCellType.get_values"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_values</span></code></a>(name[, exclude_none])</p></td>
+<td><p>Returns the set of all possible values of a field.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_complex</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_mirna</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_protein</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CellSurfaceProteinAtlasCellType.labels" title="pypath.core.annot.CellSurfaceProteinAtlasCellType.labels"><code class="xref py py-obj docutils literal notranslate"><span class="pre">labels</span></code></a>([method])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CellSurfaceProteinAtlasCellType.load" title="pypath.core.annot.CellSurfaceProteinAtlasCellType.load"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load</span></code></a>()</p></td>
+<td><p>Loads the annotation data by calling the input method.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CellSurfaceProteinAtlasCellType.load_data" title="pypath.core.annot.CellSurfaceProteinAtlasCellType.load_data"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_data</span></code></a>()</p></td>
+<td><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CellSurfaceProteinAtlasCellType.load_proteins" title="pypath.core.annot.CellSurfaceProteinAtlasCellType.load_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_proteins</span></code></a>()</p></td>
+<td><p>Retrieves a set of all UniProt IDs to have a base set of the entire proteome.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CellSurfaceProteinAtlasCellType.make_df" title="pypath.core.annot.CellSurfaceProteinAtlasCellType.make_df"><code class="xref py py-obj docutils literal notranslate"><span class="pre">make_df</span></code></a>([rebuild])</p></td>
+<td><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complex_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CellSurfaceProteinAtlasCellType.numof_entities" title="pypath.core.annot.CellSurfaceProteinAtlasCellType.numof_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_entities</span></code></a>()</p></td>
+<td><p>The number of annotated entities in the resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirna_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirnas</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_protein_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_proteins</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CellSurfaceProteinAtlasCellType.numof_records" title="pypath.core.annot.CellSurfaceProteinAtlasCellType.numof_records"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_records</span></code></a>([entity_types])</p></td>
+<td><p>The total number of annotation records.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CellSurfaceProteinAtlasCellType.numof_references" title="pypath.core.annot.CellSurfaceProteinAtlasCellType.numof_references"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_references</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CellSurfaceProteinAtlasCellType.process" title="pypath.core.annot.CellSurfaceProteinAtlasCellType.process"><code class="xref py py-obj docutils literal notranslate"><span class="pre">process</span></code></a>()</p></td>
+<td><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">proportion</span></code>(other)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CellSurfaceProteinAtlasCellType.reload" title="pypath.core.annot.CellSurfaceProteinAtlasCellType.reload"><code class="xref py py-obj docutils literal notranslate"><span class="pre">reload</span></code></a>()</p></td>
+<td><p>Reloads the object from the module level.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">save_to_pickle</span></code>(pickle_file)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CellSurfaceProteinAtlasCellType.select" title="pypath.core.annot.CellSurfaceProteinAtlasCellType.select"><code class="xref py py-obj docutils literal notranslate"><span class="pre">select</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CellSurfaceProteinAtlasCellType.set_method" title="pypath.core.annot.CellSurfaceProteinAtlasCellType.set_method"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_method</span></code></a>()</p></td>
+<td><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if necessary.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CellSurfaceProteinAtlasCellType.set_reference_set" title="pypath.core.annot.CellSurfaceProteinAtlasCellType.set_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_reference_set</span></code></a>()</p></td>
+<td><p>Assigns the reference set to the :py:attr``reference_set`` attribute.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CellSurfaceProteinAtlasCellType.show" title="pypath.core.annot.CellSurfaceProteinAtlasCellType.show"><code class="xref py py-obj docutils literal notranslate"><span class="pre">show</span></code></a>([method, table_param])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic information from the UniProt datasheets.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CellSurfaceProteinAtlasCellType.subset_intersection" title="pypath.core.annot.CellSurfaceProteinAtlasCellType.subset_intersection"><code class="xref py py-obj docutils literal notranslate"><span class="pre">subset_intersection</span></code></a>(universe, **kwargs)</p></td>
+<td><p>Calculates the proportion of entities in a subset occuring in the set <code class="docutils literal notranslate"><span class="pre">universe</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CellSurfaceProteinAtlasCellType.to_array" title="pypath.core.annot.CellSurfaceProteinAtlasCellType.to_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_array</span></code></a>([reference_set, use_fields])</p></td>
+<td><p>Returns an entity vs feature array.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CellSurfaceProteinAtlasCellType.to_bool_array" title="pypath.core.annot.CellSurfaceProteinAtlasCellType.to_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_bool_array</span></code></a>(reference_set)</p></td>
+<td><p>Returns a presence/absence boolean array for a reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CellSurfaceProteinAtlasCellType.to_set" title="pypath.core.annot.CellSurfaceProteinAtlasCellType.to_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_set</span></code></a>()</p></td>
+<td><p>Returns the entities present in this annotation resource as a set.</p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Attributes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_fields</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">summary</span></code></p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellSurfaceProteinAtlasCellType.add_complexes_by_inference">
+<span class="sig-name descname"><span class="pre">add_complexes_by_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellSurfaceProteinAtlasCellType.add_complexes_by_inference" title="Link to this definition">§</a></dt>
+<dd><p>Creates complex annotations by in silico inference and adds them
+to this annotation set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellSurfaceProteinAtlasCellType.all_complexes">
+<span class="sig-name descname"><span class="pre">all_complexes</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellSurfaceProteinAtlasCellType.all_complexes" title="Link to this definition">§</a></dt>
+<dd><p>All protein complexes annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellSurfaceProteinAtlasCellType.all_entities">
+<span class="sig-name descname"><span class="pre">all_entities</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellSurfaceProteinAtlasCellType.all_entities" title="Link to this definition">§</a></dt>
+<dd><p>All entities annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellSurfaceProteinAtlasCellType.all_mirnas">
+<span class="sig-name descname"><span class="pre">all_mirnas</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellSurfaceProteinAtlasCellType.all_mirnas" title="Link to this definition">§</a></dt>
+<dd><p>All miRNAs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellSurfaceProteinAtlasCellType.all_proteins">
+<span class="sig-name descname"><span class="pre">all_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellSurfaceProteinAtlasCellType.all_proteins" title="Link to this definition">§</a></dt>
+<dd><p>All UniProt IDs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellSurfaceProteinAtlasCellType.all_refs">
+<span class="sig-name descname"><span class="pre">all_refs</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellSurfaceProteinAtlasCellType.all_refs" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects the references
+across all records. Returns <em>list</em>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellSurfaceProteinAtlasCellType.annotate_complex">
+<span class="sig-name descname"><span class="pre">annotate_complex</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cplex</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellSurfaceProteinAtlasCellType.annotate_complex" title="Link to this definition">§</a></dt>
+<dd><p>Infers annotations for a single complex.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellSurfaceProteinAtlasCellType.browse">
+<span class="sig-name descname"><span class="pre">browse</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">field</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">start</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellSurfaceProteinAtlasCellType.browse" title="Link to this definition">§</a></dt>
+<dd><p>Print gene information as a table.</p>
+<p>Presents information about annotation categories as ascii tables
+printed in the terminal. If one category provided, prints one table.
+If multiple categories provided, prints a table for each of them one
+by one proceeding to the next one once you hit return. If no categories
+provided goes through all levels of the primary category.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>field:</dt><dd><p>The field to browse categories by.</p>
+<ul class="simple">
+<li><p>If None the primary field will be selected.
+If this annotation resource doesn’t have fields, all proteins
+will be presented as one single category.</p></li>
+<li><p>If a string it will be considered a field name and it will
+browse through all levels of this field.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">list</span></code>, set or tuple, it will be considered either a
+<code class="docutils literal notranslate"><span class="pre">list</span></code> of field names or a list of values from the primary
+field. In the former case all combinations of the values of
+the fields will be presented, in the latter case the browsing
+will be limited to the levels of the primary field contained
+in <code class="docutils literal notranslate"><span class="pre">field</span></code>.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">dict</span></code>, keys are supposed to be field names and values
+as list of levels. If any of the values are None, all levels
+from that field will be used.</p></li>
+</ul>
+</dd>
+<dt>start:</dt><dd><p>Start browsing from this category. E.g. if there are 500
+categories and start is 250 it will skip everything before the
+250th.</p>
+</dd>
+<dt>kwargs:</dt><dd><p>Passed to <code class="docutils literal notranslate"><span class="pre">pypath.utils.uniprot.info</span></code>.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellSurfaceProteinAtlasCellType.complex_inference">
+<span class="sig-name descname"><span class="pre">complex_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellSurfaceProteinAtlasCellType.complex_inference" title="Link to this definition">§</a></dt>
+<dd><p>Annotates all complexes in <cite>complexes</cite>, by default in the default
+complex database (existing in the <cite>complex</cite> module or generated
+on demand according to the module’s current settings).</p>
+<dl class="field-list simple">
+<dt class="field-odd">Returns<span class="colon">:</span></dt>
+<dd class="field-odd"><p><ul class="simple">
+<li><p><em>Dict with complexes as keys and sets of annotations as values.</em></p></li>
+<li><p><em>Complexes with no valid information in this annotation resource</em></p></li>
+<li><p><em>won’t be in the dict.</em></p></li>
+</ul>
+</p>
+</dd>
+<dt class="field-even">Parameters<span class="colon">:</span></dt>
+<dd class="field-even"><p><strong>complexes</strong> (<em>iterable</em>) – Iterable yielding complexes.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellSurfaceProteinAtlasCellType.coverage">
+<span class="sig-name descname"><span class="pre">coverage</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">other</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellSurfaceProteinAtlasCellType.coverage" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the coverage of the annotation i.e. the proportion of
+entities having at least one record in this annotation resource
+for an arbitrary set of entities.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellSurfaceProteinAtlasCellType.curation_effort">
+<span class="sig-name descname"><span class="pre">curation_effort</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellSurfaceProteinAtlasCellType.curation_effort" title="Link to this definition">§</a></dt>
+<dd><p>Counts the reference-record pairs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellSurfaceProteinAtlasCellType.get_names">
+<span class="sig-name descname"><span class="pre">get_names</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellSurfaceProteinAtlasCellType.get_names" title="Link to this definition">§</a></dt>
+<dd><p>Returns the list of field names in the records. The annotation
+consists of uniform records and each entity might be annotated
+with one or more records. Each record is a tuple of fields, for
+example <code class="docutils literal notranslate"><span class="pre">('cell_type',</span> <span class="pre">'expression_level',</span> <span class="pre">'score')</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellSurfaceProteinAtlasCellType.get_reference_set">
+<em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">get_reference_set</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">proteins</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">swissprot_only</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellSurfaceProteinAtlasCellType.get_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the reference set i.e. the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellSurfaceProteinAtlasCellType.get_subset">
+<span class="sig-name descname"><span class="pre">get_subset</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellSurfaceProteinAtlasCellType.get_subset" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellSurfaceProteinAtlasCellType.get_subset_bool_array">
+<span class="sig-name descname"><span class="pre">get_subset_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellSurfaceProteinAtlasCellType.get_subset_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a boolean vector with True and False values for each entity
+in the reference set. The values represent presence absence data
+in the simplest case, but by providing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> any kind of matching
+and filtering is possible. <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> are passed to the <code class="docutils literal notranslate"><span class="pre">select</span></code>
+method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellSurfaceProteinAtlasCellType.get_values">
+<span class="sig-name descname"><span class="pre">get_values</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">exclude_none</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellSurfaceProteinAtlasCellType.get_values" title="Link to this definition">§</a></dt>
+<dd><p>Returns the set of all possible values of a field. E.g. if the
+records of this annotation have a field <code class="docutils literal notranslate"><span class="pre">cell_type</span></code> then calling
+this method can tell you that across all records the values of
+this field might be <code class="docutils literal notranslate"><span class="pre">{'macrophage',</span> <span class="pre">'epithelial_cell',</span> <span class="pre">...}</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellSurfaceProteinAtlasCellType.labels">
+<span class="sig-name descname"><span class="pre">labels</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellSurfaceProteinAtlasCellType.labels" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellSurfaceProteinAtlasCellType.load">
+<span class="sig-name descname"><span class="pre">load</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellSurfaceProteinAtlasCellType.load" title="Link to this definition">§</a></dt>
+<dd><p>Loads the annotation data by calling the input method.
+Infers annotations for complexes in the complex database if
+py:attr:<code class="docutils literal notranslate"><span class="pre">infer_complexes</span></code> is True.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellSurfaceProteinAtlasCellType.load_data">
+<span class="sig-name descname"><span class="pre">load_data</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellSurfaceProteinAtlasCellType.load_data" title="Link to this definition">§</a></dt>
+<dd><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellSurfaceProteinAtlasCellType.load_proteins">
+<span class="sig-name descname"><span class="pre">load_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellSurfaceProteinAtlasCellType.load_proteins" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a set of all UniProt IDs to have a base set of the entire
+proteome.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellSurfaceProteinAtlasCellType.make_df">
+<span class="sig-name descname"><span class="pre">make_df</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">rebuild</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellSurfaceProteinAtlasCellType.make_df" title="Link to this definition">§</a></dt>
+<dd><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.
+The data frame will be assigned to :py:attr``df``.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellSurfaceProteinAtlasCellType.numof_entities">
+<span class="sig-name descname"><span class="pre">numof_entities</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellSurfaceProteinAtlasCellType.numof_entities" title="Link to this definition">§</a></dt>
+<dd><p>The number of annotated entities in the resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellSurfaceProteinAtlasCellType.numof_records">
+<span class="sig-name descname"><span class="pre">numof_records</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellSurfaceProteinAtlasCellType.numof_records" title="Link to this definition">§</a></dt>
+<dd><p>The total number of annotation records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellSurfaceProteinAtlasCellType.numof_references">
+<span class="sig-name descname"><span class="pre">numof_references</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellSurfaceProteinAtlasCellType.numof_references" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects and counts the
+references across all records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellSurfaceProteinAtlasCellType.process">
+<span class="sig-name descname"><span class="pre">process</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellSurfaceProteinAtlasCellType.process" title="Link to this definition">§</a></dt>
+<dd><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellSurfaceProteinAtlasCellType.reload">
+<span class="sig-name descname"><span class="pre">reload</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellSurfaceProteinAtlasCellType.reload" title="Link to this definition">§</a></dt>
+<dd><p>Reloads the object from the module level.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellSurfaceProteinAtlasCellType.select">
+<span class="sig-name descname"><span class="pre">select</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellSurfaceProteinAtlasCellType.select" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellSurfaceProteinAtlasCellType.set_method">
+<span class="sig-name descname"><span class="pre">set_method</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellSurfaceProteinAtlasCellType.set_method" title="Link to this definition">§</a></dt>
+<dd><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if
+necessary.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellSurfaceProteinAtlasCellType.set_reference_set">
+<span class="sig-name descname"><span class="pre">set_reference_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellSurfaceProteinAtlasCellType.set_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Assigns the reference set to the :py:attr``reference_set`` attribute.
+The reference set is the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellSurfaceProteinAtlasCellType.show">
+<span class="sig-name descname"><span class="pre">show</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">table_param</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellSurfaceProteinAtlasCellType.show" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic
+information from the UniProt datasheets.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellSurfaceProteinAtlasCellType.subset_intersection">
+<span class="sig-name descname"><span class="pre">subset_intersection</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">universe</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellSurfaceProteinAtlasCellType.subset_intersection" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the proportion of entities in a subset occuring in the
+set <code class="docutils literal notranslate"><span class="pre">universe</span></code>. The subset is selected by passing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> to the
+<code class="docutils literal notranslate"><span class="pre">select</span></code> method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellSurfaceProteinAtlasCellType.to_array">
+<span class="sig-name descname"><span class="pre">to_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_fields</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellSurfaceProteinAtlasCellType.to_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns an entity vs feature array. In case of more complex
+annotations this might be huge.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellSurfaceProteinAtlasCellType.to_bool_array">
+<span class="sig-name descname"><span class="pre">to_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellSurfaceProteinAtlasCellType.to_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a presence/absence boolean array for a reference set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellSurfaceProteinAtlasCellType.to_set">
+<span class="sig-name descname"><span class="pre">to_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellSurfaceProteinAtlasCellType.to_set" title="Link to this definition">§</a></dt>
+<dd><p>Returns the entities present in this annotation resource as a set.</p>
+</dd></dl>
+
+</dd></dl>
+
+</section>
+
+
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+  <section id="pypath-core-annot-cellcall">
+<h1>pypath.core.annot.Cellcall<a class="headerlink" href="#pypath-core-annot-cellcall" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.core.annot.Cellcall">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.core.annot.</span></span><span class="sig-name descname"><span class="pre">Cellcall</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#Cellcall"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.Cellcall" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <a class="reference internal" href="pypath.core.annot.AnnotationBase.html#pypath.core.annot.AnnotationBase" title="pypath.core.annot.AnnotationBase"><code class="xref py py-class docutils literal notranslate"><span class="pre">AnnotationBase</span></code></a></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cellcall.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#Cellcall.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.Cellcall.__init__" title="Link to this definition">§</a></dt>
+<dd><p>Represents annotations for a set of proteins.
+Loads the data from the original resource and provides methods
+to query the annotations.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>name</strong> (<em>str</em>) – A custom name for the annotation resource.</p></li>
+<li><p><strong>ncbi_tax_id</strong> (<em>int</em>) – NCBI Taxonomy identifier.</p></li>
+<li><p><strong>input_method</strong> (<em>callable</em><em>,</em><em>str</em>) – Either a callable or the name of a method in any submodules of
+the <code class="docutils literal notranslate"><span class="pre">pypath.inputs</span></code>  module. Should return a dict with
+UniProt IDs as keys or an object suitable for <code class="docutils literal notranslate"><span class="pre">process_method</span></code>.</p></li>
+<li><p><strong>input_args</strong> (<em>dict</em>) – Arguments for the <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Cellcall.__init__" title="pypath.core.annot.Cellcall.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>(**kwargs)</p></td>
+<td><p>Represents annotations for a set of proteins.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Cellcall.add_complexes_by_inference" title="pypath.core.annot.Cellcall.add_complexes_by_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">add_complexes_by_inference</span></code></a>([complexes])</p></td>
+<td><p>Creates complex annotations by in silico inference and adds them to this annotation set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Cellcall.all_complexes" title="pypath.core.annot.Cellcall.all_complexes"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_complexes</span></code></a>()</p></td>
+<td><p>All protein complexes annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Cellcall.all_entities" title="pypath.core.annot.Cellcall.all_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_entities</span></code></a>([entity_types])</p></td>
+<td><p>All entities annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Cellcall.all_mirnas" title="pypath.core.annot.Cellcall.all_mirnas"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_mirnas</span></code></a>()</p></td>
+<td><p>All miRNAs annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Cellcall.all_proteins" title="pypath.core.annot.Cellcall.all_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_proteins</span></code></a>()</p></td>
+<td><p>All UniProt IDs annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Cellcall.all_refs" title="pypath.core.annot.Cellcall.all_refs"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_refs</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Cellcall.annotate_complex" title="pypath.core.annot.Cellcall.annotate_complex"><code class="xref py py-obj docutils literal notranslate"><span class="pre">annotate_complex</span></code></a>(cplex)</p></td>
+<td><p>Infers annotations for a single complex.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Cellcall.browse" title="pypath.core.annot.Cellcall.browse"><code class="xref py py-obj docutils literal notranslate"><span class="pre">browse</span></code></a>([field, start])</p></td>
+<td><p>Print gene information as a table.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Cellcall.complex_inference" title="pypath.core.annot.Cellcall.complex_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">complex_inference</span></code></a>([complexes])</p></td>
+<td><p>Annotates all complexes in <cite>complexes</cite>, by default in the default complex database (existing in the <cite>complex</cite> module or generated on demand according to the module's current settings).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Cellcall.coverage" title="pypath.core.annot.Cellcall.coverage"><code class="xref py py-obj docutils literal notranslate"><span class="pre">coverage</span></code></a>(other)</p></td>
+<td><p>Calculates the coverage of the annotation i.e. the proportion of entities having at least one record in this annotation resource for an arbitrary set of entities.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Cellcall.curation_effort" title="pypath.core.annot.Cellcall.curation_effort"><code class="xref py py-obj docutils literal notranslate"><span class="pre">curation_effort</span></code></a>()</p></td>
+<td><p>Counts the reference-record pairs.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">from_dump</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_entity_type</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Cellcall.get_names" title="pypath.core.annot.Cellcall.get_names"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_names</span></code></a>()</p></td>
+<td><p>Returns the list of field names in the records.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Cellcall.get_reference_set" title="pypath.core.annot.Cellcall.get_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_reference_set</span></code></a>([proteins, complexes, ...])</p></td>
+<td><p>Retrieves the reference set i.e. the set of all entities which potentially have annotation in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Cellcall.get_subset" title="pypath.core.annot.Cellcall.get_subset"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Cellcall.get_subset_bool_array" title="pypath.core.annot.Cellcall.get_subset_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset_bool_array</span></code></a>([reference_set])</p></td>
+<td><p>Returns a boolean vector with True and False values for each entity in the reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Cellcall.get_values" title="pypath.core.annot.Cellcall.get_values"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_values</span></code></a>(name[, exclude_none])</p></td>
+<td><p>Returns the set of all possible values of a field.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_complex</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_mirna</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_protein</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Cellcall.labels" title="pypath.core.annot.Cellcall.labels"><code class="xref py py-obj docutils literal notranslate"><span class="pre">labels</span></code></a>([method])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Cellcall.load" title="pypath.core.annot.Cellcall.load"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load</span></code></a>()</p></td>
+<td><p>Loads the annotation data by calling the input method.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Cellcall.load_data" title="pypath.core.annot.Cellcall.load_data"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_data</span></code></a>()</p></td>
+<td><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Cellcall.load_proteins" title="pypath.core.annot.Cellcall.load_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_proteins</span></code></a>()</p></td>
+<td><p>Retrieves a set of all UniProt IDs to have a base set of the entire proteome.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Cellcall.make_df" title="pypath.core.annot.Cellcall.make_df"><code class="xref py py-obj docutils literal notranslate"><span class="pre">make_df</span></code></a>([rebuild])</p></td>
+<td><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complex_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Cellcall.numof_entities" title="pypath.core.annot.Cellcall.numof_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_entities</span></code></a>()</p></td>
+<td><p>The number of annotated entities in the resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirna_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirnas</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_protein_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_proteins</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Cellcall.numof_records" title="pypath.core.annot.Cellcall.numof_records"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_records</span></code></a>([entity_types])</p></td>
+<td><p>The total number of annotation records.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Cellcall.numof_references" title="pypath.core.annot.Cellcall.numof_references"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_references</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Cellcall.process" title="pypath.core.annot.Cellcall.process"><code class="xref py py-obj docutils literal notranslate"><span class="pre">process</span></code></a>()</p></td>
+<td><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">proportion</span></code>(other)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Cellcall.reload" title="pypath.core.annot.Cellcall.reload"><code class="xref py py-obj docutils literal notranslate"><span class="pre">reload</span></code></a>()</p></td>
+<td><p>Reloads the object from the module level.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">save_to_pickle</span></code>(pickle_file)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Cellcall.select" title="pypath.core.annot.Cellcall.select"><code class="xref py py-obj docutils literal notranslate"><span class="pre">select</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Cellcall.set_method" title="pypath.core.annot.Cellcall.set_method"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_method</span></code></a>()</p></td>
+<td><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if necessary.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Cellcall.set_reference_set" title="pypath.core.annot.Cellcall.set_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_reference_set</span></code></a>()</p></td>
+<td><p>Assigns the reference set to the :py:attr``reference_set`` attribute.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Cellcall.show" title="pypath.core.annot.Cellcall.show"><code class="xref py py-obj docutils literal notranslate"><span class="pre">show</span></code></a>([method, table_param])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic information from the UniProt datasheets.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Cellcall.subset_intersection" title="pypath.core.annot.Cellcall.subset_intersection"><code class="xref py py-obj docutils literal notranslate"><span class="pre">subset_intersection</span></code></a>(universe, **kwargs)</p></td>
+<td><p>Calculates the proportion of entities in a subset occuring in the set <code class="docutils literal notranslate"><span class="pre">universe</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Cellcall.to_array" title="pypath.core.annot.Cellcall.to_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_array</span></code></a>([reference_set, use_fields])</p></td>
+<td><p>Returns an entity vs feature array.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Cellcall.to_bool_array" title="pypath.core.annot.Cellcall.to_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_bool_array</span></code></a>(reference_set)</p></td>
+<td><p>Returns a presence/absence boolean array for a reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Cellcall.to_set" title="pypath.core.annot.Cellcall.to_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_set</span></code></a>()</p></td>
+<td><p>Returns the entities present in this annotation resource as a set.</p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Attributes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_fields</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">summary</span></code></p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cellcall.add_complexes_by_inference">
+<span class="sig-name descname"><span class="pre">add_complexes_by_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cellcall.add_complexes_by_inference" title="Link to this definition">§</a></dt>
+<dd><p>Creates complex annotations by in silico inference and adds them
+to this annotation set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cellcall.all_complexes">
+<span class="sig-name descname"><span class="pre">all_complexes</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cellcall.all_complexes" title="Link to this definition">§</a></dt>
+<dd><p>All protein complexes annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cellcall.all_entities">
+<span class="sig-name descname"><span class="pre">all_entities</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cellcall.all_entities" title="Link to this definition">§</a></dt>
+<dd><p>All entities annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cellcall.all_mirnas">
+<span class="sig-name descname"><span class="pre">all_mirnas</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cellcall.all_mirnas" title="Link to this definition">§</a></dt>
+<dd><p>All miRNAs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cellcall.all_proteins">
+<span class="sig-name descname"><span class="pre">all_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cellcall.all_proteins" title="Link to this definition">§</a></dt>
+<dd><p>All UniProt IDs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cellcall.all_refs">
+<span class="sig-name descname"><span class="pre">all_refs</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cellcall.all_refs" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects the references
+across all records. Returns <em>list</em>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cellcall.annotate_complex">
+<span class="sig-name descname"><span class="pre">annotate_complex</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cplex</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cellcall.annotate_complex" title="Link to this definition">§</a></dt>
+<dd><p>Infers annotations for a single complex.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cellcall.browse">
+<span class="sig-name descname"><span class="pre">browse</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">field</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">start</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cellcall.browse" title="Link to this definition">§</a></dt>
+<dd><p>Print gene information as a table.</p>
+<p>Presents information about annotation categories as ascii tables
+printed in the terminal. If one category provided, prints one table.
+If multiple categories provided, prints a table for each of them one
+by one proceeding to the next one once you hit return. If no categories
+provided goes through all levels of the primary category.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>field:</dt><dd><p>The field to browse categories by.</p>
+<ul class="simple">
+<li><p>If None the primary field will be selected.
+If this annotation resource doesn’t have fields, all proteins
+will be presented as one single category.</p></li>
+<li><p>If a string it will be considered a field name and it will
+browse through all levels of this field.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">list</span></code>, set or tuple, it will be considered either a
+<code class="docutils literal notranslate"><span class="pre">list</span></code> of field names or a list of values from the primary
+field. In the former case all combinations of the values of
+the fields will be presented, in the latter case the browsing
+will be limited to the levels of the primary field contained
+in <code class="docutils literal notranslate"><span class="pre">field</span></code>.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">dict</span></code>, keys are supposed to be field names and values
+as list of levels. If any of the values are None, all levels
+from that field will be used.</p></li>
+</ul>
+</dd>
+<dt>start:</dt><dd><p>Start browsing from this category. E.g. if there are 500
+categories and start is 250 it will skip everything before the
+250th.</p>
+</dd>
+<dt>kwargs:</dt><dd><p>Passed to <code class="docutils literal notranslate"><span class="pre">pypath.utils.uniprot.info</span></code>.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cellcall.complex_inference">
+<span class="sig-name descname"><span class="pre">complex_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cellcall.complex_inference" title="Link to this definition">§</a></dt>
+<dd><p>Annotates all complexes in <cite>complexes</cite>, by default in the default
+complex database (existing in the <cite>complex</cite> module or generated
+on demand according to the module’s current settings).</p>
+<dl class="field-list simple">
+<dt class="field-odd">Returns<span class="colon">:</span></dt>
+<dd class="field-odd"><p><ul class="simple">
+<li><p><em>Dict with complexes as keys and sets of annotations as values.</em></p></li>
+<li><p><em>Complexes with no valid information in this annotation resource</em></p></li>
+<li><p><em>won’t be in the dict.</em></p></li>
+</ul>
+</p>
+</dd>
+<dt class="field-even">Parameters<span class="colon">:</span></dt>
+<dd class="field-even"><p><strong>complexes</strong> (<em>iterable</em>) – Iterable yielding complexes.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cellcall.coverage">
+<span class="sig-name descname"><span class="pre">coverage</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">other</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cellcall.coverage" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the coverage of the annotation i.e. the proportion of
+entities having at least one record in this annotation resource
+for an arbitrary set of entities.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cellcall.curation_effort">
+<span class="sig-name descname"><span class="pre">curation_effort</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cellcall.curation_effort" title="Link to this definition">§</a></dt>
+<dd><p>Counts the reference-record pairs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cellcall.get_names">
+<span class="sig-name descname"><span class="pre">get_names</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cellcall.get_names" title="Link to this definition">§</a></dt>
+<dd><p>Returns the list of field names in the records. The annotation
+consists of uniform records and each entity might be annotated
+with one or more records. Each record is a tuple of fields, for
+example <code class="docutils literal notranslate"><span class="pre">('cell_type',</span> <span class="pre">'expression_level',</span> <span class="pre">'score')</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cellcall.get_reference_set">
+<em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">get_reference_set</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">proteins</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">swissprot_only</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cellcall.get_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the reference set i.e. the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cellcall.get_subset">
+<span class="sig-name descname"><span class="pre">get_subset</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cellcall.get_subset" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cellcall.get_subset_bool_array">
+<span class="sig-name descname"><span class="pre">get_subset_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cellcall.get_subset_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a boolean vector with True and False values for each entity
+in the reference set. The values represent presence absence data
+in the simplest case, but by providing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> any kind of matching
+and filtering is possible. <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> are passed to the <code class="docutils literal notranslate"><span class="pre">select</span></code>
+method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cellcall.get_values">
+<span class="sig-name descname"><span class="pre">get_values</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">exclude_none</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cellcall.get_values" title="Link to this definition">§</a></dt>
+<dd><p>Returns the set of all possible values of a field. E.g. if the
+records of this annotation have a field <code class="docutils literal notranslate"><span class="pre">cell_type</span></code> then calling
+this method can tell you that across all records the values of
+this field might be <code class="docutils literal notranslate"><span class="pre">{'macrophage',</span> <span class="pre">'epithelial_cell',</span> <span class="pre">...}</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cellcall.labels">
+<span class="sig-name descname"><span class="pre">labels</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cellcall.labels" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cellcall.load">
+<span class="sig-name descname"><span class="pre">load</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cellcall.load" title="Link to this definition">§</a></dt>
+<dd><p>Loads the annotation data by calling the input method.
+Infers annotations for complexes in the complex database if
+py:attr:<code class="docutils literal notranslate"><span class="pre">infer_complexes</span></code> is True.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cellcall.load_data">
+<span class="sig-name descname"><span class="pre">load_data</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cellcall.load_data" title="Link to this definition">§</a></dt>
+<dd><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cellcall.load_proteins">
+<span class="sig-name descname"><span class="pre">load_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cellcall.load_proteins" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a set of all UniProt IDs to have a base set of the entire
+proteome.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cellcall.make_df">
+<span class="sig-name descname"><span class="pre">make_df</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">rebuild</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cellcall.make_df" title="Link to this definition">§</a></dt>
+<dd><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.
+The data frame will be assigned to :py:attr``df``.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cellcall.numof_entities">
+<span class="sig-name descname"><span class="pre">numof_entities</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cellcall.numof_entities" title="Link to this definition">§</a></dt>
+<dd><p>The number of annotated entities in the resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cellcall.numof_records">
+<span class="sig-name descname"><span class="pre">numof_records</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cellcall.numof_records" title="Link to this definition">§</a></dt>
+<dd><p>The total number of annotation records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cellcall.numof_references">
+<span class="sig-name descname"><span class="pre">numof_references</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cellcall.numof_references" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects and counts the
+references across all records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cellcall.process">
+<span class="sig-name descname"><span class="pre">process</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cellcall.process" title="Link to this definition">§</a></dt>
+<dd><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cellcall.reload">
+<span class="sig-name descname"><span class="pre">reload</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cellcall.reload" title="Link to this definition">§</a></dt>
+<dd><p>Reloads the object from the module level.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cellcall.select">
+<span class="sig-name descname"><span class="pre">select</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cellcall.select" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cellcall.set_method">
+<span class="sig-name descname"><span class="pre">set_method</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cellcall.set_method" title="Link to this definition">§</a></dt>
+<dd><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if
+necessary.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cellcall.set_reference_set">
+<span class="sig-name descname"><span class="pre">set_reference_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cellcall.set_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Assigns the reference set to the :py:attr``reference_set`` attribute.
+The reference set is the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cellcall.show">
+<span class="sig-name descname"><span class="pre">show</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">table_param</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cellcall.show" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic
+information from the UniProt datasheets.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cellcall.subset_intersection">
+<span class="sig-name descname"><span class="pre">subset_intersection</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">universe</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cellcall.subset_intersection" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the proportion of entities in a subset occuring in the
+set <code class="docutils literal notranslate"><span class="pre">universe</span></code>. The subset is selected by passing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> to the
+<code class="docutils literal notranslate"><span class="pre">select</span></code> method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cellcall.to_array">
+<span class="sig-name descname"><span class="pre">to_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_fields</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cellcall.to_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns an entity vs feature array. In case of more complex
+annotations this might be huge.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cellcall.to_bool_array">
+<span class="sig-name descname"><span class="pre">to_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cellcall.to_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a presence/absence boolean array for a reference set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cellcall.to_set">
+<span class="sig-name descname"><span class="pre">to_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cellcall.to_set" title="Link to this definition">§</a></dt>
+<dd><p>Returns the entities present in this annotation resource as a set.</p>
+</dd></dl>
+
+</dd></dl>
+
+</section>
+
+
+                </article>
+              
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diff --git a/api/pypath.core.annot.Cellcellinteractions.html b/api/pypath.core.annot.Cellcellinteractions.html
new file mode 100644
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+  <section id="pypath-core-annot-cellcellinteractions">
+<h1>pypath.core.annot.Cellcellinteractions<a class="headerlink" href="#pypath-core-annot-cellcellinteractions" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.core.annot.Cellcellinteractions">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.core.annot.</span></span><span class="sig-name descname"><span class="pre">Cellcellinteractions</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#Cellcellinteractions"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.Cellcellinteractions" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <a class="reference internal" href="pypath.core.annot.AnnotationBase.html#pypath.core.annot.AnnotationBase" title="pypath.core.annot.AnnotationBase"><code class="xref py py-class docutils literal notranslate"><span class="pre">AnnotationBase</span></code></a></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cellcellinteractions.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#Cellcellinteractions.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.Cellcellinteractions.__init__" title="Link to this definition">§</a></dt>
+<dd><p>Represents annotations for a set of proteins.
+Loads the data from the original resource and provides methods
+to query the annotations.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>name</strong> (<em>str</em>) – A custom name for the annotation resource.</p></li>
+<li><p><strong>ncbi_tax_id</strong> (<em>int</em>) – NCBI Taxonomy identifier.</p></li>
+<li><p><strong>input_method</strong> (<em>callable</em><em>,</em><em>str</em>) – Either a callable or the name of a method in any submodules of
+the <code class="docutils literal notranslate"><span class="pre">pypath.inputs</span></code>  module. Should return a dict with
+UniProt IDs as keys or an object suitable for <code class="docutils literal notranslate"><span class="pre">process_method</span></code>.</p></li>
+<li><p><strong>input_args</strong> (<em>dict</em>) – Arguments for the <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Cellcellinteractions.__init__" title="pypath.core.annot.Cellcellinteractions.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>([ncbi_tax_id])</p></td>
+<td><p>Represents annotations for a set of proteins.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Cellcellinteractions.add_complexes_by_inference" title="pypath.core.annot.Cellcellinteractions.add_complexes_by_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">add_complexes_by_inference</span></code></a>([complexes])</p></td>
+<td><p>Creates complex annotations by in silico inference and adds them to this annotation set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Cellcellinteractions.all_complexes" title="pypath.core.annot.Cellcellinteractions.all_complexes"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_complexes</span></code></a>()</p></td>
+<td><p>All protein complexes annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Cellcellinteractions.all_entities" title="pypath.core.annot.Cellcellinteractions.all_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_entities</span></code></a>([entity_types])</p></td>
+<td><p>All entities annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Cellcellinteractions.all_mirnas" title="pypath.core.annot.Cellcellinteractions.all_mirnas"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_mirnas</span></code></a>()</p></td>
+<td><p>All miRNAs annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Cellcellinteractions.all_proteins" title="pypath.core.annot.Cellcellinteractions.all_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_proteins</span></code></a>()</p></td>
+<td><p>All UniProt IDs annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Cellcellinteractions.all_refs" title="pypath.core.annot.Cellcellinteractions.all_refs"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_refs</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Cellcellinteractions.annotate_complex" title="pypath.core.annot.Cellcellinteractions.annotate_complex"><code class="xref py py-obj docutils literal notranslate"><span class="pre">annotate_complex</span></code></a>(cplex)</p></td>
+<td><p>Infers annotations for a single complex.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Cellcellinteractions.browse" title="pypath.core.annot.Cellcellinteractions.browse"><code class="xref py py-obj docutils literal notranslate"><span class="pre">browse</span></code></a>([field, start])</p></td>
+<td><p>Print gene information as a table.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Cellcellinteractions.complex_inference" title="pypath.core.annot.Cellcellinteractions.complex_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">complex_inference</span></code></a>([complexes])</p></td>
+<td><p>Annotates all complexes in <cite>complexes</cite>, by default in the default complex database (existing in the <cite>complex</cite> module or generated on demand according to the module's current settings).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Cellcellinteractions.coverage" title="pypath.core.annot.Cellcellinteractions.coverage"><code class="xref py py-obj docutils literal notranslate"><span class="pre">coverage</span></code></a>(other)</p></td>
+<td><p>Calculates the coverage of the annotation i.e. the proportion of entities having at least one record in this annotation resource for an arbitrary set of entities.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Cellcellinteractions.curation_effort" title="pypath.core.annot.Cellcellinteractions.curation_effort"><code class="xref py py-obj docutils literal notranslate"><span class="pre">curation_effort</span></code></a>()</p></td>
+<td><p>Counts the reference-record pairs.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">from_dump</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_entity_type</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Cellcellinteractions.get_names" title="pypath.core.annot.Cellcellinteractions.get_names"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_names</span></code></a>()</p></td>
+<td><p>Returns the list of field names in the records.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Cellcellinteractions.get_reference_set" title="pypath.core.annot.Cellcellinteractions.get_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_reference_set</span></code></a>([proteins, complexes, ...])</p></td>
+<td><p>Retrieves the reference set i.e. the set of all entities which potentially have annotation in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Cellcellinteractions.get_subset" title="pypath.core.annot.Cellcellinteractions.get_subset"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Cellcellinteractions.get_subset_bool_array" title="pypath.core.annot.Cellcellinteractions.get_subset_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset_bool_array</span></code></a>([reference_set])</p></td>
+<td><p>Returns a boolean vector with True and False values for each entity in the reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Cellcellinteractions.get_values" title="pypath.core.annot.Cellcellinteractions.get_values"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_values</span></code></a>(name[, exclude_none])</p></td>
+<td><p>Returns the set of all possible values of a field.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_complex</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_mirna</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_protein</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Cellcellinteractions.labels" title="pypath.core.annot.Cellcellinteractions.labels"><code class="xref py py-obj docutils literal notranslate"><span class="pre">labels</span></code></a>([method])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Cellcellinteractions.load" title="pypath.core.annot.Cellcellinteractions.load"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load</span></code></a>()</p></td>
+<td><p>Loads the annotation data by calling the input method.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Cellcellinteractions.load_data" title="pypath.core.annot.Cellcellinteractions.load_data"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_data</span></code></a>()</p></td>
+<td><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Cellcellinteractions.load_proteins" title="pypath.core.annot.Cellcellinteractions.load_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_proteins</span></code></a>()</p></td>
+<td><p>Retrieves a set of all UniProt IDs to have a base set of the entire proteome.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Cellcellinteractions.make_df" title="pypath.core.annot.Cellcellinteractions.make_df"><code class="xref py py-obj docutils literal notranslate"><span class="pre">make_df</span></code></a>([rebuild])</p></td>
+<td><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complex_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Cellcellinteractions.numof_entities" title="pypath.core.annot.Cellcellinteractions.numof_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_entities</span></code></a>()</p></td>
+<td><p>The number of annotated entities in the resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirna_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirnas</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_protein_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_proteins</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Cellcellinteractions.numof_records" title="pypath.core.annot.Cellcellinteractions.numof_records"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_records</span></code></a>([entity_types])</p></td>
+<td><p>The total number of annotation records.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Cellcellinteractions.numof_references" title="pypath.core.annot.Cellcellinteractions.numof_references"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_references</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Cellcellinteractions.process" title="pypath.core.annot.Cellcellinteractions.process"><code class="xref py py-obj docutils literal notranslate"><span class="pre">process</span></code></a>()</p></td>
+<td><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">proportion</span></code>(other)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Cellcellinteractions.reload" title="pypath.core.annot.Cellcellinteractions.reload"><code class="xref py py-obj docutils literal notranslate"><span class="pre">reload</span></code></a>()</p></td>
+<td><p>Reloads the object from the module level.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">save_to_pickle</span></code>(pickle_file)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Cellcellinteractions.select" title="pypath.core.annot.Cellcellinteractions.select"><code class="xref py py-obj docutils literal notranslate"><span class="pre">select</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Cellcellinteractions.set_method" title="pypath.core.annot.Cellcellinteractions.set_method"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_method</span></code></a>()</p></td>
+<td><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if necessary.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Cellcellinteractions.set_reference_set" title="pypath.core.annot.Cellcellinteractions.set_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_reference_set</span></code></a>()</p></td>
+<td><p>Assigns the reference set to the :py:attr``reference_set`` attribute.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Cellcellinteractions.show" title="pypath.core.annot.Cellcellinteractions.show"><code class="xref py py-obj docutils literal notranslate"><span class="pre">show</span></code></a>([method, table_param])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic information from the UniProt datasheets.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Cellcellinteractions.subset_intersection" title="pypath.core.annot.Cellcellinteractions.subset_intersection"><code class="xref py py-obj docutils literal notranslate"><span class="pre">subset_intersection</span></code></a>(universe, **kwargs)</p></td>
+<td><p>Calculates the proportion of entities in a subset occuring in the set <code class="docutils literal notranslate"><span class="pre">universe</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Cellcellinteractions.to_array" title="pypath.core.annot.Cellcellinteractions.to_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_array</span></code></a>([reference_set, use_fields])</p></td>
+<td><p>Returns an entity vs feature array.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Cellcellinteractions.to_bool_array" title="pypath.core.annot.Cellcellinteractions.to_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_bool_array</span></code></a>(reference_set)</p></td>
+<td><p>Returns a presence/absence boolean array for a reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Cellcellinteractions.to_set" title="pypath.core.annot.Cellcellinteractions.to_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_set</span></code></a>()</p></td>
+<td><p>Returns the entities present in this annotation resource as a set.</p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Attributes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_fields</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">summary</span></code></p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cellcellinteractions.add_complexes_by_inference">
+<span class="sig-name descname"><span class="pre">add_complexes_by_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cellcellinteractions.add_complexes_by_inference" title="Link to this definition">§</a></dt>
+<dd><p>Creates complex annotations by in silico inference and adds them
+to this annotation set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cellcellinteractions.all_complexes">
+<span class="sig-name descname"><span class="pre">all_complexes</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cellcellinteractions.all_complexes" title="Link to this definition">§</a></dt>
+<dd><p>All protein complexes annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cellcellinteractions.all_entities">
+<span class="sig-name descname"><span class="pre">all_entities</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cellcellinteractions.all_entities" title="Link to this definition">§</a></dt>
+<dd><p>All entities annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cellcellinteractions.all_mirnas">
+<span class="sig-name descname"><span class="pre">all_mirnas</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cellcellinteractions.all_mirnas" title="Link to this definition">§</a></dt>
+<dd><p>All miRNAs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cellcellinteractions.all_proteins">
+<span class="sig-name descname"><span class="pre">all_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cellcellinteractions.all_proteins" title="Link to this definition">§</a></dt>
+<dd><p>All UniProt IDs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cellcellinteractions.all_refs">
+<span class="sig-name descname"><span class="pre">all_refs</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cellcellinteractions.all_refs" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects the references
+across all records. Returns <em>list</em>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cellcellinteractions.annotate_complex">
+<span class="sig-name descname"><span class="pre">annotate_complex</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cplex</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cellcellinteractions.annotate_complex" title="Link to this definition">§</a></dt>
+<dd><p>Infers annotations for a single complex.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cellcellinteractions.browse">
+<span class="sig-name descname"><span class="pre">browse</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">field</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">start</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cellcellinteractions.browse" title="Link to this definition">§</a></dt>
+<dd><p>Print gene information as a table.</p>
+<p>Presents information about annotation categories as ascii tables
+printed in the terminal. If one category provided, prints one table.
+If multiple categories provided, prints a table for each of them one
+by one proceeding to the next one once you hit return. If no categories
+provided goes through all levels of the primary category.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>field:</dt><dd><p>The field to browse categories by.</p>
+<ul class="simple">
+<li><p>If None the primary field will be selected.
+If this annotation resource doesn’t have fields, all proteins
+will be presented as one single category.</p></li>
+<li><p>If a string it will be considered a field name and it will
+browse through all levels of this field.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">list</span></code>, set or tuple, it will be considered either a
+<code class="docutils literal notranslate"><span class="pre">list</span></code> of field names or a list of values from the primary
+field. In the former case all combinations of the values of
+the fields will be presented, in the latter case the browsing
+will be limited to the levels of the primary field contained
+in <code class="docutils literal notranslate"><span class="pre">field</span></code>.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">dict</span></code>, keys are supposed to be field names and values
+as list of levels. If any of the values are None, all levels
+from that field will be used.</p></li>
+</ul>
+</dd>
+<dt>start:</dt><dd><p>Start browsing from this category. E.g. if there are 500
+categories and start is 250 it will skip everything before the
+250th.</p>
+</dd>
+<dt>kwargs:</dt><dd><p>Passed to <code class="docutils literal notranslate"><span class="pre">pypath.utils.uniprot.info</span></code>.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cellcellinteractions.complex_inference">
+<span class="sig-name descname"><span class="pre">complex_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cellcellinteractions.complex_inference" title="Link to this definition">§</a></dt>
+<dd><p>Annotates all complexes in <cite>complexes</cite>, by default in the default
+complex database (existing in the <cite>complex</cite> module or generated
+on demand according to the module’s current settings).</p>
+<dl class="field-list simple">
+<dt class="field-odd">Returns<span class="colon">:</span></dt>
+<dd class="field-odd"><p><ul class="simple">
+<li><p><em>Dict with complexes as keys and sets of annotations as values.</em></p></li>
+<li><p><em>Complexes with no valid information in this annotation resource</em></p></li>
+<li><p><em>won’t be in the dict.</em></p></li>
+</ul>
+</p>
+</dd>
+<dt class="field-even">Parameters<span class="colon">:</span></dt>
+<dd class="field-even"><p><strong>complexes</strong> (<em>iterable</em>) – Iterable yielding complexes.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cellcellinteractions.coverage">
+<span class="sig-name descname"><span class="pre">coverage</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">other</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cellcellinteractions.coverage" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the coverage of the annotation i.e. the proportion of
+entities having at least one record in this annotation resource
+for an arbitrary set of entities.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cellcellinteractions.curation_effort">
+<span class="sig-name descname"><span class="pre">curation_effort</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cellcellinteractions.curation_effort" title="Link to this definition">§</a></dt>
+<dd><p>Counts the reference-record pairs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cellcellinteractions.get_names">
+<span class="sig-name descname"><span class="pre">get_names</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cellcellinteractions.get_names" title="Link to this definition">§</a></dt>
+<dd><p>Returns the list of field names in the records. The annotation
+consists of uniform records and each entity might be annotated
+with one or more records. Each record is a tuple of fields, for
+example <code class="docutils literal notranslate"><span class="pre">('cell_type',</span> <span class="pre">'expression_level',</span> <span class="pre">'score')</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cellcellinteractions.get_reference_set">
+<em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">get_reference_set</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">proteins</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">swissprot_only</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cellcellinteractions.get_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the reference set i.e. the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cellcellinteractions.get_subset">
+<span class="sig-name descname"><span class="pre">get_subset</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cellcellinteractions.get_subset" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cellcellinteractions.get_subset_bool_array">
+<span class="sig-name descname"><span class="pre">get_subset_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cellcellinteractions.get_subset_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a boolean vector with True and False values for each entity
+in the reference set. The values represent presence absence data
+in the simplest case, but by providing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> any kind of matching
+and filtering is possible. <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> are passed to the <code class="docutils literal notranslate"><span class="pre">select</span></code>
+method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cellcellinteractions.get_values">
+<span class="sig-name descname"><span class="pre">get_values</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">exclude_none</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cellcellinteractions.get_values" title="Link to this definition">§</a></dt>
+<dd><p>Returns the set of all possible values of a field. E.g. if the
+records of this annotation have a field <code class="docutils literal notranslate"><span class="pre">cell_type</span></code> then calling
+this method can tell you that across all records the values of
+this field might be <code class="docutils literal notranslate"><span class="pre">{'macrophage',</span> <span class="pre">'epithelial_cell',</span> <span class="pre">...}</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cellcellinteractions.labels">
+<span class="sig-name descname"><span class="pre">labels</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cellcellinteractions.labels" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cellcellinteractions.load">
+<span class="sig-name descname"><span class="pre">load</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cellcellinteractions.load" title="Link to this definition">§</a></dt>
+<dd><p>Loads the annotation data by calling the input method.
+Infers annotations for complexes in the complex database if
+py:attr:<code class="docutils literal notranslate"><span class="pre">infer_complexes</span></code> is True.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cellcellinteractions.load_data">
+<span class="sig-name descname"><span class="pre">load_data</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cellcellinteractions.load_data" title="Link to this definition">§</a></dt>
+<dd><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cellcellinteractions.load_proteins">
+<span class="sig-name descname"><span class="pre">load_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cellcellinteractions.load_proteins" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a set of all UniProt IDs to have a base set of the entire
+proteome.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cellcellinteractions.make_df">
+<span class="sig-name descname"><span class="pre">make_df</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">rebuild</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cellcellinteractions.make_df" title="Link to this definition">§</a></dt>
+<dd><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.
+The data frame will be assigned to :py:attr``df``.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cellcellinteractions.numof_entities">
+<span class="sig-name descname"><span class="pre">numof_entities</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cellcellinteractions.numof_entities" title="Link to this definition">§</a></dt>
+<dd><p>The number of annotated entities in the resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cellcellinteractions.numof_records">
+<span class="sig-name descname"><span class="pre">numof_records</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cellcellinteractions.numof_records" title="Link to this definition">§</a></dt>
+<dd><p>The total number of annotation records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cellcellinteractions.numof_references">
+<span class="sig-name descname"><span class="pre">numof_references</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cellcellinteractions.numof_references" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects and counts the
+references across all records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cellcellinteractions.process">
+<span class="sig-name descname"><span class="pre">process</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cellcellinteractions.process" title="Link to this definition">§</a></dt>
+<dd><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cellcellinteractions.reload">
+<span class="sig-name descname"><span class="pre">reload</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cellcellinteractions.reload" title="Link to this definition">§</a></dt>
+<dd><p>Reloads the object from the module level.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cellcellinteractions.select">
+<span class="sig-name descname"><span class="pre">select</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cellcellinteractions.select" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cellcellinteractions.set_method">
+<span class="sig-name descname"><span class="pre">set_method</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cellcellinteractions.set_method" title="Link to this definition">§</a></dt>
+<dd><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if
+necessary.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cellcellinteractions.set_reference_set">
+<span class="sig-name descname"><span class="pre">set_reference_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cellcellinteractions.set_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Assigns the reference set to the :py:attr``reference_set`` attribute.
+The reference set is the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cellcellinteractions.show">
+<span class="sig-name descname"><span class="pre">show</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">table_param</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cellcellinteractions.show" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic
+information from the UniProt datasheets.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cellcellinteractions.subset_intersection">
+<span class="sig-name descname"><span class="pre">subset_intersection</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">universe</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cellcellinteractions.subset_intersection" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the proportion of entities in a subset occuring in the
+set <code class="docutils literal notranslate"><span class="pre">universe</span></code>. The subset is selected by passing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> to the
+<code class="docutils literal notranslate"><span class="pre">select</span></code> method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cellcellinteractions.to_array">
+<span class="sig-name descname"><span class="pre">to_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_fields</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cellcellinteractions.to_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns an entity vs feature array. In case of more complex
+annotations this might be huge.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cellcellinteractions.to_bool_array">
+<span class="sig-name descname"><span class="pre">to_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cellcellinteractions.to_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a presence/absence boolean array for a reference set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cellcellinteractions.to_set">
+<span class="sig-name descname"><span class="pre">to_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cellcellinteractions.to_set" title="Link to this definition">§</a></dt>
+<dd><p>Returns the entities present in this annotation resource as a set.</p>
+</dd></dl>
+
+</dd></dl>
+
+</section>
+
+
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+  <section id="pypath-core-annot-cellchatdb">
+<h1>pypath.core.annot.Cellchatdb<a class="headerlink" href="#pypath-core-annot-cellchatdb" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.core.annot.Cellchatdb">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.core.annot.</span></span><span class="sig-name descname"><span class="pre">Cellchatdb</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#Cellchatdb"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.Cellchatdb" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <a class="reference internal" href="pypath.core.annot.AnnotationBase.html#pypath.core.annot.AnnotationBase" title="pypath.core.annot.AnnotationBase"><code class="xref py py-class docutils literal notranslate"><span class="pre">AnnotationBase</span></code></a></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cellchatdb.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#Cellchatdb.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.Cellchatdb.__init__" title="Link to this definition">§</a></dt>
+<dd><p>Represents annotations for a set of proteins.
+Loads the data from the original resource and provides methods
+to query the annotations.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>name</strong> (<em>str</em>) – A custom name for the annotation resource.</p></li>
+<li><p><strong>ncbi_tax_id</strong> (<em>int</em>) – NCBI Taxonomy identifier.</p></li>
+<li><p><strong>input_method</strong> (<em>callable</em><em>,</em><em>str</em>) – Either a callable or the name of a method in any submodules of
+the <code class="docutils literal notranslate"><span class="pre">pypath.inputs</span></code>  module. Should return a dict with
+UniProt IDs as keys or an object suitable for <code class="docutils literal notranslate"><span class="pre">process_method</span></code>.</p></li>
+<li><p><strong>input_args</strong> (<em>dict</em>) – Arguments for the <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Cellchatdb.__init__" title="pypath.core.annot.Cellchatdb.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>(**kwargs)</p></td>
+<td><p>Represents annotations for a set of proteins.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Cellchatdb.add_complexes_by_inference" title="pypath.core.annot.Cellchatdb.add_complexes_by_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">add_complexes_by_inference</span></code></a>([complexes])</p></td>
+<td><p>Creates complex annotations by in silico inference and adds them to this annotation set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Cellchatdb.all_complexes" title="pypath.core.annot.Cellchatdb.all_complexes"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_complexes</span></code></a>()</p></td>
+<td><p>All protein complexes annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Cellchatdb.all_entities" title="pypath.core.annot.Cellchatdb.all_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_entities</span></code></a>([entity_types])</p></td>
+<td><p>All entities annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Cellchatdb.all_mirnas" title="pypath.core.annot.Cellchatdb.all_mirnas"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_mirnas</span></code></a>()</p></td>
+<td><p>All miRNAs annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Cellchatdb.all_proteins" title="pypath.core.annot.Cellchatdb.all_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_proteins</span></code></a>()</p></td>
+<td><p>All UniProt IDs annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Cellchatdb.all_refs" title="pypath.core.annot.Cellchatdb.all_refs"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_refs</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Cellchatdb.annotate_complex" title="pypath.core.annot.Cellchatdb.annotate_complex"><code class="xref py py-obj docutils literal notranslate"><span class="pre">annotate_complex</span></code></a>(cplex)</p></td>
+<td><p>Infers annotations for a single complex.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Cellchatdb.browse" title="pypath.core.annot.Cellchatdb.browse"><code class="xref py py-obj docutils literal notranslate"><span class="pre">browse</span></code></a>([field, start])</p></td>
+<td><p>Print gene information as a table.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Cellchatdb.complex_inference" title="pypath.core.annot.Cellchatdb.complex_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">complex_inference</span></code></a>([complexes])</p></td>
+<td><p>Annotates all complexes in <cite>complexes</cite>, by default in the default complex database (existing in the <cite>complex</cite> module or generated on demand according to the module's current settings).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Cellchatdb.coverage" title="pypath.core.annot.Cellchatdb.coverage"><code class="xref py py-obj docutils literal notranslate"><span class="pre">coverage</span></code></a>(other)</p></td>
+<td><p>Calculates the coverage of the annotation i.e. the proportion of entities having at least one record in this annotation resource for an arbitrary set of entities.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Cellchatdb.curation_effort" title="pypath.core.annot.Cellchatdb.curation_effort"><code class="xref py py-obj docutils literal notranslate"><span class="pre">curation_effort</span></code></a>()</p></td>
+<td><p>Counts the reference-record pairs.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">from_dump</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_entity_type</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Cellchatdb.get_names" title="pypath.core.annot.Cellchatdb.get_names"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_names</span></code></a>()</p></td>
+<td><p>Returns the list of field names in the records.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Cellchatdb.get_reference_set" title="pypath.core.annot.Cellchatdb.get_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_reference_set</span></code></a>([proteins, complexes, ...])</p></td>
+<td><p>Retrieves the reference set i.e. the set of all entities which potentially have annotation in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Cellchatdb.get_subset" title="pypath.core.annot.Cellchatdb.get_subset"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Cellchatdb.get_subset_bool_array" title="pypath.core.annot.Cellchatdb.get_subset_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset_bool_array</span></code></a>([reference_set])</p></td>
+<td><p>Returns a boolean vector with True and False values for each entity in the reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Cellchatdb.get_values" title="pypath.core.annot.Cellchatdb.get_values"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_values</span></code></a>(name[, exclude_none])</p></td>
+<td><p>Returns the set of all possible values of a field.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_complex</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_mirna</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_protein</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Cellchatdb.labels" title="pypath.core.annot.Cellchatdb.labels"><code class="xref py py-obj docutils literal notranslate"><span class="pre">labels</span></code></a>([method])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Cellchatdb.load" title="pypath.core.annot.Cellchatdb.load"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load</span></code></a>()</p></td>
+<td><p>Loads the annotation data by calling the input method.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Cellchatdb.load_data" title="pypath.core.annot.Cellchatdb.load_data"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_data</span></code></a>()</p></td>
+<td><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Cellchatdb.load_proteins" title="pypath.core.annot.Cellchatdb.load_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_proteins</span></code></a>()</p></td>
+<td><p>Retrieves a set of all UniProt IDs to have a base set of the entire proteome.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Cellchatdb.make_df" title="pypath.core.annot.Cellchatdb.make_df"><code class="xref py py-obj docutils literal notranslate"><span class="pre">make_df</span></code></a>([rebuild])</p></td>
+<td><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complex_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Cellchatdb.numof_entities" title="pypath.core.annot.Cellchatdb.numof_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_entities</span></code></a>()</p></td>
+<td><p>The number of annotated entities in the resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirna_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirnas</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_protein_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_proteins</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Cellchatdb.numof_records" title="pypath.core.annot.Cellchatdb.numof_records"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_records</span></code></a>([entity_types])</p></td>
+<td><p>The total number of annotation records.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Cellchatdb.numof_references" title="pypath.core.annot.Cellchatdb.numof_references"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_references</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Cellchatdb.process" title="pypath.core.annot.Cellchatdb.process"><code class="xref py py-obj docutils literal notranslate"><span class="pre">process</span></code></a>()</p></td>
+<td><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">proportion</span></code>(other)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Cellchatdb.reload" title="pypath.core.annot.Cellchatdb.reload"><code class="xref py py-obj docutils literal notranslate"><span class="pre">reload</span></code></a>()</p></td>
+<td><p>Reloads the object from the module level.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">save_to_pickle</span></code>(pickle_file)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Cellchatdb.select" title="pypath.core.annot.Cellchatdb.select"><code class="xref py py-obj docutils literal notranslate"><span class="pre">select</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Cellchatdb.set_method" title="pypath.core.annot.Cellchatdb.set_method"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_method</span></code></a>()</p></td>
+<td><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if necessary.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Cellchatdb.set_reference_set" title="pypath.core.annot.Cellchatdb.set_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_reference_set</span></code></a>()</p></td>
+<td><p>Assigns the reference set to the :py:attr``reference_set`` attribute.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Cellchatdb.show" title="pypath.core.annot.Cellchatdb.show"><code class="xref py py-obj docutils literal notranslate"><span class="pre">show</span></code></a>([method, table_param])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic information from the UniProt datasheets.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Cellchatdb.subset_intersection" title="pypath.core.annot.Cellchatdb.subset_intersection"><code class="xref py py-obj docutils literal notranslate"><span class="pre">subset_intersection</span></code></a>(universe, **kwargs)</p></td>
+<td><p>Calculates the proportion of entities in a subset occuring in the set <code class="docutils literal notranslate"><span class="pre">universe</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Cellchatdb.to_array" title="pypath.core.annot.Cellchatdb.to_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_array</span></code></a>([reference_set, use_fields])</p></td>
+<td><p>Returns an entity vs feature array.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Cellchatdb.to_bool_array" title="pypath.core.annot.Cellchatdb.to_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_bool_array</span></code></a>(reference_set)</p></td>
+<td><p>Returns a presence/absence boolean array for a reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Cellchatdb.to_set" title="pypath.core.annot.Cellchatdb.to_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_set</span></code></a>()</p></td>
+<td><p>Returns the entities present in this annotation resource as a set.</p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Attributes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_fields</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">summary</span></code></p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cellchatdb.add_complexes_by_inference">
+<span class="sig-name descname"><span class="pre">add_complexes_by_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cellchatdb.add_complexes_by_inference" title="Link to this definition">§</a></dt>
+<dd><p>Creates complex annotations by in silico inference and adds them
+to this annotation set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cellchatdb.all_complexes">
+<span class="sig-name descname"><span class="pre">all_complexes</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cellchatdb.all_complexes" title="Link to this definition">§</a></dt>
+<dd><p>All protein complexes annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cellchatdb.all_entities">
+<span class="sig-name descname"><span class="pre">all_entities</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cellchatdb.all_entities" title="Link to this definition">§</a></dt>
+<dd><p>All entities annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cellchatdb.all_mirnas">
+<span class="sig-name descname"><span class="pre">all_mirnas</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cellchatdb.all_mirnas" title="Link to this definition">§</a></dt>
+<dd><p>All miRNAs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cellchatdb.all_proteins">
+<span class="sig-name descname"><span class="pre">all_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cellchatdb.all_proteins" title="Link to this definition">§</a></dt>
+<dd><p>All UniProt IDs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cellchatdb.all_refs">
+<span class="sig-name descname"><span class="pre">all_refs</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cellchatdb.all_refs" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects the references
+across all records. Returns <em>list</em>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cellchatdb.annotate_complex">
+<span class="sig-name descname"><span class="pre">annotate_complex</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cplex</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cellchatdb.annotate_complex" title="Link to this definition">§</a></dt>
+<dd><p>Infers annotations for a single complex.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cellchatdb.browse">
+<span class="sig-name descname"><span class="pre">browse</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">field</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">start</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cellchatdb.browse" title="Link to this definition">§</a></dt>
+<dd><p>Print gene information as a table.</p>
+<p>Presents information about annotation categories as ascii tables
+printed in the terminal. If one category provided, prints one table.
+If multiple categories provided, prints a table for each of them one
+by one proceeding to the next one once you hit return. If no categories
+provided goes through all levels of the primary category.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>field:</dt><dd><p>The field to browse categories by.</p>
+<ul class="simple">
+<li><p>If None the primary field will be selected.
+If this annotation resource doesn’t have fields, all proteins
+will be presented as one single category.</p></li>
+<li><p>If a string it will be considered a field name and it will
+browse through all levels of this field.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">list</span></code>, set or tuple, it will be considered either a
+<code class="docutils literal notranslate"><span class="pre">list</span></code> of field names or a list of values from the primary
+field. In the former case all combinations of the values of
+the fields will be presented, in the latter case the browsing
+will be limited to the levels of the primary field contained
+in <code class="docutils literal notranslate"><span class="pre">field</span></code>.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">dict</span></code>, keys are supposed to be field names and values
+as list of levels. If any of the values are None, all levels
+from that field will be used.</p></li>
+</ul>
+</dd>
+<dt>start:</dt><dd><p>Start browsing from this category. E.g. if there are 500
+categories and start is 250 it will skip everything before the
+250th.</p>
+</dd>
+<dt>kwargs:</dt><dd><p>Passed to <code class="docutils literal notranslate"><span class="pre">pypath.utils.uniprot.info</span></code>.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cellchatdb.complex_inference">
+<span class="sig-name descname"><span class="pre">complex_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cellchatdb.complex_inference" title="Link to this definition">§</a></dt>
+<dd><p>Annotates all complexes in <cite>complexes</cite>, by default in the default
+complex database (existing in the <cite>complex</cite> module or generated
+on demand according to the module’s current settings).</p>
+<dl class="field-list simple">
+<dt class="field-odd">Returns<span class="colon">:</span></dt>
+<dd class="field-odd"><p><ul class="simple">
+<li><p><em>Dict with complexes as keys and sets of annotations as values.</em></p></li>
+<li><p><em>Complexes with no valid information in this annotation resource</em></p></li>
+<li><p><em>won’t be in the dict.</em></p></li>
+</ul>
+</p>
+</dd>
+<dt class="field-even">Parameters<span class="colon">:</span></dt>
+<dd class="field-even"><p><strong>complexes</strong> (<em>iterable</em>) – Iterable yielding complexes.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cellchatdb.coverage">
+<span class="sig-name descname"><span class="pre">coverage</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">other</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cellchatdb.coverage" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the coverage of the annotation i.e. the proportion of
+entities having at least one record in this annotation resource
+for an arbitrary set of entities.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cellchatdb.curation_effort">
+<span class="sig-name descname"><span class="pre">curation_effort</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cellchatdb.curation_effort" title="Link to this definition">§</a></dt>
+<dd><p>Counts the reference-record pairs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cellchatdb.get_names">
+<span class="sig-name descname"><span class="pre">get_names</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cellchatdb.get_names" title="Link to this definition">§</a></dt>
+<dd><p>Returns the list of field names in the records. The annotation
+consists of uniform records and each entity might be annotated
+with one or more records. Each record is a tuple of fields, for
+example <code class="docutils literal notranslate"><span class="pre">('cell_type',</span> <span class="pre">'expression_level',</span> <span class="pre">'score')</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cellchatdb.get_reference_set">
+<em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">get_reference_set</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">proteins</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">swissprot_only</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cellchatdb.get_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the reference set i.e. the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cellchatdb.get_subset">
+<span class="sig-name descname"><span class="pre">get_subset</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cellchatdb.get_subset" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cellchatdb.get_subset_bool_array">
+<span class="sig-name descname"><span class="pre">get_subset_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cellchatdb.get_subset_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a boolean vector with True and False values for each entity
+in the reference set. The values represent presence absence data
+in the simplest case, but by providing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> any kind of matching
+and filtering is possible. <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> are passed to the <code class="docutils literal notranslate"><span class="pre">select</span></code>
+method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cellchatdb.get_values">
+<span class="sig-name descname"><span class="pre">get_values</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">exclude_none</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cellchatdb.get_values" title="Link to this definition">§</a></dt>
+<dd><p>Returns the set of all possible values of a field. E.g. if the
+records of this annotation have a field <code class="docutils literal notranslate"><span class="pre">cell_type</span></code> then calling
+this method can tell you that across all records the values of
+this field might be <code class="docutils literal notranslate"><span class="pre">{'macrophage',</span> <span class="pre">'epithelial_cell',</span> <span class="pre">...}</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cellchatdb.labels">
+<span class="sig-name descname"><span class="pre">labels</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cellchatdb.labels" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cellchatdb.load">
+<span class="sig-name descname"><span class="pre">load</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cellchatdb.load" title="Link to this definition">§</a></dt>
+<dd><p>Loads the annotation data by calling the input method.
+Infers annotations for complexes in the complex database if
+py:attr:<code class="docutils literal notranslate"><span class="pre">infer_complexes</span></code> is True.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cellchatdb.load_data">
+<span class="sig-name descname"><span class="pre">load_data</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cellchatdb.load_data" title="Link to this definition">§</a></dt>
+<dd><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cellchatdb.load_proteins">
+<span class="sig-name descname"><span class="pre">load_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cellchatdb.load_proteins" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a set of all UniProt IDs to have a base set of the entire
+proteome.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cellchatdb.make_df">
+<span class="sig-name descname"><span class="pre">make_df</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">rebuild</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cellchatdb.make_df" title="Link to this definition">§</a></dt>
+<dd><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.
+The data frame will be assigned to :py:attr``df``.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cellchatdb.numof_entities">
+<span class="sig-name descname"><span class="pre">numof_entities</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cellchatdb.numof_entities" title="Link to this definition">§</a></dt>
+<dd><p>The number of annotated entities in the resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cellchatdb.numof_records">
+<span class="sig-name descname"><span class="pre">numof_records</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cellchatdb.numof_records" title="Link to this definition">§</a></dt>
+<dd><p>The total number of annotation records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cellchatdb.numof_references">
+<span class="sig-name descname"><span class="pre">numof_references</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cellchatdb.numof_references" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects and counts the
+references across all records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cellchatdb.process">
+<span class="sig-name descname"><span class="pre">process</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cellchatdb.process" title="Link to this definition">§</a></dt>
+<dd><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cellchatdb.reload">
+<span class="sig-name descname"><span class="pre">reload</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cellchatdb.reload" title="Link to this definition">§</a></dt>
+<dd><p>Reloads the object from the module level.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cellchatdb.select">
+<span class="sig-name descname"><span class="pre">select</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cellchatdb.select" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cellchatdb.set_method">
+<span class="sig-name descname"><span class="pre">set_method</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cellchatdb.set_method" title="Link to this definition">§</a></dt>
+<dd><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if
+necessary.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cellchatdb.set_reference_set">
+<span class="sig-name descname"><span class="pre">set_reference_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cellchatdb.set_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Assigns the reference set to the :py:attr``reference_set`` attribute.
+The reference set is the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cellchatdb.show">
+<span class="sig-name descname"><span class="pre">show</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">table_param</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cellchatdb.show" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic
+information from the UniProt datasheets.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cellchatdb.subset_intersection">
+<span class="sig-name descname"><span class="pre">subset_intersection</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">universe</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cellchatdb.subset_intersection" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the proportion of entities in a subset occuring in the
+set <code class="docutils literal notranslate"><span class="pre">universe</span></code>. The subset is selected by passing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> to the
+<code class="docutils literal notranslate"><span class="pre">select</span></code> method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cellchatdb.to_array">
+<span class="sig-name descname"><span class="pre">to_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_fields</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cellchatdb.to_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns an entity vs feature array. In case of more complex
+annotations this might be huge.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cellchatdb.to_bool_array">
+<span class="sig-name descname"><span class="pre">to_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cellchatdb.to_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a presence/absence boolean array for a reference set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cellchatdb.to_set">
+<span class="sig-name descname"><span class="pre">to_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cellchatdb.to_set" title="Link to this definition">§</a></dt>
+<dd><p>Returns the entities present in this annotation resource as a set.</p>
+</dd></dl>
+
+</dd></dl>
+
+</section>
+
+
+                </article>
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+  <section id="pypath-core-annot-cellchatdbcomplex">
+<h1>pypath.core.annot.CellchatdbComplex<a class="headerlink" href="#pypath-core-annot-cellchatdbcomplex" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.core.annot.CellchatdbComplex">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.core.annot.</span></span><span class="sig-name descname"><span class="pre">CellchatdbComplex</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#CellchatdbComplex"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.CellchatdbComplex" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <a class="reference internal" href="pypath.core.annot.AnnotationBase.html#pypath.core.annot.AnnotationBase" title="pypath.core.annot.AnnotationBase"><code class="xref py py-class docutils literal notranslate"><span class="pre">AnnotationBase</span></code></a></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellchatdbComplex.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#CellchatdbComplex.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.CellchatdbComplex.__init__" title="Link to this definition">§</a></dt>
+<dd><p>Represents annotations for a set of proteins.
+Loads the data from the original resource and provides methods
+to query the annotations.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>name</strong> (<em>str</em>) – A custom name for the annotation resource.</p></li>
+<li><p><strong>ncbi_tax_id</strong> (<em>int</em>) – NCBI Taxonomy identifier.</p></li>
+<li><p><strong>input_method</strong> (<em>callable</em><em>,</em><em>str</em>) – Either a callable or the name of a method in any submodules of
+the <code class="docutils literal notranslate"><span class="pre">pypath.inputs</span></code>  module. Should return a dict with
+UniProt IDs as keys or an object suitable for <code class="docutils literal notranslate"><span class="pre">process_method</span></code>.</p></li>
+<li><p><strong>input_args</strong> (<em>dict</em>) – Arguments for the <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CellchatdbComplex.__init__" title="pypath.core.annot.CellchatdbComplex.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>(**kwargs)</p></td>
+<td><p>Represents annotations for a set of proteins.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CellchatdbComplex.add_complexes_by_inference" title="pypath.core.annot.CellchatdbComplex.add_complexes_by_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">add_complexes_by_inference</span></code></a>([complexes])</p></td>
+<td><p>Creates complex annotations by in silico inference and adds them to this annotation set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CellchatdbComplex.all_complexes" title="pypath.core.annot.CellchatdbComplex.all_complexes"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_complexes</span></code></a>()</p></td>
+<td><p>All protein complexes annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CellchatdbComplex.all_entities" title="pypath.core.annot.CellchatdbComplex.all_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_entities</span></code></a>([entity_types])</p></td>
+<td><p>All entities annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CellchatdbComplex.all_mirnas" title="pypath.core.annot.CellchatdbComplex.all_mirnas"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_mirnas</span></code></a>()</p></td>
+<td><p>All miRNAs annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CellchatdbComplex.all_proteins" title="pypath.core.annot.CellchatdbComplex.all_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_proteins</span></code></a>()</p></td>
+<td><p>All UniProt IDs annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CellchatdbComplex.all_refs" title="pypath.core.annot.CellchatdbComplex.all_refs"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_refs</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CellchatdbComplex.annotate_complex" title="pypath.core.annot.CellchatdbComplex.annotate_complex"><code class="xref py py-obj docutils literal notranslate"><span class="pre">annotate_complex</span></code></a>(cplex)</p></td>
+<td><p>Infers annotations for a single complex.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CellchatdbComplex.browse" title="pypath.core.annot.CellchatdbComplex.browse"><code class="xref py py-obj docutils literal notranslate"><span class="pre">browse</span></code></a>([field, start])</p></td>
+<td><p>Print gene information as a table.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CellchatdbComplex.complex_inference" title="pypath.core.annot.CellchatdbComplex.complex_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">complex_inference</span></code></a>([complexes])</p></td>
+<td><p>Annotates all complexes in <cite>complexes</cite>, by default in the default complex database (existing in the <cite>complex</cite> module or generated on demand according to the module's current settings).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CellchatdbComplex.coverage" title="pypath.core.annot.CellchatdbComplex.coverage"><code class="xref py py-obj docutils literal notranslate"><span class="pre">coverage</span></code></a>(other)</p></td>
+<td><p>Calculates the coverage of the annotation i.e. the proportion of entities having at least one record in this annotation resource for an arbitrary set of entities.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CellchatdbComplex.curation_effort" title="pypath.core.annot.CellchatdbComplex.curation_effort"><code class="xref py py-obj docutils literal notranslate"><span class="pre">curation_effort</span></code></a>()</p></td>
+<td><p>Counts the reference-record pairs.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">from_dump</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_entity_type</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CellchatdbComplex.get_names" title="pypath.core.annot.CellchatdbComplex.get_names"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_names</span></code></a>()</p></td>
+<td><p>Returns the list of field names in the records.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CellchatdbComplex.get_reference_set" title="pypath.core.annot.CellchatdbComplex.get_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_reference_set</span></code></a>([proteins, complexes, ...])</p></td>
+<td><p>Retrieves the reference set i.e. the set of all entities which potentially have annotation in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CellchatdbComplex.get_subset" title="pypath.core.annot.CellchatdbComplex.get_subset"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CellchatdbComplex.get_subset_bool_array" title="pypath.core.annot.CellchatdbComplex.get_subset_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset_bool_array</span></code></a>([reference_set])</p></td>
+<td><p>Returns a boolean vector with True and False values for each entity in the reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CellchatdbComplex.get_values" title="pypath.core.annot.CellchatdbComplex.get_values"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_values</span></code></a>(name[, exclude_none])</p></td>
+<td><p>Returns the set of all possible values of a field.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_complex</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_mirna</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_protein</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CellchatdbComplex.labels" title="pypath.core.annot.CellchatdbComplex.labels"><code class="xref py py-obj docutils literal notranslate"><span class="pre">labels</span></code></a>([method])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CellchatdbComplex.load" title="pypath.core.annot.CellchatdbComplex.load"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load</span></code></a>()</p></td>
+<td><p>Loads the annotation data by calling the input method.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CellchatdbComplex.load_data" title="pypath.core.annot.CellchatdbComplex.load_data"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_data</span></code></a>()</p></td>
+<td><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CellchatdbComplex.load_proteins" title="pypath.core.annot.CellchatdbComplex.load_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_proteins</span></code></a>()</p></td>
+<td><p>Retrieves a set of all UniProt IDs to have a base set of the entire proteome.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CellchatdbComplex.make_df" title="pypath.core.annot.CellchatdbComplex.make_df"><code class="xref py py-obj docutils literal notranslate"><span class="pre">make_df</span></code></a>([rebuild])</p></td>
+<td><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complex_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CellchatdbComplex.numof_entities" title="pypath.core.annot.CellchatdbComplex.numof_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_entities</span></code></a>()</p></td>
+<td><p>The number of annotated entities in the resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirna_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirnas</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_protein_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_proteins</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CellchatdbComplex.numof_records" title="pypath.core.annot.CellchatdbComplex.numof_records"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_records</span></code></a>([entity_types])</p></td>
+<td><p>The total number of annotation records.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CellchatdbComplex.numof_references" title="pypath.core.annot.CellchatdbComplex.numof_references"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_references</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CellchatdbComplex.process" title="pypath.core.annot.CellchatdbComplex.process"><code class="xref py py-obj docutils literal notranslate"><span class="pre">process</span></code></a>()</p></td>
+<td><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">proportion</span></code>(other)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CellchatdbComplex.reload" title="pypath.core.annot.CellchatdbComplex.reload"><code class="xref py py-obj docutils literal notranslate"><span class="pre">reload</span></code></a>()</p></td>
+<td><p>Reloads the object from the module level.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">save_to_pickle</span></code>(pickle_file)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CellchatdbComplex.select" title="pypath.core.annot.CellchatdbComplex.select"><code class="xref py py-obj docutils literal notranslate"><span class="pre">select</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CellchatdbComplex.set_method" title="pypath.core.annot.CellchatdbComplex.set_method"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_method</span></code></a>()</p></td>
+<td><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if necessary.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CellchatdbComplex.set_reference_set" title="pypath.core.annot.CellchatdbComplex.set_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_reference_set</span></code></a>()</p></td>
+<td><p>Assigns the reference set to the :py:attr``reference_set`` attribute.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CellchatdbComplex.show" title="pypath.core.annot.CellchatdbComplex.show"><code class="xref py py-obj docutils literal notranslate"><span class="pre">show</span></code></a>([method, table_param])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic information from the UniProt datasheets.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CellchatdbComplex.subset_intersection" title="pypath.core.annot.CellchatdbComplex.subset_intersection"><code class="xref py py-obj docutils literal notranslate"><span class="pre">subset_intersection</span></code></a>(universe, **kwargs)</p></td>
+<td><p>Calculates the proportion of entities in a subset occuring in the set <code class="docutils literal notranslate"><span class="pre">universe</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CellchatdbComplex.to_array" title="pypath.core.annot.CellchatdbComplex.to_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_array</span></code></a>([reference_set, use_fields])</p></td>
+<td><p>Returns an entity vs feature array.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CellchatdbComplex.to_bool_array" title="pypath.core.annot.CellchatdbComplex.to_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_bool_array</span></code></a>(reference_set)</p></td>
+<td><p>Returns a presence/absence boolean array for a reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CellchatdbComplex.to_set" title="pypath.core.annot.CellchatdbComplex.to_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_set</span></code></a>()</p></td>
+<td><p>Returns the entities present in this annotation resource as a set.</p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Attributes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_fields</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">summary</span></code></p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellchatdbComplex.add_complexes_by_inference">
+<span class="sig-name descname"><span class="pre">add_complexes_by_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellchatdbComplex.add_complexes_by_inference" title="Link to this definition">§</a></dt>
+<dd><p>Creates complex annotations by in silico inference and adds them
+to this annotation set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellchatdbComplex.all_complexes">
+<span class="sig-name descname"><span class="pre">all_complexes</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellchatdbComplex.all_complexes" title="Link to this definition">§</a></dt>
+<dd><p>All protein complexes annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellchatdbComplex.all_entities">
+<span class="sig-name descname"><span class="pre">all_entities</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellchatdbComplex.all_entities" title="Link to this definition">§</a></dt>
+<dd><p>All entities annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellchatdbComplex.all_mirnas">
+<span class="sig-name descname"><span class="pre">all_mirnas</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellchatdbComplex.all_mirnas" title="Link to this definition">§</a></dt>
+<dd><p>All miRNAs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellchatdbComplex.all_proteins">
+<span class="sig-name descname"><span class="pre">all_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellchatdbComplex.all_proteins" title="Link to this definition">§</a></dt>
+<dd><p>All UniProt IDs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellchatdbComplex.all_refs">
+<span class="sig-name descname"><span class="pre">all_refs</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellchatdbComplex.all_refs" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects the references
+across all records. Returns <em>list</em>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellchatdbComplex.annotate_complex">
+<span class="sig-name descname"><span class="pre">annotate_complex</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cplex</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellchatdbComplex.annotate_complex" title="Link to this definition">§</a></dt>
+<dd><p>Infers annotations for a single complex.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellchatdbComplex.browse">
+<span class="sig-name descname"><span class="pre">browse</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">field</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">start</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellchatdbComplex.browse" title="Link to this definition">§</a></dt>
+<dd><p>Print gene information as a table.</p>
+<p>Presents information about annotation categories as ascii tables
+printed in the terminal. If one category provided, prints one table.
+If multiple categories provided, prints a table for each of them one
+by one proceeding to the next one once you hit return. If no categories
+provided goes through all levels of the primary category.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>field:</dt><dd><p>The field to browse categories by.</p>
+<ul class="simple">
+<li><p>If None the primary field will be selected.
+If this annotation resource doesn’t have fields, all proteins
+will be presented as one single category.</p></li>
+<li><p>If a string it will be considered a field name and it will
+browse through all levels of this field.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">list</span></code>, set or tuple, it will be considered either a
+<code class="docutils literal notranslate"><span class="pre">list</span></code> of field names or a list of values from the primary
+field. In the former case all combinations of the values of
+the fields will be presented, in the latter case the browsing
+will be limited to the levels of the primary field contained
+in <code class="docutils literal notranslate"><span class="pre">field</span></code>.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">dict</span></code>, keys are supposed to be field names and values
+as list of levels. If any of the values are None, all levels
+from that field will be used.</p></li>
+</ul>
+</dd>
+<dt>start:</dt><dd><p>Start browsing from this category. E.g. if there are 500
+categories and start is 250 it will skip everything before the
+250th.</p>
+</dd>
+<dt>kwargs:</dt><dd><p>Passed to <code class="docutils literal notranslate"><span class="pre">pypath.utils.uniprot.info</span></code>.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellchatdbComplex.complex_inference">
+<span class="sig-name descname"><span class="pre">complex_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellchatdbComplex.complex_inference" title="Link to this definition">§</a></dt>
+<dd><p>Annotates all complexes in <cite>complexes</cite>, by default in the default
+complex database (existing in the <cite>complex</cite> module or generated
+on demand according to the module’s current settings).</p>
+<dl class="field-list simple">
+<dt class="field-odd">Returns<span class="colon">:</span></dt>
+<dd class="field-odd"><p><ul class="simple">
+<li><p><em>Dict with complexes as keys and sets of annotations as values.</em></p></li>
+<li><p><em>Complexes with no valid information in this annotation resource</em></p></li>
+<li><p><em>won’t be in the dict.</em></p></li>
+</ul>
+</p>
+</dd>
+<dt class="field-even">Parameters<span class="colon">:</span></dt>
+<dd class="field-even"><p><strong>complexes</strong> (<em>iterable</em>) – Iterable yielding complexes.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellchatdbComplex.coverage">
+<span class="sig-name descname"><span class="pre">coverage</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">other</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellchatdbComplex.coverage" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the coverage of the annotation i.e. the proportion of
+entities having at least one record in this annotation resource
+for an arbitrary set of entities.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellchatdbComplex.curation_effort">
+<span class="sig-name descname"><span class="pre">curation_effort</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellchatdbComplex.curation_effort" title="Link to this definition">§</a></dt>
+<dd><p>Counts the reference-record pairs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellchatdbComplex.get_names">
+<span class="sig-name descname"><span class="pre">get_names</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellchatdbComplex.get_names" title="Link to this definition">§</a></dt>
+<dd><p>Returns the list of field names in the records. The annotation
+consists of uniform records and each entity might be annotated
+with one or more records. Each record is a tuple of fields, for
+example <code class="docutils literal notranslate"><span class="pre">('cell_type',</span> <span class="pre">'expression_level',</span> <span class="pre">'score')</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellchatdbComplex.get_reference_set">
+<em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">get_reference_set</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">proteins</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">swissprot_only</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellchatdbComplex.get_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the reference set i.e. the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellchatdbComplex.get_subset">
+<span class="sig-name descname"><span class="pre">get_subset</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellchatdbComplex.get_subset" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellchatdbComplex.get_subset_bool_array">
+<span class="sig-name descname"><span class="pre">get_subset_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellchatdbComplex.get_subset_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a boolean vector with True and False values for each entity
+in the reference set. The values represent presence absence data
+in the simplest case, but by providing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> any kind of matching
+and filtering is possible. <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> are passed to the <code class="docutils literal notranslate"><span class="pre">select</span></code>
+method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellchatdbComplex.get_values">
+<span class="sig-name descname"><span class="pre">get_values</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">exclude_none</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellchatdbComplex.get_values" title="Link to this definition">§</a></dt>
+<dd><p>Returns the set of all possible values of a field. E.g. if the
+records of this annotation have a field <code class="docutils literal notranslate"><span class="pre">cell_type</span></code> then calling
+this method can tell you that across all records the values of
+this field might be <code class="docutils literal notranslate"><span class="pre">{'macrophage',</span> <span class="pre">'epithelial_cell',</span> <span class="pre">...}</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellchatdbComplex.labels">
+<span class="sig-name descname"><span class="pre">labels</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellchatdbComplex.labels" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellchatdbComplex.load">
+<span class="sig-name descname"><span class="pre">load</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellchatdbComplex.load" title="Link to this definition">§</a></dt>
+<dd><p>Loads the annotation data by calling the input method.
+Infers annotations for complexes in the complex database if
+py:attr:<code class="docutils literal notranslate"><span class="pre">infer_complexes</span></code> is True.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellchatdbComplex.load_data">
+<span class="sig-name descname"><span class="pre">load_data</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellchatdbComplex.load_data" title="Link to this definition">§</a></dt>
+<dd><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellchatdbComplex.load_proteins">
+<span class="sig-name descname"><span class="pre">load_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellchatdbComplex.load_proteins" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a set of all UniProt IDs to have a base set of the entire
+proteome.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellchatdbComplex.make_df">
+<span class="sig-name descname"><span class="pre">make_df</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">rebuild</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellchatdbComplex.make_df" title="Link to this definition">§</a></dt>
+<dd><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.
+The data frame will be assigned to :py:attr``df``.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellchatdbComplex.numof_entities">
+<span class="sig-name descname"><span class="pre">numof_entities</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellchatdbComplex.numof_entities" title="Link to this definition">§</a></dt>
+<dd><p>The number of annotated entities in the resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellchatdbComplex.numof_records">
+<span class="sig-name descname"><span class="pre">numof_records</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellchatdbComplex.numof_records" title="Link to this definition">§</a></dt>
+<dd><p>The total number of annotation records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellchatdbComplex.numof_references">
+<span class="sig-name descname"><span class="pre">numof_references</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellchatdbComplex.numof_references" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects and counts the
+references across all records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellchatdbComplex.process">
+<span class="sig-name descname"><span class="pre">process</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellchatdbComplex.process" title="Link to this definition">§</a></dt>
+<dd><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellchatdbComplex.reload">
+<span class="sig-name descname"><span class="pre">reload</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellchatdbComplex.reload" title="Link to this definition">§</a></dt>
+<dd><p>Reloads the object from the module level.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellchatdbComplex.select">
+<span class="sig-name descname"><span class="pre">select</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellchatdbComplex.select" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellchatdbComplex.set_method">
+<span class="sig-name descname"><span class="pre">set_method</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellchatdbComplex.set_method" title="Link to this definition">§</a></dt>
+<dd><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if
+necessary.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellchatdbComplex.set_reference_set">
+<span class="sig-name descname"><span class="pre">set_reference_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellchatdbComplex.set_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Assigns the reference set to the :py:attr``reference_set`` attribute.
+The reference set is the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellchatdbComplex.show">
+<span class="sig-name descname"><span class="pre">show</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">table_param</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellchatdbComplex.show" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic
+information from the UniProt datasheets.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellchatdbComplex.subset_intersection">
+<span class="sig-name descname"><span class="pre">subset_intersection</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">universe</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellchatdbComplex.subset_intersection" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the proportion of entities in a subset occuring in the
+set <code class="docutils literal notranslate"><span class="pre">universe</span></code>. The subset is selected by passing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> to the
+<code class="docutils literal notranslate"><span class="pre">select</span></code> method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellchatdbComplex.to_array">
+<span class="sig-name descname"><span class="pre">to_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_fields</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellchatdbComplex.to_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns an entity vs feature array. In case of more complex
+annotations this might be huge.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellchatdbComplex.to_bool_array">
+<span class="sig-name descname"><span class="pre">to_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellchatdbComplex.to_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a presence/absence boolean array for a reference set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellchatdbComplex.to_set">
+<span class="sig-name descname"><span class="pre">to_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellchatdbComplex.to_set" title="Link to this definition">§</a></dt>
+<dd><p>Returns the entities present in this annotation resource as a set.</p>
+</dd></dl>
+
+</dd></dl>
+
+</section>
+
+
+                </article>
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+  <section id="pypath-core-annot-cellinker">
+<h1>pypath.core.annot.Cellinker<a class="headerlink" href="#pypath-core-annot-cellinker" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.core.annot.Cellinker">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.core.annot.</span></span><span class="sig-name descname"><span class="pre">Cellinker</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#Cellinker"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.Cellinker" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <a class="reference internal" href="pypath.core.annot.AnnotationBase.html#pypath.core.annot.AnnotationBase" title="pypath.core.annot.AnnotationBase"><code class="xref py py-class docutils literal notranslate"><span class="pre">AnnotationBase</span></code></a></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cellinker.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#Cellinker.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.Cellinker.__init__" title="Link to this definition">§</a></dt>
+<dd><p>Represents annotations for a set of proteins.
+Loads the data from the original resource and provides methods
+to query the annotations.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>name</strong> (<em>str</em>) – A custom name for the annotation resource.</p></li>
+<li><p><strong>ncbi_tax_id</strong> (<em>int</em>) – NCBI Taxonomy identifier.</p></li>
+<li><p><strong>input_method</strong> (<em>callable</em><em>,</em><em>str</em>) – Either a callable or the name of a method in any submodules of
+the <code class="docutils literal notranslate"><span class="pre">pypath.inputs</span></code>  module. Should return a dict with
+UniProt IDs as keys or an object suitable for <code class="docutils literal notranslate"><span class="pre">process_method</span></code>.</p></li>
+<li><p><strong>input_args</strong> (<em>dict</em>) – Arguments for the <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Cellinker.__init__" title="pypath.core.annot.Cellinker.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>([ncbi_tax_id])</p></td>
+<td><p>Represents annotations for a set of proteins.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Cellinker.add_complexes_by_inference" title="pypath.core.annot.Cellinker.add_complexes_by_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">add_complexes_by_inference</span></code></a>([complexes])</p></td>
+<td><p>Creates complex annotations by in silico inference and adds them to this annotation set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Cellinker.all_complexes" title="pypath.core.annot.Cellinker.all_complexes"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_complexes</span></code></a>()</p></td>
+<td><p>All protein complexes annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Cellinker.all_entities" title="pypath.core.annot.Cellinker.all_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_entities</span></code></a>([entity_types])</p></td>
+<td><p>All entities annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Cellinker.all_mirnas" title="pypath.core.annot.Cellinker.all_mirnas"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_mirnas</span></code></a>()</p></td>
+<td><p>All miRNAs annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Cellinker.all_proteins" title="pypath.core.annot.Cellinker.all_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_proteins</span></code></a>()</p></td>
+<td><p>All UniProt IDs annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Cellinker.all_refs" title="pypath.core.annot.Cellinker.all_refs"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_refs</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Cellinker.annotate_complex" title="pypath.core.annot.Cellinker.annotate_complex"><code class="xref py py-obj docutils literal notranslate"><span class="pre">annotate_complex</span></code></a>(cplex)</p></td>
+<td><p>Infers annotations for a single complex.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Cellinker.browse" title="pypath.core.annot.Cellinker.browse"><code class="xref py py-obj docutils literal notranslate"><span class="pre">browse</span></code></a>([field, start])</p></td>
+<td><p>Print gene information as a table.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Cellinker.complex_inference" title="pypath.core.annot.Cellinker.complex_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">complex_inference</span></code></a>([complexes])</p></td>
+<td><p>Annotates all complexes in <cite>complexes</cite>, by default in the default complex database (existing in the <cite>complex</cite> module or generated on demand according to the module's current settings).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Cellinker.coverage" title="pypath.core.annot.Cellinker.coverage"><code class="xref py py-obj docutils literal notranslate"><span class="pre">coverage</span></code></a>(other)</p></td>
+<td><p>Calculates the coverage of the annotation i.e. the proportion of entities having at least one record in this annotation resource for an arbitrary set of entities.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Cellinker.curation_effort" title="pypath.core.annot.Cellinker.curation_effort"><code class="xref py py-obj docutils literal notranslate"><span class="pre">curation_effort</span></code></a>()</p></td>
+<td><p>Counts the reference-record pairs.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">from_dump</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_entity_type</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Cellinker.get_names" title="pypath.core.annot.Cellinker.get_names"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_names</span></code></a>()</p></td>
+<td><p>Returns the list of field names in the records.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Cellinker.get_reference_set" title="pypath.core.annot.Cellinker.get_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_reference_set</span></code></a>([proteins, complexes, ...])</p></td>
+<td><p>Retrieves the reference set i.e. the set of all entities which potentially have annotation in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Cellinker.get_subset" title="pypath.core.annot.Cellinker.get_subset"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Cellinker.get_subset_bool_array" title="pypath.core.annot.Cellinker.get_subset_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset_bool_array</span></code></a>([reference_set])</p></td>
+<td><p>Returns a boolean vector with True and False values for each entity in the reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Cellinker.get_values" title="pypath.core.annot.Cellinker.get_values"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_values</span></code></a>(name[, exclude_none])</p></td>
+<td><p>Returns the set of all possible values of a field.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_complex</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_mirna</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_protein</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Cellinker.labels" title="pypath.core.annot.Cellinker.labels"><code class="xref py py-obj docutils literal notranslate"><span class="pre">labels</span></code></a>([method])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Cellinker.load" title="pypath.core.annot.Cellinker.load"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load</span></code></a>()</p></td>
+<td><p>Loads the annotation data by calling the input method.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Cellinker.load_data" title="pypath.core.annot.Cellinker.load_data"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_data</span></code></a>()</p></td>
+<td><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Cellinker.load_proteins" title="pypath.core.annot.Cellinker.load_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_proteins</span></code></a>()</p></td>
+<td><p>Retrieves a set of all UniProt IDs to have a base set of the entire proteome.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Cellinker.make_df" title="pypath.core.annot.Cellinker.make_df"><code class="xref py py-obj docutils literal notranslate"><span class="pre">make_df</span></code></a>([rebuild])</p></td>
+<td><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complex_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Cellinker.numof_entities" title="pypath.core.annot.Cellinker.numof_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_entities</span></code></a>()</p></td>
+<td><p>The number of annotated entities in the resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirna_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirnas</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_protein_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_proteins</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Cellinker.numof_records" title="pypath.core.annot.Cellinker.numof_records"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_records</span></code></a>([entity_types])</p></td>
+<td><p>The total number of annotation records.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Cellinker.numof_references" title="pypath.core.annot.Cellinker.numof_references"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_references</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Cellinker.process" title="pypath.core.annot.Cellinker.process"><code class="xref py py-obj docutils literal notranslate"><span class="pre">process</span></code></a>()</p></td>
+<td><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">proportion</span></code>(other)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Cellinker.reload" title="pypath.core.annot.Cellinker.reload"><code class="xref py py-obj docutils literal notranslate"><span class="pre">reload</span></code></a>()</p></td>
+<td><p>Reloads the object from the module level.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">save_to_pickle</span></code>(pickle_file)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Cellinker.select" title="pypath.core.annot.Cellinker.select"><code class="xref py py-obj docutils literal notranslate"><span class="pre">select</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Cellinker.set_method" title="pypath.core.annot.Cellinker.set_method"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_method</span></code></a>()</p></td>
+<td><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if necessary.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Cellinker.set_reference_set" title="pypath.core.annot.Cellinker.set_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_reference_set</span></code></a>()</p></td>
+<td><p>Assigns the reference set to the :py:attr``reference_set`` attribute.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Cellinker.show" title="pypath.core.annot.Cellinker.show"><code class="xref py py-obj docutils literal notranslate"><span class="pre">show</span></code></a>([method, table_param])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic information from the UniProt datasheets.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Cellinker.subset_intersection" title="pypath.core.annot.Cellinker.subset_intersection"><code class="xref py py-obj docutils literal notranslate"><span class="pre">subset_intersection</span></code></a>(universe, **kwargs)</p></td>
+<td><p>Calculates the proportion of entities in a subset occuring in the set <code class="docutils literal notranslate"><span class="pre">universe</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Cellinker.to_array" title="pypath.core.annot.Cellinker.to_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_array</span></code></a>([reference_set, use_fields])</p></td>
+<td><p>Returns an entity vs feature array.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Cellinker.to_bool_array" title="pypath.core.annot.Cellinker.to_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_bool_array</span></code></a>(reference_set)</p></td>
+<td><p>Returns a presence/absence boolean array for a reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Cellinker.to_set" title="pypath.core.annot.Cellinker.to_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_set</span></code></a>()</p></td>
+<td><p>Returns the entities present in this annotation resource as a set.</p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Attributes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_fields</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">summary</span></code></p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cellinker.add_complexes_by_inference">
+<span class="sig-name descname"><span class="pre">add_complexes_by_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cellinker.add_complexes_by_inference" title="Link to this definition">§</a></dt>
+<dd><p>Creates complex annotations by in silico inference and adds them
+to this annotation set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cellinker.all_complexes">
+<span class="sig-name descname"><span class="pre">all_complexes</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cellinker.all_complexes" title="Link to this definition">§</a></dt>
+<dd><p>All protein complexes annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cellinker.all_entities">
+<span class="sig-name descname"><span class="pre">all_entities</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cellinker.all_entities" title="Link to this definition">§</a></dt>
+<dd><p>All entities annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cellinker.all_mirnas">
+<span class="sig-name descname"><span class="pre">all_mirnas</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cellinker.all_mirnas" title="Link to this definition">§</a></dt>
+<dd><p>All miRNAs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cellinker.all_proteins">
+<span class="sig-name descname"><span class="pre">all_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cellinker.all_proteins" title="Link to this definition">§</a></dt>
+<dd><p>All UniProt IDs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cellinker.all_refs">
+<span class="sig-name descname"><span class="pre">all_refs</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cellinker.all_refs" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects the references
+across all records. Returns <em>list</em>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cellinker.annotate_complex">
+<span class="sig-name descname"><span class="pre">annotate_complex</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cplex</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cellinker.annotate_complex" title="Link to this definition">§</a></dt>
+<dd><p>Infers annotations for a single complex.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cellinker.browse">
+<span class="sig-name descname"><span class="pre">browse</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">field</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">start</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cellinker.browse" title="Link to this definition">§</a></dt>
+<dd><p>Print gene information as a table.</p>
+<p>Presents information about annotation categories as ascii tables
+printed in the terminal. If one category provided, prints one table.
+If multiple categories provided, prints a table for each of them one
+by one proceeding to the next one once you hit return. If no categories
+provided goes through all levels of the primary category.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>field:</dt><dd><p>The field to browse categories by.</p>
+<ul class="simple">
+<li><p>If None the primary field will be selected.
+If this annotation resource doesn’t have fields, all proteins
+will be presented as one single category.</p></li>
+<li><p>If a string it will be considered a field name and it will
+browse through all levels of this field.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">list</span></code>, set or tuple, it will be considered either a
+<code class="docutils literal notranslate"><span class="pre">list</span></code> of field names or a list of values from the primary
+field. In the former case all combinations of the values of
+the fields will be presented, in the latter case the browsing
+will be limited to the levels of the primary field contained
+in <code class="docutils literal notranslate"><span class="pre">field</span></code>.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">dict</span></code>, keys are supposed to be field names and values
+as list of levels. If any of the values are None, all levels
+from that field will be used.</p></li>
+</ul>
+</dd>
+<dt>start:</dt><dd><p>Start browsing from this category. E.g. if there are 500
+categories and start is 250 it will skip everything before the
+250th.</p>
+</dd>
+<dt>kwargs:</dt><dd><p>Passed to <code class="docutils literal notranslate"><span class="pre">pypath.utils.uniprot.info</span></code>.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cellinker.complex_inference">
+<span class="sig-name descname"><span class="pre">complex_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cellinker.complex_inference" title="Link to this definition">§</a></dt>
+<dd><p>Annotates all complexes in <cite>complexes</cite>, by default in the default
+complex database (existing in the <cite>complex</cite> module or generated
+on demand according to the module’s current settings).</p>
+<dl class="field-list simple">
+<dt class="field-odd">Returns<span class="colon">:</span></dt>
+<dd class="field-odd"><p><ul class="simple">
+<li><p><em>Dict with complexes as keys and sets of annotations as values.</em></p></li>
+<li><p><em>Complexes with no valid information in this annotation resource</em></p></li>
+<li><p><em>won’t be in the dict.</em></p></li>
+</ul>
+</p>
+</dd>
+<dt class="field-even">Parameters<span class="colon">:</span></dt>
+<dd class="field-even"><p><strong>complexes</strong> (<em>iterable</em>) – Iterable yielding complexes.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cellinker.coverage">
+<span class="sig-name descname"><span class="pre">coverage</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">other</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cellinker.coverage" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the coverage of the annotation i.e. the proportion of
+entities having at least one record in this annotation resource
+for an arbitrary set of entities.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cellinker.curation_effort">
+<span class="sig-name descname"><span class="pre">curation_effort</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cellinker.curation_effort" title="Link to this definition">§</a></dt>
+<dd><p>Counts the reference-record pairs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cellinker.get_names">
+<span class="sig-name descname"><span class="pre">get_names</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cellinker.get_names" title="Link to this definition">§</a></dt>
+<dd><p>Returns the list of field names in the records. The annotation
+consists of uniform records and each entity might be annotated
+with one or more records. Each record is a tuple of fields, for
+example <code class="docutils literal notranslate"><span class="pre">('cell_type',</span> <span class="pre">'expression_level',</span> <span class="pre">'score')</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cellinker.get_reference_set">
+<em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">get_reference_set</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">proteins</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">swissprot_only</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cellinker.get_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the reference set i.e. the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cellinker.get_subset">
+<span class="sig-name descname"><span class="pre">get_subset</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cellinker.get_subset" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cellinker.get_subset_bool_array">
+<span class="sig-name descname"><span class="pre">get_subset_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cellinker.get_subset_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a boolean vector with True and False values for each entity
+in the reference set. The values represent presence absence data
+in the simplest case, but by providing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> any kind of matching
+and filtering is possible. <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> are passed to the <code class="docutils literal notranslate"><span class="pre">select</span></code>
+method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cellinker.get_values">
+<span class="sig-name descname"><span class="pre">get_values</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">exclude_none</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cellinker.get_values" title="Link to this definition">§</a></dt>
+<dd><p>Returns the set of all possible values of a field. E.g. if the
+records of this annotation have a field <code class="docutils literal notranslate"><span class="pre">cell_type</span></code> then calling
+this method can tell you that across all records the values of
+this field might be <code class="docutils literal notranslate"><span class="pre">{'macrophage',</span> <span class="pre">'epithelial_cell',</span> <span class="pre">...}</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cellinker.labels">
+<span class="sig-name descname"><span class="pre">labels</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cellinker.labels" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cellinker.load">
+<span class="sig-name descname"><span class="pre">load</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cellinker.load" title="Link to this definition">§</a></dt>
+<dd><p>Loads the annotation data by calling the input method.
+Infers annotations for complexes in the complex database if
+py:attr:<code class="docutils literal notranslate"><span class="pre">infer_complexes</span></code> is True.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cellinker.load_data">
+<span class="sig-name descname"><span class="pre">load_data</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cellinker.load_data" title="Link to this definition">§</a></dt>
+<dd><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cellinker.load_proteins">
+<span class="sig-name descname"><span class="pre">load_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cellinker.load_proteins" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a set of all UniProt IDs to have a base set of the entire
+proteome.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cellinker.make_df">
+<span class="sig-name descname"><span class="pre">make_df</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">rebuild</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cellinker.make_df" title="Link to this definition">§</a></dt>
+<dd><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.
+The data frame will be assigned to :py:attr``df``.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cellinker.numof_entities">
+<span class="sig-name descname"><span class="pre">numof_entities</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cellinker.numof_entities" title="Link to this definition">§</a></dt>
+<dd><p>The number of annotated entities in the resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cellinker.numof_records">
+<span class="sig-name descname"><span class="pre">numof_records</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cellinker.numof_records" title="Link to this definition">§</a></dt>
+<dd><p>The total number of annotation records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cellinker.numof_references">
+<span class="sig-name descname"><span class="pre">numof_references</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cellinker.numof_references" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects and counts the
+references across all records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cellinker.process">
+<span class="sig-name descname"><span class="pre">process</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cellinker.process" title="Link to this definition">§</a></dt>
+<dd><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cellinker.reload">
+<span class="sig-name descname"><span class="pre">reload</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cellinker.reload" title="Link to this definition">§</a></dt>
+<dd><p>Reloads the object from the module level.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cellinker.select">
+<span class="sig-name descname"><span class="pre">select</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cellinker.select" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cellinker.set_method">
+<span class="sig-name descname"><span class="pre">set_method</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cellinker.set_method" title="Link to this definition">§</a></dt>
+<dd><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if
+necessary.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cellinker.set_reference_set">
+<span class="sig-name descname"><span class="pre">set_reference_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cellinker.set_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Assigns the reference set to the :py:attr``reference_set`` attribute.
+The reference set is the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cellinker.show">
+<span class="sig-name descname"><span class="pre">show</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">table_param</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cellinker.show" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic
+information from the UniProt datasheets.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cellinker.subset_intersection">
+<span class="sig-name descname"><span class="pre">subset_intersection</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">universe</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cellinker.subset_intersection" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the proportion of entities in a subset occuring in the
+set <code class="docutils literal notranslate"><span class="pre">universe</span></code>. The subset is selected by passing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> to the
+<code class="docutils literal notranslate"><span class="pre">select</span></code> method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cellinker.to_array">
+<span class="sig-name descname"><span class="pre">to_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_fields</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cellinker.to_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns an entity vs feature array. In case of more complex
+annotations this might be huge.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cellinker.to_bool_array">
+<span class="sig-name descname"><span class="pre">to_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cellinker.to_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a presence/absence boolean array for a reference set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cellinker.to_set">
+<span class="sig-name descname"><span class="pre">to_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cellinker.to_set" title="Link to this definition">§</a></dt>
+<dd><p>Returns the entities present in this annotation resource as a set.</p>
+</dd></dl>
+
+</dd></dl>
+
+</section>
+
+
+                </article>
+              
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+  <section id="pypath-core-annot-cellinkercomplex">
+<h1>pypath.core.annot.CellinkerComplex<a class="headerlink" href="#pypath-core-annot-cellinkercomplex" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.core.annot.CellinkerComplex">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.core.annot.</span></span><span class="sig-name descname"><span class="pre">CellinkerComplex</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#CellinkerComplex"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.CellinkerComplex" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <a class="reference internal" href="pypath.core.annot.AnnotationBase.html#pypath.core.annot.AnnotationBase" title="pypath.core.annot.AnnotationBase"><code class="xref py py-class docutils literal notranslate"><span class="pre">AnnotationBase</span></code></a></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellinkerComplex.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#CellinkerComplex.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.CellinkerComplex.__init__" title="Link to this definition">§</a></dt>
+<dd><p>Represents annotations for a set of proteins.
+Loads the data from the original resource and provides methods
+to query the annotations.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>name</strong> (<em>str</em>) – A custom name for the annotation resource.</p></li>
+<li><p><strong>ncbi_tax_id</strong> (<em>int</em>) – NCBI Taxonomy identifier.</p></li>
+<li><p><strong>input_method</strong> (<em>callable</em><em>,</em><em>str</em>) – Either a callable or the name of a method in any submodules of
+the <code class="docutils literal notranslate"><span class="pre">pypath.inputs</span></code>  module. Should return a dict with
+UniProt IDs as keys or an object suitable for <code class="docutils literal notranslate"><span class="pre">process_method</span></code>.</p></li>
+<li><p><strong>input_args</strong> (<em>dict</em>) – Arguments for the <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CellinkerComplex.__init__" title="pypath.core.annot.CellinkerComplex.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>([ncbi_tax_id])</p></td>
+<td><p>Represents annotations for a set of proteins.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CellinkerComplex.add_complexes_by_inference" title="pypath.core.annot.CellinkerComplex.add_complexes_by_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">add_complexes_by_inference</span></code></a>([complexes])</p></td>
+<td><p>Creates complex annotations by in silico inference and adds them to this annotation set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CellinkerComplex.all_complexes" title="pypath.core.annot.CellinkerComplex.all_complexes"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_complexes</span></code></a>()</p></td>
+<td><p>All protein complexes annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CellinkerComplex.all_entities" title="pypath.core.annot.CellinkerComplex.all_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_entities</span></code></a>([entity_types])</p></td>
+<td><p>All entities annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CellinkerComplex.all_mirnas" title="pypath.core.annot.CellinkerComplex.all_mirnas"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_mirnas</span></code></a>()</p></td>
+<td><p>All miRNAs annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CellinkerComplex.all_proteins" title="pypath.core.annot.CellinkerComplex.all_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_proteins</span></code></a>()</p></td>
+<td><p>All UniProt IDs annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CellinkerComplex.all_refs" title="pypath.core.annot.CellinkerComplex.all_refs"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_refs</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CellinkerComplex.annotate_complex" title="pypath.core.annot.CellinkerComplex.annotate_complex"><code class="xref py py-obj docutils literal notranslate"><span class="pre">annotate_complex</span></code></a>(cplex)</p></td>
+<td><p>Infers annotations for a single complex.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CellinkerComplex.browse" title="pypath.core.annot.CellinkerComplex.browse"><code class="xref py py-obj docutils literal notranslate"><span class="pre">browse</span></code></a>([field, start])</p></td>
+<td><p>Print gene information as a table.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CellinkerComplex.complex_inference" title="pypath.core.annot.CellinkerComplex.complex_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">complex_inference</span></code></a>([complexes])</p></td>
+<td><p>Annotates all complexes in <cite>complexes</cite>, by default in the default complex database (existing in the <cite>complex</cite> module or generated on demand according to the module's current settings).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CellinkerComplex.coverage" title="pypath.core.annot.CellinkerComplex.coverage"><code class="xref py py-obj docutils literal notranslate"><span class="pre">coverage</span></code></a>(other)</p></td>
+<td><p>Calculates the coverage of the annotation i.e. the proportion of entities having at least one record in this annotation resource for an arbitrary set of entities.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CellinkerComplex.curation_effort" title="pypath.core.annot.CellinkerComplex.curation_effort"><code class="xref py py-obj docutils literal notranslate"><span class="pre">curation_effort</span></code></a>()</p></td>
+<td><p>Counts the reference-record pairs.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">from_dump</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_entity_type</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CellinkerComplex.get_names" title="pypath.core.annot.CellinkerComplex.get_names"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_names</span></code></a>()</p></td>
+<td><p>Returns the list of field names in the records.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CellinkerComplex.get_reference_set" title="pypath.core.annot.CellinkerComplex.get_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_reference_set</span></code></a>([proteins, complexes, ...])</p></td>
+<td><p>Retrieves the reference set i.e. the set of all entities which potentially have annotation in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CellinkerComplex.get_subset" title="pypath.core.annot.CellinkerComplex.get_subset"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CellinkerComplex.get_subset_bool_array" title="pypath.core.annot.CellinkerComplex.get_subset_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset_bool_array</span></code></a>([reference_set])</p></td>
+<td><p>Returns a boolean vector with True and False values for each entity in the reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CellinkerComplex.get_values" title="pypath.core.annot.CellinkerComplex.get_values"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_values</span></code></a>(name[, exclude_none])</p></td>
+<td><p>Returns the set of all possible values of a field.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_complex</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_mirna</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_protein</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CellinkerComplex.labels" title="pypath.core.annot.CellinkerComplex.labels"><code class="xref py py-obj docutils literal notranslate"><span class="pre">labels</span></code></a>([method])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CellinkerComplex.load" title="pypath.core.annot.CellinkerComplex.load"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load</span></code></a>()</p></td>
+<td><p>Loads the annotation data by calling the input method.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CellinkerComplex.load_data" title="pypath.core.annot.CellinkerComplex.load_data"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_data</span></code></a>()</p></td>
+<td><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CellinkerComplex.load_proteins" title="pypath.core.annot.CellinkerComplex.load_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_proteins</span></code></a>()</p></td>
+<td><p>Retrieves a set of all UniProt IDs to have a base set of the entire proteome.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CellinkerComplex.make_df" title="pypath.core.annot.CellinkerComplex.make_df"><code class="xref py py-obj docutils literal notranslate"><span class="pre">make_df</span></code></a>([rebuild])</p></td>
+<td><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complex_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CellinkerComplex.numof_entities" title="pypath.core.annot.CellinkerComplex.numof_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_entities</span></code></a>()</p></td>
+<td><p>The number of annotated entities in the resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirna_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirnas</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_protein_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_proteins</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CellinkerComplex.numof_records" title="pypath.core.annot.CellinkerComplex.numof_records"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_records</span></code></a>([entity_types])</p></td>
+<td><p>The total number of annotation records.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CellinkerComplex.numof_references" title="pypath.core.annot.CellinkerComplex.numof_references"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_references</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CellinkerComplex.process" title="pypath.core.annot.CellinkerComplex.process"><code class="xref py py-obj docutils literal notranslate"><span class="pre">process</span></code></a>()</p></td>
+<td><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">proportion</span></code>(other)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CellinkerComplex.reload" title="pypath.core.annot.CellinkerComplex.reload"><code class="xref py py-obj docutils literal notranslate"><span class="pre">reload</span></code></a>()</p></td>
+<td><p>Reloads the object from the module level.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">save_to_pickle</span></code>(pickle_file)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CellinkerComplex.select" title="pypath.core.annot.CellinkerComplex.select"><code class="xref py py-obj docutils literal notranslate"><span class="pre">select</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CellinkerComplex.set_method" title="pypath.core.annot.CellinkerComplex.set_method"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_method</span></code></a>()</p></td>
+<td><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if necessary.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CellinkerComplex.set_reference_set" title="pypath.core.annot.CellinkerComplex.set_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_reference_set</span></code></a>()</p></td>
+<td><p>Assigns the reference set to the :py:attr``reference_set`` attribute.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CellinkerComplex.show" title="pypath.core.annot.CellinkerComplex.show"><code class="xref py py-obj docutils literal notranslate"><span class="pre">show</span></code></a>([method, table_param])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic information from the UniProt datasheets.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CellinkerComplex.subset_intersection" title="pypath.core.annot.CellinkerComplex.subset_intersection"><code class="xref py py-obj docutils literal notranslate"><span class="pre">subset_intersection</span></code></a>(universe, **kwargs)</p></td>
+<td><p>Calculates the proportion of entities in a subset occuring in the set <code class="docutils literal notranslate"><span class="pre">universe</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CellinkerComplex.to_array" title="pypath.core.annot.CellinkerComplex.to_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_array</span></code></a>([reference_set, use_fields])</p></td>
+<td><p>Returns an entity vs feature array.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CellinkerComplex.to_bool_array" title="pypath.core.annot.CellinkerComplex.to_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_bool_array</span></code></a>(reference_set)</p></td>
+<td><p>Returns a presence/absence boolean array for a reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CellinkerComplex.to_set" title="pypath.core.annot.CellinkerComplex.to_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_set</span></code></a>()</p></td>
+<td><p>Returns the entities present in this annotation resource as a set.</p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Attributes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_fields</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">summary</span></code></p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellinkerComplex.add_complexes_by_inference">
+<span class="sig-name descname"><span class="pre">add_complexes_by_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellinkerComplex.add_complexes_by_inference" title="Link to this definition">§</a></dt>
+<dd><p>Creates complex annotations by in silico inference and adds them
+to this annotation set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellinkerComplex.all_complexes">
+<span class="sig-name descname"><span class="pre">all_complexes</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellinkerComplex.all_complexes" title="Link to this definition">§</a></dt>
+<dd><p>All protein complexes annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellinkerComplex.all_entities">
+<span class="sig-name descname"><span class="pre">all_entities</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellinkerComplex.all_entities" title="Link to this definition">§</a></dt>
+<dd><p>All entities annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellinkerComplex.all_mirnas">
+<span class="sig-name descname"><span class="pre">all_mirnas</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellinkerComplex.all_mirnas" title="Link to this definition">§</a></dt>
+<dd><p>All miRNAs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellinkerComplex.all_proteins">
+<span class="sig-name descname"><span class="pre">all_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellinkerComplex.all_proteins" title="Link to this definition">§</a></dt>
+<dd><p>All UniProt IDs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellinkerComplex.all_refs">
+<span class="sig-name descname"><span class="pre">all_refs</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellinkerComplex.all_refs" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects the references
+across all records. Returns <em>list</em>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellinkerComplex.annotate_complex">
+<span class="sig-name descname"><span class="pre">annotate_complex</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cplex</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellinkerComplex.annotate_complex" title="Link to this definition">§</a></dt>
+<dd><p>Infers annotations for a single complex.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellinkerComplex.browse">
+<span class="sig-name descname"><span class="pre">browse</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">field</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">start</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellinkerComplex.browse" title="Link to this definition">§</a></dt>
+<dd><p>Print gene information as a table.</p>
+<p>Presents information about annotation categories as ascii tables
+printed in the terminal. If one category provided, prints one table.
+If multiple categories provided, prints a table for each of them one
+by one proceeding to the next one once you hit return. If no categories
+provided goes through all levels of the primary category.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>field:</dt><dd><p>The field to browse categories by.</p>
+<ul class="simple">
+<li><p>If None the primary field will be selected.
+If this annotation resource doesn’t have fields, all proteins
+will be presented as one single category.</p></li>
+<li><p>If a string it will be considered a field name and it will
+browse through all levels of this field.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">list</span></code>, set or tuple, it will be considered either a
+<code class="docutils literal notranslate"><span class="pre">list</span></code> of field names or a list of values from the primary
+field. In the former case all combinations of the values of
+the fields will be presented, in the latter case the browsing
+will be limited to the levels of the primary field contained
+in <code class="docutils literal notranslate"><span class="pre">field</span></code>.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">dict</span></code>, keys are supposed to be field names and values
+as list of levels. If any of the values are None, all levels
+from that field will be used.</p></li>
+</ul>
+</dd>
+<dt>start:</dt><dd><p>Start browsing from this category. E.g. if there are 500
+categories and start is 250 it will skip everything before the
+250th.</p>
+</dd>
+<dt>kwargs:</dt><dd><p>Passed to <code class="docutils literal notranslate"><span class="pre">pypath.utils.uniprot.info</span></code>.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellinkerComplex.complex_inference">
+<span class="sig-name descname"><span class="pre">complex_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellinkerComplex.complex_inference" title="Link to this definition">§</a></dt>
+<dd><p>Annotates all complexes in <cite>complexes</cite>, by default in the default
+complex database (existing in the <cite>complex</cite> module or generated
+on demand according to the module’s current settings).</p>
+<dl class="field-list simple">
+<dt class="field-odd">Returns<span class="colon">:</span></dt>
+<dd class="field-odd"><p><ul class="simple">
+<li><p><em>Dict with complexes as keys and sets of annotations as values.</em></p></li>
+<li><p><em>Complexes with no valid information in this annotation resource</em></p></li>
+<li><p><em>won’t be in the dict.</em></p></li>
+</ul>
+</p>
+</dd>
+<dt class="field-even">Parameters<span class="colon">:</span></dt>
+<dd class="field-even"><p><strong>complexes</strong> (<em>iterable</em>) – Iterable yielding complexes.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellinkerComplex.coverage">
+<span class="sig-name descname"><span class="pre">coverage</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">other</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellinkerComplex.coverage" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the coverage of the annotation i.e. the proportion of
+entities having at least one record in this annotation resource
+for an arbitrary set of entities.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellinkerComplex.curation_effort">
+<span class="sig-name descname"><span class="pre">curation_effort</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellinkerComplex.curation_effort" title="Link to this definition">§</a></dt>
+<dd><p>Counts the reference-record pairs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellinkerComplex.get_names">
+<span class="sig-name descname"><span class="pre">get_names</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellinkerComplex.get_names" title="Link to this definition">§</a></dt>
+<dd><p>Returns the list of field names in the records. The annotation
+consists of uniform records and each entity might be annotated
+with one or more records. Each record is a tuple of fields, for
+example <code class="docutils literal notranslate"><span class="pre">('cell_type',</span> <span class="pre">'expression_level',</span> <span class="pre">'score')</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellinkerComplex.get_reference_set">
+<em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">get_reference_set</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">proteins</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">swissprot_only</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellinkerComplex.get_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the reference set i.e. the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellinkerComplex.get_subset">
+<span class="sig-name descname"><span class="pre">get_subset</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellinkerComplex.get_subset" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellinkerComplex.get_subset_bool_array">
+<span class="sig-name descname"><span class="pre">get_subset_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellinkerComplex.get_subset_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a boolean vector with True and False values for each entity
+in the reference set. The values represent presence absence data
+in the simplest case, but by providing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> any kind of matching
+and filtering is possible. <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> are passed to the <code class="docutils literal notranslate"><span class="pre">select</span></code>
+method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellinkerComplex.get_values">
+<span class="sig-name descname"><span class="pre">get_values</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">exclude_none</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellinkerComplex.get_values" title="Link to this definition">§</a></dt>
+<dd><p>Returns the set of all possible values of a field. E.g. if the
+records of this annotation have a field <code class="docutils literal notranslate"><span class="pre">cell_type</span></code> then calling
+this method can tell you that across all records the values of
+this field might be <code class="docutils literal notranslate"><span class="pre">{'macrophage',</span> <span class="pre">'epithelial_cell',</span> <span class="pre">...}</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellinkerComplex.labels">
+<span class="sig-name descname"><span class="pre">labels</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellinkerComplex.labels" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellinkerComplex.load">
+<span class="sig-name descname"><span class="pre">load</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellinkerComplex.load" title="Link to this definition">§</a></dt>
+<dd><p>Loads the annotation data by calling the input method.
+Infers annotations for complexes in the complex database if
+py:attr:<code class="docutils literal notranslate"><span class="pre">infer_complexes</span></code> is True.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellinkerComplex.load_data">
+<span class="sig-name descname"><span class="pre">load_data</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellinkerComplex.load_data" title="Link to this definition">§</a></dt>
+<dd><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellinkerComplex.load_proteins">
+<span class="sig-name descname"><span class="pre">load_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellinkerComplex.load_proteins" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a set of all UniProt IDs to have a base set of the entire
+proteome.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellinkerComplex.make_df">
+<span class="sig-name descname"><span class="pre">make_df</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">rebuild</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellinkerComplex.make_df" title="Link to this definition">§</a></dt>
+<dd><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.
+The data frame will be assigned to :py:attr``df``.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellinkerComplex.numof_entities">
+<span class="sig-name descname"><span class="pre">numof_entities</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellinkerComplex.numof_entities" title="Link to this definition">§</a></dt>
+<dd><p>The number of annotated entities in the resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellinkerComplex.numof_records">
+<span class="sig-name descname"><span class="pre">numof_records</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellinkerComplex.numof_records" title="Link to this definition">§</a></dt>
+<dd><p>The total number of annotation records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellinkerComplex.numof_references">
+<span class="sig-name descname"><span class="pre">numof_references</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellinkerComplex.numof_references" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects and counts the
+references across all records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellinkerComplex.process">
+<span class="sig-name descname"><span class="pre">process</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellinkerComplex.process" title="Link to this definition">§</a></dt>
+<dd><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellinkerComplex.reload">
+<span class="sig-name descname"><span class="pre">reload</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellinkerComplex.reload" title="Link to this definition">§</a></dt>
+<dd><p>Reloads the object from the module level.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellinkerComplex.select">
+<span class="sig-name descname"><span class="pre">select</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellinkerComplex.select" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellinkerComplex.set_method">
+<span class="sig-name descname"><span class="pre">set_method</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellinkerComplex.set_method" title="Link to this definition">§</a></dt>
+<dd><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if
+necessary.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellinkerComplex.set_reference_set">
+<span class="sig-name descname"><span class="pre">set_reference_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellinkerComplex.set_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Assigns the reference set to the :py:attr``reference_set`` attribute.
+The reference set is the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellinkerComplex.show">
+<span class="sig-name descname"><span class="pre">show</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">table_param</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellinkerComplex.show" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic
+information from the UniProt datasheets.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellinkerComplex.subset_intersection">
+<span class="sig-name descname"><span class="pre">subset_intersection</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">universe</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellinkerComplex.subset_intersection" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the proportion of entities in a subset occuring in the
+set <code class="docutils literal notranslate"><span class="pre">universe</span></code>. The subset is selected by passing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> to the
+<code class="docutils literal notranslate"><span class="pre">select</span></code> method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellinkerComplex.to_array">
+<span class="sig-name descname"><span class="pre">to_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_fields</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellinkerComplex.to_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns an entity vs feature array. In case of more complex
+annotations this might be huge.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellinkerComplex.to_bool_array">
+<span class="sig-name descname"><span class="pre">to_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellinkerComplex.to_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a presence/absence boolean array for a reference set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CellinkerComplex.to_set">
+<span class="sig-name descname"><span class="pre">to_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CellinkerComplex.to_set" title="Link to this definition">§</a></dt>
+<dd><p>Returns the entities present in this annotation resource as a set.</p>
+</dd></dl>
+
+</dd></dl>
+
+</section>
+
+
+                </article>
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+  <section id="pypath-core-annot-celltalkdb">
+<h1>pypath.core.annot.Celltalkdb<a class="headerlink" href="#pypath-core-annot-celltalkdb" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.core.annot.Celltalkdb">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.core.annot.</span></span><span class="sig-name descname"><span class="pre">Celltalkdb</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#Celltalkdb"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.Celltalkdb" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <a class="reference internal" href="pypath.core.annot.AnnotationBase.html#pypath.core.annot.AnnotationBase" title="pypath.core.annot.AnnotationBase"><code class="xref py py-class docutils literal notranslate"><span class="pre">AnnotationBase</span></code></a></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Celltalkdb.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#Celltalkdb.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.Celltalkdb.__init__" title="Link to this definition">§</a></dt>
+<dd><p>Represents annotations for a set of proteins.
+Loads the data from the original resource and provides methods
+to query the annotations.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>name</strong> (<em>str</em>) – A custom name for the annotation resource.</p></li>
+<li><p><strong>ncbi_tax_id</strong> (<em>int</em>) – NCBI Taxonomy identifier.</p></li>
+<li><p><strong>input_method</strong> (<em>callable</em><em>,</em><em>str</em>) – Either a callable or the name of a method in any submodules of
+the <code class="docutils literal notranslate"><span class="pre">pypath.inputs</span></code>  module. Should return a dict with
+UniProt IDs as keys or an object suitable for <code class="docutils literal notranslate"><span class="pre">process_method</span></code>.</p></li>
+<li><p><strong>input_args</strong> (<em>dict</em>) – Arguments for the <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Celltalkdb.__init__" title="pypath.core.annot.Celltalkdb.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>(**kwargs)</p></td>
+<td><p>Represents annotations for a set of proteins.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Celltalkdb.add_complexes_by_inference" title="pypath.core.annot.Celltalkdb.add_complexes_by_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">add_complexes_by_inference</span></code></a>([complexes])</p></td>
+<td><p>Creates complex annotations by in silico inference and adds them to this annotation set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Celltalkdb.all_complexes" title="pypath.core.annot.Celltalkdb.all_complexes"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_complexes</span></code></a>()</p></td>
+<td><p>All protein complexes annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Celltalkdb.all_entities" title="pypath.core.annot.Celltalkdb.all_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_entities</span></code></a>([entity_types])</p></td>
+<td><p>All entities annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Celltalkdb.all_mirnas" title="pypath.core.annot.Celltalkdb.all_mirnas"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_mirnas</span></code></a>()</p></td>
+<td><p>All miRNAs annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Celltalkdb.all_proteins" title="pypath.core.annot.Celltalkdb.all_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_proteins</span></code></a>()</p></td>
+<td><p>All UniProt IDs annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Celltalkdb.all_refs" title="pypath.core.annot.Celltalkdb.all_refs"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_refs</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Celltalkdb.annotate_complex" title="pypath.core.annot.Celltalkdb.annotate_complex"><code class="xref py py-obj docutils literal notranslate"><span class="pre">annotate_complex</span></code></a>(cplex)</p></td>
+<td><p>Infers annotations for a single complex.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Celltalkdb.browse" title="pypath.core.annot.Celltalkdb.browse"><code class="xref py py-obj docutils literal notranslate"><span class="pre">browse</span></code></a>([field, start])</p></td>
+<td><p>Print gene information as a table.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Celltalkdb.complex_inference" title="pypath.core.annot.Celltalkdb.complex_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">complex_inference</span></code></a>([complexes])</p></td>
+<td><p>Annotates all complexes in <cite>complexes</cite>, by default in the default complex database (existing in the <cite>complex</cite> module or generated on demand according to the module's current settings).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Celltalkdb.coverage" title="pypath.core.annot.Celltalkdb.coverage"><code class="xref py py-obj docutils literal notranslate"><span class="pre">coverage</span></code></a>(other)</p></td>
+<td><p>Calculates the coverage of the annotation i.e. the proportion of entities having at least one record in this annotation resource for an arbitrary set of entities.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Celltalkdb.curation_effort" title="pypath.core.annot.Celltalkdb.curation_effort"><code class="xref py py-obj docutils literal notranslate"><span class="pre">curation_effort</span></code></a>()</p></td>
+<td><p>Counts the reference-record pairs.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">from_dump</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_entity_type</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Celltalkdb.get_names" title="pypath.core.annot.Celltalkdb.get_names"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_names</span></code></a>()</p></td>
+<td><p>Returns the list of field names in the records.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Celltalkdb.get_reference_set" title="pypath.core.annot.Celltalkdb.get_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_reference_set</span></code></a>([proteins, complexes, ...])</p></td>
+<td><p>Retrieves the reference set i.e. the set of all entities which potentially have annotation in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Celltalkdb.get_subset" title="pypath.core.annot.Celltalkdb.get_subset"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Celltalkdb.get_subset_bool_array" title="pypath.core.annot.Celltalkdb.get_subset_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset_bool_array</span></code></a>([reference_set])</p></td>
+<td><p>Returns a boolean vector with True and False values for each entity in the reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Celltalkdb.get_values" title="pypath.core.annot.Celltalkdb.get_values"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_values</span></code></a>(name[, exclude_none])</p></td>
+<td><p>Returns the set of all possible values of a field.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_complex</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_mirna</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_protein</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Celltalkdb.labels" title="pypath.core.annot.Celltalkdb.labels"><code class="xref py py-obj docutils literal notranslate"><span class="pre">labels</span></code></a>([method])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Celltalkdb.load" title="pypath.core.annot.Celltalkdb.load"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load</span></code></a>()</p></td>
+<td><p>Loads the annotation data by calling the input method.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Celltalkdb.load_data" title="pypath.core.annot.Celltalkdb.load_data"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_data</span></code></a>()</p></td>
+<td><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Celltalkdb.load_proteins" title="pypath.core.annot.Celltalkdb.load_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_proteins</span></code></a>()</p></td>
+<td><p>Retrieves a set of all UniProt IDs to have a base set of the entire proteome.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Celltalkdb.make_df" title="pypath.core.annot.Celltalkdb.make_df"><code class="xref py py-obj docutils literal notranslate"><span class="pre">make_df</span></code></a>([rebuild])</p></td>
+<td><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complex_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Celltalkdb.numof_entities" title="pypath.core.annot.Celltalkdb.numof_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_entities</span></code></a>()</p></td>
+<td><p>The number of annotated entities in the resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirna_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirnas</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_protein_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_proteins</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Celltalkdb.numof_records" title="pypath.core.annot.Celltalkdb.numof_records"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_records</span></code></a>([entity_types])</p></td>
+<td><p>The total number of annotation records.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Celltalkdb.numof_references" title="pypath.core.annot.Celltalkdb.numof_references"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_references</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Celltalkdb.process" title="pypath.core.annot.Celltalkdb.process"><code class="xref py py-obj docutils literal notranslate"><span class="pre">process</span></code></a>()</p></td>
+<td><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">proportion</span></code>(other)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Celltalkdb.reload" title="pypath.core.annot.Celltalkdb.reload"><code class="xref py py-obj docutils literal notranslate"><span class="pre">reload</span></code></a>()</p></td>
+<td><p>Reloads the object from the module level.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">save_to_pickle</span></code>(pickle_file)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Celltalkdb.select" title="pypath.core.annot.Celltalkdb.select"><code class="xref py py-obj docutils literal notranslate"><span class="pre">select</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Celltalkdb.set_method" title="pypath.core.annot.Celltalkdb.set_method"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_method</span></code></a>()</p></td>
+<td><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if necessary.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Celltalkdb.set_reference_set" title="pypath.core.annot.Celltalkdb.set_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_reference_set</span></code></a>()</p></td>
+<td><p>Assigns the reference set to the :py:attr``reference_set`` attribute.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Celltalkdb.show" title="pypath.core.annot.Celltalkdb.show"><code class="xref py py-obj docutils literal notranslate"><span class="pre">show</span></code></a>([method, table_param])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic information from the UniProt datasheets.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Celltalkdb.subset_intersection" title="pypath.core.annot.Celltalkdb.subset_intersection"><code class="xref py py-obj docutils literal notranslate"><span class="pre">subset_intersection</span></code></a>(universe, **kwargs)</p></td>
+<td><p>Calculates the proportion of entities in a subset occuring in the set <code class="docutils literal notranslate"><span class="pre">universe</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Celltalkdb.to_array" title="pypath.core.annot.Celltalkdb.to_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_array</span></code></a>([reference_set, use_fields])</p></td>
+<td><p>Returns an entity vs feature array.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Celltalkdb.to_bool_array" title="pypath.core.annot.Celltalkdb.to_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_bool_array</span></code></a>(reference_set)</p></td>
+<td><p>Returns a presence/absence boolean array for a reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Celltalkdb.to_set" title="pypath.core.annot.Celltalkdb.to_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_set</span></code></a>()</p></td>
+<td><p>Returns the entities present in this annotation resource as a set.</p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Attributes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_fields</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">summary</span></code></p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Celltalkdb.add_complexes_by_inference">
+<span class="sig-name descname"><span class="pre">add_complexes_by_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Celltalkdb.add_complexes_by_inference" title="Link to this definition">§</a></dt>
+<dd><p>Creates complex annotations by in silico inference and adds them
+to this annotation set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Celltalkdb.all_complexes">
+<span class="sig-name descname"><span class="pre">all_complexes</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Celltalkdb.all_complexes" title="Link to this definition">§</a></dt>
+<dd><p>All protein complexes annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Celltalkdb.all_entities">
+<span class="sig-name descname"><span class="pre">all_entities</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Celltalkdb.all_entities" title="Link to this definition">§</a></dt>
+<dd><p>All entities annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Celltalkdb.all_mirnas">
+<span class="sig-name descname"><span class="pre">all_mirnas</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Celltalkdb.all_mirnas" title="Link to this definition">§</a></dt>
+<dd><p>All miRNAs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Celltalkdb.all_proteins">
+<span class="sig-name descname"><span class="pre">all_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Celltalkdb.all_proteins" title="Link to this definition">§</a></dt>
+<dd><p>All UniProt IDs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Celltalkdb.all_refs">
+<span class="sig-name descname"><span class="pre">all_refs</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Celltalkdb.all_refs" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects the references
+across all records. Returns <em>list</em>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Celltalkdb.annotate_complex">
+<span class="sig-name descname"><span class="pre">annotate_complex</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cplex</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Celltalkdb.annotate_complex" title="Link to this definition">§</a></dt>
+<dd><p>Infers annotations for a single complex.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Celltalkdb.browse">
+<span class="sig-name descname"><span class="pre">browse</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">field</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">start</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Celltalkdb.browse" title="Link to this definition">§</a></dt>
+<dd><p>Print gene information as a table.</p>
+<p>Presents information about annotation categories as ascii tables
+printed in the terminal. If one category provided, prints one table.
+If multiple categories provided, prints a table for each of them one
+by one proceeding to the next one once you hit return. If no categories
+provided goes through all levels of the primary category.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>field:</dt><dd><p>The field to browse categories by.</p>
+<ul class="simple">
+<li><p>If None the primary field will be selected.
+If this annotation resource doesn’t have fields, all proteins
+will be presented as one single category.</p></li>
+<li><p>If a string it will be considered a field name and it will
+browse through all levels of this field.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">list</span></code>, set or tuple, it will be considered either a
+<code class="docutils literal notranslate"><span class="pre">list</span></code> of field names or a list of values from the primary
+field. In the former case all combinations of the values of
+the fields will be presented, in the latter case the browsing
+will be limited to the levels of the primary field contained
+in <code class="docutils literal notranslate"><span class="pre">field</span></code>.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">dict</span></code>, keys are supposed to be field names and values
+as list of levels. If any of the values are None, all levels
+from that field will be used.</p></li>
+</ul>
+</dd>
+<dt>start:</dt><dd><p>Start browsing from this category. E.g. if there are 500
+categories and start is 250 it will skip everything before the
+250th.</p>
+</dd>
+<dt>kwargs:</dt><dd><p>Passed to <code class="docutils literal notranslate"><span class="pre">pypath.utils.uniprot.info</span></code>.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Celltalkdb.complex_inference">
+<span class="sig-name descname"><span class="pre">complex_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Celltalkdb.complex_inference" title="Link to this definition">§</a></dt>
+<dd><p>Annotates all complexes in <cite>complexes</cite>, by default in the default
+complex database (existing in the <cite>complex</cite> module or generated
+on demand according to the module’s current settings).</p>
+<dl class="field-list simple">
+<dt class="field-odd">Returns<span class="colon">:</span></dt>
+<dd class="field-odd"><p><ul class="simple">
+<li><p><em>Dict with complexes as keys and sets of annotations as values.</em></p></li>
+<li><p><em>Complexes with no valid information in this annotation resource</em></p></li>
+<li><p><em>won’t be in the dict.</em></p></li>
+</ul>
+</p>
+</dd>
+<dt class="field-even">Parameters<span class="colon">:</span></dt>
+<dd class="field-even"><p><strong>complexes</strong> (<em>iterable</em>) – Iterable yielding complexes.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Celltalkdb.coverage">
+<span class="sig-name descname"><span class="pre">coverage</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">other</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Celltalkdb.coverage" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the coverage of the annotation i.e. the proportion of
+entities having at least one record in this annotation resource
+for an arbitrary set of entities.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Celltalkdb.curation_effort">
+<span class="sig-name descname"><span class="pre">curation_effort</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Celltalkdb.curation_effort" title="Link to this definition">§</a></dt>
+<dd><p>Counts the reference-record pairs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Celltalkdb.get_names">
+<span class="sig-name descname"><span class="pre">get_names</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Celltalkdb.get_names" title="Link to this definition">§</a></dt>
+<dd><p>Returns the list of field names in the records. The annotation
+consists of uniform records and each entity might be annotated
+with one or more records. Each record is a tuple of fields, for
+example <code class="docutils literal notranslate"><span class="pre">('cell_type',</span> <span class="pre">'expression_level',</span> <span class="pre">'score')</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Celltalkdb.get_reference_set">
+<em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">get_reference_set</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">proteins</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">swissprot_only</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Celltalkdb.get_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the reference set i.e. the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Celltalkdb.get_subset">
+<span class="sig-name descname"><span class="pre">get_subset</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Celltalkdb.get_subset" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Celltalkdb.get_subset_bool_array">
+<span class="sig-name descname"><span class="pre">get_subset_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Celltalkdb.get_subset_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a boolean vector with True and False values for each entity
+in the reference set. The values represent presence absence data
+in the simplest case, but by providing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> any kind of matching
+and filtering is possible. <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> are passed to the <code class="docutils literal notranslate"><span class="pre">select</span></code>
+method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Celltalkdb.get_values">
+<span class="sig-name descname"><span class="pre">get_values</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">exclude_none</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Celltalkdb.get_values" title="Link to this definition">§</a></dt>
+<dd><p>Returns the set of all possible values of a field. E.g. if the
+records of this annotation have a field <code class="docutils literal notranslate"><span class="pre">cell_type</span></code> then calling
+this method can tell you that across all records the values of
+this field might be <code class="docutils literal notranslate"><span class="pre">{'macrophage',</span> <span class="pre">'epithelial_cell',</span> <span class="pre">...}</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Celltalkdb.labels">
+<span class="sig-name descname"><span class="pre">labels</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Celltalkdb.labels" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Celltalkdb.load">
+<span class="sig-name descname"><span class="pre">load</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Celltalkdb.load" title="Link to this definition">§</a></dt>
+<dd><p>Loads the annotation data by calling the input method.
+Infers annotations for complexes in the complex database if
+py:attr:<code class="docutils literal notranslate"><span class="pre">infer_complexes</span></code> is True.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Celltalkdb.load_data">
+<span class="sig-name descname"><span class="pre">load_data</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Celltalkdb.load_data" title="Link to this definition">§</a></dt>
+<dd><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Celltalkdb.load_proteins">
+<span class="sig-name descname"><span class="pre">load_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Celltalkdb.load_proteins" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a set of all UniProt IDs to have a base set of the entire
+proteome.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Celltalkdb.make_df">
+<span class="sig-name descname"><span class="pre">make_df</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">rebuild</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Celltalkdb.make_df" title="Link to this definition">§</a></dt>
+<dd><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.
+The data frame will be assigned to :py:attr``df``.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Celltalkdb.numof_entities">
+<span class="sig-name descname"><span class="pre">numof_entities</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Celltalkdb.numof_entities" title="Link to this definition">§</a></dt>
+<dd><p>The number of annotated entities in the resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Celltalkdb.numof_records">
+<span class="sig-name descname"><span class="pre">numof_records</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Celltalkdb.numof_records" title="Link to this definition">§</a></dt>
+<dd><p>The total number of annotation records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Celltalkdb.numof_references">
+<span class="sig-name descname"><span class="pre">numof_references</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Celltalkdb.numof_references" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects and counts the
+references across all records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Celltalkdb.process">
+<span class="sig-name descname"><span class="pre">process</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Celltalkdb.process" title="Link to this definition">§</a></dt>
+<dd><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Celltalkdb.reload">
+<span class="sig-name descname"><span class="pre">reload</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Celltalkdb.reload" title="Link to this definition">§</a></dt>
+<dd><p>Reloads the object from the module level.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Celltalkdb.select">
+<span class="sig-name descname"><span class="pre">select</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Celltalkdb.select" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Celltalkdb.set_method">
+<span class="sig-name descname"><span class="pre">set_method</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Celltalkdb.set_method" title="Link to this definition">§</a></dt>
+<dd><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if
+necessary.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Celltalkdb.set_reference_set">
+<span class="sig-name descname"><span class="pre">set_reference_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Celltalkdb.set_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Assigns the reference set to the :py:attr``reference_set`` attribute.
+The reference set is the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Celltalkdb.show">
+<span class="sig-name descname"><span class="pre">show</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">table_param</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Celltalkdb.show" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic
+information from the UniProt datasheets.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Celltalkdb.subset_intersection">
+<span class="sig-name descname"><span class="pre">subset_intersection</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">universe</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Celltalkdb.subset_intersection" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the proportion of entities in a subset occuring in the
+set <code class="docutils literal notranslate"><span class="pre">universe</span></code>. The subset is selected by passing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> to the
+<code class="docutils literal notranslate"><span class="pre">select</span></code> method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Celltalkdb.to_array">
+<span class="sig-name descname"><span class="pre">to_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_fields</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Celltalkdb.to_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns an entity vs feature array. In case of more complex
+annotations this might be huge.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Celltalkdb.to_bool_array">
+<span class="sig-name descname"><span class="pre">to_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Celltalkdb.to_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a presence/absence boolean array for a reference set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Celltalkdb.to_set">
+<span class="sig-name descname"><span class="pre">to_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Celltalkdb.to_set" title="Link to this definition">§</a></dt>
+<dd><p>Returns the entities present in this annotation resource as a set.</p>
+</dd></dl>
+
+</dd></dl>
+
+</section>
+
+
+                </article>
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+  <section id="pypath-core-annot-celltypist">
+<h1>pypath.core.annot.Celltypist<a class="headerlink" href="#pypath-core-annot-celltypist" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.core.annot.Celltypist">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.core.annot.</span></span><span class="sig-name descname"><span class="pre">Celltypist</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#Celltypist"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.Celltypist" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <a class="reference internal" href="pypath.core.annot.AnnotationBase.html#pypath.core.annot.AnnotationBase" title="pypath.core.annot.AnnotationBase"><code class="xref py py-class docutils literal notranslate"><span class="pre">AnnotationBase</span></code></a></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Celltypist.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#Celltypist.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.Celltypist.__init__" title="Link to this definition">§</a></dt>
+<dd><p>Cell type markers from the CellTypist database.</p>
+</dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Celltypist.__init__" title="pypath.core.annot.Celltypist.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>([ncbi_tax_id])</p></td>
+<td><p>Cell type markers from the CellTypist database.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Celltypist.add_complexes_by_inference" title="pypath.core.annot.Celltypist.add_complexes_by_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">add_complexes_by_inference</span></code></a>([complexes])</p></td>
+<td><p>Creates complex annotations by in silico inference and adds them to this annotation set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Celltypist.all_complexes" title="pypath.core.annot.Celltypist.all_complexes"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_complexes</span></code></a>()</p></td>
+<td><p>All protein complexes annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Celltypist.all_entities" title="pypath.core.annot.Celltypist.all_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_entities</span></code></a>([entity_types])</p></td>
+<td><p>All entities annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Celltypist.all_mirnas" title="pypath.core.annot.Celltypist.all_mirnas"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_mirnas</span></code></a>()</p></td>
+<td><p>All miRNAs annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Celltypist.all_proteins" title="pypath.core.annot.Celltypist.all_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_proteins</span></code></a>()</p></td>
+<td><p>All UniProt IDs annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Celltypist.all_refs" title="pypath.core.annot.Celltypist.all_refs"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_refs</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Celltypist.annotate_complex" title="pypath.core.annot.Celltypist.annotate_complex"><code class="xref py py-obj docutils literal notranslate"><span class="pre">annotate_complex</span></code></a>(cplex)</p></td>
+<td><p>Infers annotations for a single complex.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Celltypist.browse" title="pypath.core.annot.Celltypist.browse"><code class="xref py py-obj docutils literal notranslate"><span class="pre">browse</span></code></a>([field, start])</p></td>
+<td><p>Print gene information as a table.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Celltypist.complex_inference" title="pypath.core.annot.Celltypist.complex_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">complex_inference</span></code></a>([complexes])</p></td>
+<td><p>Annotates all complexes in <cite>complexes</cite>, by default in the default complex database (existing in the <cite>complex</cite> module or generated on demand according to the module's current settings).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Celltypist.coverage" title="pypath.core.annot.Celltypist.coverage"><code class="xref py py-obj docutils literal notranslate"><span class="pre">coverage</span></code></a>(other)</p></td>
+<td><p>Calculates the coverage of the annotation i.e. the proportion of entities having at least one record in this annotation resource for an arbitrary set of entities.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Celltypist.curation_effort" title="pypath.core.annot.Celltypist.curation_effort"><code class="xref py py-obj docutils literal notranslate"><span class="pre">curation_effort</span></code></a>()</p></td>
+<td><p>Counts the reference-record pairs.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">from_dump</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_entity_type</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Celltypist.get_names" title="pypath.core.annot.Celltypist.get_names"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_names</span></code></a>()</p></td>
+<td><p>Returns the list of field names in the records.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Celltypist.get_reference_set" title="pypath.core.annot.Celltypist.get_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_reference_set</span></code></a>([proteins, complexes, ...])</p></td>
+<td><p>Retrieves the reference set i.e. the set of all entities which potentially have annotation in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Celltypist.get_subset" title="pypath.core.annot.Celltypist.get_subset"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Celltypist.get_subset_bool_array" title="pypath.core.annot.Celltypist.get_subset_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset_bool_array</span></code></a>([reference_set])</p></td>
+<td><p>Returns a boolean vector with True and False values for each entity in the reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Celltypist.get_values" title="pypath.core.annot.Celltypist.get_values"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_values</span></code></a>(name[, exclude_none])</p></td>
+<td><p>Returns the set of all possible values of a field.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_complex</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_mirna</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_protein</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Celltypist.labels" title="pypath.core.annot.Celltypist.labels"><code class="xref py py-obj docutils literal notranslate"><span class="pre">labels</span></code></a>([method])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Celltypist.load" title="pypath.core.annot.Celltypist.load"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load</span></code></a>()</p></td>
+<td><p>Loads the annotation data by calling the input method.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Celltypist.load_data" title="pypath.core.annot.Celltypist.load_data"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_data</span></code></a>()</p></td>
+<td><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Celltypist.load_proteins" title="pypath.core.annot.Celltypist.load_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_proteins</span></code></a>()</p></td>
+<td><p>Retrieves a set of all UniProt IDs to have a base set of the entire proteome.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Celltypist.make_df" title="pypath.core.annot.Celltypist.make_df"><code class="xref py py-obj docutils literal notranslate"><span class="pre">make_df</span></code></a>([rebuild])</p></td>
+<td><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complex_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Celltypist.numof_entities" title="pypath.core.annot.Celltypist.numof_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_entities</span></code></a>()</p></td>
+<td><p>The number of annotated entities in the resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirna_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirnas</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_protein_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_proteins</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Celltypist.numof_records" title="pypath.core.annot.Celltypist.numof_records"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_records</span></code></a>([entity_types])</p></td>
+<td><p>The total number of annotation records.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Celltypist.numof_references" title="pypath.core.annot.Celltypist.numof_references"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_references</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Celltypist.process" title="pypath.core.annot.Celltypist.process"><code class="xref py py-obj docutils literal notranslate"><span class="pre">process</span></code></a>()</p></td>
+<td><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">proportion</span></code>(other)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Celltypist.reload" title="pypath.core.annot.Celltypist.reload"><code class="xref py py-obj docutils literal notranslate"><span class="pre">reload</span></code></a>()</p></td>
+<td><p>Reloads the object from the module level.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">save_to_pickle</span></code>(pickle_file)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Celltypist.select" title="pypath.core.annot.Celltypist.select"><code class="xref py py-obj docutils literal notranslate"><span class="pre">select</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Celltypist.set_method" title="pypath.core.annot.Celltypist.set_method"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_method</span></code></a>()</p></td>
+<td><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if necessary.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Celltypist.set_reference_set" title="pypath.core.annot.Celltypist.set_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_reference_set</span></code></a>()</p></td>
+<td><p>Assigns the reference set to the :py:attr``reference_set`` attribute.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Celltypist.show" title="pypath.core.annot.Celltypist.show"><code class="xref py py-obj docutils literal notranslate"><span class="pre">show</span></code></a>([method, table_param])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic information from the UniProt datasheets.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Celltypist.subset_intersection" title="pypath.core.annot.Celltypist.subset_intersection"><code class="xref py py-obj docutils literal notranslate"><span class="pre">subset_intersection</span></code></a>(universe, **kwargs)</p></td>
+<td><p>Calculates the proportion of entities in a subset occuring in the set <code class="docutils literal notranslate"><span class="pre">universe</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Celltypist.to_array" title="pypath.core.annot.Celltypist.to_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_array</span></code></a>([reference_set, use_fields])</p></td>
+<td><p>Returns an entity vs feature array.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Celltypist.to_bool_array" title="pypath.core.annot.Celltypist.to_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_bool_array</span></code></a>(reference_set)</p></td>
+<td><p>Returns a presence/absence boolean array for a reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Celltypist.to_set" title="pypath.core.annot.Celltypist.to_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_set</span></code></a>()</p></td>
+<td><p>Returns the entities present in this annotation resource as a set.</p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Attributes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_fields</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">summary</span></code></p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Celltypist.add_complexes_by_inference">
+<span class="sig-name descname"><span class="pre">add_complexes_by_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Celltypist.add_complexes_by_inference" title="Link to this definition">§</a></dt>
+<dd><p>Creates complex annotations by in silico inference and adds them
+to this annotation set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Celltypist.all_complexes">
+<span class="sig-name descname"><span class="pre">all_complexes</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Celltypist.all_complexes" title="Link to this definition">§</a></dt>
+<dd><p>All protein complexes annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Celltypist.all_entities">
+<span class="sig-name descname"><span class="pre">all_entities</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Celltypist.all_entities" title="Link to this definition">§</a></dt>
+<dd><p>All entities annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Celltypist.all_mirnas">
+<span class="sig-name descname"><span class="pre">all_mirnas</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Celltypist.all_mirnas" title="Link to this definition">§</a></dt>
+<dd><p>All miRNAs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Celltypist.all_proteins">
+<span class="sig-name descname"><span class="pre">all_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Celltypist.all_proteins" title="Link to this definition">§</a></dt>
+<dd><p>All UniProt IDs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Celltypist.all_refs">
+<span class="sig-name descname"><span class="pre">all_refs</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Celltypist.all_refs" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects the references
+across all records. Returns <em>list</em>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Celltypist.annotate_complex">
+<span class="sig-name descname"><span class="pre">annotate_complex</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cplex</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Celltypist.annotate_complex" title="Link to this definition">§</a></dt>
+<dd><p>Infers annotations for a single complex.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Celltypist.browse">
+<span class="sig-name descname"><span class="pre">browse</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">field</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">start</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Celltypist.browse" title="Link to this definition">§</a></dt>
+<dd><p>Print gene information as a table.</p>
+<p>Presents information about annotation categories as ascii tables
+printed in the terminal. If one category provided, prints one table.
+If multiple categories provided, prints a table for each of them one
+by one proceeding to the next one once you hit return. If no categories
+provided goes through all levels of the primary category.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>field:</dt><dd><p>The field to browse categories by.</p>
+<ul class="simple">
+<li><p>If None the primary field will be selected.
+If this annotation resource doesn’t have fields, all proteins
+will be presented as one single category.</p></li>
+<li><p>If a string it will be considered a field name and it will
+browse through all levels of this field.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">list</span></code>, set or tuple, it will be considered either a
+<code class="docutils literal notranslate"><span class="pre">list</span></code> of field names or a list of values from the primary
+field. In the former case all combinations of the values of
+the fields will be presented, in the latter case the browsing
+will be limited to the levels of the primary field contained
+in <code class="docutils literal notranslate"><span class="pre">field</span></code>.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">dict</span></code>, keys are supposed to be field names and values
+as list of levels. If any of the values are None, all levels
+from that field will be used.</p></li>
+</ul>
+</dd>
+<dt>start:</dt><dd><p>Start browsing from this category. E.g. if there are 500
+categories and start is 250 it will skip everything before the
+250th.</p>
+</dd>
+<dt>kwargs:</dt><dd><p>Passed to <code class="docutils literal notranslate"><span class="pre">pypath.utils.uniprot.info</span></code>.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Celltypist.complex_inference">
+<span class="sig-name descname"><span class="pre">complex_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Celltypist.complex_inference" title="Link to this definition">§</a></dt>
+<dd><p>Annotates all complexes in <cite>complexes</cite>, by default in the default
+complex database (existing in the <cite>complex</cite> module or generated
+on demand according to the module’s current settings).</p>
+<dl class="field-list simple">
+<dt class="field-odd">Returns<span class="colon">:</span></dt>
+<dd class="field-odd"><p><ul class="simple">
+<li><p><em>Dict with complexes as keys and sets of annotations as values.</em></p></li>
+<li><p><em>Complexes with no valid information in this annotation resource</em></p></li>
+<li><p><em>won’t be in the dict.</em></p></li>
+</ul>
+</p>
+</dd>
+<dt class="field-even">Parameters<span class="colon">:</span></dt>
+<dd class="field-even"><p><strong>complexes</strong> (<em>iterable</em>) – Iterable yielding complexes.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Celltypist.coverage">
+<span class="sig-name descname"><span class="pre">coverage</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">other</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Celltypist.coverage" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the coverage of the annotation i.e. the proportion of
+entities having at least one record in this annotation resource
+for an arbitrary set of entities.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Celltypist.curation_effort">
+<span class="sig-name descname"><span class="pre">curation_effort</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Celltypist.curation_effort" title="Link to this definition">§</a></dt>
+<dd><p>Counts the reference-record pairs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Celltypist.get_names">
+<span class="sig-name descname"><span class="pre">get_names</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Celltypist.get_names" title="Link to this definition">§</a></dt>
+<dd><p>Returns the list of field names in the records. The annotation
+consists of uniform records and each entity might be annotated
+with one or more records. Each record is a tuple of fields, for
+example <code class="docutils literal notranslate"><span class="pre">('cell_type',</span> <span class="pre">'expression_level',</span> <span class="pre">'score')</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Celltypist.get_reference_set">
+<em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">get_reference_set</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">proteins</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">swissprot_only</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Celltypist.get_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the reference set i.e. the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Celltypist.get_subset">
+<span class="sig-name descname"><span class="pre">get_subset</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Celltypist.get_subset" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Celltypist.get_subset_bool_array">
+<span class="sig-name descname"><span class="pre">get_subset_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Celltypist.get_subset_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a boolean vector with True and False values for each entity
+in the reference set. The values represent presence absence data
+in the simplest case, but by providing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> any kind of matching
+and filtering is possible. <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> are passed to the <code class="docutils literal notranslate"><span class="pre">select</span></code>
+method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Celltypist.get_values">
+<span class="sig-name descname"><span class="pre">get_values</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">exclude_none</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Celltypist.get_values" title="Link to this definition">§</a></dt>
+<dd><p>Returns the set of all possible values of a field. E.g. if the
+records of this annotation have a field <code class="docutils literal notranslate"><span class="pre">cell_type</span></code> then calling
+this method can tell you that across all records the values of
+this field might be <code class="docutils literal notranslate"><span class="pre">{'macrophage',</span> <span class="pre">'epithelial_cell',</span> <span class="pre">...}</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Celltypist.labels">
+<span class="sig-name descname"><span class="pre">labels</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Celltypist.labels" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Celltypist.load">
+<span class="sig-name descname"><span class="pre">load</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Celltypist.load" title="Link to this definition">§</a></dt>
+<dd><p>Loads the annotation data by calling the input method.
+Infers annotations for complexes in the complex database if
+py:attr:<code class="docutils literal notranslate"><span class="pre">infer_complexes</span></code> is True.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Celltypist.load_data">
+<span class="sig-name descname"><span class="pre">load_data</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Celltypist.load_data" title="Link to this definition">§</a></dt>
+<dd><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Celltypist.load_proteins">
+<span class="sig-name descname"><span class="pre">load_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Celltypist.load_proteins" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a set of all UniProt IDs to have a base set of the entire
+proteome.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Celltypist.make_df">
+<span class="sig-name descname"><span class="pre">make_df</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">rebuild</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Celltypist.make_df" title="Link to this definition">§</a></dt>
+<dd><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.
+The data frame will be assigned to :py:attr``df``.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Celltypist.numof_entities">
+<span class="sig-name descname"><span class="pre">numof_entities</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Celltypist.numof_entities" title="Link to this definition">§</a></dt>
+<dd><p>The number of annotated entities in the resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Celltypist.numof_records">
+<span class="sig-name descname"><span class="pre">numof_records</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Celltypist.numof_records" title="Link to this definition">§</a></dt>
+<dd><p>The total number of annotation records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Celltypist.numof_references">
+<span class="sig-name descname"><span class="pre">numof_references</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Celltypist.numof_references" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects and counts the
+references across all records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Celltypist.process">
+<span class="sig-name descname"><span class="pre">process</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Celltypist.process" title="Link to this definition">§</a></dt>
+<dd><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Celltypist.reload">
+<span class="sig-name descname"><span class="pre">reload</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Celltypist.reload" title="Link to this definition">§</a></dt>
+<dd><p>Reloads the object from the module level.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Celltypist.select">
+<span class="sig-name descname"><span class="pre">select</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Celltypist.select" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Celltypist.set_method">
+<span class="sig-name descname"><span class="pre">set_method</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Celltypist.set_method" title="Link to this definition">§</a></dt>
+<dd><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if
+necessary.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Celltypist.set_reference_set">
+<span class="sig-name descname"><span class="pre">set_reference_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Celltypist.set_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Assigns the reference set to the :py:attr``reference_set`` attribute.
+The reference set is the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Celltypist.show">
+<span class="sig-name descname"><span class="pre">show</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">table_param</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Celltypist.show" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic
+information from the UniProt datasheets.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Celltypist.subset_intersection">
+<span class="sig-name descname"><span class="pre">subset_intersection</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">universe</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Celltypist.subset_intersection" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the proportion of entities in a subset occuring in the
+set <code class="docutils literal notranslate"><span class="pre">universe</span></code>. The subset is selected by passing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> to the
+<code class="docutils literal notranslate"><span class="pre">select</span></code> method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Celltypist.to_array">
+<span class="sig-name descname"><span class="pre">to_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_fields</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Celltypist.to_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns an entity vs feature array. In case of more complex
+annotations this might be huge.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Celltypist.to_bool_array">
+<span class="sig-name descname"><span class="pre">to_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Celltypist.to_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a presence/absence boolean array for a reference set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Celltypist.to_set">
+<span class="sig-name descname"><span class="pre">to_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Celltypist.to_set" title="Link to this definition">§</a></dt>
+<dd><p>Returns the entities present in this annotation resource as a set.</p>
+</dd></dl>
+
+</dd></dl>
+
+</section>
+
+
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+  <section id="pypath-core-annot-comppi">
+<h1>pypath.core.annot.Comppi<a class="headerlink" href="#pypath-core-annot-comppi" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.core.annot.Comppi">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.core.annot.</span></span><span class="sig-name descname"><span class="pre">Comppi</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#Comppi"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.Comppi" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <a class="reference internal" href="pypath.core.annot.AnnotationBase.html#pypath.core.annot.AnnotationBase" title="pypath.core.annot.AnnotationBase"><code class="xref py py-class docutils literal notranslate"><span class="pre">AnnotationBase</span></code></a></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Comppi.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#Comppi.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.Comppi.__init__" title="Link to this definition">§</a></dt>
+<dd><p>Represents annotations for a set of proteins.
+Loads the data from the original resource and provides methods
+to query the annotations.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>name</strong> (<em>str</em>) – A custom name for the annotation resource.</p></li>
+<li><p><strong>ncbi_tax_id</strong> (<em>int</em>) – NCBI Taxonomy identifier.</p></li>
+<li><p><strong>input_method</strong> (<em>callable</em><em>,</em><em>str</em>) – Either a callable or the name of a method in any submodules of
+the <code class="docutils literal notranslate"><span class="pre">pypath.inputs</span></code>  module. Should return a dict with
+UniProt IDs as keys or an object suitable for <code class="docutils literal notranslate"><span class="pre">process_method</span></code>.</p></li>
+<li><p><strong>input_args</strong> (<em>dict</em>) – Arguments for the <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Comppi.__init__" title="pypath.core.annot.Comppi.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>(**kwargs)</p></td>
+<td><p>Represents annotations for a set of proteins.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Comppi.add_complexes_by_inference" title="pypath.core.annot.Comppi.add_complexes_by_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">add_complexes_by_inference</span></code></a>([complexes])</p></td>
+<td><p>Creates complex annotations by in silico inference and adds them to this annotation set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Comppi.all_complexes" title="pypath.core.annot.Comppi.all_complexes"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_complexes</span></code></a>()</p></td>
+<td><p>All protein complexes annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Comppi.all_entities" title="pypath.core.annot.Comppi.all_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_entities</span></code></a>([entity_types])</p></td>
+<td><p>All entities annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Comppi.all_mirnas" title="pypath.core.annot.Comppi.all_mirnas"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_mirnas</span></code></a>()</p></td>
+<td><p>All miRNAs annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Comppi.all_proteins" title="pypath.core.annot.Comppi.all_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_proteins</span></code></a>()</p></td>
+<td><p>All UniProt IDs annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Comppi.all_refs" title="pypath.core.annot.Comppi.all_refs"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_refs</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Comppi.annotate_complex" title="pypath.core.annot.Comppi.annotate_complex"><code class="xref py py-obj docutils literal notranslate"><span class="pre">annotate_complex</span></code></a>(cplex)</p></td>
+<td><p>Infers annotations for a single complex.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Comppi.browse" title="pypath.core.annot.Comppi.browse"><code class="xref py py-obj docutils literal notranslate"><span class="pre">browse</span></code></a>([field, start])</p></td>
+<td><p>Print gene information as a table.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Comppi.complex_inference" title="pypath.core.annot.Comppi.complex_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">complex_inference</span></code></a>([complexes])</p></td>
+<td><p>Annotates all complexes in <cite>complexes</cite>, by default in the default complex database (existing in the <cite>complex</cite> module or generated on demand according to the module's current settings).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Comppi.coverage" title="pypath.core.annot.Comppi.coverage"><code class="xref py py-obj docutils literal notranslate"><span class="pre">coverage</span></code></a>(other)</p></td>
+<td><p>Calculates the coverage of the annotation i.e. the proportion of entities having at least one record in this annotation resource for an arbitrary set of entities.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Comppi.curation_effort" title="pypath.core.annot.Comppi.curation_effort"><code class="xref py py-obj docutils literal notranslate"><span class="pre">curation_effort</span></code></a>()</p></td>
+<td><p>Counts the reference-record pairs.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">from_dump</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_entity_type</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Comppi.get_names" title="pypath.core.annot.Comppi.get_names"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_names</span></code></a>()</p></td>
+<td><p>Returns the list of field names in the records.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Comppi.get_reference_set" title="pypath.core.annot.Comppi.get_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_reference_set</span></code></a>([proteins, complexes, ...])</p></td>
+<td><p>Retrieves the reference set i.e. the set of all entities which potentially have annotation in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Comppi.get_subset" title="pypath.core.annot.Comppi.get_subset"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Comppi.get_subset_bool_array" title="pypath.core.annot.Comppi.get_subset_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset_bool_array</span></code></a>([reference_set])</p></td>
+<td><p>Returns a boolean vector with True and False values for each entity in the reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Comppi.get_values" title="pypath.core.annot.Comppi.get_values"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_values</span></code></a>(name[, exclude_none])</p></td>
+<td><p>Returns the set of all possible values of a field.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_complex</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_mirna</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_protein</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Comppi.labels" title="pypath.core.annot.Comppi.labels"><code class="xref py py-obj docutils literal notranslate"><span class="pre">labels</span></code></a>([method])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Comppi.load" title="pypath.core.annot.Comppi.load"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load</span></code></a>()</p></td>
+<td><p>Loads the annotation data by calling the input method.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Comppi.load_data" title="pypath.core.annot.Comppi.load_data"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_data</span></code></a>()</p></td>
+<td><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Comppi.load_proteins" title="pypath.core.annot.Comppi.load_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_proteins</span></code></a>()</p></td>
+<td><p>Retrieves a set of all UniProt IDs to have a base set of the entire proteome.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Comppi.make_df" title="pypath.core.annot.Comppi.make_df"><code class="xref py py-obj docutils literal notranslate"><span class="pre">make_df</span></code></a>([rebuild])</p></td>
+<td><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complex_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Comppi.numof_entities" title="pypath.core.annot.Comppi.numof_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_entities</span></code></a>()</p></td>
+<td><p>The number of annotated entities in the resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirna_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirnas</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_protein_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_proteins</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Comppi.numof_records" title="pypath.core.annot.Comppi.numof_records"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_records</span></code></a>([entity_types])</p></td>
+<td><p>The total number of annotation records.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Comppi.numof_references" title="pypath.core.annot.Comppi.numof_references"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_references</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Comppi.process" title="pypath.core.annot.Comppi.process"><code class="xref py py-obj docutils literal notranslate"><span class="pre">process</span></code></a>()</p></td>
+<td><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">proportion</span></code>(other)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Comppi.reload" title="pypath.core.annot.Comppi.reload"><code class="xref py py-obj docutils literal notranslate"><span class="pre">reload</span></code></a>()</p></td>
+<td><p>Reloads the object from the module level.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">save_to_pickle</span></code>(pickle_file)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Comppi.select" title="pypath.core.annot.Comppi.select"><code class="xref py py-obj docutils literal notranslate"><span class="pre">select</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Comppi.set_method" title="pypath.core.annot.Comppi.set_method"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_method</span></code></a>()</p></td>
+<td><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if necessary.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Comppi.set_reference_set" title="pypath.core.annot.Comppi.set_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_reference_set</span></code></a>()</p></td>
+<td><p>Assigns the reference set to the :py:attr``reference_set`` attribute.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Comppi.show" title="pypath.core.annot.Comppi.show"><code class="xref py py-obj docutils literal notranslate"><span class="pre">show</span></code></a>([method, table_param])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic information from the UniProt datasheets.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Comppi.subset_intersection" title="pypath.core.annot.Comppi.subset_intersection"><code class="xref py py-obj docutils literal notranslate"><span class="pre">subset_intersection</span></code></a>(universe, **kwargs)</p></td>
+<td><p>Calculates the proportion of entities in a subset occuring in the set <code class="docutils literal notranslate"><span class="pre">universe</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Comppi.to_array" title="pypath.core.annot.Comppi.to_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_array</span></code></a>([reference_set, use_fields])</p></td>
+<td><p>Returns an entity vs feature array.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Comppi.to_bool_array" title="pypath.core.annot.Comppi.to_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_bool_array</span></code></a>(reference_set)</p></td>
+<td><p>Returns a presence/absence boolean array for a reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Comppi.to_set" title="pypath.core.annot.Comppi.to_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_set</span></code></a>()</p></td>
+<td><p>Returns the entities present in this annotation resource as a set.</p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Attributes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_fields</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">summary</span></code></p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Comppi.add_complexes_by_inference">
+<span class="sig-name descname"><span class="pre">add_complexes_by_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Comppi.add_complexes_by_inference" title="Link to this definition">§</a></dt>
+<dd><p>Creates complex annotations by in silico inference and adds them
+to this annotation set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Comppi.all_complexes">
+<span class="sig-name descname"><span class="pre">all_complexes</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Comppi.all_complexes" title="Link to this definition">§</a></dt>
+<dd><p>All protein complexes annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Comppi.all_entities">
+<span class="sig-name descname"><span class="pre">all_entities</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Comppi.all_entities" title="Link to this definition">§</a></dt>
+<dd><p>All entities annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Comppi.all_mirnas">
+<span class="sig-name descname"><span class="pre">all_mirnas</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Comppi.all_mirnas" title="Link to this definition">§</a></dt>
+<dd><p>All miRNAs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Comppi.all_proteins">
+<span class="sig-name descname"><span class="pre">all_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Comppi.all_proteins" title="Link to this definition">§</a></dt>
+<dd><p>All UniProt IDs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Comppi.all_refs">
+<span class="sig-name descname"><span class="pre">all_refs</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Comppi.all_refs" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects the references
+across all records. Returns <em>list</em>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Comppi.annotate_complex">
+<span class="sig-name descname"><span class="pre">annotate_complex</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cplex</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Comppi.annotate_complex" title="Link to this definition">§</a></dt>
+<dd><p>Infers annotations for a single complex.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Comppi.browse">
+<span class="sig-name descname"><span class="pre">browse</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">field</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">start</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Comppi.browse" title="Link to this definition">§</a></dt>
+<dd><p>Print gene information as a table.</p>
+<p>Presents information about annotation categories as ascii tables
+printed in the terminal. If one category provided, prints one table.
+If multiple categories provided, prints a table for each of them one
+by one proceeding to the next one once you hit return. If no categories
+provided goes through all levels of the primary category.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>field:</dt><dd><p>The field to browse categories by.</p>
+<ul class="simple">
+<li><p>If None the primary field will be selected.
+If this annotation resource doesn’t have fields, all proteins
+will be presented as one single category.</p></li>
+<li><p>If a string it will be considered a field name and it will
+browse through all levels of this field.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">list</span></code>, set or tuple, it will be considered either a
+<code class="docutils literal notranslate"><span class="pre">list</span></code> of field names or a list of values from the primary
+field. In the former case all combinations of the values of
+the fields will be presented, in the latter case the browsing
+will be limited to the levels of the primary field contained
+in <code class="docutils literal notranslate"><span class="pre">field</span></code>.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">dict</span></code>, keys are supposed to be field names and values
+as list of levels. If any of the values are None, all levels
+from that field will be used.</p></li>
+</ul>
+</dd>
+<dt>start:</dt><dd><p>Start browsing from this category. E.g. if there are 500
+categories and start is 250 it will skip everything before the
+250th.</p>
+</dd>
+<dt>kwargs:</dt><dd><p>Passed to <code class="docutils literal notranslate"><span class="pre">pypath.utils.uniprot.info</span></code>.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Comppi.complex_inference">
+<span class="sig-name descname"><span class="pre">complex_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Comppi.complex_inference" title="Link to this definition">§</a></dt>
+<dd><p>Annotates all complexes in <cite>complexes</cite>, by default in the default
+complex database (existing in the <cite>complex</cite> module or generated
+on demand according to the module’s current settings).</p>
+<dl class="field-list simple">
+<dt class="field-odd">Returns<span class="colon">:</span></dt>
+<dd class="field-odd"><p><ul class="simple">
+<li><p><em>Dict with complexes as keys and sets of annotations as values.</em></p></li>
+<li><p><em>Complexes with no valid information in this annotation resource</em></p></li>
+<li><p><em>won’t be in the dict.</em></p></li>
+</ul>
+</p>
+</dd>
+<dt class="field-even">Parameters<span class="colon">:</span></dt>
+<dd class="field-even"><p><strong>complexes</strong> (<em>iterable</em>) – Iterable yielding complexes.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Comppi.coverage">
+<span class="sig-name descname"><span class="pre">coverage</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">other</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Comppi.coverage" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the coverage of the annotation i.e. the proportion of
+entities having at least one record in this annotation resource
+for an arbitrary set of entities.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Comppi.curation_effort">
+<span class="sig-name descname"><span class="pre">curation_effort</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Comppi.curation_effort" title="Link to this definition">§</a></dt>
+<dd><p>Counts the reference-record pairs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Comppi.get_names">
+<span class="sig-name descname"><span class="pre">get_names</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Comppi.get_names" title="Link to this definition">§</a></dt>
+<dd><p>Returns the list of field names in the records. The annotation
+consists of uniform records and each entity might be annotated
+with one or more records. Each record is a tuple of fields, for
+example <code class="docutils literal notranslate"><span class="pre">('cell_type',</span> <span class="pre">'expression_level',</span> <span class="pre">'score')</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Comppi.get_reference_set">
+<em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">get_reference_set</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">proteins</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">swissprot_only</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Comppi.get_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the reference set i.e. the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Comppi.get_subset">
+<span class="sig-name descname"><span class="pre">get_subset</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Comppi.get_subset" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Comppi.get_subset_bool_array">
+<span class="sig-name descname"><span class="pre">get_subset_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Comppi.get_subset_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a boolean vector with True and False values for each entity
+in the reference set. The values represent presence absence data
+in the simplest case, but by providing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> any kind of matching
+and filtering is possible. <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> are passed to the <code class="docutils literal notranslate"><span class="pre">select</span></code>
+method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Comppi.get_values">
+<span class="sig-name descname"><span class="pre">get_values</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">exclude_none</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Comppi.get_values" title="Link to this definition">§</a></dt>
+<dd><p>Returns the set of all possible values of a field. E.g. if the
+records of this annotation have a field <code class="docutils literal notranslate"><span class="pre">cell_type</span></code> then calling
+this method can tell you that across all records the values of
+this field might be <code class="docutils literal notranslate"><span class="pre">{'macrophage',</span> <span class="pre">'epithelial_cell',</span> <span class="pre">...}</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Comppi.labels">
+<span class="sig-name descname"><span class="pre">labels</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Comppi.labels" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Comppi.load">
+<span class="sig-name descname"><span class="pre">load</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Comppi.load" title="Link to this definition">§</a></dt>
+<dd><p>Loads the annotation data by calling the input method.
+Infers annotations for complexes in the complex database if
+py:attr:<code class="docutils literal notranslate"><span class="pre">infer_complexes</span></code> is True.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Comppi.load_data">
+<span class="sig-name descname"><span class="pre">load_data</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Comppi.load_data" title="Link to this definition">§</a></dt>
+<dd><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Comppi.load_proteins">
+<span class="sig-name descname"><span class="pre">load_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Comppi.load_proteins" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a set of all UniProt IDs to have a base set of the entire
+proteome.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Comppi.make_df">
+<span class="sig-name descname"><span class="pre">make_df</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">rebuild</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Comppi.make_df" title="Link to this definition">§</a></dt>
+<dd><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.
+The data frame will be assigned to :py:attr``df``.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Comppi.numof_entities">
+<span class="sig-name descname"><span class="pre">numof_entities</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Comppi.numof_entities" title="Link to this definition">§</a></dt>
+<dd><p>The number of annotated entities in the resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Comppi.numof_records">
+<span class="sig-name descname"><span class="pre">numof_records</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Comppi.numof_records" title="Link to this definition">§</a></dt>
+<dd><p>The total number of annotation records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Comppi.numof_references">
+<span class="sig-name descname"><span class="pre">numof_references</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Comppi.numof_references" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects and counts the
+references across all records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Comppi.process">
+<span class="sig-name descname"><span class="pre">process</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Comppi.process" title="Link to this definition">§</a></dt>
+<dd><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Comppi.reload">
+<span class="sig-name descname"><span class="pre">reload</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Comppi.reload" title="Link to this definition">§</a></dt>
+<dd><p>Reloads the object from the module level.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Comppi.select">
+<span class="sig-name descname"><span class="pre">select</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Comppi.select" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Comppi.set_method">
+<span class="sig-name descname"><span class="pre">set_method</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Comppi.set_method" title="Link to this definition">§</a></dt>
+<dd><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if
+necessary.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Comppi.set_reference_set">
+<span class="sig-name descname"><span class="pre">set_reference_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Comppi.set_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Assigns the reference set to the :py:attr``reference_set`` attribute.
+The reference set is the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Comppi.show">
+<span class="sig-name descname"><span class="pre">show</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">table_param</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Comppi.show" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic
+information from the UniProt datasheets.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Comppi.subset_intersection">
+<span class="sig-name descname"><span class="pre">subset_intersection</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">universe</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Comppi.subset_intersection" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the proportion of entities in a subset occuring in the
+set <code class="docutils literal notranslate"><span class="pre">universe</span></code>. The subset is selected by passing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> to the
+<code class="docutils literal notranslate"><span class="pre">select</span></code> method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Comppi.to_array">
+<span class="sig-name descname"><span class="pre">to_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_fields</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Comppi.to_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns an entity vs feature array. In case of more complex
+annotations this might be huge.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Comppi.to_bool_array">
+<span class="sig-name descname"><span class="pre">to_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Comppi.to_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a presence/absence boolean array for a reference set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Comppi.to_set">
+<span class="sig-name descname"><span class="pre">to_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Comppi.to_set" title="Link to this definition">§</a></dt>
+<dd><p>Returns the entities present in this annotation resource as a set.</p>
+</dd></dl>
+
+</dd></dl>
+
+</section>
+
+
+                </article>
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+  <section id="pypath-core-annot-connectomedb">
+<h1>pypath.core.annot.Connectomedb<a class="headerlink" href="#pypath-core-annot-connectomedb" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.core.annot.Connectomedb">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.core.annot.</span></span><span class="sig-name descname"><span class="pre">Connectomedb</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#Connectomedb"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.Connectomedb" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <a class="reference internal" href="pypath.core.annot.AnnotationBase.html#pypath.core.annot.AnnotationBase" title="pypath.core.annot.AnnotationBase"><code class="xref py py-class docutils literal notranslate"><span class="pre">AnnotationBase</span></code></a></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Connectomedb.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#Connectomedb.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.Connectomedb.__init__" title="Link to this definition">§</a></dt>
+<dd><p>Represents annotations for a set of proteins.
+Loads the data from the original resource and provides methods
+to query the annotations.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>name</strong> (<em>str</em>) – A custom name for the annotation resource.</p></li>
+<li><p><strong>ncbi_tax_id</strong> (<em>int</em>) – NCBI Taxonomy identifier.</p></li>
+<li><p><strong>input_method</strong> (<em>callable</em><em>,</em><em>str</em>) – Either a callable or the name of a method in any submodules of
+the <code class="docutils literal notranslate"><span class="pre">pypath.inputs</span></code>  module. Should return a dict with
+UniProt IDs as keys or an object suitable for <code class="docutils literal notranslate"><span class="pre">process_method</span></code>.</p></li>
+<li><p><strong>input_args</strong> (<em>dict</em>) – Arguments for the <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Connectomedb.__init__" title="pypath.core.annot.Connectomedb.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>(**kwargs)</p></td>
+<td><p>Represents annotations for a set of proteins.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Connectomedb.add_complexes_by_inference" title="pypath.core.annot.Connectomedb.add_complexes_by_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">add_complexes_by_inference</span></code></a>([complexes])</p></td>
+<td><p>Creates complex annotations by in silico inference and adds them to this annotation set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Connectomedb.all_complexes" title="pypath.core.annot.Connectomedb.all_complexes"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_complexes</span></code></a>()</p></td>
+<td><p>All protein complexes annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Connectomedb.all_entities" title="pypath.core.annot.Connectomedb.all_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_entities</span></code></a>([entity_types])</p></td>
+<td><p>All entities annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Connectomedb.all_mirnas" title="pypath.core.annot.Connectomedb.all_mirnas"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_mirnas</span></code></a>()</p></td>
+<td><p>All miRNAs annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Connectomedb.all_proteins" title="pypath.core.annot.Connectomedb.all_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_proteins</span></code></a>()</p></td>
+<td><p>All UniProt IDs annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Connectomedb.all_refs" title="pypath.core.annot.Connectomedb.all_refs"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_refs</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Connectomedb.annotate_complex" title="pypath.core.annot.Connectomedb.annotate_complex"><code class="xref py py-obj docutils literal notranslate"><span class="pre">annotate_complex</span></code></a>(cplex)</p></td>
+<td><p>Infers annotations for a single complex.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Connectomedb.browse" title="pypath.core.annot.Connectomedb.browse"><code class="xref py py-obj docutils literal notranslate"><span class="pre">browse</span></code></a>([field, start])</p></td>
+<td><p>Print gene information as a table.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Connectomedb.complex_inference" title="pypath.core.annot.Connectomedb.complex_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">complex_inference</span></code></a>([complexes])</p></td>
+<td><p>Annotates all complexes in <cite>complexes</cite>, by default in the default complex database (existing in the <cite>complex</cite> module or generated on demand according to the module's current settings).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Connectomedb.coverage" title="pypath.core.annot.Connectomedb.coverage"><code class="xref py py-obj docutils literal notranslate"><span class="pre">coverage</span></code></a>(other)</p></td>
+<td><p>Calculates the coverage of the annotation i.e. the proportion of entities having at least one record in this annotation resource for an arbitrary set of entities.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Connectomedb.curation_effort" title="pypath.core.annot.Connectomedb.curation_effort"><code class="xref py py-obj docutils literal notranslate"><span class="pre">curation_effort</span></code></a>()</p></td>
+<td><p>Counts the reference-record pairs.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">from_dump</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_entity_type</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Connectomedb.get_names" title="pypath.core.annot.Connectomedb.get_names"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_names</span></code></a>()</p></td>
+<td><p>Returns the list of field names in the records.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Connectomedb.get_reference_set" title="pypath.core.annot.Connectomedb.get_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_reference_set</span></code></a>([proteins, complexes, ...])</p></td>
+<td><p>Retrieves the reference set i.e. the set of all entities which potentially have annotation in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Connectomedb.get_subset" title="pypath.core.annot.Connectomedb.get_subset"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Connectomedb.get_subset_bool_array" title="pypath.core.annot.Connectomedb.get_subset_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset_bool_array</span></code></a>([reference_set])</p></td>
+<td><p>Returns a boolean vector with True and False values for each entity in the reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Connectomedb.get_values" title="pypath.core.annot.Connectomedb.get_values"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_values</span></code></a>(name[, exclude_none])</p></td>
+<td><p>Returns the set of all possible values of a field.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_complex</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_mirna</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_protein</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Connectomedb.labels" title="pypath.core.annot.Connectomedb.labels"><code class="xref py py-obj docutils literal notranslate"><span class="pre">labels</span></code></a>([method])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Connectomedb.load" title="pypath.core.annot.Connectomedb.load"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load</span></code></a>()</p></td>
+<td><p>Loads the annotation data by calling the input method.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Connectomedb.load_data" title="pypath.core.annot.Connectomedb.load_data"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_data</span></code></a>()</p></td>
+<td><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Connectomedb.load_proteins" title="pypath.core.annot.Connectomedb.load_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_proteins</span></code></a>()</p></td>
+<td><p>Retrieves a set of all UniProt IDs to have a base set of the entire proteome.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Connectomedb.make_df" title="pypath.core.annot.Connectomedb.make_df"><code class="xref py py-obj docutils literal notranslate"><span class="pre">make_df</span></code></a>([rebuild])</p></td>
+<td><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complex_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Connectomedb.numof_entities" title="pypath.core.annot.Connectomedb.numof_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_entities</span></code></a>()</p></td>
+<td><p>The number of annotated entities in the resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirna_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirnas</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_protein_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_proteins</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Connectomedb.numof_records" title="pypath.core.annot.Connectomedb.numof_records"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_records</span></code></a>([entity_types])</p></td>
+<td><p>The total number of annotation records.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Connectomedb.numof_references" title="pypath.core.annot.Connectomedb.numof_references"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_references</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Connectomedb.process" title="pypath.core.annot.Connectomedb.process"><code class="xref py py-obj docutils literal notranslate"><span class="pre">process</span></code></a>()</p></td>
+<td><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">proportion</span></code>(other)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Connectomedb.reload" title="pypath.core.annot.Connectomedb.reload"><code class="xref py py-obj docutils literal notranslate"><span class="pre">reload</span></code></a>()</p></td>
+<td><p>Reloads the object from the module level.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">save_to_pickle</span></code>(pickle_file)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Connectomedb.select" title="pypath.core.annot.Connectomedb.select"><code class="xref py py-obj docutils literal notranslate"><span class="pre">select</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Connectomedb.set_method" title="pypath.core.annot.Connectomedb.set_method"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_method</span></code></a>()</p></td>
+<td><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if necessary.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Connectomedb.set_reference_set" title="pypath.core.annot.Connectomedb.set_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_reference_set</span></code></a>()</p></td>
+<td><p>Assigns the reference set to the :py:attr``reference_set`` attribute.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Connectomedb.show" title="pypath.core.annot.Connectomedb.show"><code class="xref py py-obj docutils literal notranslate"><span class="pre">show</span></code></a>([method, table_param])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic information from the UniProt datasheets.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Connectomedb.subset_intersection" title="pypath.core.annot.Connectomedb.subset_intersection"><code class="xref py py-obj docutils literal notranslate"><span class="pre">subset_intersection</span></code></a>(universe, **kwargs)</p></td>
+<td><p>Calculates the proportion of entities in a subset occuring in the set <code class="docutils literal notranslate"><span class="pre">universe</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Connectomedb.to_array" title="pypath.core.annot.Connectomedb.to_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_array</span></code></a>([reference_set, use_fields])</p></td>
+<td><p>Returns an entity vs feature array.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Connectomedb.to_bool_array" title="pypath.core.annot.Connectomedb.to_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_bool_array</span></code></a>(reference_set)</p></td>
+<td><p>Returns a presence/absence boolean array for a reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Connectomedb.to_set" title="pypath.core.annot.Connectomedb.to_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_set</span></code></a>()</p></td>
+<td><p>Returns the entities present in this annotation resource as a set.</p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Attributes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_fields</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">summary</span></code></p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Connectomedb.add_complexes_by_inference">
+<span class="sig-name descname"><span class="pre">add_complexes_by_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Connectomedb.add_complexes_by_inference" title="Link to this definition">§</a></dt>
+<dd><p>Creates complex annotations by in silico inference and adds them
+to this annotation set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Connectomedb.all_complexes">
+<span class="sig-name descname"><span class="pre">all_complexes</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Connectomedb.all_complexes" title="Link to this definition">§</a></dt>
+<dd><p>All protein complexes annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Connectomedb.all_entities">
+<span class="sig-name descname"><span class="pre">all_entities</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Connectomedb.all_entities" title="Link to this definition">§</a></dt>
+<dd><p>All entities annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Connectomedb.all_mirnas">
+<span class="sig-name descname"><span class="pre">all_mirnas</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Connectomedb.all_mirnas" title="Link to this definition">§</a></dt>
+<dd><p>All miRNAs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Connectomedb.all_proteins">
+<span class="sig-name descname"><span class="pre">all_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Connectomedb.all_proteins" title="Link to this definition">§</a></dt>
+<dd><p>All UniProt IDs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Connectomedb.all_refs">
+<span class="sig-name descname"><span class="pre">all_refs</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Connectomedb.all_refs" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects the references
+across all records. Returns <em>list</em>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Connectomedb.annotate_complex">
+<span class="sig-name descname"><span class="pre">annotate_complex</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cplex</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Connectomedb.annotate_complex" title="Link to this definition">§</a></dt>
+<dd><p>Infers annotations for a single complex.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Connectomedb.browse">
+<span class="sig-name descname"><span class="pre">browse</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">field</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">start</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Connectomedb.browse" title="Link to this definition">§</a></dt>
+<dd><p>Print gene information as a table.</p>
+<p>Presents information about annotation categories as ascii tables
+printed in the terminal. If one category provided, prints one table.
+If multiple categories provided, prints a table for each of them one
+by one proceeding to the next one once you hit return. If no categories
+provided goes through all levels of the primary category.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>field:</dt><dd><p>The field to browse categories by.</p>
+<ul class="simple">
+<li><p>If None the primary field will be selected.
+If this annotation resource doesn’t have fields, all proteins
+will be presented as one single category.</p></li>
+<li><p>If a string it will be considered a field name and it will
+browse through all levels of this field.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">list</span></code>, set or tuple, it will be considered either a
+<code class="docutils literal notranslate"><span class="pre">list</span></code> of field names or a list of values from the primary
+field. In the former case all combinations of the values of
+the fields will be presented, in the latter case the browsing
+will be limited to the levels of the primary field contained
+in <code class="docutils literal notranslate"><span class="pre">field</span></code>.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">dict</span></code>, keys are supposed to be field names and values
+as list of levels. If any of the values are None, all levels
+from that field will be used.</p></li>
+</ul>
+</dd>
+<dt>start:</dt><dd><p>Start browsing from this category. E.g. if there are 500
+categories and start is 250 it will skip everything before the
+250th.</p>
+</dd>
+<dt>kwargs:</dt><dd><p>Passed to <code class="docutils literal notranslate"><span class="pre">pypath.utils.uniprot.info</span></code>.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Connectomedb.complex_inference">
+<span class="sig-name descname"><span class="pre">complex_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Connectomedb.complex_inference" title="Link to this definition">§</a></dt>
+<dd><p>Annotates all complexes in <cite>complexes</cite>, by default in the default
+complex database (existing in the <cite>complex</cite> module or generated
+on demand according to the module’s current settings).</p>
+<dl class="field-list simple">
+<dt class="field-odd">Returns<span class="colon">:</span></dt>
+<dd class="field-odd"><p><ul class="simple">
+<li><p><em>Dict with complexes as keys and sets of annotations as values.</em></p></li>
+<li><p><em>Complexes with no valid information in this annotation resource</em></p></li>
+<li><p><em>won’t be in the dict.</em></p></li>
+</ul>
+</p>
+</dd>
+<dt class="field-even">Parameters<span class="colon">:</span></dt>
+<dd class="field-even"><p><strong>complexes</strong> (<em>iterable</em>) – Iterable yielding complexes.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Connectomedb.coverage">
+<span class="sig-name descname"><span class="pre">coverage</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">other</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Connectomedb.coverage" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the coverage of the annotation i.e. the proportion of
+entities having at least one record in this annotation resource
+for an arbitrary set of entities.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Connectomedb.curation_effort">
+<span class="sig-name descname"><span class="pre">curation_effort</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Connectomedb.curation_effort" title="Link to this definition">§</a></dt>
+<dd><p>Counts the reference-record pairs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Connectomedb.get_names">
+<span class="sig-name descname"><span class="pre">get_names</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Connectomedb.get_names" title="Link to this definition">§</a></dt>
+<dd><p>Returns the list of field names in the records. The annotation
+consists of uniform records and each entity might be annotated
+with one or more records. Each record is a tuple of fields, for
+example <code class="docutils literal notranslate"><span class="pre">('cell_type',</span> <span class="pre">'expression_level',</span> <span class="pre">'score')</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Connectomedb.get_reference_set">
+<em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">get_reference_set</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">proteins</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">swissprot_only</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Connectomedb.get_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the reference set i.e. the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Connectomedb.get_subset">
+<span class="sig-name descname"><span class="pre">get_subset</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Connectomedb.get_subset" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Connectomedb.get_subset_bool_array">
+<span class="sig-name descname"><span class="pre">get_subset_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Connectomedb.get_subset_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a boolean vector with True and False values for each entity
+in the reference set. The values represent presence absence data
+in the simplest case, but by providing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> any kind of matching
+and filtering is possible. <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> are passed to the <code class="docutils literal notranslate"><span class="pre">select</span></code>
+method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Connectomedb.get_values">
+<span class="sig-name descname"><span class="pre">get_values</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">exclude_none</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Connectomedb.get_values" title="Link to this definition">§</a></dt>
+<dd><p>Returns the set of all possible values of a field. E.g. if the
+records of this annotation have a field <code class="docutils literal notranslate"><span class="pre">cell_type</span></code> then calling
+this method can tell you that across all records the values of
+this field might be <code class="docutils literal notranslate"><span class="pre">{'macrophage',</span> <span class="pre">'epithelial_cell',</span> <span class="pre">...}</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Connectomedb.labels">
+<span class="sig-name descname"><span class="pre">labels</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Connectomedb.labels" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Connectomedb.load">
+<span class="sig-name descname"><span class="pre">load</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Connectomedb.load" title="Link to this definition">§</a></dt>
+<dd><p>Loads the annotation data by calling the input method.
+Infers annotations for complexes in the complex database if
+py:attr:<code class="docutils literal notranslate"><span class="pre">infer_complexes</span></code> is True.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Connectomedb.load_data">
+<span class="sig-name descname"><span class="pre">load_data</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Connectomedb.load_data" title="Link to this definition">§</a></dt>
+<dd><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Connectomedb.load_proteins">
+<span class="sig-name descname"><span class="pre">load_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Connectomedb.load_proteins" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a set of all UniProt IDs to have a base set of the entire
+proteome.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Connectomedb.make_df">
+<span class="sig-name descname"><span class="pre">make_df</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">rebuild</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Connectomedb.make_df" title="Link to this definition">§</a></dt>
+<dd><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.
+The data frame will be assigned to :py:attr``df``.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Connectomedb.numof_entities">
+<span class="sig-name descname"><span class="pre">numof_entities</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Connectomedb.numof_entities" title="Link to this definition">§</a></dt>
+<dd><p>The number of annotated entities in the resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Connectomedb.numof_records">
+<span class="sig-name descname"><span class="pre">numof_records</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Connectomedb.numof_records" title="Link to this definition">§</a></dt>
+<dd><p>The total number of annotation records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Connectomedb.numof_references">
+<span class="sig-name descname"><span class="pre">numof_references</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Connectomedb.numof_references" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects and counts the
+references across all records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Connectomedb.process">
+<span class="sig-name descname"><span class="pre">process</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Connectomedb.process" title="Link to this definition">§</a></dt>
+<dd><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Connectomedb.reload">
+<span class="sig-name descname"><span class="pre">reload</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Connectomedb.reload" title="Link to this definition">§</a></dt>
+<dd><p>Reloads the object from the module level.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Connectomedb.select">
+<span class="sig-name descname"><span class="pre">select</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Connectomedb.select" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Connectomedb.set_method">
+<span class="sig-name descname"><span class="pre">set_method</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Connectomedb.set_method" title="Link to this definition">§</a></dt>
+<dd><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if
+necessary.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Connectomedb.set_reference_set">
+<span class="sig-name descname"><span class="pre">set_reference_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Connectomedb.set_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Assigns the reference set to the :py:attr``reference_set`` attribute.
+The reference set is the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Connectomedb.show">
+<span class="sig-name descname"><span class="pre">show</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">table_param</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Connectomedb.show" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic
+information from the UniProt datasheets.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Connectomedb.subset_intersection">
+<span class="sig-name descname"><span class="pre">subset_intersection</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">universe</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Connectomedb.subset_intersection" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the proportion of entities in a subset occuring in the
+set <code class="docutils literal notranslate"><span class="pre">universe</span></code>. The subset is selected by passing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> to the
+<code class="docutils literal notranslate"><span class="pre">select</span></code> method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Connectomedb.to_array">
+<span class="sig-name descname"><span class="pre">to_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_fields</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Connectomedb.to_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns an entity vs feature array. In case of more complex
+annotations this might be huge.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Connectomedb.to_bool_array">
+<span class="sig-name descname"><span class="pre">to_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Connectomedb.to_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a presence/absence boolean array for a reference set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Connectomedb.to_set">
+<span class="sig-name descname"><span class="pre">to_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Connectomedb.to_set" title="Link to this definition">§</a></dt>
+<dd><p>Returns the entities present in this annotation resource as a set.</p>
+</dd></dl>
+
+</dd></dl>
+
+</section>
+
+
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+  <section id="pypath-core-annot-corum">
+<h1>pypath.core.annot.Corum<a class="headerlink" href="#pypath-core-annot-corum" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.core.annot.Corum">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.core.annot.</span></span><span class="sig-name descname"><span class="pre">Corum</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">annot_attr</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#Corum"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.Corum" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <a class="reference internal" href="pypath.core.annot.AnnotationBase.html#pypath.core.annot.AnnotationBase" title="pypath.core.annot.AnnotationBase"><code class="xref py py-class docutils literal notranslate"><span class="pre">AnnotationBase</span></code></a></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Corum.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">annot_attr</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#Corum.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.Corum.__init__" title="Link to this definition">§</a></dt>
+<dd><p>Represents annotations for a set of proteins.
+Loads the data from the original resource and provides methods
+to query the annotations.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>name</strong> (<em>str</em>) – A custom name for the annotation resource.</p></li>
+<li><p><strong>ncbi_tax_id</strong> (<em>int</em>) – NCBI Taxonomy identifier.</p></li>
+<li><p><strong>input_method</strong> (<em>callable</em><em>,</em><em>str</em>) – Either a callable or the name of a method in any submodules of
+the <code class="docutils literal notranslate"><span class="pre">pypath.inputs</span></code>  module. Should return a dict with
+UniProt IDs as keys or an object suitable for <code class="docutils literal notranslate"><span class="pre">process_method</span></code>.</p></li>
+<li><p><strong>input_args</strong> (<em>dict</em>) – Arguments for the <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Corum.__init__" title="pypath.core.annot.Corum.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>(name, annot_attr, **kwargs)</p></td>
+<td><p>Represents annotations for a set of proteins.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Corum.add_complexes_by_inference" title="pypath.core.annot.Corum.add_complexes_by_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">add_complexes_by_inference</span></code></a>([complexes])</p></td>
+<td><p>Creates complex annotations by in silico inference and adds them to this annotation set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Corum.all_complexes" title="pypath.core.annot.Corum.all_complexes"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_complexes</span></code></a>()</p></td>
+<td><p>All protein complexes annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Corum.all_entities" title="pypath.core.annot.Corum.all_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_entities</span></code></a>([entity_types])</p></td>
+<td><p>All entities annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Corum.all_mirnas" title="pypath.core.annot.Corum.all_mirnas"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_mirnas</span></code></a>()</p></td>
+<td><p>All miRNAs annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Corum.all_proteins" title="pypath.core.annot.Corum.all_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_proteins</span></code></a>()</p></td>
+<td><p>All UniProt IDs annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Corum.all_refs" title="pypath.core.annot.Corum.all_refs"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_refs</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Corum.annotate_complex" title="pypath.core.annot.Corum.annotate_complex"><code class="xref py py-obj docutils literal notranslate"><span class="pre">annotate_complex</span></code></a>(cplex)</p></td>
+<td><p>Infers annotations for a single complex.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Corum.browse" title="pypath.core.annot.Corum.browse"><code class="xref py py-obj docutils literal notranslate"><span class="pre">browse</span></code></a>([field, start])</p></td>
+<td><p>Print gene information as a table.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Corum.complex_inference" title="pypath.core.annot.Corum.complex_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">complex_inference</span></code></a>([complexes])</p></td>
+<td><p>Annotates all complexes in <cite>complexes</cite>, by default in the default complex database (existing in the <cite>complex</cite> module or generated on demand according to the module's current settings).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Corum.coverage" title="pypath.core.annot.Corum.coverage"><code class="xref py py-obj docutils literal notranslate"><span class="pre">coverage</span></code></a>(other)</p></td>
+<td><p>Calculates the coverage of the annotation i.e. the proportion of entities having at least one record in this annotation resource for an arbitrary set of entities.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Corum.curation_effort" title="pypath.core.annot.Corum.curation_effort"><code class="xref py py-obj docutils literal notranslate"><span class="pre">curation_effort</span></code></a>()</p></td>
+<td><p>Counts the reference-record pairs.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">from_dump</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_entity_type</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Corum.get_names" title="pypath.core.annot.Corum.get_names"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_names</span></code></a>()</p></td>
+<td><p>Returns the list of field names in the records.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Corum.get_reference_set" title="pypath.core.annot.Corum.get_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_reference_set</span></code></a>([proteins, complexes, ...])</p></td>
+<td><p>Retrieves the reference set i.e. the set of all entities which potentially have annotation in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Corum.get_subset" title="pypath.core.annot.Corum.get_subset"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Corum.get_subset_bool_array" title="pypath.core.annot.Corum.get_subset_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset_bool_array</span></code></a>([reference_set])</p></td>
+<td><p>Returns a boolean vector with True and False values for each entity in the reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Corum.get_values" title="pypath.core.annot.Corum.get_values"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_values</span></code></a>(name[, exclude_none])</p></td>
+<td><p>Returns the set of all possible values of a field.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_complex</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_mirna</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_protein</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Corum.labels" title="pypath.core.annot.Corum.labels"><code class="xref py py-obj docutils literal notranslate"><span class="pre">labels</span></code></a>([method])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Corum.load" title="pypath.core.annot.Corum.load"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load</span></code></a>()</p></td>
+<td><p>Loads the annotation data by calling the input method.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Corum.load_data" title="pypath.core.annot.Corum.load_data"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_data</span></code></a>()</p></td>
+<td><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Corum.load_proteins" title="pypath.core.annot.Corum.load_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_proteins</span></code></a>()</p></td>
+<td><p>Retrieves a set of all UniProt IDs to have a base set of the entire proteome.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Corum.make_df" title="pypath.core.annot.Corum.make_df"><code class="xref py py-obj docutils literal notranslate"><span class="pre">make_df</span></code></a>([rebuild])</p></td>
+<td><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complex_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Corum.numof_entities" title="pypath.core.annot.Corum.numof_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_entities</span></code></a>()</p></td>
+<td><p>The number of annotated entities in the resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirna_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirnas</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_protein_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_proteins</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Corum.numof_records" title="pypath.core.annot.Corum.numof_records"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_records</span></code></a>([entity_types])</p></td>
+<td><p>The total number of annotation records.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Corum.numof_references" title="pypath.core.annot.Corum.numof_references"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_references</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Corum.process" title="pypath.core.annot.Corum.process"><code class="xref py py-obj docutils literal notranslate"><span class="pre">process</span></code></a>()</p></td>
+<td><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">proportion</span></code>(other)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Corum.reload" title="pypath.core.annot.Corum.reload"><code class="xref py py-obj docutils literal notranslate"><span class="pre">reload</span></code></a>()</p></td>
+<td><p>Reloads the object from the module level.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">save_to_pickle</span></code>(pickle_file)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Corum.select" title="pypath.core.annot.Corum.select"><code class="xref py py-obj docutils literal notranslate"><span class="pre">select</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Corum.set_method" title="pypath.core.annot.Corum.set_method"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_method</span></code></a>()</p></td>
+<td><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if necessary.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Corum.set_reference_set" title="pypath.core.annot.Corum.set_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_reference_set</span></code></a>()</p></td>
+<td><p>Assigns the reference set to the :py:attr``reference_set`` attribute.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Corum.show" title="pypath.core.annot.Corum.show"><code class="xref py py-obj docutils literal notranslate"><span class="pre">show</span></code></a>([method, table_param])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic information from the UniProt datasheets.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Corum.subset_intersection" title="pypath.core.annot.Corum.subset_intersection"><code class="xref py py-obj docutils literal notranslate"><span class="pre">subset_intersection</span></code></a>(universe, **kwargs)</p></td>
+<td><p>Calculates the proportion of entities in a subset occuring in the set <code class="docutils literal notranslate"><span class="pre">universe</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Corum.to_array" title="pypath.core.annot.Corum.to_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_array</span></code></a>([reference_set, use_fields])</p></td>
+<td><p>Returns an entity vs feature array.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Corum.to_bool_array" title="pypath.core.annot.Corum.to_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_bool_array</span></code></a>(reference_set)</p></td>
+<td><p>Returns a presence/absence boolean array for a reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Corum.to_set" title="pypath.core.annot.Corum.to_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_set</span></code></a>()</p></td>
+<td><p>Returns the entities present in this annotation resource as a set.</p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Attributes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_fields</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">summary</span></code></p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Corum.add_complexes_by_inference">
+<span class="sig-name descname"><span class="pre">add_complexes_by_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Corum.add_complexes_by_inference" title="Link to this definition">§</a></dt>
+<dd><p>Creates complex annotations by in silico inference and adds them
+to this annotation set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Corum.all_complexes">
+<span class="sig-name descname"><span class="pre">all_complexes</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Corum.all_complexes" title="Link to this definition">§</a></dt>
+<dd><p>All protein complexes annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Corum.all_entities">
+<span class="sig-name descname"><span class="pre">all_entities</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Corum.all_entities" title="Link to this definition">§</a></dt>
+<dd><p>All entities annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Corum.all_mirnas">
+<span class="sig-name descname"><span class="pre">all_mirnas</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Corum.all_mirnas" title="Link to this definition">§</a></dt>
+<dd><p>All miRNAs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Corum.all_proteins">
+<span class="sig-name descname"><span class="pre">all_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Corum.all_proteins" title="Link to this definition">§</a></dt>
+<dd><p>All UniProt IDs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Corum.all_refs">
+<span class="sig-name descname"><span class="pre">all_refs</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Corum.all_refs" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects the references
+across all records. Returns <em>list</em>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Corum.annotate_complex">
+<span class="sig-name descname"><span class="pre">annotate_complex</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cplex</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Corum.annotate_complex" title="Link to this definition">§</a></dt>
+<dd><p>Infers annotations for a single complex.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Corum.browse">
+<span class="sig-name descname"><span class="pre">browse</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">field</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">start</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Corum.browse" title="Link to this definition">§</a></dt>
+<dd><p>Print gene information as a table.</p>
+<p>Presents information about annotation categories as ascii tables
+printed in the terminal. If one category provided, prints one table.
+If multiple categories provided, prints a table for each of them one
+by one proceeding to the next one once you hit return. If no categories
+provided goes through all levels of the primary category.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>field:</dt><dd><p>The field to browse categories by.</p>
+<ul class="simple">
+<li><p>If None the primary field will be selected.
+If this annotation resource doesn’t have fields, all proteins
+will be presented as one single category.</p></li>
+<li><p>If a string it will be considered a field name and it will
+browse through all levels of this field.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">list</span></code>, set or tuple, it will be considered either a
+<code class="docutils literal notranslate"><span class="pre">list</span></code> of field names or a list of values from the primary
+field. In the former case all combinations of the values of
+the fields will be presented, in the latter case the browsing
+will be limited to the levels of the primary field contained
+in <code class="docutils literal notranslate"><span class="pre">field</span></code>.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">dict</span></code>, keys are supposed to be field names and values
+as list of levels. If any of the values are None, all levels
+from that field will be used.</p></li>
+</ul>
+</dd>
+<dt>start:</dt><dd><p>Start browsing from this category. E.g. if there are 500
+categories and start is 250 it will skip everything before the
+250th.</p>
+</dd>
+<dt>kwargs:</dt><dd><p>Passed to <code class="docutils literal notranslate"><span class="pre">pypath.utils.uniprot.info</span></code>.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Corum.complex_inference">
+<span class="sig-name descname"><span class="pre">complex_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Corum.complex_inference" title="Link to this definition">§</a></dt>
+<dd><p>Annotates all complexes in <cite>complexes</cite>, by default in the default
+complex database (existing in the <cite>complex</cite> module or generated
+on demand according to the module’s current settings).</p>
+<dl class="field-list simple">
+<dt class="field-odd">Returns<span class="colon">:</span></dt>
+<dd class="field-odd"><p><ul class="simple">
+<li><p><em>Dict with complexes as keys and sets of annotations as values.</em></p></li>
+<li><p><em>Complexes with no valid information in this annotation resource</em></p></li>
+<li><p><em>won’t be in the dict.</em></p></li>
+</ul>
+</p>
+</dd>
+<dt class="field-even">Parameters<span class="colon">:</span></dt>
+<dd class="field-even"><p><strong>complexes</strong> (<em>iterable</em>) – Iterable yielding complexes.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Corum.coverage">
+<span class="sig-name descname"><span class="pre">coverage</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">other</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Corum.coverage" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the coverage of the annotation i.e. the proportion of
+entities having at least one record in this annotation resource
+for an arbitrary set of entities.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Corum.curation_effort">
+<span class="sig-name descname"><span class="pre">curation_effort</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Corum.curation_effort" title="Link to this definition">§</a></dt>
+<dd><p>Counts the reference-record pairs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Corum.get_names">
+<span class="sig-name descname"><span class="pre">get_names</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Corum.get_names" title="Link to this definition">§</a></dt>
+<dd><p>Returns the list of field names in the records. The annotation
+consists of uniform records and each entity might be annotated
+with one or more records. Each record is a tuple of fields, for
+example <code class="docutils literal notranslate"><span class="pre">('cell_type',</span> <span class="pre">'expression_level',</span> <span class="pre">'score')</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Corum.get_reference_set">
+<em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">get_reference_set</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">proteins</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">swissprot_only</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Corum.get_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the reference set i.e. the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Corum.get_subset">
+<span class="sig-name descname"><span class="pre">get_subset</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Corum.get_subset" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Corum.get_subset_bool_array">
+<span class="sig-name descname"><span class="pre">get_subset_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Corum.get_subset_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a boolean vector with True and False values for each entity
+in the reference set. The values represent presence absence data
+in the simplest case, but by providing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> any kind of matching
+and filtering is possible. <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> are passed to the <code class="docutils literal notranslate"><span class="pre">select</span></code>
+method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Corum.get_values">
+<span class="sig-name descname"><span class="pre">get_values</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">exclude_none</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Corum.get_values" title="Link to this definition">§</a></dt>
+<dd><p>Returns the set of all possible values of a field. E.g. if the
+records of this annotation have a field <code class="docutils literal notranslate"><span class="pre">cell_type</span></code> then calling
+this method can tell you that across all records the values of
+this field might be <code class="docutils literal notranslate"><span class="pre">{'macrophage',</span> <span class="pre">'epithelial_cell',</span> <span class="pre">...}</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Corum.labels">
+<span class="sig-name descname"><span class="pre">labels</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Corum.labels" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Corum.load">
+<span class="sig-name descname"><span class="pre">load</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Corum.load" title="Link to this definition">§</a></dt>
+<dd><p>Loads the annotation data by calling the input method.
+Infers annotations for complexes in the complex database if
+py:attr:<code class="docutils literal notranslate"><span class="pre">infer_complexes</span></code> is True.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Corum.load_data">
+<span class="sig-name descname"><span class="pre">load_data</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Corum.load_data" title="Link to this definition">§</a></dt>
+<dd><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Corum.load_proteins">
+<span class="sig-name descname"><span class="pre">load_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Corum.load_proteins" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a set of all UniProt IDs to have a base set of the entire
+proteome.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Corum.make_df">
+<span class="sig-name descname"><span class="pre">make_df</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">rebuild</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Corum.make_df" title="Link to this definition">§</a></dt>
+<dd><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.
+The data frame will be assigned to :py:attr``df``.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Corum.numof_entities">
+<span class="sig-name descname"><span class="pre">numof_entities</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Corum.numof_entities" title="Link to this definition">§</a></dt>
+<dd><p>The number of annotated entities in the resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Corum.numof_records">
+<span class="sig-name descname"><span class="pre">numof_records</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Corum.numof_records" title="Link to this definition">§</a></dt>
+<dd><p>The total number of annotation records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Corum.numof_references">
+<span class="sig-name descname"><span class="pre">numof_references</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Corum.numof_references" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects and counts the
+references across all records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Corum.process">
+<span class="sig-name descname"><span class="pre">process</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Corum.process" title="Link to this definition">§</a></dt>
+<dd><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Corum.reload">
+<span class="sig-name descname"><span class="pre">reload</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Corum.reload" title="Link to this definition">§</a></dt>
+<dd><p>Reloads the object from the module level.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Corum.select">
+<span class="sig-name descname"><span class="pre">select</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Corum.select" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Corum.set_method">
+<span class="sig-name descname"><span class="pre">set_method</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Corum.set_method" title="Link to this definition">§</a></dt>
+<dd><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if
+necessary.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Corum.set_reference_set">
+<span class="sig-name descname"><span class="pre">set_reference_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Corum.set_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Assigns the reference set to the :py:attr``reference_set`` attribute.
+The reference set is the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Corum.show">
+<span class="sig-name descname"><span class="pre">show</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">table_param</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Corum.show" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic
+information from the UniProt datasheets.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Corum.subset_intersection">
+<span class="sig-name descname"><span class="pre">subset_intersection</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">universe</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Corum.subset_intersection" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the proportion of entities in a subset occuring in the
+set <code class="docutils literal notranslate"><span class="pre">universe</span></code>. The subset is selected by passing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> to the
+<code class="docutils literal notranslate"><span class="pre">select</span></code> method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Corum.to_array">
+<span class="sig-name descname"><span class="pre">to_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_fields</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Corum.to_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns an entity vs feature array. In case of more complex
+annotations this might be huge.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Corum.to_bool_array">
+<span class="sig-name descname"><span class="pre">to_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Corum.to_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a presence/absence boolean array for a reference set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Corum.to_set">
+<span class="sig-name descname"><span class="pre">to_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Corum.to_set" title="Link to this definition">§</a></dt>
+<dd><p>Returns the entities present in this annotation resource as a set.</p>
+</dd></dl>
+
+</dd></dl>
+
+</section>
+
+
+                </article>
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+  <section id="pypath-core-annot-corumfuncat">
+<h1>pypath.core.annot.CorumFuncat<a class="headerlink" href="#pypath-core-annot-corumfuncat" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.core.annot.CorumFuncat">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.core.annot.</span></span><span class="sig-name descname"><span class="pre">CorumFuncat</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#CorumFuncat"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.CorumFuncat" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <a class="reference internal" href="pypath.core.annot.Corum.html#pypath.core.annot.Corum" title="pypath.core.annot.Corum"><code class="xref py py-class docutils literal notranslate"><span class="pre">Corum</span></code></a></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CorumFuncat.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#CorumFuncat.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.CorumFuncat.__init__" title="Link to this definition">§</a></dt>
+<dd><p>Represents annotations for a set of proteins.
+Loads the data from the original resource and provides methods
+to query the annotations.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>name</strong> (<em>str</em>) – A custom name for the annotation resource.</p></li>
+<li><p><strong>ncbi_tax_id</strong> (<em>int</em>) – NCBI Taxonomy identifier.</p></li>
+<li><p><strong>input_method</strong> (<em>callable</em><em>,</em><em>str</em>) – Either a callable or the name of a method in any submodules of
+the <code class="docutils literal notranslate"><span class="pre">pypath.inputs</span></code>  module. Should return a dict with
+UniProt IDs as keys or an object suitable for <code class="docutils literal notranslate"><span class="pre">process_method</span></code>.</p></li>
+<li><p><strong>input_args</strong> (<em>dict</em>) – Arguments for the <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CorumFuncat.__init__" title="pypath.core.annot.CorumFuncat.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>(**kwargs)</p></td>
+<td><p>Represents annotations for a set of proteins.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CorumFuncat.add_complexes_by_inference" title="pypath.core.annot.CorumFuncat.add_complexes_by_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">add_complexes_by_inference</span></code></a>([complexes])</p></td>
+<td><p>Creates complex annotations by in silico inference and adds them to this annotation set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CorumFuncat.all_complexes" title="pypath.core.annot.CorumFuncat.all_complexes"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_complexes</span></code></a>()</p></td>
+<td><p>All protein complexes annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CorumFuncat.all_entities" title="pypath.core.annot.CorumFuncat.all_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_entities</span></code></a>([entity_types])</p></td>
+<td><p>All entities annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CorumFuncat.all_mirnas" title="pypath.core.annot.CorumFuncat.all_mirnas"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_mirnas</span></code></a>()</p></td>
+<td><p>All miRNAs annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CorumFuncat.all_proteins" title="pypath.core.annot.CorumFuncat.all_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_proteins</span></code></a>()</p></td>
+<td><p>All UniProt IDs annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CorumFuncat.all_refs" title="pypath.core.annot.CorumFuncat.all_refs"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_refs</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CorumFuncat.annotate_complex" title="pypath.core.annot.CorumFuncat.annotate_complex"><code class="xref py py-obj docutils literal notranslate"><span class="pre">annotate_complex</span></code></a>(cplex)</p></td>
+<td><p>Infers annotations for a single complex.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CorumFuncat.browse" title="pypath.core.annot.CorumFuncat.browse"><code class="xref py py-obj docutils literal notranslate"><span class="pre">browse</span></code></a>([field, start])</p></td>
+<td><p>Print gene information as a table.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CorumFuncat.complex_inference" title="pypath.core.annot.CorumFuncat.complex_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">complex_inference</span></code></a>([complexes])</p></td>
+<td><p>Annotates all complexes in <cite>complexes</cite>, by default in the default complex database (existing in the <cite>complex</cite> module or generated on demand according to the module's current settings).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CorumFuncat.coverage" title="pypath.core.annot.CorumFuncat.coverage"><code class="xref py py-obj docutils literal notranslate"><span class="pre">coverage</span></code></a>(other)</p></td>
+<td><p>Calculates the coverage of the annotation i.e. the proportion of entities having at least one record in this annotation resource for an arbitrary set of entities.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CorumFuncat.curation_effort" title="pypath.core.annot.CorumFuncat.curation_effort"><code class="xref py py-obj docutils literal notranslate"><span class="pre">curation_effort</span></code></a>()</p></td>
+<td><p>Counts the reference-record pairs.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">from_dump</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_entity_type</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CorumFuncat.get_names" title="pypath.core.annot.CorumFuncat.get_names"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_names</span></code></a>()</p></td>
+<td><p>Returns the list of field names in the records.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CorumFuncat.get_reference_set" title="pypath.core.annot.CorumFuncat.get_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_reference_set</span></code></a>([proteins, complexes, ...])</p></td>
+<td><p>Retrieves the reference set i.e. the set of all entities which potentially have annotation in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CorumFuncat.get_subset" title="pypath.core.annot.CorumFuncat.get_subset"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CorumFuncat.get_subset_bool_array" title="pypath.core.annot.CorumFuncat.get_subset_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset_bool_array</span></code></a>([reference_set])</p></td>
+<td><p>Returns a boolean vector with True and False values for each entity in the reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CorumFuncat.get_values" title="pypath.core.annot.CorumFuncat.get_values"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_values</span></code></a>(name[, exclude_none])</p></td>
+<td><p>Returns the set of all possible values of a field.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_complex</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_mirna</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_protein</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CorumFuncat.labels" title="pypath.core.annot.CorumFuncat.labels"><code class="xref py py-obj docutils literal notranslate"><span class="pre">labels</span></code></a>([method])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CorumFuncat.load" title="pypath.core.annot.CorumFuncat.load"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load</span></code></a>()</p></td>
+<td><p>Loads the annotation data by calling the input method.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CorumFuncat.load_data" title="pypath.core.annot.CorumFuncat.load_data"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_data</span></code></a>()</p></td>
+<td><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CorumFuncat.load_proteins" title="pypath.core.annot.CorumFuncat.load_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_proteins</span></code></a>()</p></td>
+<td><p>Retrieves a set of all UniProt IDs to have a base set of the entire proteome.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CorumFuncat.make_df" title="pypath.core.annot.CorumFuncat.make_df"><code class="xref py py-obj docutils literal notranslate"><span class="pre">make_df</span></code></a>([rebuild])</p></td>
+<td><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complex_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CorumFuncat.numof_entities" title="pypath.core.annot.CorumFuncat.numof_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_entities</span></code></a>()</p></td>
+<td><p>The number of annotated entities in the resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirna_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirnas</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_protein_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_proteins</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CorumFuncat.numof_records" title="pypath.core.annot.CorumFuncat.numof_records"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_records</span></code></a>([entity_types])</p></td>
+<td><p>The total number of annotation records.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CorumFuncat.numof_references" title="pypath.core.annot.CorumFuncat.numof_references"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_references</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CorumFuncat.process" title="pypath.core.annot.CorumFuncat.process"><code class="xref py py-obj docutils literal notranslate"><span class="pre">process</span></code></a>()</p></td>
+<td><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">proportion</span></code>(other)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CorumFuncat.reload" title="pypath.core.annot.CorumFuncat.reload"><code class="xref py py-obj docutils literal notranslate"><span class="pre">reload</span></code></a>()</p></td>
+<td><p>Reloads the object from the module level.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">save_to_pickle</span></code>(pickle_file)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CorumFuncat.select" title="pypath.core.annot.CorumFuncat.select"><code class="xref py py-obj docutils literal notranslate"><span class="pre">select</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CorumFuncat.set_method" title="pypath.core.annot.CorumFuncat.set_method"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_method</span></code></a>()</p></td>
+<td><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if necessary.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CorumFuncat.set_reference_set" title="pypath.core.annot.CorumFuncat.set_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_reference_set</span></code></a>()</p></td>
+<td><p>Assigns the reference set to the :py:attr``reference_set`` attribute.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CorumFuncat.show" title="pypath.core.annot.CorumFuncat.show"><code class="xref py py-obj docutils literal notranslate"><span class="pre">show</span></code></a>([method, table_param])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic information from the UniProt datasheets.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CorumFuncat.subset_intersection" title="pypath.core.annot.CorumFuncat.subset_intersection"><code class="xref py py-obj docutils literal notranslate"><span class="pre">subset_intersection</span></code></a>(universe, **kwargs)</p></td>
+<td><p>Calculates the proportion of entities in a subset occuring in the set <code class="docutils literal notranslate"><span class="pre">universe</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CorumFuncat.to_array" title="pypath.core.annot.CorumFuncat.to_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_array</span></code></a>([reference_set, use_fields])</p></td>
+<td><p>Returns an entity vs feature array.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CorumFuncat.to_bool_array" title="pypath.core.annot.CorumFuncat.to_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_bool_array</span></code></a>(reference_set)</p></td>
+<td><p>Returns a presence/absence boolean array for a reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CorumFuncat.to_set" title="pypath.core.annot.CorumFuncat.to_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_set</span></code></a>()</p></td>
+<td><p>Returns the entities present in this annotation resource as a set.</p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Attributes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_fields</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">summary</span></code></p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CorumFuncat.add_complexes_by_inference">
+<span class="sig-name descname"><span class="pre">add_complexes_by_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CorumFuncat.add_complexes_by_inference" title="Link to this definition">§</a></dt>
+<dd><p>Creates complex annotations by in silico inference and adds them
+to this annotation set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CorumFuncat.all_complexes">
+<span class="sig-name descname"><span class="pre">all_complexes</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CorumFuncat.all_complexes" title="Link to this definition">§</a></dt>
+<dd><p>All protein complexes annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CorumFuncat.all_entities">
+<span class="sig-name descname"><span class="pre">all_entities</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CorumFuncat.all_entities" title="Link to this definition">§</a></dt>
+<dd><p>All entities annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CorumFuncat.all_mirnas">
+<span class="sig-name descname"><span class="pre">all_mirnas</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CorumFuncat.all_mirnas" title="Link to this definition">§</a></dt>
+<dd><p>All miRNAs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CorumFuncat.all_proteins">
+<span class="sig-name descname"><span class="pre">all_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CorumFuncat.all_proteins" title="Link to this definition">§</a></dt>
+<dd><p>All UniProt IDs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CorumFuncat.all_refs">
+<span class="sig-name descname"><span class="pre">all_refs</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CorumFuncat.all_refs" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects the references
+across all records. Returns <em>list</em>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CorumFuncat.annotate_complex">
+<span class="sig-name descname"><span class="pre">annotate_complex</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cplex</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CorumFuncat.annotate_complex" title="Link to this definition">§</a></dt>
+<dd><p>Infers annotations for a single complex.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CorumFuncat.browse">
+<span class="sig-name descname"><span class="pre">browse</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">field</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">start</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CorumFuncat.browse" title="Link to this definition">§</a></dt>
+<dd><p>Print gene information as a table.</p>
+<p>Presents information about annotation categories as ascii tables
+printed in the terminal. If one category provided, prints one table.
+If multiple categories provided, prints a table for each of them one
+by one proceeding to the next one once you hit return. If no categories
+provided goes through all levels of the primary category.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>field:</dt><dd><p>The field to browse categories by.</p>
+<ul class="simple">
+<li><p>If None the primary field will be selected.
+If this annotation resource doesn’t have fields, all proteins
+will be presented as one single category.</p></li>
+<li><p>If a string it will be considered a field name and it will
+browse through all levels of this field.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">list</span></code>, set or tuple, it will be considered either a
+<code class="docutils literal notranslate"><span class="pre">list</span></code> of field names or a list of values from the primary
+field. In the former case all combinations of the values of
+the fields will be presented, in the latter case the browsing
+will be limited to the levels of the primary field contained
+in <code class="docutils literal notranslate"><span class="pre">field</span></code>.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">dict</span></code>, keys are supposed to be field names and values
+as list of levels. If any of the values are None, all levels
+from that field will be used.</p></li>
+</ul>
+</dd>
+<dt>start:</dt><dd><p>Start browsing from this category. E.g. if there are 500
+categories and start is 250 it will skip everything before the
+250th.</p>
+</dd>
+<dt>kwargs:</dt><dd><p>Passed to <code class="docutils literal notranslate"><span class="pre">pypath.utils.uniprot.info</span></code>.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CorumFuncat.complex_inference">
+<span class="sig-name descname"><span class="pre">complex_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CorumFuncat.complex_inference" title="Link to this definition">§</a></dt>
+<dd><p>Annotates all complexes in <cite>complexes</cite>, by default in the default
+complex database (existing in the <cite>complex</cite> module or generated
+on demand according to the module’s current settings).</p>
+<dl class="field-list simple">
+<dt class="field-odd">Returns<span class="colon">:</span></dt>
+<dd class="field-odd"><p><ul class="simple">
+<li><p><em>Dict with complexes as keys and sets of annotations as values.</em></p></li>
+<li><p><em>Complexes with no valid information in this annotation resource</em></p></li>
+<li><p><em>won’t be in the dict.</em></p></li>
+</ul>
+</p>
+</dd>
+<dt class="field-even">Parameters<span class="colon">:</span></dt>
+<dd class="field-even"><p><strong>complexes</strong> (<em>iterable</em>) – Iterable yielding complexes.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CorumFuncat.coverage">
+<span class="sig-name descname"><span class="pre">coverage</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">other</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CorumFuncat.coverage" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the coverage of the annotation i.e. the proportion of
+entities having at least one record in this annotation resource
+for an arbitrary set of entities.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CorumFuncat.curation_effort">
+<span class="sig-name descname"><span class="pre">curation_effort</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CorumFuncat.curation_effort" title="Link to this definition">§</a></dt>
+<dd><p>Counts the reference-record pairs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CorumFuncat.get_names">
+<span class="sig-name descname"><span class="pre">get_names</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CorumFuncat.get_names" title="Link to this definition">§</a></dt>
+<dd><p>Returns the list of field names in the records. The annotation
+consists of uniform records and each entity might be annotated
+with one or more records. Each record is a tuple of fields, for
+example <code class="docutils literal notranslate"><span class="pre">('cell_type',</span> <span class="pre">'expression_level',</span> <span class="pre">'score')</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CorumFuncat.get_reference_set">
+<em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">get_reference_set</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">proteins</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">swissprot_only</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CorumFuncat.get_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the reference set i.e. the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CorumFuncat.get_subset">
+<span class="sig-name descname"><span class="pre">get_subset</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CorumFuncat.get_subset" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CorumFuncat.get_subset_bool_array">
+<span class="sig-name descname"><span class="pre">get_subset_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CorumFuncat.get_subset_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a boolean vector with True and False values for each entity
+in the reference set. The values represent presence absence data
+in the simplest case, but by providing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> any kind of matching
+and filtering is possible. <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> are passed to the <code class="docutils literal notranslate"><span class="pre">select</span></code>
+method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CorumFuncat.get_values">
+<span class="sig-name descname"><span class="pre">get_values</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">exclude_none</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CorumFuncat.get_values" title="Link to this definition">§</a></dt>
+<dd><p>Returns the set of all possible values of a field. E.g. if the
+records of this annotation have a field <code class="docutils literal notranslate"><span class="pre">cell_type</span></code> then calling
+this method can tell you that across all records the values of
+this field might be <code class="docutils literal notranslate"><span class="pre">{'macrophage',</span> <span class="pre">'epithelial_cell',</span> <span class="pre">...}</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CorumFuncat.labels">
+<span class="sig-name descname"><span class="pre">labels</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CorumFuncat.labels" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CorumFuncat.load">
+<span class="sig-name descname"><span class="pre">load</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CorumFuncat.load" title="Link to this definition">§</a></dt>
+<dd><p>Loads the annotation data by calling the input method.
+Infers annotations for complexes in the complex database if
+py:attr:<code class="docutils literal notranslate"><span class="pre">infer_complexes</span></code> is True.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CorumFuncat.load_data">
+<span class="sig-name descname"><span class="pre">load_data</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CorumFuncat.load_data" title="Link to this definition">§</a></dt>
+<dd><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CorumFuncat.load_proteins">
+<span class="sig-name descname"><span class="pre">load_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CorumFuncat.load_proteins" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a set of all UniProt IDs to have a base set of the entire
+proteome.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CorumFuncat.make_df">
+<span class="sig-name descname"><span class="pre">make_df</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">rebuild</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CorumFuncat.make_df" title="Link to this definition">§</a></dt>
+<dd><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.
+The data frame will be assigned to :py:attr``df``.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CorumFuncat.numof_entities">
+<span class="sig-name descname"><span class="pre">numof_entities</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CorumFuncat.numof_entities" title="Link to this definition">§</a></dt>
+<dd><p>The number of annotated entities in the resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CorumFuncat.numof_records">
+<span class="sig-name descname"><span class="pre">numof_records</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CorumFuncat.numof_records" title="Link to this definition">§</a></dt>
+<dd><p>The total number of annotation records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CorumFuncat.numof_references">
+<span class="sig-name descname"><span class="pre">numof_references</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CorumFuncat.numof_references" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects and counts the
+references across all records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CorumFuncat.process">
+<span class="sig-name descname"><span class="pre">process</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CorumFuncat.process" title="Link to this definition">§</a></dt>
+<dd><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CorumFuncat.reload">
+<span class="sig-name descname"><span class="pre">reload</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CorumFuncat.reload" title="Link to this definition">§</a></dt>
+<dd><p>Reloads the object from the module level.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CorumFuncat.select">
+<span class="sig-name descname"><span class="pre">select</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CorumFuncat.select" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CorumFuncat.set_method">
+<span class="sig-name descname"><span class="pre">set_method</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CorumFuncat.set_method" title="Link to this definition">§</a></dt>
+<dd><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if
+necessary.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CorumFuncat.set_reference_set">
+<span class="sig-name descname"><span class="pre">set_reference_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CorumFuncat.set_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Assigns the reference set to the :py:attr``reference_set`` attribute.
+The reference set is the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CorumFuncat.show">
+<span class="sig-name descname"><span class="pre">show</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">table_param</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CorumFuncat.show" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic
+information from the UniProt datasheets.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CorumFuncat.subset_intersection">
+<span class="sig-name descname"><span class="pre">subset_intersection</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">universe</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CorumFuncat.subset_intersection" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the proportion of entities in a subset occuring in the
+set <code class="docutils literal notranslate"><span class="pre">universe</span></code>. The subset is selected by passing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> to the
+<code class="docutils literal notranslate"><span class="pre">select</span></code> method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CorumFuncat.to_array">
+<span class="sig-name descname"><span class="pre">to_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_fields</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CorumFuncat.to_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns an entity vs feature array. In case of more complex
+annotations this might be huge.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CorumFuncat.to_bool_array">
+<span class="sig-name descname"><span class="pre">to_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CorumFuncat.to_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a presence/absence boolean array for a reference set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CorumFuncat.to_set">
+<span class="sig-name descname"><span class="pre">to_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CorumFuncat.to_set" title="Link to this definition">§</a></dt>
+<dd><p>Returns the entities present in this annotation resource as a set.</p>
+</dd></dl>
+
+</dd></dl>
+
+</section>
+
+
+                </article>
+              
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+  <section id="pypath-core-annot-corumgo">
+<h1>pypath.core.annot.CorumGO<a class="headerlink" href="#pypath-core-annot-corumgo" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.core.annot.CorumGO">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.core.annot.</span></span><span class="sig-name descname"><span class="pre">CorumGO</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#CorumGO"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.CorumGO" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <a class="reference internal" href="pypath.core.annot.Corum.html#pypath.core.annot.Corum" title="pypath.core.annot.Corum"><code class="xref py py-class docutils literal notranslate"><span class="pre">Corum</span></code></a></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CorumGO.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#CorumGO.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.CorumGO.__init__" title="Link to this definition">§</a></dt>
+<dd><p>Represents annotations for a set of proteins.
+Loads the data from the original resource and provides methods
+to query the annotations.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>name</strong> (<em>str</em>) – A custom name for the annotation resource.</p></li>
+<li><p><strong>ncbi_tax_id</strong> (<em>int</em>) – NCBI Taxonomy identifier.</p></li>
+<li><p><strong>input_method</strong> (<em>callable</em><em>,</em><em>str</em>) – Either a callable or the name of a method in any submodules of
+the <code class="docutils literal notranslate"><span class="pre">pypath.inputs</span></code>  module. Should return a dict with
+UniProt IDs as keys or an object suitable for <code class="docutils literal notranslate"><span class="pre">process_method</span></code>.</p></li>
+<li><p><strong>input_args</strong> (<em>dict</em>) – Arguments for the <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CorumGO.__init__" title="pypath.core.annot.CorumGO.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>(**kwargs)</p></td>
+<td><p>Represents annotations for a set of proteins.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CorumGO.add_complexes_by_inference" title="pypath.core.annot.CorumGO.add_complexes_by_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">add_complexes_by_inference</span></code></a>([complexes])</p></td>
+<td><p>Creates complex annotations by in silico inference and adds them to this annotation set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CorumGO.all_complexes" title="pypath.core.annot.CorumGO.all_complexes"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_complexes</span></code></a>()</p></td>
+<td><p>All protein complexes annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CorumGO.all_entities" title="pypath.core.annot.CorumGO.all_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_entities</span></code></a>([entity_types])</p></td>
+<td><p>All entities annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CorumGO.all_mirnas" title="pypath.core.annot.CorumGO.all_mirnas"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_mirnas</span></code></a>()</p></td>
+<td><p>All miRNAs annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CorumGO.all_proteins" title="pypath.core.annot.CorumGO.all_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_proteins</span></code></a>()</p></td>
+<td><p>All UniProt IDs annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CorumGO.all_refs" title="pypath.core.annot.CorumGO.all_refs"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_refs</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CorumGO.annotate_complex" title="pypath.core.annot.CorumGO.annotate_complex"><code class="xref py py-obj docutils literal notranslate"><span class="pre">annotate_complex</span></code></a>(cplex)</p></td>
+<td><p>Infers annotations for a single complex.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CorumGO.browse" title="pypath.core.annot.CorumGO.browse"><code class="xref py py-obj docutils literal notranslate"><span class="pre">browse</span></code></a>([field, start])</p></td>
+<td><p>Print gene information as a table.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CorumGO.complex_inference" title="pypath.core.annot.CorumGO.complex_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">complex_inference</span></code></a>([complexes])</p></td>
+<td><p>Annotates all complexes in <cite>complexes</cite>, by default in the default complex database (existing in the <cite>complex</cite> module or generated on demand according to the module's current settings).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CorumGO.coverage" title="pypath.core.annot.CorumGO.coverage"><code class="xref py py-obj docutils literal notranslate"><span class="pre">coverage</span></code></a>(other)</p></td>
+<td><p>Calculates the coverage of the annotation i.e. the proportion of entities having at least one record in this annotation resource for an arbitrary set of entities.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CorumGO.curation_effort" title="pypath.core.annot.CorumGO.curation_effort"><code class="xref py py-obj docutils literal notranslate"><span class="pre">curation_effort</span></code></a>()</p></td>
+<td><p>Counts the reference-record pairs.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">from_dump</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_entity_type</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CorumGO.get_names" title="pypath.core.annot.CorumGO.get_names"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_names</span></code></a>()</p></td>
+<td><p>Returns the list of field names in the records.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CorumGO.get_reference_set" title="pypath.core.annot.CorumGO.get_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_reference_set</span></code></a>([proteins, complexes, ...])</p></td>
+<td><p>Retrieves the reference set i.e. the set of all entities which potentially have annotation in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CorumGO.get_subset" title="pypath.core.annot.CorumGO.get_subset"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CorumGO.get_subset_bool_array" title="pypath.core.annot.CorumGO.get_subset_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset_bool_array</span></code></a>([reference_set])</p></td>
+<td><p>Returns a boolean vector with True and False values for each entity in the reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CorumGO.get_values" title="pypath.core.annot.CorumGO.get_values"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_values</span></code></a>(name[, exclude_none])</p></td>
+<td><p>Returns the set of all possible values of a field.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_complex</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_mirna</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_protein</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CorumGO.labels" title="pypath.core.annot.CorumGO.labels"><code class="xref py py-obj docutils literal notranslate"><span class="pre">labels</span></code></a>([method])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CorumGO.load" title="pypath.core.annot.CorumGO.load"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load</span></code></a>()</p></td>
+<td><p>Loads the annotation data by calling the input method.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CorumGO.load_data" title="pypath.core.annot.CorumGO.load_data"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_data</span></code></a>()</p></td>
+<td><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CorumGO.load_proteins" title="pypath.core.annot.CorumGO.load_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_proteins</span></code></a>()</p></td>
+<td><p>Retrieves a set of all UniProt IDs to have a base set of the entire proteome.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CorumGO.make_df" title="pypath.core.annot.CorumGO.make_df"><code class="xref py py-obj docutils literal notranslate"><span class="pre">make_df</span></code></a>([rebuild])</p></td>
+<td><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complex_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CorumGO.numof_entities" title="pypath.core.annot.CorumGO.numof_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_entities</span></code></a>()</p></td>
+<td><p>The number of annotated entities in the resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirna_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirnas</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_protein_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_proteins</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CorumGO.numof_records" title="pypath.core.annot.CorumGO.numof_records"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_records</span></code></a>([entity_types])</p></td>
+<td><p>The total number of annotation records.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CorumGO.numof_references" title="pypath.core.annot.CorumGO.numof_references"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_references</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CorumGO.process" title="pypath.core.annot.CorumGO.process"><code class="xref py py-obj docutils literal notranslate"><span class="pre">process</span></code></a>()</p></td>
+<td><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">proportion</span></code>(other)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CorumGO.reload" title="pypath.core.annot.CorumGO.reload"><code class="xref py py-obj docutils literal notranslate"><span class="pre">reload</span></code></a>()</p></td>
+<td><p>Reloads the object from the module level.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">save_to_pickle</span></code>(pickle_file)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CorumGO.select" title="pypath.core.annot.CorumGO.select"><code class="xref py py-obj docutils literal notranslate"><span class="pre">select</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CorumGO.set_method" title="pypath.core.annot.CorumGO.set_method"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_method</span></code></a>()</p></td>
+<td><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if necessary.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CorumGO.set_reference_set" title="pypath.core.annot.CorumGO.set_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_reference_set</span></code></a>()</p></td>
+<td><p>Assigns the reference set to the :py:attr``reference_set`` attribute.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CorumGO.show" title="pypath.core.annot.CorumGO.show"><code class="xref py py-obj docutils literal notranslate"><span class="pre">show</span></code></a>([method, table_param])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic information from the UniProt datasheets.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CorumGO.subset_intersection" title="pypath.core.annot.CorumGO.subset_intersection"><code class="xref py py-obj docutils literal notranslate"><span class="pre">subset_intersection</span></code></a>(universe, **kwargs)</p></td>
+<td><p>Calculates the proportion of entities in a subset occuring in the set <code class="docutils literal notranslate"><span class="pre">universe</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CorumGO.to_array" title="pypath.core.annot.CorumGO.to_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_array</span></code></a>([reference_set, use_fields])</p></td>
+<td><p>Returns an entity vs feature array.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CorumGO.to_bool_array" title="pypath.core.annot.CorumGO.to_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_bool_array</span></code></a>(reference_set)</p></td>
+<td><p>Returns a presence/absence boolean array for a reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CorumGO.to_set" title="pypath.core.annot.CorumGO.to_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_set</span></code></a>()</p></td>
+<td><p>Returns the entities present in this annotation resource as a set.</p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Attributes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_fields</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">summary</span></code></p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CorumGO.add_complexes_by_inference">
+<span class="sig-name descname"><span class="pre">add_complexes_by_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CorumGO.add_complexes_by_inference" title="Link to this definition">§</a></dt>
+<dd><p>Creates complex annotations by in silico inference and adds them
+to this annotation set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CorumGO.all_complexes">
+<span class="sig-name descname"><span class="pre">all_complexes</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CorumGO.all_complexes" title="Link to this definition">§</a></dt>
+<dd><p>All protein complexes annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CorumGO.all_entities">
+<span class="sig-name descname"><span class="pre">all_entities</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CorumGO.all_entities" title="Link to this definition">§</a></dt>
+<dd><p>All entities annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CorumGO.all_mirnas">
+<span class="sig-name descname"><span class="pre">all_mirnas</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CorumGO.all_mirnas" title="Link to this definition">§</a></dt>
+<dd><p>All miRNAs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CorumGO.all_proteins">
+<span class="sig-name descname"><span class="pre">all_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CorumGO.all_proteins" title="Link to this definition">§</a></dt>
+<dd><p>All UniProt IDs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CorumGO.all_refs">
+<span class="sig-name descname"><span class="pre">all_refs</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CorumGO.all_refs" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects the references
+across all records. Returns <em>list</em>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CorumGO.annotate_complex">
+<span class="sig-name descname"><span class="pre">annotate_complex</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cplex</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CorumGO.annotate_complex" title="Link to this definition">§</a></dt>
+<dd><p>Infers annotations for a single complex.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CorumGO.browse">
+<span class="sig-name descname"><span class="pre">browse</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">field</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">start</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CorumGO.browse" title="Link to this definition">§</a></dt>
+<dd><p>Print gene information as a table.</p>
+<p>Presents information about annotation categories as ascii tables
+printed in the terminal. If one category provided, prints one table.
+If multiple categories provided, prints a table for each of them one
+by one proceeding to the next one once you hit return. If no categories
+provided goes through all levels of the primary category.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>field:</dt><dd><p>The field to browse categories by.</p>
+<ul class="simple">
+<li><p>If None the primary field will be selected.
+If this annotation resource doesn’t have fields, all proteins
+will be presented as one single category.</p></li>
+<li><p>If a string it will be considered a field name and it will
+browse through all levels of this field.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">list</span></code>, set or tuple, it will be considered either a
+<code class="docutils literal notranslate"><span class="pre">list</span></code> of field names or a list of values from the primary
+field. In the former case all combinations of the values of
+the fields will be presented, in the latter case the browsing
+will be limited to the levels of the primary field contained
+in <code class="docutils literal notranslate"><span class="pre">field</span></code>.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">dict</span></code>, keys are supposed to be field names and values
+as list of levels. If any of the values are None, all levels
+from that field will be used.</p></li>
+</ul>
+</dd>
+<dt>start:</dt><dd><p>Start browsing from this category. E.g. if there are 500
+categories and start is 250 it will skip everything before the
+250th.</p>
+</dd>
+<dt>kwargs:</dt><dd><p>Passed to <code class="docutils literal notranslate"><span class="pre">pypath.utils.uniprot.info</span></code>.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CorumGO.complex_inference">
+<span class="sig-name descname"><span class="pre">complex_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CorumGO.complex_inference" title="Link to this definition">§</a></dt>
+<dd><p>Annotates all complexes in <cite>complexes</cite>, by default in the default
+complex database (existing in the <cite>complex</cite> module or generated
+on demand according to the module’s current settings).</p>
+<dl class="field-list simple">
+<dt class="field-odd">Returns<span class="colon">:</span></dt>
+<dd class="field-odd"><p><ul class="simple">
+<li><p><em>Dict with complexes as keys and sets of annotations as values.</em></p></li>
+<li><p><em>Complexes with no valid information in this annotation resource</em></p></li>
+<li><p><em>won’t be in the dict.</em></p></li>
+</ul>
+</p>
+</dd>
+<dt class="field-even">Parameters<span class="colon">:</span></dt>
+<dd class="field-even"><p><strong>complexes</strong> (<em>iterable</em>) – Iterable yielding complexes.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CorumGO.coverage">
+<span class="sig-name descname"><span class="pre">coverage</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">other</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CorumGO.coverage" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the coverage of the annotation i.e. the proportion of
+entities having at least one record in this annotation resource
+for an arbitrary set of entities.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CorumGO.curation_effort">
+<span class="sig-name descname"><span class="pre">curation_effort</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CorumGO.curation_effort" title="Link to this definition">§</a></dt>
+<dd><p>Counts the reference-record pairs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CorumGO.get_names">
+<span class="sig-name descname"><span class="pre">get_names</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CorumGO.get_names" title="Link to this definition">§</a></dt>
+<dd><p>Returns the list of field names in the records. The annotation
+consists of uniform records and each entity might be annotated
+with one or more records. Each record is a tuple of fields, for
+example <code class="docutils literal notranslate"><span class="pre">('cell_type',</span> <span class="pre">'expression_level',</span> <span class="pre">'score')</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CorumGO.get_reference_set">
+<em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">get_reference_set</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">proteins</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">swissprot_only</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CorumGO.get_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the reference set i.e. the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CorumGO.get_subset">
+<span class="sig-name descname"><span class="pre">get_subset</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CorumGO.get_subset" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CorumGO.get_subset_bool_array">
+<span class="sig-name descname"><span class="pre">get_subset_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CorumGO.get_subset_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a boolean vector with True and False values for each entity
+in the reference set. The values represent presence absence data
+in the simplest case, but by providing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> any kind of matching
+and filtering is possible. <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> are passed to the <code class="docutils literal notranslate"><span class="pre">select</span></code>
+method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CorumGO.get_values">
+<span class="sig-name descname"><span class="pre">get_values</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">exclude_none</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CorumGO.get_values" title="Link to this definition">§</a></dt>
+<dd><p>Returns the set of all possible values of a field. E.g. if the
+records of this annotation have a field <code class="docutils literal notranslate"><span class="pre">cell_type</span></code> then calling
+this method can tell you that across all records the values of
+this field might be <code class="docutils literal notranslate"><span class="pre">{'macrophage',</span> <span class="pre">'epithelial_cell',</span> <span class="pre">...}</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CorumGO.labels">
+<span class="sig-name descname"><span class="pre">labels</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CorumGO.labels" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CorumGO.load">
+<span class="sig-name descname"><span class="pre">load</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CorumGO.load" title="Link to this definition">§</a></dt>
+<dd><p>Loads the annotation data by calling the input method.
+Infers annotations for complexes in the complex database if
+py:attr:<code class="docutils literal notranslate"><span class="pre">infer_complexes</span></code> is True.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CorumGO.load_data">
+<span class="sig-name descname"><span class="pre">load_data</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CorumGO.load_data" title="Link to this definition">§</a></dt>
+<dd><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CorumGO.load_proteins">
+<span class="sig-name descname"><span class="pre">load_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CorumGO.load_proteins" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a set of all UniProt IDs to have a base set of the entire
+proteome.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CorumGO.make_df">
+<span class="sig-name descname"><span class="pre">make_df</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">rebuild</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CorumGO.make_df" title="Link to this definition">§</a></dt>
+<dd><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.
+The data frame will be assigned to :py:attr``df``.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CorumGO.numof_entities">
+<span class="sig-name descname"><span class="pre">numof_entities</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CorumGO.numof_entities" title="Link to this definition">§</a></dt>
+<dd><p>The number of annotated entities in the resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CorumGO.numof_records">
+<span class="sig-name descname"><span class="pre">numof_records</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CorumGO.numof_records" title="Link to this definition">§</a></dt>
+<dd><p>The total number of annotation records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CorumGO.numof_references">
+<span class="sig-name descname"><span class="pre">numof_references</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CorumGO.numof_references" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects and counts the
+references across all records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CorumGO.process">
+<span class="sig-name descname"><span class="pre">process</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CorumGO.process" title="Link to this definition">§</a></dt>
+<dd><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CorumGO.reload">
+<span class="sig-name descname"><span class="pre">reload</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CorumGO.reload" title="Link to this definition">§</a></dt>
+<dd><p>Reloads the object from the module level.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CorumGO.select">
+<span class="sig-name descname"><span class="pre">select</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CorumGO.select" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CorumGO.set_method">
+<span class="sig-name descname"><span class="pre">set_method</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CorumGO.set_method" title="Link to this definition">§</a></dt>
+<dd><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if
+necessary.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CorumGO.set_reference_set">
+<span class="sig-name descname"><span class="pre">set_reference_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CorumGO.set_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Assigns the reference set to the :py:attr``reference_set`` attribute.
+The reference set is the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CorumGO.show">
+<span class="sig-name descname"><span class="pre">show</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">table_param</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CorumGO.show" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic
+information from the UniProt datasheets.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CorumGO.subset_intersection">
+<span class="sig-name descname"><span class="pre">subset_intersection</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">universe</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CorumGO.subset_intersection" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the proportion of entities in a subset occuring in the
+set <code class="docutils literal notranslate"><span class="pre">universe</span></code>. The subset is selected by passing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> to the
+<code class="docutils literal notranslate"><span class="pre">select</span></code> method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CorumGO.to_array">
+<span class="sig-name descname"><span class="pre">to_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_fields</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CorumGO.to_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns an entity vs feature array. In case of more complex
+annotations this might be huge.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CorumGO.to_bool_array">
+<span class="sig-name descname"><span class="pre">to_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CorumGO.to_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a presence/absence boolean array for a reference set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CorumGO.to_set">
+<span class="sig-name descname"><span class="pre">to_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CorumGO.to_set" title="Link to this definition">§</a></dt>
+<dd><p>Returns the entities present in this annotation resource as a set.</p>
+</dd></dl>
+
+</dd></dl>
+
+</section>
+
+
+                </article>
+              
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+  <section id="pypath-core-annot-cpad">
+<h1>pypath.core.annot.Cpad<a class="headerlink" href="#pypath-core-annot-cpad" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.core.annot.Cpad">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.core.annot.</span></span><span class="sig-name descname"><span class="pre">Cpad</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#Cpad"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.Cpad" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <a class="reference internal" href="pypath.core.annot.AnnotationBase.html#pypath.core.annot.AnnotationBase" title="pypath.core.annot.AnnotationBase"><code class="xref py py-class docutils literal notranslate"><span class="pre">AnnotationBase</span></code></a></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cpad.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#Cpad.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.Cpad.__init__" title="Link to this definition">§</a></dt>
+<dd><p>Represents annotations for a set of proteins.
+Loads the data from the original resource and provides methods
+to query the annotations.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>name</strong> (<em>str</em>) – A custom name for the annotation resource.</p></li>
+<li><p><strong>ncbi_tax_id</strong> (<em>int</em>) – NCBI Taxonomy identifier.</p></li>
+<li><p><strong>input_method</strong> (<em>callable</em><em>,</em><em>str</em>) – Either a callable or the name of a method in any submodules of
+the <code class="docutils literal notranslate"><span class="pre">pypath.inputs</span></code>  module. Should return a dict with
+UniProt IDs as keys or an object suitable for <code class="docutils literal notranslate"><span class="pre">process_method</span></code>.</p></li>
+<li><p><strong>input_args</strong> (<em>dict</em>) – Arguments for the <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Cpad.__init__" title="pypath.core.annot.Cpad.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>([ncbi_tax_id])</p></td>
+<td><p>Represents annotations for a set of proteins.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Cpad.add_complexes_by_inference" title="pypath.core.annot.Cpad.add_complexes_by_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">add_complexes_by_inference</span></code></a>([complexes])</p></td>
+<td><p>Creates complex annotations by in silico inference and adds them to this annotation set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Cpad.all_complexes" title="pypath.core.annot.Cpad.all_complexes"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_complexes</span></code></a>()</p></td>
+<td><p>All protein complexes annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Cpad.all_entities" title="pypath.core.annot.Cpad.all_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_entities</span></code></a>([entity_types])</p></td>
+<td><p>All entities annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Cpad.all_mirnas" title="pypath.core.annot.Cpad.all_mirnas"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_mirnas</span></code></a>()</p></td>
+<td><p>All miRNAs annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Cpad.all_proteins" title="pypath.core.annot.Cpad.all_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_proteins</span></code></a>()</p></td>
+<td><p>All UniProt IDs annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Cpad.all_refs" title="pypath.core.annot.Cpad.all_refs"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_refs</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Cpad.annotate_complex" title="pypath.core.annot.Cpad.annotate_complex"><code class="xref py py-obj docutils literal notranslate"><span class="pre">annotate_complex</span></code></a>(cplex)</p></td>
+<td><p>Infers annotations for a single complex.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Cpad.browse" title="pypath.core.annot.Cpad.browse"><code class="xref py py-obj docutils literal notranslate"><span class="pre">browse</span></code></a>([field, start])</p></td>
+<td><p>Print gene information as a table.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Cpad.complex_inference" title="pypath.core.annot.Cpad.complex_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">complex_inference</span></code></a>([complexes])</p></td>
+<td><p>Annotates all complexes in <cite>complexes</cite>, by default in the default complex database (existing in the <cite>complex</cite> module or generated on demand according to the module's current settings).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Cpad.coverage" title="pypath.core.annot.Cpad.coverage"><code class="xref py py-obj docutils literal notranslate"><span class="pre">coverage</span></code></a>(other)</p></td>
+<td><p>Calculates the coverage of the annotation i.e. the proportion of entities having at least one record in this annotation resource for an arbitrary set of entities.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Cpad.curation_effort" title="pypath.core.annot.Cpad.curation_effort"><code class="xref py py-obj docutils literal notranslate"><span class="pre">curation_effort</span></code></a>()</p></td>
+<td><p>Counts the reference-record pairs.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">from_dump</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_entity_type</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Cpad.get_names" title="pypath.core.annot.Cpad.get_names"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_names</span></code></a>()</p></td>
+<td><p>Returns the list of field names in the records.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Cpad.get_reference_set" title="pypath.core.annot.Cpad.get_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_reference_set</span></code></a>([proteins, complexes, ...])</p></td>
+<td><p>Retrieves the reference set i.e. the set of all entities which potentially have annotation in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Cpad.get_subset" title="pypath.core.annot.Cpad.get_subset"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Cpad.get_subset_bool_array" title="pypath.core.annot.Cpad.get_subset_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset_bool_array</span></code></a>([reference_set])</p></td>
+<td><p>Returns a boolean vector with True and False values for each entity in the reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Cpad.get_values" title="pypath.core.annot.Cpad.get_values"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_values</span></code></a>(name[, exclude_none])</p></td>
+<td><p>Returns the set of all possible values of a field.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_complex</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_mirna</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_protein</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Cpad.labels" title="pypath.core.annot.Cpad.labels"><code class="xref py py-obj docutils literal notranslate"><span class="pre">labels</span></code></a>([method])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Cpad.load" title="pypath.core.annot.Cpad.load"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load</span></code></a>()</p></td>
+<td><p>Loads the annotation data by calling the input method.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Cpad.load_data" title="pypath.core.annot.Cpad.load_data"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_data</span></code></a>()</p></td>
+<td><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Cpad.load_proteins" title="pypath.core.annot.Cpad.load_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_proteins</span></code></a>()</p></td>
+<td><p>Retrieves a set of all UniProt IDs to have a base set of the entire proteome.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Cpad.make_df" title="pypath.core.annot.Cpad.make_df"><code class="xref py py-obj docutils literal notranslate"><span class="pre">make_df</span></code></a>([rebuild])</p></td>
+<td><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complex_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Cpad.numof_entities" title="pypath.core.annot.Cpad.numof_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_entities</span></code></a>()</p></td>
+<td><p>The number of annotated entities in the resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirna_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirnas</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_protein_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_proteins</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Cpad.numof_records" title="pypath.core.annot.Cpad.numof_records"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_records</span></code></a>([entity_types])</p></td>
+<td><p>The total number of annotation records.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Cpad.numof_references" title="pypath.core.annot.Cpad.numof_references"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_references</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Cpad.process" title="pypath.core.annot.Cpad.process"><code class="xref py py-obj docutils literal notranslate"><span class="pre">process</span></code></a>()</p></td>
+<td><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">proportion</span></code>(other)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Cpad.reload" title="pypath.core.annot.Cpad.reload"><code class="xref py py-obj docutils literal notranslate"><span class="pre">reload</span></code></a>()</p></td>
+<td><p>Reloads the object from the module level.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">save_to_pickle</span></code>(pickle_file)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Cpad.select" title="pypath.core.annot.Cpad.select"><code class="xref py py-obj docutils literal notranslate"><span class="pre">select</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Cpad.set_method" title="pypath.core.annot.Cpad.set_method"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_method</span></code></a>()</p></td>
+<td><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if necessary.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Cpad.set_reference_set" title="pypath.core.annot.Cpad.set_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_reference_set</span></code></a>()</p></td>
+<td><p>Assigns the reference set to the :py:attr``reference_set`` attribute.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Cpad.show" title="pypath.core.annot.Cpad.show"><code class="xref py py-obj docutils literal notranslate"><span class="pre">show</span></code></a>([method, table_param])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic information from the UniProt datasheets.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Cpad.subset_intersection" title="pypath.core.annot.Cpad.subset_intersection"><code class="xref py py-obj docutils literal notranslate"><span class="pre">subset_intersection</span></code></a>(universe, **kwargs)</p></td>
+<td><p>Calculates the proportion of entities in a subset occuring in the set <code class="docutils literal notranslate"><span class="pre">universe</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Cpad.to_array" title="pypath.core.annot.Cpad.to_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_array</span></code></a>([reference_set, use_fields])</p></td>
+<td><p>Returns an entity vs feature array.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Cpad.to_bool_array" title="pypath.core.annot.Cpad.to_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_bool_array</span></code></a>(reference_set)</p></td>
+<td><p>Returns a presence/absence boolean array for a reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Cpad.to_set" title="pypath.core.annot.Cpad.to_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_set</span></code></a>()</p></td>
+<td><p>Returns the entities present in this annotation resource as a set.</p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Attributes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_fields</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">summary</span></code></p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cpad.add_complexes_by_inference">
+<span class="sig-name descname"><span class="pre">add_complexes_by_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cpad.add_complexes_by_inference" title="Link to this definition">§</a></dt>
+<dd><p>Creates complex annotations by in silico inference and adds them
+to this annotation set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cpad.all_complexes">
+<span class="sig-name descname"><span class="pre">all_complexes</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cpad.all_complexes" title="Link to this definition">§</a></dt>
+<dd><p>All protein complexes annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cpad.all_entities">
+<span class="sig-name descname"><span class="pre">all_entities</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cpad.all_entities" title="Link to this definition">§</a></dt>
+<dd><p>All entities annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cpad.all_mirnas">
+<span class="sig-name descname"><span class="pre">all_mirnas</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cpad.all_mirnas" title="Link to this definition">§</a></dt>
+<dd><p>All miRNAs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cpad.all_proteins">
+<span class="sig-name descname"><span class="pre">all_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cpad.all_proteins" title="Link to this definition">§</a></dt>
+<dd><p>All UniProt IDs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cpad.all_refs">
+<span class="sig-name descname"><span class="pre">all_refs</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cpad.all_refs" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects the references
+across all records. Returns <em>list</em>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cpad.annotate_complex">
+<span class="sig-name descname"><span class="pre">annotate_complex</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cplex</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cpad.annotate_complex" title="Link to this definition">§</a></dt>
+<dd><p>Infers annotations for a single complex.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cpad.browse">
+<span class="sig-name descname"><span class="pre">browse</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">field</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">start</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cpad.browse" title="Link to this definition">§</a></dt>
+<dd><p>Print gene information as a table.</p>
+<p>Presents information about annotation categories as ascii tables
+printed in the terminal. If one category provided, prints one table.
+If multiple categories provided, prints a table for each of them one
+by one proceeding to the next one once you hit return. If no categories
+provided goes through all levels of the primary category.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>field:</dt><dd><p>The field to browse categories by.</p>
+<ul class="simple">
+<li><p>If None the primary field will be selected.
+If this annotation resource doesn’t have fields, all proteins
+will be presented as one single category.</p></li>
+<li><p>If a string it will be considered a field name and it will
+browse through all levels of this field.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">list</span></code>, set or tuple, it will be considered either a
+<code class="docutils literal notranslate"><span class="pre">list</span></code> of field names or a list of values from the primary
+field. In the former case all combinations of the values of
+the fields will be presented, in the latter case the browsing
+will be limited to the levels of the primary field contained
+in <code class="docutils literal notranslate"><span class="pre">field</span></code>.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">dict</span></code>, keys are supposed to be field names and values
+as list of levels. If any of the values are None, all levels
+from that field will be used.</p></li>
+</ul>
+</dd>
+<dt>start:</dt><dd><p>Start browsing from this category. E.g. if there are 500
+categories and start is 250 it will skip everything before the
+250th.</p>
+</dd>
+<dt>kwargs:</dt><dd><p>Passed to <code class="docutils literal notranslate"><span class="pre">pypath.utils.uniprot.info</span></code>.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cpad.complex_inference">
+<span class="sig-name descname"><span class="pre">complex_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cpad.complex_inference" title="Link to this definition">§</a></dt>
+<dd><p>Annotates all complexes in <cite>complexes</cite>, by default in the default
+complex database (existing in the <cite>complex</cite> module or generated
+on demand according to the module’s current settings).</p>
+<dl class="field-list simple">
+<dt class="field-odd">Returns<span class="colon">:</span></dt>
+<dd class="field-odd"><p><ul class="simple">
+<li><p><em>Dict with complexes as keys and sets of annotations as values.</em></p></li>
+<li><p><em>Complexes with no valid information in this annotation resource</em></p></li>
+<li><p><em>won’t be in the dict.</em></p></li>
+</ul>
+</p>
+</dd>
+<dt class="field-even">Parameters<span class="colon">:</span></dt>
+<dd class="field-even"><p><strong>complexes</strong> (<em>iterable</em>) – Iterable yielding complexes.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cpad.coverage">
+<span class="sig-name descname"><span class="pre">coverage</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">other</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cpad.coverage" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the coverage of the annotation i.e. the proportion of
+entities having at least one record in this annotation resource
+for an arbitrary set of entities.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cpad.curation_effort">
+<span class="sig-name descname"><span class="pre">curation_effort</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cpad.curation_effort" title="Link to this definition">§</a></dt>
+<dd><p>Counts the reference-record pairs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cpad.get_names">
+<span class="sig-name descname"><span class="pre">get_names</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cpad.get_names" title="Link to this definition">§</a></dt>
+<dd><p>Returns the list of field names in the records. The annotation
+consists of uniform records and each entity might be annotated
+with one or more records. Each record is a tuple of fields, for
+example <code class="docutils literal notranslate"><span class="pre">('cell_type',</span> <span class="pre">'expression_level',</span> <span class="pre">'score')</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cpad.get_reference_set">
+<em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">get_reference_set</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">proteins</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">swissprot_only</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cpad.get_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the reference set i.e. the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cpad.get_subset">
+<span class="sig-name descname"><span class="pre">get_subset</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cpad.get_subset" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cpad.get_subset_bool_array">
+<span class="sig-name descname"><span class="pre">get_subset_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cpad.get_subset_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a boolean vector with True and False values for each entity
+in the reference set. The values represent presence absence data
+in the simplest case, but by providing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> any kind of matching
+and filtering is possible. <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> are passed to the <code class="docutils literal notranslate"><span class="pre">select</span></code>
+method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cpad.get_values">
+<span class="sig-name descname"><span class="pre">get_values</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">exclude_none</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cpad.get_values" title="Link to this definition">§</a></dt>
+<dd><p>Returns the set of all possible values of a field. E.g. if the
+records of this annotation have a field <code class="docutils literal notranslate"><span class="pre">cell_type</span></code> then calling
+this method can tell you that across all records the values of
+this field might be <code class="docutils literal notranslate"><span class="pre">{'macrophage',</span> <span class="pre">'epithelial_cell',</span> <span class="pre">...}</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cpad.labels">
+<span class="sig-name descname"><span class="pre">labels</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cpad.labels" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cpad.load">
+<span class="sig-name descname"><span class="pre">load</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cpad.load" title="Link to this definition">§</a></dt>
+<dd><p>Loads the annotation data by calling the input method.
+Infers annotations for complexes in the complex database if
+py:attr:<code class="docutils literal notranslate"><span class="pre">infer_complexes</span></code> is True.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cpad.load_data">
+<span class="sig-name descname"><span class="pre">load_data</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cpad.load_data" title="Link to this definition">§</a></dt>
+<dd><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cpad.load_proteins">
+<span class="sig-name descname"><span class="pre">load_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cpad.load_proteins" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a set of all UniProt IDs to have a base set of the entire
+proteome.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cpad.make_df">
+<span class="sig-name descname"><span class="pre">make_df</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">rebuild</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cpad.make_df" title="Link to this definition">§</a></dt>
+<dd><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.
+The data frame will be assigned to :py:attr``df``.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cpad.numof_entities">
+<span class="sig-name descname"><span class="pre">numof_entities</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cpad.numof_entities" title="Link to this definition">§</a></dt>
+<dd><p>The number of annotated entities in the resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cpad.numof_records">
+<span class="sig-name descname"><span class="pre">numof_records</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cpad.numof_records" title="Link to this definition">§</a></dt>
+<dd><p>The total number of annotation records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cpad.numof_references">
+<span class="sig-name descname"><span class="pre">numof_references</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cpad.numof_references" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects and counts the
+references across all records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cpad.process">
+<span class="sig-name descname"><span class="pre">process</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cpad.process" title="Link to this definition">§</a></dt>
+<dd><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cpad.reload">
+<span class="sig-name descname"><span class="pre">reload</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cpad.reload" title="Link to this definition">§</a></dt>
+<dd><p>Reloads the object from the module level.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cpad.select">
+<span class="sig-name descname"><span class="pre">select</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cpad.select" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cpad.set_method">
+<span class="sig-name descname"><span class="pre">set_method</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cpad.set_method" title="Link to this definition">§</a></dt>
+<dd><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if
+necessary.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cpad.set_reference_set">
+<span class="sig-name descname"><span class="pre">set_reference_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cpad.set_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Assigns the reference set to the :py:attr``reference_set`` attribute.
+The reference set is the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cpad.show">
+<span class="sig-name descname"><span class="pre">show</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">table_param</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cpad.show" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic
+information from the UniProt datasheets.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cpad.subset_intersection">
+<span class="sig-name descname"><span class="pre">subset_intersection</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">universe</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cpad.subset_intersection" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the proportion of entities in a subset occuring in the
+set <code class="docutils literal notranslate"><span class="pre">universe</span></code>. The subset is selected by passing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> to the
+<code class="docutils literal notranslate"><span class="pre">select</span></code> method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cpad.to_array">
+<span class="sig-name descname"><span class="pre">to_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_fields</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cpad.to_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns an entity vs feature array. In case of more complex
+annotations this might be huge.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cpad.to_bool_array">
+<span class="sig-name descname"><span class="pre">to_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cpad.to_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a presence/absence boolean array for a reference set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cpad.to_set">
+<span class="sig-name descname"><span class="pre">to_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cpad.to_set" title="Link to this definition">§</a></dt>
+<dd><p>Returns the entities present in this annotation resource as a set.</p>
+</dd></dl>
+
+</dd></dl>
+
+</section>
+
+
+                </article>
+              
+              
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+                  
+  <section id="pypath-core-annot-customannotation">
+<h1>pypath.core.annot.CustomAnnotation<a class="headerlink" href="#pypath-core-annot-customannotation" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.core.annot.CustomAnnotation">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.core.annot.</span></span><span class="sig-name descname"><span class="pre">CustomAnnotation</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">class_definitions</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">excludes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">excludes_extra</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">build</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">pickle_file</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">annotdb_pickle_file</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">composite_resource_name</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#CustomAnnotation"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.CustomAnnotation" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">Logger</span></code></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CustomAnnotation.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">class_definitions</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">excludes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">excludes_extra</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">build</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">pickle_file</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">annotdb_pickle_file</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">composite_resource_name</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#CustomAnnotation.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.CustomAnnotation.__init__" title="Link to this definition">§</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>class_definitions</strong> (<em>tuple</em>) – A series of annotation class definitions, each represented by
+an instance of <code class="docutils literal notranslate"><span class="pre">pypath.internals.annot_formats.AnnotDef</span></code>.
+These definitions carry the attributes and instructions to
+populate the classes.</p></li>
+<li><p><strong>excludes</strong> (<em>dict</em>) – A dict with parent category names (strings) or category keys
+(tuples) as keys and sets if identifiers as values.
+The identifiers in this dict will be excluded from all the
+respective categories while building the database. E.g. if
+the UniProt ID <cite>P00533</cite> (EGFR) is in the set under the key of
+<cite>adhesion</cite> it will be excluded from the category <cite>adhesion</cite> and
+all it’s direct children.</p></li>
+<li><p><strong>excludes_extra</strong> (<em>dict</em>) – Same kind of dict as <cite>excludes</cite> but it will be added to the
+built-in default. The built in and the provided extra sets
+will be merged. If you want to overwrite or modify the built-in
+sets provide your custom dict as <cite>excludes</cite>.</p></li>
+<li><p><strong>build</strong> (<em>bool</em>) – Execute the build upon instantiation or set up an empty object
+the build can be executed on later.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CustomAnnotation.__init__" title="pypath.core.annot.CustomAnnotation.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>([class_definitions, excludes, ...])</p></td>
+<td><p><dl class="field-list simple">
+<dt class="field-odd">param tuple class_definitions<span class="colon">:</span></dt>
+<dd class="field-odd"><p></p></dd>
+</dl>
+</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">add_class_definitions</span></code>(class_definitions)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_resources</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CustomAnnotation.browse" title="pypath.core.annot.CustomAnnotation.browse"><code class="xref py py-obj docutils literal notranslate"><span class="pre">browse</span></code></a>([start])</p></td>
+<td><p>Print gene information as a table.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">build</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CustomAnnotation.class_to_class_connections" title="pypath.core.annot.CustomAnnotation.class_to_class_connections"><code class="xref py py-obj docutils literal notranslate"><span class="pre">class_to_class_connections</span></code></a>(**kwargs)</p></td>
+<td><p><code class="docutils literal notranslate"><span class="pre">kwargs</span></code> passed to <code class="docutils literal notranslate"><span class="pre">filter_interclass_network</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">class_to_class_connections_directed</span></code>(**kwargs)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">class_to_class_connections_inhibitory</span></code>(**kwargs)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">class_to_class_connections_signed</span></code>(**kwargs)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">class_to_class_connections_stimulatory</span></code>(**kwargs)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">class_to_class_connections_undirected</span></code>(**kwargs)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CustomAnnotation.classes_by_entity" title="pypath.core.annot.CustomAnnotation.classes_by_entity"><code class="xref py py-obj docutils literal notranslate"><span class="pre">classes_by_entity</span></code></a>(element[, labels])</p></td>
+<td><p>Returns a set of class keys with the classes containing at least one of the elements.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">complexes_by_resource</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">consensus_score</span></code>(name, entity)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">consensus_score_normalized</span></code>(name, entity)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_inter_class_connections</span></code>([...])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_inter_class_connections_all</span></code>([...])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_inter_class_connections_directed</span></code>([...])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_inter_class_connections_inhibitory</span></code>([...])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_inter_class_connections_signed</span></code>([...])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_inter_class_connections_stimulatory</span></code>([...])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_inter_class_connections_undirected</span></code>([...])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CustomAnnotation.counts" title="pypath.core.annot.CustomAnnotation.counts"><code class="xref py py-obj docutils literal notranslate"><span class="pre">counts</span></code></a>([entity_type, labels])</p></td>
+<td><p>Returns a dict with number of elements in each class.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CustomAnnotation.counts_by_class" title="pypath.core.annot.CustomAnnotation.counts_by_class"><code class="xref py py-obj docutils literal notranslate"><span class="pre">counts_by_class</span></code></a>([entity_type, labels])</p></td>
+<td><p>Returns a dict with number of elements in each class.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">counts_by_resource</span></code>([entity_types])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">counts_df</span></code>([groupby])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CustomAnnotation.create_class" title="pypath.core.annot.CustomAnnotation.create_class"><code class="xref py py-obj docutils literal notranslate"><span class="pre">create_class</span></code></a>(classdef[, override])</p></td>
+<td><p>Creates a category of entities by processing a custom definition.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CustomAnnotation.degree_inter_class_network" title="pypath.core.annot.CustomAnnotation.degree_inter_class_network"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degree_inter_class_network</span></code></a>([...])</p></td>
+<td><p>degrees_of : str</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">degree_inter_class_network_2</span></code>([degrees_of, ...])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">degree_inter_class_network_directed</span></code>([...])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">degree_inter_class_network_directed_2</span></code>(**kwargs)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">degree_inter_class_network_inhibitory</span></code>([...])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">degree_inter_class_network_inhibitory_2</span></code>(**kwargs)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">degree_inter_class_network_stimulatory</span></code>([...])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">degree_inter_class_network_stimulatory_2</span></code>(...)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">degree_inter_class_network_undirected</span></code>([...])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">degree_inter_class_network_undirected_2</span></code>(**kwargs)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">difference</span></code>(*args)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">ensure_annotdb</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">entities_by_resource</span></code>([entity_types])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">export</span></code>(fname, **kwargs)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CustomAnnotation.filter" title="pypath.core.annot.CustomAnnotation.filter"><code class="xref py py-obj docutils literal notranslate"><span class="pre">filter</span></code></a>([entity_type])</p></td>
+<td><p>Filters the annotated entities by annotation class attributes and <code class="docutils literal notranslate"><span class="pre">entity_type</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CustomAnnotation.filter_classes" title="pypath.core.annot.CustomAnnotation.filter_classes"><code class="xref py py-obj docutils literal notranslate"><span class="pre">filter_classes</span></code></a>(classes, **kwargs)</p></td>
+<td><p>Returns a list of annotation classes filtered by their attributes.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">filter_df</span></code>(annot_df[, entities, postfix])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">filter_entity_type</span></code>(cls[, entity_type])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CustomAnnotation.filter_interclass_network" title="pypath.core.annot.CustomAnnotation.filter_interclass_network"><code class="xref py py-obj docutils literal notranslate"><span class="pre">filter_interclass_network</span></code></a>([annot_df, ...])</p></td>
+<td><p>Combines the annotation data frame and a network data frame.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">filtered</span></code>([annot_df, entities])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_aspect</span></code>(name[, parent, resource])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CustomAnnotation.get_class" title="pypath.core.annot.CustomAnnotation.get_class"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_class</span></code></a>(definition[, parent, resource, ...])</p></td>
+<td><p>Retrieves a class by its name or definition.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_class_label</span></code>(name[, parent, resource])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_class_scope</span></code>(name[, parent, resource])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CustomAnnotation.get_df" title="pypath.core.annot.CustomAnnotation.get_df"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_df</span></code></a>()</p></td>
+<td><p>Returns the data frame of custom annotations.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_entities</span></code>([entity_types])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CustomAnnotation.get_interclass_network_df" title="pypath.core.annot.CustomAnnotation.get_interclass_network_df"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_interclass_network_df</span></code></a>(**kwargs)</p></td>
+<td><p>If the an interclass network is already present the <code class="docutils literal notranslate"><span class="pre">network</span></code> and other <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> provided not considered.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_mirnas</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_parent</span></code>(name[, parent, resource])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CustomAnnotation.get_parents" title="pypath.core.annot.CustomAnnotation.get_parents"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_parents</span></code></a>(name[, parent, resource])</p></td>
+<td><p>As names should be unique for resources, a combination of a name and resource determines the parent category.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_proteins</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CustomAnnotation.get_resource" title="pypath.core.annot.CustomAnnotation.get_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_resource</span></code></a>(name[, parent])</p></td>
+<td><p>For a category name and its parent returns a single resource name.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CustomAnnotation.get_resources" title="pypath.core.annot.CustomAnnotation.get_resources"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_resources</span></code></a>(name[, parent])</p></td>
+<td><p>Returns a set with the names of all resources defining a category with the given name and parent.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_source</span></code>(name[, parent, resource])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">inter_class_network</span></code>([annot_args_source, ...])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">inter_class_network_directed</span></code>([...])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">inter_class_network_inhibitory</span></code>([...])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">inter_class_network_signed</span></code>([...])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">inter_class_network_stimulatory</span></code>([...])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">inter_class_network_undirected</span></code>([...])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">intersection</span></code>(*args)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">isdisjoint</span></code>(*args)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">iter_classes</span></code>(**kwargs)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CustomAnnotation.labels" title="pypath.core.annot.CustomAnnotation.labels"><code class="xref py py-obj docutils literal notranslate"><span class="pre">labels</span></code></a>(name[, parent, resource, entity_type])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">load</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_from_pickle</span></code>(pickle_file)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CustomAnnotation.make_df" title="pypath.core.annot.CustomAnnotation.make_df"><code class="xref py py-obj docutils literal notranslate"><span class="pre">make_df</span></code></a>([all_annotations, full_name])</p></td>
+<td><p>Creates a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> where each record assigns a molecular entity to an annotation category.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">mirnas_by_resource</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CustomAnnotation.network_df" title="pypath.core.annot.CustomAnnotation.network_df"><code class="xref py py-obj docutils literal notranslate"><span class="pre">network_df</span></code></a>([annot_df, network, combined_df, ...])</p></td>
+<td><p>Combines the annotation data frame and a network data frame.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_classes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complex_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_entities</span></code>([entity_types])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirna_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirnas</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_protein_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_proteins</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_records</span></code>([entity_types])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CustomAnnotation.populate_classes" title="pypath.core.annot.CustomAnnotation.populate_classes"><code class="xref py py-obj docutils literal notranslate"><span class="pre">populate_classes</span></code></a>([update])</p></td>
+<td><p>Creates a classification of proteins according to the custom annotation definitions.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CustomAnnotation.populate_scores" title="pypath.core.annot.CustomAnnotation.populate_scores"><code class="xref py py-obj docutils literal notranslate"><span class="pre">populate_scores</span></code></a>()</p></td>
+<td><p>Creates the consensus score dictionaries based on the number of resources annotating an entity for each composite category.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">post_load</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">pre_build</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CustomAnnotation.process_annot" title="pypath.core.annot.CustomAnnotation.process_annot"><code class="xref py py-obj docutils literal notranslate"><span class="pre">process_annot</span></code></a>(classdef)</p></td>
+<td><p>Processes an annotation definition and returns a set of identifiers.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">proteins_by_resource</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CustomAnnotation.quality_check_table" title="pypath.core.annot.CustomAnnotation.quality_check_table"><code class="xref py py-obj docutils literal notranslate"><span class="pre">quality_check_table</span></code></a>([path, fmt, ...])</p></td>
+<td><p>Exports a table in tsv format for quality check and browsing purposes.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CustomAnnotation.register_network" title="pypath.core.annot.CustomAnnotation.register_network"><code class="xref py py-obj docutils literal notranslate"><span class="pre">register_network</span></code></a>(network)</p></td>
+<td><p>Sets <code class="docutils literal notranslate"><span class="pre">network</span></code> as the default network dataset for the instance.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CustomAnnotation.reload" title="pypath.core.annot.CustomAnnotation.reload"><code class="xref py py-obj docutils literal notranslate"><span class="pre">reload</span></code></a>()</p></td>
+<td><p>Reloads the object from the module level.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CustomAnnotation.resources_in_category" title="pypath.core.annot.CustomAnnotation.resources_in_category"><code class="xref py py-obj docutils literal notranslate"><span class="pre">resources_in_category</span></code></a>(key)</p></td>
+<td><p>Returns a list of resources contributing to the definition of a category.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">save_to_pickle</span></code>(pickle_file)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CustomAnnotation.select" title="pypath.core.annot.CustomAnnotation.select"><code class="xref py py-obj docutils literal notranslate"><span class="pre">select</span></code></a>(definition[, parent, resource, ...])</p></td>
+<td><p>Retrieves a class by its name or definition.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CustomAnnotation.set_interclass_network_df" title="pypath.core.annot.CustomAnnotation.set_interclass_network_df"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_interclass_network_df</span></code></a>(**kwargs)</p></td>
+<td><p>Creates a data frame of the whole inter-class network and keeps it assigned to the instance in order to make subsequent queries faster.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">sets</span></code>(*args)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.CustomAnnotation.show" title="pypath.core.annot.CustomAnnotation.show"><code class="xref py py-obj docutils literal notranslate"><span class="pre">show</span></code></a>(name[, parent, resource])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic information from the UniProt datasheets.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">symmetric_difference</span></code>(*args)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">union</span></code>(*args)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">unset_interclass_network_df</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">update_excludes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.CustomAnnotation.update_parents" title="pypath.core.annot.CustomAnnotation.update_parents"><code class="xref py py-obj docutils literal notranslate"><span class="pre">update_parents</span></code></a>()</p></td>
+<td><p>Creates a dict :py:attr:<code class="docutils literal notranslate"><span class="pre">children</span></code> with parent class names as keys and sets of children class keys as values.</p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CustomAnnotation.browse">
+<span class="sig-name descname"><span class="pre">browse</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">start</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#CustomAnnotation.browse"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.CustomAnnotation.browse" title="Link to this definition">§</a></dt>
+<dd><p>Print gene information as a table.</p>
+<p>Presents information about annotation classes as ascii tables printed
+in the terminal. If one class provided, prints one table. If multiple
+classes provided, prints a table for each of them one by one
+proceeding to the next one once you hit return. If no classes
+provided goes through all classes.</p>
+<p><code class="docutils literal notranslate"><span class="pre">kwargs</span></code> passed to <code class="docutils literal notranslate"><span class="pre">pypath.utils.uniprot.info</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CustomAnnotation.class_to_class_connections">
+<span class="sig-name descname"><span class="pre">class_to_class_connections</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#CustomAnnotation.class_to_class_connections"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.CustomAnnotation.class_to_class_connections" title="Link to this definition">§</a></dt>
+<dd><p><code class="docutils literal notranslate"><span class="pre">kwargs</span></code> passed to <code class="docutils literal notranslate"><span class="pre">filter_interclass_network</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CustomAnnotation.classes_by_entity">
+<span class="sig-name descname"><span class="pre">classes_by_entity</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">element</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">labels</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#CustomAnnotation.classes_by_entity"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.CustomAnnotation.classes_by_entity" title="Link to this definition">§</a></dt>
+<dd><p>Returns a set of class keys with the classes containing at least
+one of the elements.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>element</strong> (<em>str</em><em>,</em><em>set</em>) – One or more element (entity) to search for in the classes.</p></li>
+<li><p><strong>labels</strong> (<em>bool</em>) – Return labels instead of keys.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CustomAnnotation.counts">
+<span class="sig-name descname"><span class="pre">counts</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'protein'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">labels</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#CustomAnnotation.counts"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.CustomAnnotation.counts" title="Link to this definition">§</a></dt>
+<dd><p>Returns a dict with number of elements in each class.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><p><strong>labels</strong> (<em>bool</em>) – Use keys or labels as keys in the returned dict.</p>
+</dd>
+</dl>
+<p>All other arguments passed to <code class="docutils literal notranslate"><span class="pre">iter_classes</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CustomAnnotation.counts_by_class">
+<span class="sig-name descname"><span class="pre">counts_by_class</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'protein'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">labels</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CustomAnnotation.counts_by_class" title="Link to this definition">§</a></dt>
+<dd><p>Returns a dict with number of elements in each class.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><p><strong>labels</strong> (<em>bool</em>) – Use keys or labels as keys in the returned dict.</p>
+</dd>
+</dl>
+<p>All other arguments passed to <code class="docutils literal notranslate"><span class="pre">iter_classes</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CustomAnnotation.create_class">
+<span class="sig-name descname"><span class="pre">create_class</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">classdef</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">override</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#CustomAnnotation.create_class"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.CustomAnnotation.create_class" title="Link to this definition">§</a></dt>
+<dd><p>Creates a category of entities by processing a custom definition.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CustomAnnotation.degree_inter_class_network">
+<span class="sig-name descname"><span class="pre">degree_inter_class_network</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">annot_args_source</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">annot_args_target</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">degrees_of</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'target'</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#CustomAnnotation.degree_inter_class_network"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.CustomAnnotation.degree_inter_class_network" title="Link to this definition">§</a></dt>
+<dd><dl class="simple">
+<dt>degrees_of<span class="classifier">str</span></dt><dd><p>Either <em>source</em> or <em>target</em>. Count the degrees for the source
+or the target class.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CustomAnnotation.filter">
+<span class="sig-name descname"><span class="pre">filter</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#CustomAnnotation.filter"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.CustomAnnotation.filter" title="Link to this definition">§</a></dt>
+<dd><p>Filters the annotated entities by annotation class attributes and
+<code class="docutils literal notranslate"><span class="pre">entity_type</span></code>. <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> passed to <code class="docutils literal notranslate"><span class="pre">filter_classes</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CustomAnnotation.filter_classes">
+<em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">filter_classes</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">classes</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#CustomAnnotation.filter_classes"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.CustomAnnotation.filter_classes" title="Link to this definition">§</a></dt>
+<dd><p>Returns a list of annotation classes filtered by their attributes.
+<code class="docutils literal notranslate"><span class="pre">kwargs</span></code> contains attributes and values.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CustomAnnotation.filter_interclass_network">
+<span class="sig-name descname"><span class="pre">filter_interclass_network</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">annot_df</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">network</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">combined_df</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">network_args</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">annot_args</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">annot_args_source</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">annot_args_target</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entities</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entities_source</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entities_target</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">only_directed</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">only_undirected</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">only_signed</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">only_effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">only_proteins</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">swap_undirected</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">undirected_orientation</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entities_or</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CustomAnnotation.filter_interclass_network" title="Link to this definition">§</a></dt>
+<dd><p>Combines the annotation data frame and a network data frame.
+Creates a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> where each record is an interaction
+between a pair of molecular enitities labeled by their annotations.</p>
+<dl class="simple">
+<dt>network<span class="classifier">pypath.network.Network,pandas.DataFrame</span></dt><dd><p>A <code class="docutils literal notranslate"><span class="pre">pypath.network.Network</span></code> object or a data frame with network
+data.</p>
+</dd>
+<dt>combined_df<span class="classifier">pandas.DataFrame</span></dt><dd><p>Optional, a network data frame already combined with annotations
+for filtering only.</p>
+</dd>
+<dt>resources<span class="classifier">set,None</span></dt><dd><p>Use only these network resources.</p>
+</dd>
+<dt>entities<span class="classifier">set,None</span></dt><dd><p>Limit the network only to these molecular entities.</p>
+</dd>
+<dt>entities_source<span class="classifier">set,None</span></dt><dd><p>Limit the source side of network connections only to these
+molecular entities.</p>
+</dd>
+<dt>entities_target<span class="classifier">set,None</span></dt><dd><p>Limit the target side of network connections only to these
+molecular entities.</p>
+</dd>
+<dt>annot_args<span class="classifier">dict,None</span></dt><dd><p>Parameters for filtering annotation classes; note, the defaults
+might include some filtering, provide an empty dict if you want
+no filtering at all; however this might result in huge data
+frame and consequently memory issues. Passed to the <code class="docutils literal notranslate"><span class="pre">filtered</span></code>
+method.</p>
+</dd>
+<dt>annot_args_source<span class="classifier">dict,None</span></dt><dd><p>Same as <code class="docutils literal notranslate"><span class="pre">annot_args</span></code> but only for the source side of the
+network connections. These override <code class="docutils literal notranslate"><span class="pre">annot_args</span></code> but all the
+criteria not defined here will be applied from <code class="docutils literal notranslate"><span class="pre">annot_args</span></code>.</p>
+</dd>
+<dt>annot_args_target<span class="classifier">dict,None</span></dt><dd><p>Same as <code class="docutils literal notranslate"><span class="pre">annot_args</span></code> but only for the target side of the
+network connections. These override <code class="docutils literal notranslate"><span class="pre">annot_args</span></code> but all the
+criteria not defined here will be applied from <code class="docutils literal notranslate"><span class="pre">annot_args</span></code>.</p>
+</dd>
+<dt>only_directed<span class="classifier">bool</span></dt><dd><p>Use only the directed interactions.</p>
+</dd>
+<dt>only_undirected<span class="classifier">bool</span></dt><dd><p>Use only the undirected interactions. Specifically for retrieving
+and counting the interactions without direction information.</p>
+</dd>
+<dt>only_effect<span class="classifier">int,None</span></dt><dd><p>Use only the interactions with this effect. Either -1 or 1.</p>
+</dd>
+<dt>only_proteins<span class="classifier">bool</span></dt><dd><p>Use only the interactions where each of the partners is a protein
+(i.e. not complex, miRNA, small molecule or other kind of entity).</p>
+</dd>
+<dt>swap_undirected<span class="classifier">bool</span></dt><dd><p>Convert undirected interactions to a pair of mutual interactions.</p>
+</dd>
+<dt>undirected_orientation<span class="classifier">str,None</span></dt><dd><p>Ignore the direction at all interactions and make sure all of
+them have a uniform orientation. If <cite>id</cite>, all interactions will
+be oriented by the identifiers of the partenrs; if <cite>category</cite>,
+the interactions will be oriented by the categories of the
+partners.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CustomAnnotation.get_class">
+<span class="sig-name descname"><span class="pre">get_class</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">definition</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">parent</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resource</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.CustomAnnotation.get_class" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a class by its name or definition. The definition can be
+a class name (string) or a set of entities, or an AnnotDef object
+defining the contents based on original resources or an AnnotOp
+which defines the contents as an operation over other definitions.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CustomAnnotation.get_df">
+<span class="sig-name descname"><span class="pre">get_df</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#CustomAnnotation.get_df"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.CustomAnnotation.get_df" title="Link to this definition">§</a></dt>
+<dd><p>Returns the data frame of custom annotations. If it does not exist yet
+builds the data frame.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CustomAnnotation.get_interclass_network_df">
+<span class="sig-name descname"><span class="pre">get_interclass_network_df</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#CustomAnnotation.get_interclass_network_df"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.CustomAnnotation.get_interclass_network_df" title="Link to this definition">§</a></dt>
+<dd><p>If the an interclass network is already present the <code class="docutils literal notranslate"><span class="pre">network</span></code>
+and other <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> provided not considered. Otherwise these
+are passed to <code class="docutils literal notranslate"><span class="pre">network_df</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CustomAnnotation.get_parents">
+<span class="sig-name descname"><span class="pre">get_parents</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">parent</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resource</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#CustomAnnotation.get_parents"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.CustomAnnotation.get_parents" title="Link to this definition">§</a></dt>
+<dd><p>As names should be unique for resources, a combination of a name and
+resource determines the parent category. This method looks up the
+parent for a pair of name and resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CustomAnnotation.get_resource">
+<span class="sig-name descname"><span class="pre">get_resource</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">parent</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#CustomAnnotation.get_resource"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.CustomAnnotation.get_resource" title="Link to this definition">§</a></dt>
+<dd><p>For a category name and its parent returns a single resource name.
+If a category belonging to the composite database matches the name
+and the parent the name of the composite database will be returned,
+otherwise the resource name first in alphabetic order.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CustomAnnotation.get_resources">
+<span class="sig-name descname"><span class="pre">get_resources</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">parent</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#CustomAnnotation.get_resources"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.CustomAnnotation.get_resources" title="Link to this definition">§</a></dt>
+<dd><p>Returns a set with the names of all resources defining a category
+with the given name and parent.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CustomAnnotation.labels">
+<span class="sig-name descname"><span class="pre">labels</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">parent</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resource</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#CustomAnnotation.labels"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.CustomAnnotation.labels" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CustomAnnotation.make_df">
+<span class="sig-name descname"><span class="pre">make_df</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">all_annotations</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">full_name</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#CustomAnnotation.make_df"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.CustomAnnotation.make_df" title="Link to this definition">§</a></dt>
+<dd><p>Creates a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> where each record assigns a
+molecular entity to an annotation category. The data frame will
+be assigned to the <code class="docutils literal notranslate"><span class="pre">df</span></code> attribute.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CustomAnnotation.network_df">
+<span class="sig-name descname"><span class="pre">network_df</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">annot_df</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">network</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">combined_df</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">network_args</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">annot_args</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">annot_args_source</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">annot_args_target</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entities</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entities_source</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entities_target</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">only_directed</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">only_undirected</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">only_signed</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">only_effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">only_proteins</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">swap_undirected</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">undirected_orientation</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entities_or</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#CustomAnnotation.network_df"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.CustomAnnotation.network_df" title="Link to this definition">§</a></dt>
+<dd><p>Combines the annotation data frame and a network data frame.
+Creates a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> where each record is an interaction
+between a pair of molecular enitities labeled by their annotations.</p>
+<dl class="simple">
+<dt>network<span class="classifier">pypath.network.Network,pandas.DataFrame</span></dt><dd><p>A <code class="docutils literal notranslate"><span class="pre">pypath.network.Network</span></code> object or a data frame with network
+data.</p>
+</dd>
+<dt>combined_df<span class="classifier">pandas.DataFrame</span></dt><dd><p>Optional, a network data frame already combined with annotations
+for filtering only.</p>
+</dd>
+<dt>resources<span class="classifier">set,None</span></dt><dd><p>Use only these network resources.</p>
+</dd>
+<dt>entities<span class="classifier">set,None</span></dt><dd><p>Limit the network only to these molecular entities.</p>
+</dd>
+<dt>entities_source<span class="classifier">set,None</span></dt><dd><p>Limit the source side of network connections only to these
+molecular entities.</p>
+</dd>
+<dt>entities_target<span class="classifier">set,None</span></dt><dd><p>Limit the target side of network connections only to these
+molecular entities.</p>
+</dd>
+<dt>annot_args<span class="classifier">dict,None</span></dt><dd><p>Parameters for filtering annotation classes; note, the defaults
+might include some filtering, provide an empty dict if you want
+no filtering at all; however this might result in huge data
+frame and consequently memory issues. Passed to the <code class="docutils literal notranslate"><span class="pre">filtered</span></code>
+method.</p>
+</dd>
+<dt>annot_args_source<span class="classifier">dict,None</span></dt><dd><p>Same as <code class="docutils literal notranslate"><span class="pre">annot_args</span></code> but only for the source side of the
+network connections. These override <code class="docutils literal notranslate"><span class="pre">annot_args</span></code> but all the
+criteria not defined here will be applied from <code class="docutils literal notranslate"><span class="pre">annot_args</span></code>.</p>
+</dd>
+<dt>annot_args_target<span class="classifier">dict,None</span></dt><dd><p>Same as <code class="docutils literal notranslate"><span class="pre">annot_args</span></code> but only for the target side of the
+network connections. These override <code class="docutils literal notranslate"><span class="pre">annot_args</span></code> but all the
+criteria not defined here will be applied from <code class="docutils literal notranslate"><span class="pre">annot_args</span></code>.</p>
+</dd>
+<dt>only_directed<span class="classifier">bool</span></dt><dd><p>Use only the directed interactions.</p>
+</dd>
+<dt>only_undirected<span class="classifier">bool</span></dt><dd><p>Use only the undirected interactions. Specifically for retrieving
+and counting the interactions without direction information.</p>
+</dd>
+<dt>only_effect<span class="classifier">int,None</span></dt><dd><p>Use only the interactions with this effect. Either -1 or 1.</p>
+</dd>
+<dt>only_proteins<span class="classifier">bool</span></dt><dd><p>Use only the interactions where each of the partners is a protein
+(i.e. not complex, miRNA, small molecule or other kind of entity).</p>
+</dd>
+<dt>swap_undirected<span class="classifier">bool</span></dt><dd><p>Convert undirected interactions to a pair of mutual interactions.</p>
+</dd>
+<dt>undirected_orientation<span class="classifier">str,None</span></dt><dd><p>Ignore the direction at all interactions and make sure all of
+them have a uniform orientation. If <cite>id</cite>, all interactions will
+be oriented by the identifiers of the partenrs; if <cite>category</cite>,
+the interactions will be oriented by the categories of the
+partners.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CustomAnnotation.populate_classes">
+<span class="sig-name descname"><span class="pre">populate_classes</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">update</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#CustomAnnotation.populate_classes"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.CustomAnnotation.populate_classes" title="Link to this definition">§</a></dt>
+<dd><p>Creates a classification of proteins according to the custom
+annotation definitions.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CustomAnnotation.populate_scores">
+<span class="sig-name descname"><span class="pre">populate_scores</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#CustomAnnotation.populate_scores"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.CustomAnnotation.populate_scores" title="Link to this definition">§</a></dt>
+<dd><p>Creates the consensus score dictionaries based on the number of
+resources annotating an entity for each composite category.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CustomAnnotation.process_annot">
+<span class="sig-name descname"><span class="pre">process_annot</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">classdef</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#CustomAnnotation.process_annot"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.CustomAnnotation.process_annot" title="Link to this definition">§</a></dt>
+<dd><p>Processes an annotation definition and returns a set of identifiers.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CustomAnnotation.quality_check_table">
+<span class="sig-name descname"><span class="pre">quality_check_table</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">path</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">fmt</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'tsv'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">only_swissprot</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">top</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#CustomAnnotation.quality_check_table"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.CustomAnnotation.quality_check_table" title="Link to this definition">§</a></dt>
+<dd><p>Exports a table in tsv format for quality check and browsing purposes.
+Each protein represented in one row of this table with basic data
+from UniProt and the list of annotation categories from this
+database.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>path</strong> (<em>str</em>) – Path for the exported file.</p></li>
+<li><p><strong>fmt</strong> (<em>str</em>) – Format: either <cite>tsv</cite> or <cite>latex</cite>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CustomAnnotation.register_network">
+<span class="sig-name descname"><span class="pre">register_network</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">network</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#CustomAnnotation.register_network"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.CustomAnnotation.register_network" title="Link to this definition">§</a></dt>
+<dd><p>Sets <code class="docutils literal notranslate"><span class="pre">network</span></code> as the default network dataset for the instance.
+All methods afterwards will use this network.
+Also it discards the interclass network data frame if it present to
+make sure future queries will address the network registered here.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CustomAnnotation.reload">
+<span class="sig-name descname"><span class="pre">reload</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#CustomAnnotation.reload"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.CustomAnnotation.reload" title="Link to this definition">§</a></dt>
+<dd><p>Reloads the object from the module level.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CustomAnnotation.resources_in_category">
+<span class="sig-name descname"><span class="pre">resources_in_category</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">key</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#CustomAnnotation.resources_in_category"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.CustomAnnotation.resources_in_category" title="Link to this definition">§</a></dt>
+<dd><p>Returns a list of resources contributing to the definition of
+a category.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CustomAnnotation.select">
+<span class="sig-name descname"><span class="pre">select</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">definition</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">parent</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resource</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#CustomAnnotation.select"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.CustomAnnotation.select" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a class by its name or definition. The definition can be
+a class name (string) or a set of entities, or an AnnotDef object
+defining the contents based on original resources or an AnnotOp
+which defines the contents as an operation over other definitions.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CustomAnnotation.set_interclass_network_df">
+<span class="sig-name descname"><span class="pre">set_interclass_network_df</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#CustomAnnotation.set_interclass_network_df"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.CustomAnnotation.set_interclass_network_df" title="Link to this definition">§</a></dt>
+<dd><p>Creates a data frame of the whole inter-class network and keeps it
+assigned to the instance in order to make subsequent queries faster.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CustomAnnotation.show">
+<span class="sig-name descname"><span class="pre">show</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">parent</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resource</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#CustomAnnotation.show"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.CustomAnnotation.show" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic
+information from the UniProt datasheets.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.CustomAnnotation.update_parents">
+<span class="sig-name descname"><span class="pre">update_parents</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#CustomAnnotation.update_parents"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.CustomAnnotation.update_parents" title="Link to this definition">§</a></dt>
+<dd><p>Creates a dict :py:attr:<code class="docutils literal notranslate"><span class="pre">children</span></code> with parent class names as keys
+and sets of children class keys as values. Also a dict
+:py:attr:<code class="docutils literal notranslate"><span class="pre">parents</span></code> with children class keys as keys and parent
+class keys as values.</p>
+</dd></dl>
+
+</dd></dl>
+
+</section>
+
+
+                </article>
+              
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+  <section id="pypath-core-annot-cytosig">
+<h1>pypath.core.annot.Cytosig<a class="headerlink" href="#pypath-core-annot-cytosig" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.core.annot.Cytosig">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.core.annot.</span></span><span class="sig-name descname"><span class="pre">Cytosig</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#Cytosig"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.Cytosig" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <a class="reference internal" href="pypath.core.annot.AnnotationBase.html#pypath.core.annot.AnnotationBase" title="pypath.core.annot.AnnotationBase"><code class="xref py py-class docutils literal notranslate"><span class="pre">AnnotationBase</span></code></a></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cytosig.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#Cytosig.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.Cytosig.__init__" title="Link to this definition">§</a></dt>
+<dd><p>Cytokine perturbation signatures from the CytoSig database.</p>
+</dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Cytosig.__init__" title="pypath.core.annot.Cytosig.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>([ncbi_tax_id])</p></td>
+<td><p>Cytokine perturbation signatures from the CytoSig database.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Cytosig.add_complexes_by_inference" title="pypath.core.annot.Cytosig.add_complexes_by_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">add_complexes_by_inference</span></code></a>([complexes])</p></td>
+<td><p>Creates complex annotations by in silico inference and adds them to this annotation set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Cytosig.all_complexes" title="pypath.core.annot.Cytosig.all_complexes"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_complexes</span></code></a>()</p></td>
+<td><p>All protein complexes annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Cytosig.all_entities" title="pypath.core.annot.Cytosig.all_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_entities</span></code></a>([entity_types])</p></td>
+<td><p>All entities annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Cytosig.all_mirnas" title="pypath.core.annot.Cytosig.all_mirnas"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_mirnas</span></code></a>()</p></td>
+<td><p>All miRNAs annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Cytosig.all_proteins" title="pypath.core.annot.Cytosig.all_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_proteins</span></code></a>()</p></td>
+<td><p>All UniProt IDs annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Cytosig.all_refs" title="pypath.core.annot.Cytosig.all_refs"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_refs</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Cytosig.annotate_complex" title="pypath.core.annot.Cytosig.annotate_complex"><code class="xref py py-obj docutils literal notranslate"><span class="pre">annotate_complex</span></code></a>(cplex)</p></td>
+<td><p>Infers annotations for a single complex.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Cytosig.browse" title="pypath.core.annot.Cytosig.browse"><code class="xref py py-obj docutils literal notranslate"><span class="pre">browse</span></code></a>([field, start])</p></td>
+<td><p>Print gene information as a table.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Cytosig.complex_inference" title="pypath.core.annot.Cytosig.complex_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">complex_inference</span></code></a>([complexes])</p></td>
+<td><p>Annotates all complexes in <cite>complexes</cite>, by default in the default complex database (existing in the <cite>complex</cite> module or generated on demand according to the module's current settings).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Cytosig.coverage" title="pypath.core.annot.Cytosig.coverage"><code class="xref py py-obj docutils literal notranslate"><span class="pre">coverage</span></code></a>(other)</p></td>
+<td><p>Calculates the coverage of the annotation i.e. the proportion of entities having at least one record in this annotation resource for an arbitrary set of entities.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Cytosig.curation_effort" title="pypath.core.annot.Cytosig.curation_effort"><code class="xref py py-obj docutils literal notranslate"><span class="pre">curation_effort</span></code></a>()</p></td>
+<td><p>Counts the reference-record pairs.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">from_dump</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_entity_type</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Cytosig.get_names" title="pypath.core.annot.Cytosig.get_names"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_names</span></code></a>()</p></td>
+<td><p>Returns the list of field names in the records.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Cytosig.get_reference_set" title="pypath.core.annot.Cytosig.get_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_reference_set</span></code></a>([proteins, complexes, ...])</p></td>
+<td><p>Retrieves the reference set i.e. the set of all entities which potentially have annotation in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Cytosig.get_subset" title="pypath.core.annot.Cytosig.get_subset"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Cytosig.get_subset_bool_array" title="pypath.core.annot.Cytosig.get_subset_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset_bool_array</span></code></a>([reference_set])</p></td>
+<td><p>Returns a boolean vector with True and False values for each entity in the reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Cytosig.get_values" title="pypath.core.annot.Cytosig.get_values"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_values</span></code></a>(name[, exclude_none])</p></td>
+<td><p>Returns the set of all possible values of a field.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_complex</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_mirna</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_protein</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Cytosig.labels" title="pypath.core.annot.Cytosig.labels"><code class="xref py py-obj docutils literal notranslate"><span class="pre">labels</span></code></a>([method])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Cytosig.load" title="pypath.core.annot.Cytosig.load"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load</span></code></a>()</p></td>
+<td><p>Loads the annotation data by calling the input method.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Cytosig.load_data" title="pypath.core.annot.Cytosig.load_data"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_data</span></code></a>()</p></td>
+<td><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Cytosig.load_proteins" title="pypath.core.annot.Cytosig.load_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_proteins</span></code></a>()</p></td>
+<td><p>Retrieves a set of all UniProt IDs to have a base set of the entire proteome.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Cytosig.make_df" title="pypath.core.annot.Cytosig.make_df"><code class="xref py py-obj docutils literal notranslate"><span class="pre">make_df</span></code></a>([rebuild])</p></td>
+<td><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complex_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Cytosig.numof_entities" title="pypath.core.annot.Cytosig.numof_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_entities</span></code></a>()</p></td>
+<td><p>The number of annotated entities in the resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirna_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirnas</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_protein_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_proteins</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Cytosig.numof_records" title="pypath.core.annot.Cytosig.numof_records"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_records</span></code></a>([entity_types])</p></td>
+<td><p>The total number of annotation records.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Cytosig.numof_references" title="pypath.core.annot.Cytosig.numof_references"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_references</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Cytosig.process" title="pypath.core.annot.Cytosig.process"><code class="xref py py-obj docutils literal notranslate"><span class="pre">process</span></code></a>()</p></td>
+<td><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">proportion</span></code>(other)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Cytosig.reload" title="pypath.core.annot.Cytosig.reload"><code class="xref py py-obj docutils literal notranslate"><span class="pre">reload</span></code></a>()</p></td>
+<td><p>Reloads the object from the module level.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">save_to_pickle</span></code>(pickle_file)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Cytosig.select" title="pypath.core.annot.Cytosig.select"><code class="xref py py-obj docutils literal notranslate"><span class="pre">select</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Cytosig.set_method" title="pypath.core.annot.Cytosig.set_method"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_method</span></code></a>()</p></td>
+<td><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if necessary.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Cytosig.set_reference_set" title="pypath.core.annot.Cytosig.set_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_reference_set</span></code></a>()</p></td>
+<td><p>Assigns the reference set to the :py:attr``reference_set`` attribute.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Cytosig.show" title="pypath.core.annot.Cytosig.show"><code class="xref py py-obj docutils literal notranslate"><span class="pre">show</span></code></a>([method, table_param])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic information from the UniProt datasheets.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Cytosig.subset_intersection" title="pypath.core.annot.Cytosig.subset_intersection"><code class="xref py py-obj docutils literal notranslate"><span class="pre">subset_intersection</span></code></a>(universe, **kwargs)</p></td>
+<td><p>Calculates the proportion of entities in a subset occuring in the set <code class="docutils literal notranslate"><span class="pre">universe</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Cytosig.to_array" title="pypath.core.annot.Cytosig.to_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_array</span></code></a>([reference_set, use_fields])</p></td>
+<td><p>Returns an entity vs feature array.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Cytosig.to_bool_array" title="pypath.core.annot.Cytosig.to_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_bool_array</span></code></a>(reference_set)</p></td>
+<td><p>Returns a presence/absence boolean array for a reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Cytosig.to_set" title="pypath.core.annot.Cytosig.to_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_set</span></code></a>()</p></td>
+<td><p>Returns the entities present in this annotation resource as a set.</p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Attributes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_fields</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">summary</span></code></p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cytosig.add_complexes_by_inference">
+<span class="sig-name descname"><span class="pre">add_complexes_by_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cytosig.add_complexes_by_inference" title="Link to this definition">§</a></dt>
+<dd><p>Creates complex annotations by in silico inference and adds them
+to this annotation set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cytosig.all_complexes">
+<span class="sig-name descname"><span class="pre">all_complexes</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cytosig.all_complexes" title="Link to this definition">§</a></dt>
+<dd><p>All protein complexes annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cytosig.all_entities">
+<span class="sig-name descname"><span class="pre">all_entities</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cytosig.all_entities" title="Link to this definition">§</a></dt>
+<dd><p>All entities annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cytosig.all_mirnas">
+<span class="sig-name descname"><span class="pre">all_mirnas</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cytosig.all_mirnas" title="Link to this definition">§</a></dt>
+<dd><p>All miRNAs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cytosig.all_proteins">
+<span class="sig-name descname"><span class="pre">all_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cytosig.all_proteins" title="Link to this definition">§</a></dt>
+<dd><p>All UniProt IDs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cytosig.all_refs">
+<span class="sig-name descname"><span class="pre">all_refs</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cytosig.all_refs" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects the references
+across all records. Returns <em>list</em>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cytosig.annotate_complex">
+<span class="sig-name descname"><span class="pre">annotate_complex</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cplex</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cytosig.annotate_complex" title="Link to this definition">§</a></dt>
+<dd><p>Infers annotations for a single complex.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cytosig.browse">
+<span class="sig-name descname"><span class="pre">browse</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">field</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">start</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cytosig.browse" title="Link to this definition">§</a></dt>
+<dd><p>Print gene information as a table.</p>
+<p>Presents information about annotation categories as ascii tables
+printed in the terminal. If one category provided, prints one table.
+If multiple categories provided, prints a table for each of them one
+by one proceeding to the next one once you hit return. If no categories
+provided goes through all levels of the primary category.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>field:</dt><dd><p>The field to browse categories by.</p>
+<ul class="simple">
+<li><p>If None the primary field will be selected.
+If this annotation resource doesn’t have fields, all proteins
+will be presented as one single category.</p></li>
+<li><p>If a string it will be considered a field name and it will
+browse through all levels of this field.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">list</span></code>, set or tuple, it will be considered either a
+<code class="docutils literal notranslate"><span class="pre">list</span></code> of field names or a list of values from the primary
+field. In the former case all combinations of the values of
+the fields will be presented, in the latter case the browsing
+will be limited to the levels of the primary field contained
+in <code class="docutils literal notranslate"><span class="pre">field</span></code>.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">dict</span></code>, keys are supposed to be field names and values
+as list of levels. If any of the values are None, all levels
+from that field will be used.</p></li>
+</ul>
+</dd>
+<dt>start:</dt><dd><p>Start browsing from this category. E.g. if there are 500
+categories and start is 250 it will skip everything before the
+250th.</p>
+</dd>
+<dt>kwargs:</dt><dd><p>Passed to <code class="docutils literal notranslate"><span class="pre">pypath.utils.uniprot.info</span></code>.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cytosig.complex_inference">
+<span class="sig-name descname"><span class="pre">complex_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cytosig.complex_inference" title="Link to this definition">§</a></dt>
+<dd><p>Annotates all complexes in <cite>complexes</cite>, by default in the default
+complex database (existing in the <cite>complex</cite> module or generated
+on demand according to the module’s current settings).</p>
+<dl class="field-list simple">
+<dt class="field-odd">Returns<span class="colon">:</span></dt>
+<dd class="field-odd"><p><ul class="simple">
+<li><p><em>Dict with complexes as keys and sets of annotations as values.</em></p></li>
+<li><p><em>Complexes with no valid information in this annotation resource</em></p></li>
+<li><p><em>won’t be in the dict.</em></p></li>
+</ul>
+</p>
+</dd>
+<dt class="field-even">Parameters<span class="colon">:</span></dt>
+<dd class="field-even"><p><strong>complexes</strong> (<em>iterable</em>) – Iterable yielding complexes.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cytosig.coverage">
+<span class="sig-name descname"><span class="pre">coverage</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">other</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cytosig.coverage" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the coverage of the annotation i.e. the proportion of
+entities having at least one record in this annotation resource
+for an arbitrary set of entities.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cytosig.curation_effort">
+<span class="sig-name descname"><span class="pre">curation_effort</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cytosig.curation_effort" title="Link to this definition">§</a></dt>
+<dd><p>Counts the reference-record pairs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cytosig.get_names">
+<span class="sig-name descname"><span class="pre">get_names</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cytosig.get_names" title="Link to this definition">§</a></dt>
+<dd><p>Returns the list of field names in the records. The annotation
+consists of uniform records and each entity might be annotated
+with one or more records. Each record is a tuple of fields, for
+example <code class="docutils literal notranslate"><span class="pre">('cell_type',</span> <span class="pre">'expression_level',</span> <span class="pre">'score')</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cytosig.get_reference_set">
+<em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">get_reference_set</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">proteins</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">swissprot_only</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cytosig.get_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the reference set i.e. the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cytosig.get_subset">
+<span class="sig-name descname"><span class="pre">get_subset</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cytosig.get_subset" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cytosig.get_subset_bool_array">
+<span class="sig-name descname"><span class="pre">get_subset_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cytosig.get_subset_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a boolean vector with True and False values for each entity
+in the reference set. The values represent presence absence data
+in the simplest case, but by providing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> any kind of matching
+and filtering is possible. <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> are passed to the <code class="docutils literal notranslate"><span class="pre">select</span></code>
+method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cytosig.get_values">
+<span class="sig-name descname"><span class="pre">get_values</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">exclude_none</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cytosig.get_values" title="Link to this definition">§</a></dt>
+<dd><p>Returns the set of all possible values of a field. E.g. if the
+records of this annotation have a field <code class="docutils literal notranslate"><span class="pre">cell_type</span></code> then calling
+this method can tell you that across all records the values of
+this field might be <code class="docutils literal notranslate"><span class="pre">{'macrophage',</span> <span class="pre">'epithelial_cell',</span> <span class="pre">...}</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cytosig.labels">
+<span class="sig-name descname"><span class="pre">labels</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cytosig.labels" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cytosig.load">
+<span class="sig-name descname"><span class="pre">load</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cytosig.load" title="Link to this definition">§</a></dt>
+<dd><p>Loads the annotation data by calling the input method.
+Infers annotations for complexes in the complex database if
+py:attr:<code class="docutils literal notranslate"><span class="pre">infer_complexes</span></code> is True.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cytosig.load_data">
+<span class="sig-name descname"><span class="pre">load_data</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cytosig.load_data" title="Link to this definition">§</a></dt>
+<dd><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cytosig.load_proteins">
+<span class="sig-name descname"><span class="pre">load_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cytosig.load_proteins" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a set of all UniProt IDs to have a base set of the entire
+proteome.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cytosig.make_df">
+<span class="sig-name descname"><span class="pre">make_df</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">rebuild</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cytosig.make_df" title="Link to this definition">§</a></dt>
+<dd><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.
+The data frame will be assigned to :py:attr``df``.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cytosig.numof_entities">
+<span class="sig-name descname"><span class="pre">numof_entities</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cytosig.numof_entities" title="Link to this definition">§</a></dt>
+<dd><p>The number of annotated entities in the resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cytosig.numof_records">
+<span class="sig-name descname"><span class="pre">numof_records</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cytosig.numof_records" title="Link to this definition">§</a></dt>
+<dd><p>The total number of annotation records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cytosig.numof_references">
+<span class="sig-name descname"><span class="pre">numof_references</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cytosig.numof_references" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects and counts the
+references across all records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cytosig.process">
+<span class="sig-name descname"><span class="pre">process</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cytosig.process" title="Link to this definition">§</a></dt>
+<dd><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cytosig.reload">
+<span class="sig-name descname"><span class="pre">reload</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cytosig.reload" title="Link to this definition">§</a></dt>
+<dd><p>Reloads the object from the module level.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cytosig.select">
+<span class="sig-name descname"><span class="pre">select</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cytosig.select" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cytosig.set_method">
+<span class="sig-name descname"><span class="pre">set_method</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cytosig.set_method" title="Link to this definition">§</a></dt>
+<dd><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if
+necessary.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cytosig.set_reference_set">
+<span class="sig-name descname"><span class="pre">set_reference_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cytosig.set_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Assigns the reference set to the :py:attr``reference_set`` attribute.
+The reference set is the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cytosig.show">
+<span class="sig-name descname"><span class="pre">show</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">table_param</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cytosig.show" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic
+information from the UniProt datasheets.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cytosig.subset_intersection">
+<span class="sig-name descname"><span class="pre">subset_intersection</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">universe</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cytosig.subset_intersection" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the proportion of entities in a subset occuring in the
+set <code class="docutils literal notranslate"><span class="pre">universe</span></code>. The subset is selected by passing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> to the
+<code class="docutils literal notranslate"><span class="pre">select</span></code> method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cytosig.to_array">
+<span class="sig-name descname"><span class="pre">to_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_fields</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cytosig.to_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns an entity vs feature array. In case of more complex
+annotations this might be huge.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cytosig.to_bool_array">
+<span class="sig-name descname"><span class="pre">to_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cytosig.to_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a presence/absence boolean array for a reference set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Cytosig.to_set">
+<span class="sig-name descname"><span class="pre">to_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Cytosig.to_set" title="Link to this definition">§</a></dt>
+<dd><p>Returns the entities present in this annotation resource as a set.</p>
+</dd></dl>
+
+</dd></dl>
+
+</section>
+
+
+                </article>
+              
+              
+              
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+  <section id="pypath-core-annot-dgidb">
+<h1>pypath.core.annot.Dgidb<a class="headerlink" href="#pypath-core-annot-dgidb" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.core.annot.Dgidb">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.core.annot.</span></span><span class="sig-name descname"><span class="pre">Dgidb</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#Dgidb"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.Dgidb" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <a class="reference internal" href="pypath.core.annot.AnnotationBase.html#pypath.core.annot.AnnotationBase" title="pypath.core.annot.AnnotationBase"><code class="xref py py-class docutils literal notranslate"><span class="pre">AnnotationBase</span></code></a></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Dgidb.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#Dgidb.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.Dgidb.__init__" title="Link to this definition">§</a></dt>
+<dd><p>Druggable proteins from DGIdb (Drug Gene Interaction Database).</p>
+</dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Dgidb.__init__" title="pypath.core.annot.Dgidb.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>(**kwargs)</p></td>
+<td><p>Druggable proteins from DGIdb (Drug Gene Interaction Database).</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Dgidb.add_complexes_by_inference" title="pypath.core.annot.Dgidb.add_complexes_by_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">add_complexes_by_inference</span></code></a>([complexes])</p></td>
+<td><p>Creates complex annotations by in silico inference and adds them to this annotation set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Dgidb.all_complexes" title="pypath.core.annot.Dgidb.all_complexes"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_complexes</span></code></a>()</p></td>
+<td><p>All protein complexes annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Dgidb.all_entities" title="pypath.core.annot.Dgidb.all_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_entities</span></code></a>([entity_types])</p></td>
+<td><p>All entities annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Dgidb.all_mirnas" title="pypath.core.annot.Dgidb.all_mirnas"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_mirnas</span></code></a>()</p></td>
+<td><p>All miRNAs annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Dgidb.all_proteins" title="pypath.core.annot.Dgidb.all_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_proteins</span></code></a>()</p></td>
+<td><p>All UniProt IDs annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Dgidb.all_refs" title="pypath.core.annot.Dgidb.all_refs"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_refs</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Dgidb.annotate_complex" title="pypath.core.annot.Dgidb.annotate_complex"><code class="xref py py-obj docutils literal notranslate"><span class="pre">annotate_complex</span></code></a>(cplex)</p></td>
+<td><p>Infers annotations for a single complex.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Dgidb.browse" title="pypath.core.annot.Dgidb.browse"><code class="xref py py-obj docutils literal notranslate"><span class="pre">browse</span></code></a>([field, start])</p></td>
+<td><p>Print gene information as a table.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Dgidb.complex_inference" title="pypath.core.annot.Dgidb.complex_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">complex_inference</span></code></a>([complexes])</p></td>
+<td><p>Annotates all complexes in <cite>complexes</cite>, by default in the default complex database (existing in the <cite>complex</cite> module or generated on demand according to the module's current settings).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Dgidb.coverage" title="pypath.core.annot.Dgidb.coverage"><code class="xref py py-obj docutils literal notranslate"><span class="pre">coverage</span></code></a>(other)</p></td>
+<td><p>Calculates the coverage of the annotation i.e. the proportion of entities having at least one record in this annotation resource for an arbitrary set of entities.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Dgidb.curation_effort" title="pypath.core.annot.Dgidb.curation_effort"><code class="xref py py-obj docutils literal notranslate"><span class="pre">curation_effort</span></code></a>()</p></td>
+<td><p>Counts the reference-record pairs.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">from_dump</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_entity_type</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Dgidb.get_names" title="pypath.core.annot.Dgidb.get_names"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_names</span></code></a>()</p></td>
+<td><p>Returns the list of field names in the records.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Dgidb.get_reference_set" title="pypath.core.annot.Dgidb.get_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_reference_set</span></code></a>([proteins, complexes, ...])</p></td>
+<td><p>Retrieves the reference set i.e. the set of all entities which potentially have annotation in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Dgidb.get_subset" title="pypath.core.annot.Dgidb.get_subset"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Dgidb.get_subset_bool_array" title="pypath.core.annot.Dgidb.get_subset_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset_bool_array</span></code></a>([reference_set])</p></td>
+<td><p>Returns a boolean vector with True and False values for each entity in the reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Dgidb.get_values" title="pypath.core.annot.Dgidb.get_values"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_values</span></code></a>(name[, exclude_none])</p></td>
+<td><p>Returns the set of all possible values of a field.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_complex</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_mirna</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_protein</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Dgidb.labels" title="pypath.core.annot.Dgidb.labels"><code class="xref py py-obj docutils literal notranslate"><span class="pre">labels</span></code></a>([method])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Dgidb.load" title="pypath.core.annot.Dgidb.load"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load</span></code></a>()</p></td>
+<td><p>Loads the annotation data by calling the input method.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Dgidb.load_data" title="pypath.core.annot.Dgidb.load_data"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_data</span></code></a>()</p></td>
+<td><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Dgidb.load_proteins" title="pypath.core.annot.Dgidb.load_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_proteins</span></code></a>()</p></td>
+<td><p>Retrieves a set of all UniProt IDs to have a base set of the entire proteome.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Dgidb.make_df" title="pypath.core.annot.Dgidb.make_df"><code class="xref py py-obj docutils literal notranslate"><span class="pre">make_df</span></code></a>([rebuild])</p></td>
+<td><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complex_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Dgidb.numof_entities" title="pypath.core.annot.Dgidb.numof_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_entities</span></code></a>()</p></td>
+<td><p>The number of annotated entities in the resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirna_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirnas</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_protein_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_proteins</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Dgidb.numof_records" title="pypath.core.annot.Dgidb.numof_records"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_records</span></code></a>([entity_types])</p></td>
+<td><p>The total number of annotation records.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Dgidb.numof_references" title="pypath.core.annot.Dgidb.numof_references"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_references</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Dgidb.process" title="pypath.core.annot.Dgidb.process"><code class="xref py py-obj docutils literal notranslate"><span class="pre">process</span></code></a>()</p></td>
+<td><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">proportion</span></code>(other)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Dgidb.reload" title="pypath.core.annot.Dgidb.reload"><code class="xref py py-obj docutils literal notranslate"><span class="pre">reload</span></code></a>()</p></td>
+<td><p>Reloads the object from the module level.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">save_to_pickle</span></code>(pickle_file)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Dgidb.select" title="pypath.core.annot.Dgidb.select"><code class="xref py py-obj docutils literal notranslate"><span class="pre">select</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Dgidb.set_method" title="pypath.core.annot.Dgidb.set_method"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_method</span></code></a>()</p></td>
+<td><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if necessary.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Dgidb.set_reference_set" title="pypath.core.annot.Dgidb.set_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_reference_set</span></code></a>()</p></td>
+<td><p>Assigns the reference set to the :py:attr``reference_set`` attribute.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Dgidb.show" title="pypath.core.annot.Dgidb.show"><code class="xref py py-obj docutils literal notranslate"><span class="pre">show</span></code></a>([method, table_param])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic information from the UniProt datasheets.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Dgidb.subset_intersection" title="pypath.core.annot.Dgidb.subset_intersection"><code class="xref py py-obj docutils literal notranslate"><span class="pre">subset_intersection</span></code></a>(universe, **kwargs)</p></td>
+<td><p>Calculates the proportion of entities in a subset occuring in the set <code class="docutils literal notranslate"><span class="pre">universe</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Dgidb.to_array" title="pypath.core.annot.Dgidb.to_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_array</span></code></a>([reference_set, use_fields])</p></td>
+<td><p>Returns an entity vs feature array.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Dgidb.to_bool_array" title="pypath.core.annot.Dgidb.to_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_bool_array</span></code></a>(reference_set)</p></td>
+<td><p>Returns a presence/absence boolean array for a reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Dgidb.to_set" title="pypath.core.annot.Dgidb.to_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_set</span></code></a>()</p></td>
+<td><p>Returns the entities present in this annotation resource as a set.</p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Attributes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_fields</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">summary</span></code></p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Dgidb.add_complexes_by_inference">
+<span class="sig-name descname"><span class="pre">add_complexes_by_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Dgidb.add_complexes_by_inference" title="Link to this definition">§</a></dt>
+<dd><p>Creates complex annotations by in silico inference and adds them
+to this annotation set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Dgidb.all_complexes">
+<span class="sig-name descname"><span class="pre">all_complexes</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Dgidb.all_complexes" title="Link to this definition">§</a></dt>
+<dd><p>All protein complexes annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Dgidb.all_entities">
+<span class="sig-name descname"><span class="pre">all_entities</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Dgidb.all_entities" title="Link to this definition">§</a></dt>
+<dd><p>All entities annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Dgidb.all_mirnas">
+<span class="sig-name descname"><span class="pre">all_mirnas</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Dgidb.all_mirnas" title="Link to this definition">§</a></dt>
+<dd><p>All miRNAs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Dgidb.all_proteins">
+<span class="sig-name descname"><span class="pre">all_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Dgidb.all_proteins" title="Link to this definition">§</a></dt>
+<dd><p>All UniProt IDs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Dgidb.all_refs">
+<span class="sig-name descname"><span class="pre">all_refs</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Dgidb.all_refs" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects the references
+across all records. Returns <em>list</em>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Dgidb.annotate_complex">
+<span class="sig-name descname"><span class="pre">annotate_complex</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cplex</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Dgidb.annotate_complex" title="Link to this definition">§</a></dt>
+<dd><p>Infers annotations for a single complex.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Dgidb.browse">
+<span class="sig-name descname"><span class="pre">browse</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">field</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">start</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Dgidb.browse" title="Link to this definition">§</a></dt>
+<dd><p>Print gene information as a table.</p>
+<p>Presents information about annotation categories as ascii tables
+printed in the terminal. If one category provided, prints one table.
+If multiple categories provided, prints a table for each of them one
+by one proceeding to the next one once you hit return. If no categories
+provided goes through all levels of the primary category.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>field:</dt><dd><p>The field to browse categories by.</p>
+<ul class="simple">
+<li><p>If None the primary field will be selected.
+If this annotation resource doesn’t have fields, all proteins
+will be presented as one single category.</p></li>
+<li><p>If a string it will be considered a field name and it will
+browse through all levels of this field.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">list</span></code>, set or tuple, it will be considered either a
+<code class="docutils literal notranslate"><span class="pre">list</span></code> of field names or a list of values from the primary
+field. In the former case all combinations of the values of
+the fields will be presented, in the latter case the browsing
+will be limited to the levels of the primary field contained
+in <code class="docutils literal notranslate"><span class="pre">field</span></code>.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">dict</span></code>, keys are supposed to be field names and values
+as list of levels. If any of the values are None, all levels
+from that field will be used.</p></li>
+</ul>
+</dd>
+<dt>start:</dt><dd><p>Start browsing from this category. E.g. if there are 500
+categories and start is 250 it will skip everything before the
+250th.</p>
+</dd>
+<dt>kwargs:</dt><dd><p>Passed to <code class="docutils literal notranslate"><span class="pre">pypath.utils.uniprot.info</span></code>.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Dgidb.complex_inference">
+<span class="sig-name descname"><span class="pre">complex_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Dgidb.complex_inference" title="Link to this definition">§</a></dt>
+<dd><p>Annotates all complexes in <cite>complexes</cite>, by default in the default
+complex database (existing in the <cite>complex</cite> module or generated
+on demand according to the module’s current settings).</p>
+<dl class="field-list simple">
+<dt class="field-odd">Returns<span class="colon">:</span></dt>
+<dd class="field-odd"><p><ul class="simple">
+<li><p><em>Dict with complexes as keys and sets of annotations as values.</em></p></li>
+<li><p><em>Complexes with no valid information in this annotation resource</em></p></li>
+<li><p><em>won’t be in the dict.</em></p></li>
+</ul>
+</p>
+</dd>
+<dt class="field-even">Parameters<span class="colon">:</span></dt>
+<dd class="field-even"><p><strong>complexes</strong> (<em>iterable</em>) – Iterable yielding complexes.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Dgidb.coverage">
+<span class="sig-name descname"><span class="pre">coverage</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">other</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Dgidb.coverage" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the coverage of the annotation i.e. the proportion of
+entities having at least one record in this annotation resource
+for an arbitrary set of entities.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Dgidb.curation_effort">
+<span class="sig-name descname"><span class="pre">curation_effort</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Dgidb.curation_effort" title="Link to this definition">§</a></dt>
+<dd><p>Counts the reference-record pairs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Dgidb.get_names">
+<span class="sig-name descname"><span class="pre">get_names</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Dgidb.get_names" title="Link to this definition">§</a></dt>
+<dd><p>Returns the list of field names in the records. The annotation
+consists of uniform records and each entity might be annotated
+with one or more records. Each record is a tuple of fields, for
+example <code class="docutils literal notranslate"><span class="pre">('cell_type',</span> <span class="pre">'expression_level',</span> <span class="pre">'score')</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Dgidb.get_reference_set">
+<em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">get_reference_set</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">proteins</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">swissprot_only</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Dgidb.get_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the reference set i.e. the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Dgidb.get_subset">
+<span class="sig-name descname"><span class="pre">get_subset</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Dgidb.get_subset" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Dgidb.get_subset_bool_array">
+<span class="sig-name descname"><span class="pre">get_subset_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Dgidb.get_subset_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a boolean vector with True and False values for each entity
+in the reference set. The values represent presence absence data
+in the simplest case, but by providing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> any kind of matching
+and filtering is possible. <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> are passed to the <code class="docutils literal notranslate"><span class="pre">select</span></code>
+method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Dgidb.get_values">
+<span class="sig-name descname"><span class="pre">get_values</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">exclude_none</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Dgidb.get_values" title="Link to this definition">§</a></dt>
+<dd><p>Returns the set of all possible values of a field. E.g. if the
+records of this annotation have a field <code class="docutils literal notranslate"><span class="pre">cell_type</span></code> then calling
+this method can tell you that across all records the values of
+this field might be <code class="docutils literal notranslate"><span class="pre">{'macrophage',</span> <span class="pre">'epithelial_cell',</span> <span class="pre">...}</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Dgidb.labels">
+<span class="sig-name descname"><span class="pre">labels</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Dgidb.labels" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Dgidb.load">
+<span class="sig-name descname"><span class="pre">load</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Dgidb.load" title="Link to this definition">§</a></dt>
+<dd><p>Loads the annotation data by calling the input method.
+Infers annotations for complexes in the complex database if
+py:attr:<code class="docutils literal notranslate"><span class="pre">infer_complexes</span></code> is True.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Dgidb.load_data">
+<span class="sig-name descname"><span class="pre">load_data</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Dgidb.load_data" title="Link to this definition">§</a></dt>
+<dd><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Dgidb.load_proteins">
+<span class="sig-name descname"><span class="pre">load_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Dgidb.load_proteins" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a set of all UniProt IDs to have a base set of the entire
+proteome.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Dgidb.make_df">
+<span class="sig-name descname"><span class="pre">make_df</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">rebuild</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Dgidb.make_df" title="Link to this definition">§</a></dt>
+<dd><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.
+The data frame will be assigned to :py:attr``df``.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Dgidb.numof_entities">
+<span class="sig-name descname"><span class="pre">numof_entities</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Dgidb.numof_entities" title="Link to this definition">§</a></dt>
+<dd><p>The number of annotated entities in the resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Dgidb.numof_records">
+<span class="sig-name descname"><span class="pre">numof_records</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Dgidb.numof_records" title="Link to this definition">§</a></dt>
+<dd><p>The total number of annotation records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Dgidb.numof_references">
+<span class="sig-name descname"><span class="pre">numof_references</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Dgidb.numof_references" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects and counts the
+references across all records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Dgidb.process">
+<span class="sig-name descname"><span class="pre">process</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Dgidb.process" title="Link to this definition">§</a></dt>
+<dd><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Dgidb.reload">
+<span class="sig-name descname"><span class="pre">reload</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Dgidb.reload" title="Link to this definition">§</a></dt>
+<dd><p>Reloads the object from the module level.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Dgidb.select">
+<span class="sig-name descname"><span class="pre">select</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Dgidb.select" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Dgidb.set_method">
+<span class="sig-name descname"><span class="pre">set_method</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Dgidb.set_method" title="Link to this definition">§</a></dt>
+<dd><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if
+necessary.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Dgidb.set_reference_set">
+<span class="sig-name descname"><span class="pre">set_reference_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Dgidb.set_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Assigns the reference set to the :py:attr``reference_set`` attribute.
+The reference set is the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Dgidb.show">
+<span class="sig-name descname"><span class="pre">show</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">table_param</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Dgidb.show" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic
+information from the UniProt datasheets.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Dgidb.subset_intersection">
+<span class="sig-name descname"><span class="pre">subset_intersection</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">universe</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Dgidb.subset_intersection" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the proportion of entities in a subset occuring in the
+set <code class="docutils literal notranslate"><span class="pre">universe</span></code>. The subset is selected by passing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> to the
+<code class="docutils literal notranslate"><span class="pre">select</span></code> method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Dgidb.to_array">
+<span class="sig-name descname"><span class="pre">to_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_fields</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Dgidb.to_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns an entity vs feature array. In case of more complex
+annotations this might be huge.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Dgidb.to_bool_array">
+<span class="sig-name descname"><span class="pre">to_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Dgidb.to_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a presence/absence boolean array for a reference set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Dgidb.to_set">
+<span class="sig-name descname"><span class="pre">to_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Dgidb.to_set" title="Link to this definition">§</a></dt>
+<dd><p>Returns the entities present in this annotation resource as a set.</p>
+</dd></dl>
+
+</dd></dl>
+
+</section>
+
+
+                </article>
+              
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+  <section id="pypath-core-annot-disgenet">
+<h1>pypath.core.annot.Disgenet<a class="headerlink" href="#pypath-core-annot-disgenet" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.core.annot.Disgenet">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.core.annot.</span></span><span class="sig-name descname"><span class="pre">Disgenet</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#Disgenet"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.Disgenet" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <a class="reference internal" href="pypath.core.annot.AnnotationBase.html#pypath.core.annot.AnnotationBase" title="pypath.core.annot.AnnotationBase"><code class="xref py py-class docutils literal notranslate"><span class="pre">AnnotationBase</span></code></a></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Disgenet.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#Disgenet.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.Disgenet.__init__" title="Link to this definition">§</a></dt>
+<dd><p>Represents annotations for a set of proteins.
+Loads the data from the original resource and provides methods
+to query the annotations.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>name</strong> (<em>str</em>) – A custom name for the annotation resource.</p></li>
+<li><p><strong>ncbi_tax_id</strong> (<em>int</em>) – NCBI Taxonomy identifier.</p></li>
+<li><p><strong>input_method</strong> (<em>callable</em><em>,</em><em>str</em>) – Either a callable or the name of a method in any submodules of
+the <code class="docutils literal notranslate"><span class="pre">pypath.inputs</span></code>  module. Should return a dict with
+UniProt IDs as keys or an object suitable for <code class="docutils literal notranslate"><span class="pre">process_method</span></code>.</p></li>
+<li><p><strong>input_args</strong> (<em>dict</em>) – Arguments for the <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Disgenet.__init__" title="pypath.core.annot.Disgenet.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>([ncbi_tax_id])</p></td>
+<td><p>Represents annotations for a set of proteins.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Disgenet.add_complexes_by_inference" title="pypath.core.annot.Disgenet.add_complexes_by_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">add_complexes_by_inference</span></code></a>([complexes])</p></td>
+<td><p>Creates complex annotations by in silico inference and adds them to this annotation set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Disgenet.all_complexes" title="pypath.core.annot.Disgenet.all_complexes"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_complexes</span></code></a>()</p></td>
+<td><p>All protein complexes annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Disgenet.all_entities" title="pypath.core.annot.Disgenet.all_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_entities</span></code></a>([entity_types])</p></td>
+<td><p>All entities annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Disgenet.all_mirnas" title="pypath.core.annot.Disgenet.all_mirnas"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_mirnas</span></code></a>()</p></td>
+<td><p>All miRNAs annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Disgenet.all_proteins" title="pypath.core.annot.Disgenet.all_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_proteins</span></code></a>()</p></td>
+<td><p>All UniProt IDs annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Disgenet.all_refs" title="pypath.core.annot.Disgenet.all_refs"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_refs</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Disgenet.annotate_complex" title="pypath.core.annot.Disgenet.annotate_complex"><code class="xref py py-obj docutils literal notranslate"><span class="pre">annotate_complex</span></code></a>(cplex)</p></td>
+<td><p>Infers annotations for a single complex.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Disgenet.browse" title="pypath.core.annot.Disgenet.browse"><code class="xref py py-obj docutils literal notranslate"><span class="pre">browse</span></code></a>([field, start])</p></td>
+<td><p>Print gene information as a table.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Disgenet.complex_inference" title="pypath.core.annot.Disgenet.complex_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">complex_inference</span></code></a>([complexes])</p></td>
+<td><p>Annotates all complexes in <cite>complexes</cite>, by default in the default complex database (existing in the <cite>complex</cite> module or generated on demand according to the module's current settings).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Disgenet.coverage" title="pypath.core.annot.Disgenet.coverage"><code class="xref py py-obj docutils literal notranslate"><span class="pre">coverage</span></code></a>(other)</p></td>
+<td><p>Calculates the coverage of the annotation i.e. the proportion of entities having at least one record in this annotation resource for an arbitrary set of entities.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Disgenet.curation_effort" title="pypath.core.annot.Disgenet.curation_effort"><code class="xref py py-obj docutils literal notranslate"><span class="pre">curation_effort</span></code></a>()</p></td>
+<td><p>Counts the reference-record pairs.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">from_dump</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_entity_type</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Disgenet.get_names" title="pypath.core.annot.Disgenet.get_names"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_names</span></code></a>()</p></td>
+<td><p>Returns the list of field names in the records.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Disgenet.get_reference_set" title="pypath.core.annot.Disgenet.get_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_reference_set</span></code></a>([proteins, complexes, ...])</p></td>
+<td><p>Retrieves the reference set i.e. the set of all entities which potentially have annotation in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Disgenet.get_subset" title="pypath.core.annot.Disgenet.get_subset"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Disgenet.get_subset_bool_array" title="pypath.core.annot.Disgenet.get_subset_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset_bool_array</span></code></a>([reference_set])</p></td>
+<td><p>Returns a boolean vector with True and False values for each entity in the reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Disgenet.get_values" title="pypath.core.annot.Disgenet.get_values"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_values</span></code></a>(name[, exclude_none])</p></td>
+<td><p>Returns the set of all possible values of a field.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_complex</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_mirna</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_protein</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Disgenet.labels" title="pypath.core.annot.Disgenet.labels"><code class="xref py py-obj docutils literal notranslate"><span class="pre">labels</span></code></a>([method])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Disgenet.load" title="pypath.core.annot.Disgenet.load"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load</span></code></a>()</p></td>
+<td><p>Loads the annotation data by calling the input method.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Disgenet.load_data" title="pypath.core.annot.Disgenet.load_data"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_data</span></code></a>()</p></td>
+<td><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Disgenet.load_proteins" title="pypath.core.annot.Disgenet.load_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_proteins</span></code></a>()</p></td>
+<td><p>Retrieves a set of all UniProt IDs to have a base set of the entire proteome.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Disgenet.make_df" title="pypath.core.annot.Disgenet.make_df"><code class="xref py py-obj docutils literal notranslate"><span class="pre">make_df</span></code></a>([rebuild])</p></td>
+<td><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complex_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Disgenet.numof_entities" title="pypath.core.annot.Disgenet.numof_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_entities</span></code></a>()</p></td>
+<td><p>The number of annotated entities in the resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirna_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirnas</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_protein_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_proteins</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Disgenet.numof_records" title="pypath.core.annot.Disgenet.numof_records"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_records</span></code></a>([entity_types])</p></td>
+<td><p>The total number of annotation records.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Disgenet.numof_references" title="pypath.core.annot.Disgenet.numof_references"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_references</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Disgenet.process" title="pypath.core.annot.Disgenet.process"><code class="xref py py-obj docutils literal notranslate"><span class="pre">process</span></code></a>()</p></td>
+<td><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">proportion</span></code>(other)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Disgenet.reload" title="pypath.core.annot.Disgenet.reload"><code class="xref py py-obj docutils literal notranslate"><span class="pre">reload</span></code></a>()</p></td>
+<td><p>Reloads the object from the module level.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">save_to_pickle</span></code>(pickle_file)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Disgenet.select" title="pypath.core.annot.Disgenet.select"><code class="xref py py-obj docutils literal notranslate"><span class="pre">select</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Disgenet.set_method" title="pypath.core.annot.Disgenet.set_method"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_method</span></code></a>()</p></td>
+<td><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if necessary.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Disgenet.set_reference_set" title="pypath.core.annot.Disgenet.set_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_reference_set</span></code></a>()</p></td>
+<td><p>Assigns the reference set to the :py:attr``reference_set`` attribute.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Disgenet.show" title="pypath.core.annot.Disgenet.show"><code class="xref py py-obj docutils literal notranslate"><span class="pre">show</span></code></a>([method, table_param])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic information from the UniProt datasheets.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Disgenet.subset_intersection" title="pypath.core.annot.Disgenet.subset_intersection"><code class="xref py py-obj docutils literal notranslate"><span class="pre">subset_intersection</span></code></a>(universe, **kwargs)</p></td>
+<td><p>Calculates the proportion of entities in a subset occuring in the set <code class="docutils literal notranslate"><span class="pre">universe</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Disgenet.to_array" title="pypath.core.annot.Disgenet.to_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_array</span></code></a>([reference_set, use_fields])</p></td>
+<td><p>Returns an entity vs feature array.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Disgenet.to_bool_array" title="pypath.core.annot.Disgenet.to_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_bool_array</span></code></a>(reference_set)</p></td>
+<td><p>Returns a presence/absence boolean array for a reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Disgenet.to_set" title="pypath.core.annot.Disgenet.to_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_set</span></code></a>()</p></td>
+<td><p>Returns the entities present in this annotation resource as a set.</p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Attributes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_fields</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">summary</span></code></p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Disgenet.add_complexes_by_inference">
+<span class="sig-name descname"><span class="pre">add_complexes_by_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Disgenet.add_complexes_by_inference" title="Link to this definition">§</a></dt>
+<dd><p>Creates complex annotations by in silico inference and adds them
+to this annotation set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Disgenet.all_complexes">
+<span class="sig-name descname"><span class="pre">all_complexes</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Disgenet.all_complexes" title="Link to this definition">§</a></dt>
+<dd><p>All protein complexes annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Disgenet.all_entities">
+<span class="sig-name descname"><span class="pre">all_entities</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Disgenet.all_entities" title="Link to this definition">§</a></dt>
+<dd><p>All entities annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Disgenet.all_mirnas">
+<span class="sig-name descname"><span class="pre">all_mirnas</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Disgenet.all_mirnas" title="Link to this definition">§</a></dt>
+<dd><p>All miRNAs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Disgenet.all_proteins">
+<span class="sig-name descname"><span class="pre">all_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Disgenet.all_proteins" title="Link to this definition">§</a></dt>
+<dd><p>All UniProt IDs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Disgenet.all_refs">
+<span class="sig-name descname"><span class="pre">all_refs</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Disgenet.all_refs" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects the references
+across all records. Returns <em>list</em>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Disgenet.annotate_complex">
+<span class="sig-name descname"><span class="pre">annotate_complex</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cplex</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Disgenet.annotate_complex" title="Link to this definition">§</a></dt>
+<dd><p>Infers annotations for a single complex.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Disgenet.browse">
+<span class="sig-name descname"><span class="pre">browse</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">field</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">start</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Disgenet.browse" title="Link to this definition">§</a></dt>
+<dd><p>Print gene information as a table.</p>
+<p>Presents information about annotation categories as ascii tables
+printed in the terminal. If one category provided, prints one table.
+If multiple categories provided, prints a table for each of them one
+by one proceeding to the next one once you hit return. If no categories
+provided goes through all levels of the primary category.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>field:</dt><dd><p>The field to browse categories by.</p>
+<ul class="simple">
+<li><p>If None the primary field will be selected.
+If this annotation resource doesn’t have fields, all proteins
+will be presented as one single category.</p></li>
+<li><p>If a string it will be considered a field name and it will
+browse through all levels of this field.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">list</span></code>, set or tuple, it will be considered either a
+<code class="docutils literal notranslate"><span class="pre">list</span></code> of field names or a list of values from the primary
+field. In the former case all combinations of the values of
+the fields will be presented, in the latter case the browsing
+will be limited to the levels of the primary field contained
+in <code class="docutils literal notranslate"><span class="pre">field</span></code>.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">dict</span></code>, keys are supposed to be field names and values
+as list of levels. If any of the values are None, all levels
+from that field will be used.</p></li>
+</ul>
+</dd>
+<dt>start:</dt><dd><p>Start browsing from this category. E.g. if there are 500
+categories and start is 250 it will skip everything before the
+250th.</p>
+</dd>
+<dt>kwargs:</dt><dd><p>Passed to <code class="docutils literal notranslate"><span class="pre">pypath.utils.uniprot.info</span></code>.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Disgenet.complex_inference">
+<span class="sig-name descname"><span class="pre">complex_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Disgenet.complex_inference" title="Link to this definition">§</a></dt>
+<dd><p>Annotates all complexes in <cite>complexes</cite>, by default in the default
+complex database (existing in the <cite>complex</cite> module or generated
+on demand according to the module’s current settings).</p>
+<dl class="field-list simple">
+<dt class="field-odd">Returns<span class="colon">:</span></dt>
+<dd class="field-odd"><p><ul class="simple">
+<li><p><em>Dict with complexes as keys and sets of annotations as values.</em></p></li>
+<li><p><em>Complexes with no valid information in this annotation resource</em></p></li>
+<li><p><em>won’t be in the dict.</em></p></li>
+</ul>
+</p>
+</dd>
+<dt class="field-even">Parameters<span class="colon">:</span></dt>
+<dd class="field-even"><p><strong>complexes</strong> (<em>iterable</em>) – Iterable yielding complexes.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Disgenet.coverage">
+<span class="sig-name descname"><span class="pre">coverage</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">other</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Disgenet.coverage" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the coverage of the annotation i.e. the proportion of
+entities having at least one record in this annotation resource
+for an arbitrary set of entities.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Disgenet.curation_effort">
+<span class="sig-name descname"><span class="pre">curation_effort</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Disgenet.curation_effort" title="Link to this definition">§</a></dt>
+<dd><p>Counts the reference-record pairs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Disgenet.get_names">
+<span class="sig-name descname"><span class="pre">get_names</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Disgenet.get_names" title="Link to this definition">§</a></dt>
+<dd><p>Returns the list of field names in the records. The annotation
+consists of uniform records and each entity might be annotated
+with one or more records. Each record is a tuple of fields, for
+example <code class="docutils literal notranslate"><span class="pre">('cell_type',</span> <span class="pre">'expression_level',</span> <span class="pre">'score')</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Disgenet.get_reference_set">
+<em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">get_reference_set</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">proteins</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">swissprot_only</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Disgenet.get_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the reference set i.e. the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Disgenet.get_subset">
+<span class="sig-name descname"><span class="pre">get_subset</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Disgenet.get_subset" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Disgenet.get_subset_bool_array">
+<span class="sig-name descname"><span class="pre">get_subset_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Disgenet.get_subset_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a boolean vector with True and False values for each entity
+in the reference set. The values represent presence absence data
+in the simplest case, but by providing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> any kind of matching
+and filtering is possible. <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> are passed to the <code class="docutils literal notranslate"><span class="pre">select</span></code>
+method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Disgenet.get_values">
+<span class="sig-name descname"><span class="pre">get_values</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">exclude_none</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Disgenet.get_values" title="Link to this definition">§</a></dt>
+<dd><p>Returns the set of all possible values of a field. E.g. if the
+records of this annotation have a field <code class="docutils literal notranslate"><span class="pre">cell_type</span></code> then calling
+this method can tell you that across all records the values of
+this field might be <code class="docutils literal notranslate"><span class="pre">{'macrophage',</span> <span class="pre">'epithelial_cell',</span> <span class="pre">...}</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Disgenet.labels">
+<span class="sig-name descname"><span class="pre">labels</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Disgenet.labels" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Disgenet.load">
+<span class="sig-name descname"><span class="pre">load</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Disgenet.load" title="Link to this definition">§</a></dt>
+<dd><p>Loads the annotation data by calling the input method.
+Infers annotations for complexes in the complex database if
+py:attr:<code class="docutils literal notranslate"><span class="pre">infer_complexes</span></code> is True.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Disgenet.load_data">
+<span class="sig-name descname"><span class="pre">load_data</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Disgenet.load_data" title="Link to this definition">§</a></dt>
+<dd><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Disgenet.load_proteins">
+<span class="sig-name descname"><span class="pre">load_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Disgenet.load_proteins" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a set of all UniProt IDs to have a base set of the entire
+proteome.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Disgenet.make_df">
+<span class="sig-name descname"><span class="pre">make_df</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">rebuild</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Disgenet.make_df" title="Link to this definition">§</a></dt>
+<dd><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.
+The data frame will be assigned to :py:attr``df``.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Disgenet.numof_entities">
+<span class="sig-name descname"><span class="pre">numof_entities</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Disgenet.numof_entities" title="Link to this definition">§</a></dt>
+<dd><p>The number of annotated entities in the resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Disgenet.numof_records">
+<span class="sig-name descname"><span class="pre">numof_records</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Disgenet.numof_records" title="Link to this definition">§</a></dt>
+<dd><p>The total number of annotation records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Disgenet.numof_references">
+<span class="sig-name descname"><span class="pre">numof_references</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Disgenet.numof_references" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects and counts the
+references across all records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Disgenet.process">
+<span class="sig-name descname"><span class="pre">process</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Disgenet.process" title="Link to this definition">§</a></dt>
+<dd><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Disgenet.reload">
+<span class="sig-name descname"><span class="pre">reload</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Disgenet.reload" title="Link to this definition">§</a></dt>
+<dd><p>Reloads the object from the module level.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Disgenet.select">
+<span class="sig-name descname"><span class="pre">select</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Disgenet.select" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Disgenet.set_method">
+<span class="sig-name descname"><span class="pre">set_method</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Disgenet.set_method" title="Link to this definition">§</a></dt>
+<dd><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if
+necessary.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Disgenet.set_reference_set">
+<span class="sig-name descname"><span class="pre">set_reference_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Disgenet.set_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Assigns the reference set to the :py:attr``reference_set`` attribute.
+The reference set is the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Disgenet.show">
+<span class="sig-name descname"><span class="pre">show</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">table_param</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Disgenet.show" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic
+information from the UniProt datasheets.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Disgenet.subset_intersection">
+<span class="sig-name descname"><span class="pre">subset_intersection</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">universe</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Disgenet.subset_intersection" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the proportion of entities in a subset occuring in the
+set <code class="docutils literal notranslate"><span class="pre">universe</span></code>. The subset is selected by passing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> to the
+<code class="docutils literal notranslate"><span class="pre">select</span></code> method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Disgenet.to_array">
+<span class="sig-name descname"><span class="pre">to_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_fields</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Disgenet.to_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns an entity vs feature array. In case of more complex
+annotations this might be huge.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Disgenet.to_bool_array">
+<span class="sig-name descname"><span class="pre">to_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Disgenet.to_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a presence/absence boolean array for a reference set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Disgenet.to_set">
+<span class="sig-name descname"><span class="pre">to_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Disgenet.to_set" title="Link to this definition">§</a></dt>
+<dd><p>Returns the entities present in this annotation resource as a set.</p>
+</dd></dl>
+
+</dd></dl>
+
+</section>
+
+
+                </article>
+              
+              
+              
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+  <section id="pypath-core-annot-embrace">
+<h1>pypath.core.annot.Embrace<a class="headerlink" href="#pypath-core-annot-embrace" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.core.annot.Embrace">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.core.annot.</span></span><span class="sig-name descname"><span class="pre">Embrace</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#Embrace"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.Embrace" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <a class="reference internal" href="pypath.core.annot.AnnotationBase.html#pypath.core.annot.AnnotationBase" title="pypath.core.annot.AnnotationBase"><code class="xref py py-class docutils literal notranslate"><span class="pre">AnnotationBase</span></code></a></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Embrace.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#Embrace.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.Embrace.__init__" title="Link to this definition">§</a></dt>
+<dd><p>Represents annotations for a set of proteins.
+Loads the data from the original resource and provides methods
+to query the annotations.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>name</strong> (<em>str</em>) – A custom name for the annotation resource.</p></li>
+<li><p><strong>ncbi_tax_id</strong> (<em>int</em>) – NCBI Taxonomy identifier.</p></li>
+<li><p><strong>input_method</strong> (<em>callable</em><em>,</em><em>str</em>) – Either a callable or the name of a method in any submodules of
+the <code class="docutils literal notranslate"><span class="pre">pypath.inputs</span></code>  module. Should return a dict with
+UniProt IDs as keys or an object suitable for <code class="docutils literal notranslate"><span class="pre">process_method</span></code>.</p></li>
+<li><p><strong>input_args</strong> (<em>dict</em>) – Arguments for the <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Embrace.__init__" title="pypath.core.annot.Embrace.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>([ncbi_tax_id])</p></td>
+<td><p>Represents annotations for a set of proteins.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Embrace.add_complexes_by_inference" title="pypath.core.annot.Embrace.add_complexes_by_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">add_complexes_by_inference</span></code></a>([complexes])</p></td>
+<td><p>Creates complex annotations by in silico inference and adds them to this annotation set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Embrace.all_complexes" title="pypath.core.annot.Embrace.all_complexes"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_complexes</span></code></a>()</p></td>
+<td><p>All protein complexes annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Embrace.all_entities" title="pypath.core.annot.Embrace.all_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_entities</span></code></a>([entity_types])</p></td>
+<td><p>All entities annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Embrace.all_mirnas" title="pypath.core.annot.Embrace.all_mirnas"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_mirnas</span></code></a>()</p></td>
+<td><p>All miRNAs annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Embrace.all_proteins" title="pypath.core.annot.Embrace.all_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_proteins</span></code></a>()</p></td>
+<td><p>All UniProt IDs annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Embrace.all_refs" title="pypath.core.annot.Embrace.all_refs"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_refs</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Embrace.annotate_complex" title="pypath.core.annot.Embrace.annotate_complex"><code class="xref py py-obj docutils literal notranslate"><span class="pre">annotate_complex</span></code></a>(cplex)</p></td>
+<td><p>Infers annotations for a single complex.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Embrace.browse" title="pypath.core.annot.Embrace.browse"><code class="xref py py-obj docutils literal notranslate"><span class="pre">browse</span></code></a>([field, start])</p></td>
+<td><p>Print gene information as a table.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Embrace.complex_inference" title="pypath.core.annot.Embrace.complex_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">complex_inference</span></code></a>([complexes])</p></td>
+<td><p>Annotates all complexes in <cite>complexes</cite>, by default in the default complex database (existing in the <cite>complex</cite> module or generated on demand according to the module's current settings).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Embrace.coverage" title="pypath.core.annot.Embrace.coverage"><code class="xref py py-obj docutils literal notranslate"><span class="pre">coverage</span></code></a>(other)</p></td>
+<td><p>Calculates the coverage of the annotation i.e. the proportion of entities having at least one record in this annotation resource for an arbitrary set of entities.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Embrace.curation_effort" title="pypath.core.annot.Embrace.curation_effort"><code class="xref py py-obj docutils literal notranslate"><span class="pre">curation_effort</span></code></a>()</p></td>
+<td><p>Counts the reference-record pairs.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">from_dump</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_entity_type</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Embrace.get_names" title="pypath.core.annot.Embrace.get_names"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_names</span></code></a>()</p></td>
+<td><p>Returns the list of field names in the records.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Embrace.get_reference_set" title="pypath.core.annot.Embrace.get_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_reference_set</span></code></a>([proteins, complexes, ...])</p></td>
+<td><p>Retrieves the reference set i.e. the set of all entities which potentially have annotation in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Embrace.get_subset" title="pypath.core.annot.Embrace.get_subset"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Embrace.get_subset_bool_array" title="pypath.core.annot.Embrace.get_subset_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset_bool_array</span></code></a>([reference_set])</p></td>
+<td><p>Returns a boolean vector with True and False values for each entity in the reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Embrace.get_values" title="pypath.core.annot.Embrace.get_values"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_values</span></code></a>(name[, exclude_none])</p></td>
+<td><p>Returns the set of all possible values of a field.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_complex</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_mirna</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_protein</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Embrace.labels" title="pypath.core.annot.Embrace.labels"><code class="xref py py-obj docutils literal notranslate"><span class="pre">labels</span></code></a>([method])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Embrace.load" title="pypath.core.annot.Embrace.load"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load</span></code></a>()</p></td>
+<td><p>Loads the annotation data by calling the input method.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Embrace.load_data" title="pypath.core.annot.Embrace.load_data"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_data</span></code></a>()</p></td>
+<td><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Embrace.load_proteins" title="pypath.core.annot.Embrace.load_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_proteins</span></code></a>()</p></td>
+<td><p>Retrieves a set of all UniProt IDs to have a base set of the entire proteome.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Embrace.make_df" title="pypath.core.annot.Embrace.make_df"><code class="xref py py-obj docutils literal notranslate"><span class="pre">make_df</span></code></a>([rebuild])</p></td>
+<td><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complex_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Embrace.numof_entities" title="pypath.core.annot.Embrace.numof_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_entities</span></code></a>()</p></td>
+<td><p>The number of annotated entities in the resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirna_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirnas</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_protein_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_proteins</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Embrace.numof_records" title="pypath.core.annot.Embrace.numof_records"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_records</span></code></a>([entity_types])</p></td>
+<td><p>The total number of annotation records.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Embrace.numof_references" title="pypath.core.annot.Embrace.numof_references"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_references</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Embrace.process" title="pypath.core.annot.Embrace.process"><code class="xref py py-obj docutils literal notranslate"><span class="pre">process</span></code></a>()</p></td>
+<td><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">proportion</span></code>(other)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Embrace.reload" title="pypath.core.annot.Embrace.reload"><code class="xref py py-obj docutils literal notranslate"><span class="pre">reload</span></code></a>()</p></td>
+<td><p>Reloads the object from the module level.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">save_to_pickle</span></code>(pickle_file)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Embrace.select" title="pypath.core.annot.Embrace.select"><code class="xref py py-obj docutils literal notranslate"><span class="pre">select</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Embrace.set_method" title="pypath.core.annot.Embrace.set_method"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_method</span></code></a>()</p></td>
+<td><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if necessary.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Embrace.set_reference_set" title="pypath.core.annot.Embrace.set_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_reference_set</span></code></a>()</p></td>
+<td><p>Assigns the reference set to the :py:attr``reference_set`` attribute.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Embrace.show" title="pypath.core.annot.Embrace.show"><code class="xref py py-obj docutils literal notranslate"><span class="pre">show</span></code></a>([method, table_param])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic information from the UniProt datasheets.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Embrace.subset_intersection" title="pypath.core.annot.Embrace.subset_intersection"><code class="xref py py-obj docutils literal notranslate"><span class="pre">subset_intersection</span></code></a>(universe, **kwargs)</p></td>
+<td><p>Calculates the proportion of entities in a subset occuring in the set <code class="docutils literal notranslate"><span class="pre">universe</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Embrace.to_array" title="pypath.core.annot.Embrace.to_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_array</span></code></a>([reference_set, use_fields])</p></td>
+<td><p>Returns an entity vs feature array.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Embrace.to_bool_array" title="pypath.core.annot.Embrace.to_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_bool_array</span></code></a>(reference_set)</p></td>
+<td><p>Returns a presence/absence boolean array for a reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Embrace.to_set" title="pypath.core.annot.Embrace.to_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_set</span></code></a>()</p></td>
+<td><p>Returns the entities present in this annotation resource as a set.</p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Attributes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_fields</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">summary</span></code></p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Embrace.add_complexes_by_inference">
+<span class="sig-name descname"><span class="pre">add_complexes_by_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Embrace.add_complexes_by_inference" title="Link to this definition">§</a></dt>
+<dd><p>Creates complex annotations by in silico inference and adds them
+to this annotation set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Embrace.all_complexes">
+<span class="sig-name descname"><span class="pre">all_complexes</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Embrace.all_complexes" title="Link to this definition">§</a></dt>
+<dd><p>All protein complexes annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Embrace.all_entities">
+<span class="sig-name descname"><span class="pre">all_entities</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Embrace.all_entities" title="Link to this definition">§</a></dt>
+<dd><p>All entities annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Embrace.all_mirnas">
+<span class="sig-name descname"><span class="pre">all_mirnas</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Embrace.all_mirnas" title="Link to this definition">§</a></dt>
+<dd><p>All miRNAs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Embrace.all_proteins">
+<span class="sig-name descname"><span class="pre">all_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Embrace.all_proteins" title="Link to this definition">§</a></dt>
+<dd><p>All UniProt IDs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Embrace.all_refs">
+<span class="sig-name descname"><span class="pre">all_refs</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Embrace.all_refs" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects the references
+across all records. Returns <em>list</em>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Embrace.annotate_complex">
+<span class="sig-name descname"><span class="pre">annotate_complex</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cplex</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Embrace.annotate_complex" title="Link to this definition">§</a></dt>
+<dd><p>Infers annotations for a single complex.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Embrace.browse">
+<span class="sig-name descname"><span class="pre">browse</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">field</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">start</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Embrace.browse" title="Link to this definition">§</a></dt>
+<dd><p>Print gene information as a table.</p>
+<p>Presents information about annotation categories as ascii tables
+printed in the terminal. If one category provided, prints one table.
+If multiple categories provided, prints a table for each of them one
+by one proceeding to the next one once you hit return. If no categories
+provided goes through all levels of the primary category.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>field:</dt><dd><p>The field to browse categories by.</p>
+<ul class="simple">
+<li><p>If None the primary field will be selected.
+If this annotation resource doesn’t have fields, all proteins
+will be presented as one single category.</p></li>
+<li><p>If a string it will be considered a field name and it will
+browse through all levels of this field.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">list</span></code>, set or tuple, it will be considered either a
+<code class="docutils literal notranslate"><span class="pre">list</span></code> of field names or a list of values from the primary
+field. In the former case all combinations of the values of
+the fields will be presented, in the latter case the browsing
+will be limited to the levels of the primary field contained
+in <code class="docutils literal notranslate"><span class="pre">field</span></code>.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">dict</span></code>, keys are supposed to be field names and values
+as list of levels. If any of the values are None, all levels
+from that field will be used.</p></li>
+</ul>
+</dd>
+<dt>start:</dt><dd><p>Start browsing from this category. E.g. if there are 500
+categories and start is 250 it will skip everything before the
+250th.</p>
+</dd>
+<dt>kwargs:</dt><dd><p>Passed to <code class="docutils literal notranslate"><span class="pre">pypath.utils.uniprot.info</span></code>.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Embrace.complex_inference">
+<span class="sig-name descname"><span class="pre">complex_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Embrace.complex_inference" title="Link to this definition">§</a></dt>
+<dd><p>Annotates all complexes in <cite>complexes</cite>, by default in the default
+complex database (existing in the <cite>complex</cite> module or generated
+on demand according to the module’s current settings).</p>
+<dl class="field-list simple">
+<dt class="field-odd">Returns<span class="colon">:</span></dt>
+<dd class="field-odd"><p><ul class="simple">
+<li><p><em>Dict with complexes as keys and sets of annotations as values.</em></p></li>
+<li><p><em>Complexes with no valid information in this annotation resource</em></p></li>
+<li><p><em>won’t be in the dict.</em></p></li>
+</ul>
+</p>
+</dd>
+<dt class="field-even">Parameters<span class="colon">:</span></dt>
+<dd class="field-even"><p><strong>complexes</strong> (<em>iterable</em>) – Iterable yielding complexes.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Embrace.coverage">
+<span class="sig-name descname"><span class="pre">coverage</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">other</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Embrace.coverage" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the coverage of the annotation i.e. the proportion of
+entities having at least one record in this annotation resource
+for an arbitrary set of entities.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Embrace.curation_effort">
+<span class="sig-name descname"><span class="pre">curation_effort</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Embrace.curation_effort" title="Link to this definition">§</a></dt>
+<dd><p>Counts the reference-record pairs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Embrace.get_names">
+<span class="sig-name descname"><span class="pre">get_names</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Embrace.get_names" title="Link to this definition">§</a></dt>
+<dd><p>Returns the list of field names in the records. The annotation
+consists of uniform records and each entity might be annotated
+with one or more records. Each record is a tuple of fields, for
+example <code class="docutils literal notranslate"><span class="pre">('cell_type',</span> <span class="pre">'expression_level',</span> <span class="pre">'score')</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Embrace.get_reference_set">
+<em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">get_reference_set</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">proteins</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">swissprot_only</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Embrace.get_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the reference set i.e. the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Embrace.get_subset">
+<span class="sig-name descname"><span class="pre">get_subset</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Embrace.get_subset" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Embrace.get_subset_bool_array">
+<span class="sig-name descname"><span class="pre">get_subset_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Embrace.get_subset_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a boolean vector with True and False values for each entity
+in the reference set. The values represent presence absence data
+in the simplest case, but by providing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> any kind of matching
+and filtering is possible. <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> are passed to the <code class="docutils literal notranslate"><span class="pre">select</span></code>
+method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Embrace.get_values">
+<span class="sig-name descname"><span class="pre">get_values</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">exclude_none</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Embrace.get_values" title="Link to this definition">§</a></dt>
+<dd><p>Returns the set of all possible values of a field. E.g. if the
+records of this annotation have a field <code class="docutils literal notranslate"><span class="pre">cell_type</span></code> then calling
+this method can tell you that across all records the values of
+this field might be <code class="docutils literal notranslate"><span class="pre">{'macrophage',</span> <span class="pre">'epithelial_cell',</span> <span class="pre">...}</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Embrace.labels">
+<span class="sig-name descname"><span class="pre">labels</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Embrace.labels" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Embrace.load">
+<span class="sig-name descname"><span class="pre">load</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Embrace.load" title="Link to this definition">§</a></dt>
+<dd><p>Loads the annotation data by calling the input method.
+Infers annotations for complexes in the complex database if
+py:attr:<code class="docutils literal notranslate"><span class="pre">infer_complexes</span></code> is True.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Embrace.load_data">
+<span class="sig-name descname"><span class="pre">load_data</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Embrace.load_data" title="Link to this definition">§</a></dt>
+<dd><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Embrace.load_proteins">
+<span class="sig-name descname"><span class="pre">load_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Embrace.load_proteins" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a set of all UniProt IDs to have a base set of the entire
+proteome.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Embrace.make_df">
+<span class="sig-name descname"><span class="pre">make_df</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">rebuild</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Embrace.make_df" title="Link to this definition">§</a></dt>
+<dd><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.
+The data frame will be assigned to :py:attr``df``.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Embrace.numof_entities">
+<span class="sig-name descname"><span class="pre">numof_entities</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Embrace.numof_entities" title="Link to this definition">§</a></dt>
+<dd><p>The number of annotated entities in the resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Embrace.numof_records">
+<span class="sig-name descname"><span class="pre">numof_records</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Embrace.numof_records" title="Link to this definition">§</a></dt>
+<dd><p>The total number of annotation records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Embrace.numof_references">
+<span class="sig-name descname"><span class="pre">numof_references</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Embrace.numof_references" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects and counts the
+references across all records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Embrace.process">
+<span class="sig-name descname"><span class="pre">process</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Embrace.process" title="Link to this definition">§</a></dt>
+<dd><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Embrace.reload">
+<span class="sig-name descname"><span class="pre">reload</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Embrace.reload" title="Link to this definition">§</a></dt>
+<dd><p>Reloads the object from the module level.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Embrace.select">
+<span class="sig-name descname"><span class="pre">select</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Embrace.select" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Embrace.set_method">
+<span class="sig-name descname"><span class="pre">set_method</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Embrace.set_method" title="Link to this definition">§</a></dt>
+<dd><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if
+necessary.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Embrace.set_reference_set">
+<span class="sig-name descname"><span class="pre">set_reference_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Embrace.set_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Assigns the reference set to the :py:attr``reference_set`` attribute.
+The reference set is the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Embrace.show">
+<span class="sig-name descname"><span class="pre">show</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">table_param</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Embrace.show" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic
+information from the UniProt datasheets.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Embrace.subset_intersection">
+<span class="sig-name descname"><span class="pre">subset_intersection</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">universe</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Embrace.subset_intersection" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the proportion of entities in a subset occuring in the
+set <code class="docutils literal notranslate"><span class="pre">universe</span></code>. The subset is selected by passing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> to the
+<code class="docutils literal notranslate"><span class="pre">select</span></code> method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Embrace.to_array">
+<span class="sig-name descname"><span class="pre">to_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_fields</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Embrace.to_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns an entity vs feature array. In case of more complex
+annotations this might be huge.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Embrace.to_bool_array">
+<span class="sig-name descname"><span class="pre">to_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Embrace.to_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a presence/absence boolean array for a reference set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Embrace.to_set">
+<span class="sig-name descname"><span class="pre">to_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Embrace.to_set" title="Link to this definition">§</a></dt>
+<dd><p>Returns the entities present in this annotation resource as a set.</p>
+</dd></dl>
+
+</dd></dl>
+
+</section>
+
+
+                </article>
+              
+              
+              
+              
+              
+                <footer class="prev-next-footer">
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+<h1>pypath.core.annot.Exocarta<a class="headerlink" href="#pypath-core-annot-exocarta" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.core.annot.Exocarta">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.core.annot.</span></span><span class="sig-name descname"><span class="pre">Exocarta</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#Exocarta"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.Exocarta" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <a class="reference internal" href="pypath.core.annot.AnnotationBase.html#pypath.core.annot.AnnotationBase" title="pypath.core.annot.AnnotationBase"><code class="xref py py-class docutils literal notranslate"><span class="pre">AnnotationBase</span></code></a></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Exocarta.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#Exocarta.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.Exocarta.__init__" title="Link to this definition">§</a></dt>
+<dd><p>Represents annotations for a set of proteins.
+Loads the data from the original resource and provides methods
+to query the annotations.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>name</strong> (<em>str</em>) – A custom name for the annotation resource.</p></li>
+<li><p><strong>ncbi_tax_id</strong> (<em>int</em>) – NCBI Taxonomy identifier.</p></li>
+<li><p><strong>input_method</strong> (<em>callable</em><em>,</em><em>str</em>) – Either a callable or the name of a method in any submodules of
+the <code class="docutils literal notranslate"><span class="pre">pypath.inputs</span></code>  module. Should return a dict with
+UniProt IDs as keys or an object suitable for <code class="docutils literal notranslate"><span class="pre">process_method</span></code>.</p></li>
+<li><p><strong>input_args</strong> (<em>dict</em>) – Arguments for the <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Exocarta.__init__" title="pypath.core.annot.Exocarta.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>([ncbi_tax_id])</p></td>
+<td><p>Represents annotations for a set of proteins.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Exocarta.add_complexes_by_inference" title="pypath.core.annot.Exocarta.add_complexes_by_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">add_complexes_by_inference</span></code></a>([complexes])</p></td>
+<td><p>Creates complex annotations by in silico inference and adds them to this annotation set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Exocarta.all_complexes" title="pypath.core.annot.Exocarta.all_complexes"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_complexes</span></code></a>()</p></td>
+<td><p>All protein complexes annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Exocarta.all_entities" title="pypath.core.annot.Exocarta.all_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_entities</span></code></a>([entity_types])</p></td>
+<td><p>All entities annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Exocarta.all_mirnas" title="pypath.core.annot.Exocarta.all_mirnas"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_mirnas</span></code></a>()</p></td>
+<td><p>All miRNAs annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Exocarta.all_proteins" title="pypath.core.annot.Exocarta.all_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_proteins</span></code></a>()</p></td>
+<td><p>All UniProt IDs annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Exocarta.all_refs" title="pypath.core.annot.Exocarta.all_refs"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_refs</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Exocarta.annotate_complex" title="pypath.core.annot.Exocarta.annotate_complex"><code class="xref py py-obj docutils literal notranslate"><span class="pre">annotate_complex</span></code></a>(cplex)</p></td>
+<td><p>Infers annotations for a single complex.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Exocarta.browse" title="pypath.core.annot.Exocarta.browse"><code class="xref py py-obj docutils literal notranslate"><span class="pre">browse</span></code></a>([field, start])</p></td>
+<td><p>Print gene information as a table.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Exocarta.complex_inference" title="pypath.core.annot.Exocarta.complex_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">complex_inference</span></code></a>([complexes])</p></td>
+<td><p>Annotates all complexes in <cite>complexes</cite>, by default in the default complex database (existing in the <cite>complex</cite> module or generated on demand according to the module's current settings).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Exocarta.coverage" title="pypath.core.annot.Exocarta.coverage"><code class="xref py py-obj docutils literal notranslate"><span class="pre">coverage</span></code></a>(other)</p></td>
+<td><p>Calculates the coverage of the annotation i.e. the proportion of entities having at least one record in this annotation resource for an arbitrary set of entities.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Exocarta.curation_effort" title="pypath.core.annot.Exocarta.curation_effort"><code class="xref py py-obj docutils literal notranslate"><span class="pre">curation_effort</span></code></a>()</p></td>
+<td><p>Counts the reference-record pairs.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">from_dump</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_entity_type</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Exocarta.get_names" title="pypath.core.annot.Exocarta.get_names"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_names</span></code></a>()</p></td>
+<td><p>Returns the list of field names in the records.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Exocarta.get_reference_set" title="pypath.core.annot.Exocarta.get_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_reference_set</span></code></a>([proteins, complexes, ...])</p></td>
+<td><p>Retrieves the reference set i.e. the set of all entities which potentially have annotation in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Exocarta.get_subset" title="pypath.core.annot.Exocarta.get_subset"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Exocarta.get_subset_bool_array" title="pypath.core.annot.Exocarta.get_subset_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset_bool_array</span></code></a>([reference_set])</p></td>
+<td><p>Returns a boolean vector with True and False values for each entity in the reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Exocarta.get_values" title="pypath.core.annot.Exocarta.get_values"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_values</span></code></a>(name[, exclude_none])</p></td>
+<td><p>Returns the set of all possible values of a field.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_complex</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_mirna</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_protein</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Exocarta.labels" title="pypath.core.annot.Exocarta.labels"><code class="xref py py-obj docutils literal notranslate"><span class="pre">labels</span></code></a>([method])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Exocarta.load" title="pypath.core.annot.Exocarta.load"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load</span></code></a>()</p></td>
+<td><p>Loads the annotation data by calling the input method.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Exocarta.load_data" title="pypath.core.annot.Exocarta.load_data"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_data</span></code></a>()</p></td>
+<td><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Exocarta.load_proteins" title="pypath.core.annot.Exocarta.load_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_proteins</span></code></a>()</p></td>
+<td><p>Retrieves a set of all UniProt IDs to have a base set of the entire proteome.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Exocarta.make_df" title="pypath.core.annot.Exocarta.make_df"><code class="xref py py-obj docutils literal notranslate"><span class="pre">make_df</span></code></a>([rebuild])</p></td>
+<td><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complex_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Exocarta.numof_entities" title="pypath.core.annot.Exocarta.numof_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_entities</span></code></a>()</p></td>
+<td><p>The number of annotated entities in the resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirna_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirnas</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_protein_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_proteins</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Exocarta.numof_records" title="pypath.core.annot.Exocarta.numof_records"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_records</span></code></a>([entity_types])</p></td>
+<td><p>The total number of annotation records.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Exocarta.numof_references" title="pypath.core.annot.Exocarta.numof_references"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_references</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Exocarta.process" title="pypath.core.annot.Exocarta.process"><code class="xref py py-obj docutils literal notranslate"><span class="pre">process</span></code></a>()</p></td>
+<td><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">proportion</span></code>(other)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Exocarta.reload" title="pypath.core.annot.Exocarta.reload"><code class="xref py py-obj docutils literal notranslate"><span class="pre">reload</span></code></a>()</p></td>
+<td><p>Reloads the object from the module level.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">save_to_pickle</span></code>(pickle_file)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Exocarta.select" title="pypath.core.annot.Exocarta.select"><code class="xref py py-obj docutils literal notranslate"><span class="pre">select</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Exocarta.set_method" title="pypath.core.annot.Exocarta.set_method"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_method</span></code></a>()</p></td>
+<td><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if necessary.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Exocarta.set_reference_set" title="pypath.core.annot.Exocarta.set_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_reference_set</span></code></a>()</p></td>
+<td><p>Assigns the reference set to the :py:attr``reference_set`` attribute.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Exocarta.show" title="pypath.core.annot.Exocarta.show"><code class="xref py py-obj docutils literal notranslate"><span class="pre">show</span></code></a>([method, table_param])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic information from the UniProt datasheets.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Exocarta.subset_intersection" title="pypath.core.annot.Exocarta.subset_intersection"><code class="xref py py-obj docutils literal notranslate"><span class="pre">subset_intersection</span></code></a>(universe, **kwargs)</p></td>
+<td><p>Calculates the proportion of entities in a subset occuring in the set <code class="docutils literal notranslate"><span class="pre">universe</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Exocarta.to_array" title="pypath.core.annot.Exocarta.to_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_array</span></code></a>([reference_set, use_fields])</p></td>
+<td><p>Returns an entity vs feature array.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Exocarta.to_bool_array" title="pypath.core.annot.Exocarta.to_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_bool_array</span></code></a>(reference_set)</p></td>
+<td><p>Returns a presence/absence boolean array for a reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Exocarta.to_set" title="pypath.core.annot.Exocarta.to_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_set</span></code></a>()</p></td>
+<td><p>Returns the entities present in this annotation resource as a set.</p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Attributes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_fields</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">summary</span></code></p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Exocarta.add_complexes_by_inference">
+<span class="sig-name descname"><span class="pre">add_complexes_by_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Exocarta.add_complexes_by_inference" title="Link to this definition">§</a></dt>
+<dd><p>Creates complex annotations by in silico inference and adds them
+to this annotation set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Exocarta.all_complexes">
+<span class="sig-name descname"><span class="pre">all_complexes</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Exocarta.all_complexes" title="Link to this definition">§</a></dt>
+<dd><p>All protein complexes annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Exocarta.all_entities">
+<span class="sig-name descname"><span class="pre">all_entities</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Exocarta.all_entities" title="Link to this definition">§</a></dt>
+<dd><p>All entities annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Exocarta.all_mirnas">
+<span class="sig-name descname"><span class="pre">all_mirnas</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Exocarta.all_mirnas" title="Link to this definition">§</a></dt>
+<dd><p>All miRNAs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Exocarta.all_proteins">
+<span class="sig-name descname"><span class="pre">all_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Exocarta.all_proteins" title="Link to this definition">§</a></dt>
+<dd><p>All UniProt IDs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Exocarta.all_refs">
+<span class="sig-name descname"><span class="pre">all_refs</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Exocarta.all_refs" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects the references
+across all records. Returns <em>list</em>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Exocarta.annotate_complex">
+<span class="sig-name descname"><span class="pre">annotate_complex</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cplex</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Exocarta.annotate_complex" title="Link to this definition">§</a></dt>
+<dd><p>Infers annotations for a single complex.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Exocarta.browse">
+<span class="sig-name descname"><span class="pre">browse</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">field</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">start</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Exocarta.browse" title="Link to this definition">§</a></dt>
+<dd><p>Print gene information as a table.</p>
+<p>Presents information about annotation categories as ascii tables
+printed in the terminal. If one category provided, prints one table.
+If multiple categories provided, prints a table for each of them one
+by one proceeding to the next one once you hit return. If no categories
+provided goes through all levels of the primary category.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>field:</dt><dd><p>The field to browse categories by.</p>
+<ul class="simple">
+<li><p>If None the primary field will be selected.
+If this annotation resource doesn’t have fields, all proteins
+will be presented as one single category.</p></li>
+<li><p>If a string it will be considered a field name and it will
+browse through all levels of this field.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">list</span></code>, set or tuple, it will be considered either a
+<code class="docutils literal notranslate"><span class="pre">list</span></code> of field names or a list of values from the primary
+field. In the former case all combinations of the values of
+the fields will be presented, in the latter case the browsing
+will be limited to the levels of the primary field contained
+in <code class="docutils literal notranslate"><span class="pre">field</span></code>.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">dict</span></code>, keys are supposed to be field names and values
+as list of levels. If any of the values are None, all levels
+from that field will be used.</p></li>
+</ul>
+</dd>
+<dt>start:</dt><dd><p>Start browsing from this category. E.g. if there are 500
+categories and start is 250 it will skip everything before the
+250th.</p>
+</dd>
+<dt>kwargs:</dt><dd><p>Passed to <code class="docutils literal notranslate"><span class="pre">pypath.utils.uniprot.info</span></code>.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Exocarta.complex_inference">
+<span class="sig-name descname"><span class="pre">complex_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Exocarta.complex_inference" title="Link to this definition">§</a></dt>
+<dd><p>Annotates all complexes in <cite>complexes</cite>, by default in the default
+complex database (existing in the <cite>complex</cite> module or generated
+on demand according to the module’s current settings).</p>
+<dl class="field-list simple">
+<dt class="field-odd">Returns<span class="colon">:</span></dt>
+<dd class="field-odd"><p><ul class="simple">
+<li><p><em>Dict with complexes as keys and sets of annotations as values.</em></p></li>
+<li><p><em>Complexes with no valid information in this annotation resource</em></p></li>
+<li><p><em>won’t be in the dict.</em></p></li>
+</ul>
+</p>
+</dd>
+<dt class="field-even">Parameters<span class="colon">:</span></dt>
+<dd class="field-even"><p><strong>complexes</strong> (<em>iterable</em>) – Iterable yielding complexes.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Exocarta.coverage">
+<span class="sig-name descname"><span class="pre">coverage</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">other</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Exocarta.coverage" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the coverage of the annotation i.e. the proportion of
+entities having at least one record in this annotation resource
+for an arbitrary set of entities.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Exocarta.curation_effort">
+<span class="sig-name descname"><span class="pre">curation_effort</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Exocarta.curation_effort" title="Link to this definition">§</a></dt>
+<dd><p>Counts the reference-record pairs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Exocarta.get_names">
+<span class="sig-name descname"><span class="pre">get_names</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Exocarta.get_names" title="Link to this definition">§</a></dt>
+<dd><p>Returns the list of field names in the records. The annotation
+consists of uniform records and each entity might be annotated
+with one or more records. Each record is a tuple of fields, for
+example <code class="docutils literal notranslate"><span class="pre">('cell_type',</span> <span class="pre">'expression_level',</span> <span class="pre">'score')</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Exocarta.get_reference_set">
+<em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">get_reference_set</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">proteins</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">swissprot_only</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Exocarta.get_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the reference set i.e. the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Exocarta.get_subset">
+<span class="sig-name descname"><span class="pre">get_subset</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Exocarta.get_subset" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Exocarta.get_subset_bool_array">
+<span class="sig-name descname"><span class="pre">get_subset_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Exocarta.get_subset_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a boolean vector with True and False values for each entity
+in the reference set. The values represent presence absence data
+in the simplest case, but by providing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> any kind of matching
+and filtering is possible. <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> are passed to the <code class="docutils literal notranslate"><span class="pre">select</span></code>
+method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Exocarta.get_values">
+<span class="sig-name descname"><span class="pre">get_values</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">exclude_none</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Exocarta.get_values" title="Link to this definition">§</a></dt>
+<dd><p>Returns the set of all possible values of a field. E.g. if the
+records of this annotation have a field <code class="docutils literal notranslate"><span class="pre">cell_type</span></code> then calling
+this method can tell you that across all records the values of
+this field might be <code class="docutils literal notranslate"><span class="pre">{'macrophage',</span> <span class="pre">'epithelial_cell',</span> <span class="pre">...}</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Exocarta.labels">
+<span class="sig-name descname"><span class="pre">labels</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Exocarta.labels" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Exocarta.load">
+<span class="sig-name descname"><span class="pre">load</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Exocarta.load" title="Link to this definition">§</a></dt>
+<dd><p>Loads the annotation data by calling the input method.
+Infers annotations for complexes in the complex database if
+py:attr:<code class="docutils literal notranslate"><span class="pre">infer_complexes</span></code> is True.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Exocarta.load_data">
+<span class="sig-name descname"><span class="pre">load_data</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Exocarta.load_data" title="Link to this definition">§</a></dt>
+<dd><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Exocarta.load_proteins">
+<span class="sig-name descname"><span class="pre">load_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Exocarta.load_proteins" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a set of all UniProt IDs to have a base set of the entire
+proteome.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Exocarta.make_df">
+<span class="sig-name descname"><span class="pre">make_df</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">rebuild</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Exocarta.make_df" title="Link to this definition">§</a></dt>
+<dd><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.
+The data frame will be assigned to :py:attr``df``.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Exocarta.numof_entities">
+<span class="sig-name descname"><span class="pre">numof_entities</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Exocarta.numof_entities" title="Link to this definition">§</a></dt>
+<dd><p>The number of annotated entities in the resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Exocarta.numof_records">
+<span class="sig-name descname"><span class="pre">numof_records</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Exocarta.numof_records" title="Link to this definition">§</a></dt>
+<dd><p>The total number of annotation records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Exocarta.numof_references">
+<span class="sig-name descname"><span class="pre">numof_references</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Exocarta.numof_references" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects and counts the
+references across all records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Exocarta.process">
+<span class="sig-name descname"><span class="pre">process</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Exocarta.process" title="Link to this definition">§</a></dt>
+<dd><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Exocarta.reload">
+<span class="sig-name descname"><span class="pre">reload</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Exocarta.reload" title="Link to this definition">§</a></dt>
+<dd><p>Reloads the object from the module level.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Exocarta.select">
+<span class="sig-name descname"><span class="pre">select</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Exocarta.select" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Exocarta.set_method">
+<span class="sig-name descname"><span class="pre">set_method</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Exocarta.set_method" title="Link to this definition">§</a></dt>
+<dd><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if
+necessary.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Exocarta.set_reference_set">
+<span class="sig-name descname"><span class="pre">set_reference_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Exocarta.set_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Assigns the reference set to the :py:attr``reference_set`` attribute.
+The reference set is the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Exocarta.show">
+<span class="sig-name descname"><span class="pre">show</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">table_param</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Exocarta.show" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic
+information from the UniProt datasheets.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Exocarta.subset_intersection">
+<span class="sig-name descname"><span class="pre">subset_intersection</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">universe</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Exocarta.subset_intersection" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the proportion of entities in a subset occuring in the
+set <code class="docutils literal notranslate"><span class="pre">universe</span></code>. The subset is selected by passing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> to the
+<code class="docutils literal notranslate"><span class="pre">select</span></code> method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Exocarta.to_array">
+<span class="sig-name descname"><span class="pre">to_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_fields</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Exocarta.to_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns an entity vs feature array. In case of more complex
+annotations this might be huge.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Exocarta.to_bool_array">
+<span class="sig-name descname"><span class="pre">to_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Exocarta.to_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a presence/absence boolean array for a reference set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Exocarta.to_set">
+<span class="sig-name descname"><span class="pre">to_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Exocarta.to_set" title="Link to this definition">§</a></dt>
+<dd><p>Returns the entities present in this annotation resource as a set.</p>
+</dd></dl>
+
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+  <section id="pypath-core-annot-gocustomintercell">
+<h1>pypath.core.annot.GOCustomIntercell<a class="headerlink" href="#pypath-core-annot-gocustomintercell" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.core.annot.GOCustomIntercell">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.core.annot.</span></span><span class="sig-name descname"><span class="pre">GOCustomIntercell</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">categories</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">go_annot</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#GOCustomIntercell"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.GOCustomIntercell" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <a class="reference internal" href="pypath.utils.go.GOCustomAnnotation.html#pypath.utils.go.GOCustomAnnotation" title="pypath.utils.go.GOCustomAnnotation"><code class="xref py py-class docutils literal notranslate"><span class="pre">GOCustomAnnotation</span></code></a></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.GOCustomIntercell.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">categories</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">go_annot</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#GOCustomIntercell.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.GOCustomIntercell.__init__" title="Link to this definition">§</a></dt>
+<dd><p>Same as :class:<code class="docutils literal notranslate"><span class="pre">pypath.go.GOCustomAnnotation</span></code>
+initialized with the categories defined in
+<code class="docutils literal notranslate"><span class="pre">pypath.intercell_annot.intercell_categories</span></code>.</p>
+</dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.GOCustomIntercell.__init__" title="pypath.core.annot.GOCustomIntercell.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>([categories, go_annot, ncbi_tax_id])</p></td>
+<td><p>Same as :class:<code class="docutils literal notranslate"><span class="pre">pypath.go.GOCustomAnnotation</span></code> initialized with the categories defined in <code class="docutils literal notranslate"><span class="pre">pypath.intercell_annot.intercell_categories</span></code>.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.GOCustomIntercell.get_annotation" title="pypath.core.annot.GOCustomIntercell.get_annotation"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_annotation</span></code></a>(category[, uniprots])</p></td>
+<td><p>For a category name returns a set of UniProt IDs annotated with the corresponding Gene Ontology terms or expression.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.GOCustomIntercell.get_annotations" title="pypath.core.annot.GOCustomIntercell.get_annotations"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_annotations</span></code></a>([uniprots])</p></td>
+<td><p>Returns a dict with set of UniProt IDs for each category.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.GOCustomIntercell.process_categories" title="pypath.core.annot.GOCustomIntercell.process_categories"><code class="xref py py-obj docutils literal notranslate"><span class="pre">process_categories</span></code></a>()</p></td>
+<td><p>Translates GO term names listed in categories to GO terms ACs.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.GOCustomIntercell.reload" title="pypath.core.annot.GOCustomIntercell.reload"><code class="xref py py-obj docutils literal notranslate"><span class="pre">reload</span></code></a>()</p></td>
+<td><p>Reloads the object from the module level.</p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.GOCustomIntercell.get_annotation">
+<span class="sig-name descname"><span class="pre">get_annotation</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">category</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">uniprots</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.GOCustomIntercell.get_annotation" title="Link to this definition">§</a></dt>
+<dd><p>For a category name returns a set of UniProt IDs annotated with
+the corresponding Gene Ontology terms or expression.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>category</strong> (<em>str</em>) – The category name, should be a key in the <code class="docutils literal notranslate"><span class="pre">categories</span></code> dict.</p></li>
+<li><p><strong>uniprots</strong> (<em>set</em>) – A set or list of UniProt IDs. If <code class="docutils literal notranslate"><span class="pre">None</span></code>, annotations based on
+all UniProts in GO annotation will be returned.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.GOCustomIntercell.get_annotations">
+<span class="sig-name descname"><span class="pre">get_annotations</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">uniprots</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.GOCustomIntercell.get_annotations" title="Link to this definition">§</a></dt>
+<dd><p>Returns a dict with set of UniProt IDs for each category.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><p><strong>uniprots</strong> (<em>set</em>) – A set or list of UniProt IDs. If <code class="docutils literal notranslate"><span class="pre">None</span></code>, annotations based on
+all UniProts in GO annotation will be returned.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.GOCustomIntercell.process_categories">
+<span class="sig-name descname"><span class="pre">process_categories</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.GOCustomIntercell.process_categories" title="Link to this definition">§</a></dt>
+<dd><p>Translates GO term names listed in categories to GO terms ACs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.GOCustomIntercell.reload">
+<span class="sig-name descname"><span class="pre">reload</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.GOCustomIntercell.reload" title="Link to this definition">§</a></dt>
+<dd><p>Reloads the object from the module level.</p>
+</dd></dl>
+
+</dd></dl>
+
+</section>
+
+
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+  <section id="pypath-core-annot-gointercell">
+<h1>pypath.core.annot.GOIntercell<a class="headerlink" href="#pypath-core-annot-gointercell" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.core.annot.GOIntercell">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.core.annot.</span></span><span class="sig-name descname"><span class="pre">GOIntercell</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">categories</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">go_annot</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#GOIntercell"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.GOIntercell" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <a class="reference internal" href="pypath.core.annot.AnnotationBase.html#pypath.core.annot.AnnotationBase" title="pypath.core.annot.AnnotationBase"><code class="xref py py-class docutils literal notranslate"><span class="pre">AnnotationBase</span></code></a></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.GOIntercell.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">categories</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">go_annot</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#GOIntercell.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.GOIntercell.__init__" title="Link to this definition">§</a></dt>
+<dd><p>Annotation of proteins based on their roles in intercellular
+communication from Gene Ontology.</p>
+</dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.GOIntercell.__init__" title="pypath.core.annot.GOIntercell.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>([categories, go_annot, ncbi_tax_id])</p></td>
+<td><p>Annotation of proteins based on their roles in intercellular communication from Gene Ontology.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.GOIntercell.add_complexes_by_inference" title="pypath.core.annot.GOIntercell.add_complexes_by_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">add_complexes_by_inference</span></code></a>([complexes])</p></td>
+<td><p>Creates complex annotations by in silico inference and adds them to this annotation set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.GOIntercell.all_complexes" title="pypath.core.annot.GOIntercell.all_complexes"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_complexes</span></code></a>()</p></td>
+<td><p>All protein complexes annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.GOIntercell.all_entities" title="pypath.core.annot.GOIntercell.all_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_entities</span></code></a>([entity_types])</p></td>
+<td><p>All entities annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.GOIntercell.all_mirnas" title="pypath.core.annot.GOIntercell.all_mirnas"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_mirnas</span></code></a>()</p></td>
+<td><p>All miRNAs annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.GOIntercell.all_proteins" title="pypath.core.annot.GOIntercell.all_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_proteins</span></code></a>()</p></td>
+<td><p>All UniProt IDs annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.GOIntercell.all_refs" title="pypath.core.annot.GOIntercell.all_refs"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_refs</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.GOIntercell.annotate_complex" title="pypath.core.annot.GOIntercell.annotate_complex"><code class="xref py py-obj docutils literal notranslate"><span class="pre">annotate_complex</span></code></a>(cplex)</p></td>
+<td><p>Infers annotations for a single complex.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.GOIntercell.browse" title="pypath.core.annot.GOIntercell.browse"><code class="xref py py-obj docutils literal notranslate"><span class="pre">browse</span></code></a>([field, start])</p></td>
+<td><p>Print gene information as a table.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.GOIntercell.complex_inference" title="pypath.core.annot.GOIntercell.complex_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">complex_inference</span></code></a>([complexes])</p></td>
+<td><p>Annotates all complexes in <cite>complexes</cite>, by default in the default complex database (existing in the <cite>complex</cite> module or generated on demand according to the module's current settings).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.GOIntercell.coverage" title="pypath.core.annot.GOIntercell.coverage"><code class="xref py py-obj docutils literal notranslate"><span class="pre">coverage</span></code></a>(other)</p></td>
+<td><p>Calculates the coverage of the annotation i.e. the proportion of entities having at least one record in this annotation resource for an arbitrary set of entities.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.GOIntercell.curation_effort" title="pypath.core.annot.GOIntercell.curation_effort"><code class="xref py py-obj docutils literal notranslate"><span class="pre">curation_effort</span></code></a>()</p></td>
+<td><p>Counts the reference-record pairs.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">from_dump</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_entity_type</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.GOIntercell.get_names" title="pypath.core.annot.GOIntercell.get_names"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_names</span></code></a>()</p></td>
+<td><p>Returns the list of field names in the records.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.GOIntercell.get_reference_set" title="pypath.core.annot.GOIntercell.get_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_reference_set</span></code></a>([proteins, complexes, ...])</p></td>
+<td><p>Retrieves the reference set i.e. the set of all entities which potentially have annotation in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.GOIntercell.get_subset" title="pypath.core.annot.GOIntercell.get_subset"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.GOIntercell.get_subset_bool_array" title="pypath.core.annot.GOIntercell.get_subset_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset_bool_array</span></code></a>([reference_set])</p></td>
+<td><p>Returns a boolean vector with True and False values for each entity in the reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.GOIntercell.get_values" title="pypath.core.annot.GOIntercell.get_values"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_values</span></code></a>(name[, exclude_none])</p></td>
+<td><p>Returns the set of all possible values of a field.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_complex</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_mirna</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_protein</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.GOIntercell.labels" title="pypath.core.annot.GOIntercell.labels"><code class="xref py py-obj docutils literal notranslate"><span class="pre">labels</span></code></a>([method])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.GOIntercell.load" title="pypath.core.annot.GOIntercell.load"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load</span></code></a>()</p></td>
+<td><p>Loads the annotation data by calling the input method.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.GOIntercell.load_data" title="pypath.core.annot.GOIntercell.load_data"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_data</span></code></a>()</p></td>
+<td><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.GOIntercell.load_proteins" title="pypath.core.annot.GOIntercell.load_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_proteins</span></code></a>()</p></td>
+<td><p>Retrieves a set of all UniProt IDs to have a base set of the entire proteome.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.GOIntercell.make_df" title="pypath.core.annot.GOIntercell.make_df"><code class="xref py py-obj docutils literal notranslate"><span class="pre">make_df</span></code></a>([rebuild])</p></td>
+<td><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complex_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.GOIntercell.numof_entities" title="pypath.core.annot.GOIntercell.numof_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_entities</span></code></a>()</p></td>
+<td><p>The number of annotated entities in the resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirna_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirnas</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_protein_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_proteins</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.GOIntercell.numof_records" title="pypath.core.annot.GOIntercell.numof_records"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_records</span></code></a>([entity_types])</p></td>
+<td><p>The total number of annotation records.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.GOIntercell.numof_references" title="pypath.core.annot.GOIntercell.numof_references"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_references</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.GOIntercell.process" title="pypath.core.annot.GOIntercell.process"><code class="xref py py-obj docutils literal notranslate"><span class="pre">process</span></code></a>()</p></td>
+<td><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">proportion</span></code>(other)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.GOIntercell.reload" title="pypath.core.annot.GOIntercell.reload"><code class="xref py py-obj docutils literal notranslate"><span class="pre">reload</span></code></a>()</p></td>
+<td><p>Reloads the object from the module level.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">save_to_pickle</span></code>(pickle_file)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.GOIntercell.select" title="pypath.core.annot.GOIntercell.select"><code class="xref py py-obj docutils literal notranslate"><span class="pre">select</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.GOIntercell.set_method" title="pypath.core.annot.GOIntercell.set_method"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_method</span></code></a>()</p></td>
+<td><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if necessary.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.GOIntercell.set_reference_set" title="pypath.core.annot.GOIntercell.set_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_reference_set</span></code></a>()</p></td>
+<td><p>Assigns the reference set to the :py:attr``reference_set`` attribute.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.GOIntercell.show" title="pypath.core.annot.GOIntercell.show"><code class="xref py py-obj docutils literal notranslate"><span class="pre">show</span></code></a>([method, table_param])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic information from the UniProt datasheets.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.GOIntercell.subset_intersection" title="pypath.core.annot.GOIntercell.subset_intersection"><code class="xref py py-obj docutils literal notranslate"><span class="pre">subset_intersection</span></code></a>(universe, **kwargs)</p></td>
+<td><p>Calculates the proportion of entities in a subset occuring in the set <code class="docutils literal notranslate"><span class="pre">universe</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.GOIntercell.to_array" title="pypath.core.annot.GOIntercell.to_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_array</span></code></a>([reference_set, use_fields])</p></td>
+<td><p>Returns an entity vs feature array.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.GOIntercell.to_bool_array" title="pypath.core.annot.GOIntercell.to_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_bool_array</span></code></a>(reference_set)</p></td>
+<td><p>Returns a presence/absence boolean array for a reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.GOIntercell.to_set" title="pypath.core.annot.GOIntercell.to_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_set</span></code></a>()</p></td>
+<td><p>Returns the entities present in this annotation resource as a set.</p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Attributes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_fields</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">summary</span></code></p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.GOIntercell.add_complexes_by_inference">
+<span class="sig-name descname"><span class="pre">add_complexes_by_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.GOIntercell.add_complexes_by_inference" title="Link to this definition">§</a></dt>
+<dd><p>Creates complex annotations by in silico inference and adds them
+to this annotation set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.GOIntercell.all_complexes">
+<span class="sig-name descname"><span class="pre">all_complexes</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.GOIntercell.all_complexes" title="Link to this definition">§</a></dt>
+<dd><p>All protein complexes annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.GOIntercell.all_entities">
+<span class="sig-name descname"><span class="pre">all_entities</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.GOIntercell.all_entities" title="Link to this definition">§</a></dt>
+<dd><p>All entities annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.GOIntercell.all_mirnas">
+<span class="sig-name descname"><span class="pre">all_mirnas</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.GOIntercell.all_mirnas" title="Link to this definition">§</a></dt>
+<dd><p>All miRNAs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.GOIntercell.all_proteins">
+<span class="sig-name descname"><span class="pre">all_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.GOIntercell.all_proteins" title="Link to this definition">§</a></dt>
+<dd><p>All UniProt IDs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.GOIntercell.all_refs">
+<span class="sig-name descname"><span class="pre">all_refs</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.GOIntercell.all_refs" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects the references
+across all records. Returns <em>list</em>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.GOIntercell.annotate_complex">
+<span class="sig-name descname"><span class="pre">annotate_complex</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cplex</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.GOIntercell.annotate_complex" title="Link to this definition">§</a></dt>
+<dd><p>Infers annotations for a single complex.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.GOIntercell.browse">
+<span class="sig-name descname"><span class="pre">browse</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">field</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">start</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.GOIntercell.browse" title="Link to this definition">§</a></dt>
+<dd><p>Print gene information as a table.</p>
+<p>Presents information about annotation categories as ascii tables
+printed in the terminal. If one category provided, prints one table.
+If multiple categories provided, prints a table for each of them one
+by one proceeding to the next one once you hit return. If no categories
+provided goes through all levels of the primary category.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>field:</dt><dd><p>The field to browse categories by.</p>
+<ul class="simple">
+<li><p>If None the primary field will be selected.
+If this annotation resource doesn’t have fields, all proteins
+will be presented as one single category.</p></li>
+<li><p>If a string it will be considered a field name and it will
+browse through all levels of this field.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">list</span></code>, set or tuple, it will be considered either a
+<code class="docutils literal notranslate"><span class="pre">list</span></code> of field names or a list of values from the primary
+field. In the former case all combinations of the values of
+the fields will be presented, in the latter case the browsing
+will be limited to the levels of the primary field contained
+in <code class="docutils literal notranslate"><span class="pre">field</span></code>.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">dict</span></code>, keys are supposed to be field names and values
+as list of levels. If any of the values are None, all levels
+from that field will be used.</p></li>
+</ul>
+</dd>
+<dt>start:</dt><dd><p>Start browsing from this category. E.g. if there are 500
+categories and start is 250 it will skip everything before the
+250th.</p>
+</dd>
+<dt>kwargs:</dt><dd><p>Passed to <code class="docutils literal notranslate"><span class="pre">pypath.utils.uniprot.info</span></code>.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.GOIntercell.complex_inference">
+<span class="sig-name descname"><span class="pre">complex_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.GOIntercell.complex_inference" title="Link to this definition">§</a></dt>
+<dd><p>Annotates all complexes in <cite>complexes</cite>, by default in the default
+complex database (existing in the <cite>complex</cite> module or generated
+on demand according to the module’s current settings).</p>
+<dl class="field-list simple">
+<dt class="field-odd">Returns<span class="colon">:</span></dt>
+<dd class="field-odd"><p><ul class="simple">
+<li><p><em>Dict with complexes as keys and sets of annotations as values.</em></p></li>
+<li><p><em>Complexes with no valid information in this annotation resource</em></p></li>
+<li><p><em>won’t be in the dict.</em></p></li>
+</ul>
+</p>
+</dd>
+<dt class="field-even">Parameters<span class="colon">:</span></dt>
+<dd class="field-even"><p><strong>complexes</strong> (<em>iterable</em>) – Iterable yielding complexes.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.GOIntercell.coverage">
+<span class="sig-name descname"><span class="pre">coverage</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">other</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.GOIntercell.coverage" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the coverage of the annotation i.e. the proportion of
+entities having at least one record in this annotation resource
+for an arbitrary set of entities.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.GOIntercell.curation_effort">
+<span class="sig-name descname"><span class="pre">curation_effort</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.GOIntercell.curation_effort" title="Link to this definition">§</a></dt>
+<dd><p>Counts the reference-record pairs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.GOIntercell.get_names">
+<span class="sig-name descname"><span class="pre">get_names</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.GOIntercell.get_names" title="Link to this definition">§</a></dt>
+<dd><p>Returns the list of field names in the records. The annotation
+consists of uniform records and each entity might be annotated
+with one or more records. Each record is a tuple of fields, for
+example <code class="docutils literal notranslate"><span class="pre">('cell_type',</span> <span class="pre">'expression_level',</span> <span class="pre">'score')</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.GOIntercell.get_reference_set">
+<em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">get_reference_set</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">proteins</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">swissprot_only</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.GOIntercell.get_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the reference set i.e. the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.GOIntercell.get_subset">
+<span class="sig-name descname"><span class="pre">get_subset</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.GOIntercell.get_subset" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.GOIntercell.get_subset_bool_array">
+<span class="sig-name descname"><span class="pre">get_subset_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.GOIntercell.get_subset_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a boolean vector with True and False values for each entity
+in the reference set. The values represent presence absence data
+in the simplest case, but by providing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> any kind of matching
+and filtering is possible. <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> are passed to the <code class="docutils literal notranslate"><span class="pre">select</span></code>
+method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.GOIntercell.get_values">
+<span class="sig-name descname"><span class="pre">get_values</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">exclude_none</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.GOIntercell.get_values" title="Link to this definition">§</a></dt>
+<dd><p>Returns the set of all possible values of a field. E.g. if the
+records of this annotation have a field <code class="docutils literal notranslate"><span class="pre">cell_type</span></code> then calling
+this method can tell you that across all records the values of
+this field might be <code class="docutils literal notranslate"><span class="pre">{'macrophage',</span> <span class="pre">'epithelial_cell',</span> <span class="pre">...}</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.GOIntercell.labels">
+<span class="sig-name descname"><span class="pre">labels</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.GOIntercell.labels" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.GOIntercell.load">
+<span class="sig-name descname"><span class="pre">load</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#GOIntercell.load"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.GOIntercell.load" title="Link to this definition">§</a></dt>
+<dd><p>Loads the annotation data by calling the input method.
+Infers annotations for complexes in the complex database if
+py:attr:<code class="docutils literal notranslate"><span class="pre">infer_complexes</span></code> is True.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.GOIntercell.load_data">
+<span class="sig-name descname"><span class="pre">load_data</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.GOIntercell.load_data" title="Link to this definition">§</a></dt>
+<dd><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.GOIntercell.load_proteins">
+<span class="sig-name descname"><span class="pre">load_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.GOIntercell.load_proteins" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a set of all UniProt IDs to have a base set of the entire
+proteome.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.GOIntercell.make_df">
+<span class="sig-name descname"><span class="pre">make_df</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">rebuild</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.GOIntercell.make_df" title="Link to this definition">§</a></dt>
+<dd><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.
+The data frame will be assigned to :py:attr``df``.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.GOIntercell.numof_entities">
+<span class="sig-name descname"><span class="pre">numof_entities</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.GOIntercell.numof_entities" title="Link to this definition">§</a></dt>
+<dd><p>The number of annotated entities in the resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.GOIntercell.numof_records">
+<span class="sig-name descname"><span class="pre">numof_records</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.GOIntercell.numof_records" title="Link to this definition">§</a></dt>
+<dd><p>The total number of annotation records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.GOIntercell.numof_references">
+<span class="sig-name descname"><span class="pre">numof_references</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.GOIntercell.numof_references" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects and counts the
+references across all records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.GOIntercell.process">
+<span class="sig-name descname"><span class="pre">process</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.GOIntercell.process" title="Link to this definition">§</a></dt>
+<dd><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.GOIntercell.reload">
+<span class="sig-name descname"><span class="pre">reload</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.GOIntercell.reload" title="Link to this definition">§</a></dt>
+<dd><p>Reloads the object from the module level.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.GOIntercell.select">
+<span class="sig-name descname"><span class="pre">select</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.GOIntercell.select" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.GOIntercell.set_method">
+<span class="sig-name descname"><span class="pre">set_method</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.GOIntercell.set_method" title="Link to this definition">§</a></dt>
+<dd><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if
+necessary.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.GOIntercell.set_reference_set">
+<span class="sig-name descname"><span class="pre">set_reference_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.GOIntercell.set_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Assigns the reference set to the :py:attr``reference_set`` attribute.
+The reference set is the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.GOIntercell.show">
+<span class="sig-name descname"><span class="pre">show</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">table_param</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.GOIntercell.show" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic
+information from the UniProt datasheets.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.GOIntercell.subset_intersection">
+<span class="sig-name descname"><span class="pre">subset_intersection</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">universe</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.GOIntercell.subset_intersection" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the proportion of entities in a subset occuring in the
+set <code class="docutils literal notranslate"><span class="pre">universe</span></code>. The subset is selected by passing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> to the
+<code class="docutils literal notranslate"><span class="pre">select</span></code> method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.GOIntercell.to_array">
+<span class="sig-name descname"><span class="pre">to_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_fields</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.GOIntercell.to_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns an entity vs feature array. In case of more complex
+annotations this might be huge.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.GOIntercell.to_bool_array">
+<span class="sig-name descname"><span class="pre">to_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.GOIntercell.to_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a presence/absence boolean array for a reference set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.GOIntercell.to_set">
+<span class="sig-name descname"><span class="pre">to_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.GOIntercell.to_set" title="Link to this definition">§</a></dt>
+<dd><p>Returns the entities present in this annotation resource as a set.</p>
+</dd></dl>
+
+</dd></dl>
+
+</section>
+
+
+                </article>
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+  <section id="pypath-core-annot-gpcrdb">
+<h1>pypath.core.annot.Gpcrdb<a class="headerlink" href="#pypath-core-annot-gpcrdb" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.core.annot.Gpcrdb">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.core.annot.</span></span><span class="sig-name descname"><span class="pre">Gpcrdb</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#Gpcrdb"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.Gpcrdb" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <a class="reference internal" href="pypath.core.annot.AnnotationBase.html#pypath.core.annot.AnnotationBase" title="pypath.core.annot.AnnotationBase"><code class="xref py py-class docutils literal notranslate"><span class="pre">AnnotationBase</span></code></a></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Gpcrdb.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#Gpcrdb.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.Gpcrdb.__init__" title="Link to this definition">§</a></dt>
+<dd><p>GPCR classification from GPCRdb - <a class="reference external" href="https://gpcrdb.org/">https://gpcrdb.org/</a>.</p>
+</dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Gpcrdb.__init__" title="pypath.core.annot.Gpcrdb.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>([ncbi_tax_id])</p></td>
+<td><p>GPCR classification from GPCRdb - <a class="reference external" href="https://gpcrdb.org/">https://gpcrdb.org/</a>.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Gpcrdb.add_complexes_by_inference" title="pypath.core.annot.Gpcrdb.add_complexes_by_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">add_complexes_by_inference</span></code></a>([complexes])</p></td>
+<td><p>Creates complex annotations by in silico inference and adds them to this annotation set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Gpcrdb.all_complexes" title="pypath.core.annot.Gpcrdb.all_complexes"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_complexes</span></code></a>()</p></td>
+<td><p>All protein complexes annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Gpcrdb.all_entities" title="pypath.core.annot.Gpcrdb.all_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_entities</span></code></a>([entity_types])</p></td>
+<td><p>All entities annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Gpcrdb.all_mirnas" title="pypath.core.annot.Gpcrdb.all_mirnas"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_mirnas</span></code></a>()</p></td>
+<td><p>All miRNAs annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Gpcrdb.all_proteins" title="pypath.core.annot.Gpcrdb.all_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_proteins</span></code></a>()</p></td>
+<td><p>All UniProt IDs annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Gpcrdb.all_refs" title="pypath.core.annot.Gpcrdb.all_refs"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_refs</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Gpcrdb.annotate_complex" title="pypath.core.annot.Gpcrdb.annotate_complex"><code class="xref py py-obj docutils literal notranslate"><span class="pre">annotate_complex</span></code></a>(cplex)</p></td>
+<td><p>Infers annotations for a single complex.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Gpcrdb.browse" title="pypath.core.annot.Gpcrdb.browse"><code class="xref py py-obj docutils literal notranslate"><span class="pre">browse</span></code></a>([field, start])</p></td>
+<td><p>Print gene information as a table.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Gpcrdb.complex_inference" title="pypath.core.annot.Gpcrdb.complex_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">complex_inference</span></code></a>([complexes])</p></td>
+<td><p>Annotates all complexes in <cite>complexes</cite>, by default in the default complex database (existing in the <cite>complex</cite> module or generated on demand according to the module's current settings).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Gpcrdb.coverage" title="pypath.core.annot.Gpcrdb.coverage"><code class="xref py py-obj docutils literal notranslate"><span class="pre">coverage</span></code></a>(other)</p></td>
+<td><p>Calculates the coverage of the annotation i.e. the proportion of entities having at least one record in this annotation resource for an arbitrary set of entities.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Gpcrdb.curation_effort" title="pypath.core.annot.Gpcrdb.curation_effort"><code class="xref py py-obj docutils literal notranslate"><span class="pre">curation_effort</span></code></a>()</p></td>
+<td><p>Counts the reference-record pairs.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">from_dump</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_entity_type</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Gpcrdb.get_names" title="pypath.core.annot.Gpcrdb.get_names"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_names</span></code></a>()</p></td>
+<td><p>Returns the list of field names in the records.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Gpcrdb.get_reference_set" title="pypath.core.annot.Gpcrdb.get_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_reference_set</span></code></a>([proteins, complexes, ...])</p></td>
+<td><p>Retrieves the reference set i.e. the set of all entities which potentially have annotation in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Gpcrdb.get_subset" title="pypath.core.annot.Gpcrdb.get_subset"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Gpcrdb.get_subset_bool_array" title="pypath.core.annot.Gpcrdb.get_subset_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset_bool_array</span></code></a>([reference_set])</p></td>
+<td><p>Returns a boolean vector with True and False values for each entity in the reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Gpcrdb.get_values" title="pypath.core.annot.Gpcrdb.get_values"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_values</span></code></a>(name[, exclude_none])</p></td>
+<td><p>Returns the set of all possible values of a field.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_complex</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_mirna</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_protein</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Gpcrdb.labels" title="pypath.core.annot.Gpcrdb.labels"><code class="xref py py-obj docutils literal notranslate"><span class="pre">labels</span></code></a>([method])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Gpcrdb.load" title="pypath.core.annot.Gpcrdb.load"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load</span></code></a>()</p></td>
+<td><p>Loads the annotation data by calling the input method.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Gpcrdb.load_data" title="pypath.core.annot.Gpcrdb.load_data"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_data</span></code></a>()</p></td>
+<td><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Gpcrdb.load_proteins" title="pypath.core.annot.Gpcrdb.load_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_proteins</span></code></a>()</p></td>
+<td><p>Retrieves a set of all UniProt IDs to have a base set of the entire proteome.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Gpcrdb.make_df" title="pypath.core.annot.Gpcrdb.make_df"><code class="xref py py-obj docutils literal notranslate"><span class="pre">make_df</span></code></a>([rebuild])</p></td>
+<td><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complex_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Gpcrdb.numof_entities" title="pypath.core.annot.Gpcrdb.numof_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_entities</span></code></a>()</p></td>
+<td><p>The number of annotated entities in the resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirna_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirnas</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_protein_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_proteins</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Gpcrdb.numof_records" title="pypath.core.annot.Gpcrdb.numof_records"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_records</span></code></a>([entity_types])</p></td>
+<td><p>The total number of annotation records.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Gpcrdb.numof_references" title="pypath.core.annot.Gpcrdb.numof_references"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_references</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Gpcrdb.process" title="pypath.core.annot.Gpcrdb.process"><code class="xref py py-obj docutils literal notranslate"><span class="pre">process</span></code></a>()</p></td>
+<td><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">proportion</span></code>(other)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Gpcrdb.reload" title="pypath.core.annot.Gpcrdb.reload"><code class="xref py py-obj docutils literal notranslate"><span class="pre">reload</span></code></a>()</p></td>
+<td><p>Reloads the object from the module level.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">save_to_pickle</span></code>(pickle_file)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Gpcrdb.select" title="pypath.core.annot.Gpcrdb.select"><code class="xref py py-obj docutils literal notranslate"><span class="pre">select</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Gpcrdb.set_method" title="pypath.core.annot.Gpcrdb.set_method"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_method</span></code></a>()</p></td>
+<td><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if necessary.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Gpcrdb.set_reference_set" title="pypath.core.annot.Gpcrdb.set_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_reference_set</span></code></a>()</p></td>
+<td><p>Assigns the reference set to the :py:attr``reference_set`` attribute.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Gpcrdb.show" title="pypath.core.annot.Gpcrdb.show"><code class="xref py py-obj docutils literal notranslate"><span class="pre">show</span></code></a>([method, table_param])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic information from the UniProt datasheets.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Gpcrdb.subset_intersection" title="pypath.core.annot.Gpcrdb.subset_intersection"><code class="xref py py-obj docutils literal notranslate"><span class="pre">subset_intersection</span></code></a>(universe, **kwargs)</p></td>
+<td><p>Calculates the proportion of entities in a subset occuring in the set <code class="docutils literal notranslate"><span class="pre">universe</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Gpcrdb.to_array" title="pypath.core.annot.Gpcrdb.to_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_array</span></code></a>([reference_set, use_fields])</p></td>
+<td><p>Returns an entity vs feature array.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Gpcrdb.to_bool_array" title="pypath.core.annot.Gpcrdb.to_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_bool_array</span></code></a>(reference_set)</p></td>
+<td><p>Returns a presence/absence boolean array for a reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Gpcrdb.to_set" title="pypath.core.annot.Gpcrdb.to_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_set</span></code></a>()</p></td>
+<td><p>Returns the entities present in this annotation resource as a set.</p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Attributes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_fields</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">summary</span></code></p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Gpcrdb.add_complexes_by_inference">
+<span class="sig-name descname"><span class="pre">add_complexes_by_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Gpcrdb.add_complexes_by_inference" title="Link to this definition">§</a></dt>
+<dd><p>Creates complex annotations by in silico inference and adds them
+to this annotation set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Gpcrdb.all_complexes">
+<span class="sig-name descname"><span class="pre">all_complexes</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Gpcrdb.all_complexes" title="Link to this definition">§</a></dt>
+<dd><p>All protein complexes annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Gpcrdb.all_entities">
+<span class="sig-name descname"><span class="pre">all_entities</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Gpcrdb.all_entities" title="Link to this definition">§</a></dt>
+<dd><p>All entities annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Gpcrdb.all_mirnas">
+<span class="sig-name descname"><span class="pre">all_mirnas</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Gpcrdb.all_mirnas" title="Link to this definition">§</a></dt>
+<dd><p>All miRNAs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Gpcrdb.all_proteins">
+<span class="sig-name descname"><span class="pre">all_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Gpcrdb.all_proteins" title="Link to this definition">§</a></dt>
+<dd><p>All UniProt IDs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Gpcrdb.all_refs">
+<span class="sig-name descname"><span class="pre">all_refs</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Gpcrdb.all_refs" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects the references
+across all records. Returns <em>list</em>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Gpcrdb.annotate_complex">
+<span class="sig-name descname"><span class="pre">annotate_complex</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cplex</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Gpcrdb.annotate_complex" title="Link to this definition">§</a></dt>
+<dd><p>Infers annotations for a single complex.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Gpcrdb.browse">
+<span class="sig-name descname"><span class="pre">browse</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">field</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">start</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Gpcrdb.browse" title="Link to this definition">§</a></dt>
+<dd><p>Print gene information as a table.</p>
+<p>Presents information about annotation categories as ascii tables
+printed in the terminal. If one category provided, prints one table.
+If multiple categories provided, prints a table for each of them one
+by one proceeding to the next one once you hit return. If no categories
+provided goes through all levels of the primary category.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>field:</dt><dd><p>The field to browse categories by.</p>
+<ul class="simple">
+<li><p>If None the primary field will be selected.
+If this annotation resource doesn’t have fields, all proteins
+will be presented as one single category.</p></li>
+<li><p>If a string it will be considered a field name and it will
+browse through all levels of this field.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">list</span></code>, set or tuple, it will be considered either a
+<code class="docutils literal notranslate"><span class="pre">list</span></code> of field names or a list of values from the primary
+field. In the former case all combinations of the values of
+the fields will be presented, in the latter case the browsing
+will be limited to the levels of the primary field contained
+in <code class="docutils literal notranslate"><span class="pre">field</span></code>.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">dict</span></code>, keys are supposed to be field names and values
+as list of levels. If any of the values are None, all levels
+from that field will be used.</p></li>
+</ul>
+</dd>
+<dt>start:</dt><dd><p>Start browsing from this category. E.g. if there are 500
+categories and start is 250 it will skip everything before the
+250th.</p>
+</dd>
+<dt>kwargs:</dt><dd><p>Passed to <code class="docutils literal notranslate"><span class="pre">pypath.utils.uniprot.info</span></code>.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Gpcrdb.complex_inference">
+<span class="sig-name descname"><span class="pre">complex_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Gpcrdb.complex_inference" title="Link to this definition">§</a></dt>
+<dd><p>Annotates all complexes in <cite>complexes</cite>, by default in the default
+complex database (existing in the <cite>complex</cite> module or generated
+on demand according to the module’s current settings).</p>
+<dl class="field-list simple">
+<dt class="field-odd">Returns<span class="colon">:</span></dt>
+<dd class="field-odd"><p><ul class="simple">
+<li><p><em>Dict with complexes as keys and sets of annotations as values.</em></p></li>
+<li><p><em>Complexes with no valid information in this annotation resource</em></p></li>
+<li><p><em>won’t be in the dict.</em></p></li>
+</ul>
+</p>
+</dd>
+<dt class="field-even">Parameters<span class="colon">:</span></dt>
+<dd class="field-even"><p><strong>complexes</strong> (<em>iterable</em>) – Iterable yielding complexes.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Gpcrdb.coverage">
+<span class="sig-name descname"><span class="pre">coverage</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">other</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Gpcrdb.coverage" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the coverage of the annotation i.e. the proportion of
+entities having at least one record in this annotation resource
+for an arbitrary set of entities.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Gpcrdb.curation_effort">
+<span class="sig-name descname"><span class="pre">curation_effort</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Gpcrdb.curation_effort" title="Link to this definition">§</a></dt>
+<dd><p>Counts the reference-record pairs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Gpcrdb.get_names">
+<span class="sig-name descname"><span class="pre">get_names</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Gpcrdb.get_names" title="Link to this definition">§</a></dt>
+<dd><p>Returns the list of field names in the records. The annotation
+consists of uniform records and each entity might be annotated
+with one or more records. Each record is a tuple of fields, for
+example <code class="docutils literal notranslate"><span class="pre">('cell_type',</span> <span class="pre">'expression_level',</span> <span class="pre">'score')</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Gpcrdb.get_reference_set">
+<em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">get_reference_set</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">proteins</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">swissprot_only</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Gpcrdb.get_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the reference set i.e. the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Gpcrdb.get_subset">
+<span class="sig-name descname"><span class="pre">get_subset</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Gpcrdb.get_subset" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Gpcrdb.get_subset_bool_array">
+<span class="sig-name descname"><span class="pre">get_subset_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Gpcrdb.get_subset_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a boolean vector with True and False values for each entity
+in the reference set. The values represent presence absence data
+in the simplest case, but by providing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> any kind of matching
+and filtering is possible. <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> are passed to the <code class="docutils literal notranslate"><span class="pre">select</span></code>
+method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Gpcrdb.get_values">
+<span class="sig-name descname"><span class="pre">get_values</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">exclude_none</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Gpcrdb.get_values" title="Link to this definition">§</a></dt>
+<dd><p>Returns the set of all possible values of a field. E.g. if the
+records of this annotation have a field <code class="docutils literal notranslate"><span class="pre">cell_type</span></code> then calling
+this method can tell you that across all records the values of
+this field might be <code class="docutils literal notranslate"><span class="pre">{'macrophage',</span> <span class="pre">'epithelial_cell',</span> <span class="pre">...}</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Gpcrdb.labels">
+<span class="sig-name descname"><span class="pre">labels</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Gpcrdb.labels" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Gpcrdb.load">
+<span class="sig-name descname"><span class="pre">load</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Gpcrdb.load" title="Link to this definition">§</a></dt>
+<dd><p>Loads the annotation data by calling the input method.
+Infers annotations for complexes in the complex database if
+py:attr:<code class="docutils literal notranslate"><span class="pre">infer_complexes</span></code> is True.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Gpcrdb.load_data">
+<span class="sig-name descname"><span class="pre">load_data</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Gpcrdb.load_data" title="Link to this definition">§</a></dt>
+<dd><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Gpcrdb.load_proteins">
+<span class="sig-name descname"><span class="pre">load_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Gpcrdb.load_proteins" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a set of all UniProt IDs to have a base set of the entire
+proteome.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Gpcrdb.make_df">
+<span class="sig-name descname"><span class="pre">make_df</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">rebuild</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Gpcrdb.make_df" title="Link to this definition">§</a></dt>
+<dd><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.
+The data frame will be assigned to :py:attr``df``.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Gpcrdb.numof_entities">
+<span class="sig-name descname"><span class="pre">numof_entities</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Gpcrdb.numof_entities" title="Link to this definition">§</a></dt>
+<dd><p>The number of annotated entities in the resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Gpcrdb.numof_records">
+<span class="sig-name descname"><span class="pre">numof_records</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Gpcrdb.numof_records" title="Link to this definition">§</a></dt>
+<dd><p>The total number of annotation records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Gpcrdb.numof_references">
+<span class="sig-name descname"><span class="pre">numof_references</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Gpcrdb.numof_references" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects and counts the
+references across all records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Gpcrdb.process">
+<span class="sig-name descname"><span class="pre">process</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Gpcrdb.process" title="Link to this definition">§</a></dt>
+<dd><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Gpcrdb.reload">
+<span class="sig-name descname"><span class="pre">reload</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Gpcrdb.reload" title="Link to this definition">§</a></dt>
+<dd><p>Reloads the object from the module level.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Gpcrdb.select">
+<span class="sig-name descname"><span class="pre">select</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Gpcrdb.select" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Gpcrdb.set_method">
+<span class="sig-name descname"><span class="pre">set_method</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Gpcrdb.set_method" title="Link to this definition">§</a></dt>
+<dd><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if
+necessary.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Gpcrdb.set_reference_set">
+<span class="sig-name descname"><span class="pre">set_reference_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Gpcrdb.set_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Assigns the reference set to the :py:attr``reference_set`` attribute.
+The reference set is the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Gpcrdb.show">
+<span class="sig-name descname"><span class="pre">show</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">table_param</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Gpcrdb.show" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic
+information from the UniProt datasheets.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Gpcrdb.subset_intersection">
+<span class="sig-name descname"><span class="pre">subset_intersection</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">universe</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Gpcrdb.subset_intersection" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the proportion of entities in a subset occuring in the
+set <code class="docutils literal notranslate"><span class="pre">universe</span></code>. The subset is selected by passing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> to the
+<code class="docutils literal notranslate"><span class="pre">select</span></code> method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Gpcrdb.to_array">
+<span class="sig-name descname"><span class="pre">to_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_fields</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Gpcrdb.to_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns an entity vs feature array. In case of more complex
+annotations this might be huge.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Gpcrdb.to_bool_array">
+<span class="sig-name descname"><span class="pre">to_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Gpcrdb.to_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a presence/absence boolean array for a reference set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Gpcrdb.to_set">
+<span class="sig-name descname"><span class="pre">to_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Gpcrdb.to_set" title="Link to this definition">§</a></dt>
+<dd><p>Returns the entities present in this annotation resource as a set.</p>
+</dd></dl>
+
+</dd></dl>
+
+</section>
+
+
+                </article>
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+  <section id="pypath-core-annot-guidetopharmacology">
+<h1>pypath.core.annot.GuideToPharmacology<a class="headerlink" href="#pypath-core-annot-guidetopharmacology" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.core.annot.GuideToPharmacology">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.core.annot.</span></span><span class="sig-name descname"><span class="pre">GuideToPharmacology</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">load_sources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#GuideToPharmacology"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.GuideToPharmacology" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <a class="reference internal" href="pypath.core.annot.LigandReceptor.html#pypath.core.annot.LigandReceptor" title="pypath.core.annot.LigandReceptor"><code class="xref py py-class docutils literal notranslate"><span class="pre">LigandReceptor</span></code></a></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.GuideToPharmacology.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">load_sources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#GuideToPharmacology.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.GuideToPharmacology.__init__" title="Link to this definition">§</a></dt>
+<dd><p>Represents annotations for a set of proteins.
+Loads the data from the original resource and provides methods
+to query the annotations.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>name</strong> (<em>str</em>) – A custom name for the annotation resource.</p></li>
+<li><p><strong>ncbi_tax_id</strong> (<em>int</em>) – NCBI Taxonomy identifier.</p></li>
+<li><p><strong>input_method</strong> (<em>callable</em><em>,</em><em>str</em>) – Either a callable or the name of a method in any submodules of
+the <code class="docutils literal notranslate"><span class="pre">pypath.inputs</span></code>  module. Should return a dict with
+UniProt IDs as keys or an object suitable for <code class="docutils literal notranslate"><span class="pre">process_method</span></code>.</p></li>
+<li><p><strong>input_args</strong> (<em>dict</em>) – Arguments for the <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.GuideToPharmacology.__init__" title="pypath.core.annot.GuideToPharmacology.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>([load_sources])</p></td>
+<td><p>Represents annotations for a set of proteins.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.GuideToPharmacology.add_complexes_by_inference" title="pypath.core.annot.GuideToPharmacology.add_complexes_by_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">add_complexes_by_inference</span></code></a>([complexes])</p></td>
+<td><p>Creates complex annotations by in silico inference and adds them to this annotation set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.GuideToPharmacology.all_complexes" title="pypath.core.annot.GuideToPharmacology.all_complexes"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_complexes</span></code></a>()</p></td>
+<td><p>All protein complexes annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.GuideToPharmacology.all_entities" title="pypath.core.annot.GuideToPharmacology.all_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_entities</span></code></a>([entity_types])</p></td>
+<td><p>All entities annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.GuideToPharmacology.all_mirnas" title="pypath.core.annot.GuideToPharmacology.all_mirnas"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_mirnas</span></code></a>()</p></td>
+<td><p>All miRNAs annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.GuideToPharmacology.all_proteins" title="pypath.core.annot.GuideToPharmacology.all_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_proteins</span></code></a>()</p></td>
+<td><p>All UniProt IDs annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.GuideToPharmacology.all_refs" title="pypath.core.annot.GuideToPharmacology.all_refs"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_refs</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.GuideToPharmacology.annotate_complex" title="pypath.core.annot.GuideToPharmacology.annotate_complex"><code class="xref py py-obj docutils literal notranslate"><span class="pre">annotate_complex</span></code></a>(cplex)</p></td>
+<td><p>Infers annotations for a single complex.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.GuideToPharmacology.browse" title="pypath.core.annot.GuideToPharmacology.browse"><code class="xref py py-obj docutils literal notranslate"><span class="pre">browse</span></code></a>([field, start])</p></td>
+<td><p>Print gene information as a table.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.GuideToPharmacology.complex_inference" title="pypath.core.annot.GuideToPharmacology.complex_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">complex_inference</span></code></a>([complexes])</p></td>
+<td><p>Annotates all complexes in <cite>complexes</cite>, by default in the default complex database (existing in the <cite>complex</cite> module or generated on demand according to the module's current settings).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.GuideToPharmacology.coverage" title="pypath.core.annot.GuideToPharmacology.coverage"><code class="xref py py-obj docutils literal notranslate"><span class="pre">coverage</span></code></a>(other)</p></td>
+<td><p>Calculates the coverage of the annotation i.e. the proportion of entities having at least one record in this annotation resource for an arbitrary set of entities.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.GuideToPharmacology.curation_effort" title="pypath.core.annot.GuideToPharmacology.curation_effort"><code class="xref py py-obj docutils literal notranslate"><span class="pre">curation_effort</span></code></a>()</p></td>
+<td><p>Counts the reference-record pairs.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">from_dump</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_entity_type</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.GuideToPharmacology.get_names" title="pypath.core.annot.GuideToPharmacology.get_names"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_names</span></code></a>()</p></td>
+<td><p>Returns the list of field names in the records.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.GuideToPharmacology.get_reference_set" title="pypath.core.annot.GuideToPharmacology.get_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_reference_set</span></code></a>([proteins, complexes, ...])</p></td>
+<td><p>Retrieves the reference set i.e. the set of all entities which potentially have annotation in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.GuideToPharmacology.get_subset" title="pypath.core.annot.GuideToPharmacology.get_subset"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.GuideToPharmacology.get_subset_bool_array" title="pypath.core.annot.GuideToPharmacology.get_subset_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset_bool_array</span></code></a>([reference_set])</p></td>
+<td><p>Returns a boolean vector with True and False values for each entity in the reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.GuideToPharmacology.get_values" title="pypath.core.annot.GuideToPharmacology.get_values"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_values</span></code></a>(name[, exclude_none])</p></td>
+<td><p>Returns the set of all possible values of a field.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_complex</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_mirna</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_protein</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.GuideToPharmacology.labels" title="pypath.core.annot.GuideToPharmacology.labels"><code class="xref py py-obj docutils literal notranslate"><span class="pre">labels</span></code></a>([method])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.GuideToPharmacology.load" title="pypath.core.annot.GuideToPharmacology.load"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load</span></code></a>()</p></td>
+<td><p>Loads the annotation data by calling the input method.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.GuideToPharmacology.load_data" title="pypath.core.annot.GuideToPharmacology.load_data"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_data</span></code></a>()</p></td>
+<td><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.GuideToPharmacology.load_proteins" title="pypath.core.annot.GuideToPharmacology.load_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_proteins</span></code></a>()</p></td>
+<td><p>Retrieves a set of all UniProt IDs to have a base set of the entire proteome.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.GuideToPharmacology.make_df" title="pypath.core.annot.GuideToPharmacology.make_df"><code class="xref py py-obj docutils literal notranslate"><span class="pre">make_df</span></code></a>([rebuild])</p></td>
+<td><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complex_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.GuideToPharmacology.numof_entities" title="pypath.core.annot.GuideToPharmacology.numof_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_entities</span></code></a>()</p></td>
+<td><p>The number of annotated entities in the resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirna_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirnas</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_protein_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_proteins</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.GuideToPharmacology.numof_records" title="pypath.core.annot.GuideToPharmacology.numof_records"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_records</span></code></a>([entity_types])</p></td>
+<td><p>The total number of annotation records.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.GuideToPharmacology.numof_references" title="pypath.core.annot.GuideToPharmacology.numof_references"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_references</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.GuideToPharmacology.process" title="pypath.core.annot.GuideToPharmacology.process"><code class="xref py py-obj docutils literal notranslate"><span class="pre">process</span></code></a>()</p></td>
+<td><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">proportion</span></code>(other)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.GuideToPharmacology.reload" title="pypath.core.annot.GuideToPharmacology.reload"><code class="xref py py-obj docutils literal notranslate"><span class="pre">reload</span></code></a>()</p></td>
+<td><p>Reloads the object from the module level.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">save_to_pickle</span></code>(pickle_file)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.GuideToPharmacology.select" title="pypath.core.annot.GuideToPharmacology.select"><code class="xref py py-obj docutils literal notranslate"><span class="pre">select</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.GuideToPharmacology.set_method" title="pypath.core.annot.GuideToPharmacology.set_method"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_method</span></code></a>()</p></td>
+<td><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if necessary.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.GuideToPharmacology.set_reference_set" title="pypath.core.annot.GuideToPharmacology.set_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_reference_set</span></code></a>()</p></td>
+<td><p>Assigns the reference set to the :py:attr``reference_set`` attribute.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.GuideToPharmacology.show" title="pypath.core.annot.GuideToPharmacology.show"><code class="xref py py-obj docutils literal notranslate"><span class="pre">show</span></code></a>([method, table_param])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic information from the UniProt datasheets.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.GuideToPharmacology.subset_intersection" title="pypath.core.annot.GuideToPharmacology.subset_intersection"><code class="xref py py-obj docutils literal notranslate"><span class="pre">subset_intersection</span></code></a>(universe, **kwargs)</p></td>
+<td><p>Calculates the proportion of entities in a subset occuring in the set <code class="docutils literal notranslate"><span class="pre">universe</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.GuideToPharmacology.to_array" title="pypath.core.annot.GuideToPharmacology.to_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_array</span></code></a>([reference_set, use_fields])</p></td>
+<td><p>Returns an entity vs feature array.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.GuideToPharmacology.to_bool_array" title="pypath.core.annot.GuideToPharmacology.to_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_bool_array</span></code></a>(reference_set)</p></td>
+<td><p>Returns a presence/absence boolean array for a reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.GuideToPharmacology.to_set" title="pypath.core.annot.GuideToPharmacology.to_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_set</span></code></a>()</p></td>
+<td><p>Returns the entities present in this annotation resource as a set.</p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Attributes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_fields</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">summary</span></code></p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.GuideToPharmacology.add_complexes_by_inference">
+<span class="sig-name descname"><span class="pre">add_complexes_by_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.GuideToPharmacology.add_complexes_by_inference" title="Link to this definition">§</a></dt>
+<dd><p>Creates complex annotations by in silico inference and adds them
+to this annotation set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.GuideToPharmacology.all_complexes">
+<span class="sig-name descname"><span class="pre">all_complexes</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.GuideToPharmacology.all_complexes" title="Link to this definition">§</a></dt>
+<dd><p>All protein complexes annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.GuideToPharmacology.all_entities">
+<span class="sig-name descname"><span class="pre">all_entities</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.GuideToPharmacology.all_entities" title="Link to this definition">§</a></dt>
+<dd><p>All entities annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.GuideToPharmacology.all_mirnas">
+<span class="sig-name descname"><span class="pre">all_mirnas</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.GuideToPharmacology.all_mirnas" title="Link to this definition">§</a></dt>
+<dd><p>All miRNAs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.GuideToPharmacology.all_proteins">
+<span class="sig-name descname"><span class="pre">all_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.GuideToPharmacology.all_proteins" title="Link to this definition">§</a></dt>
+<dd><p>All UniProt IDs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.GuideToPharmacology.all_refs">
+<span class="sig-name descname"><span class="pre">all_refs</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.GuideToPharmacology.all_refs" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects the references
+across all records. Returns <em>list</em>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.GuideToPharmacology.annotate_complex">
+<span class="sig-name descname"><span class="pre">annotate_complex</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cplex</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.GuideToPharmacology.annotate_complex" title="Link to this definition">§</a></dt>
+<dd><p>Infers annotations for a single complex.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.GuideToPharmacology.browse">
+<span class="sig-name descname"><span class="pre">browse</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">field</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">start</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.GuideToPharmacology.browse" title="Link to this definition">§</a></dt>
+<dd><p>Print gene information as a table.</p>
+<p>Presents information about annotation categories as ascii tables
+printed in the terminal. If one category provided, prints one table.
+If multiple categories provided, prints a table for each of them one
+by one proceeding to the next one once you hit return. If no categories
+provided goes through all levels of the primary category.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>field:</dt><dd><p>The field to browse categories by.</p>
+<ul class="simple">
+<li><p>If None the primary field will be selected.
+If this annotation resource doesn’t have fields, all proteins
+will be presented as one single category.</p></li>
+<li><p>If a string it will be considered a field name and it will
+browse through all levels of this field.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">list</span></code>, set or tuple, it will be considered either a
+<code class="docutils literal notranslate"><span class="pre">list</span></code> of field names or a list of values from the primary
+field. In the former case all combinations of the values of
+the fields will be presented, in the latter case the browsing
+will be limited to the levels of the primary field contained
+in <code class="docutils literal notranslate"><span class="pre">field</span></code>.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">dict</span></code>, keys are supposed to be field names and values
+as list of levels. If any of the values are None, all levels
+from that field will be used.</p></li>
+</ul>
+</dd>
+<dt>start:</dt><dd><p>Start browsing from this category. E.g. if there are 500
+categories and start is 250 it will skip everything before the
+250th.</p>
+</dd>
+<dt>kwargs:</dt><dd><p>Passed to <code class="docutils literal notranslate"><span class="pre">pypath.utils.uniprot.info</span></code>.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.GuideToPharmacology.complex_inference">
+<span class="sig-name descname"><span class="pre">complex_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.GuideToPharmacology.complex_inference" title="Link to this definition">§</a></dt>
+<dd><p>Annotates all complexes in <cite>complexes</cite>, by default in the default
+complex database (existing in the <cite>complex</cite> module or generated
+on demand according to the module’s current settings).</p>
+<dl class="field-list simple">
+<dt class="field-odd">Returns<span class="colon">:</span></dt>
+<dd class="field-odd"><p><ul class="simple">
+<li><p><em>Dict with complexes as keys and sets of annotations as values.</em></p></li>
+<li><p><em>Complexes with no valid information in this annotation resource</em></p></li>
+<li><p><em>won’t be in the dict.</em></p></li>
+</ul>
+</p>
+</dd>
+<dt class="field-even">Parameters<span class="colon">:</span></dt>
+<dd class="field-even"><p><strong>complexes</strong> (<em>iterable</em>) – Iterable yielding complexes.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.GuideToPharmacology.coverage">
+<span class="sig-name descname"><span class="pre">coverage</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">other</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.GuideToPharmacology.coverage" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the coverage of the annotation i.e. the proportion of
+entities having at least one record in this annotation resource
+for an arbitrary set of entities.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.GuideToPharmacology.curation_effort">
+<span class="sig-name descname"><span class="pre">curation_effort</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.GuideToPharmacology.curation_effort" title="Link to this definition">§</a></dt>
+<dd><p>Counts the reference-record pairs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.GuideToPharmacology.get_names">
+<span class="sig-name descname"><span class="pre">get_names</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.GuideToPharmacology.get_names" title="Link to this definition">§</a></dt>
+<dd><p>Returns the list of field names in the records. The annotation
+consists of uniform records and each entity might be annotated
+with one or more records. Each record is a tuple of fields, for
+example <code class="docutils literal notranslate"><span class="pre">('cell_type',</span> <span class="pre">'expression_level',</span> <span class="pre">'score')</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.GuideToPharmacology.get_reference_set">
+<em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">get_reference_set</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">proteins</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">swissprot_only</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.GuideToPharmacology.get_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the reference set i.e. the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.GuideToPharmacology.get_subset">
+<span class="sig-name descname"><span class="pre">get_subset</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.GuideToPharmacology.get_subset" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.GuideToPharmacology.get_subset_bool_array">
+<span class="sig-name descname"><span class="pre">get_subset_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.GuideToPharmacology.get_subset_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a boolean vector with True and False values for each entity
+in the reference set. The values represent presence absence data
+in the simplest case, but by providing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> any kind of matching
+and filtering is possible. <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> are passed to the <code class="docutils literal notranslate"><span class="pre">select</span></code>
+method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.GuideToPharmacology.get_values">
+<span class="sig-name descname"><span class="pre">get_values</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">exclude_none</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.GuideToPharmacology.get_values" title="Link to this definition">§</a></dt>
+<dd><p>Returns the set of all possible values of a field. E.g. if the
+records of this annotation have a field <code class="docutils literal notranslate"><span class="pre">cell_type</span></code> then calling
+this method can tell you that across all records the values of
+this field might be <code class="docutils literal notranslate"><span class="pre">{'macrophage',</span> <span class="pre">'epithelial_cell',</span> <span class="pre">...}</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.GuideToPharmacology.labels">
+<span class="sig-name descname"><span class="pre">labels</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.GuideToPharmacology.labels" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.GuideToPharmacology.load">
+<span class="sig-name descname"><span class="pre">load</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.GuideToPharmacology.load" title="Link to this definition">§</a></dt>
+<dd><p>Loads the annotation data by calling the input method.
+Infers annotations for complexes in the complex database if
+py:attr:<code class="docutils literal notranslate"><span class="pre">infer_complexes</span></code> is True.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.GuideToPharmacology.load_data">
+<span class="sig-name descname"><span class="pre">load_data</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.GuideToPharmacology.load_data" title="Link to this definition">§</a></dt>
+<dd><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.GuideToPharmacology.load_proteins">
+<span class="sig-name descname"><span class="pre">load_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.GuideToPharmacology.load_proteins" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a set of all UniProt IDs to have a base set of the entire
+proteome.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.GuideToPharmacology.make_df">
+<span class="sig-name descname"><span class="pre">make_df</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">rebuild</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.GuideToPharmacology.make_df" title="Link to this definition">§</a></dt>
+<dd><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.
+The data frame will be assigned to :py:attr``df``.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.GuideToPharmacology.numof_entities">
+<span class="sig-name descname"><span class="pre">numof_entities</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.GuideToPharmacology.numof_entities" title="Link to this definition">§</a></dt>
+<dd><p>The number of annotated entities in the resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.GuideToPharmacology.numof_records">
+<span class="sig-name descname"><span class="pre">numof_records</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.GuideToPharmacology.numof_records" title="Link to this definition">§</a></dt>
+<dd><p>The total number of annotation records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.GuideToPharmacology.numof_references">
+<span class="sig-name descname"><span class="pre">numof_references</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.GuideToPharmacology.numof_references" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects and counts the
+references across all records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.GuideToPharmacology.process">
+<span class="sig-name descname"><span class="pre">process</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.GuideToPharmacology.process" title="Link to this definition">§</a></dt>
+<dd><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.GuideToPharmacology.reload">
+<span class="sig-name descname"><span class="pre">reload</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.GuideToPharmacology.reload" title="Link to this definition">§</a></dt>
+<dd><p>Reloads the object from the module level.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.GuideToPharmacology.select">
+<span class="sig-name descname"><span class="pre">select</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.GuideToPharmacology.select" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.GuideToPharmacology.set_method">
+<span class="sig-name descname"><span class="pre">set_method</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.GuideToPharmacology.set_method" title="Link to this definition">§</a></dt>
+<dd><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if
+necessary.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.GuideToPharmacology.set_reference_set">
+<span class="sig-name descname"><span class="pre">set_reference_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.GuideToPharmacology.set_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Assigns the reference set to the :py:attr``reference_set`` attribute.
+The reference set is the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.GuideToPharmacology.show">
+<span class="sig-name descname"><span class="pre">show</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">table_param</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.GuideToPharmacology.show" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic
+information from the UniProt datasheets.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.GuideToPharmacology.subset_intersection">
+<span class="sig-name descname"><span class="pre">subset_intersection</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">universe</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.GuideToPharmacology.subset_intersection" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the proportion of entities in a subset occuring in the
+set <code class="docutils literal notranslate"><span class="pre">universe</span></code>. The subset is selected by passing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> to the
+<code class="docutils literal notranslate"><span class="pre">select</span></code> method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.GuideToPharmacology.to_array">
+<span class="sig-name descname"><span class="pre">to_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_fields</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.GuideToPharmacology.to_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns an entity vs feature array. In case of more complex
+annotations this might be huge.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.GuideToPharmacology.to_bool_array">
+<span class="sig-name descname"><span class="pre">to_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.GuideToPharmacology.to_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a presence/absence boolean array for a reference set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.GuideToPharmacology.to_set">
+<span class="sig-name descname"><span class="pre">to_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.GuideToPharmacology.to_set" title="Link to this definition">§</a></dt>
+<dd><p>Returns the entities present in this annotation resource as a set.</p>
+</dd></dl>
+
+</dd></dl>
+
+</section>
+
+
+                </article>
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+  <section id="pypath-core-annot-hpo">
+<h1>pypath.core.annot.HPO<a class="headerlink" href="#pypath-core-annot-hpo" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.core.annot.HPO">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.core.annot.</span></span><span class="sig-name descname"><span class="pre">HPO</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#HPO"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.HPO" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <a class="reference internal" href="pypath.core.annot.AnnotationBase.html#pypath.core.annot.AnnotationBase" title="pypath.core.annot.AnnotationBase"><code class="xref py py-class docutils literal notranslate"><span class="pre">AnnotationBase</span></code></a></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HPO.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#HPO.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.HPO.__init__" title="Link to this definition">§</a></dt>
+<dd><p>HPO Gene Annotations from the HPO database.</p>
+</dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.HPO.__init__" title="pypath.core.annot.HPO.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>(**kwargs)</p></td>
+<td><p>HPO Gene Annotations from the HPO database.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.HPO.add_complexes_by_inference" title="pypath.core.annot.HPO.add_complexes_by_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">add_complexes_by_inference</span></code></a>([complexes])</p></td>
+<td><p>Creates complex annotations by in silico inference and adds them to this annotation set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.HPO.all_complexes" title="pypath.core.annot.HPO.all_complexes"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_complexes</span></code></a>()</p></td>
+<td><p>All protein complexes annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.HPO.all_entities" title="pypath.core.annot.HPO.all_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_entities</span></code></a>([entity_types])</p></td>
+<td><p>All entities annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.HPO.all_mirnas" title="pypath.core.annot.HPO.all_mirnas"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_mirnas</span></code></a>()</p></td>
+<td><p>All miRNAs annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.HPO.all_proteins" title="pypath.core.annot.HPO.all_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_proteins</span></code></a>()</p></td>
+<td><p>All UniProt IDs annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.HPO.all_refs" title="pypath.core.annot.HPO.all_refs"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_refs</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.HPO.annotate_complex" title="pypath.core.annot.HPO.annotate_complex"><code class="xref py py-obj docutils literal notranslate"><span class="pre">annotate_complex</span></code></a>(cplex)</p></td>
+<td><p>Infers annotations for a single complex.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.HPO.browse" title="pypath.core.annot.HPO.browse"><code class="xref py py-obj docutils literal notranslate"><span class="pre">browse</span></code></a>([field, start])</p></td>
+<td><p>Print gene information as a table.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.HPO.complex_inference" title="pypath.core.annot.HPO.complex_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">complex_inference</span></code></a>([complexes])</p></td>
+<td><p>Annotates all complexes in <cite>complexes</cite>, by default in the default complex database (existing in the <cite>complex</cite> module or generated on demand according to the module's current settings).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.HPO.coverage" title="pypath.core.annot.HPO.coverage"><code class="xref py py-obj docutils literal notranslate"><span class="pre">coverage</span></code></a>(other)</p></td>
+<td><p>Calculates the coverage of the annotation i.e. the proportion of entities having at least one record in this annotation resource for an arbitrary set of entities.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.HPO.curation_effort" title="pypath.core.annot.HPO.curation_effort"><code class="xref py py-obj docutils literal notranslate"><span class="pre">curation_effort</span></code></a>()</p></td>
+<td><p>Counts the reference-record pairs.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">from_dump</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_entity_type</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.HPO.get_names" title="pypath.core.annot.HPO.get_names"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_names</span></code></a>()</p></td>
+<td><p>Returns the list of field names in the records.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.HPO.get_reference_set" title="pypath.core.annot.HPO.get_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_reference_set</span></code></a>([proteins, complexes, ...])</p></td>
+<td><p>Retrieves the reference set i.e. the set of all entities which potentially have annotation in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.HPO.get_subset" title="pypath.core.annot.HPO.get_subset"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.HPO.get_subset_bool_array" title="pypath.core.annot.HPO.get_subset_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset_bool_array</span></code></a>([reference_set])</p></td>
+<td><p>Returns a boolean vector with True and False values for each entity in the reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.HPO.get_values" title="pypath.core.annot.HPO.get_values"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_values</span></code></a>(name[, exclude_none])</p></td>
+<td><p>Returns the set of all possible values of a field.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_complex</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_mirna</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_protein</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.HPO.labels" title="pypath.core.annot.HPO.labels"><code class="xref py py-obj docutils literal notranslate"><span class="pre">labels</span></code></a>([method])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.HPO.load" title="pypath.core.annot.HPO.load"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load</span></code></a>()</p></td>
+<td><p>Loads the annotation data by calling the input method.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.HPO.load_data" title="pypath.core.annot.HPO.load_data"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_data</span></code></a>()</p></td>
+<td><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.HPO.load_proteins" title="pypath.core.annot.HPO.load_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_proteins</span></code></a>()</p></td>
+<td><p>Retrieves a set of all UniProt IDs to have a base set of the entire proteome.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.HPO.make_df" title="pypath.core.annot.HPO.make_df"><code class="xref py py-obj docutils literal notranslate"><span class="pre">make_df</span></code></a>([rebuild])</p></td>
+<td><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complex_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.HPO.numof_entities" title="pypath.core.annot.HPO.numof_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_entities</span></code></a>()</p></td>
+<td><p>The number of annotated entities in the resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirna_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirnas</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_protein_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_proteins</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.HPO.numof_records" title="pypath.core.annot.HPO.numof_records"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_records</span></code></a>([entity_types])</p></td>
+<td><p>The total number of annotation records.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.HPO.numof_references" title="pypath.core.annot.HPO.numof_references"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_references</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.HPO.process" title="pypath.core.annot.HPO.process"><code class="xref py py-obj docutils literal notranslate"><span class="pre">process</span></code></a>()</p></td>
+<td><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">proportion</span></code>(other)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.HPO.reload" title="pypath.core.annot.HPO.reload"><code class="xref py py-obj docutils literal notranslate"><span class="pre">reload</span></code></a>()</p></td>
+<td><p>Reloads the object from the module level.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">save_to_pickle</span></code>(pickle_file)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.HPO.select" title="pypath.core.annot.HPO.select"><code class="xref py py-obj docutils literal notranslate"><span class="pre">select</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.HPO.set_method" title="pypath.core.annot.HPO.set_method"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_method</span></code></a>()</p></td>
+<td><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if necessary.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.HPO.set_reference_set" title="pypath.core.annot.HPO.set_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_reference_set</span></code></a>()</p></td>
+<td><p>Assigns the reference set to the :py:attr``reference_set`` attribute.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.HPO.show" title="pypath.core.annot.HPO.show"><code class="xref py py-obj docutils literal notranslate"><span class="pre">show</span></code></a>([method, table_param])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic information from the UniProt datasheets.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.HPO.subset_intersection" title="pypath.core.annot.HPO.subset_intersection"><code class="xref py py-obj docutils literal notranslate"><span class="pre">subset_intersection</span></code></a>(universe, **kwargs)</p></td>
+<td><p>Calculates the proportion of entities in a subset occuring in the set <code class="docutils literal notranslate"><span class="pre">universe</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.HPO.to_array" title="pypath.core.annot.HPO.to_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_array</span></code></a>([reference_set, use_fields])</p></td>
+<td><p>Returns an entity vs feature array.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.HPO.to_bool_array" title="pypath.core.annot.HPO.to_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_bool_array</span></code></a>(reference_set)</p></td>
+<td><p>Returns a presence/absence boolean array for a reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.HPO.to_set" title="pypath.core.annot.HPO.to_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_set</span></code></a>()</p></td>
+<td><p>Returns the entities present in this annotation resource as a set.</p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Attributes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_fields</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">summary</span></code></p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HPO.add_complexes_by_inference">
+<span class="sig-name descname"><span class="pre">add_complexes_by_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HPO.add_complexes_by_inference" title="Link to this definition">§</a></dt>
+<dd><p>Creates complex annotations by in silico inference and adds them
+to this annotation set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HPO.all_complexes">
+<span class="sig-name descname"><span class="pre">all_complexes</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HPO.all_complexes" title="Link to this definition">§</a></dt>
+<dd><p>All protein complexes annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HPO.all_entities">
+<span class="sig-name descname"><span class="pre">all_entities</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HPO.all_entities" title="Link to this definition">§</a></dt>
+<dd><p>All entities annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HPO.all_mirnas">
+<span class="sig-name descname"><span class="pre">all_mirnas</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HPO.all_mirnas" title="Link to this definition">§</a></dt>
+<dd><p>All miRNAs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HPO.all_proteins">
+<span class="sig-name descname"><span class="pre">all_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HPO.all_proteins" title="Link to this definition">§</a></dt>
+<dd><p>All UniProt IDs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HPO.all_refs">
+<span class="sig-name descname"><span class="pre">all_refs</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HPO.all_refs" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects the references
+across all records. Returns <em>list</em>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HPO.annotate_complex">
+<span class="sig-name descname"><span class="pre">annotate_complex</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cplex</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HPO.annotate_complex" title="Link to this definition">§</a></dt>
+<dd><p>Infers annotations for a single complex.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HPO.browse">
+<span class="sig-name descname"><span class="pre">browse</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">field</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">start</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HPO.browse" title="Link to this definition">§</a></dt>
+<dd><p>Print gene information as a table.</p>
+<p>Presents information about annotation categories as ascii tables
+printed in the terminal. If one category provided, prints one table.
+If multiple categories provided, prints a table for each of them one
+by one proceeding to the next one once you hit return. If no categories
+provided goes through all levels of the primary category.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>field:</dt><dd><p>The field to browse categories by.</p>
+<ul class="simple">
+<li><p>If None the primary field will be selected.
+If this annotation resource doesn’t have fields, all proteins
+will be presented as one single category.</p></li>
+<li><p>If a string it will be considered a field name and it will
+browse through all levels of this field.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">list</span></code>, set or tuple, it will be considered either a
+<code class="docutils literal notranslate"><span class="pre">list</span></code> of field names or a list of values from the primary
+field. In the former case all combinations of the values of
+the fields will be presented, in the latter case the browsing
+will be limited to the levels of the primary field contained
+in <code class="docutils literal notranslate"><span class="pre">field</span></code>.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">dict</span></code>, keys are supposed to be field names and values
+as list of levels. If any of the values are None, all levels
+from that field will be used.</p></li>
+</ul>
+</dd>
+<dt>start:</dt><dd><p>Start browsing from this category. E.g. if there are 500
+categories and start is 250 it will skip everything before the
+250th.</p>
+</dd>
+<dt>kwargs:</dt><dd><p>Passed to <code class="docutils literal notranslate"><span class="pre">pypath.utils.uniprot.info</span></code>.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HPO.complex_inference">
+<span class="sig-name descname"><span class="pre">complex_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HPO.complex_inference" title="Link to this definition">§</a></dt>
+<dd><p>Annotates all complexes in <cite>complexes</cite>, by default in the default
+complex database (existing in the <cite>complex</cite> module or generated
+on demand according to the module’s current settings).</p>
+<dl class="field-list simple">
+<dt class="field-odd">Returns<span class="colon">:</span></dt>
+<dd class="field-odd"><p><ul class="simple">
+<li><p><em>Dict with complexes as keys and sets of annotations as values.</em></p></li>
+<li><p><em>Complexes with no valid information in this annotation resource</em></p></li>
+<li><p><em>won’t be in the dict.</em></p></li>
+</ul>
+</p>
+</dd>
+<dt class="field-even">Parameters<span class="colon">:</span></dt>
+<dd class="field-even"><p><strong>complexes</strong> (<em>iterable</em>) – Iterable yielding complexes.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HPO.coverage">
+<span class="sig-name descname"><span class="pre">coverage</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">other</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HPO.coverage" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the coverage of the annotation i.e. the proportion of
+entities having at least one record in this annotation resource
+for an arbitrary set of entities.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HPO.curation_effort">
+<span class="sig-name descname"><span class="pre">curation_effort</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HPO.curation_effort" title="Link to this definition">§</a></dt>
+<dd><p>Counts the reference-record pairs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HPO.get_names">
+<span class="sig-name descname"><span class="pre">get_names</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HPO.get_names" title="Link to this definition">§</a></dt>
+<dd><p>Returns the list of field names in the records. The annotation
+consists of uniform records and each entity might be annotated
+with one or more records. Each record is a tuple of fields, for
+example <code class="docutils literal notranslate"><span class="pre">('cell_type',</span> <span class="pre">'expression_level',</span> <span class="pre">'score')</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HPO.get_reference_set">
+<em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">get_reference_set</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">proteins</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">swissprot_only</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HPO.get_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the reference set i.e. the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HPO.get_subset">
+<span class="sig-name descname"><span class="pre">get_subset</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HPO.get_subset" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HPO.get_subset_bool_array">
+<span class="sig-name descname"><span class="pre">get_subset_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HPO.get_subset_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a boolean vector with True and False values for each entity
+in the reference set. The values represent presence absence data
+in the simplest case, but by providing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> any kind of matching
+and filtering is possible. <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> are passed to the <code class="docutils literal notranslate"><span class="pre">select</span></code>
+method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HPO.get_values">
+<span class="sig-name descname"><span class="pre">get_values</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">exclude_none</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HPO.get_values" title="Link to this definition">§</a></dt>
+<dd><p>Returns the set of all possible values of a field. E.g. if the
+records of this annotation have a field <code class="docutils literal notranslate"><span class="pre">cell_type</span></code> then calling
+this method can tell you that across all records the values of
+this field might be <code class="docutils literal notranslate"><span class="pre">{'macrophage',</span> <span class="pre">'epithelial_cell',</span> <span class="pre">...}</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HPO.labels">
+<span class="sig-name descname"><span class="pre">labels</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HPO.labels" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HPO.load">
+<span class="sig-name descname"><span class="pre">load</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HPO.load" title="Link to this definition">§</a></dt>
+<dd><p>Loads the annotation data by calling the input method.
+Infers annotations for complexes in the complex database if
+py:attr:<code class="docutils literal notranslate"><span class="pre">infer_complexes</span></code> is True.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HPO.load_data">
+<span class="sig-name descname"><span class="pre">load_data</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HPO.load_data" title="Link to this definition">§</a></dt>
+<dd><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HPO.load_proteins">
+<span class="sig-name descname"><span class="pre">load_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HPO.load_proteins" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a set of all UniProt IDs to have a base set of the entire
+proteome.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HPO.make_df">
+<span class="sig-name descname"><span class="pre">make_df</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">rebuild</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HPO.make_df" title="Link to this definition">§</a></dt>
+<dd><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.
+The data frame will be assigned to :py:attr``df``.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HPO.numof_entities">
+<span class="sig-name descname"><span class="pre">numof_entities</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HPO.numof_entities" title="Link to this definition">§</a></dt>
+<dd><p>The number of annotated entities in the resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HPO.numof_records">
+<span class="sig-name descname"><span class="pre">numof_records</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HPO.numof_records" title="Link to this definition">§</a></dt>
+<dd><p>The total number of annotation records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HPO.numof_references">
+<span class="sig-name descname"><span class="pre">numof_references</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HPO.numof_references" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects and counts the
+references across all records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HPO.process">
+<span class="sig-name descname"><span class="pre">process</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HPO.process" title="Link to this definition">§</a></dt>
+<dd><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HPO.reload">
+<span class="sig-name descname"><span class="pre">reload</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HPO.reload" title="Link to this definition">§</a></dt>
+<dd><p>Reloads the object from the module level.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HPO.select">
+<span class="sig-name descname"><span class="pre">select</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HPO.select" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HPO.set_method">
+<span class="sig-name descname"><span class="pre">set_method</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HPO.set_method" title="Link to this definition">§</a></dt>
+<dd><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if
+necessary.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HPO.set_reference_set">
+<span class="sig-name descname"><span class="pre">set_reference_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HPO.set_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Assigns the reference set to the :py:attr``reference_set`` attribute.
+The reference set is the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HPO.show">
+<span class="sig-name descname"><span class="pre">show</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">table_param</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HPO.show" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic
+information from the UniProt datasheets.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HPO.subset_intersection">
+<span class="sig-name descname"><span class="pre">subset_intersection</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">universe</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HPO.subset_intersection" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the proportion of entities in a subset occuring in the
+set <code class="docutils literal notranslate"><span class="pre">universe</span></code>. The subset is selected by passing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> to the
+<code class="docutils literal notranslate"><span class="pre">select</span></code> method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HPO.to_array">
+<span class="sig-name descname"><span class="pre">to_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_fields</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HPO.to_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns an entity vs feature array. In case of more complex
+annotations this might be huge.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HPO.to_bool_array">
+<span class="sig-name descname"><span class="pre">to_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HPO.to_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a presence/absence boolean array for a reference set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HPO.to_set">
+<span class="sig-name descname"><span class="pre">to_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HPO.to_set" title="Link to this definition">§</a></dt>
+<dd><p>Returns the entities present in this annotation resource as a set.</p>
+</dd></dl>
+
+</dd></dl>
+
+</section>
+
+
+                </article>
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+  <section id="pypath-core-annot-hgnc">
+<h1>pypath.core.annot.Hgnc<a class="headerlink" href="#pypath-core-annot-hgnc" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.core.annot.Hgnc">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.core.annot.</span></span><span class="sig-name descname"><span class="pre">Hgnc</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#Hgnc"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.Hgnc" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <a class="reference internal" href="pypath.core.annot.AnnotationBase.html#pypath.core.annot.AnnotationBase" title="pypath.core.annot.AnnotationBase"><code class="xref py py-class docutils literal notranslate"><span class="pre">AnnotationBase</span></code></a></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Hgnc.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#Hgnc.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.Hgnc.__init__" title="Link to this definition">§</a></dt>
+<dd><p>Represents annotations for a set of proteins.
+Loads the data from the original resource and provides methods
+to query the annotations.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>name</strong> (<em>str</em>) – A custom name for the annotation resource.</p></li>
+<li><p><strong>ncbi_tax_id</strong> (<em>int</em>) – NCBI Taxonomy identifier.</p></li>
+<li><p><strong>input_method</strong> (<em>callable</em><em>,</em><em>str</em>) – Either a callable or the name of a method in any submodules of
+the <code class="docutils literal notranslate"><span class="pre">pypath.inputs</span></code>  module. Should return a dict with
+UniProt IDs as keys or an object suitable for <code class="docutils literal notranslate"><span class="pre">process_method</span></code>.</p></li>
+<li><p><strong>input_args</strong> (<em>dict</em>) – Arguments for the <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Hgnc.__init__" title="pypath.core.annot.Hgnc.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>(**kwargs)</p></td>
+<td><p>Represents annotations for a set of proteins.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Hgnc.add_complexes_by_inference" title="pypath.core.annot.Hgnc.add_complexes_by_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">add_complexes_by_inference</span></code></a>([complexes])</p></td>
+<td><p>Creates complex annotations by in silico inference and adds them to this annotation set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Hgnc.all_complexes" title="pypath.core.annot.Hgnc.all_complexes"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_complexes</span></code></a>()</p></td>
+<td><p>All protein complexes annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Hgnc.all_entities" title="pypath.core.annot.Hgnc.all_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_entities</span></code></a>([entity_types])</p></td>
+<td><p>All entities annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Hgnc.all_mirnas" title="pypath.core.annot.Hgnc.all_mirnas"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_mirnas</span></code></a>()</p></td>
+<td><p>All miRNAs annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Hgnc.all_proteins" title="pypath.core.annot.Hgnc.all_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_proteins</span></code></a>()</p></td>
+<td><p>All UniProt IDs annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Hgnc.all_refs" title="pypath.core.annot.Hgnc.all_refs"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_refs</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Hgnc.annotate_complex" title="pypath.core.annot.Hgnc.annotate_complex"><code class="xref py py-obj docutils literal notranslate"><span class="pre">annotate_complex</span></code></a>(cplex)</p></td>
+<td><p>Infers annotations for a single complex.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Hgnc.browse" title="pypath.core.annot.Hgnc.browse"><code class="xref py py-obj docutils literal notranslate"><span class="pre">browse</span></code></a>([field, start])</p></td>
+<td><p>Print gene information as a table.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Hgnc.complex_inference" title="pypath.core.annot.Hgnc.complex_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">complex_inference</span></code></a>([complexes])</p></td>
+<td><p>Annotates all complexes in <cite>complexes</cite>, by default in the default complex database (existing in the <cite>complex</cite> module or generated on demand according to the module's current settings).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Hgnc.coverage" title="pypath.core.annot.Hgnc.coverage"><code class="xref py py-obj docutils literal notranslate"><span class="pre">coverage</span></code></a>(other)</p></td>
+<td><p>Calculates the coverage of the annotation i.e. the proportion of entities having at least one record in this annotation resource for an arbitrary set of entities.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Hgnc.curation_effort" title="pypath.core.annot.Hgnc.curation_effort"><code class="xref py py-obj docutils literal notranslate"><span class="pre">curation_effort</span></code></a>()</p></td>
+<td><p>Counts the reference-record pairs.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">from_dump</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_entity_type</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Hgnc.get_names" title="pypath.core.annot.Hgnc.get_names"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_names</span></code></a>()</p></td>
+<td><p>Returns the list of field names in the records.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Hgnc.get_reference_set" title="pypath.core.annot.Hgnc.get_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_reference_set</span></code></a>([proteins, complexes, ...])</p></td>
+<td><p>Retrieves the reference set i.e. the set of all entities which potentially have annotation in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Hgnc.get_subset" title="pypath.core.annot.Hgnc.get_subset"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Hgnc.get_subset_bool_array" title="pypath.core.annot.Hgnc.get_subset_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset_bool_array</span></code></a>([reference_set])</p></td>
+<td><p>Returns a boolean vector with True and False values for each entity in the reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Hgnc.get_values" title="pypath.core.annot.Hgnc.get_values"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_values</span></code></a>(name[, exclude_none])</p></td>
+<td><p>Returns the set of all possible values of a field.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_complex</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_mirna</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_protein</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Hgnc.labels" title="pypath.core.annot.Hgnc.labels"><code class="xref py py-obj docutils literal notranslate"><span class="pre">labels</span></code></a>([method])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Hgnc.load" title="pypath.core.annot.Hgnc.load"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load</span></code></a>()</p></td>
+<td><p>Loads the annotation data by calling the input method.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Hgnc.load_data" title="pypath.core.annot.Hgnc.load_data"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_data</span></code></a>()</p></td>
+<td><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Hgnc.load_proteins" title="pypath.core.annot.Hgnc.load_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_proteins</span></code></a>()</p></td>
+<td><p>Retrieves a set of all UniProt IDs to have a base set of the entire proteome.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Hgnc.make_df" title="pypath.core.annot.Hgnc.make_df"><code class="xref py py-obj docutils literal notranslate"><span class="pre">make_df</span></code></a>([rebuild])</p></td>
+<td><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complex_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Hgnc.numof_entities" title="pypath.core.annot.Hgnc.numof_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_entities</span></code></a>()</p></td>
+<td><p>The number of annotated entities in the resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirna_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirnas</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_protein_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_proteins</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Hgnc.numof_records" title="pypath.core.annot.Hgnc.numof_records"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_records</span></code></a>([entity_types])</p></td>
+<td><p>The total number of annotation records.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Hgnc.numof_references" title="pypath.core.annot.Hgnc.numof_references"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_references</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Hgnc.process" title="pypath.core.annot.Hgnc.process"><code class="xref py py-obj docutils literal notranslate"><span class="pre">process</span></code></a>()</p></td>
+<td><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">proportion</span></code>(other)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Hgnc.reload" title="pypath.core.annot.Hgnc.reload"><code class="xref py py-obj docutils literal notranslate"><span class="pre">reload</span></code></a>()</p></td>
+<td><p>Reloads the object from the module level.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">save_to_pickle</span></code>(pickle_file)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Hgnc.select" title="pypath.core.annot.Hgnc.select"><code class="xref py py-obj docutils literal notranslate"><span class="pre">select</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Hgnc.set_method" title="pypath.core.annot.Hgnc.set_method"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_method</span></code></a>()</p></td>
+<td><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if necessary.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Hgnc.set_reference_set" title="pypath.core.annot.Hgnc.set_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_reference_set</span></code></a>()</p></td>
+<td><p>Assigns the reference set to the :py:attr``reference_set`` attribute.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Hgnc.show" title="pypath.core.annot.Hgnc.show"><code class="xref py py-obj docutils literal notranslate"><span class="pre">show</span></code></a>([method, table_param])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic information from the UniProt datasheets.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Hgnc.subset_intersection" title="pypath.core.annot.Hgnc.subset_intersection"><code class="xref py py-obj docutils literal notranslate"><span class="pre">subset_intersection</span></code></a>(universe, **kwargs)</p></td>
+<td><p>Calculates the proportion of entities in a subset occuring in the set <code class="docutils literal notranslate"><span class="pre">universe</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Hgnc.to_array" title="pypath.core.annot.Hgnc.to_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_array</span></code></a>([reference_set, use_fields])</p></td>
+<td><p>Returns an entity vs feature array.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Hgnc.to_bool_array" title="pypath.core.annot.Hgnc.to_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_bool_array</span></code></a>(reference_set)</p></td>
+<td><p>Returns a presence/absence boolean array for a reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Hgnc.to_set" title="pypath.core.annot.Hgnc.to_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_set</span></code></a>()</p></td>
+<td><p>Returns the entities present in this annotation resource as a set.</p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Attributes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_fields</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">summary</span></code></p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Hgnc.add_complexes_by_inference">
+<span class="sig-name descname"><span class="pre">add_complexes_by_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Hgnc.add_complexes_by_inference" title="Link to this definition">§</a></dt>
+<dd><p>Creates complex annotations by in silico inference and adds them
+to this annotation set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Hgnc.all_complexes">
+<span class="sig-name descname"><span class="pre">all_complexes</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Hgnc.all_complexes" title="Link to this definition">§</a></dt>
+<dd><p>All protein complexes annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Hgnc.all_entities">
+<span class="sig-name descname"><span class="pre">all_entities</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Hgnc.all_entities" title="Link to this definition">§</a></dt>
+<dd><p>All entities annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Hgnc.all_mirnas">
+<span class="sig-name descname"><span class="pre">all_mirnas</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Hgnc.all_mirnas" title="Link to this definition">§</a></dt>
+<dd><p>All miRNAs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Hgnc.all_proteins">
+<span class="sig-name descname"><span class="pre">all_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Hgnc.all_proteins" title="Link to this definition">§</a></dt>
+<dd><p>All UniProt IDs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Hgnc.all_refs">
+<span class="sig-name descname"><span class="pre">all_refs</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Hgnc.all_refs" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects the references
+across all records. Returns <em>list</em>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Hgnc.annotate_complex">
+<span class="sig-name descname"><span class="pre">annotate_complex</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cplex</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Hgnc.annotate_complex" title="Link to this definition">§</a></dt>
+<dd><p>Infers annotations for a single complex.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Hgnc.browse">
+<span class="sig-name descname"><span class="pre">browse</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">field</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">start</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Hgnc.browse" title="Link to this definition">§</a></dt>
+<dd><p>Print gene information as a table.</p>
+<p>Presents information about annotation categories as ascii tables
+printed in the terminal. If one category provided, prints one table.
+If multiple categories provided, prints a table for each of them one
+by one proceeding to the next one once you hit return. If no categories
+provided goes through all levels of the primary category.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>field:</dt><dd><p>The field to browse categories by.</p>
+<ul class="simple">
+<li><p>If None the primary field will be selected.
+If this annotation resource doesn’t have fields, all proteins
+will be presented as one single category.</p></li>
+<li><p>If a string it will be considered a field name and it will
+browse through all levels of this field.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">list</span></code>, set or tuple, it will be considered either a
+<code class="docutils literal notranslate"><span class="pre">list</span></code> of field names or a list of values from the primary
+field. In the former case all combinations of the values of
+the fields will be presented, in the latter case the browsing
+will be limited to the levels of the primary field contained
+in <code class="docutils literal notranslate"><span class="pre">field</span></code>.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">dict</span></code>, keys are supposed to be field names and values
+as list of levels. If any of the values are None, all levels
+from that field will be used.</p></li>
+</ul>
+</dd>
+<dt>start:</dt><dd><p>Start browsing from this category. E.g. if there are 500
+categories and start is 250 it will skip everything before the
+250th.</p>
+</dd>
+<dt>kwargs:</dt><dd><p>Passed to <code class="docutils literal notranslate"><span class="pre">pypath.utils.uniprot.info</span></code>.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Hgnc.complex_inference">
+<span class="sig-name descname"><span class="pre">complex_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Hgnc.complex_inference" title="Link to this definition">§</a></dt>
+<dd><p>Annotates all complexes in <cite>complexes</cite>, by default in the default
+complex database (existing in the <cite>complex</cite> module or generated
+on demand according to the module’s current settings).</p>
+<dl class="field-list simple">
+<dt class="field-odd">Returns<span class="colon">:</span></dt>
+<dd class="field-odd"><p><ul class="simple">
+<li><p><em>Dict with complexes as keys and sets of annotations as values.</em></p></li>
+<li><p><em>Complexes with no valid information in this annotation resource</em></p></li>
+<li><p><em>won’t be in the dict.</em></p></li>
+</ul>
+</p>
+</dd>
+<dt class="field-even">Parameters<span class="colon">:</span></dt>
+<dd class="field-even"><p><strong>complexes</strong> (<em>iterable</em>) – Iterable yielding complexes.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Hgnc.coverage">
+<span class="sig-name descname"><span class="pre">coverage</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">other</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Hgnc.coverage" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the coverage of the annotation i.e. the proportion of
+entities having at least one record in this annotation resource
+for an arbitrary set of entities.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Hgnc.curation_effort">
+<span class="sig-name descname"><span class="pre">curation_effort</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Hgnc.curation_effort" title="Link to this definition">§</a></dt>
+<dd><p>Counts the reference-record pairs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Hgnc.get_names">
+<span class="sig-name descname"><span class="pre">get_names</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Hgnc.get_names" title="Link to this definition">§</a></dt>
+<dd><p>Returns the list of field names in the records. The annotation
+consists of uniform records and each entity might be annotated
+with one or more records. Each record is a tuple of fields, for
+example <code class="docutils literal notranslate"><span class="pre">('cell_type',</span> <span class="pre">'expression_level',</span> <span class="pre">'score')</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Hgnc.get_reference_set">
+<em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">get_reference_set</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">proteins</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">swissprot_only</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Hgnc.get_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the reference set i.e. the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Hgnc.get_subset">
+<span class="sig-name descname"><span class="pre">get_subset</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Hgnc.get_subset" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Hgnc.get_subset_bool_array">
+<span class="sig-name descname"><span class="pre">get_subset_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Hgnc.get_subset_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a boolean vector with True and False values for each entity
+in the reference set. The values represent presence absence data
+in the simplest case, but by providing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> any kind of matching
+and filtering is possible. <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> are passed to the <code class="docutils literal notranslate"><span class="pre">select</span></code>
+method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Hgnc.get_values">
+<span class="sig-name descname"><span class="pre">get_values</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">exclude_none</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Hgnc.get_values" title="Link to this definition">§</a></dt>
+<dd><p>Returns the set of all possible values of a field. E.g. if the
+records of this annotation have a field <code class="docutils literal notranslate"><span class="pre">cell_type</span></code> then calling
+this method can tell you that across all records the values of
+this field might be <code class="docutils literal notranslate"><span class="pre">{'macrophage',</span> <span class="pre">'epithelial_cell',</span> <span class="pre">...}</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Hgnc.labels">
+<span class="sig-name descname"><span class="pre">labels</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Hgnc.labels" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Hgnc.load">
+<span class="sig-name descname"><span class="pre">load</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Hgnc.load" title="Link to this definition">§</a></dt>
+<dd><p>Loads the annotation data by calling the input method.
+Infers annotations for complexes in the complex database if
+py:attr:<code class="docutils literal notranslate"><span class="pre">infer_complexes</span></code> is True.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Hgnc.load_data">
+<span class="sig-name descname"><span class="pre">load_data</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Hgnc.load_data" title="Link to this definition">§</a></dt>
+<dd><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Hgnc.load_proteins">
+<span class="sig-name descname"><span class="pre">load_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Hgnc.load_proteins" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a set of all UniProt IDs to have a base set of the entire
+proteome.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Hgnc.make_df">
+<span class="sig-name descname"><span class="pre">make_df</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">rebuild</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Hgnc.make_df" title="Link to this definition">§</a></dt>
+<dd><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.
+The data frame will be assigned to :py:attr``df``.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Hgnc.numof_entities">
+<span class="sig-name descname"><span class="pre">numof_entities</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Hgnc.numof_entities" title="Link to this definition">§</a></dt>
+<dd><p>The number of annotated entities in the resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Hgnc.numof_records">
+<span class="sig-name descname"><span class="pre">numof_records</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Hgnc.numof_records" title="Link to this definition">§</a></dt>
+<dd><p>The total number of annotation records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Hgnc.numof_references">
+<span class="sig-name descname"><span class="pre">numof_references</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Hgnc.numof_references" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects and counts the
+references across all records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Hgnc.process">
+<span class="sig-name descname"><span class="pre">process</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Hgnc.process" title="Link to this definition">§</a></dt>
+<dd><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Hgnc.reload">
+<span class="sig-name descname"><span class="pre">reload</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Hgnc.reload" title="Link to this definition">§</a></dt>
+<dd><p>Reloads the object from the module level.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Hgnc.select">
+<span class="sig-name descname"><span class="pre">select</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Hgnc.select" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Hgnc.set_method">
+<span class="sig-name descname"><span class="pre">set_method</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Hgnc.set_method" title="Link to this definition">§</a></dt>
+<dd><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if
+necessary.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Hgnc.set_reference_set">
+<span class="sig-name descname"><span class="pre">set_reference_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Hgnc.set_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Assigns the reference set to the :py:attr``reference_set`` attribute.
+The reference set is the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Hgnc.show">
+<span class="sig-name descname"><span class="pre">show</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">table_param</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Hgnc.show" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic
+information from the UniProt datasheets.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Hgnc.subset_intersection">
+<span class="sig-name descname"><span class="pre">subset_intersection</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">universe</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Hgnc.subset_intersection" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the proportion of entities in a subset occuring in the
+set <code class="docutils literal notranslate"><span class="pre">universe</span></code>. The subset is selected by passing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> to the
+<code class="docutils literal notranslate"><span class="pre">select</span></code> method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Hgnc.to_array">
+<span class="sig-name descname"><span class="pre">to_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_fields</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Hgnc.to_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns an entity vs feature array. In case of more complex
+annotations this might be huge.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Hgnc.to_bool_array">
+<span class="sig-name descname"><span class="pre">to_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Hgnc.to_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a presence/absence boolean array for a reference set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Hgnc.to_set">
+<span class="sig-name descname"><span class="pre">to_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Hgnc.to_set" title="Link to this definition">§</a></dt>
+<dd><p>Returns the entities present in this annotation resource as a set.</p>
+</dd></dl>
+
+</dd></dl>
+
+</section>
+
+
+                </article>
+              
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+  <section id="pypath-core-annot-hpmrcomplex">
+<h1>pypath.core.annot.HpmrComplex<a class="headerlink" href="#pypath-core-annot-hpmrcomplex" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.core.annot.HpmrComplex">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.core.annot.</span></span><span class="sig-name descname"><span class="pre">HpmrComplex</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#HpmrComplex"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.HpmrComplex" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <a class="reference internal" href="pypath.core.annot.AnnotationBase.html#pypath.core.annot.AnnotationBase" title="pypath.core.annot.AnnotationBase"><code class="xref py py-class docutils literal notranslate"><span class="pre">AnnotationBase</span></code></a></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HpmrComplex.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#HpmrComplex.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.HpmrComplex.__init__" title="Link to this definition">§</a></dt>
+<dd><p>Represents annotations for a set of proteins.
+Loads the data from the original resource and provides methods
+to query the annotations.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>name</strong> (<em>str</em>) – A custom name for the annotation resource.</p></li>
+<li><p><strong>ncbi_tax_id</strong> (<em>int</em>) – NCBI Taxonomy identifier.</p></li>
+<li><p><strong>input_method</strong> (<em>callable</em><em>,</em><em>str</em>) – Either a callable or the name of a method in any submodules of
+the <code class="docutils literal notranslate"><span class="pre">pypath.inputs</span></code>  module. Should return a dict with
+UniProt IDs as keys or an object suitable for <code class="docutils literal notranslate"><span class="pre">process_method</span></code>.</p></li>
+<li><p><strong>input_args</strong> (<em>dict</em>) – Arguments for the <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.HpmrComplex.__init__" title="pypath.core.annot.HpmrComplex.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>(**kwargs)</p></td>
+<td><p>Represents annotations for a set of proteins.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.HpmrComplex.add_complexes_by_inference" title="pypath.core.annot.HpmrComplex.add_complexes_by_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">add_complexes_by_inference</span></code></a>([complexes])</p></td>
+<td><p>Creates complex annotations by in silico inference and adds them to this annotation set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.HpmrComplex.all_complexes" title="pypath.core.annot.HpmrComplex.all_complexes"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_complexes</span></code></a>()</p></td>
+<td><p>All protein complexes annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.HpmrComplex.all_entities" title="pypath.core.annot.HpmrComplex.all_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_entities</span></code></a>([entity_types])</p></td>
+<td><p>All entities annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.HpmrComplex.all_mirnas" title="pypath.core.annot.HpmrComplex.all_mirnas"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_mirnas</span></code></a>()</p></td>
+<td><p>All miRNAs annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.HpmrComplex.all_proteins" title="pypath.core.annot.HpmrComplex.all_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_proteins</span></code></a>()</p></td>
+<td><p>All UniProt IDs annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.HpmrComplex.all_refs" title="pypath.core.annot.HpmrComplex.all_refs"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_refs</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.HpmrComplex.annotate_complex" title="pypath.core.annot.HpmrComplex.annotate_complex"><code class="xref py py-obj docutils literal notranslate"><span class="pre">annotate_complex</span></code></a>(cplex)</p></td>
+<td><p>Infers annotations for a single complex.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.HpmrComplex.browse" title="pypath.core.annot.HpmrComplex.browse"><code class="xref py py-obj docutils literal notranslate"><span class="pre">browse</span></code></a>([field, start])</p></td>
+<td><p>Print gene information as a table.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.HpmrComplex.complex_inference" title="pypath.core.annot.HpmrComplex.complex_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">complex_inference</span></code></a>([complexes])</p></td>
+<td><p>Annotates all complexes in <cite>complexes</cite>, by default in the default complex database (existing in the <cite>complex</cite> module or generated on demand according to the module's current settings).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.HpmrComplex.coverage" title="pypath.core.annot.HpmrComplex.coverage"><code class="xref py py-obj docutils literal notranslate"><span class="pre">coverage</span></code></a>(other)</p></td>
+<td><p>Calculates the coverage of the annotation i.e. the proportion of entities having at least one record in this annotation resource for an arbitrary set of entities.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.HpmrComplex.curation_effort" title="pypath.core.annot.HpmrComplex.curation_effort"><code class="xref py py-obj docutils literal notranslate"><span class="pre">curation_effort</span></code></a>()</p></td>
+<td><p>Counts the reference-record pairs.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">from_dump</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_entity_type</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.HpmrComplex.get_names" title="pypath.core.annot.HpmrComplex.get_names"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_names</span></code></a>()</p></td>
+<td><p>Returns the list of field names in the records.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.HpmrComplex.get_reference_set" title="pypath.core.annot.HpmrComplex.get_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_reference_set</span></code></a>([proteins, complexes, ...])</p></td>
+<td><p>Retrieves the reference set i.e. the set of all entities which potentially have annotation in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.HpmrComplex.get_subset" title="pypath.core.annot.HpmrComplex.get_subset"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.HpmrComplex.get_subset_bool_array" title="pypath.core.annot.HpmrComplex.get_subset_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset_bool_array</span></code></a>([reference_set])</p></td>
+<td><p>Returns a boolean vector with True and False values for each entity in the reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.HpmrComplex.get_values" title="pypath.core.annot.HpmrComplex.get_values"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_values</span></code></a>(name[, exclude_none])</p></td>
+<td><p>Returns the set of all possible values of a field.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_complex</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_mirna</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_protein</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.HpmrComplex.labels" title="pypath.core.annot.HpmrComplex.labels"><code class="xref py py-obj docutils literal notranslate"><span class="pre">labels</span></code></a>([method])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.HpmrComplex.load" title="pypath.core.annot.HpmrComplex.load"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load</span></code></a>()</p></td>
+<td><p>Loads the annotation data by calling the input method.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.HpmrComplex.load_data" title="pypath.core.annot.HpmrComplex.load_data"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_data</span></code></a>()</p></td>
+<td><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.HpmrComplex.load_proteins" title="pypath.core.annot.HpmrComplex.load_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_proteins</span></code></a>()</p></td>
+<td><p>Retrieves a set of all UniProt IDs to have a base set of the entire proteome.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.HpmrComplex.make_df" title="pypath.core.annot.HpmrComplex.make_df"><code class="xref py py-obj docutils literal notranslate"><span class="pre">make_df</span></code></a>([rebuild])</p></td>
+<td><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complex_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.HpmrComplex.numof_entities" title="pypath.core.annot.HpmrComplex.numof_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_entities</span></code></a>()</p></td>
+<td><p>The number of annotated entities in the resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirna_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirnas</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_protein_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_proteins</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.HpmrComplex.numof_records" title="pypath.core.annot.HpmrComplex.numof_records"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_records</span></code></a>([entity_types])</p></td>
+<td><p>The total number of annotation records.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.HpmrComplex.numof_references" title="pypath.core.annot.HpmrComplex.numof_references"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_references</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.HpmrComplex.process" title="pypath.core.annot.HpmrComplex.process"><code class="xref py py-obj docutils literal notranslate"><span class="pre">process</span></code></a>()</p></td>
+<td><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">proportion</span></code>(other)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.HpmrComplex.reload" title="pypath.core.annot.HpmrComplex.reload"><code class="xref py py-obj docutils literal notranslate"><span class="pre">reload</span></code></a>()</p></td>
+<td><p>Reloads the object from the module level.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">save_to_pickle</span></code>(pickle_file)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.HpmrComplex.select" title="pypath.core.annot.HpmrComplex.select"><code class="xref py py-obj docutils literal notranslate"><span class="pre">select</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.HpmrComplex.set_method" title="pypath.core.annot.HpmrComplex.set_method"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_method</span></code></a>()</p></td>
+<td><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if necessary.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.HpmrComplex.set_reference_set" title="pypath.core.annot.HpmrComplex.set_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_reference_set</span></code></a>()</p></td>
+<td><p>Assigns the reference set to the :py:attr``reference_set`` attribute.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.HpmrComplex.show" title="pypath.core.annot.HpmrComplex.show"><code class="xref py py-obj docutils literal notranslate"><span class="pre">show</span></code></a>([method, table_param])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic information from the UniProt datasheets.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.HpmrComplex.subset_intersection" title="pypath.core.annot.HpmrComplex.subset_intersection"><code class="xref py py-obj docutils literal notranslate"><span class="pre">subset_intersection</span></code></a>(universe, **kwargs)</p></td>
+<td><p>Calculates the proportion of entities in a subset occuring in the set <code class="docutils literal notranslate"><span class="pre">universe</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.HpmrComplex.to_array" title="pypath.core.annot.HpmrComplex.to_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_array</span></code></a>([reference_set, use_fields])</p></td>
+<td><p>Returns an entity vs feature array.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.HpmrComplex.to_bool_array" title="pypath.core.annot.HpmrComplex.to_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_bool_array</span></code></a>(reference_set)</p></td>
+<td><p>Returns a presence/absence boolean array for a reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.HpmrComplex.to_set" title="pypath.core.annot.HpmrComplex.to_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_set</span></code></a>()</p></td>
+<td><p>Returns the entities present in this annotation resource as a set.</p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Attributes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_fields</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">summary</span></code></p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HpmrComplex.add_complexes_by_inference">
+<span class="sig-name descname"><span class="pre">add_complexes_by_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HpmrComplex.add_complexes_by_inference" title="Link to this definition">§</a></dt>
+<dd><p>Creates complex annotations by in silico inference and adds them
+to this annotation set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HpmrComplex.all_complexes">
+<span class="sig-name descname"><span class="pre">all_complexes</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HpmrComplex.all_complexes" title="Link to this definition">§</a></dt>
+<dd><p>All protein complexes annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HpmrComplex.all_entities">
+<span class="sig-name descname"><span class="pre">all_entities</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HpmrComplex.all_entities" title="Link to this definition">§</a></dt>
+<dd><p>All entities annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HpmrComplex.all_mirnas">
+<span class="sig-name descname"><span class="pre">all_mirnas</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HpmrComplex.all_mirnas" title="Link to this definition">§</a></dt>
+<dd><p>All miRNAs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HpmrComplex.all_proteins">
+<span class="sig-name descname"><span class="pre">all_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HpmrComplex.all_proteins" title="Link to this definition">§</a></dt>
+<dd><p>All UniProt IDs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HpmrComplex.all_refs">
+<span class="sig-name descname"><span class="pre">all_refs</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HpmrComplex.all_refs" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects the references
+across all records. Returns <em>list</em>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HpmrComplex.annotate_complex">
+<span class="sig-name descname"><span class="pre">annotate_complex</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cplex</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HpmrComplex.annotate_complex" title="Link to this definition">§</a></dt>
+<dd><p>Infers annotations for a single complex.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HpmrComplex.browse">
+<span class="sig-name descname"><span class="pre">browse</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">field</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">start</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HpmrComplex.browse" title="Link to this definition">§</a></dt>
+<dd><p>Print gene information as a table.</p>
+<p>Presents information about annotation categories as ascii tables
+printed in the terminal. If one category provided, prints one table.
+If multiple categories provided, prints a table for each of them one
+by one proceeding to the next one once you hit return. If no categories
+provided goes through all levels of the primary category.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>field:</dt><dd><p>The field to browse categories by.</p>
+<ul class="simple">
+<li><p>If None the primary field will be selected.
+If this annotation resource doesn’t have fields, all proteins
+will be presented as one single category.</p></li>
+<li><p>If a string it will be considered a field name and it will
+browse through all levels of this field.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">list</span></code>, set or tuple, it will be considered either a
+<code class="docutils literal notranslate"><span class="pre">list</span></code> of field names or a list of values from the primary
+field. In the former case all combinations of the values of
+the fields will be presented, in the latter case the browsing
+will be limited to the levels of the primary field contained
+in <code class="docutils literal notranslate"><span class="pre">field</span></code>.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">dict</span></code>, keys are supposed to be field names and values
+as list of levels. If any of the values are None, all levels
+from that field will be used.</p></li>
+</ul>
+</dd>
+<dt>start:</dt><dd><p>Start browsing from this category. E.g. if there are 500
+categories and start is 250 it will skip everything before the
+250th.</p>
+</dd>
+<dt>kwargs:</dt><dd><p>Passed to <code class="docutils literal notranslate"><span class="pre">pypath.utils.uniprot.info</span></code>.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HpmrComplex.complex_inference">
+<span class="sig-name descname"><span class="pre">complex_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HpmrComplex.complex_inference" title="Link to this definition">§</a></dt>
+<dd><p>Annotates all complexes in <cite>complexes</cite>, by default in the default
+complex database (existing in the <cite>complex</cite> module or generated
+on demand according to the module’s current settings).</p>
+<dl class="field-list simple">
+<dt class="field-odd">Returns<span class="colon">:</span></dt>
+<dd class="field-odd"><p><ul class="simple">
+<li><p><em>Dict with complexes as keys and sets of annotations as values.</em></p></li>
+<li><p><em>Complexes with no valid information in this annotation resource</em></p></li>
+<li><p><em>won’t be in the dict.</em></p></li>
+</ul>
+</p>
+</dd>
+<dt class="field-even">Parameters<span class="colon">:</span></dt>
+<dd class="field-even"><p><strong>complexes</strong> (<em>iterable</em>) – Iterable yielding complexes.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HpmrComplex.coverage">
+<span class="sig-name descname"><span class="pre">coverage</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">other</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HpmrComplex.coverage" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the coverage of the annotation i.e. the proportion of
+entities having at least one record in this annotation resource
+for an arbitrary set of entities.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HpmrComplex.curation_effort">
+<span class="sig-name descname"><span class="pre">curation_effort</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HpmrComplex.curation_effort" title="Link to this definition">§</a></dt>
+<dd><p>Counts the reference-record pairs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HpmrComplex.get_names">
+<span class="sig-name descname"><span class="pre">get_names</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HpmrComplex.get_names" title="Link to this definition">§</a></dt>
+<dd><p>Returns the list of field names in the records. The annotation
+consists of uniform records and each entity might be annotated
+with one or more records. Each record is a tuple of fields, for
+example <code class="docutils literal notranslate"><span class="pre">('cell_type',</span> <span class="pre">'expression_level',</span> <span class="pre">'score')</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HpmrComplex.get_reference_set">
+<em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">get_reference_set</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">proteins</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">swissprot_only</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HpmrComplex.get_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the reference set i.e. the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HpmrComplex.get_subset">
+<span class="sig-name descname"><span class="pre">get_subset</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HpmrComplex.get_subset" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HpmrComplex.get_subset_bool_array">
+<span class="sig-name descname"><span class="pre">get_subset_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HpmrComplex.get_subset_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a boolean vector with True and False values for each entity
+in the reference set. The values represent presence absence data
+in the simplest case, but by providing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> any kind of matching
+and filtering is possible. <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> are passed to the <code class="docutils literal notranslate"><span class="pre">select</span></code>
+method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HpmrComplex.get_values">
+<span class="sig-name descname"><span class="pre">get_values</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">exclude_none</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HpmrComplex.get_values" title="Link to this definition">§</a></dt>
+<dd><p>Returns the set of all possible values of a field. E.g. if the
+records of this annotation have a field <code class="docutils literal notranslate"><span class="pre">cell_type</span></code> then calling
+this method can tell you that across all records the values of
+this field might be <code class="docutils literal notranslate"><span class="pre">{'macrophage',</span> <span class="pre">'epithelial_cell',</span> <span class="pre">...}</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HpmrComplex.labels">
+<span class="sig-name descname"><span class="pre">labels</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HpmrComplex.labels" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HpmrComplex.load">
+<span class="sig-name descname"><span class="pre">load</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HpmrComplex.load" title="Link to this definition">§</a></dt>
+<dd><p>Loads the annotation data by calling the input method.
+Infers annotations for complexes in the complex database if
+py:attr:<code class="docutils literal notranslate"><span class="pre">infer_complexes</span></code> is True.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HpmrComplex.load_data">
+<span class="sig-name descname"><span class="pre">load_data</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HpmrComplex.load_data" title="Link to this definition">§</a></dt>
+<dd><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HpmrComplex.load_proteins">
+<span class="sig-name descname"><span class="pre">load_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HpmrComplex.load_proteins" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a set of all UniProt IDs to have a base set of the entire
+proteome.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HpmrComplex.make_df">
+<span class="sig-name descname"><span class="pre">make_df</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">rebuild</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HpmrComplex.make_df" title="Link to this definition">§</a></dt>
+<dd><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.
+The data frame will be assigned to :py:attr``df``.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HpmrComplex.numof_entities">
+<span class="sig-name descname"><span class="pre">numof_entities</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HpmrComplex.numof_entities" title="Link to this definition">§</a></dt>
+<dd><p>The number of annotated entities in the resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HpmrComplex.numof_records">
+<span class="sig-name descname"><span class="pre">numof_records</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HpmrComplex.numof_records" title="Link to this definition">§</a></dt>
+<dd><p>The total number of annotation records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HpmrComplex.numof_references">
+<span class="sig-name descname"><span class="pre">numof_references</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HpmrComplex.numof_references" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects and counts the
+references across all records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HpmrComplex.process">
+<span class="sig-name descname"><span class="pre">process</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HpmrComplex.process" title="Link to this definition">§</a></dt>
+<dd><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HpmrComplex.reload">
+<span class="sig-name descname"><span class="pre">reload</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HpmrComplex.reload" title="Link to this definition">§</a></dt>
+<dd><p>Reloads the object from the module level.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HpmrComplex.select">
+<span class="sig-name descname"><span class="pre">select</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HpmrComplex.select" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HpmrComplex.set_method">
+<span class="sig-name descname"><span class="pre">set_method</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HpmrComplex.set_method" title="Link to this definition">§</a></dt>
+<dd><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if
+necessary.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HpmrComplex.set_reference_set">
+<span class="sig-name descname"><span class="pre">set_reference_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HpmrComplex.set_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Assigns the reference set to the :py:attr``reference_set`` attribute.
+The reference set is the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HpmrComplex.show">
+<span class="sig-name descname"><span class="pre">show</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">table_param</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HpmrComplex.show" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic
+information from the UniProt datasheets.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HpmrComplex.subset_intersection">
+<span class="sig-name descname"><span class="pre">subset_intersection</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">universe</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HpmrComplex.subset_intersection" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the proportion of entities in a subset occuring in the
+set <code class="docutils literal notranslate"><span class="pre">universe</span></code>. The subset is selected by passing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> to the
+<code class="docutils literal notranslate"><span class="pre">select</span></code> method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HpmrComplex.to_array">
+<span class="sig-name descname"><span class="pre">to_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_fields</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HpmrComplex.to_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns an entity vs feature array. In case of more complex
+annotations this might be huge.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HpmrComplex.to_bool_array">
+<span class="sig-name descname"><span class="pre">to_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HpmrComplex.to_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a presence/absence boolean array for a reference set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HpmrComplex.to_set">
+<span class="sig-name descname"><span class="pre">to_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HpmrComplex.to_set" title="Link to this definition">§</a></dt>
+<dd><p>Returns the entities present in this annotation resource as a set.</p>
+</dd></dl>
+
+</dd></dl>
+
+</section>
+
+
+                </article>
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+  <section id="pypath-core-annot-humanplasmamembranereceptome">
+<h1>pypath.core.annot.HumanPlasmaMembraneReceptome<a class="headerlink" href="#pypath-core-annot-humanplasmamembranereceptome" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.core.annot.HumanPlasmaMembraneReceptome">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.core.annot.</span></span><span class="sig-name descname"><span class="pre">HumanPlasmaMembraneReceptome</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#HumanPlasmaMembraneReceptome"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.HumanPlasmaMembraneReceptome" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <a class="reference internal" href="pypath.core.annot.AnnotationBase.html#pypath.core.annot.AnnotationBase" title="pypath.core.annot.AnnotationBase"><code class="xref py py-class docutils literal notranslate"><span class="pre">AnnotationBase</span></code></a></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HumanPlasmaMembraneReceptome.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#HumanPlasmaMembraneReceptome.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.HumanPlasmaMembraneReceptome.__init__" title="Link to this definition">§</a></dt>
+<dd><p>The name of this resource abbreviated as <cite>HPMR</cite>.</p>
+</dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.HumanPlasmaMembraneReceptome.__init__" title="pypath.core.annot.HumanPlasmaMembraneReceptome.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>(**kwargs)</p></td>
+<td><p>The name of this resource abbreviated as <cite>HPMR</cite>.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.HumanPlasmaMembraneReceptome.add_complexes_by_inference" title="pypath.core.annot.HumanPlasmaMembraneReceptome.add_complexes_by_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">add_complexes_by_inference</span></code></a>([complexes])</p></td>
+<td><p>Creates complex annotations by in silico inference and adds them to this annotation set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.HumanPlasmaMembraneReceptome.all_complexes" title="pypath.core.annot.HumanPlasmaMembraneReceptome.all_complexes"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_complexes</span></code></a>()</p></td>
+<td><p>All protein complexes annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.HumanPlasmaMembraneReceptome.all_entities" title="pypath.core.annot.HumanPlasmaMembraneReceptome.all_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_entities</span></code></a>([entity_types])</p></td>
+<td><p>All entities annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.HumanPlasmaMembraneReceptome.all_mirnas" title="pypath.core.annot.HumanPlasmaMembraneReceptome.all_mirnas"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_mirnas</span></code></a>()</p></td>
+<td><p>All miRNAs annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.HumanPlasmaMembraneReceptome.all_proteins" title="pypath.core.annot.HumanPlasmaMembraneReceptome.all_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_proteins</span></code></a>()</p></td>
+<td><p>All UniProt IDs annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.HumanPlasmaMembraneReceptome.all_refs" title="pypath.core.annot.HumanPlasmaMembraneReceptome.all_refs"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_refs</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.HumanPlasmaMembraneReceptome.annotate_complex" title="pypath.core.annot.HumanPlasmaMembraneReceptome.annotate_complex"><code class="xref py py-obj docutils literal notranslate"><span class="pre">annotate_complex</span></code></a>(cplex)</p></td>
+<td><p>Infers annotations for a single complex.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.HumanPlasmaMembraneReceptome.browse" title="pypath.core.annot.HumanPlasmaMembraneReceptome.browse"><code class="xref py py-obj docutils literal notranslate"><span class="pre">browse</span></code></a>([field, start])</p></td>
+<td><p>Print gene information as a table.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.HumanPlasmaMembraneReceptome.complex_inference" title="pypath.core.annot.HumanPlasmaMembraneReceptome.complex_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">complex_inference</span></code></a>([complexes])</p></td>
+<td><p>Annotates all complexes in <cite>complexes</cite>, by default in the default complex database (existing in the <cite>complex</cite> module or generated on demand according to the module's current settings).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.HumanPlasmaMembraneReceptome.coverage" title="pypath.core.annot.HumanPlasmaMembraneReceptome.coverage"><code class="xref py py-obj docutils literal notranslate"><span class="pre">coverage</span></code></a>(other)</p></td>
+<td><p>Calculates the coverage of the annotation i.e. the proportion of entities having at least one record in this annotation resource for an arbitrary set of entities.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.HumanPlasmaMembraneReceptome.curation_effort" title="pypath.core.annot.HumanPlasmaMembraneReceptome.curation_effort"><code class="xref py py-obj docutils literal notranslate"><span class="pre">curation_effort</span></code></a>()</p></td>
+<td><p>Counts the reference-record pairs.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">from_dump</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_entity_type</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.HumanPlasmaMembraneReceptome.get_names" title="pypath.core.annot.HumanPlasmaMembraneReceptome.get_names"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_names</span></code></a>()</p></td>
+<td><p>Returns the list of field names in the records.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.HumanPlasmaMembraneReceptome.get_reference_set" title="pypath.core.annot.HumanPlasmaMembraneReceptome.get_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_reference_set</span></code></a>([proteins, complexes, ...])</p></td>
+<td><p>Retrieves the reference set i.e. the set of all entities which potentially have annotation in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.HumanPlasmaMembraneReceptome.get_subset" title="pypath.core.annot.HumanPlasmaMembraneReceptome.get_subset"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.HumanPlasmaMembraneReceptome.get_subset_bool_array" title="pypath.core.annot.HumanPlasmaMembraneReceptome.get_subset_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset_bool_array</span></code></a>([reference_set])</p></td>
+<td><p>Returns a boolean vector with True and False values for each entity in the reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.HumanPlasmaMembraneReceptome.get_values" title="pypath.core.annot.HumanPlasmaMembraneReceptome.get_values"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_values</span></code></a>(name[, exclude_none])</p></td>
+<td><p>Returns the set of all possible values of a field.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_complex</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_mirna</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_protein</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.HumanPlasmaMembraneReceptome.labels" title="pypath.core.annot.HumanPlasmaMembraneReceptome.labels"><code class="xref py py-obj docutils literal notranslate"><span class="pre">labels</span></code></a>([method])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.HumanPlasmaMembraneReceptome.load" title="pypath.core.annot.HumanPlasmaMembraneReceptome.load"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load</span></code></a>()</p></td>
+<td><p>Loads the annotation data by calling the input method.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.HumanPlasmaMembraneReceptome.load_data" title="pypath.core.annot.HumanPlasmaMembraneReceptome.load_data"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_data</span></code></a>()</p></td>
+<td><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.HumanPlasmaMembraneReceptome.load_proteins" title="pypath.core.annot.HumanPlasmaMembraneReceptome.load_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_proteins</span></code></a>()</p></td>
+<td><p>Retrieves a set of all UniProt IDs to have a base set of the entire proteome.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.HumanPlasmaMembraneReceptome.make_df" title="pypath.core.annot.HumanPlasmaMembraneReceptome.make_df"><code class="xref py py-obj docutils literal notranslate"><span class="pre">make_df</span></code></a>([rebuild])</p></td>
+<td><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complex_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.HumanPlasmaMembraneReceptome.numof_entities" title="pypath.core.annot.HumanPlasmaMembraneReceptome.numof_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_entities</span></code></a>()</p></td>
+<td><p>The number of annotated entities in the resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirna_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirnas</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_protein_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_proteins</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.HumanPlasmaMembraneReceptome.numof_records" title="pypath.core.annot.HumanPlasmaMembraneReceptome.numof_records"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_records</span></code></a>([entity_types])</p></td>
+<td><p>The total number of annotation records.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.HumanPlasmaMembraneReceptome.numof_references" title="pypath.core.annot.HumanPlasmaMembraneReceptome.numof_references"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_references</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.HumanPlasmaMembraneReceptome.process" title="pypath.core.annot.HumanPlasmaMembraneReceptome.process"><code class="xref py py-obj docutils literal notranslate"><span class="pre">process</span></code></a>()</p></td>
+<td><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">proportion</span></code>(other)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.HumanPlasmaMembraneReceptome.reload" title="pypath.core.annot.HumanPlasmaMembraneReceptome.reload"><code class="xref py py-obj docutils literal notranslate"><span class="pre">reload</span></code></a>()</p></td>
+<td><p>Reloads the object from the module level.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">save_to_pickle</span></code>(pickle_file)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.HumanPlasmaMembraneReceptome.select" title="pypath.core.annot.HumanPlasmaMembraneReceptome.select"><code class="xref py py-obj docutils literal notranslate"><span class="pre">select</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.HumanPlasmaMembraneReceptome.set_method" title="pypath.core.annot.HumanPlasmaMembraneReceptome.set_method"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_method</span></code></a>()</p></td>
+<td><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if necessary.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.HumanPlasmaMembraneReceptome.set_reference_set" title="pypath.core.annot.HumanPlasmaMembraneReceptome.set_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_reference_set</span></code></a>()</p></td>
+<td><p>Assigns the reference set to the :py:attr``reference_set`` attribute.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.HumanPlasmaMembraneReceptome.show" title="pypath.core.annot.HumanPlasmaMembraneReceptome.show"><code class="xref py py-obj docutils literal notranslate"><span class="pre">show</span></code></a>([method, table_param])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic information from the UniProt datasheets.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.HumanPlasmaMembraneReceptome.subset_intersection" title="pypath.core.annot.HumanPlasmaMembraneReceptome.subset_intersection"><code class="xref py py-obj docutils literal notranslate"><span class="pre">subset_intersection</span></code></a>(universe, **kwargs)</p></td>
+<td><p>Calculates the proportion of entities in a subset occuring in the set <code class="docutils literal notranslate"><span class="pre">universe</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.HumanPlasmaMembraneReceptome.to_array" title="pypath.core.annot.HumanPlasmaMembraneReceptome.to_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_array</span></code></a>([reference_set, use_fields])</p></td>
+<td><p>Returns an entity vs feature array.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.HumanPlasmaMembraneReceptome.to_bool_array" title="pypath.core.annot.HumanPlasmaMembraneReceptome.to_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_bool_array</span></code></a>(reference_set)</p></td>
+<td><p>Returns a presence/absence boolean array for a reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.HumanPlasmaMembraneReceptome.to_set" title="pypath.core.annot.HumanPlasmaMembraneReceptome.to_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_set</span></code></a>()</p></td>
+<td><p>Returns the entities present in this annotation resource as a set.</p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Attributes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_fields</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">summary</span></code></p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HumanPlasmaMembraneReceptome.add_complexes_by_inference">
+<span class="sig-name descname"><span class="pre">add_complexes_by_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HumanPlasmaMembraneReceptome.add_complexes_by_inference" title="Link to this definition">§</a></dt>
+<dd><p>Creates complex annotations by in silico inference and adds them
+to this annotation set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HumanPlasmaMembraneReceptome.all_complexes">
+<span class="sig-name descname"><span class="pre">all_complexes</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HumanPlasmaMembraneReceptome.all_complexes" title="Link to this definition">§</a></dt>
+<dd><p>All protein complexes annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HumanPlasmaMembraneReceptome.all_entities">
+<span class="sig-name descname"><span class="pre">all_entities</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HumanPlasmaMembraneReceptome.all_entities" title="Link to this definition">§</a></dt>
+<dd><p>All entities annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HumanPlasmaMembraneReceptome.all_mirnas">
+<span class="sig-name descname"><span class="pre">all_mirnas</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HumanPlasmaMembraneReceptome.all_mirnas" title="Link to this definition">§</a></dt>
+<dd><p>All miRNAs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HumanPlasmaMembraneReceptome.all_proteins">
+<span class="sig-name descname"><span class="pre">all_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HumanPlasmaMembraneReceptome.all_proteins" title="Link to this definition">§</a></dt>
+<dd><p>All UniProt IDs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HumanPlasmaMembraneReceptome.all_refs">
+<span class="sig-name descname"><span class="pre">all_refs</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HumanPlasmaMembraneReceptome.all_refs" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects the references
+across all records. Returns <em>list</em>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HumanPlasmaMembraneReceptome.annotate_complex">
+<span class="sig-name descname"><span class="pre">annotate_complex</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cplex</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HumanPlasmaMembraneReceptome.annotate_complex" title="Link to this definition">§</a></dt>
+<dd><p>Infers annotations for a single complex.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HumanPlasmaMembraneReceptome.browse">
+<span class="sig-name descname"><span class="pre">browse</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">field</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">start</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HumanPlasmaMembraneReceptome.browse" title="Link to this definition">§</a></dt>
+<dd><p>Print gene information as a table.</p>
+<p>Presents information about annotation categories as ascii tables
+printed in the terminal. If one category provided, prints one table.
+If multiple categories provided, prints a table for each of them one
+by one proceeding to the next one once you hit return. If no categories
+provided goes through all levels of the primary category.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>field:</dt><dd><p>The field to browse categories by.</p>
+<ul class="simple">
+<li><p>If None the primary field will be selected.
+If this annotation resource doesn’t have fields, all proteins
+will be presented as one single category.</p></li>
+<li><p>If a string it will be considered a field name and it will
+browse through all levels of this field.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">list</span></code>, set or tuple, it will be considered either a
+<code class="docutils literal notranslate"><span class="pre">list</span></code> of field names or a list of values from the primary
+field. In the former case all combinations of the values of
+the fields will be presented, in the latter case the browsing
+will be limited to the levels of the primary field contained
+in <code class="docutils literal notranslate"><span class="pre">field</span></code>.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">dict</span></code>, keys are supposed to be field names and values
+as list of levels. If any of the values are None, all levels
+from that field will be used.</p></li>
+</ul>
+</dd>
+<dt>start:</dt><dd><p>Start browsing from this category. E.g. if there are 500
+categories and start is 250 it will skip everything before the
+250th.</p>
+</dd>
+<dt>kwargs:</dt><dd><p>Passed to <code class="docutils literal notranslate"><span class="pre">pypath.utils.uniprot.info</span></code>.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HumanPlasmaMembraneReceptome.complex_inference">
+<span class="sig-name descname"><span class="pre">complex_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HumanPlasmaMembraneReceptome.complex_inference" title="Link to this definition">§</a></dt>
+<dd><p>Annotates all complexes in <cite>complexes</cite>, by default in the default
+complex database (existing in the <cite>complex</cite> module or generated
+on demand according to the module’s current settings).</p>
+<dl class="field-list simple">
+<dt class="field-odd">Returns<span class="colon">:</span></dt>
+<dd class="field-odd"><p><ul class="simple">
+<li><p><em>Dict with complexes as keys and sets of annotations as values.</em></p></li>
+<li><p><em>Complexes with no valid information in this annotation resource</em></p></li>
+<li><p><em>won’t be in the dict.</em></p></li>
+</ul>
+</p>
+</dd>
+<dt class="field-even">Parameters<span class="colon">:</span></dt>
+<dd class="field-even"><p><strong>complexes</strong> (<em>iterable</em>) – Iterable yielding complexes.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HumanPlasmaMembraneReceptome.coverage">
+<span class="sig-name descname"><span class="pre">coverage</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">other</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HumanPlasmaMembraneReceptome.coverage" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the coverage of the annotation i.e. the proportion of
+entities having at least one record in this annotation resource
+for an arbitrary set of entities.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HumanPlasmaMembraneReceptome.curation_effort">
+<span class="sig-name descname"><span class="pre">curation_effort</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HumanPlasmaMembraneReceptome.curation_effort" title="Link to this definition">§</a></dt>
+<dd><p>Counts the reference-record pairs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HumanPlasmaMembraneReceptome.get_names">
+<span class="sig-name descname"><span class="pre">get_names</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HumanPlasmaMembraneReceptome.get_names" title="Link to this definition">§</a></dt>
+<dd><p>Returns the list of field names in the records. The annotation
+consists of uniform records and each entity might be annotated
+with one or more records. Each record is a tuple of fields, for
+example <code class="docutils literal notranslate"><span class="pre">('cell_type',</span> <span class="pre">'expression_level',</span> <span class="pre">'score')</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HumanPlasmaMembraneReceptome.get_reference_set">
+<em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">get_reference_set</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">proteins</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">swissprot_only</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HumanPlasmaMembraneReceptome.get_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the reference set i.e. the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HumanPlasmaMembraneReceptome.get_subset">
+<span class="sig-name descname"><span class="pre">get_subset</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HumanPlasmaMembraneReceptome.get_subset" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HumanPlasmaMembraneReceptome.get_subset_bool_array">
+<span class="sig-name descname"><span class="pre">get_subset_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HumanPlasmaMembraneReceptome.get_subset_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a boolean vector with True and False values for each entity
+in the reference set. The values represent presence absence data
+in the simplest case, but by providing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> any kind of matching
+and filtering is possible. <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> are passed to the <code class="docutils literal notranslate"><span class="pre">select</span></code>
+method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HumanPlasmaMembraneReceptome.get_values">
+<span class="sig-name descname"><span class="pre">get_values</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">exclude_none</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HumanPlasmaMembraneReceptome.get_values" title="Link to this definition">§</a></dt>
+<dd><p>Returns the set of all possible values of a field. E.g. if the
+records of this annotation have a field <code class="docutils literal notranslate"><span class="pre">cell_type</span></code> then calling
+this method can tell you that across all records the values of
+this field might be <code class="docutils literal notranslate"><span class="pre">{'macrophage',</span> <span class="pre">'epithelial_cell',</span> <span class="pre">...}</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HumanPlasmaMembraneReceptome.labels">
+<span class="sig-name descname"><span class="pre">labels</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HumanPlasmaMembraneReceptome.labels" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HumanPlasmaMembraneReceptome.load">
+<span class="sig-name descname"><span class="pre">load</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HumanPlasmaMembraneReceptome.load" title="Link to this definition">§</a></dt>
+<dd><p>Loads the annotation data by calling the input method.
+Infers annotations for complexes in the complex database if
+py:attr:<code class="docutils literal notranslate"><span class="pre">infer_complexes</span></code> is True.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HumanPlasmaMembraneReceptome.load_data">
+<span class="sig-name descname"><span class="pre">load_data</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HumanPlasmaMembraneReceptome.load_data" title="Link to this definition">§</a></dt>
+<dd><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HumanPlasmaMembraneReceptome.load_proteins">
+<span class="sig-name descname"><span class="pre">load_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HumanPlasmaMembraneReceptome.load_proteins" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a set of all UniProt IDs to have a base set of the entire
+proteome.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HumanPlasmaMembraneReceptome.make_df">
+<span class="sig-name descname"><span class="pre">make_df</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">rebuild</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HumanPlasmaMembraneReceptome.make_df" title="Link to this definition">§</a></dt>
+<dd><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.
+The data frame will be assigned to :py:attr``df``.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HumanPlasmaMembraneReceptome.numof_entities">
+<span class="sig-name descname"><span class="pre">numof_entities</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HumanPlasmaMembraneReceptome.numof_entities" title="Link to this definition">§</a></dt>
+<dd><p>The number of annotated entities in the resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HumanPlasmaMembraneReceptome.numof_records">
+<span class="sig-name descname"><span class="pre">numof_records</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HumanPlasmaMembraneReceptome.numof_records" title="Link to this definition">§</a></dt>
+<dd><p>The total number of annotation records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HumanPlasmaMembraneReceptome.numof_references">
+<span class="sig-name descname"><span class="pre">numof_references</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HumanPlasmaMembraneReceptome.numof_references" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects and counts the
+references across all records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HumanPlasmaMembraneReceptome.process">
+<span class="sig-name descname"><span class="pre">process</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HumanPlasmaMembraneReceptome.process" title="Link to this definition">§</a></dt>
+<dd><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HumanPlasmaMembraneReceptome.reload">
+<span class="sig-name descname"><span class="pre">reload</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HumanPlasmaMembraneReceptome.reload" title="Link to this definition">§</a></dt>
+<dd><p>Reloads the object from the module level.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HumanPlasmaMembraneReceptome.select">
+<span class="sig-name descname"><span class="pre">select</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HumanPlasmaMembraneReceptome.select" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HumanPlasmaMembraneReceptome.set_method">
+<span class="sig-name descname"><span class="pre">set_method</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HumanPlasmaMembraneReceptome.set_method" title="Link to this definition">§</a></dt>
+<dd><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if
+necessary.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HumanPlasmaMembraneReceptome.set_reference_set">
+<span class="sig-name descname"><span class="pre">set_reference_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HumanPlasmaMembraneReceptome.set_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Assigns the reference set to the :py:attr``reference_set`` attribute.
+The reference set is the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HumanPlasmaMembraneReceptome.show">
+<span class="sig-name descname"><span class="pre">show</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">table_param</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HumanPlasmaMembraneReceptome.show" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic
+information from the UniProt datasheets.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HumanPlasmaMembraneReceptome.subset_intersection">
+<span class="sig-name descname"><span class="pre">subset_intersection</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">universe</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HumanPlasmaMembraneReceptome.subset_intersection" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the proportion of entities in a subset occuring in the
+set <code class="docutils literal notranslate"><span class="pre">universe</span></code>. The subset is selected by passing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> to the
+<code class="docutils literal notranslate"><span class="pre">select</span></code> method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HumanPlasmaMembraneReceptome.to_array">
+<span class="sig-name descname"><span class="pre">to_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_fields</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HumanPlasmaMembraneReceptome.to_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns an entity vs feature array. In case of more complex
+annotations this might be huge.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HumanPlasmaMembraneReceptome.to_bool_array">
+<span class="sig-name descname"><span class="pre">to_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HumanPlasmaMembraneReceptome.to_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a presence/absence boolean array for a reference set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HumanPlasmaMembraneReceptome.to_set">
+<span class="sig-name descname"><span class="pre">to_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HumanPlasmaMembraneReceptome.to_set" title="Link to this definition">§</a></dt>
+<dd><p>Returns the entities present in this annotation resource as a set.</p>
+</dd></dl>
+
+</dd></dl>
+
+</section>
+
+
+                </article>
+              
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+  <section id="pypath-core-annot-humanproteinatlas">
+<h1>pypath.core.annot.HumanProteinAtlas<a class="headerlink" href="#pypath-core-annot-humanproteinatlas" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.core.annot.HumanProteinAtlas">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.core.annot.</span></span><span class="sig-name descname"><span class="pre">HumanProteinAtlas</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#HumanProteinAtlas"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.HumanProteinAtlas" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <a class="reference internal" href="pypath.core.annot.AnnotationBase.html#pypath.core.annot.AnnotationBase" title="pypath.core.annot.AnnotationBase"><code class="xref py py-class docutils literal notranslate"><span class="pre">AnnotationBase</span></code></a></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HumanProteinAtlas.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#HumanProteinAtlas.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.HumanProteinAtlas.__init__" title="Link to this definition">§</a></dt>
+<dd><p>Represents annotations for a set of proteins.
+Loads the data from the original resource and provides methods
+to query the annotations.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>name</strong> (<em>str</em>) – A custom name for the annotation resource.</p></li>
+<li><p><strong>ncbi_tax_id</strong> (<em>int</em>) – NCBI Taxonomy identifier.</p></li>
+<li><p><strong>input_method</strong> (<em>callable</em><em>,</em><em>str</em>) – Either a callable or the name of a method in any submodules of
+the <code class="docutils literal notranslate"><span class="pre">pypath.inputs</span></code>  module. Should return a dict with
+UniProt IDs as keys or an object suitable for <code class="docutils literal notranslate"><span class="pre">process_method</span></code>.</p></li>
+<li><p><strong>input_args</strong> (<em>dict</em>) – Arguments for the <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.HumanProteinAtlas.__init__" title="pypath.core.annot.HumanProteinAtlas.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>(**kwargs)</p></td>
+<td><p>Represents annotations for a set of proteins.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.HumanProteinAtlas.add_complexes_by_inference" title="pypath.core.annot.HumanProteinAtlas.add_complexes_by_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">add_complexes_by_inference</span></code></a>([complexes])</p></td>
+<td><p>Creates complex annotations by in silico inference and adds them to this annotation set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.HumanProteinAtlas.all_complexes" title="pypath.core.annot.HumanProteinAtlas.all_complexes"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_complexes</span></code></a>()</p></td>
+<td><p>All protein complexes annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.HumanProteinAtlas.all_entities" title="pypath.core.annot.HumanProteinAtlas.all_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_entities</span></code></a>([entity_types])</p></td>
+<td><p>All entities annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.HumanProteinAtlas.all_mirnas" title="pypath.core.annot.HumanProteinAtlas.all_mirnas"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_mirnas</span></code></a>()</p></td>
+<td><p>All miRNAs annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.HumanProteinAtlas.all_proteins" title="pypath.core.annot.HumanProteinAtlas.all_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_proteins</span></code></a>()</p></td>
+<td><p>All UniProt IDs annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.HumanProteinAtlas.all_refs" title="pypath.core.annot.HumanProteinAtlas.all_refs"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_refs</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.HumanProteinAtlas.annotate_complex" title="pypath.core.annot.HumanProteinAtlas.annotate_complex"><code class="xref py py-obj docutils literal notranslate"><span class="pre">annotate_complex</span></code></a>(cplex)</p></td>
+<td><p>Infers annotations for a single complex.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.HumanProteinAtlas.browse" title="pypath.core.annot.HumanProteinAtlas.browse"><code class="xref py py-obj docutils literal notranslate"><span class="pre">browse</span></code></a>([field, start])</p></td>
+<td><p>Print gene information as a table.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.HumanProteinAtlas.complex_inference" title="pypath.core.annot.HumanProteinAtlas.complex_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">complex_inference</span></code></a>([complexes])</p></td>
+<td><p>Annotates all complexes in <cite>complexes</cite>, by default in the default complex database (existing in the <cite>complex</cite> module or generated on demand according to the module's current settings).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.HumanProteinAtlas.coverage" title="pypath.core.annot.HumanProteinAtlas.coverage"><code class="xref py py-obj docutils literal notranslate"><span class="pre">coverage</span></code></a>(other)</p></td>
+<td><p>Calculates the coverage of the annotation i.e. the proportion of entities having at least one record in this annotation resource for an arbitrary set of entities.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.HumanProteinAtlas.curation_effort" title="pypath.core.annot.HumanProteinAtlas.curation_effort"><code class="xref py py-obj docutils literal notranslate"><span class="pre">curation_effort</span></code></a>()</p></td>
+<td><p>Counts the reference-record pairs.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">from_dump</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_entity_type</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.HumanProteinAtlas.get_names" title="pypath.core.annot.HumanProteinAtlas.get_names"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_names</span></code></a>()</p></td>
+<td><p>Returns the list of field names in the records.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.HumanProteinAtlas.get_reference_set" title="pypath.core.annot.HumanProteinAtlas.get_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_reference_set</span></code></a>([proteins, complexes, ...])</p></td>
+<td><p>Retrieves the reference set i.e. the set of all entities which potentially have annotation in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.HumanProteinAtlas.get_subset" title="pypath.core.annot.HumanProteinAtlas.get_subset"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.HumanProteinAtlas.get_subset_bool_array" title="pypath.core.annot.HumanProteinAtlas.get_subset_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset_bool_array</span></code></a>([reference_set])</p></td>
+<td><p>Returns a boolean vector with True and False values for each entity in the reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.HumanProteinAtlas.get_values" title="pypath.core.annot.HumanProteinAtlas.get_values"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_values</span></code></a>(name[, exclude_none])</p></td>
+<td><p>Returns the set of all possible values of a field.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_complex</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_mirna</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_protein</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.HumanProteinAtlas.labels" title="pypath.core.annot.HumanProteinAtlas.labels"><code class="xref py py-obj docutils literal notranslate"><span class="pre">labels</span></code></a>([method])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.HumanProteinAtlas.load" title="pypath.core.annot.HumanProteinAtlas.load"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load</span></code></a>()</p></td>
+<td><p>Loads the annotation data by calling the input method.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.HumanProteinAtlas.load_data" title="pypath.core.annot.HumanProteinAtlas.load_data"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_data</span></code></a>()</p></td>
+<td><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.HumanProteinAtlas.load_proteins" title="pypath.core.annot.HumanProteinAtlas.load_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_proteins</span></code></a>()</p></td>
+<td><p>Retrieves a set of all UniProt IDs to have a base set of the entire proteome.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.HumanProteinAtlas.make_df" title="pypath.core.annot.HumanProteinAtlas.make_df"><code class="xref py py-obj docutils literal notranslate"><span class="pre">make_df</span></code></a>([rebuild])</p></td>
+<td><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complex_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.HumanProteinAtlas.numof_entities" title="pypath.core.annot.HumanProteinAtlas.numof_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_entities</span></code></a>()</p></td>
+<td><p>The number of annotated entities in the resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirna_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirnas</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_protein_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_proteins</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.HumanProteinAtlas.numof_records" title="pypath.core.annot.HumanProteinAtlas.numof_records"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_records</span></code></a>([entity_types])</p></td>
+<td><p>The total number of annotation records.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.HumanProteinAtlas.numof_references" title="pypath.core.annot.HumanProteinAtlas.numof_references"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_references</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.HumanProteinAtlas.process" title="pypath.core.annot.HumanProteinAtlas.process"><code class="xref py py-obj docutils literal notranslate"><span class="pre">process</span></code></a>()</p></td>
+<td><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">proportion</span></code>(other)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.HumanProteinAtlas.reload" title="pypath.core.annot.HumanProteinAtlas.reload"><code class="xref py py-obj docutils literal notranslate"><span class="pre">reload</span></code></a>()</p></td>
+<td><p>Reloads the object from the module level.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">save_to_pickle</span></code>(pickle_file)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.HumanProteinAtlas.select" title="pypath.core.annot.HumanProteinAtlas.select"><code class="xref py py-obj docutils literal notranslate"><span class="pre">select</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.HumanProteinAtlas.set_method" title="pypath.core.annot.HumanProteinAtlas.set_method"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_method</span></code></a>()</p></td>
+<td><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if necessary.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.HumanProteinAtlas.set_reference_set" title="pypath.core.annot.HumanProteinAtlas.set_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_reference_set</span></code></a>()</p></td>
+<td><p>Assigns the reference set to the :py:attr``reference_set`` attribute.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.HumanProteinAtlas.show" title="pypath.core.annot.HumanProteinAtlas.show"><code class="xref py py-obj docutils literal notranslate"><span class="pre">show</span></code></a>([method, table_param])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic information from the UniProt datasheets.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.HumanProteinAtlas.subset_intersection" title="pypath.core.annot.HumanProteinAtlas.subset_intersection"><code class="xref py py-obj docutils literal notranslate"><span class="pre">subset_intersection</span></code></a>(universe, **kwargs)</p></td>
+<td><p>Calculates the proportion of entities in a subset occuring in the set <code class="docutils literal notranslate"><span class="pre">universe</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.HumanProteinAtlas.to_array" title="pypath.core.annot.HumanProteinAtlas.to_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_array</span></code></a>([reference_set, use_fields])</p></td>
+<td><p>Returns an entity vs feature array.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.HumanProteinAtlas.to_bool_array" title="pypath.core.annot.HumanProteinAtlas.to_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_bool_array</span></code></a>(reference_set)</p></td>
+<td><p>Returns a presence/absence boolean array for a reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.HumanProteinAtlas.to_set" title="pypath.core.annot.HumanProteinAtlas.to_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_set</span></code></a>()</p></td>
+<td><p>Returns the entities present in this annotation resource as a set.</p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Attributes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_fields</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">summary</span></code></p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HumanProteinAtlas.add_complexes_by_inference">
+<span class="sig-name descname"><span class="pre">add_complexes_by_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HumanProteinAtlas.add_complexes_by_inference" title="Link to this definition">§</a></dt>
+<dd><p>Creates complex annotations by in silico inference and adds them
+to this annotation set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HumanProteinAtlas.all_complexes">
+<span class="sig-name descname"><span class="pre">all_complexes</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HumanProteinAtlas.all_complexes" title="Link to this definition">§</a></dt>
+<dd><p>All protein complexes annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HumanProteinAtlas.all_entities">
+<span class="sig-name descname"><span class="pre">all_entities</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HumanProteinAtlas.all_entities" title="Link to this definition">§</a></dt>
+<dd><p>All entities annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HumanProteinAtlas.all_mirnas">
+<span class="sig-name descname"><span class="pre">all_mirnas</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HumanProteinAtlas.all_mirnas" title="Link to this definition">§</a></dt>
+<dd><p>All miRNAs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HumanProteinAtlas.all_proteins">
+<span class="sig-name descname"><span class="pre">all_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HumanProteinAtlas.all_proteins" title="Link to this definition">§</a></dt>
+<dd><p>All UniProt IDs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HumanProteinAtlas.all_refs">
+<span class="sig-name descname"><span class="pre">all_refs</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HumanProteinAtlas.all_refs" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects the references
+across all records. Returns <em>list</em>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HumanProteinAtlas.annotate_complex">
+<span class="sig-name descname"><span class="pre">annotate_complex</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cplex</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HumanProteinAtlas.annotate_complex" title="Link to this definition">§</a></dt>
+<dd><p>Infers annotations for a single complex.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HumanProteinAtlas.browse">
+<span class="sig-name descname"><span class="pre">browse</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">field</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">start</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HumanProteinAtlas.browse" title="Link to this definition">§</a></dt>
+<dd><p>Print gene information as a table.</p>
+<p>Presents information about annotation categories as ascii tables
+printed in the terminal. If one category provided, prints one table.
+If multiple categories provided, prints a table for each of them one
+by one proceeding to the next one once you hit return. If no categories
+provided goes through all levels of the primary category.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>field:</dt><dd><p>The field to browse categories by.</p>
+<ul class="simple">
+<li><p>If None the primary field will be selected.
+If this annotation resource doesn’t have fields, all proteins
+will be presented as one single category.</p></li>
+<li><p>If a string it will be considered a field name and it will
+browse through all levels of this field.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">list</span></code>, set or tuple, it will be considered either a
+<code class="docutils literal notranslate"><span class="pre">list</span></code> of field names or a list of values from the primary
+field. In the former case all combinations of the values of
+the fields will be presented, in the latter case the browsing
+will be limited to the levels of the primary field contained
+in <code class="docutils literal notranslate"><span class="pre">field</span></code>.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">dict</span></code>, keys are supposed to be field names and values
+as list of levels. If any of the values are None, all levels
+from that field will be used.</p></li>
+</ul>
+</dd>
+<dt>start:</dt><dd><p>Start browsing from this category. E.g. if there are 500
+categories and start is 250 it will skip everything before the
+250th.</p>
+</dd>
+<dt>kwargs:</dt><dd><p>Passed to <code class="docutils literal notranslate"><span class="pre">pypath.utils.uniprot.info</span></code>.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HumanProteinAtlas.complex_inference">
+<span class="sig-name descname"><span class="pre">complex_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HumanProteinAtlas.complex_inference" title="Link to this definition">§</a></dt>
+<dd><p>Annotates all complexes in <cite>complexes</cite>, by default in the default
+complex database (existing in the <cite>complex</cite> module or generated
+on demand according to the module’s current settings).</p>
+<dl class="field-list simple">
+<dt class="field-odd">Returns<span class="colon">:</span></dt>
+<dd class="field-odd"><p><ul class="simple">
+<li><p><em>Dict with complexes as keys and sets of annotations as values.</em></p></li>
+<li><p><em>Complexes with no valid information in this annotation resource</em></p></li>
+<li><p><em>won’t be in the dict.</em></p></li>
+</ul>
+</p>
+</dd>
+<dt class="field-even">Parameters<span class="colon">:</span></dt>
+<dd class="field-even"><p><strong>complexes</strong> (<em>iterable</em>) – Iterable yielding complexes.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HumanProteinAtlas.coverage">
+<span class="sig-name descname"><span class="pre">coverage</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">other</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HumanProteinAtlas.coverage" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the coverage of the annotation i.e. the proportion of
+entities having at least one record in this annotation resource
+for an arbitrary set of entities.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HumanProteinAtlas.curation_effort">
+<span class="sig-name descname"><span class="pre">curation_effort</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HumanProteinAtlas.curation_effort" title="Link to this definition">§</a></dt>
+<dd><p>Counts the reference-record pairs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HumanProteinAtlas.get_names">
+<span class="sig-name descname"><span class="pre">get_names</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HumanProteinAtlas.get_names" title="Link to this definition">§</a></dt>
+<dd><p>Returns the list of field names in the records. The annotation
+consists of uniform records and each entity might be annotated
+with one or more records. Each record is a tuple of fields, for
+example <code class="docutils literal notranslate"><span class="pre">('cell_type',</span> <span class="pre">'expression_level',</span> <span class="pre">'score')</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HumanProteinAtlas.get_reference_set">
+<em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">get_reference_set</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">proteins</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">swissprot_only</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HumanProteinAtlas.get_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the reference set i.e. the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HumanProteinAtlas.get_subset">
+<span class="sig-name descname"><span class="pre">get_subset</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HumanProteinAtlas.get_subset" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HumanProteinAtlas.get_subset_bool_array">
+<span class="sig-name descname"><span class="pre">get_subset_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HumanProteinAtlas.get_subset_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a boolean vector with True and False values for each entity
+in the reference set. The values represent presence absence data
+in the simplest case, but by providing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> any kind of matching
+and filtering is possible. <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> are passed to the <code class="docutils literal notranslate"><span class="pre">select</span></code>
+method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HumanProteinAtlas.get_values">
+<span class="sig-name descname"><span class="pre">get_values</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">exclude_none</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HumanProteinAtlas.get_values" title="Link to this definition">§</a></dt>
+<dd><p>Returns the set of all possible values of a field. E.g. if the
+records of this annotation have a field <code class="docutils literal notranslate"><span class="pre">cell_type</span></code> then calling
+this method can tell you that across all records the values of
+this field might be <code class="docutils literal notranslate"><span class="pre">{'macrophage',</span> <span class="pre">'epithelial_cell',</span> <span class="pre">...}</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HumanProteinAtlas.labels">
+<span class="sig-name descname"><span class="pre">labels</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HumanProteinAtlas.labels" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HumanProteinAtlas.load">
+<span class="sig-name descname"><span class="pre">load</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HumanProteinAtlas.load" title="Link to this definition">§</a></dt>
+<dd><p>Loads the annotation data by calling the input method.
+Infers annotations for complexes in the complex database if
+py:attr:<code class="docutils literal notranslate"><span class="pre">infer_complexes</span></code> is True.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HumanProteinAtlas.load_data">
+<span class="sig-name descname"><span class="pre">load_data</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HumanProteinAtlas.load_data" title="Link to this definition">§</a></dt>
+<dd><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HumanProteinAtlas.load_proteins">
+<span class="sig-name descname"><span class="pre">load_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HumanProteinAtlas.load_proteins" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a set of all UniProt IDs to have a base set of the entire
+proteome.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HumanProteinAtlas.make_df">
+<span class="sig-name descname"><span class="pre">make_df</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">rebuild</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HumanProteinAtlas.make_df" title="Link to this definition">§</a></dt>
+<dd><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.
+The data frame will be assigned to :py:attr``df``.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HumanProteinAtlas.numof_entities">
+<span class="sig-name descname"><span class="pre">numof_entities</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HumanProteinAtlas.numof_entities" title="Link to this definition">§</a></dt>
+<dd><p>The number of annotated entities in the resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HumanProteinAtlas.numof_records">
+<span class="sig-name descname"><span class="pre">numof_records</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HumanProteinAtlas.numof_records" title="Link to this definition">§</a></dt>
+<dd><p>The total number of annotation records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HumanProteinAtlas.numof_references">
+<span class="sig-name descname"><span class="pre">numof_references</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HumanProteinAtlas.numof_references" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects and counts the
+references across all records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HumanProteinAtlas.process">
+<span class="sig-name descname"><span class="pre">process</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HumanProteinAtlas.process" title="Link to this definition">§</a></dt>
+<dd><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HumanProteinAtlas.reload">
+<span class="sig-name descname"><span class="pre">reload</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HumanProteinAtlas.reload" title="Link to this definition">§</a></dt>
+<dd><p>Reloads the object from the module level.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HumanProteinAtlas.select">
+<span class="sig-name descname"><span class="pre">select</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HumanProteinAtlas.select" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HumanProteinAtlas.set_method">
+<span class="sig-name descname"><span class="pre">set_method</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HumanProteinAtlas.set_method" title="Link to this definition">§</a></dt>
+<dd><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if
+necessary.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HumanProteinAtlas.set_reference_set">
+<span class="sig-name descname"><span class="pre">set_reference_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HumanProteinAtlas.set_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Assigns the reference set to the :py:attr``reference_set`` attribute.
+The reference set is the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HumanProteinAtlas.show">
+<span class="sig-name descname"><span class="pre">show</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">table_param</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HumanProteinAtlas.show" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic
+information from the UniProt datasheets.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HumanProteinAtlas.subset_intersection">
+<span class="sig-name descname"><span class="pre">subset_intersection</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">universe</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HumanProteinAtlas.subset_intersection" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the proportion of entities in a subset occuring in the
+set <code class="docutils literal notranslate"><span class="pre">universe</span></code>. The subset is selected by passing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> to the
+<code class="docutils literal notranslate"><span class="pre">select</span></code> method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HumanProteinAtlas.to_array">
+<span class="sig-name descname"><span class="pre">to_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_fields</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HumanProteinAtlas.to_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns an entity vs feature array. In case of more complex
+annotations this might be huge.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HumanProteinAtlas.to_bool_array">
+<span class="sig-name descname"><span class="pre">to_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HumanProteinAtlas.to_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a presence/absence boolean array for a reference set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HumanProteinAtlas.to_set">
+<span class="sig-name descname"><span class="pre">to_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HumanProteinAtlas.to_set" title="Link to this definition">§</a></dt>
+<dd><p>Returns the entities present in this annotation resource as a set.</p>
+</dd></dl>
+
+</dd></dl>
+
+</section>
+
+
+                </article>
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+  <section id="pypath-core-annot-humanproteinatlassecretome">
+<h1>pypath.core.annot.HumanProteinAtlasSecretome<a class="headerlink" href="#pypath-core-annot-humanproteinatlassecretome" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.core.annot.HumanProteinAtlasSecretome">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.core.annot.</span></span><span class="sig-name descname"><span class="pre">HumanProteinAtlasSecretome</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#HumanProteinAtlasSecretome"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.HumanProteinAtlasSecretome" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <a class="reference internal" href="pypath.core.annot.AnnotationBase.html#pypath.core.annot.AnnotationBase" title="pypath.core.annot.AnnotationBase"><code class="xref py py-class docutils literal notranslate"><span class="pre">AnnotationBase</span></code></a></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HumanProteinAtlasSecretome.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#HumanProteinAtlasSecretome.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.HumanProteinAtlasSecretome.__init__" title="Link to this definition">§</a></dt>
+<dd><p>Represents annotations for a set of proteins.
+Loads the data from the original resource and provides methods
+to query the annotations.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>name</strong> (<em>str</em>) – A custom name for the annotation resource.</p></li>
+<li><p><strong>ncbi_tax_id</strong> (<em>int</em>) – NCBI Taxonomy identifier.</p></li>
+<li><p><strong>input_method</strong> (<em>callable</em><em>,</em><em>str</em>) – Either a callable or the name of a method in any submodules of
+the <code class="docutils literal notranslate"><span class="pre">pypath.inputs</span></code>  module. Should return a dict with
+UniProt IDs as keys or an object suitable for <code class="docutils literal notranslate"><span class="pre">process_method</span></code>.</p></li>
+<li><p><strong>input_args</strong> (<em>dict</em>) – Arguments for the <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.HumanProteinAtlasSecretome.__init__" title="pypath.core.annot.HumanProteinAtlasSecretome.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>(**kwargs)</p></td>
+<td><p>Represents annotations for a set of proteins.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.HumanProteinAtlasSecretome.add_complexes_by_inference" title="pypath.core.annot.HumanProteinAtlasSecretome.add_complexes_by_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">add_complexes_by_inference</span></code></a>([complexes])</p></td>
+<td><p>Creates complex annotations by in silico inference and adds them to this annotation set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.HumanProteinAtlasSecretome.all_complexes" title="pypath.core.annot.HumanProteinAtlasSecretome.all_complexes"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_complexes</span></code></a>()</p></td>
+<td><p>All protein complexes annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.HumanProteinAtlasSecretome.all_entities" title="pypath.core.annot.HumanProteinAtlasSecretome.all_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_entities</span></code></a>([entity_types])</p></td>
+<td><p>All entities annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.HumanProteinAtlasSecretome.all_mirnas" title="pypath.core.annot.HumanProteinAtlasSecretome.all_mirnas"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_mirnas</span></code></a>()</p></td>
+<td><p>All miRNAs annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.HumanProteinAtlasSecretome.all_proteins" title="pypath.core.annot.HumanProteinAtlasSecretome.all_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_proteins</span></code></a>()</p></td>
+<td><p>All UniProt IDs annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.HumanProteinAtlasSecretome.all_refs" title="pypath.core.annot.HumanProteinAtlasSecretome.all_refs"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_refs</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.HumanProteinAtlasSecretome.annotate_complex" title="pypath.core.annot.HumanProteinAtlasSecretome.annotate_complex"><code class="xref py py-obj docutils literal notranslate"><span class="pre">annotate_complex</span></code></a>(cplex)</p></td>
+<td><p>Infers annotations for a single complex.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.HumanProteinAtlasSecretome.browse" title="pypath.core.annot.HumanProteinAtlasSecretome.browse"><code class="xref py py-obj docutils literal notranslate"><span class="pre">browse</span></code></a>([field, start])</p></td>
+<td><p>Print gene information as a table.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.HumanProteinAtlasSecretome.complex_inference" title="pypath.core.annot.HumanProteinAtlasSecretome.complex_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">complex_inference</span></code></a>([complexes])</p></td>
+<td><p>Annotates all complexes in <cite>complexes</cite>, by default in the default complex database (existing in the <cite>complex</cite> module or generated on demand according to the module's current settings).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.HumanProteinAtlasSecretome.coverage" title="pypath.core.annot.HumanProteinAtlasSecretome.coverage"><code class="xref py py-obj docutils literal notranslate"><span class="pre">coverage</span></code></a>(other)</p></td>
+<td><p>Calculates the coverage of the annotation i.e. the proportion of entities having at least one record in this annotation resource for an arbitrary set of entities.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.HumanProteinAtlasSecretome.curation_effort" title="pypath.core.annot.HumanProteinAtlasSecretome.curation_effort"><code class="xref py py-obj docutils literal notranslate"><span class="pre">curation_effort</span></code></a>()</p></td>
+<td><p>Counts the reference-record pairs.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">from_dump</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_entity_type</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.HumanProteinAtlasSecretome.get_names" title="pypath.core.annot.HumanProteinAtlasSecretome.get_names"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_names</span></code></a>()</p></td>
+<td><p>Returns the list of field names in the records.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.HumanProteinAtlasSecretome.get_reference_set" title="pypath.core.annot.HumanProteinAtlasSecretome.get_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_reference_set</span></code></a>([proteins, complexes, ...])</p></td>
+<td><p>Retrieves the reference set i.e. the set of all entities which potentially have annotation in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.HumanProteinAtlasSecretome.get_subset" title="pypath.core.annot.HumanProteinAtlasSecretome.get_subset"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.HumanProteinAtlasSecretome.get_subset_bool_array" title="pypath.core.annot.HumanProteinAtlasSecretome.get_subset_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset_bool_array</span></code></a>([reference_set])</p></td>
+<td><p>Returns a boolean vector with True and False values for each entity in the reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.HumanProteinAtlasSecretome.get_values" title="pypath.core.annot.HumanProteinAtlasSecretome.get_values"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_values</span></code></a>(name[, exclude_none])</p></td>
+<td><p>Returns the set of all possible values of a field.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_complex</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_mirna</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_protein</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.HumanProteinAtlasSecretome.labels" title="pypath.core.annot.HumanProteinAtlasSecretome.labels"><code class="xref py py-obj docutils literal notranslate"><span class="pre">labels</span></code></a>([method])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.HumanProteinAtlasSecretome.load" title="pypath.core.annot.HumanProteinAtlasSecretome.load"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load</span></code></a>()</p></td>
+<td><p>Loads the annotation data by calling the input method.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.HumanProteinAtlasSecretome.load_data" title="pypath.core.annot.HumanProteinAtlasSecretome.load_data"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_data</span></code></a>()</p></td>
+<td><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.HumanProteinAtlasSecretome.load_proteins" title="pypath.core.annot.HumanProteinAtlasSecretome.load_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_proteins</span></code></a>()</p></td>
+<td><p>Retrieves a set of all UniProt IDs to have a base set of the entire proteome.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.HumanProteinAtlasSecretome.make_df" title="pypath.core.annot.HumanProteinAtlasSecretome.make_df"><code class="xref py py-obj docutils literal notranslate"><span class="pre">make_df</span></code></a>([rebuild])</p></td>
+<td><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complex_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.HumanProteinAtlasSecretome.numof_entities" title="pypath.core.annot.HumanProteinAtlasSecretome.numof_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_entities</span></code></a>()</p></td>
+<td><p>The number of annotated entities in the resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirna_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirnas</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_protein_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_proteins</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.HumanProteinAtlasSecretome.numof_records" title="pypath.core.annot.HumanProteinAtlasSecretome.numof_records"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_records</span></code></a>([entity_types])</p></td>
+<td><p>The total number of annotation records.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.HumanProteinAtlasSecretome.numof_references" title="pypath.core.annot.HumanProteinAtlasSecretome.numof_references"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_references</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.HumanProteinAtlasSecretome.process" title="pypath.core.annot.HumanProteinAtlasSecretome.process"><code class="xref py py-obj docutils literal notranslate"><span class="pre">process</span></code></a>()</p></td>
+<td><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">proportion</span></code>(other)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.HumanProteinAtlasSecretome.reload" title="pypath.core.annot.HumanProteinAtlasSecretome.reload"><code class="xref py py-obj docutils literal notranslate"><span class="pre">reload</span></code></a>()</p></td>
+<td><p>Reloads the object from the module level.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">save_to_pickle</span></code>(pickle_file)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.HumanProteinAtlasSecretome.select" title="pypath.core.annot.HumanProteinAtlasSecretome.select"><code class="xref py py-obj docutils literal notranslate"><span class="pre">select</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.HumanProteinAtlasSecretome.set_method" title="pypath.core.annot.HumanProteinAtlasSecretome.set_method"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_method</span></code></a>()</p></td>
+<td><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if necessary.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.HumanProteinAtlasSecretome.set_reference_set" title="pypath.core.annot.HumanProteinAtlasSecretome.set_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_reference_set</span></code></a>()</p></td>
+<td><p>Assigns the reference set to the :py:attr``reference_set`` attribute.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.HumanProteinAtlasSecretome.show" title="pypath.core.annot.HumanProteinAtlasSecretome.show"><code class="xref py py-obj docutils literal notranslate"><span class="pre">show</span></code></a>([method, table_param])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic information from the UniProt datasheets.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.HumanProteinAtlasSecretome.subset_intersection" title="pypath.core.annot.HumanProteinAtlasSecretome.subset_intersection"><code class="xref py py-obj docutils literal notranslate"><span class="pre">subset_intersection</span></code></a>(universe, **kwargs)</p></td>
+<td><p>Calculates the proportion of entities in a subset occuring in the set <code class="docutils literal notranslate"><span class="pre">universe</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.HumanProteinAtlasSecretome.to_array" title="pypath.core.annot.HumanProteinAtlasSecretome.to_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_array</span></code></a>([reference_set, use_fields])</p></td>
+<td><p>Returns an entity vs feature array.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.HumanProteinAtlasSecretome.to_bool_array" title="pypath.core.annot.HumanProteinAtlasSecretome.to_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_bool_array</span></code></a>(reference_set)</p></td>
+<td><p>Returns a presence/absence boolean array for a reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.HumanProteinAtlasSecretome.to_set" title="pypath.core.annot.HumanProteinAtlasSecretome.to_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_set</span></code></a>()</p></td>
+<td><p>Returns the entities present in this annotation resource as a set.</p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Attributes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_fields</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">summary</span></code></p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HumanProteinAtlasSecretome.add_complexes_by_inference">
+<span class="sig-name descname"><span class="pre">add_complexes_by_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HumanProteinAtlasSecretome.add_complexes_by_inference" title="Link to this definition">§</a></dt>
+<dd><p>Creates complex annotations by in silico inference and adds them
+to this annotation set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HumanProteinAtlasSecretome.all_complexes">
+<span class="sig-name descname"><span class="pre">all_complexes</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HumanProteinAtlasSecretome.all_complexes" title="Link to this definition">§</a></dt>
+<dd><p>All protein complexes annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HumanProteinAtlasSecretome.all_entities">
+<span class="sig-name descname"><span class="pre">all_entities</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HumanProteinAtlasSecretome.all_entities" title="Link to this definition">§</a></dt>
+<dd><p>All entities annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HumanProteinAtlasSecretome.all_mirnas">
+<span class="sig-name descname"><span class="pre">all_mirnas</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HumanProteinAtlasSecretome.all_mirnas" title="Link to this definition">§</a></dt>
+<dd><p>All miRNAs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HumanProteinAtlasSecretome.all_proteins">
+<span class="sig-name descname"><span class="pre">all_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HumanProteinAtlasSecretome.all_proteins" title="Link to this definition">§</a></dt>
+<dd><p>All UniProt IDs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HumanProteinAtlasSecretome.all_refs">
+<span class="sig-name descname"><span class="pre">all_refs</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HumanProteinAtlasSecretome.all_refs" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects the references
+across all records. Returns <em>list</em>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HumanProteinAtlasSecretome.annotate_complex">
+<span class="sig-name descname"><span class="pre">annotate_complex</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cplex</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HumanProteinAtlasSecretome.annotate_complex" title="Link to this definition">§</a></dt>
+<dd><p>Infers annotations for a single complex.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HumanProteinAtlasSecretome.browse">
+<span class="sig-name descname"><span class="pre">browse</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">field</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">start</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HumanProteinAtlasSecretome.browse" title="Link to this definition">§</a></dt>
+<dd><p>Print gene information as a table.</p>
+<p>Presents information about annotation categories as ascii tables
+printed in the terminal. If one category provided, prints one table.
+If multiple categories provided, prints a table for each of them one
+by one proceeding to the next one once you hit return. If no categories
+provided goes through all levels of the primary category.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>field:</dt><dd><p>The field to browse categories by.</p>
+<ul class="simple">
+<li><p>If None the primary field will be selected.
+If this annotation resource doesn’t have fields, all proteins
+will be presented as one single category.</p></li>
+<li><p>If a string it will be considered a field name and it will
+browse through all levels of this field.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">list</span></code>, set or tuple, it will be considered either a
+<code class="docutils literal notranslate"><span class="pre">list</span></code> of field names or a list of values from the primary
+field. In the former case all combinations of the values of
+the fields will be presented, in the latter case the browsing
+will be limited to the levels of the primary field contained
+in <code class="docutils literal notranslate"><span class="pre">field</span></code>.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">dict</span></code>, keys are supposed to be field names and values
+as list of levels. If any of the values are None, all levels
+from that field will be used.</p></li>
+</ul>
+</dd>
+<dt>start:</dt><dd><p>Start browsing from this category. E.g. if there are 500
+categories and start is 250 it will skip everything before the
+250th.</p>
+</dd>
+<dt>kwargs:</dt><dd><p>Passed to <code class="docutils literal notranslate"><span class="pre">pypath.utils.uniprot.info</span></code>.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HumanProteinAtlasSecretome.complex_inference">
+<span class="sig-name descname"><span class="pre">complex_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HumanProteinAtlasSecretome.complex_inference" title="Link to this definition">§</a></dt>
+<dd><p>Annotates all complexes in <cite>complexes</cite>, by default in the default
+complex database (existing in the <cite>complex</cite> module or generated
+on demand according to the module’s current settings).</p>
+<dl class="field-list simple">
+<dt class="field-odd">Returns<span class="colon">:</span></dt>
+<dd class="field-odd"><p><ul class="simple">
+<li><p><em>Dict with complexes as keys and sets of annotations as values.</em></p></li>
+<li><p><em>Complexes with no valid information in this annotation resource</em></p></li>
+<li><p><em>won’t be in the dict.</em></p></li>
+</ul>
+</p>
+</dd>
+<dt class="field-even">Parameters<span class="colon">:</span></dt>
+<dd class="field-even"><p><strong>complexes</strong> (<em>iterable</em>) – Iterable yielding complexes.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HumanProteinAtlasSecretome.coverage">
+<span class="sig-name descname"><span class="pre">coverage</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">other</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HumanProteinAtlasSecretome.coverage" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the coverage of the annotation i.e. the proportion of
+entities having at least one record in this annotation resource
+for an arbitrary set of entities.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HumanProteinAtlasSecretome.curation_effort">
+<span class="sig-name descname"><span class="pre">curation_effort</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HumanProteinAtlasSecretome.curation_effort" title="Link to this definition">§</a></dt>
+<dd><p>Counts the reference-record pairs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HumanProteinAtlasSecretome.get_names">
+<span class="sig-name descname"><span class="pre">get_names</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HumanProteinAtlasSecretome.get_names" title="Link to this definition">§</a></dt>
+<dd><p>Returns the list of field names in the records. The annotation
+consists of uniform records and each entity might be annotated
+with one or more records. Each record is a tuple of fields, for
+example <code class="docutils literal notranslate"><span class="pre">('cell_type',</span> <span class="pre">'expression_level',</span> <span class="pre">'score')</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HumanProteinAtlasSecretome.get_reference_set">
+<em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">get_reference_set</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">proteins</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">swissprot_only</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HumanProteinAtlasSecretome.get_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the reference set i.e. the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HumanProteinAtlasSecretome.get_subset">
+<span class="sig-name descname"><span class="pre">get_subset</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HumanProteinAtlasSecretome.get_subset" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HumanProteinAtlasSecretome.get_subset_bool_array">
+<span class="sig-name descname"><span class="pre">get_subset_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HumanProteinAtlasSecretome.get_subset_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a boolean vector with True and False values for each entity
+in the reference set. The values represent presence absence data
+in the simplest case, but by providing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> any kind of matching
+and filtering is possible. <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> are passed to the <code class="docutils literal notranslate"><span class="pre">select</span></code>
+method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HumanProteinAtlasSecretome.get_values">
+<span class="sig-name descname"><span class="pre">get_values</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">exclude_none</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HumanProteinAtlasSecretome.get_values" title="Link to this definition">§</a></dt>
+<dd><p>Returns the set of all possible values of a field. E.g. if the
+records of this annotation have a field <code class="docutils literal notranslate"><span class="pre">cell_type</span></code> then calling
+this method can tell you that across all records the values of
+this field might be <code class="docutils literal notranslate"><span class="pre">{'macrophage',</span> <span class="pre">'epithelial_cell',</span> <span class="pre">...}</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HumanProteinAtlasSecretome.labels">
+<span class="sig-name descname"><span class="pre">labels</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HumanProteinAtlasSecretome.labels" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HumanProteinAtlasSecretome.load">
+<span class="sig-name descname"><span class="pre">load</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HumanProteinAtlasSecretome.load" title="Link to this definition">§</a></dt>
+<dd><p>Loads the annotation data by calling the input method.
+Infers annotations for complexes in the complex database if
+py:attr:<code class="docutils literal notranslate"><span class="pre">infer_complexes</span></code> is True.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HumanProteinAtlasSecretome.load_data">
+<span class="sig-name descname"><span class="pre">load_data</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HumanProteinAtlasSecretome.load_data" title="Link to this definition">§</a></dt>
+<dd><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HumanProteinAtlasSecretome.load_proteins">
+<span class="sig-name descname"><span class="pre">load_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HumanProteinAtlasSecretome.load_proteins" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a set of all UniProt IDs to have a base set of the entire
+proteome.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HumanProteinAtlasSecretome.make_df">
+<span class="sig-name descname"><span class="pre">make_df</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">rebuild</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HumanProteinAtlasSecretome.make_df" title="Link to this definition">§</a></dt>
+<dd><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.
+The data frame will be assigned to :py:attr``df``.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HumanProteinAtlasSecretome.numof_entities">
+<span class="sig-name descname"><span class="pre">numof_entities</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HumanProteinAtlasSecretome.numof_entities" title="Link to this definition">§</a></dt>
+<dd><p>The number of annotated entities in the resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HumanProteinAtlasSecretome.numof_records">
+<span class="sig-name descname"><span class="pre">numof_records</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HumanProteinAtlasSecretome.numof_records" title="Link to this definition">§</a></dt>
+<dd><p>The total number of annotation records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HumanProteinAtlasSecretome.numof_references">
+<span class="sig-name descname"><span class="pre">numof_references</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HumanProteinAtlasSecretome.numof_references" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects and counts the
+references across all records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HumanProteinAtlasSecretome.process">
+<span class="sig-name descname"><span class="pre">process</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HumanProteinAtlasSecretome.process" title="Link to this definition">§</a></dt>
+<dd><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HumanProteinAtlasSecretome.reload">
+<span class="sig-name descname"><span class="pre">reload</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HumanProteinAtlasSecretome.reload" title="Link to this definition">§</a></dt>
+<dd><p>Reloads the object from the module level.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HumanProteinAtlasSecretome.select">
+<span class="sig-name descname"><span class="pre">select</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HumanProteinAtlasSecretome.select" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HumanProteinAtlasSecretome.set_method">
+<span class="sig-name descname"><span class="pre">set_method</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HumanProteinAtlasSecretome.set_method" title="Link to this definition">§</a></dt>
+<dd><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if
+necessary.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HumanProteinAtlasSecretome.set_reference_set">
+<span class="sig-name descname"><span class="pre">set_reference_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HumanProteinAtlasSecretome.set_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Assigns the reference set to the :py:attr``reference_set`` attribute.
+The reference set is the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HumanProteinAtlasSecretome.show">
+<span class="sig-name descname"><span class="pre">show</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">table_param</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HumanProteinAtlasSecretome.show" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic
+information from the UniProt datasheets.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HumanProteinAtlasSecretome.subset_intersection">
+<span class="sig-name descname"><span class="pre">subset_intersection</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">universe</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HumanProteinAtlasSecretome.subset_intersection" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the proportion of entities in a subset occuring in the
+set <code class="docutils literal notranslate"><span class="pre">universe</span></code>. The subset is selected by passing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> to the
+<code class="docutils literal notranslate"><span class="pre">select</span></code> method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HumanProteinAtlasSecretome.to_array">
+<span class="sig-name descname"><span class="pre">to_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_fields</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HumanProteinAtlasSecretome.to_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns an entity vs feature array. In case of more complex
+annotations this might be huge.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HumanProteinAtlasSecretome.to_bool_array">
+<span class="sig-name descname"><span class="pre">to_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HumanProteinAtlasSecretome.to_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a presence/absence boolean array for a reference set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HumanProteinAtlasSecretome.to_set">
+<span class="sig-name descname"><span class="pre">to_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HumanProteinAtlasSecretome.to_set" title="Link to this definition">§</a></dt>
+<dd><p>Returns the entities present in this annotation resource as a set.</p>
+</dd></dl>
+
+</dd></dl>
+
+</section>
+
+
+                </article>
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diff --git a/api/pypath.core.annot.HumanProteinAtlasSubcellular.html b/api/pypath.core.annot.HumanProteinAtlasSubcellular.html
new file mode 100644
index 000000000..1ede0a736
--- /dev/null
+++ b/api/pypath.core.annot.HumanProteinAtlasSubcellular.html
@@ -0,0 +1,1116 @@
+
+<!DOCTYPE html>
+
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+  <section id="pypath-core-annot-humanproteinatlassubcellular">
+<h1>pypath.core.annot.HumanProteinAtlasSubcellular<a class="headerlink" href="#pypath-core-annot-humanproteinatlassubcellular" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.core.annot.HumanProteinAtlasSubcellular">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.core.annot.</span></span><span class="sig-name descname"><span class="pre">HumanProteinAtlasSubcellular</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#HumanProteinAtlasSubcellular"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.HumanProteinAtlasSubcellular" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <a class="reference internal" href="pypath.core.annot.AnnotationBase.html#pypath.core.annot.AnnotationBase" title="pypath.core.annot.AnnotationBase"><code class="xref py py-class docutils literal notranslate"><span class="pre">AnnotationBase</span></code></a></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HumanProteinAtlasSubcellular.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#HumanProteinAtlasSubcellular.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.HumanProteinAtlasSubcellular.__init__" title="Link to this definition">§</a></dt>
+<dd><p>Represents annotations for a set of proteins.
+Loads the data from the original resource and provides methods
+to query the annotations.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>name</strong> (<em>str</em>) – A custom name for the annotation resource.</p></li>
+<li><p><strong>ncbi_tax_id</strong> (<em>int</em>) – NCBI Taxonomy identifier.</p></li>
+<li><p><strong>input_method</strong> (<em>callable</em><em>,</em><em>str</em>) – Either a callable or the name of a method in any submodules of
+the <code class="docutils literal notranslate"><span class="pre">pypath.inputs</span></code>  module. Should return a dict with
+UniProt IDs as keys or an object suitable for <code class="docutils literal notranslate"><span class="pre">process_method</span></code>.</p></li>
+<li><p><strong>input_args</strong> (<em>dict</em>) – Arguments for the <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.HumanProteinAtlasSubcellular.__init__" title="pypath.core.annot.HumanProteinAtlasSubcellular.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>(**kwargs)</p></td>
+<td><p>Represents annotations for a set of proteins.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.HumanProteinAtlasSubcellular.add_complexes_by_inference" title="pypath.core.annot.HumanProteinAtlasSubcellular.add_complexes_by_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">add_complexes_by_inference</span></code></a>([complexes])</p></td>
+<td><p>Creates complex annotations by in silico inference and adds them to this annotation set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.HumanProteinAtlasSubcellular.all_complexes" title="pypath.core.annot.HumanProteinAtlasSubcellular.all_complexes"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_complexes</span></code></a>()</p></td>
+<td><p>All protein complexes annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.HumanProteinAtlasSubcellular.all_entities" title="pypath.core.annot.HumanProteinAtlasSubcellular.all_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_entities</span></code></a>([entity_types])</p></td>
+<td><p>All entities annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.HumanProteinAtlasSubcellular.all_mirnas" title="pypath.core.annot.HumanProteinAtlasSubcellular.all_mirnas"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_mirnas</span></code></a>()</p></td>
+<td><p>All miRNAs annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.HumanProteinAtlasSubcellular.all_proteins" title="pypath.core.annot.HumanProteinAtlasSubcellular.all_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_proteins</span></code></a>()</p></td>
+<td><p>All UniProt IDs annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.HumanProteinAtlasSubcellular.all_refs" title="pypath.core.annot.HumanProteinAtlasSubcellular.all_refs"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_refs</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.HumanProteinAtlasSubcellular.annotate_complex" title="pypath.core.annot.HumanProteinAtlasSubcellular.annotate_complex"><code class="xref py py-obj docutils literal notranslate"><span class="pre">annotate_complex</span></code></a>(cplex)</p></td>
+<td><p>Infers annotations for a single complex.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.HumanProteinAtlasSubcellular.browse" title="pypath.core.annot.HumanProteinAtlasSubcellular.browse"><code class="xref py py-obj docutils literal notranslate"><span class="pre">browse</span></code></a>([field, start])</p></td>
+<td><p>Print gene information as a table.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.HumanProteinAtlasSubcellular.complex_inference" title="pypath.core.annot.HumanProteinAtlasSubcellular.complex_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">complex_inference</span></code></a>([complexes])</p></td>
+<td><p>Annotates all complexes in <cite>complexes</cite>, by default in the default complex database (existing in the <cite>complex</cite> module or generated on demand according to the module's current settings).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.HumanProteinAtlasSubcellular.coverage" title="pypath.core.annot.HumanProteinAtlasSubcellular.coverage"><code class="xref py py-obj docutils literal notranslate"><span class="pre">coverage</span></code></a>(other)</p></td>
+<td><p>Calculates the coverage of the annotation i.e. the proportion of entities having at least one record in this annotation resource for an arbitrary set of entities.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.HumanProteinAtlasSubcellular.curation_effort" title="pypath.core.annot.HumanProteinAtlasSubcellular.curation_effort"><code class="xref py py-obj docutils literal notranslate"><span class="pre">curation_effort</span></code></a>()</p></td>
+<td><p>Counts the reference-record pairs.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">from_dump</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_entity_type</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.HumanProteinAtlasSubcellular.get_names" title="pypath.core.annot.HumanProteinAtlasSubcellular.get_names"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_names</span></code></a>()</p></td>
+<td><p>Returns the list of field names in the records.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.HumanProteinAtlasSubcellular.get_reference_set" title="pypath.core.annot.HumanProteinAtlasSubcellular.get_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_reference_set</span></code></a>([proteins, complexes, ...])</p></td>
+<td><p>Retrieves the reference set i.e. the set of all entities which potentially have annotation in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.HumanProteinAtlasSubcellular.get_subset" title="pypath.core.annot.HumanProteinAtlasSubcellular.get_subset"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.HumanProteinAtlasSubcellular.get_subset_bool_array" title="pypath.core.annot.HumanProteinAtlasSubcellular.get_subset_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset_bool_array</span></code></a>([reference_set])</p></td>
+<td><p>Returns a boolean vector with True and False values for each entity in the reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.HumanProteinAtlasSubcellular.get_values" title="pypath.core.annot.HumanProteinAtlasSubcellular.get_values"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_values</span></code></a>(name[, exclude_none])</p></td>
+<td><p>Returns the set of all possible values of a field.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_complex</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_mirna</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_protein</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.HumanProteinAtlasSubcellular.labels" title="pypath.core.annot.HumanProteinAtlasSubcellular.labels"><code class="xref py py-obj docutils literal notranslate"><span class="pre">labels</span></code></a>([method])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.HumanProteinAtlasSubcellular.load" title="pypath.core.annot.HumanProteinAtlasSubcellular.load"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load</span></code></a>()</p></td>
+<td><p>Loads the annotation data by calling the input method.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.HumanProteinAtlasSubcellular.load_data" title="pypath.core.annot.HumanProteinAtlasSubcellular.load_data"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_data</span></code></a>()</p></td>
+<td><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.HumanProteinAtlasSubcellular.load_proteins" title="pypath.core.annot.HumanProteinAtlasSubcellular.load_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_proteins</span></code></a>()</p></td>
+<td><p>Retrieves a set of all UniProt IDs to have a base set of the entire proteome.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.HumanProteinAtlasSubcellular.make_df" title="pypath.core.annot.HumanProteinAtlasSubcellular.make_df"><code class="xref py py-obj docutils literal notranslate"><span class="pre">make_df</span></code></a>([rebuild])</p></td>
+<td><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complex_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.HumanProteinAtlasSubcellular.numof_entities" title="pypath.core.annot.HumanProteinAtlasSubcellular.numof_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_entities</span></code></a>()</p></td>
+<td><p>The number of annotated entities in the resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirna_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirnas</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_protein_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_proteins</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.HumanProteinAtlasSubcellular.numof_records" title="pypath.core.annot.HumanProteinAtlasSubcellular.numof_records"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_records</span></code></a>([entity_types])</p></td>
+<td><p>The total number of annotation records.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.HumanProteinAtlasSubcellular.numof_references" title="pypath.core.annot.HumanProteinAtlasSubcellular.numof_references"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_references</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.HumanProteinAtlasSubcellular.process" title="pypath.core.annot.HumanProteinAtlasSubcellular.process"><code class="xref py py-obj docutils literal notranslate"><span class="pre">process</span></code></a>()</p></td>
+<td><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">proportion</span></code>(other)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.HumanProteinAtlasSubcellular.reload" title="pypath.core.annot.HumanProteinAtlasSubcellular.reload"><code class="xref py py-obj docutils literal notranslate"><span class="pre">reload</span></code></a>()</p></td>
+<td><p>Reloads the object from the module level.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">save_to_pickle</span></code>(pickle_file)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.HumanProteinAtlasSubcellular.select" title="pypath.core.annot.HumanProteinAtlasSubcellular.select"><code class="xref py py-obj docutils literal notranslate"><span class="pre">select</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.HumanProteinAtlasSubcellular.set_method" title="pypath.core.annot.HumanProteinAtlasSubcellular.set_method"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_method</span></code></a>()</p></td>
+<td><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if necessary.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.HumanProteinAtlasSubcellular.set_reference_set" title="pypath.core.annot.HumanProteinAtlasSubcellular.set_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_reference_set</span></code></a>()</p></td>
+<td><p>Assigns the reference set to the :py:attr``reference_set`` attribute.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.HumanProteinAtlasSubcellular.show" title="pypath.core.annot.HumanProteinAtlasSubcellular.show"><code class="xref py py-obj docutils literal notranslate"><span class="pre">show</span></code></a>([method, table_param])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic information from the UniProt datasheets.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.HumanProteinAtlasSubcellular.subset_intersection" title="pypath.core.annot.HumanProteinAtlasSubcellular.subset_intersection"><code class="xref py py-obj docutils literal notranslate"><span class="pre">subset_intersection</span></code></a>(universe, **kwargs)</p></td>
+<td><p>Calculates the proportion of entities in a subset occuring in the set <code class="docutils literal notranslate"><span class="pre">universe</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.HumanProteinAtlasSubcellular.to_array" title="pypath.core.annot.HumanProteinAtlasSubcellular.to_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_array</span></code></a>([reference_set, use_fields])</p></td>
+<td><p>Returns an entity vs feature array.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.HumanProteinAtlasSubcellular.to_bool_array" title="pypath.core.annot.HumanProteinAtlasSubcellular.to_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_bool_array</span></code></a>(reference_set)</p></td>
+<td><p>Returns a presence/absence boolean array for a reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.HumanProteinAtlasSubcellular.to_set" title="pypath.core.annot.HumanProteinAtlasSubcellular.to_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_set</span></code></a>()</p></td>
+<td><p>Returns the entities present in this annotation resource as a set.</p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Attributes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_fields</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">summary</span></code></p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HumanProteinAtlasSubcellular.add_complexes_by_inference">
+<span class="sig-name descname"><span class="pre">add_complexes_by_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HumanProteinAtlasSubcellular.add_complexes_by_inference" title="Link to this definition">§</a></dt>
+<dd><p>Creates complex annotations by in silico inference and adds them
+to this annotation set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HumanProteinAtlasSubcellular.all_complexes">
+<span class="sig-name descname"><span class="pre">all_complexes</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HumanProteinAtlasSubcellular.all_complexes" title="Link to this definition">§</a></dt>
+<dd><p>All protein complexes annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HumanProteinAtlasSubcellular.all_entities">
+<span class="sig-name descname"><span class="pre">all_entities</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HumanProteinAtlasSubcellular.all_entities" title="Link to this definition">§</a></dt>
+<dd><p>All entities annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HumanProteinAtlasSubcellular.all_mirnas">
+<span class="sig-name descname"><span class="pre">all_mirnas</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HumanProteinAtlasSubcellular.all_mirnas" title="Link to this definition">§</a></dt>
+<dd><p>All miRNAs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HumanProteinAtlasSubcellular.all_proteins">
+<span class="sig-name descname"><span class="pre">all_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HumanProteinAtlasSubcellular.all_proteins" title="Link to this definition">§</a></dt>
+<dd><p>All UniProt IDs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HumanProteinAtlasSubcellular.all_refs">
+<span class="sig-name descname"><span class="pre">all_refs</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HumanProteinAtlasSubcellular.all_refs" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects the references
+across all records. Returns <em>list</em>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HumanProteinAtlasSubcellular.annotate_complex">
+<span class="sig-name descname"><span class="pre">annotate_complex</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cplex</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HumanProteinAtlasSubcellular.annotate_complex" title="Link to this definition">§</a></dt>
+<dd><p>Infers annotations for a single complex.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HumanProteinAtlasSubcellular.browse">
+<span class="sig-name descname"><span class="pre">browse</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">field</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">start</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HumanProteinAtlasSubcellular.browse" title="Link to this definition">§</a></dt>
+<dd><p>Print gene information as a table.</p>
+<p>Presents information about annotation categories as ascii tables
+printed in the terminal. If one category provided, prints one table.
+If multiple categories provided, prints a table for each of them one
+by one proceeding to the next one once you hit return. If no categories
+provided goes through all levels of the primary category.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>field:</dt><dd><p>The field to browse categories by.</p>
+<ul class="simple">
+<li><p>If None the primary field will be selected.
+If this annotation resource doesn’t have fields, all proteins
+will be presented as one single category.</p></li>
+<li><p>If a string it will be considered a field name and it will
+browse through all levels of this field.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">list</span></code>, set or tuple, it will be considered either a
+<code class="docutils literal notranslate"><span class="pre">list</span></code> of field names or a list of values from the primary
+field. In the former case all combinations of the values of
+the fields will be presented, in the latter case the browsing
+will be limited to the levels of the primary field contained
+in <code class="docutils literal notranslate"><span class="pre">field</span></code>.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">dict</span></code>, keys are supposed to be field names and values
+as list of levels. If any of the values are None, all levels
+from that field will be used.</p></li>
+</ul>
+</dd>
+<dt>start:</dt><dd><p>Start browsing from this category. E.g. if there are 500
+categories and start is 250 it will skip everything before the
+250th.</p>
+</dd>
+<dt>kwargs:</dt><dd><p>Passed to <code class="docutils literal notranslate"><span class="pre">pypath.utils.uniprot.info</span></code>.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HumanProteinAtlasSubcellular.complex_inference">
+<span class="sig-name descname"><span class="pre">complex_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HumanProteinAtlasSubcellular.complex_inference" title="Link to this definition">§</a></dt>
+<dd><p>Annotates all complexes in <cite>complexes</cite>, by default in the default
+complex database (existing in the <cite>complex</cite> module or generated
+on demand according to the module’s current settings).</p>
+<dl class="field-list simple">
+<dt class="field-odd">Returns<span class="colon">:</span></dt>
+<dd class="field-odd"><p><ul class="simple">
+<li><p><em>Dict with complexes as keys and sets of annotations as values.</em></p></li>
+<li><p><em>Complexes with no valid information in this annotation resource</em></p></li>
+<li><p><em>won’t be in the dict.</em></p></li>
+</ul>
+</p>
+</dd>
+<dt class="field-even">Parameters<span class="colon">:</span></dt>
+<dd class="field-even"><p><strong>complexes</strong> (<em>iterable</em>) – Iterable yielding complexes.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HumanProteinAtlasSubcellular.coverage">
+<span class="sig-name descname"><span class="pre">coverage</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">other</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HumanProteinAtlasSubcellular.coverage" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the coverage of the annotation i.e. the proportion of
+entities having at least one record in this annotation resource
+for an arbitrary set of entities.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HumanProteinAtlasSubcellular.curation_effort">
+<span class="sig-name descname"><span class="pre">curation_effort</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HumanProteinAtlasSubcellular.curation_effort" title="Link to this definition">§</a></dt>
+<dd><p>Counts the reference-record pairs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HumanProteinAtlasSubcellular.get_names">
+<span class="sig-name descname"><span class="pre">get_names</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HumanProteinAtlasSubcellular.get_names" title="Link to this definition">§</a></dt>
+<dd><p>Returns the list of field names in the records. The annotation
+consists of uniform records and each entity might be annotated
+with one or more records. Each record is a tuple of fields, for
+example <code class="docutils literal notranslate"><span class="pre">('cell_type',</span> <span class="pre">'expression_level',</span> <span class="pre">'score')</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HumanProteinAtlasSubcellular.get_reference_set">
+<em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">get_reference_set</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">proteins</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">swissprot_only</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HumanProteinAtlasSubcellular.get_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the reference set i.e. the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HumanProteinAtlasSubcellular.get_subset">
+<span class="sig-name descname"><span class="pre">get_subset</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HumanProteinAtlasSubcellular.get_subset" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HumanProteinAtlasSubcellular.get_subset_bool_array">
+<span class="sig-name descname"><span class="pre">get_subset_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HumanProteinAtlasSubcellular.get_subset_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a boolean vector with True and False values for each entity
+in the reference set. The values represent presence absence data
+in the simplest case, but by providing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> any kind of matching
+and filtering is possible. <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> are passed to the <code class="docutils literal notranslate"><span class="pre">select</span></code>
+method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HumanProteinAtlasSubcellular.get_values">
+<span class="sig-name descname"><span class="pre">get_values</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">exclude_none</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HumanProteinAtlasSubcellular.get_values" title="Link to this definition">§</a></dt>
+<dd><p>Returns the set of all possible values of a field. E.g. if the
+records of this annotation have a field <code class="docutils literal notranslate"><span class="pre">cell_type</span></code> then calling
+this method can tell you that across all records the values of
+this field might be <code class="docutils literal notranslate"><span class="pre">{'macrophage',</span> <span class="pre">'epithelial_cell',</span> <span class="pre">...}</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HumanProteinAtlasSubcellular.labels">
+<span class="sig-name descname"><span class="pre">labels</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HumanProteinAtlasSubcellular.labels" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HumanProteinAtlasSubcellular.load">
+<span class="sig-name descname"><span class="pre">load</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HumanProteinAtlasSubcellular.load" title="Link to this definition">§</a></dt>
+<dd><p>Loads the annotation data by calling the input method.
+Infers annotations for complexes in the complex database if
+py:attr:<code class="docutils literal notranslate"><span class="pre">infer_complexes</span></code> is True.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HumanProteinAtlasSubcellular.load_data">
+<span class="sig-name descname"><span class="pre">load_data</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HumanProteinAtlasSubcellular.load_data" title="Link to this definition">§</a></dt>
+<dd><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HumanProteinAtlasSubcellular.load_proteins">
+<span class="sig-name descname"><span class="pre">load_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HumanProteinAtlasSubcellular.load_proteins" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a set of all UniProt IDs to have a base set of the entire
+proteome.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HumanProteinAtlasSubcellular.make_df">
+<span class="sig-name descname"><span class="pre">make_df</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">rebuild</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HumanProteinAtlasSubcellular.make_df" title="Link to this definition">§</a></dt>
+<dd><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.
+The data frame will be assigned to :py:attr``df``.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HumanProteinAtlasSubcellular.numof_entities">
+<span class="sig-name descname"><span class="pre">numof_entities</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HumanProteinAtlasSubcellular.numof_entities" title="Link to this definition">§</a></dt>
+<dd><p>The number of annotated entities in the resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HumanProteinAtlasSubcellular.numof_records">
+<span class="sig-name descname"><span class="pre">numof_records</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HumanProteinAtlasSubcellular.numof_records" title="Link to this definition">§</a></dt>
+<dd><p>The total number of annotation records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HumanProteinAtlasSubcellular.numof_references">
+<span class="sig-name descname"><span class="pre">numof_references</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HumanProteinAtlasSubcellular.numof_references" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects and counts the
+references across all records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HumanProteinAtlasSubcellular.process">
+<span class="sig-name descname"><span class="pre">process</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HumanProteinAtlasSubcellular.process" title="Link to this definition">§</a></dt>
+<dd><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HumanProteinAtlasSubcellular.reload">
+<span class="sig-name descname"><span class="pre">reload</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HumanProteinAtlasSubcellular.reload" title="Link to this definition">§</a></dt>
+<dd><p>Reloads the object from the module level.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HumanProteinAtlasSubcellular.select">
+<span class="sig-name descname"><span class="pre">select</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HumanProteinAtlasSubcellular.select" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HumanProteinAtlasSubcellular.set_method">
+<span class="sig-name descname"><span class="pre">set_method</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HumanProteinAtlasSubcellular.set_method" title="Link to this definition">§</a></dt>
+<dd><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if
+necessary.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HumanProteinAtlasSubcellular.set_reference_set">
+<span class="sig-name descname"><span class="pre">set_reference_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HumanProteinAtlasSubcellular.set_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Assigns the reference set to the :py:attr``reference_set`` attribute.
+The reference set is the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HumanProteinAtlasSubcellular.show">
+<span class="sig-name descname"><span class="pre">show</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">table_param</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HumanProteinAtlasSubcellular.show" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic
+information from the UniProt datasheets.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HumanProteinAtlasSubcellular.subset_intersection">
+<span class="sig-name descname"><span class="pre">subset_intersection</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">universe</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HumanProteinAtlasSubcellular.subset_intersection" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the proportion of entities in a subset occuring in the
+set <code class="docutils literal notranslate"><span class="pre">universe</span></code>. The subset is selected by passing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> to the
+<code class="docutils literal notranslate"><span class="pre">select</span></code> method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HumanProteinAtlasSubcellular.to_array">
+<span class="sig-name descname"><span class="pre">to_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_fields</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HumanProteinAtlasSubcellular.to_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns an entity vs feature array. In case of more complex
+annotations this might be huge.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HumanProteinAtlasSubcellular.to_bool_array">
+<span class="sig-name descname"><span class="pre">to_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HumanProteinAtlasSubcellular.to_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a presence/absence boolean array for a reference set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.HumanProteinAtlasSubcellular.to_set">
+<span class="sig-name descname"><span class="pre">to_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.HumanProteinAtlasSubcellular.to_set" title="Link to this definition">§</a></dt>
+<dd><p>Returns the entities present in this annotation resource as a set.</p>
+</dd></dl>
+
+</dd></dl>
+
+</section>
+
+
+                </article>
+              
+              
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+  <section id="pypath-core-annot-humancellmap">
+<h1>pypath.core.annot.Humancellmap<a class="headerlink" href="#pypath-core-annot-humancellmap" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.core.annot.Humancellmap">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.core.annot.</span></span><span class="sig-name descname"><span class="pre">Humancellmap</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#Humancellmap"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.Humancellmap" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <a class="reference internal" href="pypath.core.annot.AnnotationBase.html#pypath.core.annot.AnnotationBase" title="pypath.core.annot.AnnotationBase"><code class="xref py py-class docutils literal notranslate"><span class="pre">AnnotationBase</span></code></a></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Humancellmap.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#Humancellmap.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.Humancellmap.__init__" title="Link to this definition">§</a></dt>
+<dd><p>Protein families from UniProt.</p>
+</dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Humancellmap.__init__" title="pypath.core.annot.Humancellmap.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>([ncbi_tax_id])</p></td>
+<td><p>Protein families from UniProt.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Humancellmap.add_complexes_by_inference" title="pypath.core.annot.Humancellmap.add_complexes_by_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">add_complexes_by_inference</span></code></a>([complexes])</p></td>
+<td><p>Creates complex annotations by in silico inference and adds them to this annotation set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Humancellmap.all_complexes" title="pypath.core.annot.Humancellmap.all_complexes"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_complexes</span></code></a>()</p></td>
+<td><p>All protein complexes annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Humancellmap.all_entities" title="pypath.core.annot.Humancellmap.all_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_entities</span></code></a>([entity_types])</p></td>
+<td><p>All entities annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Humancellmap.all_mirnas" title="pypath.core.annot.Humancellmap.all_mirnas"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_mirnas</span></code></a>()</p></td>
+<td><p>All miRNAs annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Humancellmap.all_proteins" title="pypath.core.annot.Humancellmap.all_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_proteins</span></code></a>()</p></td>
+<td><p>All UniProt IDs annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Humancellmap.all_refs" title="pypath.core.annot.Humancellmap.all_refs"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_refs</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Humancellmap.annotate_complex" title="pypath.core.annot.Humancellmap.annotate_complex"><code class="xref py py-obj docutils literal notranslate"><span class="pre">annotate_complex</span></code></a>(cplex)</p></td>
+<td><p>Infers annotations for a single complex.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Humancellmap.browse" title="pypath.core.annot.Humancellmap.browse"><code class="xref py py-obj docutils literal notranslate"><span class="pre">browse</span></code></a>([field, start])</p></td>
+<td><p>Print gene information as a table.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Humancellmap.complex_inference" title="pypath.core.annot.Humancellmap.complex_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">complex_inference</span></code></a>([complexes])</p></td>
+<td><p>Annotates all complexes in <cite>complexes</cite>, by default in the default complex database (existing in the <cite>complex</cite> module or generated on demand according to the module's current settings).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Humancellmap.coverage" title="pypath.core.annot.Humancellmap.coverage"><code class="xref py py-obj docutils literal notranslate"><span class="pre">coverage</span></code></a>(other)</p></td>
+<td><p>Calculates the coverage of the annotation i.e. the proportion of entities having at least one record in this annotation resource for an arbitrary set of entities.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Humancellmap.curation_effort" title="pypath.core.annot.Humancellmap.curation_effort"><code class="xref py py-obj docutils literal notranslate"><span class="pre">curation_effort</span></code></a>()</p></td>
+<td><p>Counts the reference-record pairs.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">from_dump</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_entity_type</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Humancellmap.get_names" title="pypath.core.annot.Humancellmap.get_names"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_names</span></code></a>()</p></td>
+<td><p>Returns the list of field names in the records.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Humancellmap.get_reference_set" title="pypath.core.annot.Humancellmap.get_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_reference_set</span></code></a>([proteins, complexes, ...])</p></td>
+<td><p>Retrieves the reference set i.e. the set of all entities which potentially have annotation in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Humancellmap.get_subset" title="pypath.core.annot.Humancellmap.get_subset"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Humancellmap.get_subset_bool_array" title="pypath.core.annot.Humancellmap.get_subset_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset_bool_array</span></code></a>([reference_set])</p></td>
+<td><p>Returns a boolean vector with True and False values for each entity in the reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Humancellmap.get_values" title="pypath.core.annot.Humancellmap.get_values"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_values</span></code></a>(name[, exclude_none])</p></td>
+<td><p>Returns the set of all possible values of a field.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_complex</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_mirna</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_protein</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Humancellmap.labels" title="pypath.core.annot.Humancellmap.labels"><code class="xref py py-obj docutils literal notranslate"><span class="pre">labels</span></code></a>([method])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Humancellmap.load" title="pypath.core.annot.Humancellmap.load"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load</span></code></a>()</p></td>
+<td><p>Loads the annotation data by calling the input method.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Humancellmap.load_data" title="pypath.core.annot.Humancellmap.load_data"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_data</span></code></a>()</p></td>
+<td><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Humancellmap.load_proteins" title="pypath.core.annot.Humancellmap.load_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_proteins</span></code></a>()</p></td>
+<td><p>Retrieves a set of all UniProt IDs to have a base set of the entire proteome.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Humancellmap.make_df" title="pypath.core.annot.Humancellmap.make_df"><code class="xref py py-obj docutils literal notranslate"><span class="pre">make_df</span></code></a>([rebuild])</p></td>
+<td><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complex_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Humancellmap.numof_entities" title="pypath.core.annot.Humancellmap.numof_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_entities</span></code></a>()</p></td>
+<td><p>The number of annotated entities in the resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirna_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirnas</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_protein_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_proteins</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Humancellmap.numof_records" title="pypath.core.annot.Humancellmap.numof_records"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_records</span></code></a>([entity_types])</p></td>
+<td><p>The total number of annotation records.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Humancellmap.numof_references" title="pypath.core.annot.Humancellmap.numof_references"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_references</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Humancellmap.process" title="pypath.core.annot.Humancellmap.process"><code class="xref py py-obj docutils literal notranslate"><span class="pre">process</span></code></a>()</p></td>
+<td><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">proportion</span></code>(other)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Humancellmap.reload" title="pypath.core.annot.Humancellmap.reload"><code class="xref py py-obj docutils literal notranslate"><span class="pre">reload</span></code></a>()</p></td>
+<td><p>Reloads the object from the module level.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">save_to_pickle</span></code>(pickle_file)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Humancellmap.select" title="pypath.core.annot.Humancellmap.select"><code class="xref py py-obj docutils literal notranslate"><span class="pre">select</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Humancellmap.set_method" title="pypath.core.annot.Humancellmap.set_method"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_method</span></code></a>()</p></td>
+<td><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if necessary.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Humancellmap.set_reference_set" title="pypath.core.annot.Humancellmap.set_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_reference_set</span></code></a>()</p></td>
+<td><p>Assigns the reference set to the :py:attr``reference_set`` attribute.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Humancellmap.show" title="pypath.core.annot.Humancellmap.show"><code class="xref py py-obj docutils literal notranslate"><span class="pre">show</span></code></a>([method, table_param])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic information from the UniProt datasheets.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Humancellmap.subset_intersection" title="pypath.core.annot.Humancellmap.subset_intersection"><code class="xref py py-obj docutils literal notranslate"><span class="pre">subset_intersection</span></code></a>(universe, **kwargs)</p></td>
+<td><p>Calculates the proportion of entities in a subset occuring in the set <code class="docutils literal notranslate"><span class="pre">universe</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Humancellmap.to_array" title="pypath.core.annot.Humancellmap.to_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_array</span></code></a>([reference_set, use_fields])</p></td>
+<td><p>Returns an entity vs feature array.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Humancellmap.to_bool_array" title="pypath.core.annot.Humancellmap.to_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_bool_array</span></code></a>(reference_set)</p></td>
+<td><p>Returns a presence/absence boolean array for a reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Humancellmap.to_set" title="pypath.core.annot.Humancellmap.to_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_set</span></code></a>()</p></td>
+<td><p>Returns the entities present in this annotation resource as a set.</p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Attributes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_fields</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">summary</span></code></p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Humancellmap.add_complexes_by_inference">
+<span class="sig-name descname"><span class="pre">add_complexes_by_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Humancellmap.add_complexes_by_inference" title="Link to this definition">§</a></dt>
+<dd><p>Creates complex annotations by in silico inference and adds them
+to this annotation set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Humancellmap.all_complexes">
+<span class="sig-name descname"><span class="pre">all_complexes</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Humancellmap.all_complexes" title="Link to this definition">§</a></dt>
+<dd><p>All protein complexes annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Humancellmap.all_entities">
+<span class="sig-name descname"><span class="pre">all_entities</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Humancellmap.all_entities" title="Link to this definition">§</a></dt>
+<dd><p>All entities annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Humancellmap.all_mirnas">
+<span class="sig-name descname"><span class="pre">all_mirnas</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Humancellmap.all_mirnas" title="Link to this definition">§</a></dt>
+<dd><p>All miRNAs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Humancellmap.all_proteins">
+<span class="sig-name descname"><span class="pre">all_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Humancellmap.all_proteins" title="Link to this definition">§</a></dt>
+<dd><p>All UniProt IDs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Humancellmap.all_refs">
+<span class="sig-name descname"><span class="pre">all_refs</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Humancellmap.all_refs" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects the references
+across all records. Returns <em>list</em>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Humancellmap.annotate_complex">
+<span class="sig-name descname"><span class="pre">annotate_complex</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cplex</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Humancellmap.annotate_complex" title="Link to this definition">§</a></dt>
+<dd><p>Infers annotations for a single complex.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Humancellmap.browse">
+<span class="sig-name descname"><span class="pre">browse</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">field</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">start</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Humancellmap.browse" title="Link to this definition">§</a></dt>
+<dd><p>Print gene information as a table.</p>
+<p>Presents information about annotation categories as ascii tables
+printed in the terminal. If one category provided, prints one table.
+If multiple categories provided, prints a table for each of them one
+by one proceeding to the next one once you hit return. If no categories
+provided goes through all levels of the primary category.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>field:</dt><dd><p>The field to browse categories by.</p>
+<ul class="simple">
+<li><p>If None the primary field will be selected.
+If this annotation resource doesn’t have fields, all proteins
+will be presented as one single category.</p></li>
+<li><p>If a string it will be considered a field name and it will
+browse through all levels of this field.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">list</span></code>, set or tuple, it will be considered either a
+<code class="docutils literal notranslate"><span class="pre">list</span></code> of field names or a list of values from the primary
+field. In the former case all combinations of the values of
+the fields will be presented, in the latter case the browsing
+will be limited to the levels of the primary field contained
+in <code class="docutils literal notranslate"><span class="pre">field</span></code>.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">dict</span></code>, keys are supposed to be field names and values
+as list of levels. If any of the values are None, all levels
+from that field will be used.</p></li>
+</ul>
+</dd>
+<dt>start:</dt><dd><p>Start browsing from this category. E.g. if there are 500
+categories and start is 250 it will skip everything before the
+250th.</p>
+</dd>
+<dt>kwargs:</dt><dd><p>Passed to <code class="docutils literal notranslate"><span class="pre">pypath.utils.uniprot.info</span></code>.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Humancellmap.complex_inference">
+<span class="sig-name descname"><span class="pre">complex_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Humancellmap.complex_inference" title="Link to this definition">§</a></dt>
+<dd><p>Annotates all complexes in <cite>complexes</cite>, by default in the default
+complex database (existing in the <cite>complex</cite> module or generated
+on demand according to the module’s current settings).</p>
+<dl class="field-list simple">
+<dt class="field-odd">Returns<span class="colon">:</span></dt>
+<dd class="field-odd"><p><ul class="simple">
+<li><p><em>Dict with complexes as keys and sets of annotations as values.</em></p></li>
+<li><p><em>Complexes with no valid information in this annotation resource</em></p></li>
+<li><p><em>won’t be in the dict.</em></p></li>
+</ul>
+</p>
+</dd>
+<dt class="field-even">Parameters<span class="colon">:</span></dt>
+<dd class="field-even"><p><strong>complexes</strong> (<em>iterable</em>) – Iterable yielding complexes.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Humancellmap.coverage">
+<span class="sig-name descname"><span class="pre">coverage</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">other</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Humancellmap.coverage" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the coverage of the annotation i.e. the proportion of
+entities having at least one record in this annotation resource
+for an arbitrary set of entities.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Humancellmap.curation_effort">
+<span class="sig-name descname"><span class="pre">curation_effort</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Humancellmap.curation_effort" title="Link to this definition">§</a></dt>
+<dd><p>Counts the reference-record pairs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Humancellmap.get_names">
+<span class="sig-name descname"><span class="pre">get_names</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Humancellmap.get_names" title="Link to this definition">§</a></dt>
+<dd><p>Returns the list of field names in the records. The annotation
+consists of uniform records and each entity might be annotated
+with one or more records. Each record is a tuple of fields, for
+example <code class="docutils literal notranslate"><span class="pre">('cell_type',</span> <span class="pre">'expression_level',</span> <span class="pre">'score')</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Humancellmap.get_reference_set">
+<em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">get_reference_set</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">proteins</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">swissprot_only</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Humancellmap.get_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the reference set i.e. the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Humancellmap.get_subset">
+<span class="sig-name descname"><span class="pre">get_subset</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Humancellmap.get_subset" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Humancellmap.get_subset_bool_array">
+<span class="sig-name descname"><span class="pre">get_subset_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Humancellmap.get_subset_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a boolean vector with True and False values for each entity
+in the reference set. The values represent presence absence data
+in the simplest case, but by providing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> any kind of matching
+and filtering is possible. <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> are passed to the <code class="docutils literal notranslate"><span class="pre">select</span></code>
+method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Humancellmap.get_values">
+<span class="sig-name descname"><span class="pre">get_values</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">exclude_none</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Humancellmap.get_values" title="Link to this definition">§</a></dt>
+<dd><p>Returns the set of all possible values of a field. E.g. if the
+records of this annotation have a field <code class="docutils literal notranslate"><span class="pre">cell_type</span></code> then calling
+this method can tell you that across all records the values of
+this field might be <code class="docutils literal notranslate"><span class="pre">{'macrophage',</span> <span class="pre">'epithelial_cell',</span> <span class="pre">...}</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Humancellmap.labels">
+<span class="sig-name descname"><span class="pre">labels</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Humancellmap.labels" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Humancellmap.load">
+<span class="sig-name descname"><span class="pre">load</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Humancellmap.load" title="Link to this definition">§</a></dt>
+<dd><p>Loads the annotation data by calling the input method.
+Infers annotations for complexes in the complex database if
+py:attr:<code class="docutils literal notranslate"><span class="pre">infer_complexes</span></code> is True.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Humancellmap.load_data">
+<span class="sig-name descname"><span class="pre">load_data</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Humancellmap.load_data" title="Link to this definition">§</a></dt>
+<dd><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Humancellmap.load_proteins">
+<span class="sig-name descname"><span class="pre">load_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Humancellmap.load_proteins" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a set of all UniProt IDs to have a base set of the entire
+proteome.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Humancellmap.make_df">
+<span class="sig-name descname"><span class="pre">make_df</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">rebuild</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Humancellmap.make_df" title="Link to this definition">§</a></dt>
+<dd><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.
+The data frame will be assigned to :py:attr``df``.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Humancellmap.numof_entities">
+<span class="sig-name descname"><span class="pre">numof_entities</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Humancellmap.numof_entities" title="Link to this definition">§</a></dt>
+<dd><p>The number of annotated entities in the resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Humancellmap.numof_records">
+<span class="sig-name descname"><span class="pre">numof_records</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Humancellmap.numof_records" title="Link to this definition">§</a></dt>
+<dd><p>The total number of annotation records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Humancellmap.numof_references">
+<span class="sig-name descname"><span class="pre">numof_references</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Humancellmap.numof_references" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects and counts the
+references across all records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Humancellmap.process">
+<span class="sig-name descname"><span class="pre">process</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Humancellmap.process" title="Link to this definition">§</a></dt>
+<dd><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Humancellmap.reload">
+<span class="sig-name descname"><span class="pre">reload</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Humancellmap.reload" title="Link to this definition">§</a></dt>
+<dd><p>Reloads the object from the module level.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Humancellmap.select">
+<span class="sig-name descname"><span class="pre">select</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Humancellmap.select" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Humancellmap.set_method">
+<span class="sig-name descname"><span class="pre">set_method</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Humancellmap.set_method" title="Link to this definition">§</a></dt>
+<dd><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if
+necessary.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Humancellmap.set_reference_set">
+<span class="sig-name descname"><span class="pre">set_reference_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Humancellmap.set_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Assigns the reference set to the :py:attr``reference_set`` attribute.
+The reference set is the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Humancellmap.show">
+<span class="sig-name descname"><span class="pre">show</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">table_param</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Humancellmap.show" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic
+information from the UniProt datasheets.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Humancellmap.subset_intersection">
+<span class="sig-name descname"><span class="pre">subset_intersection</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">universe</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Humancellmap.subset_intersection" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the proportion of entities in a subset occuring in the
+set <code class="docutils literal notranslate"><span class="pre">universe</span></code>. The subset is selected by passing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> to the
+<code class="docutils literal notranslate"><span class="pre">select</span></code> method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Humancellmap.to_array">
+<span class="sig-name descname"><span class="pre">to_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_fields</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Humancellmap.to_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns an entity vs feature array. In case of more complex
+annotations this might be huge.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Humancellmap.to_bool_array">
+<span class="sig-name descname"><span class="pre">to_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Humancellmap.to_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a presence/absence boolean array for a reference set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Humancellmap.to_set">
+<span class="sig-name descname"><span class="pre">to_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Humancellmap.to_set" title="Link to this definition">§</a></dt>
+<dd><p>Returns the entities present in this annotation resource as a set.</p>
+</dd></dl>
+
+</dd></dl>
+
+</section>
+
+
+                </article>
+              
+              
+              
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+  <section id="pypath-core-annot-icellnet">
+<h1>pypath.core.annot.Icellnet<a class="headerlink" href="#pypath-core-annot-icellnet" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.core.annot.Icellnet">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.core.annot.</span></span><span class="sig-name descname"><span class="pre">Icellnet</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#Icellnet"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.Icellnet" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <a class="reference internal" href="pypath.core.annot.AnnotationBase.html#pypath.core.annot.AnnotationBase" title="pypath.core.annot.AnnotationBase"><code class="xref py py-class docutils literal notranslate"><span class="pre">AnnotationBase</span></code></a></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Icellnet.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#Icellnet.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.Icellnet.__init__" title="Link to this definition">§</a></dt>
+<dd><p>Represents annotations for a set of proteins.
+Loads the data from the original resource and provides methods
+to query the annotations.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>name</strong> (<em>str</em>) – A custom name for the annotation resource.</p></li>
+<li><p><strong>ncbi_tax_id</strong> (<em>int</em>) – NCBI Taxonomy identifier.</p></li>
+<li><p><strong>input_method</strong> (<em>callable</em><em>,</em><em>str</em>) – Either a callable or the name of a method in any submodules of
+the <code class="docutils literal notranslate"><span class="pre">pypath.inputs</span></code>  module. Should return a dict with
+UniProt IDs as keys or an object suitable for <code class="docutils literal notranslate"><span class="pre">process_method</span></code>.</p></li>
+<li><p><strong>input_args</strong> (<em>dict</em>) – Arguments for the <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Icellnet.__init__" title="pypath.core.annot.Icellnet.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>(**kwargs)</p></td>
+<td><p>Represents annotations for a set of proteins.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Icellnet.add_complexes_by_inference" title="pypath.core.annot.Icellnet.add_complexes_by_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">add_complexes_by_inference</span></code></a>([complexes])</p></td>
+<td><p>Creates complex annotations by in silico inference and adds them to this annotation set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Icellnet.all_complexes" title="pypath.core.annot.Icellnet.all_complexes"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_complexes</span></code></a>()</p></td>
+<td><p>All protein complexes annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Icellnet.all_entities" title="pypath.core.annot.Icellnet.all_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_entities</span></code></a>([entity_types])</p></td>
+<td><p>All entities annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Icellnet.all_mirnas" title="pypath.core.annot.Icellnet.all_mirnas"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_mirnas</span></code></a>()</p></td>
+<td><p>All miRNAs annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Icellnet.all_proteins" title="pypath.core.annot.Icellnet.all_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_proteins</span></code></a>()</p></td>
+<td><p>All UniProt IDs annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Icellnet.all_refs" title="pypath.core.annot.Icellnet.all_refs"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_refs</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Icellnet.annotate_complex" title="pypath.core.annot.Icellnet.annotate_complex"><code class="xref py py-obj docutils literal notranslate"><span class="pre">annotate_complex</span></code></a>(cplex)</p></td>
+<td><p>Infers annotations for a single complex.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Icellnet.browse" title="pypath.core.annot.Icellnet.browse"><code class="xref py py-obj docutils literal notranslate"><span class="pre">browse</span></code></a>([field, start])</p></td>
+<td><p>Print gene information as a table.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Icellnet.complex_inference" title="pypath.core.annot.Icellnet.complex_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">complex_inference</span></code></a>([complexes])</p></td>
+<td><p>Annotates all complexes in <cite>complexes</cite>, by default in the default complex database (existing in the <cite>complex</cite> module or generated on demand according to the module's current settings).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Icellnet.coverage" title="pypath.core.annot.Icellnet.coverage"><code class="xref py py-obj docutils literal notranslate"><span class="pre">coverage</span></code></a>(other)</p></td>
+<td><p>Calculates the coverage of the annotation i.e. the proportion of entities having at least one record in this annotation resource for an arbitrary set of entities.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Icellnet.curation_effort" title="pypath.core.annot.Icellnet.curation_effort"><code class="xref py py-obj docutils literal notranslate"><span class="pre">curation_effort</span></code></a>()</p></td>
+<td><p>Counts the reference-record pairs.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">from_dump</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_entity_type</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Icellnet.get_names" title="pypath.core.annot.Icellnet.get_names"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_names</span></code></a>()</p></td>
+<td><p>Returns the list of field names in the records.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Icellnet.get_reference_set" title="pypath.core.annot.Icellnet.get_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_reference_set</span></code></a>([proteins, complexes, ...])</p></td>
+<td><p>Retrieves the reference set i.e. the set of all entities which potentially have annotation in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Icellnet.get_subset" title="pypath.core.annot.Icellnet.get_subset"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Icellnet.get_subset_bool_array" title="pypath.core.annot.Icellnet.get_subset_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset_bool_array</span></code></a>([reference_set])</p></td>
+<td><p>Returns a boolean vector with True and False values for each entity in the reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Icellnet.get_values" title="pypath.core.annot.Icellnet.get_values"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_values</span></code></a>(name[, exclude_none])</p></td>
+<td><p>Returns the set of all possible values of a field.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_complex</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_mirna</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_protein</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Icellnet.labels" title="pypath.core.annot.Icellnet.labels"><code class="xref py py-obj docutils literal notranslate"><span class="pre">labels</span></code></a>([method])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Icellnet.load" title="pypath.core.annot.Icellnet.load"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load</span></code></a>()</p></td>
+<td><p>Loads the annotation data by calling the input method.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Icellnet.load_data" title="pypath.core.annot.Icellnet.load_data"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_data</span></code></a>()</p></td>
+<td><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Icellnet.load_proteins" title="pypath.core.annot.Icellnet.load_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_proteins</span></code></a>()</p></td>
+<td><p>Retrieves a set of all UniProt IDs to have a base set of the entire proteome.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Icellnet.make_df" title="pypath.core.annot.Icellnet.make_df"><code class="xref py py-obj docutils literal notranslate"><span class="pre">make_df</span></code></a>([rebuild])</p></td>
+<td><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complex_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Icellnet.numof_entities" title="pypath.core.annot.Icellnet.numof_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_entities</span></code></a>()</p></td>
+<td><p>The number of annotated entities in the resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirna_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirnas</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_protein_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_proteins</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Icellnet.numof_records" title="pypath.core.annot.Icellnet.numof_records"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_records</span></code></a>([entity_types])</p></td>
+<td><p>The total number of annotation records.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Icellnet.numof_references" title="pypath.core.annot.Icellnet.numof_references"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_references</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Icellnet.process" title="pypath.core.annot.Icellnet.process"><code class="xref py py-obj docutils literal notranslate"><span class="pre">process</span></code></a>()</p></td>
+<td><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">proportion</span></code>(other)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Icellnet.reload" title="pypath.core.annot.Icellnet.reload"><code class="xref py py-obj docutils literal notranslate"><span class="pre">reload</span></code></a>()</p></td>
+<td><p>Reloads the object from the module level.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">save_to_pickle</span></code>(pickle_file)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Icellnet.select" title="pypath.core.annot.Icellnet.select"><code class="xref py py-obj docutils literal notranslate"><span class="pre">select</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Icellnet.set_method" title="pypath.core.annot.Icellnet.set_method"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_method</span></code></a>()</p></td>
+<td><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if necessary.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Icellnet.set_reference_set" title="pypath.core.annot.Icellnet.set_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_reference_set</span></code></a>()</p></td>
+<td><p>Assigns the reference set to the :py:attr``reference_set`` attribute.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Icellnet.show" title="pypath.core.annot.Icellnet.show"><code class="xref py py-obj docutils literal notranslate"><span class="pre">show</span></code></a>([method, table_param])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic information from the UniProt datasheets.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Icellnet.subset_intersection" title="pypath.core.annot.Icellnet.subset_intersection"><code class="xref py py-obj docutils literal notranslate"><span class="pre">subset_intersection</span></code></a>(universe, **kwargs)</p></td>
+<td><p>Calculates the proportion of entities in a subset occuring in the set <code class="docutils literal notranslate"><span class="pre">universe</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Icellnet.to_array" title="pypath.core.annot.Icellnet.to_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_array</span></code></a>([reference_set, use_fields])</p></td>
+<td><p>Returns an entity vs feature array.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Icellnet.to_bool_array" title="pypath.core.annot.Icellnet.to_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_bool_array</span></code></a>(reference_set)</p></td>
+<td><p>Returns a presence/absence boolean array for a reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Icellnet.to_set" title="pypath.core.annot.Icellnet.to_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_set</span></code></a>()</p></td>
+<td><p>Returns the entities present in this annotation resource as a set.</p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Attributes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_fields</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">summary</span></code></p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Icellnet.add_complexes_by_inference">
+<span class="sig-name descname"><span class="pre">add_complexes_by_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Icellnet.add_complexes_by_inference" title="Link to this definition">§</a></dt>
+<dd><p>Creates complex annotations by in silico inference and adds them
+to this annotation set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Icellnet.all_complexes">
+<span class="sig-name descname"><span class="pre">all_complexes</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Icellnet.all_complexes" title="Link to this definition">§</a></dt>
+<dd><p>All protein complexes annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Icellnet.all_entities">
+<span class="sig-name descname"><span class="pre">all_entities</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Icellnet.all_entities" title="Link to this definition">§</a></dt>
+<dd><p>All entities annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Icellnet.all_mirnas">
+<span class="sig-name descname"><span class="pre">all_mirnas</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Icellnet.all_mirnas" title="Link to this definition">§</a></dt>
+<dd><p>All miRNAs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Icellnet.all_proteins">
+<span class="sig-name descname"><span class="pre">all_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Icellnet.all_proteins" title="Link to this definition">§</a></dt>
+<dd><p>All UniProt IDs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Icellnet.all_refs">
+<span class="sig-name descname"><span class="pre">all_refs</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Icellnet.all_refs" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects the references
+across all records. Returns <em>list</em>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Icellnet.annotate_complex">
+<span class="sig-name descname"><span class="pre">annotate_complex</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cplex</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Icellnet.annotate_complex" title="Link to this definition">§</a></dt>
+<dd><p>Infers annotations for a single complex.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Icellnet.browse">
+<span class="sig-name descname"><span class="pre">browse</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">field</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">start</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Icellnet.browse" title="Link to this definition">§</a></dt>
+<dd><p>Print gene information as a table.</p>
+<p>Presents information about annotation categories as ascii tables
+printed in the terminal. If one category provided, prints one table.
+If multiple categories provided, prints a table for each of them one
+by one proceeding to the next one once you hit return. If no categories
+provided goes through all levels of the primary category.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>field:</dt><dd><p>The field to browse categories by.</p>
+<ul class="simple">
+<li><p>If None the primary field will be selected.
+If this annotation resource doesn’t have fields, all proteins
+will be presented as one single category.</p></li>
+<li><p>If a string it will be considered a field name and it will
+browse through all levels of this field.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">list</span></code>, set or tuple, it will be considered either a
+<code class="docutils literal notranslate"><span class="pre">list</span></code> of field names or a list of values from the primary
+field. In the former case all combinations of the values of
+the fields will be presented, in the latter case the browsing
+will be limited to the levels of the primary field contained
+in <code class="docutils literal notranslate"><span class="pre">field</span></code>.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">dict</span></code>, keys are supposed to be field names and values
+as list of levels. If any of the values are None, all levels
+from that field will be used.</p></li>
+</ul>
+</dd>
+<dt>start:</dt><dd><p>Start browsing from this category. E.g. if there are 500
+categories and start is 250 it will skip everything before the
+250th.</p>
+</dd>
+<dt>kwargs:</dt><dd><p>Passed to <code class="docutils literal notranslate"><span class="pre">pypath.utils.uniprot.info</span></code>.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Icellnet.complex_inference">
+<span class="sig-name descname"><span class="pre">complex_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Icellnet.complex_inference" title="Link to this definition">§</a></dt>
+<dd><p>Annotates all complexes in <cite>complexes</cite>, by default in the default
+complex database (existing in the <cite>complex</cite> module or generated
+on demand according to the module’s current settings).</p>
+<dl class="field-list simple">
+<dt class="field-odd">Returns<span class="colon">:</span></dt>
+<dd class="field-odd"><p><ul class="simple">
+<li><p><em>Dict with complexes as keys and sets of annotations as values.</em></p></li>
+<li><p><em>Complexes with no valid information in this annotation resource</em></p></li>
+<li><p><em>won’t be in the dict.</em></p></li>
+</ul>
+</p>
+</dd>
+<dt class="field-even">Parameters<span class="colon">:</span></dt>
+<dd class="field-even"><p><strong>complexes</strong> (<em>iterable</em>) – Iterable yielding complexes.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Icellnet.coverage">
+<span class="sig-name descname"><span class="pre">coverage</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">other</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Icellnet.coverage" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the coverage of the annotation i.e. the proportion of
+entities having at least one record in this annotation resource
+for an arbitrary set of entities.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Icellnet.curation_effort">
+<span class="sig-name descname"><span class="pre">curation_effort</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Icellnet.curation_effort" title="Link to this definition">§</a></dt>
+<dd><p>Counts the reference-record pairs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Icellnet.get_names">
+<span class="sig-name descname"><span class="pre">get_names</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Icellnet.get_names" title="Link to this definition">§</a></dt>
+<dd><p>Returns the list of field names in the records. The annotation
+consists of uniform records and each entity might be annotated
+with one or more records. Each record is a tuple of fields, for
+example <code class="docutils literal notranslate"><span class="pre">('cell_type',</span> <span class="pre">'expression_level',</span> <span class="pre">'score')</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Icellnet.get_reference_set">
+<em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">get_reference_set</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">proteins</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">swissprot_only</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Icellnet.get_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the reference set i.e. the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Icellnet.get_subset">
+<span class="sig-name descname"><span class="pre">get_subset</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Icellnet.get_subset" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Icellnet.get_subset_bool_array">
+<span class="sig-name descname"><span class="pre">get_subset_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Icellnet.get_subset_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a boolean vector with True and False values for each entity
+in the reference set. The values represent presence absence data
+in the simplest case, but by providing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> any kind of matching
+and filtering is possible. <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> are passed to the <code class="docutils literal notranslate"><span class="pre">select</span></code>
+method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Icellnet.get_values">
+<span class="sig-name descname"><span class="pre">get_values</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">exclude_none</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Icellnet.get_values" title="Link to this definition">§</a></dt>
+<dd><p>Returns the set of all possible values of a field. E.g. if the
+records of this annotation have a field <code class="docutils literal notranslate"><span class="pre">cell_type</span></code> then calling
+this method can tell you that across all records the values of
+this field might be <code class="docutils literal notranslate"><span class="pre">{'macrophage',</span> <span class="pre">'epithelial_cell',</span> <span class="pre">...}</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Icellnet.labels">
+<span class="sig-name descname"><span class="pre">labels</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Icellnet.labels" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Icellnet.load">
+<span class="sig-name descname"><span class="pre">load</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Icellnet.load" title="Link to this definition">§</a></dt>
+<dd><p>Loads the annotation data by calling the input method.
+Infers annotations for complexes in the complex database if
+py:attr:<code class="docutils literal notranslate"><span class="pre">infer_complexes</span></code> is True.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Icellnet.load_data">
+<span class="sig-name descname"><span class="pre">load_data</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Icellnet.load_data" title="Link to this definition">§</a></dt>
+<dd><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Icellnet.load_proteins">
+<span class="sig-name descname"><span class="pre">load_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Icellnet.load_proteins" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a set of all UniProt IDs to have a base set of the entire
+proteome.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Icellnet.make_df">
+<span class="sig-name descname"><span class="pre">make_df</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">rebuild</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Icellnet.make_df" title="Link to this definition">§</a></dt>
+<dd><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.
+The data frame will be assigned to :py:attr``df``.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Icellnet.numof_entities">
+<span class="sig-name descname"><span class="pre">numof_entities</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Icellnet.numof_entities" title="Link to this definition">§</a></dt>
+<dd><p>The number of annotated entities in the resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Icellnet.numof_records">
+<span class="sig-name descname"><span class="pre">numof_records</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Icellnet.numof_records" title="Link to this definition">§</a></dt>
+<dd><p>The total number of annotation records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Icellnet.numof_references">
+<span class="sig-name descname"><span class="pre">numof_references</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Icellnet.numof_references" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects and counts the
+references across all records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Icellnet.process">
+<span class="sig-name descname"><span class="pre">process</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Icellnet.process" title="Link to this definition">§</a></dt>
+<dd><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Icellnet.reload">
+<span class="sig-name descname"><span class="pre">reload</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Icellnet.reload" title="Link to this definition">§</a></dt>
+<dd><p>Reloads the object from the module level.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Icellnet.select">
+<span class="sig-name descname"><span class="pre">select</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Icellnet.select" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Icellnet.set_method">
+<span class="sig-name descname"><span class="pre">set_method</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Icellnet.set_method" title="Link to this definition">§</a></dt>
+<dd><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if
+necessary.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Icellnet.set_reference_set">
+<span class="sig-name descname"><span class="pre">set_reference_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Icellnet.set_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Assigns the reference set to the :py:attr``reference_set`` attribute.
+The reference set is the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Icellnet.show">
+<span class="sig-name descname"><span class="pre">show</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">table_param</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Icellnet.show" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic
+information from the UniProt datasheets.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Icellnet.subset_intersection">
+<span class="sig-name descname"><span class="pre">subset_intersection</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">universe</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Icellnet.subset_intersection" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the proportion of entities in a subset occuring in the
+set <code class="docutils literal notranslate"><span class="pre">universe</span></code>. The subset is selected by passing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> to the
+<code class="docutils literal notranslate"><span class="pre">select</span></code> method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Icellnet.to_array">
+<span class="sig-name descname"><span class="pre">to_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_fields</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Icellnet.to_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns an entity vs feature array. In case of more complex
+annotations this might be huge.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Icellnet.to_bool_array">
+<span class="sig-name descname"><span class="pre">to_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Icellnet.to_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a presence/absence boolean array for a reference set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Icellnet.to_set">
+<span class="sig-name descname"><span class="pre">to_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Icellnet.to_set" title="Link to this definition">§</a></dt>
+<dd><p>Returns the entities present in this annotation resource as a set.</p>
+</dd></dl>
+
+</dd></dl>
+
+</section>
+
+
+                </article>
+              
+              
+              
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+  <section id="pypath-core-annot-icellnetcomplex">
+<h1>pypath.core.annot.IcellnetComplex<a class="headerlink" href="#pypath-core-annot-icellnetcomplex" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.core.annot.IcellnetComplex">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.core.annot.</span></span><span class="sig-name descname"><span class="pre">IcellnetComplex</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#IcellnetComplex"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.IcellnetComplex" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <a class="reference internal" href="pypath.core.annot.AnnotationBase.html#pypath.core.annot.AnnotationBase" title="pypath.core.annot.AnnotationBase"><code class="xref py py-class docutils literal notranslate"><span class="pre">AnnotationBase</span></code></a></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.IcellnetComplex.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#IcellnetComplex.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.IcellnetComplex.__init__" title="Link to this definition">§</a></dt>
+<dd><p>Represents annotations for a set of proteins.
+Loads the data from the original resource and provides methods
+to query the annotations.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>name</strong> (<em>str</em>) – A custom name for the annotation resource.</p></li>
+<li><p><strong>ncbi_tax_id</strong> (<em>int</em>) – NCBI Taxonomy identifier.</p></li>
+<li><p><strong>input_method</strong> (<em>callable</em><em>,</em><em>str</em>) – Either a callable or the name of a method in any submodules of
+the <code class="docutils literal notranslate"><span class="pre">pypath.inputs</span></code>  module. Should return a dict with
+UniProt IDs as keys or an object suitable for <code class="docutils literal notranslate"><span class="pre">process_method</span></code>.</p></li>
+<li><p><strong>input_args</strong> (<em>dict</em>) – Arguments for the <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.IcellnetComplex.__init__" title="pypath.core.annot.IcellnetComplex.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>(**kwargs)</p></td>
+<td><p>Represents annotations for a set of proteins.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.IcellnetComplex.add_complexes_by_inference" title="pypath.core.annot.IcellnetComplex.add_complexes_by_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">add_complexes_by_inference</span></code></a>([complexes])</p></td>
+<td><p>Creates complex annotations by in silico inference and adds them to this annotation set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.IcellnetComplex.all_complexes" title="pypath.core.annot.IcellnetComplex.all_complexes"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_complexes</span></code></a>()</p></td>
+<td><p>All protein complexes annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.IcellnetComplex.all_entities" title="pypath.core.annot.IcellnetComplex.all_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_entities</span></code></a>([entity_types])</p></td>
+<td><p>All entities annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.IcellnetComplex.all_mirnas" title="pypath.core.annot.IcellnetComplex.all_mirnas"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_mirnas</span></code></a>()</p></td>
+<td><p>All miRNAs annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.IcellnetComplex.all_proteins" title="pypath.core.annot.IcellnetComplex.all_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_proteins</span></code></a>()</p></td>
+<td><p>All UniProt IDs annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.IcellnetComplex.all_refs" title="pypath.core.annot.IcellnetComplex.all_refs"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_refs</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.IcellnetComplex.annotate_complex" title="pypath.core.annot.IcellnetComplex.annotate_complex"><code class="xref py py-obj docutils literal notranslate"><span class="pre">annotate_complex</span></code></a>(cplex)</p></td>
+<td><p>Infers annotations for a single complex.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.IcellnetComplex.browse" title="pypath.core.annot.IcellnetComplex.browse"><code class="xref py py-obj docutils literal notranslate"><span class="pre">browse</span></code></a>([field, start])</p></td>
+<td><p>Print gene information as a table.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.IcellnetComplex.complex_inference" title="pypath.core.annot.IcellnetComplex.complex_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">complex_inference</span></code></a>([complexes])</p></td>
+<td><p>Annotates all complexes in <cite>complexes</cite>, by default in the default complex database (existing in the <cite>complex</cite> module or generated on demand according to the module's current settings).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.IcellnetComplex.coverage" title="pypath.core.annot.IcellnetComplex.coverage"><code class="xref py py-obj docutils literal notranslate"><span class="pre">coverage</span></code></a>(other)</p></td>
+<td><p>Calculates the coverage of the annotation i.e. the proportion of entities having at least one record in this annotation resource for an arbitrary set of entities.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.IcellnetComplex.curation_effort" title="pypath.core.annot.IcellnetComplex.curation_effort"><code class="xref py py-obj docutils literal notranslate"><span class="pre">curation_effort</span></code></a>()</p></td>
+<td><p>Counts the reference-record pairs.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">from_dump</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_entity_type</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.IcellnetComplex.get_names" title="pypath.core.annot.IcellnetComplex.get_names"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_names</span></code></a>()</p></td>
+<td><p>Returns the list of field names in the records.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.IcellnetComplex.get_reference_set" title="pypath.core.annot.IcellnetComplex.get_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_reference_set</span></code></a>([proteins, complexes, ...])</p></td>
+<td><p>Retrieves the reference set i.e. the set of all entities which potentially have annotation in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.IcellnetComplex.get_subset" title="pypath.core.annot.IcellnetComplex.get_subset"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.IcellnetComplex.get_subset_bool_array" title="pypath.core.annot.IcellnetComplex.get_subset_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset_bool_array</span></code></a>([reference_set])</p></td>
+<td><p>Returns a boolean vector with True and False values for each entity in the reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.IcellnetComplex.get_values" title="pypath.core.annot.IcellnetComplex.get_values"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_values</span></code></a>(name[, exclude_none])</p></td>
+<td><p>Returns the set of all possible values of a field.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_complex</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_mirna</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_protein</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.IcellnetComplex.labels" title="pypath.core.annot.IcellnetComplex.labels"><code class="xref py py-obj docutils literal notranslate"><span class="pre">labels</span></code></a>([method])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.IcellnetComplex.load" title="pypath.core.annot.IcellnetComplex.load"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load</span></code></a>()</p></td>
+<td><p>Loads the annotation data by calling the input method.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.IcellnetComplex.load_data" title="pypath.core.annot.IcellnetComplex.load_data"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_data</span></code></a>()</p></td>
+<td><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.IcellnetComplex.load_proteins" title="pypath.core.annot.IcellnetComplex.load_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_proteins</span></code></a>()</p></td>
+<td><p>Retrieves a set of all UniProt IDs to have a base set of the entire proteome.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.IcellnetComplex.make_df" title="pypath.core.annot.IcellnetComplex.make_df"><code class="xref py py-obj docutils literal notranslate"><span class="pre">make_df</span></code></a>([rebuild])</p></td>
+<td><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complex_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.IcellnetComplex.numof_entities" title="pypath.core.annot.IcellnetComplex.numof_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_entities</span></code></a>()</p></td>
+<td><p>The number of annotated entities in the resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirna_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirnas</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_protein_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_proteins</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.IcellnetComplex.numof_records" title="pypath.core.annot.IcellnetComplex.numof_records"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_records</span></code></a>([entity_types])</p></td>
+<td><p>The total number of annotation records.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.IcellnetComplex.numof_references" title="pypath.core.annot.IcellnetComplex.numof_references"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_references</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.IcellnetComplex.process" title="pypath.core.annot.IcellnetComplex.process"><code class="xref py py-obj docutils literal notranslate"><span class="pre">process</span></code></a>()</p></td>
+<td><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">proportion</span></code>(other)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.IcellnetComplex.reload" title="pypath.core.annot.IcellnetComplex.reload"><code class="xref py py-obj docutils literal notranslate"><span class="pre">reload</span></code></a>()</p></td>
+<td><p>Reloads the object from the module level.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">save_to_pickle</span></code>(pickle_file)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.IcellnetComplex.select" title="pypath.core.annot.IcellnetComplex.select"><code class="xref py py-obj docutils literal notranslate"><span class="pre">select</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.IcellnetComplex.set_method" title="pypath.core.annot.IcellnetComplex.set_method"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_method</span></code></a>()</p></td>
+<td><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if necessary.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.IcellnetComplex.set_reference_set" title="pypath.core.annot.IcellnetComplex.set_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_reference_set</span></code></a>()</p></td>
+<td><p>Assigns the reference set to the :py:attr``reference_set`` attribute.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.IcellnetComplex.show" title="pypath.core.annot.IcellnetComplex.show"><code class="xref py py-obj docutils literal notranslate"><span class="pre">show</span></code></a>([method, table_param])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic information from the UniProt datasheets.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.IcellnetComplex.subset_intersection" title="pypath.core.annot.IcellnetComplex.subset_intersection"><code class="xref py py-obj docutils literal notranslate"><span class="pre">subset_intersection</span></code></a>(universe, **kwargs)</p></td>
+<td><p>Calculates the proportion of entities in a subset occuring in the set <code class="docutils literal notranslate"><span class="pre">universe</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.IcellnetComplex.to_array" title="pypath.core.annot.IcellnetComplex.to_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_array</span></code></a>([reference_set, use_fields])</p></td>
+<td><p>Returns an entity vs feature array.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.IcellnetComplex.to_bool_array" title="pypath.core.annot.IcellnetComplex.to_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_bool_array</span></code></a>(reference_set)</p></td>
+<td><p>Returns a presence/absence boolean array for a reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.IcellnetComplex.to_set" title="pypath.core.annot.IcellnetComplex.to_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_set</span></code></a>()</p></td>
+<td><p>Returns the entities present in this annotation resource as a set.</p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Attributes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_fields</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">summary</span></code></p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.IcellnetComplex.add_complexes_by_inference">
+<span class="sig-name descname"><span class="pre">add_complexes_by_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.IcellnetComplex.add_complexes_by_inference" title="Link to this definition">§</a></dt>
+<dd><p>Creates complex annotations by in silico inference and adds them
+to this annotation set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.IcellnetComplex.all_complexes">
+<span class="sig-name descname"><span class="pre">all_complexes</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.IcellnetComplex.all_complexes" title="Link to this definition">§</a></dt>
+<dd><p>All protein complexes annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.IcellnetComplex.all_entities">
+<span class="sig-name descname"><span class="pre">all_entities</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.IcellnetComplex.all_entities" title="Link to this definition">§</a></dt>
+<dd><p>All entities annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.IcellnetComplex.all_mirnas">
+<span class="sig-name descname"><span class="pre">all_mirnas</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.IcellnetComplex.all_mirnas" title="Link to this definition">§</a></dt>
+<dd><p>All miRNAs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.IcellnetComplex.all_proteins">
+<span class="sig-name descname"><span class="pre">all_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.IcellnetComplex.all_proteins" title="Link to this definition">§</a></dt>
+<dd><p>All UniProt IDs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.IcellnetComplex.all_refs">
+<span class="sig-name descname"><span class="pre">all_refs</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.IcellnetComplex.all_refs" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects the references
+across all records. Returns <em>list</em>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.IcellnetComplex.annotate_complex">
+<span class="sig-name descname"><span class="pre">annotate_complex</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cplex</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.IcellnetComplex.annotate_complex" title="Link to this definition">§</a></dt>
+<dd><p>Infers annotations for a single complex.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.IcellnetComplex.browse">
+<span class="sig-name descname"><span class="pre">browse</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">field</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">start</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.IcellnetComplex.browse" title="Link to this definition">§</a></dt>
+<dd><p>Print gene information as a table.</p>
+<p>Presents information about annotation categories as ascii tables
+printed in the terminal. If one category provided, prints one table.
+If multiple categories provided, prints a table for each of them one
+by one proceeding to the next one once you hit return. If no categories
+provided goes through all levels of the primary category.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>field:</dt><dd><p>The field to browse categories by.</p>
+<ul class="simple">
+<li><p>If None the primary field will be selected.
+If this annotation resource doesn’t have fields, all proteins
+will be presented as one single category.</p></li>
+<li><p>If a string it will be considered a field name and it will
+browse through all levels of this field.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">list</span></code>, set or tuple, it will be considered either a
+<code class="docutils literal notranslate"><span class="pre">list</span></code> of field names or a list of values from the primary
+field. In the former case all combinations of the values of
+the fields will be presented, in the latter case the browsing
+will be limited to the levels of the primary field contained
+in <code class="docutils literal notranslate"><span class="pre">field</span></code>.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">dict</span></code>, keys are supposed to be field names and values
+as list of levels. If any of the values are None, all levels
+from that field will be used.</p></li>
+</ul>
+</dd>
+<dt>start:</dt><dd><p>Start browsing from this category. E.g. if there are 500
+categories and start is 250 it will skip everything before the
+250th.</p>
+</dd>
+<dt>kwargs:</dt><dd><p>Passed to <code class="docutils literal notranslate"><span class="pre">pypath.utils.uniprot.info</span></code>.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.IcellnetComplex.complex_inference">
+<span class="sig-name descname"><span class="pre">complex_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.IcellnetComplex.complex_inference" title="Link to this definition">§</a></dt>
+<dd><p>Annotates all complexes in <cite>complexes</cite>, by default in the default
+complex database (existing in the <cite>complex</cite> module or generated
+on demand according to the module’s current settings).</p>
+<dl class="field-list simple">
+<dt class="field-odd">Returns<span class="colon">:</span></dt>
+<dd class="field-odd"><p><ul class="simple">
+<li><p><em>Dict with complexes as keys and sets of annotations as values.</em></p></li>
+<li><p><em>Complexes with no valid information in this annotation resource</em></p></li>
+<li><p><em>won’t be in the dict.</em></p></li>
+</ul>
+</p>
+</dd>
+<dt class="field-even">Parameters<span class="colon">:</span></dt>
+<dd class="field-even"><p><strong>complexes</strong> (<em>iterable</em>) – Iterable yielding complexes.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.IcellnetComplex.coverage">
+<span class="sig-name descname"><span class="pre">coverage</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">other</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.IcellnetComplex.coverage" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the coverage of the annotation i.e. the proportion of
+entities having at least one record in this annotation resource
+for an arbitrary set of entities.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.IcellnetComplex.curation_effort">
+<span class="sig-name descname"><span class="pre">curation_effort</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.IcellnetComplex.curation_effort" title="Link to this definition">§</a></dt>
+<dd><p>Counts the reference-record pairs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.IcellnetComplex.get_names">
+<span class="sig-name descname"><span class="pre">get_names</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.IcellnetComplex.get_names" title="Link to this definition">§</a></dt>
+<dd><p>Returns the list of field names in the records. The annotation
+consists of uniform records and each entity might be annotated
+with one or more records. Each record is a tuple of fields, for
+example <code class="docutils literal notranslate"><span class="pre">('cell_type',</span> <span class="pre">'expression_level',</span> <span class="pre">'score')</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.IcellnetComplex.get_reference_set">
+<em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">get_reference_set</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">proteins</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">swissprot_only</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.IcellnetComplex.get_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the reference set i.e. the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.IcellnetComplex.get_subset">
+<span class="sig-name descname"><span class="pre">get_subset</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.IcellnetComplex.get_subset" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.IcellnetComplex.get_subset_bool_array">
+<span class="sig-name descname"><span class="pre">get_subset_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.IcellnetComplex.get_subset_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a boolean vector with True and False values for each entity
+in the reference set. The values represent presence absence data
+in the simplest case, but by providing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> any kind of matching
+and filtering is possible. <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> are passed to the <code class="docutils literal notranslate"><span class="pre">select</span></code>
+method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.IcellnetComplex.get_values">
+<span class="sig-name descname"><span class="pre">get_values</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">exclude_none</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.IcellnetComplex.get_values" title="Link to this definition">§</a></dt>
+<dd><p>Returns the set of all possible values of a field. E.g. if the
+records of this annotation have a field <code class="docutils literal notranslate"><span class="pre">cell_type</span></code> then calling
+this method can tell you that across all records the values of
+this field might be <code class="docutils literal notranslate"><span class="pre">{'macrophage',</span> <span class="pre">'epithelial_cell',</span> <span class="pre">...}</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.IcellnetComplex.labels">
+<span class="sig-name descname"><span class="pre">labels</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.IcellnetComplex.labels" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.IcellnetComplex.load">
+<span class="sig-name descname"><span class="pre">load</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.IcellnetComplex.load" title="Link to this definition">§</a></dt>
+<dd><p>Loads the annotation data by calling the input method.
+Infers annotations for complexes in the complex database if
+py:attr:<code class="docutils literal notranslate"><span class="pre">infer_complexes</span></code> is True.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.IcellnetComplex.load_data">
+<span class="sig-name descname"><span class="pre">load_data</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.IcellnetComplex.load_data" title="Link to this definition">§</a></dt>
+<dd><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.IcellnetComplex.load_proteins">
+<span class="sig-name descname"><span class="pre">load_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.IcellnetComplex.load_proteins" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a set of all UniProt IDs to have a base set of the entire
+proteome.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.IcellnetComplex.make_df">
+<span class="sig-name descname"><span class="pre">make_df</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">rebuild</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.IcellnetComplex.make_df" title="Link to this definition">§</a></dt>
+<dd><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.
+The data frame will be assigned to :py:attr``df``.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.IcellnetComplex.numof_entities">
+<span class="sig-name descname"><span class="pre">numof_entities</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.IcellnetComplex.numof_entities" title="Link to this definition">§</a></dt>
+<dd><p>The number of annotated entities in the resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.IcellnetComplex.numof_records">
+<span class="sig-name descname"><span class="pre">numof_records</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.IcellnetComplex.numof_records" title="Link to this definition">§</a></dt>
+<dd><p>The total number of annotation records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.IcellnetComplex.numof_references">
+<span class="sig-name descname"><span class="pre">numof_references</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.IcellnetComplex.numof_references" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects and counts the
+references across all records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.IcellnetComplex.process">
+<span class="sig-name descname"><span class="pre">process</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.IcellnetComplex.process" title="Link to this definition">§</a></dt>
+<dd><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.IcellnetComplex.reload">
+<span class="sig-name descname"><span class="pre">reload</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.IcellnetComplex.reload" title="Link to this definition">§</a></dt>
+<dd><p>Reloads the object from the module level.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.IcellnetComplex.select">
+<span class="sig-name descname"><span class="pre">select</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.IcellnetComplex.select" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.IcellnetComplex.set_method">
+<span class="sig-name descname"><span class="pre">set_method</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.IcellnetComplex.set_method" title="Link to this definition">§</a></dt>
+<dd><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if
+necessary.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.IcellnetComplex.set_reference_set">
+<span class="sig-name descname"><span class="pre">set_reference_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.IcellnetComplex.set_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Assigns the reference set to the :py:attr``reference_set`` attribute.
+The reference set is the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.IcellnetComplex.show">
+<span class="sig-name descname"><span class="pre">show</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">table_param</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.IcellnetComplex.show" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic
+information from the UniProt datasheets.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.IcellnetComplex.subset_intersection">
+<span class="sig-name descname"><span class="pre">subset_intersection</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">universe</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.IcellnetComplex.subset_intersection" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the proportion of entities in a subset occuring in the
+set <code class="docutils literal notranslate"><span class="pre">universe</span></code>. The subset is selected by passing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> to the
+<code class="docutils literal notranslate"><span class="pre">select</span></code> method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.IcellnetComplex.to_array">
+<span class="sig-name descname"><span class="pre">to_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_fields</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.IcellnetComplex.to_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns an entity vs feature array. In case of more complex
+annotations this might be huge.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.IcellnetComplex.to_bool_array">
+<span class="sig-name descname"><span class="pre">to_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.IcellnetComplex.to_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a presence/absence boolean array for a reference set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.IcellnetComplex.to_set">
+<span class="sig-name descname"><span class="pre">to_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.IcellnetComplex.to_set" title="Link to this definition">§</a></dt>
+<dd><p>Returns the entities present in this annotation resource as a set.</p>
+</dd></dl>
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+  <section id="pypath-core-annot-integrins">
+<h1>pypath.core.annot.Integrins<a class="headerlink" href="#pypath-core-annot-integrins" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.core.annot.Integrins">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.core.annot.</span></span><span class="sig-name descname"><span class="pre">Integrins</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#Integrins"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.Integrins" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <a class="reference internal" href="pypath.core.annot.AnnotationBase.html#pypath.core.annot.AnnotationBase" title="pypath.core.annot.AnnotationBase"><code class="xref py py-class docutils literal notranslate"><span class="pre">AnnotationBase</span></code></a></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Integrins.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#Integrins.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.Integrins.__init__" title="Link to this definition">§</a></dt>
+<dd><p>Represents annotations for a set of proteins.
+Loads the data from the original resource and provides methods
+to query the annotations.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>name</strong> (<em>str</em>) – A custom name for the annotation resource.</p></li>
+<li><p><strong>ncbi_tax_id</strong> (<em>int</em>) – NCBI Taxonomy identifier.</p></li>
+<li><p><strong>input_method</strong> (<em>callable</em><em>,</em><em>str</em>) – Either a callable or the name of a method in any submodules of
+the <code class="docutils literal notranslate"><span class="pre">pypath.inputs</span></code>  module. Should return a dict with
+UniProt IDs as keys or an object suitable for <code class="docutils literal notranslate"><span class="pre">process_method</span></code>.</p></li>
+<li><p><strong>input_args</strong> (<em>dict</em>) – Arguments for the <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Integrins.__init__" title="pypath.core.annot.Integrins.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>(**kwargs)</p></td>
+<td><p>Represents annotations for a set of proteins.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Integrins.add_complexes_by_inference" title="pypath.core.annot.Integrins.add_complexes_by_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">add_complexes_by_inference</span></code></a>([complexes])</p></td>
+<td><p>Creates complex annotations by in silico inference and adds them to this annotation set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Integrins.all_complexes" title="pypath.core.annot.Integrins.all_complexes"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_complexes</span></code></a>()</p></td>
+<td><p>All protein complexes annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Integrins.all_entities" title="pypath.core.annot.Integrins.all_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_entities</span></code></a>([entity_types])</p></td>
+<td><p>All entities annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Integrins.all_mirnas" title="pypath.core.annot.Integrins.all_mirnas"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_mirnas</span></code></a>()</p></td>
+<td><p>All miRNAs annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Integrins.all_proteins" title="pypath.core.annot.Integrins.all_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_proteins</span></code></a>()</p></td>
+<td><p>All UniProt IDs annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Integrins.all_refs" title="pypath.core.annot.Integrins.all_refs"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_refs</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Integrins.annotate_complex" title="pypath.core.annot.Integrins.annotate_complex"><code class="xref py py-obj docutils literal notranslate"><span class="pre">annotate_complex</span></code></a>(cplex)</p></td>
+<td><p>Infers annotations for a single complex.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Integrins.browse" title="pypath.core.annot.Integrins.browse"><code class="xref py py-obj docutils literal notranslate"><span class="pre">browse</span></code></a>([field, start])</p></td>
+<td><p>Print gene information as a table.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Integrins.complex_inference" title="pypath.core.annot.Integrins.complex_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">complex_inference</span></code></a>([complexes])</p></td>
+<td><p>Annotates all complexes in <cite>complexes</cite>, by default in the default complex database (existing in the <cite>complex</cite> module or generated on demand according to the module's current settings).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Integrins.coverage" title="pypath.core.annot.Integrins.coverage"><code class="xref py py-obj docutils literal notranslate"><span class="pre">coverage</span></code></a>(other)</p></td>
+<td><p>Calculates the coverage of the annotation i.e. the proportion of entities having at least one record in this annotation resource for an arbitrary set of entities.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Integrins.curation_effort" title="pypath.core.annot.Integrins.curation_effort"><code class="xref py py-obj docutils literal notranslate"><span class="pre">curation_effort</span></code></a>()</p></td>
+<td><p>Counts the reference-record pairs.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">from_dump</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_entity_type</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Integrins.get_names" title="pypath.core.annot.Integrins.get_names"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_names</span></code></a>()</p></td>
+<td><p>Returns the list of field names in the records.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Integrins.get_reference_set" title="pypath.core.annot.Integrins.get_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_reference_set</span></code></a>([proteins, complexes, ...])</p></td>
+<td><p>Retrieves the reference set i.e. the set of all entities which potentially have annotation in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Integrins.get_subset" title="pypath.core.annot.Integrins.get_subset"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Integrins.get_subset_bool_array" title="pypath.core.annot.Integrins.get_subset_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset_bool_array</span></code></a>([reference_set])</p></td>
+<td><p>Returns a boolean vector with True and False values for each entity in the reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Integrins.get_values" title="pypath.core.annot.Integrins.get_values"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_values</span></code></a>(name[, exclude_none])</p></td>
+<td><p>Returns the set of all possible values of a field.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_complex</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_mirna</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_protein</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Integrins.labels" title="pypath.core.annot.Integrins.labels"><code class="xref py py-obj docutils literal notranslate"><span class="pre">labels</span></code></a>([method])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Integrins.load" title="pypath.core.annot.Integrins.load"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load</span></code></a>()</p></td>
+<td><p>Loads the annotation data by calling the input method.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Integrins.load_data" title="pypath.core.annot.Integrins.load_data"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_data</span></code></a>()</p></td>
+<td><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Integrins.load_proteins" title="pypath.core.annot.Integrins.load_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_proteins</span></code></a>()</p></td>
+<td><p>Retrieves a set of all UniProt IDs to have a base set of the entire proteome.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Integrins.make_df" title="pypath.core.annot.Integrins.make_df"><code class="xref py py-obj docutils literal notranslate"><span class="pre">make_df</span></code></a>([rebuild])</p></td>
+<td><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complex_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Integrins.numof_entities" title="pypath.core.annot.Integrins.numof_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_entities</span></code></a>()</p></td>
+<td><p>The number of annotated entities in the resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirna_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirnas</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_protein_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_proteins</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Integrins.numof_records" title="pypath.core.annot.Integrins.numof_records"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_records</span></code></a>([entity_types])</p></td>
+<td><p>The total number of annotation records.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Integrins.numof_references" title="pypath.core.annot.Integrins.numof_references"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_references</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Integrins.process" title="pypath.core.annot.Integrins.process"><code class="xref py py-obj docutils literal notranslate"><span class="pre">process</span></code></a>()</p></td>
+<td><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">proportion</span></code>(other)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Integrins.reload" title="pypath.core.annot.Integrins.reload"><code class="xref py py-obj docutils literal notranslate"><span class="pre">reload</span></code></a>()</p></td>
+<td><p>Reloads the object from the module level.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">save_to_pickle</span></code>(pickle_file)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Integrins.select" title="pypath.core.annot.Integrins.select"><code class="xref py py-obj docutils literal notranslate"><span class="pre">select</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Integrins.set_method" title="pypath.core.annot.Integrins.set_method"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_method</span></code></a>()</p></td>
+<td><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if necessary.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Integrins.set_reference_set" title="pypath.core.annot.Integrins.set_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_reference_set</span></code></a>()</p></td>
+<td><p>Assigns the reference set to the :py:attr``reference_set`` attribute.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Integrins.show" title="pypath.core.annot.Integrins.show"><code class="xref py py-obj docutils literal notranslate"><span class="pre">show</span></code></a>([method, table_param])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic information from the UniProt datasheets.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Integrins.subset_intersection" title="pypath.core.annot.Integrins.subset_intersection"><code class="xref py py-obj docutils literal notranslate"><span class="pre">subset_intersection</span></code></a>(universe, **kwargs)</p></td>
+<td><p>Calculates the proportion of entities in a subset occuring in the set <code class="docutils literal notranslate"><span class="pre">universe</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Integrins.to_array" title="pypath.core.annot.Integrins.to_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_array</span></code></a>([reference_set, use_fields])</p></td>
+<td><p>Returns an entity vs feature array.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Integrins.to_bool_array" title="pypath.core.annot.Integrins.to_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_bool_array</span></code></a>(reference_set)</p></td>
+<td><p>Returns a presence/absence boolean array for a reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Integrins.to_set" title="pypath.core.annot.Integrins.to_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_set</span></code></a>()</p></td>
+<td><p>Returns the entities present in this annotation resource as a set.</p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Attributes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_fields</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">summary</span></code></p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Integrins.add_complexes_by_inference">
+<span class="sig-name descname"><span class="pre">add_complexes_by_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Integrins.add_complexes_by_inference" title="Link to this definition">§</a></dt>
+<dd><p>Creates complex annotations by in silico inference and adds them
+to this annotation set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Integrins.all_complexes">
+<span class="sig-name descname"><span class="pre">all_complexes</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Integrins.all_complexes" title="Link to this definition">§</a></dt>
+<dd><p>All protein complexes annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Integrins.all_entities">
+<span class="sig-name descname"><span class="pre">all_entities</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Integrins.all_entities" title="Link to this definition">§</a></dt>
+<dd><p>All entities annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Integrins.all_mirnas">
+<span class="sig-name descname"><span class="pre">all_mirnas</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Integrins.all_mirnas" title="Link to this definition">§</a></dt>
+<dd><p>All miRNAs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Integrins.all_proteins">
+<span class="sig-name descname"><span class="pre">all_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Integrins.all_proteins" title="Link to this definition">§</a></dt>
+<dd><p>All UniProt IDs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Integrins.all_refs">
+<span class="sig-name descname"><span class="pre">all_refs</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Integrins.all_refs" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects the references
+across all records. Returns <em>list</em>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Integrins.annotate_complex">
+<span class="sig-name descname"><span class="pre">annotate_complex</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cplex</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Integrins.annotate_complex" title="Link to this definition">§</a></dt>
+<dd><p>Infers annotations for a single complex.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Integrins.browse">
+<span class="sig-name descname"><span class="pre">browse</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">field</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">start</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Integrins.browse" title="Link to this definition">§</a></dt>
+<dd><p>Print gene information as a table.</p>
+<p>Presents information about annotation categories as ascii tables
+printed in the terminal. If one category provided, prints one table.
+If multiple categories provided, prints a table for each of them one
+by one proceeding to the next one once you hit return. If no categories
+provided goes through all levels of the primary category.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>field:</dt><dd><p>The field to browse categories by.</p>
+<ul class="simple">
+<li><p>If None the primary field will be selected.
+If this annotation resource doesn’t have fields, all proteins
+will be presented as one single category.</p></li>
+<li><p>If a string it will be considered a field name and it will
+browse through all levels of this field.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">list</span></code>, set or tuple, it will be considered either a
+<code class="docutils literal notranslate"><span class="pre">list</span></code> of field names or a list of values from the primary
+field. In the former case all combinations of the values of
+the fields will be presented, in the latter case the browsing
+will be limited to the levels of the primary field contained
+in <code class="docutils literal notranslate"><span class="pre">field</span></code>.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">dict</span></code>, keys are supposed to be field names and values
+as list of levels. If any of the values are None, all levels
+from that field will be used.</p></li>
+</ul>
+</dd>
+<dt>start:</dt><dd><p>Start browsing from this category. E.g. if there are 500
+categories and start is 250 it will skip everything before the
+250th.</p>
+</dd>
+<dt>kwargs:</dt><dd><p>Passed to <code class="docutils literal notranslate"><span class="pre">pypath.utils.uniprot.info</span></code>.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Integrins.complex_inference">
+<span class="sig-name descname"><span class="pre">complex_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Integrins.complex_inference" title="Link to this definition">§</a></dt>
+<dd><p>Annotates all complexes in <cite>complexes</cite>, by default in the default
+complex database (existing in the <cite>complex</cite> module or generated
+on demand according to the module’s current settings).</p>
+<dl class="field-list simple">
+<dt class="field-odd">Returns<span class="colon">:</span></dt>
+<dd class="field-odd"><p><ul class="simple">
+<li><p><em>Dict with complexes as keys and sets of annotations as values.</em></p></li>
+<li><p><em>Complexes with no valid information in this annotation resource</em></p></li>
+<li><p><em>won’t be in the dict.</em></p></li>
+</ul>
+</p>
+</dd>
+<dt class="field-even">Parameters<span class="colon">:</span></dt>
+<dd class="field-even"><p><strong>complexes</strong> (<em>iterable</em>) – Iterable yielding complexes.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Integrins.coverage">
+<span class="sig-name descname"><span class="pre">coverage</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">other</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Integrins.coverage" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the coverage of the annotation i.e. the proportion of
+entities having at least one record in this annotation resource
+for an arbitrary set of entities.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Integrins.curation_effort">
+<span class="sig-name descname"><span class="pre">curation_effort</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Integrins.curation_effort" title="Link to this definition">§</a></dt>
+<dd><p>Counts the reference-record pairs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Integrins.get_names">
+<span class="sig-name descname"><span class="pre">get_names</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Integrins.get_names" title="Link to this definition">§</a></dt>
+<dd><p>Returns the list of field names in the records. The annotation
+consists of uniform records and each entity might be annotated
+with one or more records. Each record is a tuple of fields, for
+example <code class="docutils literal notranslate"><span class="pre">('cell_type',</span> <span class="pre">'expression_level',</span> <span class="pre">'score')</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Integrins.get_reference_set">
+<em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">get_reference_set</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">proteins</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">swissprot_only</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Integrins.get_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the reference set i.e. the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Integrins.get_subset">
+<span class="sig-name descname"><span class="pre">get_subset</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Integrins.get_subset" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Integrins.get_subset_bool_array">
+<span class="sig-name descname"><span class="pre">get_subset_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Integrins.get_subset_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a boolean vector with True and False values for each entity
+in the reference set. The values represent presence absence data
+in the simplest case, but by providing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> any kind of matching
+and filtering is possible. <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> are passed to the <code class="docutils literal notranslate"><span class="pre">select</span></code>
+method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Integrins.get_values">
+<span class="sig-name descname"><span class="pre">get_values</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">exclude_none</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Integrins.get_values" title="Link to this definition">§</a></dt>
+<dd><p>Returns the set of all possible values of a field. E.g. if the
+records of this annotation have a field <code class="docutils literal notranslate"><span class="pre">cell_type</span></code> then calling
+this method can tell you that across all records the values of
+this field might be <code class="docutils literal notranslate"><span class="pre">{'macrophage',</span> <span class="pre">'epithelial_cell',</span> <span class="pre">...}</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Integrins.labels">
+<span class="sig-name descname"><span class="pre">labels</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Integrins.labels" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Integrins.load">
+<span class="sig-name descname"><span class="pre">load</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Integrins.load" title="Link to this definition">§</a></dt>
+<dd><p>Loads the annotation data by calling the input method.
+Infers annotations for complexes in the complex database if
+py:attr:<code class="docutils literal notranslate"><span class="pre">infer_complexes</span></code> is True.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Integrins.load_data">
+<span class="sig-name descname"><span class="pre">load_data</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Integrins.load_data" title="Link to this definition">§</a></dt>
+<dd><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Integrins.load_proteins">
+<span class="sig-name descname"><span class="pre">load_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Integrins.load_proteins" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a set of all UniProt IDs to have a base set of the entire
+proteome.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Integrins.make_df">
+<span class="sig-name descname"><span class="pre">make_df</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">rebuild</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Integrins.make_df" title="Link to this definition">§</a></dt>
+<dd><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.
+The data frame will be assigned to :py:attr``df``.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Integrins.numof_entities">
+<span class="sig-name descname"><span class="pre">numof_entities</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Integrins.numof_entities" title="Link to this definition">§</a></dt>
+<dd><p>The number of annotated entities in the resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Integrins.numof_records">
+<span class="sig-name descname"><span class="pre">numof_records</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Integrins.numof_records" title="Link to this definition">§</a></dt>
+<dd><p>The total number of annotation records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Integrins.numof_references">
+<span class="sig-name descname"><span class="pre">numof_references</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Integrins.numof_references" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects and counts the
+references across all records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Integrins.process">
+<span class="sig-name descname"><span class="pre">process</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Integrins.process" title="Link to this definition">§</a></dt>
+<dd><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Integrins.reload">
+<span class="sig-name descname"><span class="pre">reload</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Integrins.reload" title="Link to this definition">§</a></dt>
+<dd><p>Reloads the object from the module level.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Integrins.select">
+<span class="sig-name descname"><span class="pre">select</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Integrins.select" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Integrins.set_method">
+<span class="sig-name descname"><span class="pre">set_method</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Integrins.set_method" title="Link to this definition">§</a></dt>
+<dd><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if
+necessary.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Integrins.set_reference_set">
+<span class="sig-name descname"><span class="pre">set_reference_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Integrins.set_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Assigns the reference set to the :py:attr``reference_set`` attribute.
+The reference set is the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Integrins.show">
+<span class="sig-name descname"><span class="pre">show</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">table_param</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Integrins.show" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic
+information from the UniProt datasheets.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Integrins.subset_intersection">
+<span class="sig-name descname"><span class="pre">subset_intersection</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">universe</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Integrins.subset_intersection" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the proportion of entities in a subset occuring in the
+set <code class="docutils literal notranslate"><span class="pre">universe</span></code>. The subset is selected by passing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> to the
+<code class="docutils literal notranslate"><span class="pre">select</span></code> method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Integrins.to_array">
+<span class="sig-name descname"><span class="pre">to_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_fields</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Integrins.to_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns an entity vs feature array. In case of more complex
+annotations this might be huge.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Integrins.to_bool_array">
+<span class="sig-name descname"><span class="pre">to_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Integrins.to_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a presence/absence boolean array for a reference set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Integrins.to_set">
+<span class="sig-name descname"><span class="pre">to_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Integrins.to_set" title="Link to this definition">§</a></dt>
+<dd><p>Returns the entities present in this annotation resource as a set.</p>
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+  </ul>
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+                  
+  <section id="pypath-core-annot-interpro">
+<h1>pypath.core.annot.InterPro<a class="headerlink" href="#pypath-core-annot-interpro" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.core.annot.InterPro">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.core.annot.</span></span><span class="sig-name descname"><span class="pre">InterPro</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#InterPro"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.InterPro" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <a class="reference internal" href="pypath.core.annot.AnnotationBase.html#pypath.core.annot.AnnotationBase" title="pypath.core.annot.AnnotationBase"><code class="xref py py-class docutils literal notranslate"><span class="pre">AnnotationBase</span></code></a></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.InterPro.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#InterPro.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.InterPro.__init__" title="Link to this definition">§</a></dt>
+<dd><p>Protein signatures from the InterPro database.</p>
+</dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.InterPro.__init__" title="pypath.core.annot.InterPro.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>([ncbi_tax_id])</p></td>
+<td><p>Protein signatures from the InterPro database.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.InterPro.add_complexes_by_inference" title="pypath.core.annot.InterPro.add_complexes_by_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">add_complexes_by_inference</span></code></a>([complexes])</p></td>
+<td><p>Creates complex annotations by in silico inference and adds them to this annotation set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.InterPro.all_complexes" title="pypath.core.annot.InterPro.all_complexes"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_complexes</span></code></a>()</p></td>
+<td><p>All protein complexes annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.InterPro.all_entities" title="pypath.core.annot.InterPro.all_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_entities</span></code></a>([entity_types])</p></td>
+<td><p>All entities annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.InterPro.all_mirnas" title="pypath.core.annot.InterPro.all_mirnas"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_mirnas</span></code></a>()</p></td>
+<td><p>All miRNAs annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.InterPro.all_proteins" title="pypath.core.annot.InterPro.all_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_proteins</span></code></a>()</p></td>
+<td><p>All UniProt IDs annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.InterPro.all_refs" title="pypath.core.annot.InterPro.all_refs"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_refs</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.InterPro.annotate_complex" title="pypath.core.annot.InterPro.annotate_complex"><code class="xref py py-obj docutils literal notranslate"><span class="pre">annotate_complex</span></code></a>(cplex)</p></td>
+<td><p>Infers annotations for a single complex.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.InterPro.browse" title="pypath.core.annot.InterPro.browse"><code class="xref py py-obj docutils literal notranslate"><span class="pre">browse</span></code></a>([field, start])</p></td>
+<td><p>Print gene information as a table.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.InterPro.complex_inference" title="pypath.core.annot.InterPro.complex_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">complex_inference</span></code></a>([complexes])</p></td>
+<td><p>Annotates all complexes in <cite>complexes</cite>, by default in the default complex database (existing in the <cite>complex</cite> module or generated on demand according to the module's current settings).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.InterPro.coverage" title="pypath.core.annot.InterPro.coverage"><code class="xref py py-obj docutils literal notranslate"><span class="pre">coverage</span></code></a>(other)</p></td>
+<td><p>Calculates the coverage of the annotation i.e. the proportion of entities having at least one record in this annotation resource for an arbitrary set of entities.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.InterPro.curation_effort" title="pypath.core.annot.InterPro.curation_effort"><code class="xref py py-obj docutils literal notranslate"><span class="pre">curation_effort</span></code></a>()</p></td>
+<td><p>Counts the reference-record pairs.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">from_dump</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_entity_type</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.InterPro.get_names" title="pypath.core.annot.InterPro.get_names"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_names</span></code></a>()</p></td>
+<td><p>Returns the list of field names in the records.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.InterPro.get_reference_set" title="pypath.core.annot.InterPro.get_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_reference_set</span></code></a>([proteins, complexes, ...])</p></td>
+<td><p>Retrieves the reference set i.e. the set of all entities which potentially have annotation in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.InterPro.get_subset" title="pypath.core.annot.InterPro.get_subset"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.InterPro.get_subset_bool_array" title="pypath.core.annot.InterPro.get_subset_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset_bool_array</span></code></a>([reference_set])</p></td>
+<td><p>Returns a boolean vector with True and False values for each entity in the reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.InterPro.get_values" title="pypath.core.annot.InterPro.get_values"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_values</span></code></a>(name[, exclude_none])</p></td>
+<td><p>Returns the set of all possible values of a field.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_complex</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_mirna</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_protein</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.InterPro.labels" title="pypath.core.annot.InterPro.labels"><code class="xref py py-obj docutils literal notranslate"><span class="pre">labels</span></code></a>([method])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.InterPro.load" title="pypath.core.annot.InterPro.load"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load</span></code></a>()</p></td>
+<td><p>Loads the annotation data by calling the input method.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.InterPro.load_data" title="pypath.core.annot.InterPro.load_data"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_data</span></code></a>()</p></td>
+<td><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.InterPro.load_proteins" title="pypath.core.annot.InterPro.load_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_proteins</span></code></a>()</p></td>
+<td><p>Retrieves a set of all UniProt IDs to have a base set of the entire proteome.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.InterPro.make_df" title="pypath.core.annot.InterPro.make_df"><code class="xref py py-obj docutils literal notranslate"><span class="pre">make_df</span></code></a>([rebuild])</p></td>
+<td><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complex_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.InterPro.numof_entities" title="pypath.core.annot.InterPro.numof_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_entities</span></code></a>()</p></td>
+<td><p>The number of annotated entities in the resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirna_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirnas</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_protein_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_proteins</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.InterPro.numof_records" title="pypath.core.annot.InterPro.numof_records"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_records</span></code></a>([entity_types])</p></td>
+<td><p>The total number of annotation records.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.InterPro.numof_references" title="pypath.core.annot.InterPro.numof_references"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_references</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.InterPro.process" title="pypath.core.annot.InterPro.process"><code class="xref py py-obj docutils literal notranslate"><span class="pre">process</span></code></a>()</p></td>
+<td><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">proportion</span></code>(other)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.InterPro.reload" title="pypath.core.annot.InterPro.reload"><code class="xref py py-obj docutils literal notranslate"><span class="pre">reload</span></code></a>()</p></td>
+<td><p>Reloads the object from the module level.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">save_to_pickle</span></code>(pickle_file)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.InterPro.select" title="pypath.core.annot.InterPro.select"><code class="xref py py-obj docutils literal notranslate"><span class="pre">select</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.InterPro.set_method" title="pypath.core.annot.InterPro.set_method"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_method</span></code></a>()</p></td>
+<td><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if necessary.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.InterPro.set_reference_set" title="pypath.core.annot.InterPro.set_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_reference_set</span></code></a>()</p></td>
+<td><p>Assigns the reference set to the :py:attr``reference_set`` attribute.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.InterPro.show" title="pypath.core.annot.InterPro.show"><code class="xref py py-obj docutils literal notranslate"><span class="pre">show</span></code></a>([method, table_param])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic information from the UniProt datasheets.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.InterPro.subset_intersection" title="pypath.core.annot.InterPro.subset_intersection"><code class="xref py py-obj docutils literal notranslate"><span class="pre">subset_intersection</span></code></a>(universe, **kwargs)</p></td>
+<td><p>Calculates the proportion of entities in a subset occuring in the set <code class="docutils literal notranslate"><span class="pre">universe</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.InterPro.to_array" title="pypath.core.annot.InterPro.to_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_array</span></code></a>([reference_set, use_fields])</p></td>
+<td><p>Returns an entity vs feature array.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.InterPro.to_bool_array" title="pypath.core.annot.InterPro.to_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_bool_array</span></code></a>(reference_set)</p></td>
+<td><p>Returns a presence/absence boolean array for a reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.InterPro.to_set" title="pypath.core.annot.InterPro.to_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_set</span></code></a>()</p></td>
+<td><p>Returns the entities present in this annotation resource as a set.</p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Attributes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_fields</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">summary</span></code></p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.InterPro.add_complexes_by_inference">
+<span class="sig-name descname"><span class="pre">add_complexes_by_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.InterPro.add_complexes_by_inference" title="Link to this definition">§</a></dt>
+<dd><p>Creates complex annotations by in silico inference and adds them
+to this annotation set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.InterPro.all_complexes">
+<span class="sig-name descname"><span class="pre">all_complexes</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.InterPro.all_complexes" title="Link to this definition">§</a></dt>
+<dd><p>All protein complexes annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.InterPro.all_entities">
+<span class="sig-name descname"><span class="pre">all_entities</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.InterPro.all_entities" title="Link to this definition">§</a></dt>
+<dd><p>All entities annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.InterPro.all_mirnas">
+<span class="sig-name descname"><span class="pre">all_mirnas</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.InterPro.all_mirnas" title="Link to this definition">§</a></dt>
+<dd><p>All miRNAs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.InterPro.all_proteins">
+<span class="sig-name descname"><span class="pre">all_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.InterPro.all_proteins" title="Link to this definition">§</a></dt>
+<dd><p>All UniProt IDs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.InterPro.all_refs">
+<span class="sig-name descname"><span class="pre">all_refs</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.InterPro.all_refs" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects the references
+across all records. Returns <em>list</em>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.InterPro.annotate_complex">
+<span class="sig-name descname"><span class="pre">annotate_complex</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cplex</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.InterPro.annotate_complex" title="Link to this definition">§</a></dt>
+<dd><p>Infers annotations for a single complex.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.InterPro.browse">
+<span class="sig-name descname"><span class="pre">browse</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">field</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">start</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.InterPro.browse" title="Link to this definition">§</a></dt>
+<dd><p>Print gene information as a table.</p>
+<p>Presents information about annotation categories as ascii tables
+printed in the terminal. If one category provided, prints one table.
+If multiple categories provided, prints a table for each of them one
+by one proceeding to the next one once you hit return. If no categories
+provided goes through all levels of the primary category.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>field:</dt><dd><p>The field to browse categories by.</p>
+<ul class="simple">
+<li><p>If None the primary field will be selected.
+If this annotation resource doesn’t have fields, all proteins
+will be presented as one single category.</p></li>
+<li><p>If a string it will be considered a field name and it will
+browse through all levels of this field.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">list</span></code>, set or tuple, it will be considered either a
+<code class="docutils literal notranslate"><span class="pre">list</span></code> of field names or a list of values from the primary
+field. In the former case all combinations of the values of
+the fields will be presented, in the latter case the browsing
+will be limited to the levels of the primary field contained
+in <code class="docutils literal notranslate"><span class="pre">field</span></code>.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">dict</span></code>, keys are supposed to be field names and values
+as list of levels. If any of the values are None, all levels
+from that field will be used.</p></li>
+</ul>
+</dd>
+<dt>start:</dt><dd><p>Start browsing from this category. E.g. if there are 500
+categories and start is 250 it will skip everything before the
+250th.</p>
+</dd>
+<dt>kwargs:</dt><dd><p>Passed to <code class="docutils literal notranslate"><span class="pre">pypath.utils.uniprot.info</span></code>.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.InterPro.complex_inference">
+<span class="sig-name descname"><span class="pre">complex_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.InterPro.complex_inference" title="Link to this definition">§</a></dt>
+<dd><p>Annotates all complexes in <cite>complexes</cite>, by default in the default
+complex database (existing in the <cite>complex</cite> module or generated
+on demand according to the module’s current settings).</p>
+<dl class="field-list simple">
+<dt class="field-odd">Returns<span class="colon">:</span></dt>
+<dd class="field-odd"><p><ul class="simple">
+<li><p><em>Dict with complexes as keys and sets of annotations as values.</em></p></li>
+<li><p><em>Complexes with no valid information in this annotation resource</em></p></li>
+<li><p><em>won’t be in the dict.</em></p></li>
+</ul>
+</p>
+</dd>
+<dt class="field-even">Parameters<span class="colon">:</span></dt>
+<dd class="field-even"><p><strong>complexes</strong> (<em>iterable</em>) – Iterable yielding complexes.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.InterPro.coverage">
+<span class="sig-name descname"><span class="pre">coverage</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">other</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.InterPro.coverage" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the coverage of the annotation i.e. the proportion of
+entities having at least one record in this annotation resource
+for an arbitrary set of entities.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.InterPro.curation_effort">
+<span class="sig-name descname"><span class="pre">curation_effort</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.InterPro.curation_effort" title="Link to this definition">§</a></dt>
+<dd><p>Counts the reference-record pairs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.InterPro.get_names">
+<span class="sig-name descname"><span class="pre">get_names</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.InterPro.get_names" title="Link to this definition">§</a></dt>
+<dd><p>Returns the list of field names in the records. The annotation
+consists of uniform records and each entity might be annotated
+with one or more records. Each record is a tuple of fields, for
+example <code class="docutils literal notranslate"><span class="pre">('cell_type',</span> <span class="pre">'expression_level',</span> <span class="pre">'score')</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.InterPro.get_reference_set">
+<em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">get_reference_set</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">proteins</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">swissprot_only</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.InterPro.get_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the reference set i.e. the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.InterPro.get_subset">
+<span class="sig-name descname"><span class="pre">get_subset</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.InterPro.get_subset" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.InterPro.get_subset_bool_array">
+<span class="sig-name descname"><span class="pre">get_subset_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.InterPro.get_subset_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a boolean vector with True and False values for each entity
+in the reference set. The values represent presence absence data
+in the simplest case, but by providing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> any kind of matching
+and filtering is possible. <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> are passed to the <code class="docutils literal notranslate"><span class="pre">select</span></code>
+method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.InterPro.get_values">
+<span class="sig-name descname"><span class="pre">get_values</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">exclude_none</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.InterPro.get_values" title="Link to this definition">§</a></dt>
+<dd><p>Returns the set of all possible values of a field. E.g. if the
+records of this annotation have a field <code class="docutils literal notranslate"><span class="pre">cell_type</span></code> then calling
+this method can tell you that across all records the values of
+this field might be <code class="docutils literal notranslate"><span class="pre">{'macrophage',</span> <span class="pre">'epithelial_cell',</span> <span class="pre">...}</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.InterPro.labels">
+<span class="sig-name descname"><span class="pre">labels</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.InterPro.labels" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.InterPro.load">
+<span class="sig-name descname"><span class="pre">load</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.InterPro.load" title="Link to this definition">§</a></dt>
+<dd><p>Loads the annotation data by calling the input method.
+Infers annotations for complexes in the complex database if
+py:attr:<code class="docutils literal notranslate"><span class="pre">infer_complexes</span></code> is True.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.InterPro.load_data">
+<span class="sig-name descname"><span class="pre">load_data</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.InterPro.load_data" title="Link to this definition">§</a></dt>
+<dd><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.InterPro.load_proteins">
+<span class="sig-name descname"><span class="pre">load_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.InterPro.load_proteins" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a set of all UniProt IDs to have a base set of the entire
+proteome.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.InterPro.make_df">
+<span class="sig-name descname"><span class="pre">make_df</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">rebuild</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.InterPro.make_df" title="Link to this definition">§</a></dt>
+<dd><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.
+The data frame will be assigned to :py:attr``df``.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.InterPro.numof_entities">
+<span class="sig-name descname"><span class="pre">numof_entities</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.InterPro.numof_entities" title="Link to this definition">§</a></dt>
+<dd><p>The number of annotated entities in the resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.InterPro.numof_records">
+<span class="sig-name descname"><span class="pre">numof_records</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.InterPro.numof_records" title="Link to this definition">§</a></dt>
+<dd><p>The total number of annotation records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.InterPro.numof_references">
+<span class="sig-name descname"><span class="pre">numof_references</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.InterPro.numof_references" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects and counts the
+references across all records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.InterPro.process">
+<span class="sig-name descname"><span class="pre">process</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.InterPro.process" title="Link to this definition">§</a></dt>
+<dd><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.InterPro.reload">
+<span class="sig-name descname"><span class="pre">reload</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.InterPro.reload" title="Link to this definition">§</a></dt>
+<dd><p>Reloads the object from the module level.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.InterPro.select">
+<span class="sig-name descname"><span class="pre">select</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.InterPro.select" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.InterPro.set_method">
+<span class="sig-name descname"><span class="pre">set_method</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.InterPro.set_method" title="Link to this definition">§</a></dt>
+<dd><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if
+necessary.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.InterPro.set_reference_set">
+<span class="sig-name descname"><span class="pre">set_reference_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.InterPro.set_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Assigns the reference set to the :py:attr``reference_set`` attribute.
+The reference set is the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.InterPro.show">
+<span class="sig-name descname"><span class="pre">show</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">table_param</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.InterPro.show" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic
+information from the UniProt datasheets.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.InterPro.subset_intersection">
+<span class="sig-name descname"><span class="pre">subset_intersection</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">universe</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.InterPro.subset_intersection" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the proportion of entities in a subset occuring in the
+set <code class="docutils literal notranslate"><span class="pre">universe</span></code>. The subset is selected by passing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> to the
+<code class="docutils literal notranslate"><span class="pre">select</span></code> method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.InterPro.to_array">
+<span class="sig-name descname"><span class="pre">to_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_fields</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.InterPro.to_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns an entity vs feature array. In case of more complex
+annotations this might be huge.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.InterPro.to_bool_array">
+<span class="sig-name descname"><span class="pre">to_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.InterPro.to_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a presence/absence boolean array for a reference set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.InterPro.to_set">
+<span class="sig-name descname"><span class="pre">to_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.InterPro.to_set" title="Link to this definition">§</a></dt>
+<dd><p>Returns the entities present in this annotation resource as a set.</p>
+</dd></dl>
+
+</dd></dl>
+
+</section>
+
+
+                </article>
+              
+              
+              
+              
+              
+                <footer class="prev-next-footer">
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+  <section id="pypath-core-annot-intogen">
+<h1>pypath.core.annot.Intogen<a class="headerlink" href="#pypath-core-annot-intogen" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.core.annot.Intogen">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.core.annot.</span></span><span class="sig-name descname"><span class="pre">Intogen</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#Intogen"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.Intogen" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <a class="reference internal" href="pypath.core.annot.AnnotationBase.html#pypath.core.annot.AnnotationBase" title="pypath.core.annot.AnnotationBase"><code class="xref py py-class docutils literal notranslate"><span class="pre">AnnotationBase</span></code></a></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Intogen.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#Intogen.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.Intogen.__init__" title="Link to this definition">§</a></dt>
+<dd><p>Represents annotations for a set of proteins.
+Loads the data from the original resource and provides methods
+to query the annotations.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>name</strong> (<em>str</em>) – A custom name for the annotation resource.</p></li>
+<li><p><strong>ncbi_tax_id</strong> (<em>int</em>) – NCBI Taxonomy identifier.</p></li>
+<li><p><strong>input_method</strong> (<em>callable</em><em>,</em><em>str</em>) – Either a callable or the name of a method in any submodules of
+the <code class="docutils literal notranslate"><span class="pre">pypath.inputs</span></code>  module. Should return a dict with
+UniProt IDs as keys or an object suitable for <code class="docutils literal notranslate"><span class="pre">process_method</span></code>.</p></li>
+<li><p><strong>input_args</strong> (<em>dict</em>) – Arguments for the <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Intogen.__init__" title="pypath.core.annot.Intogen.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>(**kwargs)</p></td>
+<td><p>Represents annotations for a set of proteins.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Intogen.add_complexes_by_inference" title="pypath.core.annot.Intogen.add_complexes_by_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">add_complexes_by_inference</span></code></a>([complexes])</p></td>
+<td><p>Creates complex annotations by in silico inference and adds them to this annotation set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Intogen.all_complexes" title="pypath.core.annot.Intogen.all_complexes"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_complexes</span></code></a>()</p></td>
+<td><p>All protein complexes annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Intogen.all_entities" title="pypath.core.annot.Intogen.all_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_entities</span></code></a>([entity_types])</p></td>
+<td><p>All entities annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Intogen.all_mirnas" title="pypath.core.annot.Intogen.all_mirnas"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_mirnas</span></code></a>()</p></td>
+<td><p>All miRNAs annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Intogen.all_proteins" title="pypath.core.annot.Intogen.all_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_proteins</span></code></a>()</p></td>
+<td><p>All UniProt IDs annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Intogen.all_refs" title="pypath.core.annot.Intogen.all_refs"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_refs</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Intogen.annotate_complex" title="pypath.core.annot.Intogen.annotate_complex"><code class="xref py py-obj docutils literal notranslate"><span class="pre">annotate_complex</span></code></a>(cplex)</p></td>
+<td><p>Infers annotations for a single complex.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Intogen.browse" title="pypath.core.annot.Intogen.browse"><code class="xref py py-obj docutils literal notranslate"><span class="pre">browse</span></code></a>([field, start])</p></td>
+<td><p>Print gene information as a table.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Intogen.complex_inference" title="pypath.core.annot.Intogen.complex_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">complex_inference</span></code></a>([complexes])</p></td>
+<td><p>Annotates all complexes in <cite>complexes</cite>, by default in the default complex database (existing in the <cite>complex</cite> module or generated on demand according to the module's current settings).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Intogen.coverage" title="pypath.core.annot.Intogen.coverage"><code class="xref py py-obj docutils literal notranslate"><span class="pre">coverage</span></code></a>(other)</p></td>
+<td><p>Calculates the coverage of the annotation i.e. the proportion of entities having at least one record in this annotation resource for an arbitrary set of entities.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Intogen.curation_effort" title="pypath.core.annot.Intogen.curation_effort"><code class="xref py py-obj docutils literal notranslate"><span class="pre">curation_effort</span></code></a>()</p></td>
+<td><p>Counts the reference-record pairs.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">from_dump</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_entity_type</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Intogen.get_names" title="pypath.core.annot.Intogen.get_names"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_names</span></code></a>()</p></td>
+<td><p>Returns the list of field names in the records.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Intogen.get_reference_set" title="pypath.core.annot.Intogen.get_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_reference_set</span></code></a>([proteins, complexes, ...])</p></td>
+<td><p>Retrieves the reference set i.e. the set of all entities which potentially have annotation in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Intogen.get_subset" title="pypath.core.annot.Intogen.get_subset"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Intogen.get_subset_bool_array" title="pypath.core.annot.Intogen.get_subset_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset_bool_array</span></code></a>([reference_set])</p></td>
+<td><p>Returns a boolean vector with True and False values for each entity in the reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Intogen.get_values" title="pypath.core.annot.Intogen.get_values"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_values</span></code></a>(name[, exclude_none])</p></td>
+<td><p>Returns the set of all possible values of a field.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_complex</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_mirna</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_protein</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Intogen.labels" title="pypath.core.annot.Intogen.labels"><code class="xref py py-obj docutils literal notranslate"><span class="pre">labels</span></code></a>([method])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Intogen.load" title="pypath.core.annot.Intogen.load"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load</span></code></a>()</p></td>
+<td><p>Loads the annotation data by calling the input method.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Intogen.load_data" title="pypath.core.annot.Intogen.load_data"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_data</span></code></a>()</p></td>
+<td><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Intogen.load_proteins" title="pypath.core.annot.Intogen.load_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_proteins</span></code></a>()</p></td>
+<td><p>Retrieves a set of all UniProt IDs to have a base set of the entire proteome.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Intogen.make_df" title="pypath.core.annot.Intogen.make_df"><code class="xref py py-obj docutils literal notranslate"><span class="pre">make_df</span></code></a>([rebuild])</p></td>
+<td><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complex_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Intogen.numof_entities" title="pypath.core.annot.Intogen.numof_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_entities</span></code></a>()</p></td>
+<td><p>The number of annotated entities in the resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirna_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirnas</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_protein_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_proteins</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Intogen.numof_records" title="pypath.core.annot.Intogen.numof_records"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_records</span></code></a>([entity_types])</p></td>
+<td><p>The total number of annotation records.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Intogen.numof_references" title="pypath.core.annot.Intogen.numof_references"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_references</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Intogen.process" title="pypath.core.annot.Intogen.process"><code class="xref py py-obj docutils literal notranslate"><span class="pre">process</span></code></a>()</p></td>
+<td><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">proportion</span></code>(other)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Intogen.reload" title="pypath.core.annot.Intogen.reload"><code class="xref py py-obj docutils literal notranslate"><span class="pre">reload</span></code></a>()</p></td>
+<td><p>Reloads the object from the module level.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">save_to_pickle</span></code>(pickle_file)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Intogen.select" title="pypath.core.annot.Intogen.select"><code class="xref py py-obj docutils literal notranslate"><span class="pre">select</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Intogen.set_method" title="pypath.core.annot.Intogen.set_method"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_method</span></code></a>()</p></td>
+<td><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if necessary.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Intogen.set_reference_set" title="pypath.core.annot.Intogen.set_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_reference_set</span></code></a>()</p></td>
+<td><p>Assigns the reference set to the :py:attr``reference_set`` attribute.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Intogen.show" title="pypath.core.annot.Intogen.show"><code class="xref py py-obj docutils literal notranslate"><span class="pre">show</span></code></a>([method, table_param])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic information from the UniProt datasheets.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Intogen.subset_intersection" title="pypath.core.annot.Intogen.subset_intersection"><code class="xref py py-obj docutils literal notranslate"><span class="pre">subset_intersection</span></code></a>(universe, **kwargs)</p></td>
+<td><p>Calculates the proportion of entities in a subset occuring in the set <code class="docutils literal notranslate"><span class="pre">universe</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Intogen.to_array" title="pypath.core.annot.Intogen.to_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_array</span></code></a>([reference_set, use_fields])</p></td>
+<td><p>Returns an entity vs feature array.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Intogen.to_bool_array" title="pypath.core.annot.Intogen.to_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_bool_array</span></code></a>(reference_set)</p></td>
+<td><p>Returns a presence/absence boolean array for a reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Intogen.to_set" title="pypath.core.annot.Intogen.to_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_set</span></code></a>()</p></td>
+<td><p>Returns the entities present in this annotation resource as a set.</p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Attributes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_fields</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">summary</span></code></p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Intogen.add_complexes_by_inference">
+<span class="sig-name descname"><span class="pre">add_complexes_by_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Intogen.add_complexes_by_inference" title="Link to this definition">§</a></dt>
+<dd><p>Creates complex annotations by in silico inference and adds them
+to this annotation set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Intogen.all_complexes">
+<span class="sig-name descname"><span class="pre">all_complexes</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Intogen.all_complexes" title="Link to this definition">§</a></dt>
+<dd><p>All protein complexes annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Intogen.all_entities">
+<span class="sig-name descname"><span class="pre">all_entities</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Intogen.all_entities" title="Link to this definition">§</a></dt>
+<dd><p>All entities annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Intogen.all_mirnas">
+<span class="sig-name descname"><span class="pre">all_mirnas</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Intogen.all_mirnas" title="Link to this definition">§</a></dt>
+<dd><p>All miRNAs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Intogen.all_proteins">
+<span class="sig-name descname"><span class="pre">all_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Intogen.all_proteins" title="Link to this definition">§</a></dt>
+<dd><p>All UniProt IDs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Intogen.all_refs">
+<span class="sig-name descname"><span class="pre">all_refs</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Intogen.all_refs" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects the references
+across all records. Returns <em>list</em>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Intogen.annotate_complex">
+<span class="sig-name descname"><span class="pre">annotate_complex</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cplex</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Intogen.annotate_complex" title="Link to this definition">§</a></dt>
+<dd><p>Infers annotations for a single complex.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Intogen.browse">
+<span class="sig-name descname"><span class="pre">browse</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">field</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">start</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Intogen.browse" title="Link to this definition">§</a></dt>
+<dd><p>Print gene information as a table.</p>
+<p>Presents information about annotation categories as ascii tables
+printed in the terminal. If one category provided, prints one table.
+If multiple categories provided, prints a table for each of them one
+by one proceeding to the next one once you hit return. If no categories
+provided goes through all levels of the primary category.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>field:</dt><dd><p>The field to browse categories by.</p>
+<ul class="simple">
+<li><p>If None the primary field will be selected.
+If this annotation resource doesn’t have fields, all proteins
+will be presented as one single category.</p></li>
+<li><p>If a string it will be considered a field name and it will
+browse through all levels of this field.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">list</span></code>, set or tuple, it will be considered either a
+<code class="docutils literal notranslate"><span class="pre">list</span></code> of field names or a list of values from the primary
+field. In the former case all combinations of the values of
+the fields will be presented, in the latter case the browsing
+will be limited to the levels of the primary field contained
+in <code class="docutils literal notranslate"><span class="pre">field</span></code>.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">dict</span></code>, keys are supposed to be field names and values
+as list of levels. If any of the values are None, all levels
+from that field will be used.</p></li>
+</ul>
+</dd>
+<dt>start:</dt><dd><p>Start browsing from this category. E.g. if there are 500
+categories and start is 250 it will skip everything before the
+250th.</p>
+</dd>
+<dt>kwargs:</dt><dd><p>Passed to <code class="docutils literal notranslate"><span class="pre">pypath.utils.uniprot.info</span></code>.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Intogen.complex_inference">
+<span class="sig-name descname"><span class="pre">complex_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Intogen.complex_inference" title="Link to this definition">§</a></dt>
+<dd><p>Annotates all complexes in <cite>complexes</cite>, by default in the default
+complex database (existing in the <cite>complex</cite> module or generated
+on demand according to the module’s current settings).</p>
+<dl class="field-list simple">
+<dt class="field-odd">Returns<span class="colon">:</span></dt>
+<dd class="field-odd"><p><ul class="simple">
+<li><p><em>Dict with complexes as keys and sets of annotations as values.</em></p></li>
+<li><p><em>Complexes with no valid information in this annotation resource</em></p></li>
+<li><p><em>won’t be in the dict.</em></p></li>
+</ul>
+</p>
+</dd>
+<dt class="field-even">Parameters<span class="colon">:</span></dt>
+<dd class="field-even"><p><strong>complexes</strong> (<em>iterable</em>) – Iterable yielding complexes.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Intogen.coverage">
+<span class="sig-name descname"><span class="pre">coverage</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">other</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Intogen.coverage" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the coverage of the annotation i.e. the proportion of
+entities having at least one record in this annotation resource
+for an arbitrary set of entities.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Intogen.curation_effort">
+<span class="sig-name descname"><span class="pre">curation_effort</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Intogen.curation_effort" title="Link to this definition">§</a></dt>
+<dd><p>Counts the reference-record pairs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Intogen.get_names">
+<span class="sig-name descname"><span class="pre">get_names</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Intogen.get_names" title="Link to this definition">§</a></dt>
+<dd><p>Returns the list of field names in the records. The annotation
+consists of uniform records and each entity might be annotated
+with one or more records. Each record is a tuple of fields, for
+example <code class="docutils literal notranslate"><span class="pre">('cell_type',</span> <span class="pre">'expression_level',</span> <span class="pre">'score')</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Intogen.get_reference_set">
+<em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">get_reference_set</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">proteins</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">swissprot_only</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Intogen.get_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the reference set i.e. the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Intogen.get_subset">
+<span class="sig-name descname"><span class="pre">get_subset</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Intogen.get_subset" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Intogen.get_subset_bool_array">
+<span class="sig-name descname"><span class="pre">get_subset_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Intogen.get_subset_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a boolean vector with True and False values for each entity
+in the reference set. The values represent presence absence data
+in the simplest case, but by providing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> any kind of matching
+and filtering is possible. <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> are passed to the <code class="docutils literal notranslate"><span class="pre">select</span></code>
+method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Intogen.get_values">
+<span class="sig-name descname"><span class="pre">get_values</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">exclude_none</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Intogen.get_values" title="Link to this definition">§</a></dt>
+<dd><p>Returns the set of all possible values of a field. E.g. if the
+records of this annotation have a field <code class="docutils literal notranslate"><span class="pre">cell_type</span></code> then calling
+this method can tell you that across all records the values of
+this field might be <code class="docutils literal notranslate"><span class="pre">{'macrophage',</span> <span class="pre">'epithelial_cell',</span> <span class="pre">...}</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Intogen.labels">
+<span class="sig-name descname"><span class="pre">labels</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Intogen.labels" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Intogen.load">
+<span class="sig-name descname"><span class="pre">load</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Intogen.load" title="Link to this definition">§</a></dt>
+<dd><p>Loads the annotation data by calling the input method.
+Infers annotations for complexes in the complex database if
+py:attr:<code class="docutils literal notranslate"><span class="pre">infer_complexes</span></code> is True.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Intogen.load_data">
+<span class="sig-name descname"><span class="pre">load_data</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Intogen.load_data" title="Link to this definition">§</a></dt>
+<dd><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Intogen.load_proteins">
+<span class="sig-name descname"><span class="pre">load_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Intogen.load_proteins" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a set of all UniProt IDs to have a base set of the entire
+proteome.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Intogen.make_df">
+<span class="sig-name descname"><span class="pre">make_df</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">rebuild</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Intogen.make_df" title="Link to this definition">§</a></dt>
+<dd><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.
+The data frame will be assigned to :py:attr``df``.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Intogen.numof_entities">
+<span class="sig-name descname"><span class="pre">numof_entities</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Intogen.numof_entities" title="Link to this definition">§</a></dt>
+<dd><p>The number of annotated entities in the resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Intogen.numof_records">
+<span class="sig-name descname"><span class="pre">numof_records</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Intogen.numof_records" title="Link to this definition">§</a></dt>
+<dd><p>The total number of annotation records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Intogen.numof_references">
+<span class="sig-name descname"><span class="pre">numof_references</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Intogen.numof_references" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects and counts the
+references across all records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Intogen.process">
+<span class="sig-name descname"><span class="pre">process</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Intogen.process" title="Link to this definition">§</a></dt>
+<dd><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Intogen.reload">
+<span class="sig-name descname"><span class="pre">reload</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Intogen.reload" title="Link to this definition">§</a></dt>
+<dd><p>Reloads the object from the module level.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Intogen.select">
+<span class="sig-name descname"><span class="pre">select</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Intogen.select" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Intogen.set_method">
+<span class="sig-name descname"><span class="pre">set_method</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Intogen.set_method" title="Link to this definition">§</a></dt>
+<dd><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if
+necessary.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Intogen.set_reference_set">
+<span class="sig-name descname"><span class="pre">set_reference_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Intogen.set_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Assigns the reference set to the :py:attr``reference_set`` attribute.
+The reference set is the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Intogen.show">
+<span class="sig-name descname"><span class="pre">show</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">table_param</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Intogen.show" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic
+information from the UniProt datasheets.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Intogen.subset_intersection">
+<span class="sig-name descname"><span class="pre">subset_intersection</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">universe</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Intogen.subset_intersection" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the proportion of entities in a subset occuring in the
+set <code class="docutils literal notranslate"><span class="pre">universe</span></code>. The subset is selected by passing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> to the
+<code class="docutils literal notranslate"><span class="pre">select</span></code> method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Intogen.to_array">
+<span class="sig-name descname"><span class="pre">to_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_fields</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Intogen.to_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns an entity vs feature array. In case of more complex
+annotations this might be huge.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Intogen.to_bool_array">
+<span class="sig-name descname"><span class="pre">to_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Intogen.to_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a presence/absence boolean array for a reference set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Intogen.to_set">
+<span class="sig-name descname"><span class="pre">to_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Intogen.to_set" title="Link to this definition">§</a></dt>
+<dd><p>Returns the entities present in this annotation resource as a set.</p>
+</dd></dl>
+
+</dd></dl>
+
+</section>
+
+
+                </article>
+              
+              
+              
+              
+              
+                <footer class="prev-next-footer">
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+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.core.annot.Italk">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.core.annot.</span></span><span class="sig-name descname"><span class="pre">Italk</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#Italk"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.Italk" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <a class="reference internal" href="pypath.core.annot.AnnotationBase.html#pypath.core.annot.AnnotationBase" title="pypath.core.annot.AnnotationBase"><code class="xref py py-class docutils literal notranslate"><span class="pre">AnnotationBase</span></code></a></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Italk.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#Italk.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.Italk.__init__" title="Link to this definition">§</a></dt>
+<dd><p>Represents annotations for a set of proteins.
+Loads the data from the original resource and provides methods
+to query the annotations.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>name</strong> (<em>str</em>) – A custom name for the annotation resource.</p></li>
+<li><p><strong>ncbi_tax_id</strong> (<em>int</em>) – NCBI Taxonomy identifier.</p></li>
+<li><p><strong>input_method</strong> (<em>callable</em><em>,</em><em>str</em>) – Either a callable or the name of a method in any submodules of
+the <code class="docutils literal notranslate"><span class="pre">pypath.inputs</span></code>  module. Should return a dict with
+UniProt IDs as keys or an object suitable for <code class="docutils literal notranslate"><span class="pre">process_method</span></code>.</p></li>
+<li><p><strong>input_args</strong> (<em>dict</em>) – Arguments for the <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Italk.__init__" title="pypath.core.annot.Italk.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>([ncbi_tax_id])</p></td>
+<td><p>Represents annotations for a set of proteins.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Italk.add_complexes_by_inference" title="pypath.core.annot.Italk.add_complexes_by_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">add_complexes_by_inference</span></code></a>([complexes])</p></td>
+<td><p>Creates complex annotations by in silico inference and adds them to this annotation set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Italk.all_complexes" title="pypath.core.annot.Italk.all_complexes"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_complexes</span></code></a>()</p></td>
+<td><p>All protein complexes annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Italk.all_entities" title="pypath.core.annot.Italk.all_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_entities</span></code></a>([entity_types])</p></td>
+<td><p>All entities annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Italk.all_mirnas" title="pypath.core.annot.Italk.all_mirnas"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_mirnas</span></code></a>()</p></td>
+<td><p>All miRNAs annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Italk.all_proteins" title="pypath.core.annot.Italk.all_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_proteins</span></code></a>()</p></td>
+<td><p>All UniProt IDs annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Italk.all_refs" title="pypath.core.annot.Italk.all_refs"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_refs</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Italk.annotate_complex" title="pypath.core.annot.Italk.annotate_complex"><code class="xref py py-obj docutils literal notranslate"><span class="pre">annotate_complex</span></code></a>(cplex)</p></td>
+<td><p>Infers annotations for a single complex.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Italk.browse" title="pypath.core.annot.Italk.browse"><code class="xref py py-obj docutils literal notranslate"><span class="pre">browse</span></code></a>([field, start])</p></td>
+<td><p>Print gene information as a table.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Italk.complex_inference" title="pypath.core.annot.Italk.complex_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">complex_inference</span></code></a>([complexes])</p></td>
+<td><p>Annotates all complexes in <cite>complexes</cite>, by default in the default complex database (existing in the <cite>complex</cite> module or generated on demand according to the module's current settings).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Italk.coverage" title="pypath.core.annot.Italk.coverage"><code class="xref py py-obj docutils literal notranslate"><span class="pre">coverage</span></code></a>(other)</p></td>
+<td><p>Calculates the coverage of the annotation i.e. the proportion of entities having at least one record in this annotation resource for an arbitrary set of entities.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Italk.curation_effort" title="pypath.core.annot.Italk.curation_effort"><code class="xref py py-obj docutils literal notranslate"><span class="pre">curation_effort</span></code></a>()</p></td>
+<td><p>Counts the reference-record pairs.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">from_dump</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_entity_type</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Italk.get_names" title="pypath.core.annot.Italk.get_names"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_names</span></code></a>()</p></td>
+<td><p>Returns the list of field names in the records.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Italk.get_reference_set" title="pypath.core.annot.Italk.get_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_reference_set</span></code></a>([proteins, complexes, ...])</p></td>
+<td><p>Retrieves the reference set i.e. the set of all entities which potentially have annotation in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Italk.get_subset" title="pypath.core.annot.Italk.get_subset"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Italk.get_subset_bool_array" title="pypath.core.annot.Italk.get_subset_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset_bool_array</span></code></a>([reference_set])</p></td>
+<td><p>Returns a boolean vector with True and False values for each entity in the reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Italk.get_values" title="pypath.core.annot.Italk.get_values"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_values</span></code></a>(name[, exclude_none])</p></td>
+<td><p>Returns the set of all possible values of a field.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_complex</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_mirna</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_protein</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Italk.labels" title="pypath.core.annot.Italk.labels"><code class="xref py py-obj docutils literal notranslate"><span class="pre">labels</span></code></a>([method])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Italk.load" title="pypath.core.annot.Italk.load"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load</span></code></a>()</p></td>
+<td><p>Loads the annotation data by calling the input method.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Italk.load_data" title="pypath.core.annot.Italk.load_data"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_data</span></code></a>()</p></td>
+<td><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Italk.load_proteins" title="pypath.core.annot.Italk.load_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_proteins</span></code></a>()</p></td>
+<td><p>Retrieves a set of all UniProt IDs to have a base set of the entire proteome.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Italk.make_df" title="pypath.core.annot.Italk.make_df"><code class="xref py py-obj docutils literal notranslate"><span class="pre">make_df</span></code></a>([rebuild])</p></td>
+<td><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complex_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Italk.numof_entities" title="pypath.core.annot.Italk.numof_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_entities</span></code></a>()</p></td>
+<td><p>The number of annotated entities in the resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirna_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirnas</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_protein_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_proteins</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Italk.numof_records" title="pypath.core.annot.Italk.numof_records"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_records</span></code></a>([entity_types])</p></td>
+<td><p>The total number of annotation records.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Italk.numof_references" title="pypath.core.annot.Italk.numof_references"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_references</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Italk.process" title="pypath.core.annot.Italk.process"><code class="xref py py-obj docutils literal notranslate"><span class="pre">process</span></code></a>()</p></td>
+<td><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">proportion</span></code>(other)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Italk.reload" title="pypath.core.annot.Italk.reload"><code class="xref py py-obj docutils literal notranslate"><span class="pre">reload</span></code></a>()</p></td>
+<td><p>Reloads the object from the module level.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">save_to_pickle</span></code>(pickle_file)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Italk.select" title="pypath.core.annot.Italk.select"><code class="xref py py-obj docutils literal notranslate"><span class="pre">select</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Italk.set_method" title="pypath.core.annot.Italk.set_method"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_method</span></code></a>()</p></td>
+<td><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if necessary.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Italk.set_reference_set" title="pypath.core.annot.Italk.set_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_reference_set</span></code></a>()</p></td>
+<td><p>Assigns the reference set to the :py:attr``reference_set`` attribute.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Italk.show" title="pypath.core.annot.Italk.show"><code class="xref py py-obj docutils literal notranslate"><span class="pre">show</span></code></a>([method, table_param])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic information from the UniProt datasheets.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Italk.subset_intersection" title="pypath.core.annot.Italk.subset_intersection"><code class="xref py py-obj docutils literal notranslate"><span class="pre">subset_intersection</span></code></a>(universe, **kwargs)</p></td>
+<td><p>Calculates the proportion of entities in a subset occuring in the set <code class="docutils literal notranslate"><span class="pre">universe</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Italk.to_array" title="pypath.core.annot.Italk.to_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_array</span></code></a>([reference_set, use_fields])</p></td>
+<td><p>Returns an entity vs feature array.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Italk.to_bool_array" title="pypath.core.annot.Italk.to_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_bool_array</span></code></a>(reference_set)</p></td>
+<td><p>Returns a presence/absence boolean array for a reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Italk.to_set" title="pypath.core.annot.Italk.to_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_set</span></code></a>()</p></td>
+<td><p>Returns the entities present in this annotation resource as a set.</p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Attributes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_fields</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">summary</span></code></p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Italk.add_complexes_by_inference">
+<span class="sig-name descname"><span class="pre">add_complexes_by_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Italk.add_complexes_by_inference" title="Link to this definition">§</a></dt>
+<dd><p>Creates complex annotations by in silico inference and adds them
+to this annotation set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Italk.all_complexes">
+<span class="sig-name descname"><span class="pre">all_complexes</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Italk.all_complexes" title="Link to this definition">§</a></dt>
+<dd><p>All protein complexes annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Italk.all_entities">
+<span class="sig-name descname"><span class="pre">all_entities</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Italk.all_entities" title="Link to this definition">§</a></dt>
+<dd><p>All entities annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Italk.all_mirnas">
+<span class="sig-name descname"><span class="pre">all_mirnas</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Italk.all_mirnas" title="Link to this definition">§</a></dt>
+<dd><p>All miRNAs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Italk.all_proteins">
+<span class="sig-name descname"><span class="pre">all_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Italk.all_proteins" title="Link to this definition">§</a></dt>
+<dd><p>All UniProt IDs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Italk.all_refs">
+<span class="sig-name descname"><span class="pre">all_refs</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Italk.all_refs" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects the references
+across all records. Returns <em>list</em>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Italk.annotate_complex">
+<span class="sig-name descname"><span class="pre">annotate_complex</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cplex</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Italk.annotate_complex" title="Link to this definition">§</a></dt>
+<dd><p>Infers annotations for a single complex.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Italk.browse">
+<span class="sig-name descname"><span class="pre">browse</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">field</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">start</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Italk.browse" title="Link to this definition">§</a></dt>
+<dd><p>Print gene information as a table.</p>
+<p>Presents information about annotation categories as ascii tables
+printed in the terminal. If one category provided, prints one table.
+If multiple categories provided, prints a table for each of them one
+by one proceeding to the next one once you hit return. If no categories
+provided goes through all levels of the primary category.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>field:</dt><dd><p>The field to browse categories by.</p>
+<ul class="simple">
+<li><p>If None the primary field will be selected.
+If this annotation resource doesn’t have fields, all proteins
+will be presented as one single category.</p></li>
+<li><p>If a string it will be considered a field name and it will
+browse through all levels of this field.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">list</span></code>, set or tuple, it will be considered either a
+<code class="docutils literal notranslate"><span class="pre">list</span></code> of field names or a list of values from the primary
+field. In the former case all combinations of the values of
+the fields will be presented, in the latter case the browsing
+will be limited to the levels of the primary field contained
+in <code class="docutils literal notranslate"><span class="pre">field</span></code>.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">dict</span></code>, keys are supposed to be field names and values
+as list of levels. If any of the values are None, all levels
+from that field will be used.</p></li>
+</ul>
+</dd>
+<dt>start:</dt><dd><p>Start browsing from this category. E.g. if there are 500
+categories and start is 250 it will skip everything before the
+250th.</p>
+</dd>
+<dt>kwargs:</dt><dd><p>Passed to <code class="docutils literal notranslate"><span class="pre">pypath.utils.uniprot.info</span></code>.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Italk.complex_inference">
+<span class="sig-name descname"><span class="pre">complex_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Italk.complex_inference" title="Link to this definition">§</a></dt>
+<dd><p>Annotates all complexes in <cite>complexes</cite>, by default in the default
+complex database (existing in the <cite>complex</cite> module or generated
+on demand according to the module’s current settings).</p>
+<dl class="field-list simple">
+<dt class="field-odd">Returns<span class="colon">:</span></dt>
+<dd class="field-odd"><p><ul class="simple">
+<li><p><em>Dict with complexes as keys and sets of annotations as values.</em></p></li>
+<li><p><em>Complexes with no valid information in this annotation resource</em></p></li>
+<li><p><em>won’t be in the dict.</em></p></li>
+</ul>
+</p>
+</dd>
+<dt class="field-even">Parameters<span class="colon">:</span></dt>
+<dd class="field-even"><p><strong>complexes</strong> (<em>iterable</em>) – Iterable yielding complexes.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Italk.coverage">
+<span class="sig-name descname"><span class="pre">coverage</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">other</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Italk.coverage" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the coverage of the annotation i.e. the proportion of
+entities having at least one record in this annotation resource
+for an arbitrary set of entities.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Italk.curation_effort">
+<span class="sig-name descname"><span class="pre">curation_effort</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Italk.curation_effort" title="Link to this definition">§</a></dt>
+<dd><p>Counts the reference-record pairs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Italk.get_names">
+<span class="sig-name descname"><span class="pre">get_names</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Italk.get_names" title="Link to this definition">§</a></dt>
+<dd><p>Returns the list of field names in the records. The annotation
+consists of uniform records and each entity might be annotated
+with one or more records. Each record is a tuple of fields, for
+example <code class="docutils literal notranslate"><span class="pre">('cell_type',</span> <span class="pre">'expression_level',</span> <span class="pre">'score')</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Italk.get_reference_set">
+<em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">get_reference_set</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">proteins</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">swissprot_only</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Italk.get_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the reference set i.e. the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Italk.get_subset">
+<span class="sig-name descname"><span class="pre">get_subset</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Italk.get_subset" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Italk.get_subset_bool_array">
+<span class="sig-name descname"><span class="pre">get_subset_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Italk.get_subset_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a boolean vector with True and False values for each entity
+in the reference set. The values represent presence absence data
+in the simplest case, but by providing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> any kind of matching
+and filtering is possible. <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> are passed to the <code class="docutils literal notranslate"><span class="pre">select</span></code>
+method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Italk.get_values">
+<span class="sig-name descname"><span class="pre">get_values</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">exclude_none</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Italk.get_values" title="Link to this definition">§</a></dt>
+<dd><p>Returns the set of all possible values of a field. E.g. if the
+records of this annotation have a field <code class="docutils literal notranslate"><span class="pre">cell_type</span></code> then calling
+this method can tell you that across all records the values of
+this field might be <code class="docutils literal notranslate"><span class="pre">{'macrophage',</span> <span class="pre">'epithelial_cell',</span> <span class="pre">...}</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Italk.labels">
+<span class="sig-name descname"><span class="pre">labels</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Italk.labels" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Italk.load">
+<span class="sig-name descname"><span class="pre">load</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Italk.load" title="Link to this definition">§</a></dt>
+<dd><p>Loads the annotation data by calling the input method.
+Infers annotations for complexes in the complex database if
+py:attr:<code class="docutils literal notranslate"><span class="pre">infer_complexes</span></code> is True.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Italk.load_data">
+<span class="sig-name descname"><span class="pre">load_data</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Italk.load_data" title="Link to this definition">§</a></dt>
+<dd><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Italk.load_proteins">
+<span class="sig-name descname"><span class="pre">load_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Italk.load_proteins" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a set of all UniProt IDs to have a base set of the entire
+proteome.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Italk.make_df">
+<span class="sig-name descname"><span class="pre">make_df</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">rebuild</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Italk.make_df" title="Link to this definition">§</a></dt>
+<dd><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.
+The data frame will be assigned to :py:attr``df``.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Italk.numof_entities">
+<span class="sig-name descname"><span class="pre">numof_entities</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Italk.numof_entities" title="Link to this definition">§</a></dt>
+<dd><p>The number of annotated entities in the resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Italk.numof_records">
+<span class="sig-name descname"><span class="pre">numof_records</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Italk.numof_records" title="Link to this definition">§</a></dt>
+<dd><p>The total number of annotation records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Italk.numof_references">
+<span class="sig-name descname"><span class="pre">numof_references</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Italk.numof_references" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects and counts the
+references across all records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Italk.process">
+<span class="sig-name descname"><span class="pre">process</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Italk.process" title="Link to this definition">§</a></dt>
+<dd><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Italk.reload">
+<span class="sig-name descname"><span class="pre">reload</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Italk.reload" title="Link to this definition">§</a></dt>
+<dd><p>Reloads the object from the module level.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Italk.select">
+<span class="sig-name descname"><span class="pre">select</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Italk.select" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Italk.set_method">
+<span class="sig-name descname"><span class="pre">set_method</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Italk.set_method" title="Link to this definition">§</a></dt>
+<dd><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if
+necessary.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Italk.set_reference_set">
+<span class="sig-name descname"><span class="pre">set_reference_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Italk.set_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Assigns the reference set to the :py:attr``reference_set`` attribute.
+The reference set is the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Italk.show">
+<span class="sig-name descname"><span class="pre">show</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">table_param</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Italk.show" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic
+information from the UniProt datasheets.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Italk.subset_intersection">
+<span class="sig-name descname"><span class="pre">subset_intersection</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">universe</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Italk.subset_intersection" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the proportion of entities in a subset occuring in the
+set <code class="docutils literal notranslate"><span class="pre">universe</span></code>. The subset is selected by passing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> to the
+<code class="docutils literal notranslate"><span class="pre">select</span></code> method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Italk.to_array">
+<span class="sig-name descname"><span class="pre">to_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_fields</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Italk.to_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns an entity vs feature array. In case of more complex
+annotations this might be huge.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Italk.to_bool_array">
+<span class="sig-name descname"><span class="pre">to_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Italk.to_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a presence/absence boolean array for a reference set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Italk.to_set">
+<span class="sig-name descname"><span class="pre">to_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Italk.to_set" title="Link to this definition">§</a></dt>
+<dd><p>Returns the entities present in this annotation resource as a set.</p>
+</dd></dl>
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+    <li class="breadcrumb-item active" aria-current="page">pypath.core....</li>
+  </ul>
+</nav>
+</div>
+      
+    </div>
+  
+  
+</div>
+</div>
+              
+              
+              
+                
+<div id="searchbox"></div>
+                <article class="bd-article">
+                  
+  <section id="pypath-core-annot-keggpathways">
+<h1>pypath.core.annot.KeggPathways<a class="headerlink" href="#pypath-core-annot-keggpathways" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.core.annot.KeggPathways">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.core.annot.</span></span><span class="sig-name descname"><span class="pre">KeggPathways</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#KeggPathways"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.KeggPathways" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <a class="reference internal" href="pypath.core.annot.AnnotationBase.html#pypath.core.annot.AnnotationBase" title="pypath.core.annot.AnnotationBase"><code class="xref py py-class docutils literal notranslate"><span class="pre">AnnotationBase</span></code></a></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.KeggPathways.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#KeggPathways.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.KeggPathways.__init__" title="Link to this definition">§</a></dt>
+<dd><p>Pathway annotations from KEGG.</p>
+</dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.KeggPathways.__init__" title="pypath.core.annot.KeggPathways.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>([ncbi_tax_id])</p></td>
+<td><p>Pathway annotations from KEGG.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.KeggPathways.add_complexes_by_inference" title="pypath.core.annot.KeggPathways.add_complexes_by_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">add_complexes_by_inference</span></code></a>([complexes])</p></td>
+<td><p>Creates complex annotations by in silico inference and adds them to this annotation set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.KeggPathways.all_complexes" title="pypath.core.annot.KeggPathways.all_complexes"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_complexes</span></code></a>()</p></td>
+<td><p>All protein complexes annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.KeggPathways.all_entities" title="pypath.core.annot.KeggPathways.all_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_entities</span></code></a>([entity_types])</p></td>
+<td><p>All entities annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.KeggPathways.all_mirnas" title="pypath.core.annot.KeggPathways.all_mirnas"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_mirnas</span></code></a>()</p></td>
+<td><p>All miRNAs annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.KeggPathways.all_proteins" title="pypath.core.annot.KeggPathways.all_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_proteins</span></code></a>()</p></td>
+<td><p>All UniProt IDs annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.KeggPathways.all_refs" title="pypath.core.annot.KeggPathways.all_refs"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_refs</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.KeggPathways.annotate_complex" title="pypath.core.annot.KeggPathways.annotate_complex"><code class="xref py py-obj docutils literal notranslate"><span class="pre">annotate_complex</span></code></a>(cplex)</p></td>
+<td><p>Infers annotations for a single complex.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.KeggPathways.browse" title="pypath.core.annot.KeggPathways.browse"><code class="xref py py-obj docutils literal notranslate"><span class="pre">browse</span></code></a>([field, start])</p></td>
+<td><p>Print gene information as a table.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.KeggPathways.complex_inference" title="pypath.core.annot.KeggPathways.complex_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">complex_inference</span></code></a>([complexes])</p></td>
+<td><p>Annotates all complexes in <cite>complexes</cite>, by default in the default complex database (existing in the <cite>complex</cite> module or generated on demand according to the module's current settings).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.KeggPathways.coverage" title="pypath.core.annot.KeggPathways.coverage"><code class="xref py py-obj docutils literal notranslate"><span class="pre">coverage</span></code></a>(other)</p></td>
+<td><p>Calculates the coverage of the annotation i.e. the proportion of entities having at least one record in this annotation resource for an arbitrary set of entities.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.KeggPathways.curation_effort" title="pypath.core.annot.KeggPathways.curation_effort"><code class="xref py py-obj docutils literal notranslate"><span class="pre">curation_effort</span></code></a>()</p></td>
+<td><p>Counts the reference-record pairs.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">from_dump</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_entity_type</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.KeggPathways.get_names" title="pypath.core.annot.KeggPathways.get_names"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_names</span></code></a>()</p></td>
+<td><p>Returns the list of field names in the records.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.KeggPathways.get_reference_set" title="pypath.core.annot.KeggPathways.get_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_reference_set</span></code></a>([proteins, complexes, ...])</p></td>
+<td><p>Retrieves the reference set i.e. the set of all entities which potentially have annotation in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.KeggPathways.get_subset" title="pypath.core.annot.KeggPathways.get_subset"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.KeggPathways.get_subset_bool_array" title="pypath.core.annot.KeggPathways.get_subset_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset_bool_array</span></code></a>([reference_set])</p></td>
+<td><p>Returns a boolean vector with True and False values for each entity in the reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.KeggPathways.get_values" title="pypath.core.annot.KeggPathways.get_values"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_values</span></code></a>(name[, exclude_none])</p></td>
+<td><p>Returns the set of all possible values of a field.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_complex</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_mirna</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_protein</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.KeggPathways.labels" title="pypath.core.annot.KeggPathways.labels"><code class="xref py py-obj docutils literal notranslate"><span class="pre">labels</span></code></a>([method])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.KeggPathways.load" title="pypath.core.annot.KeggPathways.load"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load</span></code></a>()</p></td>
+<td><p>Loads the annotation data by calling the input method.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.KeggPathways.load_data" title="pypath.core.annot.KeggPathways.load_data"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_data</span></code></a>()</p></td>
+<td><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.KeggPathways.load_proteins" title="pypath.core.annot.KeggPathways.load_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_proteins</span></code></a>()</p></td>
+<td><p>Retrieves a set of all UniProt IDs to have a base set of the entire proteome.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.KeggPathways.make_df" title="pypath.core.annot.KeggPathways.make_df"><code class="xref py py-obj docutils literal notranslate"><span class="pre">make_df</span></code></a>([rebuild])</p></td>
+<td><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complex_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.KeggPathways.numof_entities" title="pypath.core.annot.KeggPathways.numof_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_entities</span></code></a>()</p></td>
+<td><p>The number of annotated entities in the resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirna_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirnas</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_protein_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_proteins</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.KeggPathways.numof_records" title="pypath.core.annot.KeggPathways.numof_records"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_records</span></code></a>([entity_types])</p></td>
+<td><p>The total number of annotation records.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.KeggPathways.numof_references" title="pypath.core.annot.KeggPathways.numof_references"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_references</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.KeggPathways.process" title="pypath.core.annot.KeggPathways.process"><code class="xref py py-obj docutils literal notranslate"><span class="pre">process</span></code></a>()</p></td>
+<td><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">proportion</span></code>(other)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.KeggPathways.reload" title="pypath.core.annot.KeggPathways.reload"><code class="xref py py-obj docutils literal notranslate"><span class="pre">reload</span></code></a>()</p></td>
+<td><p>Reloads the object from the module level.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">save_to_pickle</span></code>(pickle_file)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.KeggPathways.select" title="pypath.core.annot.KeggPathways.select"><code class="xref py py-obj docutils literal notranslate"><span class="pre">select</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.KeggPathways.set_method" title="pypath.core.annot.KeggPathways.set_method"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_method</span></code></a>()</p></td>
+<td><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if necessary.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.KeggPathways.set_reference_set" title="pypath.core.annot.KeggPathways.set_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_reference_set</span></code></a>()</p></td>
+<td><p>Assigns the reference set to the :py:attr``reference_set`` attribute.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.KeggPathways.show" title="pypath.core.annot.KeggPathways.show"><code class="xref py py-obj docutils literal notranslate"><span class="pre">show</span></code></a>([method, table_param])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic information from the UniProt datasheets.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.KeggPathways.subset_intersection" title="pypath.core.annot.KeggPathways.subset_intersection"><code class="xref py py-obj docutils literal notranslate"><span class="pre">subset_intersection</span></code></a>(universe, **kwargs)</p></td>
+<td><p>Calculates the proportion of entities in a subset occuring in the set <code class="docutils literal notranslate"><span class="pre">universe</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.KeggPathways.to_array" title="pypath.core.annot.KeggPathways.to_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_array</span></code></a>([reference_set, use_fields])</p></td>
+<td><p>Returns an entity vs feature array.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.KeggPathways.to_bool_array" title="pypath.core.annot.KeggPathways.to_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_bool_array</span></code></a>(reference_set)</p></td>
+<td><p>Returns a presence/absence boolean array for a reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.KeggPathways.to_set" title="pypath.core.annot.KeggPathways.to_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_set</span></code></a>()</p></td>
+<td><p>Returns the entities present in this annotation resource as a set.</p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Attributes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_fields</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">summary</span></code></p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.KeggPathways.add_complexes_by_inference">
+<span class="sig-name descname"><span class="pre">add_complexes_by_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.KeggPathways.add_complexes_by_inference" title="Link to this definition">§</a></dt>
+<dd><p>Creates complex annotations by in silico inference and adds them
+to this annotation set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.KeggPathways.all_complexes">
+<span class="sig-name descname"><span class="pre">all_complexes</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.KeggPathways.all_complexes" title="Link to this definition">§</a></dt>
+<dd><p>All protein complexes annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.KeggPathways.all_entities">
+<span class="sig-name descname"><span class="pre">all_entities</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.KeggPathways.all_entities" title="Link to this definition">§</a></dt>
+<dd><p>All entities annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.KeggPathways.all_mirnas">
+<span class="sig-name descname"><span class="pre">all_mirnas</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.KeggPathways.all_mirnas" title="Link to this definition">§</a></dt>
+<dd><p>All miRNAs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.KeggPathways.all_proteins">
+<span class="sig-name descname"><span class="pre">all_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.KeggPathways.all_proteins" title="Link to this definition">§</a></dt>
+<dd><p>All UniProt IDs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.KeggPathways.all_refs">
+<span class="sig-name descname"><span class="pre">all_refs</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.KeggPathways.all_refs" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects the references
+across all records. Returns <em>list</em>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.KeggPathways.annotate_complex">
+<span class="sig-name descname"><span class="pre">annotate_complex</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cplex</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.KeggPathways.annotate_complex" title="Link to this definition">§</a></dt>
+<dd><p>Infers annotations for a single complex.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.KeggPathways.browse">
+<span class="sig-name descname"><span class="pre">browse</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">field</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">start</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.KeggPathways.browse" title="Link to this definition">§</a></dt>
+<dd><p>Print gene information as a table.</p>
+<p>Presents information about annotation categories as ascii tables
+printed in the terminal. If one category provided, prints one table.
+If multiple categories provided, prints a table for each of them one
+by one proceeding to the next one once you hit return. If no categories
+provided goes through all levels of the primary category.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>field:</dt><dd><p>The field to browse categories by.</p>
+<ul class="simple">
+<li><p>If None the primary field will be selected.
+If this annotation resource doesn’t have fields, all proteins
+will be presented as one single category.</p></li>
+<li><p>If a string it will be considered a field name and it will
+browse through all levels of this field.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">list</span></code>, set or tuple, it will be considered either a
+<code class="docutils literal notranslate"><span class="pre">list</span></code> of field names or a list of values from the primary
+field. In the former case all combinations of the values of
+the fields will be presented, in the latter case the browsing
+will be limited to the levels of the primary field contained
+in <code class="docutils literal notranslate"><span class="pre">field</span></code>.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">dict</span></code>, keys are supposed to be field names and values
+as list of levels. If any of the values are None, all levels
+from that field will be used.</p></li>
+</ul>
+</dd>
+<dt>start:</dt><dd><p>Start browsing from this category. E.g. if there are 500
+categories and start is 250 it will skip everything before the
+250th.</p>
+</dd>
+<dt>kwargs:</dt><dd><p>Passed to <code class="docutils literal notranslate"><span class="pre">pypath.utils.uniprot.info</span></code>.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.KeggPathways.complex_inference">
+<span class="sig-name descname"><span class="pre">complex_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.KeggPathways.complex_inference" title="Link to this definition">§</a></dt>
+<dd><p>Annotates all complexes in <cite>complexes</cite>, by default in the default
+complex database (existing in the <cite>complex</cite> module or generated
+on demand according to the module’s current settings).</p>
+<dl class="field-list simple">
+<dt class="field-odd">Returns<span class="colon">:</span></dt>
+<dd class="field-odd"><p><ul class="simple">
+<li><p><em>Dict with complexes as keys and sets of annotations as values.</em></p></li>
+<li><p><em>Complexes with no valid information in this annotation resource</em></p></li>
+<li><p><em>won’t be in the dict.</em></p></li>
+</ul>
+</p>
+</dd>
+<dt class="field-even">Parameters<span class="colon">:</span></dt>
+<dd class="field-even"><p><strong>complexes</strong> (<em>iterable</em>) – Iterable yielding complexes.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.KeggPathways.coverage">
+<span class="sig-name descname"><span class="pre">coverage</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">other</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.KeggPathways.coverage" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the coverage of the annotation i.e. the proportion of
+entities having at least one record in this annotation resource
+for an arbitrary set of entities.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.KeggPathways.curation_effort">
+<span class="sig-name descname"><span class="pre">curation_effort</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.KeggPathways.curation_effort" title="Link to this definition">§</a></dt>
+<dd><p>Counts the reference-record pairs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.KeggPathways.get_names">
+<span class="sig-name descname"><span class="pre">get_names</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.KeggPathways.get_names" title="Link to this definition">§</a></dt>
+<dd><p>Returns the list of field names in the records. The annotation
+consists of uniform records and each entity might be annotated
+with one or more records. Each record is a tuple of fields, for
+example <code class="docutils literal notranslate"><span class="pre">('cell_type',</span> <span class="pre">'expression_level',</span> <span class="pre">'score')</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.KeggPathways.get_reference_set">
+<em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">get_reference_set</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">proteins</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">swissprot_only</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.KeggPathways.get_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the reference set i.e. the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.KeggPathways.get_subset">
+<span class="sig-name descname"><span class="pre">get_subset</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.KeggPathways.get_subset" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.KeggPathways.get_subset_bool_array">
+<span class="sig-name descname"><span class="pre">get_subset_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.KeggPathways.get_subset_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a boolean vector with True and False values for each entity
+in the reference set. The values represent presence absence data
+in the simplest case, but by providing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> any kind of matching
+and filtering is possible. <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> are passed to the <code class="docutils literal notranslate"><span class="pre">select</span></code>
+method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.KeggPathways.get_values">
+<span class="sig-name descname"><span class="pre">get_values</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">exclude_none</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.KeggPathways.get_values" title="Link to this definition">§</a></dt>
+<dd><p>Returns the set of all possible values of a field. E.g. if the
+records of this annotation have a field <code class="docutils literal notranslate"><span class="pre">cell_type</span></code> then calling
+this method can tell you that across all records the values of
+this field might be <code class="docutils literal notranslate"><span class="pre">{'macrophage',</span> <span class="pre">'epithelial_cell',</span> <span class="pre">...}</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.KeggPathways.labels">
+<span class="sig-name descname"><span class="pre">labels</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.KeggPathways.labels" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.KeggPathways.load">
+<span class="sig-name descname"><span class="pre">load</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.KeggPathways.load" title="Link to this definition">§</a></dt>
+<dd><p>Loads the annotation data by calling the input method.
+Infers annotations for complexes in the complex database if
+py:attr:<code class="docutils literal notranslate"><span class="pre">infer_complexes</span></code> is True.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.KeggPathways.load_data">
+<span class="sig-name descname"><span class="pre">load_data</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.KeggPathways.load_data" title="Link to this definition">§</a></dt>
+<dd><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.KeggPathways.load_proteins">
+<span class="sig-name descname"><span class="pre">load_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.KeggPathways.load_proteins" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a set of all UniProt IDs to have a base set of the entire
+proteome.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.KeggPathways.make_df">
+<span class="sig-name descname"><span class="pre">make_df</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">rebuild</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.KeggPathways.make_df" title="Link to this definition">§</a></dt>
+<dd><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.
+The data frame will be assigned to :py:attr``df``.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.KeggPathways.numof_entities">
+<span class="sig-name descname"><span class="pre">numof_entities</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.KeggPathways.numof_entities" title="Link to this definition">§</a></dt>
+<dd><p>The number of annotated entities in the resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.KeggPathways.numof_records">
+<span class="sig-name descname"><span class="pre">numof_records</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.KeggPathways.numof_records" title="Link to this definition">§</a></dt>
+<dd><p>The total number of annotation records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.KeggPathways.numof_references">
+<span class="sig-name descname"><span class="pre">numof_references</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.KeggPathways.numof_references" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects and counts the
+references across all records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.KeggPathways.process">
+<span class="sig-name descname"><span class="pre">process</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.KeggPathways.process" title="Link to this definition">§</a></dt>
+<dd><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.KeggPathways.reload">
+<span class="sig-name descname"><span class="pre">reload</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.KeggPathways.reload" title="Link to this definition">§</a></dt>
+<dd><p>Reloads the object from the module level.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.KeggPathways.select">
+<span class="sig-name descname"><span class="pre">select</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.KeggPathways.select" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.KeggPathways.set_method">
+<span class="sig-name descname"><span class="pre">set_method</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.KeggPathways.set_method" title="Link to this definition">§</a></dt>
+<dd><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if
+necessary.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.KeggPathways.set_reference_set">
+<span class="sig-name descname"><span class="pre">set_reference_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.KeggPathways.set_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Assigns the reference set to the :py:attr``reference_set`` attribute.
+The reference set is the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.KeggPathways.show">
+<span class="sig-name descname"><span class="pre">show</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">table_param</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.KeggPathways.show" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic
+information from the UniProt datasheets.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.KeggPathways.subset_intersection">
+<span class="sig-name descname"><span class="pre">subset_intersection</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">universe</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.KeggPathways.subset_intersection" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the proportion of entities in a subset occuring in the
+set <code class="docutils literal notranslate"><span class="pre">universe</span></code>. The subset is selected by passing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> to the
+<code class="docutils literal notranslate"><span class="pre">select</span></code> method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.KeggPathways.to_array">
+<span class="sig-name descname"><span class="pre">to_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_fields</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.KeggPathways.to_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns an entity vs feature array. In case of more complex
+annotations this might be huge.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.KeggPathways.to_bool_array">
+<span class="sig-name descname"><span class="pre">to_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.KeggPathways.to_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a presence/absence boolean array for a reference set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.KeggPathways.to_set">
+<span class="sig-name descname"><span class="pre">to_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.KeggPathways.to_set" title="Link to this definition">§</a></dt>
+<dd><p>Returns the entities present in this annotation resource as a set.</p>
+</dd></dl>
+
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+  <section id="pypath-core-annot-keggpathwayspc">
+<h1>pypath.core.annot.KeggPathwaysPC<a class="headerlink" href="#pypath-core-annot-keggpathwayspc" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.core.annot.KeggPathwaysPC">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.core.annot.</span></span><span class="sig-name descname"><span class="pre">KeggPathwaysPC</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#KeggPathwaysPC"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.KeggPathwaysPC" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <a class="reference internal" href="pypath.core.annot.AnnotationBase.html#pypath.core.annot.AnnotationBase" title="pypath.core.annot.AnnotationBase"><code class="xref py py-class docutils literal notranslate"><span class="pre">AnnotationBase</span></code></a></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.KeggPathwaysPC.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#KeggPathwaysPC.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.KeggPathwaysPC.__init__" title="Link to this definition">§</a></dt>
+<dd><p>Pathway annotations from KEGG via PathwayCommons.</p>
+</dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.KeggPathwaysPC.__init__" title="pypath.core.annot.KeggPathwaysPC.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>([ncbi_tax_id])</p></td>
+<td><p>Pathway annotations from KEGG via PathwayCommons.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.KeggPathwaysPC.add_complexes_by_inference" title="pypath.core.annot.KeggPathwaysPC.add_complexes_by_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">add_complexes_by_inference</span></code></a>([complexes])</p></td>
+<td><p>Creates complex annotations by in silico inference and adds them to this annotation set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.KeggPathwaysPC.all_complexes" title="pypath.core.annot.KeggPathwaysPC.all_complexes"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_complexes</span></code></a>()</p></td>
+<td><p>All protein complexes annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.KeggPathwaysPC.all_entities" title="pypath.core.annot.KeggPathwaysPC.all_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_entities</span></code></a>([entity_types])</p></td>
+<td><p>All entities annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.KeggPathwaysPC.all_mirnas" title="pypath.core.annot.KeggPathwaysPC.all_mirnas"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_mirnas</span></code></a>()</p></td>
+<td><p>All miRNAs annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.KeggPathwaysPC.all_proteins" title="pypath.core.annot.KeggPathwaysPC.all_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_proteins</span></code></a>()</p></td>
+<td><p>All UniProt IDs annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.KeggPathwaysPC.all_refs" title="pypath.core.annot.KeggPathwaysPC.all_refs"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_refs</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.KeggPathwaysPC.annotate_complex" title="pypath.core.annot.KeggPathwaysPC.annotate_complex"><code class="xref py py-obj docutils literal notranslate"><span class="pre">annotate_complex</span></code></a>(cplex)</p></td>
+<td><p>Infers annotations for a single complex.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.KeggPathwaysPC.browse" title="pypath.core.annot.KeggPathwaysPC.browse"><code class="xref py py-obj docutils literal notranslate"><span class="pre">browse</span></code></a>([field, start])</p></td>
+<td><p>Print gene information as a table.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.KeggPathwaysPC.complex_inference" title="pypath.core.annot.KeggPathwaysPC.complex_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">complex_inference</span></code></a>([complexes])</p></td>
+<td><p>Annotates all complexes in <cite>complexes</cite>, by default in the default complex database (existing in the <cite>complex</cite> module or generated on demand according to the module's current settings).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.KeggPathwaysPC.coverage" title="pypath.core.annot.KeggPathwaysPC.coverage"><code class="xref py py-obj docutils literal notranslate"><span class="pre">coverage</span></code></a>(other)</p></td>
+<td><p>Calculates the coverage of the annotation i.e. the proportion of entities having at least one record in this annotation resource for an arbitrary set of entities.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.KeggPathwaysPC.curation_effort" title="pypath.core.annot.KeggPathwaysPC.curation_effort"><code class="xref py py-obj docutils literal notranslate"><span class="pre">curation_effort</span></code></a>()</p></td>
+<td><p>Counts the reference-record pairs.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">from_dump</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_entity_type</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.KeggPathwaysPC.get_names" title="pypath.core.annot.KeggPathwaysPC.get_names"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_names</span></code></a>()</p></td>
+<td><p>Returns the list of field names in the records.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.KeggPathwaysPC.get_reference_set" title="pypath.core.annot.KeggPathwaysPC.get_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_reference_set</span></code></a>([proteins, complexes, ...])</p></td>
+<td><p>Retrieves the reference set i.e. the set of all entities which potentially have annotation in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.KeggPathwaysPC.get_subset" title="pypath.core.annot.KeggPathwaysPC.get_subset"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.KeggPathwaysPC.get_subset_bool_array" title="pypath.core.annot.KeggPathwaysPC.get_subset_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset_bool_array</span></code></a>([reference_set])</p></td>
+<td><p>Returns a boolean vector with True and False values for each entity in the reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.KeggPathwaysPC.get_values" title="pypath.core.annot.KeggPathwaysPC.get_values"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_values</span></code></a>(name[, exclude_none])</p></td>
+<td><p>Returns the set of all possible values of a field.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_complex</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_mirna</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_protein</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.KeggPathwaysPC.labels" title="pypath.core.annot.KeggPathwaysPC.labels"><code class="xref py py-obj docutils literal notranslate"><span class="pre">labels</span></code></a>([method])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.KeggPathwaysPC.load" title="pypath.core.annot.KeggPathwaysPC.load"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load</span></code></a>()</p></td>
+<td><p>Loads the annotation data by calling the input method.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.KeggPathwaysPC.load_data" title="pypath.core.annot.KeggPathwaysPC.load_data"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_data</span></code></a>()</p></td>
+<td><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.KeggPathwaysPC.load_proteins" title="pypath.core.annot.KeggPathwaysPC.load_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_proteins</span></code></a>()</p></td>
+<td><p>Retrieves a set of all UniProt IDs to have a base set of the entire proteome.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.KeggPathwaysPC.make_df" title="pypath.core.annot.KeggPathwaysPC.make_df"><code class="xref py py-obj docutils literal notranslate"><span class="pre">make_df</span></code></a>([rebuild])</p></td>
+<td><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complex_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.KeggPathwaysPC.numof_entities" title="pypath.core.annot.KeggPathwaysPC.numof_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_entities</span></code></a>()</p></td>
+<td><p>The number of annotated entities in the resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirna_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirnas</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_protein_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_proteins</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.KeggPathwaysPC.numof_records" title="pypath.core.annot.KeggPathwaysPC.numof_records"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_records</span></code></a>([entity_types])</p></td>
+<td><p>The total number of annotation records.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.KeggPathwaysPC.numof_references" title="pypath.core.annot.KeggPathwaysPC.numof_references"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_references</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.KeggPathwaysPC.process" title="pypath.core.annot.KeggPathwaysPC.process"><code class="xref py py-obj docutils literal notranslate"><span class="pre">process</span></code></a>()</p></td>
+<td><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">proportion</span></code>(other)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.KeggPathwaysPC.reload" title="pypath.core.annot.KeggPathwaysPC.reload"><code class="xref py py-obj docutils literal notranslate"><span class="pre">reload</span></code></a>()</p></td>
+<td><p>Reloads the object from the module level.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">save_to_pickle</span></code>(pickle_file)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.KeggPathwaysPC.select" title="pypath.core.annot.KeggPathwaysPC.select"><code class="xref py py-obj docutils literal notranslate"><span class="pre">select</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.KeggPathwaysPC.set_method" title="pypath.core.annot.KeggPathwaysPC.set_method"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_method</span></code></a>()</p></td>
+<td><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if necessary.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.KeggPathwaysPC.set_reference_set" title="pypath.core.annot.KeggPathwaysPC.set_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_reference_set</span></code></a>()</p></td>
+<td><p>Assigns the reference set to the :py:attr``reference_set`` attribute.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.KeggPathwaysPC.show" title="pypath.core.annot.KeggPathwaysPC.show"><code class="xref py py-obj docutils literal notranslate"><span class="pre">show</span></code></a>([method, table_param])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic information from the UniProt datasheets.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.KeggPathwaysPC.subset_intersection" title="pypath.core.annot.KeggPathwaysPC.subset_intersection"><code class="xref py py-obj docutils literal notranslate"><span class="pre">subset_intersection</span></code></a>(universe, **kwargs)</p></td>
+<td><p>Calculates the proportion of entities in a subset occuring in the set <code class="docutils literal notranslate"><span class="pre">universe</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.KeggPathwaysPC.to_array" title="pypath.core.annot.KeggPathwaysPC.to_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_array</span></code></a>([reference_set, use_fields])</p></td>
+<td><p>Returns an entity vs feature array.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.KeggPathwaysPC.to_bool_array" title="pypath.core.annot.KeggPathwaysPC.to_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_bool_array</span></code></a>(reference_set)</p></td>
+<td><p>Returns a presence/absence boolean array for a reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.KeggPathwaysPC.to_set" title="pypath.core.annot.KeggPathwaysPC.to_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_set</span></code></a>()</p></td>
+<td><p>Returns the entities present in this annotation resource as a set.</p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Attributes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_fields</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">summary</span></code></p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.KeggPathwaysPC.add_complexes_by_inference">
+<span class="sig-name descname"><span class="pre">add_complexes_by_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.KeggPathwaysPC.add_complexes_by_inference" title="Link to this definition">§</a></dt>
+<dd><p>Creates complex annotations by in silico inference and adds them
+to this annotation set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.KeggPathwaysPC.all_complexes">
+<span class="sig-name descname"><span class="pre">all_complexes</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.KeggPathwaysPC.all_complexes" title="Link to this definition">§</a></dt>
+<dd><p>All protein complexes annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.KeggPathwaysPC.all_entities">
+<span class="sig-name descname"><span class="pre">all_entities</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.KeggPathwaysPC.all_entities" title="Link to this definition">§</a></dt>
+<dd><p>All entities annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.KeggPathwaysPC.all_mirnas">
+<span class="sig-name descname"><span class="pre">all_mirnas</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.KeggPathwaysPC.all_mirnas" title="Link to this definition">§</a></dt>
+<dd><p>All miRNAs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.KeggPathwaysPC.all_proteins">
+<span class="sig-name descname"><span class="pre">all_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.KeggPathwaysPC.all_proteins" title="Link to this definition">§</a></dt>
+<dd><p>All UniProt IDs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.KeggPathwaysPC.all_refs">
+<span class="sig-name descname"><span class="pre">all_refs</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.KeggPathwaysPC.all_refs" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects the references
+across all records. Returns <em>list</em>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.KeggPathwaysPC.annotate_complex">
+<span class="sig-name descname"><span class="pre">annotate_complex</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cplex</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.KeggPathwaysPC.annotate_complex" title="Link to this definition">§</a></dt>
+<dd><p>Infers annotations for a single complex.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.KeggPathwaysPC.browse">
+<span class="sig-name descname"><span class="pre">browse</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">field</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">start</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.KeggPathwaysPC.browse" title="Link to this definition">§</a></dt>
+<dd><p>Print gene information as a table.</p>
+<p>Presents information about annotation categories as ascii tables
+printed in the terminal. If one category provided, prints one table.
+If multiple categories provided, prints a table for each of them one
+by one proceeding to the next one once you hit return. If no categories
+provided goes through all levels of the primary category.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>field:</dt><dd><p>The field to browse categories by.</p>
+<ul class="simple">
+<li><p>If None the primary field will be selected.
+If this annotation resource doesn’t have fields, all proteins
+will be presented as one single category.</p></li>
+<li><p>If a string it will be considered a field name and it will
+browse through all levels of this field.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">list</span></code>, set or tuple, it will be considered either a
+<code class="docutils literal notranslate"><span class="pre">list</span></code> of field names or a list of values from the primary
+field. In the former case all combinations of the values of
+the fields will be presented, in the latter case the browsing
+will be limited to the levels of the primary field contained
+in <code class="docutils literal notranslate"><span class="pre">field</span></code>.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">dict</span></code>, keys are supposed to be field names and values
+as list of levels. If any of the values are None, all levels
+from that field will be used.</p></li>
+</ul>
+</dd>
+<dt>start:</dt><dd><p>Start browsing from this category. E.g. if there are 500
+categories and start is 250 it will skip everything before the
+250th.</p>
+</dd>
+<dt>kwargs:</dt><dd><p>Passed to <code class="docutils literal notranslate"><span class="pre">pypath.utils.uniprot.info</span></code>.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.KeggPathwaysPC.complex_inference">
+<span class="sig-name descname"><span class="pre">complex_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.KeggPathwaysPC.complex_inference" title="Link to this definition">§</a></dt>
+<dd><p>Annotates all complexes in <cite>complexes</cite>, by default in the default
+complex database (existing in the <cite>complex</cite> module or generated
+on demand according to the module’s current settings).</p>
+<dl class="field-list simple">
+<dt class="field-odd">Returns<span class="colon">:</span></dt>
+<dd class="field-odd"><p><ul class="simple">
+<li><p><em>Dict with complexes as keys and sets of annotations as values.</em></p></li>
+<li><p><em>Complexes with no valid information in this annotation resource</em></p></li>
+<li><p><em>won’t be in the dict.</em></p></li>
+</ul>
+</p>
+</dd>
+<dt class="field-even">Parameters<span class="colon">:</span></dt>
+<dd class="field-even"><p><strong>complexes</strong> (<em>iterable</em>) – Iterable yielding complexes.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.KeggPathwaysPC.coverage">
+<span class="sig-name descname"><span class="pre">coverage</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">other</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.KeggPathwaysPC.coverage" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the coverage of the annotation i.e. the proportion of
+entities having at least one record in this annotation resource
+for an arbitrary set of entities.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.KeggPathwaysPC.curation_effort">
+<span class="sig-name descname"><span class="pre">curation_effort</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.KeggPathwaysPC.curation_effort" title="Link to this definition">§</a></dt>
+<dd><p>Counts the reference-record pairs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.KeggPathwaysPC.get_names">
+<span class="sig-name descname"><span class="pre">get_names</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.KeggPathwaysPC.get_names" title="Link to this definition">§</a></dt>
+<dd><p>Returns the list of field names in the records. The annotation
+consists of uniform records and each entity might be annotated
+with one or more records. Each record is a tuple of fields, for
+example <code class="docutils literal notranslate"><span class="pre">('cell_type',</span> <span class="pre">'expression_level',</span> <span class="pre">'score')</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.KeggPathwaysPC.get_reference_set">
+<em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">get_reference_set</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">proteins</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">swissprot_only</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.KeggPathwaysPC.get_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the reference set i.e. the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.KeggPathwaysPC.get_subset">
+<span class="sig-name descname"><span class="pre">get_subset</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.KeggPathwaysPC.get_subset" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.KeggPathwaysPC.get_subset_bool_array">
+<span class="sig-name descname"><span class="pre">get_subset_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.KeggPathwaysPC.get_subset_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a boolean vector with True and False values for each entity
+in the reference set. The values represent presence absence data
+in the simplest case, but by providing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> any kind of matching
+and filtering is possible. <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> are passed to the <code class="docutils literal notranslate"><span class="pre">select</span></code>
+method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.KeggPathwaysPC.get_values">
+<span class="sig-name descname"><span class="pre">get_values</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">exclude_none</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.KeggPathwaysPC.get_values" title="Link to this definition">§</a></dt>
+<dd><p>Returns the set of all possible values of a field. E.g. if the
+records of this annotation have a field <code class="docutils literal notranslate"><span class="pre">cell_type</span></code> then calling
+this method can tell you that across all records the values of
+this field might be <code class="docutils literal notranslate"><span class="pre">{'macrophage',</span> <span class="pre">'epithelial_cell',</span> <span class="pre">...}</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.KeggPathwaysPC.labels">
+<span class="sig-name descname"><span class="pre">labels</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.KeggPathwaysPC.labels" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.KeggPathwaysPC.load">
+<span class="sig-name descname"><span class="pre">load</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.KeggPathwaysPC.load" title="Link to this definition">§</a></dt>
+<dd><p>Loads the annotation data by calling the input method.
+Infers annotations for complexes in the complex database if
+py:attr:<code class="docutils literal notranslate"><span class="pre">infer_complexes</span></code> is True.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.KeggPathwaysPC.load_data">
+<span class="sig-name descname"><span class="pre">load_data</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.KeggPathwaysPC.load_data" title="Link to this definition">§</a></dt>
+<dd><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.KeggPathwaysPC.load_proteins">
+<span class="sig-name descname"><span class="pre">load_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.KeggPathwaysPC.load_proteins" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a set of all UniProt IDs to have a base set of the entire
+proteome.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.KeggPathwaysPC.make_df">
+<span class="sig-name descname"><span class="pre">make_df</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">rebuild</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.KeggPathwaysPC.make_df" title="Link to this definition">§</a></dt>
+<dd><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.
+The data frame will be assigned to :py:attr``df``.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.KeggPathwaysPC.numof_entities">
+<span class="sig-name descname"><span class="pre">numof_entities</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.KeggPathwaysPC.numof_entities" title="Link to this definition">§</a></dt>
+<dd><p>The number of annotated entities in the resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.KeggPathwaysPC.numof_records">
+<span class="sig-name descname"><span class="pre">numof_records</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.KeggPathwaysPC.numof_records" title="Link to this definition">§</a></dt>
+<dd><p>The total number of annotation records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.KeggPathwaysPC.numof_references">
+<span class="sig-name descname"><span class="pre">numof_references</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.KeggPathwaysPC.numof_references" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects and counts the
+references across all records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.KeggPathwaysPC.process">
+<span class="sig-name descname"><span class="pre">process</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.KeggPathwaysPC.process" title="Link to this definition">§</a></dt>
+<dd><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.KeggPathwaysPC.reload">
+<span class="sig-name descname"><span class="pre">reload</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.KeggPathwaysPC.reload" title="Link to this definition">§</a></dt>
+<dd><p>Reloads the object from the module level.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.KeggPathwaysPC.select">
+<span class="sig-name descname"><span class="pre">select</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.KeggPathwaysPC.select" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.KeggPathwaysPC.set_method">
+<span class="sig-name descname"><span class="pre">set_method</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.KeggPathwaysPC.set_method" title="Link to this definition">§</a></dt>
+<dd><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if
+necessary.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.KeggPathwaysPC.set_reference_set">
+<span class="sig-name descname"><span class="pre">set_reference_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.KeggPathwaysPC.set_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Assigns the reference set to the :py:attr``reference_set`` attribute.
+The reference set is the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.KeggPathwaysPC.show">
+<span class="sig-name descname"><span class="pre">show</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">table_param</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.KeggPathwaysPC.show" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic
+information from the UniProt datasheets.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.KeggPathwaysPC.subset_intersection">
+<span class="sig-name descname"><span class="pre">subset_intersection</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">universe</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.KeggPathwaysPC.subset_intersection" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the proportion of entities in a subset occuring in the
+set <code class="docutils literal notranslate"><span class="pre">universe</span></code>. The subset is selected by passing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> to the
+<code class="docutils literal notranslate"><span class="pre">select</span></code> method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.KeggPathwaysPC.to_array">
+<span class="sig-name descname"><span class="pre">to_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_fields</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.KeggPathwaysPC.to_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns an entity vs feature array. In case of more complex
+annotations this might be huge.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.KeggPathwaysPC.to_bool_array">
+<span class="sig-name descname"><span class="pre">to_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.KeggPathwaysPC.to_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a presence/absence boolean array for a reference set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.KeggPathwaysPC.to_set">
+<span class="sig-name descname"><span class="pre">to_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.KeggPathwaysPC.to_set" title="Link to this definition">§</a></dt>
+<dd><p>Returns the entities present in this annotation resource as a set.</p>
+</dd></dl>
+
+</dd></dl>
+
+</section>
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+  <section id="pypath-core-annot-kinasedotcom">
+<h1>pypath.core.annot.Kinasedotcom<a class="headerlink" href="#pypath-core-annot-kinasedotcom" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.core.annot.Kinasedotcom">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.core.annot.</span></span><span class="sig-name descname"><span class="pre">Kinasedotcom</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#Kinasedotcom"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.Kinasedotcom" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <a class="reference internal" href="pypath.core.annot.AnnotationBase.html#pypath.core.annot.AnnotationBase" title="pypath.core.annot.AnnotationBase"><code class="xref py py-class docutils literal notranslate"><span class="pre">AnnotationBase</span></code></a></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Kinasedotcom.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#Kinasedotcom.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.Kinasedotcom.__init__" title="Link to this definition">§</a></dt>
+<dd><p>Kinases from <cite>kinase.com</cite>.</p>
+</dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Kinasedotcom.__init__" title="pypath.core.annot.Kinasedotcom.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>(**kwargs)</p></td>
+<td><p>Kinases from <cite>kinase.com</cite>.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Kinasedotcom.add_complexes_by_inference" title="pypath.core.annot.Kinasedotcom.add_complexes_by_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">add_complexes_by_inference</span></code></a>([complexes])</p></td>
+<td><p>Creates complex annotations by in silico inference and adds them to this annotation set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Kinasedotcom.all_complexes" title="pypath.core.annot.Kinasedotcom.all_complexes"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_complexes</span></code></a>()</p></td>
+<td><p>All protein complexes annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Kinasedotcom.all_entities" title="pypath.core.annot.Kinasedotcom.all_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_entities</span></code></a>([entity_types])</p></td>
+<td><p>All entities annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Kinasedotcom.all_mirnas" title="pypath.core.annot.Kinasedotcom.all_mirnas"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_mirnas</span></code></a>()</p></td>
+<td><p>All miRNAs annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Kinasedotcom.all_proteins" title="pypath.core.annot.Kinasedotcom.all_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_proteins</span></code></a>()</p></td>
+<td><p>All UniProt IDs annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Kinasedotcom.all_refs" title="pypath.core.annot.Kinasedotcom.all_refs"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_refs</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Kinasedotcom.annotate_complex" title="pypath.core.annot.Kinasedotcom.annotate_complex"><code class="xref py py-obj docutils literal notranslate"><span class="pre">annotate_complex</span></code></a>(cplex)</p></td>
+<td><p>Infers annotations for a single complex.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Kinasedotcom.browse" title="pypath.core.annot.Kinasedotcom.browse"><code class="xref py py-obj docutils literal notranslate"><span class="pre">browse</span></code></a>([field, start])</p></td>
+<td><p>Print gene information as a table.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Kinasedotcom.complex_inference" title="pypath.core.annot.Kinasedotcom.complex_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">complex_inference</span></code></a>([complexes])</p></td>
+<td><p>Annotates all complexes in <cite>complexes</cite>, by default in the default complex database (existing in the <cite>complex</cite> module or generated on demand according to the module's current settings).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Kinasedotcom.coverage" title="pypath.core.annot.Kinasedotcom.coverage"><code class="xref py py-obj docutils literal notranslate"><span class="pre">coverage</span></code></a>(other)</p></td>
+<td><p>Calculates the coverage of the annotation i.e. the proportion of entities having at least one record in this annotation resource for an arbitrary set of entities.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Kinasedotcom.curation_effort" title="pypath.core.annot.Kinasedotcom.curation_effort"><code class="xref py py-obj docutils literal notranslate"><span class="pre">curation_effort</span></code></a>()</p></td>
+<td><p>Counts the reference-record pairs.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">from_dump</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_entity_type</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Kinasedotcom.get_names" title="pypath.core.annot.Kinasedotcom.get_names"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_names</span></code></a>()</p></td>
+<td><p>Returns the list of field names in the records.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Kinasedotcom.get_reference_set" title="pypath.core.annot.Kinasedotcom.get_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_reference_set</span></code></a>([proteins, complexes, ...])</p></td>
+<td><p>Retrieves the reference set i.e. the set of all entities which potentially have annotation in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Kinasedotcom.get_subset" title="pypath.core.annot.Kinasedotcom.get_subset"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Kinasedotcom.get_subset_bool_array" title="pypath.core.annot.Kinasedotcom.get_subset_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset_bool_array</span></code></a>([reference_set])</p></td>
+<td><p>Returns a boolean vector with True and False values for each entity in the reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Kinasedotcom.get_values" title="pypath.core.annot.Kinasedotcom.get_values"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_values</span></code></a>(name[, exclude_none])</p></td>
+<td><p>Returns the set of all possible values of a field.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_complex</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_mirna</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_protein</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Kinasedotcom.labels" title="pypath.core.annot.Kinasedotcom.labels"><code class="xref py py-obj docutils literal notranslate"><span class="pre">labels</span></code></a>([method])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Kinasedotcom.load" title="pypath.core.annot.Kinasedotcom.load"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load</span></code></a>()</p></td>
+<td><p>Loads the annotation data by calling the input method.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Kinasedotcom.load_data" title="pypath.core.annot.Kinasedotcom.load_data"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_data</span></code></a>()</p></td>
+<td><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Kinasedotcom.load_proteins" title="pypath.core.annot.Kinasedotcom.load_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_proteins</span></code></a>()</p></td>
+<td><p>Retrieves a set of all UniProt IDs to have a base set of the entire proteome.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Kinasedotcom.make_df" title="pypath.core.annot.Kinasedotcom.make_df"><code class="xref py py-obj docutils literal notranslate"><span class="pre">make_df</span></code></a>([rebuild])</p></td>
+<td><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complex_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Kinasedotcom.numof_entities" title="pypath.core.annot.Kinasedotcom.numof_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_entities</span></code></a>()</p></td>
+<td><p>The number of annotated entities in the resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirna_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirnas</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_protein_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_proteins</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Kinasedotcom.numof_records" title="pypath.core.annot.Kinasedotcom.numof_records"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_records</span></code></a>([entity_types])</p></td>
+<td><p>The total number of annotation records.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Kinasedotcom.numof_references" title="pypath.core.annot.Kinasedotcom.numof_references"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_references</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Kinasedotcom.process" title="pypath.core.annot.Kinasedotcom.process"><code class="xref py py-obj docutils literal notranslate"><span class="pre">process</span></code></a>()</p></td>
+<td><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">proportion</span></code>(other)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Kinasedotcom.reload" title="pypath.core.annot.Kinasedotcom.reload"><code class="xref py py-obj docutils literal notranslate"><span class="pre">reload</span></code></a>()</p></td>
+<td><p>Reloads the object from the module level.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">save_to_pickle</span></code>(pickle_file)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Kinasedotcom.select" title="pypath.core.annot.Kinasedotcom.select"><code class="xref py py-obj docutils literal notranslate"><span class="pre">select</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Kinasedotcom.set_method" title="pypath.core.annot.Kinasedotcom.set_method"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_method</span></code></a>()</p></td>
+<td><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if necessary.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Kinasedotcom.set_reference_set" title="pypath.core.annot.Kinasedotcom.set_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_reference_set</span></code></a>()</p></td>
+<td><p>Assigns the reference set to the :py:attr``reference_set`` attribute.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Kinasedotcom.show" title="pypath.core.annot.Kinasedotcom.show"><code class="xref py py-obj docutils literal notranslate"><span class="pre">show</span></code></a>([method, table_param])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic information from the UniProt datasheets.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Kinasedotcom.subset_intersection" title="pypath.core.annot.Kinasedotcom.subset_intersection"><code class="xref py py-obj docutils literal notranslate"><span class="pre">subset_intersection</span></code></a>(universe, **kwargs)</p></td>
+<td><p>Calculates the proportion of entities in a subset occuring in the set <code class="docutils literal notranslate"><span class="pre">universe</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Kinasedotcom.to_array" title="pypath.core.annot.Kinasedotcom.to_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_array</span></code></a>([reference_set, use_fields])</p></td>
+<td><p>Returns an entity vs feature array.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Kinasedotcom.to_bool_array" title="pypath.core.annot.Kinasedotcom.to_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_bool_array</span></code></a>(reference_set)</p></td>
+<td><p>Returns a presence/absence boolean array for a reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Kinasedotcom.to_set" title="pypath.core.annot.Kinasedotcom.to_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_set</span></code></a>()</p></td>
+<td><p>Returns the entities present in this annotation resource as a set.</p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Attributes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_fields</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">summary</span></code></p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Kinasedotcom.add_complexes_by_inference">
+<span class="sig-name descname"><span class="pre">add_complexes_by_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Kinasedotcom.add_complexes_by_inference" title="Link to this definition">§</a></dt>
+<dd><p>Creates complex annotations by in silico inference and adds them
+to this annotation set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Kinasedotcom.all_complexes">
+<span class="sig-name descname"><span class="pre">all_complexes</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Kinasedotcom.all_complexes" title="Link to this definition">§</a></dt>
+<dd><p>All protein complexes annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Kinasedotcom.all_entities">
+<span class="sig-name descname"><span class="pre">all_entities</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Kinasedotcom.all_entities" title="Link to this definition">§</a></dt>
+<dd><p>All entities annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Kinasedotcom.all_mirnas">
+<span class="sig-name descname"><span class="pre">all_mirnas</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Kinasedotcom.all_mirnas" title="Link to this definition">§</a></dt>
+<dd><p>All miRNAs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Kinasedotcom.all_proteins">
+<span class="sig-name descname"><span class="pre">all_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Kinasedotcom.all_proteins" title="Link to this definition">§</a></dt>
+<dd><p>All UniProt IDs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Kinasedotcom.all_refs">
+<span class="sig-name descname"><span class="pre">all_refs</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Kinasedotcom.all_refs" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects the references
+across all records. Returns <em>list</em>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Kinasedotcom.annotate_complex">
+<span class="sig-name descname"><span class="pre">annotate_complex</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cplex</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Kinasedotcom.annotate_complex" title="Link to this definition">§</a></dt>
+<dd><p>Infers annotations for a single complex.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Kinasedotcom.browse">
+<span class="sig-name descname"><span class="pre">browse</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">field</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">start</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Kinasedotcom.browse" title="Link to this definition">§</a></dt>
+<dd><p>Print gene information as a table.</p>
+<p>Presents information about annotation categories as ascii tables
+printed in the terminal. If one category provided, prints one table.
+If multiple categories provided, prints a table for each of them one
+by one proceeding to the next one once you hit return. If no categories
+provided goes through all levels of the primary category.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>field:</dt><dd><p>The field to browse categories by.</p>
+<ul class="simple">
+<li><p>If None the primary field will be selected.
+If this annotation resource doesn’t have fields, all proteins
+will be presented as one single category.</p></li>
+<li><p>If a string it will be considered a field name and it will
+browse through all levels of this field.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">list</span></code>, set or tuple, it will be considered either a
+<code class="docutils literal notranslate"><span class="pre">list</span></code> of field names or a list of values from the primary
+field. In the former case all combinations of the values of
+the fields will be presented, in the latter case the browsing
+will be limited to the levels of the primary field contained
+in <code class="docutils literal notranslate"><span class="pre">field</span></code>.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">dict</span></code>, keys are supposed to be field names and values
+as list of levels. If any of the values are None, all levels
+from that field will be used.</p></li>
+</ul>
+</dd>
+<dt>start:</dt><dd><p>Start browsing from this category. E.g. if there are 500
+categories and start is 250 it will skip everything before the
+250th.</p>
+</dd>
+<dt>kwargs:</dt><dd><p>Passed to <code class="docutils literal notranslate"><span class="pre">pypath.utils.uniprot.info</span></code>.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Kinasedotcom.complex_inference">
+<span class="sig-name descname"><span class="pre">complex_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Kinasedotcom.complex_inference" title="Link to this definition">§</a></dt>
+<dd><p>Annotates all complexes in <cite>complexes</cite>, by default in the default
+complex database (existing in the <cite>complex</cite> module or generated
+on demand according to the module’s current settings).</p>
+<dl class="field-list simple">
+<dt class="field-odd">Returns<span class="colon">:</span></dt>
+<dd class="field-odd"><p><ul class="simple">
+<li><p><em>Dict with complexes as keys and sets of annotations as values.</em></p></li>
+<li><p><em>Complexes with no valid information in this annotation resource</em></p></li>
+<li><p><em>won’t be in the dict.</em></p></li>
+</ul>
+</p>
+</dd>
+<dt class="field-even">Parameters<span class="colon">:</span></dt>
+<dd class="field-even"><p><strong>complexes</strong> (<em>iterable</em>) – Iterable yielding complexes.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Kinasedotcom.coverage">
+<span class="sig-name descname"><span class="pre">coverage</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">other</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Kinasedotcom.coverage" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the coverage of the annotation i.e. the proportion of
+entities having at least one record in this annotation resource
+for an arbitrary set of entities.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Kinasedotcom.curation_effort">
+<span class="sig-name descname"><span class="pre">curation_effort</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Kinasedotcom.curation_effort" title="Link to this definition">§</a></dt>
+<dd><p>Counts the reference-record pairs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Kinasedotcom.get_names">
+<span class="sig-name descname"><span class="pre">get_names</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Kinasedotcom.get_names" title="Link to this definition">§</a></dt>
+<dd><p>Returns the list of field names in the records. The annotation
+consists of uniform records and each entity might be annotated
+with one or more records. Each record is a tuple of fields, for
+example <code class="docutils literal notranslate"><span class="pre">('cell_type',</span> <span class="pre">'expression_level',</span> <span class="pre">'score')</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Kinasedotcom.get_reference_set">
+<em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">get_reference_set</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">proteins</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">swissprot_only</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Kinasedotcom.get_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the reference set i.e. the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Kinasedotcom.get_subset">
+<span class="sig-name descname"><span class="pre">get_subset</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Kinasedotcom.get_subset" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Kinasedotcom.get_subset_bool_array">
+<span class="sig-name descname"><span class="pre">get_subset_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Kinasedotcom.get_subset_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a boolean vector with True and False values for each entity
+in the reference set. The values represent presence absence data
+in the simplest case, but by providing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> any kind of matching
+and filtering is possible. <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> are passed to the <code class="docutils literal notranslate"><span class="pre">select</span></code>
+method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Kinasedotcom.get_values">
+<span class="sig-name descname"><span class="pre">get_values</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">exclude_none</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Kinasedotcom.get_values" title="Link to this definition">§</a></dt>
+<dd><p>Returns the set of all possible values of a field. E.g. if the
+records of this annotation have a field <code class="docutils literal notranslate"><span class="pre">cell_type</span></code> then calling
+this method can tell you that across all records the values of
+this field might be <code class="docutils literal notranslate"><span class="pre">{'macrophage',</span> <span class="pre">'epithelial_cell',</span> <span class="pre">...}</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Kinasedotcom.labels">
+<span class="sig-name descname"><span class="pre">labels</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Kinasedotcom.labels" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Kinasedotcom.load">
+<span class="sig-name descname"><span class="pre">load</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Kinasedotcom.load" title="Link to this definition">§</a></dt>
+<dd><p>Loads the annotation data by calling the input method.
+Infers annotations for complexes in the complex database if
+py:attr:<code class="docutils literal notranslate"><span class="pre">infer_complexes</span></code> is True.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Kinasedotcom.load_data">
+<span class="sig-name descname"><span class="pre">load_data</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Kinasedotcom.load_data" title="Link to this definition">§</a></dt>
+<dd><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Kinasedotcom.load_proteins">
+<span class="sig-name descname"><span class="pre">load_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Kinasedotcom.load_proteins" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a set of all UniProt IDs to have a base set of the entire
+proteome.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Kinasedotcom.make_df">
+<span class="sig-name descname"><span class="pre">make_df</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">rebuild</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Kinasedotcom.make_df" title="Link to this definition">§</a></dt>
+<dd><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.
+The data frame will be assigned to :py:attr``df``.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Kinasedotcom.numof_entities">
+<span class="sig-name descname"><span class="pre">numof_entities</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Kinasedotcom.numof_entities" title="Link to this definition">§</a></dt>
+<dd><p>The number of annotated entities in the resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Kinasedotcom.numof_records">
+<span class="sig-name descname"><span class="pre">numof_records</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Kinasedotcom.numof_records" title="Link to this definition">§</a></dt>
+<dd><p>The total number of annotation records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Kinasedotcom.numof_references">
+<span class="sig-name descname"><span class="pre">numof_references</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Kinasedotcom.numof_references" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects and counts the
+references across all records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Kinasedotcom.process">
+<span class="sig-name descname"><span class="pre">process</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Kinasedotcom.process" title="Link to this definition">§</a></dt>
+<dd><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Kinasedotcom.reload">
+<span class="sig-name descname"><span class="pre">reload</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Kinasedotcom.reload" title="Link to this definition">§</a></dt>
+<dd><p>Reloads the object from the module level.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Kinasedotcom.select">
+<span class="sig-name descname"><span class="pre">select</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Kinasedotcom.select" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Kinasedotcom.set_method">
+<span class="sig-name descname"><span class="pre">set_method</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Kinasedotcom.set_method" title="Link to this definition">§</a></dt>
+<dd><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if
+necessary.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Kinasedotcom.set_reference_set">
+<span class="sig-name descname"><span class="pre">set_reference_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Kinasedotcom.set_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Assigns the reference set to the :py:attr``reference_set`` attribute.
+The reference set is the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Kinasedotcom.show">
+<span class="sig-name descname"><span class="pre">show</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">table_param</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Kinasedotcom.show" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic
+information from the UniProt datasheets.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Kinasedotcom.subset_intersection">
+<span class="sig-name descname"><span class="pre">subset_intersection</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">universe</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Kinasedotcom.subset_intersection" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the proportion of entities in a subset occuring in the
+set <code class="docutils literal notranslate"><span class="pre">universe</span></code>. The subset is selected by passing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> to the
+<code class="docutils literal notranslate"><span class="pre">select</span></code> method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Kinasedotcom.to_array">
+<span class="sig-name descname"><span class="pre">to_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_fields</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Kinasedotcom.to_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns an entity vs feature array. In case of more complex
+annotations this might be huge.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Kinasedotcom.to_bool_array">
+<span class="sig-name descname"><span class="pre">to_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Kinasedotcom.to_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a presence/absence boolean array for a reference set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Kinasedotcom.to_set">
+<span class="sig-name descname"><span class="pre">to_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Kinasedotcom.to_set" title="Link to this definition">§</a></dt>
+<dd><p>Returns the entities present in this annotation resource as a set.</p>
+</dd></dl>
+
+</dd></dl>
+
+</section>
+
+
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+  <section id="pypath-core-annot-kirouac2010">
+<h1>pypath.core.annot.Kirouac2010<a class="headerlink" href="#pypath-core-annot-kirouac2010" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.core.annot.Kirouac2010">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.core.annot.</span></span><span class="sig-name descname"><span class="pre">Kirouac2010</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">load_sources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#Kirouac2010"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.Kirouac2010" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <a class="reference internal" href="pypath.core.annot.LigandReceptor.html#pypath.core.annot.LigandReceptor" title="pypath.core.annot.LigandReceptor"><code class="xref py py-class docutils literal notranslate"><span class="pre">LigandReceptor</span></code></a></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Kirouac2010.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">load_sources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#Kirouac2010.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.Kirouac2010.__init__" title="Link to this definition">§</a></dt>
+<dd><p>Represents annotations for a set of proteins.
+Loads the data from the original resource and provides methods
+to query the annotations.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>name</strong> (<em>str</em>) – A custom name for the annotation resource.</p></li>
+<li><p><strong>ncbi_tax_id</strong> (<em>int</em>) – NCBI Taxonomy identifier.</p></li>
+<li><p><strong>input_method</strong> (<em>callable</em><em>,</em><em>str</em>) – Either a callable or the name of a method in any submodules of
+the <code class="docutils literal notranslate"><span class="pre">pypath.inputs</span></code>  module. Should return a dict with
+UniProt IDs as keys or an object suitable for <code class="docutils literal notranslate"><span class="pre">process_method</span></code>.</p></li>
+<li><p><strong>input_args</strong> (<em>dict</em>) – Arguments for the <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Kirouac2010.__init__" title="pypath.core.annot.Kirouac2010.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>([load_sources])</p></td>
+<td><p>Represents annotations for a set of proteins.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Kirouac2010.add_complexes_by_inference" title="pypath.core.annot.Kirouac2010.add_complexes_by_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">add_complexes_by_inference</span></code></a>([complexes])</p></td>
+<td><p>Creates complex annotations by in silico inference and adds them to this annotation set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Kirouac2010.all_complexes" title="pypath.core.annot.Kirouac2010.all_complexes"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_complexes</span></code></a>()</p></td>
+<td><p>All protein complexes annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Kirouac2010.all_entities" title="pypath.core.annot.Kirouac2010.all_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_entities</span></code></a>([entity_types])</p></td>
+<td><p>All entities annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Kirouac2010.all_mirnas" title="pypath.core.annot.Kirouac2010.all_mirnas"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_mirnas</span></code></a>()</p></td>
+<td><p>All miRNAs annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Kirouac2010.all_proteins" title="pypath.core.annot.Kirouac2010.all_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_proteins</span></code></a>()</p></td>
+<td><p>All UniProt IDs annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Kirouac2010.all_refs" title="pypath.core.annot.Kirouac2010.all_refs"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_refs</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Kirouac2010.annotate_complex" title="pypath.core.annot.Kirouac2010.annotate_complex"><code class="xref py py-obj docutils literal notranslate"><span class="pre">annotate_complex</span></code></a>(cplex)</p></td>
+<td><p>Infers annotations for a single complex.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Kirouac2010.browse" title="pypath.core.annot.Kirouac2010.browse"><code class="xref py py-obj docutils literal notranslate"><span class="pre">browse</span></code></a>([field, start])</p></td>
+<td><p>Print gene information as a table.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Kirouac2010.complex_inference" title="pypath.core.annot.Kirouac2010.complex_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">complex_inference</span></code></a>([complexes])</p></td>
+<td><p>Annotates all complexes in <cite>complexes</cite>, by default in the default complex database (existing in the <cite>complex</cite> module or generated on demand according to the module's current settings).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Kirouac2010.coverage" title="pypath.core.annot.Kirouac2010.coverage"><code class="xref py py-obj docutils literal notranslate"><span class="pre">coverage</span></code></a>(other)</p></td>
+<td><p>Calculates the coverage of the annotation i.e. the proportion of entities having at least one record in this annotation resource for an arbitrary set of entities.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Kirouac2010.curation_effort" title="pypath.core.annot.Kirouac2010.curation_effort"><code class="xref py py-obj docutils literal notranslate"><span class="pre">curation_effort</span></code></a>()</p></td>
+<td><p>Counts the reference-record pairs.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">from_dump</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_entity_type</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Kirouac2010.get_names" title="pypath.core.annot.Kirouac2010.get_names"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_names</span></code></a>()</p></td>
+<td><p>Returns the list of field names in the records.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Kirouac2010.get_reference_set" title="pypath.core.annot.Kirouac2010.get_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_reference_set</span></code></a>([proteins, complexes, ...])</p></td>
+<td><p>Retrieves the reference set i.e. the set of all entities which potentially have annotation in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Kirouac2010.get_subset" title="pypath.core.annot.Kirouac2010.get_subset"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Kirouac2010.get_subset_bool_array" title="pypath.core.annot.Kirouac2010.get_subset_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset_bool_array</span></code></a>([reference_set])</p></td>
+<td><p>Returns a boolean vector with True and False values for each entity in the reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Kirouac2010.get_values" title="pypath.core.annot.Kirouac2010.get_values"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_values</span></code></a>(name[, exclude_none])</p></td>
+<td><p>Returns the set of all possible values of a field.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_complex</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_mirna</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_protein</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Kirouac2010.labels" title="pypath.core.annot.Kirouac2010.labels"><code class="xref py py-obj docutils literal notranslate"><span class="pre">labels</span></code></a>([method])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Kirouac2010.load" title="pypath.core.annot.Kirouac2010.load"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load</span></code></a>()</p></td>
+<td><p>Loads the annotation data by calling the input method.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Kirouac2010.load_data" title="pypath.core.annot.Kirouac2010.load_data"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_data</span></code></a>()</p></td>
+<td><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Kirouac2010.load_proteins" title="pypath.core.annot.Kirouac2010.load_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_proteins</span></code></a>()</p></td>
+<td><p>Retrieves a set of all UniProt IDs to have a base set of the entire proteome.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Kirouac2010.make_df" title="pypath.core.annot.Kirouac2010.make_df"><code class="xref py py-obj docutils literal notranslate"><span class="pre">make_df</span></code></a>([rebuild])</p></td>
+<td><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complex_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Kirouac2010.numof_entities" title="pypath.core.annot.Kirouac2010.numof_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_entities</span></code></a>()</p></td>
+<td><p>The number of annotated entities in the resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirna_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirnas</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_protein_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_proteins</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Kirouac2010.numof_records" title="pypath.core.annot.Kirouac2010.numof_records"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_records</span></code></a>([entity_types])</p></td>
+<td><p>The total number of annotation records.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Kirouac2010.numof_references" title="pypath.core.annot.Kirouac2010.numof_references"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_references</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Kirouac2010.process" title="pypath.core.annot.Kirouac2010.process"><code class="xref py py-obj docutils literal notranslate"><span class="pre">process</span></code></a>()</p></td>
+<td><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">proportion</span></code>(other)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Kirouac2010.reload" title="pypath.core.annot.Kirouac2010.reload"><code class="xref py py-obj docutils literal notranslate"><span class="pre">reload</span></code></a>()</p></td>
+<td><p>Reloads the object from the module level.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">save_to_pickle</span></code>(pickle_file)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Kirouac2010.select" title="pypath.core.annot.Kirouac2010.select"><code class="xref py py-obj docutils literal notranslate"><span class="pre">select</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Kirouac2010.set_method" title="pypath.core.annot.Kirouac2010.set_method"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_method</span></code></a>()</p></td>
+<td><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if necessary.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Kirouac2010.set_reference_set" title="pypath.core.annot.Kirouac2010.set_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_reference_set</span></code></a>()</p></td>
+<td><p>Assigns the reference set to the :py:attr``reference_set`` attribute.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Kirouac2010.show" title="pypath.core.annot.Kirouac2010.show"><code class="xref py py-obj docutils literal notranslate"><span class="pre">show</span></code></a>([method, table_param])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic information from the UniProt datasheets.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Kirouac2010.subset_intersection" title="pypath.core.annot.Kirouac2010.subset_intersection"><code class="xref py py-obj docutils literal notranslate"><span class="pre">subset_intersection</span></code></a>(universe, **kwargs)</p></td>
+<td><p>Calculates the proportion of entities in a subset occuring in the set <code class="docutils literal notranslate"><span class="pre">universe</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Kirouac2010.to_array" title="pypath.core.annot.Kirouac2010.to_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_array</span></code></a>([reference_set, use_fields])</p></td>
+<td><p>Returns an entity vs feature array.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Kirouac2010.to_bool_array" title="pypath.core.annot.Kirouac2010.to_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_bool_array</span></code></a>(reference_set)</p></td>
+<td><p>Returns a presence/absence boolean array for a reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Kirouac2010.to_set" title="pypath.core.annot.Kirouac2010.to_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_set</span></code></a>()</p></td>
+<td><p>Returns the entities present in this annotation resource as a set.</p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Attributes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_fields</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">summary</span></code></p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Kirouac2010.add_complexes_by_inference">
+<span class="sig-name descname"><span class="pre">add_complexes_by_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Kirouac2010.add_complexes_by_inference" title="Link to this definition">§</a></dt>
+<dd><p>Creates complex annotations by in silico inference and adds them
+to this annotation set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Kirouac2010.all_complexes">
+<span class="sig-name descname"><span class="pre">all_complexes</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Kirouac2010.all_complexes" title="Link to this definition">§</a></dt>
+<dd><p>All protein complexes annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Kirouac2010.all_entities">
+<span class="sig-name descname"><span class="pre">all_entities</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Kirouac2010.all_entities" title="Link to this definition">§</a></dt>
+<dd><p>All entities annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Kirouac2010.all_mirnas">
+<span class="sig-name descname"><span class="pre">all_mirnas</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Kirouac2010.all_mirnas" title="Link to this definition">§</a></dt>
+<dd><p>All miRNAs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Kirouac2010.all_proteins">
+<span class="sig-name descname"><span class="pre">all_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Kirouac2010.all_proteins" title="Link to this definition">§</a></dt>
+<dd><p>All UniProt IDs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Kirouac2010.all_refs">
+<span class="sig-name descname"><span class="pre">all_refs</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Kirouac2010.all_refs" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects the references
+across all records. Returns <em>list</em>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Kirouac2010.annotate_complex">
+<span class="sig-name descname"><span class="pre">annotate_complex</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cplex</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Kirouac2010.annotate_complex" title="Link to this definition">§</a></dt>
+<dd><p>Infers annotations for a single complex.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Kirouac2010.browse">
+<span class="sig-name descname"><span class="pre">browse</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">field</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">start</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Kirouac2010.browse" title="Link to this definition">§</a></dt>
+<dd><p>Print gene information as a table.</p>
+<p>Presents information about annotation categories as ascii tables
+printed in the terminal. If one category provided, prints one table.
+If multiple categories provided, prints a table for each of them one
+by one proceeding to the next one once you hit return. If no categories
+provided goes through all levels of the primary category.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>field:</dt><dd><p>The field to browse categories by.</p>
+<ul class="simple">
+<li><p>If None the primary field will be selected.
+If this annotation resource doesn’t have fields, all proteins
+will be presented as one single category.</p></li>
+<li><p>If a string it will be considered a field name and it will
+browse through all levels of this field.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">list</span></code>, set or tuple, it will be considered either a
+<code class="docutils literal notranslate"><span class="pre">list</span></code> of field names or a list of values from the primary
+field. In the former case all combinations of the values of
+the fields will be presented, in the latter case the browsing
+will be limited to the levels of the primary field contained
+in <code class="docutils literal notranslate"><span class="pre">field</span></code>.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">dict</span></code>, keys are supposed to be field names and values
+as list of levels. If any of the values are None, all levels
+from that field will be used.</p></li>
+</ul>
+</dd>
+<dt>start:</dt><dd><p>Start browsing from this category. E.g. if there are 500
+categories and start is 250 it will skip everything before the
+250th.</p>
+</dd>
+<dt>kwargs:</dt><dd><p>Passed to <code class="docutils literal notranslate"><span class="pre">pypath.utils.uniprot.info</span></code>.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Kirouac2010.complex_inference">
+<span class="sig-name descname"><span class="pre">complex_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Kirouac2010.complex_inference" title="Link to this definition">§</a></dt>
+<dd><p>Annotates all complexes in <cite>complexes</cite>, by default in the default
+complex database (existing in the <cite>complex</cite> module or generated
+on demand according to the module’s current settings).</p>
+<dl class="field-list simple">
+<dt class="field-odd">Returns<span class="colon">:</span></dt>
+<dd class="field-odd"><p><ul class="simple">
+<li><p><em>Dict with complexes as keys and sets of annotations as values.</em></p></li>
+<li><p><em>Complexes with no valid information in this annotation resource</em></p></li>
+<li><p><em>won’t be in the dict.</em></p></li>
+</ul>
+</p>
+</dd>
+<dt class="field-even">Parameters<span class="colon">:</span></dt>
+<dd class="field-even"><p><strong>complexes</strong> (<em>iterable</em>) – Iterable yielding complexes.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Kirouac2010.coverage">
+<span class="sig-name descname"><span class="pre">coverage</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">other</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Kirouac2010.coverage" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the coverage of the annotation i.e. the proportion of
+entities having at least one record in this annotation resource
+for an arbitrary set of entities.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Kirouac2010.curation_effort">
+<span class="sig-name descname"><span class="pre">curation_effort</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Kirouac2010.curation_effort" title="Link to this definition">§</a></dt>
+<dd><p>Counts the reference-record pairs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Kirouac2010.get_names">
+<span class="sig-name descname"><span class="pre">get_names</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Kirouac2010.get_names" title="Link to this definition">§</a></dt>
+<dd><p>Returns the list of field names in the records. The annotation
+consists of uniform records and each entity might be annotated
+with one or more records. Each record is a tuple of fields, for
+example <code class="docutils literal notranslate"><span class="pre">('cell_type',</span> <span class="pre">'expression_level',</span> <span class="pre">'score')</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Kirouac2010.get_reference_set">
+<em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">get_reference_set</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">proteins</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">swissprot_only</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Kirouac2010.get_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the reference set i.e. the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Kirouac2010.get_subset">
+<span class="sig-name descname"><span class="pre">get_subset</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Kirouac2010.get_subset" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Kirouac2010.get_subset_bool_array">
+<span class="sig-name descname"><span class="pre">get_subset_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Kirouac2010.get_subset_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a boolean vector with True and False values for each entity
+in the reference set. The values represent presence absence data
+in the simplest case, but by providing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> any kind of matching
+and filtering is possible. <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> are passed to the <code class="docutils literal notranslate"><span class="pre">select</span></code>
+method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Kirouac2010.get_values">
+<span class="sig-name descname"><span class="pre">get_values</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">exclude_none</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Kirouac2010.get_values" title="Link to this definition">§</a></dt>
+<dd><p>Returns the set of all possible values of a field. E.g. if the
+records of this annotation have a field <code class="docutils literal notranslate"><span class="pre">cell_type</span></code> then calling
+this method can tell you that across all records the values of
+this field might be <code class="docutils literal notranslate"><span class="pre">{'macrophage',</span> <span class="pre">'epithelial_cell',</span> <span class="pre">...}</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Kirouac2010.labels">
+<span class="sig-name descname"><span class="pre">labels</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Kirouac2010.labels" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Kirouac2010.load">
+<span class="sig-name descname"><span class="pre">load</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Kirouac2010.load" title="Link to this definition">§</a></dt>
+<dd><p>Loads the annotation data by calling the input method.
+Infers annotations for complexes in the complex database if
+py:attr:<code class="docutils literal notranslate"><span class="pre">infer_complexes</span></code> is True.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Kirouac2010.load_data">
+<span class="sig-name descname"><span class="pre">load_data</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Kirouac2010.load_data" title="Link to this definition">§</a></dt>
+<dd><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Kirouac2010.load_proteins">
+<span class="sig-name descname"><span class="pre">load_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Kirouac2010.load_proteins" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a set of all UniProt IDs to have a base set of the entire
+proteome.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Kirouac2010.make_df">
+<span class="sig-name descname"><span class="pre">make_df</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">rebuild</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Kirouac2010.make_df" title="Link to this definition">§</a></dt>
+<dd><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.
+The data frame will be assigned to :py:attr``df``.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Kirouac2010.numof_entities">
+<span class="sig-name descname"><span class="pre">numof_entities</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Kirouac2010.numof_entities" title="Link to this definition">§</a></dt>
+<dd><p>The number of annotated entities in the resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Kirouac2010.numof_records">
+<span class="sig-name descname"><span class="pre">numof_records</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Kirouac2010.numof_records" title="Link to this definition">§</a></dt>
+<dd><p>The total number of annotation records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Kirouac2010.numof_references">
+<span class="sig-name descname"><span class="pre">numof_references</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Kirouac2010.numof_references" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects and counts the
+references across all records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Kirouac2010.process">
+<span class="sig-name descname"><span class="pre">process</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Kirouac2010.process" title="Link to this definition">§</a></dt>
+<dd><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Kirouac2010.reload">
+<span class="sig-name descname"><span class="pre">reload</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Kirouac2010.reload" title="Link to this definition">§</a></dt>
+<dd><p>Reloads the object from the module level.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Kirouac2010.select">
+<span class="sig-name descname"><span class="pre">select</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Kirouac2010.select" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Kirouac2010.set_method">
+<span class="sig-name descname"><span class="pre">set_method</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Kirouac2010.set_method" title="Link to this definition">§</a></dt>
+<dd><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if
+necessary.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Kirouac2010.set_reference_set">
+<span class="sig-name descname"><span class="pre">set_reference_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Kirouac2010.set_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Assigns the reference set to the :py:attr``reference_set`` attribute.
+The reference set is the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Kirouac2010.show">
+<span class="sig-name descname"><span class="pre">show</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">table_param</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Kirouac2010.show" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic
+information from the UniProt datasheets.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Kirouac2010.subset_intersection">
+<span class="sig-name descname"><span class="pre">subset_intersection</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">universe</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Kirouac2010.subset_intersection" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the proportion of entities in a subset occuring in the
+set <code class="docutils literal notranslate"><span class="pre">universe</span></code>. The subset is selected by passing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> to the
+<code class="docutils literal notranslate"><span class="pre">select</span></code> method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Kirouac2010.to_array">
+<span class="sig-name descname"><span class="pre">to_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_fields</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Kirouac2010.to_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns an entity vs feature array. In case of more complex
+annotations this might be huge.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Kirouac2010.to_bool_array">
+<span class="sig-name descname"><span class="pre">to_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Kirouac2010.to_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a presence/absence boolean array for a reference set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Kirouac2010.to_set">
+<span class="sig-name descname"><span class="pre">to_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Kirouac2010.to_set" title="Link to this definition">§</a></dt>
+<dd><p>Returns the entities present in this annotation resource as a set.</p>
+</dd></dl>
+
+</dd></dl>
+
+</section>
+
+
+                </article>
+              
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+  <section id="pypath-core-annot-lambert2018">
+<h1>pypath.core.annot.Lambert2018<a class="headerlink" href="#pypath-core-annot-lambert2018" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.core.annot.Lambert2018">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.core.annot.</span></span><span class="sig-name descname"><span class="pre">Lambert2018</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#Lambert2018"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.Lambert2018" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <a class="reference internal" href="pypath.core.annot.AnnotationBase.html#pypath.core.annot.AnnotationBase" title="pypath.core.annot.AnnotationBase"><code class="xref py py-class docutils literal notranslate"><span class="pre">AnnotationBase</span></code></a></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Lambert2018.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#Lambert2018.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.Lambert2018.__init__" title="Link to this definition">§</a></dt>
+<dd><p>Cell type markers from PanglaoDB</p>
+</dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Lambert2018.__init__" title="pypath.core.annot.Lambert2018.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>([ncbi_tax_id])</p></td>
+<td><p>Cell type markers from PanglaoDB</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Lambert2018.add_complexes_by_inference" title="pypath.core.annot.Lambert2018.add_complexes_by_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">add_complexes_by_inference</span></code></a>([complexes])</p></td>
+<td><p>Creates complex annotations by in silico inference and adds them to this annotation set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Lambert2018.all_complexes" title="pypath.core.annot.Lambert2018.all_complexes"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_complexes</span></code></a>()</p></td>
+<td><p>All protein complexes annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Lambert2018.all_entities" title="pypath.core.annot.Lambert2018.all_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_entities</span></code></a>([entity_types])</p></td>
+<td><p>All entities annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Lambert2018.all_mirnas" title="pypath.core.annot.Lambert2018.all_mirnas"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_mirnas</span></code></a>()</p></td>
+<td><p>All miRNAs annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Lambert2018.all_proteins" title="pypath.core.annot.Lambert2018.all_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_proteins</span></code></a>()</p></td>
+<td><p>All UniProt IDs annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Lambert2018.all_refs" title="pypath.core.annot.Lambert2018.all_refs"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_refs</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Lambert2018.annotate_complex" title="pypath.core.annot.Lambert2018.annotate_complex"><code class="xref py py-obj docutils literal notranslate"><span class="pre">annotate_complex</span></code></a>(cplex)</p></td>
+<td><p>Infers annotations for a single complex.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Lambert2018.browse" title="pypath.core.annot.Lambert2018.browse"><code class="xref py py-obj docutils literal notranslate"><span class="pre">browse</span></code></a>([field, start])</p></td>
+<td><p>Print gene information as a table.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Lambert2018.complex_inference" title="pypath.core.annot.Lambert2018.complex_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">complex_inference</span></code></a>([complexes])</p></td>
+<td><p>Annotates all complexes in <cite>complexes</cite>, by default in the default complex database (existing in the <cite>complex</cite> module or generated on demand according to the module's current settings).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Lambert2018.coverage" title="pypath.core.annot.Lambert2018.coverage"><code class="xref py py-obj docutils literal notranslate"><span class="pre">coverage</span></code></a>(other)</p></td>
+<td><p>Calculates the coverage of the annotation i.e. the proportion of entities having at least one record in this annotation resource for an arbitrary set of entities.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Lambert2018.curation_effort" title="pypath.core.annot.Lambert2018.curation_effort"><code class="xref py py-obj docutils literal notranslate"><span class="pre">curation_effort</span></code></a>()</p></td>
+<td><p>Counts the reference-record pairs.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">from_dump</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_entity_type</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Lambert2018.get_names" title="pypath.core.annot.Lambert2018.get_names"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_names</span></code></a>()</p></td>
+<td><p>Returns the list of field names in the records.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Lambert2018.get_reference_set" title="pypath.core.annot.Lambert2018.get_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_reference_set</span></code></a>([proteins, complexes, ...])</p></td>
+<td><p>Retrieves the reference set i.e. the set of all entities which potentially have annotation in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Lambert2018.get_subset" title="pypath.core.annot.Lambert2018.get_subset"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Lambert2018.get_subset_bool_array" title="pypath.core.annot.Lambert2018.get_subset_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset_bool_array</span></code></a>([reference_set])</p></td>
+<td><p>Returns a boolean vector with True and False values for each entity in the reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Lambert2018.get_values" title="pypath.core.annot.Lambert2018.get_values"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_values</span></code></a>(name[, exclude_none])</p></td>
+<td><p>Returns the set of all possible values of a field.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_complex</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_mirna</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_protein</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Lambert2018.labels" title="pypath.core.annot.Lambert2018.labels"><code class="xref py py-obj docutils literal notranslate"><span class="pre">labels</span></code></a>([method])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Lambert2018.load" title="pypath.core.annot.Lambert2018.load"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load</span></code></a>()</p></td>
+<td><p>Loads the annotation data by calling the input method.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Lambert2018.load_data" title="pypath.core.annot.Lambert2018.load_data"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_data</span></code></a>()</p></td>
+<td><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Lambert2018.load_proteins" title="pypath.core.annot.Lambert2018.load_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_proteins</span></code></a>()</p></td>
+<td><p>Retrieves a set of all UniProt IDs to have a base set of the entire proteome.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Lambert2018.make_df" title="pypath.core.annot.Lambert2018.make_df"><code class="xref py py-obj docutils literal notranslate"><span class="pre">make_df</span></code></a>([rebuild])</p></td>
+<td><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complex_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Lambert2018.numof_entities" title="pypath.core.annot.Lambert2018.numof_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_entities</span></code></a>()</p></td>
+<td><p>The number of annotated entities in the resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirna_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirnas</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_protein_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_proteins</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Lambert2018.numof_records" title="pypath.core.annot.Lambert2018.numof_records"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_records</span></code></a>([entity_types])</p></td>
+<td><p>The total number of annotation records.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Lambert2018.numof_references" title="pypath.core.annot.Lambert2018.numof_references"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_references</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Lambert2018.process" title="pypath.core.annot.Lambert2018.process"><code class="xref py py-obj docutils literal notranslate"><span class="pre">process</span></code></a>()</p></td>
+<td><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">proportion</span></code>(other)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Lambert2018.reload" title="pypath.core.annot.Lambert2018.reload"><code class="xref py py-obj docutils literal notranslate"><span class="pre">reload</span></code></a>()</p></td>
+<td><p>Reloads the object from the module level.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">save_to_pickle</span></code>(pickle_file)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Lambert2018.select" title="pypath.core.annot.Lambert2018.select"><code class="xref py py-obj docutils literal notranslate"><span class="pre">select</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Lambert2018.set_method" title="pypath.core.annot.Lambert2018.set_method"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_method</span></code></a>()</p></td>
+<td><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if necessary.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Lambert2018.set_reference_set" title="pypath.core.annot.Lambert2018.set_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_reference_set</span></code></a>()</p></td>
+<td><p>Assigns the reference set to the :py:attr``reference_set`` attribute.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Lambert2018.show" title="pypath.core.annot.Lambert2018.show"><code class="xref py py-obj docutils literal notranslate"><span class="pre">show</span></code></a>([method, table_param])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic information from the UniProt datasheets.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Lambert2018.subset_intersection" title="pypath.core.annot.Lambert2018.subset_intersection"><code class="xref py py-obj docutils literal notranslate"><span class="pre">subset_intersection</span></code></a>(universe, **kwargs)</p></td>
+<td><p>Calculates the proportion of entities in a subset occuring in the set <code class="docutils literal notranslate"><span class="pre">universe</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Lambert2018.to_array" title="pypath.core.annot.Lambert2018.to_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_array</span></code></a>([reference_set, use_fields])</p></td>
+<td><p>Returns an entity vs feature array.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Lambert2018.to_bool_array" title="pypath.core.annot.Lambert2018.to_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_bool_array</span></code></a>(reference_set)</p></td>
+<td><p>Returns a presence/absence boolean array for a reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Lambert2018.to_set" title="pypath.core.annot.Lambert2018.to_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_set</span></code></a>()</p></td>
+<td><p>Returns the entities present in this annotation resource as a set.</p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Attributes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_fields</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">summary</span></code></p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Lambert2018.add_complexes_by_inference">
+<span class="sig-name descname"><span class="pre">add_complexes_by_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Lambert2018.add_complexes_by_inference" title="Link to this definition">§</a></dt>
+<dd><p>Creates complex annotations by in silico inference and adds them
+to this annotation set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Lambert2018.all_complexes">
+<span class="sig-name descname"><span class="pre">all_complexes</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Lambert2018.all_complexes" title="Link to this definition">§</a></dt>
+<dd><p>All protein complexes annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Lambert2018.all_entities">
+<span class="sig-name descname"><span class="pre">all_entities</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Lambert2018.all_entities" title="Link to this definition">§</a></dt>
+<dd><p>All entities annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Lambert2018.all_mirnas">
+<span class="sig-name descname"><span class="pre">all_mirnas</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Lambert2018.all_mirnas" title="Link to this definition">§</a></dt>
+<dd><p>All miRNAs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Lambert2018.all_proteins">
+<span class="sig-name descname"><span class="pre">all_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Lambert2018.all_proteins" title="Link to this definition">§</a></dt>
+<dd><p>All UniProt IDs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Lambert2018.all_refs">
+<span class="sig-name descname"><span class="pre">all_refs</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Lambert2018.all_refs" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects the references
+across all records. Returns <em>list</em>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Lambert2018.annotate_complex">
+<span class="sig-name descname"><span class="pre">annotate_complex</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cplex</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Lambert2018.annotate_complex" title="Link to this definition">§</a></dt>
+<dd><p>Infers annotations for a single complex.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Lambert2018.browse">
+<span class="sig-name descname"><span class="pre">browse</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">field</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">start</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Lambert2018.browse" title="Link to this definition">§</a></dt>
+<dd><p>Print gene information as a table.</p>
+<p>Presents information about annotation categories as ascii tables
+printed in the terminal. If one category provided, prints one table.
+If multiple categories provided, prints a table for each of them one
+by one proceeding to the next one once you hit return. If no categories
+provided goes through all levels of the primary category.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>field:</dt><dd><p>The field to browse categories by.</p>
+<ul class="simple">
+<li><p>If None the primary field will be selected.
+If this annotation resource doesn’t have fields, all proteins
+will be presented as one single category.</p></li>
+<li><p>If a string it will be considered a field name and it will
+browse through all levels of this field.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">list</span></code>, set or tuple, it will be considered either a
+<code class="docutils literal notranslate"><span class="pre">list</span></code> of field names or a list of values from the primary
+field. In the former case all combinations of the values of
+the fields will be presented, in the latter case the browsing
+will be limited to the levels of the primary field contained
+in <code class="docutils literal notranslate"><span class="pre">field</span></code>.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">dict</span></code>, keys are supposed to be field names and values
+as list of levels. If any of the values are None, all levels
+from that field will be used.</p></li>
+</ul>
+</dd>
+<dt>start:</dt><dd><p>Start browsing from this category. E.g. if there are 500
+categories and start is 250 it will skip everything before the
+250th.</p>
+</dd>
+<dt>kwargs:</dt><dd><p>Passed to <code class="docutils literal notranslate"><span class="pre">pypath.utils.uniprot.info</span></code>.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Lambert2018.complex_inference">
+<span class="sig-name descname"><span class="pre">complex_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Lambert2018.complex_inference" title="Link to this definition">§</a></dt>
+<dd><p>Annotates all complexes in <cite>complexes</cite>, by default in the default
+complex database (existing in the <cite>complex</cite> module or generated
+on demand according to the module’s current settings).</p>
+<dl class="field-list simple">
+<dt class="field-odd">Returns<span class="colon">:</span></dt>
+<dd class="field-odd"><p><ul class="simple">
+<li><p><em>Dict with complexes as keys and sets of annotations as values.</em></p></li>
+<li><p><em>Complexes with no valid information in this annotation resource</em></p></li>
+<li><p><em>won’t be in the dict.</em></p></li>
+</ul>
+</p>
+</dd>
+<dt class="field-even">Parameters<span class="colon">:</span></dt>
+<dd class="field-even"><p><strong>complexes</strong> (<em>iterable</em>) – Iterable yielding complexes.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Lambert2018.coverage">
+<span class="sig-name descname"><span class="pre">coverage</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">other</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Lambert2018.coverage" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the coverage of the annotation i.e. the proportion of
+entities having at least one record in this annotation resource
+for an arbitrary set of entities.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Lambert2018.curation_effort">
+<span class="sig-name descname"><span class="pre">curation_effort</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Lambert2018.curation_effort" title="Link to this definition">§</a></dt>
+<dd><p>Counts the reference-record pairs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Lambert2018.get_names">
+<span class="sig-name descname"><span class="pre">get_names</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Lambert2018.get_names" title="Link to this definition">§</a></dt>
+<dd><p>Returns the list of field names in the records. The annotation
+consists of uniform records and each entity might be annotated
+with one or more records. Each record is a tuple of fields, for
+example <code class="docutils literal notranslate"><span class="pre">('cell_type',</span> <span class="pre">'expression_level',</span> <span class="pre">'score')</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Lambert2018.get_reference_set">
+<em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">get_reference_set</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">proteins</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">swissprot_only</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Lambert2018.get_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the reference set i.e. the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Lambert2018.get_subset">
+<span class="sig-name descname"><span class="pre">get_subset</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Lambert2018.get_subset" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Lambert2018.get_subset_bool_array">
+<span class="sig-name descname"><span class="pre">get_subset_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Lambert2018.get_subset_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a boolean vector with True and False values for each entity
+in the reference set. The values represent presence absence data
+in the simplest case, but by providing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> any kind of matching
+and filtering is possible. <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> are passed to the <code class="docutils literal notranslate"><span class="pre">select</span></code>
+method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Lambert2018.get_values">
+<span class="sig-name descname"><span class="pre">get_values</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">exclude_none</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Lambert2018.get_values" title="Link to this definition">§</a></dt>
+<dd><p>Returns the set of all possible values of a field. E.g. if the
+records of this annotation have a field <code class="docutils literal notranslate"><span class="pre">cell_type</span></code> then calling
+this method can tell you that across all records the values of
+this field might be <code class="docutils literal notranslate"><span class="pre">{'macrophage',</span> <span class="pre">'epithelial_cell',</span> <span class="pre">...}</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Lambert2018.labels">
+<span class="sig-name descname"><span class="pre">labels</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Lambert2018.labels" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Lambert2018.load">
+<span class="sig-name descname"><span class="pre">load</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Lambert2018.load" title="Link to this definition">§</a></dt>
+<dd><p>Loads the annotation data by calling the input method.
+Infers annotations for complexes in the complex database if
+py:attr:<code class="docutils literal notranslate"><span class="pre">infer_complexes</span></code> is True.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Lambert2018.load_data">
+<span class="sig-name descname"><span class="pre">load_data</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Lambert2018.load_data" title="Link to this definition">§</a></dt>
+<dd><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Lambert2018.load_proteins">
+<span class="sig-name descname"><span class="pre">load_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Lambert2018.load_proteins" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a set of all UniProt IDs to have a base set of the entire
+proteome.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Lambert2018.make_df">
+<span class="sig-name descname"><span class="pre">make_df</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">rebuild</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Lambert2018.make_df" title="Link to this definition">§</a></dt>
+<dd><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.
+The data frame will be assigned to :py:attr``df``.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Lambert2018.numof_entities">
+<span class="sig-name descname"><span class="pre">numof_entities</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Lambert2018.numof_entities" title="Link to this definition">§</a></dt>
+<dd><p>The number of annotated entities in the resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Lambert2018.numof_records">
+<span class="sig-name descname"><span class="pre">numof_records</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Lambert2018.numof_records" title="Link to this definition">§</a></dt>
+<dd><p>The total number of annotation records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Lambert2018.numof_references">
+<span class="sig-name descname"><span class="pre">numof_references</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Lambert2018.numof_references" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects and counts the
+references across all records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Lambert2018.process">
+<span class="sig-name descname"><span class="pre">process</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Lambert2018.process" title="Link to this definition">§</a></dt>
+<dd><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Lambert2018.reload">
+<span class="sig-name descname"><span class="pre">reload</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Lambert2018.reload" title="Link to this definition">§</a></dt>
+<dd><p>Reloads the object from the module level.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Lambert2018.select">
+<span class="sig-name descname"><span class="pre">select</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Lambert2018.select" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Lambert2018.set_method">
+<span class="sig-name descname"><span class="pre">set_method</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Lambert2018.set_method" title="Link to this definition">§</a></dt>
+<dd><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if
+necessary.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Lambert2018.set_reference_set">
+<span class="sig-name descname"><span class="pre">set_reference_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Lambert2018.set_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Assigns the reference set to the :py:attr``reference_set`` attribute.
+The reference set is the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Lambert2018.show">
+<span class="sig-name descname"><span class="pre">show</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">table_param</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Lambert2018.show" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic
+information from the UniProt datasheets.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Lambert2018.subset_intersection">
+<span class="sig-name descname"><span class="pre">subset_intersection</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">universe</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Lambert2018.subset_intersection" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the proportion of entities in a subset occuring in the
+set <code class="docutils literal notranslate"><span class="pre">universe</span></code>. The subset is selected by passing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> to the
+<code class="docutils literal notranslate"><span class="pre">select</span></code> method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Lambert2018.to_array">
+<span class="sig-name descname"><span class="pre">to_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_fields</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Lambert2018.to_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns an entity vs feature array. In case of more complex
+annotations this might be huge.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Lambert2018.to_bool_array">
+<span class="sig-name descname"><span class="pre">to_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Lambert2018.to_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a presence/absence boolean array for a reference set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Lambert2018.to_set">
+<span class="sig-name descname"><span class="pre">to_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Lambert2018.to_set" title="Link to this definition">§</a></dt>
+<dd><p>Returns the entities present in this annotation resource as a set.</p>
+</dd></dl>
+
+</dd></dl>
+
+</section>
+
+
+                </article>
+              
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diff --git a/api/pypath.core.annot.LigandReceptor.html b/api/pypath.core.annot.LigandReceptor.html
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+  <section id="pypath-core-annot-ligandreceptor">
+<h1>pypath.core.annot.LigandReceptor<a class="headerlink" href="#pypath-core-annot-ligandreceptor" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.core.annot.LigandReceptor">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.core.annot.</span></span><span class="sig-name descname"><span class="pre">LigandReceptor</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ligand_col</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">receptor_col</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ligand_id_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">receptor_id_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">record_processor_method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">record_extra_fields</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">record_defaults</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">extra_fields_methods</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#LigandReceptor"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.LigandReceptor" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <a class="reference internal" href="pypath.core.annot.AnnotationBase.html#pypath.core.annot.AnnotationBase" title="pypath.core.annot.AnnotationBase"><code class="xref py py-class docutils literal notranslate"><span class="pre">AnnotationBase</span></code></a></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.LigandReceptor.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ligand_col</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">receptor_col</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ligand_id_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">receptor_id_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">record_processor_method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">record_extra_fields</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">record_defaults</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">extra_fields_methods</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#LigandReceptor.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.LigandReceptor.__init__" title="Link to this definition">§</a></dt>
+<dd><p>Represents annotations for a set of proteins.
+Loads the data from the original resource and provides methods
+to query the annotations.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>name</strong> (<em>str</em>) – A custom name for the annotation resource.</p></li>
+<li><p><strong>ncbi_tax_id</strong> (<em>int</em>) – NCBI Taxonomy identifier.</p></li>
+<li><p><strong>input_method</strong> (<em>callable</em><em>,</em><em>str</em>) – Either a callable or the name of a method in any submodules of
+the <code class="docutils literal notranslate"><span class="pre">pypath.inputs</span></code>  module. Should return a dict with
+UniProt IDs as keys or an object suitable for <code class="docutils literal notranslate"><span class="pre">process_method</span></code>.</p></li>
+<li><p><strong>input_args</strong> (<em>dict</em>) – Arguments for the <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.LigandReceptor.__init__" title="pypath.core.annot.LigandReceptor.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>(name[, ligand_col, receptor_col, ...])</p></td>
+<td><p>Represents annotations for a set of proteins.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.LigandReceptor.add_complexes_by_inference" title="pypath.core.annot.LigandReceptor.add_complexes_by_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">add_complexes_by_inference</span></code></a>([complexes])</p></td>
+<td><p>Creates complex annotations by in silico inference and adds them to this annotation set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.LigandReceptor.all_complexes" title="pypath.core.annot.LigandReceptor.all_complexes"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_complexes</span></code></a>()</p></td>
+<td><p>All protein complexes annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.LigandReceptor.all_entities" title="pypath.core.annot.LigandReceptor.all_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_entities</span></code></a>([entity_types])</p></td>
+<td><p>All entities annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.LigandReceptor.all_mirnas" title="pypath.core.annot.LigandReceptor.all_mirnas"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_mirnas</span></code></a>()</p></td>
+<td><p>All miRNAs annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.LigandReceptor.all_proteins" title="pypath.core.annot.LigandReceptor.all_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_proteins</span></code></a>()</p></td>
+<td><p>All UniProt IDs annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.LigandReceptor.all_refs" title="pypath.core.annot.LigandReceptor.all_refs"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_refs</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.LigandReceptor.annotate_complex" title="pypath.core.annot.LigandReceptor.annotate_complex"><code class="xref py py-obj docutils literal notranslate"><span class="pre">annotate_complex</span></code></a>(cplex)</p></td>
+<td><p>Infers annotations for a single complex.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.LigandReceptor.browse" title="pypath.core.annot.LigandReceptor.browse"><code class="xref py py-obj docutils literal notranslate"><span class="pre">browse</span></code></a>([field, start])</p></td>
+<td><p>Print gene information as a table.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.LigandReceptor.complex_inference" title="pypath.core.annot.LigandReceptor.complex_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">complex_inference</span></code></a>([complexes])</p></td>
+<td><p>Annotates all complexes in <cite>complexes</cite>, by default in the default complex database (existing in the <cite>complex</cite> module or generated on demand according to the module's current settings).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.LigandReceptor.coverage" title="pypath.core.annot.LigandReceptor.coverage"><code class="xref py py-obj docutils literal notranslate"><span class="pre">coverage</span></code></a>(other)</p></td>
+<td><p>Calculates the coverage of the annotation i.e. the proportion of entities having at least one record in this annotation resource for an arbitrary set of entities.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.LigandReceptor.curation_effort" title="pypath.core.annot.LigandReceptor.curation_effort"><code class="xref py py-obj docutils literal notranslate"><span class="pre">curation_effort</span></code></a>()</p></td>
+<td><p>Counts the reference-record pairs.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">from_dump</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_entity_type</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.LigandReceptor.get_names" title="pypath.core.annot.LigandReceptor.get_names"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_names</span></code></a>()</p></td>
+<td><p>Returns the list of field names in the records.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.LigandReceptor.get_reference_set" title="pypath.core.annot.LigandReceptor.get_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_reference_set</span></code></a>([proteins, complexes, ...])</p></td>
+<td><p>Retrieves the reference set i.e. the set of all entities which potentially have annotation in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.LigandReceptor.get_subset" title="pypath.core.annot.LigandReceptor.get_subset"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.LigandReceptor.get_subset_bool_array" title="pypath.core.annot.LigandReceptor.get_subset_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset_bool_array</span></code></a>([reference_set])</p></td>
+<td><p>Returns a boolean vector with True and False values for each entity in the reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.LigandReceptor.get_values" title="pypath.core.annot.LigandReceptor.get_values"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_values</span></code></a>(name[, exclude_none])</p></td>
+<td><p>Returns the set of all possible values of a field.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_complex</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_mirna</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_protein</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.LigandReceptor.labels" title="pypath.core.annot.LigandReceptor.labels"><code class="xref py py-obj docutils literal notranslate"><span class="pre">labels</span></code></a>([method])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.LigandReceptor.load" title="pypath.core.annot.LigandReceptor.load"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load</span></code></a>()</p></td>
+<td><p>Loads the annotation data by calling the input method.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.LigandReceptor.load_data" title="pypath.core.annot.LigandReceptor.load_data"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_data</span></code></a>()</p></td>
+<td><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.LigandReceptor.load_proteins" title="pypath.core.annot.LigandReceptor.load_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_proteins</span></code></a>()</p></td>
+<td><p>Retrieves a set of all UniProt IDs to have a base set of the entire proteome.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.LigandReceptor.make_df" title="pypath.core.annot.LigandReceptor.make_df"><code class="xref py py-obj docutils literal notranslate"><span class="pre">make_df</span></code></a>([rebuild])</p></td>
+<td><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complex_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.LigandReceptor.numof_entities" title="pypath.core.annot.LigandReceptor.numof_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_entities</span></code></a>()</p></td>
+<td><p>The number of annotated entities in the resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirna_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirnas</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_protein_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_proteins</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.LigandReceptor.numof_records" title="pypath.core.annot.LigandReceptor.numof_records"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_records</span></code></a>([entity_types])</p></td>
+<td><p>The total number of annotation records.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.LigandReceptor.numof_references" title="pypath.core.annot.LigandReceptor.numof_references"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_references</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.LigandReceptor.process" title="pypath.core.annot.LigandReceptor.process"><code class="xref py py-obj docutils literal notranslate"><span class="pre">process</span></code></a>()</p></td>
+<td><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">proportion</span></code>(other)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.LigandReceptor.reload" title="pypath.core.annot.LigandReceptor.reload"><code class="xref py py-obj docutils literal notranslate"><span class="pre">reload</span></code></a>()</p></td>
+<td><p>Reloads the object from the module level.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">save_to_pickle</span></code>(pickle_file)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.LigandReceptor.select" title="pypath.core.annot.LigandReceptor.select"><code class="xref py py-obj docutils literal notranslate"><span class="pre">select</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.LigandReceptor.set_method" title="pypath.core.annot.LigandReceptor.set_method"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_method</span></code></a>()</p></td>
+<td><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if necessary.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.LigandReceptor.set_reference_set" title="pypath.core.annot.LigandReceptor.set_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_reference_set</span></code></a>()</p></td>
+<td><p>Assigns the reference set to the :py:attr``reference_set`` attribute.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.LigandReceptor.show" title="pypath.core.annot.LigandReceptor.show"><code class="xref py py-obj docutils literal notranslate"><span class="pre">show</span></code></a>([method, table_param])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic information from the UniProt datasheets.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.LigandReceptor.subset_intersection" title="pypath.core.annot.LigandReceptor.subset_intersection"><code class="xref py py-obj docutils literal notranslate"><span class="pre">subset_intersection</span></code></a>(universe, **kwargs)</p></td>
+<td><p>Calculates the proportion of entities in a subset occuring in the set <code class="docutils literal notranslate"><span class="pre">universe</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.LigandReceptor.to_array" title="pypath.core.annot.LigandReceptor.to_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_array</span></code></a>([reference_set, use_fields])</p></td>
+<td><p>Returns an entity vs feature array.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.LigandReceptor.to_bool_array" title="pypath.core.annot.LigandReceptor.to_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_bool_array</span></code></a>(reference_set)</p></td>
+<td><p>Returns a presence/absence boolean array for a reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.LigandReceptor.to_set" title="pypath.core.annot.LigandReceptor.to_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_set</span></code></a>()</p></td>
+<td><p>Returns the entities present in this annotation resource as a set.</p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Attributes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_fields</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">summary</span></code></p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.LigandReceptor.add_complexes_by_inference">
+<span class="sig-name descname"><span class="pre">add_complexes_by_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.LigandReceptor.add_complexes_by_inference" title="Link to this definition">§</a></dt>
+<dd><p>Creates complex annotations by in silico inference and adds them
+to this annotation set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.LigandReceptor.all_complexes">
+<span class="sig-name descname"><span class="pre">all_complexes</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.LigandReceptor.all_complexes" title="Link to this definition">§</a></dt>
+<dd><p>All protein complexes annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.LigandReceptor.all_entities">
+<span class="sig-name descname"><span class="pre">all_entities</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.LigandReceptor.all_entities" title="Link to this definition">§</a></dt>
+<dd><p>All entities annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.LigandReceptor.all_mirnas">
+<span class="sig-name descname"><span class="pre">all_mirnas</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.LigandReceptor.all_mirnas" title="Link to this definition">§</a></dt>
+<dd><p>All miRNAs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.LigandReceptor.all_proteins">
+<span class="sig-name descname"><span class="pre">all_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.LigandReceptor.all_proteins" title="Link to this definition">§</a></dt>
+<dd><p>All UniProt IDs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.LigandReceptor.all_refs">
+<span class="sig-name descname"><span class="pre">all_refs</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.LigandReceptor.all_refs" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects the references
+across all records. Returns <em>list</em>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.LigandReceptor.annotate_complex">
+<span class="sig-name descname"><span class="pre">annotate_complex</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cplex</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.LigandReceptor.annotate_complex" title="Link to this definition">§</a></dt>
+<dd><p>Infers annotations for a single complex.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.LigandReceptor.browse">
+<span class="sig-name descname"><span class="pre">browse</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">field</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">start</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.LigandReceptor.browse" title="Link to this definition">§</a></dt>
+<dd><p>Print gene information as a table.</p>
+<p>Presents information about annotation categories as ascii tables
+printed in the terminal. If one category provided, prints one table.
+If multiple categories provided, prints a table for each of them one
+by one proceeding to the next one once you hit return. If no categories
+provided goes through all levels of the primary category.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>field:</dt><dd><p>The field to browse categories by.</p>
+<ul class="simple">
+<li><p>If None the primary field will be selected.
+If this annotation resource doesn’t have fields, all proteins
+will be presented as one single category.</p></li>
+<li><p>If a string it will be considered a field name and it will
+browse through all levels of this field.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">list</span></code>, set or tuple, it will be considered either a
+<code class="docutils literal notranslate"><span class="pre">list</span></code> of field names or a list of values from the primary
+field. In the former case all combinations of the values of
+the fields will be presented, in the latter case the browsing
+will be limited to the levels of the primary field contained
+in <code class="docutils literal notranslate"><span class="pre">field</span></code>.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">dict</span></code>, keys are supposed to be field names and values
+as list of levels. If any of the values are None, all levels
+from that field will be used.</p></li>
+</ul>
+</dd>
+<dt>start:</dt><dd><p>Start browsing from this category. E.g. if there are 500
+categories and start is 250 it will skip everything before the
+250th.</p>
+</dd>
+<dt>kwargs:</dt><dd><p>Passed to <code class="docutils literal notranslate"><span class="pre">pypath.utils.uniprot.info</span></code>.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.LigandReceptor.complex_inference">
+<span class="sig-name descname"><span class="pre">complex_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.LigandReceptor.complex_inference" title="Link to this definition">§</a></dt>
+<dd><p>Annotates all complexes in <cite>complexes</cite>, by default in the default
+complex database (existing in the <cite>complex</cite> module or generated
+on demand according to the module’s current settings).</p>
+<dl class="field-list simple">
+<dt class="field-odd">Returns<span class="colon">:</span></dt>
+<dd class="field-odd"><p><ul class="simple">
+<li><p><em>Dict with complexes as keys and sets of annotations as values.</em></p></li>
+<li><p><em>Complexes with no valid information in this annotation resource</em></p></li>
+<li><p><em>won’t be in the dict.</em></p></li>
+</ul>
+</p>
+</dd>
+<dt class="field-even">Parameters<span class="colon">:</span></dt>
+<dd class="field-even"><p><strong>complexes</strong> (<em>iterable</em>) – Iterable yielding complexes.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.LigandReceptor.coverage">
+<span class="sig-name descname"><span class="pre">coverage</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">other</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.LigandReceptor.coverage" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the coverage of the annotation i.e. the proportion of
+entities having at least one record in this annotation resource
+for an arbitrary set of entities.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.LigandReceptor.curation_effort">
+<span class="sig-name descname"><span class="pre">curation_effort</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.LigandReceptor.curation_effort" title="Link to this definition">§</a></dt>
+<dd><p>Counts the reference-record pairs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.LigandReceptor.get_names">
+<span class="sig-name descname"><span class="pre">get_names</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.LigandReceptor.get_names" title="Link to this definition">§</a></dt>
+<dd><p>Returns the list of field names in the records. The annotation
+consists of uniform records and each entity might be annotated
+with one or more records. Each record is a tuple of fields, for
+example <code class="docutils literal notranslate"><span class="pre">('cell_type',</span> <span class="pre">'expression_level',</span> <span class="pre">'score')</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.LigandReceptor.get_reference_set">
+<em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">get_reference_set</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">proteins</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">swissprot_only</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.LigandReceptor.get_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the reference set i.e. the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.LigandReceptor.get_subset">
+<span class="sig-name descname"><span class="pre">get_subset</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.LigandReceptor.get_subset" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.LigandReceptor.get_subset_bool_array">
+<span class="sig-name descname"><span class="pre">get_subset_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.LigandReceptor.get_subset_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a boolean vector with True and False values for each entity
+in the reference set. The values represent presence absence data
+in the simplest case, but by providing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> any kind of matching
+and filtering is possible. <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> are passed to the <code class="docutils literal notranslate"><span class="pre">select</span></code>
+method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.LigandReceptor.get_values">
+<span class="sig-name descname"><span class="pre">get_values</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">exclude_none</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.LigandReceptor.get_values" title="Link to this definition">§</a></dt>
+<dd><p>Returns the set of all possible values of a field. E.g. if the
+records of this annotation have a field <code class="docutils literal notranslate"><span class="pre">cell_type</span></code> then calling
+this method can tell you that across all records the values of
+this field might be <code class="docutils literal notranslate"><span class="pre">{'macrophage',</span> <span class="pre">'epithelial_cell',</span> <span class="pre">...}</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.LigandReceptor.labels">
+<span class="sig-name descname"><span class="pre">labels</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.LigandReceptor.labels" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.LigandReceptor.load">
+<span class="sig-name descname"><span class="pre">load</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.LigandReceptor.load" title="Link to this definition">§</a></dt>
+<dd><p>Loads the annotation data by calling the input method.
+Infers annotations for complexes in the complex database if
+py:attr:<code class="docutils literal notranslate"><span class="pre">infer_complexes</span></code> is True.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.LigandReceptor.load_data">
+<span class="sig-name descname"><span class="pre">load_data</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.LigandReceptor.load_data" title="Link to this definition">§</a></dt>
+<dd><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.LigandReceptor.load_proteins">
+<span class="sig-name descname"><span class="pre">load_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.LigandReceptor.load_proteins" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a set of all UniProt IDs to have a base set of the entire
+proteome.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.LigandReceptor.make_df">
+<span class="sig-name descname"><span class="pre">make_df</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">rebuild</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.LigandReceptor.make_df" title="Link to this definition">§</a></dt>
+<dd><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.
+The data frame will be assigned to :py:attr``df``.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.LigandReceptor.numof_entities">
+<span class="sig-name descname"><span class="pre">numof_entities</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.LigandReceptor.numof_entities" title="Link to this definition">§</a></dt>
+<dd><p>The number of annotated entities in the resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.LigandReceptor.numof_records">
+<span class="sig-name descname"><span class="pre">numof_records</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.LigandReceptor.numof_records" title="Link to this definition">§</a></dt>
+<dd><p>The total number of annotation records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.LigandReceptor.numof_references">
+<span class="sig-name descname"><span class="pre">numof_references</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.LigandReceptor.numof_references" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects and counts the
+references across all records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.LigandReceptor.process">
+<span class="sig-name descname"><span class="pre">process</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.LigandReceptor.process" title="Link to this definition">§</a></dt>
+<dd><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.LigandReceptor.reload">
+<span class="sig-name descname"><span class="pre">reload</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.LigandReceptor.reload" title="Link to this definition">§</a></dt>
+<dd><p>Reloads the object from the module level.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.LigandReceptor.select">
+<span class="sig-name descname"><span class="pre">select</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.LigandReceptor.select" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.LigandReceptor.set_method">
+<span class="sig-name descname"><span class="pre">set_method</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.LigandReceptor.set_method" title="Link to this definition">§</a></dt>
+<dd><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if
+necessary.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.LigandReceptor.set_reference_set">
+<span class="sig-name descname"><span class="pre">set_reference_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.LigandReceptor.set_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Assigns the reference set to the :py:attr``reference_set`` attribute.
+The reference set is the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.LigandReceptor.show">
+<span class="sig-name descname"><span class="pre">show</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">table_param</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.LigandReceptor.show" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic
+information from the UniProt datasheets.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.LigandReceptor.subset_intersection">
+<span class="sig-name descname"><span class="pre">subset_intersection</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">universe</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.LigandReceptor.subset_intersection" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the proportion of entities in a subset occuring in the
+set <code class="docutils literal notranslate"><span class="pre">universe</span></code>. The subset is selected by passing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> to the
+<code class="docutils literal notranslate"><span class="pre">select</span></code> method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.LigandReceptor.to_array">
+<span class="sig-name descname"><span class="pre">to_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_fields</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.LigandReceptor.to_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns an entity vs feature array. In case of more complex
+annotations this might be huge.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.LigandReceptor.to_bool_array">
+<span class="sig-name descname"><span class="pre">to_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.LigandReceptor.to_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a presence/absence boolean array for a reference set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.LigandReceptor.to_set">
+<span class="sig-name descname"><span class="pre">to_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.LigandReceptor.to_set" title="Link to this definition">§</a></dt>
+<dd><p>Returns the entities present in this annotation resource as a set.</p>
+</dd></dl>
+
+</dd></dl>
+
+</section>
+
+
+                </article>
+              
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+  <section id="pypath-core-annot-locate">
+<h1>pypath.core.annot.Locate<a class="headerlink" href="#pypath-core-annot-locate" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.core.annot.Locate">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.core.annot.</span></span><span class="sig-name descname"><span class="pre">Locate</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">literature</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">external</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">predictions</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#Locate"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.Locate" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <a class="reference internal" href="pypath.core.annot.AnnotationBase.html#pypath.core.annot.AnnotationBase" title="pypath.core.annot.AnnotationBase"><code class="xref py py-class docutils literal notranslate"><span class="pre">AnnotationBase</span></code></a></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Locate.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">literature</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">external</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">predictions</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#Locate.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.Locate.__init__" title="Link to this definition">§</a></dt>
+<dd><p>Represents annotations for a set of proteins.
+Loads the data from the original resource and provides methods
+to query the annotations.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>name</strong> (<em>str</em>) – A custom name for the annotation resource.</p></li>
+<li><p><strong>ncbi_tax_id</strong> (<em>int</em>) – NCBI Taxonomy identifier.</p></li>
+<li><p><strong>input_method</strong> (<em>callable</em><em>,</em><em>str</em>) – Either a callable or the name of a method in any submodules of
+the <code class="docutils literal notranslate"><span class="pre">pypath.inputs</span></code>  module. Should return a dict with
+UniProt IDs as keys or an object suitable for <code class="docutils literal notranslate"><span class="pre">process_method</span></code>.</p></li>
+<li><p><strong>input_args</strong> (<em>dict</em>) – Arguments for the <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Locate.__init__" title="pypath.core.annot.Locate.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>([ncbi_tax_id, literature, ...])</p></td>
+<td><p>Represents annotations for a set of proteins.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Locate.add_complexes_by_inference" title="pypath.core.annot.Locate.add_complexes_by_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">add_complexes_by_inference</span></code></a>([complexes])</p></td>
+<td><p>Creates complex annotations by in silico inference and adds them to this annotation set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Locate.all_complexes" title="pypath.core.annot.Locate.all_complexes"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_complexes</span></code></a>()</p></td>
+<td><p>All protein complexes annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Locate.all_entities" title="pypath.core.annot.Locate.all_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_entities</span></code></a>([entity_types])</p></td>
+<td><p>All entities annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Locate.all_mirnas" title="pypath.core.annot.Locate.all_mirnas"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_mirnas</span></code></a>()</p></td>
+<td><p>All miRNAs annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Locate.all_proteins" title="pypath.core.annot.Locate.all_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_proteins</span></code></a>()</p></td>
+<td><p>All UniProt IDs annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Locate.all_refs" title="pypath.core.annot.Locate.all_refs"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_refs</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Locate.annotate_complex" title="pypath.core.annot.Locate.annotate_complex"><code class="xref py py-obj docutils literal notranslate"><span class="pre">annotate_complex</span></code></a>(cplex)</p></td>
+<td><p>Infers annotations for a single complex.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Locate.browse" title="pypath.core.annot.Locate.browse"><code class="xref py py-obj docutils literal notranslate"><span class="pre">browse</span></code></a>([field, start])</p></td>
+<td><p>Print gene information as a table.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Locate.complex_inference" title="pypath.core.annot.Locate.complex_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">complex_inference</span></code></a>([complexes])</p></td>
+<td><p>Annotates all complexes in <cite>complexes</cite>, by default in the default complex database (existing in the <cite>complex</cite> module or generated on demand according to the module's current settings).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Locate.coverage" title="pypath.core.annot.Locate.coverage"><code class="xref py py-obj docutils literal notranslate"><span class="pre">coverage</span></code></a>(other)</p></td>
+<td><p>Calculates the coverage of the annotation i.e. the proportion of entities having at least one record in this annotation resource for an arbitrary set of entities.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Locate.curation_effort" title="pypath.core.annot.Locate.curation_effort"><code class="xref py py-obj docutils literal notranslate"><span class="pre">curation_effort</span></code></a>()</p></td>
+<td><p>Counts the reference-record pairs.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">from_dump</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_entity_type</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Locate.get_names" title="pypath.core.annot.Locate.get_names"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_names</span></code></a>()</p></td>
+<td><p>Returns the list of field names in the records.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Locate.get_reference_set" title="pypath.core.annot.Locate.get_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_reference_set</span></code></a>([proteins, complexes, ...])</p></td>
+<td><p>Retrieves the reference set i.e. the set of all entities which potentially have annotation in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Locate.get_subset" title="pypath.core.annot.Locate.get_subset"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Locate.get_subset_bool_array" title="pypath.core.annot.Locate.get_subset_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset_bool_array</span></code></a>([reference_set])</p></td>
+<td><p>Returns a boolean vector with True and False values for each entity in the reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Locate.get_values" title="pypath.core.annot.Locate.get_values"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_values</span></code></a>(name[, exclude_none])</p></td>
+<td><p>Returns the set of all possible values of a field.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_complex</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_mirna</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_protein</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Locate.labels" title="pypath.core.annot.Locate.labels"><code class="xref py py-obj docutils literal notranslate"><span class="pre">labels</span></code></a>([method])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Locate.load" title="pypath.core.annot.Locate.load"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load</span></code></a>()</p></td>
+<td><p>Loads the annotation data by calling the input method.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Locate.load_data" title="pypath.core.annot.Locate.load_data"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_data</span></code></a>()</p></td>
+<td><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Locate.load_proteins" title="pypath.core.annot.Locate.load_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_proteins</span></code></a>()</p></td>
+<td><p>Retrieves a set of all UniProt IDs to have a base set of the entire proteome.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Locate.make_df" title="pypath.core.annot.Locate.make_df"><code class="xref py py-obj docutils literal notranslate"><span class="pre">make_df</span></code></a>([rebuild])</p></td>
+<td><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complex_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Locate.numof_entities" title="pypath.core.annot.Locate.numof_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_entities</span></code></a>()</p></td>
+<td><p>The number of annotated entities in the resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirna_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirnas</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_protein_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_proteins</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Locate.numof_records" title="pypath.core.annot.Locate.numof_records"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_records</span></code></a>([entity_types])</p></td>
+<td><p>The total number of annotation records.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Locate.numof_references" title="pypath.core.annot.Locate.numof_references"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_references</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Locate.process" title="pypath.core.annot.Locate.process"><code class="xref py py-obj docutils literal notranslate"><span class="pre">process</span></code></a>()</p></td>
+<td><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">proportion</span></code>(other)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Locate.reload" title="pypath.core.annot.Locate.reload"><code class="xref py py-obj docutils literal notranslate"><span class="pre">reload</span></code></a>()</p></td>
+<td><p>Reloads the object from the module level.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">save_to_pickle</span></code>(pickle_file)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Locate.select" title="pypath.core.annot.Locate.select"><code class="xref py py-obj docutils literal notranslate"><span class="pre">select</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Locate.set_method" title="pypath.core.annot.Locate.set_method"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_method</span></code></a>()</p></td>
+<td><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if necessary.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Locate.set_reference_set" title="pypath.core.annot.Locate.set_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_reference_set</span></code></a>()</p></td>
+<td><p>Assigns the reference set to the :py:attr``reference_set`` attribute.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Locate.show" title="pypath.core.annot.Locate.show"><code class="xref py py-obj docutils literal notranslate"><span class="pre">show</span></code></a>([method, table_param])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic information from the UniProt datasheets.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Locate.subset_intersection" title="pypath.core.annot.Locate.subset_intersection"><code class="xref py py-obj docutils literal notranslate"><span class="pre">subset_intersection</span></code></a>(universe, **kwargs)</p></td>
+<td><p>Calculates the proportion of entities in a subset occuring in the set <code class="docutils literal notranslate"><span class="pre">universe</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Locate.to_array" title="pypath.core.annot.Locate.to_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_array</span></code></a>([reference_set, use_fields])</p></td>
+<td><p>Returns an entity vs feature array.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Locate.to_bool_array" title="pypath.core.annot.Locate.to_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_bool_array</span></code></a>(reference_set)</p></td>
+<td><p>Returns a presence/absence boolean array for a reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Locate.to_set" title="pypath.core.annot.Locate.to_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_set</span></code></a>()</p></td>
+<td><p>Returns the entities present in this annotation resource as a set.</p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Attributes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_fields</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">summary</span></code></p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Locate.add_complexes_by_inference">
+<span class="sig-name descname"><span class="pre">add_complexes_by_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Locate.add_complexes_by_inference" title="Link to this definition">§</a></dt>
+<dd><p>Creates complex annotations by in silico inference and adds them
+to this annotation set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Locate.all_complexes">
+<span class="sig-name descname"><span class="pre">all_complexes</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Locate.all_complexes" title="Link to this definition">§</a></dt>
+<dd><p>All protein complexes annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Locate.all_entities">
+<span class="sig-name descname"><span class="pre">all_entities</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Locate.all_entities" title="Link to this definition">§</a></dt>
+<dd><p>All entities annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Locate.all_mirnas">
+<span class="sig-name descname"><span class="pre">all_mirnas</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Locate.all_mirnas" title="Link to this definition">§</a></dt>
+<dd><p>All miRNAs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Locate.all_proteins">
+<span class="sig-name descname"><span class="pre">all_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Locate.all_proteins" title="Link to this definition">§</a></dt>
+<dd><p>All UniProt IDs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Locate.all_refs">
+<span class="sig-name descname"><span class="pre">all_refs</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Locate.all_refs" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects the references
+across all records. Returns <em>list</em>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Locate.annotate_complex">
+<span class="sig-name descname"><span class="pre">annotate_complex</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cplex</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Locate.annotate_complex" title="Link to this definition">§</a></dt>
+<dd><p>Infers annotations for a single complex.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Locate.browse">
+<span class="sig-name descname"><span class="pre">browse</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">field</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">start</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Locate.browse" title="Link to this definition">§</a></dt>
+<dd><p>Print gene information as a table.</p>
+<p>Presents information about annotation categories as ascii tables
+printed in the terminal. If one category provided, prints one table.
+If multiple categories provided, prints a table for each of them one
+by one proceeding to the next one once you hit return. If no categories
+provided goes through all levels of the primary category.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>field:</dt><dd><p>The field to browse categories by.</p>
+<ul class="simple">
+<li><p>If None the primary field will be selected.
+If this annotation resource doesn’t have fields, all proteins
+will be presented as one single category.</p></li>
+<li><p>If a string it will be considered a field name and it will
+browse through all levels of this field.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">list</span></code>, set or tuple, it will be considered either a
+<code class="docutils literal notranslate"><span class="pre">list</span></code> of field names or a list of values from the primary
+field. In the former case all combinations of the values of
+the fields will be presented, in the latter case the browsing
+will be limited to the levels of the primary field contained
+in <code class="docutils literal notranslate"><span class="pre">field</span></code>.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">dict</span></code>, keys are supposed to be field names and values
+as list of levels. If any of the values are None, all levels
+from that field will be used.</p></li>
+</ul>
+</dd>
+<dt>start:</dt><dd><p>Start browsing from this category. E.g. if there are 500
+categories and start is 250 it will skip everything before the
+250th.</p>
+</dd>
+<dt>kwargs:</dt><dd><p>Passed to <code class="docutils literal notranslate"><span class="pre">pypath.utils.uniprot.info</span></code>.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Locate.complex_inference">
+<span class="sig-name descname"><span class="pre">complex_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Locate.complex_inference" title="Link to this definition">§</a></dt>
+<dd><p>Annotates all complexes in <cite>complexes</cite>, by default in the default
+complex database (existing in the <cite>complex</cite> module or generated
+on demand according to the module’s current settings).</p>
+<dl class="field-list simple">
+<dt class="field-odd">Returns<span class="colon">:</span></dt>
+<dd class="field-odd"><p><ul class="simple">
+<li><p><em>Dict with complexes as keys and sets of annotations as values.</em></p></li>
+<li><p><em>Complexes with no valid information in this annotation resource</em></p></li>
+<li><p><em>won’t be in the dict.</em></p></li>
+</ul>
+</p>
+</dd>
+<dt class="field-even">Parameters<span class="colon">:</span></dt>
+<dd class="field-even"><p><strong>complexes</strong> (<em>iterable</em>) – Iterable yielding complexes.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Locate.coverage">
+<span class="sig-name descname"><span class="pre">coverage</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">other</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Locate.coverage" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the coverage of the annotation i.e. the proportion of
+entities having at least one record in this annotation resource
+for an arbitrary set of entities.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Locate.curation_effort">
+<span class="sig-name descname"><span class="pre">curation_effort</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Locate.curation_effort" title="Link to this definition">§</a></dt>
+<dd><p>Counts the reference-record pairs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Locate.get_names">
+<span class="sig-name descname"><span class="pre">get_names</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Locate.get_names" title="Link to this definition">§</a></dt>
+<dd><p>Returns the list of field names in the records. The annotation
+consists of uniform records and each entity might be annotated
+with one or more records. Each record is a tuple of fields, for
+example <code class="docutils literal notranslate"><span class="pre">('cell_type',</span> <span class="pre">'expression_level',</span> <span class="pre">'score')</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Locate.get_reference_set">
+<em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">get_reference_set</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">proteins</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">swissprot_only</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Locate.get_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the reference set i.e. the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Locate.get_subset">
+<span class="sig-name descname"><span class="pre">get_subset</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Locate.get_subset" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Locate.get_subset_bool_array">
+<span class="sig-name descname"><span class="pre">get_subset_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Locate.get_subset_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a boolean vector with True and False values for each entity
+in the reference set. The values represent presence absence data
+in the simplest case, but by providing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> any kind of matching
+and filtering is possible. <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> are passed to the <code class="docutils literal notranslate"><span class="pre">select</span></code>
+method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Locate.get_values">
+<span class="sig-name descname"><span class="pre">get_values</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">exclude_none</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Locate.get_values" title="Link to this definition">§</a></dt>
+<dd><p>Returns the set of all possible values of a field. E.g. if the
+records of this annotation have a field <code class="docutils literal notranslate"><span class="pre">cell_type</span></code> then calling
+this method can tell you that across all records the values of
+this field might be <code class="docutils literal notranslate"><span class="pre">{'macrophage',</span> <span class="pre">'epithelial_cell',</span> <span class="pre">...}</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Locate.labels">
+<span class="sig-name descname"><span class="pre">labels</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Locate.labels" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Locate.load">
+<span class="sig-name descname"><span class="pre">load</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Locate.load" title="Link to this definition">§</a></dt>
+<dd><p>Loads the annotation data by calling the input method.
+Infers annotations for complexes in the complex database if
+py:attr:<code class="docutils literal notranslate"><span class="pre">infer_complexes</span></code> is True.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Locate.load_data">
+<span class="sig-name descname"><span class="pre">load_data</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Locate.load_data" title="Link to this definition">§</a></dt>
+<dd><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Locate.load_proteins">
+<span class="sig-name descname"><span class="pre">load_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Locate.load_proteins" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a set of all UniProt IDs to have a base set of the entire
+proteome.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Locate.make_df">
+<span class="sig-name descname"><span class="pre">make_df</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">rebuild</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Locate.make_df" title="Link to this definition">§</a></dt>
+<dd><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.
+The data frame will be assigned to :py:attr``df``.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Locate.numof_entities">
+<span class="sig-name descname"><span class="pre">numof_entities</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Locate.numof_entities" title="Link to this definition">§</a></dt>
+<dd><p>The number of annotated entities in the resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Locate.numof_records">
+<span class="sig-name descname"><span class="pre">numof_records</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Locate.numof_records" title="Link to this definition">§</a></dt>
+<dd><p>The total number of annotation records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Locate.numof_references">
+<span class="sig-name descname"><span class="pre">numof_references</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Locate.numof_references" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects and counts the
+references across all records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Locate.process">
+<span class="sig-name descname"><span class="pre">process</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Locate.process" title="Link to this definition">§</a></dt>
+<dd><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Locate.reload">
+<span class="sig-name descname"><span class="pre">reload</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Locate.reload" title="Link to this definition">§</a></dt>
+<dd><p>Reloads the object from the module level.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Locate.select">
+<span class="sig-name descname"><span class="pre">select</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Locate.select" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Locate.set_method">
+<span class="sig-name descname"><span class="pre">set_method</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Locate.set_method" title="Link to this definition">§</a></dt>
+<dd><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if
+necessary.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Locate.set_reference_set">
+<span class="sig-name descname"><span class="pre">set_reference_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Locate.set_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Assigns the reference set to the :py:attr``reference_set`` attribute.
+The reference set is the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Locate.show">
+<span class="sig-name descname"><span class="pre">show</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">table_param</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Locate.show" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic
+information from the UniProt datasheets.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Locate.subset_intersection">
+<span class="sig-name descname"><span class="pre">subset_intersection</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">universe</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Locate.subset_intersection" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the proportion of entities in a subset occuring in the
+set <code class="docutils literal notranslate"><span class="pre">universe</span></code>. The subset is selected by passing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> to the
+<code class="docutils literal notranslate"><span class="pre">select</span></code> method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Locate.to_array">
+<span class="sig-name descname"><span class="pre">to_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_fields</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Locate.to_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns an entity vs feature array. In case of more complex
+annotations this might be huge.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Locate.to_bool_array">
+<span class="sig-name descname"><span class="pre">to_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Locate.to_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a presence/absence boolean array for a reference set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Locate.to_set">
+<span class="sig-name descname"><span class="pre">to_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Locate.to_set" title="Link to this definition">§</a></dt>
+<dd><p>Returns the entities present in this annotation resource as a set.</p>
+</dd></dl>
+
+</dd></dl>
+
+</section>
+
+
+                </article>
+              
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+  <section id="pypath-core-annot-lrdb">
+<h1>pypath.core.annot.Lrdb<a class="headerlink" href="#pypath-core-annot-lrdb" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.core.annot.Lrdb">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.core.annot.</span></span><span class="sig-name descname"><span class="pre">Lrdb</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#Lrdb"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.Lrdb" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <a class="reference internal" href="pypath.core.annot.AnnotationBase.html#pypath.core.annot.AnnotationBase" title="pypath.core.annot.AnnotationBase"><code class="xref py py-class docutils literal notranslate"><span class="pre">AnnotationBase</span></code></a></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Lrdb.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#Lrdb.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.Lrdb.__init__" title="Link to this definition">§</a></dt>
+<dd><p>Represents annotations for a set of proteins.
+Loads the data from the original resource and provides methods
+to query the annotations.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>name</strong> (<em>str</em>) – A custom name for the annotation resource.</p></li>
+<li><p><strong>ncbi_tax_id</strong> (<em>int</em>) – NCBI Taxonomy identifier.</p></li>
+<li><p><strong>input_method</strong> (<em>callable</em><em>,</em><em>str</em>) – Either a callable or the name of a method in any submodules of
+the <code class="docutils literal notranslate"><span class="pre">pypath.inputs</span></code>  module. Should return a dict with
+UniProt IDs as keys or an object suitable for <code class="docutils literal notranslate"><span class="pre">process_method</span></code>.</p></li>
+<li><p><strong>input_args</strong> (<em>dict</em>) – Arguments for the <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Lrdb.__init__" title="pypath.core.annot.Lrdb.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>(**kwargs)</p></td>
+<td><p>Represents annotations for a set of proteins.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Lrdb.add_complexes_by_inference" title="pypath.core.annot.Lrdb.add_complexes_by_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">add_complexes_by_inference</span></code></a>([complexes])</p></td>
+<td><p>Creates complex annotations by in silico inference and adds them to this annotation set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Lrdb.all_complexes" title="pypath.core.annot.Lrdb.all_complexes"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_complexes</span></code></a>()</p></td>
+<td><p>All protein complexes annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Lrdb.all_entities" title="pypath.core.annot.Lrdb.all_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_entities</span></code></a>([entity_types])</p></td>
+<td><p>All entities annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Lrdb.all_mirnas" title="pypath.core.annot.Lrdb.all_mirnas"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_mirnas</span></code></a>()</p></td>
+<td><p>All miRNAs annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Lrdb.all_proteins" title="pypath.core.annot.Lrdb.all_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_proteins</span></code></a>()</p></td>
+<td><p>All UniProt IDs annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Lrdb.all_refs" title="pypath.core.annot.Lrdb.all_refs"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_refs</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Lrdb.annotate_complex" title="pypath.core.annot.Lrdb.annotate_complex"><code class="xref py py-obj docutils literal notranslate"><span class="pre">annotate_complex</span></code></a>(cplex)</p></td>
+<td><p>Infers annotations for a single complex.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Lrdb.browse" title="pypath.core.annot.Lrdb.browse"><code class="xref py py-obj docutils literal notranslate"><span class="pre">browse</span></code></a>([field, start])</p></td>
+<td><p>Print gene information as a table.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Lrdb.complex_inference" title="pypath.core.annot.Lrdb.complex_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">complex_inference</span></code></a>([complexes])</p></td>
+<td><p>Annotates all complexes in <cite>complexes</cite>, by default in the default complex database (existing in the <cite>complex</cite> module or generated on demand according to the module's current settings).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Lrdb.coverage" title="pypath.core.annot.Lrdb.coverage"><code class="xref py py-obj docutils literal notranslate"><span class="pre">coverage</span></code></a>(other)</p></td>
+<td><p>Calculates the coverage of the annotation i.e. the proportion of entities having at least one record in this annotation resource for an arbitrary set of entities.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Lrdb.curation_effort" title="pypath.core.annot.Lrdb.curation_effort"><code class="xref py py-obj docutils literal notranslate"><span class="pre">curation_effort</span></code></a>()</p></td>
+<td><p>Counts the reference-record pairs.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">from_dump</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_entity_type</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Lrdb.get_names" title="pypath.core.annot.Lrdb.get_names"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_names</span></code></a>()</p></td>
+<td><p>Returns the list of field names in the records.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Lrdb.get_reference_set" title="pypath.core.annot.Lrdb.get_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_reference_set</span></code></a>([proteins, complexes, ...])</p></td>
+<td><p>Retrieves the reference set i.e. the set of all entities which potentially have annotation in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Lrdb.get_subset" title="pypath.core.annot.Lrdb.get_subset"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Lrdb.get_subset_bool_array" title="pypath.core.annot.Lrdb.get_subset_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset_bool_array</span></code></a>([reference_set])</p></td>
+<td><p>Returns a boolean vector with True and False values for each entity in the reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Lrdb.get_values" title="pypath.core.annot.Lrdb.get_values"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_values</span></code></a>(name[, exclude_none])</p></td>
+<td><p>Returns the set of all possible values of a field.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_complex</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_mirna</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_protein</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Lrdb.labels" title="pypath.core.annot.Lrdb.labels"><code class="xref py py-obj docutils literal notranslate"><span class="pre">labels</span></code></a>([method])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Lrdb.load" title="pypath.core.annot.Lrdb.load"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load</span></code></a>()</p></td>
+<td><p>Loads the annotation data by calling the input method.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Lrdb.load_data" title="pypath.core.annot.Lrdb.load_data"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_data</span></code></a>()</p></td>
+<td><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Lrdb.load_proteins" title="pypath.core.annot.Lrdb.load_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_proteins</span></code></a>()</p></td>
+<td><p>Retrieves a set of all UniProt IDs to have a base set of the entire proteome.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Lrdb.make_df" title="pypath.core.annot.Lrdb.make_df"><code class="xref py py-obj docutils literal notranslate"><span class="pre">make_df</span></code></a>([rebuild])</p></td>
+<td><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complex_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Lrdb.numof_entities" title="pypath.core.annot.Lrdb.numof_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_entities</span></code></a>()</p></td>
+<td><p>The number of annotated entities in the resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirna_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirnas</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_protein_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_proteins</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Lrdb.numof_records" title="pypath.core.annot.Lrdb.numof_records"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_records</span></code></a>([entity_types])</p></td>
+<td><p>The total number of annotation records.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Lrdb.numof_references" title="pypath.core.annot.Lrdb.numof_references"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_references</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Lrdb.process" title="pypath.core.annot.Lrdb.process"><code class="xref py py-obj docutils literal notranslate"><span class="pre">process</span></code></a>()</p></td>
+<td><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">proportion</span></code>(other)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Lrdb.reload" title="pypath.core.annot.Lrdb.reload"><code class="xref py py-obj docutils literal notranslate"><span class="pre">reload</span></code></a>()</p></td>
+<td><p>Reloads the object from the module level.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">save_to_pickle</span></code>(pickle_file)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Lrdb.select" title="pypath.core.annot.Lrdb.select"><code class="xref py py-obj docutils literal notranslate"><span class="pre">select</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Lrdb.set_method" title="pypath.core.annot.Lrdb.set_method"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_method</span></code></a>()</p></td>
+<td><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if necessary.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Lrdb.set_reference_set" title="pypath.core.annot.Lrdb.set_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_reference_set</span></code></a>()</p></td>
+<td><p>Assigns the reference set to the :py:attr``reference_set`` attribute.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Lrdb.show" title="pypath.core.annot.Lrdb.show"><code class="xref py py-obj docutils literal notranslate"><span class="pre">show</span></code></a>([method, table_param])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic information from the UniProt datasheets.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Lrdb.subset_intersection" title="pypath.core.annot.Lrdb.subset_intersection"><code class="xref py py-obj docutils literal notranslate"><span class="pre">subset_intersection</span></code></a>(universe, **kwargs)</p></td>
+<td><p>Calculates the proportion of entities in a subset occuring in the set <code class="docutils literal notranslate"><span class="pre">universe</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Lrdb.to_array" title="pypath.core.annot.Lrdb.to_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_array</span></code></a>([reference_set, use_fields])</p></td>
+<td><p>Returns an entity vs feature array.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Lrdb.to_bool_array" title="pypath.core.annot.Lrdb.to_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_bool_array</span></code></a>(reference_set)</p></td>
+<td><p>Returns a presence/absence boolean array for a reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Lrdb.to_set" title="pypath.core.annot.Lrdb.to_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_set</span></code></a>()</p></td>
+<td><p>Returns the entities present in this annotation resource as a set.</p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Attributes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_fields</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">summary</span></code></p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Lrdb.add_complexes_by_inference">
+<span class="sig-name descname"><span class="pre">add_complexes_by_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Lrdb.add_complexes_by_inference" title="Link to this definition">§</a></dt>
+<dd><p>Creates complex annotations by in silico inference and adds them
+to this annotation set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Lrdb.all_complexes">
+<span class="sig-name descname"><span class="pre">all_complexes</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Lrdb.all_complexes" title="Link to this definition">§</a></dt>
+<dd><p>All protein complexes annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Lrdb.all_entities">
+<span class="sig-name descname"><span class="pre">all_entities</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Lrdb.all_entities" title="Link to this definition">§</a></dt>
+<dd><p>All entities annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Lrdb.all_mirnas">
+<span class="sig-name descname"><span class="pre">all_mirnas</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Lrdb.all_mirnas" title="Link to this definition">§</a></dt>
+<dd><p>All miRNAs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Lrdb.all_proteins">
+<span class="sig-name descname"><span class="pre">all_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Lrdb.all_proteins" title="Link to this definition">§</a></dt>
+<dd><p>All UniProt IDs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Lrdb.all_refs">
+<span class="sig-name descname"><span class="pre">all_refs</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Lrdb.all_refs" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects the references
+across all records. Returns <em>list</em>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Lrdb.annotate_complex">
+<span class="sig-name descname"><span class="pre">annotate_complex</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cplex</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Lrdb.annotate_complex" title="Link to this definition">§</a></dt>
+<dd><p>Infers annotations for a single complex.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Lrdb.browse">
+<span class="sig-name descname"><span class="pre">browse</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">field</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">start</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Lrdb.browse" title="Link to this definition">§</a></dt>
+<dd><p>Print gene information as a table.</p>
+<p>Presents information about annotation categories as ascii tables
+printed in the terminal. If one category provided, prints one table.
+If multiple categories provided, prints a table for each of them one
+by one proceeding to the next one once you hit return. If no categories
+provided goes through all levels of the primary category.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>field:</dt><dd><p>The field to browse categories by.</p>
+<ul class="simple">
+<li><p>If None the primary field will be selected.
+If this annotation resource doesn’t have fields, all proteins
+will be presented as one single category.</p></li>
+<li><p>If a string it will be considered a field name and it will
+browse through all levels of this field.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">list</span></code>, set or tuple, it will be considered either a
+<code class="docutils literal notranslate"><span class="pre">list</span></code> of field names or a list of values from the primary
+field. In the former case all combinations of the values of
+the fields will be presented, in the latter case the browsing
+will be limited to the levels of the primary field contained
+in <code class="docutils literal notranslate"><span class="pre">field</span></code>.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">dict</span></code>, keys are supposed to be field names and values
+as list of levels. If any of the values are None, all levels
+from that field will be used.</p></li>
+</ul>
+</dd>
+<dt>start:</dt><dd><p>Start browsing from this category. E.g. if there are 500
+categories and start is 250 it will skip everything before the
+250th.</p>
+</dd>
+<dt>kwargs:</dt><dd><p>Passed to <code class="docutils literal notranslate"><span class="pre">pypath.utils.uniprot.info</span></code>.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Lrdb.complex_inference">
+<span class="sig-name descname"><span class="pre">complex_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Lrdb.complex_inference" title="Link to this definition">§</a></dt>
+<dd><p>Annotates all complexes in <cite>complexes</cite>, by default in the default
+complex database (existing in the <cite>complex</cite> module or generated
+on demand according to the module’s current settings).</p>
+<dl class="field-list simple">
+<dt class="field-odd">Returns<span class="colon">:</span></dt>
+<dd class="field-odd"><p><ul class="simple">
+<li><p><em>Dict with complexes as keys and sets of annotations as values.</em></p></li>
+<li><p><em>Complexes with no valid information in this annotation resource</em></p></li>
+<li><p><em>won’t be in the dict.</em></p></li>
+</ul>
+</p>
+</dd>
+<dt class="field-even">Parameters<span class="colon">:</span></dt>
+<dd class="field-even"><p><strong>complexes</strong> (<em>iterable</em>) – Iterable yielding complexes.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Lrdb.coverage">
+<span class="sig-name descname"><span class="pre">coverage</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">other</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Lrdb.coverage" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the coverage of the annotation i.e. the proportion of
+entities having at least one record in this annotation resource
+for an arbitrary set of entities.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Lrdb.curation_effort">
+<span class="sig-name descname"><span class="pre">curation_effort</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Lrdb.curation_effort" title="Link to this definition">§</a></dt>
+<dd><p>Counts the reference-record pairs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Lrdb.get_names">
+<span class="sig-name descname"><span class="pre">get_names</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Lrdb.get_names" title="Link to this definition">§</a></dt>
+<dd><p>Returns the list of field names in the records. The annotation
+consists of uniform records and each entity might be annotated
+with one or more records. Each record is a tuple of fields, for
+example <code class="docutils literal notranslate"><span class="pre">('cell_type',</span> <span class="pre">'expression_level',</span> <span class="pre">'score')</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Lrdb.get_reference_set">
+<em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">get_reference_set</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">proteins</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">swissprot_only</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Lrdb.get_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the reference set i.e. the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Lrdb.get_subset">
+<span class="sig-name descname"><span class="pre">get_subset</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Lrdb.get_subset" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Lrdb.get_subset_bool_array">
+<span class="sig-name descname"><span class="pre">get_subset_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Lrdb.get_subset_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a boolean vector with True and False values for each entity
+in the reference set. The values represent presence absence data
+in the simplest case, but by providing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> any kind of matching
+and filtering is possible. <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> are passed to the <code class="docutils literal notranslate"><span class="pre">select</span></code>
+method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Lrdb.get_values">
+<span class="sig-name descname"><span class="pre">get_values</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">exclude_none</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Lrdb.get_values" title="Link to this definition">§</a></dt>
+<dd><p>Returns the set of all possible values of a field. E.g. if the
+records of this annotation have a field <code class="docutils literal notranslate"><span class="pre">cell_type</span></code> then calling
+this method can tell you that across all records the values of
+this field might be <code class="docutils literal notranslate"><span class="pre">{'macrophage',</span> <span class="pre">'epithelial_cell',</span> <span class="pre">...}</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Lrdb.labels">
+<span class="sig-name descname"><span class="pre">labels</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Lrdb.labels" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Lrdb.load">
+<span class="sig-name descname"><span class="pre">load</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Lrdb.load" title="Link to this definition">§</a></dt>
+<dd><p>Loads the annotation data by calling the input method.
+Infers annotations for complexes in the complex database if
+py:attr:<code class="docutils literal notranslate"><span class="pre">infer_complexes</span></code> is True.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Lrdb.load_data">
+<span class="sig-name descname"><span class="pre">load_data</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Lrdb.load_data" title="Link to this definition">§</a></dt>
+<dd><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Lrdb.load_proteins">
+<span class="sig-name descname"><span class="pre">load_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Lrdb.load_proteins" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a set of all UniProt IDs to have a base set of the entire
+proteome.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Lrdb.make_df">
+<span class="sig-name descname"><span class="pre">make_df</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">rebuild</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Lrdb.make_df" title="Link to this definition">§</a></dt>
+<dd><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.
+The data frame will be assigned to :py:attr``df``.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Lrdb.numof_entities">
+<span class="sig-name descname"><span class="pre">numof_entities</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Lrdb.numof_entities" title="Link to this definition">§</a></dt>
+<dd><p>The number of annotated entities in the resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Lrdb.numof_records">
+<span class="sig-name descname"><span class="pre">numof_records</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Lrdb.numof_records" title="Link to this definition">§</a></dt>
+<dd><p>The total number of annotation records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Lrdb.numof_references">
+<span class="sig-name descname"><span class="pre">numof_references</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Lrdb.numof_references" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects and counts the
+references across all records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Lrdb.process">
+<span class="sig-name descname"><span class="pre">process</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Lrdb.process" title="Link to this definition">§</a></dt>
+<dd><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Lrdb.reload">
+<span class="sig-name descname"><span class="pre">reload</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Lrdb.reload" title="Link to this definition">§</a></dt>
+<dd><p>Reloads the object from the module level.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Lrdb.select">
+<span class="sig-name descname"><span class="pre">select</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Lrdb.select" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Lrdb.set_method">
+<span class="sig-name descname"><span class="pre">set_method</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Lrdb.set_method" title="Link to this definition">§</a></dt>
+<dd><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if
+necessary.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Lrdb.set_reference_set">
+<span class="sig-name descname"><span class="pre">set_reference_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Lrdb.set_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Assigns the reference set to the :py:attr``reference_set`` attribute.
+The reference set is the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Lrdb.show">
+<span class="sig-name descname"><span class="pre">show</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">table_param</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Lrdb.show" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic
+information from the UniProt datasheets.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Lrdb.subset_intersection">
+<span class="sig-name descname"><span class="pre">subset_intersection</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">universe</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Lrdb.subset_intersection" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the proportion of entities in a subset occuring in the
+set <code class="docutils literal notranslate"><span class="pre">universe</span></code>. The subset is selected by passing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> to the
+<code class="docutils literal notranslate"><span class="pre">select</span></code> method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Lrdb.to_array">
+<span class="sig-name descname"><span class="pre">to_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_fields</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Lrdb.to_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns an entity vs feature array. In case of more complex
+annotations this might be huge.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Lrdb.to_bool_array">
+<span class="sig-name descname"><span class="pre">to_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Lrdb.to_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a presence/absence boolean array for a reference set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Lrdb.to_set">
+<span class="sig-name descname"><span class="pre">to_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Lrdb.to_set" title="Link to this definition">§</a></dt>
+<dd><p>Returns the entities present in this annotation resource as a set.</p>
+</dd></dl>
+
+</dd></dl>
+
+</section>
+
+
+                </article>
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+  <section id="pypath-core-annot-matrisome">
+<h1>pypath.core.annot.Matrisome<a class="headerlink" href="#pypath-core-annot-matrisome" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.core.annot.Matrisome">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.core.annot.</span></span><span class="sig-name descname"><span class="pre">Matrisome</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#Matrisome"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.Matrisome" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <a class="reference internal" href="pypath.core.annot.AnnotationBase.html#pypath.core.annot.AnnotationBase" title="pypath.core.annot.AnnotationBase"><code class="xref py py-class docutils literal notranslate"><span class="pre">AnnotationBase</span></code></a></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Matrisome.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#Matrisome.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.Matrisome.__init__" title="Link to this definition">§</a></dt>
+<dd><p>Represents annotations for a set of proteins.
+Loads the data from the original resource and provides methods
+to query the annotations.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>name</strong> (<em>str</em>) – A custom name for the annotation resource.</p></li>
+<li><p><strong>ncbi_tax_id</strong> (<em>int</em>) – NCBI Taxonomy identifier.</p></li>
+<li><p><strong>input_method</strong> (<em>callable</em><em>,</em><em>str</em>) – Either a callable or the name of a method in any submodules of
+the <code class="docutils literal notranslate"><span class="pre">pypath.inputs</span></code>  module. Should return a dict with
+UniProt IDs as keys or an object suitable for <code class="docutils literal notranslate"><span class="pre">process_method</span></code>.</p></li>
+<li><p><strong>input_args</strong> (<em>dict</em>) – Arguments for the <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Matrisome.__init__" title="pypath.core.annot.Matrisome.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>([ncbi_tax_id])</p></td>
+<td><p>Represents annotations for a set of proteins.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Matrisome.add_complexes_by_inference" title="pypath.core.annot.Matrisome.add_complexes_by_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">add_complexes_by_inference</span></code></a>([complexes])</p></td>
+<td><p>Creates complex annotations by in silico inference and adds them to this annotation set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Matrisome.all_complexes" title="pypath.core.annot.Matrisome.all_complexes"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_complexes</span></code></a>()</p></td>
+<td><p>All protein complexes annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Matrisome.all_entities" title="pypath.core.annot.Matrisome.all_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_entities</span></code></a>([entity_types])</p></td>
+<td><p>All entities annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Matrisome.all_mirnas" title="pypath.core.annot.Matrisome.all_mirnas"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_mirnas</span></code></a>()</p></td>
+<td><p>All miRNAs annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Matrisome.all_proteins" title="pypath.core.annot.Matrisome.all_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_proteins</span></code></a>()</p></td>
+<td><p>All UniProt IDs annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Matrisome.all_refs" title="pypath.core.annot.Matrisome.all_refs"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_refs</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Matrisome.annotate_complex" title="pypath.core.annot.Matrisome.annotate_complex"><code class="xref py py-obj docutils literal notranslate"><span class="pre">annotate_complex</span></code></a>(cplex)</p></td>
+<td><p>Infers annotations for a single complex.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Matrisome.browse" title="pypath.core.annot.Matrisome.browse"><code class="xref py py-obj docutils literal notranslate"><span class="pre">browse</span></code></a>([field, start])</p></td>
+<td><p>Print gene information as a table.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Matrisome.complex_inference" title="pypath.core.annot.Matrisome.complex_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">complex_inference</span></code></a>([complexes])</p></td>
+<td><p>Annotates all complexes in <cite>complexes</cite>, by default in the default complex database (existing in the <cite>complex</cite> module or generated on demand according to the module's current settings).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Matrisome.coverage" title="pypath.core.annot.Matrisome.coverage"><code class="xref py py-obj docutils literal notranslate"><span class="pre">coverage</span></code></a>(other)</p></td>
+<td><p>Calculates the coverage of the annotation i.e. the proportion of entities having at least one record in this annotation resource for an arbitrary set of entities.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Matrisome.curation_effort" title="pypath.core.annot.Matrisome.curation_effort"><code class="xref py py-obj docutils literal notranslate"><span class="pre">curation_effort</span></code></a>()</p></td>
+<td><p>Counts the reference-record pairs.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">from_dump</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_entity_type</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Matrisome.get_names" title="pypath.core.annot.Matrisome.get_names"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_names</span></code></a>()</p></td>
+<td><p>Returns the list of field names in the records.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Matrisome.get_reference_set" title="pypath.core.annot.Matrisome.get_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_reference_set</span></code></a>([proteins, complexes, ...])</p></td>
+<td><p>Retrieves the reference set i.e. the set of all entities which potentially have annotation in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Matrisome.get_subset" title="pypath.core.annot.Matrisome.get_subset"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Matrisome.get_subset_bool_array" title="pypath.core.annot.Matrisome.get_subset_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset_bool_array</span></code></a>([reference_set])</p></td>
+<td><p>Returns a boolean vector with True and False values for each entity in the reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Matrisome.get_values" title="pypath.core.annot.Matrisome.get_values"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_values</span></code></a>(name[, exclude_none])</p></td>
+<td><p>Returns the set of all possible values of a field.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_complex</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_mirna</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_protein</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Matrisome.labels" title="pypath.core.annot.Matrisome.labels"><code class="xref py py-obj docutils literal notranslate"><span class="pre">labels</span></code></a>([method])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Matrisome.load" title="pypath.core.annot.Matrisome.load"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load</span></code></a>()</p></td>
+<td><p>Loads the annotation data by calling the input method.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Matrisome.load_data" title="pypath.core.annot.Matrisome.load_data"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_data</span></code></a>()</p></td>
+<td><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Matrisome.load_proteins" title="pypath.core.annot.Matrisome.load_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_proteins</span></code></a>()</p></td>
+<td><p>Retrieves a set of all UniProt IDs to have a base set of the entire proteome.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Matrisome.make_df" title="pypath.core.annot.Matrisome.make_df"><code class="xref py py-obj docutils literal notranslate"><span class="pre">make_df</span></code></a>([rebuild])</p></td>
+<td><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complex_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Matrisome.numof_entities" title="pypath.core.annot.Matrisome.numof_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_entities</span></code></a>()</p></td>
+<td><p>The number of annotated entities in the resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirna_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirnas</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_protein_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_proteins</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Matrisome.numof_records" title="pypath.core.annot.Matrisome.numof_records"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_records</span></code></a>([entity_types])</p></td>
+<td><p>The total number of annotation records.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Matrisome.numof_references" title="pypath.core.annot.Matrisome.numof_references"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_references</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Matrisome.process" title="pypath.core.annot.Matrisome.process"><code class="xref py py-obj docutils literal notranslate"><span class="pre">process</span></code></a>()</p></td>
+<td><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">proportion</span></code>(other)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Matrisome.reload" title="pypath.core.annot.Matrisome.reload"><code class="xref py py-obj docutils literal notranslate"><span class="pre">reload</span></code></a>()</p></td>
+<td><p>Reloads the object from the module level.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">save_to_pickle</span></code>(pickle_file)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Matrisome.select" title="pypath.core.annot.Matrisome.select"><code class="xref py py-obj docutils literal notranslate"><span class="pre">select</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Matrisome.set_method" title="pypath.core.annot.Matrisome.set_method"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_method</span></code></a>()</p></td>
+<td><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if necessary.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Matrisome.set_reference_set" title="pypath.core.annot.Matrisome.set_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_reference_set</span></code></a>()</p></td>
+<td><p>Assigns the reference set to the :py:attr``reference_set`` attribute.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Matrisome.show" title="pypath.core.annot.Matrisome.show"><code class="xref py py-obj docutils literal notranslate"><span class="pre">show</span></code></a>([method, table_param])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic information from the UniProt datasheets.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Matrisome.subset_intersection" title="pypath.core.annot.Matrisome.subset_intersection"><code class="xref py py-obj docutils literal notranslate"><span class="pre">subset_intersection</span></code></a>(universe, **kwargs)</p></td>
+<td><p>Calculates the proportion of entities in a subset occuring in the set <code class="docutils literal notranslate"><span class="pre">universe</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Matrisome.to_array" title="pypath.core.annot.Matrisome.to_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_array</span></code></a>([reference_set, use_fields])</p></td>
+<td><p>Returns an entity vs feature array.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Matrisome.to_bool_array" title="pypath.core.annot.Matrisome.to_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_bool_array</span></code></a>(reference_set)</p></td>
+<td><p>Returns a presence/absence boolean array for a reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Matrisome.to_set" title="pypath.core.annot.Matrisome.to_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_set</span></code></a>()</p></td>
+<td><p>Returns the entities present in this annotation resource as a set.</p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Attributes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_fields</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">summary</span></code></p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Matrisome.add_complexes_by_inference">
+<span class="sig-name descname"><span class="pre">add_complexes_by_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Matrisome.add_complexes_by_inference" title="Link to this definition">§</a></dt>
+<dd><p>Creates complex annotations by in silico inference and adds them
+to this annotation set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Matrisome.all_complexes">
+<span class="sig-name descname"><span class="pre">all_complexes</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Matrisome.all_complexes" title="Link to this definition">§</a></dt>
+<dd><p>All protein complexes annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Matrisome.all_entities">
+<span class="sig-name descname"><span class="pre">all_entities</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Matrisome.all_entities" title="Link to this definition">§</a></dt>
+<dd><p>All entities annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Matrisome.all_mirnas">
+<span class="sig-name descname"><span class="pre">all_mirnas</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Matrisome.all_mirnas" title="Link to this definition">§</a></dt>
+<dd><p>All miRNAs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Matrisome.all_proteins">
+<span class="sig-name descname"><span class="pre">all_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Matrisome.all_proteins" title="Link to this definition">§</a></dt>
+<dd><p>All UniProt IDs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Matrisome.all_refs">
+<span class="sig-name descname"><span class="pre">all_refs</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Matrisome.all_refs" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects the references
+across all records. Returns <em>list</em>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Matrisome.annotate_complex">
+<span class="sig-name descname"><span class="pre">annotate_complex</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cplex</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Matrisome.annotate_complex" title="Link to this definition">§</a></dt>
+<dd><p>Infers annotations for a single complex.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Matrisome.browse">
+<span class="sig-name descname"><span class="pre">browse</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">field</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">start</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Matrisome.browse" title="Link to this definition">§</a></dt>
+<dd><p>Print gene information as a table.</p>
+<p>Presents information about annotation categories as ascii tables
+printed in the terminal. If one category provided, prints one table.
+If multiple categories provided, prints a table for each of them one
+by one proceeding to the next one once you hit return. If no categories
+provided goes through all levels of the primary category.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>field:</dt><dd><p>The field to browse categories by.</p>
+<ul class="simple">
+<li><p>If None the primary field will be selected.
+If this annotation resource doesn’t have fields, all proteins
+will be presented as one single category.</p></li>
+<li><p>If a string it will be considered a field name and it will
+browse through all levels of this field.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">list</span></code>, set or tuple, it will be considered either a
+<code class="docutils literal notranslate"><span class="pre">list</span></code> of field names or a list of values from the primary
+field. In the former case all combinations of the values of
+the fields will be presented, in the latter case the browsing
+will be limited to the levels of the primary field contained
+in <code class="docutils literal notranslate"><span class="pre">field</span></code>.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">dict</span></code>, keys are supposed to be field names and values
+as list of levels. If any of the values are None, all levels
+from that field will be used.</p></li>
+</ul>
+</dd>
+<dt>start:</dt><dd><p>Start browsing from this category. E.g. if there are 500
+categories and start is 250 it will skip everything before the
+250th.</p>
+</dd>
+<dt>kwargs:</dt><dd><p>Passed to <code class="docutils literal notranslate"><span class="pre">pypath.utils.uniprot.info</span></code>.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Matrisome.complex_inference">
+<span class="sig-name descname"><span class="pre">complex_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Matrisome.complex_inference" title="Link to this definition">§</a></dt>
+<dd><p>Annotates all complexes in <cite>complexes</cite>, by default in the default
+complex database (existing in the <cite>complex</cite> module or generated
+on demand according to the module’s current settings).</p>
+<dl class="field-list simple">
+<dt class="field-odd">Returns<span class="colon">:</span></dt>
+<dd class="field-odd"><p><ul class="simple">
+<li><p><em>Dict with complexes as keys and sets of annotations as values.</em></p></li>
+<li><p><em>Complexes with no valid information in this annotation resource</em></p></li>
+<li><p><em>won’t be in the dict.</em></p></li>
+</ul>
+</p>
+</dd>
+<dt class="field-even">Parameters<span class="colon">:</span></dt>
+<dd class="field-even"><p><strong>complexes</strong> (<em>iterable</em>) – Iterable yielding complexes.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Matrisome.coverage">
+<span class="sig-name descname"><span class="pre">coverage</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">other</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Matrisome.coverage" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the coverage of the annotation i.e. the proportion of
+entities having at least one record in this annotation resource
+for an arbitrary set of entities.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Matrisome.curation_effort">
+<span class="sig-name descname"><span class="pre">curation_effort</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Matrisome.curation_effort" title="Link to this definition">§</a></dt>
+<dd><p>Counts the reference-record pairs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Matrisome.get_names">
+<span class="sig-name descname"><span class="pre">get_names</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Matrisome.get_names" title="Link to this definition">§</a></dt>
+<dd><p>Returns the list of field names in the records. The annotation
+consists of uniform records and each entity might be annotated
+with one or more records. Each record is a tuple of fields, for
+example <code class="docutils literal notranslate"><span class="pre">('cell_type',</span> <span class="pre">'expression_level',</span> <span class="pre">'score')</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Matrisome.get_reference_set">
+<em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">get_reference_set</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">proteins</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">swissprot_only</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Matrisome.get_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the reference set i.e. the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Matrisome.get_subset">
+<span class="sig-name descname"><span class="pre">get_subset</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Matrisome.get_subset" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Matrisome.get_subset_bool_array">
+<span class="sig-name descname"><span class="pre">get_subset_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Matrisome.get_subset_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a boolean vector with True and False values for each entity
+in the reference set. The values represent presence absence data
+in the simplest case, but by providing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> any kind of matching
+and filtering is possible. <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> are passed to the <code class="docutils literal notranslate"><span class="pre">select</span></code>
+method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Matrisome.get_values">
+<span class="sig-name descname"><span class="pre">get_values</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">exclude_none</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Matrisome.get_values" title="Link to this definition">§</a></dt>
+<dd><p>Returns the set of all possible values of a field. E.g. if the
+records of this annotation have a field <code class="docutils literal notranslate"><span class="pre">cell_type</span></code> then calling
+this method can tell you that across all records the values of
+this field might be <code class="docutils literal notranslate"><span class="pre">{'macrophage',</span> <span class="pre">'epithelial_cell',</span> <span class="pre">...}</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Matrisome.labels">
+<span class="sig-name descname"><span class="pre">labels</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Matrisome.labels" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Matrisome.load">
+<span class="sig-name descname"><span class="pre">load</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Matrisome.load" title="Link to this definition">§</a></dt>
+<dd><p>Loads the annotation data by calling the input method.
+Infers annotations for complexes in the complex database if
+py:attr:<code class="docutils literal notranslate"><span class="pre">infer_complexes</span></code> is True.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Matrisome.load_data">
+<span class="sig-name descname"><span class="pre">load_data</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Matrisome.load_data" title="Link to this definition">§</a></dt>
+<dd><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Matrisome.load_proteins">
+<span class="sig-name descname"><span class="pre">load_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Matrisome.load_proteins" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a set of all UniProt IDs to have a base set of the entire
+proteome.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Matrisome.make_df">
+<span class="sig-name descname"><span class="pre">make_df</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">rebuild</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Matrisome.make_df" title="Link to this definition">§</a></dt>
+<dd><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.
+The data frame will be assigned to :py:attr``df``.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Matrisome.numof_entities">
+<span class="sig-name descname"><span class="pre">numof_entities</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Matrisome.numof_entities" title="Link to this definition">§</a></dt>
+<dd><p>The number of annotated entities in the resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Matrisome.numof_records">
+<span class="sig-name descname"><span class="pre">numof_records</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Matrisome.numof_records" title="Link to this definition">§</a></dt>
+<dd><p>The total number of annotation records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Matrisome.numof_references">
+<span class="sig-name descname"><span class="pre">numof_references</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Matrisome.numof_references" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects and counts the
+references across all records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Matrisome.process">
+<span class="sig-name descname"><span class="pre">process</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Matrisome.process" title="Link to this definition">§</a></dt>
+<dd><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Matrisome.reload">
+<span class="sig-name descname"><span class="pre">reload</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Matrisome.reload" title="Link to this definition">§</a></dt>
+<dd><p>Reloads the object from the module level.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Matrisome.select">
+<span class="sig-name descname"><span class="pre">select</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Matrisome.select" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Matrisome.set_method">
+<span class="sig-name descname"><span class="pre">set_method</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Matrisome.set_method" title="Link to this definition">§</a></dt>
+<dd><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if
+necessary.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Matrisome.set_reference_set">
+<span class="sig-name descname"><span class="pre">set_reference_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Matrisome.set_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Assigns the reference set to the :py:attr``reference_set`` attribute.
+The reference set is the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Matrisome.show">
+<span class="sig-name descname"><span class="pre">show</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">table_param</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Matrisome.show" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic
+information from the UniProt datasheets.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Matrisome.subset_intersection">
+<span class="sig-name descname"><span class="pre">subset_intersection</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">universe</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Matrisome.subset_intersection" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the proportion of entities in a subset occuring in the
+set <code class="docutils literal notranslate"><span class="pre">universe</span></code>. The subset is selected by passing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> to the
+<code class="docutils literal notranslate"><span class="pre">select</span></code> method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Matrisome.to_array">
+<span class="sig-name descname"><span class="pre">to_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_fields</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Matrisome.to_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns an entity vs feature array. In case of more complex
+annotations this might be huge.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Matrisome.to_bool_array">
+<span class="sig-name descname"><span class="pre">to_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Matrisome.to_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a presence/absence boolean array for a reference set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Matrisome.to_set">
+<span class="sig-name descname"><span class="pre">to_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Matrisome.to_set" title="Link to this definition">§</a></dt>
+<dd><p>Returns the entities present in this annotation resource as a set.</p>
+</dd></dl>
+
+</dd></dl>
+
+</section>
+
+
+                </article>
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+  <section id="pypath-core-annot-matrixdb">
+<h1>pypath.core.annot.Matrixdb<a class="headerlink" href="#pypath-core-annot-matrixdb" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.core.annot.Matrixdb">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.core.annot.</span></span><span class="sig-name descname"><span class="pre">Matrixdb</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#Matrixdb"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.Matrixdb" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <a class="reference internal" href="pypath.core.annot.AnnotationBase.html#pypath.core.annot.AnnotationBase" title="pypath.core.annot.AnnotationBase"><code class="xref py py-class docutils literal notranslate"><span class="pre">AnnotationBase</span></code></a></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Matrixdb.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#Matrixdb.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.Matrixdb.__init__" title="Link to this definition">§</a></dt>
+<dd><p>Protein annotations from MatrixDB.</p>
+</dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Matrixdb.__init__" title="pypath.core.annot.Matrixdb.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>([ncbi_tax_id])</p></td>
+<td><p>Protein annotations from MatrixDB.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Matrixdb.add_complexes_by_inference" title="pypath.core.annot.Matrixdb.add_complexes_by_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">add_complexes_by_inference</span></code></a>([complexes])</p></td>
+<td><p>Creates complex annotations by in silico inference and adds them to this annotation set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Matrixdb.all_complexes" title="pypath.core.annot.Matrixdb.all_complexes"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_complexes</span></code></a>()</p></td>
+<td><p>All protein complexes annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Matrixdb.all_entities" title="pypath.core.annot.Matrixdb.all_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_entities</span></code></a>([entity_types])</p></td>
+<td><p>All entities annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Matrixdb.all_mirnas" title="pypath.core.annot.Matrixdb.all_mirnas"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_mirnas</span></code></a>()</p></td>
+<td><p>All miRNAs annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Matrixdb.all_proteins" title="pypath.core.annot.Matrixdb.all_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_proteins</span></code></a>()</p></td>
+<td><p>All UniProt IDs annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Matrixdb.all_refs" title="pypath.core.annot.Matrixdb.all_refs"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_refs</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Matrixdb.annotate_complex" title="pypath.core.annot.Matrixdb.annotate_complex"><code class="xref py py-obj docutils literal notranslate"><span class="pre">annotate_complex</span></code></a>(cplex)</p></td>
+<td><p>Infers annotations for a single complex.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Matrixdb.browse" title="pypath.core.annot.Matrixdb.browse"><code class="xref py py-obj docutils literal notranslate"><span class="pre">browse</span></code></a>([field, start])</p></td>
+<td><p>Print gene information as a table.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Matrixdb.complex_inference" title="pypath.core.annot.Matrixdb.complex_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">complex_inference</span></code></a>([complexes])</p></td>
+<td><p>Annotates all complexes in <cite>complexes</cite>, by default in the default complex database (existing in the <cite>complex</cite> module or generated on demand according to the module's current settings).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Matrixdb.coverage" title="pypath.core.annot.Matrixdb.coverage"><code class="xref py py-obj docutils literal notranslate"><span class="pre">coverage</span></code></a>(other)</p></td>
+<td><p>Calculates the coverage of the annotation i.e. the proportion of entities having at least one record in this annotation resource for an arbitrary set of entities.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Matrixdb.curation_effort" title="pypath.core.annot.Matrixdb.curation_effort"><code class="xref py py-obj docutils literal notranslate"><span class="pre">curation_effort</span></code></a>()</p></td>
+<td><p>Counts the reference-record pairs.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">from_dump</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_entity_type</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Matrixdb.get_names" title="pypath.core.annot.Matrixdb.get_names"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_names</span></code></a>()</p></td>
+<td><p>Returns the list of field names in the records.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Matrixdb.get_reference_set" title="pypath.core.annot.Matrixdb.get_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_reference_set</span></code></a>([proteins, complexes, ...])</p></td>
+<td><p>Retrieves the reference set i.e. the set of all entities which potentially have annotation in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Matrixdb.get_subset" title="pypath.core.annot.Matrixdb.get_subset"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Matrixdb.get_subset_bool_array" title="pypath.core.annot.Matrixdb.get_subset_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset_bool_array</span></code></a>([reference_set])</p></td>
+<td><p>Returns a boolean vector with True and False values for each entity in the reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Matrixdb.get_values" title="pypath.core.annot.Matrixdb.get_values"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_values</span></code></a>(name[, exclude_none])</p></td>
+<td><p>Returns the set of all possible values of a field.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_complex</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_mirna</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_protein</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Matrixdb.labels" title="pypath.core.annot.Matrixdb.labels"><code class="xref py py-obj docutils literal notranslate"><span class="pre">labels</span></code></a>([method])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Matrixdb.load" title="pypath.core.annot.Matrixdb.load"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load</span></code></a>()</p></td>
+<td><p>Loads the annotation data by calling the input method.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Matrixdb.load_data" title="pypath.core.annot.Matrixdb.load_data"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_data</span></code></a>()</p></td>
+<td><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Matrixdb.load_proteins" title="pypath.core.annot.Matrixdb.load_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_proteins</span></code></a>()</p></td>
+<td><p>Retrieves a set of all UniProt IDs to have a base set of the entire proteome.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Matrixdb.make_df" title="pypath.core.annot.Matrixdb.make_df"><code class="xref py py-obj docutils literal notranslate"><span class="pre">make_df</span></code></a>([rebuild])</p></td>
+<td><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complex_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Matrixdb.numof_entities" title="pypath.core.annot.Matrixdb.numof_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_entities</span></code></a>()</p></td>
+<td><p>The number of annotated entities in the resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirna_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirnas</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_protein_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_proteins</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Matrixdb.numof_records" title="pypath.core.annot.Matrixdb.numof_records"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_records</span></code></a>([entity_types])</p></td>
+<td><p>The total number of annotation records.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Matrixdb.numof_references" title="pypath.core.annot.Matrixdb.numof_references"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_references</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Matrixdb.process" title="pypath.core.annot.Matrixdb.process"><code class="xref py py-obj docutils literal notranslate"><span class="pre">process</span></code></a>()</p></td>
+<td><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">proportion</span></code>(other)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Matrixdb.reload" title="pypath.core.annot.Matrixdb.reload"><code class="xref py py-obj docutils literal notranslate"><span class="pre">reload</span></code></a>()</p></td>
+<td><p>Reloads the object from the module level.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">save_to_pickle</span></code>(pickle_file)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Matrixdb.select" title="pypath.core.annot.Matrixdb.select"><code class="xref py py-obj docutils literal notranslate"><span class="pre">select</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Matrixdb.set_method" title="pypath.core.annot.Matrixdb.set_method"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_method</span></code></a>()</p></td>
+<td><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if necessary.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Matrixdb.set_reference_set" title="pypath.core.annot.Matrixdb.set_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_reference_set</span></code></a>()</p></td>
+<td><p>Assigns the reference set to the :py:attr``reference_set`` attribute.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Matrixdb.show" title="pypath.core.annot.Matrixdb.show"><code class="xref py py-obj docutils literal notranslate"><span class="pre">show</span></code></a>([method, table_param])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic information from the UniProt datasheets.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Matrixdb.subset_intersection" title="pypath.core.annot.Matrixdb.subset_intersection"><code class="xref py py-obj docutils literal notranslate"><span class="pre">subset_intersection</span></code></a>(universe, **kwargs)</p></td>
+<td><p>Calculates the proportion of entities in a subset occuring in the set <code class="docutils literal notranslate"><span class="pre">universe</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Matrixdb.to_array" title="pypath.core.annot.Matrixdb.to_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_array</span></code></a>([reference_set, use_fields])</p></td>
+<td><p>Returns an entity vs feature array.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Matrixdb.to_bool_array" title="pypath.core.annot.Matrixdb.to_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_bool_array</span></code></a>(reference_set)</p></td>
+<td><p>Returns a presence/absence boolean array for a reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Matrixdb.to_set" title="pypath.core.annot.Matrixdb.to_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_set</span></code></a>()</p></td>
+<td><p>Returns the entities present in this annotation resource as a set.</p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Attributes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_fields</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">summary</span></code></p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Matrixdb.add_complexes_by_inference">
+<span class="sig-name descname"><span class="pre">add_complexes_by_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Matrixdb.add_complexes_by_inference" title="Link to this definition">§</a></dt>
+<dd><p>Creates complex annotations by in silico inference and adds them
+to this annotation set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Matrixdb.all_complexes">
+<span class="sig-name descname"><span class="pre">all_complexes</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Matrixdb.all_complexes" title="Link to this definition">§</a></dt>
+<dd><p>All protein complexes annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Matrixdb.all_entities">
+<span class="sig-name descname"><span class="pre">all_entities</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Matrixdb.all_entities" title="Link to this definition">§</a></dt>
+<dd><p>All entities annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Matrixdb.all_mirnas">
+<span class="sig-name descname"><span class="pre">all_mirnas</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Matrixdb.all_mirnas" title="Link to this definition">§</a></dt>
+<dd><p>All miRNAs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Matrixdb.all_proteins">
+<span class="sig-name descname"><span class="pre">all_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Matrixdb.all_proteins" title="Link to this definition">§</a></dt>
+<dd><p>All UniProt IDs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Matrixdb.all_refs">
+<span class="sig-name descname"><span class="pre">all_refs</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Matrixdb.all_refs" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects the references
+across all records. Returns <em>list</em>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Matrixdb.annotate_complex">
+<span class="sig-name descname"><span class="pre">annotate_complex</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cplex</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Matrixdb.annotate_complex" title="Link to this definition">§</a></dt>
+<dd><p>Infers annotations for a single complex.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Matrixdb.browse">
+<span class="sig-name descname"><span class="pre">browse</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">field</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">start</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Matrixdb.browse" title="Link to this definition">§</a></dt>
+<dd><p>Print gene information as a table.</p>
+<p>Presents information about annotation categories as ascii tables
+printed in the terminal. If one category provided, prints one table.
+If multiple categories provided, prints a table for each of them one
+by one proceeding to the next one once you hit return. If no categories
+provided goes through all levels of the primary category.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>field:</dt><dd><p>The field to browse categories by.</p>
+<ul class="simple">
+<li><p>If None the primary field will be selected.
+If this annotation resource doesn’t have fields, all proteins
+will be presented as one single category.</p></li>
+<li><p>If a string it will be considered a field name and it will
+browse through all levels of this field.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">list</span></code>, set or tuple, it will be considered either a
+<code class="docutils literal notranslate"><span class="pre">list</span></code> of field names or a list of values from the primary
+field. In the former case all combinations of the values of
+the fields will be presented, in the latter case the browsing
+will be limited to the levels of the primary field contained
+in <code class="docutils literal notranslate"><span class="pre">field</span></code>.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">dict</span></code>, keys are supposed to be field names and values
+as list of levels. If any of the values are None, all levels
+from that field will be used.</p></li>
+</ul>
+</dd>
+<dt>start:</dt><dd><p>Start browsing from this category. E.g. if there are 500
+categories and start is 250 it will skip everything before the
+250th.</p>
+</dd>
+<dt>kwargs:</dt><dd><p>Passed to <code class="docutils literal notranslate"><span class="pre">pypath.utils.uniprot.info</span></code>.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Matrixdb.complex_inference">
+<span class="sig-name descname"><span class="pre">complex_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Matrixdb.complex_inference" title="Link to this definition">§</a></dt>
+<dd><p>Annotates all complexes in <cite>complexes</cite>, by default in the default
+complex database (existing in the <cite>complex</cite> module or generated
+on demand according to the module’s current settings).</p>
+<dl class="field-list simple">
+<dt class="field-odd">Returns<span class="colon">:</span></dt>
+<dd class="field-odd"><p><ul class="simple">
+<li><p><em>Dict with complexes as keys and sets of annotations as values.</em></p></li>
+<li><p><em>Complexes with no valid information in this annotation resource</em></p></li>
+<li><p><em>won’t be in the dict.</em></p></li>
+</ul>
+</p>
+</dd>
+<dt class="field-even">Parameters<span class="colon">:</span></dt>
+<dd class="field-even"><p><strong>complexes</strong> (<em>iterable</em>) – Iterable yielding complexes.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Matrixdb.coverage">
+<span class="sig-name descname"><span class="pre">coverage</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">other</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Matrixdb.coverage" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the coverage of the annotation i.e. the proportion of
+entities having at least one record in this annotation resource
+for an arbitrary set of entities.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Matrixdb.curation_effort">
+<span class="sig-name descname"><span class="pre">curation_effort</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Matrixdb.curation_effort" title="Link to this definition">§</a></dt>
+<dd><p>Counts the reference-record pairs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Matrixdb.get_names">
+<span class="sig-name descname"><span class="pre">get_names</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Matrixdb.get_names" title="Link to this definition">§</a></dt>
+<dd><p>Returns the list of field names in the records. The annotation
+consists of uniform records and each entity might be annotated
+with one or more records. Each record is a tuple of fields, for
+example <code class="docutils literal notranslate"><span class="pre">('cell_type',</span> <span class="pre">'expression_level',</span> <span class="pre">'score')</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Matrixdb.get_reference_set">
+<em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">get_reference_set</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">proteins</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">swissprot_only</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Matrixdb.get_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the reference set i.e. the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Matrixdb.get_subset">
+<span class="sig-name descname"><span class="pre">get_subset</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Matrixdb.get_subset" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Matrixdb.get_subset_bool_array">
+<span class="sig-name descname"><span class="pre">get_subset_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Matrixdb.get_subset_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a boolean vector with True and False values for each entity
+in the reference set. The values represent presence absence data
+in the simplest case, but by providing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> any kind of matching
+and filtering is possible. <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> are passed to the <code class="docutils literal notranslate"><span class="pre">select</span></code>
+method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Matrixdb.get_values">
+<span class="sig-name descname"><span class="pre">get_values</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">exclude_none</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Matrixdb.get_values" title="Link to this definition">§</a></dt>
+<dd><p>Returns the set of all possible values of a field. E.g. if the
+records of this annotation have a field <code class="docutils literal notranslate"><span class="pre">cell_type</span></code> then calling
+this method can tell you that across all records the values of
+this field might be <code class="docutils literal notranslate"><span class="pre">{'macrophage',</span> <span class="pre">'epithelial_cell',</span> <span class="pre">...}</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Matrixdb.labels">
+<span class="sig-name descname"><span class="pre">labels</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Matrixdb.labels" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Matrixdb.load">
+<span class="sig-name descname"><span class="pre">load</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Matrixdb.load" title="Link to this definition">§</a></dt>
+<dd><p>Loads the annotation data by calling the input method.
+Infers annotations for complexes in the complex database if
+py:attr:<code class="docutils literal notranslate"><span class="pre">infer_complexes</span></code> is True.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Matrixdb.load_data">
+<span class="sig-name descname"><span class="pre">load_data</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Matrixdb.load_data" title="Link to this definition">§</a></dt>
+<dd><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Matrixdb.load_proteins">
+<span class="sig-name descname"><span class="pre">load_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Matrixdb.load_proteins" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a set of all UniProt IDs to have a base set of the entire
+proteome.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Matrixdb.make_df">
+<span class="sig-name descname"><span class="pre">make_df</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">rebuild</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Matrixdb.make_df" title="Link to this definition">§</a></dt>
+<dd><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.
+The data frame will be assigned to :py:attr``df``.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Matrixdb.numof_entities">
+<span class="sig-name descname"><span class="pre">numof_entities</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Matrixdb.numof_entities" title="Link to this definition">§</a></dt>
+<dd><p>The number of annotated entities in the resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Matrixdb.numof_records">
+<span class="sig-name descname"><span class="pre">numof_records</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Matrixdb.numof_records" title="Link to this definition">§</a></dt>
+<dd><p>The total number of annotation records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Matrixdb.numof_references">
+<span class="sig-name descname"><span class="pre">numof_references</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Matrixdb.numof_references" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects and counts the
+references across all records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Matrixdb.process">
+<span class="sig-name descname"><span class="pre">process</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Matrixdb.process" title="Link to this definition">§</a></dt>
+<dd><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Matrixdb.reload">
+<span class="sig-name descname"><span class="pre">reload</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Matrixdb.reload" title="Link to this definition">§</a></dt>
+<dd><p>Reloads the object from the module level.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Matrixdb.select">
+<span class="sig-name descname"><span class="pre">select</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Matrixdb.select" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Matrixdb.set_method">
+<span class="sig-name descname"><span class="pre">set_method</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Matrixdb.set_method" title="Link to this definition">§</a></dt>
+<dd><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if
+necessary.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Matrixdb.set_reference_set">
+<span class="sig-name descname"><span class="pre">set_reference_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Matrixdb.set_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Assigns the reference set to the :py:attr``reference_set`` attribute.
+The reference set is the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Matrixdb.show">
+<span class="sig-name descname"><span class="pre">show</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">table_param</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Matrixdb.show" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic
+information from the UniProt datasheets.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Matrixdb.subset_intersection">
+<span class="sig-name descname"><span class="pre">subset_intersection</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">universe</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Matrixdb.subset_intersection" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the proportion of entities in a subset occuring in the
+set <code class="docutils literal notranslate"><span class="pre">universe</span></code>. The subset is selected by passing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> to the
+<code class="docutils literal notranslate"><span class="pre">select</span></code> method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Matrixdb.to_array">
+<span class="sig-name descname"><span class="pre">to_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_fields</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Matrixdb.to_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns an entity vs feature array. In case of more complex
+annotations this might be huge.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Matrixdb.to_bool_array">
+<span class="sig-name descname"><span class="pre">to_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Matrixdb.to_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a presence/absence boolean array for a reference set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Matrixdb.to_set">
+<span class="sig-name descname"><span class="pre">to_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Matrixdb.to_set" title="Link to this definition">§</a></dt>
+<dd><p>Returns the entities present in this annotation resource as a set.</p>
+</dd></dl>
+
+</dd></dl>
+
+</section>
+
+
+                </article>
+              
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+  <section id="pypath-core-annot-mcam">
+<h1>pypath.core.annot.Mcam<a class="headerlink" href="#pypath-core-annot-mcam" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.core.annot.Mcam">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.core.annot.</span></span><span class="sig-name descname"><span class="pre">Mcam</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#Mcam"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.Mcam" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <a class="reference internal" href="pypath.core.annot.AnnotationBase.html#pypath.core.annot.AnnotationBase" title="pypath.core.annot.AnnotationBase"><code class="xref py py-class docutils literal notranslate"><span class="pre">AnnotationBase</span></code></a></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Mcam.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#Mcam.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.Mcam.__init__" title="Link to this definition">§</a></dt>
+<dd><p>List of cell adhesion molecules (CAMs) from 10.4137/cin.s341.</p>
+</dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Mcam.__init__" title="pypath.core.annot.Mcam.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>(**kwargs)</p></td>
+<td><p>List of cell adhesion molecules (CAMs) from 10.4137/cin.s341.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Mcam.add_complexes_by_inference" title="pypath.core.annot.Mcam.add_complexes_by_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">add_complexes_by_inference</span></code></a>([complexes])</p></td>
+<td><p>Creates complex annotations by in silico inference and adds them to this annotation set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Mcam.all_complexes" title="pypath.core.annot.Mcam.all_complexes"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_complexes</span></code></a>()</p></td>
+<td><p>All protein complexes annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Mcam.all_entities" title="pypath.core.annot.Mcam.all_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_entities</span></code></a>([entity_types])</p></td>
+<td><p>All entities annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Mcam.all_mirnas" title="pypath.core.annot.Mcam.all_mirnas"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_mirnas</span></code></a>()</p></td>
+<td><p>All miRNAs annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Mcam.all_proteins" title="pypath.core.annot.Mcam.all_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_proteins</span></code></a>()</p></td>
+<td><p>All UniProt IDs annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Mcam.all_refs" title="pypath.core.annot.Mcam.all_refs"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_refs</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Mcam.annotate_complex" title="pypath.core.annot.Mcam.annotate_complex"><code class="xref py py-obj docutils literal notranslate"><span class="pre">annotate_complex</span></code></a>(cplex)</p></td>
+<td><p>Infers annotations for a single complex.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Mcam.browse" title="pypath.core.annot.Mcam.browse"><code class="xref py py-obj docutils literal notranslate"><span class="pre">browse</span></code></a>([field, start])</p></td>
+<td><p>Print gene information as a table.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Mcam.complex_inference" title="pypath.core.annot.Mcam.complex_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">complex_inference</span></code></a>([complexes])</p></td>
+<td><p>Annotates all complexes in <cite>complexes</cite>, by default in the default complex database (existing in the <cite>complex</cite> module or generated on demand according to the module's current settings).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Mcam.coverage" title="pypath.core.annot.Mcam.coverage"><code class="xref py py-obj docutils literal notranslate"><span class="pre">coverage</span></code></a>(other)</p></td>
+<td><p>Calculates the coverage of the annotation i.e. the proportion of entities having at least one record in this annotation resource for an arbitrary set of entities.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Mcam.curation_effort" title="pypath.core.annot.Mcam.curation_effort"><code class="xref py py-obj docutils literal notranslate"><span class="pre">curation_effort</span></code></a>()</p></td>
+<td><p>Counts the reference-record pairs.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">from_dump</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_entity_type</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Mcam.get_names" title="pypath.core.annot.Mcam.get_names"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_names</span></code></a>()</p></td>
+<td><p>Returns the list of field names in the records.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Mcam.get_reference_set" title="pypath.core.annot.Mcam.get_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_reference_set</span></code></a>([proteins, complexes, ...])</p></td>
+<td><p>Retrieves the reference set i.e. the set of all entities which potentially have annotation in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Mcam.get_subset" title="pypath.core.annot.Mcam.get_subset"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Mcam.get_subset_bool_array" title="pypath.core.annot.Mcam.get_subset_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset_bool_array</span></code></a>([reference_set])</p></td>
+<td><p>Returns a boolean vector with True and False values for each entity in the reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Mcam.get_values" title="pypath.core.annot.Mcam.get_values"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_values</span></code></a>(name[, exclude_none])</p></td>
+<td><p>Returns the set of all possible values of a field.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_complex</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_mirna</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_protein</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Mcam.labels" title="pypath.core.annot.Mcam.labels"><code class="xref py py-obj docutils literal notranslate"><span class="pre">labels</span></code></a>([method])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Mcam.load" title="pypath.core.annot.Mcam.load"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load</span></code></a>()</p></td>
+<td><p>Loads the annotation data by calling the input method.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Mcam.load_data" title="pypath.core.annot.Mcam.load_data"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_data</span></code></a>()</p></td>
+<td><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Mcam.load_proteins" title="pypath.core.annot.Mcam.load_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_proteins</span></code></a>()</p></td>
+<td><p>Retrieves a set of all UniProt IDs to have a base set of the entire proteome.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Mcam.make_df" title="pypath.core.annot.Mcam.make_df"><code class="xref py py-obj docutils literal notranslate"><span class="pre">make_df</span></code></a>([rebuild])</p></td>
+<td><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complex_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Mcam.numof_entities" title="pypath.core.annot.Mcam.numof_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_entities</span></code></a>()</p></td>
+<td><p>The number of annotated entities in the resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirna_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirnas</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_protein_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_proteins</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Mcam.numof_records" title="pypath.core.annot.Mcam.numof_records"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_records</span></code></a>([entity_types])</p></td>
+<td><p>The total number of annotation records.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Mcam.numof_references" title="pypath.core.annot.Mcam.numof_references"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_references</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Mcam.process" title="pypath.core.annot.Mcam.process"><code class="xref py py-obj docutils literal notranslate"><span class="pre">process</span></code></a>()</p></td>
+<td><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">proportion</span></code>(other)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Mcam.reload" title="pypath.core.annot.Mcam.reload"><code class="xref py py-obj docutils literal notranslate"><span class="pre">reload</span></code></a>()</p></td>
+<td><p>Reloads the object from the module level.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">save_to_pickle</span></code>(pickle_file)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Mcam.select" title="pypath.core.annot.Mcam.select"><code class="xref py py-obj docutils literal notranslate"><span class="pre">select</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Mcam.set_method" title="pypath.core.annot.Mcam.set_method"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_method</span></code></a>()</p></td>
+<td><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if necessary.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Mcam.set_reference_set" title="pypath.core.annot.Mcam.set_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_reference_set</span></code></a>()</p></td>
+<td><p>Assigns the reference set to the :py:attr``reference_set`` attribute.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Mcam.show" title="pypath.core.annot.Mcam.show"><code class="xref py py-obj docutils literal notranslate"><span class="pre">show</span></code></a>([method, table_param])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic information from the UniProt datasheets.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Mcam.subset_intersection" title="pypath.core.annot.Mcam.subset_intersection"><code class="xref py py-obj docutils literal notranslate"><span class="pre">subset_intersection</span></code></a>(universe, **kwargs)</p></td>
+<td><p>Calculates the proportion of entities in a subset occuring in the set <code class="docutils literal notranslate"><span class="pre">universe</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Mcam.to_array" title="pypath.core.annot.Mcam.to_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_array</span></code></a>([reference_set, use_fields])</p></td>
+<td><p>Returns an entity vs feature array.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Mcam.to_bool_array" title="pypath.core.annot.Mcam.to_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_bool_array</span></code></a>(reference_set)</p></td>
+<td><p>Returns a presence/absence boolean array for a reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Mcam.to_set" title="pypath.core.annot.Mcam.to_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_set</span></code></a>()</p></td>
+<td><p>Returns the entities present in this annotation resource as a set.</p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Attributes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_fields</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">summary</span></code></p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Mcam.add_complexes_by_inference">
+<span class="sig-name descname"><span class="pre">add_complexes_by_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Mcam.add_complexes_by_inference" title="Link to this definition">§</a></dt>
+<dd><p>Creates complex annotations by in silico inference and adds them
+to this annotation set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Mcam.all_complexes">
+<span class="sig-name descname"><span class="pre">all_complexes</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Mcam.all_complexes" title="Link to this definition">§</a></dt>
+<dd><p>All protein complexes annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Mcam.all_entities">
+<span class="sig-name descname"><span class="pre">all_entities</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Mcam.all_entities" title="Link to this definition">§</a></dt>
+<dd><p>All entities annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Mcam.all_mirnas">
+<span class="sig-name descname"><span class="pre">all_mirnas</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Mcam.all_mirnas" title="Link to this definition">§</a></dt>
+<dd><p>All miRNAs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Mcam.all_proteins">
+<span class="sig-name descname"><span class="pre">all_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Mcam.all_proteins" title="Link to this definition">§</a></dt>
+<dd><p>All UniProt IDs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Mcam.all_refs">
+<span class="sig-name descname"><span class="pre">all_refs</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Mcam.all_refs" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects the references
+across all records. Returns <em>list</em>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Mcam.annotate_complex">
+<span class="sig-name descname"><span class="pre">annotate_complex</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cplex</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Mcam.annotate_complex" title="Link to this definition">§</a></dt>
+<dd><p>Infers annotations for a single complex.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Mcam.browse">
+<span class="sig-name descname"><span class="pre">browse</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">field</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">start</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Mcam.browse" title="Link to this definition">§</a></dt>
+<dd><p>Print gene information as a table.</p>
+<p>Presents information about annotation categories as ascii tables
+printed in the terminal. If one category provided, prints one table.
+If multiple categories provided, prints a table for each of them one
+by one proceeding to the next one once you hit return. If no categories
+provided goes through all levels of the primary category.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>field:</dt><dd><p>The field to browse categories by.</p>
+<ul class="simple">
+<li><p>If None the primary field will be selected.
+If this annotation resource doesn’t have fields, all proteins
+will be presented as one single category.</p></li>
+<li><p>If a string it will be considered a field name and it will
+browse through all levels of this field.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">list</span></code>, set or tuple, it will be considered either a
+<code class="docutils literal notranslate"><span class="pre">list</span></code> of field names or a list of values from the primary
+field. In the former case all combinations of the values of
+the fields will be presented, in the latter case the browsing
+will be limited to the levels of the primary field contained
+in <code class="docutils literal notranslate"><span class="pre">field</span></code>.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">dict</span></code>, keys are supposed to be field names and values
+as list of levels. If any of the values are None, all levels
+from that field will be used.</p></li>
+</ul>
+</dd>
+<dt>start:</dt><dd><p>Start browsing from this category. E.g. if there are 500
+categories and start is 250 it will skip everything before the
+250th.</p>
+</dd>
+<dt>kwargs:</dt><dd><p>Passed to <code class="docutils literal notranslate"><span class="pre">pypath.utils.uniprot.info</span></code>.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Mcam.complex_inference">
+<span class="sig-name descname"><span class="pre">complex_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Mcam.complex_inference" title="Link to this definition">§</a></dt>
+<dd><p>Annotates all complexes in <cite>complexes</cite>, by default in the default
+complex database (existing in the <cite>complex</cite> module or generated
+on demand according to the module’s current settings).</p>
+<dl class="field-list simple">
+<dt class="field-odd">Returns<span class="colon">:</span></dt>
+<dd class="field-odd"><p><ul class="simple">
+<li><p><em>Dict with complexes as keys and sets of annotations as values.</em></p></li>
+<li><p><em>Complexes with no valid information in this annotation resource</em></p></li>
+<li><p><em>won’t be in the dict.</em></p></li>
+</ul>
+</p>
+</dd>
+<dt class="field-even">Parameters<span class="colon">:</span></dt>
+<dd class="field-even"><p><strong>complexes</strong> (<em>iterable</em>) – Iterable yielding complexes.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Mcam.coverage">
+<span class="sig-name descname"><span class="pre">coverage</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">other</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Mcam.coverage" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the coverage of the annotation i.e. the proportion of
+entities having at least one record in this annotation resource
+for an arbitrary set of entities.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Mcam.curation_effort">
+<span class="sig-name descname"><span class="pre">curation_effort</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Mcam.curation_effort" title="Link to this definition">§</a></dt>
+<dd><p>Counts the reference-record pairs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Mcam.get_names">
+<span class="sig-name descname"><span class="pre">get_names</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Mcam.get_names" title="Link to this definition">§</a></dt>
+<dd><p>Returns the list of field names in the records. The annotation
+consists of uniform records and each entity might be annotated
+with one or more records. Each record is a tuple of fields, for
+example <code class="docutils literal notranslate"><span class="pre">('cell_type',</span> <span class="pre">'expression_level',</span> <span class="pre">'score')</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Mcam.get_reference_set">
+<em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">get_reference_set</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">proteins</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">swissprot_only</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Mcam.get_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the reference set i.e. the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Mcam.get_subset">
+<span class="sig-name descname"><span class="pre">get_subset</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Mcam.get_subset" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Mcam.get_subset_bool_array">
+<span class="sig-name descname"><span class="pre">get_subset_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Mcam.get_subset_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a boolean vector with True and False values for each entity
+in the reference set. The values represent presence absence data
+in the simplest case, but by providing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> any kind of matching
+and filtering is possible. <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> are passed to the <code class="docutils literal notranslate"><span class="pre">select</span></code>
+method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Mcam.get_values">
+<span class="sig-name descname"><span class="pre">get_values</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">exclude_none</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Mcam.get_values" title="Link to this definition">§</a></dt>
+<dd><p>Returns the set of all possible values of a field. E.g. if the
+records of this annotation have a field <code class="docutils literal notranslate"><span class="pre">cell_type</span></code> then calling
+this method can tell you that across all records the values of
+this field might be <code class="docutils literal notranslate"><span class="pre">{'macrophage',</span> <span class="pre">'epithelial_cell',</span> <span class="pre">...}</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Mcam.labels">
+<span class="sig-name descname"><span class="pre">labels</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Mcam.labels" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Mcam.load">
+<span class="sig-name descname"><span class="pre">load</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Mcam.load" title="Link to this definition">§</a></dt>
+<dd><p>Loads the annotation data by calling the input method.
+Infers annotations for complexes in the complex database if
+py:attr:<code class="docutils literal notranslate"><span class="pre">infer_complexes</span></code> is True.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Mcam.load_data">
+<span class="sig-name descname"><span class="pre">load_data</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Mcam.load_data" title="Link to this definition">§</a></dt>
+<dd><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Mcam.load_proteins">
+<span class="sig-name descname"><span class="pre">load_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Mcam.load_proteins" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a set of all UniProt IDs to have a base set of the entire
+proteome.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Mcam.make_df">
+<span class="sig-name descname"><span class="pre">make_df</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">rebuild</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Mcam.make_df" title="Link to this definition">§</a></dt>
+<dd><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.
+The data frame will be assigned to :py:attr``df``.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Mcam.numof_entities">
+<span class="sig-name descname"><span class="pre">numof_entities</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Mcam.numof_entities" title="Link to this definition">§</a></dt>
+<dd><p>The number of annotated entities in the resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Mcam.numof_records">
+<span class="sig-name descname"><span class="pre">numof_records</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Mcam.numof_records" title="Link to this definition">§</a></dt>
+<dd><p>The total number of annotation records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Mcam.numof_references">
+<span class="sig-name descname"><span class="pre">numof_references</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Mcam.numof_references" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects and counts the
+references across all records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Mcam.process">
+<span class="sig-name descname"><span class="pre">process</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Mcam.process" title="Link to this definition">§</a></dt>
+<dd><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Mcam.reload">
+<span class="sig-name descname"><span class="pre">reload</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Mcam.reload" title="Link to this definition">§</a></dt>
+<dd><p>Reloads the object from the module level.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Mcam.select">
+<span class="sig-name descname"><span class="pre">select</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Mcam.select" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Mcam.set_method">
+<span class="sig-name descname"><span class="pre">set_method</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Mcam.set_method" title="Link to this definition">§</a></dt>
+<dd><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if
+necessary.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Mcam.set_reference_set">
+<span class="sig-name descname"><span class="pre">set_reference_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Mcam.set_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Assigns the reference set to the :py:attr``reference_set`` attribute.
+The reference set is the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Mcam.show">
+<span class="sig-name descname"><span class="pre">show</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">table_param</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Mcam.show" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic
+information from the UniProt datasheets.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Mcam.subset_intersection">
+<span class="sig-name descname"><span class="pre">subset_intersection</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">universe</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Mcam.subset_intersection" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the proportion of entities in a subset occuring in the
+set <code class="docutils literal notranslate"><span class="pre">universe</span></code>. The subset is selected by passing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> to the
+<code class="docutils literal notranslate"><span class="pre">select</span></code> method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Mcam.to_array">
+<span class="sig-name descname"><span class="pre">to_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_fields</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Mcam.to_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns an entity vs feature array. In case of more complex
+annotations this might be huge.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Mcam.to_bool_array">
+<span class="sig-name descname"><span class="pre">to_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Mcam.to_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a presence/absence boolean array for a reference set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Mcam.to_set">
+<span class="sig-name descname"><span class="pre">to_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Mcam.to_set" title="Link to this definition">§</a></dt>
+<dd><p>Returns the entities present in this annotation resource as a set.</p>
+</dd></dl>
+
+</dd></dl>
+
+</section>
+
+
+                </article>
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+  <section id="pypath-core-annot-membranome">
+<h1>pypath.core.annot.Membranome<a class="headerlink" href="#pypath-core-annot-membranome" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.core.annot.Membranome">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.core.annot.</span></span><span class="sig-name descname"><span class="pre">Membranome</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#Membranome"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.Membranome" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <a class="reference internal" href="pypath.core.annot.AnnotationBase.html#pypath.core.annot.AnnotationBase" title="pypath.core.annot.AnnotationBase"><code class="xref py py-class docutils literal notranslate"><span class="pre">AnnotationBase</span></code></a></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Membranome.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#Membranome.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.Membranome.__init__" title="Link to this definition">§</a></dt>
+<dd><p>Represents annotations for a set of proteins.
+Loads the data from the original resource and provides methods
+to query the annotations.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>name</strong> (<em>str</em>) – A custom name for the annotation resource.</p></li>
+<li><p><strong>ncbi_tax_id</strong> (<em>int</em>) – NCBI Taxonomy identifier.</p></li>
+<li><p><strong>input_method</strong> (<em>callable</em><em>,</em><em>str</em>) – Either a callable or the name of a method in any submodules of
+the <code class="docutils literal notranslate"><span class="pre">pypath.inputs</span></code>  module. Should return a dict with
+UniProt IDs as keys or an object suitable for <code class="docutils literal notranslate"><span class="pre">process_method</span></code>.</p></li>
+<li><p><strong>input_args</strong> (<em>dict</em>) – Arguments for the <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Membranome.__init__" title="pypath.core.annot.Membranome.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>(**kwargs)</p></td>
+<td><p>Represents annotations for a set of proteins.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Membranome.add_complexes_by_inference" title="pypath.core.annot.Membranome.add_complexes_by_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">add_complexes_by_inference</span></code></a>([complexes])</p></td>
+<td><p>Creates complex annotations by in silico inference and adds them to this annotation set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Membranome.all_complexes" title="pypath.core.annot.Membranome.all_complexes"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_complexes</span></code></a>()</p></td>
+<td><p>All protein complexes annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Membranome.all_entities" title="pypath.core.annot.Membranome.all_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_entities</span></code></a>([entity_types])</p></td>
+<td><p>All entities annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Membranome.all_mirnas" title="pypath.core.annot.Membranome.all_mirnas"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_mirnas</span></code></a>()</p></td>
+<td><p>All miRNAs annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Membranome.all_proteins" title="pypath.core.annot.Membranome.all_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_proteins</span></code></a>()</p></td>
+<td><p>All UniProt IDs annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Membranome.all_refs" title="pypath.core.annot.Membranome.all_refs"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_refs</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Membranome.annotate_complex" title="pypath.core.annot.Membranome.annotate_complex"><code class="xref py py-obj docutils literal notranslate"><span class="pre">annotate_complex</span></code></a>(cplex)</p></td>
+<td><p>Infers annotations for a single complex.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Membranome.browse" title="pypath.core.annot.Membranome.browse"><code class="xref py py-obj docutils literal notranslate"><span class="pre">browse</span></code></a>([field, start])</p></td>
+<td><p>Print gene information as a table.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Membranome.complex_inference" title="pypath.core.annot.Membranome.complex_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">complex_inference</span></code></a>([complexes])</p></td>
+<td><p>Annotates all complexes in <cite>complexes</cite>, by default in the default complex database (existing in the <cite>complex</cite> module or generated on demand according to the module's current settings).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Membranome.coverage" title="pypath.core.annot.Membranome.coverage"><code class="xref py py-obj docutils literal notranslate"><span class="pre">coverage</span></code></a>(other)</p></td>
+<td><p>Calculates the coverage of the annotation i.e. the proportion of entities having at least one record in this annotation resource for an arbitrary set of entities.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Membranome.curation_effort" title="pypath.core.annot.Membranome.curation_effort"><code class="xref py py-obj docutils literal notranslate"><span class="pre">curation_effort</span></code></a>()</p></td>
+<td><p>Counts the reference-record pairs.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">from_dump</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_entity_type</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Membranome.get_names" title="pypath.core.annot.Membranome.get_names"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_names</span></code></a>()</p></td>
+<td><p>Returns the list of field names in the records.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Membranome.get_reference_set" title="pypath.core.annot.Membranome.get_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_reference_set</span></code></a>([proteins, complexes, ...])</p></td>
+<td><p>Retrieves the reference set i.e. the set of all entities which potentially have annotation in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Membranome.get_subset" title="pypath.core.annot.Membranome.get_subset"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Membranome.get_subset_bool_array" title="pypath.core.annot.Membranome.get_subset_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset_bool_array</span></code></a>([reference_set])</p></td>
+<td><p>Returns a boolean vector with True and False values for each entity in the reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Membranome.get_values" title="pypath.core.annot.Membranome.get_values"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_values</span></code></a>(name[, exclude_none])</p></td>
+<td><p>Returns the set of all possible values of a field.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_complex</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_mirna</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_protein</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Membranome.labels" title="pypath.core.annot.Membranome.labels"><code class="xref py py-obj docutils literal notranslate"><span class="pre">labels</span></code></a>([method])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Membranome.load" title="pypath.core.annot.Membranome.load"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load</span></code></a>()</p></td>
+<td><p>Loads the annotation data by calling the input method.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Membranome.load_data" title="pypath.core.annot.Membranome.load_data"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_data</span></code></a>()</p></td>
+<td><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Membranome.load_proteins" title="pypath.core.annot.Membranome.load_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_proteins</span></code></a>()</p></td>
+<td><p>Retrieves a set of all UniProt IDs to have a base set of the entire proteome.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Membranome.make_df" title="pypath.core.annot.Membranome.make_df"><code class="xref py py-obj docutils literal notranslate"><span class="pre">make_df</span></code></a>([rebuild])</p></td>
+<td><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complex_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Membranome.numof_entities" title="pypath.core.annot.Membranome.numof_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_entities</span></code></a>()</p></td>
+<td><p>The number of annotated entities in the resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirna_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirnas</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_protein_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_proteins</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Membranome.numof_records" title="pypath.core.annot.Membranome.numof_records"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_records</span></code></a>([entity_types])</p></td>
+<td><p>The total number of annotation records.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Membranome.numof_references" title="pypath.core.annot.Membranome.numof_references"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_references</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Membranome.process" title="pypath.core.annot.Membranome.process"><code class="xref py py-obj docutils literal notranslate"><span class="pre">process</span></code></a>()</p></td>
+<td><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">proportion</span></code>(other)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Membranome.reload" title="pypath.core.annot.Membranome.reload"><code class="xref py py-obj docutils literal notranslate"><span class="pre">reload</span></code></a>()</p></td>
+<td><p>Reloads the object from the module level.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">save_to_pickle</span></code>(pickle_file)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Membranome.select" title="pypath.core.annot.Membranome.select"><code class="xref py py-obj docutils literal notranslate"><span class="pre">select</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Membranome.set_method" title="pypath.core.annot.Membranome.set_method"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_method</span></code></a>()</p></td>
+<td><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if necessary.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Membranome.set_reference_set" title="pypath.core.annot.Membranome.set_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_reference_set</span></code></a>()</p></td>
+<td><p>Assigns the reference set to the :py:attr``reference_set`` attribute.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Membranome.show" title="pypath.core.annot.Membranome.show"><code class="xref py py-obj docutils literal notranslate"><span class="pre">show</span></code></a>([method, table_param])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic information from the UniProt datasheets.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Membranome.subset_intersection" title="pypath.core.annot.Membranome.subset_intersection"><code class="xref py py-obj docutils literal notranslate"><span class="pre">subset_intersection</span></code></a>(universe, **kwargs)</p></td>
+<td><p>Calculates the proportion of entities in a subset occuring in the set <code class="docutils literal notranslate"><span class="pre">universe</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Membranome.to_array" title="pypath.core.annot.Membranome.to_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_array</span></code></a>([reference_set, use_fields])</p></td>
+<td><p>Returns an entity vs feature array.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Membranome.to_bool_array" title="pypath.core.annot.Membranome.to_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_bool_array</span></code></a>(reference_set)</p></td>
+<td><p>Returns a presence/absence boolean array for a reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Membranome.to_set" title="pypath.core.annot.Membranome.to_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_set</span></code></a>()</p></td>
+<td><p>Returns the entities present in this annotation resource as a set.</p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Attributes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_fields</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">summary</span></code></p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Membranome.add_complexes_by_inference">
+<span class="sig-name descname"><span class="pre">add_complexes_by_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Membranome.add_complexes_by_inference" title="Link to this definition">§</a></dt>
+<dd><p>Creates complex annotations by in silico inference and adds them
+to this annotation set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Membranome.all_complexes">
+<span class="sig-name descname"><span class="pre">all_complexes</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Membranome.all_complexes" title="Link to this definition">§</a></dt>
+<dd><p>All protein complexes annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Membranome.all_entities">
+<span class="sig-name descname"><span class="pre">all_entities</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Membranome.all_entities" title="Link to this definition">§</a></dt>
+<dd><p>All entities annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Membranome.all_mirnas">
+<span class="sig-name descname"><span class="pre">all_mirnas</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Membranome.all_mirnas" title="Link to this definition">§</a></dt>
+<dd><p>All miRNAs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Membranome.all_proteins">
+<span class="sig-name descname"><span class="pre">all_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Membranome.all_proteins" title="Link to this definition">§</a></dt>
+<dd><p>All UniProt IDs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Membranome.all_refs">
+<span class="sig-name descname"><span class="pre">all_refs</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Membranome.all_refs" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects the references
+across all records. Returns <em>list</em>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Membranome.annotate_complex">
+<span class="sig-name descname"><span class="pre">annotate_complex</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cplex</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Membranome.annotate_complex" title="Link to this definition">§</a></dt>
+<dd><p>Infers annotations for a single complex.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Membranome.browse">
+<span class="sig-name descname"><span class="pre">browse</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">field</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">start</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Membranome.browse" title="Link to this definition">§</a></dt>
+<dd><p>Print gene information as a table.</p>
+<p>Presents information about annotation categories as ascii tables
+printed in the terminal. If one category provided, prints one table.
+If multiple categories provided, prints a table for each of them one
+by one proceeding to the next one once you hit return. If no categories
+provided goes through all levels of the primary category.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>field:</dt><dd><p>The field to browse categories by.</p>
+<ul class="simple">
+<li><p>If None the primary field will be selected.
+If this annotation resource doesn’t have fields, all proteins
+will be presented as one single category.</p></li>
+<li><p>If a string it will be considered a field name and it will
+browse through all levels of this field.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">list</span></code>, set or tuple, it will be considered either a
+<code class="docutils literal notranslate"><span class="pre">list</span></code> of field names or a list of values from the primary
+field. In the former case all combinations of the values of
+the fields will be presented, in the latter case the browsing
+will be limited to the levels of the primary field contained
+in <code class="docutils literal notranslate"><span class="pre">field</span></code>.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">dict</span></code>, keys are supposed to be field names and values
+as list of levels. If any of the values are None, all levels
+from that field will be used.</p></li>
+</ul>
+</dd>
+<dt>start:</dt><dd><p>Start browsing from this category. E.g. if there are 500
+categories and start is 250 it will skip everything before the
+250th.</p>
+</dd>
+<dt>kwargs:</dt><dd><p>Passed to <code class="docutils literal notranslate"><span class="pre">pypath.utils.uniprot.info</span></code>.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Membranome.complex_inference">
+<span class="sig-name descname"><span class="pre">complex_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Membranome.complex_inference" title="Link to this definition">§</a></dt>
+<dd><p>Annotates all complexes in <cite>complexes</cite>, by default in the default
+complex database (existing in the <cite>complex</cite> module or generated
+on demand according to the module’s current settings).</p>
+<dl class="field-list simple">
+<dt class="field-odd">Returns<span class="colon">:</span></dt>
+<dd class="field-odd"><p><ul class="simple">
+<li><p><em>Dict with complexes as keys and sets of annotations as values.</em></p></li>
+<li><p><em>Complexes with no valid information in this annotation resource</em></p></li>
+<li><p><em>won’t be in the dict.</em></p></li>
+</ul>
+</p>
+</dd>
+<dt class="field-even">Parameters<span class="colon">:</span></dt>
+<dd class="field-even"><p><strong>complexes</strong> (<em>iterable</em>) – Iterable yielding complexes.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Membranome.coverage">
+<span class="sig-name descname"><span class="pre">coverage</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">other</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Membranome.coverage" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the coverage of the annotation i.e. the proportion of
+entities having at least one record in this annotation resource
+for an arbitrary set of entities.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Membranome.curation_effort">
+<span class="sig-name descname"><span class="pre">curation_effort</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Membranome.curation_effort" title="Link to this definition">§</a></dt>
+<dd><p>Counts the reference-record pairs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Membranome.get_names">
+<span class="sig-name descname"><span class="pre">get_names</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Membranome.get_names" title="Link to this definition">§</a></dt>
+<dd><p>Returns the list of field names in the records. The annotation
+consists of uniform records and each entity might be annotated
+with one or more records. Each record is a tuple of fields, for
+example <code class="docutils literal notranslate"><span class="pre">('cell_type',</span> <span class="pre">'expression_level',</span> <span class="pre">'score')</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Membranome.get_reference_set">
+<em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">get_reference_set</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">proteins</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">swissprot_only</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Membranome.get_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the reference set i.e. the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Membranome.get_subset">
+<span class="sig-name descname"><span class="pre">get_subset</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Membranome.get_subset" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Membranome.get_subset_bool_array">
+<span class="sig-name descname"><span class="pre">get_subset_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Membranome.get_subset_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a boolean vector with True and False values for each entity
+in the reference set. The values represent presence absence data
+in the simplest case, but by providing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> any kind of matching
+and filtering is possible. <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> are passed to the <code class="docutils literal notranslate"><span class="pre">select</span></code>
+method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Membranome.get_values">
+<span class="sig-name descname"><span class="pre">get_values</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">exclude_none</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Membranome.get_values" title="Link to this definition">§</a></dt>
+<dd><p>Returns the set of all possible values of a field. E.g. if the
+records of this annotation have a field <code class="docutils literal notranslate"><span class="pre">cell_type</span></code> then calling
+this method can tell you that across all records the values of
+this field might be <code class="docutils literal notranslate"><span class="pre">{'macrophage',</span> <span class="pre">'epithelial_cell',</span> <span class="pre">...}</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Membranome.labels">
+<span class="sig-name descname"><span class="pre">labels</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Membranome.labels" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Membranome.load">
+<span class="sig-name descname"><span class="pre">load</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Membranome.load" title="Link to this definition">§</a></dt>
+<dd><p>Loads the annotation data by calling the input method.
+Infers annotations for complexes in the complex database if
+py:attr:<code class="docutils literal notranslate"><span class="pre">infer_complexes</span></code> is True.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Membranome.load_data">
+<span class="sig-name descname"><span class="pre">load_data</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Membranome.load_data" title="Link to this definition">§</a></dt>
+<dd><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Membranome.load_proteins">
+<span class="sig-name descname"><span class="pre">load_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Membranome.load_proteins" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a set of all UniProt IDs to have a base set of the entire
+proteome.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Membranome.make_df">
+<span class="sig-name descname"><span class="pre">make_df</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">rebuild</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Membranome.make_df" title="Link to this definition">§</a></dt>
+<dd><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.
+The data frame will be assigned to :py:attr``df``.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Membranome.numof_entities">
+<span class="sig-name descname"><span class="pre">numof_entities</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Membranome.numof_entities" title="Link to this definition">§</a></dt>
+<dd><p>The number of annotated entities in the resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Membranome.numof_records">
+<span class="sig-name descname"><span class="pre">numof_records</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Membranome.numof_records" title="Link to this definition">§</a></dt>
+<dd><p>The total number of annotation records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Membranome.numof_references">
+<span class="sig-name descname"><span class="pre">numof_references</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Membranome.numof_references" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects and counts the
+references across all records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Membranome.process">
+<span class="sig-name descname"><span class="pre">process</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Membranome.process" title="Link to this definition">§</a></dt>
+<dd><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Membranome.reload">
+<span class="sig-name descname"><span class="pre">reload</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Membranome.reload" title="Link to this definition">§</a></dt>
+<dd><p>Reloads the object from the module level.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Membranome.select">
+<span class="sig-name descname"><span class="pre">select</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Membranome.select" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Membranome.set_method">
+<span class="sig-name descname"><span class="pre">set_method</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Membranome.set_method" title="Link to this definition">§</a></dt>
+<dd><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if
+necessary.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Membranome.set_reference_set">
+<span class="sig-name descname"><span class="pre">set_reference_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Membranome.set_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Assigns the reference set to the :py:attr``reference_set`` attribute.
+The reference set is the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Membranome.show">
+<span class="sig-name descname"><span class="pre">show</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">table_param</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Membranome.show" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic
+information from the UniProt datasheets.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Membranome.subset_intersection">
+<span class="sig-name descname"><span class="pre">subset_intersection</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">universe</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Membranome.subset_intersection" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the proportion of entities in a subset occuring in the
+set <code class="docutils literal notranslate"><span class="pre">universe</span></code>. The subset is selected by passing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> to the
+<code class="docutils literal notranslate"><span class="pre">select</span></code> method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Membranome.to_array">
+<span class="sig-name descname"><span class="pre">to_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_fields</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Membranome.to_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns an entity vs feature array. In case of more complex
+annotations this might be huge.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Membranome.to_bool_array">
+<span class="sig-name descname"><span class="pre">to_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Membranome.to_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a presence/absence boolean array for a reference set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Membranome.to_set">
+<span class="sig-name descname"><span class="pre">to_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Membranome.to_set" title="Link to this definition">§</a></dt>
+<dd><p>Returns the entities present in this annotation resource as a set.</p>
+</dd></dl>
+
+</dd></dl>
+
+</section>
+
+
+                </article>
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+  <section id="pypath-core-annot-msigdb">
+<h1>pypath.core.annot.Msigdb<a class="headerlink" href="#pypath-core-annot-msigdb" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.core.annot.Msigdb">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.core.annot.</span></span><span class="sig-name descname"><span class="pre">Msigdb</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#Msigdb"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.Msigdb" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <a class="reference internal" href="pypath.core.annot.AnnotationBase.html#pypath.core.annot.AnnotationBase" title="pypath.core.annot.AnnotationBase"><code class="xref py py-class docutils literal notranslate"><span class="pre">AnnotationBase</span></code></a></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Msigdb.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#Msigdb.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.Msigdb.__init__" title="Link to this definition">§</a></dt>
+<dd><p>Represents annotations for a set of proteins.
+Loads the data from the original resource and provides methods
+to query the annotations.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>name</strong> (<em>str</em>) – A custom name for the annotation resource.</p></li>
+<li><p><strong>ncbi_tax_id</strong> (<em>int</em>) – NCBI Taxonomy identifier.</p></li>
+<li><p><strong>input_method</strong> (<em>callable</em><em>,</em><em>str</em>) – Either a callable or the name of a method in any submodules of
+the <code class="docutils literal notranslate"><span class="pre">pypath.inputs</span></code>  module. Should return a dict with
+UniProt IDs as keys or an object suitable for <code class="docutils literal notranslate"><span class="pre">process_method</span></code>.</p></li>
+<li><p><strong>input_args</strong> (<em>dict</em>) – Arguments for the <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Msigdb.__init__" title="pypath.core.annot.Msigdb.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>([ncbi_tax_id])</p></td>
+<td><p>Represents annotations for a set of proteins.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Msigdb.add_complexes_by_inference" title="pypath.core.annot.Msigdb.add_complexes_by_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">add_complexes_by_inference</span></code></a>([complexes])</p></td>
+<td><p>Creates complex annotations by in silico inference and adds them to this annotation set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Msigdb.all_complexes" title="pypath.core.annot.Msigdb.all_complexes"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_complexes</span></code></a>()</p></td>
+<td><p>All protein complexes annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Msigdb.all_entities" title="pypath.core.annot.Msigdb.all_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_entities</span></code></a>([entity_types])</p></td>
+<td><p>All entities annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Msigdb.all_mirnas" title="pypath.core.annot.Msigdb.all_mirnas"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_mirnas</span></code></a>()</p></td>
+<td><p>All miRNAs annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Msigdb.all_proteins" title="pypath.core.annot.Msigdb.all_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_proteins</span></code></a>()</p></td>
+<td><p>All UniProt IDs annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Msigdb.all_refs" title="pypath.core.annot.Msigdb.all_refs"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_refs</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Msigdb.annotate_complex" title="pypath.core.annot.Msigdb.annotate_complex"><code class="xref py py-obj docutils literal notranslate"><span class="pre">annotate_complex</span></code></a>(cplex)</p></td>
+<td><p>Infers annotations for a single complex.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Msigdb.browse" title="pypath.core.annot.Msigdb.browse"><code class="xref py py-obj docutils literal notranslate"><span class="pre">browse</span></code></a>([field, start])</p></td>
+<td><p>Print gene information as a table.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Msigdb.complex_inference" title="pypath.core.annot.Msigdb.complex_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">complex_inference</span></code></a>([complexes])</p></td>
+<td><p>Annotates all complexes in <cite>complexes</cite>, by default in the default complex database (existing in the <cite>complex</cite> module or generated on demand according to the module's current settings).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Msigdb.coverage" title="pypath.core.annot.Msigdb.coverage"><code class="xref py py-obj docutils literal notranslate"><span class="pre">coverage</span></code></a>(other)</p></td>
+<td><p>Calculates the coverage of the annotation i.e. the proportion of entities having at least one record in this annotation resource for an arbitrary set of entities.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Msigdb.curation_effort" title="pypath.core.annot.Msigdb.curation_effort"><code class="xref py py-obj docutils literal notranslate"><span class="pre">curation_effort</span></code></a>()</p></td>
+<td><p>Counts the reference-record pairs.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">from_dump</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_entity_type</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Msigdb.get_names" title="pypath.core.annot.Msigdb.get_names"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_names</span></code></a>()</p></td>
+<td><p>Returns the list of field names in the records.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Msigdb.get_reference_set" title="pypath.core.annot.Msigdb.get_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_reference_set</span></code></a>([proteins, complexes, ...])</p></td>
+<td><p>Retrieves the reference set i.e. the set of all entities which potentially have annotation in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Msigdb.get_subset" title="pypath.core.annot.Msigdb.get_subset"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Msigdb.get_subset_bool_array" title="pypath.core.annot.Msigdb.get_subset_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset_bool_array</span></code></a>([reference_set])</p></td>
+<td><p>Returns a boolean vector with True and False values for each entity in the reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Msigdb.get_values" title="pypath.core.annot.Msigdb.get_values"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_values</span></code></a>(name[, exclude_none])</p></td>
+<td><p>Returns the set of all possible values of a field.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_complex</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_mirna</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_protein</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Msigdb.labels" title="pypath.core.annot.Msigdb.labels"><code class="xref py py-obj docutils literal notranslate"><span class="pre">labels</span></code></a>([method])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Msigdb.load" title="pypath.core.annot.Msigdb.load"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load</span></code></a>()</p></td>
+<td><p>Loads the annotation data by calling the input method.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Msigdb.load_data" title="pypath.core.annot.Msigdb.load_data"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_data</span></code></a>()</p></td>
+<td><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Msigdb.load_proteins" title="pypath.core.annot.Msigdb.load_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_proteins</span></code></a>()</p></td>
+<td><p>Retrieves a set of all UniProt IDs to have a base set of the entire proteome.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Msigdb.make_df" title="pypath.core.annot.Msigdb.make_df"><code class="xref py py-obj docutils literal notranslate"><span class="pre">make_df</span></code></a>([rebuild])</p></td>
+<td><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complex_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Msigdb.numof_entities" title="pypath.core.annot.Msigdb.numof_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_entities</span></code></a>()</p></td>
+<td><p>The number of annotated entities in the resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirna_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirnas</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_protein_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_proteins</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Msigdb.numof_records" title="pypath.core.annot.Msigdb.numof_records"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_records</span></code></a>([entity_types])</p></td>
+<td><p>The total number of annotation records.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Msigdb.numof_references" title="pypath.core.annot.Msigdb.numof_references"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_references</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Msigdb.process" title="pypath.core.annot.Msigdb.process"><code class="xref py py-obj docutils literal notranslate"><span class="pre">process</span></code></a>()</p></td>
+<td><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">proportion</span></code>(other)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Msigdb.reload" title="pypath.core.annot.Msigdb.reload"><code class="xref py py-obj docutils literal notranslate"><span class="pre">reload</span></code></a>()</p></td>
+<td><p>Reloads the object from the module level.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">save_to_pickle</span></code>(pickle_file)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Msigdb.select" title="pypath.core.annot.Msigdb.select"><code class="xref py py-obj docutils literal notranslate"><span class="pre">select</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Msigdb.set_method" title="pypath.core.annot.Msigdb.set_method"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_method</span></code></a>()</p></td>
+<td><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if necessary.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Msigdb.set_reference_set" title="pypath.core.annot.Msigdb.set_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_reference_set</span></code></a>()</p></td>
+<td><p>Assigns the reference set to the :py:attr``reference_set`` attribute.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Msigdb.show" title="pypath.core.annot.Msigdb.show"><code class="xref py py-obj docutils literal notranslate"><span class="pre">show</span></code></a>([method, table_param])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic information from the UniProt datasheets.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Msigdb.subset_intersection" title="pypath.core.annot.Msigdb.subset_intersection"><code class="xref py py-obj docutils literal notranslate"><span class="pre">subset_intersection</span></code></a>(universe, **kwargs)</p></td>
+<td><p>Calculates the proportion of entities in a subset occuring in the set <code class="docutils literal notranslate"><span class="pre">universe</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Msigdb.to_array" title="pypath.core.annot.Msigdb.to_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_array</span></code></a>([reference_set, use_fields])</p></td>
+<td><p>Returns an entity vs feature array.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Msigdb.to_bool_array" title="pypath.core.annot.Msigdb.to_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_bool_array</span></code></a>(reference_set)</p></td>
+<td><p>Returns a presence/absence boolean array for a reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Msigdb.to_set" title="pypath.core.annot.Msigdb.to_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_set</span></code></a>()</p></td>
+<td><p>Returns the entities present in this annotation resource as a set.</p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Attributes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_fields</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">summary</span></code></p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Msigdb.add_complexes_by_inference">
+<span class="sig-name descname"><span class="pre">add_complexes_by_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Msigdb.add_complexes_by_inference" title="Link to this definition">§</a></dt>
+<dd><p>Creates complex annotations by in silico inference and adds them
+to this annotation set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Msigdb.all_complexes">
+<span class="sig-name descname"><span class="pre">all_complexes</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Msigdb.all_complexes" title="Link to this definition">§</a></dt>
+<dd><p>All protein complexes annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Msigdb.all_entities">
+<span class="sig-name descname"><span class="pre">all_entities</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Msigdb.all_entities" title="Link to this definition">§</a></dt>
+<dd><p>All entities annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Msigdb.all_mirnas">
+<span class="sig-name descname"><span class="pre">all_mirnas</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Msigdb.all_mirnas" title="Link to this definition">§</a></dt>
+<dd><p>All miRNAs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Msigdb.all_proteins">
+<span class="sig-name descname"><span class="pre">all_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Msigdb.all_proteins" title="Link to this definition">§</a></dt>
+<dd><p>All UniProt IDs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Msigdb.all_refs">
+<span class="sig-name descname"><span class="pre">all_refs</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Msigdb.all_refs" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects the references
+across all records. Returns <em>list</em>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Msigdb.annotate_complex">
+<span class="sig-name descname"><span class="pre">annotate_complex</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cplex</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Msigdb.annotate_complex" title="Link to this definition">§</a></dt>
+<dd><p>Infers annotations for a single complex.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Msigdb.browse">
+<span class="sig-name descname"><span class="pre">browse</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">field</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">start</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Msigdb.browse" title="Link to this definition">§</a></dt>
+<dd><p>Print gene information as a table.</p>
+<p>Presents information about annotation categories as ascii tables
+printed in the terminal. If one category provided, prints one table.
+If multiple categories provided, prints a table for each of them one
+by one proceeding to the next one once you hit return. If no categories
+provided goes through all levels of the primary category.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>field:</dt><dd><p>The field to browse categories by.</p>
+<ul class="simple">
+<li><p>If None the primary field will be selected.
+If this annotation resource doesn’t have fields, all proteins
+will be presented as one single category.</p></li>
+<li><p>If a string it will be considered a field name and it will
+browse through all levels of this field.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">list</span></code>, set or tuple, it will be considered either a
+<code class="docutils literal notranslate"><span class="pre">list</span></code> of field names or a list of values from the primary
+field. In the former case all combinations of the values of
+the fields will be presented, in the latter case the browsing
+will be limited to the levels of the primary field contained
+in <code class="docutils literal notranslate"><span class="pre">field</span></code>.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">dict</span></code>, keys are supposed to be field names and values
+as list of levels. If any of the values are None, all levels
+from that field will be used.</p></li>
+</ul>
+</dd>
+<dt>start:</dt><dd><p>Start browsing from this category. E.g. if there are 500
+categories and start is 250 it will skip everything before the
+250th.</p>
+</dd>
+<dt>kwargs:</dt><dd><p>Passed to <code class="docutils literal notranslate"><span class="pre">pypath.utils.uniprot.info</span></code>.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Msigdb.complex_inference">
+<span class="sig-name descname"><span class="pre">complex_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Msigdb.complex_inference" title="Link to this definition">§</a></dt>
+<dd><p>Annotates all complexes in <cite>complexes</cite>, by default in the default
+complex database (existing in the <cite>complex</cite> module or generated
+on demand according to the module’s current settings).</p>
+<dl class="field-list simple">
+<dt class="field-odd">Returns<span class="colon">:</span></dt>
+<dd class="field-odd"><p><ul class="simple">
+<li><p><em>Dict with complexes as keys and sets of annotations as values.</em></p></li>
+<li><p><em>Complexes with no valid information in this annotation resource</em></p></li>
+<li><p><em>won’t be in the dict.</em></p></li>
+</ul>
+</p>
+</dd>
+<dt class="field-even">Parameters<span class="colon">:</span></dt>
+<dd class="field-even"><p><strong>complexes</strong> (<em>iterable</em>) – Iterable yielding complexes.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Msigdb.coverage">
+<span class="sig-name descname"><span class="pre">coverage</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">other</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Msigdb.coverage" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the coverage of the annotation i.e. the proportion of
+entities having at least one record in this annotation resource
+for an arbitrary set of entities.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Msigdb.curation_effort">
+<span class="sig-name descname"><span class="pre">curation_effort</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Msigdb.curation_effort" title="Link to this definition">§</a></dt>
+<dd><p>Counts the reference-record pairs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Msigdb.get_names">
+<span class="sig-name descname"><span class="pre">get_names</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Msigdb.get_names" title="Link to this definition">§</a></dt>
+<dd><p>Returns the list of field names in the records. The annotation
+consists of uniform records and each entity might be annotated
+with one or more records. Each record is a tuple of fields, for
+example <code class="docutils literal notranslate"><span class="pre">('cell_type',</span> <span class="pre">'expression_level',</span> <span class="pre">'score')</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Msigdb.get_reference_set">
+<em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">get_reference_set</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">proteins</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">swissprot_only</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Msigdb.get_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the reference set i.e. the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Msigdb.get_subset">
+<span class="sig-name descname"><span class="pre">get_subset</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Msigdb.get_subset" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Msigdb.get_subset_bool_array">
+<span class="sig-name descname"><span class="pre">get_subset_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Msigdb.get_subset_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a boolean vector with True and False values for each entity
+in the reference set. The values represent presence absence data
+in the simplest case, but by providing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> any kind of matching
+and filtering is possible. <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> are passed to the <code class="docutils literal notranslate"><span class="pre">select</span></code>
+method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Msigdb.get_values">
+<span class="sig-name descname"><span class="pre">get_values</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">exclude_none</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Msigdb.get_values" title="Link to this definition">§</a></dt>
+<dd><p>Returns the set of all possible values of a field. E.g. if the
+records of this annotation have a field <code class="docutils literal notranslate"><span class="pre">cell_type</span></code> then calling
+this method can tell you that across all records the values of
+this field might be <code class="docutils literal notranslate"><span class="pre">{'macrophage',</span> <span class="pre">'epithelial_cell',</span> <span class="pre">...}</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Msigdb.labels">
+<span class="sig-name descname"><span class="pre">labels</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Msigdb.labels" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Msigdb.load">
+<span class="sig-name descname"><span class="pre">load</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Msigdb.load" title="Link to this definition">§</a></dt>
+<dd><p>Loads the annotation data by calling the input method.
+Infers annotations for complexes in the complex database if
+py:attr:<code class="docutils literal notranslate"><span class="pre">infer_complexes</span></code> is True.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Msigdb.load_data">
+<span class="sig-name descname"><span class="pre">load_data</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Msigdb.load_data" title="Link to this definition">§</a></dt>
+<dd><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Msigdb.load_proteins">
+<span class="sig-name descname"><span class="pre">load_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Msigdb.load_proteins" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a set of all UniProt IDs to have a base set of the entire
+proteome.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Msigdb.make_df">
+<span class="sig-name descname"><span class="pre">make_df</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">rebuild</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Msigdb.make_df" title="Link to this definition">§</a></dt>
+<dd><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.
+The data frame will be assigned to :py:attr``df``.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Msigdb.numof_entities">
+<span class="sig-name descname"><span class="pre">numof_entities</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Msigdb.numof_entities" title="Link to this definition">§</a></dt>
+<dd><p>The number of annotated entities in the resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Msigdb.numof_records">
+<span class="sig-name descname"><span class="pre">numof_records</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Msigdb.numof_records" title="Link to this definition">§</a></dt>
+<dd><p>The total number of annotation records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Msigdb.numof_references">
+<span class="sig-name descname"><span class="pre">numof_references</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Msigdb.numof_references" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects and counts the
+references across all records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Msigdb.process">
+<span class="sig-name descname"><span class="pre">process</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Msigdb.process" title="Link to this definition">§</a></dt>
+<dd><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Msigdb.reload">
+<span class="sig-name descname"><span class="pre">reload</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Msigdb.reload" title="Link to this definition">§</a></dt>
+<dd><p>Reloads the object from the module level.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Msigdb.select">
+<span class="sig-name descname"><span class="pre">select</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Msigdb.select" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Msigdb.set_method">
+<span class="sig-name descname"><span class="pre">set_method</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Msigdb.set_method" title="Link to this definition">§</a></dt>
+<dd><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if
+necessary.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Msigdb.set_reference_set">
+<span class="sig-name descname"><span class="pre">set_reference_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Msigdb.set_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Assigns the reference set to the :py:attr``reference_set`` attribute.
+The reference set is the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Msigdb.show">
+<span class="sig-name descname"><span class="pre">show</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">table_param</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Msigdb.show" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic
+information from the UniProt datasheets.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Msigdb.subset_intersection">
+<span class="sig-name descname"><span class="pre">subset_intersection</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">universe</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Msigdb.subset_intersection" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the proportion of entities in a subset occuring in the
+set <code class="docutils literal notranslate"><span class="pre">universe</span></code>. The subset is selected by passing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> to the
+<code class="docutils literal notranslate"><span class="pre">select</span></code> method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Msigdb.to_array">
+<span class="sig-name descname"><span class="pre">to_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_fields</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Msigdb.to_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns an entity vs feature array. In case of more complex
+annotations this might be huge.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Msigdb.to_bool_array">
+<span class="sig-name descname"><span class="pre">to_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Msigdb.to_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a presence/absence boolean array for a reference set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Msigdb.to_set">
+<span class="sig-name descname"><span class="pre">to_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Msigdb.to_set" title="Link to this definition">§</a></dt>
+<dd><p>Returns the entities present in this annotation resource as a set.</p>
+</dd></dl>
+
+</dd></dl>
+
+</section>
+
+
+                </article>
+              
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+  <section id="pypath-core-annot-netpathpathways">
+<h1>pypath.core.annot.NetpathPathways<a class="headerlink" href="#pypath-core-annot-netpathpathways" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.core.annot.NetpathPathways">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.core.annot.</span></span><span class="sig-name descname"><span class="pre">NetpathPathways</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#NetpathPathways"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.NetpathPathways" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <a class="reference internal" href="pypath.core.annot.AnnotationBase.html#pypath.core.annot.AnnotationBase" title="pypath.core.annot.AnnotationBase"><code class="xref py py-class docutils literal notranslate"><span class="pre">AnnotationBase</span></code></a></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.NetpathPathways.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#NetpathPathways.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.NetpathPathways.__init__" title="Link to this definition">§</a></dt>
+<dd><p>Pathway annotations from NetPath.</p>
+</dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.NetpathPathways.__init__" title="pypath.core.annot.NetpathPathways.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>([ncbi_tax_id])</p></td>
+<td><p>Pathway annotations from NetPath.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.NetpathPathways.add_complexes_by_inference" title="pypath.core.annot.NetpathPathways.add_complexes_by_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">add_complexes_by_inference</span></code></a>([complexes])</p></td>
+<td><p>Creates complex annotations by in silico inference and adds them to this annotation set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.NetpathPathways.all_complexes" title="pypath.core.annot.NetpathPathways.all_complexes"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_complexes</span></code></a>()</p></td>
+<td><p>All protein complexes annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.NetpathPathways.all_entities" title="pypath.core.annot.NetpathPathways.all_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_entities</span></code></a>([entity_types])</p></td>
+<td><p>All entities annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.NetpathPathways.all_mirnas" title="pypath.core.annot.NetpathPathways.all_mirnas"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_mirnas</span></code></a>()</p></td>
+<td><p>All miRNAs annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.NetpathPathways.all_proteins" title="pypath.core.annot.NetpathPathways.all_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_proteins</span></code></a>()</p></td>
+<td><p>All UniProt IDs annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.NetpathPathways.all_refs" title="pypath.core.annot.NetpathPathways.all_refs"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_refs</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.NetpathPathways.annotate_complex" title="pypath.core.annot.NetpathPathways.annotate_complex"><code class="xref py py-obj docutils literal notranslate"><span class="pre">annotate_complex</span></code></a>(cplex)</p></td>
+<td><p>Infers annotations for a single complex.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.NetpathPathways.browse" title="pypath.core.annot.NetpathPathways.browse"><code class="xref py py-obj docutils literal notranslate"><span class="pre">browse</span></code></a>([field, start])</p></td>
+<td><p>Print gene information as a table.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.NetpathPathways.complex_inference" title="pypath.core.annot.NetpathPathways.complex_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">complex_inference</span></code></a>([complexes])</p></td>
+<td><p>Annotates all complexes in <cite>complexes</cite>, by default in the default complex database (existing in the <cite>complex</cite> module or generated on demand according to the module's current settings).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.NetpathPathways.coverage" title="pypath.core.annot.NetpathPathways.coverage"><code class="xref py py-obj docutils literal notranslate"><span class="pre">coverage</span></code></a>(other)</p></td>
+<td><p>Calculates the coverage of the annotation i.e. the proportion of entities having at least one record in this annotation resource for an arbitrary set of entities.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.NetpathPathways.curation_effort" title="pypath.core.annot.NetpathPathways.curation_effort"><code class="xref py py-obj docutils literal notranslate"><span class="pre">curation_effort</span></code></a>()</p></td>
+<td><p>Counts the reference-record pairs.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">from_dump</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_entity_type</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.NetpathPathways.get_names" title="pypath.core.annot.NetpathPathways.get_names"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_names</span></code></a>()</p></td>
+<td><p>Returns the list of field names in the records.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.NetpathPathways.get_reference_set" title="pypath.core.annot.NetpathPathways.get_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_reference_set</span></code></a>([proteins, complexes, ...])</p></td>
+<td><p>Retrieves the reference set i.e. the set of all entities which potentially have annotation in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.NetpathPathways.get_subset" title="pypath.core.annot.NetpathPathways.get_subset"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.NetpathPathways.get_subset_bool_array" title="pypath.core.annot.NetpathPathways.get_subset_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset_bool_array</span></code></a>([reference_set])</p></td>
+<td><p>Returns a boolean vector with True and False values for each entity in the reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.NetpathPathways.get_values" title="pypath.core.annot.NetpathPathways.get_values"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_values</span></code></a>(name[, exclude_none])</p></td>
+<td><p>Returns the set of all possible values of a field.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_complex</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_mirna</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_protein</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.NetpathPathways.labels" title="pypath.core.annot.NetpathPathways.labels"><code class="xref py py-obj docutils literal notranslate"><span class="pre">labels</span></code></a>([method])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.NetpathPathways.load" title="pypath.core.annot.NetpathPathways.load"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load</span></code></a>()</p></td>
+<td><p>Loads the annotation data by calling the input method.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.NetpathPathways.load_data" title="pypath.core.annot.NetpathPathways.load_data"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_data</span></code></a>()</p></td>
+<td><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.NetpathPathways.load_proteins" title="pypath.core.annot.NetpathPathways.load_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_proteins</span></code></a>()</p></td>
+<td><p>Retrieves a set of all UniProt IDs to have a base set of the entire proteome.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.NetpathPathways.make_df" title="pypath.core.annot.NetpathPathways.make_df"><code class="xref py py-obj docutils literal notranslate"><span class="pre">make_df</span></code></a>([rebuild])</p></td>
+<td><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complex_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.NetpathPathways.numof_entities" title="pypath.core.annot.NetpathPathways.numof_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_entities</span></code></a>()</p></td>
+<td><p>The number of annotated entities in the resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirna_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirnas</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_protein_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_proteins</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.NetpathPathways.numof_records" title="pypath.core.annot.NetpathPathways.numof_records"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_records</span></code></a>([entity_types])</p></td>
+<td><p>The total number of annotation records.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.NetpathPathways.numof_references" title="pypath.core.annot.NetpathPathways.numof_references"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_references</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.NetpathPathways.process" title="pypath.core.annot.NetpathPathways.process"><code class="xref py py-obj docutils literal notranslate"><span class="pre">process</span></code></a>()</p></td>
+<td><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">proportion</span></code>(other)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.NetpathPathways.reload" title="pypath.core.annot.NetpathPathways.reload"><code class="xref py py-obj docutils literal notranslate"><span class="pre">reload</span></code></a>()</p></td>
+<td><p>Reloads the object from the module level.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">save_to_pickle</span></code>(pickle_file)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.NetpathPathways.select" title="pypath.core.annot.NetpathPathways.select"><code class="xref py py-obj docutils literal notranslate"><span class="pre">select</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.NetpathPathways.set_method" title="pypath.core.annot.NetpathPathways.set_method"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_method</span></code></a>()</p></td>
+<td><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if necessary.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.NetpathPathways.set_reference_set" title="pypath.core.annot.NetpathPathways.set_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_reference_set</span></code></a>()</p></td>
+<td><p>Assigns the reference set to the :py:attr``reference_set`` attribute.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.NetpathPathways.show" title="pypath.core.annot.NetpathPathways.show"><code class="xref py py-obj docutils literal notranslate"><span class="pre">show</span></code></a>([method, table_param])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic information from the UniProt datasheets.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.NetpathPathways.subset_intersection" title="pypath.core.annot.NetpathPathways.subset_intersection"><code class="xref py py-obj docutils literal notranslate"><span class="pre">subset_intersection</span></code></a>(universe, **kwargs)</p></td>
+<td><p>Calculates the proportion of entities in a subset occuring in the set <code class="docutils literal notranslate"><span class="pre">universe</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.NetpathPathways.to_array" title="pypath.core.annot.NetpathPathways.to_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_array</span></code></a>([reference_set, use_fields])</p></td>
+<td><p>Returns an entity vs feature array.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.NetpathPathways.to_bool_array" title="pypath.core.annot.NetpathPathways.to_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_bool_array</span></code></a>(reference_set)</p></td>
+<td><p>Returns a presence/absence boolean array for a reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.NetpathPathways.to_set" title="pypath.core.annot.NetpathPathways.to_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_set</span></code></a>()</p></td>
+<td><p>Returns the entities present in this annotation resource as a set.</p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Attributes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_fields</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">summary</span></code></p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.NetpathPathways.add_complexes_by_inference">
+<span class="sig-name descname"><span class="pre">add_complexes_by_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.NetpathPathways.add_complexes_by_inference" title="Link to this definition">§</a></dt>
+<dd><p>Creates complex annotations by in silico inference and adds them
+to this annotation set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.NetpathPathways.all_complexes">
+<span class="sig-name descname"><span class="pre">all_complexes</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.NetpathPathways.all_complexes" title="Link to this definition">§</a></dt>
+<dd><p>All protein complexes annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.NetpathPathways.all_entities">
+<span class="sig-name descname"><span class="pre">all_entities</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.NetpathPathways.all_entities" title="Link to this definition">§</a></dt>
+<dd><p>All entities annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.NetpathPathways.all_mirnas">
+<span class="sig-name descname"><span class="pre">all_mirnas</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.NetpathPathways.all_mirnas" title="Link to this definition">§</a></dt>
+<dd><p>All miRNAs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.NetpathPathways.all_proteins">
+<span class="sig-name descname"><span class="pre">all_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.NetpathPathways.all_proteins" title="Link to this definition">§</a></dt>
+<dd><p>All UniProt IDs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.NetpathPathways.all_refs">
+<span class="sig-name descname"><span class="pre">all_refs</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.NetpathPathways.all_refs" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects the references
+across all records. Returns <em>list</em>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.NetpathPathways.annotate_complex">
+<span class="sig-name descname"><span class="pre">annotate_complex</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cplex</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.NetpathPathways.annotate_complex" title="Link to this definition">§</a></dt>
+<dd><p>Infers annotations for a single complex.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.NetpathPathways.browse">
+<span class="sig-name descname"><span class="pre">browse</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">field</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">start</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.NetpathPathways.browse" title="Link to this definition">§</a></dt>
+<dd><p>Print gene information as a table.</p>
+<p>Presents information about annotation categories as ascii tables
+printed in the terminal. If one category provided, prints one table.
+If multiple categories provided, prints a table for each of them one
+by one proceeding to the next one once you hit return. If no categories
+provided goes through all levels of the primary category.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>field:</dt><dd><p>The field to browse categories by.</p>
+<ul class="simple">
+<li><p>If None the primary field will be selected.
+If this annotation resource doesn’t have fields, all proteins
+will be presented as one single category.</p></li>
+<li><p>If a string it will be considered a field name and it will
+browse through all levels of this field.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">list</span></code>, set or tuple, it will be considered either a
+<code class="docutils literal notranslate"><span class="pre">list</span></code> of field names or a list of values from the primary
+field. In the former case all combinations of the values of
+the fields will be presented, in the latter case the browsing
+will be limited to the levels of the primary field contained
+in <code class="docutils literal notranslate"><span class="pre">field</span></code>.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">dict</span></code>, keys are supposed to be field names and values
+as list of levels. If any of the values are None, all levels
+from that field will be used.</p></li>
+</ul>
+</dd>
+<dt>start:</dt><dd><p>Start browsing from this category. E.g. if there are 500
+categories and start is 250 it will skip everything before the
+250th.</p>
+</dd>
+<dt>kwargs:</dt><dd><p>Passed to <code class="docutils literal notranslate"><span class="pre">pypath.utils.uniprot.info</span></code>.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.NetpathPathways.complex_inference">
+<span class="sig-name descname"><span class="pre">complex_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.NetpathPathways.complex_inference" title="Link to this definition">§</a></dt>
+<dd><p>Annotates all complexes in <cite>complexes</cite>, by default in the default
+complex database (existing in the <cite>complex</cite> module or generated
+on demand according to the module’s current settings).</p>
+<dl class="field-list simple">
+<dt class="field-odd">Returns<span class="colon">:</span></dt>
+<dd class="field-odd"><p><ul class="simple">
+<li><p><em>Dict with complexes as keys and sets of annotations as values.</em></p></li>
+<li><p><em>Complexes with no valid information in this annotation resource</em></p></li>
+<li><p><em>won’t be in the dict.</em></p></li>
+</ul>
+</p>
+</dd>
+<dt class="field-even">Parameters<span class="colon">:</span></dt>
+<dd class="field-even"><p><strong>complexes</strong> (<em>iterable</em>) – Iterable yielding complexes.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.NetpathPathways.coverage">
+<span class="sig-name descname"><span class="pre">coverage</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">other</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.NetpathPathways.coverage" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the coverage of the annotation i.e. the proportion of
+entities having at least one record in this annotation resource
+for an arbitrary set of entities.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.NetpathPathways.curation_effort">
+<span class="sig-name descname"><span class="pre">curation_effort</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.NetpathPathways.curation_effort" title="Link to this definition">§</a></dt>
+<dd><p>Counts the reference-record pairs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.NetpathPathways.get_names">
+<span class="sig-name descname"><span class="pre">get_names</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.NetpathPathways.get_names" title="Link to this definition">§</a></dt>
+<dd><p>Returns the list of field names in the records. The annotation
+consists of uniform records and each entity might be annotated
+with one or more records. Each record is a tuple of fields, for
+example <code class="docutils literal notranslate"><span class="pre">('cell_type',</span> <span class="pre">'expression_level',</span> <span class="pre">'score')</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.NetpathPathways.get_reference_set">
+<em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">get_reference_set</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">proteins</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">swissprot_only</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.NetpathPathways.get_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the reference set i.e. the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.NetpathPathways.get_subset">
+<span class="sig-name descname"><span class="pre">get_subset</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.NetpathPathways.get_subset" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.NetpathPathways.get_subset_bool_array">
+<span class="sig-name descname"><span class="pre">get_subset_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.NetpathPathways.get_subset_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a boolean vector with True and False values for each entity
+in the reference set. The values represent presence absence data
+in the simplest case, but by providing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> any kind of matching
+and filtering is possible. <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> are passed to the <code class="docutils literal notranslate"><span class="pre">select</span></code>
+method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.NetpathPathways.get_values">
+<span class="sig-name descname"><span class="pre">get_values</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">exclude_none</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.NetpathPathways.get_values" title="Link to this definition">§</a></dt>
+<dd><p>Returns the set of all possible values of a field. E.g. if the
+records of this annotation have a field <code class="docutils literal notranslate"><span class="pre">cell_type</span></code> then calling
+this method can tell you that across all records the values of
+this field might be <code class="docutils literal notranslate"><span class="pre">{'macrophage',</span> <span class="pre">'epithelial_cell',</span> <span class="pre">...}</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.NetpathPathways.labels">
+<span class="sig-name descname"><span class="pre">labels</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.NetpathPathways.labels" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.NetpathPathways.load">
+<span class="sig-name descname"><span class="pre">load</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.NetpathPathways.load" title="Link to this definition">§</a></dt>
+<dd><p>Loads the annotation data by calling the input method.
+Infers annotations for complexes in the complex database if
+py:attr:<code class="docutils literal notranslate"><span class="pre">infer_complexes</span></code> is True.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.NetpathPathways.load_data">
+<span class="sig-name descname"><span class="pre">load_data</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.NetpathPathways.load_data" title="Link to this definition">§</a></dt>
+<dd><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.NetpathPathways.load_proteins">
+<span class="sig-name descname"><span class="pre">load_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.NetpathPathways.load_proteins" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a set of all UniProt IDs to have a base set of the entire
+proteome.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.NetpathPathways.make_df">
+<span class="sig-name descname"><span class="pre">make_df</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">rebuild</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.NetpathPathways.make_df" title="Link to this definition">§</a></dt>
+<dd><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.
+The data frame will be assigned to :py:attr``df``.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.NetpathPathways.numof_entities">
+<span class="sig-name descname"><span class="pre">numof_entities</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.NetpathPathways.numof_entities" title="Link to this definition">§</a></dt>
+<dd><p>The number of annotated entities in the resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.NetpathPathways.numof_records">
+<span class="sig-name descname"><span class="pre">numof_records</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.NetpathPathways.numof_records" title="Link to this definition">§</a></dt>
+<dd><p>The total number of annotation records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.NetpathPathways.numof_references">
+<span class="sig-name descname"><span class="pre">numof_references</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.NetpathPathways.numof_references" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects and counts the
+references across all records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.NetpathPathways.process">
+<span class="sig-name descname"><span class="pre">process</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.NetpathPathways.process" title="Link to this definition">§</a></dt>
+<dd><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.NetpathPathways.reload">
+<span class="sig-name descname"><span class="pre">reload</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.NetpathPathways.reload" title="Link to this definition">§</a></dt>
+<dd><p>Reloads the object from the module level.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.NetpathPathways.select">
+<span class="sig-name descname"><span class="pre">select</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.NetpathPathways.select" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.NetpathPathways.set_method">
+<span class="sig-name descname"><span class="pre">set_method</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.NetpathPathways.set_method" title="Link to this definition">§</a></dt>
+<dd><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if
+necessary.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.NetpathPathways.set_reference_set">
+<span class="sig-name descname"><span class="pre">set_reference_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.NetpathPathways.set_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Assigns the reference set to the :py:attr``reference_set`` attribute.
+The reference set is the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.NetpathPathways.show">
+<span class="sig-name descname"><span class="pre">show</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">table_param</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.NetpathPathways.show" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic
+information from the UniProt datasheets.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.NetpathPathways.subset_intersection">
+<span class="sig-name descname"><span class="pre">subset_intersection</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">universe</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.NetpathPathways.subset_intersection" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the proportion of entities in a subset occuring in the
+set <code class="docutils literal notranslate"><span class="pre">universe</span></code>. The subset is selected by passing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> to the
+<code class="docutils literal notranslate"><span class="pre">select</span></code> method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.NetpathPathways.to_array">
+<span class="sig-name descname"><span class="pre">to_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_fields</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.NetpathPathways.to_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns an entity vs feature array. In case of more complex
+annotations this might be huge.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.NetpathPathways.to_bool_array">
+<span class="sig-name descname"><span class="pre">to_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.NetpathPathways.to_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a presence/absence boolean array for a reference set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.NetpathPathways.to_set">
+<span class="sig-name descname"><span class="pre">to_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.NetpathPathways.to_set" title="Link to this definition">§</a></dt>
+<dd><p>Returns the entities present in this annotation resource as a set.</p>
+</dd></dl>
+
+</dd></dl>
+
+</section>
+
+
+                </article>
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+  <section id="pypath-core-annot-opm">
+<h1>pypath.core.annot.Opm<a class="headerlink" href="#pypath-core-annot-opm" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.core.annot.Opm">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.core.annot.</span></span><span class="sig-name descname"><span class="pre">Opm</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#Opm"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.Opm" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <a class="reference internal" href="pypath.core.annot.AnnotationBase.html#pypath.core.annot.AnnotationBase" title="pypath.core.annot.AnnotationBase"><code class="xref py py-class docutils literal notranslate"><span class="pre">AnnotationBase</span></code></a></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Opm.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#Opm.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.Opm.__init__" title="Link to this definition">§</a></dt>
+<dd><p>Represents annotations for a set of proteins.
+Loads the data from the original resource and provides methods
+to query the annotations.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>name</strong> (<em>str</em>) – A custom name for the annotation resource.</p></li>
+<li><p><strong>ncbi_tax_id</strong> (<em>int</em>) – NCBI Taxonomy identifier.</p></li>
+<li><p><strong>input_method</strong> (<em>callable</em><em>,</em><em>str</em>) – Either a callable or the name of a method in any submodules of
+the <code class="docutils literal notranslate"><span class="pre">pypath.inputs</span></code>  module. Should return a dict with
+UniProt IDs as keys or an object suitable for <code class="docutils literal notranslate"><span class="pre">process_method</span></code>.</p></li>
+<li><p><strong>input_args</strong> (<em>dict</em>) – Arguments for the <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Opm.__init__" title="pypath.core.annot.Opm.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>([ncbi_tax_id])</p></td>
+<td><p>Represents annotations for a set of proteins.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Opm.add_complexes_by_inference" title="pypath.core.annot.Opm.add_complexes_by_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">add_complexes_by_inference</span></code></a>([complexes])</p></td>
+<td><p>Creates complex annotations by in silico inference and adds them to this annotation set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Opm.all_complexes" title="pypath.core.annot.Opm.all_complexes"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_complexes</span></code></a>()</p></td>
+<td><p>All protein complexes annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Opm.all_entities" title="pypath.core.annot.Opm.all_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_entities</span></code></a>([entity_types])</p></td>
+<td><p>All entities annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Opm.all_mirnas" title="pypath.core.annot.Opm.all_mirnas"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_mirnas</span></code></a>()</p></td>
+<td><p>All miRNAs annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Opm.all_proteins" title="pypath.core.annot.Opm.all_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_proteins</span></code></a>()</p></td>
+<td><p>All UniProt IDs annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Opm.all_refs" title="pypath.core.annot.Opm.all_refs"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_refs</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Opm.annotate_complex" title="pypath.core.annot.Opm.annotate_complex"><code class="xref py py-obj docutils literal notranslate"><span class="pre">annotate_complex</span></code></a>(cplex)</p></td>
+<td><p>Infers annotations for a single complex.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Opm.browse" title="pypath.core.annot.Opm.browse"><code class="xref py py-obj docutils literal notranslate"><span class="pre">browse</span></code></a>([field, start])</p></td>
+<td><p>Print gene information as a table.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Opm.complex_inference" title="pypath.core.annot.Opm.complex_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">complex_inference</span></code></a>([complexes])</p></td>
+<td><p>Annotates all complexes in <cite>complexes</cite>, by default in the default complex database (existing in the <cite>complex</cite> module or generated on demand according to the module's current settings).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Opm.coverage" title="pypath.core.annot.Opm.coverage"><code class="xref py py-obj docutils literal notranslate"><span class="pre">coverage</span></code></a>(other)</p></td>
+<td><p>Calculates the coverage of the annotation i.e. the proportion of entities having at least one record in this annotation resource for an arbitrary set of entities.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Opm.curation_effort" title="pypath.core.annot.Opm.curation_effort"><code class="xref py py-obj docutils literal notranslate"><span class="pre">curation_effort</span></code></a>()</p></td>
+<td><p>Counts the reference-record pairs.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">from_dump</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_entity_type</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Opm.get_names" title="pypath.core.annot.Opm.get_names"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_names</span></code></a>()</p></td>
+<td><p>Returns the list of field names in the records.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Opm.get_reference_set" title="pypath.core.annot.Opm.get_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_reference_set</span></code></a>([proteins, complexes, ...])</p></td>
+<td><p>Retrieves the reference set i.e. the set of all entities which potentially have annotation in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Opm.get_subset" title="pypath.core.annot.Opm.get_subset"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Opm.get_subset_bool_array" title="pypath.core.annot.Opm.get_subset_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset_bool_array</span></code></a>([reference_set])</p></td>
+<td><p>Returns a boolean vector with True and False values for each entity in the reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Opm.get_values" title="pypath.core.annot.Opm.get_values"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_values</span></code></a>(name[, exclude_none])</p></td>
+<td><p>Returns the set of all possible values of a field.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_complex</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_mirna</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_protein</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Opm.labels" title="pypath.core.annot.Opm.labels"><code class="xref py py-obj docutils literal notranslate"><span class="pre">labels</span></code></a>([method])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Opm.load" title="pypath.core.annot.Opm.load"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load</span></code></a>()</p></td>
+<td><p>Loads the annotation data by calling the input method.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Opm.load_data" title="pypath.core.annot.Opm.load_data"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_data</span></code></a>()</p></td>
+<td><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Opm.load_proteins" title="pypath.core.annot.Opm.load_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_proteins</span></code></a>()</p></td>
+<td><p>Retrieves a set of all UniProt IDs to have a base set of the entire proteome.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Opm.make_df" title="pypath.core.annot.Opm.make_df"><code class="xref py py-obj docutils literal notranslate"><span class="pre">make_df</span></code></a>([rebuild])</p></td>
+<td><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complex_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Opm.numof_entities" title="pypath.core.annot.Opm.numof_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_entities</span></code></a>()</p></td>
+<td><p>The number of annotated entities in the resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirna_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirnas</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_protein_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_proteins</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Opm.numof_records" title="pypath.core.annot.Opm.numof_records"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_records</span></code></a>([entity_types])</p></td>
+<td><p>The total number of annotation records.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Opm.numof_references" title="pypath.core.annot.Opm.numof_references"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_references</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Opm.process" title="pypath.core.annot.Opm.process"><code class="xref py py-obj docutils literal notranslate"><span class="pre">process</span></code></a>()</p></td>
+<td><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">proportion</span></code>(other)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Opm.reload" title="pypath.core.annot.Opm.reload"><code class="xref py py-obj docutils literal notranslate"><span class="pre">reload</span></code></a>()</p></td>
+<td><p>Reloads the object from the module level.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">save_to_pickle</span></code>(pickle_file)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Opm.select" title="pypath.core.annot.Opm.select"><code class="xref py py-obj docutils literal notranslate"><span class="pre">select</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Opm.set_method" title="pypath.core.annot.Opm.set_method"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_method</span></code></a>()</p></td>
+<td><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if necessary.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Opm.set_reference_set" title="pypath.core.annot.Opm.set_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_reference_set</span></code></a>()</p></td>
+<td><p>Assigns the reference set to the :py:attr``reference_set`` attribute.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Opm.show" title="pypath.core.annot.Opm.show"><code class="xref py py-obj docutils literal notranslate"><span class="pre">show</span></code></a>([method, table_param])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic information from the UniProt datasheets.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Opm.subset_intersection" title="pypath.core.annot.Opm.subset_intersection"><code class="xref py py-obj docutils literal notranslate"><span class="pre">subset_intersection</span></code></a>(universe, **kwargs)</p></td>
+<td><p>Calculates the proportion of entities in a subset occuring in the set <code class="docutils literal notranslate"><span class="pre">universe</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Opm.to_array" title="pypath.core.annot.Opm.to_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_array</span></code></a>([reference_set, use_fields])</p></td>
+<td><p>Returns an entity vs feature array.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Opm.to_bool_array" title="pypath.core.annot.Opm.to_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_bool_array</span></code></a>(reference_set)</p></td>
+<td><p>Returns a presence/absence boolean array for a reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Opm.to_set" title="pypath.core.annot.Opm.to_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_set</span></code></a>()</p></td>
+<td><p>Returns the entities present in this annotation resource as a set.</p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Attributes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_fields</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">summary</span></code></p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Opm.add_complexes_by_inference">
+<span class="sig-name descname"><span class="pre">add_complexes_by_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Opm.add_complexes_by_inference" title="Link to this definition">§</a></dt>
+<dd><p>Creates complex annotations by in silico inference and adds them
+to this annotation set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Opm.all_complexes">
+<span class="sig-name descname"><span class="pre">all_complexes</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Opm.all_complexes" title="Link to this definition">§</a></dt>
+<dd><p>All protein complexes annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Opm.all_entities">
+<span class="sig-name descname"><span class="pre">all_entities</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Opm.all_entities" title="Link to this definition">§</a></dt>
+<dd><p>All entities annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Opm.all_mirnas">
+<span class="sig-name descname"><span class="pre">all_mirnas</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Opm.all_mirnas" title="Link to this definition">§</a></dt>
+<dd><p>All miRNAs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Opm.all_proteins">
+<span class="sig-name descname"><span class="pre">all_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Opm.all_proteins" title="Link to this definition">§</a></dt>
+<dd><p>All UniProt IDs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Opm.all_refs">
+<span class="sig-name descname"><span class="pre">all_refs</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Opm.all_refs" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects the references
+across all records. Returns <em>list</em>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Opm.annotate_complex">
+<span class="sig-name descname"><span class="pre">annotate_complex</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cplex</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Opm.annotate_complex" title="Link to this definition">§</a></dt>
+<dd><p>Infers annotations for a single complex.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Opm.browse">
+<span class="sig-name descname"><span class="pre">browse</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">field</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">start</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Opm.browse" title="Link to this definition">§</a></dt>
+<dd><p>Print gene information as a table.</p>
+<p>Presents information about annotation categories as ascii tables
+printed in the terminal. If one category provided, prints one table.
+If multiple categories provided, prints a table for each of them one
+by one proceeding to the next one once you hit return. If no categories
+provided goes through all levels of the primary category.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>field:</dt><dd><p>The field to browse categories by.</p>
+<ul class="simple">
+<li><p>If None the primary field will be selected.
+If this annotation resource doesn’t have fields, all proteins
+will be presented as one single category.</p></li>
+<li><p>If a string it will be considered a field name and it will
+browse through all levels of this field.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">list</span></code>, set or tuple, it will be considered either a
+<code class="docutils literal notranslate"><span class="pre">list</span></code> of field names or a list of values from the primary
+field. In the former case all combinations of the values of
+the fields will be presented, in the latter case the browsing
+will be limited to the levels of the primary field contained
+in <code class="docutils literal notranslate"><span class="pre">field</span></code>.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">dict</span></code>, keys are supposed to be field names and values
+as list of levels. If any of the values are None, all levels
+from that field will be used.</p></li>
+</ul>
+</dd>
+<dt>start:</dt><dd><p>Start browsing from this category. E.g. if there are 500
+categories and start is 250 it will skip everything before the
+250th.</p>
+</dd>
+<dt>kwargs:</dt><dd><p>Passed to <code class="docutils literal notranslate"><span class="pre">pypath.utils.uniprot.info</span></code>.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Opm.complex_inference">
+<span class="sig-name descname"><span class="pre">complex_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Opm.complex_inference" title="Link to this definition">§</a></dt>
+<dd><p>Annotates all complexes in <cite>complexes</cite>, by default in the default
+complex database (existing in the <cite>complex</cite> module or generated
+on demand according to the module’s current settings).</p>
+<dl class="field-list simple">
+<dt class="field-odd">Returns<span class="colon">:</span></dt>
+<dd class="field-odd"><p><ul class="simple">
+<li><p><em>Dict with complexes as keys and sets of annotations as values.</em></p></li>
+<li><p><em>Complexes with no valid information in this annotation resource</em></p></li>
+<li><p><em>won’t be in the dict.</em></p></li>
+</ul>
+</p>
+</dd>
+<dt class="field-even">Parameters<span class="colon">:</span></dt>
+<dd class="field-even"><p><strong>complexes</strong> (<em>iterable</em>) – Iterable yielding complexes.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Opm.coverage">
+<span class="sig-name descname"><span class="pre">coverage</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">other</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Opm.coverage" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the coverage of the annotation i.e. the proportion of
+entities having at least one record in this annotation resource
+for an arbitrary set of entities.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Opm.curation_effort">
+<span class="sig-name descname"><span class="pre">curation_effort</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Opm.curation_effort" title="Link to this definition">§</a></dt>
+<dd><p>Counts the reference-record pairs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Opm.get_names">
+<span class="sig-name descname"><span class="pre">get_names</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Opm.get_names" title="Link to this definition">§</a></dt>
+<dd><p>Returns the list of field names in the records. The annotation
+consists of uniform records and each entity might be annotated
+with one or more records. Each record is a tuple of fields, for
+example <code class="docutils literal notranslate"><span class="pre">('cell_type',</span> <span class="pre">'expression_level',</span> <span class="pre">'score')</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Opm.get_reference_set">
+<em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">get_reference_set</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">proteins</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">swissprot_only</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Opm.get_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the reference set i.e. the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Opm.get_subset">
+<span class="sig-name descname"><span class="pre">get_subset</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Opm.get_subset" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Opm.get_subset_bool_array">
+<span class="sig-name descname"><span class="pre">get_subset_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Opm.get_subset_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a boolean vector with True and False values for each entity
+in the reference set. The values represent presence absence data
+in the simplest case, but by providing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> any kind of matching
+and filtering is possible. <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> are passed to the <code class="docutils literal notranslate"><span class="pre">select</span></code>
+method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Opm.get_values">
+<span class="sig-name descname"><span class="pre">get_values</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">exclude_none</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Opm.get_values" title="Link to this definition">§</a></dt>
+<dd><p>Returns the set of all possible values of a field. E.g. if the
+records of this annotation have a field <code class="docutils literal notranslate"><span class="pre">cell_type</span></code> then calling
+this method can tell you that across all records the values of
+this field might be <code class="docutils literal notranslate"><span class="pre">{'macrophage',</span> <span class="pre">'epithelial_cell',</span> <span class="pre">...}</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Opm.labels">
+<span class="sig-name descname"><span class="pre">labels</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Opm.labels" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Opm.load">
+<span class="sig-name descname"><span class="pre">load</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Opm.load" title="Link to this definition">§</a></dt>
+<dd><p>Loads the annotation data by calling the input method.
+Infers annotations for complexes in the complex database if
+py:attr:<code class="docutils literal notranslate"><span class="pre">infer_complexes</span></code> is True.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Opm.load_data">
+<span class="sig-name descname"><span class="pre">load_data</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Opm.load_data" title="Link to this definition">§</a></dt>
+<dd><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Opm.load_proteins">
+<span class="sig-name descname"><span class="pre">load_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Opm.load_proteins" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a set of all UniProt IDs to have a base set of the entire
+proteome.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Opm.make_df">
+<span class="sig-name descname"><span class="pre">make_df</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">rebuild</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Opm.make_df" title="Link to this definition">§</a></dt>
+<dd><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.
+The data frame will be assigned to :py:attr``df``.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Opm.numof_entities">
+<span class="sig-name descname"><span class="pre">numof_entities</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Opm.numof_entities" title="Link to this definition">§</a></dt>
+<dd><p>The number of annotated entities in the resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Opm.numof_records">
+<span class="sig-name descname"><span class="pre">numof_records</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Opm.numof_records" title="Link to this definition">§</a></dt>
+<dd><p>The total number of annotation records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Opm.numof_references">
+<span class="sig-name descname"><span class="pre">numof_references</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Opm.numof_references" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects and counts the
+references across all records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Opm.process">
+<span class="sig-name descname"><span class="pre">process</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Opm.process" title="Link to this definition">§</a></dt>
+<dd><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Opm.reload">
+<span class="sig-name descname"><span class="pre">reload</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Opm.reload" title="Link to this definition">§</a></dt>
+<dd><p>Reloads the object from the module level.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Opm.select">
+<span class="sig-name descname"><span class="pre">select</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Opm.select" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Opm.set_method">
+<span class="sig-name descname"><span class="pre">set_method</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Opm.set_method" title="Link to this definition">§</a></dt>
+<dd><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if
+necessary.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Opm.set_reference_set">
+<span class="sig-name descname"><span class="pre">set_reference_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Opm.set_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Assigns the reference set to the :py:attr``reference_set`` attribute.
+The reference set is the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Opm.show">
+<span class="sig-name descname"><span class="pre">show</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">table_param</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Opm.show" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic
+information from the UniProt datasheets.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Opm.subset_intersection">
+<span class="sig-name descname"><span class="pre">subset_intersection</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">universe</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Opm.subset_intersection" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the proportion of entities in a subset occuring in the
+set <code class="docutils literal notranslate"><span class="pre">universe</span></code>. The subset is selected by passing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> to the
+<code class="docutils literal notranslate"><span class="pre">select</span></code> method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Opm.to_array">
+<span class="sig-name descname"><span class="pre">to_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_fields</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Opm.to_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns an entity vs feature array. In case of more complex
+annotations this might be huge.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Opm.to_bool_array">
+<span class="sig-name descname"><span class="pre">to_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Opm.to_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a presence/absence boolean array for a reference set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Opm.to_set">
+<span class="sig-name descname"><span class="pre">to_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Opm.to_set" title="Link to this definition">§</a></dt>
+<dd><p>Returns the entities present in this annotation resource as a set.</p>
+</dd></dl>
+
+</dd></dl>
+
+</section>
+
+
+                </article>
+              
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+  <section id="pypath-core-annot-panglaodb">
+<h1>pypath.core.annot.Panglaodb<a class="headerlink" href="#pypath-core-annot-panglaodb" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.core.annot.Panglaodb">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.core.annot.</span></span><span class="sig-name descname"><span class="pre">Panglaodb</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#Panglaodb"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.Panglaodb" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <a class="reference internal" href="pypath.core.annot.AnnotationBase.html#pypath.core.annot.AnnotationBase" title="pypath.core.annot.AnnotationBase"><code class="xref py py-class docutils literal notranslate"><span class="pre">AnnotationBase</span></code></a></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Panglaodb.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#Panglaodb.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.Panglaodb.__init__" title="Link to this definition">§</a></dt>
+<dd><p>Cell type markers from PanglaoDB</p>
+</dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Panglaodb.__init__" title="pypath.core.annot.Panglaodb.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>([ncbi_tax_id])</p></td>
+<td><p>Cell type markers from PanglaoDB</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Panglaodb.add_complexes_by_inference" title="pypath.core.annot.Panglaodb.add_complexes_by_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">add_complexes_by_inference</span></code></a>([complexes])</p></td>
+<td><p>Creates complex annotations by in silico inference and adds them to this annotation set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Panglaodb.all_complexes" title="pypath.core.annot.Panglaodb.all_complexes"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_complexes</span></code></a>()</p></td>
+<td><p>All protein complexes annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Panglaodb.all_entities" title="pypath.core.annot.Panglaodb.all_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_entities</span></code></a>([entity_types])</p></td>
+<td><p>All entities annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Panglaodb.all_mirnas" title="pypath.core.annot.Panglaodb.all_mirnas"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_mirnas</span></code></a>()</p></td>
+<td><p>All miRNAs annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Panglaodb.all_proteins" title="pypath.core.annot.Panglaodb.all_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_proteins</span></code></a>()</p></td>
+<td><p>All UniProt IDs annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Panglaodb.all_refs" title="pypath.core.annot.Panglaodb.all_refs"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_refs</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Panglaodb.annotate_complex" title="pypath.core.annot.Panglaodb.annotate_complex"><code class="xref py py-obj docutils literal notranslate"><span class="pre">annotate_complex</span></code></a>(cplex)</p></td>
+<td><p>Infers annotations for a single complex.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Panglaodb.browse" title="pypath.core.annot.Panglaodb.browse"><code class="xref py py-obj docutils literal notranslate"><span class="pre">browse</span></code></a>([field, start])</p></td>
+<td><p>Print gene information as a table.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Panglaodb.complex_inference" title="pypath.core.annot.Panglaodb.complex_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">complex_inference</span></code></a>([complexes])</p></td>
+<td><p>Annotates all complexes in <cite>complexes</cite>, by default in the default complex database (existing in the <cite>complex</cite> module or generated on demand according to the module's current settings).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Panglaodb.coverage" title="pypath.core.annot.Panglaodb.coverage"><code class="xref py py-obj docutils literal notranslate"><span class="pre">coverage</span></code></a>(other)</p></td>
+<td><p>Calculates the coverage of the annotation i.e. the proportion of entities having at least one record in this annotation resource for an arbitrary set of entities.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Panglaodb.curation_effort" title="pypath.core.annot.Panglaodb.curation_effort"><code class="xref py py-obj docutils literal notranslate"><span class="pre">curation_effort</span></code></a>()</p></td>
+<td><p>Counts the reference-record pairs.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">from_dump</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_entity_type</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Panglaodb.get_names" title="pypath.core.annot.Panglaodb.get_names"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_names</span></code></a>()</p></td>
+<td><p>Returns the list of field names in the records.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Panglaodb.get_reference_set" title="pypath.core.annot.Panglaodb.get_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_reference_set</span></code></a>([proteins, complexes, ...])</p></td>
+<td><p>Retrieves the reference set i.e. the set of all entities which potentially have annotation in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Panglaodb.get_subset" title="pypath.core.annot.Panglaodb.get_subset"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Panglaodb.get_subset_bool_array" title="pypath.core.annot.Panglaodb.get_subset_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset_bool_array</span></code></a>([reference_set])</p></td>
+<td><p>Returns a boolean vector with True and False values for each entity in the reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Panglaodb.get_values" title="pypath.core.annot.Panglaodb.get_values"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_values</span></code></a>(name[, exclude_none])</p></td>
+<td><p>Returns the set of all possible values of a field.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_complex</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_mirna</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_protein</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Panglaodb.labels" title="pypath.core.annot.Panglaodb.labels"><code class="xref py py-obj docutils literal notranslate"><span class="pre">labels</span></code></a>([method])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Panglaodb.load" title="pypath.core.annot.Panglaodb.load"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load</span></code></a>()</p></td>
+<td><p>Loads the annotation data by calling the input method.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Panglaodb.load_data" title="pypath.core.annot.Panglaodb.load_data"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_data</span></code></a>()</p></td>
+<td><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Panglaodb.load_proteins" title="pypath.core.annot.Panglaodb.load_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_proteins</span></code></a>()</p></td>
+<td><p>Retrieves a set of all UniProt IDs to have a base set of the entire proteome.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Panglaodb.make_df" title="pypath.core.annot.Panglaodb.make_df"><code class="xref py py-obj docutils literal notranslate"><span class="pre">make_df</span></code></a>([rebuild])</p></td>
+<td><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complex_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Panglaodb.numof_entities" title="pypath.core.annot.Panglaodb.numof_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_entities</span></code></a>()</p></td>
+<td><p>The number of annotated entities in the resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirna_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirnas</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_protein_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_proteins</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Panglaodb.numof_records" title="pypath.core.annot.Panglaodb.numof_records"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_records</span></code></a>([entity_types])</p></td>
+<td><p>The total number of annotation records.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Panglaodb.numof_references" title="pypath.core.annot.Panglaodb.numof_references"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_references</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Panglaodb.process" title="pypath.core.annot.Panglaodb.process"><code class="xref py py-obj docutils literal notranslate"><span class="pre">process</span></code></a>()</p></td>
+<td><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">proportion</span></code>(other)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Panglaodb.reload" title="pypath.core.annot.Panglaodb.reload"><code class="xref py py-obj docutils literal notranslate"><span class="pre">reload</span></code></a>()</p></td>
+<td><p>Reloads the object from the module level.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">save_to_pickle</span></code>(pickle_file)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Panglaodb.select" title="pypath.core.annot.Panglaodb.select"><code class="xref py py-obj docutils literal notranslate"><span class="pre">select</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Panglaodb.set_method" title="pypath.core.annot.Panglaodb.set_method"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_method</span></code></a>()</p></td>
+<td><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if necessary.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Panglaodb.set_reference_set" title="pypath.core.annot.Panglaodb.set_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_reference_set</span></code></a>()</p></td>
+<td><p>Assigns the reference set to the :py:attr``reference_set`` attribute.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Panglaodb.show" title="pypath.core.annot.Panglaodb.show"><code class="xref py py-obj docutils literal notranslate"><span class="pre">show</span></code></a>([method, table_param])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic information from the UniProt datasheets.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Panglaodb.subset_intersection" title="pypath.core.annot.Panglaodb.subset_intersection"><code class="xref py py-obj docutils literal notranslate"><span class="pre">subset_intersection</span></code></a>(universe, **kwargs)</p></td>
+<td><p>Calculates the proportion of entities in a subset occuring in the set <code class="docutils literal notranslate"><span class="pre">universe</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Panglaodb.to_array" title="pypath.core.annot.Panglaodb.to_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_array</span></code></a>([reference_set, use_fields])</p></td>
+<td><p>Returns an entity vs feature array.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Panglaodb.to_bool_array" title="pypath.core.annot.Panglaodb.to_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_bool_array</span></code></a>(reference_set)</p></td>
+<td><p>Returns a presence/absence boolean array for a reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Panglaodb.to_set" title="pypath.core.annot.Panglaodb.to_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_set</span></code></a>()</p></td>
+<td><p>Returns the entities present in this annotation resource as a set.</p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Attributes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_fields</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">summary</span></code></p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Panglaodb.add_complexes_by_inference">
+<span class="sig-name descname"><span class="pre">add_complexes_by_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Panglaodb.add_complexes_by_inference" title="Link to this definition">§</a></dt>
+<dd><p>Creates complex annotations by in silico inference and adds them
+to this annotation set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Panglaodb.all_complexes">
+<span class="sig-name descname"><span class="pre">all_complexes</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Panglaodb.all_complexes" title="Link to this definition">§</a></dt>
+<dd><p>All protein complexes annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Panglaodb.all_entities">
+<span class="sig-name descname"><span class="pre">all_entities</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Panglaodb.all_entities" title="Link to this definition">§</a></dt>
+<dd><p>All entities annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Panglaodb.all_mirnas">
+<span class="sig-name descname"><span class="pre">all_mirnas</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Panglaodb.all_mirnas" title="Link to this definition">§</a></dt>
+<dd><p>All miRNAs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Panglaodb.all_proteins">
+<span class="sig-name descname"><span class="pre">all_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Panglaodb.all_proteins" title="Link to this definition">§</a></dt>
+<dd><p>All UniProt IDs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Panglaodb.all_refs">
+<span class="sig-name descname"><span class="pre">all_refs</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Panglaodb.all_refs" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects the references
+across all records. Returns <em>list</em>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Panglaodb.annotate_complex">
+<span class="sig-name descname"><span class="pre">annotate_complex</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cplex</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Panglaodb.annotate_complex" title="Link to this definition">§</a></dt>
+<dd><p>Infers annotations for a single complex.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Panglaodb.browse">
+<span class="sig-name descname"><span class="pre">browse</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">field</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">start</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Panglaodb.browse" title="Link to this definition">§</a></dt>
+<dd><p>Print gene information as a table.</p>
+<p>Presents information about annotation categories as ascii tables
+printed in the terminal. If one category provided, prints one table.
+If multiple categories provided, prints a table for each of them one
+by one proceeding to the next one once you hit return. If no categories
+provided goes through all levels of the primary category.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>field:</dt><dd><p>The field to browse categories by.</p>
+<ul class="simple">
+<li><p>If None the primary field will be selected.
+If this annotation resource doesn’t have fields, all proteins
+will be presented as one single category.</p></li>
+<li><p>If a string it will be considered a field name and it will
+browse through all levels of this field.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">list</span></code>, set or tuple, it will be considered either a
+<code class="docutils literal notranslate"><span class="pre">list</span></code> of field names or a list of values from the primary
+field. In the former case all combinations of the values of
+the fields will be presented, in the latter case the browsing
+will be limited to the levels of the primary field contained
+in <code class="docutils literal notranslate"><span class="pre">field</span></code>.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">dict</span></code>, keys are supposed to be field names and values
+as list of levels. If any of the values are None, all levels
+from that field will be used.</p></li>
+</ul>
+</dd>
+<dt>start:</dt><dd><p>Start browsing from this category. E.g. if there are 500
+categories and start is 250 it will skip everything before the
+250th.</p>
+</dd>
+<dt>kwargs:</dt><dd><p>Passed to <code class="docutils literal notranslate"><span class="pre">pypath.utils.uniprot.info</span></code>.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Panglaodb.complex_inference">
+<span class="sig-name descname"><span class="pre">complex_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Panglaodb.complex_inference" title="Link to this definition">§</a></dt>
+<dd><p>Annotates all complexes in <cite>complexes</cite>, by default in the default
+complex database (existing in the <cite>complex</cite> module or generated
+on demand according to the module’s current settings).</p>
+<dl class="field-list simple">
+<dt class="field-odd">Returns<span class="colon">:</span></dt>
+<dd class="field-odd"><p><ul class="simple">
+<li><p><em>Dict with complexes as keys and sets of annotations as values.</em></p></li>
+<li><p><em>Complexes with no valid information in this annotation resource</em></p></li>
+<li><p><em>won’t be in the dict.</em></p></li>
+</ul>
+</p>
+</dd>
+<dt class="field-even">Parameters<span class="colon">:</span></dt>
+<dd class="field-even"><p><strong>complexes</strong> (<em>iterable</em>) – Iterable yielding complexes.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Panglaodb.coverage">
+<span class="sig-name descname"><span class="pre">coverage</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">other</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Panglaodb.coverage" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the coverage of the annotation i.e. the proportion of
+entities having at least one record in this annotation resource
+for an arbitrary set of entities.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Panglaodb.curation_effort">
+<span class="sig-name descname"><span class="pre">curation_effort</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Panglaodb.curation_effort" title="Link to this definition">§</a></dt>
+<dd><p>Counts the reference-record pairs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Panglaodb.get_names">
+<span class="sig-name descname"><span class="pre">get_names</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Panglaodb.get_names" title="Link to this definition">§</a></dt>
+<dd><p>Returns the list of field names in the records. The annotation
+consists of uniform records and each entity might be annotated
+with one or more records. Each record is a tuple of fields, for
+example <code class="docutils literal notranslate"><span class="pre">('cell_type',</span> <span class="pre">'expression_level',</span> <span class="pre">'score')</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Panglaodb.get_reference_set">
+<em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">get_reference_set</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">proteins</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">swissprot_only</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Panglaodb.get_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the reference set i.e. the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Panglaodb.get_subset">
+<span class="sig-name descname"><span class="pre">get_subset</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Panglaodb.get_subset" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Panglaodb.get_subset_bool_array">
+<span class="sig-name descname"><span class="pre">get_subset_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Panglaodb.get_subset_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a boolean vector with True and False values for each entity
+in the reference set. The values represent presence absence data
+in the simplest case, but by providing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> any kind of matching
+and filtering is possible. <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> are passed to the <code class="docutils literal notranslate"><span class="pre">select</span></code>
+method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Panglaodb.get_values">
+<span class="sig-name descname"><span class="pre">get_values</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">exclude_none</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Panglaodb.get_values" title="Link to this definition">§</a></dt>
+<dd><p>Returns the set of all possible values of a field. E.g. if the
+records of this annotation have a field <code class="docutils literal notranslate"><span class="pre">cell_type</span></code> then calling
+this method can tell you that across all records the values of
+this field might be <code class="docutils literal notranslate"><span class="pre">{'macrophage',</span> <span class="pre">'epithelial_cell',</span> <span class="pre">...}</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Panglaodb.labels">
+<span class="sig-name descname"><span class="pre">labels</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Panglaodb.labels" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Panglaodb.load">
+<span class="sig-name descname"><span class="pre">load</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Panglaodb.load" title="Link to this definition">§</a></dt>
+<dd><p>Loads the annotation data by calling the input method.
+Infers annotations for complexes in the complex database if
+py:attr:<code class="docutils literal notranslate"><span class="pre">infer_complexes</span></code> is True.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Panglaodb.load_data">
+<span class="sig-name descname"><span class="pre">load_data</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Panglaodb.load_data" title="Link to this definition">§</a></dt>
+<dd><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Panglaodb.load_proteins">
+<span class="sig-name descname"><span class="pre">load_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Panglaodb.load_proteins" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a set of all UniProt IDs to have a base set of the entire
+proteome.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Panglaodb.make_df">
+<span class="sig-name descname"><span class="pre">make_df</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">rebuild</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Panglaodb.make_df" title="Link to this definition">§</a></dt>
+<dd><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.
+The data frame will be assigned to :py:attr``df``.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Panglaodb.numof_entities">
+<span class="sig-name descname"><span class="pre">numof_entities</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Panglaodb.numof_entities" title="Link to this definition">§</a></dt>
+<dd><p>The number of annotated entities in the resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Panglaodb.numof_records">
+<span class="sig-name descname"><span class="pre">numof_records</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Panglaodb.numof_records" title="Link to this definition">§</a></dt>
+<dd><p>The total number of annotation records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Panglaodb.numof_references">
+<span class="sig-name descname"><span class="pre">numof_references</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Panglaodb.numof_references" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects and counts the
+references across all records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Panglaodb.process">
+<span class="sig-name descname"><span class="pre">process</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Panglaodb.process" title="Link to this definition">§</a></dt>
+<dd><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Panglaodb.reload">
+<span class="sig-name descname"><span class="pre">reload</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Panglaodb.reload" title="Link to this definition">§</a></dt>
+<dd><p>Reloads the object from the module level.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Panglaodb.select">
+<span class="sig-name descname"><span class="pre">select</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Panglaodb.select" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Panglaodb.set_method">
+<span class="sig-name descname"><span class="pre">set_method</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Panglaodb.set_method" title="Link to this definition">§</a></dt>
+<dd><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if
+necessary.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Panglaodb.set_reference_set">
+<span class="sig-name descname"><span class="pre">set_reference_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Panglaodb.set_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Assigns the reference set to the :py:attr``reference_set`` attribute.
+The reference set is the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Panglaodb.show">
+<span class="sig-name descname"><span class="pre">show</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">table_param</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Panglaodb.show" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic
+information from the UniProt datasheets.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Panglaodb.subset_intersection">
+<span class="sig-name descname"><span class="pre">subset_intersection</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">universe</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Panglaodb.subset_intersection" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the proportion of entities in a subset occuring in the
+set <code class="docutils literal notranslate"><span class="pre">universe</span></code>. The subset is selected by passing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> to the
+<code class="docutils literal notranslate"><span class="pre">select</span></code> method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Panglaodb.to_array">
+<span class="sig-name descname"><span class="pre">to_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_fields</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Panglaodb.to_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns an entity vs feature array. In case of more complex
+annotations this might be huge.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Panglaodb.to_bool_array">
+<span class="sig-name descname"><span class="pre">to_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Panglaodb.to_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a presence/absence boolean array for a reference set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Panglaodb.to_set">
+<span class="sig-name descname"><span class="pre">to_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Panglaodb.to_set" title="Link to this definition">§</a></dt>
+<dd><p>Returns the entities present in this annotation resource as a set.</p>
+</dd></dl>
+
+</dd></dl>
+
+</section>
+
+
+                </article>
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+  <section id="pypath-core-annot-phobius">
+<h1>pypath.core.annot.Phobius<a class="headerlink" href="#pypath-core-annot-phobius" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.core.annot.Phobius">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.core.annot.</span></span><span class="sig-name descname"><span class="pre">Phobius</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#Phobius"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.Phobius" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <a class="reference internal" href="pypath.core.annot.AnnotationBase.html#pypath.core.annot.AnnotationBase" title="pypath.core.annot.AnnotationBase"><code class="xref py py-class docutils literal notranslate"><span class="pre">AnnotationBase</span></code></a></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Phobius.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#Phobius.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.Phobius.__init__" title="Link to this definition">§</a></dt>
+<dd><p>Represents annotations for a set of proteins.
+Loads the data from the original resource and provides methods
+to query the annotations.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>name</strong> (<em>str</em>) – A custom name for the annotation resource.</p></li>
+<li><p><strong>ncbi_tax_id</strong> (<em>int</em>) – NCBI Taxonomy identifier.</p></li>
+<li><p><strong>input_method</strong> (<em>callable</em><em>,</em><em>str</em>) – Either a callable or the name of a method in any submodules of
+the <code class="docutils literal notranslate"><span class="pre">pypath.inputs</span></code>  module. Should return a dict with
+UniProt IDs as keys or an object suitable for <code class="docutils literal notranslate"><span class="pre">process_method</span></code>.</p></li>
+<li><p><strong>input_args</strong> (<em>dict</em>) – Arguments for the <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Phobius.__init__" title="pypath.core.annot.Phobius.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>(**kwargs)</p></td>
+<td><p>Represents annotations for a set of proteins.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Phobius.add_complexes_by_inference" title="pypath.core.annot.Phobius.add_complexes_by_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">add_complexes_by_inference</span></code></a>([complexes])</p></td>
+<td><p>Creates complex annotations by in silico inference and adds them to this annotation set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Phobius.all_complexes" title="pypath.core.annot.Phobius.all_complexes"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_complexes</span></code></a>()</p></td>
+<td><p>All protein complexes annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Phobius.all_entities" title="pypath.core.annot.Phobius.all_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_entities</span></code></a>([entity_types])</p></td>
+<td><p>All entities annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Phobius.all_mirnas" title="pypath.core.annot.Phobius.all_mirnas"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_mirnas</span></code></a>()</p></td>
+<td><p>All miRNAs annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Phobius.all_proteins" title="pypath.core.annot.Phobius.all_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_proteins</span></code></a>()</p></td>
+<td><p>All UniProt IDs annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Phobius.all_refs" title="pypath.core.annot.Phobius.all_refs"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_refs</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Phobius.annotate_complex" title="pypath.core.annot.Phobius.annotate_complex"><code class="xref py py-obj docutils literal notranslate"><span class="pre">annotate_complex</span></code></a>(cplex)</p></td>
+<td><p>Infers annotations for a single complex.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Phobius.browse" title="pypath.core.annot.Phobius.browse"><code class="xref py py-obj docutils literal notranslate"><span class="pre">browse</span></code></a>([field, start])</p></td>
+<td><p>Print gene information as a table.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Phobius.complex_inference" title="pypath.core.annot.Phobius.complex_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">complex_inference</span></code></a>([complexes])</p></td>
+<td><p>Annotates all complexes in <cite>complexes</cite>, by default in the default complex database (existing in the <cite>complex</cite> module or generated on demand according to the module's current settings).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Phobius.coverage" title="pypath.core.annot.Phobius.coverage"><code class="xref py py-obj docutils literal notranslate"><span class="pre">coverage</span></code></a>(other)</p></td>
+<td><p>Calculates the coverage of the annotation i.e. the proportion of entities having at least one record in this annotation resource for an arbitrary set of entities.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Phobius.curation_effort" title="pypath.core.annot.Phobius.curation_effort"><code class="xref py py-obj docutils literal notranslate"><span class="pre">curation_effort</span></code></a>()</p></td>
+<td><p>Counts the reference-record pairs.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">from_dump</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_entity_type</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Phobius.get_names" title="pypath.core.annot.Phobius.get_names"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_names</span></code></a>()</p></td>
+<td><p>Returns the list of field names in the records.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Phobius.get_reference_set" title="pypath.core.annot.Phobius.get_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_reference_set</span></code></a>([proteins, complexes, ...])</p></td>
+<td><p>Retrieves the reference set i.e. the set of all entities which potentially have annotation in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Phobius.get_subset" title="pypath.core.annot.Phobius.get_subset"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Phobius.get_subset_bool_array" title="pypath.core.annot.Phobius.get_subset_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset_bool_array</span></code></a>([reference_set])</p></td>
+<td><p>Returns a boolean vector with True and False values for each entity in the reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Phobius.get_values" title="pypath.core.annot.Phobius.get_values"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_values</span></code></a>(name[, exclude_none])</p></td>
+<td><p>Returns the set of all possible values of a field.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_complex</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_mirna</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_protein</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Phobius.labels" title="pypath.core.annot.Phobius.labels"><code class="xref py py-obj docutils literal notranslate"><span class="pre">labels</span></code></a>([method])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Phobius.load" title="pypath.core.annot.Phobius.load"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load</span></code></a>()</p></td>
+<td><p>Loads the annotation data by calling the input method.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Phobius.load_data" title="pypath.core.annot.Phobius.load_data"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_data</span></code></a>()</p></td>
+<td><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Phobius.load_proteins" title="pypath.core.annot.Phobius.load_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_proteins</span></code></a>()</p></td>
+<td><p>Retrieves a set of all UniProt IDs to have a base set of the entire proteome.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Phobius.make_df" title="pypath.core.annot.Phobius.make_df"><code class="xref py py-obj docutils literal notranslate"><span class="pre">make_df</span></code></a>([rebuild])</p></td>
+<td><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complex_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Phobius.numof_entities" title="pypath.core.annot.Phobius.numof_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_entities</span></code></a>()</p></td>
+<td><p>The number of annotated entities in the resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirna_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirnas</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_protein_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_proteins</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Phobius.numof_records" title="pypath.core.annot.Phobius.numof_records"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_records</span></code></a>([entity_types])</p></td>
+<td><p>The total number of annotation records.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Phobius.numof_references" title="pypath.core.annot.Phobius.numof_references"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_references</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Phobius.process" title="pypath.core.annot.Phobius.process"><code class="xref py py-obj docutils literal notranslate"><span class="pre">process</span></code></a>()</p></td>
+<td><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">proportion</span></code>(other)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Phobius.reload" title="pypath.core.annot.Phobius.reload"><code class="xref py py-obj docutils literal notranslate"><span class="pre">reload</span></code></a>()</p></td>
+<td><p>Reloads the object from the module level.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">save_to_pickle</span></code>(pickle_file)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Phobius.select" title="pypath.core.annot.Phobius.select"><code class="xref py py-obj docutils literal notranslate"><span class="pre">select</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Phobius.set_method" title="pypath.core.annot.Phobius.set_method"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_method</span></code></a>()</p></td>
+<td><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if necessary.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Phobius.set_reference_set" title="pypath.core.annot.Phobius.set_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_reference_set</span></code></a>()</p></td>
+<td><p>Assigns the reference set to the :py:attr``reference_set`` attribute.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Phobius.show" title="pypath.core.annot.Phobius.show"><code class="xref py py-obj docutils literal notranslate"><span class="pre">show</span></code></a>([method, table_param])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic information from the UniProt datasheets.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Phobius.subset_intersection" title="pypath.core.annot.Phobius.subset_intersection"><code class="xref py py-obj docutils literal notranslate"><span class="pre">subset_intersection</span></code></a>(universe, **kwargs)</p></td>
+<td><p>Calculates the proportion of entities in a subset occuring in the set <code class="docutils literal notranslate"><span class="pre">universe</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Phobius.to_array" title="pypath.core.annot.Phobius.to_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_array</span></code></a>([reference_set, use_fields])</p></td>
+<td><p>Returns an entity vs feature array.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Phobius.to_bool_array" title="pypath.core.annot.Phobius.to_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_bool_array</span></code></a>(reference_set)</p></td>
+<td><p>Returns a presence/absence boolean array for a reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Phobius.to_set" title="pypath.core.annot.Phobius.to_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_set</span></code></a>()</p></td>
+<td><p>Returns the entities present in this annotation resource as a set.</p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Attributes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_fields</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">summary</span></code></p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Phobius.add_complexes_by_inference">
+<span class="sig-name descname"><span class="pre">add_complexes_by_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Phobius.add_complexes_by_inference" title="Link to this definition">§</a></dt>
+<dd><p>Creates complex annotations by in silico inference and adds them
+to this annotation set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Phobius.all_complexes">
+<span class="sig-name descname"><span class="pre">all_complexes</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Phobius.all_complexes" title="Link to this definition">§</a></dt>
+<dd><p>All protein complexes annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Phobius.all_entities">
+<span class="sig-name descname"><span class="pre">all_entities</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Phobius.all_entities" title="Link to this definition">§</a></dt>
+<dd><p>All entities annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Phobius.all_mirnas">
+<span class="sig-name descname"><span class="pre">all_mirnas</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Phobius.all_mirnas" title="Link to this definition">§</a></dt>
+<dd><p>All miRNAs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Phobius.all_proteins">
+<span class="sig-name descname"><span class="pre">all_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Phobius.all_proteins" title="Link to this definition">§</a></dt>
+<dd><p>All UniProt IDs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Phobius.all_refs">
+<span class="sig-name descname"><span class="pre">all_refs</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Phobius.all_refs" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects the references
+across all records. Returns <em>list</em>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Phobius.annotate_complex">
+<span class="sig-name descname"><span class="pre">annotate_complex</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cplex</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Phobius.annotate_complex" title="Link to this definition">§</a></dt>
+<dd><p>Infers annotations for a single complex.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Phobius.browse">
+<span class="sig-name descname"><span class="pre">browse</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">field</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">start</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Phobius.browse" title="Link to this definition">§</a></dt>
+<dd><p>Print gene information as a table.</p>
+<p>Presents information about annotation categories as ascii tables
+printed in the terminal. If one category provided, prints one table.
+If multiple categories provided, prints a table for each of them one
+by one proceeding to the next one once you hit return. If no categories
+provided goes through all levels of the primary category.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>field:</dt><dd><p>The field to browse categories by.</p>
+<ul class="simple">
+<li><p>If None the primary field will be selected.
+If this annotation resource doesn’t have fields, all proteins
+will be presented as one single category.</p></li>
+<li><p>If a string it will be considered a field name and it will
+browse through all levels of this field.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">list</span></code>, set or tuple, it will be considered either a
+<code class="docutils literal notranslate"><span class="pre">list</span></code> of field names or a list of values from the primary
+field. In the former case all combinations of the values of
+the fields will be presented, in the latter case the browsing
+will be limited to the levels of the primary field contained
+in <code class="docutils literal notranslate"><span class="pre">field</span></code>.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">dict</span></code>, keys are supposed to be field names and values
+as list of levels. If any of the values are None, all levels
+from that field will be used.</p></li>
+</ul>
+</dd>
+<dt>start:</dt><dd><p>Start browsing from this category. E.g. if there are 500
+categories and start is 250 it will skip everything before the
+250th.</p>
+</dd>
+<dt>kwargs:</dt><dd><p>Passed to <code class="docutils literal notranslate"><span class="pre">pypath.utils.uniprot.info</span></code>.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Phobius.complex_inference">
+<span class="sig-name descname"><span class="pre">complex_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Phobius.complex_inference" title="Link to this definition">§</a></dt>
+<dd><p>Annotates all complexes in <cite>complexes</cite>, by default in the default
+complex database (existing in the <cite>complex</cite> module or generated
+on demand according to the module’s current settings).</p>
+<dl class="field-list simple">
+<dt class="field-odd">Returns<span class="colon">:</span></dt>
+<dd class="field-odd"><p><ul class="simple">
+<li><p><em>Dict with complexes as keys and sets of annotations as values.</em></p></li>
+<li><p><em>Complexes with no valid information in this annotation resource</em></p></li>
+<li><p><em>won’t be in the dict.</em></p></li>
+</ul>
+</p>
+</dd>
+<dt class="field-even">Parameters<span class="colon">:</span></dt>
+<dd class="field-even"><p><strong>complexes</strong> (<em>iterable</em>) – Iterable yielding complexes.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Phobius.coverage">
+<span class="sig-name descname"><span class="pre">coverage</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">other</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Phobius.coverage" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the coverage of the annotation i.e. the proportion of
+entities having at least one record in this annotation resource
+for an arbitrary set of entities.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Phobius.curation_effort">
+<span class="sig-name descname"><span class="pre">curation_effort</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Phobius.curation_effort" title="Link to this definition">§</a></dt>
+<dd><p>Counts the reference-record pairs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Phobius.get_names">
+<span class="sig-name descname"><span class="pre">get_names</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Phobius.get_names" title="Link to this definition">§</a></dt>
+<dd><p>Returns the list of field names in the records. The annotation
+consists of uniform records and each entity might be annotated
+with one or more records. Each record is a tuple of fields, for
+example <code class="docutils literal notranslate"><span class="pre">('cell_type',</span> <span class="pre">'expression_level',</span> <span class="pre">'score')</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Phobius.get_reference_set">
+<em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">get_reference_set</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">proteins</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">swissprot_only</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Phobius.get_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the reference set i.e. the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Phobius.get_subset">
+<span class="sig-name descname"><span class="pre">get_subset</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Phobius.get_subset" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Phobius.get_subset_bool_array">
+<span class="sig-name descname"><span class="pre">get_subset_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Phobius.get_subset_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a boolean vector with True and False values for each entity
+in the reference set. The values represent presence absence data
+in the simplest case, but by providing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> any kind of matching
+and filtering is possible. <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> are passed to the <code class="docutils literal notranslate"><span class="pre">select</span></code>
+method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Phobius.get_values">
+<span class="sig-name descname"><span class="pre">get_values</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">exclude_none</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Phobius.get_values" title="Link to this definition">§</a></dt>
+<dd><p>Returns the set of all possible values of a field. E.g. if the
+records of this annotation have a field <code class="docutils literal notranslate"><span class="pre">cell_type</span></code> then calling
+this method can tell you that across all records the values of
+this field might be <code class="docutils literal notranslate"><span class="pre">{'macrophage',</span> <span class="pre">'epithelial_cell',</span> <span class="pre">...}</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Phobius.labels">
+<span class="sig-name descname"><span class="pre">labels</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Phobius.labels" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Phobius.load">
+<span class="sig-name descname"><span class="pre">load</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Phobius.load" title="Link to this definition">§</a></dt>
+<dd><p>Loads the annotation data by calling the input method.
+Infers annotations for complexes in the complex database if
+py:attr:<code class="docutils literal notranslate"><span class="pre">infer_complexes</span></code> is True.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Phobius.load_data">
+<span class="sig-name descname"><span class="pre">load_data</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Phobius.load_data" title="Link to this definition">§</a></dt>
+<dd><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Phobius.load_proteins">
+<span class="sig-name descname"><span class="pre">load_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Phobius.load_proteins" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a set of all UniProt IDs to have a base set of the entire
+proteome.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Phobius.make_df">
+<span class="sig-name descname"><span class="pre">make_df</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">rebuild</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Phobius.make_df" title="Link to this definition">§</a></dt>
+<dd><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.
+The data frame will be assigned to :py:attr``df``.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Phobius.numof_entities">
+<span class="sig-name descname"><span class="pre">numof_entities</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Phobius.numof_entities" title="Link to this definition">§</a></dt>
+<dd><p>The number of annotated entities in the resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Phobius.numof_records">
+<span class="sig-name descname"><span class="pre">numof_records</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Phobius.numof_records" title="Link to this definition">§</a></dt>
+<dd><p>The total number of annotation records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Phobius.numof_references">
+<span class="sig-name descname"><span class="pre">numof_references</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Phobius.numof_references" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects and counts the
+references across all records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Phobius.process">
+<span class="sig-name descname"><span class="pre">process</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Phobius.process" title="Link to this definition">§</a></dt>
+<dd><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Phobius.reload">
+<span class="sig-name descname"><span class="pre">reload</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Phobius.reload" title="Link to this definition">§</a></dt>
+<dd><p>Reloads the object from the module level.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Phobius.select">
+<span class="sig-name descname"><span class="pre">select</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Phobius.select" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Phobius.set_method">
+<span class="sig-name descname"><span class="pre">set_method</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Phobius.set_method" title="Link to this definition">§</a></dt>
+<dd><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if
+necessary.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Phobius.set_reference_set">
+<span class="sig-name descname"><span class="pre">set_reference_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Phobius.set_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Assigns the reference set to the :py:attr``reference_set`` attribute.
+The reference set is the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Phobius.show">
+<span class="sig-name descname"><span class="pre">show</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">table_param</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Phobius.show" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic
+information from the UniProt datasheets.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Phobius.subset_intersection">
+<span class="sig-name descname"><span class="pre">subset_intersection</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">universe</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Phobius.subset_intersection" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the proportion of entities in a subset occuring in the
+set <code class="docutils literal notranslate"><span class="pre">universe</span></code>. The subset is selected by passing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> to the
+<code class="docutils literal notranslate"><span class="pre">select</span></code> method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Phobius.to_array">
+<span class="sig-name descname"><span class="pre">to_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_fields</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Phobius.to_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns an entity vs feature array. In case of more complex
+annotations this might be huge.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Phobius.to_bool_array">
+<span class="sig-name descname"><span class="pre">to_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Phobius.to_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a presence/absence boolean array for a reference set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Phobius.to_set">
+<span class="sig-name descname"><span class="pre">to_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Phobius.to_set" title="Link to this definition">§</a></dt>
+<dd><p>Returns the entities present in this annotation resource as a set.</p>
+</dd></dl>
+
+</dd></dl>
+
+</section>
+
+
+                </article>
+              
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+  <section id="pypath-core-annot-phosphatome">
+<h1>pypath.core.annot.Phosphatome<a class="headerlink" href="#pypath-core-annot-phosphatome" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.core.annot.Phosphatome">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.core.annot.</span></span><span class="sig-name descname"><span class="pre">Phosphatome</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#Phosphatome"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.Phosphatome" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <a class="reference internal" href="pypath.core.annot.AnnotationBase.html#pypath.core.annot.AnnotationBase" title="pypath.core.annot.AnnotationBase"><code class="xref py py-class docutils literal notranslate"><span class="pre">AnnotationBase</span></code></a></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Phosphatome.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#Phosphatome.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.Phosphatome.__init__" title="Link to this definition">§</a></dt>
+<dd><p>The list of phosphatases from Chen et al, Science Signaling (2017)
+Table S1.</p>
+</dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Phosphatome.__init__" title="pypath.core.annot.Phosphatome.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>(**kwargs)</p></td>
+<td><p>The list of phosphatases from Chen et al, Science Signaling (2017) Table S1.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Phosphatome.add_complexes_by_inference" title="pypath.core.annot.Phosphatome.add_complexes_by_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">add_complexes_by_inference</span></code></a>([complexes])</p></td>
+<td><p>Creates complex annotations by in silico inference and adds them to this annotation set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Phosphatome.all_complexes" title="pypath.core.annot.Phosphatome.all_complexes"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_complexes</span></code></a>()</p></td>
+<td><p>All protein complexes annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Phosphatome.all_entities" title="pypath.core.annot.Phosphatome.all_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_entities</span></code></a>([entity_types])</p></td>
+<td><p>All entities annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Phosphatome.all_mirnas" title="pypath.core.annot.Phosphatome.all_mirnas"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_mirnas</span></code></a>()</p></td>
+<td><p>All miRNAs annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Phosphatome.all_proteins" title="pypath.core.annot.Phosphatome.all_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_proteins</span></code></a>()</p></td>
+<td><p>All UniProt IDs annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Phosphatome.all_refs" title="pypath.core.annot.Phosphatome.all_refs"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_refs</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Phosphatome.annotate_complex" title="pypath.core.annot.Phosphatome.annotate_complex"><code class="xref py py-obj docutils literal notranslate"><span class="pre">annotate_complex</span></code></a>(cplex)</p></td>
+<td><p>Infers annotations for a single complex.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Phosphatome.browse" title="pypath.core.annot.Phosphatome.browse"><code class="xref py py-obj docutils literal notranslate"><span class="pre">browse</span></code></a>([field, start])</p></td>
+<td><p>Print gene information as a table.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Phosphatome.complex_inference" title="pypath.core.annot.Phosphatome.complex_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">complex_inference</span></code></a>([complexes])</p></td>
+<td><p>Annotates all complexes in <cite>complexes</cite>, by default in the default complex database (existing in the <cite>complex</cite> module or generated on demand according to the module's current settings).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Phosphatome.coverage" title="pypath.core.annot.Phosphatome.coverage"><code class="xref py py-obj docutils literal notranslate"><span class="pre">coverage</span></code></a>(other)</p></td>
+<td><p>Calculates the coverage of the annotation i.e. the proportion of entities having at least one record in this annotation resource for an arbitrary set of entities.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Phosphatome.curation_effort" title="pypath.core.annot.Phosphatome.curation_effort"><code class="xref py py-obj docutils literal notranslate"><span class="pre">curation_effort</span></code></a>()</p></td>
+<td><p>Counts the reference-record pairs.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">from_dump</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_entity_type</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Phosphatome.get_names" title="pypath.core.annot.Phosphatome.get_names"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_names</span></code></a>()</p></td>
+<td><p>Returns the list of field names in the records.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Phosphatome.get_reference_set" title="pypath.core.annot.Phosphatome.get_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_reference_set</span></code></a>([proteins, complexes, ...])</p></td>
+<td><p>Retrieves the reference set i.e. the set of all entities which potentially have annotation in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Phosphatome.get_subset" title="pypath.core.annot.Phosphatome.get_subset"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Phosphatome.get_subset_bool_array" title="pypath.core.annot.Phosphatome.get_subset_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset_bool_array</span></code></a>([reference_set])</p></td>
+<td><p>Returns a boolean vector with True and False values for each entity in the reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Phosphatome.get_values" title="pypath.core.annot.Phosphatome.get_values"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_values</span></code></a>(name[, exclude_none])</p></td>
+<td><p>Returns the set of all possible values of a field.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_complex</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_mirna</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_protein</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Phosphatome.labels" title="pypath.core.annot.Phosphatome.labels"><code class="xref py py-obj docutils literal notranslate"><span class="pre">labels</span></code></a>([method])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Phosphatome.load" title="pypath.core.annot.Phosphatome.load"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load</span></code></a>()</p></td>
+<td><p>Loads the annotation data by calling the input method.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Phosphatome.load_data" title="pypath.core.annot.Phosphatome.load_data"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_data</span></code></a>()</p></td>
+<td><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Phosphatome.load_proteins" title="pypath.core.annot.Phosphatome.load_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_proteins</span></code></a>()</p></td>
+<td><p>Retrieves a set of all UniProt IDs to have a base set of the entire proteome.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Phosphatome.make_df" title="pypath.core.annot.Phosphatome.make_df"><code class="xref py py-obj docutils literal notranslate"><span class="pre">make_df</span></code></a>([rebuild])</p></td>
+<td><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complex_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Phosphatome.numof_entities" title="pypath.core.annot.Phosphatome.numof_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_entities</span></code></a>()</p></td>
+<td><p>The number of annotated entities in the resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirna_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirnas</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_protein_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_proteins</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Phosphatome.numof_records" title="pypath.core.annot.Phosphatome.numof_records"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_records</span></code></a>([entity_types])</p></td>
+<td><p>The total number of annotation records.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Phosphatome.numof_references" title="pypath.core.annot.Phosphatome.numof_references"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_references</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Phosphatome.process" title="pypath.core.annot.Phosphatome.process"><code class="xref py py-obj docutils literal notranslate"><span class="pre">process</span></code></a>()</p></td>
+<td><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">proportion</span></code>(other)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Phosphatome.reload" title="pypath.core.annot.Phosphatome.reload"><code class="xref py py-obj docutils literal notranslate"><span class="pre">reload</span></code></a>()</p></td>
+<td><p>Reloads the object from the module level.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">save_to_pickle</span></code>(pickle_file)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Phosphatome.select" title="pypath.core.annot.Phosphatome.select"><code class="xref py py-obj docutils literal notranslate"><span class="pre">select</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Phosphatome.set_method" title="pypath.core.annot.Phosphatome.set_method"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_method</span></code></a>()</p></td>
+<td><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if necessary.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Phosphatome.set_reference_set" title="pypath.core.annot.Phosphatome.set_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_reference_set</span></code></a>()</p></td>
+<td><p>Assigns the reference set to the :py:attr``reference_set`` attribute.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Phosphatome.show" title="pypath.core.annot.Phosphatome.show"><code class="xref py py-obj docutils literal notranslate"><span class="pre">show</span></code></a>([method, table_param])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic information from the UniProt datasheets.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Phosphatome.subset_intersection" title="pypath.core.annot.Phosphatome.subset_intersection"><code class="xref py py-obj docutils literal notranslate"><span class="pre">subset_intersection</span></code></a>(universe, **kwargs)</p></td>
+<td><p>Calculates the proportion of entities in a subset occuring in the set <code class="docutils literal notranslate"><span class="pre">universe</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Phosphatome.to_array" title="pypath.core.annot.Phosphatome.to_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_array</span></code></a>([reference_set, use_fields])</p></td>
+<td><p>Returns an entity vs feature array.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Phosphatome.to_bool_array" title="pypath.core.annot.Phosphatome.to_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_bool_array</span></code></a>(reference_set)</p></td>
+<td><p>Returns a presence/absence boolean array for a reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Phosphatome.to_set" title="pypath.core.annot.Phosphatome.to_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_set</span></code></a>()</p></td>
+<td><p>Returns the entities present in this annotation resource as a set.</p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Attributes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_fields</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">summary</span></code></p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Phosphatome.add_complexes_by_inference">
+<span class="sig-name descname"><span class="pre">add_complexes_by_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Phosphatome.add_complexes_by_inference" title="Link to this definition">§</a></dt>
+<dd><p>Creates complex annotations by in silico inference and adds them
+to this annotation set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Phosphatome.all_complexes">
+<span class="sig-name descname"><span class="pre">all_complexes</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Phosphatome.all_complexes" title="Link to this definition">§</a></dt>
+<dd><p>All protein complexes annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Phosphatome.all_entities">
+<span class="sig-name descname"><span class="pre">all_entities</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Phosphatome.all_entities" title="Link to this definition">§</a></dt>
+<dd><p>All entities annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Phosphatome.all_mirnas">
+<span class="sig-name descname"><span class="pre">all_mirnas</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Phosphatome.all_mirnas" title="Link to this definition">§</a></dt>
+<dd><p>All miRNAs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Phosphatome.all_proteins">
+<span class="sig-name descname"><span class="pre">all_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Phosphatome.all_proteins" title="Link to this definition">§</a></dt>
+<dd><p>All UniProt IDs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Phosphatome.all_refs">
+<span class="sig-name descname"><span class="pre">all_refs</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Phosphatome.all_refs" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects the references
+across all records. Returns <em>list</em>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Phosphatome.annotate_complex">
+<span class="sig-name descname"><span class="pre">annotate_complex</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cplex</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Phosphatome.annotate_complex" title="Link to this definition">§</a></dt>
+<dd><p>Infers annotations for a single complex.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Phosphatome.browse">
+<span class="sig-name descname"><span class="pre">browse</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">field</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">start</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Phosphatome.browse" title="Link to this definition">§</a></dt>
+<dd><p>Print gene information as a table.</p>
+<p>Presents information about annotation categories as ascii tables
+printed in the terminal. If one category provided, prints one table.
+If multiple categories provided, prints a table for each of them one
+by one proceeding to the next one once you hit return. If no categories
+provided goes through all levels of the primary category.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>field:</dt><dd><p>The field to browse categories by.</p>
+<ul class="simple">
+<li><p>If None the primary field will be selected.
+If this annotation resource doesn’t have fields, all proteins
+will be presented as one single category.</p></li>
+<li><p>If a string it will be considered a field name and it will
+browse through all levels of this field.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">list</span></code>, set or tuple, it will be considered either a
+<code class="docutils literal notranslate"><span class="pre">list</span></code> of field names or a list of values from the primary
+field. In the former case all combinations of the values of
+the fields will be presented, in the latter case the browsing
+will be limited to the levels of the primary field contained
+in <code class="docutils literal notranslate"><span class="pre">field</span></code>.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">dict</span></code>, keys are supposed to be field names and values
+as list of levels. If any of the values are None, all levels
+from that field will be used.</p></li>
+</ul>
+</dd>
+<dt>start:</dt><dd><p>Start browsing from this category. E.g. if there are 500
+categories and start is 250 it will skip everything before the
+250th.</p>
+</dd>
+<dt>kwargs:</dt><dd><p>Passed to <code class="docutils literal notranslate"><span class="pre">pypath.utils.uniprot.info</span></code>.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Phosphatome.complex_inference">
+<span class="sig-name descname"><span class="pre">complex_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Phosphatome.complex_inference" title="Link to this definition">§</a></dt>
+<dd><p>Annotates all complexes in <cite>complexes</cite>, by default in the default
+complex database (existing in the <cite>complex</cite> module or generated
+on demand according to the module’s current settings).</p>
+<dl class="field-list simple">
+<dt class="field-odd">Returns<span class="colon">:</span></dt>
+<dd class="field-odd"><p><ul class="simple">
+<li><p><em>Dict with complexes as keys and sets of annotations as values.</em></p></li>
+<li><p><em>Complexes with no valid information in this annotation resource</em></p></li>
+<li><p><em>won’t be in the dict.</em></p></li>
+</ul>
+</p>
+</dd>
+<dt class="field-even">Parameters<span class="colon">:</span></dt>
+<dd class="field-even"><p><strong>complexes</strong> (<em>iterable</em>) – Iterable yielding complexes.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Phosphatome.coverage">
+<span class="sig-name descname"><span class="pre">coverage</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">other</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Phosphatome.coverage" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the coverage of the annotation i.e. the proportion of
+entities having at least one record in this annotation resource
+for an arbitrary set of entities.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Phosphatome.curation_effort">
+<span class="sig-name descname"><span class="pre">curation_effort</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Phosphatome.curation_effort" title="Link to this definition">§</a></dt>
+<dd><p>Counts the reference-record pairs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Phosphatome.get_names">
+<span class="sig-name descname"><span class="pre">get_names</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Phosphatome.get_names" title="Link to this definition">§</a></dt>
+<dd><p>Returns the list of field names in the records. The annotation
+consists of uniform records and each entity might be annotated
+with one or more records. Each record is a tuple of fields, for
+example <code class="docutils literal notranslate"><span class="pre">('cell_type',</span> <span class="pre">'expression_level',</span> <span class="pre">'score')</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Phosphatome.get_reference_set">
+<em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">get_reference_set</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">proteins</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">swissprot_only</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Phosphatome.get_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the reference set i.e. the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Phosphatome.get_subset">
+<span class="sig-name descname"><span class="pre">get_subset</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Phosphatome.get_subset" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Phosphatome.get_subset_bool_array">
+<span class="sig-name descname"><span class="pre">get_subset_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Phosphatome.get_subset_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a boolean vector with True and False values for each entity
+in the reference set. The values represent presence absence data
+in the simplest case, but by providing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> any kind of matching
+and filtering is possible. <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> are passed to the <code class="docutils literal notranslate"><span class="pre">select</span></code>
+method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Phosphatome.get_values">
+<span class="sig-name descname"><span class="pre">get_values</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">exclude_none</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Phosphatome.get_values" title="Link to this definition">§</a></dt>
+<dd><p>Returns the set of all possible values of a field. E.g. if the
+records of this annotation have a field <code class="docutils literal notranslate"><span class="pre">cell_type</span></code> then calling
+this method can tell you that across all records the values of
+this field might be <code class="docutils literal notranslate"><span class="pre">{'macrophage',</span> <span class="pre">'epithelial_cell',</span> <span class="pre">...}</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Phosphatome.labels">
+<span class="sig-name descname"><span class="pre">labels</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Phosphatome.labels" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Phosphatome.load">
+<span class="sig-name descname"><span class="pre">load</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Phosphatome.load" title="Link to this definition">§</a></dt>
+<dd><p>Loads the annotation data by calling the input method.
+Infers annotations for complexes in the complex database if
+py:attr:<code class="docutils literal notranslate"><span class="pre">infer_complexes</span></code> is True.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Phosphatome.load_data">
+<span class="sig-name descname"><span class="pre">load_data</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Phosphatome.load_data" title="Link to this definition">§</a></dt>
+<dd><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Phosphatome.load_proteins">
+<span class="sig-name descname"><span class="pre">load_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Phosphatome.load_proteins" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a set of all UniProt IDs to have a base set of the entire
+proteome.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Phosphatome.make_df">
+<span class="sig-name descname"><span class="pre">make_df</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">rebuild</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Phosphatome.make_df" title="Link to this definition">§</a></dt>
+<dd><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.
+The data frame will be assigned to :py:attr``df``.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Phosphatome.numof_entities">
+<span class="sig-name descname"><span class="pre">numof_entities</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Phosphatome.numof_entities" title="Link to this definition">§</a></dt>
+<dd><p>The number of annotated entities in the resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Phosphatome.numof_records">
+<span class="sig-name descname"><span class="pre">numof_records</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Phosphatome.numof_records" title="Link to this definition">§</a></dt>
+<dd><p>The total number of annotation records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Phosphatome.numof_references">
+<span class="sig-name descname"><span class="pre">numof_references</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Phosphatome.numof_references" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects and counts the
+references across all records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Phosphatome.process">
+<span class="sig-name descname"><span class="pre">process</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Phosphatome.process" title="Link to this definition">§</a></dt>
+<dd><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Phosphatome.reload">
+<span class="sig-name descname"><span class="pre">reload</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Phosphatome.reload" title="Link to this definition">§</a></dt>
+<dd><p>Reloads the object from the module level.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Phosphatome.select">
+<span class="sig-name descname"><span class="pre">select</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Phosphatome.select" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Phosphatome.set_method">
+<span class="sig-name descname"><span class="pre">set_method</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Phosphatome.set_method" title="Link to this definition">§</a></dt>
+<dd><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if
+necessary.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Phosphatome.set_reference_set">
+<span class="sig-name descname"><span class="pre">set_reference_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Phosphatome.set_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Assigns the reference set to the :py:attr``reference_set`` attribute.
+The reference set is the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Phosphatome.show">
+<span class="sig-name descname"><span class="pre">show</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">table_param</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Phosphatome.show" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic
+information from the UniProt datasheets.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Phosphatome.subset_intersection">
+<span class="sig-name descname"><span class="pre">subset_intersection</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">universe</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Phosphatome.subset_intersection" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the proportion of entities in a subset occuring in the
+set <code class="docutils literal notranslate"><span class="pre">universe</span></code>. The subset is selected by passing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> to the
+<code class="docutils literal notranslate"><span class="pre">select</span></code> method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Phosphatome.to_array">
+<span class="sig-name descname"><span class="pre">to_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_fields</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Phosphatome.to_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns an entity vs feature array. In case of more complex
+annotations this might be huge.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Phosphatome.to_bool_array">
+<span class="sig-name descname"><span class="pre">to_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Phosphatome.to_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a presence/absence boolean array for a reference set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Phosphatome.to_set">
+<span class="sig-name descname"><span class="pre">to_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Phosphatome.to_set" title="Link to this definition">§</a></dt>
+<dd><p>Returns the entities present in this annotation resource as a set.</p>
+</dd></dl>
+
+</dd></dl>
+
+</section>
+
+
+                </article>
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+  <section id="pypath-core-annot-progeny">
+<h1>pypath.core.annot.Progeny<a class="headerlink" href="#pypath-core-annot-progeny" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.core.annot.Progeny">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.core.annot.</span></span><span class="sig-name descname"><span class="pre">Progeny</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#Progeny"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.Progeny" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <a class="reference internal" href="pypath.core.annot.AnnotationBase.html#pypath.core.annot.AnnotationBase" title="pypath.core.annot.AnnotationBase"><code class="xref py py-class docutils literal notranslate"><span class="pre">AnnotationBase</span></code></a></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Progeny.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#Progeny.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.Progeny.__init__" title="Link to this definition">§</a></dt>
+<dd><p>Pathway responsive genes: signatures based on transcriptomics data
+from PROGENy (<a class="github reference external" href="https://github.com/saezlab/progeny">saezlab/progeny</a>).</p>
+</dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Progeny.__init__" title="pypath.core.annot.Progeny.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>([ncbi_tax_id])</p></td>
+<td><p>Pathway responsive genes: signatures based on transcriptomics data from PROGENy (<a class="github reference external" href="https://github.com/saezlab/progeny">saezlab/progeny</a>).</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Progeny.add_complexes_by_inference" title="pypath.core.annot.Progeny.add_complexes_by_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">add_complexes_by_inference</span></code></a>([complexes])</p></td>
+<td><p>Creates complex annotations by in silico inference and adds them to this annotation set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Progeny.all_complexes" title="pypath.core.annot.Progeny.all_complexes"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_complexes</span></code></a>()</p></td>
+<td><p>All protein complexes annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Progeny.all_entities" title="pypath.core.annot.Progeny.all_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_entities</span></code></a>([entity_types])</p></td>
+<td><p>All entities annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Progeny.all_mirnas" title="pypath.core.annot.Progeny.all_mirnas"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_mirnas</span></code></a>()</p></td>
+<td><p>All miRNAs annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Progeny.all_proteins" title="pypath.core.annot.Progeny.all_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_proteins</span></code></a>()</p></td>
+<td><p>All UniProt IDs annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Progeny.all_refs" title="pypath.core.annot.Progeny.all_refs"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_refs</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Progeny.annotate_complex" title="pypath.core.annot.Progeny.annotate_complex"><code class="xref py py-obj docutils literal notranslate"><span class="pre">annotate_complex</span></code></a>(cplex)</p></td>
+<td><p>Infers annotations for a single complex.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Progeny.browse" title="pypath.core.annot.Progeny.browse"><code class="xref py py-obj docutils literal notranslate"><span class="pre">browse</span></code></a>([field, start])</p></td>
+<td><p>Print gene information as a table.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Progeny.complex_inference" title="pypath.core.annot.Progeny.complex_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">complex_inference</span></code></a>([complexes])</p></td>
+<td><p>Annotates all complexes in <cite>complexes</cite>, by default in the default complex database (existing in the <cite>complex</cite> module or generated on demand according to the module's current settings).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Progeny.coverage" title="pypath.core.annot.Progeny.coverage"><code class="xref py py-obj docutils literal notranslate"><span class="pre">coverage</span></code></a>(other)</p></td>
+<td><p>Calculates the coverage of the annotation i.e. the proportion of entities having at least one record in this annotation resource for an arbitrary set of entities.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Progeny.curation_effort" title="pypath.core.annot.Progeny.curation_effort"><code class="xref py py-obj docutils literal notranslate"><span class="pre">curation_effort</span></code></a>()</p></td>
+<td><p>Counts the reference-record pairs.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">from_dump</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_entity_type</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Progeny.get_names" title="pypath.core.annot.Progeny.get_names"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_names</span></code></a>()</p></td>
+<td><p>Returns the list of field names in the records.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Progeny.get_reference_set" title="pypath.core.annot.Progeny.get_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_reference_set</span></code></a>([proteins, complexes, ...])</p></td>
+<td><p>Retrieves the reference set i.e. the set of all entities which potentially have annotation in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Progeny.get_subset" title="pypath.core.annot.Progeny.get_subset"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Progeny.get_subset_bool_array" title="pypath.core.annot.Progeny.get_subset_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset_bool_array</span></code></a>([reference_set])</p></td>
+<td><p>Returns a boolean vector with True and False values for each entity in the reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Progeny.get_values" title="pypath.core.annot.Progeny.get_values"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_values</span></code></a>(name[, exclude_none])</p></td>
+<td><p>Returns the set of all possible values of a field.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_complex</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_mirna</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_protein</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Progeny.labels" title="pypath.core.annot.Progeny.labels"><code class="xref py py-obj docutils literal notranslate"><span class="pre">labels</span></code></a>([method])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Progeny.load" title="pypath.core.annot.Progeny.load"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load</span></code></a>()</p></td>
+<td><p>Loads the annotation data by calling the input method.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Progeny.load_data" title="pypath.core.annot.Progeny.load_data"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_data</span></code></a>()</p></td>
+<td><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Progeny.load_proteins" title="pypath.core.annot.Progeny.load_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_proteins</span></code></a>()</p></td>
+<td><p>Retrieves a set of all UniProt IDs to have a base set of the entire proteome.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Progeny.make_df" title="pypath.core.annot.Progeny.make_df"><code class="xref py py-obj docutils literal notranslate"><span class="pre">make_df</span></code></a>([rebuild])</p></td>
+<td><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complex_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Progeny.numof_entities" title="pypath.core.annot.Progeny.numof_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_entities</span></code></a>()</p></td>
+<td><p>The number of annotated entities in the resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirna_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirnas</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_protein_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_proteins</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Progeny.numof_records" title="pypath.core.annot.Progeny.numof_records"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_records</span></code></a>([entity_types])</p></td>
+<td><p>The total number of annotation records.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Progeny.numof_references" title="pypath.core.annot.Progeny.numof_references"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_references</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Progeny.process" title="pypath.core.annot.Progeny.process"><code class="xref py py-obj docutils literal notranslate"><span class="pre">process</span></code></a>()</p></td>
+<td><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">proportion</span></code>(other)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Progeny.reload" title="pypath.core.annot.Progeny.reload"><code class="xref py py-obj docutils literal notranslate"><span class="pre">reload</span></code></a>()</p></td>
+<td><p>Reloads the object from the module level.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">save_to_pickle</span></code>(pickle_file)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Progeny.select" title="pypath.core.annot.Progeny.select"><code class="xref py py-obj docutils literal notranslate"><span class="pre">select</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Progeny.set_method" title="pypath.core.annot.Progeny.set_method"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_method</span></code></a>()</p></td>
+<td><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if necessary.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Progeny.set_reference_set" title="pypath.core.annot.Progeny.set_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_reference_set</span></code></a>()</p></td>
+<td><p>Assigns the reference set to the :py:attr``reference_set`` attribute.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Progeny.show" title="pypath.core.annot.Progeny.show"><code class="xref py py-obj docutils literal notranslate"><span class="pre">show</span></code></a>([method, table_param])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic information from the UniProt datasheets.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Progeny.subset_intersection" title="pypath.core.annot.Progeny.subset_intersection"><code class="xref py py-obj docutils literal notranslate"><span class="pre">subset_intersection</span></code></a>(universe, **kwargs)</p></td>
+<td><p>Calculates the proportion of entities in a subset occuring in the set <code class="docutils literal notranslate"><span class="pre">universe</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Progeny.to_array" title="pypath.core.annot.Progeny.to_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_array</span></code></a>([reference_set, use_fields])</p></td>
+<td><p>Returns an entity vs feature array.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Progeny.to_bool_array" title="pypath.core.annot.Progeny.to_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_bool_array</span></code></a>(reference_set)</p></td>
+<td><p>Returns a presence/absence boolean array for a reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Progeny.to_set" title="pypath.core.annot.Progeny.to_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_set</span></code></a>()</p></td>
+<td><p>Returns the entities present in this annotation resource as a set.</p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Attributes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_fields</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">summary</span></code></p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Progeny.add_complexes_by_inference">
+<span class="sig-name descname"><span class="pre">add_complexes_by_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Progeny.add_complexes_by_inference" title="Link to this definition">§</a></dt>
+<dd><p>Creates complex annotations by in silico inference and adds them
+to this annotation set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Progeny.all_complexes">
+<span class="sig-name descname"><span class="pre">all_complexes</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Progeny.all_complexes" title="Link to this definition">§</a></dt>
+<dd><p>All protein complexes annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Progeny.all_entities">
+<span class="sig-name descname"><span class="pre">all_entities</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Progeny.all_entities" title="Link to this definition">§</a></dt>
+<dd><p>All entities annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Progeny.all_mirnas">
+<span class="sig-name descname"><span class="pre">all_mirnas</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Progeny.all_mirnas" title="Link to this definition">§</a></dt>
+<dd><p>All miRNAs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Progeny.all_proteins">
+<span class="sig-name descname"><span class="pre">all_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Progeny.all_proteins" title="Link to this definition">§</a></dt>
+<dd><p>All UniProt IDs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Progeny.all_refs">
+<span class="sig-name descname"><span class="pre">all_refs</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Progeny.all_refs" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects the references
+across all records. Returns <em>list</em>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Progeny.annotate_complex">
+<span class="sig-name descname"><span class="pre">annotate_complex</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cplex</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Progeny.annotate_complex" title="Link to this definition">§</a></dt>
+<dd><p>Infers annotations for a single complex.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Progeny.browse">
+<span class="sig-name descname"><span class="pre">browse</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">field</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">start</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Progeny.browse" title="Link to this definition">§</a></dt>
+<dd><p>Print gene information as a table.</p>
+<p>Presents information about annotation categories as ascii tables
+printed in the terminal. If one category provided, prints one table.
+If multiple categories provided, prints a table for each of them one
+by one proceeding to the next one once you hit return. If no categories
+provided goes through all levels of the primary category.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>field:</dt><dd><p>The field to browse categories by.</p>
+<ul class="simple">
+<li><p>If None the primary field will be selected.
+If this annotation resource doesn’t have fields, all proteins
+will be presented as one single category.</p></li>
+<li><p>If a string it will be considered a field name and it will
+browse through all levels of this field.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">list</span></code>, set or tuple, it will be considered either a
+<code class="docutils literal notranslate"><span class="pre">list</span></code> of field names or a list of values from the primary
+field. In the former case all combinations of the values of
+the fields will be presented, in the latter case the browsing
+will be limited to the levels of the primary field contained
+in <code class="docutils literal notranslate"><span class="pre">field</span></code>.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">dict</span></code>, keys are supposed to be field names and values
+as list of levels. If any of the values are None, all levels
+from that field will be used.</p></li>
+</ul>
+</dd>
+<dt>start:</dt><dd><p>Start browsing from this category. E.g. if there are 500
+categories and start is 250 it will skip everything before the
+250th.</p>
+</dd>
+<dt>kwargs:</dt><dd><p>Passed to <code class="docutils literal notranslate"><span class="pre">pypath.utils.uniprot.info</span></code>.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Progeny.complex_inference">
+<span class="sig-name descname"><span class="pre">complex_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Progeny.complex_inference" title="Link to this definition">§</a></dt>
+<dd><p>Annotates all complexes in <cite>complexes</cite>, by default in the default
+complex database (existing in the <cite>complex</cite> module or generated
+on demand according to the module’s current settings).</p>
+<dl class="field-list simple">
+<dt class="field-odd">Returns<span class="colon">:</span></dt>
+<dd class="field-odd"><p><ul class="simple">
+<li><p><em>Dict with complexes as keys and sets of annotations as values.</em></p></li>
+<li><p><em>Complexes with no valid information in this annotation resource</em></p></li>
+<li><p><em>won’t be in the dict.</em></p></li>
+</ul>
+</p>
+</dd>
+<dt class="field-even">Parameters<span class="colon">:</span></dt>
+<dd class="field-even"><p><strong>complexes</strong> (<em>iterable</em>) – Iterable yielding complexes.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Progeny.coverage">
+<span class="sig-name descname"><span class="pre">coverage</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">other</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Progeny.coverage" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the coverage of the annotation i.e. the proportion of
+entities having at least one record in this annotation resource
+for an arbitrary set of entities.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Progeny.curation_effort">
+<span class="sig-name descname"><span class="pre">curation_effort</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Progeny.curation_effort" title="Link to this definition">§</a></dt>
+<dd><p>Counts the reference-record pairs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Progeny.get_names">
+<span class="sig-name descname"><span class="pre">get_names</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Progeny.get_names" title="Link to this definition">§</a></dt>
+<dd><p>Returns the list of field names in the records. The annotation
+consists of uniform records and each entity might be annotated
+with one or more records. Each record is a tuple of fields, for
+example <code class="docutils literal notranslate"><span class="pre">('cell_type',</span> <span class="pre">'expression_level',</span> <span class="pre">'score')</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Progeny.get_reference_set">
+<em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">get_reference_set</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">proteins</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">swissprot_only</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Progeny.get_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the reference set i.e. the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Progeny.get_subset">
+<span class="sig-name descname"><span class="pre">get_subset</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Progeny.get_subset" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Progeny.get_subset_bool_array">
+<span class="sig-name descname"><span class="pre">get_subset_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Progeny.get_subset_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a boolean vector with True and False values for each entity
+in the reference set. The values represent presence absence data
+in the simplest case, but by providing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> any kind of matching
+and filtering is possible. <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> are passed to the <code class="docutils literal notranslate"><span class="pre">select</span></code>
+method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Progeny.get_values">
+<span class="sig-name descname"><span class="pre">get_values</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">exclude_none</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Progeny.get_values" title="Link to this definition">§</a></dt>
+<dd><p>Returns the set of all possible values of a field. E.g. if the
+records of this annotation have a field <code class="docutils literal notranslate"><span class="pre">cell_type</span></code> then calling
+this method can tell you that across all records the values of
+this field might be <code class="docutils literal notranslate"><span class="pre">{'macrophage',</span> <span class="pre">'epithelial_cell',</span> <span class="pre">...}</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Progeny.labels">
+<span class="sig-name descname"><span class="pre">labels</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Progeny.labels" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Progeny.load">
+<span class="sig-name descname"><span class="pre">load</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Progeny.load" title="Link to this definition">§</a></dt>
+<dd><p>Loads the annotation data by calling the input method.
+Infers annotations for complexes in the complex database if
+py:attr:<code class="docutils literal notranslate"><span class="pre">infer_complexes</span></code> is True.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Progeny.load_data">
+<span class="sig-name descname"><span class="pre">load_data</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Progeny.load_data" title="Link to this definition">§</a></dt>
+<dd><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Progeny.load_proteins">
+<span class="sig-name descname"><span class="pre">load_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Progeny.load_proteins" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a set of all UniProt IDs to have a base set of the entire
+proteome.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Progeny.make_df">
+<span class="sig-name descname"><span class="pre">make_df</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">rebuild</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Progeny.make_df" title="Link to this definition">§</a></dt>
+<dd><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.
+The data frame will be assigned to :py:attr``df``.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Progeny.numof_entities">
+<span class="sig-name descname"><span class="pre">numof_entities</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Progeny.numof_entities" title="Link to this definition">§</a></dt>
+<dd><p>The number of annotated entities in the resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Progeny.numof_records">
+<span class="sig-name descname"><span class="pre">numof_records</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Progeny.numof_records" title="Link to this definition">§</a></dt>
+<dd><p>The total number of annotation records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Progeny.numof_references">
+<span class="sig-name descname"><span class="pre">numof_references</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Progeny.numof_references" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects and counts the
+references across all records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Progeny.process">
+<span class="sig-name descname"><span class="pre">process</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Progeny.process" title="Link to this definition">§</a></dt>
+<dd><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Progeny.reload">
+<span class="sig-name descname"><span class="pre">reload</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Progeny.reload" title="Link to this definition">§</a></dt>
+<dd><p>Reloads the object from the module level.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Progeny.select">
+<span class="sig-name descname"><span class="pre">select</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Progeny.select" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Progeny.set_method">
+<span class="sig-name descname"><span class="pre">set_method</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Progeny.set_method" title="Link to this definition">§</a></dt>
+<dd><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if
+necessary.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Progeny.set_reference_set">
+<span class="sig-name descname"><span class="pre">set_reference_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Progeny.set_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Assigns the reference set to the :py:attr``reference_set`` attribute.
+The reference set is the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Progeny.show">
+<span class="sig-name descname"><span class="pre">show</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">table_param</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Progeny.show" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic
+information from the UniProt datasheets.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Progeny.subset_intersection">
+<span class="sig-name descname"><span class="pre">subset_intersection</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">universe</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Progeny.subset_intersection" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the proportion of entities in a subset occuring in the
+set <code class="docutils literal notranslate"><span class="pre">universe</span></code>. The subset is selected by passing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> to the
+<code class="docutils literal notranslate"><span class="pre">select</span></code> method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Progeny.to_array">
+<span class="sig-name descname"><span class="pre">to_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_fields</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Progeny.to_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns an entity vs feature array. In case of more complex
+annotations this might be huge.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Progeny.to_bool_array">
+<span class="sig-name descname"><span class="pre">to_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Progeny.to_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a presence/absence boolean array for a reference set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Progeny.to_set">
+<span class="sig-name descname"><span class="pre">to_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Progeny.to_set" title="Link to this definition">§</a></dt>
+<dd><p>Returns the entities present in this annotation resource as a set.</p>
+</dd></dl>
+
+</dd></dl>
+
+</section>
+
+
+                </article>
+              
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+  <section id="pypath-core-annot-ramilowski2015">
+<h1>pypath.core.annot.Ramilowski2015<a class="headerlink" href="#pypath-core-annot-ramilowski2015" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.core.annot.Ramilowski2015">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.core.annot.</span></span><span class="sig-name descname"><span class="pre">Ramilowski2015</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">load_sources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#Ramilowski2015"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.Ramilowski2015" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <a class="reference internal" href="pypath.core.annot.LigandReceptor.html#pypath.core.annot.LigandReceptor" title="pypath.core.annot.LigandReceptor"><code class="xref py py-class docutils literal notranslate"><span class="pre">LigandReceptor</span></code></a></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Ramilowski2015.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">load_sources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#Ramilowski2015.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.Ramilowski2015.__init__" title="Link to this definition">§</a></dt>
+<dd><p>Represents annotations for a set of proteins.
+Loads the data from the original resource and provides methods
+to query the annotations.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>name</strong> (<em>str</em>) – A custom name for the annotation resource.</p></li>
+<li><p><strong>ncbi_tax_id</strong> (<em>int</em>) – NCBI Taxonomy identifier.</p></li>
+<li><p><strong>input_method</strong> (<em>callable</em><em>,</em><em>str</em>) – Either a callable or the name of a method in any submodules of
+the <code class="docutils literal notranslate"><span class="pre">pypath.inputs</span></code>  module. Should return a dict with
+UniProt IDs as keys or an object suitable for <code class="docutils literal notranslate"><span class="pre">process_method</span></code>.</p></li>
+<li><p><strong>input_args</strong> (<em>dict</em>) – Arguments for the <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Ramilowski2015.__init__" title="pypath.core.annot.Ramilowski2015.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>([load_sources])</p></td>
+<td><p>Represents annotations for a set of proteins.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Ramilowski2015.add_complexes_by_inference" title="pypath.core.annot.Ramilowski2015.add_complexes_by_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">add_complexes_by_inference</span></code></a>([complexes])</p></td>
+<td><p>Creates complex annotations by in silico inference and adds them to this annotation set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Ramilowski2015.all_complexes" title="pypath.core.annot.Ramilowski2015.all_complexes"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_complexes</span></code></a>()</p></td>
+<td><p>All protein complexes annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Ramilowski2015.all_entities" title="pypath.core.annot.Ramilowski2015.all_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_entities</span></code></a>([entity_types])</p></td>
+<td><p>All entities annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Ramilowski2015.all_mirnas" title="pypath.core.annot.Ramilowski2015.all_mirnas"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_mirnas</span></code></a>()</p></td>
+<td><p>All miRNAs annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Ramilowski2015.all_proteins" title="pypath.core.annot.Ramilowski2015.all_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_proteins</span></code></a>()</p></td>
+<td><p>All UniProt IDs annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Ramilowski2015.all_refs" title="pypath.core.annot.Ramilowski2015.all_refs"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_refs</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Ramilowski2015.annotate_complex" title="pypath.core.annot.Ramilowski2015.annotate_complex"><code class="xref py py-obj docutils literal notranslate"><span class="pre">annotate_complex</span></code></a>(cplex)</p></td>
+<td><p>Infers annotations for a single complex.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Ramilowski2015.browse" title="pypath.core.annot.Ramilowski2015.browse"><code class="xref py py-obj docutils literal notranslate"><span class="pre">browse</span></code></a>([field, start])</p></td>
+<td><p>Print gene information as a table.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Ramilowski2015.complex_inference" title="pypath.core.annot.Ramilowski2015.complex_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">complex_inference</span></code></a>([complexes])</p></td>
+<td><p>Annotates all complexes in <cite>complexes</cite>, by default in the default complex database (existing in the <cite>complex</cite> module or generated on demand according to the module's current settings).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Ramilowski2015.coverage" title="pypath.core.annot.Ramilowski2015.coverage"><code class="xref py py-obj docutils literal notranslate"><span class="pre">coverage</span></code></a>(other)</p></td>
+<td><p>Calculates the coverage of the annotation i.e. the proportion of entities having at least one record in this annotation resource for an arbitrary set of entities.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Ramilowski2015.curation_effort" title="pypath.core.annot.Ramilowski2015.curation_effort"><code class="xref py py-obj docutils literal notranslate"><span class="pre">curation_effort</span></code></a>()</p></td>
+<td><p>Counts the reference-record pairs.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">from_dump</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_entity_type</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Ramilowski2015.get_names" title="pypath.core.annot.Ramilowski2015.get_names"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_names</span></code></a>()</p></td>
+<td><p>Returns the list of field names in the records.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Ramilowski2015.get_reference_set" title="pypath.core.annot.Ramilowski2015.get_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_reference_set</span></code></a>([proteins, complexes, ...])</p></td>
+<td><p>Retrieves the reference set i.e. the set of all entities which potentially have annotation in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Ramilowski2015.get_subset" title="pypath.core.annot.Ramilowski2015.get_subset"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Ramilowski2015.get_subset_bool_array" title="pypath.core.annot.Ramilowski2015.get_subset_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset_bool_array</span></code></a>([reference_set])</p></td>
+<td><p>Returns a boolean vector with True and False values for each entity in the reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Ramilowski2015.get_values" title="pypath.core.annot.Ramilowski2015.get_values"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_values</span></code></a>(name[, exclude_none])</p></td>
+<td><p>Returns the set of all possible values of a field.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_complex</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_mirna</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_protein</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Ramilowski2015.labels" title="pypath.core.annot.Ramilowski2015.labels"><code class="xref py py-obj docutils literal notranslate"><span class="pre">labels</span></code></a>([method])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Ramilowski2015.load" title="pypath.core.annot.Ramilowski2015.load"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load</span></code></a>()</p></td>
+<td><p>Loads the annotation data by calling the input method.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Ramilowski2015.load_data" title="pypath.core.annot.Ramilowski2015.load_data"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_data</span></code></a>()</p></td>
+<td><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Ramilowski2015.load_proteins" title="pypath.core.annot.Ramilowski2015.load_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_proteins</span></code></a>()</p></td>
+<td><p>Retrieves a set of all UniProt IDs to have a base set of the entire proteome.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Ramilowski2015.make_df" title="pypath.core.annot.Ramilowski2015.make_df"><code class="xref py py-obj docutils literal notranslate"><span class="pre">make_df</span></code></a>([rebuild])</p></td>
+<td><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complex_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Ramilowski2015.numof_entities" title="pypath.core.annot.Ramilowski2015.numof_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_entities</span></code></a>()</p></td>
+<td><p>The number of annotated entities in the resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirna_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirnas</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_protein_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_proteins</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Ramilowski2015.numof_records" title="pypath.core.annot.Ramilowski2015.numof_records"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_records</span></code></a>([entity_types])</p></td>
+<td><p>The total number of annotation records.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Ramilowski2015.numof_references" title="pypath.core.annot.Ramilowski2015.numof_references"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_references</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Ramilowski2015.process" title="pypath.core.annot.Ramilowski2015.process"><code class="xref py py-obj docutils literal notranslate"><span class="pre">process</span></code></a>()</p></td>
+<td><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">proportion</span></code>(other)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Ramilowski2015.reload" title="pypath.core.annot.Ramilowski2015.reload"><code class="xref py py-obj docutils literal notranslate"><span class="pre">reload</span></code></a>()</p></td>
+<td><p>Reloads the object from the module level.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">save_to_pickle</span></code>(pickle_file)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Ramilowski2015.select" title="pypath.core.annot.Ramilowski2015.select"><code class="xref py py-obj docutils literal notranslate"><span class="pre">select</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Ramilowski2015.set_method" title="pypath.core.annot.Ramilowski2015.set_method"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_method</span></code></a>()</p></td>
+<td><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if necessary.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Ramilowski2015.set_reference_set" title="pypath.core.annot.Ramilowski2015.set_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_reference_set</span></code></a>()</p></td>
+<td><p>Assigns the reference set to the :py:attr``reference_set`` attribute.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Ramilowski2015.show" title="pypath.core.annot.Ramilowski2015.show"><code class="xref py py-obj docutils literal notranslate"><span class="pre">show</span></code></a>([method, table_param])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic information from the UniProt datasheets.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Ramilowski2015.subset_intersection" title="pypath.core.annot.Ramilowski2015.subset_intersection"><code class="xref py py-obj docutils literal notranslate"><span class="pre">subset_intersection</span></code></a>(universe, **kwargs)</p></td>
+<td><p>Calculates the proportion of entities in a subset occuring in the set <code class="docutils literal notranslate"><span class="pre">universe</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Ramilowski2015.to_array" title="pypath.core.annot.Ramilowski2015.to_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_array</span></code></a>([reference_set, use_fields])</p></td>
+<td><p>Returns an entity vs feature array.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Ramilowski2015.to_bool_array" title="pypath.core.annot.Ramilowski2015.to_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_bool_array</span></code></a>(reference_set)</p></td>
+<td><p>Returns a presence/absence boolean array for a reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Ramilowski2015.to_set" title="pypath.core.annot.Ramilowski2015.to_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_set</span></code></a>()</p></td>
+<td><p>Returns the entities present in this annotation resource as a set.</p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Attributes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_fields</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">summary</span></code></p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Ramilowski2015.add_complexes_by_inference">
+<span class="sig-name descname"><span class="pre">add_complexes_by_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Ramilowski2015.add_complexes_by_inference" title="Link to this definition">§</a></dt>
+<dd><p>Creates complex annotations by in silico inference and adds them
+to this annotation set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Ramilowski2015.all_complexes">
+<span class="sig-name descname"><span class="pre">all_complexes</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Ramilowski2015.all_complexes" title="Link to this definition">§</a></dt>
+<dd><p>All protein complexes annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Ramilowski2015.all_entities">
+<span class="sig-name descname"><span class="pre">all_entities</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Ramilowski2015.all_entities" title="Link to this definition">§</a></dt>
+<dd><p>All entities annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Ramilowski2015.all_mirnas">
+<span class="sig-name descname"><span class="pre">all_mirnas</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Ramilowski2015.all_mirnas" title="Link to this definition">§</a></dt>
+<dd><p>All miRNAs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Ramilowski2015.all_proteins">
+<span class="sig-name descname"><span class="pre">all_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Ramilowski2015.all_proteins" title="Link to this definition">§</a></dt>
+<dd><p>All UniProt IDs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Ramilowski2015.all_refs">
+<span class="sig-name descname"><span class="pre">all_refs</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Ramilowski2015.all_refs" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects the references
+across all records. Returns <em>list</em>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Ramilowski2015.annotate_complex">
+<span class="sig-name descname"><span class="pre">annotate_complex</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cplex</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Ramilowski2015.annotate_complex" title="Link to this definition">§</a></dt>
+<dd><p>Infers annotations for a single complex.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Ramilowski2015.browse">
+<span class="sig-name descname"><span class="pre">browse</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">field</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">start</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Ramilowski2015.browse" title="Link to this definition">§</a></dt>
+<dd><p>Print gene information as a table.</p>
+<p>Presents information about annotation categories as ascii tables
+printed in the terminal. If one category provided, prints one table.
+If multiple categories provided, prints a table for each of them one
+by one proceeding to the next one once you hit return. If no categories
+provided goes through all levels of the primary category.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>field:</dt><dd><p>The field to browse categories by.</p>
+<ul class="simple">
+<li><p>If None the primary field will be selected.
+If this annotation resource doesn’t have fields, all proteins
+will be presented as one single category.</p></li>
+<li><p>If a string it will be considered a field name and it will
+browse through all levels of this field.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">list</span></code>, set or tuple, it will be considered either a
+<code class="docutils literal notranslate"><span class="pre">list</span></code> of field names or a list of values from the primary
+field. In the former case all combinations of the values of
+the fields will be presented, in the latter case the browsing
+will be limited to the levels of the primary field contained
+in <code class="docutils literal notranslate"><span class="pre">field</span></code>.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">dict</span></code>, keys are supposed to be field names and values
+as list of levels. If any of the values are None, all levels
+from that field will be used.</p></li>
+</ul>
+</dd>
+<dt>start:</dt><dd><p>Start browsing from this category. E.g. if there are 500
+categories and start is 250 it will skip everything before the
+250th.</p>
+</dd>
+<dt>kwargs:</dt><dd><p>Passed to <code class="docutils literal notranslate"><span class="pre">pypath.utils.uniprot.info</span></code>.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Ramilowski2015.complex_inference">
+<span class="sig-name descname"><span class="pre">complex_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Ramilowski2015.complex_inference" title="Link to this definition">§</a></dt>
+<dd><p>Annotates all complexes in <cite>complexes</cite>, by default in the default
+complex database (existing in the <cite>complex</cite> module or generated
+on demand according to the module’s current settings).</p>
+<dl class="field-list simple">
+<dt class="field-odd">Returns<span class="colon">:</span></dt>
+<dd class="field-odd"><p><ul class="simple">
+<li><p><em>Dict with complexes as keys and sets of annotations as values.</em></p></li>
+<li><p><em>Complexes with no valid information in this annotation resource</em></p></li>
+<li><p><em>won’t be in the dict.</em></p></li>
+</ul>
+</p>
+</dd>
+<dt class="field-even">Parameters<span class="colon">:</span></dt>
+<dd class="field-even"><p><strong>complexes</strong> (<em>iterable</em>) – Iterable yielding complexes.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Ramilowski2015.coverage">
+<span class="sig-name descname"><span class="pre">coverage</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">other</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Ramilowski2015.coverage" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the coverage of the annotation i.e. the proportion of
+entities having at least one record in this annotation resource
+for an arbitrary set of entities.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Ramilowski2015.curation_effort">
+<span class="sig-name descname"><span class="pre">curation_effort</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Ramilowski2015.curation_effort" title="Link to this definition">§</a></dt>
+<dd><p>Counts the reference-record pairs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Ramilowski2015.get_names">
+<span class="sig-name descname"><span class="pre">get_names</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Ramilowski2015.get_names" title="Link to this definition">§</a></dt>
+<dd><p>Returns the list of field names in the records. The annotation
+consists of uniform records and each entity might be annotated
+with one or more records. Each record is a tuple of fields, for
+example <code class="docutils literal notranslate"><span class="pre">('cell_type',</span> <span class="pre">'expression_level',</span> <span class="pre">'score')</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Ramilowski2015.get_reference_set">
+<em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">get_reference_set</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">proteins</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">swissprot_only</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Ramilowski2015.get_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the reference set i.e. the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Ramilowski2015.get_subset">
+<span class="sig-name descname"><span class="pre">get_subset</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Ramilowski2015.get_subset" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Ramilowski2015.get_subset_bool_array">
+<span class="sig-name descname"><span class="pre">get_subset_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Ramilowski2015.get_subset_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a boolean vector with True and False values for each entity
+in the reference set. The values represent presence absence data
+in the simplest case, but by providing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> any kind of matching
+and filtering is possible. <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> are passed to the <code class="docutils literal notranslate"><span class="pre">select</span></code>
+method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Ramilowski2015.get_values">
+<span class="sig-name descname"><span class="pre">get_values</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">exclude_none</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Ramilowski2015.get_values" title="Link to this definition">§</a></dt>
+<dd><p>Returns the set of all possible values of a field. E.g. if the
+records of this annotation have a field <code class="docutils literal notranslate"><span class="pre">cell_type</span></code> then calling
+this method can tell you that across all records the values of
+this field might be <code class="docutils literal notranslate"><span class="pre">{'macrophage',</span> <span class="pre">'epithelial_cell',</span> <span class="pre">...}</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Ramilowski2015.labels">
+<span class="sig-name descname"><span class="pre">labels</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Ramilowski2015.labels" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Ramilowski2015.load">
+<span class="sig-name descname"><span class="pre">load</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Ramilowski2015.load" title="Link to this definition">§</a></dt>
+<dd><p>Loads the annotation data by calling the input method.
+Infers annotations for complexes in the complex database if
+py:attr:<code class="docutils literal notranslate"><span class="pre">infer_complexes</span></code> is True.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Ramilowski2015.load_data">
+<span class="sig-name descname"><span class="pre">load_data</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Ramilowski2015.load_data" title="Link to this definition">§</a></dt>
+<dd><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Ramilowski2015.load_proteins">
+<span class="sig-name descname"><span class="pre">load_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Ramilowski2015.load_proteins" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a set of all UniProt IDs to have a base set of the entire
+proteome.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Ramilowski2015.make_df">
+<span class="sig-name descname"><span class="pre">make_df</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">rebuild</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Ramilowski2015.make_df" title="Link to this definition">§</a></dt>
+<dd><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.
+The data frame will be assigned to :py:attr``df``.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Ramilowski2015.numof_entities">
+<span class="sig-name descname"><span class="pre">numof_entities</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Ramilowski2015.numof_entities" title="Link to this definition">§</a></dt>
+<dd><p>The number of annotated entities in the resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Ramilowski2015.numof_records">
+<span class="sig-name descname"><span class="pre">numof_records</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Ramilowski2015.numof_records" title="Link to this definition">§</a></dt>
+<dd><p>The total number of annotation records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Ramilowski2015.numof_references">
+<span class="sig-name descname"><span class="pre">numof_references</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Ramilowski2015.numof_references" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects and counts the
+references across all records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Ramilowski2015.process">
+<span class="sig-name descname"><span class="pre">process</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Ramilowski2015.process" title="Link to this definition">§</a></dt>
+<dd><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Ramilowski2015.reload">
+<span class="sig-name descname"><span class="pre">reload</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Ramilowski2015.reload" title="Link to this definition">§</a></dt>
+<dd><p>Reloads the object from the module level.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Ramilowski2015.select">
+<span class="sig-name descname"><span class="pre">select</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Ramilowski2015.select" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Ramilowski2015.set_method">
+<span class="sig-name descname"><span class="pre">set_method</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Ramilowski2015.set_method" title="Link to this definition">§</a></dt>
+<dd><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if
+necessary.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Ramilowski2015.set_reference_set">
+<span class="sig-name descname"><span class="pre">set_reference_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Ramilowski2015.set_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Assigns the reference set to the :py:attr``reference_set`` attribute.
+The reference set is the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Ramilowski2015.show">
+<span class="sig-name descname"><span class="pre">show</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">table_param</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Ramilowski2015.show" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic
+information from the UniProt datasheets.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Ramilowski2015.subset_intersection">
+<span class="sig-name descname"><span class="pre">subset_intersection</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">universe</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Ramilowski2015.subset_intersection" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the proportion of entities in a subset occuring in the
+set <code class="docutils literal notranslate"><span class="pre">universe</span></code>. The subset is selected by passing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> to the
+<code class="docutils literal notranslate"><span class="pre">select</span></code> method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Ramilowski2015.to_array">
+<span class="sig-name descname"><span class="pre">to_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_fields</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Ramilowski2015.to_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns an entity vs feature array. In case of more complex
+annotations this might be huge.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Ramilowski2015.to_bool_array">
+<span class="sig-name descname"><span class="pre">to_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Ramilowski2015.to_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a presence/absence boolean array for a reference set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Ramilowski2015.to_set">
+<span class="sig-name descname"><span class="pre">to_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Ramilowski2015.to_set" title="Link to this definition">§</a></dt>
+<dd><p>Returns the entities present in this annotation resource as a set.</p>
+</dd></dl>
+
+</dd></dl>
+
+</section>
+
+
+                </article>
+              
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+  <section id="pypath-core-annot-ramilowski2015location">
+<h1>pypath.core.annot.Ramilowski2015Location<a class="headerlink" href="#pypath-core-annot-ramilowski2015location" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.core.annot.Ramilowski2015Location">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.core.annot.</span></span><span class="sig-name descname"><span class="pre">Ramilowski2015Location</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#Ramilowski2015Location"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.Ramilowski2015Location" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <a class="reference internal" href="pypath.core.annot.AnnotationBase.html#pypath.core.annot.AnnotationBase" title="pypath.core.annot.AnnotationBase"><code class="xref py py-class docutils literal notranslate"><span class="pre">AnnotationBase</span></code></a></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Ramilowski2015Location.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#Ramilowski2015Location.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.Ramilowski2015Location.__init__" title="Link to this definition">§</a></dt>
+<dd><p>Represents annotations for a set of proteins.
+Loads the data from the original resource and provides methods
+to query the annotations.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>name</strong> (<em>str</em>) – A custom name for the annotation resource.</p></li>
+<li><p><strong>ncbi_tax_id</strong> (<em>int</em>) – NCBI Taxonomy identifier.</p></li>
+<li><p><strong>input_method</strong> (<em>callable</em><em>,</em><em>str</em>) – Either a callable or the name of a method in any submodules of
+the <code class="docutils literal notranslate"><span class="pre">pypath.inputs</span></code>  module. Should return a dict with
+UniProt IDs as keys or an object suitable for <code class="docutils literal notranslate"><span class="pre">process_method</span></code>.</p></li>
+<li><p><strong>input_args</strong> (<em>dict</em>) – Arguments for the <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Ramilowski2015Location.__init__" title="pypath.core.annot.Ramilowski2015Location.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>(**kwargs)</p></td>
+<td><p>Represents annotations for a set of proteins.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Ramilowski2015Location.add_complexes_by_inference" title="pypath.core.annot.Ramilowski2015Location.add_complexes_by_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">add_complexes_by_inference</span></code></a>([complexes])</p></td>
+<td><p>Creates complex annotations by in silico inference and adds them to this annotation set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Ramilowski2015Location.all_complexes" title="pypath.core.annot.Ramilowski2015Location.all_complexes"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_complexes</span></code></a>()</p></td>
+<td><p>All protein complexes annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Ramilowski2015Location.all_entities" title="pypath.core.annot.Ramilowski2015Location.all_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_entities</span></code></a>([entity_types])</p></td>
+<td><p>All entities annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Ramilowski2015Location.all_mirnas" title="pypath.core.annot.Ramilowski2015Location.all_mirnas"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_mirnas</span></code></a>()</p></td>
+<td><p>All miRNAs annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Ramilowski2015Location.all_proteins" title="pypath.core.annot.Ramilowski2015Location.all_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_proteins</span></code></a>()</p></td>
+<td><p>All UniProt IDs annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Ramilowski2015Location.all_refs" title="pypath.core.annot.Ramilowski2015Location.all_refs"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_refs</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Ramilowski2015Location.annotate_complex" title="pypath.core.annot.Ramilowski2015Location.annotate_complex"><code class="xref py py-obj docutils literal notranslate"><span class="pre">annotate_complex</span></code></a>(cplex)</p></td>
+<td><p>Infers annotations for a single complex.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Ramilowski2015Location.browse" title="pypath.core.annot.Ramilowski2015Location.browse"><code class="xref py py-obj docutils literal notranslate"><span class="pre">browse</span></code></a>([field, start])</p></td>
+<td><p>Print gene information as a table.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Ramilowski2015Location.complex_inference" title="pypath.core.annot.Ramilowski2015Location.complex_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">complex_inference</span></code></a>([complexes])</p></td>
+<td><p>Annotates all complexes in <cite>complexes</cite>, by default in the default complex database (existing in the <cite>complex</cite> module or generated on demand according to the module's current settings).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Ramilowski2015Location.coverage" title="pypath.core.annot.Ramilowski2015Location.coverage"><code class="xref py py-obj docutils literal notranslate"><span class="pre">coverage</span></code></a>(other)</p></td>
+<td><p>Calculates the coverage of the annotation i.e. the proportion of entities having at least one record in this annotation resource for an arbitrary set of entities.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Ramilowski2015Location.curation_effort" title="pypath.core.annot.Ramilowski2015Location.curation_effort"><code class="xref py py-obj docutils literal notranslate"><span class="pre">curation_effort</span></code></a>()</p></td>
+<td><p>Counts the reference-record pairs.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">from_dump</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_entity_type</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Ramilowski2015Location.get_names" title="pypath.core.annot.Ramilowski2015Location.get_names"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_names</span></code></a>()</p></td>
+<td><p>Returns the list of field names in the records.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Ramilowski2015Location.get_reference_set" title="pypath.core.annot.Ramilowski2015Location.get_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_reference_set</span></code></a>([proteins, complexes, ...])</p></td>
+<td><p>Retrieves the reference set i.e. the set of all entities which potentially have annotation in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Ramilowski2015Location.get_subset" title="pypath.core.annot.Ramilowski2015Location.get_subset"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Ramilowski2015Location.get_subset_bool_array" title="pypath.core.annot.Ramilowski2015Location.get_subset_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset_bool_array</span></code></a>([reference_set])</p></td>
+<td><p>Returns a boolean vector with True and False values for each entity in the reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Ramilowski2015Location.get_values" title="pypath.core.annot.Ramilowski2015Location.get_values"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_values</span></code></a>(name[, exclude_none])</p></td>
+<td><p>Returns the set of all possible values of a field.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_complex</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_mirna</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_protein</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Ramilowski2015Location.labels" title="pypath.core.annot.Ramilowski2015Location.labels"><code class="xref py py-obj docutils literal notranslate"><span class="pre">labels</span></code></a>([method])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Ramilowski2015Location.load" title="pypath.core.annot.Ramilowski2015Location.load"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load</span></code></a>()</p></td>
+<td><p>Loads the annotation data by calling the input method.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Ramilowski2015Location.load_data" title="pypath.core.annot.Ramilowski2015Location.load_data"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_data</span></code></a>()</p></td>
+<td><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Ramilowski2015Location.load_proteins" title="pypath.core.annot.Ramilowski2015Location.load_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_proteins</span></code></a>()</p></td>
+<td><p>Retrieves a set of all UniProt IDs to have a base set of the entire proteome.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Ramilowski2015Location.make_df" title="pypath.core.annot.Ramilowski2015Location.make_df"><code class="xref py py-obj docutils literal notranslate"><span class="pre">make_df</span></code></a>([rebuild])</p></td>
+<td><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complex_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Ramilowski2015Location.numof_entities" title="pypath.core.annot.Ramilowski2015Location.numof_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_entities</span></code></a>()</p></td>
+<td><p>The number of annotated entities in the resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirna_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirnas</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_protein_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_proteins</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Ramilowski2015Location.numof_records" title="pypath.core.annot.Ramilowski2015Location.numof_records"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_records</span></code></a>([entity_types])</p></td>
+<td><p>The total number of annotation records.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Ramilowski2015Location.numof_references" title="pypath.core.annot.Ramilowski2015Location.numof_references"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_references</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Ramilowski2015Location.process" title="pypath.core.annot.Ramilowski2015Location.process"><code class="xref py py-obj docutils literal notranslate"><span class="pre">process</span></code></a>()</p></td>
+<td><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">proportion</span></code>(other)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Ramilowski2015Location.reload" title="pypath.core.annot.Ramilowski2015Location.reload"><code class="xref py py-obj docutils literal notranslate"><span class="pre">reload</span></code></a>()</p></td>
+<td><p>Reloads the object from the module level.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">save_to_pickle</span></code>(pickle_file)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Ramilowski2015Location.select" title="pypath.core.annot.Ramilowski2015Location.select"><code class="xref py py-obj docutils literal notranslate"><span class="pre">select</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Ramilowski2015Location.set_method" title="pypath.core.annot.Ramilowski2015Location.set_method"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_method</span></code></a>()</p></td>
+<td><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if necessary.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Ramilowski2015Location.set_reference_set" title="pypath.core.annot.Ramilowski2015Location.set_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_reference_set</span></code></a>()</p></td>
+<td><p>Assigns the reference set to the :py:attr``reference_set`` attribute.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Ramilowski2015Location.show" title="pypath.core.annot.Ramilowski2015Location.show"><code class="xref py py-obj docutils literal notranslate"><span class="pre">show</span></code></a>([method, table_param])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic information from the UniProt datasheets.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Ramilowski2015Location.subset_intersection" title="pypath.core.annot.Ramilowski2015Location.subset_intersection"><code class="xref py py-obj docutils literal notranslate"><span class="pre">subset_intersection</span></code></a>(universe, **kwargs)</p></td>
+<td><p>Calculates the proportion of entities in a subset occuring in the set <code class="docutils literal notranslate"><span class="pre">universe</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Ramilowski2015Location.to_array" title="pypath.core.annot.Ramilowski2015Location.to_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_array</span></code></a>([reference_set, use_fields])</p></td>
+<td><p>Returns an entity vs feature array.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Ramilowski2015Location.to_bool_array" title="pypath.core.annot.Ramilowski2015Location.to_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_bool_array</span></code></a>(reference_set)</p></td>
+<td><p>Returns a presence/absence boolean array for a reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Ramilowski2015Location.to_set" title="pypath.core.annot.Ramilowski2015Location.to_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_set</span></code></a>()</p></td>
+<td><p>Returns the entities present in this annotation resource as a set.</p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Attributes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_fields</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">summary</span></code></p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Ramilowski2015Location.add_complexes_by_inference">
+<span class="sig-name descname"><span class="pre">add_complexes_by_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Ramilowski2015Location.add_complexes_by_inference" title="Link to this definition">§</a></dt>
+<dd><p>Creates complex annotations by in silico inference and adds them
+to this annotation set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Ramilowski2015Location.all_complexes">
+<span class="sig-name descname"><span class="pre">all_complexes</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Ramilowski2015Location.all_complexes" title="Link to this definition">§</a></dt>
+<dd><p>All protein complexes annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Ramilowski2015Location.all_entities">
+<span class="sig-name descname"><span class="pre">all_entities</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Ramilowski2015Location.all_entities" title="Link to this definition">§</a></dt>
+<dd><p>All entities annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Ramilowski2015Location.all_mirnas">
+<span class="sig-name descname"><span class="pre">all_mirnas</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Ramilowski2015Location.all_mirnas" title="Link to this definition">§</a></dt>
+<dd><p>All miRNAs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Ramilowski2015Location.all_proteins">
+<span class="sig-name descname"><span class="pre">all_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Ramilowski2015Location.all_proteins" title="Link to this definition">§</a></dt>
+<dd><p>All UniProt IDs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Ramilowski2015Location.all_refs">
+<span class="sig-name descname"><span class="pre">all_refs</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Ramilowski2015Location.all_refs" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects the references
+across all records. Returns <em>list</em>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Ramilowski2015Location.annotate_complex">
+<span class="sig-name descname"><span class="pre">annotate_complex</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cplex</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Ramilowski2015Location.annotate_complex" title="Link to this definition">§</a></dt>
+<dd><p>Infers annotations for a single complex.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Ramilowski2015Location.browse">
+<span class="sig-name descname"><span class="pre">browse</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">field</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">start</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Ramilowski2015Location.browse" title="Link to this definition">§</a></dt>
+<dd><p>Print gene information as a table.</p>
+<p>Presents information about annotation categories as ascii tables
+printed in the terminal. If one category provided, prints one table.
+If multiple categories provided, prints a table for each of them one
+by one proceeding to the next one once you hit return. If no categories
+provided goes through all levels of the primary category.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>field:</dt><dd><p>The field to browse categories by.</p>
+<ul class="simple">
+<li><p>If None the primary field will be selected.
+If this annotation resource doesn’t have fields, all proteins
+will be presented as one single category.</p></li>
+<li><p>If a string it will be considered a field name and it will
+browse through all levels of this field.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">list</span></code>, set or tuple, it will be considered either a
+<code class="docutils literal notranslate"><span class="pre">list</span></code> of field names or a list of values from the primary
+field. In the former case all combinations of the values of
+the fields will be presented, in the latter case the browsing
+will be limited to the levels of the primary field contained
+in <code class="docutils literal notranslate"><span class="pre">field</span></code>.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">dict</span></code>, keys are supposed to be field names and values
+as list of levels. If any of the values are None, all levels
+from that field will be used.</p></li>
+</ul>
+</dd>
+<dt>start:</dt><dd><p>Start browsing from this category. E.g. if there are 500
+categories and start is 250 it will skip everything before the
+250th.</p>
+</dd>
+<dt>kwargs:</dt><dd><p>Passed to <code class="docutils literal notranslate"><span class="pre">pypath.utils.uniprot.info</span></code>.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Ramilowski2015Location.complex_inference">
+<span class="sig-name descname"><span class="pre">complex_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Ramilowski2015Location.complex_inference" title="Link to this definition">§</a></dt>
+<dd><p>Annotates all complexes in <cite>complexes</cite>, by default in the default
+complex database (existing in the <cite>complex</cite> module or generated
+on demand according to the module’s current settings).</p>
+<dl class="field-list simple">
+<dt class="field-odd">Returns<span class="colon">:</span></dt>
+<dd class="field-odd"><p><ul class="simple">
+<li><p><em>Dict with complexes as keys and sets of annotations as values.</em></p></li>
+<li><p><em>Complexes with no valid information in this annotation resource</em></p></li>
+<li><p><em>won’t be in the dict.</em></p></li>
+</ul>
+</p>
+</dd>
+<dt class="field-even">Parameters<span class="colon">:</span></dt>
+<dd class="field-even"><p><strong>complexes</strong> (<em>iterable</em>) – Iterable yielding complexes.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Ramilowski2015Location.coverage">
+<span class="sig-name descname"><span class="pre">coverage</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">other</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Ramilowski2015Location.coverage" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the coverage of the annotation i.e. the proportion of
+entities having at least one record in this annotation resource
+for an arbitrary set of entities.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Ramilowski2015Location.curation_effort">
+<span class="sig-name descname"><span class="pre">curation_effort</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Ramilowski2015Location.curation_effort" title="Link to this definition">§</a></dt>
+<dd><p>Counts the reference-record pairs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Ramilowski2015Location.get_names">
+<span class="sig-name descname"><span class="pre">get_names</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Ramilowski2015Location.get_names" title="Link to this definition">§</a></dt>
+<dd><p>Returns the list of field names in the records. The annotation
+consists of uniform records and each entity might be annotated
+with one or more records. Each record is a tuple of fields, for
+example <code class="docutils literal notranslate"><span class="pre">('cell_type',</span> <span class="pre">'expression_level',</span> <span class="pre">'score')</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Ramilowski2015Location.get_reference_set">
+<em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">get_reference_set</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">proteins</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">swissprot_only</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Ramilowski2015Location.get_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the reference set i.e. the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Ramilowski2015Location.get_subset">
+<span class="sig-name descname"><span class="pre">get_subset</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Ramilowski2015Location.get_subset" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Ramilowski2015Location.get_subset_bool_array">
+<span class="sig-name descname"><span class="pre">get_subset_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Ramilowski2015Location.get_subset_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a boolean vector with True and False values for each entity
+in the reference set. The values represent presence absence data
+in the simplest case, but by providing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> any kind of matching
+and filtering is possible. <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> are passed to the <code class="docutils literal notranslate"><span class="pre">select</span></code>
+method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Ramilowski2015Location.get_values">
+<span class="sig-name descname"><span class="pre">get_values</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">exclude_none</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Ramilowski2015Location.get_values" title="Link to this definition">§</a></dt>
+<dd><p>Returns the set of all possible values of a field. E.g. if the
+records of this annotation have a field <code class="docutils literal notranslate"><span class="pre">cell_type</span></code> then calling
+this method can tell you that across all records the values of
+this field might be <code class="docutils literal notranslate"><span class="pre">{'macrophage',</span> <span class="pre">'epithelial_cell',</span> <span class="pre">...}</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Ramilowski2015Location.labels">
+<span class="sig-name descname"><span class="pre">labels</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Ramilowski2015Location.labels" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Ramilowski2015Location.load">
+<span class="sig-name descname"><span class="pre">load</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Ramilowski2015Location.load" title="Link to this definition">§</a></dt>
+<dd><p>Loads the annotation data by calling the input method.
+Infers annotations for complexes in the complex database if
+py:attr:<code class="docutils literal notranslate"><span class="pre">infer_complexes</span></code> is True.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Ramilowski2015Location.load_data">
+<span class="sig-name descname"><span class="pre">load_data</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Ramilowski2015Location.load_data" title="Link to this definition">§</a></dt>
+<dd><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Ramilowski2015Location.load_proteins">
+<span class="sig-name descname"><span class="pre">load_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Ramilowski2015Location.load_proteins" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a set of all UniProt IDs to have a base set of the entire
+proteome.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Ramilowski2015Location.make_df">
+<span class="sig-name descname"><span class="pre">make_df</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">rebuild</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Ramilowski2015Location.make_df" title="Link to this definition">§</a></dt>
+<dd><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.
+The data frame will be assigned to :py:attr``df``.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Ramilowski2015Location.numof_entities">
+<span class="sig-name descname"><span class="pre">numof_entities</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Ramilowski2015Location.numof_entities" title="Link to this definition">§</a></dt>
+<dd><p>The number of annotated entities in the resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Ramilowski2015Location.numof_records">
+<span class="sig-name descname"><span class="pre">numof_records</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Ramilowski2015Location.numof_records" title="Link to this definition">§</a></dt>
+<dd><p>The total number of annotation records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Ramilowski2015Location.numof_references">
+<span class="sig-name descname"><span class="pre">numof_references</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Ramilowski2015Location.numof_references" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects and counts the
+references across all records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Ramilowski2015Location.process">
+<span class="sig-name descname"><span class="pre">process</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Ramilowski2015Location.process" title="Link to this definition">§</a></dt>
+<dd><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Ramilowski2015Location.reload">
+<span class="sig-name descname"><span class="pre">reload</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Ramilowski2015Location.reload" title="Link to this definition">§</a></dt>
+<dd><p>Reloads the object from the module level.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Ramilowski2015Location.select">
+<span class="sig-name descname"><span class="pre">select</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Ramilowski2015Location.select" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Ramilowski2015Location.set_method">
+<span class="sig-name descname"><span class="pre">set_method</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Ramilowski2015Location.set_method" title="Link to this definition">§</a></dt>
+<dd><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if
+necessary.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Ramilowski2015Location.set_reference_set">
+<span class="sig-name descname"><span class="pre">set_reference_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Ramilowski2015Location.set_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Assigns the reference set to the :py:attr``reference_set`` attribute.
+The reference set is the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Ramilowski2015Location.show">
+<span class="sig-name descname"><span class="pre">show</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">table_param</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Ramilowski2015Location.show" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic
+information from the UniProt datasheets.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Ramilowski2015Location.subset_intersection">
+<span class="sig-name descname"><span class="pre">subset_intersection</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">universe</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Ramilowski2015Location.subset_intersection" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the proportion of entities in a subset occuring in the
+set <code class="docutils literal notranslate"><span class="pre">universe</span></code>. The subset is selected by passing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> to the
+<code class="docutils literal notranslate"><span class="pre">select</span></code> method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Ramilowski2015Location.to_array">
+<span class="sig-name descname"><span class="pre">to_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_fields</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Ramilowski2015Location.to_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns an entity vs feature array. In case of more complex
+annotations this might be huge.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Ramilowski2015Location.to_bool_array">
+<span class="sig-name descname"><span class="pre">to_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Ramilowski2015Location.to_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a presence/absence boolean array for a reference set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Ramilowski2015Location.to_set">
+<span class="sig-name descname"><span class="pre">to_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Ramilowski2015Location.to_set" title="Link to this definition">§</a></dt>
+<dd><p>Returns the entities present in this annotation resource as a set.</p>
+</dd></dl>
+
+</dd></dl>
+
+</section>
+
+
+                </article>
+              
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+  <section id="pypath-core-annot-scconnect">
+<h1>pypath.core.annot.Scconnect<a class="headerlink" href="#pypath-core-annot-scconnect" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.core.annot.Scconnect">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.core.annot.</span></span><span class="sig-name descname"><span class="pre">Scconnect</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#Scconnect"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.Scconnect" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <a class="reference internal" href="pypath.core.annot.AnnotationBase.html#pypath.core.annot.AnnotationBase" title="pypath.core.annot.AnnotationBase"><code class="xref py py-class docutils literal notranslate"><span class="pre">AnnotationBase</span></code></a></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Scconnect.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#Scconnect.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.Scconnect.__init__" title="Link to this definition">§</a></dt>
+<dd><p>Represents annotations for a set of proteins.
+Loads the data from the original resource and provides methods
+to query the annotations.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>name</strong> (<em>str</em>) – A custom name for the annotation resource.</p></li>
+<li><p><strong>ncbi_tax_id</strong> (<em>int</em>) – NCBI Taxonomy identifier.</p></li>
+<li><p><strong>input_method</strong> (<em>callable</em><em>,</em><em>str</em>) – Either a callable or the name of a method in any submodules of
+the <code class="docutils literal notranslate"><span class="pre">pypath.inputs</span></code>  module. Should return a dict with
+UniProt IDs as keys or an object suitable for <code class="docutils literal notranslate"><span class="pre">process_method</span></code>.</p></li>
+<li><p><strong>input_args</strong> (<em>dict</em>) – Arguments for the <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Scconnect.__init__" title="pypath.core.annot.Scconnect.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>([ncbi_tax_id])</p></td>
+<td><p>Represents annotations for a set of proteins.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Scconnect.add_complexes_by_inference" title="pypath.core.annot.Scconnect.add_complexes_by_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">add_complexes_by_inference</span></code></a>([complexes])</p></td>
+<td><p>Creates complex annotations by in silico inference and adds them to this annotation set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Scconnect.all_complexes" title="pypath.core.annot.Scconnect.all_complexes"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_complexes</span></code></a>()</p></td>
+<td><p>All protein complexes annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Scconnect.all_entities" title="pypath.core.annot.Scconnect.all_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_entities</span></code></a>([entity_types])</p></td>
+<td><p>All entities annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Scconnect.all_mirnas" title="pypath.core.annot.Scconnect.all_mirnas"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_mirnas</span></code></a>()</p></td>
+<td><p>All miRNAs annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Scconnect.all_proteins" title="pypath.core.annot.Scconnect.all_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_proteins</span></code></a>()</p></td>
+<td><p>All UniProt IDs annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Scconnect.all_refs" title="pypath.core.annot.Scconnect.all_refs"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_refs</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Scconnect.annotate_complex" title="pypath.core.annot.Scconnect.annotate_complex"><code class="xref py py-obj docutils literal notranslate"><span class="pre">annotate_complex</span></code></a>(cplex)</p></td>
+<td><p>Infers annotations for a single complex.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Scconnect.browse" title="pypath.core.annot.Scconnect.browse"><code class="xref py py-obj docutils literal notranslate"><span class="pre">browse</span></code></a>([field, start])</p></td>
+<td><p>Print gene information as a table.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Scconnect.complex_inference" title="pypath.core.annot.Scconnect.complex_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">complex_inference</span></code></a>([complexes])</p></td>
+<td><p>Annotates all complexes in <cite>complexes</cite>, by default in the default complex database (existing in the <cite>complex</cite> module or generated on demand according to the module's current settings).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Scconnect.coverage" title="pypath.core.annot.Scconnect.coverage"><code class="xref py py-obj docutils literal notranslate"><span class="pre">coverage</span></code></a>(other)</p></td>
+<td><p>Calculates the coverage of the annotation i.e. the proportion of entities having at least one record in this annotation resource for an arbitrary set of entities.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Scconnect.curation_effort" title="pypath.core.annot.Scconnect.curation_effort"><code class="xref py py-obj docutils literal notranslate"><span class="pre">curation_effort</span></code></a>()</p></td>
+<td><p>Counts the reference-record pairs.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">from_dump</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_entity_type</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Scconnect.get_names" title="pypath.core.annot.Scconnect.get_names"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_names</span></code></a>()</p></td>
+<td><p>Returns the list of field names in the records.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Scconnect.get_reference_set" title="pypath.core.annot.Scconnect.get_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_reference_set</span></code></a>([proteins, complexes, ...])</p></td>
+<td><p>Retrieves the reference set i.e. the set of all entities which potentially have annotation in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Scconnect.get_subset" title="pypath.core.annot.Scconnect.get_subset"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Scconnect.get_subset_bool_array" title="pypath.core.annot.Scconnect.get_subset_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset_bool_array</span></code></a>([reference_set])</p></td>
+<td><p>Returns a boolean vector with True and False values for each entity in the reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Scconnect.get_values" title="pypath.core.annot.Scconnect.get_values"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_values</span></code></a>(name[, exclude_none])</p></td>
+<td><p>Returns the set of all possible values of a field.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_complex</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_mirna</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_protein</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Scconnect.labels" title="pypath.core.annot.Scconnect.labels"><code class="xref py py-obj docutils literal notranslate"><span class="pre">labels</span></code></a>([method])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Scconnect.load" title="pypath.core.annot.Scconnect.load"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load</span></code></a>()</p></td>
+<td><p>Loads the annotation data by calling the input method.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Scconnect.load_data" title="pypath.core.annot.Scconnect.load_data"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_data</span></code></a>()</p></td>
+<td><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Scconnect.load_proteins" title="pypath.core.annot.Scconnect.load_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_proteins</span></code></a>()</p></td>
+<td><p>Retrieves a set of all UniProt IDs to have a base set of the entire proteome.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Scconnect.make_df" title="pypath.core.annot.Scconnect.make_df"><code class="xref py py-obj docutils literal notranslate"><span class="pre">make_df</span></code></a>([rebuild])</p></td>
+<td><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complex_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Scconnect.numof_entities" title="pypath.core.annot.Scconnect.numof_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_entities</span></code></a>()</p></td>
+<td><p>The number of annotated entities in the resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirna_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirnas</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_protein_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_proteins</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Scconnect.numof_records" title="pypath.core.annot.Scconnect.numof_records"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_records</span></code></a>([entity_types])</p></td>
+<td><p>The total number of annotation records.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Scconnect.numof_references" title="pypath.core.annot.Scconnect.numof_references"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_references</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Scconnect.process" title="pypath.core.annot.Scconnect.process"><code class="xref py py-obj docutils literal notranslate"><span class="pre">process</span></code></a>()</p></td>
+<td><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">proportion</span></code>(other)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Scconnect.reload" title="pypath.core.annot.Scconnect.reload"><code class="xref py py-obj docutils literal notranslate"><span class="pre">reload</span></code></a>()</p></td>
+<td><p>Reloads the object from the module level.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">save_to_pickle</span></code>(pickle_file)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Scconnect.select" title="pypath.core.annot.Scconnect.select"><code class="xref py py-obj docutils literal notranslate"><span class="pre">select</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Scconnect.set_method" title="pypath.core.annot.Scconnect.set_method"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_method</span></code></a>()</p></td>
+<td><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if necessary.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Scconnect.set_reference_set" title="pypath.core.annot.Scconnect.set_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_reference_set</span></code></a>()</p></td>
+<td><p>Assigns the reference set to the :py:attr``reference_set`` attribute.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Scconnect.show" title="pypath.core.annot.Scconnect.show"><code class="xref py py-obj docutils literal notranslate"><span class="pre">show</span></code></a>([method, table_param])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic information from the UniProt datasheets.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Scconnect.subset_intersection" title="pypath.core.annot.Scconnect.subset_intersection"><code class="xref py py-obj docutils literal notranslate"><span class="pre">subset_intersection</span></code></a>(universe, **kwargs)</p></td>
+<td><p>Calculates the proportion of entities in a subset occuring in the set <code class="docutils literal notranslate"><span class="pre">universe</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Scconnect.to_array" title="pypath.core.annot.Scconnect.to_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_array</span></code></a>([reference_set, use_fields])</p></td>
+<td><p>Returns an entity vs feature array.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Scconnect.to_bool_array" title="pypath.core.annot.Scconnect.to_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_bool_array</span></code></a>(reference_set)</p></td>
+<td><p>Returns a presence/absence boolean array for a reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Scconnect.to_set" title="pypath.core.annot.Scconnect.to_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_set</span></code></a>()</p></td>
+<td><p>Returns the entities present in this annotation resource as a set.</p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Attributes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_fields</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">summary</span></code></p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Scconnect.add_complexes_by_inference">
+<span class="sig-name descname"><span class="pre">add_complexes_by_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Scconnect.add_complexes_by_inference" title="Link to this definition">§</a></dt>
+<dd><p>Creates complex annotations by in silico inference and adds them
+to this annotation set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Scconnect.all_complexes">
+<span class="sig-name descname"><span class="pre">all_complexes</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Scconnect.all_complexes" title="Link to this definition">§</a></dt>
+<dd><p>All protein complexes annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Scconnect.all_entities">
+<span class="sig-name descname"><span class="pre">all_entities</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Scconnect.all_entities" title="Link to this definition">§</a></dt>
+<dd><p>All entities annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Scconnect.all_mirnas">
+<span class="sig-name descname"><span class="pre">all_mirnas</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Scconnect.all_mirnas" title="Link to this definition">§</a></dt>
+<dd><p>All miRNAs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Scconnect.all_proteins">
+<span class="sig-name descname"><span class="pre">all_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Scconnect.all_proteins" title="Link to this definition">§</a></dt>
+<dd><p>All UniProt IDs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Scconnect.all_refs">
+<span class="sig-name descname"><span class="pre">all_refs</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Scconnect.all_refs" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects the references
+across all records. Returns <em>list</em>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Scconnect.annotate_complex">
+<span class="sig-name descname"><span class="pre">annotate_complex</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cplex</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Scconnect.annotate_complex" title="Link to this definition">§</a></dt>
+<dd><p>Infers annotations for a single complex.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Scconnect.browse">
+<span class="sig-name descname"><span class="pre">browse</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">field</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">start</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Scconnect.browse" title="Link to this definition">§</a></dt>
+<dd><p>Print gene information as a table.</p>
+<p>Presents information about annotation categories as ascii tables
+printed in the terminal. If one category provided, prints one table.
+If multiple categories provided, prints a table for each of them one
+by one proceeding to the next one once you hit return. If no categories
+provided goes through all levels of the primary category.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>field:</dt><dd><p>The field to browse categories by.</p>
+<ul class="simple">
+<li><p>If None the primary field will be selected.
+If this annotation resource doesn’t have fields, all proteins
+will be presented as one single category.</p></li>
+<li><p>If a string it will be considered a field name and it will
+browse through all levels of this field.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">list</span></code>, set or tuple, it will be considered either a
+<code class="docutils literal notranslate"><span class="pre">list</span></code> of field names or a list of values from the primary
+field. In the former case all combinations of the values of
+the fields will be presented, in the latter case the browsing
+will be limited to the levels of the primary field contained
+in <code class="docutils literal notranslate"><span class="pre">field</span></code>.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">dict</span></code>, keys are supposed to be field names and values
+as list of levels. If any of the values are None, all levels
+from that field will be used.</p></li>
+</ul>
+</dd>
+<dt>start:</dt><dd><p>Start browsing from this category. E.g. if there are 500
+categories and start is 250 it will skip everything before the
+250th.</p>
+</dd>
+<dt>kwargs:</dt><dd><p>Passed to <code class="docutils literal notranslate"><span class="pre">pypath.utils.uniprot.info</span></code>.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Scconnect.complex_inference">
+<span class="sig-name descname"><span class="pre">complex_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Scconnect.complex_inference" title="Link to this definition">§</a></dt>
+<dd><p>Annotates all complexes in <cite>complexes</cite>, by default in the default
+complex database (existing in the <cite>complex</cite> module or generated
+on demand according to the module’s current settings).</p>
+<dl class="field-list simple">
+<dt class="field-odd">Returns<span class="colon">:</span></dt>
+<dd class="field-odd"><p><ul class="simple">
+<li><p><em>Dict with complexes as keys and sets of annotations as values.</em></p></li>
+<li><p><em>Complexes with no valid information in this annotation resource</em></p></li>
+<li><p><em>won’t be in the dict.</em></p></li>
+</ul>
+</p>
+</dd>
+<dt class="field-even">Parameters<span class="colon">:</span></dt>
+<dd class="field-even"><p><strong>complexes</strong> (<em>iterable</em>) – Iterable yielding complexes.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Scconnect.coverage">
+<span class="sig-name descname"><span class="pre">coverage</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">other</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Scconnect.coverage" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the coverage of the annotation i.e. the proportion of
+entities having at least one record in this annotation resource
+for an arbitrary set of entities.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Scconnect.curation_effort">
+<span class="sig-name descname"><span class="pre">curation_effort</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Scconnect.curation_effort" title="Link to this definition">§</a></dt>
+<dd><p>Counts the reference-record pairs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Scconnect.get_names">
+<span class="sig-name descname"><span class="pre">get_names</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Scconnect.get_names" title="Link to this definition">§</a></dt>
+<dd><p>Returns the list of field names in the records. The annotation
+consists of uniform records and each entity might be annotated
+with one or more records. Each record is a tuple of fields, for
+example <code class="docutils literal notranslate"><span class="pre">('cell_type',</span> <span class="pre">'expression_level',</span> <span class="pre">'score')</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Scconnect.get_reference_set">
+<em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">get_reference_set</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">proteins</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">swissprot_only</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Scconnect.get_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the reference set i.e. the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Scconnect.get_subset">
+<span class="sig-name descname"><span class="pre">get_subset</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Scconnect.get_subset" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Scconnect.get_subset_bool_array">
+<span class="sig-name descname"><span class="pre">get_subset_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Scconnect.get_subset_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a boolean vector with True and False values for each entity
+in the reference set. The values represent presence absence data
+in the simplest case, but by providing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> any kind of matching
+and filtering is possible. <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> are passed to the <code class="docutils literal notranslate"><span class="pre">select</span></code>
+method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Scconnect.get_values">
+<span class="sig-name descname"><span class="pre">get_values</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">exclude_none</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Scconnect.get_values" title="Link to this definition">§</a></dt>
+<dd><p>Returns the set of all possible values of a field. E.g. if the
+records of this annotation have a field <code class="docutils literal notranslate"><span class="pre">cell_type</span></code> then calling
+this method can tell you that across all records the values of
+this field might be <code class="docutils literal notranslate"><span class="pre">{'macrophage',</span> <span class="pre">'epithelial_cell',</span> <span class="pre">...}</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Scconnect.labels">
+<span class="sig-name descname"><span class="pre">labels</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Scconnect.labels" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Scconnect.load">
+<span class="sig-name descname"><span class="pre">load</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Scconnect.load" title="Link to this definition">§</a></dt>
+<dd><p>Loads the annotation data by calling the input method.
+Infers annotations for complexes in the complex database if
+py:attr:<code class="docutils literal notranslate"><span class="pre">infer_complexes</span></code> is True.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Scconnect.load_data">
+<span class="sig-name descname"><span class="pre">load_data</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Scconnect.load_data" title="Link to this definition">§</a></dt>
+<dd><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Scconnect.load_proteins">
+<span class="sig-name descname"><span class="pre">load_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Scconnect.load_proteins" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a set of all UniProt IDs to have a base set of the entire
+proteome.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Scconnect.make_df">
+<span class="sig-name descname"><span class="pre">make_df</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">rebuild</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Scconnect.make_df" title="Link to this definition">§</a></dt>
+<dd><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.
+The data frame will be assigned to :py:attr``df``.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Scconnect.numof_entities">
+<span class="sig-name descname"><span class="pre">numof_entities</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Scconnect.numof_entities" title="Link to this definition">§</a></dt>
+<dd><p>The number of annotated entities in the resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Scconnect.numof_records">
+<span class="sig-name descname"><span class="pre">numof_records</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Scconnect.numof_records" title="Link to this definition">§</a></dt>
+<dd><p>The total number of annotation records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Scconnect.numof_references">
+<span class="sig-name descname"><span class="pre">numof_references</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Scconnect.numof_references" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects and counts the
+references across all records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Scconnect.process">
+<span class="sig-name descname"><span class="pre">process</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Scconnect.process" title="Link to this definition">§</a></dt>
+<dd><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Scconnect.reload">
+<span class="sig-name descname"><span class="pre">reload</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Scconnect.reload" title="Link to this definition">§</a></dt>
+<dd><p>Reloads the object from the module level.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Scconnect.select">
+<span class="sig-name descname"><span class="pre">select</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Scconnect.select" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Scconnect.set_method">
+<span class="sig-name descname"><span class="pre">set_method</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Scconnect.set_method" title="Link to this definition">§</a></dt>
+<dd><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if
+necessary.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Scconnect.set_reference_set">
+<span class="sig-name descname"><span class="pre">set_reference_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Scconnect.set_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Assigns the reference set to the :py:attr``reference_set`` attribute.
+The reference set is the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Scconnect.show">
+<span class="sig-name descname"><span class="pre">show</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">table_param</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Scconnect.show" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic
+information from the UniProt datasheets.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Scconnect.subset_intersection">
+<span class="sig-name descname"><span class="pre">subset_intersection</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">universe</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Scconnect.subset_intersection" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the proportion of entities in a subset occuring in the
+set <code class="docutils literal notranslate"><span class="pre">universe</span></code>. The subset is selected by passing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> to the
+<code class="docutils literal notranslate"><span class="pre">select</span></code> method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Scconnect.to_array">
+<span class="sig-name descname"><span class="pre">to_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_fields</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Scconnect.to_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns an entity vs feature array. In case of more complex
+annotations this might be huge.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Scconnect.to_bool_array">
+<span class="sig-name descname"><span class="pre">to_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Scconnect.to_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a presence/absence boolean array for a reference set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Scconnect.to_set">
+<span class="sig-name descname"><span class="pre">to_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Scconnect.to_set" title="Link to this definition">§</a></dt>
+<dd><p>Returns the entities present in this annotation resource as a set.</p>
+</dd></dl>
+
+</dd></dl>
+
+</section>
+
+
+                </article>
+              
+              
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diff --git a/api/pypath.core.annot.ScconnectComplex.html b/api/pypath.core.annot.ScconnectComplex.html
new file mode 100644
index 000000000..335e679e3
--- /dev/null
+++ b/api/pypath.core.annot.ScconnectComplex.html
@@ -0,0 +1,1116 @@
+
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+  <section id="pypath-core-annot-scconnectcomplex">
+<h1>pypath.core.annot.ScconnectComplex<a class="headerlink" href="#pypath-core-annot-scconnectcomplex" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.core.annot.ScconnectComplex">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.core.annot.</span></span><span class="sig-name descname"><span class="pre">ScconnectComplex</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#ScconnectComplex"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.ScconnectComplex" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <a class="reference internal" href="pypath.core.annot.AnnotationBase.html#pypath.core.annot.AnnotationBase" title="pypath.core.annot.AnnotationBase"><code class="xref py py-class docutils literal notranslate"><span class="pre">AnnotationBase</span></code></a></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.ScconnectComplex.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#ScconnectComplex.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.ScconnectComplex.__init__" title="Link to this definition">§</a></dt>
+<dd><p>Represents annotations for a set of proteins.
+Loads the data from the original resource and provides methods
+to query the annotations.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>name</strong> (<em>str</em>) – A custom name for the annotation resource.</p></li>
+<li><p><strong>ncbi_tax_id</strong> (<em>int</em>) – NCBI Taxonomy identifier.</p></li>
+<li><p><strong>input_method</strong> (<em>callable</em><em>,</em><em>str</em>) – Either a callable or the name of a method in any submodules of
+the <code class="docutils literal notranslate"><span class="pre">pypath.inputs</span></code>  module. Should return a dict with
+UniProt IDs as keys or an object suitable for <code class="docutils literal notranslate"><span class="pre">process_method</span></code>.</p></li>
+<li><p><strong>input_args</strong> (<em>dict</em>) – Arguments for the <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.ScconnectComplex.__init__" title="pypath.core.annot.ScconnectComplex.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>([ncbi_tax_id])</p></td>
+<td><p>Represents annotations for a set of proteins.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.ScconnectComplex.add_complexes_by_inference" title="pypath.core.annot.ScconnectComplex.add_complexes_by_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">add_complexes_by_inference</span></code></a>([complexes])</p></td>
+<td><p>Creates complex annotations by in silico inference and adds them to this annotation set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.ScconnectComplex.all_complexes" title="pypath.core.annot.ScconnectComplex.all_complexes"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_complexes</span></code></a>()</p></td>
+<td><p>All protein complexes annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.ScconnectComplex.all_entities" title="pypath.core.annot.ScconnectComplex.all_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_entities</span></code></a>([entity_types])</p></td>
+<td><p>All entities annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.ScconnectComplex.all_mirnas" title="pypath.core.annot.ScconnectComplex.all_mirnas"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_mirnas</span></code></a>()</p></td>
+<td><p>All miRNAs annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.ScconnectComplex.all_proteins" title="pypath.core.annot.ScconnectComplex.all_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_proteins</span></code></a>()</p></td>
+<td><p>All UniProt IDs annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.ScconnectComplex.all_refs" title="pypath.core.annot.ScconnectComplex.all_refs"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_refs</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.ScconnectComplex.annotate_complex" title="pypath.core.annot.ScconnectComplex.annotate_complex"><code class="xref py py-obj docutils literal notranslate"><span class="pre">annotate_complex</span></code></a>(cplex)</p></td>
+<td><p>Infers annotations for a single complex.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.ScconnectComplex.browse" title="pypath.core.annot.ScconnectComplex.browse"><code class="xref py py-obj docutils literal notranslate"><span class="pre">browse</span></code></a>([field, start])</p></td>
+<td><p>Print gene information as a table.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.ScconnectComplex.complex_inference" title="pypath.core.annot.ScconnectComplex.complex_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">complex_inference</span></code></a>([complexes])</p></td>
+<td><p>Annotates all complexes in <cite>complexes</cite>, by default in the default complex database (existing in the <cite>complex</cite> module or generated on demand according to the module's current settings).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.ScconnectComplex.coverage" title="pypath.core.annot.ScconnectComplex.coverage"><code class="xref py py-obj docutils literal notranslate"><span class="pre">coverage</span></code></a>(other)</p></td>
+<td><p>Calculates the coverage of the annotation i.e. the proportion of entities having at least one record in this annotation resource for an arbitrary set of entities.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.ScconnectComplex.curation_effort" title="pypath.core.annot.ScconnectComplex.curation_effort"><code class="xref py py-obj docutils literal notranslate"><span class="pre">curation_effort</span></code></a>()</p></td>
+<td><p>Counts the reference-record pairs.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">from_dump</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_entity_type</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.ScconnectComplex.get_names" title="pypath.core.annot.ScconnectComplex.get_names"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_names</span></code></a>()</p></td>
+<td><p>Returns the list of field names in the records.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.ScconnectComplex.get_reference_set" title="pypath.core.annot.ScconnectComplex.get_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_reference_set</span></code></a>([proteins, complexes, ...])</p></td>
+<td><p>Retrieves the reference set i.e. the set of all entities which potentially have annotation in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.ScconnectComplex.get_subset" title="pypath.core.annot.ScconnectComplex.get_subset"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.ScconnectComplex.get_subset_bool_array" title="pypath.core.annot.ScconnectComplex.get_subset_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset_bool_array</span></code></a>([reference_set])</p></td>
+<td><p>Returns a boolean vector with True and False values for each entity in the reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.ScconnectComplex.get_values" title="pypath.core.annot.ScconnectComplex.get_values"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_values</span></code></a>(name[, exclude_none])</p></td>
+<td><p>Returns the set of all possible values of a field.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_complex</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_mirna</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_protein</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.ScconnectComplex.labels" title="pypath.core.annot.ScconnectComplex.labels"><code class="xref py py-obj docutils literal notranslate"><span class="pre">labels</span></code></a>([method])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.ScconnectComplex.load" title="pypath.core.annot.ScconnectComplex.load"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load</span></code></a>()</p></td>
+<td><p>Loads the annotation data by calling the input method.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.ScconnectComplex.load_data" title="pypath.core.annot.ScconnectComplex.load_data"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_data</span></code></a>()</p></td>
+<td><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.ScconnectComplex.load_proteins" title="pypath.core.annot.ScconnectComplex.load_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_proteins</span></code></a>()</p></td>
+<td><p>Retrieves a set of all UniProt IDs to have a base set of the entire proteome.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.ScconnectComplex.make_df" title="pypath.core.annot.ScconnectComplex.make_df"><code class="xref py py-obj docutils literal notranslate"><span class="pre">make_df</span></code></a>([rebuild])</p></td>
+<td><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complex_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.ScconnectComplex.numof_entities" title="pypath.core.annot.ScconnectComplex.numof_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_entities</span></code></a>()</p></td>
+<td><p>The number of annotated entities in the resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirna_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirnas</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_protein_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_proteins</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.ScconnectComplex.numof_records" title="pypath.core.annot.ScconnectComplex.numof_records"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_records</span></code></a>([entity_types])</p></td>
+<td><p>The total number of annotation records.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.ScconnectComplex.numof_references" title="pypath.core.annot.ScconnectComplex.numof_references"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_references</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.ScconnectComplex.process" title="pypath.core.annot.ScconnectComplex.process"><code class="xref py py-obj docutils literal notranslate"><span class="pre">process</span></code></a>()</p></td>
+<td><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">proportion</span></code>(other)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.ScconnectComplex.reload" title="pypath.core.annot.ScconnectComplex.reload"><code class="xref py py-obj docutils literal notranslate"><span class="pre">reload</span></code></a>()</p></td>
+<td><p>Reloads the object from the module level.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">save_to_pickle</span></code>(pickle_file)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.ScconnectComplex.select" title="pypath.core.annot.ScconnectComplex.select"><code class="xref py py-obj docutils literal notranslate"><span class="pre">select</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.ScconnectComplex.set_method" title="pypath.core.annot.ScconnectComplex.set_method"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_method</span></code></a>()</p></td>
+<td><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if necessary.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.ScconnectComplex.set_reference_set" title="pypath.core.annot.ScconnectComplex.set_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_reference_set</span></code></a>()</p></td>
+<td><p>Assigns the reference set to the :py:attr``reference_set`` attribute.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.ScconnectComplex.show" title="pypath.core.annot.ScconnectComplex.show"><code class="xref py py-obj docutils literal notranslate"><span class="pre">show</span></code></a>([method, table_param])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic information from the UniProt datasheets.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.ScconnectComplex.subset_intersection" title="pypath.core.annot.ScconnectComplex.subset_intersection"><code class="xref py py-obj docutils literal notranslate"><span class="pre">subset_intersection</span></code></a>(universe, **kwargs)</p></td>
+<td><p>Calculates the proportion of entities in a subset occuring in the set <code class="docutils literal notranslate"><span class="pre">universe</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.ScconnectComplex.to_array" title="pypath.core.annot.ScconnectComplex.to_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_array</span></code></a>([reference_set, use_fields])</p></td>
+<td><p>Returns an entity vs feature array.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.ScconnectComplex.to_bool_array" title="pypath.core.annot.ScconnectComplex.to_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_bool_array</span></code></a>(reference_set)</p></td>
+<td><p>Returns a presence/absence boolean array for a reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.ScconnectComplex.to_set" title="pypath.core.annot.ScconnectComplex.to_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_set</span></code></a>()</p></td>
+<td><p>Returns the entities present in this annotation resource as a set.</p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Attributes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_fields</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">summary</span></code></p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.ScconnectComplex.add_complexes_by_inference">
+<span class="sig-name descname"><span class="pre">add_complexes_by_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.ScconnectComplex.add_complexes_by_inference" title="Link to this definition">§</a></dt>
+<dd><p>Creates complex annotations by in silico inference and adds them
+to this annotation set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.ScconnectComplex.all_complexes">
+<span class="sig-name descname"><span class="pre">all_complexes</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.ScconnectComplex.all_complexes" title="Link to this definition">§</a></dt>
+<dd><p>All protein complexes annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.ScconnectComplex.all_entities">
+<span class="sig-name descname"><span class="pre">all_entities</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.ScconnectComplex.all_entities" title="Link to this definition">§</a></dt>
+<dd><p>All entities annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.ScconnectComplex.all_mirnas">
+<span class="sig-name descname"><span class="pre">all_mirnas</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.ScconnectComplex.all_mirnas" title="Link to this definition">§</a></dt>
+<dd><p>All miRNAs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.ScconnectComplex.all_proteins">
+<span class="sig-name descname"><span class="pre">all_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.ScconnectComplex.all_proteins" title="Link to this definition">§</a></dt>
+<dd><p>All UniProt IDs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.ScconnectComplex.all_refs">
+<span class="sig-name descname"><span class="pre">all_refs</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.ScconnectComplex.all_refs" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects the references
+across all records. Returns <em>list</em>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.ScconnectComplex.annotate_complex">
+<span class="sig-name descname"><span class="pre">annotate_complex</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cplex</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.ScconnectComplex.annotate_complex" title="Link to this definition">§</a></dt>
+<dd><p>Infers annotations for a single complex.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.ScconnectComplex.browse">
+<span class="sig-name descname"><span class="pre">browse</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">field</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">start</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.ScconnectComplex.browse" title="Link to this definition">§</a></dt>
+<dd><p>Print gene information as a table.</p>
+<p>Presents information about annotation categories as ascii tables
+printed in the terminal. If one category provided, prints one table.
+If multiple categories provided, prints a table for each of them one
+by one proceeding to the next one once you hit return. If no categories
+provided goes through all levels of the primary category.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>field:</dt><dd><p>The field to browse categories by.</p>
+<ul class="simple">
+<li><p>If None the primary field will be selected.
+If this annotation resource doesn’t have fields, all proteins
+will be presented as one single category.</p></li>
+<li><p>If a string it will be considered a field name and it will
+browse through all levels of this field.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">list</span></code>, set or tuple, it will be considered either a
+<code class="docutils literal notranslate"><span class="pre">list</span></code> of field names or a list of values from the primary
+field. In the former case all combinations of the values of
+the fields will be presented, in the latter case the browsing
+will be limited to the levels of the primary field contained
+in <code class="docutils literal notranslate"><span class="pre">field</span></code>.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">dict</span></code>, keys are supposed to be field names and values
+as list of levels. If any of the values are None, all levels
+from that field will be used.</p></li>
+</ul>
+</dd>
+<dt>start:</dt><dd><p>Start browsing from this category. E.g. if there are 500
+categories and start is 250 it will skip everything before the
+250th.</p>
+</dd>
+<dt>kwargs:</dt><dd><p>Passed to <code class="docutils literal notranslate"><span class="pre">pypath.utils.uniprot.info</span></code>.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.ScconnectComplex.complex_inference">
+<span class="sig-name descname"><span class="pre">complex_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.ScconnectComplex.complex_inference" title="Link to this definition">§</a></dt>
+<dd><p>Annotates all complexes in <cite>complexes</cite>, by default in the default
+complex database (existing in the <cite>complex</cite> module or generated
+on demand according to the module’s current settings).</p>
+<dl class="field-list simple">
+<dt class="field-odd">Returns<span class="colon">:</span></dt>
+<dd class="field-odd"><p><ul class="simple">
+<li><p><em>Dict with complexes as keys and sets of annotations as values.</em></p></li>
+<li><p><em>Complexes with no valid information in this annotation resource</em></p></li>
+<li><p><em>won’t be in the dict.</em></p></li>
+</ul>
+</p>
+</dd>
+<dt class="field-even">Parameters<span class="colon">:</span></dt>
+<dd class="field-even"><p><strong>complexes</strong> (<em>iterable</em>) – Iterable yielding complexes.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.ScconnectComplex.coverage">
+<span class="sig-name descname"><span class="pre">coverage</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">other</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.ScconnectComplex.coverage" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the coverage of the annotation i.e. the proportion of
+entities having at least one record in this annotation resource
+for an arbitrary set of entities.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.ScconnectComplex.curation_effort">
+<span class="sig-name descname"><span class="pre">curation_effort</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.ScconnectComplex.curation_effort" title="Link to this definition">§</a></dt>
+<dd><p>Counts the reference-record pairs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.ScconnectComplex.get_names">
+<span class="sig-name descname"><span class="pre">get_names</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.ScconnectComplex.get_names" title="Link to this definition">§</a></dt>
+<dd><p>Returns the list of field names in the records. The annotation
+consists of uniform records and each entity might be annotated
+with one or more records. Each record is a tuple of fields, for
+example <code class="docutils literal notranslate"><span class="pre">('cell_type',</span> <span class="pre">'expression_level',</span> <span class="pre">'score')</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.ScconnectComplex.get_reference_set">
+<em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">get_reference_set</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">proteins</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">swissprot_only</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.ScconnectComplex.get_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the reference set i.e. the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.ScconnectComplex.get_subset">
+<span class="sig-name descname"><span class="pre">get_subset</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.ScconnectComplex.get_subset" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.ScconnectComplex.get_subset_bool_array">
+<span class="sig-name descname"><span class="pre">get_subset_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.ScconnectComplex.get_subset_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a boolean vector with True and False values for each entity
+in the reference set. The values represent presence absence data
+in the simplest case, but by providing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> any kind of matching
+and filtering is possible. <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> are passed to the <code class="docutils literal notranslate"><span class="pre">select</span></code>
+method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.ScconnectComplex.get_values">
+<span class="sig-name descname"><span class="pre">get_values</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">exclude_none</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.ScconnectComplex.get_values" title="Link to this definition">§</a></dt>
+<dd><p>Returns the set of all possible values of a field. E.g. if the
+records of this annotation have a field <code class="docutils literal notranslate"><span class="pre">cell_type</span></code> then calling
+this method can tell you that across all records the values of
+this field might be <code class="docutils literal notranslate"><span class="pre">{'macrophage',</span> <span class="pre">'epithelial_cell',</span> <span class="pre">...}</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.ScconnectComplex.labels">
+<span class="sig-name descname"><span class="pre">labels</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.ScconnectComplex.labels" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.ScconnectComplex.load">
+<span class="sig-name descname"><span class="pre">load</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.ScconnectComplex.load" title="Link to this definition">§</a></dt>
+<dd><p>Loads the annotation data by calling the input method.
+Infers annotations for complexes in the complex database if
+py:attr:<code class="docutils literal notranslate"><span class="pre">infer_complexes</span></code> is True.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.ScconnectComplex.load_data">
+<span class="sig-name descname"><span class="pre">load_data</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.ScconnectComplex.load_data" title="Link to this definition">§</a></dt>
+<dd><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.ScconnectComplex.load_proteins">
+<span class="sig-name descname"><span class="pre">load_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.ScconnectComplex.load_proteins" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a set of all UniProt IDs to have a base set of the entire
+proteome.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.ScconnectComplex.make_df">
+<span class="sig-name descname"><span class="pre">make_df</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">rebuild</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.ScconnectComplex.make_df" title="Link to this definition">§</a></dt>
+<dd><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.
+The data frame will be assigned to :py:attr``df``.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.ScconnectComplex.numof_entities">
+<span class="sig-name descname"><span class="pre">numof_entities</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.ScconnectComplex.numof_entities" title="Link to this definition">§</a></dt>
+<dd><p>The number of annotated entities in the resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.ScconnectComplex.numof_records">
+<span class="sig-name descname"><span class="pre">numof_records</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.ScconnectComplex.numof_records" title="Link to this definition">§</a></dt>
+<dd><p>The total number of annotation records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.ScconnectComplex.numof_references">
+<span class="sig-name descname"><span class="pre">numof_references</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.ScconnectComplex.numof_references" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects and counts the
+references across all records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.ScconnectComplex.process">
+<span class="sig-name descname"><span class="pre">process</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.ScconnectComplex.process" title="Link to this definition">§</a></dt>
+<dd><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.ScconnectComplex.reload">
+<span class="sig-name descname"><span class="pre">reload</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.ScconnectComplex.reload" title="Link to this definition">§</a></dt>
+<dd><p>Reloads the object from the module level.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.ScconnectComplex.select">
+<span class="sig-name descname"><span class="pre">select</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.ScconnectComplex.select" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.ScconnectComplex.set_method">
+<span class="sig-name descname"><span class="pre">set_method</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.ScconnectComplex.set_method" title="Link to this definition">§</a></dt>
+<dd><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if
+necessary.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.ScconnectComplex.set_reference_set">
+<span class="sig-name descname"><span class="pre">set_reference_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.ScconnectComplex.set_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Assigns the reference set to the :py:attr``reference_set`` attribute.
+The reference set is the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.ScconnectComplex.show">
+<span class="sig-name descname"><span class="pre">show</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">table_param</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.ScconnectComplex.show" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic
+information from the UniProt datasheets.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.ScconnectComplex.subset_intersection">
+<span class="sig-name descname"><span class="pre">subset_intersection</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">universe</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.ScconnectComplex.subset_intersection" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the proportion of entities in a subset occuring in the
+set <code class="docutils literal notranslate"><span class="pre">universe</span></code>. The subset is selected by passing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> to the
+<code class="docutils literal notranslate"><span class="pre">select</span></code> method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.ScconnectComplex.to_array">
+<span class="sig-name descname"><span class="pre">to_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_fields</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.ScconnectComplex.to_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns an entity vs feature array. In case of more complex
+annotations this might be huge.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.ScconnectComplex.to_bool_array">
+<span class="sig-name descname"><span class="pre">to_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.ScconnectComplex.to_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a presence/absence boolean array for a reference set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.ScconnectComplex.to_set">
+<span class="sig-name descname"><span class="pre">to_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.ScconnectComplex.to_set" title="Link to this definition">§</a></dt>
+<dd><p>Returns the entities present in this annotation resource as a set.</p>
+</dd></dl>
+
+</dd></dl>
+
+</section>
+
+
+                </article>
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+  <section id="pypath-core-annot-signalinkfunctions">
+<h1>pypath.core.annot.SignalinkFunctions<a class="headerlink" href="#pypath-core-annot-signalinkfunctions" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.core.annot.SignalinkFunctions">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.core.annot.</span></span><span class="sig-name descname"><span class="pre">SignalinkFunctions</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#SignalinkFunctions"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.SignalinkFunctions" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <a class="reference internal" href="pypath.core.annot.AnnotationBase.html#pypath.core.annot.AnnotationBase" title="pypath.core.annot.AnnotationBase"><code class="xref py py-class docutils literal notranslate"><span class="pre">AnnotationBase</span></code></a></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.SignalinkFunctions.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#SignalinkFunctions.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.SignalinkFunctions.__init__" title="Link to this definition">§</a></dt>
+<dd><p>Functional annotations from SignaLink.</p>
+</dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.SignalinkFunctions.__init__" title="pypath.core.annot.SignalinkFunctions.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>([ncbi_tax_id])</p></td>
+<td><p>Functional annotations from SignaLink.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.SignalinkFunctions.add_complexes_by_inference" title="pypath.core.annot.SignalinkFunctions.add_complexes_by_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">add_complexes_by_inference</span></code></a>([complexes])</p></td>
+<td><p>Creates complex annotations by in silico inference and adds them to this annotation set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.SignalinkFunctions.all_complexes" title="pypath.core.annot.SignalinkFunctions.all_complexes"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_complexes</span></code></a>()</p></td>
+<td><p>All protein complexes annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.SignalinkFunctions.all_entities" title="pypath.core.annot.SignalinkFunctions.all_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_entities</span></code></a>([entity_types])</p></td>
+<td><p>All entities annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.SignalinkFunctions.all_mirnas" title="pypath.core.annot.SignalinkFunctions.all_mirnas"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_mirnas</span></code></a>()</p></td>
+<td><p>All miRNAs annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.SignalinkFunctions.all_proteins" title="pypath.core.annot.SignalinkFunctions.all_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_proteins</span></code></a>()</p></td>
+<td><p>All UniProt IDs annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.SignalinkFunctions.all_refs" title="pypath.core.annot.SignalinkFunctions.all_refs"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_refs</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.SignalinkFunctions.annotate_complex" title="pypath.core.annot.SignalinkFunctions.annotate_complex"><code class="xref py py-obj docutils literal notranslate"><span class="pre">annotate_complex</span></code></a>(cplex)</p></td>
+<td><p>Infers annotations for a single complex.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.SignalinkFunctions.browse" title="pypath.core.annot.SignalinkFunctions.browse"><code class="xref py py-obj docutils literal notranslate"><span class="pre">browse</span></code></a>([field, start])</p></td>
+<td><p>Print gene information as a table.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.SignalinkFunctions.complex_inference" title="pypath.core.annot.SignalinkFunctions.complex_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">complex_inference</span></code></a>([complexes])</p></td>
+<td><p>Annotates all complexes in <cite>complexes</cite>, by default in the default complex database (existing in the <cite>complex</cite> module or generated on demand according to the module's current settings).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.SignalinkFunctions.coverage" title="pypath.core.annot.SignalinkFunctions.coverage"><code class="xref py py-obj docutils literal notranslate"><span class="pre">coverage</span></code></a>(other)</p></td>
+<td><p>Calculates the coverage of the annotation i.e. the proportion of entities having at least one record in this annotation resource for an arbitrary set of entities.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.SignalinkFunctions.curation_effort" title="pypath.core.annot.SignalinkFunctions.curation_effort"><code class="xref py py-obj docutils literal notranslate"><span class="pre">curation_effort</span></code></a>()</p></td>
+<td><p>Counts the reference-record pairs.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">from_dump</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_entity_type</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.SignalinkFunctions.get_names" title="pypath.core.annot.SignalinkFunctions.get_names"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_names</span></code></a>()</p></td>
+<td><p>Returns the list of field names in the records.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.SignalinkFunctions.get_reference_set" title="pypath.core.annot.SignalinkFunctions.get_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_reference_set</span></code></a>([proteins, complexes, ...])</p></td>
+<td><p>Retrieves the reference set i.e. the set of all entities which potentially have annotation in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.SignalinkFunctions.get_subset" title="pypath.core.annot.SignalinkFunctions.get_subset"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.SignalinkFunctions.get_subset_bool_array" title="pypath.core.annot.SignalinkFunctions.get_subset_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset_bool_array</span></code></a>([reference_set])</p></td>
+<td><p>Returns a boolean vector with True and False values for each entity in the reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.SignalinkFunctions.get_values" title="pypath.core.annot.SignalinkFunctions.get_values"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_values</span></code></a>(name[, exclude_none])</p></td>
+<td><p>Returns the set of all possible values of a field.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_complex</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_mirna</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_protein</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.SignalinkFunctions.labels" title="pypath.core.annot.SignalinkFunctions.labels"><code class="xref py py-obj docutils literal notranslate"><span class="pre">labels</span></code></a>([method])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.SignalinkFunctions.load" title="pypath.core.annot.SignalinkFunctions.load"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load</span></code></a>()</p></td>
+<td><p>Loads the annotation data by calling the input method.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.SignalinkFunctions.load_data" title="pypath.core.annot.SignalinkFunctions.load_data"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_data</span></code></a>()</p></td>
+<td><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.SignalinkFunctions.load_proteins" title="pypath.core.annot.SignalinkFunctions.load_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_proteins</span></code></a>()</p></td>
+<td><p>Retrieves a set of all UniProt IDs to have a base set of the entire proteome.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.SignalinkFunctions.make_df" title="pypath.core.annot.SignalinkFunctions.make_df"><code class="xref py py-obj docutils literal notranslate"><span class="pre">make_df</span></code></a>([rebuild])</p></td>
+<td><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complex_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.SignalinkFunctions.numof_entities" title="pypath.core.annot.SignalinkFunctions.numof_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_entities</span></code></a>()</p></td>
+<td><p>The number of annotated entities in the resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirna_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirnas</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_protein_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_proteins</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.SignalinkFunctions.numof_records" title="pypath.core.annot.SignalinkFunctions.numof_records"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_records</span></code></a>([entity_types])</p></td>
+<td><p>The total number of annotation records.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.SignalinkFunctions.numof_references" title="pypath.core.annot.SignalinkFunctions.numof_references"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_references</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.SignalinkFunctions.process" title="pypath.core.annot.SignalinkFunctions.process"><code class="xref py py-obj docutils literal notranslate"><span class="pre">process</span></code></a>()</p></td>
+<td><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">proportion</span></code>(other)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.SignalinkFunctions.reload" title="pypath.core.annot.SignalinkFunctions.reload"><code class="xref py py-obj docutils literal notranslate"><span class="pre">reload</span></code></a>()</p></td>
+<td><p>Reloads the object from the module level.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">save_to_pickle</span></code>(pickle_file)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.SignalinkFunctions.select" title="pypath.core.annot.SignalinkFunctions.select"><code class="xref py py-obj docutils literal notranslate"><span class="pre">select</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.SignalinkFunctions.set_method" title="pypath.core.annot.SignalinkFunctions.set_method"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_method</span></code></a>()</p></td>
+<td><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if necessary.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.SignalinkFunctions.set_reference_set" title="pypath.core.annot.SignalinkFunctions.set_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_reference_set</span></code></a>()</p></td>
+<td><p>Assigns the reference set to the :py:attr``reference_set`` attribute.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.SignalinkFunctions.show" title="pypath.core.annot.SignalinkFunctions.show"><code class="xref py py-obj docutils literal notranslate"><span class="pre">show</span></code></a>([method, table_param])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic information from the UniProt datasheets.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.SignalinkFunctions.subset_intersection" title="pypath.core.annot.SignalinkFunctions.subset_intersection"><code class="xref py py-obj docutils literal notranslate"><span class="pre">subset_intersection</span></code></a>(universe, **kwargs)</p></td>
+<td><p>Calculates the proportion of entities in a subset occuring in the set <code class="docutils literal notranslate"><span class="pre">universe</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.SignalinkFunctions.to_array" title="pypath.core.annot.SignalinkFunctions.to_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_array</span></code></a>([reference_set, use_fields])</p></td>
+<td><p>Returns an entity vs feature array.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.SignalinkFunctions.to_bool_array" title="pypath.core.annot.SignalinkFunctions.to_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_bool_array</span></code></a>(reference_set)</p></td>
+<td><p>Returns a presence/absence boolean array for a reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.SignalinkFunctions.to_set" title="pypath.core.annot.SignalinkFunctions.to_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_set</span></code></a>()</p></td>
+<td><p>Returns the entities present in this annotation resource as a set.</p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Attributes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_fields</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">summary</span></code></p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.SignalinkFunctions.add_complexes_by_inference">
+<span class="sig-name descname"><span class="pre">add_complexes_by_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.SignalinkFunctions.add_complexes_by_inference" title="Link to this definition">§</a></dt>
+<dd><p>Creates complex annotations by in silico inference and adds them
+to this annotation set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.SignalinkFunctions.all_complexes">
+<span class="sig-name descname"><span class="pre">all_complexes</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.SignalinkFunctions.all_complexes" title="Link to this definition">§</a></dt>
+<dd><p>All protein complexes annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.SignalinkFunctions.all_entities">
+<span class="sig-name descname"><span class="pre">all_entities</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.SignalinkFunctions.all_entities" title="Link to this definition">§</a></dt>
+<dd><p>All entities annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.SignalinkFunctions.all_mirnas">
+<span class="sig-name descname"><span class="pre">all_mirnas</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.SignalinkFunctions.all_mirnas" title="Link to this definition">§</a></dt>
+<dd><p>All miRNAs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.SignalinkFunctions.all_proteins">
+<span class="sig-name descname"><span class="pre">all_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.SignalinkFunctions.all_proteins" title="Link to this definition">§</a></dt>
+<dd><p>All UniProt IDs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.SignalinkFunctions.all_refs">
+<span class="sig-name descname"><span class="pre">all_refs</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.SignalinkFunctions.all_refs" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects the references
+across all records. Returns <em>list</em>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.SignalinkFunctions.annotate_complex">
+<span class="sig-name descname"><span class="pre">annotate_complex</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cplex</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.SignalinkFunctions.annotate_complex" title="Link to this definition">§</a></dt>
+<dd><p>Infers annotations for a single complex.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.SignalinkFunctions.browse">
+<span class="sig-name descname"><span class="pre">browse</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">field</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">start</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.SignalinkFunctions.browse" title="Link to this definition">§</a></dt>
+<dd><p>Print gene information as a table.</p>
+<p>Presents information about annotation categories as ascii tables
+printed in the terminal. If one category provided, prints one table.
+If multiple categories provided, prints a table for each of them one
+by one proceeding to the next one once you hit return. If no categories
+provided goes through all levels of the primary category.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>field:</dt><dd><p>The field to browse categories by.</p>
+<ul class="simple">
+<li><p>If None the primary field will be selected.
+If this annotation resource doesn’t have fields, all proteins
+will be presented as one single category.</p></li>
+<li><p>If a string it will be considered a field name and it will
+browse through all levels of this field.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">list</span></code>, set or tuple, it will be considered either a
+<code class="docutils literal notranslate"><span class="pre">list</span></code> of field names or a list of values from the primary
+field. In the former case all combinations of the values of
+the fields will be presented, in the latter case the browsing
+will be limited to the levels of the primary field contained
+in <code class="docutils literal notranslate"><span class="pre">field</span></code>.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">dict</span></code>, keys are supposed to be field names and values
+as list of levels. If any of the values are None, all levels
+from that field will be used.</p></li>
+</ul>
+</dd>
+<dt>start:</dt><dd><p>Start browsing from this category. E.g. if there are 500
+categories and start is 250 it will skip everything before the
+250th.</p>
+</dd>
+<dt>kwargs:</dt><dd><p>Passed to <code class="docutils literal notranslate"><span class="pre">pypath.utils.uniprot.info</span></code>.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.SignalinkFunctions.complex_inference">
+<span class="sig-name descname"><span class="pre">complex_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.SignalinkFunctions.complex_inference" title="Link to this definition">§</a></dt>
+<dd><p>Annotates all complexes in <cite>complexes</cite>, by default in the default
+complex database (existing in the <cite>complex</cite> module or generated
+on demand according to the module’s current settings).</p>
+<dl class="field-list simple">
+<dt class="field-odd">Returns<span class="colon">:</span></dt>
+<dd class="field-odd"><p><ul class="simple">
+<li><p><em>Dict with complexes as keys and sets of annotations as values.</em></p></li>
+<li><p><em>Complexes with no valid information in this annotation resource</em></p></li>
+<li><p><em>won’t be in the dict.</em></p></li>
+</ul>
+</p>
+</dd>
+<dt class="field-even">Parameters<span class="colon">:</span></dt>
+<dd class="field-even"><p><strong>complexes</strong> (<em>iterable</em>) – Iterable yielding complexes.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.SignalinkFunctions.coverage">
+<span class="sig-name descname"><span class="pre">coverage</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">other</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.SignalinkFunctions.coverage" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the coverage of the annotation i.e. the proportion of
+entities having at least one record in this annotation resource
+for an arbitrary set of entities.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.SignalinkFunctions.curation_effort">
+<span class="sig-name descname"><span class="pre">curation_effort</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.SignalinkFunctions.curation_effort" title="Link to this definition">§</a></dt>
+<dd><p>Counts the reference-record pairs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.SignalinkFunctions.get_names">
+<span class="sig-name descname"><span class="pre">get_names</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.SignalinkFunctions.get_names" title="Link to this definition">§</a></dt>
+<dd><p>Returns the list of field names in the records. The annotation
+consists of uniform records and each entity might be annotated
+with one or more records. Each record is a tuple of fields, for
+example <code class="docutils literal notranslate"><span class="pre">('cell_type',</span> <span class="pre">'expression_level',</span> <span class="pre">'score')</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.SignalinkFunctions.get_reference_set">
+<em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">get_reference_set</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">proteins</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">swissprot_only</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.SignalinkFunctions.get_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the reference set i.e. the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.SignalinkFunctions.get_subset">
+<span class="sig-name descname"><span class="pre">get_subset</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.SignalinkFunctions.get_subset" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.SignalinkFunctions.get_subset_bool_array">
+<span class="sig-name descname"><span class="pre">get_subset_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.SignalinkFunctions.get_subset_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a boolean vector with True and False values for each entity
+in the reference set. The values represent presence absence data
+in the simplest case, but by providing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> any kind of matching
+and filtering is possible. <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> are passed to the <code class="docutils literal notranslate"><span class="pre">select</span></code>
+method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.SignalinkFunctions.get_values">
+<span class="sig-name descname"><span class="pre">get_values</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">exclude_none</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.SignalinkFunctions.get_values" title="Link to this definition">§</a></dt>
+<dd><p>Returns the set of all possible values of a field. E.g. if the
+records of this annotation have a field <code class="docutils literal notranslate"><span class="pre">cell_type</span></code> then calling
+this method can tell you that across all records the values of
+this field might be <code class="docutils literal notranslate"><span class="pre">{'macrophage',</span> <span class="pre">'epithelial_cell',</span> <span class="pre">...}</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.SignalinkFunctions.labels">
+<span class="sig-name descname"><span class="pre">labels</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.SignalinkFunctions.labels" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.SignalinkFunctions.load">
+<span class="sig-name descname"><span class="pre">load</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.SignalinkFunctions.load" title="Link to this definition">§</a></dt>
+<dd><p>Loads the annotation data by calling the input method.
+Infers annotations for complexes in the complex database if
+py:attr:<code class="docutils literal notranslate"><span class="pre">infer_complexes</span></code> is True.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.SignalinkFunctions.load_data">
+<span class="sig-name descname"><span class="pre">load_data</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.SignalinkFunctions.load_data" title="Link to this definition">§</a></dt>
+<dd><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.SignalinkFunctions.load_proteins">
+<span class="sig-name descname"><span class="pre">load_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.SignalinkFunctions.load_proteins" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a set of all UniProt IDs to have a base set of the entire
+proteome.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.SignalinkFunctions.make_df">
+<span class="sig-name descname"><span class="pre">make_df</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">rebuild</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.SignalinkFunctions.make_df" title="Link to this definition">§</a></dt>
+<dd><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.
+The data frame will be assigned to :py:attr``df``.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.SignalinkFunctions.numof_entities">
+<span class="sig-name descname"><span class="pre">numof_entities</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.SignalinkFunctions.numof_entities" title="Link to this definition">§</a></dt>
+<dd><p>The number of annotated entities in the resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.SignalinkFunctions.numof_records">
+<span class="sig-name descname"><span class="pre">numof_records</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.SignalinkFunctions.numof_records" title="Link to this definition">§</a></dt>
+<dd><p>The total number of annotation records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.SignalinkFunctions.numof_references">
+<span class="sig-name descname"><span class="pre">numof_references</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.SignalinkFunctions.numof_references" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects and counts the
+references across all records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.SignalinkFunctions.process">
+<span class="sig-name descname"><span class="pre">process</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.SignalinkFunctions.process" title="Link to this definition">§</a></dt>
+<dd><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.SignalinkFunctions.reload">
+<span class="sig-name descname"><span class="pre">reload</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.SignalinkFunctions.reload" title="Link to this definition">§</a></dt>
+<dd><p>Reloads the object from the module level.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.SignalinkFunctions.select">
+<span class="sig-name descname"><span class="pre">select</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.SignalinkFunctions.select" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.SignalinkFunctions.set_method">
+<span class="sig-name descname"><span class="pre">set_method</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.SignalinkFunctions.set_method" title="Link to this definition">§</a></dt>
+<dd><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if
+necessary.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.SignalinkFunctions.set_reference_set">
+<span class="sig-name descname"><span class="pre">set_reference_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.SignalinkFunctions.set_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Assigns the reference set to the :py:attr``reference_set`` attribute.
+The reference set is the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.SignalinkFunctions.show">
+<span class="sig-name descname"><span class="pre">show</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">table_param</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.SignalinkFunctions.show" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic
+information from the UniProt datasheets.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.SignalinkFunctions.subset_intersection">
+<span class="sig-name descname"><span class="pre">subset_intersection</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">universe</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.SignalinkFunctions.subset_intersection" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the proportion of entities in a subset occuring in the
+set <code class="docutils literal notranslate"><span class="pre">universe</span></code>. The subset is selected by passing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> to the
+<code class="docutils literal notranslate"><span class="pre">select</span></code> method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.SignalinkFunctions.to_array">
+<span class="sig-name descname"><span class="pre">to_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_fields</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.SignalinkFunctions.to_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns an entity vs feature array. In case of more complex
+annotations this might be huge.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.SignalinkFunctions.to_bool_array">
+<span class="sig-name descname"><span class="pre">to_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.SignalinkFunctions.to_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a presence/absence boolean array for a reference set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.SignalinkFunctions.to_set">
+<span class="sig-name descname"><span class="pre">to_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.SignalinkFunctions.to_set" title="Link to this definition">§</a></dt>
+<dd><p>Returns the entities present in this annotation resource as a set.</p>
+</dd></dl>
+
+</dd></dl>
+
+</section>
+
+
+                </article>
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+  <section id="pypath-core-annot-signalinkpathways">
+<h1>pypath.core.annot.SignalinkPathways<a class="headerlink" href="#pypath-core-annot-signalinkpathways" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.core.annot.SignalinkPathways">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.core.annot.</span></span><span class="sig-name descname"><span class="pre">SignalinkPathways</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#SignalinkPathways"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.SignalinkPathways" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <a class="reference internal" href="pypath.core.annot.AnnotationBase.html#pypath.core.annot.AnnotationBase" title="pypath.core.annot.AnnotationBase"><code class="xref py py-class docutils literal notranslate"><span class="pre">AnnotationBase</span></code></a></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.SignalinkPathways.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#SignalinkPathways.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.SignalinkPathways.__init__" title="Link to this definition">§</a></dt>
+<dd><p>Pathway annotations from SignaLink.</p>
+</dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.SignalinkPathways.__init__" title="pypath.core.annot.SignalinkPathways.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>([ncbi_tax_id])</p></td>
+<td><p>Pathway annotations from SignaLink.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.SignalinkPathways.add_complexes_by_inference" title="pypath.core.annot.SignalinkPathways.add_complexes_by_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">add_complexes_by_inference</span></code></a>([complexes])</p></td>
+<td><p>Creates complex annotations by in silico inference and adds them to this annotation set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.SignalinkPathways.all_complexes" title="pypath.core.annot.SignalinkPathways.all_complexes"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_complexes</span></code></a>()</p></td>
+<td><p>All protein complexes annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.SignalinkPathways.all_entities" title="pypath.core.annot.SignalinkPathways.all_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_entities</span></code></a>([entity_types])</p></td>
+<td><p>All entities annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.SignalinkPathways.all_mirnas" title="pypath.core.annot.SignalinkPathways.all_mirnas"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_mirnas</span></code></a>()</p></td>
+<td><p>All miRNAs annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.SignalinkPathways.all_proteins" title="pypath.core.annot.SignalinkPathways.all_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_proteins</span></code></a>()</p></td>
+<td><p>All UniProt IDs annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.SignalinkPathways.all_refs" title="pypath.core.annot.SignalinkPathways.all_refs"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_refs</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.SignalinkPathways.annotate_complex" title="pypath.core.annot.SignalinkPathways.annotate_complex"><code class="xref py py-obj docutils literal notranslate"><span class="pre">annotate_complex</span></code></a>(cplex)</p></td>
+<td><p>Infers annotations for a single complex.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.SignalinkPathways.browse" title="pypath.core.annot.SignalinkPathways.browse"><code class="xref py py-obj docutils literal notranslate"><span class="pre">browse</span></code></a>([field, start])</p></td>
+<td><p>Print gene information as a table.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.SignalinkPathways.complex_inference" title="pypath.core.annot.SignalinkPathways.complex_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">complex_inference</span></code></a>([complexes])</p></td>
+<td><p>Annotates all complexes in <cite>complexes</cite>, by default in the default complex database (existing in the <cite>complex</cite> module or generated on demand according to the module's current settings).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.SignalinkPathways.coverage" title="pypath.core.annot.SignalinkPathways.coverage"><code class="xref py py-obj docutils literal notranslate"><span class="pre">coverage</span></code></a>(other)</p></td>
+<td><p>Calculates the coverage of the annotation i.e. the proportion of entities having at least one record in this annotation resource for an arbitrary set of entities.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.SignalinkPathways.curation_effort" title="pypath.core.annot.SignalinkPathways.curation_effort"><code class="xref py py-obj docutils literal notranslate"><span class="pre">curation_effort</span></code></a>()</p></td>
+<td><p>Counts the reference-record pairs.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">from_dump</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_entity_type</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.SignalinkPathways.get_names" title="pypath.core.annot.SignalinkPathways.get_names"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_names</span></code></a>()</p></td>
+<td><p>Returns the list of field names in the records.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.SignalinkPathways.get_reference_set" title="pypath.core.annot.SignalinkPathways.get_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_reference_set</span></code></a>([proteins, complexes, ...])</p></td>
+<td><p>Retrieves the reference set i.e. the set of all entities which potentially have annotation in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.SignalinkPathways.get_subset" title="pypath.core.annot.SignalinkPathways.get_subset"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.SignalinkPathways.get_subset_bool_array" title="pypath.core.annot.SignalinkPathways.get_subset_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset_bool_array</span></code></a>([reference_set])</p></td>
+<td><p>Returns a boolean vector with True and False values for each entity in the reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.SignalinkPathways.get_values" title="pypath.core.annot.SignalinkPathways.get_values"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_values</span></code></a>(name[, exclude_none])</p></td>
+<td><p>Returns the set of all possible values of a field.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_complex</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_mirna</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_protein</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.SignalinkPathways.labels" title="pypath.core.annot.SignalinkPathways.labels"><code class="xref py py-obj docutils literal notranslate"><span class="pre">labels</span></code></a>([method])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.SignalinkPathways.load" title="pypath.core.annot.SignalinkPathways.load"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load</span></code></a>()</p></td>
+<td><p>Loads the annotation data by calling the input method.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.SignalinkPathways.load_data" title="pypath.core.annot.SignalinkPathways.load_data"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_data</span></code></a>()</p></td>
+<td><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.SignalinkPathways.load_proteins" title="pypath.core.annot.SignalinkPathways.load_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_proteins</span></code></a>()</p></td>
+<td><p>Retrieves a set of all UniProt IDs to have a base set of the entire proteome.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.SignalinkPathways.make_df" title="pypath.core.annot.SignalinkPathways.make_df"><code class="xref py py-obj docutils literal notranslate"><span class="pre">make_df</span></code></a>([rebuild])</p></td>
+<td><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complex_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.SignalinkPathways.numof_entities" title="pypath.core.annot.SignalinkPathways.numof_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_entities</span></code></a>()</p></td>
+<td><p>The number of annotated entities in the resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirna_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirnas</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_protein_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_proteins</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.SignalinkPathways.numof_records" title="pypath.core.annot.SignalinkPathways.numof_records"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_records</span></code></a>([entity_types])</p></td>
+<td><p>The total number of annotation records.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.SignalinkPathways.numof_references" title="pypath.core.annot.SignalinkPathways.numof_references"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_references</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.SignalinkPathways.process" title="pypath.core.annot.SignalinkPathways.process"><code class="xref py py-obj docutils literal notranslate"><span class="pre">process</span></code></a>()</p></td>
+<td><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">proportion</span></code>(other)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.SignalinkPathways.reload" title="pypath.core.annot.SignalinkPathways.reload"><code class="xref py py-obj docutils literal notranslate"><span class="pre">reload</span></code></a>()</p></td>
+<td><p>Reloads the object from the module level.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">save_to_pickle</span></code>(pickle_file)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.SignalinkPathways.select" title="pypath.core.annot.SignalinkPathways.select"><code class="xref py py-obj docutils literal notranslate"><span class="pre">select</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.SignalinkPathways.set_method" title="pypath.core.annot.SignalinkPathways.set_method"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_method</span></code></a>()</p></td>
+<td><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if necessary.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.SignalinkPathways.set_reference_set" title="pypath.core.annot.SignalinkPathways.set_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_reference_set</span></code></a>()</p></td>
+<td><p>Assigns the reference set to the :py:attr``reference_set`` attribute.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.SignalinkPathways.show" title="pypath.core.annot.SignalinkPathways.show"><code class="xref py py-obj docutils literal notranslate"><span class="pre">show</span></code></a>([method, table_param])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic information from the UniProt datasheets.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.SignalinkPathways.subset_intersection" title="pypath.core.annot.SignalinkPathways.subset_intersection"><code class="xref py py-obj docutils literal notranslate"><span class="pre">subset_intersection</span></code></a>(universe, **kwargs)</p></td>
+<td><p>Calculates the proportion of entities in a subset occuring in the set <code class="docutils literal notranslate"><span class="pre">universe</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.SignalinkPathways.to_array" title="pypath.core.annot.SignalinkPathways.to_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_array</span></code></a>([reference_set, use_fields])</p></td>
+<td><p>Returns an entity vs feature array.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.SignalinkPathways.to_bool_array" title="pypath.core.annot.SignalinkPathways.to_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_bool_array</span></code></a>(reference_set)</p></td>
+<td><p>Returns a presence/absence boolean array for a reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.SignalinkPathways.to_set" title="pypath.core.annot.SignalinkPathways.to_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_set</span></code></a>()</p></td>
+<td><p>Returns the entities present in this annotation resource as a set.</p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Attributes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_fields</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">summary</span></code></p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.SignalinkPathways.add_complexes_by_inference">
+<span class="sig-name descname"><span class="pre">add_complexes_by_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.SignalinkPathways.add_complexes_by_inference" title="Link to this definition">§</a></dt>
+<dd><p>Creates complex annotations by in silico inference and adds them
+to this annotation set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.SignalinkPathways.all_complexes">
+<span class="sig-name descname"><span class="pre">all_complexes</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.SignalinkPathways.all_complexes" title="Link to this definition">§</a></dt>
+<dd><p>All protein complexes annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.SignalinkPathways.all_entities">
+<span class="sig-name descname"><span class="pre">all_entities</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.SignalinkPathways.all_entities" title="Link to this definition">§</a></dt>
+<dd><p>All entities annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.SignalinkPathways.all_mirnas">
+<span class="sig-name descname"><span class="pre">all_mirnas</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.SignalinkPathways.all_mirnas" title="Link to this definition">§</a></dt>
+<dd><p>All miRNAs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.SignalinkPathways.all_proteins">
+<span class="sig-name descname"><span class="pre">all_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.SignalinkPathways.all_proteins" title="Link to this definition">§</a></dt>
+<dd><p>All UniProt IDs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.SignalinkPathways.all_refs">
+<span class="sig-name descname"><span class="pre">all_refs</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.SignalinkPathways.all_refs" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects the references
+across all records. Returns <em>list</em>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.SignalinkPathways.annotate_complex">
+<span class="sig-name descname"><span class="pre">annotate_complex</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cplex</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.SignalinkPathways.annotate_complex" title="Link to this definition">§</a></dt>
+<dd><p>Infers annotations for a single complex.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.SignalinkPathways.browse">
+<span class="sig-name descname"><span class="pre">browse</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">field</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">start</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.SignalinkPathways.browse" title="Link to this definition">§</a></dt>
+<dd><p>Print gene information as a table.</p>
+<p>Presents information about annotation categories as ascii tables
+printed in the terminal. If one category provided, prints one table.
+If multiple categories provided, prints a table for each of them one
+by one proceeding to the next one once you hit return. If no categories
+provided goes through all levels of the primary category.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>field:</dt><dd><p>The field to browse categories by.</p>
+<ul class="simple">
+<li><p>If None the primary field will be selected.
+If this annotation resource doesn’t have fields, all proteins
+will be presented as one single category.</p></li>
+<li><p>If a string it will be considered a field name and it will
+browse through all levels of this field.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">list</span></code>, set or tuple, it will be considered either a
+<code class="docutils literal notranslate"><span class="pre">list</span></code> of field names or a list of values from the primary
+field. In the former case all combinations of the values of
+the fields will be presented, in the latter case the browsing
+will be limited to the levels of the primary field contained
+in <code class="docutils literal notranslate"><span class="pre">field</span></code>.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">dict</span></code>, keys are supposed to be field names and values
+as list of levels. If any of the values are None, all levels
+from that field will be used.</p></li>
+</ul>
+</dd>
+<dt>start:</dt><dd><p>Start browsing from this category. E.g. if there are 500
+categories and start is 250 it will skip everything before the
+250th.</p>
+</dd>
+<dt>kwargs:</dt><dd><p>Passed to <code class="docutils literal notranslate"><span class="pre">pypath.utils.uniprot.info</span></code>.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.SignalinkPathways.complex_inference">
+<span class="sig-name descname"><span class="pre">complex_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.SignalinkPathways.complex_inference" title="Link to this definition">§</a></dt>
+<dd><p>Annotates all complexes in <cite>complexes</cite>, by default in the default
+complex database (existing in the <cite>complex</cite> module or generated
+on demand according to the module’s current settings).</p>
+<dl class="field-list simple">
+<dt class="field-odd">Returns<span class="colon">:</span></dt>
+<dd class="field-odd"><p><ul class="simple">
+<li><p><em>Dict with complexes as keys and sets of annotations as values.</em></p></li>
+<li><p><em>Complexes with no valid information in this annotation resource</em></p></li>
+<li><p><em>won’t be in the dict.</em></p></li>
+</ul>
+</p>
+</dd>
+<dt class="field-even">Parameters<span class="colon">:</span></dt>
+<dd class="field-even"><p><strong>complexes</strong> (<em>iterable</em>) – Iterable yielding complexes.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.SignalinkPathways.coverage">
+<span class="sig-name descname"><span class="pre">coverage</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">other</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.SignalinkPathways.coverage" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the coverage of the annotation i.e. the proportion of
+entities having at least one record in this annotation resource
+for an arbitrary set of entities.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.SignalinkPathways.curation_effort">
+<span class="sig-name descname"><span class="pre">curation_effort</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.SignalinkPathways.curation_effort" title="Link to this definition">§</a></dt>
+<dd><p>Counts the reference-record pairs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.SignalinkPathways.get_names">
+<span class="sig-name descname"><span class="pre">get_names</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.SignalinkPathways.get_names" title="Link to this definition">§</a></dt>
+<dd><p>Returns the list of field names in the records. The annotation
+consists of uniform records and each entity might be annotated
+with one or more records. Each record is a tuple of fields, for
+example <code class="docutils literal notranslate"><span class="pre">('cell_type',</span> <span class="pre">'expression_level',</span> <span class="pre">'score')</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.SignalinkPathways.get_reference_set">
+<em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">get_reference_set</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">proteins</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">swissprot_only</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.SignalinkPathways.get_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the reference set i.e. the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.SignalinkPathways.get_subset">
+<span class="sig-name descname"><span class="pre">get_subset</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.SignalinkPathways.get_subset" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.SignalinkPathways.get_subset_bool_array">
+<span class="sig-name descname"><span class="pre">get_subset_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.SignalinkPathways.get_subset_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a boolean vector with True and False values for each entity
+in the reference set. The values represent presence absence data
+in the simplest case, but by providing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> any kind of matching
+and filtering is possible. <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> are passed to the <code class="docutils literal notranslate"><span class="pre">select</span></code>
+method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.SignalinkPathways.get_values">
+<span class="sig-name descname"><span class="pre">get_values</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">exclude_none</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.SignalinkPathways.get_values" title="Link to this definition">§</a></dt>
+<dd><p>Returns the set of all possible values of a field. E.g. if the
+records of this annotation have a field <code class="docutils literal notranslate"><span class="pre">cell_type</span></code> then calling
+this method can tell you that across all records the values of
+this field might be <code class="docutils literal notranslate"><span class="pre">{'macrophage',</span> <span class="pre">'epithelial_cell',</span> <span class="pre">...}</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.SignalinkPathways.labels">
+<span class="sig-name descname"><span class="pre">labels</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.SignalinkPathways.labels" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.SignalinkPathways.load">
+<span class="sig-name descname"><span class="pre">load</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.SignalinkPathways.load" title="Link to this definition">§</a></dt>
+<dd><p>Loads the annotation data by calling the input method.
+Infers annotations for complexes in the complex database if
+py:attr:<code class="docutils literal notranslate"><span class="pre">infer_complexes</span></code> is True.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.SignalinkPathways.load_data">
+<span class="sig-name descname"><span class="pre">load_data</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.SignalinkPathways.load_data" title="Link to this definition">§</a></dt>
+<dd><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.SignalinkPathways.load_proteins">
+<span class="sig-name descname"><span class="pre">load_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.SignalinkPathways.load_proteins" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a set of all UniProt IDs to have a base set of the entire
+proteome.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.SignalinkPathways.make_df">
+<span class="sig-name descname"><span class="pre">make_df</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">rebuild</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.SignalinkPathways.make_df" title="Link to this definition">§</a></dt>
+<dd><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.
+The data frame will be assigned to :py:attr``df``.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.SignalinkPathways.numof_entities">
+<span class="sig-name descname"><span class="pre">numof_entities</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.SignalinkPathways.numof_entities" title="Link to this definition">§</a></dt>
+<dd><p>The number of annotated entities in the resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.SignalinkPathways.numof_records">
+<span class="sig-name descname"><span class="pre">numof_records</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.SignalinkPathways.numof_records" title="Link to this definition">§</a></dt>
+<dd><p>The total number of annotation records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.SignalinkPathways.numof_references">
+<span class="sig-name descname"><span class="pre">numof_references</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.SignalinkPathways.numof_references" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects and counts the
+references across all records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.SignalinkPathways.process">
+<span class="sig-name descname"><span class="pre">process</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.SignalinkPathways.process" title="Link to this definition">§</a></dt>
+<dd><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.SignalinkPathways.reload">
+<span class="sig-name descname"><span class="pre">reload</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.SignalinkPathways.reload" title="Link to this definition">§</a></dt>
+<dd><p>Reloads the object from the module level.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.SignalinkPathways.select">
+<span class="sig-name descname"><span class="pre">select</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.SignalinkPathways.select" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.SignalinkPathways.set_method">
+<span class="sig-name descname"><span class="pre">set_method</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.SignalinkPathways.set_method" title="Link to this definition">§</a></dt>
+<dd><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if
+necessary.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.SignalinkPathways.set_reference_set">
+<span class="sig-name descname"><span class="pre">set_reference_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.SignalinkPathways.set_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Assigns the reference set to the :py:attr``reference_set`` attribute.
+The reference set is the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.SignalinkPathways.show">
+<span class="sig-name descname"><span class="pre">show</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">table_param</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.SignalinkPathways.show" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic
+information from the UniProt datasheets.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.SignalinkPathways.subset_intersection">
+<span class="sig-name descname"><span class="pre">subset_intersection</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">universe</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.SignalinkPathways.subset_intersection" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the proportion of entities in a subset occuring in the
+set <code class="docutils literal notranslate"><span class="pre">universe</span></code>. The subset is selected by passing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> to the
+<code class="docutils literal notranslate"><span class="pre">select</span></code> method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.SignalinkPathways.to_array">
+<span class="sig-name descname"><span class="pre">to_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_fields</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.SignalinkPathways.to_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns an entity vs feature array. In case of more complex
+annotations this might be huge.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.SignalinkPathways.to_bool_array">
+<span class="sig-name descname"><span class="pre">to_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.SignalinkPathways.to_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a presence/absence boolean array for a reference set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.SignalinkPathways.to_set">
+<span class="sig-name descname"><span class="pre">to_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.SignalinkPathways.to_set" title="Link to this definition">§</a></dt>
+<dd><p>Returns the entities present in this annotation resource as a set.</p>
+</dd></dl>
+
+</dd></dl>
+
+</section>
+
+
+                </article>
+              
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+  <section id="pypath-core-annot-signorpathways">
+<h1>pypath.core.annot.SignorPathways<a class="headerlink" href="#pypath-core-annot-signorpathways" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.core.annot.SignorPathways">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.core.annot.</span></span><span class="sig-name descname"><span class="pre">SignorPathways</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#SignorPathways"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.SignorPathways" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <a class="reference internal" href="pypath.core.annot.AnnotationBase.html#pypath.core.annot.AnnotationBase" title="pypath.core.annot.AnnotationBase"><code class="xref py py-class docutils literal notranslate"><span class="pre">AnnotationBase</span></code></a></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.SignorPathways.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#SignorPathways.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.SignorPathways.__init__" title="Link to this definition">§</a></dt>
+<dd><p>Pathway annotations from Signor.</p>
+</dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.SignorPathways.__init__" title="pypath.core.annot.SignorPathways.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>([ncbi_tax_id])</p></td>
+<td><p>Pathway annotations from Signor.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.SignorPathways.add_complexes_by_inference" title="pypath.core.annot.SignorPathways.add_complexes_by_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">add_complexes_by_inference</span></code></a>([complexes])</p></td>
+<td><p>Creates complex annotations by in silico inference and adds them to this annotation set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.SignorPathways.all_complexes" title="pypath.core.annot.SignorPathways.all_complexes"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_complexes</span></code></a>()</p></td>
+<td><p>All protein complexes annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.SignorPathways.all_entities" title="pypath.core.annot.SignorPathways.all_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_entities</span></code></a>([entity_types])</p></td>
+<td><p>All entities annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.SignorPathways.all_mirnas" title="pypath.core.annot.SignorPathways.all_mirnas"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_mirnas</span></code></a>()</p></td>
+<td><p>All miRNAs annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.SignorPathways.all_proteins" title="pypath.core.annot.SignorPathways.all_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_proteins</span></code></a>()</p></td>
+<td><p>All UniProt IDs annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.SignorPathways.all_refs" title="pypath.core.annot.SignorPathways.all_refs"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_refs</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.SignorPathways.annotate_complex" title="pypath.core.annot.SignorPathways.annotate_complex"><code class="xref py py-obj docutils literal notranslate"><span class="pre">annotate_complex</span></code></a>(cplex)</p></td>
+<td><p>Infers annotations for a single complex.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.SignorPathways.browse" title="pypath.core.annot.SignorPathways.browse"><code class="xref py py-obj docutils literal notranslate"><span class="pre">browse</span></code></a>([field, start])</p></td>
+<td><p>Print gene information as a table.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.SignorPathways.complex_inference" title="pypath.core.annot.SignorPathways.complex_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">complex_inference</span></code></a>([complexes])</p></td>
+<td><p>Annotates all complexes in <cite>complexes</cite>, by default in the default complex database (existing in the <cite>complex</cite> module or generated on demand according to the module's current settings).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.SignorPathways.coverage" title="pypath.core.annot.SignorPathways.coverage"><code class="xref py py-obj docutils literal notranslate"><span class="pre">coverage</span></code></a>(other)</p></td>
+<td><p>Calculates the coverage of the annotation i.e. the proportion of entities having at least one record in this annotation resource for an arbitrary set of entities.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.SignorPathways.curation_effort" title="pypath.core.annot.SignorPathways.curation_effort"><code class="xref py py-obj docutils literal notranslate"><span class="pre">curation_effort</span></code></a>()</p></td>
+<td><p>Counts the reference-record pairs.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">from_dump</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_entity_type</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.SignorPathways.get_names" title="pypath.core.annot.SignorPathways.get_names"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_names</span></code></a>()</p></td>
+<td><p>Returns the list of field names in the records.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.SignorPathways.get_reference_set" title="pypath.core.annot.SignorPathways.get_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_reference_set</span></code></a>([proteins, complexes, ...])</p></td>
+<td><p>Retrieves the reference set i.e. the set of all entities which potentially have annotation in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.SignorPathways.get_subset" title="pypath.core.annot.SignorPathways.get_subset"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.SignorPathways.get_subset_bool_array" title="pypath.core.annot.SignorPathways.get_subset_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset_bool_array</span></code></a>([reference_set])</p></td>
+<td><p>Returns a boolean vector with True and False values for each entity in the reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.SignorPathways.get_values" title="pypath.core.annot.SignorPathways.get_values"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_values</span></code></a>(name[, exclude_none])</p></td>
+<td><p>Returns the set of all possible values of a field.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_complex</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_mirna</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_protein</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.SignorPathways.labels" title="pypath.core.annot.SignorPathways.labels"><code class="xref py py-obj docutils literal notranslate"><span class="pre">labels</span></code></a>([method])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.SignorPathways.load" title="pypath.core.annot.SignorPathways.load"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load</span></code></a>()</p></td>
+<td><p>Loads the annotation data by calling the input method.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.SignorPathways.load_data" title="pypath.core.annot.SignorPathways.load_data"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_data</span></code></a>()</p></td>
+<td><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.SignorPathways.load_proteins" title="pypath.core.annot.SignorPathways.load_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_proteins</span></code></a>()</p></td>
+<td><p>Retrieves a set of all UniProt IDs to have a base set of the entire proteome.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.SignorPathways.make_df" title="pypath.core.annot.SignorPathways.make_df"><code class="xref py py-obj docutils literal notranslate"><span class="pre">make_df</span></code></a>([rebuild])</p></td>
+<td><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complex_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.SignorPathways.numof_entities" title="pypath.core.annot.SignorPathways.numof_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_entities</span></code></a>()</p></td>
+<td><p>The number of annotated entities in the resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirna_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirnas</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_protein_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_proteins</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.SignorPathways.numof_records" title="pypath.core.annot.SignorPathways.numof_records"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_records</span></code></a>([entity_types])</p></td>
+<td><p>The total number of annotation records.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.SignorPathways.numof_references" title="pypath.core.annot.SignorPathways.numof_references"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_references</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.SignorPathways.process" title="pypath.core.annot.SignorPathways.process"><code class="xref py py-obj docutils literal notranslate"><span class="pre">process</span></code></a>()</p></td>
+<td><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">proportion</span></code>(other)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.SignorPathways.reload" title="pypath.core.annot.SignorPathways.reload"><code class="xref py py-obj docutils literal notranslate"><span class="pre">reload</span></code></a>()</p></td>
+<td><p>Reloads the object from the module level.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">save_to_pickle</span></code>(pickle_file)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.SignorPathways.select" title="pypath.core.annot.SignorPathways.select"><code class="xref py py-obj docutils literal notranslate"><span class="pre">select</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.SignorPathways.set_method" title="pypath.core.annot.SignorPathways.set_method"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_method</span></code></a>()</p></td>
+<td><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if necessary.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.SignorPathways.set_reference_set" title="pypath.core.annot.SignorPathways.set_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_reference_set</span></code></a>()</p></td>
+<td><p>Assigns the reference set to the :py:attr``reference_set`` attribute.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.SignorPathways.show" title="pypath.core.annot.SignorPathways.show"><code class="xref py py-obj docutils literal notranslate"><span class="pre">show</span></code></a>([method, table_param])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic information from the UniProt datasheets.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.SignorPathways.subset_intersection" title="pypath.core.annot.SignorPathways.subset_intersection"><code class="xref py py-obj docutils literal notranslate"><span class="pre">subset_intersection</span></code></a>(universe, **kwargs)</p></td>
+<td><p>Calculates the proportion of entities in a subset occuring in the set <code class="docutils literal notranslate"><span class="pre">universe</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.SignorPathways.to_array" title="pypath.core.annot.SignorPathways.to_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_array</span></code></a>([reference_set, use_fields])</p></td>
+<td><p>Returns an entity vs feature array.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.SignorPathways.to_bool_array" title="pypath.core.annot.SignorPathways.to_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_bool_array</span></code></a>(reference_set)</p></td>
+<td><p>Returns a presence/absence boolean array for a reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.SignorPathways.to_set" title="pypath.core.annot.SignorPathways.to_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_set</span></code></a>()</p></td>
+<td><p>Returns the entities present in this annotation resource as a set.</p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Attributes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_fields</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">summary</span></code></p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.SignorPathways.add_complexes_by_inference">
+<span class="sig-name descname"><span class="pre">add_complexes_by_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.SignorPathways.add_complexes_by_inference" title="Link to this definition">§</a></dt>
+<dd><p>Creates complex annotations by in silico inference and adds them
+to this annotation set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.SignorPathways.all_complexes">
+<span class="sig-name descname"><span class="pre">all_complexes</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.SignorPathways.all_complexes" title="Link to this definition">§</a></dt>
+<dd><p>All protein complexes annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.SignorPathways.all_entities">
+<span class="sig-name descname"><span class="pre">all_entities</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.SignorPathways.all_entities" title="Link to this definition">§</a></dt>
+<dd><p>All entities annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.SignorPathways.all_mirnas">
+<span class="sig-name descname"><span class="pre">all_mirnas</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.SignorPathways.all_mirnas" title="Link to this definition">§</a></dt>
+<dd><p>All miRNAs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.SignorPathways.all_proteins">
+<span class="sig-name descname"><span class="pre">all_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.SignorPathways.all_proteins" title="Link to this definition">§</a></dt>
+<dd><p>All UniProt IDs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.SignorPathways.all_refs">
+<span class="sig-name descname"><span class="pre">all_refs</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.SignorPathways.all_refs" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects the references
+across all records. Returns <em>list</em>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.SignorPathways.annotate_complex">
+<span class="sig-name descname"><span class="pre">annotate_complex</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cplex</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.SignorPathways.annotate_complex" title="Link to this definition">§</a></dt>
+<dd><p>Infers annotations for a single complex.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.SignorPathways.browse">
+<span class="sig-name descname"><span class="pre">browse</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">field</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">start</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.SignorPathways.browse" title="Link to this definition">§</a></dt>
+<dd><p>Print gene information as a table.</p>
+<p>Presents information about annotation categories as ascii tables
+printed in the terminal. If one category provided, prints one table.
+If multiple categories provided, prints a table for each of them one
+by one proceeding to the next one once you hit return. If no categories
+provided goes through all levels of the primary category.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>field:</dt><dd><p>The field to browse categories by.</p>
+<ul class="simple">
+<li><p>If None the primary field will be selected.
+If this annotation resource doesn’t have fields, all proteins
+will be presented as one single category.</p></li>
+<li><p>If a string it will be considered a field name and it will
+browse through all levels of this field.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">list</span></code>, set or tuple, it will be considered either a
+<code class="docutils literal notranslate"><span class="pre">list</span></code> of field names or a list of values from the primary
+field. In the former case all combinations of the values of
+the fields will be presented, in the latter case the browsing
+will be limited to the levels of the primary field contained
+in <code class="docutils literal notranslate"><span class="pre">field</span></code>.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">dict</span></code>, keys are supposed to be field names and values
+as list of levels. If any of the values are None, all levels
+from that field will be used.</p></li>
+</ul>
+</dd>
+<dt>start:</dt><dd><p>Start browsing from this category. E.g. if there are 500
+categories and start is 250 it will skip everything before the
+250th.</p>
+</dd>
+<dt>kwargs:</dt><dd><p>Passed to <code class="docutils literal notranslate"><span class="pre">pypath.utils.uniprot.info</span></code>.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.SignorPathways.complex_inference">
+<span class="sig-name descname"><span class="pre">complex_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.SignorPathways.complex_inference" title="Link to this definition">§</a></dt>
+<dd><p>Annotates all complexes in <cite>complexes</cite>, by default in the default
+complex database (existing in the <cite>complex</cite> module or generated
+on demand according to the module’s current settings).</p>
+<dl class="field-list simple">
+<dt class="field-odd">Returns<span class="colon">:</span></dt>
+<dd class="field-odd"><p><ul class="simple">
+<li><p><em>Dict with complexes as keys and sets of annotations as values.</em></p></li>
+<li><p><em>Complexes with no valid information in this annotation resource</em></p></li>
+<li><p><em>won’t be in the dict.</em></p></li>
+</ul>
+</p>
+</dd>
+<dt class="field-even">Parameters<span class="colon">:</span></dt>
+<dd class="field-even"><p><strong>complexes</strong> (<em>iterable</em>) – Iterable yielding complexes.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.SignorPathways.coverage">
+<span class="sig-name descname"><span class="pre">coverage</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">other</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.SignorPathways.coverage" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the coverage of the annotation i.e. the proportion of
+entities having at least one record in this annotation resource
+for an arbitrary set of entities.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.SignorPathways.curation_effort">
+<span class="sig-name descname"><span class="pre">curation_effort</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.SignorPathways.curation_effort" title="Link to this definition">§</a></dt>
+<dd><p>Counts the reference-record pairs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.SignorPathways.get_names">
+<span class="sig-name descname"><span class="pre">get_names</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.SignorPathways.get_names" title="Link to this definition">§</a></dt>
+<dd><p>Returns the list of field names in the records. The annotation
+consists of uniform records and each entity might be annotated
+with one or more records. Each record is a tuple of fields, for
+example <code class="docutils literal notranslate"><span class="pre">('cell_type',</span> <span class="pre">'expression_level',</span> <span class="pre">'score')</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.SignorPathways.get_reference_set">
+<em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">get_reference_set</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">proteins</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">swissprot_only</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.SignorPathways.get_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the reference set i.e. the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.SignorPathways.get_subset">
+<span class="sig-name descname"><span class="pre">get_subset</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.SignorPathways.get_subset" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.SignorPathways.get_subset_bool_array">
+<span class="sig-name descname"><span class="pre">get_subset_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.SignorPathways.get_subset_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a boolean vector with True and False values for each entity
+in the reference set. The values represent presence absence data
+in the simplest case, but by providing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> any kind of matching
+and filtering is possible. <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> are passed to the <code class="docutils literal notranslate"><span class="pre">select</span></code>
+method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.SignorPathways.get_values">
+<span class="sig-name descname"><span class="pre">get_values</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">exclude_none</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.SignorPathways.get_values" title="Link to this definition">§</a></dt>
+<dd><p>Returns the set of all possible values of a field. E.g. if the
+records of this annotation have a field <code class="docutils literal notranslate"><span class="pre">cell_type</span></code> then calling
+this method can tell you that across all records the values of
+this field might be <code class="docutils literal notranslate"><span class="pre">{'macrophage',</span> <span class="pre">'epithelial_cell',</span> <span class="pre">...}</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.SignorPathways.labels">
+<span class="sig-name descname"><span class="pre">labels</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.SignorPathways.labels" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.SignorPathways.load">
+<span class="sig-name descname"><span class="pre">load</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.SignorPathways.load" title="Link to this definition">§</a></dt>
+<dd><p>Loads the annotation data by calling the input method.
+Infers annotations for complexes in the complex database if
+py:attr:<code class="docutils literal notranslate"><span class="pre">infer_complexes</span></code> is True.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.SignorPathways.load_data">
+<span class="sig-name descname"><span class="pre">load_data</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.SignorPathways.load_data" title="Link to this definition">§</a></dt>
+<dd><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.SignorPathways.load_proteins">
+<span class="sig-name descname"><span class="pre">load_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.SignorPathways.load_proteins" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a set of all UniProt IDs to have a base set of the entire
+proteome.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.SignorPathways.make_df">
+<span class="sig-name descname"><span class="pre">make_df</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">rebuild</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.SignorPathways.make_df" title="Link to this definition">§</a></dt>
+<dd><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.
+The data frame will be assigned to :py:attr``df``.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.SignorPathways.numof_entities">
+<span class="sig-name descname"><span class="pre">numof_entities</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.SignorPathways.numof_entities" title="Link to this definition">§</a></dt>
+<dd><p>The number of annotated entities in the resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.SignorPathways.numof_records">
+<span class="sig-name descname"><span class="pre">numof_records</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.SignorPathways.numof_records" title="Link to this definition">§</a></dt>
+<dd><p>The total number of annotation records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.SignorPathways.numof_references">
+<span class="sig-name descname"><span class="pre">numof_references</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.SignorPathways.numof_references" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects and counts the
+references across all records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.SignorPathways.process">
+<span class="sig-name descname"><span class="pre">process</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.SignorPathways.process" title="Link to this definition">§</a></dt>
+<dd><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.SignorPathways.reload">
+<span class="sig-name descname"><span class="pre">reload</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.SignorPathways.reload" title="Link to this definition">§</a></dt>
+<dd><p>Reloads the object from the module level.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.SignorPathways.select">
+<span class="sig-name descname"><span class="pre">select</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.SignorPathways.select" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.SignorPathways.set_method">
+<span class="sig-name descname"><span class="pre">set_method</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.SignorPathways.set_method" title="Link to this definition">§</a></dt>
+<dd><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if
+necessary.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.SignorPathways.set_reference_set">
+<span class="sig-name descname"><span class="pre">set_reference_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.SignorPathways.set_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Assigns the reference set to the :py:attr``reference_set`` attribute.
+The reference set is the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.SignorPathways.show">
+<span class="sig-name descname"><span class="pre">show</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">table_param</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.SignorPathways.show" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic
+information from the UniProt datasheets.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.SignorPathways.subset_intersection">
+<span class="sig-name descname"><span class="pre">subset_intersection</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">universe</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.SignorPathways.subset_intersection" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the proportion of entities in a subset occuring in the
+set <code class="docutils literal notranslate"><span class="pre">universe</span></code>. The subset is selected by passing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> to the
+<code class="docutils literal notranslate"><span class="pre">select</span></code> method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.SignorPathways.to_array">
+<span class="sig-name descname"><span class="pre">to_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_fields</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.SignorPathways.to_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns an entity vs feature array. In case of more complex
+annotations this might be huge.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.SignorPathways.to_bool_array">
+<span class="sig-name descname"><span class="pre">to_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.SignorPathways.to_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a presence/absence boolean array for a reference set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.SignorPathways.to_set">
+<span class="sig-name descname"><span class="pre">to_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.SignorPathways.to_set" title="Link to this definition">§</a></dt>
+<dd><p>Returns the entities present in this annotation resource as a set.</p>
+</dd></dl>
+
+</dd></dl>
+
+</section>
+
+
+                </article>
+              
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+  <section id="pypath-core-annot-surfaceome">
+<h1>pypath.core.annot.Surfaceome<a class="headerlink" href="#pypath-core-annot-surfaceome" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.core.annot.Surfaceome">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.core.annot.</span></span><span class="sig-name descname"><span class="pre">Surfaceome</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#Surfaceome"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.Surfaceome" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <a class="reference internal" href="pypath.core.annot.AnnotationBase.html#pypath.core.annot.AnnotationBase" title="pypath.core.annot.AnnotationBase"><code class="xref py py-class docutils literal notranslate"><span class="pre">AnnotationBase</span></code></a></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Surfaceome.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#Surfaceome.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.Surfaceome.__init__" title="Link to this definition">§</a></dt>
+<dd><p>Represents annotations for a set of proteins.
+Loads the data from the original resource and provides methods
+to query the annotations.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>name</strong> (<em>str</em>) – A custom name for the annotation resource.</p></li>
+<li><p><strong>ncbi_tax_id</strong> (<em>int</em>) – NCBI Taxonomy identifier.</p></li>
+<li><p><strong>input_method</strong> (<em>callable</em><em>,</em><em>str</em>) – Either a callable or the name of a method in any submodules of
+the <code class="docutils literal notranslate"><span class="pre">pypath.inputs</span></code>  module. Should return a dict with
+UniProt IDs as keys or an object suitable for <code class="docutils literal notranslate"><span class="pre">process_method</span></code>.</p></li>
+<li><p><strong>input_args</strong> (<em>dict</em>) – Arguments for the <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Surfaceome.__init__" title="pypath.core.annot.Surfaceome.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>(**kwargs)</p></td>
+<td><p>Represents annotations for a set of proteins.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Surfaceome.add_complexes_by_inference" title="pypath.core.annot.Surfaceome.add_complexes_by_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">add_complexes_by_inference</span></code></a>([complexes])</p></td>
+<td><p>Creates complex annotations by in silico inference and adds them to this annotation set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Surfaceome.all_complexes" title="pypath.core.annot.Surfaceome.all_complexes"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_complexes</span></code></a>()</p></td>
+<td><p>All protein complexes annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Surfaceome.all_entities" title="pypath.core.annot.Surfaceome.all_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_entities</span></code></a>([entity_types])</p></td>
+<td><p>All entities annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Surfaceome.all_mirnas" title="pypath.core.annot.Surfaceome.all_mirnas"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_mirnas</span></code></a>()</p></td>
+<td><p>All miRNAs annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Surfaceome.all_proteins" title="pypath.core.annot.Surfaceome.all_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_proteins</span></code></a>()</p></td>
+<td><p>All UniProt IDs annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Surfaceome.all_refs" title="pypath.core.annot.Surfaceome.all_refs"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_refs</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Surfaceome.annotate_complex" title="pypath.core.annot.Surfaceome.annotate_complex"><code class="xref py py-obj docutils literal notranslate"><span class="pre">annotate_complex</span></code></a>(cplex)</p></td>
+<td><p>Infers annotations for a single complex.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Surfaceome.browse" title="pypath.core.annot.Surfaceome.browse"><code class="xref py py-obj docutils literal notranslate"><span class="pre">browse</span></code></a>([field, start])</p></td>
+<td><p>Print gene information as a table.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Surfaceome.complex_inference" title="pypath.core.annot.Surfaceome.complex_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">complex_inference</span></code></a>([complexes])</p></td>
+<td><p>Annotates all complexes in <cite>complexes</cite>, by default in the default complex database (existing in the <cite>complex</cite> module or generated on demand according to the module's current settings).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Surfaceome.coverage" title="pypath.core.annot.Surfaceome.coverage"><code class="xref py py-obj docutils literal notranslate"><span class="pre">coverage</span></code></a>(other)</p></td>
+<td><p>Calculates the coverage of the annotation i.e. the proportion of entities having at least one record in this annotation resource for an arbitrary set of entities.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Surfaceome.curation_effort" title="pypath.core.annot.Surfaceome.curation_effort"><code class="xref py py-obj docutils literal notranslate"><span class="pre">curation_effort</span></code></a>()</p></td>
+<td><p>Counts the reference-record pairs.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">from_dump</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_entity_type</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Surfaceome.get_names" title="pypath.core.annot.Surfaceome.get_names"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_names</span></code></a>()</p></td>
+<td><p>Returns the list of field names in the records.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Surfaceome.get_reference_set" title="pypath.core.annot.Surfaceome.get_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_reference_set</span></code></a>([proteins, complexes, ...])</p></td>
+<td><p>Retrieves the reference set i.e. the set of all entities which potentially have annotation in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Surfaceome.get_subset" title="pypath.core.annot.Surfaceome.get_subset"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Surfaceome.get_subset_bool_array" title="pypath.core.annot.Surfaceome.get_subset_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset_bool_array</span></code></a>([reference_set])</p></td>
+<td><p>Returns a boolean vector with True and False values for each entity in the reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Surfaceome.get_values" title="pypath.core.annot.Surfaceome.get_values"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_values</span></code></a>(name[, exclude_none])</p></td>
+<td><p>Returns the set of all possible values of a field.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_complex</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_mirna</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_protein</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Surfaceome.labels" title="pypath.core.annot.Surfaceome.labels"><code class="xref py py-obj docutils literal notranslate"><span class="pre">labels</span></code></a>([method])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Surfaceome.load" title="pypath.core.annot.Surfaceome.load"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load</span></code></a>()</p></td>
+<td><p>Loads the annotation data by calling the input method.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Surfaceome.load_data" title="pypath.core.annot.Surfaceome.load_data"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_data</span></code></a>()</p></td>
+<td><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Surfaceome.load_proteins" title="pypath.core.annot.Surfaceome.load_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_proteins</span></code></a>()</p></td>
+<td><p>Retrieves a set of all UniProt IDs to have a base set of the entire proteome.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Surfaceome.make_df" title="pypath.core.annot.Surfaceome.make_df"><code class="xref py py-obj docutils literal notranslate"><span class="pre">make_df</span></code></a>([rebuild])</p></td>
+<td><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complex_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Surfaceome.numof_entities" title="pypath.core.annot.Surfaceome.numof_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_entities</span></code></a>()</p></td>
+<td><p>The number of annotated entities in the resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirna_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirnas</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_protein_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_proteins</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Surfaceome.numof_records" title="pypath.core.annot.Surfaceome.numof_records"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_records</span></code></a>([entity_types])</p></td>
+<td><p>The total number of annotation records.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Surfaceome.numof_references" title="pypath.core.annot.Surfaceome.numof_references"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_references</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Surfaceome.process" title="pypath.core.annot.Surfaceome.process"><code class="xref py py-obj docutils literal notranslate"><span class="pre">process</span></code></a>()</p></td>
+<td><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">proportion</span></code>(other)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Surfaceome.reload" title="pypath.core.annot.Surfaceome.reload"><code class="xref py py-obj docutils literal notranslate"><span class="pre">reload</span></code></a>()</p></td>
+<td><p>Reloads the object from the module level.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">save_to_pickle</span></code>(pickle_file)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Surfaceome.select" title="pypath.core.annot.Surfaceome.select"><code class="xref py py-obj docutils literal notranslate"><span class="pre">select</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Surfaceome.set_method" title="pypath.core.annot.Surfaceome.set_method"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_method</span></code></a>()</p></td>
+<td><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if necessary.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Surfaceome.set_reference_set" title="pypath.core.annot.Surfaceome.set_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_reference_set</span></code></a>()</p></td>
+<td><p>Assigns the reference set to the :py:attr``reference_set`` attribute.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Surfaceome.show" title="pypath.core.annot.Surfaceome.show"><code class="xref py py-obj docutils literal notranslate"><span class="pre">show</span></code></a>([method, table_param])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic information from the UniProt datasheets.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Surfaceome.subset_intersection" title="pypath.core.annot.Surfaceome.subset_intersection"><code class="xref py py-obj docutils literal notranslate"><span class="pre">subset_intersection</span></code></a>(universe, **kwargs)</p></td>
+<td><p>Calculates the proportion of entities in a subset occuring in the set <code class="docutils literal notranslate"><span class="pre">universe</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Surfaceome.to_array" title="pypath.core.annot.Surfaceome.to_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_array</span></code></a>([reference_set, use_fields])</p></td>
+<td><p>Returns an entity vs feature array.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Surfaceome.to_bool_array" title="pypath.core.annot.Surfaceome.to_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_bool_array</span></code></a>(reference_set)</p></td>
+<td><p>Returns a presence/absence boolean array for a reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Surfaceome.to_set" title="pypath.core.annot.Surfaceome.to_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_set</span></code></a>()</p></td>
+<td><p>Returns the entities present in this annotation resource as a set.</p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Attributes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_fields</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">summary</span></code></p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Surfaceome.add_complexes_by_inference">
+<span class="sig-name descname"><span class="pre">add_complexes_by_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Surfaceome.add_complexes_by_inference" title="Link to this definition">§</a></dt>
+<dd><p>Creates complex annotations by in silico inference and adds them
+to this annotation set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Surfaceome.all_complexes">
+<span class="sig-name descname"><span class="pre">all_complexes</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Surfaceome.all_complexes" title="Link to this definition">§</a></dt>
+<dd><p>All protein complexes annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Surfaceome.all_entities">
+<span class="sig-name descname"><span class="pre">all_entities</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Surfaceome.all_entities" title="Link to this definition">§</a></dt>
+<dd><p>All entities annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Surfaceome.all_mirnas">
+<span class="sig-name descname"><span class="pre">all_mirnas</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Surfaceome.all_mirnas" title="Link to this definition">§</a></dt>
+<dd><p>All miRNAs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Surfaceome.all_proteins">
+<span class="sig-name descname"><span class="pre">all_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Surfaceome.all_proteins" title="Link to this definition">§</a></dt>
+<dd><p>All UniProt IDs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Surfaceome.all_refs">
+<span class="sig-name descname"><span class="pre">all_refs</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Surfaceome.all_refs" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects the references
+across all records. Returns <em>list</em>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Surfaceome.annotate_complex">
+<span class="sig-name descname"><span class="pre">annotate_complex</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cplex</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Surfaceome.annotate_complex" title="Link to this definition">§</a></dt>
+<dd><p>Infers annotations for a single complex.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Surfaceome.browse">
+<span class="sig-name descname"><span class="pre">browse</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">field</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">start</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Surfaceome.browse" title="Link to this definition">§</a></dt>
+<dd><p>Print gene information as a table.</p>
+<p>Presents information about annotation categories as ascii tables
+printed in the terminal. If one category provided, prints one table.
+If multiple categories provided, prints a table for each of them one
+by one proceeding to the next one once you hit return. If no categories
+provided goes through all levels of the primary category.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>field:</dt><dd><p>The field to browse categories by.</p>
+<ul class="simple">
+<li><p>If None the primary field will be selected.
+If this annotation resource doesn’t have fields, all proteins
+will be presented as one single category.</p></li>
+<li><p>If a string it will be considered a field name and it will
+browse through all levels of this field.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">list</span></code>, set or tuple, it will be considered either a
+<code class="docutils literal notranslate"><span class="pre">list</span></code> of field names or a list of values from the primary
+field. In the former case all combinations of the values of
+the fields will be presented, in the latter case the browsing
+will be limited to the levels of the primary field contained
+in <code class="docutils literal notranslate"><span class="pre">field</span></code>.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">dict</span></code>, keys are supposed to be field names and values
+as list of levels. If any of the values are None, all levels
+from that field will be used.</p></li>
+</ul>
+</dd>
+<dt>start:</dt><dd><p>Start browsing from this category. E.g. if there are 500
+categories and start is 250 it will skip everything before the
+250th.</p>
+</dd>
+<dt>kwargs:</dt><dd><p>Passed to <code class="docutils literal notranslate"><span class="pre">pypath.utils.uniprot.info</span></code>.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Surfaceome.complex_inference">
+<span class="sig-name descname"><span class="pre">complex_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Surfaceome.complex_inference" title="Link to this definition">§</a></dt>
+<dd><p>Annotates all complexes in <cite>complexes</cite>, by default in the default
+complex database (existing in the <cite>complex</cite> module or generated
+on demand according to the module’s current settings).</p>
+<dl class="field-list simple">
+<dt class="field-odd">Returns<span class="colon">:</span></dt>
+<dd class="field-odd"><p><ul class="simple">
+<li><p><em>Dict with complexes as keys and sets of annotations as values.</em></p></li>
+<li><p><em>Complexes with no valid information in this annotation resource</em></p></li>
+<li><p><em>won’t be in the dict.</em></p></li>
+</ul>
+</p>
+</dd>
+<dt class="field-even">Parameters<span class="colon">:</span></dt>
+<dd class="field-even"><p><strong>complexes</strong> (<em>iterable</em>) – Iterable yielding complexes.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Surfaceome.coverage">
+<span class="sig-name descname"><span class="pre">coverage</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">other</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Surfaceome.coverage" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the coverage of the annotation i.e. the proportion of
+entities having at least one record in this annotation resource
+for an arbitrary set of entities.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Surfaceome.curation_effort">
+<span class="sig-name descname"><span class="pre">curation_effort</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Surfaceome.curation_effort" title="Link to this definition">§</a></dt>
+<dd><p>Counts the reference-record pairs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Surfaceome.get_names">
+<span class="sig-name descname"><span class="pre">get_names</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Surfaceome.get_names" title="Link to this definition">§</a></dt>
+<dd><p>Returns the list of field names in the records. The annotation
+consists of uniform records and each entity might be annotated
+with one or more records. Each record is a tuple of fields, for
+example <code class="docutils literal notranslate"><span class="pre">('cell_type',</span> <span class="pre">'expression_level',</span> <span class="pre">'score')</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Surfaceome.get_reference_set">
+<em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">get_reference_set</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">proteins</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">swissprot_only</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Surfaceome.get_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the reference set i.e. the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Surfaceome.get_subset">
+<span class="sig-name descname"><span class="pre">get_subset</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Surfaceome.get_subset" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Surfaceome.get_subset_bool_array">
+<span class="sig-name descname"><span class="pre">get_subset_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Surfaceome.get_subset_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a boolean vector with True and False values for each entity
+in the reference set. The values represent presence absence data
+in the simplest case, but by providing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> any kind of matching
+and filtering is possible. <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> are passed to the <code class="docutils literal notranslate"><span class="pre">select</span></code>
+method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Surfaceome.get_values">
+<span class="sig-name descname"><span class="pre">get_values</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">exclude_none</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Surfaceome.get_values" title="Link to this definition">§</a></dt>
+<dd><p>Returns the set of all possible values of a field. E.g. if the
+records of this annotation have a field <code class="docutils literal notranslate"><span class="pre">cell_type</span></code> then calling
+this method can tell you that across all records the values of
+this field might be <code class="docutils literal notranslate"><span class="pre">{'macrophage',</span> <span class="pre">'epithelial_cell',</span> <span class="pre">...}</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Surfaceome.labels">
+<span class="sig-name descname"><span class="pre">labels</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Surfaceome.labels" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Surfaceome.load">
+<span class="sig-name descname"><span class="pre">load</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Surfaceome.load" title="Link to this definition">§</a></dt>
+<dd><p>Loads the annotation data by calling the input method.
+Infers annotations for complexes in the complex database if
+py:attr:<code class="docutils literal notranslate"><span class="pre">infer_complexes</span></code> is True.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Surfaceome.load_data">
+<span class="sig-name descname"><span class="pre">load_data</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Surfaceome.load_data" title="Link to this definition">§</a></dt>
+<dd><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Surfaceome.load_proteins">
+<span class="sig-name descname"><span class="pre">load_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Surfaceome.load_proteins" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a set of all UniProt IDs to have a base set of the entire
+proteome.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Surfaceome.make_df">
+<span class="sig-name descname"><span class="pre">make_df</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">rebuild</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Surfaceome.make_df" title="Link to this definition">§</a></dt>
+<dd><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.
+The data frame will be assigned to :py:attr``df``.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Surfaceome.numof_entities">
+<span class="sig-name descname"><span class="pre">numof_entities</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Surfaceome.numof_entities" title="Link to this definition">§</a></dt>
+<dd><p>The number of annotated entities in the resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Surfaceome.numof_records">
+<span class="sig-name descname"><span class="pre">numof_records</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Surfaceome.numof_records" title="Link to this definition">§</a></dt>
+<dd><p>The total number of annotation records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Surfaceome.numof_references">
+<span class="sig-name descname"><span class="pre">numof_references</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Surfaceome.numof_references" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects and counts the
+references across all records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Surfaceome.process">
+<span class="sig-name descname"><span class="pre">process</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Surfaceome.process" title="Link to this definition">§</a></dt>
+<dd><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Surfaceome.reload">
+<span class="sig-name descname"><span class="pre">reload</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Surfaceome.reload" title="Link to this definition">§</a></dt>
+<dd><p>Reloads the object from the module level.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Surfaceome.select">
+<span class="sig-name descname"><span class="pre">select</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Surfaceome.select" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Surfaceome.set_method">
+<span class="sig-name descname"><span class="pre">set_method</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Surfaceome.set_method" title="Link to this definition">§</a></dt>
+<dd><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if
+necessary.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Surfaceome.set_reference_set">
+<span class="sig-name descname"><span class="pre">set_reference_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Surfaceome.set_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Assigns the reference set to the :py:attr``reference_set`` attribute.
+The reference set is the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Surfaceome.show">
+<span class="sig-name descname"><span class="pre">show</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">table_param</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Surfaceome.show" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic
+information from the UniProt datasheets.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Surfaceome.subset_intersection">
+<span class="sig-name descname"><span class="pre">subset_intersection</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">universe</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Surfaceome.subset_intersection" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the proportion of entities in a subset occuring in the
+set <code class="docutils literal notranslate"><span class="pre">universe</span></code>. The subset is selected by passing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> to the
+<code class="docutils literal notranslate"><span class="pre">select</span></code> method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Surfaceome.to_array">
+<span class="sig-name descname"><span class="pre">to_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_fields</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Surfaceome.to_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns an entity vs feature array. In case of more complex
+annotations this might be huge.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Surfaceome.to_bool_array">
+<span class="sig-name descname"><span class="pre">to_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Surfaceome.to_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a presence/absence boolean array for a reference set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Surfaceome.to_set">
+<span class="sig-name descname"><span class="pre">to_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Surfaceome.to_set" title="Link to this definition">§</a></dt>
+<dd><p>Returns the entities present in this annotation resource as a set.</p>
+</dd></dl>
+
+</dd></dl>
+
+</section>
+
+
+                </article>
+              
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+  <section id="pypath-core-annot-talklr">
+<h1>pypath.core.annot.Talklr<a class="headerlink" href="#pypath-core-annot-talklr" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.core.annot.Talklr">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.core.annot.</span></span><span class="sig-name descname"><span class="pre">Talklr</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#Talklr"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.Talklr" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <a class="reference internal" href="pypath.core.annot.AnnotationBase.html#pypath.core.annot.AnnotationBase" title="pypath.core.annot.AnnotationBase"><code class="xref py py-class docutils literal notranslate"><span class="pre">AnnotationBase</span></code></a></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Talklr.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#Talklr.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.Talklr.__init__" title="Link to this definition">§</a></dt>
+<dd><p>Represents annotations for a set of proteins.
+Loads the data from the original resource and provides methods
+to query the annotations.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>name</strong> (<em>str</em>) – A custom name for the annotation resource.</p></li>
+<li><p><strong>ncbi_tax_id</strong> (<em>int</em>) – NCBI Taxonomy identifier.</p></li>
+<li><p><strong>input_method</strong> (<em>callable</em><em>,</em><em>str</em>) – Either a callable or the name of a method in any submodules of
+the <code class="docutils literal notranslate"><span class="pre">pypath.inputs</span></code>  module. Should return a dict with
+UniProt IDs as keys or an object suitable for <code class="docutils literal notranslate"><span class="pre">process_method</span></code>.</p></li>
+<li><p><strong>input_args</strong> (<em>dict</em>) – Arguments for the <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Talklr.__init__" title="pypath.core.annot.Talklr.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>(**kwargs)</p></td>
+<td><p>Represents annotations for a set of proteins.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Talklr.add_complexes_by_inference" title="pypath.core.annot.Talklr.add_complexes_by_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">add_complexes_by_inference</span></code></a>([complexes])</p></td>
+<td><p>Creates complex annotations by in silico inference and adds them to this annotation set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Talklr.all_complexes" title="pypath.core.annot.Talklr.all_complexes"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_complexes</span></code></a>()</p></td>
+<td><p>All protein complexes annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Talklr.all_entities" title="pypath.core.annot.Talklr.all_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_entities</span></code></a>([entity_types])</p></td>
+<td><p>All entities annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Talklr.all_mirnas" title="pypath.core.annot.Talklr.all_mirnas"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_mirnas</span></code></a>()</p></td>
+<td><p>All miRNAs annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Talklr.all_proteins" title="pypath.core.annot.Talklr.all_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_proteins</span></code></a>()</p></td>
+<td><p>All UniProt IDs annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Talklr.all_refs" title="pypath.core.annot.Talklr.all_refs"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_refs</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Talklr.annotate_complex" title="pypath.core.annot.Talklr.annotate_complex"><code class="xref py py-obj docutils literal notranslate"><span class="pre">annotate_complex</span></code></a>(cplex)</p></td>
+<td><p>Infers annotations for a single complex.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Talklr.browse" title="pypath.core.annot.Talklr.browse"><code class="xref py py-obj docutils literal notranslate"><span class="pre">browse</span></code></a>([field, start])</p></td>
+<td><p>Print gene information as a table.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Talklr.complex_inference" title="pypath.core.annot.Talklr.complex_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">complex_inference</span></code></a>([complexes])</p></td>
+<td><p>Annotates all complexes in <cite>complexes</cite>, by default in the default complex database (existing in the <cite>complex</cite> module or generated on demand according to the module's current settings).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Talklr.coverage" title="pypath.core.annot.Talklr.coverage"><code class="xref py py-obj docutils literal notranslate"><span class="pre">coverage</span></code></a>(other)</p></td>
+<td><p>Calculates the coverage of the annotation i.e. the proportion of entities having at least one record in this annotation resource for an arbitrary set of entities.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Talklr.curation_effort" title="pypath.core.annot.Talklr.curation_effort"><code class="xref py py-obj docutils literal notranslate"><span class="pre">curation_effort</span></code></a>()</p></td>
+<td><p>Counts the reference-record pairs.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">from_dump</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_entity_type</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Talklr.get_names" title="pypath.core.annot.Talklr.get_names"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_names</span></code></a>()</p></td>
+<td><p>Returns the list of field names in the records.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Talklr.get_reference_set" title="pypath.core.annot.Talklr.get_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_reference_set</span></code></a>([proteins, complexes, ...])</p></td>
+<td><p>Retrieves the reference set i.e. the set of all entities which potentially have annotation in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Talklr.get_subset" title="pypath.core.annot.Talklr.get_subset"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Talklr.get_subset_bool_array" title="pypath.core.annot.Talklr.get_subset_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset_bool_array</span></code></a>([reference_set])</p></td>
+<td><p>Returns a boolean vector with True and False values for each entity in the reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Talklr.get_values" title="pypath.core.annot.Talklr.get_values"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_values</span></code></a>(name[, exclude_none])</p></td>
+<td><p>Returns the set of all possible values of a field.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_complex</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_mirna</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_protein</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Talklr.labels" title="pypath.core.annot.Talklr.labels"><code class="xref py py-obj docutils literal notranslate"><span class="pre">labels</span></code></a>([method])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Talklr.load" title="pypath.core.annot.Talklr.load"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load</span></code></a>()</p></td>
+<td><p>Loads the annotation data by calling the input method.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Talklr.load_data" title="pypath.core.annot.Talklr.load_data"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_data</span></code></a>()</p></td>
+<td><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Talklr.load_proteins" title="pypath.core.annot.Talklr.load_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_proteins</span></code></a>()</p></td>
+<td><p>Retrieves a set of all UniProt IDs to have a base set of the entire proteome.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Talklr.make_df" title="pypath.core.annot.Talklr.make_df"><code class="xref py py-obj docutils literal notranslate"><span class="pre">make_df</span></code></a>([rebuild])</p></td>
+<td><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complex_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Talklr.numof_entities" title="pypath.core.annot.Talklr.numof_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_entities</span></code></a>()</p></td>
+<td><p>The number of annotated entities in the resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirna_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirnas</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_protein_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_proteins</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Talklr.numof_records" title="pypath.core.annot.Talklr.numof_records"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_records</span></code></a>([entity_types])</p></td>
+<td><p>The total number of annotation records.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Talklr.numof_references" title="pypath.core.annot.Talklr.numof_references"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_references</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Talklr.process" title="pypath.core.annot.Talklr.process"><code class="xref py py-obj docutils literal notranslate"><span class="pre">process</span></code></a>()</p></td>
+<td><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">proportion</span></code>(other)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Talklr.reload" title="pypath.core.annot.Talklr.reload"><code class="xref py py-obj docutils literal notranslate"><span class="pre">reload</span></code></a>()</p></td>
+<td><p>Reloads the object from the module level.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">save_to_pickle</span></code>(pickle_file)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Talklr.select" title="pypath.core.annot.Talklr.select"><code class="xref py py-obj docutils literal notranslate"><span class="pre">select</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Talklr.set_method" title="pypath.core.annot.Talklr.set_method"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_method</span></code></a>()</p></td>
+<td><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if necessary.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Talklr.set_reference_set" title="pypath.core.annot.Talklr.set_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_reference_set</span></code></a>()</p></td>
+<td><p>Assigns the reference set to the :py:attr``reference_set`` attribute.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Talklr.show" title="pypath.core.annot.Talklr.show"><code class="xref py py-obj docutils literal notranslate"><span class="pre">show</span></code></a>([method, table_param])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic information from the UniProt datasheets.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Talklr.subset_intersection" title="pypath.core.annot.Talklr.subset_intersection"><code class="xref py py-obj docutils literal notranslate"><span class="pre">subset_intersection</span></code></a>(universe, **kwargs)</p></td>
+<td><p>Calculates the proportion of entities in a subset occuring in the set <code class="docutils literal notranslate"><span class="pre">universe</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Talklr.to_array" title="pypath.core.annot.Talklr.to_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_array</span></code></a>([reference_set, use_fields])</p></td>
+<td><p>Returns an entity vs feature array.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Talklr.to_bool_array" title="pypath.core.annot.Talklr.to_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_bool_array</span></code></a>(reference_set)</p></td>
+<td><p>Returns a presence/absence boolean array for a reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Talklr.to_set" title="pypath.core.annot.Talklr.to_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_set</span></code></a>()</p></td>
+<td><p>Returns the entities present in this annotation resource as a set.</p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Attributes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_fields</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">summary</span></code></p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Talklr.add_complexes_by_inference">
+<span class="sig-name descname"><span class="pre">add_complexes_by_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Talklr.add_complexes_by_inference" title="Link to this definition">§</a></dt>
+<dd><p>Creates complex annotations by in silico inference and adds them
+to this annotation set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Talklr.all_complexes">
+<span class="sig-name descname"><span class="pre">all_complexes</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Talklr.all_complexes" title="Link to this definition">§</a></dt>
+<dd><p>All protein complexes annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Talklr.all_entities">
+<span class="sig-name descname"><span class="pre">all_entities</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Talklr.all_entities" title="Link to this definition">§</a></dt>
+<dd><p>All entities annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Talklr.all_mirnas">
+<span class="sig-name descname"><span class="pre">all_mirnas</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Talklr.all_mirnas" title="Link to this definition">§</a></dt>
+<dd><p>All miRNAs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Talklr.all_proteins">
+<span class="sig-name descname"><span class="pre">all_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Talklr.all_proteins" title="Link to this definition">§</a></dt>
+<dd><p>All UniProt IDs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Talklr.all_refs">
+<span class="sig-name descname"><span class="pre">all_refs</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Talklr.all_refs" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects the references
+across all records. Returns <em>list</em>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Talklr.annotate_complex">
+<span class="sig-name descname"><span class="pre">annotate_complex</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cplex</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Talklr.annotate_complex" title="Link to this definition">§</a></dt>
+<dd><p>Infers annotations for a single complex.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Talklr.browse">
+<span class="sig-name descname"><span class="pre">browse</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">field</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">start</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Talklr.browse" title="Link to this definition">§</a></dt>
+<dd><p>Print gene information as a table.</p>
+<p>Presents information about annotation categories as ascii tables
+printed in the terminal. If one category provided, prints one table.
+If multiple categories provided, prints a table for each of them one
+by one proceeding to the next one once you hit return. If no categories
+provided goes through all levels of the primary category.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>field:</dt><dd><p>The field to browse categories by.</p>
+<ul class="simple">
+<li><p>If None the primary field will be selected.
+If this annotation resource doesn’t have fields, all proteins
+will be presented as one single category.</p></li>
+<li><p>If a string it will be considered a field name and it will
+browse through all levels of this field.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">list</span></code>, set or tuple, it will be considered either a
+<code class="docutils literal notranslate"><span class="pre">list</span></code> of field names or a list of values from the primary
+field. In the former case all combinations of the values of
+the fields will be presented, in the latter case the browsing
+will be limited to the levels of the primary field contained
+in <code class="docutils literal notranslate"><span class="pre">field</span></code>.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">dict</span></code>, keys are supposed to be field names and values
+as list of levels. If any of the values are None, all levels
+from that field will be used.</p></li>
+</ul>
+</dd>
+<dt>start:</dt><dd><p>Start browsing from this category. E.g. if there are 500
+categories and start is 250 it will skip everything before the
+250th.</p>
+</dd>
+<dt>kwargs:</dt><dd><p>Passed to <code class="docutils literal notranslate"><span class="pre">pypath.utils.uniprot.info</span></code>.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Talklr.complex_inference">
+<span class="sig-name descname"><span class="pre">complex_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Talklr.complex_inference" title="Link to this definition">§</a></dt>
+<dd><p>Annotates all complexes in <cite>complexes</cite>, by default in the default
+complex database (existing in the <cite>complex</cite> module or generated
+on demand according to the module’s current settings).</p>
+<dl class="field-list simple">
+<dt class="field-odd">Returns<span class="colon">:</span></dt>
+<dd class="field-odd"><p><ul class="simple">
+<li><p><em>Dict with complexes as keys and sets of annotations as values.</em></p></li>
+<li><p><em>Complexes with no valid information in this annotation resource</em></p></li>
+<li><p><em>won’t be in the dict.</em></p></li>
+</ul>
+</p>
+</dd>
+<dt class="field-even">Parameters<span class="colon">:</span></dt>
+<dd class="field-even"><p><strong>complexes</strong> (<em>iterable</em>) – Iterable yielding complexes.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Talklr.coverage">
+<span class="sig-name descname"><span class="pre">coverage</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">other</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Talklr.coverage" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the coverage of the annotation i.e. the proportion of
+entities having at least one record in this annotation resource
+for an arbitrary set of entities.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Talklr.curation_effort">
+<span class="sig-name descname"><span class="pre">curation_effort</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Talklr.curation_effort" title="Link to this definition">§</a></dt>
+<dd><p>Counts the reference-record pairs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Talklr.get_names">
+<span class="sig-name descname"><span class="pre">get_names</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Talklr.get_names" title="Link to this definition">§</a></dt>
+<dd><p>Returns the list of field names in the records. The annotation
+consists of uniform records and each entity might be annotated
+with one or more records. Each record is a tuple of fields, for
+example <code class="docutils literal notranslate"><span class="pre">('cell_type',</span> <span class="pre">'expression_level',</span> <span class="pre">'score')</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Talklr.get_reference_set">
+<em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">get_reference_set</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">proteins</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">swissprot_only</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Talklr.get_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the reference set i.e. the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Talklr.get_subset">
+<span class="sig-name descname"><span class="pre">get_subset</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Talklr.get_subset" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Talklr.get_subset_bool_array">
+<span class="sig-name descname"><span class="pre">get_subset_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Talklr.get_subset_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a boolean vector with True and False values for each entity
+in the reference set. The values represent presence absence data
+in the simplest case, but by providing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> any kind of matching
+and filtering is possible. <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> are passed to the <code class="docutils literal notranslate"><span class="pre">select</span></code>
+method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Talklr.get_values">
+<span class="sig-name descname"><span class="pre">get_values</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">exclude_none</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Talklr.get_values" title="Link to this definition">§</a></dt>
+<dd><p>Returns the set of all possible values of a field. E.g. if the
+records of this annotation have a field <code class="docutils literal notranslate"><span class="pre">cell_type</span></code> then calling
+this method can tell you that across all records the values of
+this field might be <code class="docutils literal notranslate"><span class="pre">{'macrophage',</span> <span class="pre">'epithelial_cell',</span> <span class="pre">...}</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Talklr.labels">
+<span class="sig-name descname"><span class="pre">labels</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Talklr.labels" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Talklr.load">
+<span class="sig-name descname"><span class="pre">load</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Talklr.load" title="Link to this definition">§</a></dt>
+<dd><p>Loads the annotation data by calling the input method.
+Infers annotations for complexes in the complex database if
+py:attr:<code class="docutils literal notranslate"><span class="pre">infer_complexes</span></code> is True.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Talklr.load_data">
+<span class="sig-name descname"><span class="pre">load_data</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Talklr.load_data" title="Link to this definition">§</a></dt>
+<dd><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Talklr.load_proteins">
+<span class="sig-name descname"><span class="pre">load_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Talklr.load_proteins" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a set of all UniProt IDs to have a base set of the entire
+proteome.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Talklr.make_df">
+<span class="sig-name descname"><span class="pre">make_df</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">rebuild</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Talklr.make_df" title="Link to this definition">§</a></dt>
+<dd><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.
+The data frame will be assigned to :py:attr``df``.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Talklr.numof_entities">
+<span class="sig-name descname"><span class="pre">numof_entities</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Talklr.numof_entities" title="Link to this definition">§</a></dt>
+<dd><p>The number of annotated entities in the resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Talklr.numof_records">
+<span class="sig-name descname"><span class="pre">numof_records</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Talklr.numof_records" title="Link to this definition">§</a></dt>
+<dd><p>The total number of annotation records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Talklr.numof_references">
+<span class="sig-name descname"><span class="pre">numof_references</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Talklr.numof_references" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects and counts the
+references across all records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Talklr.process">
+<span class="sig-name descname"><span class="pre">process</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Talklr.process" title="Link to this definition">§</a></dt>
+<dd><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Talklr.reload">
+<span class="sig-name descname"><span class="pre">reload</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Talklr.reload" title="Link to this definition">§</a></dt>
+<dd><p>Reloads the object from the module level.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Talklr.select">
+<span class="sig-name descname"><span class="pre">select</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Talklr.select" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Talklr.set_method">
+<span class="sig-name descname"><span class="pre">set_method</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Talklr.set_method" title="Link to this definition">§</a></dt>
+<dd><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if
+necessary.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Talklr.set_reference_set">
+<span class="sig-name descname"><span class="pre">set_reference_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Talklr.set_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Assigns the reference set to the :py:attr``reference_set`` attribute.
+The reference set is the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Talklr.show">
+<span class="sig-name descname"><span class="pre">show</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">table_param</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Talklr.show" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic
+information from the UniProt datasheets.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Talklr.subset_intersection">
+<span class="sig-name descname"><span class="pre">subset_intersection</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">universe</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Talklr.subset_intersection" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the proportion of entities in a subset occuring in the
+set <code class="docutils literal notranslate"><span class="pre">universe</span></code>. The subset is selected by passing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> to the
+<code class="docutils literal notranslate"><span class="pre">select</span></code> method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Talklr.to_array">
+<span class="sig-name descname"><span class="pre">to_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_fields</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Talklr.to_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns an entity vs feature array. In case of more complex
+annotations this might be huge.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Talklr.to_bool_array">
+<span class="sig-name descname"><span class="pre">to_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Talklr.to_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a presence/absence boolean array for a reference set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Talklr.to_set">
+<span class="sig-name descname"><span class="pre">to_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Talklr.to_set" title="Link to this definition">§</a></dt>
+<dd><p>Returns the entities present in this annotation resource as a set.</p>
+</dd></dl>
+
+</dd></dl>
+
+</section>
+
+
+                </article>
+              
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+  <section id="pypath-core-annot-tcdb">
+<h1>pypath.core.annot.Tcdb<a class="headerlink" href="#pypath-core-annot-tcdb" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.core.annot.Tcdb">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.core.annot.</span></span><span class="sig-name descname"><span class="pre">Tcdb</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#Tcdb"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.Tcdb" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <a class="reference internal" href="pypath.core.annot.AnnotationBase.html#pypath.core.annot.AnnotationBase" title="pypath.core.annot.AnnotationBase"><code class="xref py py-class docutils literal notranslate"><span class="pre">AnnotationBase</span></code></a></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Tcdb.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#Tcdb.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.Tcdb.__init__" title="Link to this definition">§</a></dt>
+<dd><p>Topological domains and transmembrane segments from UniProt.</p>
+</dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Tcdb.__init__" title="pypath.core.annot.Tcdb.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>([ncbi_tax_id])</p></td>
+<td><p>Topological domains and transmembrane segments from UniProt.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Tcdb.add_complexes_by_inference" title="pypath.core.annot.Tcdb.add_complexes_by_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">add_complexes_by_inference</span></code></a>([complexes])</p></td>
+<td><p>Creates complex annotations by in silico inference and adds them to this annotation set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Tcdb.all_complexes" title="pypath.core.annot.Tcdb.all_complexes"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_complexes</span></code></a>()</p></td>
+<td><p>All protein complexes annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Tcdb.all_entities" title="pypath.core.annot.Tcdb.all_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_entities</span></code></a>([entity_types])</p></td>
+<td><p>All entities annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Tcdb.all_mirnas" title="pypath.core.annot.Tcdb.all_mirnas"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_mirnas</span></code></a>()</p></td>
+<td><p>All miRNAs annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Tcdb.all_proteins" title="pypath.core.annot.Tcdb.all_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_proteins</span></code></a>()</p></td>
+<td><p>All UniProt IDs annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Tcdb.all_refs" title="pypath.core.annot.Tcdb.all_refs"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_refs</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Tcdb.annotate_complex" title="pypath.core.annot.Tcdb.annotate_complex"><code class="xref py py-obj docutils literal notranslate"><span class="pre">annotate_complex</span></code></a>(cplex)</p></td>
+<td><p>Infers annotations for a single complex.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Tcdb.browse" title="pypath.core.annot.Tcdb.browse"><code class="xref py py-obj docutils literal notranslate"><span class="pre">browse</span></code></a>([field, start])</p></td>
+<td><p>Print gene information as a table.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Tcdb.complex_inference" title="pypath.core.annot.Tcdb.complex_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">complex_inference</span></code></a>([complexes])</p></td>
+<td><p>Annotates all complexes in <cite>complexes</cite>, by default in the default complex database (existing in the <cite>complex</cite> module or generated on demand according to the module's current settings).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Tcdb.coverage" title="pypath.core.annot.Tcdb.coverage"><code class="xref py py-obj docutils literal notranslate"><span class="pre">coverage</span></code></a>(other)</p></td>
+<td><p>Calculates the coverage of the annotation i.e. the proportion of entities having at least one record in this annotation resource for an arbitrary set of entities.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Tcdb.curation_effort" title="pypath.core.annot.Tcdb.curation_effort"><code class="xref py py-obj docutils literal notranslate"><span class="pre">curation_effort</span></code></a>()</p></td>
+<td><p>Counts the reference-record pairs.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">from_dump</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_entity_type</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Tcdb.get_names" title="pypath.core.annot.Tcdb.get_names"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_names</span></code></a>()</p></td>
+<td><p>Returns the list of field names in the records.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Tcdb.get_reference_set" title="pypath.core.annot.Tcdb.get_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_reference_set</span></code></a>([proteins, complexes, ...])</p></td>
+<td><p>Retrieves the reference set i.e. the set of all entities which potentially have annotation in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Tcdb.get_subset" title="pypath.core.annot.Tcdb.get_subset"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Tcdb.get_subset_bool_array" title="pypath.core.annot.Tcdb.get_subset_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset_bool_array</span></code></a>([reference_set])</p></td>
+<td><p>Returns a boolean vector with True and False values for each entity in the reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Tcdb.get_values" title="pypath.core.annot.Tcdb.get_values"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_values</span></code></a>(name[, exclude_none])</p></td>
+<td><p>Returns the set of all possible values of a field.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_complex</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_mirna</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_protein</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Tcdb.labels" title="pypath.core.annot.Tcdb.labels"><code class="xref py py-obj docutils literal notranslate"><span class="pre">labels</span></code></a>([method])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Tcdb.load" title="pypath.core.annot.Tcdb.load"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load</span></code></a>()</p></td>
+<td><p>Loads the annotation data by calling the input method.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Tcdb.load_data" title="pypath.core.annot.Tcdb.load_data"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_data</span></code></a>()</p></td>
+<td><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Tcdb.load_proteins" title="pypath.core.annot.Tcdb.load_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_proteins</span></code></a>()</p></td>
+<td><p>Retrieves a set of all UniProt IDs to have a base set of the entire proteome.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Tcdb.make_df" title="pypath.core.annot.Tcdb.make_df"><code class="xref py py-obj docutils literal notranslate"><span class="pre">make_df</span></code></a>([rebuild])</p></td>
+<td><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complex_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Tcdb.numof_entities" title="pypath.core.annot.Tcdb.numof_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_entities</span></code></a>()</p></td>
+<td><p>The number of annotated entities in the resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirna_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirnas</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_protein_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_proteins</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Tcdb.numof_records" title="pypath.core.annot.Tcdb.numof_records"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_records</span></code></a>([entity_types])</p></td>
+<td><p>The total number of annotation records.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Tcdb.numof_references" title="pypath.core.annot.Tcdb.numof_references"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_references</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Tcdb.process" title="pypath.core.annot.Tcdb.process"><code class="xref py py-obj docutils literal notranslate"><span class="pre">process</span></code></a>()</p></td>
+<td><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">proportion</span></code>(other)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Tcdb.reload" title="pypath.core.annot.Tcdb.reload"><code class="xref py py-obj docutils literal notranslate"><span class="pre">reload</span></code></a>()</p></td>
+<td><p>Reloads the object from the module level.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">save_to_pickle</span></code>(pickle_file)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Tcdb.select" title="pypath.core.annot.Tcdb.select"><code class="xref py py-obj docutils literal notranslate"><span class="pre">select</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Tcdb.set_method" title="pypath.core.annot.Tcdb.set_method"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_method</span></code></a>()</p></td>
+<td><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if necessary.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Tcdb.set_reference_set" title="pypath.core.annot.Tcdb.set_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_reference_set</span></code></a>()</p></td>
+<td><p>Assigns the reference set to the :py:attr``reference_set`` attribute.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Tcdb.show" title="pypath.core.annot.Tcdb.show"><code class="xref py py-obj docutils literal notranslate"><span class="pre">show</span></code></a>([method, table_param])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic information from the UniProt datasheets.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Tcdb.subset_intersection" title="pypath.core.annot.Tcdb.subset_intersection"><code class="xref py py-obj docutils literal notranslate"><span class="pre">subset_intersection</span></code></a>(universe, **kwargs)</p></td>
+<td><p>Calculates the proportion of entities in a subset occuring in the set <code class="docutils literal notranslate"><span class="pre">universe</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Tcdb.to_array" title="pypath.core.annot.Tcdb.to_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_array</span></code></a>([reference_set, use_fields])</p></td>
+<td><p>Returns an entity vs feature array.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Tcdb.to_bool_array" title="pypath.core.annot.Tcdb.to_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_bool_array</span></code></a>(reference_set)</p></td>
+<td><p>Returns a presence/absence boolean array for a reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Tcdb.to_set" title="pypath.core.annot.Tcdb.to_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_set</span></code></a>()</p></td>
+<td><p>Returns the entities present in this annotation resource as a set.</p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Attributes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_fields</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">summary</span></code></p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Tcdb.add_complexes_by_inference">
+<span class="sig-name descname"><span class="pre">add_complexes_by_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Tcdb.add_complexes_by_inference" title="Link to this definition">§</a></dt>
+<dd><p>Creates complex annotations by in silico inference and adds them
+to this annotation set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Tcdb.all_complexes">
+<span class="sig-name descname"><span class="pre">all_complexes</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Tcdb.all_complexes" title="Link to this definition">§</a></dt>
+<dd><p>All protein complexes annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Tcdb.all_entities">
+<span class="sig-name descname"><span class="pre">all_entities</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Tcdb.all_entities" title="Link to this definition">§</a></dt>
+<dd><p>All entities annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Tcdb.all_mirnas">
+<span class="sig-name descname"><span class="pre">all_mirnas</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Tcdb.all_mirnas" title="Link to this definition">§</a></dt>
+<dd><p>All miRNAs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Tcdb.all_proteins">
+<span class="sig-name descname"><span class="pre">all_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Tcdb.all_proteins" title="Link to this definition">§</a></dt>
+<dd><p>All UniProt IDs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Tcdb.all_refs">
+<span class="sig-name descname"><span class="pre">all_refs</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Tcdb.all_refs" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects the references
+across all records. Returns <em>list</em>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Tcdb.annotate_complex">
+<span class="sig-name descname"><span class="pre">annotate_complex</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cplex</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Tcdb.annotate_complex" title="Link to this definition">§</a></dt>
+<dd><p>Infers annotations for a single complex.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Tcdb.browse">
+<span class="sig-name descname"><span class="pre">browse</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">field</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">start</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Tcdb.browse" title="Link to this definition">§</a></dt>
+<dd><p>Print gene information as a table.</p>
+<p>Presents information about annotation categories as ascii tables
+printed in the terminal. If one category provided, prints one table.
+If multiple categories provided, prints a table for each of them one
+by one proceeding to the next one once you hit return. If no categories
+provided goes through all levels of the primary category.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>field:</dt><dd><p>The field to browse categories by.</p>
+<ul class="simple">
+<li><p>If None the primary field will be selected.
+If this annotation resource doesn’t have fields, all proteins
+will be presented as one single category.</p></li>
+<li><p>If a string it will be considered a field name and it will
+browse through all levels of this field.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">list</span></code>, set or tuple, it will be considered either a
+<code class="docutils literal notranslate"><span class="pre">list</span></code> of field names or a list of values from the primary
+field. In the former case all combinations of the values of
+the fields will be presented, in the latter case the browsing
+will be limited to the levels of the primary field contained
+in <code class="docutils literal notranslate"><span class="pre">field</span></code>.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">dict</span></code>, keys are supposed to be field names and values
+as list of levels. If any of the values are None, all levels
+from that field will be used.</p></li>
+</ul>
+</dd>
+<dt>start:</dt><dd><p>Start browsing from this category. E.g. if there are 500
+categories and start is 250 it will skip everything before the
+250th.</p>
+</dd>
+<dt>kwargs:</dt><dd><p>Passed to <code class="docutils literal notranslate"><span class="pre">pypath.utils.uniprot.info</span></code>.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Tcdb.complex_inference">
+<span class="sig-name descname"><span class="pre">complex_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Tcdb.complex_inference" title="Link to this definition">§</a></dt>
+<dd><p>Annotates all complexes in <cite>complexes</cite>, by default in the default
+complex database (existing in the <cite>complex</cite> module or generated
+on demand according to the module’s current settings).</p>
+<dl class="field-list simple">
+<dt class="field-odd">Returns<span class="colon">:</span></dt>
+<dd class="field-odd"><p><ul class="simple">
+<li><p><em>Dict with complexes as keys and sets of annotations as values.</em></p></li>
+<li><p><em>Complexes with no valid information in this annotation resource</em></p></li>
+<li><p><em>won’t be in the dict.</em></p></li>
+</ul>
+</p>
+</dd>
+<dt class="field-even">Parameters<span class="colon">:</span></dt>
+<dd class="field-even"><p><strong>complexes</strong> (<em>iterable</em>) – Iterable yielding complexes.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Tcdb.coverage">
+<span class="sig-name descname"><span class="pre">coverage</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">other</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Tcdb.coverage" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the coverage of the annotation i.e. the proportion of
+entities having at least one record in this annotation resource
+for an arbitrary set of entities.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Tcdb.curation_effort">
+<span class="sig-name descname"><span class="pre">curation_effort</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Tcdb.curation_effort" title="Link to this definition">§</a></dt>
+<dd><p>Counts the reference-record pairs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Tcdb.get_names">
+<span class="sig-name descname"><span class="pre">get_names</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Tcdb.get_names" title="Link to this definition">§</a></dt>
+<dd><p>Returns the list of field names in the records. The annotation
+consists of uniform records and each entity might be annotated
+with one or more records. Each record is a tuple of fields, for
+example <code class="docutils literal notranslate"><span class="pre">('cell_type',</span> <span class="pre">'expression_level',</span> <span class="pre">'score')</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Tcdb.get_reference_set">
+<em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">get_reference_set</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">proteins</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">swissprot_only</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Tcdb.get_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the reference set i.e. the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Tcdb.get_subset">
+<span class="sig-name descname"><span class="pre">get_subset</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Tcdb.get_subset" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Tcdb.get_subset_bool_array">
+<span class="sig-name descname"><span class="pre">get_subset_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Tcdb.get_subset_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a boolean vector with True and False values for each entity
+in the reference set. The values represent presence absence data
+in the simplest case, but by providing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> any kind of matching
+and filtering is possible. <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> are passed to the <code class="docutils literal notranslate"><span class="pre">select</span></code>
+method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Tcdb.get_values">
+<span class="sig-name descname"><span class="pre">get_values</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">exclude_none</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Tcdb.get_values" title="Link to this definition">§</a></dt>
+<dd><p>Returns the set of all possible values of a field. E.g. if the
+records of this annotation have a field <code class="docutils literal notranslate"><span class="pre">cell_type</span></code> then calling
+this method can tell you that across all records the values of
+this field might be <code class="docutils literal notranslate"><span class="pre">{'macrophage',</span> <span class="pre">'epithelial_cell',</span> <span class="pre">...}</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Tcdb.labels">
+<span class="sig-name descname"><span class="pre">labels</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Tcdb.labels" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Tcdb.load">
+<span class="sig-name descname"><span class="pre">load</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Tcdb.load" title="Link to this definition">§</a></dt>
+<dd><p>Loads the annotation data by calling the input method.
+Infers annotations for complexes in the complex database if
+py:attr:<code class="docutils literal notranslate"><span class="pre">infer_complexes</span></code> is True.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Tcdb.load_data">
+<span class="sig-name descname"><span class="pre">load_data</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Tcdb.load_data" title="Link to this definition">§</a></dt>
+<dd><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Tcdb.load_proteins">
+<span class="sig-name descname"><span class="pre">load_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Tcdb.load_proteins" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a set of all UniProt IDs to have a base set of the entire
+proteome.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Tcdb.make_df">
+<span class="sig-name descname"><span class="pre">make_df</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">rebuild</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Tcdb.make_df" title="Link to this definition">§</a></dt>
+<dd><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.
+The data frame will be assigned to :py:attr``df``.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Tcdb.numof_entities">
+<span class="sig-name descname"><span class="pre">numof_entities</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Tcdb.numof_entities" title="Link to this definition">§</a></dt>
+<dd><p>The number of annotated entities in the resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Tcdb.numof_records">
+<span class="sig-name descname"><span class="pre">numof_records</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Tcdb.numof_records" title="Link to this definition">§</a></dt>
+<dd><p>The total number of annotation records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Tcdb.numof_references">
+<span class="sig-name descname"><span class="pre">numof_references</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Tcdb.numof_references" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects and counts the
+references across all records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Tcdb.process">
+<span class="sig-name descname"><span class="pre">process</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Tcdb.process" title="Link to this definition">§</a></dt>
+<dd><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Tcdb.reload">
+<span class="sig-name descname"><span class="pre">reload</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Tcdb.reload" title="Link to this definition">§</a></dt>
+<dd><p>Reloads the object from the module level.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Tcdb.select">
+<span class="sig-name descname"><span class="pre">select</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Tcdb.select" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Tcdb.set_method">
+<span class="sig-name descname"><span class="pre">set_method</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Tcdb.set_method" title="Link to this definition">§</a></dt>
+<dd><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if
+necessary.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Tcdb.set_reference_set">
+<span class="sig-name descname"><span class="pre">set_reference_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Tcdb.set_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Assigns the reference set to the :py:attr``reference_set`` attribute.
+The reference set is the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Tcdb.show">
+<span class="sig-name descname"><span class="pre">show</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">table_param</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Tcdb.show" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic
+information from the UniProt datasheets.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Tcdb.subset_intersection">
+<span class="sig-name descname"><span class="pre">subset_intersection</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">universe</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Tcdb.subset_intersection" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the proportion of entities in a subset occuring in the
+set <code class="docutils literal notranslate"><span class="pre">universe</span></code>. The subset is selected by passing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> to the
+<code class="docutils literal notranslate"><span class="pre">select</span></code> method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Tcdb.to_array">
+<span class="sig-name descname"><span class="pre">to_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_fields</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Tcdb.to_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns an entity vs feature array. In case of more complex
+annotations this might be huge.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Tcdb.to_bool_array">
+<span class="sig-name descname"><span class="pre">to_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Tcdb.to_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a presence/absence boolean array for a reference set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Tcdb.to_set">
+<span class="sig-name descname"><span class="pre">to_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Tcdb.to_set" title="Link to this definition">§</a></dt>
+<dd><p>Returns the entities present in this annotation resource as a set.</p>
+</dd></dl>
+
+</dd></dl>
+
+</section>
+
+
+                </article>
+              
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+  <section id="pypath-core-annot-tfcensus">
+<h1>pypath.core.annot.Tfcensus<a class="headerlink" href="#pypath-core-annot-tfcensus" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.core.annot.Tfcensus">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.core.annot.</span></span><span class="sig-name descname"><span class="pre">Tfcensus</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#Tfcensus"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.Tfcensus" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <a class="reference internal" href="pypath.core.annot.AnnotationBase.html#pypath.core.annot.AnnotationBase" title="pypath.core.annot.AnnotationBase"><code class="xref py py-class docutils literal notranslate"><span class="pre">AnnotationBase</span></code></a></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Tfcensus.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#Tfcensus.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.Tfcensus.__init__" title="Link to this definition">§</a></dt>
+<dd><p>Transcription factors from TF census (Vaquerizas et al 2009).</p>
+</dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Tfcensus.__init__" title="pypath.core.annot.Tfcensus.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>(**kwargs)</p></td>
+<td><p>Transcription factors from TF census (Vaquerizas et al 2009).</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Tfcensus.add_complexes_by_inference" title="pypath.core.annot.Tfcensus.add_complexes_by_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">add_complexes_by_inference</span></code></a>([complexes])</p></td>
+<td><p>Creates complex annotations by in silico inference and adds them to this annotation set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Tfcensus.all_complexes" title="pypath.core.annot.Tfcensus.all_complexes"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_complexes</span></code></a>()</p></td>
+<td><p>All protein complexes annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Tfcensus.all_entities" title="pypath.core.annot.Tfcensus.all_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_entities</span></code></a>([entity_types])</p></td>
+<td><p>All entities annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Tfcensus.all_mirnas" title="pypath.core.annot.Tfcensus.all_mirnas"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_mirnas</span></code></a>()</p></td>
+<td><p>All miRNAs annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Tfcensus.all_proteins" title="pypath.core.annot.Tfcensus.all_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_proteins</span></code></a>()</p></td>
+<td><p>All UniProt IDs annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Tfcensus.all_refs" title="pypath.core.annot.Tfcensus.all_refs"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_refs</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Tfcensus.annotate_complex" title="pypath.core.annot.Tfcensus.annotate_complex"><code class="xref py py-obj docutils literal notranslate"><span class="pre">annotate_complex</span></code></a>(cplex)</p></td>
+<td><p>Infers annotations for a single complex.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Tfcensus.browse" title="pypath.core.annot.Tfcensus.browse"><code class="xref py py-obj docutils literal notranslate"><span class="pre">browse</span></code></a>([field, start])</p></td>
+<td><p>Print gene information as a table.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Tfcensus.complex_inference" title="pypath.core.annot.Tfcensus.complex_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">complex_inference</span></code></a>([complexes])</p></td>
+<td><p>Annotates all complexes in <cite>complexes</cite>, by default in the default complex database (existing in the <cite>complex</cite> module or generated on demand according to the module's current settings).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Tfcensus.coverage" title="pypath.core.annot.Tfcensus.coverage"><code class="xref py py-obj docutils literal notranslate"><span class="pre">coverage</span></code></a>(other)</p></td>
+<td><p>Calculates the coverage of the annotation i.e. the proportion of entities having at least one record in this annotation resource for an arbitrary set of entities.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Tfcensus.curation_effort" title="pypath.core.annot.Tfcensus.curation_effort"><code class="xref py py-obj docutils literal notranslate"><span class="pre">curation_effort</span></code></a>()</p></td>
+<td><p>Counts the reference-record pairs.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">from_dump</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_entity_type</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Tfcensus.get_names" title="pypath.core.annot.Tfcensus.get_names"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_names</span></code></a>()</p></td>
+<td><p>Returns the list of field names in the records.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Tfcensus.get_reference_set" title="pypath.core.annot.Tfcensus.get_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_reference_set</span></code></a>([proteins, complexes, ...])</p></td>
+<td><p>Retrieves the reference set i.e. the set of all entities which potentially have annotation in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Tfcensus.get_subset" title="pypath.core.annot.Tfcensus.get_subset"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Tfcensus.get_subset_bool_array" title="pypath.core.annot.Tfcensus.get_subset_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset_bool_array</span></code></a>([reference_set])</p></td>
+<td><p>Returns a boolean vector with True and False values for each entity in the reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Tfcensus.get_values" title="pypath.core.annot.Tfcensus.get_values"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_values</span></code></a>(name[, exclude_none])</p></td>
+<td><p>Returns the set of all possible values of a field.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_complex</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_mirna</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_protein</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Tfcensus.labels" title="pypath.core.annot.Tfcensus.labels"><code class="xref py py-obj docutils literal notranslate"><span class="pre">labels</span></code></a>([method])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Tfcensus.load" title="pypath.core.annot.Tfcensus.load"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load</span></code></a>()</p></td>
+<td><p>Loads the annotation data by calling the input method.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Tfcensus.load_data" title="pypath.core.annot.Tfcensus.load_data"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_data</span></code></a>()</p></td>
+<td><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Tfcensus.load_proteins" title="pypath.core.annot.Tfcensus.load_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_proteins</span></code></a>()</p></td>
+<td><p>Retrieves a set of all UniProt IDs to have a base set of the entire proteome.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Tfcensus.make_df" title="pypath.core.annot.Tfcensus.make_df"><code class="xref py py-obj docutils literal notranslate"><span class="pre">make_df</span></code></a>([rebuild])</p></td>
+<td><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complex_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Tfcensus.numof_entities" title="pypath.core.annot.Tfcensus.numof_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_entities</span></code></a>()</p></td>
+<td><p>The number of annotated entities in the resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirna_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirnas</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_protein_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_proteins</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Tfcensus.numof_records" title="pypath.core.annot.Tfcensus.numof_records"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_records</span></code></a>([entity_types])</p></td>
+<td><p>The total number of annotation records.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Tfcensus.numof_references" title="pypath.core.annot.Tfcensus.numof_references"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_references</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Tfcensus.process" title="pypath.core.annot.Tfcensus.process"><code class="xref py py-obj docutils literal notranslate"><span class="pre">process</span></code></a>()</p></td>
+<td><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">proportion</span></code>(other)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Tfcensus.reload" title="pypath.core.annot.Tfcensus.reload"><code class="xref py py-obj docutils literal notranslate"><span class="pre">reload</span></code></a>()</p></td>
+<td><p>Reloads the object from the module level.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">save_to_pickle</span></code>(pickle_file)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Tfcensus.select" title="pypath.core.annot.Tfcensus.select"><code class="xref py py-obj docutils literal notranslate"><span class="pre">select</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Tfcensus.set_method" title="pypath.core.annot.Tfcensus.set_method"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_method</span></code></a>()</p></td>
+<td><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if necessary.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Tfcensus.set_reference_set" title="pypath.core.annot.Tfcensus.set_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_reference_set</span></code></a>()</p></td>
+<td><p>Assigns the reference set to the :py:attr``reference_set`` attribute.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Tfcensus.show" title="pypath.core.annot.Tfcensus.show"><code class="xref py py-obj docutils literal notranslate"><span class="pre">show</span></code></a>([method, table_param])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic information from the UniProt datasheets.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Tfcensus.subset_intersection" title="pypath.core.annot.Tfcensus.subset_intersection"><code class="xref py py-obj docutils literal notranslate"><span class="pre">subset_intersection</span></code></a>(universe, **kwargs)</p></td>
+<td><p>Calculates the proportion of entities in a subset occuring in the set <code class="docutils literal notranslate"><span class="pre">universe</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Tfcensus.to_array" title="pypath.core.annot.Tfcensus.to_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_array</span></code></a>([reference_set, use_fields])</p></td>
+<td><p>Returns an entity vs feature array.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Tfcensus.to_bool_array" title="pypath.core.annot.Tfcensus.to_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_bool_array</span></code></a>(reference_set)</p></td>
+<td><p>Returns a presence/absence boolean array for a reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Tfcensus.to_set" title="pypath.core.annot.Tfcensus.to_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_set</span></code></a>()</p></td>
+<td><p>Returns the entities present in this annotation resource as a set.</p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Attributes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_fields</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">summary</span></code></p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Tfcensus.add_complexes_by_inference">
+<span class="sig-name descname"><span class="pre">add_complexes_by_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Tfcensus.add_complexes_by_inference" title="Link to this definition">§</a></dt>
+<dd><p>Creates complex annotations by in silico inference and adds them
+to this annotation set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Tfcensus.all_complexes">
+<span class="sig-name descname"><span class="pre">all_complexes</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Tfcensus.all_complexes" title="Link to this definition">§</a></dt>
+<dd><p>All protein complexes annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Tfcensus.all_entities">
+<span class="sig-name descname"><span class="pre">all_entities</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Tfcensus.all_entities" title="Link to this definition">§</a></dt>
+<dd><p>All entities annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Tfcensus.all_mirnas">
+<span class="sig-name descname"><span class="pre">all_mirnas</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Tfcensus.all_mirnas" title="Link to this definition">§</a></dt>
+<dd><p>All miRNAs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Tfcensus.all_proteins">
+<span class="sig-name descname"><span class="pre">all_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Tfcensus.all_proteins" title="Link to this definition">§</a></dt>
+<dd><p>All UniProt IDs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Tfcensus.all_refs">
+<span class="sig-name descname"><span class="pre">all_refs</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Tfcensus.all_refs" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects the references
+across all records. Returns <em>list</em>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Tfcensus.annotate_complex">
+<span class="sig-name descname"><span class="pre">annotate_complex</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cplex</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Tfcensus.annotate_complex" title="Link to this definition">§</a></dt>
+<dd><p>Infers annotations for a single complex.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Tfcensus.browse">
+<span class="sig-name descname"><span class="pre">browse</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">field</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">start</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Tfcensus.browse" title="Link to this definition">§</a></dt>
+<dd><p>Print gene information as a table.</p>
+<p>Presents information about annotation categories as ascii tables
+printed in the terminal. If one category provided, prints one table.
+If multiple categories provided, prints a table for each of them one
+by one proceeding to the next one once you hit return. If no categories
+provided goes through all levels of the primary category.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>field:</dt><dd><p>The field to browse categories by.</p>
+<ul class="simple">
+<li><p>If None the primary field will be selected.
+If this annotation resource doesn’t have fields, all proteins
+will be presented as one single category.</p></li>
+<li><p>If a string it will be considered a field name and it will
+browse through all levels of this field.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">list</span></code>, set or tuple, it will be considered either a
+<code class="docutils literal notranslate"><span class="pre">list</span></code> of field names or a list of values from the primary
+field. In the former case all combinations of the values of
+the fields will be presented, in the latter case the browsing
+will be limited to the levels of the primary field contained
+in <code class="docutils literal notranslate"><span class="pre">field</span></code>.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">dict</span></code>, keys are supposed to be field names and values
+as list of levels. If any of the values are None, all levels
+from that field will be used.</p></li>
+</ul>
+</dd>
+<dt>start:</dt><dd><p>Start browsing from this category. E.g. if there are 500
+categories and start is 250 it will skip everything before the
+250th.</p>
+</dd>
+<dt>kwargs:</dt><dd><p>Passed to <code class="docutils literal notranslate"><span class="pre">pypath.utils.uniprot.info</span></code>.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Tfcensus.complex_inference">
+<span class="sig-name descname"><span class="pre">complex_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Tfcensus.complex_inference" title="Link to this definition">§</a></dt>
+<dd><p>Annotates all complexes in <cite>complexes</cite>, by default in the default
+complex database (existing in the <cite>complex</cite> module or generated
+on demand according to the module’s current settings).</p>
+<dl class="field-list simple">
+<dt class="field-odd">Returns<span class="colon">:</span></dt>
+<dd class="field-odd"><p><ul class="simple">
+<li><p><em>Dict with complexes as keys and sets of annotations as values.</em></p></li>
+<li><p><em>Complexes with no valid information in this annotation resource</em></p></li>
+<li><p><em>won’t be in the dict.</em></p></li>
+</ul>
+</p>
+</dd>
+<dt class="field-even">Parameters<span class="colon">:</span></dt>
+<dd class="field-even"><p><strong>complexes</strong> (<em>iterable</em>) – Iterable yielding complexes.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Tfcensus.coverage">
+<span class="sig-name descname"><span class="pre">coverage</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">other</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Tfcensus.coverage" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the coverage of the annotation i.e. the proportion of
+entities having at least one record in this annotation resource
+for an arbitrary set of entities.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Tfcensus.curation_effort">
+<span class="sig-name descname"><span class="pre">curation_effort</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Tfcensus.curation_effort" title="Link to this definition">§</a></dt>
+<dd><p>Counts the reference-record pairs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Tfcensus.get_names">
+<span class="sig-name descname"><span class="pre">get_names</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Tfcensus.get_names" title="Link to this definition">§</a></dt>
+<dd><p>Returns the list of field names in the records. The annotation
+consists of uniform records and each entity might be annotated
+with one or more records. Each record is a tuple of fields, for
+example <code class="docutils literal notranslate"><span class="pre">('cell_type',</span> <span class="pre">'expression_level',</span> <span class="pre">'score')</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Tfcensus.get_reference_set">
+<em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">get_reference_set</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">proteins</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">swissprot_only</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Tfcensus.get_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the reference set i.e. the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Tfcensus.get_subset">
+<span class="sig-name descname"><span class="pre">get_subset</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Tfcensus.get_subset" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Tfcensus.get_subset_bool_array">
+<span class="sig-name descname"><span class="pre">get_subset_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Tfcensus.get_subset_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a boolean vector with True and False values for each entity
+in the reference set. The values represent presence absence data
+in the simplest case, but by providing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> any kind of matching
+and filtering is possible. <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> are passed to the <code class="docutils literal notranslate"><span class="pre">select</span></code>
+method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Tfcensus.get_values">
+<span class="sig-name descname"><span class="pre">get_values</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">exclude_none</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Tfcensus.get_values" title="Link to this definition">§</a></dt>
+<dd><p>Returns the set of all possible values of a field. E.g. if the
+records of this annotation have a field <code class="docutils literal notranslate"><span class="pre">cell_type</span></code> then calling
+this method can tell you that across all records the values of
+this field might be <code class="docutils literal notranslate"><span class="pre">{'macrophage',</span> <span class="pre">'epithelial_cell',</span> <span class="pre">...}</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Tfcensus.labels">
+<span class="sig-name descname"><span class="pre">labels</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Tfcensus.labels" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Tfcensus.load">
+<span class="sig-name descname"><span class="pre">load</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Tfcensus.load" title="Link to this definition">§</a></dt>
+<dd><p>Loads the annotation data by calling the input method.
+Infers annotations for complexes in the complex database if
+py:attr:<code class="docutils literal notranslate"><span class="pre">infer_complexes</span></code> is True.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Tfcensus.load_data">
+<span class="sig-name descname"><span class="pre">load_data</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Tfcensus.load_data" title="Link to this definition">§</a></dt>
+<dd><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Tfcensus.load_proteins">
+<span class="sig-name descname"><span class="pre">load_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Tfcensus.load_proteins" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a set of all UniProt IDs to have a base set of the entire
+proteome.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Tfcensus.make_df">
+<span class="sig-name descname"><span class="pre">make_df</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">rebuild</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Tfcensus.make_df" title="Link to this definition">§</a></dt>
+<dd><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.
+The data frame will be assigned to :py:attr``df``.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Tfcensus.numof_entities">
+<span class="sig-name descname"><span class="pre">numof_entities</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Tfcensus.numof_entities" title="Link to this definition">§</a></dt>
+<dd><p>The number of annotated entities in the resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Tfcensus.numof_records">
+<span class="sig-name descname"><span class="pre">numof_records</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Tfcensus.numof_records" title="Link to this definition">§</a></dt>
+<dd><p>The total number of annotation records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Tfcensus.numof_references">
+<span class="sig-name descname"><span class="pre">numof_references</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Tfcensus.numof_references" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects and counts the
+references across all records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Tfcensus.process">
+<span class="sig-name descname"><span class="pre">process</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Tfcensus.process" title="Link to this definition">§</a></dt>
+<dd><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Tfcensus.reload">
+<span class="sig-name descname"><span class="pre">reload</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Tfcensus.reload" title="Link to this definition">§</a></dt>
+<dd><p>Reloads the object from the module level.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Tfcensus.select">
+<span class="sig-name descname"><span class="pre">select</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Tfcensus.select" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Tfcensus.set_method">
+<span class="sig-name descname"><span class="pre">set_method</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Tfcensus.set_method" title="Link to this definition">§</a></dt>
+<dd><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if
+necessary.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Tfcensus.set_reference_set">
+<span class="sig-name descname"><span class="pre">set_reference_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Tfcensus.set_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Assigns the reference set to the :py:attr``reference_set`` attribute.
+The reference set is the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Tfcensus.show">
+<span class="sig-name descname"><span class="pre">show</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">table_param</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Tfcensus.show" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic
+information from the UniProt datasheets.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Tfcensus.subset_intersection">
+<span class="sig-name descname"><span class="pre">subset_intersection</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">universe</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Tfcensus.subset_intersection" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the proportion of entities in a subset occuring in the
+set <code class="docutils literal notranslate"><span class="pre">universe</span></code>. The subset is selected by passing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> to the
+<code class="docutils literal notranslate"><span class="pre">select</span></code> method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Tfcensus.to_array">
+<span class="sig-name descname"><span class="pre">to_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_fields</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Tfcensus.to_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns an entity vs feature array. In case of more complex
+annotations this might be huge.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Tfcensus.to_bool_array">
+<span class="sig-name descname"><span class="pre">to_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Tfcensus.to_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a presence/absence boolean array for a reference set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Tfcensus.to_set">
+<span class="sig-name descname"><span class="pre">to_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Tfcensus.to_set" title="Link to this definition">§</a></dt>
+<dd><p>Returns the entities present in this annotation resource as a set.</p>
+</dd></dl>
+
+</dd></dl>
+
+</section>
+
+
+                </article>
+              
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+  <section id="pypath-core-annot-topdb">
+<h1>pypath.core.annot.Topdb<a class="headerlink" href="#pypath-core-annot-topdb" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.core.annot.Topdb">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.core.annot.</span></span><span class="sig-name descname"><span class="pre">Topdb</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#Topdb"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.Topdb" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <a class="reference internal" href="pypath.core.annot.AnnotationBase.html#pypath.core.annot.AnnotationBase" title="pypath.core.annot.AnnotationBase"><code class="xref py py-class docutils literal notranslate"><span class="pre">AnnotationBase</span></code></a></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Topdb.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#Topdb.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.Topdb.__init__" title="Link to this definition">§</a></dt>
+<dd><p>Represents annotations for a set of proteins.
+Loads the data from the original resource and provides methods
+to query the annotations.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>name</strong> (<em>str</em>) – A custom name for the annotation resource.</p></li>
+<li><p><strong>ncbi_tax_id</strong> (<em>int</em>) – NCBI Taxonomy identifier.</p></li>
+<li><p><strong>input_method</strong> (<em>callable</em><em>,</em><em>str</em>) – Either a callable or the name of a method in any submodules of
+the <code class="docutils literal notranslate"><span class="pre">pypath.inputs</span></code>  module. Should return a dict with
+UniProt IDs as keys or an object suitable for <code class="docutils literal notranslate"><span class="pre">process_method</span></code>.</p></li>
+<li><p><strong>input_args</strong> (<em>dict</em>) – Arguments for the <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Topdb.__init__" title="pypath.core.annot.Topdb.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>([ncbi_tax_id])</p></td>
+<td><p>Represents annotations for a set of proteins.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Topdb.add_complexes_by_inference" title="pypath.core.annot.Topdb.add_complexes_by_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">add_complexes_by_inference</span></code></a>([complexes])</p></td>
+<td><p>Creates complex annotations by in silico inference and adds them to this annotation set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Topdb.all_complexes" title="pypath.core.annot.Topdb.all_complexes"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_complexes</span></code></a>()</p></td>
+<td><p>All protein complexes annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Topdb.all_entities" title="pypath.core.annot.Topdb.all_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_entities</span></code></a>([entity_types])</p></td>
+<td><p>All entities annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Topdb.all_mirnas" title="pypath.core.annot.Topdb.all_mirnas"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_mirnas</span></code></a>()</p></td>
+<td><p>All miRNAs annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Topdb.all_proteins" title="pypath.core.annot.Topdb.all_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_proteins</span></code></a>()</p></td>
+<td><p>All UniProt IDs annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Topdb.all_refs" title="pypath.core.annot.Topdb.all_refs"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_refs</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Topdb.annotate_complex" title="pypath.core.annot.Topdb.annotate_complex"><code class="xref py py-obj docutils literal notranslate"><span class="pre">annotate_complex</span></code></a>(cplex)</p></td>
+<td><p>Infers annotations for a single complex.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Topdb.browse" title="pypath.core.annot.Topdb.browse"><code class="xref py py-obj docutils literal notranslate"><span class="pre">browse</span></code></a>([field, start])</p></td>
+<td><p>Print gene information as a table.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Topdb.complex_inference" title="pypath.core.annot.Topdb.complex_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">complex_inference</span></code></a>([complexes])</p></td>
+<td><p>Annotates all complexes in <cite>complexes</cite>, by default in the default complex database (existing in the <cite>complex</cite> module or generated on demand according to the module's current settings).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Topdb.coverage" title="pypath.core.annot.Topdb.coverage"><code class="xref py py-obj docutils literal notranslate"><span class="pre">coverage</span></code></a>(other)</p></td>
+<td><p>Calculates the coverage of the annotation i.e. the proportion of entities having at least one record in this annotation resource for an arbitrary set of entities.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Topdb.curation_effort" title="pypath.core.annot.Topdb.curation_effort"><code class="xref py py-obj docutils literal notranslate"><span class="pre">curation_effort</span></code></a>()</p></td>
+<td><p>Counts the reference-record pairs.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">from_dump</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_entity_type</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Topdb.get_names" title="pypath.core.annot.Topdb.get_names"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_names</span></code></a>()</p></td>
+<td><p>Returns the list of field names in the records.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Topdb.get_reference_set" title="pypath.core.annot.Topdb.get_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_reference_set</span></code></a>([proteins, complexes, ...])</p></td>
+<td><p>Retrieves the reference set i.e. the set of all entities which potentially have annotation in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Topdb.get_subset" title="pypath.core.annot.Topdb.get_subset"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Topdb.get_subset_bool_array" title="pypath.core.annot.Topdb.get_subset_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset_bool_array</span></code></a>([reference_set])</p></td>
+<td><p>Returns a boolean vector with True and False values for each entity in the reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Topdb.get_values" title="pypath.core.annot.Topdb.get_values"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_values</span></code></a>(name[, exclude_none])</p></td>
+<td><p>Returns the set of all possible values of a field.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_complex</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_mirna</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_protein</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Topdb.labels" title="pypath.core.annot.Topdb.labels"><code class="xref py py-obj docutils literal notranslate"><span class="pre">labels</span></code></a>([method])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Topdb.load" title="pypath.core.annot.Topdb.load"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load</span></code></a>()</p></td>
+<td><p>Loads the annotation data by calling the input method.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Topdb.load_data" title="pypath.core.annot.Topdb.load_data"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_data</span></code></a>()</p></td>
+<td><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Topdb.load_proteins" title="pypath.core.annot.Topdb.load_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_proteins</span></code></a>()</p></td>
+<td><p>Retrieves a set of all UniProt IDs to have a base set of the entire proteome.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Topdb.make_df" title="pypath.core.annot.Topdb.make_df"><code class="xref py py-obj docutils literal notranslate"><span class="pre">make_df</span></code></a>([rebuild])</p></td>
+<td><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complex_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Topdb.numof_entities" title="pypath.core.annot.Topdb.numof_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_entities</span></code></a>()</p></td>
+<td><p>The number of annotated entities in the resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirna_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirnas</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_protein_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_proteins</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Topdb.numof_records" title="pypath.core.annot.Topdb.numof_records"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_records</span></code></a>([entity_types])</p></td>
+<td><p>The total number of annotation records.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Topdb.numof_references" title="pypath.core.annot.Topdb.numof_references"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_references</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Topdb.process" title="pypath.core.annot.Topdb.process"><code class="xref py py-obj docutils literal notranslate"><span class="pre">process</span></code></a>()</p></td>
+<td><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">proportion</span></code>(other)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Topdb.reload" title="pypath.core.annot.Topdb.reload"><code class="xref py py-obj docutils literal notranslate"><span class="pre">reload</span></code></a>()</p></td>
+<td><p>Reloads the object from the module level.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">save_to_pickle</span></code>(pickle_file)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Topdb.select" title="pypath.core.annot.Topdb.select"><code class="xref py py-obj docutils literal notranslate"><span class="pre">select</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Topdb.set_method" title="pypath.core.annot.Topdb.set_method"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_method</span></code></a>()</p></td>
+<td><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if necessary.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Topdb.set_reference_set" title="pypath.core.annot.Topdb.set_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_reference_set</span></code></a>()</p></td>
+<td><p>Assigns the reference set to the :py:attr``reference_set`` attribute.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Topdb.show" title="pypath.core.annot.Topdb.show"><code class="xref py py-obj docutils literal notranslate"><span class="pre">show</span></code></a>([method, table_param])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic information from the UniProt datasheets.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Topdb.subset_intersection" title="pypath.core.annot.Topdb.subset_intersection"><code class="xref py py-obj docutils literal notranslate"><span class="pre">subset_intersection</span></code></a>(universe, **kwargs)</p></td>
+<td><p>Calculates the proportion of entities in a subset occuring in the set <code class="docutils literal notranslate"><span class="pre">universe</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Topdb.to_array" title="pypath.core.annot.Topdb.to_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_array</span></code></a>([reference_set, use_fields])</p></td>
+<td><p>Returns an entity vs feature array.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Topdb.to_bool_array" title="pypath.core.annot.Topdb.to_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_bool_array</span></code></a>(reference_set)</p></td>
+<td><p>Returns a presence/absence boolean array for a reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Topdb.to_set" title="pypath.core.annot.Topdb.to_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_set</span></code></a>()</p></td>
+<td><p>Returns the entities present in this annotation resource as a set.</p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Attributes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_fields</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">summary</span></code></p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Topdb.add_complexes_by_inference">
+<span class="sig-name descname"><span class="pre">add_complexes_by_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Topdb.add_complexes_by_inference" title="Link to this definition">§</a></dt>
+<dd><p>Creates complex annotations by in silico inference and adds them
+to this annotation set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Topdb.all_complexes">
+<span class="sig-name descname"><span class="pre">all_complexes</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Topdb.all_complexes" title="Link to this definition">§</a></dt>
+<dd><p>All protein complexes annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Topdb.all_entities">
+<span class="sig-name descname"><span class="pre">all_entities</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Topdb.all_entities" title="Link to this definition">§</a></dt>
+<dd><p>All entities annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Topdb.all_mirnas">
+<span class="sig-name descname"><span class="pre">all_mirnas</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Topdb.all_mirnas" title="Link to this definition">§</a></dt>
+<dd><p>All miRNAs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Topdb.all_proteins">
+<span class="sig-name descname"><span class="pre">all_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Topdb.all_proteins" title="Link to this definition">§</a></dt>
+<dd><p>All UniProt IDs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Topdb.all_refs">
+<span class="sig-name descname"><span class="pre">all_refs</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Topdb.all_refs" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects the references
+across all records. Returns <em>list</em>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Topdb.annotate_complex">
+<span class="sig-name descname"><span class="pre">annotate_complex</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cplex</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Topdb.annotate_complex" title="Link to this definition">§</a></dt>
+<dd><p>Infers annotations for a single complex.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Topdb.browse">
+<span class="sig-name descname"><span class="pre">browse</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">field</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">start</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Topdb.browse" title="Link to this definition">§</a></dt>
+<dd><p>Print gene information as a table.</p>
+<p>Presents information about annotation categories as ascii tables
+printed in the terminal. If one category provided, prints one table.
+If multiple categories provided, prints a table for each of them one
+by one proceeding to the next one once you hit return. If no categories
+provided goes through all levels of the primary category.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>field:</dt><dd><p>The field to browse categories by.</p>
+<ul class="simple">
+<li><p>If None the primary field will be selected.
+If this annotation resource doesn’t have fields, all proteins
+will be presented as one single category.</p></li>
+<li><p>If a string it will be considered a field name and it will
+browse through all levels of this field.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">list</span></code>, set or tuple, it will be considered either a
+<code class="docutils literal notranslate"><span class="pre">list</span></code> of field names or a list of values from the primary
+field. In the former case all combinations of the values of
+the fields will be presented, in the latter case the browsing
+will be limited to the levels of the primary field contained
+in <code class="docutils literal notranslate"><span class="pre">field</span></code>.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">dict</span></code>, keys are supposed to be field names and values
+as list of levels. If any of the values are None, all levels
+from that field will be used.</p></li>
+</ul>
+</dd>
+<dt>start:</dt><dd><p>Start browsing from this category. E.g. if there are 500
+categories and start is 250 it will skip everything before the
+250th.</p>
+</dd>
+<dt>kwargs:</dt><dd><p>Passed to <code class="docutils literal notranslate"><span class="pre">pypath.utils.uniprot.info</span></code>.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Topdb.complex_inference">
+<span class="sig-name descname"><span class="pre">complex_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Topdb.complex_inference" title="Link to this definition">§</a></dt>
+<dd><p>Annotates all complexes in <cite>complexes</cite>, by default in the default
+complex database (existing in the <cite>complex</cite> module or generated
+on demand according to the module’s current settings).</p>
+<dl class="field-list simple">
+<dt class="field-odd">Returns<span class="colon">:</span></dt>
+<dd class="field-odd"><p><ul class="simple">
+<li><p><em>Dict with complexes as keys and sets of annotations as values.</em></p></li>
+<li><p><em>Complexes with no valid information in this annotation resource</em></p></li>
+<li><p><em>won’t be in the dict.</em></p></li>
+</ul>
+</p>
+</dd>
+<dt class="field-even">Parameters<span class="colon">:</span></dt>
+<dd class="field-even"><p><strong>complexes</strong> (<em>iterable</em>) – Iterable yielding complexes.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Topdb.coverage">
+<span class="sig-name descname"><span class="pre">coverage</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">other</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Topdb.coverage" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the coverage of the annotation i.e. the proportion of
+entities having at least one record in this annotation resource
+for an arbitrary set of entities.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Topdb.curation_effort">
+<span class="sig-name descname"><span class="pre">curation_effort</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Topdb.curation_effort" title="Link to this definition">§</a></dt>
+<dd><p>Counts the reference-record pairs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Topdb.get_names">
+<span class="sig-name descname"><span class="pre">get_names</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Topdb.get_names" title="Link to this definition">§</a></dt>
+<dd><p>Returns the list of field names in the records. The annotation
+consists of uniform records and each entity might be annotated
+with one or more records. Each record is a tuple of fields, for
+example <code class="docutils literal notranslate"><span class="pre">('cell_type',</span> <span class="pre">'expression_level',</span> <span class="pre">'score')</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Topdb.get_reference_set">
+<em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">get_reference_set</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">proteins</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">swissprot_only</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Topdb.get_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the reference set i.e. the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Topdb.get_subset">
+<span class="sig-name descname"><span class="pre">get_subset</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Topdb.get_subset" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Topdb.get_subset_bool_array">
+<span class="sig-name descname"><span class="pre">get_subset_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Topdb.get_subset_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a boolean vector with True and False values for each entity
+in the reference set. The values represent presence absence data
+in the simplest case, but by providing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> any kind of matching
+and filtering is possible. <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> are passed to the <code class="docutils literal notranslate"><span class="pre">select</span></code>
+method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Topdb.get_values">
+<span class="sig-name descname"><span class="pre">get_values</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">exclude_none</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Topdb.get_values" title="Link to this definition">§</a></dt>
+<dd><p>Returns the set of all possible values of a field. E.g. if the
+records of this annotation have a field <code class="docutils literal notranslate"><span class="pre">cell_type</span></code> then calling
+this method can tell you that across all records the values of
+this field might be <code class="docutils literal notranslate"><span class="pre">{'macrophage',</span> <span class="pre">'epithelial_cell',</span> <span class="pre">...}</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Topdb.labels">
+<span class="sig-name descname"><span class="pre">labels</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Topdb.labels" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Topdb.load">
+<span class="sig-name descname"><span class="pre">load</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Topdb.load" title="Link to this definition">§</a></dt>
+<dd><p>Loads the annotation data by calling the input method.
+Infers annotations for complexes in the complex database if
+py:attr:<code class="docutils literal notranslate"><span class="pre">infer_complexes</span></code> is True.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Topdb.load_data">
+<span class="sig-name descname"><span class="pre">load_data</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Topdb.load_data" title="Link to this definition">§</a></dt>
+<dd><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Topdb.load_proteins">
+<span class="sig-name descname"><span class="pre">load_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Topdb.load_proteins" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a set of all UniProt IDs to have a base set of the entire
+proteome.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Topdb.make_df">
+<span class="sig-name descname"><span class="pre">make_df</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">rebuild</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Topdb.make_df" title="Link to this definition">§</a></dt>
+<dd><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.
+The data frame will be assigned to :py:attr``df``.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Topdb.numof_entities">
+<span class="sig-name descname"><span class="pre">numof_entities</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Topdb.numof_entities" title="Link to this definition">§</a></dt>
+<dd><p>The number of annotated entities in the resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Topdb.numof_records">
+<span class="sig-name descname"><span class="pre">numof_records</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Topdb.numof_records" title="Link to this definition">§</a></dt>
+<dd><p>The total number of annotation records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Topdb.numof_references">
+<span class="sig-name descname"><span class="pre">numof_references</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Topdb.numof_references" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects and counts the
+references across all records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Topdb.process">
+<span class="sig-name descname"><span class="pre">process</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Topdb.process" title="Link to this definition">§</a></dt>
+<dd><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Topdb.reload">
+<span class="sig-name descname"><span class="pre">reload</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Topdb.reload" title="Link to this definition">§</a></dt>
+<dd><p>Reloads the object from the module level.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Topdb.select">
+<span class="sig-name descname"><span class="pre">select</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Topdb.select" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Topdb.set_method">
+<span class="sig-name descname"><span class="pre">set_method</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Topdb.set_method" title="Link to this definition">§</a></dt>
+<dd><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if
+necessary.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Topdb.set_reference_set">
+<span class="sig-name descname"><span class="pre">set_reference_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Topdb.set_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Assigns the reference set to the :py:attr``reference_set`` attribute.
+The reference set is the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Topdb.show">
+<span class="sig-name descname"><span class="pre">show</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">table_param</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Topdb.show" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic
+information from the UniProt datasheets.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Topdb.subset_intersection">
+<span class="sig-name descname"><span class="pre">subset_intersection</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">universe</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Topdb.subset_intersection" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the proportion of entities in a subset occuring in the
+set <code class="docutils literal notranslate"><span class="pre">universe</span></code>. The subset is selected by passing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> to the
+<code class="docutils literal notranslate"><span class="pre">select</span></code> method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Topdb.to_array">
+<span class="sig-name descname"><span class="pre">to_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_fields</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Topdb.to_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns an entity vs feature array. In case of more complex
+annotations this might be huge.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Topdb.to_bool_array">
+<span class="sig-name descname"><span class="pre">to_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Topdb.to_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a presence/absence boolean array for a reference set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Topdb.to_set">
+<span class="sig-name descname"><span class="pre">to_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Topdb.to_set" title="Link to this definition">§</a></dt>
+<dd><p>Returns the entities present in this annotation resource as a set.</p>
+</dd></dl>
+
+</dd></dl>
+
+</section>
+
+
+                </article>
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+  <section id="pypath-core-annot-uniprotfamilies">
+<h1>pypath.core.annot.UniprotFamilies<a class="headerlink" href="#pypath-core-annot-uniprotfamilies" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotFamilies">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.core.annot.</span></span><span class="sig-name descname"><span class="pre">UniprotFamilies</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#UniprotFamilies"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.UniprotFamilies" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <a class="reference internal" href="pypath.core.annot.AnnotationBase.html#pypath.core.annot.AnnotationBase" title="pypath.core.annot.AnnotationBase"><code class="xref py py-class docutils literal notranslate"><span class="pre">AnnotationBase</span></code></a></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotFamilies.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#UniprotFamilies.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.UniprotFamilies.__init__" title="Link to this definition">§</a></dt>
+<dd><p>Protein families from UniProt.</p>
+</dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotFamilies.__init__" title="pypath.core.annot.UniprotFamilies.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>([ncbi_tax_id])</p></td>
+<td><p>Protein families from UniProt.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotFamilies.add_complexes_by_inference" title="pypath.core.annot.UniprotFamilies.add_complexes_by_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">add_complexes_by_inference</span></code></a>([complexes])</p></td>
+<td><p>Creates complex annotations by in silico inference and adds them to this annotation set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotFamilies.all_complexes" title="pypath.core.annot.UniprotFamilies.all_complexes"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_complexes</span></code></a>()</p></td>
+<td><p>All protein complexes annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotFamilies.all_entities" title="pypath.core.annot.UniprotFamilies.all_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_entities</span></code></a>([entity_types])</p></td>
+<td><p>All entities annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotFamilies.all_mirnas" title="pypath.core.annot.UniprotFamilies.all_mirnas"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_mirnas</span></code></a>()</p></td>
+<td><p>All miRNAs annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotFamilies.all_proteins" title="pypath.core.annot.UniprotFamilies.all_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_proteins</span></code></a>()</p></td>
+<td><p>All UniProt IDs annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotFamilies.all_refs" title="pypath.core.annot.UniprotFamilies.all_refs"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_refs</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotFamilies.annotate_complex" title="pypath.core.annot.UniprotFamilies.annotate_complex"><code class="xref py py-obj docutils literal notranslate"><span class="pre">annotate_complex</span></code></a>(cplex)</p></td>
+<td><p>Infers annotations for a single complex.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotFamilies.browse" title="pypath.core.annot.UniprotFamilies.browse"><code class="xref py py-obj docutils literal notranslate"><span class="pre">browse</span></code></a>([field, start])</p></td>
+<td><p>Print gene information as a table.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotFamilies.complex_inference" title="pypath.core.annot.UniprotFamilies.complex_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">complex_inference</span></code></a>([complexes])</p></td>
+<td><p>Annotates all complexes in <cite>complexes</cite>, by default in the default complex database (existing in the <cite>complex</cite> module or generated on demand according to the module's current settings).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotFamilies.coverage" title="pypath.core.annot.UniprotFamilies.coverage"><code class="xref py py-obj docutils literal notranslate"><span class="pre">coverage</span></code></a>(other)</p></td>
+<td><p>Calculates the coverage of the annotation i.e. the proportion of entities having at least one record in this annotation resource for an arbitrary set of entities.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotFamilies.curation_effort" title="pypath.core.annot.UniprotFamilies.curation_effort"><code class="xref py py-obj docutils literal notranslate"><span class="pre">curation_effort</span></code></a>()</p></td>
+<td><p>Counts the reference-record pairs.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">from_dump</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_entity_type</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotFamilies.get_names" title="pypath.core.annot.UniprotFamilies.get_names"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_names</span></code></a>()</p></td>
+<td><p>Returns the list of field names in the records.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotFamilies.get_reference_set" title="pypath.core.annot.UniprotFamilies.get_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_reference_set</span></code></a>([proteins, complexes, ...])</p></td>
+<td><p>Retrieves the reference set i.e. the set of all entities which potentially have annotation in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotFamilies.get_subset" title="pypath.core.annot.UniprotFamilies.get_subset"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotFamilies.get_subset_bool_array" title="pypath.core.annot.UniprotFamilies.get_subset_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset_bool_array</span></code></a>([reference_set])</p></td>
+<td><p>Returns a boolean vector with True and False values for each entity in the reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotFamilies.get_values" title="pypath.core.annot.UniprotFamilies.get_values"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_values</span></code></a>(name[, exclude_none])</p></td>
+<td><p>Returns the set of all possible values of a field.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_complex</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_mirna</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_protein</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotFamilies.labels" title="pypath.core.annot.UniprotFamilies.labels"><code class="xref py py-obj docutils literal notranslate"><span class="pre">labels</span></code></a>([method])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotFamilies.load" title="pypath.core.annot.UniprotFamilies.load"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load</span></code></a>()</p></td>
+<td><p>Loads the annotation data by calling the input method.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotFamilies.load_data" title="pypath.core.annot.UniprotFamilies.load_data"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_data</span></code></a>()</p></td>
+<td><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotFamilies.load_proteins" title="pypath.core.annot.UniprotFamilies.load_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_proteins</span></code></a>()</p></td>
+<td><p>Retrieves a set of all UniProt IDs to have a base set of the entire proteome.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotFamilies.make_df" title="pypath.core.annot.UniprotFamilies.make_df"><code class="xref py py-obj docutils literal notranslate"><span class="pre">make_df</span></code></a>([rebuild])</p></td>
+<td><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complex_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotFamilies.numof_entities" title="pypath.core.annot.UniprotFamilies.numof_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_entities</span></code></a>()</p></td>
+<td><p>The number of annotated entities in the resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirna_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirnas</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_protein_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_proteins</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotFamilies.numof_records" title="pypath.core.annot.UniprotFamilies.numof_records"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_records</span></code></a>([entity_types])</p></td>
+<td><p>The total number of annotation records.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotFamilies.numof_references" title="pypath.core.annot.UniprotFamilies.numof_references"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_references</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotFamilies.process" title="pypath.core.annot.UniprotFamilies.process"><code class="xref py py-obj docutils literal notranslate"><span class="pre">process</span></code></a>()</p></td>
+<td><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">proportion</span></code>(other)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotFamilies.reload" title="pypath.core.annot.UniprotFamilies.reload"><code class="xref py py-obj docutils literal notranslate"><span class="pre">reload</span></code></a>()</p></td>
+<td><p>Reloads the object from the module level.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">save_to_pickle</span></code>(pickle_file)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotFamilies.select" title="pypath.core.annot.UniprotFamilies.select"><code class="xref py py-obj docutils literal notranslate"><span class="pre">select</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotFamilies.set_method" title="pypath.core.annot.UniprotFamilies.set_method"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_method</span></code></a>()</p></td>
+<td><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if necessary.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotFamilies.set_reference_set" title="pypath.core.annot.UniprotFamilies.set_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_reference_set</span></code></a>()</p></td>
+<td><p>Assigns the reference set to the :py:attr``reference_set`` attribute.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotFamilies.show" title="pypath.core.annot.UniprotFamilies.show"><code class="xref py py-obj docutils literal notranslate"><span class="pre">show</span></code></a>([method, table_param])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic information from the UniProt datasheets.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotFamilies.subset_intersection" title="pypath.core.annot.UniprotFamilies.subset_intersection"><code class="xref py py-obj docutils literal notranslate"><span class="pre">subset_intersection</span></code></a>(universe, **kwargs)</p></td>
+<td><p>Calculates the proportion of entities in a subset occuring in the set <code class="docutils literal notranslate"><span class="pre">universe</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotFamilies.to_array" title="pypath.core.annot.UniprotFamilies.to_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_array</span></code></a>([reference_set, use_fields])</p></td>
+<td><p>Returns an entity vs feature array.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotFamilies.to_bool_array" title="pypath.core.annot.UniprotFamilies.to_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_bool_array</span></code></a>(reference_set)</p></td>
+<td><p>Returns a presence/absence boolean array for a reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotFamilies.to_set" title="pypath.core.annot.UniprotFamilies.to_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_set</span></code></a>()</p></td>
+<td><p>Returns the entities present in this annotation resource as a set.</p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Attributes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_fields</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">summary</span></code></p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotFamilies.add_complexes_by_inference">
+<span class="sig-name descname"><span class="pre">add_complexes_by_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotFamilies.add_complexes_by_inference" title="Link to this definition">§</a></dt>
+<dd><p>Creates complex annotations by in silico inference and adds them
+to this annotation set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotFamilies.all_complexes">
+<span class="sig-name descname"><span class="pre">all_complexes</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotFamilies.all_complexes" title="Link to this definition">§</a></dt>
+<dd><p>All protein complexes annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotFamilies.all_entities">
+<span class="sig-name descname"><span class="pre">all_entities</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotFamilies.all_entities" title="Link to this definition">§</a></dt>
+<dd><p>All entities annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotFamilies.all_mirnas">
+<span class="sig-name descname"><span class="pre">all_mirnas</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotFamilies.all_mirnas" title="Link to this definition">§</a></dt>
+<dd><p>All miRNAs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotFamilies.all_proteins">
+<span class="sig-name descname"><span class="pre">all_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotFamilies.all_proteins" title="Link to this definition">§</a></dt>
+<dd><p>All UniProt IDs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotFamilies.all_refs">
+<span class="sig-name descname"><span class="pre">all_refs</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotFamilies.all_refs" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects the references
+across all records. Returns <em>list</em>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotFamilies.annotate_complex">
+<span class="sig-name descname"><span class="pre">annotate_complex</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cplex</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotFamilies.annotate_complex" title="Link to this definition">§</a></dt>
+<dd><p>Infers annotations for a single complex.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotFamilies.browse">
+<span class="sig-name descname"><span class="pre">browse</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">field</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">start</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotFamilies.browse" title="Link to this definition">§</a></dt>
+<dd><p>Print gene information as a table.</p>
+<p>Presents information about annotation categories as ascii tables
+printed in the terminal. If one category provided, prints one table.
+If multiple categories provided, prints a table for each of them one
+by one proceeding to the next one once you hit return. If no categories
+provided goes through all levels of the primary category.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>field:</dt><dd><p>The field to browse categories by.</p>
+<ul class="simple">
+<li><p>If None the primary field will be selected.
+If this annotation resource doesn’t have fields, all proteins
+will be presented as one single category.</p></li>
+<li><p>If a string it will be considered a field name and it will
+browse through all levels of this field.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">list</span></code>, set or tuple, it will be considered either a
+<code class="docutils literal notranslate"><span class="pre">list</span></code> of field names or a list of values from the primary
+field. In the former case all combinations of the values of
+the fields will be presented, in the latter case the browsing
+will be limited to the levels of the primary field contained
+in <code class="docutils literal notranslate"><span class="pre">field</span></code>.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">dict</span></code>, keys are supposed to be field names and values
+as list of levels. If any of the values are None, all levels
+from that field will be used.</p></li>
+</ul>
+</dd>
+<dt>start:</dt><dd><p>Start browsing from this category. E.g. if there are 500
+categories and start is 250 it will skip everything before the
+250th.</p>
+</dd>
+<dt>kwargs:</dt><dd><p>Passed to <code class="docutils literal notranslate"><span class="pre">pypath.utils.uniprot.info</span></code>.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotFamilies.complex_inference">
+<span class="sig-name descname"><span class="pre">complex_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotFamilies.complex_inference" title="Link to this definition">§</a></dt>
+<dd><p>Annotates all complexes in <cite>complexes</cite>, by default in the default
+complex database (existing in the <cite>complex</cite> module or generated
+on demand according to the module’s current settings).</p>
+<dl class="field-list simple">
+<dt class="field-odd">Returns<span class="colon">:</span></dt>
+<dd class="field-odd"><p><ul class="simple">
+<li><p><em>Dict with complexes as keys and sets of annotations as values.</em></p></li>
+<li><p><em>Complexes with no valid information in this annotation resource</em></p></li>
+<li><p><em>won’t be in the dict.</em></p></li>
+</ul>
+</p>
+</dd>
+<dt class="field-even">Parameters<span class="colon">:</span></dt>
+<dd class="field-even"><p><strong>complexes</strong> (<em>iterable</em>) – Iterable yielding complexes.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotFamilies.coverage">
+<span class="sig-name descname"><span class="pre">coverage</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">other</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotFamilies.coverage" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the coverage of the annotation i.e. the proportion of
+entities having at least one record in this annotation resource
+for an arbitrary set of entities.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotFamilies.curation_effort">
+<span class="sig-name descname"><span class="pre">curation_effort</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotFamilies.curation_effort" title="Link to this definition">§</a></dt>
+<dd><p>Counts the reference-record pairs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotFamilies.get_names">
+<span class="sig-name descname"><span class="pre">get_names</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotFamilies.get_names" title="Link to this definition">§</a></dt>
+<dd><p>Returns the list of field names in the records. The annotation
+consists of uniform records and each entity might be annotated
+with one or more records. Each record is a tuple of fields, for
+example <code class="docutils literal notranslate"><span class="pre">('cell_type',</span> <span class="pre">'expression_level',</span> <span class="pre">'score')</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotFamilies.get_reference_set">
+<em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">get_reference_set</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">proteins</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">swissprot_only</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotFamilies.get_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the reference set i.e. the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotFamilies.get_subset">
+<span class="sig-name descname"><span class="pre">get_subset</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotFamilies.get_subset" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotFamilies.get_subset_bool_array">
+<span class="sig-name descname"><span class="pre">get_subset_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotFamilies.get_subset_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a boolean vector with True and False values for each entity
+in the reference set. The values represent presence absence data
+in the simplest case, but by providing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> any kind of matching
+and filtering is possible. <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> are passed to the <code class="docutils literal notranslate"><span class="pre">select</span></code>
+method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotFamilies.get_values">
+<span class="sig-name descname"><span class="pre">get_values</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">exclude_none</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotFamilies.get_values" title="Link to this definition">§</a></dt>
+<dd><p>Returns the set of all possible values of a field. E.g. if the
+records of this annotation have a field <code class="docutils literal notranslate"><span class="pre">cell_type</span></code> then calling
+this method can tell you that across all records the values of
+this field might be <code class="docutils literal notranslate"><span class="pre">{'macrophage',</span> <span class="pre">'epithelial_cell',</span> <span class="pre">...}</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotFamilies.labels">
+<span class="sig-name descname"><span class="pre">labels</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotFamilies.labels" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotFamilies.load">
+<span class="sig-name descname"><span class="pre">load</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotFamilies.load" title="Link to this definition">§</a></dt>
+<dd><p>Loads the annotation data by calling the input method.
+Infers annotations for complexes in the complex database if
+py:attr:<code class="docutils literal notranslate"><span class="pre">infer_complexes</span></code> is True.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotFamilies.load_data">
+<span class="sig-name descname"><span class="pre">load_data</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotFamilies.load_data" title="Link to this definition">§</a></dt>
+<dd><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotFamilies.load_proteins">
+<span class="sig-name descname"><span class="pre">load_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotFamilies.load_proteins" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a set of all UniProt IDs to have a base set of the entire
+proteome.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotFamilies.make_df">
+<span class="sig-name descname"><span class="pre">make_df</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">rebuild</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotFamilies.make_df" title="Link to this definition">§</a></dt>
+<dd><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.
+The data frame will be assigned to :py:attr``df``.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotFamilies.numof_entities">
+<span class="sig-name descname"><span class="pre">numof_entities</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotFamilies.numof_entities" title="Link to this definition">§</a></dt>
+<dd><p>The number of annotated entities in the resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotFamilies.numof_records">
+<span class="sig-name descname"><span class="pre">numof_records</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotFamilies.numof_records" title="Link to this definition">§</a></dt>
+<dd><p>The total number of annotation records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotFamilies.numof_references">
+<span class="sig-name descname"><span class="pre">numof_references</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotFamilies.numof_references" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects and counts the
+references across all records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotFamilies.process">
+<span class="sig-name descname"><span class="pre">process</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotFamilies.process" title="Link to this definition">§</a></dt>
+<dd><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotFamilies.reload">
+<span class="sig-name descname"><span class="pre">reload</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotFamilies.reload" title="Link to this definition">§</a></dt>
+<dd><p>Reloads the object from the module level.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotFamilies.select">
+<span class="sig-name descname"><span class="pre">select</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotFamilies.select" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotFamilies.set_method">
+<span class="sig-name descname"><span class="pre">set_method</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotFamilies.set_method" title="Link to this definition">§</a></dt>
+<dd><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if
+necessary.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotFamilies.set_reference_set">
+<span class="sig-name descname"><span class="pre">set_reference_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotFamilies.set_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Assigns the reference set to the :py:attr``reference_set`` attribute.
+The reference set is the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotFamilies.show">
+<span class="sig-name descname"><span class="pre">show</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">table_param</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotFamilies.show" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic
+information from the UniProt datasheets.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotFamilies.subset_intersection">
+<span class="sig-name descname"><span class="pre">subset_intersection</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">universe</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotFamilies.subset_intersection" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the proportion of entities in a subset occuring in the
+set <code class="docutils literal notranslate"><span class="pre">universe</span></code>. The subset is selected by passing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> to the
+<code class="docutils literal notranslate"><span class="pre">select</span></code> method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotFamilies.to_array">
+<span class="sig-name descname"><span class="pre">to_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_fields</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotFamilies.to_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns an entity vs feature array. In case of more complex
+annotations this might be huge.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotFamilies.to_bool_array">
+<span class="sig-name descname"><span class="pre">to_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotFamilies.to_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a presence/absence boolean array for a reference set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotFamilies.to_set">
+<span class="sig-name descname"><span class="pre">to_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotFamilies.to_set" title="Link to this definition">§</a></dt>
+<dd><p>Returns the entities present in this annotation resource as a set.</p>
+</dd></dl>
+
+</dd></dl>
+
+</section>
+
+
+                </article>
+              
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+  <section id="pypath-core-annot-uniprotkeywords">
+<h1>pypath.core.annot.UniprotKeywords<a class="headerlink" href="#pypath-core-annot-uniprotkeywords" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotKeywords">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.core.annot.</span></span><span class="sig-name descname"><span class="pre">UniprotKeywords</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#UniprotKeywords"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.UniprotKeywords" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <a class="reference internal" href="pypath.core.annot.AnnotationBase.html#pypath.core.annot.AnnotationBase" title="pypath.core.annot.AnnotationBase"><code class="xref py py-class docutils literal notranslate"><span class="pre">AnnotationBase</span></code></a></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotKeywords.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#UniprotKeywords.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.UniprotKeywords.__init__" title="Link to this definition">§</a></dt>
+<dd><p>Tissue expression levels from UniProt.</p>
+</dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotKeywords.__init__" title="pypath.core.annot.UniprotKeywords.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>([ncbi_tax_id])</p></td>
+<td><p>Tissue expression levels from UniProt.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotKeywords.add_complexes_by_inference" title="pypath.core.annot.UniprotKeywords.add_complexes_by_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">add_complexes_by_inference</span></code></a>([complexes])</p></td>
+<td><p>Creates complex annotations by in silico inference and adds them to this annotation set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotKeywords.all_complexes" title="pypath.core.annot.UniprotKeywords.all_complexes"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_complexes</span></code></a>()</p></td>
+<td><p>All protein complexes annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotKeywords.all_entities" title="pypath.core.annot.UniprotKeywords.all_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_entities</span></code></a>([entity_types])</p></td>
+<td><p>All entities annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotKeywords.all_mirnas" title="pypath.core.annot.UniprotKeywords.all_mirnas"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_mirnas</span></code></a>()</p></td>
+<td><p>All miRNAs annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotKeywords.all_proteins" title="pypath.core.annot.UniprotKeywords.all_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_proteins</span></code></a>()</p></td>
+<td><p>All UniProt IDs annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotKeywords.all_refs" title="pypath.core.annot.UniprotKeywords.all_refs"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_refs</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotKeywords.annotate_complex" title="pypath.core.annot.UniprotKeywords.annotate_complex"><code class="xref py py-obj docutils literal notranslate"><span class="pre">annotate_complex</span></code></a>(cplex)</p></td>
+<td><p>Infers annotations for a single complex.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotKeywords.browse" title="pypath.core.annot.UniprotKeywords.browse"><code class="xref py py-obj docutils literal notranslate"><span class="pre">browse</span></code></a>([field, start])</p></td>
+<td><p>Print gene information as a table.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotKeywords.complex_inference" title="pypath.core.annot.UniprotKeywords.complex_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">complex_inference</span></code></a>([complexes])</p></td>
+<td><p>Annotates all complexes in <cite>complexes</cite>, by default in the default complex database (existing in the <cite>complex</cite> module or generated on demand according to the module's current settings).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotKeywords.coverage" title="pypath.core.annot.UniprotKeywords.coverage"><code class="xref py py-obj docutils literal notranslate"><span class="pre">coverage</span></code></a>(other)</p></td>
+<td><p>Calculates the coverage of the annotation i.e. the proportion of entities having at least one record in this annotation resource for an arbitrary set of entities.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotKeywords.curation_effort" title="pypath.core.annot.UniprotKeywords.curation_effort"><code class="xref py py-obj docutils literal notranslate"><span class="pre">curation_effort</span></code></a>()</p></td>
+<td><p>Counts the reference-record pairs.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">from_dump</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_entity_type</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotKeywords.get_names" title="pypath.core.annot.UniprotKeywords.get_names"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_names</span></code></a>()</p></td>
+<td><p>Returns the list of field names in the records.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotKeywords.get_reference_set" title="pypath.core.annot.UniprotKeywords.get_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_reference_set</span></code></a>([proteins, complexes, ...])</p></td>
+<td><p>Retrieves the reference set i.e. the set of all entities which potentially have annotation in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotKeywords.get_subset" title="pypath.core.annot.UniprotKeywords.get_subset"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotKeywords.get_subset_bool_array" title="pypath.core.annot.UniprotKeywords.get_subset_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset_bool_array</span></code></a>([reference_set])</p></td>
+<td><p>Returns a boolean vector with True and False values for each entity in the reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotKeywords.get_values" title="pypath.core.annot.UniprotKeywords.get_values"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_values</span></code></a>(name[, exclude_none])</p></td>
+<td><p>Returns the set of all possible values of a field.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_complex</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_mirna</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_protein</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotKeywords.labels" title="pypath.core.annot.UniprotKeywords.labels"><code class="xref py py-obj docutils literal notranslate"><span class="pre">labels</span></code></a>([method])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotKeywords.load" title="pypath.core.annot.UniprotKeywords.load"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load</span></code></a>()</p></td>
+<td><p>Loads the annotation data by calling the input method.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotKeywords.load_data" title="pypath.core.annot.UniprotKeywords.load_data"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_data</span></code></a>()</p></td>
+<td><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotKeywords.load_proteins" title="pypath.core.annot.UniprotKeywords.load_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_proteins</span></code></a>()</p></td>
+<td><p>Retrieves a set of all UniProt IDs to have a base set of the entire proteome.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotKeywords.make_df" title="pypath.core.annot.UniprotKeywords.make_df"><code class="xref py py-obj docutils literal notranslate"><span class="pre">make_df</span></code></a>([rebuild])</p></td>
+<td><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complex_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotKeywords.numof_entities" title="pypath.core.annot.UniprotKeywords.numof_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_entities</span></code></a>()</p></td>
+<td><p>The number of annotated entities in the resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirna_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirnas</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_protein_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_proteins</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotKeywords.numof_records" title="pypath.core.annot.UniprotKeywords.numof_records"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_records</span></code></a>([entity_types])</p></td>
+<td><p>The total number of annotation records.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotKeywords.numof_references" title="pypath.core.annot.UniprotKeywords.numof_references"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_references</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotKeywords.process" title="pypath.core.annot.UniprotKeywords.process"><code class="xref py py-obj docutils literal notranslate"><span class="pre">process</span></code></a>()</p></td>
+<td><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">proportion</span></code>(other)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotKeywords.reload" title="pypath.core.annot.UniprotKeywords.reload"><code class="xref py py-obj docutils literal notranslate"><span class="pre">reload</span></code></a>()</p></td>
+<td><p>Reloads the object from the module level.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">save_to_pickle</span></code>(pickle_file)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotKeywords.select" title="pypath.core.annot.UniprotKeywords.select"><code class="xref py py-obj docutils literal notranslate"><span class="pre">select</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotKeywords.set_method" title="pypath.core.annot.UniprotKeywords.set_method"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_method</span></code></a>()</p></td>
+<td><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if necessary.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotKeywords.set_reference_set" title="pypath.core.annot.UniprotKeywords.set_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_reference_set</span></code></a>()</p></td>
+<td><p>Assigns the reference set to the :py:attr``reference_set`` attribute.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotKeywords.show" title="pypath.core.annot.UniprotKeywords.show"><code class="xref py py-obj docutils literal notranslate"><span class="pre">show</span></code></a>([method, table_param])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic information from the UniProt datasheets.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotKeywords.subset_intersection" title="pypath.core.annot.UniprotKeywords.subset_intersection"><code class="xref py py-obj docutils literal notranslate"><span class="pre">subset_intersection</span></code></a>(universe, **kwargs)</p></td>
+<td><p>Calculates the proportion of entities in a subset occuring in the set <code class="docutils literal notranslate"><span class="pre">universe</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotKeywords.to_array" title="pypath.core.annot.UniprotKeywords.to_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_array</span></code></a>([reference_set, use_fields])</p></td>
+<td><p>Returns an entity vs feature array.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotKeywords.to_bool_array" title="pypath.core.annot.UniprotKeywords.to_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_bool_array</span></code></a>(reference_set)</p></td>
+<td><p>Returns a presence/absence boolean array for a reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotKeywords.to_set" title="pypath.core.annot.UniprotKeywords.to_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_set</span></code></a>()</p></td>
+<td><p>Returns the entities present in this annotation resource as a set.</p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Attributes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_fields</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">summary</span></code></p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotKeywords.add_complexes_by_inference">
+<span class="sig-name descname"><span class="pre">add_complexes_by_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotKeywords.add_complexes_by_inference" title="Link to this definition">§</a></dt>
+<dd><p>Creates complex annotations by in silico inference and adds them
+to this annotation set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotKeywords.all_complexes">
+<span class="sig-name descname"><span class="pre">all_complexes</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotKeywords.all_complexes" title="Link to this definition">§</a></dt>
+<dd><p>All protein complexes annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotKeywords.all_entities">
+<span class="sig-name descname"><span class="pre">all_entities</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotKeywords.all_entities" title="Link to this definition">§</a></dt>
+<dd><p>All entities annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotKeywords.all_mirnas">
+<span class="sig-name descname"><span class="pre">all_mirnas</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotKeywords.all_mirnas" title="Link to this definition">§</a></dt>
+<dd><p>All miRNAs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotKeywords.all_proteins">
+<span class="sig-name descname"><span class="pre">all_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotKeywords.all_proteins" title="Link to this definition">§</a></dt>
+<dd><p>All UniProt IDs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotKeywords.all_refs">
+<span class="sig-name descname"><span class="pre">all_refs</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotKeywords.all_refs" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects the references
+across all records. Returns <em>list</em>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotKeywords.annotate_complex">
+<span class="sig-name descname"><span class="pre">annotate_complex</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cplex</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotKeywords.annotate_complex" title="Link to this definition">§</a></dt>
+<dd><p>Infers annotations for a single complex.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotKeywords.browse">
+<span class="sig-name descname"><span class="pre">browse</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">field</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">start</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotKeywords.browse" title="Link to this definition">§</a></dt>
+<dd><p>Print gene information as a table.</p>
+<p>Presents information about annotation categories as ascii tables
+printed in the terminal. If one category provided, prints one table.
+If multiple categories provided, prints a table for each of them one
+by one proceeding to the next one once you hit return. If no categories
+provided goes through all levels of the primary category.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>field:</dt><dd><p>The field to browse categories by.</p>
+<ul class="simple">
+<li><p>If None the primary field will be selected.
+If this annotation resource doesn’t have fields, all proteins
+will be presented as one single category.</p></li>
+<li><p>If a string it will be considered a field name and it will
+browse through all levels of this field.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">list</span></code>, set or tuple, it will be considered either a
+<code class="docutils literal notranslate"><span class="pre">list</span></code> of field names or a list of values from the primary
+field. In the former case all combinations of the values of
+the fields will be presented, in the latter case the browsing
+will be limited to the levels of the primary field contained
+in <code class="docutils literal notranslate"><span class="pre">field</span></code>.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">dict</span></code>, keys are supposed to be field names and values
+as list of levels. If any of the values are None, all levels
+from that field will be used.</p></li>
+</ul>
+</dd>
+<dt>start:</dt><dd><p>Start browsing from this category. E.g. if there are 500
+categories and start is 250 it will skip everything before the
+250th.</p>
+</dd>
+<dt>kwargs:</dt><dd><p>Passed to <code class="docutils literal notranslate"><span class="pre">pypath.utils.uniprot.info</span></code>.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotKeywords.complex_inference">
+<span class="sig-name descname"><span class="pre">complex_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotKeywords.complex_inference" title="Link to this definition">§</a></dt>
+<dd><p>Annotates all complexes in <cite>complexes</cite>, by default in the default
+complex database (existing in the <cite>complex</cite> module or generated
+on demand according to the module’s current settings).</p>
+<dl class="field-list simple">
+<dt class="field-odd">Returns<span class="colon">:</span></dt>
+<dd class="field-odd"><p><ul class="simple">
+<li><p><em>Dict with complexes as keys and sets of annotations as values.</em></p></li>
+<li><p><em>Complexes with no valid information in this annotation resource</em></p></li>
+<li><p><em>won’t be in the dict.</em></p></li>
+</ul>
+</p>
+</dd>
+<dt class="field-even">Parameters<span class="colon">:</span></dt>
+<dd class="field-even"><p><strong>complexes</strong> (<em>iterable</em>) – Iterable yielding complexes.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotKeywords.coverage">
+<span class="sig-name descname"><span class="pre">coverage</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">other</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotKeywords.coverage" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the coverage of the annotation i.e. the proportion of
+entities having at least one record in this annotation resource
+for an arbitrary set of entities.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotKeywords.curation_effort">
+<span class="sig-name descname"><span class="pre">curation_effort</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotKeywords.curation_effort" title="Link to this definition">§</a></dt>
+<dd><p>Counts the reference-record pairs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotKeywords.get_names">
+<span class="sig-name descname"><span class="pre">get_names</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotKeywords.get_names" title="Link to this definition">§</a></dt>
+<dd><p>Returns the list of field names in the records. The annotation
+consists of uniform records and each entity might be annotated
+with one or more records. Each record is a tuple of fields, for
+example <code class="docutils literal notranslate"><span class="pre">('cell_type',</span> <span class="pre">'expression_level',</span> <span class="pre">'score')</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotKeywords.get_reference_set">
+<em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">get_reference_set</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">proteins</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">swissprot_only</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotKeywords.get_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the reference set i.e. the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotKeywords.get_subset">
+<span class="sig-name descname"><span class="pre">get_subset</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotKeywords.get_subset" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotKeywords.get_subset_bool_array">
+<span class="sig-name descname"><span class="pre">get_subset_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotKeywords.get_subset_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a boolean vector with True and False values for each entity
+in the reference set. The values represent presence absence data
+in the simplest case, but by providing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> any kind of matching
+and filtering is possible. <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> are passed to the <code class="docutils literal notranslate"><span class="pre">select</span></code>
+method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotKeywords.get_values">
+<span class="sig-name descname"><span class="pre">get_values</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">exclude_none</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotKeywords.get_values" title="Link to this definition">§</a></dt>
+<dd><p>Returns the set of all possible values of a field. E.g. if the
+records of this annotation have a field <code class="docutils literal notranslate"><span class="pre">cell_type</span></code> then calling
+this method can tell you that across all records the values of
+this field might be <code class="docutils literal notranslate"><span class="pre">{'macrophage',</span> <span class="pre">'epithelial_cell',</span> <span class="pre">...}</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotKeywords.labels">
+<span class="sig-name descname"><span class="pre">labels</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotKeywords.labels" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotKeywords.load">
+<span class="sig-name descname"><span class="pre">load</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotKeywords.load" title="Link to this definition">§</a></dt>
+<dd><p>Loads the annotation data by calling the input method.
+Infers annotations for complexes in the complex database if
+py:attr:<code class="docutils literal notranslate"><span class="pre">infer_complexes</span></code> is True.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotKeywords.load_data">
+<span class="sig-name descname"><span class="pre">load_data</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotKeywords.load_data" title="Link to this definition">§</a></dt>
+<dd><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotKeywords.load_proteins">
+<span class="sig-name descname"><span class="pre">load_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotKeywords.load_proteins" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a set of all UniProt IDs to have a base set of the entire
+proteome.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotKeywords.make_df">
+<span class="sig-name descname"><span class="pre">make_df</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">rebuild</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotKeywords.make_df" title="Link to this definition">§</a></dt>
+<dd><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.
+The data frame will be assigned to :py:attr``df``.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotKeywords.numof_entities">
+<span class="sig-name descname"><span class="pre">numof_entities</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotKeywords.numof_entities" title="Link to this definition">§</a></dt>
+<dd><p>The number of annotated entities in the resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotKeywords.numof_records">
+<span class="sig-name descname"><span class="pre">numof_records</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotKeywords.numof_records" title="Link to this definition">§</a></dt>
+<dd><p>The total number of annotation records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotKeywords.numof_references">
+<span class="sig-name descname"><span class="pre">numof_references</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotKeywords.numof_references" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects and counts the
+references across all records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotKeywords.process">
+<span class="sig-name descname"><span class="pre">process</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotKeywords.process" title="Link to this definition">§</a></dt>
+<dd><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotKeywords.reload">
+<span class="sig-name descname"><span class="pre">reload</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotKeywords.reload" title="Link to this definition">§</a></dt>
+<dd><p>Reloads the object from the module level.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotKeywords.select">
+<span class="sig-name descname"><span class="pre">select</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotKeywords.select" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotKeywords.set_method">
+<span class="sig-name descname"><span class="pre">set_method</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotKeywords.set_method" title="Link to this definition">§</a></dt>
+<dd><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if
+necessary.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotKeywords.set_reference_set">
+<span class="sig-name descname"><span class="pre">set_reference_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotKeywords.set_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Assigns the reference set to the :py:attr``reference_set`` attribute.
+The reference set is the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotKeywords.show">
+<span class="sig-name descname"><span class="pre">show</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">table_param</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotKeywords.show" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic
+information from the UniProt datasheets.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotKeywords.subset_intersection">
+<span class="sig-name descname"><span class="pre">subset_intersection</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">universe</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotKeywords.subset_intersection" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the proportion of entities in a subset occuring in the
+set <code class="docutils literal notranslate"><span class="pre">universe</span></code>. The subset is selected by passing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> to the
+<code class="docutils literal notranslate"><span class="pre">select</span></code> method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotKeywords.to_array">
+<span class="sig-name descname"><span class="pre">to_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_fields</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotKeywords.to_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns an entity vs feature array. In case of more complex
+annotations this might be huge.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotKeywords.to_bool_array">
+<span class="sig-name descname"><span class="pre">to_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotKeywords.to_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a presence/absence boolean array for a reference set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotKeywords.to_set">
+<span class="sig-name descname"><span class="pre">to_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotKeywords.to_set" title="Link to this definition">§</a></dt>
+<dd><p>Returns the entities present in this annotation resource as a set.</p>
+</dd></dl>
+
+</dd></dl>
+
+</section>
+
+
+                </article>
+              
+              
+              
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+  <section id="pypath-core-annot-uniprotlocations">
+<h1>pypath.core.annot.UniprotLocations<a class="headerlink" href="#pypath-core-annot-uniprotlocations" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotLocations">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.core.annot.</span></span><span class="sig-name descname"><span class="pre">UniprotLocations</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#UniprotLocations"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.UniprotLocations" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <a class="reference internal" href="pypath.core.annot.AnnotationBase.html#pypath.core.annot.AnnotationBase" title="pypath.core.annot.AnnotationBase"><code class="xref py py-class docutils literal notranslate"><span class="pre">AnnotationBase</span></code></a></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotLocations.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#UniprotLocations.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.UniprotLocations.__init__" title="Link to this definition">§</a></dt>
+<dd><p>Subcellular localizations from UniProt.</p>
+</dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotLocations.__init__" title="pypath.core.annot.UniprotLocations.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>([ncbi_tax_id])</p></td>
+<td><p>Subcellular localizations from UniProt.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotLocations.add_complexes_by_inference" title="pypath.core.annot.UniprotLocations.add_complexes_by_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">add_complexes_by_inference</span></code></a>([complexes])</p></td>
+<td><p>Creates complex annotations by in silico inference and adds them to this annotation set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotLocations.all_complexes" title="pypath.core.annot.UniprotLocations.all_complexes"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_complexes</span></code></a>()</p></td>
+<td><p>All protein complexes annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotLocations.all_entities" title="pypath.core.annot.UniprotLocations.all_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_entities</span></code></a>([entity_types])</p></td>
+<td><p>All entities annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotLocations.all_mirnas" title="pypath.core.annot.UniprotLocations.all_mirnas"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_mirnas</span></code></a>()</p></td>
+<td><p>All miRNAs annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotLocations.all_proteins" title="pypath.core.annot.UniprotLocations.all_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_proteins</span></code></a>()</p></td>
+<td><p>All UniProt IDs annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotLocations.all_refs" title="pypath.core.annot.UniprotLocations.all_refs"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_refs</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotLocations.annotate_complex" title="pypath.core.annot.UniprotLocations.annotate_complex"><code class="xref py py-obj docutils literal notranslate"><span class="pre">annotate_complex</span></code></a>(cplex)</p></td>
+<td><p>Infers annotations for a single complex.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotLocations.browse" title="pypath.core.annot.UniprotLocations.browse"><code class="xref py py-obj docutils literal notranslate"><span class="pre">browse</span></code></a>([field, start])</p></td>
+<td><p>Print gene information as a table.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotLocations.complex_inference" title="pypath.core.annot.UniprotLocations.complex_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">complex_inference</span></code></a>([complexes])</p></td>
+<td><p>Annotates all complexes in <cite>complexes</cite>, by default in the default complex database (existing in the <cite>complex</cite> module or generated on demand according to the module's current settings).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotLocations.coverage" title="pypath.core.annot.UniprotLocations.coverage"><code class="xref py py-obj docutils literal notranslate"><span class="pre">coverage</span></code></a>(other)</p></td>
+<td><p>Calculates the coverage of the annotation i.e. the proportion of entities having at least one record in this annotation resource for an arbitrary set of entities.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotLocations.curation_effort" title="pypath.core.annot.UniprotLocations.curation_effort"><code class="xref py py-obj docutils literal notranslate"><span class="pre">curation_effort</span></code></a>()</p></td>
+<td><p>Counts the reference-record pairs.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">from_dump</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_entity_type</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotLocations.get_names" title="pypath.core.annot.UniprotLocations.get_names"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_names</span></code></a>()</p></td>
+<td><p>Returns the list of field names in the records.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotLocations.get_reference_set" title="pypath.core.annot.UniprotLocations.get_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_reference_set</span></code></a>([proteins, complexes, ...])</p></td>
+<td><p>Retrieves the reference set i.e. the set of all entities which potentially have annotation in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotLocations.get_subset" title="pypath.core.annot.UniprotLocations.get_subset"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotLocations.get_subset_bool_array" title="pypath.core.annot.UniprotLocations.get_subset_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset_bool_array</span></code></a>([reference_set])</p></td>
+<td><p>Returns a boolean vector with True and False values for each entity in the reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotLocations.get_values" title="pypath.core.annot.UniprotLocations.get_values"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_values</span></code></a>(name[, exclude_none])</p></td>
+<td><p>Returns the set of all possible values of a field.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_complex</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_mirna</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_protein</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotLocations.labels" title="pypath.core.annot.UniprotLocations.labels"><code class="xref py py-obj docutils literal notranslate"><span class="pre">labels</span></code></a>([method])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotLocations.load" title="pypath.core.annot.UniprotLocations.load"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load</span></code></a>()</p></td>
+<td><p>Loads the annotation data by calling the input method.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotLocations.load_data" title="pypath.core.annot.UniprotLocations.load_data"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_data</span></code></a>()</p></td>
+<td><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotLocations.load_proteins" title="pypath.core.annot.UniprotLocations.load_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_proteins</span></code></a>()</p></td>
+<td><p>Retrieves a set of all UniProt IDs to have a base set of the entire proteome.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotLocations.make_df" title="pypath.core.annot.UniprotLocations.make_df"><code class="xref py py-obj docutils literal notranslate"><span class="pre">make_df</span></code></a>([rebuild])</p></td>
+<td><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complex_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotLocations.numof_entities" title="pypath.core.annot.UniprotLocations.numof_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_entities</span></code></a>()</p></td>
+<td><p>The number of annotated entities in the resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirna_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirnas</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_protein_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_proteins</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotLocations.numof_records" title="pypath.core.annot.UniprotLocations.numof_records"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_records</span></code></a>([entity_types])</p></td>
+<td><p>The total number of annotation records.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotLocations.numof_references" title="pypath.core.annot.UniprotLocations.numof_references"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_references</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotLocations.process" title="pypath.core.annot.UniprotLocations.process"><code class="xref py py-obj docutils literal notranslate"><span class="pre">process</span></code></a>()</p></td>
+<td><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">proportion</span></code>(other)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotLocations.reload" title="pypath.core.annot.UniprotLocations.reload"><code class="xref py py-obj docutils literal notranslate"><span class="pre">reload</span></code></a>()</p></td>
+<td><p>Reloads the object from the module level.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">save_to_pickle</span></code>(pickle_file)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotLocations.select" title="pypath.core.annot.UniprotLocations.select"><code class="xref py py-obj docutils literal notranslate"><span class="pre">select</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotLocations.set_method" title="pypath.core.annot.UniprotLocations.set_method"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_method</span></code></a>()</p></td>
+<td><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if necessary.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotLocations.set_reference_set" title="pypath.core.annot.UniprotLocations.set_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_reference_set</span></code></a>()</p></td>
+<td><p>Assigns the reference set to the :py:attr``reference_set`` attribute.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotLocations.show" title="pypath.core.annot.UniprotLocations.show"><code class="xref py py-obj docutils literal notranslate"><span class="pre">show</span></code></a>([method, table_param])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic information from the UniProt datasheets.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotLocations.subset_intersection" title="pypath.core.annot.UniprotLocations.subset_intersection"><code class="xref py py-obj docutils literal notranslate"><span class="pre">subset_intersection</span></code></a>(universe, **kwargs)</p></td>
+<td><p>Calculates the proportion of entities in a subset occuring in the set <code class="docutils literal notranslate"><span class="pre">universe</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotLocations.to_array" title="pypath.core.annot.UniprotLocations.to_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_array</span></code></a>([reference_set, use_fields])</p></td>
+<td><p>Returns an entity vs feature array.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotLocations.to_bool_array" title="pypath.core.annot.UniprotLocations.to_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_bool_array</span></code></a>(reference_set)</p></td>
+<td><p>Returns a presence/absence boolean array for a reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotLocations.to_set" title="pypath.core.annot.UniprotLocations.to_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_set</span></code></a>()</p></td>
+<td><p>Returns the entities present in this annotation resource as a set.</p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Attributes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_fields</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">summary</span></code></p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotLocations.add_complexes_by_inference">
+<span class="sig-name descname"><span class="pre">add_complexes_by_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotLocations.add_complexes_by_inference" title="Link to this definition">§</a></dt>
+<dd><p>Creates complex annotations by in silico inference and adds them
+to this annotation set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotLocations.all_complexes">
+<span class="sig-name descname"><span class="pre">all_complexes</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotLocations.all_complexes" title="Link to this definition">§</a></dt>
+<dd><p>All protein complexes annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotLocations.all_entities">
+<span class="sig-name descname"><span class="pre">all_entities</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotLocations.all_entities" title="Link to this definition">§</a></dt>
+<dd><p>All entities annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotLocations.all_mirnas">
+<span class="sig-name descname"><span class="pre">all_mirnas</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotLocations.all_mirnas" title="Link to this definition">§</a></dt>
+<dd><p>All miRNAs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotLocations.all_proteins">
+<span class="sig-name descname"><span class="pre">all_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotLocations.all_proteins" title="Link to this definition">§</a></dt>
+<dd><p>All UniProt IDs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotLocations.all_refs">
+<span class="sig-name descname"><span class="pre">all_refs</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotLocations.all_refs" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects the references
+across all records. Returns <em>list</em>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotLocations.annotate_complex">
+<span class="sig-name descname"><span class="pre">annotate_complex</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cplex</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotLocations.annotate_complex" title="Link to this definition">§</a></dt>
+<dd><p>Infers annotations for a single complex.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotLocations.browse">
+<span class="sig-name descname"><span class="pre">browse</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">field</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">start</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotLocations.browse" title="Link to this definition">§</a></dt>
+<dd><p>Print gene information as a table.</p>
+<p>Presents information about annotation categories as ascii tables
+printed in the terminal. If one category provided, prints one table.
+If multiple categories provided, prints a table for each of them one
+by one proceeding to the next one once you hit return. If no categories
+provided goes through all levels of the primary category.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>field:</dt><dd><p>The field to browse categories by.</p>
+<ul class="simple">
+<li><p>If None the primary field will be selected.
+If this annotation resource doesn’t have fields, all proteins
+will be presented as one single category.</p></li>
+<li><p>If a string it will be considered a field name and it will
+browse through all levels of this field.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">list</span></code>, set or tuple, it will be considered either a
+<code class="docutils literal notranslate"><span class="pre">list</span></code> of field names or a list of values from the primary
+field. In the former case all combinations of the values of
+the fields will be presented, in the latter case the browsing
+will be limited to the levels of the primary field contained
+in <code class="docutils literal notranslate"><span class="pre">field</span></code>.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">dict</span></code>, keys are supposed to be field names and values
+as list of levels. If any of the values are None, all levels
+from that field will be used.</p></li>
+</ul>
+</dd>
+<dt>start:</dt><dd><p>Start browsing from this category. E.g. if there are 500
+categories and start is 250 it will skip everything before the
+250th.</p>
+</dd>
+<dt>kwargs:</dt><dd><p>Passed to <code class="docutils literal notranslate"><span class="pre">pypath.utils.uniprot.info</span></code>.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotLocations.complex_inference">
+<span class="sig-name descname"><span class="pre">complex_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotLocations.complex_inference" title="Link to this definition">§</a></dt>
+<dd><p>Annotates all complexes in <cite>complexes</cite>, by default in the default
+complex database (existing in the <cite>complex</cite> module or generated
+on demand according to the module’s current settings).</p>
+<dl class="field-list simple">
+<dt class="field-odd">Returns<span class="colon">:</span></dt>
+<dd class="field-odd"><p><ul class="simple">
+<li><p><em>Dict with complexes as keys and sets of annotations as values.</em></p></li>
+<li><p><em>Complexes with no valid information in this annotation resource</em></p></li>
+<li><p><em>won’t be in the dict.</em></p></li>
+</ul>
+</p>
+</dd>
+<dt class="field-even">Parameters<span class="colon">:</span></dt>
+<dd class="field-even"><p><strong>complexes</strong> (<em>iterable</em>) – Iterable yielding complexes.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotLocations.coverage">
+<span class="sig-name descname"><span class="pre">coverage</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">other</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotLocations.coverage" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the coverage of the annotation i.e. the proportion of
+entities having at least one record in this annotation resource
+for an arbitrary set of entities.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotLocations.curation_effort">
+<span class="sig-name descname"><span class="pre">curation_effort</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotLocations.curation_effort" title="Link to this definition">§</a></dt>
+<dd><p>Counts the reference-record pairs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotLocations.get_names">
+<span class="sig-name descname"><span class="pre">get_names</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotLocations.get_names" title="Link to this definition">§</a></dt>
+<dd><p>Returns the list of field names in the records. The annotation
+consists of uniform records and each entity might be annotated
+with one or more records. Each record is a tuple of fields, for
+example <code class="docutils literal notranslate"><span class="pre">('cell_type',</span> <span class="pre">'expression_level',</span> <span class="pre">'score')</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotLocations.get_reference_set">
+<em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">get_reference_set</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">proteins</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">swissprot_only</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotLocations.get_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the reference set i.e. the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotLocations.get_subset">
+<span class="sig-name descname"><span class="pre">get_subset</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotLocations.get_subset" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotLocations.get_subset_bool_array">
+<span class="sig-name descname"><span class="pre">get_subset_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotLocations.get_subset_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a boolean vector with True and False values for each entity
+in the reference set. The values represent presence absence data
+in the simplest case, but by providing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> any kind of matching
+and filtering is possible. <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> are passed to the <code class="docutils literal notranslate"><span class="pre">select</span></code>
+method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotLocations.get_values">
+<span class="sig-name descname"><span class="pre">get_values</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">exclude_none</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotLocations.get_values" title="Link to this definition">§</a></dt>
+<dd><p>Returns the set of all possible values of a field. E.g. if the
+records of this annotation have a field <code class="docutils literal notranslate"><span class="pre">cell_type</span></code> then calling
+this method can tell you that across all records the values of
+this field might be <code class="docutils literal notranslate"><span class="pre">{'macrophage',</span> <span class="pre">'epithelial_cell',</span> <span class="pre">...}</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotLocations.labels">
+<span class="sig-name descname"><span class="pre">labels</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotLocations.labels" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotLocations.load">
+<span class="sig-name descname"><span class="pre">load</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotLocations.load" title="Link to this definition">§</a></dt>
+<dd><p>Loads the annotation data by calling the input method.
+Infers annotations for complexes in the complex database if
+py:attr:<code class="docutils literal notranslate"><span class="pre">infer_complexes</span></code> is True.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotLocations.load_data">
+<span class="sig-name descname"><span class="pre">load_data</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotLocations.load_data" title="Link to this definition">§</a></dt>
+<dd><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotLocations.load_proteins">
+<span class="sig-name descname"><span class="pre">load_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotLocations.load_proteins" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a set of all UniProt IDs to have a base set of the entire
+proteome.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotLocations.make_df">
+<span class="sig-name descname"><span class="pre">make_df</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">rebuild</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotLocations.make_df" title="Link to this definition">§</a></dt>
+<dd><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.
+The data frame will be assigned to :py:attr``df``.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotLocations.numof_entities">
+<span class="sig-name descname"><span class="pre">numof_entities</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotLocations.numof_entities" title="Link to this definition">§</a></dt>
+<dd><p>The number of annotated entities in the resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotLocations.numof_records">
+<span class="sig-name descname"><span class="pre">numof_records</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotLocations.numof_records" title="Link to this definition">§</a></dt>
+<dd><p>The total number of annotation records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotLocations.numof_references">
+<span class="sig-name descname"><span class="pre">numof_references</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotLocations.numof_references" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects and counts the
+references across all records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotLocations.process">
+<span class="sig-name descname"><span class="pre">process</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotLocations.process" title="Link to this definition">§</a></dt>
+<dd><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotLocations.reload">
+<span class="sig-name descname"><span class="pre">reload</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotLocations.reload" title="Link to this definition">§</a></dt>
+<dd><p>Reloads the object from the module level.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotLocations.select">
+<span class="sig-name descname"><span class="pre">select</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotLocations.select" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotLocations.set_method">
+<span class="sig-name descname"><span class="pre">set_method</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotLocations.set_method" title="Link to this definition">§</a></dt>
+<dd><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if
+necessary.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotLocations.set_reference_set">
+<span class="sig-name descname"><span class="pre">set_reference_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotLocations.set_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Assigns the reference set to the :py:attr``reference_set`` attribute.
+The reference set is the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotLocations.show">
+<span class="sig-name descname"><span class="pre">show</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">table_param</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotLocations.show" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic
+information from the UniProt datasheets.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotLocations.subset_intersection">
+<span class="sig-name descname"><span class="pre">subset_intersection</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">universe</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotLocations.subset_intersection" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the proportion of entities in a subset occuring in the
+set <code class="docutils literal notranslate"><span class="pre">universe</span></code>. The subset is selected by passing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> to the
+<code class="docutils literal notranslate"><span class="pre">select</span></code> method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotLocations.to_array">
+<span class="sig-name descname"><span class="pre">to_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_fields</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotLocations.to_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns an entity vs feature array. In case of more complex
+annotations this might be huge.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotLocations.to_bool_array">
+<span class="sig-name descname"><span class="pre">to_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotLocations.to_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a presence/absence boolean array for a reference set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotLocations.to_set">
+<span class="sig-name descname"><span class="pre">to_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotLocations.to_set" title="Link to this definition">§</a></dt>
+<dd><p>Returns the entities present in this annotation resource as a set.</p>
+</dd></dl>
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+    <li class="breadcrumb-item"><a href="pypath.core.annot.html" class="nav-link">pypath.core.annot</a></li>
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+    <li class="breadcrumb-item active" aria-current="page">pypath.core....</li>
+  </ul>
+</nav>
+</div>
+      
+    </div>
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+  
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+</div>
+              
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+<div id="searchbox"></div>
+                <article class="bd-article">
+                  
+  <section id="pypath-core-annot-uniprottissues">
+<h1>pypath.core.annot.UniprotTissues<a class="headerlink" href="#pypath-core-annot-uniprottissues" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotTissues">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.core.annot.</span></span><span class="sig-name descname"><span class="pre">UniprotTissues</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#UniprotTissues"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.UniprotTissues" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <a class="reference internal" href="pypath.core.annot.AnnotationBase.html#pypath.core.annot.AnnotationBase" title="pypath.core.annot.AnnotationBase"><code class="xref py py-class docutils literal notranslate"><span class="pre">AnnotationBase</span></code></a></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotTissues.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#UniprotTissues.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.UniprotTissues.__init__" title="Link to this definition">§</a></dt>
+<dd><p>Tissue expression levels from UniProt.</p>
+</dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotTissues.__init__" title="pypath.core.annot.UniprotTissues.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>([ncbi_tax_id])</p></td>
+<td><p>Tissue expression levels from UniProt.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotTissues.add_complexes_by_inference" title="pypath.core.annot.UniprotTissues.add_complexes_by_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">add_complexes_by_inference</span></code></a>([complexes])</p></td>
+<td><p>Creates complex annotations by in silico inference and adds them to this annotation set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotTissues.all_complexes" title="pypath.core.annot.UniprotTissues.all_complexes"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_complexes</span></code></a>()</p></td>
+<td><p>All protein complexes annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotTissues.all_entities" title="pypath.core.annot.UniprotTissues.all_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_entities</span></code></a>([entity_types])</p></td>
+<td><p>All entities annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotTissues.all_mirnas" title="pypath.core.annot.UniprotTissues.all_mirnas"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_mirnas</span></code></a>()</p></td>
+<td><p>All miRNAs annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotTissues.all_proteins" title="pypath.core.annot.UniprotTissues.all_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_proteins</span></code></a>()</p></td>
+<td><p>All UniProt IDs annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotTissues.all_refs" title="pypath.core.annot.UniprotTissues.all_refs"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_refs</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotTissues.annotate_complex" title="pypath.core.annot.UniprotTissues.annotate_complex"><code class="xref py py-obj docutils literal notranslate"><span class="pre">annotate_complex</span></code></a>(cplex)</p></td>
+<td><p>Infers annotations for a single complex.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotTissues.browse" title="pypath.core.annot.UniprotTissues.browse"><code class="xref py py-obj docutils literal notranslate"><span class="pre">browse</span></code></a>([field, start])</p></td>
+<td><p>Print gene information as a table.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotTissues.complex_inference" title="pypath.core.annot.UniprotTissues.complex_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">complex_inference</span></code></a>([complexes])</p></td>
+<td><p>Annotates all complexes in <cite>complexes</cite>, by default in the default complex database (existing in the <cite>complex</cite> module or generated on demand according to the module's current settings).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotTissues.coverage" title="pypath.core.annot.UniprotTissues.coverage"><code class="xref py py-obj docutils literal notranslate"><span class="pre">coverage</span></code></a>(other)</p></td>
+<td><p>Calculates the coverage of the annotation i.e. the proportion of entities having at least one record in this annotation resource for an arbitrary set of entities.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotTissues.curation_effort" title="pypath.core.annot.UniprotTissues.curation_effort"><code class="xref py py-obj docutils literal notranslate"><span class="pre">curation_effort</span></code></a>()</p></td>
+<td><p>Counts the reference-record pairs.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">from_dump</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_entity_type</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotTissues.get_names" title="pypath.core.annot.UniprotTissues.get_names"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_names</span></code></a>()</p></td>
+<td><p>Returns the list of field names in the records.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotTissues.get_reference_set" title="pypath.core.annot.UniprotTissues.get_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_reference_set</span></code></a>([proteins, complexes, ...])</p></td>
+<td><p>Retrieves the reference set i.e. the set of all entities which potentially have annotation in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotTissues.get_subset" title="pypath.core.annot.UniprotTissues.get_subset"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotTissues.get_subset_bool_array" title="pypath.core.annot.UniprotTissues.get_subset_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset_bool_array</span></code></a>([reference_set])</p></td>
+<td><p>Returns a boolean vector with True and False values for each entity in the reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotTissues.get_values" title="pypath.core.annot.UniprotTissues.get_values"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_values</span></code></a>(name[, exclude_none])</p></td>
+<td><p>Returns the set of all possible values of a field.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_complex</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_mirna</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_protein</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotTissues.labels" title="pypath.core.annot.UniprotTissues.labels"><code class="xref py py-obj docutils literal notranslate"><span class="pre">labels</span></code></a>([method])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotTissues.load" title="pypath.core.annot.UniprotTissues.load"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load</span></code></a>()</p></td>
+<td><p>Loads the annotation data by calling the input method.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotTissues.load_data" title="pypath.core.annot.UniprotTissues.load_data"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_data</span></code></a>()</p></td>
+<td><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotTissues.load_proteins" title="pypath.core.annot.UniprotTissues.load_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_proteins</span></code></a>()</p></td>
+<td><p>Retrieves a set of all UniProt IDs to have a base set of the entire proteome.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotTissues.make_df" title="pypath.core.annot.UniprotTissues.make_df"><code class="xref py py-obj docutils literal notranslate"><span class="pre">make_df</span></code></a>([rebuild])</p></td>
+<td><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complex_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotTissues.numof_entities" title="pypath.core.annot.UniprotTissues.numof_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_entities</span></code></a>()</p></td>
+<td><p>The number of annotated entities in the resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirna_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirnas</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_protein_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_proteins</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotTissues.numof_records" title="pypath.core.annot.UniprotTissues.numof_records"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_records</span></code></a>([entity_types])</p></td>
+<td><p>The total number of annotation records.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotTissues.numof_references" title="pypath.core.annot.UniprotTissues.numof_references"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_references</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotTissues.process" title="pypath.core.annot.UniprotTissues.process"><code class="xref py py-obj docutils literal notranslate"><span class="pre">process</span></code></a>()</p></td>
+<td><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">proportion</span></code>(other)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotTissues.reload" title="pypath.core.annot.UniprotTissues.reload"><code class="xref py py-obj docutils literal notranslate"><span class="pre">reload</span></code></a>()</p></td>
+<td><p>Reloads the object from the module level.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">save_to_pickle</span></code>(pickle_file)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotTissues.select" title="pypath.core.annot.UniprotTissues.select"><code class="xref py py-obj docutils literal notranslate"><span class="pre">select</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotTissues.set_method" title="pypath.core.annot.UniprotTissues.set_method"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_method</span></code></a>()</p></td>
+<td><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if necessary.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotTissues.set_reference_set" title="pypath.core.annot.UniprotTissues.set_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_reference_set</span></code></a>()</p></td>
+<td><p>Assigns the reference set to the :py:attr``reference_set`` attribute.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotTissues.show" title="pypath.core.annot.UniprotTissues.show"><code class="xref py py-obj docutils literal notranslate"><span class="pre">show</span></code></a>([method, table_param])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic information from the UniProt datasheets.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotTissues.subset_intersection" title="pypath.core.annot.UniprotTissues.subset_intersection"><code class="xref py py-obj docutils literal notranslate"><span class="pre">subset_intersection</span></code></a>(universe, **kwargs)</p></td>
+<td><p>Calculates the proportion of entities in a subset occuring in the set <code class="docutils literal notranslate"><span class="pre">universe</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotTissues.to_array" title="pypath.core.annot.UniprotTissues.to_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_array</span></code></a>([reference_set, use_fields])</p></td>
+<td><p>Returns an entity vs feature array.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotTissues.to_bool_array" title="pypath.core.annot.UniprotTissues.to_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_bool_array</span></code></a>(reference_set)</p></td>
+<td><p>Returns a presence/absence boolean array for a reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotTissues.to_set" title="pypath.core.annot.UniprotTissues.to_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_set</span></code></a>()</p></td>
+<td><p>Returns the entities present in this annotation resource as a set.</p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Attributes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_fields</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">summary</span></code></p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotTissues.add_complexes_by_inference">
+<span class="sig-name descname"><span class="pre">add_complexes_by_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotTissues.add_complexes_by_inference" title="Link to this definition">§</a></dt>
+<dd><p>Creates complex annotations by in silico inference and adds them
+to this annotation set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotTissues.all_complexes">
+<span class="sig-name descname"><span class="pre">all_complexes</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotTissues.all_complexes" title="Link to this definition">§</a></dt>
+<dd><p>All protein complexes annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotTissues.all_entities">
+<span class="sig-name descname"><span class="pre">all_entities</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotTissues.all_entities" title="Link to this definition">§</a></dt>
+<dd><p>All entities annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotTissues.all_mirnas">
+<span class="sig-name descname"><span class="pre">all_mirnas</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotTissues.all_mirnas" title="Link to this definition">§</a></dt>
+<dd><p>All miRNAs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotTissues.all_proteins">
+<span class="sig-name descname"><span class="pre">all_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotTissues.all_proteins" title="Link to this definition">§</a></dt>
+<dd><p>All UniProt IDs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotTissues.all_refs">
+<span class="sig-name descname"><span class="pre">all_refs</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotTissues.all_refs" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects the references
+across all records. Returns <em>list</em>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotTissues.annotate_complex">
+<span class="sig-name descname"><span class="pre">annotate_complex</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cplex</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotTissues.annotate_complex" title="Link to this definition">§</a></dt>
+<dd><p>Infers annotations for a single complex.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotTissues.browse">
+<span class="sig-name descname"><span class="pre">browse</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">field</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">start</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotTissues.browse" title="Link to this definition">§</a></dt>
+<dd><p>Print gene information as a table.</p>
+<p>Presents information about annotation categories as ascii tables
+printed in the terminal. If one category provided, prints one table.
+If multiple categories provided, prints a table for each of them one
+by one proceeding to the next one once you hit return. If no categories
+provided goes through all levels of the primary category.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>field:</dt><dd><p>The field to browse categories by.</p>
+<ul class="simple">
+<li><p>If None the primary field will be selected.
+If this annotation resource doesn’t have fields, all proteins
+will be presented as one single category.</p></li>
+<li><p>If a string it will be considered a field name and it will
+browse through all levels of this field.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">list</span></code>, set or tuple, it will be considered either a
+<code class="docutils literal notranslate"><span class="pre">list</span></code> of field names or a list of values from the primary
+field. In the former case all combinations of the values of
+the fields will be presented, in the latter case the browsing
+will be limited to the levels of the primary field contained
+in <code class="docutils literal notranslate"><span class="pre">field</span></code>.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">dict</span></code>, keys are supposed to be field names and values
+as list of levels. If any of the values are None, all levels
+from that field will be used.</p></li>
+</ul>
+</dd>
+<dt>start:</dt><dd><p>Start browsing from this category. E.g. if there are 500
+categories and start is 250 it will skip everything before the
+250th.</p>
+</dd>
+<dt>kwargs:</dt><dd><p>Passed to <code class="docutils literal notranslate"><span class="pre">pypath.utils.uniprot.info</span></code>.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotTissues.complex_inference">
+<span class="sig-name descname"><span class="pre">complex_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotTissues.complex_inference" title="Link to this definition">§</a></dt>
+<dd><p>Annotates all complexes in <cite>complexes</cite>, by default in the default
+complex database (existing in the <cite>complex</cite> module or generated
+on demand according to the module’s current settings).</p>
+<dl class="field-list simple">
+<dt class="field-odd">Returns<span class="colon">:</span></dt>
+<dd class="field-odd"><p><ul class="simple">
+<li><p><em>Dict with complexes as keys and sets of annotations as values.</em></p></li>
+<li><p><em>Complexes with no valid information in this annotation resource</em></p></li>
+<li><p><em>won’t be in the dict.</em></p></li>
+</ul>
+</p>
+</dd>
+<dt class="field-even">Parameters<span class="colon">:</span></dt>
+<dd class="field-even"><p><strong>complexes</strong> (<em>iterable</em>) – Iterable yielding complexes.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotTissues.coverage">
+<span class="sig-name descname"><span class="pre">coverage</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">other</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotTissues.coverage" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the coverage of the annotation i.e. the proportion of
+entities having at least one record in this annotation resource
+for an arbitrary set of entities.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotTissues.curation_effort">
+<span class="sig-name descname"><span class="pre">curation_effort</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotTissues.curation_effort" title="Link to this definition">§</a></dt>
+<dd><p>Counts the reference-record pairs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotTissues.get_names">
+<span class="sig-name descname"><span class="pre">get_names</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotTissues.get_names" title="Link to this definition">§</a></dt>
+<dd><p>Returns the list of field names in the records. The annotation
+consists of uniform records and each entity might be annotated
+with one or more records. Each record is a tuple of fields, for
+example <code class="docutils literal notranslate"><span class="pre">('cell_type',</span> <span class="pre">'expression_level',</span> <span class="pre">'score')</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotTissues.get_reference_set">
+<em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">get_reference_set</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">proteins</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">swissprot_only</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotTissues.get_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the reference set i.e. the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotTissues.get_subset">
+<span class="sig-name descname"><span class="pre">get_subset</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotTissues.get_subset" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotTissues.get_subset_bool_array">
+<span class="sig-name descname"><span class="pre">get_subset_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotTissues.get_subset_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a boolean vector with True and False values for each entity
+in the reference set. The values represent presence absence data
+in the simplest case, but by providing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> any kind of matching
+and filtering is possible. <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> are passed to the <code class="docutils literal notranslate"><span class="pre">select</span></code>
+method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotTissues.get_values">
+<span class="sig-name descname"><span class="pre">get_values</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">exclude_none</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotTissues.get_values" title="Link to this definition">§</a></dt>
+<dd><p>Returns the set of all possible values of a field. E.g. if the
+records of this annotation have a field <code class="docutils literal notranslate"><span class="pre">cell_type</span></code> then calling
+this method can tell you that across all records the values of
+this field might be <code class="docutils literal notranslate"><span class="pre">{'macrophage',</span> <span class="pre">'epithelial_cell',</span> <span class="pre">...}</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotTissues.labels">
+<span class="sig-name descname"><span class="pre">labels</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotTissues.labels" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotTissues.load">
+<span class="sig-name descname"><span class="pre">load</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotTissues.load" title="Link to this definition">§</a></dt>
+<dd><p>Loads the annotation data by calling the input method.
+Infers annotations for complexes in the complex database if
+py:attr:<code class="docutils literal notranslate"><span class="pre">infer_complexes</span></code> is True.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotTissues.load_data">
+<span class="sig-name descname"><span class="pre">load_data</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotTissues.load_data" title="Link to this definition">§</a></dt>
+<dd><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotTissues.load_proteins">
+<span class="sig-name descname"><span class="pre">load_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotTissues.load_proteins" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a set of all UniProt IDs to have a base set of the entire
+proteome.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotTissues.make_df">
+<span class="sig-name descname"><span class="pre">make_df</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">rebuild</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotTissues.make_df" title="Link to this definition">§</a></dt>
+<dd><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.
+The data frame will be assigned to :py:attr``df``.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotTissues.numof_entities">
+<span class="sig-name descname"><span class="pre">numof_entities</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotTissues.numof_entities" title="Link to this definition">§</a></dt>
+<dd><p>The number of annotated entities in the resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotTissues.numof_records">
+<span class="sig-name descname"><span class="pre">numof_records</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotTissues.numof_records" title="Link to this definition">§</a></dt>
+<dd><p>The total number of annotation records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotTissues.numof_references">
+<span class="sig-name descname"><span class="pre">numof_references</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotTissues.numof_references" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects and counts the
+references across all records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotTissues.process">
+<span class="sig-name descname"><span class="pre">process</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotTissues.process" title="Link to this definition">§</a></dt>
+<dd><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotTissues.reload">
+<span class="sig-name descname"><span class="pre">reload</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotTissues.reload" title="Link to this definition">§</a></dt>
+<dd><p>Reloads the object from the module level.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotTissues.select">
+<span class="sig-name descname"><span class="pre">select</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotTissues.select" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotTissues.set_method">
+<span class="sig-name descname"><span class="pre">set_method</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotTissues.set_method" title="Link to this definition">§</a></dt>
+<dd><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if
+necessary.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotTissues.set_reference_set">
+<span class="sig-name descname"><span class="pre">set_reference_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotTissues.set_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Assigns the reference set to the :py:attr``reference_set`` attribute.
+The reference set is the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotTissues.show">
+<span class="sig-name descname"><span class="pre">show</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">table_param</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotTissues.show" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic
+information from the UniProt datasheets.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotTissues.subset_intersection">
+<span class="sig-name descname"><span class="pre">subset_intersection</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">universe</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotTissues.subset_intersection" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the proportion of entities in a subset occuring in the
+set <code class="docutils literal notranslate"><span class="pre">universe</span></code>. The subset is selected by passing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> to the
+<code class="docutils literal notranslate"><span class="pre">select</span></code> method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotTissues.to_array">
+<span class="sig-name descname"><span class="pre">to_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_fields</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotTissues.to_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns an entity vs feature array. In case of more complex
+annotations this might be huge.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotTissues.to_bool_array">
+<span class="sig-name descname"><span class="pre">to_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotTissues.to_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a presence/absence boolean array for a reference set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotTissues.to_set">
+<span class="sig-name descname"><span class="pre">to_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotTissues.to_set" title="Link to this definition">§</a></dt>
+<dd><p>Returns the entities present in this annotation resource as a set.</p>
+</dd></dl>
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+  <section id="pypath-core-annot-uniprottopologies">
+<h1>pypath.core.annot.UniprotTopologies<a class="headerlink" href="#pypath-core-annot-uniprottopologies" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotTopologies">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.core.annot.</span></span><span class="sig-name descname"><span class="pre">UniprotTopologies</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#UniprotTopologies"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.UniprotTopologies" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <a class="reference internal" href="pypath.core.annot.AnnotationBase.html#pypath.core.annot.AnnotationBase" title="pypath.core.annot.AnnotationBase"><code class="xref py py-class docutils literal notranslate"><span class="pre">AnnotationBase</span></code></a></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotTopologies.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#UniprotTopologies.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.UniprotTopologies.__init__" title="Link to this definition">§</a></dt>
+<dd><p>Topological domains and transmembrane segments from UniProt.</p>
+</dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotTopologies.__init__" title="pypath.core.annot.UniprotTopologies.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>([ncbi_tax_id])</p></td>
+<td><p>Topological domains and transmembrane segments from UniProt.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotTopologies.add_complexes_by_inference" title="pypath.core.annot.UniprotTopologies.add_complexes_by_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">add_complexes_by_inference</span></code></a>([complexes])</p></td>
+<td><p>Creates complex annotations by in silico inference and adds them to this annotation set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotTopologies.all_complexes" title="pypath.core.annot.UniprotTopologies.all_complexes"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_complexes</span></code></a>()</p></td>
+<td><p>All protein complexes annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotTopologies.all_entities" title="pypath.core.annot.UniprotTopologies.all_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_entities</span></code></a>([entity_types])</p></td>
+<td><p>All entities annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotTopologies.all_mirnas" title="pypath.core.annot.UniprotTopologies.all_mirnas"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_mirnas</span></code></a>()</p></td>
+<td><p>All miRNAs annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotTopologies.all_proteins" title="pypath.core.annot.UniprotTopologies.all_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_proteins</span></code></a>()</p></td>
+<td><p>All UniProt IDs annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotTopologies.all_refs" title="pypath.core.annot.UniprotTopologies.all_refs"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_refs</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotTopologies.annotate_complex" title="pypath.core.annot.UniprotTopologies.annotate_complex"><code class="xref py py-obj docutils literal notranslate"><span class="pre">annotate_complex</span></code></a>(cplex)</p></td>
+<td><p>Infers annotations for a single complex.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotTopologies.browse" title="pypath.core.annot.UniprotTopologies.browse"><code class="xref py py-obj docutils literal notranslate"><span class="pre">browse</span></code></a>([field, start])</p></td>
+<td><p>Print gene information as a table.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotTopologies.complex_inference" title="pypath.core.annot.UniprotTopologies.complex_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">complex_inference</span></code></a>([complexes])</p></td>
+<td><p>Annotates all complexes in <cite>complexes</cite>, by default in the default complex database (existing in the <cite>complex</cite> module or generated on demand according to the module's current settings).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotTopologies.coverage" title="pypath.core.annot.UniprotTopologies.coverage"><code class="xref py py-obj docutils literal notranslate"><span class="pre">coverage</span></code></a>(other)</p></td>
+<td><p>Calculates the coverage of the annotation i.e. the proportion of entities having at least one record in this annotation resource for an arbitrary set of entities.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotTopologies.curation_effort" title="pypath.core.annot.UniprotTopologies.curation_effort"><code class="xref py py-obj docutils literal notranslate"><span class="pre">curation_effort</span></code></a>()</p></td>
+<td><p>Counts the reference-record pairs.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">from_dump</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_entity_type</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotTopologies.get_names" title="pypath.core.annot.UniprotTopologies.get_names"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_names</span></code></a>()</p></td>
+<td><p>Returns the list of field names in the records.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotTopologies.get_reference_set" title="pypath.core.annot.UniprotTopologies.get_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_reference_set</span></code></a>([proteins, complexes, ...])</p></td>
+<td><p>Retrieves the reference set i.e. the set of all entities which potentially have annotation in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotTopologies.get_subset" title="pypath.core.annot.UniprotTopologies.get_subset"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotTopologies.get_subset_bool_array" title="pypath.core.annot.UniprotTopologies.get_subset_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset_bool_array</span></code></a>([reference_set])</p></td>
+<td><p>Returns a boolean vector with True and False values for each entity in the reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotTopologies.get_values" title="pypath.core.annot.UniprotTopologies.get_values"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_values</span></code></a>(name[, exclude_none])</p></td>
+<td><p>Returns the set of all possible values of a field.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_complex</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_mirna</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_protein</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotTopologies.labels" title="pypath.core.annot.UniprotTopologies.labels"><code class="xref py py-obj docutils literal notranslate"><span class="pre">labels</span></code></a>([method])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotTopologies.load" title="pypath.core.annot.UniprotTopologies.load"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load</span></code></a>()</p></td>
+<td><p>Loads the annotation data by calling the input method.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotTopologies.load_data" title="pypath.core.annot.UniprotTopologies.load_data"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_data</span></code></a>()</p></td>
+<td><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotTopologies.load_proteins" title="pypath.core.annot.UniprotTopologies.load_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_proteins</span></code></a>()</p></td>
+<td><p>Retrieves a set of all UniProt IDs to have a base set of the entire proteome.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotTopologies.make_df" title="pypath.core.annot.UniprotTopologies.make_df"><code class="xref py py-obj docutils literal notranslate"><span class="pre">make_df</span></code></a>([rebuild])</p></td>
+<td><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complex_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotTopologies.numof_entities" title="pypath.core.annot.UniprotTopologies.numof_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_entities</span></code></a>()</p></td>
+<td><p>The number of annotated entities in the resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirna_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirnas</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_protein_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_proteins</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotTopologies.numof_records" title="pypath.core.annot.UniprotTopologies.numof_records"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_records</span></code></a>([entity_types])</p></td>
+<td><p>The total number of annotation records.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotTopologies.numof_references" title="pypath.core.annot.UniprotTopologies.numof_references"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_references</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotTopologies.process" title="pypath.core.annot.UniprotTopologies.process"><code class="xref py py-obj docutils literal notranslate"><span class="pre">process</span></code></a>()</p></td>
+<td><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">proportion</span></code>(other)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotTopologies.reload" title="pypath.core.annot.UniprotTopologies.reload"><code class="xref py py-obj docutils literal notranslate"><span class="pre">reload</span></code></a>()</p></td>
+<td><p>Reloads the object from the module level.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">save_to_pickle</span></code>(pickle_file)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotTopologies.select" title="pypath.core.annot.UniprotTopologies.select"><code class="xref py py-obj docutils literal notranslate"><span class="pre">select</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotTopologies.set_method" title="pypath.core.annot.UniprotTopologies.set_method"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_method</span></code></a>()</p></td>
+<td><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if necessary.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotTopologies.set_reference_set" title="pypath.core.annot.UniprotTopologies.set_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_reference_set</span></code></a>()</p></td>
+<td><p>Assigns the reference set to the :py:attr``reference_set`` attribute.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotTopologies.show" title="pypath.core.annot.UniprotTopologies.show"><code class="xref py py-obj docutils literal notranslate"><span class="pre">show</span></code></a>([method, table_param])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic information from the UniProt datasheets.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotTopologies.subset_intersection" title="pypath.core.annot.UniprotTopologies.subset_intersection"><code class="xref py py-obj docutils literal notranslate"><span class="pre">subset_intersection</span></code></a>(universe, **kwargs)</p></td>
+<td><p>Calculates the proportion of entities in a subset occuring in the set <code class="docutils literal notranslate"><span class="pre">universe</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotTopologies.to_array" title="pypath.core.annot.UniprotTopologies.to_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_array</span></code></a>([reference_set, use_fields])</p></td>
+<td><p>Returns an entity vs feature array.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotTopologies.to_bool_array" title="pypath.core.annot.UniprotTopologies.to_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_bool_array</span></code></a>(reference_set)</p></td>
+<td><p>Returns a presence/absence boolean array for a reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.UniprotTopologies.to_set" title="pypath.core.annot.UniprotTopologies.to_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_set</span></code></a>()</p></td>
+<td><p>Returns the entities present in this annotation resource as a set.</p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Attributes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_fields</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">summary</span></code></p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotTopologies.add_complexes_by_inference">
+<span class="sig-name descname"><span class="pre">add_complexes_by_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotTopologies.add_complexes_by_inference" title="Link to this definition">§</a></dt>
+<dd><p>Creates complex annotations by in silico inference and adds them
+to this annotation set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotTopologies.all_complexes">
+<span class="sig-name descname"><span class="pre">all_complexes</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotTopologies.all_complexes" title="Link to this definition">§</a></dt>
+<dd><p>All protein complexes annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotTopologies.all_entities">
+<span class="sig-name descname"><span class="pre">all_entities</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotTopologies.all_entities" title="Link to this definition">§</a></dt>
+<dd><p>All entities annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotTopologies.all_mirnas">
+<span class="sig-name descname"><span class="pre">all_mirnas</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotTopologies.all_mirnas" title="Link to this definition">§</a></dt>
+<dd><p>All miRNAs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotTopologies.all_proteins">
+<span class="sig-name descname"><span class="pre">all_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotTopologies.all_proteins" title="Link to this definition">§</a></dt>
+<dd><p>All UniProt IDs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotTopologies.all_refs">
+<span class="sig-name descname"><span class="pre">all_refs</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotTopologies.all_refs" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects the references
+across all records. Returns <em>list</em>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotTopologies.annotate_complex">
+<span class="sig-name descname"><span class="pre">annotate_complex</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cplex</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotTopologies.annotate_complex" title="Link to this definition">§</a></dt>
+<dd><p>Infers annotations for a single complex.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotTopologies.browse">
+<span class="sig-name descname"><span class="pre">browse</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">field</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">start</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotTopologies.browse" title="Link to this definition">§</a></dt>
+<dd><p>Print gene information as a table.</p>
+<p>Presents information about annotation categories as ascii tables
+printed in the terminal. If one category provided, prints one table.
+If multiple categories provided, prints a table for each of them one
+by one proceeding to the next one once you hit return. If no categories
+provided goes through all levels of the primary category.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>field:</dt><dd><p>The field to browse categories by.</p>
+<ul class="simple">
+<li><p>If None the primary field will be selected.
+If this annotation resource doesn’t have fields, all proteins
+will be presented as one single category.</p></li>
+<li><p>If a string it will be considered a field name and it will
+browse through all levels of this field.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">list</span></code>, set or tuple, it will be considered either a
+<code class="docutils literal notranslate"><span class="pre">list</span></code> of field names or a list of values from the primary
+field. In the former case all combinations of the values of
+the fields will be presented, in the latter case the browsing
+will be limited to the levels of the primary field contained
+in <code class="docutils literal notranslate"><span class="pre">field</span></code>.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">dict</span></code>, keys are supposed to be field names and values
+as list of levels. If any of the values are None, all levels
+from that field will be used.</p></li>
+</ul>
+</dd>
+<dt>start:</dt><dd><p>Start browsing from this category. E.g. if there are 500
+categories and start is 250 it will skip everything before the
+250th.</p>
+</dd>
+<dt>kwargs:</dt><dd><p>Passed to <code class="docutils literal notranslate"><span class="pre">pypath.utils.uniprot.info</span></code>.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotTopologies.complex_inference">
+<span class="sig-name descname"><span class="pre">complex_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotTopologies.complex_inference" title="Link to this definition">§</a></dt>
+<dd><p>Annotates all complexes in <cite>complexes</cite>, by default in the default
+complex database (existing in the <cite>complex</cite> module or generated
+on demand according to the module’s current settings).</p>
+<dl class="field-list simple">
+<dt class="field-odd">Returns<span class="colon">:</span></dt>
+<dd class="field-odd"><p><ul class="simple">
+<li><p><em>Dict with complexes as keys and sets of annotations as values.</em></p></li>
+<li><p><em>Complexes with no valid information in this annotation resource</em></p></li>
+<li><p><em>won’t be in the dict.</em></p></li>
+</ul>
+</p>
+</dd>
+<dt class="field-even">Parameters<span class="colon">:</span></dt>
+<dd class="field-even"><p><strong>complexes</strong> (<em>iterable</em>) – Iterable yielding complexes.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotTopologies.coverage">
+<span class="sig-name descname"><span class="pre">coverage</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">other</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotTopologies.coverage" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the coverage of the annotation i.e. the proportion of
+entities having at least one record in this annotation resource
+for an arbitrary set of entities.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotTopologies.curation_effort">
+<span class="sig-name descname"><span class="pre">curation_effort</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotTopologies.curation_effort" title="Link to this definition">§</a></dt>
+<dd><p>Counts the reference-record pairs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotTopologies.get_names">
+<span class="sig-name descname"><span class="pre">get_names</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotTopologies.get_names" title="Link to this definition">§</a></dt>
+<dd><p>Returns the list of field names in the records. The annotation
+consists of uniform records and each entity might be annotated
+with one or more records. Each record is a tuple of fields, for
+example <code class="docutils literal notranslate"><span class="pre">('cell_type',</span> <span class="pre">'expression_level',</span> <span class="pre">'score')</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotTopologies.get_reference_set">
+<em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">get_reference_set</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">proteins</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">swissprot_only</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotTopologies.get_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the reference set i.e. the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotTopologies.get_subset">
+<span class="sig-name descname"><span class="pre">get_subset</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotTopologies.get_subset" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotTopologies.get_subset_bool_array">
+<span class="sig-name descname"><span class="pre">get_subset_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotTopologies.get_subset_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a boolean vector with True and False values for each entity
+in the reference set. The values represent presence absence data
+in the simplest case, but by providing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> any kind of matching
+and filtering is possible. <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> are passed to the <code class="docutils literal notranslate"><span class="pre">select</span></code>
+method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotTopologies.get_values">
+<span class="sig-name descname"><span class="pre">get_values</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">exclude_none</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotTopologies.get_values" title="Link to this definition">§</a></dt>
+<dd><p>Returns the set of all possible values of a field. E.g. if the
+records of this annotation have a field <code class="docutils literal notranslate"><span class="pre">cell_type</span></code> then calling
+this method can tell you that across all records the values of
+this field might be <code class="docutils literal notranslate"><span class="pre">{'macrophage',</span> <span class="pre">'epithelial_cell',</span> <span class="pre">...}</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotTopologies.labels">
+<span class="sig-name descname"><span class="pre">labels</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotTopologies.labels" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotTopologies.load">
+<span class="sig-name descname"><span class="pre">load</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotTopologies.load" title="Link to this definition">§</a></dt>
+<dd><p>Loads the annotation data by calling the input method.
+Infers annotations for complexes in the complex database if
+py:attr:<code class="docutils literal notranslate"><span class="pre">infer_complexes</span></code> is True.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotTopologies.load_data">
+<span class="sig-name descname"><span class="pre">load_data</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotTopologies.load_data" title="Link to this definition">§</a></dt>
+<dd><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotTopologies.load_proteins">
+<span class="sig-name descname"><span class="pre">load_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotTopologies.load_proteins" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a set of all UniProt IDs to have a base set of the entire
+proteome.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotTopologies.make_df">
+<span class="sig-name descname"><span class="pre">make_df</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">rebuild</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotTopologies.make_df" title="Link to this definition">§</a></dt>
+<dd><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.
+The data frame will be assigned to :py:attr``df``.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotTopologies.numof_entities">
+<span class="sig-name descname"><span class="pre">numof_entities</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotTopologies.numof_entities" title="Link to this definition">§</a></dt>
+<dd><p>The number of annotated entities in the resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotTopologies.numof_records">
+<span class="sig-name descname"><span class="pre">numof_records</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotTopologies.numof_records" title="Link to this definition">§</a></dt>
+<dd><p>The total number of annotation records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotTopologies.numof_references">
+<span class="sig-name descname"><span class="pre">numof_references</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotTopologies.numof_references" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects and counts the
+references across all records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotTopologies.process">
+<span class="sig-name descname"><span class="pre">process</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotTopologies.process" title="Link to this definition">§</a></dt>
+<dd><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotTopologies.reload">
+<span class="sig-name descname"><span class="pre">reload</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotTopologies.reload" title="Link to this definition">§</a></dt>
+<dd><p>Reloads the object from the module level.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotTopologies.select">
+<span class="sig-name descname"><span class="pre">select</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotTopologies.select" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotTopologies.set_method">
+<span class="sig-name descname"><span class="pre">set_method</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotTopologies.set_method" title="Link to this definition">§</a></dt>
+<dd><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if
+necessary.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotTopologies.set_reference_set">
+<span class="sig-name descname"><span class="pre">set_reference_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotTopologies.set_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Assigns the reference set to the :py:attr``reference_set`` attribute.
+The reference set is the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotTopologies.show">
+<span class="sig-name descname"><span class="pre">show</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">table_param</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotTopologies.show" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic
+information from the UniProt datasheets.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotTopologies.subset_intersection">
+<span class="sig-name descname"><span class="pre">subset_intersection</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">universe</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotTopologies.subset_intersection" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the proportion of entities in a subset occuring in the
+set <code class="docutils literal notranslate"><span class="pre">universe</span></code>. The subset is selected by passing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> to the
+<code class="docutils literal notranslate"><span class="pre">select</span></code> method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotTopologies.to_array">
+<span class="sig-name descname"><span class="pre">to_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_fields</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotTopologies.to_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns an entity vs feature array. In case of more complex
+annotations this might be huge.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotTopologies.to_bool_array">
+<span class="sig-name descname"><span class="pre">to_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotTopologies.to_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a presence/absence boolean array for a reference set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.UniprotTopologies.to_set">
+<span class="sig-name descname"><span class="pre">to_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.UniprotTopologies.to_set" title="Link to this definition">§</a></dt>
+<dd><p>Returns the entities present in this annotation resource as a set.</p>
+</dd></dl>
+
+</dd></dl>
+
+</section>
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+
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+  <section id="pypath-core-annot-vesiclepedia">
+<h1>pypath.core.annot.Vesiclepedia<a class="headerlink" href="#pypath-core-annot-vesiclepedia" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.core.annot.Vesiclepedia">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.core.annot.</span></span><span class="sig-name descname"><span class="pre">Vesiclepedia</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#Vesiclepedia"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.Vesiclepedia" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <a class="reference internal" href="pypath.core.annot.Exocarta.html#pypath.core.annot.Exocarta" title="pypath.core.annot.Exocarta"><code class="xref py py-class docutils literal notranslate"><span class="pre">Exocarta</span></code></a></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Vesiclepedia.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#Vesiclepedia.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.Vesiclepedia.__init__" title="Link to this definition">§</a></dt>
+<dd><p>Represents annotations for a set of proteins.
+Loads the data from the original resource and provides methods
+to query the annotations.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>name</strong> (<em>str</em>) – A custom name for the annotation resource.</p></li>
+<li><p><strong>ncbi_tax_id</strong> (<em>int</em>) – NCBI Taxonomy identifier.</p></li>
+<li><p><strong>input_method</strong> (<em>callable</em><em>,</em><em>str</em>) – Either a callable or the name of a method in any submodules of
+the <code class="docutils literal notranslate"><span class="pre">pypath.inputs</span></code>  module. Should return a dict with
+UniProt IDs as keys or an object suitable for <code class="docutils literal notranslate"><span class="pre">process_method</span></code>.</p></li>
+<li><p><strong>input_args</strong> (<em>dict</em>) – Arguments for the <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Vesiclepedia.__init__" title="pypath.core.annot.Vesiclepedia.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>([ncbi_tax_id])</p></td>
+<td><p>Represents annotations for a set of proteins.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Vesiclepedia.add_complexes_by_inference" title="pypath.core.annot.Vesiclepedia.add_complexes_by_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">add_complexes_by_inference</span></code></a>([complexes])</p></td>
+<td><p>Creates complex annotations by in silico inference and adds them to this annotation set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Vesiclepedia.all_complexes" title="pypath.core.annot.Vesiclepedia.all_complexes"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_complexes</span></code></a>()</p></td>
+<td><p>All protein complexes annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Vesiclepedia.all_entities" title="pypath.core.annot.Vesiclepedia.all_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_entities</span></code></a>([entity_types])</p></td>
+<td><p>All entities annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Vesiclepedia.all_mirnas" title="pypath.core.annot.Vesiclepedia.all_mirnas"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_mirnas</span></code></a>()</p></td>
+<td><p>All miRNAs annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Vesiclepedia.all_proteins" title="pypath.core.annot.Vesiclepedia.all_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_proteins</span></code></a>()</p></td>
+<td><p>All UniProt IDs annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Vesiclepedia.all_refs" title="pypath.core.annot.Vesiclepedia.all_refs"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_refs</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Vesiclepedia.annotate_complex" title="pypath.core.annot.Vesiclepedia.annotate_complex"><code class="xref py py-obj docutils literal notranslate"><span class="pre">annotate_complex</span></code></a>(cplex)</p></td>
+<td><p>Infers annotations for a single complex.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Vesiclepedia.browse" title="pypath.core.annot.Vesiclepedia.browse"><code class="xref py py-obj docutils literal notranslate"><span class="pre">browse</span></code></a>([field, start])</p></td>
+<td><p>Print gene information as a table.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Vesiclepedia.complex_inference" title="pypath.core.annot.Vesiclepedia.complex_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">complex_inference</span></code></a>([complexes])</p></td>
+<td><p>Annotates all complexes in <cite>complexes</cite>, by default in the default complex database (existing in the <cite>complex</cite> module or generated on demand according to the module's current settings).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Vesiclepedia.coverage" title="pypath.core.annot.Vesiclepedia.coverage"><code class="xref py py-obj docutils literal notranslate"><span class="pre">coverage</span></code></a>(other)</p></td>
+<td><p>Calculates the coverage of the annotation i.e. the proportion of entities having at least one record in this annotation resource for an arbitrary set of entities.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Vesiclepedia.curation_effort" title="pypath.core.annot.Vesiclepedia.curation_effort"><code class="xref py py-obj docutils literal notranslate"><span class="pre">curation_effort</span></code></a>()</p></td>
+<td><p>Counts the reference-record pairs.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">from_dump</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_entity_type</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Vesiclepedia.get_names" title="pypath.core.annot.Vesiclepedia.get_names"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_names</span></code></a>()</p></td>
+<td><p>Returns the list of field names in the records.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Vesiclepedia.get_reference_set" title="pypath.core.annot.Vesiclepedia.get_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_reference_set</span></code></a>([proteins, complexes, ...])</p></td>
+<td><p>Retrieves the reference set i.e. the set of all entities which potentially have annotation in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Vesiclepedia.get_subset" title="pypath.core.annot.Vesiclepedia.get_subset"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Vesiclepedia.get_subset_bool_array" title="pypath.core.annot.Vesiclepedia.get_subset_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset_bool_array</span></code></a>([reference_set])</p></td>
+<td><p>Returns a boolean vector with True and False values for each entity in the reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Vesiclepedia.get_values" title="pypath.core.annot.Vesiclepedia.get_values"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_values</span></code></a>(name[, exclude_none])</p></td>
+<td><p>Returns the set of all possible values of a field.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_complex</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_mirna</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_protein</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Vesiclepedia.labels" title="pypath.core.annot.Vesiclepedia.labels"><code class="xref py py-obj docutils literal notranslate"><span class="pre">labels</span></code></a>([method])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Vesiclepedia.load" title="pypath.core.annot.Vesiclepedia.load"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load</span></code></a>()</p></td>
+<td><p>Loads the annotation data by calling the input method.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Vesiclepedia.load_data" title="pypath.core.annot.Vesiclepedia.load_data"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_data</span></code></a>()</p></td>
+<td><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Vesiclepedia.load_proteins" title="pypath.core.annot.Vesiclepedia.load_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_proteins</span></code></a>()</p></td>
+<td><p>Retrieves a set of all UniProt IDs to have a base set of the entire proteome.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Vesiclepedia.make_df" title="pypath.core.annot.Vesiclepedia.make_df"><code class="xref py py-obj docutils literal notranslate"><span class="pre">make_df</span></code></a>([rebuild])</p></td>
+<td><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complex_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Vesiclepedia.numof_entities" title="pypath.core.annot.Vesiclepedia.numof_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_entities</span></code></a>()</p></td>
+<td><p>The number of annotated entities in the resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirna_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirnas</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_protein_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_proteins</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Vesiclepedia.numof_records" title="pypath.core.annot.Vesiclepedia.numof_records"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_records</span></code></a>([entity_types])</p></td>
+<td><p>The total number of annotation records.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Vesiclepedia.numof_references" title="pypath.core.annot.Vesiclepedia.numof_references"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_references</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Vesiclepedia.process" title="pypath.core.annot.Vesiclepedia.process"><code class="xref py py-obj docutils literal notranslate"><span class="pre">process</span></code></a>()</p></td>
+<td><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">proportion</span></code>(other)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Vesiclepedia.reload" title="pypath.core.annot.Vesiclepedia.reload"><code class="xref py py-obj docutils literal notranslate"><span class="pre">reload</span></code></a>()</p></td>
+<td><p>Reloads the object from the module level.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">save_to_pickle</span></code>(pickle_file)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Vesiclepedia.select" title="pypath.core.annot.Vesiclepedia.select"><code class="xref py py-obj docutils literal notranslate"><span class="pre">select</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Vesiclepedia.set_method" title="pypath.core.annot.Vesiclepedia.set_method"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_method</span></code></a>()</p></td>
+<td><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if necessary.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Vesiclepedia.set_reference_set" title="pypath.core.annot.Vesiclepedia.set_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_reference_set</span></code></a>()</p></td>
+<td><p>Assigns the reference set to the :py:attr``reference_set`` attribute.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Vesiclepedia.show" title="pypath.core.annot.Vesiclepedia.show"><code class="xref py py-obj docutils literal notranslate"><span class="pre">show</span></code></a>([method, table_param])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic information from the UniProt datasheets.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Vesiclepedia.subset_intersection" title="pypath.core.annot.Vesiclepedia.subset_intersection"><code class="xref py py-obj docutils literal notranslate"><span class="pre">subset_intersection</span></code></a>(universe, **kwargs)</p></td>
+<td><p>Calculates the proportion of entities in a subset occuring in the set <code class="docutils literal notranslate"><span class="pre">universe</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Vesiclepedia.to_array" title="pypath.core.annot.Vesiclepedia.to_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_array</span></code></a>([reference_set, use_fields])</p></td>
+<td><p>Returns an entity vs feature array.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Vesiclepedia.to_bool_array" title="pypath.core.annot.Vesiclepedia.to_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_bool_array</span></code></a>(reference_set)</p></td>
+<td><p>Returns a presence/absence boolean array for a reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Vesiclepedia.to_set" title="pypath.core.annot.Vesiclepedia.to_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_set</span></code></a>()</p></td>
+<td><p>Returns the entities present in this annotation resource as a set.</p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Attributes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_fields</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">summary</span></code></p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Vesiclepedia.add_complexes_by_inference">
+<span class="sig-name descname"><span class="pre">add_complexes_by_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Vesiclepedia.add_complexes_by_inference" title="Link to this definition">§</a></dt>
+<dd><p>Creates complex annotations by in silico inference and adds them
+to this annotation set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Vesiclepedia.all_complexes">
+<span class="sig-name descname"><span class="pre">all_complexes</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Vesiclepedia.all_complexes" title="Link to this definition">§</a></dt>
+<dd><p>All protein complexes annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Vesiclepedia.all_entities">
+<span class="sig-name descname"><span class="pre">all_entities</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Vesiclepedia.all_entities" title="Link to this definition">§</a></dt>
+<dd><p>All entities annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Vesiclepedia.all_mirnas">
+<span class="sig-name descname"><span class="pre">all_mirnas</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Vesiclepedia.all_mirnas" title="Link to this definition">§</a></dt>
+<dd><p>All miRNAs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Vesiclepedia.all_proteins">
+<span class="sig-name descname"><span class="pre">all_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Vesiclepedia.all_proteins" title="Link to this definition">§</a></dt>
+<dd><p>All UniProt IDs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Vesiclepedia.all_refs">
+<span class="sig-name descname"><span class="pre">all_refs</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Vesiclepedia.all_refs" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects the references
+across all records. Returns <em>list</em>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Vesiclepedia.annotate_complex">
+<span class="sig-name descname"><span class="pre">annotate_complex</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cplex</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Vesiclepedia.annotate_complex" title="Link to this definition">§</a></dt>
+<dd><p>Infers annotations for a single complex.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Vesiclepedia.browse">
+<span class="sig-name descname"><span class="pre">browse</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">field</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">start</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Vesiclepedia.browse" title="Link to this definition">§</a></dt>
+<dd><p>Print gene information as a table.</p>
+<p>Presents information about annotation categories as ascii tables
+printed in the terminal. If one category provided, prints one table.
+If multiple categories provided, prints a table for each of them one
+by one proceeding to the next one once you hit return. If no categories
+provided goes through all levels of the primary category.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>field:</dt><dd><p>The field to browse categories by.</p>
+<ul class="simple">
+<li><p>If None the primary field will be selected.
+If this annotation resource doesn’t have fields, all proteins
+will be presented as one single category.</p></li>
+<li><p>If a string it will be considered a field name and it will
+browse through all levels of this field.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">list</span></code>, set or tuple, it will be considered either a
+<code class="docutils literal notranslate"><span class="pre">list</span></code> of field names or a list of values from the primary
+field. In the former case all combinations of the values of
+the fields will be presented, in the latter case the browsing
+will be limited to the levels of the primary field contained
+in <code class="docutils literal notranslate"><span class="pre">field</span></code>.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">dict</span></code>, keys are supposed to be field names and values
+as list of levels. If any of the values are None, all levels
+from that field will be used.</p></li>
+</ul>
+</dd>
+<dt>start:</dt><dd><p>Start browsing from this category. E.g. if there are 500
+categories and start is 250 it will skip everything before the
+250th.</p>
+</dd>
+<dt>kwargs:</dt><dd><p>Passed to <code class="docutils literal notranslate"><span class="pre">pypath.utils.uniprot.info</span></code>.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Vesiclepedia.complex_inference">
+<span class="sig-name descname"><span class="pre">complex_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Vesiclepedia.complex_inference" title="Link to this definition">§</a></dt>
+<dd><p>Annotates all complexes in <cite>complexes</cite>, by default in the default
+complex database (existing in the <cite>complex</cite> module or generated
+on demand according to the module’s current settings).</p>
+<dl class="field-list simple">
+<dt class="field-odd">Returns<span class="colon">:</span></dt>
+<dd class="field-odd"><p><ul class="simple">
+<li><p><em>Dict with complexes as keys and sets of annotations as values.</em></p></li>
+<li><p><em>Complexes with no valid information in this annotation resource</em></p></li>
+<li><p><em>won’t be in the dict.</em></p></li>
+</ul>
+</p>
+</dd>
+<dt class="field-even">Parameters<span class="colon">:</span></dt>
+<dd class="field-even"><p><strong>complexes</strong> (<em>iterable</em>) – Iterable yielding complexes.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Vesiclepedia.coverage">
+<span class="sig-name descname"><span class="pre">coverage</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">other</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Vesiclepedia.coverage" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the coverage of the annotation i.e. the proportion of
+entities having at least one record in this annotation resource
+for an arbitrary set of entities.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Vesiclepedia.curation_effort">
+<span class="sig-name descname"><span class="pre">curation_effort</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Vesiclepedia.curation_effort" title="Link to this definition">§</a></dt>
+<dd><p>Counts the reference-record pairs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Vesiclepedia.get_names">
+<span class="sig-name descname"><span class="pre">get_names</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Vesiclepedia.get_names" title="Link to this definition">§</a></dt>
+<dd><p>Returns the list of field names in the records. The annotation
+consists of uniform records and each entity might be annotated
+with one or more records. Each record is a tuple of fields, for
+example <code class="docutils literal notranslate"><span class="pre">('cell_type',</span> <span class="pre">'expression_level',</span> <span class="pre">'score')</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Vesiclepedia.get_reference_set">
+<em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">get_reference_set</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">proteins</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">swissprot_only</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Vesiclepedia.get_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the reference set i.e. the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Vesiclepedia.get_subset">
+<span class="sig-name descname"><span class="pre">get_subset</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Vesiclepedia.get_subset" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Vesiclepedia.get_subset_bool_array">
+<span class="sig-name descname"><span class="pre">get_subset_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Vesiclepedia.get_subset_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a boolean vector with True and False values for each entity
+in the reference set. The values represent presence absence data
+in the simplest case, but by providing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> any kind of matching
+and filtering is possible. <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> are passed to the <code class="docutils literal notranslate"><span class="pre">select</span></code>
+method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Vesiclepedia.get_values">
+<span class="sig-name descname"><span class="pre">get_values</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">exclude_none</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Vesiclepedia.get_values" title="Link to this definition">§</a></dt>
+<dd><p>Returns the set of all possible values of a field. E.g. if the
+records of this annotation have a field <code class="docutils literal notranslate"><span class="pre">cell_type</span></code> then calling
+this method can tell you that across all records the values of
+this field might be <code class="docutils literal notranslate"><span class="pre">{'macrophage',</span> <span class="pre">'epithelial_cell',</span> <span class="pre">...}</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Vesiclepedia.labels">
+<span class="sig-name descname"><span class="pre">labels</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Vesiclepedia.labels" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Vesiclepedia.load">
+<span class="sig-name descname"><span class="pre">load</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Vesiclepedia.load" title="Link to this definition">§</a></dt>
+<dd><p>Loads the annotation data by calling the input method.
+Infers annotations for complexes in the complex database if
+py:attr:<code class="docutils literal notranslate"><span class="pre">infer_complexes</span></code> is True.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Vesiclepedia.load_data">
+<span class="sig-name descname"><span class="pre">load_data</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Vesiclepedia.load_data" title="Link to this definition">§</a></dt>
+<dd><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Vesiclepedia.load_proteins">
+<span class="sig-name descname"><span class="pre">load_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Vesiclepedia.load_proteins" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a set of all UniProt IDs to have a base set of the entire
+proteome.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Vesiclepedia.make_df">
+<span class="sig-name descname"><span class="pre">make_df</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">rebuild</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Vesiclepedia.make_df" title="Link to this definition">§</a></dt>
+<dd><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.
+The data frame will be assigned to :py:attr``df``.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Vesiclepedia.numof_entities">
+<span class="sig-name descname"><span class="pre">numof_entities</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Vesiclepedia.numof_entities" title="Link to this definition">§</a></dt>
+<dd><p>The number of annotated entities in the resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Vesiclepedia.numof_records">
+<span class="sig-name descname"><span class="pre">numof_records</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Vesiclepedia.numof_records" title="Link to this definition">§</a></dt>
+<dd><p>The total number of annotation records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Vesiclepedia.numof_references">
+<span class="sig-name descname"><span class="pre">numof_references</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Vesiclepedia.numof_references" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects and counts the
+references across all records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Vesiclepedia.process">
+<span class="sig-name descname"><span class="pre">process</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Vesiclepedia.process" title="Link to this definition">§</a></dt>
+<dd><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Vesiclepedia.reload">
+<span class="sig-name descname"><span class="pre">reload</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Vesiclepedia.reload" title="Link to this definition">§</a></dt>
+<dd><p>Reloads the object from the module level.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Vesiclepedia.select">
+<span class="sig-name descname"><span class="pre">select</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Vesiclepedia.select" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Vesiclepedia.set_method">
+<span class="sig-name descname"><span class="pre">set_method</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Vesiclepedia.set_method" title="Link to this definition">§</a></dt>
+<dd><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if
+necessary.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Vesiclepedia.set_reference_set">
+<span class="sig-name descname"><span class="pre">set_reference_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Vesiclepedia.set_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Assigns the reference set to the :py:attr``reference_set`` attribute.
+The reference set is the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Vesiclepedia.show">
+<span class="sig-name descname"><span class="pre">show</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">table_param</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Vesiclepedia.show" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic
+information from the UniProt datasheets.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Vesiclepedia.subset_intersection">
+<span class="sig-name descname"><span class="pre">subset_intersection</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">universe</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Vesiclepedia.subset_intersection" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the proportion of entities in a subset occuring in the
+set <code class="docutils literal notranslate"><span class="pre">universe</span></code>. The subset is selected by passing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> to the
+<code class="docutils literal notranslate"><span class="pre">select</span></code> method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Vesiclepedia.to_array">
+<span class="sig-name descname"><span class="pre">to_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_fields</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Vesiclepedia.to_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns an entity vs feature array. In case of more complex
+annotations this might be huge.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Vesiclepedia.to_bool_array">
+<span class="sig-name descname"><span class="pre">to_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Vesiclepedia.to_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a presence/absence boolean array for a reference set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Vesiclepedia.to_set">
+<span class="sig-name descname"><span class="pre">to_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Vesiclepedia.to_set" title="Link to this definition">§</a></dt>
+<dd><p>Returns the entities present in this annotation resource as a set.</p>
+</dd></dl>
+
+</dd></dl>
+
+</section>
+
+
+                </article>
+              
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+  <section id="pypath-core-annot-wang">
+<h1>pypath.core.annot.Wang<a class="headerlink" href="#pypath-core-annot-wang" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.core.annot.Wang">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.core.annot.</span></span><span class="sig-name descname"><span class="pre">Wang</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#Wang"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.Wang" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <a class="reference internal" href="pypath.core.annot.AnnotationBase.html#pypath.core.annot.AnnotationBase" title="pypath.core.annot.AnnotationBase"><code class="xref py py-class docutils literal notranslate"><span class="pre">AnnotationBase</span></code></a></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Wang.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#Wang.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.Wang.__init__" title="Link to this definition">§</a></dt>
+<dd><p>Cytokine perturbation signatures from the CytoSig database.</p>
+</dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Wang.__init__" title="pypath.core.annot.Wang.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>([ncbi_tax_id])</p></td>
+<td><p>Cytokine perturbation signatures from the CytoSig database.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Wang.add_complexes_by_inference" title="pypath.core.annot.Wang.add_complexes_by_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">add_complexes_by_inference</span></code></a>([complexes])</p></td>
+<td><p>Creates complex annotations by in silico inference and adds them to this annotation set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Wang.all_complexes" title="pypath.core.annot.Wang.all_complexes"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_complexes</span></code></a>()</p></td>
+<td><p>All protein complexes annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Wang.all_entities" title="pypath.core.annot.Wang.all_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_entities</span></code></a>([entity_types])</p></td>
+<td><p>All entities annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Wang.all_mirnas" title="pypath.core.annot.Wang.all_mirnas"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_mirnas</span></code></a>()</p></td>
+<td><p>All miRNAs annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Wang.all_proteins" title="pypath.core.annot.Wang.all_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_proteins</span></code></a>()</p></td>
+<td><p>All UniProt IDs annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Wang.all_refs" title="pypath.core.annot.Wang.all_refs"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_refs</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Wang.annotate_complex" title="pypath.core.annot.Wang.annotate_complex"><code class="xref py py-obj docutils literal notranslate"><span class="pre">annotate_complex</span></code></a>(cplex)</p></td>
+<td><p>Infers annotations for a single complex.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Wang.browse" title="pypath.core.annot.Wang.browse"><code class="xref py py-obj docutils literal notranslate"><span class="pre">browse</span></code></a>([field, start])</p></td>
+<td><p>Print gene information as a table.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Wang.complex_inference" title="pypath.core.annot.Wang.complex_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">complex_inference</span></code></a>([complexes])</p></td>
+<td><p>Annotates all complexes in <cite>complexes</cite>, by default in the default complex database (existing in the <cite>complex</cite> module or generated on demand according to the module's current settings).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Wang.coverage" title="pypath.core.annot.Wang.coverage"><code class="xref py py-obj docutils literal notranslate"><span class="pre">coverage</span></code></a>(other)</p></td>
+<td><p>Calculates the coverage of the annotation i.e. the proportion of entities having at least one record in this annotation resource for an arbitrary set of entities.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Wang.curation_effort" title="pypath.core.annot.Wang.curation_effort"><code class="xref py py-obj docutils literal notranslate"><span class="pre">curation_effort</span></code></a>()</p></td>
+<td><p>Counts the reference-record pairs.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">from_dump</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_entity_type</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Wang.get_names" title="pypath.core.annot.Wang.get_names"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_names</span></code></a>()</p></td>
+<td><p>Returns the list of field names in the records.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Wang.get_reference_set" title="pypath.core.annot.Wang.get_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_reference_set</span></code></a>([proteins, complexes, ...])</p></td>
+<td><p>Retrieves the reference set i.e. the set of all entities which potentially have annotation in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Wang.get_subset" title="pypath.core.annot.Wang.get_subset"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Wang.get_subset_bool_array" title="pypath.core.annot.Wang.get_subset_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset_bool_array</span></code></a>([reference_set])</p></td>
+<td><p>Returns a boolean vector with True and False values for each entity in the reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Wang.get_values" title="pypath.core.annot.Wang.get_values"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_values</span></code></a>(name[, exclude_none])</p></td>
+<td><p>Returns the set of all possible values of a field.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_complex</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_mirna</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_protein</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Wang.labels" title="pypath.core.annot.Wang.labels"><code class="xref py py-obj docutils literal notranslate"><span class="pre">labels</span></code></a>([method])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Wang.load" title="pypath.core.annot.Wang.load"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load</span></code></a>()</p></td>
+<td><p>Loads the annotation data by calling the input method.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Wang.load_data" title="pypath.core.annot.Wang.load_data"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_data</span></code></a>()</p></td>
+<td><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Wang.load_proteins" title="pypath.core.annot.Wang.load_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_proteins</span></code></a>()</p></td>
+<td><p>Retrieves a set of all UniProt IDs to have a base set of the entire proteome.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Wang.make_df" title="pypath.core.annot.Wang.make_df"><code class="xref py py-obj docutils literal notranslate"><span class="pre">make_df</span></code></a>([rebuild])</p></td>
+<td><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complex_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Wang.numof_entities" title="pypath.core.annot.Wang.numof_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_entities</span></code></a>()</p></td>
+<td><p>The number of annotated entities in the resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirna_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirnas</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_protein_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_proteins</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Wang.numof_records" title="pypath.core.annot.Wang.numof_records"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_records</span></code></a>([entity_types])</p></td>
+<td><p>The total number of annotation records.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Wang.numof_references" title="pypath.core.annot.Wang.numof_references"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_references</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Wang.process" title="pypath.core.annot.Wang.process"><code class="xref py py-obj docutils literal notranslate"><span class="pre">process</span></code></a>()</p></td>
+<td><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">proportion</span></code>(other)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Wang.reload" title="pypath.core.annot.Wang.reload"><code class="xref py py-obj docutils literal notranslate"><span class="pre">reload</span></code></a>()</p></td>
+<td><p>Reloads the object from the module level.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">save_to_pickle</span></code>(pickle_file)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Wang.select" title="pypath.core.annot.Wang.select"><code class="xref py py-obj docutils literal notranslate"><span class="pre">select</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Wang.set_method" title="pypath.core.annot.Wang.set_method"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_method</span></code></a>()</p></td>
+<td><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if necessary.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Wang.set_reference_set" title="pypath.core.annot.Wang.set_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_reference_set</span></code></a>()</p></td>
+<td><p>Assigns the reference set to the :py:attr``reference_set`` attribute.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Wang.show" title="pypath.core.annot.Wang.show"><code class="xref py py-obj docutils literal notranslate"><span class="pre">show</span></code></a>([method, table_param])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic information from the UniProt datasheets.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Wang.subset_intersection" title="pypath.core.annot.Wang.subset_intersection"><code class="xref py py-obj docutils literal notranslate"><span class="pre">subset_intersection</span></code></a>(universe, **kwargs)</p></td>
+<td><p>Calculates the proportion of entities in a subset occuring in the set <code class="docutils literal notranslate"><span class="pre">universe</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Wang.to_array" title="pypath.core.annot.Wang.to_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_array</span></code></a>([reference_set, use_fields])</p></td>
+<td><p>Returns an entity vs feature array.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Wang.to_bool_array" title="pypath.core.annot.Wang.to_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_bool_array</span></code></a>(reference_set)</p></td>
+<td><p>Returns a presence/absence boolean array for a reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Wang.to_set" title="pypath.core.annot.Wang.to_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_set</span></code></a>()</p></td>
+<td><p>Returns the entities present in this annotation resource as a set.</p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Attributes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_fields</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">summary</span></code></p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Wang.add_complexes_by_inference">
+<span class="sig-name descname"><span class="pre">add_complexes_by_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Wang.add_complexes_by_inference" title="Link to this definition">§</a></dt>
+<dd><p>Creates complex annotations by in silico inference and adds them
+to this annotation set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Wang.all_complexes">
+<span class="sig-name descname"><span class="pre">all_complexes</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Wang.all_complexes" title="Link to this definition">§</a></dt>
+<dd><p>All protein complexes annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Wang.all_entities">
+<span class="sig-name descname"><span class="pre">all_entities</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Wang.all_entities" title="Link to this definition">§</a></dt>
+<dd><p>All entities annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Wang.all_mirnas">
+<span class="sig-name descname"><span class="pre">all_mirnas</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Wang.all_mirnas" title="Link to this definition">§</a></dt>
+<dd><p>All miRNAs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Wang.all_proteins">
+<span class="sig-name descname"><span class="pre">all_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Wang.all_proteins" title="Link to this definition">§</a></dt>
+<dd><p>All UniProt IDs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Wang.all_refs">
+<span class="sig-name descname"><span class="pre">all_refs</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Wang.all_refs" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects the references
+across all records. Returns <em>list</em>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Wang.annotate_complex">
+<span class="sig-name descname"><span class="pre">annotate_complex</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cplex</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Wang.annotate_complex" title="Link to this definition">§</a></dt>
+<dd><p>Infers annotations for a single complex.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Wang.browse">
+<span class="sig-name descname"><span class="pre">browse</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">field</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">start</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Wang.browse" title="Link to this definition">§</a></dt>
+<dd><p>Print gene information as a table.</p>
+<p>Presents information about annotation categories as ascii tables
+printed in the terminal. If one category provided, prints one table.
+If multiple categories provided, prints a table for each of them one
+by one proceeding to the next one once you hit return. If no categories
+provided goes through all levels of the primary category.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>field:</dt><dd><p>The field to browse categories by.</p>
+<ul class="simple">
+<li><p>If None the primary field will be selected.
+If this annotation resource doesn’t have fields, all proteins
+will be presented as one single category.</p></li>
+<li><p>If a string it will be considered a field name and it will
+browse through all levels of this field.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">list</span></code>, set or tuple, it will be considered either a
+<code class="docutils literal notranslate"><span class="pre">list</span></code> of field names or a list of values from the primary
+field. In the former case all combinations of the values of
+the fields will be presented, in the latter case the browsing
+will be limited to the levels of the primary field contained
+in <code class="docutils literal notranslate"><span class="pre">field</span></code>.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">dict</span></code>, keys are supposed to be field names and values
+as list of levels. If any of the values are None, all levels
+from that field will be used.</p></li>
+</ul>
+</dd>
+<dt>start:</dt><dd><p>Start browsing from this category. E.g. if there are 500
+categories and start is 250 it will skip everything before the
+250th.</p>
+</dd>
+<dt>kwargs:</dt><dd><p>Passed to <code class="docutils literal notranslate"><span class="pre">pypath.utils.uniprot.info</span></code>.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Wang.complex_inference">
+<span class="sig-name descname"><span class="pre">complex_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Wang.complex_inference" title="Link to this definition">§</a></dt>
+<dd><p>Annotates all complexes in <cite>complexes</cite>, by default in the default
+complex database (existing in the <cite>complex</cite> module or generated
+on demand according to the module’s current settings).</p>
+<dl class="field-list simple">
+<dt class="field-odd">Returns<span class="colon">:</span></dt>
+<dd class="field-odd"><p><ul class="simple">
+<li><p><em>Dict with complexes as keys and sets of annotations as values.</em></p></li>
+<li><p><em>Complexes with no valid information in this annotation resource</em></p></li>
+<li><p><em>won’t be in the dict.</em></p></li>
+</ul>
+</p>
+</dd>
+<dt class="field-even">Parameters<span class="colon">:</span></dt>
+<dd class="field-even"><p><strong>complexes</strong> (<em>iterable</em>) – Iterable yielding complexes.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Wang.coverage">
+<span class="sig-name descname"><span class="pre">coverage</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">other</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Wang.coverage" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the coverage of the annotation i.e. the proportion of
+entities having at least one record in this annotation resource
+for an arbitrary set of entities.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Wang.curation_effort">
+<span class="sig-name descname"><span class="pre">curation_effort</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Wang.curation_effort" title="Link to this definition">§</a></dt>
+<dd><p>Counts the reference-record pairs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Wang.get_names">
+<span class="sig-name descname"><span class="pre">get_names</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Wang.get_names" title="Link to this definition">§</a></dt>
+<dd><p>Returns the list of field names in the records. The annotation
+consists of uniform records and each entity might be annotated
+with one or more records. Each record is a tuple of fields, for
+example <code class="docutils literal notranslate"><span class="pre">('cell_type',</span> <span class="pre">'expression_level',</span> <span class="pre">'score')</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Wang.get_reference_set">
+<em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">get_reference_set</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">proteins</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">swissprot_only</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Wang.get_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the reference set i.e. the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Wang.get_subset">
+<span class="sig-name descname"><span class="pre">get_subset</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Wang.get_subset" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Wang.get_subset_bool_array">
+<span class="sig-name descname"><span class="pre">get_subset_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Wang.get_subset_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a boolean vector with True and False values for each entity
+in the reference set. The values represent presence absence data
+in the simplest case, but by providing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> any kind of matching
+and filtering is possible. <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> are passed to the <code class="docutils literal notranslate"><span class="pre">select</span></code>
+method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Wang.get_values">
+<span class="sig-name descname"><span class="pre">get_values</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">exclude_none</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Wang.get_values" title="Link to this definition">§</a></dt>
+<dd><p>Returns the set of all possible values of a field. E.g. if the
+records of this annotation have a field <code class="docutils literal notranslate"><span class="pre">cell_type</span></code> then calling
+this method can tell you that across all records the values of
+this field might be <code class="docutils literal notranslate"><span class="pre">{'macrophage',</span> <span class="pre">'epithelial_cell',</span> <span class="pre">...}</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Wang.labels">
+<span class="sig-name descname"><span class="pre">labels</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Wang.labels" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Wang.load">
+<span class="sig-name descname"><span class="pre">load</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Wang.load" title="Link to this definition">§</a></dt>
+<dd><p>Loads the annotation data by calling the input method.
+Infers annotations for complexes in the complex database if
+py:attr:<code class="docutils literal notranslate"><span class="pre">infer_complexes</span></code> is True.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Wang.load_data">
+<span class="sig-name descname"><span class="pre">load_data</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Wang.load_data" title="Link to this definition">§</a></dt>
+<dd><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Wang.load_proteins">
+<span class="sig-name descname"><span class="pre">load_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Wang.load_proteins" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a set of all UniProt IDs to have a base set of the entire
+proteome.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Wang.make_df">
+<span class="sig-name descname"><span class="pre">make_df</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">rebuild</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Wang.make_df" title="Link to this definition">§</a></dt>
+<dd><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.
+The data frame will be assigned to :py:attr``df``.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Wang.numof_entities">
+<span class="sig-name descname"><span class="pre">numof_entities</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Wang.numof_entities" title="Link to this definition">§</a></dt>
+<dd><p>The number of annotated entities in the resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Wang.numof_records">
+<span class="sig-name descname"><span class="pre">numof_records</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Wang.numof_records" title="Link to this definition">§</a></dt>
+<dd><p>The total number of annotation records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Wang.numof_references">
+<span class="sig-name descname"><span class="pre">numof_references</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Wang.numof_references" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects and counts the
+references across all records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Wang.process">
+<span class="sig-name descname"><span class="pre">process</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Wang.process" title="Link to this definition">§</a></dt>
+<dd><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Wang.reload">
+<span class="sig-name descname"><span class="pre">reload</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Wang.reload" title="Link to this definition">§</a></dt>
+<dd><p>Reloads the object from the module level.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Wang.select">
+<span class="sig-name descname"><span class="pre">select</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Wang.select" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Wang.set_method">
+<span class="sig-name descname"><span class="pre">set_method</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Wang.set_method" title="Link to this definition">§</a></dt>
+<dd><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if
+necessary.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Wang.set_reference_set">
+<span class="sig-name descname"><span class="pre">set_reference_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Wang.set_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Assigns the reference set to the :py:attr``reference_set`` attribute.
+The reference set is the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Wang.show">
+<span class="sig-name descname"><span class="pre">show</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">table_param</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Wang.show" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic
+information from the UniProt datasheets.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Wang.subset_intersection">
+<span class="sig-name descname"><span class="pre">subset_intersection</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">universe</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Wang.subset_intersection" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the proportion of entities in a subset occuring in the
+set <code class="docutils literal notranslate"><span class="pre">universe</span></code>. The subset is selected by passing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> to the
+<code class="docutils literal notranslate"><span class="pre">select</span></code> method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Wang.to_array">
+<span class="sig-name descname"><span class="pre">to_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_fields</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Wang.to_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns an entity vs feature array. In case of more complex
+annotations this might be huge.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Wang.to_bool_array">
+<span class="sig-name descname"><span class="pre">to_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Wang.to_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a presence/absence boolean array for a reference set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Wang.to_set">
+<span class="sig-name descname"><span class="pre">to_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Wang.to_set" title="Link to this definition">§</a></dt>
+<dd><p>Returns the entities present in this annotation resource as a set.</p>
+</dd></dl>
+
+</dd></dl>
+
+</section>
+
+
+                </article>
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+  <section id="pypath-core-annot-zhong2015">
+<h1>pypath.core.annot.Zhong2015<a class="headerlink" href="#pypath-core-annot-zhong2015" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.core.annot.Zhong2015">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.core.annot.</span></span><span class="sig-name descname"><span class="pre">Zhong2015</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#Zhong2015"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.Zhong2015" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <a class="reference internal" href="pypath.core.annot.AnnotationBase.html#pypath.core.annot.AnnotationBase" title="pypath.core.annot.AnnotationBase"><code class="xref py py-class docutils literal notranslate"><span class="pre">AnnotationBase</span></code></a></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Zhong2015.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#Zhong2015.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.Zhong2015.__init__" title="Link to this definition">§</a></dt>
+<dd><p>Represents annotations for a set of proteins.
+Loads the data from the original resource and provides methods
+to query the annotations.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>name</strong> (<em>str</em>) – A custom name for the annotation resource.</p></li>
+<li><p><strong>ncbi_tax_id</strong> (<em>int</em>) – NCBI Taxonomy identifier.</p></li>
+<li><p><strong>input_method</strong> (<em>callable</em><em>,</em><em>str</em>) – Either a callable or the name of a method in any submodules of
+the <code class="docutils literal notranslate"><span class="pre">pypath.inputs</span></code>  module. Should return a dict with
+UniProt IDs as keys or an object suitable for <code class="docutils literal notranslate"><span class="pre">process_method</span></code>.</p></li>
+<li><p><strong>input_args</strong> (<em>dict</em>) – Arguments for the <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Zhong2015.__init__" title="pypath.core.annot.Zhong2015.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>(**kwargs)</p></td>
+<td><p>Represents annotations for a set of proteins.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Zhong2015.add_complexes_by_inference" title="pypath.core.annot.Zhong2015.add_complexes_by_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">add_complexes_by_inference</span></code></a>([complexes])</p></td>
+<td><p>Creates complex annotations by in silico inference and adds them to this annotation set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Zhong2015.all_complexes" title="pypath.core.annot.Zhong2015.all_complexes"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_complexes</span></code></a>()</p></td>
+<td><p>All protein complexes annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Zhong2015.all_entities" title="pypath.core.annot.Zhong2015.all_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_entities</span></code></a>([entity_types])</p></td>
+<td><p>All entities annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Zhong2015.all_mirnas" title="pypath.core.annot.Zhong2015.all_mirnas"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_mirnas</span></code></a>()</p></td>
+<td><p>All miRNAs annotated in this resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Zhong2015.all_proteins" title="pypath.core.annot.Zhong2015.all_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_proteins</span></code></a>()</p></td>
+<td><p>All UniProt IDs annotated in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Zhong2015.all_refs" title="pypath.core.annot.Zhong2015.all_refs"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_refs</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Zhong2015.annotate_complex" title="pypath.core.annot.Zhong2015.annotate_complex"><code class="xref py py-obj docutils literal notranslate"><span class="pre">annotate_complex</span></code></a>(cplex)</p></td>
+<td><p>Infers annotations for a single complex.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Zhong2015.browse" title="pypath.core.annot.Zhong2015.browse"><code class="xref py py-obj docutils literal notranslate"><span class="pre">browse</span></code></a>([field, start])</p></td>
+<td><p>Print gene information as a table.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Zhong2015.complex_inference" title="pypath.core.annot.Zhong2015.complex_inference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">complex_inference</span></code></a>([complexes])</p></td>
+<td><p>Annotates all complexes in <cite>complexes</cite>, by default in the default complex database (existing in the <cite>complex</cite> module or generated on demand according to the module's current settings).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Zhong2015.coverage" title="pypath.core.annot.Zhong2015.coverage"><code class="xref py py-obj docutils literal notranslate"><span class="pre">coverage</span></code></a>(other)</p></td>
+<td><p>Calculates the coverage of the annotation i.e. the proportion of entities having at least one record in this annotation resource for an arbitrary set of entities.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Zhong2015.curation_effort" title="pypath.core.annot.Zhong2015.curation_effort"><code class="xref py py-obj docutils literal notranslate"><span class="pre">curation_effort</span></code></a>()</p></td>
+<td><p>Counts the reference-record pairs.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">from_dump</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_entity_type</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Zhong2015.get_names" title="pypath.core.annot.Zhong2015.get_names"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_names</span></code></a>()</p></td>
+<td><p>Returns the list of field names in the records.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Zhong2015.get_reference_set" title="pypath.core.annot.Zhong2015.get_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_reference_set</span></code></a>([proteins, complexes, ...])</p></td>
+<td><p>Retrieves the reference set i.e. the set of all entities which potentially have annotation in this resource.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Zhong2015.get_subset" title="pypath.core.annot.Zhong2015.get_subset"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Zhong2015.get_subset_bool_array" title="pypath.core.annot.Zhong2015.get_subset_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_subset_bool_array</span></code></a>([reference_set])</p></td>
+<td><p>Returns a boolean vector with True and False values for each entity in the reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Zhong2015.get_values" title="pypath.core.annot.Zhong2015.get_values"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_values</span></code></a>(name[, exclude_none])</p></td>
+<td><p>Returns the set of all possible values of a field.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_complex</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_mirna</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_protein</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Zhong2015.labels" title="pypath.core.annot.Zhong2015.labels"><code class="xref py py-obj docutils literal notranslate"><span class="pre">labels</span></code></a>([method])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Zhong2015.load" title="pypath.core.annot.Zhong2015.load"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load</span></code></a>()</p></td>
+<td><p>Loads the annotation data by calling the input method.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Zhong2015.load_data" title="pypath.core.annot.Zhong2015.load_data"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_data</span></code></a>()</p></td>
+<td><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Zhong2015.load_proteins" title="pypath.core.annot.Zhong2015.load_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_proteins</span></code></a>()</p></td>
+<td><p>Retrieves a set of all UniProt IDs to have a base set of the entire proteome.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Zhong2015.make_df" title="pypath.core.annot.Zhong2015.make_df"><code class="xref py py-obj docutils literal notranslate"><span class="pre">make_df</span></code></a>([rebuild])</p></td>
+<td><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complex_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Zhong2015.numof_entities" title="pypath.core.annot.Zhong2015.numof_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_entities</span></code></a>()</p></td>
+<td><p>The number of annotated entities in the resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirna_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirnas</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_protein_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_proteins</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Zhong2015.numof_records" title="pypath.core.annot.Zhong2015.numof_records"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_records</span></code></a>([entity_types])</p></td>
+<td><p>The total number of annotation records.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Zhong2015.numof_references" title="pypath.core.annot.Zhong2015.numof_references"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_references</span></code></a>()</p></td>
+<td><p>Some annotations contain references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Zhong2015.process" title="pypath.core.annot.Zhong2015.process"><code class="xref py py-obj docutils literal notranslate"><span class="pre">process</span></code></a>()</p></td>
+<td><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">proportion</span></code>(other)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Zhong2015.reload" title="pypath.core.annot.Zhong2015.reload"><code class="xref py py-obj docutils literal notranslate"><span class="pre">reload</span></code></a>()</p></td>
+<td><p>Reloads the object from the module level.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">save_to_pickle</span></code>(pickle_file)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Zhong2015.select" title="pypath.core.annot.Zhong2015.select"><code class="xref py py-obj docutils literal notranslate"><span class="pre">select</span></code></a>([method, entity_type])</p></td>
+<td><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Zhong2015.set_method" title="pypath.core.annot.Zhong2015.set_method"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_method</span></code></a>()</p></td>
+<td><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if necessary.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Zhong2015.set_reference_set" title="pypath.core.annot.Zhong2015.set_reference_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_reference_set</span></code></a>()</p></td>
+<td><p>Assigns the reference set to the :py:attr``reference_set`` attribute.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Zhong2015.show" title="pypath.core.annot.Zhong2015.show"><code class="xref py py-obj docutils literal notranslate"><span class="pre">show</span></code></a>([method, table_param])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic information from the UniProt datasheets.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Zhong2015.subset_intersection" title="pypath.core.annot.Zhong2015.subset_intersection"><code class="xref py py-obj docutils literal notranslate"><span class="pre">subset_intersection</span></code></a>(universe, **kwargs)</p></td>
+<td><p>Calculates the proportion of entities in a subset occuring in the set <code class="docutils literal notranslate"><span class="pre">universe</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Zhong2015.to_array" title="pypath.core.annot.Zhong2015.to_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_array</span></code></a>([reference_set, use_fields])</p></td>
+<td><p>Returns an entity vs feature array.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.annot.Zhong2015.to_bool_array" title="pypath.core.annot.Zhong2015.to_bool_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_bool_array</span></code></a>(reference_set)</p></td>
+<td><p>Returns a presence/absence boolean array for a reference set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.annot.Zhong2015.to_set" title="pypath.core.annot.Zhong2015.to_set"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_set</span></code></a>()</p></td>
+<td><p>Returns the entities present in this annotation resource as a set.</p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Attributes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_fields</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">summary</span></code></p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Zhong2015.add_complexes_by_inference">
+<span class="sig-name descname"><span class="pre">add_complexes_by_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Zhong2015.add_complexes_by_inference" title="Link to this definition">§</a></dt>
+<dd><p>Creates complex annotations by in silico inference and adds them
+to this annotation set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Zhong2015.all_complexes">
+<span class="sig-name descname"><span class="pre">all_complexes</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Zhong2015.all_complexes" title="Link to this definition">§</a></dt>
+<dd><p>All protein complexes annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Zhong2015.all_entities">
+<span class="sig-name descname"><span class="pre">all_entities</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Zhong2015.all_entities" title="Link to this definition">§</a></dt>
+<dd><p>All entities annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Zhong2015.all_mirnas">
+<span class="sig-name descname"><span class="pre">all_mirnas</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Zhong2015.all_mirnas" title="Link to this definition">§</a></dt>
+<dd><p>All miRNAs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Zhong2015.all_proteins">
+<span class="sig-name descname"><span class="pre">all_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Zhong2015.all_proteins" title="Link to this definition">§</a></dt>
+<dd><p>All UniProt IDs annotated in this resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Zhong2015.all_refs">
+<span class="sig-name descname"><span class="pre">all_refs</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Zhong2015.all_refs" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects the references
+across all records. Returns <em>list</em>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Zhong2015.annotate_complex">
+<span class="sig-name descname"><span class="pre">annotate_complex</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cplex</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Zhong2015.annotate_complex" title="Link to this definition">§</a></dt>
+<dd><p>Infers annotations for a single complex.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Zhong2015.browse">
+<span class="sig-name descname"><span class="pre">browse</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">field</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">start</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Zhong2015.browse" title="Link to this definition">§</a></dt>
+<dd><p>Print gene information as a table.</p>
+<p>Presents information about annotation categories as ascii tables
+printed in the terminal. If one category provided, prints one table.
+If multiple categories provided, prints a table for each of them one
+by one proceeding to the next one once you hit return. If no categories
+provided goes through all levels of the primary category.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>field:</dt><dd><p>The field to browse categories by.</p>
+<ul class="simple">
+<li><p>If None the primary field will be selected.
+If this annotation resource doesn’t have fields, all proteins
+will be presented as one single category.</p></li>
+<li><p>If a string it will be considered a field name and it will
+browse through all levels of this field.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">list</span></code>, set or tuple, it will be considered either a
+<code class="docutils literal notranslate"><span class="pre">list</span></code> of field names or a list of values from the primary
+field. In the former case all combinations of the values of
+the fields will be presented, in the latter case the browsing
+will be limited to the levels of the primary field contained
+in <code class="docutils literal notranslate"><span class="pre">field</span></code>.</p></li>
+<li><p>If a <code class="docutils literal notranslate"><span class="pre">dict</span></code>, keys are supposed to be field names and values
+as list of levels. If any of the values are None, all levels
+from that field will be used.</p></li>
+</ul>
+</dd>
+<dt>start:</dt><dd><p>Start browsing from this category. E.g. if there are 500
+categories and start is 250 it will skip everything before the
+250th.</p>
+</dd>
+<dt>kwargs:</dt><dd><p>Passed to <code class="docutils literal notranslate"><span class="pre">pypath.utils.uniprot.info</span></code>.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Zhong2015.complex_inference">
+<span class="sig-name descname"><span class="pre">complex_inference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Zhong2015.complex_inference" title="Link to this definition">§</a></dt>
+<dd><p>Annotates all complexes in <cite>complexes</cite>, by default in the default
+complex database (existing in the <cite>complex</cite> module or generated
+on demand according to the module’s current settings).</p>
+<dl class="field-list simple">
+<dt class="field-odd">Returns<span class="colon">:</span></dt>
+<dd class="field-odd"><p><ul class="simple">
+<li><p><em>Dict with complexes as keys and sets of annotations as values.</em></p></li>
+<li><p><em>Complexes with no valid information in this annotation resource</em></p></li>
+<li><p><em>won’t be in the dict.</em></p></li>
+</ul>
+</p>
+</dd>
+<dt class="field-even">Parameters<span class="colon">:</span></dt>
+<dd class="field-even"><p><strong>complexes</strong> (<em>iterable</em>) – Iterable yielding complexes.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Zhong2015.coverage">
+<span class="sig-name descname"><span class="pre">coverage</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">other</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Zhong2015.coverage" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the coverage of the annotation i.e. the proportion of
+entities having at least one record in this annotation resource
+for an arbitrary set of entities.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Zhong2015.curation_effort">
+<span class="sig-name descname"><span class="pre">curation_effort</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Zhong2015.curation_effort" title="Link to this definition">§</a></dt>
+<dd><p>Counts the reference-record pairs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Zhong2015.get_names">
+<span class="sig-name descname"><span class="pre">get_names</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Zhong2015.get_names" title="Link to this definition">§</a></dt>
+<dd><p>Returns the list of field names in the records. The annotation
+consists of uniform records and each entity might be annotated
+with one or more records. Each record is a tuple of fields, for
+example <code class="docutils literal notranslate"><span class="pre">('cell_type',</span> <span class="pre">'expression_level',</span> <span class="pre">'score')</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Zhong2015.get_reference_set">
+<em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">get_reference_set</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">proteins</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">swissprot_only</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Zhong2015.get_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the reference set i.e. the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Zhong2015.get_subset">
+<span class="sig-name descname"><span class="pre">get_subset</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Zhong2015.get_subset" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Zhong2015.get_subset_bool_array">
+<span class="sig-name descname"><span class="pre">get_subset_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Zhong2015.get_subset_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a boolean vector with True and False values for each entity
+in the reference set. The values represent presence absence data
+in the simplest case, but by providing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> any kind of matching
+and filtering is possible. <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> are passed to the <code class="docutils literal notranslate"><span class="pre">select</span></code>
+method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Zhong2015.get_values">
+<span class="sig-name descname"><span class="pre">get_values</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">exclude_none</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Zhong2015.get_values" title="Link to this definition">§</a></dt>
+<dd><p>Returns the set of all possible values of a field. E.g. if the
+records of this annotation have a field <code class="docutils literal notranslate"><span class="pre">cell_type</span></code> then calling
+this method can tell you that across all records the values of
+this field might be <code class="docutils literal notranslate"><span class="pre">{'macrophage',</span> <span class="pre">'epithelial_cell',</span> <span class="pre">...}</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Zhong2015.labels">
+<span class="sig-name descname"><span class="pre">labels</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Zhong2015.labels" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Zhong2015.load">
+<span class="sig-name descname"><span class="pre">load</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Zhong2015.load" title="Link to this definition">§</a></dt>
+<dd><p>Loads the annotation data by calling the input method.
+Infers annotations for complexes in the complex database if
+py:attr:<code class="docutils literal notranslate"><span class="pre">infer_complexes</span></code> is True.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Zhong2015.load_data">
+<span class="sig-name descname"><span class="pre">load_data</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Zhong2015.load_data" title="Link to this definition">§</a></dt>
+<dd><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Zhong2015.load_proteins">
+<span class="sig-name descname"><span class="pre">load_proteins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Zhong2015.load_proteins" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a set of all UniProt IDs to have a base set of the entire
+proteome.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Zhong2015.make_df">
+<span class="sig-name descname"><span class="pre">make_df</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">rebuild</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Zhong2015.make_df" title="Link to this definition">§</a></dt>
+<dd><p>Compiles a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the annotation data.
+The data frame will be assigned to :py:attr``df``.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Zhong2015.numof_entities">
+<span class="sig-name descname"><span class="pre">numof_entities</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Zhong2015.numof_entities" title="Link to this definition">§</a></dt>
+<dd><p>The number of annotated entities in the resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Zhong2015.numof_records">
+<span class="sig-name descname"><span class="pre">numof_records</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Zhong2015.numof_records" title="Link to this definition">§</a></dt>
+<dd><p>The total number of annotation records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Zhong2015.numof_references">
+<span class="sig-name descname"><span class="pre">numof_references</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Zhong2015.numof_references" title="Link to this definition">§</a></dt>
+<dd><p>Some annotations contain references. The field name for references
+is always <code class="docutils literal notranslate"><span class="pre">pmid</span></code> (PubMed ID). This method collects and counts the
+references across all records.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Zhong2015.process">
+<span class="sig-name descname"><span class="pre">process</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Zhong2015.process" title="Link to this definition">§</a></dt>
+<dd><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Zhong2015.reload">
+<span class="sig-name descname"><span class="pre">reload</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Zhong2015.reload" title="Link to this definition">§</a></dt>
+<dd><p>Reloads the object from the module level.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Zhong2015.select">
+<span class="sig-name descname"><span class="pre">select</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Zhong2015.select" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a subset by filtering based on <code class="docutils literal notranslate"><span class="pre">kwargs</span></code>.
+Each argument should be a name and a value or set of values.
+Elements having the provided values in the annotation will be
+returned.
+Returns a set of UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Zhong2015.set_method">
+<span class="sig-name descname"><span class="pre">set_method</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Zhong2015.set_method" title="Link to this definition">§</a></dt>
+<dd><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if
+necessary.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Zhong2015.set_reference_set">
+<span class="sig-name descname"><span class="pre">set_reference_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Zhong2015.set_reference_set" title="Link to this definition">§</a></dt>
+<dd><p>Assigns the reference set to the :py:attr``reference_set`` attribute.
+The reference set is the set of all entities which
+potentially have annotation in this resource. Typically this is the
+proteome of the organism from UniProt optionally with all the protein
+complexes from the complex database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Zhong2015.show">
+<span class="sig-name descname"><span class="pre">show</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">table_param</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Zhong2015.show" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic
+information from the UniProt datasheets.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Zhong2015.subset_intersection">
+<span class="sig-name descname"><span class="pre">subset_intersection</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">universe</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Zhong2015.subset_intersection" title="Link to this definition">§</a></dt>
+<dd><p>Calculates the proportion of entities in a subset occuring in the
+set <code class="docutils literal notranslate"><span class="pre">universe</span></code>. The subset is selected by passing <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> to the
+<code class="docutils literal notranslate"><span class="pre">select</span></code> method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Zhong2015.to_array">
+<span class="sig-name descname"><span class="pre">to_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_fields</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Zhong2015.to_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns an entity vs feature array. In case of more complex
+annotations this might be huge.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Zhong2015.to_bool_array">
+<span class="sig-name descname"><span class="pre">to_bool_array</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reference_set</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Zhong2015.to_bool_array" title="Link to this definition">§</a></dt>
+<dd><p>Returns a presence/absence boolean array for a reference set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.annot.Zhong2015.to_set">
+<span class="sig-name descname"><span class="pre">to_set</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.annot.Zhong2015.to_set" title="Link to this definition">§</a></dt>
+<dd><p>Returns the entities present in this annotation resource as a set.</p>
+</dd></dl>
+
+</dd></dl>
+
+</section>
+
+
+                </article>
+              
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+<dl class="py function">
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+<span class="sig-prename descclassname"><span class="pre">pypath.core.annot.</span></span><span class="sig-name descname"><span class="pre">get_db</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">keep_annotators</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">create_dataframe</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#get_db"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.get_db" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the current database instance and initializes it if does
+not exist yet.</p>
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+                  
+  <section id="module-pypath.core.annot">
+<span id="pypath-core-annot"></span><h1>pypath.core.annot<a class="headerlink" href="#module-pypath.core.annot" title="Link to this heading">§</a></h1>
+<dl class="field-list simple">
+<dt class="field-odd">members<span class="colon">:</span></dt>
+<dd class="field-odd"><p></p></dd>
+</dl>
+<p class="rubric">Functions</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.core.annot.get_db.html#pypath.core.annot.get_db" title="pypath.core.annot.get_db"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_db</span></code></a>([keep_annotators, create_dataframe, ...])</p></td>
+<td><p>Retrieves the current database instance and initializes it if does not exist yet.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.core.annot.init_db.html#pypath.core.annot.init_db" title="pypath.core.annot.init_db"><code class="xref py py-obj docutils literal notranslate"><span class="pre">init_db</span></code></a>([keep_annotators, create_dataframe, ...])</p></td>
+<td><p>Initializes or reloads the annotation database.</p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Classes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.core.annot.Adhesome.html#pypath.core.annot.Adhesome" title="pypath.core.annot.Adhesome"><code class="xref py py-obj docutils literal notranslate"><span class="pre">Adhesome</span></code></a>(**kwargs)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.core.annot.Almen2009.html#pypath.core.annot.Almen2009" title="pypath.core.annot.Almen2009"><code class="xref py py-obj docutils literal notranslate"><span class="pre">Almen2009</span></code></a>([ncbi_tax_id])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.core.annot.AnnotationBase.html#pypath.core.annot.AnnotationBase" title="pypath.core.annot.AnnotationBase"><code class="xref py py-obj docutils literal notranslate"><span class="pre">AnnotationBase</span></code></a>(name[, ncbi_tax_id, ...])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.core.annot.AnnotationTable.html#pypath.core.annot.AnnotationTable" title="pypath.core.annot.AnnotationTable"><code class="xref py py-obj docutils literal notranslate"><span class="pre">AnnotationTable</span></code></a>([proteins, complexes, ...])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.core.annot.Baccin2019.html#pypath.core.annot.Baccin2019" title="pypath.core.annot.Baccin2019"><code class="xref py py-obj docutils literal notranslate"><span class="pre">Baccin2019</span></code></a>([ncbi_tax_id])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.core.annot.Biogps.html#pypath.core.annot.Biogps" title="pypath.core.annot.Biogps"><code class="xref py py-obj docutils literal notranslate"><span class="pre">Biogps</span></code></a>([ncbi_tax_id])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.core.annot.CancerGeneCensus.html#pypath.core.annot.CancerGeneCensus" title="pypath.core.annot.CancerGeneCensus"><code class="xref py py-obj docutils literal notranslate"><span class="pre">CancerGeneCensus</span></code></a>(**kwargs)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.core.annot.Cancerdrugsdb.html#pypath.core.annot.Cancerdrugsdb" title="pypath.core.annot.Cancerdrugsdb"><code class="xref py py-obj docutils literal notranslate"><span class="pre">Cancerdrugsdb</span></code></a>(**kwargs)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.core.annot.Cancersea.html#pypath.core.annot.Cancersea" title="pypath.core.annot.Cancersea"><code class="xref py py-obj docutils literal notranslate"><span class="pre">Cancersea</span></code></a>(**kwargs)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.core.annot.CellPhoneDB.html#pypath.core.annot.CellPhoneDB" title="pypath.core.annot.CellPhoneDB"><code class="xref py py-obj docutils literal notranslate"><span class="pre">CellPhoneDB</span></code></a>(**kwargs)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.core.annot.CellPhoneDBComplex.html#pypath.core.annot.CellPhoneDBComplex" title="pypath.core.annot.CellPhoneDBComplex"><code class="xref py py-obj docutils literal notranslate"><span class="pre">CellPhoneDBComplex</span></code></a>(**kwargs)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.core.annot.CellSurfaceProteinAtlas.html#pypath.core.annot.CellSurfaceProteinAtlas" title="pypath.core.annot.CellSurfaceProteinAtlas"><code class="xref py py-obj docutils literal notranslate"><span class="pre">CellSurfaceProteinAtlas</span></code></a>([ncbi_tax_id])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.core.annot.CellSurfaceProteinAtlasCellType.html#pypath.core.annot.CellSurfaceProteinAtlasCellType" title="pypath.core.annot.CellSurfaceProteinAtlasCellType"><code class="xref py py-obj docutils literal notranslate"><span class="pre">CellSurfaceProteinAtlasCellType</span></code></a>([ncbi_tax_id])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.core.annot.Cellcall.html#pypath.core.annot.Cellcall" title="pypath.core.annot.Cellcall"><code class="xref py py-obj docutils literal notranslate"><span class="pre">Cellcall</span></code></a>(**kwargs)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.core.annot.Cellcellinteractions.html#pypath.core.annot.Cellcellinteractions" title="pypath.core.annot.Cellcellinteractions"><code class="xref py py-obj docutils literal notranslate"><span class="pre">Cellcellinteractions</span></code></a>([ncbi_tax_id])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.core.annot.Cellchatdb.html#pypath.core.annot.Cellchatdb" title="pypath.core.annot.Cellchatdb"><code class="xref py py-obj docutils literal notranslate"><span class="pre">Cellchatdb</span></code></a>(**kwargs)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.core.annot.CellchatdbComplex.html#pypath.core.annot.CellchatdbComplex" title="pypath.core.annot.CellchatdbComplex"><code class="xref py py-obj docutils literal notranslate"><span class="pre">CellchatdbComplex</span></code></a>(**kwargs)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.core.annot.Cellinker.html#pypath.core.annot.Cellinker" title="pypath.core.annot.Cellinker"><code class="xref py py-obj docutils literal notranslate"><span class="pre">Cellinker</span></code></a>([ncbi_tax_id])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.core.annot.CellinkerComplex.html#pypath.core.annot.CellinkerComplex" title="pypath.core.annot.CellinkerComplex"><code class="xref py py-obj docutils literal notranslate"><span class="pre">CellinkerComplex</span></code></a>([ncbi_tax_id])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.core.annot.Celltalkdb.html#pypath.core.annot.Celltalkdb" title="pypath.core.annot.Celltalkdb"><code class="xref py py-obj docutils literal notranslate"><span class="pre">Celltalkdb</span></code></a>(**kwargs)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.core.annot.Celltypist.html#pypath.core.annot.Celltypist" title="pypath.core.annot.Celltypist"><code class="xref py py-obj docutils literal notranslate"><span class="pre">Celltypist</span></code></a>([ncbi_tax_id])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.core.annot.Comppi.html#pypath.core.annot.Comppi" title="pypath.core.annot.Comppi"><code class="xref py py-obj docutils literal notranslate"><span class="pre">Comppi</span></code></a>(**kwargs)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.core.annot.Connectomedb.html#pypath.core.annot.Connectomedb" title="pypath.core.annot.Connectomedb"><code class="xref py py-obj docutils literal notranslate"><span class="pre">Connectomedb</span></code></a>(**kwargs)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.core.annot.Corum.html#pypath.core.annot.Corum" title="pypath.core.annot.Corum"><code class="xref py py-obj docutils literal notranslate"><span class="pre">Corum</span></code></a>(name, annot_attr, **kwargs)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.core.annot.CorumFuncat.html#pypath.core.annot.CorumFuncat" title="pypath.core.annot.CorumFuncat"><code class="xref py py-obj docutils literal notranslate"><span class="pre">CorumFuncat</span></code></a>(**kwargs)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.core.annot.CorumGO.html#pypath.core.annot.CorumGO" title="pypath.core.annot.CorumGO"><code class="xref py py-obj docutils literal notranslate"><span class="pre">CorumGO</span></code></a>(**kwargs)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.core.annot.Cpad.html#pypath.core.annot.Cpad" title="pypath.core.annot.Cpad"><code class="xref py py-obj docutils literal notranslate"><span class="pre">Cpad</span></code></a>([ncbi_tax_id])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.core.annot.CustomAnnotation.html#pypath.core.annot.CustomAnnotation" title="pypath.core.annot.CustomAnnotation"><code class="xref py py-obj docutils literal notranslate"><span class="pre">CustomAnnotation</span></code></a>([class_definitions, ...])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.core.annot.Cytosig.html#pypath.core.annot.Cytosig" title="pypath.core.annot.Cytosig"><code class="xref py py-obj docutils literal notranslate"><span class="pre">Cytosig</span></code></a>([ncbi_tax_id])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.core.annot.Dgidb.html#pypath.core.annot.Dgidb" title="pypath.core.annot.Dgidb"><code class="xref py py-obj docutils literal notranslate"><span class="pre">Dgidb</span></code></a>(**kwargs)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.core.annot.Disgenet.html#pypath.core.annot.Disgenet" title="pypath.core.annot.Disgenet"><code class="xref py py-obj docutils literal notranslate"><span class="pre">Disgenet</span></code></a>([ncbi_tax_id])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.core.annot.Embrace.html#pypath.core.annot.Embrace" title="pypath.core.annot.Embrace"><code class="xref py py-obj docutils literal notranslate"><span class="pre">Embrace</span></code></a>([ncbi_tax_id])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.core.annot.Exocarta.html#pypath.core.annot.Exocarta" title="pypath.core.annot.Exocarta"><code class="xref py py-obj docutils literal notranslate"><span class="pre">Exocarta</span></code></a>([ncbi_tax_id])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.core.annot.GOCustomIntercell.html#pypath.core.annot.GOCustomIntercell" title="pypath.core.annot.GOCustomIntercell"><code class="xref py py-obj docutils literal notranslate"><span class="pre">GOCustomIntercell</span></code></a>([categories, go_annot, ...])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.core.annot.GOIntercell.html#pypath.core.annot.GOIntercell" title="pypath.core.annot.GOIntercell"><code class="xref py py-obj docutils literal notranslate"><span class="pre">GOIntercell</span></code></a>([categories, go_annot, ncbi_tax_id])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.core.annot.Gpcrdb.html#pypath.core.annot.Gpcrdb" title="pypath.core.annot.Gpcrdb"><code class="xref py py-obj docutils literal notranslate"><span class="pre">Gpcrdb</span></code></a>([ncbi_tax_id])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.core.annot.GuideToPharmacology.html#pypath.core.annot.GuideToPharmacology" title="pypath.core.annot.GuideToPharmacology"><code class="xref py py-obj docutils literal notranslate"><span class="pre">GuideToPharmacology</span></code></a>([load_sources])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.core.annot.HPO.html#pypath.core.annot.HPO" title="pypath.core.annot.HPO"><code class="xref py py-obj docutils literal notranslate"><span class="pre">HPO</span></code></a>(**kwargs)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.core.annot.Hgnc.html#pypath.core.annot.Hgnc" title="pypath.core.annot.Hgnc"><code class="xref py py-obj docutils literal notranslate"><span class="pre">Hgnc</span></code></a>(**kwargs)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.core.annot.HpmrComplex.html#pypath.core.annot.HpmrComplex" title="pypath.core.annot.HpmrComplex"><code class="xref py py-obj docutils literal notranslate"><span class="pre">HpmrComplex</span></code></a>(**kwargs)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.core.annot.HumanPlasmaMembraneReceptome.html#pypath.core.annot.HumanPlasmaMembraneReceptome" title="pypath.core.annot.HumanPlasmaMembraneReceptome"><code class="xref py py-obj docutils literal notranslate"><span class="pre">HumanPlasmaMembraneReceptome</span></code></a>(**kwargs)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.core.annot.HumanProteinAtlas.html#pypath.core.annot.HumanProteinAtlas" title="pypath.core.annot.HumanProteinAtlas"><code class="xref py py-obj docutils literal notranslate"><span class="pre">HumanProteinAtlas</span></code></a>(**kwargs)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.core.annot.HumanProteinAtlasSecretome.html#pypath.core.annot.HumanProteinAtlasSecretome" title="pypath.core.annot.HumanProteinAtlasSecretome"><code class="xref py py-obj docutils literal notranslate"><span class="pre">HumanProteinAtlasSecretome</span></code></a>(**kwargs)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.core.annot.HumanProteinAtlasSubcellular.html#pypath.core.annot.HumanProteinAtlasSubcellular" title="pypath.core.annot.HumanProteinAtlasSubcellular"><code class="xref py py-obj docutils literal notranslate"><span class="pre">HumanProteinAtlasSubcellular</span></code></a>(**kwargs)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.core.annot.Humancellmap.html#pypath.core.annot.Humancellmap" title="pypath.core.annot.Humancellmap"><code class="xref py py-obj docutils literal notranslate"><span class="pre">Humancellmap</span></code></a>([ncbi_tax_id])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.core.annot.Icellnet.html#pypath.core.annot.Icellnet" title="pypath.core.annot.Icellnet"><code class="xref py py-obj docutils literal notranslate"><span class="pre">Icellnet</span></code></a>(**kwargs)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.core.annot.IcellnetComplex.html#pypath.core.annot.IcellnetComplex" title="pypath.core.annot.IcellnetComplex"><code class="xref py py-obj docutils literal notranslate"><span class="pre">IcellnetComplex</span></code></a>(**kwargs)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.core.annot.Integrins.html#pypath.core.annot.Integrins" title="pypath.core.annot.Integrins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">Integrins</span></code></a>(**kwargs)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.core.annot.InterPro.html#pypath.core.annot.InterPro" title="pypath.core.annot.InterPro"><code class="xref py py-obj docutils literal notranslate"><span class="pre">InterPro</span></code></a>([ncbi_tax_id])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.core.annot.Intogen.html#pypath.core.annot.Intogen" title="pypath.core.annot.Intogen"><code class="xref py py-obj docutils literal notranslate"><span class="pre">Intogen</span></code></a>(**kwargs)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.core.annot.Italk.html#pypath.core.annot.Italk" title="pypath.core.annot.Italk"><code class="xref py py-obj docutils literal notranslate"><span class="pre">Italk</span></code></a>([ncbi_tax_id])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.core.annot.KeggPathways.html#pypath.core.annot.KeggPathways" title="pypath.core.annot.KeggPathways"><code class="xref py py-obj docutils literal notranslate"><span class="pre">KeggPathways</span></code></a>([ncbi_tax_id])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.core.annot.KeggPathwaysPC.html#pypath.core.annot.KeggPathwaysPC" title="pypath.core.annot.KeggPathwaysPC"><code class="xref py py-obj docutils literal notranslate"><span class="pre">KeggPathwaysPC</span></code></a>([ncbi_tax_id])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.core.annot.Kinasedotcom.html#pypath.core.annot.Kinasedotcom" title="pypath.core.annot.Kinasedotcom"><code class="xref py py-obj docutils literal notranslate"><span class="pre">Kinasedotcom</span></code></a>(**kwargs)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.core.annot.Kirouac2010.html#pypath.core.annot.Kirouac2010" title="pypath.core.annot.Kirouac2010"><code class="xref py py-obj docutils literal notranslate"><span class="pre">Kirouac2010</span></code></a>([load_sources])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.core.annot.Lambert2018.html#pypath.core.annot.Lambert2018" title="pypath.core.annot.Lambert2018"><code class="xref py py-obj docutils literal notranslate"><span class="pre">Lambert2018</span></code></a>([ncbi_tax_id])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.core.annot.LigandReceptor.html#pypath.core.annot.LigandReceptor" title="pypath.core.annot.LigandReceptor"><code class="xref py py-obj docutils literal notranslate"><span class="pre">LigandReceptor</span></code></a>(name[, ligand_col, ...])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.core.annot.Locate.html#pypath.core.annot.Locate" title="pypath.core.annot.Locate"><code class="xref py py-obj docutils literal notranslate"><span class="pre">Locate</span></code></a>([ncbi_tax_id, literature, external, ...])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.core.annot.Lrdb.html#pypath.core.annot.Lrdb" title="pypath.core.annot.Lrdb"><code class="xref py py-obj docutils literal notranslate"><span class="pre">Lrdb</span></code></a>(**kwargs)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.core.annot.Matrisome.html#pypath.core.annot.Matrisome" title="pypath.core.annot.Matrisome"><code class="xref py py-obj docutils literal notranslate"><span class="pre">Matrisome</span></code></a>([ncbi_tax_id])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.core.annot.Matrixdb.html#pypath.core.annot.Matrixdb" title="pypath.core.annot.Matrixdb"><code class="xref py py-obj docutils literal notranslate"><span class="pre">Matrixdb</span></code></a>([ncbi_tax_id])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.core.annot.Mcam.html#pypath.core.annot.Mcam" title="pypath.core.annot.Mcam"><code class="xref py py-obj docutils literal notranslate"><span class="pre">Mcam</span></code></a>(**kwargs)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.core.annot.Membranome.html#pypath.core.annot.Membranome" title="pypath.core.annot.Membranome"><code class="xref py py-obj docutils literal notranslate"><span class="pre">Membranome</span></code></a>(**kwargs)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.core.annot.Msigdb.html#pypath.core.annot.Msigdb" title="pypath.core.annot.Msigdb"><code class="xref py py-obj docutils literal notranslate"><span class="pre">Msigdb</span></code></a>([ncbi_tax_id])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.core.annot.NetpathPathways.html#pypath.core.annot.NetpathPathways" title="pypath.core.annot.NetpathPathways"><code class="xref py py-obj docutils literal notranslate"><span class="pre">NetpathPathways</span></code></a>([ncbi_tax_id])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.core.annot.Opm.html#pypath.core.annot.Opm" title="pypath.core.annot.Opm"><code class="xref py py-obj docutils literal notranslate"><span class="pre">Opm</span></code></a>([ncbi_tax_id])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.core.annot.Panglaodb.html#pypath.core.annot.Panglaodb" title="pypath.core.annot.Panglaodb"><code class="xref py py-obj docutils literal notranslate"><span class="pre">Panglaodb</span></code></a>([ncbi_tax_id])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.core.annot.Phobius.html#pypath.core.annot.Phobius" title="pypath.core.annot.Phobius"><code class="xref py py-obj docutils literal notranslate"><span class="pre">Phobius</span></code></a>(**kwargs)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.core.annot.Phosphatome.html#pypath.core.annot.Phosphatome" title="pypath.core.annot.Phosphatome"><code class="xref py py-obj docutils literal notranslate"><span class="pre">Phosphatome</span></code></a>(**kwargs)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.core.annot.Progeny.html#pypath.core.annot.Progeny" title="pypath.core.annot.Progeny"><code class="xref py py-obj docutils literal notranslate"><span class="pre">Progeny</span></code></a>([ncbi_tax_id])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.core.annot.Ramilowski2015.html#pypath.core.annot.Ramilowski2015" title="pypath.core.annot.Ramilowski2015"><code class="xref py py-obj docutils literal notranslate"><span class="pre">Ramilowski2015</span></code></a>([load_sources])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.core.annot.Ramilowski2015Location.html#pypath.core.annot.Ramilowski2015Location" title="pypath.core.annot.Ramilowski2015Location"><code class="xref py py-obj docutils literal notranslate"><span class="pre">Ramilowski2015Location</span></code></a>(**kwargs)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.core.annot.Scconnect.html#pypath.core.annot.Scconnect" title="pypath.core.annot.Scconnect"><code class="xref py py-obj docutils literal notranslate"><span class="pre">Scconnect</span></code></a>([ncbi_tax_id])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.core.annot.ScconnectComplex.html#pypath.core.annot.ScconnectComplex" title="pypath.core.annot.ScconnectComplex"><code class="xref py py-obj docutils literal notranslate"><span class="pre">ScconnectComplex</span></code></a>([ncbi_tax_id])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.core.annot.SignalinkFunctions.html#pypath.core.annot.SignalinkFunctions" title="pypath.core.annot.SignalinkFunctions"><code class="xref py py-obj docutils literal notranslate"><span class="pre">SignalinkFunctions</span></code></a>([ncbi_tax_id])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.core.annot.SignalinkPathways.html#pypath.core.annot.SignalinkPathways" title="pypath.core.annot.SignalinkPathways"><code class="xref py py-obj docutils literal notranslate"><span class="pre">SignalinkPathways</span></code></a>([ncbi_tax_id])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.core.annot.SignorPathways.html#pypath.core.annot.SignorPathways" title="pypath.core.annot.SignorPathways"><code class="xref py py-obj docutils literal notranslate"><span class="pre">SignorPathways</span></code></a>([ncbi_tax_id])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.core.annot.Surfaceome.html#pypath.core.annot.Surfaceome" title="pypath.core.annot.Surfaceome"><code class="xref py py-obj docutils literal notranslate"><span class="pre">Surfaceome</span></code></a>(**kwargs)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.core.annot.Talklr.html#pypath.core.annot.Talklr" title="pypath.core.annot.Talklr"><code class="xref py py-obj docutils literal notranslate"><span class="pre">Talklr</span></code></a>(**kwargs)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.core.annot.Tcdb.html#pypath.core.annot.Tcdb" title="pypath.core.annot.Tcdb"><code class="xref py py-obj docutils literal notranslate"><span class="pre">Tcdb</span></code></a>([ncbi_tax_id])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.core.annot.Tfcensus.html#pypath.core.annot.Tfcensus" title="pypath.core.annot.Tfcensus"><code class="xref py py-obj docutils literal notranslate"><span class="pre">Tfcensus</span></code></a>(**kwargs)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.core.annot.Topdb.html#pypath.core.annot.Topdb" title="pypath.core.annot.Topdb"><code class="xref py py-obj docutils literal notranslate"><span class="pre">Topdb</span></code></a>([ncbi_tax_id])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.core.annot.UniprotFamilies.html#pypath.core.annot.UniprotFamilies" title="pypath.core.annot.UniprotFamilies"><code class="xref py py-obj docutils literal notranslate"><span class="pre">UniprotFamilies</span></code></a>([ncbi_tax_id])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.core.annot.UniprotKeywords.html#pypath.core.annot.UniprotKeywords" title="pypath.core.annot.UniprotKeywords"><code class="xref py py-obj docutils literal notranslate"><span class="pre">UniprotKeywords</span></code></a>([ncbi_tax_id])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.core.annot.UniprotLocations.html#pypath.core.annot.UniprotLocations" title="pypath.core.annot.UniprotLocations"><code class="xref py py-obj docutils literal notranslate"><span class="pre">UniprotLocations</span></code></a>([ncbi_tax_id])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.core.annot.UniprotTissues.html#pypath.core.annot.UniprotTissues" title="pypath.core.annot.UniprotTissues"><code class="xref py py-obj docutils literal notranslate"><span class="pre">UniprotTissues</span></code></a>([ncbi_tax_id])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.core.annot.UniprotTopologies.html#pypath.core.annot.UniprotTopologies" title="pypath.core.annot.UniprotTopologies"><code class="xref py py-obj docutils literal notranslate"><span class="pre">UniprotTopologies</span></code></a>([ncbi_tax_id])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.core.annot.Vesiclepedia.html#pypath.core.annot.Vesiclepedia" title="pypath.core.annot.Vesiclepedia"><code class="xref py py-obj docutils literal notranslate"><span class="pre">Vesiclepedia</span></code></a>([ncbi_tax_id])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.core.annot.Wang.html#pypath.core.annot.Wang" title="pypath.core.annot.Wang"><code class="xref py py-obj docutils literal notranslate"><span class="pre">Wang</span></code></a>([ncbi_tax_id])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.core.annot.Zhong2015.html#pypath.core.annot.Zhong2015" title="pypath.core.annot.Zhong2015"><code class="xref py py-obj docutils literal notranslate"><span class="pre">Zhong2015</span></code></a>(**kwargs)</p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+</section>
+
+
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+  <section id="pypath-core-annot-init-db">
+<h1>pypath.core.annot.init_db<a class="headerlink" href="#pypath-core-annot-init-db" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.core.annot.init_db">
+<span class="sig-prename descclassname"><span class="pre">pypath.core.annot.</span></span><span class="sig-name descname"><span class="pre">init_db</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">keep_annotators</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">create_dataframe</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/annot.html#init_db"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.annot.init_db" title="Link to this definition">§</a></dt>
+<dd><p>Initializes or reloads the annotation database.
+The database will be assigned to the <code class="docutils literal notranslate"><span class="pre">db</span></code> attribute of this module.</p>
+</dd></dl>
+
+</section>
+
+
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diff --git a/api/pypath.core.attrs.html b/api/pypath.core.attrs.html
index d3284a1aa..328124c1f 100644
--- a/api/pypath.core.attrs.html
+++ b/api/pypath.core.attrs.html
@@ -48,7 +48,7 @@
     <link rel="index" title="Index" href="../genindex.html" />
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     <link rel="next" title="pypath.core.attrs.AttributeHandler" href="pypath.core.attrs.AttributeHandler.html" />
-    <link rel="prev" title="pypath.core" href="pypath.core.html" />
+    <link rel="prev" title="pypath.core.annot.Zhong2015" href="pypath.core.annot.Zhong2015.html" />
   <meta name="viewport" content="width=device-width, initial-scale=1"/>
   <meta name="docsearch:language" content="en"/>
   </head>
@@ -542,12 +542,12 @@
                   
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-       href="pypath.core.html"
+       href="pypath.core.annot.Zhong2015.html"
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-        <p class="prev-next-title">pypath.core</p>
+        <p class="prev-next-title">pypath.core.annot.Zhong2015</p>
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     <a class="right-next"
diff --git a/api/pypath.core.common.filter_network_df.html b/api/pypath.core.common.filter_network_df.html
index 0856d1fbc..12b829826 100644
--- a/api/pypath.core.common.filter_network_df.html
+++ b/api/pypath.core.common.filter_network_df.html
@@ -47,7 +47,7 @@
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+  <section id="pypath-core-complex-abstractcomplexresource">
+<h1>pypath.core.complex.AbstractComplexResource<a class="headerlink" href="#pypath-core-complex-abstractcomplexresource" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.core.complex.AbstractComplexResource">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.core.complex.</span></span><span class="sig-name descname"><span class="pre">AbstractComplexResource</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">input_method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">input_args</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">dump</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/complex.html#AbstractComplexResource"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.complex.AbstractComplexResource" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <a class="reference internal" href="pypath.internals.resource.AbstractResource.html#pypath.internals.resource.AbstractResource" title="pypath.internals.resource.AbstractResource"><code class="xref py py-class docutils literal notranslate"><span class="pre">AbstractResource</span></code></a></p>
+<p>A resource which provides information about molecular complexes.</p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.complex.AbstractComplexResource.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">input_method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">input_args</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">dump</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/complex.html#AbstractComplexResource.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.complex.AbstractComplexResource.__init__" title="Link to this definition">§</a></dt>
+<dd><dl class="simple">
+<dt>name<span class="classifier">str</span></dt><dd><p>Custom name for the resource.</p>
+</dd>
+<dt>input_method<span class="classifier">callable</span></dt><dd><p>Method providing the input data.</p>
+</dd>
+<dt>process_method<span class="classifier">callable</span></dt><dd><p>Method processing the data and yielding <code class="docutils literal notranslate"><span class="pre">intera.Complex</span></code>
+instances.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.complex.AbstractComplexResource.__init__" title="pypath.core.complex.AbstractComplexResource.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>(name[, ncbi_tax_id, input_method, ...])</p></td>
+<td><p>name : str</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">from_dump</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">load</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.complex.AbstractComplexResource.load_data" title="pypath.core.complex.AbstractComplexResource.load_data"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_data</span></code></a>()</p></td>
+<td><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">make_df</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.complex.AbstractComplexResource.process" title="pypath.core.complex.AbstractComplexResource.process"><code class="xref py py-obj docutils literal notranslate"><span class="pre">process</span></code></a>()</p></td>
+<td><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">save_to_pickle</span></code>(pickle_file)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.complex.AbstractComplexResource.set_method" title="pypath.core.complex.AbstractComplexResource.set_method"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_method</span></code></a>()</p></td>
+<td><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if necessary.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">update_index</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Attributes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_sources</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">curation_effort</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_stoichiometry</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">heteromers</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">homomers</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_references</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">summary</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">summary_str</span></code></p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.complex.AbstractComplexResource.load_data">
+<span class="sig-name descname"><span class="pre">load_data</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.complex.AbstractComplexResource.load_data" title="Link to this definition">§</a></dt>
+<dd><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.complex.AbstractComplexResource.process">
+<span class="sig-name descname"><span class="pre">process</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.complex.AbstractComplexResource.process" title="Link to this definition">§</a></dt>
+<dd><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.complex.AbstractComplexResource.set_method">
+<span class="sig-name descname"><span class="pre">set_method</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.complex.AbstractComplexResource.set_method" title="Link to this definition">§</a></dt>
+<dd><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if
+necessary.</p>
+</dd></dl>
+
+</dd></dl>
+
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+  <section id="pypath-core-complex-cellphonedb">
+<h1>pypath.core.complex.CellPhoneDB<a class="headerlink" href="#pypath-core-complex-cellphonedb" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.core.complex.CellPhoneDB">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.core.complex.</span></span><span class="sig-name descname"><span class="pre">CellPhoneDB</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/complex.html#CellPhoneDB"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.complex.CellPhoneDB" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <a class="reference internal" href="pypath.core.complex.AbstractComplexResource.html#pypath.core.complex.AbstractComplexResource" title="pypath.core.complex.AbstractComplexResource"><code class="xref py py-class docutils literal notranslate"><span class="pre">AbstractComplexResource</span></code></a></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.complex.CellPhoneDB.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/complex.html#CellPhoneDB.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.complex.CellPhoneDB.__init__" title="Link to this definition">§</a></dt>
+<dd><dl class="simple">
+<dt>name<span class="classifier">str</span></dt><dd><p>Custom name for the resource.</p>
+</dd>
+<dt>input_method<span class="classifier">callable</span></dt><dd><p>Method providing the input data.</p>
+</dd>
+<dt>process_method<span class="classifier">callable</span></dt><dd><p>Method processing the data and yielding <code class="docutils literal notranslate"><span class="pre">intera.Complex</span></code>
+instances.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.complex.CellPhoneDB.__init__" title="pypath.core.complex.CellPhoneDB.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>(**kwargs)</p></td>
+<td><p>name : str</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">from_dump</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">load</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.complex.CellPhoneDB.load_data" title="pypath.core.complex.CellPhoneDB.load_data"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_data</span></code></a>()</p></td>
+<td><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">make_df</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.complex.CellPhoneDB.process" title="pypath.core.complex.CellPhoneDB.process"><code class="xref py py-obj docutils literal notranslate"><span class="pre">process</span></code></a>()</p></td>
+<td><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">save_to_pickle</span></code>(pickle_file)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.complex.CellPhoneDB.set_method" title="pypath.core.complex.CellPhoneDB.set_method"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_method</span></code></a>()</p></td>
+<td><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if necessary.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">update_index</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Attributes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_sources</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">curation_effort</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_stoichiometry</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">heteromers</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">homomers</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_references</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">summary</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">summary_str</span></code></p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.complex.CellPhoneDB.load_data">
+<span class="sig-name descname"><span class="pre">load_data</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.complex.CellPhoneDB.load_data" title="Link to this definition">§</a></dt>
+<dd><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.complex.CellPhoneDB.process">
+<span class="sig-name descname"><span class="pre">process</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.complex.CellPhoneDB.process" title="Link to this definition">§</a></dt>
+<dd><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.complex.CellPhoneDB.set_method">
+<span class="sig-name descname"><span class="pre">set_method</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.complex.CellPhoneDB.set_method" title="Link to this definition">§</a></dt>
+<dd><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if
+necessary.</p>
+</dd></dl>
+
+</dd></dl>
+
+</section>
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+  <section id="pypath-core-complex-cellchatdb">
+<h1>pypath.core.complex.Cellchatdb<a class="headerlink" href="#pypath-core-complex-cellchatdb" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.core.complex.Cellchatdb">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.core.complex.</span></span><span class="sig-name descname"><span class="pre">Cellchatdb</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">input_args</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/complex.html#Cellchatdb"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.complex.Cellchatdb" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <a class="reference internal" href="pypath.core.complex.AbstractComplexResource.html#pypath.core.complex.AbstractComplexResource" title="pypath.core.complex.AbstractComplexResource"><code class="xref py py-class docutils literal notranslate"><span class="pre">AbstractComplexResource</span></code></a></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.complex.Cellchatdb.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">input_args</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/complex.html#Cellchatdb.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.complex.Cellchatdb.__init__" title="Link to this definition">§</a></dt>
+<dd><dl class="simple">
+<dt>name<span class="classifier">str</span></dt><dd><p>Custom name for the resource.</p>
+</dd>
+<dt>input_method<span class="classifier">callable</span></dt><dd><p>Method providing the input data.</p>
+</dd>
+<dt>process_method<span class="classifier">callable</span></dt><dd><p>Method processing the data and yielding <code class="docutils literal notranslate"><span class="pre">intera.Complex</span></code>
+instances.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.complex.Cellchatdb.__init__" title="pypath.core.complex.Cellchatdb.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>([input_args])</p></td>
+<td><p>name : str</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">from_dump</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">load</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.complex.Cellchatdb.load_data" title="pypath.core.complex.Cellchatdb.load_data"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_data</span></code></a>()</p></td>
+<td><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">make_df</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.complex.Cellchatdb.process" title="pypath.core.complex.Cellchatdb.process"><code class="xref py py-obj docutils literal notranslate"><span class="pre">process</span></code></a>()</p></td>
+<td><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">save_to_pickle</span></code>(pickle_file)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.complex.Cellchatdb.set_method" title="pypath.core.complex.Cellchatdb.set_method"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_method</span></code></a>()</p></td>
+<td><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if necessary.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">update_index</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Attributes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_sources</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">curation_effort</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_stoichiometry</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">heteromers</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">homomers</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_references</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">summary</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">summary_str</span></code></p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.complex.Cellchatdb.load_data">
+<span class="sig-name descname"><span class="pre">load_data</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.complex.Cellchatdb.load_data" title="Link to this definition">§</a></dt>
+<dd><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.complex.Cellchatdb.process">
+<span class="sig-name descname"><span class="pre">process</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.complex.Cellchatdb.process" title="Link to this definition">§</a></dt>
+<dd><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.complex.Cellchatdb.set_method">
+<span class="sig-name descname"><span class="pre">set_method</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.complex.Cellchatdb.set_method" title="Link to this definition">§</a></dt>
+<dd><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if
+necessary.</p>
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+  <section id="pypath-core-complex-cellinker">
+<h1>pypath.core.complex.Cellinker<a class="headerlink" href="#pypath-core-complex-cellinker" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.core.complex.Cellinker">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.core.complex.</span></span><span class="sig-name descname"><span class="pre">Cellinker</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">input_args</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/complex.html#Cellinker"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.complex.Cellinker" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <a class="reference internal" href="pypath.core.complex.AbstractComplexResource.html#pypath.core.complex.AbstractComplexResource" title="pypath.core.complex.AbstractComplexResource"><code class="xref py py-class docutils literal notranslate"><span class="pre">AbstractComplexResource</span></code></a></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.complex.Cellinker.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">input_args</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/complex.html#Cellinker.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.complex.Cellinker.__init__" title="Link to this definition">§</a></dt>
+<dd><dl class="simple">
+<dt>name<span class="classifier">str</span></dt><dd><p>Custom name for the resource.</p>
+</dd>
+<dt>input_method<span class="classifier">callable</span></dt><dd><p>Method providing the input data.</p>
+</dd>
+<dt>process_method<span class="classifier">callable</span></dt><dd><p>Method processing the data and yielding <code class="docutils literal notranslate"><span class="pre">intera.Complex</span></code>
+instances.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.complex.Cellinker.__init__" title="pypath.core.complex.Cellinker.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>([input_args])</p></td>
+<td><p>name : str</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">from_dump</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">load</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.complex.Cellinker.load_data" title="pypath.core.complex.Cellinker.load_data"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_data</span></code></a>()</p></td>
+<td><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">make_df</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.complex.Cellinker.process" title="pypath.core.complex.Cellinker.process"><code class="xref py py-obj docutils literal notranslate"><span class="pre">process</span></code></a>()</p></td>
+<td><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">save_to_pickle</span></code>(pickle_file)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.complex.Cellinker.set_method" title="pypath.core.complex.Cellinker.set_method"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_method</span></code></a>()</p></td>
+<td><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if necessary.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">update_index</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Attributes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_sources</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">curation_effort</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_stoichiometry</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">heteromers</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">homomers</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_references</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">summary</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">summary_str</span></code></p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.complex.Cellinker.load_data">
+<span class="sig-name descname"><span class="pre">load_data</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.complex.Cellinker.load_data" title="Link to this definition">§</a></dt>
+<dd><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.complex.Cellinker.process">
+<span class="sig-name descname"><span class="pre">process</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.complex.Cellinker.process" title="Link to this definition">§</a></dt>
+<dd><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.complex.Cellinker.set_method">
+<span class="sig-name descname"><span class="pre">set_method</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.complex.Cellinker.set_method" title="Link to this definition">§</a></dt>
+<dd><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if
+necessary.</p>
+</dd></dl>
+
+</dd></dl>
+
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+  <section id="pypath-core-complex-compleat">
+<h1>pypath.core.complex.Compleat<a class="headerlink" href="#pypath-core-complex-compleat" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.core.complex.Compleat">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.core.complex.</span></span><span class="sig-name descname"><span class="pre">Compleat</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">input_args</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/complex.html#Compleat"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.complex.Compleat" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <a class="reference internal" href="pypath.core.complex.AbstractComplexResource.html#pypath.core.complex.AbstractComplexResource" title="pypath.core.complex.AbstractComplexResource"><code class="xref py py-class docutils literal notranslate"><span class="pre">AbstractComplexResource</span></code></a></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.complex.Compleat.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">input_args</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/complex.html#Compleat.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.complex.Compleat.__init__" title="Link to this definition">§</a></dt>
+<dd><dl class="simple">
+<dt>name<span class="classifier">str</span></dt><dd><p>Custom name for the resource.</p>
+</dd>
+<dt>input_method<span class="classifier">callable</span></dt><dd><p>Method providing the input data.</p>
+</dd>
+<dt>process_method<span class="classifier">callable</span></dt><dd><p>Method processing the data and yielding <code class="docutils literal notranslate"><span class="pre">intera.Complex</span></code>
+instances.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.complex.Compleat.__init__" title="pypath.core.complex.Compleat.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>([input_args])</p></td>
+<td><p>name : str</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">from_dump</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">load</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.complex.Compleat.load_data" title="pypath.core.complex.Compleat.load_data"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_data</span></code></a>()</p></td>
+<td><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">make_df</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.complex.Compleat.process" title="pypath.core.complex.Compleat.process"><code class="xref py py-obj docutils literal notranslate"><span class="pre">process</span></code></a>()</p></td>
+<td><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">save_to_pickle</span></code>(pickle_file)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.complex.Compleat.set_method" title="pypath.core.complex.Compleat.set_method"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_method</span></code></a>()</p></td>
+<td><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if necessary.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">update_index</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Attributes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_sources</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">curation_effort</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_stoichiometry</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">heteromers</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">homomers</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_references</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">summary</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">summary_str</span></code></p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.complex.Compleat.load_data">
+<span class="sig-name descname"><span class="pre">load_data</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.complex.Compleat.load_data" title="Link to this definition">§</a></dt>
+<dd><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.complex.Compleat.process">
+<span class="sig-name descname"><span class="pre">process</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.complex.Compleat.process" title="Link to this definition">§</a></dt>
+<dd><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.complex.Compleat.set_method">
+<span class="sig-name descname"><span class="pre">set_method</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.complex.Compleat.set_method" title="Link to this definition">§</a></dt>
+<dd><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if
+necessary.</p>
+</dd></dl>
+
+</dd></dl>
+
+</section>
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+  <section id="pypath-core-complex-complexaggregator">
+<h1>pypath.core.complex.ComplexAggregator<a class="headerlink" href="#pypath-core-complex-complexaggregator" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.core.complex.ComplexAggregator">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.core.complex.</span></span><span class="sig-name descname"><span class="pre">ComplexAggregator</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">pickle_file</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/complex.html#ComplexAggregator"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.complex.ComplexAggregator" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <a class="reference internal" href="pypath.core.complex.AbstractComplexResource.html#pypath.core.complex.AbstractComplexResource" title="pypath.core.complex.AbstractComplexResource"><code class="xref py py-class docutils literal notranslate"><span class="pre">AbstractComplexResource</span></code></a></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.complex.ComplexAggregator.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">pickle_file</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/complex.html#ComplexAggregator.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.complex.ComplexAggregator.__init__" title="Link to this definition">§</a></dt>
+<dd><p>Combines complexes from multiple resources.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><p><strong>resources</strong> (<em>list</em>) – List of resources. Names of complex resource classes in this
+module or custom</p>
+</dd>
+</dl>
+</dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.complex.ComplexAggregator.__init__" title="pypath.core.complex.ComplexAggregator.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>([resources, pickle_file])</p></td>
+<td><p>Combines complexes from multiple resources.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">from_dump</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">load</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.complex.ComplexAggregator.load_data" title="pypath.core.complex.ComplexAggregator.load_data"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_data</span></code></a>()</p></td>
+<td><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_from_pickle</span></code>(pickle_file)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">make_df</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.complex.ComplexAggregator.process" title="pypath.core.complex.ComplexAggregator.process"><code class="xref py py-obj docutils literal notranslate"><span class="pre">process</span></code></a>()</p></td>
+<td><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.complex.ComplexAggregator.reload" title="pypath.core.complex.ComplexAggregator.reload"><code class="xref py py-obj docutils literal notranslate"><span class="pre">reload</span></code></a>()</p></td>
+<td><p>Reloads the object from the module level.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">save_to_pickle</span></code>(pickle_file)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.complex.ComplexAggregator.set_method" title="pypath.core.complex.ComplexAggregator.set_method"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_method</span></code></a>()</p></td>
+<td><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if necessary.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">summaries_tab</span></code>([outfile, return_table])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">update_index</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">update_summaries</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Attributes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_sources</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">curation_effort</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_stoichiometry</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">heteromers</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">homomers</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_references</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">summary</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">summary_str</span></code></p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.complex.ComplexAggregator.load_data">
+<span class="sig-name descname"><span class="pre">load_data</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.complex.ComplexAggregator.load_data" title="Link to this definition">§</a></dt>
+<dd><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.complex.ComplexAggregator.process">
+<span class="sig-name descname"><span class="pre">process</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.complex.ComplexAggregator.process" title="Link to this definition">§</a></dt>
+<dd><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.complex.ComplexAggregator.reload">
+<span class="sig-name descname"><span class="pre">reload</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/complex.html#ComplexAggregator.reload"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.complex.ComplexAggregator.reload" title="Link to this definition">§</a></dt>
+<dd><p>Reloads the object from the module level.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.complex.ComplexAggregator.set_method">
+<span class="sig-name descname"><span class="pre">set_method</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.complex.ComplexAggregator.set_method" title="Link to this definition">§</a></dt>
+<dd><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if
+necessary.</p>
+</dd></dl>
+
+</dd></dl>
+
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+  <section id="pypath-core-complex-complexportal">
+<h1>pypath.core.complex.ComplexPortal<a class="headerlink" href="#pypath-core-complex-complexportal" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.core.complex.ComplexPortal">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.core.complex.</span></span><span class="sig-name descname"><span class="pre">ComplexPortal</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">input_args</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/complex.html#ComplexPortal"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.complex.ComplexPortal" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <a class="reference internal" href="pypath.core.complex.AbstractComplexResource.html#pypath.core.complex.AbstractComplexResource" title="pypath.core.complex.AbstractComplexResource"><code class="xref py py-class docutils literal notranslate"><span class="pre">AbstractComplexResource</span></code></a></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.complex.ComplexPortal.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">input_args</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/complex.html#ComplexPortal.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.complex.ComplexPortal.__init__" title="Link to this definition">§</a></dt>
+<dd><dl class="simple">
+<dt>name<span class="classifier">str</span></dt><dd><p>Custom name for the resource.</p>
+</dd>
+<dt>input_method<span class="classifier">callable</span></dt><dd><p>Method providing the input data.</p>
+</dd>
+<dt>process_method<span class="classifier">callable</span></dt><dd><p>Method processing the data and yielding <code class="docutils literal notranslate"><span class="pre">intera.Complex</span></code>
+instances.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.complex.ComplexPortal.__init__" title="pypath.core.complex.ComplexPortal.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>([input_args])</p></td>
+<td><p>name : str</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">from_dump</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">load</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.complex.ComplexPortal.load_data" title="pypath.core.complex.ComplexPortal.load_data"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_data</span></code></a>()</p></td>
+<td><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">make_df</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.complex.ComplexPortal.process" title="pypath.core.complex.ComplexPortal.process"><code class="xref py py-obj docutils literal notranslate"><span class="pre">process</span></code></a>()</p></td>
+<td><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">save_to_pickle</span></code>(pickle_file)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.complex.ComplexPortal.set_method" title="pypath.core.complex.ComplexPortal.set_method"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_method</span></code></a>()</p></td>
+<td><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if necessary.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">update_index</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Attributes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_sources</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">curation_effort</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_stoichiometry</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">heteromers</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">homomers</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_references</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">summary</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">summary_str</span></code></p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.complex.ComplexPortal.load_data">
+<span class="sig-name descname"><span class="pre">load_data</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.complex.ComplexPortal.load_data" title="Link to this definition">§</a></dt>
+<dd><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.complex.ComplexPortal.process">
+<span class="sig-name descname"><span class="pre">process</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.complex.ComplexPortal.process" title="Link to this definition">§</a></dt>
+<dd><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.complex.ComplexPortal.set_method">
+<span class="sig-name descname"><span class="pre">set_method</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.complex.ComplexPortal.set_method" title="Link to this definition">§</a></dt>
+<dd><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if
+necessary.</p>
+</dd></dl>
+
+</dd></dl>
+
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+  <section id="pypath-core-complex-corum">
+<h1>pypath.core.complex.Corum<a class="headerlink" href="#pypath-core-complex-corum" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.core.complex.Corum">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.core.complex.</span></span><span class="sig-name descname"><span class="pre">Corum</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">input_args</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/complex.html#Corum"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.complex.Corum" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <a class="reference internal" href="pypath.core.complex.AbstractComplexResource.html#pypath.core.complex.AbstractComplexResource" title="pypath.core.complex.AbstractComplexResource"><code class="xref py py-class docutils literal notranslate"><span class="pre">AbstractComplexResource</span></code></a></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.complex.Corum.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">input_args</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/complex.html#Corum.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.complex.Corum.__init__" title="Link to this definition">§</a></dt>
+<dd><dl class="simple">
+<dt>name<span class="classifier">str</span></dt><dd><p>Custom name for the resource.</p>
+</dd>
+<dt>input_method<span class="classifier">callable</span></dt><dd><p>Method providing the input data.</p>
+</dd>
+<dt>process_method<span class="classifier">callable</span></dt><dd><p>Method processing the data and yielding <code class="docutils literal notranslate"><span class="pre">intera.Complex</span></code>
+instances.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.complex.Corum.__init__" title="pypath.core.complex.Corum.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>([input_args])</p></td>
+<td><p>name : str</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">from_dump</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">load</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.complex.Corum.load_data" title="pypath.core.complex.Corum.load_data"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_data</span></code></a>()</p></td>
+<td><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">make_df</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.complex.Corum.process" title="pypath.core.complex.Corum.process"><code class="xref py py-obj docutils literal notranslate"><span class="pre">process</span></code></a>()</p></td>
+<td><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">save_to_pickle</span></code>(pickle_file)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.complex.Corum.set_method" title="pypath.core.complex.Corum.set_method"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_method</span></code></a>()</p></td>
+<td><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if necessary.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">update_index</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Attributes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_sources</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">curation_effort</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_stoichiometry</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">heteromers</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">homomers</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_references</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">summary</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">summary_str</span></code></p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.complex.Corum.load_data">
+<span class="sig-name descname"><span class="pre">load_data</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.complex.Corum.load_data" title="Link to this definition">§</a></dt>
+<dd><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.complex.Corum.process">
+<span class="sig-name descname"><span class="pre">process</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.complex.Corum.process" title="Link to this definition">§</a></dt>
+<dd><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.complex.Corum.set_method">
+<span class="sig-name descname"><span class="pre">set_method</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.complex.Corum.set_method" title="Link to this definition">§</a></dt>
+<dd><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if
+necessary.</p>
+</dd></dl>
+
+</dd></dl>
+
+</section>
+
+
+                </article>
+              
+              
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+  <section id="pypath-core-complex-guidetopharmacology">
+<h1>pypath.core.complex.GuideToPharmacology<a class="headerlink" href="#pypath-core-complex-guidetopharmacology" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.core.complex.GuideToPharmacology">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.core.complex.</span></span><span class="sig-name descname"><span class="pre">GuideToPharmacology</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">input_args</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/complex.html#GuideToPharmacology"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.complex.GuideToPharmacology" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <a class="reference internal" href="pypath.core.complex.AbstractComplexResource.html#pypath.core.complex.AbstractComplexResource" title="pypath.core.complex.AbstractComplexResource"><code class="xref py py-class docutils literal notranslate"><span class="pre">AbstractComplexResource</span></code></a></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.complex.GuideToPharmacology.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">input_args</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/complex.html#GuideToPharmacology.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.complex.GuideToPharmacology.__init__" title="Link to this definition">§</a></dt>
+<dd><dl class="simple">
+<dt>name<span class="classifier">str</span></dt><dd><p>Custom name for the resource.</p>
+</dd>
+<dt>input_method<span class="classifier">callable</span></dt><dd><p>Method providing the input data.</p>
+</dd>
+<dt>process_method<span class="classifier">callable</span></dt><dd><p>Method processing the data and yielding <code class="docutils literal notranslate"><span class="pre">intera.Complex</span></code>
+instances.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.complex.GuideToPharmacology.__init__" title="pypath.core.complex.GuideToPharmacology.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>([input_args])</p></td>
+<td><p>name : str</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">from_dump</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">load</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.complex.GuideToPharmacology.load_data" title="pypath.core.complex.GuideToPharmacology.load_data"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_data</span></code></a>()</p></td>
+<td><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">make_df</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.complex.GuideToPharmacology.process" title="pypath.core.complex.GuideToPharmacology.process"><code class="xref py py-obj docutils literal notranslate"><span class="pre">process</span></code></a>()</p></td>
+<td><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">save_to_pickle</span></code>(pickle_file)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.complex.GuideToPharmacology.set_method" title="pypath.core.complex.GuideToPharmacology.set_method"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_method</span></code></a>()</p></td>
+<td><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if necessary.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">update_index</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Attributes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_sources</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">curation_effort</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_stoichiometry</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">heteromers</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">homomers</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_references</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">summary</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">summary_str</span></code></p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.complex.GuideToPharmacology.load_data">
+<span class="sig-name descname"><span class="pre">load_data</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.complex.GuideToPharmacology.load_data" title="Link to this definition">§</a></dt>
+<dd><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.complex.GuideToPharmacology.process">
+<span class="sig-name descname"><span class="pre">process</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.complex.GuideToPharmacology.process" title="Link to this definition">§</a></dt>
+<dd><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.complex.GuideToPharmacology.set_method">
+<span class="sig-name descname"><span class="pre">set_method</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.complex.GuideToPharmacology.set_method" title="Link to this definition">§</a></dt>
+<dd><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if
+necessary.</p>
+</dd></dl>
+
+</dd></dl>
+
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+  <section id="pypath-core-complex-havugimana">
+<h1>pypath.core.complex.Havugimana<a class="headerlink" href="#pypath-core-complex-havugimana" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.core.complex.Havugimana">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.core.complex.</span></span><span class="sig-name descname"><span class="pre">Havugimana</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">input_args</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/complex.html#Havugimana"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.complex.Havugimana" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <a class="reference internal" href="pypath.core.complex.AbstractComplexResource.html#pypath.core.complex.AbstractComplexResource" title="pypath.core.complex.AbstractComplexResource"><code class="xref py py-class docutils literal notranslate"><span class="pre">AbstractComplexResource</span></code></a></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.complex.Havugimana.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">input_args</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/complex.html#Havugimana.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.complex.Havugimana.__init__" title="Link to this definition">§</a></dt>
+<dd><dl class="simple">
+<dt>name<span class="classifier">str</span></dt><dd><p>Custom name for the resource.</p>
+</dd>
+<dt>input_method<span class="classifier">callable</span></dt><dd><p>Method providing the input data.</p>
+</dd>
+<dt>process_method<span class="classifier">callable</span></dt><dd><p>Method processing the data and yielding <code class="docutils literal notranslate"><span class="pre">intera.Complex</span></code>
+instances.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.complex.Havugimana.__init__" title="pypath.core.complex.Havugimana.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>([input_args])</p></td>
+<td><p>name : str</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">from_dump</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">load</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.complex.Havugimana.load_data" title="pypath.core.complex.Havugimana.load_data"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_data</span></code></a>()</p></td>
+<td><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">make_df</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.complex.Havugimana.process" title="pypath.core.complex.Havugimana.process"><code class="xref py py-obj docutils literal notranslate"><span class="pre">process</span></code></a>()</p></td>
+<td><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">save_to_pickle</span></code>(pickle_file)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.complex.Havugimana.set_method" title="pypath.core.complex.Havugimana.set_method"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_method</span></code></a>()</p></td>
+<td><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if necessary.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">update_index</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Attributes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_sources</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">curation_effort</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_stoichiometry</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">heteromers</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">homomers</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_references</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">summary</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">summary_str</span></code></p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.complex.Havugimana.load_data">
+<span class="sig-name descname"><span class="pre">load_data</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.complex.Havugimana.load_data" title="Link to this definition">§</a></dt>
+<dd><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.complex.Havugimana.process">
+<span class="sig-name descname"><span class="pre">process</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.complex.Havugimana.process" title="Link to this definition">§</a></dt>
+<dd><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.complex.Havugimana.set_method">
+<span class="sig-name descname"><span class="pre">set_method</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.complex.Havugimana.set_method" title="Link to this definition">§</a></dt>
+<dd><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if
+necessary.</p>
+</dd></dl>
+
+</dd></dl>
+
+</section>
+
+
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+  <section id="pypath-core-complex-hpmr">
+<h1>pypath.core.complex.Hpmr<a class="headerlink" href="#pypath-core-complex-hpmr" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.core.complex.Hpmr">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.core.complex.</span></span><span class="sig-name descname"><span class="pre">Hpmr</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">input_args</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/complex.html#Hpmr"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.complex.Hpmr" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <a class="reference internal" href="pypath.core.complex.AbstractComplexResource.html#pypath.core.complex.AbstractComplexResource" title="pypath.core.complex.AbstractComplexResource"><code class="xref py py-class docutils literal notranslate"><span class="pre">AbstractComplexResource</span></code></a></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.complex.Hpmr.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">input_args</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/complex.html#Hpmr.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.complex.Hpmr.__init__" title="Link to this definition">§</a></dt>
+<dd><dl class="simple">
+<dt>name<span class="classifier">str</span></dt><dd><p>Custom name for the resource.</p>
+</dd>
+<dt>input_method<span class="classifier">callable</span></dt><dd><p>Method providing the input data.</p>
+</dd>
+<dt>process_method<span class="classifier">callable</span></dt><dd><p>Method processing the data and yielding <code class="docutils literal notranslate"><span class="pre">intera.Complex</span></code>
+instances.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.complex.Hpmr.__init__" title="pypath.core.complex.Hpmr.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>([input_args])</p></td>
+<td><p>name : str</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">from_dump</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">load</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.complex.Hpmr.load_data" title="pypath.core.complex.Hpmr.load_data"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_data</span></code></a>()</p></td>
+<td><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">make_df</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.complex.Hpmr.process" title="pypath.core.complex.Hpmr.process"><code class="xref py py-obj docutils literal notranslate"><span class="pre">process</span></code></a>()</p></td>
+<td><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">save_to_pickle</span></code>(pickle_file)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.complex.Hpmr.set_method" title="pypath.core.complex.Hpmr.set_method"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_method</span></code></a>()</p></td>
+<td><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if necessary.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">update_index</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Attributes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_sources</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">curation_effort</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_stoichiometry</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">heteromers</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">homomers</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_references</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">summary</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">summary_str</span></code></p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.complex.Hpmr.load_data">
+<span class="sig-name descname"><span class="pre">load_data</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.complex.Hpmr.load_data" title="Link to this definition">§</a></dt>
+<dd><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.complex.Hpmr.process">
+<span class="sig-name descname"><span class="pre">process</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.complex.Hpmr.process" title="Link to this definition">§</a></dt>
+<dd><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.complex.Hpmr.set_method">
+<span class="sig-name descname"><span class="pre">set_method</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.complex.Hpmr.set_method" title="Link to this definition">§</a></dt>
+<dd><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if
+necessary.</p>
+</dd></dl>
+
+</dd></dl>
+
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+  <section id="pypath-core-complex-humap">
+<h1>pypath.core.complex.Humap<a class="headerlink" href="#pypath-core-complex-humap" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.core.complex.Humap">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.core.complex.</span></span><span class="sig-name descname"><span class="pre">Humap</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">input_args</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/complex.html#Humap"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.complex.Humap" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <a class="reference internal" href="pypath.core.complex.AbstractComplexResource.html#pypath.core.complex.AbstractComplexResource" title="pypath.core.complex.AbstractComplexResource"><code class="xref py py-class docutils literal notranslate"><span class="pre">AbstractComplexResource</span></code></a></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.complex.Humap.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">input_args</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/complex.html#Humap.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.complex.Humap.__init__" title="Link to this definition">§</a></dt>
+<dd><dl class="simple">
+<dt>name<span class="classifier">str</span></dt><dd><p>Custom name for the resource.</p>
+</dd>
+<dt>input_method<span class="classifier">callable</span></dt><dd><p>Method providing the input data.</p>
+</dd>
+<dt>process_method<span class="classifier">callable</span></dt><dd><p>Method processing the data and yielding <code class="docutils literal notranslate"><span class="pre">intera.Complex</span></code>
+instances.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.complex.Humap.__init__" title="pypath.core.complex.Humap.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>([input_args])</p></td>
+<td><p>name : str</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">from_dump</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">load</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.complex.Humap.load_data" title="pypath.core.complex.Humap.load_data"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_data</span></code></a>()</p></td>
+<td><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">make_df</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.complex.Humap.process" title="pypath.core.complex.Humap.process"><code class="xref py py-obj docutils literal notranslate"><span class="pre">process</span></code></a>()</p></td>
+<td><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">save_to_pickle</span></code>(pickle_file)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.complex.Humap.set_method" title="pypath.core.complex.Humap.set_method"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_method</span></code></a>()</p></td>
+<td><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if necessary.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">update_index</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Attributes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_sources</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">curation_effort</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_stoichiometry</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">heteromers</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">homomers</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_references</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">summary</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">summary_str</span></code></p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.complex.Humap.load_data">
+<span class="sig-name descname"><span class="pre">load_data</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.complex.Humap.load_data" title="Link to this definition">§</a></dt>
+<dd><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.complex.Humap.process">
+<span class="sig-name descname"><span class="pre">process</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.complex.Humap.process" title="Link to this definition">§</a></dt>
+<dd><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.complex.Humap.set_method">
+<span class="sig-name descname"><span class="pre">set_method</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.complex.Humap.set_method" title="Link to this definition">§</a></dt>
+<dd><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if
+necessary.</p>
+</dd></dl>
+
+</dd></dl>
+
+</section>
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+  <section id="pypath-core-complex-humap2">
+<h1>pypath.core.complex.Humap2<a class="headerlink" href="#pypath-core-complex-humap2" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.core.complex.Humap2">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.core.complex.</span></span><span class="sig-name descname"><span class="pre">Humap2</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">input_args</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/complex.html#Humap2"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.complex.Humap2" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <a class="reference internal" href="pypath.core.complex.AbstractComplexResource.html#pypath.core.complex.AbstractComplexResource" title="pypath.core.complex.AbstractComplexResource"><code class="xref py py-class docutils literal notranslate"><span class="pre">AbstractComplexResource</span></code></a></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.complex.Humap2.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">input_args</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/complex.html#Humap2.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.complex.Humap2.__init__" title="Link to this definition">§</a></dt>
+<dd><dl class="simple">
+<dt>name<span class="classifier">str</span></dt><dd><p>Custom name for the resource.</p>
+</dd>
+<dt>input_method<span class="classifier">callable</span></dt><dd><p>Method providing the input data.</p>
+</dd>
+<dt>process_method<span class="classifier">callable</span></dt><dd><p>Method processing the data and yielding <code class="docutils literal notranslate"><span class="pre">intera.Complex</span></code>
+instances.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.complex.Humap2.__init__" title="pypath.core.complex.Humap2.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>([input_args])</p></td>
+<td><p>name : str</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">from_dump</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">load</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.complex.Humap2.load_data" title="pypath.core.complex.Humap2.load_data"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_data</span></code></a>()</p></td>
+<td><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">make_df</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.complex.Humap2.process" title="pypath.core.complex.Humap2.process"><code class="xref py py-obj docutils literal notranslate"><span class="pre">process</span></code></a>()</p></td>
+<td><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">save_to_pickle</span></code>(pickle_file)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.complex.Humap2.set_method" title="pypath.core.complex.Humap2.set_method"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_method</span></code></a>()</p></td>
+<td><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if necessary.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">update_index</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Attributes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_sources</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">curation_effort</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_stoichiometry</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">heteromers</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">homomers</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_references</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">summary</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">summary_str</span></code></p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.complex.Humap2.load_data">
+<span class="sig-name descname"><span class="pre">load_data</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.complex.Humap2.load_data" title="Link to this definition">§</a></dt>
+<dd><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.complex.Humap2.process">
+<span class="sig-name descname"><span class="pre">process</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.complex.Humap2.process" title="Link to this definition">§</a></dt>
+<dd><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.complex.Humap2.set_method">
+<span class="sig-name descname"><span class="pre">set_method</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.complex.Humap2.set_method" title="Link to this definition">§</a></dt>
+<dd><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if
+necessary.</p>
+</dd></dl>
+
+</dd></dl>
+
+</section>
+
+
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+  <section id="pypath-core-complex-icellnet">
+<h1>pypath.core.complex.Icellnet<a class="headerlink" href="#pypath-core-complex-icellnet" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.core.complex.Icellnet">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.core.complex.</span></span><span class="sig-name descname"><span class="pre">Icellnet</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">input_args</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/complex.html#Icellnet"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.complex.Icellnet" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <a class="reference internal" href="pypath.core.complex.AbstractComplexResource.html#pypath.core.complex.AbstractComplexResource" title="pypath.core.complex.AbstractComplexResource"><code class="xref py py-class docutils literal notranslate"><span class="pre">AbstractComplexResource</span></code></a></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.complex.Icellnet.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">input_args</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/complex.html#Icellnet.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.complex.Icellnet.__init__" title="Link to this definition">§</a></dt>
+<dd><dl class="simple">
+<dt>name<span class="classifier">str</span></dt><dd><p>Custom name for the resource.</p>
+</dd>
+<dt>input_method<span class="classifier">callable</span></dt><dd><p>Method providing the input data.</p>
+</dd>
+<dt>process_method<span class="classifier">callable</span></dt><dd><p>Method processing the data and yielding <code class="docutils literal notranslate"><span class="pre">intera.Complex</span></code>
+instances.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.complex.Icellnet.__init__" title="pypath.core.complex.Icellnet.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>([input_args])</p></td>
+<td><p>name : str</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">from_dump</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">load</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.complex.Icellnet.load_data" title="pypath.core.complex.Icellnet.load_data"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_data</span></code></a>()</p></td>
+<td><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">make_df</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.complex.Icellnet.process" title="pypath.core.complex.Icellnet.process"><code class="xref py py-obj docutils literal notranslate"><span class="pre">process</span></code></a>()</p></td>
+<td><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">save_to_pickle</span></code>(pickle_file)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.complex.Icellnet.set_method" title="pypath.core.complex.Icellnet.set_method"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_method</span></code></a>()</p></td>
+<td><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if necessary.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">update_index</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Attributes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_sources</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">curation_effort</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_stoichiometry</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">heteromers</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">homomers</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_references</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">summary</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">summary_str</span></code></p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.complex.Icellnet.load_data">
+<span class="sig-name descname"><span class="pre">load_data</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.complex.Icellnet.load_data" title="Link to this definition">§</a></dt>
+<dd><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.complex.Icellnet.process">
+<span class="sig-name descname"><span class="pre">process</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.complex.Icellnet.process" title="Link to this definition">§</a></dt>
+<dd><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.complex.Icellnet.set_method">
+<span class="sig-name descname"><span class="pre">set_method</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.complex.Icellnet.set_method" title="Link to this definition">§</a></dt>
+<dd><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if
+necessary.</p>
+</dd></dl>
+
+</dd></dl>
+
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+                <article class="bd-article">
+                  
+  <section id="pypath-core-complex-kegg">
+<h1>pypath.core.complex.Kegg<a class="headerlink" href="#pypath-core-complex-kegg" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.core.complex.Kegg">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.core.complex.</span></span><span class="sig-name descname"><span class="pre">Kegg</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">input_args</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/complex.html#Kegg"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.complex.Kegg" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <a class="reference internal" href="pypath.core.complex.AbstractComplexResource.html#pypath.core.complex.AbstractComplexResource" title="pypath.core.complex.AbstractComplexResource"><code class="xref py py-class docutils literal notranslate"><span class="pre">AbstractComplexResource</span></code></a></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.complex.Kegg.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">input_args</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/complex.html#Kegg.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.complex.Kegg.__init__" title="Link to this definition">§</a></dt>
+<dd><dl class="simple">
+<dt>name<span class="classifier">str</span></dt><dd><p>Custom name for the resource.</p>
+</dd>
+<dt>input_method<span class="classifier">callable</span></dt><dd><p>Method providing the input data.</p>
+</dd>
+<dt>process_method<span class="classifier">callable</span></dt><dd><p>Method processing the data and yielding <code class="docutils literal notranslate"><span class="pre">intera.Complex</span></code>
+instances.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.complex.Kegg.__init__" title="pypath.core.complex.Kegg.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>([input_args])</p></td>
+<td><p>name : str</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">from_dump</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">load</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.complex.Kegg.load_data" title="pypath.core.complex.Kegg.load_data"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_data</span></code></a>()</p></td>
+<td><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">make_df</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.complex.Kegg.process" title="pypath.core.complex.Kegg.process"><code class="xref py py-obj docutils literal notranslate"><span class="pre">process</span></code></a>()</p></td>
+<td><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">save_to_pickle</span></code>(pickle_file)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.complex.Kegg.set_method" title="pypath.core.complex.Kegg.set_method"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_method</span></code></a>()</p></td>
+<td><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if necessary.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">update_index</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Attributes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_sources</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">curation_effort</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_stoichiometry</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">heteromers</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">homomers</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_references</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">summary</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">summary_str</span></code></p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.complex.Kegg.load_data">
+<span class="sig-name descname"><span class="pre">load_data</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.complex.Kegg.load_data" title="Link to this definition">§</a></dt>
+<dd><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.complex.Kegg.process">
+<span class="sig-name descname"><span class="pre">process</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.complex.Kegg.process" title="Link to this definition">§</a></dt>
+<dd><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.complex.Kegg.set_method">
+<span class="sig-name descname"><span class="pre">set_method</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.complex.Kegg.set_method" title="Link to this definition">§</a></dt>
+<dd><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if
+necessary.</p>
+</dd></dl>
+
+</dd></dl>
+
+</section>
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+  <section id="pypath-core-complex-pdb">
+<h1>pypath.core.complex.Pdb<a class="headerlink" href="#pypath-core-complex-pdb" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.core.complex.Pdb">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.core.complex.</span></span><span class="sig-name descname"><span class="pre">Pdb</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">input_args</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/complex.html#Pdb"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.complex.Pdb" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <a class="reference internal" href="pypath.core.complex.AbstractComplexResource.html#pypath.core.complex.AbstractComplexResource" title="pypath.core.complex.AbstractComplexResource"><code class="xref py py-class docutils literal notranslate"><span class="pre">AbstractComplexResource</span></code></a></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.complex.Pdb.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">input_args</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/complex.html#Pdb.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.complex.Pdb.__init__" title="Link to this definition">§</a></dt>
+<dd><dl class="simple">
+<dt>name<span class="classifier">str</span></dt><dd><p>Custom name for the resource.</p>
+</dd>
+<dt>input_method<span class="classifier">callable</span></dt><dd><p>Method providing the input data.</p>
+</dd>
+<dt>process_method<span class="classifier">callable</span></dt><dd><p>Method processing the data and yielding <code class="docutils literal notranslate"><span class="pre">intera.Complex</span></code>
+instances.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.complex.Pdb.__init__" title="pypath.core.complex.Pdb.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>([input_args])</p></td>
+<td><p>name : str</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">from_dump</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">load</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.complex.Pdb.load_data" title="pypath.core.complex.Pdb.load_data"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_data</span></code></a>()</p></td>
+<td><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">make_df</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.complex.Pdb.process" title="pypath.core.complex.Pdb.process"><code class="xref py py-obj docutils literal notranslate"><span class="pre">process</span></code></a>()</p></td>
+<td><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">save_to_pickle</span></code>(pickle_file)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.complex.Pdb.set_method" title="pypath.core.complex.Pdb.set_method"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_method</span></code></a>()</p></td>
+<td><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if necessary.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">update_index</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Attributes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_sources</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">curation_effort</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_stoichiometry</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">heteromers</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">homomers</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_references</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">summary</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">summary_str</span></code></p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.complex.Pdb.load_data">
+<span class="sig-name descname"><span class="pre">load_data</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.complex.Pdb.load_data" title="Link to this definition">§</a></dt>
+<dd><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.complex.Pdb.process">
+<span class="sig-name descname"><span class="pre">process</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.complex.Pdb.process" title="Link to this definition">§</a></dt>
+<dd><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.complex.Pdb.set_method">
+<span class="sig-name descname"><span class="pre">set_method</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.complex.Pdb.set_method" title="Link to this definition">§</a></dt>
+<dd><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if
+necessary.</p>
+</dd></dl>
+
+</dd></dl>
+
+</section>
+
+
+                </article>
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+  <section id="pypath-core-complex-signor">
+<h1>pypath.core.complex.Signor<a class="headerlink" href="#pypath-core-complex-signor" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.core.complex.Signor">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.core.complex.</span></span><span class="sig-name descname"><span class="pre">Signor</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">input_args</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/complex.html#Signor"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.complex.Signor" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <a class="reference internal" href="pypath.core.complex.AbstractComplexResource.html#pypath.core.complex.AbstractComplexResource" title="pypath.core.complex.AbstractComplexResource"><code class="xref py py-class docutils literal notranslate"><span class="pre">AbstractComplexResource</span></code></a></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.complex.Signor.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">input_args</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/complex.html#Signor.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.complex.Signor.__init__" title="Link to this definition">§</a></dt>
+<dd><dl class="simple">
+<dt>name<span class="classifier">str</span></dt><dd><p>Custom name for the resource.</p>
+</dd>
+<dt>input_method<span class="classifier">callable</span></dt><dd><p>Method providing the input data.</p>
+</dd>
+<dt>process_method<span class="classifier">callable</span></dt><dd><p>Method processing the data and yielding <code class="docutils literal notranslate"><span class="pre">intera.Complex</span></code>
+instances.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.complex.Signor.__init__" title="pypath.core.complex.Signor.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>([input_args])</p></td>
+<td><p>name : str</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">from_dump</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">load</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.complex.Signor.load_data" title="pypath.core.complex.Signor.load_data"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_data</span></code></a>()</p></td>
+<td><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">make_df</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.complex.Signor.process" title="pypath.core.complex.Signor.process"><code class="xref py py-obj docutils literal notranslate"><span class="pre">process</span></code></a>()</p></td>
+<td><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">save_to_pickle</span></code>(pickle_file)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.complex.Signor.set_method" title="pypath.core.complex.Signor.set_method"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_method</span></code></a>()</p></td>
+<td><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if necessary.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">update_index</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Attributes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_sources</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">curation_effort</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_stoichiometry</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">heteromers</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">homomers</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_references</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">summary</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">summary_str</span></code></p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.complex.Signor.load_data">
+<span class="sig-name descname"><span class="pre">load_data</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.complex.Signor.load_data" title="Link to this definition">§</a></dt>
+<dd><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.complex.Signor.process">
+<span class="sig-name descname"><span class="pre">process</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.complex.Signor.process" title="Link to this definition">§</a></dt>
+<dd><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.complex.Signor.set_method">
+<span class="sig-name descname"><span class="pre">set_method</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.complex.Signor.set_method" title="Link to this definition">§</a></dt>
+<dd><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if
+necessary.</p>
+</dd></dl>
+
+</dd></dl>
+
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+  <section id="pypath-core-complex-spike">
+<h1>pypath.core.complex.Spike<a class="headerlink" href="#pypath-core-complex-spike" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.core.complex.Spike">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.core.complex.</span></span><span class="sig-name descname"><span class="pre">Spike</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">input_args</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/complex.html#Spike"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.complex.Spike" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <a class="reference internal" href="pypath.core.complex.AbstractComplexResource.html#pypath.core.complex.AbstractComplexResource" title="pypath.core.complex.AbstractComplexResource"><code class="xref py py-class docutils literal notranslate"><span class="pre">AbstractComplexResource</span></code></a></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.complex.Spike.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">input_args</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/complex.html#Spike.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.complex.Spike.__init__" title="Link to this definition">§</a></dt>
+<dd><dl class="simple">
+<dt>name<span class="classifier">str</span></dt><dd><p>Custom name for the resource.</p>
+</dd>
+<dt>input_method<span class="classifier">callable</span></dt><dd><p>Method providing the input data.</p>
+</dd>
+<dt>process_method<span class="classifier">callable</span></dt><dd><p>Method processing the data and yielding <code class="docutils literal notranslate"><span class="pre">intera.Complex</span></code>
+instances.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.complex.Spike.__init__" title="pypath.core.complex.Spike.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>([input_args])</p></td>
+<td><p>name : str</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">from_dump</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">load</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.complex.Spike.load_data" title="pypath.core.complex.Spike.load_data"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_data</span></code></a>()</p></td>
+<td><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">make_df</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.complex.Spike.process" title="pypath.core.complex.Spike.process"><code class="xref py py-obj docutils literal notranslate"><span class="pre">process</span></code></a>()</p></td>
+<td><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">save_to_pickle</span></code>(pickle_file)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.complex.Spike.set_method" title="pypath.core.complex.Spike.set_method"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_method</span></code></a>()</p></td>
+<td><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if necessary.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">update_index</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Attributes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_sources</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">curation_effort</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_stoichiometry</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">heteromers</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">homomers</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_references</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">summary</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">summary_str</span></code></p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.complex.Spike.load_data">
+<span class="sig-name descname"><span class="pre">load_data</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.complex.Spike.load_data" title="Link to this definition">§</a></dt>
+<dd><p>Loads the data by calling <code class="docutils literal notranslate"><span class="pre">input_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.complex.Spike.process">
+<span class="sig-name descname"><span class="pre">process</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.complex.Spike.process" title="Link to this definition">§</a></dt>
+<dd><p>Calls the <code class="docutils literal notranslate"><span class="pre">_process_method</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.complex.Spike.set_method">
+<span class="sig-name descname"><span class="pre">set_method</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.complex.Spike.set_method" title="Link to this definition">§</a></dt>
+<dd><p>Sets the data input method by looking up in <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module if
+necessary.</p>
+</dd></dl>
+
+</dd></dl>
+
+</section>
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+  <section id="pypath-core-complex-all-complexes">
+<h1>pypath.core.complex.all_complexes<a class="headerlink" href="#pypath-core-complex-all-complexes" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.core.complex.all_complexes">
+<span class="sig-prename descclassname"><span class="pre">pypath.core.complex.</span></span><span class="sig-name descname"><span class="pre">all_complexes</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/complex.html#all_complexes"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.complex.all_complexes" title="Link to this definition">§</a></dt>
+<dd><p>Returns a set of all complexes in the database which serves as a
+reference set for many methods, just like
+<code class="docutils literal notranslate"><span class="pre">inputs.uniprot_db.all_uniprots</span></code> represents the proteome.</p>
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+<dl class="py function">
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+<span class="sig-prename descclassname"><span class="pre">pypath.core.complex.</span></span><span class="sig-name descname"><span class="pre">get_db</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/complex.html#get_db"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.complex.get_db" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the current database instance and initializes it if does
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+                  
+  <section id="module-pypath.core.complex">
+<span id="pypath-core-complex"></span><h1>pypath.core.complex<a class="headerlink" href="#module-pypath.core.complex" title="Link to this heading">§</a></h1>
+<dl class="field-list simple">
+<dt class="field-odd">members<span class="colon">:</span></dt>
+<dd class="field-odd"><p></p></dd>
+</dl>
+<p class="rubric">Functions</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.core.complex.all_complexes.html#pypath.core.complex.all_complexes" title="pypath.core.complex.all_complexes"><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_complexes</span></code></a>()</p></td>
+<td><p>Returns a set of all complexes in the database which serves as a reference set for many methods, just like <code class="docutils literal notranslate"><span class="pre">inputs.uniprot_db.all_uniprots</span></code> represents the proteome.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.core.complex.get_db.html#pypath.core.complex.get_db" title="pypath.core.complex.get_db"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_db</span></code></a>(**kwargs)</p></td>
+<td><p>Retrieves the current database instance and initializes it if does not exist yet.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.core.complex.init_db.html#pypath.core.complex.init_db" title="pypath.core.complex.init_db"><code class="xref py py-obj docutils literal notranslate"><span class="pre">init_db</span></code></a>(**kwargs)</p></td>
+<td><p>Initializes or reloads the complex database.</p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Classes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.core.complex.AbstractComplexResource.html#pypath.core.complex.AbstractComplexResource" title="pypath.core.complex.AbstractComplexResource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">AbstractComplexResource</span></code></a>(name[, ncbi_tax_id, ...])</p></td>
+<td><p>A resource which provides information about molecular complexes.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.core.complex.CellPhoneDB.html#pypath.core.complex.CellPhoneDB" title="pypath.core.complex.CellPhoneDB"><code class="xref py py-obj docutils literal notranslate"><span class="pre">CellPhoneDB</span></code></a>(**kwargs)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.core.complex.Cellchatdb.html#pypath.core.complex.Cellchatdb" title="pypath.core.complex.Cellchatdb"><code class="xref py py-obj docutils literal notranslate"><span class="pre">Cellchatdb</span></code></a>([input_args])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.core.complex.Cellinker.html#pypath.core.complex.Cellinker" title="pypath.core.complex.Cellinker"><code class="xref py py-obj docutils literal notranslate"><span class="pre">Cellinker</span></code></a>([input_args])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.core.complex.Compleat.html#pypath.core.complex.Compleat" title="pypath.core.complex.Compleat"><code class="xref py py-obj docutils literal notranslate"><span class="pre">Compleat</span></code></a>([input_args])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.core.complex.ComplexAggregator.html#pypath.core.complex.ComplexAggregator" title="pypath.core.complex.ComplexAggregator"><code class="xref py py-obj docutils literal notranslate"><span class="pre">ComplexAggregator</span></code></a>([resources, pickle_file])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.core.complex.ComplexPortal.html#pypath.core.complex.ComplexPortal" title="pypath.core.complex.ComplexPortal"><code class="xref py py-obj docutils literal notranslate"><span class="pre">ComplexPortal</span></code></a>([input_args])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.core.complex.Corum.html#pypath.core.complex.Corum" title="pypath.core.complex.Corum"><code class="xref py py-obj docutils literal notranslate"><span class="pre">Corum</span></code></a>([input_args])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.core.complex.GuideToPharmacology.html#pypath.core.complex.GuideToPharmacology" title="pypath.core.complex.GuideToPharmacology"><code class="xref py py-obj docutils literal notranslate"><span class="pre">GuideToPharmacology</span></code></a>([input_args])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.core.complex.Havugimana.html#pypath.core.complex.Havugimana" title="pypath.core.complex.Havugimana"><code class="xref py py-obj docutils literal notranslate"><span class="pre">Havugimana</span></code></a>([input_args])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.core.complex.Hpmr.html#pypath.core.complex.Hpmr" title="pypath.core.complex.Hpmr"><code class="xref py py-obj docutils literal notranslate"><span class="pre">Hpmr</span></code></a>([input_args])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.core.complex.Humap.html#pypath.core.complex.Humap" title="pypath.core.complex.Humap"><code class="xref py py-obj docutils literal notranslate"><span class="pre">Humap</span></code></a>([input_args])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.core.complex.Humap2.html#pypath.core.complex.Humap2" title="pypath.core.complex.Humap2"><code class="xref py py-obj docutils literal notranslate"><span class="pre">Humap2</span></code></a>([input_args])</p></td>
+<td><p></p></td>
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+<tr class="row-even"><td><p><a class="reference internal" href="pypath.core.complex.Icellnet.html#pypath.core.complex.Icellnet" title="pypath.core.complex.Icellnet"><code class="xref py py-obj docutils literal notranslate"><span class="pre">Icellnet</span></code></a>([input_args])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.core.complex.Kegg.html#pypath.core.complex.Kegg" title="pypath.core.complex.Kegg"><code class="xref py py-obj docutils literal notranslate"><span class="pre">Kegg</span></code></a>([input_args])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.core.complex.Pdb.html#pypath.core.complex.Pdb" title="pypath.core.complex.Pdb"><code class="xref py py-obj docutils literal notranslate"><span class="pre">Pdb</span></code></a>([input_args])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.core.complex.Signor.html#pypath.core.complex.Signor" title="pypath.core.complex.Signor"><code class="xref py py-obj docutils literal notranslate"><span class="pre">Signor</span></code></a>([input_args])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.core.complex.Spike.html#pypath.core.complex.Spike" title="pypath.core.complex.Spike"><code class="xref py py-obj docutils literal notranslate"><span class="pre">Spike</span></code></a>([input_args])</p></td>
+<td><p></p></td>
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+<dd><p>Initializes or reloads the complex database.
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+  <section id="pypath-core-entity-entity">
+<h1>pypath.core.entity.Entity<a class="headerlink" href="#pypath-core-entity-entity" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.core.entity.Entity">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.core.entity.</span></span><span class="sig-name descname"><span class="pre">Entity</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">identifier</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">id_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">taxon</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">attrs</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/entity.html#Entity"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.entity.Entity" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">Logger</span></code>, <a class="reference internal" href="pypath.core.attrs.AttributeHandler.html#pypath.core.attrs.AttributeHandler" title="pypath.core.attrs.AttributeHandler"><code class="xref py py-class docutils literal notranslate"><span class="pre">AttributeHandler</span></code></a></p>
+<p>Represents a molecular entity such as protein, miRNA, lncRNA or small
+molecule.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>identifier</strong> (<em>str</em>) – An identifier from the reference database e.g. UniProt ID for
+proteins.</p></li>
+<li><p><strong>entity_type</strong> (<em>str</em>) – The type of the molecular entity, defaults to <code class="docutils literal notranslate"><span class="pre">'protein'</span></code>.</p></li>
+<li><p><strong>id_type</strong> (<em>str</em>) – The type of the identifier (the reference database), default is
+<code class="docutils literal notranslate"><span class="pre">'uniprot'</span></code>.</p></li>
+<li><p><strong>taxon</strong> (<em>int</em>) – The NCBI Taxonomy Identifier of the molecular entity, e.g. <code class="docutils literal notranslate"><span class="pre">9606</span></code>
+for human. Use <code class="docutils literal notranslate"><span class="pre">0</span></code> for non taxon specific molecules e.g. metabolites
+or drug compounds.</p></li>
+<li><p><strong>attrs</strong> (<em>NoneType</em><em>,</em><em>dict</em>) – A dictionary of additional attributes.</p></li>
+</ul>
+</dd>
+</dl>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.entity.Entity.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">identifier</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">id_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">taxon</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">attrs</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/entity.html#Entity.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.entity.Entity.__init__" title="Link to this definition">§</a></dt>
+<dd><p>Make this instance a logger.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>name</strong> – The label of this instance that will be prepended to all
+messages it sends to the logger.</p></li>
+<li><p><strong>module</strong> – Send the messages by the logger of this module.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.entity.Entity.__init__" title="pypath.core.entity.Entity.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>(identifier[, entity_type, id_type, ...])</p></td>
+<td><p>Make this instance a logger.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.entity.Entity.count_entity_type" title="pypath.core.entity.Entity.count_entity_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_entity_type</span></code></a>(entities, entity_type)</p></td>
+<td><p>Counts elements in an iterable of entities or identifiers of type(s) in <code class="docutils literal notranslate"><span class="pre">entity_type</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">entity_info</span></code>(identifier)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">entity_name_str</span></code>(entity)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.entity.Entity.filter_entity_type" title="pypath.core.entity.Entity.filter_entity_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">filter_entity_type</span></code></a>(entities, entity_type)</p></td>
+<td><p>Filters an iterable of entities or identifiers keeping only the ones of type(s) in <code class="docutils literal notranslate"><span class="pre">entity_type</span></code>.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_entity_type</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">igraph_vertex_label</span></code>(igraph_v)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">igraph_vertex_name</span></code>(igraph_v)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">igraph_vertex_name_label</span></code>(igraph_v)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">info</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_complex</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_mirna</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_protein</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_small_molecule</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">only_complexes</span></code>(entities)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">only_mirnas</span></code>(entities)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">only_proteins</span></code>(entities)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">reload</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.entity.Entity.serialize" title="pypath.core.entity.Entity.serialize"><code class="xref py py-obj docutils literal notranslate"><span class="pre">serialize</span></code></a>(**kwargs)</p></td>
+<td><p>Generates a JSON string with the full contents of the attributes, without any whitespace or line break.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_label</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.entity.Entity.update_attrs" title="pypath.core.entity.Entity.update_attrs"><code class="xref py py-obj docutils literal notranslate"><span class="pre">update_attrs</span></code></a>([attrs])</p></td>
+<td><p>Updates the attributes stored here.</p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Attributes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">identifier</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">entity_type</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">id_type</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">taxon</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">label</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">key</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">attrs</span></code></p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.entity.Entity.count_entity_type">
+<em class="property"><span class="pre">classmethod</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">count_entity_type</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entities</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/entity.html#Entity.count_entity_type"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.entity.Entity.count_entity_type" title="Link to this definition">§</a></dt>
+<dd><p>Counts elements in an iterable of entities or identifiers of type(s)
+in <code class="docutils literal notranslate"><span class="pre">entity_type</span></code>.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>entities</strong> (<em>iterable</em>) – A list, set, tuple or other iterable yielding entities or
+identifiers.</p></li>
+<li><p><strong>entity_type</strong> (<em>str</em><em>,</em><em>set</em>) – One or more entity types e.g. <code class="docutils literal notranslate"><span class="pre">{'protein',</span> <span class="pre">'mirna'}</span></code>.</p></li>
+</ul>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p>int</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.entity.Entity.filter_entity_type">
+<em class="property"><span class="pre">classmethod</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">filter_entity_type</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entities</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/entity.html#Entity.filter_entity_type"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.entity.Entity.filter_entity_type" title="Link to this definition">§</a></dt>
+<dd><p>Filters an iterable of entities or identifiers keeping only the ones
+of type(s) in <code class="docutils literal notranslate"><span class="pre">entity_type</span></code>.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>entities</strong> (<em>iterable</em>) – A list, set, tuple or other iterable yielding entities or
+identifiers.</p></li>
+<li><p><strong>entity_type</strong> (<em>str</em><em>,</em><em>set</em>) – One or more entity types e.g. <code class="docutils literal notranslate"><span class="pre">{'protein',</span> <span class="pre">'mirna'}</span></code>.</p></li>
+</ul>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p>Same type of object as <code class="docutils literal notranslate"><span class="pre">entities</span></code> if the type of the object is
+list, set or tuple, otherwise a generator.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.entity.Entity.serialize">
+<span class="sig-name descname"><span class="pre">serialize</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.entity.Entity.serialize" title="Link to this definition">§</a></dt>
+<dd><p>Generates a JSON string with the full contents of the attributes,
+without any whitespace or line break.</p>
+<dl class="simple">
+<dt>Returns</dt><dd><p>(str): The attributes JSON serialized.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.entity.Entity.update_attrs">
+<span class="sig-name descname"><span class="pre">update_attrs</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">attrs</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.entity.Entity.update_attrs" title="Link to this definition">§</a></dt>
+<dd><p>Updates the attributes stored here. The attributes with identical
+keys are merged using the <code class="xref py py-func docutils literal notranslate"><span class="pre">pypath.share.common.combine_attrs()</span></code>
+function.</p>
+<p>The new attributes can be provided three ways: an object with an
+attribute called <cite>attrs</cite>; a dictionary of attributes; or the
+attributes as keyword arguments.</p>
+</dd></dl>
+
+</dd></dl>
+
+</section>
+
+
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+  <section id="pypath-core-entity-entitykey">
+<h1>pypath.core.entity.EntityKey<a class="headerlink" href="#pypath-core-entity-entitykey" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.core.entity.EntityKey">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.core.entity.</span></span><span class="sig-name descname"><span class="pre">EntityKey</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">identifier</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">id_type</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">taxon</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.entity.EntityKey" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">tuple</span></code></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.entity.EntityKey.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.entity.EntityKey.__init__" title="Link to this definition">§</a></dt>
+<dd></dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.entity.EntityKey.__init__" title="pypath.core.entity.EntityKey.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.entity.EntityKey.count" title="pypath.core.entity.EntityKey.count"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count</span></code></a>(value, /)</p></td>
+<td><p>Return number of occurrences of value.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.entity.EntityKey.index" title="pypath.core.entity.EntityKey.index"><code class="xref py py-obj docutils literal notranslate"><span class="pre">index</span></code></a>(value[, start, stop])</p></td>
+<td><p>Return first index of value.</p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Attributes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.entity.EntityKey.entity_type" title="pypath.core.entity.EntityKey.entity_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">entity_type</span></code></a></p></td>
+<td><p>Alias for field number 2</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.entity.EntityKey.id_type" title="pypath.core.entity.EntityKey.id_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">id_type</span></code></a></p></td>
+<td><p>Alias for field number 1</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.entity.EntityKey.identifier" title="pypath.core.entity.EntityKey.identifier"><code class="xref py py-obj docutils literal notranslate"><span class="pre">identifier</span></code></a></p></td>
+<td><p>Alias for field number 0</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.entity.EntityKey.taxon" title="pypath.core.entity.EntityKey.taxon"><code class="xref py py-obj docutils literal notranslate"><span class="pre">taxon</span></code></a></p></td>
+<td><p>Alias for field number 3</p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.entity.EntityKey.count">
+<span class="sig-name descname"><span class="pre">count</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">value</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">/</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.entity.EntityKey.count" title="Link to this definition">§</a></dt>
+<dd><p>Return number of occurrences of value.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.entity.EntityKey.entity_type">
+<span class="sig-name descname"><span class="pre">entity_type</span></span><a class="headerlink" href="#pypath.core.entity.EntityKey.entity_type" title="Link to this definition">§</a></dt>
+<dd><p>Alias for field number 2</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.entity.EntityKey.id_type">
+<span class="sig-name descname"><span class="pre">id_type</span></span><a class="headerlink" href="#pypath.core.entity.EntityKey.id_type" title="Link to this definition">§</a></dt>
+<dd><p>Alias for field number 1</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.entity.EntityKey.identifier">
+<span class="sig-name descname"><span class="pre">identifier</span></span><a class="headerlink" href="#pypath.core.entity.EntityKey.identifier" title="Link to this definition">§</a></dt>
+<dd><p>Alias for field number 0</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.entity.EntityKey.index">
+<span class="sig-name descname"><span class="pre">index</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">value</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">start</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">stop</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9223372036854775807</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">/</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.entity.EntityKey.index" title="Link to this definition">§</a></dt>
+<dd><p>Return first index of value.</p>
+<p>Raises ValueError if the value is not present.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.entity.EntityKey.taxon">
+<span class="sig-name descname"><span class="pre">taxon</span></span><a class="headerlink" href="#pypath.core.entity.EntityKey.taxon" title="Link to this definition">§</a></dt>
+<dd><p>Alias for field number 3</p>
+</dd></dl>
+
+</dd></dl>
+
+</section>
+
+
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diff --git a/api/pypath.core.entity.EntityList.html b/api/pypath.core.entity.EntityList.html
new file mode 100644
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+              
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+                <article class="bd-article">
+                  
+  <section id="pypath-core-entity-entitylist">
+<h1>pypath.core.entity.EntityList<a class="headerlink" href="#pypath-core-entity-entitylist" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.core.entity.EntityList">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.core.entity.</span></span><span class="sig-name descname"><span class="pre">EntityList</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entities</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/entity.html#EntityList"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.entity.EntityList" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.entity.EntityList.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entities</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/entity.html#EntityList.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.entity.EntityList.__init__" title="Link to this definition">§</a></dt>
+<dd></dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.entity.EntityList.__init__" title="pypath.core.entity.EntityList.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>(entities)</p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Attributes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">e</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">entities</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">i</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">identifiers</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">ids</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">l</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">labels</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">le</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">li</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">list_entities</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">list_ids</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">list_labels</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">ll</span></code></p></td>
+<td><p></p></td>
+</tr>
+</tbody>
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diff --git a/api/pypath.core.enz_sub.EnzymeSubstrateAggregator.html b/api/pypath.core.enz_sub.EnzymeSubstrateAggregator.html
new file mode 100644
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+                  
+  <section id="pypath-core-enz-sub-enzymesubstrateaggregator">
+<h1>pypath.core.enz_sub.EnzymeSubstrateAggregator<a class="headerlink" href="#pypath-core-enz-sub-enzymesubstrateaggregator" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.core.enz_sub.EnzymeSubstrateAggregator">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.core.enz_sub.</span></span><span class="sig-name descname"><span class="pre">EnzymeSubstrateAggregator</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">input_param</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">exclude</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">map_by_orthology_from</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">trace</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">orthology_only_swissprot</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ptm_orthology_strict</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">nonhuman_direct_lookup</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">inputargs</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">pickle_file</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/enz_sub.html#EnzymeSubstrateAggregator"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.enz_sub.EnzymeSubstrateAggregator" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">Logger</span></code></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.enz_sub.EnzymeSubstrateAggregator.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">input_param</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">exclude</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">map_by_orthology_from</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">trace</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">orthology_only_swissprot</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ptm_orthology_strict</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">nonhuman_direct_lookup</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">inputargs</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">pickle_file</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/enz_sub.html#EnzymeSubstrateAggregator.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.enz_sub.EnzymeSubstrateAggregator.__init__" title="Link to this definition">§</a></dt>
+<dd><p>Docs not written yet.</p>
+</dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.enz_sub.EnzymeSubstrateAggregator.__init__" title="pypath.core.enz_sub.EnzymeSubstrateAggregator.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>([input_param, exclude, ...])</p></td>
+<td><p>Docs not written yet.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.enz_sub.EnzymeSubstrateAggregator.assign_to_network" title="pypath.core.enz_sub.EnzymeSubstrateAggregator.assign_to_network"><code class="xref py py-obj docutils literal notranslate"><span class="pre">assign_to_network</span></code></a>(pa)</p></td>
+<td><p>Assigns enzyme-substrate interactions to the edges of a network in a py:class:<code class="docutils literal notranslate"><span class="pre">pypath.legacy.main.PyPath</span></code> instance.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">build</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.enz_sub.EnzymeSubstrateAggregator.build_list" title="pypath.core.enz_sub.EnzymeSubstrateAggregator.build_list"><code class="xref py py-obj docutils literal notranslate"><span class="pre">build_list</span></code></a>()</p></td>
+<td><p>Builds a full list of enzyme-substrate interactions from all the requested sources.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">export_table</span></code>(fname)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_enzyme_substrate</span></code>(enzyme, substrate)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_from_pickle</span></code>([pickle_file])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">main</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">make_df</span></code>([tax_id, resources_only_primary])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">reload</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">save_to_pickle</span></code>(pickle_file)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_inputs</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">summaries_tab</span></code>([outfile, return_table])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">uniq_enz_sub</span></code>(enz_sub)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.enz_sub.EnzymeSubstrateAggregator.unique" title="pypath.core.enz_sub.EnzymeSubstrateAggregator.unique"><code class="xref py py-obj docutils literal notranslate"><span class="pre">unique</span></code></a>()</p></td>
+<td><p>Merges the redundant elements of the interaction list.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">update_ptm_lookup_dict</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">update_summaries</span></code>([collect_args])</p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Attributes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">resources</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">resources_sorted</span></code></p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.enz_sub.EnzymeSubstrateAggregator.assign_to_network">
+<span class="sig-name descname"><span class="pre">assign_to_network</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">pa</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/enz_sub.html#EnzymeSubstrateAggregator.assign_to_network"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.enz_sub.EnzymeSubstrateAggregator.assign_to_network" title="Link to this definition">§</a></dt>
+<dd><p>Assigns enzyme-substrate interactions to the edges of a
+network in a py:class:<code class="docutils literal notranslate"><span class="pre">pypath.legacy.main.PyPath</span></code> instance.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.enz_sub.EnzymeSubstrateAggregator.build_list">
+<span class="sig-name descname"><span class="pre">build_list</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/enz_sub.html#EnzymeSubstrateAggregator.build_list"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.enz_sub.EnzymeSubstrateAggregator.build_list" title="Link to this definition">§</a></dt>
+<dd><p>Builds a full list of enzyme-substrate interactions from
+all the requested sources. This list might contain redundant
+elements which later will be merged by <cite>unique</cite>.
+This ‘full list’ is organised into a dict by pairs of proteins
+in order to make it more efficient to compile a unique set
+for each pair.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.enz_sub.EnzymeSubstrateAggregator.unique">
+<span class="sig-name descname"><span class="pre">unique</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/enz_sub.html#EnzymeSubstrateAggregator.unique"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.enz_sub.EnzymeSubstrateAggregator.unique" title="Link to this definition">§</a></dt>
+<dd><p>Merges the redundant elements of the interaction list.
+Elements are redundant if they agree in all their attributes
+except the sources, references and isoforms.</p>
+</dd></dl>
+
+</dd></dl>
+
+</section>
+
+
+                </article>
+              
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+                <article class="bd-article">
+                  
+  <section id="pypath-core-enz-sub-enzymesubstrateorthologyprocessor">
+<h1>pypath.core.enz_sub.EnzymeSubstrateOrthologyProcessor<a class="headerlink" href="#pypath-core-enz-sub-enzymesubstrateorthologyprocessor" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.core.enz_sub.EnzymeSubstrateOrthologyProcessor">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.core.enz_sub.</span></span><span class="sig-name descname"><span class="pre">EnzymeSubstrateOrthologyProcessor</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">input_param</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">input_method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">map_by_orthology_from</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">trace</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">id_type_enzyme</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">id_type_substrate</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">name</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">orthology_only_swissprot</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ptm_orthology_strict</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/enz_sub.html#EnzymeSubstrateOrthologyProcessor"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.enz_sub.EnzymeSubstrateOrthologyProcessor" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <a class="reference internal" href="pypath.utils.orthology.PtmOrthology.html#pypath.utils.orthology.PtmOrthology" title="pypath.utils.orthology.PtmOrthology"><code class="xref py py-class docutils literal notranslate"><span class="pre">PtmOrthology</span></code></a>, <a class="reference internal" href="pypath.core.enz_sub.EnzymeSubstrateProcessor.html#pypath.core.enz_sub.EnzymeSubstrateProcessor" title="pypath.core.enz_sub.EnzymeSubstrateProcessor"><code class="xref py py-class docutils literal notranslate"><span class="pre">EnzymeSubstrateProcessor</span></code></a>, <code class="xref py py-class docutils literal notranslate"><span class="pre">Logger</span></code></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.enz_sub.EnzymeSubstrateOrthologyProcessor.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">input_param</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">input_method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">map_by_orthology_from</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">trace</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">id_type_enzyme</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">id_type_substrate</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">name</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">orthology_only_swissprot</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ptm_orthology_strict</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/enz_sub.html#EnzymeSubstrateOrthologyProcessor.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.enz_sub.EnzymeSubstrateOrthologyProcessor.__init__" title="Link to this definition">§</a></dt>
+<dd><p>Unifies a <cite>pypath.core.enz_sub.EnzymeSubstrateProcessor</cite> and
+a <cite>pypath.utils.orthology.PtmOrthology</cite> object to build
+a set of enzyme-substrate interactions from a database and
+subsequently translate them by orthology to one different organism.
+Multiple organism can be chosen as the source of the
+enzyme-substrate interactions. For example if you want mouse
+interactions, you can translate them from human and from rat.
+To get the original mouse interactions themselves, use an
+other instance of the <cite>EnzymeSubstrateProcessor</cite>.
+To have both the original and the orthology translated set,
+and also from multiple databases, whatmore all these merged
+into a single set, use the <cite>EnzymeSubstrateAggregator</cite>.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>input_method</strong> (<em>str</em>) – Data source for <cite>EnzymeSubstrateProcessor</cite>.</p></li>
+<li><p><strong>ncbi_tax_id</strong> (<em>int</em>) – The NCBI Taxonomy ID the interactions
+should be translated to.</p></li>
+<li><p><strong>orthology_only_swissprot</strong> (<em>bool</em>) – Use only SwissProt
+(i.e. not Trembl) at orthology
+translation.</p></li>
+<li><p><strong>ptm_orthology_strict</strong> (<em>bool</em>) – Use only those homologous PTM pairs
+which are in PhosphoSite data, i.e.
+do not look for residues with same
+offset in protein sequence.</p></li>
+</ul>
+</dd>
+</dl>
+<p>See further options at <cite>EnzymeSubstrateProcessor</cite>.</p>
+</dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.enz_sub.EnzymeSubstrateOrthologyProcessor.__init__" title="pypath.core.enz_sub.EnzymeSubstrateOrthologyProcessor.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>(ncbi_tax_id[, input_param, ...])</p></td>
+<td><p>Unifies a <cite>pypath.core.enz_sub.EnzymeSubstrateProcessor</cite> and a <cite>pypath.utils.orthology.PtmOrthology</cite> object to build a set of enzyme-substrate interactions from a database and subsequently translate them by orthology to one different organism.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_seq</span></code>(protein[, taxon])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_taxon</span></code>(protein[, only_swissprot])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_taxon_trembl</span></code>(protein)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_protein</span></code>(protein)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">input_is</span></code>(i[, op])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_swissprot</span></code>(protein)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.enz_sub.EnzymeSubstrateOrthologyProcessor.load_data" title="pypath.core.enz_sub.EnzymeSubstrateOrthologyProcessor.load_data"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_data</span></code></a>()</p></td>
+<td><p>Loads the data by the defined input method.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_enz_sub</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_proteome</span></code>(taxon[, only_swissprot])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_seq</span></code>(taxon)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_taxonomy</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.enz_sub.EnzymeSubstrateOrthologyProcessor.ptm_orthology" title="pypath.core.enz_sub.EnzymeSubstrateOrthologyProcessor.ptm_orthology"><code class="xref py py-obj docutils literal notranslate"><span class="pre">ptm_orthology</span></code></a>()</p></td>
+<td><p>Load PTM orthology data from PhosphoSite.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">reload</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">reset_ptmprocessor</span></code>([seq, ncbi_tax_id])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.enz_sub.EnzymeSubstrateOrthologyProcessor.set_inputargs" title="pypath.core.enz_sub.EnzymeSubstrateOrthologyProcessor.set_inputargs"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_inputargs</span></code></a>(**inputargs)</p></td>
+<td><p>Sets the arguments to be provided for the input method.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.enz_sub.EnzymeSubstrateOrthologyProcessor.set_method" title="pypath.core.enz_sub.EnzymeSubstrateOrthologyProcessor.set_method"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_method</span></code></a>()</p></td>
+<td><p>Selects the input method.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_taxon</span></code>(ncbi_tax_id)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">setup</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.enz_sub.EnzymeSubstrateOrthologyProcessor.translate" title="pypath.core.enz_sub.EnzymeSubstrateOrthologyProcessor.translate"><code class="xref py py-obj docutils literal notranslate"><span class="pre">translate</span></code></a>(x[, return_strings])</p></td>
+<td><p>Translates anything: string notation, intera objects, tuples.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">translate_domain</span></code>(domain)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">translate_domain_motif</span></code>(dmotif)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">translate_ptm</span></code>(ptm)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">translate_residue</span></code>(residue)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.enz_sub.EnzymeSubstrateOrthologyProcessor.translate_site" title="pypath.core.enz_sub.EnzymeSubstrateOrthologyProcessor.translate_site"><code class="xref py py-obj docutils literal notranslate"><span class="pre">translate_site</span></code></a>(protein, res, offset[, ...])</p></td>
+<td><p>Translates one PTM site.</p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.enz_sub.EnzymeSubstrateOrthologyProcessor.load_data">
+<span class="sig-name descname"><span class="pre">load_data</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.enz_sub.EnzymeSubstrateOrthologyProcessor.load_data" title="Link to this definition">§</a></dt>
+<dd><p>Loads the data by the defined input method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.enz_sub.EnzymeSubstrateOrthologyProcessor.ptm_orthology">
+<span class="sig-name descname"><span class="pre">ptm_orthology</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.enz_sub.EnzymeSubstrateOrthologyProcessor.ptm_orthology" title="Link to this definition">§</a></dt>
+<dd><p>Load PTM orthology data from PhosphoSite.</p>
+<p>Creates an orthology translation dict of phosphosites
+based on phosphorylation sites table from PhosphoSitePlus.
+In the result all PTMs represented by a tuple of the following
+6 elements: UniProt ID, isoform (int), residue one letter code,
+residue number (int), NCBI Taxonomy ID (int), modification type.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.enz_sub.EnzymeSubstrateOrthologyProcessor.set_inputargs">
+<span class="sig-name descname"><span class="pre">set_inputargs</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">inputargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.enz_sub.EnzymeSubstrateOrthologyProcessor.set_inputargs" title="Link to this definition">§</a></dt>
+<dd><p>Sets the arguments to be provided for the input method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.enz_sub.EnzymeSubstrateOrthologyProcessor.set_method">
+<span class="sig-name descname"><span class="pre">set_method</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.enz_sub.EnzymeSubstrateOrthologyProcessor.set_method" title="Link to this definition">§</a></dt>
+<dd><p>Selects the input method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.enz_sub.EnzymeSubstrateOrthologyProcessor.translate">
+<span class="sig-name descname"><span class="pre">translate</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">x</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">return_strings</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.enz_sub.EnzymeSubstrateOrthologyProcessor.translate" title="Link to this definition">§</a></dt>
+<dd><p>Translates anything: string notation, intera objects, tuples.</p>
+<ul class="simple">
+<li><p>one PTM provided as tuple of (UniProt, amino acid, offest)</p></li>
+<li><p>one PTM provided as string (e.g. <cite>P00533_S231</cite>)</p></li>
+<li><p>instance from pypath.intera: DomainMotif, Domain or Ptm</p></li>
+</ul>
+<p>Additional arguments can be isoform and typ (modification type).</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.enz_sub.EnzymeSubstrateOrthologyProcessor.translate_site">
+<span class="sig-name descname"><span class="pre">translate_site</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">protein</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">intera.Protein</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">res</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">offset</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">isoform</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">typ</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">'phosphorylation'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">source_organism</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">int</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><span class="pre">set</span><span class="p"><span class="pre">[</span></span><span class="pre">tuple</span><span class="p"><span class="pre">]</span></span></span></span><a class="headerlink" href="#pypath.core.enz_sub.EnzymeSubstrateOrthologyProcessor.translate_site" title="Link to this definition">§</a></dt>
+<dd><p>Translates one PTM site.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>protein</strong> – A protein identifier or an intera.Protein object.</p></li>
+<li><p><strong>res</strong> – Single letter code of the residue.</p></li>
+<li><p><strong>offset</strong> – Sequence offset of the site.</p></li>
+<li><p><strong>isoform</strong> – Sequence isoform.</p></li>
+<li><p><strong>typ</strong> – Modification type.</p></li>
+<li><p><strong>source_organism</strong> – Name or NCBI Taxonomy ID of the source organism.</p></li>
+</ul>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p>A list of tuples with the identifier, isoform, residue, offset,
+taxon and modification type of the orthologous PTM sites.</p>
+</dd>
+</dl>
+</dd></dl>
+
+</dd></dl>
+
+</section>
+
+
+                </article>
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diff --git a/api/pypath.core.enz_sub.EnzymeSubstrateProcessor.html b/api/pypath.core.enz_sub.EnzymeSubstrateProcessor.html
new file mode 100644
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+  <section id="pypath-core-enz-sub-enzymesubstrateprocessor">
+<h1>pypath.core.enz_sub.EnzymeSubstrateProcessor<a class="headerlink" href="#pypath-core-enz-sub-enzymesubstrateprocessor" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.core.enz_sub.EnzymeSubstrateProcessor">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.core.enz_sub.</span></span><span class="sig-name descname"><span class="pre">EnzymeSubstrateProcessor</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">input_param</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">input_method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">trace</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">id_type_enzyme</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">id_type_substrate</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">name</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">allow_mixed_organisms</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">organisms_supported</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/enz_sub.html#EnzymeSubstrateProcessor"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.enz_sub.EnzymeSubstrateProcessor" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <a class="reference internal" href="pypath.utils.orthology.Proteomes.html#pypath.utils.orthology.Proteomes" title="pypath.utils.orthology.Proteomes"><code class="xref py py-class docutils literal notranslate"><span class="pre">Proteomes</span></code></a>, <a class="reference internal" href="pypath.utils.orthology.SequenceContainer.html#pypath.utils.orthology.SequenceContainer" title="pypath.utils.orthology.SequenceContainer"><code class="xref py py-class docutils literal notranslate"><span class="pre">SequenceContainer</span></code></a></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.enz_sub.EnzymeSubstrateProcessor.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">input_param</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">input_method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">trace</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">id_type_enzyme</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">id_type_substrate</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">name</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">allow_mixed_organisms</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">organisms_supported</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/enz_sub.html#EnzymeSubstrateProcessor.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.enz_sub.EnzymeSubstrateProcessor.__init__" title="Link to this definition">§</a></dt>
+<dd><p>Processes enzyme-substrate interaction data from various databases.
+Provides generators to iterate over these interactions.
+For organisms other than human obtains the organism specific
+interactions from databases.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>input_method</strong> (<em>str</em>) – Either a method name in the <code class="docutils literal notranslate"><span class="pre">inputs</span></code> module or a database
+name e.g. <cite>PhosphoSite</cite> or a callable which returns data in
+list of dicts format.</p></li>
+<li><p><strong>ncbi_tax_id</strong> (<em>int</em>) – NCBI Taxonomy ID used at the database lookups.</p></li>
+<li><p><strong>trace</strong> (<em>bool</em>) – Keep data about ambiguous ID mappings and PTM data
+in mismatch with UniProt sequences.</p></li>
+<li><p><strong>pypath.mapping.Mapper</strong> – A <cite>Mapper</cite> instance. If <cite>None</cite> a new
+instance will be created.</p></li>
+<li><p><strong>id_type_enzyme</strong> (<em>str</em>) – The ID type of the enzyme in the database.</p></li>
+<li><p><strong>id_type_substrate</strong> (<em>str</em>) – The ID type of the substrate in the
+database.</p></li>
+<li><p><strong>nonhuman_direct_lookup</strong> (<em>bool</em>) – Use direct lookup at non-human
+target species.</p></li>
+<li><p><strong>**kwargs</strong> – <p>Args to be forwarded to the input method.</p>
+</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.enz_sub.EnzymeSubstrateProcessor.__init__" title="pypath.core.enz_sub.EnzymeSubstrateProcessor.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>([input_param, input_method, ...])</p></td>
+<td><p>Processes enzyme-substrate interaction data from various databases.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_seq</span></code>(protein[, taxon])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_taxon</span></code>(protein[, only_swissprot])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_taxon_trembl</span></code>(protein)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_protein</span></code>(protein)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">input_is</span></code>(i[, op])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_swissprot</span></code>(protein)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.enz_sub.EnzymeSubstrateProcessor.load_data" title="pypath.core.enz_sub.EnzymeSubstrateProcessor.load_data"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_data</span></code></a>()</p></td>
+<td><p>Loads the data by the defined input method.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_enz_sub</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_proteome</span></code>(taxon[, only_swissprot])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_seq</span></code>(taxon)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_taxonomy</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">reload</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">reset_ptmprocessor</span></code>([seq, ncbi_tax_id])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.enz_sub.EnzymeSubstrateProcessor.set_inputargs" title="pypath.core.enz_sub.EnzymeSubstrateProcessor.set_inputargs"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_inputargs</span></code></a>(**inputargs)</p></td>
+<td><p>Sets the arguments to be provided for the input method.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.enz_sub.EnzymeSubstrateProcessor.set_method" title="pypath.core.enz_sub.EnzymeSubstrateProcessor.set_method"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_method</span></code></a>()</p></td>
+<td><p>Selects the input method.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_taxon</span></code>(ncbi_tax_id)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">setup</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.enz_sub.EnzymeSubstrateProcessor.load_data">
+<span class="sig-name descname"><span class="pre">load_data</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/enz_sub.html#EnzymeSubstrateProcessor.load_data"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.enz_sub.EnzymeSubstrateProcessor.load_data" title="Link to this definition">§</a></dt>
+<dd><p>Loads the data by the defined input method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.enz_sub.EnzymeSubstrateProcessor.set_inputargs">
+<span class="sig-name descname"><span class="pre">set_inputargs</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">inputargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/enz_sub.html#EnzymeSubstrateProcessor.set_inputargs"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.enz_sub.EnzymeSubstrateProcessor.set_inputargs" title="Link to this definition">§</a></dt>
+<dd><p>Sets the arguments to be provided for the input method.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.enz_sub.EnzymeSubstrateProcessor.set_method">
+<span class="sig-name descname"><span class="pre">set_method</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/enz_sub.html#EnzymeSubstrateProcessor.set_method"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.enz_sub.EnzymeSubstrateProcessor.set_method" title="Link to this definition">§</a></dt>
+<dd><p>Selects the input method.</p>
+</dd></dl>
+
+</dd></dl>
+
+</section>
+
+
+                </article>
+              
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diff --git a/api/pypath.core.evidence.Evidence.html b/api/pypath.core.evidence.Evidence.html
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+  <section id="pypath-core-evidence-evidence">
+<h1>pypath.core.evidence.Evidence<a class="headerlink" href="#pypath-core-evidence-evidence" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.core.evidence.Evidence">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.core.evidence.</span></span><span class="sig-name descname"><span class="pre">Evidence</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">resource</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">attrs</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/evidence.html#Evidence"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.evidence.Evidence" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <a class="reference internal" href="pypath.core.attrs.AttributeHandler.html#pypath.core.attrs.AttributeHandler" title="pypath.core.attrs.AttributeHandler"><code class="xref py py-class docutils literal notranslate"><span class="pre">AttributeHandler</span></code></a></p>
+<p>Represents an evidence supporting a relationship such as molecular
+interaction, molecular complex, enzyme-PTM interaction, annotation, etc.</p>
+<p>The evidence consists of two main parts: the database and the literature
+references. If a relationship is supported by multiple databases, for
+each one <cite>Evidence</cite> object should be created and</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>resource</strong> (<em>pypath.resource.ResourceAttributes</em>) – An object derived from <code class="xref py py-class docutils literal notranslate"><span class="pre">pypath.resource.ResourceAttributes</span></code>.</p></li>
+<li><p><strong>references</strong> (<em>str</em><em>,</em><em>list</em><em>,</em><em>set</em><em>,</em><em>NoneType</em>) – Optional, one or more literature references (preferably PubMed IDs).</p></li>
+</ul>
+</dd>
+</dl>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.evidence.Evidence.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">resource</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">attrs</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/evidence.html#Evidence.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.evidence.Evidence.__init__" title="Link to this definition">§</a></dt>
+<dd></dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.evidence.Evidence.__init__" title="pypath.core.evidence.Evidence.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>(resource[, references, attrs])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.evidence.Evidence.asdict" title="pypath.core.evidence.Evidence.asdict"><code class="xref py py-obj docutils literal notranslate"><span class="pre">asdict</span></code></a>()</p></td>
+<td><p>Dictionary representation of the evidence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">contains_database</span></code>(database)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">contains_reference</span></code>(reference)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_data_model</span></code>(data_model)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_database_via</span></code>(database, via)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.evidence.Evidence.has_interaction_type" title="pypath.core.evidence.Evidence.has_interaction_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_interaction_type</span></code></a>(interaction_type[, ...])</p></td>
+<td><p>If <code class="docutils literal notranslate"><span class="pre">via</span></code> is <code class="docutils literal notranslate"><span class="pre">False</span></code> then it will be ignored, otherwise if <code class="docutils literal notranslate"><span class="pre">None</span></code> only primary resources are considered.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">match</span></code>([resource, data_model, ...])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.evidence.Evidence.merge" title="pypath.core.evidence.Evidence.merge"><code class="xref py py-obj docutils literal notranslate"><span class="pre">merge</span></code></a>(other)</p></td>
+<td><p>Merges two evidences.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.evidence.Evidence.reload" title="pypath.core.evidence.Evidence.reload"><code class="xref py py-obj docutils literal notranslate"><span class="pre">reload</span></code></a>()</p></td>
+<td><p>Reloads the object from the module level.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.evidence.Evidence.serialize" title="pypath.core.evidence.Evidence.serialize"><code class="xref py py-obj docutils literal notranslate"><span class="pre">serialize</span></code></a>(**kwargs)</p></td>
+<td><p>Generates a JSON string with the full contents of the attributes, without any whitespace or line break.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.evidence.Evidence.update_attrs" title="pypath.core.evidence.Evidence.update_attrs"><code class="xref py py-obj docutils literal notranslate"><span class="pre">update_attrs</span></code></a>([attrs])</p></td>
+<td><p>Updates the attributes stored here.</p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Attributes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">resource</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">references</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">dataset</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">attrs</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">key</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.evidence.Evidence.pubmeds" title="pypath.core.evidence.Evidence.pubmeds"><code class="xref py py-obj docutils literal notranslate"><span class="pre">pubmeds</span></code></a></p></td>
+<td><p>PubMed IDs of the references supporting this evidence.</p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.evidence.Evidence.asdict">
+<span class="sig-name descname"><span class="pre">asdict</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><span class="pre">dict</span></span></span><a class="reference internal" href="../_modules/pypath/core/evidence.html#Evidence.asdict"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.evidence.Evidence.asdict" title="Link to this definition">§</a></dt>
+<dd><p>Dictionary representation of the evidence.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.evidence.Evidence.has_interaction_type">
+<span class="sig-name descname"><span class="pre">has_interaction_type</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">database</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/evidence.html#Evidence.has_interaction_type"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.evidence.Evidence.has_interaction_type" title="Link to this definition">§</a></dt>
+<dd><p>If <code class="docutils literal notranslate"><span class="pre">via</span></code> is <code class="docutils literal notranslate"><span class="pre">False</span></code> then it will be ignored, otherwise if <code class="docutils literal notranslate"><span class="pre">None</span></code>
+only primary resources are considered.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.evidence.Evidence.merge">
+<span class="sig-name descname"><span class="pre">merge</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">other</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/evidence.html#Evidence.merge"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.evidence.Evidence.merge" title="Link to this definition">§</a></dt>
+<dd><p>Merges two evidences. Returns set of either one or two evidences
+depending on whether the two evidences are from the same resource.</p>
+</dd></dl>
+
+<dl class="py property">
+<dt class="sig sig-object py" id="pypath.core.evidence.Evidence.pubmeds">
+<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">pubmeds</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span></em><a class="headerlink" href="#pypath.core.evidence.Evidence.pubmeds" title="Link to this definition">§</a></dt>
+<dd><p>PubMed IDs of the references supporting this evidence.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.evidence.Evidence.reload">
+<span class="sig-name descname"><span class="pre">reload</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/evidence.html#Evidence.reload"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.evidence.Evidence.reload" title="Link to this definition">§</a></dt>
+<dd><p>Reloads the object from the module level.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.evidence.Evidence.serialize">
+<span class="sig-name descname"><span class="pre">serialize</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.evidence.Evidence.serialize" title="Link to this definition">§</a></dt>
+<dd><p>Generates a JSON string with the full contents of the attributes,
+without any whitespace or line break.</p>
+<dl class="simple">
+<dt>Returns</dt><dd><p>(str): The attributes JSON serialized.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.evidence.Evidence.update_attrs">
+<span class="sig-name descname"><span class="pre">update_attrs</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">attrs</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.evidence.Evidence.update_attrs" title="Link to this definition">§</a></dt>
+<dd><p>Updates the attributes stored here. The attributes with identical
+keys are merged using the <code class="xref py py-func docutils literal notranslate"><span class="pre">pypath.share.common.combine_attrs()</span></code>
+function.</p>
+<p>The new attributes can be provided three ways: an object with an
+attribute called <cite>attrs</cite>; a dictionary of attributes; or the
+attributes as keyword arguments.</p>
+</dd></dl>
+
+</dd></dl>
+
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+  <section id="pypath-core-evidence-evidences">
+<h1>pypath.core.evidence.Evidences<a class="headerlink" href="#pypath-core-evidence-evidences" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.core.evidence.Evidences">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.core.evidence.</span></span><span class="sig-name descname"><span class="pre">Evidences</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">evidences</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/evidence.html#Evidences"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.evidence.Evidences" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></p>
+<p>A collection of evidences. All evidences supporting a relationship such
+as molecular interaction, molecular complex, enzyme-PTM interaction,
+annotation, etc should be collected in one <cite>Evidences</cite> object. This way
+the set of evidences can be queried a comprehensive way.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><p><strong>evidences</strong> (<em>tuple</em><em>,</em><em>list</em><em>,</em><em>set</em><em>,</em><a class="reference internal" href="#pypath.core.evidence.Evidences" title="pypath.core.evidence.Evidences"><em>Evidences</em></a>) – An iterable providing <a class="reference internal" href="pypath.core.evidence.Evidence.html#pypath.core.evidence.Evidence" title="pypath.core.evidence.Evidence"><code class="xref py py-class docutils literal notranslate"><span class="pre">Evidence</span></code></a> instances. It is possible
+to create an empty evidence collection and populate it later or to
+show this way that certain relationship has no supporting evidences.</p>
+</dd>
+</dl>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.evidence.Evidences.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">evidences</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/evidence.html#Evidences.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.evidence.Evidences.__init__" title="Link to this definition">§</a></dt>
+<dd></dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.evidence.Evidences.__init__" title="pypath.core.evidence.Evidences.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>([evidences])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.evidence.Evidences.asdict" title="pypath.core.evidence.Evidences.asdict"><code class="xref py py-obj docutils literal notranslate"><span class="pre">asdict</span></code></a>()</p></td>
+<td><p>Evidence set as a list of dictionaries.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">contains_database</span></code>(database, **kwargs)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">contains_reference</span></code>(reference, **kwargs)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_curation_effort</span></code>(**kwargs)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_references</span></code>(**kwargs)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_resources</span></code>(**kwargs)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">filter</span></code>([resource, data_model, ...])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_curation_effort</span></code>(**kwargs)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_data_models</span></code>(**kwargs)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_datasets</span></code>(**kwargs)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_interaction_types</span></code>(**kwargs)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_references</span></code>(**kwargs)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_resource_names</span></code>(**kwargs)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_resource_names_via</span></code>(**kwargs)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_resources</span></code>(**kwargs)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_resources_via</span></code>(**kwargs)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_data_model</span></code>(data_model, **kwargs)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_database_via</span></code>(database, via, **kwargs)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.evidence.Evidences.has_dataset" title="pypath.core.evidence.Evidences.has_dataset"><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_dataset</span></code></a>(dataset, **kwargs)</p></td>
+<td><p>Contains evidence(s) from a given dataset meeting the criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.evidence.Evidences.has_interaction_type" title="pypath.core.evidence.Evidences.has_interaction_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_interaction_type</span></code></a>(interaction_type[, ...])</p></td>
+<td><p>If <code class="docutils literal notranslate"><span class="pre">via</span></code> is <code class="docutils literal notranslate"><span class="pre">False</span></code> then it will be ignored, otherwise if <code class="docutils literal notranslate"><span class="pre">None</span></code> only primary resources are considered.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">intersection</span></code>(other)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.evidence.Evidences.items" title="pypath.core.evidence.Evidences.items"><code class="xref py py-obj docutils literal notranslate"><span class="pre">items</span></code></a>()</p></td>
+<td><p>Returns</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.evidence.Evidences.keys" title="pypath.core.evidence.Evidences.keys"><code class="xref py py-obj docutils literal notranslate"><span class="pre">keys</span></code></a>()</p></td>
+<td><p>Returns</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">match</span></code>([resource, data_model, ...])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.evidence.Evidences.reload" title="pypath.core.evidence.Evidences.reload"><code class="xref py py-obj docutils literal notranslate"><span class="pre">reload</span></code></a>()</p></td>
+<td><p>Reloads the object from the module level.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">remove</span></code>([resource, interaction_type, via])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.evidence.Evidences.serialize_attrs" title="pypath.core.evidence.Evidences.serialize_attrs"><code class="xref py py-obj docutils literal notranslate"><span class="pre">serialize_attrs</span></code></a>([top_key_prefix])</p></td>
+<td><p>Serialize the extra attributes of the evidences as a JSON string.</p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Attributes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">evidences</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.evidence.Evidences.attrs" title="pypath.core.evidence.Evidences.attrs"><code class="xref py py-obj docutils literal notranslate"><span class="pre">attrs</span></code></a></p></td>
+<td><p>Combines the custom attributes from all evidences within this set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.evidence.Evidences.datasets" title="pypath.core.evidence.Evidences.datasets"><code class="xref py py-obj docutils literal notranslate"><span class="pre">datasets</span></code></a></p></td>
+<td><p>Datasets in this evidence set.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.evidence.Evidences.simple_dict" title="pypath.core.evidence.Evidences.simple_dict"><code class="xref py py-obj docutils literal notranslate"><span class="pre">simple_dict</span></code></a></p></td>
+<td><p>Returns Keys are resource labels, values are <code class="docutils literal notranslate"><span class="pre">Evidence</span></code> objects.</p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.evidence.Evidences.asdict">
+<span class="sig-name descname"><span class="pre">asdict</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">dict</span><span class="p"><span class="pre">]</span></span></span></span><a class="reference internal" href="../_modules/pypath/core/evidence.html#Evidences.asdict"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.evidence.Evidences.asdict" title="Link to this definition">§</a></dt>
+<dd><p>Evidence set as a list of dictionaries.</p>
+</dd></dl>
+
+<dl class="py property">
+<dt class="sig sig-object py" id="pypath.core.evidence.Evidences.attrs">
+<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">attrs</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">dict</span></em><a class="headerlink" href="#pypath.core.evidence.Evidences.attrs" title="Link to this definition">§</a></dt>
+<dd><p>Combines the custom attributes from all evidences within this set.</p>
+</dd></dl>
+
+<dl class="py property">
+<dt class="sig sig-object py" id="pypath.core.evidence.Evidences.datasets">
+<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">datasets</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">set</span></em><a class="headerlink" href="#pypath.core.evidence.Evidences.datasets" title="Link to this definition">§</a></dt>
+<dd><p>Datasets in this evidence set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.evidence.Evidences.has_dataset">
+<span class="sig-name descname"><span class="pre">has_dataset</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">dataset</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><span class="pre">bool</span></span></span><a class="reference internal" href="../_modules/pypath/core/evidence.html#Evidences.has_dataset"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.evidence.Evidences.has_dataset" title="Link to this definition">§</a></dt>
+<dd><p>Contains evidence(s) from a given dataset meeting the criteria.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>dataset</strong> – Name of the dataset.</p></li>
+<li><p><strong>kwargs</strong> – Filtering criteria for evidences.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.evidence.Evidences.has_interaction_type">
+<span class="sig-name descname"><span class="pre">has_interaction_type</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">database</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/evidence.html#Evidences.has_interaction_type"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.evidence.Evidences.has_interaction_type" title="Link to this definition">§</a></dt>
+<dd><p>If <code class="docutils literal notranslate"><span class="pre">via</span></code> is <code class="docutils literal notranslate"><span class="pre">False</span></code> then it will be ignored, otherwise if <code class="docutils literal notranslate"><span class="pre">None</span></code>
+only primary resources are considered.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.evidence.Evidences.items">
+<span class="sig-name descname"><span class="pre">items</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/evidence.html#Evidences.items"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.evidence.Evidences.items" title="Link to this definition">§</a></dt>
+<dd><dl class="simple">
+<dt>Returns</dt><dd><dl class="simple">
+<dt>(dict_items): The evidences as a mapping, with</dt><dd><p><a class="reference internal" href="pypath.internals.resource.NetworkResourceKey.html#pypath.internals.resource.NetworkResourceKey" title="pypath.internals.resource.NetworkResourceKey"><code class="xref py py-class docutils literal notranslate"><span class="pre">pypath.internals.resource.NetworkResourceKey</span></code></a>
+objects as keys and <a class="reference internal" href="pypath.core.evidence.Evidence.html#pypath.core.evidence.Evidence" title="pypath.core.evidence.Evidence"><code class="xref py py-class docutils literal notranslate"><span class="pre">pypath.core.evidence.Evidence</span></code></a>
+objects as values.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.evidence.Evidences.keys">
+<span class="sig-name descname"><span class="pre">keys</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/evidence.html#Evidences.keys"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.evidence.Evidences.keys" title="Link to this definition">§</a></dt>
+<dd><dl class="simple">
+<dt>Returns</dt><dd><dl class="simple">
+<dt>(dict_keys): The keys of this dictionary are</dt><dd><p><a class="reference internal" href="pypath.internals.resource.NetworkResourceKey.html#pypath.internals.resource.NetworkResourceKey" title="pypath.internals.resource.NetworkResourceKey"><code class="xref py py-class docutils literal notranslate"><span class="pre">pypath.internals.resource.NetworkResourceKey</span></code></a>
+objects.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.evidence.Evidences.reload">
+<span class="sig-name descname"><span class="pre">reload</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/evidence.html#Evidences.reload"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.evidence.Evidences.reload" title="Link to this definition">§</a></dt>
+<dd><p>Reloads the object from the module level.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.evidence.Evidences.serialize_attrs">
+<span class="sig-name descname"><span class="pre">serialize_attrs</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">top_key_prefix</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><span class="pre">str</span></span></span><a class="reference internal" href="../_modules/pypath/core/evidence.html#Evidences.serialize_attrs"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.evidence.Evidences.serialize_attrs" title="Link to this definition">§</a></dt>
+<dd><p>Serialize the extra attributes of the evidences as a JSON string.</p>
+<dl class="simple">
+<dt>Returns</dt><dd><p>A JSON serialized string with the evidences from each resource.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py property">
+<dt class="sig sig-object py" id="pypath.core.evidence.Evidences.simple_dict">
+<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">simple_dict</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><a class="reference internal" href="pypath.core.evidence.Evidence.html#pypath.core.evidence.Evidence" title="pypath.core.evidence.Evidence"><span class="pre">evidence.Evidence</span></a><span class="p"><span class="pre">]</span></span></em><a class="headerlink" href="#pypath.core.evidence.Evidences.simple_dict" title="Link to this definition">§</a></dt>
+<dd><p>Returns
+Keys are resource labels, values are <code class="docutils literal notranslate"><span class="pre">Evidence</span></code> objects.</p>
+</dd></dl>
+
+</dd></dl>
+
+</section>
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+  </ul>
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+</div>
+      
+    </div>
+  
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+</div>
+              
+              
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+<div id="searchbox"></div>
+                <article class="bd-article">
+                  
+  <section id="module-pypath.core.evidence">
+<span id="pypath-core-evidence"></span><h1>pypath.core.evidence<a class="headerlink" href="#module-pypath.core.evidence" title="Link to this heading">§</a></h1>
+<p>Provides classes for representing and processing evidences supporting
+relationships. The evidences hold information about the databases and
+literature references, they can be organized into collections. A number
+of operations are available on evidences and their collections, for
+example they can be combined or filtered.</p>
+<dl class="field-list simple">
+<dt class="field-odd">members<span class="colon">:</span></dt>
+<dd class="field-odd"><p></p></dd>
+</dl>
+<p class="rubric">Classes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.core.evidence.Evidence.html#pypath.core.evidence.Evidence" title="pypath.core.evidence.Evidence"><code class="xref py py-obj docutils literal notranslate"><span class="pre">Evidence</span></code></a>(resource[, references, attrs])</p></td>
+<td><p>Represents an evidence supporting a relationship such as molecular interaction, molecular complex, enzyme-PTM interaction, annotation, etc.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.core.evidence.Evidences.html#pypath.core.evidence.Evidences" title="pypath.core.evidence.Evidences"><code class="xref py py-obj docutils literal notranslate"><span class="pre">Evidences</span></code></a>([evidences])</p></td>
+<td><p>A collection of evidences.</p></td>
+</tr>
+</tbody>
+</table>
+</section>
+
+
+                </article>
+              
+              
+              
+              
+              
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+<li class="toctree-l1 toc-h1 nav-item toc-entry"><a class="reference internal nav-link" href="../webservice.html">Webservice</a></li>
+<li class="toctree-l1 toc-h1 nav-item toc-entry"><a class="reference internal nav-link" href="../releasehistory.html">Release history</a></li>
+<li class="toctree-l1 toc-h1 nav-item toc-entry"><a class="reference internal nav-link" href="../reference.html">Reference</a></li>
+<li class="toctree-l1 toc-h1 nav-item toc-entry"><a class="reference internal nav-link" href="../notebooks/manual.html">The pypath book</a></li>
+</ul>
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\ No newline at end of file
diff --git a/api/pypath.core.html b/api/pypath.core.html
index cb92adb60..e1eb6c3ef 100644
--- a/api/pypath.core.html
+++ b/api/pypath.core.html
@@ -47,7 +47,7 @@
     <link rel="icon" href="../_static/omnipath-logo.svg"/>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
-    <link rel="next" title="pypath.core.attrs" href="pypath.core.attrs.html" />
+    <link rel="next" title="pypath.core.annot" href="pypath.core.annot.html" />
     <link rel="prev" title="pypath.log" href="pypath.log.html" />
   <meta name="viewport" content="width=device-width, initial-scale=1"/>
   <meta name="docsearch:language" content="en"/>
@@ -519,12 +519,39 @@
 <p class="rubric">Modules</p>
 <table class="autosummary longtable table autosummary">
 <tbody>
-<tr class="row-odd"><td><p><a class="reference internal" href="pypath.core.attrs.html#module-pypath.core.attrs" title="pypath.core.attrs"><code class="xref py py-obj docutils literal notranslate"><span class="pre">pypath.core.attrs</span></code></a></p></td>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.core.annot.html#module-pypath.core.annot" title="pypath.core.annot"><code class="xref py py-obj docutils literal notranslate"><span class="pre">pypath.core.annot</span></code></a></p></td>
 <td><p></p></td>
 </tr>
-<tr class="row-even"><td><p><a class="reference internal" href="pypath.core.common.html#module-pypath.core.common" title="pypath.core.common"><code class="xref py py-obj docutils literal notranslate"><span class="pre">pypath.core.common</span></code></a></p></td>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.core.attrs.html#module-pypath.core.attrs" title="pypath.core.attrs"><code class="xref py py-obj docutils literal notranslate"><span class="pre">pypath.core.attrs</span></code></a></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.core.common.html#module-pypath.core.common" title="pypath.core.common"><code class="xref py py-obj docutils literal notranslate"><span class="pre">pypath.core.common</span></code></a></p></td>
 <td><p>Methods working on objects from <cite>pypath.core</cite> which might be useful to access without importing the main modules.</p></td>
 </tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.core.complex.html#module-pypath.core.complex" title="pypath.core.complex"><code class="xref py py-obj docutils literal notranslate"><span class="pre">pypath.core.complex</span></code></a></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.core.entity.html#module-pypath.core.entity" title="pypath.core.entity"><code class="xref py py-obj docutils literal notranslate"><span class="pre">pypath.core.entity</span></code></a></p></td>
+<td><p>Provides classes for representing molecular entities and their collections.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.core.enz_sub.html#module-pypath.core.enz_sub" title="pypath.core.enz_sub"><code class="xref py py-obj docutils literal notranslate"><span class="pre">pypath.core.enz_sub</span></code></a></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.core.evidence.html#module-pypath.core.evidence" title="pypath.core.evidence"><code class="xref py py-obj docutils literal notranslate"><span class="pre">pypath.core.evidence</span></code></a></p></td>
+<td><p>Provides classes for representing and processing evidences supporting relationships.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.core.interaction.html#module-pypath.core.interaction" title="pypath.core.interaction"><code class="xref py py-obj docutils literal notranslate"><span class="pre">pypath.core.interaction</span></code></a></p></td>
+<td><p>Here we define one class, the <code class="xref py py-class docutils literal notranslate"><span class="pre">Interaction`</span></code> which provides a rich API for representing and querying molecular interactions.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.core.intercell.html#module-pypath.core.intercell" title="pypath.core.intercell"><code class="xref py py-obj docutils literal notranslate"><span class="pre">pypath.core.intercell</span></code></a></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.core.intercell_annot.html#module-pypath.core.intercell_annot" title="pypath.core.intercell_annot"><code class="xref py py-obj docutils literal notranslate"><span class="pre">pypath.core.intercell_annot</span></code></a></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.core.network.html#module-pypath.core.network" title="pypath.core.network"><code class="xref py py-obj docutils literal notranslate"><span class="pre">pypath.core.network</span></code></a></p></td>
+<td><p></p></td>
+</tr>
 </tbody>
 </table>
 </section>
@@ -549,11 +576,11 @@
       </div>
     </a>
     <a class="right-next"
-       href="pypath.core.attrs.html"
+       href="pypath.core.annot.html"
        title="next page">
       <div class="prev-next-info">
         <p class="prev-next-subtitle">next</p>
-        <p class="prev-next-title">pypath.core.attrs</p>
+        <p class="prev-next-title">pypath.core.annot</p>
       </div>
       <i class="fa-solid fa-angle-right"></i>
     </a>
diff --git a/api/pypath.core.interaction.Interaction.html b/api/pypath.core.interaction.Interaction.html
new file mode 100644
index 000000000..6d37ba92a
--- /dev/null
+++ b/api/pypath.core.interaction.Interaction.html
@@ -0,0 +1,10401 @@
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+
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+
+    <title>pypath.core.interaction.Interaction &#8212; pypath 0.16.9 documentation</title>
+  
+  
+  
+  <script data-cfasync="false">
+    document.documentElement.dataset.mode = localStorage.getItem("mode") || "";
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+    <script>DOCUMENTATION_OPTIONS.pagename = 'api/pypath.core.interaction.Interaction';</script>
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+  <section id="pypath-core-interaction-interaction">
+<h1>pypath.core.interaction.Interaction<a class="headerlink" href="#pypath-core-interaction-interaction" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.core.interaction.</span></span><span class="sig-name descname"><span class="pre">Interaction</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">a</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">b</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">id_type_a</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'uniprot'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">id_type_b</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'uniprot'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type_a</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'protein'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type_b</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'protein'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">taxon_a</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">taxon_b</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">attrs</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/interaction.html#Interaction"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.interaction.Interaction" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <a class="reference internal" href="pypath.core.attrs.AttributeHandler.html#pypath.core.attrs.AttributeHandler" title="pypath.core.attrs.AttributeHandler"><code class="xref py py-class docutils literal notranslate"><span class="pre">AttributeHandler</span></code></a></p>
+<p>Represents a unique pair of molecular entities interacting with each
+other. One <a class="reference internal" href="#pypath.core.interaction.Interaction" title="pypath.core.interaction.Interaction"><code class="xref py py-class docutils literal notranslate"><span class="pre">Interaction</span></code></a> object might represent multiple
+interactions i.e. with different direction or effect or type (e.g.
+transcriptional regulation and post-translational regulation),
+each supported by different evidences.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>a</strong><strong>,</strong><strong>b</strong> (<em>str</em><em>,</em><em>pypath.entity.Entity</em>) – The two interacting partners. If an <code class="xref py py-class docutils literal notranslate"><span class="pre">pypath.entity.Entity</span></code>
+objects provided the other attributes (entity_type, id_type, taxon)
+will be ignored.</p></li>
+<li><p><strong>id_type_a</strong><strong>,</strong><strong>id_type_b</strong> (<em>str</em>) – The identifier types for partner <code class="docutils literal notranslate"><span class="pre">a</span></code> and <code class="docutils literal notranslate"><span class="pre">b</span></code> e.g. <code class="docutils literal notranslate"><span class="pre">'uniprot'</span></code>.</p></li>
+<li><p><strong>entity_type_a</strong><strong>,</strong><strong>entity_type_b</strong> (<em>str</em>) – The types of the molecular entities <code class="docutils literal notranslate"><span class="pre">a</span></code> and <code class="docutils literal notranslate"><span class="pre">b</span></code>
+e.g. <code class="docutils literal notranslate"><span class="pre">'protein'</span></code>.</p></li>
+<li><p><strong>taxon_a</strong><strong>,</strong><strong>taxon_b</strong> (<em>int</em>) – The NCBI Taxonomy Identifiers of partner <code class="docutils literal notranslate"><span class="pre">a</span></code> and <code class="docutils literal notranslate"><span class="pre">b</span></code>
+e.g. <code class="docutils literal notranslate"><span class="pre">9606</span></code> for human.</p></li>
+</ul>
+</dd>
+<dt class="field-even">Details<span class="colon">:</span></dt>
+<dd class="field-even"><p>The arguments <code class="docutils literal notranslate"><span class="pre">a</span></code> and <code class="docutils literal notranslate"><span class="pre">b</span></code> will be assigned to the attribute <code class="docutils literal notranslate"><span class="pre">a</span></code>
+and <code class="docutils literal notranslate"><span class="pre">b</span></code> in an alphabetical order, hence it’s possible that
+argument <code class="docutils literal notranslate"><span class="pre">a</span></code> becomes attribute <code class="docutils literal notranslate"><span class="pre">b</span></code>.</p>
+</dd>
+</dl>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">a</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">b</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">id_type_a</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'uniprot'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">id_type_b</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'uniprot'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type_a</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'protein'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type_b</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'protein'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">taxon_a</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">taxon_b</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">attrs</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/interaction.html#Interaction.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.interaction.Interaction.__init__" title="Link to this definition">§</a></dt>
+<dd></dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.__init__" title="pypath.core.interaction.Interaction.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>(a, b[, id_type_a, id_type_b, ...])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.add_evidence" title="pypath.core.interaction.Interaction.add_evidence"><code class="xref py py-obj docutils literal notranslate"><span class="pre">add_evidence</span></code></a>(evidence[, direction, effect, ...])</p></td>
+<td><p>Adds directionality information with the corresponding data source named.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.add_sign" title="pypath.core.interaction.Interaction.add_sign"><code class="xref py py-obj docutils literal notranslate"><span class="pre">add_sign</span></code></a>(direction, sign[, resource, ...])</p></td>
+<td><p>Sets sign and source information on a given direction of the edge.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.asdict" title="pypath.core.interaction.Interaction.asdict"><code class="xref py py-obj docutils literal notranslate"><span class="pre">asdict</span></code></a>(direction)</p></td>
+<td><p>Dictionary representation of the evidences.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.complex_identifiers_by_data_model" title="pypath.core.interaction.Interaction.complex_identifiers_by_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">complex_identifiers_by_data_model</span></code></a>([effect, ...])</p></td>
+<td><p>Retrieves the entities involved in interactions matching the criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.complex_identifiers_by_interaction_type" title="pypath.core.interaction.Interaction.complex_identifiers_by_interaction_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">complex_identifiers_by_interaction_type</span></code></a>([...])</p></td>
+<td><p>Retrieves the entities involved in interactions matching the criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.complex_identifiers_by_interaction_type_and_data_model" title="pypath.core.interaction.Interaction.complex_identifiers_by_interaction_type_and_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">complex_identifiers_by_interaction_type_and_data_model</span></code></a>([...])</p></td>
+<td><p>Retrieves the entities involved in interactions matching the criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.complex_identifiers_by_interaction_type_and_data_model_and_resource" title="pypath.core.interaction.Interaction.complex_identifiers_by_interaction_type_and_data_model_and_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">complex_identifiers_by_interaction_type_and_data_model_and_resource</span></code></a>([...])</p></td>
+<td><p>Retrieves the entities involved in interactions matching the criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.complex_identifiers_by_reference" title="pypath.core.interaction.Interaction.complex_identifiers_by_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">complex_identifiers_by_reference</span></code></a>([effect, ...])</p></td>
+<td><p>Retrieves the entities involved in interactions matching the criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.complex_identifiers_by_resource" title="pypath.core.interaction.Interaction.complex_identifiers_by_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">complex_identifiers_by_resource</span></code></a>([effect, ...])</p></td>
+<td><p>Retrieves the entities involved in interactions matching the criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.complex_labels_by_data_model" title="pypath.core.interaction.Interaction.complex_labels_by_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">complex_labels_by_data_model</span></code></a>([effect, ...])</p></td>
+<td><p>Retrieves the entities involved in interactions matching the criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.complex_labels_by_interaction_type" title="pypath.core.interaction.Interaction.complex_labels_by_interaction_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">complex_labels_by_interaction_type</span></code></a>([effect, ...])</p></td>
+<td><p>Retrieves the entities involved in interactions matching the criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.complex_labels_by_interaction_type_and_data_model" title="pypath.core.interaction.Interaction.complex_labels_by_interaction_type_and_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">complex_labels_by_interaction_type_and_data_model</span></code></a>([...])</p></td>
+<td><p>Retrieves the entities involved in interactions matching the criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.complex_labels_by_interaction_type_and_data_model_and_resource" title="pypath.core.interaction.Interaction.complex_labels_by_interaction_type_and_data_model_and_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">complex_labels_by_interaction_type_and_data_model_and_resource</span></code></a>([...])</p></td>
+<td><p>Retrieves the entities involved in interactions matching the criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.complex_labels_by_reference" title="pypath.core.interaction.Interaction.complex_labels_by_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">complex_labels_by_reference</span></code></a>([effect, ...])</p></td>
+<td><p>Retrieves the entities involved in interactions matching the criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.complex_labels_by_resource" title="pypath.core.interaction.Interaction.complex_labels_by_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">complex_labels_by_resource</span></code></a>([effect, ...])</p></td>
+<td><p>Retrieves the entities involved in interactions matching the criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.complexes_by_data_model" title="pypath.core.interaction.Interaction.complexes_by_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">complexes_by_data_model</span></code></a>([effect, resources, ...])</p></td>
+<td><p>Retrieves the entities involved in interactions matching the criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.complexes_by_interaction_type" title="pypath.core.interaction.Interaction.complexes_by_interaction_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">complexes_by_interaction_type</span></code></a>([effect, ...])</p></td>
+<td><p>Retrieves the entities involved in interactions matching the criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.complexes_by_interaction_type_and_data_model" title="pypath.core.interaction.Interaction.complexes_by_interaction_type_and_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">complexes_by_interaction_type_and_data_model</span></code></a>([...])</p></td>
+<td><p>Retrieves the entities involved in interactions matching the criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.complexes_by_interaction_type_and_data_model_and_resource" title="pypath.core.interaction.Interaction.complexes_by_interaction_type_and_data_model_and_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">complexes_by_interaction_type_and_data_model_and_resource</span></code></a>([...])</p></td>
+<td><p>Retrieves the entities involved in interactions matching the criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.complexes_by_reference" title="pypath.core.interaction.Interaction.complexes_by_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">complexes_by_reference</span></code></a>([effect, resources, ...])</p></td>
+<td><p>Retrieves the entities involved in interactions matching the criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.complexes_by_resource" title="pypath.core.interaction.Interaction.complexes_by_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">complexes_by_resource</span></code></a>([effect, resources, ...])</p></td>
+<td><p>Retrieves the entities involved in interactions matching the criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.consensus" title="pypath.core.interaction.Interaction.consensus"><code class="xref py py-obj docutils literal notranslate"><span class="pre">consensus</span></code></a>([only_interaction_type, ...])</p></td>
+<td><p>Infers the consensus edge(s) according to the number of supporting sources.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.consensus_edges" title="pypath.core.interaction.Interaction.consensus_edges"><code class="xref py py-obj docutils literal notranslate"><span class="pre">consensus_edges</span></code></a>([only_interaction_type, ...])</p></td>
+<td><p>Infers the consensus edge(s) according to the number of supporting sources.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.count_complex_identifiers" title="pypath.core.interaction.Interaction.count_complex_identifiers"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_complex_identifiers</span></code></a>([effect, ...])</p></td>
+<td><p>Retrieves the entities involved in interactions matching the criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.count_complex_labels" title="pypath.core.interaction.Interaction.count_complex_labels"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_complex_labels</span></code></a>([effect, resources, ...])</p></td>
+<td><p>Retrieves the entities involved in interactions matching the criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.count_complexes" title="pypath.core.interaction.Interaction.count_complexes"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_complexes</span></code></a>([effect, resources, ...])</p></td>
+<td><p>Retrieves the entities involved in interactions matching the criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_curation_effort</span></code>([effect, resources, ...])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.count_entities" title="pypath.core.interaction.Interaction.count_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_entities</span></code></a>([effect, resources, ...])</p></td>
+<td><p>Retrieves the entities involved in interactions matching the criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.count_identifiers" title="pypath.core.interaction.Interaction.count_identifiers"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_identifiers</span></code></a>([effect, resources, ...])</p></td>
+<td><p>Retrieves the entities involved in interactions matching the criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.count_interactions" title="pypath.core.interaction.Interaction.count_interactions"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_interactions</span></code></a>([effect, resources, ...])</p></td>
+<td><p>Returns one or two tuples of the interacting partners: one if only one direction, two if both directions match the query criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.count_interactions_0" title="pypath.core.interaction.Interaction.count_interactions_0"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_interactions_0</span></code></a>([effect, resources, ...])</p></td>
+<td><p>Returns unique interacting pairs without being aware of the direction.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.count_interactions_directed" title="pypath.core.interaction.Interaction.count_interactions_directed"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_interactions_directed</span></code></a>([effect, ...])</p></td>
+<td><p>Args</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.count_interactions_mutual" title="pypath.core.interaction.Interaction.count_interactions_mutual"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_interactions_mutual</span></code></a>(**kwargs)</p></td>
+<td><p>Note: undirected interactions does not count as mutual but only interactions with explicit direction information for both directions.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.count_interactions_negative" title="pypath.core.interaction.Interaction.count_interactions_negative"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_interactions_negative</span></code></a>([effect, ...])</p></td>
+<td><p>Args</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.count_interactions_non_directed" title="pypath.core.interaction.Interaction.count_interactions_non_directed"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_interactions_non_directed</span></code></a>(**kwargs)</p></td>
+<td><p>Returns <cite>True</cite> if any resource annotates this interaction without and no resource with direction.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.count_interactions_positive" title="pypath.core.interaction.Interaction.count_interactions_positive"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_interactions_positive</span></code></a>([effect, ...])</p></td>
+<td><p>Args</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.count_interactions_signed" title="pypath.core.interaction.Interaction.count_interactions_signed"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_interactions_signed</span></code></a>([effect, ...])</p></td>
+<td><p>Args</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.count_interactions_undirected" title="pypath.core.interaction.Interaction.count_interactions_undirected"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_interactions_undirected</span></code></a>(**kwargs)</p></td>
+<td><p>Returns <cite>True</cite> if any resource annotates this interaction without direction.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.count_labels" title="pypath.core.interaction.Interaction.count_labels"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_labels</span></code></a>([effect, resources, ...])</p></td>
+<td><p>Retrieves the entities involved in interactions matching the criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.count_lncrna_identifiers" title="pypath.core.interaction.Interaction.count_lncrna_identifiers"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_lncrna_identifiers</span></code></a>([effect, ...])</p></td>
+<td><p>Retrieves the entities involved in interactions matching the criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.count_lncrna_labels" title="pypath.core.interaction.Interaction.count_lncrna_labels"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_lncrna_labels</span></code></a>([effect, resources, ...])</p></td>
+<td><p>Retrieves the entities involved in interactions matching the criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.count_lncrnas" title="pypath.core.interaction.Interaction.count_lncrnas"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_lncrnas</span></code></a>([effect, resources, ...])</p></td>
+<td><p>Retrieves the entities involved in interactions matching the criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.count_mirna_identifiers" title="pypath.core.interaction.Interaction.count_mirna_identifiers"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_mirna_identifiers</span></code></a>([effect, resources, ...])</p></td>
+<td><p>Retrieves the entities involved in interactions matching the criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.count_mirna_labels" title="pypath.core.interaction.Interaction.count_mirna_labels"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_mirna_labels</span></code></a>([effect, resources, ...])</p></td>
+<td><p>Retrieves the entities involved in interactions matching the criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.count_mirnas" title="pypath.core.interaction.Interaction.count_mirnas"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_mirnas</span></code></a>([effect, resources, ...])</p></td>
+<td><p>Retrieves the entities involved in interactions matching the criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.count_protein_identifiers" title="pypath.core.interaction.Interaction.count_protein_identifiers"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_protein_identifiers</span></code></a>([effect, ...])</p></td>
+<td><p>Retrieves the entities involved in interactions matching the criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.count_protein_labels" title="pypath.core.interaction.Interaction.count_protein_labels"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_protein_labels</span></code></a>([effect, resources, ...])</p></td>
+<td><p>Retrieves the entities involved in interactions matching the criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.count_proteins" title="pypath.core.interaction.Interaction.count_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_proteins</span></code></a>([effect, resources, ...])</p></td>
+<td><p>Retrieves the entities involved in interactions matching the criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.count_small_molecule_identifiers" title="pypath.core.interaction.Interaction.count_small_molecule_identifiers"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_small_molecule_identifiers</span></code></a>([effect, ...])</p></td>
+<td><p>Retrieves the entities involved in interactions matching the criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.count_small_molecule_labels" title="pypath.core.interaction.Interaction.count_small_molecule_labels"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_small_molecule_labels</span></code></a>([effect, ...])</p></td>
+<td><p>Retrieves the entities involved in interactions matching the criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.count_small_molecules" title="pypath.core.interaction.Interaction.count_small_molecules"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_small_molecules</span></code></a>([effect, resources, ...])</p></td>
+<td><p>Retrieves the entities involved in interactions matching the criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">curation_effort_by_data_model</span></code>([effect, ...])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">curation_effort_by_interaction_type</span></code>([...])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">curation_effort_by_interaction_type_and_data_model</span></code>([...])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">curation_effort_by_interaction_type_and_data_model_and_resource</span></code>([...])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">curation_effort_by_reference</span></code>([effect, ...])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">curation_effort_by_resource</span></code>([effect, ...])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.direction_key" title="pypath.core.interaction.Interaction.direction_key"><code class="xref py py-obj docutils literal notranslate"><span class="pre">direction_key</span></code></a>(direction)</p></td>
+<td><p>The direction keys are tuples of <cite>Entity</cite> objects; this method creates these tuples from a tuple of strings.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">direction_key_identifiers</span></code>(direction)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.dorothea_level" title="pypath.core.interaction.Interaction.dorothea_level"><code class="xref py py-obj docutils literal notranslate"><span class="pre">dorothea_level</span></code></a>(direction)</p></td>
+<td><p>DoRothEA confidence level for one direction as a single letter.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.dorothea_levels" title="pypath.core.interaction.Interaction.dorothea_levels"><code class="xref py py-obj docutils literal notranslate"><span class="pre">dorothea_levels</span></code></a>([direction])</p></td>
+<td><p>Retrieves the DoRothEA confidence levels.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.entities_by_data_model" title="pypath.core.interaction.Interaction.entities_by_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">entities_by_data_model</span></code></a>([effect, resources, ...])</p></td>
+<td><p>Retrieves the entities involved in interactions matching the criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.entities_by_interaction_type" title="pypath.core.interaction.Interaction.entities_by_interaction_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">entities_by_interaction_type</span></code></a>([effect, ...])</p></td>
+<td><p>Retrieves the entities involved in interactions matching the criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.entities_by_interaction_type_and_data_model" title="pypath.core.interaction.Interaction.entities_by_interaction_type_and_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">entities_by_interaction_type_and_data_model</span></code></a>([...])</p></td>
+<td><p>Retrieves the entities involved in interactions matching the criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.entities_by_interaction_type_and_data_model_and_resource" title="pypath.core.interaction.Interaction.entities_by_interaction_type_and_data_model_and_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">entities_by_interaction_type_and_data_model_and_resource</span></code></a>([...])</p></td>
+<td><p>Retrieves the entities involved in interactions matching the criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.entities_by_reference" title="pypath.core.interaction.Interaction.entities_by_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">entities_by_reference</span></code></a>([effect, resources, ...])</p></td>
+<td><p>Retrieves the entities involved in interactions matching the criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.entities_by_resource" title="pypath.core.interaction.Interaction.entities_by_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">entities_by_resource</span></code></a>([effect, resources, ...])</p></td>
+<td><p>Retrieves the entities involved in interactions matching the criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.evaluate_evidences" title="pypath.core.interaction.Interaction.evaluate_evidences"><code class="xref py py-obj docutils literal notranslate"><span class="pre">evaluate_evidences</span></code></a>(this_direction[, ...])</p></td>
+<td><p>Selects the evidence collections matching the direction and effect criteria and then evaluates if any of the evidences in these collections match the evidence criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">evidences_by_data_model</span></code>([effect, resources, ...])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">evidences_by_interaction_type</span></code>([effect, ...])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">evidences_by_interaction_type_and_data_model</span></code>([...])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">evidences_by_interaction_type_and_data_model_and_resource</span></code>([...])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">evidences_by_reference</span></code>([effect, resources, ...])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">evidences_by_resource</span></code>([effect, resources, ...])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.generate_df_records" title="pypath.core.interaction.Interaction.generate_df_records"><code class="xref py py-obj docutils literal notranslate"><span class="pre">generate_df_records</span></code></a>([by_source, with_references])</p></td>
+<td><p>Yields interaction records.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.get_attr" title="pypath.core.interaction.Interaction.get_attr"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_attr</span></code></a>(resource, key[, direction])</p></td>
+<td><p>Extracts the values of one specific attribute.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.get_complex_identifiers" title="pypath.core.interaction.Interaction.get_complex_identifiers"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_complex_identifiers</span></code></a>([entity_type, ...])</p></td>
+<td><p>Retrieves the entities involved in interactions matching the criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.get_complex_labels" title="pypath.core.interaction.Interaction.get_complex_labels"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_complex_labels</span></code></a>([entity_type, direction, ...])</p></td>
+<td><p>Retrieves the entities involved in interactions matching the criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.get_complexes" title="pypath.core.interaction.Interaction.get_complexes"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_complexes</span></code></a>([entity_type, direction, ...])</p></td>
+<td><p>Retrieves the entities involved in interactions matching the criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_curation_effort</span></code>(**kwargs)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.get_degrees" title="pypath.core.interaction.Interaction.get_degrees"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_degrees</span></code></a>(mode[, direction, effect, ...])</p></td>
+<td><p>Returns a <em>set</em> of nodes with the connections matching the direction, effect and evidence criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.get_direction" title="pypath.core.interaction.Interaction.get_direction"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_direction</span></code></a>(direction[, resources, ...])</p></td>
+<td><p>Returns the state (or <em>resources</em> if specified) of the given <em>direction</em>.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.get_directions" title="pypath.core.interaction.Interaction.get_directions"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_directions</span></code></a>(src, tgt[, resources, ...])</p></td>
+<td><p>Returns all directions with boolean values or list of sources.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.get_entities" title="pypath.core.interaction.Interaction.get_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_entities</span></code></a>([entity_type, direction, ...])</p></td>
+<td><p>Retrieves the entities involved in interactions matching the criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_evidences</span></code>([direction, effect, ...])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.get_identifiers" title="pypath.core.interaction.Interaction.get_identifiers"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_identifiers</span></code></a>([entity_type, direction, ...])</p></td>
+<td><p>Retrieves the entities involved in interactions matching the criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.get_interactions" title="pypath.core.interaction.Interaction.get_interactions"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_interactions</span></code></a>([direction, effect, ...])</p></td>
+<td><p>Returns one or two tuples of the interacting partners: one if only one direction, two if both directions match the query criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.get_interactions_0" title="pypath.core.interaction.Interaction.get_interactions_0"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_interactions_0</span></code></a>(**kwargs)</p></td>
+<td><p>Returns unique interacting pairs without being aware of the direction.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.get_interactions_directed" title="pypath.core.interaction.Interaction.get_interactions_directed"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_interactions_directed</span></code></a>(**kwargs)</p></td>
+<td><p>Args</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.get_interactions_mutual" title="pypath.core.interaction.Interaction.get_interactions_mutual"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_interactions_mutual</span></code></a>(**kwargs)</p></td>
+<td><p>Note: undirected interactions does not count as mutual but only interactions with explicit direction information for both directions.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.get_interactions_negative" title="pypath.core.interaction.Interaction.get_interactions_negative"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_interactions_negative</span></code></a>(**kwargs)</p></td>
+<td><p>Args</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.get_interactions_non_directed" title="pypath.core.interaction.Interaction.get_interactions_non_directed"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_interactions_non_directed</span></code></a>(**kwargs)</p></td>
+<td><p>Only the undirected interactions will be considered, if any resource annotates this interaction as undirected both directions will be returned, but only if no resource provide direction.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.get_interactions_non_directed_0" title="pypath.core.interaction.Interaction.get_interactions_non_directed_0"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_interactions_non_directed_0</span></code></a>(**kwargs)</p></td>
+<td><p>Only the undirected interactions will be considered, if any resource annotates this interaction as undirected and none as directed, the interacting pair as a sorted tuple will be returned inside a one element tuple.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.get_interactions_positive" title="pypath.core.interaction.Interaction.get_interactions_positive"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_interactions_positive</span></code></a>(**kwargs)</p></td>
+<td><p>Args</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.get_interactions_signed" title="pypath.core.interaction.Interaction.get_interactions_signed"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_interactions_signed</span></code></a>(**kwargs)</p></td>
+<td><p>Args</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.get_interactions_undirected" title="pypath.core.interaction.Interaction.get_interactions_undirected"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_interactions_undirected</span></code></a>(**kwargs)</p></td>
+<td><p>Only the undirected interactions will be considered, if any resource annotates this interaction as undirected both directions will be returned, no matter if certain resources provide direction.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.get_interactions_undirected_0" title="pypath.core.interaction.Interaction.get_interactions_undirected_0"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_interactions_undirected_0</span></code></a>(**kwargs)</p></td>
+<td><p>Only the undirected interactions will be considered, if any resource annotates this interaction as undirected the interacting pair as a sorted tuple will be returned inside a one element tuple.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.get_labels" title="pypath.core.interaction.Interaction.get_labels"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_labels</span></code></a>([entity_type, direction, effect, ...])</p></td>
+<td><p>Retrieves the entities involved in interactions matching the criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.get_lncrna_identifiers" title="pypath.core.interaction.Interaction.get_lncrna_identifiers"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_lncrna_identifiers</span></code></a>([entity_type, ...])</p></td>
+<td><p>Retrieves the entities involved in interactions matching the criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.get_lncrna_labels" title="pypath.core.interaction.Interaction.get_lncrna_labels"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_lncrna_labels</span></code></a>([entity_type, direction, ...])</p></td>
+<td><p>Retrieves the entities involved in interactions matching the criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.get_lncrnas" title="pypath.core.interaction.Interaction.get_lncrnas"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_lncrnas</span></code></a>([entity_type, direction, ...])</p></td>
+<td><p>Retrieves the entities involved in interactions matching the criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.get_mirna_identifiers" title="pypath.core.interaction.Interaction.get_mirna_identifiers"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_mirna_identifiers</span></code></a>([entity_type, ...])</p></td>
+<td><p>Retrieves the entities involved in interactions matching the criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.get_mirna_labels" title="pypath.core.interaction.Interaction.get_mirna_labels"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_mirna_labels</span></code></a>([entity_type, direction, ...])</p></td>
+<td><p>Retrieves the entities involved in interactions matching the criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.get_mirnas" title="pypath.core.interaction.Interaction.get_mirnas"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_mirnas</span></code></a>([entity_type, direction, effect, ...])</p></td>
+<td><p>Retrieves the entities involved in interactions matching the criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.get_protein_identifiers" title="pypath.core.interaction.Interaction.get_protein_identifiers"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_protein_identifiers</span></code></a>([entity_type, ...])</p></td>
+<td><p>Retrieves the entities involved in interactions matching the criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.get_protein_labels" title="pypath.core.interaction.Interaction.get_protein_labels"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_protein_labels</span></code></a>([entity_type, direction, ...])</p></td>
+<td><p>Retrieves the entities involved in interactions matching the criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.get_proteins" title="pypath.core.interaction.Interaction.get_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_proteins</span></code></a>([entity_type, direction, ...])</p></td>
+<td><p>Retrieves the entities involved in interactions matching the criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.get_sign" title="pypath.core.interaction.Interaction.get_sign"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_sign</span></code></a>(direction[, sign, evidences, ...])</p></td>
+<td><p>Retrieves the sign information of the edge in the given diretion.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.get_small_molecule_identifiers" title="pypath.core.interaction.Interaction.get_small_molecule_identifiers"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_small_molecule_identifiers</span></code></a>([...])</p></td>
+<td><p>Retrieves the entities involved in interactions matching the criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.get_small_molecule_labels" title="pypath.core.interaction.Interaction.get_small_molecule_labels"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_small_molecule_labels</span></code></a>([entity_type, ...])</p></td>
+<td><p>Retrieves the entities involved in interactions matching the criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.get_small_molecules" title="pypath.core.interaction.Interaction.get_small_molecules"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_small_molecules</span></code></a>([entity_type, ...])</p></td>
+<td><p>Retrieves the entities involved in interactions matching the criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_data_model</span></code>(data_model)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_dataset</span></code>(dataset[, direction, effect])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.has_sign" title="pypath.core.interaction.Interaction.has_sign"><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_sign</span></code></a>([direction, resources])</p></td>
+<td><p>Checks whether the edge (or for a specific <em>direction</em>) has any signed information (about positive/negative interactions).</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">id_to_entity</span></code>(identifier)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.identifiers_by_data_model" title="pypath.core.interaction.Interaction.identifiers_by_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">identifiers_by_data_model</span></code></a>([effect, ...])</p></td>
+<td><p>Retrieves the entities involved in interactions matching the criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.identifiers_by_interaction_type" title="pypath.core.interaction.Interaction.identifiers_by_interaction_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">identifiers_by_interaction_type</span></code></a>([effect, ...])</p></td>
+<td><p>Retrieves the entities involved in interactions matching the criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.identifiers_by_interaction_type_and_data_model" title="pypath.core.interaction.Interaction.identifiers_by_interaction_type_and_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">identifiers_by_interaction_type_and_data_model</span></code></a>([...])</p></td>
+<td><p>Retrieves the entities involved in interactions matching the criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.identifiers_by_interaction_type_and_data_model_and_resource" title="pypath.core.interaction.Interaction.identifiers_by_interaction_type_and_data_model_and_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">identifiers_by_interaction_type_and_data_model_and_resource</span></code></a>([...])</p></td>
+<td><p>Retrieves the entities involved in interactions matching the criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.identifiers_by_reference" title="pypath.core.interaction.Interaction.identifiers_by_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">identifiers_by_reference</span></code></a>([effect, ...])</p></td>
+<td><p>Retrieves the entities involved in interactions matching the criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.identifiers_by_resource" title="pypath.core.interaction.Interaction.identifiers_by_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">identifiers_by_resource</span></code></a>([effect, resources, ...])</p></td>
+<td><p>Retrieves the entities involved in interactions matching the criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.interactions_0_by_data_model" title="pypath.core.interaction.Interaction.interactions_0_by_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">interactions_0_by_data_model</span></code></a>([effect, ...])</p></td>
+<td><p>Returns unique interacting pairs without being aware of the direction.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.interactions_0_by_interaction_type" title="pypath.core.interaction.Interaction.interactions_0_by_interaction_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">interactions_0_by_interaction_type</span></code></a>([effect, ...])</p></td>
+<td><p>Returns unique interacting pairs without being aware of the direction.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.interactions_0_by_interaction_type_and_data_model" title="pypath.core.interaction.Interaction.interactions_0_by_interaction_type_and_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">interactions_0_by_interaction_type_and_data_model</span></code></a>([...])</p></td>
+<td><p>Returns unique interacting pairs without being aware of the direction.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.interactions_0_by_interaction_type_and_data_model_and_resource" title="pypath.core.interaction.Interaction.interactions_0_by_interaction_type_and_data_model_and_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">interactions_0_by_interaction_type_and_data_model_and_resource</span></code></a>([...])</p></td>
+<td><p>Returns unique interacting pairs without being aware of the direction.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.interactions_0_by_reference" title="pypath.core.interaction.Interaction.interactions_0_by_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">interactions_0_by_reference</span></code></a>([effect, ...])</p></td>
+<td><p>Returns unique interacting pairs without being aware of the direction.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.interactions_0_by_resource" title="pypath.core.interaction.Interaction.interactions_0_by_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">interactions_0_by_resource</span></code></a>([effect, ...])</p></td>
+<td><p>Returns unique interacting pairs without being aware of the direction.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.interactions_by_data_model" title="pypath.core.interaction.Interaction.interactions_by_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">interactions_by_data_model</span></code></a>([effect, ...])</p></td>
+<td><p>Returns one or two tuples of the interacting partners: one if only one direction, two if both directions match the query criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.interactions_by_interaction_type" title="pypath.core.interaction.Interaction.interactions_by_interaction_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">interactions_by_interaction_type</span></code></a>([effect, ...])</p></td>
+<td><p>Returns one or two tuples of the interacting partners: one if only one direction, two if both directions match the query criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.interactions_by_interaction_type_and_data_model" title="pypath.core.interaction.Interaction.interactions_by_interaction_type_and_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">interactions_by_interaction_type_and_data_model</span></code></a>([...])</p></td>
+<td><p>Returns one or two tuples of the interacting partners: one if only one direction, two if both directions match the query criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.interactions_by_interaction_type_and_data_model_and_resource" title="pypath.core.interaction.Interaction.interactions_by_interaction_type_and_data_model_and_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">interactions_by_interaction_type_and_data_model_and_resource</span></code></a>([...])</p></td>
+<td><p>Returns one or two tuples of the interacting partners: one if only one direction, two if both directions match the query criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.interactions_by_reference" title="pypath.core.interaction.Interaction.interactions_by_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">interactions_by_reference</span></code></a>([effect, ...])</p></td>
+<td><p>Returns one or two tuples of the interacting partners: one if only one direction, two if both directions match the query criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.interactions_by_resource" title="pypath.core.interaction.Interaction.interactions_by_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">interactions_by_resource</span></code></a>([effect, ...])</p></td>
+<td><p>Returns one or two tuples of the interacting partners: one if only one direction, two if both directions match the query criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.interactions_directed_by_data_model" title="pypath.core.interaction.Interaction.interactions_directed_by_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">interactions_directed_by_data_model</span></code></a>([...])</p></td>
+<td><p>Args</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.interactions_directed_by_interaction_type" title="pypath.core.interaction.Interaction.interactions_directed_by_interaction_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">interactions_directed_by_interaction_type</span></code></a>([...])</p></td>
+<td><p>Args</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.interactions_directed_by_interaction_type_and_data_model" title="pypath.core.interaction.Interaction.interactions_directed_by_interaction_type_and_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">interactions_directed_by_interaction_type_and_data_model</span></code></a>([...])</p></td>
+<td><p>Args</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.interactions_directed_by_interaction_type_and_data_model_and_resource" title="pypath.core.interaction.Interaction.interactions_directed_by_interaction_type_and_data_model_and_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">interactions_directed_by_interaction_type_and_data_model_and_resource</span></code></a>([...])</p></td>
+<td><p>Args</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.interactions_directed_by_reference" title="pypath.core.interaction.Interaction.interactions_directed_by_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">interactions_directed_by_reference</span></code></a>([effect, ...])</p></td>
+<td><p>Args</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.interactions_directed_by_resource" title="pypath.core.interaction.Interaction.interactions_directed_by_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">interactions_directed_by_resource</span></code></a>([effect, ...])</p></td>
+<td><p>Args</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.interactions_mutual_by_data_model" title="pypath.core.interaction.Interaction.interactions_mutual_by_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">interactions_mutual_by_data_model</span></code></a>([effect, ...])</p></td>
+<td><p>Note: undirected interactions does not count as mutual but only interactions with explicit direction information for both directions.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.interactions_mutual_by_interaction_type" title="pypath.core.interaction.Interaction.interactions_mutual_by_interaction_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">interactions_mutual_by_interaction_type</span></code></a>([...])</p></td>
+<td><p>Note: undirected interactions does not count as mutual but only interactions with explicit direction information for both directions.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.interactions_mutual_by_interaction_type_and_data_model" title="pypath.core.interaction.Interaction.interactions_mutual_by_interaction_type_and_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">interactions_mutual_by_interaction_type_and_data_model</span></code></a>([...])</p></td>
+<td><p>Note: undirected interactions does not count as mutual but only interactions with explicit direction information for both directions.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.interactions_mutual_by_interaction_type_and_data_model_and_resource" title="pypath.core.interaction.Interaction.interactions_mutual_by_interaction_type_and_data_model_and_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">interactions_mutual_by_interaction_type_and_data_model_and_resource</span></code></a>([...])</p></td>
+<td><p>Note: undirected interactions does not count as mutual but only interactions with explicit direction information for both directions.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.interactions_mutual_by_reference" title="pypath.core.interaction.Interaction.interactions_mutual_by_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">interactions_mutual_by_reference</span></code></a>([effect, ...])</p></td>
+<td><p>Note: undirected interactions does not count as mutual but only interactions with explicit direction information for both directions.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.interactions_mutual_by_resource" title="pypath.core.interaction.Interaction.interactions_mutual_by_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">interactions_mutual_by_resource</span></code></a>([effect, ...])</p></td>
+<td><p>Note: undirected interactions does not count as mutual but only interactions with explicit direction information for both directions.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.interactions_negative_by_data_model" title="pypath.core.interaction.Interaction.interactions_negative_by_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">interactions_negative_by_data_model</span></code></a>([...])</p></td>
+<td><p>Args</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.interactions_negative_by_interaction_type" title="pypath.core.interaction.Interaction.interactions_negative_by_interaction_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">interactions_negative_by_interaction_type</span></code></a>([...])</p></td>
+<td><p>Args</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.interactions_negative_by_interaction_type_and_data_model" title="pypath.core.interaction.Interaction.interactions_negative_by_interaction_type_and_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">interactions_negative_by_interaction_type_and_data_model</span></code></a>([...])</p></td>
+<td><p>Args</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.interactions_negative_by_interaction_type_and_data_model_and_resource" title="pypath.core.interaction.Interaction.interactions_negative_by_interaction_type_and_data_model_and_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">interactions_negative_by_interaction_type_and_data_model_and_resource</span></code></a>([...])</p></td>
+<td><p>Args</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.interactions_negative_by_reference" title="pypath.core.interaction.Interaction.interactions_negative_by_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">interactions_negative_by_reference</span></code></a>([effect, ...])</p></td>
+<td><p>Args</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.interactions_negative_by_resource" title="pypath.core.interaction.Interaction.interactions_negative_by_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">interactions_negative_by_resource</span></code></a>([effect, ...])</p></td>
+<td><p>Args</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.interactions_non_directed_0_by_data_model" title="pypath.core.interaction.Interaction.interactions_non_directed_0_by_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">interactions_non_directed_0_by_data_model</span></code></a>([...])</p></td>
+<td><p>Only the undirected interactions will be considered, if any resource annotates this interaction as undirected and none as directed, the interacting pair as a sorted tuple will be returned inside a one element tuple.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.interactions_non_directed_0_by_interaction_type" title="pypath.core.interaction.Interaction.interactions_non_directed_0_by_interaction_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">interactions_non_directed_0_by_interaction_type</span></code></a>([...])</p></td>
+<td><p>Only the undirected interactions will be considered, if any resource annotates this interaction as undirected and none as directed, the interacting pair as a sorted tuple will be returned inside a one element tuple.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.interactions_non_directed_0_by_interaction_type_and_data_model" title="pypath.core.interaction.Interaction.interactions_non_directed_0_by_interaction_type_and_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">interactions_non_directed_0_by_interaction_type_and_data_model</span></code></a>([...])</p></td>
+<td><p>Only the undirected interactions will be considered, if any resource annotates this interaction as undirected and none as directed, the interacting pair as a sorted tuple will be returned inside a one element tuple.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.interactions_non_directed_0_by_interaction_type_and_data_model_and_resource" title="pypath.core.interaction.Interaction.interactions_non_directed_0_by_interaction_type_and_data_model_and_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">interactions_non_directed_0_by_interaction_type_and_data_model_and_resource</span></code></a>([...])</p></td>
+<td><p>Only the undirected interactions will be considered, if any resource annotates this interaction as undirected and none as directed, the interacting pair as a sorted tuple will be returned inside a one element tuple.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.interactions_non_directed_0_by_reference" title="pypath.core.interaction.Interaction.interactions_non_directed_0_by_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">interactions_non_directed_0_by_reference</span></code></a>([...])</p></td>
+<td><p>Only the undirected interactions will be considered, if any resource annotates this interaction as undirected and none as directed, the interacting pair as a sorted tuple will be returned inside a one element tuple.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.interactions_non_directed_0_by_resource" title="pypath.core.interaction.Interaction.interactions_non_directed_0_by_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">interactions_non_directed_0_by_resource</span></code></a>([...])</p></td>
+<td><p>Only the undirected interactions will be considered, if any resource annotates this interaction as undirected and none as directed, the interacting pair as a sorted tuple will be returned inside a one element tuple.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.interactions_non_directed_by_data_model" title="pypath.core.interaction.Interaction.interactions_non_directed_by_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">interactions_non_directed_by_data_model</span></code></a>([...])</p></td>
+<td><p>Only the undirected interactions will be considered, if any resource annotates this interaction as undirected both directions will be returned, but only if no resource provide direction.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.interactions_non_directed_by_interaction_type" title="pypath.core.interaction.Interaction.interactions_non_directed_by_interaction_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">interactions_non_directed_by_interaction_type</span></code></a>([...])</p></td>
+<td><p>Only the undirected interactions will be considered, if any resource annotates this interaction as undirected both directions will be returned, but only if no resource provide direction.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.interactions_non_directed_by_interaction_type_and_data_model" title="pypath.core.interaction.Interaction.interactions_non_directed_by_interaction_type_and_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">interactions_non_directed_by_interaction_type_and_data_model</span></code></a>([...])</p></td>
+<td><p>Only the undirected interactions will be considered, if any resource annotates this interaction as undirected both directions will be returned, but only if no resource provide direction.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.interactions_non_directed_by_interaction_type_and_data_model_and_resource" title="pypath.core.interaction.Interaction.interactions_non_directed_by_interaction_type_and_data_model_and_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">interactions_non_directed_by_interaction_type_and_data_model_and_resource</span></code></a>([...])</p></td>
+<td><p>Only the undirected interactions will be considered, if any resource annotates this interaction as undirected both directions will be returned, but only if no resource provide direction.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.interactions_non_directed_by_reference" title="pypath.core.interaction.Interaction.interactions_non_directed_by_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">interactions_non_directed_by_reference</span></code></a>([...])</p></td>
+<td><p>Only the undirected interactions will be considered, if any resource annotates this interaction as undirected both directions will be returned, but only if no resource provide direction.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.interactions_non_directed_by_resource" title="pypath.core.interaction.Interaction.interactions_non_directed_by_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">interactions_non_directed_by_resource</span></code></a>([...])</p></td>
+<td><p>Only the undirected interactions will be considered, if any resource annotates this interaction as undirected both directions will be returned, but only if no resource provide direction.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.interactions_positive_by_data_model" title="pypath.core.interaction.Interaction.interactions_positive_by_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">interactions_positive_by_data_model</span></code></a>([...])</p></td>
+<td><p>Args</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.interactions_positive_by_interaction_type" title="pypath.core.interaction.Interaction.interactions_positive_by_interaction_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">interactions_positive_by_interaction_type</span></code></a>([...])</p></td>
+<td><p>Args</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.interactions_positive_by_interaction_type_and_data_model" title="pypath.core.interaction.Interaction.interactions_positive_by_interaction_type_and_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">interactions_positive_by_interaction_type_and_data_model</span></code></a>([...])</p></td>
+<td><p>Args</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.interactions_positive_by_interaction_type_and_data_model_and_resource" title="pypath.core.interaction.Interaction.interactions_positive_by_interaction_type_and_data_model_and_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">interactions_positive_by_interaction_type_and_data_model_and_resource</span></code></a>([...])</p></td>
+<td><p>Args</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.interactions_positive_by_reference" title="pypath.core.interaction.Interaction.interactions_positive_by_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">interactions_positive_by_reference</span></code></a>([effect, ...])</p></td>
+<td><p>Args</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.interactions_positive_by_resource" title="pypath.core.interaction.Interaction.interactions_positive_by_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">interactions_positive_by_resource</span></code></a>([effect, ...])</p></td>
+<td><p>Args</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.interactions_signed_by_data_model" title="pypath.core.interaction.Interaction.interactions_signed_by_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">interactions_signed_by_data_model</span></code></a>([effect, ...])</p></td>
+<td><p>Args</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.interactions_signed_by_interaction_type" title="pypath.core.interaction.Interaction.interactions_signed_by_interaction_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">interactions_signed_by_interaction_type</span></code></a>([...])</p></td>
+<td><p>Args</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.interactions_signed_by_interaction_type_and_data_model" title="pypath.core.interaction.Interaction.interactions_signed_by_interaction_type_and_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">interactions_signed_by_interaction_type_and_data_model</span></code></a>([...])</p></td>
+<td><p>Args</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.interactions_signed_by_interaction_type_and_data_model_and_resource" title="pypath.core.interaction.Interaction.interactions_signed_by_interaction_type_and_data_model_and_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">interactions_signed_by_interaction_type_and_data_model_and_resource</span></code></a>([...])</p></td>
+<td><p>Args</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.interactions_signed_by_reference" title="pypath.core.interaction.Interaction.interactions_signed_by_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">interactions_signed_by_reference</span></code></a>([effect, ...])</p></td>
+<td><p>Args</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.interactions_signed_by_resource" title="pypath.core.interaction.Interaction.interactions_signed_by_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">interactions_signed_by_resource</span></code></a>([effect, ...])</p></td>
+<td><p>Args</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.interactions_undirected_0_by_data_model" title="pypath.core.interaction.Interaction.interactions_undirected_0_by_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">interactions_undirected_0_by_data_model</span></code></a>([...])</p></td>
+<td><p>Only the undirected interactions will be considered, if any resource annotates this interaction as undirected the interacting pair as a sorted tuple will be returned inside a one element tuple.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.interactions_undirected_0_by_interaction_type" title="pypath.core.interaction.Interaction.interactions_undirected_0_by_interaction_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">interactions_undirected_0_by_interaction_type</span></code></a>([...])</p></td>
+<td><p>Only the undirected interactions will be considered, if any resource annotates this interaction as undirected the interacting pair as a sorted tuple will be returned inside a one element tuple.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.interactions_undirected_0_by_interaction_type_and_data_model" title="pypath.core.interaction.Interaction.interactions_undirected_0_by_interaction_type_and_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">interactions_undirected_0_by_interaction_type_and_data_model</span></code></a>([...])</p></td>
+<td><p>Only the undirected interactions will be considered, if any resource annotates this interaction as undirected the interacting pair as a sorted tuple will be returned inside a one element tuple.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.interactions_undirected_0_by_interaction_type_and_data_model_and_resource" title="pypath.core.interaction.Interaction.interactions_undirected_0_by_interaction_type_and_data_model_and_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">interactions_undirected_0_by_interaction_type_and_data_model_and_resource</span></code></a>([...])</p></td>
+<td><p>Only the undirected interactions will be considered, if any resource annotates this interaction as undirected the interacting pair as a sorted tuple will be returned inside a one element tuple.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.interactions_undirected_0_by_reference" title="pypath.core.interaction.Interaction.interactions_undirected_0_by_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">interactions_undirected_0_by_reference</span></code></a>([...])</p></td>
+<td><p>Only the undirected interactions will be considered, if any resource annotates this interaction as undirected the interacting pair as a sorted tuple will be returned inside a one element tuple.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.interactions_undirected_0_by_resource" title="pypath.core.interaction.Interaction.interactions_undirected_0_by_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">interactions_undirected_0_by_resource</span></code></a>([...])</p></td>
+<td><p>Only the undirected interactions will be considered, if any resource annotates this interaction as undirected the interacting pair as a sorted tuple will be returned inside a one element tuple.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.interactions_undirected_by_data_model" title="pypath.core.interaction.Interaction.interactions_undirected_by_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">interactions_undirected_by_data_model</span></code></a>([...])</p></td>
+<td><p>Only the undirected interactions will be considered, if any resource annotates this interaction as undirected both directions will be returned, no matter if certain resources provide direction.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.interactions_undirected_by_interaction_type" title="pypath.core.interaction.Interaction.interactions_undirected_by_interaction_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">interactions_undirected_by_interaction_type</span></code></a>([...])</p></td>
+<td><p>Only the undirected interactions will be considered, if any resource annotates this interaction as undirected both directions will be returned, no matter if certain resources provide direction.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.interactions_undirected_by_interaction_type_and_data_model" title="pypath.core.interaction.Interaction.interactions_undirected_by_interaction_type_and_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">interactions_undirected_by_interaction_type_and_data_model</span></code></a>([...])</p></td>
+<td><p>Only the undirected interactions will be considered, if any resource annotates this interaction as undirected both directions will be returned, no matter if certain resources provide direction.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.interactions_undirected_by_interaction_type_and_data_model_and_resource" title="pypath.core.interaction.Interaction.interactions_undirected_by_interaction_type_and_data_model_and_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">interactions_undirected_by_interaction_type_and_data_model_and_resource</span></code></a>([...])</p></td>
+<td><p>Only the undirected interactions will be considered, if any resource annotates this interaction as undirected both directions will be returned, no matter if certain resources provide direction.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.interactions_undirected_by_reference" title="pypath.core.interaction.Interaction.interactions_undirected_by_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">interactions_undirected_by_reference</span></code></a>([...])</p></td>
+<td><p>Only the undirected interactions will be considered, if any resource annotates this interaction as undirected both directions will be returned, no matter if certain resources provide direction.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.interactions_undirected_by_resource" title="pypath.core.interaction.Interaction.interactions_undirected_by_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">interactions_undirected_by_resource</span></code></a>([...])</p></td>
+<td><p>Only the undirected interactions will be considered, if any resource annotates this interaction as undirected both directions will be returned, no matter if certain resources provide direction.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.is_directed" title="pypath.core.interaction.Interaction.is_directed"><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_directed</span></code></a>()</p></td>
+<td><p>Checks if edge has any directionality information.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.is_directed_by_resources" title="pypath.core.interaction.Interaction.is_directed_by_resources"><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_directed_by_resources</span></code></a>([resources])</p></td>
+<td><p>Checks if edge has any directionality information from some resource(s).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.is_inhibition" title="pypath.core.interaction.Interaction.is_inhibition"><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_inhibition</span></code></a>([direction, resources])</p></td>
+<td><p>Checks if any (or for a specific <em>direction</em>) interaction is inhibition (negative interaction).</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.is_loop" title="pypath.core.interaction.Interaction.is_loop"><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_loop</span></code></a>()</p></td>
+<td><p><dl class="field-list simple">
+<dt class="field-odd">returns<span class="colon">:</span></dt>
+<dd class="field-odd"><p></p></dd>
+</dl>
+</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.is_mutual" title="pypath.core.interaction.Interaction.is_mutual"><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_mutual</span></code></a>(**kwargs)</p></td>
+<td><p>Note: undirected interactions does not count as mutual but only interactions with explicit direction information for both directions.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.is_mutual_by_resources" title="pypath.core.interaction.Interaction.is_mutual_by_resources"><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_mutual_by_resources</span></code></a>([resources])</p></td>
+<td><p>Checks if the edge has mutual directions (both A--&gt;B and B--&gt;A) according to some resource(s).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.is_stimulation" title="pypath.core.interaction.Interaction.is_stimulation"><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_stimulation</span></code></a>([direction, resources])</p></td>
+<td><p>Checks if any (or for a specific <em>direction</em>) interaction is activation (positive interaction).</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.iter_evidences" title="pypath.core.interaction.Interaction.iter_evidences"><code class="xref py py-obj docutils literal notranslate"><span class="pre">iter_evidences</span></code></a>(this_direction[, direction, ...])</p></td>
+<td><p>Selects and yields evidence collections matching the direction and effect criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.iter_match_evidences" title="pypath.core.interaction.Interaction.iter_match_evidences"><code class="xref py py-obj docutils literal notranslate"><span class="pre">iter_match_evidences</span></code></a>(this_direction[, ...])</p></td>
+<td><p>Selects the evidence collections matching the direction and effect criteria and yields collections matching the evidence criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.labels_by_data_model" title="pypath.core.interaction.Interaction.labels_by_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">labels_by_data_model</span></code></a>([effect, resources, ...])</p></td>
+<td><p>Retrieves the entities involved in interactions matching the criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.labels_by_interaction_type" title="pypath.core.interaction.Interaction.labels_by_interaction_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">labels_by_interaction_type</span></code></a>([effect, ...])</p></td>
+<td><p>Retrieves the entities involved in interactions matching the criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.labels_by_interaction_type_and_data_model" title="pypath.core.interaction.Interaction.labels_by_interaction_type_and_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">labels_by_interaction_type_and_data_model</span></code></a>([...])</p></td>
+<td><p>Retrieves the entities involved in interactions matching the criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.labels_by_interaction_type_and_data_model_and_resource" title="pypath.core.interaction.Interaction.labels_by_interaction_type_and_data_model_and_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">labels_by_interaction_type_and_data_model_and_resource</span></code></a>([...])</p></td>
+<td><p>Retrieves the entities involved in interactions matching the criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.labels_by_reference" title="pypath.core.interaction.Interaction.labels_by_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">labels_by_reference</span></code></a>([effect, resources, ...])</p></td>
+<td><p>Retrieves the entities involved in interactions matching the criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.labels_by_resource" title="pypath.core.interaction.Interaction.labels_by_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">labels_by_resource</span></code></a>([effect, resources, ...])</p></td>
+<td><p>Retrieves the entities involved in interactions matching the criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.lncrna_identifiers_by_data_model" title="pypath.core.interaction.Interaction.lncrna_identifiers_by_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">lncrna_identifiers_by_data_model</span></code></a>([effect, ...])</p></td>
+<td><p>Retrieves the entities involved in interactions matching the criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.lncrna_identifiers_by_interaction_type" title="pypath.core.interaction.Interaction.lncrna_identifiers_by_interaction_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">lncrna_identifiers_by_interaction_type</span></code></a>([...])</p></td>
+<td><p>Retrieves the entities involved in interactions matching the criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.lncrna_identifiers_by_interaction_type_and_data_model" title="pypath.core.interaction.Interaction.lncrna_identifiers_by_interaction_type_and_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">lncrna_identifiers_by_interaction_type_and_data_model</span></code></a>([...])</p></td>
+<td><p>Retrieves the entities involved in interactions matching the criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.lncrna_identifiers_by_interaction_type_and_data_model_and_resource" title="pypath.core.interaction.Interaction.lncrna_identifiers_by_interaction_type_and_data_model_and_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">lncrna_identifiers_by_interaction_type_and_data_model_and_resource</span></code></a>([...])</p></td>
+<td><p>Retrieves the entities involved in interactions matching the criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.lncrna_identifiers_by_reference" title="pypath.core.interaction.Interaction.lncrna_identifiers_by_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">lncrna_identifiers_by_reference</span></code></a>([effect, ...])</p></td>
+<td><p>Retrieves the entities involved in interactions matching the criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.lncrna_identifiers_by_resource" title="pypath.core.interaction.Interaction.lncrna_identifiers_by_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">lncrna_identifiers_by_resource</span></code></a>([effect, ...])</p></td>
+<td><p>Retrieves the entities involved in interactions matching the criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.lncrna_labels_by_data_model" title="pypath.core.interaction.Interaction.lncrna_labels_by_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">lncrna_labels_by_data_model</span></code></a>([effect, ...])</p></td>
+<td><p>Retrieves the entities involved in interactions matching the criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.lncrna_labels_by_interaction_type" title="pypath.core.interaction.Interaction.lncrna_labels_by_interaction_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">lncrna_labels_by_interaction_type</span></code></a>([effect, ...])</p></td>
+<td><p>Retrieves the entities involved in interactions matching the criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.lncrna_labels_by_interaction_type_and_data_model" title="pypath.core.interaction.Interaction.lncrna_labels_by_interaction_type_and_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">lncrna_labels_by_interaction_type_and_data_model</span></code></a>([...])</p></td>
+<td><p>Retrieves the entities involved in interactions matching the criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.lncrna_labels_by_interaction_type_and_data_model_and_resource" title="pypath.core.interaction.Interaction.lncrna_labels_by_interaction_type_and_data_model_and_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">lncrna_labels_by_interaction_type_and_data_model_and_resource</span></code></a>([...])</p></td>
+<td><p>Retrieves the entities involved in interactions matching the criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.lncrna_labels_by_reference" title="pypath.core.interaction.Interaction.lncrna_labels_by_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">lncrna_labels_by_reference</span></code></a>([effect, ...])</p></td>
+<td><p>Retrieves the entities involved in interactions matching the criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.lncrna_labels_by_resource" title="pypath.core.interaction.Interaction.lncrna_labels_by_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">lncrna_labels_by_resource</span></code></a>([effect, ...])</p></td>
+<td><p>Retrieves the entities involved in interactions matching the criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.lncrnas_by_data_model" title="pypath.core.interaction.Interaction.lncrnas_by_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">lncrnas_by_data_model</span></code></a>([effect, resources, ...])</p></td>
+<td><p>Retrieves the entities involved in interactions matching the criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.lncrnas_by_interaction_type" title="pypath.core.interaction.Interaction.lncrnas_by_interaction_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">lncrnas_by_interaction_type</span></code></a>([effect, ...])</p></td>
+<td><p>Retrieves the entities involved in interactions matching the criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.lncrnas_by_interaction_type_and_data_model" title="pypath.core.interaction.Interaction.lncrnas_by_interaction_type_and_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">lncrnas_by_interaction_type_and_data_model</span></code></a>([...])</p></td>
+<td><p>Retrieves the entities involved in interactions matching the criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.lncrnas_by_interaction_type_and_data_model_and_resource" title="pypath.core.interaction.Interaction.lncrnas_by_interaction_type_and_data_model_and_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">lncrnas_by_interaction_type_and_data_model_and_resource</span></code></a>([...])</p></td>
+<td><p>Retrieves the entities involved in interactions matching the criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.lncrnas_by_reference" title="pypath.core.interaction.Interaction.lncrnas_by_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">lncrnas_by_reference</span></code></a>([effect, resources, ...])</p></td>
+<td><p>Retrieves the entities involved in interactions matching the criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.lncrnas_by_resource" title="pypath.core.interaction.Interaction.lncrnas_by_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">lncrnas_by_resource</span></code></a>([effect, resources, ...])</p></td>
+<td><p>Retrieves the entities involved in interactions matching the criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.majority_dir" title="pypath.core.interaction.Interaction.majority_dir"><code class="xref py py-obj docutils literal notranslate"><span class="pre">majority_dir</span></code></a>([only_interaction_type, ...])</p></td>
+<td><p>Infers which is the major directionality of the edge by number of supporting sources.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.majority_sign" title="pypath.core.interaction.Interaction.majority_sign"><code class="xref py py-obj docutils literal notranslate"><span class="pre">majority_sign</span></code></a>([only_interaction_type, ...])</p></td>
+<td><p>Infers which is the major sign (activation/inhibition) of the edge by number of supporting sources on both directions.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.merge" title="pypath.core.interaction.Interaction.merge"><code class="xref py py-obj docutils literal notranslate"><span class="pre">merge</span></code></a>(other)</p></td>
+<td><p>Merges current Interaction with another (if and only if they are the same class and contain the same nodes).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.mirna_identifiers_by_data_model" title="pypath.core.interaction.Interaction.mirna_identifiers_by_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">mirna_identifiers_by_data_model</span></code></a>([effect, ...])</p></td>
+<td><p>Retrieves the entities involved in interactions matching the criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.mirna_identifiers_by_interaction_type" title="pypath.core.interaction.Interaction.mirna_identifiers_by_interaction_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">mirna_identifiers_by_interaction_type</span></code></a>([...])</p></td>
+<td><p>Retrieves the entities involved in interactions matching the criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.mirna_identifiers_by_interaction_type_and_data_model" title="pypath.core.interaction.Interaction.mirna_identifiers_by_interaction_type_and_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">mirna_identifiers_by_interaction_type_and_data_model</span></code></a>([...])</p></td>
+<td><p>Retrieves the entities involved in interactions matching the criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.mirna_identifiers_by_interaction_type_and_data_model_and_resource" title="pypath.core.interaction.Interaction.mirna_identifiers_by_interaction_type_and_data_model_and_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">mirna_identifiers_by_interaction_type_and_data_model_and_resource</span></code></a>([...])</p></td>
+<td><p>Retrieves the entities involved in interactions matching the criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.mirna_identifiers_by_reference" title="pypath.core.interaction.Interaction.mirna_identifiers_by_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">mirna_identifiers_by_reference</span></code></a>([effect, ...])</p></td>
+<td><p>Retrieves the entities involved in interactions matching the criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.mirna_identifiers_by_resource" title="pypath.core.interaction.Interaction.mirna_identifiers_by_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">mirna_identifiers_by_resource</span></code></a>([effect, ...])</p></td>
+<td><p>Retrieves the entities involved in interactions matching the criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.mirna_labels_by_data_model" title="pypath.core.interaction.Interaction.mirna_labels_by_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">mirna_labels_by_data_model</span></code></a>([effect, ...])</p></td>
+<td><p>Retrieves the entities involved in interactions matching the criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.mirna_labels_by_interaction_type" title="pypath.core.interaction.Interaction.mirna_labels_by_interaction_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">mirna_labels_by_interaction_type</span></code></a>([effect, ...])</p></td>
+<td><p>Retrieves the entities involved in interactions matching the criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.mirna_labels_by_interaction_type_and_data_model" title="pypath.core.interaction.Interaction.mirna_labels_by_interaction_type_and_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">mirna_labels_by_interaction_type_and_data_model</span></code></a>([...])</p></td>
+<td><p>Retrieves the entities involved in interactions matching the criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.mirna_labels_by_interaction_type_and_data_model_and_resource" title="pypath.core.interaction.Interaction.mirna_labels_by_interaction_type_and_data_model_and_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">mirna_labels_by_interaction_type_and_data_model_and_resource</span></code></a>([...])</p></td>
+<td><p>Retrieves the entities involved in interactions matching the criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.mirna_labels_by_reference" title="pypath.core.interaction.Interaction.mirna_labels_by_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">mirna_labels_by_reference</span></code></a>([effect, ...])</p></td>
+<td><p>Retrieves the entities involved in interactions matching the criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.mirna_labels_by_resource" title="pypath.core.interaction.Interaction.mirna_labels_by_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">mirna_labels_by_resource</span></code></a>([effect, ...])</p></td>
+<td><p>Retrieves the entities involved in interactions matching the criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.mirnas_by_data_model" title="pypath.core.interaction.Interaction.mirnas_by_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">mirnas_by_data_model</span></code></a>([effect, resources, ...])</p></td>
+<td><p>Retrieves the entities involved in interactions matching the criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.mirnas_by_interaction_type" title="pypath.core.interaction.Interaction.mirnas_by_interaction_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">mirnas_by_interaction_type</span></code></a>([effect, ...])</p></td>
+<td><p>Retrieves the entities involved in interactions matching the criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.mirnas_by_interaction_type_and_data_model" title="pypath.core.interaction.Interaction.mirnas_by_interaction_type_and_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">mirnas_by_interaction_type_and_data_model</span></code></a>([...])</p></td>
+<td><p>Retrieves the entities involved in interactions matching the criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.mirnas_by_interaction_type_and_data_model_and_resource" title="pypath.core.interaction.Interaction.mirnas_by_interaction_type_and_data_model_and_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">mirnas_by_interaction_type_and_data_model_and_resource</span></code></a>([...])</p></td>
+<td><p>Retrieves the entities involved in interactions matching the criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.mirnas_by_reference" title="pypath.core.interaction.Interaction.mirnas_by_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">mirnas_by_reference</span></code></a>([effect, resources, ...])</p></td>
+<td><p>Retrieves the entities involved in interactions matching the criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.mirnas_by_resource" title="pypath.core.interaction.Interaction.mirnas_by_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">mirnas_by_resource</span></code></a>([effect, resources, ...])</p></td>
+<td><p>Retrieves the entities involved in interactions matching the criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.negative_a_b" title="pypath.core.interaction.Interaction.negative_a_b"><code class="xref py py-obj docutils literal notranslate"><span class="pre">negative_a_b</span></code></a>()</p></td>
+<td><p>Checks if the <code class="xref py py-attr docutils literal notranslate"><span class="pre">a_b</span></code> directionality is a negative interaction.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.negative_b_a" title="pypath.core.interaction.Interaction.negative_b_a"><code class="xref py py-obj docutils literal notranslate"><span class="pre">negative_b_a</span></code></a>()</p></td>
+<td><p>Checks if the <code class="xref py py-attr docutils literal notranslate"><span class="pre">b_a</span></code> directionality is a negative interaction.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.negative_resources_a_b" title="pypath.core.interaction.Interaction.negative_resources_a_b"><code class="xref py py-obj docutils literal notranslate"><span class="pre">negative_resources_a_b</span></code></a>(**kwargs)</p></td>
+<td><p>Retrieves the list of resources for the <code class="xref py py-attr docutils literal notranslate"><span class="pre">a_b</span></code> direction and negative sign.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.negative_resources_b_a" title="pypath.core.interaction.Interaction.negative_resources_b_a"><code class="xref py py-obj docutils literal notranslate"><span class="pre">negative_resources_b_a</span></code></a>(**kwargs)</p></td>
+<td><p>Retrieves the list of resources for the <code class="xref py py-attr docutils literal notranslate"><span class="pre">b_a</span></code> direction and negative sign.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.negative_reverse" title="pypath.core.interaction.Interaction.negative_reverse"><code class="xref py py-obj docutils literal notranslate"><span class="pre">negative_reverse</span></code></a>()</p></td>
+<td><p>Checks if the <code class="xref py py-attr docutils literal notranslate"><span class="pre">b_a</span></code> directionality is a negative interaction.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.negative_straight" title="pypath.core.interaction.Interaction.negative_straight"><code class="xref py py-obj docutils literal notranslate"><span class="pre">negative_straight</span></code></a>()</p></td>
+<td><p>Checks if the <code class="xref py py-attr docutils literal notranslate"><span class="pre">a_b</span></code> directionality is a negative interaction.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">orthology_translate</span></code>(taxon[, exclude])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">orthology_translate_one</span></code>(id_a, id_b, taxon)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.positive_a_b" title="pypath.core.interaction.Interaction.positive_a_b"><code class="xref py py-obj docutils literal notranslate"><span class="pre">positive_a_b</span></code></a>()</p></td>
+<td><p>Checks if the <code class="xref py py-attr docutils literal notranslate"><span class="pre">a_b</span></code> directionality is a positive interaction.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.positive_b_a" title="pypath.core.interaction.Interaction.positive_b_a"><code class="xref py py-obj docutils literal notranslate"><span class="pre">positive_b_a</span></code></a>()</p></td>
+<td><p>Checks if the <code class="xref py py-attr docutils literal notranslate"><span class="pre">b_a</span></code> directionality is a positive interaction.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.positive_resources_a_b" title="pypath.core.interaction.Interaction.positive_resources_a_b"><code class="xref py py-obj docutils literal notranslate"><span class="pre">positive_resources_a_b</span></code></a>(**kwargs)</p></td>
+<td><p>Retrieves the list of resources for the <code class="xref py py-attr docutils literal notranslate"><span class="pre">a_b</span></code> direction and positive sign.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.positive_resources_b_a" title="pypath.core.interaction.Interaction.positive_resources_b_a"><code class="xref py py-obj docutils literal notranslate"><span class="pre">positive_resources_b_a</span></code></a>(**kwargs)</p></td>
+<td><p>Retrieves the list of resources for the <code class="xref py py-attr docutils literal notranslate"><span class="pre">b_a</span></code> direction and positive sign.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.positive_reverse" title="pypath.core.interaction.Interaction.positive_reverse"><code class="xref py py-obj docutils literal notranslate"><span class="pre">positive_reverse</span></code></a>()</p></td>
+<td><p>Checks if the <code class="xref py py-attr docutils literal notranslate"><span class="pre">b_a</span></code> directionality is a positive interaction.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.positive_straight" title="pypath.core.interaction.Interaction.positive_straight"><code class="xref py py-obj docutils literal notranslate"><span class="pre">positive_straight</span></code></a>()</p></td>
+<td><p>Checks if the <code class="xref py py-attr docutils literal notranslate"><span class="pre">a_b</span></code> directionality is a positive interaction.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.protein_identifiers_by_data_model" title="pypath.core.interaction.Interaction.protein_identifiers_by_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">protein_identifiers_by_data_model</span></code></a>([effect, ...])</p></td>
+<td><p>Retrieves the entities involved in interactions matching the criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.protein_identifiers_by_interaction_type" title="pypath.core.interaction.Interaction.protein_identifiers_by_interaction_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">protein_identifiers_by_interaction_type</span></code></a>([...])</p></td>
+<td><p>Retrieves the entities involved in interactions matching the criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.protein_identifiers_by_interaction_type_and_data_model" title="pypath.core.interaction.Interaction.protein_identifiers_by_interaction_type_and_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">protein_identifiers_by_interaction_type_and_data_model</span></code></a>([...])</p></td>
+<td><p>Retrieves the entities involved in interactions matching the criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.protein_identifiers_by_interaction_type_and_data_model_and_resource" title="pypath.core.interaction.Interaction.protein_identifiers_by_interaction_type_and_data_model_and_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">protein_identifiers_by_interaction_type_and_data_model_and_resource</span></code></a>([...])</p></td>
+<td><p>Retrieves the entities involved in interactions matching the criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.protein_identifiers_by_reference" title="pypath.core.interaction.Interaction.protein_identifiers_by_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">protein_identifiers_by_reference</span></code></a>([effect, ...])</p></td>
+<td><p>Retrieves the entities involved in interactions matching the criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.protein_identifiers_by_resource" title="pypath.core.interaction.Interaction.protein_identifiers_by_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">protein_identifiers_by_resource</span></code></a>([effect, ...])</p></td>
+<td><p>Retrieves the entities involved in interactions matching the criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.protein_labels_by_data_model" title="pypath.core.interaction.Interaction.protein_labels_by_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">protein_labels_by_data_model</span></code></a>([effect, ...])</p></td>
+<td><p>Retrieves the entities involved in interactions matching the criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.protein_labels_by_interaction_type" title="pypath.core.interaction.Interaction.protein_labels_by_interaction_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">protein_labels_by_interaction_type</span></code></a>([effect, ...])</p></td>
+<td><p>Retrieves the entities involved in interactions matching the criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.protein_labels_by_interaction_type_and_data_model" title="pypath.core.interaction.Interaction.protein_labels_by_interaction_type_and_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">protein_labels_by_interaction_type_and_data_model</span></code></a>([...])</p></td>
+<td><p>Retrieves the entities involved in interactions matching the criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.protein_labels_by_interaction_type_and_data_model_and_resource" title="pypath.core.interaction.Interaction.protein_labels_by_interaction_type_and_data_model_and_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">protein_labels_by_interaction_type_and_data_model_and_resource</span></code></a>([...])</p></td>
+<td><p>Retrieves the entities involved in interactions matching the criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.protein_labels_by_reference" title="pypath.core.interaction.Interaction.protein_labels_by_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">protein_labels_by_reference</span></code></a>([effect, ...])</p></td>
+<td><p>Retrieves the entities involved in interactions matching the criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.protein_labels_by_resource" title="pypath.core.interaction.Interaction.protein_labels_by_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">protein_labels_by_resource</span></code></a>([effect, ...])</p></td>
+<td><p>Retrieves the entities involved in interactions matching the criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.proteins_by_data_model" title="pypath.core.interaction.Interaction.proteins_by_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">proteins_by_data_model</span></code></a>([effect, resources, ...])</p></td>
+<td><p>Retrieves the entities involved in interactions matching the criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.proteins_by_interaction_type" title="pypath.core.interaction.Interaction.proteins_by_interaction_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">proteins_by_interaction_type</span></code></a>([effect, ...])</p></td>
+<td><p>Retrieves the entities involved in interactions matching the criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.proteins_by_interaction_type_and_data_model" title="pypath.core.interaction.Interaction.proteins_by_interaction_type_and_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">proteins_by_interaction_type_and_data_model</span></code></a>([...])</p></td>
+<td><p>Retrieves the entities involved in interactions matching the criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.proteins_by_interaction_type_and_data_model_and_resource" title="pypath.core.interaction.Interaction.proteins_by_interaction_type_and_data_model_and_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">proteins_by_interaction_type_and_data_model_and_resource</span></code></a>([...])</p></td>
+<td><p>Retrieves the entities involved in interactions matching the criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.proteins_by_reference" title="pypath.core.interaction.Interaction.proteins_by_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">proteins_by_reference</span></code></a>([effect, resources, ...])</p></td>
+<td><p>Retrieves the entities involved in interactions matching the criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.proteins_by_resource" title="pypath.core.interaction.Interaction.proteins_by_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">proteins_by_resource</span></code></a>([effect, resources, ...])</p></td>
+<td><p>Retrieves the entities involved in interactions matching the criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.reload" title="pypath.core.interaction.Interaction.reload"><code class="xref py py-obj docutils literal notranslate"><span class="pre">reload</span></code></a>()</p></td>
+<td><p>Reloads the object from the module level.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.resources_a_b" title="pypath.core.interaction.Interaction.resources_a_b"><code class="xref py py-obj docutils literal notranslate"><span class="pre">resources_a_b</span></code></a>([resources, evidences, ...])</p></td>
+<td><p>Retrieves the list of resources for the <code class="xref py py-attr docutils literal notranslate"><span class="pre">a_b</span></code> direction.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.resources_b_a" title="pypath.core.interaction.Interaction.resources_b_a"><code class="xref py py-obj docutils literal notranslate"><span class="pre">resources_b_a</span></code></a>([resources, evidences, ...])</p></td>
+<td><p>Retrieves the list of sources for the <code class="xref py py-attr docutils literal notranslate"><span class="pre">b_a</span></code> direction.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.resources_undirected" title="pypath.core.interaction.Interaction.resources_undirected"><code class="xref py py-obj docutils literal notranslate"><span class="pre">resources_undirected</span></code></a>([resources, evidences, ...])</p></td>
+<td><p>Retrieves the list of resources without directed information.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.serialize" title="pypath.core.interaction.Interaction.serialize"><code class="xref py py-obj docutils literal notranslate"><span class="pre">serialize</span></code></a>(**kwargs)</p></td>
+<td><p>Generates a JSON string with the full contents of the attributes, without any whitespace or line break.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.serialize_attrs" title="pypath.core.interaction.Interaction.serialize_attrs"><code class="xref py py-obj docutils literal notranslate"><span class="pre">serialize_attrs</span></code></a>([direction])</p></td>
+<td><p>Serialize the resource specific attributes into a JSON string.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.serialize_evidences" title="pypath.core.interaction.Interaction.serialize_evidences"><code class="xref py py-obj docutils literal notranslate"><span class="pre">serialize_evidences</span></code></a>(direction)</p></td>
+<td><p>Serialize the evidences into a JSON string.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.small_molecule_identifiers_by_data_model" title="pypath.core.interaction.Interaction.small_molecule_identifiers_by_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">small_molecule_identifiers_by_data_model</span></code></a>([...])</p></td>
+<td><p>Retrieves the entities involved in interactions matching the criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.small_molecule_identifiers_by_interaction_type" title="pypath.core.interaction.Interaction.small_molecule_identifiers_by_interaction_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">small_molecule_identifiers_by_interaction_type</span></code></a>([...])</p></td>
+<td><p>Retrieves the entities involved in interactions matching the criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.small_molecule_identifiers_by_interaction_type_and_data_model" title="pypath.core.interaction.Interaction.small_molecule_identifiers_by_interaction_type_and_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">small_molecule_identifiers_by_interaction_type_and_data_model</span></code></a>([...])</p></td>
+<td><p>Retrieves the entities involved in interactions matching the criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.small_molecule_identifiers_by_interaction_type_and_data_model_and_resource" title="pypath.core.interaction.Interaction.small_molecule_identifiers_by_interaction_type_and_data_model_and_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">small_molecule_identifiers_by_interaction_type_and_data_model_and_resource</span></code></a>([...])</p></td>
+<td><p>Retrieves the entities involved in interactions matching the criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.small_molecule_identifiers_by_reference" title="pypath.core.interaction.Interaction.small_molecule_identifiers_by_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">small_molecule_identifiers_by_reference</span></code></a>([...])</p></td>
+<td><p>Retrieves the entities involved in interactions matching the criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.small_molecule_identifiers_by_resource" title="pypath.core.interaction.Interaction.small_molecule_identifiers_by_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">small_molecule_identifiers_by_resource</span></code></a>([...])</p></td>
+<td><p>Retrieves the entities involved in interactions matching the criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.small_molecule_labels_by_data_model" title="pypath.core.interaction.Interaction.small_molecule_labels_by_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">small_molecule_labels_by_data_model</span></code></a>([...])</p></td>
+<td><p>Retrieves the entities involved in interactions matching the criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.small_molecule_labels_by_interaction_type" title="pypath.core.interaction.Interaction.small_molecule_labels_by_interaction_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">small_molecule_labels_by_interaction_type</span></code></a>([...])</p></td>
+<td><p>Retrieves the entities involved in interactions matching the criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.small_molecule_labels_by_interaction_type_and_data_model" title="pypath.core.interaction.Interaction.small_molecule_labels_by_interaction_type_and_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">small_molecule_labels_by_interaction_type_and_data_model</span></code></a>([...])</p></td>
+<td><p>Retrieves the entities involved in interactions matching the criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.small_molecule_labels_by_interaction_type_and_data_model_and_resource" title="pypath.core.interaction.Interaction.small_molecule_labels_by_interaction_type_and_data_model_and_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">small_molecule_labels_by_interaction_type_and_data_model_and_resource</span></code></a>([...])</p></td>
+<td><p>Retrieves the entities involved in interactions matching the criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.small_molecule_labels_by_reference" title="pypath.core.interaction.Interaction.small_molecule_labels_by_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">small_molecule_labels_by_reference</span></code></a>([effect, ...])</p></td>
+<td><p>Retrieves the entities involved in interactions matching the criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.small_molecule_labels_by_resource" title="pypath.core.interaction.Interaction.small_molecule_labels_by_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">small_molecule_labels_by_resource</span></code></a>([effect, ...])</p></td>
+<td><p>Retrieves the entities involved in interactions matching the criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.small_molecules_by_data_model" title="pypath.core.interaction.Interaction.small_molecules_by_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">small_molecules_by_data_model</span></code></a>([effect, ...])</p></td>
+<td><p>Retrieves the entities involved in interactions matching the criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.small_molecules_by_interaction_type" title="pypath.core.interaction.Interaction.small_molecules_by_interaction_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">small_molecules_by_interaction_type</span></code></a>([...])</p></td>
+<td><p>Retrieves the entities involved in interactions matching the criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.small_molecules_by_interaction_type_and_data_model" title="pypath.core.interaction.Interaction.small_molecules_by_interaction_type_and_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">small_molecules_by_interaction_type_and_data_model</span></code></a>([...])</p></td>
+<td><p>Retrieves the entities involved in interactions matching the criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.small_molecules_by_interaction_type_and_data_model_and_resource" title="pypath.core.interaction.Interaction.small_molecules_by_interaction_type_and_data_model_and_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">small_molecules_by_interaction_type_and_data_model_and_resource</span></code></a>([...])</p></td>
+<td><p>Retrieves the entities involved in interactions matching the criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.small_molecules_by_reference" title="pypath.core.interaction.Interaction.small_molecules_by_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">small_molecules_by_reference</span></code></a>([effect, ...])</p></td>
+<td><p>Retrieves the entities involved in interactions matching the criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.small_molecules_by_resource" title="pypath.core.interaction.Interaction.small_molecules_by_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">small_molecules_by_resource</span></code></a>([effect, ...])</p></td>
+<td><p>Retrieves the entities involved in interactions matching the criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.source" title="pypath.core.interaction.Interaction.source"><code class="xref py py-obj docutils literal notranslate"><span class="pre">source</span></code></a>([undirected, resources])</p></td>
+<td><p>Returns the name(s) of the source node(s) for each existing direction on the interaction.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.sources_reverse" title="pypath.core.interaction.Interaction.sources_reverse"><code class="xref py py-obj docutils literal notranslate"><span class="pre">sources_reverse</span></code></a>([resources, evidences, ...])</p></td>
+<td><p>Retrieves the list of sources for the <code class="xref py py-attr docutils literal notranslate"><span class="pre">b_a</span></code> direction.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.sources_straight" title="pypath.core.interaction.Interaction.sources_straight"><code class="xref py py-obj docutils literal notranslate"><span class="pre">sources_straight</span></code></a>([resources, evidences, ...])</p></td>
+<td><p>Retrieves the list of resources for the <code class="xref py py-attr docutils literal notranslate"><span class="pre">a_b</span></code> direction.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.sources_undirected" title="pypath.core.interaction.Interaction.sources_undirected"><code class="xref py py-obj docutils literal notranslate"><span class="pre">sources_undirected</span></code></a>([resources, evidences, ...])</p></td>
+<td><p>Retrieves the list of resources without directed information.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.src" title="pypath.core.interaction.Interaction.src"><code class="xref py py-obj docutils literal notranslate"><span class="pre">src</span></code></a>([undirected, resources])</p></td>
+<td><p>Returns the name(s) of the source node(s) for each existing direction on the interaction.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.src_by_resource" title="pypath.core.interaction.Interaction.src_by_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">src_by_resource</span></code></a>(resource)</p></td>
+<td><p>Returns the name(s) of the source node(s) for each existing direction on the interaction for a specific <em>resource</em>.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.target" title="pypath.core.interaction.Interaction.target"><code class="xref py py-obj docutils literal notranslate"><span class="pre">target</span></code></a>([undirected, resources])</p></td>
+<td><p>Returns the name(s) of the target node(s) for each existing direction on the interaction.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.tgt" title="pypath.core.interaction.Interaction.tgt"><code class="xref py py-obj docutils literal notranslate"><span class="pre">tgt</span></code></a>([undirected, resources])</p></td>
+<td><p>Returns the name(s) of the target node(s) for each existing direction on the interaction.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.tgt_by_resource" title="pypath.core.interaction.Interaction.tgt_by_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">tgt_by_resource</span></code></a>(resource)</p></td>
+<td><p>Returns the name(s) of the target node(s) for each existing direction on the interaction for a specific <em>resource</em>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.translate" title="pypath.core.interaction.Interaction.translate"><code class="xref py py-obj docutils literal notranslate"><span class="pre">translate</span></code></a>(ids[, new_attrs])</p></td>
+<td><p>Translates the node names/identifiers according to the dictionary <em>ids</em>.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.unset_dir" title="pypath.core.interaction.Interaction.unset_dir"><code class="xref py py-obj docutils literal notranslate"><span class="pre">unset_dir</span></code></a>(direction[, only_sign, resource, ...])</p></td>
+<td><p>Removes directionality and/or source information of the specified <em>direction</em>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.unset_direction" title="pypath.core.interaction.Interaction.unset_direction"><code class="xref py py-obj docutils literal notranslate"><span class="pre">unset_direction</span></code></a>(direction[, only_sign, ...])</p></td>
+<td><p>Removes directionality and/or source information of the specified <em>direction</em>.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.unset_interaction_type" title="pypath.core.interaction.Interaction.unset_interaction_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">unset_interaction_type</span></code></a>(interaction_type)</p></td>
+<td><p>Removes all evidences with a certain <code class="docutils literal notranslate"><span class="pre">interaction_type</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.unset_sign" title="pypath.core.interaction.Interaction.unset_sign"><code class="xref py py-obj docutils literal notranslate"><span class="pre">unset_sign</span></code></a>(direction, sign[, resource, ...])</p></td>
+<td><p>Removes sign and/or source information of the specified <em>direction</em> and <em>sign</em>.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.update_attrs" title="pypath.core.interaction.Interaction.update_attrs"><code class="xref py py-obj docutils literal notranslate"><span class="pre">update_attrs</span></code></a>([attrs])</p></td>
+<td><p>Updates the attributes stored here.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.which_directions" title="pypath.core.interaction.Interaction.which_directions"><code class="xref py py-obj docutils literal notranslate"><span class="pre">which_directions</span></code></a>([resources, effect])</p></td>
+<td><p>Returns the pair(s) of nodes for which there is information about their directionality.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.which_dirs" title="pypath.core.interaction.Interaction.which_dirs"><code class="xref py py-obj docutils literal notranslate"><span class="pre">which_dirs</span></code></a>([resources, effect])</p></td>
+<td><p>Returns the pair(s) of nodes for which there is information about their directionality.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.which_signs" title="pypath.core.interaction.Interaction.which_signs"><code class="xref py py-obj docutils literal notranslate"><span class="pre">which_signs</span></code></a>([resources, effect])</p></td>
+<td><p>Returns the pair(s) of nodes for which there is information about their effect signs.</p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Attributes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">a</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">b</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">a_b</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">b_a</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">nodes</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">key</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">evidences</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">direction</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">positive</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">negative</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">unknown_effect</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">attrs</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.count_data_models" title="pypath.core.interaction.Interaction.count_data_models"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_data_models</span></code></a></p></td>
+<td><p>Retrieves data models matching the criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.count_degrees_directed" title="pypath.core.interaction.Interaction.count_degrees_directed"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_degrees_directed</span></code></a></p></td>
+<td><p>Returns a <em>set</em> of nodes with the connections matching the direction, effect and evidence criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.count_degrees_directed_in" title="pypath.core.interaction.Interaction.count_degrees_directed_in"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_degrees_directed_in</span></code></a></p></td>
+<td><p>Returns a <em>set</em> of nodes with the connections matching the direction, effect and evidence criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.count_degrees_directed_out" title="pypath.core.interaction.Interaction.count_degrees_directed_out"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_degrees_directed_out</span></code></a></p></td>
+<td><p>Returns a <em>set</em> of nodes with the connections matching the direction, effect and evidence criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.count_degrees_negative" title="pypath.core.interaction.Interaction.count_degrees_negative"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_degrees_negative</span></code></a></p></td>
+<td><p>Returns a <em>set</em> of nodes with the connections matching the direction, effect and evidence criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.count_degrees_negative_in" title="pypath.core.interaction.Interaction.count_degrees_negative_in"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_degrees_negative_in</span></code></a></p></td>
+<td><p>Returns a <em>set</em> of nodes with the connections matching the direction, effect and evidence criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.count_degrees_negative_out" title="pypath.core.interaction.Interaction.count_degrees_negative_out"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_degrees_negative_out</span></code></a></p></td>
+<td><p>Returns a <em>set</em> of nodes with the connections matching the direction, effect and evidence criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.count_degrees_non_directed" title="pypath.core.interaction.Interaction.count_degrees_non_directed"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_degrees_non_directed</span></code></a></p></td>
+<td><p>Returns a <em>set</em> of nodes with the connections matching the direction, effect and evidence criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.count_degrees_positive" title="pypath.core.interaction.Interaction.count_degrees_positive"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_degrees_positive</span></code></a></p></td>
+<td><p>Returns a <em>set</em> of nodes with the connections matching the direction, effect and evidence criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.count_degrees_positive_in" title="pypath.core.interaction.Interaction.count_degrees_positive_in"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_degrees_positive_in</span></code></a></p></td>
+<td><p>Returns a <em>set</em> of nodes with the connections matching the direction, effect and evidence criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.count_degrees_positive_out" title="pypath.core.interaction.Interaction.count_degrees_positive_out"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_degrees_positive_out</span></code></a></p></td>
+<td><p>Returns a <em>set</em> of nodes with the connections matching the direction, effect and evidence criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.count_degrees_signed" title="pypath.core.interaction.Interaction.count_degrees_signed"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_degrees_signed</span></code></a></p></td>
+<td><p>Returns a <em>set</em> of nodes with the connections matching the direction, effect and evidence criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.count_degrees_signed_in" title="pypath.core.interaction.Interaction.count_degrees_signed_in"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_degrees_signed_in</span></code></a></p></td>
+<td><p>Returns a <em>set</em> of nodes with the connections matching the direction, effect and evidence criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.count_degrees_signed_out" title="pypath.core.interaction.Interaction.count_degrees_signed_out"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_degrees_signed_out</span></code></a></p></td>
+<td><p>Returns a <em>set</em> of nodes with the connections matching the direction, effect and evidence criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.count_degrees_undirected" title="pypath.core.interaction.Interaction.count_degrees_undirected"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_degrees_undirected</span></code></a></p></td>
+<td><p>Returns a <em>set</em> of nodes with the connections matching the direction, effect and evidence criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.count_interaction_types" title="pypath.core.interaction.Interaction.count_interaction_types"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_interaction_types</span></code></a></p></td>
+<td><p>Retrieves interaction types matching the criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.count_references" title="pypath.core.interaction.Interaction.count_references"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_references</span></code></a></p></td>
+<td><p>Retrieves references matching the criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.count_resource_names" title="pypath.core.interaction.Interaction.count_resource_names"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_resource_names</span></code></a></p></td>
+<td><p>Retrieves resource names matching the criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.count_resource_names_via" title="pypath.core.interaction.Interaction.count_resource_names_via"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_resource_names_via</span></code></a></p></td>
+<td><p>Retrieves resource names via matching the criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.count_resources" title="pypath.core.interaction.Interaction.count_resources"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_resources</span></code></a></p></td>
+<td><p>Retrieves resources matching the criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.count_resources_via" title="pypath.core.interaction.Interaction.count_resources_via"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_resources_via</span></code></a></p></td>
+<td><p>Retrieves resources via matching the criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">data_models</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.data_models_by_data_model" title="pypath.core.interaction.Interaction.data_models_by_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">data_models_by_data_model</span></code></a></p></td>
+<td><p>Retrieves data models matching the criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.data_models_by_interaction_type" title="pypath.core.interaction.Interaction.data_models_by_interaction_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">data_models_by_interaction_type</span></code></a></p></td>
+<td><p>Retrieves data models matching the criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.data_models_by_interaction_type_and_data_model" title="pypath.core.interaction.Interaction.data_models_by_interaction_type_and_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">data_models_by_interaction_type_and_data_model</span></code></a></p></td>
+<td><p>Retrieves data models matching the criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.data_models_by_interaction_type_and_data_model_and_resource" title="pypath.core.interaction.Interaction.data_models_by_interaction_type_and_data_model_and_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">data_models_by_interaction_type_and_data_model_and_resource</span></code></a></p></td>
+<td><p>Retrieves data models matching the criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.data_models_by_reference" title="pypath.core.interaction.Interaction.data_models_by_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">data_models_by_reference</span></code></a></p></td>
+<td><p>Retrieves data models matching the criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.data_models_by_resource" title="pypath.core.interaction.Interaction.data_models_by_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">data_models_by_resource</span></code></a></p></td>
+<td><p>Retrieves data models matching the criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.datasets_by_data_model" title="pypath.core.interaction.Interaction.datasets_by_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">datasets_by_data_model</span></code></a></p></td>
+<td><p>Retrieves datasets matching the criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.datasets_by_interaction_type" title="pypath.core.interaction.Interaction.datasets_by_interaction_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">datasets_by_interaction_type</span></code></a></p></td>
+<td><p>Retrieves datasets matching the criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.datasets_by_interaction_type_and_data_model" title="pypath.core.interaction.Interaction.datasets_by_interaction_type_and_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">datasets_by_interaction_type_and_data_model</span></code></a></p></td>
+<td><p>Retrieves datasets matching the criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.datasets_by_interaction_type_and_data_model_and_resource" title="pypath.core.interaction.Interaction.datasets_by_interaction_type_and_data_model_and_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">datasets_by_interaction_type_and_data_model_and_resource</span></code></a></p></td>
+<td><p>Retrieves datasets matching the criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.datasets_by_reference" title="pypath.core.interaction.Interaction.datasets_by_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">datasets_by_reference</span></code></a></p></td>
+<td><p>Retrieves datasets matching the criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.datasets_by_resource" title="pypath.core.interaction.Interaction.datasets_by_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">datasets_by_resource</span></code></a></p></td>
+<td><p>Retrieves datasets matching the criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.degrees_directed_by_data_model" title="pypath.core.interaction.Interaction.degrees_directed_by_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_directed_by_data_model</span></code></a></p></td>
+<td><p>Returns a <em>set</em> of nodes with the connections matching the direction, effect and evidence criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.degrees_directed_by_interaction_type" title="pypath.core.interaction.Interaction.degrees_directed_by_interaction_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_directed_by_interaction_type</span></code></a></p></td>
+<td><p>Returns a <em>set</em> of nodes with the connections matching the direction, effect and evidence criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.degrees_directed_by_interaction_type_and_data_model" title="pypath.core.interaction.Interaction.degrees_directed_by_interaction_type_and_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_directed_by_interaction_type_and_data_model</span></code></a></p></td>
+<td><p>Returns a <em>set</em> of nodes with the connections matching the direction, effect and evidence criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.degrees_directed_by_interaction_type_and_data_model_and_resource" title="pypath.core.interaction.Interaction.degrees_directed_by_interaction_type_and_data_model_and_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_directed_by_interaction_type_and_data_model_and_resource</span></code></a></p></td>
+<td><p>Returns a <em>set</em> of nodes with the connections matching the direction, effect and evidence criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.degrees_directed_by_reference" title="pypath.core.interaction.Interaction.degrees_directed_by_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_directed_by_reference</span></code></a></p></td>
+<td><p>Returns a <em>set</em> of nodes with the connections matching the direction, effect and evidence criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.degrees_directed_by_resource" title="pypath.core.interaction.Interaction.degrees_directed_by_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_directed_by_resource</span></code></a></p></td>
+<td><p>Returns a <em>set</em> of nodes with the connections matching the direction, effect and evidence criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.degrees_directed_in_by_data_model" title="pypath.core.interaction.Interaction.degrees_directed_in_by_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_directed_in_by_data_model</span></code></a></p></td>
+<td><p>Returns a <em>set</em> of nodes with the connections matching the direction, effect and evidence criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.degrees_directed_in_by_interaction_type" title="pypath.core.interaction.Interaction.degrees_directed_in_by_interaction_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_directed_in_by_interaction_type</span></code></a></p></td>
+<td><p>Returns a <em>set</em> of nodes with the connections matching the direction, effect and evidence criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.degrees_directed_in_by_interaction_type_and_data_model" title="pypath.core.interaction.Interaction.degrees_directed_in_by_interaction_type_and_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_directed_in_by_interaction_type_and_data_model</span></code></a></p></td>
+<td><p>Returns a <em>set</em> of nodes with the connections matching the direction, effect and evidence criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.degrees_directed_in_by_interaction_type_and_data_model_and_resource" title="pypath.core.interaction.Interaction.degrees_directed_in_by_interaction_type_and_data_model_and_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_directed_in_by_interaction_type_and_data_model_and_resource</span></code></a></p></td>
+<td><p>Returns a <em>set</em> of nodes with the connections matching the direction, effect and evidence criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.degrees_directed_in_by_reference" title="pypath.core.interaction.Interaction.degrees_directed_in_by_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_directed_in_by_reference</span></code></a></p></td>
+<td><p>Returns a <em>set</em> of nodes with the connections matching the direction, effect and evidence criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.degrees_directed_in_by_resource" title="pypath.core.interaction.Interaction.degrees_directed_in_by_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_directed_in_by_resource</span></code></a></p></td>
+<td><p>Returns a <em>set</em> of nodes with the connections matching the direction, effect and evidence criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.degrees_directed_out_by_data_model" title="pypath.core.interaction.Interaction.degrees_directed_out_by_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_directed_out_by_data_model</span></code></a></p></td>
+<td><p>Returns a <em>set</em> of nodes with the connections matching the direction, effect and evidence criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.degrees_directed_out_by_interaction_type" title="pypath.core.interaction.Interaction.degrees_directed_out_by_interaction_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_directed_out_by_interaction_type</span></code></a></p></td>
+<td><p>Returns a <em>set</em> of nodes with the connections matching the direction, effect and evidence criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.degrees_directed_out_by_interaction_type_and_data_model" title="pypath.core.interaction.Interaction.degrees_directed_out_by_interaction_type_and_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_directed_out_by_interaction_type_and_data_model</span></code></a></p></td>
+<td><p>Returns a <em>set</em> of nodes with the connections matching the direction, effect and evidence criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.degrees_directed_out_by_interaction_type_and_data_model_and_resource" title="pypath.core.interaction.Interaction.degrees_directed_out_by_interaction_type_and_data_model_and_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_directed_out_by_interaction_type_and_data_model_and_resource</span></code></a></p></td>
+<td><p>Returns a <em>set</em> of nodes with the connections matching the direction, effect and evidence criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.degrees_directed_out_by_reference" title="pypath.core.interaction.Interaction.degrees_directed_out_by_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_directed_out_by_reference</span></code></a></p></td>
+<td><p>Returns a <em>set</em> of nodes with the connections matching the direction, effect and evidence criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.degrees_directed_out_by_resource" title="pypath.core.interaction.Interaction.degrees_directed_out_by_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_directed_out_by_resource</span></code></a></p></td>
+<td><p>Returns a <em>set</em> of nodes with the connections matching the direction, effect and evidence criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.degrees_negative_by_data_model" title="pypath.core.interaction.Interaction.degrees_negative_by_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_negative_by_data_model</span></code></a></p></td>
+<td><p>Returns a <em>set</em> of nodes with the connections matching the direction, effect and evidence criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.degrees_negative_by_interaction_type" title="pypath.core.interaction.Interaction.degrees_negative_by_interaction_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_negative_by_interaction_type</span></code></a></p></td>
+<td><p>Returns a <em>set</em> of nodes with the connections matching the direction, effect and evidence criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.degrees_negative_by_interaction_type_and_data_model" title="pypath.core.interaction.Interaction.degrees_negative_by_interaction_type_and_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_negative_by_interaction_type_and_data_model</span></code></a></p></td>
+<td><p>Returns a <em>set</em> of nodes with the connections matching the direction, effect and evidence criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.degrees_negative_by_interaction_type_and_data_model_and_resource" title="pypath.core.interaction.Interaction.degrees_negative_by_interaction_type_and_data_model_and_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_negative_by_interaction_type_and_data_model_and_resource</span></code></a></p></td>
+<td><p>Returns a <em>set</em> of nodes with the connections matching the direction, effect and evidence criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.degrees_negative_by_reference" title="pypath.core.interaction.Interaction.degrees_negative_by_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_negative_by_reference</span></code></a></p></td>
+<td><p>Returns a <em>set</em> of nodes with the connections matching the direction, effect and evidence criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.degrees_negative_by_resource" title="pypath.core.interaction.Interaction.degrees_negative_by_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_negative_by_resource</span></code></a></p></td>
+<td><p>Returns a <em>set</em> of nodes with the connections matching the direction, effect and evidence criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.degrees_negative_in_by_data_model" title="pypath.core.interaction.Interaction.degrees_negative_in_by_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_negative_in_by_data_model</span></code></a></p></td>
+<td><p>Returns a <em>set</em> of nodes with the connections matching the direction, effect and evidence criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.degrees_negative_in_by_interaction_type" title="pypath.core.interaction.Interaction.degrees_negative_in_by_interaction_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_negative_in_by_interaction_type</span></code></a></p></td>
+<td><p>Returns a <em>set</em> of nodes with the connections matching the direction, effect and evidence criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.degrees_negative_in_by_interaction_type_and_data_model" title="pypath.core.interaction.Interaction.degrees_negative_in_by_interaction_type_and_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_negative_in_by_interaction_type_and_data_model</span></code></a></p></td>
+<td><p>Returns a <em>set</em> of nodes with the connections matching the direction, effect and evidence criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.degrees_negative_in_by_interaction_type_and_data_model_and_resource" title="pypath.core.interaction.Interaction.degrees_negative_in_by_interaction_type_and_data_model_and_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_negative_in_by_interaction_type_and_data_model_and_resource</span></code></a></p></td>
+<td><p>Returns a <em>set</em> of nodes with the connections matching the direction, effect and evidence criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.degrees_negative_in_by_reference" title="pypath.core.interaction.Interaction.degrees_negative_in_by_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_negative_in_by_reference</span></code></a></p></td>
+<td><p>Returns a <em>set</em> of nodes with the connections matching the direction, effect and evidence criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.degrees_negative_in_by_resource" title="pypath.core.interaction.Interaction.degrees_negative_in_by_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_negative_in_by_resource</span></code></a></p></td>
+<td><p>Returns a <em>set</em> of nodes with the connections matching the direction, effect and evidence criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.degrees_negative_out_by_data_model" title="pypath.core.interaction.Interaction.degrees_negative_out_by_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_negative_out_by_data_model</span></code></a></p></td>
+<td><p>Returns a <em>set</em> of nodes with the connections matching the direction, effect and evidence criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.degrees_negative_out_by_interaction_type" title="pypath.core.interaction.Interaction.degrees_negative_out_by_interaction_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_negative_out_by_interaction_type</span></code></a></p></td>
+<td><p>Returns a <em>set</em> of nodes with the connections matching the direction, effect and evidence criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.degrees_negative_out_by_interaction_type_and_data_model" title="pypath.core.interaction.Interaction.degrees_negative_out_by_interaction_type_and_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_negative_out_by_interaction_type_and_data_model</span></code></a></p></td>
+<td><p>Returns a <em>set</em> of nodes with the connections matching the direction, effect and evidence criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.degrees_negative_out_by_interaction_type_and_data_model_and_resource" title="pypath.core.interaction.Interaction.degrees_negative_out_by_interaction_type_and_data_model_and_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_negative_out_by_interaction_type_and_data_model_and_resource</span></code></a></p></td>
+<td><p>Returns a <em>set</em> of nodes with the connections matching the direction, effect and evidence criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.degrees_negative_out_by_reference" title="pypath.core.interaction.Interaction.degrees_negative_out_by_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_negative_out_by_reference</span></code></a></p></td>
+<td><p>Returns a <em>set</em> of nodes with the connections matching the direction, effect and evidence criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.degrees_negative_out_by_resource" title="pypath.core.interaction.Interaction.degrees_negative_out_by_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_negative_out_by_resource</span></code></a></p></td>
+<td><p>Returns a <em>set</em> of nodes with the connections matching the direction, effect and evidence criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.degrees_non_directed_by_data_model" title="pypath.core.interaction.Interaction.degrees_non_directed_by_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_non_directed_by_data_model</span></code></a></p></td>
+<td><p>Returns a <em>set</em> of nodes with the connections matching the direction, effect and evidence criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.degrees_non_directed_by_interaction_type" title="pypath.core.interaction.Interaction.degrees_non_directed_by_interaction_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_non_directed_by_interaction_type</span></code></a></p></td>
+<td><p>Returns a <em>set</em> of nodes with the connections matching the direction, effect and evidence criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.degrees_non_directed_by_interaction_type_and_data_model" title="pypath.core.interaction.Interaction.degrees_non_directed_by_interaction_type_and_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_non_directed_by_interaction_type_and_data_model</span></code></a></p></td>
+<td><p>Returns a <em>set</em> of nodes with the connections matching the direction, effect and evidence criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.degrees_non_directed_by_interaction_type_and_data_model_and_resource" title="pypath.core.interaction.Interaction.degrees_non_directed_by_interaction_type_and_data_model_and_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_non_directed_by_interaction_type_and_data_model_and_resource</span></code></a></p></td>
+<td><p>Returns a <em>set</em> of nodes with the connections matching the direction, effect and evidence criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.degrees_non_directed_by_reference" title="pypath.core.interaction.Interaction.degrees_non_directed_by_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_non_directed_by_reference</span></code></a></p></td>
+<td><p>Returns a <em>set</em> of nodes with the connections matching the direction, effect and evidence criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.degrees_non_directed_by_resource" title="pypath.core.interaction.Interaction.degrees_non_directed_by_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_non_directed_by_resource</span></code></a></p></td>
+<td><p>Returns a <em>set</em> of nodes with the connections matching the direction, effect and evidence criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.degrees_positive_by_data_model" title="pypath.core.interaction.Interaction.degrees_positive_by_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_positive_by_data_model</span></code></a></p></td>
+<td><p>Returns a <em>set</em> of nodes with the connections matching the direction, effect and evidence criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.degrees_positive_by_interaction_type" title="pypath.core.interaction.Interaction.degrees_positive_by_interaction_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_positive_by_interaction_type</span></code></a></p></td>
+<td><p>Returns a <em>set</em> of nodes with the connections matching the direction, effect and evidence criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.degrees_positive_by_interaction_type_and_data_model" title="pypath.core.interaction.Interaction.degrees_positive_by_interaction_type_and_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_positive_by_interaction_type_and_data_model</span></code></a></p></td>
+<td><p>Returns a <em>set</em> of nodes with the connections matching the direction, effect and evidence criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.degrees_positive_by_interaction_type_and_data_model_and_resource" title="pypath.core.interaction.Interaction.degrees_positive_by_interaction_type_and_data_model_and_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_positive_by_interaction_type_and_data_model_and_resource</span></code></a></p></td>
+<td><p>Returns a <em>set</em> of nodes with the connections matching the direction, effect and evidence criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.degrees_positive_by_reference" title="pypath.core.interaction.Interaction.degrees_positive_by_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_positive_by_reference</span></code></a></p></td>
+<td><p>Returns a <em>set</em> of nodes with the connections matching the direction, effect and evidence criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.degrees_positive_by_resource" title="pypath.core.interaction.Interaction.degrees_positive_by_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_positive_by_resource</span></code></a></p></td>
+<td><p>Returns a <em>set</em> of nodes with the connections matching the direction, effect and evidence criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.degrees_positive_in_by_data_model" title="pypath.core.interaction.Interaction.degrees_positive_in_by_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_positive_in_by_data_model</span></code></a></p></td>
+<td><p>Returns a <em>set</em> of nodes with the connections matching the direction, effect and evidence criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.degrees_positive_in_by_interaction_type" title="pypath.core.interaction.Interaction.degrees_positive_in_by_interaction_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_positive_in_by_interaction_type</span></code></a></p></td>
+<td><p>Returns a <em>set</em> of nodes with the connections matching the direction, effect and evidence criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.degrees_positive_in_by_interaction_type_and_data_model" title="pypath.core.interaction.Interaction.degrees_positive_in_by_interaction_type_and_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_positive_in_by_interaction_type_and_data_model</span></code></a></p></td>
+<td><p>Returns a <em>set</em> of nodes with the connections matching the direction, effect and evidence criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.degrees_positive_in_by_interaction_type_and_data_model_and_resource" title="pypath.core.interaction.Interaction.degrees_positive_in_by_interaction_type_and_data_model_and_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_positive_in_by_interaction_type_and_data_model_and_resource</span></code></a></p></td>
+<td><p>Returns a <em>set</em> of nodes with the connections matching the direction, effect and evidence criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.degrees_positive_in_by_reference" title="pypath.core.interaction.Interaction.degrees_positive_in_by_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_positive_in_by_reference</span></code></a></p></td>
+<td><p>Returns a <em>set</em> of nodes with the connections matching the direction, effect and evidence criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.degrees_positive_in_by_resource" title="pypath.core.interaction.Interaction.degrees_positive_in_by_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_positive_in_by_resource</span></code></a></p></td>
+<td><p>Returns a <em>set</em> of nodes with the connections matching the direction, effect and evidence criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.degrees_positive_out_by_data_model" title="pypath.core.interaction.Interaction.degrees_positive_out_by_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_positive_out_by_data_model</span></code></a></p></td>
+<td><p>Returns a <em>set</em> of nodes with the connections matching the direction, effect and evidence criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.degrees_positive_out_by_interaction_type" title="pypath.core.interaction.Interaction.degrees_positive_out_by_interaction_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_positive_out_by_interaction_type</span></code></a></p></td>
+<td><p>Returns a <em>set</em> of nodes with the connections matching the direction, effect and evidence criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.degrees_positive_out_by_interaction_type_and_data_model" title="pypath.core.interaction.Interaction.degrees_positive_out_by_interaction_type_and_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_positive_out_by_interaction_type_and_data_model</span></code></a></p></td>
+<td><p>Returns a <em>set</em> of nodes with the connections matching the direction, effect and evidence criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.degrees_positive_out_by_interaction_type_and_data_model_and_resource" title="pypath.core.interaction.Interaction.degrees_positive_out_by_interaction_type_and_data_model_and_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_positive_out_by_interaction_type_and_data_model_and_resource</span></code></a></p></td>
+<td><p>Returns a <em>set</em> of nodes with the connections matching the direction, effect and evidence criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.degrees_positive_out_by_reference" title="pypath.core.interaction.Interaction.degrees_positive_out_by_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_positive_out_by_reference</span></code></a></p></td>
+<td><p>Returns a <em>set</em> of nodes with the connections matching the direction, effect and evidence criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.degrees_positive_out_by_resource" title="pypath.core.interaction.Interaction.degrees_positive_out_by_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_positive_out_by_resource</span></code></a></p></td>
+<td><p>Returns a <em>set</em> of nodes with the connections matching the direction, effect and evidence criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.degrees_signed_by_data_model" title="pypath.core.interaction.Interaction.degrees_signed_by_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_signed_by_data_model</span></code></a></p></td>
+<td><p>Returns a <em>set</em> of nodes with the connections matching the direction, effect and evidence criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.degrees_signed_by_interaction_type" title="pypath.core.interaction.Interaction.degrees_signed_by_interaction_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_signed_by_interaction_type</span></code></a></p></td>
+<td><p>Returns a <em>set</em> of nodes with the connections matching the direction, effect and evidence criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.degrees_signed_by_interaction_type_and_data_model" title="pypath.core.interaction.Interaction.degrees_signed_by_interaction_type_and_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_signed_by_interaction_type_and_data_model</span></code></a></p></td>
+<td><p>Returns a <em>set</em> of nodes with the connections matching the direction, effect and evidence criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.degrees_signed_by_interaction_type_and_data_model_and_resource" title="pypath.core.interaction.Interaction.degrees_signed_by_interaction_type_and_data_model_and_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_signed_by_interaction_type_and_data_model_and_resource</span></code></a></p></td>
+<td><p>Returns a <em>set</em> of nodes with the connections matching the direction, effect and evidence criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.degrees_signed_by_reference" title="pypath.core.interaction.Interaction.degrees_signed_by_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_signed_by_reference</span></code></a></p></td>
+<td><p>Returns a <em>set</em> of nodes with the connections matching the direction, effect and evidence criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.degrees_signed_by_resource" title="pypath.core.interaction.Interaction.degrees_signed_by_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_signed_by_resource</span></code></a></p></td>
+<td><p>Returns a <em>set</em> of nodes with the connections matching the direction, effect and evidence criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.degrees_signed_in_by_data_model" title="pypath.core.interaction.Interaction.degrees_signed_in_by_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_signed_in_by_data_model</span></code></a></p></td>
+<td><p>Returns a <em>set</em> of nodes with the connections matching the direction, effect and evidence criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.degrees_signed_in_by_interaction_type" title="pypath.core.interaction.Interaction.degrees_signed_in_by_interaction_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_signed_in_by_interaction_type</span></code></a></p></td>
+<td><p>Returns a <em>set</em> of nodes with the connections matching the direction, effect and evidence criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.degrees_signed_in_by_interaction_type_and_data_model" title="pypath.core.interaction.Interaction.degrees_signed_in_by_interaction_type_and_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_signed_in_by_interaction_type_and_data_model</span></code></a></p></td>
+<td><p>Returns a <em>set</em> of nodes with the connections matching the direction, effect and evidence criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.degrees_signed_in_by_interaction_type_and_data_model_and_resource" title="pypath.core.interaction.Interaction.degrees_signed_in_by_interaction_type_and_data_model_and_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_signed_in_by_interaction_type_and_data_model_and_resource</span></code></a></p></td>
+<td><p>Returns a <em>set</em> of nodes with the connections matching the direction, effect and evidence criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.degrees_signed_in_by_reference" title="pypath.core.interaction.Interaction.degrees_signed_in_by_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_signed_in_by_reference</span></code></a></p></td>
+<td><p>Returns a <em>set</em> of nodes with the connections matching the direction, effect and evidence criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.degrees_signed_in_by_resource" title="pypath.core.interaction.Interaction.degrees_signed_in_by_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_signed_in_by_resource</span></code></a></p></td>
+<td><p>Returns a <em>set</em> of nodes with the connections matching the direction, effect and evidence criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.degrees_signed_out_by_data_model" title="pypath.core.interaction.Interaction.degrees_signed_out_by_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_signed_out_by_data_model</span></code></a></p></td>
+<td><p>Returns a <em>set</em> of nodes with the connections matching the direction, effect and evidence criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.degrees_signed_out_by_interaction_type" title="pypath.core.interaction.Interaction.degrees_signed_out_by_interaction_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_signed_out_by_interaction_type</span></code></a></p></td>
+<td><p>Returns a <em>set</em> of nodes with the connections matching the direction, effect and evidence criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.degrees_signed_out_by_interaction_type_and_data_model" title="pypath.core.interaction.Interaction.degrees_signed_out_by_interaction_type_and_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_signed_out_by_interaction_type_and_data_model</span></code></a></p></td>
+<td><p>Returns a <em>set</em> of nodes with the connections matching the direction, effect and evidence criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.degrees_signed_out_by_interaction_type_and_data_model_and_resource" title="pypath.core.interaction.Interaction.degrees_signed_out_by_interaction_type_and_data_model_and_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_signed_out_by_interaction_type_and_data_model_and_resource</span></code></a></p></td>
+<td><p>Returns a <em>set</em> of nodes with the connections matching the direction, effect and evidence criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.degrees_signed_out_by_reference" title="pypath.core.interaction.Interaction.degrees_signed_out_by_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_signed_out_by_reference</span></code></a></p></td>
+<td><p>Returns a <em>set</em> of nodes with the connections matching the direction, effect and evidence criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.degrees_signed_out_by_resource" title="pypath.core.interaction.Interaction.degrees_signed_out_by_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_signed_out_by_resource</span></code></a></p></td>
+<td><p>Returns a <em>set</em> of nodes with the connections matching the direction, effect and evidence criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.degrees_undirected_by_data_model" title="pypath.core.interaction.Interaction.degrees_undirected_by_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_undirected_by_data_model</span></code></a></p></td>
+<td><p>Returns a <em>set</em> of nodes with the connections matching the direction, effect and evidence criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.degrees_undirected_by_interaction_type" title="pypath.core.interaction.Interaction.degrees_undirected_by_interaction_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_undirected_by_interaction_type</span></code></a></p></td>
+<td><p>Returns a <em>set</em> of nodes with the connections matching the direction, effect and evidence criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.degrees_undirected_by_interaction_type_and_data_model" title="pypath.core.interaction.Interaction.degrees_undirected_by_interaction_type_and_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_undirected_by_interaction_type_and_data_model</span></code></a></p></td>
+<td><p>Returns a <em>set</em> of nodes with the connections matching the direction, effect and evidence criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.degrees_undirected_by_interaction_type_and_data_model_and_resource" title="pypath.core.interaction.Interaction.degrees_undirected_by_interaction_type_and_data_model_and_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_undirected_by_interaction_type_and_data_model_and_resource</span></code></a></p></td>
+<td><p>Returns a <em>set</em> of nodes with the connections matching the direction, effect and evidence criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.degrees_undirected_by_reference" title="pypath.core.interaction.Interaction.degrees_undirected_by_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_undirected_by_reference</span></code></a></p></td>
+<td><p>Returns a <em>set</em> of nodes with the connections matching the direction, effect and evidence criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.degrees_undirected_by_resource" title="pypath.core.interaction.Interaction.degrees_undirected_by_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_undirected_by_resource</span></code></a></p></td>
+<td><p>Returns a <em>set</em> of nodes with the connections matching the direction, effect and evidence criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.get_data_models" title="pypath.core.interaction.Interaction.get_data_models"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_data_models</span></code></a></p></td>
+<td><p>Retrieves data models matching the criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.get_datasets" title="pypath.core.interaction.Interaction.get_datasets"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_datasets</span></code></a></p></td>
+<td><p>Retrieves datasets matching the criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.get_degrees_directed" title="pypath.core.interaction.Interaction.get_degrees_directed"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_degrees_directed</span></code></a></p></td>
+<td><p>Returns a <em>set</em> of nodes with the connections matching the direction, effect and evidence criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.get_degrees_directed_in" title="pypath.core.interaction.Interaction.get_degrees_directed_in"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_degrees_directed_in</span></code></a></p></td>
+<td><p>Returns a <em>set</em> of nodes with the connections matching the direction, effect and evidence criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.get_degrees_directed_out" title="pypath.core.interaction.Interaction.get_degrees_directed_out"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_degrees_directed_out</span></code></a></p></td>
+<td><p>Returns a <em>set</em> of nodes with the connections matching the direction, effect and evidence criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.get_degrees_negative" title="pypath.core.interaction.Interaction.get_degrees_negative"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_degrees_negative</span></code></a></p></td>
+<td><p>Returns a <em>set</em> of nodes with the connections matching the direction, effect and evidence criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.get_degrees_negative_in" title="pypath.core.interaction.Interaction.get_degrees_negative_in"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_degrees_negative_in</span></code></a></p></td>
+<td><p>Returns a <em>set</em> of nodes with the connections matching the direction, effect and evidence criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.get_degrees_negative_out" title="pypath.core.interaction.Interaction.get_degrees_negative_out"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_degrees_negative_out</span></code></a></p></td>
+<td><p>Returns a <em>set</em> of nodes with the connections matching the direction, effect and evidence criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.get_degrees_non_directed" title="pypath.core.interaction.Interaction.get_degrees_non_directed"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_degrees_non_directed</span></code></a></p></td>
+<td><p>Returns a <em>set</em> of nodes with the connections matching the direction, effect and evidence criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.get_degrees_positive" title="pypath.core.interaction.Interaction.get_degrees_positive"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_degrees_positive</span></code></a></p></td>
+<td><p>Returns a <em>set</em> of nodes with the connections matching the direction, effect and evidence criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.get_degrees_positive_in" title="pypath.core.interaction.Interaction.get_degrees_positive_in"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_degrees_positive_in</span></code></a></p></td>
+<td><p>Returns a <em>set</em> of nodes with the connections matching the direction, effect and evidence criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.get_degrees_positive_out" title="pypath.core.interaction.Interaction.get_degrees_positive_out"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_degrees_positive_out</span></code></a></p></td>
+<td><p>Returns a <em>set</em> of nodes with the connections matching the direction, effect and evidence criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.get_degrees_signed" title="pypath.core.interaction.Interaction.get_degrees_signed"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_degrees_signed</span></code></a></p></td>
+<td><p>Returns a <em>set</em> of nodes with the connections matching the direction, effect and evidence criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.get_degrees_signed_in" title="pypath.core.interaction.Interaction.get_degrees_signed_in"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_degrees_signed_in</span></code></a></p></td>
+<td><p>Returns a <em>set</em> of nodes with the connections matching the direction, effect and evidence criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.get_degrees_signed_out" title="pypath.core.interaction.Interaction.get_degrees_signed_out"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_degrees_signed_out</span></code></a></p></td>
+<td><p>Returns a <em>set</em> of nodes with the connections matching the direction, effect and evidence criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.get_degrees_undirected" title="pypath.core.interaction.Interaction.get_degrees_undirected"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_degrees_undirected</span></code></a></p></td>
+<td><p>Returns a <em>set</em> of nodes with the connections matching the direction, effect and evidence criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.get_interaction_types" title="pypath.core.interaction.Interaction.get_interaction_types"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_interaction_types</span></code></a></p></td>
+<td><p>Retrieves interaction types matching the criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.get_references" title="pypath.core.interaction.Interaction.get_references"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_references</span></code></a></p></td>
+<td><p>Retrieves references matching the criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.get_resource_names" title="pypath.core.interaction.Interaction.get_resource_names"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_resource_names</span></code></a></p></td>
+<td><p>Retrieves resource names matching the criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.get_resource_names_via" title="pypath.core.interaction.Interaction.get_resource_names_via"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_resource_names_via</span></code></a></p></td>
+<td><p>Retrieves resource names via matching the criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.get_resources" title="pypath.core.interaction.Interaction.get_resources"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_resources</span></code></a></p></td>
+<td><p>Retrieves resources matching the criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.get_resources_via" title="pypath.core.interaction.Interaction.get_resources_via"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_resources_via</span></code></a></p></td>
+<td><p>Retrieves resources via matching the criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.interaction_types_by_data_model" title="pypath.core.interaction.Interaction.interaction_types_by_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">interaction_types_by_data_model</span></code></a></p></td>
+<td><p>Retrieves interaction types matching the criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.interaction_types_by_interaction_type" title="pypath.core.interaction.Interaction.interaction_types_by_interaction_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">interaction_types_by_interaction_type</span></code></a></p></td>
+<td><p>Retrieves interaction types matching the criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.interaction_types_by_interaction_type_and_data_model" title="pypath.core.interaction.Interaction.interaction_types_by_interaction_type_and_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">interaction_types_by_interaction_type_and_data_model</span></code></a></p></td>
+<td><p>Retrieves interaction types matching the criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.interaction_types_by_interaction_type_and_data_model_and_resource" title="pypath.core.interaction.Interaction.interaction_types_by_interaction_type_and_data_model_and_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">interaction_types_by_interaction_type_and_data_model_and_resource</span></code></a></p></td>
+<td><p>Retrieves interaction types matching the criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.interaction_types_by_reference" title="pypath.core.interaction.Interaction.interaction_types_by_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">interaction_types_by_reference</span></code></a></p></td>
+<td><p>Retrieves interaction types matching the criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.interaction_types_by_resource" title="pypath.core.interaction.Interaction.interaction_types_by_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">interaction_types_by_resource</span></code></a></p></td>
+<td><p>Retrieves interaction types matching the criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.references_by_data_model" title="pypath.core.interaction.Interaction.references_by_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">references_by_data_model</span></code></a></p></td>
+<td><p>Retrieves references matching the criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.references_by_interaction_type" title="pypath.core.interaction.Interaction.references_by_interaction_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">references_by_interaction_type</span></code></a></p></td>
+<td><p>Retrieves references matching the criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.references_by_interaction_type_and_data_model" title="pypath.core.interaction.Interaction.references_by_interaction_type_and_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">references_by_interaction_type_and_data_model</span></code></a></p></td>
+<td><p>Retrieves references matching the criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.references_by_interaction_type_and_data_model_and_resource" title="pypath.core.interaction.Interaction.references_by_interaction_type_and_data_model_and_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">references_by_interaction_type_and_data_model_and_resource</span></code></a></p></td>
+<td><p>Retrieves references matching the criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.references_by_reference" title="pypath.core.interaction.Interaction.references_by_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">references_by_reference</span></code></a></p></td>
+<td><p>Retrieves references matching the criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.references_by_resource" title="pypath.core.interaction.Interaction.references_by_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">references_by_resource</span></code></a></p></td>
+<td><p>Retrieves references matching the criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.resource_names_by_data_model" title="pypath.core.interaction.Interaction.resource_names_by_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">resource_names_by_data_model</span></code></a></p></td>
+<td><p>Retrieves resource names matching the criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.resource_names_by_interaction_type" title="pypath.core.interaction.Interaction.resource_names_by_interaction_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">resource_names_by_interaction_type</span></code></a></p></td>
+<td><p>Retrieves resource names matching the criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.resource_names_by_interaction_type_and_data_model" title="pypath.core.interaction.Interaction.resource_names_by_interaction_type_and_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">resource_names_by_interaction_type_and_data_model</span></code></a></p></td>
+<td><p>Retrieves resource names matching the criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.resource_names_by_interaction_type_and_data_model_and_resource" title="pypath.core.interaction.Interaction.resource_names_by_interaction_type_and_data_model_and_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">resource_names_by_interaction_type_and_data_model_and_resource</span></code></a></p></td>
+<td><p>Retrieves resource names matching the criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.resource_names_by_reference" title="pypath.core.interaction.Interaction.resource_names_by_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">resource_names_by_reference</span></code></a></p></td>
+<td><p>Retrieves resource names matching the criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.resource_names_by_resource" title="pypath.core.interaction.Interaction.resource_names_by_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">resource_names_by_resource</span></code></a></p></td>
+<td><p>Retrieves resource names matching the criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.resource_names_via_by_data_model" title="pypath.core.interaction.Interaction.resource_names_via_by_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">resource_names_via_by_data_model</span></code></a></p></td>
+<td><p>Retrieves resource names via matching the criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.resource_names_via_by_interaction_type" title="pypath.core.interaction.Interaction.resource_names_via_by_interaction_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">resource_names_via_by_interaction_type</span></code></a></p></td>
+<td><p>Retrieves resource names via matching the criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.resource_names_via_by_interaction_type_and_data_model" title="pypath.core.interaction.Interaction.resource_names_via_by_interaction_type_and_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">resource_names_via_by_interaction_type_and_data_model</span></code></a></p></td>
+<td><p>Retrieves resource names via matching the criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.resource_names_via_by_interaction_type_and_data_model_and_resource" title="pypath.core.interaction.Interaction.resource_names_via_by_interaction_type_and_data_model_and_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">resource_names_via_by_interaction_type_and_data_model_and_resource</span></code></a></p></td>
+<td><p>Retrieves resource names via matching the criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.resource_names_via_by_reference" title="pypath.core.interaction.Interaction.resource_names_via_by_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">resource_names_via_by_reference</span></code></a></p></td>
+<td><p>Retrieves resource names via matching the criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.resource_names_via_by_resource" title="pypath.core.interaction.Interaction.resource_names_via_by_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">resource_names_via_by_resource</span></code></a></p></td>
+<td><p>Retrieves resource names via matching the criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.resources_by_data_model" title="pypath.core.interaction.Interaction.resources_by_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">resources_by_data_model</span></code></a></p></td>
+<td><p>Retrieves resources matching the criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.resources_by_interaction_type" title="pypath.core.interaction.Interaction.resources_by_interaction_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">resources_by_interaction_type</span></code></a></p></td>
+<td><p>Retrieves resources matching the criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.resources_by_interaction_type_and_data_model" title="pypath.core.interaction.Interaction.resources_by_interaction_type_and_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">resources_by_interaction_type_and_data_model</span></code></a></p></td>
+<td><p>Retrieves resources matching the criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.resources_by_interaction_type_and_data_model_and_resource" title="pypath.core.interaction.Interaction.resources_by_interaction_type_and_data_model_and_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">resources_by_interaction_type_and_data_model_and_resource</span></code></a></p></td>
+<td><p>Retrieves resources matching the criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.resources_by_reference" title="pypath.core.interaction.Interaction.resources_by_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">resources_by_reference</span></code></a></p></td>
+<td><p>Retrieves resources matching the criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.resources_by_resource" title="pypath.core.interaction.Interaction.resources_by_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">resources_by_resource</span></code></a></p></td>
+<td><p>Retrieves resources matching the criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.resources_via_by_data_model" title="pypath.core.interaction.Interaction.resources_via_by_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">resources_via_by_data_model</span></code></a></p></td>
+<td><p>Retrieves resources via matching the criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.resources_via_by_interaction_type" title="pypath.core.interaction.Interaction.resources_via_by_interaction_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">resources_via_by_interaction_type</span></code></a></p></td>
+<td><p>Retrieves resources via matching the criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.resources_via_by_interaction_type_and_data_model" title="pypath.core.interaction.Interaction.resources_via_by_interaction_type_and_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">resources_via_by_interaction_type_and_data_model</span></code></a></p></td>
+<td><p>Retrieves resources via matching the criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.resources_via_by_interaction_type_and_data_model_and_resource" title="pypath.core.interaction.Interaction.resources_via_by_interaction_type_and_data_model_and_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">resources_via_by_interaction_type_and_data_model_and_resource</span></code></a></p></td>
+<td><p>Retrieves resources via matching the criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.resources_via_by_reference" title="pypath.core.interaction.Interaction.resources_via_by_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">resources_via_by_reference</span></code></a></p></td>
+<td><p>Retrieves resources via matching the criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.Interaction.resources_via_by_resource" title="pypath.core.interaction.Interaction.resources_via_by_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">resources_via_by_resource</span></code></a></p></td>
+<td><p>Retrieves resources via matching the criteria.</p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.add_evidence">
+<span class="sig-name descname"><span class="pre">add_evidence</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">evidence</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">direction</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'undirected'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">attrs</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/interaction.html#Interaction.add_evidence"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.interaction.Interaction.add_evidence" title="Link to this definition">§</a></dt>
+<dd><p>Adds directionality information with the corresponding data
+source named. Modifies self attributes <code class="xref py py-attr docutils literal notranslate"><span class="pre">dirs</span></code> and
+<code class="xref py py-attr docutils literal notranslate"><span class="pre">sources</span></code>.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>evidence</strong> (<a class="reference internal" href="pypath.internals.resource.NetworkResource.html#pypath.internals.resource.NetworkResource" title="pypath.internals.resource.NetworkResource"><em>resource.NetworkResource</em></a><em>,</em><a class="reference internal" href="pypath.core.evidence.Evidence.html#pypath.core.evidence.Evidence" title="pypath.core.evidence.Evidence"><em>evidence.Evidence</em></a>) – Either a <code class="docutils literal notranslate"><span class="pre">pypath.evidence.Evidence</span></code> object or a resource as
+<code class="docutils literal notranslate"><span class="pre">pypath.resource.NetworkResource</span></code> object. In the latter case
+the references can be provided in a separate argument.</p></li>
+<li><p><strong>direction</strong> (<em>tuple</em>) – Or [str], the directionality key for which the value on
+<code class="xref py py-attr docutils literal notranslate"><span class="pre">dirs</span></code> has to be set <code class="docutils literal notranslate"><span class="pre">True</span></code>.</p></li>
+<li><p><strong>effect</strong> (<em>int</em>) – The causal effect of the interaction. 1 or ‘stimulation’
+corresponds to a stimulatory, -1 or ‘inhibition’ to an
+inhibitory while 0 to an unknown or neutral effect.</p></li>
+<li><p><strong>references</strong> (<em>set</em><em>,</em><em>NoneType</em>) – A set of references, used only if the resource have been provided
+as <code class="docutils literal notranslate"><span class="pre">NetworkResource</span></code> object.</p></li>
+<li><p><strong>attrs</strong> (<em>dict</em>) – Custom (resource specific) attributes.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.add_sign">
+<span class="sig-name descname"><span class="pre">add_sign</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">direction</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">tuple</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">sign</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resource</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">set</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resource_name</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">'PPI'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">attrs</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">dict</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/interaction.html#Interaction.add_sign"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.interaction.Interaction.add_sign" title="Link to this definition">§</a></dt>
+<dd><p>Sets sign and source information on a given direction of the
+edge. Modifies the attributes <code class="xref py py-attr docutils literal notranslate"><span class="pre">positive</span></code> and
+<code class="xref py py-attr docutils literal notranslate"><span class="pre">positive_sources</span></code> or <code class="xref py py-attr docutils literal notranslate"><span class="pre">negative</span></code> and
+<code class="xref py py-attr docutils literal notranslate"><span class="pre">negative_sources</span></code> depending on the sign. Direction is
+also updated accordingly, which also modifies the attributes
+<code class="xref py py-attr docutils literal notranslate"><span class="pre">dirs</span></code> and <code class="xref py py-attr docutils literal notranslate"><span class="pre">sources</span></code>.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>direction:</dt><dd><p>Pair of edge nodes specifying the direction from which the
+information is to be set/updated.</p>
+</dd>
+<dt>sign:</dt><dd><p>Specifies the type of interaction. Either <code class="docutils literal notranslate"><span class="pre">'positive'</span></code> or
+<code class="docutils literal notranslate"><span class="pre">'negative'</span></code>.</p>
+</dd>
+<dt>resource:</dt><dd><p>Contains the name(s) of the source(s) from which the
+information was obtained.</p>
+</dd>
+<dt>attrs:</dt><dd><p>Custom (resource specific) edge attributes.</p>
+</dd>
+<dt>kwargs:</dt><dd><p>Passed to <code class="docutils literal notranslate"><span class="pre">pypath.resource.NetworkResource</span></code> if <code class="docutils literal notranslate"><span class="pre">resource</span></code>
+is not already a <code class="docutils literal notranslate"><span class="pre">NetworkResource</span></code> or <code class="docutils literal notranslate"><span class="pre">Evidence</span></code>
+instance.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.asdict">
+<span class="sig-name descname"><span class="pre">asdict</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">direction</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">tuple</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><span class="pre">dict</span></span></span><a class="reference internal" href="../_modules/pypath/core/interaction.html#Interaction.asdict"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.interaction.Interaction.asdict" title="Link to this definition">§</a></dt>
+<dd><p>Dictionary representation of the evidences.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.complex_identifiers_by_data_model">
+<span class="sig-name descname"><span class="pre">complex_identifiers_by_data_model</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.complex_identifiers_by_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the entities involved in interactions matching the criteria.
+It either returns both interacting entities in a <em>set</em> or an empty
+<em>set</em>. This may not sound so useful at the level of this object but
+becomes more useful once we want to collect entities having certain
+kind of interactions across a series of <cite>Interaction</cite> objects.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>entity_type</strong> (<em>str</em>) – The type of the molecular entity. Possible values: <cite>protein</cite>,
+<cite>complex</cite>, <cite>mirna</cite>, <cite>small_molecule</cite>.</p></li>
+<li><p><strong>return_type</strong> (<em>str</em>) – The type of values to return. Default is
+py:class:<code class="docutils literal notranslate"><span class="pre">pypath.entity.Entity</span></code> objects, alternatives are
+<code class="docutils literal notranslate"><span class="pre">labels</span></code>  <code class="docutils literal notranslate"><span class="pre">identifiers</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.complex_identifiers_by_interaction_type">
+<span class="sig-name descname"><span class="pre">complex_identifiers_by_interaction_type</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.complex_identifiers_by_interaction_type" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the entities involved in interactions matching the criteria.
+It either returns both interacting entities in a <em>set</em> or an empty
+<em>set</em>. This may not sound so useful at the level of this object but
+becomes more useful once we want to collect entities having certain
+kind of interactions across a series of <cite>Interaction</cite> objects.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>entity_type</strong> (<em>str</em>) – The type of the molecular entity. Possible values: <cite>protein</cite>,
+<cite>complex</cite>, <cite>mirna</cite>, <cite>small_molecule</cite>.</p></li>
+<li><p><strong>return_type</strong> (<em>str</em>) – The type of values to return. Default is
+py:class:<code class="docutils literal notranslate"><span class="pre">pypath.entity.Entity</span></code> objects, alternatives are
+<code class="docutils literal notranslate"><span class="pre">labels</span></code>  <code class="docutils literal notranslate"><span class="pre">identifiers</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.complex_identifiers_by_interaction_type_and_data_model">
+<span class="sig-name descname"><span class="pre">complex_identifiers_by_interaction_type_and_data_model</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.complex_identifiers_by_interaction_type_and_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the entities involved in interactions matching the criteria.
+It either returns both interacting entities in a <em>set</em> or an empty
+<em>set</em>. This may not sound so useful at the level of this object but
+becomes more useful once we want to collect entities having certain
+kind of interactions across a series of <cite>Interaction</cite> objects.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>entity_type</strong> (<em>str</em>) – The type of the molecular entity. Possible values: <cite>protein</cite>,
+<cite>complex</cite>, <cite>mirna</cite>, <cite>small_molecule</cite>.</p></li>
+<li><p><strong>return_type</strong> (<em>str</em>) – The type of values to return. Default is
+py:class:<code class="docutils literal notranslate"><span class="pre">pypath.entity.Entity</span></code> objects, alternatives are
+<code class="docutils literal notranslate"><span class="pre">labels</span></code>  <code class="docutils literal notranslate"><span class="pre">identifiers</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.complex_identifiers_by_interaction_type_and_data_model_and_resource">
+<span class="sig-name descname"><span class="pre">complex_identifiers_by_interaction_type_and_data_model_and_resource</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.complex_identifiers_by_interaction_type_and_data_model_and_resource" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the entities involved in interactions matching the criteria.
+It either returns both interacting entities in a <em>set</em> or an empty
+<em>set</em>. This may not sound so useful at the level of this object but
+becomes more useful once we want to collect entities having certain
+kind of interactions across a series of <cite>Interaction</cite> objects.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>entity_type</strong> (<em>str</em>) – The type of the molecular entity. Possible values: <cite>protein</cite>,
+<cite>complex</cite>, <cite>mirna</cite>, <cite>small_molecule</cite>.</p></li>
+<li><p><strong>return_type</strong> (<em>str</em>) – The type of values to return. Default is
+py:class:<code class="docutils literal notranslate"><span class="pre">pypath.entity.Entity</span></code> objects, alternatives are
+<code class="docutils literal notranslate"><span class="pre">labels</span></code>  <code class="docutils literal notranslate"><span class="pre">identifiers</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.complex_identifiers_by_reference">
+<span class="sig-name descname"><span class="pre">complex_identifiers_by_reference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.complex_identifiers_by_reference" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the entities involved in interactions matching the criteria.
+It either returns both interacting entities in a <em>set</em> or an empty
+<em>set</em>. This may not sound so useful at the level of this object but
+becomes more useful once we want to collect entities having certain
+kind of interactions across a series of <cite>Interaction</cite> objects.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>entity_type</strong> (<em>str</em>) – The type of the molecular entity. Possible values: <cite>protein</cite>,
+<cite>complex</cite>, <cite>mirna</cite>, <cite>small_molecule</cite>.</p></li>
+<li><p><strong>return_type</strong> (<em>str</em>) – The type of values to return. Default is
+py:class:<code class="docutils literal notranslate"><span class="pre">pypath.entity.Entity</span></code> objects, alternatives are
+<code class="docutils literal notranslate"><span class="pre">labels</span></code>  <code class="docutils literal notranslate"><span class="pre">identifiers</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.complex_identifiers_by_resource">
+<span class="sig-name descname"><span class="pre">complex_identifiers_by_resource</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.complex_identifiers_by_resource" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the entities involved in interactions matching the criteria.
+It either returns both interacting entities in a <em>set</em> or an empty
+<em>set</em>. This may not sound so useful at the level of this object but
+becomes more useful once we want to collect entities having certain
+kind of interactions across a series of <cite>Interaction</cite> objects.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>entity_type</strong> (<em>str</em>) – The type of the molecular entity. Possible values: <cite>protein</cite>,
+<cite>complex</cite>, <cite>mirna</cite>, <cite>small_molecule</cite>.</p></li>
+<li><p><strong>return_type</strong> (<em>str</em>) – The type of values to return. Default is
+py:class:<code class="docutils literal notranslate"><span class="pre">pypath.entity.Entity</span></code> objects, alternatives are
+<code class="docutils literal notranslate"><span class="pre">labels</span></code>  <code class="docutils literal notranslate"><span class="pre">identifiers</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.complex_labels_by_data_model">
+<span class="sig-name descname"><span class="pre">complex_labels_by_data_model</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.complex_labels_by_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the entities involved in interactions matching the criteria.
+It either returns both interacting entities in a <em>set</em> or an empty
+<em>set</em>. This may not sound so useful at the level of this object but
+becomes more useful once we want to collect entities having certain
+kind of interactions across a series of <cite>Interaction</cite> objects.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>entity_type</strong> (<em>str</em>) – The type of the molecular entity. Possible values: <cite>protein</cite>,
+<cite>complex</cite>, <cite>mirna</cite>, <cite>small_molecule</cite>.</p></li>
+<li><p><strong>return_type</strong> (<em>str</em>) – The type of values to return. Default is
+py:class:<code class="docutils literal notranslate"><span class="pre">pypath.entity.Entity</span></code> objects, alternatives are
+<code class="docutils literal notranslate"><span class="pre">labels</span></code>  <code class="docutils literal notranslate"><span class="pre">identifiers</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.complex_labels_by_interaction_type">
+<span class="sig-name descname"><span class="pre">complex_labels_by_interaction_type</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.complex_labels_by_interaction_type" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the entities involved in interactions matching the criteria.
+It either returns both interacting entities in a <em>set</em> or an empty
+<em>set</em>. This may not sound so useful at the level of this object but
+becomes more useful once we want to collect entities having certain
+kind of interactions across a series of <cite>Interaction</cite> objects.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>entity_type</strong> (<em>str</em>) – The type of the molecular entity. Possible values: <cite>protein</cite>,
+<cite>complex</cite>, <cite>mirna</cite>, <cite>small_molecule</cite>.</p></li>
+<li><p><strong>return_type</strong> (<em>str</em>) – The type of values to return. Default is
+py:class:<code class="docutils literal notranslate"><span class="pre">pypath.entity.Entity</span></code> objects, alternatives are
+<code class="docutils literal notranslate"><span class="pre">labels</span></code>  <code class="docutils literal notranslate"><span class="pre">identifiers</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.complex_labels_by_interaction_type_and_data_model">
+<span class="sig-name descname"><span class="pre">complex_labels_by_interaction_type_and_data_model</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.complex_labels_by_interaction_type_and_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the entities involved in interactions matching the criteria.
+It either returns both interacting entities in a <em>set</em> or an empty
+<em>set</em>. This may not sound so useful at the level of this object but
+becomes more useful once we want to collect entities having certain
+kind of interactions across a series of <cite>Interaction</cite> objects.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>entity_type</strong> (<em>str</em>) – The type of the molecular entity. Possible values: <cite>protein</cite>,
+<cite>complex</cite>, <cite>mirna</cite>, <cite>small_molecule</cite>.</p></li>
+<li><p><strong>return_type</strong> (<em>str</em>) – The type of values to return. Default is
+py:class:<code class="docutils literal notranslate"><span class="pre">pypath.entity.Entity</span></code> objects, alternatives are
+<code class="docutils literal notranslate"><span class="pre">labels</span></code>  <code class="docutils literal notranslate"><span class="pre">identifiers</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.complex_labels_by_interaction_type_and_data_model_and_resource">
+<span class="sig-name descname"><span class="pre">complex_labels_by_interaction_type_and_data_model_and_resource</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.complex_labels_by_interaction_type_and_data_model_and_resource" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the entities involved in interactions matching the criteria.
+It either returns both interacting entities in a <em>set</em> or an empty
+<em>set</em>. This may not sound so useful at the level of this object but
+becomes more useful once we want to collect entities having certain
+kind of interactions across a series of <cite>Interaction</cite> objects.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>entity_type</strong> (<em>str</em>) – The type of the molecular entity. Possible values: <cite>protein</cite>,
+<cite>complex</cite>, <cite>mirna</cite>, <cite>small_molecule</cite>.</p></li>
+<li><p><strong>return_type</strong> (<em>str</em>) – The type of values to return. Default is
+py:class:<code class="docutils literal notranslate"><span class="pre">pypath.entity.Entity</span></code> objects, alternatives are
+<code class="docutils literal notranslate"><span class="pre">labels</span></code>  <code class="docutils literal notranslate"><span class="pre">identifiers</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.complex_labels_by_reference">
+<span class="sig-name descname"><span class="pre">complex_labels_by_reference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.complex_labels_by_reference" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the entities involved in interactions matching the criteria.
+It either returns both interacting entities in a <em>set</em> or an empty
+<em>set</em>. This may not sound so useful at the level of this object but
+becomes more useful once we want to collect entities having certain
+kind of interactions across a series of <cite>Interaction</cite> objects.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>entity_type</strong> (<em>str</em>) – The type of the molecular entity. Possible values: <cite>protein</cite>,
+<cite>complex</cite>, <cite>mirna</cite>, <cite>small_molecule</cite>.</p></li>
+<li><p><strong>return_type</strong> (<em>str</em>) – The type of values to return. Default is
+py:class:<code class="docutils literal notranslate"><span class="pre">pypath.entity.Entity</span></code> objects, alternatives are
+<code class="docutils literal notranslate"><span class="pre">labels</span></code>  <code class="docutils literal notranslate"><span class="pre">identifiers</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.complex_labels_by_resource">
+<span class="sig-name descname"><span class="pre">complex_labels_by_resource</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.complex_labels_by_resource" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the entities involved in interactions matching the criteria.
+It either returns both interacting entities in a <em>set</em> or an empty
+<em>set</em>. This may not sound so useful at the level of this object but
+becomes more useful once we want to collect entities having certain
+kind of interactions across a series of <cite>Interaction</cite> objects.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>entity_type</strong> (<em>str</em>) – The type of the molecular entity. Possible values: <cite>protein</cite>,
+<cite>complex</cite>, <cite>mirna</cite>, <cite>small_molecule</cite>.</p></li>
+<li><p><strong>return_type</strong> (<em>str</em>) – The type of values to return. Default is
+py:class:<code class="docutils literal notranslate"><span class="pre">pypath.entity.Entity</span></code> objects, alternatives are
+<code class="docutils literal notranslate"><span class="pre">labels</span></code>  <code class="docutils literal notranslate"><span class="pre">identifiers</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.complexes_by_data_model">
+<span class="sig-name descname"><span class="pre">complexes_by_data_model</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.complexes_by_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the entities involved in interactions matching the criteria.
+It either returns both interacting entities in a <em>set</em> or an empty
+<em>set</em>. This may not sound so useful at the level of this object but
+becomes more useful once we want to collect entities having certain
+kind of interactions across a series of <cite>Interaction</cite> objects.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>entity_type</strong> (<em>str</em>) – The type of the molecular entity. Possible values: <cite>protein</cite>,
+<cite>complex</cite>, <cite>mirna</cite>, <cite>small_molecule</cite>.</p></li>
+<li><p><strong>return_type</strong> (<em>str</em>) – The type of values to return. Default is
+py:class:<code class="docutils literal notranslate"><span class="pre">pypath.entity.Entity</span></code> objects, alternatives are
+<code class="docutils literal notranslate"><span class="pre">labels</span></code>  <code class="docutils literal notranslate"><span class="pre">identifiers</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.complexes_by_interaction_type">
+<span class="sig-name descname"><span class="pre">complexes_by_interaction_type</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.complexes_by_interaction_type" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the entities involved in interactions matching the criteria.
+It either returns both interacting entities in a <em>set</em> or an empty
+<em>set</em>. This may not sound so useful at the level of this object but
+becomes more useful once we want to collect entities having certain
+kind of interactions across a series of <cite>Interaction</cite> objects.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>entity_type</strong> (<em>str</em>) – The type of the molecular entity. Possible values: <cite>protein</cite>,
+<cite>complex</cite>, <cite>mirna</cite>, <cite>small_molecule</cite>.</p></li>
+<li><p><strong>return_type</strong> (<em>str</em>) – The type of values to return. Default is
+py:class:<code class="docutils literal notranslate"><span class="pre">pypath.entity.Entity</span></code> objects, alternatives are
+<code class="docutils literal notranslate"><span class="pre">labels</span></code>  <code class="docutils literal notranslate"><span class="pre">identifiers</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.complexes_by_interaction_type_and_data_model">
+<span class="sig-name descname"><span class="pre">complexes_by_interaction_type_and_data_model</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.complexes_by_interaction_type_and_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the entities involved in interactions matching the criteria.
+It either returns both interacting entities in a <em>set</em> or an empty
+<em>set</em>. This may not sound so useful at the level of this object but
+becomes more useful once we want to collect entities having certain
+kind of interactions across a series of <cite>Interaction</cite> objects.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>entity_type</strong> (<em>str</em>) – The type of the molecular entity. Possible values: <cite>protein</cite>,
+<cite>complex</cite>, <cite>mirna</cite>, <cite>small_molecule</cite>.</p></li>
+<li><p><strong>return_type</strong> (<em>str</em>) – The type of values to return. Default is
+py:class:<code class="docutils literal notranslate"><span class="pre">pypath.entity.Entity</span></code> objects, alternatives are
+<code class="docutils literal notranslate"><span class="pre">labels</span></code>  <code class="docutils literal notranslate"><span class="pre">identifiers</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.complexes_by_interaction_type_and_data_model_and_resource">
+<span class="sig-name descname"><span class="pre">complexes_by_interaction_type_and_data_model_and_resource</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.complexes_by_interaction_type_and_data_model_and_resource" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the entities involved in interactions matching the criteria.
+It either returns both interacting entities in a <em>set</em> or an empty
+<em>set</em>. This may not sound so useful at the level of this object but
+becomes more useful once we want to collect entities having certain
+kind of interactions across a series of <cite>Interaction</cite> objects.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>entity_type</strong> (<em>str</em>) – The type of the molecular entity. Possible values: <cite>protein</cite>,
+<cite>complex</cite>, <cite>mirna</cite>, <cite>small_molecule</cite>.</p></li>
+<li><p><strong>return_type</strong> (<em>str</em>) – The type of values to return. Default is
+py:class:<code class="docutils literal notranslate"><span class="pre">pypath.entity.Entity</span></code> objects, alternatives are
+<code class="docutils literal notranslate"><span class="pre">labels</span></code>  <code class="docutils literal notranslate"><span class="pre">identifiers</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.complexes_by_reference">
+<span class="sig-name descname"><span class="pre">complexes_by_reference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.complexes_by_reference" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the entities involved in interactions matching the criteria.
+It either returns both interacting entities in a <em>set</em> or an empty
+<em>set</em>. This may not sound so useful at the level of this object but
+becomes more useful once we want to collect entities having certain
+kind of interactions across a series of <cite>Interaction</cite> objects.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>entity_type</strong> (<em>str</em>) – The type of the molecular entity. Possible values: <cite>protein</cite>,
+<cite>complex</cite>, <cite>mirna</cite>, <cite>small_molecule</cite>.</p></li>
+<li><p><strong>return_type</strong> (<em>str</em>) – The type of values to return. Default is
+py:class:<code class="docutils literal notranslate"><span class="pre">pypath.entity.Entity</span></code> objects, alternatives are
+<code class="docutils literal notranslate"><span class="pre">labels</span></code>  <code class="docutils literal notranslate"><span class="pre">identifiers</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.complexes_by_resource">
+<span class="sig-name descname"><span class="pre">complexes_by_resource</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.complexes_by_resource" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the entities involved in interactions matching the criteria.
+It either returns both interacting entities in a <em>set</em> or an empty
+<em>set</em>. This may not sound so useful at the level of this object but
+becomes more useful once we want to collect entities having certain
+kind of interactions across a series of <cite>Interaction</cite> objects.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>entity_type</strong> (<em>str</em>) – The type of the molecular entity. Possible values: <cite>protein</cite>,
+<cite>complex</cite>, <cite>mirna</cite>, <cite>small_molecule</cite>.</p></li>
+<li><p><strong>return_type</strong> (<em>str</em>) – The type of values to return. Default is
+py:class:<code class="docutils literal notranslate"><span class="pre">pypath.entity.Entity</span></code> objects, alternatives are
+<code class="docutils literal notranslate"><span class="pre">labels</span></code>  <code class="docutils literal notranslate"><span class="pre">identifiers</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.consensus">
+<span class="sig-name descname"><span class="pre">consensus</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">only_interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">only_primary</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">by_references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">by_reference_resource_pairs</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/interaction.html#Interaction.consensus"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.interaction.Interaction.consensus" title="Link to this definition">§</a></dt>
+<dd><p>Infers the consensus edge(s) according to the number of
+supporting sources. This includes direction and sign.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Returns<span class="colon">:</span></dt>
+<dd class="field-odd"><p>(<em>list</em>) – Contains the consensus edge(s) along with the
+consensus sign. If there is no major directionality, both
+are returned. The structure is as follows:
+<code class="docutils literal notranslate"><span class="pre">['&lt;source&gt;',</span> <span class="pre">'&lt;target&gt;',</span> <span class="pre">'&lt;(un)directed&gt;',</span> <span class="pre">'&lt;sign&gt;']</span></code></p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.consensus_edges">
+<span class="sig-name descname"><span class="pre">consensus_edges</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">only_interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">only_primary</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">by_references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">by_reference_resource_pairs</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.consensus_edges" title="Link to this definition">§</a></dt>
+<dd><p>Infers the consensus edge(s) according to the number of
+supporting sources. This includes direction and sign.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Returns<span class="colon">:</span></dt>
+<dd class="field-odd"><p>(<em>list</em>) – Contains the consensus edge(s) along with the
+consensus sign. If there is no major directionality, both
+are returned. The structure is as follows:
+<code class="docutils literal notranslate"><span class="pre">['&lt;source&gt;',</span> <span class="pre">'&lt;target&gt;',</span> <span class="pre">'&lt;(un)directed&gt;',</span> <span class="pre">'&lt;sign&gt;']</span></code></p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.count_complex_identifiers">
+<span class="sig-name descname"><span class="pre">count_complex_identifiers</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.count_complex_identifiers" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the entities involved in interactions matching the criteria.
+It either returns both interacting entities in a <em>set</em> or an empty
+<em>set</em>. This may not sound so useful at the level of this object but
+becomes more useful once we want to collect entities having certain
+kind of interactions across a series of <cite>Interaction</cite> objects.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>entity_type</strong> (<em>str</em>) – The type of the molecular entity. Possible values: <cite>protein</cite>,
+<cite>complex</cite>, <cite>mirna</cite>, <cite>small_molecule</cite>.</p></li>
+<li><p><strong>return_type</strong> (<em>str</em>) – The type of values to return. Default is
+py:class:<code class="docutils literal notranslate"><span class="pre">pypath.entity.Entity</span></code> objects, alternatives are
+<code class="docutils literal notranslate"><span class="pre">labels</span></code>  <code class="docutils literal notranslate"><span class="pre">identifiers</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.count_complex_labels">
+<span class="sig-name descname"><span class="pre">count_complex_labels</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.count_complex_labels" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the entities involved in interactions matching the criteria.
+It either returns both interacting entities in a <em>set</em> or an empty
+<em>set</em>. This may not sound so useful at the level of this object but
+becomes more useful once we want to collect entities having certain
+kind of interactions across a series of <cite>Interaction</cite> objects.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>entity_type</strong> (<em>str</em>) – The type of the molecular entity. Possible values: <cite>protein</cite>,
+<cite>complex</cite>, <cite>mirna</cite>, <cite>small_molecule</cite>.</p></li>
+<li><p><strong>return_type</strong> (<em>str</em>) – The type of values to return. Default is
+py:class:<code class="docutils literal notranslate"><span class="pre">pypath.entity.Entity</span></code> objects, alternatives are
+<code class="docutils literal notranslate"><span class="pre">labels</span></code>  <code class="docutils literal notranslate"><span class="pre">identifiers</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.count_complexes">
+<span class="sig-name descname"><span class="pre">count_complexes</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.count_complexes" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the entities involved in interactions matching the criteria.
+It either returns both interacting entities in a <em>set</em> or an empty
+<em>set</em>. This may not sound so useful at the level of this object but
+becomes more useful once we want to collect entities having certain
+kind of interactions across a series of <cite>Interaction</cite> objects.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>entity_type</strong> (<em>str</em>) – The type of the molecular entity. Possible values: <cite>protein</cite>,
+<cite>complex</cite>, <cite>mirna</cite>, <cite>small_molecule</cite>.</p></li>
+<li><p><strong>return_type</strong> (<em>str</em>) – The type of values to return. Default is
+py:class:<code class="docutils literal notranslate"><span class="pre">pypath.entity.Entity</span></code> objects, alternatives are
+<code class="docutils literal notranslate"><span class="pre">labels</span></code>  <code class="docutils literal notranslate"><span class="pre">identifiers</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.count_data_models">
+<span class="sig-name descname"><span class="pre">count_data_models</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.count_data_models" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves data models matching the criteria.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.count_degrees_directed">
+<span class="sig-name descname"><span class="pre">count_degrees_directed</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.count_degrees_directed" title="Link to this definition">§</a></dt>
+<dd><p>Returns a <em>set</em> of nodes with the connections matching the direction,
+effect and evidence criteria. E.g. if the query concerns the incoming
+degrees with positive effect and the matching evidences show A
+activates B, but not the other way around, only “B” will be returned.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>mode:</dt><dd><p>The type of degrees to be considered. Three possible values are
+<code class="docutils literal notranslate"><span class="pre">'IN'</span></code>, <cite>‘OUT’`</cite> and <code class="docutils literal notranslate"><span class="pre">'ALL'</span></code> for incoming, outgoing and all
+connections, respectively. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is <code class="docutils literal notranslate"><span class="pre">False</span></code>
+the only possible mode is <code class="docutils literal notranslate"><span class="pre">ALL</span></code>. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is
+<code class="docutils literal notranslate"><span class="pre">None</span></code> and also directed evidence(s) match the criteria these
+will overwrite the undirected evidences and only the directed
+result will be returned.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.count_degrees_directed_in">
+<span class="sig-name descname"><span class="pre">count_degrees_directed_in</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.count_degrees_directed_in" title="Link to this definition">§</a></dt>
+<dd><p>Returns a <em>set</em> of nodes with the connections matching the direction,
+effect and evidence criteria. E.g. if the query concerns the incoming
+degrees with positive effect and the matching evidences show A
+activates B, but not the other way around, only “B” will be returned.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>mode:</dt><dd><p>The type of degrees to be considered. Three possible values are
+<code class="docutils literal notranslate"><span class="pre">'IN'</span></code>, <cite>‘OUT’`</cite> and <code class="docutils literal notranslate"><span class="pre">'ALL'</span></code> for incoming, outgoing and all
+connections, respectively. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is <code class="docutils literal notranslate"><span class="pre">False</span></code>
+the only possible mode is <code class="docutils literal notranslate"><span class="pre">ALL</span></code>. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is
+<code class="docutils literal notranslate"><span class="pre">None</span></code> and also directed evidence(s) match the criteria these
+will overwrite the undirected evidences and only the directed
+result will be returned.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.count_degrees_directed_out">
+<span class="sig-name descname"><span class="pre">count_degrees_directed_out</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.count_degrees_directed_out" title="Link to this definition">§</a></dt>
+<dd><p>Returns a <em>set</em> of nodes with the connections matching the direction,
+effect and evidence criteria. E.g. if the query concerns the incoming
+degrees with positive effect and the matching evidences show A
+activates B, but not the other way around, only “B” will be returned.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>mode:</dt><dd><p>The type of degrees to be considered. Three possible values are
+<code class="docutils literal notranslate"><span class="pre">'IN'</span></code>, <cite>‘OUT’`</cite> and <code class="docutils literal notranslate"><span class="pre">'ALL'</span></code> for incoming, outgoing and all
+connections, respectively. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is <code class="docutils literal notranslate"><span class="pre">False</span></code>
+the only possible mode is <code class="docutils literal notranslate"><span class="pre">ALL</span></code>. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is
+<code class="docutils literal notranslate"><span class="pre">None</span></code> and also directed evidence(s) match the criteria these
+will overwrite the undirected evidences and only the directed
+result will be returned.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.count_degrees_negative">
+<span class="sig-name descname"><span class="pre">count_degrees_negative</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.count_degrees_negative" title="Link to this definition">§</a></dt>
+<dd><p>Returns a <em>set</em> of nodes with the connections matching the direction,
+effect and evidence criteria. E.g. if the query concerns the incoming
+degrees with positive effect and the matching evidences show A
+activates B, but not the other way around, only “B” will be returned.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>mode:</dt><dd><p>The type of degrees to be considered. Three possible values are
+<code class="docutils literal notranslate"><span class="pre">'IN'</span></code>, <cite>‘OUT’`</cite> and <code class="docutils literal notranslate"><span class="pre">'ALL'</span></code> for incoming, outgoing and all
+connections, respectively. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is <code class="docutils literal notranslate"><span class="pre">False</span></code>
+the only possible mode is <code class="docutils literal notranslate"><span class="pre">ALL</span></code>. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is
+<code class="docutils literal notranslate"><span class="pre">None</span></code> and also directed evidence(s) match the criteria these
+will overwrite the undirected evidences and only the directed
+result will be returned.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.count_degrees_negative_in">
+<span class="sig-name descname"><span class="pre">count_degrees_negative_in</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.count_degrees_negative_in" title="Link to this definition">§</a></dt>
+<dd><p>Returns a <em>set</em> of nodes with the connections matching the direction,
+effect and evidence criteria. E.g. if the query concerns the incoming
+degrees with positive effect and the matching evidences show A
+activates B, but not the other way around, only “B” will be returned.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>mode:</dt><dd><p>The type of degrees to be considered. Three possible values are
+<code class="docutils literal notranslate"><span class="pre">'IN'</span></code>, <cite>‘OUT’`</cite> and <code class="docutils literal notranslate"><span class="pre">'ALL'</span></code> for incoming, outgoing and all
+connections, respectively. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is <code class="docutils literal notranslate"><span class="pre">False</span></code>
+the only possible mode is <code class="docutils literal notranslate"><span class="pre">ALL</span></code>. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is
+<code class="docutils literal notranslate"><span class="pre">None</span></code> and also directed evidence(s) match the criteria these
+will overwrite the undirected evidences and only the directed
+result will be returned.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.count_degrees_negative_out">
+<span class="sig-name descname"><span class="pre">count_degrees_negative_out</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.count_degrees_negative_out" title="Link to this definition">§</a></dt>
+<dd><p>Returns a <em>set</em> of nodes with the connections matching the direction,
+effect and evidence criteria. E.g. if the query concerns the incoming
+degrees with positive effect and the matching evidences show A
+activates B, but not the other way around, only “B” will be returned.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>mode:</dt><dd><p>The type of degrees to be considered. Three possible values are
+<code class="docutils literal notranslate"><span class="pre">'IN'</span></code>, <cite>‘OUT’`</cite> and <code class="docutils literal notranslate"><span class="pre">'ALL'</span></code> for incoming, outgoing and all
+connections, respectively. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is <code class="docutils literal notranslate"><span class="pre">False</span></code>
+the only possible mode is <code class="docutils literal notranslate"><span class="pre">ALL</span></code>. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is
+<code class="docutils literal notranslate"><span class="pre">None</span></code> and also directed evidence(s) match the criteria these
+will overwrite the undirected evidences and only the directed
+result will be returned.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.count_degrees_non_directed">
+<span class="sig-name descname"><span class="pre">count_degrees_non_directed</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.count_degrees_non_directed" title="Link to this definition">§</a></dt>
+<dd><p>Returns a <em>set</em> of nodes with the connections matching the direction,
+effect and evidence criteria. E.g. if the query concerns the incoming
+degrees with positive effect and the matching evidences show A
+activates B, but not the other way around, only “B” will be returned.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>mode:</dt><dd><p>The type of degrees to be considered. Three possible values are
+<code class="docutils literal notranslate"><span class="pre">'IN'</span></code>, <cite>‘OUT’`</cite> and <code class="docutils literal notranslate"><span class="pre">'ALL'</span></code> for incoming, outgoing and all
+connections, respectively. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is <code class="docutils literal notranslate"><span class="pre">False</span></code>
+the only possible mode is <code class="docutils literal notranslate"><span class="pre">ALL</span></code>. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is
+<code class="docutils literal notranslate"><span class="pre">None</span></code> and also directed evidence(s) match the criteria these
+will overwrite the undirected evidences and only the directed
+result will be returned.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.count_degrees_positive">
+<span class="sig-name descname"><span class="pre">count_degrees_positive</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.count_degrees_positive" title="Link to this definition">§</a></dt>
+<dd><p>Returns a <em>set</em> of nodes with the connections matching the direction,
+effect and evidence criteria. E.g. if the query concerns the incoming
+degrees with positive effect and the matching evidences show A
+activates B, but not the other way around, only “B” will be returned.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>mode:</dt><dd><p>The type of degrees to be considered. Three possible values are
+<code class="docutils literal notranslate"><span class="pre">'IN'</span></code>, <cite>‘OUT’`</cite> and <code class="docutils literal notranslate"><span class="pre">'ALL'</span></code> for incoming, outgoing and all
+connections, respectively. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is <code class="docutils literal notranslate"><span class="pre">False</span></code>
+the only possible mode is <code class="docutils literal notranslate"><span class="pre">ALL</span></code>. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is
+<code class="docutils literal notranslate"><span class="pre">None</span></code> and also directed evidence(s) match the criteria these
+will overwrite the undirected evidences and only the directed
+result will be returned.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.count_degrees_positive_in">
+<span class="sig-name descname"><span class="pre">count_degrees_positive_in</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.count_degrees_positive_in" title="Link to this definition">§</a></dt>
+<dd><p>Returns a <em>set</em> of nodes with the connections matching the direction,
+effect and evidence criteria. E.g. if the query concerns the incoming
+degrees with positive effect and the matching evidences show A
+activates B, but not the other way around, only “B” will be returned.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>mode:</dt><dd><p>The type of degrees to be considered. Three possible values are
+<code class="docutils literal notranslate"><span class="pre">'IN'</span></code>, <cite>‘OUT’`</cite> and <code class="docutils literal notranslate"><span class="pre">'ALL'</span></code> for incoming, outgoing and all
+connections, respectively. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is <code class="docutils literal notranslate"><span class="pre">False</span></code>
+the only possible mode is <code class="docutils literal notranslate"><span class="pre">ALL</span></code>. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is
+<code class="docutils literal notranslate"><span class="pre">None</span></code> and also directed evidence(s) match the criteria these
+will overwrite the undirected evidences and only the directed
+result will be returned.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.count_degrees_positive_out">
+<span class="sig-name descname"><span class="pre">count_degrees_positive_out</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.count_degrees_positive_out" title="Link to this definition">§</a></dt>
+<dd><p>Returns a <em>set</em> of nodes with the connections matching the direction,
+effect and evidence criteria. E.g. if the query concerns the incoming
+degrees with positive effect and the matching evidences show A
+activates B, but not the other way around, only “B” will be returned.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>mode:</dt><dd><p>The type of degrees to be considered. Three possible values are
+<code class="docutils literal notranslate"><span class="pre">'IN'</span></code>, <cite>‘OUT’`</cite> and <code class="docutils literal notranslate"><span class="pre">'ALL'</span></code> for incoming, outgoing and all
+connections, respectively. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is <code class="docutils literal notranslate"><span class="pre">False</span></code>
+the only possible mode is <code class="docutils literal notranslate"><span class="pre">ALL</span></code>. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is
+<code class="docutils literal notranslate"><span class="pre">None</span></code> and also directed evidence(s) match the criteria these
+will overwrite the undirected evidences and only the directed
+result will be returned.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.count_degrees_signed">
+<span class="sig-name descname"><span class="pre">count_degrees_signed</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.count_degrees_signed" title="Link to this definition">§</a></dt>
+<dd><p>Returns a <em>set</em> of nodes with the connections matching the direction,
+effect and evidence criteria. E.g. if the query concerns the incoming
+degrees with positive effect and the matching evidences show A
+activates B, but not the other way around, only “B” will be returned.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>mode:</dt><dd><p>The type of degrees to be considered. Three possible values are
+<code class="docutils literal notranslate"><span class="pre">'IN'</span></code>, <cite>‘OUT’`</cite> and <code class="docutils literal notranslate"><span class="pre">'ALL'</span></code> for incoming, outgoing and all
+connections, respectively. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is <code class="docutils literal notranslate"><span class="pre">False</span></code>
+the only possible mode is <code class="docutils literal notranslate"><span class="pre">ALL</span></code>. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is
+<code class="docutils literal notranslate"><span class="pre">None</span></code> and also directed evidence(s) match the criteria these
+will overwrite the undirected evidences and only the directed
+result will be returned.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.count_degrees_signed_in">
+<span class="sig-name descname"><span class="pre">count_degrees_signed_in</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.count_degrees_signed_in" title="Link to this definition">§</a></dt>
+<dd><p>Returns a <em>set</em> of nodes with the connections matching the direction,
+effect and evidence criteria. E.g. if the query concerns the incoming
+degrees with positive effect and the matching evidences show A
+activates B, but not the other way around, only “B” will be returned.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>mode:</dt><dd><p>The type of degrees to be considered. Three possible values are
+<code class="docutils literal notranslate"><span class="pre">'IN'</span></code>, <cite>‘OUT’`</cite> and <code class="docutils literal notranslate"><span class="pre">'ALL'</span></code> for incoming, outgoing and all
+connections, respectively. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is <code class="docutils literal notranslate"><span class="pre">False</span></code>
+the only possible mode is <code class="docutils literal notranslate"><span class="pre">ALL</span></code>. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is
+<code class="docutils literal notranslate"><span class="pre">None</span></code> and also directed evidence(s) match the criteria these
+will overwrite the undirected evidences and only the directed
+result will be returned.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.count_degrees_signed_out">
+<span class="sig-name descname"><span class="pre">count_degrees_signed_out</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.count_degrees_signed_out" title="Link to this definition">§</a></dt>
+<dd><p>Returns a <em>set</em> of nodes with the connections matching the direction,
+effect and evidence criteria. E.g. if the query concerns the incoming
+degrees with positive effect and the matching evidences show A
+activates B, but not the other way around, only “B” will be returned.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>mode:</dt><dd><p>The type of degrees to be considered. Three possible values are
+<code class="docutils literal notranslate"><span class="pre">'IN'</span></code>, <cite>‘OUT’`</cite> and <code class="docutils literal notranslate"><span class="pre">'ALL'</span></code> for incoming, outgoing and all
+connections, respectively. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is <code class="docutils literal notranslate"><span class="pre">False</span></code>
+the only possible mode is <code class="docutils literal notranslate"><span class="pre">ALL</span></code>. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is
+<code class="docutils literal notranslate"><span class="pre">None</span></code> and also directed evidence(s) match the criteria these
+will overwrite the undirected evidences and only the directed
+result will be returned.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.count_degrees_undirected">
+<span class="sig-name descname"><span class="pre">count_degrees_undirected</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.count_degrees_undirected" title="Link to this definition">§</a></dt>
+<dd><p>Returns a <em>set</em> of nodes with the connections matching the direction,
+effect and evidence criteria. E.g. if the query concerns the incoming
+degrees with positive effect and the matching evidences show A
+activates B, but not the other way around, only “B” will be returned.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>mode:</dt><dd><p>The type of degrees to be considered. Three possible values are
+<code class="docutils literal notranslate"><span class="pre">'IN'</span></code>, <cite>‘OUT’`</cite> and <code class="docutils literal notranslate"><span class="pre">'ALL'</span></code> for incoming, outgoing and all
+connections, respectively. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is <code class="docutils literal notranslate"><span class="pre">False</span></code>
+the only possible mode is <code class="docutils literal notranslate"><span class="pre">ALL</span></code>. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is
+<code class="docutils literal notranslate"><span class="pre">None</span></code> and also directed evidence(s) match the criteria these
+will overwrite the undirected evidences and only the directed
+result will be returned.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.count_entities">
+<span class="sig-name descname"><span class="pre">count_entities</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.count_entities" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the entities involved in interactions matching the criteria.
+It either returns both interacting entities in a <em>set</em> or an empty
+<em>set</em>. This may not sound so useful at the level of this object but
+becomes more useful once we want to collect entities having certain
+kind of interactions across a series of <cite>Interaction</cite> objects.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>entity_type</strong> (<em>str</em>) – The type of the molecular entity. Possible values: <cite>protein</cite>,
+<cite>complex</cite>, <cite>mirna</cite>, <cite>small_molecule</cite>.</p></li>
+<li><p><strong>return_type</strong> (<em>str</em>) – The type of values to return. Default is
+py:class:<code class="docutils literal notranslate"><span class="pre">pypath.entity.Entity</span></code> objects, alternatives are
+<code class="docutils literal notranslate"><span class="pre">labels</span></code>  <code class="docutils literal notranslate"><span class="pre">identifiers</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.count_identifiers">
+<span class="sig-name descname"><span class="pre">count_identifiers</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.count_identifiers" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the entities involved in interactions matching the criteria.
+It either returns both interacting entities in a <em>set</em> or an empty
+<em>set</em>. This may not sound so useful at the level of this object but
+becomes more useful once we want to collect entities having certain
+kind of interactions across a series of <cite>Interaction</cite> objects.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>entity_type</strong> (<em>str</em>) – The type of the molecular entity. Possible values: <cite>protein</cite>,
+<cite>complex</cite>, <cite>mirna</cite>, <cite>small_molecule</cite>.</p></li>
+<li><p><strong>return_type</strong> (<em>str</em>) – The type of values to return. Default is
+py:class:<code class="docutils literal notranslate"><span class="pre">pypath.entity.Entity</span></code> objects, alternatives are
+<code class="docutils literal notranslate"><span class="pre">labels</span></code>  <code class="docutils literal notranslate"><span class="pre">identifiers</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.count_interaction_types">
+<span class="sig-name descname"><span class="pre">count_interaction_types</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.count_interaction_types" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves interaction types matching the criteria.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.count_interactions">
+<span class="sig-name descname"><span class="pre">count_interactions</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.count_interactions" title="Link to this definition">§</a></dt>
+<dd><p>Returns one or two tuples of the interacting partners: one if only
+one direction, two if both directions match the query criteria.
+The tuple will be empty if no evidence matches the criteria.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>direction</strong> (<em>NontType</em><em>,</em><em>bool</em><em>,</em><em>tuple</em>) – If <cite>None</cite> both undirected and directed, if <cite>True</cite> only directed,
+if a <em>tuple</em> of entities only the interactions with that specific
+direction will be considered. Unless you set this parameter to
+<cite>True</cite> this method will return both directions if one or more
+undirected resources present.
+If <cite>False</cite>, only the undirected interactions will be considered,
+and if any resource annotates this interaction as undirected
+both directions will be returned. However the
+<code class="docutils literal notranslate"><span class="pre">count_interactions_undirected</span></code> method will return <cite>1</cite>
+in this case.</p></li>
+<li><p><strong>effect</strong> (<em>NoneType</em><em>,</em><em>bool</em><em>,</em><em>str</em>) – If <cite>None</cite> also interactions without effect, if <cite>True</cite> only
+the ones with any effect, if a string naming an effect only the
+interactions with that specific effect will be considered.</p></li>
+<li><p><strong>resources</strong> (<em>NontType</em><em>,</em><em>str</em><em>,</em><em>set</em>) – Optionally limit the query to one or more resources.</p></li>
+<li><p><strong>data_model</strong> (<em>NontType</em><em>,</em><em>str</em><em>,</em><em>set</em>) – Optionally limit the query to one or more data models e.g.
+<cite>activity_flow</cite>.</p></li>
+<li><p><strong>interaction_type</strong> (<em>NontType</em><em>,</em><em>str</em><em>,</em><em>set</em>) – Optionally limit the query to one or more interaction types
+e.g. <cite>PPI</cite>.</p></li>
+<li><p><strong>via</strong> (<em>NontType</em><em>,</em><em>bool</em><em>,</em><em>str</em><em>,</em><em>set</em>) – Optionally limit the query to certain secondary databases or
+if <cite>False</cite> consider only data from primary databases.</p></li>
+<li><p><strong>entity_type</strong> (<em>str</em>) – Molecule type for both of the entities.</p></li>
+<li><p><strong>source_entity_type</strong> (<em>str</em>) – Molecule type for the source entity.</p></li>
+<li><p><strong>target_entity_type</strong> (<em>str</em>) – Molecule type for the target entity.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.count_interactions_0">
+<span class="sig-name descname"><span class="pre">count_interactions_0</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.count_interactions_0" title="Link to this definition">§</a></dt>
+<dd><p>Returns unique interacting pairs without being aware of the direction.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.count_interactions_directed">
+<span class="sig-name descname"><span class="pre">count_interactions_directed</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.count_interactions_directed" title="Link to this definition">§</a></dt>
+<dd><dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>kwargs:</dt><dd><p>See the docs of method <code class="docutils literal notranslate"><span class="pre">get_interactions</span></code>.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.count_interactions_mutual">
+<span class="sig-name descname"><span class="pre">count_interactions_mutual</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/interaction.html#Interaction.count_interactions_mutual"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.interaction.Interaction.count_interactions_mutual" title="Link to this definition">§</a></dt>
+<dd><p>Note: undirected interactions does not count as mutual but only
+interactions with explicit direction information for both directions.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>kwargs:</dt><dd><p>See the docs of method <code class="docutils literal notranslate"><span class="pre">get_interactions</span></code>.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.count_interactions_negative">
+<span class="sig-name descname"><span class="pre">count_interactions_negative</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.count_interactions_negative" title="Link to this definition">§</a></dt>
+<dd><dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>kwargs:</dt><dd><p>See the docs of method <code class="docutils literal notranslate"><span class="pre">get_interactions</span></code>.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.count_interactions_non_directed">
+<span class="sig-name descname"><span class="pre">count_interactions_non_directed</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/interaction.html#Interaction.count_interactions_non_directed"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.interaction.Interaction.count_interactions_non_directed" title="Link to this definition">§</a></dt>
+<dd><p>Returns <cite>True</cite> if any resource annotates this interaction without
+and no resource with direction.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>kwargs:</dt><dd><p>See the docs of method <code class="docutils literal notranslate"><span class="pre">get_interactions</span></code>.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.count_interactions_positive">
+<span class="sig-name descname"><span class="pre">count_interactions_positive</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.count_interactions_positive" title="Link to this definition">§</a></dt>
+<dd><dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>kwargs:</dt><dd><p>See the docs of method <code class="docutils literal notranslate"><span class="pre">get_interactions</span></code>.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.count_interactions_signed">
+<span class="sig-name descname"><span class="pre">count_interactions_signed</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.count_interactions_signed" title="Link to this definition">§</a></dt>
+<dd><dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>kwargs:</dt><dd><p>See the docs of method <code class="docutils literal notranslate"><span class="pre">get_interactions</span></code>.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.count_interactions_undirected">
+<span class="sig-name descname"><span class="pre">count_interactions_undirected</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/interaction.html#Interaction.count_interactions_undirected"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.interaction.Interaction.count_interactions_undirected" title="Link to this definition">§</a></dt>
+<dd><p>Returns <cite>True</cite> if any resource annotates this interaction without
+direction.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>kwargs:</dt><dd><p>See the docs of method <code class="docutils literal notranslate"><span class="pre">get_interactions</span></code>.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.count_labels">
+<span class="sig-name descname"><span class="pre">count_labels</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.count_labels" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the entities involved in interactions matching the criteria.
+It either returns both interacting entities in a <em>set</em> or an empty
+<em>set</em>. This may not sound so useful at the level of this object but
+becomes more useful once we want to collect entities having certain
+kind of interactions across a series of <cite>Interaction</cite> objects.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>entity_type</strong> (<em>str</em>) – The type of the molecular entity. Possible values: <cite>protein</cite>,
+<cite>complex</cite>, <cite>mirna</cite>, <cite>small_molecule</cite>.</p></li>
+<li><p><strong>return_type</strong> (<em>str</em>) – The type of values to return. Default is
+py:class:<code class="docutils literal notranslate"><span class="pre">pypath.entity.Entity</span></code> objects, alternatives are
+<code class="docutils literal notranslate"><span class="pre">labels</span></code>  <code class="docutils literal notranslate"><span class="pre">identifiers</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.count_lncrna_identifiers">
+<span class="sig-name descname"><span class="pre">count_lncrna_identifiers</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.count_lncrna_identifiers" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the entities involved in interactions matching the criteria.
+It either returns both interacting entities in a <em>set</em> or an empty
+<em>set</em>. This may not sound so useful at the level of this object but
+becomes more useful once we want to collect entities having certain
+kind of interactions across a series of <cite>Interaction</cite> objects.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>entity_type</strong> (<em>str</em>) – The type of the molecular entity. Possible values: <cite>protein</cite>,
+<cite>complex</cite>, <cite>mirna</cite>, <cite>small_molecule</cite>.</p></li>
+<li><p><strong>return_type</strong> (<em>str</em>) – The type of values to return. Default is
+py:class:<code class="docutils literal notranslate"><span class="pre">pypath.entity.Entity</span></code> objects, alternatives are
+<code class="docutils literal notranslate"><span class="pre">labels</span></code>  <code class="docutils literal notranslate"><span class="pre">identifiers</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.count_lncrna_labels">
+<span class="sig-name descname"><span class="pre">count_lncrna_labels</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.count_lncrna_labels" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the entities involved in interactions matching the criteria.
+It either returns both interacting entities in a <em>set</em> or an empty
+<em>set</em>. This may not sound so useful at the level of this object but
+becomes more useful once we want to collect entities having certain
+kind of interactions across a series of <cite>Interaction</cite> objects.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>entity_type</strong> (<em>str</em>) – The type of the molecular entity. Possible values: <cite>protein</cite>,
+<cite>complex</cite>, <cite>mirna</cite>, <cite>small_molecule</cite>.</p></li>
+<li><p><strong>return_type</strong> (<em>str</em>) – The type of values to return. Default is
+py:class:<code class="docutils literal notranslate"><span class="pre">pypath.entity.Entity</span></code> objects, alternatives are
+<code class="docutils literal notranslate"><span class="pre">labels</span></code>  <code class="docutils literal notranslate"><span class="pre">identifiers</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.count_lncrnas">
+<span class="sig-name descname"><span class="pre">count_lncrnas</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.count_lncrnas" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the entities involved in interactions matching the criteria.
+It either returns both interacting entities in a <em>set</em> or an empty
+<em>set</em>. This may not sound so useful at the level of this object but
+becomes more useful once we want to collect entities having certain
+kind of interactions across a series of <cite>Interaction</cite> objects.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>entity_type</strong> (<em>str</em>) – The type of the molecular entity. Possible values: <cite>protein</cite>,
+<cite>complex</cite>, <cite>mirna</cite>, <cite>small_molecule</cite>.</p></li>
+<li><p><strong>return_type</strong> (<em>str</em>) – The type of values to return. Default is
+py:class:<code class="docutils literal notranslate"><span class="pre">pypath.entity.Entity</span></code> objects, alternatives are
+<code class="docutils literal notranslate"><span class="pre">labels</span></code>  <code class="docutils literal notranslate"><span class="pre">identifiers</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.count_mirna_identifiers">
+<span class="sig-name descname"><span class="pre">count_mirna_identifiers</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.count_mirna_identifiers" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the entities involved in interactions matching the criteria.
+It either returns both interacting entities in a <em>set</em> or an empty
+<em>set</em>. This may not sound so useful at the level of this object but
+becomes more useful once we want to collect entities having certain
+kind of interactions across a series of <cite>Interaction</cite> objects.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>entity_type</strong> (<em>str</em>) – The type of the molecular entity. Possible values: <cite>protein</cite>,
+<cite>complex</cite>, <cite>mirna</cite>, <cite>small_molecule</cite>.</p></li>
+<li><p><strong>return_type</strong> (<em>str</em>) – The type of values to return. Default is
+py:class:<code class="docutils literal notranslate"><span class="pre">pypath.entity.Entity</span></code> objects, alternatives are
+<code class="docutils literal notranslate"><span class="pre">labels</span></code>  <code class="docutils literal notranslate"><span class="pre">identifiers</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.count_mirna_labels">
+<span class="sig-name descname"><span class="pre">count_mirna_labels</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.count_mirna_labels" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the entities involved in interactions matching the criteria.
+It either returns both interacting entities in a <em>set</em> or an empty
+<em>set</em>. This may not sound so useful at the level of this object but
+becomes more useful once we want to collect entities having certain
+kind of interactions across a series of <cite>Interaction</cite> objects.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>entity_type</strong> (<em>str</em>) – The type of the molecular entity. Possible values: <cite>protein</cite>,
+<cite>complex</cite>, <cite>mirna</cite>, <cite>small_molecule</cite>.</p></li>
+<li><p><strong>return_type</strong> (<em>str</em>) – The type of values to return. Default is
+py:class:<code class="docutils literal notranslate"><span class="pre">pypath.entity.Entity</span></code> objects, alternatives are
+<code class="docutils literal notranslate"><span class="pre">labels</span></code>  <code class="docutils literal notranslate"><span class="pre">identifiers</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.count_mirnas">
+<span class="sig-name descname"><span class="pre">count_mirnas</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.count_mirnas" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the entities involved in interactions matching the criteria.
+It either returns both interacting entities in a <em>set</em> or an empty
+<em>set</em>. This may not sound so useful at the level of this object but
+becomes more useful once we want to collect entities having certain
+kind of interactions across a series of <cite>Interaction</cite> objects.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>entity_type</strong> (<em>str</em>) – The type of the molecular entity. Possible values: <cite>protein</cite>,
+<cite>complex</cite>, <cite>mirna</cite>, <cite>small_molecule</cite>.</p></li>
+<li><p><strong>return_type</strong> (<em>str</em>) – The type of values to return. Default is
+py:class:<code class="docutils literal notranslate"><span class="pre">pypath.entity.Entity</span></code> objects, alternatives are
+<code class="docutils literal notranslate"><span class="pre">labels</span></code>  <code class="docutils literal notranslate"><span class="pre">identifiers</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.count_protein_identifiers">
+<span class="sig-name descname"><span class="pre">count_protein_identifiers</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.count_protein_identifiers" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the entities involved in interactions matching the criteria.
+It either returns both interacting entities in a <em>set</em> or an empty
+<em>set</em>. This may not sound so useful at the level of this object but
+becomes more useful once we want to collect entities having certain
+kind of interactions across a series of <cite>Interaction</cite> objects.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>entity_type</strong> (<em>str</em>) – The type of the molecular entity. Possible values: <cite>protein</cite>,
+<cite>complex</cite>, <cite>mirna</cite>, <cite>small_molecule</cite>.</p></li>
+<li><p><strong>return_type</strong> (<em>str</em>) – The type of values to return. Default is
+py:class:<code class="docutils literal notranslate"><span class="pre">pypath.entity.Entity</span></code> objects, alternatives are
+<code class="docutils literal notranslate"><span class="pre">labels</span></code>  <code class="docutils literal notranslate"><span class="pre">identifiers</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.count_protein_labels">
+<span class="sig-name descname"><span class="pre">count_protein_labels</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.count_protein_labels" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the entities involved in interactions matching the criteria.
+It either returns both interacting entities in a <em>set</em> or an empty
+<em>set</em>. This may not sound so useful at the level of this object but
+becomes more useful once we want to collect entities having certain
+kind of interactions across a series of <cite>Interaction</cite> objects.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>entity_type</strong> (<em>str</em>) – The type of the molecular entity. Possible values: <cite>protein</cite>,
+<cite>complex</cite>, <cite>mirna</cite>, <cite>small_molecule</cite>.</p></li>
+<li><p><strong>return_type</strong> (<em>str</em>) – The type of values to return. Default is
+py:class:<code class="docutils literal notranslate"><span class="pre">pypath.entity.Entity</span></code> objects, alternatives are
+<code class="docutils literal notranslate"><span class="pre">labels</span></code>  <code class="docutils literal notranslate"><span class="pre">identifiers</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.count_proteins">
+<span class="sig-name descname"><span class="pre">count_proteins</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.count_proteins" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the entities involved in interactions matching the criteria.
+It either returns both interacting entities in a <em>set</em> or an empty
+<em>set</em>. This may not sound so useful at the level of this object but
+becomes more useful once we want to collect entities having certain
+kind of interactions across a series of <cite>Interaction</cite> objects.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>entity_type</strong> (<em>str</em>) – The type of the molecular entity. Possible values: <cite>protein</cite>,
+<cite>complex</cite>, <cite>mirna</cite>, <cite>small_molecule</cite>.</p></li>
+<li><p><strong>return_type</strong> (<em>str</em>) – The type of values to return. Default is
+py:class:<code class="docutils literal notranslate"><span class="pre">pypath.entity.Entity</span></code> objects, alternatives are
+<code class="docutils literal notranslate"><span class="pre">labels</span></code>  <code class="docutils literal notranslate"><span class="pre">identifiers</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.count_references">
+<span class="sig-name descname"><span class="pre">count_references</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.count_references" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves references matching the criteria.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.count_resource_names">
+<span class="sig-name descname"><span class="pre">count_resource_names</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.count_resource_names" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves resource names matching the criteria.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.count_resource_names_via">
+<span class="sig-name descname"><span class="pre">count_resource_names_via</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.count_resource_names_via" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves resource names via matching the criteria.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.count_resources">
+<span class="sig-name descname"><span class="pre">count_resources</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.count_resources" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves resources matching the criteria.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.count_resources_via">
+<span class="sig-name descname"><span class="pre">count_resources_via</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.count_resources_via" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves resources via matching the criteria.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.count_small_molecule_identifiers">
+<span class="sig-name descname"><span class="pre">count_small_molecule_identifiers</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.count_small_molecule_identifiers" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the entities involved in interactions matching the criteria.
+It either returns both interacting entities in a <em>set</em> or an empty
+<em>set</em>. This may not sound so useful at the level of this object but
+becomes more useful once we want to collect entities having certain
+kind of interactions across a series of <cite>Interaction</cite> objects.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>entity_type</strong> (<em>str</em>) – The type of the molecular entity. Possible values: <cite>protein</cite>,
+<cite>complex</cite>, <cite>mirna</cite>, <cite>small_molecule</cite>.</p></li>
+<li><p><strong>return_type</strong> (<em>str</em>) – The type of values to return. Default is
+py:class:<code class="docutils literal notranslate"><span class="pre">pypath.entity.Entity</span></code> objects, alternatives are
+<code class="docutils literal notranslate"><span class="pre">labels</span></code>  <code class="docutils literal notranslate"><span class="pre">identifiers</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.count_small_molecule_labels">
+<span class="sig-name descname"><span class="pre">count_small_molecule_labels</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.count_small_molecule_labels" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the entities involved in interactions matching the criteria.
+It either returns both interacting entities in a <em>set</em> or an empty
+<em>set</em>. This may not sound so useful at the level of this object but
+becomes more useful once we want to collect entities having certain
+kind of interactions across a series of <cite>Interaction</cite> objects.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>entity_type</strong> (<em>str</em>) – The type of the molecular entity. Possible values: <cite>protein</cite>,
+<cite>complex</cite>, <cite>mirna</cite>, <cite>small_molecule</cite>.</p></li>
+<li><p><strong>return_type</strong> (<em>str</em>) – The type of values to return. Default is
+py:class:<code class="docutils literal notranslate"><span class="pre">pypath.entity.Entity</span></code> objects, alternatives are
+<code class="docutils literal notranslate"><span class="pre">labels</span></code>  <code class="docutils literal notranslate"><span class="pre">identifiers</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.count_small_molecules">
+<span class="sig-name descname"><span class="pre">count_small_molecules</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.count_small_molecules" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the entities involved in interactions matching the criteria.
+It either returns both interacting entities in a <em>set</em> or an empty
+<em>set</em>. This may not sound so useful at the level of this object but
+becomes more useful once we want to collect entities having certain
+kind of interactions across a series of <cite>Interaction</cite> objects.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>entity_type</strong> (<em>str</em>) – The type of the molecular entity. Possible values: <cite>protein</cite>,
+<cite>complex</cite>, <cite>mirna</cite>, <cite>small_molecule</cite>.</p></li>
+<li><p><strong>return_type</strong> (<em>str</em>) – The type of values to return. Default is
+py:class:<code class="docutils literal notranslate"><span class="pre">pypath.entity.Entity</span></code> objects, alternatives are
+<code class="docutils literal notranslate"><span class="pre">labels</span></code>  <code class="docutils literal notranslate"><span class="pre">identifiers</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.data_models_by_data_model">
+<span class="sig-name descname"><span class="pre">data_models_by_data_model</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.data_models_by_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves data models matching the criteria.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.data_models_by_interaction_type">
+<span class="sig-name descname"><span class="pre">data_models_by_interaction_type</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.data_models_by_interaction_type" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves data models matching the criteria.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.data_models_by_interaction_type_and_data_model">
+<span class="sig-name descname"><span class="pre">data_models_by_interaction_type_and_data_model</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.data_models_by_interaction_type_and_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves data models matching the criteria.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.data_models_by_interaction_type_and_data_model_and_resource">
+<span class="sig-name descname"><span class="pre">data_models_by_interaction_type_and_data_model_and_resource</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.data_models_by_interaction_type_and_data_model_and_resource" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves data models matching the criteria.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.data_models_by_reference">
+<span class="sig-name descname"><span class="pre">data_models_by_reference</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.data_models_by_reference" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves data models matching the criteria.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.data_models_by_resource">
+<span class="sig-name descname"><span class="pre">data_models_by_resource</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.data_models_by_resource" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves data models matching the criteria.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.datasets_by_data_model">
+<span class="sig-name descname"><span class="pre">datasets_by_data_model</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.datasets_by_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves datasets matching the criteria.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.datasets_by_interaction_type">
+<span class="sig-name descname"><span class="pre">datasets_by_interaction_type</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.datasets_by_interaction_type" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves datasets matching the criteria.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.datasets_by_interaction_type_and_data_model">
+<span class="sig-name descname"><span class="pre">datasets_by_interaction_type_and_data_model</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.datasets_by_interaction_type_and_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves datasets matching the criteria.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.datasets_by_interaction_type_and_data_model_and_resource">
+<span class="sig-name descname"><span class="pre">datasets_by_interaction_type_and_data_model_and_resource</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.datasets_by_interaction_type_and_data_model_and_resource" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves datasets matching the criteria.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.datasets_by_reference">
+<span class="sig-name descname"><span class="pre">datasets_by_reference</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.datasets_by_reference" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves datasets matching the criteria.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.datasets_by_resource">
+<span class="sig-name descname"><span class="pre">datasets_by_resource</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.datasets_by_resource" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves datasets matching the criteria.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.degrees_directed_by_data_model">
+<span class="sig-name descname"><span class="pre">degrees_directed_by_data_model</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.degrees_directed_by_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Returns a <em>set</em> of nodes with the connections matching the direction,
+effect and evidence criteria. E.g. if the query concerns the incoming
+degrees with positive effect and the matching evidences show A
+activates B, but not the other way around, only “B” will be returned.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>mode:</dt><dd><p>The type of degrees to be considered. Three possible values are
+<code class="docutils literal notranslate"><span class="pre">'IN'</span></code>, <cite>‘OUT’`</cite> and <code class="docutils literal notranslate"><span class="pre">'ALL'</span></code> for incoming, outgoing and all
+connections, respectively. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is <code class="docutils literal notranslate"><span class="pre">False</span></code>
+the only possible mode is <code class="docutils literal notranslate"><span class="pre">ALL</span></code>. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is
+<code class="docutils literal notranslate"><span class="pre">None</span></code> and also directed evidence(s) match the criteria these
+will overwrite the undirected evidences and only the directed
+result will be returned.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.degrees_directed_by_interaction_type">
+<span class="sig-name descname"><span class="pre">degrees_directed_by_interaction_type</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.degrees_directed_by_interaction_type" title="Link to this definition">§</a></dt>
+<dd><p>Returns a <em>set</em> of nodes with the connections matching the direction,
+effect and evidence criteria. E.g. if the query concerns the incoming
+degrees with positive effect and the matching evidences show A
+activates B, but not the other way around, only “B” will be returned.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>mode:</dt><dd><p>The type of degrees to be considered. Three possible values are
+<code class="docutils literal notranslate"><span class="pre">'IN'</span></code>, <cite>‘OUT’`</cite> and <code class="docutils literal notranslate"><span class="pre">'ALL'</span></code> for incoming, outgoing and all
+connections, respectively. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is <code class="docutils literal notranslate"><span class="pre">False</span></code>
+the only possible mode is <code class="docutils literal notranslate"><span class="pre">ALL</span></code>. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is
+<code class="docutils literal notranslate"><span class="pre">None</span></code> and also directed evidence(s) match the criteria these
+will overwrite the undirected evidences and only the directed
+result will be returned.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.degrees_directed_by_interaction_type_and_data_model">
+<span class="sig-name descname"><span class="pre">degrees_directed_by_interaction_type_and_data_model</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.degrees_directed_by_interaction_type_and_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Returns a <em>set</em> of nodes with the connections matching the direction,
+effect and evidence criteria. E.g. if the query concerns the incoming
+degrees with positive effect and the matching evidences show A
+activates B, but not the other way around, only “B” will be returned.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>mode:</dt><dd><p>The type of degrees to be considered. Three possible values are
+<code class="docutils literal notranslate"><span class="pre">'IN'</span></code>, <cite>‘OUT’`</cite> and <code class="docutils literal notranslate"><span class="pre">'ALL'</span></code> for incoming, outgoing and all
+connections, respectively. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is <code class="docutils literal notranslate"><span class="pre">False</span></code>
+the only possible mode is <code class="docutils literal notranslate"><span class="pre">ALL</span></code>. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is
+<code class="docutils literal notranslate"><span class="pre">None</span></code> and also directed evidence(s) match the criteria these
+will overwrite the undirected evidences and only the directed
+result will be returned.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.degrees_directed_by_interaction_type_and_data_model_and_resource">
+<span class="sig-name descname"><span class="pre">degrees_directed_by_interaction_type_and_data_model_and_resource</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.degrees_directed_by_interaction_type_and_data_model_and_resource" title="Link to this definition">§</a></dt>
+<dd><p>Returns a <em>set</em> of nodes with the connections matching the direction,
+effect and evidence criteria. E.g. if the query concerns the incoming
+degrees with positive effect and the matching evidences show A
+activates B, but not the other way around, only “B” will be returned.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>mode:</dt><dd><p>The type of degrees to be considered. Three possible values are
+<code class="docutils literal notranslate"><span class="pre">'IN'</span></code>, <cite>‘OUT’`</cite> and <code class="docutils literal notranslate"><span class="pre">'ALL'</span></code> for incoming, outgoing and all
+connections, respectively. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is <code class="docutils literal notranslate"><span class="pre">False</span></code>
+the only possible mode is <code class="docutils literal notranslate"><span class="pre">ALL</span></code>. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is
+<code class="docutils literal notranslate"><span class="pre">None</span></code> and also directed evidence(s) match the criteria these
+will overwrite the undirected evidences and only the directed
+result will be returned.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.degrees_directed_by_reference">
+<span class="sig-name descname"><span class="pre">degrees_directed_by_reference</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.degrees_directed_by_reference" title="Link to this definition">§</a></dt>
+<dd><p>Returns a <em>set</em> of nodes with the connections matching the direction,
+effect and evidence criteria. E.g. if the query concerns the incoming
+degrees with positive effect and the matching evidences show A
+activates B, but not the other way around, only “B” will be returned.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>mode:</dt><dd><p>The type of degrees to be considered. Three possible values are
+<code class="docutils literal notranslate"><span class="pre">'IN'</span></code>, <cite>‘OUT’`</cite> and <code class="docutils literal notranslate"><span class="pre">'ALL'</span></code> for incoming, outgoing and all
+connections, respectively. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is <code class="docutils literal notranslate"><span class="pre">False</span></code>
+the only possible mode is <code class="docutils literal notranslate"><span class="pre">ALL</span></code>. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is
+<code class="docutils literal notranslate"><span class="pre">None</span></code> and also directed evidence(s) match the criteria these
+will overwrite the undirected evidences and only the directed
+result will be returned.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.degrees_directed_by_resource">
+<span class="sig-name descname"><span class="pre">degrees_directed_by_resource</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.degrees_directed_by_resource" title="Link to this definition">§</a></dt>
+<dd><p>Returns a <em>set</em> of nodes with the connections matching the direction,
+effect and evidence criteria. E.g. if the query concerns the incoming
+degrees with positive effect and the matching evidences show A
+activates B, but not the other way around, only “B” will be returned.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>mode:</dt><dd><p>The type of degrees to be considered. Three possible values are
+<code class="docutils literal notranslate"><span class="pre">'IN'</span></code>, <cite>‘OUT’`</cite> and <code class="docutils literal notranslate"><span class="pre">'ALL'</span></code> for incoming, outgoing and all
+connections, respectively. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is <code class="docutils literal notranslate"><span class="pre">False</span></code>
+the only possible mode is <code class="docutils literal notranslate"><span class="pre">ALL</span></code>. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is
+<code class="docutils literal notranslate"><span class="pre">None</span></code> and also directed evidence(s) match the criteria these
+will overwrite the undirected evidences and only the directed
+result will be returned.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.degrees_directed_in_by_data_model">
+<span class="sig-name descname"><span class="pre">degrees_directed_in_by_data_model</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.degrees_directed_in_by_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Returns a <em>set</em> of nodes with the connections matching the direction,
+effect and evidence criteria. E.g. if the query concerns the incoming
+degrees with positive effect and the matching evidences show A
+activates B, but not the other way around, only “B” will be returned.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>mode:</dt><dd><p>The type of degrees to be considered. Three possible values are
+<code class="docutils literal notranslate"><span class="pre">'IN'</span></code>, <cite>‘OUT’`</cite> and <code class="docutils literal notranslate"><span class="pre">'ALL'</span></code> for incoming, outgoing and all
+connections, respectively. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is <code class="docutils literal notranslate"><span class="pre">False</span></code>
+the only possible mode is <code class="docutils literal notranslate"><span class="pre">ALL</span></code>. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is
+<code class="docutils literal notranslate"><span class="pre">None</span></code> and also directed evidence(s) match the criteria these
+will overwrite the undirected evidences and only the directed
+result will be returned.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.degrees_directed_in_by_interaction_type">
+<span class="sig-name descname"><span class="pre">degrees_directed_in_by_interaction_type</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.degrees_directed_in_by_interaction_type" title="Link to this definition">§</a></dt>
+<dd><p>Returns a <em>set</em> of nodes with the connections matching the direction,
+effect and evidence criteria. E.g. if the query concerns the incoming
+degrees with positive effect and the matching evidences show A
+activates B, but not the other way around, only “B” will be returned.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>mode:</dt><dd><p>The type of degrees to be considered. Three possible values are
+<code class="docutils literal notranslate"><span class="pre">'IN'</span></code>, <cite>‘OUT’`</cite> and <code class="docutils literal notranslate"><span class="pre">'ALL'</span></code> for incoming, outgoing and all
+connections, respectively. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is <code class="docutils literal notranslate"><span class="pre">False</span></code>
+the only possible mode is <code class="docutils literal notranslate"><span class="pre">ALL</span></code>. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is
+<code class="docutils literal notranslate"><span class="pre">None</span></code> and also directed evidence(s) match the criteria these
+will overwrite the undirected evidences and only the directed
+result will be returned.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.degrees_directed_in_by_interaction_type_and_data_model">
+<span class="sig-name descname"><span class="pre">degrees_directed_in_by_interaction_type_and_data_model</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.degrees_directed_in_by_interaction_type_and_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Returns a <em>set</em> of nodes with the connections matching the direction,
+effect and evidence criteria. E.g. if the query concerns the incoming
+degrees with positive effect and the matching evidences show A
+activates B, but not the other way around, only “B” will be returned.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>mode:</dt><dd><p>The type of degrees to be considered. Three possible values are
+<code class="docutils literal notranslate"><span class="pre">'IN'</span></code>, <cite>‘OUT’`</cite> and <code class="docutils literal notranslate"><span class="pre">'ALL'</span></code> for incoming, outgoing and all
+connections, respectively. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is <code class="docutils literal notranslate"><span class="pre">False</span></code>
+the only possible mode is <code class="docutils literal notranslate"><span class="pre">ALL</span></code>. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is
+<code class="docutils literal notranslate"><span class="pre">None</span></code> and also directed evidence(s) match the criteria these
+will overwrite the undirected evidences and only the directed
+result will be returned.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.degrees_directed_in_by_interaction_type_and_data_model_and_resource">
+<span class="sig-name descname"><span class="pre">degrees_directed_in_by_interaction_type_and_data_model_and_resource</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.degrees_directed_in_by_interaction_type_and_data_model_and_resource" title="Link to this definition">§</a></dt>
+<dd><p>Returns a <em>set</em> of nodes with the connections matching the direction,
+effect and evidence criteria. E.g. if the query concerns the incoming
+degrees with positive effect and the matching evidences show A
+activates B, but not the other way around, only “B” will be returned.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>mode:</dt><dd><p>The type of degrees to be considered. Three possible values are
+<code class="docutils literal notranslate"><span class="pre">'IN'</span></code>, <cite>‘OUT’`</cite> and <code class="docutils literal notranslate"><span class="pre">'ALL'</span></code> for incoming, outgoing and all
+connections, respectively. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is <code class="docutils literal notranslate"><span class="pre">False</span></code>
+the only possible mode is <code class="docutils literal notranslate"><span class="pre">ALL</span></code>. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is
+<code class="docutils literal notranslate"><span class="pre">None</span></code> and also directed evidence(s) match the criteria these
+will overwrite the undirected evidences and only the directed
+result will be returned.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.degrees_directed_in_by_reference">
+<span class="sig-name descname"><span class="pre">degrees_directed_in_by_reference</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.degrees_directed_in_by_reference" title="Link to this definition">§</a></dt>
+<dd><p>Returns a <em>set</em> of nodes with the connections matching the direction,
+effect and evidence criteria. E.g. if the query concerns the incoming
+degrees with positive effect and the matching evidences show A
+activates B, but not the other way around, only “B” will be returned.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>mode:</dt><dd><p>The type of degrees to be considered. Three possible values are
+<code class="docutils literal notranslate"><span class="pre">'IN'</span></code>, <cite>‘OUT’`</cite> and <code class="docutils literal notranslate"><span class="pre">'ALL'</span></code> for incoming, outgoing and all
+connections, respectively. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is <code class="docutils literal notranslate"><span class="pre">False</span></code>
+the only possible mode is <code class="docutils literal notranslate"><span class="pre">ALL</span></code>. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is
+<code class="docutils literal notranslate"><span class="pre">None</span></code> and also directed evidence(s) match the criteria these
+will overwrite the undirected evidences and only the directed
+result will be returned.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.degrees_directed_in_by_resource">
+<span class="sig-name descname"><span class="pre">degrees_directed_in_by_resource</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.degrees_directed_in_by_resource" title="Link to this definition">§</a></dt>
+<dd><p>Returns a <em>set</em> of nodes with the connections matching the direction,
+effect and evidence criteria. E.g. if the query concerns the incoming
+degrees with positive effect and the matching evidences show A
+activates B, but not the other way around, only “B” will be returned.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>mode:</dt><dd><p>The type of degrees to be considered. Three possible values are
+<code class="docutils literal notranslate"><span class="pre">'IN'</span></code>, <cite>‘OUT’`</cite> and <code class="docutils literal notranslate"><span class="pre">'ALL'</span></code> for incoming, outgoing and all
+connections, respectively. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is <code class="docutils literal notranslate"><span class="pre">False</span></code>
+the only possible mode is <code class="docutils literal notranslate"><span class="pre">ALL</span></code>. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is
+<code class="docutils literal notranslate"><span class="pre">None</span></code> and also directed evidence(s) match the criteria these
+will overwrite the undirected evidences and only the directed
+result will be returned.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.degrees_directed_out_by_data_model">
+<span class="sig-name descname"><span class="pre">degrees_directed_out_by_data_model</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.degrees_directed_out_by_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Returns a <em>set</em> of nodes with the connections matching the direction,
+effect and evidence criteria. E.g. if the query concerns the incoming
+degrees with positive effect and the matching evidences show A
+activates B, but not the other way around, only “B” will be returned.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>mode:</dt><dd><p>The type of degrees to be considered. Three possible values are
+<code class="docutils literal notranslate"><span class="pre">'IN'</span></code>, <cite>‘OUT’`</cite> and <code class="docutils literal notranslate"><span class="pre">'ALL'</span></code> for incoming, outgoing and all
+connections, respectively. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is <code class="docutils literal notranslate"><span class="pre">False</span></code>
+the only possible mode is <code class="docutils literal notranslate"><span class="pre">ALL</span></code>. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is
+<code class="docutils literal notranslate"><span class="pre">None</span></code> and also directed evidence(s) match the criteria these
+will overwrite the undirected evidences and only the directed
+result will be returned.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.degrees_directed_out_by_interaction_type">
+<span class="sig-name descname"><span class="pre">degrees_directed_out_by_interaction_type</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.degrees_directed_out_by_interaction_type" title="Link to this definition">§</a></dt>
+<dd><p>Returns a <em>set</em> of nodes with the connections matching the direction,
+effect and evidence criteria. E.g. if the query concerns the incoming
+degrees with positive effect and the matching evidences show A
+activates B, but not the other way around, only “B” will be returned.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>mode:</dt><dd><p>The type of degrees to be considered. Three possible values are
+<code class="docutils literal notranslate"><span class="pre">'IN'</span></code>, <cite>‘OUT’`</cite> and <code class="docutils literal notranslate"><span class="pre">'ALL'</span></code> for incoming, outgoing and all
+connections, respectively. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is <code class="docutils literal notranslate"><span class="pre">False</span></code>
+the only possible mode is <code class="docutils literal notranslate"><span class="pre">ALL</span></code>. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is
+<code class="docutils literal notranslate"><span class="pre">None</span></code> and also directed evidence(s) match the criteria these
+will overwrite the undirected evidences and only the directed
+result will be returned.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.degrees_directed_out_by_interaction_type_and_data_model">
+<span class="sig-name descname"><span class="pre">degrees_directed_out_by_interaction_type_and_data_model</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.degrees_directed_out_by_interaction_type_and_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Returns a <em>set</em> of nodes with the connections matching the direction,
+effect and evidence criteria. E.g. if the query concerns the incoming
+degrees with positive effect and the matching evidences show A
+activates B, but not the other way around, only “B” will be returned.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>mode:</dt><dd><p>The type of degrees to be considered. Three possible values are
+<code class="docutils literal notranslate"><span class="pre">'IN'</span></code>, <cite>‘OUT’`</cite> and <code class="docutils literal notranslate"><span class="pre">'ALL'</span></code> for incoming, outgoing and all
+connections, respectively. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is <code class="docutils literal notranslate"><span class="pre">False</span></code>
+the only possible mode is <code class="docutils literal notranslate"><span class="pre">ALL</span></code>. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is
+<code class="docutils literal notranslate"><span class="pre">None</span></code> and also directed evidence(s) match the criteria these
+will overwrite the undirected evidences and only the directed
+result will be returned.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.degrees_directed_out_by_interaction_type_and_data_model_and_resource">
+<span class="sig-name descname"><span class="pre">degrees_directed_out_by_interaction_type_and_data_model_and_resource</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.degrees_directed_out_by_interaction_type_and_data_model_and_resource" title="Link to this definition">§</a></dt>
+<dd><p>Returns a <em>set</em> of nodes with the connections matching the direction,
+effect and evidence criteria. E.g. if the query concerns the incoming
+degrees with positive effect and the matching evidences show A
+activates B, but not the other way around, only “B” will be returned.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>mode:</dt><dd><p>The type of degrees to be considered. Three possible values are
+<code class="docutils literal notranslate"><span class="pre">'IN'</span></code>, <cite>‘OUT’`</cite> and <code class="docutils literal notranslate"><span class="pre">'ALL'</span></code> for incoming, outgoing and all
+connections, respectively. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is <code class="docutils literal notranslate"><span class="pre">False</span></code>
+the only possible mode is <code class="docutils literal notranslate"><span class="pre">ALL</span></code>. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is
+<code class="docutils literal notranslate"><span class="pre">None</span></code> and also directed evidence(s) match the criteria these
+will overwrite the undirected evidences and only the directed
+result will be returned.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.degrees_directed_out_by_reference">
+<span class="sig-name descname"><span class="pre">degrees_directed_out_by_reference</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.degrees_directed_out_by_reference" title="Link to this definition">§</a></dt>
+<dd><p>Returns a <em>set</em> of nodes with the connections matching the direction,
+effect and evidence criteria. E.g. if the query concerns the incoming
+degrees with positive effect and the matching evidences show A
+activates B, but not the other way around, only “B” will be returned.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>mode:</dt><dd><p>The type of degrees to be considered. Three possible values are
+<code class="docutils literal notranslate"><span class="pre">'IN'</span></code>, <cite>‘OUT’`</cite> and <code class="docutils literal notranslate"><span class="pre">'ALL'</span></code> for incoming, outgoing and all
+connections, respectively. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is <code class="docutils literal notranslate"><span class="pre">False</span></code>
+the only possible mode is <code class="docutils literal notranslate"><span class="pre">ALL</span></code>. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is
+<code class="docutils literal notranslate"><span class="pre">None</span></code> and also directed evidence(s) match the criteria these
+will overwrite the undirected evidences and only the directed
+result will be returned.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.degrees_directed_out_by_resource">
+<span class="sig-name descname"><span class="pre">degrees_directed_out_by_resource</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.degrees_directed_out_by_resource" title="Link to this definition">§</a></dt>
+<dd><p>Returns a <em>set</em> of nodes with the connections matching the direction,
+effect and evidence criteria. E.g. if the query concerns the incoming
+degrees with positive effect and the matching evidences show A
+activates B, but not the other way around, only “B” will be returned.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>mode:</dt><dd><p>The type of degrees to be considered. Three possible values are
+<code class="docutils literal notranslate"><span class="pre">'IN'</span></code>, <cite>‘OUT’`</cite> and <code class="docutils literal notranslate"><span class="pre">'ALL'</span></code> for incoming, outgoing and all
+connections, respectively. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is <code class="docutils literal notranslate"><span class="pre">False</span></code>
+the only possible mode is <code class="docutils literal notranslate"><span class="pre">ALL</span></code>. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is
+<code class="docutils literal notranslate"><span class="pre">None</span></code> and also directed evidence(s) match the criteria these
+will overwrite the undirected evidences and only the directed
+result will be returned.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.degrees_negative_by_data_model">
+<span class="sig-name descname"><span class="pre">degrees_negative_by_data_model</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.degrees_negative_by_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Returns a <em>set</em> of nodes with the connections matching the direction,
+effect and evidence criteria. E.g. if the query concerns the incoming
+degrees with positive effect and the matching evidences show A
+activates B, but not the other way around, only “B” will be returned.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>mode:</dt><dd><p>The type of degrees to be considered. Three possible values are
+<code class="docutils literal notranslate"><span class="pre">'IN'</span></code>, <cite>‘OUT’`</cite> and <code class="docutils literal notranslate"><span class="pre">'ALL'</span></code> for incoming, outgoing and all
+connections, respectively. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is <code class="docutils literal notranslate"><span class="pre">False</span></code>
+the only possible mode is <code class="docutils literal notranslate"><span class="pre">ALL</span></code>. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is
+<code class="docutils literal notranslate"><span class="pre">None</span></code> and also directed evidence(s) match the criteria these
+will overwrite the undirected evidences and only the directed
+result will be returned.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.degrees_negative_by_interaction_type">
+<span class="sig-name descname"><span class="pre">degrees_negative_by_interaction_type</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.degrees_negative_by_interaction_type" title="Link to this definition">§</a></dt>
+<dd><p>Returns a <em>set</em> of nodes with the connections matching the direction,
+effect and evidence criteria. E.g. if the query concerns the incoming
+degrees with positive effect and the matching evidences show A
+activates B, but not the other way around, only “B” will be returned.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>mode:</dt><dd><p>The type of degrees to be considered. Three possible values are
+<code class="docutils literal notranslate"><span class="pre">'IN'</span></code>, <cite>‘OUT’`</cite> and <code class="docutils literal notranslate"><span class="pre">'ALL'</span></code> for incoming, outgoing and all
+connections, respectively. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is <code class="docutils literal notranslate"><span class="pre">False</span></code>
+the only possible mode is <code class="docutils literal notranslate"><span class="pre">ALL</span></code>. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is
+<code class="docutils literal notranslate"><span class="pre">None</span></code> and also directed evidence(s) match the criteria these
+will overwrite the undirected evidences and only the directed
+result will be returned.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.degrees_negative_by_interaction_type_and_data_model">
+<span class="sig-name descname"><span class="pre">degrees_negative_by_interaction_type_and_data_model</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.degrees_negative_by_interaction_type_and_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Returns a <em>set</em> of nodes with the connections matching the direction,
+effect and evidence criteria. E.g. if the query concerns the incoming
+degrees with positive effect and the matching evidences show A
+activates B, but not the other way around, only “B” will be returned.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>mode:</dt><dd><p>The type of degrees to be considered. Three possible values are
+<code class="docutils literal notranslate"><span class="pre">'IN'</span></code>, <cite>‘OUT’`</cite> and <code class="docutils literal notranslate"><span class="pre">'ALL'</span></code> for incoming, outgoing and all
+connections, respectively. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is <code class="docutils literal notranslate"><span class="pre">False</span></code>
+the only possible mode is <code class="docutils literal notranslate"><span class="pre">ALL</span></code>. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is
+<code class="docutils literal notranslate"><span class="pre">None</span></code> and also directed evidence(s) match the criteria these
+will overwrite the undirected evidences and only the directed
+result will be returned.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.degrees_negative_by_interaction_type_and_data_model_and_resource">
+<span class="sig-name descname"><span class="pre">degrees_negative_by_interaction_type_and_data_model_and_resource</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.degrees_negative_by_interaction_type_and_data_model_and_resource" title="Link to this definition">§</a></dt>
+<dd><p>Returns a <em>set</em> of nodes with the connections matching the direction,
+effect and evidence criteria. E.g. if the query concerns the incoming
+degrees with positive effect and the matching evidences show A
+activates B, but not the other way around, only “B” will be returned.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>mode:</dt><dd><p>The type of degrees to be considered. Three possible values are
+<code class="docutils literal notranslate"><span class="pre">'IN'</span></code>, <cite>‘OUT’`</cite> and <code class="docutils literal notranslate"><span class="pre">'ALL'</span></code> for incoming, outgoing and all
+connections, respectively. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is <code class="docutils literal notranslate"><span class="pre">False</span></code>
+the only possible mode is <code class="docutils literal notranslate"><span class="pre">ALL</span></code>. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is
+<code class="docutils literal notranslate"><span class="pre">None</span></code> and also directed evidence(s) match the criteria these
+will overwrite the undirected evidences and only the directed
+result will be returned.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.degrees_negative_by_reference">
+<span class="sig-name descname"><span class="pre">degrees_negative_by_reference</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.degrees_negative_by_reference" title="Link to this definition">§</a></dt>
+<dd><p>Returns a <em>set</em> of nodes with the connections matching the direction,
+effect and evidence criteria. E.g. if the query concerns the incoming
+degrees with positive effect and the matching evidences show A
+activates B, but not the other way around, only “B” will be returned.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>mode:</dt><dd><p>The type of degrees to be considered. Three possible values are
+<code class="docutils literal notranslate"><span class="pre">'IN'</span></code>, <cite>‘OUT’`</cite> and <code class="docutils literal notranslate"><span class="pre">'ALL'</span></code> for incoming, outgoing and all
+connections, respectively. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is <code class="docutils literal notranslate"><span class="pre">False</span></code>
+the only possible mode is <code class="docutils literal notranslate"><span class="pre">ALL</span></code>. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is
+<code class="docutils literal notranslate"><span class="pre">None</span></code> and also directed evidence(s) match the criteria these
+will overwrite the undirected evidences and only the directed
+result will be returned.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.degrees_negative_by_resource">
+<span class="sig-name descname"><span class="pre">degrees_negative_by_resource</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.degrees_negative_by_resource" title="Link to this definition">§</a></dt>
+<dd><p>Returns a <em>set</em> of nodes with the connections matching the direction,
+effect and evidence criteria. E.g. if the query concerns the incoming
+degrees with positive effect and the matching evidences show A
+activates B, but not the other way around, only “B” will be returned.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>mode:</dt><dd><p>The type of degrees to be considered. Three possible values are
+<code class="docutils literal notranslate"><span class="pre">'IN'</span></code>, <cite>‘OUT’`</cite> and <code class="docutils literal notranslate"><span class="pre">'ALL'</span></code> for incoming, outgoing and all
+connections, respectively. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is <code class="docutils literal notranslate"><span class="pre">False</span></code>
+the only possible mode is <code class="docutils literal notranslate"><span class="pre">ALL</span></code>. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is
+<code class="docutils literal notranslate"><span class="pre">None</span></code> and also directed evidence(s) match the criteria these
+will overwrite the undirected evidences and only the directed
+result will be returned.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.degrees_negative_in_by_data_model">
+<span class="sig-name descname"><span class="pre">degrees_negative_in_by_data_model</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.degrees_negative_in_by_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Returns a <em>set</em> of nodes with the connections matching the direction,
+effect and evidence criteria. E.g. if the query concerns the incoming
+degrees with positive effect and the matching evidences show A
+activates B, but not the other way around, only “B” will be returned.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>mode:</dt><dd><p>The type of degrees to be considered. Three possible values are
+<code class="docutils literal notranslate"><span class="pre">'IN'</span></code>, <cite>‘OUT’`</cite> and <code class="docutils literal notranslate"><span class="pre">'ALL'</span></code> for incoming, outgoing and all
+connections, respectively. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is <code class="docutils literal notranslate"><span class="pre">False</span></code>
+the only possible mode is <code class="docutils literal notranslate"><span class="pre">ALL</span></code>. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is
+<code class="docutils literal notranslate"><span class="pre">None</span></code> and also directed evidence(s) match the criteria these
+will overwrite the undirected evidences and only the directed
+result will be returned.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.degrees_negative_in_by_interaction_type">
+<span class="sig-name descname"><span class="pre">degrees_negative_in_by_interaction_type</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.degrees_negative_in_by_interaction_type" title="Link to this definition">§</a></dt>
+<dd><p>Returns a <em>set</em> of nodes with the connections matching the direction,
+effect and evidence criteria. E.g. if the query concerns the incoming
+degrees with positive effect and the matching evidences show A
+activates B, but not the other way around, only “B” will be returned.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>mode:</dt><dd><p>The type of degrees to be considered. Three possible values are
+<code class="docutils literal notranslate"><span class="pre">'IN'</span></code>, <cite>‘OUT’`</cite> and <code class="docutils literal notranslate"><span class="pre">'ALL'</span></code> for incoming, outgoing and all
+connections, respectively. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is <code class="docutils literal notranslate"><span class="pre">False</span></code>
+the only possible mode is <code class="docutils literal notranslate"><span class="pre">ALL</span></code>. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is
+<code class="docutils literal notranslate"><span class="pre">None</span></code> and also directed evidence(s) match the criteria these
+will overwrite the undirected evidences and only the directed
+result will be returned.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.degrees_negative_in_by_interaction_type_and_data_model">
+<span class="sig-name descname"><span class="pre">degrees_negative_in_by_interaction_type_and_data_model</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.degrees_negative_in_by_interaction_type_and_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Returns a <em>set</em> of nodes with the connections matching the direction,
+effect and evidence criteria. E.g. if the query concerns the incoming
+degrees with positive effect and the matching evidences show A
+activates B, but not the other way around, only “B” will be returned.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>mode:</dt><dd><p>The type of degrees to be considered. Three possible values are
+<code class="docutils literal notranslate"><span class="pre">'IN'</span></code>, <cite>‘OUT’`</cite> and <code class="docutils literal notranslate"><span class="pre">'ALL'</span></code> for incoming, outgoing and all
+connections, respectively. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is <code class="docutils literal notranslate"><span class="pre">False</span></code>
+the only possible mode is <code class="docutils literal notranslate"><span class="pre">ALL</span></code>. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is
+<code class="docutils literal notranslate"><span class="pre">None</span></code> and also directed evidence(s) match the criteria these
+will overwrite the undirected evidences and only the directed
+result will be returned.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.degrees_negative_in_by_interaction_type_and_data_model_and_resource">
+<span class="sig-name descname"><span class="pre">degrees_negative_in_by_interaction_type_and_data_model_and_resource</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.degrees_negative_in_by_interaction_type_and_data_model_and_resource" title="Link to this definition">§</a></dt>
+<dd><p>Returns a <em>set</em> of nodes with the connections matching the direction,
+effect and evidence criteria. E.g. if the query concerns the incoming
+degrees with positive effect and the matching evidences show A
+activates B, but not the other way around, only “B” will be returned.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>mode:</dt><dd><p>The type of degrees to be considered. Three possible values are
+<code class="docutils literal notranslate"><span class="pre">'IN'</span></code>, <cite>‘OUT’`</cite> and <code class="docutils literal notranslate"><span class="pre">'ALL'</span></code> for incoming, outgoing and all
+connections, respectively. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is <code class="docutils literal notranslate"><span class="pre">False</span></code>
+the only possible mode is <code class="docutils literal notranslate"><span class="pre">ALL</span></code>. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is
+<code class="docutils literal notranslate"><span class="pre">None</span></code> and also directed evidence(s) match the criteria these
+will overwrite the undirected evidences and only the directed
+result will be returned.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.degrees_negative_in_by_reference">
+<span class="sig-name descname"><span class="pre">degrees_negative_in_by_reference</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.degrees_negative_in_by_reference" title="Link to this definition">§</a></dt>
+<dd><p>Returns a <em>set</em> of nodes with the connections matching the direction,
+effect and evidence criteria. E.g. if the query concerns the incoming
+degrees with positive effect and the matching evidences show A
+activates B, but not the other way around, only “B” will be returned.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>mode:</dt><dd><p>The type of degrees to be considered. Three possible values are
+<code class="docutils literal notranslate"><span class="pre">'IN'</span></code>, <cite>‘OUT’`</cite> and <code class="docutils literal notranslate"><span class="pre">'ALL'</span></code> for incoming, outgoing and all
+connections, respectively. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is <code class="docutils literal notranslate"><span class="pre">False</span></code>
+the only possible mode is <code class="docutils literal notranslate"><span class="pre">ALL</span></code>. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is
+<code class="docutils literal notranslate"><span class="pre">None</span></code> and also directed evidence(s) match the criteria these
+will overwrite the undirected evidences and only the directed
+result will be returned.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.degrees_negative_in_by_resource">
+<span class="sig-name descname"><span class="pre">degrees_negative_in_by_resource</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.degrees_negative_in_by_resource" title="Link to this definition">§</a></dt>
+<dd><p>Returns a <em>set</em> of nodes with the connections matching the direction,
+effect and evidence criteria. E.g. if the query concerns the incoming
+degrees with positive effect and the matching evidences show A
+activates B, but not the other way around, only “B” will be returned.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>mode:</dt><dd><p>The type of degrees to be considered. Three possible values are
+<code class="docutils literal notranslate"><span class="pre">'IN'</span></code>, <cite>‘OUT’`</cite> and <code class="docutils literal notranslate"><span class="pre">'ALL'</span></code> for incoming, outgoing and all
+connections, respectively. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is <code class="docutils literal notranslate"><span class="pre">False</span></code>
+the only possible mode is <code class="docutils literal notranslate"><span class="pre">ALL</span></code>. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is
+<code class="docutils literal notranslate"><span class="pre">None</span></code> and also directed evidence(s) match the criteria these
+will overwrite the undirected evidences and only the directed
+result will be returned.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.degrees_negative_out_by_data_model">
+<span class="sig-name descname"><span class="pre">degrees_negative_out_by_data_model</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.degrees_negative_out_by_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Returns a <em>set</em> of nodes with the connections matching the direction,
+effect and evidence criteria. E.g. if the query concerns the incoming
+degrees with positive effect and the matching evidences show A
+activates B, but not the other way around, only “B” will be returned.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>mode:</dt><dd><p>The type of degrees to be considered. Three possible values are
+<code class="docutils literal notranslate"><span class="pre">'IN'</span></code>, <cite>‘OUT’`</cite> and <code class="docutils literal notranslate"><span class="pre">'ALL'</span></code> for incoming, outgoing and all
+connections, respectively. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is <code class="docutils literal notranslate"><span class="pre">False</span></code>
+the only possible mode is <code class="docutils literal notranslate"><span class="pre">ALL</span></code>. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is
+<code class="docutils literal notranslate"><span class="pre">None</span></code> and also directed evidence(s) match the criteria these
+will overwrite the undirected evidences and only the directed
+result will be returned.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.degrees_negative_out_by_interaction_type">
+<span class="sig-name descname"><span class="pre">degrees_negative_out_by_interaction_type</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.degrees_negative_out_by_interaction_type" title="Link to this definition">§</a></dt>
+<dd><p>Returns a <em>set</em> of nodes with the connections matching the direction,
+effect and evidence criteria. E.g. if the query concerns the incoming
+degrees with positive effect and the matching evidences show A
+activates B, but not the other way around, only “B” will be returned.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>mode:</dt><dd><p>The type of degrees to be considered. Three possible values are
+<code class="docutils literal notranslate"><span class="pre">'IN'</span></code>, <cite>‘OUT’`</cite> and <code class="docutils literal notranslate"><span class="pre">'ALL'</span></code> for incoming, outgoing and all
+connections, respectively. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is <code class="docutils literal notranslate"><span class="pre">False</span></code>
+the only possible mode is <code class="docutils literal notranslate"><span class="pre">ALL</span></code>. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is
+<code class="docutils literal notranslate"><span class="pre">None</span></code> and also directed evidence(s) match the criteria these
+will overwrite the undirected evidences and only the directed
+result will be returned.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.degrees_negative_out_by_interaction_type_and_data_model">
+<span class="sig-name descname"><span class="pre">degrees_negative_out_by_interaction_type_and_data_model</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.degrees_negative_out_by_interaction_type_and_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Returns a <em>set</em> of nodes with the connections matching the direction,
+effect and evidence criteria. E.g. if the query concerns the incoming
+degrees with positive effect and the matching evidences show A
+activates B, but not the other way around, only “B” will be returned.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>mode:</dt><dd><p>The type of degrees to be considered. Three possible values are
+<code class="docutils literal notranslate"><span class="pre">'IN'</span></code>, <cite>‘OUT’`</cite> and <code class="docutils literal notranslate"><span class="pre">'ALL'</span></code> for incoming, outgoing and all
+connections, respectively. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is <code class="docutils literal notranslate"><span class="pre">False</span></code>
+the only possible mode is <code class="docutils literal notranslate"><span class="pre">ALL</span></code>. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is
+<code class="docutils literal notranslate"><span class="pre">None</span></code> and also directed evidence(s) match the criteria these
+will overwrite the undirected evidences and only the directed
+result will be returned.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.degrees_negative_out_by_interaction_type_and_data_model_and_resource">
+<span class="sig-name descname"><span class="pre">degrees_negative_out_by_interaction_type_and_data_model_and_resource</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.degrees_negative_out_by_interaction_type_and_data_model_and_resource" title="Link to this definition">§</a></dt>
+<dd><p>Returns a <em>set</em> of nodes with the connections matching the direction,
+effect and evidence criteria. E.g. if the query concerns the incoming
+degrees with positive effect and the matching evidences show A
+activates B, but not the other way around, only “B” will be returned.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>mode:</dt><dd><p>The type of degrees to be considered. Three possible values are
+<code class="docutils literal notranslate"><span class="pre">'IN'</span></code>, <cite>‘OUT’`</cite> and <code class="docutils literal notranslate"><span class="pre">'ALL'</span></code> for incoming, outgoing and all
+connections, respectively. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is <code class="docutils literal notranslate"><span class="pre">False</span></code>
+the only possible mode is <code class="docutils literal notranslate"><span class="pre">ALL</span></code>. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is
+<code class="docutils literal notranslate"><span class="pre">None</span></code> and also directed evidence(s) match the criteria these
+will overwrite the undirected evidences and only the directed
+result will be returned.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.degrees_negative_out_by_reference">
+<span class="sig-name descname"><span class="pre">degrees_negative_out_by_reference</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.degrees_negative_out_by_reference" title="Link to this definition">§</a></dt>
+<dd><p>Returns a <em>set</em> of nodes with the connections matching the direction,
+effect and evidence criteria. E.g. if the query concerns the incoming
+degrees with positive effect and the matching evidences show A
+activates B, but not the other way around, only “B” will be returned.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>mode:</dt><dd><p>The type of degrees to be considered. Three possible values are
+<code class="docutils literal notranslate"><span class="pre">'IN'</span></code>, <cite>‘OUT’`</cite> and <code class="docutils literal notranslate"><span class="pre">'ALL'</span></code> for incoming, outgoing and all
+connections, respectively. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is <code class="docutils literal notranslate"><span class="pre">False</span></code>
+the only possible mode is <code class="docutils literal notranslate"><span class="pre">ALL</span></code>. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is
+<code class="docutils literal notranslate"><span class="pre">None</span></code> and also directed evidence(s) match the criteria these
+will overwrite the undirected evidences and only the directed
+result will be returned.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.degrees_negative_out_by_resource">
+<span class="sig-name descname"><span class="pre">degrees_negative_out_by_resource</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.degrees_negative_out_by_resource" title="Link to this definition">§</a></dt>
+<dd><p>Returns a <em>set</em> of nodes with the connections matching the direction,
+effect and evidence criteria. E.g. if the query concerns the incoming
+degrees with positive effect and the matching evidences show A
+activates B, but not the other way around, only “B” will be returned.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>mode:</dt><dd><p>The type of degrees to be considered. Three possible values are
+<code class="docutils literal notranslate"><span class="pre">'IN'</span></code>, <cite>‘OUT’`</cite> and <code class="docutils literal notranslate"><span class="pre">'ALL'</span></code> for incoming, outgoing and all
+connections, respectively. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is <code class="docutils literal notranslate"><span class="pre">False</span></code>
+the only possible mode is <code class="docutils literal notranslate"><span class="pre">ALL</span></code>. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is
+<code class="docutils literal notranslate"><span class="pre">None</span></code> and also directed evidence(s) match the criteria these
+will overwrite the undirected evidences and only the directed
+result will be returned.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.degrees_non_directed_by_data_model">
+<span class="sig-name descname"><span class="pre">degrees_non_directed_by_data_model</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.degrees_non_directed_by_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Returns a <em>set</em> of nodes with the connections matching the direction,
+effect and evidence criteria. E.g. if the query concerns the incoming
+degrees with positive effect and the matching evidences show A
+activates B, but not the other way around, only “B” will be returned.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>mode:</dt><dd><p>The type of degrees to be considered. Three possible values are
+<code class="docutils literal notranslate"><span class="pre">'IN'</span></code>, <cite>‘OUT’`</cite> and <code class="docutils literal notranslate"><span class="pre">'ALL'</span></code> for incoming, outgoing and all
+connections, respectively. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is <code class="docutils literal notranslate"><span class="pre">False</span></code>
+the only possible mode is <code class="docutils literal notranslate"><span class="pre">ALL</span></code>. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is
+<code class="docutils literal notranslate"><span class="pre">None</span></code> and also directed evidence(s) match the criteria these
+will overwrite the undirected evidences and only the directed
+result will be returned.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.degrees_non_directed_by_interaction_type">
+<span class="sig-name descname"><span class="pre">degrees_non_directed_by_interaction_type</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.degrees_non_directed_by_interaction_type" title="Link to this definition">§</a></dt>
+<dd><p>Returns a <em>set</em> of nodes with the connections matching the direction,
+effect and evidence criteria. E.g. if the query concerns the incoming
+degrees with positive effect and the matching evidences show A
+activates B, but not the other way around, only “B” will be returned.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>mode:</dt><dd><p>The type of degrees to be considered. Three possible values are
+<code class="docutils literal notranslate"><span class="pre">'IN'</span></code>, <cite>‘OUT’`</cite> and <code class="docutils literal notranslate"><span class="pre">'ALL'</span></code> for incoming, outgoing and all
+connections, respectively. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is <code class="docutils literal notranslate"><span class="pre">False</span></code>
+the only possible mode is <code class="docutils literal notranslate"><span class="pre">ALL</span></code>. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is
+<code class="docutils literal notranslate"><span class="pre">None</span></code> and also directed evidence(s) match the criteria these
+will overwrite the undirected evidences and only the directed
+result will be returned.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.degrees_non_directed_by_interaction_type_and_data_model">
+<span class="sig-name descname"><span class="pre">degrees_non_directed_by_interaction_type_and_data_model</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.degrees_non_directed_by_interaction_type_and_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Returns a <em>set</em> of nodes with the connections matching the direction,
+effect and evidence criteria. E.g. if the query concerns the incoming
+degrees with positive effect and the matching evidences show A
+activates B, but not the other way around, only “B” will be returned.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>mode:</dt><dd><p>The type of degrees to be considered. Three possible values are
+<code class="docutils literal notranslate"><span class="pre">'IN'</span></code>, <cite>‘OUT’`</cite> and <code class="docutils literal notranslate"><span class="pre">'ALL'</span></code> for incoming, outgoing and all
+connections, respectively. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is <code class="docutils literal notranslate"><span class="pre">False</span></code>
+the only possible mode is <code class="docutils literal notranslate"><span class="pre">ALL</span></code>. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is
+<code class="docutils literal notranslate"><span class="pre">None</span></code> and also directed evidence(s) match the criteria these
+will overwrite the undirected evidences and only the directed
+result will be returned.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.degrees_non_directed_by_interaction_type_and_data_model_and_resource">
+<span class="sig-name descname"><span class="pre">degrees_non_directed_by_interaction_type_and_data_model_and_resource</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.degrees_non_directed_by_interaction_type_and_data_model_and_resource" title="Link to this definition">§</a></dt>
+<dd><p>Returns a <em>set</em> of nodes with the connections matching the direction,
+effect and evidence criteria. E.g. if the query concerns the incoming
+degrees with positive effect and the matching evidences show A
+activates B, but not the other way around, only “B” will be returned.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>mode:</dt><dd><p>The type of degrees to be considered. Three possible values are
+<code class="docutils literal notranslate"><span class="pre">'IN'</span></code>, <cite>‘OUT’`</cite> and <code class="docutils literal notranslate"><span class="pre">'ALL'</span></code> for incoming, outgoing and all
+connections, respectively. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is <code class="docutils literal notranslate"><span class="pre">False</span></code>
+the only possible mode is <code class="docutils literal notranslate"><span class="pre">ALL</span></code>. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is
+<code class="docutils literal notranslate"><span class="pre">None</span></code> and also directed evidence(s) match the criteria these
+will overwrite the undirected evidences and only the directed
+result will be returned.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.degrees_non_directed_by_reference">
+<span class="sig-name descname"><span class="pre">degrees_non_directed_by_reference</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.degrees_non_directed_by_reference" title="Link to this definition">§</a></dt>
+<dd><p>Returns a <em>set</em> of nodes with the connections matching the direction,
+effect and evidence criteria. E.g. if the query concerns the incoming
+degrees with positive effect and the matching evidences show A
+activates B, but not the other way around, only “B” will be returned.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>mode:</dt><dd><p>The type of degrees to be considered. Three possible values are
+<code class="docutils literal notranslate"><span class="pre">'IN'</span></code>, <cite>‘OUT’`</cite> and <code class="docutils literal notranslate"><span class="pre">'ALL'</span></code> for incoming, outgoing and all
+connections, respectively. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is <code class="docutils literal notranslate"><span class="pre">False</span></code>
+the only possible mode is <code class="docutils literal notranslate"><span class="pre">ALL</span></code>. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is
+<code class="docutils literal notranslate"><span class="pre">None</span></code> and also directed evidence(s) match the criteria these
+will overwrite the undirected evidences and only the directed
+result will be returned.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.degrees_non_directed_by_resource">
+<span class="sig-name descname"><span class="pre">degrees_non_directed_by_resource</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.degrees_non_directed_by_resource" title="Link to this definition">§</a></dt>
+<dd><p>Returns a <em>set</em> of nodes with the connections matching the direction,
+effect and evidence criteria. E.g. if the query concerns the incoming
+degrees with positive effect and the matching evidences show A
+activates B, but not the other way around, only “B” will be returned.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>mode:</dt><dd><p>The type of degrees to be considered. Three possible values are
+<code class="docutils literal notranslate"><span class="pre">'IN'</span></code>, <cite>‘OUT’`</cite> and <code class="docutils literal notranslate"><span class="pre">'ALL'</span></code> for incoming, outgoing and all
+connections, respectively. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is <code class="docutils literal notranslate"><span class="pre">False</span></code>
+the only possible mode is <code class="docutils literal notranslate"><span class="pre">ALL</span></code>. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is
+<code class="docutils literal notranslate"><span class="pre">None</span></code> and also directed evidence(s) match the criteria these
+will overwrite the undirected evidences and only the directed
+result will be returned.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.degrees_positive_by_data_model">
+<span class="sig-name descname"><span class="pre">degrees_positive_by_data_model</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.degrees_positive_by_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Returns a <em>set</em> of nodes with the connections matching the direction,
+effect and evidence criteria. E.g. if the query concerns the incoming
+degrees with positive effect and the matching evidences show A
+activates B, but not the other way around, only “B” will be returned.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>mode:</dt><dd><p>The type of degrees to be considered. Three possible values are
+<code class="docutils literal notranslate"><span class="pre">'IN'</span></code>, <cite>‘OUT’`</cite> and <code class="docutils literal notranslate"><span class="pre">'ALL'</span></code> for incoming, outgoing and all
+connections, respectively. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is <code class="docutils literal notranslate"><span class="pre">False</span></code>
+the only possible mode is <code class="docutils literal notranslate"><span class="pre">ALL</span></code>. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is
+<code class="docutils literal notranslate"><span class="pre">None</span></code> and also directed evidence(s) match the criteria these
+will overwrite the undirected evidences and only the directed
+result will be returned.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.degrees_positive_by_interaction_type">
+<span class="sig-name descname"><span class="pre">degrees_positive_by_interaction_type</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.degrees_positive_by_interaction_type" title="Link to this definition">§</a></dt>
+<dd><p>Returns a <em>set</em> of nodes with the connections matching the direction,
+effect and evidence criteria. E.g. if the query concerns the incoming
+degrees with positive effect and the matching evidences show A
+activates B, but not the other way around, only “B” will be returned.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>mode:</dt><dd><p>The type of degrees to be considered. Three possible values are
+<code class="docutils literal notranslate"><span class="pre">'IN'</span></code>, <cite>‘OUT’`</cite> and <code class="docutils literal notranslate"><span class="pre">'ALL'</span></code> for incoming, outgoing and all
+connections, respectively. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is <code class="docutils literal notranslate"><span class="pre">False</span></code>
+the only possible mode is <code class="docutils literal notranslate"><span class="pre">ALL</span></code>. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is
+<code class="docutils literal notranslate"><span class="pre">None</span></code> and also directed evidence(s) match the criteria these
+will overwrite the undirected evidences and only the directed
+result will be returned.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.degrees_positive_by_interaction_type_and_data_model">
+<span class="sig-name descname"><span class="pre">degrees_positive_by_interaction_type_and_data_model</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.degrees_positive_by_interaction_type_and_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Returns a <em>set</em> of nodes with the connections matching the direction,
+effect and evidence criteria. E.g. if the query concerns the incoming
+degrees with positive effect and the matching evidences show A
+activates B, but not the other way around, only “B” will be returned.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>mode:</dt><dd><p>The type of degrees to be considered. Three possible values are
+<code class="docutils literal notranslate"><span class="pre">'IN'</span></code>, <cite>‘OUT’`</cite> and <code class="docutils literal notranslate"><span class="pre">'ALL'</span></code> for incoming, outgoing and all
+connections, respectively. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is <code class="docutils literal notranslate"><span class="pre">False</span></code>
+the only possible mode is <code class="docutils literal notranslate"><span class="pre">ALL</span></code>. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is
+<code class="docutils literal notranslate"><span class="pre">None</span></code> and also directed evidence(s) match the criteria these
+will overwrite the undirected evidences and only the directed
+result will be returned.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.degrees_positive_by_interaction_type_and_data_model_and_resource">
+<span class="sig-name descname"><span class="pre">degrees_positive_by_interaction_type_and_data_model_and_resource</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.degrees_positive_by_interaction_type_and_data_model_and_resource" title="Link to this definition">§</a></dt>
+<dd><p>Returns a <em>set</em> of nodes with the connections matching the direction,
+effect and evidence criteria. E.g. if the query concerns the incoming
+degrees with positive effect and the matching evidences show A
+activates B, but not the other way around, only “B” will be returned.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>mode:</dt><dd><p>The type of degrees to be considered. Three possible values are
+<code class="docutils literal notranslate"><span class="pre">'IN'</span></code>, <cite>‘OUT’`</cite> and <code class="docutils literal notranslate"><span class="pre">'ALL'</span></code> for incoming, outgoing and all
+connections, respectively. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is <code class="docutils literal notranslate"><span class="pre">False</span></code>
+the only possible mode is <code class="docutils literal notranslate"><span class="pre">ALL</span></code>. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is
+<code class="docutils literal notranslate"><span class="pre">None</span></code> and also directed evidence(s) match the criteria these
+will overwrite the undirected evidences and only the directed
+result will be returned.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.degrees_positive_by_reference">
+<span class="sig-name descname"><span class="pre">degrees_positive_by_reference</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.degrees_positive_by_reference" title="Link to this definition">§</a></dt>
+<dd><p>Returns a <em>set</em> of nodes with the connections matching the direction,
+effect and evidence criteria. E.g. if the query concerns the incoming
+degrees with positive effect and the matching evidences show A
+activates B, but not the other way around, only “B” will be returned.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>mode:</dt><dd><p>The type of degrees to be considered. Three possible values are
+<code class="docutils literal notranslate"><span class="pre">'IN'</span></code>, <cite>‘OUT’`</cite> and <code class="docutils literal notranslate"><span class="pre">'ALL'</span></code> for incoming, outgoing and all
+connections, respectively. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is <code class="docutils literal notranslate"><span class="pre">False</span></code>
+the only possible mode is <code class="docutils literal notranslate"><span class="pre">ALL</span></code>. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is
+<code class="docutils literal notranslate"><span class="pre">None</span></code> and also directed evidence(s) match the criteria these
+will overwrite the undirected evidences and only the directed
+result will be returned.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.degrees_positive_by_resource">
+<span class="sig-name descname"><span class="pre">degrees_positive_by_resource</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.degrees_positive_by_resource" title="Link to this definition">§</a></dt>
+<dd><p>Returns a <em>set</em> of nodes with the connections matching the direction,
+effect and evidence criteria. E.g. if the query concerns the incoming
+degrees with positive effect and the matching evidences show A
+activates B, but not the other way around, only “B” will be returned.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>mode:</dt><dd><p>The type of degrees to be considered. Three possible values are
+<code class="docutils literal notranslate"><span class="pre">'IN'</span></code>, <cite>‘OUT’`</cite> and <code class="docutils literal notranslate"><span class="pre">'ALL'</span></code> for incoming, outgoing and all
+connections, respectively. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is <code class="docutils literal notranslate"><span class="pre">False</span></code>
+the only possible mode is <code class="docutils literal notranslate"><span class="pre">ALL</span></code>. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is
+<code class="docutils literal notranslate"><span class="pre">None</span></code> and also directed evidence(s) match the criteria these
+will overwrite the undirected evidences and only the directed
+result will be returned.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.degrees_positive_in_by_data_model">
+<span class="sig-name descname"><span class="pre">degrees_positive_in_by_data_model</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.degrees_positive_in_by_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Returns a <em>set</em> of nodes with the connections matching the direction,
+effect and evidence criteria. E.g. if the query concerns the incoming
+degrees with positive effect and the matching evidences show A
+activates B, but not the other way around, only “B” will be returned.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>mode:</dt><dd><p>The type of degrees to be considered. Three possible values are
+<code class="docutils literal notranslate"><span class="pre">'IN'</span></code>, <cite>‘OUT’`</cite> and <code class="docutils literal notranslate"><span class="pre">'ALL'</span></code> for incoming, outgoing and all
+connections, respectively. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is <code class="docutils literal notranslate"><span class="pre">False</span></code>
+the only possible mode is <code class="docutils literal notranslate"><span class="pre">ALL</span></code>. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is
+<code class="docutils literal notranslate"><span class="pre">None</span></code> and also directed evidence(s) match the criteria these
+will overwrite the undirected evidences and only the directed
+result will be returned.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.degrees_positive_in_by_interaction_type">
+<span class="sig-name descname"><span class="pre">degrees_positive_in_by_interaction_type</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.degrees_positive_in_by_interaction_type" title="Link to this definition">§</a></dt>
+<dd><p>Returns a <em>set</em> of nodes with the connections matching the direction,
+effect and evidence criteria. E.g. if the query concerns the incoming
+degrees with positive effect and the matching evidences show A
+activates B, but not the other way around, only “B” will be returned.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>mode:</dt><dd><p>The type of degrees to be considered. Three possible values are
+<code class="docutils literal notranslate"><span class="pre">'IN'</span></code>, <cite>‘OUT’`</cite> and <code class="docutils literal notranslate"><span class="pre">'ALL'</span></code> for incoming, outgoing and all
+connections, respectively. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is <code class="docutils literal notranslate"><span class="pre">False</span></code>
+the only possible mode is <code class="docutils literal notranslate"><span class="pre">ALL</span></code>. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is
+<code class="docutils literal notranslate"><span class="pre">None</span></code> and also directed evidence(s) match the criteria these
+will overwrite the undirected evidences and only the directed
+result will be returned.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.degrees_positive_in_by_interaction_type_and_data_model">
+<span class="sig-name descname"><span class="pre">degrees_positive_in_by_interaction_type_and_data_model</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.degrees_positive_in_by_interaction_type_and_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Returns a <em>set</em> of nodes with the connections matching the direction,
+effect and evidence criteria. E.g. if the query concerns the incoming
+degrees with positive effect and the matching evidences show A
+activates B, but not the other way around, only “B” will be returned.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>mode:</dt><dd><p>The type of degrees to be considered. Three possible values are
+<code class="docutils literal notranslate"><span class="pre">'IN'</span></code>, <cite>‘OUT’`</cite> and <code class="docutils literal notranslate"><span class="pre">'ALL'</span></code> for incoming, outgoing and all
+connections, respectively. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is <code class="docutils literal notranslate"><span class="pre">False</span></code>
+the only possible mode is <code class="docutils literal notranslate"><span class="pre">ALL</span></code>. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is
+<code class="docutils literal notranslate"><span class="pre">None</span></code> and also directed evidence(s) match the criteria these
+will overwrite the undirected evidences and only the directed
+result will be returned.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.degrees_positive_in_by_interaction_type_and_data_model_and_resource">
+<span class="sig-name descname"><span class="pre">degrees_positive_in_by_interaction_type_and_data_model_and_resource</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.degrees_positive_in_by_interaction_type_and_data_model_and_resource" title="Link to this definition">§</a></dt>
+<dd><p>Returns a <em>set</em> of nodes with the connections matching the direction,
+effect and evidence criteria. E.g. if the query concerns the incoming
+degrees with positive effect and the matching evidences show A
+activates B, but not the other way around, only “B” will be returned.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>mode:</dt><dd><p>The type of degrees to be considered. Three possible values are
+<code class="docutils literal notranslate"><span class="pre">'IN'</span></code>, <cite>‘OUT’`</cite> and <code class="docutils literal notranslate"><span class="pre">'ALL'</span></code> for incoming, outgoing and all
+connections, respectively. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is <code class="docutils literal notranslate"><span class="pre">False</span></code>
+the only possible mode is <code class="docutils literal notranslate"><span class="pre">ALL</span></code>. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is
+<code class="docutils literal notranslate"><span class="pre">None</span></code> and also directed evidence(s) match the criteria these
+will overwrite the undirected evidences and only the directed
+result will be returned.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.degrees_positive_in_by_reference">
+<span class="sig-name descname"><span class="pre">degrees_positive_in_by_reference</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.degrees_positive_in_by_reference" title="Link to this definition">§</a></dt>
+<dd><p>Returns a <em>set</em> of nodes with the connections matching the direction,
+effect and evidence criteria. E.g. if the query concerns the incoming
+degrees with positive effect and the matching evidences show A
+activates B, but not the other way around, only “B” will be returned.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>mode:</dt><dd><p>The type of degrees to be considered. Three possible values are
+<code class="docutils literal notranslate"><span class="pre">'IN'</span></code>, <cite>‘OUT’`</cite> and <code class="docutils literal notranslate"><span class="pre">'ALL'</span></code> for incoming, outgoing and all
+connections, respectively. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is <code class="docutils literal notranslate"><span class="pre">False</span></code>
+the only possible mode is <code class="docutils literal notranslate"><span class="pre">ALL</span></code>. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is
+<code class="docutils literal notranslate"><span class="pre">None</span></code> and also directed evidence(s) match the criteria these
+will overwrite the undirected evidences and only the directed
+result will be returned.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.degrees_positive_in_by_resource">
+<span class="sig-name descname"><span class="pre">degrees_positive_in_by_resource</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.degrees_positive_in_by_resource" title="Link to this definition">§</a></dt>
+<dd><p>Returns a <em>set</em> of nodes with the connections matching the direction,
+effect and evidence criteria. E.g. if the query concerns the incoming
+degrees with positive effect and the matching evidences show A
+activates B, but not the other way around, only “B” will be returned.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>mode:</dt><dd><p>The type of degrees to be considered. Three possible values are
+<code class="docutils literal notranslate"><span class="pre">'IN'</span></code>, <cite>‘OUT’`</cite> and <code class="docutils literal notranslate"><span class="pre">'ALL'</span></code> for incoming, outgoing and all
+connections, respectively. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is <code class="docutils literal notranslate"><span class="pre">False</span></code>
+the only possible mode is <code class="docutils literal notranslate"><span class="pre">ALL</span></code>. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is
+<code class="docutils literal notranslate"><span class="pre">None</span></code> and also directed evidence(s) match the criteria these
+will overwrite the undirected evidences and only the directed
+result will be returned.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.degrees_positive_out_by_data_model">
+<span class="sig-name descname"><span class="pre">degrees_positive_out_by_data_model</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.degrees_positive_out_by_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Returns a <em>set</em> of nodes with the connections matching the direction,
+effect and evidence criteria. E.g. if the query concerns the incoming
+degrees with positive effect and the matching evidences show A
+activates B, but not the other way around, only “B” will be returned.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>mode:</dt><dd><p>The type of degrees to be considered. Three possible values are
+<code class="docutils literal notranslate"><span class="pre">'IN'</span></code>, <cite>‘OUT’`</cite> and <code class="docutils literal notranslate"><span class="pre">'ALL'</span></code> for incoming, outgoing and all
+connections, respectively. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is <code class="docutils literal notranslate"><span class="pre">False</span></code>
+the only possible mode is <code class="docutils literal notranslate"><span class="pre">ALL</span></code>. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is
+<code class="docutils literal notranslate"><span class="pre">None</span></code> and also directed evidence(s) match the criteria these
+will overwrite the undirected evidences and only the directed
+result will be returned.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.degrees_positive_out_by_interaction_type">
+<span class="sig-name descname"><span class="pre">degrees_positive_out_by_interaction_type</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.degrees_positive_out_by_interaction_type" title="Link to this definition">§</a></dt>
+<dd><p>Returns a <em>set</em> of nodes with the connections matching the direction,
+effect and evidence criteria. E.g. if the query concerns the incoming
+degrees with positive effect and the matching evidences show A
+activates B, but not the other way around, only “B” will be returned.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>mode:</dt><dd><p>The type of degrees to be considered. Three possible values are
+<code class="docutils literal notranslate"><span class="pre">'IN'</span></code>, <cite>‘OUT’`</cite> and <code class="docutils literal notranslate"><span class="pre">'ALL'</span></code> for incoming, outgoing and all
+connections, respectively. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is <code class="docutils literal notranslate"><span class="pre">False</span></code>
+the only possible mode is <code class="docutils literal notranslate"><span class="pre">ALL</span></code>. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is
+<code class="docutils literal notranslate"><span class="pre">None</span></code> and also directed evidence(s) match the criteria these
+will overwrite the undirected evidences and only the directed
+result will be returned.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.degrees_positive_out_by_interaction_type_and_data_model">
+<span class="sig-name descname"><span class="pre">degrees_positive_out_by_interaction_type_and_data_model</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.degrees_positive_out_by_interaction_type_and_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Returns a <em>set</em> of nodes with the connections matching the direction,
+effect and evidence criteria. E.g. if the query concerns the incoming
+degrees with positive effect and the matching evidences show A
+activates B, but not the other way around, only “B” will be returned.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>mode:</dt><dd><p>The type of degrees to be considered. Three possible values are
+<code class="docutils literal notranslate"><span class="pre">'IN'</span></code>, <cite>‘OUT’`</cite> and <code class="docutils literal notranslate"><span class="pre">'ALL'</span></code> for incoming, outgoing and all
+connections, respectively. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is <code class="docutils literal notranslate"><span class="pre">False</span></code>
+the only possible mode is <code class="docutils literal notranslate"><span class="pre">ALL</span></code>. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is
+<code class="docutils literal notranslate"><span class="pre">None</span></code> and also directed evidence(s) match the criteria these
+will overwrite the undirected evidences and only the directed
+result will be returned.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.degrees_positive_out_by_interaction_type_and_data_model_and_resource">
+<span class="sig-name descname"><span class="pre">degrees_positive_out_by_interaction_type_and_data_model_and_resource</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.degrees_positive_out_by_interaction_type_and_data_model_and_resource" title="Link to this definition">§</a></dt>
+<dd><p>Returns a <em>set</em> of nodes with the connections matching the direction,
+effect and evidence criteria. E.g. if the query concerns the incoming
+degrees with positive effect and the matching evidences show A
+activates B, but not the other way around, only “B” will be returned.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>mode:</dt><dd><p>The type of degrees to be considered. Three possible values are
+<code class="docutils literal notranslate"><span class="pre">'IN'</span></code>, <cite>‘OUT’`</cite> and <code class="docutils literal notranslate"><span class="pre">'ALL'</span></code> for incoming, outgoing and all
+connections, respectively. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is <code class="docutils literal notranslate"><span class="pre">False</span></code>
+the only possible mode is <code class="docutils literal notranslate"><span class="pre">ALL</span></code>. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is
+<code class="docutils literal notranslate"><span class="pre">None</span></code> and also directed evidence(s) match the criteria these
+will overwrite the undirected evidences and only the directed
+result will be returned.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.degrees_positive_out_by_reference">
+<span class="sig-name descname"><span class="pre">degrees_positive_out_by_reference</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.degrees_positive_out_by_reference" title="Link to this definition">§</a></dt>
+<dd><p>Returns a <em>set</em> of nodes with the connections matching the direction,
+effect and evidence criteria. E.g. if the query concerns the incoming
+degrees with positive effect and the matching evidences show A
+activates B, but not the other way around, only “B” will be returned.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>mode:</dt><dd><p>The type of degrees to be considered. Three possible values are
+<code class="docutils literal notranslate"><span class="pre">'IN'</span></code>, <cite>‘OUT’`</cite> and <code class="docutils literal notranslate"><span class="pre">'ALL'</span></code> for incoming, outgoing and all
+connections, respectively. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is <code class="docutils literal notranslate"><span class="pre">False</span></code>
+the only possible mode is <code class="docutils literal notranslate"><span class="pre">ALL</span></code>. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is
+<code class="docutils literal notranslate"><span class="pre">None</span></code> and also directed evidence(s) match the criteria these
+will overwrite the undirected evidences and only the directed
+result will be returned.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.degrees_positive_out_by_resource">
+<span class="sig-name descname"><span class="pre">degrees_positive_out_by_resource</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.degrees_positive_out_by_resource" title="Link to this definition">§</a></dt>
+<dd><p>Returns a <em>set</em> of nodes with the connections matching the direction,
+effect and evidence criteria. E.g. if the query concerns the incoming
+degrees with positive effect and the matching evidences show A
+activates B, but not the other way around, only “B” will be returned.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>mode:</dt><dd><p>The type of degrees to be considered. Three possible values are
+<code class="docutils literal notranslate"><span class="pre">'IN'</span></code>, <cite>‘OUT’`</cite> and <code class="docutils literal notranslate"><span class="pre">'ALL'</span></code> for incoming, outgoing and all
+connections, respectively. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is <code class="docutils literal notranslate"><span class="pre">False</span></code>
+the only possible mode is <code class="docutils literal notranslate"><span class="pre">ALL</span></code>. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is
+<code class="docutils literal notranslate"><span class="pre">None</span></code> and also directed evidence(s) match the criteria these
+will overwrite the undirected evidences and only the directed
+result will be returned.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.degrees_signed_by_data_model">
+<span class="sig-name descname"><span class="pre">degrees_signed_by_data_model</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.degrees_signed_by_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Returns a <em>set</em> of nodes with the connections matching the direction,
+effect and evidence criteria. E.g. if the query concerns the incoming
+degrees with positive effect and the matching evidences show A
+activates B, but not the other way around, only “B” will be returned.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>mode:</dt><dd><p>The type of degrees to be considered. Three possible values are
+<code class="docutils literal notranslate"><span class="pre">'IN'</span></code>, <cite>‘OUT’`</cite> and <code class="docutils literal notranslate"><span class="pre">'ALL'</span></code> for incoming, outgoing and all
+connections, respectively. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is <code class="docutils literal notranslate"><span class="pre">False</span></code>
+the only possible mode is <code class="docutils literal notranslate"><span class="pre">ALL</span></code>. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is
+<code class="docutils literal notranslate"><span class="pre">None</span></code> and also directed evidence(s) match the criteria these
+will overwrite the undirected evidences and only the directed
+result will be returned.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.degrees_signed_by_interaction_type">
+<span class="sig-name descname"><span class="pre">degrees_signed_by_interaction_type</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.degrees_signed_by_interaction_type" title="Link to this definition">§</a></dt>
+<dd><p>Returns a <em>set</em> of nodes with the connections matching the direction,
+effect and evidence criteria. E.g. if the query concerns the incoming
+degrees with positive effect and the matching evidences show A
+activates B, but not the other way around, only “B” will be returned.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>mode:</dt><dd><p>The type of degrees to be considered. Three possible values are
+<code class="docutils literal notranslate"><span class="pre">'IN'</span></code>, <cite>‘OUT’`</cite> and <code class="docutils literal notranslate"><span class="pre">'ALL'</span></code> for incoming, outgoing and all
+connections, respectively. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is <code class="docutils literal notranslate"><span class="pre">False</span></code>
+the only possible mode is <code class="docutils literal notranslate"><span class="pre">ALL</span></code>. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is
+<code class="docutils literal notranslate"><span class="pre">None</span></code> and also directed evidence(s) match the criteria these
+will overwrite the undirected evidences and only the directed
+result will be returned.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.degrees_signed_by_interaction_type_and_data_model">
+<span class="sig-name descname"><span class="pre">degrees_signed_by_interaction_type_and_data_model</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.degrees_signed_by_interaction_type_and_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Returns a <em>set</em> of nodes with the connections matching the direction,
+effect and evidence criteria. E.g. if the query concerns the incoming
+degrees with positive effect and the matching evidences show A
+activates B, but not the other way around, only “B” will be returned.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>mode:</dt><dd><p>The type of degrees to be considered. Three possible values are
+<code class="docutils literal notranslate"><span class="pre">'IN'</span></code>, <cite>‘OUT’`</cite> and <code class="docutils literal notranslate"><span class="pre">'ALL'</span></code> for incoming, outgoing and all
+connections, respectively. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is <code class="docutils literal notranslate"><span class="pre">False</span></code>
+the only possible mode is <code class="docutils literal notranslate"><span class="pre">ALL</span></code>. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is
+<code class="docutils literal notranslate"><span class="pre">None</span></code> and also directed evidence(s) match the criteria these
+will overwrite the undirected evidences and only the directed
+result will be returned.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.degrees_signed_by_interaction_type_and_data_model_and_resource">
+<span class="sig-name descname"><span class="pre">degrees_signed_by_interaction_type_and_data_model_and_resource</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.degrees_signed_by_interaction_type_and_data_model_and_resource" title="Link to this definition">§</a></dt>
+<dd><p>Returns a <em>set</em> of nodes with the connections matching the direction,
+effect and evidence criteria. E.g. if the query concerns the incoming
+degrees with positive effect and the matching evidences show A
+activates B, but not the other way around, only “B” will be returned.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>mode:</dt><dd><p>The type of degrees to be considered. Three possible values are
+<code class="docutils literal notranslate"><span class="pre">'IN'</span></code>, <cite>‘OUT’`</cite> and <code class="docutils literal notranslate"><span class="pre">'ALL'</span></code> for incoming, outgoing and all
+connections, respectively. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is <code class="docutils literal notranslate"><span class="pre">False</span></code>
+the only possible mode is <code class="docutils literal notranslate"><span class="pre">ALL</span></code>. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is
+<code class="docutils literal notranslate"><span class="pre">None</span></code> and also directed evidence(s) match the criteria these
+will overwrite the undirected evidences and only the directed
+result will be returned.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.degrees_signed_by_reference">
+<span class="sig-name descname"><span class="pre">degrees_signed_by_reference</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.degrees_signed_by_reference" title="Link to this definition">§</a></dt>
+<dd><p>Returns a <em>set</em> of nodes with the connections matching the direction,
+effect and evidence criteria. E.g. if the query concerns the incoming
+degrees with positive effect and the matching evidences show A
+activates B, but not the other way around, only “B” will be returned.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>mode:</dt><dd><p>The type of degrees to be considered. Three possible values are
+<code class="docutils literal notranslate"><span class="pre">'IN'</span></code>, <cite>‘OUT’`</cite> and <code class="docutils literal notranslate"><span class="pre">'ALL'</span></code> for incoming, outgoing and all
+connections, respectively. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is <code class="docutils literal notranslate"><span class="pre">False</span></code>
+the only possible mode is <code class="docutils literal notranslate"><span class="pre">ALL</span></code>. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is
+<code class="docutils literal notranslate"><span class="pre">None</span></code> and also directed evidence(s) match the criteria these
+will overwrite the undirected evidences and only the directed
+result will be returned.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.degrees_signed_by_resource">
+<span class="sig-name descname"><span class="pre">degrees_signed_by_resource</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.degrees_signed_by_resource" title="Link to this definition">§</a></dt>
+<dd><p>Returns a <em>set</em> of nodes with the connections matching the direction,
+effect and evidence criteria. E.g. if the query concerns the incoming
+degrees with positive effect and the matching evidences show A
+activates B, but not the other way around, only “B” will be returned.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>mode:</dt><dd><p>The type of degrees to be considered. Three possible values are
+<code class="docutils literal notranslate"><span class="pre">'IN'</span></code>, <cite>‘OUT’`</cite> and <code class="docutils literal notranslate"><span class="pre">'ALL'</span></code> for incoming, outgoing and all
+connections, respectively. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is <code class="docutils literal notranslate"><span class="pre">False</span></code>
+the only possible mode is <code class="docutils literal notranslate"><span class="pre">ALL</span></code>. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is
+<code class="docutils literal notranslate"><span class="pre">None</span></code> and also directed evidence(s) match the criteria these
+will overwrite the undirected evidences and only the directed
+result will be returned.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.degrees_signed_in_by_data_model">
+<span class="sig-name descname"><span class="pre">degrees_signed_in_by_data_model</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.degrees_signed_in_by_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Returns a <em>set</em> of nodes with the connections matching the direction,
+effect and evidence criteria. E.g. if the query concerns the incoming
+degrees with positive effect and the matching evidences show A
+activates B, but not the other way around, only “B” will be returned.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>mode:</dt><dd><p>The type of degrees to be considered. Three possible values are
+<code class="docutils literal notranslate"><span class="pre">'IN'</span></code>, <cite>‘OUT’`</cite> and <code class="docutils literal notranslate"><span class="pre">'ALL'</span></code> for incoming, outgoing and all
+connections, respectively. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is <code class="docutils literal notranslate"><span class="pre">False</span></code>
+the only possible mode is <code class="docutils literal notranslate"><span class="pre">ALL</span></code>. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is
+<code class="docutils literal notranslate"><span class="pre">None</span></code> and also directed evidence(s) match the criteria these
+will overwrite the undirected evidences and only the directed
+result will be returned.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.degrees_signed_in_by_interaction_type">
+<span class="sig-name descname"><span class="pre">degrees_signed_in_by_interaction_type</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.degrees_signed_in_by_interaction_type" title="Link to this definition">§</a></dt>
+<dd><p>Returns a <em>set</em> of nodes with the connections matching the direction,
+effect and evidence criteria. E.g. if the query concerns the incoming
+degrees with positive effect and the matching evidences show A
+activates B, but not the other way around, only “B” will be returned.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>mode:</dt><dd><p>The type of degrees to be considered. Three possible values are
+<code class="docutils literal notranslate"><span class="pre">'IN'</span></code>, <cite>‘OUT’`</cite> and <code class="docutils literal notranslate"><span class="pre">'ALL'</span></code> for incoming, outgoing and all
+connections, respectively. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is <code class="docutils literal notranslate"><span class="pre">False</span></code>
+the only possible mode is <code class="docutils literal notranslate"><span class="pre">ALL</span></code>. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is
+<code class="docutils literal notranslate"><span class="pre">None</span></code> and also directed evidence(s) match the criteria these
+will overwrite the undirected evidences and only the directed
+result will be returned.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.degrees_signed_in_by_interaction_type_and_data_model">
+<span class="sig-name descname"><span class="pre">degrees_signed_in_by_interaction_type_and_data_model</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.degrees_signed_in_by_interaction_type_and_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Returns a <em>set</em> of nodes with the connections matching the direction,
+effect and evidence criteria. E.g. if the query concerns the incoming
+degrees with positive effect and the matching evidences show A
+activates B, but not the other way around, only “B” will be returned.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>mode:</dt><dd><p>The type of degrees to be considered. Three possible values are
+<code class="docutils literal notranslate"><span class="pre">'IN'</span></code>, <cite>‘OUT’`</cite> and <code class="docutils literal notranslate"><span class="pre">'ALL'</span></code> for incoming, outgoing and all
+connections, respectively. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is <code class="docutils literal notranslate"><span class="pre">False</span></code>
+the only possible mode is <code class="docutils literal notranslate"><span class="pre">ALL</span></code>. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is
+<code class="docutils literal notranslate"><span class="pre">None</span></code> and also directed evidence(s) match the criteria these
+will overwrite the undirected evidences and only the directed
+result will be returned.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.degrees_signed_in_by_interaction_type_and_data_model_and_resource">
+<span class="sig-name descname"><span class="pre">degrees_signed_in_by_interaction_type_and_data_model_and_resource</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.degrees_signed_in_by_interaction_type_and_data_model_and_resource" title="Link to this definition">§</a></dt>
+<dd><p>Returns a <em>set</em> of nodes with the connections matching the direction,
+effect and evidence criteria. E.g. if the query concerns the incoming
+degrees with positive effect and the matching evidences show A
+activates B, but not the other way around, only “B” will be returned.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>mode:</dt><dd><p>The type of degrees to be considered. Three possible values are
+<code class="docutils literal notranslate"><span class="pre">'IN'</span></code>, <cite>‘OUT’`</cite> and <code class="docutils literal notranslate"><span class="pre">'ALL'</span></code> for incoming, outgoing and all
+connections, respectively. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is <code class="docutils literal notranslate"><span class="pre">False</span></code>
+the only possible mode is <code class="docutils literal notranslate"><span class="pre">ALL</span></code>. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is
+<code class="docutils literal notranslate"><span class="pre">None</span></code> and also directed evidence(s) match the criteria these
+will overwrite the undirected evidences and only the directed
+result will be returned.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.degrees_signed_in_by_reference">
+<span class="sig-name descname"><span class="pre">degrees_signed_in_by_reference</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.degrees_signed_in_by_reference" title="Link to this definition">§</a></dt>
+<dd><p>Returns a <em>set</em> of nodes with the connections matching the direction,
+effect and evidence criteria. E.g. if the query concerns the incoming
+degrees with positive effect and the matching evidences show A
+activates B, but not the other way around, only “B” will be returned.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>mode:</dt><dd><p>The type of degrees to be considered. Three possible values are
+<code class="docutils literal notranslate"><span class="pre">'IN'</span></code>, <cite>‘OUT’`</cite> and <code class="docutils literal notranslate"><span class="pre">'ALL'</span></code> for incoming, outgoing and all
+connections, respectively. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is <code class="docutils literal notranslate"><span class="pre">False</span></code>
+the only possible mode is <code class="docutils literal notranslate"><span class="pre">ALL</span></code>. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is
+<code class="docutils literal notranslate"><span class="pre">None</span></code> and also directed evidence(s) match the criteria these
+will overwrite the undirected evidences and only the directed
+result will be returned.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.degrees_signed_in_by_resource">
+<span class="sig-name descname"><span class="pre">degrees_signed_in_by_resource</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.degrees_signed_in_by_resource" title="Link to this definition">§</a></dt>
+<dd><p>Returns a <em>set</em> of nodes with the connections matching the direction,
+effect and evidence criteria. E.g. if the query concerns the incoming
+degrees with positive effect and the matching evidences show A
+activates B, but not the other way around, only “B” will be returned.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>mode:</dt><dd><p>The type of degrees to be considered. Three possible values are
+<code class="docutils literal notranslate"><span class="pre">'IN'</span></code>, <cite>‘OUT’`</cite> and <code class="docutils literal notranslate"><span class="pre">'ALL'</span></code> for incoming, outgoing and all
+connections, respectively. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is <code class="docutils literal notranslate"><span class="pre">False</span></code>
+the only possible mode is <code class="docutils literal notranslate"><span class="pre">ALL</span></code>. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is
+<code class="docutils literal notranslate"><span class="pre">None</span></code> and also directed evidence(s) match the criteria these
+will overwrite the undirected evidences and only the directed
+result will be returned.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.degrees_signed_out_by_data_model">
+<span class="sig-name descname"><span class="pre">degrees_signed_out_by_data_model</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.degrees_signed_out_by_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Returns a <em>set</em> of nodes with the connections matching the direction,
+effect and evidence criteria. E.g. if the query concerns the incoming
+degrees with positive effect and the matching evidences show A
+activates B, but not the other way around, only “B” will be returned.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>mode:</dt><dd><p>The type of degrees to be considered. Three possible values are
+<code class="docutils literal notranslate"><span class="pre">'IN'</span></code>, <cite>‘OUT’`</cite> and <code class="docutils literal notranslate"><span class="pre">'ALL'</span></code> for incoming, outgoing and all
+connections, respectively. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is <code class="docutils literal notranslate"><span class="pre">False</span></code>
+the only possible mode is <code class="docutils literal notranslate"><span class="pre">ALL</span></code>. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is
+<code class="docutils literal notranslate"><span class="pre">None</span></code> and also directed evidence(s) match the criteria these
+will overwrite the undirected evidences and only the directed
+result will be returned.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.degrees_signed_out_by_interaction_type">
+<span class="sig-name descname"><span class="pre">degrees_signed_out_by_interaction_type</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.degrees_signed_out_by_interaction_type" title="Link to this definition">§</a></dt>
+<dd><p>Returns a <em>set</em> of nodes with the connections matching the direction,
+effect and evidence criteria. E.g. if the query concerns the incoming
+degrees with positive effect and the matching evidences show A
+activates B, but not the other way around, only “B” will be returned.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>mode:</dt><dd><p>The type of degrees to be considered. Three possible values are
+<code class="docutils literal notranslate"><span class="pre">'IN'</span></code>, <cite>‘OUT’`</cite> and <code class="docutils literal notranslate"><span class="pre">'ALL'</span></code> for incoming, outgoing and all
+connections, respectively. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is <code class="docutils literal notranslate"><span class="pre">False</span></code>
+the only possible mode is <code class="docutils literal notranslate"><span class="pre">ALL</span></code>. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is
+<code class="docutils literal notranslate"><span class="pre">None</span></code> and also directed evidence(s) match the criteria these
+will overwrite the undirected evidences and only the directed
+result will be returned.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.degrees_signed_out_by_interaction_type_and_data_model">
+<span class="sig-name descname"><span class="pre">degrees_signed_out_by_interaction_type_and_data_model</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.degrees_signed_out_by_interaction_type_and_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Returns a <em>set</em> of nodes with the connections matching the direction,
+effect and evidence criteria. E.g. if the query concerns the incoming
+degrees with positive effect and the matching evidences show A
+activates B, but not the other way around, only “B” will be returned.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>mode:</dt><dd><p>The type of degrees to be considered. Three possible values are
+<code class="docutils literal notranslate"><span class="pre">'IN'</span></code>, <cite>‘OUT’`</cite> and <code class="docutils literal notranslate"><span class="pre">'ALL'</span></code> for incoming, outgoing and all
+connections, respectively. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is <code class="docutils literal notranslate"><span class="pre">False</span></code>
+the only possible mode is <code class="docutils literal notranslate"><span class="pre">ALL</span></code>. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is
+<code class="docutils literal notranslate"><span class="pre">None</span></code> and also directed evidence(s) match the criteria these
+will overwrite the undirected evidences and only the directed
+result will be returned.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.degrees_signed_out_by_interaction_type_and_data_model_and_resource">
+<span class="sig-name descname"><span class="pre">degrees_signed_out_by_interaction_type_and_data_model_and_resource</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.degrees_signed_out_by_interaction_type_and_data_model_and_resource" title="Link to this definition">§</a></dt>
+<dd><p>Returns a <em>set</em> of nodes with the connections matching the direction,
+effect and evidence criteria. E.g. if the query concerns the incoming
+degrees with positive effect and the matching evidences show A
+activates B, but not the other way around, only “B” will be returned.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>mode:</dt><dd><p>The type of degrees to be considered. Three possible values are
+<code class="docutils literal notranslate"><span class="pre">'IN'</span></code>, <cite>‘OUT’`</cite> and <code class="docutils literal notranslate"><span class="pre">'ALL'</span></code> for incoming, outgoing and all
+connections, respectively. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is <code class="docutils literal notranslate"><span class="pre">False</span></code>
+the only possible mode is <code class="docutils literal notranslate"><span class="pre">ALL</span></code>. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is
+<code class="docutils literal notranslate"><span class="pre">None</span></code> and also directed evidence(s) match the criteria these
+will overwrite the undirected evidences and only the directed
+result will be returned.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.degrees_signed_out_by_reference">
+<span class="sig-name descname"><span class="pre">degrees_signed_out_by_reference</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.degrees_signed_out_by_reference" title="Link to this definition">§</a></dt>
+<dd><p>Returns a <em>set</em> of nodes with the connections matching the direction,
+effect and evidence criteria. E.g. if the query concerns the incoming
+degrees with positive effect and the matching evidences show A
+activates B, but not the other way around, only “B” will be returned.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>mode:</dt><dd><p>The type of degrees to be considered. Three possible values are
+<code class="docutils literal notranslate"><span class="pre">'IN'</span></code>, <cite>‘OUT’`</cite> and <code class="docutils literal notranslate"><span class="pre">'ALL'</span></code> for incoming, outgoing and all
+connections, respectively. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is <code class="docutils literal notranslate"><span class="pre">False</span></code>
+the only possible mode is <code class="docutils literal notranslate"><span class="pre">ALL</span></code>. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is
+<code class="docutils literal notranslate"><span class="pre">None</span></code> and also directed evidence(s) match the criteria these
+will overwrite the undirected evidences and only the directed
+result will be returned.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.degrees_signed_out_by_resource">
+<span class="sig-name descname"><span class="pre">degrees_signed_out_by_resource</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.degrees_signed_out_by_resource" title="Link to this definition">§</a></dt>
+<dd><p>Returns a <em>set</em> of nodes with the connections matching the direction,
+effect and evidence criteria. E.g. if the query concerns the incoming
+degrees with positive effect and the matching evidences show A
+activates B, but not the other way around, only “B” will be returned.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>mode:</dt><dd><p>The type of degrees to be considered. Three possible values are
+<code class="docutils literal notranslate"><span class="pre">'IN'</span></code>, <cite>‘OUT’`</cite> and <code class="docutils literal notranslate"><span class="pre">'ALL'</span></code> for incoming, outgoing and all
+connections, respectively. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is <code class="docutils literal notranslate"><span class="pre">False</span></code>
+the only possible mode is <code class="docutils literal notranslate"><span class="pre">ALL</span></code>. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is
+<code class="docutils literal notranslate"><span class="pre">None</span></code> and also directed evidence(s) match the criteria these
+will overwrite the undirected evidences and only the directed
+result will be returned.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.degrees_undirected_by_data_model">
+<span class="sig-name descname"><span class="pre">degrees_undirected_by_data_model</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.degrees_undirected_by_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Returns a <em>set</em> of nodes with the connections matching the direction,
+effect and evidence criteria. E.g. if the query concerns the incoming
+degrees with positive effect and the matching evidences show A
+activates B, but not the other way around, only “B” will be returned.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>mode:</dt><dd><p>The type of degrees to be considered. Three possible values are
+<code class="docutils literal notranslate"><span class="pre">'IN'</span></code>, <cite>‘OUT’`</cite> and <code class="docutils literal notranslate"><span class="pre">'ALL'</span></code> for incoming, outgoing and all
+connections, respectively. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is <code class="docutils literal notranslate"><span class="pre">False</span></code>
+the only possible mode is <code class="docutils literal notranslate"><span class="pre">ALL</span></code>. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is
+<code class="docutils literal notranslate"><span class="pre">None</span></code> and also directed evidence(s) match the criteria these
+will overwrite the undirected evidences and only the directed
+result will be returned.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.degrees_undirected_by_interaction_type">
+<span class="sig-name descname"><span class="pre">degrees_undirected_by_interaction_type</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.degrees_undirected_by_interaction_type" title="Link to this definition">§</a></dt>
+<dd><p>Returns a <em>set</em> of nodes with the connections matching the direction,
+effect and evidence criteria. E.g. if the query concerns the incoming
+degrees with positive effect and the matching evidences show A
+activates B, but not the other way around, only “B” will be returned.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>mode:</dt><dd><p>The type of degrees to be considered. Three possible values are
+<code class="docutils literal notranslate"><span class="pre">'IN'</span></code>, <cite>‘OUT’`</cite> and <code class="docutils literal notranslate"><span class="pre">'ALL'</span></code> for incoming, outgoing and all
+connections, respectively. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is <code class="docutils literal notranslate"><span class="pre">False</span></code>
+the only possible mode is <code class="docutils literal notranslate"><span class="pre">ALL</span></code>. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is
+<code class="docutils literal notranslate"><span class="pre">None</span></code> and also directed evidence(s) match the criteria these
+will overwrite the undirected evidences and only the directed
+result will be returned.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.degrees_undirected_by_interaction_type_and_data_model">
+<span class="sig-name descname"><span class="pre">degrees_undirected_by_interaction_type_and_data_model</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.degrees_undirected_by_interaction_type_and_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Returns a <em>set</em> of nodes with the connections matching the direction,
+effect and evidence criteria. E.g. if the query concerns the incoming
+degrees with positive effect and the matching evidences show A
+activates B, but not the other way around, only “B” will be returned.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>mode:</dt><dd><p>The type of degrees to be considered. Three possible values are
+<code class="docutils literal notranslate"><span class="pre">'IN'</span></code>, <cite>‘OUT’`</cite> and <code class="docutils literal notranslate"><span class="pre">'ALL'</span></code> for incoming, outgoing and all
+connections, respectively. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is <code class="docutils literal notranslate"><span class="pre">False</span></code>
+the only possible mode is <code class="docutils literal notranslate"><span class="pre">ALL</span></code>. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is
+<code class="docutils literal notranslate"><span class="pre">None</span></code> and also directed evidence(s) match the criteria these
+will overwrite the undirected evidences and only the directed
+result will be returned.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.degrees_undirected_by_interaction_type_and_data_model_and_resource">
+<span class="sig-name descname"><span class="pre">degrees_undirected_by_interaction_type_and_data_model_and_resource</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.degrees_undirected_by_interaction_type_and_data_model_and_resource" title="Link to this definition">§</a></dt>
+<dd><p>Returns a <em>set</em> of nodes with the connections matching the direction,
+effect and evidence criteria. E.g. if the query concerns the incoming
+degrees with positive effect and the matching evidences show A
+activates B, but not the other way around, only “B” will be returned.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>mode:</dt><dd><p>The type of degrees to be considered. Three possible values are
+<code class="docutils literal notranslate"><span class="pre">'IN'</span></code>, <cite>‘OUT’`</cite> and <code class="docutils literal notranslate"><span class="pre">'ALL'</span></code> for incoming, outgoing and all
+connections, respectively. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is <code class="docutils literal notranslate"><span class="pre">False</span></code>
+the only possible mode is <code class="docutils literal notranslate"><span class="pre">ALL</span></code>. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is
+<code class="docutils literal notranslate"><span class="pre">None</span></code> and also directed evidence(s) match the criteria these
+will overwrite the undirected evidences and only the directed
+result will be returned.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.degrees_undirected_by_reference">
+<span class="sig-name descname"><span class="pre">degrees_undirected_by_reference</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.degrees_undirected_by_reference" title="Link to this definition">§</a></dt>
+<dd><p>Returns a <em>set</em> of nodes with the connections matching the direction,
+effect and evidence criteria. E.g. if the query concerns the incoming
+degrees with positive effect and the matching evidences show A
+activates B, but not the other way around, only “B” will be returned.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>mode:</dt><dd><p>The type of degrees to be considered. Three possible values are
+<code class="docutils literal notranslate"><span class="pre">'IN'</span></code>, <cite>‘OUT’`</cite> and <code class="docutils literal notranslate"><span class="pre">'ALL'</span></code> for incoming, outgoing and all
+connections, respectively. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is <code class="docutils literal notranslate"><span class="pre">False</span></code>
+the only possible mode is <code class="docutils literal notranslate"><span class="pre">ALL</span></code>. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is
+<code class="docutils literal notranslate"><span class="pre">None</span></code> and also directed evidence(s) match the criteria these
+will overwrite the undirected evidences and only the directed
+result will be returned.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.degrees_undirected_by_resource">
+<span class="sig-name descname"><span class="pre">degrees_undirected_by_resource</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.degrees_undirected_by_resource" title="Link to this definition">§</a></dt>
+<dd><p>Returns a <em>set</em> of nodes with the connections matching the direction,
+effect and evidence criteria. E.g. if the query concerns the incoming
+degrees with positive effect and the matching evidences show A
+activates B, but not the other way around, only “B” will be returned.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>mode:</dt><dd><p>The type of degrees to be considered. Three possible values are
+<code class="docutils literal notranslate"><span class="pre">'IN'</span></code>, <cite>‘OUT’`</cite> and <code class="docutils literal notranslate"><span class="pre">'ALL'</span></code> for incoming, outgoing and all
+connections, respectively. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is <code class="docutils literal notranslate"><span class="pre">False</span></code>
+the only possible mode is <code class="docutils literal notranslate"><span class="pre">ALL</span></code>. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is
+<code class="docutils literal notranslate"><span class="pre">None</span></code> and also directed evidence(s) match the criteria these
+will overwrite the undirected evidences and only the directed
+result will be returned.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.direction_key">
+<span class="sig-name descname"><span class="pre">direction_key</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">direction</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/interaction.html#Interaction.direction_key"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.interaction.Interaction.direction_key" title="Link to this definition">§</a></dt>
+<dd><p>The direction keys are tuples of <cite>Entity</cite> objects; this method
+creates these tuples from a tuple of strings. The two strings
+can be labels or identifiers.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.dorothea_level">
+<span class="sig-name descname"><span class="pre">dorothea_level</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">direction</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">tuple</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><span class="pre">Literal</span><span class="p"><span class="pre">[</span></span><span class="s"><span class="pre">'A'</span></span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="s"><span class="pre">'B'</span></span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="s"><span class="pre">'C'</span></span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="s"><span class="pre">'D'</span></span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="s"><span class="pre">'E'</span></span><span class="p"><span class="pre">]</span></span></span></span><a class="reference internal" href="../_modules/pypath/core/interaction.html#Interaction.dorothea_level"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.interaction.Interaction.dorothea_level" title="Link to this definition">§</a></dt>
+<dd><p>DoRothEA confidence level for one direction as a single letter.</p>
+<p>Some interactions might have multiple levels due to the ambiguous
+nature of translating gene symbols to UniProt IDs. Here we take the
+highest level and drop the rest. For interactions without DoRothEA
+levels None is returned.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.dorothea_levels">
+<span class="sig-name descname"><span class="pre">dorothea_levels</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">direction</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">tuple</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/interaction.html#Interaction.dorothea_levels"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.interaction.Interaction.dorothea_levels" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the DoRothEA confidence levels.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>direction:</dt><dd><p>Direction(s) to consider, either a tuple of entities or
+entity names, or the string <cite>undirected</cite>.</p>
+</dd>
+</dl>
+</dd>
+<dt>Returns</dt><dd><p>List of unique single letter strings representing the five
+confidence levels (A-E).</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.entities_by_data_model">
+<span class="sig-name descname"><span class="pre">entities_by_data_model</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.entities_by_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the entities involved in interactions matching the criteria.
+It either returns both interacting entities in a <em>set</em> or an empty
+<em>set</em>. This may not sound so useful at the level of this object but
+becomes more useful once we want to collect entities having certain
+kind of interactions across a series of <cite>Interaction</cite> objects.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>entity_type</strong> (<em>str</em>) – The type of the molecular entity. Possible values: <cite>protein</cite>,
+<cite>complex</cite>, <cite>mirna</cite>, <cite>small_molecule</cite>.</p></li>
+<li><p><strong>return_type</strong> (<em>str</em>) – The type of values to return. Default is
+py:class:<code class="docutils literal notranslate"><span class="pre">pypath.entity.Entity</span></code> objects, alternatives are
+<code class="docutils literal notranslate"><span class="pre">labels</span></code>  <code class="docutils literal notranslate"><span class="pre">identifiers</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.entities_by_interaction_type">
+<span class="sig-name descname"><span class="pre">entities_by_interaction_type</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.entities_by_interaction_type" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the entities involved in interactions matching the criteria.
+It either returns both interacting entities in a <em>set</em> or an empty
+<em>set</em>. This may not sound so useful at the level of this object but
+becomes more useful once we want to collect entities having certain
+kind of interactions across a series of <cite>Interaction</cite> objects.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>entity_type</strong> (<em>str</em>) – The type of the molecular entity. Possible values: <cite>protein</cite>,
+<cite>complex</cite>, <cite>mirna</cite>, <cite>small_molecule</cite>.</p></li>
+<li><p><strong>return_type</strong> (<em>str</em>) – The type of values to return. Default is
+py:class:<code class="docutils literal notranslate"><span class="pre">pypath.entity.Entity</span></code> objects, alternatives are
+<code class="docutils literal notranslate"><span class="pre">labels</span></code>  <code class="docutils literal notranslate"><span class="pre">identifiers</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.entities_by_interaction_type_and_data_model">
+<span class="sig-name descname"><span class="pre">entities_by_interaction_type_and_data_model</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.entities_by_interaction_type_and_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the entities involved in interactions matching the criteria.
+It either returns both interacting entities in a <em>set</em> or an empty
+<em>set</em>. This may not sound so useful at the level of this object but
+becomes more useful once we want to collect entities having certain
+kind of interactions across a series of <cite>Interaction</cite> objects.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>entity_type</strong> (<em>str</em>) – The type of the molecular entity. Possible values: <cite>protein</cite>,
+<cite>complex</cite>, <cite>mirna</cite>, <cite>small_molecule</cite>.</p></li>
+<li><p><strong>return_type</strong> (<em>str</em>) – The type of values to return. Default is
+py:class:<code class="docutils literal notranslate"><span class="pre">pypath.entity.Entity</span></code> objects, alternatives are
+<code class="docutils literal notranslate"><span class="pre">labels</span></code>  <code class="docutils literal notranslate"><span class="pre">identifiers</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.entities_by_interaction_type_and_data_model_and_resource">
+<span class="sig-name descname"><span class="pre">entities_by_interaction_type_and_data_model_and_resource</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.entities_by_interaction_type_and_data_model_and_resource" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the entities involved in interactions matching the criteria.
+It either returns both interacting entities in a <em>set</em> or an empty
+<em>set</em>. This may not sound so useful at the level of this object but
+becomes more useful once we want to collect entities having certain
+kind of interactions across a series of <cite>Interaction</cite> objects.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>entity_type</strong> (<em>str</em>) – The type of the molecular entity. Possible values: <cite>protein</cite>,
+<cite>complex</cite>, <cite>mirna</cite>, <cite>small_molecule</cite>.</p></li>
+<li><p><strong>return_type</strong> (<em>str</em>) – The type of values to return. Default is
+py:class:<code class="docutils literal notranslate"><span class="pre">pypath.entity.Entity</span></code> objects, alternatives are
+<code class="docutils literal notranslate"><span class="pre">labels</span></code>  <code class="docutils literal notranslate"><span class="pre">identifiers</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.entities_by_reference">
+<span class="sig-name descname"><span class="pre">entities_by_reference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.entities_by_reference" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the entities involved in interactions matching the criteria.
+It either returns both interacting entities in a <em>set</em> or an empty
+<em>set</em>. This may not sound so useful at the level of this object but
+becomes more useful once we want to collect entities having certain
+kind of interactions across a series of <cite>Interaction</cite> objects.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>entity_type</strong> (<em>str</em>) – The type of the molecular entity. Possible values: <cite>protein</cite>,
+<cite>complex</cite>, <cite>mirna</cite>, <cite>small_molecule</cite>.</p></li>
+<li><p><strong>return_type</strong> (<em>str</em>) – The type of values to return. Default is
+py:class:<code class="docutils literal notranslate"><span class="pre">pypath.entity.Entity</span></code> objects, alternatives are
+<code class="docutils literal notranslate"><span class="pre">labels</span></code>  <code class="docutils literal notranslate"><span class="pre">identifiers</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.entities_by_resource">
+<span class="sig-name descname"><span class="pre">entities_by_resource</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.entities_by_resource" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the entities involved in interactions matching the criteria.
+It either returns both interacting entities in a <em>set</em> or an empty
+<em>set</em>. This may not sound so useful at the level of this object but
+becomes more useful once we want to collect entities having certain
+kind of interactions across a series of <cite>Interaction</cite> objects.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>entity_type</strong> (<em>str</em>) – The type of the molecular entity. Possible values: <cite>protein</cite>,
+<cite>complex</cite>, <cite>mirna</cite>, <cite>small_molecule</cite>.</p></li>
+<li><p><strong>return_type</strong> (<em>str</em>) – The type of values to return. Default is
+py:class:<code class="docutils literal notranslate"><span class="pre">pypath.entity.Entity</span></code> objects, alternatives are
+<code class="docutils literal notranslate"><span class="pre">labels</span></code>  <code class="docutils literal notranslate"><span class="pre">identifiers</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.evaluate_evidences">
+<span class="sig-name descname"><span class="pre">evaluate_evidences</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">this_direction</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">direction</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">datasets</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/interaction.html#Interaction.evaluate_evidences"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.interaction.Interaction.evaluate_evidences" title="Link to this definition">§</a></dt>
+<dd><p>Selects the evidence collections matching the direction and effect
+criteria and then evaluates if any of the evidences in these
+collections match the evidence criteria.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.generate_df_records">
+<span class="sig-name descname"><span class="pre">generate_df_records</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">by_source</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">with_references</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/interaction.html#Interaction.generate_df_records"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.interaction.Interaction.generate_df_records" title="Link to this definition">§</a></dt>
+<dd><p>Yields interaction records. It is a generator because one edge can
+be represented by one or more records depending on the signs and
+directions and other parameters</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>by_source:</dt><dd><p>Yield separate records by resources. This way the node pairs
+will be redundant and you need to group later if you want
+unique interacting pairs. By default is <code class="docutils literal notranslate"><span class="pre">False</span></code> because for
+most applications unique interactions are preferred.
+If <code class="docutils literal notranslate"><span class="pre">False</span></code> the <em>refrences</em> field will still be present
+but with <code class="docutils literal notranslate"><span class="pre">None</span></code> values.</p>
+</dd>
+<dt>with_references:</dt><dd><p>Include the literature references. By default is <code class="docutils literal notranslate"><span class="pre">False</span></code>
+because you rarely need these and they increase the data size
+significantly.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.get_attr">
+<span class="sig-name descname"><span class="pre">get_attr</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">resource</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">key</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">direction</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">tuple</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/interaction.html#Interaction.get_attr"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.interaction.Interaction.get_attr" title="Link to this definition">§</a></dt>
+<dd><p>Extracts the values of one specific attribute.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>resource:</dt><dd><p>Name of the resource.</p>
+</dd>
+<dt>key:</dt><dd><p>Name of the attribute.</p>
+</dd>
+<dt>direction:</dt><dd><p>Direction(s) to consider, either a tuple of entities or
+entity names, or the string <cite>undirected</cite>.</p>
+</dd>
+</dl>
+</dd>
+<dt>Returns</dt><dd><p>Depends on the arguments. The value of the attribute if direction
+is defined. Otherwise a dict with the value of the attribute for
+each direction. The value of the attribute is <cite>None</cite> if the
+resource or the attribute does not belong to this interaction.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.get_complex_identifiers">
+<span class="sig-name descname"><span class="pre">get_complex_identifiers</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">direction</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">return_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.get_complex_identifiers" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the entities involved in interactions matching the criteria.
+It either returns both interacting entities in a <em>set</em> or an empty
+<em>set</em>. This may not sound so useful at the level of this object but
+becomes more useful once we want to collect entities having certain
+kind of interactions across a series of <cite>Interaction</cite> objects.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>entity_type</strong> (<em>str</em>) – The type of the molecular entity. Possible values: <cite>protein</cite>,
+<cite>complex</cite>, <cite>mirna</cite>, <cite>small_molecule</cite>.</p></li>
+<li><p><strong>return_type</strong> (<em>str</em>) – The type of values to return. Default is
+py:class:<code class="docutils literal notranslate"><span class="pre">pypath.entity.Entity</span></code> objects, alternatives are
+<code class="docutils literal notranslate"><span class="pre">labels</span></code>  <code class="docutils literal notranslate"><span class="pre">identifiers</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.get_complex_labels">
+<span class="sig-name descname"><span class="pre">get_complex_labels</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">direction</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">return_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.get_complex_labels" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the entities involved in interactions matching the criteria.
+It either returns both interacting entities in a <em>set</em> or an empty
+<em>set</em>. This may not sound so useful at the level of this object but
+becomes more useful once we want to collect entities having certain
+kind of interactions across a series of <cite>Interaction</cite> objects.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>entity_type</strong> (<em>str</em>) – The type of the molecular entity. Possible values: <cite>protein</cite>,
+<cite>complex</cite>, <cite>mirna</cite>, <cite>small_molecule</cite>.</p></li>
+<li><p><strong>return_type</strong> (<em>str</em>) – The type of values to return. Default is
+py:class:<code class="docutils literal notranslate"><span class="pre">pypath.entity.Entity</span></code> objects, alternatives are
+<code class="docutils literal notranslate"><span class="pre">labels</span></code>  <code class="docutils literal notranslate"><span class="pre">identifiers</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.get_complexes">
+<span class="sig-name descname"><span class="pre">get_complexes</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">direction</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">return_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.get_complexes" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the entities involved in interactions matching the criteria.
+It either returns both interacting entities in a <em>set</em> or an empty
+<em>set</em>. This may not sound so useful at the level of this object but
+becomes more useful once we want to collect entities having certain
+kind of interactions across a series of <cite>Interaction</cite> objects.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>entity_type</strong> (<em>str</em>) – The type of the molecular entity. Possible values: <cite>protein</cite>,
+<cite>complex</cite>, <cite>mirna</cite>, <cite>small_molecule</cite>.</p></li>
+<li><p><strong>return_type</strong> (<em>str</em>) – The type of values to return. Default is
+py:class:<code class="docutils literal notranslate"><span class="pre">pypath.entity.Entity</span></code> objects, alternatives are
+<code class="docutils literal notranslate"><span class="pre">labels</span></code>  <code class="docutils literal notranslate"><span class="pre">identifiers</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.get_data_models">
+<span class="sig-name descname"><span class="pre">get_data_models</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.get_data_models" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves data models matching the criteria.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.get_datasets">
+<span class="sig-name descname"><span class="pre">get_datasets</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.get_datasets" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves datasets matching the criteria.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.get_degrees">
+<span class="sig-name descname"><span class="pre">get_degrees</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">mode</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">direction</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/interaction.html#Interaction.get_degrees"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.interaction.Interaction.get_degrees" title="Link to this definition">§</a></dt>
+<dd><p>Returns a <em>set</em> of nodes with the connections matching the direction,
+effect and evidence criteria. E.g. if the query concerns the incoming
+degrees with positive effect and the matching evidences show A
+activates B, but not the other way around, only “B” will be returned.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>mode:</dt><dd><p>The type of degrees to be considered. Three possible values are
+<code class="docutils literal notranslate"><span class="pre">'IN'</span></code>, <cite>‘OUT’`</cite> and <code class="docutils literal notranslate"><span class="pre">'ALL'</span></code> for incoming, outgoing and all
+connections, respectively. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is <code class="docutils literal notranslate"><span class="pre">False</span></code>
+the only possible mode is <code class="docutils literal notranslate"><span class="pre">ALL</span></code>. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is
+<code class="docutils literal notranslate"><span class="pre">None</span></code> and also directed evidence(s) match the criteria these
+will overwrite the undirected evidences and only the directed
+result will be returned.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.get_degrees_directed">
+<span class="sig-name descname"><span class="pre">get_degrees_directed</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.get_degrees_directed" title="Link to this definition">§</a></dt>
+<dd><p>Returns a <em>set</em> of nodes with the connections matching the direction,
+effect and evidence criteria. E.g. if the query concerns the incoming
+degrees with positive effect and the matching evidences show A
+activates B, but not the other way around, only “B” will be returned.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>mode:</dt><dd><p>The type of degrees to be considered. Three possible values are
+<code class="docutils literal notranslate"><span class="pre">'IN'</span></code>, <cite>‘OUT’`</cite> and <code class="docutils literal notranslate"><span class="pre">'ALL'</span></code> for incoming, outgoing and all
+connections, respectively. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is <code class="docutils literal notranslate"><span class="pre">False</span></code>
+the only possible mode is <code class="docutils literal notranslate"><span class="pre">ALL</span></code>. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is
+<code class="docutils literal notranslate"><span class="pre">None</span></code> and also directed evidence(s) match the criteria these
+will overwrite the undirected evidences and only the directed
+result will be returned.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.get_degrees_directed_in">
+<span class="sig-name descname"><span class="pre">get_degrees_directed_in</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.get_degrees_directed_in" title="Link to this definition">§</a></dt>
+<dd><p>Returns a <em>set</em> of nodes with the connections matching the direction,
+effect and evidence criteria. E.g. if the query concerns the incoming
+degrees with positive effect and the matching evidences show A
+activates B, but not the other way around, only “B” will be returned.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>mode:</dt><dd><p>The type of degrees to be considered. Three possible values are
+<code class="docutils literal notranslate"><span class="pre">'IN'</span></code>, <cite>‘OUT’`</cite> and <code class="docutils literal notranslate"><span class="pre">'ALL'</span></code> for incoming, outgoing and all
+connections, respectively. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is <code class="docutils literal notranslate"><span class="pre">False</span></code>
+the only possible mode is <code class="docutils literal notranslate"><span class="pre">ALL</span></code>. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is
+<code class="docutils literal notranslate"><span class="pre">None</span></code> and also directed evidence(s) match the criteria these
+will overwrite the undirected evidences and only the directed
+result will be returned.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.get_degrees_directed_out">
+<span class="sig-name descname"><span class="pre">get_degrees_directed_out</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.get_degrees_directed_out" title="Link to this definition">§</a></dt>
+<dd><p>Returns a <em>set</em> of nodes with the connections matching the direction,
+effect and evidence criteria. E.g. if the query concerns the incoming
+degrees with positive effect and the matching evidences show A
+activates B, but not the other way around, only “B” will be returned.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>mode:</dt><dd><p>The type of degrees to be considered. Three possible values are
+<code class="docutils literal notranslate"><span class="pre">'IN'</span></code>, <cite>‘OUT’`</cite> and <code class="docutils literal notranslate"><span class="pre">'ALL'</span></code> for incoming, outgoing and all
+connections, respectively. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is <code class="docutils literal notranslate"><span class="pre">False</span></code>
+the only possible mode is <code class="docutils literal notranslate"><span class="pre">ALL</span></code>. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is
+<code class="docutils literal notranslate"><span class="pre">None</span></code> and also directed evidence(s) match the criteria these
+will overwrite the undirected evidences and only the directed
+result will be returned.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.get_degrees_negative">
+<span class="sig-name descname"><span class="pre">get_degrees_negative</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.get_degrees_negative" title="Link to this definition">§</a></dt>
+<dd><p>Returns a <em>set</em> of nodes with the connections matching the direction,
+effect and evidence criteria. E.g. if the query concerns the incoming
+degrees with positive effect and the matching evidences show A
+activates B, but not the other way around, only “B” will be returned.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>mode:</dt><dd><p>The type of degrees to be considered. Three possible values are
+<code class="docutils literal notranslate"><span class="pre">'IN'</span></code>, <cite>‘OUT’`</cite> and <code class="docutils literal notranslate"><span class="pre">'ALL'</span></code> for incoming, outgoing and all
+connections, respectively. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is <code class="docutils literal notranslate"><span class="pre">False</span></code>
+the only possible mode is <code class="docutils literal notranslate"><span class="pre">ALL</span></code>. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is
+<code class="docutils literal notranslate"><span class="pre">None</span></code> and also directed evidence(s) match the criteria these
+will overwrite the undirected evidences and only the directed
+result will be returned.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.get_degrees_negative_in">
+<span class="sig-name descname"><span class="pre">get_degrees_negative_in</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.get_degrees_negative_in" title="Link to this definition">§</a></dt>
+<dd><p>Returns a <em>set</em> of nodes with the connections matching the direction,
+effect and evidence criteria. E.g. if the query concerns the incoming
+degrees with positive effect and the matching evidences show A
+activates B, but not the other way around, only “B” will be returned.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>mode:</dt><dd><p>The type of degrees to be considered. Three possible values are
+<code class="docutils literal notranslate"><span class="pre">'IN'</span></code>, <cite>‘OUT’`</cite> and <code class="docutils literal notranslate"><span class="pre">'ALL'</span></code> for incoming, outgoing and all
+connections, respectively. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is <code class="docutils literal notranslate"><span class="pre">False</span></code>
+the only possible mode is <code class="docutils literal notranslate"><span class="pre">ALL</span></code>. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is
+<code class="docutils literal notranslate"><span class="pre">None</span></code> and also directed evidence(s) match the criteria these
+will overwrite the undirected evidences and only the directed
+result will be returned.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.get_degrees_negative_out">
+<span class="sig-name descname"><span class="pre">get_degrees_negative_out</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.get_degrees_negative_out" title="Link to this definition">§</a></dt>
+<dd><p>Returns a <em>set</em> of nodes with the connections matching the direction,
+effect and evidence criteria. E.g. if the query concerns the incoming
+degrees with positive effect and the matching evidences show A
+activates B, but not the other way around, only “B” will be returned.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>mode:</dt><dd><p>The type of degrees to be considered. Three possible values are
+<code class="docutils literal notranslate"><span class="pre">'IN'</span></code>, <cite>‘OUT’`</cite> and <code class="docutils literal notranslate"><span class="pre">'ALL'</span></code> for incoming, outgoing and all
+connections, respectively. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is <code class="docutils literal notranslate"><span class="pre">False</span></code>
+the only possible mode is <code class="docutils literal notranslate"><span class="pre">ALL</span></code>. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is
+<code class="docutils literal notranslate"><span class="pre">None</span></code> and also directed evidence(s) match the criteria these
+will overwrite the undirected evidences and only the directed
+result will be returned.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.get_degrees_non_directed">
+<span class="sig-name descname"><span class="pre">get_degrees_non_directed</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.get_degrees_non_directed" title="Link to this definition">§</a></dt>
+<dd><p>Returns a <em>set</em> of nodes with the connections matching the direction,
+effect and evidence criteria. E.g. if the query concerns the incoming
+degrees with positive effect and the matching evidences show A
+activates B, but not the other way around, only “B” will be returned.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>mode:</dt><dd><p>The type of degrees to be considered. Three possible values are
+<code class="docutils literal notranslate"><span class="pre">'IN'</span></code>, <cite>‘OUT’`</cite> and <code class="docutils literal notranslate"><span class="pre">'ALL'</span></code> for incoming, outgoing and all
+connections, respectively. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is <code class="docutils literal notranslate"><span class="pre">False</span></code>
+the only possible mode is <code class="docutils literal notranslate"><span class="pre">ALL</span></code>. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is
+<code class="docutils literal notranslate"><span class="pre">None</span></code> and also directed evidence(s) match the criteria these
+will overwrite the undirected evidences and only the directed
+result will be returned.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.get_degrees_positive">
+<span class="sig-name descname"><span class="pre">get_degrees_positive</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.get_degrees_positive" title="Link to this definition">§</a></dt>
+<dd><p>Returns a <em>set</em> of nodes with the connections matching the direction,
+effect and evidence criteria. E.g. if the query concerns the incoming
+degrees with positive effect and the matching evidences show A
+activates B, but not the other way around, only “B” will be returned.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>mode:</dt><dd><p>The type of degrees to be considered. Three possible values are
+<code class="docutils literal notranslate"><span class="pre">'IN'</span></code>, <cite>‘OUT’`</cite> and <code class="docutils literal notranslate"><span class="pre">'ALL'</span></code> for incoming, outgoing and all
+connections, respectively. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is <code class="docutils literal notranslate"><span class="pre">False</span></code>
+the only possible mode is <code class="docutils literal notranslate"><span class="pre">ALL</span></code>. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is
+<code class="docutils literal notranslate"><span class="pre">None</span></code> and also directed evidence(s) match the criteria these
+will overwrite the undirected evidences and only the directed
+result will be returned.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.get_degrees_positive_in">
+<span class="sig-name descname"><span class="pre">get_degrees_positive_in</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.get_degrees_positive_in" title="Link to this definition">§</a></dt>
+<dd><p>Returns a <em>set</em> of nodes with the connections matching the direction,
+effect and evidence criteria. E.g. if the query concerns the incoming
+degrees with positive effect and the matching evidences show A
+activates B, but not the other way around, only “B” will be returned.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>mode:</dt><dd><p>The type of degrees to be considered. Three possible values are
+<code class="docutils literal notranslate"><span class="pre">'IN'</span></code>, <cite>‘OUT’`</cite> and <code class="docutils literal notranslate"><span class="pre">'ALL'</span></code> for incoming, outgoing and all
+connections, respectively. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is <code class="docutils literal notranslate"><span class="pre">False</span></code>
+the only possible mode is <code class="docutils literal notranslate"><span class="pre">ALL</span></code>. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is
+<code class="docutils literal notranslate"><span class="pre">None</span></code> and also directed evidence(s) match the criteria these
+will overwrite the undirected evidences and only the directed
+result will be returned.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.get_degrees_positive_out">
+<span class="sig-name descname"><span class="pre">get_degrees_positive_out</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.get_degrees_positive_out" title="Link to this definition">§</a></dt>
+<dd><p>Returns a <em>set</em> of nodes with the connections matching the direction,
+effect and evidence criteria. E.g. if the query concerns the incoming
+degrees with positive effect and the matching evidences show A
+activates B, but not the other way around, only “B” will be returned.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>mode:</dt><dd><p>The type of degrees to be considered. Three possible values are
+<code class="docutils literal notranslate"><span class="pre">'IN'</span></code>, <cite>‘OUT’`</cite> and <code class="docutils literal notranslate"><span class="pre">'ALL'</span></code> for incoming, outgoing and all
+connections, respectively. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is <code class="docutils literal notranslate"><span class="pre">False</span></code>
+the only possible mode is <code class="docutils literal notranslate"><span class="pre">ALL</span></code>. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is
+<code class="docutils literal notranslate"><span class="pre">None</span></code> and also directed evidence(s) match the criteria these
+will overwrite the undirected evidences and only the directed
+result will be returned.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.get_degrees_signed">
+<span class="sig-name descname"><span class="pre">get_degrees_signed</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.get_degrees_signed" title="Link to this definition">§</a></dt>
+<dd><p>Returns a <em>set</em> of nodes with the connections matching the direction,
+effect and evidence criteria. E.g. if the query concerns the incoming
+degrees with positive effect and the matching evidences show A
+activates B, but not the other way around, only “B” will be returned.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>mode:</dt><dd><p>The type of degrees to be considered. Three possible values are
+<code class="docutils literal notranslate"><span class="pre">'IN'</span></code>, <cite>‘OUT’`</cite> and <code class="docutils literal notranslate"><span class="pre">'ALL'</span></code> for incoming, outgoing and all
+connections, respectively. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is <code class="docutils literal notranslate"><span class="pre">False</span></code>
+the only possible mode is <code class="docutils literal notranslate"><span class="pre">ALL</span></code>. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is
+<code class="docutils literal notranslate"><span class="pre">None</span></code> and also directed evidence(s) match the criteria these
+will overwrite the undirected evidences and only the directed
+result will be returned.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.get_degrees_signed_in">
+<span class="sig-name descname"><span class="pre">get_degrees_signed_in</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.get_degrees_signed_in" title="Link to this definition">§</a></dt>
+<dd><p>Returns a <em>set</em> of nodes with the connections matching the direction,
+effect and evidence criteria. E.g. if the query concerns the incoming
+degrees with positive effect and the matching evidences show A
+activates B, but not the other way around, only “B” will be returned.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>mode:</dt><dd><p>The type of degrees to be considered. Three possible values are
+<code class="docutils literal notranslate"><span class="pre">'IN'</span></code>, <cite>‘OUT’`</cite> and <code class="docutils literal notranslate"><span class="pre">'ALL'</span></code> for incoming, outgoing and all
+connections, respectively. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is <code class="docutils literal notranslate"><span class="pre">False</span></code>
+the only possible mode is <code class="docutils literal notranslate"><span class="pre">ALL</span></code>. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is
+<code class="docutils literal notranslate"><span class="pre">None</span></code> and also directed evidence(s) match the criteria these
+will overwrite the undirected evidences and only the directed
+result will be returned.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.get_degrees_signed_out">
+<span class="sig-name descname"><span class="pre">get_degrees_signed_out</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.get_degrees_signed_out" title="Link to this definition">§</a></dt>
+<dd><p>Returns a <em>set</em> of nodes with the connections matching the direction,
+effect and evidence criteria. E.g. if the query concerns the incoming
+degrees with positive effect and the matching evidences show A
+activates B, but not the other way around, only “B” will be returned.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>mode:</dt><dd><p>The type of degrees to be considered. Three possible values are
+<code class="docutils literal notranslate"><span class="pre">'IN'</span></code>, <cite>‘OUT’`</cite> and <code class="docutils literal notranslate"><span class="pre">'ALL'</span></code> for incoming, outgoing and all
+connections, respectively. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is <code class="docutils literal notranslate"><span class="pre">False</span></code>
+the only possible mode is <code class="docutils literal notranslate"><span class="pre">ALL</span></code>. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is
+<code class="docutils literal notranslate"><span class="pre">None</span></code> and also directed evidence(s) match the criteria these
+will overwrite the undirected evidences and only the directed
+result will be returned.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.get_degrees_undirected">
+<span class="sig-name descname"><span class="pre">get_degrees_undirected</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.get_degrees_undirected" title="Link to this definition">§</a></dt>
+<dd><p>Returns a <em>set</em> of nodes with the connections matching the direction,
+effect and evidence criteria. E.g. if the query concerns the incoming
+degrees with positive effect and the matching evidences show A
+activates B, but not the other way around, only “B” will be returned.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>mode:</dt><dd><p>The type of degrees to be considered. Three possible values are
+<code class="docutils literal notranslate"><span class="pre">'IN'</span></code>, <cite>‘OUT’`</cite> and <code class="docutils literal notranslate"><span class="pre">'ALL'</span></code> for incoming, outgoing and all
+connections, respectively. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is <code class="docutils literal notranslate"><span class="pre">False</span></code>
+the only possible mode is <code class="docutils literal notranslate"><span class="pre">ALL</span></code>. If the <code class="docutils literal notranslate"><span class="pre">direction</span></code> is
+<code class="docutils literal notranslate"><span class="pre">None</span></code> and also directed evidence(s) match the criteria these
+will overwrite the undirected evidences and only the directed
+result will be returned.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.get_direction">
+<span class="sig-name descname"><span class="pre">get_direction</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">direction</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">evidences</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">sources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resource_names</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/interaction.html#Interaction.get_direction"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.interaction.Interaction.get_direction" title="Link to this definition">§</a></dt>
+<dd><p>Returns the state (or <em>resources</em> if specified) of the given
+<em>direction</em>.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>direction</strong> (<em>tuple</em>) – Or [str] (if <code class="docutils literal notranslate"><span class="pre">'undirected'</span></code>). Pair of nodes from which
+direction information is to be retrieved.</p></li>
+<li><p><strong>resources</strong> (<em>bool</em>) – Optional, <code class="docutils literal notranslate"><span class="pre">'False'</span></code> by default. Specifies if the
+<code class="xref py py-attr docutils literal notranslate"><span class="pre">resources</span></code> information of the given direction is to
+be retrieved instead.</p></li>
+</ul>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p>(<em>bool</em> or <em>set</em>) – (if <code class="docutils literal notranslate"><span class="pre">resources=True</span></code>). Presence/absence
+of the requested direction (or the list of resources if
+specified). Returns <code class="docutils literal notranslate"><span class="pre">None</span></code> if <em>direction</em> is not valid.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.get_directions">
+<span class="sig-name descname"><span class="pre">get_directions</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">src</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">tgt</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">evidences</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resource_names</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">sources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/interaction.html#Interaction.get_directions"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.interaction.Interaction.get_directions" title="Link to this definition">§</a></dt>
+<dd><p>Returns all directions with boolean values or list of sources.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>src</strong> (<em>str</em>) – Source node.</p></li>
+<li><p><strong>tgt</strong> (<em>str</em>) – Target node.</p></li>
+<li><p><strong>resources</strong> (<em>bool</em>) – Optional, <code class="docutils literal notranslate"><span class="pre">False</span></code> by default. Specifies whether to return
+the <code class="xref py py-attr docutils literal notranslate"><span class="pre">resources</span></code> attribute instead of <code class="xref py py-attr docutils literal notranslate"><span class="pre">dirs</span></code>.</p></li>
+</ul>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p>Contains the <code class="xref py py-attr docutils literal notranslate"><span class="pre">dirs</span></code> (or <code class="xref py py-attr docutils literal notranslate"><span class="pre">resources</span></code> if
+specified) of the given edge.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.get_entities">
+<span class="sig-name descname"><span class="pre">get_entities</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">direction</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">datasets</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">return_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/interaction.html#Interaction.get_entities"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.interaction.Interaction.get_entities" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the entities involved in interactions matching the criteria.
+It either returns both interacting entities in a <em>set</em> or an empty
+<em>set</em>. This may not sound so useful at the level of this object but
+becomes more useful once we want to collect entities having certain
+kind of interactions across a series of <cite>Interaction</cite> objects.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>entity_type</strong> (<em>str</em>) – The type of the molecular entity. Possible values: <cite>protein</cite>,
+<cite>complex</cite>, <cite>mirna</cite>, <cite>small_molecule</cite>.</p></li>
+<li><p><strong>return_type</strong> (<em>str</em>) – The type of values to return. Default is
+py:class:<code class="docutils literal notranslate"><span class="pre">pypath.entity.Entity</span></code> objects, alternatives are
+<code class="docutils literal notranslate"><span class="pre">labels</span></code>  <code class="docutils literal notranslate"><span class="pre">identifiers</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.get_identifiers">
+<span class="sig-name descname"><span class="pre">get_identifiers</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">direction</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">return_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.get_identifiers" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the entities involved in interactions matching the criteria.
+It either returns both interacting entities in a <em>set</em> or an empty
+<em>set</em>. This may not sound so useful at the level of this object but
+becomes more useful once we want to collect entities having certain
+kind of interactions across a series of <cite>Interaction</cite> objects.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>entity_type</strong> (<em>str</em>) – The type of the molecular entity. Possible values: <cite>protein</cite>,
+<cite>complex</cite>, <cite>mirna</cite>, <cite>small_molecule</cite>.</p></li>
+<li><p><strong>return_type</strong> (<em>str</em>) – The type of values to return. Default is
+py:class:<code class="docutils literal notranslate"><span class="pre">pypath.entity.Entity</span></code> objects, alternatives are
+<code class="docutils literal notranslate"><span class="pre">labels</span></code>  <code class="docutils literal notranslate"><span class="pre">identifiers</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.get_interaction_types">
+<span class="sig-name descname"><span class="pre">get_interaction_types</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.get_interaction_types" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves interaction types matching the criteria.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.get_interactions">
+<span class="sig-name descname"><span class="pre">get_interactions</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">direction</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">source_entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">target_entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">datasets</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/interaction.html#Interaction.get_interactions"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.interaction.Interaction.get_interactions" title="Link to this definition">§</a></dt>
+<dd><p>Returns one or two tuples of the interacting partners: one if only
+one direction, two if both directions match the query criteria.
+The tuple will be empty if no evidence matches the criteria.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>direction</strong> (<em>NontType</em><em>,</em><em>bool</em><em>,</em><em>tuple</em>) – If <cite>None</cite> both undirected and directed, if <cite>True</cite> only directed,
+if a <em>tuple</em> of entities only the interactions with that specific
+direction will be considered. Unless you set this parameter to
+<cite>True</cite> this method will return both directions if one or more
+undirected resources present.
+If <cite>False</cite>, only the undirected interactions will be considered,
+and if any resource annotates this interaction as undirected
+both directions will be returned. However the
+<code class="docutils literal notranslate"><span class="pre">count_interactions_undirected</span></code> method will return <cite>1</cite>
+in this case.</p></li>
+<li><p><strong>effect</strong> (<em>NoneType</em><em>,</em><em>bool</em><em>,</em><em>str</em>) – If <cite>None</cite> also interactions without effect, if <cite>True</cite> only
+the ones with any effect, if a string naming an effect only the
+interactions with that specific effect will be considered.</p></li>
+<li><p><strong>resources</strong> (<em>NontType</em><em>,</em><em>str</em><em>,</em><em>set</em>) – Optionally limit the query to one or more resources.</p></li>
+<li><p><strong>data_model</strong> (<em>NontType</em><em>,</em><em>str</em><em>,</em><em>set</em>) – Optionally limit the query to one or more data models e.g.
+<cite>activity_flow</cite>.</p></li>
+<li><p><strong>interaction_type</strong> (<em>NontType</em><em>,</em><em>str</em><em>,</em><em>set</em>) – Optionally limit the query to one or more interaction types
+e.g. <cite>PPI</cite>.</p></li>
+<li><p><strong>via</strong> (<em>NontType</em><em>,</em><em>bool</em><em>,</em><em>str</em><em>,</em><em>set</em>) – Optionally limit the query to certain secondary databases or
+if <cite>False</cite> consider only data from primary databases.</p></li>
+<li><p><strong>entity_type</strong> (<em>str</em>) – Molecule type for both of the entities.</p></li>
+<li><p><strong>source_entity_type</strong> (<em>str</em>) – Molecule type for the source entity.</p></li>
+<li><p><strong>target_entity_type</strong> (<em>str</em>) – Molecule type for the target entity.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.get_interactions_0">
+<span class="sig-name descname"><span class="pre">get_interactions_0</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/interaction.html#Interaction.get_interactions_0"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.interaction.Interaction.get_interactions_0" title="Link to this definition">§</a></dt>
+<dd><p>Returns unique interacting pairs without being aware of the direction.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.get_interactions_directed">
+<span class="sig-name descname"><span class="pre">get_interactions_directed</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/interaction.html#Interaction.get_interactions_directed"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.interaction.Interaction.get_interactions_directed" title="Link to this definition">§</a></dt>
+<dd><dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>kwargs:</dt><dd><p>See the docs of method <code class="docutils literal notranslate"><span class="pre">get_interactions</span></code>.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.get_interactions_mutual">
+<span class="sig-name descname"><span class="pre">get_interactions_mutual</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/interaction.html#Interaction.get_interactions_mutual"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.interaction.Interaction.get_interactions_mutual" title="Link to this definition">§</a></dt>
+<dd><p>Note: undirected interactions does not count as mutual but only
+interactions with explicit direction information for both directions.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>kwargs:</dt><dd><p>See the docs of method <code class="docutils literal notranslate"><span class="pre">get_interactions</span></code>.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.get_interactions_negative">
+<span class="sig-name descname"><span class="pre">get_interactions_negative</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/interaction.html#Interaction.get_interactions_negative"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.interaction.Interaction.get_interactions_negative" title="Link to this definition">§</a></dt>
+<dd><dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>kwargs:</dt><dd><p>See the docs of method <code class="docutils literal notranslate"><span class="pre">get_interactions</span></code>.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.get_interactions_non_directed">
+<span class="sig-name descname"><span class="pre">get_interactions_non_directed</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/interaction.html#Interaction.get_interactions_non_directed"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.interaction.Interaction.get_interactions_non_directed" title="Link to this definition">§</a></dt>
+<dd><p>Only the undirected interactions will be considered, if any resource
+annotates this interaction as undirected both directions will be
+returned, but only if no resource provide direction. However
+the <code class="docutils literal notranslate"><span class="pre">count_interactions_non_directed</span></code> method will return <cite>1</cite> in
+this case.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>kwargs:</dt><dd><p>See the docs of method <code class="docutils literal notranslate"><span class="pre">get_interactions</span></code>.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.get_interactions_non_directed_0">
+<span class="sig-name descname"><span class="pre">get_interactions_non_directed_0</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/interaction.html#Interaction.get_interactions_non_directed_0"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.interaction.Interaction.get_interactions_non_directed_0" title="Link to this definition">§</a></dt>
+<dd><p>Only the undirected interactions will be considered, if any resource
+annotates this interaction as undirected and none as directed, the
+interacting pair as a sorted tuple will be returned inside a one
+element tuple.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>kwargs:</dt><dd><p>See the docs of method <code class="docutils literal notranslate"><span class="pre">get_interactions</span></code>.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.get_interactions_positive">
+<span class="sig-name descname"><span class="pre">get_interactions_positive</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/interaction.html#Interaction.get_interactions_positive"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.interaction.Interaction.get_interactions_positive" title="Link to this definition">§</a></dt>
+<dd><dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>kwargs:</dt><dd><p>See the docs of method <code class="docutils literal notranslate"><span class="pre">get_interactions</span></code>.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.get_interactions_signed">
+<span class="sig-name descname"><span class="pre">get_interactions_signed</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/interaction.html#Interaction.get_interactions_signed"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.interaction.Interaction.get_interactions_signed" title="Link to this definition">§</a></dt>
+<dd><dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>kwargs:</dt><dd><p>See the docs of method <code class="docutils literal notranslate"><span class="pre">get_interactions</span></code>.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.get_interactions_undirected">
+<span class="sig-name descname"><span class="pre">get_interactions_undirected</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/interaction.html#Interaction.get_interactions_undirected"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.interaction.Interaction.get_interactions_undirected" title="Link to this definition">§</a></dt>
+<dd><p>Only the undirected interactions will be considered, if any resource
+annotates this interaction as undirected both directions will be
+returned, no matter if certain resources provide direction. However
+the <code class="docutils literal notranslate"><span class="pre">count_interactions_undirected</span></code> method will return <cite>1</cite> in this
+case.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>kwargs:</dt><dd><p>See the docs of method <code class="docutils literal notranslate"><span class="pre">get_interactions</span></code>.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.get_interactions_undirected_0">
+<span class="sig-name descname"><span class="pre">get_interactions_undirected_0</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/interaction.html#Interaction.get_interactions_undirected_0"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.interaction.Interaction.get_interactions_undirected_0" title="Link to this definition">§</a></dt>
+<dd><p>Only the undirected interactions will be considered, if any resource
+annotates this interaction as undirected the interacting pair as
+a sorted tuple will be returned inside a one element tuple.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>kwargs:</dt><dd><p>See the docs of method <code class="docutils literal notranslate"><span class="pre">get_interactions</span></code>.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.get_labels">
+<span class="sig-name descname"><span class="pre">get_labels</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">direction</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">return_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.get_labels" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the entities involved in interactions matching the criteria.
+It either returns both interacting entities in a <em>set</em> or an empty
+<em>set</em>. This may not sound so useful at the level of this object but
+becomes more useful once we want to collect entities having certain
+kind of interactions across a series of <cite>Interaction</cite> objects.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>entity_type</strong> (<em>str</em>) – The type of the molecular entity. Possible values: <cite>protein</cite>,
+<cite>complex</cite>, <cite>mirna</cite>, <cite>small_molecule</cite>.</p></li>
+<li><p><strong>return_type</strong> (<em>str</em>) – The type of values to return. Default is
+py:class:<code class="docutils literal notranslate"><span class="pre">pypath.entity.Entity</span></code> objects, alternatives are
+<code class="docutils literal notranslate"><span class="pre">labels</span></code>  <code class="docutils literal notranslate"><span class="pre">identifiers</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.get_lncrna_identifiers">
+<span class="sig-name descname"><span class="pre">get_lncrna_identifiers</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">direction</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">return_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.get_lncrna_identifiers" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the entities involved in interactions matching the criteria.
+It either returns both interacting entities in a <em>set</em> or an empty
+<em>set</em>. This may not sound so useful at the level of this object but
+becomes more useful once we want to collect entities having certain
+kind of interactions across a series of <cite>Interaction</cite> objects.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>entity_type</strong> (<em>str</em>) – The type of the molecular entity. Possible values: <cite>protein</cite>,
+<cite>complex</cite>, <cite>mirna</cite>, <cite>small_molecule</cite>.</p></li>
+<li><p><strong>return_type</strong> (<em>str</em>) – The type of values to return. Default is
+py:class:<code class="docutils literal notranslate"><span class="pre">pypath.entity.Entity</span></code> objects, alternatives are
+<code class="docutils literal notranslate"><span class="pre">labels</span></code>  <code class="docutils literal notranslate"><span class="pre">identifiers</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.get_lncrna_labels">
+<span class="sig-name descname"><span class="pre">get_lncrna_labels</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">direction</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">return_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.get_lncrna_labels" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the entities involved in interactions matching the criteria.
+It either returns both interacting entities in a <em>set</em> or an empty
+<em>set</em>. This may not sound so useful at the level of this object but
+becomes more useful once we want to collect entities having certain
+kind of interactions across a series of <cite>Interaction</cite> objects.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>entity_type</strong> (<em>str</em>) – The type of the molecular entity. Possible values: <cite>protein</cite>,
+<cite>complex</cite>, <cite>mirna</cite>, <cite>small_molecule</cite>.</p></li>
+<li><p><strong>return_type</strong> (<em>str</em>) – The type of values to return. Default is
+py:class:<code class="docutils literal notranslate"><span class="pre">pypath.entity.Entity</span></code> objects, alternatives are
+<code class="docutils literal notranslate"><span class="pre">labels</span></code>  <code class="docutils literal notranslate"><span class="pre">identifiers</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.get_lncrnas">
+<span class="sig-name descname"><span class="pre">get_lncrnas</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">direction</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">return_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.get_lncrnas" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the entities involved in interactions matching the criteria.
+It either returns both interacting entities in a <em>set</em> or an empty
+<em>set</em>. This may not sound so useful at the level of this object but
+becomes more useful once we want to collect entities having certain
+kind of interactions across a series of <cite>Interaction</cite> objects.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>entity_type</strong> (<em>str</em>) – The type of the molecular entity. Possible values: <cite>protein</cite>,
+<cite>complex</cite>, <cite>mirna</cite>, <cite>small_molecule</cite>.</p></li>
+<li><p><strong>return_type</strong> (<em>str</em>) – The type of values to return. Default is
+py:class:<code class="docutils literal notranslate"><span class="pre">pypath.entity.Entity</span></code> objects, alternatives are
+<code class="docutils literal notranslate"><span class="pre">labels</span></code>  <code class="docutils literal notranslate"><span class="pre">identifiers</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.get_mirna_identifiers">
+<span class="sig-name descname"><span class="pre">get_mirna_identifiers</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">direction</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">return_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.get_mirna_identifiers" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the entities involved in interactions matching the criteria.
+It either returns both interacting entities in a <em>set</em> or an empty
+<em>set</em>. This may not sound so useful at the level of this object but
+becomes more useful once we want to collect entities having certain
+kind of interactions across a series of <cite>Interaction</cite> objects.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>entity_type</strong> (<em>str</em>) – The type of the molecular entity. Possible values: <cite>protein</cite>,
+<cite>complex</cite>, <cite>mirna</cite>, <cite>small_molecule</cite>.</p></li>
+<li><p><strong>return_type</strong> (<em>str</em>) – The type of values to return. Default is
+py:class:<code class="docutils literal notranslate"><span class="pre">pypath.entity.Entity</span></code> objects, alternatives are
+<code class="docutils literal notranslate"><span class="pre">labels</span></code>  <code class="docutils literal notranslate"><span class="pre">identifiers</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.get_mirna_labels">
+<span class="sig-name descname"><span class="pre">get_mirna_labels</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">direction</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">return_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.get_mirna_labels" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the entities involved in interactions matching the criteria.
+It either returns both interacting entities in a <em>set</em> or an empty
+<em>set</em>. This may not sound so useful at the level of this object but
+becomes more useful once we want to collect entities having certain
+kind of interactions across a series of <cite>Interaction</cite> objects.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>entity_type</strong> (<em>str</em>) – The type of the molecular entity. Possible values: <cite>protein</cite>,
+<cite>complex</cite>, <cite>mirna</cite>, <cite>small_molecule</cite>.</p></li>
+<li><p><strong>return_type</strong> (<em>str</em>) – The type of values to return. Default is
+py:class:<code class="docutils literal notranslate"><span class="pre">pypath.entity.Entity</span></code> objects, alternatives are
+<code class="docutils literal notranslate"><span class="pre">labels</span></code>  <code class="docutils literal notranslate"><span class="pre">identifiers</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.get_mirnas">
+<span class="sig-name descname"><span class="pre">get_mirnas</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">direction</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">return_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.get_mirnas" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the entities involved in interactions matching the criteria.
+It either returns both interacting entities in a <em>set</em> or an empty
+<em>set</em>. This may not sound so useful at the level of this object but
+becomes more useful once we want to collect entities having certain
+kind of interactions across a series of <cite>Interaction</cite> objects.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>entity_type</strong> (<em>str</em>) – The type of the molecular entity. Possible values: <cite>protein</cite>,
+<cite>complex</cite>, <cite>mirna</cite>, <cite>small_molecule</cite>.</p></li>
+<li><p><strong>return_type</strong> (<em>str</em>) – The type of values to return. Default is
+py:class:<code class="docutils literal notranslate"><span class="pre">pypath.entity.Entity</span></code> objects, alternatives are
+<code class="docutils literal notranslate"><span class="pre">labels</span></code>  <code class="docutils literal notranslate"><span class="pre">identifiers</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.get_protein_identifiers">
+<span class="sig-name descname"><span class="pre">get_protein_identifiers</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">direction</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">return_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.get_protein_identifiers" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the entities involved in interactions matching the criteria.
+It either returns both interacting entities in a <em>set</em> or an empty
+<em>set</em>. This may not sound so useful at the level of this object but
+becomes more useful once we want to collect entities having certain
+kind of interactions across a series of <cite>Interaction</cite> objects.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>entity_type</strong> (<em>str</em>) – The type of the molecular entity. Possible values: <cite>protein</cite>,
+<cite>complex</cite>, <cite>mirna</cite>, <cite>small_molecule</cite>.</p></li>
+<li><p><strong>return_type</strong> (<em>str</em>) – The type of values to return. Default is
+py:class:<code class="docutils literal notranslate"><span class="pre">pypath.entity.Entity</span></code> objects, alternatives are
+<code class="docutils literal notranslate"><span class="pre">labels</span></code>  <code class="docutils literal notranslate"><span class="pre">identifiers</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.get_protein_labels">
+<span class="sig-name descname"><span class="pre">get_protein_labels</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">direction</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">return_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.get_protein_labels" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the entities involved in interactions matching the criteria.
+It either returns both interacting entities in a <em>set</em> or an empty
+<em>set</em>. This may not sound so useful at the level of this object but
+becomes more useful once we want to collect entities having certain
+kind of interactions across a series of <cite>Interaction</cite> objects.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>entity_type</strong> (<em>str</em>) – The type of the molecular entity. Possible values: <cite>protein</cite>,
+<cite>complex</cite>, <cite>mirna</cite>, <cite>small_molecule</cite>.</p></li>
+<li><p><strong>return_type</strong> (<em>str</em>) – The type of values to return. Default is
+py:class:<code class="docutils literal notranslate"><span class="pre">pypath.entity.Entity</span></code> objects, alternatives are
+<code class="docutils literal notranslate"><span class="pre">labels</span></code>  <code class="docutils literal notranslate"><span class="pre">identifiers</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.get_proteins">
+<span class="sig-name descname"><span class="pre">get_proteins</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">direction</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">return_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.get_proteins" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the entities involved in interactions matching the criteria.
+It either returns both interacting entities in a <em>set</em> or an empty
+<em>set</em>. This may not sound so useful at the level of this object but
+becomes more useful once we want to collect entities having certain
+kind of interactions across a series of <cite>Interaction</cite> objects.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>entity_type</strong> (<em>str</em>) – The type of the molecular entity. Possible values: <cite>protein</cite>,
+<cite>complex</cite>, <cite>mirna</cite>, <cite>small_molecule</cite>.</p></li>
+<li><p><strong>return_type</strong> (<em>str</em>) – The type of values to return. Default is
+py:class:<code class="docutils literal notranslate"><span class="pre">pypath.entity.Entity</span></code> objects, alternatives are
+<code class="docutils literal notranslate"><span class="pre">labels</span></code>  <code class="docutils literal notranslate"><span class="pre">identifiers</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.get_references">
+<span class="sig-name descname"><span class="pre">get_references</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.get_references" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves references matching the criteria.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.get_resource_names">
+<span class="sig-name descname"><span class="pre">get_resource_names</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.get_resource_names" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves resource names matching the criteria.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.get_resource_names_via">
+<span class="sig-name descname"><span class="pre">get_resource_names_via</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.get_resource_names_via" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves resource names via matching the criteria.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.get_resources">
+<span class="sig-name descname"><span class="pre">get_resources</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.get_resources" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves resources matching the criteria.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.get_resources_via">
+<span class="sig-name descname"><span class="pre">get_resources_via</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.get_resources_via" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves resources via matching the criteria.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.get_sign">
+<span class="sig-name descname"><span class="pre">get_sign</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">direction</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">tuple</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">sign</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">evidences</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resource_names</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">sources</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">bool</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">str</span><span class="p"><span class="pre">]</span></span></span></span><a class="reference internal" href="../_modules/pypath/core/interaction.html#Interaction.get_sign"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.interaction.Interaction.get_sign" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the sign information of the edge in the given
+diretion. If specified in <em>sign</em>, only that sign’s information
+will be retrieved. If specified in <em>sources</em>, the sources of
+that information will be retrieved instead.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>direction:</dt><dd><p>Contains the pair of nodes specifying the directionality of
+the edge from which th information is to be retrieved.</p>
+</dd>
+<dt>sign:</dt><dd><p>Optional, <code class="docutils literal notranslate"><span class="pre">None</span></code> by default. Denotes whether to retrieve
+the <code class="docutils literal notranslate"><span class="pre">'positive'</span></code> or <code class="docutils literal notranslate"><span class="pre">'negative'</span></code> specific information.</p>
+</dd>
+<dt>resources:</dt><dd><p>Optional, <code class="docutils literal notranslate"><span class="pre">False</span></code> by default. Specifies whether to return
+the resources instead of sign.</p>
+</dd>
+</dl>
+</dd>
+<dt>Returns</dt><dd><p>If <code class="docutils literal notranslate"><span class="pre">sign=None</span></code> containing [bool] values
+denoting the presence of positive and negative sign on that
+direction, if <code class="docutils literal notranslate"><span class="pre">sources=True</span></code> the [set] of sources for each
+of them will be returned instead. If <em>sign</em> is specified,
+returns [bool] or [set] (if <code class="docutils literal notranslate"><span class="pre">sources=True</span></code>) of that
+specific direction and sign.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.get_small_molecule_identifiers">
+<span class="sig-name descname"><span class="pre">get_small_molecule_identifiers</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">direction</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">return_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.get_small_molecule_identifiers" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the entities involved in interactions matching the criteria.
+It either returns both interacting entities in a <em>set</em> or an empty
+<em>set</em>. This may not sound so useful at the level of this object but
+becomes more useful once we want to collect entities having certain
+kind of interactions across a series of <cite>Interaction</cite> objects.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>entity_type</strong> (<em>str</em>) – The type of the molecular entity. Possible values: <cite>protein</cite>,
+<cite>complex</cite>, <cite>mirna</cite>, <cite>small_molecule</cite>.</p></li>
+<li><p><strong>return_type</strong> (<em>str</em>) – The type of values to return. Default is
+py:class:<code class="docutils literal notranslate"><span class="pre">pypath.entity.Entity</span></code> objects, alternatives are
+<code class="docutils literal notranslate"><span class="pre">labels</span></code>  <code class="docutils literal notranslate"><span class="pre">identifiers</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.get_small_molecule_labels">
+<span class="sig-name descname"><span class="pre">get_small_molecule_labels</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">direction</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">return_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.get_small_molecule_labels" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the entities involved in interactions matching the criteria.
+It either returns both interacting entities in a <em>set</em> or an empty
+<em>set</em>. This may not sound so useful at the level of this object but
+becomes more useful once we want to collect entities having certain
+kind of interactions across a series of <cite>Interaction</cite> objects.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>entity_type</strong> (<em>str</em>) – The type of the molecular entity. Possible values: <cite>protein</cite>,
+<cite>complex</cite>, <cite>mirna</cite>, <cite>small_molecule</cite>.</p></li>
+<li><p><strong>return_type</strong> (<em>str</em>) – The type of values to return. Default is
+py:class:<code class="docutils literal notranslate"><span class="pre">pypath.entity.Entity</span></code> objects, alternatives are
+<code class="docutils literal notranslate"><span class="pre">labels</span></code>  <code class="docutils literal notranslate"><span class="pre">identifiers</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.get_small_molecules">
+<span class="sig-name descname"><span class="pre">get_small_molecules</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">direction</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">return_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.get_small_molecules" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the entities involved in interactions matching the criteria.
+It either returns both interacting entities in a <em>set</em> or an empty
+<em>set</em>. This may not sound so useful at the level of this object but
+becomes more useful once we want to collect entities having certain
+kind of interactions across a series of <cite>Interaction</cite> objects.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>entity_type</strong> (<em>str</em>) – The type of the molecular entity. Possible values: <cite>protein</cite>,
+<cite>complex</cite>, <cite>mirna</cite>, <cite>small_molecule</cite>.</p></li>
+<li><p><strong>return_type</strong> (<em>str</em>) – The type of values to return. Default is
+py:class:<code class="docutils literal notranslate"><span class="pre">pypath.entity.Entity</span></code> objects, alternatives are
+<code class="docutils literal notranslate"><span class="pre">labels</span></code>  <code class="docutils literal notranslate"><span class="pre">identifiers</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.has_sign">
+<span class="sig-name descname"><span class="pre">has_sign</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">direction</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/interaction.html#Interaction.has_sign"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.interaction.Interaction.has_sign" title="Link to this definition">§</a></dt>
+<dd><p>Checks whether the edge (or for a specific <em>direction</em>) has
+any signed information (about positive/negative interactions).</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><p><strong>direction</strong> (<em>tuple</em>) – Optional, <code class="docutils literal notranslate"><span class="pre">None</span></code> by default. If specified, only the
+information of that direction is checked for sign.</p>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p><dl class="simple">
+<dt>(<em>bool</em>) – <code class="docutils literal notranslate"><span class="pre">True</span></code> if there exist any information on the</dt><dd><p>sign of the interaction, <code class="docutils literal notranslate"><span class="pre">False</span></code> otherwise.</p>
+</dd>
+</dl>
+</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.identifiers_by_data_model">
+<span class="sig-name descname"><span class="pre">identifiers_by_data_model</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.identifiers_by_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the entities involved in interactions matching the criteria.
+It either returns both interacting entities in a <em>set</em> or an empty
+<em>set</em>. This may not sound so useful at the level of this object but
+becomes more useful once we want to collect entities having certain
+kind of interactions across a series of <cite>Interaction</cite> objects.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>entity_type</strong> (<em>str</em>) – The type of the molecular entity. Possible values: <cite>protein</cite>,
+<cite>complex</cite>, <cite>mirna</cite>, <cite>small_molecule</cite>.</p></li>
+<li><p><strong>return_type</strong> (<em>str</em>) – The type of values to return. Default is
+py:class:<code class="docutils literal notranslate"><span class="pre">pypath.entity.Entity</span></code> objects, alternatives are
+<code class="docutils literal notranslate"><span class="pre">labels</span></code>  <code class="docutils literal notranslate"><span class="pre">identifiers</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.identifiers_by_interaction_type">
+<span class="sig-name descname"><span class="pre">identifiers_by_interaction_type</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.identifiers_by_interaction_type" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the entities involved in interactions matching the criteria.
+It either returns both interacting entities in a <em>set</em> or an empty
+<em>set</em>. This may not sound so useful at the level of this object but
+becomes more useful once we want to collect entities having certain
+kind of interactions across a series of <cite>Interaction</cite> objects.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>entity_type</strong> (<em>str</em>) – The type of the molecular entity. Possible values: <cite>protein</cite>,
+<cite>complex</cite>, <cite>mirna</cite>, <cite>small_molecule</cite>.</p></li>
+<li><p><strong>return_type</strong> (<em>str</em>) – The type of values to return. Default is
+py:class:<code class="docutils literal notranslate"><span class="pre">pypath.entity.Entity</span></code> objects, alternatives are
+<code class="docutils literal notranslate"><span class="pre">labels</span></code>  <code class="docutils literal notranslate"><span class="pre">identifiers</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.identifiers_by_interaction_type_and_data_model">
+<span class="sig-name descname"><span class="pre">identifiers_by_interaction_type_and_data_model</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.identifiers_by_interaction_type_and_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the entities involved in interactions matching the criteria.
+It either returns both interacting entities in a <em>set</em> or an empty
+<em>set</em>. This may not sound so useful at the level of this object but
+becomes more useful once we want to collect entities having certain
+kind of interactions across a series of <cite>Interaction</cite> objects.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>entity_type</strong> (<em>str</em>) – The type of the molecular entity. Possible values: <cite>protein</cite>,
+<cite>complex</cite>, <cite>mirna</cite>, <cite>small_molecule</cite>.</p></li>
+<li><p><strong>return_type</strong> (<em>str</em>) – The type of values to return. Default is
+py:class:<code class="docutils literal notranslate"><span class="pre">pypath.entity.Entity</span></code> objects, alternatives are
+<code class="docutils literal notranslate"><span class="pre">labels</span></code>  <code class="docutils literal notranslate"><span class="pre">identifiers</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.identifiers_by_interaction_type_and_data_model_and_resource">
+<span class="sig-name descname"><span class="pre">identifiers_by_interaction_type_and_data_model_and_resource</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.identifiers_by_interaction_type_and_data_model_and_resource" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the entities involved in interactions matching the criteria.
+It either returns both interacting entities in a <em>set</em> or an empty
+<em>set</em>. This may not sound so useful at the level of this object but
+becomes more useful once we want to collect entities having certain
+kind of interactions across a series of <cite>Interaction</cite> objects.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>entity_type</strong> (<em>str</em>) – The type of the molecular entity. Possible values: <cite>protein</cite>,
+<cite>complex</cite>, <cite>mirna</cite>, <cite>small_molecule</cite>.</p></li>
+<li><p><strong>return_type</strong> (<em>str</em>) – The type of values to return. Default is
+py:class:<code class="docutils literal notranslate"><span class="pre">pypath.entity.Entity</span></code> objects, alternatives are
+<code class="docutils literal notranslate"><span class="pre">labels</span></code>  <code class="docutils literal notranslate"><span class="pre">identifiers</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.identifiers_by_reference">
+<span class="sig-name descname"><span class="pre">identifiers_by_reference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.identifiers_by_reference" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the entities involved in interactions matching the criteria.
+It either returns both interacting entities in a <em>set</em> or an empty
+<em>set</em>. This may not sound so useful at the level of this object but
+becomes more useful once we want to collect entities having certain
+kind of interactions across a series of <cite>Interaction</cite> objects.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>entity_type</strong> (<em>str</em>) – The type of the molecular entity. Possible values: <cite>protein</cite>,
+<cite>complex</cite>, <cite>mirna</cite>, <cite>small_molecule</cite>.</p></li>
+<li><p><strong>return_type</strong> (<em>str</em>) – The type of values to return. Default is
+py:class:<code class="docutils literal notranslate"><span class="pre">pypath.entity.Entity</span></code> objects, alternatives are
+<code class="docutils literal notranslate"><span class="pre">labels</span></code>  <code class="docutils literal notranslate"><span class="pre">identifiers</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.identifiers_by_resource">
+<span class="sig-name descname"><span class="pre">identifiers_by_resource</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.identifiers_by_resource" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the entities involved in interactions matching the criteria.
+It either returns both interacting entities in a <em>set</em> or an empty
+<em>set</em>. This may not sound so useful at the level of this object but
+becomes more useful once we want to collect entities having certain
+kind of interactions across a series of <cite>Interaction</cite> objects.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>entity_type</strong> (<em>str</em>) – The type of the molecular entity. Possible values: <cite>protein</cite>,
+<cite>complex</cite>, <cite>mirna</cite>, <cite>small_molecule</cite>.</p></li>
+<li><p><strong>return_type</strong> (<em>str</em>) – The type of values to return. Default is
+py:class:<code class="docutils literal notranslate"><span class="pre">pypath.entity.Entity</span></code> objects, alternatives are
+<code class="docutils literal notranslate"><span class="pre">labels</span></code>  <code class="docutils literal notranslate"><span class="pre">identifiers</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.interaction_types_by_data_model">
+<span class="sig-name descname"><span class="pre">interaction_types_by_data_model</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.interaction_types_by_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves interaction types matching the criteria.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.interaction_types_by_interaction_type">
+<span class="sig-name descname"><span class="pre">interaction_types_by_interaction_type</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.interaction_types_by_interaction_type" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves interaction types matching the criteria.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.interaction_types_by_interaction_type_and_data_model">
+<span class="sig-name descname"><span class="pre">interaction_types_by_interaction_type_and_data_model</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.interaction_types_by_interaction_type_and_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves interaction types matching the criteria.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.interaction_types_by_interaction_type_and_data_model_and_resource">
+<span class="sig-name descname"><span class="pre">interaction_types_by_interaction_type_and_data_model_and_resource</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.interaction_types_by_interaction_type_and_data_model_and_resource" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves interaction types matching the criteria.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.interaction_types_by_reference">
+<span class="sig-name descname"><span class="pre">interaction_types_by_reference</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.interaction_types_by_reference" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves interaction types matching the criteria.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.interaction_types_by_resource">
+<span class="sig-name descname"><span class="pre">interaction_types_by_resource</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.interaction_types_by_resource" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves interaction types matching the criteria.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.interactions_0_by_data_model">
+<span class="sig-name descname"><span class="pre">interactions_0_by_data_model</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.interactions_0_by_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Returns unique interacting pairs without being aware of the direction.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.interactions_0_by_interaction_type">
+<span class="sig-name descname"><span class="pre">interactions_0_by_interaction_type</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.interactions_0_by_interaction_type" title="Link to this definition">§</a></dt>
+<dd><p>Returns unique interacting pairs without being aware of the direction.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.interactions_0_by_interaction_type_and_data_model">
+<span class="sig-name descname"><span class="pre">interactions_0_by_interaction_type_and_data_model</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.interactions_0_by_interaction_type_and_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Returns unique interacting pairs without being aware of the direction.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.interactions_0_by_interaction_type_and_data_model_and_resource">
+<span class="sig-name descname"><span class="pre">interactions_0_by_interaction_type_and_data_model_and_resource</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.interactions_0_by_interaction_type_and_data_model_and_resource" title="Link to this definition">§</a></dt>
+<dd><p>Returns unique interacting pairs without being aware of the direction.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.interactions_0_by_reference">
+<span class="sig-name descname"><span class="pre">interactions_0_by_reference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.interactions_0_by_reference" title="Link to this definition">§</a></dt>
+<dd><p>Returns unique interacting pairs without being aware of the direction.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.interactions_0_by_resource">
+<span class="sig-name descname"><span class="pre">interactions_0_by_resource</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.interactions_0_by_resource" title="Link to this definition">§</a></dt>
+<dd><p>Returns unique interacting pairs without being aware of the direction.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.interactions_by_data_model">
+<span class="sig-name descname"><span class="pre">interactions_by_data_model</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.interactions_by_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Returns one or two tuples of the interacting partners: one if only
+one direction, two if both directions match the query criteria.
+The tuple will be empty if no evidence matches the criteria.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>direction</strong> (<em>NontType</em><em>,</em><em>bool</em><em>,</em><em>tuple</em>) – If <cite>None</cite> both undirected and directed, if <cite>True</cite> only directed,
+if a <em>tuple</em> of entities only the interactions with that specific
+direction will be considered. Unless you set this parameter to
+<cite>True</cite> this method will return both directions if one or more
+undirected resources present.
+If <cite>False</cite>, only the undirected interactions will be considered,
+and if any resource annotates this interaction as undirected
+both directions will be returned. However the
+<code class="docutils literal notranslate"><span class="pre">count_interactions_undirected</span></code> method will return <cite>1</cite>
+in this case.</p></li>
+<li><p><strong>effect</strong> (<em>NoneType</em><em>,</em><em>bool</em><em>,</em><em>str</em>) – If <cite>None</cite> also interactions without effect, if <cite>True</cite> only
+the ones with any effect, if a string naming an effect only the
+interactions with that specific effect will be considered.</p></li>
+<li><p><strong>resources</strong> (<em>NontType</em><em>,</em><em>str</em><em>,</em><em>set</em>) – Optionally limit the query to one or more resources.</p></li>
+<li><p><strong>data_model</strong> (<em>NontType</em><em>,</em><em>str</em><em>,</em><em>set</em>) – Optionally limit the query to one or more data models e.g.
+<cite>activity_flow</cite>.</p></li>
+<li><p><strong>interaction_type</strong> (<em>NontType</em><em>,</em><em>str</em><em>,</em><em>set</em>) – Optionally limit the query to one or more interaction types
+e.g. <cite>PPI</cite>.</p></li>
+<li><p><strong>via</strong> (<em>NontType</em><em>,</em><em>bool</em><em>,</em><em>str</em><em>,</em><em>set</em>) – Optionally limit the query to certain secondary databases or
+if <cite>False</cite> consider only data from primary databases.</p></li>
+<li><p><strong>entity_type</strong> (<em>str</em>) – Molecule type for both of the entities.</p></li>
+<li><p><strong>source_entity_type</strong> (<em>str</em>) – Molecule type for the source entity.</p></li>
+<li><p><strong>target_entity_type</strong> (<em>str</em>) – Molecule type for the target entity.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.interactions_by_interaction_type">
+<span class="sig-name descname"><span class="pre">interactions_by_interaction_type</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.interactions_by_interaction_type" title="Link to this definition">§</a></dt>
+<dd><p>Returns one or two tuples of the interacting partners: one if only
+one direction, two if both directions match the query criteria.
+The tuple will be empty if no evidence matches the criteria.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>direction</strong> (<em>NontType</em><em>,</em><em>bool</em><em>,</em><em>tuple</em>) – If <cite>None</cite> both undirected and directed, if <cite>True</cite> only directed,
+if a <em>tuple</em> of entities only the interactions with that specific
+direction will be considered. Unless you set this parameter to
+<cite>True</cite> this method will return both directions if one or more
+undirected resources present.
+If <cite>False</cite>, only the undirected interactions will be considered,
+and if any resource annotates this interaction as undirected
+both directions will be returned. However the
+<code class="docutils literal notranslate"><span class="pre">count_interactions_undirected</span></code> method will return <cite>1</cite>
+in this case.</p></li>
+<li><p><strong>effect</strong> (<em>NoneType</em><em>,</em><em>bool</em><em>,</em><em>str</em>) – If <cite>None</cite> also interactions without effect, if <cite>True</cite> only
+the ones with any effect, if a string naming an effect only the
+interactions with that specific effect will be considered.</p></li>
+<li><p><strong>resources</strong> (<em>NontType</em><em>,</em><em>str</em><em>,</em><em>set</em>) – Optionally limit the query to one or more resources.</p></li>
+<li><p><strong>data_model</strong> (<em>NontType</em><em>,</em><em>str</em><em>,</em><em>set</em>) – Optionally limit the query to one or more data models e.g.
+<cite>activity_flow</cite>.</p></li>
+<li><p><strong>interaction_type</strong> (<em>NontType</em><em>,</em><em>str</em><em>,</em><em>set</em>) – Optionally limit the query to one or more interaction types
+e.g. <cite>PPI</cite>.</p></li>
+<li><p><strong>via</strong> (<em>NontType</em><em>,</em><em>bool</em><em>,</em><em>str</em><em>,</em><em>set</em>) – Optionally limit the query to certain secondary databases or
+if <cite>False</cite> consider only data from primary databases.</p></li>
+<li><p><strong>entity_type</strong> (<em>str</em>) – Molecule type for both of the entities.</p></li>
+<li><p><strong>source_entity_type</strong> (<em>str</em>) – Molecule type for the source entity.</p></li>
+<li><p><strong>target_entity_type</strong> (<em>str</em>) – Molecule type for the target entity.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.interactions_by_interaction_type_and_data_model">
+<span class="sig-name descname"><span class="pre">interactions_by_interaction_type_and_data_model</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.interactions_by_interaction_type_and_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Returns one or two tuples of the interacting partners: one if only
+one direction, two if both directions match the query criteria.
+The tuple will be empty if no evidence matches the criteria.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>direction</strong> (<em>NontType</em><em>,</em><em>bool</em><em>,</em><em>tuple</em>) – If <cite>None</cite> both undirected and directed, if <cite>True</cite> only directed,
+if a <em>tuple</em> of entities only the interactions with that specific
+direction will be considered. Unless you set this parameter to
+<cite>True</cite> this method will return both directions if one or more
+undirected resources present.
+If <cite>False</cite>, only the undirected interactions will be considered,
+and if any resource annotates this interaction as undirected
+both directions will be returned. However the
+<code class="docutils literal notranslate"><span class="pre">count_interactions_undirected</span></code> method will return <cite>1</cite>
+in this case.</p></li>
+<li><p><strong>effect</strong> (<em>NoneType</em><em>,</em><em>bool</em><em>,</em><em>str</em>) – If <cite>None</cite> also interactions without effect, if <cite>True</cite> only
+the ones with any effect, if a string naming an effect only the
+interactions with that specific effect will be considered.</p></li>
+<li><p><strong>resources</strong> (<em>NontType</em><em>,</em><em>str</em><em>,</em><em>set</em>) – Optionally limit the query to one or more resources.</p></li>
+<li><p><strong>data_model</strong> (<em>NontType</em><em>,</em><em>str</em><em>,</em><em>set</em>) – Optionally limit the query to one or more data models e.g.
+<cite>activity_flow</cite>.</p></li>
+<li><p><strong>interaction_type</strong> (<em>NontType</em><em>,</em><em>str</em><em>,</em><em>set</em>) – Optionally limit the query to one or more interaction types
+e.g. <cite>PPI</cite>.</p></li>
+<li><p><strong>via</strong> (<em>NontType</em><em>,</em><em>bool</em><em>,</em><em>str</em><em>,</em><em>set</em>) – Optionally limit the query to certain secondary databases or
+if <cite>False</cite> consider only data from primary databases.</p></li>
+<li><p><strong>entity_type</strong> (<em>str</em>) – Molecule type for both of the entities.</p></li>
+<li><p><strong>source_entity_type</strong> (<em>str</em>) – Molecule type for the source entity.</p></li>
+<li><p><strong>target_entity_type</strong> (<em>str</em>) – Molecule type for the target entity.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.interactions_by_interaction_type_and_data_model_and_resource">
+<span class="sig-name descname"><span class="pre">interactions_by_interaction_type_and_data_model_and_resource</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.interactions_by_interaction_type_and_data_model_and_resource" title="Link to this definition">§</a></dt>
+<dd><p>Returns one or two tuples of the interacting partners: one if only
+one direction, two if both directions match the query criteria.
+The tuple will be empty if no evidence matches the criteria.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>direction</strong> (<em>NontType</em><em>,</em><em>bool</em><em>,</em><em>tuple</em>) – If <cite>None</cite> both undirected and directed, if <cite>True</cite> only directed,
+if a <em>tuple</em> of entities only the interactions with that specific
+direction will be considered. Unless you set this parameter to
+<cite>True</cite> this method will return both directions if one or more
+undirected resources present.
+If <cite>False</cite>, only the undirected interactions will be considered,
+and if any resource annotates this interaction as undirected
+both directions will be returned. However the
+<code class="docutils literal notranslate"><span class="pre">count_interactions_undirected</span></code> method will return <cite>1</cite>
+in this case.</p></li>
+<li><p><strong>effect</strong> (<em>NoneType</em><em>,</em><em>bool</em><em>,</em><em>str</em>) – If <cite>None</cite> also interactions without effect, if <cite>True</cite> only
+the ones with any effect, if a string naming an effect only the
+interactions with that specific effect will be considered.</p></li>
+<li><p><strong>resources</strong> (<em>NontType</em><em>,</em><em>str</em><em>,</em><em>set</em>) – Optionally limit the query to one or more resources.</p></li>
+<li><p><strong>data_model</strong> (<em>NontType</em><em>,</em><em>str</em><em>,</em><em>set</em>) – Optionally limit the query to one or more data models e.g.
+<cite>activity_flow</cite>.</p></li>
+<li><p><strong>interaction_type</strong> (<em>NontType</em><em>,</em><em>str</em><em>,</em><em>set</em>) – Optionally limit the query to one or more interaction types
+e.g. <cite>PPI</cite>.</p></li>
+<li><p><strong>via</strong> (<em>NontType</em><em>,</em><em>bool</em><em>,</em><em>str</em><em>,</em><em>set</em>) – Optionally limit the query to certain secondary databases or
+if <cite>False</cite> consider only data from primary databases.</p></li>
+<li><p><strong>entity_type</strong> (<em>str</em>) – Molecule type for both of the entities.</p></li>
+<li><p><strong>source_entity_type</strong> (<em>str</em>) – Molecule type for the source entity.</p></li>
+<li><p><strong>target_entity_type</strong> (<em>str</em>) – Molecule type for the target entity.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.interactions_by_reference">
+<span class="sig-name descname"><span class="pre">interactions_by_reference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.interactions_by_reference" title="Link to this definition">§</a></dt>
+<dd><p>Returns one or two tuples of the interacting partners: one if only
+one direction, two if both directions match the query criteria.
+The tuple will be empty if no evidence matches the criteria.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>direction</strong> (<em>NontType</em><em>,</em><em>bool</em><em>,</em><em>tuple</em>) – If <cite>None</cite> both undirected and directed, if <cite>True</cite> only directed,
+if a <em>tuple</em> of entities only the interactions with that specific
+direction will be considered. Unless you set this parameter to
+<cite>True</cite> this method will return both directions if one or more
+undirected resources present.
+If <cite>False</cite>, only the undirected interactions will be considered,
+and if any resource annotates this interaction as undirected
+both directions will be returned. However the
+<code class="docutils literal notranslate"><span class="pre">count_interactions_undirected</span></code> method will return <cite>1</cite>
+in this case.</p></li>
+<li><p><strong>effect</strong> (<em>NoneType</em><em>,</em><em>bool</em><em>,</em><em>str</em>) – If <cite>None</cite> also interactions without effect, if <cite>True</cite> only
+the ones with any effect, if a string naming an effect only the
+interactions with that specific effect will be considered.</p></li>
+<li><p><strong>resources</strong> (<em>NontType</em><em>,</em><em>str</em><em>,</em><em>set</em>) – Optionally limit the query to one or more resources.</p></li>
+<li><p><strong>data_model</strong> (<em>NontType</em><em>,</em><em>str</em><em>,</em><em>set</em>) – Optionally limit the query to one or more data models e.g.
+<cite>activity_flow</cite>.</p></li>
+<li><p><strong>interaction_type</strong> (<em>NontType</em><em>,</em><em>str</em><em>,</em><em>set</em>) – Optionally limit the query to one or more interaction types
+e.g. <cite>PPI</cite>.</p></li>
+<li><p><strong>via</strong> (<em>NontType</em><em>,</em><em>bool</em><em>,</em><em>str</em><em>,</em><em>set</em>) – Optionally limit the query to certain secondary databases or
+if <cite>False</cite> consider only data from primary databases.</p></li>
+<li><p><strong>entity_type</strong> (<em>str</em>) – Molecule type for both of the entities.</p></li>
+<li><p><strong>source_entity_type</strong> (<em>str</em>) – Molecule type for the source entity.</p></li>
+<li><p><strong>target_entity_type</strong> (<em>str</em>) – Molecule type for the target entity.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.interactions_by_resource">
+<span class="sig-name descname"><span class="pre">interactions_by_resource</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.interactions_by_resource" title="Link to this definition">§</a></dt>
+<dd><p>Returns one or two tuples of the interacting partners: one if only
+one direction, two if both directions match the query criteria.
+The tuple will be empty if no evidence matches the criteria.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>direction</strong> (<em>NontType</em><em>,</em><em>bool</em><em>,</em><em>tuple</em>) – If <cite>None</cite> both undirected and directed, if <cite>True</cite> only directed,
+if a <em>tuple</em> of entities only the interactions with that specific
+direction will be considered. Unless you set this parameter to
+<cite>True</cite> this method will return both directions if one or more
+undirected resources present.
+If <cite>False</cite>, only the undirected interactions will be considered,
+and if any resource annotates this interaction as undirected
+both directions will be returned. However the
+<code class="docutils literal notranslate"><span class="pre">count_interactions_undirected</span></code> method will return <cite>1</cite>
+in this case.</p></li>
+<li><p><strong>effect</strong> (<em>NoneType</em><em>,</em><em>bool</em><em>,</em><em>str</em>) – If <cite>None</cite> also interactions without effect, if <cite>True</cite> only
+the ones with any effect, if a string naming an effect only the
+interactions with that specific effect will be considered.</p></li>
+<li><p><strong>resources</strong> (<em>NontType</em><em>,</em><em>str</em><em>,</em><em>set</em>) – Optionally limit the query to one or more resources.</p></li>
+<li><p><strong>data_model</strong> (<em>NontType</em><em>,</em><em>str</em><em>,</em><em>set</em>) – Optionally limit the query to one or more data models e.g.
+<cite>activity_flow</cite>.</p></li>
+<li><p><strong>interaction_type</strong> (<em>NontType</em><em>,</em><em>str</em><em>,</em><em>set</em>) – Optionally limit the query to one or more interaction types
+e.g. <cite>PPI</cite>.</p></li>
+<li><p><strong>via</strong> (<em>NontType</em><em>,</em><em>bool</em><em>,</em><em>str</em><em>,</em><em>set</em>) – Optionally limit the query to certain secondary databases or
+if <cite>False</cite> consider only data from primary databases.</p></li>
+<li><p><strong>entity_type</strong> (<em>str</em>) – Molecule type for both of the entities.</p></li>
+<li><p><strong>source_entity_type</strong> (<em>str</em>) – Molecule type for the source entity.</p></li>
+<li><p><strong>target_entity_type</strong> (<em>str</em>) – Molecule type for the target entity.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.interactions_directed_by_data_model">
+<span class="sig-name descname"><span class="pre">interactions_directed_by_data_model</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.interactions_directed_by_data_model" title="Link to this definition">§</a></dt>
+<dd><dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>kwargs:</dt><dd><p>See the docs of method <code class="docutils literal notranslate"><span class="pre">get_interactions</span></code>.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.interactions_directed_by_interaction_type">
+<span class="sig-name descname"><span class="pre">interactions_directed_by_interaction_type</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.interactions_directed_by_interaction_type" title="Link to this definition">§</a></dt>
+<dd><dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>kwargs:</dt><dd><p>See the docs of method <code class="docutils literal notranslate"><span class="pre">get_interactions</span></code>.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.interactions_directed_by_interaction_type_and_data_model">
+<span class="sig-name descname"><span class="pre">interactions_directed_by_interaction_type_and_data_model</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.interactions_directed_by_interaction_type_and_data_model" title="Link to this definition">§</a></dt>
+<dd><dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>kwargs:</dt><dd><p>See the docs of method <code class="docutils literal notranslate"><span class="pre">get_interactions</span></code>.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.interactions_directed_by_interaction_type_and_data_model_and_resource">
+<span class="sig-name descname"><span class="pre">interactions_directed_by_interaction_type_and_data_model_and_resource</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.interactions_directed_by_interaction_type_and_data_model_and_resource" title="Link to this definition">§</a></dt>
+<dd><dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>kwargs:</dt><dd><p>See the docs of method <code class="docutils literal notranslate"><span class="pre">get_interactions</span></code>.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.interactions_directed_by_reference">
+<span class="sig-name descname"><span class="pre">interactions_directed_by_reference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.interactions_directed_by_reference" title="Link to this definition">§</a></dt>
+<dd><dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>kwargs:</dt><dd><p>See the docs of method <code class="docutils literal notranslate"><span class="pre">get_interactions</span></code>.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.interactions_directed_by_resource">
+<span class="sig-name descname"><span class="pre">interactions_directed_by_resource</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.interactions_directed_by_resource" title="Link to this definition">§</a></dt>
+<dd><dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>kwargs:</dt><dd><p>See the docs of method <code class="docutils literal notranslate"><span class="pre">get_interactions</span></code>.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.interactions_mutual_by_data_model">
+<span class="sig-name descname"><span class="pre">interactions_mutual_by_data_model</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.interactions_mutual_by_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Note: undirected interactions does not count as mutual but only
+interactions with explicit direction information for both directions.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>kwargs:</dt><dd><p>See the docs of method <code class="docutils literal notranslate"><span class="pre">get_interactions</span></code>.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.interactions_mutual_by_interaction_type">
+<span class="sig-name descname"><span class="pre">interactions_mutual_by_interaction_type</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.interactions_mutual_by_interaction_type" title="Link to this definition">§</a></dt>
+<dd><p>Note: undirected interactions does not count as mutual but only
+interactions with explicit direction information for both directions.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>kwargs:</dt><dd><p>See the docs of method <code class="docutils literal notranslate"><span class="pre">get_interactions</span></code>.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.interactions_mutual_by_interaction_type_and_data_model">
+<span class="sig-name descname"><span class="pre">interactions_mutual_by_interaction_type_and_data_model</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.interactions_mutual_by_interaction_type_and_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Note: undirected interactions does not count as mutual but only
+interactions with explicit direction information for both directions.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>kwargs:</dt><dd><p>See the docs of method <code class="docutils literal notranslate"><span class="pre">get_interactions</span></code>.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.interactions_mutual_by_interaction_type_and_data_model_and_resource">
+<span class="sig-name descname"><span class="pre">interactions_mutual_by_interaction_type_and_data_model_and_resource</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.interactions_mutual_by_interaction_type_and_data_model_and_resource" title="Link to this definition">§</a></dt>
+<dd><p>Note: undirected interactions does not count as mutual but only
+interactions with explicit direction information for both directions.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>kwargs:</dt><dd><p>See the docs of method <code class="docutils literal notranslate"><span class="pre">get_interactions</span></code>.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.interactions_mutual_by_reference">
+<span class="sig-name descname"><span class="pre">interactions_mutual_by_reference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.interactions_mutual_by_reference" title="Link to this definition">§</a></dt>
+<dd><p>Note: undirected interactions does not count as mutual but only
+interactions with explicit direction information for both directions.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>kwargs:</dt><dd><p>See the docs of method <code class="docutils literal notranslate"><span class="pre">get_interactions</span></code>.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.interactions_mutual_by_resource">
+<span class="sig-name descname"><span class="pre">interactions_mutual_by_resource</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.interactions_mutual_by_resource" title="Link to this definition">§</a></dt>
+<dd><p>Note: undirected interactions does not count as mutual but only
+interactions with explicit direction information for both directions.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>kwargs:</dt><dd><p>See the docs of method <code class="docutils literal notranslate"><span class="pre">get_interactions</span></code>.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.interactions_negative_by_data_model">
+<span class="sig-name descname"><span class="pre">interactions_negative_by_data_model</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.interactions_negative_by_data_model" title="Link to this definition">§</a></dt>
+<dd><dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>kwargs:</dt><dd><p>See the docs of method <code class="docutils literal notranslate"><span class="pre">get_interactions</span></code>.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.interactions_negative_by_interaction_type">
+<span class="sig-name descname"><span class="pre">interactions_negative_by_interaction_type</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.interactions_negative_by_interaction_type" title="Link to this definition">§</a></dt>
+<dd><dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>kwargs:</dt><dd><p>See the docs of method <code class="docutils literal notranslate"><span class="pre">get_interactions</span></code>.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.interactions_negative_by_interaction_type_and_data_model">
+<span class="sig-name descname"><span class="pre">interactions_negative_by_interaction_type_and_data_model</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.interactions_negative_by_interaction_type_and_data_model" title="Link to this definition">§</a></dt>
+<dd><dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>kwargs:</dt><dd><p>See the docs of method <code class="docutils literal notranslate"><span class="pre">get_interactions</span></code>.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.interactions_negative_by_interaction_type_and_data_model_and_resource">
+<span class="sig-name descname"><span class="pre">interactions_negative_by_interaction_type_and_data_model_and_resource</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.interactions_negative_by_interaction_type_and_data_model_and_resource" title="Link to this definition">§</a></dt>
+<dd><dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>kwargs:</dt><dd><p>See the docs of method <code class="docutils literal notranslate"><span class="pre">get_interactions</span></code>.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.interactions_negative_by_reference">
+<span class="sig-name descname"><span class="pre">interactions_negative_by_reference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.interactions_negative_by_reference" title="Link to this definition">§</a></dt>
+<dd><dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>kwargs:</dt><dd><p>See the docs of method <code class="docutils literal notranslate"><span class="pre">get_interactions</span></code>.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.interactions_negative_by_resource">
+<span class="sig-name descname"><span class="pre">interactions_negative_by_resource</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.interactions_negative_by_resource" title="Link to this definition">§</a></dt>
+<dd><dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>kwargs:</dt><dd><p>See the docs of method <code class="docutils literal notranslate"><span class="pre">get_interactions</span></code>.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.interactions_non_directed_0_by_data_model">
+<span class="sig-name descname"><span class="pre">interactions_non_directed_0_by_data_model</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.interactions_non_directed_0_by_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Only the undirected interactions will be considered, if any resource
+annotates this interaction as undirected and none as directed, the
+interacting pair as a sorted tuple will be returned inside a one
+element tuple.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>kwargs:</dt><dd><p>See the docs of method <code class="docutils literal notranslate"><span class="pre">get_interactions</span></code>.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.interactions_non_directed_0_by_interaction_type">
+<span class="sig-name descname"><span class="pre">interactions_non_directed_0_by_interaction_type</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.interactions_non_directed_0_by_interaction_type" title="Link to this definition">§</a></dt>
+<dd><p>Only the undirected interactions will be considered, if any resource
+annotates this interaction as undirected and none as directed, the
+interacting pair as a sorted tuple will be returned inside a one
+element tuple.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>kwargs:</dt><dd><p>See the docs of method <code class="docutils literal notranslate"><span class="pre">get_interactions</span></code>.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.interactions_non_directed_0_by_interaction_type_and_data_model">
+<span class="sig-name descname"><span class="pre">interactions_non_directed_0_by_interaction_type_and_data_model</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.interactions_non_directed_0_by_interaction_type_and_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Only the undirected interactions will be considered, if any resource
+annotates this interaction as undirected and none as directed, the
+interacting pair as a sorted tuple will be returned inside a one
+element tuple.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>kwargs:</dt><dd><p>See the docs of method <code class="docutils literal notranslate"><span class="pre">get_interactions</span></code>.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.interactions_non_directed_0_by_interaction_type_and_data_model_and_resource">
+<span class="sig-name descname"><span class="pre">interactions_non_directed_0_by_interaction_type_and_data_model_and_resource</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.interactions_non_directed_0_by_interaction_type_and_data_model_and_resource" title="Link to this definition">§</a></dt>
+<dd><p>Only the undirected interactions will be considered, if any resource
+annotates this interaction as undirected and none as directed, the
+interacting pair as a sorted tuple will be returned inside a one
+element tuple.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>kwargs:</dt><dd><p>See the docs of method <code class="docutils literal notranslate"><span class="pre">get_interactions</span></code>.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.interactions_non_directed_0_by_reference">
+<span class="sig-name descname"><span class="pre">interactions_non_directed_0_by_reference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.interactions_non_directed_0_by_reference" title="Link to this definition">§</a></dt>
+<dd><p>Only the undirected interactions will be considered, if any resource
+annotates this interaction as undirected and none as directed, the
+interacting pair as a sorted tuple will be returned inside a one
+element tuple.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>kwargs:</dt><dd><p>See the docs of method <code class="docutils literal notranslate"><span class="pre">get_interactions</span></code>.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.interactions_non_directed_0_by_resource">
+<span class="sig-name descname"><span class="pre">interactions_non_directed_0_by_resource</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.interactions_non_directed_0_by_resource" title="Link to this definition">§</a></dt>
+<dd><p>Only the undirected interactions will be considered, if any resource
+annotates this interaction as undirected and none as directed, the
+interacting pair as a sorted tuple will be returned inside a one
+element tuple.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>kwargs:</dt><dd><p>See the docs of method <code class="docutils literal notranslate"><span class="pre">get_interactions</span></code>.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.interactions_non_directed_by_data_model">
+<span class="sig-name descname"><span class="pre">interactions_non_directed_by_data_model</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.interactions_non_directed_by_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Only the undirected interactions will be considered, if any resource
+annotates this interaction as undirected both directions will be
+returned, but only if no resource provide direction. However
+the <code class="docutils literal notranslate"><span class="pre">count_interactions_non_directed</span></code> method will return <cite>1</cite> in
+this case.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>kwargs:</dt><dd><p>See the docs of method <code class="docutils literal notranslate"><span class="pre">get_interactions</span></code>.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.interactions_non_directed_by_interaction_type">
+<span class="sig-name descname"><span class="pre">interactions_non_directed_by_interaction_type</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.interactions_non_directed_by_interaction_type" title="Link to this definition">§</a></dt>
+<dd><p>Only the undirected interactions will be considered, if any resource
+annotates this interaction as undirected both directions will be
+returned, but only if no resource provide direction. However
+the <code class="docutils literal notranslate"><span class="pre">count_interactions_non_directed</span></code> method will return <cite>1</cite> in
+this case.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>kwargs:</dt><dd><p>See the docs of method <code class="docutils literal notranslate"><span class="pre">get_interactions</span></code>.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.interactions_non_directed_by_interaction_type_and_data_model">
+<span class="sig-name descname"><span class="pre">interactions_non_directed_by_interaction_type_and_data_model</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.interactions_non_directed_by_interaction_type_and_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Only the undirected interactions will be considered, if any resource
+annotates this interaction as undirected both directions will be
+returned, but only if no resource provide direction. However
+the <code class="docutils literal notranslate"><span class="pre">count_interactions_non_directed</span></code> method will return <cite>1</cite> in
+this case.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>kwargs:</dt><dd><p>See the docs of method <code class="docutils literal notranslate"><span class="pre">get_interactions</span></code>.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.interactions_non_directed_by_interaction_type_and_data_model_and_resource">
+<span class="sig-name descname"><span class="pre">interactions_non_directed_by_interaction_type_and_data_model_and_resource</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.interactions_non_directed_by_interaction_type_and_data_model_and_resource" title="Link to this definition">§</a></dt>
+<dd><p>Only the undirected interactions will be considered, if any resource
+annotates this interaction as undirected both directions will be
+returned, but only if no resource provide direction. However
+the <code class="docutils literal notranslate"><span class="pre">count_interactions_non_directed</span></code> method will return <cite>1</cite> in
+this case.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>kwargs:</dt><dd><p>See the docs of method <code class="docutils literal notranslate"><span class="pre">get_interactions</span></code>.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.interactions_non_directed_by_reference">
+<span class="sig-name descname"><span class="pre">interactions_non_directed_by_reference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.interactions_non_directed_by_reference" title="Link to this definition">§</a></dt>
+<dd><p>Only the undirected interactions will be considered, if any resource
+annotates this interaction as undirected both directions will be
+returned, but only if no resource provide direction. However
+the <code class="docutils literal notranslate"><span class="pre">count_interactions_non_directed</span></code> method will return <cite>1</cite> in
+this case.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>kwargs:</dt><dd><p>See the docs of method <code class="docutils literal notranslate"><span class="pre">get_interactions</span></code>.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.interactions_non_directed_by_resource">
+<span class="sig-name descname"><span class="pre">interactions_non_directed_by_resource</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.interactions_non_directed_by_resource" title="Link to this definition">§</a></dt>
+<dd><p>Only the undirected interactions will be considered, if any resource
+annotates this interaction as undirected both directions will be
+returned, but only if no resource provide direction. However
+the <code class="docutils literal notranslate"><span class="pre">count_interactions_non_directed</span></code> method will return <cite>1</cite> in
+this case.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>kwargs:</dt><dd><p>See the docs of method <code class="docutils literal notranslate"><span class="pre">get_interactions</span></code>.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.interactions_positive_by_data_model">
+<span class="sig-name descname"><span class="pre">interactions_positive_by_data_model</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.interactions_positive_by_data_model" title="Link to this definition">§</a></dt>
+<dd><dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>kwargs:</dt><dd><p>See the docs of method <code class="docutils literal notranslate"><span class="pre">get_interactions</span></code>.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.interactions_positive_by_interaction_type">
+<span class="sig-name descname"><span class="pre">interactions_positive_by_interaction_type</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.interactions_positive_by_interaction_type" title="Link to this definition">§</a></dt>
+<dd><dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>kwargs:</dt><dd><p>See the docs of method <code class="docutils literal notranslate"><span class="pre">get_interactions</span></code>.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.interactions_positive_by_interaction_type_and_data_model">
+<span class="sig-name descname"><span class="pre">interactions_positive_by_interaction_type_and_data_model</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.interactions_positive_by_interaction_type_and_data_model" title="Link to this definition">§</a></dt>
+<dd><dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>kwargs:</dt><dd><p>See the docs of method <code class="docutils literal notranslate"><span class="pre">get_interactions</span></code>.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.interactions_positive_by_interaction_type_and_data_model_and_resource">
+<span class="sig-name descname"><span class="pre">interactions_positive_by_interaction_type_and_data_model_and_resource</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.interactions_positive_by_interaction_type_and_data_model_and_resource" title="Link to this definition">§</a></dt>
+<dd><dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>kwargs:</dt><dd><p>See the docs of method <code class="docutils literal notranslate"><span class="pre">get_interactions</span></code>.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.interactions_positive_by_reference">
+<span class="sig-name descname"><span class="pre">interactions_positive_by_reference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.interactions_positive_by_reference" title="Link to this definition">§</a></dt>
+<dd><dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>kwargs:</dt><dd><p>See the docs of method <code class="docutils literal notranslate"><span class="pre">get_interactions</span></code>.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.interactions_positive_by_resource">
+<span class="sig-name descname"><span class="pre">interactions_positive_by_resource</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.interactions_positive_by_resource" title="Link to this definition">§</a></dt>
+<dd><dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>kwargs:</dt><dd><p>See the docs of method <code class="docutils literal notranslate"><span class="pre">get_interactions</span></code>.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.interactions_signed_by_data_model">
+<span class="sig-name descname"><span class="pre">interactions_signed_by_data_model</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.interactions_signed_by_data_model" title="Link to this definition">§</a></dt>
+<dd><dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>kwargs:</dt><dd><p>See the docs of method <code class="docutils literal notranslate"><span class="pre">get_interactions</span></code>.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.interactions_signed_by_interaction_type">
+<span class="sig-name descname"><span class="pre">interactions_signed_by_interaction_type</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.interactions_signed_by_interaction_type" title="Link to this definition">§</a></dt>
+<dd><dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>kwargs:</dt><dd><p>See the docs of method <code class="docutils literal notranslate"><span class="pre">get_interactions</span></code>.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.interactions_signed_by_interaction_type_and_data_model">
+<span class="sig-name descname"><span class="pre">interactions_signed_by_interaction_type_and_data_model</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.interactions_signed_by_interaction_type_and_data_model" title="Link to this definition">§</a></dt>
+<dd><dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>kwargs:</dt><dd><p>See the docs of method <code class="docutils literal notranslate"><span class="pre">get_interactions</span></code>.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.interactions_signed_by_interaction_type_and_data_model_and_resource">
+<span class="sig-name descname"><span class="pre">interactions_signed_by_interaction_type_and_data_model_and_resource</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.interactions_signed_by_interaction_type_and_data_model_and_resource" title="Link to this definition">§</a></dt>
+<dd><dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>kwargs:</dt><dd><p>See the docs of method <code class="docutils literal notranslate"><span class="pre">get_interactions</span></code>.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.interactions_signed_by_reference">
+<span class="sig-name descname"><span class="pre">interactions_signed_by_reference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.interactions_signed_by_reference" title="Link to this definition">§</a></dt>
+<dd><dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>kwargs:</dt><dd><p>See the docs of method <code class="docutils literal notranslate"><span class="pre">get_interactions</span></code>.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.interactions_signed_by_resource">
+<span class="sig-name descname"><span class="pre">interactions_signed_by_resource</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.interactions_signed_by_resource" title="Link to this definition">§</a></dt>
+<dd><dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>kwargs:</dt><dd><p>See the docs of method <code class="docutils literal notranslate"><span class="pre">get_interactions</span></code>.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.interactions_undirected_0_by_data_model">
+<span class="sig-name descname"><span class="pre">interactions_undirected_0_by_data_model</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.interactions_undirected_0_by_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Only the undirected interactions will be considered, if any resource
+annotates this interaction as undirected the interacting pair as
+a sorted tuple will be returned inside a one element tuple.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>kwargs:</dt><dd><p>See the docs of method <code class="docutils literal notranslate"><span class="pre">get_interactions</span></code>.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.interactions_undirected_0_by_interaction_type">
+<span class="sig-name descname"><span class="pre">interactions_undirected_0_by_interaction_type</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.interactions_undirected_0_by_interaction_type" title="Link to this definition">§</a></dt>
+<dd><p>Only the undirected interactions will be considered, if any resource
+annotates this interaction as undirected the interacting pair as
+a sorted tuple will be returned inside a one element tuple.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>kwargs:</dt><dd><p>See the docs of method <code class="docutils literal notranslate"><span class="pre">get_interactions</span></code>.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.interactions_undirected_0_by_interaction_type_and_data_model">
+<span class="sig-name descname"><span class="pre">interactions_undirected_0_by_interaction_type_and_data_model</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.interactions_undirected_0_by_interaction_type_and_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Only the undirected interactions will be considered, if any resource
+annotates this interaction as undirected the interacting pair as
+a sorted tuple will be returned inside a one element tuple.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>kwargs:</dt><dd><p>See the docs of method <code class="docutils literal notranslate"><span class="pre">get_interactions</span></code>.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.interactions_undirected_0_by_interaction_type_and_data_model_and_resource">
+<span class="sig-name descname"><span class="pre">interactions_undirected_0_by_interaction_type_and_data_model_and_resource</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.interactions_undirected_0_by_interaction_type_and_data_model_and_resource" title="Link to this definition">§</a></dt>
+<dd><p>Only the undirected interactions will be considered, if any resource
+annotates this interaction as undirected the interacting pair as
+a sorted tuple will be returned inside a one element tuple.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>kwargs:</dt><dd><p>See the docs of method <code class="docutils literal notranslate"><span class="pre">get_interactions</span></code>.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.interactions_undirected_0_by_reference">
+<span class="sig-name descname"><span class="pre">interactions_undirected_0_by_reference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.interactions_undirected_0_by_reference" title="Link to this definition">§</a></dt>
+<dd><p>Only the undirected interactions will be considered, if any resource
+annotates this interaction as undirected the interacting pair as
+a sorted tuple will be returned inside a one element tuple.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>kwargs:</dt><dd><p>See the docs of method <code class="docutils literal notranslate"><span class="pre">get_interactions</span></code>.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.interactions_undirected_0_by_resource">
+<span class="sig-name descname"><span class="pre">interactions_undirected_0_by_resource</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.interactions_undirected_0_by_resource" title="Link to this definition">§</a></dt>
+<dd><p>Only the undirected interactions will be considered, if any resource
+annotates this interaction as undirected the interacting pair as
+a sorted tuple will be returned inside a one element tuple.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>kwargs:</dt><dd><p>See the docs of method <code class="docutils literal notranslate"><span class="pre">get_interactions</span></code>.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.interactions_undirected_by_data_model">
+<span class="sig-name descname"><span class="pre">interactions_undirected_by_data_model</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.interactions_undirected_by_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Only the undirected interactions will be considered, if any resource
+annotates this interaction as undirected both directions will be
+returned, no matter if certain resources provide direction. However
+the <code class="docutils literal notranslate"><span class="pre">count_interactions_undirected</span></code> method will return <cite>1</cite> in this
+case.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>kwargs:</dt><dd><p>See the docs of method <code class="docutils literal notranslate"><span class="pre">get_interactions</span></code>.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.interactions_undirected_by_interaction_type">
+<span class="sig-name descname"><span class="pre">interactions_undirected_by_interaction_type</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.interactions_undirected_by_interaction_type" title="Link to this definition">§</a></dt>
+<dd><p>Only the undirected interactions will be considered, if any resource
+annotates this interaction as undirected both directions will be
+returned, no matter if certain resources provide direction. However
+the <code class="docutils literal notranslate"><span class="pre">count_interactions_undirected</span></code> method will return <cite>1</cite> in this
+case.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>kwargs:</dt><dd><p>See the docs of method <code class="docutils literal notranslate"><span class="pre">get_interactions</span></code>.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.interactions_undirected_by_interaction_type_and_data_model">
+<span class="sig-name descname"><span class="pre">interactions_undirected_by_interaction_type_and_data_model</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.interactions_undirected_by_interaction_type_and_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Only the undirected interactions will be considered, if any resource
+annotates this interaction as undirected both directions will be
+returned, no matter if certain resources provide direction. However
+the <code class="docutils literal notranslate"><span class="pre">count_interactions_undirected</span></code> method will return <cite>1</cite> in this
+case.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>kwargs:</dt><dd><p>See the docs of method <code class="docutils literal notranslate"><span class="pre">get_interactions</span></code>.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.interactions_undirected_by_interaction_type_and_data_model_and_resource">
+<span class="sig-name descname"><span class="pre">interactions_undirected_by_interaction_type_and_data_model_and_resource</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.interactions_undirected_by_interaction_type_and_data_model_and_resource" title="Link to this definition">§</a></dt>
+<dd><p>Only the undirected interactions will be considered, if any resource
+annotates this interaction as undirected both directions will be
+returned, no matter if certain resources provide direction. However
+the <code class="docutils literal notranslate"><span class="pre">count_interactions_undirected</span></code> method will return <cite>1</cite> in this
+case.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>kwargs:</dt><dd><p>See the docs of method <code class="docutils literal notranslate"><span class="pre">get_interactions</span></code>.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.interactions_undirected_by_reference">
+<span class="sig-name descname"><span class="pre">interactions_undirected_by_reference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.interactions_undirected_by_reference" title="Link to this definition">§</a></dt>
+<dd><p>Only the undirected interactions will be considered, if any resource
+annotates this interaction as undirected both directions will be
+returned, no matter if certain resources provide direction. However
+the <code class="docutils literal notranslate"><span class="pre">count_interactions_undirected</span></code> method will return <cite>1</cite> in this
+case.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>kwargs:</dt><dd><p>See the docs of method <code class="docutils literal notranslate"><span class="pre">get_interactions</span></code>.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.interactions_undirected_by_resource">
+<span class="sig-name descname"><span class="pre">interactions_undirected_by_resource</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.interactions_undirected_by_resource" title="Link to this definition">§</a></dt>
+<dd><p>Only the undirected interactions will be considered, if any resource
+annotates this interaction as undirected both directions will be
+returned, no matter if certain resources provide direction. However
+the <code class="docutils literal notranslate"><span class="pre">count_interactions_undirected</span></code> method will return <cite>1</cite> in this
+case.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>kwargs:</dt><dd><p>See the docs of method <code class="docutils literal notranslate"><span class="pre">get_interactions</span></code>.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.is_directed">
+<span class="sig-name descname"><span class="pre">is_directed</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/interaction.html#Interaction.is_directed"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.interaction.Interaction.is_directed" title="Link to this definition">§</a></dt>
+<dd><p>Checks if edge has any directionality information.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Returns<span class="colon">:</span></dt>
+<dd class="field-odd"><p>(<em>bool</em>) – Returns <code class="docutils literal notranslate"><span class="pre">True</span></code> if any of the <code class="xref py py-attr docutils literal notranslate"><span class="pre">dirs</span></code>
+attribute values is <code class="docutils literal notranslate"><span class="pre">True</span></code> (except <code class="docutils literal notranslate"><span class="pre">'undirected'</span></code>),
+<code class="docutils literal notranslate"><span class="pre">False</span></code> otherwise.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.is_directed_by_resources">
+<span class="sig-name descname"><span class="pre">is_directed_by_resources</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/interaction.html#Interaction.is_directed_by_resources"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.interaction.Interaction.is_directed_by_resources" title="Link to this definition">§</a></dt>
+<dd><p>Checks if edge has any directionality information from some
+resource(s).</p>
+<dl class="field-list simple">
+<dt class="field-odd">Returns<span class="colon">:</span></dt>
+<dd class="field-odd"><p>(<em>bool</em>) – Returns <code class="docutils literal notranslate"><span class="pre">True</span></code> if any of the <code class="xref py py-attr docutils literal notranslate"><span class="pre">dirs</span></code>
+attribute values is <code class="docutils literal notranslate"><span class="pre">True</span></code> (except <code class="docutils literal notranslate"><span class="pre">'undirected'</span></code>),
+<code class="docutils literal notranslate"><span class="pre">False</span></code> otherwise.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.is_inhibition">
+<span class="sig-name descname"><span class="pre">is_inhibition</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">direction</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/interaction.html#Interaction.is_inhibition"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.interaction.Interaction.is_inhibition" title="Link to this definition">§</a></dt>
+<dd><p>Checks if any (or for a specific <em>direction</em>) interaction is
+inhibition (negative interaction).</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><p><strong>direction</strong> (<em>tuple</em>) – Optional, <code class="docutils literal notranslate"><span class="pre">None</span></code> by default. If specified, checks the
+<code class="xref py py-attr docutils literal notranslate"><span class="pre">negative</span></code> attribute of that specific
+directionality. If not specified, checks both.</p>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p>(<em>bool</em>) – <code class="docutils literal notranslate"><span class="pre">True</span></code> if any interaction (or the specified
+<em>direction</em>) is inhibitory (negative).</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.is_loop">
+<span class="sig-name descname"><span class="pre">is_loop</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/interaction.html#Interaction.is_loop"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.interaction.Interaction.is_loop" title="Link to this definition">§</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Returns<span class="colon">:</span></dt>
+<dd class="field-odd"><p></p>
+</dd>
+</dl>
+<p><code class="docutils literal notranslate"><span class="pre">True</span></code> if the interaction is a loop edge i.e. its endpoints are the
+same node.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.is_mutual">
+<span class="sig-name descname"><span class="pre">is_mutual</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/interaction.html#Interaction.is_mutual"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.interaction.Interaction.is_mutual" title="Link to this definition">§</a></dt>
+<dd><p>Note: undirected interactions does not count as mutual but only
+interactions with explicit direction information for both directions.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>kwargs:</dt><dd><p>See the docs of method <code class="docutils literal notranslate"><span class="pre">get_interactions</span></code>.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.is_mutual_by_resources">
+<span class="sig-name descname"><span class="pre">is_mutual_by_resources</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/interaction.html#Interaction.is_mutual_by_resources"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.interaction.Interaction.is_mutual_by_resources" title="Link to this definition">§</a></dt>
+<dd><p>Checks if the edge has mutual directions (both A–&gt;B and B–&gt;A)
+according to some resource(s).</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.is_stimulation">
+<span class="sig-name descname"><span class="pre">is_stimulation</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">direction</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/interaction.html#Interaction.is_stimulation"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.interaction.Interaction.is_stimulation" title="Link to this definition">§</a></dt>
+<dd><p>Checks if any (or for a specific <em>direction</em>) interaction is
+activation (positive interaction).</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><p><strong>direction</strong> (<em>tuple</em>) – Optional, <code class="docutils literal notranslate"><span class="pre">None</span></code> by default. If specified, checks the
+<code class="xref py py-attr docutils literal notranslate"><span class="pre">positive</span></code> attribute of that specific
+directionality. If not specified, checks both.</p>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p>(<em>bool</em>) – <code class="docutils literal notranslate"><span class="pre">True</span></code> if any interaction (or the specified
+<em>direction</em>) is activatory (positive).</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.iter_evidences">
+<span class="sig-name descname"><span class="pre">iter_evidences</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">this_direction</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">direction</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/interaction.html#Interaction.iter_evidences"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.interaction.Interaction.iter_evidences" title="Link to this definition">§</a></dt>
+<dd><p>Selects and yields evidence collections matching the direction and
+effect criteria.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.iter_match_evidences">
+<span class="sig-name descname"><span class="pre">iter_match_evidences</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">this_direction</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">direction</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">datasets</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/interaction.html#Interaction.iter_match_evidences"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.interaction.Interaction.iter_match_evidences" title="Link to this definition">§</a></dt>
+<dd><p>Selects the evidence collections matching the direction and effect
+criteria and yields collections matching the evidence criteria.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.labels_by_data_model">
+<span class="sig-name descname"><span class="pre">labels_by_data_model</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.labels_by_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the entities involved in interactions matching the criteria.
+It either returns both interacting entities in a <em>set</em> or an empty
+<em>set</em>. This may not sound so useful at the level of this object but
+becomes more useful once we want to collect entities having certain
+kind of interactions across a series of <cite>Interaction</cite> objects.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>entity_type</strong> (<em>str</em>) – The type of the molecular entity. Possible values: <cite>protein</cite>,
+<cite>complex</cite>, <cite>mirna</cite>, <cite>small_molecule</cite>.</p></li>
+<li><p><strong>return_type</strong> (<em>str</em>) – The type of values to return. Default is
+py:class:<code class="docutils literal notranslate"><span class="pre">pypath.entity.Entity</span></code> objects, alternatives are
+<code class="docutils literal notranslate"><span class="pre">labels</span></code>  <code class="docutils literal notranslate"><span class="pre">identifiers</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.labels_by_interaction_type">
+<span class="sig-name descname"><span class="pre">labels_by_interaction_type</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.labels_by_interaction_type" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the entities involved in interactions matching the criteria.
+It either returns both interacting entities in a <em>set</em> or an empty
+<em>set</em>. This may not sound so useful at the level of this object but
+becomes more useful once we want to collect entities having certain
+kind of interactions across a series of <cite>Interaction</cite> objects.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>entity_type</strong> (<em>str</em>) – The type of the molecular entity. Possible values: <cite>protein</cite>,
+<cite>complex</cite>, <cite>mirna</cite>, <cite>small_molecule</cite>.</p></li>
+<li><p><strong>return_type</strong> (<em>str</em>) – The type of values to return. Default is
+py:class:<code class="docutils literal notranslate"><span class="pre">pypath.entity.Entity</span></code> objects, alternatives are
+<code class="docutils literal notranslate"><span class="pre">labels</span></code>  <code class="docutils literal notranslate"><span class="pre">identifiers</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.labels_by_interaction_type_and_data_model">
+<span class="sig-name descname"><span class="pre">labels_by_interaction_type_and_data_model</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.labels_by_interaction_type_and_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the entities involved in interactions matching the criteria.
+It either returns both interacting entities in a <em>set</em> or an empty
+<em>set</em>. This may not sound so useful at the level of this object but
+becomes more useful once we want to collect entities having certain
+kind of interactions across a series of <cite>Interaction</cite> objects.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>entity_type</strong> (<em>str</em>) – The type of the molecular entity. Possible values: <cite>protein</cite>,
+<cite>complex</cite>, <cite>mirna</cite>, <cite>small_molecule</cite>.</p></li>
+<li><p><strong>return_type</strong> (<em>str</em>) – The type of values to return. Default is
+py:class:<code class="docutils literal notranslate"><span class="pre">pypath.entity.Entity</span></code> objects, alternatives are
+<code class="docutils literal notranslate"><span class="pre">labels</span></code>  <code class="docutils literal notranslate"><span class="pre">identifiers</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.labels_by_interaction_type_and_data_model_and_resource">
+<span class="sig-name descname"><span class="pre">labels_by_interaction_type_and_data_model_and_resource</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.labels_by_interaction_type_and_data_model_and_resource" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the entities involved in interactions matching the criteria.
+It either returns both interacting entities in a <em>set</em> or an empty
+<em>set</em>. This may not sound so useful at the level of this object but
+becomes more useful once we want to collect entities having certain
+kind of interactions across a series of <cite>Interaction</cite> objects.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>entity_type</strong> (<em>str</em>) – The type of the molecular entity. Possible values: <cite>protein</cite>,
+<cite>complex</cite>, <cite>mirna</cite>, <cite>small_molecule</cite>.</p></li>
+<li><p><strong>return_type</strong> (<em>str</em>) – The type of values to return. Default is
+py:class:<code class="docutils literal notranslate"><span class="pre">pypath.entity.Entity</span></code> objects, alternatives are
+<code class="docutils literal notranslate"><span class="pre">labels</span></code>  <code class="docutils literal notranslate"><span class="pre">identifiers</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.labels_by_reference">
+<span class="sig-name descname"><span class="pre">labels_by_reference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.labels_by_reference" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the entities involved in interactions matching the criteria.
+It either returns both interacting entities in a <em>set</em> or an empty
+<em>set</em>. This may not sound so useful at the level of this object but
+becomes more useful once we want to collect entities having certain
+kind of interactions across a series of <cite>Interaction</cite> objects.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>entity_type</strong> (<em>str</em>) – The type of the molecular entity. Possible values: <cite>protein</cite>,
+<cite>complex</cite>, <cite>mirna</cite>, <cite>small_molecule</cite>.</p></li>
+<li><p><strong>return_type</strong> (<em>str</em>) – The type of values to return. Default is
+py:class:<code class="docutils literal notranslate"><span class="pre">pypath.entity.Entity</span></code> objects, alternatives are
+<code class="docutils literal notranslate"><span class="pre">labels</span></code>  <code class="docutils literal notranslate"><span class="pre">identifiers</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.labels_by_resource">
+<span class="sig-name descname"><span class="pre">labels_by_resource</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.labels_by_resource" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the entities involved in interactions matching the criteria.
+It either returns both interacting entities in a <em>set</em> or an empty
+<em>set</em>. This may not sound so useful at the level of this object but
+becomes more useful once we want to collect entities having certain
+kind of interactions across a series of <cite>Interaction</cite> objects.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>entity_type</strong> (<em>str</em>) – The type of the molecular entity. Possible values: <cite>protein</cite>,
+<cite>complex</cite>, <cite>mirna</cite>, <cite>small_molecule</cite>.</p></li>
+<li><p><strong>return_type</strong> (<em>str</em>) – The type of values to return. Default is
+py:class:<code class="docutils literal notranslate"><span class="pre">pypath.entity.Entity</span></code> objects, alternatives are
+<code class="docutils literal notranslate"><span class="pre">labels</span></code>  <code class="docutils literal notranslate"><span class="pre">identifiers</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.lncrna_identifiers_by_data_model">
+<span class="sig-name descname"><span class="pre">lncrna_identifiers_by_data_model</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.lncrna_identifiers_by_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the entities involved in interactions matching the criteria.
+It either returns both interacting entities in a <em>set</em> or an empty
+<em>set</em>. This may not sound so useful at the level of this object but
+becomes more useful once we want to collect entities having certain
+kind of interactions across a series of <cite>Interaction</cite> objects.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>entity_type</strong> (<em>str</em>) – The type of the molecular entity. Possible values: <cite>protein</cite>,
+<cite>complex</cite>, <cite>mirna</cite>, <cite>small_molecule</cite>.</p></li>
+<li><p><strong>return_type</strong> (<em>str</em>) – The type of values to return. Default is
+py:class:<code class="docutils literal notranslate"><span class="pre">pypath.entity.Entity</span></code> objects, alternatives are
+<code class="docutils literal notranslate"><span class="pre">labels</span></code>  <code class="docutils literal notranslate"><span class="pre">identifiers</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.lncrna_identifiers_by_interaction_type">
+<span class="sig-name descname"><span class="pre">lncrna_identifiers_by_interaction_type</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.lncrna_identifiers_by_interaction_type" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the entities involved in interactions matching the criteria.
+It either returns both interacting entities in a <em>set</em> or an empty
+<em>set</em>. This may not sound so useful at the level of this object but
+becomes more useful once we want to collect entities having certain
+kind of interactions across a series of <cite>Interaction</cite> objects.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>entity_type</strong> (<em>str</em>) – The type of the molecular entity. Possible values: <cite>protein</cite>,
+<cite>complex</cite>, <cite>mirna</cite>, <cite>small_molecule</cite>.</p></li>
+<li><p><strong>return_type</strong> (<em>str</em>) – The type of values to return. Default is
+py:class:<code class="docutils literal notranslate"><span class="pre">pypath.entity.Entity</span></code> objects, alternatives are
+<code class="docutils literal notranslate"><span class="pre">labels</span></code>  <code class="docutils literal notranslate"><span class="pre">identifiers</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.lncrna_identifiers_by_interaction_type_and_data_model">
+<span class="sig-name descname"><span class="pre">lncrna_identifiers_by_interaction_type_and_data_model</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.lncrna_identifiers_by_interaction_type_and_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the entities involved in interactions matching the criteria.
+It either returns both interacting entities in a <em>set</em> or an empty
+<em>set</em>. This may not sound so useful at the level of this object but
+becomes more useful once we want to collect entities having certain
+kind of interactions across a series of <cite>Interaction</cite> objects.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>entity_type</strong> (<em>str</em>) – The type of the molecular entity. Possible values: <cite>protein</cite>,
+<cite>complex</cite>, <cite>mirna</cite>, <cite>small_molecule</cite>.</p></li>
+<li><p><strong>return_type</strong> (<em>str</em>) – The type of values to return. Default is
+py:class:<code class="docutils literal notranslate"><span class="pre">pypath.entity.Entity</span></code> objects, alternatives are
+<code class="docutils literal notranslate"><span class="pre">labels</span></code>  <code class="docutils literal notranslate"><span class="pre">identifiers</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.lncrna_identifiers_by_interaction_type_and_data_model_and_resource">
+<span class="sig-name descname"><span class="pre">lncrna_identifiers_by_interaction_type_and_data_model_and_resource</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.lncrna_identifiers_by_interaction_type_and_data_model_and_resource" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the entities involved in interactions matching the criteria.
+It either returns both interacting entities in a <em>set</em> or an empty
+<em>set</em>. This may not sound so useful at the level of this object but
+becomes more useful once we want to collect entities having certain
+kind of interactions across a series of <cite>Interaction</cite> objects.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>entity_type</strong> (<em>str</em>) – The type of the molecular entity. Possible values: <cite>protein</cite>,
+<cite>complex</cite>, <cite>mirna</cite>, <cite>small_molecule</cite>.</p></li>
+<li><p><strong>return_type</strong> (<em>str</em>) – The type of values to return. Default is
+py:class:<code class="docutils literal notranslate"><span class="pre">pypath.entity.Entity</span></code> objects, alternatives are
+<code class="docutils literal notranslate"><span class="pre">labels</span></code>  <code class="docutils literal notranslate"><span class="pre">identifiers</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.lncrna_identifiers_by_reference">
+<span class="sig-name descname"><span class="pre">lncrna_identifiers_by_reference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.lncrna_identifiers_by_reference" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the entities involved in interactions matching the criteria.
+It either returns both interacting entities in a <em>set</em> or an empty
+<em>set</em>. This may not sound so useful at the level of this object but
+becomes more useful once we want to collect entities having certain
+kind of interactions across a series of <cite>Interaction</cite> objects.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>entity_type</strong> (<em>str</em>) – The type of the molecular entity. Possible values: <cite>protein</cite>,
+<cite>complex</cite>, <cite>mirna</cite>, <cite>small_molecule</cite>.</p></li>
+<li><p><strong>return_type</strong> (<em>str</em>) – The type of values to return. Default is
+py:class:<code class="docutils literal notranslate"><span class="pre">pypath.entity.Entity</span></code> objects, alternatives are
+<code class="docutils literal notranslate"><span class="pre">labels</span></code>  <code class="docutils literal notranslate"><span class="pre">identifiers</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.lncrna_identifiers_by_resource">
+<span class="sig-name descname"><span class="pre">lncrna_identifiers_by_resource</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.lncrna_identifiers_by_resource" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the entities involved in interactions matching the criteria.
+It either returns both interacting entities in a <em>set</em> or an empty
+<em>set</em>. This may not sound so useful at the level of this object but
+becomes more useful once we want to collect entities having certain
+kind of interactions across a series of <cite>Interaction</cite> objects.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>entity_type</strong> (<em>str</em>) – The type of the molecular entity. Possible values: <cite>protein</cite>,
+<cite>complex</cite>, <cite>mirna</cite>, <cite>small_molecule</cite>.</p></li>
+<li><p><strong>return_type</strong> (<em>str</em>) – The type of values to return. Default is
+py:class:<code class="docutils literal notranslate"><span class="pre">pypath.entity.Entity</span></code> objects, alternatives are
+<code class="docutils literal notranslate"><span class="pre">labels</span></code>  <code class="docutils literal notranslate"><span class="pre">identifiers</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.lncrna_labels_by_data_model">
+<span class="sig-name descname"><span class="pre">lncrna_labels_by_data_model</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.lncrna_labels_by_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the entities involved in interactions matching the criteria.
+It either returns both interacting entities in a <em>set</em> or an empty
+<em>set</em>. This may not sound so useful at the level of this object but
+becomes more useful once we want to collect entities having certain
+kind of interactions across a series of <cite>Interaction</cite> objects.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>entity_type</strong> (<em>str</em>) – The type of the molecular entity. Possible values: <cite>protein</cite>,
+<cite>complex</cite>, <cite>mirna</cite>, <cite>small_molecule</cite>.</p></li>
+<li><p><strong>return_type</strong> (<em>str</em>) – The type of values to return. Default is
+py:class:<code class="docutils literal notranslate"><span class="pre">pypath.entity.Entity</span></code> objects, alternatives are
+<code class="docutils literal notranslate"><span class="pre">labels</span></code>  <code class="docutils literal notranslate"><span class="pre">identifiers</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.lncrna_labels_by_interaction_type">
+<span class="sig-name descname"><span class="pre">lncrna_labels_by_interaction_type</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.lncrna_labels_by_interaction_type" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the entities involved in interactions matching the criteria.
+It either returns both interacting entities in a <em>set</em> or an empty
+<em>set</em>. This may not sound so useful at the level of this object but
+becomes more useful once we want to collect entities having certain
+kind of interactions across a series of <cite>Interaction</cite> objects.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>entity_type</strong> (<em>str</em>) – The type of the molecular entity. Possible values: <cite>protein</cite>,
+<cite>complex</cite>, <cite>mirna</cite>, <cite>small_molecule</cite>.</p></li>
+<li><p><strong>return_type</strong> (<em>str</em>) – The type of values to return. Default is
+py:class:<code class="docutils literal notranslate"><span class="pre">pypath.entity.Entity</span></code> objects, alternatives are
+<code class="docutils literal notranslate"><span class="pre">labels</span></code>  <code class="docutils literal notranslate"><span class="pre">identifiers</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.lncrna_labels_by_interaction_type_and_data_model">
+<span class="sig-name descname"><span class="pre">lncrna_labels_by_interaction_type_and_data_model</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.lncrna_labels_by_interaction_type_and_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the entities involved in interactions matching the criteria.
+It either returns both interacting entities in a <em>set</em> or an empty
+<em>set</em>. This may not sound so useful at the level of this object but
+becomes more useful once we want to collect entities having certain
+kind of interactions across a series of <cite>Interaction</cite> objects.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>entity_type</strong> (<em>str</em>) – The type of the molecular entity. Possible values: <cite>protein</cite>,
+<cite>complex</cite>, <cite>mirna</cite>, <cite>small_molecule</cite>.</p></li>
+<li><p><strong>return_type</strong> (<em>str</em>) – The type of values to return. Default is
+py:class:<code class="docutils literal notranslate"><span class="pre">pypath.entity.Entity</span></code> objects, alternatives are
+<code class="docutils literal notranslate"><span class="pre">labels</span></code>  <code class="docutils literal notranslate"><span class="pre">identifiers</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.lncrna_labels_by_interaction_type_and_data_model_and_resource">
+<span class="sig-name descname"><span class="pre">lncrna_labels_by_interaction_type_and_data_model_and_resource</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.lncrna_labels_by_interaction_type_and_data_model_and_resource" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the entities involved in interactions matching the criteria.
+It either returns both interacting entities in a <em>set</em> or an empty
+<em>set</em>. This may not sound so useful at the level of this object but
+becomes more useful once we want to collect entities having certain
+kind of interactions across a series of <cite>Interaction</cite> objects.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>entity_type</strong> (<em>str</em>) – The type of the molecular entity. Possible values: <cite>protein</cite>,
+<cite>complex</cite>, <cite>mirna</cite>, <cite>small_molecule</cite>.</p></li>
+<li><p><strong>return_type</strong> (<em>str</em>) – The type of values to return. Default is
+py:class:<code class="docutils literal notranslate"><span class="pre">pypath.entity.Entity</span></code> objects, alternatives are
+<code class="docutils literal notranslate"><span class="pre">labels</span></code>  <code class="docutils literal notranslate"><span class="pre">identifiers</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.lncrna_labels_by_reference">
+<span class="sig-name descname"><span class="pre">lncrna_labels_by_reference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.lncrna_labels_by_reference" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the entities involved in interactions matching the criteria.
+It either returns both interacting entities in a <em>set</em> or an empty
+<em>set</em>. This may not sound so useful at the level of this object but
+becomes more useful once we want to collect entities having certain
+kind of interactions across a series of <cite>Interaction</cite> objects.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>entity_type</strong> (<em>str</em>) – The type of the molecular entity. Possible values: <cite>protein</cite>,
+<cite>complex</cite>, <cite>mirna</cite>, <cite>small_molecule</cite>.</p></li>
+<li><p><strong>return_type</strong> (<em>str</em>) – The type of values to return. Default is
+py:class:<code class="docutils literal notranslate"><span class="pre">pypath.entity.Entity</span></code> objects, alternatives are
+<code class="docutils literal notranslate"><span class="pre">labels</span></code>  <code class="docutils literal notranslate"><span class="pre">identifiers</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.lncrna_labels_by_resource">
+<span class="sig-name descname"><span class="pre">lncrna_labels_by_resource</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.lncrna_labels_by_resource" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the entities involved in interactions matching the criteria.
+It either returns both interacting entities in a <em>set</em> or an empty
+<em>set</em>. This may not sound so useful at the level of this object but
+becomes more useful once we want to collect entities having certain
+kind of interactions across a series of <cite>Interaction</cite> objects.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>entity_type</strong> (<em>str</em>) – The type of the molecular entity. Possible values: <cite>protein</cite>,
+<cite>complex</cite>, <cite>mirna</cite>, <cite>small_molecule</cite>.</p></li>
+<li><p><strong>return_type</strong> (<em>str</em>) – The type of values to return. Default is
+py:class:<code class="docutils literal notranslate"><span class="pre">pypath.entity.Entity</span></code> objects, alternatives are
+<code class="docutils literal notranslate"><span class="pre">labels</span></code>  <code class="docutils literal notranslate"><span class="pre">identifiers</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.lncrnas_by_data_model">
+<span class="sig-name descname"><span class="pre">lncrnas_by_data_model</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.lncrnas_by_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the entities involved in interactions matching the criteria.
+It either returns both interacting entities in a <em>set</em> or an empty
+<em>set</em>. This may not sound so useful at the level of this object but
+becomes more useful once we want to collect entities having certain
+kind of interactions across a series of <cite>Interaction</cite> objects.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>entity_type</strong> (<em>str</em>) – The type of the molecular entity. Possible values: <cite>protein</cite>,
+<cite>complex</cite>, <cite>mirna</cite>, <cite>small_molecule</cite>.</p></li>
+<li><p><strong>return_type</strong> (<em>str</em>) – The type of values to return. Default is
+py:class:<code class="docutils literal notranslate"><span class="pre">pypath.entity.Entity</span></code> objects, alternatives are
+<code class="docutils literal notranslate"><span class="pre">labels</span></code>  <code class="docutils literal notranslate"><span class="pre">identifiers</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.lncrnas_by_interaction_type">
+<span class="sig-name descname"><span class="pre">lncrnas_by_interaction_type</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.lncrnas_by_interaction_type" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the entities involved in interactions matching the criteria.
+It either returns both interacting entities in a <em>set</em> or an empty
+<em>set</em>. This may not sound so useful at the level of this object but
+becomes more useful once we want to collect entities having certain
+kind of interactions across a series of <cite>Interaction</cite> objects.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>entity_type</strong> (<em>str</em>) – The type of the molecular entity. Possible values: <cite>protein</cite>,
+<cite>complex</cite>, <cite>mirna</cite>, <cite>small_molecule</cite>.</p></li>
+<li><p><strong>return_type</strong> (<em>str</em>) – The type of values to return. Default is
+py:class:<code class="docutils literal notranslate"><span class="pre">pypath.entity.Entity</span></code> objects, alternatives are
+<code class="docutils literal notranslate"><span class="pre">labels</span></code>  <code class="docutils literal notranslate"><span class="pre">identifiers</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.lncrnas_by_interaction_type_and_data_model">
+<span class="sig-name descname"><span class="pre">lncrnas_by_interaction_type_and_data_model</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.lncrnas_by_interaction_type_and_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the entities involved in interactions matching the criteria.
+It either returns both interacting entities in a <em>set</em> or an empty
+<em>set</em>. This may not sound so useful at the level of this object but
+becomes more useful once we want to collect entities having certain
+kind of interactions across a series of <cite>Interaction</cite> objects.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>entity_type</strong> (<em>str</em>) – The type of the molecular entity. Possible values: <cite>protein</cite>,
+<cite>complex</cite>, <cite>mirna</cite>, <cite>small_molecule</cite>.</p></li>
+<li><p><strong>return_type</strong> (<em>str</em>) – The type of values to return. Default is
+py:class:<code class="docutils literal notranslate"><span class="pre">pypath.entity.Entity</span></code> objects, alternatives are
+<code class="docutils literal notranslate"><span class="pre">labels</span></code>  <code class="docutils literal notranslate"><span class="pre">identifiers</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.lncrnas_by_interaction_type_and_data_model_and_resource">
+<span class="sig-name descname"><span class="pre">lncrnas_by_interaction_type_and_data_model_and_resource</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.lncrnas_by_interaction_type_and_data_model_and_resource" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the entities involved in interactions matching the criteria.
+It either returns both interacting entities in a <em>set</em> or an empty
+<em>set</em>. This may not sound so useful at the level of this object but
+becomes more useful once we want to collect entities having certain
+kind of interactions across a series of <cite>Interaction</cite> objects.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>entity_type</strong> (<em>str</em>) – The type of the molecular entity. Possible values: <cite>protein</cite>,
+<cite>complex</cite>, <cite>mirna</cite>, <cite>small_molecule</cite>.</p></li>
+<li><p><strong>return_type</strong> (<em>str</em>) – The type of values to return. Default is
+py:class:<code class="docutils literal notranslate"><span class="pre">pypath.entity.Entity</span></code> objects, alternatives are
+<code class="docutils literal notranslate"><span class="pre">labels</span></code>  <code class="docutils literal notranslate"><span class="pre">identifiers</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.lncrnas_by_reference">
+<span class="sig-name descname"><span class="pre">lncrnas_by_reference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.lncrnas_by_reference" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the entities involved in interactions matching the criteria.
+It either returns both interacting entities in a <em>set</em> or an empty
+<em>set</em>. This may not sound so useful at the level of this object but
+becomes more useful once we want to collect entities having certain
+kind of interactions across a series of <cite>Interaction</cite> objects.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>entity_type</strong> (<em>str</em>) – The type of the molecular entity. Possible values: <cite>protein</cite>,
+<cite>complex</cite>, <cite>mirna</cite>, <cite>small_molecule</cite>.</p></li>
+<li><p><strong>return_type</strong> (<em>str</em>) – The type of values to return. Default is
+py:class:<code class="docutils literal notranslate"><span class="pre">pypath.entity.Entity</span></code> objects, alternatives are
+<code class="docutils literal notranslate"><span class="pre">labels</span></code>  <code class="docutils literal notranslate"><span class="pre">identifiers</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.lncrnas_by_resource">
+<span class="sig-name descname"><span class="pre">lncrnas_by_resource</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.lncrnas_by_resource" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the entities involved in interactions matching the criteria.
+It either returns both interacting entities in a <em>set</em> or an empty
+<em>set</em>. This may not sound so useful at the level of this object but
+becomes more useful once we want to collect entities having certain
+kind of interactions across a series of <cite>Interaction</cite> objects.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>entity_type</strong> (<em>str</em>) – The type of the molecular entity. Possible values: <cite>protein</cite>,
+<cite>complex</cite>, <cite>mirna</cite>, <cite>small_molecule</cite>.</p></li>
+<li><p><strong>return_type</strong> (<em>str</em>) – The type of values to return. Default is
+py:class:<code class="docutils literal notranslate"><span class="pre">pypath.entity.Entity</span></code> objects, alternatives are
+<code class="docutils literal notranslate"><span class="pre">labels</span></code>  <code class="docutils literal notranslate"><span class="pre">identifiers</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.majority_dir">
+<span class="sig-name descname"><span class="pre">majority_dir</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">only_interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">only_primary</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">by_references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">by_reference_resource_pairs</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/interaction.html#Interaction.majority_dir"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.interaction.Interaction.majority_dir" title="Link to this definition">§</a></dt>
+<dd><p>Infers which is the major directionality of the edge by number
+of supporting sources.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Returns<span class="colon">:</span></dt>
+<dd class="field-odd"><p>(<em>tuple</em>) – Contains the pair of nodes denoting the
+consensus directionality. If the number of sources on both
+directions is equal, <code class="docutils literal notranslate"><span class="pre">None</span></code> is returned. If there is no
+directionality information, <code class="docutils literal notranslate"><span class="pre">'undirected'`</span></code> will be
+returned.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.majority_sign">
+<span class="sig-name descname"><span class="pre">majority_sign</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">only_interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">only_primary</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">by_references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">by_reference_resource_pairs</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/interaction.html#Interaction.majority_sign"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.interaction.Interaction.majority_sign" title="Link to this definition">§</a></dt>
+<dd><p>Infers which is the major sign (activation/inhibition) of the
+edge by number of supporting sources on both directions.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Returns<span class="colon">:</span></dt>
+<dd class="field-odd"><p>(<em>dict</em>) – Keys are the node tuples on both directions
+(<code class="xref py py-attr docutils literal notranslate"><span class="pre">straight</span></code>/<code class="xref py py-attr docutils literal notranslate"><span class="pre">reverse</span></code>) and values can be
+either <code class="docutils literal notranslate"><span class="pre">None</span></code> if that direction has no sign information or
+a list of two [bool] elements corresponding to majority of
+positive and majority of negative support. In case both
+elements of the list are <code class="docutils literal notranslate"><span class="pre">True</span></code>, this means the number of
+supporting sources for both signs in that direction is
+equal.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.merge">
+<span class="sig-name descname"><span class="pre">merge</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">other</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/interaction.html#Interaction.merge"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.interaction.Interaction.merge" title="Link to this definition">§</a></dt>
+<dd><p>Merges current Interaction with another (if and only if they are the
+same class and contain the same nodes). Updates the attributes
+<code class="xref py py-attr docutils literal notranslate"><span class="pre">direction</span></code>, <code class="xref py py-attr docutils literal notranslate"><span class="pre">positive</span></code> and <code class="xref py py-attr docutils literal notranslate"><span class="pre">negative</span></code>.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><p><strong>other</strong> (<em>pypath.interaction.Interaction</em>) – The new Interaction object to be merged with the current one.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.mirna_identifiers_by_data_model">
+<span class="sig-name descname"><span class="pre">mirna_identifiers_by_data_model</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.mirna_identifiers_by_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the entities involved in interactions matching the criteria.
+It either returns both interacting entities in a <em>set</em> or an empty
+<em>set</em>. This may not sound so useful at the level of this object but
+becomes more useful once we want to collect entities having certain
+kind of interactions across a series of <cite>Interaction</cite> objects.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>entity_type</strong> (<em>str</em>) – The type of the molecular entity. Possible values: <cite>protein</cite>,
+<cite>complex</cite>, <cite>mirna</cite>, <cite>small_molecule</cite>.</p></li>
+<li><p><strong>return_type</strong> (<em>str</em>) – The type of values to return. Default is
+py:class:<code class="docutils literal notranslate"><span class="pre">pypath.entity.Entity</span></code> objects, alternatives are
+<code class="docutils literal notranslate"><span class="pre">labels</span></code>  <code class="docutils literal notranslate"><span class="pre">identifiers</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.mirna_identifiers_by_interaction_type">
+<span class="sig-name descname"><span class="pre">mirna_identifiers_by_interaction_type</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.mirna_identifiers_by_interaction_type" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the entities involved in interactions matching the criteria.
+It either returns both interacting entities in a <em>set</em> or an empty
+<em>set</em>. This may not sound so useful at the level of this object but
+becomes more useful once we want to collect entities having certain
+kind of interactions across a series of <cite>Interaction</cite> objects.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>entity_type</strong> (<em>str</em>) – The type of the molecular entity. Possible values: <cite>protein</cite>,
+<cite>complex</cite>, <cite>mirna</cite>, <cite>small_molecule</cite>.</p></li>
+<li><p><strong>return_type</strong> (<em>str</em>) – The type of values to return. Default is
+py:class:<code class="docutils literal notranslate"><span class="pre">pypath.entity.Entity</span></code> objects, alternatives are
+<code class="docutils literal notranslate"><span class="pre">labels</span></code>  <code class="docutils literal notranslate"><span class="pre">identifiers</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.mirna_identifiers_by_interaction_type_and_data_model">
+<span class="sig-name descname"><span class="pre">mirna_identifiers_by_interaction_type_and_data_model</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.mirna_identifiers_by_interaction_type_and_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the entities involved in interactions matching the criteria.
+It either returns both interacting entities in a <em>set</em> or an empty
+<em>set</em>. This may not sound so useful at the level of this object but
+becomes more useful once we want to collect entities having certain
+kind of interactions across a series of <cite>Interaction</cite> objects.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>entity_type</strong> (<em>str</em>) – The type of the molecular entity. Possible values: <cite>protein</cite>,
+<cite>complex</cite>, <cite>mirna</cite>, <cite>small_molecule</cite>.</p></li>
+<li><p><strong>return_type</strong> (<em>str</em>) – The type of values to return. Default is
+py:class:<code class="docutils literal notranslate"><span class="pre">pypath.entity.Entity</span></code> objects, alternatives are
+<code class="docutils literal notranslate"><span class="pre">labels</span></code>  <code class="docutils literal notranslate"><span class="pre">identifiers</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.mirna_identifiers_by_interaction_type_and_data_model_and_resource">
+<span class="sig-name descname"><span class="pre">mirna_identifiers_by_interaction_type_and_data_model_and_resource</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.mirna_identifiers_by_interaction_type_and_data_model_and_resource" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the entities involved in interactions matching the criteria.
+It either returns both interacting entities in a <em>set</em> or an empty
+<em>set</em>. This may not sound so useful at the level of this object but
+becomes more useful once we want to collect entities having certain
+kind of interactions across a series of <cite>Interaction</cite> objects.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>entity_type</strong> (<em>str</em>) – The type of the molecular entity. Possible values: <cite>protein</cite>,
+<cite>complex</cite>, <cite>mirna</cite>, <cite>small_molecule</cite>.</p></li>
+<li><p><strong>return_type</strong> (<em>str</em>) – The type of values to return. Default is
+py:class:<code class="docutils literal notranslate"><span class="pre">pypath.entity.Entity</span></code> objects, alternatives are
+<code class="docutils literal notranslate"><span class="pre">labels</span></code>  <code class="docutils literal notranslate"><span class="pre">identifiers</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.mirna_identifiers_by_reference">
+<span class="sig-name descname"><span class="pre">mirna_identifiers_by_reference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.mirna_identifiers_by_reference" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the entities involved in interactions matching the criteria.
+It either returns both interacting entities in a <em>set</em> or an empty
+<em>set</em>. This may not sound so useful at the level of this object but
+becomes more useful once we want to collect entities having certain
+kind of interactions across a series of <cite>Interaction</cite> objects.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>entity_type</strong> (<em>str</em>) – The type of the molecular entity. Possible values: <cite>protein</cite>,
+<cite>complex</cite>, <cite>mirna</cite>, <cite>small_molecule</cite>.</p></li>
+<li><p><strong>return_type</strong> (<em>str</em>) – The type of values to return. Default is
+py:class:<code class="docutils literal notranslate"><span class="pre">pypath.entity.Entity</span></code> objects, alternatives are
+<code class="docutils literal notranslate"><span class="pre">labels</span></code>  <code class="docutils literal notranslate"><span class="pre">identifiers</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.mirna_identifiers_by_resource">
+<span class="sig-name descname"><span class="pre">mirna_identifiers_by_resource</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.mirna_identifiers_by_resource" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the entities involved in interactions matching the criteria.
+It either returns both interacting entities in a <em>set</em> or an empty
+<em>set</em>. This may not sound so useful at the level of this object but
+becomes more useful once we want to collect entities having certain
+kind of interactions across a series of <cite>Interaction</cite> objects.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>entity_type</strong> (<em>str</em>) – The type of the molecular entity. Possible values: <cite>protein</cite>,
+<cite>complex</cite>, <cite>mirna</cite>, <cite>small_molecule</cite>.</p></li>
+<li><p><strong>return_type</strong> (<em>str</em>) – The type of values to return. Default is
+py:class:<code class="docutils literal notranslate"><span class="pre">pypath.entity.Entity</span></code> objects, alternatives are
+<code class="docutils literal notranslate"><span class="pre">labels</span></code>  <code class="docutils literal notranslate"><span class="pre">identifiers</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.mirna_labels_by_data_model">
+<span class="sig-name descname"><span class="pre">mirna_labels_by_data_model</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.mirna_labels_by_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the entities involved in interactions matching the criteria.
+It either returns both interacting entities in a <em>set</em> or an empty
+<em>set</em>. This may not sound so useful at the level of this object but
+becomes more useful once we want to collect entities having certain
+kind of interactions across a series of <cite>Interaction</cite> objects.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>entity_type</strong> (<em>str</em>) – The type of the molecular entity. Possible values: <cite>protein</cite>,
+<cite>complex</cite>, <cite>mirna</cite>, <cite>small_molecule</cite>.</p></li>
+<li><p><strong>return_type</strong> (<em>str</em>) – The type of values to return. Default is
+py:class:<code class="docutils literal notranslate"><span class="pre">pypath.entity.Entity</span></code> objects, alternatives are
+<code class="docutils literal notranslate"><span class="pre">labels</span></code>  <code class="docutils literal notranslate"><span class="pre">identifiers</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.mirna_labels_by_interaction_type">
+<span class="sig-name descname"><span class="pre">mirna_labels_by_interaction_type</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.mirna_labels_by_interaction_type" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the entities involved in interactions matching the criteria.
+It either returns both interacting entities in a <em>set</em> or an empty
+<em>set</em>. This may not sound so useful at the level of this object but
+becomes more useful once we want to collect entities having certain
+kind of interactions across a series of <cite>Interaction</cite> objects.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>entity_type</strong> (<em>str</em>) – The type of the molecular entity. Possible values: <cite>protein</cite>,
+<cite>complex</cite>, <cite>mirna</cite>, <cite>small_molecule</cite>.</p></li>
+<li><p><strong>return_type</strong> (<em>str</em>) – The type of values to return. Default is
+py:class:<code class="docutils literal notranslate"><span class="pre">pypath.entity.Entity</span></code> objects, alternatives are
+<code class="docutils literal notranslate"><span class="pre">labels</span></code>  <code class="docutils literal notranslate"><span class="pre">identifiers</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.mirna_labels_by_interaction_type_and_data_model">
+<span class="sig-name descname"><span class="pre">mirna_labels_by_interaction_type_and_data_model</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.mirna_labels_by_interaction_type_and_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the entities involved in interactions matching the criteria.
+It either returns both interacting entities in a <em>set</em> or an empty
+<em>set</em>. This may not sound so useful at the level of this object but
+becomes more useful once we want to collect entities having certain
+kind of interactions across a series of <cite>Interaction</cite> objects.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>entity_type</strong> (<em>str</em>) – The type of the molecular entity. Possible values: <cite>protein</cite>,
+<cite>complex</cite>, <cite>mirna</cite>, <cite>small_molecule</cite>.</p></li>
+<li><p><strong>return_type</strong> (<em>str</em>) – The type of values to return. Default is
+py:class:<code class="docutils literal notranslate"><span class="pre">pypath.entity.Entity</span></code> objects, alternatives are
+<code class="docutils literal notranslate"><span class="pre">labels</span></code>  <code class="docutils literal notranslate"><span class="pre">identifiers</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.mirna_labels_by_interaction_type_and_data_model_and_resource">
+<span class="sig-name descname"><span class="pre">mirna_labels_by_interaction_type_and_data_model_and_resource</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.mirna_labels_by_interaction_type_and_data_model_and_resource" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the entities involved in interactions matching the criteria.
+It either returns both interacting entities in a <em>set</em> or an empty
+<em>set</em>. This may not sound so useful at the level of this object but
+becomes more useful once we want to collect entities having certain
+kind of interactions across a series of <cite>Interaction</cite> objects.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>entity_type</strong> (<em>str</em>) – The type of the molecular entity. Possible values: <cite>protein</cite>,
+<cite>complex</cite>, <cite>mirna</cite>, <cite>small_molecule</cite>.</p></li>
+<li><p><strong>return_type</strong> (<em>str</em>) – The type of values to return. Default is
+py:class:<code class="docutils literal notranslate"><span class="pre">pypath.entity.Entity</span></code> objects, alternatives are
+<code class="docutils literal notranslate"><span class="pre">labels</span></code>  <code class="docutils literal notranslate"><span class="pre">identifiers</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.mirna_labels_by_reference">
+<span class="sig-name descname"><span class="pre">mirna_labels_by_reference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.mirna_labels_by_reference" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the entities involved in interactions matching the criteria.
+It either returns both interacting entities in a <em>set</em> or an empty
+<em>set</em>. This may not sound so useful at the level of this object but
+becomes more useful once we want to collect entities having certain
+kind of interactions across a series of <cite>Interaction</cite> objects.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>entity_type</strong> (<em>str</em>) – The type of the molecular entity. Possible values: <cite>protein</cite>,
+<cite>complex</cite>, <cite>mirna</cite>, <cite>small_molecule</cite>.</p></li>
+<li><p><strong>return_type</strong> (<em>str</em>) – The type of values to return. Default is
+py:class:<code class="docutils literal notranslate"><span class="pre">pypath.entity.Entity</span></code> objects, alternatives are
+<code class="docutils literal notranslate"><span class="pre">labels</span></code>  <code class="docutils literal notranslate"><span class="pre">identifiers</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.mirna_labels_by_resource">
+<span class="sig-name descname"><span class="pre">mirna_labels_by_resource</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.mirna_labels_by_resource" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the entities involved in interactions matching the criteria.
+It either returns both interacting entities in a <em>set</em> or an empty
+<em>set</em>. This may not sound so useful at the level of this object but
+becomes more useful once we want to collect entities having certain
+kind of interactions across a series of <cite>Interaction</cite> objects.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>entity_type</strong> (<em>str</em>) – The type of the molecular entity. Possible values: <cite>protein</cite>,
+<cite>complex</cite>, <cite>mirna</cite>, <cite>small_molecule</cite>.</p></li>
+<li><p><strong>return_type</strong> (<em>str</em>) – The type of values to return. Default is
+py:class:<code class="docutils literal notranslate"><span class="pre">pypath.entity.Entity</span></code> objects, alternatives are
+<code class="docutils literal notranslate"><span class="pre">labels</span></code>  <code class="docutils literal notranslate"><span class="pre">identifiers</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.mirnas_by_data_model">
+<span class="sig-name descname"><span class="pre">mirnas_by_data_model</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.mirnas_by_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the entities involved in interactions matching the criteria.
+It either returns both interacting entities in a <em>set</em> or an empty
+<em>set</em>. This may not sound so useful at the level of this object but
+becomes more useful once we want to collect entities having certain
+kind of interactions across a series of <cite>Interaction</cite> objects.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>entity_type</strong> (<em>str</em>) – The type of the molecular entity. Possible values: <cite>protein</cite>,
+<cite>complex</cite>, <cite>mirna</cite>, <cite>small_molecule</cite>.</p></li>
+<li><p><strong>return_type</strong> (<em>str</em>) – The type of values to return. Default is
+py:class:<code class="docutils literal notranslate"><span class="pre">pypath.entity.Entity</span></code> objects, alternatives are
+<code class="docutils literal notranslate"><span class="pre">labels</span></code>  <code class="docutils literal notranslate"><span class="pre">identifiers</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.mirnas_by_interaction_type">
+<span class="sig-name descname"><span class="pre">mirnas_by_interaction_type</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.mirnas_by_interaction_type" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the entities involved in interactions matching the criteria.
+It either returns both interacting entities in a <em>set</em> or an empty
+<em>set</em>. This may not sound so useful at the level of this object but
+becomes more useful once we want to collect entities having certain
+kind of interactions across a series of <cite>Interaction</cite> objects.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>entity_type</strong> (<em>str</em>) – The type of the molecular entity. Possible values: <cite>protein</cite>,
+<cite>complex</cite>, <cite>mirna</cite>, <cite>small_molecule</cite>.</p></li>
+<li><p><strong>return_type</strong> (<em>str</em>) – The type of values to return. Default is
+py:class:<code class="docutils literal notranslate"><span class="pre">pypath.entity.Entity</span></code> objects, alternatives are
+<code class="docutils literal notranslate"><span class="pre">labels</span></code>  <code class="docutils literal notranslate"><span class="pre">identifiers</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.mirnas_by_interaction_type_and_data_model">
+<span class="sig-name descname"><span class="pre">mirnas_by_interaction_type_and_data_model</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.mirnas_by_interaction_type_and_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the entities involved in interactions matching the criteria.
+It either returns both interacting entities in a <em>set</em> or an empty
+<em>set</em>. This may not sound so useful at the level of this object but
+becomes more useful once we want to collect entities having certain
+kind of interactions across a series of <cite>Interaction</cite> objects.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>entity_type</strong> (<em>str</em>) – The type of the molecular entity. Possible values: <cite>protein</cite>,
+<cite>complex</cite>, <cite>mirna</cite>, <cite>small_molecule</cite>.</p></li>
+<li><p><strong>return_type</strong> (<em>str</em>) – The type of values to return. Default is
+py:class:<code class="docutils literal notranslate"><span class="pre">pypath.entity.Entity</span></code> objects, alternatives are
+<code class="docutils literal notranslate"><span class="pre">labels</span></code>  <code class="docutils literal notranslate"><span class="pre">identifiers</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.mirnas_by_interaction_type_and_data_model_and_resource">
+<span class="sig-name descname"><span class="pre">mirnas_by_interaction_type_and_data_model_and_resource</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.mirnas_by_interaction_type_and_data_model_and_resource" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the entities involved in interactions matching the criteria.
+It either returns both interacting entities in a <em>set</em> or an empty
+<em>set</em>. This may not sound so useful at the level of this object but
+becomes more useful once we want to collect entities having certain
+kind of interactions across a series of <cite>Interaction</cite> objects.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>entity_type</strong> (<em>str</em>) – The type of the molecular entity. Possible values: <cite>protein</cite>,
+<cite>complex</cite>, <cite>mirna</cite>, <cite>small_molecule</cite>.</p></li>
+<li><p><strong>return_type</strong> (<em>str</em>) – The type of values to return. Default is
+py:class:<code class="docutils literal notranslate"><span class="pre">pypath.entity.Entity</span></code> objects, alternatives are
+<code class="docutils literal notranslate"><span class="pre">labels</span></code>  <code class="docutils literal notranslate"><span class="pre">identifiers</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.mirnas_by_reference">
+<span class="sig-name descname"><span class="pre">mirnas_by_reference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.mirnas_by_reference" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the entities involved in interactions matching the criteria.
+It either returns both interacting entities in a <em>set</em> or an empty
+<em>set</em>. This may not sound so useful at the level of this object but
+becomes more useful once we want to collect entities having certain
+kind of interactions across a series of <cite>Interaction</cite> objects.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>entity_type</strong> (<em>str</em>) – The type of the molecular entity. Possible values: <cite>protein</cite>,
+<cite>complex</cite>, <cite>mirna</cite>, <cite>small_molecule</cite>.</p></li>
+<li><p><strong>return_type</strong> (<em>str</em>) – The type of values to return. Default is
+py:class:<code class="docutils literal notranslate"><span class="pre">pypath.entity.Entity</span></code> objects, alternatives are
+<code class="docutils literal notranslate"><span class="pre">labels</span></code>  <code class="docutils literal notranslate"><span class="pre">identifiers</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.mirnas_by_resource">
+<span class="sig-name descname"><span class="pre">mirnas_by_resource</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.mirnas_by_resource" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the entities involved in interactions matching the criteria.
+It either returns both interacting entities in a <em>set</em> or an empty
+<em>set</em>. This may not sound so useful at the level of this object but
+becomes more useful once we want to collect entities having certain
+kind of interactions across a series of <cite>Interaction</cite> objects.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>entity_type</strong> (<em>str</em>) – The type of the molecular entity. Possible values: <cite>protein</cite>,
+<cite>complex</cite>, <cite>mirna</cite>, <cite>small_molecule</cite>.</p></li>
+<li><p><strong>return_type</strong> (<em>str</em>) – The type of values to return. Default is
+py:class:<code class="docutils literal notranslate"><span class="pre">pypath.entity.Entity</span></code> objects, alternatives are
+<code class="docutils literal notranslate"><span class="pre">labels</span></code>  <code class="docutils literal notranslate"><span class="pre">identifiers</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.negative_a_b">
+<span class="sig-name descname"><span class="pre">negative_a_b</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/interaction.html#Interaction.negative_a_b"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.interaction.Interaction.negative_a_b" title="Link to this definition">§</a></dt>
+<dd><p>Checks if the <code class="xref py py-attr docutils literal notranslate"><span class="pre">a_b</span></code> directionality is a negative
+interaction.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Returns<span class="colon">:</span></dt>
+<dd class="field-odd"><p>(<em>bool</em>) – <code class="docutils literal notranslate"><span class="pre">True</span></code> if there is supporting information on
+the <code class="xref py py-attr docutils literal notranslate"><span class="pre">a_b</span></code> direction of the edge as inhibition.
+<code class="docutils literal notranslate"><span class="pre">False</span></code> otherwise.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.negative_b_a">
+<span class="sig-name descname"><span class="pre">negative_b_a</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/interaction.html#Interaction.negative_b_a"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.interaction.Interaction.negative_b_a" title="Link to this definition">§</a></dt>
+<dd><p>Checks if the <code class="xref py py-attr docutils literal notranslate"><span class="pre">b_a</span></code> directionality is a negative
+interaction.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Returns<span class="colon">:</span></dt>
+<dd class="field-odd"><p>(<em>bool</em>) – <code class="docutils literal notranslate"><span class="pre">True</span></code> if there is supporting information on
+the <code class="xref py py-attr docutils literal notranslate"><span class="pre">b_a</span></code> direction of the edge as inhibition.
+<code class="docutils literal notranslate"><span class="pre">False</span></code> otherwise.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.negative_resources_a_b">
+<span class="sig-name descname"><span class="pre">negative_resources_a_b</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/interaction.html#Interaction.negative_resources_a_b"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.interaction.Interaction.negative_resources_a_b" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the list of resources for the <code class="xref py py-attr docutils literal notranslate"><span class="pre">a_b</span></code>
+direction and negative sign.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Returns<span class="colon">:</span></dt>
+<dd class="field-odd"><p>(<em>set</em>) – Contains the names of the resources supporting the
+<code class="xref py py-attr docutils literal notranslate"><span class="pre">a_b</span></code> directionality of the edge with a
+negative sign.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.negative_resources_b_a">
+<span class="sig-name descname"><span class="pre">negative_resources_b_a</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/interaction.html#Interaction.negative_resources_b_a"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.interaction.Interaction.negative_resources_b_a" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the list of resources for the <code class="xref py py-attr docutils literal notranslate"><span class="pre">b_a</span></code>
+direction and negative sign.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Returns<span class="colon">:</span></dt>
+<dd class="field-odd"><p>(<em>set</em>) – Contains the names of the resources supporting the
+<code class="xref py py-attr docutils literal notranslate"><span class="pre">b_a</span></code> directionality of the edge with a
+negative sign.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.negative_reverse">
+<span class="sig-name descname"><span class="pre">negative_reverse</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.negative_reverse" title="Link to this definition">§</a></dt>
+<dd><p>Checks if the <code class="xref py py-attr docutils literal notranslate"><span class="pre">b_a</span></code> directionality is a negative
+interaction.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Returns<span class="colon">:</span></dt>
+<dd class="field-odd"><p>(<em>bool</em>) – <code class="docutils literal notranslate"><span class="pre">True</span></code> if there is supporting information on
+the <code class="xref py py-attr docutils literal notranslate"><span class="pre">b_a</span></code> direction of the edge as inhibition.
+<code class="docutils literal notranslate"><span class="pre">False</span></code> otherwise.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.negative_straight">
+<span class="sig-name descname"><span class="pre">negative_straight</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.negative_straight" title="Link to this definition">§</a></dt>
+<dd><p>Checks if the <code class="xref py py-attr docutils literal notranslate"><span class="pre">a_b</span></code> directionality is a negative
+interaction.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Returns<span class="colon">:</span></dt>
+<dd class="field-odd"><p>(<em>bool</em>) – <code class="docutils literal notranslate"><span class="pre">True</span></code> if there is supporting information on
+the <code class="xref py py-attr docutils literal notranslate"><span class="pre">a_b</span></code> direction of the edge as inhibition.
+<code class="docutils literal notranslate"><span class="pre">False</span></code> otherwise.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.positive_a_b">
+<span class="sig-name descname"><span class="pre">positive_a_b</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/interaction.html#Interaction.positive_a_b"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.interaction.Interaction.positive_a_b" title="Link to this definition">§</a></dt>
+<dd><p>Checks if the <code class="xref py py-attr docutils literal notranslate"><span class="pre">a_b</span></code> directionality is a positive
+interaction.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Returns<span class="colon">:</span></dt>
+<dd class="field-odd"><p>(<em>bool</em>) – <code class="docutils literal notranslate"><span class="pre">True</span></code> if there is supporting information on
+the <code class="xref py py-attr docutils literal notranslate"><span class="pre">a_b</span></code> direction of the edge as activation.
+<code class="docutils literal notranslate"><span class="pre">False</span></code> otherwise.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.positive_b_a">
+<span class="sig-name descname"><span class="pre">positive_b_a</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/interaction.html#Interaction.positive_b_a"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.interaction.Interaction.positive_b_a" title="Link to this definition">§</a></dt>
+<dd><p>Checks if the <code class="xref py py-attr docutils literal notranslate"><span class="pre">b_a</span></code> directionality is a positive
+interaction.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Returns<span class="colon">:</span></dt>
+<dd class="field-odd"><p>(<em>bool</em>) – <code class="docutils literal notranslate"><span class="pre">True</span></code> if there is supporting information on
+the <code class="xref py py-attr docutils literal notranslate"><span class="pre">b_a</span></code> direction of the edge as activation.
+<code class="docutils literal notranslate"><span class="pre">False</span></code> otherwise.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.positive_resources_a_b">
+<span class="sig-name descname"><span class="pre">positive_resources_a_b</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/interaction.html#Interaction.positive_resources_a_b"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.interaction.Interaction.positive_resources_a_b" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the list of resources for the <code class="xref py py-attr docutils literal notranslate"><span class="pre">a_b</span></code>
+direction and positive sign.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Returns<span class="colon">:</span></dt>
+<dd class="field-odd"><p>(<em>set</em>) – Contains the names of the resources supporting the
+<code class="xref py py-attr docutils literal notranslate"><span class="pre">a_b</span></code> directionality of the edge with a
+positive sign.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.positive_resources_b_a">
+<span class="sig-name descname"><span class="pre">positive_resources_b_a</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/interaction.html#Interaction.positive_resources_b_a"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.interaction.Interaction.positive_resources_b_a" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the list of resources for the <code class="xref py py-attr docutils literal notranslate"><span class="pre">b_a</span></code>
+direction and positive sign.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Returns<span class="colon">:</span></dt>
+<dd class="field-odd"><p>(<em>set</em>) – Contains the names of the resources supporting the
+<code class="xref py py-attr docutils literal notranslate"><span class="pre">b_a</span></code> directionality of the edge with a
+positive sign.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.positive_reverse">
+<span class="sig-name descname"><span class="pre">positive_reverse</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.positive_reverse" title="Link to this definition">§</a></dt>
+<dd><p>Checks if the <code class="xref py py-attr docutils literal notranslate"><span class="pre">b_a</span></code> directionality is a positive
+interaction.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Returns<span class="colon">:</span></dt>
+<dd class="field-odd"><p>(<em>bool</em>) – <code class="docutils literal notranslate"><span class="pre">True</span></code> if there is supporting information on
+the <code class="xref py py-attr docutils literal notranslate"><span class="pre">b_a</span></code> direction of the edge as activation.
+<code class="docutils literal notranslate"><span class="pre">False</span></code> otherwise.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.positive_straight">
+<span class="sig-name descname"><span class="pre">positive_straight</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.positive_straight" title="Link to this definition">§</a></dt>
+<dd><p>Checks if the <code class="xref py py-attr docutils literal notranslate"><span class="pre">a_b</span></code> directionality is a positive
+interaction.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Returns<span class="colon">:</span></dt>
+<dd class="field-odd"><p>(<em>bool</em>) – <code class="docutils literal notranslate"><span class="pre">True</span></code> if there is supporting information on
+the <code class="xref py py-attr docutils literal notranslate"><span class="pre">a_b</span></code> direction of the edge as activation.
+<code class="docutils literal notranslate"><span class="pre">False</span></code> otherwise.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.protein_identifiers_by_data_model">
+<span class="sig-name descname"><span class="pre">protein_identifiers_by_data_model</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.protein_identifiers_by_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the entities involved in interactions matching the criteria.
+It either returns both interacting entities in a <em>set</em> or an empty
+<em>set</em>. This may not sound so useful at the level of this object but
+becomes more useful once we want to collect entities having certain
+kind of interactions across a series of <cite>Interaction</cite> objects.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>entity_type</strong> (<em>str</em>) – The type of the molecular entity. Possible values: <cite>protein</cite>,
+<cite>complex</cite>, <cite>mirna</cite>, <cite>small_molecule</cite>.</p></li>
+<li><p><strong>return_type</strong> (<em>str</em>) – The type of values to return. Default is
+py:class:<code class="docutils literal notranslate"><span class="pre">pypath.entity.Entity</span></code> objects, alternatives are
+<code class="docutils literal notranslate"><span class="pre">labels</span></code>  <code class="docutils literal notranslate"><span class="pre">identifiers</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.protein_identifiers_by_interaction_type">
+<span class="sig-name descname"><span class="pre">protein_identifiers_by_interaction_type</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.protein_identifiers_by_interaction_type" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the entities involved in interactions matching the criteria.
+It either returns both interacting entities in a <em>set</em> or an empty
+<em>set</em>. This may not sound so useful at the level of this object but
+becomes more useful once we want to collect entities having certain
+kind of interactions across a series of <cite>Interaction</cite> objects.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>entity_type</strong> (<em>str</em>) – The type of the molecular entity. Possible values: <cite>protein</cite>,
+<cite>complex</cite>, <cite>mirna</cite>, <cite>small_molecule</cite>.</p></li>
+<li><p><strong>return_type</strong> (<em>str</em>) – The type of values to return. Default is
+py:class:<code class="docutils literal notranslate"><span class="pre">pypath.entity.Entity</span></code> objects, alternatives are
+<code class="docutils literal notranslate"><span class="pre">labels</span></code>  <code class="docutils literal notranslate"><span class="pre">identifiers</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.protein_identifiers_by_interaction_type_and_data_model">
+<span class="sig-name descname"><span class="pre">protein_identifiers_by_interaction_type_and_data_model</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.protein_identifiers_by_interaction_type_and_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the entities involved in interactions matching the criteria.
+It either returns both interacting entities in a <em>set</em> or an empty
+<em>set</em>. This may not sound so useful at the level of this object but
+becomes more useful once we want to collect entities having certain
+kind of interactions across a series of <cite>Interaction</cite> objects.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>entity_type</strong> (<em>str</em>) – The type of the molecular entity. Possible values: <cite>protein</cite>,
+<cite>complex</cite>, <cite>mirna</cite>, <cite>small_molecule</cite>.</p></li>
+<li><p><strong>return_type</strong> (<em>str</em>) – The type of values to return. Default is
+py:class:<code class="docutils literal notranslate"><span class="pre">pypath.entity.Entity</span></code> objects, alternatives are
+<code class="docutils literal notranslate"><span class="pre">labels</span></code>  <code class="docutils literal notranslate"><span class="pre">identifiers</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.protein_identifiers_by_interaction_type_and_data_model_and_resource">
+<span class="sig-name descname"><span class="pre">protein_identifiers_by_interaction_type_and_data_model_and_resource</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.protein_identifiers_by_interaction_type_and_data_model_and_resource" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the entities involved in interactions matching the criteria.
+It either returns both interacting entities in a <em>set</em> or an empty
+<em>set</em>. This may not sound so useful at the level of this object but
+becomes more useful once we want to collect entities having certain
+kind of interactions across a series of <cite>Interaction</cite> objects.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>entity_type</strong> (<em>str</em>) – The type of the molecular entity. Possible values: <cite>protein</cite>,
+<cite>complex</cite>, <cite>mirna</cite>, <cite>small_molecule</cite>.</p></li>
+<li><p><strong>return_type</strong> (<em>str</em>) – The type of values to return. Default is
+py:class:<code class="docutils literal notranslate"><span class="pre">pypath.entity.Entity</span></code> objects, alternatives are
+<code class="docutils literal notranslate"><span class="pre">labels</span></code>  <code class="docutils literal notranslate"><span class="pre">identifiers</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.protein_identifiers_by_reference">
+<span class="sig-name descname"><span class="pre">protein_identifiers_by_reference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.protein_identifiers_by_reference" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the entities involved in interactions matching the criteria.
+It either returns both interacting entities in a <em>set</em> or an empty
+<em>set</em>. This may not sound so useful at the level of this object but
+becomes more useful once we want to collect entities having certain
+kind of interactions across a series of <cite>Interaction</cite> objects.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>entity_type</strong> (<em>str</em>) – The type of the molecular entity. Possible values: <cite>protein</cite>,
+<cite>complex</cite>, <cite>mirna</cite>, <cite>small_molecule</cite>.</p></li>
+<li><p><strong>return_type</strong> (<em>str</em>) – The type of values to return. Default is
+py:class:<code class="docutils literal notranslate"><span class="pre">pypath.entity.Entity</span></code> objects, alternatives are
+<code class="docutils literal notranslate"><span class="pre">labels</span></code>  <code class="docutils literal notranslate"><span class="pre">identifiers</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.protein_identifiers_by_resource">
+<span class="sig-name descname"><span class="pre">protein_identifiers_by_resource</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.protein_identifiers_by_resource" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the entities involved in interactions matching the criteria.
+It either returns both interacting entities in a <em>set</em> or an empty
+<em>set</em>. This may not sound so useful at the level of this object but
+becomes more useful once we want to collect entities having certain
+kind of interactions across a series of <cite>Interaction</cite> objects.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>entity_type</strong> (<em>str</em>) – The type of the molecular entity. Possible values: <cite>protein</cite>,
+<cite>complex</cite>, <cite>mirna</cite>, <cite>small_molecule</cite>.</p></li>
+<li><p><strong>return_type</strong> (<em>str</em>) – The type of values to return. Default is
+py:class:<code class="docutils literal notranslate"><span class="pre">pypath.entity.Entity</span></code> objects, alternatives are
+<code class="docutils literal notranslate"><span class="pre">labels</span></code>  <code class="docutils literal notranslate"><span class="pre">identifiers</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.protein_labels_by_data_model">
+<span class="sig-name descname"><span class="pre">protein_labels_by_data_model</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.protein_labels_by_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the entities involved in interactions matching the criteria.
+It either returns both interacting entities in a <em>set</em> or an empty
+<em>set</em>. This may not sound so useful at the level of this object but
+becomes more useful once we want to collect entities having certain
+kind of interactions across a series of <cite>Interaction</cite> objects.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>entity_type</strong> (<em>str</em>) – The type of the molecular entity. Possible values: <cite>protein</cite>,
+<cite>complex</cite>, <cite>mirna</cite>, <cite>small_molecule</cite>.</p></li>
+<li><p><strong>return_type</strong> (<em>str</em>) – The type of values to return. Default is
+py:class:<code class="docutils literal notranslate"><span class="pre">pypath.entity.Entity</span></code> objects, alternatives are
+<code class="docutils literal notranslate"><span class="pre">labels</span></code>  <code class="docutils literal notranslate"><span class="pre">identifiers</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.protein_labels_by_interaction_type">
+<span class="sig-name descname"><span class="pre">protein_labels_by_interaction_type</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.protein_labels_by_interaction_type" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the entities involved in interactions matching the criteria.
+It either returns both interacting entities in a <em>set</em> or an empty
+<em>set</em>. This may not sound so useful at the level of this object but
+becomes more useful once we want to collect entities having certain
+kind of interactions across a series of <cite>Interaction</cite> objects.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>entity_type</strong> (<em>str</em>) – The type of the molecular entity. Possible values: <cite>protein</cite>,
+<cite>complex</cite>, <cite>mirna</cite>, <cite>small_molecule</cite>.</p></li>
+<li><p><strong>return_type</strong> (<em>str</em>) – The type of values to return. Default is
+py:class:<code class="docutils literal notranslate"><span class="pre">pypath.entity.Entity</span></code> objects, alternatives are
+<code class="docutils literal notranslate"><span class="pre">labels</span></code>  <code class="docutils literal notranslate"><span class="pre">identifiers</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.protein_labels_by_interaction_type_and_data_model">
+<span class="sig-name descname"><span class="pre">protein_labels_by_interaction_type_and_data_model</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.protein_labels_by_interaction_type_and_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the entities involved in interactions matching the criteria.
+It either returns both interacting entities in a <em>set</em> or an empty
+<em>set</em>. This may not sound so useful at the level of this object but
+becomes more useful once we want to collect entities having certain
+kind of interactions across a series of <cite>Interaction</cite> objects.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>entity_type</strong> (<em>str</em>) – The type of the molecular entity. Possible values: <cite>protein</cite>,
+<cite>complex</cite>, <cite>mirna</cite>, <cite>small_molecule</cite>.</p></li>
+<li><p><strong>return_type</strong> (<em>str</em>) – The type of values to return. Default is
+py:class:<code class="docutils literal notranslate"><span class="pre">pypath.entity.Entity</span></code> objects, alternatives are
+<code class="docutils literal notranslate"><span class="pre">labels</span></code>  <code class="docutils literal notranslate"><span class="pre">identifiers</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.protein_labels_by_interaction_type_and_data_model_and_resource">
+<span class="sig-name descname"><span class="pre">protein_labels_by_interaction_type_and_data_model_and_resource</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.protein_labels_by_interaction_type_and_data_model_and_resource" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the entities involved in interactions matching the criteria.
+It either returns both interacting entities in a <em>set</em> or an empty
+<em>set</em>. This may not sound so useful at the level of this object but
+becomes more useful once we want to collect entities having certain
+kind of interactions across a series of <cite>Interaction</cite> objects.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>entity_type</strong> (<em>str</em>) – The type of the molecular entity. Possible values: <cite>protein</cite>,
+<cite>complex</cite>, <cite>mirna</cite>, <cite>small_molecule</cite>.</p></li>
+<li><p><strong>return_type</strong> (<em>str</em>) – The type of values to return. Default is
+py:class:<code class="docutils literal notranslate"><span class="pre">pypath.entity.Entity</span></code> objects, alternatives are
+<code class="docutils literal notranslate"><span class="pre">labels</span></code>  <code class="docutils literal notranslate"><span class="pre">identifiers</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.protein_labels_by_reference">
+<span class="sig-name descname"><span class="pre">protein_labels_by_reference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.protein_labels_by_reference" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the entities involved in interactions matching the criteria.
+It either returns both interacting entities in a <em>set</em> or an empty
+<em>set</em>. This may not sound so useful at the level of this object but
+becomes more useful once we want to collect entities having certain
+kind of interactions across a series of <cite>Interaction</cite> objects.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>entity_type</strong> (<em>str</em>) – The type of the molecular entity. Possible values: <cite>protein</cite>,
+<cite>complex</cite>, <cite>mirna</cite>, <cite>small_molecule</cite>.</p></li>
+<li><p><strong>return_type</strong> (<em>str</em>) – The type of values to return. Default is
+py:class:<code class="docutils literal notranslate"><span class="pre">pypath.entity.Entity</span></code> objects, alternatives are
+<code class="docutils literal notranslate"><span class="pre">labels</span></code>  <code class="docutils literal notranslate"><span class="pre">identifiers</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.protein_labels_by_resource">
+<span class="sig-name descname"><span class="pre">protein_labels_by_resource</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.protein_labels_by_resource" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the entities involved in interactions matching the criteria.
+It either returns both interacting entities in a <em>set</em> or an empty
+<em>set</em>. This may not sound so useful at the level of this object but
+becomes more useful once we want to collect entities having certain
+kind of interactions across a series of <cite>Interaction</cite> objects.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>entity_type</strong> (<em>str</em>) – The type of the molecular entity. Possible values: <cite>protein</cite>,
+<cite>complex</cite>, <cite>mirna</cite>, <cite>small_molecule</cite>.</p></li>
+<li><p><strong>return_type</strong> (<em>str</em>) – The type of values to return. Default is
+py:class:<code class="docutils literal notranslate"><span class="pre">pypath.entity.Entity</span></code> objects, alternatives are
+<code class="docutils literal notranslate"><span class="pre">labels</span></code>  <code class="docutils literal notranslate"><span class="pre">identifiers</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.proteins_by_data_model">
+<span class="sig-name descname"><span class="pre">proteins_by_data_model</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.proteins_by_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the entities involved in interactions matching the criteria.
+It either returns both interacting entities in a <em>set</em> or an empty
+<em>set</em>. This may not sound so useful at the level of this object but
+becomes more useful once we want to collect entities having certain
+kind of interactions across a series of <cite>Interaction</cite> objects.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>entity_type</strong> (<em>str</em>) – The type of the molecular entity. Possible values: <cite>protein</cite>,
+<cite>complex</cite>, <cite>mirna</cite>, <cite>small_molecule</cite>.</p></li>
+<li><p><strong>return_type</strong> (<em>str</em>) – The type of values to return. Default is
+py:class:<code class="docutils literal notranslate"><span class="pre">pypath.entity.Entity</span></code> objects, alternatives are
+<code class="docutils literal notranslate"><span class="pre">labels</span></code>  <code class="docutils literal notranslate"><span class="pre">identifiers</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.proteins_by_interaction_type">
+<span class="sig-name descname"><span class="pre">proteins_by_interaction_type</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.proteins_by_interaction_type" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the entities involved in interactions matching the criteria.
+It either returns both interacting entities in a <em>set</em> or an empty
+<em>set</em>. This may not sound so useful at the level of this object but
+becomes more useful once we want to collect entities having certain
+kind of interactions across a series of <cite>Interaction</cite> objects.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>entity_type</strong> (<em>str</em>) – The type of the molecular entity. Possible values: <cite>protein</cite>,
+<cite>complex</cite>, <cite>mirna</cite>, <cite>small_molecule</cite>.</p></li>
+<li><p><strong>return_type</strong> (<em>str</em>) – The type of values to return. Default is
+py:class:<code class="docutils literal notranslate"><span class="pre">pypath.entity.Entity</span></code> objects, alternatives are
+<code class="docutils literal notranslate"><span class="pre">labels</span></code>  <code class="docutils literal notranslate"><span class="pre">identifiers</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.proteins_by_interaction_type_and_data_model">
+<span class="sig-name descname"><span class="pre">proteins_by_interaction_type_and_data_model</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.proteins_by_interaction_type_and_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the entities involved in interactions matching the criteria.
+It either returns both interacting entities in a <em>set</em> or an empty
+<em>set</em>. This may not sound so useful at the level of this object but
+becomes more useful once we want to collect entities having certain
+kind of interactions across a series of <cite>Interaction</cite> objects.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>entity_type</strong> (<em>str</em>) – The type of the molecular entity. Possible values: <cite>protein</cite>,
+<cite>complex</cite>, <cite>mirna</cite>, <cite>small_molecule</cite>.</p></li>
+<li><p><strong>return_type</strong> (<em>str</em>) – The type of values to return. Default is
+py:class:<code class="docutils literal notranslate"><span class="pre">pypath.entity.Entity</span></code> objects, alternatives are
+<code class="docutils literal notranslate"><span class="pre">labels</span></code>  <code class="docutils literal notranslate"><span class="pre">identifiers</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.proteins_by_interaction_type_and_data_model_and_resource">
+<span class="sig-name descname"><span class="pre">proteins_by_interaction_type_and_data_model_and_resource</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.proteins_by_interaction_type_and_data_model_and_resource" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the entities involved in interactions matching the criteria.
+It either returns both interacting entities in a <em>set</em> or an empty
+<em>set</em>. This may not sound so useful at the level of this object but
+becomes more useful once we want to collect entities having certain
+kind of interactions across a series of <cite>Interaction</cite> objects.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>entity_type</strong> (<em>str</em>) – The type of the molecular entity. Possible values: <cite>protein</cite>,
+<cite>complex</cite>, <cite>mirna</cite>, <cite>small_molecule</cite>.</p></li>
+<li><p><strong>return_type</strong> (<em>str</em>) – The type of values to return. Default is
+py:class:<code class="docutils literal notranslate"><span class="pre">pypath.entity.Entity</span></code> objects, alternatives are
+<code class="docutils literal notranslate"><span class="pre">labels</span></code>  <code class="docutils literal notranslate"><span class="pre">identifiers</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.proteins_by_reference">
+<span class="sig-name descname"><span class="pre">proteins_by_reference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.proteins_by_reference" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the entities involved in interactions matching the criteria.
+It either returns both interacting entities in a <em>set</em> or an empty
+<em>set</em>. This may not sound so useful at the level of this object but
+becomes more useful once we want to collect entities having certain
+kind of interactions across a series of <cite>Interaction</cite> objects.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>entity_type</strong> (<em>str</em>) – The type of the molecular entity. Possible values: <cite>protein</cite>,
+<cite>complex</cite>, <cite>mirna</cite>, <cite>small_molecule</cite>.</p></li>
+<li><p><strong>return_type</strong> (<em>str</em>) – The type of values to return. Default is
+py:class:<code class="docutils literal notranslate"><span class="pre">pypath.entity.Entity</span></code> objects, alternatives are
+<code class="docutils literal notranslate"><span class="pre">labels</span></code>  <code class="docutils literal notranslate"><span class="pre">identifiers</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.proteins_by_resource">
+<span class="sig-name descname"><span class="pre">proteins_by_resource</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.proteins_by_resource" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the entities involved in interactions matching the criteria.
+It either returns both interacting entities in a <em>set</em> or an empty
+<em>set</em>. This may not sound so useful at the level of this object but
+becomes more useful once we want to collect entities having certain
+kind of interactions across a series of <cite>Interaction</cite> objects.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>entity_type</strong> (<em>str</em>) – The type of the molecular entity. Possible values: <cite>protein</cite>,
+<cite>complex</cite>, <cite>mirna</cite>, <cite>small_molecule</cite>.</p></li>
+<li><p><strong>return_type</strong> (<em>str</em>) – The type of values to return. Default is
+py:class:<code class="docutils literal notranslate"><span class="pre">pypath.entity.Entity</span></code> objects, alternatives are
+<code class="docutils literal notranslate"><span class="pre">labels</span></code>  <code class="docutils literal notranslate"><span class="pre">identifiers</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.references_by_data_model">
+<span class="sig-name descname"><span class="pre">references_by_data_model</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.references_by_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves references matching the criteria.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.references_by_interaction_type">
+<span class="sig-name descname"><span class="pre">references_by_interaction_type</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.references_by_interaction_type" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves references matching the criteria.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.references_by_interaction_type_and_data_model">
+<span class="sig-name descname"><span class="pre">references_by_interaction_type_and_data_model</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.references_by_interaction_type_and_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves references matching the criteria.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.references_by_interaction_type_and_data_model_and_resource">
+<span class="sig-name descname"><span class="pre">references_by_interaction_type_and_data_model_and_resource</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.references_by_interaction_type_and_data_model_and_resource" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves references matching the criteria.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.references_by_reference">
+<span class="sig-name descname"><span class="pre">references_by_reference</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.references_by_reference" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves references matching the criteria.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.references_by_resource">
+<span class="sig-name descname"><span class="pre">references_by_resource</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.references_by_resource" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves references matching the criteria.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.reload">
+<span class="sig-name descname"><span class="pre">reload</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/interaction.html#Interaction.reload"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.interaction.Interaction.reload" title="Link to this definition">§</a></dt>
+<dd><p>Reloads the object from the module level.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.resource_names_by_data_model">
+<span class="sig-name descname"><span class="pre">resource_names_by_data_model</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.resource_names_by_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves resource names matching the criteria.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.resource_names_by_interaction_type">
+<span class="sig-name descname"><span class="pre">resource_names_by_interaction_type</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.resource_names_by_interaction_type" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves resource names matching the criteria.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.resource_names_by_interaction_type_and_data_model">
+<span class="sig-name descname"><span class="pre">resource_names_by_interaction_type_and_data_model</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.resource_names_by_interaction_type_and_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves resource names matching the criteria.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.resource_names_by_interaction_type_and_data_model_and_resource">
+<span class="sig-name descname"><span class="pre">resource_names_by_interaction_type_and_data_model_and_resource</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.resource_names_by_interaction_type_and_data_model_and_resource" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves resource names matching the criteria.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.resource_names_by_reference">
+<span class="sig-name descname"><span class="pre">resource_names_by_reference</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.resource_names_by_reference" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves resource names matching the criteria.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.resource_names_by_resource">
+<span class="sig-name descname"><span class="pre">resource_names_by_resource</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.resource_names_by_resource" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves resource names matching the criteria.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.resource_names_via_by_data_model">
+<span class="sig-name descname"><span class="pre">resource_names_via_by_data_model</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.resource_names_via_by_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves resource names via matching the criteria.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.resource_names_via_by_interaction_type">
+<span class="sig-name descname"><span class="pre">resource_names_via_by_interaction_type</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.resource_names_via_by_interaction_type" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves resource names via matching the criteria.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.resource_names_via_by_interaction_type_and_data_model">
+<span class="sig-name descname"><span class="pre">resource_names_via_by_interaction_type_and_data_model</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.resource_names_via_by_interaction_type_and_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves resource names via matching the criteria.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.resource_names_via_by_interaction_type_and_data_model_and_resource">
+<span class="sig-name descname"><span class="pre">resource_names_via_by_interaction_type_and_data_model_and_resource</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.resource_names_via_by_interaction_type_and_data_model_and_resource" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves resource names via matching the criteria.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.resource_names_via_by_reference">
+<span class="sig-name descname"><span class="pre">resource_names_via_by_reference</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.resource_names_via_by_reference" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves resource names via matching the criteria.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.resource_names_via_by_resource">
+<span class="sig-name descname"><span class="pre">resource_names_via_by_resource</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.resource_names_via_by_resource" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves resource names via matching the criteria.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.resources_a_b">
+<span class="sig-name descname"><span class="pre">resources_a_b</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">evidences</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resource_names</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">sources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/interaction.html#Interaction.resources_a_b"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.interaction.Interaction.resources_a_b" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the list of resources for the <code class="xref py py-attr docutils literal notranslate"><span class="pre">a_b</span></code>
+direction.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Returns<span class="colon">:</span></dt>
+<dd class="field-odd"><p>(<em>set</em>) – Contains the names of the sources supporting the
+<code class="xref py py-attr docutils literal notranslate"><span class="pre">a_b</span></code> directionality of the edge.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.resources_b_a">
+<span class="sig-name descname"><span class="pre">resources_b_a</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">evidences</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resource_names</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">sources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/interaction.html#Interaction.resources_b_a"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.interaction.Interaction.resources_b_a" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the list of sources for the <code class="xref py py-attr docutils literal notranslate"><span class="pre">b_a</span></code> direction.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Returns<span class="colon">:</span></dt>
+<dd class="field-odd"><p>(<em>set</em>) – Contains the names of the sources supporting the
+<code class="xref py py-attr docutils literal notranslate"><span class="pre">b_a</span></code> directionality of the edge.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.resources_by_data_model">
+<span class="sig-name descname"><span class="pre">resources_by_data_model</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.resources_by_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves resources matching the criteria.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.resources_by_interaction_type">
+<span class="sig-name descname"><span class="pre">resources_by_interaction_type</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.resources_by_interaction_type" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves resources matching the criteria.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.resources_by_interaction_type_and_data_model">
+<span class="sig-name descname"><span class="pre">resources_by_interaction_type_and_data_model</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.resources_by_interaction_type_and_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves resources matching the criteria.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.resources_by_interaction_type_and_data_model_and_resource">
+<span class="sig-name descname"><span class="pre">resources_by_interaction_type_and_data_model_and_resource</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.resources_by_interaction_type_and_data_model_and_resource" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves resources matching the criteria.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.resources_by_reference">
+<span class="sig-name descname"><span class="pre">resources_by_reference</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.resources_by_reference" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves resources matching the criteria.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.resources_by_resource">
+<span class="sig-name descname"><span class="pre">resources_by_resource</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.resources_by_resource" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves resources matching the criteria.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.resources_undirected">
+<span class="sig-name descname"><span class="pre">resources_undirected</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">evidences</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resource_names</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">sources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/interaction.html#Interaction.resources_undirected"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.interaction.Interaction.resources_undirected" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the list of resources without directed information.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Returns<span class="colon">:</span></dt>
+<dd class="field-odd"><p>(<em>set</em>) – Contains the names of the sources supporting the
+edge presence but without specific directionality
+information.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.resources_via_by_data_model">
+<span class="sig-name descname"><span class="pre">resources_via_by_data_model</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.resources_via_by_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves resources via matching the criteria.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.resources_via_by_interaction_type">
+<span class="sig-name descname"><span class="pre">resources_via_by_interaction_type</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.resources_via_by_interaction_type" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves resources via matching the criteria.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.resources_via_by_interaction_type_and_data_model">
+<span class="sig-name descname"><span class="pre">resources_via_by_interaction_type_and_data_model</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.resources_via_by_interaction_type_and_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves resources via matching the criteria.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.resources_via_by_interaction_type_and_data_model_and_resource">
+<span class="sig-name descname"><span class="pre">resources_via_by_interaction_type_and_data_model_and_resource</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.resources_via_by_interaction_type_and_data_model_and_resource" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves resources via matching the criteria.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.resources_via_by_reference">
+<span class="sig-name descname"><span class="pre">resources_via_by_reference</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.resources_via_by_reference" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves resources via matching the criteria.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.resources_via_by_resource">
+<span class="sig-name descname"><span class="pre">resources_via_by_resource</span></span><a class="headerlink" href="#pypath.core.interaction.Interaction.resources_via_by_resource" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves resources via matching the criteria.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.serialize">
+<span class="sig-name descname"><span class="pre">serialize</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.serialize" title="Link to this definition">§</a></dt>
+<dd><p>Generates a JSON string with the full contents of the attributes,
+without any whitespace or line break.</p>
+<dl class="simple">
+<dt>Returns</dt><dd><p>(str): The attributes JSON serialized.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.serialize_attrs">
+<span class="sig-name descname"><span class="pre">serialize_attrs</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">direction</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">tuple</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><span class="pre">str</span></span></span><a class="reference internal" href="../_modules/pypath/core/interaction.html#Interaction.serialize_attrs"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.interaction.Interaction.serialize_attrs" title="Link to this definition">§</a></dt>
+<dd><p>Serialize the resource specific attributes into a JSON string.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.serialize_evidences">
+<span class="sig-name descname"><span class="pre">serialize_evidences</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">direction</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">tuple</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><span class="pre">str</span></span></span><a class="reference internal" href="../_modules/pypath/core/interaction.html#Interaction.serialize_evidences"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.interaction.Interaction.serialize_evidences" title="Link to this definition">§</a></dt>
+<dd><p>Serialize the evidences into a JSON string.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.small_molecule_identifiers_by_data_model">
+<span class="sig-name descname"><span class="pre">small_molecule_identifiers_by_data_model</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.small_molecule_identifiers_by_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the entities involved in interactions matching the criteria.
+It either returns both interacting entities in a <em>set</em> or an empty
+<em>set</em>. This may not sound so useful at the level of this object but
+becomes more useful once we want to collect entities having certain
+kind of interactions across a series of <cite>Interaction</cite> objects.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>entity_type</strong> (<em>str</em>) – The type of the molecular entity. Possible values: <cite>protein</cite>,
+<cite>complex</cite>, <cite>mirna</cite>, <cite>small_molecule</cite>.</p></li>
+<li><p><strong>return_type</strong> (<em>str</em>) – The type of values to return. Default is
+py:class:<code class="docutils literal notranslate"><span class="pre">pypath.entity.Entity</span></code> objects, alternatives are
+<code class="docutils literal notranslate"><span class="pre">labels</span></code>  <code class="docutils literal notranslate"><span class="pre">identifiers</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.small_molecule_identifiers_by_interaction_type">
+<span class="sig-name descname"><span class="pre">small_molecule_identifiers_by_interaction_type</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.small_molecule_identifiers_by_interaction_type" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the entities involved in interactions matching the criteria.
+It either returns both interacting entities in a <em>set</em> or an empty
+<em>set</em>. This may not sound so useful at the level of this object but
+becomes more useful once we want to collect entities having certain
+kind of interactions across a series of <cite>Interaction</cite> objects.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>entity_type</strong> (<em>str</em>) – The type of the molecular entity. Possible values: <cite>protein</cite>,
+<cite>complex</cite>, <cite>mirna</cite>, <cite>small_molecule</cite>.</p></li>
+<li><p><strong>return_type</strong> (<em>str</em>) – The type of values to return. Default is
+py:class:<code class="docutils literal notranslate"><span class="pre">pypath.entity.Entity</span></code> objects, alternatives are
+<code class="docutils literal notranslate"><span class="pre">labels</span></code>  <code class="docutils literal notranslate"><span class="pre">identifiers</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.small_molecule_identifiers_by_interaction_type_and_data_model">
+<span class="sig-name descname"><span class="pre">small_molecule_identifiers_by_interaction_type_and_data_model</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.small_molecule_identifiers_by_interaction_type_and_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the entities involved in interactions matching the criteria.
+It either returns both interacting entities in a <em>set</em> or an empty
+<em>set</em>. This may not sound so useful at the level of this object but
+becomes more useful once we want to collect entities having certain
+kind of interactions across a series of <cite>Interaction</cite> objects.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>entity_type</strong> (<em>str</em>) – The type of the molecular entity. Possible values: <cite>protein</cite>,
+<cite>complex</cite>, <cite>mirna</cite>, <cite>small_molecule</cite>.</p></li>
+<li><p><strong>return_type</strong> (<em>str</em>) – The type of values to return. Default is
+py:class:<code class="docutils literal notranslate"><span class="pre">pypath.entity.Entity</span></code> objects, alternatives are
+<code class="docutils literal notranslate"><span class="pre">labels</span></code>  <code class="docutils literal notranslate"><span class="pre">identifiers</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.small_molecule_identifiers_by_interaction_type_and_data_model_and_resource">
+<span class="sig-name descname"><span class="pre">small_molecule_identifiers_by_interaction_type_and_data_model_and_resource</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.small_molecule_identifiers_by_interaction_type_and_data_model_and_resource" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the entities involved in interactions matching the criteria.
+It either returns both interacting entities in a <em>set</em> or an empty
+<em>set</em>. This may not sound so useful at the level of this object but
+becomes more useful once we want to collect entities having certain
+kind of interactions across a series of <cite>Interaction</cite> objects.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>entity_type</strong> (<em>str</em>) – The type of the molecular entity. Possible values: <cite>protein</cite>,
+<cite>complex</cite>, <cite>mirna</cite>, <cite>small_molecule</cite>.</p></li>
+<li><p><strong>return_type</strong> (<em>str</em>) – The type of values to return. Default is
+py:class:<code class="docutils literal notranslate"><span class="pre">pypath.entity.Entity</span></code> objects, alternatives are
+<code class="docutils literal notranslate"><span class="pre">labels</span></code>  <code class="docutils literal notranslate"><span class="pre">identifiers</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.small_molecule_identifiers_by_reference">
+<span class="sig-name descname"><span class="pre">small_molecule_identifiers_by_reference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.small_molecule_identifiers_by_reference" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the entities involved in interactions matching the criteria.
+It either returns both interacting entities in a <em>set</em> or an empty
+<em>set</em>. This may not sound so useful at the level of this object but
+becomes more useful once we want to collect entities having certain
+kind of interactions across a series of <cite>Interaction</cite> objects.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>entity_type</strong> (<em>str</em>) – The type of the molecular entity. Possible values: <cite>protein</cite>,
+<cite>complex</cite>, <cite>mirna</cite>, <cite>small_molecule</cite>.</p></li>
+<li><p><strong>return_type</strong> (<em>str</em>) – The type of values to return. Default is
+py:class:<code class="docutils literal notranslate"><span class="pre">pypath.entity.Entity</span></code> objects, alternatives are
+<code class="docutils literal notranslate"><span class="pre">labels</span></code>  <code class="docutils literal notranslate"><span class="pre">identifiers</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.small_molecule_identifiers_by_resource">
+<span class="sig-name descname"><span class="pre">small_molecule_identifiers_by_resource</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.small_molecule_identifiers_by_resource" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the entities involved in interactions matching the criteria.
+It either returns both interacting entities in a <em>set</em> or an empty
+<em>set</em>. This may not sound so useful at the level of this object but
+becomes more useful once we want to collect entities having certain
+kind of interactions across a series of <cite>Interaction</cite> objects.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>entity_type</strong> (<em>str</em>) – The type of the molecular entity. Possible values: <cite>protein</cite>,
+<cite>complex</cite>, <cite>mirna</cite>, <cite>small_molecule</cite>.</p></li>
+<li><p><strong>return_type</strong> (<em>str</em>) – The type of values to return. Default is
+py:class:<code class="docutils literal notranslate"><span class="pre">pypath.entity.Entity</span></code> objects, alternatives are
+<code class="docutils literal notranslate"><span class="pre">labels</span></code>  <code class="docutils literal notranslate"><span class="pre">identifiers</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.small_molecule_labels_by_data_model">
+<span class="sig-name descname"><span class="pre">small_molecule_labels_by_data_model</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.small_molecule_labels_by_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the entities involved in interactions matching the criteria.
+It either returns both interacting entities in a <em>set</em> or an empty
+<em>set</em>. This may not sound so useful at the level of this object but
+becomes more useful once we want to collect entities having certain
+kind of interactions across a series of <cite>Interaction</cite> objects.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>entity_type</strong> (<em>str</em>) – The type of the molecular entity. Possible values: <cite>protein</cite>,
+<cite>complex</cite>, <cite>mirna</cite>, <cite>small_molecule</cite>.</p></li>
+<li><p><strong>return_type</strong> (<em>str</em>) – The type of values to return. Default is
+py:class:<code class="docutils literal notranslate"><span class="pre">pypath.entity.Entity</span></code> objects, alternatives are
+<code class="docutils literal notranslate"><span class="pre">labels</span></code>  <code class="docutils literal notranslate"><span class="pre">identifiers</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.small_molecule_labels_by_interaction_type">
+<span class="sig-name descname"><span class="pre">small_molecule_labels_by_interaction_type</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.small_molecule_labels_by_interaction_type" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the entities involved in interactions matching the criteria.
+It either returns both interacting entities in a <em>set</em> or an empty
+<em>set</em>. This may not sound so useful at the level of this object but
+becomes more useful once we want to collect entities having certain
+kind of interactions across a series of <cite>Interaction</cite> objects.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>entity_type</strong> (<em>str</em>) – The type of the molecular entity. Possible values: <cite>protein</cite>,
+<cite>complex</cite>, <cite>mirna</cite>, <cite>small_molecule</cite>.</p></li>
+<li><p><strong>return_type</strong> (<em>str</em>) – The type of values to return. Default is
+py:class:<code class="docutils literal notranslate"><span class="pre">pypath.entity.Entity</span></code> objects, alternatives are
+<code class="docutils literal notranslate"><span class="pre">labels</span></code>  <code class="docutils literal notranslate"><span class="pre">identifiers</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.small_molecule_labels_by_interaction_type_and_data_model">
+<span class="sig-name descname"><span class="pre">small_molecule_labels_by_interaction_type_and_data_model</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.small_molecule_labels_by_interaction_type_and_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the entities involved in interactions matching the criteria.
+It either returns both interacting entities in a <em>set</em> or an empty
+<em>set</em>. This may not sound so useful at the level of this object but
+becomes more useful once we want to collect entities having certain
+kind of interactions across a series of <cite>Interaction</cite> objects.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>entity_type</strong> (<em>str</em>) – The type of the molecular entity. Possible values: <cite>protein</cite>,
+<cite>complex</cite>, <cite>mirna</cite>, <cite>small_molecule</cite>.</p></li>
+<li><p><strong>return_type</strong> (<em>str</em>) – The type of values to return. Default is
+py:class:<code class="docutils literal notranslate"><span class="pre">pypath.entity.Entity</span></code> objects, alternatives are
+<code class="docutils literal notranslate"><span class="pre">labels</span></code>  <code class="docutils literal notranslate"><span class="pre">identifiers</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.small_molecule_labels_by_interaction_type_and_data_model_and_resource">
+<span class="sig-name descname"><span class="pre">small_molecule_labels_by_interaction_type_and_data_model_and_resource</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.small_molecule_labels_by_interaction_type_and_data_model_and_resource" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the entities involved in interactions matching the criteria.
+It either returns both interacting entities in a <em>set</em> or an empty
+<em>set</em>. This may not sound so useful at the level of this object but
+becomes more useful once we want to collect entities having certain
+kind of interactions across a series of <cite>Interaction</cite> objects.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>entity_type</strong> (<em>str</em>) – The type of the molecular entity. Possible values: <cite>protein</cite>,
+<cite>complex</cite>, <cite>mirna</cite>, <cite>small_molecule</cite>.</p></li>
+<li><p><strong>return_type</strong> (<em>str</em>) – The type of values to return. Default is
+py:class:<code class="docutils literal notranslate"><span class="pre">pypath.entity.Entity</span></code> objects, alternatives are
+<code class="docutils literal notranslate"><span class="pre">labels</span></code>  <code class="docutils literal notranslate"><span class="pre">identifiers</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.small_molecule_labels_by_reference">
+<span class="sig-name descname"><span class="pre">small_molecule_labels_by_reference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.small_molecule_labels_by_reference" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the entities involved in interactions matching the criteria.
+It either returns both interacting entities in a <em>set</em> or an empty
+<em>set</em>. This may not sound so useful at the level of this object but
+becomes more useful once we want to collect entities having certain
+kind of interactions across a series of <cite>Interaction</cite> objects.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>entity_type</strong> (<em>str</em>) – The type of the molecular entity. Possible values: <cite>protein</cite>,
+<cite>complex</cite>, <cite>mirna</cite>, <cite>small_molecule</cite>.</p></li>
+<li><p><strong>return_type</strong> (<em>str</em>) – The type of values to return. Default is
+py:class:<code class="docutils literal notranslate"><span class="pre">pypath.entity.Entity</span></code> objects, alternatives are
+<code class="docutils literal notranslate"><span class="pre">labels</span></code>  <code class="docutils literal notranslate"><span class="pre">identifiers</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.small_molecule_labels_by_resource">
+<span class="sig-name descname"><span class="pre">small_molecule_labels_by_resource</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.small_molecule_labels_by_resource" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the entities involved in interactions matching the criteria.
+It either returns both interacting entities in a <em>set</em> or an empty
+<em>set</em>. This may not sound so useful at the level of this object but
+becomes more useful once we want to collect entities having certain
+kind of interactions across a series of <cite>Interaction</cite> objects.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>entity_type</strong> (<em>str</em>) – The type of the molecular entity. Possible values: <cite>protein</cite>,
+<cite>complex</cite>, <cite>mirna</cite>, <cite>small_molecule</cite>.</p></li>
+<li><p><strong>return_type</strong> (<em>str</em>) – The type of values to return. Default is
+py:class:<code class="docutils literal notranslate"><span class="pre">pypath.entity.Entity</span></code> objects, alternatives are
+<code class="docutils literal notranslate"><span class="pre">labels</span></code>  <code class="docutils literal notranslate"><span class="pre">identifiers</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.small_molecules_by_data_model">
+<span class="sig-name descname"><span class="pre">small_molecules_by_data_model</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.small_molecules_by_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the entities involved in interactions matching the criteria.
+It either returns both interacting entities in a <em>set</em> or an empty
+<em>set</em>. This may not sound so useful at the level of this object but
+becomes more useful once we want to collect entities having certain
+kind of interactions across a series of <cite>Interaction</cite> objects.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>entity_type</strong> (<em>str</em>) – The type of the molecular entity. Possible values: <cite>protein</cite>,
+<cite>complex</cite>, <cite>mirna</cite>, <cite>small_molecule</cite>.</p></li>
+<li><p><strong>return_type</strong> (<em>str</em>) – The type of values to return. Default is
+py:class:<code class="docutils literal notranslate"><span class="pre">pypath.entity.Entity</span></code> objects, alternatives are
+<code class="docutils literal notranslate"><span class="pre">labels</span></code>  <code class="docutils literal notranslate"><span class="pre">identifiers</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.small_molecules_by_interaction_type">
+<span class="sig-name descname"><span class="pre">small_molecules_by_interaction_type</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.small_molecules_by_interaction_type" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the entities involved in interactions matching the criteria.
+It either returns both interacting entities in a <em>set</em> or an empty
+<em>set</em>. This may not sound so useful at the level of this object but
+becomes more useful once we want to collect entities having certain
+kind of interactions across a series of <cite>Interaction</cite> objects.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>entity_type</strong> (<em>str</em>) – The type of the molecular entity. Possible values: <cite>protein</cite>,
+<cite>complex</cite>, <cite>mirna</cite>, <cite>small_molecule</cite>.</p></li>
+<li><p><strong>return_type</strong> (<em>str</em>) – The type of values to return. Default is
+py:class:<code class="docutils literal notranslate"><span class="pre">pypath.entity.Entity</span></code> objects, alternatives are
+<code class="docutils literal notranslate"><span class="pre">labels</span></code>  <code class="docutils literal notranslate"><span class="pre">identifiers</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.small_molecules_by_interaction_type_and_data_model">
+<span class="sig-name descname"><span class="pre">small_molecules_by_interaction_type_and_data_model</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.small_molecules_by_interaction_type_and_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the entities involved in interactions matching the criteria.
+It either returns both interacting entities in a <em>set</em> or an empty
+<em>set</em>. This may not sound so useful at the level of this object but
+becomes more useful once we want to collect entities having certain
+kind of interactions across a series of <cite>Interaction</cite> objects.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>entity_type</strong> (<em>str</em>) – The type of the molecular entity. Possible values: <cite>protein</cite>,
+<cite>complex</cite>, <cite>mirna</cite>, <cite>small_molecule</cite>.</p></li>
+<li><p><strong>return_type</strong> (<em>str</em>) – The type of values to return. Default is
+py:class:<code class="docutils literal notranslate"><span class="pre">pypath.entity.Entity</span></code> objects, alternatives are
+<code class="docutils literal notranslate"><span class="pre">labels</span></code>  <code class="docutils literal notranslate"><span class="pre">identifiers</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.small_molecules_by_interaction_type_and_data_model_and_resource">
+<span class="sig-name descname"><span class="pre">small_molecules_by_interaction_type_and_data_model_and_resource</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.small_molecules_by_interaction_type_and_data_model_and_resource" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the entities involved in interactions matching the criteria.
+It either returns both interacting entities in a <em>set</em> or an empty
+<em>set</em>. This may not sound so useful at the level of this object but
+becomes more useful once we want to collect entities having certain
+kind of interactions across a series of <cite>Interaction</cite> objects.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>entity_type</strong> (<em>str</em>) – The type of the molecular entity. Possible values: <cite>protein</cite>,
+<cite>complex</cite>, <cite>mirna</cite>, <cite>small_molecule</cite>.</p></li>
+<li><p><strong>return_type</strong> (<em>str</em>) – The type of values to return. Default is
+py:class:<code class="docutils literal notranslate"><span class="pre">pypath.entity.Entity</span></code> objects, alternatives are
+<code class="docutils literal notranslate"><span class="pre">labels</span></code>  <code class="docutils literal notranslate"><span class="pre">identifiers</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.small_molecules_by_reference">
+<span class="sig-name descname"><span class="pre">small_molecules_by_reference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.small_molecules_by_reference" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the entities involved in interactions matching the criteria.
+It either returns both interacting entities in a <em>set</em> or an empty
+<em>set</em>. This may not sound so useful at the level of this object but
+becomes more useful once we want to collect entities having certain
+kind of interactions across a series of <cite>Interaction</cite> objects.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>entity_type</strong> (<em>str</em>) – The type of the molecular entity. Possible values: <cite>protein</cite>,
+<cite>complex</cite>, <cite>mirna</cite>, <cite>small_molecule</cite>.</p></li>
+<li><p><strong>return_type</strong> (<em>str</em>) – The type of values to return. Default is
+py:class:<code class="docutils literal notranslate"><span class="pre">pypath.entity.Entity</span></code> objects, alternatives are
+<code class="docutils literal notranslate"><span class="pre">labels</span></code>  <code class="docutils literal notranslate"><span class="pre">identifiers</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.small_molecules_by_resource">
+<span class="sig-name descname"><span class="pre">small_molecules_by_resource</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.small_molecules_by_resource" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the entities involved in interactions matching the criteria.
+It either returns both interacting entities in a <em>set</em> or an empty
+<em>set</em>. This may not sound so useful at the level of this object but
+becomes more useful once we want to collect entities having certain
+kind of interactions across a series of <cite>Interaction</cite> objects.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>entity_type</strong> (<em>str</em>) – The type of the molecular entity. Possible values: <cite>protein</cite>,
+<cite>complex</cite>, <cite>mirna</cite>, <cite>small_molecule</cite>.</p></li>
+<li><p><strong>return_type</strong> (<em>str</em>) – The type of values to return. Default is
+py:class:<code class="docutils literal notranslate"><span class="pre">pypath.entity.Entity</span></code> objects, alternatives are
+<code class="docutils literal notranslate"><span class="pre">labels</span></code>  <code class="docutils literal notranslate"><span class="pre">identifiers</span></code>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.source">
+<span class="sig-name descname"><span class="pre">source</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">undirected</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/interaction.html#Interaction.source"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.interaction.Interaction.source" title="Link to this definition">§</a></dt>
+<dd><p>Returns the name(s) of the source node(s) for each existing
+direction on the interaction.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>undirected:</dt><dd><p>Optional, <code class="docutils literal notranslate"><span class="pre">False</span></code> by default.</p>
+</dd>
+</dl>
+</dd>
+<dt>Returns</dt><dd><p>(<em>list</em>) – Contains the name(s) for the source node(s).
+This means if the interaction is bidirectional, the list
+will contain both identifiers on the edge. If the
+interaction is undirected, an empty list will be returned.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.sources_reverse">
+<span class="sig-name descname"><span class="pre">sources_reverse</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">evidences</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resource_names</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">sources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.sources_reverse" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the list of sources for the <code class="xref py py-attr docutils literal notranslate"><span class="pre">b_a</span></code> direction.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Returns<span class="colon">:</span></dt>
+<dd class="field-odd"><p>(<em>set</em>) – Contains the names of the sources supporting the
+<code class="xref py py-attr docutils literal notranslate"><span class="pre">b_a</span></code> directionality of the edge.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.sources_straight">
+<span class="sig-name descname"><span class="pre">sources_straight</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">evidences</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resource_names</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">sources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.sources_straight" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the list of resources for the <code class="xref py py-attr docutils literal notranslate"><span class="pre">a_b</span></code>
+direction.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Returns<span class="colon">:</span></dt>
+<dd class="field-odd"><p>(<em>set</em>) – Contains the names of the sources supporting the
+<code class="xref py py-attr docutils literal notranslate"><span class="pre">a_b</span></code> directionality of the edge.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.sources_undirected">
+<span class="sig-name descname"><span class="pre">sources_undirected</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">evidences</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resource_names</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">sources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.sources_undirected" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the list of resources without directed information.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Returns<span class="colon">:</span></dt>
+<dd class="field-odd"><p>(<em>set</em>) – Contains the names of the sources supporting the
+edge presence but without specific directionality
+information.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.src">
+<span class="sig-name descname"><span class="pre">src</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">undirected</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.src" title="Link to this definition">§</a></dt>
+<dd><p>Returns the name(s) of the source node(s) for each existing
+direction on the interaction.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>undirected:</dt><dd><p>Optional, <code class="docutils literal notranslate"><span class="pre">False</span></code> by default.</p>
+</dd>
+</dl>
+</dd>
+<dt>Returns</dt><dd><p>(<em>list</em>) – Contains the name(s) for the source node(s).
+This means if the interaction is bidirectional, the list
+will contain both identifiers on the edge. If the
+interaction is undirected, an empty list will be returned.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.src_by_resource">
+<span class="sig-name descname"><span class="pre">src_by_resource</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">resource</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/interaction.html#Interaction.src_by_resource"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.interaction.Interaction.src_by_resource" title="Link to this definition">§</a></dt>
+<dd><p>Returns the name(s) of the source node(s) for each existing
+direction on the interaction for a specific <em>resource</em>.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><p><strong>resource</strong> (<em>str</em>) – Name of the resource according to which the information is to
+be retrieved.</p>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p>(<em>list</em>) – Contains the name(s) for the source node(s)
+according to the specified <em>resource</em>. This means if the
+interaction is bidirectional, the list will contain both
+identifiers on the edge. If the specified <em>source</em> is not
+found or invalid, an empty list will be returned.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.target">
+<span class="sig-name descname"><span class="pre">target</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">undirected</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/interaction.html#Interaction.target"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.interaction.Interaction.target" title="Link to this definition">§</a></dt>
+<dd><p>Returns the name(s) of the target node(s) for each existing
+direction on the interaction.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>undirected:</dt><dd><p>Optional, <code class="docutils literal notranslate"><span class="pre">False</span></code> by default.</p>
+</dd>
+</dl>
+</dd>
+<dt>Returns</dt><dd><p>(<em>list</em>) – Contains the name(s) for the target node(s).
+This means if the interaction is bidirectional, the list
+will contain both identifiers on the edge. If the
+interaction is undirected, an empty list will be returned.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.tgt">
+<span class="sig-name descname"><span class="pre">tgt</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">undirected</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.tgt" title="Link to this definition">§</a></dt>
+<dd><p>Returns the name(s) of the target node(s) for each existing
+direction on the interaction.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>undirected:</dt><dd><p>Optional, <code class="docutils literal notranslate"><span class="pre">False</span></code> by default.</p>
+</dd>
+</dl>
+</dd>
+<dt>Returns</dt><dd><p>(<em>list</em>) – Contains the name(s) for the target node(s).
+This means if the interaction is bidirectional, the list
+will contain both identifiers on the edge. If the
+interaction is undirected, an empty list will be returned.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.tgt_by_resource">
+<span class="sig-name descname"><span class="pre">tgt_by_resource</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">resource</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/interaction.html#Interaction.tgt_by_resource"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.interaction.Interaction.tgt_by_resource" title="Link to this definition">§</a></dt>
+<dd><p>Returns the name(s) of the target node(s) for each existing
+direction on the interaction for a specific <em>resource</em>.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><p><strong>resource</strong> (<em>str</em>) – Name of the resource according to which the information is to
+be retrieved.</p>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p>(<em>list</em>) – Contains the name(s) for the target node(s)
+according to the specified <em>resource</em>. This means if the
+interaction is bidirectional, the list will contain both
+identifiers on the edge. If the specified <em>source</em> is not
+found or invalid, an empty list will be returned.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.translate">
+<span class="sig-name descname"><span class="pre">translate</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">ids</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">new_attrs</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/interaction.html#Interaction.translate"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.interaction.Interaction.translate" title="Link to this definition">§</a></dt>
+<dd><p>Translates the node names/identifiers according to the
+dictionary <em>ids</em>. Also is able to change attributes like <cite>id_type</cite>,
+<cite>taxon</cite> and <cite>entity_type</cite>.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>ids</strong> (<em>dict</em>) – Dictionary containing (at least) the current names of the
+nodes as keys and their translation as values.</p></li>
+<li><p><strong>new_attrs</strong> (<em>dict</em>) – Dictionary with new IDs as keys and their dicts of their new
+attributes as values. For any attribute not provided here
+the attributes from the original instance will be used.
+E.g. you can provide <a href="#id1"><span class="problematic" id="id2">`</span></a>{‘1956’: {‘id_type’: ‘entrez’}}’ if the
+new ID type for protein EGFR is Entrez Gene ID.</p></li>
+</ul>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p>(<em>pypath.main.Direction</em>) – The copy of current edge object
+with translated node names.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.unset_dir">
+<span class="sig-name descname"><span class="pre">unset_dir</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">direction</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">only_sign</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resource</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">source</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.unset_dir" title="Link to this definition">§</a></dt>
+<dd><p>Removes directionality and/or source information of the
+specified <em>direction</em>. Modifies attribute <code class="xref py py-attr docutils literal notranslate"><span class="pre">dirs</span></code> and
+<code class="xref py py-attr docutils literal notranslate"><span class="pre">sources</span></code>.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>direction</strong> (<em>tuple</em>) – Or [str] (if <code class="docutils literal notranslate"><span class="pre">'undirected'</span></code>) the pair of nodes specifying
+the directionality from which the information is to be
+removed.</p></li>
+<li><p><strong>resource</strong> (<em>set</em>) – Optional, <code class="docutils literal notranslate"><span class="pre">None</span></code> by default. If specified, determines
+which specific source(s) is(are) to be removed from
+<code class="xref py py-attr docutils literal notranslate"><span class="pre">sources</span></code> attribute in the specified <em>direction</em>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.unset_direction">
+<span class="sig-name descname"><span class="pre">unset_direction</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">direction</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">only_sign</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resource</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">source</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/interaction.html#Interaction.unset_direction"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.interaction.Interaction.unset_direction" title="Link to this definition">§</a></dt>
+<dd><p>Removes directionality and/or source information of the
+specified <em>direction</em>. Modifies attribute <code class="xref py py-attr docutils literal notranslate"><span class="pre">dirs</span></code> and
+<code class="xref py py-attr docutils literal notranslate"><span class="pre">sources</span></code>.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>direction</strong> (<em>tuple</em>) – Or [str] (if <code class="docutils literal notranslate"><span class="pre">'undirected'</span></code>) the pair of nodes specifying
+the directionality from which the information is to be
+removed.</p></li>
+<li><p><strong>resource</strong> (<em>set</em>) – Optional, <code class="docutils literal notranslate"><span class="pre">None</span></code> by default. If specified, determines
+which specific source(s) is(are) to be removed from
+<code class="xref py py-attr docutils literal notranslate"><span class="pre">sources</span></code> attribute in the specified <em>direction</em>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.unset_interaction_type">
+<span class="sig-name descname"><span class="pre">unset_interaction_type</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/interaction.html#Interaction.unset_interaction_type"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.interaction.Interaction.unset_interaction_type" title="Link to this definition">§</a></dt>
+<dd><p>Removes all evidences with a certain <code class="docutils literal notranslate"><span class="pre">interaction_type</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.unset_sign">
+<span class="sig-name descname"><span class="pre">unset_sign</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">direction</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">sign</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resource</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">source</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/interaction.html#Interaction.unset_sign"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.interaction.Interaction.unset_sign" title="Link to this definition">§</a></dt>
+<dd><p>Removes sign and/or source information of the specified
+<em>direction</em> and <em>sign</em>. Modifies attribute <code class="xref py py-attr docutils literal notranslate"><span class="pre">positive</span></code>
+and <code class="xref py py-attr docutils literal notranslate"><span class="pre">positive_sources</span></code> or <code class="xref py py-attr docutils literal notranslate"><span class="pre">negative</span></code> and
+<code class="xref py py-attr docutils literal notranslate"><span class="pre">negative_sources</span></code> (or
+<code class="xref py py-attr docutils literal notranslate"><span class="pre">positive_attributes</span></code>/<code class="xref py py-attr docutils literal notranslate"><span class="pre">negative_sources</span></code>
+only if <code class="docutils literal notranslate"><span class="pre">source=True</span></code>).</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>direction</strong> (<em>tuple</em>) – The pair of nodes specifying the directionality from which
+the information is to be removed.</p></li>
+<li><p><strong>sign</strong> (<em>str</em>) – Sign from which the information is to be removed. Must be
+either <code class="docutils literal notranslate"><span class="pre">'positive'</span></code> or <code class="docutils literal notranslate"><span class="pre">'negative'</span></code>.</p></li>
+<li><p><strong>source</strong> (<em>set</em>) – Optional, <code class="docutils literal notranslate"><span class="pre">None</span></code> by default. If specified, determines
+which source(s) is(are) to be removed from the sources in
+the specified <em>direction</em> and <em>sign</em>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.update_attrs">
+<span class="sig-name descname"><span class="pre">update_attrs</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">attrs</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.update_attrs" title="Link to this definition">§</a></dt>
+<dd><p>Updates the attributes stored here. The attributes with identical
+keys are merged using the <code class="xref py py-func docutils literal notranslate"><span class="pre">pypath.share.common.combine_attrs()</span></code>
+function.</p>
+<p>The new attributes can be provided three ways: an object with an
+attribute called <cite>attrs</cite>; a dictionary of attributes; or the
+attributes as keyword arguments.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.which_directions">
+<span class="sig-name descname"><span class="pre">which_directions</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/interaction.html#Interaction.which_directions"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.interaction.Interaction.which_directions" title="Link to this definition">§</a></dt>
+<dd><p>Returns the pair(s) of nodes for which there is information
+about their directionality.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>effect</strong> (<em>str</em>) – Either <em>positive</em> or <em>negative</em>.</p></li>
+<li><p><strong>resources</strong> (<em>str</em><em>,</em><em>set</em>) – Limits the query to one or more resources. Optional.</p></li>
+</ul>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p>(<em>tuple</em>) – Tuple of tuples with pairs of nodes where the
+first element is the source and the second is the target
+entity, according to the given resources and limited to the
+effect.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.which_dirs">
+<span class="sig-name descname"><span class="pre">which_dirs</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.Interaction.which_dirs" title="Link to this definition">§</a></dt>
+<dd><p>Returns the pair(s) of nodes for which there is information
+about their directionality.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>effect</strong> (<em>str</em>) – Either <em>positive</em> or <em>negative</em>.</p></li>
+<li><p><strong>resources</strong> (<em>str</em><em>,</em><em>set</em>) – Limits the query to one or more resources. Optional.</p></li>
+</ul>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p>(<em>tuple</em>) – Tuple of tuples with pairs of nodes where the
+first element is the source and the second is the target
+entity, according to the given resources and limited to the
+effect.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.Interaction.which_signs">
+<span class="sig-name descname"><span class="pre">which_signs</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/interaction.html#Interaction.which_signs"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.interaction.Interaction.which_signs" title="Link to this definition">§</a></dt>
+<dd><p>Returns the pair(s) of nodes for which there is information
+about their effect signs.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>resources</strong> (<em>str</em><em>,</em><em>set</em>) – Limits the query to one or more resources. Optional.</p></li>
+<li><p><strong>effect</strong> (<em>str</em>) – Either <em>positive</em> or <em>negative</em>, limiting the query to positive
+or negative effects; for any other values effects of both
+signs will be returned.</p></li>
+</ul>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p>(<em>tuple</em>) – Tuple of tuples with pairs of nodes where the
+first element is a tuple of the source and the target entity,
+while the second element is the effect sign, according to
+the given resources. E.g. (((‘A’, ‘B’), ‘positive’),)</p>
+</dd>
+</dl>
+</dd></dl>
+
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+
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+  <section id="pypath-core-interaction-interactiondataframerecord">
+<h1>pypath.core.interaction.InteractionDataFrameRecord<a class="headerlink" href="#pypath-core-interaction-interactiondataframerecord" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.core.interaction.InteractionDataFrameRecord">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.core.interaction.</span></span><span class="sig-name descname"><span class="pre">InteractionDataFrameRecord</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">id_a</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">id_b</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">type_a</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">type_b</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">directed</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">effect</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">type</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">dmodel</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">sources</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.InteractionDataFrameRecord" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">tuple</span></code></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.InteractionDataFrameRecord.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.InteractionDataFrameRecord.__init__" title="Link to this definition">§</a></dt>
+<dd></dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.InteractionDataFrameRecord.__init__" title="pypath.core.interaction.InteractionDataFrameRecord.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.InteractionDataFrameRecord.count" title="pypath.core.interaction.InteractionDataFrameRecord.count"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count</span></code></a>(value, /)</p></td>
+<td><p>Return number of occurrences of value.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.InteractionDataFrameRecord.index" title="pypath.core.interaction.InteractionDataFrameRecord.index"><code class="xref py py-obj docutils literal notranslate"><span class="pre">index</span></code></a>(value[, start, stop])</p></td>
+<td><p>Return first index of value.</p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Attributes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.InteractionDataFrameRecord.directed" title="pypath.core.interaction.InteractionDataFrameRecord.directed"><code class="xref py py-obj docutils literal notranslate"><span class="pre">directed</span></code></a></p></td>
+<td><p>Alias for field number 4</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.InteractionDataFrameRecord.dmodel" title="pypath.core.interaction.InteractionDataFrameRecord.dmodel"><code class="xref py py-obj docutils literal notranslate"><span class="pre">dmodel</span></code></a></p></td>
+<td><p>Alias for field number 7</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.InteractionDataFrameRecord.effect" title="pypath.core.interaction.InteractionDataFrameRecord.effect"><code class="xref py py-obj docutils literal notranslate"><span class="pre">effect</span></code></a></p></td>
+<td><p>Alias for field number 5</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.InteractionDataFrameRecord.id_a" title="pypath.core.interaction.InteractionDataFrameRecord.id_a"><code class="xref py py-obj docutils literal notranslate"><span class="pre">id_a</span></code></a></p></td>
+<td><p>Alias for field number 0</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.InteractionDataFrameRecord.id_b" title="pypath.core.interaction.InteractionDataFrameRecord.id_b"><code class="xref py py-obj docutils literal notranslate"><span class="pre">id_b</span></code></a></p></td>
+<td><p>Alias for field number 1</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.InteractionDataFrameRecord.references" title="pypath.core.interaction.InteractionDataFrameRecord.references"><code class="xref py py-obj docutils literal notranslate"><span class="pre">references</span></code></a></p></td>
+<td><p>Alias for field number 9</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.InteractionDataFrameRecord.sources" title="pypath.core.interaction.InteractionDataFrameRecord.sources"><code class="xref py py-obj docutils literal notranslate"><span class="pre">sources</span></code></a></p></td>
+<td><p>Alias for field number 8</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.InteractionDataFrameRecord.type" title="pypath.core.interaction.InteractionDataFrameRecord.type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">type</span></code></a></p></td>
+<td><p>Alias for field number 6</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.InteractionDataFrameRecord.type_a" title="pypath.core.interaction.InteractionDataFrameRecord.type_a"><code class="xref py py-obj docutils literal notranslate"><span class="pre">type_a</span></code></a></p></td>
+<td><p>Alias for field number 2</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.InteractionDataFrameRecord.type_b" title="pypath.core.interaction.InteractionDataFrameRecord.type_b"><code class="xref py py-obj docutils literal notranslate"><span class="pre">type_b</span></code></a></p></td>
+<td><p>Alias for field number 3</p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.InteractionDataFrameRecord.count">
+<span class="sig-name descname"><span class="pre">count</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">value</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">/</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.InteractionDataFrameRecord.count" title="Link to this definition">§</a></dt>
+<dd><p>Return number of occurrences of value.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.InteractionDataFrameRecord.directed">
+<span class="sig-name descname"><span class="pre">directed</span></span><a class="headerlink" href="#pypath.core.interaction.InteractionDataFrameRecord.directed" title="Link to this definition">§</a></dt>
+<dd><p>Alias for field number 4</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.InteractionDataFrameRecord.dmodel">
+<span class="sig-name descname"><span class="pre">dmodel</span></span><a class="headerlink" href="#pypath.core.interaction.InteractionDataFrameRecord.dmodel" title="Link to this definition">§</a></dt>
+<dd><p>Alias for field number 7</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.InteractionDataFrameRecord.effect">
+<span class="sig-name descname"><span class="pre">effect</span></span><a class="headerlink" href="#pypath.core.interaction.InteractionDataFrameRecord.effect" title="Link to this definition">§</a></dt>
+<dd><p>Alias for field number 5</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.InteractionDataFrameRecord.id_a">
+<span class="sig-name descname"><span class="pre">id_a</span></span><a class="headerlink" href="#pypath.core.interaction.InteractionDataFrameRecord.id_a" title="Link to this definition">§</a></dt>
+<dd><p>Alias for field number 0</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.InteractionDataFrameRecord.id_b">
+<span class="sig-name descname"><span class="pre">id_b</span></span><a class="headerlink" href="#pypath.core.interaction.InteractionDataFrameRecord.id_b" title="Link to this definition">§</a></dt>
+<dd><p>Alias for field number 1</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.InteractionDataFrameRecord.index">
+<span class="sig-name descname"><span class="pre">index</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">value</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">start</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">stop</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9223372036854775807</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">/</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.InteractionDataFrameRecord.index" title="Link to this definition">§</a></dt>
+<dd><p>Return first index of value.</p>
+<p>Raises ValueError if the value is not present.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.InteractionDataFrameRecord.references">
+<span class="sig-name descname"><span class="pre">references</span></span><a class="headerlink" href="#pypath.core.interaction.InteractionDataFrameRecord.references" title="Link to this definition">§</a></dt>
+<dd><p>Alias for field number 9</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.InteractionDataFrameRecord.sources">
+<span class="sig-name descname"><span class="pre">sources</span></span><a class="headerlink" href="#pypath.core.interaction.InteractionDataFrameRecord.sources" title="Link to this definition">§</a></dt>
+<dd><p>Alias for field number 8</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.InteractionDataFrameRecord.type">
+<span class="sig-name descname"><span class="pre">type</span></span><a class="headerlink" href="#pypath.core.interaction.InteractionDataFrameRecord.type" title="Link to this definition">§</a></dt>
+<dd><p>Alias for field number 6</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.InteractionDataFrameRecord.type_a">
+<span class="sig-name descname"><span class="pre">type_a</span></span><a class="headerlink" href="#pypath.core.interaction.InteractionDataFrameRecord.type_a" title="Link to this definition">§</a></dt>
+<dd><p>Alias for field number 2</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.InteractionDataFrameRecord.type_b">
+<span class="sig-name descname"><span class="pre">type_b</span></span><a class="headerlink" href="#pypath.core.interaction.InteractionDataFrameRecord.type_b" title="Link to this definition">§</a></dt>
+<dd><p>Alias for field number 3</p>
+</dd></dl>
+
+</dd></dl>
+
+</section>
+
+
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new file mode 100644
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+  <section id="pypath-core-interaction-interactionkey">
+<h1>pypath.core.interaction.InteractionKey<a class="headerlink" href="#pypath-core-interaction-interactionkey" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.core.interaction.InteractionKey">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.core.interaction.</span></span><span class="sig-name descname"><span class="pre">InteractionKey</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_a</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_b</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.InteractionKey" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">tuple</span></code></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.InteractionKey.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.InteractionKey.__init__" title="Link to this definition">§</a></dt>
+<dd></dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.InteractionKey.__init__" title="pypath.core.interaction.InteractionKey.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.InteractionKey.count" title="pypath.core.interaction.InteractionKey.count"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count</span></code></a>(value, /)</p></td>
+<td><p>Return number of occurrences of value.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.InteractionKey.index" title="pypath.core.interaction.InteractionKey.index"><code class="xref py py-obj docutils literal notranslate"><span class="pre">index</span></code></a>(value[, start, stop])</p></td>
+<td><p>Return first index of value.</p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Attributes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.interaction.InteractionKey.entity_a" title="pypath.core.interaction.InteractionKey.entity_a"><code class="xref py py-obj docutils literal notranslate"><span class="pre">entity_a</span></code></a></p></td>
+<td><p>Alias for field number 0</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.interaction.InteractionKey.entity_b" title="pypath.core.interaction.InteractionKey.entity_b"><code class="xref py py-obj docutils literal notranslate"><span class="pre">entity_b</span></code></a></p></td>
+<td><p>Alias for field number 1</p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.InteractionKey.count">
+<span class="sig-name descname"><span class="pre">count</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">value</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">/</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.InteractionKey.count" title="Link to this definition">§</a></dt>
+<dd><p>Return number of occurrences of value.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.InteractionKey.entity_a">
+<span class="sig-name descname"><span class="pre">entity_a</span></span><a class="headerlink" href="#pypath.core.interaction.InteractionKey.entity_a" title="Link to this definition">§</a></dt>
+<dd><p>Alias for field number 0</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.interaction.InteractionKey.entity_b">
+<span class="sig-name descname"><span class="pre">entity_b</span></span><a class="headerlink" href="#pypath.core.interaction.InteractionKey.entity_b" title="Link to this definition">§</a></dt>
+<dd><p>Alias for field number 1</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.interaction.InteractionKey.index">
+<span class="sig-name descname"><span class="pre">index</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">value</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">start</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">stop</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9223372036854775807</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">/</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.interaction.InteractionKey.index" title="Link to this definition">§</a></dt>
+<dd><p>Return first index of value.</p>
+<p>Raises ValueError if the value is not present.</p>
+</dd></dl>
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+<p>Here we define one class, the <code class="xref py py-class docutils literal notranslate"><span class="pre">Interaction`</span></code> which provides a
+rich API for representing and querying molecular interactions. The
+interactions serve as the building elements of the network and the
+<code class="xref py py-class docutils literal notranslate"><span class="pre">pypath.network.Network</span></code> object largely relies on methods
+of the <code class="xref py py-class docutils literal notranslate"><span class="pre">Interaction`</span></code> objects.</p>
+<dl class="field-list simple">
+<dt class="field-odd">members<span class="colon">:</span></dt>
+<dd class="field-odd"><p></p></dd>
+</dl>
+<p class="rubric">Classes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction" title="pypath.core.interaction.Interaction"><code class="xref py py-obj docutils literal notranslate"><span class="pre">Interaction</span></code></a>(a, b[, id_type_a, id_type_b, ...])</p></td>
+<td><p>Represents a unique pair of molecular entities interacting with each other.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.core.interaction.InteractionDataFrameRecord.html#pypath.core.interaction.InteractionDataFrameRecord" title="pypath.core.interaction.InteractionDataFrameRecord"><code class="xref py py-obj docutils literal notranslate"><span class="pre">InteractionDataFrameRecord</span></code></a>(id_a, id_b, ...)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.core.interaction.InteractionKey.html#pypath.core.interaction.InteractionKey" title="pypath.core.interaction.InteractionKey"><code class="xref py py-obj docutils literal notranslate"><span class="pre">InteractionKey</span></code></a>(entity_a, entity_b)</p></td>
+<td><p></p></td>
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+  <section id="pypath-core-intercell-intercellannotation">
+<h1>pypath.core.intercell.IntercellAnnotation<a class="headerlink" href="#pypath-core-intercell-intercellannotation" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.core.intercell.IntercellAnnotation">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.core.intercell.</span></span><span class="sig-name descname"><span class="pre">IntercellAnnotation</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">class_definitions</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">excludes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">excludes_extra</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cellphonedb_categories</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">baccin_categories</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">hpmr_categories</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">surfaceome_categories</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">gpcrdb_categories</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">icellnet_categories</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">build</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">composite_resource_name</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/intercell.html#IntercellAnnotation"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.intercell.IntercellAnnotation" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <a class="reference internal" href="pypath.core.annot.CustomAnnotation.html#pypath.core.annot.CustomAnnotation" title="pypath.core.annot.CustomAnnotation"><code class="xref py py-class docutils literal notranslate"><span class="pre">CustomAnnotation</span></code></a></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.intercell.IntercellAnnotation.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">class_definitions</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">excludes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">excludes_extra</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cellphonedb_categories</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">baccin_categories</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">hpmr_categories</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">surfaceome_categories</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">gpcrdb_categories</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">icellnet_categories</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">build</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">composite_resource_name</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/intercell.html#IntercellAnnotation.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.intercell.IntercellAnnotation.__init__" title="Link to this definition">§</a></dt>
+<dd><p>Builds a database about roles of proteins and complexes in
+intercellular communication. The built-in category definitions
+defining the default contents of this database can be found in the
+<code class="docutils literal notranslate"><span class="pre">pypath.core.intercell_annot</span></code> module.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>class_definitions</strong> (<em>tuple</em>) – A series of annotation class definitions, each represented by
+an instance of <code class="docutils literal notranslate"><span class="pre">pypath.internals.annot_formats.AnnotDef</span></code>.
+These definitions carry the attributes and instructions to
+populate the classes.</p></li>
+<li><p><strong>excludes</strong> (<em>dict</em>) – A dict with parent category names (strings) or category keys
+(tuples) as keys and sets if identifiers as values.
+The identifiers in this dict will be excluded from all the
+respective categories while building the database. E.g. if
+the UniProt ID <cite>P00533</cite> (EGFR) is in the set under the key of
+<cite>adhesion</cite> it will be excluded from the category <cite>adhesion</cite> and
+all it’s direct children.</p></li>
+<li><p><strong>excludes_extra</strong> (<em>dict</em>) – Same kind of dict as <cite>excludes</cite> but it will be added to the
+built-in default. The built in and the provided extra sets
+will be merged. If you want to overwrite or modify the built-in
+sets provide your custom dict as <cite>excludes</cite>.</p></li>
+<li><p><strong>build</strong> (<em>bool</em>) – Execute the build upon instantiation or set up an empty object
+the build can be executed on later.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.intercell.IntercellAnnotation.__init__" title="pypath.core.intercell.IntercellAnnotation.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>([class_definitions, excludes, ...])</p></td>
+<td><p>Builds a database about roles of proteins and complexes in intercellular communication.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">add_baccin_categories</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">add_cellphonedb_categories</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">add_class_definitions</span></code>(class_definitions)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">add_classes_to_df</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">add_extra_categories</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">add_gpcrdb_categories</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">add_hpmr_categories</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">add_icellnet_categories</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">add_surfaceome_categories</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">all_resources</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.intercell.IntercellAnnotation.browse" title="pypath.core.intercell.IntercellAnnotation.browse"><code class="xref py py-obj docutils literal notranslate"><span class="pre">browse</span></code></a>([start])</p></td>
+<td><p>Print gene information as a table.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">build</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.intercell.IntercellAnnotation.class_to_class_connections" title="pypath.core.intercell.IntercellAnnotation.class_to_class_connections"><code class="xref py py-obj docutils literal notranslate"><span class="pre">class_to_class_connections</span></code></a>(**kwargs)</p></td>
+<td><p><code class="docutils literal notranslate"><span class="pre">kwargs</span></code> passed to <code class="docutils literal notranslate"><span class="pre">filter_interclass_network</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">class_to_class_connections_directed</span></code>(**kwargs)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">class_to_class_connections_inhibitory</span></code>(**kwargs)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">class_to_class_connections_signed</span></code>(**kwargs)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">class_to_class_connections_stimulatory</span></code>(**kwargs)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">class_to_class_connections_undirected</span></code>(**kwargs)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.intercell.IntercellAnnotation.classes_by_entity" title="pypath.core.intercell.IntercellAnnotation.classes_by_entity"><code class="xref py py-obj docutils literal notranslate"><span class="pre">classes_by_entity</span></code></a>(element[, labels])</p></td>
+<td><p>Returns a set of class keys with the classes containing at least one of the elements.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">collect_classes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">complexes_by_resource</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">consensus_score</span></code>(name, entity)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">consensus_score_normalized</span></code>(name, entity)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_inter_class_connections</span></code>([...])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_inter_class_connections_all</span></code>([...])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_inter_class_connections_directed</span></code>([...])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_inter_class_connections_inhibitory</span></code>([...])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_inter_class_connections_signed</span></code>([...])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_inter_class_connections_stimulatory</span></code>([...])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_inter_class_connections_undirected</span></code>([...])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.intercell.IntercellAnnotation.counts" title="pypath.core.intercell.IntercellAnnotation.counts"><code class="xref py py-obj docutils literal notranslate"><span class="pre">counts</span></code></a>([entity_type, labels])</p></td>
+<td><p>Returns a dict with number of elements in each class.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.intercell.IntercellAnnotation.counts_by_class" title="pypath.core.intercell.IntercellAnnotation.counts_by_class"><code class="xref py py-obj docutils literal notranslate"><span class="pre">counts_by_class</span></code></a>([entity_type, labels])</p></td>
+<td><p>Returns a dict with number of elements in each class.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">counts_by_resource</span></code>([entity_types])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">counts_df</span></code>([groupby])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.intercell.IntercellAnnotation.create_class" title="pypath.core.intercell.IntercellAnnotation.create_class"><code class="xref py py-obj docutils literal notranslate"><span class="pre">create_class</span></code></a>(classdef[, override])</p></td>
+<td><p>Creates a category of entities by processing a custom definition.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.intercell.IntercellAnnotation.degree_inter_class_network" title="pypath.core.intercell.IntercellAnnotation.degree_inter_class_network"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degree_inter_class_network</span></code></a>([...])</p></td>
+<td><p>degrees_of : str</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">degree_inter_class_network_2</span></code>([degrees_of, ...])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">degree_inter_class_network_directed</span></code>([...])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">degree_inter_class_network_directed_2</span></code>(**kwargs)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">degree_inter_class_network_inhibitory</span></code>([...])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">degree_inter_class_network_inhibitory_2</span></code>(**kwargs)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">degree_inter_class_network_stimulatory</span></code>([...])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">degree_inter_class_network_stimulatory_2</span></code>(...)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">degree_inter_class_network_undirected</span></code>([...])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">degree_inter_class_network_undirected_2</span></code>(**kwargs)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">df_add_causality</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">df_add_locations</span></code>([locations])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">difference</span></code>(*args)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">ensure_annotdb</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">entities_by_resource</span></code>([entity_types])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">export</span></code>(fname, **kwargs)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.intercell.IntercellAnnotation.filter" title="pypath.core.intercell.IntercellAnnotation.filter"><code class="xref py py-obj docutils literal notranslate"><span class="pre">filter</span></code></a>([entity_type])</p></td>
+<td><p>Filters the annotated entities by annotation class attributes and <code class="docutils literal notranslate"><span class="pre">entity_type</span></code>.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.intercell.IntercellAnnotation.filter_classes" title="pypath.core.intercell.IntercellAnnotation.filter_classes"><code class="xref py py-obj docutils literal notranslate"><span class="pre">filter_classes</span></code></a>(classes, **kwargs)</p></td>
+<td><p>Returns a list of annotation classes filtered by their attributes.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">filter_df</span></code>(annot_df[, category, name, ...])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">filter_entity_type</span></code>(cls[, entity_type])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.intercell.IntercellAnnotation.filter_interclass_network" title="pypath.core.intercell.IntercellAnnotation.filter_interclass_network"><code class="xref py py-obj docutils literal notranslate"><span class="pre">filter_interclass_network</span></code></a>([annot_df, ...])</p></td>
+<td><p>Combines the annotation data frame and a network data frame.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">filtered</span></code>([annot_df, entities])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_aspect</span></code>(name[, parent, resource])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.intercell.IntercellAnnotation.get_class" title="pypath.core.intercell.IntercellAnnotation.get_class"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_class</span></code></a>(definition[, parent, resource, ...])</p></td>
+<td><p>Retrieves a class by its name or definition.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_class_label</span></code>(name[, parent, resource])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_class_scope</span></code>(name[, parent, resource])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.intercell.IntercellAnnotation.get_df" title="pypath.core.intercell.IntercellAnnotation.get_df"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_df</span></code></a>()</p></td>
+<td><p>Returns the data frame of custom annotations.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_entities</span></code>([entity_types])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.intercell.IntercellAnnotation.get_interclass_network_df" title="pypath.core.intercell.IntercellAnnotation.get_interclass_network_df"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_interclass_network_df</span></code></a>(**kwargs)</p></td>
+<td><p>If the an interclass network is already present the <code class="docutils literal notranslate"><span class="pre">network</span></code> and other <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> provided not considered.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_mirnas</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_parent</span></code>(name[, parent, resource])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.intercell.IntercellAnnotation.get_parents" title="pypath.core.intercell.IntercellAnnotation.get_parents"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_parents</span></code></a>(name[, parent, resource])</p></td>
+<td><p>As names should be unique for resources, a combination of a name and resource determines the parent category.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_proteins</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.intercell.IntercellAnnotation.get_resource" title="pypath.core.intercell.IntercellAnnotation.get_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_resource</span></code></a>(name[, parent])</p></td>
+<td><p>For a category name and its parent returns a single resource name.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.intercell.IntercellAnnotation.get_resources" title="pypath.core.intercell.IntercellAnnotation.get_resources"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_resources</span></code></a>(name[, parent])</p></td>
+<td><p>Returns a set with the names of all resources defining a category with the given name and parent.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_source</span></code>(name[, parent, resource])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">inter_class_network</span></code>([annot_args_source, ...])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">inter_class_network_directed</span></code>([...])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">inter_class_network_inhibitory</span></code>([...])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">inter_class_network_signed</span></code>([...])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">inter_class_network_stimulatory</span></code>([...])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">inter_class_network_undirected</span></code>([...])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">intersection</span></code>(*args)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">isdisjoint</span></code>(*args)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">iter_classes</span></code>(**kwargs)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.intercell.IntercellAnnotation.labels" title="pypath.core.intercell.IntercellAnnotation.labels"><code class="xref py py-obj docutils literal notranslate"><span class="pre">labels</span></code></a>(name[, parent, resource, entity_type])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">load</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_from_pickle</span></code>(pickle_file)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.intercell.IntercellAnnotation.make_df" title="pypath.core.intercell.IntercellAnnotation.make_df"><code class="xref py py-obj docutils literal notranslate"><span class="pre">make_df</span></code></a>()</p></td>
+<td><p>Creates a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> where each record assigns a molecular entity to an annotation category.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">mirnas_by_resource</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.intercell.IntercellAnnotation.network_df" title="pypath.core.intercell.IntercellAnnotation.network_df"><code class="xref py py-obj docutils literal notranslate"><span class="pre">network_df</span></code></a>([annot_df, network, combined_df, ...])</p></td>
+<td><p>Combines the annotation data frame and a network data frame.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_classes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complex_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_entities</span></code>([entity_types])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirna_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_mirnas</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_protein_records</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_proteins</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_records</span></code>([entity_types])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.intercell.IntercellAnnotation.populate_classes" title="pypath.core.intercell.IntercellAnnotation.populate_classes"><code class="xref py py-obj docutils literal notranslate"><span class="pre">populate_classes</span></code></a>([update])</p></td>
+<td><p>Creates a classification of proteins according to the custom annotation definitions.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.intercell.IntercellAnnotation.populate_scores" title="pypath.core.intercell.IntercellAnnotation.populate_scores"><code class="xref py py-obj docutils literal notranslate"><span class="pre">populate_scores</span></code></a>()</p></td>
+<td><p>Creates the consensus score dictionaries based on the number of resources annotating an entity for each composite category.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">post_load</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">pre_build</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.intercell.IntercellAnnotation.process_annot" title="pypath.core.intercell.IntercellAnnotation.process_annot"><code class="xref py py-obj docutils literal notranslate"><span class="pre">process_annot</span></code></a>(classdef)</p></td>
+<td><p>Processes an annotation definition and returns a set of identifiers.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">proteins_by_resource</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.intercell.IntercellAnnotation.quality_check_table" title="pypath.core.intercell.IntercellAnnotation.quality_check_table"><code class="xref py py-obj docutils literal notranslate"><span class="pre">quality_check_table</span></code></a>([path, fmt, ...])</p></td>
+<td><p>Exports a table in tsv format for quality check and browsing purposes.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.intercell.IntercellAnnotation.register_network" title="pypath.core.intercell.IntercellAnnotation.register_network"><code class="xref py py-obj docutils literal notranslate"><span class="pre">register_network</span></code></a>(network)</p></td>
+<td><p>Sets <code class="docutils literal notranslate"><span class="pre">network</span></code> as the default network dataset for the instance.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.intercell.IntercellAnnotation.reload" title="pypath.core.intercell.IntercellAnnotation.reload"><code class="xref py py-obj docutils literal notranslate"><span class="pre">reload</span></code></a>()</p></td>
+<td><p>Reloads the object from the module level.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.intercell.IntercellAnnotation.resources_in_category" title="pypath.core.intercell.IntercellAnnotation.resources_in_category"><code class="xref py py-obj docutils literal notranslate"><span class="pre">resources_in_category</span></code></a>(key)</p></td>
+<td><p>Returns a list of resources contributing to the definition of a category.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">save_to_pickle</span></code>(pickle_file)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.intercell.IntercellAnnotation.select" title="pypath.core.intercell.IntercellAnnotation.select"><code class="xref py py-obj docutils literal notranslate"><span class="pre">select</span></code></a>(definition[, parent, resource, ...])</p></td>
+<td><p>Retrieves a class by its name or definition.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_classes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.intercell.IntercellAnnotation.set_interclass_network_df" title="pypath.core.intercell.IntercellAnnotation.set_interclass_network_df"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_interclass_network_df</span></code></a>(**kwargs)</p></td>
+<td><p>Creates a data frame of the whole inter-class network and keeps it assigned to the instance in order to make subsequent queries faster.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">sets</span></code>(*args)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.intercell.IntercellAnnotation.show" title="pypath.core.intercell.IntercellAnnotation.show"><code class="xref py py-obj docutils literal notranslate"><span class="pre">show</span></code></a>(name[, parent, resource])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic information from the UniProt datasheets.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">summaries_tab</span></code>([outfile, return_table])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">symmetric_difference</span></code>(*args)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">union</span></code>(*args)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">unset_interclass_network_df</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">update_excludes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.intercell.IntercellAnnotation.update_parents" title="pypath.core.intercell.IntercellAnnotation.update_parents"><code class="xref py py-obj docutils literal notranslate"><span class="pre">update_parents</span></code></a>()</p></td>
+<td><p>Creates a dict :py:attr:<code class="docutils literal notranslate"><span class="pre">children</span></code> with parent class names as keys and sets of children class keys as values.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">update_summaries</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.intercell.IntercellAnnotation.browse">
+<span class="sig-name descname"><span class="pre">browse</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">start</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.intercell.IntercellAnnotation.browse" title="Link to this definition">§</a></dt>
+<dd><p>Print gene information as a table.</p>
+<p>Presents information about annotation classes as ascii tables printed
+in the terminal. If one class provided, prints one table. If multiple
+classes provided, prints a table for each of them one by one
+proceeding to the next one once you hit return. If no classes
+provided goes through all classes.</p>
+<p><code class="docutils literal notranslate"><span class="pre">kwargs</span></code> passed to <code class="docutils literal notranslate"><span class="pre">pypath.utils.uniprot.info</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.intercell.IntercellAnnotation.class_to_class_connections">
+<span class="sig-name descname"><span class="pre">class_to_class_connections</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.intercell.IntercellAnnotation.class_to_class_connections" title="Link to this definition">§</a></dt>
+<dd><p><code class="docutils literal notranslate"><span class="pre">kwargs</span></code> passed to <code class="docutils literal notranslate"><span class="pre">filter_interclass_network</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.intercell.IntercellAnnotation.classes_by_entity">
+<span class="sig-name descname"><span class="pre">classes_by_entity</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">element</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">labels</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.intercell.IntercellAnnotation.classes_by_entity" title="Link to this definition">§</a></dt>
+<dd><p>Returns a set of class keys with the classes containing at least
+one of the elements.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>element</strong> (<em>str</em><em>,</em><em>set</em>) – One or more element (entity) to search for in the classes.</p></li>
+<li><p><strong>labels</strong> (<em>bool</em>) – Return labels instead of keys.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.intercell.IntercellAnnotation.counts">
+<span class="sig-name descname"><span class="pre">counts</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'protein'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">labels</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.intercell.IntercellAnnotation.counts" title="Link to this definition">§</a></dt>
+<dd><p>Returns a dict with number of elements in each class.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><p><strong>labels</strong> (<em>bool</em>) – Use keys or labels as keys in the returned dict.</p>
+</dd>
+</dl>
+<p>All other arguments passed to <code class="docutils literal notranslate"><span class="pre">iter_classes</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.intercell.IntercellAnnotation.counts_by_class">
+<span class="sig-name descname"><span class="pre">counts_by_class</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'protein'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">labels</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.intercell.IntercellAnnotation.counts_by_class" title="Link to this definition">§</a></dt>
+<dd><p>Returns a dict with number of elements in each class.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><p><strong>labels</strong> (<em>bool</em>) – Use keys or labels as keys in the returned dict.</p>
+</dd>
+</dl>
+<p>All other arguments passed to <code class="docutils literal notranslate"><span class="pre">iter_classes</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.intercell.IntercellAnnotation.create_class">
+<span class="sig-name descname"><span class="pre">create_class</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">classdef</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">override</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.intercell.IntercellAnnotation.create_class" title="Link to this definition">§</a></dt>
+<dd><p>Creates a category of entities by processing a custom definition.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.intercell.IntercellAnnotation.degree_inter_class_network">
+<span class="sig-name descname"><span class="pre">degree_inter_class_network</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">annot_args_source</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">annot_args_target</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">degrees_of</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'target'</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.intercell.IntercellAnnotation.degree_inter_class_network" title="Link to this definition">§</a></dt>
+<dd><dl class="simple">
+<dt>degrees_of<span class="classifier">str</span></dt><dd><p>Either <em>source</em> or <em>target</em>. Count the degrees for the source
+or the target class.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.intercell.IntercellAnnotation.filter">
+<span class="sig-name descname"><span class="pre">filter</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.intercell.IntercellAnnotation.filter" title="Link to this definition">§</a></dt>
+<dd><p>Filters the annotated entities by annotation class attributes and
+<code class="docutils literal notranslate"><span class="pre">entity_type</span></code>. <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> passed to <code class="docutils literal notranslate"><span class="pre">filter_classes</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.intercell.IntercellAnnotation.filter_classes">
+<em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">filter_classes</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">classes</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.intercell.IntercellAnnotation.filter_classes" title="Link to this definition">§</a></dt>
+<dd><p>Returns a list of annotation classes filtered by their attributes.
+<code class="docutils literal notranslate"><span class="pre">kwargs</span></code> contains attributes and values.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.intercell.IntercellAnnotation.filter_interclass_network">
+<span class="sig-name descname"><span class="pre">filter_interclass_network</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">annot_df</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">network</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">combined_df</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">network_args</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">annot_args</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">annot_args_source</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">annot_args_target</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entities</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">only_directed</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">only_undirected</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">undirected_orientation</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">only_signed</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">only_effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">only_proteins</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">swap_undirected</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entities_or</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">transmitter_receiver</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">only_generic</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">only_composite</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">only_functional</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">exclude_intracellular</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.intercell.IntercellAnnotation.filter_interclass_network" title="Link to this definition">§</a></dt>
+<dd><p>Combines the annotation data frame and a network data frame.
+Creates a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> where each record is an interaction
+between a pair of molecular enitities labeled by their annotations.</p>
+<dl class="simple">
+<dt>network<span class="classifier">pypath.network.Network,pandas.DataFrame</span></dt><dd><p>A <code class="docutils literal notranslate"><span class="pre">pypath.network.Network</span></code> object or a data frame with network
+data.</p>
+</dd>
+<dt>combined_df<span class="classifier">pandas.DataFrame</span></dt><dd><p>Optional, a network data frame already combined with annotations
+for filtering only.</p>
+</dd>
+<dt>resources<span class="classifier">set,None</span></dt><dd><p>Use only these network resources.</p>
+</dd>
+<dt>entities<span class="classifier">set,None</span></dt><dd><p>Limit the network only to these molecular entities.</p>
+</dd>
+<dt>entities_source<span class="classifier">set,None</span></dt><dd><p>Limit the source side of network connections only to these
+molecular entities.</p>
+</dd>
+<dt>entities_target<span class="classifier">set,None</span></dt><dd><p>Limit the target side of network connections only to these
+molecular entities.</p>
+</dd>
+<dt>annot_args<span class="classifier">dict,None</span></dt><dd><p>Parameters for filtering annotation classes; note, the defaults
+might include some filtering, provide an empty dict if you want
+no filtering at all; however this might result in huge data
+frame and consequently memory issues. Passed to the <code class="docutils literal notranslate"><span class="pre">filtered</span></code>
+method.</p>
+</dd>
+<dt>annot_args_source<span class="classifier">dict,None</span></dt><dd><p>Same as <code class="docutils literal notranslate"><span class="pre">annot_args</span></code> but only for the source side of the
+network connections.</p>
+</dd>
+<dt>annot_args_target<span class="classifier">dict,None</span></dt><dd><p>Same as <code class="docutils literal notranslate"><span class="pre">annot_args</span></code> but only for the target side of the
+network connections.</p>
+</dd>
+<dt>only_directed<span class="classifier">bool</span></dt><dd><p>Use only the directed interactions.</p>
+</dd>
+<dt>only_undirected<span class="classifier">bool</span></dt><dd><p>Use only the undirected interactions. Specifically for retrieving
+and counting the interactions without direction information.</p>
+</dd>
+<dt>undirected_orientation<span class="classifier">str,None</span></dt><dd><p>Ignore the direction at all interactions and make sure all of
+them have a uniform orientation. If <cite>id</cite>, all interactions will
+be oriented by the identifiers of the partenrs; if <cite>category</cite>,
+the interactions will be oriented by the categories of the
+partners.</p>
+</dd>
+<dt>only_effect<span class="classifier">int,None</span></dt><dd><p>Use only the interactions with this effect. Either -1 or 1.</p>
+</dd>
+<dt>only_signed<span class="classifier">bool</span></dt><dd><p>Use only the interactions with effect sign.</p>
+</dd>
+<dt>only_proteins<span class="classifier">bool</span></dt><dd><p>Use only the interactions where each of the partners is a protein
+(i.e. not complex, miRNA, small molecule or other kind of entity).</p>
+</dd>
+<dt>transmitter_receiver<span class="classifier">bool</span></dt><dd><p>On the source side only transmitters, on the target side only
+receivers.</p>
+</dd>
+<dt>only_generic<span class="classifier">bool</span></dt><dd><p>Use only the generic classes. If specific classes allowed the
+size of the combined data frame might be huge.</p>
+</dd>
+<dt>only_composite<span class="classifier">bool</span></dt><dd><p>Use only the composite classes. If resource_specific classes
+allowed the size of the combined data frame might be huge.</p>
+</dd>
+<dt>only_functional<span class="classifier">bool</span></dt><dd><p>Use only the functional classes. Locational classes are often
+not relevant and they largely increase the size of the
+combined data frame.</p>
+</dd>
+<dt>exclude_intracellular<span class="classifier">bool</span></dt><dd><p>Remove the intracellular parent class and it’s children. These
+classes are not relevant in intercellular signaling and having
+them largely increases the size of the combined data frame.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.intercell.IntercellAnnotation.get_class">
+<span class="sig-name descname"><span class="pre">get_class</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">definition</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">parent</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resource</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.intercell.IntercellAnnotation.get_class" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a class by its name or definition. The definition can be
+a class name (string) or a set of entities, or an AnnotDef object
+defining the contents based on original resources or an AnnotOp
+which defines the contents as an operation over other definitions.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.intercell.IntercellAnnotation.get_df">
+<span class="sig-name descname"><span class="pre">get_df</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.intercell.IntercellAnnotation.get_df" title="Link to this definition">§</a></dt>
+<dd><p>Returns the data frame of custom annotations. If it does not exist yet
+builds the data frame.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.intercell.IntercellAnnotation.get_interclass_network_df">
+<span class="sig-name descname"><span class="pre">get_interclass_network_df</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.intercell.IntercellAnnotation.get_interclass_network_df" title="Link to this definition">§</a></dt>
+<dd><p>If the an interclass network is already present the <code class="docutils literal notranslate"><span class="pre">network</span></code>
+and other <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> provided not considered. Otherwise these
+are passed to <code class="docutils literal notranslate"><span class="pre">network_df</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.intercell.IntercellAnnotation.get_parents">
+<span class="sig-name descname"><span class="pre">get_parents</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">parent</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resource</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.intercell.IntercellAnnotation.get_parents" title="Link to this definition">§</a></dt>
+<dd><p>As names should be unique for resources, a combination of a name and
+resource determines the parent category. This method looks up the
+parent for a pair of name and resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.intercell.IntercellAnnotation.get_resource">
+<span class="sig-name descname"><span class="pre">get_resource</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">parent</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.intercell.IntercellAnnotation.get_resource" title="Link to this definition">§</a></dt>
+<dd><p>For a category name and its parent returns a single resource name.
+If a category belonging to the composite database matches the name
+and the parent the name of the composite database will be returned,
+otherwise the resource name first in alphabetic order.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.intercell.IntercellAnnotation.get_resources">
+<span class="sig-name descname"><span class="pre">get_resources</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">parent</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.intercell.IntercellAnnotation.get_resources" title="Link to this definition">§</a></dt>
+<dd><p>Returns a set with the names of all resources defining a category
+with the given name and parent.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.intercell.IntercellAnnotation.labels">
+<span class="sig-name descname"><span class="pre">labels</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">parent</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resource</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.intercell.IntercellAnnotation.labels" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but returns a list of labels (more human readable).</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.intercell.IntercellAnnotation.make_df">
+<span class="sig-name descname"><span class="pre">make_df</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/intercell.html#IntercellAnnotation.make_df"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.intercell.IntercellAnnotation.make_df" title="Link to this definition">§</a></dt>
+<dd><p>Creates a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> where each record assigns a
+molecular entity to an annotation category. The data frame will
+be assigned to the <code class="docutils literal notranslate"><span class="pre">df</span></code> attribute.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.intercell.IntercellAnnotation.network_df">
+<span class="sig-name descname"><span class="pre">network_df</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">annot_df</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">network</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">combined_df</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">network_args</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">annot_args</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">annot_args_source</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">annot_args_target</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entities</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">only_directed</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">only_undirected</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">undirected_orientation</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">only_signed</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">only_effect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">only_proteins</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">swap_undirected</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entities_or</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">transmitter_receiver</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">only_generic</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">only_composite</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">only_functional</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">exclude_intracellular</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/intercell.html#IntercellAnnotation.network_df"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.intercell.IntercellAnnotation.network_df" title="Link to this definition">§</a></dt>
+<dd><p>Combines the annotation data frame and a network data frame.
+Creates a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> where each record is an interaction
+between a pair of molecular enitities labeled by their annotations.</p>
+<dl class="simple">
+<dt>network<span class="classifier">pypath.network.Network,pandas.DataFrame</span></dt><dd><p>A <code class="docutils literal notranslate"><span class="pre">pypath.network.Network</span></code> object or a data frame with network
+data.</p>
+</dd>
+<dt>combined_df<span class="classifier">pandas.DataFrame</span></dt><dd><p>Optional, a network data frame already combined with annotations
+for filtering only.</p>
+</dd>
+<dt>resources<span class="classifier">set,None</span></dt><dd><p>Use only these network resources.</p>
+</dd>
+<dt>entities<span class="classifier">set,None</span></dt><dd><p>Limit the network only to these molecular entities.</p>
+</dd>
+<dt>entities_source<span class="classifier">set,None</span></dt><dd><p>Limit the source side of network connections only to these
+molecular entities.</p>
+</dd>
+<dt>entities_target<span class="classifier">set,None</span></dt><dd><p>Limit the target side of network connections only to these
+molecular entities.</p>
+</dd>
+<dt>annot_args<span class="classifier">dict,None</span></dt><dd><p>Parameters for filtering annotation classes; note, the defaults
+might include some filtering, provide an empty dict if you want
+no filtering at all; however this might result in huge data
+frame and consequently memory issues. Passed to the <code class="docutils literal notranslate"><span class="pre">filtered</span></code>
+method.</p>
+</dd>
+<dt>annot_args_source<span class="classifier">dict,None</span></dt><dd><p>Same as <code class="docutils literal notranslate"><span class="pre">annot_args</span></code> but only for the source side of the
+network connections.</p>
+</dd>
+<dt>annot_args_target<span class="classifier">dict,None</span></dt><dd><p>Same as <code class="docutils literal notranslate"><span class="pre">annot_args</span></code> but only for the target side of the
+network connections.</p>
+</dd>
+<dt>only_directed<span class="classifier">bool</span></dt><dd><p>Use only the directed interactions.</p>
+</dd>
+<dt>only_undirected<span class="classifier">bool</span></dt><dd><p>Use only the undirected interactions. Specifically for retrieving
+and counting the interactions without direction information.</p>
+</dd>
+<dt>undirected_orientation<span class="classifier">str,None</span></dt><dd><p>Ignore the direction at all interactions and make sure all of
+them have a uniform orientation. If <cite>id</cite>, all interactions will
+be oriented by the identifiers of the partenrs; if <cite>category</cite>,
+the interactions will be oriented by the categories of the
+partners.</p>
+</dd>
+<dt>only_effect<span class="classifier">int,None</span></dt><dd><p>Use only the interactions with this effect. Either -1 or 1.</p>
+</dd>
+<dt>only_signed<span class="classifier">bool</span></dt><dd><p>Use only the interactions with effect sign.</p>
+</dd>
+<dt>only_proteins<span class="classifier">bool</span></dt><dd><p>Use only the interactions where each of the partners is a protein
+(i.e. not complex, miRNA, small molecule or other kind of entity).</p>
+</dd>
+<dt>transmitter_receiver<span class="classifier">bool</span></dt><dd><p>On the source side only transmitters, on the target side only
+receivers.</p>
+</dd>
+<dt>only_generic<span class="classifier">bool</span></dt><dd><p>Use only the generic classes. If specific classes allowed the
+size of the combined data frame might be huge.</p>
+</dd>
+<dt>only_composite<span class="classifier">bool</span></dt><dd><p>Use only the composite classes. If resource_specific classes
+allowed the size of the combined data frame might be huge.</p>
+</dd>
+<dt>only_functional<span class="classifier">bool</span></dt><dd><p>Use only the functional classes. Locational classes are often
+not relevant and they largely increase the size of the
+combined data frame.</p>
+</dd>
+<dt>exclude_intracellular<span class="classifier">bool</span></dt><dd><p>Remove the intracellular parent class and it’s children. These
+classes are not relevant in intercellular signaling and having
+them largely increases the size of the combined data frame.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.intercell.IntercellAnnotation.populate_classes">
+<span class="sig-name descname"><span class="pre">populate_classes</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">update</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.intercell.IntercellAnnotation.populate_classes" title="Link to this definition">§</a></dt>
+<dd><p>Creates a classification of proteins according to the custom
+annotation definitions.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.intercell.IntercellAnnotation.populate_scores">
+<span class="sig-name descname"><span class="pre">populate_scores</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.intercell.IntercellAnnotation.populate_scores" title="Link to this definition">§</a></dt>
+<dd><p>Creates the consensus score dictionaries based on the number of
+resources annotating an entity for each composite category.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.intercell.IntercellAnnotation.process_annot">
+<span class="sig-name descname"><span class="pre">process_annot</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">classdef</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.intercell.IntercellAnnotation.process_annot" title="Link to this definition">§</a></dt>
+<dd><p>Processes an annotation definition and returns a set of identifiers.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.intercell.IntercellAnnotation.quality_check_table">
+<span class="sig-name descname"><span class="pre">quality_check_table</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">path</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">fmt</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'tsv'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">only_swissprot</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">top</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.intercell.IntercellAnnotation.quality_check_table" title="Link to this definition">§</a></dt>
+<dd><p>Exports a table in tsv format for quality check and browsing purposes.
+Each protein represented in one row of this table with basic data
+from UniProt and the list of annotation categories from this
+database.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>path</strong> (<em>str</em>) – Path for the exported file.</p></li>
+<li><p><strong>fmt</strong> (<em>str</em>) – Format: either <cite>tsv</cite> or <cite>latex</cite>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.intercell.IntercellAnnotation.register_network">
+<span class="sig-name descname"><span class="pre">register_network</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">network</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.intercell.IntercellAnnotation.register_network" title="Link to this definition">§</a></dt>
+<dd><p>Sets <code class="docutils literal notranslate"><span class="pre">network</span></code> as the default network dataset for the instance.
+All methods afterwards will use this network.
+Also it discards the interclass network data frame if it present to
+make sure future queries will address the network registered here.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.intercell.IntercellAnnotation.reload">
+<span class="sig-name descname"><span class="pre">reload</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/intercell.html#IntercellAnnotation.reload"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.intercell.IntercellAnnotation.reload" title="Link to this definition">§</a></dt>
+<dd><p>Reloads the object from the module level.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.intercell.IntercellAnnotation.resources_in_category">
+<span class="sig-name descname"><span class="pre">resources_in_category</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">key</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.intercell.IntercellAnnotation.resources_in_category" title="Link to this definition">§</a></dt>
+<dd><p>Returns a list of resources contributing to the definition of
+a category.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.intercell.IntercellAnnotation.select">
+<span class="sig-name descname"><span class="pre">select</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">definition</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">parent</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resource</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.intercell.IntercellAnnotation.select" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a class by its name or definition. The definition can be
+a class name (string) or a set of entities, or an AnnotDef object
+defining the contents based on original resources or an AnnotOp
+which defines the contents as an operation over other definitions.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.intercell.IntercellAnnotation.set_interclass_network_df">
+<span class="sig-name descname"><span class="pre">set_interclass_network_df</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.intercell.IntercellAnnotation.set_interclass_network_df" title="Link to this definition">§</a></dt>
+<dd><p>Creates a data frame of the whole inter-class network and keeps it
+assigned to the instance in order to make subsequent queries faster.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.intercell.IntercellAnnotation.show">
+<span class="sig-name descname"><span class="pre">show</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">parent</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resource</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.intercell.IntercellAnnotation.show" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">select</span></code> but prints a table to the console with basic
+information from the UniProt datasheets.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.intercell.IntercellAnnotation.update_parents">
+<span class="sig-name descname"><span class="pre">update_parents</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.intercell.IntercellAnnotation.update_parents" title="Link to this definition">§</a></dt>
+<dd><p>Creates a dict :py:attr:<code class="docutils literal notranslate"><span class="pre">children</span></code> with parent class names as keys
+and sets of children class keys as values. Also a dict
+:py:attr:<code class="docutils literal notranslate"><span class="pre">parents</span></code> with children class keys as keys and parent
+class keys as values.</p>
+</dd></dl>
+
+</dd></dl>
+
+</section>
+
+
+                </article>
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+  <section id="module-pypath.core.intercell">
+<span id="pypath-core-intercell"></span><h1>pypath.core.intercell<a class="headerlink" href="#module-pypath.core.intercell" title="Link to this heading">§</a></h1>
+<dl class="field-list simple">
+<dt class="field-odd">members<span class="colon">:</span></dt>
+<dd class="field-odd"><p></p></dd>
+</dl>
+<p class="rubric">Functions</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.core.intercell.get_db.html#pypath.core.intercell.get_db" title="pypath.core.intercell.get_db"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_db</span></code></a>(**kwargs)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.core.intercell.init_db.html#pypath.core.intercell.init_db" title="pypath.core.intercell.init_db"><code class="xref py py-obj docutils literal notranslate"><span class="pre">init_db</span></code></a>(**kwargs)</p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Classes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.core.intercell.IntercellAnnotation.html#pypath.core.intercell.IntercellAnnotation" title="pypath.core.intercell.IntercellAnnotation"><code class="xref py py-obj docutils literal notranslate"><span class="pre">IntercellAnnotation</span></code></a>([class_definitions, ...])</p></td>
+<td><p></p></td>
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+<span class="sig-prename descclassname"><span class="pre">pypath.core.intercell.</span></span><span class="sig-name descname"><span class="pre">init_db</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/intercell.html#init_db"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.intercell.init_db" title="Link to this definition">§</a></dt>
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+  <section id="pypath-core-intercell-annot-excludes">
+<h1>pypath.core.intercell_annot.excludes<a class="headerlink" href="#pypath-core-intercell-annot-excludes" title="Link to this heading">§</a></h1>
+<dl class="py data">
+<dt class="sig sig-object py" id="pypath.core.intercell_annot.excludes">
+<span class="sig-prename descclassname"><span class="pre">pypath.core.intercell_annot.</span></span><span class="sig-name descname"><span class="pre">excludes</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">{'adhesion':</span> <span class="pre">{'O14976',</span> <span class="pre">'O15231',</span> <span class="pre">'O43294',</span> <span class="pre">'O60711',</span> <span class="pre">'O60759',</span> <span class="pre">'P07332',</span> <span class="pre">'P29965',</span> <span class="pre">'P35221',</span> <span class="pre">'P35222',</span> <span class="pre">'P50552',</span> <span class="pre">'P56945',</span> <span class="pre">'Q02297',</span> <span class="pre">'Q03001',</span> <span class="pre">'Q13153',</span> <span class="pre">'Q13895',</span> <span class="pre">'Q14451',</span> <span class="pre">'Q14511',</span> <span class="pre">'Q14943',</span> <span class="pre">'Q14952',</span> <span 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class="pre">'Q9Y6Y9'}}</span></em><a class="headerlink" href="#pypath.core.intercell_annot.excludes" title="Link to this definition">§</a></dt>
+<dd><p>Higher level classes of intercellular communication roles.</p>
+</dd></dl>
+
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+<dl class="field-list simple">
+<dt class="field-odd">members<span class="colon">:</span></dt>
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+  <section id="pypath-core-network-network">
+<h1>pypath.core.network.Network<a class="headerlink" href="#pypath-core-network-network" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.core.network.Network">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.core.network.</span></span><span class="sig-name descname"><span class="pre">Network</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">make_df</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">df_by_source</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">df_with_references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">df_columns</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">df_dtype</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">pickle_file</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">allow_loops</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/network.html#Network"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.network.Network" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">Logger</span></code></p>
+<p>Represents a molecular interaction network. Provides various methods to
+query the network and its components. Optionally converts the network
+to a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> of interactions.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>resources</strong> (<em>list</em><em>,</em><em>dict</em>) – One or more lists or dictionaries containing
+<code class="docutils literal notranslate"><span class="pre">pypath.resource.NetworkResource</span></code> objects.</p></li>
+<li><p><strong>make_df</strong> (<em>bool</em>) – Create a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> already when creating the instance.
+If no network data loaded no data frame will be created.</p></li>
+<li><p><strong>ncbi_tax_id</strong> (<em>int</em>) – Restrict the network only to this organism. If <code class="docutils literal notranslate"><span class="pre">None</span></code> identifiers
+from any organism will be allowed.</p></li>
+<li><p><strong>allow_loops</strong> (<em>bool</em>) – Allow interactions with the their two endpoints being the same entity.</p></li>
+</ul>
+</dd>
+</dl>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.network.Network.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">make_df</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">df_by_source</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">df_with_references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">df_columns</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">df_dtype</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">pickle_file</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">allow_loops</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/network.html#Network.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.network.Network.__init__" title="Link to this definition">§</a></dt>
+<dd><p>Make this instance a logger.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>name</strong> – The label of this instance that will be prepended to all
+messages it sends to the logger.</p></li>
+<li><p><strong>module</strong> – Send the messages by the logger of this module.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.__init__" title="pypath.core.network.Network.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>([resources, make_df, df_by_source, ...])</p></td>
+<td><p>Make this instance a logger.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.add_interaction" title="pypath.core.network.Network.add_interaction"><code class="xref py py-obj docutils literal notranslate"><span class="pre">add_interaction</span></code></a>(interaction[, attrs, ...])</p></td>
+<td><p>Adds a ready <code class="docutils literal notranslate"><span class="pre">pypath.interaction.Interaction</span></code> object to the network.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.add_node" title="pypath.core.network.Network.add_node"><code class="xref py py-obj docutils literal notranslate"><span class="pre">add_node</span></code></a>(entity[, attrs, add])</p></td>
+<td><p>Adds a molecular entity to the py:attr:<code class="docutils literal notranslate"><span class="pre">nodes</span></code> and py:attr:<code class="docutils literal notranslate"><span class="pre">nodes_by_label</span></code> dictionaries.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.collectri" title="pypath.core.network.Network.collectri"><code class="xref py py-obj docutils literal notranslate"><span class="pre">collectri</span></code></a>([ncbi_tax_id])</p></td>
+<td><p>Initializes a new <code class="docutils literal notranslate"><span class="pre">Network</span></code> object with loading the transcriptional regulation network from CollecTRI.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_loops</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_partners" title="pypath.core.network.Network.count_partners"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_partners</span></code></a>(entity, **kwargs)</p></td>
+<td><p>Returns the count of the interacting partners for one or more entities according to the specified criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.direction_consistency" title="pypath.core.network.Network.direction_consistency"><code class="xref py py-obj docutils literal notranslate"><span class="pre">direction_consistency</span></code></a>()</p></td>
+<td><p>Collects statistics about the consistency of interaction directions between resources. * total_directed: number of directed edges * shared_directed: number of directed edges in overlap with other   resources * consistent_edges: number of edges consistent with other resources * inconsistent_edges: number of edges inconsistent with other   resources * total_consistency: sum of consistencies (for all edges and all   resources) * total_inconsistency: sum of inconsistencies (for all edges and all   resources).</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.dorothea" title="pypath.core.network.Network.dorothea"><code class="xref py py-obj docutils literal notranslate"><span class="pre">dorothea</span></code></a>([levels, ncbi_tax_id])</p></td>
+<td><p>Initializes a new <code class="docutils literal notranslate"><span class="pre">Network</span></code> object with loading the transcriptional regulation network from DoRothEA.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">dorothea_resources</span></code>([levels, expand_levels])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">entity</span></code>(entity)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.entity_by_id" title="pypath.core.network.Network.entity_by_id"><code class="xref py py-obj docutils literal notranslate"><span class="pre">entity_by_id</span></code></a>(identifier)</p></td>
+<td><p>Returns a <code class="docutils literal notranslate"><span class="pre">pypath.entity.Entity</span></code> object representing a molecular entity by looking it up by its identifier.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.entity_by_label" title="pypath.core.network.Network.entity_by_label"><code class="xref py py-obj docutils literal notranslate"><span class="pre">entity_by_label</span></code></a>(label)</p></td>
+<td><p>Returns a <code class="docutils literal notranslate"><span class="pre">pypath.entity.Entity</span></code> object representing a molecular entity by looking it up by its label.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.extra_directions" title="pypath.core.network.Network.extra_directions"><code class="xref py py-obj docutils literal notranslate"><span class="pre">extra_directions</span></code></a>([resources, use_laudanna, ...])</p></td>
+<td><p>Adds additional direction &amp; effect information from resources having no literature curated references, but giving sufficient evidence about the directionality for interactions already supported by literature evidences from other sources.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">filter_df</span></code>(*args, **kwargs)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">filtered</span></code>([resource, entity_type, ...])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.find_paths" title="pypath.core.network.Network.find_paths"><code class="xref py py-obj docutils literal notranslate"><span class="pre">find_paths</span></code></a>(start[, end, loops, mode, ...])</p></td>
+<td><p>Find paths or motifs in a network.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.from_igraph" title="pypath.core.network.Network.from_igraph"><code class="xref py py-obj docutils literal notranslate"><span class="pre">from_igraph</span></code></a>(pa, **kwargs)</p></td>
+<td><p>Creates an instance from an <code class="docutils literal notranslate"><span class="pre">igraph.Graph</span></code> based <code class="docutils literal notranslate"><span class="pre">pypath.main.PyPath</span></code> object.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.from_pickle" title="pypath.core.network.Network.from_pickle"><code class="xref py py-obj docutils literal notranslate"><span class="pre">from_pickle</span></code></a>(pickle_file, **kwargs)</p></td>
+<td><p>Initializes a new <code class="docutils literal notranslate"><span class="pre">Network</span></code> object by loading it from a pickle file.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">generate_df_records</span></code>([by_source, with_references])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_df</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.get_organisms" title="pypath.core.network.Network.get_organisms"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_organisms</span></code></a>()</p></td>
+<td><p>Returns the set of all NCBI Taxonomy IDs occurring in the network.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">homology_translate</span></code>(taxon[, exclude])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.htp_interactions" title="pypath.core.network.Network.htp_interactions"><code class="xref py py-obj docutils literal notranslate"><span class="pre">htp_interactions</span></code></a>([threshold, ignore_directed])</p></td>
+<td><p>Collects the interactions only from high-throughput studies.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.htp_references" title="pypath.core.network.Network.htp_references"><code class="xref py py-obj docutils literal notranslate"><span class="pre">htp_references</span></code></a>([threshold])</p></td>
+<td><p>Collects the high-throughput references i.e. the ones cited at a higher number of interactions than <code class="docutils literal notranslate"><span class="pre">threshold</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.init_network" title="pypath.core.network.Network.init_network"><code class="xref py py-obj docutils literal notranslate"><span class="pre">init_network</span></code></a>([resources, make_df, exclude, ...])</p></td>
+<td><p>Loads data from a network resource or a collection of resources.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.interaction" title="pypath.core.network.Network.interaction"><code class="xref py py-obj docutils literal notranslate"><span class="pre">interaction</span></code></a>(a, b)</p></td>
+<td><p>Retrieves the interaction <cite>a --&gt; b</cite> if it exists in the network, otherwise <cite>b --&gt; a</cite>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.interaction_by_id" title="pypath.core.network.Network.interaction_by_id"><code class="xref py py-obj docutils literal notranslate"><span class="pre">interaction_by_id</span></code></a>(id_a, id_b)</p></td>
+<td><p>Returns a <code class="docutils literal notranslate"><span class="pre">pypath.interaction.Interaction</span></code> object by looking it up based on a pair of identifiers.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.interaction_by_label" title="pypath.core.network.Network.interaction_by_label"><code class="xref py py-obj docutils literal notranslate"><span class="pre">interaction_by_label</span></code></a>(label_a, label_b)</p></td>
+<td><p>Returns a <code class="docutils literal notranslate"><span class="pre">pypath.interaction.Interaction</span></code> object by looking it up based on a pair of labels.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.load" title="pypath.core.network.Network.load"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load</span></code></a>([resources, make_df, exclude, reread, ...])</p></td>
+<td><p>Loads data from a network resource or a collection of resources.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_collectri</span></code>(**kwargs)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_dorothea</span></code>([levels, expand_levels])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.load_from_pickle" title="pypath.core.network.Network.load_from_pickle"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_from_pickle</span></code></a>(pickle_file)</p></td>
+<td><p>Loads the network to a pickle file.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_mirna_target</span></code>(**kwargs)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_omnipath</span></code>([omnipath, ...])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.load_resource" title="pypath.core.network.Network.load_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_resource</span></code></a>(resource[, clean, reread, ...])</p></td>
+<td><p>Loads the data from a single resource and attaches it to the network</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.load_resources" title="pypath.core.network.Network.load_resources"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_resources</span></code></a>([resources, make_df, ...])</p></td>
+<td><p>Loads data from a network resource or a collection of resources.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_transcription</span></code>([collectri, dorothea, ...])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.make_df" title="pypath.core.network.Network.make_df"><code class="xref py py-obj docutils literal notranslate"><span class="pre">make_df</span></code></a>([records, by_source, ...])</p></td>
+<td><p>Creates a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the interactions.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.mirna_target" title="pypath.core.network.Network.mirna_target"><code class="xref py py-obj docutils literal notranslate"><span class="pre">mirna_target</span></code></a>([resources, make_df, reread, ...])</p></td>
+<td><p>Initializes a new <code class="docutils literal notranslate"><span class="pre">Network</span></code> object with loading a miRNA-mRNA regulation network from all databases by default.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.numof_interactions_per_reference" title="pypath.core.network.Network.numof_interactions_per_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_interactions_per_reference</span></code></a>()</p></td>
+<td><p>Counts the number of interactions for each literature reference.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">omnipath</span></code>([omnipath, kinase_substrate_extra, ...])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">omnipath_resources</span></code>([omnipath, ...])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.organisms_check" title="pypath.core.network.Network.organisms_check"><code class="xref py py-obj docutils literal notranslate"><span class="pre">organisms_check</span></code></a>([organisms, ...])</p></td>
+<td><p>Scans the network for one or more organisms and removes the nodes and interactions which belong to any other organism.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.partners" title="pypath.core.network.Network.partners"><code class="xref py py-obj docutils literal notranslate"><span class="pre">partners</span></code></a>(entity[, mode, direction, effect, ...])</p></td>
+<td><p><dl class="field-list simple">
+<dt class="field-odd">arg str,Entity,list,set,tuple,EntityList entity<span class="colon">:</span></dt>
+<dd class="field-odd"><p></p></dd>
+</dl>
+</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.random_interaction" title="pypath.core.network.Network.random_interaction"><code class="xref py py-obj docutils literal notranslate"><span class="pre">random_interaction</span></code></a>(**kwargs)</p></td>
+<td><p>Picks a random interaction from the network.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.reload" title="pypath.core.network.Network.reload"><code class="xref py py-obj docutils literal notranslate"><span class="pre">reload</span></code></a>([recursive])</p></td>
+<td><p>Reloads the object from the module level.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">remove_htp</span></code>([threshold, keep_directed])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.remove_interaction" title="pypath.core.network.Network.remove_interaction"><code class="xref py py-obj docutils literal notranslate"><span class="pre">remove_interaction</span></code></a>(entity_a, entity_b)</p></td>
+<td><p>Removes the interaction between two nodes if exists.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.remove_loops" title="pypath.core.network.Network.remove_loops"><code class="xref py py-obj docutils literal notranslate"><span class="pre">remove_loops</span></code></a>()</p></td>
+<td><p>Removes the loop interactions from the network i.e. the ones with their two endpoints being the same entity.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.remove_node" title="pypath.core.network.Network.remove_node"><code class="xref py py-obj docutils literal notranslate"><span class="pre">remove_node</span></code></a>(entity)</p></td>
+<td><p>Removes a node with all its interactions.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">remove_undirected</span></code>([min_refs, min_resources])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.remove_zero_degree" title="pypath.core.network.Network.remove_zero_degree"><code class="xref py py-obj docutils literal notranslate"><span class="pre">remove_zero_degree</span></code></a>()</p></td>
+<td><p>Removes all nodes with no interaction.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.reset" title="pypath.core.network.Network.reset"><code class="xref py py-obj docutils literal notranslate"><span class="pre">reset</span></code></a>()</p></td>
+<td><p>Removes network data i.e. creates empty interaction and node dictionaries.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.save_to_pickle" title="pypath.core.network.Network.save_to_pickle"><code class="xref py py-obj docutils literal notranslate"><span class="pre">save_to_pickle</span></code></a>(pickle_file)</p></td>
+<td><p>Saves the network to a pickle file.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.summaries_tab" title="pypath.core.network.Network.summaries_tab"><code class="xref py py-obj docutils literal notranslate"><span class="pre">summaries_tab</span></code></a>([outfile, return_table, ...])</p></td>
+<td><p>Creates a table from resource vs.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.to_igraph" title="pypath.core.network.Network.to_igraph"><code class="xref py py-obj docutils literal notranslate"><span class="pre">to_igraph</span></code></a>()</p></td>
+<td><p>Converts the network to the legacy <code class="docutils literal notranslate"><span class="pre">igraph.Graph</span></code> based <code class="docutils literal notranslate"><span class="pre">PyPath</span></code> object.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.transcription" title="pypath.core.network.Network.transcription"><code class="xref py py-obj docutils literal notranslate"><span class="pre">transcription</span></code></a>([dorothea, ...])</p></td>
+<td><p>Initializes a new <code class="docutils literal notranslate"><span class="pre">Network</span></code> object with loading a transcriptional regulation network from all databases by default.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">update_summaries</span></code>([collect_args])</p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Attributes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.activated_by" title="pypath.core.network.Network.activated_by"><code class="xref py py-obj docutils literal notranslate"><span class="pre">activated_by</span></code></a></p></td>
+<td><p>arg str,Entity,list,set,tuple,EntityList entity:</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.activates" title="pypath.core.network.Network.activates"><code class="xref py py-obj docutils literal notranslate"><span class="pre">activates</span></code></a></p></td>
+<td><p>arg str,Entity,list,set,tuple,EntityList entity:</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.collect_complex_identifiers" title="pypath.core.network.Network.collect_complex_identifiers"><code class="xref py py-obj docutils literal notranslate"><span class="pre">collect_complex_identifiers</span></code></a></p></td>
+<td><p>Builds a comprehensive collection of <cite>complex_identifiers</cite> entities across the network, counts unique and shared objects by resource, data model and interaction types.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.collect_complex_labels" title="pypath.core.network.Network.collect_complex_labels"><code class="xref py py-obj docutils literal notranslate"><span class="pre">collect_complex_labels</span></code></a></p></td>
+<td><p>Builds a comprehensive collection of <cite>complex_labels</cite> entities across the network, counts unique and shared objects by resource, data model and interaction types.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.collect_complexes" title="pypath.core.network.Network.collect_complexes"><code class="xref py py-obj docutils literal notranslate"><span class="pre">collect_complexes</span></code></a></p></td>
+<td><p>Builds a comprehensive collection of <cite>complexes</cite> entities across the network, counts unique and shared objects by resource, data model and interaction types.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.collect_curation_effort" title="pypath.core.network.Network.collect_curation_effort"><code class="xref py py-obj docutils literal notranslate"><span class="pre">collect_curation_effort</span></code></a></p></td>
+<td><p>Builds a comprehensive collection of <cite>curation_effort</cite> entities across the network, counts unique and shared objects by resource, data model and interaction types.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.collect_data_models" title="pypath.core.network.Network.collect_data_models"><code class="xref py py-obj docutils literal notranslate"><span class="pre">collect_data_models</span></code></a></p></td>
+<td><p>Builds a comprehensive collection of <cite>data_models</cite> entities across the network, counts unique and shared objects by resource, data model and interaction types.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.collect_datasets" title="pypath.core.network.Network.collect_datasets"><code class="xref py py-obj docutils literal notranslate"><span class="pre">collect_datasets</span></code></a></p></td>
+<td><p>Builds a comprehensive collection of <cite>datasets</cite> entities across the network, counts unique and shared objects by resource, data model and interaction types.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.collect_degrees_directed" title="pypath.core.network.Network.collect_degrees_directed"><code class="xref py py-obj docutils literal notranslate"><span class="pre">collect_degrees_directed</span></code></a></p></td>
+<td><p>Builds a comprehensive collection of <cite>degrees_directed</cite> entities across the network, counts unique and shared objects by resource, data model and interaction types.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.collect_degrees_directed_in" title="pypath.core.network.Network.collect_degrees_directed_in"><code class="xref py py-obj docutils literal notranslate"><span class="pre">collect_degrees_directed_in</span></code></a></p></td>
+<td><p>Builds a comprehensive collection of <cite>degrees_directed_in</cite> entities across the network, counts unique and shared objects by resource, data model and interaction types.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.collect_degrees_directed_out" title="pypath.core.network.Network.collect_degrees_directed_out"><code class="xref py py-obj docutils literal notranslate"><span class="pre">collect_degrees_directed_out</span></code></a></p></td>
+<td><p>Builds a comprehensive collection of <cite>degrees_directed_out</cite> entities across the network, counts unique and shared objects by resource, data model and interaction types.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.collect_degrees_negative" title="pypath.core.network.Network.collect_degrees_negative"><code class="xref py py-obj docutils literal notranslate"><span class="pre">collect_degrees_negative</span></code></a></p></td>
+<td><p>Builds a comprehensive collection of <cite>degrees_negative</cite> entities across the network, counts unique and shared objects by resource, data model and interaction types.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.collect_degrees_negative_in" title="pypath.core.network.Network.collect_degrees_negative_in"><code class="xref py py-obj docutils literal notranslate"><span class="pre">collect_degrees_negative_in</span></code></a></p></td>
+<td><p>Builds a comprehensive collection of <cite>degrees_negative_in</cite> entities across the network, counts unique and shared objects by resource, data model and interaction types.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.collect_degrees_negative_out" title="pypath.core.network.Network.collect_degrees_negative_out"><code class="xref py py-obj docutils literal notranslate"><span class="pre">collect_degrees_negative_out</span></code></a></p></td>
+<td><p>Builds a comprehensive collection of <cite>degrees_negative_out</cite> entities across the network, counts unique and shared objects by resource, data model and interaction types.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.collect_degrees_non_directed" title="pypath.core.network.Network.collect_degrees_non_directed"><code class="xref py py-obj docutils literal notranslate"><span class="pre">collect_degrees_non_directed</span></code></a></p></td>
+<td><p>Builds a comprehensive collection of <cite>degrees_non_directed</cite> entities across the network, counts unique and shared objects by resource, data model and interaction types.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.collect_degrees_positive" title="pypath.core.network.Network.collect_degrees_positive"><code class="xref py py-obj docutils literal notranslate"><span class="pre">collect_degrees_positive</span></code></a></p></td>
+<td><p>Builds a comprehensive collection of <cite>degrees_positive</cite> entities across the network, counts unique and shared objects by resource, data model and interaction types.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.collect_degrees_positive_in" title="pypath.core.network.Network.collect_degrees_positive_in"><code class="xref py py-obj docutils literal notranslate"><span class="pre">collect_degrees_positive_in</span></code></a></p></td>
+<td><p>Builds a comprehensive collection of <cite>degrees_positive_in</cite> entities across the network, counts unique and shared objects by resource, data model and interaction types.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.collect_degrees_positive_out" title="pypath.core.network.Network.collect_degrees_positive_out"><code class="xref py py-obj docutils literal notranslate"><span class="pre">collect_degrees_positive_out</span></code></a></p></td>
+<td><p>Builds a comprehensive collection of <cite>degrees_positive_out</cite> entities across the network, counts unique and shared objects by resource, data model and interaction types.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.collect_degrees_signed" title="pypath.core.network.Network.collect_degrees_signed"><code class="xref py py-obj docutils literal notranslate"><span class="pre">collect_degrees_signed</span></code></a></p></td>
+<td><p>Builds a comprehensive collection of <cite>degrees_signed</cite> entities across the network, counts unique and shared objects by resource, data model and interaction types.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.collect_degrees_signed_in" title="pypath.core.network.Network.collect_degrees_signed_in"><code class="xref py py-obj docutils literal notranslate"><span class="pre">collect_degrees_signed_in</span></code></a></p></td>
+<td><p>Builds a comprehensive collection of <cite>degrees_signed_in</cite> entities across the network, counts unique and shared objects by resource, data model and interaction types.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.collect_degrees_signed_out" title="pypath.core.network.Network.collect_degrees_signed_out"><code class="xref py py-obj docutils literal notranslate"><span class="pre">collect_degrees_signed_out</span></code></a></p></td>
+<td><p>Builds a comprehensive collection of <cite>degrees_signed_out</cite> entities across the network, counts unique and shared objects by resource, data model and interaction types.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.collect_degrees_undirected" title="pypath.core.network.Network.collect_degrees_undirected"><code class="xref py py-obj docutils literal notranslate"><span class="pre">collect_degrees_undirected</span></code></a></p></td>
+<td><p>Builds a comprehensive collection of <cite>degrees_undirected</cite> entities across the network, counts unique and shared objects by resource, data model and interaction types.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.collect_entities" title="pypath.core.network.Network.collect_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">collect_entities</span></code></a></p></td>
+<td><p>Builds a comprehensive collection of <cite>entities</cite> entities across the network, counts unique and shared objects by resource, data model and interaction types.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.collect_evidences" title="pypath.core.network.Network.collect_evidences"><code class="xref py py-obj docutils literal notranslate"><span class="pre">collect_evidences</span></code></a></p></td>
+<td><p>Builds a comprehensive collection of <cite>evidences</cite> entities across the network, counts unique and shared objects by resource, data model and interaction types.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.collect_identifiers" title="pypath.core.network.Network.collect_identifiers"><code class="xref py py-obj docutils literal notranslate"><span class="pre">collect_identifiers</span></code></a></p></td>
+<td><p>Builds a comprehensive collection of <cite>identifiers</cite> entities across the network, counts unique and shared objects by resource, data model and interaction types.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.collect_interaction_types" title="pypath.core.network.Network.collect_interaction_types"><code class="xref py py-obj docutils literal notranslate"><span class="pre">collect_interaction_types</span></code></a></p></td>
+<td><p>Builds a comprehensive collection of <cite>interaction_types</cite> entities across the network, counts unique and shared objects by resource, data model and interaction types.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.collect_interactions" title="pypath.core.network.Network.collect_interactions"><code class="xref py py-obj docutils literal notranslate"><span class="pre">collect_interactions</span></code></a></p></td>
+<td><p>Builds a comprehensive collection of <cite>interactions</cite> entities across the network, counts unique and shared objects by resource, data model and interaction types.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.collect_interactions_0" title="pypath.core.network.Network.collect_interactions_0"><code class="xref py py-obj docutils literal notranslate"><span class="pre">collect_interactions_0</span></code></a></p></td>
+<td><p>Builds a comprehensive collection of <cite>interactions_0</cite> entities across the network, counts unique and shared objects by resource, data model and interaction types.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.collect_interactions_directed" title="pypath.core.network.Network.collect_interactions_directed"><code class="xref py py-obj docutils literal notranslate"><span class="pre">collect_interactions_directed</span></code></a></p></td>
+<td><p>Builds a comprehensive collection of <cite>interactions_directed</cite> entities across the network, counts unique and shared objects by resource, data model and interaction types.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.collect_interactions_mutual" title="pypath.core.network.Network.collect_interactions_mutual"><code class="xref py py-obj docutils literal notranslate"><span class="pre">collect_interactions_mutual</span></code></a></p></td>
+<td><p>Builds a comprehensive collection of <cite>interactions_mutual</cite> entities across the network, counts unique and shared objects by resource, data model and interaction types.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.collect_interactions_negative" title="pypath.core.network.Network.collect_interactions_negative"><code class="xref py py-obj docutils literal notranslate"><span class="pre">collect_interactions_negative</span></code></a></p></td>
+<td><p>Builds a comprehensive collection of <cite>interactions_negative</cite> entities across the network, counts unique and shared objects by resource, data model and interaction types.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.collect_interactions_non_directed" title="pypath.core.network.Network.collect_interactions_non_directed"><code class="xref py py-obj docutils literal notranslate"><span class="pre">collect_interactions_non_directed</span></code></a></p></td>
+<td><p>Builds a comprehensive collection of <cite>interactions_non_directed</cite> entities across the network, counts unique and shared objects by resource, data model and interaction types.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.collect_interactions_non_directed_0" title="pypath.core.network.Network.collect_interactions_non_directed_0"><code class="xref py py-obj docutils literal notranslate"><span class="pre">collect_interactions_non_directed_0</span></code></a></p></td>
+<td><p>Builds a comprehensive collection of <cite>interactions_non_directed_0</cite> entities across the network, counts unique and shared objects by resource, data model and interaction types.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.collect_interactions_positive" title="pypath.core.network.Network.collect_interactions_positive"><code class="xref py py-obj docutils literal notranslate"><span class="pre">collect_interactions_positive</span></code></a></p></td>
+<td><p>Builds a comprehensive collection of <cite>interactions_positive</cite> entities across the network, counts unique and shared objects by resource, data model and interaction types.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.collect_interactions_signed" title="pypath.core.network.Network.collect_interactions_signed"><code class="xref py py-obj docutils literal notranslate"><span class="pre">collect_interactions_signed</span></code></a></p></td>
+<td><p>Builds a comprehensive collection of <cite>interactions_signed</cite> entities across the network, counts unique and shared objects by resource, data model and interaction types.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.collect_interactions_undirected" title="pypath.core.network.Network.collect_interactions_undirected"><code class="xref py py-obj docutils literal notranslate"><span class="pre">collect_interactions_undirected</span></code></a></p></td>
+<td><p>Builds a comprehensive collection of <cite>interactions_undirected</cite> entities across the network, counts unique and shared objects by resource, data model and interaction types.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.collect_interactions_undirected_0" title="pypath.core.network.Network.collect_interactions_undirected_0"><code class="xref py py-obj docutils literal notranslate"><span class="pre">collect_interactions_undirected_0</span></code></a></p></td>
+<td><p>Builds a comprehensive collection of <cite>interactions_undirected_0</cite> entities across the network, counts unique and shared objects by resource, data model and interaction types.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.collect_labels" title="pypath.core.network.Network.collect_labels"><code class="xref py py-obj docutils literal notranslate"><span class="pre">collect_labels</span></code></a></p></td>
+<td><p>Builds a comprehensive collection of <cite>labels</cite> entities across the network, counts unique and shared objects by resource, data model and interaction types.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.collect_lncrna_identifiers" title="pypath.core.network.Network.collect_lncrna_identifiers"><code class="xref py py-obj docutils literal notranslate"><span class="pre">collect_lncrna_identifiers</span></code></a></p></td>
+<td><p>Builds a comprehensive collection of <cite>lncrna_identifiers</cite> entities across the network, counts unique and shared objects by resource, data model and interaction types.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.collect_lncrna_labels" title="pypath.core.network.Network.collect_lncrna_labels"><code class="xref py py-obj docutils literal notranslate"><span class="pre">collect_lncrna_labels</span></code></a></p></td>
+<td><p>Builds a comprehensive collection of <cite>lncrna_labels</cite> entities across the network, counts unique and shared objects by resource, data model and interaction types.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.collect_lncrnas" title="pypath.core.network.Network.collect_lncrnas"><code class="xref py py-obj docutils literal notranslate"><span class="pre">collect_lncrnas</span></code></a></p></td>
+<td><p>Builds a comprehensive collection of <cite>lncrnas</cite> entities across the network, counts unique and shared objects by resource, data model and interaction types.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.collect_mirna_identifiers" title="pypath.core.network.Network.collect_mirna_identifiers"><code class="xref py py-obj docutils literal notranslate"><span class="pre">collect_mirna_identifiers</span></code></a></p></td>
+<td><p>Builds a comprehensive collection of <cite>mirna_identifiers</cite> entities across the network, counts unique and shared objects by resource, data model and interaction types.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.collect_mirna_labels" title="pypath.core.network.Network.collect_mirna_labels"><code class="xref py py-obj docutils literal notranslate"><span class="pre">collect_mirna_labels</span></code></a></p></td>
+<td><p>Builds a comprehensive collection of <cite>mirna_labels</cite> entities across the network, counts unique and shared objects by resource, data model and interaction types.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.collect_mirnas" title="pypath.core.network.Network.collect_mirnas"><code class="xref py py-obj docutils literal notranslate"><span class="pre">collect_mirnas</span></code></a></p></td>
+<td><p>Builds a comprehensive collection of <cite>mirnas</cite> entities across the network, counts unique and shared objects by resource, data model and interaction types.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.collect_protein_identifiers" title="pypath.core.network.Network.collect_protein_identifiers"><code class="xref py py-obj docutils literal notranslate"><span class="pre">collect_protein_identifiers</span></code></a></p></td>
+<td><p>Builds a comprehensive collection of <cite>protein_identifiers</cite> entities across the network, counts unique and shared objects by resource, data model and interaction types.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.collect_protein_labels" title="pypath.core.network.Network.collect_protein_labels"><code class="xref py py-obj docutils literal notranslate"><span class="pre">collect_protein_labels</span></code></a></p></td>
+<td><p>Builds a comprehensive collection of <cite>protein_labels</cite> entities across the network, counts unique and shared objects by resource, data model and interaction types.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.collect_proteins" title="pypath.core.network.Network.collect_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">collect_proteins</span></code></a></p></td>
+<td><p>Builds a comprehensive collection of <cite>proteins</cite> entities across the network, counts unique and shared objects by resource, data model and interaction types.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.collect_references" title="pypath.core.network.Network.collect_references"><code class="xref py py-obj docutils literal notranslate"><span class="pre">collect_references</span></code></a></p></td>
+<td><p>Builds a comprehensive collection of <cite>references</cite> entities across the network, counts unique and shared objects by resource, data model and interaction types.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.collect_resource_names" title="pypath.core.network.Network.collect_resource_names"><code class="xref py py-obj docutils literal notranslate"><span class="pre">collect_resource_names</span></code></a></p></td>
+<td><p>Builds a comprehensive collection of <cite>resource_names</cite> entities across the network, counts unique and shared objects by resource, data model and interaction types.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.collect_resource_names_via" title="pypath.core.network.Network.collect_resource_names_via"><code class="xref py py-obj docutils literal notranslate"><span class="pre">collect_resource_names_via</span></code></a></p></td>
+<td><p>Builds a comprehensive collection of <cite>resource_names_via</cite> entities across the network, counts unique and shared objects by resource, data model and interaction types.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.collect_resources" title="pypath.core.network.Network.collect_resources"><code class="xref py py-obj docutils literal notranslate"><span class="pre">collect_resources</span></code></a></p></td>
+<td><p>Builds a comprehensive collection of <cite>resources</cite> entities across the network, counts unique and shared objects by resource, data model and interaction types.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.collect_resources_via" title="pypath.core.network.Network.collect_resources_via"><code class="xref py py-obj docutils literal notranslate"><span class="pre">collect_resources_via</span></code></a></p></td>
+<td><p>Builds a comprehensive collection of <cite>resources_via</cite> entities across the network, counts unique and shared objects by resource, data model and interaction types.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.collect_small_molecule_identifiers" title="pypath.core.network.Network.collect_small_molecule_identifiers"><code class="xref py py-obj docutils literal notranslate"><span class="pre">collect_small_molecule_identifiers</span></code></a></p></td>
+<td><p>Builds a comprehensive collection of <cite>small_molecule_identifiers</cite> entities across the network, counts unique and shared objects by resource, data model and interaction types.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.collect_small_molecule_labels" title="pypath.core.network.Network.collect_small_molecule_labels"><code class="xref py py-obj docutils literal notranslate"><span class="pre">collect_small_molecule_labels</span></code></a></p></td>
+<td><p>Builds a comprehensive collection of <cite>small_molecule_labels</cite> entities across the network, counts unique and shared objects by resource, data model and interaction types.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.collect_small_molecules" title="pypath.core.network.Network.collect_small_molecules"><code class="xref py py-obj docutils literal notranslate"><span class="pre">collect_small_molecules</span></code></a></p></td>
+<td><p>Builds a comprehensive collection of <cite>small_molecules</cite> entities across the network, counts unique and shared objects by resource, data model and interaction types.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.complex_identifiers_by_data_model" title="pypath.core.network.Network.complex_identifiers_by_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">complex_identifiers_by_data_model</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.complex_identifiers_by_interaction_type" title="pypath.core.network.Network.complex_identifiers_by_interaction_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">complex_identifiers_by_interaction_type</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.complex_identifiers_by_interaction_type_and_data_model" title="pypath.core.network.Network.complex_identifiers_by_interaction_type_and_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">complex_identifiers_by_interaction_type_and_data_model</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.complex_identifiers_by_interaction_type_and_data_model_and_resource" title="pypath.core.network.Network.complex_identifiers_by_interaction_type_and_data_model_and_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">complex_identifiers_by_interaction_type_and_data_model_and_resource</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.complex_identifiers_by_reference" title="pypath.core.network.Network.complex_identifiers_by_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">complex_identifiers_by_reference</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.complex_identifiers_by_resource" title="pypath.core.network.Network.complex_identifiers_by_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">complex_identifiers_by_resource</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.complex_labels_by_data_model" title="pypath.core.network.Network.complex_labels_by_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">complex_labels_by_data_model</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.complex_labels_by_interaction_type" title="pypath.core.network.Network.complex_labels_by_interaction_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">complex_labels_by_interaction_type</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.complex_labels_by_interaction_type_and_data_model" title="pypath.core.network.Network.complex_labels_by_interaction_type_and_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">complex_labels_by_interaction_type_and_data_model</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.complex_labels_by_interaction_type_and_data_model_and_resource" title="pypath.core.network.Network.complex_labels_by_interaction_type_and_data_model_and_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">complex_labels_by_interaction_type_and_data_model_and_resource</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.complex_labels_by_reference" title="pypath.core.network.Network.complex_labels_by_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">complex_labels_by_reference</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.complex_labels_by_resource" title="pypath.core.network.Network.complex_labels_by_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">complex_labels_by_resource</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.complexes_by_data_model" title="pypath.core.network.Network.complexes_by_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">complexes_by_data_model</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.complexes_by_interaction_type" title="pypath.core.network.Network.complexes_by_interaction_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">complexes_by_interaction_type</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.complexes_by_interaction_type_and_data_model" title="pypath.core.network.Network.complexes_by_interaction_type_and_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">complexes_by_interaction_type_and_data_model</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.complexes_by_interaction_type_and_data_model_and_resource" title="pypath.core.network.Network.complexes_by_interaction_type_and_data_model_and_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">complexes_by_interaction_type_and_data_model_and_resource</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.complexes_by_reference" title="pypath.core.network.Network.complexes_by_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">complexes_by_reference</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.complexes_by_resource" title="pypath.core.network.Network.complexes_by_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">complexes_by_resource</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_activated_by" title="pypath.core.network.Network.count_activated_by"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_activated_by</span></code></a></p></td>
+<td><p>Returns the count of the interacting partners for one or more entities according to the specified criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_activates" title="pypath.core.network.Network.count_activates"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_activates</span></code></a></p></td>
+<td><p>Returns the count of the interacting partners for one or more entities according to the specified criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_complex_identifiers" title="pypath.core.network.Network.count_complex_identifiers"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_complex_identifiers</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_complex_identifiers_by_data_model" title="pypath.core.network.Network.count_complex_identifiers_by_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_complex_identifiers_by_data_model</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_complex_identifiers_by_interaction_type" title="pypath.core.network.Network.count_complex_identifiers_by_interaction_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_complex_identifiers_by_interaction_type</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_complex_identifiers_by_interaction_type_and_data_model" title="pypath.core.network.Network.count_complex_identifiers_by_interaction_type_and_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_complex_identifiers_by_interaction_type_and_data_model</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_complex_identifiers_by_interaction_type_and_data_model_and_resource" title="pypath.core.network.Network.count_complex_identifiers_by_interaction_type_and_data_model_and_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_complex_identifiers_by_interaction_type_and_data_model_and_resource</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_complex_identifiers_by_reference" title="pypath.core.network.Network.count_complex_identifiers_by_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_complex_identifiers_by_reference</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_complex_identifiers_by_resource" title="pypath.core.network.Network.count_complex_identifiers_by_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_complex_identifiers_by_resource</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_complex_labels" title="pypath.core.network.Network.count_complex_labels"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_complex_labels</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_complex_labels_by_data_model" title="pypath.core.network.Network.count_complex_labels_by_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_complex_labels_by_data_model</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_complex_labels_by_interaction_type" title="pypath.core.network.Network.count_complex_labels_by_interaction_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_complex_labels_by_interaction_type</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_complex_labels_by_interaction_type_and_data_model" title="pypath.core.network.Network.count_complex_labels_by_interaction_type_and_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_complex_labels_by_interaction_type_and_data_model</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_complex_labels_by_interaction_type_and_data_model_and_resource" title="pypath.core.network.Network.count_complex_labels_by_interaction_type_and_data_model_and_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_complex_labels_by_interaction_type_and_data_model_and_resource</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_complex_labels_by_reference" title="pypath.core.network.Network.count_complex_labels_by_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_complex_labels_by_reference</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_complex_labels_by_resource" title="pypath.core.network.Network.count_complex_labels_by_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_complex_labels_by_resource</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_complexes" title="pypath.core.network.Network.count_complexes"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_complexes</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_complexes_by_data_model" title="pypath.core.network.Network.count_complexes_by_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_complexes_by_data_model</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_complexes_by_interaction_type" title="pypath.core.network.Network.count_complexes_by_interaction_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_complexes_by_interaction_type</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_complexes_by_interaction_type_and_data_model" title="pypath.core.network.Network.count_complexes_by_interaction_type_and_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_complexes_by_interaction_type_and_data_model</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_complexes_by_interaction_type_and_data_model_and_resource" title="pypath.core.network.Network.count_complexes_by_interaction_type_and_data_model_and_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_complexes_by_interaction_type_and_data_model_and_resource</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_complexes_by_reference" title="pypath.core.network.Network.count_complexes_by_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_complexes_by_reference</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_complexes_by_resource" title="pypath.core.network.Network.count_complexes_by_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_complexes_by_resource</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_curation_effort" title="pypath.core.network.Network.count_curation_effort"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_curation_effort</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_curation_effort_by_data_model" title="pypath.core.network.Network.count_curation_effort_by_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_curation_effort_by_data_model</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_curation_effort_by_interaction_type" title="pypath.core.network.Network.count_curation_effort_by_interaction_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_curation_effort_by_interaction_type</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_curation_effort_by_interaction_type_and_data_model" title="pypath.core.network.Network.count_curation_effort_by_interaction_type_and_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_curation_effort_by_interaction_type_and_data_model</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_curation_effort_by_interaction_type_and_data_model_and_resource" title="pypath.core.network.Network.count_curation_effort_by_interaction_type_and_data_model_and_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_curation_effort_by_interaction_type_and_data_model_and_resource</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_curation_effort_by_reference" title="pypath.core.network.Network.count_curation_effort_by_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_curation_effort_by_reference</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_curation_effort_by_resource" title="pypath.core.network.Network.count_curation_effort_by_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_curation_effort_by_resource</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_data_models" title="pypath.core.network.Network.count_data_models"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_data_models</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_data_models_by_data_model" title="pypath.core.network.Network.count_data_models_by_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_data_models_by_data_model</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_data_models_by_interaction_type" title="pypath.core.network.Network.count_data_models_by_interaction_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_data_models_by_interaction_type</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_data_models_by_interaction_type_and_data_model" title="pypath.core.network.Network.count_data_models_by_interaction_type_and_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_data_models_by_interaction_type_and_data_model</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_data_models_by_interaction_type_and_data_model_and_resource" title="pypath.core.network.Network.count_data_models_by_interaction_type_and_data_model_and_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_data_models_by_interaction_type_and_data_model_and_resource</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_data_models_by_reference" title="pypath.core.network.Network.count_data_models_by_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_data_models_by_reference</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_data_models_by_resource" title="pypath.core.network.Network.count_data_models_by_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_data_models_by_resource</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_datasets" title="pypath.core.network.Network.count_datasets"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_datasets</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_datasets_by_data_model" title="pypath.core.network.Network.count_datasets_by_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_datasets_by_data_model</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_datasets_by_interaction_type" title="pypath.core.network.Network.count_datasets_by_interaction_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_datasets_by_interaction_type</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_datasets_by_interaction_type_and_data_model" title="pypath.core.network.Network.count_datasets_by_interaction_type_and_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_datasets_by_interaction_type_and_data_model</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_datasets_by_interaction_type_and_data_model_and_resource" title="pypath.core.network.Network.count_datasets_by_interaction_type_and_data_model_and_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_datasets_by_interaction_type_and_data_model_and_resource</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_datasets_by_reference" title="pypath.core.network.Network.count_datasets_by_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_datasets_by_reference</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_datasets_by_resource" title="pypath.core.network.Network.count_datasets_by_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_datasets_by_resource</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_degrees_directed" title="pypath.core.network.Network.count_degrees_directed"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_degrees_directed</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_degrees_directed_by_data_model" title="pypath.core.network.Network.count_degrees_directed_by_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_degrees_directed_by_data_model</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_degrees_directed_by_interaction_type" title="pypath.core.network.Network.count_degrees_directed_by_interaction_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_degrees_directed_by_interaction_type</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_degrees_directed_by_interaction_type_and_data_model" title="pypath.core.network.Network.count_degrees_directed_by_interaction_type_and_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_degrees_directed_by_interaction_type_and_data_model</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_degrees_directed_by_interaction_type_and_data_model_and_resource" title="pypath.core.network.Network.count_degrees_directed_by_interaction_type_and_data_model_and_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_degrees_directed_by_interaction_type_and_data_model_and_resource</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_degrees_directed_by_reference" title="pypath.core.network.Network.count_degrees_directed_by_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_degrees_directed_by_reference</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_degrees_directed_by_resource" title="pypath.core.network.Network.count_degrees_directed_by_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_degrees_directed_by_resource</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_degrees_directed_in" title="pypath.core.network.Network.count_degrees_directed_in"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_degrees_directed_in</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_degrees_directed_in_by_data_model" title="pypath.core.network.Network.count_degrees_directed_in_by_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_degrees_directed_in_by_data_model</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_degrees_directed_in_by_interaction_type" title="pypath.core.network.Network.count_degrees_directed_in_by_interaction_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_degrees_directed_in_by_interaction_type</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_degrees_directed_in_by_interaction_type_and_data_model" title="pypath.core.network.Network.count_degrees_directed_in_by_interaction_type_and_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_degrees_directed_in_by_interaction_type_and_data_model</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_degrees_directed_in_by_interaction_type_and_data_model_and_resource" title="pypath.core.network.Network.count_degrees_directed_in_by_interaction_type_and_data_model_and_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_degrees_directed_in_by_interaction_type_and_data_model_and_resource</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_degrees_directed_in_by_reference" title="pypath.core.network.Network.count_degrees_directed_in_by_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_degrees_directed_in_by_reference</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_degrees_directed_in_by_resource" title="pypath.core.network.Network.count_degrees_directed_in_by_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_degrees_directed_in_by_resource</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_degrees_directed_out" title="pypath.core.network.Network.count_degrees_directed_out"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_degrees_directed_out</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_degrees_directed_out_by_data_model" title="pypath.core.network.Network.count_degrees_directed_out_by_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_degrees_directed_out_by_data_model</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_degrees_directed_out_by_interaction_type" title="pypath.core.network.Network.count_degrees_directed_out_by_interaction_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_degrees_directed_out_by_interaction_type</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_degrees_directed_out_by_interaction_type_and_data_model" title="pypath.core.network.Network.count_degrees_directed_out_by_interaction_type_and_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_degrees_directed_out_by_interaction_type_and_data_model</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_degrees_directed_out_by_interaction_type_and_data_model_and_resource" title="pypath.core.network.Network.count_degrees_directed_out_by_interaction_type_and_data_model_and_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_degrees_directed_out_by_interaction_type_and_data_model_and_resource</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_degrees_directed_out_by_reference" title="pypath.core.network.Network.count_degrees_directed_out_by_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_degrees_directed_out_by_reference</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_degrees_directed_out_by_resource" title="pypath.core.network.Network.count_degrees_directed_out_by_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_degrees_directed_out_by_resource</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_degrees_negative" title="pypath.core.network.Network.count_degrees_negative"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_degrees_negative</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_degrees_negative_by_data_model" title="pypath.core.network.Network.count_degrees_negative_by_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_degrees_negative_by_data_model</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_degrees_negative_by_interaction_type" title="pypath.core.network.Network.count_degrees_negative_by_interaction_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_degrees_negative_by_interaction_type</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_degrees_negative_by_interaction_type_and_data_model" title="pypath.core.network.Network.count_degrees_negative_by_interaction_type_and_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_degrees_negative_by_interaction_type_and_data_model</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_degrees_negative_by_interaction_type_and_data_model_and_resource" title="pypath.core.network.Network.count_degrees_negative_by_interaction_type_and_data_model_and_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_degrees_negative_by_interaction_type_and_data_model_and_resource</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_degrees_negative_by_reference" title="pypath.core.network.Network.count_degrees_negative_by_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_degrees_negative_by_reference</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_degrees_negative_by_resource" title="pypath.core.network.Network.count_degrees_negative_by_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_degrees_negative_by_resource</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_degrees_negative_in" title="pypath.core.network.Network.count_degrees_negative_in"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_degrees_negative_in</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_degrees_negative_in_by_data_model" title="pypath.core.network.Network.count_degrees_negative_in_by_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_degrees_negative_in_by_data_model</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_degrees_negative_in_by_interaction_type" title="pypath.core.network.Network.count_degrees_negative_in_by_interaction_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_degrees_negative_in_by_interaction_type</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_degrees_negative_in_by_interaction_type_and_data_model" title="pypath.core.network.Network.count_degrees_negative_in_by_interaction_type_and_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_degrees_negative_in_by_interaction_type_and_data_model</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_degrees_negative_in_by_interaction_type_and_data_model_and_resource" title="pypath.core.network.Network.count_degrees_negative_in_by_interaction_type_and_data_model_and_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_degrees_negative_in_by_interaction_type_and_data_model_and_resource</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_degrees_negative_in_by_reference" title="pypath.core.network.Network.count_degrees_negative_in_by_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_degrees_negative_in_by_reference</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_degrees_negative_in_by_resource" title="pypath.core.network.Network.count_degrees_negative_in_by_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_degrees_negative_in_by_resource</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_degrees_negative_out" title="pypath.core.network.Network.count_degrees_negative_out"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_degrees_negative_out</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_degrees_negative_out_by_data_model" title="pypath.core.network.Network.count_degrees_negative_out_by_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_degrees_negative_out_by_data_model</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_degrees_negative_out_by_interaction_type" title="pypath.core.network.Network.count_degrees_negative_out_by_interaction_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_degrees_negative_out_by_interaction_type</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_degrees_negative_out_by_interaction_type_and_data_model" title="pypath.core.network.Network.count_degrees_negative_out_by_interaction_type_and_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_degrees_negative_out_by_interaction_type_and_data_model</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_degrees_negative_out_by_interaction_type_and_data_model_and_resource" title="pypath.core.network.Network.count_degrees_negative_out_by_interaction_type_and_data_model_and_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_degrees_negative_out_by_interaction_type_and_data_model_and_resource</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_degrees_negative_out_by_reference" title="pypath.core.network.Network.count_degrees_negative_out_by_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_degrees_negative_out_by_reference</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_degrees_negative_out_by_resource" title="pypath.core.network.Network.count_degrees_negative_out_by_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_degrees_negative_out_by_resource</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_degrees_non_directed" title="pypath.core.network.Network.count_degrees_non_directed"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_degrees_non_directed</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_degrees_non_directed_by_data_model" title="pypath.core.network.Network.count_degrees_non_directed_by_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_degrees_non_directed_by_data_model</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_degrees_non_directed_by_interaction_type" title="pypath.core.network.Network.count_degrees_non_directed_by_interaction_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_degrees_non_directed_by_interaction_type</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_degrees_non_directed_by_interaction_type_and_data_model" title="pypath.core.network.Network.count_degrees_non_directed_by_interaction_type_and_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_degrees_non_directed_by_interaction_type_and_data_model</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_degrees_non_directed_by_interaction_type_and_data_model_and_resource" title="pypath.core.network.Network.count_degrees_non_directed_by_interaction_type_and_data_model_and_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_degrees_non_directed_by_interaction_type_and_data_model_and_resource</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_degrees_non_directed_by_reference" title="pypath.core.network.Network.count_degrees_non_directed_by_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_degrees_non_directed_by_reference</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_degrees_non_directed_by_resource" title="pypath.core.network.Network.count_degrees_non_directed_by_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_degrees_non_directed_by_resource</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_degrees_positive" title="pypath.core.network.Network.count_degrees_positive"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_degrees_positive</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_degrees_positive_by_data_model" title="pypath.core.network.Network.count_degrees_positive_by_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_degrees_positive_by_data_model</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_degrees_positive_by_interaction_type" title="pypath.core.network.Network.count_degrees_positive_by_interaction_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_degrees_positive_by_interaction_type</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_degrees_positive_by_interaction_type_and_data_model" title="pypath.core.network.Network.count_degrees_positive_by_interaction_type_and_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_degrees_positive_by_interaction_type_and_data_model</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_degrees_positive_by_interaction_type_and_data_model_and_resource" title="pypath.core.network.Network.count_degrees_positive_by_interaction_type_and_data_model_and_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_degrees_positive_by_interaction_type_and_data_model_and_resource</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_degrees_positive_by_reference" title="pypath.core.network.Network.count_degrees_positive_by_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_degrees_positive_by_reference</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_degrees_positive_by_resource" title="pypath.core.network.Network.count_degrees_positive_by_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_degrees_positive_by_resource</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_degrees_positive_in" title="pypath.core.network.Network.count_degrees_positive_in"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_degrees_positive_in</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_degrees_positive_in_by_data_model" title="pypath.core.network.Network.count_degrees_positive_in_by_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_degrees_positive_in_by_data_model</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_degrees_positive_in_by_interaction_type" title="pypath.core.network.Network.count_degrees_positive_in_by_interaction_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_degrees_positive_in_by_interaction_type</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_degrees_positive_in_by_interaction_type_and_data_model" title="pypath.core.network.Network.count_degrees_positive_in_by_interaction_type_and_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_degrees_positive_in_by_interaction_type_and_data_model</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_degrees_positive_in_by_interaction_type_and_data_model_and_resource" title="pypath.core.network.Network.count_degrees_positive_in_by_interaction_type_and_data_model_and_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_degrees_positive_in_by_interaction_type_and_data_model_and_resource</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_degrees_positive_in_by_reference" title="pypath.core.network.Network.count_degrees_positive_in_by_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_degrees_positive_in_by_reference</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_degrees_positive_in_by_resource" title="pypath.core.network.Network.count_degrees_positive_in_by_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_degrees_positive_in_by_resource</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_degrees_positive_out" title="pypath.core.network.Network.count_degrees_positive_out"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_degrees_positive_out</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_degrees_positive_out_by_data_model" title="pypath.core.network.Network.count_degrees_positive_out_by_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_degrees_positive_out_by_data_model</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_degrees_positive_out_by_interaction_type" title="pypath.core.network.Network.count_degrees_positive_out_by_interaction_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_degrees_positive_out_by_interaction_type</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_degrees_positive_out_by_interaction_type_and_data_model" title="pypath.core.network.Network.count_degrees_positive_out_by_interaction_type_and_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_degrees_positive_out_by_interaction_type_and_data_model</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_degrees_positive_out_by_interaction_type_and_data_model_and_resource" title="pypath.core.network.Network.count_degrees_positive_out_by_interaction_type_and_data_model_and_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_degrees_positive_out_by_interaction_type_and_data_model_and_resource</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_degrees_positive_out_by_reference" title="pypath.core.network.Network.count_degrees_positive_out_by_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_degrees_positive_out_by_reference</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_degrees_positive_out_by_resource" title="pypath.core.network.Network.count_degrees_positive_out_by_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_degrees_positive_out_by_resource</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_degrees_signed" title="pypath.core.network.Network.count_degrees_signed"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_degrees_signed</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_degrees_signed_by_data_model" title="pypath.core.network.Network.count_degrees_signed_by_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_degrees_signed_by_data_model</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_degrees_signed_by_interaction_type" title="pypath.core.network.Network.count_degrees_signed_by_interaction_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_degrees_signed_by_interaction_type</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_degrees_signed_by_interaction_type_and_data_model" title="pypath.core.network.Network.count_degrees_signed_by_interaction_type_and_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_degrees_signed_by_interaction_type_and_data_model</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_degrees_signed_by_interaction_type_and_data_model_and_resource" title="pypath.core.network.Network.count_degrees_signed_by_interaction_type_and_data_model_and_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_degrees_signed_by_interaction_type_and_data_model_and_resource</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_degrees_signed_by_reference" title="pypath.core.network.Network.count_degrees_signed_by_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_degrees_signed_by_reference</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_degrees_signed_by_resource" title="pypath.core.network.Network.count_degrees_signed_by_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_degrees_signed_by_resource</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_degrees_signed_in" title="pypath.core.network.Network.count_degrees_signed_in"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_degrees_signed_in</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_degrees_signed_in_by_data_model" title="pypath.core.network.Network.count_degrees_signed_in_by_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_degrees_signed_in_by_data_model</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_degrees_signed_in_by_interaction_type" title="pypath.core.network.Network.count_degrees_signed_in_by_interaction_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_degrees_signed_in_by_interaction_type</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_degrees_signed_in_by_interaction_type_and_data_model" title="pypath.core.network.Network.count_degrees_signed_in_by_interaction_type_and_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_degrees_signed_in_by_interaction_type_and_data_model</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_degrees_signed_in_by_interaction_type_and_data_model_and_resource" title="pypath.core.network.Network.count_degrees_signed_in_by_interaction_type_and_data_model_and_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_degrees_signed_in_by_interaction_type_and_data_model_and_resource</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_degrees_signed_in_by_reference" title="pypath.core.network.Network.count_degrees_signed_in_by_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_degrees_signed_in_by_reference</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_degrees_signed_in_by_resource" title="pypath.core.network.Network.count_degrees_signed_in_by_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_degrees_signed_in_by_resource</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_degrees_signed_out" title="pypath.core.network.Network.count_degrees_signed_out"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_degrees_signed_out</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_degrees_signed_out_by_data_model" title="pypath.core.network.Network.count_degrees_signed_out_by_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_degrees_signed_out_by_data_model</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_degrees_signed_out_by_interaction_type" title="pypath.core.network.Network.count_degrees_signed_out_by_interaction_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_degrees_signed_out_by_interaction_type</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_degrees_signed_out_by_interaction_type_and_data_model" title="pypath.core.network.Network.count_degrees_signed_out_by_interaction_type_and_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_degrees_signed_out_by_interaction_type_and_data_model</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_degrees_signed_out_by_interaction_type_and_data_model_and_resource" title="pypath.core.network.Network.count_degrees_signed_out_by_interaction_type_and_data_model_and_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_degrees_signed_out_by_interaction_type_and_data_model_and_resource</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_degrees_signed_out_by_reference" title="pypath.core.network.Network.count_degrees_signed_out_by_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_degrees_signed_out_by_reference</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_degrees_signed_out_by_resource" title="pypath.core.network.Network.count_degrees_signed_out_by_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_degrees_signed_out_by_resource</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_degrees_undirected" title="pypath.core.network.Network.count_degrees_undirected"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_degrees_undirected</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_degrees_undirected_by_data_model" title="pypath.core.network.Network.count_degrees_undirected_by_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_degrees_undirected_by_data_model</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_degrees_undirected_by_interaction_type" title="pypath.core.network.Network.count_degrees_undirected_by_interaction_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_degrees_undirected_by_interaction_type</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_degrees_undirected_by_interaction_type_and_data_model" title="pypath.core.network.Network.count_degrees_undirected_by_interaction_type_and_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_degrees_undirected_by_interaction_type_and_data_model</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_degrees_undirected_by_interaction_type_and_data_model_and_resource" title="pypath.core.network.Network.count_degrees_undirected_by_interaction_type_and_data_model_and_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_degrees_undirected_by_interaction_type_and_data_model_and_resource</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_degrees_undirected_by_reference" title="pypath.core.network.Network.count_degrees_undirected_by_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_degrees_undirected_by_reference</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_degrees_undirected_by_resource" title="pypath.core.network.Network.count_degrees_undirected_by_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_degrees_undirected_by_resource</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_entities" title="pypath.core.network.Network.count_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_entities</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_entities_by_data_model" title="pypath.core.network.Network.count_entities_by_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_entities_by_data_model</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_entities_by_interaction_type" title="pypath.core.network.Network.count_entities_by_interaction_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_entities_by_interaction_type</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_entities_by_interaction_type_and_data_model" title="pypath.core.network.Network.count_entities_by_interaction_type_and_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_entities_by_interaction_type_and_data_model</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_entities_by_interaction_type_and_data_model_and_resource" title="pypath.core.network.Network.count_entities_by_interaction_type_and_data_model_and_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_entities_by_interaction_type_and_data_model_and_resource</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_entities_by_reference" title="pypath.core.network.Network.count_entities_by_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_entities_by_reference</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_entities_by_resource" title="pypath.core.network.Network.count_entities_by_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_entities_by_resource</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_evidences" title="pypath.core.network.Network.count_evidences"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_evidences</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_evidences_by_data_model" title="pypath.core.network.Network.count_evidences_by_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_evidences_by_data_model</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_evidences_by_interaction_type" title="pypath.core.network.Network.count_evidences_by_interaction_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_evidences_by_interaction_type</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_evidences_by_interaction_type_and_data_model" title="pypath.core.network.Network.count_evidences_by_interaction_type_and_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_evidences_by_interaction_type_and_data_model</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_evidences_by_interaction_type_and_data_model_and_resource" title="pypath.core.network.Network.count_evidences_by_interaction_type_and_data_model_and_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_evidences_by_interaction_type_and_data_model_and_resource</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_evidences_by_reference" title="pypath.core.network.Network.count_evidences_by_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_evidences_by_reference</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_evidences_by_resource" title="pypath.core.network.Network.count_evidences_by_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_evidences_by_resource</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_identifiers" title="pypath.core.network.Network.count_identifiers"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_identifiers</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_identifiers_by_data_model" title="pypath.core.network.Network.count_identifiers_by_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_identifiers_by_data_model</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_identifiers_by_interaction_type" title="pypath.core.network.Network.count_identifiers_by_interaction_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_identifiers_by_interaction_type</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_identifiers_by_interaction_type_and_data_model" title="pypath.core.network.Network.count_identifiers_by_interaction_type_and_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_identifiers_by_interaction_type_and_data_model</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_identifiers_by_interaction_type_and_data_model_and_resource" title="pypath.core.network.Network.count_identifiers_by_interaction_type_and_data_model_and_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_identifiers_by_interaction_type_and_data_model_and_resource</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_identifiers_by_reference" title="pypath.core.network.Network.count_identifiers_by_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_identifiers_by_reference</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_identifiers_by_resource" title="pypath.core.network.Network.count_identifiers_by_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_identifiers_by_resource</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_interaction_types" title="pypath.core.network.Network.count_interaction_types"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_interaction_types</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_interaction_types_by_data_model" title="pypath.core.network.Network.count_interaction_types_by_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_interaction_types_by_data_model</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_interaction_types_by_interaction_type" title="pypath.core.network.Network.count_interaction_types_by_interaction_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_interaction_types_by_interaction_type</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_interaction_types_by_interaction_type_and_data_model" title="pypath.core.network.Network.count_interaction_types_by_interaction_type_and_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_interaction_types_by_interaction_type_and_data_model</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_interaction_types_by_interaction_type_and_data_model_and_resource" title="pypath.core.network.Network.count_interaction_types_by_interaction_type_and_data_model_and_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_interaction_types_by_interaction_type_and_data_model_and_resource</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_interaction_types_by_reference" title="pypath.core.network.Network.count_interaction_types_by_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_interaction_types_by_reference</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_interaction_types_by_resource" title="pypath.core.network.Network.count_interaction_types_by_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_interaction_types_by_resource</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_interactions" title="pypath.core.network.Network.count_interactions"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_interactions</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_interactions_0" title="pypath.core.network.Network.count_interactions_0"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_interactions_0</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_interactions_0_by_data_model" title="pypath.core.network.Network.count_interactions_0_by_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_interactions_0_by_data_model</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_interactions_0_by_interaction_type" title="pypath.core.network.Network.count_interactions_0_by_interaction_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_interactions_0_by_interaction_type</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_interactions_0_by_interaction_type_and_data_model" title="pypath.core.network.Network.count_interactions_0_by_interaction_type_and_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_interactions_0_by_interaction_type_and_data_model</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_interactions_0_by_interaction_type_and_data_model_and_resource" title="pypath.core.network.Network.count_interactions_0_by_interaction_type_and_data_model_and_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_interactions_0_by_interaction_type_and_data_model_and_resource</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_interactions_0_by_reference" title="pypath.core.network.Network.count_interactions_0_by_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_interactions_0_by_reference</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_interactions_0_by_resource" title="pypath.core.network.Network.count_interactions_0_by_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_interactions_0_by_resource</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_interactions_by_data_model" title="pypath.core.network.Network.count_interactions_by_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_interactions_by_data_model</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_interactions_by_interaction_type" title="pypath.core.network.Network.count_interactions_by_interaction_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_interactions_by_interaction_type</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_interactions_by_interaction_type_and_data_model" title="pypath.core.network.Network.count_interactions_by_interaction_type_and_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_interactions_by_interaction_type_and_data_model</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_interactions_by_interaction_type_and_data_model_and_resource" title="pypath.core.network.Network.count_interactions_by_interaction_type_and_data_model_and_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_interactions_by_interaction_type_and_data_model_and_resource</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_interactions_by_reference" title="pypath.core.network.Network.count_interactions_by_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_interactions_by_reference</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_interactions_by_resource" title="pypath.core.network.Network.count_interactions_by_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_interactions_by_resource</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_interactions_directed" title="pypath.core.network.Network.count_interactions_directed"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_interactions_directed</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_interactions_directed_by_data_model" title="pypath.core.network.Network.count_interactions_directed_by_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_interactions_directed_by_data_model</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_interactions_directed_by_interaction_type" title="pypath.core.network.Network.count_interactions_directed_by_interaction_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_interactions_directed_by_interaction_type</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_interactions_directed_by_interaction_type_and_data_model" title="pypath.core.network.Network.count_interactions_directed_by_interaction_type_and_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_interactions_directed_by_interaction_type_and_data_model</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_interactions_directed_by_interaction_type_and_data_model_and_resource" title="pypath.core.network.Network.count_interactions_directed_by_interaction_type_and_data_model_and_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_interactions_directed_by_interaction_type_and_data_model_and_resource</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_interactions_directed_by_reference" title="pypath.core.network.Network.count_interactions_directed_by_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_interactions_directed_by_reference</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_interactions_directed_by_resource" title="pypath.core.network.Network.count_interactions_directed_by_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_interactions_directed_by_resource</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_interactions_mutual" title="pypath.core.network.Network.count_interactions_mutual"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_interactions_mutual</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_interactions_mutual_by_data_model" title="pypath.core.network.Network.count_interactions_mutual_by_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_interactions_mutual_by_data_model</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_interactions_mutual_by_interaction_type" title="pypath.core.network.Network.count_interactions_mutual_by_interaction_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_interactions_mutual_by_interaction_type</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_interactions_mutual_by_interaction_type_and_data_model" title="pypath.core.network.Network.count_interactions_mutual_by_interaction_type_and_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_interactions_mutual_by_interaction_type_and_data_model</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_interactions_mutual_by_interaction_type_and_data_model_and_resource" title="pypath.core.network.Network.count_interactions_mutual_by_interaction_type_and_data_model_and_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_interactions_mutual_by_interaction_type_and_data_model_and_resource</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_interactions_mutual_by_reference" title="pypath.core.network.Network.count_interactions_mutual_by_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_interactions_mutual_by_reference</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_interactions_mutual_by_resource" title="pypath.core.network.Network.count_interactions_mutual_by_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_interactions_mutual_by_resource</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_interactions_negative" title="pypath.core.network.Network.count_interactions_negative"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_interactions_negative</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_interactions_negative_by_data_model" title="pypath.core.network.Network.count_interactions_negative_by_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_interactions_negative_by_data_model</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_interactions_negative_by_interaction_type" title="pypath.core.network.Network.count_interactions_negative_by_interaction_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_interactions_negative_by_interaction_type</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_interactions_negative_by_interaction_type_and_data_model" title="pypath.core.network.Network.count_interactions_negative_by_interaction_type_and_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_interactions_negative_by_interaction_type_and_data_model</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_interactions_negative_by_interaction_type_and_data_model_and_resource" title="pypath.core.network.Network.count_interactions_negative_by_interaction_type_and_data_model_and_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_interactions_negative_by_interaction_type_and_data_model_and_resource</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_interactions_negative_by_reference" title="pypath.core.network.Network.count_interactions_negative_by_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_interactions_negative_by_reference</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_interactions_negative_by_resource" title="pypath.core.network.Network.count_interactions_negative_by_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_interactions_negative_by_resource</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_interactions_non_directed" title="pypath.core.network.Network.count_interactions_non_directed"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_interactions_non_directed</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_interactions_non_directed_0" title="pypath.core.network.Network.count_interactions_non_directed_0"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_interactions_non_directed_0</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_interactions_non_directed_0_by_data_model" title="pypath.core.network.Network.count_interactions_non_directed_0_by_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_interactions_non_directed_0_by_data_model</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_interactions_non_directed_0_by_interaction_type" title="pypath.core.network.Network.count_interactions_non_directed_0_by_interaction_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_interactions_non_directed_0_by_interaction_type</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_interactions_non_directed_0_by_interaction_type_and_data_model" title="pypath.core.network.Network.count_interactions_non_directed_0_by_interaction_type_and_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_interactions_non_directed_0_by_interaction_type_and_data_model</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_interactions_non_directed_0_by_interaction_type_and_data_model_and_resource" title="pypath.core.network.Network.count_interactions_non_directed_0_by_interaction_type_and_data_model_and_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_interactions_non_directed_0_by_interaction_type_and_data_model_and_resource</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_interactions_non_directed_0_by_reference" title="pypath.core.network.Network.count_interactions_non_directed_0_by_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_interactions_non_directed_0_by_reference</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_interactions_non_directed_0_by_resource" title="pypath.core.network.Network.count_interactions_non_directed_0_by_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_interactions_non_directed_0_by_resource</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_interactions_non_directed_by_data_model" title="pypath.core.network.Network.count_interactions_non_directed_by_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_interactions_non_directed_by_data_model</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_interactions_non_directed_by_interaction_type" title="pypath.core.network.Network.count_interactions_non_directed_by_interaction_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_interactions_non_directed_by_interaction_type</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_interactions_non_directed_by_interaction_type_and_data_model" title="pypath.core.network.Network.count_interactions_non_directed_by_interaction_type_and_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_interactions_non_directed_by_interaction_type_and_data_model</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_interactions_non_directed_by_interaction_type_and_data_model_and_resource" title="pypath.core.network.Network.count_interactions_non_directed_by_interaction_type_and_data_model_and_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_interactions_non_directed_by_interaction_type_and_data_model_and_resource</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_interactions_non_directed_by_reference" title="pypath.core.network.Network.count_interactions_non_directed_by_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_interactions_non_directed_by_reference</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_interactions_non_directed_by_resource" title="pypath.core.network.Network.count_interactions_non_directed_by_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_interactions_non_directed_by_resource</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_interactions_positive" title="pypath.core.network.Network.count_interactions_positive"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_interactions_positive</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_interactions_positive_by_data_model" title="pypath.core.network.Network.count_interactions_positive_by_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_interactions_positive_by_data_model</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_interactions_positive_by_interaction_type" title="pypath.core.network.Network.count_interactions_positive_by_interaction_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_interactions_positive_by_interaction_type</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_interactions_positive_by_interaction_type_and_data_model" title="pypath.core.network.Network.count_interactions_positive_by_interaction_type_and_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_interactions_positive_by_interaction_type_and_data_model</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_interactions_positive_by_interaction_type_and_data_model_and_resource" title="pypath.core.network.Network.count_interactions_positive_by_interaction_type_and_data_model_and_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_interactions_positive_by_interaction_type_and_data_model_and_resource</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_interactions_positive_by_reference" title="pypath.core.network.Network.count_interactions_positive_by_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_interactions_positive_by_reference</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_interactions_positive_by_resource" title="pypath.core.network.Network.count_interactions_positive_by_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_interactions_positive_by_resource</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_interactions_signed" title="pypath.core.network.Network.count_interactions_signed"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_interactions_signed</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_interactions_signed_by_data_model" title="pypath.core.network.Network.count_interactions_signed_by_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_interactions_signed_by_data_model</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_interactions_signed_by_interaction_type" title="pypath.core.network.Network.count_interactions_signed_by_interaction_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_interactions_signed_by_interaction_type</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_interactions_signed_by_interaction_type_and_data_model" title="pypath.core.network.Network.count_interactions_signed_by_interaction_type_and_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_interactions_signed_by_interaction_type_and_data_model</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_interactions_signed_by_interaction_type_and_data_model_and_resource" title="pypath.core.network.Network.count_interactions_signed_by_interaction_type_and_data_model_and_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_interactions_signed_by_interaction_type_and_data_model_and_resource</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_interactions_signed_by_reference" title="pypath.core.network.Network.count_interactions_signed_by_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_interactions_signed_by_reference</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_interactions_signed_by_resource" title="pypath.core.network.Network.count_interactions_signed_by_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_interactions_signed_by_resource</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_interactions_undirected" title="pypath.core.network.Network.count_interactions_undirected"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_interactions_undirected</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_interactions_undirected_0" title="pypath.core.network.Network.count_interactions_undirected_0"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_interactions_undirected_0</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_interactions_undirected_0_by_data_model" title="pypath.core.network.Network.count_interactions_undirected_0_by_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_interactions_undirected_0_by_data_model</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_interactions_undirected_0_by_interaction_type" title="pypath.core.network.Network.count_interactions_undirected_0_by_interaction_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_interactions_undirected_0_by_interaction_type</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_interactions_undirected_0_by_interaction_type_and_data_model" title="pypath.core.network.Network.count_interactions_undirected_0_by_interaction_type_and_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_interactions_undirected_0_by_interaction_type_and_data_model</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_interactions_undirected_0_by_interaction_type_and_data_model_and_resource" title="pypath.core.network.Network.count_interactions_undirected_0_by_interaction_type_and_data_model_and_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_interactions_undirected_0_by_interaction_type_and_data_model_and_resource</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_interactions_undirected_0_by_reference" title="pypath.core.network.Network.count_interactions_undirected_0_by_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_interactions_undirected_0_by_reference</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_interactions_undirected_0_by_resource" title="pypath.core.network.Network.count_interactions_undirected_0_by_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_interactions_undirected_0_by_resource</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_interactions_undirected_by_data_model" title="pypath.core.network.Network.count_interactions_undirected_by_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_interactions_undirected_by_data_model</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_interactions_undirected_by_interaction_type" title="pypath.core.network.Network.count_interactions_undirected_by_interaction_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_interactions_undirected_by_interaction_type</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_interactions_undirected_by_interaction_type_and_data_model" title="pypath.core.network.Network.count_interactions_undirected_by_interaction_type_and_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_interactions_undirected_by_interaction_type_and_data_model</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_interactions_undirected_by_interaction_type_and_data_model_and_resource" title="pypath.core.network.Network.count_interactions_undirected_by_interaction_type_and_data_model_and_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_interactions_undirected_by_interaction_type_and_data_model_and_resource</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_interactions_undirected_by_reference" title="pypath.core.network.Network.count_interactions_undirected_by_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_interactions_undirected_by_reference</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_interactions_undirected_by_resource" title="pypath.core.network.Network.count_interactions_undirected_by_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_interactions_undirected_by_resource</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_labels" title="pypath.core.network.Network.count_labels"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_labels</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_labels_by_data_model" title="pypath.core.network.Network.count_labels_by_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_labels_by_data_model</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_labels_by_interaction_type" title="pypath.core.network.Network.count_labels_by_interaction_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_labels_by_interaction_type</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_labels_by_interaction_type_and_data_model" title="pypath.core.network.Network.count_labels_by_interaction_type_and_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_labels_by_interaction_type_and_data_model</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_labels_by_interaction_type_and_data_model_and_resource" title="pypath.core.network.Network.count_labels_by_interaction_type_and_data_model_and_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_labels_by_interaction_type_and_data_model_and_resource</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_labels_by_reference" title="pypath.core.network.Network.count_labels_by_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_labels_by_reference</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_labels_by_resource" title="pypath.core.network.Network.count_labels_by_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_labels_by_resource</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_lncrna_identifiers" title="pypath.core.network.Network.count_lncrna_identifiers"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_lncrna_identifiers</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_lncrna_identifiers_by_data_model" title="pypath.core.network.Network.count_lncrna_identifiers_by_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_lncrna_identifiers_by_data_model</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_lncrna_identifiers_by_interaction_type" title="pypath.core.network.Network.count_lncrna_identifiers_by_interaction_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_lncrna_identifiers_by_interaction_type</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_lncrna_identifiers_by_interaction_type_and_data_model" title="pypath.core.network.Network.count_lncrna_identifiers_by_interaction_type_and_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_lncrna_identifiers_by_interaction_type_and_data_model</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_lncrna_identifiers_by_interaction_type_and_data_model_and_resource" title="pypath.core.network.Network.count_lncrna_identifiers_by_interaction_type_and_data_model_and_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_lncrna_identifiers_by_interaction_type_and_data_model_and_resource</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_lncrna_identifiers_by_reference" title="pypath.core.network.Network.count_lncrna_identifiers_by_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_lncrna_identifiers_by_reference</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_lncrna_identifiers_by_resource" title="pypath.core.network.Network.count_lncrna_identifiers_by_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_lncrna_identifiers_by_resource</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_lncrna_labels" title="pypath.core.network.Network.count_lncrna_labels"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_lncrna_labels</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_lncrna_labels_by_data_model" title="pypath.core.network.Network.count_lncrna_labels_by_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_lncrna_labels_by_data_model</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_lncrna_labels_by_interaction_type" title="pypath.core.network.Network.count_lncrna_labels_by_interaction_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_lncrna_labels_by_interaction_type</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_lncrna_labels_by_interaction_type_and_data_model" title="pypath.core.network.Network.count_lncrna_labels_by_interaction_type_and_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_lncrna_labels_by_interaction_type_and_data_model</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_lncrna_labels_by_interaction_type_and_data_model_and_resource" title="pypath.core.network.Network.count_lncrna_labels_by_interaction_type_and_data_model_and_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_lncrna_labels_by_interaction_type_and_data_model_and_resource</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_lncrna_labels_by_reference" title="pypath.core.network.Network.count_lncrna_labels_by_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_lncrna_labels_by_reference</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_lncrna_labels_by_resource" title="pypath.core.network.Network.count_lncrna_labels_by_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_lncrna_labels_by_resource</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_lncrnas" title="pypath.core.network.Network.count_lncrnas"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_lncrnas</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_lncrnas_by_data_model" title="pypath.core.network.Network.count_lncrnas_by_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_lncrnas_by_data_model</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_lncrnas_by_interaction_type" title="pypath.core.network.Network.count_lncrnas_by_interaction_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_lncrnas_by_interaction_type</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_lncrnas_by_interaction_type_and_data_model" title="pypath.core.network.Network.count_lncrnas_by_interaction_type_and_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_lncrnas_by_interaction_type_and_data_model</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_lncrnas_by_interaction_type_and_data_model_and_resource" title="pypath.core.network.Network.count_lncrnas_by_interaction_type_and_data_model_and_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_lncrnas_by_interaction_type_and_data_model_and_resource</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_lncrnas_by_reference" title="pypath.core.network.Network.count_lncrnas_by_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_lncrnas_by_reference</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_lncrnas_by_resource" title="pypath.core.network.Network.count_lncrnas_by_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_lncrnas_by_resource</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_mirna_identifiers" title="pypath.core.network.Network.count_mirna_identifiers"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_mirna_identifiers</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_mirna_identifiers_by_data_model" title="pypath.core.network.Network.count_mirna_identifiers_by_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_mirna_identifiers_by_data_model</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_mirna_identifiers_by_interaction_type" title="pypath.core.network.Network.count_mirna_identifiers_by_interaction_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_mirna_identifiers_by_interaction_type</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_mirna_identifiers_by_interaction_type_and_data_model" title="pypath.core.network.Network.count_mirna_identifiers_by_interaction_type_and_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_mirna_identifiers_by_interaction_type_and_data_model</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_mirna_identifiers_by_interaction_type_and_data_model_and_resource" title="pypath.core.network.Network.count_mirna_identifiers_by_interaction_type_and_data_model_and_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_mirna_identifiers_by_interaction_type_and_data_model_and_resource</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_mirna_identifiers_by_reference" title="pypath.core.network.Network.count_mirna_identifiers_by_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_mirna_identifiers_by_reference</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_mirna_identifiers_by_resource" title="pypath.core.network.Network.count_mirna_identifiers_by_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_mirna_identifiers_by_resource</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_mirna_labels" title="pypath.core.network.Network.count_mirna_labels"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_mirna_labels</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_mirna_labels_by_data_model" title="pypath.core.network.Network.count_mirna_labels_by_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_mirna_labels_by_data_model</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_mirna_labels_by_interaction_type" title="pypath.core.network.Network.count_mirna_labels_by_interaction_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_mirna_labels_by_interaction_type</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_mirna_labels_by_interaction_type_and_data_model" title="pypath.core.network.Network.count_mirna_labels_by_interaction_type_and_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_mirna_labels_by_interaction_type_and_data_model</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_mirna_labels_by_interaction_type_and_data_model_and_resource" title="pypath.core.network.Network.count_mirna_labels_by_interaction_type_and_data_model_and_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_mirna_labels_by_interaction_type_and_data_model_and_resource</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_mirna_labels_by_reference" title="pypath.core.network.Network.count_mirna_labels_by_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_mirna_labels_by_reference</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_mirna_labels_by_resource" title="pypath.core.network.Network.count_mirna_labels_by_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_mirna_labels_by_resource</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_mirnas" title="pypath.core.network.Network.count_mirnas"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_mirnas</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_mirnas_by_data_model" title="pypath.core.network.Network.count_mirnas_by_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_mirnas_by_data_model</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_mirnas_by_interaction_type" title="pypath.core.network.Network.count_mirnas_by_interaction_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_mirnas_by_interaction_type</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_mirnas_by_interaction_type_and_data_model" title="pypath.core.network.Network.count_mirnas_by_interaction_type_and_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_mirnas_by_interaction_type_and_data_model</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_mirnas_by_interaction_type_and_data_model_and_resource" title="pypath.core.network.Network.count_mirnas_by_interaction_type_and_data_model_and_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_mirnas_by_interaction_type_and_data_model_and_resource</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_mirnas_by_reference" title="pypath.core.network.Network.count_mirnas_by_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_mirnas_by_reference</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_mirnas_by_resource" title="pypath.core.network.Network.count_mirnas_by_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_mirnas_by_resource</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_post_transcriptionally_activated_by" title="pypath.core.network.Network.count_post_transcriptionally_activated_by"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_post_transcriptionally_activated_by</span></code></a></p></td>
+<td><p>Returns the count of the interacting partners for one or more entities according to the specified criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_post_transcriptionally_activates" title="pypath.core.network.Network.count_post_transcriptionally_activates"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_post_transcriptionally_activates</span></code></a></p></td>
+<td><p>Returns the count of the interacting partners for one or more entities according to the specified criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_post_transcriptionally_regulated_by" title="pypath.core.network.Network.count_post_transcriptionally_regulated_by"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_post_transcriptionally_regulated_by</span></code></a></p></td>
+<td><p>Returns the count of the interacting partners for one or more entities according to the specified criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_post_transcriptionally_regulates" title="pypath.core.network.Network.count_post_transcriptionally_regulates"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_post_transcriptionally_regulates</span></code></a></p></td>
+<td><p>Returns the count of the interacting partners for one or more entities according to the specified criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_post_transcriptionally_suppressed_by" title="pypath.core.network.Network.count_post_transcriptionally_suppressed_by"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_post_transcriptionally_suppressed_by</span></code></a></p></td>
+<td><p>Returns the count of the interacting partners for one or more entities according to the specified criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_post_transcriptionally_suppresses" title="pypath.core.network.Network.count_post_transcriptionally_suppresses"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_post_transcriptionally_suppresses</span></code></a></p></td>
+<td><p>Returns the count of the interacting partners for one or more entities according to the specified criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_post_translationally_activated_by" title="pypath.core.network.Network.count_post_translationally_activated_by"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_post_translationally_activated_by</span></code></a></p></td>
+<td><p>Returns the count of the interacting partners for one or more entities according to the specified criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_post_translationally_activates" title="pypath.core.network.Network.count_post_translationally_activates"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_post_translationally_activates</span></code></a></p></td>
+<td><p>Returns the count of the interacting partners for one or more entities according to the specified criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_post_translationally_regulated_by" title="pypath.core.network.Network.count_post_translationally_regulated_by"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_post_translationally_regulated_by</span></code></a></p></td>
+<td><p>Returns the count of the interacting partners for one or more entities according to the specified criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_post_translationally_regulates" title="pypath.core.network.Network.count_post_translationally_regulates"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_post_translationally_regulates</span></code></a></p></td>
+<td><p>Returns the count of the interacting partners for one or more entities according to the specified criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_post_translationally_suppressed_by" title="pypath.core.network.Network.count_post_translationally_suppressed_by"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_post_translationally_suppressed_by</span></code></a></p></td>
+<td><p>Returns the count of the interacting partners for one or more entities according to the specified criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_post_translationally_suppresses" title="pypath.core.network.Network.count_post_translationally_suppresses"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_post_translationally_suppresses</span></code></a></p></td>
+<td><p>Returns the count of the interacting partners for one or more entities according to the specified criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_protein_identifiers" title="pypath.core.network.Network.count_protein_identifiers"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_protein_identifiers</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_protein_identifiers_by_data_model" title="pypath.core.network.Network.count_protein_identifiers_by_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_protein_identifiers_by_data_model</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_protein_identifiers_by_interaction_type" title="pypath.core.network.Network.count_protein_identifiers_by_interaction_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_protein_identifiers_by_interaction_type</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_protein_identifiers_by_interaction_type_and_data_model" title="pypath.core.network.Network.count_protein_identifiers_by_interaction_type_and_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_protein_identifiers_by_interaction_type_and_data_model</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_protein_identifiers_by_interaction_type_and_data_model_and_resource" title="pypath.core.network.Network.count_protein_identifiers_by_interaction_type_and_data_model_and_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_protein_identifiers_by_interaction_type_and_data_model_and_resource</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_protein_identifiers_by_reference" title="pypath.core.network.Network.count_protein_identifiers_by_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_protein_identifiers_by_reference</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_protein_identifiers_by_resource" title="pypath.core.network.Network.count_protein_identifiers_by_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_protein_identifiers_by_resource</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_protein_labels" title="pypath.core.network.Network.count_protein_labels"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_protein_labels</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_protein_labels_by_data_model" title="pypath.core.network.Network.count_protein_labels_by_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_protein_labels_by_data_model</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_protein_labels_by_interaction_type" title="pypath.core.network.Network.count_protein_labels_by_interaction_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_protein_labels_by_interaction_type</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_protein_labels_by_interaction_type_and_data_model" title="pypath.core.network.Network.count_protein_labels_by_interaction_type_and_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_protein_labels_by_interaction_type_and_data_model</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_protein_labels_by_interaction_type_and_data_model_and_resource" title="pypath.core.network.Network.count_protein_labels_by_interaction_type_and_data_model_and_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_protein_labels_by_interaction_type_and_data_model_and_resource</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_protein_labels_by_reference" title="pypath.core.network.Network.count_protein_labels_by_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_protein_labels_by_reference</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_protein_labels_by_resource" title="pypath.core.network.Network.count_protein_labels_by_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_protein_labels_by_resource</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_proteins" title="pypath.core.network.Network.count_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_proteins</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_proteins_by_data_model" title="pypath.core.network.Network.count_proteins_by_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_proteins_by_data_model</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_proteins_by_interaction_type" title="pypath.core.network.Network.count_proteins_by_interaction_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_proteins_by_interaction_type</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_proteins_by_interaction_type_and_data_model" title="pypath.core.network.Network.count_proteins_by_interaction_type_and_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_proteins_by_interaction_type_and_data_model</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_proteins_by_interaction_type_and_data_model_and_resource" title="pypath.core.network.Network.count_proteins_by_interaction_type_and_data_model_and_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_proteins_by_interaction_type_and_data_model_and_resource</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_proteins_by_reference" title="pypath.core.network.Network.count_proteins_by_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_proteins_by_reference</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_proteins_by_resource" title="pypath.core.network.Network.count_proteins_by_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_proteins_by_resource</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_references" title="pypath.core.network.Network.count_references"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_references</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_references_by_data_model" title="pypath.core.network.Network.count_references_by_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_references_by_data_model</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_references_by_interaction_type" title="pypath.core.network.Network.count_references_by_interaction_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_references_by_interaction_type</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_references_by_interaction_type_and_data_model" title="pypath.core.network.Network.count_references_by_interaction_type_and_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_references_by_interaction_type_and_data_model</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_references_by_interaction_type_and_data_model_and_resource" title="pypath.core.network.Network.count_references_by_interaction_type_and_data_model_and_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_references_by_interaction_type_and_data_model_and_resource</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_references_by_reference" title="pypath.core.network.Network.count_references_by_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_references_by_reference</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_references_by_resource" title="pypath.core.network.Network.count_references_by_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_references_by_resource</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_regulated_by" title="pypath.core.network.Network.count_regulated_by"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_regulated_by</span></code></a></p></td>
+<td><p>Returns the count of the interacting partners for one or more entities according to the specified criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_regulates" title="pypath.core.network.Network.count_regulates"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_regulates</span></code></a></p></td>
+<td><p>Returns the count of the interacting partners for one or more entities according to the specified criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_resource_names" title="pypath.core.network.Network.count_resource_names"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_resource_names</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_resource_names_by_data_model" title="pypath.core.network.Network.count_resource_names_by_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_resource_names_by_data_model</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_resource_names_by_interaction_type" title="pypath.core.network.Network.count_resource_names_by_interaction_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_resource_names_by_interaction_type</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_resource_names_by_interaction_type_and_data_model" title="pypath.core.network.Network.count_resource_names_by_interaction_type_and_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_resource_names_by_interaction_type_and_data_model</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_resource_names_by_interaction_type_and_data_model_and_resource" title="pypath.core.network.Network.count_resource_names_by_interaction_type_and_data_model_and_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_resource_names_by_interaction_type_and_data_model_and_resource</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_resource_names_by_reference" title="pypath.core.network.Network.count_resource_names_by_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_resource_names_by_reference</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_resource_names_by_resource" title="pypath.core.network.Network.count_resource_names_by_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_resource_names_by_resource</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_resource_names_via" title="pypath.core.network.Network.count_resource_names_via"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_resource_names_via</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_resource_names_via_by_data_model" title="pypath.core.network.Network.count_resource_names_via_by_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_resource_names_via_by_data_model</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_resource_names_via_by_interaction_type" title="pypath.core.network.Network.count_resource_names_via_by_interaction_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_resource_names_via_by_interaction_type</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_resource_names_via_by_interaction_type_and_data_model" title="pypath.core.network.Network.count_resource_names_via_by_interaction_type_and_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_resource_names_via_by_interaction_type_and_data_model</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_resource_names_via_by_interaction_type_and_data_model_and_resource" title="pypath.core.network.Network.count_resource_names_via_by_interaction_type_and_data_model_and_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_resource_names_via_by_interaction_type_and_data_model_and_resource</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_resource_names_via_by_reference" title="pypath.core.network.Network.count_resource_names_via_by_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_resource_names_via_by_reference</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_resource_names_via_by_resource" title="pypath.core.network.Network.count_resource_names_via_by_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_resource_names_via_by_resource</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_resources" title="pypath.core.network.Network.count_resources"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_resources</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_resources_by_data_model" title="pypath.core.network.Network.count_resources_by_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_resources_by_data_model</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_resources_by_interaction_type" title="pypath.core.network.Network.count_resources_by_interaction_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_resources_by_interaction_type</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_resources_by_interaction_type_and_data_model" title="pypath.core.network.Network.count_resources_by_interaction_type_and_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_resources_by_interaction_type_and_data_model</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_resources_by_interaction_type_and_data_model_and_resource" title="pypath.core.network.Network.count_resources_by_interaction_type_and_data_model_and_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_resources_by_interaction_type_and_data_model_and_resource</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_resources_by_reference" title="pypath.core.network.Network.count_resources_by_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_resources_by_reference</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_resources_by_resource" title="pypath.core.network.Network.count_resources_by_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_resources_by_resource</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_resources_via" title="pypath.core.network.Network.count_resources_via"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_resources_via</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_resources_via_by_data_model" title="pypath.core.network.Network.count_resources_via_by_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_resources_via_by_data_model</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_resources_via_by_interaction_type" title="pypath.core.network.Network.count_resources_via_by_interaction_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_resources_via_by_interaction_type</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_resources_via_by_interaction_type_and_data_model" title="pypath.core.network.Network.count_resources_via_by_interaction_type_and_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_resources_via_by_interaction_type_and_data_model</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_resources_via_by_interaction_type_and_data_model_and_resource" title="pypath.core.network.Network.count_resources_via_by_interaction_type_and_data_model_and_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_resources_via_by_interaction_type_and_data_model_and_resource</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_resources_via_by_reference" title="pypath.core.network.Network.count_resources_via_by_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_resources_via_by_reference</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_resources_via_by_resource" title="pypath.core.network.Network.count_resources_via_by_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_resources_via_by_resource</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_small_molecule_identifiers" title="pypath.core.network.Network.count_small_molecule_identifiers"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_small_molecule_identifiers</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_small_molecule_identifiers_by_data_model" title="pypath.core.network.Network.count_small_molecule_identifiers_by_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_small_molecule_identifiers_by_data_model</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_small_molecule_identifiers_by_interaction_type" title="pypath.core.network.Network.count_small_molecule_identifiers_by_interaction_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_small_molecule_identifiers_by_interaction_type</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_small_molecule_identifiers_by_interaction_type_and_data_model" title="pypath.core.network.Network.count_small_molecule_identifiers_by_interaction_type_and_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_small_molecule_identifiers_by_interaction_type_and_data_model</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_small_molecule_identifiers_by_interaction_type_and_data_model_and_resource" title="pypath.core.network.Network.count_small_molecule_identifiers_by_interaction_type_and_data_model_and_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_small_molecule_identifiers_by_interaction_type_and_data_model_and_resource</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_small_molecule_identifiers_by_reference" title="pypath.core.network.Network.count_small_molecule_identifiers_by_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_small_molecule_identifiers_by_reference</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_small_molecule_identifiers_by_resource" title="pypath.core.network.Network.count_small_molecule_identifiers_by_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_small_molecule_identifiers_by_resource</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_small_molecule_labels" title="pypath.core.network.Network.count_small_molecule_labels"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_small_molecule_labels</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_small_molecule_labels_by_data_model" title="pypath.core.network.Network.count_small_molecule_labels_by_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_small_molecule_labels_by_data_model</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_small_molecule_labels_by_interaction_type" title="pypath.core.network.Network.count_small_molecule_labels_by_interaction_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_small_molecule_labels_by_interaction_type</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_small_molecule_labels_by_interaction_type_and_data_model" title="pypath.core.network.Network.count_small_molecule_labels_by_interaction_type_and_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_small_molecule_labels_by_interaction_type_and_data_model</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_small_molecule_labels_by_interaction_type_and_data_model_and_resource" title="pypath.core.network.Network.count_small_molecule_labels_by_interaction_type_and_data_model_and_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_small_molecule_labels_by_interaction_type_and_data_model_and_resource</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_small_molecule_labels_by_reference" title="pypath.core.network.Network.count_small_molecule_labels_by_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_small_molecule_labels_by_reference</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_small_molecule_labels_by_resource" title="pypath.core.network.Network.count_small_molecule_labels_by_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_small_molecule_labels_by_resource</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_small_molecules" title="pypath.core.network.Network.count_small_molecules"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_small_molecules</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_small_molecules_by_data_model" title="pypath.core.network.Network.count_small_molecules_by_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_small_molecules_by_data_model</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_small_molecules_by_interaction_type" title="pypath.core.network.Network.count_small_molecules_by_interaction_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_small_molecules_by_interaction_type</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_small_molecules_by_interaction_type_and_data_model" title="pypath.core.network.Network.count_small_molecules_by_interaction_type_and_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_small_molecules_by_interaction_type_and_data_model</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_small_molecules_by_interaction_type_and_data_model_and_resource" title="pypath.core.network.Network.count_small_molecules_by_interaction_type_and_data_model_and_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_small_molecules_by_interaction_type_and_data_model_and_resource</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_small_molecules_by_reference" title="pypath.core.network.Network.count_small_molecules_by_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_small_molecules_by_reference</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_small_molecules_by_resource" title="pypath.core.network.Network.count_small_molecules_by_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_small_molecules_by_resource</span></code></a></p></td>
+<td><p>str(object='') -&gt; str str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_suppressed_by" title="pypath.core.network.Network.count_suppressed_by"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_suppressed_by</span></code></a></p></td>
+<td><p>Returns the count of the interacting partners for one or more entities according to the specified criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_suppresses" title="pypath.core.network.Network.count_suppresses"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_suppresses</span></code></a></p></td>
+<td><p>Returns the count of the interacting partners for one or more entities according to the specified criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_transcriptionally_activated_by" title="pypath.core.network.Network.count_transcriptionally_activated_by"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_transcriptionally_activated_by</span></code></a></p></td>
+<td><p>Returns the count of the interacting partners for one or more entities according to the specified criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_transcriptionally_activates" title="pypath.core.network.Network.count_transcriptionally_activates"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_transcriptionally_activates</span></code></a></p></td>
+<td><p>Returns the count of the interacting partners for one or more entities according to the specified criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_transcriptionally_regulated_by" title="pypath.core.network.Network.count_transcriptionally_regulated_by"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_transcriptionally_regulated_by</span></code></a></p></td>
+<td><p>Returns the count of the interacting partners for one or more entities according to the specified criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_transcriptionally_regulates" title="pypath.core.network.Network.count_transcriptionally_regulates"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_transcriptionally_regulates</span></code></a></p></td>
+<td><p>Returns the count of the interacting partners for one or more entities according to the specified criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_transcriptionally_suppressed_by" title="pypath.core.network.Network.count_transcriptionally_suppressed_by"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_transcriptionally_suppressed_by</span></code></a></p></td>
+<td><p>Returns the count of the interacting partners for one or more entities according to the specified criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.count_transcriptionally_suppresses" title="pypath.core.network.Network.count_transcriptionally_suppresses"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_transcriptionally_suppresses</span></code></a></p></td>
+<td><p>Returns the count of the interacting partners for one or more entities according to the specified criteria.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.curation_effort_by_data_model" title="pypath.core.network.Network.curation_effort_by_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">curation_effort_by_data_model</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.curation_effort_by_interaction_type" title="pypath.core.network.Network.curation_effort_by_interaction_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">curation_effort_by_interaction_type</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.curation_effort_by_interaction_type_and_data_model" title="pypath.core.network.Network.curation_effort_by_interaction_type_and_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">curation_effort_by_interaction_type_and_data_model</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.curation_effort_by_interaction_type_and_data_model_and_resource" title="pypath.core.network.Network.curation_effort_by_interaction_type_and_data_model_and_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">curation_effort_by_interaction_type_and_data_model_and_resource</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.curation_effort_by_reference" title="pypath.core.network.Network.curation_effort_by_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">curation_effort_by_reference</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.curation_effort_by_resource" title="pypath.core.network.Network.curation_effort_by_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">curation_effort_by_resource</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.data_models_by_data_model" title="pypath.core.network.Network.data_models_by_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">data_models_by_data_model</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.data_models_by_interaction_type" title="pypath.core.network.Network.data_models_by_interaction_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">data_models_by_interaction_type</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.data_models_by_interaction_type_and_data_model" title="pypath.core.network.Network.data_models_by_interaction_type_and_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">data_models_by_interaction_type_and_data_model</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.data_models_by_interaction_type_and_data_model_and_resource" title="pypath.core.network.Network.data_models_by_interaction_type_and_data_model_and_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">data_models_by_interaction_type_and_data_model_and_resource</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.data_models_by_reference" title="pypath.core.network.Network.data_models_by_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">data_models_by_reference</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.data_models_by_resource" title="pypath.core.network.Network.data_models_by_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">data_models_by_resource</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.datasets_by_data_model" title="pypath.core.network.Network.datasets_by_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">datasets_by_data_model</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.datasets_by_interaction_type" title="pypath.core.network.Network.datasets_by_interaction_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">datasets_by_interaction_type</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.datasets_by_interaction_type_and_data_model" title="pypath.core.network.Network.datasets_by_interaction_type_and_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">datasets_by_interaction_type_and_data_model</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.datasets_by_interaction_type_and_data_model_and_resource" title="pypath.core.network.Network.datasets_by_interaction_type_and_data_model_and_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">datasets_by_interaction_type_and_data_model_and_resource</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.datasets_by_reference" title="pypath.core.network.Network.datasets_by_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">datasets_by_reference</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.datasets_by_resource" title="pypath.core.network.Network.datasets_by_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">datasets_by_resource</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.degrees_directed_by_data_model" title="pypath.core.network.Network.degrees_directed_by_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_directed_by_data_model</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.degrees_directed_by_interaction_type" title="pypath.core.network.Network.degrees_directed_by_interaction_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_directed_by_interaction_type</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.degrees_directed_by_interaction_type_and_data_model" title="pypath.core.network.Network.degrees_directed_by_interaction_type_and_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_directed_by_interaction_type_and_data_model</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.degrees_directed_by_interaction_type_and_data_model_and_resource" title="pypath.core.network.Network.degrees_directed_by_interaction_type_and_data_model_and_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_directed_by_interaction_type_and_data_model_and_resource</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.degrees_directed_by_reference" title="pypath.core.network.Network.degrees_directed_by_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_directed_by_reference</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.degrees_directed_by_resource" title="pypath.core.network.Network.degrees_directed_by_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_directed_by_resource</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.degrees_directed_in_by_data_model" title="pypath.core.network.Network.degrees_directed_in_by_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_directed_in_by_data_model</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.degrees_directed_in_by_interaction_type" title="pypath.core.network.Network.degrees_directed_in_by_interaction_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_directed_in_by_interaction_type</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.degrees_directed_in_by_interaction_type_and_data_model" title="pypath.core.network.Network.degrees_directed_in_by_interaction_type_and_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_directed_in_by_interaction_type_and_data_model</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.degrees_directed_in_by_interaction_type_and_data_model_and_resource" title="pypath.core.network.Network.degrees_directed_in_by_interaction_type_and_data_model_and_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_directed_in_by_interaction_type_and_data_model_and_resource</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.degrees_directed_in_by_reference" title="pypath.core.network.Network.degrees_directed_in_by_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_directed_in_by_reference</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.degrees_directed_in_by_resource" title="pypath.core.network.Network.degrees_directed_in_by_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_directed_in_by_resource</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.degrees_directed_out_by_data_model" title="pypath.core.network.Network.degrees_directed_out_by_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_directed_out_by_data_model</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.degrees_directed_out_by_interaction_type" title="pypath.core.network.Network.degrees_directed_out_by_interaction_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_directed_out_by_interaction_type</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.degrees_directed_out_by_interaction_type_and_data_model" title="pypath.core.network.Network.degrees_directed_out_by_interaction_type_and_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_directed_out_by_interaction_type_and_data_model</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.degrees_directed_out_by_interaction_type_and_data_model_and_resource" title="pypath.core.network.Network.degrees_directed_out_by_interaction_type_and_data_model_and_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_directed_out_by_interaction_type_and_data_model_and_resource</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.degrees_directed_out_by_reference" title="pypath.core.network.Network.degrees_directed_out_by_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_directed_out_by_reference</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.degrees_directed_out_by_resource" title="pypath.core.network.Network.degrees_directed_out_by_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_directed_out_by_resource</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.degrees_negative_by_data_model" title="pypath.core.network.Network.degrees_negative_by_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_negative_by_data_model</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.degrees_negative_by_interaction_type" title="pypath.core.network.Network.degrees_negative_by_interaction_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_negative_by_interaction_type</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.degrees_negative_by_interaction_type_and_data_model" title="pypath.core.network.Network.degrees_negative_by_interaction_type_and_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_negative_by_interaction_type_and_data_model</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.degrees_negative_by_interaction_type_and_data_model_and_resource" title="pypath.core.network.Network.degrees_negative_by_interaction_type_and_data_model_and_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_negative_by_interaction_type_and_data_model_and_resource</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.degrees_negative_by_reference" title="pypath.core.network.Network.degrees_negative_by_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_negative_by_reference</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.degrees_negative_by_resource" title="pypath.core.network.Network.degrees_negative_by_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_negative_by_resource</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.degrees_negative_in_by_data_model" title="pypath.core.network.Network.degrees_negative_in_by_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_negative_in_by_data_model</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.degrees_negative_in_by_interaction_type" title="pypath.core.network.Network.degrees_negative_in_by_interaction_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_negative_in_by_interaction_type</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.degrees_negative_in_by_interaction_type_and_data_model" title="pypath.core.network.Network.degrees_negative_in_by_interaction_type_and_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_negative_in_by_interaction_type_and_data_model</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.degrees_negative_in_by_interaction_type_and_data_model_and_resource" title="pypath.core.network.Network.degrees_negative_in_by_interaction_type_and_data_model_and_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_negative_in_by_interaction_type_and_data_model_and_resource</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.degrees_negative_in_by_reference" title="pypath.core.network.Network.degrees_negative_in_by_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_negative_in_by_reference</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.degrees_negative_in_by_resource" title="pypath.core.network.Network.degrees_negative_in_by_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_negative_in_by_resource</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.degrees_negative_out_by_data_model" title="pypath.core.network.Network.degrees_negative_out_by_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_negative_out_by_data_model</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.degrees_negative_out_by_interaction_type" title="pypath.core.network.Network.degrees_negative_out_by_interaction_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_negative_out_by_interaction_type</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.degrees_negative_out_by_interaction_type_and_data_model" title="pypath.core.network.Network.degrees_negative_out_by_interaction_type_and_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_negative_out_by_interaction_type_and_data_model</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.degrees_negative_out_by_interaction_type_and_data_model_and_resource" title="pypath.core.network.Network.degrees_negative_out_by_interaction_type_and_data_model_and_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_negative_out_by_interaction_type_and_data_model_and_resource</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.degrees_negative_out_by_reference" title="pypath.core.network.Network.degrees_negative_out_by_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_negative_out_by_reference</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.degrees_negative_out_by_resource" title="pypath.core.network.Network.degrees_negative_out_by_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_negative_out_by_resource</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.degrees_non_directed_by_data_model" title="pypath.core.network.Network.degrees_non_directed_by_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_non_directed_by_data_model</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.degrees_non_directed_by_interaction_type" title="pypath.core.network.Network.degrees_non_directed_by_interaction_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_non_directed_by_interaction_type</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.degrees_non_directed_by_interaction_type_and_data_model" title="pypath.core.network.Network.degrees_non_directed_by_interaction_type_and_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_non_directed_by_interaction_type_and_data_model</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.degrees_non_directed_by_interaction_type_and_data_model_and_resource" title="pypath.core.network.Network.degrees_non_directed_by_interaction_type_and_data_model_and_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_non_directed_by_interaction_type_and_data_model_and_resource</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.degrees_non_directed_by_reference" title="pypath.core.network.Network.degrees_non_directed_by_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_non_directed_by_reference</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.degrees_non_directed_by_resource" title="pypath.core.network.Network.degrees_non_directed_by_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_non_directed_by_resource</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.degrees_positive_by_data_model" title="pypath.core.network.Network.degrees_positive_by_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_positive_by_data_model</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.degrees_positive_by_interaction_type" title="pypath.core.network.Network.degrees_positive_by_interaction_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_positive_by_interaction_type</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.degrees_positive_by_interaction_type_and_data_model" title="pypath.core.network.Network.degrees_positive_by_interaction_type_and_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_positive_by_interaction_type_and_data_model</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.degrees_positive_by_interaction_type_and_data_model_and_resource" title="pypath.core.network.Network.degrees_positive_by_interaction_type_and_data_model_and_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_positive_by_interaction_type_and_data_model_and_resource</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.degrees_positive_by_reference" title="pypath.core.network.Network.degrees_positive_by_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_positive_by_reference</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.degrees_positive_by_resource" title="pypath.core.network.Network.degrees_positive_by_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_positive_by_resource</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.degrees_positive_in_by_data_model" title="pypath.core.network.Network.degrees_positive_in_by_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_positive_in_by_data_model</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.degrees_positive_in_by_interaction_type" title="pypath.core.network.Network.degrees_positive_in_by_interaction_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_positive_in_by_interaction_type</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.degrees_positive_in_by_interaction_type_and_data_model" title="pypath.core.network.Network.degrees_positive_in_by_interaction_type_and_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_positive_in_by_interaction_type_and_data_model</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.degrees_positive_in_by_interaction_type_and_data_model_and_resource" title="pypath.core.network.Network.degrees_positive_in_by_interaction_type_and_data_model_and_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_positive_in_by_interaction_type_and_data_model_and_resource</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.degrees_positive_in_by_reference" title="pypath.core.network.Network.degrees_positive_in_by_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_positive_in_by_reference</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.degrees_positive_in_by_resource" title="pypath.core.network.Network.degrees_positive_in_by_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_positive_in_by_resource</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.degrees_positive_out_by_data_model" title="pypath.core.network.Network.degrees_positive_out_by_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_positive_out_by_data_model</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.degrees_positive_out_by_interaction_type" title="pypath.core.network.Network.degrees_positive_out_by_interaction_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_positive_out_by_interaction_type</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.degrees_positive_out_by_interaction_type_and_data_model" title="pypath.core.network.Network.degrees_positive_out_by_interaction_type_and_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_positive_out_by_interaction_type_and_data_model</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.degrees_positive_out_by_interaction_type_and_data_model_and_resource" title="pypath.core.network.Network.degrees_positive_out_by_interaction_type_and_data_model_and_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_positive_out_by_interaction_type_and_data_model_and_resource</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.degrees_positive_out_by_reference" title="pypath.core.network.Network.degrees_positive_out_by_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_positive_out_by_reference</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.degrees_positive_out_by_resource" title="pypath.core.network.Network.degrees_positive_out_by_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_positive_out_by_resource</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.degrees_signed_by_data_model" title="pypath.core.network.Network.degrees_signed_by_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_signed_by_data_model</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.degrees_signed_by_interaction_type" title="pypath.core.network.Network.degrees_signed_by_interaction_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_signed_by_interaction_type</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.degrees_signed_by_interaction_type_and_data_model" title="pypath.core.network.Network.degrees_signed_by_interaction_type_and_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_signed_by_interaction_type_and_data_model</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.degrees_signed_by_interaction_type_and_data_model_and_resource" title="pypath.core.network.Network.degrees_signed_by_interaction_type_and_data_model_and_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_signed_by_interaction_type_and_data_model_and_resource</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.degrees_signed_by_reference" title="pypath.core.network.Network.degrees_signed_by_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_signed_by_reference</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.degrees_signed_by_resource" title="pypath.core.network.Network.degrees_signed_by_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_signed_by_resource</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.degrees_signed_in_by_data_model" title="pypath.core.network.Network.degrees_signed_in_by_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_signed_in_by_data_model</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.degrees_signed_in_by_interaction_type" title="pypath.core.network.Network.degrees_signed_in_by_interaction_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_signed_in_by_interaction_type</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.degrees_signed_in_by_interaction_type_and_data_model" title="pypath.core.network.Network.degrees_signed_in_by_interaction_type_and_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_signed_in_by_interaction_type_and_data_model</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.degrees_signed_in_by_interaction_type_and_data_model_and_resource" title="pypath.core.network.Network.degrees_signed_in_by_interaction_type_and_data_model_and_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_signed_in_by_interaction_type_and_data_model_and_resource</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.degrees_signed_in_by_reference" title="pypath.core.network.Network.degrees_signed_in_by_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_signed_in_by_reference</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.degrees_signed_in_by_resource" title="pypath.core.network.Network.degrees_signed_in_by_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_signed_in_by_resource</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.degrees_signed_out_by_data_model" title="pypath.core.network.Network.degrees_signed_out_by_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_signed_out_by_data_model</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.degrees_signed_out_by_interaction_type" title="pypath.core.network.Network.degrees_signed_out_by_interaction_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_signed_out_by_interaction_type</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.degrees_signed_out_by_interaction_type_and_data_model" title="pypath.core.network.Network.degrees_signed_out_by_interaction_type_and_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_signed_out_by_interaction_type_and_data_model</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.degrees_signed_out_by_interaction_type_and_data_model_and_resource" title="pypath.core.network.Network.degrees_signed_out_by_interaction_type_and_data_model_and_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_signed_out_by_interaction_type_and_data_model_and_resource</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.degrees_signed_out_by_reference" title="pypath.core.network.Network.degrees_signed_out_by_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_signed_out_by_reference</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.degrees_signed_out_by_resource" title="pypath.core.network.Network.degrees_signed_out_by_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_signed_out_by_resource</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.degrees_undirected_by_data_model" title="pypath.core.network.Network.degrees_undirected_by_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_undirected_by_data_model</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.degrees_undirected_by_interaction_type" title="pypath.core.network.Network.degrees_undirected_by_interaction_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_undirected_by_interaction_type</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.degrees_undirected_by_interaction_type_and_data_model" title="pypath.core.network.Network.degrees_undirected_by_interaction_type_and_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_undirected_by_interaction_type_and_data_model</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.degrees_undirected_by_interaction_type_and_data_model_and_resource" title="pypath.core.network.Network.degrees_undirected_by_interaction_type_and_data_model_and_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_undirected_by_interaction_type_and_data_model_and_resource</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.degrees_undirected_by_reference" title="pypath.core.network.Network.degrees_undirected_by_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_undirected_by_reference</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.degrees_undirected_by_resource" title="pypath.core.network.Network.degrees_undirected_by_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">degrees_undirected_by_resource</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">ecount</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.entities_by_data_model" title="pypath.core.network.Network.entities_by_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">entities_by_data_model</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.entities_by_interaction_type" title="pypath.core.network.Network.entities_by_interaction_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">entities_by_interaction_type</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.entities_by_interaction_type_and_data_model" title="pypath.core.network.Network.entities_by_interaction_type_and_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">entities_by_interaction_type_and_data_model</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.entities_by_interaction_type_and_data_model_and_resource" title="pypath.core.network.Network.entities_by_interaction_type_and_data_model_and_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">entities_by_interaction_type_and_data_model_and_resource</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.entities_by_reference" title="pypath.core.network.Network.entities_by_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">entities_by_reference</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.entities_by_resource" title="pypath.core.network.Network.entities_by_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">entities_by_resource</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.evidences_by_data_model" title="pypath.core.network.Network.evidences_by_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">evidences_by_data_model</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.evidences_by_interaction_type" title="pypath.core.network.Network.evidences_by_interaction_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">evidences_by_interaction_type</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.evidences_by_interaction_type_and_data_model" title="pypath.core.network.Network.evidences_by_interaction_type_and_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">evidences_by_interaction_type_and_data_model</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.evidences_by_interaction_type_and_data_model_and_resource" title="pypath.core.network.Network.evidences_by_interaction_type_and_data_model_and_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">evidences_by_interaction_type_and_data_model_and_resource</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.evidences_by_reference" title="pypath.core.network.Network.evidences_by_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">evidences_by_reference</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.evidences_by_resource" title="pypath.core.network.Network.evidences_by_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">evidences_by_resource</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.get_complex_identifiers" title="pypath.core.network.Network.get_complex_identifiers"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_complex_identifiers</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.get_complex_labels" title="pypath.core.network.Network.get_complex_labels"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_complex_labels</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.get_complexes" title="pypath.core.network.Network.get_complexes"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_complexes</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.get_curation_effort" title="pypath.core.network.Network.get_curation_effort"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_curation_effort</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.get_data_models" title="pypath.core.network.Network.get_data_models"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_data_models</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.get_datasets" title="pypath.core.network.Network.get_datasets"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_datasets</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.get_degrees_directed" title="pypath.core.network.Network.get_degrees_directed"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_degrees_directed</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.get_degrees_directed_in" title="pypath.core.network.Network.get_degrees_directed_in"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_degrees_directed_in</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.get_degrees_directed_out" title="pypath.core.network.Network.get_degrees_directed_out"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_degrees_directed_out</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.get_degrees_negative" title="pypath.core.network.Network.get_degrees_negative"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_degrees_negative</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.get_degrees_negative_in" title="pypath.core.network.Network.get_degrees_negative_in"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_degrees_negative_in</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.get_degrees_negative_out" title="pypath.core.network.Network.get_degrees_negative_out"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_degrees_negative_out</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.get_degrees_non_directed" title="pypath.core.network.Network.get_degrees_non_directed"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_degrees_non_directed</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.get_degrees_positive" title="pypath.core.network.Network.get_degrees_positive"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_degrees_positive</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.get_degrees_positive_in" title="pypath.core.network.Network.get_degrees_positive_in"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_degrees_positive_in</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.get_degrees_positive_out" title="pypath.core.network.Network.get_degrees_positive_out"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_degrees_positive_out</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.get_degrees_signed" title="pypath.core.network.Network.get_degrees_signed"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_degrees_signed</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.get_degrees_signed_in" title="pypath.core.network.Network.get_degrees_signed_in"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_degrees_signed_in</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.get_degrees_signed_out" title="pypath.core.network.Network.get_degrees_signed_out"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_degrees_signed_out</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.get_degrees_undirected" title="pypath.core.network.Network.get_degrees_undirected"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_degrees_undirected</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.get_entities" title="pypath.core.network.Network.get_entities"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_entities</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.get_evidences" title="pypath.core.network.Network.get_evidences"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_evidences</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.get_identifiers" title="pypath.core.network.Network.get_identifiers"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_identifiers</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.get_interaction_types" title="pypath.core.network.Network.get_interaction_types"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_interaction_types</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.get_interactions" title="pypath.core.network.Network.get_interactions"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_interactions</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.get_interactions_0" title="pypath.core.network.Network.get_interactions_0"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_interactions_0</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.get_interactions_directed" title="pypath.core.network.Network.get_interactions_directed"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_interactions_directed</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.get_interactions_mutual" title="pypath.core.network.Network.get_interactions_mutual"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_interactions_mutual</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.get_interactions_negative" title="pypath.core.network.Network.get_interactions_negative"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_interactions_negative</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.get_interactions_non_directed" title="pypath.core.network.Network.get_interactions_non_directed"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_interactions_non_directed</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.get_interactions_non_directed_0" title="pypath.core.network.Network.get_interactions_non_directed_0"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_interactions_non_directed_0</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.get_interactions_positive" title="pypath.core.network.Network.get_interactions_positive"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_interactions_positive</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.get_interactions_signed" title="pypath.core.network.Network.get_interactions_signed"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_interactions_signed</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.get_interactions_undirected" title="pypath.core.network.Network.get_interactions_undirected"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_interactions_undirected</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.get_interactions_undirected_0" title="pypath.core.network.Network.get_interactions_undirected_0"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_interactions_undirected_0</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.get_labels" title="pypath.core.network.Network.get_labels"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_labels</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.get_lncrna_identifiers" title="pypath.core.network.Network.get_lncrna_identifiers"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_lncrna_identifiers</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.get_lncrna_labels" title="pypath.core.network.Network.get_lncrna_labels"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_lncrna_labels</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.get_lncrnas" title="pypath.core.network.Network.get_lncrnas"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_lncrnas</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.get_mirna_identifiers" title="pypath.core.network.Network.get_mirna_identifiers"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_mirna_identifiers</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.get_mirna_labels" title="pypath.core.network.Network.get_mirna_labels"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_mirna_labels</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.get_mirnas" title="pypath.core.network.Network.get_mirnas"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_mirnas</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.get_protein_identifiers" title="pypath.core.network.Network.get_protein_identifiers"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_protein_identifiers</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.get_protein_labels" title="pypath.core.network.Network.get_protein_labels"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_protein_labels</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.get_proteins" title="pypath.core.network.Network.get_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_proteins</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.get_references" title="pypath.core.network.Network.get_references"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_references</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.get_resource_names" title="pypath.core.network.Network.get_resource_names"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_resource_names</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.get_resource_names_via" title="pypath.core.network.Network.get_resource_names_via"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_resource_names_via</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.get_resources" title="pypath.core.network.Network.get_resources"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_resources</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.get_resources_via" title="pypath.core.network.Network.get_resources_via"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_resources_via</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.get_small_molecule_identifiers" title="pypath.core.network.Network.get_small_molecule_identifiers"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_small_molecule_identifiers</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.get_small_molecule_labels" title="pypath.core.network.Network.get_small_molecule_labels"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_small_molecule_labels</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.get_small_molecules" title="pypath.core.network.Network.get_small_molecules"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_small_molecules</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.identifiers_by_data_model" title="pypath.core.network.Network.identifiers_by_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">identifiers_by_data_model</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.identifiers_by_interaction_type" title="pypath.core.network.Network.identifiers_by_interaction_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">identifiers_by_interaction_type</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.identifiers_by_interaction_type_and_data_model" title="pypath.core.network.Network.identifiers_by_interaction_type_and_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">identifiers_by_interaction_type_and_data_model</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.identifiers_by_interaction_type_and_data_model_and_resource" title="pypath.core.network.Network.identifiers_by_interaction_type_and_data_model_and_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">identifiers_by_interaction_type_and_data_model_and_resource</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.identifiers_by_reference" title="pypath.core.network.Network.identifiers_by_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">identifiers_by_reference</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.identifiers_by_resource" title="pypath.core.network.Network.identifiers_by_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">identifiers_by_resource</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.interaction_types_by_data_model" title="pypath.core.network.Network.interaction_types_by_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">interaction_types_by_data_model</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.interaction_types_by_interaction_type" title="pypath.core.network.Network.interaction_types_by_interaction_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">interaction_types_by_interaction_type</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.interaction_types_by_interaction_type_and_data_model" title="pypath.core.network.Network.interaction_types_by_interaction_type_and_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">interaction_types_by_interaction_type_and_data_model</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.interaction_types_by_interaction_type_and_data_model_and_resource" title="pypath.core.network.Network.interaction_types_by_interaction_type_and_data_model_and_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">interaction_types_by_interaction_type_and_data_model_and_resource</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.interaction_types_by_reference" title="pypath.core.network.Network.interaction_types_by_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">interaction_types_by_reference</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.interaction_types_by_resource" title="pypath.core.network.Network.interaction_types_by_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">interaction_types_by_resource</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.interactions_0_by_data_model" title="pypath.core.network.Network.interactions_0_by_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">interactions_0_by_data_model</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.interactions_0_by_interaction_type" title="pypath.core.network.Network.interactions_0_by_interaction_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">interactions_0_by_interaction_type</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.interactions_0_by_interaction_type_and_data_model" title="pypath.core.network.Network.interactions_0_by_interaction_type_and_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">interactions_0_by_interaction_type_and_data_model</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.interactions_0_by_interaction_type_and_data_model_and_resource" title="pypath.core.network.Network.interactions_0_by_interaction_type_and_data_model_and_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">interactions_0_by_interaction_type_and_data_model_and_resource</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.interactions_0_by_reference" title="pypath.core.network.Network.interactions_0_by_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">interactions_0_by_reference</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.interactions_0_by_resource" title="pypath.core.network.Network.interactions_0_by_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">interactions_0_by_resource</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.interactions_by_data_model" title="pypath.core.network.Network.interactions_by_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">interactions_by_data_model</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.interactions_by_interaction_type" title="pypath.core.network.Network.interactions_by_interaction_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">interactions_by_interaction_type</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.interactions_by_interaction_type_and_data_model" title="pypath.core.network.Network.interactions_by_interaction_type_and_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">interactions_by_interaction_type_and_data_model</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.interactions_by_interaction_type_and_data_model_and_resource" title="pypath.core.network.Network.interactions_by_interaction_type_and_data_model_and_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">interactions_by_interaction_type_and_data_model_and_resource</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.interactions_by_reference" title="pypath.core.network.Network.interactions_by_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">interactions_by_reference</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.interactions_by_resource" title="pypath.core.network.Network.interactions_by_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">interactions_by_resource</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.interactions_directed_by_data_model" title="pypath.core.network.Network.interactions_directed_by_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">interactions_directed_by_data_model</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.interactions_directed_by_interaction_type" title="pypath.core.network.Network.interactions_directed_by_interaction_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">interactions_directed_by_interaction_type</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.interactions_directed_by_interaction_type_and_data_model" title="pypath.core.network.Network.interactions_directed_by_interaction_type_and_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">interactions_directed_by_interaction_type_and_data_model</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.interactions_directed_by_interaction_type_and_data_model_and_resource" title="pypath.core.network.Network.interactions_directed_by_interaction_type_and_data_model_and_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">interactions_directed_by_interaction_type_and_data_model_and_resource</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.interactions_directed_by_reference" title="pypath.core.network.Network.interactions_directed_by_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">interactions_directed_by_reference</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.interactions_directed_by_resource" title="pypath.core.network.Network.interactions_directed_by_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">interactions_directed_by_resource</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.interactions_mutual_by_data_model" title="pypath.core.network.Network.interactions_mutual_by_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">interactions_mutual_by_data_model</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.interactions_mutual_by_interaction_type" title="pypath.core.network.Network.interactions_mutual_by_interaction_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">interactions_mutual_by_interaction_type</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.interactions_mutual_by_interaction_type_and_data_model" title="pypath.core.network.Network.interactions_mutual_by_interaction_type_and_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">interactions_mutual_by_interaction_type_and_data_model</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.interactions_mutual_by_interaction_type_and_data_model_and_resource" title="pypath.core.network.Network.interactions_mutual_by_interaction_type_and_data_model_and_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">interactions_mutual_by_interaction_type_and_data_model_and_resource</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.interactions_mutual_by_reference" title="pypath.core.network.Network.interactions_mutual_by_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">interactions_mutual_by_reference</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.interactions_mutual_by_resource" title="pypath.core.network.Network.interactions_mutual_by_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">interactions_mutual_by_resource</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.interactions_negative_by_data_model" title="pypath.core.network.Network.interactions_negative_by_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">interactions_negative_by_data_model</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.interactions_negative_by_interaction_type" title="pypath.core.network.Network.interactions_negative_by_interaction_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">interactions_negative_by_interaction_type</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.interactions_negative_by_interaction_type_and_data_model" title="pypath.core.network.Network.interactions_negative_by_interaction_type_and_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">interactions_negative_by_interaction_type_and_data_model</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.interactions_negative_by_interaction_type_and_data_model_and_resource" title="pypath.core.network.Network.interactions_negative_by_interaction_type_and_data_model_and_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">interactions_negative_by_interaction_type_and_data_model_and_resource</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.interactions_negative_by_reference" title="pypath.core.network.Network.interactions_negative_by_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">interactions_negative_by_reference</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.interactions_negative_by_resource" title="pypath.core.network.Network.interactions_negative_by_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">interactions_negative_by_resource</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.interactions_non_directed_0_by_data_model" title="pypath.core.network.Network.interactions_non_directed_0_by_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">interactions_non_directed_0_by_data_model</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.interactions_non_directed_0_by_interaction_type" title="pypath.core.network.Network.interactions_non_directed_0_by_interaction_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">interactions_non_directed_0_by_interaction_type</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.interactions_non_directed_0_by_interaction_type_and_data_model" title="pypath.core.network.Network.interactions_non_directed_0_by_interaction_type_and_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">interactions_non_directed_0_by_interaction_type_and_data_model</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.interactions_non_directed_0_by_interaction_type_and_data_model_and_resource" title="pypath.core.network.Network.interactions_non_directed_0_by_interaction_type_and_data_model_and_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">interactions_non_directed_0_by_interaction_type_and_data_model_and_resource</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.interactions_non_directed_0_by_reference" title="pypath.core.network.Network.interactions_non_directed_0_by_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">interactions_non_directed_0_by_reference</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.interactions_non_directed_0_by_resource" title="pypath.core.network.Network.interactions_non_directed_0_by_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">interactions_non_directed_0_by_resource</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.interactions_non_directed_by_data_model" title="pypath.core.network.Network.interactions_non_directed_by_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">interactions_non_directed_by_data_model</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.interactions_non_directed_by_interaction_type" title="pypath.core.network.Network.interactions_non_directed_by_interaction_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">interactions_non_directed_by_interaction_type</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.interactions_non_directed_by_interaction_type_and_data_model" title="pypath.core.network.Network.interactions_non_directed_by_interaction_type_and_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">interactions_non_directed_by_interaction_type_and_data_model</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.interactions_non_directed_by_interaction_type_and_data_model_and_resource" title="pypath.core.network.Network.interactions_non_directed_by_interaction_type_and_data_model_and_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">interactions_non_directed_by_interaction_type_and_data_model_and_resource</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.interactions_non_directed_by_reference" title="pypath.core.network.Network.interactions_non_directed_by_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">interactions_non_directed_by_reference</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.interactions_non_directed_by_resource" title="pypath.core.network.Network.interactions_non_directed_by_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">interactions_non_directed_by_resource</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.interactions_positive_by_data_model" title="pypath.core.network.Network.interactions_positive_by_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">interactions_positive_by_data_model</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.interactions_positive_by_interaction_type" title="pypath.core.network.Network.interactions_positive_by_interaction_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">interactions_positive_by_interaction_type</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.interactions_positive_by_interaction_type_and_data_model" title="pypath.core.network.Network.interactions_positive_by_interaction_type_and_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">interactions_positive_by_interaction_type_and_data_model</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.interactions_positive_by_interaction_type_and_data_model_and_resource" title="pypath.core.network.Network.interactions_positive_by_interaction_type_and_data_model_and_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">interactions_positive_by_interaction_type_and_data_model_and_resource</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.interactions_positive_by_reference" title="pypath.core.network.Network.interactions_positive_by_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">interactions_positive_by_reference</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.interactions_positive_by_resource" title="pypath.core.network.Network.interactions_positive_by_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">interactions_positive_by_resource</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.interactions_signed_by_data_model" title="pypath.core.network.Network.interactions_signed_by_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">interactions_signed_by_data_model</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.interactions_signed_by_interaction_type" title="pypath.core.network.Network.interactions_signed_by_interaction_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">interactions_signed_by_interaction_type</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.interactions_signed_by_interaction_type_and_data_model" title="pypath.core.network.Network.interactions_signed_by_interaction_type_and_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">interactions_signed_by_interaction_type_and_data_model</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.interactions_signed_by_interaction_type_and_data_model_and_resource" title="pypath.core.network.Network.interactions_signed_by_interaction_type_and_data_model_and_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">interactions_signed_by_interaction_type_and_data_model_and_resource</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.interactions_signed_by_reference" title="pypath.core.network.Network.interactions_signed_by_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">interactions_signed_by_reference</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.interactions_signed_by_resource" title="pypath.core.network.Network.interactions_signed_by_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">interactions_signed_by_resource</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.interactions_undirected_0_by_data_model" title="pypath.core.network.Network.interactions_undirected_0_by_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">interactions_undirected_0_by_data_model</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.interactions_undirected_0_by_interaction_type" title="pypath.core.network.Network.interactions_undirected_0_by_interaction_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">interactions_undirected_0_by_interaction_type</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.interactions_undirected_0_by_interaction_type_and_data_model" title="pypath.core.network.Network.interactions_undirected_0_by_interaction_type_and_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">interactions_undirected_0_by_interaction_type_and_data_model</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.interactions_undirected_0_by_interaction_type_and_data_model_and_resource" title="pypath.core.network.Network.interactions_undirected_0_by_interaction_type_and_data_model_and_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">interactions_undirected_0_by_interaction_type_and_data_model_and_resource</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.interactions_undirected_0_by_reference" title="pypath.core.network.Network.interactions_undirected_0_by_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">interactions_undirected_0_by_reference</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.interactions_undirected_0_by_resource" title="pypath.core.network.Network.interactions_undirected_0_by_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">interactions_undirected_0_by_resource</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.interactions_undirected_by_data_model" title="pypath.core.network.Network.interactions_undirected_by_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">interactions_undirected_by_data_model</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.interactions_undirected_by_interaction_type" title="pypath.core.network.Network.interactions_undirected_by_interaction_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">interactions_undirected_by_interaction_type</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.interactions_undirected_by_interaction_type_and_data_model" title="pypath.core.network.Network.interactions_undirected_by_interaction_type_and_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">interactions_undirected_by_interaction_type_and_data_model</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.interactions_undirected_by_interaction_type_and_data_model_and_resource" title="pypath.core.network.Network.interactions_undirected_by_interaction_type_and_data_model_and_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">interactions_undirected_by_interaction_type_and_data_model_and_resource</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.interactions_undirected_by_reference" title="pypath.core.network.Network.interactions_undirected_by_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">interactions_undirected_by_reference</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.interactions_undirected_by_resource" title="pypath.core.network.Network.interactions_undirected_by_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">interactions_undirected_by_resource</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.labels_by_data_model" title="pypath.core.network.Network.labels_by_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">labels_by_data_model</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.labels_by_interaction_type" title="pypath.core.network.Network.labels_by_interaction_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">labels_by_interaction_type</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.labels_by_interaction_type_and_data_model" title="pypath.core.network.Network.labels_by_interaction_type_and_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">labels_by_interaction_type_and_data_model</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.labels_by_interaction_type_and_data_model_and_resource" title="pypath.core.network.Network.labels_by_interaction_type_and_data_model_and_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">labels_by_interaction_type_and_data_model_and_resource</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.labels_by_reference" title="pypath.core.network.Network.labels_by_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">labels_by_reference</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.labels_by_resource" title="pypath.core.network.Network.labels_by_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">labels_by_resource</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.lncrna_identifiers_by_data_model" title="pypath.core.network.Network.lncrna_identifiers_by_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">lncrna_identifiers_by_data_model</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.lncrna_identifiers_by_interaction_type" title="pypath.core.network.Network.lncrna_identifiers_by_interaction_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">lncrna_identifiers_by_interaction_type</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.lncrna_identifiers_by_interaction_type_and_data_model" title="pypath.core.network.Network.lncrna_identifiers_by_interaction_type_and_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">lncrna_identifiers_by_interaction_type_and_data_model</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.lncrna_identifiers_by_interaction_type_and_data_model_and_resource" title="pypath.core.network.Network.lncrna_identifiers_by_interaction_type_and_data_model_and_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">lncrna_identifiers_by_interaction_type_and_data_model_and_resource</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.lncrna_identifiers_by_reference" title="pypath.core.network.Network.lncrna_identifiers_by_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">lncrna_identifiers_by_reference</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.lncrna_identifiers_by_resource" title="pypath.core.network.Network.lncrna_identifiers_by_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">lncrna_identifiers_by_resource</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.lncrna_labels_by_data_model" title="pypath.core.network.Network.lncrna_labels_by_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">lncrna_labels_by_data_model</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.lncrna_labels_by_interaction_type" title="pypath.core.network.Network.lncrna_labels_by_interaction_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">lncrna_labels_by_interaction_type</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.lncrna_labels_by_interaction_type_and_data_model" title="pypath.core.network.Network.lncrna_labels_by_interaction_type_and_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">lncrna_labels_by_interaction_type_and_data_model</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.lncrna_labels_by_interaction_type_and_data_model_and_resource" title="pypath.core.network.Network.lncrna_labels_by_interaction_type_and_data_model_and_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">lncrna_labels_by_interaction_type_and_data_model_and_resource</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.lncrna_labels_by_reference" title="pypath.core.network.Network.lncrna_labels_by_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">lncrna_labels_by_reference</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.lncrna_labels_by_resource" title="pypath.core.network.Network.lncrna_labels_by_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">lncrna_labels_by_resource</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.lncrnas_by_data_model" title="pypath.core.network.Network.lncrnas_by_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">lncrnas_by_data_model</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.lncrnas_by_interaction_type" title="pypath.core.network.Network.lncrnas_by_interaction_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">lncrnas_by_interaction_type</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.lncrnas_by_interaction_type_and_data_model" title="pypath.core.network.Network.lncrnas_by_interaction_type_and_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">lncrnas_by_interaction_type_and_data_model</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.lncrnas_by_interaction_type_and_data_model_and_resource" title="pypath.core.network.Network.lncrnas_by_interaction_type_and_data_model_and_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">lncrnas_by_interaction_type_and_data_model_and_resource</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.lncrnas_by_reference" title="pypath.core.network.Network.lncrnas_by_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">lncrnas_by_reference</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.lncrnas_by_resource" title="pypath.core.network.Network.lncrnas_by_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">lncrnas_by_resource</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.mirna_identifiers_by_data_model" title="pypath.core.network.Network.mirna_identifiers_by_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">mirna_identifiers_by_data_model</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.mirna_identifiers_by_interaction_type" title="pypath.core.network.Network.mirna_identifiers_by_interaction_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">mirna_identifiers_by_interaction_type</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.mirna_identifiers_by_interaction_type_and_data_model" title="pypath.core.network.Network.mirna_identifiers_by_interaction_type_and_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">mirna_identifiers_by_interaction_type_and_data_model</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.mirna_identifiers_by_interaction_type_and_data_model_and_resource" title="pypath.core.network.Network.mirna_identifiers_by_interaction_type_and_data_model_and_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">mirna_identifiers_by_interaction_type_and_data_model_and_resource</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.mirna_identifiers_by_reference" title="pypath.core.network.Network.mirna_identifiers_by_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">mirna_identifiers_by_reference</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.mirna_identifiers_by_resource" title="pypath.core.network.Network.mirna_identifiers_by_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">mirna_identifiers_by_resource</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.mirna_labels_by_data_model" title="pypath.core.network.Network.mirna_labels_by_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">mirna_labels_by_data_model</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.mirna_labels_by_interaction_type" title="pypath.core.network.Network.mirna_labels_by_interaction_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">mirna_labels_by_interaction_type</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.mirna_labels_by_interaction_type_and_data_model" title="pypath.core.network.Network.mirna_labels_by_interaction_type_and_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">mirna_labels_by_interaction_type_and_data_model</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.mirna_labels_by_interaction_type_and_data_model_and_resource" title="pypath.core.network.Network.mirna_labels_by_interaction_type_and_data_model_and_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">mirna_labels_by_interaction_type_and_data_model_and_resource</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.mirna_labels_by_reference" title="pypath.core.network.Network.mirna_labels_by_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">mirna_labels_by_reference</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.mirna_labels_by_resource" title="pypath.core.network.Network.mirna_labels_by_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">mirna_labels_by_resource</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.mirnas_by_data_model" title="pypath.core.network.Network.mirnas_by_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">mirnas_by_data_model</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.mirnas_by_interaction_type" title="pypath.core.network.Network.mirnas_by_interaction_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">mirnas_by_interaction_type</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.mirnas_by_interaction_type_and_data_model" title="pypath.core.network.Network.mirnas_by_interaction_type_and_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">mirnas_by_interaction_type_and_data_model</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.mirnas_by_interaction_type_and_data_model_and_resource" title="pypath.core.network.Network.mirnas_by_interaction_type_and_data_model_and_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">mirnas_by_interaction_type_and_data_model_and_resource</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.mirnas_by_reference" title="pypath.core.network.Network.mirnas_by_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">mirnas_by_reference</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.mirnas_by_resource" title="pypath.core.network.Network.mirnas_by_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">mirnas_by_resource</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.post_transcriptionally_activated_by" title="pypath.core.network.Network.post_transcriptionally_activated_by"><code class="xref py py-obj docutils literal notranslate"><span class="pre">post_transcriptionally_activated_by</span></code></a></p></td>
+<td><p>arg str,Entity,list,set,tuple,EntityList entity:</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.post_transcriptionally_activates" title="pypath.core.network.Network.post_transcriptionally_activates"><code class="xref py py-obj docutils literal notranslate"><span class="pre">post_transcriptionally_activates</span></code></a></p></td>
+<td><p>arg str,Entity,list,set,tuple,EntityList entity:</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.post_transcriptionally_regulated_by" title="pypath.core.network.Network.post_transcriptionally_regulated_by"><code class="xref py py-obj docutils literal notranslate"><span class="pre">post_transcriptionally_regulated_by</span></code></a></p></td>
+<td><p>arg str,Entity,list,set,tuple,EntityList entity:</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.post_transcriptionally_regulates" title="pypath.core.network.Network.post_transcriptionally_regulates"><code class="xref py py-obj docutils literal notranslate"><span class="pre">post_transcriptionally_regulates</span></code></a></p></td>
+<td><p>arg str,Entity,list,set,tuple,EntityList entity:</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.post_transcriptionally_suppressed_by" title="pypath.core.network.Network.post_transcriptionally_suppressed_by"><code class="xref py py-obj docutils literal notranslate"><span class="pre">post_transcriptionally_suppressed_by</span></code></a></p></td>
+<td><p>arg str,Entity,list,set,tuple,EntityList entity:</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.post_transcriptionally_suppresses" title="pypath.core.network.Network.post_transcriptionally_suppresses"><code class="xref py py-obj docutils literal notranslate"><span class="pre">post_transcriptionally_suppresses</span></code></a></p></td>
+<td><p>arg str,Entity,list,set,tuple,EntityList entity:</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.post_translationally_activated_by" title="pypath.core.network.Network.post_translationally_activated_by"><code class="xref py py-obj docutils literal notranslate"><span class="pre">post_translationally_activated_by</span></code></a></p></td>
+<td><p>arg str,Entity,list,set,tuple,EntityList entity:</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.post_translationally_activates" title="pypath.core.network.Network.post_translationally_activates"><code class="xref py py-obj docutils literal notranslate"><span class="pre">post_translationally_activates</span></code></a></p></td>
+<td><p>arg str,Entity,list,set,tuple,EntityList entity:</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.post_translationally_regulated_by" title="pypath.core.network.Network.post_translationally_regulated_by"><code class="xref py py-obj docutils literal notranslate"><span class="pre">post_translationally_regulated_by</span></code></a></p></td>
+<td><p>arg str,Entity,list,set,tuple,EntityList entity:</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.post_translationally_regulates" title="pypath.core.network.Network.post_translationally_regulates"><code class="xref py py-obj docutils literal notranslate"><span class="pre">post_translationally_regulates</span></code></a></p></td>
+<td><p>arg str,Entity,list,set,tuple,EntityList entity:</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.post_translationally_suppressed_by" title="pypath.core.network.Network.post_translationally_suppressed_by"><code class="xref py py-obj docutils literal notranslate"><span class="pre">post_translationally_suppressed_by</span></code></a></p></td>
+<td><p>arg str,Entity,list,set,tuple,EntityList entity:</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.post_translationally_suppresses" title="pypath.core.network.Network.post_translationally_suppresses"><code class="xref py py-obj docutils literal notranslate"><span class="pre">post_translationally_suppresses</span></code></a></p></td>
+<td><p>arg str,Entity,list,set,tuple,EntityList entity:</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.protein_identifiers_by_data_model" title="pypath.core.network.Network.protein_identifiers_by_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">protein_identifiers_by_data_model</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.protein_identifiers_by_interaction_type" title="pypath.core.network.Network.protein_identifiers_by_interaction_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">protein_identifiers_by_interaction_type</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.protein_identifiers_by_interaction_type_and_data_model" title="pypath.core.network.Network.protein_identifiers_by_interaction_type_and_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">protein_identifiers_by_interaction_type_and_data_model</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.protein_identifiers_by_interaction_type_and_data_model_and_resource" title="pypath.core.network.Network.protein_identifiers_by_interaction_type_and_data_model_and_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">protein_identifiers_by_interaction_type_and_data_model_and_resource</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.protein_identifiers_by_reference" title="pypath.core.network.Network.protein_identifiers_by_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">protein_identifiers_by_reference</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.protein_identifiers_by_resource" title="pypath.core.network.Network.protein_identifiers_by_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">protein_identifiers_by_resource</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.protein_labels_by_data_model" title="pypath.core.network.Network.protein_labels_by_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">protein_labels_by_data_model</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.protein_labels_by_interaction_type" title="pypath.core.network.Network.protein_labels_by_interaction_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">protein_labels_by_interaction_type</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.protein_labels_by_interaction_type_and_data_model" title="pypath.core.network.Network.protein_labels_by_interaction_type_and_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">protein_labels_by_interaction_type_and_data_model</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.protein_labels_by_interaction_type_and_data_model_and_resource" title="pypath.core.network.Network.protein_labels_by_interaction_type_and_data_model_and_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">protein_labels_by_interaction_type_and_data_model_and_resource</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.protein_labels_by_reference" title="pypath.core.network.Network.protein_labels_by_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">protein_labels_by_reference</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.protein_labels_by_resource" title="pypath.core.network.Network.protein_labels_by_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">protein_labels_by_resource</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.proteins_by_data_model" title="pypath.core.network.Network.proteins_by_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">proteins_by_data_model</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.proteins_by_interaction_type" title="pypath.core.network.Network.proteins_by_interaction_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">proteins_by_interaction_type</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.proteins_by_interaction_type_and_data_model" title="pypath.core.network.Network.proteins_by_interaction_type_and_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">proteins_by_interaction_type_and_data_model</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.proteins_by_interaction_type_and_data_model_and_resource" title="pypath.core.network.Network.proteins_by_interaction_type_and_data_model_and_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">proteins_by_interaction_type_and_data_model_and_resource</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.proteins_by_reference" title="pypath.core.network.Network.proteins_by_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">proteins_by_reference</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.proteins_by_resource" title="pypath.core.network.Network.proteins_by_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">proteins_by_resource</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.references_by_data_model" title="pypath.core.network.Network.references_by_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">references_by_data_model</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.references_by_interaction_type" title="pypath.core.network.Network.references_by_interaction_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">references_by_interaction_type</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.references_by_interaction_type_and_data_model" title="pypath.core.network.Network.references_by_interaction_type_and_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">references_by_interaction_type_and_data_model</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.references_by_interaction_type_and_data_model_and_resource" title="pypath.core.network.Network.references_by_interaction_type_and_data_model_and_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">references_by_interaction_type_and_data_model_and_resource</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.references_by_reference" title="pypath.core.network.Network.references_by_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">references_by_reference</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.references_by_resource" title="pypath.core.network.Network.references_by_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">references_by_resource</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.regulated_by" title="pypath.core.network.Network.regulated_by"><code class="xref py py-obj docutils literal notranslate"><span class="pre">regulated_by</span></code></a></p></td>
+<td><p>arg str,Entity,list,set,tuple,EntityList entity:</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.regulates" title="pypath.core.network.Network.regulates"><code class="xref py py-obj docutils literal notranslate"><span class="pre">regulates</span></code></a></p></td>
+<td><p>arg str,Entity,list,set,tuple,EntityList entity:</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.resource_names" title="pypath.core.network.Network.resource_names"><code class="xref py py-obj docutils literal notranslate"><span class="pre">resource_names</span></code></a></p></td>
+<td><p>Returns a set of all resource names.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.resource_names_by_data_model" title="pypath.core.network.Network.resource_names_by_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">resource_names_by_data_model</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.resource_names_by_interaction_type" title="pypath.core.network.Network.resource_names_by_interaction_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">resource_names_by_interaction_type</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.resource_names_by_interaction_type_and_data_model" title="pypath.core.network.Network.resource_names_by_interaction_type_and_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">resource_names_by_interaction_type_and_data_model</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.resource_names_by_interaction_type_and_data_model_and_resource" title="pypath.core.network.Network.resource_names_by_interaction_type_and_data_model_and_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">resource_names_by_interaction_type_and_data_model_and_resource</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.resource_names_by_reference" title="pypath.core.network.Network.resource_names_by_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">resource_names_by_reference</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.resource_names_by_resource" title="pypath.core.network.Network.resource_names_by_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">resource_names_by_resource</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.resource_names_via_by_data_model" title="pypath.core.network.Network.resource_names_via_by_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">resource_names_via_by_data_model</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.resource_names_via_by_interaction_type" title="pypath.core.network.Network.resource_names_via_by_interaction_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">resource_names_via_by_interaction_type</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.resource_names_via_by_interaction_type_and_data_model" title="pypath.core.network.Network.resource_names_via_by_interaction_type_and_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">resource_names_via_by_interaction_type_and_data_model</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.resource_names_via_by_interaction_type_and_data_model_and_resource" title="pypath.core.network.Network.resource_names_via_by_interaction_type_and_data_model_and_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">resource_names_via_by_interaction_type_and_data_model_and_resource</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.resource_names_via_by_reference" title="pypath.core.network.Network.resource_names_via_by_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">resource_names_via_by_reference</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.resource_names_via_by_resource" title="pypath.core.network.Network.resource_names_via_by_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">resource_names_via_by_resource</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.resources" title="pypath.core.network.Network.resources"><code class="xref py py-obj docutils literal notranslate"><span class="pre">resources</span></code></a></p></td>
+<td><p>Returns a set of all resources.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.resources_by_data_model" title="pypath.core.network.Network.resources_by_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">resources_by_data_model</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.resources_by_interaction_type" title="pypath.core.network.Network.resources_by_interaction_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">resources_by_interaction_type</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.resources_by_interaction_type_and_data_model" title="pypath.core.network.Network.resources_by_interaction_type_and_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">resources_by_interaction_type_and_data_model</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.resources_by_interaction_type_and_data_model_and_resource" title="pypath.core.network.Network.resources_by_interaction_type_and_data_model_and_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">resources_by_interaction_type_and_data_model_and_resource</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.resources_by_reference" title="pypath.core.network.Network.resources_by_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">resources_by_reference</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.resources_by_resource" title="pypath.core.network.Network.resources_by_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">resources_by_resource</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.resources_via_by_data_model" title="pypath.core.network.Network.resources_via_by_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">resources_via_by_data_model</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.resources_via_by_interaction_type" title="pypath.core.network.Network.resources_via_by_interaction_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">resources_via_by_interaction_type</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.resources_via_by_interaction_type_and_data_model" title="pypath.core.network.Network.resources_via_by_interaction_type_and_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">resources_via_by_interaction_type_and_data_model</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.resources_via_by_interaction_type_and_data_model_and_resource" title="pypath.core.network.Network.resources_via_by_interaction_type_and_data_model_and_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">resources_via_by_interaction_type_and_data_model_and_resource</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.resources_via_by_reference" title="pypath.core.network.Network.resources_via_by_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">resources_via_by_reference</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.resources_via_by_resource" title="pypath.core.network.Network.resources_via_by_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">resources_via_by_resource</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.small_molecule_identifiers_by_data_model" title="pypath.core.network.Network.small_molecule_identifiers_by_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">small_molecule_identifiers_by_data_model</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.small_molecule_identifiers_by_interaction_type" title="pypath.core.network.Network.small_molecule_identifiers_by_interaction_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">small_molecule_identifiers_by_interaction_type</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.small_molecule_identifiers_by_interaction_type_and_data_model" title="pypath.core.network.Network.small_molecule_identifiers_by_interaction_type_and_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">small_molecule_identifiers_by_interaction_type_and_data_model</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.small_molecule_identifiers_by_interaction_type_and_data_model_and_resource" title="pypath.core.network.Network.small_molecule_identifiers_by_interaction_type_and_data_model_and_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">small_molecule_identifiers_by_interaction_type_and_data_model_and_resource</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.small_molecule_identifiers_by_reference" title="pypath.core.network.Network.small_molecule_identifiers_by_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">small_molecule_identifiers_by_reference</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.small_molecule_identifiers_by_resource" title="pypath.core.network.Network.small_molecule_identifiers_by_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">small_molecule_identifiers_by_resource</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.small_molecule_labels_by_data_model" title="pypath.core.network.Network.small_molecule_labels_by_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">small_molecule_labels_by_data_model</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.small_molecule_labels_by_interaction_type" title="pypath.core.network.Network.small_molecule_labels_by_interaction_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">small_molecule_labels_by_interaction_type</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.small_molecule_labels_by_interaction_type_and_data_model" title="pypath.core.network.Network.small_molecule_labels_by_interaction_type_and_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">small_molecule_labels_by_interaction_type_and_data_model</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.small_molecule_labels_by_interaction_type_and_data_model_and_resource" title="pypath.core.network.Network.small_molecule_labels_by_interaction_type_and_data_model_and_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">small_molecule_labels_by_interaction_type_and_data_model_and_resource</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.small_molecule_labels_by_reference" title="pypath.core.network.Network.small_molecule_labels_by_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">small_molecule_labels_by_reference</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.small_molecule_labels_by_resource" title="pypath.core.network.Network.small_molecule_labels_by_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">small_molecule_labels_by_resource</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.small_molecules_by_data_model" title="pypath.core.network.Network.small_molecules_by_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">small_molecules_by_data_model</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.small_molecules_by_interaction_type" title="pypath.core.network.Network.small_molecules_by_interaction_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">small_molecules_by_interaction_type</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.small_molecules_by_interaction_type_and_data_model" title="pypath.core.network.Network.small_molecules_by_interaction_type_and_data_model"><code class="xref py py-obj docutils literal notranslate"><span class="pre">small_molecules_by_interaction_type_and_data_model</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.small_molecules_by_interaction_type_and_data_model_and_resource" title="pypath.core.network.Network.small_molecules_by_interaction_type_and_data_model_and_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">small_molecules_by_interaction_type_and_data_model_and_resource</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.small_molecules_by_reference" title="pypath.core.network.Network.small_molecules_by_reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">small_molecules_by_reference</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.small_molecules_by_resource" title="pypath.core.network.Network.small_molecules_by_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">small_molecules_by_resource</span></code></a></p></td>
+<td><p>Built-in immutable sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.suppressed_by" title="pypath.core.network.Network.suppressed_by"><code class="xref py py-obj docutils literal notranslate"><span class="pre">suppressed_by</span></code></a></p></td>
+<td><p>arg str,Entity,list,set,tuple,EntityList entity:</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.suppresses" title="pypath.core.network.Network.suppresses"><code class="xref py py-obj docutils literal notranslate"><span class="pre">suppresses</span></code></a></p></td>
+<td><p>arg str,Entity,list,set,tuple,EntityList entity:</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.transcriptionally_activated_by" title="pypath.core.network.Network.transcriptionally_activated_by"><code class="xref py py-obj docutils literal notranslate"><span class="pre">transcriptionally_activated_by</span></code></a></p></td>
+<td><p>arg str,Entity,list,set,tuple,EntityList entity:</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.transcriptionally_activates" title="pypath.core.network.Network.transcriptionally_activates"><code class="xref py py-obj docutils literal notranslate"><span class="pre">transcriptionally_activates</span></code></a></p></td>
+<td><p>arg str,Entity,list,set,tuple,EntityList entity:</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.transcriptionally_regulated_by" title="pypath.core.network.Network.transcriptionally_regulated_by"><code class="xref py py-obj docutils literal notranslate"><span class="pre">transcriptionally_regulated_by</span></code></a></p></td>
+<td><p>arg str,Entity,list,set,tuple,EntityList entity:</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.transcriptionally_regulates" title="pypath.core.network.Network.transcriptionally_regulates"><code class="xref py py-obj docutils literal notranslate"><span class="pre">transcriptionally_regulates</span></code></a></p></td>
+<td><p>arg str,Entity,list,set,tuple,EntityList entity:</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.Network.transcriptionally_suppressed_by" title="pypath.core.network.Network.transcriptionally_suppressed_by"><code class="xref py py-obj docutils literal notranslate"><span class="pre">transcriptionally_suppressed_by</span></code></a></p></td>
+<td><p>arg str,Entity,list,set,tuple,EntityList entity:</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.Network.transcriptionally_suppresses" title="pypath.core.network.Network.transcriptionally_suppresses"><code class="xref py py-obj docutils literal notranslate"><span class="pre">transcriptionally_suppresses</span></code></a></p></td>
+<td><p>arg str,Entity,list,set,tuple,EntityList entity:</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">vcount</span></code></p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.activated_by">
+<span class="sig-name descname"><span class="pre">activated_by</span></span><a class="headerlink" href="#pypath.core.network.Network.activated_by" title="Link to this definition">§</a></dt>
+<dd><dl class="simple">
+<dt>arg str,Entity,list,set,tuple,EntityList entity:</dt><dd><p>An identifier or label of a molecular entity or an
+<code class="xref py py-class docutils literal notranslate"><span class="pre">Entity</span></code> object. Alternatively an iterator with the
+elements of any of the types valid for a single entity argument,
+e.g. a list of gene symbols.</p>
+</dd>
+</dl>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><p><strong>mode</strong> (<em>str</em>) – Mode of counting the interactions: <cite>IN</cite>, <cite>OUT</cite> or <cite>ALL</cite> , whether
+to consider incoming, outgoing or all edges, respectively,
+respective to the <cite>node defined in `entity`</cite>.</p>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p><code class="xref py py-class docutils literal notranslate"><span class="pre">EntityList</span></code> object containing the partners having
+interactions to the queried node(s) matching all the criteria.
+If <code class="docutils literal notranslate"><span class="pre">entity</span></code> doesn’t present in the network the returned
+<code class="docutils literal notranslate"><span class="pre">EntityList</span></code> will be empty just like if no interaction matches
+the criteria.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.activates">
+<span class="sig-name descname"><span class="pre">activates</span></span><a class="headerlink" href="#pypath.core.network.Network.activates" title="Link to this definition">§</a></dt>
+<dd><dl class="simple">
+<dt>arg str,Entity,list,set,tuple,EntityList entity:</dt><dd><p>An identifier or label of a molecular entity or an
+<code class="xref py py-class docutils literal notranslate"><span class="pre">Entity</span></code> object. Alternatively an iterator with the
+elements of any of the types valid for a single entity argument,
+e.g. a list of gene symbols.</p>
+</dd>
+</dl>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><p><strong>mode</strong> (<em>str</em>) – Mode of counting the interactions: <cite>IN</cite>, <cite>OUT</cite> or <cite>ALL</cite> , whether
+to consider incoming, outgoing or all edges, respectively,
+respective to the <cite>node defined in `entity`</cite>.</p>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p><code class="xref py py-class docutils literal notranslate"><span class="pre">EntityList</span></code> object containing the partners having
+interactions to the queried node(s) matching all the criteria.
+If <code class="docutils literal notranslate"><span class="pre">entity</span></code> doesn’t present in the network the returned
+<code class="docutils literal notranslate"><span class="pre">EntityList</span></code> will be empty just like if no interaction matches
+the criteria.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.network.Network.add_interaction">
+<span class="sig-name descname"><span class="pre">add_interaction</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">interaction</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">attrs</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">only_directions</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/network.html#Network.add_interaction"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.network.Network.add_interaction" title="Link to this definition">§</a></dt>
+<dd><p>Adds a ready <code class="docutils literal notranslate"><span class="pre">pypath.interaction.Interaction</span></code> object to the network.
+If an interaction between the two endpoints already exists, the
+interactions will be merged: this stands for the directions, signs,
+evidences and other attributes.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>interaction</strong> (<a class="reference internal" href="pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction" title="pypath.core.interaction.Interaction"><em>interaction.Interaction</em></a>) – A <code class="docutils literal notranslate"><span class="pre">pypath.interaction.Interaction</span></code> object.</p></li>
+<li><p><strong>attrs</strong> (<em>NoneType</em><em>,</em><em>dict</em>) – Optional, a dictionary of extra (usually resource specific)
+attributes.</p></li>
+<li><p><strong>only_directions</strong> (<em>bool</em>) – If the interaction between the two endpoints does not exist it
+won’t be added to the network. Otherwise all attributes
+(direction, effect sign, evidences, etc) will be merged to the
+existing interaction. Apart from the endpoints also the
+<code class="docutils literal notranslate"><span class="pre">interaction_type</span></code> of the existing interaction has to match the
+interaction added here.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.network.Network.add_node">
+<span class="sig-name descname"><span class="pre">add_node</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">attrs</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">add</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/network.html#Network.add_node"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.network.Network.add_node" title="Link to this definition">§</a></dt>
+<dd><p>Adds a molecular entity to the py:attr:<code class="docutils literal notranslate"><span class="pre">nodes</span></code> and
+py:attr:<code class="docutils literal notranslate"><span class="pre">nodes_by_label</span></code> dictionaries.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>entity</strong> (<a class="reference internal" href="pypath.core.entity.Entity.html#pypath.core.entity.Entity" title="pypath.core.entity.Entity"><em>entity.Entity</em></a>) – An object representing a molecular entity.</p></li>
+<li><p><strong>attrs</strong> (<em>NoneType</em><em>,</em><em>dict</em>) – Optional extra attributes to be assigned to the entity.</p></li>
+<li><p><strong>add</strong> (<em>bool</em>) – Whether to add a new molecular entity to the network if it does
+not exist yet. If <code class="docutils literal notranslate"><span class="pre">False</span></code> will only update attributes for
+existing entities otherwise will do nothing.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.collect_complex_identifiers">
+<span class="sig-name descname"><span class="pre">collect_complex_identifiers</span></span><a class="headerlink" href="#pypath.core.network.Network.collect_complex_identifiers" title="Link to this definition">§</a></dt>
+<dd><p>Builds a comprehensive collection of <cite>complex_identifiers</cite> entities across the network, counts unique and shared objects by resource, data model and interaction types.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.collect_complex_labels">
+<span class="sig-name descname"><span class="pre">collect_complex_labels</span></span><a class="headerlink" href="#pypath.core.network.Network.collect_complex_labels" title="Link to this definition">§</a></dt>
+<dd><p>Builds a comprehensive collection of <cite>complex_labels</cite> entities across the network, counts unique and shared objects by resource, data model and interaction types.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.collect_complexes">
+<span class="sig-name descname"><span class="pre">collect_complexes</span></span><a class="headerlink" href="#pypath.core.network.Network.collect_complexes" title="Link to this definition">§</a></dt>
+<dd><p>Builds a comprehensive collection of <cite>complexes</cite> entities across the network, counts unique and shared objects by resource, data model and interaction types.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.collect_curation_effort">
+<span class="sig-name descname"><span class="pre">collect_curation_effort</span></span><a class="headerlink" href="#pypath.core.network.Network.collect_curation_effort" title="Link to this definition">§</a></dt>
+<dd><p>Builds a comprehensive collection of <cite>curation_effort</cite> entities across the network, counts unique and shared objects by resource, data model and interaction types.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.collect_data_models">
+<span class="sig-name descname"><span class="pre">collect_data_models</span></span><a class="headerlink" href="#pypath.core.network.Network.collect_data_models" title="Link to this definition">§</a></dt>
+<dd><p>Builds a comprehensive collection of <cite>data_models</cite> entities across the network, counts unique and shared objects by resource, data model and interaction types.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.collect_datasets">
+<span class="sig-name descname"><span class="pre">collect_datasets</span></span><a class="headerlink" href="#pypath.core.network.Network.collect_datasets" title="Link to this definition">§</a></dt>
+<dd><p>Builds a comprehensive collection of <cite>datasets</cite> entities across the network, counts unique and shared objects by resource, data model and interaction types.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.collect_degrees_directed">
+<span class="sig-name descname"><span class="pre">collect_degrees_directed</span></span><a class="headerlink" href="#pypath.core.network.Network.collect_degrees_directed" title="Link to this definition">§</a></dt>
+<dd><p>Builds a comprehensive collection of <cite>degrees_directed</cite> entities across the network, counts unique and shared objects by resource, data model and interaction types.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.collect_degrees_directed_in">
+<span class="sig-name descname"><span class="pre">collect_degrees_directed_in</span></span><a class="headerlink" href="#pypath.core.network.Network.collect_degrees_directed_in" title="Link to this definition">§</a></dt>
+<dd><p>Builds a comprehensive collection of <cite>degrees_directed_in</cite> entities across the network, counts unique and shared objects by resource, data model and interaction types.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.collect_degrees_directed_out">
+<span class="sig-name descname"><span class="pre">collect_degrees_directed_out</span></span><a class="headerlink" href="#pypath.core.network.Network.collect_degrees_directed_out" title="Link to this definition">§</a></dt>
+<dd><p>Builds a comprehensive collection of <cite>degrees_directed_out</cite> entities across the network, counts unique and shared objects by resource, data model and interaction types.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.collect_degrees_negative">
+<span class="sig-name descname"><span class="pre">collect_degrees_negative</span></span><a class="headerlink" href="#pypath.core.network.Network.collect_degrees_negative" title="Link to this definition">§</a></dt>
+<dd><p>Builds a comprehensive collection of <cite>degrees_negative</cite> entities across the network, counts unique and shared objects by resource, data model and interaction types.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.collect_degrees_negative_in">
+<span class="sig-name descname"><span class="pre">collect_degrees_negative_in</span></span><a class="headerlink" href="#pypath.core.network.Network.collect_degrees_negative_in" title="Link to this definition">§</a></dt>
+<dd><p>Builds a comprehensive collection of <cite>degrees_negative_in</cite> entities across the network, counts unique and shared objects by resource, data model and interaction types.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.collect_degrees_negative_out">
+<span class="sig-name descname"><span class="pre">collect_degrees_negative_out</span></span><a class="headerlink" href="#pypath.core.network.Network.collect_degrees_negative_out" title="Link to this definition">§</a></dt>
+<dd><p>Builds a comprehensive collection of <cite>degrees_negative_out</cite> entities across the network, counts unique and shared objects by resource, data model and interaction types.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.collect_degrees_non_directed">
+<span class="sig-name descname"><span class="pre">collect_degrees_non_directed</span></span><a class="headerlink" href="#pypath.core.network.Network.collect_degrees_non_directed" title="Link to this definition">§</a></dt>
+<dd><p>Builds a comprehensive collection of <cite>degrees_non_directed</cite> entities across the network, counts unique and shared objects by resource, data model and interaction types.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.collect_degrees_positive">
+<span class="sig-name descname"><span class="pre">collect_degrees_positive</span></span><a class="headerlink" href="#pypath.core.network.Network.collect_degrees_positive" title="Link to this definition">§</a></dt>
+<dd><p>Builds a comprehensive collection of <cite>degrees_positive</cite> entities across the network, counts unique and shared objects by resource, data model and interaction types.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.collect_degrees_positive_in">
+<span class="sig-name descname"><span class="pre">collect_degrees_positive_in</span></span><a class="headerlink" href="#pypath.core.network.Network.collect_degrees_positive_in" title="Link to this definition">§</a></dt>
+<dd><p>Builds a comprehensive collection of <cite>degrees_positive_in</cite> entities across the network, counts unique and shared objects by resource, data model and interaction types.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.collect_degrees_positive_out">
+<span class="sig-name descname"><span class="pre">collect_degrees_positive_out</span></span><a class="headerlink" href="#pypath.core.network.Network.collect_degrees_positive_out" title="Link to this definition">§</a></dt>
+<dd><p>Builds a comprehensive collection of <cite>degrees_positive_out</cite> entities across the network, counts unique and shared objects by resource, data model and interaction types.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.collect_degrees_signed">
+<span class="sig-name descname"><span class="pre">collect_degrees_signed</span></span><a class="headerlink" href="#pypath.core.network.Network.collect_degrees_signed" title="Link to this definition">§</a></dt>
+<dd><p>Builds a comprehensive collection of <cite>degrees_signed</cite> entities across the network, counts unique and shared objects by resource, data model and interaction types.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.collect_degrees_signed_in">
+<span class="sig-name descname"><span class="pre">collect_degrees_signed_in</span></span><a class="headerlink" href="#pypath.core.network.Network.collect_degrees_signed_in" title="Link to this definition">§</a></dt>
+<dd><p>Builds a comprehensive collection of <cite>degrees_signed_in</cite> entities across the network, counts unique and shared objects by resource, data model and interaction types.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.collect_degrees_signed_out">
+<span class="sig-name descname"><span class="pre">collect_degrees_signed_out</span></span><a class="headerlink" href="#pypath.core.network.Network.collect_degrees_signed_out" title="Link to this definition">§</a></dt>
+<dd><p>Builds a comprehensive collection of <cite>degrees_signed_out</cite> entities across the network, counts unique and shared objects by resource, data model and interaction types.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.collect_degrees_undirected">
+<span class="sig-name descname"><span class="pre">collect_degrees_undirected</span></span><a class="headerlink" href="#pypath.core.network.Network.collect_degrees_undirected" title="Link to this definition">§</a></dt>
+<dd><p>Builds a comprehensive collection of <cite>degrees_undirected</cite> entities across the network, counts unique and shared objects by resource, data model and interaction types.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.collect_entities">
+<span class="sig-name descname"><span class="pre">collect_entities</span></span><a class="headerlink" href="#pypath.core.network.Network.collect_entities" title="Link to this definition">§</a></dt>
+<dd><p>Builds a comprehensive collection of <cite>entities</cite> entities across the network, counts unique and shared objects by resource, data model and interaction types.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.collect_evidences">
+<span class="sig-name descname"><span class="pre">collect_evidences</span></span><a class="headerlink" href="#pypath.core.network.Network.collect_evidences" title="Link to this definition">§</a></dt>
+<dd><p>Builds a comprehensive collection of <cite>evidences</cite> entities across the network, counts unique and shared objects by resource, data model and interaction types.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.collect_identifiers">
+<span class="sig-name descname"><span class="pre">collect_identifiers</span></span><a class="headerlink" href="#pypath.core.network.Network.collect_identifiers" title="Link to this definition">§</a></dt>
+<dd><p>Builds a comprehensive collection of <cite>identifiers</cite> entities across the network, counts unique and shared objects by resource, data model and interaction types.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.collect_interaction_types">
+<span class="sig-name descname"><span class="pre">collect_interaction_types</span></span><a class="headerlink" href="#pypath.core.network.Network.collect_interaction_types" title="Link to this definition">§</a></dt>
+<dd><p>Builds a comprehensive collection of <cite>interaction_types</cite> entities across the network, counts unique and shared objects by resource, data model and interaction types.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.collect_interactions">
+<span class="sig-name descname"><span class="pre">collect_interactions</span></span><a class="headerlink" href="#pypath.core.network.Network.collect_interactions" title="Link to this definition">§</a></dt>
+<dd><p>Builds a comprehensive collection of <cite>interactions</cite> entities across the network, counts unique and shared objects by resource, data model and interaction types.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.collect_interactions_0">
+<span class="sig-name descname"><span class="pre">collect_interactions_0</span></span><a class="headerlink" href="#pypath.core.network.Network.collect_interactions_0" title="Link to this definition">§</a></dt>
+<dd><p>Builds a comprehensive collection of <cite>interactions_0</cite> entities across the network, counts unique and shared objects by resource, data model and interaction types.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.collect_interactions_directed">
+<span class="sig-name descname"><span class="pre">collect_interactions_directed</span></span><a class="headerlink" href="#pypath.core.network.Network.collect_interactions_directed" title="Link to this definition">§</a></dt>
+<dd><p>Builds a comprehensive collection of <cite>interactions_directed</cite> entities across the network, counts unique and shared objects by resource, data model and interaction types.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.collect_interactions_mutual">
+<span class="sig-name descname"><span class="pre">collect_interactions_mutual</span></span><a class="headerlink" href="#pypath.core.network.Network.collect_interactions_mutual" title="Link to this definition">§</a></dt>
+<dd><p>Builds a comprehensive collection of <cite>interactions_mutual</cite> entities across the network, counts unique and shared objects by resource, data model and interaction types.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.collect_interactions_negative">
+<span class="sig-name descname"><span class="pre">collect_interactions_negative</span></span><a class="headerlink" href="#pypath.core.network.Network.collect_interactions_negative" title="Link to this definition">§</a></dt>
+<dd><p>Builds a comprehensive collection of <cite>interactions_negative</cite> entities across the network, counts unique and shared objects by resource, data model and interaction types.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.collect_interactions_non_directed">
+<span class="sig-name descname"><span class="pre">collect_interactions_non_directed</span></span><a class="headerlink" href="#pypath.core.network.Network.collect_interactions_non_directed" title="Link to this definition">§</a></dt>
+<dd><p>Builds a comprehensive collection of <cite>interactions_non_directed</cite> entities across the network, counts unique and shared objects by resource, data model and interaction types.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.collect_interactions_non_directed_0">
+<span class="sig-name descname"><span class="pre">collect_interactions_non_directed_0</span></span><a class="headerlink" href="#pypath.core.network.Network.collect_interactions_non_directed_0" title="Link to this definition">§</a></dt>
+<dd><p>Builds a comprehensive collection of <cite>interactions_non_directed_0</cite> entities across the network, counts unique and shared objects by resource, data model and interaction types.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.collect_interactions_positive">
+<span class="sig-name descname"><span class="pre">collect_interactions_positive</span></span><a class="headerlink" href="#pypath.core.network.Network.collect_interactions_positive" title="Link to this definition">§</a></dt>
+<dd><p>Builds a comprehensive collection of <cite>interactions_positive</cite> entities across the network, counts unique and shared objects by resource, data model and interaction types.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.collect_interactions_signed">
+<span class="sig-name descname"><span class="pre">collect_interactions_signed</span></span><a class="headerlink" href="#pypath.core.network.Network.collect_interactions_signed" title="Link to this definition">§</a></dt>
+<dd><p>Builds a comprehensive collection of <cite>interactions_signed</cite> entities across the network, counts unique and shared objects by resource, data model and interaction types.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.collect_interactions_undirected">
+<span class="sig-name descname"><span class="pre">collect_interactions_undirected</span></span><a class="headerlink" href="#pypath.core.network.Network.collect_interactions_undirected" title="Link to this definition">§</a></dt>
+<dd><p>Builds a comprehensive collection of <cite>interactions_undirected</cite> entities across the network, counts unique and shared objects by resource, data model and interaction types.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.collect_interactions_undirected_0">
+<span class="sig-name descname"><span class="pre">collect_interactions_undirected_0</span></span><a class="headerlink" href="#pypath.core.network.Network.collect_interactions_undirected_0" title="Link to this definition">§</a></dt>
+<dd><p>Builds a comprehensive collection of <cite>interactions_undirected_0</cite> entities across the network, counts unique and shared objects by resource, data model and interaction types.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.collect_labels">
+<span class="sig-name descname"><span class="pre">collect_labels</span></span><a class="headerlink" href="#pypath.core.network.Network.collect_labels" title="Link to this definition">§</a></dt>
+<dd><p>Builds a comprehensive collection of <cite>labels</cite> entities across the network, counts unique and shared objects by resource, data model and interaction types.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.collect_lncrna_identifiers">
+<span class="sig-name descname"><span class="pre">collect_lncrna_identifiers</span></span><a class="headerlink" href="#pypath.core.network.Network.collect_lncrna_identifiers" title="Link to this definition">§</a></dt>
+<dd><p>Builds a comprehensive collection of <cite>lncrna_identifiers</cite> entities across the network, counts unique and shared objects by resource, data model and interaction types.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.collect_lncrna_labels">
+<span class="sig-name descname"><span class="pre">collect_lncrna_labels</span></span><a class="headerlink" href="#pypath.core.network.Network.collect_lncrna_labels" title="Link to this definition">§</a></dt>
+<dd><p>Builds a comprehensive collection of <cite>lncrna_labels</cite> entities across the network, counts unique and shared objects by resource, data model and interaction types.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.collect_lncrnas">
+<span class="sig-name descname"><span class="pre">collect_lncrnas</span></span><a class="headerlink" href="#pypath.core.network.Network.collect_lncrnas" title="Link to this definition">§</a></dt>
+<dd><p>Builds a comprehensive collection of <cite>lncrnas</cite> entities across the network, counts unique and shared objects by resource, data model and interaction types.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.collect_mirna_identifiers">
+<span class="sig-name descname"><span class="pre">collect_mirna_identifiers</span></span><a class="headerlink" href="#pypath.core.network.Network.collect_mirna_identifiers" title="Link to this definition">§</a></dt>
+<dd><p>Builds a comprehensive collection of <cite>mirna_identifiers</cite> entities across the network, counts unique and shared objects by resource, data model and interaction types.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.collect_mirna_labels">
+<span class="sig-name descname"><span class="pre">collect_mirna_labels</span></span><a class="headerlink" href="#pypath.core.network.Network.collect_mirna_labels" title="Link to this definition">§</a></dt>
+<dd><p>Builds a comprehensive collection of <cite>mirna_labels</cite> entities across the network, counts unique and shared objects by resource, data model and interaction types.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.collect_mirnas">
+<span class="sig-name descname"><span class="pre">collect_mirnas</span></span><a class="headerlink" href="#pypath.core.network.Network.collect_mirnas" title="Link to this definition">§</a></dt>
+<dd><p>Builds a comprehensive collection of <cite>mirnas</cite> entities across the network, counts unique and shared objects by resource, data model and interaction types.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.collect_protein_identifiers">
+<span class="sig-name descname"><span class="pre">collect_protein_identifiers</span></span><a class="headerlink" href="#pypath.core.network.Network.collect_protein_identifiers" title="Link to this definition">§</a></dt>
+<dd><p>Builds a comprehensive collection of <cite>protein_identifiers</cite> entities across the network, counts unique and shared objects by resource, data model and interaction types.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.collect_protein_labels">
+<span class="sig-name descname"><span class="pre">collect_protein_labels</span></span><a class="headerlink" href="#pypath.core.network.Network.collect_protein_labels" title="Link to this definition">§</a></dt>
+<dd><p>Builds a comprehensive collection of <cite>protein_labels</cite> entities across the network, counts unique and shared objects by resource, data model and interaction types.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.collect_proteins">
+<span class="sig-name descname"><span class="pre">collect_proteins</span></span><a class="headerlink" href="#pypath.core.network.Network.collect_proteins" title="Link to this definition">§</a></dt>
+<dd><p>Builds a comprehensive collection of <cite>proteins</cite> entities across the network, counts unique and shared objects by resource, data model and interaction types.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.collect_references">
+<span class="sig-name descname"><span class="pre">collect_references</span></span><a class="headerlink" href="#pypath.core.network.Network.collect_references" title="Link to this definition">§</a></dt>
+<dd><p>Builds a comprehensive collection of <cite>references</cite> entities across the network, counts unique and shared objects by resource, data model and interaction types.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.collect_resource_names">
+<span class="sig-name descname"><span class="pre">collect_resource_names</span></span><a class="headerlink" href="#pypath.core.network.Network.collect_resource_names" title="Link to this definition">§</a></dt>
+<dd><p>Builds a comprehensive collection of <cite>resource_names</cite> entities across the network, counts unique and shared objects by resource, data model and interaction types.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.collect_resource_names_via">
+<span class="sig-name descname"><span class="pre">collect_resource_names_via</span></span><a class="headerlink" href="#pypath.core.network.Network.collect_resource_names_via" title="Link to this definition">§</a></dt>
+<dd><p>Builds a comprehensive collection of <cite>resource_names_via</cite> entities across the network, counts unique and shared objects by resource, data model and interaction types.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.collect_resources">
+<span class="sig-name descname"><span class="pre">collect_resources</span></span><a class="headerlink" href="#pypath.core.network.Network.collect_resources" title="Link to this definition">§</a></dt>
+<dd><p>Builds a comprehensive collection of <cite>resources</cite> entities across the network, counts unique and shared objects by resource, data model and interaction types.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.collect_resources_via">
+<span class="sig-name descname"><span class="pre">collect_resources_via</span></span><a class="headerlink" href="#pypath.core.network.Network.collect_resources_via" title="Link to this definition">§</a></dt>
+<dd><p>Builds a comprehensive collection of <cite>resources_via</cite> entities across the network, counts unique and shared objects by resource, data model and interaction types.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.collect_small_molecule_identifiers">
+<span class="sig-name descname"><span class="pre">collect_small_molecule_identifiers</span></span><a class="headerlink" href="#pypath.core.network.Network.collect_small_molecule_identifiers" title="Link to this definition">§</a></dt>
+<dd><p>Builds a comprehensive collection of <cite>small_molecule_identifiers</cite> entities across the network, counts unique and shared objects by resource, data model and interaction types.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.collect_small_molecule_labels">
+<span class="sig-name descname"><span class="pre">collect_small_molecule_labels</span></span><a class="headerlink" href="#pypath.core.network.Network.collect_small_molecule_labels" title="Link to this definition">§</a></dt>
+<dd><p>Builds a comprehensive collection of <cite>small_molecule_labels</cite> entities across the network, counts unique and shared objects by resource, data model and interaction types.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.collect_small_molecules">
+<span class="sig-name descname"><span class="pre">collect_small_molecules</span></span><a class="headerlink" href="#pypath.core.network.Network.collect_small_molecules" title="Link to this definition">§</a></dt>
+<dd><p>Builds a comprehensive collection of <cite>small_molecules</cite> entities across the network, counts unique and shared objects by resource, data model and interaction types.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.network.Network.collectri">
+<em class="property"><span class="pre">classmethod</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">collectri</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/network.html#Network.collectri"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.network.Network.collectri" title="Link to this definition">§</a></dt>
+<dd><p>Initializes a new <code class="docutils literal notranslate"><span class="pre">Network</span></code> object with loading the transcriptional
+regulation network from CollecTRI.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.complex_identifiers_by_data_model">
+<span class="sig-name descname"><span class="pre">complex_identifiers_by_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.complex_identifiers_by_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.complex_identifiers_by_interaction_type">
+<span class="sig-name descname"><span class="pre">complex_identifiers_by_interaction_type</span></span><a class="headerlink" href="#pypath.core.network.Network.complex_identifiers_by_interaction_type" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.complex_identifiers_by_interaction_type_and_data_model">
+<span class="sig-name descname"><span class="pre">complex_identifiers_by_interaction_type_and_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.complex_identifiers_by_interaction_type_and_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.complex_identifiers_by_interaction_type_and_data_model_and_resource">
+<span class="sig-name descname"><span class="pre">complex_identifiers_by_interaction_type_and_data_model_and_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.complex_identifiers_by_interaction_type_and_data_model_and_resource" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.complex_identifiers_by_reference">
+<span class="sig-name descname"><span class="pre">complex_identifiers_by_reference</span></span><a class="headerlink" href="#pypath.core.network.Network.complex_identifiers_by_reference" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.complex_identifiers_by_resource">
+<span class="sig-name descname"><span class="pre">complex_identifiers_by_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.complex_identifiers_by_resource" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.complex_labels_by_data_model">
+<span class="sig-name descname"><span class="pre">complex_labels_by_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.complex_labels_by_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.complex_labels_by_interaction_type">
+<span class="sig-name descname"><span class="pre">complex_labels_by_interaction_type</span></span><a class="headerlink" href="#pypath.core.network.Network.complex_labels_by_interaction_type" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.complex_labels_by_interaction_type_and_data_model">
+<span class="sig-name descname"><span class="pre">complex_labels_by_interaction_type_and_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.complex_labels_by_interaction_type_and_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.complex_labels_by_interaction_type_and_data_model_and_resource">
+<span class="sig-name descname"><span class="pre">complex_labels_by_interaction_type_and_data_model_and_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.complex_labels_by_interaction_type_and_data_model_and_resource" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.complex_labels_by_reference">
+<span class="sig-name descname"><span class="pre">complex_labels_by_reference</span></span><a class="headerlink" href="#pypath.core.network.Network.complex_labels_by_reference" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.complex_labels_by_resource">
+<span class="sig-name descname"><span class="pre">complex_labels_by_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.complex_labels_by_resource" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.complexes_by_data_model">
+<span class="sig-name descname"><span class="pre">complexes_by_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.complexes_by_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.complexes_by_interaction_type">
+<span class="sig-name descname"><span class="pre">complexes_by_interaction_type</span></span><a class="headerlink" href="#pypath.core.network.Network.complexes_by_interaction_type" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.complexes_by_interaction_type_and_data_model">
+<span class="sig-name descname"><span class="pre">complexes_by_interaction_type_and_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.complexes_by_interaction_type_and_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.complexes_by_interaction_type_and_data_model_and_resource">
+<span class="sig-name descname"><span class="pre">complexes_by_interaction_type_and_data_model_and_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.complexes_by_interaction_type_and_data_model_and_resource" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.complexes_by_reference">
+<span class="sig-name descname"><span class="pre">complexes_by_reference</span></span><a class="headerlink" href="#pypath.core.network.Network.complexes_by_reference" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.complexes_by_resource">
+<span class="sig-name descname"><span class="pre">complexes_by_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.complexes_by_resource" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_activated_by">
+<span class="sig-name descname"><span class="pre">count_activated_by</span></span><a class="headerlink" href="#pypath.core.network.Network.count_activated_by" title="Link to this definition">§</a></dt>
+<dd><p>Returns the count of the interacting partners for one or more
+entities according to the specified criteria.
+Please refer to the docs of the <code class="docutils literal notranslate"><span class="pre">partners</span></code> method.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_activates">
+<span class="sig-name descname"><span class="pre">count_activates</span></span><a class="headerlink" href="#pypath.core.network.Network.count_activates" title="Link to this definition">§</a></dt>
+<dd><p>Returns the count of the interacting partners for one or more
+entities according to the specified criteria.
+Please refer to the docs of the <code class="docutils literal notranslate"><span class="pre">partners</span></code> method.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_complex_identifiers">
+<span class="sig-name descname"><span class="pre">count_complex_identifiers</span></span><a class="headerlink" href="#pypath.core.network.Network.count_complex_identifiers" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_complex_identifiers_by_data_model">
+<span class="sig-name descname"><span class="pre">count_complex_identifiers_by_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.count_complex_identifiers_by_data_model" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_complex_identifiers_by_interaction_type">
+<span class="sig-name descname"><span class="pre">count_complex_identifiers_by_interaction_type</span></span><a class="headerlink" href="#pypath.core.network.Network.count_complex_identifiers_by_interaction_type" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_complex_identifiers_by_interaction_type_and_data_model">
+<span class="sig-name descname"><span class="pre">count_complex_identifiers_by_interaction_type_and_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.count_complex_identifiers_by_interaction_type_and_data_model" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_complex_identifiers_by_interaction_type_and_data_model_and_resource">
+<span class="sig-name descname"><span class="pre">count_complex_identifiers_by_interaction_type_and_data_model_and_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.count_complex_identifiers_by_interaction_type_and_data_model_and_resource" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_complex_identifiers_by_reference">
+<span class="sig-name descname"><span class="pre">count_complex_identifiers_by_reference</span></span><a class="headerlink" href="#pypath.core.network.Network.count_complex_identifiers_by_reference" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_complex_identifiers_by_resource">
+<span class="sig-name descname"><span class="pre">count_complex_identifiers_by_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.count_complex_identifiers_by_resource" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_complex_labels">
+<span class="sig-name descname"><span class="pre">count_complex_labels</span></span><a class="headerlink" href="#pypath.core.network.Network.count_complex_labels" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_complex_labels_by_data_model">
+<span class="sig-name descname"><span class="pre">count_complex_labels_by_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.count_complex_labels_by_data_model" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_complex_labels_by_interaction_type">
+<span class="sig-name descname"><span class="pre">count_complex_labels_by_interaction_type</span></span><a class="headerlink" href="#pypath.core.network.Network.count_complex_labels_by_interaction_type" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_complex_labels_by_interaction_type_and_data_model">
+<span class="sig-name descname"><span class="pre">count_complex_labels_by_interaction_type_and_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.count_complex_labels_by_interaction_type_and_data_model" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_complex_labels_by_interaction_type_and_data_model_and_resource">
+<span class="sig-name descname"><span class="pre">count_complex_labels_by_interaction_type_and_data_model_and_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.count_complex_labels_by_interaction_type_and_data_model_and_resource" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_complex_labels_by_reference">
+<span class="sig-name descname"><span class="pre">count_complex_labels_by_reference</span></span><a class="headerlink" href="#pypath.core.network.Network.count_complex_labels_by_reference" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_complex_labels_by_resource">
+<span class="sig-name descname"><span class="pre">count_complex_labels_by_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.count_complex_labels_by_resource" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_complexes">
+<span class="sig-name descname"><span class="pre">count_complexes</span></span><a class="headerlink" href="#pypath.core.network.Network.count_complexes" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_complexes_by_data_model">
+<span class="sig-name descname"><span class="pre">count_complexes_by_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.count_complexes_by_data_model" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_complexes_by_interaction_type">
+<span class="sig-name descname"><span class="pre">count_complexes_by_interaction_type</span></span><a class="headerlink" href="#pypath.core.network.Network.count_complexes_by_interaction_type" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_complexes_by_interaction_type_and_data_model">
+<span class="sig-name descname"><span class="pre">count_complexes_by_interaction_type_and_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.count_complexes_by_interaction_type_and_data_model" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_complexes_by_interaction_type_and_data_model_and_resource">
+<span class="sig-name descname"><span class="pre">count_complexes_by_interaction_type_and_data_model_and_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.count_complexes_by_interaction_type_and_data_model_and_resource" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_complexes_by_reference">
+<span class="sig-name descname"><span class="pre">count_complexes_by_reference</span></span><a class="headerlink" href="#pypath.core.network.Network.count_complexes_by_reference" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_complexes_by_resource">
+<span class="sig-name descname"><span class="pre">count_complexes_by_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.count_complexes_by_resource" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_curation_effort">
+<span class="sig-name descname"><span class="pre">count_curation_effort</span></span><a class="headerlink" href="#pypath.core.network.Network.count_curation_effort" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_curation_effort_by_data_model">
+<span class="sig-name descname"><span class="pre">count_curation_effort_by_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.count_curation_effort_by_data_model" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_curation_effort_by_interaction_type">
+<span class="sig-name descname"><span class="pre">count_curation_effort_by_interaction_type</span></span><a class="headerlink" href="#pypath.core.network.Network.count_curation_effort_by_interaction_type" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_curation_effort_by_interaction_type_and_data_model">
+<span class="sig-name descname"><span class="pre">count_curation_effort_by_interaction_type_and_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.count_curation_effort_by_interaction_type_and_data_model" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_curation_effort_by_interaction_type_and_data_model_and_resource">
+<span class="sig-name descname"><span class="pre">count_curation_effort_by_interaction_type_and_data_model_and_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.count_curation_effort_by_interaction_type_and_data_model_and_resource" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_curation_effort_by_reference">
+<span class="sig-name descname"><span class="pre">count_curation_effort_by_reference</span></span><a class="headerlink" href="#pypath.core.network.Network.count_curation_effort_by_reference" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_curation_effort_by_resource">
+<span class="sig-name descname"><span class="pre">count_curation_effort_by_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.count_curation_effort_by_resource" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_data_models">
+<span class="sig-name descname"><span class="pre">count_data_models</span></span><a class="headerlink" href="#pypath.core.network.Network.count_data_models" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_data_models_by_data_model">
+<span class="sig-name descname"><span class="pre">count_data_models_by_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.count_data_models_by_data_model" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_data_models_by_interaction_type">
+<span class="sig-name descname"><span class="pre">count_data_models_by_interaction_type</span></span><a class="headerlink" href="#pypath.core.network.Network.count_data_models_by_interaction_type" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_data_models_by_interaction_type_and_data_model">
+<span class="sig-name descname"><span class="pre">count_data_models_by_interaction_type_and_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.count_data_models_by_interaction_type_and_data_model" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_data_models_by_interaction_type_and_data_model_and_resource">
+<span class="sig-name descname"><span class="pre">count_data_models_by_interaction_type_and_data_model_and_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.count_data_models_by_interaction_type_and_data_model_and_resource" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_data_models_by_reference">
+<span class="sig-name descname"><span class="pre">count_data_models_by_reference</span></span><a class="headerlink" href="#pypath.core.network.Network.count_data_models_by_reference" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_data_models_by_resource">
+<span class="sig-name descname"><span class="pre">count_data_models_by_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.count_data_models_by_resource" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_datasets">
+<span class="sig-name descname"><span class="pre">count_datasets</span></span><a class="headerlink" href="#pypath.core.network.Network.count_datasets" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_datasets_by_data_model">
+<span class="sig-name descname"><span class="pre">count_datasets_by_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.count_datasets_by_data_model" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_datasets_by_interaction_type">
+<span class="sig-name descname"><span class="pre">count_datasets_by_interaction_type</span></span><a class="headerlink" href="#pypath.core.network.Network.count_datasets_by_interaction_type" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_datasets_by_interaction_type_and_data_model">
+<span class="sig-name descname"><span class="pre">count_datasets_by_interaction_type_and_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.count_datasets_by_interaction_type_and_data_model" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_datasets_by_interaction_type_and_data_model_and_resource">
+<span class="sig-name descname"><span class="pre">count_datasets_by_interaction_type_and_data_model_and_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.count_datasets_by_interaction_type_and_data_model_and_resource" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_datasets_by_reference">
+<span class="sig-name descname"><span class="pre">count_datasets_by_reference</span></span><a class="headerlink" href="#pypath.core.network.Network.count_datasets_by_reference" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_datasets_by_resource">
+<span class="sig-name descname"><span class="pre">count_datasets_by_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.count_datasets_by_resource" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_degrees_directed">
+<span class="sig-name descname"><span class="pre">count_degrees_directed</span></span><a class="headerlink" href="#pypath.core.network.Network.count_degrees_directed" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_degrees_directed_by_data_model">
+<span class="sig-name descname"><span class="pre">count_degrees_directed_by_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.count_degrees_directed_by_data_model" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_degrees_directed_by_interaction_type">
+<span class="sig-name descname"><span class="pre">count_degrees_directed_by_interaction_type</span></span><a class="headerlink" href="#pypath.core.network.Network.count_degrees_directed_by_interaction_type" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_degrees_directed_by_interaction_type_and_data_model">
+<span class="sig-name descname"><span class="pre">count_degrees_directed_by_interaction_type_and_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.count_degrees_directed_by_interaction_type_and_data_model" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_degrees_directed_by_interaction_type_and_data_model_and_resource">
+<span class="sig-name descname"><span class="pre">count_degrees_directed_by_interaction_type_and_data_model_and_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.count_degrees_directed_by_interaction_type_and_data_model_and_resource" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_degrees_directed_by_reference">
+<span class="sig-name descname"><span class="pre">count_degrees_directed_by_reference</span></span><a class="headerlink" href="#pypath.core.network.Network.count_degrees_directed_by_reference" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_degrees_directed_by_resource">
+<span class="sig-name descname"><span class="pre">count_degrees_directed_by_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.count_degrees_directed_by_resource" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_degrees_directed_in">
+<span class="sig-name descname"><span class="pre">count_degrees_directed_in</span></span><a class="headerlink" href="#pypath.core.network.Network.count_degrees_directed_in" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_degrees_directed_in_by_data_model">
+<span class="sig-name descname"><span class="pre">count_degrees_directed_in_by_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.count_degrees_directed_in_by_data_model" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_degrees_directed_in_by_interaction_type">
+<span class="sig-name descname"><span class="pre">count_degrees_directed_in_by_interaction_type</span></span><a class="headerlink" href="#pypath.core.network.Network.count_degrees_directed_in_by_interaction_type" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_degrees_directed_in_by_interaction_type_and_data_model">
+<span class="sig-name descname"><span class="pre">count_degrees_directed_in_by_interaction_type_and_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.count_degrees_directed_in_by_interaction_type_and_data_model" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_degrees_directed_in_by_interaction_type_and_data_model_and_resource">
+<span class="sig-name descname"><span class="pre">count_degrees_directed_in_by_interaction_type_and_data_model_and_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.count_degrees_directed_in_by_interaction_type_and_data_model_and_resource" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_degrees_directed_in_by_reference">
+<span class="sig-name descname"><span class="pre">count_degrees_directed_in_by_reference</span></span><a class="headerlink" href="#pypath.core.network.Network.count_degrees_directed_in_by_reference" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_degrees_directed_in_by_resource">
+<span class="sig-name descname"><span class="pre">count_degrees_directed_in_by_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.count_degrees_directed_in_by_resource" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_degrees_directed_out">
+<span class="sig-name descname"><span class="pre">count_degrees_directed_out</span></span><a class="headerlink" href="#pypath.core.network.Network.count_degrees_directed_out" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_degrees_directed_out_by_data_model">
+<span class="sig-name descname"><span class="pre">count_degrees_directed_out_by_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.count_degrees_directed_out_by_data_model" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_degrees_directed_out_by_interaction_type">
+<span class="sig-name descname"><span class="pre">count_degrees_directed_out_by_interaction_type</span></span><a class="headerlink" href="#pypath.core.network.Network.count_degrees_directed_out_by_interaction_type" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_degrees_directed_out_by_interaction_type_and_data_model">
+<span class="sig-name descname"><span class="pre">count_degrees_directed_out_by_interaction_type_and_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.count_degrees_directed_out_by_interaction_type_and_data_model" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_degrees_directed_out_by_interaction_type_and_data_model_and_resource">
+<span class="sig-name descname"><span class="pre">count_degrees_directed_out_by_interaction_type_and_data_model_and_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.count_degrees_directed_out_by_interaction_type_and_data_model_and_resource" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_degrees_directed_out_by_reference">
+<span class="sig-name descname"><span class="pre">count_degrees_directed_out_by_reference</span></span><a class="headerlink" href="#pypath.core.network.Network.count_degrees_directed_out_by_reference" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_degrees_directed_out_by_resource">
+<span class="sig-name descname"><span class="pre">count_degrees_directed_out_by_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.count_degrees_directed_out_by_resource" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_degrees_negative">
+<span class="sig-name descname"><span class="pre">count_degrees_negative</span></span><a class="headerlink" href="#pypath.core.network.Network.count_degrees_negative" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_degrees_negative_by_data_model">
+<span class="sig-name descname"><span class="pre">count_degrees_negative_by_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.count_degrees_negative_by_data_model" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_degrees_negative_by_interaction_type">
+<span class="sig-name descname"><span class="pre">count_degrees_negative_by_interaction_type</span></span><a class="headerlink" href="#pypath.core.network.Network.count_degrees_negative_by_interaction_type" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_degrees_negative_by_interaction_type_and_data_model">
+<span class="sig-name descname"><span class="pre">count_degrees_negative_by_interaction_type_and_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.count_degrees_negative_by_interaction_type_and_data_model" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_degrees_negative_by_interaction_type_and_data_model_and_resource">
+<span class="sig-name descname"><span class="pre">count_degrees_negative_by_interaction_type_and_data_model_and_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.count_degrees_negative_by_interaction_type_and_data_model_and_resource" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_degrees_negative_by_reference">
+<span class="sig-name descname"><span class="pre">count_degrees_negative_by_reference</span></span><a class="headerlink" href="#pypath.core.network.Network.count_degrees_negative_by_reference" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_degrees_negative_by_resource">
+<span class="sig-name descname"><span class="pre">count_degrees_negative_by_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.count_degrees_negative_by_resource" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_degrees_negative_in">
+<span class="sig-name descname"><span class="pre">count_degrees_negative_in</span></span><a class="headerlink" href="#pypath.core.network.Network.count_degrees_negative_in" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_degrees_negative_in_by_data_model">
+<span class="sig-name descname"><span class="pre">count_degrees_negative_in_by_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.count_degrees_negative_in_by_data_model" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_degrees_negative_in_by_interaction_type">
+<span class="sig-name descname"><span class="pre">count_degrees_negative_in_by_interaction_type</span></span><a class="headerlink" href="#pypath.core.network.Network.count_degrees_negative_in_by_interaction_type" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_degrees_negative_in_by_interaction_type_and_data_model">
+<span class="sig-name descname"><span class="pre">count_degrees_negative_in_by_interaction_type_and_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.count_degrees_negative_in_by_interaction_type_and_data_model" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_degrees_negative_in_by_interaction_type_and_data_model_and_resource">
+<span class="sig-name descname"><span class="pre">count_degrees_negative_in_by_interaction_type_and_data_model_and_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.count_degrees_negative_in_by_interaction_type_and_data_model_and_resource" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_degrees_negative_in_by_reference">
+<span class="sig-name descname"><span class="pre">count_degrees_negative_in_by_reference</span></span><a class="headerlink" href="#pypath.core.network.Network.count_degrees_negative_in_by_reference" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_degrees_negative_in_by_resource">
+<span class="sig-name descname"><span class="pre">count_degrees_negative_in_by_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.count_degrees_negative_in_by_resource" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_degrees_negative_out">
+<span class="sig-name descname"><span class="pre">count_degrees_negative_out</span></span><a class="headerlink" href="#pypath.core.network.Network.count_degrees_negative_out" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_degrees_negative_out_by_data_model">
+<span class="sig-name descname"><span class="pre">count_degrees_negative_out_by_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.count_degrees_negative_out_by_data_model" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_degrees_negative_out_by_interaction_type">
+<span class="sig-name descname"><span class="pre">count_degrees_negative_out_by_interaction_type</span></span><a class="headerlink" href="#pypath.core.network.Network.count_degrees_negative_out_by_interaction_type" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_degrees_negative_out_by_interaction_type_and_data_model">
+<span class="sig-name descname"><span class="pre">count_degrees_negative_out_by_interaction_type_and_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.count_degrees_negative_out_by_interaction_type_and_data_model" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_degrees_negative_out_by_interaction_type_and_data_model_and_resource">
+<span class="sig-name descname"><span class="pre">count_degrees_negative_out_by_interaction_type_and_data_model_and_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.count_degrees_negative_out_by_interaction_type_and_data_model_and_resource" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_degrees_negative_out_by_reference">
+<span class="sig-name descname"><span class="pre">count_degrees_negative_out_by_reference</span></span><a class="headerlink" href="#pypath.core.network.Network.count_degrees_negative_out_by_reference" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_degrees_negative_out_by_resource">
+<span class="sig-name descname"><span class="pre">count_degrees_negative_out_by_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.count_degrees_negative_out_by_resource" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_degrees_non_directed">
+<span class="sig-name descname"><span class="pre">count_degrees_non_directed</span></span><a class="headerlink" href="#pypath.core.network.Network.count_degrees_non_directed" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_degrees_non_directed_by_data_model">
+<span class="sig-name descname"><span class="pre">count_degrees_non_directed_by_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.count_degrees_non_directed_by_data_model" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_degrees_non_directed_by_interaction_type">
+<span class="sig-name descname"><span class="pre">count_degrees_non_directed_by_interaction_type</span></span><a class="headerlink" href="#pypath.core.network.Network.count_degrees_non_directed_by_interaction_type" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_degrees_non_directed_by_interaction_type_and_data_model">
+<span class="sig-name descname"><span class="pre">count_degrees_non_directed_by_interaction_type_and_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.count_degrees_non_directed_by_interaction_type_and_data_model" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_degrees_non_directed_by_interaction_type_and_data_model_and_resource">
+<span class="sig-name descname"><span class="pre">count_degrees_non_directed_by_interaction_type_and_data_model_and_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.count_degrees_non_directed_by_interaction_type_and_data_model_and_resource" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_degrees_non_directed_by_reference">
+<span class="sig-name descname"><span class="pre">count_degrees_non_directed_by_reference</span></span><a class="headerlink" href="#pypath.core.network.Network.count_degrees_non_directed_by_reference" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_degrees_non_directed_by_resource">
+<span class="sig-name descname"><span class="pre">count_degrees_non_directed_by_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.count_degrees_non_directed_by_resource" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_degrees_positive">
+<span class="sig-name descname"><span class="pre">count_degrees_positive</span></span><a class="headerlink" href="#pypath.core.network.Network.count_degrees_positive" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_degrees_positive_by_data_model">
+<span class="sig-name descname"><span class="pre">count_degrees_positive_by_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.count_degrees_positive_by_data_model" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_degrees_positive_by_interaction_type">
+<span class="sig-name descname"><span class="pre">count_degrees_positive_by_interaction_type</span></span><a class="headerlink" href="#pypath.core.network.Network.count_degrees_positive_by_interaction_type" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_degrees_positive_by_interaction_type_and_data_model">
+<span class="sig-name descname"><span class="pre">count_degrees_positive_by_interaction_type_and_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.count_degrees_positive_by_interaction_type_and_data_model" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_degrees_positive_by_interaction_type_and_data_model_and_resource">
+<span class="sig-name descname"><span class="pre">count_degrees_positive_by_interaction_type_and_data_model_and_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.count_degrees_positive_by_interaction_type_and_data_model_and_resource" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_degrees_positive_by_reference">
+<span class="sig-name descname"><span class="pre">count_degrees_positive_by_reference</span></span><a class="headerlink" href="#pypath.core.network.Network.count_degrees_positive_by_reference" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_degrees_positive_by_resource">
+<span class="sig-name descname"><span class="pre">count_degrees_positive_by_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.count_degrees_positive_by_resource" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_degrees_positive_in">
+<span class="sig-name descname"><span class="pre">count_degrees_positive_in</span></span><a class="headerlink" href="#pypath.core.network.Network.count_degrees_positive_in" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_degrees_positive_in_by_data_model">
+<span class="sig-name descname"><span class="pre">count_degrees_positive_in_by_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.count_degrees_positive_in_by_data_model" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_degrees_positive_in_by_interaction_type">
+<span class="sig-name descname"><span class="pre">count_degrees_positive_in_by_interaction_type</span></span><a class="headerlink" href="#pypath.core.network.Network.count_degrees_positive_in_by_interaction_type" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_degrees_positive_in_by_interaction_type_and_data_model">
+<span class="sig-name descname"><span class="pre">count_degrees_positive_in_by_interaction_type_and_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.count_degrees_positive_in_by_interaction_type_and_data_model" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_degrees_positive_in_by_interaction_type_and_data_model_and_resource">
+<span class="sig-name descname"><span class="pre">count_degrees_positive_in_by_interaction_type_and_data_model_and_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.count_degrees_positive_in_by_interaction_type_and_data_model_and_resource" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_degrees_positive_in_by_reference">
+<span class="sig-name descname"><span class="pre">count_degrees_positive_in_by_reference</span></span><a class="headerlink" href="#pypath.core.network.Network.count_degrees_positive_in_by_reference" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_degrees_positive_in_by_resource">
+<span class="sig-name descname"><span class="pre">count_degrees_positive_in_by_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.count_degrees_positive_in_by_resource" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_degrees_positive_out">
+<span class="sig-name descname"><span class="pre">count_degrees_positive_out</span></span><a class="headerlink" href="#pypath.core.network.Network.count_degrees_positive_out" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_degrees_positive_out_by_data_model">
+<span class="sig-name descname"><span class="pre">count_degrees_positive_out_by_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.count_degrees_positive_out_by_data_model" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_degrees_positive_out_by_interaction_type">
+<span class="sig-name descname"><span class="pre">count_degrees_positive_out_by_interaction_type</span></span><a class="headerlink" href="#pypath.core.network.Network.count_degrees_positive_out_by_interaction_type" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_degrees_positive_out_by_interaction_type_and_data_model">
+<span class="sig-name descname"><span class="pre">count_degrees_positive_out_by_interaction_type_and_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.count_degrees_positive_out_by_interaction_type_and_data_model" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_degrees_positive_out_by_interaction_type_and_data_model_and_resource">
+<span class="sig-name descname"><span class="pre">count_degrees_positive_out_by_interaction_type_and_data_model_and_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.count_degrees_positive_out_by_interaction_type_and_data_model_and_resource" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_degrees_positive_out_by_reference">
+<span class="sig-name descname"><span class="pre">count_degrees_positive_out_by_reference</span></span><a class="headerlink" href="#pypath.core.network.Network.count_degrees_positive_out_by_reference" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_degrees_positive_out_by_resource">
+<span class="sig-name descname"><span class="pre">count_degrees_positive_out_by_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.count_degrees_positive_out_by_resource" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_degrees_signed">
+<span class="sig-name descname"><span class="pre">count_degrees_signed</span></span><a class="headerlink" href="#pypath.core.network.Network.count_degrees_signed" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_degrees_signed_by_data_model">
+<span class="sig-name descname"><span class="pre">count_degrees_signed_by_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.count_degrees_signed_by_data_model" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_degrees_signed_by_interaction_type">
+<span class="sig-name descname"><span class="pre">count_degrees_signed_by_interaction_type</span></span><a class="headerlink" href="#pypath.core.network.Network.count_degrees_signed_by_interaction_type" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_degrees_signed_by_interaction_type_and_data_model">
+<span class="sig-name descname"><span class="pre">count_degrees_signed_by_interaction_type_and_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.count_degrees_signed_by_interaction_type_and_data_model" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_degrees_signed_by_interaction_type_and_data_model_and_resource">
+<span class="sig-name descname"><span class="pre">count_degrees_signed_by_interaction_type_and_data_model_and_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.count_degrees_signed_by_interaction_type_and_data_model_and_resource" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_degrees_signed_by_reference">
+<span class="sig-name descname"><span class="pre">count_degrees_signed_by_reference</span></span><a class="headerlink" href="#pypath.core.network.Network.count_degrees_signed_by_reference" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_degrees_signed_by_resource">
+<span class="sig-name descname"><span class="pre">count_degrees_signed_by_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.count_degrees_signed_by_resource" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_degrees_signed_in">
+<span class="sig-name descname"><span class="pre">count_degrees_signed_in</span></span><a class="headerlink" href="#pypath.core.network.Network.count_degrees_signed_in" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_degrees_signed_in_by_data_model">
+<span class="sig-name descname"><span class="pre">count_degrees_signed_in_by_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.count_degrees_signed_in_by_data_model" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_degrees_signed_in_by_interaction_type">
+<span class="sig-name descname"><span class="pre">count_degrees_signed_in_by_interaction_type</span></span><a class="headerlink" href="#pypath.core.network.Network.count_degrees_signed_in_by_interaction_type" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_degrees_signed_in_by_interaction_type_and_data_model">
+<span class="sig-name descname"><span class="pre">count_degrees_signed_in_by_interaction_type_and_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.count_degrees_signed_in_by_interaction_type_and_data_model" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_degrees_signed_in_by_interaction_type_and_data_model_and_resource">
+<span class="sig-name descname"><span class="pre">count_degrees_signed_in_by_interaction_type_and_data_model_and_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.count_degrees_signed_in_by_interaction_type_and_data_model_and_resource" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_degrees_signed_in_by_reference">
+<span class="sig-name descname"><span class="pre">count_degrees_signed_in_by_reference</span></span><a class="headerlink" href="#pypath.core.network.Network.count_degrees_signed_in_by_reference" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_degrees_signed_in_by_resource">
+<span class="sig-name descname"><span class="pre">count_degrees_signed_in_by_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.count_degrees_signed_in_by_resource" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_degrees_signed_out">
+<span class="sig-name descname"><span class="pre">count_degrees_signed_out</span></span><a class="headerlink" href="#pypath.core.network.Network.count_degrees_signed_out" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_degrees_signed_out_by_data_model">
+<span class="sig-name descname"><span class="pre">count_degrees_signed_out_by_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.count_degrees_signed_out_by_data_model" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_degrees_signed_out_by_interaction_type">
+<span class="sig-name descname"><span class="pre">count_degrees_signed_out_by_interaction_type</span></span><a class="headerlink" href="#pypath.core.network.Network.count_degrees_signed_out_by_interaction_type" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_degrees_signed_out_by_interaction_type_and_data_model">
+<span class="sig-name descname"><span class="pre">count_degrees_signed_out_by_interaction_type_and_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.count_degrees_signed_out_by_interaction_type_and_data_model" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_degrees_signed_out_by_interaction_type_and_data_model_and_resource">
+<span class="sig-name descname"><span class="pre">count_degrees_signed_out_by_interaction_type_and_data_model_and_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.count_degrees_signed_out_by_interaction_type_and_data_model_and_resource" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_degrees_signed_out_by_reference">
+<span class="sig-name descname"><span class="pre">count_degrees_signed_out_by_reference</span></span><a class="headerlink" href="#pypath.core.network.Network.count_degrees_signed_out_by_reference" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_degrees_signed_out_by_resource">
+<span class="sig-name descname"><span class="pre">count_degrees_signed_out_by_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.count_degrees_signed_out_by_resource" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_degrees_undirected">
+<span class="sig-name descname"><span class="pre">count_degrees_undirected</span></span><a class="headerlink" href="#pypath.core.network.Network.count_degrees_undirected" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_degrees_undirected_by_data_model">
+<span class="sig-name descname"><span class="pre">count_degrees_undirected_by_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.count_degrees_undirected_by_data_model" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_degrees_undirected_by_interaction_type">
+<span class="sig-name descname"><span class="pre">count_degrees_undirected_by_interaction_type</span></span><a class="headerlink" href="#pypath.core.network.Network.count_degrees_undirected_by_interaction_type" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_degrees_undirected_by_interaction_type_and_data_model">
+<span class="sig-name descname"><span class="pre">count_degrees_undirected_by_interaction_type_and_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.count_degrees_undirected_by_interaction_type_and_data_model" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_degrees_undirected_by_interaction_type_and_data_model_and_resource">
+<span class="sig-name descname"><span class="pre">count_degrees_undirected_by_interaction_type_and_data_model_and_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.count_degrees_undirected_by_interaction_type_and_data_model_and_resource" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_degrees_undirected_by_reference">
+<span class="sig-name descname"><span class="pre">count_degrees_undirected_by_reference</span></span><a class="headerlink" href="#pypath.core.network.Network.count_degrees_undirected_by_reference" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_degrees_undirected_by_resource">
+<span class="sig-name descname"><span class="pre">count_degrees_undirected_by_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.count_degrees_undirected_by_resource" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_entities">
+<span class="sig-name descname"><span class="pre">count_entities</span></span><a class="headerlink" href="#pypath.core.network.Network.count_entities" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_entities_by_data_model">
+<span class="sig-name descname"><span class="pre">count_entities_by_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.count_entities_by_data_model" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_entities_by_interaction_type">
+<span class="sig-name descname"><span class="pre">count_entities_by_interaction_type</span></span><a class="headerlink" href="#pypath.core.network.Network.count_entities_by_interaction_type" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_entities_by_interaction_type_and_data_model">
+<span class="sig-name descname"><span class="pre">count_entities_by_interaction_type_and_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.count_entities_by_interaction_type_and_data_model" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_entities_by_interaction_type_and_data_model_and_resource">
+<span class="sig-name descname"><span class="pre">count_entities_by_interaction_type_and_data_model_and_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.count_entities_by_interaction_type_and_data_model_and_resource" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_entities_by_reference">
+<span class="sig-name descname"><span class="pre">count_entities_by_reference</span></span><a class="headerlink" href="#pypath.core.network.Network.count_entities_by_reference" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_entities_by_resource">
+<span class="sig-name descname"><span class="pre">count_entities_by_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.count_entities_by_resource" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_evidences">
+<span class="sig-name descname"><span class="pre">count_evidences</span></span><a class="headerlink" href="#pypath.core.network.Network.count_evidences" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_evidences_by_data_model">
+<span class="sig-name descname"><span class="pre">count_evidences_by_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.count_evidences_by_data_model" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_evidences_by_interaction_type">
+<span class="sig-name descname"><span class="pre">count_evidences_by_interaction_type</span></span><a class="headerlink" href="#pypath.core.network.Network.count_evidences_by_interaction_type" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_evidences_by_interaction_type_and_data_model">
+<span class="sig-name descname"><span class="pre">count_evidences_by_interaction_type_and_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.count_evidences_by_interaction_type_and_data_model" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_evidences_by_interaction_type_and_data_model_and_resource">
+<span class="sig-name descname"><span class="pre">count_evidences_by_interaction_type_and_data_model_and_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.count_evidences_by_interaction_type_and_data_model_and_resource" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_evidences_by_reference">
+<span class="sig-name descname"><span class="pre">count_evidences_by_reference</span></span><a class="headerlink" href="#pypath.core.network.Network.count_evidences_by_reference" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_evidences_by_resource">
+<span class="sig-name descname"><span class="pre">count_evidences_by_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.count_evidences_by_resource" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_identifiers">
+<span class="sig-name descname"><span class="pre">count_identifiers</span></span><a class="headerlink" href="#pypath.core.network.Network.count_identifiers" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_identifiers_by_data_model">
+<span class="sig-name descname"><span class="pre">count_identifiers_by_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.count_identifiers_by_data_model" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_identifiers_by_interaction_type">
+<span class="sig-name descname"><span class="pre">count_identifiers_by_interaction_type</span></span><a class="headerlink" href="#pypath.core.network.Network.count_identifiers_by_interaction_type" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_identifiers_by_interaction_type_and_data_model">
+<span class="sig-name descname"><span class="pre">count_identifiers_by_interaction_type_and_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.count_identifiers_by_interaction_type_and_data_model" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_identifiers_by_interaction_type_and_data_model_and_resource">
+<span class="sig-name descname"><span class="pre">count_identifiers_by_interaction_type_and_data_model_and_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.count_identifiers_by_interaction_type_and_data_model_and_resource" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_identifiers_by_reference">
+<span class="sig-name descname"><span class="pre">count_identifiers_by_reference</span></span><a class="headerlink" href="#pypath.core.network.Network.count_identifiers_by_reference" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_identifiers_by_resource">
+<span class="sig-name descname"><span class="pre">count_identifiers_by_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.count_identifiers_by_resource" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_interaction_types">
+<span class="sig-name descname"><span class="pre">count_interaction_types</span></span><a class="headerlink" href="#pypath.core.network.Network.count_interaction_types" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_interaction_types_by_data_model">
+<span class="sig-name descname"><span class="pre">count_interaction_types_by_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.count_interaction_types_by_data_model" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_interaction_types_by_interaction_type">
+<span class="sig-name descname"><span class="pre">count_interaction_types_by_interaction_type</span></span><a class="headerlink" href="#pypath.core.network.Network.count_interaction_types_by_interaction_type" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_interaction_types_by_interaction_type_and_data_model">
+<span class="sig-name descname"><span class="pre">count_interaction_types_by_interaction_type_and_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.count_interaction_types_by_interaction_type_and_data_model" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_interaction_types_by_interaction_type_and_data_model_and_resource">
+<span class="sig-name descname"><span class="pre">count_interaction_types_by_interaction_type_and_data_model_and_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.count_interaction_types_by_interaction_type_and_data_model_and_resource" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_interaction_types_by_reference">
+<span class="sig-name descname"><span class="pre">count_interaction_types_by_reference</span></span><a class="headerlink" href="#pypath.core.network.Network.count_interaction_types_by_reference" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_interaction_types_by_resource">
+<span class="sig-name descname"><span class="pre">count_interaction_types_by_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.count_interaction_types_by_resource" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_interactions">
+<span class="sig-name descname"><span class="pre">count_interactions</span></span><a class="headerlink" href="#pypath.core.network.Network.count_interactions" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_interactions_0">
+<span class="sig-name descname"><span class="pre">count_interactions_0</span></span><a class="headerlink" href="#pypath.core.network.Network.count_interactions_0" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_interactions_0_by_data_model">
+<span class="sig-name descname"><span class="pre">count_interactions_0_by_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.count_interactions_0_by_data_model" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_interactions_0_by_interaction_type">
+<span class="sig-name descname"><span class="pre">count_interactions_0_by_interaction_type</span></span><a class="headerlink" href="#pypath.core.network.Network.count_interactions_0_by_interaction_type" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_interactions_0_by_interaction_type_and_data_model">
+<span class="sig-name descname"><span class="pre">count_interactions_0_by_interaction_type_and_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.count_interactions_0_by_interaction_type_and_data_model" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_interactions_0_by_interaction_type_and_data_model_and_resource">
+<span class="sig-name descname"><span class="pre">count_interactions_0_by_interaction_type_and_data_model_and_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.count_interactions_0_by_interaction_type_and_data_model_and_resource" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_interactions_0_by_reference">
+<span class="sig-name descname"><span class="pre">count_interactions_0_by_reference</span></span><a class="headerlink" href="#pypath.core.network.Network.count_interactions_0_by_reference" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_interactions_0_by_resource">
+<span class="sig-name descname"><span class="pre">count_interactions_0_by_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.count_interactions_0_by_resource" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_interactions_by_data_model">
+<span class="sig-name descname"><span class="pre">count_interactions_by_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.count_interactions_by_data_model" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_interactions_by_interaction_type">
+<span class="sig-name descname"><span class="pre">count_interactions_by_interaction_type</span></span><a class="headerlink" href="#pypath.core.network.Network.count_interactions_by_interaction_type" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_interactions_by_interaction_type_and_data_model">
+<span class="sig-name descname"><span class="pre">count_interactions_by_interaction_type_and_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.count_interactions_by_interaction_type_and_data_model" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_interactions_by_interaction_type_and_data_model_and_resource">
+<span class="sig-name descname"><span class="pre">count_interactions_by_interaction_type_and_data_model_and_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.count_interactions_by_interaction_type_and_data_model_and_resource" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_interactions_by_reference">
+<span class="sig-name descname"><span class="pre">count_interactions_by_reference</span></span><a class="headerlink" href="#pypath.core.network.Network.count_interactions_by_reference" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_interactions_by_resource">
+<span class="sig-name descname"><span class="pre">count_interactions_by_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.count_interactions_by_resource" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_interactions_directed">
+<span class="sig-name descname"><span class="pre">count_interactions_directed</span></span><a class="headerlink" href="#pypath.core.network.Network.count_interactions_directed" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_interactions_directed_by_data_model">
+<span class="sig-name descname"><span class="pre">count_interactions_directed_by_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.count_interactions_directed_by_data_model" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_interactions_directed_by_interaction_type">
+<span class="sig-name descname"><span class="pre">count_interactions_directed_by_interaction_type</span></span><a class="headerlink" href="#pypath.core.network.Network.count_interactions_directed_by_interaction_type" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_interactions_directed_by_interaction_type_and_data_model">
+<span class="sig-name descname"><span class="pre">count_interactions_directed_by_interaction_type_and_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.count_interactions_directed_by_interaction_type_and_data_model" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_interactions_directed_by_interaction_type_and_data_model_and_resource">
+<span class="sig-name descname"><span class="pre">count_interactions_directed_by_interaction_type_and_data_model_and_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.count_interactions_directed_by_interaction_type_and_data_model_and_resource" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_interactions_directed_by_reference">
+<span class="sig-name descname"><span class="pre">count_interactions_directed_by_reference</span></span><a class="headerlink" href="#pypath.core.network.Network.count_interactions_directed_by_reference" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_interactions_directed_by_resource">
+<span class="sig-name descname"><span class="pre">count_interactions_directed_by_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.count_interactions_directed_by_resource" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_interactions_mutual">
+<span class="sig-name descname"><span class="pre">count_interactions_mutual</span></span><a class="headerlink" href="#pypath.core.network.Network.count_interactions_mutual" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_interactions_mutual_by_data_model">
+<span class="sig-name descname"><span class="pre">count_interactions_mutual_by_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.count_interactions_mutual_by_data_model" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_interactions_mutual_by_interaction_type">
+<span class="sig-name descname"><span class="pre">count_interactions_mutual_by_interaction_type</span></span><a class="headerlink" href="#pypath.core.network.Network.count_interactions_mutual_by_interaction_type" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_interactions_mutual_by_interaction_type_and_data_model">
+<span class="sig-name descname"><span class="pre">count_interactions_mutual_by_interaction_type_and_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.count_interactions_mutual_by_interaction_type_and_data_model" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_interactions_mutual_by_interaction_type_and_data_model_and_resource">
+<span class="sig-name descname"><span class="pre">count_interactions_mutual_by_interaction_type_and_data_model_and_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.count_interactions_mutual_by_interaction_type_and_data_model_and_resource" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_interactions_mutual_by_reference">
+<span class="sig-name descname"><span class="pre">count_interactions_mutual_by_reference</span></span><a class="headerlink" href="#pypath.core.network.Network.count_interactions_mutual_by_reference" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_interactions_mutual_by_resource">
+<span class="sig-name descname"><span class="pre">count_interactions_mutual_by_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.count_interactions_mutual_by_resource" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_interactions_negative">
+<span class="sig-name descname"><span class="pre">count_interactions_negative</span></span><a class="headerlink" href="#pypath.core.network.Network.count_interactions_negative" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_interactions_negative_by_data_model">
+<span class="sig-name descname"><span class="pre">count_interactions_negative_by_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.count_interactions_negative_by_data_model" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_interactions_negative_by_interaction_type">
+<span class="sig-name descname"><span class="pre">count_interactions_negative_by_interaction_type</span></span><a class="headerlink" href="#pypath.core.network.Network.count_interactions_negative_by_interaction_type" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_interactions_negative_by_interaction_type_and_data_model">
+<span class="sig-name descname"><span class="pre">count_interactions_negative_by_interaction_type_and_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.count_interactions_negative_by_interaction_type_and_data_model" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_interactions_negative_by_interaction_type_and_data_model_and_resource">
+<span class="sig-name descname"><span class="pre">count_interactions_negative_by_interaction_type_and_data_model_and_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.count_interactions_negative_by_interaction_type_and_data_model_and_resource" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_interactions_negative_by_reference">
+<span class="sig-name descname"><span class="pre">count_interactions_negative_by_reference</span></span><a class="headerlink" href="#pypath.core.network.Network.count_interactions_negative_by_reference" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_interactions_negative_by_resource">
+<span class="sig-name descname"><span class="pre">count_interactions_negative_by_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.count_interactions_negative_by_resource" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_interactions_non_directed">
+<span class="sig-name descname"><span class="pre">count_interactions_non_directed</span></span><a class="headerlink" href="#pypath.core.network.Network.count_interactions_non_directed" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_interactions_non_directed_0">
+<span class="sig-name descname"><span class="pre">count_interactions_non_directed_0</span></span><a class="headerlink" href="#pypath.core.network.Network.count_interactions_non_directed_0" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_interactions_non_directed_0_by_data_model">
+<span class="sig-name descname"><span class="pre">count_interactions_non_directed_0_by_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.count_interactions_non_directed_0_by_data_model" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_interactions_non_directed_0_by_interaction_type">
+<span class="sig-name descname"><span class="pre">count_interactions_non_directed_0_by_interaction_type</span></span><a class="headerlink" href="#pypath.core.network.Network.count_interactions_non_directed_0_by_interaction_type" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_interactions_non_directed_0_by_interaction_type_and_data_model">
+<span class="sig-name descname"><span class="pre">count_interactions_non_directed_0_by_interaction_type_and_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.count_interactions_non_directed_0_by_interaction_type_and_data_model" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_interactions_non_directed_0_by_interaction_type_and_data_model_and_resource">
+<span class="sig-name descname"><span class="pre">count_interactions_non_directed_0_by_interaction_type_and_data_model_and_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.count_interactions_non_directed_0_by_interaction_type_and_data_model_and_resource" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_interactions_non_directed_0_by_reference">
+<span class="sig-name descname"><span class="pre">count_interactions_non_directed_0_by_reference</span></span><a class="headerlink" href="#pypath.core.network.Network.count_interactions_non_directed_0_by_reference" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_interactions_non_directed_0_by_resource">
+<span class="sig-name descname"><span class="pre">count_interactions_non_directed_0_by_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.count_interactions_non_directed_0_by_resource" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_interactions_non_directed_by_data_model">
+<span class="sig-name descname"><span class="pre">count_interactions_non_directed_by_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.count_interactions_non_directed_by_data_model" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_interactions_non_directed_by_interaction_type">
+<span class="sig-name descname"><span class="pre">count_interactions_non_directed_by_interaction_type</span></span><a class="headerlink" href="#pypath.core.network.Network.count_interactions_non_directed_by_interaction_type" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_interactions_non_directed_by_interaction_type_and_data_model">
+<span class="sig-name descname"><span class="pre">count_interactions_non_directed_by_interaction_type_and_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.count_interactions_non_directed_by_interaction_type_and_data_model" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_interactions_non_directed_by_interaction_type_and_data_model_and_resource">
+<span class="sig-name descname"><span class="pre">count_interactions_non_directed_by_interaction_type_and_data_model_and_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.count_interactions_non_directed_by_interaction_type_and_data_model_and_resource" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_interactions_non_directed_by_reference">
+<span class="sig-name descname"><span class="pre">count_interactions_non_directed_by_reference</span></span><a class="headerlink" href="#pypath.core.network.Network.count_interactions_non_directed_by_reference" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_interactions_non_directed_by_resource">
+<span class="sig-name descname"><span class="pre">count_interactions_non_directed_by_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.count_interactions_non_directed_by_resource" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_interactions_positive">
+<span class="sig-name descname"><span class="pre">count_interactions_positive</span></span><a class="headerlink" href="#pypath.core.network.Network.count_interactions_positive" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_interactions_positive_by_data_model">
+<span class="sig-name descname"><span class="pre">count_interactions_positive_by_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.count_interactions_positive_by_data_model" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_interactions_positive_by_interaction_type">
+<span class="sig-name descname"><span class="pre">count_interactions_positive_by_interaction_type</span></span><a class="headerlink" href="#pypath.core.network.Network.count_interactions_positive_by_interaction_type" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_interactions_positive_by_interaction_type_and_data_model">
+<span class="sig-name descname"><span class="pre">count_interactions_positive_by_interaction_type_and_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.count_interactions_positive_by_interaction_type_and_data_model" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_interactions_positive_by_interaction_type_and_data_model_and_resource">
+<span class="sig-name descname"><span class="pre">count_interactions_positive_by_interaction_type_and_data_model_and_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.count_interactions_positive_by_interaction_type_and_data_model_and_resource" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_interactions_positive_by_reference">
+<span class="sig-name descname"><span class="pre">count_interactions_positive_by_reference</span></span><a class="headerlink" href="#pypath.core.network.Network.count_interactions_positive_by_reference" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_interactions_positive_by_resource">
+<span class="sig-name descname"><span class="pre">count_interactions_positive_by_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.count_interactions_positive_by_resource" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_interactions_signed">
+<span class="sig-name descname"><span class="pre">count_interactions_signed</span></span><a class="headerlink" href="#pypath.core.network.Network.count_interactions_signed" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_interactions_signed_by_data_model">
+<span class="sig-name descname"><span class="pre">count_interactions_signed_by_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.count_interactions_signed_by_data_model" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_interactions_signed_by_interaction_type">
+<span class="sig-name descname"><span class="pre">count_interactions_signed_by_interaction_type</span></span><a class="headerlink" href="#pypath.core.network.Network.count_interactions_signed_by_interaction_type" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_interactions_signed_by_interaction_type_and_data_model">
+<span class="sig-name descname"><span class="pre">count_interactions_signed_by_interaction_type_and_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.count_interactions_signed_by_interaction_type_and_data_model" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_interactions_signed_by_interaction_type_and_data_model_and_resource">
+<span class="sig-name descname"><span class="pre">count_interactions_signed_by_interaction_type_and_data_model_and_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.count_interactions_signed_by_interaction_type_and_data_model_and_resource" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_interactions_signed_by_reference">
+<span class="sig-name descname"><span class="pre">count_interactions_signed_by_reference</span></span><a class="headerlink" href="#pypath.core.network.Network.count_interactions_signed_by_reference" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_interactions_signed_by_resource">
+<span class="sig-name descname"><span class="pre">count_interactions_signed_by_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.count_interactions_signed_by_resource" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_interactions_undirected">
+<span class="sig-name descname"><span class="pre">count_interactions_undirected</span></span><a class="headerlink" href="#pypath.core.network.Network.count_interactions_undirected" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_interactions_undirected_0">
+<span class="sig-name descname"><span class="pre">count_interactions_undirected_0</span></span><a class="headerlink" href="#pypath.core.network.Network.count_interactions_undirected_0" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_interactions_undirected_0_by_data_model">
+<span class="sig-name descname"><span class="pre">count_interactions_undirected_0_by_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.count_interactions_undirected_0_by_data_model" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_interactions_undirected_0_by_interaction_type">
+<span class="sig-name descname"><span class="pre">count_interactions_undirected_0_by_interaction_type</span></span><a class="headerlink" href="#pypath.core.network.Network.count_interactions_undirected_0_by_interaction_type" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_interactions_undirected_0_by_interaction_type_and_data_model">
+<span class="sig-name descname"><span class="pre">count_interactions_undirected_0_by_interaction_type_and_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.count_interactions_undirected_0_by_interaction_type_and_data_model" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_interactions_undirected_0_by_interaction_type_and_data_model_and_resource">
+<span class="sig-name descname"><span class="pre">count_interactions_undirected_0_by_interaction_type_and_data_model_and_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.count_interactions_undirected_0_by_interaction_type_and_data_model_and_resource" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_interactions_undirected_0_by_reference">
+<span class="sig-name descname"><span class="pre">count_interactions_undirected_0_by_reference</span></span><a class="headerlink" href="#pypath.core.network.Network.count_interactions_undirected_0_by_reference" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_interactions_undirected_0_by_resource">
+<span class="sig-name descname"><span class="pre">count_interactions_undirected_0_by_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.count_interactions_undirected_0_by_resource" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_interactions_undirected_by_data_model">
+<span class="sig-name descname"><span class="pre">count_interactions_undirected_by_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.count_interactions_undirected_by_data_model" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_interactions_undirected_by_interaction_type">
+<span class="sig-name descname"><span class="pre">count_interactions_undirected_by_interaction_type</span></span><a class="headerlink" href="#pypath.core.network.Network.count_interactions_undirected_by_interaction_type" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_interactions_undirected_by_interaction_type_and_data_model">
+<span class="sig-name descname"><span class="pre">count_interactions_undirected_by_interaction_type_and_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.count_interactions_undirected_by_interaction_type_and_data_model" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_interactions_undirected_by_interaction_type_and_data_model_and_resource">
+<span class="sig-name descname"><span class="pre">count_interactions_undirected_by_interaction_type_and_data_model_and_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.count_interactions_undirected_by_interaction_type_and_data_model_and_resource" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_interactions_undirected_by_reference">
+<span class="sig-name descname"><span class="pre">count_interactions_undirected_by_reference</span></span><a class="headerlink" href="#pypath.core.network.Network.count_interactions_undirected_by_reference" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_interactions_undirected_by_resource">
+<span class="sig-name descname"><span class="pre">count_interactions_undirected_by_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.count_interactions_undirected_by_resource" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_labels">
+<span class="sig-name descname"><span class="pre">count_labels</span></span><a class="headerlink" href="#pypath.core.network.Network.count_labels" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_labels_by_data_model">
+<span class="sig-name descname"><span class="pre">count_labels_by_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.count_labels_by_data_model" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_labels_by_interaction_type">
+<span class="sig-name descname"><span class="pre">count_labels_by_interaction_type</span></span><a class="headerlink" href="#pypath.core.network.Network.count_labels_by_interaction_type" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_labels_by_interaction_type_and_data_model">
+<span class="sig-name descname"><span class="pre">count_labels_by_interaction_type_and_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.count_labels_by_interaction_type_and_data_model" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_labels_by_interaction_type_and_data_model_and_resource">
+<span class="sig-name descname"><span class="pre">count_labels_by_interaction_type_and_data_model_and_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.count_labels_by_interaction_type_and_data_model_and_resource" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_labels_by_reference">
+<span class="sig-name descname"><span class="pre">count_labels_by_reference</span></span><a class="headerlink" href="#pypath.core.network.Network.count_labels_by_reference" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_labels_by_resource">
+<span class="sig-name descname"><span class="pre">count_labels_by_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.count_labels_by_resource" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_lncrna_identifiers">
+<span class="sig-name descname"><span class="pre">count_lncrna_identifiers</span></span><a class="headerlink" href="#pypath.core.network.Network.count_lncrna_identifiers" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_lncrna_identifiers_by_data_model">
+<span class="sig-name descname"><span class="pre">count_lncrna_identifiers_by_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.count_lncrna_identifiers_by_data_model" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_lncrna_identifiers_by_interaction_type">
+<span class="sig-name descname"><span class="pre">count_lncrna_identifiers_by_interaction_type</span></span><a class="headerlink" href="#pypath.core.network.Network.count_lncrna_identifiers_by_interaction_type" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_lncrna_identifiers_by_interaction_type_and_data_model">
+<span class="sig-name descname"><span class="pre">count_lncrna_identifiers_by_interaction_type_and_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.count_lncrna_identifiers_by_interaction_type_and_data_model" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_lncrna_identifiers_by_interaction_type_and_data_model_and_resource">
+<span class="sig-name descname"><span class="pre">count_lncrna_identifiers_by_interaction_type_and_data_model_and_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.count_lncrna_identifiers_by_interaction_type_and_data_model_and_resource" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_lncrna_identifiers_by_reference">
+<span class="sig-name descname"><span class="pre">count_lncrna_identifiers_by_reference</span></span><a class="headerlink" href="#pypath.core.network.Network.count_lncrna_identifiers_by_reference" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_lncrna_identifiers_by_resource">
+<span class="sig-name descname"><span class="pre">count_lncrna_identifiers_by_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.count_lncrna_identifiers_by_resource" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_lncrna_labels">
+<span class="sig-name descname"><span class="pre">count_lncrna_labels</span></span><a class="headerlink" href="#pypath.core.network.Network.count_lncrna_labels" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_lncrna_labels_by_data_model">
+<span class="sig-name descname"><span class="pre">count_lncrna_labels_by_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.count_lncrna_labels_by_data_model" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_lncrna_labels_by_interaction_type">
+<span class="sig-name descname"><span class="pre">count_lncrna_labels_by_interaction_type</span></span><a class="headerlink" href="#pypath.core.network.Network.count_lncrna_labels_by_interaction_type" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_lncrna_labels_by_interaction_type_and_data_model">
+<span class="sig-name descname"><span class="pre">count_lncrna_labels_by_interaction_type_and_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.count_lncrna_labels_by_interaction_type_and_data_model" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_lncrna_labels_by_interaction_type_and_data_model_and_resource">
+<span class="sig-name descname"><span class="pre">count_lncrna_labels_by_interaction_type_and_data_model_and_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.count_lncrna_labels_by_interaction_type_and_data_model_and_resource" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_lncrna_labels_by_reference">
+<span class="sig-name descname"><span class="pre">count_lncrna_labels_by_reference</span></span><a class="headerlink" href="#pypath.core.network.Network.count_lncrna_labels_by_reference" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_lncrna_labels_by_resource">
+<span class="sig-name descname"><span class="pre">count_lncrna_labels_by_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.count_lncrna_labels_by_resource" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_lncrnas">
+<span class="sig-name descname"><span class="pre">count_lncrnas</span></span><a class="headerlink" href="#pypath.core.network.Network.count_lncrnas" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_lncrnas_by_data_model">
+<span class="sig-name descname"><span class="pre">count_lncrnas_by_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.count_lncrnas_by_data_model" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_lncrnas_by_interaction_type">
+<span class="sig-name descname"><span class="pre">count_lncrnas_by_interaction_type</span></span><a class="headerlink" href="#pypath.core.network.Network.count_lncrnas_by_interaction_type" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_lncrnas_by_interaction_type_and_data_model">
+<span class="sig-name descname"><span class="pre">count_lncrnas_by_interaction_type_and_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.count_lncrnas_by_interaction_type_and_data_model" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_lncrnas_by_interaction_type_and_data_model_and_resource">
+<span class="sig-name descname"><span class="pre">count_lncrnas_by_interaction_type_and_data_model_and_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.count_lncrnas_by_interaction_type_and_data_model_and_resource" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_lncrnas_by_reference">
+<span class="sig-name descname"><span class="pre">count_lncrnas_by_reference</span></span><a class="headerlink" href="#pypath.core.network.Network.count_lncrnas_by_reference" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_lncrnas_by_resource">
+<span class="sig-name descname"><span class="pre">count_lncrnas_by_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.count_lncrnas_by_resource" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_mirna_identifiers">
+<span class="sig-name descname"><span class="pre">count_mirna_identifiers</span></span><a class="headerlink" href="#pypath.core.network.Network.count_mirna_identifiers" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_mirna_identifiers_by_data_model">
+<span class="sig-name descname"><span class="pre">count_mirna_identifiers_by_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.count_mirna_identifiers_by_data_model" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_mirna_identifiers_by_interaction_type">
+<span class="sig-name descname"><span class="pre">count_mirna_identifiers_by_interaction_type</span></span><a class="headerlink" href="#pypath.core.network.Network.count_mirna_identifiers_by_interaction_type" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_mirna_identifiers_by_interaction_type_and_data_model">
+<span class="sig-name descname"><span class="pre">count_mirna_identifiers_by_interaction_type_and_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.count_mirna_identifiers_by_interaction_type_and_data_model" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_mirna_identifiers_by_interaction_type_and_data_model_and_resource">
+<span class="sig-name descname"><span class="pre">count_mirna_identifiers_by_interaction_type_and_data_model_and_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.count_mirna_identifiers_by_interaction_type_and_data_model_and_resource" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_mirna_identifiers_by_reference">
+<span class="sig-name descname"><span class="pre">count_mirna_identifiers_by_reference</span></span><a class="headerlink" href="#pypath.core.network.Network.count_mirna_identifiers_by_reference" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_mirna_identifiers_by_resource">
+<span class="sig-name descname"><span class="pre">count_mirna_identifiers_by_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.count_mirna_identifiers_by_resource" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_mirna_labels">
+<span class="sig-name descname"><span class="pre">count_mirna_labels</span></span><a class="headerlink" href="#pypath.core.network.Network.count_mirna_labels" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_mirna_labels_by_data_model">
+<span class="sig-name descname"><span class="pre">count_mirna_labels_by_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.count_mirna_labels_by_data_model" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_mirna_labels_by_interaction_type">
+<span class="sig-name descname"><span class="pre">count_mirna_labels_by_interaction_type</span></span><a class="headerlink" href="#pypath.core.network.Network.count_mirna_labels_by_interaction_type" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_mirna_labels_by_interaction_type_and_data_model">
+<span class="sig-name descname"><span class="pre">count_mirna_labels_by_interaction_type_and_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.count_mirna_labels_by_interaction_type_and_data_model" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_mirna_labels_by_interaction_type_and_data_model_and_resource">
+<span class="sig-name descname"><span class="pre">count_mirna_labels_by_interaction_type_and_data_model_and_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.count_mirna_labels_by_interaction_type_and_data_model_and_resource" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_mirna_labels_by_reference">
+<span class="sig-name descname"><span class="pre">count_mirna_labels_by_reference</span></span><a class="headerlink" href="#pypath.core.network.Network.count_mirna_labels_by_reference" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_mirna_labels_by_resource">
+<span class="sig-name descname"><span class="pre">count_mirna_labels_by_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.count_mirna_labels_by_resource" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_mirnas">
+<span class="sig-name descname"><span class="pre">count_mirnas</span></span><a class="headerlink" href="#pypath.core.network.Network.count_mirnas" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_mirnas_by_data_model">
+<span class="sig-name descname"><span class="pre">count_mirnas_by_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.count_mirnas_by_data_model" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_mirnas_by_interaction_type">
+<span class="sig-name descname"><span class="pre">count_mirnas_by_interaction_type</span></span><a class="headerlink" href="#pypath.core.network.Network.count_mirnas_by_interaction_type" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_mirnas_by_interaction_type_and_data_model">
+<span class="sig-name descname"><span class="pre">count_mirnas_by_interaction_type_and_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.count_mirnas_by_interaction_type_and_data_model" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_mirnas_by_interaction_type_and_data_model_and_resource">
+<span class="sig-name descname"><span class="pre">count_mirnas_by_interaction_type_and_data_model_and_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.count_mirnas_by_interaction_type_and_data_model_and_resource" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_mirnas_by_reference">
+<span class="sig-name descname"><span class="pre">count_mirnas_by_reference</span></span><a class="headerlink" href="#pypath.core.network.Network.count_mirnas_by_reference" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_mirnas_by_resource">
+<span class="sig-name descname"><span class="pre">count_mirnas_by_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.count_mirnas_by_resource" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_partners">
+<span class="sig-name descname"><span class="pre">count_partners</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/network.html#Network.count_partners"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.network.Network.count_partners" title="Link to this definition">§</a></dt>
+<dd><p>Returns the count of the interacting partners for one or more
+entities according to the specified criteria.
+Please refer to the docs of the <code class="docutils literal notranslate"><span class="pre">partners</span></code> method.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_post_transcriptionally_activated_by">
+<span class="sig-name descname"><span class="pre">count_post_transcriptionally_activated_by</span></span><a class="headerlink" href="#pypath.core.network.Network.count_post_transcriptionally_activated_by" title="Link to this definition">§</a></dt>
+<dd><p>Returns the count of the interacting partners for one or more
+entities according to the specified criteria.
+Please refer to the docs of the <code class="docutils literal notranslate"><span class="pre">partners</span></code> method.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_post_transcriptionally_activates">
+<span class="sig-name descname"><span class="pre">count_post_transcriptionally_activates</span></span><a class="headerlink" href="#pypath.core.network.Network.count_post_transcriptionally_activates" title="Link to this definition">§</a></dt>
+<dd><p>Returns the count of the interacting partners for one or more
+entities according to the specified criteria.
+Please refer to the docs of the <code class="docutils literal notranslate"><span class="pre">partners</span></code> method.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_post_transcriptionally_regulated_by">
+<span class="sig-name descname"><span class="pre">count_post_transcriptionally_regulated_by</span></span><a class="headerlink" href="#pypath.core.network.Network.count_post_transcriptionally_regulated_by" title="Link to this definition">§</a></dt>
+<dd><p>Returns the count of the interacting partners for one or more
+entities according to the specified criteria.
+Please refer to the docs of the <code class="docutils literal notranslate"><span class="pre">partners</span></code> method.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_post_transcriptionally_regulates">
+<span class="sig-name descname"><span class="pre">count_post_transcriptionally_regulates</span></span><a class="headerlink" href="#pypath.core.network.Network.count_post_transcriptionally_regulates" title="Link to this definition">§</a></dt>
+<dd><p>Returns the count of the interacting partners for one or more
+entities according to the specified criteria.
+Please refer to the docs of the <code class="docutils literal notranslate"><span class="pre">partners</span></code> method.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_post_transcriptionally_suppressed_by">
+<span class="sig-name descname"><span class="pre">count_post_transcriptionally_suppressed_by</span></span><a class="headerlink" href="#pypath.core.network.Network.count_post_transcriptionally_suppressed_by" title="Link to this definition">§</a></dt>
+<dd><p>Returns the count of the interacting partners for one or more
+entities according to the specified criteria.
+Please refer to the docs of the <code class="docutils literal notranslate"><span class="pre">partners</span></code> method.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_post_transcriptionally_suppresses">
+<span class="sig-name descname"><span class="pre">count_post_transcriptionally_suppresses</span></span><a class="headerlink" href="#pypath.core.network.Network.count_post_transcriptionally_suppresses" title="Link to this definition">§</a></dt>
+<dd><p>Returns the count of the interacting partners for one or more
+entities according to the specified criteria.
+Please refer to the docs of the <code class="docutils literal notranslate"><span class="pre">partners</span></code> method.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_post_translationally_activated_by">
+<span class="sig-name descname"><span class="pre">count_post_translationally_activated_by</span></span><a class="headerlink" href="#pypath.core.network.Network.count_post_translationally_activated_by" title="Link to this definition">§</a></dt>
+<dd><p>Returns the count of the interacting partners for one or more
+entities according to the specified criteria.
+Please refer to the docs of the <code class="docutils literal notranslate"><span class="pre">partners</span></code> method.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_post_translationally_activates">
+<span class="sig-name descname"><span class="pre">count_post_translationally_activates</span></span><a class="headerlink" href="#pypath.core.network.Network.count_post_translationally_activates" title="Link to this definition">§</a></dt>
+<dd><p>Returns the count of the interacting partners for one or more
+entities according to the specified criteria.
+Please refer to the docs of the <code class="docutils literal notranslate"><span class="pre">partners</span></code> method.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_post_translationally_regulated_by">
+<span class="sig-name descname"><span class="pre">count_post_translationally_regulated_by</span></span><a class="headerlink" href="#pypath.core.network.Network.count_post_translationally_regulated_by" title="Link to this definition">§</a></dt>
+<dd><p>Returns the count of the interacting partners for one or more
+entities according to the specified criteria.
+Please refer to the docs of the <code class="docutils literal notranslate"><span class="pre">partners</span></code> method.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_post_translationally_regulates">
+<span class="sig-name descname"><span class="pre">count_post_translationally_regulates</span></span><a class="headerlink" href="#pypath.core.network.Network.count_post_translationally_regulates" title="Link to this definition">§</a></dt>
+<dd><p>Returns the count of the interacting partners for one or more
+entities according to the specified criteria.
+Please refer to the docs of the <code class="docutils literal notranslate"><span class="pre">partners</span></code> method.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_post_translationally_suppressed_by">
+<span class="sig-name descname"><span class="pre">count_post_translationally_suppressed_by</span></span><a class="headerlink" href="#pypath.core.network.Network.count_post_translationally_suppressed_by" title="Link to this definition">§</a></dt>
+<dd><p>Returns the count of the interacting partners for one or more
+entities according to the specified criteria.
+Please refer to the docs of the <code class="docutils literal notranslate"><span class="pre">partners</span></code> method.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_post_translationally_suppresses">
+<span class="sig-name descname"><span class="pre">count_post_translationally_suppresses</span></span><a class="headerlink" href="#pypath.core.network.Network.count_post_translationally_suppresses" title="Link to this definition">§</a></dt>
+<dd><p>Returns the count of the interacting partners for one or more
+entities according to the specified criteria.
+Please refer to the docs of the <code class="docutils literal notranslate"><span class="pre">partners</span></code> method.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_protein_identifiers">
+<span class="sig-name descname"><span class="pre">count_protein_identifiers</span></span><a class="headerlink" href="#pypath.core.network.Network.count_protein_identifiers" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_protein_identifiers_by_data_model">
+<span class="sig-name descname"><span class="pre">count_protein_identifiers_by_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.count_protein_identifiers_by_data_model" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_protein_identifiers_by_interaction_type">
+<span class="sig-name descname"><span class="pre">count_protein_identifiers_by_interaction_type</span></span><a class="headerlink" href="#pypath.core.network.Network.count_protein_identifiers_by_interaction_type" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_protein_identifiers_by_interaction_type_and_data_model">
+<span class="sig-name descname"><span class="pre">count_protein_identifiers_by_interaction_type_and_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.count_protein_identifiers_by_interaction_type_and_data_model" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_protein_identifiers_by_interaction_type_and_data_model_and_resource">
+<span class="sig-name descname"><span class="pre">count_protein_identifiers_by_interaction_type_and_data_model_and_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.count_protein_identifiers_by_interaction_type_and_data_model_and_resource" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_protein_identifiers_by_reference">
+<span class="sig-name descname"><span class="pre">count_protein_identifiers_by_reference</span></span><a class="headerlink" href="#pypath.core.network.Network.count_protein_identifiers_by_reference" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_protein_identifiers_by_resource">
+<span class="sig-name descname"><span class="pre">count_protein_identifiers_by_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.count_protein_identifiers_by_resource" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_protein_labels">
+<span class="sig-name descname"><span class="pre">count_protein_labels</span></span><a class="headerlink" href="#pypath.core.network.Network.count_protein_labels" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_protein_labels_by_data_model">
+<span class="sig-name descname"><span class="pre">count_protein_labels_by_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.count_protein_labels_by_data_model" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_protein_labels_by_interaction_type">
+<span class="sig-name descname"><span class="pre">count_protein_labels_by_interaction_type</span></span><a class="headerlink" href="#pypath.core.network.Network.count_protein_labels_by_interaction_type" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_protein_labels_by_interaction_type_and_data_model">
+<span class="sig-name descname"><span class="pre">count_protein_labels_by_interaction_type_and_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.count_protein_labels_by_interaction_type_and_data_model" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_protein_labels_by_interaction_type_and_data_model_and_resource">
+<span class="sig-name descname"><span class="pre">count_protein_labels_by_interaction_type_and_data_model_and_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.count_protein_labels_by_interaction_type_and_data_model_and_resource" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_protein_labels_by_reference">
+<span class="sig-name descname"><span class="pre">count_protein_labels_by_reference</span></span><a class="headerlink" href="#pypath.core.network.Network.count_protein_labels_by_reference" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_protein_labels_by_resource">
+<span class="sig-name descname"><span class="pre">count_protein_labels_by_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.count_protein_labels_by_resource" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_proteins">
+<span class="sig-name descname"><span class="pre">count_proteins</span></span><a class="headerlink" href="#pypath.core.network.Network.count_proteins" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_proteins_by_data_model">
+<span class="sig-name descname"><span class="pre">count_proteins_by_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.count_proteins_by_data_model" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_proteins_by_interaction_type">
+<span class="sig-name descname"><span class="pre">count_proteins_by_interaction_type</span></span><a class="headerlink" href="#pypath.core.network.Network.count_proteins_by_interaction_type" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_proteins_by_interaction_type_and_data_model">
+<span class="sig-name descname"><span class="pre">count_proteins_by_interaction_type_and_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.count_proteins_by_interaction_type_and_data_model" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_proteins_by_interaction_type_and_data_model_and_resource">
+<span class="sig-name descname"><span class="pre">count_proteins_by_interaction_type_and_data_model_and_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.count_proteins_by_interaction_type_and_data_model_and_resource" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_proteins_by_reference">
+<span class="sig-name descname"><span class="pre">count_proteins_by_reference</span></span><a class="headerlink" href="#pypath.core.network.Network.count_proteins_by_reference" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_proteins_by_resource">
+<span class="sig-name descname"><span class="pre">count_proteins_by_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.count_proteins_by_resource" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_references">
+<span class="sig-name descname"><span class="pre">count_references</span></span><a class="headerlink" href="#pypath.core.network.Network.count_references" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_references_by_data_model">
+<span class="sig-name descname"><span class="pre">count_references_by_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.count_references_by_data_model" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_references_by_interaction_type">
+<span class="sig-name descname"><span class="pre">count_references_by_interaction_type</span></span><a class="headerlink" href="#pypath.core.network.Network.count_references_by_interaction_type" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_references_by_interaction_type_and_data_model">
+<span class="sig-name descname"><span class="pre">count_references_by_interaction_type_and_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.count_references_by_interaction_type_and_data_model" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_references_by_interaction_type_and_data_model_and_resource">
+<span class="sig-name descname"><span class="pre">count_references_by_interaction_type_and_data_model_and_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.count_references_by_interaction_type_and_data_model_and_resource" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_references_by_reference">
+<span class="sig-name descname"><span class="pre">count_references_by_reference</span></span><a class="headerlink" href="#pypath.core.network.Network.count_references_by_reference" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_references_by_resource">
+<span class="sig-name descname"><span class="pre">count_references_by_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.count_references_by_resource" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_regulated_by">
+<span class="sig-name descname"><span class="pre">count_regulated_by</span></span><a class="headerlink" href="#pypath.core.network.Network.count_regulated_by" title="Link to this definition">§</a></dt>
+<dd><p>Returns the count of the interacting partners for one or more
+entities according to the specified criteria.
+Please refer to the docs of the <code class="docutils literal notranslate"><span class="pre">partners</span></code> method.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_regulates">
+<span class="sig-name descname"><span class="pre">count_regulates</span></span><a class="headerlink" href="#pypath.core.network.Network.count_regulates" title="Link to this definition">§</a></dt>
+<dd><p>Returns the count of the interacting partners for one or more
+entities according to the specified criteria.
+Please refer to the docs of the <code class="docutils literal notranslate"><span class="pre">partners</span></code> method.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_resource_names">
+<span class="sig-name descname"><span class="pre">count_resource_names</span></span><a class="headerlink" href="#pypath.core.network.Network.count_resource_names" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_resource_names_by_data_model">
+<span class="sig-name descname"><span class="pre">count_resource_names_by_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.count_resource_names_by_data_model" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_resource_names_by_interaction_type">
+<span class="sig-name descname"><span class="pre">count_resource_names_by_interaction_type</span></span><a class="headerlink" href="#pypath.core.network.Network.count_resource_names_by_interaction_type" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_resource_names_by_interaction_type_and_data_model">
+<span class="sig-name descname"><span class="pre">count_resource_names_by_interaction_type_and_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.count_resource_names_by_interaction_type_and_data_model" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_resource_names_by_interaction_type_and_data_model_and_resource">
+<span class="sig-name descname"><span class="pre">count_resource_names_by_interaction_type_and_data_model_and_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.count_resource_names_by_interaction_type_and_data_model_and_resource" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_resource_names_by_reference">
+<span class="sig-name descname"><span class="pre">count_resource_names_by_reference</span></span><a class="headerlink" href="#pypath.core.network.Network.count_resource_names_by_reference" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_resource_names_by_resource">
+<span class="sig-name descname"><span class="pre">count_resource_names_by_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.count_resource_names_by_resource" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_resource_names_via">
+<span class="sig-name descname"><span class="pre">count_resource_names_via</span></span><a class="headerlink" href="#pypath.core.network.Network.count_resource_names_via" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_resource_names_via_by_data_model">
+<span class="sig-name descname"><span class="pre">count_resource_names_via_by_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.count_resource_names_via_by_data_model" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_resource_names_via_by_interaction_type">
+<span class="sig-name descname"><span class="pre">count_resource_names_via_by_interaction_type</span></span><a class="headerlink" href="#pypath.core.network.Network.count_resource_names_via_by_interaction_type" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_resource_names_via_by_interaction_type_and_data_model">
+<span class="sig-name descname"><span class="pre">count_resource_names_via_by_interaction_type_and_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.count_resource_names_via_by_interaction_type_and_data_model" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_resource_names_via_by_interaction_type_and_data_model_and_resource">
+<span class="sig-name descname"><span class="pre">count_resource_names_via_by_interaction_type_and_data_model_and_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.count_resource_names_via_by_interaction_type_and_data_model_and_resource" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_resource_names_via_by_reference">
+<span class="sig-name descname"><span class="pre">count_resource_names_via_by_reference</span></span><a class="headerlink" href="#pypath.core.network.Network.count_resource_names_via_by_reference" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_resource_names_via_by_resource">
+<span class="sig-name descname"><span class="pre">count_resource_names_via_by_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.count_resource_names_via_by_resource" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_resources">
+<span class="sig-name descname"><span class="pre">count_resources</span></span><a class="headerlink" href="#pypath.core.network.Network.count_resources" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_resources_by_data_model">
+<span class="sig-name descname"><span class="pre">count_resources_by_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.count_resources_by_data_model" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_resources_by_interaction_type">
+<span class="sig-name descname"><span class="pre">count_resources_by_interaction_type</span></span><a class="headerlink" href="#pypath.core.network.Network.count_resources_by_interaction_type" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_resources_by_interaction_type_and_data_model">
+<span class="sig-name descname"><span class="pre">count_resources_by_interaction_type_and_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.count_resources_by_interaction_type_and_data_model" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_resources_by_interaction_type_and_data_model_and_resource">
+<span class="sig-name descname"><span class="pre">count_resources_by_interaction_type_and_data_model_and_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.count_resources_by_interaction_type_and_data_model_and_resource" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_resources_by_reference">
+<span class="sig-name descname"><span class="pre">count_resources_by_reference</span></span><a class="headerlink" href="#pypath.core.network.Network.count_resources_by_reference" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_resources_by_resource">
+<span class="sig-name descname"><span class="pre">count_resources_by_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.count_resources_by_resource" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_resources_via">
+<span class="sig-name descname"><span class="pre">count_resources_via</span></span><a class="headerlink" href="#pypath.core.network.Network.count_resources_via" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_resources_via_by_data_model">
+<span class="sig-name descname"><span class="pre">count_resources_via_by_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.count_resources_via_by_data_model" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_resources_via_by_interaction_type">
+<span class="sig-name descname"><span class="pre">count_resources_via_by_interaction_type</span></span><a class="headerlink" href="#pypath.core.network.Network.count_resources_via_by_interaction_type" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_resources_via_by_interaction_type_and_data_model">
+<span class="sig-name descname"><span class="pre">count_resources_via_by_interaction_type_and_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.count_resources_via_by_interaction_type_and_data_model" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_resources_via_by_interaction_type_and_data_model_and_resource">
+<span class="sig-name descname"><span class="pre">count_resources_via_by_interaction_type_and_data_model_and_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.count_resources_via_by_interaction_type_and_data_model_and_resource" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_resources_via_by_reference">
+<span class="sig-name descname"><span class="pre">count_resources_via_by_reference</span></span><a class="headerlink" href="#pypath.core.network.Network.count_resources_via_by_reference" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_resources_via_by_resource">
+<span class="sig-name descname"><span class="pre">count_resources_via_by_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.count_resources_via_by_resource" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_small_molecule_identifiers">
+<span class="sig-name descname"><span class="pre">count_small_molecule_identifiers</span></span><a class="headerlink" href="#pypath.core.network.Network.count_small_molecule_identifiers" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_small_molecule_identifiers_by_data_model">
+<span class="sig-name descname"><span class="pre">count_small_molecule_identifiers_by_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.count_small_molecule_identifiers_by_data_model" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_small_molecule_identifiers_by_interaction_type">
+<span class="sig-name descname"><span class="pre">count_small_molecule_identifiers_by_interaction_type</span></span><a class="headerlink" href="#pypath.core.network.Network.count_small_molecule_identifiers_by_interaction_type" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_small_molecule_identifiers_by_interaction_type_and_data_model">
+<span class="sig-name descname"><span class="pre">count_small_molecule_identifiers_by_interaction_type_and_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.count_small_molecule_identifiers_by_interaction_type_and_data_model" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_small_molecule_identifiers_by_interaction_type_and_data_model_and_resource">
+<span class="sig-name descname"><span class="pre">count_small_molecule_identifiers_by_interaction_type_and_data_model_and_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.count_small_molecule_identifiers_by_interaction_type_and_data_model_and_resource" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_small_molecule_identifiers_by_reference">
+<span class="sig-name descname"><span class="pre">count_small_molecule_identifiers_by_reference</span></span><a class="headerlink" href="#pypath.core.network.Network.count_small_molecule_identifiers_by_reference" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_small_molecule_identifiers_by_resource">
+<span class="sig-name descname"><span class="pre">count_small_molecule_identifiers_by_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.count_small_molecule_identifiers_by_resource" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_small_molecule_labels">
+<span class="sig-name descname"><span class="pre">count_small_molecule_labels</span></span><a class="headerlink" href="#pypath.core.network.Network.count_small_molecule_labels" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_small_molecule_labels_by_data_model">
+<span class="sig-name descname"><span class="pre">count_small_molecule_labels_by_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.count_small_molecule_labels_by_data_model" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_small_molecule_labels_by_interaction_type">
+<span class="sig-name descname"><span class="pre">count_small_molecule_labels_by_interaction_type</span></span><a class="headerlink" href="#pypath.core.network.Network.count_small_molecule_labels_by_interaction_type" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_small_molecule_labels_by_interaction_type_and_data_model">
+<span class="sig-name descname"><span class="pre">count_small_molecule_labels_by_interaction_type_and_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.count_small_molecule_labels_by_interaction_type_and_data_model" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_small_molecule_labels_by_interaction_type_and_data_model_and_resource">
+<span class="sig-name descname"><span class="pre">count_small_molecule_labels_by_interaction_type_and_data_model_and_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.count_small_molecule_labels_by_interaction_type_and_data_model_and_resource" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_small_molecule_labels_by_reference">
+<span class="sig-name descname"><span class="pre">count_small_molecule_labels_by_reference</span></span><a class="headerlink" href="#pypath.core.network.Network.count_small_molecule_labels_by_reference" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_small_molecule_labels_by_resource">
+<span class="sig-name descname"><span class="pre">count_small_molecule_labels_by_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.count_small_molecule_labels_by_resource" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_small_molecules">
+<span class="sig-name descname"><span class="pre">count_small_molecules</span></span><a class="headerlink" href="#pypath.core.network.Network.count_small_molecules" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_small_molecules_by_data_model">
+<span class="sig-name descname"><span class="pre">count_small_molecules_by_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.count_small_molecules_by_data_model" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_small_molecules_by_interaction_type">
+<span class="sig-name descname"><span class="pre">count_small_molecules_by_interaction_type</span></span><a class="headerlink" href="#pypath.core.network.Network.count_small_molecules_by_interaction_type" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_small_molecules_by_interaction_type_and_data_model">
+<span class="sig-name descname"><span class="pre">count_small_molecules_by_interaction_type_and_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.count_small_molecules_by_interaction_type_and_data_model" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_small_molecules_by_interaction_type_and_data_model_and_resource">
+<span class="sig-name descname"><span class="pre">count_small_molecules_by_interaction_type_and_data_model_and_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.count_small_molecules_by_interaction_type_and_data_model_and_resource" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_small_molecules_by_reference">
+<span class="sig-name descname"><span class="pre">count_small_molecules_by_reference</span></span><a class="headerlink" href="#pypath.core.network.Network.count_small_molecules_by_reference" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_small_molecules_by_resource">
+<span class="sig-name descname"><span class="pre">count_small_molecules_by_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.count_small_molecules_by_resource" title="Link to this definition">§</a></dt>
+<dd><p>str(object=’’) -&gt; str
+str(bytes_or_buffer[, encoding[, errors]]) -&gt; str</p>
+<p>Create a new string object from the given object. If encoding or
+errors is specified, then the object must expose a data buffer
+that will be decoded using the given encoding and error handler.
+Otherwise, returns the result of object.__str__() (if defined)
+or repr(object).
+encoding defaults to sys.getdefaultencoding().
+errors defaults to ‘strict’.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_suppressed_by">
+<span class="sig-name descname"><span class="pre">count_suppressed_by</span></span><a class="headerlink" href="#pypath.core.network.Network.count_suppressed_by" title="Link to this definition">§</a></dt>
+<dd><p>Returns the count of the interacting partners for one or more
+entities according to the specified criteria.
+Please refer to the docs of the <code class="docutils literal notranslate"><span class="pre">partners</span></code> method.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_suppresses">
+<span class="sig-name descname"><span class="pre">count_suppresses</span></span><a class="headerlink" href="#pypath.core.network.Network.count_suppresses" title="Link to this definition">§</a></dt>
+<dd><p>Returns the count of the interacting partners for one or more
+entities according to the specified criteria.
+Please refer to the docs of the <code class="docutils literal notranslate"><span class="pre">partners</span></code> method.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_transcriptionally_activated_by">
+<span class="sig-name descname"><span class="pre">count_transcriptionally_activated_by</span></span><a class="headerlink" href="#pypath.core.network.Network.count_transcriptionally_activated_by" title="Link to this definition">§</a></dt>
+<dd><p>Returns the count of the interacting partners for one or more
+entities according to the specified criteria.
+Please refer to the docs of the <code class="docutils literal notranslate"><span class="pre">partners</span></code> method.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_transcriptionally_activates">
+<span class="sig-name descname"><span class="pre">count_transcriptionally_activates</span></span><a class="headerlink" href="#pypath.core.network.Network.count_transcriptionally_activates" title="Link to this definition">§</a></dt>
+<dd><p>Returns the count of the interacting partners for one or more
+entities according to the specified criteria.
+Please refer to the docs of the <code class="docutils literal notranslate"><span class="pre">partners</span></code> method.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_transcriptionally_regulated_by">
+<span class="sig-name descname"><span class="pre">count_transcriptionally_regulated_by</span></span><a class="headerlink" href="#pypath.core.network.Network.count_transcriptionally_regulated_by" title="Link to this definition">§</a></dt>
+<dd><p>Returns the count of the interacting partners for one or more
+entities according to the specified criteria.
+Please refer to the docs of the <code class="docutils literal notranslate"><span class="pre">partners</span></code> method.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_transcriptionally_regulates">
+<span class="sig-name descname"><span class="pre">count_transcriptionally_regulates</span></span><a class="headerlink" href="#pypath.core.network.Network.count_transcriptionally_regulates" title="Link to this definition">§</a></dt>
+<dd><p>Returns the count of the interacting partners for one or more
+entities according to the specified criteria.
+Please refer to the docs of the <code class="docutils literal notranslate"><span class="pre">partners</span></code> method.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_transcriptionally_suppressed_by">
+<span class="sig-name descname"><span class="pre">count_transcriptionally_suppressed_by</span></span><a class="headerlink" href="#pypath.core.network.Network.count_transcriptionally_suppressed_by" title="Link to this definition">§</a></dt>
+<dd><p>Returns the count of the interacting partners for one or more
+entities according to the specified criteria.
+Please refer to the docs of the <code class="docutils literal notranslate"><span class="pre">partners</span></code> method.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.count_transcriptionally_suppresses">
+<span class="sig-name descname"><span class="pre">count_transcriptionally_suppresses</span></span><a class="headerlink" href="#pypath.core.network.Network.count_transcriptionally_suppresses" title="Link to this definition">§</a></dt>
+<dd><p>Returns the count of the interacting partners for one or more
+entities according to the specified criteria.
+Please refer to the docs of the <code class="docutils literal notranslate"><span class="pre">partners</span></code> method.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.curation_effort_by_data_model">
+<span class="sig-name descname"><span class="pre">curation_effort_by_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.curation_effort_by_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.curation_effort_by_interaction_type">
+<span class="sig-name descname"><span class="pre">curation_effort_by_interaction_type</span></span><a class="headerlink" href="#pypath.core.network.Network.curation_effort_by_interaction_type" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.curation_effort_by_interaction_type_and_data_model">
+<span class="sig-name descname"><span class="pre">curation_effort_by_interaction_type_and_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.curation_effort_by_interaction_type_and_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.curation_effort_by_interaction_type_and_data_model_and_resource">
+<span class="sig-name descname"><span class="pre">curation_effort_by_interaction_type_and_data_model_and_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.curation_effort_by_interaction_type_and_data_model_and_resource" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.curation_effort_by_reference">
+<span class="sig-name descname"><span class="pre">curation_effort_by_reference</span></span><a class="headerlink" href="#pypath.core.network.Network.curation_effort_by_reference" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.curation_effort_by_resource">
+<span class="sig-name descname"><span class="pre">curation_effort_by_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.curation_effort_by_resource" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.data_models_by_data_model">
+<span class="sig-name descname"><span class="pre">data_models_by_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.data_models_by_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.data_models_by_interaction_type">
+<span class="sig-name descname"><span class="pre">data_models_by_interaction_type</span></span><a class="headerlink" href="#pypath.core.network.Network.data_models_by_interaction_type" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.data_models_by_interaction_type_and_data_model">
+<span class="sig-name descname"><span class="pre">data_models_by_interaction_type_and_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.data_models_by_interaction_type_and_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.data_models_by_interaction_type_and_data_model_and_resource">
+<span class="sig-name descname"><span class="pre">data_models_by_interaction_type_and_data_model_and_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.data_models_by_interaction_type_and_data_model_and_resource" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.data_models_by_reference">
+<span class="sig-name descname"><span class="pre">data_models_by_reference</span></span><a class="headerlink" href="#pypath.core.network.Network.data_models_by_reference" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.data_models_by_resource">
+<span class="sig-name descname"><span class="pre">data_models_by_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.data_models_by_resource" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.datasets_by_data_model">
+<span class="sig-name descname"><span class="pre">datasets_by_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.datasets_by_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.datasets_by_interaction_type">
+<span class="sig-name descname"><span class="pre">datasets_by_interaction_type</span></span><a class="headerlink" href="#pypath.core.network.Network.datasets_by_interaction_type" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.datasets_by_interaction_type_and_data_model">
+<span class="sig-name descname"><span class="pre">datasets_by_interaction_type_and_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.datasets_by_interaction_type_and_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.datasets_by_interaction_type_and_data_model_and_resource">
+<span class="sig-name descname"><span class="pre">datasets_by_interaction_type_and_data_model_and_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.datasets_by_interaction_type_and_data_model_and_resource" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.datasets_by_reference">
+<span class="sig-name descname"><span class="pre">datasets_by_reference</span></span><a class="headerlink" href="#pypath.core.network.Network.datasets_by_reference" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.datasets_by_resource">
+<span class="sig-name descname"><span class="pre">datasets_by_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.datasets_by_resource" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.degrees_directed_by_data_model">
+<span class="sig-name descname"><span class="pre">degrees_directed_by_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.degrees_directed_by_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.degrees_directed_by_interaction_type">
+<span class="sig-name descname"><span class="pre">degrees_directed_by_interaction_type</span></span><a class="headerlink" href="#pypath.core.network.Network.degrees_directed_by_interaction_type" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.degrees_directed_by_interaction_type_and_data_model">
+<span class="sig-name descname"><span class="pre">degrees_directed_by_interaction_type_and_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.degrees_directed_by_interaction_type_and_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.degrees_directed_by_interaction_type_and_data_model_and_resource">
+<span class="sig-name descname"><span class="pre">degrees_directed_by_interaction_type_and_data_model_and_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.degrees_directed_by_interaction_type_and_data_model_and_resource" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.degrees_directed_by_reference">
+<span class="sig-name descname"><span class="pre">degrees_directed_by_reference</span></span><a class="headerlink" href="#pypath.core.network.Network.degrees_directed_by_reference" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.degrees_directed_by_resource">
+<span class="sig-name descname"><span class="pre">degrees_directed_by_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.degrees_directed_by_resource" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.degrees_directed_in_by_data_model">
+<span class="sig-name descname"><span class="pre">degrees_directed_in_by_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.degrees_directed_in_by_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.degrees_directed_in_by_interaction_type">
+<span class="sig-name descname"><span class="pre">degrees_directed_in_by_interaction_type</span></span><a class="headerlink" href="#pypath.core.network.Network.degrees_directed_in_by_interaction_type" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.degrees_directed_in_by_interaction_type_and_data_model">
+<span class="sig-name descname"><span class="pre">degrees_directed_in_by_interaction_type_and_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.degrees_directed_in_by_interaction_type_and_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.degrees_directed_in_by_interaction_type_and_data_model_and_resource">
+<span class="sig-name descname"><span class="pre">degrees_directed_in_by_interaction_type_and_data_model_and_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.degrees_directed_in_by_interaction_type_and_data_model_and_resource" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.degrees_directed_in_by_reference">
+<span class="sig-name descname"><span class="pre">degrees_directed_in_by_reference</span></span><a class="headerlink" href="#pypath.core.network.Network.degrees_directed_in_by_reference" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.degrees_directed_in_by_resource">
+<span class="sig-name descname"><span class="pre">degrees_directed_in_by_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.degrees_directed_in_by_resource" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.degrees_directed_out_by_data_model">
+<span class="sig-name descname"><span class="pre">degrees_directed_out_by_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.degrees_directed_out_by_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.degrees_directed_out_by_interaction_type">
+<span class="sig-name descname"><span class="pre">degrees_directed_out_by_interaction_type</span></span><a class="headerlink" href="#pypath.core.network.Network.degrees_directed_out_by_interaction_type" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.degrees_directed_out_by_interaction_type_and_data_model">
+<span class="sig-name descname"><span class="pre">degrees_directed_out_by_interaction_type_and_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.degrees_directed_out_by_interaction_type_and_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.degrees_directed_out_by_interaction_type_and_data_model_and_resource">
+<span class="sig-name descname"><span class="pre">degrees_directed_out_by_interaction_type_and_data_model_and_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.degrees_directed_out_by_interaction_type_and_data_model_and_resource" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.degrees_directed_out_by_reference">
+<span class="sig-name descname"><span class="pre">degrees_directed_out_by_reference</span></span><a class="headerlink" href="#pypath.core.network.Network.degrees_directed_out_by_reference" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.degrees_directed_out_by_resource">
+<span class="sig-name descname"><span class="pre">degrees_directed_out_by_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.degrees_directed_out_by_resource" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.degrees_negative_by_data_model">
+<span class="sig-name descname"><span class="pre">degrees_negative_by_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.degrees_negative_by_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.degrees_negative_by_interaction_type">
+<span class="sig-name descname"><span class="pre">degrees_negative_by_interaction_type</span></span><a class="headerlink" href="#pypath.core.network.Network.degrees_negative_by_interaction_type" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.degrees_negative_by_interaction_type_and_data_model">
+<span class="sig-name descname"><span class="pre">degrees_negative_by_interaction_type_and_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.degrees_negative_by_interaction_type_and_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.degrees_negative_by_interaction_type_and_data_model_and_resource">
+<span class="sig-name descname"><span class="pre">degrees_negative_by_interaction_type_and_data_model_and_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.degrees_negative_by_interaction_type_and_data_model_and_resource" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.degrees_negative_by_reference">
+<span class="sig-name descname"><span class="pre">degrees_negative_by_reference</span></span><a class="headerlink" href="#pypath.core.network.Network.degrees_negative_by_reference" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.degrees_negative_by_resource">
+<span class="sig-name descname"><span class="pre">degrees_negative_by_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.degrees_negative_by_resource" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.degrees_negative_in_by_data_model">
+<span class="sig-name descname"><span class="pre">degrees_negative_in_by_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.degrees_negative_in_by_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.degrees_negative_in_by_interaction_type">
+<span class="sig-name descname"><span class="pre">degrees_negative_in_by_interaction_type</span></span><a class="headerlink" href="#pypath.core.network.Network.degrees_negative_in_by_interaction_type" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.degrees_negative_in_by_interaction_type_and_data_model">
+<span class="sig-name descname"><span class="pre">degrees_negative_in_by_interaction_type_and_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.degrees_negative_in_by_interaction_type_and_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.degrees_negative_in_by_interaction_type_and_data_model_and_resource">
+<span class="sig-name descname"><span class="pre">degrees_negative_in_by_interaction_type_and_data_model_and_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.degrees_negative_in_by_interaction_type_and_data_model_and_resource" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.degrees_negative_in_by_reference">
+<span class="sig-name descname"><span class="pre">degrees_negative_in_by_reference</span></span><a class="headerlink" href="#pypath.core.network.Network.degrees_negative_in_by_reference" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.degrees_negative_in_by_resource">
+<span class="sig-name descname"><span class="pre">degrees_negative_in_by_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.degrees_negative_in_by_resource" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.degrees_negative_out_by_data_model">
+<span class="sig-name descname"><span class="pre">degrees_negative_out_by_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.degrees_negative_out_by_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.degrees_negative_out_by_interaction_type">
+<span class="sig-name descname"><span class="pre">degrees_negative_out_by_interaction_type</span></span><a class="headerlink" href="#pypath.core.network.Network.degrees_negative_out_by_interaction_type" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.degrees_negative_out_by_interaction_type_and_data_model">
+<span class="sig-name descname"><span class="pre">degrees_negative_out_by_interaction_type_and_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.degrees_negative_out_by_interaction_type_and_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.degrees_negative_out_by_interaction_type_and_data_model_and_resource">
+<span class="sig-name descname"><span class="pre">degrees_negative_out_by_interaction_type_and_data_model_and_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.degrees_negative_out_by_interaction_type_and_data_model_and_resource" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.degrees_negative_out_by_reference">
+<span class="sig-name descname"><span class="pre">degrees_negative_out_by_reference</span></span><a class="headerlink" href="#pypath.core.network.Network.degrees_negative_out_by_reference" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.degrees_negative_out_by_resource">
+<span class="sig-name descname"><span class="pre">degrees_negative_out_by_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.degrees_negative_out_by_resource" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.degrees_non_directed_by_data_model">
+<span class="sig-name descname"><span class="pre">degrees_non_directed_by_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.degrees_non_directed_by_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.degrees_non_directed_by_interaction_type">
+<span class="sig-name descname"><span class="pre">degrees_non_directed_by_interaction_type</span></span><a class="headerlink" href="#pypath.core.network.Network.degrees_non_directed_by_interaction_type" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.degrees_non_directed_by_interaction_type_and_data_model">
+<span class="sig-name descname"><span class="pre">degrees_non_directed_by_interaction_type_and_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.degrees_non_directed_by_interaction_type_and_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.degrees_non_directed_by_interaction_type_and_data_model_and_resource">
+<span class="sig-name descname"><span class="pre">degrees_non_directed_by_interaction_type_and_data_model_and_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.degrees_non_directed_by_interaction_type_and_data_model_and_resource" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.degrees_non_directed_by_reference">
+<span class="sig-name descname"><span class="pre">degrees_non_directed_by_reference</span></span><a class="headerlink" href="#pypath.core.network.Network.degrees_non_directed_by_reference" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.degrees_non_directed_by_resource">
+<span class="sig-name descname"><span class="pre">degrees_non_directed_by_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.degrees_non_directed_by_resource" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.degrees_positive_by_data_model">
+<span class="sig-name descname"><span class="pre">degrees_positive_by_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.degrees_positive_by_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.degrees_positive_by_interaction_type">
+<span class="sig-name descname"><span class="pre">degrees_positive_by_interaction_type</span></span><a class="headerlink" href="#pypath.core.network.Network.degrees_positive_by_interaction_type" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.degrees_positive_by_interaction_type_and_data_model">
+<span class="sig-name descname"><span class="pre">degrees_positive_by_interaction_type_and_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.degrees_positive_by_interaction_type_and_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.degrees_positive_by_interaction_type_and_data_model_and_resource">
+<span class="sig-name descname"><span class="pre">degrees_positive_by_interaction_type_and_data_model_and_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.degrees_positive_by_interaction_type_and_data_model_and_resource" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.degrees_positive_by_reference">
+<span class="sig-name descname"><span class="pre">degrees_positive_by_reference</span></span><a class="headerlink" href="#pypath.core.network.Network.degrees_positive_by_reference" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.degrees_positive_by_resource">
+<span class="sig-name descname"><span class="pre">degrees_positive_by_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.degrees_positive_by_resource" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.degrees_positive_in_by_data_model">
+<span class="sig-name descname"><span class="pre">degrees_positive_in_by_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.degrees_positive_in_by_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.degrees_positive_in_by_interaction_type">
+<span class="sig-name descname"><span class="pre">degrees_positive_in_by_interaction_type</span></span><a class="headerlink" href="#pypath.core.network.Network.degrees_positive_in_by_interaction_type" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.degrees_positive_in_by_interaction_type_and_data_model">
+<span class="sig-name descname"><span class="pre">degrees_positive_in_by_interaction_type_and_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.degrees_positive_in_by_interaction_type_and_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.degrees_positive_in_by_interaction_type_and_data_model_and_resource">
+<span class="sig-name descname"><span class="pre">degrees_positive_in_by_interaction_type_and_data_model_and_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.degrees_positive_in_by_interaction_type_and_data_model_and_resource" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.degrees_positive_in_by_reference">
+<span class="sig-name descname"><span class="pre">degrees_positive_in_by_reference</span></span><a class="headerlink" href="#pypath.core.network.Network.degrees_positive_in_by_reference" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.degrees_positive_in_by_resource">
+<span class="sig-name descname"><span class="pre">degrees_positive_in_by_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.degrees_positive_in_by_resource" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.degrees_positive_out_by_data_model">
+<span class="sig-name descname"><span class="pre">degrees_positive_out_by_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.degrees_positive_out_by_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.degrees_positive_out_by_interaction_type">
+<span class="sig-name descname"><span class="pre">degrees_positive_out_by_interaction_type</span></span><a class="headerlink" href="#pypath.core.network.Network.degrees_positive_out_by_interaction_type" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.degrees_positive_out_by_interaction_type_and_data_model">
+<span class="sig-name descname"><span class="pre">degrees_positive_out_by_interaction_type_and_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.degrees_positive_out_by_interaction_type_and_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.degrees_positive_out_by_interaction_type_and_data_model_and_resource">
+<span class="sig-name descname"><span class="pre">degrees_positive_out_by_interaction_type_and_data_model_and_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.degrees_positive_out_by_interaction_type_and_data_model_and_resource" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.degrees_positive_out_by_reference">
+<span class="sig-name descname"><span class="pre">degrees_positive_out_by_reference</span></span><a class="headerlink" href="#pypath.core.network.Network.degrees_positive_out_by_reference" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.degrees_positive_out_by_resource">
+<span class="sig-name descname"><span class="pre">degrees_positive_out_by_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.degrees_positive_out_by_resource" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.degrees_signed_by_data_model">
+<span class="sig-name descname"><span class="pre">degrees_signed_by_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.degrees_signed_by_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.degrees_signed_by_interaction_type">
+<span class="sig-name descname"><span class="pre">degrees_signed_by_interaction_type</span></span><a class="headerlink" href="#pypath.core.network.Network.degrees_signed_by_interaction_type" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.degrees_signed_by_interaction_type_and_data_model">
+<span class="sig-name descname"><span class="pre">degrees_signed_by_interaction_type_and_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.degrees_signed_by_interaction_type_and_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.degrees_signed_by_interaction_type_and_data_model_and_resource">
+<span class="sig-name descname"><span class="pre">degrees_signed_by_interaction_type_and_data_model_and_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.degrees_signed_by_interaction_type_and_data_model_and_resource" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.degrees_signed_by_reference">
+<span class="sig-name descname"><span class="pre">degrees_signed_by_reference</span></span><a class="headerlink" href="#pypath.core.network.Network.degrees_signed_by_reference" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.degrees_signed_by_resource">
+<span class="sig-name descname"><span class="pre">degrees_signed_by_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.degrees_signed_by_resource" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.degrees_signed_in_by_data_model">
+<span class="sig-name descname"><span class="pre">degrees_signed_in_by_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.degrees_signed_in_by_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.degrees_signed_in_by_interaction_type">
+<span class="sig-name descname"><span class="pre">degrees_signed_in_by_interaction_type</span></span><a class="headerlink" href="#pypath.core.network.Network.degrees_signed_in_by_interaction_type" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.degrees_signed_in_by_interaction_type_and_data_model">
+<span class="sig-name descname"><span class="pre">degrees_signed_in_by_interaction_type_and_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.degrees_signed_in_by_interaction_type_and_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.degrees_signed_in_by_interaction_type_and_data_model_and_resource">
+<span class="sig-name descname"><span class="pre">degrees_signed_in_by_interaction_type_and_data_model_and_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.degrees_signed_in_by_interaction_type_and_data_model_and_resource" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.degrees_signed_in_by_reference">
+<span class="sig-name descname"><span class="pre">degrees_signed_in_by_reference</span></span><a class="headerlink" href="#pypath.core.network.Network.degrees_signed_in_by_reference" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.degrees_signed_in_by_resource">
+<span class="sig-name descname"><span class="pre">degrees_signed_in_by_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.degrees_signed_in_by_resource" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.degrees_signed_out_by_data_model">
+<span class="sig-name descname"><span class="pre">degrees_signed_out_by_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.degrees_signed_out_by_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.degrees_signed_out_by_interaction_type">
+<span class="sig-name descname"><span class="pre">degrees_signed_out_by_interaction_type</span></span><a class="headerlink" href="#pypath.core.network.Network.degrees_signed_out_by_interaction_type" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.degrees_signed_out_by_interaction_type_and_data_model">
+<span class="sig-name descname"><span class="pre">degrees_signed_out_by_interaction_type_and_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.degrees_signed_out_by_interaction_type_and_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.degrees_signed_out_by_interaction_type_and_data_model_and_resource">
+<span class="sig-name descname"><span class="pre">degrees_signed_out_by_interaction_type_and_data_model_and_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.degrees_signed_out_by_interaction_type_and_data_model_and_resource" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.degrees_signed_out_by_reference">
+<span class="sig-name descname"><span class="pre">degrees_signed_out_by_reference</span></span><a class="headerlink" href="#pypath.core.network.Network.degrees_signed_out_by_reference" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.degrees_signed_out_by_resource">
+<span class="sig-name descname"><span class="pre">degrees_signed_out_by_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.degrees_signed_out_by_resource" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.degrees_undirected_by_data_model">
+<span class="sig-name descname"><span class="pre">degrees_undirected_by_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.degrees_undirected_by_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.degrees_undirected_by_interaction_type">
+<span class="sig-name descname"><span class="pre">degrees_undirected_by_interaction_type</span></span><a class="headerlink" href="#pypath.core.network.Network.degrees_undirected_by_interaction_type" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.degrees_undirected_by_interaction_type_and_data_model">
+<span class="sig-name descname"><span class="pre">degrees_undirected_by_interaction_type_and_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.degrees_undirected_by_interaction_type_and_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.degrees_undirected_by_interaction_type_and_data_model_and_resource">
+<span class="sig-name descname"><span class="pre">degrees_undirected_by_interaction_type_and_data_model_and_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.degrees_undirected_by_interaction_type_and_data_model_and_resource" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.degrees_undirected_by_reference">
+<span class="sig-name descname"><span class="pre">degrees_undirected_by_reference</span></span><a class="headerlink" href="#pypath.core.network.Network.degrees_undirected_by_reference" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.degrees_undirected_by_resource">
+<span class="sig-name descname"><span class="pre">degrees_undirected_by_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.degrees_undirected_by_resource" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.network.Network.direction_consistency">
+<span class="sig-name descname"><span class="pre">direction_consistency</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/network.html#Network.direction_consistency"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.network.Network.direction_consistency" title="Link to this definition">§</a></dt>
+<dd><p>Collects statistics about the consistency of interaction
+directions between resources.
+* total_directed: number of directed edges
+* shared_directed: number of directed edges in overlap with other</p>
+<blockquote>
+<div><p>resources</p>
+</div></blockquote>
+<ul class="simple">
+<li><p>consistent_edges: number of edges consistent with other resources</p></li>
+<li><p>inconsistent_edges: number of edges inconsistent with other
+resources</p></li>
+<li><p>total_consistency: sum of consistencies (for all edges and all
+resources)</p></li>
+<li><p>total_inconsistency: sum of inconsistencies (for all edges and all
+resources)</p></li>
+</ul>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.network.Network.dorothea">
+<em class="property"><span class="pre">classmethod</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">dorothea</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">levels</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/network.html#Network.dorothea"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.network.Network.dorothea" title="Link to this definition">§</a></dt>
+<dd><p>Initializes a new <code class="docutils literal notranslate"><span class="pre">Network</span></code> object with loading the transcriptional
+regulation network from DoRothEA.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><p><strong>levels</strong> (<em>NontType</em><em>,</em><em>set</em>) – The confidence levels to include.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.entities_by_data_model">
+<span class="sig-name descname"><span class="pre">entities_by_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.entities_by_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.entities_by_interaction_type">
+<span class="sig-name descname"><span class="pre">entities_by_interaction_type</span></span><a class="headerlink" href="#pypath.core.network.Network.entities_by_interaction_type" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.entities_by_interaction_type_and_data_model">
+<span class="sig-name descname"><span class="pre">entities_by_interaction_type_and_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.entities_by_interaction_type_and_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.entities_by_interaction_type_and_data_model_and_resource">
+<span class="sig-name descname"><span class="pre">entities_by_interaction_type_and_data_model_and_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.entities_by_interaction_type_and_data_model_and_resource" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.entities_by_reference">
+<span class="sig-name descname"><span class="pre">entities_by_reference</span></span><a class="headerlink" href="#pypath.core.network.Network.entities_by_reference" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.entities_by_resource">
+<span class="sig-name descname"><span class="pre">entities_by_resource</span></span><a class="reference internal" href="../_modules/pypath/core/network.html#Network.entities_by_resource"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.network.Network.entities_by_resource" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.network.Network.entity_by_id">
+<span class="sig-name descname"><span class="pre">entity_by_id</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">identifier</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/network.html#Network.entity_by_id"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.network.Network.entity_by_id" title="Link to this definition">§</a></dt>
+<dd><p>Returns a <code class="docutils literal notranslate"><span class="pre">pypath.entity.Entity</span></code> object representing a molecular
+entity by looking it up by its identifier. If the molecule does not
+present in the current network <code class="docutils literal notranslate"><span class="pre">None</span></code> will be returned.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><p><strong>identifier</strong> (<em>str</em>) – The identifier of a molecular entity. Unless it’s been set
+otherwise for genes/proteins it is the UniProt ID.
+E.g. <code class="docutils literal notranslate"><span class="pre">'P00533'</span></code>.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.network.Network.entity_by_label">
+<span class="sig-name descname"><span class="pre">entity_by_label</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">label</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/network.html#Network.entity_by_label"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.network.Network.entity_by_label" title="Link to this definition">§</a></dt>
+<dd><p>Returns a <code class="docutils literal notranslate"><span class="pre">pypath.entity.Entity</span></code> object representing a molecular
+entity by looking it up by its label. If the molecule does not
+present in the current network <code class="docutils literal notranslate"><span class="pre">None</span></code> will be returned.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><p><strong>label</strong> (<em>str</em>) – The label of a molecular entity. Unless it’s been set otherwise
+for genes/proteins it is the Gene Symbol. E.g. <code class="docutils literal notranslate"><span class="pre">'EGFR'</span></code>.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.evidences_by_data_model">
+<span class="sig-name descname"><span class="pre">evidences_by_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.evidences_by_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.evidences_by_interaction_type">
+<span class="sig-name descname"><span class="pre">evidences_by_interaction_type</span></span><a class="headerlink" href="#pypath.core.network.Network.evidences_by_interaction_type" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.evidences_by_interaction_type_and_data_model">
+<span class="sig-name descname"><span class="pre">evidences_by_interaction_type_and_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.evidences_by_interaction_type_and_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.evidences_by_interaction_type_and_data_model_and_resource">
+<span class="sig-name descname"><span class="pre">evidences_by_interaction_type_and_data_model_and_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.evidences_by_interaction_type_and_data_model_and_resource" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.evidences_by_reference">
+<span class="sig-name descname"><span class="pre">evidences_by_reference</span></span><a class="headerlink" href="#pypath.core.network.Network.evidences_by_reference" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.evidences_by_resource">
+<span class="sig-name descname"><span class="pre">evidences_by_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.evidences_by_resource" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.network.Network.extra_directions">
+<span class="sig-name descname"><span class="pre">extra_directions</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'extra_directions'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_laudanna</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_string</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">dataset</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'directionextra'</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/network.html#Network.extra_directions"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.network.Network.extra_directions" title="Link to this definition">§</a></dt>
+<dd><p>Adds additional direction &amp; effect information from resources having
+no literature curated references, but giving sufficient evidence
+about the directionality for interactions already supported by
+literature evidences from other sources.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.network.Network.find_paths">
+<span class="sig-name descname"><span class="pre">find_paths</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">start</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference internal" href="pypath.core.entity.Entity.html#pypath.core.entity.Entity" title="pypath.core.entity.Entity"><span class="pre">entity.Entity</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference internal" href="pypath.core.entity.EntityList.html#pypath.core.entity.EntityList" title="pypath.core.entity.EntityList"><span class="pre">entity.EntityList</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">Iterable</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference internal" href="pypath.core.entity.Entity.html#pypath.core.entity.Entity" title="pypath.core.entity.Entity"><span class="pre">entity.Entity</span></a><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="n"><span class="pre">end</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference internal" href="pypath.core.entity.Entity.html#pypath.core.entity.Entity" title="pypath.core.entity.Entity"><span class="pre">entity.Entity</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference internal" href="pypath.core.entity.EntityList.html#pypath.core.entity.EntityList" title="pypath.core.entity.EntityList"><span class="pre">entity.EntityList</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">Iterable</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference internal" href="pypath.core.entity.Entity.html#pypath.core.entity.Entity" title="pypath.core.entity.Entity"><span class="pre">entity.Entity</span></a><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">loops</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">mode</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">Literal</span><span class="p"><span class="pre">[</span></span><span class="s"><span class="pre">'OUT'</span></span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="s"><span class="pre">'IN'</span></span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="s"><span class="pre">'ALL'</span></span><span class="p"><span class="pre">]</span></span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">'OUT'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">maxlen</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">2</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">minlen</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">direction</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">tuple</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">set</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">set</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">set</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">set</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">set</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">silent</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/network.html#Network.find_paths"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.network.Network.find_paths" title="Link to this definition">§</a></dt>
+<dd><p>Find paths or motifs in a network.</p>
+<p>Finds all paths up to length <code class="docutils literal notranslate"><span class="pre">maxlen</span></code> between groups of nodes.
+In addition is able to search for motifs or select the nodes of a
+subnetwork around certain nodes.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>start:</dt><dd><p>Starting node(s) of the paths.</p>
+</dd>
+<dt>end:</dt><dd><p>Target node(s) of the paths. If <code class="docutils literal notranslate"><span class="pre">None</span></code> any target node will
+be accepted and all paths from the starting nodes with length
+<code class="docutils literal notranslate"><span class="pre">maxlen</span></code> will be returned.</p>
+</dd>
+<dt>loops:</dt><dd><p>Search for loops, i.e. the start and end nodes of each path
+should be the same.</p>
+</dd>
+<dt>mode:</dt><dd><p>Direction of the paths. <code class="docutils literal notranslate"><span class="pre">'OUT'</span></code> means from <code class="docutils literal notranslate"><span class="pre">start</span></code> to <code class="docutils literal notranslate"><span class="pre">end</span></code>,
+<code class="docutils literal notranslate"><span class="pre">'IN'</span></code> the opposite direction while <code class="docutils literal notranslate"><span class="pre">'ALL'</span></code> both directions.</p>
+</dd>
+<dt>maxlen:</dt><dd><p>Maximum length of paths in steps, i.e. if maxlen = 3, then
+the longest path may consist of 3 edges and 4 nodes.</p>
+</dd>
+<dt>minlen:</dt><dd><p>Minimum length of the path.</p>
+</dd>
+<dt>silent:</dt><dd><p>Indicate progress by showing a progress bar.</p>
+</dd>
+</dl>
+</dd>
+<dt>Details</dt><dd><p>The arguments: <code class="docutils literal notranslate"><span class="pre">direction</span></code>, <code class="docutils literal notranslate"><span class="pre">effect</span></code>, <code class="docutils literal notranslate"><span class="pre">resources</span></code>,
+<code class="docutils literal notranslate"><span class="pre">interaction_type</span></code>, <code class="docutils literal notranslate"><span class="pre">data_model</span></code>, <code class="docutils literal notranslate"><span class="pre">via</span></code> and <code class="docutils literal notranslate"><span class="pre">references</span></code>
+will be passed to the <code class="docutils literal notranslate"><span class="pre">partners</span></code> method of this object and from
+there to the relevant methods of the <code class="docutils literal notranslate"><span class="pre">Interaction</span></code> and
+<code class="docutils literal notranslate"><span class="pre">Evidence</span></code> objects. By these arguments it is possible to filter
+the interactions in the paths according to custom criteria. If any
+of these arguments is a <code class="docutils literal notranslate"><span class="pre">tuple</span></code> or <code class="docutils literal notranslate"><span class="pre">list</span></code>, its first value will
+be used to match the first interaction in the path, the second for
+the second one and so on. If the list or tuple is shorter then
+<code class="docutils literal notranslate"><span class="pre">maxlen</span></code>, its last element will be used for all interactions.
+If it’s longer than <code class="docutils literal notranslate"><span class="pre">maxlen</span></code>, the remaining elements will be
+discarded. This way the method is able to search for custom
+motives. For example, let’s say you want to find the motives
+where the estrogen receptor transcription factor <em>ESR1</em>
+transcriptionally regulates a gene encoding a protein which
+then has some effect post-translationally on <em>ESR1</em>:</p>
+</dd>
+</dl>
+<p>Examples</p>
+<blockquote>
+<div><dl class="simple">
+<dt>n.find_paths(</dt><dd><p>‘ESR1’,
+loops = True,
+minlen = 2,
+interaction_type = (‘transcriptional’, ‘post_translational’),</p>
+</dd>
+</dl>
+<p>)</p>
+<p># Or if you are interested only in the -/+ feedback loops i.e.
+# <em>ESR1 –(-)–&gt; X –(+)–&gt; ESR1</em>:</p>
+<dl class="simple">
+<dt>n.find_paths(</dt><dd><p>‘ESR1’,
+loops = True,
+minlen = 2,
+interaction_type = (‘transcriptional’, ‘post_translational’),
+effect = (‘negative’, ‘positive’),</p>
+</dd>
+</dl>
+<p>)</p>
+</div></blockquote>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.network.Network.from_igraph">
+<em class="property"><span class="pre">classmethod</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">from_igraph</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">pa</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/network.html#Network.from_igraph"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.network.Network.from_igraph" title="Link to this definition">§</a></dt>
+<dd><p>Creates an instance from an <code class="docutils literal notranslate"><span class="pre">igraph.Graph</span></code> based
+<code class="docutils literal notranslate"><span class="pre">pypath.main.PyPath</span></code> object.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><p><strong>pa</strong> (<em>pypath.main.PyPath</em>) – A <code class="docutils literal notranslate"><span class="pre">pypath.main.PyPath</span></code> object with network data loaded.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.network.Network.from_pickle">
+<em class="property"><span class="pre">classmethod</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">from_pickle</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">pickle_file</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/network.html#Network.from_pickle"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.network.Network.from_pickle" title="Link to this definition">§</a></dt>
+<dd><p>Initializes a new <code class="docutils literal notranslate"><span class="pre">Network</span></code> object by loading it from a pickle
+file. Returns a <code class="docutils literal notranslate"><span class="pre">Network</span></code> object.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>pickle_file:</dt><dd><p>Path to a pickle file.</p>
+</dd>
+<dt>kwargs:</dt><dd><p>Passed to <code class="docutils literal notranslate"><span class="pre">Network.__init__</span></code>.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.get_complex_identifiers">
+<span class="sig-name descname"><span class="pre">get_complex_identifiers</span></span><a class="headerlink" href="#pypath.core.network.Network.get_complex_identifiers" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.get_complex_labels">
+<span class="sig-name descname"><span class="pre">get_complex_labels</span></span><a class="headerlink" href="#pypath.core.network.Network.get_complex_labels" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.get_complexes">
+<span class="sig-name descname"><span class="pre">get_complexes</span></span><a class="headerlink" href="#pypath.core.network.Network.get_complexes" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.get_curation_effort">
+<span class="sig-name descname"><span class="pre">get_curation_effort</span></span><a class="headerlink" href="#pypath.core.network.Network.get_curation_effort" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.get_data_models">
+<span class="sig-name descname"><span class="pre">get_data_models</span></span><a class="headerlink" href="#pypath.core.network.Network.get_data_models" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.get_datasets">
+<span class="sig-name descname"><span class="pre">get_datasets</span></span><a class="headerlink" href="#pypath.core.network.Network.get_datasets" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.get_degrees_directed">
+<span class="sig-name descname"><span class="pre">get_degrees_directed</span></span><a class="headerlink" href="#pypath.core.network.Network.get_degrees_directed" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.get_degrees_directed_in">
+<span class="sig-name descname"><span class="pre">get_degrees_directed_in</span></span><a class="headerlink" href="#pypath.core.network.Network.get_degrees_directed_in" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.get_degrees_directed_out">
+<span class="sig-name descname"><span class="pre">get_degrees_directed_out</span></span><a class="headerlink" href="#pypath.core.network.Network.get_degrees_directed_out" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.get_degrees_negative">
+<span class="sig-name descname"><span class="pre">get_degrees_negative</span></span><a class="headerlink" href="#pypath.core.network.Network.get_degrees_negative" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.get_degrees_negative_in">
+<span class="sig-name descname"><span class="pre">get_degrees_negative_in</span></span><a class="headerlink" href="#pypath.core.network.Network.get_degrees_negative_in" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.get_degrees_negative_out">
+<span class="sig-name descname"><span class="pre">get_degrees_negative_out</span></span><a class="headerlink" href="#pypath.core.network.Network.get_degrees_negative_out" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.get_degrees_non_directed">
+<span class="sig-name descname"><span class="pre">get_degrees_non_directed</span></span><a class="headerlink" href="#pypath.core.network.Network.get_degrees_non_directed" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.get_degrees_positive">
+<span class="sig-name descname"><span class="pre">get_degrees_positive</span></span><a class="headerlink" href="#pypath.core.network.Network.get_degrees_positive" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.get_degrees_positive_in">
+<span class="sig-name descname"><span class="pre">get_degrees_positive_in</span></span><a class="headerlink" href="#pypath.core.network.Network.get_degrees_positive_in" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.get_degrees_positive_out">
+<span class="sig-name descname"><span class="pre">get_degrees_positive_out</span></span><a class="headerlink" href="#pypath.core.network.Network.get_degrees_positive_out" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.get_degrees_signed">
+<span class="sig-name descname"><span class="pre">get_degrees_signed</span></span><a class="headerlink" href="#pypath.core.network.Network.get_degrees_signed" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.get_degrees_signed_in">
+<span class="sig-name descname"><span class="pre">get_degrees_signed_in</span></span><a class="headerlink" href="#pypath.core.network.Network.get_degrees_signed_in" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.get_degrees_signed_out">
+<span class="sig-name descname"><span class="pre">get_degrees_signed_out</span></span><a class="headerlink" href="#pypath.core.network.Network.get_degrees_signed_out" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.get_degrees_undirected">
+<span class="sig-name descname"><span class="pre">get_degrees_undirected</span></span><a class="headerlink" href="#pypath.core.network.Network.get_degrees_undirected" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.get_entities">
+<span class="sig-name descname"><span class="pre">get_entities</span></span><a class="headerlink" href="#pypath.core.network.Network.get_entities" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.get_evidences">
+<span class="sig-name descname"><span class="pre">get_evidences</span></span><a class="headerlink" href="#pypath.core.network.Network.get_evidences" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.get_identifiers">
+<span class="sig-name descname"><span class="pre">get_identifiers</span></span><a class="headerlink" href="#pypath.core.network.Network.get_identifiers" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.get_interaction_types">
+<span class="sig-name descname"><span class="pre">get_interaction_types</span></span><a class="headerlink" href="#pypath.core.network.Network.get_interaction_types" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.get_interactions">
+<span class="sig-name descname"><span class="pre">get_interactions</span></span><a class="headerlink" href="#pypath.core.network.Network.get_interactions" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.get_interactions_0">
+<span class="sig-name descname"><span class="pre">get_interactions_0</span></span><a class="headerlink" href="#pypath.core.network.Network.get_interactions_0" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.get_interactions_directed">
+<span class="sig-name descname"><span class="pre">get_interactions_directed</span></span><a class="headerlink" href="#pypath.core.network.Network.get_interactions_directed" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.get_interactions_mutual">
+<span class="sig-name descname"><span class="pre">get_interactions_mutual</span></span><a class="headerlink" href="#pypath.core.network.Network.get_interactions_mutual" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.get_interactions_negative">
+<span class="sig-name descname"><span class="pre">get_interactions_negative</span></span><a class="headerlink" href="#pypath.core.network.Network.get_interactions_negative" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.get_interactions_non_directed">
+<span class="sig-name descname"><span class="pre">get_interactions_non_directed</span></span><a class="headerlink" href="#pypath.core.network.Network.get_interactions_non_directed" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.get_interactions_non_directed_0">
+<span class="sig-name descname"><span class="pre">get_interactions_non_directed_0</span></span><a class="headerlink" href="#pypath.core.network.Network.get_interactions_non_directed_0" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.get_interactions_positive">
+<span class="sig-name descname"><span class="pre">get_interactions_positive</span></span><a class="headerlink" href="#pypath.core.network.Network.get_interactions_positive" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.get_interactions_signed">
+<span class="sig-name descname"><span class="pre">get_interactions_signed</span></span><a class="headerlink" href="#pypath.core.network.Network.get_interactions_signed" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.get_interactions_undirected">
+<span class="sig-name descname"><span class="pre">get_interactions_undirected</span></span><a class="headerlink" href="#pypath.core.network.Network.get_interactions_undirected" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.get_interactions_undirected_0">
+<span class="sig-name descname"><span class="pre">get_interactions_undirected_0</span></span><a class="headerlink" href="#pypath.core.network.Network.get_interactions_undirected_0" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.get_labels">
+<span class="sig-name descname"><span class="pre">get_labels</span></span><a class="headerlink" href="#pypath.core.network.Network.get_labels" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.get_lncrna_identifiers">
+<span class="sig-name descname"><span class="pre">get_lncrna_identifiers</span></span><a class="headerlink" href="#pypath.core.network.Network.get_lncrna_identifiers" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.get_lncrna_labels">
+<span class="sig-name descname"><span class="pre">get_lncrna_labels</span></span><a class="headerlink" href="#pypath.core.network.Network.get_lncrna_labels" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.get_lncrnas">
+<span class="sig-name descname"><span class="pre">get_lncrnas</span></span><a class="headerlink" href="#pypath.core.network.Network.get_lncrnas" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.get_mirna_identifiers">
+<span class="sig-name descname"><span class="pre">get_mirna_identifiers</span></span><a class="headerlink" href="#pypath.core.network.Network.get_mirna_identifiers" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.get_mirna_labels">
+<span class="sig-name descname"><span class="pre">get_mirna_labels</span></span><a class="headerlink" href="#pypath.core.network.Network.get_mirna_labels" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.get_mirnas">
+<span class="sig-name descname"><span class="pre">get_mirnas</span></span><a class="headerlink" href="#pypath.core.network.Network.get_mirnas" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.network.Network.get_organisms">
+<span class="sig-name descname"><span class="pre">get_organisms</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/network.html#Network.get_organisms"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.network.Network.get_organisms" title="Link to this definition">§</a></dt>
+<dd><p>Returns the set of all NCBI Taxonomy IDs occurring in the network.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.get_protein_identifiers">
+<span class="sig-name descname"><span class="pre">get_protein_identifiers</span></span><a class="headerlink" href="#pypath.core.network.Network.get_protein_identifiers" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.get_protein_labels">
+<span class="sig-name descname"><span class="pre">get_protein_labels</span></span><a class="headerlink" href="#pypath.core.network.Network.get_protein_labels" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.get_proteins">
+<span class="sig-name descname"><span class="pre">get_proteins</span></span><a class="headerlink" href="#pypath.core.network.Network.get_proteins" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.get_references">
+<span class="sig-name descname"><span class="pre">get_references</span></span><a class="headerlink" href="#pypath.core.network.Network.get_references" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.get_resource_names">
+<span class="sig-name descname"><span class="pre">get_resource_names</span></span><a class="headerlink" href="#pypath.core.network.Network.get_resource_names" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.get_resource_names_via">
+<span class="sig-name descname"><span class="pre">get_resource_names_via</span></span><a class="headerlink" href="#pypath.core.network.Network.get_resource_names_via" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.get_resources">
+<span class="sig-name descname"><span class="pre">get_resources</span></span><a class="headerlink" href="#pypath.core.network.Network.get_resources" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.get_resources_via">
+<span class="sig-name descname"><span class="pre">get_resources_via</span></span><a class="headerlink" href="#pypath.core.network.Network.get_resources_via" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.get_small_molecule_identifiers">
+<span class="sig-name descname"><span class="pre">get_small_molecule_identifiers</span></span><a class="headerlink" href="#pypath.core.network.Network.get_small_molecule_identifiers" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.get_small_molecule_labels">
+<span class="sig-name descname"><span class="pre">get_small_molecule_labels</span></span><a class="headerlink" href="#pypath.core.network.Network.get_small_molecule_labels" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.get_small_molecules">
+<span class="sig-name descname"><span class="pre">get_small_molecules</span></span><a class="headerlink" href="#pypath.core.network.Network.get_small_molecules" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.network.Network.htp_interactions">
+<span class="sig-name descname"><span class="pre">htp_interactions</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">threshold</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">50</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ignore_directed</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/network.html#Network.htp_interactions"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.network.Network.htp_interactions" title="Link to this definition">§</a></dt>
+<dd><p>Collects the interactions only from high-throughput studies.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Returns<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Set of interaction keys (tuples of entities).</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.network.Network.htp_references">
+<span class="sig-name descname"><span class="pre">htp_references</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">threshold</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">50</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/network.html#Network.htp_references"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.network.Network.htp_references" title="Link to this definition">§</a></dt>
+<dd><p>Collects the high-throughput references i.e. the ones cited at a
+higher number of interactions than <code class="docutils literal notranslate"><span class="pre">threshold</span></code>.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.identifiers_by_data_model">
+<span class="sig-name descname"><span class="pre">identifiers_by_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.identifiers_by_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.identifiers_by_interaction_type">
+<span class="sig-name descname"><span class="pre">identifiers_by_interaction_type</span></span><a class="headerlink" href="#pypath.core.network.Network.identifiers_by_interaction_type" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.identifiers_by_interaction_type_and_data_model">
+<span class="sig-name descname"><span class="pre">identifiers_by_interaction_type_and_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.identifiers_by_interaction_type_and_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.identifiers_by_interaction_type_and_data_model_and_resource">
+<span class="sig-name descname"><span class="pre">identifiers_by_interaction_type_and_data_model_and_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.identifiers_by_interaction_type_and_data_model_and_resource" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.identifiers_by_reference">
+<span class="sig-name descname"><span class="pre">identifiers_by_reference</span></span><a class="headerlink" href="#pypath.core.network.Network.identifiers_by_reference" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.identifiers_by_resource">
+<span class="sig-name descname"><span class="pre">identifiers_by_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.identifiers_by_resource" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.network.Network.init_network">
+<span class="sig-name descname"><span class="pre">init_network</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">make_df</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">exclude</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">reread</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">redownload</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">keep_raw</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">top_call</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cache_files</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">only_directions</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">pickle_file</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">allow_loops</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">first_n</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.network.Network.init_network" title="Link to this definition">§</a></dt>
+<dd><p>Loads data from a network resource or a collection of resources.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>resources</strong> (<em>str</em><em>,</em><em>dict</em><em>,</em><em>list</em><em>,</em><a class="reference internal" href="pypath.internals.resource.NetworkResource.html#pypath.internals.resource.NetworkResource" title="pypath.internals.resource.NetworkResource"><em>resource.NetworkResource</em></a>) – An object defining one or more network resources. If <em>str</em> it
+will be looked up among the collections in the
+<code class="docutils literal notranslate"><span class="pre">pypath.resources.network</span></code> module (e.g. <code class="docutils literal notranslate"><span class="pre">'pathway'</span></code> will load
+all resources in the <cite>pathway</cite> collection). If <em>dict</em> or <em>list</em>
+it will be processed recursively i.e. the <code class="docutils literal notranslate"><span class="pre">load</span></code> method will be
+called for each element. If it is a
+<code class="docutils literal notranslate"><span class="pre">pypath.resource.NetworkResource</span></code> object it will be processed
+and added to the network.</p></li>
+<li><p><strong>make_df</strong> (<em>bool</em>) – Whether to create a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> after loading all
+resources.</p></li>
+<li><p><strong>exclude</strong> (<em>NoneType</em><em>,</em><em>set</em>) – A <em>set</em> of resource names to be ignored. It is useful if you want
+to load a collection with the exception of a few resources.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.network.Network.interaction">
+<span class="sig-name descname"><span class="pre">interaction</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">a</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">b</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/network.html#Network.interaction"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.network.Network.interaction" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the interaction <cite>a –&gt; b</cite> if it exists in the network,
+otherwise <cite>b –&gt; a</cite>. If no interaction exist between <cite>a</cite> and <cite>b</cite>
+returns <cite>None</cite>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.network.Network.interaction_by_id">
+<span class="sig-name descname"><span class="pre">interaction_by_id</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">id_a</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">id_b</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/network.html#Network.interaction_by_id"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.network.Network.interaction_by_id" title="Link to this definition">§</a></dt>
+<dd><p>Returns a <code class="docutils literal notranslate"><span class="pre">pypath.interaction.Interaction</span></code> object by looking it up
+based on a pair of identifiers. If the interaction does not exist
+in the network <code class="docutils literal notranslate"><span class="pre">None</span></code> will be returned.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>id_a</strong> (<em>str</em>) – The identifier of one of the partners in the interaction. Unless
+it’s been set otherwise for genes/proteins it is the UniProt ID.
+E.g. <code class="docutils literal notranslate"><span class="pre">'P00533'</span></code>.</p></li>
+<li><p><strong>id_b</strong> (<em>str</em>) – The other partner, similarly to <code class="docutils literal notranslate"><span class="pre">id_a</span></code>. The order of the
+partners does not matter here.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.network.Network.interaction_by_label">
+<span class="sig-name descname"><span class="pre">interaction_by_label</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">label_a</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">label_b</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/network.html#Network.interaction_by_label"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.network.Network.interaction_by_label" title="Link to this definition">§</a></dt>
+<dd><p>Returns a <code class="docutils literal notranslate"><span class="pre">pypath.interaction.Interaction</span></code> object by looking it up
+based on a pair of labels. If the interaction does not exist
+in the network <code class="docutils literal notranslate"><span class="pre">None</span></code> will be returned.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>label_a</strong> (<em>str</em>) – The label of one of the partners in the interaction. Unless
+it’s been set otherwise for genes/proteins it is the Gene Symbol.
+E.g. <code class="docutils literal notranslate"><span class="pre">'EGFR'</span></code>.</p></li>
+<li><p><strong>label_b</strong> (<em>str</em>) – The other partner, similarly to <code class="docutils literal notranslate"><span class="pre">label_a</span></code>. The order of the
+partners does not matter here.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.interaction_types_by_data_model">
+<span class="sig-name descname"><span class="pre">interaction_types_by_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.interaction_types_by_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.interaction_types_by_interaction_type">
+<span class="sig-name descname"><span class="pre">interaction_types_by_interaction_type</span></span><a class="headerlink" href="#pypath.core.network.Network.interaction_types_by_interaction_type" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.interaction_types_by_interaction_type_and_data_model">
+<span class="sig-name descname"><span class="pre">interaction_types_by_interaction_type_and_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.interaction_types_by_interaction_type_and_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.interaction_types_by_interaction_type_and_data_model_and_resource">
+<span class="sig-name descname"><span class="pre">interaction_types_by_interaction_type_and_data_model_and_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.interaction_types_by_interaction_type_and_data_model_and_resource" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.interaction_types_by_reference">
+<span class="sig-name descname"><span class="pre">interaction_types_by_reference</span></span><a class="headerlink" href="#pypath.core.network.Network.interaction_types_by_reference" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.interaction_types_by_resource">
+<span class="sig-name descname"><span class="pre">interaction_types_by_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.interaction_types_by_resource" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.interactions_0_by_data_model">
+<span class="sig-name descname"><span class="pre">interactions_0_by_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.interactions_0_by_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.interactions_0_by_interaction_type">
+<span class="sig-name descname"><span class="pre">interactions_0_by_interaction_type</span></span><a class="headerlink" href="#pypath.core.network.Network.interactions_0_by_interaction_type" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.interactions_0_by_interaction_type_and_data_model">
+<span class="sig-name descname"><span class="pre">interactions_0_by_interaction_type_and_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.interactions_0_by_interaction_type_and_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.interactions_0_by_interaction_type_and_data_model_and_resource">
+<span class="sig-name descname"><span class="pre">interactions_0_by_interaction_type_and_data_model_and_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.interactions_0_by_interaction_type_and_data_model_and_resource" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.interactions_0_by_reference">
+<span class="sig-name descname"><span class="pre">interactions_0_by_reference</span></span><a class="headerlink" href="#pypath.core.network.Network.interactions_0_by_reference" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.interactions_0_by_resource">
+<span class="sig-name descname"><span class="pre">interactions_0_by_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.interactions_0_by_resource" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.interactions_by_data_model">
+<span class="sig-name descname"><span class="pre">interactions_by_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.interactions_by_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.interactions_by_interaction_type">
+<span class="sig-name descname"><span class="pre">interactions_by_interaction_type</span></span><a class="headerlink" href="#pypath.core.network.Network.interactions_by_interaction_type" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.interactions_by_interaction_type_and_data_model">
+<span class="sig-name descname"><span class="pre">interactions_by_interaction_type_and_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.interactions_by_interaction_type_and_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.interactions_by_interaction_type_and_data_model_and_resource">
+<span class="sig-name descname"><span class="pre">interactions_by_interaction_type_and_data_model_and_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.interactions_by_interaction_type_and_data_model_and_resource" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.interactions_by_reference">
+<span class="sig-name descname"><span class="pre">interactions_by_reference</span></span><a class="reference internal" href="../_modules/pypath/core/network.html#Network.interactions_by_reference"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.network.Network.interactions_by_reference" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.interactions_by_resource">
+<span class="sig-name descname"><span class="pre">interactions_by_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.interactions_by_resource" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.interactions_directed_by_data_model">
+<span class="sig-name descname"><span class="pre">interactions_directed_by_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.interactions_directed_by_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.interactions_directed_by_interaction_type">
+<span class="sig-name descname"><span class="pre">interactions_directed_by_interaction_type</span></span><a class="headerlink" href="#pypath.core.network.Network.interactions_directed_by_interaction_type" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.interactions_directed_by_interaction_type_and_data_model">
+<span class="sig-name descname"><span class="pre">interactions_directed_by_interaction_type_and_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.interactions_directed_by_interaction_type_and_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.interactions_directed_by_interaction_type_and_data_model_and_resource">
+<span class="sig-name descname"><span class="pre">interactions_directed_by_interaction_type_and_data_model_and_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.interactions_directed_by_interaction_type_and_data_model_and_resource" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.interactions_directed_by_reference">
+<span class="sig-name descname"><span class="pre">interactions_directed_by_reference</span></span><a class="headerlink" href="#pypath.core.network.Network.interactions_directed_by_reference" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.interactions_directed_by_resource">
+<span class="sig-name descname"><span class="pre">interactions_directed_by_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.interactions_directed_by_resource" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.interactions_mutual_by_data_model">
+<span class="sig-name descname"><span class="pre">interactions_mutual_by_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.interactions_mutual_by_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.interactions_mutual_by_interaction_type">
+<span class="sig-name descname"><span class="pre">interactions_mutual_by_interaction_type</span></span><a class="headerlink" href="#pypath.core.network.Network.interactions_mutual_by_interaction_type" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.interactions_mutual_by_interaction_type_and_data_model">
+<span class="sig-name descname"><span class="pre">interactions_mutual_by_interaction_type_and_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.interactions_mutual_by_interaction_type_and_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.interactions_mutual_by_interaction_type_and_data_model_and_resource">
+<span class="sig-name descname"><span class="pre">interactions_mutual_by_interaction_type_and_data_model_and_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.interactions_mutual_by_interaction_type_and_data_model_and_resource" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.interactions_mutual_by_reference">
+<span class="sig-name descname"><span class="pre">interactions_mutual_by_reference</span></span><a class="headerlink" href="#pypath.core.network.Network.interactions_mutual_by_reference" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.interactions_mutual_by_resource">
+<span class="sig-name descname"><span class="pre">interactions_mutual_by_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.interactions_mutual_by_resource" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.interactions_negative_by_data_model">
+<span class="sig-name descname"><span class="pre">interactions_negative_by_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.interactions_negative_by_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.interactions_negative_by_interaction_type">
+<span class="sig-name descname"><span class="pre">interactions_negative_by_interaction_type</span></span><a class="headerlink" href="#pypath.core.network.Network.interactions_negative_by_interaction_type" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.interactions_negative_by_interaction_type_and_data_model">
+<span class="sig-name descname"><span class="pre">interactions_negative_by_interaction_type_and_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.interactions_negative_by_interaction_type_and_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.interactions_negative_by_interaction_type_and_data_model_and_resource">
+<span class="sig-name descname"><span class="pre">interactions_negative_by_interaction_type_and_data_model_and_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.interactions_negative_by_interaction_type_and_data_model_and_resource" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.interactions_negative_by_reference">
+<span class="sig-name descname"><span class="pre">interactions_negative_by_reference</span></span><a class="headerlink" href="#pypath.core.network.Network.interactions_negative_by_reference" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.interactions_negative_by_resource">
+<span class="sig-name descname"><span class="pre">interactions_negative_by_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.interactions_negative_by_resource" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.interactions_non_directed_0_by_data_model">
+<span class="sig-name descname"><span class="pre">interactions_non_directed_0_by_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.interactions_non_directed_0_by_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.interactions_non_directed_0_by_interaction_type">
+<span class="sig-name descname"><span class="pre">interactions_non_directed_0_by_interaction_type</span></span><a class="headerlink" href="#pypath.core.network.Network.interactions_non_directed_0_by_interaction_type" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.interactions_non_directed_0_by_interaction_type_and_data_model">
+<span class="sig-name descname"><span class="pre">interactions_non_directed_0_by_interaction_type_and_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.interactions_non_directed_0_by_interaction_type_and_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.interactions_non_directed_0_by_interaction_type_and_data_model_and_resource">
+<span class="sig-name descname"><span class="pre">interactions_non_directed_0_by_interaction_type_and_data_model_and_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.interactions_non_directed_0_by_interaction_type_and_data_model_and_resource" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.interactions_non_directed_0_by_reference">
+<span class="sig-name descname"><span class="pre">interactions_non_directed_0_by_reference</span></span><a class="headerlink" href="#pypath.core.network.Network.interactions_non_directed_0_by_reference" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.interactions_non_directed_0_by_resource">
+<span class="sig-name descname"><span class="pre">interactions_non_directed_0_by_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.interactions_non_directed_0_by_resource" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.interactions_non_directed_by_data_model">
+<span class="sig-name descname"><span class="pre">interactions_non_directed_by_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.interactions_non_directed_by_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.interactions_non_directed_by_interaction_type">
+<span class="sig-name descname"><span class="pre">interactions_non_directed_by_interaction_type</span></span><a class="headerlink" href="#pypath.core.network.Network.interactions_non_directed_by_interaction_type" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.interactions_non_directed_by_interaction_type_and_data_model">
+<span class="sig-name descname"><span class="pre">interactions_non_directed_by_interaction_type_and_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.interactions_non_directed_by_interaction_type_and_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.interactions_non_directed_by_interaction_type_and_data_model_and_resource">
+<span class="sig-name descname"><span class="pre">interactions_non_directed_by_interaction_type_and_data_model_and_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.interactions_non_directed_by_interaction_type_and_data_model_and_resource" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.interactions_non_directed_by_reference">
+<span class="sig-name descname"><span class="pre">interactions_non_directed_by_reference</span></span><a class="headerlink" href="#pypath.core.network.Network.interactions_non_directed_by_reference" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.interactions_non_directed_by_resource">
+<span class="sig-name descname"><span class="pre">interactions_non_directed_by_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.interactions_non_directed_by_resource" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.interactions_positive_by_data_model">
+<span class="sig-name descname"><span class="pre">interactions_positive_by_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.interactions_positive_by_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.interactions_positive_by_interaction_type">
+<span class="sig-name descname"><span class="pre">interactions_positive_by_interaction_type</span></span><a class="headerlink" href="#pypath.core.network.Network.interactions_positive_by_interaction_type" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.interactions_positive_by_interaction_type_and_data_model">
+<span class="sig-name descname"><span class="pre">interactions_positive_by_interaction_type_and_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.interactions_positive_by_interaction_type_and_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.interactions_positive_by_interaction_type_and_data_model_and_resource">
+<span class="sig-name descname"><span class="pre">interactions_positive_by_interaction_type_and_data_model_and_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.interactions_positive_by_interaction_type_and_data_model_and_resource" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.interactions_positive_by_reference">
+<span class="sig-name descname"><span class="pre">interactions_positive_by_reference</span></span><a class="headerlink" href="#pypath.core.network.Network.interactions_positive_by_reference" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.interactions_positive_by_resource">
+<span class="sig-name descname"><span class="pre">interactions_positive_by_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.interactions_positive_by_resource" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.interactions_signed_by_data_model">
+<span class="sig-name descname"><span class="pre">interactions_signed_by_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.interactions_signed_by_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.interactions_signed_by_interaction_type">
+<span class="sig-name descname"><span class="pre">interactions_signed_by_interaction_type</span></span><a class="headerlink" href="#pypath.core.network.Network.interactions_signed_by_interaction_type" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.interactions_signed_by_interaction_type_and_data_model">
+<span class="sig-name descname"><span class="pre">interactions_signed_by_interaction_type_and_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.interactions_signed_by_interaction_type_and_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.interactions_signed_by_interaction_type_and_data_model_and_resource">
+<span class="sig-name descname"><span class="pre">interactions_signed_by_interaction_type_and_data_model_and_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.interactions_signed_by_interaction_type_and_data_model_and_resource" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.interactions_signed_by_reference">
+<span class="sig-name descname"><span class="pre">interactions_signed_by_reference</span></span><a class="headerlink" href="#pypath.core.network.Network.interactions_signed_by_reference" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.interactions_signed_by_resource">
+<span class="sig-name descname"><span class="pre">interactions_signed_by_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.interactions_signed_by_resource" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.interactions_undirected_0_by_data_model">
+<span class="sig-name descname"><span class="pre">interactions_undirected_0_by_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.interactions_undirected_0_by_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.interactions_undirected_0_by_interaction_type">
+<span class="sig-name descname"><span class="pre">interactions_undirected_0_by_interaction_type</span></span><a class="headerlink" href="#pypath.core.network.Network.interactions_undirected_0_by_interaction_type" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.interactions_undirected_0_by_interaction_type_and_data_model">
+<span class="sig-name descname"><span class="pre">interactions_undirected_0_by_interaction_type_and_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.interactions_undirected_0_by_interaction_type_and_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.interactions_undirected_0_by_interaction_type_and_data_model_and_resource">
+<span class="sig-name descname"><span class="pre">interactions_undirected_0_by_interaction_type_and_data_model_and_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.interactions_undirected_0_by_interaction_type_and_data_model_and_resource" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.interactions_undirected_0_by_reference">
+<span class="sig-name descname"><span class="pre">interactions_undirected_0_by_reference</span></span><a class="headerlink" href="#pypath.core.network.Network.interactions_undirected_0_by_reference" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.interactions_undirected_0_by_resource">
+<span class="sig-name descname"><span class="pre">interactions_undirected_0_by_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.interactions_undirected_0_by_resource" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.interactions_undirected_by_data_model">
+<span class="sig-name descname"><span class="pre">interactions_undirected_by_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.interactions_undirected_by_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.interactions_undirected_by_interaction_type">
+<span class="sig-name descname"><span class="pre">interactions_undirected_by_interaction_type</span></span><a class="headerlink" href="#pypath.core.network.Network.interactions_undirected_by_interaction_type" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.interactions_undirected_by_interaction_type_and_data_model">
+<span class="sig-name descname"><span class="pre">interactions_undirected_by_interaction_type_and_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.interactions_undirected_by_interaction_type_and_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.interactions_undirected_by_interaction_type_and_data_model_and_resource">
+<span class="sig-name descname"><span class="pre">interactions_undirected_by_interaction_type_and_data_model_and_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.interactions_undirected_by_interaction_type_and_data_model_and_resource" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.interactions_undirected_by_reference">
+<span class="sig-name descname"><span class="pre">interactions_undirected_by_reference</span></span><a class="headerlink" href="#pypath.core.network.Network.interactions_undirected_by_reference" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.interactions_undirected_by_resource">
+<span class="sig-name descname"><span class="pre">interactions_undirected_by_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.interactions_undirected_by_resource" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.labels_by_data_model">
+<span class="sig-name descname"><span class="pre">labels_by_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.labels_by_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.labels_by_interaction_type">
+<span class="sig-name descname"><span class="pre">labels_by_interaction_type</span></span><a class="headerlink" href="#pypath.core.network.Network.labels_by_interaction_type" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.labels_by_interaction_type_and_data_model">
+<span class="sig-name descname"><span class="pre">labels_by_interaction_type_and_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.labels_by_interaction_type_and_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.labels_by_interaction_type_and_data_model_and_resource">
+<span class="sig-name descname"><span class="pre">labels_by_interaction_type_and_data_model_and_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.labels_by_interaction_type_and_data_model_and_resource" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.labels_by_reference">
+<span class="sig-name descname"><span class="pre">labels_by_reference</span></span><a class="headerlink" href="#pypath.core.network.Network.labels_by_reference" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.labels_by_resource">
+<span class="sig-name descname"><span class="pre">labels_by_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.labels_by_resource" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.lncrna_identifiers_by_data_model">
+<span class="sig-name descname"><span class="pre">lncrna_identifiers_by_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.lncrna_identifiers_by_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.lncrna_identifiers_by_interaction_type">
+<span class="sig-name descname"><span class="pre">lncrna_identifiers_by_interaction_type</span></span><a class="headerlink" href="#pypath.core.network.Network.lncrna_identifiers_by_interaction_type" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.lncrna_identifiers_by_interaction_type_and_data_model">
+<span class="sig-name descname"><span class="pre">lncrna_identifiers_by_interaction_type_and_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.lncrna_identifiers_by_interaction_type_and_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.lncrna_identifiers_by_interaction_type_and_data_model_and_resource">
+<span class="sig-name descname"><span class="pre">lncrna_identifiers_by_interaction_type_and_data_model_and_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.lncrna_identifiers_by_interaction_type_and_data_model_and_resource" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.lncrna_identifiers_by_reference">
+<span class="sig-name descname"><span class="pre">lncrna_identifiers_by_reference</span></span><a class="headerlink" href="#pypath.core.network.Network.lncrna_identifiers_by_reference" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.lncrna_identifiers_by_resource">
+<span class="sig-name descname"><span class="pre">lncrna_identifiers_by_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.lncrna_identifiers_by_resource" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.lncrna_labels_by_data_model">
+<span class="sig-name descname"><span class="pre">lncrna_labels_by_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.lncrna_labels_by_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.lncrna_labels_by_interaction_type">
+<span class="sig-name descname"><span class="pre">lncrna_labels_by_interaction_type</span></span><a class="headerlink" href="#pypath.core.network.Network.lncrna_labels_by_interaction_type" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.lncrna_labels_by_interaction_type_and_data_model">
+<span class="sig-name descname"><span class="pre">lncrna_labels_by_interaction_type_and_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.lncrna_labels_by_interaction_type_and_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.lncrna_labels_by_interaction_type_and_data_model_and_resource">
+<span class="sig-name descname"><span class="pre">lncrna_labels_by_interaction_type_and_data_model_and_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.lncrna_labels_by_interaction_type_and_data_model_and_resource" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.lncrna_labels_by_reference">
+<span class="sig-name descname"><span class="pre">lncrna_labels_by_reference</span></span><a class="headerlink" href="#pypath.core.network.Network.lncrna_labels_by_reference" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.lncrna_labels_by_resource">
+<span class="sig-name descname"><span class="pre">lncrna_labels_by_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.lncrna_labels_by_resource" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.lncrnas_by_data_model">
+<span class="sig-name descname"><span class="pre">lncrnas_by_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.lncrnas_by_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.lncrnas_by_interaction_type">
+<span class="sig-name descname"><span class="pre">lncrnas_by_interaction_type</span></span><a class="headerlink" href="#pypath.core.network.Network.lncrnas_by_interaction_type" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.lncrnas_by_interaction_type_and_data_model">
+<span class="sig-name descname"><span class="pre">lncrnas_by_interaction_type_and_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.lncrnas_by_interaction_type_and_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.lncrnas_by_interaction_type_and_data_model_and_resource">
+<span class="sig-name descname"><span class="pre">lncrnas_by_interaction_type_and_data_model_and_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.lncrnas_by_interaction_type_and_data_model_and_resource" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.lncrnas_by_reference">
+<span class="sig-name descname"><span class="pre">lncrnas_by_reference</span></span><a class="headerlink" href="#pypath.core.network.Network.lncrnas_by_reference" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.lncrnas_by_resource">
+<span class="sig-name descname"><span class="pre">lncrnas_by_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.lncrnas_by_resource" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.network.Network.load">
+<span class="sig-name descname"><span class="pre">load</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">make_df</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">exclude</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">reread</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">redownload</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">keep_raw</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">top_call</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cache_files</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">only_directions</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">pickle_file</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">allow_loops</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">first_n</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/network.html#Network.load"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.network.Network.load" title="Link to this definition">§</a></dt>
+<dd><p>Loads data from a network resource or a collection of resources.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>resources</strong> (<em>str</em><em>,</em><em>dict</em><em>,</em><em>list</em><em>,</em><a class="reference internal" href="pypath.internals.resource.NetworkResource.html#pypath.internals.resource.NetworkResource" title="pypath.internals.resource.NetworkResource"><em>resource.NetworkResource</em></a>) – An object defining one or more network resources. If <em>str</em> it
+will be looked up among the collections in the
+<code class="docutils literal notranslate"><span class="pre">pypath.resources.network</span></code> module (e.g. <code class="docutils literal notranslate"><span class="pre">'pathway'</span></code> will load
+all resources in the <cite>pathway</cite> collection). If <em>dict</em> or <em>list</em>
+it will be processed recursively i.e. the <code class="docutils literal notranslate"><span class="pre">load</span></code> method will be
+called for each element. If it is a
+<code class="docutils literal notranslate"><span class="pre">pypath.resource.NetworkResource</span></code> object it will be processed
+and added to the network.</p></li>
+<li><p><strong>make_df</strong> (<em>bool</em>) – Whether to create a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> after loading all
+resources.</p></li>
+<li><p><strong>exclude</strong> (<em>NoneType</em><em>,</em><em>set</em>) – A <em>set</em> of resource names to be ignored. It is useful if you want
+to load a collection with the exception of a few resources.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.network.Network.load_from_pickle">
+<span class="sig-name descname"><span class="pre">load_from_pickle</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">pickle_file</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/network.html#Network.load_from_pickle"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.network.Network.load_from_pickle" title="Link to this definition">§</a></dt>
+<dd><p>Loads the network to a pickle file.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><p><strong>pickle_file</strong> (<em>str</em>) – Path to the pickle file.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.network.Network.load_resource">
+<span class="sig-name descname"><span class="pre">load_resource</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">resource</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">clean</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">reread</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">redownload</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">keep_raw</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">only_directions</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">allow_loops</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">first_n</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/network.html#Network.load_resource"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.network.Network.load_resource" title="Link to this definition">§</a></dt>
+<dd><p>Loads the data from a single resource and attaches it to the
+network</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>resource</strong> (<em>pypath.input_formats.NetworkInput</em>) – <code class="xref py py-class docutils literal notranslate"><span class="pre">pypath.input_formats.NetworkInput</span></code> instance
+containing the detailed definition of the input format to
+the downloaded file.</p></li>
+<li><p><strong>clean</strong> (<em>bool</em>) – Legacy parameter, has no effect at the moment.
+Optional, <code class="docutils literal notranslate"><span class="pre">True</span></code> by default. Whether to clean the graph
+after importing the data or not. See
+<code class="xref py py-meth docutils literal notranslate"><span class="pre">pypath.main.PyPath.clean_graph()</span></code> for more
+information.</p></li>
+<li><p><strong>cache_files</strong> (<em>dict</em>) – Legacy parameter, has no effect at the moment.
+Optional, <code class="docutils literal notranslate"><span class="pre">{}</span></code> by default. Contains the resource name(s)
+[str] (keys) and the corresponding cached file name [str].
+If provided (and file exists) bypasses the download of the
+data for that resource and uses the cache file instead.</p></li>
+<li><p><strong>reread</strong> (<em>bool</em>) – Optional, <code class="docutils literal notranslate"><span class="pre">False</span></code> by default. Specifies whether to reread
+the data files from the cache or omit them (similar to
+<em>redownload</em>).</p></li>
+<li><p><strong>redownload</strong> (<em>bool</em>) – Optional, <code class="docutils literal notranslate"><span class="pre">False</span></code> by default. Specifies whether to
+re-download the data and ignore the cache.</p></li>
+<li><p><strong>only_directions</strong> (<em>bool</em>) – If <code class="docutils literal notranslate"><span class="pre">True</span></code>, no new interactions will be created but direction
+and effect sign evidences will be added to existing interactions.</p></li>
+<li><p><strong>first_n</strong> (<em>int</em>) – Load only the first n interactions.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.network.Network.load_resources">
+<span class="sig-name descname"><span class="pre">load_resources</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">make_df</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">exclude</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">reread</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">redownload</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">keep_raw</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">top_call</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cache_files</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">only_directions</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">pickle_file</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">allow_loops</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">first_n</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.network.Network.load_resources" title="Link to this definition">§</a></dt>
+<dd><p>Loads data from a network resource or a collection of resources.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>resources</strong> (<em>str</em><em>,</em><em>dict</em><em>,</em><em>list</em><em>,</em><a class="reference internal" href="pypath.internals.resource.NetworkResource.html#pypath.internals.resource.NetworkResource" title="pypath.internals.resource.NetworkResource"><em>resource.NetworkResource</em></a>) – An object defining one or more network resources. If <em>str</em> it
+will be looked up among the collections in the
+<code class="docutils literal notranslate"><span class="pre">pypath.resources.network</span></code> module (e.g. <code class="docutils literal notranslate"><span class="pre">'pathway'</span></code> will load
+all resources in the <cite>pathway</cite> collection). If <em>dict</em> or <em>list</em>
+it will be processed recursively i.e. the <code class="docutils literal notranslate"><span class="pre">load</span></code> method will be
+called for each element. If it is a
+<code class="docutils literal notranslate"><span class="pre">pypath.resource.NetworkResource</span></code> object it will be processed
+and added to the network.</p></li>
+<li><p><strong>make_df</strong> (<em>bool</em>) – Whether to create a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> after loading all
+resources.</p></li>
+<li><p><strong>exclude</strong> (<em>NoneType</em><em>,</em><em>set</em>) – A <em>set</em> of resource names to be ignored. It is useful if you want
+to load a collection with the exception of a few resources.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.network.Network.make_df">
+<span class="sig-name descname"><span class="pre">make_df</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">records</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">by_source</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">with_references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">columns</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">dtype</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/network.html#Network.make_df"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.network.Network.make_df" title="Link to this definition">§</a></dt>
+<dd><p>Creates a <code class="docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code> from the interactions.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.mirna_identifiers_by_data_model">
+<span class="sig-name descname"><span class="pre">mirna_identifiers_by_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.mirna_identifiers_by_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.mirna_identifiers_by_interaction_type">
+<span class="sig-name descname"><span class="pre">mirna_identifiers_by_interaction_type</span></span><a class="headerlink" href="#pypath.core.network.Network.mirna_identifiers_by_interaction_type" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.mirna_identifiers_by_interaction_type_and_data_model">
+<span class="sig-name descname"><span class="pre">mirna_identifiers_by_interaction_type_and_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.mirna_identifiers_by_interaction_type_and_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.mirna_identifiers_by_interaction_type_and_data_model_and_resource">
+<span class="sig-name descname"><span class="pre">mirna_identifiers_by_interaction_type_and_data_model_and_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.mirna_identifiers_by_interaction_type_and_data_model_and_resource" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.mirna_identifiers_by_reference">
+<span class="sig-name descname"><span class="pre">mirna_identifiers_by_reference</span></span><a class="headerlink" href="#pypath.core.network.Network.mirna_identifiers_by_reference" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.mirna_identifiers_by_resource">
+<span class="sig-name descname"><span class="pre">mirna_identifiers_by_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.mirna_identifiers_by_resource" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.mirna_labels_by_data_model">
+<span class="sig-name descname"><span class="pre">mirna_labels_by_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.mirna_labels_by_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.mirna_labels_by_interaction_type">
+<span class="sig-name descname"><span class="pre">mirna_labels_by_interaction_type</span></span><a class="headerlink" href="#pypath.core.network.Network.mirna_labels_by_interaction_type" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.mirna_labels_by_interaction_type_and_data_model">
+<span class="sig-name descname"><span class="pre">mirna_labels_by_interaction_type_and_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.mirna_labels_by_interaction_type_and_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.mirna_labels_by_interaction_type_and_data_model_and_resource">
+<span class="sig-name descname"><span class="pre">mirna_labels_by_interaction_type_and_data_model_and_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.mirna_labels_by_interaction_type_and_data_model_and_resource" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.mirna_labels_by_reference">
+<span class="sig-name descname"><span class="pre">mirna_labels_by_reference</span></span><a class="headerlink" href="#pypath.core.network.Network.mirna_labels_by_reference" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.mirna_labels_by_resource">
+<span class="sig-name descname"><span class="pre">mirna_labels_by_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.mirna_labels_by_resource" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.network.Network.mirna_target">
+<em class="property"><span class="pre">classmethod</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">mirna_target</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">make_df</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">reread</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">redownload</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">exclude</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/network.html#Network.mirna_target"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.network.Network.mirna_target" title="Link to this definition">§</a></dt>
+<dd><p>Initializes a new <code class="docutils literal notranslate"><span class="pre">Network</span></code> object with loading a miRNA-mRNA
+regulation network from all databases by default.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>kwargs:</dt><dd><p>Passed to <code class="docutils literal notranslate"><span class="pre">Network.__init__</span></code>.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.mirnas_by_data_model">
+<span class="sig-name descname"><span class="pre">mirnas_by_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.mirnas_by_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.mirnas_by_interaction_type">
+<span class="sig-name descname"><span class="pre">mirnas_by_interaction_type</span></span><a class="headerlink" href="#pypath.core.network.Network.mirnas_by_interaction_type" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.mirnas_by_interaction_type_and_data_model">
+<span class="sig-name descname"><span class="pre">mirnas_by_interaction_type_and_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.mirnas_by_interaction_type_and_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.mirnas_by_interaction_type_and_data_model_and_resource">
+<span class="sig-name descname"><span class="pre">mirnas_by_interaction_type_and_data_model_and_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.mirnas_by_interaction_type_and_data_model_and_resource" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.mirnas_by_reference">
+<span class="sig-name descname"><span class="pre">mirnas_by_reference</span></span><a class="headerlink" href="#pypath.core.network.Network.mirnas_by_reference" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.mirnas_by_resource">
+<span class="sig-name descname"><span class="pre">mirnas_by_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.mirnas_by_resource" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.network.Network.numof_interactions_per_reference">
+<span class="sig-name descname"><span class="pre">numof_interactions_per_reference</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/network.html#Network.numof_interactions_per_reference"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.network.Network.numof_interactions_per_reference" title="Link to this definition">§</a></dt>
+<dd><p>Counts the number of interactions for each literature reference.
+Returns a <code class="docutils literal notranslate"><span class="pre">collections.Counter</span></code> object (similar to <code class="docutils literal notranslate"><span class="pre">dict</span></code>).</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.network.Network.organisms_check">
+<span class="sig-name descname"><span class="pre">organisms_check</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">organisms</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">remove_mismatches</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">remove_nonspecific</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/network.html#Network.organisms_check"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.network.Network.organisms_check" title="Link to this definition">§</a></dt>
+<dd><p>Scans the network for one or more organisms and removes the nodes
+and interactions which belong to any other organism.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>organisms</strong> (<em>int</em><em>,</em><em>set</em><em>,</em><em>NoneType</em>) – One or more NCBI Taxonomy IDs. If <code class="docutils literal notranslate"><span class="pre">None</span></code> the value in
+<code class="xref py py-attr docutils literal notranslate"><span class="pre">ncbi_tax_id</span></code> will be used. If that’s too is <code class="docutils literal notranslate"><span class="pre">None</span></code>
+then only the entities with discrepancy between their stated
+organism and their identifier.</p></li>
+<li><p><strong>remove_mismatches</strong> (<em>bool</em>) – Remove the entities where their <code class="docutils literal notranslate"><span class="pre">identifier</span></code> can not be found
+in the reference list from the database for their <code class="docutils literal notranslate"><span class="pre">taxon</span></code>.</p></li>
+<li><p><strong>remove_nonspecific</strong> (<em>bool</em>) – Remove the entities with taxonomy ID zero, which is used to
+represent the non taxon specific entities such as metabolites
+or drug compounds.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.network.Network.partners">
+<span class="sig-name descname"><span class="pre">partners</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">mode</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'ALL'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">direction</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">tuple</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">effect</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">set</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interaction_type</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">set</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data_model</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">set</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">via</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">set</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">set</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">return_interactions</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/network.html#Network.partners"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.network.Network.partners" title="Link to this definition">§</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>entity</strong> (<em>str</em><em>,</em><a class="reference internal" href="pypath.core.entity.Entity.html#pypath.core.entity.Entity" title="pypath.core.entity.Entity"><em>Entity</em></a><em>,</em><em>list</em><em>,</em><em>set</em><em>,</em><em>tuple</em><em>,</em><a class="reference internal" href="pypath.core.entity.EntityList.html#pypath.core.entity.EntityList" title="pypath.core.entity.EntityList"><em>EntityList</em></a>) – An identifier or label of a molecular entity or an
+<code class="xref py py-class docutils literal notranslate"><span class="pre">Entity</span></code> object. Alternatively an iterator with the
+elements of any of the types valid for a single entity argument,
+e.g. a list of gene symbols.</p></li>
+<li><p><strong>mode</strong> (<em>str</em>) – Mode of counting the interactions: <cite>IN</cite>, <cite>OUT</cite> or <cite>ALL</cite> , whether
+to consider incoming, outgoing or all edges, respectively,
+respective to the <cite>node defined in `entity`</cite>.</p></li>
+</ul>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p><code class="xref py py-class docutils literal notranslate"><span class="pre">EntityList</span></code> object containing the partners having
+interactions to the queried node(s) matching all the criteria.
+If <code class="docutils literal notranslate"><span class="pre">entity</span></code> doesn’t present in the network the returned
+<code class="docutils literal notranslate"><span class="pre">EntityList</span></code> will be empty just like if no interaction matches
+the criteria.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.post_transcriptionally_activated_by">
+<span class="sig-name descname"><span class="pre">post_transcriptionally_activated_by</span></span><a class="headerlink" href="#pypath.core.network.Network.post_transcriptionally_activated_by" title="Link to this definition">§</a></dt>
+<dd><dl class="simple">
+<dt>arg str,Entity,list,set,tuple,EntityList entity:</dt><dd><p>An identifier or label of a molecular entity or an
+<code class="xref py py-class docutils literal notranslate"><span class="pre">Entity</span></code> object. Alternatively an iterator with the
+elements of any of the types valid for a single entity argument,
+e.g. a list of gene symbols.</p>
+</dd>
+</dl>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><p><strong>mode</strong> (<em>str</em>) – Mode of counting the interactions: <cite>IN</cite>, <cite>OUT</cite> or <cite>ALL</cite> , whether
+to consider incoming, outgoing or all edges, respectively,
+respective to the <cite>node defined in `entity`</cite>.</p>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p><code class="xref py py-class docutils literal notranslate"><span class="pre">EntityList</span></code> object containing the partners having
+interactions to the queried node(s) matching all the criteria.
+If <code class="docutils literal notranslate"><span class="pre">entity</span></code> doesn’t present in the network the returned
+<code class="docutils literal notranslate"><span class="pre">EntityList</span></code> will be empty just like if no interaction matches
+the criteria.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.post_transcriptionally_activates">
+<span class="sig-name descname"><span class="pre">post_transcriptionally_activates</span></span><a class="headerlink" href="#pypath.core.network.Network.post_transcriptionally_activates" title="Link to this definition">§</a></dt>
+<dd><dl class="simple">
+<dt>arg str,Entity,list,set,tuple,EntityList entity:</dt><dd><p>An identifier or label of a molecular entity or an
+<code class="xref py py-class docutils literal notranslate"><span class="pre">Entity</span></code> object. Alternatively an iterator with the
+elements of any of the types valid for a single entity argument,
+e.g. a list of gene symbols.</p>
+</dd>
+</dl>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><p><strong>mode</strong> (<em>str</em>) – Mode of counting the interactions: <cite>IN</cite>, <cite>OUT</cite> or <cite>ALL</cite> , whether
+to consider incoming, outgoing or all edges, respectively,
+respective to the <cite>node defined in `entity`</cite>.</p>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p><code class="xref py py-class docutils literal notranslate"><span class="pre">EntityList</span></code> object containing the partners having
+interactions to the queried node(s) matching all the criteria.
+If <code class="docutils literal notranslate"><span class="pre">entity</span></code> doesn’t present in the network the returned
+<code class="docutils literal notranslate"><span class="pre">EntityList</span></code> will be empty just like if no interaction matches
+the criteria.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.post_transcriptionally_regulated_by">
+<span class="sig-name descname"><span class="pre">post_transcriptionally_regulated_by</span></span><a class="headerlink" href="#pypath.core.network.Network.post_transcriptionally_regulated_by" title="Link to this definition">§</a></dt>
+<dd><dl class="simple">
+<dt>arg str,Entity,list,set,tuple,EntityList entity:</dt><dd><p>An identifier or label of a molecular entity or an
+<code class="xref py py-class docutils literal notranslate"><span class="pre">Entity</span></code> object. Alternatively an iterator with the
+elements of any of the types valid for a single entity argument,
+e.g. a list of gene symbols.</p>
+</dd>
+</dl>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><p><strong>mode</strong> (<em>str</em>) – Mode of counting the interactions: <cite>IN</cite>, <cite>OUT</cite> or <cite>ALL</cite> , whether
+to consider incoming, outgoing or all edges, respectively,
+respective to the <cite>node defined in `entity`</cite>.</p>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p><code class="xref py py-class docutils literal notranslate"><span class="pre">EntityList</span></code> object containing the partners having
+interactions to the queried node(s) matching all the criteria.
+If <code class="docutils literal notranslate"><span class="pre">entity</span></code> doesn’t present in the network the returned
+<code class="docutils literal notranslate"><span class="pre">EntityList</span></code> will be empty just like if no interaction matches
+the criteria.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.post_transcriptionally_regulates">
+<span class="sig-name descname"><span class="pre">post_transcriptionally_regulates</span></span><a class="headerlink" href="#pypath.core.network.Network.post_transcriptionally_regulates" title="Link to this definition">§</a></dt>
+<dd><dl class="simple">
+<dt>arg str,Entity,list,set,tuple,EntityList entity:</dt><dd><p>An identifier or label of a molecular entity or an
+<code class="xref py py-class docutils literal notranslate"><span class="pre">Entity</span></code> object. Alternatively an iterator with the
+elements of any of the types valid for a single entity argument,
+e.g. a list of gene symbols.</p>
+</dd>
+</dl>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><p><strong>mode</strong> (<em>str</em>) – Mode of counting the interactions: <cite>IN</cite>, <cite>OUT</cite> or <cite>ALL</cite> , whether
+to consider incoming, outgoing or all edges, respectively,
+respective to the <cite>node defined in `entity`</cite>.</p>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p><code class="xref py py-class docutils literal notranslate"><span class="pre">EntityList</span></code> object containing the partners having
+interactions to the queried node(s) matching all the criteria.
+If <code class="docutils literal notranslate"><span class="pre">entity</span></code> doesn’t present in the network the returned
+<code class="docutils literal notranslate"><span class="pre">EntityList</span></code> will be empty just like if no interaction matches
+the criteria.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.post_transcriptionally_suppressed_by">
+<span class="sig-name descname"><span class="pre">post_transcriptionally_suppressed_by</span></span><a class="headerlink" href="#pypath.core.network.Network.post_transcriptionally_suppressed_by" title="Link to this definition">§</a></dt>
+<dd><dl class="simple">
+<dt>arg str,Entity,list,set,tuple,EntityList entity:</dt><dd><p>An identifier or label of a molecular entity or an
+<code class="xref py py-class docutils literal notranslate"><span class="pre">Entity</span></code> object. Alternatively an iterator with the
+elements of any of the types valid for a single entity argument,
+e.g. a list of gene symbols.</p>
+</dd>
+</dl>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><p><strong>mode</strong> (<em>str</em>) – Mode of counting the interactions: <cite>IN</cite>, <cite>OUT</cite> or <cite>ALL</cite> , whether
+to consider incoming, outgoing or all edges, respectively,
+respective to the <cite>node defined in `entity`</cite>.</p>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p><code class="xref py py-class docutils literal notranslate"><span class="pre">EntityList</span></code> object containing the partners having
+interactions to the queried node(s) matching all the criteria.
+If <code class="docutils literal notranslate"><span class="pre">entity</span></code> doesn’t present in the network the returned
+<code class="docutils literal notranslate"><span class="pre">EntityList</span></code> will be empty just like if no interaction matches
+the criteria.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.post_transcriptionally_suppresses">
+<span class="sig-name descname"><span class="pre">post_transcriptionally_suppresses</span></span><a class="headerlink" href="#pypath.core.network.Network.post_transcriptionally_suppresses" title="Link to this definition">§</a></dt>
+<dd><dl class="simple">
+<dt>arg str,Entity,list,set,tuple,EntityList entity:</dt><dd><p>An identifier or label of a molecular entity or an
+<code class="xref py py-class docutils literal notranslate"><span class="pre">Entity</span></code> object. Alternatively an iterator with the
+elements of any of the types valid for a single entity argument,
+e.g. a list of gene symbols.</p>
+</dd>
+</dl>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><p><strong>mode</strong> (<em>str</em>) – Mode of counting the interactions: <cite>IN</cite>, <cite>OUT</cite> or <cite>ALL</cite> , whether
+to consider incoming, outgoing or all edges, respectively,
+respective to the <cite>node defined in `entity`</cite>.</p>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p><code class="xref py py-class docutils literal notranslate"><span class="pre">EntityList</span></code> object containing the partners having
+interactions to the queried node(s) matching all the criteria.
+If <code class="docutils literal notranslate"><span class="pre">entity</span></code> doesn’t present in the network the returned
+<code class="docutils literal notranslate"><span class="pre">EntityList</span></code> will be empty just like if no interaction matches
+the criteria.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.post_translationally_activated_by">
+<span class="sig-name descname"><span class="pre">post_translationally_activated_by</span></span><a class="headerlink" href="#pypath.core.network.Network.post_translationally_activated_by" title="Link to this definition">§</a></dt>
+<dd><dl class="simple">
+<dt>arg str,Entity,list,set,tuple,EntityList entity:</dt><dd><p>An identifier or label of a molecular entity or an
+<code class="xref py py-class docutils literal notranslate"><span class="pre">Entity</span></code> object. Alternatively an iterator with the
+elements of any of the types valid for a single entity argument,
+e.g. a list of gene symbols.</p>
+</dd>
+</dl>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><p><strong>mode</strong> (<em>str</em>) – Mode of counting the interactions: <cite>IN</cite>, <cite>OUT</cite> or <cite>ALL</cite> , whether
+to consider incoming, outgoing or all edges, respectively,
+respective to the <cite>node defined in `entity`</cite>.</p>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p><code class="xref py py-class docutils literal notranslate"><span class="pre">EntityList</span></code> object containing the partners having
+interactions to the queried node(s) matching all the criteria.
+If <code class="docutils literal notranslate"><span class="pre">entity</span></code> doesn’t present in the network the returned
+<code class="docutils literal notranslate"><span class="pre">EntityList</span></code> will be empty just like if no interaction matches
+the criteria.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.post_translationally_activates">
+<span class="sig-name descname"><span class="pre">post_translationally_activates</span></span><a class="headerlink" href="#pypath.core.network.Network.post_translationally_activates" title="Link to this definition">§</a></dt>
+<dd><dl class="simple">
+<dt>arg str,Entity,list,set,tuple,EntityList entity:</dt><dd><p>An identifier or label of a molecular entity or an
+<code class="xref py py-class docutils literal notranslate"><span class="pre">Entity</span></code> object. Alternatively an iterator with the
+elements of any of the types valid for a single entity argument,
+e.g. a list of gene symbols.</p>
+</dd>
+</dl>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><p><strong>mode</strong> (<em>str</em>) – Mode of counting the interactions: <cite>IN</cite>, <cite>OUT</cite> or <cite>ALL</cite> , whether
+to consider incoming, outgoing or all edges, respectively,
+respective to the <cite>node defined in `entity`</cite>.</p>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p><code class="xref py py-class docutils literal notranslate"><span class="pre">EntityList</span></code> object containing the partners having
+interactions to the queried node(s) matching all the criteria.
+If <code class="docutils literal notranslate"><span class="pre">entity</span></code> doesn’t present in the network the returned
+<code class="docutils literal notranslate"><span class="pre">EntityList</span></code> will be empty just like if no interaction matches
+the criteria.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.post_translationally_regulated_by">
+<span class="sig-name descname"><span class="pre">post_translationally_regulated_by</span></span><a class="headerlink" href="#pypath.core.network.Network.post_translationally_regulated_by" title="Link to this definition">§</a></dt>
+<dd><dl class="simple">
+<dt>arg str,Entity,list,set,tuple,EntityList entity:</dt><dd><p>An identifier or label of a molecular entity or an
+<code class="xref py py-class docutils literal notranslate"><span class="pre">Entity</span></code> object. Alternatively an iterator with the
+elements of any of the types valid for a single entity argument,
+e.g. a list of gene symbols.</p>
+</dd>
+</dl>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><p><strong>mode</strong> (<em>str</em>) – Mode of counting the interactions: <cite>IN</cite>, <cite>OUT</cite> or <cite>ALL</cite> , whether
+to consider incoming, outgoing or all edges, respectively,
+respective to the <cite>node defined in `entity`</cite>.</p>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p><code class="xref py py-class docutils literal notranslate"><span class="pre">EntityList</span></code> object containing the partners having
+interactions to the queried node(s) matching all the criteria.
+If <code class="docutils literal notranslate"><span class="pre">entity</span></code> doesn’t present in the network the returned
+<code class="docutils literal notranslate"><span class="pre">EntityList</span></code> will be empty just like if no interaction matches
+the criteria.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.post_translationally_regulates">
+<span class="sig-name descname"><span class="pre">post_translationally_regulates</span></span><a class="headerlink" href="#pypath.core.network.Network.post_translationally_regulates" title="Link to this definition">§</a></dt>
+<dd><dl class="simple">
+<dt>arg str,Entity,list,set,tuple,EntityList entity:</dt><dd><p>An identifier or label of a molecular entity or an
+<code class="xref py py-class docutils literal notranslate"><span class="pre">Entity</span></code> object. Alternatively an iterator with the
+elements of any of the types valid for a single entity argument,
+e.g. a list of gene symbols.</p>
+</dd>
+</dl>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><p><strong>mode</strong> (<em>str</em>) – Mode of counting the interactions: <cite>IN</cite>, <cite>OUT</cite> or <cite>ALL</cite> , whether
+to consider incoming, outgoing or all edges, respectively,
+respective to the <cite>node defined in `entity`</cite>.</p>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p><code class="xref py py-class docutils literal notranslate"><span class="pre">EntityList</span></code> object containing the partners having
+interactions to the queried node(s) matching all the criteria.
+If <code class="docutils literal notranslate"><span class="pre">entity</span></code> doesn’t present in the network the returned
+<code class="docutils literal notranslate"><span class="pre">EntityList</span></code> will be empty just like if no interaction matches
+the criteria.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.post_translationally_suppressed_by">
+<span class="sig-name descname"><span class="pre">post_translationally_suppressed_by</span></span><a class="headerlink" href="#pypath.core.network.Network.post_translationally_suppressed_by" title="Link to this definition">§</a></dt>
+<dd><dl class="simple">
+<dt>arg str,Entity,list,set,tuple,EntityList entity:</dt><dd><p>An identifier or label of a molecular entity or an
+<code class="xref py py-class docutils literal notranslate"><span class="pre">Entity</span></code> object. Alternatively an iterator with the
+elements of any of the types valid for a single entity argument,
+e.g. a list of gene symbols.</p>
+</dd>
+</dl>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><p><strong>mode</strong> (<em>str</em>) – Mode of counting the interactions: <cite>IN</cite>, <cite>OUT</cite> or <cite>ALL</cite> , whether
+to consider incoming, outgoing or all edges, respectively,
+respective to the <cite>node defined in `entity`</cite>.</p>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p><code class="xref py py-class docutils literal notranslate"><span class="pre">EntityList</span></code> object containing the partners having
+interactions to the queried node(s) matching all the criteria.
+If <code class="docutils literal notranslate"><span class="pre">entity</span></code> doesn’t present in the network the returned
+<code class="docutils literal notranslate"><span class="pre">EntityList</span></code> will be empty just like if no interaction matches
+the criteria.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.post_translationally_suppresses">
+<span class="sig-name descname"><span class="pre">post_translationally_suppresses</span></span><a class="headerlink" href="#pypath.core.network.Network.post_translationally_suppresses" title="Link to this definition">§</a></dt>
+<dd><dl class="simple">
+<dt>arg str,Entity,list,set,tuple,EntityList entity:</dt><dd><p>An identifier or label of a molecular entity or an
+<code class="xref py py-class docutils literal notranslate"><span class="pre">Entity</span></code> object. Alternatively an iterator with the
+elements of any of the types valid for a single entity argument,
+e.g. a list of gene symbols.</p>
+</dd>
+</dl>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><p><strong>mode</strong> (<em>str</em>) – Mode of counting the interactions: <cite>IN</cite>, <cite>OUT</cite> or <cite>ALL</cite> , whether
+to consider incoming, outgoing or all edges, respectively,
+respective to the <cite>node defined in `entity`</cite>.</p>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p><code class="xref py py-class docutils literal notranslate"><span class="pre">EntityList</span></code> object containing the partners having
+interactions to the queried node(s) matching all the criteria.
+If <code class="docutils literal notranslate"><span class="pre">entity</span></code> doesn’t present in the network the returned
+<code class="docutils literal notranslate"><span class="pre">EntityList</span></code> will be empty just like if no interaction matches
+the criteria.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.protein_identifiers_by_data_model">
+<span class="sig-name descname"><span class="pre">protein_identifiers_by_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.protein_identifiers_by_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.protein_identifiers_by_interaction_type">
+<span class="sig-name descname"><span class="pre">protein_identifiers_by_interaction_type</span></span><a class="headerlink" href="#pypath.core.network.Network.protein_identifiers_by_interaction_type" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.protein_identifiers_by_interaction_type_and_data_model">
+<span class="sig-name descname"><span class="pre">protein_identifiers_by_interaction_type_and_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.protein_identifiers_by_interaction_type_and_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.protein_identifiers_by_interaction_type_and_data_model_and_resource">
+<span class="sig-name descname"><span class="pre">protein_identifiers_by_interaction_type_and_data_model_and_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.protein_identifiers_by_interaction_type_and_data_model_and_resource" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.protein_identifiers_by_reference">
+<span class="sig-name descname"><span class="pre">protein_identifiers_by_reference</span></span><a class="headerlink" href="#pypath.core.network.Network.protein_identifiers_by_reference" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.protein_identifiers_by_resource">
+<span class="sig-name descname"><span class="pre">protein_identifiers_by_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.protein_identifiers_by_resource" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.protein_labels_by_data_model">
+<span class="sig-name descname"><span class="pre">protein_labels_by_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.protein_labels_by_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.protein_labels_by_interaction_type">
+<span class="sig-name descname"><span class="pre">protein_labels_by_interaction_type</span></span><a class="headerlink" href="#pypath.core.network.Network.protein_labels_by_interaction_type" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.protein_labels_by_interaction_type_and_data_model">
+<span class="sig-name descname"><span class="pre">protein_labels_by_interaction_type_and_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.protein_labels_by_interaction_type_and_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.protein_labels_by_interaction_type_and_data_model_and_resource">
+<span class="sig-name descname"><span class="pre">protein_labels_by_interaction_type_and_data_model_and_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.protein_labels_by_interaction_type_and_data_model_and_resource" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.protein_labels_by_reference">
+<span class="sig-name descname"><span class="pre">protein_labels_by_reference</span></span><a class="headerlink" href="#pypath.core.network.Network.protein_labels_by_reference" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.protein_labels_by_resource">
+<span class="sig-name descname"><span class="pre">protein_labels_by_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.protein_labels_by_resource" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.proteins_by_data_model">
+<span class="sig-name descname"><span class="pre">proteins_by_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.proteins_by_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.proteins_by_interaction_type">
+<span class="sig-name descname"><span class="pre">proteins_by_interaction_type</span></span><a class="headerlink" href="#pypath.core.network.Network.proteins_by_interaction_type" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.proteins_by_interaction_type_and_data_model">
+<span class="sig-name descname"><span class="pre">proteins_by_interaction_type_and_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.proteins_by_interaction_type_and_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.proteins_by_interaction_type_and_data_model_and_resource">
+<span class="sig-name descname"><span class="pre">proteins_by_interaction_type_and_data_model_and_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.proteins_by_interaction_type_and_data_model_and_resource" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.proteins_by_reference">
+<span class="sig-name descname"><span class="pre">proteins_by_reference</span></span><a class="headerlink" href="#pypath.core.network.Network.proteins_by_reference" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.proteins_by_resource">
+<span class="sig-name descname"><span class="pre">proteins_by_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.proteins_by_resource" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.network.Network.random_interaction">
+<span class="sig-name descname"><span class="pre">random_interaction</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/network.html#Network.random_interaction"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.network.Network.random_interaction" title="Link to this definition">§</a></dt>
+<dd><p>Picks a random interaction from the network.</p>
+<dl class="simple">
+<dt>Returns</dt><dd><p>An Interaction object, or None if the network is empty.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.references_by_data_model">
+<span class="sig-name descname"><span class="pre">references_by_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.references_by_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.references_by_interaction_type">
+<span class="sig-name descname"><span class="pre">references_by_interaction_type</span></span><a class="headerlink" href="#pypath.core.network.Network.references_by_interaction_type" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.references_by_interaction_type_and_data_model">
+<span class="sig-name descname"><span class="pre">references_by_interaction_type_and_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.references_by_interaction_type_and_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.references_by_interaction_type_and_data_model_and_resource">
+<span class="sig-name descname"><span class="pre">references_by_interaction_type_and_data_model_and_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.references_by_interaction_type_and_data_model_and_resource" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.references_by_reference">
+<span class="sig-name descname"><span class="pre">references_by_reference</span></span><a class="headerlink" href="#pypath.core.network.Network.references_by_reference" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.references_by_resource">
+<span class="sig-name descname"><span class="pre">references_by_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.references_by_resource" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.regulated_by">
+<span class="sig-name descname"><span class="pre">regulated_by</span></span><a class="headerlink" href="#pypath.core.network.Network.regulated_by" title="Link to this definition">§</a></dt>
+<dd><dl class="simple">
+<dt>arg str,Entity,list,set,tuple,EntityList entity:</dt><dd><p>An identifier or label of a molecular entity or an
+<code class="xref py py-class docutils literal notranslate"><span class="pre">Entity</span></code> object. Alternatively an iterator with the
+elements of any of the types valid for a single entity argument,
+e.g. a list of gene symbols.</p>
+</dd>
+</dl>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><p><strong>mode</strong> (<em>str</em>) – Mode of counting the interactions: <cite>IN</cite>, <cite>OUT</cite> or <cite>ALL</cite> , whether
+to consider incoming, outgoing or all edges, respectively,
+respective to the <cite>node defined in `entity`</cite>.</p>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p><code class="xref py py-class docutils literal notranslate"><span class="pre">EntityList</span></code> object containing the partners having
+interactions to the queried node(s) matching all the criteria.
+If <code class="docutils literal notranslate"><span class="pre">entity</span></code> doesn’t present in the network the returned
+<code class="docutils literal notranslate"><span class="pre">EntityList</span></code> will be empty just like if no interaction matches
+the criteria.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.regulates">
+<span class="sig-name descname"><span class="pre">regulates</span></span><a class="headerlink" href="#pypath.core.network.Network.regulates" title="Link to this definition">§</a></dt>
+<dd><dl class="simple">
+<dt>arg str,Entity,list,set,tuple,EntityList entity:</dt><dd><p>An identifier or label of a molecular entity or an
+<code class="xref py py-class docutils literal notranslate"><span class="pre">Entity</span></code> object. Alternatively an iterator with the
+elements of any of the types valid for a single entity argument,
+e.g. a list of gene symbols.</p>
+</dd>
+</dl>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><p><strong>mode</strong> (<em>str</em>) – Mode of counting the interactions: <cite>IN</cite>, <cite>OUT</cite> or <cite>ALL</cite> , whether
+to consider incoming, outgoing or all edges, respectively,
+respective to the <cite>node defined in `entity`</cite>.</p>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p><code class="xref py py-class docutils literal notranslate"><span class="pre">EntityList</span></code> object containing the partners having
+interactions to the queried node(s) matching all the criteria.
+If <code class="docutils literal notranslate"><span class="pre">entity</span></code> doesn’t present in the network the returned
+<code class="docutils literal notranslate"><span class="pre">EntityList</span></code> will be empty just like if no interaction matches
+the criteria.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.network.Network.reload">
+<span class="sig-name descname"><span class="pre">reload</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">recursive</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/network.html#Network.reload"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.network.Network.reload" title="Link to this definition">§</a></dt>
+<dd><p>Reloads the object from the module level.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.network.Network.remove_interaction">
+<span class="sig-name descname"><span class="pre">remove_interaction</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_a</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_b</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/network.html#Network.remove_interaction"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.network.Network.remove_interaction" title="Link to this definition">§</a></dt>
+<dd><p>Removes the interaction between two nodes if exists.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><p><strong>entity_a</strong><strong>,</strong><strong>entity_b</strong> (<em>str</em><em>,</em><a class="reference internal" href="pypath.core.entity.Entity.html#pypath.core.entity.Entity" title="pypath.core.entity.Entity"><em>Entity</em></a>) – A pair of molecular entity identifiers, labels or <code class="docutils literal notranslate"><span class="pre">Entity</span></code>
+objects.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.network.Network.remove_loops">
+<span class="sig-name descname"><span class="pre">remove_loops</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/network.html#Network.remove_loops"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.network.Network.remove_loops" title="Link to this definition">§</a></dt>
+<dd><p>Removes the loop interactions from the network i.e. the ones with
+their two endpoints being the same entity.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.network.Network.remove_node">
+<span class="sig-name descname"><span class="pre">remove_node</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/network.html#Network.remove_node"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.network.Network.remove_node" title="Link to this definition">§</a></dt>
+<dd><p>Removes a node with all its interactions.
+If the removal of the interactions leaves any of the partner nodes
+without interactions it will be removed too.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><p><strong>entity</strong> (<em>str</em><em>,</em><a class="reference internal" href="pypath.core.entity.Entity.html#pypath.core.entity.Entity" title="pypath.core.entity.Entity"><em>Entity</em></a>) – A molecular entity identifier, label or <code class="docutils literal notranslate"><span class="pre">Entity</span></code> object.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.network.Network.remove_zero_degree">
+<span class="sig-name descname"><span class="pre">remove_zero_degree</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/network.html#Network.remove_zero_degree"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.network.Network.remove_zero_degree" title="Link to this definition">§</a></dt>
+<dd><p>Removes all nodes with no interaction.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.network.Network.reset">
+<span class="sig-name descname"><span class="pre">reset</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/network.html#Network.reset"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.network.Network.reset" title="Link to this definition">§</a></dt>
+<dd><p>Removes network data i.e. creates empty interaction and node
+dictionaries.</p>
+</dd></dl>
+
+<dl class="py property">
+<dt class="sig sig-object py" id="pypath.core.network.Network.resource_names">
+<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">resource_names</span></span><a class="headerlink" href="#pypath.core.network.Network.resource_names" title="Link to this definition">§</a></dt>
+<dd><p>Returns a set of all resource names.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.resource_names_by_data_model">
+<span class="sig-name descname"><span class="pre">resource_names_by_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.resource_names_by_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.resource_names_by_interaction_type">
+<span class="sig-name descname"><span class="pre">resource_names_by_interaction_type</span></span><a class="headerlink" href="#pypath.core.network.Network.resource_names_by_interaction_type" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.resource_names_by_interaction_type_and_data_model">
+<span class="sig-name descname"><span class="pre">resource_names_by_interaction_type_and_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.resource_names_by_interaction_type_and_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.resource_names_by_interaction_type_and_data_model_and_resource">
+<span class="sig-name descname"><span class="pre">resource_names_by_interaction_type_and_data_model_and_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.resource_names_by_interaction_type_and_data_model_and_resource" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.resource_names_by_reference">
+<span class="sig-name descname"><span class="pre">resource_names_by_reference</span></span><a class="headerlink" href="#pypath.core.network.Network.resource_names_by_reference" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.resource_names_by_resource">
+<span class="sig-name descname"><span class="pre">resource_names_by_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.resource_names_by_resource" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.resource_names_via_by_data_model">
+<span class="sig-name descname"><span class="pre">resource_names_via_by_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.resource_names_via_by_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.resource_names_via_by_interaction_type">
+<span class="sig-name descname"><span class="pre">resource_names_via_by_interaction_type</span></span><a class="headerlink" href="#pypath.core.network.Network.resource_names_via_by_interaction_type" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.resource_names_via_by_interaction_type_and_data_model">
+<span class="sig-name descname"><span class="pre">resource_names_via_by_interaction_type_and_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.resource_names_via_by_interaction_type_and_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.resource_names_via_by_interaction_type_and_data_model_and_resource">
+<span class="sig-name descname"><span class="pre">resource_names_via_by_interaction_type_and_data_model_and_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.resource_names_via_by_interaction_type_and_data_model_and_resource" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.resource_names_via_by_reference">
+<span class="sig-name descname"><span class="pre">resource_names_via_by_reference</span></span><a class="headerlink" href="#pypath.core.network.Network.resource_names_via_by_reference" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.resource_names_via_by_resource">
+<span class="sig-name descname"><span class="pre">resource_names_via_by_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.resource_names_via_by_resource" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py property">
+<dt class="sig sig-object py" id="pypath.core.network.Network.resources">
+<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">resources</span></span><a class="headerlink" href="#pypath.core.network.Network.resources" title="Link to this definition">§</a></dt>
+<dd><p>Returns a set of all resources.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.resources_by_data_model">
+<span class="sig-name descname"><span class="pre">resources_by_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.resources_by_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.resources_by_interaction_type">
+<span class="sig-name descname"><span class="pre">resources_by_interaction_type</span></span><a class="headerlink" href="#pypath.core.network.Network.resources_by_interaction_type" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.resources_by_interaction_type_and_data_model">
+<span class="sig-name descname"><span class="pre">resources_by_interaction_type_and_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.resources_by_interaction_type_and_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.resources_by_interaction_type_and_data_model_and_resource">
+<span class="sig-name descname"><span class="pre">resources_by_interaction_type_and_data_model_and_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.resources_by_interaction_type_and_data_model_and_resource" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.resources_by_reference">
+<span class="sig-name descname"><span class="pre">resources_by_reference</span></span><a class="headerlink" href="#pypath.core.network.Network.resources_by_reference" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.resources_by_resource">
+<span class="sig-name descname"><span class="pre">resources_by_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.resources_by_resource" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.resources_via_by_data_model">
+<span class="sig-name descname"><span class="pre">resources_via_by_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.resources_via_by_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.resources_via_by_interaction_type">
+<span class="sig-name descname"><span class="pre">resources_via_by_interaction_type</span></span><a class="headerlink" href="#pypath.core.network.Network.resources_via_by_interaction_type" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.resources_via_by_interaction_type_and_data_model">
+<span class="sig-name descname"><span class="pre">resources_via_by_interaction_type_and_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.resources_via_by_interaction_type_and_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.resources_via_by_interaction_type_and_data_model_and_resource">
+<span class="sig-name descname"><span class="pre">resources_via_by_interaction_type_and_data_model_and_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.resources_via_by_interaction_type_and_data_model_and_resource" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.resources_via_by_reference">
+<span class="sig-name descname"><span class="pre">resources_via_by_reference</span></span><a class="headerlink" href="#pypath.core.network.Network.resources_via_by_reference" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.resources_via_by_resource">
+<span class="sig-name descname"><span class="pre">resources_via_by_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.resources_via_by_resource" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.network.Network.save_to_pickle">
+<span class="sig-name descname"><span class="pre">save_to_pickle</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">pickle_file</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/network.html#Network.save_to_pickle"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.network.Network.save_to_pickle" title="Link to this definition">§</a></dt>
+<dd><p>Saves the network to a pickle file.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><p><strong>pickle_file</strong> (<em>str</em>) – Path to the pickle file.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.small_molecule_identifiers_by_data_model">
+<span class="sig-name descname"><span class="pre">small_molecule_identifiers_by_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.small_molecule_identifiers_by_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.small_molecule_identifiers_by_interaction_type">
+<span class="sig-name descname"><span class="pre">small_molecule_identifiers_by_interaction_type</span></span><a class="headerlink" href="#pypath.core.network.Network.small_molecule_identifiers_by_interaction_type" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.small_molecule_identifiers_by_interaction_type_and_data_model">
+<span class="sig-name descname"><span class="pre">small_molecule_identifiers_by_interaction_type_and_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.small_molecule_identifiers_by_interaction_type_and_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.small_molecule_identifiers_by_interaction_type_and_data_model_and_resource">
+<span class="sig-name descname"><span class="pre">small_molecule_identifiers_by_interaction_type_and_data_model_and_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.small_molecule_identifiers_by_interaction_type_and_data_model_and_resource" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.small_molecule_identifiers_by_reference">
+<span class="sig-name descname"><span class="pre">small_molecule_identifiers_by_reference</span></span><a class="headerlink" href="#pypath.core.network.Network.small_molecule_identifiers_by_reference" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.small_molecule_identifiers_by_resource">
+<span class="sig-name descname"><span class="pre">small_molecule_identifiers_by_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.small_molecule_identifiers_by_resource" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.small_molecule_labels_by_data_model">
+<span class="sig-name descname"><span class="pre">small_molecule_labels_by_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.small_molecule_labels_by_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.small_molecule_labels_by_interaction_type">
+<span class="sig-name descname"><span class="pre">small_molecule_labels_by_interaction_type</span></span><a class="headerlink" href="#pypath.core.network.Network.small_molecule_labels_by_interaction_type" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.small_molecule_labels_by_interaction_type_and_data_model">
+<span class="sig-name descname"><span class="pre">small_molecule_labels_by_interaction_type_and_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.small_molecule_labels_by_interaction_type_and_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.small_molecule_labels_by_interaction_type_and_data_model_and_resource">
+<span class="sig-name descname"><span class="pre">small_molecule_labels_by_interaction_type_and_data_model_and_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.small_molecule_labels_by_interaction_type_and_data_model_and_resource" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.small_molecule_labels_by_reference">
+<span class="sig-name descname"><span class="pre">small_molecule_labels_by_reference</span></span><a class="headerlink" href="#pypath.core.network.Network.small_molecule_labels_by_reference" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.small_molecule_labels_by_resource">
+<span class="sig-name descname"><span class="pre">small_molecule_labels_by_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.small_molecule_labels_by_resource" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.small_molecules_by_data_model">
+<span class="sig-name descname"><span class="pre">small_molecules_by_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.small_molecules_by_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.small_molecules_by_interaction_type">
+<span class="sig-name descname"><span class="pre">small_molecules_by_interaction_type</span></span><a class="headerlink" href="#pypath.core.network.Network.small_molecules_by_interaction_type" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.small_molecules_by_interaction_type_and_data_model">
+<span class="sig-name descname"><span class="pre">small_molecules_by_interaction_type_and_data_model</span></span><a class="headerlink" href="#pypath.core.network.Network.small_molecules_by_interaction_type_and_data_model" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.small_molecules_by_interaction_type_and_data_model_and_resource">
+<span class="sig-name descname"><span class="pre">small_molecules_by_interaction_type_and_data_model_and_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.small_molecules_by_interaction_type_and_data_model_and_resource" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.small_molecules_by_reference">
+<span class="sig-name descname"><span class="pre">small_molecules_by_reference</span></span><a class="headerlink" href="#pypath.core.network.Network.small_molecules_by_reference" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.small_molecules_by_resource">
+<span class="sig-name descname"><span class="pre">small_molecules_by_resource</span></span><a class="headerlink" href="#pypath.core.network.Network.small_molecules_by_resource" title="Link to this definition">§</a></dt>
+<dd><p>Built-in immutable sequence.</p>
+<p>If no argument is given, the constructor returns an empty tuple.
+If iterable is specified the tuple is initialized from iterable’s items.</p>
+<p>If the argument is a tuple, the return value is the same object.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.network.Network.summaries_tab">
+<span class="sig-name descname"><span class="pre">summaries_tab</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">outfile</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">return_table</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">label_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/network.html#Network.summaries_tab"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.network.Network.summaries_tab" title="Link to this definition">§</a></dt>
+<dd><p>Creates a table from resource vs. entity counts and optionally
+writes it to <code class="docutils literal notranslate"><span class="pre">outfile</span></code> and returns it.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.suppressed_by">
+<span class="sig-name descname"><span class="pre">suppressed_by</span></span><a class="headerlink" href="#pypath.core.network.Network.suppressed_by" title="Link to this definition">§</a></dt>
+<dd><dl class="simple">
+<dt>arg str,Entity,list,set,tuple,EntityList entity:</dt><dd><p>An identifier or label of a molecular entity or an
+<code class="xref py py-class docutils literal notranslate"><span class="pre">Entity</span></code> object. Alternatively an iterator with the
+elements of any of the types valid for a single entity argument,
+e.g. a list of gene symbols.</p>
+</dd>
+</dl>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><p><strong>mode</strong> (<em>str</em>) – Mode of counting the interactions: <cite>IN</cite>, <cite>OUT</cite> or <cite>ALL</cite> , whether
+to consider incoming, outgoing or all edges, respectively,
+respective to the <cite>node defined in `entity`</cite>.</p>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p><code class="xref py py-class docutils literal notranslate"><span class="pre">EntityList</span></code> object containing the partners having
+interactions to the queried node(s) matching all the criteria.
+If <code class="docutils literal notranslate"><span class="pre">entity</span></code> doesn’t present in the network the returned
+<code class="docutils literal notranslate"><span class="pre">EntityList</span></code> will be empty just like if no interaction matches
+the criteria.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.suppresses">
+<span class="sig-name descname"><span class="pre">suppresses</span></span><a class="headerlink" href="#pypath.core.network.Network.suppresses" title="Link to this definition">§</a></dt>
+<dd><dl class="simple">
+<dt>arg str,Entity,list,set,tuple,EntityList entity:</dt><dd><p>An identifier or label of a molecular entity or an
+<code class="xref py py-class docutils literal notranslate"><span class="pre">Entity</span></code> object. Alternatively an iterator with the
+elements of any of the types valid for a single entity argument,
+e.g. a list of gene symbols.</p>
+</dd>
+</dl>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><p><strong>mode</strong> (<em>str</em>) – Mode of counting the interactions: <cite>IN</cite>, <cite>OUT</cite> or <cite>ALL</cite> , whether
+to consider incoming, outgoing or all edges, respectively,
+respective to the <cite>node defined in `entity`</cite>.</p>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p><code class="xref py py-class docutils literal notranslate"><span class="pre">EntityList</span></code> object containing the partners having
+interactions to the queried node(s) matching all the criteria.
+If <code class="docutils literal notranslate"><span class="pre">entity</span></code> doesn’t present in the network the returned
+<code class="docutils literal notranslate"><span class="pre">EntityList</span></code> will be empty just like if no interaction matches
+the criteria.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.network.Network.to_igraph">
+<span class="sig-name descname"><span class="pre">to_igraph</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/network.html#Network.to_igraph"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.network.Network.to_igraph" title="Link to this definition">§</a></dt>
+<dd><p>Converts the network to the legacy <code class="docutils literal notranslate"><span class="pre">igraph.Graph</span></code> based <code class="docutils literal notranslate"><span class="pre">PyPath</span></code>
+object.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.network.Network.transcription">
+<em class="property"><span class="pre">classmethod</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">transcription</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">dorothea</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">original_resources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">dorothea_levels</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">exclude</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">reread</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">redownload</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">make_df</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">allow_loops</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/network.html#Network.transcription"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.network.Network.transcription" title="Link to this definition">§</a></dt>
+<dd><p>Initializes a new <code class="docutils literal notranslate"><span class="pre">Network</span></code> object with loading a transcriptional
+regulation network from all databases by default.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>kwargs:</dt><dd><p>Passed to <code class="docutils literal notranslate"><span class="pre">Network.__init__</span></code>.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.transcriptionally_activated_by">
+<span class="sig-name descname"><span class="pre">transcriptionally_activated_by</span></span><a class="headerlink" href="#pypath.core.network.Network.transcriptionally_activated_by" title="Link to this definition">§</a></dt>
+<dd><dl class="simple">
+<dt>arg str,Entity,list,set,tuple,EntityList entity:</dt><dd><p>An identifier or label of a molecular entity or an
+<code class="xref py py-class docutils literal notranslate"><span class="pre">Entity</span></code> object. Alternatively an iterator with the
+elements of any of the types valid for a single entity argument,
+e.g. a list of gene symbols.</p>
+</dd>
+</dl>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><p><strong>mode</strong> (<em>str</em>) – Mode of counting the interactions: <cite>IN</cite>, <cite>OUT</cite> or <cite>ALL</cite> , whether
+to consider incoming, outgoing or all edges, respectively,
+respective to the <cite>node defined in `entity`</cite>.</p>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p><code class="xref py py-class docutils literal notranslate"><span class="pre">EntityList</span></code> object containing the partners having
+interactions to the queried node(s) matching all the criteria.
+If <code class="docutils literal notranslate"><span class="pre">entity</span></code> doesn’t present in the network the returned
+<code class="docutils literal notranslate"><span class="pre">EntityList</span></code> will be empty just like if no interaction matches
+the criteria.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.transcriptionally_activates">
+<span class="sig-name descname"><span class="pre">transcriptionally_activates</span></span><a class="headerlink" href="#pypath.core.network.Network.transcriptionally_activates" title="Link to this definition">§</a></dt>
+<dd><dl class="simple">
+<dt>arg str,Entity,list,set,tuple,EntityList entity:</dt><dd><p>An identifier or label of a molecular entity or an
+<code class="xref py py-class docutils literal notranslate"><span class="pre">Entity</span></code> object. Alternatively an iterator with the
+elements of any of the types valid for a single entity argument,
+e.g. a list of gene symbols.</p>
+</dd>
+</dl>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><p><strong>mode</strong> (<em>str</em>) – Mode of counting the interactions: <cite>IN</cite>, <cite>OUT</cite> or <cite>ALL</cite> , whether
+to consider incoming, outgoing or all edges, respectively,
+respective to the <cite>node defined in `entity`</cite>.</p>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p><code class="xref py py-class docutils literal notranslate"><span class="pre">EntityList</span></code> object containing the partners having
+interactions to the queried node(s) matching all the criteria.
+If <code class="docutils literal notranslate"><span class="pre">entity</span></code> doesn’t present in the network the returned
+<code class="docutils literal notranslate"><span class="pre">EntityList</span></code> will be empty just like if no interaction matches
+the criteria.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.transcriptionally_regulated_by">
+<span class="sig-name descname"><span class="pre">transcriptionally_regulated_by</span></span><a class="headerlink" href="#pypath.core.network.Network.transcriptionally_regulated_by" title="Link to this definition">§</a></dt>
+<dd><dl class="simple">
+<dt>arg str,Entity,list,set,tuple,EntityList entity:</dt><dd><p>An identifier or label of a molecular entity or an
+<code class="xref py py-class docutils literal notranslate"><span class="pre">Entity</span></code> object. Alternatively an iterator with the
+elements of any of the types valid for a single entity argument,
+e.g. a list of gene symbols.</p>
+</dd>
+</dl>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><p><strong>mode</strong> (<em>str</em>) – Mode of counting the interactions: <cite>IN</cite>, <cite>OUT</cite> or <cite>ALL</cite> , whether
+to consider incoming, outgoing or all edges, respectively,
+respective to the <cite>node defined in `entity`</cite>.</p>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p><code class="xref py py-class docutils literal notranslate"><span class="pre">EntityList</span></code> object containing the partners having
+interactions to the queried node(s) matching all the criteria.
+If <code class="docutils literal notranslate"><span class="pre">entity</span></code> doesn’t present in the network the returned
+<code class="docutils literal notranslate"><span class="pre">EntityList</span></code> will be empty just like if no interaction matches
+the criteria.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.transcriptionally_regulates">
+<span class="sig-name descname"><span class="pre">transcriptionally_regulates</span></span><a class="headerlink" href="#pypath.core.network.Network.transcriptionally_regulates" title="Link to this definition">§</a></dt>
+<dd><dl class="simple">
+<dt>arg str,Entity,list,set,tuple,EntityList entity:</dt><dd><p>An identifier or label of a molecular entity or an
+<code class="xref py py-class docutils literal notranslate"><span class="pre">Entity</span></code> object. Alternatively an iterator with the
+elements of any of the types valid for a single entity argument,
+e.g. a list of gene symbols.</p>
+</dd>
+</dl>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><p><strong>mode</strong> (<em>str</em>) – Mode of counting the interactions: <cite>IN</cite>, <cite>OUT</cite> or <cite>ALL</cite> , whether
+to consider incoming, outgoing or all edges, respectively,
+respective to the <cite>node defined in `entity`</cite>.</p>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p><code class="xref py py-class docutils literal notranslate"><span class="pre">EntityList</span></code> object containing the partners having
+interactions to the queried node(s) matching all the criteria.
+If <code class="docutils literal notranslate"><span class="pre">entity</span></code> doesn’t present in the network the returned
+<code class="docutils literal notranslate"><span class="pre">EntityList</span></code> will be empty just like if no interaction matches
+the criteria.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.transcriptionally_suppressed_by">
+<span class="sig-name descname"><span class="pre">transcriptionally_suppressed_by</span></span><a class="headerlink" href="#pypath.core.network.Network.transcriptionally_suppressed_by" title="Link to this definition">§</a></dt>
+<dd><dl class="simple">
+<dt>arg str,Entity,list,set,tuple,EntityList entity:</dt><dd><p>An identifier or label of a molecular entity or an
+<code class="xref py py-class docutils literal notranslate"><span class="pre">Entity</span></code> object. Alternatively an iterator with the
+elements of any of the types valid for a single entity argument,
+e.g. a list of gene symbols.</p>
+</dd>
+</dl>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><p><strong>mode</strong> (<em>str</em>) – Mode of counting the interactions: <cite>IN</cite>, <cite>OUT</cite> or <cite>ALL</cite> , whether
+to consider incoming, outgoing or all edges, respectively,
+respective to the <cite>node defined in `entity`</cite>.</p>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p><code class="xref py py-class docutils literal notranslate"><span class="pre">EntityList</span></code> object containing the partners having
+interactions to the queried node(s) matching all the criteria.
+If <code class="docutils literal notranslate"><span class="pre">entity</span></code> doesn’t present in the network the returned
+<code class="docutils literal notranslate"><span class="pre">EntityList</span></code> will be empty just like if no interaction matches
+the criteria.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.Network.transcriptionally_suppresses">
+<span class="sig-name descname"><span class="pre">transcriptionally_suppresses</span></span><a class="headerlink" href="#pypath.core.network.Network.transcriptionally_suppresses" title="Link to this definition">§</a></dt>
+<dd><dl class="simple">
+<dt>arg str,Entity,list,set,tuple,EntityList entity:</dt><dd><p>An identifier or label of a molecular entity or an
+<code class="xref py py-class docutils literal notranslate"><span class="pre">Entity</span></code> object. Alternatively an iterator with the
+elements of any of the types valid for a single entity argument,
+e.g. a list of gene symbols.</p>
+</dd>
+</dl>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><p><strong>mode</strong> (<em>str</em>) – Mode of counting the interactions: <cite>IN</cite>, <cite>OUT</cite> or <cite>ALL</cite> , whether
+to consider incoming, outgoing or all edges, respectively,
+respective to the <cite>node defined in `entity`</cite>.</p>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p><code class="xref py py-class docutils literal notranslate"><span class="pre">EntityList</span></code> object containing the partners having
+interactions to the queried node(s) matching all the criteria.
+If <code class="docutils literal notranslate"><span class="pre">entity</span></code> doesn’t present in the network the returned
+<code class="docutils literal notranslate"><span class="pre">EntityList</span></code> will be empty just like if no interaction matches
+the criteria.</p>
+</dd>
+</dl>
+</dd></dl>
+
+</dd></dl>
+
+</section>
+
+
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+  <section id="pypath-core-network-networkentitycollection">
+<h1>pypath.core.network.NetworkEntityCollection<a class="headerlink" href="#pypath-core-network-networkentitycollection" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.core.network.NetworkEntityCollection">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.core.network.</span></span><span class="sig-name descname"><span class="pre">NetworkEntityCollection</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">collection</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">label</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/network.html#NetworkEntityCollection"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.network.NetworkEntityCollection" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.network.NetworkEntityCollection.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">collection</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">label</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/network.html#NetworkEntityCollection.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.network.NetworkEntityCollection.__init__" title="Link to this definition">§</a></dt>
+<dd></dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.NetworkEntityCollection.__init__" title="pypath.core.network.NetworkEntityCollection.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>(collection[, label])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">collection_add_total</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">main</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">setup</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">update</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">update_collection_counts</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Attributes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">collection</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">label</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">shared_within_data_model</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">unique_within_data_model</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">shared_within_interaction_type</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">unique_within_interaction_type</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">n_collection</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">n_shared_within_data_model</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">n_unique_within_data_model</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">n_shared_within_interaction_type</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">n_unique_within_interaction_type</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">pct_collection</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">pct_within_data_model</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">pct_within_interaction_type</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">pct_shared_within_data_model</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">pct_unique_within_data_model</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">pct_shared_within_interaction_type</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">pct_unique_within_interaction_type</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">by_data_model</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">by_interaction_type</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">unique_by_data_model</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">shared_by_data_model</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">unique_by_interaction_type</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">shared_by_interaction_type</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">n_by_data_model</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">n_by_interaction_type</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">n_unique_by_data_model</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">n_shared_by_data_model</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">n_unique_by_interaction_type</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">n_shared_by_interaction_type</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">pct_by_data_model</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">pct_by_interaction_type</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">pct_unique_by_data_model</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">pct_shared_by_data_model</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">pct_unique_by_interaction_type</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">pct_shared_by_interaction_type</span></code></p></td>
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+                  
+  <section id="pypath-core-network-networkstatsrecord">
+<h1>pypath.core.network.NetworkStatsRecord<a class="headerlink" href="#pypath-core-network-networkstatsrecord" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.core.network.NetworkStatsRecord">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.core.network.</span></span><span class="sig-name descname"><span class="pre">NetworkStatsRecord</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">total</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">by_resource</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">by_category</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">shared</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">unique</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">percent</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">shared_res_cat</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">unique_res_cat</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">percent_res_cat</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">shared_cat</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">unique_cat</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">percent_cat</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resource_cat</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cat_resource</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">method</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">label</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.network.NetworkStatsRecord" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">tuple</span></code></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.network.NetworkStatsRecord.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.network.NetworkStatsRecord.__init__" title="Link to this definition">§</a></dt>
+<dd></dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.NetworkStatsRecord.__init__" title="pypath.core.network.NetworkStatsRecord.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.NetworkStatsRecord.count" title="pypath.core.network.NetworkStatsRecord.count"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count</span></code></a>(value, /)</p></td>
+<td><p>Return number of occurrences of value.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.NetworkStatsRecord.index" title="pypath.core.network.NetworkStatsRecord.index"><code class="xref py py-obj docutils literal notranslate"><span class="pre">index</span></code></a>(value[, start, stop])</p></td>
+<td><p>Return first index of value.</p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Attributes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.NetworkStatsRecord.by_category" title="pypath.core.network.NetworkStatsRecord.by_category"><code class="xref py py-obj docutils literal notranslate"><span class="pre">by_category</span></code></a></p></td>
+<td><p>Alias for field number 2</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.NetworkStatsRecord.by_resource" title="pypath.core.network.NetworkStatsRecord.by_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">by_resource</span></code></a></p></td>
+<td><p>Alias for field number 1</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.NetworkStatsRecord.cat_resource" title="pypath.core.network.NetworkStatsRecord.cat_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">cat_resource</span></code></a></p></td>
+<td><p>Alias for field number 13</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.NetworkStatsRecord.label" title="pypath.core.network.NetworkStatsRecord.label"><code class="xref py py-obj docutils literal notranslate"><span class="pre">label</span></code></a></p></td>
+<td><p>Alias for field number 15</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.NetworkStatsRecord.method" title="pypath.core.network.NetworkStatsRecord.method"><code class="xref py py-obj docutils literal notranslate"><span class="pre">method</span></code></a></p></td>
+<td><p>Alias for field number 14</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.NetworkStatsRecord.percent" title="pypath.core.network.NetworkStatsRecord.percent"><code class="xref py py-obj docutils literal notranslate"><span class="pre">percent</span></code></a></p></td>
+<td><p>Alias for field number 5</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.NetworkStatsRecord.percent_cat" title="pypath.core.network.NetworkStatsRecord.percent_cat"><code class="xref py py-obj docutils literal notranslate"><span class="pre">percent_cat</span></code></a></p></td>
+<td><p>Alias for field number 11</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.NetworkStatsRecord.percent_res_cat" title="pypath.core.network.NetworkStatsRecord.percent_res_cat"><code class="xref py py-obj docutils literal notranslate"><span class="pre">percent_res_cat</span></code></a></p></td>
+<td><p>Alias for field number 8</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.NetworkStatsRecord.resource_cat" title="pypath.core.network.NetworkStatsRecord.resource_cat"><code class="xref py py-obj docutils literal notranslate"><span class="pre">resource_cat</span></code></a></p></td>
+<td><p>Alias for field number 12</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.NetworkStatsRecord.shared" title="pypath.core.network.NetworkStatsRecord.shared"><code class="xref py py-obj docutils literal notranslate"><span class="pre">shared</span></code></a></p></td>
+<td><p>Alias for field number 3</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.NetworkStatsRecord.shared_cat" title="pypath.core.network.NetworkStatsRecord.shared_cat"><code class="xref py py-obj docutils literal notranslate"><span class="pre">shared_cat</span></code></a></p></td>
+<td><p>Alias for field number 9</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.NetworkStatsRecord.shared_res_cat" title="pypath.core.network.NetworkStatsRecord.shared_res_cat"><code class="xref py py-obj docutils literal notranslate"><span class="pre">shared_res_cat</span></code></a></p></td>
+<td><p>Alias for field number 6</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.NetworkStatsRecord.total" title="pypath.core.network.NetworkStatsRecord.total"><code class="xref py py-obj docutils literal notranslate"><span class="pre">total</span></code></a></p></td>
+<td><p>Alias for field number 0</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.NetworkStatsRecord.unique" title="pypath.core.network.NetworkStatsRecord.unique"><code class="xref py py-obj docutils literal notranslate"><span class="pre">unique</span></code></a></p></td>
+<td><p>Alias for field number 4</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.core.network.NetworkStatsRecord.unique_cat" title="pypath.core.network.NetworkStatsRecord.unique_cat"><code class="xref py py-obj docutils literal notranslate"><span class="pre">unique_cat</span></code></a></p></td>
+<td><p>Alias for field number 10</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.core.network.NetworkStatsRecord.unique_res_cat" title="pypath.core.network.NetworkStatsRecord.unique_res_cat"><code class="xref py py-obj docutils literal notranslate"><span class="pre">unique_res_cat</span></code></a></p></td>
+<td><p>Alias for field number 7</p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.NetworkStatsRecord.by_category">
+<span class="sig-name descname"><span class="pre">by_category</span></span><a class="headerlink" href="#pypath.core.network.NetworkStatsRecord.by_category" title="Link to this definition">§</a></dt>
+<dd><p>Alias for field number 2</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.NetworkStatsRecord.by_resource">
+<span class="sig-name descname"><span class="pre">by_resource</span></span><a class="headerlink" href="#pypath.core.network.NetworkStatsRecord.by_resource" title="Link to this definition">§</a></dt>
+<dd><p>Alias for field number 1</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.NetworkStatsRecord.cat_resource">
+<span class="sig-name descname"><span class="pre">cat_resource</span></span><a class="headerlink" href="#pypath.core.network.NetworkStatsRecord.cat_resource" title="Link to this definition">§</a></dt>
+<dd><p>Alias for field number 13</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.network.NetworkStatsRecord.count">
+<span class="sig-name descname"><span class="pre">count</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">value</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">/</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.network.NetworkStatsRecord.count" title="Link to this definition">§</a></dt>
+<dd><p>Return number of occurrences of value.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.core.network.NetworkStatsRecord.index">
+<span class="sig-name descname"><span class="pre">index</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">value</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">start</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">stop</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9223372036854775807</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">/</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.core.network.NetworkStatsRecord.index" title="Link to this definition">§</a></dt>
+<dd><p>Return first index of value.</p>
+<p>Raises ValueError if the value is not present.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.NetworkStatsRecord.label">
+<span class="sig-name descname"><span class="pre">label</span></span><a class="headerlink" href="#pypath.core.network.NetworkStatsRecord.label" title="Link to this definition">§</a></dt>
+<dd><p>Alias for field number 15</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.NetworkStatsRecord.method">
+<span class="sig-name descname"><span class="pre">method</span></span><a class="headerlink" href="#pypath.core.network.NetworkStatsRecord.method" title="Link to this definition">§</a></dt>
+<dd><p>Alias for field number 14</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.NetworkStatsRecord.percent">
+<span class="sig-name descname"><span class="pre">percent</span></span><a class="headerlink" href="#pypath.core.network.NetworkStatsRecord.percent" title="Link to this definition">§</a></dt>
+<dd><p>Alias for field number 5</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.NetworkStatsRecord.percent_cat">
+<span class="sig-name descname"><span class="pre">percent_cat</span></span><a class="headerlink" href="#pypath.core.network.NetworkStatsRecord.percent_cat" title="Link to this definition">§</a></dt>
+<dd><p>Alias for field number 11</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.NetworkStatsRecord.percent_res_cat">
+<span class="sig-name descname"><span class="pre">percent_res_cat</span></span><a class="headerlink" href="#pypath.core.network.NetworkStatsRecord.percent_res_cat" title="Link to this definition">§</a></dt>
+<dd><p>Alias for field number 8</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.NetworkStatsRecord.resource_cat">
+<span class="sig-name descname"><span class="pre">resource_cat</span></span><a class="headerlink" href="#pypath.core.network.NetworkStatsRecord.resource_cat" title="Link to this definition">§</a></dt>
+<dd><p>Alias for field number 12</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.NetworkStatsRecord.shared">
+<span class="sig-name descname"><span class="pre">shared</span></span><a class="headerlink" href="#pypath.core.network.NetworkStatsRecord.shared" title="Link to this definition">§</a></dt>
+<dd><p>Alias for field number 3</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.NetworkStatsRecord.shared_cat">
+<span class="sig-name descname"><span class="pre">shared_cat</span></span><a class="headerlink" href="#pypath.core.network.NetworkStatsRecord.shared_cat" title="Link to this definition">§</a></dt>
+<dd><p>Alias for field number 9</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.NetworkStatsRecord.shared_res_cat">
+<span class="sig-name descname"><span class="pre">shared_res_cat</span></span><a class="headerlink" href="#pypath.core.network.NetworkStatsRecord.shared_res_cat" title="Link to this definition">§</a></dt>
+<dd><p>Alias for field number 6</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.NetworkStatsRecord.total">
+<span class="sig-name descname"><span class="pre">total</span></span><a class="headerlink" href="#pypath.core.network.NetworkStatsRecord.total" title="Link to this definition">§</a></dt>
+<dd><p>Alias for field number 0</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.NetworkStatsRecord.unique">
+<span class="sig-name descname"><span class="pre">unique</span></span><a class="headerlink" href="#pypath.core.network.NetworkStatsRecord.unique" title="Link to this definition">§</a></dt>
+<dd><p>Alias for field number 4</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.NetworkStatsRecord.unique_cat">
+<span class="sig-name descname"><span class="pre">unique_cat</span></span><a class="headerlink" href="#pypath.core.network.NetworkStatsRecord.unique_cat" title="Link to this definition">§</a></dt>
+<dd><p>Alias for field number 10</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.core.network.NetworkStatsRecord.unique_res_cat">
+<span class="sig-name descname"><span class="pre">unique_res_cat</span></span><a class="headerlink" href="#pypath.core.network.NetworkStatsRecord.unique_res_cat" title="Link to this definition">§</a></dt>
+<dd><p>Alias for field number 7</p>
+</dd></dl>
+
+</dd></dl>
+
+</section>
+
+
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+<span id="pypath-core-network"></span><h1>pypath.core.network<a class="headerlink" href="#module-pypath.core.network" title="Link to this heading">§</a></h1>
+<dl class="field-list simple">
+<dt class="field-odd">members<span class="colon">:</span></dt>
+<dd class="field-odd"><p></p></dd>
+</dl>
+<p class="rubric">Functions</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.core.network.get_db.html#pypath.core.network.get_db" title="pypath.core.network.get_db"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_db</span></code></a>(**kwargs)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.core.network.init_db.html#pypath.core.network.init_db" title="pypath.core.network.init_db"><code class="xref py py-obj docutils literal notranslate"><span class="pre">init_db</span></code></a>([use_omnipath, method])</p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Classes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.core.network.Network.html#pypath.core.network.Network" title="pypath.core.network.Network"><code class="xref py py-obj docutils literal notranslate"><span class="pre">Network</span></code></a>([resources, make_df, df_by_source, ...])</p></td>
+<td><p>Represents a molecular interaction network.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.core.network.NetworkEntityCollection.html#pypath.core.network.NetworkEntityCollection" title="pypath.core.network.NetworkEntityCollection"><code class="xref py py-obj docutils literal notranslate"><span class="pre">NetworkEntityCollection</span></code></a>(collection[, label])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.core.network.NetworkStatsRecord.html#pypath.core.network.NetworkStatsRecord" title="pypath.core.network.NetworkStatsRecord"><code class="xref py py-obj docutils literal notranslate"><span class="pre">NetworkStatsRecord</span></code></a>(total, by_resource, ...)</p></td>
+<td><p></p></td>
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+  <section id="pypath-core-network-init-db">
+<h1>pypath.core.network.init_db<a class="headerlink" href="#pypath-core-network-init-db" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.core.network.init_db">
+<span class="sig-prename descclassname"><span class="pre">pypath.core.network.</span></span><span class="sig-name descname"><span class="pre">init_db</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">use_omnipath</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/core/network.html#init_db"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.core.network.init_db" title="Link to this definition">§</a></dt>
+<dd></dd></dl>
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+<li class="toctree-l1 toc-h1 nav-item toc-entry"><a class="reference internal nav-link" href="../notebooks/manual.html">The pypath book</a></li>
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diff --git a/api/pypath.data.html b/api/pypath.data.html
index 144ebffea..82ca2a729 100644
--- a/api/pypath.data.html
+++ b/api/pypath.data.html
@@ -48,7 +48,7 @@
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
     <link rel="next" title="pypath.inputs" href="pypath.inputs.html" />
-    <link rel="prev" title="pypath.core.common.filter_network_df" href="pypath.core.common.filter_network_df.html" />
+    <link rel="prev" title="pypath.core.network.NetworkStatsRecord" href="pypath.core.network.NetworkStatsRecord.html" />
   <meta name="viewport" content="width=device-width, initial-scale=1"/>
   <meta name="docsearch:language" content="en"/>
   </head>
@@ -536,12 +536,12 @@
                   
 <div class="prev-next-area">
     <a class="left-prev"
-       href="pypath.core.common.filter_network_df.html"
+       href="pypath.core.network.NetworkStatsRecord.html"
        title="previous page">
       <i class="fa-solid fa-angle-left"></i>
       <div class="prev-next-info">
         <p class="prev-next-subtitle">previous</p>
-        <p class="prev-next-title">pypath.core.common.filter_network_df</p>
+        <p class="prev-next-title">pypath.core.network.NetworkStatsRecord</p>
       </div>
     </a>
     <a class="right-next"
diff --git a/api/pypath.html b/api/pypath.html
index 0e512a344..3ce192ddf 100644
--- a/api/pypath.html
+++ b/api/pypath.html
@@ -552,16 +552,19 @@
 <tr class="row-odd"><td><p><a class="reference internal" href="pypath.legacy.html#module-pypath.legacy" title="pypath.legacy"><code class="xref py py-obj docutils literal notranslate"><span class="pre">pypath.legacy</span></code></a></p></td>
 <td><p></p></td>
 </tr>
-<tr class="row-even"><td><p><a class="reference internal" href="pypath.resources.html#module-pypath.resources" title="pypath.resources"><code class="xref py py-obj docutils literal notranslate"><span class="pre">pypath.resources</span></code></a></p></td>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.omnipath.html#module-pypath.omnipath" title="pypath.omnipath"><code class="xref py py-obj docutils literal notranslate"><span class="pre">pypath.omnipath</span></code></a></p></td>
 <td><p></p></td>
 </tr>
-<tr class="row-odd"><td><p><a class="reference internal" href="pypath.share.html#module-pypath.share" title="pypath.share"><code class="xref py py-obj docutils literal notranslate"><span class="pre">pypath.share</span></code></a></p></td>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.resources.html#module-pypath.resources" title="pypath.resources"><code class="xref py py-obj docutils literal notranslate"><span class="pre">pypath.resources</span></code></a></p></td>
 <td><p></p></td>
 </tr>
-<tr class="row-even"><td><p><a class="reference internal" href="pypath.utils.html#module-pypath.utils" title="pypath.utils"><code class="xref py py-obj docutils literal notranslate"><span class="pre">pypath.utils</span></code></a></p></td>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.share.html#module-pypath.share" title="pypath.share"><code class="xref py py-obj docutils literal notranslate"><span class="pre">pypath.share</span></code></a></p></td>
 <td><p></p></td>
 </tr>
-<tr class="row-odd"><td><p><a class="reference internal" href="pypath.visual.html#module-pypath.visual" title="pypath.visual"><code class="xref py py-obj docutils literal notranslate"><span class="pre">pypath.visual</span></code></a></p></td>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.utils.html#module-pypath.utils" title="pypath.utils"><code class="xref py py-obj docutils literal notranslate"><span class="pre">pypath.utils</span></code></a></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.visual.html#module-pypath.visual" title="pypath.visual"><code class="xref py py-obj docutils literal notranslate"><span class="pre">pypath.visual</span></code></a></p></td>
 <td><p></p></td>
 </tr>
 </tbody>
diff --git a/api/pypath.inputs.acsn.acsn_interactions_sif.html b/api/pypath.inputs.acsn.acsn_interactions_sif.html
index 516d5e6d2..fb62b2110 100644
--- a/api/pypath.inputs.acsn.acsn_interactions_sif.html
+++ b/api/pypath.inputs.acsn.acsn_interactions_sif.html
@@ -47,7 +47,7 @@
     <link rel="icon" href="../_static/omnipath-logo.svg"/>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
-    <link rel="next" title="pypath.inputs.adrecs" href="pypath.inputs.adrecs.html" />
+    <link rel="next" title="pypath.inputs.adhesome" href="pypath.inputs.adhesome.html" />
     <link rel="prev" title="pypath.inputs.acsn.acsn_interactions" href="pypath.inputs.acsn.acsn_interactions.html" />
   <meta name="viewport" content="width=device-width, initial-scale=1"/>
   <meta name="docsearch:language" content="en"/>
@@ -546,11 +546,11 @@ <h1>pypath.inputs.acsn.acsn_interactions_sif<a class="headerlink" href="#pypath-
       </div>
     </a>
     <a class="right-next"
-       href="pypath.inputs.adrecs.html"
+       href="pypath.inputs.adhesome.html"
        title="next page">
       <div class="prev-next-info">
         <p class="prev-next-subtitle">next</p>
-        <p class="prev-next-title">pypath.inputs.adrecs</p>
+        <p class="prev-next-title">pypath.inputs.adhesome</p>
       </div>
       <i class="fa-solid fa-angle-right"></i>
     </a>
diff --git a/api/pypath.inputs.adhesome.adhesome_annotations.html b/api/pypath.inputs.adhesome.adhesome_annotations.html
new file mode 100644
index 000000000..bc12e882a
--- /dev/null
+++ b/api/pypath.inputs.adhesome.adhesome_annotations.html
@@ -0,0 +1,638 @@
+
+<!DOCTYPE html>
+
+
+<html lang="en" data-content_root="../" >
+
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+    <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="viewport" content="width=device-width, initial-scale=1" />
+
+    <title>pypath.inputs.adhesome.adhesome_annotations &#8212; pypath 0.16.9 documentation</title>
+  
+  
+  
+  <script data-cfasync="false">
+    document.documentElement.dataset.mode = localStorage.getItem("mode") || "";
+    document.documentElement.dataset.theme = localStorage.getItem("theme") || "light";
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+  <link href="../_static/vendor/fontawesome/6.5.1/css/all.min.css?digest=8d27b9dea8ad943066ae" rel="stylesheet" />
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+<link rel="preload" as="font" type="font/woff2" crossorigin href="../_static/vendor/fontawesome/6.5.1/webfonts/fa-regular-400.woff2" />
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+    <script>DOCUMENTATION_OPTIONS.pagename = 'api/pypath.inputs.adhesome.adhesome_annotations';</script>
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+  <meta name="viewport" content="width=device-width, initial-scale=1"/>
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+  
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+  <input type="search"
+         class="form-control"
+         name="q"
+         id="search-input"
+         placeholder="Search the docs ..."
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+  <span class="search-button__kbd-shortcut"><kbd class="kbd-shortcut__modifier">Ctrl</kbd>+<kbd>K</kbd></span>
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+                    <li class="nav-item">
+                      <a class="nav-link nav-internal" href="../index.html">
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+                
+
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+                      <a class="nav-link nav-internal" href="../webservice.html">
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+                      <a class="nav-link nav-internal" href="../releasehistory.html">
+                        Release history
+                      </a>
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+                
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+                    <li class="nav-item current active">
+                      <a class="nav-link nav-internal" href="../reference.html">
+                        Reference
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+                
+
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+                      <a class="nav-link nav-internal" href="../notebooks/manual.html">
+                        The pypath book
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+                      <a class="nav-link nav-internal" href="../notebooks/manual.html">
+                        The pypath book
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+document.write(`
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diff --git a/api/pypath.inputs.adhesome.adhesome_interactions.html b/api/pypath.inputs.adhesome.adhesome_interactions.html
new file mode 100644
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+<dl class="field-list simple">
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diff --git a/api/pypath.inputs.adrecs.AdrecsTerm.html b/api/pypath.inputs.adrecs.AdrecsTerm.html
index 6d1a0cc86..5c18aa7f4 100644
--- a/api/pypath.inputs.adrecs.AdrecsTerm.html
+++ b/api/pypath.inputs.adrecs.AdrecsTerm.html
@@ -47,7 +47,7 @@
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     <link rel="prev" title="pypath.inputs.adrecs.AdrecsDrugAdr" href="pypath.inputs.adrecs.AdrecsDrugAdr.html" />
   <meta name="viewport" content="width=device-width, initial-scale=1"/>
   <meta name="docsearch:language" content="en"/>
@@ -627,11 +627,11 @@ <h1>pypath.inputs.adrecs.AdrecsTerm<a class="headerlink" href="#pypath-inputs-ad
       </div>
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diff --git a/api/pypath.inputs.adrecs.html b/api/pypath.inputs.adrecs.html
index 5d80fa482..2ef4952f8 100644
--- a/api/pypath.inputs.adrecs.html
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-    <link rel="prev" title="pypath.inputs.acsn.acsn_interactions_sif" href="pypath.inputs.acsn.acsn_interactions_sif.html" />
+    <link rel="prev" title="pypath.inputs.adhesome.adhesome_interactions" href="pypath.inputs.adhesome.adhesome_interactions.html" />
   <meta name="viewport" content="width=device-width, initial-scale=1"/>
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@@ -571,12 +571,12 @@
                   
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+       href="pypath.inputs.adhesome.adhesome_interactions.html"
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         <p class="prev-next-subtitle">previous</p>
-        <p class="prev-next-title">pypath.inputs.acsn.acsn_interactions_sif</p>
+        <p class="prev-next-title">pypath.inputs.adhesome.adhesome_interactions</p>
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diff --git a/api/pypath.inputs.almen2009.almen2009_annotations.html b/api/pypath.inputs.almen2009.almen2009_annotations.html
new file mode 100644
index 000000000..1407751ad
--- /dev/null
+++ b/api/pypath.inputs.almen2009.almen2009_annotations.html
@@ -0,0 +1,638 @@
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diff --git a/api/pypath.inputs.almen2009.html b/api/pypath.inputs.almen2009.html
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diff --git a/api/pypath.inputs.baccin2019.baccin2019_annotations.html b/api/pypath.inputs.baccin2019.baccin2019_annotations.html
new file mode 100644
index 000000000..38c250045
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+<dl class="py function">
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diff --git a/api/pypath.inputs.baccin2019.html b/api/pypath.inputs.baccin2019.html
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diff --git a/api/pypath.inputs.biogps.BiogpsDataset.html b/api/pypath.inputs.biogps.BiogpsDataset.html
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+  <section id="pypath-inputs-biogps-biogpsdataset">
+<h1>pypath.inputs.biogps.BiogpsDataset<a class="headerlink" href="#pypath-inputs-biogps-biogpsdataset" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.inputs.biogps.BiogpsDataset">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.inputs.biogps.</span></span><span class="sig-name descname"><span class="pre">BiogpsDataset</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">organism</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">label</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">url</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.inputs.biogps.BiogpsDataset" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">tuple</span></code></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.inputs.biogps.BiogpsDataset.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.inputs.biogps.BiogpsDataset.__init__" title="Link to this definition">§</a></dt>
+<dd></dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.inputs.biogps.BiogpsDataset.__init__" title="pypath.inputs.biogps.BiogpsDataset.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.inputs.biogps.BiogpsDataset.count" title="pypath.inputs.biogps.BiogpsDataset.count"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count</span></code></a>(value, /)</p></td>
+<td><p>Return number of occurrences of value.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.inputs.biogps.BiogpsDataset.index" title="pypath.inputs.biogps.BiogpsDataset.index"><code class="xref py py-obj docutils literal notranslate"><span class="pre">index</span></code></a>(value[, start, stop])</p></td>
+<td><p>Return first index of value.</p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Attributes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.inputs.biogps.BiogpsDataset.label" title="pypath.inputs.biogps.BiogpsDataset.label"><code class="xref py py-obj docutils literal notranslate"><span class="pre">label</span></code></a></p></td>
+<td><p>Alias for field number 1</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.inputs.biogps.BiogpsDataset.organism" title="pypath.inputs.biogps.BiogpsDataset.organism"><code class="xref py py-obj docutils literal notranslate"><span class="pre">organism</span></code></a></p></td>
+<td><p>Alias for field number 0</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.inputs.biogps.BiogpsDataset.url" title="pypath.inputs.biogps.BiogpsDataset.url"><code class="xref py py-obj docutils literal notranslate"><span class="pre">url</span></code></a></p></td>
+<td><p>Alias for field number 2</p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.inputs.biogps.BiogpsDataset.count">
+<span class="sig-name descname"><span class="pre">count</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">value</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">/</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.inputs.biogps.BiogpsDataset.count" title="Link to this definition">§</a></dt>
+<dd><p>Return number of occurrences of value.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.inputs.biogps.BiogpsDataset.index">
+<span class="sig-name descname"><span class="pre">index</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">value</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">start</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">stop</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9223372036854775807</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">/</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.inputs.biogps.BiogpsDataset.index" title="Link to this definition">§</a></dt>
+<dd><p>Return first index of value.</p>
+<p>Raises ValueError if the value is not present.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.inputs.biogps.BiogpsDataset.label">
+<span class="sig-name descname"><span class="pre">label</span></span><a class="headerlink" href="#pypath.inputs.biogps.BiogpsDataset.label" title="Link to this definition">§</a></dt>
+<dd><p>Alias for field number 1</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.inputs.biogps.BiogpsDataset.organism">
+<span class="sig-name descname"><span class="pre">organism</span></span><a class="headerlink" href="#pypath.inputs.biogps.BiogpsDataset.organism" title="Link to this definition">§</a></dt>
+<dd><p>Alias for field number 0</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.inputs.biogps.BiogpsDataset.url">
+<span class="sig-name descname"><span class="pre">url</span></span><a class="headerlink" href="#pypath.inputs.biogps.BiogpsDataset.url" title="Link to this definition">§</a></dt>
+<dd><p>Alias for field number 2</p>
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+<h1>pypath.inputs.biogps.biogps_annotations<a class="headerlink" href="#pypath-inputs-biogps-biogps-annotations" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.inputs.biogps.biogps_annotations">
+<span class="sig-prename descclassname"><span class="pre">pypath.inputs.biogps.</span></span><span class="sig-name descname"><span class="pre">biogps_annotations</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">organism</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">exclude</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">only</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/inputs/biogps.html#biogps_annotations"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.biogps.biogps_annotations" title="Link to this definition">§</a></dt>
+<dd><p>Expression data from BioGPS compiled in the annotation format commonly
+used in this module.</p>
+<dl>
+<dt>Args</dt><dd><dl class="simple">
+<dt>organism (int,str): Name or ID of the organism. This function</dt><dd><p>is able to process data for one organism at once.</p>
+</dd>
+<dt>exclude (str,set): One or more datasets to exclude. Should be</dt><dd><p>dataset labels as shown by <cite>biogps_datasets</cite>.</p>
+</dd>
+</dl>
+<p>only (str,set): Restrict the download only to these datasets.</p>
+</dd>
+<dt>Returns</dt><dd><dl class="simple">
+<dt>(dict): Dict of annotations, keys are UniProt IDs, values are</dt><dd><p>sets of named tuples of annotations.</p>
+</dd>
+</dl>
+</dd>
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+
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+<h1>pypath.inputs.biogps.biogps_datasets<a class="headerlink" href="#pypath-inputs-biogps-biogps-datasets" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.inputs.biogps.biogps_datasets">
+<span class="sig-prename descclassname"><span class="pre">pypath.inputs.biogps.</span></span><span class="sig-name descname"><span class="pre">biogps_datasets</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/inputs/biogps.html#biogps_datasets"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.biogps.biogps_datasets" title="Link to this definition">§</a></dt>
+<dd><p>List the expression profile datasets available from BioGPS.</p>
+<dl class="simple">
+<dt>Returns</dt><dd><p>(list): Named tuples with the label, organism and URL of the datasets.</p>
+</dd>
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+  <section id="pypath-inputs-biogps-biogps-download">
+<h1>pypath.inputs.biogps.biogps_download<a class="headerlink" href="#pypath-inputs-biogps-biogps-download" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.inputs.biogps.biogps_download">
+<span class="sig-prename descclassname"><span class="pre">pypath.inputs.biogps.</span></span><span class="sig-name descname"><span class="pre">biogps_download</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">dataset</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/inputs/biogps.html#biogps_download"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.biogps.biogps_download" title="Link to this definition">§</a></dt>
+<dd><p>Retrieve one BioGPS expression profile dataset.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>dataset (str,BiogpsDataset): Either the label of a dataset or a</dt><dd><p><cite>BiogpsDataset</cite> object. For a list of available datasets, see
+<cite>biogps_datasets</cite>.</p>
+</dd>
+</dl>
+</dd>
+<dt>Returns</dt><dd><dl class="simple">
+<dt>(pandas.DataFrame): A data frame of expression values, columns are</dt><dd><p>tissues, cell types or cell lines, rows are microarray probes
+representing transcripts.</p>
+</dd>
+</dl>
+</dd>
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+<h1>pypath.inputs.biogps.biogps_download_all<a class="headerlink" href="#pypath-inputs-biogps-biogps-download-all" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.inputs.biogps.biogps_download_all">
+<span class="sig-prename descclassname"><span class="pre">pypath.inputs.biogps.</span></span><span class="sig-name descname"><span class="pre">biogps_download_all</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">organism</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">exclude</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">only</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/inputs/biogps.html#biogps_download_all"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.biogps.biogps_download_all" title="Link to this definition">§</a></dt>
+<dd><p>Downloads all expression data from BioGPS.</p>
+<dl>
+<dt>Args</dt><dd><dl class="simple">
+<dt>organism (str,int): Restrict the download to this organism. Human,</dt><dd><p>mouse and rat datasets are available.</p>
+</dd>
+<dt>exclude (str,set): One or more datasets to exclude. Should be</dt><dd><p>dataset labels as shown by <cite>biogps_datasets</cite>.</p>
+</dd>
+</dl>
+<p>only (str,set): Restrict the download only to these datasets.</p>
+</dd>
+<dt>Returns</dt><dd><dl class="simple">
+<dt>(dict): Dict of pandas data frames, keys are dataset labels, values</dt><dd><p>are data frames of expression values, columns are tissues, cell
+types or cell lines, rows are microarray probes representing
+transcripts.</p>
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+  <section id="module-pypath.inputs.biogps">
+<span id="pypath-inputs-biogps"></span><h1>pypath.inputs.biogps<a class="headerlink" href="#module-pypath.inputs.biogps" title="Link to this heading">§</a></h1>
+<dl class="field-list simple">
+<dt class="field-odd">members<span class="colon">:</span></dt>
+<dd class="field-odd"><p></p></dd>
+</dl>
+<p class="rubric">Functions</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.inputs.biogps.biogps_annotations.html#pypath.inputs.biogps.biogps_annotations" title="pypath.inputs.biogps.biogps_annotations"><code class="xref py py-obj docutils literal notranslate"><span class="pre">biogps_annotations</span></code></a>([organism, exclude, only])</p></td>
+<td><p>Expression data from BioGPS compiled in the annotation format commonly used in this module.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.inputs.biogps.biogps_datasets.html#pypath.inputs.biogps.biogps_datasets" title="pypath.inputs.biogps.biogps_datasets"><code class="xref py py-obj docutils literal notranslate"><span class="pre">biogps_datasets</span></code></a>()</p></td>
+<td><p>List the expression profile datasets available from BioGPS.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.inputs.biogps.biogps_download.html#pypath.inputs.biogps.biogps_download" title="pypath.inputs.biogps.biogps_download"><code class="xref py py-obj docutils literal notranslate"><span class="pre">biogps_download</span></code></a>(dataset)</p></td>
+<td><p>Retrieve one BioGPS expression profile dataset.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.inputs.biogps.biogps_download_all.html#pypath.inputs.biogps.biogps_download_all" title="pypath.inputs.biogps.biogps_download_all"><code class="xref py py-obj docutils literal notranslate"><span class="pre">biogps_download_all</span></code></a>([organism, exclude, only])</p></td>
+<td><p>Downloads all expression data from BioGPS.</p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Classes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.inputs.biogps.BiogpsDataset.html#pypath.inputs.biogps.BiogpsDataset" title="pypath.inputs.biogps.BiogpsDataset"><code class="xref py py-obj docutils literal notranslate"><span class="pre">BiogpsDataset</span></code></a>(organism, label, url)</p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+</section>
+
+
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diff --git a/api/pypath.inputs.biogrid.html b/api/pypath.inputs.biogrid.html
index 45ede9aa3..b68fae04a 100644
--- a/api/pypath.inputs.biogrid.html
+++ b/api/pypath.inputs.biogrid.html
@@ -48,7 +48,7 @@
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-    <link rel="prev" title="pypath.inputs.adrecs.AdrecsTerm" href="pypath.inputs.adrecs.AdrecsTerm.html" />
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   <meta name="viewport" content="width=device-width, initial-scale=1"/>
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@@ -545,12 +545,12 @@
                   
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+       href="pypath.inputs.biogps.BiogpsDataset.html"
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       <div class="prev-next-info">
         <p class="prev-next-subtitle">previous</p>
-        <p class="prev-next-title">pypath.inputs.adrecs.AdrecsTerm</p>
+        <p class="prev-next-title">pypath.inputs.biogps.BiogpsDataset</p>
       </div>
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diff --git a/api/pypath.inputs.cancercellmap.ccmap_interactions.html b/api/pypath.inputs.cancercellmap.ccmap_interactions.html
index 93be1a37b..24ae19cce 100644
--- a/api/pypath.inputs.cancercellmap.ccmap_interactions.html
+++ b/api/pypath.inputs.cancercellmap.ccmap_interactions.html
@@ -47,7 +47,7 @@
     <link rel="icon" href="../_static/omnipath-logo.svg"/>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
-    <link rel="next" title="pypath.inputs.cell" href="pypath.inputs.cell.html" />
+    <link rel="next" title="pypath.inputs.cancerdrugsdb" href="pypath.inputs.cancerdrugsdb.html" />
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   <meta name="viewport" content="width=device-width, initial-scale=1"/>
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@@ -550,11 +550,11 @@ <h1>pypath.inputs.cancercellmap.ccmap_interactions<a class="headerlink" href="#p
       </div>
     </a>
     <a class="right-next"
-       href="pypath.inputs.cell.html"
+       href="pypath.inputs.cancerdrugsdb.html"
        title="next page">
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         <p class="prev-next-subtitle">next</p>
-        <p class="prev-next-title">pypath.inputs.cell</p>
+        <p class="prev-next-title">pypath.inputs.cancerdrugsdb</p>
       </div>
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diff --git a/api/pypath.inputs.cancerdrugsdb.cancerdrugsdb_annotations.html b/api/pypath.inputs.cancerdrugsdb.cancerdrugsdb_annotations.html
new file mode 100644
index 000000000..59ade24d1
--- /dev/null
+++ b/api/pypath.inputs.cancerdrugsdb.cancerdrugsdb_annotations.html
@@ -0,0 +1,645 @@
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+    <script>DOCUMENTATION_OPTIONS.pagename = 'api/pypath.inputs.cancerdrugsdb.cancerdrugsdb_annotations';</script>
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+<h1>pypath.inputs.cancerdrugsdb.cancerdrugsdb_annotations<a class="headerlink" href="#pypath-inputs-cancerdrugsdb-cancerdrugsdb-annotations" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.inputs.cancerdrugsdb.cancerdrugsdb_annotations">
+<span class="sig-prename descclassname"><span class="pre">pypath.inputs.cancerdrugsdb.</span></span><span class="sig-name descname"><span class="pre">cancerdrugsdb_annotations</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/inputs/cancerdrugsdb.html#cancerdrugsdb_annotations"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.cancerdrugsdb.cancerdrugsdb_annotations" title="Link to this definition">§</a></dt>
+<dd><p>Returns drug annotations from CancerDrugs_DB.</p>
+<dl class="simple">
+<dt>Args</dt><dd><p>None.</p>
+</dd>
+<dt>Returns</dt><dd><p>(dict): Keys are PubChem IDs, values are sets of annotations.</p>
+</dd>
+</dl>
+</dd></dl>
+
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diff --git a/api/pypath.inputs.cancerdrugsdb.cancerdrugsdb_download.html b/api/pypath.inputs.cancerdrugsdb.cancerdrugsdb_download.html
new file mode 100644
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+  <section id="pypath-inputs-cancerdrugsdb-cancerdrugsdb-download">
+<h1>pypath.inputs.cancerdrugsdb.cancerdrugsdb_download<a class="headerlink" href="#pypath-inputs-cancerdrugsdb-cancerdrugsdb-download" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.inputs.cancerdrugsdb.cancerdrugsdb_download">
+<span class="sig-prename descclassname"><span class="pre">pypath.inputs.cancerdrugsdb.</span></span><span class="sig-name descname"><span class="pre">cancerdrugsdb_download</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/inputs/cancerdrugsdb.html#cancerdrugsdb_download"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.cancerdrugsdb.cancerdrugsdb_download" title="Link to this definition">§</a></dt>
+<dd><p>Downloads a curated set of interactions of cancer drugs licensed
+in most parts of the world with gene targets (where available).
+From <a class="reference external" href="https://www.anticancerfund.org/en/cancerdrugs-db">https://www.anticancerfund.org/en/cancerdrugs-db</a>.
+This function downloads a single dataset.</p>
+<dl class="simple">
+<dt>Args</dt><dd><p>None.</p>
+</dd>
+<dt>Returns</dt><dd><p>A list of dicts, each is a record as it provided by the database.</p>
+</dd>
+</dl>
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+
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+  <section id="pypath-inputs-cancerdrugsdb-cancerdrugsdb-interactions">
+<h1>pypath.inputs.cancerdrugsdb.cancerdrugsdb_interactions<a class="headerlink" href="#pypath-inputs-cancerdrugsdb-cancerdrugsdb-interactions" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.inputs.cancerdrugsdb.cancerdrugsdb_interactions">
+<span class="sig-prename descclassname"><span class="pre">pypath.inputs.cancerdrugsdb.</span></span><span class="sig-name descname"><span class="pre">cancerdrugsdb_interactions</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/inputs/cancerdrugsdb.html#cancerdrugsdb_interactions"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.cancerdrugsdb.cancerdrugsdb_interactions" title="Link to this definition">§</a></dt>
+<dd><p>Returns drug-gene interactions from Cancer Drugs Database
+(<a class="reference external" href="https://www.anticancerfund.org/en/cancerdrugs-db">https://www.anticancerfund.org/en/cancerdrugs-db</a>).</p>
+<dl class="simple">
+<dt>Args</dt><dd><p>None.</p>
+</dd>
+<dt>Returns</dt><dd><p>List of named tuples, each describing a drug-gene interaction.
+Identifiers of type PubChem and UniProt.</p>
+</dd>
+</dl>
+</dd></dl>
+
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diff --git a/api/pypath.inputs.cancerdrugsdb.html b/api/pypath.inputs.cancerdrugsdb.html
new file mode 100644
index 000000000..ecdb31e8c
--- /dev/null
+++ b/api/pypath.inputs.cancerdrugsdb.html
@@ -0,0 +1,652 @@
+
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+  <section id="module-pypath.inputs.cancerdrugsdb">
+<span id="pypath-inputs-cancerdrugsdb"></span><h1>pypath.inputs.cancerdrugsdb<a class="headerlink" href="#module-pypath.inputs.cancerdrugsdb" title="Link to this heading">§</a></h1>
+<p>Web scraper for the CancerDrugs_DB database.</p>
+<dl class="field-list simple">
+<dt class="field-odd">members<span class="colon">:</span></dt>
+<dd class="field-odd"><p></p></dd>
+</dl>
+<p class="rubric">Functions</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.inputs.cancerdrugsdb.cancerdrugsdb_annotations.html#pypath.inputs.cancerdrugsdb.cancerdrugsdb_annotations" title="pypath.inputs.cancerdrugsdb.cancerdrugsdb_annotations"><code class="xref py py-obj docutils literal notranslate"><span class="pre">cancerdrugsdb_annotations</span></code></a>()</p></td>
+<td><p>Returns drug annotations from CancerDrugs_DB.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.inputs.cancerdrugsdb.cancerdrugsdb_download.html#pypath.inputs.cancerdrugsdb.cancerdrugsdb_download" title="pypath.inputs.cancerdrugsdb.cancerdrugsdb_download"><code class="xref py py-obj docutils literal notranslate"><span class="pre">cancerdrugsdb_download</span></code></a>()</p></td>
+<td><p>Downloads a curated set of interactions of cancer drugs licensed in most parts of the world with gene targets (where available).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.inputs.cancerdrugsdb.cancerdrugsdb_interactions.html#pypath.inputs.cancerdrugsdb.cancerdrugsdb_interactions" title="pypath.inputs.cancerdrugsdb.cancerdrugsdb_interactions"><code class="xref py py-obj docutils literal notranslate"><span class="pre">cancerdrugsdb_interactions</span></code></a>()</p></td>
+<td><p>Returns drug-gene interactions from Cancer Drugs Database (<a class="reference external" href="https://www.anticancerfund.org/en/cancerdrugs-db">https://www.anticancerfund.org/en/cancerdrugs-db</a>).</p></td>
+</tr>
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+  <section id="pypath-inputs-cancersea-cancersea-annotations">
+<h1>pypath.inputs.cancersea.cancersea_annotations<a class="headerlink" href="#pypath-inputs-cancersea-cancersea-annotations" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.inputs.cancersea.cancersea_annotations">
+<span class="sig-prename descclassname"><span class="pre">pypath.inputs.cancersea.</span></span><span class="sig-name descname"><span class="pre">cancersea_annotations</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/inputs/cancersea.html#cancersea_annotations"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.cancersea.cancersea_annotations" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves genes annotated with cancer funcitonal states from the
+CancerSEA database.</p>
+</dd></dl>
+
+</section>
+
+
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+  <section id="module-pypath.inputs.cancersea">
+<span id="pypath-inputs-cancersea"></span><h1>pypath.inputs.cancersea<a class="headerlink" href="#module-pypath.inputs.cancersea" title="Link to this heading">§</a></h1>
+<dl class="field-list simple">
+<dt class="field-odd">members<span class="colon">:</span></dt>
+<dd class="field-odd"><p></p></dd>
+</dl>
+<p class="rubric">Functions</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.inputs.cancersea.cancersea_annotations.html#pypath.inputs.cancersea.cancersea_annotations" title="pypath.inputs.cancersea.cancersea_annotations"><code class="xref py py-obj docutils literal notranslate"><span class="pre">cancersea_annotations</span></code></a>()</p></td>
+<td><p>Retrieves genes annotated with cancer funcitonal states from the CancerSEA database.</p></td>
+</tr>
+</tbody>
+</table>
+</section>
+
+
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diff --git a/api/pypath.inputs.cell.cell_supplementary.html b/api/pypath.inputs.cell.cell_supplementary.html
index f93e883cc..c84591954 100644
--- a/api/pypath.inputs.cell.cell_supplementary.html
+++ b/api/pypath.inputs.cell.cell_supplementary.html
@@ -47,7 +47,7 @@
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   <meta name="viewport" content="width=device-width, initial-scale=1"/>
   <meta name="docsearch:language" content="en"/>
@@ -556,11 +556,11 @@ <h1>pypath.inputs.cell.cell_supplementary<a class="headerlink" href="#pypath-inp
       </div>
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-       href="pypath.inputs.chembl.html"
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+        <p class="prev-next-title">pypath.inputs.cellcall</p>
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diff --git a/api/pypath.inputs.cell.html b/api/pypath.inputs.cell.html
index 94db44385..ec4289abe 100644
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   <meta name="viewport" content="width=device-width, initial-scale=1"/>
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@@ -542,12 +542,12 @@
                   
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-       href="pypath.inputs.cancercellmap.ccmap_interactions.html"
+       href="pypath.inputs.cancersea.cancersea_annotations.html"
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         <p class="prev-next-subtitle">previous</p>
-        <p class="prev-next-title">pypath.inputs.cancercellmap.ccmap_interactions</p>
+        <p class="prev-next-title">pypath.inputs.cancersea.cancersea_annotations</p>
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diff --git a/api/pypath.inputs.cellcall.cellcall_annotations.html b/api/pypath.inputs.cellcall.cellcall_annotations.html
new file mode 100644
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--- /dev/null
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+  <section id="pypath-inputs-cellcall-cellcall-annotations">
+<h1>pypath.inputs.cellcall.cellcall_annotations<a class="headerlink" href="#pypath-inputs-cellcall-cellcall-annotations" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.inputs.cellcall.cellcall_annotations">
+<span class="sig-prename descclassname"><span class="pre">pypath.inputs.cellcall.</span></span><span class="sig-name descname"><span class="pre">cellcall_annotations</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">extended</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">organism</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/inputs/cellcall.html#cellcall_annotations"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.cellcall.cellcall_annotations" title="Link to this definition">§</a></dt>
+<dd><p>Ligand and receptor annotations from the CellCall database
+(<a class="github reference external" href="https://github.com/ShellyCoder/cellcall">ShellyCoder/cellcall</a>).</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>extended (bool): Include not only the core but also the extended</dt><dd><p>set of interactions.</p>
+</dd>
+<dt>organism (int,str): The organism to use, human (9606) and mouse</dt><dd><ol class="arabic simple" start="10090">
+<li><p>are supported.</p></li>
+</ol>
+</dd>
+</dl>
+</dd>
+<dt>Returns</dt><dd><p>Dict of annotations, keys are UniProt IDs, values are sets of
+annotations.</p>
+</dd>
+</dl>
+</dd></dl>
+
+</section>
+
+
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+  <section id="pypath-inputs-cellcall-cellcall-download">
+<h1>pypath.inputs.cellcall.cellcall_download<a class="headerlink" href="#pypath-inputs-cellcall-cellcall-download" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.inputs.cellcall.cellcall_download">
+<span class="sig-prename descclassname"><span class="pre">pypath.inputs.cellcall.</span></span><span class="sig-name descname"><span class="pre">cellcall_download</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">extended</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">mouse</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/inputs/cellcall.html#cellcall_download"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.cellcall.cellcall_download" title="Link to this definition">§</a></dt>
+<dd><p>Downloads a ligand-receptor-TF pathway dataset from CellCall
+(<a class="github reference external" href="https://github.com/ShellyCoder/cellcall">ShellyCoder/cellcall</a>). This function downloads a
+single dataset, to download multiple datasets, see
+<code class="docutils literal notranslate"><span class="pre">cellcall_download_all</span></code>. The pathway identifiers refer to KEGG
+pathways.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>extended (bool): CellCall has core and extended datasets, if this</dt><dd><p>argument is True, the extended dataset will be retrieved.</p>
+</dd>
+<dt>mouse (bool): CellCall has human and homology inferred mouse</dt><dd><p>datasets. If this argument is True, the homology inferred
+dataset will be retrieved with mouse identifiers.</p>
+</dd>
+</dl>
+</dd>
+<dt>Returns</dt><dd><p>A list of dicts, each is a record as it provided by the CellCall
+database.</p>
+</dd>
+</dl>
+</dd></dl>
+
+</section>
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diff --git a/api/pypath.inputs.cellcall.cellcall_download_all.html b/api/pypath.inputs.cellcall.cellcall_download_all.html
new file mode 100644
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+  <section id="pypath-inputs-cellcall-cellcall-download-all">
+<h1>pypath.inputs.cellcall.cellcall_download_all<a class="headerlink" href="#pypath-inputs-cellcall-cellcall-download-all" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.inputs.cellcall.cellcall_download_all">
+<span class="sig-prename descclassname"><span class="pre">pypath.inputs.cellcall.</span></span><span class="sig-name descname"><span class="pre">cellcall_download_all</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">extended</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">human</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">mouse</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/inputs/cellcall.html#cellcall_download_all"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.cellcall.cellcall_download_all" title="Link to this definition">§</a></dt>
+<dd><p>Downloads ligand-receptor-TF pathway data from CellCall
+(<a class="github reference external" href="https://github.com/ShellyCoder/cellcall">ShellyCoder/cellcall</a>). CellCall has core (high
+confidence) and extended datasets, human and homology inferred mouse
+datasets, 4 datasets in total. By default all these are downloaded
+here, with the parameters you can exclude the extended part and select
+the organism. The pathway identifiers refer to KEGG pathways.</p>
+<dl class="simple">
+<dt>Args</dt><dd><p>extended (bool): Use also the extended datasets.
+human (bool): Include human interactions.
+mouse (bool): Include mouse interactions.</p>
+</dd>
+<dt>Returns</dt><dd><p>A list of dicts, each is a record as it provided by the CellCall
+database.</p>
+</dd>
+</dl>
+</dd></dl>
+
+</section>
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diff --git a/api/pypath.inputs.cellcall.cellcall_interactions.html b/api/pypath.inputs.cellcall.cellcall_interactions.html
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+  <section id="pypath-inputs-cellcall-cellcall-interactions">
+<h1>pypath.inputs.cellcall.cellcall_interactions<a class="headerlink" href="#pypath-inputs-cellcall-cellcall-interactions" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.inputs.cellcall.cellcall_interactions">
+<span class="sig-prename descclassname"><span class="pre">pypath.inputs.cellcall.</span></span><span class="sig-name descname"><span class="pre">cellcall_interactions</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">extended</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">organism</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/inputs/cellcall.html#cellcall_interactions"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.cellcall.cellcall_interactions" title="Link to this definition">§</a></dt>
+<dd><p>Ligand-receptor interactions from the CellCall database
+(<a class="github reference external" href="https://github.com/ShellyCoder/cellcall">ShellyCoder/cellcall</a>).</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>extended (bool): Include not only the core but also the extended</dt><dd><p>set of interactions.</p>
+</dd>
+<dt>organism (int,str): The organism to use, human (9606) and mouse</dt><dd><ol class="arabic simple" start="10090">
+<li><p>are supported.</p></li>
+</ol>
+</dd>
+</dl>
+</dd>
+<dt>Returns</dt><dd><p>List of named tuples, each describing a ligand-receptor interaction.</p>
+</dd>
+</dl>
+</dd></dl>
+
+</section>
+
+
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+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.inputs.cellcall.cellcall_annotations.html#pypath.inputs.cellcall.cellcall_annotations" title="pypath.inputs.cellcall.cellcall_annotations"><code class="xref py py-obj docutils literal notranslate"><span class="pre">cellcall_annotations</span></code></a>([extended, organism])</p></td>
+<td><p>Ligand and receptor annotations from the CellCall database (<a class="github reference external" href="https://github.com/ShellyCoder/cellcall">ShellyCoder/cellcall</a>).</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.inputs.cellcall.cellcall_download.html#pypath.inputs.cellcall.cellcall_download" title="pypath.inputs.cellcall.cellcall_download"><code class="xref py py-obj docutils literal notranslate"><span class="pre">cellcall_download</span></code></a>([extended, mouse])</p></td>
+<td><p>Downloads a ligand-receptor-TF pathway dataset from CellCall (<a class="github reference external" href="https://github.com/ShellyCoder/cellcall">ShellyCoder/cellcall</a>).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.inputs.cellcall.cellcall_download_all.html#pypath.inputs.cellcall.cellcall_download_all" title="pypath.inputs.cellcall.cellcall_download_all"><code class="xref py py-obj docutils literal notranslate"><span class="pre">cellcall_download_all</span></code></a>([extended, human, mouse])</p></td>
+<td><p>Downloads ligand-receptor-TF pathway data from CellCall (<a class="github reference external" href="https://github.com/ShellyCoder/cellcall">ShellyCoder/cellcall</a>).</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.inputs.cellcall.cellcall_interactions.html#pypath.inputs.cellcall.cellcall_interactions" title="pypath.inputs.cellcall.cellcall_interactions"><code class="xref py py-obj docutils literal notranslate"><span class="pre">cellcall_interactions</span></code></a>([extended, organism])</p></td>
+<td><p>Ligand-receptor interactions from the CellCall database (<a class="github reference external" href="https://github.com/ShellyCoder/cellcall">ShellyCoder/cellcall</a>).</p></td>
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diff --git a/api/pypath.inputs.cellcellinteractions.cellcellinteractions_annotations.html b/api/pypath.inputs.cellcellinteractions.cellcellinteractions_annotations.html
new file mode 100644
index 000000000..b103d9016
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diff --git a/api/pypath.inputs.cellcellinteractions.html b/api/pypath.inputs.cellcellinteractions.html
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diff --git a/api/pypath.inputs.cellchatdb.cellchatdb_annotations.html b/api/pypath.inputs.cellchatdb.cellchatdb_annotations.html
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diff --git a/api/pypath.inputs.cellchatdb.cellchatdb_cofactors.html b/api/pypath.inputs.cellchatdb.cellchatdb_cofactors.html
new file mode 100644
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diff --git a/api/pypath.inputs.cellchatdb.cellchatdb_complexes.html b/api/pypath.inputs.cellchatdb.cellchatdb_complexes.html
new file mode 100644
index 000000000..f7049c0a3
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+  <section id="pypath-inputs-cellchatdb-cellchatdb-complexes">
+<h1>pypath.inputs.cellchatdb.cellchatdb_complexes<a class="headerlink" href="#pypath-inputs-cellchatdb-cellchatdb-complexes" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.inputs.cellchatdb.cellchatdb_complexes">
+<span class="sig-prename descclassname"><span class="pre">pypath.inputs.cellchatdb.</span></span><span class="sig-name descname"><span class="pre">cellchatdb_complexes</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">organism</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/inputs/cellchatdb.html#cellchatdb_complexes"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.cellchatdb.cellchatdb_complexes" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves data from CellChatDB and processes protein complexes.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><p><strong>organism</strong> (<em>int</em><em>,</em><em>str</em>) – Human and mouse are available, for incomprehensive values falls back
+to human.</p>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p>Dictionary of complexes.</p>
+</dd>
+</dl>
+</dd></dl>
+
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+  <section id="pypath-inputs-cellchatdb-cellchatdb-download">
+<h1>pypath.inputs.cellchatdb.cellchatdb_download<a class="headerlink" href="#pypath-inputs-cellchatdb-cellchatdb-download" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.inputs.cellchatdb.cellchatdb_download">
+<span class="sig-prename descclassname"><span class="pre">pypath.inputs.cellchatdb.</span></span><span class="sig-name descname"><span class="pre">cellchatdb_download</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">organism</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">dataset</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'CellChatDB'</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/inputs/cellchatdb.html#cellchatdb_download"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.cellchatdb.cellchatdb_download" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves data from CellChatDB, extracts fhe R objects from the RDA
+format and returns the raw data.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>organism</strong> (<em>int</em><em>,</em><em>str</em>) – Human and mouse are available, for incomprehensive values falls back
+to human.</p></li>
+<li><p><strong>dataset</strong> (<em>str</em>) – Either <em>CellChatDB</em> or <em>PPI</em>.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
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+  <section id="pypath-inputs-cellchatdb-cellchatdb-interactions">
+<h1>pypath.inputs.cellchatdb.cellchatdb_interactions<a class="headerlink" href="#pypath-inputs-cellchatdb-cellchatdb-interactions" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.inputs.cellchatdb.cellchatdb_interactions">
+<span class="sig-prename descclassname"><span class="pre">pypath.inputs.cellchatdb.</span></span><span class="sig-name descname"><span class="pre">cellchatdb_interactions</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">organism</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ligand_receptor</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cofactors</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/inputs/cellchatdb.html#cellchatdb_interactions"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.cellchatdb.cellchatdb_interactions" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves data from CellChatDB and processes interactions.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>organism</strong> (<em>int</em><em>,</em><em>str</em>) – Human and mouse are available, for incomprehensive values falls back
+to human.</p></li>
+<li><p><strong>ligand_receptor</strong> (<em>bool</em>) – Include ligand-receptor interactions.</p></li>
+<li><p><strong>cofactors</strong> (<em>bool</em>) – Include interactions between cofactors (agonists, antagonists),
+coreceptors and receptors.</p></li>
+</ul>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p>Interactions as list of named tuples.</p>
+</dd>
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+  <section id="module-pypath.inputs.cellchatdb">
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+<dl class="field-list simple">
+<dt class="field-odd">members<span class="colon">:</span></dt>
+<dd class="field-odd"><p></p></dd>
+</dl>
+<p class="rubric">Functions</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.inputs.cellchatdb.cellchatdb_annotations.html#pypath.inputs.cellchatdb.cellchatdb_annotations" title="pypath.inputs.cellchatdb.cellchatdb_annotations"><code class="xref py py-obj docutils literal notranslate"><span class="pre">cellchatdb_annotations</span></code></a>([organism])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.inputs.cellchatdb.cellchatdb_cofactors.html#pypath.inputs.cellchatdb.cellchatdb_cofactors" title="pypath.inputs.cellchatdb.cellchatdb_cofactors"><code class="xref py py-obj docutils literal notranslate"><span class="pre">cellchatdb_cofactors</span></code></a>([organism])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.inputs.cellchatdb.cellchatdb_complexes.html#pypath.inputs.cellchatdb.cellchatdb_complexes" title="pypath.inputs.cellchatdb.cellchatdb_complexes"><code class="xref py py-obj docutils literal notranslate"><span class="pre">cellchatdb_complexes</span></code></a>([organism])</p></td>
+<td><p>Retrieves data from CellChatDB and processes protein complexes.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.inputs.cellchatdb.cellchatdb_download.html#pypath.inputs.cellchatdb.cellchatdb_download" title="pypath.inputs.cellchatdb.cellchatdb_download"><code class="xref py py-obj docutils literal notranslate"><span class="pre">cellchatdb_download</span></code></a>([organism, dataset])</p></td>
+<td><p>Retrieves data from CellChatDB, extracts fhe R objects from the RDA format and returns the raw data.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.inputs.cellchatdb.cellchatdb_interactions.html#pypath.inputs.cellchatdb.cellchatdb_interactions" title="pypath.inputs.cellchatdb.cellchatdb_interactions"><code class="xref py py-obj docutils literal notranslate"><span class="pre">cellchatdb_interactions</span></code></a>([organism, ...])</p></td>
+<td><p>Retrieves data from CellChatDB and processes interactions.</p></td>
+</tr>
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+  <section id="pypath-inputs-cellinker-cellinkerinteraction">
+<h1>pypath.inputs.cellinker.CellinkerInteraction<a class="headerlink" href="#pypath-inputs-cellinker-cellinkerinteraction" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.inputs.cellinker.CellinkerInteraction">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.inputs.cellinker.</span></span><span class="sig-name descname"><span class="pre">CellinkerInteraction</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">ligand</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">receptor</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ligand_location</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">receptor_location</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">pmids</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">type</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.inputs.cellinker.CellinkerInteraction" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">tuple</span></code></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.inputs.cellinker.CellinkerInteraction.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.inputs.cellinker.CellinkerInteraction.__init__" title="Link to this definition">§</a></dt>
+<dd></dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.inputs.cellinker.CellinkerInteraction.__init__" title="pypath.inputs.cellinker.CellinkerInteraction.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.inputs.cellinker.CellinkerInteraction.count" title="pypath.inputs.cellinker.CellinkerInteraction.count"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count</span></code></a>(value, /)</p></td>
+<td><p>Return number of occurrences of value.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.inputs.cellinker.CellinkerInteraction.index" title="pypath.inputs.cellinker.CellinkerInteraction.index"><code class="xref py py-obj docutils literal notranslate"><span class="pre">index</span></code></a>(value[, start, stop])</p></td>
+<td><p>Return first index of value.</p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Attributes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.inputs.cellinker.CellinkerInteraction.ligand" title="pypath.inputs.cellinker.CellinkerInteraction.ligand"><code class="xref py py-obj docutils literal notranslate"><span class="pre">ligand</span></code></a></p></td>
+<td><p>Alias for field number 0</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.inputs.cellinker.CellinkerInteraction.ligand_location" title="pypath.inputs.cellinker.CellinkerInteraction.ligand_location"><code class="xref py py-obj docutils literal notranslate"><span class="pre">ligand_location</span></code></a></p></td>
+<td><p>Alias for field number 2</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.inputs.cellinker.CellinkerInteraction.pmids" title="pypath.inputs.cellinker.CellinkerInteraction.pmids"><code class="xref py py-obj docutils literal notranslate"><span class="pre">pmids</span></code></a></p></td>
+<td><p>Alias for field number 5</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.inputs.cellinker.CellinkerInteraction.receptor" title="pypath.inputs.cellinker.CellinkerInteraction.receptor"><code class="xref py py-obj docutils literal notranslate"><span class="pre">receptor</span></code></a></p></td>
+<td><p>Alias for field number 1</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.inputs.cellinker.CellinkerInteraction.receptor_location" title="pypath.inputs.cellinker.CellinkerInteraction.receptor_location"><code class="xref py py-obj docutils literal notranslate"><span class="pre">receptor_location</span></code></a></p></td>
+<td><p>Alias for field number 3</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.inputs.cellinker.CellinkerInteraction.resources" title="pypath.inputs.cellinker.CellinkerInteraction.resources"><code class="xref py py-obj docutils literal notranslate"><span class="pre">resources</span></code></a></p></td>
+<td><p>Alias for field number 4</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.inputs.cellinker.CellinkerInteraction.type" title="pypath.inputs.cellinker.CellinkerInteraction.type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">type</span></code></a></p></td>
+<td><p>Alias for field number 6</p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.inputs.cellinker.CellinkerInteraction.count">
+<span class="sig-name descname"><span class="pre">count</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">value</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">/</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.inputs.cellinker.CellinkerInteraction.count" title="Link to this definition">§</a></dt>
+<dd><p>Return number of occurrences of value.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.inputs.cellinker.CellinkerInteraction.index">
+<span class="sig-name descname"><span class="pre">index</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">value</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">start</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">stop</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9223372036854775807</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">/</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.inputs.cellinker.CellinkerInteraction.index" title="Link to this definition">§</a></dt>
+<dd><p>Return first index of value.</p>
+<p>Raises ValueError if the value is not present.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.inputs.cellinker.CellinkerInteraction.ligand">
+<span class="sig-name descname"><span class="pre">ligand</span></span><a class="headerlink" href="#pypath.inputs.cellinker.CellinkerInteraction.ligand" title="Link to this definition">§</a></dt>
+<dd><p>Alias for field number 0</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.inputs.cellinker.CellinkerInteraction.ligand_location">
+<span class="sig-name descname"><span class="pre">ligand_location</span></span><a class="headerlink" href="#pypath.inputs.cellinker.CellinkerInteraction.ligand_location" title="Link to this definition">§</a></dt>
+<dd><p>Alias for field number 2</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.inputs.cellinker.CellinkerInteraction.pmids">
+<span class="sig-name descname"><span class="pre">pmids</span></span><a class="headerlink" href="#pypath.inputs.cellinker.CellinkerInteraction.pmids" title="Link to this definition">§</a></dt>
+<dd><p>Alias for field number 5</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.inputs.cellinker.CellinkerInteraction.receptor">
+<span class="sig-name descname"><span class="pre">receptor</span></span><a class="headerlink" href="#pypath.inputs.cellinker.CellinkerInteraction.receptor" title="Link to this definition">§</a></dt>
+<dd><p>Alias for field number 1</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.inputs.cellinker.CellinkerInteraction.receptor_location">
+<span class="sig-name descname"><span class="pre">receptor_location</span></span><a class="headerlink" href="#pypath.inputs.cellinker.CellinkerInteraction.receptor_location" title="Link to this definition">§</a></dt>
+<dd><p>Alias for field number 3</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.inputs.cellinker.CellinkerInteraction.resources">
+<span class="sig-name descname"><span class="pre">resources</span></span><a class="headerlink" href="#pypath.inputs.cellinker.CellinkerInteraction.resources" title="Link to this definition">§</a></dt>
+<dd><p>Alias for field number 4</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.inputs.cellinker.CellinkerInteraction.type">
+<span class="sig-name descname"><span class="pre">type</span></span><a class="headerlink" href="#pypath.inputs.cellinker.CellinkerInteraction.type" title="Link to this definition">§</a></dt>
+<dd><p>Alias for field number 6</p>
+</dd></dl>
+
+</dd></dl>
+
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+
+
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+  <section id="pypath-inputs-cellinker-cellinker-annotations">
+<h1>pypath.inputs.cellinker.cellinker_annotations<a class="headerlink" href="#pypath-inputs-cellinker-cellinker-annotations" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.inputs.cellinker.cellinker_annotations">
+<span class="sig-prename descclassname"><span class="pre">pypath.inputs.cellinker.</span></span><span class="sig-name descname"><span class="pre">cellinker_annotations</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">organism</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/inputs/cellinker.html#cellinker_annotations"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.cellinker.cellinker_annotations" title="Link to this definition">§</a></dt>
+<dd><p>Ligand and receptor annotations from the Cellinker database
+(<a class="reference external" href="http://www.rna-society.org/cellinker/">http://www.rna-society.org/cellinker/</a>).</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>organism (int,str): Name or identifier of the organism. Only mouse</dt><dd><p>and human are available.</p>
+</dd>
+<dt>entity_type (str): Either <cite>protein</cite> or <cite>complex</cite>. If <cite>None</cite>, both</dt><dd><p>proteins and protein complexes will be included.</p>
+</dd>
+</dl>
+</dd>
+<dt>Returns</dt><dd><dl class="simple">
+<dt>(dict): A dict of sets of tuples, keys are UniProt IDs for proteins</dt><dd><p>and <cite>Complex</cite> objects for protein complexes. The tuples are
+annotations with ligand or receptor role, localization and
+type.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
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diff --git a/api/pypath.inputs.cellinker.cellinker_complex_annotations.html b/api/pypath.inputs.cellinker.cellinker_complex_annotations.html
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+  <section id="pypath-inputs-cellinker-cellinker-complex-annotations">
+<h1>pypath.inputs.cellinker.cellinker_complex_annotations<a class="headerlink" href="#pypath-inputs-cellinker-cellinker-complex-annotations" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.inputs.cellinker.cellinker_complex_annotations">
+<span class="sig-prename descclassname"><span class="pre">pypath.inputs.cellinker.</span></span><span class="sig-name descname"><span class="pre">cellinker_complex_annotations</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">organism</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/inputs/cellinker.html#cellinker_complex_annotations"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.cellinker.cellinker_complex_annotations" title="Link to this definition">§</a></dt>
+<dd><p>Ligand and receptor annotations from the Cellinker database
+(<a class="reference external" href="http://www.rna-society.org/cellinker/">http://www.rna-society.org/cellinker/</a>).</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>organism (int,str): Name or identifier of the organism. Only mouse</dt><dd><p>and human are available.</p>
+</dd>
+</dl>
+</dd>
+<dt>Returns</dt><dd><dl class="simple">
+<dt>(dict): A dict of sets of tuples, keys are <cite>Complex</cite> objects.</dt><dd><p>The tuples are annotations with ligand or receptor role,
+localization and type.</p>
+</dd>
+</dl>
+</dd>
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+  <section id="pypath-inputs-cellinker-cellinker-complexes">
+<h1>pypath.inputs.cellinker.cellinker_complexes<a class="headerlink" href="#pypath-inputs-cellinker-cellinker-complexes" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.inputs.cellinker.cellinker_complexes">
+<span class="sig-prename descclassname"><span class="pre">pypath.inputs.cellinker.</span></span><span class="sig-name descname"><span class="pre">cellinker_complexes</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">organism</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/inputs/cellinker.html#cellinker_complexes"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.cellinker.cellinker_complexes" title="Link to this definition">§</a></dt>
+<dd><p>Protein complex information from the Cellinker database
+(<a class="reference external" href="http://www.rna-society.org/cellinker/">http://www.rna-society.org/cellinker/</a>).</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>organism (int,str): Name or identifier of the organism. Only mouse</dt><dd><p>and human are available.</p>
+</dd>
+</dl>
+</dd>
+<dt>Returns</dt><dd><dl class="simple">
+<dt>(dict): A dict of complexes, with string representations as keys and</dt><dd><p><cite>pypath.internals.intera.Complex</cite> objects as values.</p>
+</dd>
+</dl>
+</dd>
+</dl>
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diff --git a/api/pypath.inputs.cellinker.cellinker_complexes_raw.html b/api/pypath.inputs.cellinker.cellinker_complexes_raw.html
new file mode 100644
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+  <section id="pypath-inputs-cellinker-cellinker-complexes-raw">
+<h1>pypath.inputs.cellinker.cellinker_complexes_raw<a class="headerlink" href="#pypath-inputs-cellinker-cellinker-complexes-raw" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.inputs.cellinker.cellinker_complexes_raw">
+<span class="sig-prename descclassname"><span class="pre">pypath.inputs.cellinker.</span></span><span class="sig-name descname"><span class="pre">cellinker_complexes_raw</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">organism</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/inputs/cellinker.html#cellinker_complexes_raw"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.cellinker.cellinker_complexes_raw" title="Link to this definition">§</a></dt>
+<dd><p>Downloads protein complex data from the Cellinker database
+(<a class="reference external" href="http://www.rna-society.org/cellinker/">http://www.rna-society.org/cellinker/</a>).</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>organism (int,str): Name or identifier of the organism. Only mouse</dt><dd><p>and human are available.</p>
+</dd>
+</dl>
+</dd>
+<dt>Returns</dt><dd><dl class="simple">
+<dt>(list): List of tuples each describing a protein complex with its</dt><dd><p>role (ligand or receptor), components, localization and
+Cellinker ID.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
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+  <section id="pypath-inputs-cellinker-cellinker-lr-interactions">
+<h1>pypath.inputs.cellinker.cellinker_lr_interactions<a class="headerlink" href="#pypath-inputs-cellinker-cellinker-lr-interactions" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.inputs.cellinker.cellinker_lr_interactions">
+<span class="sig-prename descclassname"><span class="pre">pypath.inputs.cellinker.</span></span><span class="sig-name descname"><span class="pre">cellinker_lr_interactions</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">organism</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/inputs/cellinker.html#cellinker_lr_interactions"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.cellinker.cellinker_lr_interactions" title="Link to this definition">§</a></dt>
+<dd><p>Ligand-receptor interactions from the Cellinker database
+(<a class="reference external" href="http://www.rna-society.org/cellinker/">http://www.rna-society.org/cellinker/</a>).</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>organism (int,str): Name or identifier of the organism. Only mouse</dt><dd><p>and human are available.</p>
+</dd>
+</dl>
+</dd>
+<dt>Returns</dt><dd><dl class="simple">
+<dt>(set): A set of tuples, each representing a preprocessed Cellinker</dt><dd><p>interaction. The proteins are represented by their UniProt IDs,
+while the protein complexes by <cite>Complex</cite> objects.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
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+  <section id="pypath-inputs-cellinker-cellinker-lr-interactions-raw">
+<h1>pypath.inputs.cellinker.cellinker_lr_interactions_raw<a class="headerlink" href="#pypath-inputs-cellinker-cellinker-lr-interactions-raw" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.inputs.cellinker.cellinker_lr_interactions_raw">
+<span class="sig-prename descclassname"><span class="pre">pypath.inputs.cellinker.</span></span><span class="sig-name descname"><span class="pre">cellinker_lr_interactions_raw</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">organism</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/inputs/cellinker.html#cellinker_lr_interactions_raw"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.cellinker.cellinker_lr_interactions_raw" title="Link to this definition">§</a></dt>
+<dd><p>Ligand-receptor interactions from the Cellinker database
+(<a class="reference external" href="http://www.rna-society.org/cellinker/">http://www.rna-society.org/cellinker/</a>).</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>organism (int,str): Name or identifier of the organism. Only mouse</dt><dd><p>and human are available.</p>
+</dd>
+</dl>
+</dd>
+<dt>Returns</dt><dd><dl class="simple">
+<dt>(list): A list of dicts, each representing an interaction records</dt><dd><p>as it is provided by the database.</p>
+</dd>
+</dl>
+</dd>
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+
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+  <section id="pypath-inputs-cellinker-cellinker-protein-annotations">
+<h1>pypath.inputs.cellinker.cellinker_protein_annotations<a class="headerlink" href="#pypath-inputs-cellinker-cellinker-protein-annotations" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.inputs.cellinker.cellinker_protein_annotations">
+<span class="sig-prename descclassname"><span class="pre">pypath.inputs.cellinker.</span></span><span class="sig-name descname"><span class="pre">cellinker_protein_annotations</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">organism</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/inputs/cellinker.html#cellinker_protein_annotations"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.cellinker.cellinker_protein_annotations" title="Link to this definition">§</a></dt>
+<dd><p>Ligand and receptor annotations from the Cellinker database
+(<a class="reference external" href="http://www.rna-society.org/cellinker/">http://www.rna-society.org/cellinker/</a>).</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>organism (int,str): Name or identifier of the organism. Only mouse</dt><dd><p>and human are available.</p>
+</dd>
+</dl>
+</dd>
+<dt>Returns</dt><dd><dl class="simple">
+<dt>(dict): A dict of sets of tuples, keys are UniProt IDs. The tuples</dt><dd><p>are annotations with ligand or receptor role, localization and
+type.</p>
+</dd>
+</dl>
+</dd>
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diff --git a/api/pypath.inputs.cellinker.cellinker_smol_interactions.html b/api/pypath.inputs.cellinker.cellinker_smol_interactions.html
new file mode 100644
index 000000000..8c0f39aef
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+  <section id="pypath-inputs-cellinker-cellinker-smol-interactions">
+<h1>pypath.inputs.cellinker.cellinker_smol_interactions<a class="headerlink" href="#pypath-inputs-cellinker-cellinker-smol-interactions" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.inputs.cellinker.cellinker_smol_interactions">
+<span class="sig-prename descclassname"><span class="pre">pypath.inputs.cellinker.</span></span><span class="sig-name descname"><span class="pre">cellinker_smol_interactions</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">organism</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/inputs/cellinker.html#cellinker_smol_interactions"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.cellinker.cellinker_smol_interactions" title="Link to this definition">§</a></dt>
+<dd><p>Small molecule ligand-protein receptor interactions from the Cellinker
+database (<a class="reference external" href="http://www.rna-society.org/cellinker/">http://www.rna-society.org/cellinker/</a>).</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>organism (int,str): Name or identifier of the organism. Only mouse</dt><dd><p>and human are available.</p>
+</dd>
+</dl>
+</dd>
+<dt>Returns</dt><dd><dl class="simple">
+<dt>(set): A set of tuples, each representing a preprocessed Cellinker</dt><dd><p>interaction. The proteins are represented by their UniProt IDs,
+the small molecules by PubChem CIDs, while the protein complexes
+by <cite>Complex</cite> objects.</p>
+</dd>
+</dl>
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+<h1>pypath.inputs.cellinker.cellinker_smol_interactions_raw<a class="headerlink" href="#pypath-inputs-cellinker-cellinker-smol-interactions-raw" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.inputs.cellinker.cellinker_smol_interactions_raw">
+<span class="sig-prename descclassname"><span class="pre">pypath.inputs.cellinker.</span></span><span class="sig-name descname"><span class="pre">cellinker_smol_interactions_raw</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">organism</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/inputs/cellinker.html#cellinker_smol_interactions_raw"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.cellinker.cellinker_smol_interactions_raw" title="Link to this definition">§</a></dt>
+<dd><p>Small molecule ligand-protein receptor interactions from the Cellinker
+database (<a class="reference external" href="http://www.rna-society.org/cellinker/">http://www.rna-society.org/cellinker/</a>).</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>organism (int,str): Name or identifier of the organism. Only mouse</dt><dd><p>and human are available.</p>
+</dd>
+</dl>
+</dd>
+<dt>Returns</dt><dd><dl class="simple">
+<dt>(list): A list of dicts, each representing an interaction records</dt><dd><p>as it is provided by the database.</p>
+</dd>
+</dl>
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+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.inputs.cellinker.components_to_complex">
+<span class="sig-prename descclassname"><span class="pre">pypath.inputs.cellinker.</span></span><span class="sig-name descname"><span class="pre">components_to_complex</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">components</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">organism</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/inputs/cellinker.html#components_to_complex"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.cellinker.components_to_complex" title="Link to this definition">§</a></dt>
+<dd><p>Converts a set of components to <cite>pypath.internals.intera.Complex</cite>
+objects.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>components (tuple): Components of a complex, as returned by</dt><dd><p><cite>cellinker_complexes_raw</cite>.</p>
+</dd>
+<dt>organism (int,str): Name or identifier of the organism. Only mouse</dt><dd><p>and human are available. Optional, because organism can be
+guessed from the identifiers.</p>
+</dd>
+</dl>
+</dd>
+<dt>Returns</dt><dd><p>(set): A set of <cite>pypath.internals.intera.Complex</cite> objects.</p>
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+  <section id="module-pypath.inputs.cellinker">
+<span id="pypath-inputs-cellinker"></span><h1>pypath.inputs.cellinker<a class="headerlink" href="#module-pypath.inputs.cellinker" title="Link to this heading">§</a></h1>
+<dl class="field-list simple">
+<dt class="field-odd">members<span class="colon">:</span></dt>
+<dd class="field-odd"><p></p></dd>
+</dl>
+<p class="rubric">Functions</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.inputs.cellinker.cellinker_annotations.html#pypath.inputs.cellinker.cellinker_annotations" title="pypath.inputs.cellinker.cellinker_annotations"><code class="xref py py-obj docutils literal notranslate"><span class="pre">cellinker_annotations</span></code></a>([organism, entity_type])</p></td>
+<td><p>Ligand and receptor annotations from the Cellinker database (<a class="reference external" href="http://www.rna-society.org/cellinker/">http://www.rna-society.org/cellinker/</a>).</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.inputs.cellinker.cellinker_complex_annotations.html#pypath.inputs.cellinker.cellinker_complex_annotations" title="pypath.inputs.cellinker.cellinker_complex_annotations"><code class="xref py py-obj docutils literal notranslate"><span class="pre">cellinker_complex_annotations</span></code></a>([organism])</p></td>
+<td><p>Ligand and receptor annotations from the Cellinker database (<a class="reference external" href="http://www.rna-society.org/cellinker/">http://www.rna-society.org/cellinker/</a>).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.inputs.cellinker.cellinker_complexes.html#pypath.inputs.cellinker.cellinker_complexes" title="pypath.inputs.cellinker.cellinker_complexes"><code class="xref py py-obj docutils literal notranslate"><span class="pre">cellinker_complexes</span></code></a>([organism])</p></td>
+<td><p>Protein complex information from the Cellinker database (<a class="reference external" href="http://www.rna-society.org/cellinker/">http://www.rna-society.org/cellinker/</a>).</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.inputs.cellinker.cellinker_complexes_raw.html#pypath.inputs.cellinker.cellinker_complexes_raw" title="pypath.inputs.cellinker.cellinker_complexes_raw"><code class="xref py py-obj docutils literal notranslate"><span class="pre">cellinker_complexes_raw</span></code></a>([organism])</p></td>
+<td><p>Downloads protein complex data from the Cellinker database (<a class="reference external" href="http://www.rna-society.org/cellinker/">http://www.rna-society.org/cellinker/</a>).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.inputs.cellinker.cellinker_lr_interactions.html#pypath.inputs.cellinker.cellinker_lr_interactions" title="pypath.inputs.cellinker.cellinker_lr_interactions"><code class="xref py py-obj docutils literal notranslate"><span class="pre">cellinker_lr_interactions</span></code></a>([organism])</p></td>
+<td><p>Ligand-receptor interactions from the Cellinker database (<a class="reference external" href="http://www.rna-society.org/cellinker/">http://www.rna-society.org/cellinker/</a>).</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.inputs.cellinker.cellinker_lr_interactions_raw.html#pypath.inputs.cellinker.cellinker_lr_interactions_raw" title="pypath.inputs.cellinker.cellinker_lr_interactions_raw"><code class="xref py py-obj docutils literal notranslate"><span class="pre">cellinker_lr_interactions_raw</span></code></a>([organism])</p></td>
+<td><p>Ligand-receptor interactions from the Cellinker database (<a class="reference external" href="http://www.rna-society.org/cellinker/">http://www.rna-society.org/cellinker/</a>).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.inputs.cellinker.cellinker_protein_annotations.html#pypath.inputs.cellinker.cellinker_protein_annotations" title="pypath.inputs.cellinker.cellinker_protein_annotations"><code class="xref py py-obj docutils literal notranslate"><span class="pre">cellinker_protein_annotations</span></code></a>([organism])</p></td>
+<td><p>Ligand and receptor annotations from the Cellinker database (<a class="reference external" href="http://www.rna-society.org/cellinker/">http://www.rna-society.org/cellinker/</a>).</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.inputs.cellinker.cellinker_smol_interactions.html#pypath.inputs.cellinker.cellinker_smol_interactions" title="pypath.inputs.cellinker.cellinker_smol_interactions"><code class="xref py py-obj docutils literal notranslate"><span class="pre">cellinker_smol_interactions</span></code></a>([organism])</p></td>
+<td><p>Small molecule ligand-protein receptor interactions from the Cellinker database (<a class="reference external" href="http://www.rna-society.org/cellinker/">http://www.rna-society.org/cellinker/</a>).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.inputs.cellinker.cellinker_smol_interactions_raw.html#pypath.inputs.cellinker.cellinker_smol_interactions_raw" title="pypath.inputs.cellinker.cellinker_smol_interactions_raw"><code class="xref py py-obj docutils literal notranslate"><span class="pre">cellinker_smol_interactions_raw</span></code></a>([organism])</p></td>
+<td><p>Small molecule ligand-protein receptor interactions from the Cellinker database (<a class="reference external" href="http://www.rna-society.org/cellinker/">http://www.rna-society.org/cellinker/</a>).</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.inputs.cellinker.components_to_complex.html#pypath.inputs.cellinker.components_to_complex" title="pypath.inputs.cellinker.components_to_complex"><code class="xref py py-obj docutils literal notranslate"><span class="pre">components_to_complex</span></code></a>(components[, organism])</p></td>
+<td><p>Converts a set of components to <cite>pypath.internals.intera.Complex</cite> objects.</p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Classes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.inputs.cellinker.CellinkerInteraction.html#pypath.inputs.cellinker.CellinkerInteraction" title="pypath.inputs.cellinker.CellinkerInteraction"><code class="xref py py-obj docutils literal notranslate"><span class="pre">CellinkerInteraction</span></code></a>(ligand, receptor, ...)</p></td>
+<td><p></p></td>
+</tr>
+</tbody>
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diff --git a/api/pypath.inputs.cellphonedb.CellPhoneDBAnnotation.html b/api/pypath.inputs.cellphonedb.CellPhoneDBAnnotation.html
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+  <section id="pypath-inputs-cellphonedb-cellphonedbannotation">
+<h1>pypath.inputs.cellphonedb.CellPhoneDBAnnotation<a class="headerlink" href="#pypath-inputs-cellphonedb-cellphonedbannotation" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.inputs.cellphonedb.CellPhoneDBAnnotation">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.inputs.cellphonedb.</span></span><span class="sig-name descname"><span class="pre">CellPhoneDBAnnotation</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">receptor</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">receptor_class</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">peripheral</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">secreted</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">secreted_class</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">transmembrane</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">integrin</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.inputs.cellphonedb.CellPhoneDBAnnotation" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">tuple</span></code></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.inputs.cellphonedb.CellPhoneDBAnnotation.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.inputs.cellphonedb.CellPhoneDBAnnotation.__init__" title="Link to this definition">§</a></dt>
+<dd></dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.inputs.cellphonedb.CellPhoneDBAnnotation.__init__" title="pypath.inputs.cellphonedb.CellPhoneDBAnnotation.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.inputs.cellphonedb.CellPhoneDBAnnotation.count" title="pypath.inputs.cellphonedb.CellPhoneDBAnnotation.count"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count</span></code></a>(value, /)</p></td>
+<td><p>Return number of occurrences of value.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.inputs.cellphonedb.CellPhoneDBAnnotation.index" title="pypath.inputs.cellphonedb.CellPhoneDBAnnotation.index"><code class="xref py py-obj docutils literal notranslate"><span class="pre">index</span></code></a>(value[, start, stop])</p></td>
+<td><p>Return first index of value.</p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Attributes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.inputs.cellphonedb.CellPhoneDBAnnotation.integrin" title="pypath.inputs.cellphonedb.CellPhoneDBAnnotation.integrin"><code class="xref py py-obj docutils literal notranslate"><span class="pre">integrin</span></code></a></p></td>
+<td><p>Alias for field number 6</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.inputs.cellphonedb.CellPhoneDBAnnotation.peripheral" title="pypath.inputs.cellphonedb.CellPhoneDBAnnotation.peripheral"><code class="xref py py-obj docutils literal notranslate"><span class="pre">peripheral</span></code></a></p></td>
+<td><p>Alias for field number 2</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.inputs.cellphonedb.CellPhoneDBAnnotation.receptor" title="pypath.inputs.cellphonedb.CellPhoneDBAnnotation.receptor"><code class="xref py py-obj docutils literal notranslate"><span class="pre">receptor</span></code></a></p></td>
+<td><p>Alias for field number 0</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.inputs.cellphonedb.CellPhoneDBAnnotation.receptor_class" title="pypath.inputs.cellphonedb.CellPhoneDBAnnotation.receptor_class"><code class="xref py py-obj docutils literal notranslate"><span class="pre">receptor_class</span></code></a></p></td>
+<td><p>Alias for field number 1</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.inputs.cellphonedb.CellPhoneDBAnnotation.secreted" title="pypath.inputs.cellphonedb.CellPhoneDBAnnotation.secreted"><code class="xref py py-obj docutils literal notranslate"><span class="pre">secreted</span></code></a></p></td>
+<td><p>Alias for field number 3</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.inputs.cellphonedb.CellPhoneDBAnnotation.secreted_class" title="pypath.inputs.cellphonedb.CellPhoneDBAnnotation.secreted_class"><code class="xref py py-obj docutils literal notranslate"><span class="pre">secreted_class</span></code></a></p></td>
+<td><p>Alias for field number 4</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.inputs.cellphonedb.CellPhoneDBAnnotation.transmembrane" title="pypath.inputs.cellphonedb.CellPhoneDBAnnotation.transmembrane"><code class="xref py py-obj docutils literal notranslate"><span class="pre">transmembrane</span></code></a></p></td>
+<td><p>Alias for field number 5</p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.inputs.cellphonedb.CellPhoneDBAnnotation.count">
+<span class="sig-name descname"><span class="pre">count</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">value</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">/</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.inputs.cellphonedb.CellPhoneDBAnnotation.count" title="Link to this definition">§</a></dt>
+<dd><p>Return number of occurrences of value.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.inputs.cellphonedb.CellPhoneDBAnnotation.index">
+<span class="sig-name descname"><span class="pre">index</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">value</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">start</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">stop</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9223372036854775807</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">/</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.inputs.cellphonedb.CellPhoneDBAnnotation.index" title="Link to this definition">§</a></dt>
+<dd><p>Return first index of value.</p>
+<p>Raises ValueError if the value is not present.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.inputs.cellphonedb.CellPhoneDBAnnotation.integrin">
+<span class="sig-name descname"><span class="pre">integrin</span></span><a class="headerlink" href="#pypath.inputs.cellphonedb.CellPhoneDBAnnotation.integrin" title="Link to this definition">§</a></dt>
+<dd><p>Alias for field number 6</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.inputs.cellphonedb.CellPhoneDBAnnotation.peripheral">
+<span class="sig-name descname"><span class="pre">peripheral</span></span><a class="headerlink" href="#pypath.inputs.cellphonedb.CellPhoneDBAnnotation.peripheral" title="Link to this definition">§</a></dt>
+<dd><p>Alias for field number 2</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.inputs.cellphonedb.CellPhoneDBAnnotation.receptor">
+<span class="sig-name descname"><span class="pre">receptor</span></span><a class="headerlink" href="#pypath.inputs.cellphonedb.CellPhoneDBAnnotation.receptor" title="Link to this definition">§</a></dt>
+<dd><p>Alias for field number 0</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.inputs.cellphonedb.CellPhoneDBAnnotation.receptor_class">
+<span class="sig-name descname"><span class="pre">receptor_class</span></span><a class="headerlink" href="#pypath.inputs.cellphonedb.CellPhoneDBAnnotation.receptor_class" title="Link to this definition">§</a></dt>
+<dd><p>Alias for field number 1</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.inputs.cellphonedb.CellPhoneDBAnnotation.secreted">
+<span class="sig-name descname"><span class="pre">secreted</span></span><a class="headerlink" href="#pypath.inputs.cellphonedb.CellPhoneDBAnnotation.secreted" title="Link to this definition">§</a></dt>
+<dd><p>Alias for field number 3</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.inputs.cellphonedb.CellPhoneDBAnnotation.secreted_class">
+<span class="sig-name descname"><span class="pre">secreted_class</span></span><a class="headerlink" href="#pypath.inputs.cellphonedb.CellPhoneDBAnnotation.secreted_class" title="Link to this definition">§</a></dt>
+<dd><p>Alias for field number 4</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.inputs.cellphonedb.CellPhoneDBAnnotation.transmembrane">
+<span class="sig-name descname"><span class="pre">transmembrane</span></span><a class="headerlink" href="#pypath.inputs.cellphonedb.CellPhoneDBAnnotation.transmembrane" title="Link to this definition">§</a></dt>
+<dd><p>Alias for field number 5</p>
+</dd></dl>
+
+</dd></dl>
+
+</section>
+
+
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diff --git a/api/pypath.inputs.cellphonedb.cellphonedb_complex_annotations.html b/api/pypath.inputs.cellphonedb.cellphonedb_complex_annotations.html
new file mode 100644
index 000000000..dccdcea87
--- /dev/null
+++ b/api/pypath.inputs.cellphonedb.cellphonedb_complex_annotations.html
@@ -0,0 +1,638 @@
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+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.inputs.cellphonedb.cellphonedb_interactions">
+<span class="sig-prename descclassname"><span class="pre">pypath.inputs.cellphonedb.</span></span><span class="sig-name descname"><span class="pre">cellphonedb_interactions</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/inputs/cellphonedb.html#cellphonedb_interactions"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.cellphonedb.cellphonedb_interactions" title="Link to this definition">§</a></dt>
+<dd><p>Interactions between ligands and receptors from CellPhoneDB.</p>
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diff --git a/api/pypath.inputs.cellphonedb.cellphonedb_ligands_receptors.html b/api/pypath.inputs.cellphonedb.cellphonedb_ligands_receptors.html
new file mode 100644
index 000000000..f4f22f039
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+  <section id="pypath-inputs-cellphonedb-cellphonedb-ligands-receptors">
+<h1>pypath.inputs.cellphonedb.cellphonedb_ligands_receptors<a class="headerlink" href="#pypath-inputs-cellphonedb-cellphonedb-ligands-receptors" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.inputs.cellphonedb.cellphonedb_ligands_receptors">
+<span class="sig-prename descclassname"><span class="pre">pypath.inputs.cellphonedb.</span></span><span class="sig-name descname"><span class="pre">cellphonedb_ligands_receptors</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/inputs/cellphonedb.html#cellphonedb_ligands_receptors"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.cellphonedb.cellphonedb_ligands_receptors" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the set of ligands and receptors from CellPhoneDB.
+Returns tuple of sets.</p>
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diff --git a/api/pypath.inputs.cellphonedb.cellphonedb_protein_annotations.html b/api/pypath.inputs.cellphonedb.cellphonedb_protein_annotations.html
new file mode 100644
index 000000000..bea837b18
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+  <section id="pypath-inputs-cellphonedb-cellphonedb-protein-annotations">
+<h1>pypath.inputs.cellphonedb.cellphonedb_protein_annotations<a class="headerlink" href="#pypath-inputs-cellphonedb-cellphonedb-protein-annotations" title="Link to this heading">§</a></h1>
+<dl class="py function">
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+<span class="sig-prename descclassname"><span class="pre">pypath.inputs.cellphonedb.</span></span><span class="sig-name descname"><span class="pre">cellphonedb_protein_annotations</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">add_complex_annotations</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/inputs/cellphonedb.html#cellphonedb_protein_annotations"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.cellphonedb.cellphonedb_protein_annotations" title="Link to this definition">§</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><p><strong>add_complex_annotations</strong> (<em>bool</em>) – Deprecated because results wrong annotations.
+Copy the annotations of complexes to each of their member proteins.</p>
+</dd>
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diff --git a/api/pypath.inputs.cellphonedb.html b/api/pypath.inputs.cellphonedb.html
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+<span id="pypath-inputs-cellphonedb"></span><h1>pypath.inputs.cellphonedb<a class="headerlink" href="#module-pypath.inputs.cellphonedb" title="Link to this heading">§</a></h1>
+<dl class="field-list simple">
+<dt class="field-odd">members<span class="colon">:</span></dt>
+<dd class="field-odd"><p></p></dd>
+</dl>
+<p class="rubric">Functions</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.inputs.cellphonedb.cellphonedb_complex_annotations.html#pypath.inputs.cellphonedb.cellphonedb_complex_annotations" title="pypath.inputs.cellphonedb.cellphonedb_complex_annotations"><code class="xref py py-obj docutils literal notranslate"><span class="pre">cellphonedb_complex_annotations</span></code></a>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.inputs.cellphonedb.cellphonedb_complexes.html#pypath.inputs.cellphonedb.cellphonedb_complexes" title="pypath.inputs.cellphonedb.cellphonedb_complexes"><code class="xref py py-obj docutils literal notranslate"><span class="pre">cellphonedb_complexes</span></code></a>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.inputs.cellphonedb.cellphonedb_interactions.html#pypath.inputs.cellphonedb.cellphonedb_interactions" title="pypath.inputs.cellphonedb.cellphonedb_interactions"><code class="xref py py-obj docutils literal notranslate"><span class="pre">cellphonedb_interactions</span></code></a>()</p></td>
+<td><p>Interactions between ligands and receptors from CellPhoneDB.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.inputs.cellphonedb.cellphonedb_ligands_receptors.html#pypath.inputs.cellphonedb.cellphonedb_ligands_receptors" title="pypath.inputs.cellphonedb.cellphonedb_ligands_receptors"><code class="xref py py-obj docutils literal notranslate"><span class="pre">cellphonedb_ligands_receptors</span></code></a>()</p></td>
+<td><p>Retrieves the set of ligands and receptors from CellPhoneDB.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.inputs.cellphonedb.cellphonedb_protein_annotations.html#pypath.inputs.cellphonedb.cellphonedb_protein_annotations" title="pypath.inputs.cellphonedb.cellphonedb_protein_annotations"><code class="xref py py-obj docutils literal notranslate"><span class="pre">cellphonedb_protein_annotations</span></code></a>([...])</p></td>
+<td><p><dl class="field-list simple">
+<dt class="field-odd">arg bool add_complex_annotations<span class="colon">:</span></dt>
+<dd class="field-odd"><p></p></dd>
+</dl>
+</p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Classes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.inputs.cellphonedb.CellPhoneDBAnnotation.html#pypath.inputs.cellphonedb.CellPhoneDBAnnotation" title="pypath.inputs.cellphonedb.CellPhoneDBAnnotation"><code class="xref py py-obj docutils literal notranslate"><span class="pre">CellPhoneDBAnnotation</span></code></a>(receptor, ...)</p></td>
+<td><p></p></td>
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+
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diff --git a/api/pypath.inputs.celltalkdb.celltalkdb_annotations.html b/api/pypath.inputs.celltalkdb.celltalkdb_annotations.html
new file mode 100644
index 000000000..7bb6d8c3c
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+  <section id="pypath-inputs-celltalkdb-celltalkdb-annotations">
+<h1>pypath.inputs.celltalkdb.celltalkdb_annotations<a class="headerlink" href="#pypath-inputs-celltalkdb-celltalkdb-annotations" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.inputs.celltalkdb.celltalkdb_annotations">
+<span class="sig-prename descclassname"><span class="pre">pypath.inputs.celltalkdb.</span></span><span class="sig-name descname"><span class="pre">celltalkdb_annotations</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">organism</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/inputs/celltalkdb.html#celltalkdb_annotations"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.celltalkdb.celltalkdb_annotations" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves annotation of protein ligand and receptor roles from CellTalkDB
+<a class="reference external" href="http://tcm.zju.edu.cn/celltalkdb/index.php">http://tcm.zju.edu.cn/celltalkdb/index.php</a></p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><p><strong>organism</strong> (<em>int</em><em>,</em><em>str</em>) – Human and mouse supported, in case of incomprehensible value will
+fall back to human.</p>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p>Dictionary of annotations with UniProt IDs as keys.</p>
+</dd>
+</dl>
+</dd></dl>
+
+</section>
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+  <section id="pypath-inputs-celltalkdb-celltalkdb-download">
+<h1>pypath.inputs.celltalkdb.celltalkdb_download<a class="headerlink" href="#pypath-inputs-celltalkdb-celltalkdb-download" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.inputs.celltalkdb.celltalkdb_download">
+<span class="sig-prename descclassname"><span class="pre">pypath.inputs.celltalkdb.</span></span><span class="sig-name descname"><span class="pre">celltalkdb_download</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">filename</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'lr_pair'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">organism</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/inputs/celltalkdb.html#celltalkdb_download"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.celltalkdb.celltalkdb_download" title="Link to this definition">§</a></dt>
+<dd><p>Downloads a file from CellTalkDB.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>filename</strong> (<em>str</em>) – The file name of the dataset to download. Possible values:
+lr_pair, gene_info, gene2ensembl, uniprot.</p></li>
+<li><p><strong>organism</strong> (<em>int</em><em>,</em><em>str</em>) – Human and mouse supported, in case of incomprehensible value will
+fall back to human.</p></li>
+</ul>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p>Generator yielding dataset specific records as named tuples.</p>
+</dd>
+</dl>
+</dd></dl>
+
+</section>
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diff --git a/api/pypath.inputs.celltalkdb.celltalkdb_interactions.html b/api/pypath.inputs.celltalkdb.celltalkdb_interactions.html
new file mode 100644
index 000000000..1e221a177
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+  <section id="pypath-inputs-celltalkdb-celltalkdb-interactions">
+<h1>pypath.inputs.celltalkdb.celltalkdb_interactions<a class="headerlink" href="#pypath-inputs-celltalkdb-celltalkdb-interactions" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.inputs.celltalkdb.celltalkdb_interactions">
+<span class="sig-prename descclassname"><span class="pre">pypath.inputs.celltalkdb.</span></span><span class="sig-name descname"><span class="pre">celltalkdb_interactions</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">organism</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/inputs/celltalkdb.html#celltalkdb_interactions"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.celltalkdb.celltalkdb_interactions" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves ligand-receptor interactions from CellTalkDB
+<a class="reference external" href="http://tcm.zju.edu.cn/celltalkdb/index.php">http://tcm.zju.edu.cn/celltalkdb/index.php</a></p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><p><strong>organism</strong> (<em>int</em><em>,</em><em>str</em>) – Human and mouse supported, in case of incomprehensible value will
+fall back to human.</p>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p>List of interactions as named tuples.</p>
+</dd>
+</dl>
+</dd></dl>
+
+</section>
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diff --git a/api/pypath.inputs.celltalkdb.html b/api/pypath.inputs.celltalkdb.html
new file mode 100644
index 000000000..0559bf411
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@@ -0,0 +1,651 @@
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+  <section id="module-pypath.inputs.celltalkdb">
+<span id="pypath-inputs-celltalkdb"></span><h1>pypath.inputs.celltalkdb<a class="headerlink" href="#module-pypath.inputs.celltalkdb" title="Link to this heading">§</a></h1>
+<dl class="field-list simple">
+<dt class="field-odd">members<span class="colon">:</span></dt>
+<dd class="field-odd"><p></p></dd>
+</dl>
+<p class="rubric">Functions</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.inputs.celltalkdb.celltalkdb_annotations.html#pypath.inputs.celltalkdb.celltalkdb_annotations" title="pypath.inputs.celltalkdb.celltalkdb_annotations"><code class="xref py py-obj docutils literal notranslate"><span class="pre">celltalkdb_annotations</span></code></a>([organism])</p></td>
+<td><p>Retrieves annotation of protein ligand and receptor roles from CellTalkDB <a class="reference external" href="http://tcm.zju.edu.cn/celltalkdb/index.php">http://tcm.zju.edu.cn/celltalkdb/index.php</a></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.inputs.celltalkdb.celltalkdb_download.html#pypath.inputs.celltalkdb.celltalkdb_download" title="pypath.inputs.celltalkdb.celltalkdb_download"><code class="xref py py-obj docutils literal notranslate"><span class="pre">celltalkdb_download</span></code></a>([filename, organism])</p></td>
+<td><p>Downloads a file from CellTalkDB.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.inputs.celltalkdb.celltalkdb_interactions.html#pypath.inputs.celltalkdb.celltalkdb_interactions" title="pypath.inputs.celltalkdb.celltalkdb_interactions"><code class="xref py py-obj docutils literal notranslate"><span class="pre">celltalkdb_interactions</span></code></a>([organism])</p></td>
+<td><p>Retrieves ligand-receptor interactions from CellTalkDB <a class="reference external" href="http://tcm.zju.edu.cn/celltalkdb/index.php">http://tcm.zju.edu.cn/celltalkdb/index.php</a></p></td>
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+  <section id="pypath-inputs-celltypist-celltypist-annotations">
+<h1>pypath.inputs.celltypist.celltypist_annotations<a class="headerlink" href="#pypath-inputs-celltypist-celltypist-annotations" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.inputs.celltypist.celltypist_annotations">
+<span class="sig-prename descclassname"><span class="pre">pypath.inputs.celltypist.</span></span><span class="sig-name descname"><span class="pre">celltypist_annotations</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/inputs/celltypist.html#celltypist_annotations"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.celltypist.celltypist_annotations" title="Link to this definition">§</a></dt>
+<dd><p>Immune cell type marker genes from Celltypist
+(<a class="github reference external" href="https://github.com/Teichlab/celltypist_wiki">Teichlab/celltypist_wiki</a>).</p>
+</dd></dl>
+
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+  <section id="module-pypath.inputs.celltypist">
+<span id="pypath-inputs-celltypist"></span><h1>pypath.inputs.celltypist<a class="headerlink" href="#module-pypath.inputs.celltypist" title="Link to this heading">§</a></h1>
+<dl class="field-list simple">
+<dt class="field-odd">members<span class="colon">:</span></dt>
+<dd class="field-odd"><p></p></dd>
+</dl>
+<p class="rubric">Functions</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.inputs.celltypist.celltypist_annotations.html#pypath.inputs.celltypist.celltypist_annotations" title="pypath.inputs.celltypist.celltypist_annotations"><code class="xref py py-obj docutils literal notranslate"><span class="pre">celltypist_annotations</span></code></a>()</p></td>
+<td><p>Immune cell type marker genes from Celltypist (<a class="github reference external" href="https://github.com/Teichlab/celltypist_wiki">Teichlab/celltypist_wiki</a>).</p></td>
+</tr>
+</tbody>
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diff --git a/api/pypath.inputs.chembl.html b/api/pypath.inputs.chembl.html
index 562a56e93..40c0a1b64 100644
--- a/api/pypath.inputs.chembl.html
+++ b/api/pypath.inputs.chembl.html
@@ -48,7 +48,7 @@
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-    <link rel="prev" title="pypath.inputs.cell.cell_supplementary" href="pypath.inputs.cell.cell_supplementary.html" />
+    <link rel="prev" title="pypath.inputs.celltypist.celltypist_annotations" href="pypath.inputs.celltypist.celltypist_annotations.html" />
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@@ -560,12 +560,12 @@
                   
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+       href="pypath.inputs.celltypist.celltypist_annotations.html"
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+        <p class="prev-next-title">pypath.inputs.celltypist.celltypist_annotations</p>
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diff --git a/api/pypath.inputs.clinvar.clinvar_raw.html b/api/pypath.inputs.clinvar.clinvar_raw.html
index b203db505..54832b358 100644
--- a/api/pypath.inputs.clinvar.clinvar_raw.html
+++ b/api/pypath.inputs.clinvar.clinvar_raw.html
@@ -47,7 +47,7 @@
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+    <link rel="next" title="pypath.inputs.collectri" href="pypath.inputs.collectri.html" />
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   <meta name="viewport" content="width=device-width, initial-scale=1"/>
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@@ -550,11 +550,11 @@ <h1>pypath.inputs.clinvar.clinvar_raw<a class="headerlink" href="#pypath-inputs-
       </div>
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+       href="pypath.inputs.collectri.html"
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+        <p class="prev-next-title">pypath.inputs.collectri</p>
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diff --git a/api/pypath.inputs.collectri.collectri_interactions.html b/api/pypath.inputs.collectri.collectri_interactions.html
new file mode 100644
index 000000000..9c15224e1
--- /dev/null
+++ b/api/pypath.inputs.collectri.collectri_interactions.html
@@ -0,0 +1,650 @@
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+<h1>pypath.inputs.collectri.collectri_interactions<a class="headerlink" href="#pypath-inputs-collectri-collectri-interactions" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.inputs.collectri.collectri_interactions">
+<span class="sig-prename descclassname"><span class="pre">pypath.inputs.collectri.</span></span><span class="sig-name descname"><span class="pre">collectri_interactions</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">protein_coding</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">mirna</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">tuple</span><span class="p"><span class="pre">]</span></span></span></span><a class="reference internal" href="../_modules/pypath/inputs/collectri.html#collectri_interactions"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.collectri.collectri_interactions" title="Link to this definition">§</a></dt>
+<dd><p>TF-target interactions from the CollecTRI database.</p>
+<p>While <cite>collectri_raw</cite> returns the records in the same format as in the
+original data, here we translate identifiers to UniProt IDs, and use
+<cite>Complex</cite> objects to represent protein complexes.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>protein_coding</strong> – Include regulation of protein coding genes.</p></li>
+<li><p><strong>mirna</strong> – Include regulation of miRNA coding genes.</p></li>
+</ul>
+</dd>
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+<h1>pypath.inputs.collectri.collectri_raw<a class="headerlink" href="#pypath-inputs-collectri-collectri-raw" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.inputs.collectri.collectri_raw">
+<span class="sig-prename descclassname"><span class="pre">pypath.inputs.collectri.</span></span><span class="sig-name descname"><span class="pre">collectri_raw</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">protein_coding</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">mirna</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">tuple</span><span class="p"><span class="pre">]</span></span></span></span><a class="reference internal" href="../_modules/pypath/inputs/collectri.html#collectri_raw"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.collectri.collectri_raw" title="Link to this definition">§</a></dt>
+<dd><p>TF-target interactions from the CollecTRI database.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>protein_coding</strong> – Include regulation of protein coding genes.</p></li>
+<li><p><strong>mirna</strong> – Include regulation of miRNA coding genes.</p></li>
+</ul>
+</dd>
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+              
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+                <article class="bd-article">
+                  
+  <section id="module-pypath.inputs.collectri">
+<span id="pypath-inputs-collectri"></span><h1>pypath.inputs.collectri<a class="headerlink" href="#module-pypath.inputs.collectri" title="Link to this heading">§</a></h1>
+<dl class="field-list simple">
+<dt class="field-odd">members<span class="colon">:</span></dt>
+<dd class="field-odd"><p></p></dd>
+</dl>
+<p class="rubric">Functions</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.inputs.collectri.collectri_interactions.html#pypath.inputs.collectri.collectri_interactions" title="pypath.inputs.collectri.collectri_interactions"><code class="xref py py-obj docutils literal notranslate"><span class="pre">collectri_interactions</span></code></a>([protein_coding, mirna])</p></td>
+<td><p>TF-target interactions from the CollecTRI database.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.inputs.collectri.collectri_raw.html#pypath.inputs.collectri.collectri_raw" title="pypath.inputs.collectri.collectri_raw"><code class="xref py py-obj docutils literal notranslate"><span class="pre">collectri_raw</span></code></a>([protein_coding, mirna])</p></td>
+<td><p>TF-target interactions from the CollecTRI database.</p></td>
+</tr>
+</tbody>
+</table>
+</section>
+
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diff --git a/api/pypath.inputs.common.html b/api/pypath.inputs.common.html
index f75a8b872..3480e35e0 100644
--- a/api/pypath.inputs.common.html
+++ b/api/pypath.inputs.common.html
@@ -48,7 +48,7 @@
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
     <link rel="next" title="pypath.inputs.common.csv_sep_change" href="pypath.inputs.common.csv_sep_change.html" />
-    <link rel="prev" title="pypath.inputs.clinvar.clinvar_raw" href="pypath.inputs.clinvar.clinvar_raw.html" />
+    <link rel="prev" title="pypath.inputs.collectri.collectri_raw" href="pypath.inputs.collectri.collectri_raw.html" />
   <meta name="viewport" content="width=device-width, initial-scale=1"/>
   <meta name="docsearch:language" content="en"/>
   </head>
@@ -557,12 +557,12 @@
                   
 <div class="prev-next-area">
     <a class="left-prev"
-       href="pypath.inputs.clinvar.clinvar_raw.html"
+       href="pypath.inputs.collectri.collectri_raw.html"
        title="previous page">
       <i class="fa-solid fa-angle-left"></i>
       <div class="prev-next-info">
         <p class="prev-next-subtitle">previous</p>
-        <p class="prev-next-title">pypath.inputs.clinvar.clinvar_raw</p>
+        <p class="prev-next-title">pypath.inputs.collectri.collectri_raw</p>
       </div>
     </a>
     <a class="right-next"
diff --git a/api/pypath.inputs.compath.compath_mappings.html b/api/pypath.inputs.compath.compath_mappings.html
index 521964b1d..94d9608af 100644
--- a/api/pypath.inputs.compath.compath_mappings.html
+++ b/api/pypath.inputs.compath.compath_mappings.html
@@ -47,7 +47,7 @@
     <link rel="icon" href="../_static/omnipath-logo.svg"/>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
-    <link rel="next" title="pypath.inputs.cpdb" href="pypath.inputs.cpdb.html" />
+    <link rel="next" title="pypath.inputs.compleat" href="pypath.inputs.compleat.html" />
     <link rel="prev" title="pypath.inputs.compath" href="pypath.inputs.compath.html" />
   <meta name="viewport" content="width=device-width, initial-scale=1"/>
   <meta name="docsearch:language" content="en"/>
@@ -560,11 +560,11 @@ <h1>pypath.inputs.compath.compath_mappings<a class="headerlink" href="#pypath-in
       </div>
     </a>
     <a class="right-next"
-       href="pypath.inputs.cpdb.html"
+       href="pypath.inputs.compleat.html"
        title="next page">
       <div class="prev-next-info">
         <p class="prev-next-subtitle">next</p>
-        <p class="prev-next-title">pypath.inputs.cpdb</p>
+        <p class="prev-next-title">pypath.inputs.compleat</p>
       </div>
       <i class="fa-solid fa-angle-right"></i>
     </a>
diff --git a/api/pypath.inputs.compleat.compleat_complexes.html b/api/pypath.inputs.compleat.compleat_complexes.html
new file mode 100644
index 000000000..4551652a0
--- /dev/null
+++ b/api/pypath.inputs.compleat.compleat_complexes.html
@@ -0,0 +1,639 @@
+
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+    document.documentElement.dataset.mode = localStorage.getItem("mode") || "";
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+  <section id="pypath-inputs-compleat-compleat-complexes">
+<h1>pypath.inputs.compleat.compleat_complexes<a class="headerlink" href="#pypath-inputs-compleat-compleat-complexes" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.inputs.compleat.compleat_complexes">
+<span class="sig-prename descclassname"><span class="pre">pypath.inputs.compleat.</span></span><span class="sig-name descname"><span class="pre">compleat_complexes</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">predicted</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/inputs/compleat.html#compleat_complexes"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.compleat.compleat_complexes" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves and processes protein complexes from the Compleat database.</p>
+</dd></dl>
+
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+
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+  <section id="pypath-inputs-compleat-compleat-raw">
+<h1>pypath.inputs.compleat.compleat_raw<a class="headerlink" href="#pypath-inputs-compleat-compleat-raw" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.inputs.compleat.compleat_raw">
+<span class="sig-prename descclassname"><span class="pre">pypath.inputs.compleat.</span></span><span class="sig-name descname"><span class="pre">compleat_raw</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/inputs/compleat.html#compleat_raw"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.compleat.compleat_raw" title="Link to this definition">§</a></dt>
+<dd><p>Raw protein complex data from the Compleat database.</p>
+</dd></dl>
+
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+<dt class="field-odd">members<span class="colon">:</span></dt>
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+<p class="rubric">Functions</p>
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+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.inputs.compleat.compleat_complexes.html#pypath.inputs.compleat.compleat_complexes" title="pypath.inputs.compleat.compleat_complexes"><code class="xref py py-obj docutils literal notranslate"><span class="pre">compleat_complexes</span></code></a>([predicted])</p></td>
+<td><p>Retrieves and processes protein complexes from the Compleat database.</p></td>
+</tr>
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+<td><p>Raw protein complex data from the Compleat database.</p></td>
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diff --git a/api/pypath.inputs.complexportal.complexportal_complexes.html b/api/pypath.inputs.complexportal.complexportal_complexes.html
new file mode 100644
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+  <section id="pypath-inputs-complexportal-complexportal-complexes">
+<h1>pypath.inputs.complexportal.complexportal_complexes<a class="headerlink" href="#pypath-inputs-complexportal-complexportal-complexes" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.inputs.complexportal.complexportal_complexes">
+<span class="sig-prename descclassname"><span class="pre">pypath.inputs.complexportal.</span></span><span class="sig-name descname"><span class="pre">complexportal_complexes</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">organism</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">return_details</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/inputs/complexportal.html#complexportal_complexes"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.complexportal.complexportal_complexes" title="Link to this definition">§</a></dt>
+<dd><p>Complex dataset from IntAct.
+See more:
+<a class="reference external" href="http://www.ebi.ac.uk/intact/complex/">http://www.ebi.ac.uk/intact/complex/</a>
+<a class="reference external" href="http://nar.oxfordjournals.org/content/early/2014/10/13/nar.gku975.full.pdf">http://nar.oxfordjournals.org/content/early/2014/10/13/nar.gku975.full.pdf</a></p>
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+  <section id="module-pypath.inputs.complexportal">
+<span id="pypath-inputs-complexportal"></span><h1>pypath.inputs.complexportal<a class="headerlink" href="#module-pypath.inputs.complexportal" title="Link to this heading">§</a></h1>
+<dl class="field-list simple">
+<dt class="field-odd">members<span class="colon">:</span></dt>
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+<p class="rubric">Functions</p>
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+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.inputs.complexportal.complexportal_complexes.html#pypath.inputs.complexportal.complexportal_complexes" title="pypath.inputs.complexportal.complexportal_complexes"><code class="xref py py-obj docutils literal notranslate"><span class="pre">complexportal_complexes</span></code></a>([organism, ...])</p></td>
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diff --git a/api/pypath.inputs.comppi.comppi_interaction_locations.html b/api/pypath.inputs.comppi.comppi_interaction_locations.html
new file mode 100644
index 000000000..42bfe33c7
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+  <section id="pypath-inputs-comppi-comppi-interaction-locations">
+<h1>pypath.inputs.comppi.comppi_interaction_locations<a class="headerlink" href="#pypath-inputs-comppi-comppi-interaction-locations" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.inputs.comppi.comppi_interaction_locations">
+<span class="sig-prename descclassname"><span class="pre">pypath.inputs.comppi.</span></span><span class="sig-name descname"><span class="pre">comppi_interaction_locations</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">organism</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/inputs/comppi.html#comppi_interaction_locations"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.comppi.comppi_interaction_locations" title="Link to this definition">§</a></dt>
+<dd><p>Downloads and preprocesses protein interaction and cellular compartment
+association data from the ComPPI database.
+This data provides scores for occurrence of protein-protein interactions
+in various compartments.</p>
+</dd></dl>
+
+</section>
+
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diff --git a/api/pypath.inputs.comppi.comppi_locations.html b/api/pypath.inputs.comppi.comppi_locations.html
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+  <section id="pypath-inputs-comppi-comppi-locations">
+<h1>pypath.inputs.comppi.comppi_locations<a class="headerlink" href="#pypath-inputs-comppi-comppi-locations" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.inputs.comppi.comppi_locations">
+<span class="sig-prename descclassname"><span class="pre">pypath.inputs.comppi.</span></span><span class="sig-name descname"><span class="pre">comppi_locations</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">organism</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">score_threshold</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0.7</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/inputs/comppi.html#comppi_locations"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.comppi.comppi_locations" title="Link to this definition">§</a></dt>
+<dd></dd></dl>
+
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+  <section id="module-pypath.inputs.comppi">
+<span id="pypath-inputs-comppi"></span><h1>pypath.inputs.comppi<a class="headerlink" href="#module-pypath.inputs.comppi" title="Link to this heading">§</a></h1>
+<dl class="field-list simple">
+<dt class="field-odd">members<span class="colon">:</span></dt>
+<dd class="field-odd"><p></p></dd>
+</dl>
+<p class="rubric">Functions</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.inputs.comppi.comppi_interaction_locations.html#pypath.inputs.comppi.comppi_interaction_locations" title="pypath.inputs.comppi.comppi_interaction_locations"><code class="xref py py-obj docutils literal notranslate"><span class="pre">comppi_interaction_locations</span></code></a>([organism])</p></td>
+<td><p>Downloads and preprocesses protein interaction and cellular compartment association data from the ComPPI database.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.inputs.comppi.comppi_locations.html#pypath.inputs.comppi.comppi_locations" title="pypath.inputs.comppi.comppi_locations"><code class="xref py py-obj docutils literal notranslate"><span class="pre">comppi_locations</span></code></a>([organism, score_threshold])</p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+</section>
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+  <section id="pypath-inputs-connectomedb-connectomedb-annotations">
+<h1>pypath.inputs.connectomedb.connectomedb_annotations<a class="headerlink" href="#pypath-inputs-connectomedb-connectomedb-annotations" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.inputs.connectomedb.connectomedb_annotations">
+<span class="sig-prename descclassname"><span class="pre">pypath.inputs.connectomedb.</span></span><span class="sig-name descname"><span class="pre">connectomedb_annotations</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/inputs/connectomedb.html#connectomedb_annotations"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.connectomedb.connectomedb_annotations" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves ligand and receptor annotations from connectomeDB2020
+<a class="reference external" href="https://asrhou.github.io/NATMI/">https://asrhou.github.io/NATMI/</a></p>
+</dd></dl>
+
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new file mode 100644
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+  <section id="pypath-inputs-connectomedb-connectomedb-interactions">
+<h1>pypath.inputs.connectomedb.connectomedb_interactions<a class="headerlink" href="#pypath-inputs-connectomedb-connectomedb-interactions" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.inputs.connectomedb.connectomedb_interactions">
+<span class="sig-prename descclassname"><span class="pre">pypath.inputs.connectomedb.</span></span><span class="sig-name descname"><span class="pre">connectomedb_interactions</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/inputs/connectomedb.html#connectomedb_interactions"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.connectomedb.connectomedb_interactions" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves ligand-receptor interactions from connectomeDB2020
+<a class="reference external" href="https://asrhou.github.io/NATMI/">https://asrhou.github.io/NATMI/</a></p>
+</dd></dl>
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+<td><p>Retrieves ligand-receptor interactions from connectomeDB2020 <a class="reference external" href="https://asrhou.github.io/NATMI/">https://asrhou.github.io/NATMI/</a></p></td>
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+<h1>pypath.inputs.corum.corum_complexes<a class="headerlink" href="#pypath-inputs-corum-corum-complexes" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.inputs.corum.corum_complexes">
+<span class="sig-prename descclassname"><span class="pre">pypath.inputs.corum.</span></span><span class="sig-name descname"><span class="pre">corum_complexes</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">organism</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/inputs/corum.html#corum_complexes"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.corum.corum_complexes" title="Link to this definition">§</a></dt>
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diff --git a/api/pypath.inputs.cosmic.cancer_gene_census_annotations.html b/api/pypath.inputs.cosmic.cancer_gene_census_annotations.html
new file mode 100644
index 000000000..7d483315a
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+  <section id="pypath-inputs-cosmic-cancer-gene-census-annotations">
+<h1>pypath.inputs.cosmic.cancer_gene_census_annotations<a class="headerlink" href="#pypath-inputs-cosmic-cancer-gene-census-annotations" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.inputs.cosmic.cancer_gene_census_annotations">
+<span class="sig-prename descclassname"><span class="pre">pypath.inputs.cosmic.</span></span><span class="sig-name descname"><span class="pre">cancer_gene_census_annotations</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">user</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">passwd</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">credentials_fname</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'cosmic_credentials'</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/inputs/cosmic.html#cancer_gene_census_annotations"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.cosmic.cancer_gene_census_annotations" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a list of cancer driver genes (Cancer Gene Census) from
+the Sanger COSMIC (Catalogue of Somatic Mutations in Cancer) database.
+Returns dict of annotations.</p>
+</dd></dl>
+
+</section>
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diff --git a/api/pypath.inputs.cpad.cpad_annotations.html b/api/pypath.inputs.cpad.cpad_annotations.html
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diff --git a/api/pypath.inputs.cpad.cpad_pathway_cancer.html b/api/pypath.inputs.cpad.cpad_pathway_cancer.html
new file mode 100644
index 000000000..f4548a720
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+  <section id="pypath-inputs-cpad-cpad-pathway-cancer">
+<h1>pypath.inputs.cpad.cpad_pathway_cancer<a class="headerlink" href="#pypath-inputs-cpad-cpad-pathway-cancer" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.inputs.cpad.cpad_pathway_cancer">
+<span class="sig-prename descclassname"><span class="pre">pypath.inputs.cpad.</span></span><span class="sig-name descname"><span class="pre">cpad_pathway_cancer</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/inputs/cpad.html#cpad_pathway_cancer"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.cpad.cpad_pathway_cancer" title="Link to this definition">§</a></dt>
+<dd><p>Collects only the pathway-cancer relationships. Returns sets of records
+grouped in dicts by cancer and by pathway.</p>
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+  <section id="module-pypath.inputs.cpad">
+<span id="pypath-inputs-cpad"></span><h1>pypath.inputs.cpad<a class="headerlink" href="#module-pypath.inputs.cpad" title="Link to this heading">§</a></h1>
+<dl class="field-list simple">
+<dt class="field-odd">members<span class="colon">:</span></dt>
+<dd class="field-odd"><p></p></dd>
+</dl>
+<p class="rubric">Functions</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.inputs.cpad.cpad_annotations.html#pypath.inputs.cpad.cpad_annotations" title="pypath.inputs.cpad.cpad_annotations"><code class="xref py py-obj docutils literal notranslate"><span class="pre">cpad_annotations</span></code></a>([include_unknown_type])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.inputs.cpad.cpad_pathway_cancer.html#pypath.inputs.cpad.cpad_pathway_cancer" title="pypath.inputs.cpad.cpad_pathway_cancer"><code class="xref py py-obj docutils literal notranslate"><span class="pre">cpad_pathway_cancer</span></code></a>()</p></td>
+<td><p>Collects only the pathway-cancer relationships.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.inputs.cpad.get_cpad.html#pypath.inputs.cpad.get_cpad" title="pypath.inputs.cpad.get_cpad"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_cpad</span></code></a>()</p></td>
+<td><p></p></td>
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diff --git a/api/pypath.inputs.cpdb.html b/api/pypath.inputs.cpdb.html
index 288e39807..390c97d60 100644
--- a/api/pypath.inputs.cpdb.html
+++ b/api/pypath.inputs.cpdb.html
@@ -48,7 +48,7 @@
     <link rel="index" title="Index" href="../genindex.html" />
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     <link rel="next" title="pypath.inputs.cpdb.cpdb_interactions" href="pypath.inputs.cpdb.cpdb_interactions.html" />
-    <link rel="prev" title="pypath.inputs.compath.compath_mappings" href="pypath.inputs.compath.compath_mappings.html" />
+    <link rel="prev" title="pypath.inputs.cpad.get_cpad" href="pypath.inputs.cpad.get_cpad.html" />
   <meta name="viewport" content="width=device-width, initial-scale=1"/>
   <meta name="docsearch:language" content="en"/>
   </head>
@@ -545,12 +545,12 @@
                   
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     <a class="left-prev"
-       href="pypath.inputs.compath.compath_mappings.html"
+       href="pypath.inputs.cpad.get_cpad.html"
        title="previous page">
       <i class="fa-solid fa-angle-left"></i>
       <div class="prev-next-info">
         <p class="prev-next-subtitle">previous</p>
-        <p class="prev-next-title">pypath.inputs.compath.compath_mappings</p>
+        <p class="prev-next-title">pypath.inputs.cpad.get_cpad</p>
       </div>
     </a>
     <a class="right-next"
diff --git a/api/pypath.inputs.credentials.credentials.html b/api/pypath.inputs.credentials.credentials.html
index 497490f25..d1be2ddc0 100644
--- a/api/pypath.inputs.credentials.credentials.html
+++ b/api/pypath.inputs.credentials.credentials.html
@@ -47,7 +47,7 @@
     <link rel="icon" href="../_static/omnipath-logo.svg"/>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
-    <link rel="next" title="pypath.inputs.ctdbase" href="pypath.inputs.ctdbase.html" />
+    <link rel="next" title="pypath.inputs.csa" href="pypath.inputs.csa.html" />
     <link rel="prev" title="pypath.inputs.credentials" href="pypath.inputs.credentials.html" />
   <meta name="viewport" content="width=device-width, initial-scale=1"/>
   <meta name="docsearch:language" content="en"/>
@@ -568,11 +568,11 @@ <h1>pypath.inputs.credentials.credentials<a class="headerlink" href="#pypath-inp
       </div>
     </a>
     <a class="right-next"
-       href="pypath.inputs.ctdbase.html"
+       href="pypath.inputs.csa.html"
        title="next page">
       <div class="prev-next-info">
         <p class="prev-next-subtitle">next</p>
-        <p class="prev-next-title">pypath.inputs.ctdbase</p>
+        <p class="prev-next-title">pypath.inputs.csa</p>
       </div>
       <i class="fa-solid fa-angle-right"></i>
     </a>
diff --git a/api/pypath.inputs.csa.get_csa.html b/api/pypath.inputs.csa.get_csa.html
new file mode 100644
index 000000000..e7f91c869
--- /dev/null
+++ b/api/pypath.inputs.csa.get_csa.html
@@ -0,0 +1,641 @@
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+  <section id="pypath-inputs-csa-get-csa">
+<h1>pypath.inputs.csa.get_csa<a class="headerlink" href="#pypath-inputs-csa-get-csa" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.inputs.csa.get_csa">
+<span class="sig-prename descclassname"><span class="pre">pypath.inputs.csa.</span></span><span class="sig-name descname"><span class="pre">get_csa</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">uniprots</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/inputs/csa.html#get_csa"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.csa.get_csa" title="Link to this definition">§</a></dt>
+<dd><p>Downloads and preprocesses catalytic sites data.
+This data tells which residues are involved in the catalytic
+activity of one protein.</p>
+</dd></dl>
+
+</section>
+
+
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diff --git a/api/pypath.inputs.csa.html b/api/pypath.inputs.csa.html
new file mode 100644
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diff --git a/api/pypath.inputs.cspa.cspa_annotations.html b/api/pypath.inputs.cspa.cspa_annotations.html
new file mode 100644
index 000000000..780c87e01
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diff --git a/api/pypath.inputs.cspa.cspa_cell_type_annotations.html b/api/pypath.inputs.cspa.cspa_cell_type_annotations.html
new file mode 100644
index 000000000..f9a837ea1
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+<dl class="py function">
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+<span class="sig-prename descclassname"><span class="pre">pypath.inputs.cspa.</span></span><span class="sig-name descname"><span class="pre">cspa_cell_type_annotations</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">organism</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/inputs/cspa.html#cspa_cell_type_annotations"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.cspa.cspa_cell_type_annotations" title="Link to this definition">§</a></dt>
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diff --git a/api/pypath.inputs.cspa.cspa_cell_types.html b/api/pypath.inputs.cspa.cspa_cell_types.html
new file mode 100644
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+<span class="sig-prename descclassname"><span class="pre">pypath.inputs.cspa.</span></span><span class="sig-name descname"><span class="pre">cspa_cell_types</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">organism</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/inputs/cspa.html#cspa_cell_types"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.cspa.cspa_cell_types" title="Link to this definition">§</a></dt>
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+                  
+  <section id="module-pypath.inputs.cspa">
+<span id="pypath-inputs-cspa"></span><h1>pypath.inputs.cspa<a class="headerlink" href="#module-pypath.inputs.cspa" title="Link to this heading">§</a></h1>
+<dl class="field-list simple">
+<dt class="field-odd">members<span class="colon">:</span></dt>
+<dd class="field-odd"><p></p></dd>
+</dl>
+<p class="rubric">Functions</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.inputs.cspa.cspa_annotations.html#pypath.inputs.cspa.cspa_annotations" title="pypath.inputs.cspa.cspa_annotations"><code class="xref py py-obj docutils literal notranslate"><span class="pre">cspa_annotations</span></code></a>([organism])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.inputs.cspa.cspa_cell_type_annotations.html#pypath.inputs.cspa.cspa_cell_type_annotations" title="pypath.inputs.cspa.cspa_cell_type_annotations"><code class="xref py py-obj docutils literal notranslate"><span class="pre">cspa_cell_type_annotations</span></code></a>([organism])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.inputs.cspa.cspa_cell_types.html#pypath.inputs.cspa.cspa_cell_types" title="pypath.inputs.cspa.cspa_cell_types"><code class="xref py py-obj docutils literal notranslate"><span class="pre">cspa_cell_types</span></code></a>([organism])</p></td>
+<td><p></p></td>
+</tr>
+</tbody>
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diff --git a/api/pypath.inputs.ctdbase.ctdbase_vocabulary.html b/api/pypath.inputs.ctdbase.ctdbase_vocabulary.html
index a00c44b10..198479477 100644
--- a/api/pypath.inputs.ctdbase.ctdbase_vocabulary.html
+++ b/api/pypath.inputs.ctdbase.ctdbase_vocabulary.html
@@ -47,7 +47,7 @@
     <link rel="icon" href="../_static/omnipath-logo.svg"/>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
-    <link rel="next" title="pypath.inputs.dbptm" href="pypath.inputs.dbptm.html" />
+    <link rel="next" title="pypath.inputs.cytosig" href="pypath.inputs.cytosig.html" />
     <link rel="prev" title="pypath.inputs.ctdbase.ctdbase_relations" href="pypath.inputs.ctdbase.ctdbase_relations.html" />
   <meta name="viewport" content="width=device-width, initial-scale=1"/>
   <meta name="docsearch:language" content="en"/>
@@ -559,11 +559,11 @@ <h1>pypath.inputs.ctdbase.ctdbase_vocabulary<a class="headerlink" href="#pypath-
       </div>
     </a>
     <a class="right-next"
-       href="pypath.inputs.dbptm.html"
+       href="pypath.inputs.cytosig.html"
        title="next page">
       <div class="prev-next-info">
         <p class="prev-next-subtitle">next</p>
-        <p class="prev-next-title">pypath.inputs.dbptm</p>
+        <p class="prev-next-title">pypath.inputs.cytosig</p>
       </div>
       <i class="fa-solid fa-angle-right"></i>
     </a>
diff --git a/api/pypath.inputs.ctdbase.html b/api/pypath.inputs.ctdbase.html
index a7881c1bf..bc9d555bc 100644
--- a/api/pypath.inputs.ctdbase.html
+++ b/api/pypath.inputs.ctdbase.html
@@ -48,7 +48,7 @@
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
     <link rel="next" title="pypath.inputs.ctdbase.ctdbase_relations" href="pypath.inputs.ctdbase.ctdbase_relations.html" />
-    <link rel="prev" title="pypath.inputs.credentials.credentials" href="pypath.inputs.credentials.credentials.html" />
+    <link rel="prev" title="pypath.inputs.cspa.cspa_cell_types" href="pypath.inputs.cspa.cspa_cell_types.html" />
   <meta name="viewport" content="width=device-width, initial-scale=1"/>
   <meta name="docsearch:language" content="en"/>
   </head>
@@ -545,12 +545,12 @@
                   
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     <a class="left-prev"
-       href="pypath.inputs.credentials.credentials.html"
+       href="pypath.inputs.cspa.cspa_cell_types.html"
        title="previous page">
       <i class="fa-solid fa-angle-left"></i>
       <div class="prev-next-info">
         <p class="prev-next-subtitle">previous</p>
-        <p class="prev-next-title">pypath.inputs.credentials.credentials</p>
+        <p class="prev-next-title">pypath.inputs.cspa.cspa_cell_types</p>
       </div>
     </a>
     <a class="right-next"
diff --git a/api/pypath.inputs.cytosig.cytosig_annotations.html b/api/pypath.inputs.cytosig.cytosig_annotations.html
new file mode 100644
index 000000000..c7f8a896d
--- /dev/null
+++ b/api/pypath.inputs.cytosig.cytosig_annotations.html
@@ -0,0 +1,644 @@
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+  <section id="pypath-inputs-cytosig-cytosig-annotations">
+<h1>pypath.inputs.cytosig.cytosig_annotations<a class="headerlink" href="#pypath-inputs-cytosig-cytosig-annotations" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.inputs.cytosig.cytosig_annotations">
+<span class="sig-prename descclassname"><span class="pre">pypath.inputs.cytosig.</span></span><span class="sig-name descname"><span class="pre">cytosig_annotations</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><span class="pre">dict</span></span></span><a class="reference internal" href="../_modules/pypath/inputs/cytosig.html#cytosig_annotations"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.cytosig.cytosig_annotations" title="Link to this definition">§</a></dt>
+<dd><p>CytoSig is a compendium of expression signatures from cytokine
+perturbation experiments.</p>
+<dl class="simple">
+<dt>Returns</dt><dd><p>Dict of sets of annotations.</p>
+</dd>
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+
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+<h1>pypath.inputs.cytosig.cytosig_df<a class="headerlink" href="#pypath-inputs-cytosig-cytosig-df" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.inputs.cytosig.cytosig_df">
+<span class="sig-prename descclassname"><span class="pre">pypath.inputs.cytosig.</span></span><span class="sig-name descname"><span class="pre">cytosig_df</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">long</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><span class="pre">DataFrame</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">Series</span></span></span><a class="reference internal" href="../_modules/pypath/inputs/cytosig.html#cytosig_df"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.cytosig.cytosig_df" title="Link to this definition">§</a></dt>
+<dd><p>CytoSig core data is a matrix of cytokines vs. targets. Here this matrix
+is returned as a pandas data frame, either in a wide or long format.</p>
+<dl class="simple">
+<dt>Args</dt><dd><p>long: Convert the data frame to long format.</p>
+</dd>
+<dt>Returns</dt><dd><p>The original matrix format data frame (rows are signature genes,
+columns are cytokines) by default; if <cite>long</cite> is <cite>True</cite>, a series
+with multi index is returned.</p>
+</dd>
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+<span id="pypath-inputs-cytosig"></span><h1>pypath.inputs.cytosig<a class="headerlink" href="#module-pypath.inputs.cytosig" title="Link to this heading">§</a></h1>
+<dl class="field-list simple">
+<dt class="field-odd">members<span class="colon">:</span></dt>
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+</dl>
+<p class="rubric">Functions</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.inputs.cytosig.cytosig_annotations.html#pypath.inputs.cytosig.cytosig_annotations" title="pypath.inputs.cytosig.cytosig_annotations"><code class="xref py py-obj docutils literal notranslate"><span class="pre">cytosig_annotations</span></code></a>()</p></td>
+<td><p>CytoSig is a compendium of expression signatures from cytokine perturbation experiments.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.inputs.cytosig.cytosig_df.html#pypath.inputs.cytosig.cytosig_df" title="pypath.inputs.cytosig.cytosig_df"><code class="xref py py-obj docutils literal notranslate"><span class="pre">cytosig_df</span></code></a>([long])</p></td>
+<td><p>CytoSig core data is a matrix of cytokines vs.</p></td>
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diff --git a/api/pypath.inputs.dbptm.html b/api/pypath.inputs.dbptm.html
index 5f8943beb..2123ee108 100644
--- a/api/pypath.inputs.dbptm.html
+++ b/api/pypath.inputs.dbptm.html
@@ -48,7 +48,7 @@
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   <meta name="viewport" content="width=device-width, initial-scale=1"/>
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@@ -548,12 +548,12 @@
                   
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+       href="pypath.inputs.cytosig.cytosig_df.html"
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diff --git a/api/pypath.inputs.deathdomain.deathdomain_interactions_rescued.html b/api/pypath.inputs.deathdomain.deathdomain_interactions_rescued.html
index e537ce707..eae9dc888 100644
--- a/api/pypath.inputs.deathdomain.deathdomain_interactions_rescued.html
+++ b/api/pypath.inputs.deathdomain.deathdomain_interactions_rescued.html
@@ -47,7 +47,7 @@
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+    <link rel="next" title="pypath.inputs.depod" href="pypath.inputs.depod.html" />
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   <meta name="viewport" content="width=device-width, initial-scale=1"/>
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@@ -545,11 +545,11 @@ <h1>pypath.inputs.deathdomain.deathdomain_interactions_rescued<a class="headerli
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-       href="pypath.inputs.dip.html"
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diff --git a/api/pypath.inputs.depod.depod_enzyme_substrate.html b/api/pypath.inputs.depod.depod_enzyme_substrate.html
new file mode 100644
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--- /dev/null
+++ b/api/pypath.inputs.depod.depod_enzyme_substrate.html
@@ -0,0 +1,638 @@
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diff --git a/api/pypath.inputs.depod.depod_interactions.html b/api/pypath.inputs.depod.depod_interactions.html
new file mode 100644
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diff --git a/api/pypath.inputs.depod.html b/api/pypath.inputs.depod.html
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diff --git a/api/pypath.inputs.dgidb.dgidb_annotations.html b/api/pypath.inputs.dgidb.dgidb_annotations.html
new file mode 100644
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+  <section id="pypath-inputs-dgidb-dgidb-annotations">
+<h1>pypath.inputs.dgidb.dgidb_annotations<a class="headerlink" href="#pypath-inputs-dgidb-dgidb-annotations" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.inputs.dgidb.dgidb_annotations">
+<span class="sig-prename descclassname"><span class="pre">pypath.inputs.dgidb.</span></span><span class="sig-name descname"><span class="pre">dgidb_annotations</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/inputs/dgidb.html#dgidb_annotations"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.dgidb.dgidb_annotations" title="Link to this definition">§</a></dt>
+<dd><p>Downloads druggable protein annotations from DGIdb.</p>
+</dd></dl>
+
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+
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diff --git a/api/pypath.inputs.dgidb.dgidb_interactions.html b/api/pypath.inputs.dgidb.dgidb_interactions.html
new file mode 100644
index 000000000..2f78a8229
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+<h1>pypath.inputs.dgidb.dgidb_interactions<a class="headerlink" href="#pypath-inputs-dgidb-dgidb-interactions" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.inputs.dgidb.dgidb_interactions">
+<span class="sig-prename descclassname"><span class="pre">pypath.inputs.dgidb.</span></span><span class="sig-name descname"><span class="pre">dgidb_interactions</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">tuple</span><span class="p"><span class="pre">]</span></span></span></span><a class="reference internal" href="../_modules/pypath/inputs/dgidb.html#dgidb_interactions"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.dgidb.dgidb_interactions" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves drug-gene interactions from DGIdb.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Returns<span class="colon">:</span></dt>
+<dd class="field-odd"><p>A list with tuples. Tuples are dgidb interactons</p>
+</dd>
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+<h1>pypath.inputs.dgidb.get_dgidb_old<a class="headerlink" href="#pypath-inputs-dgidb-get-dgidb-old" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.inputs.dgidb.get_dgidb_old">
+<span class="sig-prename descclassname"><span class="pre">pypath.inputs.dgidb.</span></span><span class="sig-name descname"><span class="pre">get_dgidb_old</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/inputs/dgidb.html#get_dgidb_old"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.dgidb.get_dgidb_old" title="Link to this definition">§</a></dt>
+<dd><p>Deprecated. Will be removed soon.</p>
+<p>Downloads and processes the list of all human druggable proteins.
+Returns a list of GeneSymbols.</p>
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+                  
+  <section id="module-pypath.inputs.dgidb">
+<span id="pypath-inputs-dgidb"></span><h1>pypath.inputs.dgidb<a class="headerlink" href="#module-pypath.inputs.dgidb" title="Link to this heading">§</a></h1>
+<dl class="field-list simple">
+<dt class="field-odd">members<span class="colon">:</span></dt>
+<dd class="field-odd"><p></p></dd>
+</dl>
+<p class="rubric">Functions</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.inputs.dgidb.dgidb_annotations.html#pypath.inputs.dgidb.dgidb_annotations" title="pypath.inputs.dgidb.dgidb_annotations"><code class="xref py py-obj docutils literal notranslate"><span class="pre">dgidb_annotations</span></code></a>()</p></td>
+<td><p>Downloads druggable protein annotations from DGIdb.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.inputs.dgidb.dgidb_interactions.html#pypath.inputs.dgidb.dgidb_interactions" title="pypath.inputs.dgidb.dgidb_interactions"><code class="xref py py-obj docutils literal notranslate"><span class="pre">dgidb_interactions</span></code></a>()</p></td>
+<td><p>Retrieves drug-gene interactions from DGIdb.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.inputs.dgidb.get_dgidb_old.html#pypath.inputs.dgidb.get_dgidb_old" title="pypath.inputs.dgidb.get_dgidb_old"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_dgidb_old</span></code></a>()</p></td>
+<td><p>Deprecated.</p></td>
+</tr>
+</tbody>
+</table>
+</section>
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+
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diff --git a/api/pypath.inputs.dip.html b/api/pypath.inputs.dip.html
index c9ac439fb..2f0c54eed 100644
--- a/api/pypath.inputs.dip.html
+++ b/api/pypath.inputs.dip.html
@@ -48,7 +48,7 @@
     <link rel="index" title="Index" href="../genindex.html" />
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     <link rel="next" title="pypath.inputs.dip.dip_interactions" href="pypath.inputs.dip.dip_interactions.html" />
-    <link rel="prev" title="pypath.inputs.deathdomain.deathdomain_interactions_rescued" href="pypath.inputs.deathdomain.deathdomain_interactions_rescued.html" />
+    <link rel="prev" title="pypath.inputs.dgidb.get_dgidb_old" href="pypath.inputs.dgidb.get_dgidb_old.html" />
   <meta name="viewport" content="width=device-width, initial-scale=1"/>
   <meta name="docsearch:language" content="en"/>
   </head>
@@ -545,12 +545,12 @@
                   
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-       href="pypath.inputs.deathdomain.deathdomain_interactions_rescued.html"
+       href="pypath.inputs.dgidb.get_dgidb_old.html"
        title="previous page">
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       <div class="prev-next-info">
         <p class="prev-next-subtitle">previous</p>
-        <p class="prev-next-title">pypath.inputs.deathdomain.deathdomain_interactions_rescued</p>
+        <p class="prev-next-title">pypath.inputs.dgidb.get_dgidb_old</p>
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     </a>
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diff --git a/api/pypath.inputs.diseases.textmining_full.html b/api/pypath.inputs.diseases.textmining_full.html
index d4bb92061..441f1fbbf 100644
--- a/api/pypath.inputs.diseases.textmining_full.html
+++ b/api/pypath.inputs.diseases.textmining_full.html
@@ -47,7 +47,7 @@
     <link rel="icon" href="../_static/omnipath-logo.svg"/>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
-    <link rel="next" title="pypath.inputs.dorothea" href="pypath.inputs.dorothea.html" />
+    <link rel="next" title="pypath.inputs.domino" href="pypath.inputs.domino.html" />
     <link rel="prev" title="pypath.inputs.diseases.textmining_filtered" href="pypath.inputs.diseases.textmining_filtered.html" />
   <meta name="viewport" content="width=device-width, initial-scale=1"/>
   <meta name="docsearch:language" content="en"/>
@@ -551,11 +551,11 @@ <h1>pypath.inputs.diseases.textmining_full<a class="headerlink" href="#pypath-in
       </div>
     </a>
     <a class="right-next"
-       href="pypath.inputs.dorothea.html"
+       href="pypath.inputs.domino.html"
        title="next page">
       <div class="prev-next-info">
         <p class="prev-next-subtitle">next</p>
-        <p class="prev-next-title">pypath.inputs.dorothea</p>
+        <p class="prev-next-title">pypath.inputs.domino</p>
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diff --git a/api/pypath.inputs.domino.domino_ddi.html b/api/pypath.inputs.domino.domino_ddi.html
new file mode 100644
index 000000000..f2db8811d
--- /dev/null
+++ b/api/pypath.inputs.domino.domino_ddi.html
@@ -0,0 +1,638 @@
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+  <section id="pypath-inputs-domino-domino-ddi">
+<h1>pypath.inputs.domino.domino_ddi<a class="headerlink" href="#pypath-inputs-domino-domino-ddi" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.inputs.domino.domino_ddi">
+<span class="sig-prename descclassname"><span class="pre">pypath.inputs.domino.</span></span><span class="sig-name descname"><span class="pre">domino_ddi</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/inputs/domino.html#domino_ddi"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.domino.domino_ddi" title="Link to this definition">§</a></dt>
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+<h1>pypath.inputs.domino.domino_enzsub<a class="headerlink" href="#pypath-inputs-domino-domino-enzsub" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.inputs.domino.domino_enzsub">
+<span class="sig-prename descclassname"><span class="pre">pypath.inputs.domino.</span></span><span class="sig-name descname"><span class="pre">domino_enzsub</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/inputs/domino.html#domino_enzsub"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.domino.domino_enzsub" title="Link to this definition">§</a></dt>
+<dd><dl class="simple">
+<dt>Returns</dt><dd><p>A dict of two elements: <cite>ddi</cite> contains domain-domain, while <cite>dmi</cite>
+domain-motif interactions. The latter includes protein-PTM
+interactions.</p>
+</dd>
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+<h1>pypath.inputs.domino.get_domino<a class="headerlink" href="#pypath-inputs-domino-get-domino" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.inputs.domino.get_domino">
+<span class="sig-prename descclassname"><span class="pre">pypath.inputs.domino.</span></span><span class="sig-name descname"><span class="pre">get_domino</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">none_values</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">outfile</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/inputs/domino.html#get_domino"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.domino.get_domino" title="Link to this definition">§</a></dt>
+<dd><dl class="simple">
+<dt>Returns</dt><dd><p>A list of records with the following fields:
+header = [‘uniprot_A’, ‘uniprot_B’, ‘isoform_A’, ‘isoform_B’, #3
+‘exp_method’, ‘references’, ‘taxon_A’, ‘taxon_B’, #7
+‘role_A’, ‘role_B’, ‘binding_site_range_A’, ‘binding_site_range_B’, #11
+‘domains_A’, ‘domains_B’, ‘ptm_residue_A’, ‘ptm_residue_B’, #15
+‘ptm_type_mi_A’, ‘ptm_type_mi_B’, ‘ptm_type_A’, ‘ptm_type_B’, #19
+‘ptm_res_name_A’, ‘ptm_res_name_B’, ‘mutations_A’, ‘mutations_B’, #23
+‘mutation_effects_A’, ‘mutation_effects_B’, ‘domains_interpro_A’, #26
+‘domains_interpro_B’, ‘negative’] #28</p>
+</dd>
+</dl>
+</dd></dl>
+
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diff --git a/api/pypath.inputs.domino.html b/api/pypath.inputs.domino.html
new file mode 100644
index 000000000..69f3f9849
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+                  
+  <section id="module-pypath.inputs.domino">
+<span id="pypath-inputs-domino"></span><h1>pypath.inputs.domino<a class="headerlink" href="#module-pypath.inputs.domino" title="Link to this heading">§</a></h1>
+<dl class="field-list simple">
+<dt class="field-odd">members<span class="colon">:</span></dt>
+<dd class="field-odd"><p></p></dd>
+</dl>
+<p class="rubric">Functions</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.inputs.domino.domino_ddi.html#pypath.inputs.domino.domino_ddi" title="pypath.inputs.domino.domino_ddi"><code class="xref py py-obj docutils literal notranslate"><span class="pre">domino_ddi</span></code></a>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.inputs.domino.domino_enzsub.html#pypath.inputs.domino.domino_enzsub" title="pypath.inputs.domino.domino_enzsub"><code class="xref py py-obj docutils literal notranslate"><span class="pre">domino_enzsub</span></code></a>()</p></td>
+<td><p>Returns</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.inputs.domino.domino_interactions.html#pypath.inputs.domino.domino_interactions" title="pypath.inputs.domino.domino_interactions"><code class="xref py py-obj docutils literal notranslate"><span class="pre">domino_interactions</span></code></a>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.inputs.domino.get_domino.html#pypath.inputs.domino.get_domino" title="pypath.inputs.domino.get_domino"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_domino</span></code></a>([none_values, outfile])</p></td>
+<td><p>Returns</p></td>
+</tr>
+</tbody>
+</table>
+</section>
+
+
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diff --git a/api/pypath.inputs.dorothea.html b/api/pypath.inputs.dorothea.html
index 9136afd62..897cae499 100644
--- a/api/pypath.inputs.dorothea.html
+++ b/api/pypath.inputs.dorothea.html
@@ -48,7 +48,7 @@
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-    <link rel="prev" title="pypath.inputs.diseases.textmining_full" href="pypath.inputs.diseases.textmining_full.html" />
+    <link rel="prev" title="pypath.inputs.domino.get_domino" href="pypath.inputs.domino.get_domino.html" />
   <meta name="viewport" content="width=device-width, initial-scale=1"/>
   <meta name="docsearch:language" content="en"/>
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@@ -582,12 +582,12 @@
                   
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-       href="pypath.inputs.diseases.textmining_full.html"
+       href="pypath.inputs.domino.get_domino.html"
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         <p class="prev-next-subtitle">previous</p>
-        <p class="prev-next-title">pypath.inputs.diseases.textmining_full</p>
+        <p class="prev-next-title">pypath.inputs.domino.get_domino</p>
       </div>
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diff --git a/api/pypath.inputs.embopress.embopress_supplementary.html b/api/pypath.inputs.embopress.embopress_supplementary.html
index aaef73f58..c242a7265 100644
--- a/api/pypath.inputs.embopress.embopress_supplementary.html
+++ b/api/pypath.inputs.embopress.embopress_supplementary.html
@@ -47,7 +47,7 @@
     <link rel="icon" href="../_static/omnipath-logo.svg"/>
     <link rel="index" title="Index" href="../genindex.html" />
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-    <link rel="next" title="pypath.inputs.encode" href="pypath.inputs.encode.html" />
+    <link rel="next" title="pypath.inputs.embrace" href="pypath.inputs.embrace.html" />
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   <meta name="viewport" content="width=device-width, initial-scale=1"/>
   <meta name="docsearch:language" content="en"/>
@@ -544,11 +544,11 @@ <h1>pypath.inputs.embopress.embopress_supplementary<a class="headerlink" href="#
       </div>
     </a>
     <a class="right-next"
-       href="pypath.inputs.encode.html"
+       href="pypath.inputs.embrace.html"
        title="next page">
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-        <p class="prev-next-title">pypath.inputs.encode</p>
+        <p class="prev-next-title">pypath.inputs.embrace</p>
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diff --git a/api/pypath.inputs.embrace.embrace_annotations.html b/api/pypath.inputs.embrace.embrace_annotations.html
new file mode 100644
index 000000000..c3f1fc2ba
--- /dev/null
+++ b/api/pypath.inputs.embrace.embrace_annotations.html
@@ -0,0 +1,643 @@
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+    <script>DOCUMENTATION_OPTIONS.pagename = 'api/pypath.inputs.embrace.embrace_annotations';</script>
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+<h1>pypath.inputs.embrace.embrace_annotations<a class="headerlink" href="#pypath-inputs-embrace-embrace-annotations" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.inputs.embrace.embrace_annotations">
+<span class="sig-prename descclassname"><span class="pre">pypath.inputs.embrace.</span></span><span class="sig-name descname"><span class="pre">embrace_annotations</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">organism</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/inputs/embrace.html#embrace_annotations"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.embrace.embrace_annotations" title="Link to this definition">§</a></dt>
+<dd><p>Returns protein annotations from Supplementary Table S11 of
+10.1016/j.isci.2019.10.026 (Sheikh et al. 2019) translated to UniProt IDs
+of the requested organism.
+Returns dict with UniProt IDs as keys and sets of annotation tuples as
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diff --git a/api/pypath.inputs.embrace.embrace_interactions.html b/api/pypath.inputs.embrace.embrace_interactions.html
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+<h1>pypath.inputs.embrace.embrace_interactions<a class="headerlink" href="#pypath-inputs-embrace-embrace-interactions" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.inputs.embrace.embrace_interactions">
+<span class="sig-prename descclassname"><span class="pre">pypath.inputs.embrace.</span></span><span class="sig-name descname"><span class="pre">embrace_interactions</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">organism</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/inputs/embrace.html#embrace_interactions"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.embrace.embrace_interactions" title="Link to this definition">§</a></dt>
+<dd><p>Returns ligand-receptor interactions from Supplementary Table S11 of
+10.1016/j.isci.2019.10.026 (Sheikh et al. 2019) translated to UniProt IDs
+of the requested organism.</p>
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+<h1>pypath.inputs.embrace.embrace_raw<a class="headerlink" href="#pypath-inputs-embrace-embrace-raw" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.inputs.embrace.embrace_raw">
+<span class="sig-prename descclassname"><span class="pre">pypath.inputs.embrace.</span></span><span class="sig-name descname"><span class="pre">embrace_raw</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/inputs/embrace.html#embrace_raw"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.embrace.embrace_raw" title="Link to this definition">§</a></dt>
+<dd><p>Returns Supplementary Table S11 from 10.1016/j.isci.2019.10.026
+(Sheikh et al. 2019) as a list of tuples.</p>
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+<h1>pypath.inputs.embrace.embrace_translated<a class="headerlink" href="#pypath-inputs-embrace-embrace-translated" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.inputs.embrace.embrace_translated">
+<span class="sig-prename descclassname"><span class="pre">pypath.inputs.embrace.</span></span><span class="sig-name descname"><span class="pre">embrace_translated</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">organism</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/inputs/embrace.html#embrace_translated"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.embrace.embrace_translated" title="Link to this definition">§</a></dt>
+<dd><p>Returns Supplementary Table S11 from 10.1016/j.isci.2019.10.026
+(Sheikh et al. 2019) translated to UniProt IDs of the requested organism.</p>
+</dd></dl>
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+                <article class="bd-article">
+                  
+  <section id="module-pypath.inputs.embrace">
+<span id="pypath-inputs-embrace"></span><h1>pypath.inputs.embrace<a class="headerlink" href="#module-pypath.inputs.embrace" title="Link to this heading">§</a></h1>
+<dl class="field-list simple">
+<dt class="field-odd">members<span class="colon">:</span></dt>
+<dd class="field-odd"><p></p></dd>
+</dl>
+<p class="rubric">Functions</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.inputs.embrace.embrace_annotations.html#pypath.inputs.embrace.embrace_annotations" title="pypath.inputs.embrace.embrace_annotations"><code class="xref py py-obj docutils literal notranslate"><span class="pre">embrace_annotations</span></code></a>([organism, ncbi_tax_id])</p></td>
+<td><p>Returns protein annotations from Supplementary Table S11 of 10.1016/j.isci.2019.10.026 (Sheikh et al. 2019) translated to UniProt IDs of the requested organism.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.inputs.embrace.embrace_interactions.html#pypath.inputs.embrace.embrace_interactions" title="pypath.inputs.embrace.embrace_interactions"><code class="xref py py-obj docutils literal notranslate"><span class="pre">embrace_interactions</span></code></a>([organism])</p></td>
+<td><p>Returns ligand-receptor interactions from Supplementary Table S11 of 10.1016/j.isci.2019.10.026 (Sheikh et al. 2019) translated to UniProt IDs of the requested organism.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.inputs.embrace.embrace_raw.html#pypath.inputs.embrace.embrace_raw" title="pypath.inputs.embrace.embrace_raw"><code class="xref py py-obj docutils literal notranslate"><span class="pre">embrace_raw</span></code></a>()</p></td>
+<td><p>Returns Supplementary Table S11 from 10.1016/j.isci.2019.10.026 (Sheikh et al. 2019) as a list of tuples.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.inputs.embrace.embrace_translated.html#pypath.inputs.embrace.embrace_translated" title="pypath.inputs.embrace.embrace_translated"><code class="xref py py-obj docutils literal notranslate"><span class="pre">embrace_translated</span></code></a>([organism])</p></td>
+<td><p>Returns Supplementary Table S11 from 10.1016/j.isci.2019.10.026 (Sheikh et al. 2019) translated to UniProt IDs of the requested organism.</p></td>
+</tr>
+</tbody>
+</table>
+</section>
+
+
+                </article>
+              
+              
+              
+              
+              
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diff --git a/api/pypath.inputs.encode.html b/api/pypath.inputs.encode.html
index c44af24b3..54da1e325 100644
--- a/api/pypath.inputs.encode.html
+++ b/api/pypath.inputs.encode.html
@@ -48,7 +48,7 @@
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
     <link rel="next" title="pypath.inputs.encode.encode_tf_mirna_interactions" href="pypath.inputs.encode.encode_tf_mirna_interactions.html" />
-    <link rel="prev" title="pypath.inputs.embopress.embopress_supplementary" href="pypath.inputs.embopress.embopress_supplementary.html" />
+    <link rel="prev" title="pypath.inputs.embrace.embrace_translated" href="pypath.inputs.embrace.embrace_translated.html" />
   <meta name="viewport" content="width=device-width, initial-scale=1"/>
   <meta name="docsearch:language" content="en"/>
   </head>
@@ -542,12 +542,12 @@
                   
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     <a class="left-prev"
-       href="pypath.inputs.embopress.embopress_supplementary.html"
+       href="pypath.inputs.embrace.embrace_translated.html"
        title="previous page">
       <i class="fa-solid fa-angle-left"></i>
       <div class="prev-next-info">
         <p class="prev-next-subtitle">previous</p>
-        <p class="prev-next-title">pypath.inputs.embopress.embopress_supplementary</p>
+        <p class="prev-next-title">pypath.inputs.embrace.embrace_translated</p>
       </div>
     </a>
     <a class="right-next"
diff --git a/api/pypath.inputs.graphviz.graphviz_attrs.html b/api/pypath.inputs.graphviz.graphviz_attrs.html
index a33158a3e..b0a7391b4 100644
--- a/api/pypath.inputs.graphviz.graphviz_attrs.html
+++ b/api/pypath.inputs.graphviz.graphviz_attrs.html
@@ -47,7 +47,7 @@
     <link rel="icon" href="../_static/omnipath-logo.svg"/>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
-    <link rel="next" title="pypath.inputs.hmdb" href="pypath.inputs.hmdb.html" />
+    <link rel="next" title="pypath.inputs.guide2pharma" href="pypath.inputs.guide2pharma.html" />
     <link rel="prev" title="pypath.inputs.graphviz" href="pypath.inputs.graphviz.html" />
   <meta name="viewport" content="width=device-width, initial-scale=1"/>
   <meta name="docsearch:language" content="en"/>
@@ -546,11 +546,11 @@ <h1>pypath.inputs.graphviz.graphviz_attrs<a class="headerlink" href="#pypath-inp
       </div>
     </a>
     <a class="right-next"
-       href="pypath.inputs.hmdb.html"
+       href="pypath.inputs.guide2pharma.html"
        title="next page">
       <div class="prev-next-info">
         <p class="prev-next-subtitle">next</p>
-        <p class="prev-next-title">pypath.inputs.hmdb</p>
+        <p class="prev-next-title">pypath.inputs.guide2pharma</p>
       </div>
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+<h1>pypath.inputs.guide2pharma.guide2pharma_complexes<a class="headerlink" href="#pypath-inputs-guide2pharma-guide2pharma-complexes" title="Link to this heading">§</a></h1>
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+<span class="sig-prename descclassname"><span class="pre">pypath.inputs.guide2pharma.</span></span><span class="sig-name descname"><span class="pre">guide2pharma_complexes</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/inputs/guide2pharma.html#guide2pharma_complexes"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.guide2pharma.guide2pharma_complexes" title="Link to this definition">§</a></dt>
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+  <section id="pypath-inputs-guide2pharma-guide2pharma-download">
+<h1>pypath.inputs.guide2pharma.guide2pharma_download<a class="headerlink" href="#pypath-inputs-guide2pharma-guide2pharma-download" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.inputs.guide2pharma.guide2pharma_download">
+<span class="sig-prename descclassname"><span class="pre">pypath.inputs.guide2pharma.</span></span><span class="sig-name descname"><span class="pre">guide2pharma_download</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">organism</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">int</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">'human'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">endogenous</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">process_interactions</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">process_complexes</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><span class="pre">tuple</span><span class="p"><span class="pre">[</span></span><span class="pre">list</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">dict</span><span class="p"><span class="pre">]</span></span></span></span><a class="reference internal" href="../_modules/pypath/inputs/guide2pharma.html#guide2pharma_download"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.guide2pharma.guide2pharma_download" title="Link to this definition">§</a></dt>
+<dd><p>Downloads and processes Guide to Pharmacology data.
+Returns list of dicts.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>organism</strong> – Name of the organism, e.g. <cite>human</cite>.</p></li>
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diff --git a/api/pypath.inputs.guide2pharma.html b/api/pypath.inputs.guide2pharma.html
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diff --git a/api/pypath.inputs.gutmgene.GutmgeneAnnotation.html b/api/pypath.inputs.gutmgene.GutmgeneAnnotation.html
new file mode 100644
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+  <section id="pypath-inputs-gutmgene-gutmgeneannotation">
+<h1>pypath.inputs.gutmgene.GutmgeneAnnotation<a class="headerlink" href="#pypath-inputs-gutmgene-gutmgeneannotation" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.inputs.gutmgene.GutmgeneAnnotation">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.inputs.gutmgene.</span></span><span class="sig-name descname"><span class="pre">GutmgeneAnnotation</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">microbe_taxon</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">microbe_ncbi_tax_id</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">gut_microbiota_id</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">classification</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">effect</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">throughput</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/inputs/gutmgene.html#GutmgeneAnnotation"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.gutmgene.GutmgeneAnnotation" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">NamedTuple</span></code></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.inputs.gutmgene.GutmgeneAnnotation.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.inputs.gutmgene.GutmgeneAnnotation.__init__" title="Link to this definition">§</a></dt>
+<dd></dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.inputs.gutmgene.GutmgeneAnnotation.__init__" title="pypath.inputs.gutmgene.GutmgeneAnnotation.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.inputs.gutmgene.GutmgeneAnnotation.count" title="pypath.inputs.gutmgene.GutmgeneAnnotation.count"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count</span></code></a>(value, /)</p></td>
+<td><p>Return number of occurrences of value.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.inputs.gutmgene.GutmgeneAnnotation.index" title="pypath.inputs.gutmgene.GutmgeneAnnotation.index"><code class="xref py py-obj docutils literal notranslate"><span class="pre">index</span></code></a>(value[, start, stop])</p></td>
+<td><p>Return first index of value.</p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Attributes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.inputs.gutmgene.GutmgeneAnnotation.classification" title="pypath.inputs.gutmgene.GutmgeneAnnotation.classification"><code class="xref py py-obj docutils literal notranslate"><span class="pre">classification</span></code></a></p></td>
+<td><p>Alias for field number 3</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.inputs.gutmgene.GutmgeneAnnotation.effect" title="pypath.inputs.gutmgene.GutmgeneAnnotation.effect"><code class="xref py py-obj docutils literal notranslate"><span class="pre">effect</span></code></a></p></td>
+<td><p>Alias for field number 4</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.inputs.gutmgene.GutmgeneAnnotation.gut_microbiota_id" title="pypath.inputs.gutmgene.GutmgeneAnnotation.gut_microbiota_id"><code class="xref py py-obj docutils literal notranslate"><span class="pre">gut_microbiota_id</span></code></a></p></td>
+<td><p>Alias for field number 2</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.inputs.gutmgene.GutmgeneAnnotation.microbe_ncbi_tax_id" title="pypath.inputs.gutmgene.GutmgeneAnnotation.microbe_ncbi_tax_id"><code class="xref py py-obj docutils literal notranslate"><span class="pre">microbe_ncbi_tax_id</span></code></a></p></td>
+<td><p>Alias for field number 1</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.inputs.gutmgene.GutmgeneAnnotation.microbe_taxon" title="pypath.inputs.gutmgene.GutmgeneAnnotation.microbe_taxon"><code class="xref py py-obj docutils literal notranslate"><span class="pre">microbe_taxon</span></code></a></p></td>
+<td><p>Alias for field number 0</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.inputs.gutmgene.GutmgeneAnnotation.throughput" title="pypath.inputs.gutmgene.GutmgeneAnnotation.throughput"><code class="xref py py-obj docutils literal notranslate"><span class="pre">throughput</span></code></a></p></td>
+<td><p>Alias for field number 5</p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.inputs.gutmgene.GutmgeneAnnotation.classification">
+<span class="sig-name descname"><span class="pre">classification</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">str</span></em><a class="headerlink" href="#pypath.inputs.gutmgene.GutmgeneAnnotation.classification" title="Link to this definition">§</a></dt>
+<dd><p>Alias for field number 3</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.inputs.gutmgene.GutmgeneAnnotation.count">
+<span class="sig-name descname"><span class="pre">count</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">value</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">/</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.inputs.gutmgene.GutmgeneAnnotation.count" title="Link to this definition">§</a></dt>
+<dd><p>Return number of occurrences of value.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.inputs.gutmgene.GutmgeneAnnotation.effect">
+<span class="sig-name descname"><span class="pre">effect</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">str</span></em><a class="headerlink" href="#pypath.inputs.gutmgene.GutmgeneAnnotation.effect" title="Link to this definition">§</a></dt>
+<dd><p>Alias for field number 4</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.inputs.gutmgene.GutmgeneAnnotation.gut_microbiota_id">
+<span class="sig-name descname"><span class="pre">gut_microbiota_id</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">str</span></em><a class="headerlink" href="#pypath.inputs.gutmgene.GutmgeneAnnotation.gut_microbiota_id" title="Link to this definition">§</a></dt>
+<dd><p>Alias for field number 2</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.inputs.gutmgene.GutmgeneAnnotation.index">
+<span class="sig-name descname"><span class="pre">index</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">value</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">start</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">stop</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9223372036854775807</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">/</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.inputs.gutmgene.GutmgeneAnnotation.index" title="Link to this definition">§</a></dt>
+<dd><p>Return first index of value.</p>
+<p>Raises ValueError if the value is not present.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.inputs.gutmgene.GutmgeneAnnotation.microbe_ncbi_tax_id">
+<span class="sig-name descname"><span class="pre">microbe_ncbi_tax_id</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">str</span></em><a class="headerlink" href="#pypath.inputs.gutmgene.GutmgeneAnnotation.microbe_ncbi_tax_id" title="Link to this definition">§</a></dt>
+<dd><p>Alias for field number 1</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.inputs.gutmgene.GutmgeneAnnotation.microbe_taxon">
+<span class="sig-name descname"><span class="pre">microbe_taxon</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">str</span></em><a class="headerlink" href="#pypath.inputs.gutmgene.GutmgeneAnnotation.microbe_taxon" title="Link to this definition">§</a></dt>
+<dd><p>Alias for field number 0</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.inputs.gutmgene.GutmgeneAnnotation.throughput">
+<span class="sig-name descname"><span class="pre">throughput</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">str</span></em><a class="headerlink" href="#pypath.inputs.gutmgene.GutmgeneAnnotation.throughput" title="Link to this definition">§</a></dt>
+<dd><p>Alias for field number 5</p>
+</dd></dl>
+
+</dd></dl>
+
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+  <section id="pypath-inputs-gutmgene-gutmgeneraw">
+<h1>pypath.inputs.gutmgene.GutmgeneRaw<a class="headerlink" href="#pypath-inputs-gutmgene-gutmgeneraw" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.inputs.gutmgene.GutmgeneRaw">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.inputs.gutmgene.</span></span><span class="sig-name descname"><span class="pre">GutmgeneRaw</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">microbe_taxon</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">microbe_ncbi_tax_id</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">gut_microbiota_id</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">classification</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">genesymbol</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entrez</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">effect</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">throughput</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/inputs/gutmgene.html#GutmgeneRaw"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.gutmgene.GutmgeneRaw" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">NamedTuple</span></code></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.inputs.gutmgene.GutmgeneRaw.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.inputs.gutmgene.GutmgeneRaw.__init__" title="Link to this definition">§</a></dt>
+<dd></dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.inputs.gutmgene.GutmgeneRaw.__init__" title="pypath.inputs.gutmgene.GutmgeneRaw.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.inputs.gutmgene.GutmgeneRaw.count" title="pypath.inputs.gutmgene.GutmgeneRaw.count"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count</span></code></a>(value, /)</p></td>
+<td><p>Return number of occurrences of value.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.inputs.gutmgene.GutmgeneRaw.index" title="pypath.inputs.gutmgene.GutmgeneRaw.index"><code class="xref py py-obj docutils literal notranslate"><span class="pre">index</span></code></a>(value[, start, stop])</p></td>
+<td><p>Return first index of value.</p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Attributes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.inputs.gutmgene.GutmgeneRaw.classification" title="pypath.inputs.gutmgene.GutmgeneRaw.classification"><code class="xref py py-obj docutils literal notranslate"><span class="pre">classification</span></code></a></p></td>
+<td><p>Alias for field number 3</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.inputs.gutmgene.GutmgeneRaw.effect" title="pypath.inputs.gutmgene.GutmgeneRaw.effect"><code class="xref py py-obj docutils literal notranslate"><span class="pre">effect</span></code></a></p></td>
+<td><p>Alias for field number 6</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.inputs.gutmgene.GutmgeneRaw.entrez" title="pypath.inputs.gutmgene.GutmgeneRaw.entrez"><code class="xref py py-obj docutils literal notranslate"><span class="pre">entrez</span></code></a></p></td>
+<td><p>Alias for field number 5</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.inputs.gutmgene.GutmgeneRaw.genesymbol" title="pypath.inputs.gutmgene.GutmgeneRaw.genesymbol"><code class="xref py py-obj docutils literal notranslate"><span class="pre">genesymbol</span></code></a></p></td>
+<td><p>Alias for field number 4</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.inputs.gutmgene.GutmgeneRaw.gut_microbiota_id" title="pypath.inputs.gutmgene.GutmgeneRaw.gut_microbiota_id"><code class="xref py py-obj docutils literal notranslate"><span class="pre">gut_microbiota_id</span></code></a></p></td>
+<td><p>Alias for field number 2</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.inputs.gutmgene.GutmgeneRaw.microbe_ncbi_tax_id" title="pypath.inputs.gutmgene.GutmgeneRaw.microbe_ncbi_tax_id"><code class="xref py py-obj docutils literal notranslate"><span class="pre">microbe_ncbi_tax_id</span></code></a></p></td>
+<td><p>Alias for field number 1</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.inputs.gutmgene.GutmgeneRaw.microbe_taxon" title="pypath.inputs.gutmgene.GutmgeneRaw.microbe_taxon"><code class="xref py py-obj docutils literal notranslate"><span class="pre">microbe_taxon</span></code></a></p></td>
+<td><p>Alias for field number 0</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.inputs.gutmgene.GutmgeneRaw.throughput" title="pypath.inputs.gutmgene.GutmgeneRaw.throughput"><code class="xref py py-obj docutils literal notranslate"><span class="pre">throughput</span></code></a></p></td>
+<td><p>Alias for field number 7</p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.inputs.gutmgene.GutmgeneRaw.classification">
+<span class="sig-name descname"><span class="pre">classification</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">str</span></em><a class="headerlink" href="#pypath.inputs.gutmgene.GutmgeneRaw.classification" title="Link to this definition">§</a></dt>
+<dd><p>Alias for field number 3</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.inputs.gutmgene.GutmgeneRaw.count">
+<span class="sig-name descname"><span class="pre">count</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">value</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">/</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.inputs.gutmgene.GutmgeneRaw.count" title="Link to this definition">§</a></dt>
+<dd><p>Return number of occurrences of value.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.inputs.gutmgene.GutmgeneRaw.effect">
+<span class="sig-name descname"><span class="pre">effect</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">str</span></em><a class="headerlink" href="#pypath.inputs.gutmgene.GutmgeneRaw.effect" title="Link to this definition">§</a></dt>
+<dd><p>Alias for field number 6</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.inputs.gutmgene.GutmgeneRaw.entrez">
+<span class="sig-name descname"><span class="pre">entrez</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">str</span></em><a class="headerlink" href="#pypath.inputs.gutmgene.GutmgeneRaw.entrez" title="Link to this definition">§</a></dt>
+<dd><p>Alias for field number 5</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.inputs.gutmgene.GutmgeneRaw.genesymbol">
+<span class="sig-name descname"><span class="pre">genesymbol</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">str</span></em><a class="headerlink" href="#pypath.inputs.gutmgene.GutmgeneRaw.genesymbol" title="Link to this definition">§</a></dt>
+<dd><p>Alias for field number 4</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.inputs.gutmgene.GutmgeneRaw.gut_microbiota_id">
+<span class="sig-name descname"><span class="pre">gut_microbiota_id</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">str</span></em><a class="headerlink" href="#pypath.inputs.gutmgene.GutmgeneRaw.gut_microbiota_id" title="Link to this definition">§</a></dt>
+<dd><p>Alias for field number 2</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.inputs.gutmgene.GutmgeneRaw.index">
+<span class="sig-name descname"><span class="pre">index</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">value</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">start</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">stop</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9223372036854775807</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">/</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.inputs.gutmgene.GutmgeneRaw.index" title="Link to this definition">§</a></dt>
+<dd><p>Return first index of value.</p>
+<p>Raises ValueError if the value is not present.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.inputs.gutmgene.GutmgeneRaw.microbe_ncbi_tax_id">
+<span class="sig-name descname"><span class="pre">microbe_ncbi_tax_id</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">str</span></em><a class="headerlink" href="#pypath.inputs.gutmgene.GutmgeneRaw.microbe_ncbi_tax_id" title="Link to this definition">§</a></dt>
+<dd><p>Alias for field number 1</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.inputs.gutmgene.GutmgeneRaw.microbe_taxon">
+<span class="sig-name descname"><span class="pre">microbe_taxon</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">str</span></em><a class="headerlink" href="#pypath.inputs.gutmgene.GutmgeneRaw.microbe_taxon" title="Link to this definition">§</a></dt>
+<dd><p>Alias for field number 0</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.inputs.gutmgene.GutmgeneRaw.throughput">
+<span class="sig-name descname"><span class="pre">throughput</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">str</span></em><a class="headerlink" href="#pypath.inputs.gutmgene.GutmgeneRaw.throughput" title="Link to this definition">§</a></dt>
+<dd><p>Alias for field number 7</p>
+</dd></dl>
+
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+
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diff --git a/api/pypath.inputs.gutmgene.gutmgene_annotations.html b/api/pypath.inputs.gutmgene.gutmgene_annotations.html
new file mode 100644
index 000000000..cc3c9b741
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+  <section id="pypath-inputs-gutmgene-gutmgene-annotations">
+<h1>pypath.inputs.gutmgene.gutmgene_annotations<a class="headerlink" href="#pypath-inputs-gutmgene-gutmgene-annotations" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.inputs.gutmgene.gutmgene_annotations">
+<span class="sig-prename descclassname"><span class="pre">pypath.inputs.gutmgene.</span></span><span class="sig-name descname"><span class="pre">gutmgene_annotations</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">organism</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">Literal</span><span class="p"><span class="pre">[</span></span><span class="s"><span class="pre">'human'</span></span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="s"><span class="pre">'mouse'</span></span><span class="p"><span class="pre">]</span></span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">'human'</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">set</span><span class="p"><span class="pre">[</span></span><a class="reference internal" href="pypath.inputs.gutmgene.GutmgeneAnnotation.html#pypath.inputs.gutmgene.GutmgeneAnnotation" title="pypath.inputs.gutmgene.GutmgeneAnnotation"><span class="pre">GutmgeneAnnotation</span></a><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span></span></span><a class="reference internal" href="../_modules/pypath/inputs/gutmgene.html#gutmgene_annotations"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.gutmgene.gutmgene_annotations" title="Link to this definition">§</a></dt>
+<dd><p>Microbial effectors of human or mouse genes from the gutMGene database.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><p><strong>organism</strong> – Organism ID or name; human and mouse are available.</p>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p>A dict of sets of named tuples representing microbial relationships;
+top level keys are UniProt IDs.</p>
+</dd>
+</dl>
+</dd></dl>
+
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+  <section id="pypath-inputs-gutmgene-gutmgene-raw">
+<h1>pypath.inputs.gutmgene.gutmgene_raw<a class="headerlink" href="#pypath-inputs-gutmgene-gutmgene-raw" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.inputs.gutmgene.gutmgene_raw">
+<span class="sig-prename descclassname"><span class="pre">pypath.inputs.gutmgene.</span></span><span class="sig-name descname"><span class="pre">gutmgene_raw</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">organism</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">Literal</span><span class="p"><span class="pre">[</span></span><span class="s"><span class="pre">'human'</span></span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="s"><span class="pre">'mouse'</span></span><span class="p"><span class="pre">]</span></span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">'human'</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">tuple</span><span class="p"><span class="pre">]</span></span></span></span><a class="reference internal" href="../_modules/pypath/inputs/gutmgene.html#gutmgene_raw"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.gutmgene.gutmgene_raw" title="Link to this definition">§</a></dt>
+<dd><p>Gut microbiota genes from the gut microbiota gene database (gutMGene).</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><p><strong>organism</strong> – Organism ID or name; human and mouse are available.</p>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p>A list of named tuples containing information about gut microbiota
+genes in human.</p>
+</dd>
+</dl>
+</dd></dl>
+
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+<td><p>Microbial effectors of human or mouse genes from the gutMGene database.</p></td>
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+<tr class="row-even"><td><p><a class="reference internal" href="pypath.inputs.gutmgene.gutmgene_raw.html#pypath.inputs.gutmgene.gutmgene_raw" title="pypath.inputs.gutmgene.gutmgene_raw"><code class="xref py py-obj docutils literal notranslate"><span class="pre">gutmgene_raw</span></code></a>([organism])</p></td>
+<td><p>Gut microbiota genes from the gut microbiota gene database (gutMGene).</p></td>
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diff --git a/api/pypath.inputs.havugimana.get_havugimana.html b/api/pypath.inputs.havugimana.get_havugimana.html
new file mode 100644
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+  <section id="pypath-inputs-havugimana-get-havugimana">
+<h1>pypath.inputs.havugimana.get_havugimana<a class="headerlink" href="#pypath-inputs-havugimana-get-havugimana" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.inputs.havugimana.get_havugimana">
+<span class="sig-prename descclassname"><span class="pre">pypath.inputs.havugimana.</span></span><span class="sig-name descname"><span class="pre">get_havugimana</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/inputs/havugimana.html#get_havugimana"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.havugimana.get_havugimana" title="Link to this definition">§</a></dt>
+<dd><p>Downloads data from
+Supplement Table S3/1 from Havugimana 2012
+Cell. 150(5): 1068–1081.</p>
+</dd></dl>
+
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+  <section id="pypath-inputs-havugimana-havugimana-complexes">
+<h1>pypath.inputs.havugimana.havugimana_complexes<a class="headerlink" href="#pypath-inputs-havugimana-havugimana-complexes" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.inputs.havugimana.havugimana_complexes">
+<span class="sig-prename descclassname"><span class="pre">pypath.inputs.havugimana.</span></span><span class="sig-name descname"><span class="pre">havugimana_complexes</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/inputs/havugimana.html#havugimana_complexes"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.havugimana.havugimana_complexes" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves complexes from
+Supplement Table S3/1 from Havugimana 2012
+Cell. 150(5): 1068–1081.</p>
+</dd></dl>
+
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diff --git a/api/pypath.inputs.havugimana.html b/api/pypath.inputs.havugimana.html
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+<dl class="field-list simple">
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+<td><p>Retrieves complexes from Supplement Table S3/1 from Havugimana 2012 Cell.</p></td>
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diff --git a/api/pypath.inputs.hgnc.hgnc_genegroups.html b/api/pypath.inputs.hgnc.hgnc_genegroups.html
new file mode 100644
index 000000000..b7ef4a1c7
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diff --git a/api/pypath.inputs.hippie.hippie_interactions.html b/api/pypath.inputs.hippie.hippie_interactions.html
new file mode 100644
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+<h1>pypath.inputs.hippie.hippie_interactions<a class="headerlink" href="#pypath-inputs-hippie-hippie-interactions" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.inputs.hippie.hippie_interactions">
+<span class="sig-prename descclassname"><span class="pre">pypath.inputs.hippie.</span></span><span class="sig-name descname"><span class="pre">hippie_interactions</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">score_threshold</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0.75</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">only_human</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">only_sources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">only_methods</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">methods</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">sources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">organisms</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/inputs/hippie.html#hippie_interactions"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.hippie.hippie_interactions" title="Link to this definition">§</a></dt>
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diff --git a/api/pypath.inputs.hippie.html b/api/pypath.inputs.hippie.html
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+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.inputs.hippie.hippie_interactions.html#pypath.inputs.hippie.hippie_interactions" title="pypath.inputs.hippie.hippie_interactions"><code class="xref py py-obj docutils literal notranslate"><span class="pre">hippie_interactions</span></code></a>([score_threshold, ...])</p></td>
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diff --git a/api/pypath.inputs.hmdb.html b/api/pypath.inputs.hmdb.html
index 23a54b3b2..011b7aed9 100644
--- a/api/pypath.inputs.hmdb.html
+++ b/api/pypath.inputs.hmdb.html
@@ -48,7 +48,7 @@
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+    <link rel="prev" title="pypath.inputs.hippie.hippie_interactions" href="pypath.inputs.hippie.hippie_interactions.html" />
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@@ -560,12 +560,12 @@
                   
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+       href="pypath.inputs.hippie.hippie_interactions.html"
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diff --git a/api/pypath.inputs.hmdb.xml.hmdb_xml.html b/api/pypath.inputs.hmdb.xml.hmdb_xml.html
index d65e51e0a..e90a3b320 100644
--- a/api/pypath.inputs.hmdb.xml.hmdb_xml.html
+++ b/api/pypath.inputs.hmdb.xml.hmdb_xml.html
@@ -47,7 +47,7 @@
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@@ -545,11 +545,11 @@ <h1>pypath.inputs.hmdb.xml.hmdb_xml<a class="headerlink" href="#pypath-inputs-hm
       </div>
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-        <p class="prev-next-title">pypath.inputs.hprd</p>
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diff --git a/api/pypath.inputs.homologene.get_homologene.html b/api/pypath.inputs.homologene.get_homologene.html
new file mode 100644
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--- /dev/null
+++ b/api/pypath.inputs.homologene.get_homologene.html
@@ -0,0 +1,640 @@
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+  <section id="pypath-inputs-homologene-get-homologene">
+<h1>pypath.inputs.homologene.get_homologene<a class="headerlink" href="#pypath-inputs-homologene-get-homologene" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.inputs.homologene.get_homologene">
+<span class="sig-prename descclassname"><span class="pre">pypath.inputs.homologene.</span></span><span class="sig-name descname"><span class="pre">get_homologene</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/inputs/homologene.html#get_homologene"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.homologene.get_homologene" title="Link to this definition">§</a></dt>
+<dd><p>Downloads the latest release of the NCBI HomoloGene database.
+Returns file pointer.</p>
+</dd></dl>
+
+</section>
+
+
+                </article>
+              
+              
+              
+              
+              
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+<h1>pypath.inputs.homologene.homologene_dict<a class="headerlink" href="#pypath-inputs-homologene-homologene-dict" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.inputs.homologene.homologene_dict">
+<span class="sig-prename descclassname"><span class="pre">pypath.inputs.homologene.</span></span><span class="sig-name descname"><span class="pre">homologene_dict</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">source</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">target</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">id_type</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/inputs/homologene.html#homologene_dict"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.homologene.homologene_dict" title="Link to this definition">§</a></dt>
+<dd><p>Returns orthology translation table as dict, obtained
+from NCBI HomoloGene data.</p>
+<dl>
+<dt>Args</dt><dd><p>source (int): NCBI Taxonomy ID of the source species (keys).
+target (int): NCBI Taxonomy ID of the target species (values).
+id_type (str): ID type to be used in the dict. Possible values:</p>
+<blockquote>
+<div><p>‘RefSeq’, ‘Entrez’, ‘GI’, ‘GeneSymbol’.</p>
+</div></blockquote>
+</dd>
+<dt>Returns</dt><dd><p>Dict of sets: keys are IDs of the source organism, values are sets
+of IDs of the target organism.</p>
+</dd>
+</dl>
+</dd></dl>
+
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+<h1>pypath.inputs.homologene.homologene_uniprot_dict<a class="headerlink" href="#pypath-inputs-homologene-homologene-uniprot-dict" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.inputs.homologene.homologene_uniprot_dict">
+<span class="sig-prename descclassname"><span class="pre">pypath.inputs.homologene.</span></span><span class="sig-name descname"><span class="pre">homologene_uniprot_dict</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">source</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">target</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">only_swissprot</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/inputs/homologene.html#homologene_uniprot_dict"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.homologene.homologene_uniprot_dict" title="Link to this definition">§</a></dt>
+<dd><p>Returns orthology translation table as dict from UniProt to Uniprot,
+obtained from NCBI HomoloGene data. Uses RefSeq and Entrez IDs for
+translation.</p>
+<dl class="simple">
+<dt>Args</dt><dd><p>source (int): NCBI Taxonomy ID of the source species (keys).
+target(int): NCBI Taxonomy ID of the target species (values).
+only_swissprot (bool): Use only SwissProt IDs.</p>
+</dd>
+<dt>Returns</dt><dd><p>Dict of sets: keys are UniProt IDs of the source organism, values
+are sets of UniProt IDs of the target organism.</p>
+</dd>
+</dl>
+</dd></dl>
+
+</section>
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+<p class="rubric">Functions</p>
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+<td><p>Downloads the latest release of the NCBI HomoloGene database.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.inputs.homologene.homologene_dict.html#pypath.inputs.homologene.homologene_dict" title="pypath.inputs.homologene.homologene_dict"><code class="xref py py-obj docutils literal notranslate"><span class="pre">homologene_dict</span></code></a>(source, target, id_type)</p></td>
+<td><p>Returns orthology translation table as dict, obtained from NCBI HomoloGene data.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.inputs.homologene.homologene_uniprot_dict.html#pypath.inputs.homologene.homologene_uniprot_dict" title="pypath.inputs.homologene.homologene_uniprot_dict"><code class="xref py py-obj docutils literal notranslate"><span class="pre">homologene_uniprot_dict</span></code></a>(source, target[, ...])</p></td>
+<td><p>Returns orthology translation table as dict from UniProt to Uniprot, obtained from NCBI HomoloGene data.</p></td>
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diff --git a/api/pypath.inputs.hpmr.HpmrInteraction.html b/api/pypath.inputs.hpmr.HpmrInteraction.html
new file mode 100644
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+                  
+  <section id="pypath-inputs-hpmr-hpmrinteraction">
+<h1>pypath.inputs.hpmr.HpmrInteraction<a class="headerlink" href="#pypath-inputs-hpmr-hpmrinteraction" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.inputs.hpmr.HpmrInteraction">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.inputs.hpmr.</span></span><span class="sig-name descname"><span class="pre">HpmrInteraction</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">receptor</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">partner_role</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">partner</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">unambiguous</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.inputs.hpmr.HpmrInteraction" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">tuple</span></code></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.inputs.hpmr.HpmrInteraction.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.inputs.hpmr.HpmrInteraction.__init__" title="Link to this definition">§</a></dt>
+<dd></dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.inputs.hpmr.HpmrInteraction.__init__" title="pypath.inputs.hpmr.HpmrInteraction.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.inputs.hpmr.HpmrInteraction.count" title="pypath.inputs.hpmr.HpmrInteraction.count"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count</span></code></a>(value, /)</p></td>
+<td><p>Return number of occurrences of value.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.inputs.hpmr.HpmrInteraction.index" title="pypath.inputs.hpmr.HpmrInteraction.index"><code class="xref py py-obj docutils literal notranslate"><span class="pre">index</span></code></a>(value[, start, stop])</p></td>
+<td><p>Return first index of value.</p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Attributes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.inputs.hpmr.HpmrInteraction.partner" title="pypath.inputs.hpmr.HpmrInteraction.partner"><code class="xref py py-obj docutils literal notranslate"><span class="pre">partner</span></code></a></p></td>
+<td><p>Alias for field number 2</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.inputs.hpmr.HpmrInteraction.partner_role" title="pypath.inputs.hpmr.HpmrInteraction.partner_role"><code class="xref py py-obj docutils literal notranslate"><span class="pre">partner_role</span></code></a></p></td>
+<td><p>Alias for field number 1</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.inputs.hpmr.HpmrInteraction.receptor" title="pypath.inputs.hpmr.HpmrInteraction.receptor"><code class="xref py py-obj docutils literal notranslate"><span class="pre">receptor</span></code></a></p></td>
+<td><p>Alias for field number 0</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.inputs.hpmr.HpmrInteraction.references" title="pypath.inputs.hpmr.HpmrInteraction.references"><code class="xref py py-obj docutils literal notranslate"><span class="pre">references</span></code></a></p></td>
+<td><p>Alias for field number 3</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.inputs.hpmr.HpmrInteraction.unambiguous" title="pypath.inputs.hpmr.HpmrInteraction.unambiguous"><code class="xref py py-obj docutils literal notranslate"><span class="pre">unambiguous</span></code></a></p></td>
+<td><p>Alias for field number 4</p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.inputs.hpmr.HpmrInteraction.count">
+<span class="sig-name descname"><span class="pre">count</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">value</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">/</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.inputs.hpmr.HpmrInteraction.count" title="Link to this definition">§</a></dt>
+<dd><p>Return number of occurrences of value.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.inputs.hpmr.HpmrInteraction.index">
+<span class="sig-name descname"><span class="pre">index</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">value</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">start</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">stop</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9223372036854775807</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">/</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.inputs.hpmr.HpmrInteraction.index" title="Link to this definition">§</a></dt>
+<dd><p>Return first index of value.</p>
+<p>Raises ValueError if the value is not present.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.inputs.hpmr.HpmrInteraction.partner">
+<span class="sig-name descname"><span class="pre">partner</span></span><a class="headerlink" href="#pypath.inputs.hpmr.HpmrInteraction.partner" title="Link to this definition">§</a></dt>
+<dd><p>Alias for field number 2</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.inputs.hpmr.HpmrInteraction.partner_role">
+<span class="sig-name descname"><span class="pre">partner_role</span></span><a class="headerlink" href="#pypath.inputs.hpmr.HpmrInteraction.partner_role" title="Link to this definition">§</a></dt>
+<dd><p>Alias for field number 1</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.inputs.hpmr.HpmrInteraction.receptor">
+<span class="sig-name descname"><span class="pre">receptor</span></span><a class="headerlink" href="#pypath.inputs.hpmr.HpmrInteraction.receptor" title="Link to this definition">§</a></dt>
+<dd><p>Alias for field number 0</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.inputs.hpmr.HpmrInteraction.references">
+<span class="sig-name descname"><span class="pre">references</span></span><a class="headerlink" href="#pypath.inputs.hpmr.HpmrInteraction.references" title="Link to this definition">§</a></dt>
+<dd><p>Alias for field number 3</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.inputs.hpmr.HpmrInteraction.unambiguous">
+<span class="sig-name descname"><span class="pre">unambiguous</span></span><a class="headerlink" href="#pypath.inputs.hpmr.HpmrInteraction.unambiguous" title="Link to this definition">§</a></dt>
+<dd><p>Alias for field number 4</p>
+</dd></dl>
+
+</dd></dl>
+
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+<h1>pypath.inputs.hpmr.get_hpmr<a class="headerlink" href="#pypath-inputs-hpmr-get-hpmr" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.inputs.hpmr.get_hpmr">
+<span class="sig-prename descclassname"><span class="pre">pypath.inputs.hpmr.</span></span><span class="sig-name descname"><span class="pre">get_hpmr</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">use_cache</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/inputs/hpmr.html#get_hpmr"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.hpmr.get_hpmr" title="Link to this definition">§</a></dt>
+<dd><p>Downloads ligand-receptor and receptor-receptor interactions from the
+Human Plasma Membrane Receptome database.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>use_cache (bool): Use the intermediate cache (pickle file of</dt><dd><p>processed data).</p>
+</dd>
+</dl>
+</dd>
+<dt>Returns</dt><dd><p>(dict): Two elements: “interactions” and “families”.</p>
+</dd>
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+
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diff --git a/api/pypath.inputs.hpmr.hpmr_annotations.html b/api/pypath.inputs.hpmr.hpmr_annotations.html
new file mode 100644
index 000000000..b4d048885
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+  <section id="pypath-inputs-hpmr-hpmr-complexes">
+<h1>pypath.inputs.hpmr.hpmr_complexes<a class="headerlink" href="#pypath-inputs-hpmr-hpmr-complexes" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.inputs.hpmr.hpmr_complexes">
+<span class="sig-prename descclassname"><span class="pre">pypath.inputs.hpmr.</span></span><span class="sig-name descname"><span class="pre">hpmr_complexes</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">use_cache</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/inputs/hpmr.html#hpmr_complexes"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.hpmr.hpmr_complexes" title="Link to this definition">§</a></dt>
+<dd><p>HPMR does not contain unambiguous protein complex data, and considering
+the resource is unmaintained, probably it never will. Hence this function
+always returns an empty dict.</p>
+</dd></dl>
+
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diff --git a/api/pypath.inputs.hpmr.hpmr_interactions.html b/api/pypath.inputs.hpmr.hpmr_interactions.html
new file mode 100644
index 000000000..b14c73e2a
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+                  
+  <section id="module-pypath.inputs.hpmr">
+<span id="pypath-inputs-hpmr"></span><h1>pypath.inputs.hpmr<a class="headerlink" href="#module-pypath.inputs.hpmr" title="Link to this heading">§</a></h1>
+<dl class="field-list simple">
+<dt class="field-odd">members<span class="colon">:</span></dt>
+<dd class="field-odd"><p></p></dd>
+</dl>
+<p class="rubric">Functions</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.inputs.hpmr.get_hpmr.html#pypath.inputs.hpmr.get_hpmr" title="pypath.inputs.hpmr.get_hpmr"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_hpmr</span></code></a>([use_cache])</p></td>
+<td><p>Downloads ligand-receptor and receptor-receptor interactions from the Human Plasma Membrane Receptome database.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.inputs.hpmr.hpmr_annotations.html#pypath.inputs.hpmr.hpmr_annotations" title="pypath.inputs.hpmr.hpmr_annotations"><code class="xref py py-obj docutils literal notranslate"><span class="pre">hpmr_annotations</span></code></a>([use_cache])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.inputs.hpmr.hpmr_complexes.html#pypath.inputs.hpmr.hpmr_complexes" title="pypath.inputs.hpmr.hpmr_complexes"><code class="xref py py-obj docutils literal notranslate"><span class="pre">hpmr_complexes</span></code></a>([use_cache])</p></td>
+<td><p>HPMR does not contain unambiguous protein complex data, and considering the resource is unmaintained, probably it never will.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.inputs.hpmr.hpmr_interactions.html#pypath.inputs.hpmr.hpmr_interactions" title="pypath.inputs.hpmr.hpmr_interactions"><code class="xref py py-obj docutils literal notranslate"><span class="pre">hpmr_interactions</span></code></a>([use_cache])</p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Classes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.inputs.hpmr.HpmrInteraction.html#pypath.inputs.hpmr.HpmrInteraction" title="pypath.inputs.hpmr.HpmrInteraction"><code class="xref py py-obj docutils literal notranslate"><span class="pre">HpmrInteraction</span></code></a>(receptor, partner_role, ...)</p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+</section>
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+
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+  <section id="pypath-inputs-hpo-hpo-annotations">
+<h1>pypath.inputs.hpo.hpo_annotations<a class="headerlink" href="#pypath-inputs-hpo-hpo-annotations" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.inputs.hpo.hpo_annotations">
+<span class="sig-prename descclassname"><span class="pre">pypath.inputs.hpo.</span></span><span class="sig-name descname"><span class="pre">hpo_annotations</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">set</span><span class="p"><span class="pre">[</span></span><span class="pre">tuple</span><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span></span></span><a class="reference internal" href="../_modules/pypath/inputs/hpo.html#hpo_annotations"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.hpo.hpo_annotations" title="Link to this definition">§</a></dt>
+<dd><p>Human Phenotype Ontology annotations.</p>
+<dl class="simple">
+<dt>Returns</dt><dd><p>Dict of proteins as keys and sets of HPO annotations as values.</p>
+</dd>
+</dl>
+</dd></dl>
+
+</section>
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+
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+<h1>pypath.inputs.hpo.hpo_diseases<a class="headerlink" href="#pypath-inputs-hpo-hpo-diseases" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.inputs.hpo.hpo_diseases">
+<span class="sig-prename descclassname"><span class="pre">pypath.inputs.hpo.</span></span><span class="sig-name descname"><span class="pre">hpo_diseases</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">set</span><span class="p"><span class="pre">[</span></span><span class="pre">tuple</span><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span></span></span><a class="reference internal" href="../_modules/pypath/inputs/hpo.html#hpo_diseases"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.hpo.hpo_diseases" title="Link to this definition">§</a></dt>
+<dd><p>HPO term-disease relationships from Human Phenotype Ontology.</p>
+<dl class="simple">
+<dt>Returns</dt><dd><p>A set of disease records for each HPO term.</p>
+</dd>
+</dl>
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+<h1>pypath.inputs.hpo.hpo_ontology<a class="headerlink" href="#pypath-inputs-hpo-hpo-ontology" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.inputs.hpo.hpo_ontology">
+<span class="sig-prename descclassname"><span class="pre">pypath.inputs.hpo.</span></span><span class="sig-name descname"><span class="pre">hpo_ontology</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">set</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span></span></span><a class="reference internal" href="../_modules/pypath/inputs/hpo.html#hpo_ontology"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.hpo.hpo_ontology" title="Link to this definition">§</a></dt>
+<dd><p>Ontology data from HPO.</p>
+<dl class="simple">
+<dt>Returns</dt><dd><p>Five dictionaries with term names, term definitions, parents in the
+ontology tree, term synonyms and cross references to other databases.
+The dicts “terms” and “defs” are one-to-one, while “parents”,
+“synonyms” and “xrefs” are one-to-many mappings, the keys are always
+HPO terms.</p>
+</dd>
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+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.inputs.hpo.hpo_terms">
+<span class="sig-prename descclassname"><span class="pre">pypath.inputs.hpo.</span></span><span class="sig-name descname"><span class="pre">hpo_terms</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">str</span><span class="p"><span class="pre">]</span></span></span></span><a class="reference internal" href="../_modules/pypath/inputs/hpo.html#hpo_terms"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.hpo.hpo_terms" title="Link to this definition">§</a></dt>
+<dd><p>Human Phenotype Ontology accession to term mapping.</p>
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+              
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+                <article class="bd-article">
+                  
+  <section id="module-pypath.inputs.hpo">
+<span id="pypath-inputs-hpo"></span><h1>pypath.inputs.hpo<a class="headerlink" href="#module-pypath.inputs.hpo" title="Link to this heading">§</a></h1>
+<dl class="field-list simple">
+<dt class="field-odd">members<span class="colon">:</span></dt>
+<dd class="field-odd"><p></p></dd>
+</dl>
+<p class="rubric">Functions</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.inputs.hpo.hpo_annotations.html#pypath.inputs.hpo.hpo_annotations" title="pypath.inputs.hpo.hpo_annotations"><code class="xref py py-obj docutils literal notranslate"><span class="pre">hpo_annotations</span></code></a>()</p></td>
+<td><p>Human Phenotype Ontology annotations.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.inputs.hpo.hpo_diseases.html#pypath.inputs.hpo.hpo_diseases" title="pypath.inputs.hpo.hpo_diseases"><code class="xref py py-obj docutils literal notranslate"><span class="pre">hpo_diseases</span></code></a>()</p></td>
+<td><p>HPO term-disease relationships from Human Phenotype Ontology.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.inputs.hpo.hpo_ontology.html#pypath.inputs.hpo.hpo_ontology" title="pypath.inputs.hpo.hpo_ontology"><code class="xref py py-obj docutils literal notranslate"><span class="pre">hpo_ontology</span></code></a>()</p></td>
+<td><p>Ontology data from HPO.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.inputs.hpo.hpo_terms.html#pypath.inputs.hpo.hpo_terms" title="pypath.inputs.hpo.hpo_terms"><code class="xref py py-obj docutils literal notranslate"><span class="pre">hpo_terms</span></code></a>()</p></td>
+<td><p>Human Phenotype Ontology accession to term mapping.</p></td>
+</tr>
+</tbody>
+</table>
+</section>
+
+
+                </article>
+              
+              
+              
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diff --git a/api/pypath.inputs.hprd.html b/api/pypath.inputs.hprd.html
index 9dfa687dd..e0aabc9a0 100644
--- a/api/pypath.inputs.hprd.html
+++ b/api/pypath.inputs.hprd.html
@@ -48,7 +48,7 @@
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
     <link rel="next" title="pypath.inputs.hprd.get_hprd" href="pypath.inputs.hprd.get_hprd.html" />
-    <link rel="prev" title="pypath.inputs.hmdb.xml.hmdb_xml" href="pypath.inputs.hmdb.xml.hmdb_xml.html" />
+    <link rel="prev" title="pypath.inputs.hpo.hpo_terms" href="pypath.inputs.hpo.hpo_terms.html" />
   <meta name="viewport" content="width=device-width, initial-scale=1"/>
   <meta name="docsearch:language" content="en"/>
   </head>
@@ -551,12 +551,12 @@
                   
 <div class="prev-next-area">
     <a class="left-prev"
-       href="pypath.inputs.hmdb.xml.hmdb_xml.html"
+       href="pypath.inputs.hpo.hpo_terms.html"
        title="previous page">
       <i class="fa-solid fa-angle-left"></i>
       <div class="prev-next-info">
         <p class="prev-next-subtitle">previous</p>
-        <p class="prev-next-title">pypath.inputs.hmdb.xml.hmdb_xml</p>
+        <p class="prev-next-title">pypath.inputs.hpo.hpo_terms</p>
       </div>
     </a>
     <a class="right-next"
diff --git a/api/pypath.inputs.html b/api/pypath.inputs.html
index 33a9e1bc1..29a64f35c 100644
--- a/api/pypath.inputs.html
+++ b/api/pypath.inputs.html
@@ -533,7 +533,19 @@
 <tr class="row-even"><td><p><a class="reference internal" href="pypath.inputs.acsn.html#module-pypath.inputs.acsn" title="pypath.inputs.acsn"><code class="xref py py-obj docutils literal notranslate"><span class="pre">pypath.inputs.acsn</span></code></a></p></td>
 <td><p></p></td>
 </tr>
-<tr class="row-odd"><td><p><a class="reference internal" href="pypath.inputs.adrecs.html#module-pypath.inputs.adrecs" title="pypath.inputs.adrecs"><code class="xref py py-obj docutils literal notranslate"><span class="pre">pypath.inputs.adrecs</span></code></a></p></td>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.inputs.adhesome.html#module-pypath.inputs.adhesome" title="pypath.inputs.adhesome"><code class="xref py py-obj docutils literal notranslate"><span class="pre">pypath.inputs.adhesome</span></code></a></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.inputs.adrecs.html#module-pypath.inputs.adrecs" title="pypath.inputs.adrecs"><code class="xref py py-obj docutils literal notranslate"><span class="pre">pypath.inputs.adrecs</span></code></a></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.inputs.almen2009.html#module-pypath.inputs.almen2009" title="pypath.inputs.almen2009"><code class="xref py py-obj docutils literal notranslate"><span class="pre">pypath.inputs.almen2009</span></code></a></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.inputs.baccin2019.html#module-pypath.inputs.baccin2019" title="pypath.inputs.baccin2019"><code class="xref py py-obj docutils literal notranslate"><span class="pre">pypath.inputs.baccin2019</span></code></a></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.inputs.biogps.html#module-pypath.inputs.biogps" title="pypath.inputs.biogps"><code class="xref py py-obj docutils literal notranslate"><span class="pre">pypath.inputs.biogps</span></code></a></p></td>
 <td><p></p></td>
 </tr>
 <tr class="row-even"><td><p><a class="reference internal" href="pypath.inputs.biogrid.html#module-pypath.inputs.biogrid" title="pypath.inputs.biogrid"><code class="xref py py-obj docutils literal notranslate"><span class="pre">pypath.inputs.biogrid</span></code></a></p></td>
@@ -551,28 +563,88 @@
 <tr class="row-even"><td><p><a class="reference internal" href="pypath.inputs.cancercellmap.html#module-pypath.inputs.cancercellmap" title="pypath.inputs.cancercellmap"><code class="xref py py-obj docutils literal notranslate"><span class="pre">pypath.inputs.cancercellmap</span></code></a></p></td>
 <td><p></p></td>
 </tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.inputs.cancerdrugsdb.html#module-pypath.inputs.cancerdrugsdb" title="pypath.inputs.cancerdrugsdb"><code class="xref py py-obj docutils literal notranslate"><span class="pre">pypath.inputs.cancerdrugsdb</span></code></a></p></td>
+<td><p>Web scraper for the CancerDrugs_DB database.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.inputs.cancersea.html#module-pypath.inputs.cancersea" title="pypath.inputs.cancersea"><code class="xref py py-obj docutils literal notranslate"><span class="pre">pypath.inputs.cancersea</span></code></a></p></td>
+<td><p></p></td>
+</tr>
 <tr class="row-odd"><td><p><a class="reference internal" href="pypath.inputs.cell.html#module-pypath.inputs.cell" title="pypath.inputs.cell"><code class="xref py py-obj docutils literal notranslate"><span class="pre">pypath.inputs.cell</span></code></a></p></td>
 <td><p></p></td>
 </tr>
-<tr class="row-even"><td><p><a class="reference internal" href="pypath.inputs.chembl.html#module-pypath.inputs.chembl" title="pypath.inputs.chembl"><code class="xref py py-obj docutils literal notranslate"><span class="pre">pypath.inputs.chembl</span></code></a></p></td>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.inputs.cellcall.html#module-pypath.inputs.cellcall" title="pypath.inputs.cellcall"><code class="xref py py-obj docutils literal notranslate"><span class="pre">pypath.inputs.cellcall</span></code></a></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.inputs.cellcellinteractions.html#module-pypath.inputs.cellcellinteractions" title="pypath.inputs.cellcellinteractions"><code class="xref py py-obj docutils literal notranslate"><span class="pre">pypath.inputs.cellcellinteractions</span></code></a></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.inputs.cellchatdb.html#module-pypath.inputs.cellchatdb" title="pypath.inputs.cellchatdb"><code class="xref py py-obj docutils literal notranslate"><span class="pre">pypath.inputs.cellchatdb</span></code></a></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.inputs.cellinker.html#module-pypath.inputs.cellinker" title="pypath.inputs.cellinker"><code class="xref py py-obj docutils literal notranslate"><span class="pre">pypath.inputs.cellinker</span></code></a></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.inputs.cellphonedb.html#module-pypath.inputs.cellphonedb" title="pypath.inputs.cellphonedb"><code class="xref py py-obj docutils literal notranslate"><span class="pre">pypath.inputs.cellphonedb</span></code></a></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.inputs.celltalkdb.html#module-pypath.inputs.celltalkdb" title="pypath.inputs.celltalkdb"><code class="xref py py-obj docutils literal notranslate"><span class="pre">pypath.inputs.celltalkdb</span></code></a></p></td>
 <td><p></p></td>
 </tr>
-<tr class="row-odd"><td><p><a class="reference internal" href="pypath.inputs.clinvar.html#module-pypath.inputs.clinvar" title="pypath.inputs.clinvar"><code class="xref py py-obj docutils literal notranslate"><span class="pre">pypath.inputs.clinvar</span></code></a></p></td>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.inputs.celltypist.html#module-pypath.inputs.celltypist" title="pypath.inputs.celltypist"><code class="xref py py-obj docutils literal notranslate"><span class="pre">pypath.inputs.celltypist</span></code></a></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.inputs.chembl.html#module-pypath.inputs.chembl" title="pypath.inputs.chembl"><code class="xref py py-obj docutils literal notranslate"><span class="pre">pypath.inputs.chembl</span></code></a></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.inputs.clinvar.html#module-pypath.inputs.clinvar" title="pypath.inputs.clinvar"><code class="xref py py-obj docutils literal notranslate"><span class="pre">pypath.inputs.clinvar</span></code></a></p></td>
 <td><p>Variant data from the Clinvar database.</p></td>
 </tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.inputs.collectri.html#module-pypath.inputs.collectri" title="pypath.inputs.collectri"><code class="xref py py-obj docutils literal notranslate"><span class="pre">pypath.inputs.collectri</span></code></a></p></td>
+<td><p></p></td>
+</tr>
 <tr class="row-even"><td><p><a class="reference internal" href="pypath.inputs.common.html#module-pypath.inputs.common" title="pypath.inputs.common"><code class="xref py py-obj docutils literal notranslate"><span class="pre">pypath.inputs.common</span></code></a></p></td>
 <td><p></p></td>
 </tr>
 <tr class="row-odd"><td><p><a class="reference internal" href="pypath.inputs.compath.html#module-pypath.inputs.compath" title="pypath.inputs.compath"><code class="xref py py-obj docutils literal notranslate"><span class="pre">pypath.inputs.compath</span></code></a></p></td>
 <td><p></p></td>
 </tr>
-<tr class="row-even"><td><p><a class="reference internal" href="pypath.inputs.cpdb.html#module-pypath.inputs.cpdb" title="pypath.inputs.cpdb"><code class="xref py py-obj docutils literal notranslate"><span class="pre">pypath.inputs.cpdb</span></code></a></p></td>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.inputs.compleat.html#module-pypath.inputs.compleat" title="pypath.inputs.compleat"><code class="xref py py-obj docutils literal notranslate"><span class="pre">pypath.inputs.compleat</span></code></a></p></td>
+<td><p></p></td>
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 <td><p></p></td>
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@@ -812,28 +1028,58 @@
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+<tr class="row-even"><td><p><a class="reference internal" href="pypath.inputs.surfaceome.html#module-pypath.inputs.surfaceome" title="pypath.inputs.surfaceome"><code class="xref py py-obj docutils literal notranslate"><span class="pre">pypath.inputs.surfaceome</span></code></a></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.inputs.switches_elm.html#module-pypath.inputs.switches_elm" title="pypath.inputs.switches_elm"><code class="xref py py-obj docutils literal notranslate"><span class="pre">pypath.inputs.switches_elm</span></code></a></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.inputs.talklr.html#module-pypath.inputs.talklr" title="pypath.inputs.talklr"><code class="xref py py-obj docutils literal notranslate"><span class="pre">pypath.inputs.talklr</span></code></a></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.inputs.tcdb.html#module-pypath.inputs.tcdb" title="pypath.inputs.tcdb"><code class="xref py py-obj docutils literal notranslate"><span class="pre">pypath.inputs.tcdb</span></code></a></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.inputs.tfcensus.html#module-pypath.inputs.tfcensus" title="pypath.inputs.tfcensus"><code class="xref py py-obj docutils literal notranslate"><span class="pre">pypath.inputs.tfcensus</span></code></a></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.inputs.threedcomplex.html#module-pypath.inputs.threedcomplex" title="pypath.inputs.threedcomplex"><code class="xref py py-obj docutils literal notranslate"><span class="pre">pypath.inputs.threedcomplex</span></code></a></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.inputs.threedid.html#module-pypath.inputs.threedid" title="pypath.inputs.threedid"><code class="xref py py-obj docutils literal notranslate"><span class="pre">pypath.inputs.threedid</span></code></a></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.inputs.topdb.html#module-pypath.inputs.topdb" title="pypath.inputs.topdb"><code class="xref py py-obj docutils literal notranslate"><span class="pre">pypath.inputs.topdb</span></code></a></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.inputs.transmir.html#module-pypath.inputs.transmir" title="pypath.inputs.transmir"><code class="xref py py-obj docutils literal notranslate"><span class="pre">pypath.inputs.transmir</span></code></a></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.inputs.trip.html#module-pypath.inputs.trip" title="pypath.inputs.trip"><code class="xref py py-obj docutils literal notranslate"><span class="pre">pypath.inputs.trip</span></code></a></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.inputs.trrust.html#module-pypath.inputs.trrust" title="pypath.inputs.trrust"><code class="xref py py-obj docutils literal notranslate"><span class="pre">pypath.inputs.trrust</span></code></a></p></td>
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+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.inputs.twosides.html#module-pypath.inputs.twosides" title="pypath.inputs.twosides"><code class="xref py py-obj docutils literal notranslate"><span class="pre">pypath.inputs.twosides</span></code></a></p></td>
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+<tr class="row-even"><td><p><a class="reference internal" href="pypath.inputs.unichem.html#module-pypath.inputs.unichem" title="pypath.inputs.unichem"><code class="xref py py-obj docutils literal notranslate"><span class="pre">pypath.inputs.unichem</span></code></a></p></td>
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+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.inputs.uniprot.html#module-pypath.inputs.uniprot" title="pypath.inputs.uniprot"><code class="xref py py-obj docutils literal notranslate"><span class="pre">pypath.inputs.uniprot</span></code></a></p></td>
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+<tr class="row-even"><td><p><a class="reference internal" href="pypath.inputs.uniprot_db.html#module-pypath.inputs.uniprot_db" title="pypath.inputs.uniprot_db"><code class="xref py py-obj docutils literal notranslate"><span class="pre">pypath.inputs.uniprot_db</span></code></a></p></td>
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+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.inputs.wang.html#module-pypath.inputs.wang" title="pypath.inputs.wang"><code class="xref py py-obj docutils literal notranslate"><span class="pre">pypath.inputs.wang</span></code></a></p></td>
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+<tr class="row-even"><td><p><a class="reference internal" href="pypath.inputs.wojtowicz2020.html#module-pypath.inputs.wojtowicz2020" title="pypath.inputs.wojtowicz2020"><code class="xref py py-obj docutils literal notranslate"><span class="pre">pypath.inputs.wojtowicz2020</span></code></a></p></td>
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+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.inputs.zhong2015.html#module-pypath.inputs.zhong2015" title="pypath.inputs.zhong2015"><code class="xref py py-obj docutils literal notranslate"><span class="pre">pypath.inputs.zhong2015</span></code></a></p></td>
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diff --git a/api/pypath.inputs.htri.htri_interactions.html b/api/pypath.inputs.htri.htri_interactions.html
index 086835561..4d3b814c3 100644
--- a/api/pypath.inputs.htri.htri_interactions.html
+++ b/api/pypath.inputs.htri.htri_interactions.html
@@ -47,7 +47,7 @@
     <link rel="icon" href="../_static/omnipath-logo.svg"/>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
-    <link rel="next" title="pypath.inputs.humsavar" href="pypath.inputs.humsavar.html" />
+    <link rel="next" title="pypath.inputs.humancellmap" href="pypath.inputs.humancellmap.html" />
     <link rel="prev" title="pypath.inputs.htri" href="pypath.inputs.htri.html" />
   <meta name="viewport" content="width=device-width, initial-scale=1"/>
   <meta name="docsearch:language" content="en"/>
@@ -544,11 +544,11 @@ <h1>pypath.inputs.htri.htri_interactions<a class="headerlink" href="#pypath-inpu
       </div>
     </a>
     <a class="right-next"
-       href="pypath.inputs.humsavar.html"
+       href="pypath.inputs.humancellmap.html"
        title="next page">
       <div class="prev-next-info">
         <p class="prev-next-subtitle">next</p>
-        <p class="prev-next-title">pypath.inputs.humsavar</p>
+        <p class="prev-next-title">pypath.inputs.humancellmap</p>
       </div>
       <i class="fa-solid fa-angle-right"></i>
     </a>
diff --git a/api/pypath.inputs.humancellmap.html b/api/pypath.inputs.humancellmap.html
new file mode 100644
index 000000000..6846285bb
--- /dev/null
+++ b/api/pypath.inputs.humancellmap.html
@@ -0,0 +1,645 @@
+
+<!DOCTYPE html>
+
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+<html lang="en" data-content_root="../" >
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+
+    <title>pypath.inputs.humancellmap &#8212; pypath 0.16.9 documentation</title>
+  
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+  
+  <script data-cfasync="false">
+    document.documentElement.dataset.mode = localStorage.getItem("mode") || "";
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+    <script>DOCUMENTATION_OPTIONS.pagename = 'api/pypath.inputs.humancellmap';</script>
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+  
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+         placeholder="Search the docs ..."
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+  <span class="search-button__kbd-shortcut"><kbd class="kbd-shortcut__modifier">Ctrl</kbd>+<kbd>K</kbd></span>
+</form></div>
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+            <span class="sr-only">Saez Lab</span></a>
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diff --git a/api/pypath.inputs.humancellmap.humancellmap_annotations.html b/api/pypath.inputs.humancellmap.humancellmap_annotations.html
new file mode 100644
index 000000000..9ecd2300d
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new file mode 100644
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+<h1>pypath.inputs.humap.humap2_complexes<a class="headerlink" href="#pypath-inputs-humap-humap2-complexes" title="Link to this heading">§</a></h1>
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+<span class="sig-prename descclassname"><span class="pre">pypath.inputs.humap.</span></span><span class="sig-name descname"><span class="pre">humap2_complexes</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">min_confidence</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/inputs/humap.html#humap2_complexes"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.humap.humap2_complexes" title="Link to this definition">§</a></dt>
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+<dl class="py function">
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diff --git a/api/pypath.inputs.humsavar.html b/api/pypath.inputs.humsavar.html
index f62ce258e..a2ccd52c9 100644
--- a/api/pypath.inputs.humsavar.html
+++ b/api/pypath.inputs.humsavar.html
@@ -48,7 +48,7 @@
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
     <link rel="next" title="pypath.inputs.humsavar.uniprot_variants" href="pypath.inputs.humsavar.uniprot_variants.html" />
-    <link rel="prev" title="pypath.inputs.htri.htri_interactions" href="pypath.inputs.htri.htri_interactions.html" />
+    <link rel="prev" title="pypath.inputs.humap.humap_complexes" href="pypath.inputs.humap.humap_complexes.html" />
   <meta name="viewport" content="width=device-width, initial-scale=1"/>
   <meta name="docsearch:language" content="en"/>
   </head>
@@ -542,12 +542,12 @@
                   
 <div class="prev-next-area">
     <a class="left-prev"
-       href="pypath.inputs.htri.htri_interactions.html"
+       href="pypath.inputs.humap.humap_complexes.html"
        title="previous page">
       <i class="fa-solid fa-angle-left"></i>
       <div class="prev-next-info">
         <p class="prev-next-subtitle">previous</p>
-        <p class="prev-next-title">pypath.inputs.htri.htri_interactions</p>
+        <p class="prev-next-title">pypath.inputs.humap.humap_complexes</p>
       </div>
     </a>
     <a class="right-next"
diff --git a/api/pypath.inputs.humsavar.uniprot_variants.html b/api/pypath.inputs.humsavar.uniprot_variants.html
index 5ae613f55..b943da15b 100644
--- a/api/pypath.inputs.humsavar.uniprot_variants.html
+++ b/api/pypath.inputs.humsavar.uniprot_variants.html
@@ -47,7 +47,7 @@
     <link rel="icon" href="../_static/omnipath-logo.svg"/>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
-    <link rel="next" title="pypath.inputs.i3d" href="pypath.inputs.i3d.html" />
+    <link rel="next" title="pypath.inputs.huri" href="pypath.inputs.huri.html" />
     <link rel="prev" title="pypath.inputs.humsavar" href="pypath.inputs.humsavar.html" />
   <meta name="viewport" content="width=device-width, initial-scale=1"/>
   <meta name="docsearch:language" content="en"/>
@@ -550,11 +550,11 @@ <h1>pypath.inputs.humsavar.uniprot_variants<a class="headerlink" href="#pypath-i
       </div>
     </a>
     <a class="right-next"
-       href="pypath.inputs.i3d.html"
+       href="pypath.inputs.huri.html"
        title="next page">
       <div class="prev-next-info">
         <p class="prev-next-subtitle">next</p>
-        <p class="prev-next-title">pypath.inputs.i3d</p>
+        <p class="prev-next-title">pypath.inputs.huri</p>
       </div>
       <i class="fa-solid fa-angle-right"></i>
     </a>
diff --git a/api/pypath.inputs.huri.hi_i_interactions.html b/api/pypath.inputs.huri.hi_i_interactions.html
new file mode 100644
index 000000000..94c25e908
--- /dev/null
+++ b/api/pypath.inputs.huri.hi_i_interactions.html
@@ -0,0 +1,639 @@
+
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+  <section id="pypath-inputs-huri-hi-i-interactions">
+<h1>pypath.inputs.huri.hi_i_interactions<a class="headerlink" href="#pypath-inputs-huri-hi-i-interactions" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.inputs.huri.hi_i_interactions">
+<span class="sig-prename descclassname"><span class="pre">pypath.inputs.huri.</span></span><span class="sig-name descname"><span class="pre">hi_i_interactions</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/inputs/huri.html#hi_i_interactions"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.huri.hi_i_interactions" title="Link to this definition">§</a></dt>
+<dd><p>Interactions from Rual 2005 <a class="reference external" href="https://pubmed.ncbi.nlm.nih.gov/16189514/">https://pubmed.ncbi.nlm.nih.gov/16189514/</a>.</p>
+</dd></dl>
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diff --git a/api/pypath.inputs.huri.hi_ii_interactions.html b/api/pypath.inputs.huri.hi_ii_interactions.html
new file mode 100644
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+<h1>pypath.inputs.huri.hi_ii_interactions<a class="headerlink" href="#pypath-inputs-huri-hi-ii-interactions" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.inputs.huri.hi_ii_interactions">
+<span class="sig-prename descclassname"><span class="pre">pypath.inputs.huri.</span></span><span class="sig-name descname"><span class="pre">hi_ii_interactions</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/inputs/huri.html#hi_ii_interactions"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.huri.hi_ii_interactions" title="Link to this definition">§</a></dt>
+<dd><p>Interactions from Rolland 2014 <a class="reference external" href="https://pubmed.ncbi.nlm.nih.gov/25416956/">https://pubmed.ncbi.nlm.nih.gov/25416956/</a>.</p>
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diff --git a/api/pypath.inputs.huri.hi_iii_old.html b/api/pypath.inputs.huri.hi_iii_old.html
new file mode 100644
index 000000000..fc48079d7
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+  <section id="pypath-inputs-huri-hi-iii-old">
+<h1>pypath.inputs.huri.hi_iii_old<a class="headerlink" href="#pypath-inputs-huri-hi-iii-old" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.inputs.huri.hi_iii_old">
+<span class="sig-prename descclassname"><span class="pre">pypath.inputs.huri.</span></span><span class="sig-name descname"><span class="pre">hi_iii_old</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/inputs/huri.html#hi_iii_old"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.huri.hi_iii_old" title="Link to this definition">§</a></dt>
+<dd><p>Loads the unbiased human interactome version III (HI-III).
+This is an unpublished data and its use is limited.
+Please check the conditions and licensing terms carefully at
+<a class="reference external" href="http://interactome.baderlab.org">http://interactome.baderlab.org</a>.</p>
+</dd></dl>
+
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diff --git a/api/pypath.inputs.huri.hi_union_interactions.html b/api/pypath.inputs.huri.hi_union_interactions.html
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+<h1>pypath.inputs.huri.hi_union_interactions<a class="headerlink" href="#pypath-inputs-huri-hi-union-interactions" title="Link to this heading">§</a></h1>
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+<span class="sig-prename descclassname"><span class="pre">pypath.inputs.huri.</span></span><span class="sig-name descname"><span class="pre">hi_union_interactions</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/inputs/huri.html#hi_union_interactions"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.huri.hi_union_interactions" title="Link to this definition">§</a></dt>
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+  <section id="module-pypath.inputs.huri">
+<span id="pypath-inputs-huri"></span><h1>pypath.inputs.huri<a class="headerlink" href="#module-pypath.inputs.huri" title="Link to this heading">§</a></h1>
+<dl class="field-list simple">
+<dt class="field-odd">members<span class="colon">:</span></dt>
+<dd class="field-odd"><p></p></dd>
+</dl>
+<p class="rubric">Functions</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.inputs.huri.hi_i_interactions.html#pypath.inputs.huri.hi_i_interactions" title="pypath.inputs.huri.hi_i_interactions"><code class="xref py py-obj docutils literal notranslate"><span class="pre">hi_i_interactions</span></code></a>()</p></td>
+<td><p>Interactions from Rual 2005 <a class="reference external" href="https://pubmed.ncbi.nlm.nih.gov/16189514/">https://pubmed.ncbi.nlm.nih.gov/16189514/</a>.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.inputs.huri.hi_ii_interactions.html#pypath.inputs.huri.hi_ii_interactions" title="pypath.inputs.huri.hi_ii_interactions"><code class="xref py py-obj docutils literal notranslate"><span class="pre">hi_ii_interactions</span></code></a>()</p></td>
+<td><p>Interactions from Rolland 2014 <a class="reference external" href="https://pubmed.ncbi.nlm.nih.gov/25416956/">https://pubmed.ncbi.nlm.nih.gov/25416956/</a>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.inputs.huri.hi_iii_old.html#pypath.inputs.huri.hi_iii_old" title="pypath.inputs.huri.hi_iii_old"><code class="xref py py-obj docutils literal notranslate"><span class="pre">hi_iii_old</span></code></a>()</p></td>
+<td><p>Loads the unbiased human interactome version III (HI-III).</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.inputs.huri.hi_union_interactions.html#pypath.inputs.huri.hi_union_interactions" title="pypath.inputs.huri.hi_union_interactions"><code class="xref py py-obj docutils literal notranslate"><span class="pre">hi_union_interactions</span></code></a>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.inputs.huri.huri_interactions.html#pypath.inputs.huri.huri_interactions" title="pypath.inputs.huri.huri_interactions"><code class="xref py py-obj docutils literal notranslate"><span class="pre">huri_interactions</span></code></a>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.inputs.huri.lit_bm_13_interactions.html#pypath.inputs.huri.lit_bm_13_interactions" title="pypath.inputs.huri.lit_bm_13_interactions"><code class="xref py py-obj docutils literal notranslate"><span class="pre">lit_bm_13_interactions</span></code></a>()</p></td>
+<td><p>Downloads and processes Lit-BM-13 dataset, the 2013 version of the high confidence literature curated interactions from CCSB.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.inputs.huri.lit_bm_17_interactions.html#pypath.inputs.huri.lit_bm_17_interactions" title="pypath.inputs.huri.lit_bm_17_interactions"><code class="xref py py-obj docutils literal notranslate"><span class="pre">lit_bm_17_interactions</span></code></a>()</p></td>
+<td><p>Downloads and processes Lit-BM-13 dataset, the 2017 version of the high confidence literature curated interactions from CCSB.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.inputs.huri.lit_bm_interactions.html#pypath.inputs.huri.lit_bm_interactions" title="pypath.inputs.huri.lit_bm_interactions"><code class="xref py py-obj docutils literal notranslate"><span class="pre">lit_bm_interactions</span></code></a>()</p></td>
+<td><p>Literature collected interactions from Luck 2020.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.inputs.huri.rolland_hi_ii_14.html#pypath.inputs.huri.rolland_hi_ii_14" title="pypath.inputs.huri.rolland_hi_ii_14"><code class="xref py py-obj docutils literal notranslate"><span class="pre">rolland_hi_ii_14</span></code></a>()</p></td>
+<td><p>Loads the HI-II-14 unbiased interactome from the large scale screening of from Rolland 2014.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.inputs.huri.vidal_hi_iii_old.html#pypath.inputs.huri.vidal_hi_iii_old" title="pypath.inputs.huri.vidal_hi_iii_old"><code class="xref py py-obj docutils literal notranslate"><span class="pre">vidal_hi_iii_old</span></code></a>(fname)</p></td>
+<td><p>Loads the HI-III  unbiased interactome from preliminary data of the next large scale screening of Vidal Lab.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.inputs.huri.yang2016_interactions.html#pypath.inputs.huri.yang2016_interactions" title="pypath.inputs.huri.yang2016_interactions"><code class="xref py py-obj docutils literal notranslate"><span class="pre">yang2016_interactions</span></code></a>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.inputs.huri.yu2011_interactions.html#pypath.inputs.huri.yu2011_interactions" title="pypath.inputs.huri.yu2011_interactions"><code class="xref py py-obj docutils literal notranslate"><span class="pre">yu2011_interactions</span></code></a>()</p></td>
+<td><p></p></td>
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diff --git a/api/pypath.inputs.huri.lit_bm_13_interactions.html b/api/pypath.inputs.huri.lit_bm_13_interactions.html
new file mode 100644
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+  <section id="pypath-inputs-huri-lit-bm-13-interactions">
+<h1>pypath.inputs.huri.lit_bm_13_interactions<a class="headerlink" href="#pypath-inputs-huri-lit-bm-13-interactions" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.inputs.huri.lit_bm_13_interactions">
+<span class="sig-prename descclassname"><span class="pre">pypath.inputs.huri.</span></span><span class="sig-name descname"><span class="pre">lit_bm_13_interactions</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/inputs/huri.html#lit_bm_13_interactions"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.huri.lit_bm_13_interactions" title="Link to this definition">§</a></dt>
+<dd><p>Downloads and processes Lit-BM-13 dataset, the 2013 version of the
+high confidence literature curated interactions from CCSB.
+Returns list of interactions.</p>
+</dd></dl>
+
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diff --git a/api/pypath.inputs.huri.lit_bm_17_interactions.html b/api/pypath.inputs.huri.lit_bm_17_interactions.html
new file mode 100644
index 000000000..8975fe046
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+  <section id="pypath-inputs-huri-lit-bm-17-interactions">
+<h1>pypath.inputs.huri.lit_bm_17_interactions<a class="headerlink" href="#pypath-inputs-huri-lit-bm-17-interactions" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.inputs.huri.lit_bm_17_interactions">
+<span class="sig-prename descclassname"><span class="pre">pypath.inputs.huri.</span></span><span class="sig-name descname"><span class="pre">lit_bm_17_interactions</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/inputs/huri.html#lit_bm_17_interactions"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.huri.lit_bm_17_interactions" title="Link to this definition">§</a></dt>
+<dd><p>Downloads and processes Lit-BM-13 dataset, the 2017 version of the
+high confidence literature curated interactions from CCSB.
+Returns list of interactions.</p>
+</dd></dl>
+
+</section>
+
+
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diff --git a/api/pypath.inputs.huri.lit_bm_interactions.html b/api/pypath.inputs.huri.lit_bm_interactions.html
new file mode 100644
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+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.inputs.huri.lit_bm_interactions">
+<span class="sig-prename descclassname"><span class="pre">pypath.inputs.huri.</span></span><span class="sig-name descname"><span class="pre">lit_bm_interactions</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/inputs/huri.html#lit_bm_interactions"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.huri.lit_bm_interactions" title="Link to this definition">§</a></dt>
+<dd><p>Literature collected interactions from Luck 2020.</p>
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+  <section id="pypath-inputs-huri-rolland-hi-ii-14">
+<h1>pypath.inputs.huri.rolland_hi_ii_14<a class="headerlink" href="#pypath-inputs-huri-rolland-hi-ii-14" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.inputs.huri.rolland_hi_ii_14">
+<span class="sig-prename descclassname"><span class="pre">pypath.inputs.huri.</span></span><span class="sig-name descname"><span class="pre">rolland_hi_ii_14</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/inputs/huri.html#rolland_hi_ii_14"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.huri.rolland_hi_ii_14" title="Link to this definition">§</a></dt>
+<dd><p>Loads the HI-II-14 unbiased interactome from the large scale screening
+of from Rolland 2014.
+Returns list of interactions.</p>
+</dd></dl>
+
+</section>
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new file mode 100644
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+  <section id="pypath-inputs-huri-vidal-hi-iii-old">
+<h1>pypath.inputs.huri.vidal_hi_iii_old<a class="headerlink" href="#pypath-inputs-huri-vidal-hi-iii-old" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.inputs.huri.vidal_hi_iii_old">
+<span class="sig-prename descclassname"><span class="pre">pypath.inputs.huri.</span></span><span class="sig-name descname"><span class="pre">vidal_hi_iii_old</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">fname</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/inputs/huri.html#vidal_hi_iii_old"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.huri.vidal_hi_iii_old" title="Link to this definition">§</a></dt>
+<dd><p>Loads the HI-III  unbiased interactome from preliminary data of
+the next large scale screening of Vidal Lab.</p>
+<dl class="simple">
+<dt>The data is accessible here:</dt><dd><p><a class="reference external" href="http://interactome.dfci.harvard.edu/H_sapiens/dload_trk.php">http://interactome.dfci.harvard.edu/H_sapiens/dload_trk.php</a></p>
+</dd>
+</dl>
+<p>You need to register and accept the license terms.</p>
+<p>Returns list of interactions.</p>
+</dd></dl>
+
+</section>
+
+
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diff --git a/api/pypath.inputs.huri.yang2016_interactions.html b/api/pypath.inputs.huri.yang2016_interactions.html
new file mode 100644
index 000000000..b3bc789d6
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diff --git a/api/pypath.inputs.i3d.get_i3d.html b/api/pypath.inputs.i3d.get_i3d.html
index 91a73a897..9df1010a7 100644
--- a/api/pypath.inputs.i3d.get_i3d.html
+++ b/api/pypath.inputs.i3d.get_i3d.html
@@ -47,7 +47,7 @@
     <link rel="icon" href="../_static/omnipath-logo.svg"/>
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-    <link rel="next" title="pypath.inputs.ielm" href="pypath.inputs.ielm.html" />
+    <link rel="next" title="pypath.inputs.icellnet" href="pypath.inputs.icellnet.html" />
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   <meta name="viewport" content="width=device-width, initial-scale=1"/>
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@@ -548,11 +548,11 @@ <h1>pypath.inputs.i3d.get_i3d<a class="headerlink" href="#pypath-inputs-i3d-get-
       </div>
     </a>
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-       href="pypath.inputs.ielm.html"
+       href="pypath.inputs.icellnet.html"
        title="next page">
       <div class="prev-next-info">
         <p class="prev-next-subtitle">next</p>
-        <p class="prev-next-title">pypath.inputs.ielm</p>
+        <p class="prev-next-title">pypath.inputs.icellnet</p>
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diff --git a/api/pypath.inputs.i3d.html b/api/pypath.inputs.i3d.html
index a42d88d4c..7d21b5c9b 100644
--- a/api/pypath.inputs.i3d.html
+++ b/api/pypath.inputs.i3d.html
@@ -48,7 +48,7 @@
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+    <link rel="prev" title="pypath.inputs.huri.yu2011_interactions" href="pypath.inputs.huri.yu2011_interactions.html" />
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@@ -542,12 +542,12 @@
                   
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+       href="pypath.inputs.huri.yu2011_interactions.html"
        title="previous page">
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       <div class="prev-next-info">
         <p class="prev-next-subtitle">previous</p>
-        <p class="prev-next-title">pypath.inputs.humsavar.uniprot_variants</p>
+        <p class="prev-next-title">pypath.inputs.huri.yu2011_interactions</p>
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diff --git a/api/pypath.inputs.icellnet.IcellnetRecord.html b/api/pypath.inputs.icellnet.IcellnetRecord.html
new file mode 100644
index 000000000..73fa4daac
--- /dev/null
+++ b/api/pypath.inputs.icellnet.IcellnetRecord.html
@@ -0,0 +1,739 @@
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+  <section id="pypath-inputs-icellnet-icellnetrecord">
+<h1>pypath.inputs.icellnet.IcellnetRecord<a class="headerlink" href="#pypath-inputs-icellnet-icellnetrecord" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.inputs.icellnet.IcellnetRecord">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.inputs.icellnet.</span></span><span class="sig-name descname"><span class="pre">IcellnetRecord</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">ligand</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">receptor</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">family</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">subfamily</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">classification</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resources</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.inputs.icellnet.IcellnetRecord" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">tuple</span></code></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.inputs.icellnet.IcellnetRecord.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.inputs.icellnet.IcellnetRecord.__init__" title="Link to this definition">§</a></dt>
+<dd></dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.inputs.icellnet.IcellnetRecord.__init__" title="pypath.inputs.icellnet.IcellnetRecord.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.inputs.icellnet.IcellnetRecord.count" title="pypath.inputs.icellnet.IcellnetRecord.count"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count</span></code></a>(value, /)</p></td>
+<td><p>Return number of occurrences of value.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.inputs.icellnet.IcellnetRecord.index" title="pypath.inputs.icellnet.IcellnetRecord.index"><code class="xref py py-obj docutils literal notranslate"><span class="pre">index</span></code></a>(value[, start, stop])</p></td>
+<td><p>Return first index of value.</p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Attributes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.inputs.icellnet.IcellnetRecord.classification" title="pypath.inputs.icellnet.IcellnetRecord.classification"><code class="xref py py-obj docutils literal notranslate"><span class="pre">classification</span></code></a></p></td>
+<td><p>Alias for field number 4</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.inputs.icellnet.IcellnetRecord.family" title="pypath.inputs.icellnet.IcellnetRecord.family"><code class="xref py py-obj docutils literal notranslate"><span class="pre">family</span></code></a></p></td>
+<td><p>Alias for field number 2</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.inputs.icellnet.IcellnetRecord.ligand" title="pypath.inputs.icellnet.IcellnetRecord.ligand"><code class="xref py py-obj docutils literal notranslate"><span class="pre">ligand</span></code></a></p></td>
+<td><p>Alias for field number 0</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.inputs.icellnet.IcellnetRecord.receptor" title="pypath.inputs.icellnet.IcellnetRecord.receptor"><code class="xref py py-obj docutils literal notranslate"><span class="pre">receptor</span></code></a></p></td>
+<td><p>Alias for field number 1</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.inputs.icellnet.IcellnetRecord.references" title="pypath.inputs.icellnet.IcellnetRecord.references"><code class="xref py py-obj docutils literal notranslate"><span class="pre">references</span></code></a></p></td>
+<td><p>Alias for field number 6</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.inputs.icellnet.IcellnetRecord.resources" title="pypath.inputs.icellnet.IcellnetRecord.resources"><code class="xref py py-obj docutils literal notranslate"><span class="pre">resources</span></code></a></p></td>
+<td><p>Alias for field number 5</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.inputs.icellnet.IcellnetRecord.subfamily" title="pypath.inputs.icellnet.IcellnetRecord.subfamily"><code class="xref py py-obj docutils literal notranslate"><span class="pre">subfamily</span></code></a></p></td>
+<td><p>Alias for field number 3</p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.inputs.icellnet.IcellnetRecord.classification">
+<span class="sig-name descname"><span class="pre">classification</span></span><a class="headerlink" href="#pypath.inputs.icellnet.IcellnetRecord.classification" title="Link to this definition">§</a></dt>
+<dd><p>Alias for field number 4</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.inputs.icellnet.IcellnetRecord.count">
+<span class="sig-name descname"><span class="pre">count</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">value</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">/</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.inputs.icellnet.IcellnetRecord.count" title="Link to this definition">§</a></dt>
+<dd><p>Return number of occurrences of value.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.inputs.icellnet.IcellnetRecord.family">
+<span class="sig-name descname"><span class="pre">family</span></span><a class="headerlink" href="#pypath.inputs.icellnet.IcellnetRecord.family" title="Link to this definition">§</a></dt>
+<dd><p>Alias for field number 2</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.inputs.icellnet.IcellnetRecord.index">
+<span class="sig-name descname"><span class="pre">index</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">value</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">start</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">stop</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9223372036854775807</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">/</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.inputs.icellnet.IcellnetRecord.index" title="Link to this definition">§</a></dt>
+<dd><p>Return first index of value.</p>
+<p>Raises ValueError if the value is not present.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.inputs.icellnet.IcellnetRecord.ligand">
+<span class="sig-name descname"><span class="pre">ligand</span></span><a class="headerlink" href="#pypath.inputs.icellnet.IcellnetRecord.ligand" title="Link to this definition">§</a></dt>
+<dd><p>Alias for field number 0</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.inputs.icellnet.IcellnetRecord.receptor">
+<span class="sig-name descname"><span class="pre">receptor</span></span><a class="headerlink" href="#pypath.inputs.icellnet.IcellnetRecord.receptor" title="Link to this definition">§</a></dt>
+<dd><p>Alias for field number 1</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.inputs.icellnet.IcellnetRecord.references">
+<span class="sig-name descname"><span class="pre">references</span></span><a class="headerlink" href="#pypath.inputs.icellnet.IcellnetRecord.references" title="Link to this definition">§</a></dt>
+<dd><p>Alias for field number 6</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.inputs.icellnet.IcellnetRecord.resources">
+<span class="sig-name descname"><span class="pre">resources</span></span><a class="headerlink" href="#pypath.inputs.icellnet.IcellnetRecord.resources" title="Link to this definition">§</a></dt>
+<dd><p>Alias for field number 5</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.inputs.icellnet.IcellnetRecord.subfamily">
+<span class="sig-name descname"><span class="pre">subfamily</span></span><a class="headerlink" href="#pypath.inputs.icellnet.IcellnetRecord.subfamily" title="Link to this definition">§</a></dt>
+<dd><p>Alias for field number 3</p>
+</dd></dl>
+
+</dd></dl>
+
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+
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diff --git a/api/pypath.inputs.icellnet.html b/api/pypath.inputs.icellnet.html
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diff --git a/api/pypath.inputs.icellnet.icellnet_annotations.html b/api/pypath.inputs.icellnet.icellnet_annotations.html
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new file mode 100644
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diff --git a/api/pypath.inputs.ielm.html b/api/pypath.inputs.ielm.html
index 91bcea950..7b146c304 100644
--- a/api/pypath.inputs.ielm.html
+++ b/api/pypath.inputs.ielm.html
@@ -48,7 +48,7 @@
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-    <link rel="prev" title="pypath.inputs.i3d.get_i3d" href="pypath.inputs.i3d.get_i3d.html" />
+    <link rel="prev" title="pypath.inputs.icellnet.IcellnetRecord" href="pypath.inputs.icellnet.IcellnetRecord.html" />
   <meta name="viewport" content="width=device-width, initial-scale=1"/>
   <meta name="docsearch:language" content="en"/>
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@@ -545,12 +545,12 @@
                   
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+       href="pypath.inputs.icellnet.IcellnetRecord.html"
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         <p class="prev-next-subtitle">previous</p>
-        <p class="prev-next-title">pypath.inputs.i3d.get_i3d</p>
+        <p class="prev-next-title">pypath.inputs.icellnet.IcellnetRecord</p>
       </div>
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diff --git a/api/pypath.inputs.intact.intact_interactions.html b/api/pypath.inputs.intact.intact_interactions.html
index a375a21c6..b227bb541 100644
--- a/api/pypath.inputs.intact.intact_interactions.html
+++ b/api/pypath.inputs.intact.intact_interactions.html
@@ -47,7 +47,7 @@
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-    <link rel="next" title="pypath.inputs.interpro" href="pypath.inputs.interpro.html" />
+    <link rel="next" title="pypath.inputs.integrins" href="pypath.inputs.integrins.html" />
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   <meta name="viewport" content="width=device-width, initial-scale=1"/>
   <meta name="docsearch:language" content="en"/>
@@ -551,11 +551,11 @@ <h1>pypath.inputs.intact.intact_interactions<a class="headerlink" href="#pypath-
       </div>
     </a>
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-       href="pypath.inputs.interpro.html"
+       href="pypath.inputs.integrins.html"
        title="next page">
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         <p class="prev-next-subtitle">next</p>
-        <p class="prev-next-title">pypath.inputs.interpro</p>
+        <p class="prev-next-title">pypath.inputs.integrins</p>
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diff --git a/api/pypath.inputs.integrins.get_integrins.html b/api/pypath.inputs.integrins.get_integrins.html
new file mode 100644
index 000000000..efb9f9c9a
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+++ b/api/pypath.inputs.integrins.get_integrins.html
@@ -0,0 +1,640 @@
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+  <section id="pypath-inputs-integrins-get-integrins">
+<h1>pypath.inputs.integrins.get_integrins<a class="headerlink" href="#pypath-inputs-integrins-get-integrins" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.inputs.integrins.get_integrins">
+<span class="sig-prename descclassname"><span class="pre">pypath.inputs.integrins.</span></span><span class="sig-name descname"><span class="pre">get_integrins</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/inputs/integrins.html#get_integrins"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.integrins.get_integrins" title="Link to this definition">§</a></dt>
+<dd><p>Returns a set of the UniProt IDs of the human integrins from
+Table 1 of Takada et al 2007 (10.1186/gb-2007-8-5-215).</p>
+</dd></dl>
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+  <section id="module-pypath.inputs.integrins">
+<span id="pypath-inputs-integrins"></span><h1>pypath.inputs.integrins<a class="headerlink" href="#module-pypath.inputs.integrins" title="Link to this heading">§</a></h1>
+<dl class="field-list simple">
+<dt class="field-odd">members<span class="colon">:</span></dt>
+<dd class="field-odd"><p></p></dd>
+</dl>
+<p class="rubric">Functions</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.inputs.integrins.get_integrins.html#pypath.inputs.integrins.get_integrins" title="pypath.inputs.integrins.get_integrins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_integrins</span></code></a>()</p></td>
+<td><p>Returns a set of the UniProt IDs of the human integrins from Table 1 of Takada et al 2007 (10.1186/gb-2007-8-5-215).</p></td>
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diff --git a/api/pypath.inputs.interpro.html b/api/pypath.inputs.interpro.html
index 878596946..ca868817d 100644
--- a/api/pypath.inputs.interpro.html
+++ b/api/pypath.inputs.interpro.html
@@ -48,7 +48,7 @@
     <link rel="index" title="Index" href="../genindex.html" />
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     <link rel="next" title="pypath.inputs.interpro.interpro2go_annotations" href="pypath.inputs.interpro.interpro2go_annotations.html" />
-    <link rel="prev" title="pypath.inputs.intact.intact_interactions" href="pypath.inputs.intact.intact_interactions.html" />
+    <link rel="prev" title="pypath.inputs.integrins.get_integrins" href="pypath.inputs.integrins.get_integrins.html" />
   <meta name="viewport" content="width=device-width, initial-scale=1"/>
   <meta name="docsearch:language" content="en"/>
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@@ -551,12 +551,12 @@
                   
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-       href="pypath.inputs.intact.intact_interactions.html"
+       href="pypath.inputs.integrins.get_integrins.html"
        title="previous page">
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       <div class="prev-next-info">
         <p class="prev-next-subtitle">previous</p>
-        <p class="prev-next-title">pypath.inputs.intact.intact_interactions</p>
+        <p class="prev-next-title">pypath.inputs.integrins.get_integrins</p>
       </div>
     </a>
     <a class="right-next"
diff --git a/api/pypath.inputs.interpro.interpro_xrefs.html b/api/pypath.inputs.interpro.interpro_xrefs.html
index d27edef8d..32951b125 100644
--- a/api/pypath.inputs.interpro.interpro_xrefs.html
+++ b/api/pypath.inputs.interpro.interpro_xrefs.html
@@ -47,7 +47,7 @@
     <link rel="icon" href="../_static/omnipath-logo.svg"/>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
-    <link rel="next" title="pypath.inputs.ipi" href="pypath.inputs.ipi.html" />
+    <link rel="next" title="pypath.inputs.intogen" href="pypath.inputs.intogen.html" />
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   <meta name="viewport" content="width=device-width, initial-scale=1"/>
   <meta name="docsearch:language" content="en"/>
@@ -556,11 +556,11 @@ <h1>pypath.inputs.interpro.interpro_xrefs<a class="headerlink" href="#pypath-inp
       </div>
     </a>
     <a class="right-next"
-       href="pypath.inputs.ipi.html"
+       href="pypath.inputs.intogen.html"
        title="next page">
       <div class="prev-next-info">
         <p class="prev-next-subtitle">next</p>
-        <p class="prev-next-title">pypath.inputs.ipi</p>
+        <p class="prev-next-title">pypath.inputs.intogen</p>
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diff --git a/api/pypath.inputs.intogen.html b/api/pypath.inputs.intogen.html
new file mode 100644
index 000000000..73b89577d
--- /dev/null
+++ b/api/pypath.inputs.intogen.html
@@ -0,0 +1,645 @@
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+  <section id="module-pypath.inputs.intogen">
+<span id="pypath-inputs-intogen"></span><h1>pypath.inputs.intogen<a class="headerlink" href="#module-pypath.inputs.intogen" title="Link to this heading">§</a></h1>
+<dl class="field-list simple">
+<dt class="field-odd">members<span class="colon">:</span></dt>
+<dd class="field-odd"><p></p></dd>
+</dl>
+<p class="rubric">Functions</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.inputs.intogen.intogen_annotations.html#pypath.inputs.intogen.intogen_annotations" title="pypath.inputs.intogen.intogen_annotations"><code class="xref py py-obj docutils literal notranslate"><span class="pre">intogen_annotations</span></code></a>()</p></td>
+<td><p>Returns a list of cancer driver genes with their annotations, according to the IntOGen database.</p></td>
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diff --git a/api/pypath.inputs.intogen.intogen_annotations.html b/api/pypath.inputs.intogen.intogen_annotations.html
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+    
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+  </ul>
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+</div>
+      
+    </div>
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+                <article class="bd-article">
+                  
+  <section id="pypath-inputs-intogen-intogen-annotations">
+<h1>pypath.inputs.intogen.intogen_annotations<a class="headerlink" href="#pypath-inputs-intogen-intogen-annotations" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.inputs.intogen.intogen_annotations">
+<span class="sig-prename descclassname"><span class="pre">pypath.inputs.intogen.</span></span><span class="sig-name descname"><span class="pre">intogen_annotations</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/inputs/intogen.html#intogen_annotations"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.intogen.intogen_annotations" title="Link to this definition">§</a></dt>
+<dd><p>Returns a list of cancer driver genes with their annotations,
+according to the IntOGen database.</p>
+</dd></dl>
+
+</section>
+
+
+                </article>
+              
+              
+              
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\ No newline at end of file
diff --git a/api/pypath.inputs.ipi.html b/api/pypath.inputs.ipi.html
index a539f5bd0..b218b6252 100644
--- a/api/pypath.inputs.ipi.html
+++ b/api/pypath.inputs.ipi.html
@@ -48,7 +48,7 @@
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
     <link rel="next" title="pypath.inputs.ipi.ipi_uniprot" href="pypath.inputs.ipi.ipi_uniprot.html" />
-    <link rel="prev" title="pypath.inputs.interpro.interpro_xrefs" href="pypath.inputs.interpro.interpro_xrefs.html" />
+    <link rel="prev" title="pypath.inputs.intogen.intogen_annotations" href="pypath.inputs.intogen.intogen_annotations.html" />
   <meta name="viewport" content="width=device-width, initial-scale=1"/>
   <meta name="docsearch:language" content="en"/>
   </head>
@@ -542,12 +542,12 @@
                   
 <div class="prev-next-area">
     <a class="left-prev"
-       href="pypath.inputs.interpro.interpro_xrefs.html"
+       href="pypath.inputs.intogen.intogen_annotations.html"
        title="previous page">
       <i class="fa-solid fa-angle-left"></i>
       <div class="prev-next-info">
         <p class="prev-next-subtitle">previous</p>
-        <p class="prev-next-title">pypath.inputs.interpro.interpro_xrefs</p>
+        <p class="prev-next-title">pypath.inputs.intogen.intogen_annotations</p>
       </div>
     </a>
     <a class="right-next"
diff --git a/api/pypath.inputs.ipi.ipi_uniprot.html b/api/pypath.inputs.ipi.ipi_uniprot.html
index 7bec66bb2..4e31bf63c 100644
--- a/api/pypath.inputs.ipi.ipi_uniprot.html
+++ b/api/pypath.inputs.ipi.ipi_uniprot.html
@@ -47,7 +47,7 @@
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@@ -545,11 +545,11 @@ <h1>pypath.inputs.ipi.ipi_uniprot<a class="headerlink" href="#pypath-inputs-ipi-
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diff --git a/api/pypath.inputs.iptmnet.IptmnetInteraction.html b/api/pypath.inputs.iptmnet.IptmnetInteraction.html
new file mode 100644
index 000000000..98b4fb171
--- /dev/null
+++ b/api/pypath.inputs.iptmnet.IptmnetInteraction.html
@@ -0,0 +1,757 @@
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+  <section id="pypath-inputs-iptmnet-iptmnetinteraction">
+<h1>pypath.inputs.iptmnet.IptmnetInteraction<a class="headerlink" href="#pypath-inputs-iptmnet-iptmnetinteraction" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.inputs.iptmnet.IptmnetInteraction">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.inputs.iptmnet.</span></span><span class="sig-name descname"><span class="pre">IptmnetInteraction</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">enzyme</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">substrate</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">enzyme_isoform</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">substrate_isoform</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ptm_type</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resaa</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resnum</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">score</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.inputs.iptmnet.IptmnetInteraction" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">tuple</span></code></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.inputs.iptmnet.IptmnetInteraction.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.inputs.iptmnet.IptmnetInteraction.__init__" title="Link to this definition">§</a></dt>
+<dd></dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.inputs.iptmnet.IptmnetInteraction.__init__" title="pypath.inputs.iptmnet.IptmnetInteraction.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.inputs.iptmnet.IptmnetInteraction.count" title="pypath.inputs.iptmnet.IptmnetInteraction.count"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count</span></code></a>(value, /)</p></td>
+<td><p>Return number of occurrences of value.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.inputs.iptmnet.IptmnetInteraction.index" title="pypath.inputs.iptmnet.IptmnetInteraction.index"><code class="xref py py-obj docutils literal notranslate"><span class="pre">index</span></code></a>(value[, start, stop])</p></td>
+<td><p>Return first index of value.</p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Attributes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.inputs.iptmnet.IptmnetInteraction.enzyme" title="pypath.inputs.iptmnet.IptmnetInteraction.enzyme"><code class="xref py py-obj docutils literal notranslate"><span class="pre">enzyme</span></code></a></p></td>
+<td><p>Alias for field number 0</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.inputs.iptmnet.IptmnetInteraction.enzyme_isoform" title="pypath.inputs.iptmnet.IptmnetInteraction.enzyme_isoform"><code class="xref py py-obj docutils literal notranslate"><span class="pre">enzyme_isoform</span></code></a></p></td>
+<td><p>Alias for field number 2</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.inputs.iptmnet.IptmnetInteraction.ptm_type" title="pypath.inputs.iptmnet.IptmnetInteraction.ptm_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">ptm_type</span></code></a></p></td>
+<td><p>Alias for field number 4</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.inputs.iptmnet.IptmnetInteraction.references" title="pypath.inputs.iptmnet.IptmnetInteraction.references"><code class="xref py py-obj docutils literal notranslate"><span class="pre">references</span></code></a></p></td>
+<td><p>Alias for field number 8</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.inputs.iptmnet.IptmnetInteraction.resaa" title="pypath.inputs.iptmnet.IptmnetInteraction.resaa"><code class="xref py py-obj docutils literal notranslate"><span class="pre">resaa</span></code></a></p></td>
+<td><p>Alias for field number 5</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.inputs.iptmnet.IptmnetInteraction.resnum" title="pypath.inputs.iptmnet.IptmnetInteraction.resnum"><code class="xref py py-obj docutils literal notranslate"><span class="pre">resnum</span></code></a></p></td>
+<td><p>Alias for field number 6</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.inputs.iptmnet.IptmnetInteraction.score" title="pypath.inputs.iptmnet.IptmnetInteraction.score"><code class="xref py py-obj docutils literal notranslate"><span class="pre">score</span></code></a></p></td>
+<td><p>Alias for field number 7</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.inputs.iptmnet.IptmnetInteraction.substrate" title="pypath.inputs.iptmnet.IptmnetInteraction.substrate"><code class="xref py py-obj docutils literal notranslate"><span class="pre">substrate</span></code></a></p></td>
+<td><p>Alias for field number 1</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.inputs.iptmnet.IptmnetInteraction.substrate_isoform" title="pypath.inputs.iptmnet.IptmnetInteraction.substrate_isoform"><code class="xref py py-obj docutils literal notranslate"><span class="pre">substrate_isoform</span></code></a></p></td>
+<td><p>Alias for field number 3</p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.inputs.iptmnet.IptmnetInteraction.count">
+<span class="sig-name descname"><span class="pre">count</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">value</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">/</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.inputs.iptmnet.IptmnetInteraction.count" title="Link to this definition">§</a></dt>
+<dd><p>Return number of occurrences of value.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.inputs.iptmnet.IptmnetInteraction.enzyme">
+<span class="sig-name descname"><span class="pre">enzyme</span></span><a class="headerlink" href="#pypath.inputs.iptmnet.IptmnetInteraction.enzyme" title="Link to this definition">§</a></dt>
+<dd><p>Alias for field number 0</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.inputs.iptmnet.IptmnetInteraction.enzyme_isoform">
+<span class="sig-name descname"><span class="pre">enzyme_isoform</span></span><a class="headerlink" href="#pypath.inputs.iptmnet.IptmnetInteraction.enzyme_isoform" title="Link to this definition">§</a></dt>
+<dd><p>Alias for field number 2</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.inputs.iptmnet.IptmnetInteraction.index">
+<span class="sig-name descname"><span class="pre">index</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">value</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">start</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">stop</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9223372036854775807</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">/</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.inputs.iptmnet.IptmnetInteraction.index" title="Link to this definition">§</a></dt>
+<dd><p>Return first index of value.</p>
+<p>Raises ValueError if the value is not present.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.inputs.iptmnet.IptmnetInteraction.ptm_type">
+<span class="sig-name descname"><span class="pre">ptm_type</span></span><a class="headerlink" href="#pypath.inputs.iptmnet.IptmnetInteraction.ptm_type" title="Link to this definition">§</a></dt>
+<dd><p>Alias for field number 4</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.inputs.iptmnet.IptmnetInteraction.references">
+<span class="sig-name descname"><span class="pre">references</span></span><a class="headerlink" href="#pypath.inputs.iptmnet.IptmnetInteraction.references" title="Link to this definition">§</a></dt>
+<dd><p>Alias for field number 8</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.inputs.iptmnet.IptmnetInteraction.resaa">
+<span class="sig-name descname"><span class="pre">resaa</span></span><a class="headerlink" href="#pypath.inputs.iptmnet.IptmnetInteraction.resaa" title="Link to this definition">§</a></dt>
+<dd><p>Alias for field number 5</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.inputs.iptmnet.IptmnetInteraction.resnum">
+<span class="sig-name descname"><span class="pre">resnum</span></span><a class="headerlink" href="#pypath.inputs.iptmnet.IptmnetInteraction.resnum" title="Link to this definition">§</a></dt>
+<dd><p>Alias for field number 6</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.inputs.iptmnet.IptmnetInteraction.score">
+<span class="sig-name descname"><span class="pre">score</span></span><a class="headerlink" href="#pypath.inputs.iptmnet.IptmnetInteraction.score" title="Link to this definition">§</a></dt>
+<dd><p>Alias for field number 7</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.inputs.iptmnet.IptmnetInteraction.substrate">
+<span class="sig-name descname"><span class="pre">substrate</span></span><a class="headerlink" href="#pypath.inputs.iptmnet.IptmnetInteraction.substrate" title="Link to this definition">§</a></dt>
+<dd><p>Alias for field number 1</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.inputs.iptmnet.IptmnetInteraction.substrate_isoform">
+<span class="sig-name descname"><span class="pre">substrate_isoform</span></span><a class="headerlink" href="#pypath.inputs.iptmnet.IptmnetInteraction.substrate_isoform" title="Link to this definition">§</a></dt>
+<dd><p>Alias for field number 3</p>
+</dd></dl>
+
+</dd></dl>
+
+</section>
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diff --git a/api/pypath.inputs.iptmnet.iptmnet_interactions.html b/api/pypath.inputs.iptmnet.iptmnet_interactions.html
new file mode 100644
index 000000000..1b4ab2f69
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diff --git a/api/pypath.inputs.italk.italk_interactions.html b/api/pypath.inputs.italk.italk_interactions.html
new file mode 100644
index 000000000..906cc95b5
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diff --git a/api/pypath.inputs.italk.italk_raw.html b/api/pypath.inputs.italk.italk_raw.html
new file mode 100644
index 000000000..d0b946e5e
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+<span class="sig-prename descclassname"><span class="pre">pypath.inputs.italk.</span></span><span class="sig-name descname"><span class="pre">italk_raw</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/inputs/italk.html#italk_raw"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.italk.italk_raw" title="Link to this definition">§</a></dt>
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diff --git a/api/pypath.inputs.kea.kea_enzyme_substrate.html b/api/pypath.inputs.kea.kea_enzyme_substrate.html
new file mode 100644
index 000000000..f6a5c13c4
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diff --git a/api/pypath.inputs.kea.kea_interactions.html b/api/pypath.inputs.kea.kea_interactions.html
new file mode 100644
index 000000000..23c441ec4
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+  <section id="pypath-inputs-kegg-keggpathway">
+<h1>pypath.inputs.kegg.KeggPathway<a class="headerlink" href="#pypath-inputs-kegg-keggpathway" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.inputs.kegg.KeggPathway">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.inputs.kegg.</span></span><span class="sig-name descname"><span class="pre">KeggPathway</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">pathway</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.inputs.kegg.KeggPathway" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">tuple</span></code></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.inputs.kegg.KeggPathway.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.inputs.kegg.KeggPathway.__init__" title="Link to this definition">§</a></dt>
+<dd></dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.inputs.kegg.KeggPathway.__init__" title="pypath.inputs.kegg.KeggPathway.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.inputs.kegg.KeggPathway.count" title="pypath.inputs.kegg.KeggPathway.count"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count</span></code></a>(value, /)</p></td>
+<td><p>Return number of occurrences of value.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.inputs.kegg.KeggPathway.index" title="pypath.inputs.kegg.KeggPathway.index"><code class="xref py py-obj docutils literal notranslate"><span class="pre">index</span></code></a>(value[, start, stop])</p></td>
+<td><p>Return first index of value.</p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Attributes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.inputs.kegg.KeggPathway.pathway" title="pypath.inputs.kegg.KeggPathway.pathway"><code class="xref py py-obj docutils literal notranslate"><span class="pre">pathway</span></code></a></p></td>
+<td><p>Alias for field number 0</p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.inputs.kegg.KeggPathway.count">
+<span class="sig-name descname"><span class="pre">count</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">value</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">/</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.inputs.kegg.KeggPathway.count" title="Link to this definition">§</a></dt>
+<dd><p>Return number of occurrences of value.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.inputs.kegg.KeggPathway.index">
+<span class="sig-name descname"><span class="pre">index</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">value</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">start</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">stop</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9223372036854775807</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">/</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.inputs.kegg.KeggPathway.index" title="Link to this definition">§</a></dt>
+<dd><p>Return first index of value.</p>
+<p>Raises ValueError if the value is not present.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.inputs.kegg.KeggPathway.pathway">
+<span class="sig-name descname"><span class="pre">pathway</span></span><a class="headerlink" href="#pypath.inputs.kegg.KeggPathway.pathway" title="Link to this definition">§</a></dt>
+<dd><p>Alias for field number 0</p>
+</dd></dl>
+
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+  <section id="module-pypath.inputs.kegg">
+<span id="pypath-inputs-kegg"></span><h1>pypath.inputs.kegg<a class="headerlink" href="#module-pypath.inputs.kegg" title="Link to this heading">§</a></h1>
+<dl class="field-list simple">
+<dt class="field-odd">members<span class="colon">:</span></dt>
+<dd class="field-odd"><p></p></dd>
+</dl>
+<p class="rubric">Functions</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.inputs.kegg.kegg_dbget.html#pypath.inputs.kegg.kegg_dbget" title="pypath.inputs.kegg.kegg_dbget"><code class="xref py py-obj docutils literal notranslate"><span class="pre">kegg_dbget</span></code></a>(entry)</p></td>
+<td><p>Retrieves an entry (e.g. compounds, network modules) by the KEGG DBGET interface (kegg.jp/dbget-bin/www_bget).</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.inputs.kegg.kegg_interactions.html#pypath.inputs.kegg.kegg_interactions" title="pypath.inputs.kegg.kegg_interactions"><code class="xref py py-obj docutils literal notranslate"><span class="pre">kegg_interactions</span></code></a>()</p></td>
+<td><p>Downloads and processes KEGG Pathways.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.inputs.kegg.kegg_medicus.html#pypath.inputs.kegg.kegg_medicus" title="pypath.inputs.kegg.kegg_medicus"><code class="xref py py-obj docutils literal notranslate"><span class="pre">kegg_medicus</span></code></a>([max_entity_variations])</p></td>
+<td><p>Retrieves and preprocesses the KEGG MEDICUS database.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.inputs.kegg.kegg_medicus_complexes.html#pypath.inputs.kegg.kegg_medicus_complexes" title="pypath.inputs.kegg.kegg_medicus_complexes"><code class="xref py py-obj docutils literal notranslate"><span class="pre">kegg_medicus_complexes</span></code></a>([max_entity_variations])</p></td>
+<td><p>Extracts a <cite>dict</cite> of protein complexes from the KEGG MEDICUS database.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.inputs.kegg.kegg_medicus_interactions.html#pypath.inputs.kegg.kegg_medicus_interactions" title="pypath.inputs.kegg.kegg_medicus_interactions"><code class="xref py py-obj docutils literal notranslate"><span class="pre">kegg_medicus_interactions</span></code></a>([...])</p></td>
+<td><p>Retrieves and preprocesses human protein-protein and transcriptional regulatory interactions from the KEGG MEDICUS database.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.inputs.kegg.kegg_pathway_annotations.html#pypath.inputs.kegg.kegg_pathway_annotations" title="pypath.inputs.kegg.kegg_pathway_annotations"><code class="xref py py-obj docutils literal notranslate"><span class="pre">kegg_pathway_annotations</span></code></a>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.inputs.kegg.kegg_pathway_annotations_pathwaycommons.html#pypath.inputs.kegg.kegg_pathway_annotations_pathwaycommons" title="pypath.inputs.kegg.kegg_pathway_annotations_pathwaycommons"><code class="xref py py-obj docutils literal notranslate"><span class="pre">kegg_pathway_annotations_pathwaycommons</span></code></a>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.inputs.kegg.kegg_pathways.html#pypath.inputs.kegg.kegg_pathways" title="pypath.inputs.kegg.kegg_pathways"><code class="xref py py-obj docutils literal notranslate"><span class="pre">kegg_pathways</span></code></a>()</p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Classes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.inputs.kegg.KeggPathway.html#pypath.inputs.kegg.KeggPathway" title="pypath.inputs.kegg.KeggPathway"><code class="xref py py-obj docutils literal notranslate"><span class="pre">KeggPathway</span></code></a>(pathway)</p></td>
+<td><p></p></td>
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+<h1>pypath.inputs.kegg.kegg_dbget<a class="headerlink" href="#pypath-inputs-kegg-kegg-dbget" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.inputs.kegg.kegg_dbget">
+<span class="sig-prename descclassname"><span class="pre">pypath.inputs.kegg.</span></span><span class="sig-name descname"><span class="pre">kegg_dbget</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entry</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/inputs/kegg.html#kegg_dbget"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.kegg.kegg_dbget" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves an entry (e.g. compounds, network modules) by the KEGG DBGET
+interface (kegg.jp/dbget-bin/www_bget).</p>
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diff --git a/api/pypath.inputs.kegg.kegg_interactions.html b/api/pypath.inputs.kegg.kegg_interactions.html
new file mode 100644
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+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.inputs.kegg.kegg_interactions">
+<span class="sig-prename descclassname"><span class="pre">pypath.inputs.kegg.</span></span><span class="sig-name descname"><span class="pre">kegg_interactions</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/inputs/kegg.html#kegg_interactions"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.kegg.kegg_interactions" title="Link to this definition">§</a></dt>
+<dd><p>Downloads and processes KEGG Pathways.
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diff --git a/api/pypath.inputs.kegg.kegg_medicus.html b/api/pypath.inputs.kegg.kegg_medicus.html
new file mode 100644
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+  <section id="pypath-inputs-kegg-kegg-medicus">
+<h1>pypath.inputs.kegg.kegg_medicus<a class="headerlink" href="#pypath-inputs-kegg-kegg-medicus" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.inputs.kegg.kegg_medicus">
+<span class="sig-prename descclassname"><span class="pre">pypath.inputs.kegg.</span></span><span class="sig-name descname"><span class="pre">kegg_medicus</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">max_entity_variations</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">10</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/inputs/kegg.html#kegg_medicus"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.kegg.kegg_medicus" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves and preprocesses the KEGG MEDICUS database. Returns a set of
+raw interaction records (with the original identifiers and some further
+attributes). Nested complexes and protein families are flattened which
+means each interacting pair is either a single protein or a protein
+complex. Then the combination of all variants of each interacting partner
+yields a separate record. E.g. if a family of 3 proteins interacts with
+a protein complex where one of the members can be 2 alternative proteins
+then this interaction yields 6 records.</p>
+<dl class="simple">
+<dt>max_entity_variations<span class="classifier">int</span></dt><dd><p>In KEGG MEDICUS many molecular entities are protein families or
+families of often large and nested protein complexes. By this option
+you can limit largest number of variants a single entity might yield,
+so you won’t end up with one complex yielding hundreds of
+combinatiorial variants.</p>
+</dd>
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+
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diff --git a/api/pypath.inputs.kegg.kegg_medicus_complexes.html b/api/pypath.inputs.kegg.kegg_medicus_complexes.html
new file mode 100644
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+  <section id="pypath-inputs-kegg-kegg-medicus-complexes">
+<h1>pypath.inputs.kegg.kegg_medicus_complexes<a class="headerlink" href="#pypath-inputs-kegg-kegg-medicus-complexes" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.inputs.kegg.kegg_medicus_complexes">
+<span class="sig-prename descclassname"><span class="pre">pypath.inputs.kegg.</span></span><span class="sig-name descname"><span class="pre">kegg_medicus_complexes</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">max_entity_variations</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">10</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/inputs/kegg.html#kegg_medicus_complexes"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.kegg.kegg_medicus_complexes" title="Link to this definition">§</a></dt>
+<dd><p>Extracts a <cite>dict</cite> of protein complexes from the KEGG MEDICUS database.</p>
+<dl class="simple">
+<dt>max_entity_variations<span class="classifier">int</span></dt><dd><p>In KEGG MEDICUS many molecular entities are protein families or
+families of often large and nested protein complexes. By this option
+you can limit largest number of variants a single entity might yield,
+so you won’t end up with one complex yielding hundreds of
+combinatiorial variants.</p>
+</dd>
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diff --git a/api/pypath.inputs.kegg.kegg_medicus_interactions.html b/api/pypath.inputs.kegg.kegg_medicus_interactions.html
new file mode 100644
index 000000000..95d354a23
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+  <section id="pypath-inputs-kegg-kegg-medicus-interactions">
+<h1>pypath.inputs.kegg.kegg_medicus_interactions<a class="headerlink" href="#pypath-inputs-kegg-kegg-medicus-interactions" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.inputs.kegg.kegg_medicus_interactions">
+<span class="sig-prename descclassname"><span class="pre">pypath.inputs.kegg.</span></span><span class="sig-name descname"><span class="pre">kegg_medicus_interactions</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">max_entity_variations</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">10</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/inputs/kegg.html#kegg_medicus_interactions"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.kegg.kegg_medicus_interactions" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves and preprocesses human protein-protein and transcriptional
+regulatory interactions from the KEGG MEDICUS database. Optionally
+it returns protein complexes instead of interactions.</p>
+<dl class="simple">
+<dt>max_entity_variations<span class="classifier">int</span></dt><dd><p>In KEGG MEDICUS many molecular entities are protein families or
+families of often large and nested protein complexes. By this option
+you can limit largest number of variants a single entity might yield,
+so you won’t end up with one complex yielding hundreds of
+combinatiorial variants.</p>
+</dd>
+<dt>complexes<span class="classifier">bool</span></dt><dd><p>Return a set of protein complexes instead of a list of molecular
+interactions.</p>
+</dd>
+</dl>
+</dd></dl>
+
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diff --git a/api/pypath.inputs.kegg.kegg_pathway_annotations.html b/api/pypath.inputs.kegg.kegg_pathway_annotations.html
new file mode 100644
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diff --git a/api/pypath.inputs.kegg.kegg_pathway_annotations_pathwaycommons.html b/api/pypath.inputs.kegg.kegg_pathway_annotations_pathwaycommons.html
new file mode 100644
index 000000000..9d05c1ad0
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diff --git a/api/pypath.inputs.kegg.kegg_pathways.html b/api/pypath.inputs.kegg.kegg_pathways.html
new file mode 100644
index 000000000..b1b9462c8
--- /dev/null
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@@ -0,0 +1,638 @@
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\ No newline at end of file
diff --git a/api/pypath.inputs.kegg_api.html b/api/pypath.inputs.kegg_api.html
index b53820f53..be8704b59 100644
--- a/api/pypath.inputs.kegg_api.html
+++ b/api/pypath.inputs.kegg_api.html
@@ -48,7 +48,7 @@
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
     <link rel="next" title="pypath.inputs.kegg_api.disease_to_drug" href="pypath.inputs.kegg_api.disease_to_drug.html" />
-    <link rel="prev" title="pypath.inputs.ipi.ipi_uniprot" href="pypath.inputs.ipi.ipi_uniprot.html" />
+    <link rel="prev" title="pypath.inputs.kegg.KeggPathway" href="pypath.inputs.kegg.KeggPathway.html" />
   <meta name="viewport" content="width=device-width, initial-scale=1"/>
   <meta name="docsearch:language" content="en"/>
   </head>
@@ -587,12 +587,12 @@
                   
 <div class="prev-next-area">
     <a class="left-prev"
-       href="pypath.inputs.ipi.ipi_uniprot.html"
+       href="pypath.inputs.kegg.KeggPathway.html"
        title="previous page">
       <i class="fa-solid fa-angle-left"></i>
       <div class="prev-next-info">
         <p class="prev-next-subtitle">previous</p>
-        <p class="prev-next-title">pypath.inputs.ipi.ipi_uniprot</p>
+        <p class="prev-next-title">pypath.inputs.kegg.KeggPathway</p>
       </div>
     </a>
     <a class="right-next"
diff --git a/api/pypath.inputs.kegg_api.pathway_to_gene.html b/api/pypath.inputs.kegg_api.pathway_to_gene.html
index 13b74f358..22b6a76b8 100644
--- a/api/pypath.inputs.kegg_api.pathway_to_gene.html
+++ b/api/pypath.inputs.kegg_api.pathway_to_gene.html
@@ -47,7 +47,7 @@
     <link rel="icon" href="../_static/omnipath-logo.svg"/>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
-    <link rel="next" title="pypath.inputs.kirouac2010" href="pypath.inputs.kirouac2010.html" />
+    <link rel="next" title="pypath.inputs.kinasedotcom" href="pypath.inputs.kinasedotcom.html" />
     <link rel="prev" title="pypath.inputs.kegg_api.pathway_to_drug" href="pypath.inputs.kegg_api.pathway_to_drug.html" />
   <meta name="viewport" content="width=device-width, initial-scale=1"/>
   <meta name="docsearch:language" content="en"/>
@@ -552,11 +552,11 @@ <h1>pypath.inputs.kegg_api.pathway_to_gene<a class="headerlink" href="#pypath-in
       </div>
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-        <p class="prev-next-title">pypath.inputs.kirouac2010</p>
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diff --git a/api/pypath.inputs.kinasedotcom.html b/api/pypath.inputs.kinasedotcom.html
new file mode 100644
index 000000000..4b126f655
--- /dev/null
+++ b/api/pypath.inputs.kinasedotcom.html
@@ -0,0 +1,645 @@
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+  <section id="module-pypath.inputs.kinasedotcom">
+<span id="pypath-inputs-kinasedotcom"></span><h1>pypath.inputs.kinasedotcom<a class="headerlink" href="#module-pypath.inputs.kinasedotcom" title="Link to this heading">§</a></h1>
+<dl class="field-list simple">
+<dt class="field-odd">members<span class="colon">:</span></dt>
+<dd class="field-odd"><p></p></dd>
+</dl>
+<p class="rubric">Functions</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.inputs.kinasedotcom.kinasedotcom_annotations.html#pypath.inputs.kinasedotcom.kinasedotcom_annotations" title="pypath.inputs.kinasedotcom.kinasedotcom_annotations"><code class="xref py py-obj docutils literal notranslate"><span class="pre">kinasedotcom_annotations</span></code></a>()</p></td>
+<td><p>Downloads and processes kinase annotations from kinase.com.</p></td>
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+  <section id="pypath-inputs-kinasedotcom-kinasedotcom-annotations">
+<h1>pypath.inputs.kinasedotcom.kinasedotcom_annotations<a class="headerlink" href="#pypath-inputs-kinasedotcom-kinasedotcom-annotations" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.inputs.kinasedotcom.kinasedotcom_annotations">
+<span class="sig-prename descclassname"><span class="pre">pypath.inputs.kinasedotcom.</span></span><span class="sig-name descname"><span class="pre">kinasedotcom_annotations</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/inputs/kinasedotcom.html#kinasedotcom_annotations"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.kinasedotcom.kinasedotcom_annotations" title="Link to this definition">§</a></dt>
+<dd><p>Downloads and processes kinase annotations from kinase.com.</p>
+</dd></dl>
+
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+
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diff --git a/api/pypath.inputs.kirouac2010.html b/api/pypath.inputs.kirouac2010.html
index ad6709f28..818e0a3cc 100644
--- a/api/pypath.inputs.kirouac2010.html
+++ b/api/pypath.inputs.kirouac2010.html
@@ -48,7 +48,7 @@
     <link rel="index" title="Index" href="../genindex.html" />
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     <link rel="next" title="pypath.inputs.kirouac2010.kirouac2010_interactions" href="pypath.inputs.kirouac2010.kirouac2010_interactions.html" />
-    <link rel="prev" title="pypath.inputs.kegg_api.pathway_to_gene" href="pypath.inputs.kegg_api.pathway_to_gene.html" />
+    <link rel="prev" title="pypath.inputs.kinasedotcom.kinasedotcom_annotations" href="pypath.inputs.kinasedotcom.kinasedotcom_annotations.html" />
   <meta name="viewport" content="width=device-width, initial-scale=1"/>
   <meta name="docsearch:language" content="en"/>
   </head>
@@ -542,12 +542,12 @@
                   
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     <a class="left-prev"
-       href="pypath.inputs.kegg_api.pathway_to_gene.html"
+       href="pypath.inputs.kinasedotcom.kinasedotcom_annotations.html"
        title="previous page">
       <i class="fa-solid fa-angle-left"></i>
       <div class="prev-next-info">
         <p class="prev-next-subtitle">previous</p>
-        <p class="prev-next-title">pypath.inputs.kegg_api.pathway_to_gene</p>
+        <p class="prev-next-title">pypath.inputs.kinasedotcom.kinasedotcom_annotations</p>
       </div>
     </a>
     <a class="right-next"
diff --git a/api/pypath.inputs.kirouac2010.kirouac2010_interactions.html b/api/pypath.inputs.kirouac2010.kirouac2010_interactions.html
index eff8d678c..e43ef7cb9 100644
--- a/api/pypath.inputs.kirouac2010.kirouac2010_interactions.html
+++ b/api/pypath.inputs.kirouac2010.kirouac2010_interactions.html
@@ -47,7 +47,7 @@
     <link rel="icon" href="../_static/omnipath-logo.svg"/>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
-    <link rel="next" title="pypath.inputs.laudanna" href="pypath.inputs.laudanna.html" />
+    <link rel="next" title="pypath.inputs.lambert2018" href="pypath.inputs.lambert2018.html" />
     <link rel="prev" title="pypath.inputs.kirouac2010" href="pypath.inputs.kirouac2010.html" />
   <meta name="viewport" content="width=device-width, initial-scale=1"/>
   <meta name="docsearch:language" content="en"/>
@@ -546,11 +546,11 @@ <h1>pypath.inputs.kirouac2010.kirouac2010_interactions<a class="headerlink" href
       </div>
     </a>
     <a class="right-next"
-       href="pypath.inputs.laudanna.html"
+       href="pypath.inputs.lambert2018.html"
        title="next page">
       <div class="prev-next-info">
         <p class="prev-next-subtitle">next</p>
-        <p class="prev-next-title">pypath.inputs.laudanna</p>
+        <p class="prev-next-title">pypath.inputs.lambert2018</p>
       </div>
       <i class="fa-solid fa-angle-right"></i>
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diff --git a/api/pypath.inputs.lambert2018.html b/api/pypath.inputs.lambert2018.html
new file mode 100644
index 000000000..b19a2ef13
--- /dev/null
+++ b/api/pypath.inputs.lambert2018.html
@@ -0,0 +1,648 @@
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diff --git a/api/pypath.inputs.laudanna.html b/api/pypath.inputs.laudanna.html
index 262aa95c6..51ac64cc9 100644
--- a/api/pypath.inputs.laudanna.html
+++ b/api/pypath.inputs.laudanna.html
@@ -48,7 +48,7 @@
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-    <link rel="prev" title="pypath.inputs.kirouac2010.kirouac2010_interactions" href="pypath.inputs.kirouac2010.kirouac2010_interactions.html" />
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   <meta name="viewport" content="width=device-width, initial-scale=1"/>
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@@ -545,12 +545,12 @@
                   
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diff --git a/api/pypath.inputs.laudanna.laudanna_effects.html b/api/pypath.inputs.laudanna.laudanna_effects.html
index 0900e100e..8b54fc49c 100644
--- a/api/pypath.inputs.laudanna.laudanna_effects.html
+++ b/api/pypath.inputs.laudanna.laudanna_effects.html
@@ -47,7 +47,7 @@
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   <meta name="viewport" content="width=device-width, initial-scale=1"/>
   <meta name="docsearch:language" content="en"/>
@@ -547,11 +547,11 @@ <h1>pypath.inputs.laudanna.laudanna_effects<a class="headerlink" href="#pypath-i
       </div>
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diff --git a/api/pypath.inputs.li2012.get_li2012.html b/api/pypath.inputs.li2012.get_li2012.html
new file mode 100644
index 000000000..aee77f95c
--- /dev/null
+++ b/api/pypath.inputs.li2012.get_li2012.html
@@ -0,0 +1,640 @@
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+  <section id="pypath-inputs-li2012-get-li2012">
+<h1>pypath.inputs.li2012.get_li2012<a class="headerlink" href="#pypath-inputs-li2012-get-li2012" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.inputs.li2012.get_li2012">
+<span class="sig-prename descclassname"><span class="pre">pypath.inputs.li2012.</span></span><span class="sig-name descname"><span class="pre">get_li2012</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/inputs/li2012.html#get_li2012"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.li2012.get_li2012" title="Link to this definition">§</a></dt>
+<dd><p>Reads supplementary data of Li 2012 from local file.
+Returns table (list of lists).</p>
+</dd></dl>
+
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+  <section id="module-pypath.inputs.li2012">
+<span id="pypath-inputs-li2012"></span><h1>pypath.inputs.li2012<a class="headerlink" href="#module-pypath.inputs.li2012" title="Link to this heading">§</a></h1>
+<dl class="field-list simple">
+<dt class="field-odd">members<span class="colon">:</span></dt>
+<dd class="field-odd"><p></p></dd>
+</dl>
+<p class="rubric">Functions</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.inputs.li2012.get_li2012.html#pypath.inputs.li2012.get_li2012" title="pypath.inputs.li2012.get_li2012"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_li2012</span></code></a>()</p></td>
+<td><p>Reads supplementary data of Li 2012 from local file.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.inputs.li2012.li2012_dmi.html#pypath.inputs.li2012.li2012_dmi" title="pypath.inputs.li2012.li2012_dmi"><code class="xref py py-obj docutils literal notranslate"><span class="pre">li2012_dmi</span></code></a>()</p></td>
+<td><p>Converts table read by <code class="docutils literal notranslate"><span class="pre">pypath.inputs.li2012.get_li2012</span></code> to list of <code class="docutils literal notranslate"><span class="pre">pypath.internals.intera.DomainMotif</span></code> objects.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.inputs.li2012.li2012_enzyme_substrate.html#pypath.inputs.li2012.li2012_enzyme_substrate" title="pypath.inputs.li2012.li2012_enzyme_substrate"><code class="xref py py-obj docutils literal notranslate"><span class="pre">li2012_enzyme_substrate</span></code></a>()</p></td>
+<td><p>Converts table read by <code class="docutils literal notranslate"><span class="pre">pypath.inputs.li2012.get_li2012</span></code> to list of dicts of kinase-substrate interactions.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.inputs.li2012.li2012_interactions.html#pypath.inputs.li2012.li2012_interactions" title="pypath.inputs.li2012.li2012_interactions"><code class="xref py py-obj docutils literal notranslate"><span class="pre">li2012_interactions</span></code></a>()</p></td>
+<td><p>Converts table read by <code class="docutils literal notranslate"><span class="pre">pypath.inputs.li2012.get_li2012</span></code> to list of interactions.</p></td>
+</tr>
+</tbody>
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diff --git a/api/pypath.inputs.li2012.li2012_dmi.html b/api/pypath.inputs.li2012.li2012_dmi.html
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+  <section id="pypath-inputs-li2012-li2012-dmi">
+<h1>pypath.inputs.li2012.li2012_dmi<a class="headerlink" href="#pypath-inputs-li2012-li2012-dmi" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.inputs.li2012.li2012_dmi">
+<span class="sig-prename descclassname"><span class="pre">pypath.inputs.li2012.</span></span><span class="sig-name descname"><span class="pre">li2012_dmi</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/inputs/li2012.html#li2012_dmi"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.li2012.li2012_dmi" title="Link to this definition">§</a></dt>
+<dd><p>Converts table read by <code class="docutils literal notranslate"><span class="pre">pypath.inputs.li2012.get_li2012</span></code> to
+list of <code class="docutils literal notranslate"><span class="pre">pypath.internals.intera.DomainMotif</span></code> objects.
+Translates GeneSymbols to UniProt IDs.</p>
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diff --git a/api/pypath.inputs.li2012.li2012_enzyme_substrate.html b/api/pypath.inputs.li2012.li2012_enzyme_substrate.html
new file mode 100644
index 000000000..b72973469
--- /dev/null
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@@ -0,0 +1,640 @@
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+  <section id="pypath-inputs-li2012-li2012-enzyme-substrate">
+<h1>pypath.inputs.li2012.li2012_enzyme_substrate<a class="headerlink" href="#pypath-inputs-li2012-li2012-enzyme-substrate" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.inputs.li2012.li2012_enzyme_substrate">
+<span class="sig-prename descclassname"><span class="pre">pypath.inputs.li2012.</span></span><span class="sig-name descname"><span class="pre">li2012_enzyme_substrate</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/inputs/li2012.html#li2012_enzyme_substrate"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.li2012.li2012_enzyme_substrate" title="Link to this definition">§</a></dt>
+<dd><p>Converts table read by <code class="docutils literal notranslate"><span class="pre">pypath.inputs.li2012.get_li2012</span></code> to
+list of dicts of kinase-substrate interactions.</p>
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diff --git a/api/pypath.inputs.li2012.li2012_interactions.html b/api/pypath.inputs.li2012.li2012_interactions.html
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+                  
+  <section id="pypath-inputs-li2012-li2012-interactions">
+<h1>pypath.inputs.li2012.li2012_interactions<a class="headerlink" href="#pypath-inputs-li2012-li2012-interactions" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.inputs.li2012.li2012_interactions">
+<span class="sig-prename descclassname"><span class="pre">pypath.inputs.li2012.</span></span><span class="sig-name descname"><span class="pre">li2012_interactions</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/inputs/li2012.html#li2012_interactions"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.li2012.li2012_interactions" title="Link to this definition">§</a></dt>
+<dd><p>Converts table read by <code class="docutils literal notranslate"><span class="pre">pypath.inputs.li2012.get_li2012</span></code> to
+list of interactions.</p>
+</dd></dl>
+
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+
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\ No newline at end of file
diff --git a/api/pypath.inputs.lincs.html b/api/pypath.inputs.lincs.html
index 4d13bf072..afb76085d 100644
--- a/api/pypath.inputs.lincs.html
+++ b/api/pypath.inputs.lincs.html
@@ -48,7 +48,7 @@
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
     <link rel="next" title="pypath.inputs.lincs.lincs_compounds" href="pypath.inputs.lincs.lincs_compounds.html" />
-    <link rel="prev" title="pypath.inputs.laudanna.laudanna_effects" href="pypath.inputs.laudanna.laudanna_effects.html" />
+    <link rel="prev" title="pypath.inputs.li2012.li2012_interactions" href="pypath.inputs.li2012.li2012_interactions.html" />
   <meta name="viewport" content="width=device-width, initial-scale=1"/>
   <meta name="docsearch:language" content="en"/>
   </head>
@@ -542,12 +542,12 @@
                   
 <div class="prev-next-area">
     <a class="left-prev"
-       href="pypath.inputs.laudanna.laudanna_effects.html"
+       href="pypath.inputs.li2012.li2012_interactions.html"
        title="previous page">
       <i class="fa-solid fa-angle-left"></i>
       <div class="prev-next-info">
         <p class="prev-next-subtitle">previous</p>
-        <p class="prev-next-title">pypath.inputs.laudanna.laudanna_effects</p>
+        <p class="prev-next-title">pypath.inputs.li2012.li2012_interactions</p>
       </div>
     </a>
     <a class="right-next"
diff --git a/api/pypath.inputs.lincs.lincs_compounds.html b/api/pypath.inputs.lincs.lincs_compounds.html
index 55ba13d7f..8009c993c 100644
--- a/api/pypath.inputs.lincs.lincs_compounds.html
+++ b/api/pypath.inputs.lincs.lincs_compounds.html
@@ -47,7 +47,7 @@
     <link rel="icon" href="../_static/omnipath-logo.svg"/>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
-    <link rel="next" title="pypath.inputs.lncdisease" href="pypath.inputs.lncdisease.html" />
+    <link rel="next" title="pypath.inputs.lmpid" href="pypath.inputs.lmpid.html" />
     <link rel="prev" title="pypath.inputs.lincs" href="pypath.inputs.lincs.html" />
   <meta name="viewport" content="width=device-width, initial-scale=1"/>
   <meta name="docsearch:language" content="en"/>
@@ -547,11 +547,11 @@ <h1>pypath.inputs.lincs.lincs_compounds<a class="headerlink" href="#pypath-input
       </div>
     </a>
     <a class="right-next"
-       href="pypath.inputs.lncdisease.html"
+       href="pypath.inputs.lmpid.html"
        title="next page">
       <div class="prev-next-info">
         <p class="prev-next-subtitle">next</p>
-        <p class="prev-next-title">pypath.inputs.lncdisease</p>
+        <p class="prev-next-title">pypath.inputs.lmpid</p>
       </div>
       <i class="fa-solid fa-angle-right"></i>
     </a>
diff --git a/api/pypath.inputs.lmpid.html b/api/pypath.inputs.lmpid.html
new file mode 100644
index 000000000..72f8213c0
--- /dev/null
+++ b/api/pypath.inputs.lmpid.html
@@ -0,0 +1,651 @@
+
+<!DOCTYPE html>
+
+
+<html lang="en" data-content_root="../" >
+
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+    <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="viewport" content="width=device-width, initial-scale=1" />
+
+    <title>pypath.inputs.lmpid &#8212; pypath 0.16.9 documentation</title>
+  
+  
+  
+  <script data-cfasync="false">
+    document.documentElement.dataset.mode = localStorage.getItem("mode") || "";
+    document.documentElement.dataset.theme = localStorage.getItem("theme") || "light";
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+  <section id="module-pypath.inputs.lmpid">
+<span id="pypath-inputs-lmpid"></span><h1>pypath.inputs.lmpid<a class="headerlink" href="#module-pypath.inputs.lmpid" title="Link to this heading">§</a></h1>
+<dl class="field-list simple">
+<dt class="field-odd">members<span class="colon">:</span></dt>
+<dd class="field-odd"><p></p></dd>
+</dl>
+<p class="rubric">Functions</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.inputs.lmpid.lmpid_dmi.html#pypath.inputs.lmpid.lmpid_dmi" title="pypath.inputs.lmpid.lmpid_dmi"><code class="xref py py-obj docutils literal notranslate"><span class="pre">lmpid_dmi</span></code></a>([organism])</p></td>
+<td><p>Converts list of domain-motif interactions supplied by <code class="docutils literal notranslate"><span class="pre">pypath.inputs.lmpid.load_lmpid</span></code> to list of <code class="docutils literal notranslate"><span class="pre">pypath.intera.DomainMotif</span></code> objects.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.inputs.lmpid.lmpid_interactions.html#pypath.inputs.lmpid.lmpid_interactions" title="pypath.inputs.lmpid.lmpid_interactions"><code class="xref py py-obj docutils literal notranslate"><span class="pre">lmpid_interactions</span></code></a>([organism])</p></td>
+<td><p>Converts list of domain-motif interactions supplied by <code class="docutils literal notranslate"><span class="pre">pypath.inputs.lmpid.load_lmpid</span></code> to list of interactions.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.inputs.lmpid.load_lmpid.html#pypath.inputs.lmpid.load_lmpid" title="pypath.inputs.lmpid.load_lmpid"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_lmpid</span></code></a>([organism])</p></td>
+<td><p>Reads and processes LMPID data from local file <cite>pypath.data/LMPID_DATA_pubmed_ref.xml</cite>.</p></td>
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+</tbody>
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+  <section id="pypath-inputs-lmpid-lmpid-dmi">
+<h1>pypath.inputs.lmpid.lmpid_dmi<a class="headerlink" href="#pypath-inputs-lmpid-lmpid-dmi" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.inputs.lmpid.lmpid_dmi">
+<span class="sig-prename descclassname"><span class="pre">pypath.inputs.lmpid.</span></span><span class="sig-name descname"><span class="pre">lmpid_dmi</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">organism</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/inputs/lmpid.html#lmpid_dmi"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.lmpid.lmpid_dmi" title="Link to this definition">§</a></dt>
+<dd><p>Converts list of domain-motif interactions supplied by
+<code class="docutils literal notranslate"><span class="pre">pypath.inputs.lmpid.load_lmpid</span></code> to list of
+<code class="docutils literal notranslate"><span class="pre">pypath.intera.DomainMotif</span></code> objects.</p>
+</dd></dl>
+
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+  <section id="pypath-inputs-lmpid-lmpid-interactions">
+<h1>pypath.inputs.lmpid.lmpid_interactions<a class="headerlink" href="#pypath-inputs-lmpid-lmpid-interactions" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.inputs.lmpid.lmpid_interactions">
+<span class="sig-prename descclassname"><span class="pre">pypath.inputs.lmpid.</span></span><span class="sig-name descname"><span class="pre">lmpid_interactions</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">organism</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/inputs/lmpid.html#lmpid_interactions"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.lmpid.lmpid_interactions" title="Link to this definition">§</a></dt>
+<dd><p>Converts list of domain-motif interactions supplied by
+<code class="docutils literal notranslate"><span class="pre">pypath.inputs.lmpid.load_lmpid</span></code> to list of interactions.</p>
+</dd></dl>
+
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new file mode 100644
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+<h1>pypath.inputs.lmpid.load_lmpid<a class="headerlink" href="#pypath-inputs-lmpid-load-lmpid" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.inputs.lmpid.load_lmpid">
+<span class="sig-prename descclassname"><span class="pre">pypath.inputs.lmpid.</span></span><span class="sig-name descname"><span class="pre">load_lmpid</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">organism</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/inputs/lmpid.html#load_lmpid"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.lmpid.load_lmpid" title="Link to this definition">§</a></dt>
+<dd><p>Reads and processes LMPID data from local file
+<cite>pypath.data/LMPID_DATA_pubmed_ref.xml</cite>.
+The file was provided by LMPID authors and is now
+redistributed with the module.
+Returns list of domain-motif interactions.</p>
+</dd></dl>
+
+</section>
+
+
+                </article>
+              
+              
+              
+              
+              
+                <footer class="prev-next-footer">
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+        <p class="prev-next-subtitle">previous</p>
+        <p class="prev-next-title">pypath.inputs.lmpid.lmpid_interactions</p>
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+<li class="toctree-l1 toc-h1 nav-item toc-entry"><a class="reference internal nav-link" href="../notebooks/manual.html">The pypath book</a></li>
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\ No newline at end of file
diff --git a/api/pypath.inputs.lncdisease.html b/api/pypath.inputs.lncdisease.html
index 91e456589..a6f56e457 100644
--- a/api/pypath.inputs.lncdisease.html
+++ b/api/pypath.inputs.lncdisease.html
@@ -48,7 +48,7 @@
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
     <link rel="next" title="pypath.inputs.lncdisease.lncdisease_interactions" href="pypath.inputs.lncdisease.lncdisease_interactions.html" />
-    <link rel="prev" title="pypath.inputs.lincs.lincs_compounds" href="pypath.inputs.lincs.lincs_compounds.html" />
+    <link rel="prev" title="pypath.inputs.lmpid.load_lmpid" href="pypath.inputs.lmpid.load_lmpid.html" />
   <meta name="viewport" content="width=device-width, initial-scale=1"/>
   <meta name="docsearch:language" content="en"/>
   </head>
@@ -542,12 +542,12 @@
                   
 <div class="prev-next-area">
     <a class="left-prev"
-       href="pypath.inputs.lincs.lincs_compounds.html"
+       href="pypath.inputs.lmpid.load_lmpid.html"
        title="previous page">
       <i class="fa-solid fa-angle-left"></i>
       <div class="prev-next-info">
         <p class="prev-next-subtitle">previous</p>
-        <p class="prev-next-title">pypath.inputs.lincs.lincs_compounds</p>
+        <p class="prev-next-title">pypath.inputs.lmpid.load_lmpid</p>
       </div>
     </a>
     <a class="right-next"
diff --git a/api/pypath.inputs.lncrnadb.lncrnadb_interactions.html b/api/pypath.inputs.lncrnadb.lncrnadb_interactions.html
index e37edd269..0627be1df 100644
--- a/api/pypath.inputs.lncrnadb.lncrnadb_interactions.html
+++ b/api/pypath.inputs.lncrnadb.lncrnadb_interactions.html
@@ -47,7 +47,7 @@
     <link rel="icon" href="../_static/omnipath-logo.svg"/>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
-    <link rel="next" title="pypath.inputs.macrophage" href="pypath.inputs.macrophage.html" />
+    <link rel="next" title="pypath.inputs.locate" href="pypath.inputs.locate.html" />
     <link rel="prev" title="pypath.inputs.lncrnadb" href="pypath.inputs.lncrnadb.html" />
   <meta name="viewport" content="width=device-width, initial-scale=1"/>
   <meta name="docsearch:language" content="en"/>
@@ -544,11 +544,11 @@ <h1>pypath.inputs.lncrnadb.lncrnadb_interactions<a class="headerlink" href="#pyp
       </div>
     </a>
     <a class="right-next"
-       href="pypath.inputs.macrophage.html"
+       href="pypath.inputs.locate.html"
        title="next page">
       <div class="prev-next-info">
         <p class="prev-next-subtitle">next</p>
-        <p class="prev-next-title">pypath.inputs.macrophage</p>
+        <p class="prev-next-title">pypath.inputs.locate</p>
       </div>
       <i class="fa-solid fa-angle-right"></i>
     </a>
diff --git a/api/pypath.inputs.locate.html b/api/pypath.inputs.locate.html
new file mode 100644
index 000000000..bddc4ea0f
--- /dev/null
+++ b/api/pypath.inputs.locate.html
@@ -0,0 +1,645 @@
+
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+
+    <title>pypath.inputs.locate &#8212; pypath 0.16.9 documentation</title>
+  
+  
+  
+  <script data-cfasync="false">
+    document.documentElement.dataset.mode = localStorage.getItem("mode") || "";
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diff --git a/api/pypath.inputs.locate.locate_localizations.html b/api/pypath.inputs.locate.locate_localizations.html
new file mode 100644
index 000000000..73ae3241a
--- /dev/null
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@@ -0,0 +1,638 @@
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diff --git a/api/pypath.inputs.lrdb.LrdbAnnotation.html b/api/pypath.inputs.lrdb.LrdbAnnotation.html
new file mode 100644
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+  <section id="pypath-inputs-lrdb-lrdbannotation">
+<h1>pypath.inputs.lrdb.LrdbAnnotation<a class="headerlink" href="#pypath-inputs-lrdb-lrdbannotation" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.inputs.lrdb.LrdbAnnotation">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.inputs.lrdb.</span></span><span class="sig-name descname"><span class="pre">LrdbAnnotation</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">role</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cell_type</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">sources</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.inputs.lrdb.LrdbAnnotation" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">tuple</span></code></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.inputs.lrdb.LrdbAnnotation.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.inputs.lrdb.LrdbAnnotation.__init__" title="Link to this definition">§</a></dt>
+<dd></dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.inputs.lrdb.LrdbAnnotation.__init__" title="pypath.inputs.lrdb.LrdbAnnotation.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.inputs.lrdb.LrdbAnnotation.count" title="pypath.inputs.lrdb.LrdbAnnotation.count"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count</span></code></a>(value, /)</p></td>
+<td><p>Return number of occurrences of value.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.inputs.lrdb.LrdbAnnotation.index" title="pypath.inputs.lrdb.LrdbAnnotation.index"><code class="xref py py-obj docutils literal notranslate"><span class="pre">index</span></code></a>(value[, start, stop])</p></td>
+<td><p>Return first index of value.</p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Attributes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.inputs.lrdb.LrdbAnnotation.cell_type" title="pypath.inputs.lrdb.LrdbAnnotation.cell_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">cell_type</span></code></a></p></td>
+<td><p>Alias for field number 1</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.inputs.lrdb.LrdbAnnotation.references" title="pypath.inputs.lrdb.LrdbAnnotation.references"><code class="xref py py-obj docutils literal notranslate"><span class="pre">references</span></code></a></p></td>
+<td><p>Alias for field number 3</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.inputs.lrdb.LrdbAnnotation.role" title="pypath.inputs.lrdb.LrdbAnnotation.role"><code class="xref py py-obj docutils literal notranslate"><span class="pre">role</span></code></a></p></td>
+<td><p>Alias for field number 0</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.inputs.lrdb.LrdbAnnotation.sources" title="pypath.inputs.lrdb.LrdbAnnotation.sources"><code class="xref py py-obj docutils literal notranslate"><span class="pre">sources</span></code></a></p></td>
+<td><p>Alias for field number 2</p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.inputs.lrdb.LrdbAnnotation.cell_type">
+<span class="sig-name descname"><span class="pre">cell_type</span></span><a class="headerlink" href="#pypath.inputs.lrdb.LrdbAnnotation.cell_type" title="Link to this definition">§</a></dt>
+<dd><p>Alias for field number 1</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.inputs.lrdb.LrdbAnnotation.count">
+<span class="sig-name descname"><span class="pre">count</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">value</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">/</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.inputs.lrdb.LrdbAnnotation.count" title="Link to this definition">§</a></dt>
+<dd><p>Return number of occurrences of value.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.inputs.lrdb.LrdbAnnotation.index">
+<span class="sig-name descname"><span class="pre">index</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">value</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">start</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">stop</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9223372036854775807</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">/</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.inputs.lrdb.LrdbAnnotation.index" title="Link to this definition">§</a></dt>
+<dd><p>Return first index of value.</p>
+<p>Raises ValueError if the value is not present.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.inputs.lrdb.LrdbAnnotation.references">
+<span class="sig-name descname"><span class="pre">references</span></span><a class="headerlink" href="#pypath.inputs.lrdb.LrdbAnnotation.references" title="Link to this definition">§</a></dt>
+<dd><p>Alias for field number 3</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.inputs.lrdb.LrdbAnnotation.role">
+<span class="sig-name descname"><span class="pre">role</span></span><a class="headerlink" href="#pypath.inputs.lrdb.LrdbAnnotation.role" title="Link to this definition">§</a></dt>
+<dd><p>Alias for field number 0</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.inputs.lrdb.LrdbAnnotation.sources">
+<span class="sig-name descname"><span class="pre">sources</span></span><a class="headerlink" href="#pypath.inputs.lrdb.LrdbAnnotation.sources" title="Link to this definition">§</a></dt>
+<dd><p>Alias for field number 2</p>
+</dd></dl>
+
+</dd></dl>
+
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diff --git a/api/pypath.inputs.lrdb.lrdb_interactions.html b/api/pypath.inputs.lrdb.lrdb_interactions.html
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diff --git a/api/pypath.inputs.macrophage.html b/api/pypath.inputs.macrophage.html
index 485e7ebad..dd2886542 100644
--- a/api/pypath.inputs.macrophage.html
+++ b/api/pypath.inputs.macrophage.html
@@ -48,7 +48,7 @@
     <link rel="index" title="Index" href="../genindex.html" />
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     <link rel="next" title="pypath.inputs.macrophage.macrophage_interactions" href="pypath.inputs.macrophage.macrophage_interactions.html" />
-    <link rel="prev" title="pypath.inputs.lncrnadb.lncrnadb_interactions" href="pypath.inputs.lncrnadb.lncrnadb_interactions.html" />
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   <meta name="viewport" content="width=device-width, initial-scale=1"/>
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   </head>
@@ -542,12 +542,12 @@
                   
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         <p class="prev-next-subtitle">previous</p>
-        <p class="prev-next-title">pypath.inputs.lncrnadb.lncrnadb_interactions</p>
+        <p class="prev-next-title">pypath.inputs.lrdb.LrdbAnnotation</p>
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diff --git a/api/pypath.inputs.main.html b/api/pypath.inputs.main.html
index 5a16efbd0..ab4564a34 100644
--- a/api/pypath.inputs.main.html
+++ b/api/pypath.inputs.main.html
@@ -47,7 +47,7 @@
     <link rel="icon" href="../_static/omnipath-logo.svg"/>
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-    <link rel="next" title="pypath.inputs.mimp" href="pypath.inputs.mimp.html" />
+    <link rel="next" title="pypath.inputs.matrisome" href="pypath.inputs.matrisome.html" />
     <link rel="prev" title="pypath.inputs.macrophage.macrophage_interactions" href="pypath.inputs.macrophage.macrophage_interactions.html" />
   <meta name="viewport" content="width=device-width, initial-scale=1"/>
   <meta name="docsearch:language" content="en"/>
@@ -543,11 +543,11 @@
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+       href="pypath.inputs.matrisome.html"
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         <p class="prev-next-subtitle">next</p>
-        <p class="prev-next-title">pypath.inputs.mimp</p>
+        <p class="prev-next-title">pypath.inputs.matrisome</p>
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diff --git a/api/pypath.inputs.matrisome.html b/api/pypath.inputs.matrisome.html
new file mode 100644
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+++ b/api/pypath.inputs.matrisome.html
@@ -0,0 +1,645 @@
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+  <section id="module-pypath.inputs.matrisome">
+<span id="pypath-inputs-matrisome"></span><h1>pypath.inputs.matrisome<a class="headerlink" href="#module-pypath.inputs.matrisome" title="Link to this heading">§</a></h1>
+<dl class="field-list simple">
+<dt class="field-odd">members<span class="colon">:</span></dt>
+<dd class="field-odd"><p></p></dd>
+</dl>
+<p class="rubric">Functions</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.inputs.matrisome.matrisome_annotations.html#pypath.inputs.matrisome.matrisome_annotations" title="pypath.inputs.matrisome.matrisome_annotations"><code class="xref py py-obj docutils literal notranslate"><span class="pre">matrisome_annotations</span></code></a>([organism])</p></td>
+<td><p>Downloads MatrisomeDB 2.0, a database of extracellular matrix proteins.</p></td>
+</tr>
+</tbody>
+</table>
+</section>
+
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+  <section id="pypath-inputs-matrisome-matrisome-annotations">
+<h1>pypath.inputs.matrisome.matrisome_annotations<a class="headerlink" href="#pypath-inputs-matrisome-matrisome-annotations" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.inputs.matrisome.matrisome_annotations">
+<span class="sig-prename descclassname"><span class="pre">pypath.inputs.matrisome.</span></span><span class="sig-name descname"><span class="pre">matrisome_annotations</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">organism</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/inputs/matrisome.html#matrisome_annotations"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.matrisome.matrisome_annotations" title="Link to this definition">§</a></dt>
+<dd><p>Downloads MatrisomeDB 2.0, a database of extracellular matrix proteins.
+Returns dict where keys are UniProt IDs and values are tuples of
+classes, subclasses and notes.</p>
+</dd></dl>
+
+</section>
+
+
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+<span id="pypath-inputs-matrixdb"></span><h1>pypath.inputs.matrixdb<a class="headerlink" href="#module-pypath.inputs.matrixdb" title="Link to this heading">§</a></h1>
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+<dd class="field-odd"><p></p></dd>
+</dl>
+<p class="rubric">Functions</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.inputs.matrixdb.matrixdb_annotations.html#pypath.inputs.matrixdb.matrixdb_annotations" title="pypath.inputs.matrixdb.matrixdb_annotations"><code class="xref py py-obj docutils literal notranslate"><span class="pre">matrixdb_annotations</span></code></a>([organism])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.inputs.matrixdb.matrixdb_ecm_proteins.html#pypath.inputs.matrixdb.matrixdb_ecm_proteins" title="pypath.inputs.matrixdb.matrixdb_ecm_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">matrixdb_ecm_proteins</span></code></a>([organism])</p></td>
+<td><p>Returns a set of ECM (extracellular matrix) protein UniProt IDs retrieved from MatrixDB.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.inputs.matrixdb.matrixdb_interactions.html#pypath.inputs.matrixdb.matrixdb_interactions" title="pypath.inputs.matrixdb.matrixdb_interactions"><code class="xref py py-obj docutils literal notranslate"><span class="pre">matrixdb_interactions</span></code></a>([organism])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.inputs.matrixdb.matrixdb_membrane_proteins.html#pypath.inputs.matrixdb.matrixdb_membrane_proteins" title="pypath.inputs.matrixdb.matrixdb_membrane_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">matrixdb_membrane_proteins</span></code></a>([organism])</p></td>
+<td><p>Returns a set of membrane protein UniProt IDs retrieved from MatrixDB.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.inputs.matrixdb.matrixdb_secreted_proteins.html#pypath.inputs.matrixdb.matrixdb_secreted_proteins" title="pypath.inputs.matrixdb.matrixdb_secreted_proteins"><code class="xref py py-obj docutils literal notranslate"><span class="pre">matrixdb_secreted_proteins</span></code></a>([organism])</p></td>
+<td><p>Returns a set of secreted protein UniProt IDs retrieved from MatrixDB.</p></td>
+</tr>
+</tbody>
+</table>
+</section>
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new file mode 100644
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+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.inputs.matrixdb.matrixdb_ecm_proteins">
+<span class="sig-prename descclassname"><span class="pre">pypath.inputs.matrixdb.</span></span><span class="sig-name descname"><span class="pre">matrixdb_ecm_proteins</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">organism</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/inputs/matrixdb.html#matrixdb_ecm_proteins"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.matrixdb.matrixdb_ecm_proteins" title="Link to this definition">§</a></dt>
+<dd><p>Returns a set of ECM (extracellular matrix) protein UniProt IDs
+retrieved from MatrixDB.</p>
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+<h1>pypath.inputs.matrixdb.matrixdb_membrane_proteins<a class="headerlink" href="#pypath-inputs-matrixdb-matrixdb-membrane-proteins" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.inputs.matrixdb.matrixdb_membrane_proteins">
+<span class="sig-prename descclassname"><span class="pre">pypath.inputs.matrixdb.</span></span><span class="sig-name descname"><span class="pre">matrixdb_membrane_proteins</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">organism</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/inputs/matrixdb.html#matrixdb_membrane_proteins"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.matrixdb.matrixdb_membrane_proteins" title="Link to this definition">§</a></dt>
+<dd><p>Returns a set of membrane protein UniProt IDs retrieved from MatrixDB.</p>
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+<dl class="py function">
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+<span class="sig-prename descclassname"><span class="pre">pypath.inputs.matrixdb.</span></span><span class="sig-name descname"><span class="pre">matrixdb_secreted_proteins</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">organism</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/inputs/matrixdb.html#matrixdb_secreted_proteins"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.matrixdb.matrixdb_secreted_proteins" title="Link to this definition">§</a></dt>
+<dd><p>Returns a set of secreted protein UniProt IDs retrieved from MatrixDB.</p>
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diff --git a/api/pypath.inputs.mcam.mcam_cell_adhesion_molecules.html b/api/pypath.inputs.mcam.mcam_cell_adhesion_molecules.html
new file mode 100644
index 000000000..0c3d5609b
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diff --git a/api/pypath.inputs.membranome.membranome_annotations.html b/api/pypath.inputs.membranome.membranome_annotations.html
new file mode 100644
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+                        The pypath book
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+    
+    
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+    
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+              
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+                
+<div id="searchbox"></div>
+                <article class="bd-article">
+                  
+  <section id="pypath-inputs-membranome-membranome-annotations">
+<h1>pypath.inputs.membranome.membranome_annotations<a class="headerlink" href="#pypath-inputs-membranome-membranome-annotations" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.inputs.membranome.membranome_annotations">
+<span class="sig-prename descclassname"><span class="pre">pypath.inputs.membranome.</span></span><span class="sig-name descname"><span class="pre">membranome_annotations</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/inputs/membranome.html#membranome_annotations"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.membranome.membranome_annotations" title="Link to this definition">§</a></dt>
+<dd></dd></dl>
+
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diff --git a/api/pypath.inputs.mimp.html b/api/pypath.inputs.mimp.html
index 18ef95de5..238256639 100644
--- a/api/pypath.inputs.mimp.html
+++ b/api/pypath.inputs.mimp.html
@@ -48,7 +48,7 @@
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
     <link rel="next" title="pypath.inputs.mimp.get_kinase_class" href="pypath.inputs.mimp.get_kinase_class.html" />
-    <link rel="prev" title="pypath.inputs.main" href="pypath.inputs.main.html" />
+    <link rel="prev" title="pypath.inputs.membranome.membranome_annotations" href="pypath.inputs.membranome.membranome_annotations.html" />
   <meta name="viewport" content="width=device-width, initial-scale=1"/>
   <meta name="docsearch:language" content="en"/>
   </head>
@@ -548,12 +548,12 @@
                   
 <div class="prev-next-area">
     <a class="left-prev"
-       href="pypath.inputs.main.html"
+       href="pypath.inputs.membranome.membranome_annotations.html"
        title="previous page">
       <i class="fa-solid fa-angle-left"></i>
       <div class="prev-next-info">
         <p class="prev-next-subtitle">previous</p>
-        <p class="prev-next-title">pypath.inputs.main</p>
+        <p class="prev-next-title">pypath.inputs.membranome.membranome_annotations</p>
       </div>
     </a>
     <a class="right-next"
diff --git a/api/pypath.inputs.mppi.mppi_interactions.html b/api/pypath.inputs.mppi.mppi_interactions.html
index 4d6aca86f..74ec90554 100644
--- a/api/pypath.inputs.mppi.mppi_interactions.html
+++ b/api/pypath.inputs.mppi.mppi_interactions.html
@@ -47,7 +47,7 @@
     <link rel="icon" href="../_static/omnipath-logo.svg"/>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
-    <link rel="next" title="pypath.inputs.ncrdeathdb" href="pypath.inputs.ncrdeathdb.html" />
+    <link rel="next" title="pypath.inputs.msigdb" href="pypath.inputs.msigdb.html" />
     <link rel="prev" title="pypath.inputs.mppi" href="pypath.inputs.mppi.html" />
   <meta name="viewport" content="width=device-width, initial-scale=1"/>
   <meta name="docsearch:language" content="en"/>
@@ -544,11 +544,11 @@ <h1>pypath.inputs.mppi.mppi_interactions<a class="headerlink" href="#pypath-inpu
       </div>
     </a>
     <a class="right-next"
-       href="pypath.inputs.ncrdeathdb.html"
+       href="pypath.inputs.msigdb.html"
        title="next page">
       <div class="prev-next-info">
         <p class="prev-next-subtitle">next</p>
-        <p class="prev-next-title">pypath.inputs.ncrdeathdb</p>
+        <p class="prev-next-title">pypath.inputs.msigdb</p>
       </div>
       <i class="fa-solid fa-angle-right"></i>
     </a>
diff --git a/api/pypath.inputs.msigdb.html b/api/pypath.inputs.msigdb.html
new file mode 100644
index 000000000..65abaebda
--- /dev/null
+++ b/api/pypath.inputs.msigdb.html
@@ -0,0 +1,651 @@
+
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+
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+
+    <title>pypath.inputs.msigdb &#8212; pypath 0.16.9 documentation</title>
+  
+  
+  
+  <script data-cfasync="false">
+    document.documentElement.dataset.mode = localStorage.getItem("mode") || "";
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+  <section id="module-pypath.inputs.msigdb">
+<span id="pypath-inputs-msigdb"></span><h1>pypath.inputs.msigdb<a class="headerlink" href="#module-pypath.inputs.msigdb" title="Link to this heading">§</a></h1>
+<dl class="field-list simple">
+<dt class="field-odd">members<span class="colon">:</span></dt>
+<dd class="field-odd"><p></p></dd>
+</dl>
+<p class="rubric">Functions</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.inputs.msigdb.msigdb_annotations.html#pypath.inputs.msigdb.msigdb_annotations" title="pypath.inputs.msigdb.msigdb_annotations"><code class="xref py py-obj docutils literal notranslate"><span class="pre">msigdb_annotations</span></code></a>([registered_email, ...])</p></td>
+<td><p>Downloads all or some MSigDB gene set collections and processes them to an annotation type dictionary.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.inputs.msigdb.msigdb_download.html#pypath.inputs.msigdb.msigdb_download" title="pypath.inputs.msigdb.msigdb_download"><code class="xref py py-obj docutils literal notranslate"><span class="pre">msigdb_download</span></code></a>([registered_email, ...])</p></td>
+<td><p>Downloads and preprocesses a collection of gmt format gene sets from MSigDB.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.inputs.msigdb.msigdb_download_collections.html#pypath.inputs.msigdb.msigdb_download_collections" title="pypath.inputs.msigdb.msigdb_download_collections"><code class="xref py py-obj docutils literal notranslate"><span class="pre">msigdb_download_collections</span></code></a>([...])</p></td>
+<td><p>Downloads all or some MSigDB gene set collections.</p></td>
+</tr>
+</tbody>
+</table>
+</section>
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diff --git a/api/pypath.inputs.msigdb.msigdb_annotations.html b/api/pypath.inputs.msigdb.msigdb_annotations.html
new file mode 100644
index 000000000..2ad865d22
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@@ -0,0 +1,653 @@
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+  <section id="pypath-inputs-msigdb-msigdb-annotations">
+<h1>pypath.inputs.msigdb.msigdb_annotations<a class="headerlink" href="#pypath-inputs-msigdb-msigdb-annotations" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.inputs.msigdb.msigdb_annotations">
+<span class="sig-prename descclassname"><span class="pre">pypath.inputs.msigdb.</span></span><span class="sig-name descname"><span class="pre">msigdb_annotations</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">registered_email</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">only_collections</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">exclude</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">('c5',</span> <span class="pre">'m5')</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">organism</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'human'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">version</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/inputs/msigdb.html#msigdb_annotations"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.msigdb.msigdb_annotations" title="Link to this definition">§</a></dt>
+<dd><p>Downloads all or some MSigDB gene set collections and processes them
+to an annotation type dictionary.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>registered_email</strong> (<em>str</em><em>,</em><em>NoneType</em>) – An email address registered at MSigDB. If <cite>None</cite> the <cite>msigdb_email</cite>
+from <code class="docutils literal notranslate"><span class="pre">pypath.settings</span></code> will be used.</p></li>
+<li><p><strong>only_collections</strong> (<em>set</em><em>,</em><em>NoneType</em>) – Limit the annotations only to these collections. For available
+collections e.g. <code class="docutils literal notranslate"><span class="pre">{'h.all',</span> <span class="pre">'c2cgp'}</span></code> refer to the MSigDB webpage:
+<a class="reference external" href="http://software.broadinstitute.org/gsea/downloads.jsp#msigdb">http://software.broadinstitute.org/gsea/downloads.jsp#msigdb</a></p></li>
+<li><p><strong>exclude</strong> (<em>tuple</em>) – Exclude the collections having their name starting with any of the
+strings in this tuple. By default <cite>c5</cite> (Gene Ontology) is excluded.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
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diff --git a/api/pypath.inputs.msigdb.msigdb_download.html b/api/pypath.inputs.msigdb.msigdb_download.html
new file mode 100644
index 000000000..3f6bf9d2e
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+<h1>pypath.inputs.msigdb.msigdb_download<a class="headerlink" href="#pypath-inputs-msigdb-msigdb-download" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.inputs.msigdb.msigdb_download">
+<span class="sig-prename descclassname"><span class="pre">pypath.inputs.msigdb.</span></span><span class="sig-name descname"><span class="pre">msigdb_download</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">registered_email</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">collection</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'msigdb'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">id_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'symbols'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">force_download</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">organism</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'human'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">version</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/inputs/msigdb.html#msigdb_download"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.msigdb.msigdb_download" title="Link to this definition">§</a></dt>
+<dd><p>Downloads and preprocesses a collection of gmt format gene sets from
+MSigDB. Returns dict of sets with gene set names as keys and molecular
+identifiers as values.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>registered_email</strong> (<em>str</em><em>,</em><em>NoneType</em>) – An email address registered at MSigDB. If <cite>None</cite> the <cite>msigdb_email</cite>
+from <code class="docutils literal notranslate"><span class="pre">pypath.settings</span></code> will be used.</p></li>
+<li><p><strong>collection</strong> (<em>str</em>) – The name of the gene set collection. For available collections (e.g.
+<cite>h.all</cite> or <cite>c2.cpg</cite>) refer to the MSigDB website:
+<a class="reference external" href="http://software.broadinstitute.org/gsea/downloads.jsp#msigdb">http://software.broadinstitute.org/gsea/downloads.jsp#msigdb</a>
+The default value <cite>msigdb</cite> contains all the genesets however you
+won’t be able to distinguish which geneset comes from which
+collection. For this you need to download the collections one by one.</p></li>
+<li><p><strong>id_type</strong> (<em>str</em>) – MSigDB provides Gene Symbols (<cite>symbols</cite>) and Entrez Gene IDs
+(<cite>entrez</cite>).</p></li>
+<li><p><strong>force_download</strong> (<em>bool</em>) – Download even if cache content is available.</p></li>
+</ul>
+</dd>
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+                <article class="bd-article">
+                  
+  <section id="pypath-inputs-msigdb-msigdb-download-collections">
+<h1>pypath.inputs.msigdb.msigdb_download_collections<a class="headerlink" href="#pypath-inputs-msigdb-msigdb-download-collections" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.inputs.msigdb.msigdb_download_collections">
+<span class="sig-prename descclassname"><span class="pre">pypath.inputs.msigdb.</span></span><span class="sig-name descname"><span class="pre">msigdb_download_collections</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">registered_email</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">only_collections</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">exclude</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">('c5',</span> <span class="pre">'m5')</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">id_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'symbols'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">organism</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'human'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">version</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/inputs/msigdb.html#msigdb_download_collections"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.msigdb.msigdb_download_collections" title="Link to this definition">§</a></dt>
+<dd><p>Downloads all or some MSigDB gene set collections.
+Returns a dict of dicts where upper level keys are collections while
+lower level keys are geneset names and values are molecular identifiers.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>registered_email</strong> (<em>str</em><em>,</em><em>NoneType</em>) – An email address registered at MSigDB. If <cite>None</cite> the <cite>msigdb_email</cite>
+from <code class="docutils literal notranslate"><span class="pre">pypath.settings</span></code> will be used.</p></li>
+<li><p><strong>only_collections</strong> (<em>set</em><em>,</em><em>NoneType</em>) – Limit the annotations only to these collections. For available
+collections e.g. <code class="docutils literal notranslate"><span class="pre">{'h.all',</span> <span class="pre">'c2.cgp'}</span></code> refer to the MSigDB webpage:
+<a class="reference external" href="http://software.broadinstitute.org/gsea/downloads.jsp#msigdb">http://software.broadinstitute.org/gsea/downloads.jsp#msigdb</a></p></li>
+<li><p><strong>exclude</strong> (<em>tuple</em>) – Exclude the collections having their name starting with any of the
+strings in this tuple. By default <cite>c5</cite> and <cite>m5</cite> (Gene Ontology and
+Human/Mouse Phenotype Ontology) is excluded.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+</section>
+
+
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\ No newline at end of file
diff --git a/api/pypath.inputs.ncrdeathdb.html b/api/pypath.inputs.ncrdeathdb.html
index 77dac40cf..e62079e4b 100644
--- a/api/pypath.inputs.ncrdeathdb.html
+++ b/api/pypath.inputs.ncrdeathdb.html
@@ -48,7 +48,7 @@
     <link rel="index" title="Index" href="../genindex.html" />
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     <link rel="next" title="pypath.inputs.ncrdeathdb.ncrdeathdb_interactions" href="pypath.inputs.ncrdeathdb.ncrdeathdb_interactions.html" />
-    <link rel="prev" title="pypath.inputs.mppi.mppi_interactions" href="pypath.inputs.mppi.mppi_interactions.html" />
+    <link rel="prev" title="pypath.inputs.msigdb.msigdb_download_collections" href="pypath.inputs.msigdb.msigdb_download_collections.html" />
   <meta name="viewport" content="width=device-width, initial-scale=1"/>
   <meta name="docsearch:language" content="en"/>
   </head>
@@ -542,12 +542,12 @@
                   
 <div class="prev-next-area">
     <a class="left-prev"
-       href="pypath.inputs.mppi.mppi_interactions.html"
+       href="pypath.inputs.msigdb.msigdb_download_collections.html"
        title="previous page">
       <i class="fa-solid fa-angle-left"></i>
       <div class="prev-next-info">
         <p class="prev-next-subtitle">previous</p>
-        <p class="prev-next-title">pypath.inputs.mppi.mppi_interactions</p>
+        <p class="prev-next-title">pypath.inputs.msigdb.msigdb_download_collections</p>
       </div>
     </a>
     <a class="right-next"
diff --git a/api/pypath.inputs.netbiol.nrf2ome_interactions.html b/api/pypath.inputs.netbiol.nrf2ome_interactions.html
index db4962b87..cf5637eab 100644
--- a/api/pypath.inputs.netbiol.nrf2ome_interactions.html
+++ b/api/pypath.inputs.netbiol.nrf2ome_interactions.html
@@ -47,7 +47,7 @@
     <link rel="icon" href="../_static/omnipath-logo.svg"/>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
-    <link rel="next" title="pypath.inputs.offsides" href="pypath.inputs.offsides.html" />
+    <link rel="next" title="pypath.inputs.netpath" href="pypath.inputs.netpath.html" />
     <link rel="prev" title="pypath.inputs.netbiol.arn_interactions" href="pypath.inputs.netbiol.arn_interactions.html" />
   <meta name="viewport" content="width=device-width, initial-scale=1"/>
   <meta name="docsearch:language" content="en"/>
@@ -546,11 +546,11 @@ <h1>pypath.inputs.netbiol.nrf2ome_interactions<a class="headerlink" href="#pypat
       </div>
     </a>
     <a class="right-next"
-       href="pypath.inputs.offsides.html"
+       href="pypath.inputs.netpath.html"
        title="next page">
       <div class="prev-next-info">
         <p class="prev-next-subtitle">next</p>
-        <p class="prev-next-title">pypath.inputs.offsides</p>
+        <p class="prev-next-title">pypath.inputs.netpath</p>
       </div>
       <i class="fa-solid fa-angle-right"></i>
     </a>
diff --git a/api/pypath.inputs.netpath.html b/api/pypath.inputs.netpath.html
new file mode 100644
index 000000000..19a9ae85c
--- /dev/null
+++ b/api/pypath.inputs.netpath.html
@@ -0,0 +1,651 @@
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diff --git a/api/pypath.inputs.netpath.netpath_interactions.html b/api/pypath.inputs.netpath.netpath_interactions.html
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diff --git a/api/pypath.inputs.netpath.netpath_names.html b/api/pypath.inputs.netpath.netpath_names.html
new file mode 100644
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diff --git a/api/pypath.inputs.netpath.netpath_pathway_annotations.html b/api/pypath.inputs.netpath.netpath_pathway_annotations.html
new file mode 100644
index 000000000..c2b10c4a2
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+  <section id="pypath-inputs-netpath-netpath-pathway-annotations">
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+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.inputs.netpath.netpath_pathway_annotations">
+<span class="sig-prename descclassname"><span class="pre">pypath.inputs.netpath.</span></span><span class="sig-name descname"><span class="pre">netpath_pathway_annotations</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/inputs/netpath.html#netpath_pathway_annotations"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.netpath.netpath_pathway_annotations" title="Link to this definition">§</a></dt>
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diff --git a/api/pypath.inputs.offsides.html b/api/pypath.inputs.offsides.html
index 8d600ca17..222e19ebf 100644
--- a/api/pypath.inputs.offsides.html
+++ b/api/pypath.inputs.offsides.html
@@ -48,7 +48,7 @@
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
     <link rel="next" title="pypath.inputs.offsides.offsides_side_effects" href="pypath.inputs.offsides.offsides_side_effects.html" />
-    <link rel="prev" title="pypath.inputs.netbiol.nrf2ome_interactions" href="pypath.inputs.netbiol.nrf2ome_interactions.html" />
+    <link rel="prev" title="pypath.inputs.netpath.netpath_pathway_annotations" href="pypath.inputs.netpath.netpath_pathway_annotations.html" />
   <meta name="viewport" content="width=device-width, initial-scale=1"/>
   <meta name="docsearch:language" content="en"/>
   </head>
@@ -542,12 +542,12 @@
                   
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-       href="pypath.inputs.netbiol.nrf2ome_interactions.html"
+       href="pypath.inputs.netpath.netpath_pathway_annotations.html"
        title="previous page">
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       <div class="prev-next-info">
         <p class="prev-next-subtitle">previous</p>
-        <p class="prev-next-title">pypath.inputs.netbiol.nrf2ome_interactions</p>
+        <p class="prev-next-title">pypath.inputs.netpath.netpath_pathway_annotations</p>
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     <a class="right-next"
diff --git a/api/pypath.inputs.offsides.offsides_side_effects.html b/api/pypath.inputs.offsides.offsides_side_effects.html
index 67e72f7e6..6c63d8515 100644
--- a/api/pypath.inputs.offsides.offsides_side_effects.html
+++ b/api/pypath.inputs.offsides.offsides_side_effects.html
@@ -47,7 +47,7 @@
     <link rel="icon" href="../_static/omnipath-logo.svg"/>
     <link rel="index" title="Index" href="../genindex.html" />
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-    <link rel="next" title="pypath.inputs.ontology" href="pypath.inputs.ontology.html" />
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   <meta name="viewport" content="width=device-width, initial-scale=1"/>
   <meta name="docsearch:language" content="en"/>
@@ -552,11 +552,11 @@ <h1>pypath.inputs.offsides.offsides_side_effects<a class="headerlink" href="#pyp
       </div>
     </a>
     <a class="right-next"
-       href="pypath.inputs.ontology.html"
+       href="pypath.inputs.oma.html"
        title="next page">
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         <p class="prev-next-subtitle">next</p>
-        <p class="prev-next-title">pypath.inputs.ontology</p>
+        <p class="prev-next-title">pypath.inputs.oma</p>
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diff --git a/api/pypath.inputs.oma.html b/api/pypath.inputs.oma.html
new file mode 100644
index 000000000..f21be8056
--- /dev/null
+++ b/api/pypath.inputs.oma.html
@@ -0,0 +1,648 @@
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+  <section id="module-pypath.inputs.oma">
+<span id="pypath-inputs-oma"></span><h1>pypath.inputs.oma<a class="headerlink" href="#module-pypath.inputs.oma" title="Link to this heading">§</a></h1>
+<dl class="field-list simple">
+<dt class="field-odd">members<span class="colon">:</span></dt>
+<dd class="field-odd"><p></p></dd>
+</dl>
+<p class="rubric">Functions</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.inputs.oma.oma_orthologs.html#pypath.inputs.oma.oma_orthologs" title="pypath.inputs.oma.oma_orthologs"><code class="xref py py-obj docutils literal notranslate"><span class="pre">oma_orthologs</span></code></a>([organism_a, organism_b, ...])</p></td>
+<td><p>Retrieves pairwise relations between two genomes from the OMA (Orthologous Matrix) database (<a class="reference external" href="https://omabrowser.org/oma/home/">https://omabrowser.org/oma/home/</a>).</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.inputs.oma.oma_table.html#pypath.inputs.oma.oma_table" title="pypath.inputs.oma.oma_table"><code class="xref py py-obj docutils literal notranslate"><span class="pre">oma_table</span></code></a>([organism_a, organism_b, id_type, ...])</p></td>
+<td><p>Translation table of orthologous gene pairs between two organisms from the OMA (Orthologous Matrix) database (<a class="reference external" href="https://omabrowser.org/oma/home/">https://omabrowser.org/oma/home/</a>).</p></td>
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+  <section id="pypath-inputs-oma-oma-orthologs">
+<h1>pypath.inputs.oma.oma_orthologs<a class="headerlink" href="#pypath-inputs-oma-oma-orthologs" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.inputs.oma.oma_orthologs">
+<span class="sig-prename descclassname"><span class="pre">pypath.inputs.oma.</span></span><span class="sig-name descname"><span class="pre">oma_orthologs</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">organism_a</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">int</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">'human'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">organism_b</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">int</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">'mouse'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">id_type</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">rel_type</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">set</span><span class="p"><span class="pre">[</span></span><span class="pre">Literal</span><span class="p"><span class="pre">[</span></span><span class="s"><span class="pre">'1:1'</span></span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="s"><span class="pre">'1:n'</span></span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="s"><span class="pre">'m:1'</span></span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="s"><span class="pre">'m:n'</span></span><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">score</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">float</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">return_df</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">tuple</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">DataFrame</span></span></span><a class="reference internal" href="../_modules/pypath/inputs/oma.html#oma_orthologs"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.oma.oma_orthologs" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves pairwise relations between two genomes from the OMA
+(Orthologous Matrix) database (<a class="reference external" href="https://omabrowser.org/oma/home/">https://omabrowser.org/oma/home/</a>).</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>organism_a</strong> – Name or NCBI Taxonomy ID of the first organism.</p></li>
+<li><p><strong>organism_b</strong> – Name or NCBI Taxonomy ID of the second organism.</p></li>
+<li><p><strong>id_type</strong> – OMA by default uses UniProt entry IDs and sometimes other
+identifiers for genes. Set this parameter to control which
+ID type all the identifiers are to be mapped to.</p></li>
+<li><p><strong>rel_type</strong> – Restrict relations to certain types.</p></li>
+<li><p><strong>score</strong> – Lower threshold for similarity metric.</p></li>
+<li><p><strong>return_df</strong> – If True, returns a data frame instead of a list of tuples.</p></li>
+</ul>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p>A list with tuples of pairwise orthologous relationships or a data
+frame with the same records.</p>
+</dd>
+</dl>
+</dd></dl>
+
+</section>
+
+
+                </article>
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+  <section id="pypath-inputs-oma-oma-table">
+<h1>pypath.inputs.oma.oma_table<a class="headerlink" href="#pypath-inputs-oma-oma-table" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.inputs.oma.oma_table">
+<span class="sig-prename descclassname"><span class="pre">pypath.inputs.oma.</span></span><span class="sig-name descname"><span class="pre">oma_table</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">organism_a</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">int</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">'human'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">organism_b</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">int</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">'mouse'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">id_type</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">rel_type</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">set</span><span class="p"><span class="pre">[</span></span><span class="pre">Literal</span><span class="p"><span class="pre">[</span></span><span class="s"><span class="pre">'1:1'</span></span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="s"><span class="pre">'1:n'</span></span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="s"><span class="pre">'m:1'</span></span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="s"><span class="pre">'m:n'</span></span><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">score</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">float</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">return_df</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">[</span></span><span class="pre">set</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">pd.DataFrame</span></span></span><a class="reference internal" href="../_modules/pypath/inputs/oma.html#oma_table"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.oma.oma_table" title="Link to this definition">§</a></dt>
+<dd><p>Translation table of orthologous gene pairs between two organisms from the
+OMA (Orthologous Matrix) database (<a class="reference external" href="https://omabrowser.org/oma/home/">https://omabrowser.org/oma/home/</a>).</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>organism_a</strong> – Name or NCBI Taxonomy ID of the first organism.</p></li>
+<li><p><strong>organism_b</strong> – Name or NCBI Taxonomy ID of the second organism.</p></li>
+<li><p><strong>id_type</strong> – OMA by default uses UniProt entry IDs and sometimes other
+identifiers for genes. Set this parameter to control which
+ID type all the identifiers are to be mapped to.</p></li>
+<li><p><strong>rel_type</strong> – Restrict relations to certain types.</p></li>
+<li><p><strong>score</strong> – Lower threshold for similarity metric.</p></li>
+<li><p><strong>return_df</strong> – If True, returns a data frame instead of a list of tuples.</p></li>
+</ul>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p>A dict with source organism identifiers as keys and sets of target
+organism identifiers as values; or a two column data frame with
+source organism-target organism identifier pairs.</p>
+</dd>
+</dl>
+</dd></dl>
+
+</section>
+
+
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diff --git a/api/pypath.inputs.ontology.html b/api/pypath.inputs.ontology.html
index 6eab4eb7f..6e9bc475c 100644
--- a/api/pypath.inputs.ontology.html
+++ b/api/pypath.inputs.ontology.html
@@ -48,7 +48,7 @@
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-    <link rel="prev" title="pypath.inputs.offsides.offsides_side_effects" href="pypath.inputs.offsides.offsides_side_effects.html" />
+    <link rel="prev" title="pypath.inputs.oma.oma_table" href="pypath.inputs.oma.oma_table.html" />
   <meta name="viewport" content="width=device-width, initial-scale=1"/>
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@@ -545,12 +545,12 @@
                   
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+       href="pypath.inputs.oma.oma_table.html"
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+        <p class="prev-next-title">pypath.inputs.oma.oma_table</p>
       </div>
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diff --git a/api/pypath.inputs.opentargets.opentargets_indirect_score.html b/api/pypath.inputs.opentargets.opentargets_indirect_score.html
index e38af6b83..fa38071c3 100644
--- a/api/pypath.inputs.opentargets.opentargets_indirect_score.html
+++ b/api/pypath.inputs.opentargets.opentargets_indirect_score.html
@@ -47,7 +47,7 @@
     <link rel="icon" href="../_static/omnipath-logo.svg"/>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
-    <link rel="next" title="pypath.inputs.oreganno" href="pypath.inputs.oreganno.html" />
+    <link rel="next" title="pypath.inputs.opm" href="pypath.inputs.opm.html" />
     <link rel="prev" title="pypath.inputs.opentargets.opentargets_general" href="pypath.inputs.opentargets.opentargets_general.html" />
   <meta name="viewport" content="width=device-width, initial-scale=1"/>
   <meta name="docsearch:language" content="en"/>
@@ -560,11 +560,11 @@ <h1>pypath.inputs.opentargets.opentargets_indirect_score<a class="headerlink" hr
       </div>
     </a>
     <a class="right-next"
-       href="pypath.inputs.oreganno.html"
+       href="pypath.inputs.opm.html"
        title="next page">
       <div class="prev-next-info">
         <p class="prev-next-subtitle">next</p>
-        <p class="prev-next-title">pypath.inputs.oreganno</p>
+        <p class="prev-next-title">pypath.inputs.opm</p>
       </div>
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     </a>
diff --git a/api/pypath.inputs.opm.html b/api/pypath.inputs.opm.html
new file mode 100644
index 000000000..6d30fef71
--- /dev/null
+++ b/api/pypath.inputs.opm.html
@@ -0,0 +1,645 @@
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diff --git a/api/pypath.inputs.opm.opm_annotations.html b/api/pypath.inputs.opm.opm_annotations.html
new file mode 100644
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+                        Reference
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+                
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+                    <li class="nav-item">
+                      <a class="nav-link nav-internal" href="../notebooks/manual.html">
+                        The pypath book
+                      </a>
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+    
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+      <div class="sidebar-header-items__end">
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+    <span class="theme-switch nav-link" data-mode="dark"><i class="fa-solid fa-moon fa-lg"></i></span>
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+            <span class="sr-only">GitHub</span></a>
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+          
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+          <a href="https://omnipathdb.org/" title="OmniPath" class="nav-link" rel="noopener" target="_blank" data-bs-toggle="tooltip" data-bs-placement="bottom"><span><i class="fa-solid fa-university fa-lg" aria-hidden="true"></i></span>
+            <span class="sr-only">OmniPath</span></a>
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+        <li class="nav-item">
+          
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+          <a href="https://saezlab.org/" title="Saez Lab" class="nav-link" rel="noopener" target="_blank" data-bs-toggle="tooltip" data-bs-placement="bottom"><span><i class="fa-solid fa-users fa-lg" aria-hidden="true"></i></span>
+            <span class="sr-only">Saez Lab</span></a>
+        </li>
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+      <a href="../contents.html" class="nav-link" aria-label="Home">
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+    
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+    
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+    
+    <li class="breadcrumb-item active" aria-current="page">pypath.input...</li>
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+</div>
+      
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+</div>
+              
+              
+              
+                
+<div id="searchbox"></div>
+                <article class="bd-article">
+                  
+  <section id="pypath-inputs-opm-opm-annotations">
+<h1>pypath.inputs.opm.opm_annotations<a class="headerlink" href="#pypath-inputs-opm-opm-annotations" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.inputs.opm.opm_annotations">
+<span class="sig-prename descclassname"><span class="pre">pypath.inputs.opm.</span></span><span class="sig-name descname"><span class="pre">opm_annotations</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">organism</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/inputs/opm.html#opm_annotations"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.opm.opm_annotations" title="Link to this definition">§</a></dt>
+<dd></dd></dl>
+
+</section>
+
+
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+              
+              
+              
+              
+              
+                <footer class="prev-next-footer">
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+      <div class="prev-next-info">
+        <p class="prev-next-subtitle">previous</p>
+        <p class="prev-next-title">pypath.inputs.opm</p>
+      </div>
+    </a>
+    <a class="right-next"
+       href="pypath.inputs.oreganno.html"
+       title="next page">
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+        <p class="prev-next-subtitle">next</p>
+        <p class="prev-next-title">pypath.inputs.oreganno</p>
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+<div
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+    class="page-toc tocsection onthispage">
+    <i class="fa-solid fa-list"></i> On this page
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+  <nav class="bd-toc-nav page-toc" aria-labelledby="pst-page-navigation-heading-2">
+    <ul class="visible nav section-nav flex-column">
+<li class="toctree-l1 toc-h1 nav-item toc-entry"><a class="reference internal nav-link" href="../index.html">Welcome to pypath!</a></li>
+<li class="toctree-l1 toc-h1 nav-item toc-entry"><a class="reference internal nav-link" href="../webservice.html">Webservice</a></li>
+<li class="toctree-l1 toc-h1 nav-item toc-entry"><a class="reference internal nav-link" href="../releasehistory.html">Release history</a></li>
+<li class="toctree-l1 toc-h1 nav-item toc-entry"><a class="reference internal nav-link" href="../reference.html">Reference</a></li>
+<li class="toctree-l1 toc-h1 nav-item toc-entry"><a class="reference internal nav-link" href="../notebooks/manual.html">The pypath book</a></li>
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+    
+      © Copyright 2024, Denes Turei &lt;turei.denes@gmail.com&gt;, Nicolàs Palacio, Sebastian Lobentanzer, Olga Ivanova, Melih Darcan, Erva Ulusoy, Tennur Kilic, Omer Kaan Vural, Ahmet Rifaioglu, Charles Tapley Hoyt.
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+</html>
\ No newline at end of file
diff --git a/api/pypath.inputs.oreganno.html b/api/pypath.inputs.oreganno.html
index b0b4b24c1..5a291bf6d 100644
--- a/api/pypath.inputs.oreganno.html
+++ b/api/pypath.inputs.oreganno.html
@@ -48,7 +48,7 @@
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
     <link rel="next" title="pypath.inputs.oreganno.oreganno_interactions" href="pypath.inputs.oreganno.oreganno_interactions.html" />
-    <link rel="prev" title="pypath.inputs.opentargets.opentargets_indirect_score" href="pypath.inputs.opentargets.opentargets_indirect_score.html" />
+    <link rel="prev" title="pypath.inputs.opm.opm_annotations" href="pypath.inputs.opm.opm_annotations.html" />
   <meta name="viewport" content="width=device-width, initial-scale=1"/>
   <meta name="docsearch:language" content="en"/>
   </head>
@@ -545,12 +545,12 @@
                   
 <div class="prev-next-area">
     <a class="left-prev"
-       href="pypath.inputs.opentargets.opentargets_indirect_score.html"
+       href="pypath.inputs.opm.opm_annotations.html"
        title="previous page">
       <i class="fa-solid fa-angle-left"></i>
       <div class="prev-next-info">
         <p class="prev-next-subtitle">previous</p>
-        <p class="prev-next-title">pypath.inputs.opentargets.opentargets_indirect_score</p>
+        <p class="prev-next-title">pypath.inputs.opm.opm_annotations</p>
       </div>
     </a>
     <a class="right-next"
diff --git a/api/pypath.inputs.oreganno.oreganno_raw.html b/api/pypath.inputs.oreganno.oreganno_raw.html
index 518d5770e..02de35afa 100644
--- a/api/pypath.inputs.oreganno.oreganno_raw.html
+++ b/api/pypath.inputs.oreganno.oreganno_raw.html
@@ -47,7 +47,7 @@
     <link rel="icon" href="../_static/omnipath-logo.svg"/>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
-    <link rel="next" title="pypath.inputs.pathophenodb" href="pypath.inputs.pathophenodb.html" />
+    <link rel="next" title="pypath.inputs.panglaodb" href="pypath.inputs.panglaodb.html" />
     <link rel="prev" title="pypath.inputs.oreganno.oreganno_interactions" href="pypath.inputs.oreganno.oreganno_interactions.html" />
   <meta name="viewport" content="width=device-width, initial-scale=1"/>
   <meta name="docsearch:language" content="en"/>
@@ -550,11 +550,11 @@ <h1>pypath.inputs.oreganno.oreganno_raw<a class="headerlink" href="#pypath-input
       </div>
     </a>
     <a class="right-next"
-       href="pypath.inputs.pathophenodb.html"
+       href="pypath.inputs.panglaodb.html"
        title="next page">
       <div class="prev-next-info">
         <p class="prev-next-subtitle">next</p>
-        <p class="prev-next-title">pypath.inputs.pathophenodb</p>
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+                  
+  <section id="module-pypath.inputs.panglaodb">
+<span id="pypath-inputs-panglaodb"></span><h1>pypath.inputs.panglaodb<a class="headerlink" href="#module-pypath.inputs.panglaodb" title="Link to this heading">§</a></h1>
+<dl class="field-list simple">
+<dt class="field-odd">members<span class="colon">:</span></dt>
+<dd class="field-odd"><p></p></dd>
+</dl>
+<p class="rubric">Functions</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.inputs.panglaodb.panglaodb_annotations.html#pypath.inputs.panglaodb.panglaodb_annotations" title="pypath.inputs.panglaodb.panglaodb_annotations"><code class="xref py py-obj docutils literal notranslate"><span class="pre">panglaodb_annotations</span></code></a>()</p></td>
+<td><p>Cell type marker genes from PanglaoDB (<a class="reference external" href="https://panglaodb.se/index.html">https://panglaodb.se/index.html</a>).</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.inputs.panglaodb.panglaodb_raw.html#pypath.inputs.panglaodb.panglaodb_raw" title="pypath.inputs.panglaodb.panglaodb_raw"><code class="xref py py-obj docutils literal notranslate"><span class="pre">panglaodb_raw</span></code></a>()</p></td>
+<td><p>Cell type marker genes from PanglaoDB (<a class="reference external" href="https://panglaodb.se/index.html">https://panglaodb.se/index.html</a>).</p></td>
+</tr>
+</tbody>
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+  <section id="pypath-inputs-panglaodb-panglaodb-annotations">
+<h1>pypath.inputs.panglaodb.panglaodb_annotations<a class="headerlink" href="#pypath-inputs-panglaodb-panglaodb-annotations" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.inputs.panglaodb.panglaodb_annotations">
+<span class="sig-prename descclassname"><span class="pre">pypath.inputs.panglaodb.</span></span><span class="sig-name descname"><span class="pre">panglaodb_annotations</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/inputs/panglaodb.html#panglaodb_annotations"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.panglaodb.panglaodb_annotations" title="Link to this definition">§</a></dt>
+<dd><p>Cell type marker genes from PanglaoDB (<a class="reference external" href="https://panglaodb.se/index.html">https://panglaodb.se/index.html</a>).</p>
+</dd></dl>
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+  <section id="pypath-inputs-panglaodb-panglaodb-raw">
+<h1>pypath.inputs.panglaodb.panglaodb_raw<a class="headerlink" href="#pypath-inputs-panglaodb-panglaodb-raw" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.inputs.panglaodb.panglaodb_raw">
+<span class="sig-prename descclassname"><span class="pre">pypath.inputs.panglaodb.</span></span><span class="sig-name descname"><span class="pre">panglaodb_raw</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/inputs/panglaodb.html#panglaodb_raw"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.panglaodb.panglaodb_raw" title="Link to this definition">§</a></dt>
+<dd><p>Cell type marker genes from PanglaoDB (<a class="reference external" href="https://panglaodb.se/index.html">https://panglaodb.se/index.html</a>).</p>
+</dd></dl>
+
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diff --git a/api/pypath.inputs.pathophenodb.html b/api/pypath.inputs.pathophenodb.html
index 637389a4d..11883a7b7 100644
--- a/api/pypath.inputs.pathophenodb.html
+++ b/api/pypath.inputs.pathophenodb.html
@@ -48,7 +48,7 @@
     <link rel="index" title="Index" href="../genindex.html" />
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     <link rel="next" title="pypath.inputs.pathophenodb.disease_pathogen_interactions" href="pypath.inputs.pathophenodb.disease_pathogen_interactions.html" />
-    <link rel="prev" title="pypath.inputs.oreganno.oreganno_raw" href="pypath.inputs.oreganno.oreganno_raw.html" />
+    <link rel="prev" title="pypath.inputs.panglaodb.panglaodb_raw" href="pypath.inputs.panglaodb.panglaodb_raw.html" />
   <meta name="viewport" content="width=device-width, initial-scale=1"/>
   <meta name="docsearch:language" content="en"/>
   </head>
@@ -550,12 +550,12 @@
                   
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     <a class="left-prev"
-       href="pypath.inputs.oreganno.oreganno_raw.html"
+       href="pypath.inputs.panglaodb.panglaodb_raw.html"
        title="previous page">
       <i class="fa-solid fa-angle-left"></i>
       <div class="prev-next-info">
         <p class="prev-next-subtitle">previous</p>
-        <p class="prev-next-title">pypath.inputs.oreganno.oreganno_raw</p>
+        <p class="prev-next-title">pypath.inputs.panglaodb.panglaodb_raw</p>
       </div>
     </a>
     <a class="right-next"
diff --git a/api/pypath.inputs.pazar.pazar_interactions.html b/api/pypath.inputs.pazar.pazar_interactions.html
index 662aa9f0c..ce50a57fc 100644
--- a/api/pypath.inputs.pazar.pazar_interactions.html
+++ b/api/pypath.inputs.pazar.pazar_interactions.html
@@ -47,7 +47,7 @@
     <link rel="icon" href="../_static/omnipath-logo.svg"/>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
-    <link rel="next" title="pypath.inputs.pdzbase" href="pypath.inputs.pdzbase.html" />
+    <link rel="next" title="pypath.inputs.pdb" href="pypath.inputs.pdb.html" />
     <link rel="prev" title="pypath.inputs.pazar" href="pypath.inputs.pazar.html" />
   <meta name="viewport" content="width=device-width, initial-scale=1"/>
   <meta name="docsearch:language" content="en"/>
@@ -544,11 +544,11 @@ <h1>pypath.inputs.pazar.pazar_interactions<a class="headerlink" href="#pypath-in
       </div>
     </a>
     <a class="right-next"
-       href="pypath.inputs.pdzbase.html"
+       href="pypath.inputs.pdb.html"
        title="next page">
       <div class="prev-next-info">
         <p class="prev-next-subtitle">next</p>
-        <p class="prev-next-title">pypath.inputs.pdzbase</p>
+        <p class="prev-next-title">pypath.inputs.pdb</p>
       </div>
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diff --git a/api/pypath.inputs.pdb.html b/api/pypath.inputs.pdb.html
new file mode 100644
index 000000000..9850f96e9
--- /dev/null
+++ b/api/pypath.inputs.pdb.html
@@ -0,0 +1,651 @@
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+
+    <title>pypath.inputs.pdb &#8212; pypath 0.16.9 documentation</title>
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+  <script data-cfasync="false">
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+<dl class="field-list simple">
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+<p class="rubric">Functions</p>
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+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.inputs.pdb.pdb_chains.html#pypath.inputs.pdb.pdb_chains" title="pypath.inputs.pdb.pdb_chains"><code class="xref py py-obj docutils literal notranslate"><span class="pre">pdb_chains</span></code></a>()</p></td>
+<td><p>Amino acid chain level mapping between PDB and UniProt. Returns two dictionaries: * The first has UniProt IDs as keys and lists of dicts as values. Each   of these dicts defines a mapping between UniProt and PDB amino acid   chains with the chain identifier, PDB structure identifier and the   start and end of the chain in the UniProt sequence and the PDB   structure; the offset value is an integer if the PDB and the UniProt   chain are the same length, otherwise None. * The second dict has PDB IDs as keys and dicts of chain mapping dicts   as values, which are similar to the ones in the previous point, but   here the chain identifiers are the keys.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.inputs.pdb.pdb_complexes.html#pypath.inputs.pdb.pdb_complexes" title="pypath.inputs.pdb.pdb_complexes"><code class="xref py py-obj docutils literal notranslate"><span class="pre">pdb_complexes</span></code></a>([organism])</p></td>
+<td><p>Extracts protein complex data from PDB.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.inputs.pdb.pdb_uniprot.html#pypath.inputs.pdb.pdb_uniprot" title="pypath.inputs.pdb.pdb_uniprot"><code class="xref py py-obj docutils literal notranslate"><span class="pre">pdb_uniprot</span></code></a>()</p></td>
+<td><p>Mapping between UniProt and PDB identifiers. Returns two dictionaries: * UniProt to PDB mapping: keys are UniProt IDs, values are sets of   tuples, each tuple with three values: the PDB structure ID, the   structure analysis method and the structure resolution * PDB to UniProt mapping: keys are PDB IDs, values are sets of UniProt   IDs.</p></td>
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+  <section id="pypath-inputs-pdb-pdb-chains">
+<h1>pypath.inputs.pdb.pdb_chains<a class="headerlink" href="#pypath-inputs-pdb-pdb-chains" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.inputs.pdb.pdb_chains">
+<span class="sig-prename descclassname"><span class="pre">pypath.inputs.pdb.</span></span><span class="sig-name descname"><span class="pre">pdb_chains</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/inputs/pdb.html#pdb_chains"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.pdb.pdb_chains" title="Link to this definition">§</a></dt>
+<dd><p>Amino acid chain level mapping between PDB and UniProt.
+Returns two dictionaries:
+* The first has UniProt IDs as keys and lists of dicts as values. Each</p>
+<blockquote>
+<div><p>of these dicts defines a mapping between UniProt and PDB amino acid
+chains with the chain identifier, PDB structure identifier and the
+start and end of the chain in the UniProt sequence and the PDB
+structure; the offset value is an integer if the PDB and the UniProt
+chain are the same length, otherwise None.</p>
+</div></blockquote>
+<ul class="simple">
+<li><p>The second dict has PDB IDs as keys and dicts of chain mapping dicts
+as values, which are similar to the ones in the previous point, but
+here the chain identifiers are the keys.</p></li>
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+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.inputs.pdb.pdb_complexes">
+<span class="sig-prename descclassname"><span class="pre">pypath.inputs.pdb.</span></span><span class="sig-name descname"><span class="pre">pdb_complexes</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">organism</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/inputs/pdb.html#pdb_complexes"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.pdb.pdb_complexes" title="Link to this definition">§</a></dt>
+<dd><p>Extracts protein complex data from PDB. The complexes are returned in
+a dict with string keys and <code class="docutils literal notranslate"><span class="pre">pypath.internals.intera.Complex</span></code>
+objects as values. These latter carry their constitution, stoichiometry
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+            <span class="sr-only">Saez Lab</span></a>
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+</nav></div>
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+      
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+<div id="searchbox"></div>
+                <article class="bd-article">
+                  
+  <section id="pypath-inputs-pdb-pdb-uniprot">
+<h1>pypath.inputs.pdb.pdb_uniprot<a class="headerlink" href="#pypath-inputs-pdb-pdb-uniprot" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.inputs.pdb.pdb_uniprot">
+<span class="sig-prename descclassname"><span class="pre">pypath.inputs.pdb.</span></span><span class="sig-name descname"><span class="pre">pdb_uniprot</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/inputs/pdb.html#pdb_uniprot"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.pdb.pdb_uniprot" title="Link to this definition">§</a></dt>
+<dd><p>Mapping between UniProt and PDB identifiers.
+Returns two dictionaries:
+* UniProt to PDB mapping: keys are UniProt IDs, values are sets of</p>
+<blockquote>
+<div><p>tuples, each tuple with three values: the PDB structure ID, the
+structure analysis method and the structure resolution</p>
+</div></blockquote>
+<ul class="simple">
+<li><p>PDB to UniProt mapping: keys are PDB IDs, values are sets of UniProt
+IDs</p></li>
+</ul>
+</dd></dl>
+
+</section>
+
+
+                </article>
+              
+              
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+              
+                <footer class="prev-next-footer">
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+        <p class="prev-next-title">pypath.inputs.pdb.pdb_complexes</p>
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\ No newline at end of file
diff --git a/api/pypath.inputs.pdzbase.html b/api/pypath.inputs.pdzbase.html
index 68650901e..ef010bcb1 100644
--- a/api/pypath.inputs.pdzbase.html
+++ b/api/pypath.inputs.pdzbase.html
@@ -48,7 +48,7 @@
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
     <link rel="next" title="pypath.inputs.pdzbase.pdzbase_interactions" href="pypath.inputs.pdzbase.pdzbase_interactions.html" />
-    <link rel="prev" title="pypath.inputs.pazar.pazar_interactions" href="pypath.inputs.pazar.pazar_interactions.html" />
+    <link rel="prev" title="pypath.inputs.pdb.pdb_uniprot" href="pypath.inputs.pdb.pdb_uniprot.html" />
   <meta name="viewport" content="width=device-width, initial-scale=1"/>
   <meta name="docsearch:language" content="en"/>
   </head>
@@ -542,12 +542,12 @@
                   
 <div class="prev-next-area">
     <a class="left-prev"
-       href="pypath.inputs.pazar.pazar_interactions.html"
+       href="pypath.inputs.pdb.pdb_uniprot.html"
        title="previous page">
       <i class="fa-solid fa-angle-left"></i>
       <div class="prev-next-info">
         <p class="prev-next-subtitle">previous</p>
-        <p class="prev-next-title">pypath.inputs.pazar.pazar_interactions</p>
+        <p class="prev-next-title">pypath.inputs.pdb.pdb_uniprot</p>
       </div>
     </a>
     <a class="right-next"
diff --git a/api/pypath.inputs.phobius.phobius_annotations.html b/api/pypath.inputs.phobius.phobius_annotations.html
index a77bfe17d..9a738d696 100644
--- a/api/pypath.inputs.phobius.phobius_annotations.html
+++ b/api/pypath.inputs.phobius.phobius_annotations.html
@@ -47,7 +47,7 @@
     <link rel="icon" href="../_static/omnipath-logo.svg"/>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
-    <link rel="next" title="pypath.inputs.phosphoelm" href="pypath.inputs.phosphoelm.html" />
+    <link rel="next" title="pypath.inputs.phosphatome" href="pypath.inputs.phosphatome.html" />
     <link rel="prev" title="pypath.inputs.phobius" href="pypath.inputs.phobius.html" />
   <meta name="viewport" content="width=device-width, initial-scale=1"/>
   <meta name="docsearch:language" content="en"/>
@@ -544,11 +544,11 @@ <h1>pypath.inputs.phobius.phobius_annotations<a class="headerlink" href="#pypath
       </div>
     </a>
     <a class="right-next"
-       href="pypath.inputs.phosphoelm.html"
+       href="pypath.inputs.phosphatome.html"
        title="next page">
       <div class="prev-next-info">
         <p class="prev-next-subtitle">next</p>
-        <p class="prev-next-title">pypath.inputs.phosphoelm</p>
+        <p class="prev-next-title">pypath.inputs.phosphatome</p>
       </div>
       <i class="fa-solid fa-angle-right"></i>
     </a>
diff --git a/api/pypath.inputs.phosphatome.html b/api/pypath.inputs.phosphatome.html
new file mode 100644
index 000000000..7ec45bd1a
--- /dev/null
+++ b/api/pypath.inputs.phosphatome.html
@@ -0,0 +1,645 @@
+
+<!DOCTYPE html>
+
+
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+
+    <title>pypath.inputs.phosphatome &#8212; pypath 0.16.9 documentation</title>
+  
+  
+  
+  <script data-cfasync="false">
+    document.documentElement.dataset.mode = localStorage.getItem("mode") || "";
+    document.documentElement.dataset.theme = localStorage.getItem("theme") || "light";
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+    <script>DOCUMENTATION_OPTIONS.pagename = 'api/pypath.inputs.phosphatome';</script>
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+  <section id="module-pypath.inputs.phosphatome">
+<span id="pypath-inputs-phosphatome"></span><h1>pypath.inputs.phosphatome<a class="headerlink" href="#module-pypath.inputs.phosphatome" title="Link to this heading">§</a></h1>
+<dl class="field-list simple">
+<dt class="field-odd">members<span class="colon">:</span></dt>
+<dd class="field-odd"><p></p></dd>
+</dl>
+<p class="rubric">Functions</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.inputs.phosphatome.phosphatome_annotations.html#pypath.inputs.phosphatome.phosphatome_annotations" title="pypath.inputs.phosphatome.phosphatome_annotations"><code class="xref py py-obj docutils literal notranslate"><span class="pre">phosphatome_annotations</span></code></a>()</p></td>
+<td><p>Downloads the list of phosphatases from Chen et al, Science Signaling (2017) Table S1.</p></td>
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diff --git a/api/pypath.inputs.phosphatome.phosphatome_annotations.html b/api/pypath.inputs.phosphatome.phosphatome_annotations.html
new file mode 100644
index 000000000..249cfff3f
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@@ -0,0 +1,640 @@
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+    
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+    <li class="breadcrumb-item"><a href="pypath.inputs.phosphatome.html" class="nav-link">pypath.inputs.phosphatome</a></li>
+    
+    <li class="breadcrumb-item active" aria-current="page">pypath.input...</li>
+  </ul>
+</nav>
+</div>
+      
+    </div>
+  
+  
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+</div>
+              
+              
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+                
+<div id="searchbox"></div>
+                <article class="bd-article">
+                  
+  <section id="pypath-inputs-phosphatome-phosphatome-annotations">
+<h1>pypath.inputs.phosphatome.phosphatome_annotations<a class="headerlink" href="#pypath-inputs-phosphatome-phosphatome-annotations" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.inputs.phosphatome.phosphatome_annotations">
+<span class="sig-prename descclassname"><span class="pre">pypath.inputs.phosphatome.</span></span><span class="sig-name descname"><span class="pre">phosphatome_annotations</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/inputs/phosphatome.html#phosphatome_annotations"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.phosphatome.phosphatome_annotations" title="Link to this definition">§</a></dt>
+<dd><p>Downloads the list of phosphatases from Chen et al, Science Signaling
+(2017) Table S1.</p>
+</dd></dl>
+
+</section>
+
+
+                </article>
+              
+              
+              
+              
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\ No newline at end of file
diff --git a/api/pypath.inputs.phosphoelm.html b/api/pypath.inputs.phosphoelm.html
index f5bfd32aa..8bf022109 100644
--- a/api/pypath.inputs.phosphoelm.html
+++ b/api/pypath.inputs.phosphoelm.html
@@ -48,7 +48,7 @@
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
     <link rel="next" title="pypath.inputs.phosphoelm.phosphoelm_enzyme_substrate" href="pypath.inputs.phosphoelm.phosphoelm_enzyme_substrate.html" />
-    <link rel="prev" title="pypath.inputs.phobius.phobius_annotations" href="pypath.inputs.phobius.phobius_annotations.html" />
+    <link rel="prev" title="pypath.inputs.phosphatome.phosphatome_annotations" href="pypath.inputs.phosphatome.phosphatome_annotations.html" />
   <meta name="viewport" content="width=device-width, initial-scale=1"/>
   <meta name="docsearch:language" content="en"/>
   </head>
@@ -548,12 +548,12 @@
                   
 <div class="prev-next-area">
     <a class="left-prev"
-       href="pypath.inputs.phobius.phobius_annotations.html"
+       href="pypath.inputs.phosphatome.phosphatome_annotations.html"
        title="previous page">
       <i class="fa-solid fa-angle-left"></i>
       <div class="prev-next-info">
         <p class="prev-next-subtitle">previous</p>
-        <p class="prev-next-title">pypath.inputs.phobius.phobius_annotations</p>
+        <p class="prev-next-title">pypath.inputs.phosphatome.phosphatome_annotations</p>
       </div>
     </a>
     <a class="right-next"
diff --git a/api/pypath.inputs.phosphopoint.phosphopoint_interactions.html b/api/pypath.inputs.phosphopoint.phosphopoint_interactions.html
index cc056277d..e9e9d77d0 100644
--- a/api/pypath.inputs.phosphopoint.phosphopoint_interactions.html
+++ b/api/pypath.inputs.phosphopoint.phosphopoint_interactions.html
@@ -47,7 +47,7 @@
     <link rel="icon" href="../_static/omnipath-logo.svg"/>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
-    <link rel="next" title="pypath.inputs.pro" href="pypath.inputs.pro.html" />
+    <link rel="next" title="pypath.inputs.phosphosite" href="pypath.inputs.phosphosite.html" />
     <link rel="prev" title="pypath.inputs.phosphopoint.phosphopoint_directions" href="pypath.inputs.phosphopoint.phosphopoint_directions.html" />
   <meta name="viewport" content="width=device-width, initial-scale=1"/>
   <meta name="docsearch:language" content="en"/>
@@ -544,11 +544,11 @@ <h1>pypath.inputs.phosphopoint.phosphopoint_interactions<a class="headerlink" hr
       </div>
     </a>
     <a class="right-next"
-       href="pypath.inputs.pro.html"
+       href="pypath.inputs.phosphosite.html"
        title="next page">
       <div class="prev-next-info">
         <p class="prev-next-subtitle">next</p>
-        <p class="prev-next-title">pypath.inputs.pro</p>
+        <p class="prev-next-title">pypath.inputs.phosphosite</p>
       </div>
       <i class="fa-solid fa-angle-right"></i>
     </a>
diff --git a/api/pypath.inputs.phosphosite.html b/api/pypath.inputs.phosphosite.html
new file mode 100644
index 000000000..3454ad046
--- /dev/null
+++ b/api/pypath.inputs.phosphosite.html
@@ -0,0 +1,678 @@
+
+<!DOCTYPE html>
+
+
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+
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+    <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="viewport" content="width=device-width, initial-scale=1" />
+
+    <title>pypath.inputs.phosphosite &#8212; pypath 0.16.9 documentation</title>
+  
+  
+  
+  <script data-cfasync="false">
+    document.documentElement.dataset.mode = localStorage.getItem("mode") || "";
+    document.documentElement.dataset.theme = localStorage.getItem("theme") || "light";
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+  <section id="module-pypath.inputs.phosphosite">
+<span id="pypath-inputs-phosphosite"></span><h1>pypath.inputs.phosphosite<a class="headerlink" href="#module-pypath.inputs.phosphosite" title="Link to this heading">§</a></h1>
+<dl class="field-list simple">
+<dt class="field-odd">members<span class="colon">:</span></dt>
+<dd class="field-odd"><p></p></dd>
+</dl>
+<p class="rubric">Functions</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.inputs.phosphosite.phosphosite_directions.html#pypath.inputs.phosphosite.phosphosite_directions" title="pypath.inputs.phosphosite.phosphosite_directions"><code class="xref py py-obj docutils literal notranslate"><span class="pre">phosphosite_directions</span></code></a>([organism])</p></td>
+<td><p>From curated and HTP PhosphoSite data generates a list of directions.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.inputs.phosphosite.phosphosite_enzyme_substrate.html#pypath.inputs.phosphosite.phosphosite_enzyme_substrate" title="pypath.inputs.phosphosite.phosphosite_enzyme_substrate"><code class="xref py py-obj docutils literal notranslate"><span class="pre">phosphosite_enzyme_substrate</span></code></a>([raw, ...])</p></td>
+<td><p>Downloads and preprocesses phosphorylation site data from PhosphoSitePlus.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.inputs.phosphosite.phosphosite_interactions.html#pypath.inputs.phosphosite.phosphosite_interactions" title="pypath.inputs.phosphosite.phosphosite_interactions"><code class="xref py py-obj docutils literal notranslate"><span class="pre">phosphosite_interactions</span></code></a>([cache, ncbi_tax_id])</p></td>
+<td><p>Downloads curated and HTP data from Phosphosite, from preprocessed cache file if available.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.inputs.phosphosite.phosphosite_interactions_all.html#pypath.inputs.phosphosite.phosphosite_interactions_all" title="pypath.inputs.phosphosite.phosphosite_interactions_all"><code class="xref py py-obj docutils literal notranslate"><span class="pre">phosphosite_interactions_all</span></code></a>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.inputs.phosphosite.phosphosite_interactions_curated.html#pypath.inputs.phosphosite.phosphosite_interactions_curated" title="pypath.inputs.phosphosite.phosphosite_interactions_curated"><code class="xref py py-obj docutils literal notranslate"><span class="pre">phosphosite_interactions_curated</span></code></a>([ncbi_tax_id])</p></td>
+<td><p>Loads literature curated PhosphoSite data, from preprocessed cache file if available.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.inputs.phosphosite.phosphosite_interactions_new.html#pypath.inputs.phosphosite.phosphosite_interactions_new" title="pypath.inputs.phosphosite.phosphosite_interactions_new"><code class="xref py py-obj docutils literal notranslate"><span class="pre">phosphosite_interactions_new</span></code></a>([cache])</p></td>
+<td><p>Downloads curated and HTP data from Phosphosite, from preprocessed cache file if available.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.inputs.phosphosite.phosphosite_interactions_noref.html#pypath.inputs.phosphosite.phosphosite_interactions_noref" title="pypath.inputs.phosphosite.phosphosite_interactions_noref"><code class="xref py py-obj docutils literal notranslate"><span class="pre">phosphosite_interactions_noref</span></code></a>([ncbi_tax_id])</p></td>
+<td><p>Loads HTP PhosphoSite data, from preprocessed cache file if available.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.inputs.phosphosite.phosphosite_ptm_orthology.html#pypath.inputs.phosphosite.phosphosite_ptm_orthology" title="pypath.inputs.phosphosite.phosphosite_ptm_orthology"><code class="xref py py-obj docutils literal notranslate"><span class="pre">phosphosite_ptm_orthology</span></code></a>()</p></td>
+<td><p>Returns an orthology translation dict of phosphosites based on phosphorylation sites table from PhosphoSitePlus.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.inputs.phosphosite.phosphosite_ptms.html#pypath.inputs.phosphosite.phosphosite_ptms" title="pypath.inputs.phosphosite.phosphosite_ptms"><code class="xref py py-obj docutils literal notranslate"><span class="pre">phosphosite_ptms</span></code></a>([organism])</p></td>
+<td><p>Downloads the phosphorylation site dataset from PhosphoSitePlus.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.inputs.phosphosite.phosphosite_regsites.html#pypath.inputs.phosphosite.phosphosite_regsites" title="pypath.inputs.phosphosite.phosphosite_regsites"><code class="xref py py-obj docutils literal notranslate"><span class="pre">phosphosite_regsites</span></code></a>()</p></td>
+<td><p>Downloads and preprocesses the regulatory sites dataset from PhosphoSitePlus.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.inputs.phosphosite.phosphosite_regsites_one_organism.html#pypath.inputs.phosphosite.phosphosite_regsites_one_organism" title="pypath.inputs.phosphosite.phosphosite_regsites_one_organism"><code class="xref py py-obj docutils literal notranslate"><span class="pre">phosphosite_regsites_one_organism</span></code></a>([organism])</p></td>
+<td><p>Returns PhosphoSitePlus regulatory sites translated to one organism by orthology.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.inputs.phosphosite.regsites_tab.html#pypath.inputs.phosphosite.regsites_tab" title="pypath.inputs.phosphosite.regsites_tab"><code class="xref py py-obj docutils literal notranslate"><span class="pre">regsites_tab</span></code></a>(regsites[, outfile])</p></td>
+<td><p>Exports PhosphoSite regulatory sites as a tabular file, all IDs translated to UniProt.</p></td>
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+  <section id="pypath-inputs-phosphosite-phosphosite-directions">
+<h1>pypath.inputs.phosphosite.phosphosite_directions<a class="headerlink" href="#pypath-inputs-phosphosite-phosphosite-directions" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.inputs.phosphosite.phosphosite_directions">
+<span class="sig-prename descclassname"><span class="pre">pypath.inputs.phosphosite.</span></span><span class="sig-name descname"><span class="pre">phosphosite_directions</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">organism</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'human'</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/inputs/phosphosite.html#phosphosite_directions"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.phosphosite.phosphosite_directions" title="Link to this definition">§</a></dt>
+<dd><p>From curated and HTP PhosphoSite data generates a
+list of directions.</p>
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diff --git a/api/pypath.inputs.phosphosite.phosphosite_enzyme_substrate.html b/api/pypath.inputs.phosphosite.phosphosite_enzyme_substrate.html
new file mode 100644
index 000000000..51526af5c
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+  <section id="pypath-inputs-phosphosite-phosphosite-enzyme-substrate">
+<h1>pypath.inputs.phosphosite.phosphosite_enzyme_substrate<a class="headerlink" href="#pypath-inputs-phosphosite-phosphosite-enzyme-substrate" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.inputs.phosphosite.phosphosite_enzyme_substrate">
+<span class="sig-prename descclassname"><span class="pre">pypath.inputs.phosphosite.</span></span><span class="sig-name descname"><span class="pre">phosphosite_enzyme_substrate</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">raw</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">organism</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'human'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">strict</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/inputs/phosphosite.html#phosphosite_enzyme_substrate"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.phosphosite.phosphosite_enzyme_substrate" title="Link to this definition">§</a></dt>
+<dd><p>Downloads and preprocesses phosphorylation site data from PhosphoSitePlus.</p>
+</dd></dl>
+
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diff --git a/api/pypath.inputs.phosphosite.phosphosite_interactions.html b/api/pypath.inputs.phosphosite.phosphosite_interactions.html
new file mode 100644
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+  <section id="pypath-inputs-phosphosite-phosphosite-interactions">
+<h1>pypath.inputs.phosphosite.phosphosite_interactions<a class="headerlink" href="#pypath-inputs-phosphosite-phosphosite-interactions" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.inputs.phosphosite.phosphosite_interactions">
+<span class="sig-prename descclassname"><span class="pre">pypath.inputs.phosphosite.</span></span><span class="sig-name descname"><span class="pre">phosphosite_interactions</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cache</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/inputs/phosphosite.html#phosphosite_interactions"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.phosphosite.phosphosite_interactions" title="Link to this definition">§</a></dt>
+<dd><p>Downloads curated and HTP data from Phosphosite,
+from preprocessed cache file if available.
+Processes BioPAX format.
+Returns list of interactions.</p>
+</dd></dl>
+
+</section>
+
+
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diff --git a/api/pypath.inputs.phosphosite.phosphosite_interactions_all.html b/api/pypath.inputs.phosphosite.phosphosite_interactions_all.html
new file mode 100644
index 000000000..f729e4170
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diff --git a/api/pypath.inputs.phosphosite.phosphosite_interactions_curated.html b/api/pypath.inputs.phosphosite.phosphosite_interactions_curated.html
new file mode 100644
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+  <section id="pypath-inputs-phosphosite-phosphosite-interactions-curated">
+<h1>pypath.inputs.phosphosite.phosphosite_interactions_curated<a class="headerlink" href="#pypath-inputs-phosphosite-phosphosite-interactions-curated" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.inputs.phosphosite.phosphosite_interactions_curated">
+<span class="sig-prename descclassname"><span class="pre">pypath.inputs.phosphosite.</span></span><span class="sig-name descname"><span class="pre">phosphosite_interactions_curated</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/inputs/phosphosite.html#phosphosite_interactions_curated"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.phosphosite.phosphosite_interactions_curated" title="Link to this definition">§</a></dt>
+<dd><p>Loads literature curated PhosphoSite data,
+from preprocessed cache file if available.
+Returns list of interactions.</p>
+</dd></dl>
+
+</section>
+
+
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new file mode 100644
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+  <section id="pypath-inputs-phosphosite-phosphosite-interactions-new">
+<h1>pypath.inputs.phosphosite.phosphosite_interactions_new<a class="headerlink" href="#pypath-inputs-phosphosite-phosphosite-interactions-new" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.inputs.phosphosite.phosphosite_interactions_new">
+<span class="sig-prename descclassname"><span class="pre">pypath.inputs.phosphosite.</span></span><span class="sig-name descname"><span class="pre">phosphosite_interactions_new</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cache</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/inputs/phosphosite.html#phosphosite_interactions_new"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.phosphosite.phosphosite_interactions_new" title="Link to this definition">§</a></dt>
+<dd><p>Downloads curated and HTP data from Phosphosite,
+from preprocessed cache file if available.
+Processes BioPAX format.
+Returns list of interactions.</p>
+</dd></dl>
+
+</section>
+
+
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diff --git a/api/pypath.inputs.phosphosite.phosphosite_interactions_noref.html b/api/pypath.inputs.phosphosite.phosphosite_interactions_noref.html
new file mode 100644
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+<h1>pypath.inputs.phosphosite.phosphosite_interactions_noref<a class="headerlink" href="#pypath-inputs-phosphosite-phosphosite-interactions-noref" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.inputs.phosphosite.phosphosite_interactions_noref">
+<span class="sig-prename descclassname"><span class="pre">pypath.inputs.phosphosite.</span></span><span class="sig-name descname"><span class="pre">phosphosite_interactions_noref</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/inputs/phosphosite.html#phosphosite_interactions_noref"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.phosphosite.phosphosite_interactions_noref" title="Link to this definition">§</a></dt>
+<dd><p>Loads HTP PhosphoSite data,
+from preprocessed cache file if available.
+Returns list of interactions.</p>
+</dd></dl>
+
+</section>
+
+
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diff --git a/api/pypath.inputs.phosphosite.phosphosite_ptm_orthology.html b/api/pypath.inputs.phosphosite.phosphosite_ptm_orthology.html
new file mode 100644
index 000000000..3f70fdba8
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+  <section id="pypath-inputs-phosphosite-phosphosite-ptm-orthology">
+<h1>pypath.inputs.phosphosite.phosphosite_ptm_orthology<a class="headerlink" href="#pypath-inputs-phosphosite-phosphosite-ptm-orthology" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.inputs.phosphosite.phosphosite_ptm_orthology">
+<span class="sig-prename descclassname"><span class="pre">pypath.inputs.phosphosite.</span></span><span class="sig-name descname"><span class="pre">phosphosite_ptm_orthology</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/inputs/phosphosite.html#phosphosite_ptm_orthology"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.phosphosite.phosphosite_ptm_orthology" title="Link to this definition">§</a></dt>
+<dd><p>Returns an orthology translation dict of phosphosites
+based on phosphorylation sites table from PhosphoSitePlus.
+In the result all PTMs represented by a tuple of the following
+6 elements: UniProt ID, isoform (int), residue one letter code,
+residue number (int), NCBI Taxonomy ID (int), modification type.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>source</strong> (<em>int</em>) – Source taxon (NCBI Taxonomy).</p></li>
+<li><p><strong>target</strong> (<em>int</em>) – Target taxon (NCBI Taxonomy).</p></li>
+</ul>
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diff --git a/api/pypath.inputs.phosphosite.phosphosite_ptms.html b/api/pypath.inputs.phosphosite.phosphosite_ptms.html
new file mode 100644
index 000000000..25519b247
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+  <section id="pypath-inputs-phosphosite-phosphosite-ptms">
+<h1>pypath.inputs.phosphosite.phosphosite_ptms<a class="headerlink" href="#pypath-inputs-phosphosite-phosphosite-ptms" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.inputs.phosphosite.phosphosite_ptms">
+<span class="sig-prename descclassname"><span class="pre">pypath.inputs.phosphosite.</span></span><span class="sig-name descname"><span class="pre">phosphosite_ptms</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">organism</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'human'</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/inputs/phosphosite.html#phosphosite_ptms"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.phosphosite.phosphosite_ptms" title="Link to this definition">§</a></dt>
+<dd><p>Downloads the phosphorylation site dataset from PhosphoSitePlus.</p>
+</dd></dl>
+
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diff --git a/api/pypath.inputs.phosphosite.phosphosite_regsites.html b/api/pypath.inputs.phosphosite.phosphosite_regsites.html
new file mode 100644
index 000000000..019464e8f
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@@ -0,0 +1,641 @@
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+  <section id="pypath-inputs-phosphosite-phosphosite-regsites">
+<h1>pypath.inputs.phosphosite.phosphosite_regsites<a class="headerlink" href="#pypath-inputs-phosphosite-phosphosite-regsites" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.inputs.phosphosite.phosphosite_regsites">
+<span class="sig-prename descclassname"><span class="pre">pypath.inputs.phosphosite.</span></span><span class="sig-name descname"><span class="pre">phosphosite_regsites</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/inputs/phosphosite.html#phosphosite_regsites"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.phosphosite.phosphosite_regsites" title="Link to this definition">§</a></dt>
+<dd><p>Downloads and preprocesses the regulatory sites dataset from
+PhosphoSitePlus. This data provides information about which
+proteins a PTM disrupts or induces the interaction with.</p>
+</dd></dl>
+
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+
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diff --git a/api/pypath.inputs.phosphosite.phosphosite_regsites_one_organism.html b/api/pypath.inputs.phosphosite.phosphosite_regsites_one_organism.html
new file mode 100644
index 000000000..7e85a2ace
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+  <section id="pypath-inputs-phosphosite-phosphosite-regsites-one-organism">
+<h1>pypath.inputs.phosphosite.phosphosite_regsites_one_organism<a class="headerlink" href="#pypath-inputs-phosphosite-phosphosite-regsites-one-organism" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.inputs.phosphosite.phosphosite_regsites_one_organism">
+<span class="sig-prename descclassname"><span class="pre">pypath.inputs.phosphosite.</span></span><span class="sig-name descname"><span class="pre">phosphosite_regsites_one_organism</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">organism</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/inputs/phosphosite.html#phosphosite_regsites_one_organism"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.phosphosite.phosphosite_regsites_one_organism" title="Link to this definition">§</a></dt>
+<dd><p>Returns PhosphoSitePlus regulatory sites translated to
+one organism by orthology. Residue numbers will be translated
+where necessary, while gene symbols will be translated to
+UniProt IDs of the given organism.
+This works with human, mouse or rat.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><p><strong>organism</strong> (<em>int</em>) – NCBI Taxonomy ID of the target organism. In this
+method possible values are human, mouse or rat, as these species
+provide the vast majority of the data, and are close enough to each
+other that the sites can be safely translated between orthologous
+proteins by sequence alignement.</p>
+</dd>
+</dl>
+</dd></dl>
+
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diff --git a/api/pypath.inputs.phosphosite.regsites_tab.html b/api/pypath.inputs.phosphosite.regsites_tab.html
new file mode 100644
index 000000000..7dacd8b05
--- /dev/null
+++ b/api/pypath.inputs.phosphosite.regsites_tab.html
@@ -0,0 +1,640 @@
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+  <section id="pypath-inputs-phosphosite-regsites-tab">
+<h1>pypath.inputs.phosphosite.regsites_tab<a class="headerlink" href="#pypath-inputs-phosphosite-regsites-tab" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.inputs.phosphosite.regsites_tab">
+<span class="sig-prename descclassname"><span class="pre">pypath.inputs.phosphosite.</span></span><span class="sig-name descname"><span class="pre">regsites_tab</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">regsites</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">outfile</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/inputs/phosphosite.html#regsites_tab"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.phosphosite.regsites_tab" title="Link to this definition">§</a></dt>
+<dd><p>Exports PhosphoSite regulatory sites as a tabular file, all
+IDs translated to UniProt.</p>
+</dd></dl>
+
+</section>
+
+
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diff --git a/api/pypath.inputs.pisa.PisaBond.html b/api/pypath.inputs.pisa.PisaBond.html
new file mode 100644
index 000000000..8b4212ed9
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+  <section id="pypath-inputs-pisa-pisabond">
+<h1>pypath.inputs.pisa.PisaBond<a class="headerlink" href="#pypath-inputs-pisa-pisabond" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.inputs.pisa.PisaBond">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.inputs.pisa.</span></span><span class="sig-name descname"><span class="pre">PisaBond</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">uniprot_1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">chain_1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">residue_1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">seqnum_1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">uniprot_2</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">chain_2</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">residue_2</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">seqnum_2</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.inputs.pisa.PisaBond" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">tuple</span></code></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.inputs.pisa.PisaBond.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.inputs.pisa.PisaBond.__init__" title="Link to this definition">§</a></dt>
+<dd></dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.inputs.pisa.PisaBond.__init__" title="pypath.inputs.pisa.PisaBond.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.inputs.pisa.PisaBond.count" title="pypath.inputs.pisa.PisaBond.count"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count</span></code></a>(value, /)</p></td>
+<td><p>Return number of occurrences of value.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.inputs.pisa.PisaBond.index" title="pypath.inputs.pisa.PisaBond.index"><code class="xref py py-obj docutils literal notranslate"><span class="pre">index</span></code></a>(value[, start, stop])</p></td>
+<td><p>Return first index of value.</p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Attributes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.inputs.pisa.PisaBond.chain_1" title="pypath.inputs.pisa.PisaBond.chain_1"><code class="xref py py-obj docutils literal notranslate"><span class="pre">chain_1</span></code></a></p></td>
+<td><p>Alias for field number 1</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.inputs.pisa.PisaBond.chain_2" title="pypath.inputs.pisa.PisaBond.chain_2"><code class="xref py py-obj docutils literal notranslate"><span class="pre">chain_2</span></code></a></p></td>
+<td><p>Alias for field number 5</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.inputs.pisa.PisaBond.residue_1" title="pypath.inputs.pisa.PisaBond.residue_1"><code class="xref py py-obj docutils literal notranslate"><span class="pre">residue_1</span></code></a></p></td>
+<td><p>Alias for field number 2</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.inputs.pisa.PisaBond.residue_2" title="pypath.inputs.pisa.PisaBond.residue_2"><code class="xref py py-obj docutils literal notranslate"><span class="pre">residue_2</span></code></a></p></td>
+<td><p>Alias for field number 6</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.inputs.pisa.PisaBond.seqnum_1" title="pypath.inputs.pisa.PisaBond.seqnum_1"><code class="xref py py-obj docutils literal notranslate"><span class="pre">seqnum_1</span></code></a></p></td>
+<td><p>Alias for field number 3</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.inputs.pisa.PisaBond.seqnum_2" title="pypath.inputs.pisa.PisaBond.seqnum_2"><code class="xref py py-obj docutils literal notranslate"><span class="pre">seqnum_2</span></code></a></p></td>
+<td><p>Alias for field number 7</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.inputs.pisa.PisaBond.uniprot_1" title="pypath.inputs.pisa.PisaBond.uniprot_1"><code class="xref py py-obj docutils literal notranslate"><span class="pre">uniprot_1</span></code></a></p></td>
+<td><p>Alias for field number 0</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.inputs.pisa.PisaBond.uniprot_2" title="pypath.inputs.pisa.PisaBond.uniprot_2"><code class="xref py py-obj docutils literal notranslate"><span class="pre">uniprot_2</span></code></a></p></td>
+<td><p>Alias for field number 4</p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.inputs.pisa.PisaBond.chain_1">
+<span class="sig-name descname"><span class="pre">chain_1</span></span><a class="headerlink" href="#pypath.inputs.pisa.PisaBond.chain_1" title="Link to this definition">§</a></dt>
+<dd><p>Alias for field number 1</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.inputs.pisa.PisaBond.chain_2">
+<span class="sig-name descname"><span class="pre">chain_2</span></span><a class="headerlink" href="#pypath.inputs.pisa.PisaBond.chain_2" title="Link to this definition">§</a></dt>
+<dd><p>Alias for field number 5</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.inputs.pisa.PisaBond.count">
+<span class="sig-name descname"><span class="pre">count</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">value</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">/</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.inputs.pisa.PisaBond.count" title="Link to this definition">§</a></dt>
+<dd><p>Return number of occurrences of value.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.inputs.pisa.PisaBond.index">
+<span class="sig-name descname"><span class="pre">index</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">value</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">start</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">stop</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9223372036854775807</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">/</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.inputs.pisa.PisaBond.index" title="Link to this definition">§</a></dt>
+<dd><p>Return first index of value.</p>
+<p>Raises ValueError if the value is not present.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.inputs.pisa.PisaBond.residue_1">
+<span class="sig-name descname"><span class="pre">residue_1</span></span><a class="headerlink" href="#pypath.inputs.pisa.PisaBond.residue_1" title="Link to this definition">§</a></dt>
+<dd><p>Alias for field number 2</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.inputs.pisa.PisaBond.residue_2">
+<span class="sig-name descname"><span class="pre">residue_2</span></span><a class="headerlink" href="#pypath.inputs.pisa.PisaBond.residue_2" title="Link to this definition">§</a></dt>
+<dd><p>Alias for field number 6</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.inputs.pisa.PisaBond.seqnum_1">
+<span class="sig-name descname"><span class="pre">seqnum_1</span></span><a class="headerlink" href="#pypath.inputs.pisa.PisaBond.seqnum_1" title="Link to this definition">§</a></dt>
+<dd><p>Alias for field number 3</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.inputs.pisa.PisaBond.seqnum_2">
+<span class="sig-name descname"><span class="pre">seqnum_2</span></span><a class="headerlink" href="#pypath.inputs.pisa.PisaBond.seqnum_2" title="Link to this definition">§</a></dt>
+<dd><p>Alias for field number 7</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.inputs.pisa.PisaBond.uniprot_1">
+<span class="sig-name descname"><span class="pre">uniprot_1</span></span><a class="headerlink" href="#pypath.inputs.pisa.PisaBond.uniprot_1" title="Link to this definition">§</a></dt>
+<dd><p>Alias for field number 0</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.inputs.pisa.PisaBond.uniprot_2">
+<span class="sig-name descname"><span class="pre">uniprot_2</span></span><a class="headerlink" href="#pypath.inputs.pisa.PisaBond.uniprot_2" title="Link to this definition">§</a></dt>
+<dd><p>Alias for field number 4</p>
+</dd></dl>
+
+</dd></dl>
+
+</section>
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diff --git a/api/pypath.inputs.pisa.html b/api/pypath.inputs.pisa.html
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+  <section id="module-pypath.inputs.pisa">
+<span id="pypath-inputs-pisa"></span><h1>pypath.inputs.pisa<a class="headerlink" href="#module-pypath.inputs.pisa" title="Link to this heading">§</a></h1>
+<dl class="field-list simple">
+<dt class="field-odd">members<span class="colon">:</span></dt>
+<dd class="field-odd"><p></p></dd>
+</dl>
+<p class="rubric">Functions</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.inputs.pisa.pisa_bonds.html#pypath.inputs.pisa.pisa_bonds" title="pypath.inputs.pisa.pisa_bonds"><code class="xref py py-obj docutils literal notranslate"><span class="pre">pisa_bonds</span></code></a>(bonds, chains)</p></td>
+<td><p>To be refactored in the future.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.inputs.pisa.pisa_interfaces.html#pypath.inputs.pisa.pisa_interfaces" title="pypath.inputs.pisa.pisa_interfaces"><code class="xref py py-obj docutils literal notranslate"><span class="pre">pisa_interfaces</span></code></a>(pdbs[, return_unmapped])</p></td>
+<td><p>To be refactored in the future.</p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Classes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.inputs.pisa.PisaBond.html#pypath.inputs.pisa.PisaBond" title="pypath.inputs.pisa.PisaBond"><code class="xref py py-obj docutils literal notranslate"><span class="pre">PisaBond</span></code></a>(uniprot_1, chain_1, residue_1, ...)</p></td>
+<td><p></p></td>
+</tr>
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diff --git a/api/pypath.inputs.pisa.pisa_bonds.html b/api/pypath.inputs.pisa.pisa_bonds.html
new file mode 100644
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+  <section id="pypath-inputs-pisa-pisa-bonds">
+<h1>pypath.inputs.pisa.pisa_bonds<a class="headerlink" href="#pypath-inputs-pisa-pisa-bonds" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.inputs.pisa.pisa_bonds">
+<span class="sig-prename descclassname"><span class="pre">pypath.inputs.pisa.</span></span><span class="sig-name descname"><span class="pre">pisa_bonds</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">bonds</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">chains</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/inputs/pisa.html#pisa_bonds"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.pisa.pisa_bonds" title="Link to this definition">§</a></dt>
+<dd><p>To be refactored in the future. If you are interested in using this
+function, please contact the authors.</p>
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diff --git a/api/pypath.inputs.pisa.pisa_interfaces.html b/api/pypath.inputs.pisa.pisa_interfaces.html
new file mode 100644
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+  <section id="pypath-inputs-pisa-pisa-interfaces">
+<h1>pypath.inputs.pisa.pisa_interfaces<a class="headerlink" href="#pypath-inputs-pisa-pisa-interfaces" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.inputs.pisa.pisa_interfaces">
+<span class="sig-prename descclassname"><span class="pre">pypath.inputs.pisa.</span></span><span class="sig-name descname"><span class="pre">pisa_interfaces</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">pdbs</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">return_unmapped</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/inputs/pisa.html#pisa_interfaces"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.pisa.pisa_interfaces" title="Link to this definition">§</a></dt>
+<dd><p>To be refactored in the future. If you are interested in using this
+function, please contact the authors.</p>
+<dl class="simple">
+<dt>Args</dt><dd><p>pdbs (set): A set of PDB IDs to query.
+return_unmapped (bool): Return also a list of unmapped residues.
+In this case, a tuple is returned, its first element is a dict of
+interfaces, while its second element is a list of unmapped
+residues (normally empty, if all residues could be mapped
+between PDB and UniProt sequences).</p>
+</dd>
+<dt>Returns</dt><dd><p>A dict of dicts with interfaces. The upper level keys are PDB
+structure IDs, the lower level keys are tuples of UniProt IDs,
+the values are <code class="docutils literal notranslate"><span class="pre">pypath.internals.intera.Interface</span></code> objects.</p>
+</dd>
+</dl>
+</dd></dl>
+
+</section>
+
+
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diff --git a/api/pypath.inputs.pro.html b/api/pypath.inputs.pro.html
index 642af9dbd..ebd8e3fd7 100644
--- a/api/pypath.inputs.pro.html
+++ b/api/pypath.inputs.pro.html
@@ -48,7 +48,7 @@
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
     <link rel="next" title="pypath.inputs.pro.get_pro" href="pypath.inputs.pro.get_pro.html" />
-    <link rel="prev" title="pypath.inputs.phosphopoint.phosphopoint_interactions" href="pypath.inputs.phosphopoint.phosphopoint_interactions.html" />
+    <link rel="prev" title="pypath.inputs.pisa.PisaBond" href="pypath.inputs.pisa.PisaBond.html" />
   <meta name="viewport" content="width=device-width, initial-scale=1"/>
   <meta name="docsearch:language" content="en"/>
   </head>
@@ -545,12 +545,12 @@
                   
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     <a class="left-prev"
-       href="pypath.inputs.phosphopoint.phosphopoint_interactions.html"
+       href="pypath.inputs.pisa.PisaBond.html"
        title="previous page">
       <i class="fa-solid fa-angle-left"></i>
       <div class="prev-next-info">
         <p class="prev-next-subtitle">previous</p>
-        <p class="prev-next-title">pypath.inputs.phosphopoint.phosphopoint_interactions</p>
+        <p class="prev-next-title">pypath.inputs.pisa.PisaBond</p>
       </div>
     </a>
     <a class="right-next"
diff --git a/api/pypath.inputs.pro.pro_mapping.html b/api/pypath.inputs.pro.pro_mapping.html
index 13a233400..174d0ed56 100644
--- a/api/pypath.inputs.pro.pro_mapping.html
+++ b/api/pypath.inputs.pro.pro_mapping.html
@@ -47,7 +47,7 @@
     <link rel="icon" href="../_static/omnipath-logo.svg"/>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
-    <link rel="next" title="pypath.inputs.proteins" href="pypath.inputs.proteins.html" />
+    <link rel="next" title="pypath.inputs.progeny" href="pypath.inputs.progeny.html" />
     <link rel="prev" title="pypath.inputs.pro.get_pro" href="pypath.inputs.pro.get_pro.html" />
   <meta name="viewport" content="width=device-width, initial-scale=1"/>
   <meta name="docsearch:language" content="en"/>
@@ -544,11 +544,11 @@ <h1>pypath.inputs.pro.pro_mapping<a class="headerlink" href="#pypath-inputs-pro-
       </div>
     </a>
     <a class="right-next"
-       href="pypath.inputs.proteins.html"
+       href="pypath.inputs.progeny.html"
        title="next page">
       <div class="prev-next-info">
         <p class="prev-next-subtitle">next</p>
-        <p class="prev-next-title">pypath.inputs.proteins</p>
+        <p class="prev-next-title">pypath.inputs.progeny</p>
       </div>
       <i class="fa-solid fa-angle-right"></i>
     </a>
diff --git a/api/pypath.inputs.progeny.html b/api/pypath.inputs.progeny.html
new file mode 100644
index 000000000..5561df169
--- /dev/null
+++ b/api/pypath.inputs.progeny.html
@@ -0,0 +1,648 @@
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+  <section id="module-pypath.inputs.progeny">
+<span id="pypath-inputs-progeny"></span><h1>pypath.inputs.progeny<a class="headerlink" href="#module-pypath.inputs.progeny" title="Link to this heading">§</a></h1>
+<dl class="field-list simple">
+<dt class="field-odd">members<span class="colon">:</span></dt>
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+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.inputs.progeny.progeny_annotations.html#pypath.inputs.progeny.progeny_annotations" title="pypath.inputs.progeny.progeny_annotations"><code class="xref py py-obj docutils literal notranslate"><span class="pre">progeny_annotations</span></code></a>([organism])</p></td>
+<td><p>Pathway responsive genes: signatures based on transcriptomics data from PROGENy (<a class="github reference external" href="https://github.com/saezlab/progeny">saezlab/progeny</a>).</p></td>
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+<td><p>Pathway responsive genes: signatures based on transcriptomics data from PROGENy (<a class="github reference external" href="https://github.com/saezlab/progeny">saezlab/progeny</a>).</p></td>
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+  <section id="pypath-inputs-progeny-progeny-annotations">
+<h1>pypath.inputs.progeny.progeny_annotations<a class="headerlink" href="#pypath-inputs-progeny-progeny-annotations" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.inputs.progeny.progeny_annotations">
+<span class="sig-prename descclassname"><span class="pre">pypath.inputs.progeny.</span></span><span class="sig-name descname"><span class="pre">progeny_annotations</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">organism</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/inputs/progeny.html#progeny_annotations"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.progeny.progeny_annotations" title="Link to this definition">§</a></dt>
+<dd><p>Pathway responsive genes: signatures based on transcriptomics data
+from PROGENy (<a class="github reference external" href="https://github.com/saezlab/progeny">saezlab/progeny</a>).</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>organism (int,str): Name or NCBI Taxonomy ID of the organism. Human</dt><dd><p>and mouse are supported.</p>
+</dd>
+</dl>
+</dd>
+<dt>Returns</dt><dd><dl class="simple">
+<dt>(dict): Dict of sets, keys are UniProt IDs, values are pathway</dt><dd><p>association records, each with a weight and p-value.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
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+  <section id="pypath-inputs-progeny-progeny-raw">
+<h1>pypath.inputs.progeny.progeny_raw<a class="headerlink" href="#pypath-inputs-progeny-progeny-raw" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.inputs.progeny.progeny_raw">
+<span class="sig-prename descclassname"><span class="pre">pypath.inputs.progeny.</span></span><span class="sig-name descname"><span class="pre">progeny_raw</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">organism</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/inputs/progeny.html#progeny_raw"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.progeny.progeny_raw" title="Link to this definition">§</a></dt>
+<dd><p>Pathway responsive genes: signatures based on transcriptomics data
+from PROGENy (<a class="github reference external" href="https://github.com/saezlab/progeny">saezlab/progeny</a>).</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>organism (int,str): Name or NCBI Taxonomy ID of the organism. Human</dt><dd><p>and mouse are supported.</p>
+</dd>
+</dl>
+</dd>
+<dt>Returns</dt><dd><dl class="simple">
+<dt>(pandas.DataFrame): A data frame of genes, pathways, weights and</dt><dd><p>p-values for each association.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
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diff --git a/api/pypath.inputs.proteinatlas.get_proteinatlas.html b/api/pypath.inputs.proteinatlas.get_proteinatlas.html
new file mode 100644
index 000000000..a5bd50ebf
--- /dev/null
+++ b/api/pypath.inputs.proteinatlas.get_proteinatlas.html
@@ -0,0 +1,638 @@
+
+<!DOCTYPE html>
+
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+    <title>pypath.inputs.proteinatlas.get_proteinatlas &#8212; pypath 0.16.9 documentation</title>
+  
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+<h1>pypath.inputs.proteinatlas.get_proteinatlas<a class="headerlink" href="#pypath-inputs-proteinatlas-get-proteinatlas" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.inputs.proteinatlas.get_proteinatlas">
+<span class="sig-prename descclassname"><span class="pre">pypath.inputs.proteinatlas.</span></span><span class="sig-name descname"><span class="pre">get_proteinatlas</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">normal</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">pathology</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cancer</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/inputs/proteinatlas.html#get_proteinatlas"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.proteinatlas.get_proteinatlas" title="Link to this definition">§</a></dt>
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+  <section id="module-pypath.inputs.proteinatlas">
+<span id="pypath-inputs-proteinatlas"></span><h1>pypath.inputs.proteinatlas<a class="headerlink" href="#module-pypath.inputs.proteinatlas" title="Link to this heading">§</a></h1>
+<dl class="field-list simple">
+<dt class="field-odd">members<span class="colon">:</span></dt>
+<dd class="field-odd"><p></p></dd>
+</dl>
+<p class="rubric">Functions</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.inputs.proteinatlas.get_proteinatlas.html#pypath.inputs.proteinatlas.get_proteinatlas" title="pypath.inputs.proteinatlas.get_proteinatlas"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_proteinatlas</span></code></a>([normal, pathology, cancer])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.inputs.proteinatlas.proteinatlas_annotations.html#pypath.inputs.proteinatlas.proteinatlas_annotations" title="pypath.inputs.proteinatlas.proteinatlas_annotations"><code class="xref py py-obj docutils literal notranslate"><span class="pre">proteinatlas_annotations</span></code></a>([normal, ...])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.inputs.proteinatlas.proteinatlas_secretome_annotations.html#pypath.inputs.proteinatlas.proteinatlas_secretome_annotations" title="pypath.inputs.proteinatlas.proteinatlas_secretome_annotations"><code class="xref py py-obj docutils literal notranslate"><span class="pre">proteinatlas_secretome_annotations</span></code></a>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.inputs.proteinatlas.proteinatlas_subcellular_annotations.html#pypath.inputs.proteinatlas.proteinatlas_subcellular_annotations" title="pypath.inputs.proteinatlas.proteinatlas_subcellular_annotations"><code class="xref py py-obj docutils literal notranslate"><span class="pre">proteinatlas_subcellular_annotations</span></code></a>()</p></td>
+<td><p></p></td>
+</tr>
+</tbody>
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+  <section id="pypath-inputs-proteinatlas-proteinatlas-annotations">
+<h1>pypath.inputs.proteinatlas.proteinatlas_annotations<a class="headerlink" href="#pypath-inputs-proteinatlas-proteinatlas-annotations" title="Link to this heading">§</a></h1>
+<dl class="py function">
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diff --git a/api/pypath.inputs.proteinatlas.proteinatlas_secretome_annotations.html b/api/pypath.inputs.proteinatlas.proteinatlas_secretome_annotations.html
new file mode 100644
index 000000000..af388c5c9
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new file mode 100644
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+<dl class="py function">
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diff --git a/api/pypath.inputs.proteins.html b/api/pypath.inputs.proteins.html
index 99afd619d..3ce8f5542 100644
--- a/api/pypath.inputs.proteins.html
+++ b/api/pypath.inputs.proteins.html
@@ -48,7 +48,7 @@
     <link rel="index" title="Index" href="../genindex.html" />
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     <link rel="next" title="pypath.inputs.proteins.variants" href="pypath.inputs.proteins.variants.html" />
-    <link rel="prev" title="pypath.inputs.pro.pro_mapping" href="pypath.inputs.pro.pro_mapping.html" />
+    <link rel="prev" title="pypath.inputs.proteinatlas.proteinatlas_subcellular_annotations" href="pypath.inputs.proteinatlas.proteinatlas_subcellular_annotations.html" />
   <meta name="viewport" content="width=device-width, initial-scale=1"/>
   <meta name="docsearch:language" content="en"/>
   </head>
@@ -542,12 +542,12 @@
                   
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-       href="pypath.inputs.pro.pro_mapping.html"
+       href="pypath.inputs.proteinatlas.proteinatlas_subcellular_annotations.html"
        title="previous page">
       <i class="fa-solid fa-angle-left"></i>
       <div class="prev-next-info">
         <p class="prev-next-subtitle">previous</p>
-        <p class="prev-next-title">pypath.inputs.pro.pro_mapping</p>
+        <p class="prev-next-title">pypath.inputs.proteinatlas.proteinatlas_subcellular_annotations</p>
       </div>
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diff --git a/api/pypath.inputs.pubmed.pmids_list.html b/api/pypath.inputs.pubmed.pmids_list.html
index 84e5f2736..55fbff844 100644
--- a/api/pypath.inputs.pubmed.pmids_list.html
+++ b/api/pypath.inputs.pubmed.pmids_list.html
@@ -47,7 +47,7 @@
     <link rel="icon" href="../_static/omnipath-logo.svg"/>
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-    <link rel="next" title="pypath.inputs.ramp" href="pypath.inputs.ramp.html" />
+    <link rel="next" title="pypath.inputs.ramilowski2015" href="pypath.inputs.ramilowski2015.html" />
     <link rel="prev" title="pypath.inputs.pubmed.pmids_dict" href="pypath.inputs.pubmed.pmids_dict.html" />
   <meta name="viewport" content="width=device-width, initial-scale=1"/>
   <meta name="docsearch:language" content="en"/>
@@ -544,11 +544,11 @@ <h1>pypath.inputs.pubmed.pmids_list<a class="headerlink" href="#pypath-inputs-pu
       </div>
     </a>
     <a class="right-next"
-       href="pypath.inputs.ramp.html"
+       href="pypath.inputs.ramilowski2015.html"
        title="next page">
       <div class="prev-next-info">
         <p class="prev-next-subtitle">next</p>
-        <p class="prev-next-title">pypath.inputs.ramp</p>
+        <p class="prev-next-title">pypath.inputs.ramilowski2015</p>
       </div>
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diff --git a/api/pypath.inputs.ramilowski2015.html b/api/pypath.inputs.ramilowski2015.html
new file mode 100644
index 000000000..2e5c1c137
--- /dev/null
+++ b/api/pypath.inputs.ramilowski2015.html
@@ -0,0 +1,648 @@
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+  <section id="module-pypath.inputs.ramilowski2015">
+<span id="pypath-inputs-ramilowski2015"></span><h1>pypath.inputs.ramilowski2015<a class="headerlink" href="#module-pypath.inputs.ramilowski2015" title="Link to this heading">§</a></h1>
+<dl class="field-list simple">
+<dt class="field-odd">members<span class="colon">:</span></dt>
+<dd class="field-odd"><p></p></dd>
+</dl>
+<p class="rubric">Functions</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.inputs.ramilowski2015.ramilowski_interactions.html#pypath.inputs.ramilowski2015.ramilowski_interactions" title="pypath.inputs.ramilowski2015.ramilowski_interactions"><code class="xref py py-obj docutils literal notranslate"><span class="pre">ramilowski_interactions</span></code></a>([putative])</p></td>
+<td><p>Downloads and processes ligand-receptor interactions from Supplementary Table 2 of Ramilowski 2015.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.inputs.ramilowski2015.ramilowski_locations.html#pypath.inputs.ramilowski2015.ramilowski_locations" title="pypath.inputs.ramilowski2015.ramilowski_locations"><code class="xref py py-obj docutils literal notranslate"><span class="pre">ramilowski_locations</span></code></a>([long_notes])</p></td>
+<td><p>Subcellular location annotations from Ramilowski 2015.</p></td>
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new file mode 100644
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+  <section id="pypath-inputs-ramilowski2015-ramilowski-interactions">
+<h1>pypath.inputs.ramilowski2015.ramilowski_interactions<a class="headerlink" href="#pypath-inputs-ramilowski2015-ramilowski-interactions" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.inputs.ramilowski2015.ramilowski_interactions">
+<span class="sig-prename descclassname"><span class="pre">pypath.inputs.ramilowski2015.</span></span><span class="sig-name descname"><span class="pre">ramilowski_interactions</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">putative</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/inputs/ramilowski2015.html#ramilowski_interactions"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.ramilowski2015.ramilowski_interactions" title="Link to this definition">§</a></dt>
+<dd><p>Downloads and processes ligand-receptor interactions from
+Supplementary Table 2 of Ramilowski 2015.</p>
+<p>Returns list of lists with ligand and receptor gene symbols, reference
+and resources as elements.</p>
+</dd></dl>
+
+</section>
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+  <section id="pypath-inputs-ramilowski2015-ramilowski-locations">
+<h1>pypath.inputs.ramilowski2015.ramilowski_locations<a class="headerlink" href="#pypath-inputs-ramilowski2015-ramilowski-locations" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.inputs.ramilowski2015.ramilowski_locations">
+<span class="sig-prename descclassname"><span class="pre">pypath.inputs.ramilowski2015.</span></span><span class="sig-name descname"><span class="pre">ramilowski_locations</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">long_notes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/inputs/ramilowski2015.html#ramilowski_locations"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.ramilowski2015.ramilowski_locations" title="Link to this definition">§</a></dt>
+<dd><p>Subcellular location annotations from Ramilowski 2015.</p>
+</dd></dl>
+
+</section>
+
+
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diff --git a/api/pypath.inputs.ramp.html b/api/pypath.inputs.ramp.html
index a0ac7e60a..630eb8b64 100644
--- a/api/pypath.inputs.ramp.html
+++ b/api/pypath.inputs.ramp.html
@@ -48,7 +48,7 @@
     <link rel="index" title="Index" href="../genindex.html" />
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     <link rel="next" title="pypath.inputs.ramp.ramp_id_types" href="pypath.inputs.ramp.ramp_id_types.html" />
-    <link rel="prev" title="pypath.inputs.pubmed.pmids_list" href="pypath.inputs.pubmed.pmids_list.html" />
+    <link rel="prev" title="pypath.inputs.ramilowski2015.ramilowski_locations" href="pypath.inputs.ramilowski2015.ramilowski_locations.html" />
   <meta name="viewport" content="width=device-width, initial-scale=1"/>
   <meta name="docsearch:language" content="en"/>
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@@ -557,12 +557,12 @@
                   
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-       href="pypath.inputs.pubmed.pmids_list.html"
+       href="pypath.inputs.ramilowski2015.ramilowski_locations.html"
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       <div class="prev-next-info">
         <p class="prev-next-subtitle">previous</p>
-        <p class="prev-next-title">pypath.inputs.pubmed.pmids_list</p>
+        <p class="prev-next-title">pypath.inputs.ramilowski2015.ramilowski_locations</p>
       </div>
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diff --git a/api/pypath.inputs.reactome.reactome_uniprots.html b/api/pypath.inputs.reactome.reactome_uniprots.html
index 0690a4819..cd168154c 100644
--- a/api/pypath.inputs.reactome.reactome_uniprots.html
+++ b/api/pypath.inputs.reactome.reactome_uniprots.html
@@ -47,7 +47,7 @@
     <link rel="icon" href="../_static/omnipath-logo.svg"/>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
-    <link rel="next" title="pypath.inputs.science" href="pypath.inputs.science.html" />
+    <link rel="next" title="pypath.inputs.scconnect" href="pypath.inputs.scconnect.html" />
     <link rel="prev" title="pypath.inputs.reactome.reactome_pathways" href="pypath.inputs.reactome.reactome_pathways.html" />
   <meta name="viewport" content="width=device-width, initial-scale=1"/>
   <meta name="docsearch:language" content="en"/>
@@ -550,11 +550,11 @@ <h1>pypath.inputs.reactome.reactome_uniprots<a class="headerlink" href="#pypath-
       </div>
     </a>
     <a class="right-next"
-       href="pypath.inputs.science.html"
+       href="pypath.inputs.scconnect.html"
        title="next page">
       <div class="prev-next-info">
         <p class="prev-next-subtitle">next</p>
-        <p class="prev-next-title">pypath.inputs.science</p>
+        <p class="prev-next-title">pypath.inputs.scconnect</p>
       </div>
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diff --git a/api/pypath.inputs.scconnect.html b/api/pypath.inputs.scconnect.html
new file mode 100644
index 000000000..d61de020d
--- /dev/null
+++ b/api/pypath.inputs.scconnect.html
@@ -0,0 +1,651 @@
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+<dl class="field-list simple">
+<dt class="field-odd">members<span class="colon">:</span></dt>
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+<p class="rubric">Functions</p>
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+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.inputs.scconnect.scconnect_annotations.html#pypath.inputs.scconnect.scconnect_annotations" title="pypath.inputs.scconnect.scconnect_annotations"><code class="xref py py-obj docutils literal notranslate"><span class="pre">scconnect_annotations</span></code></a>([organism])</p></td>
+<td><p>Ligand and receptor annotations from scConnect (<a class="github reference external" href="https://github.com/JonETJakobsson/scConnect">JonETJakobsson/scConnect</a>).</p></td>
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+<tr class="row-even"><td><p><a class="reference internal" href="pypath.inputs.scconnect.scconnect_complexes.html#pypath.inputs.scconnect.scconnect_complexes" title="pypath.inputs.scconnect.scconnect_complexes"><code class="xref py py-obj docutils literal notranslate"><span class="pre">scconnect_complexes</span></code></a>([organism])</p></td>
+<td><p>Protein complexes from scConnect (<a class="github reference external" href="https://github.com/JonETJakobsson/scConnect">JonETJakobsson/scConnect</a>).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.inputs.scconnect.scconnect_interactions.html#pypath.inputs.scconnect.scconnect_interactions" title="pypath.inputs.scconnect.scconnect_interactions"><code class="xref py py-obj docutils literal notranslate"><span class="pre">scconnect_interactions</span></code></a>()</p></td>
+<td><p>Ligand-receptor interactions from scConnect (<a class="github reference external" href="https://github.com/JonETJakobsson/scConnect">JonETJakobsson/scConnect</a>).</p></td>
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diff --git a/api/pypath.inputs.scconnect.scconnect_annotations.html b/api/pypath.inputs.scconnect.scconnect_annotations.html
new file mode 100644
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+  <section id="pypath-inputs-scconnect-scconnect-annotations">
+<h1>pypath.inputs.scconnect.scconnect_annotations<a class="headerlink" href="#pypath-inputs-scconnect-scconnect-annotations" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.inputs.scconnect.scconnect_annotations">
+<span class="sig-prename descclassname"><span class="pre">pypath.inputs.scconnect.</span></span><span class="sig-name descname"><span class="pre">scconnect_annotations</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">organism</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/inputs/scconnect.html#scconnect_annotations"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.scconnect.scconnect_annotations" title="Link to this definition">§</a></dt>
+<dd><p>Ligand and receptor annotations from scConnect
+(<a class="github reference external" href="https://github.com/JonETJakobsson/scConnect">JonETJakobsson/scConnect</a>).</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>organism (int,str): Name or identifier of the organism. Human, mouse,</dt><dd><p>fruitfly, zebrafish, chicken, C. elegans, Xenopus tropicalis,
+yeast and Anolis carolinensis are available.</p>
+</dd>
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index 000000000..c65f78ca3
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+  <section id="pypath-inputs-scconnect-scconnect-complexes">
+<h1>pypath.inputs.scconnect.scconnect_complexes<a class="headerlink" href="#pypath-inputs-scconnect-scconnect-complexes" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.inputs.scconnect.scconnect_complexes">
+<span class="sig-prename descclassname"><span class="pre">pypath.inputs.scconnect.</span></span><span class="sig-name descname"><span class="pre">scconnect_complexes</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">organism</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/inputs/scconnect.html#scconnect_complexes"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.scconnect.scconnect_complexes" title="Link to this definition">§</a></dt>
+<dd><p>Protein complexes from scConnect
+(<a class="github reference external" href="https://github.com/JonETJakobsson/scConnect">JonETJakobsson/scConnect</a>).</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>organism (int,str): Name or identifier of the organism. Human, mouse,</dt><dd><p>fruitfly, zebrafish, chicken, C. elegans, Xenopus tropicalis,
+yeast and Anolis carolinensis are available.</p>
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+  <section id="pypath-inputs-scconnect-scconnect-interactions">
+<h1>pypath.inputs.scconnect.scconnect_interactions<a class="headerlink" href="#pypath-inputs-scconnect-scconnect-interactions" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.inputs.scconnect.scconnect_interactions">
+<span class="sig-prename descclassname"><span class="pre">pypath.inputs.scconnect.</span></span><span class="sig-name descname"><span class="pre">scconnect_interactions</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/inputs/scconnect.html#scconnect_interactions"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.scconnect.scconnect_interactions" title="Link to this definition">§</a></dt>
+<dd><p>Ligand-receptor interactions from scConnect
+(<a class="github reference external" href="https://github.com/JonETJakobsson/scConnect">JonETJakobsson/scConnect</a>).</p>
+<dl class="simple">
+<dt>Returns</dt><dd><dl class="simple">
+<dt>(list): List of interactions, each represented as a named tuple.</dt><dd><p>Proteins and protein complexes are translated to UniProt IDs,
+small molecule IDs are left intact.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
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diff --git a/api/pypath.inputs.science.html b/api/pypath.inputs.science.html
index 8cff90f9d..a4e2c5f52 100644
--- a/api/pypath.inputs.science.html
+++ b/api/pypath.inputs.science.html
@@ -48,7 +48,7 @@
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
     <link rel="next" title="pypath.inputs.science.science_download" href="pypath.inputs.science.science_download.html" />
-    <link rel="prev" title="pypath.inputs.reactome.reactome_uniprots" href="pypath.inputs.reactome.reactome_uniprots.html" />
+    <link rel="prev" title="pypath.inputs.scconnect.scconnect_interactions" href="pypath.inputs.scconnect.scconnect_interactions.html" />
   <meta name="viewport" content="width=device-width, initial-scale=1"/>
   <meta name="docsearch:language" content="en"/>
   </head>
@@ -542,12 +542,12 @@
                   
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     <a class="left-prev"
-       href="pypath.inputs.reactome.reactome_uniprots.html"
+       href="pypath.inputs.scconnect.scconnect_interactions.html"
        title="previous page">
       <i class="fa-solid fa-angle-left"></i>
       <div class="prev-next-info">
         <p class="prev-next-subtitle">previous</p>
-        <p class="prev-next-title">pypath.inputs.reactome.reactome_uniprots</p>
+        <p class="prev-next-title">pypath.inputs.scconnect.scconnect_interactions</p>
       </div>
     </a>
     <a class="right-next"
diff --git a/api/pypath.inputs.sider.SiderSideeffetFrequency.html b/api/pypath.inputs.sider.SiderSideeffetFrequency.html
index f6b9d5e98..8d471adea 100644
--- a/api/pypath.inputs.sider.SiderSideeffetFrequency.html
+++ b/api/pypath.inputs.sider.SiderSideeffetFrequency.html
@@ -47,7 +47,7 @@
     <link rel="icon" href="../_static/omnipath-logo.svg"/>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
-    <link rel="next" title="pypath.inputs.stitch" href="pypath.inputs.stitch.html" />
+    <link rel="next" title="pypath.inputs.signalink" href="pypath.inputs.signalink.html" />
     <link rel="prev" title="pypath.inputs.sider.SiderSideeffectMeddra" href="pypath.inputs.sider.SiderSideeffectMeddra.html" />
   <meta name="viewport" content="width=device-width, initial-scale=1"/>
   <meta name="docsearch:language" content="en"/>
@@ -618,11 +618,11 @@ <h1>pypath.inputs.sider.SiderSideeffetFrequency<a class="headerlink" href="#pypa
       </div>
     </a>
     <a class="right-next"
-       href="pypath.inputs.stitch.html"
+       href="pypath.inputs.signalink.html"
        title="next page">
       <div class="prev-next-info">
         <p class="prev-next-subtitle">next</p>
-        <p class="prev-next-title">pypath.inputs.stitch</p>
+        <p class="prev-next-title">pypath.inputs.signalink</p>
       </div>
       <i class="fa-solid fa-angle-right"></i>
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diff --git a/api/pypath.inputs.signalink.html b/api/pypath.inputs.signalink.html
new file mode 100644
index 000000000..13351ba07
--- /dev/null
+++ b/api/pypath.inputs.signalink.html
@@ -0,0 +1,654 @@
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+
+    <title>pypath.inputs.signalink &#8212; pypath 0.16.9 documentation</title>
+  
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+    document.documentElement.dataset.mode = localStorage.getItem("mode") || "";
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+  <section id="module-pypath.inputs.signalink">
+<span id="pypath-inputs-signalink"></span><h1>pypath.inputs.signalink<a class="headerlink" href="#module-pypath.inputs.signalink" title="Link to this heading">§</a></h1>
+<dl class="field-list simple">
+<dt class="field-odd">members<span class="colon">:</span></dt>
+<dd class="field-odd"><p></p></dd>
+</dl>
+<p class="rubric">Functions</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.inputs.signalink.signalink_annotations.html#pypath.inputs.signalink.signalink_annotations" title="pypath.inputs.signalink.signalink_annotations"><code class="xref py py-obj docutils literal notranslate"><span class="pre">signalink_annotations</span></code></a>([organism])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.inputs.signalink.signalink_function_annotations.html#pypath.inputs.signalink.signalink_function_annotations" title="pypath.inputs.signalink.signalink_function_annotations"><code class="xref py py-obj docutils literal notranslate"><span class="pre">signalink_function_annotations</span></code></a>([organism])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.inputs.signalink.signalink_interactions.html#pypath.inputs.signalink.signalink_interactions" title="pypath.inputs.signalink.signalink_interactions"><code class="xref py py-obj docutils literal notranslate"><span class="pre">signalink_interactions</span></code></a>([organism, ...])</p></td>
+<td><p>Reads and processes SignaLink3 interactions from local file.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.inputs.signalink.signalink_pathway_annotations.html#pypath.inputs.signalink.signalink_pathway_annotations" title="pypath.inputs.signalink.signalink_pathway_annotations"><code class="xref py py-obj docutils literal notranslate"><span class="pre">signalink_pathway_annotations</span></code></a>([organism])</p></td>
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diff --git a/api/pypath.inputs.signalink.signalink_annotations.html b/api/pypath.inputs.signalink.signalink_annotations.html
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diff --git a/api/pypath.inputs.signalink.signalink_function_annotations.html b/api/pypath.inputs.signalink.signalink_function_annotations.html
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+  <section id="module-pypath.inputs.signor">
+<span id="pypath-inputs-signor"></span><h1>pypath.inputs.signor<a class="headerlink" href="#module-pypath.inputs.signor" title="Link to this heading">§</a></h1>
+<dl class="field-list simple">
+<dt class="field-odd">members<span class="colon">:</span></dt>
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+<p class="rubric">Functions</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.inputs.signor.signor_complexes.html#pypath.inputs.signor.signor_complexes" title="pypath.inputs.signor.signor_complexes"><code class="xref py py-obj docutils literal notranslate"><span class="pre">signor_complexes</span></code></a>([organism])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.inputs.signor.signor_enzyme_substrate.html#pypath.inputs.signor.signor_enzyme_substrate" title="pypath.inputs.signor.signor_enzyme_substrate"><code class="xref py py-obj docutils literal notranslate"><span class="pre">signor_enzyme_substrate</span></code></a>([organism])</p></td>
+<td><p>Loads and processes Signor PTMs.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.inputs.signor.signor_interactions.html#pypath.inputs.signor.signor_interactions" title="pypath.inputs.signor.signor_interactions"><code class="xref py py-obj docutils literal notranslate"><span class="pre">signor_interactions</span></code></a>([organism, raw_records, ...])</p></td>
+<td><p>Downloads the full dataset from SIGNOR (<a class="reference external" href="https://signor.uniroma2.it/">https://signor.uniroma2.it/</a>).</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.inputs.signor.signor_pathway_annotations.html#pypath.inputs.signor.signor_pathway_annotations" title="pypath.inputs.signor.signor_pathway_annotations"><code class="xref py py-obj docutils literal notranslate"><span class="pre">signor_pathway_annotations</span></code></a>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.inputs.signor.signor_pathways.html#pypath.inputs.signor.signor_pathways" title="pypath.inputs.signor.signor_pathways"><code class="xref py py-obj docutils literal notranslate"><span class="pre">signor_pathways</span></code></a>(**kwargs)</p></td>
+<td><p>Obtains pathway annotations from Signor.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.inputs.signor.signor_protein_families.html#pypath.inputs.signor.signor_protein_families" title="pypath.inputs.signor.signor_protein_families"><code class="xref py py-obj docutils literal notranslate"><span class="pre">signor_protein_families</span></code></a>([organism])</p></td>
+<td><p></p></td>
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diff --git a/api/pypath.inputs.signor.signor_complexes.html b/api/pypath.inputs.signor.signor_complexes.html
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diff --git a/api/pypath.inputs.signor.signor_enzyme_substrate.html b/api/pypath.inputs.signor.signor_enzyme_substrate.html
new file mode 100644
index 000000000..9bcb1d1fb
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+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.inputs.signor.signor_enzyme_substrate">
+<span class="sig-prename descclassname"><span class="pre">pypath.inputs.signor.</span></span><span class="sig-name descname"><span class="pre">signor_enzyme_substrate</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">organism</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/inputs/signor.html#signor_enzyme_substrate"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.signor.signor_enzyme_substrate" title="Link to this definition">§</a></dt>
+<dd><p>Loads and processes Signor PTMs.
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diff --git a/api/pypath.inputs.signor.signor_interactions.html b/api/pypath.inputs.signor.signor_interactions.html
new file mode 100644
index 000000000..2d3e0a3d4
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+<h1>pypath.inputs.signor.signor_interactions<a class="headerlink" href="#pypath-inputs-signor-signor-interactions" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.inputs.signor.signor_interactions">
+<span class="sig-prename descclassname"><span class="pre">pypath.inputs.signor.</span></span><span class="sig-name descname"><span class="pre">signor_interactions</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">organism</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">raw_records</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">expand_families</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/inputs/signor.html#signor_interactions"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.signor.signor_interactions" title="Link to this definition">§</a></dt>
+<dd><p>Downloads the full dataset from SIGNOR (<a class="reference external" href="https://signor.uniroma2.it/">https://signor.uniroma2.it/</a>).
+Returns the records with the most important fields.
+If <code class="docutils literal notranslate"><span class="pre">raw_records</span></code> is <cite>True</cite> it returns the table split to list of
+lists but unchanged content.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>organism (int, str): The NCBI Taxonomy ID or name of the organism.</dt><dd><p>Human (9606), mouse (10090) and rat (10116) are available.</p>
+</dd>
+<dt>raw_records (bool): Process the records or return them raw,</dt><dd><p>as they are.</p>
+</dd>
+<dt>expand_families (int): Expand protein families up to this size.</dt><dd><p>Zero or one means no expansion.</p>
+</dd>
+</dl>
+</dd>
+<dt>Return</dt><dd><dl class="simple">
+<dt>list: A list with processed records as named tuples or dicts of</dt><dd><p>raw records if <code class="docutils literal notranslate"><span class="pre">raw_records</span></code> is True.</p>
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diff --git a/api/pypath.inputs.signor.signor_pathways.html b/api/pypath.inputs.signor.signor_pathways.html
new file mode 100644
index 000000000..e8f626da7
--- /dev/null
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@@ -0,0 +1,639 @@
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+<h1>pypath.inputs.signor.signor_pathways<a class="headerlink" href="#pypath-inputs-signor-signor-pathways" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.inputs.signor.signor_pathways">
+<span class="sig-prename descclassname"><span class="pre">pypath.inputs.signor.</span></span><span class="sig-name descname"><span class="pre">signor_pathways</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/inputs/signor.html#signor_pathways"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.signor.signor_pathways" title="Link to this definition">§</a></dt>
+<dd><p>Obtains pathway annotations from Signor.</p>
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+
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diff --git a/api/pypath.inputs.signor.signor_protein_families.html b/api/pypath.inputs.signor.signor_protein_families.html
new file mode 100644
index 000000000..11bab1b5c
--- /dev/null
+++ b/api/pypath.inputs.signor.signor_protein_families.html
@@ -0,0 +1,638 @@
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diff --git a/api/pypath.inputs.spike.html b/api/pypath.inputs.spike.html
new file mode 100644
index 000000000..ed34afe3e
--- /dev/null
+++ b/api/pypath.inputs.spike.html
@@ -0,0 +1,648 @@
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+  <section id="module-pypath.inputs.spike">
+<span id="pypath-inputs-spike"></span><h1>pypath.inputs.spike<a class="headerlink" href="#module-pypath.inputs.spike" title="Link to this heading">§</a></h1>
+<dl class="field-list simple">
+<dt class="field-odd">members<span class="colon">:</span></dt>
+<dd class="field-odd"><p></p></dd>
+</dl>
+<p class="rubric">Functions</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.inputs.spike.spike_complexes.html#pypath.inputs.spike.spike_complexes" title="pypath.inputs.spike.spike_complexes"><code class="xref py py-obj docutils literal notranslate"><span class="pre">spike_complexes</span></code></a>([min_confidence])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.inputs.spike.spike_interactions.html#pypath.inputs.spike.spike_interactions" title="pypath.inputs.spike.spike_interactions"><code class="xref py py-obj docutils literal notranslate"><span class="pre">spike_interactions</span></code></a>([min_confidence])</p></td>
+<td><p>Args</p></td>
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+  <section id="pypath-inputs-spike-spike-complexes">
+<h1>pypath.inputs.spike.spike_complexes<a class="headerlink" href="#pypath-inputs-spike-spike-complexes" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.inputs.spike.spike_complexes">
+<span class="sig-prename descclassname"><span class="pre">pypath.inputs.spike.</span></span><span class="sig-name descname"><span class="pre">spike_complexes</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">min_confidence</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">2</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><span class="pre">Dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><a class="reference internal" href="pypath.internals.intera.Complex.html#pypath.internals.intera.Complex" title="pypath.internals.intera.Complex"><span class="pre">Complex</span></a><span class="p"><span class="pre">]</span></span></span></span><a class="reference internal" href="../_modules/pypath/inputs/spike.html#spike_complexes"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.spike.spike_complexes" title="Link to this definition">§</a></dt>
+<dd></dd></dl>
+
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+  <section id="pypath-inputs-spike-spike-interactions">
+<h1>pypath.inputs.spike.spike_interactions<a class="headerlink" href="#pypath-inputs-spike-spike-interactions" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.inputs.spike.spike_interactions">
+<span class="sig-prename descclassname"><span class="pre">pypath.inputs.spike.</span></span><span class="sig-name descname"><span class="pre">spike_interactions</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">min_confidence</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">2</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><span class="pre">List</span><span class="p"><span class="pre">[</span></span><span class="pre">tuple</span><span class="p"><span class="pre">]</span></span></span></span><a class="reference internal" href="../_modules/pypath/inputs/spike.html#spike_interactions"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.spike.spike_interactions" title="Link to this definition">§</a></dt>
+<dd><dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>min_confidence:</dt><dd><p>Confidence (integrity) levels in SPIKE span from 1 to 4, 1
+being the highest confidence.</p>
+</dd>
+</dl>
+</dd>
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diff --git a/api/pypath.inputs.stitch.html b/api/pypath.inputs.stitch.html
index defc170f4..ec1a445a1 100644
--- a/api/pypath.inputs.stitch.html
+++ b/api/pypath.inputs.stitch.html
@@ -48,7 +48,7 @@
     <link rel="index" title="Index" href="../genindex.html" />
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     <link rel="next" title="pypath.inputs.stitch.stitch_actions_interactions" href="pypath.inputs.stitch.stitch_actions_interactions.html" />
-    <link rel="prev" title="pypath.inputs.sider.SiderSideeffetFrequency" href="pypath.inputs.sider.SiderSideeffetFrequency.html" />
+    <link rel="prev" title="pypath.inputs.spike.spike_interactions" href="pypath.inputs.spike.spike_interactions.html" />
   <meta name="viewport" content="width=device-width, initial-scale=1"/>
   <meta name="docsearch:language" content="en"/>
   </head>
@@ -545,12 +545,12 @@
                   
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     <a class="left-prev"
-       href="pypath.inputs.sider.SiderSideeffetFrequency.html"
+       href="pypath.inputs.spike.spike_interactions.html"
        title="previous page">
       <i class="fa-solid fa-angle-left"></i>
       <div class="prev-next-info">
         <p class="prev-next-subtitle">previous</p>
-        <p class="prev-next-title">pypath.inputs.sider.SiderSideeffetFrequency</p>
+        <p class="prev-next-title">pypath.inputs.spike.spike_interactions</p>
       </div>
     </a>
     <a class="right-next"
diff --git a/api/pypath.inputs.string.string_species.html b/api/pypath.inputs.string.string_species.html
index 2128895a1..843108b7f 100644
--- a/api/pypath.inputs.string.string_species.html
+++ b/api/pypath.inputs.string.string_species.html
@@ -47,7 +47,7 @@
     <link rel="icon" href="../_static/omnipath-logo.svg"/>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
-    <link rel="next" title="pypath.inputs.switches_elm" href="pypath.inputs.switches_elm.html" />
+    <link rel="next" title="pypath.inputs.surfaceome" href="pypath.inputs.surfaceome.html" />
     <link rel="prev" title="pypath.inputs.string.string_physical_interactions" href="pypath.inputs.string.string_physical_interactions.html" />
   <meta name="viewport" content="width=device-width, initial-scale=1"/>
   <meta name="docsearch:language" content="en"/>
@@ -549,11 +549,11 @@ <h1>pypath.inputs.string.string_species<a class="headerlink" href="#pypath-input
       </div>
     </a>
     <a class="right-next"
-       href="pypath.inputs.switches_elm.html"
+       href="pypath.inputs.surfaceome.html"
        title="next page">
       <div class="prev-next-info">
         <p class="prev-next-subtitle">next</p>
-        <p class="prev-next-title">pypath.inputs.switches_elm</p>
+        <p class="prev-next-title">pypath.inputs.surfaceome</p>
       </div>
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     </a>
diff --git a/api/pypath.inputs.surfaceome.html b/api/pypath.inputs.surfaceome.html
new file mode 100644
index 000000000..2808f6a3f
--- /dev/null
+++ b/api/pypath.inputs.surfaceome.html
@@ -0,0 +1,645 @@
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+<dl class="field-list simple">
+<dt class="field-odd">members<span class="colon">:</span></dt>
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+<p class="rubric">Functions</p>
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diff --git a/api/pypath.inputs.surfaceome.surfaceome_annotations.html b/api/pypath.inputs.surfaceome.surfaceome_annotations.html
new file mode 100644
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+  <section id="pypath-inputs-surfaceome-surfaceome-annotations">
+<h1>pypath.inputs.surfaceome.surfaceome_annotations<a class="headerlink" href="#pypath-inputs-surfaceome-surfaceome-annotations" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.inputs.surfaceome.surfaceome_annotations">
+<span class="sig-prename descclassname"><span class="pre">pypath.inputs.surfaceome.</span></span><span class="sig-name descname"><span class="pre">surfaceome_annotations</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/inputs/surfaceome.html#surfaceome_annotations"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.surfaceome.surfaceome_annotations" title="Link to this definition">§</a></dt>
+<dd><p>Downloads the “In silico human surfaceome”.
+Dict with UniProt IDs as key and tuples of surface prediction score,
+class and subclass as values (columns B, N, S and T of table S3).</p>
+</dd></dl>
+
+</section>
+
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diff --git a/api/pypath.inputs.switches_elm.get_switches_elm.html b/api/pypath.inputs.switches_elm.get_switches_elm.html
index 17691ca3a..656245769 100644
--- a/api/pypath.inputs.switches_elm.get_switches_elm.html
+++ b/api/pypath.inputs.switches_elm.get_switches_elm.html
@@ -47,7 +47,7 @@
     <link rel="icon" href="../_static/omnipath-logo.svg"/>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
-    <link rel="next" title="pypath.inputs.transmir" href="pypath.inputs.transmir.html" />
+    <link rel="next" title="pypath.inputs.talklr" href="pypath.inputs.talklr.html" />
     <link rel="prev" title="pypath.inputs.switches_elm" href="pypath.inputs.switches_elm.html" />
   <meta name="viewport" content="width=device-width, initial-scale=1"/>
   <meta name="docsearch:language" content="en"/>
@@ -547,11 +547,11 @@ <h1>pypath.inputs.switches_elm.get_switches_elm<a class="headerlink" href="#pypa
       </div>
     </a>
     <a class="right-next"
-       href="pypath.inputs.transmir.html"
+       href="pypath.inputs.talklr.html"
        title="next page">
       <div class="prev-next-info">
         <p class="prev-next-subtitle">next</p>
-        <p class="prev-next-title">pypath.inputs.transmir</p>
+        <p class="prev-next-title">pypath.inputs.talklr</p>
       </div>
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     </a>
diff --git a/api/pypath.inputs.switches_elm.html b/api/pypath.inputs.switches_elm.html
index 969425eeb..cbece45ae 100644
--- a/api/pypath.inputs.switches_elm.html
+++ b/api/pypath.inputs.switches_elm.html
@@ -48,7 +48,7 @@
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
     <link rel="next" title="pypath.inputs.switches_elm.get_switches_elm" href="pypath.inputs.switches_elm.get_switches_elm.html" />
-    <link rel="prev" title="pypath.inputs.string.string_species" href="pypath.inputs.string.string_species.html" />
+    <link rel="prev" title="pypath.inputs.surfaceome.surfaceome_annotations" href="pypath.inputs.surfaceome.surfaceome_annotations.html" />
   <meta name="viewport" content="width=device-width, initial-scale=1"/>
   <meta name="docsearch:language" content="en"/>
   </head>
@@ -542,12 +542,12 @@
                   
 <div class="prev-next-area">
     <a class="left-prev"
-       href="pypath.inputs.string.string_species.html"
+       href="pypath.inputs.surfaceome.surfaceome_annotations.html"
        title="previous page">
       <i class="fa-solid fa-angle-left"></i>
       <div class="prev-next-info">
         <p class="prev-next-subtitle">previous</p>
-        <p class="prev-next-title">pypath.inputs.string.string_species</p>
+        <p class="prev-next-title">pypath.inputs.surfaceome.surfaceome_annotations</p>
       </div>
     </a>
     <a class="right-next"
diff --git a/api/pypath.inputs.talklr.html b/api/pypath.inputs.talklr.html
new file mode 100644
index 000000000..40d8a03ac
--- /dev/null
+++ b/api/pypath.inputs.talklr.html
@@ -0,0 +1,651 @@
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+  
+  
+  
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+    document.documentElement.dataset.mode = localStorage.getItem("mode") || "";
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diff --git a/api/pypath.inputs.talklr.talklr_annotations.html b/api/pypath.inputs.talklr.talklr_annotations.html
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diff --git a/api/pypath.inputs.talklr.talklr_interactions.html b/api/pypath.inputs.talklr.talklr_interactions.html
new file mode 100644
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diff --git a/api/pypath.inputs.tcdb.tcdb_annotations.html b/api/pypath.inputs.tcdb.tcdb_annotations.html
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diff --git a/api/pypath.inputs.tcdb.tcdb_classes.html b/api/pypath.inputs.tcdb.tcdb_classes.html
new file mode 100644
index 000000000..6c00d4a3c
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diff --git a/api/pypath.inputs.tcdb.tcdb_families.html b/api/pypath.inputs.tcdb.tcdb_families.html
new file mode 100644
index 000000000..ac21f5152
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+  <section id="module-pypath.inputs.tfcensus">
+<span id="pypath-inputs-tfcensus"></span><h1>pypath.inputs.tfcensus<a class="headerlink" href="#module-pypath.inputs.tfcensus" title="Link to this heading">§</a></h1>
+<dl class="field-list simple">
+<dt class="field-odd">members<span class="colon">:</span></dt>
+<dd class="field-odd"><p></p></dd>
+</dl>
+<p class="rubric">Functions</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.inputs.tfcensus.tfcensus_annotations.html#pypath.inputs.tfcensus.tfcensus_annotations" title="pypath.inputs.tfcensus.tfcensus_annotations"><code class="xref py py-obj docutils literal notranslate"><span class="pre">tfcensus_annotations</span></code></a>([only_classes])</p></td>
+<td><p>Downloads and processes the list of all known transcription factors from TF census (Vaquerizas 2009).</p></td>
+</tr>
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diff --git a/api/pypath.inputs.tfcensus.tfcensus_annotations.html b/api/pypath.inputs.tfcensus.tfcensus_annotations.html
new file mode 100644
index 000000000..13a39dda8
--- /dev/null
+++ b/api/pypath.inputs.tfcensus.tfcensus_annotations.html
@@ -0,0 +1,641 @@
+
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+  <section id="pypath-inputs-tfcensus-tfcensus-annotations">
+<h1>pypath.inputs.tfcensus.tfcensus_annotations<a class="headerlink" href="#pypath-inputs-tfcensus-tfcensus-annotations" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.inputs.tfcensus.tfcensus_annotations">
+<span class="sig-prename descclassname"><span class="pre">pypath.inputs.tfcensus.</span></span><span class="sig-name descname"><span class="pre">tfcensus_annotations</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">only_classes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/inputs/tfcensus.html#tfcensus_annotations"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.tfcensus.tfcensus_annotations" title="Link to this definition">§</a></dt>
+<dd><p>Downloads and processes the list of all known transcription factors from
+TF census (Vaquerizas 2009). This resource is human only.
+Returns dict with UniProt IDs as keys and TF annotations as values.</p>
+</dd></dl>
+
+</section>
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+
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+  <section id="module-pypath.inputs.threedcomplex">
+<span id="pypath-inputs-threedcomplex"></span><h1>pypath.inputs.threedcomplex<a class="headerlink" href="#module-pypath.inputs.threedcomplex" title="Link to this heading">§</a></h1>
+<dl class="field-list simple">
+<dt class="field-odd">members<span class="colon">:</span></dt>
+<dd class="field-odd"><p></p></dd>
+</dl>
+<p class="rubric">Functions</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.inputs.threedcomplex.threedcomplex_chains.html#pypath.inputs.threedcomplex.threedcomplex_chains" title="pypath.inputs.threedcomplex.threedcomplex_chains"><code class="xref py py-obj docutils literal notranslate"><span class="pre">threedcomplex_chains</span></code></a>()</p></td>
+<td><p>Returns the chain correspondancy map of the 3D Complex database.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.inputs.threedcomplex.threedcomplex_complexes.html#pypath.inputs.threedcomplex.threedcomplex_complexes" title="pypath.inputs.threedcomplex.threedcomplex_complexes"><code class="xref py py-obj docutils literal notranslate"><span class="pre">threedcomplex_complexes</span></code></a>()</p></td>
+<td><p>To be implemented later.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.inputs.threedcomplex.threedcomplex_contacts.html#pypath.inputs.threedcomplex.threedcomplex_contacts" title="pypath.inputs.threedcomplex.threedcomplex_contacts"><code class="xref py py-obj docutils literal notranslate"><span class="pre">threedcomplex_contacts</span></code></a>([chains, pdb_uniprot])</p></td>
+<td><p>Returns the 3D structure based domain-domain contact map from the 3D Complex database.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.inputs.threedcomplex.threedcomplex_ddi.html#pypath.inputs.threedcomplex.threedcomplex_ddi" title="pypath.inputs.threedcomplex.threedcomplex_ddi"><code class="xref py py-obj docutils literal notranslate"><span class="pre">threedcomplex_ddi</span></code></a>([contacts])</p></td>
+<td><p>Downloads and preprocesses data from the 3DComplex database (<a class="reference external" href="http://shmoo.weizmann.ac.il/elevy/3dcomplexV6/Home.cgi">http://shmoo.weizmann.ac.il/elevy/3dcomplexV6/Home.cgi</a>).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.inputs.threedcomplex.threedcomplex_nresidues.html#pypath.inputs.threedcomplex.threedcomplex_nresidues" title="pypath.inputs.threedcomplex.threedcomplex_nresidues"><code class="xref py py-obj docutils literal notranslate"><span class="pre">threedcomplex_nresidues</span></code></a>()</p></td>
+<td><p>Downloads and preprocesses data from the 3DComplex database (<a class="reference external" href="http://shmoo.weizmann.ac.il/elevy/3dcomplexV6/Home.cgi">http://shmoo.weizmann.ac.il/elevy/3dcomplexV6/Home.cgi</a>).</p></td>
+</tr>
+</tbody>
+</table>
+</section>
+
+
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+  <section id="pypath-inputs-threedcomplex-threedcomplex-chains">
+<h1>pypath.inputs.threedcomplex.threedcomplex_chains<a class="headerlink" href="#pypath-inputs-threedcomplex-threedcomplex-chains" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.inputs.threedcomplex.threedcomplex_chains">
+<span class="sig-prename descclassname"><span class="pre">pypath.inputs.threedcomplex.</span></span><span class="sig-name descname"><span class="pre">threedcomplex_chains</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/inputs/threedcomplex.html#threedcomplex_chains"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.threedcomplex.threedcomplex_chains" title="Link to this definition">§</a></dt>
+<dd><p>Returns the chain correspondancy map of the 3D Complex database.</p>
+</dd></dl>
+
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+  <section id="pypath-inputs-threedcomplex-threedcomplex-complexes">
+<h1>pypath.inputs.threedcomplex.threedcomplex_complexes<a class="headerlink" href="#pypath-inputs-threedcomplex-threedcomplex-complexes" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.inputs.threedcomplex.threedcomplex_complexes">
+<span class="sig-prename descclassname"><span class="pre">pypath.inputs.threedcomplex.</span></span><span class="sig-name descname"><span class="pre">threedcomplex_complexes</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/inputs/threedcomplex.html#threedcomplex_complexes"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.threedcomplex.threedcomplex_complexes" title="Link to this definition">§</a></dt>
+<dd><p>To be implemented later. Should return dictionary of
+pypath.internals.intera.Complex objects.</p>
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+  <section id="pypath-inputs-threedcomplex-threedcomplex-contacts">
+<h1>pypath.inputs.threedcomplex.threedcomplex_contacts<a class="headerlink" href="#pypath-inputs-threedcomplex-threedcomplex-contacts" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.inputs.threedcomplex.threedcomplex_contacts">
+<span class="sig-prename descclassname"><span class="pre">pypath.inputs.threedcomplex.</span></span><span class="sig-name descname"><span class="pre">threedcomplex_contacts</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">chains</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">pdb_uniprot</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/inputs/threedcomplex.html#threedcomplex_contacts"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.threedcomplex.threedcomplex_contacts" title="Link to this definition">§</a></dt>
+<dd><p>Returns the 3D structure based domain-domain contact map from the
+3D Complex database.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>chains (dict): A dict of chain correspondancy map, as created by</dt><dd><p><code class="docutils literal notranslate"><span class="pre">threedcomplex_chains</span></code>. If None, it will be obtained
+automatically.</p>
+</dd>
+<dt>pdb_uniprot (dict): A dict of PDB-UniProt mappings, as created by</dt><dd><p><code class="docutils literal notranslate"><span class="pre">pypath.inputs.pdb.pdb_chains</span></code>. If None, it will be obtained
+automatically.</p>
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+  <section id="pypath-inputs-threedcomplex-threedcomplex-ddi">
+<h1>pypath.inputs.threedcomplex.threedcomplex_ddi<a class="headerlink" href="#pypath-inputs-threedcomplex-threedcomplex-ddi" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.inputs.threedcomplex.threedcomplex_ddi">
+<span class="sig-prename descclassname"><span class="pre">pypath.inputs.threedcomplex.</span></span><span class="sig-name descname"><span class="pre">threedcomplex_ddi</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">contacts</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/inputs/threedcomplex.html#threedcomplex_ddi"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.threedcomplex.threedcomplex_ddi" title="Link to this definition">§</a></dt>
+<dd><p>Downloads and preprocesses data from the 3DComplex database
+(<a class="reference external" href="http://shmoo.weizmann.ac.il/elevy/3dcomplexV6/Home.cgi">http://shmoo.weizmann.ac.il/elevy/3dcomplexV6/Home.cgi</a>).</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>contacts (set): A map of 3D structure based contacts, as provided by</dt><dd><p><code class="docutils literal notranslate"><span class="pre">threedcomplex_contacts</span></code>. If None, it will be obtained
+automatically.</p>
+</dd>
+</dl>
+</dd>
+<dt>Returns</dt><dd><p>A list of domain-domain interaction objects.</p>
+</dd>
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new file mode 100644
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+<h1>pypath.inputs.threedcomplex.threedcomplex_nresidues<a class="headerlink" href="#pypath-inputs-threedcomplex-threedcomplex-nresidues" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.inputs.threedcomplex.threedcomplex_nresidues">
+<span class="sig-prename descclassname"><span class="pre">pypath.inputs.threedcomplex.</span></span><span class="sig-name descname"><span class="pre">threedcomplex_nresidues</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/inputs/threedcomplex.html#threedcomplex_nresidues"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.threedcomplex.threedcomplex_nresidues" title="Link to this definition">§</a></dt>
+<dd><p>Downloads and preprocesses data from the 3DComplex database
+(<a class="reference external" href="http://shmoo.weizmann.ac.il/elevy/3dcomplexV6/Home.cgi">http://shmoo.weizmann.ac.il/elevy/3dcomplexV6/Home.cgi</a>).</p>
+<p>Returns dict of dicts where top level keys are PDB IDs, second level
+keys are pairs of tuples of UniProt IDs and values are list with the
+number of amino acids in contact.</p>
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+<h1>pypath.inputs.threedid.get_3did<a class="headerlink" href="#pypath-inputs-threedid-get-3did" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.inputs.threedid.get_3did">
+<span class="sig-prename descclassname"><span class="pre">pypath.inputs.threedid.</span></span><span class="sig-name descname"><span class="pre">get_3did</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">ddi_flat</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">res</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">organism</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">pickl</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/inputs/threedid.html#get_3did"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.threedid.get_3did" title="Link to this definition">§</a></dt>
+<dd></dd></dl>
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diff --git a/api/pypath.inputs.threedid.get_3did_ddi.html b/api/pypath.inputs.threedid.get_3did_ddi.html
new file mode 100644
index 000000000..1348161fe
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+<h1>pypath.inputs.threedid.get_3did_ddi<a class="headerlink" href="#pypath-inputs-threedid-get-3did-ddi" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.inputs.threedid.get_3did_ddi">
+<span class="sig-prename descclassname"><span class="pre">pypath.inputs.threedid.</span></span><span class="sig-name descname"><span class="pre">get_3did_ddi</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">residues</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ddi_flat</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">organism</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/inputs/threedid.html#get_3did_ddi"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.threedid.get_3did_ddi" title="Link to this definition">§</a></dt>
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diff --git a/api/pypath.inputs.threedid.get_3did_dmi.html b/api/pypath.inputs.threedid.get_3did_dmi.html
new file mode 100644
index 000000000..8bcb05db8
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diff --git a/api/pypath.inputs.threedid.html b/api/pypath.inputs.threedid.html
new file mode 100644
index 000000000..f378e0f1d
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+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.inputs.threedid.get_3did.html#pypath.inputs.threedid.get_3did" title="pypath.inputs.threedid.get_3did"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_3did</span></code></a>([ddi_flat, res, organism, pickl])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.inputs.threedid.get_3did_ddi.html#pypath.inputs.threedid.get_3did_ddi" title="pypath.inputs.threedid.get_3did_ddi"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_3did_ddi</span></code></a>([residues, ddi_flat, organism])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.inputs.threedid.get_3did_dmi.html#pypath.inputs.threedid.get_3did_dmi" title="pypath.inputs.threedid.get_3did_dmi"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_3did_dmi</span></code></a>([dmi_flat])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.inputs.threedid.process_3did_dmi.html#pypath.inputs.threedid.process_3did_dmi" title="pypath.inputs.threedid.process_3did_dmi"><code class="xref py py-obj docutils literal notranslate"><span class="pre">process_3did_dmi</span></code></a>()</p></td>
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diff --git a/api/pypath.inputs.threedid.process_3did_dmi.html b/api/pypath.inputs.threedid.process_3did_dmi.html
new file mode 100644
index 000000000..b2d466139
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diff --git a/api/pypath.inputs.topdb.topdb_annotations.html b/api/pypath.inputs.topdb.topdb_annotations.html
new file mode 100644
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+                    <li class="nav-item">
+                      <a class="nav-link nav-internal" href="../webservice.html">
+                        Webservice
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+                      <a class="nav-link nav-internal" href="../releasehistory.html">
+                        Release history
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+
+                    <li class="nav-item current active">
+                      <a class="nav-link nav-internal" href="../reference.html">
+                        Reference
+                      </a>
+                    </li>
+                
+
+                    <li class="nav-item">
+                      <a class="nav-link nav-internal" href="../notebooks/manual.html">
+                        The pypath book
+                      </a>
+                    </li>
+                
+  </ul>
+</nav></div>
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+    
+    
+    
+      <div class="sidebar-header-items__end">
+        
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+<script>
+document.write(`
+  <button class="btn btn-sm navbar-btn theme-switch-button" title="light/dark" aria-label="light/dark" data-bs-placement="bottom" data-bs-toggle="tooltip">
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+    <span class="theme-switch nav-link" data-mode="dark"><i class="fa-solid fa-moon fa-lg"></i></span>
+    <span class="theme-switch nav-link" data-mode="auto"><i class="fa-solid fa-circle-half-stroke fa-lg"></i></span>
+  </button>
+`);
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+            <span class="sr-only">OmniPath</span></a>
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+        <li class="nav-item">
+          
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+          
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+          <a href="https://saezlab.org/" title="Saez Lab" class="nav-link" rel="noopener" target="_blank" data-bs-toggle="tooltip" data-bs-placement="bottom"><span><i class="fa-solid fa-users fa-lg" aria-hidden="true"></i></span>
+            <span class="sr-only">Saez Lab</span></a>
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+      
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+<div id="searchbox"></div>
+                <article class="bd-article">
+                  
+  <section id="pypath-inputs-topdb-topdb-annotations">
+<h1>pypath.inputs.topdb.topdb_annotations<a class="headerlink" href="#pypath-inputs-topdb-topdb-annotations" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.inputs.topdb.topdb_annotations">
+<span class="sig-prename descclassname"><span class="pre">pypath.inputs.topdb.</span></span><span class="sig-name descname"><span class="pre">topdb_annotations</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/inputs/topdb.html#topdb_annotations"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.topdb.topdb_annotations" title="Link to this definition">§</a></dt>
+<dd></dd></dl>
+
+</section>
+
+
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+              
+              
+              
+              
+              
+                <footer class="prev-next-footer">
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+      <div class="prev-next-info">
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+        <p class="prev-next-title">pypath.inputs.topdb</p>
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+    <a class="right-next"
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+    <i class="fa-solid fa-list"></i> On this page
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+  <nav class="bd-toc-nav page-toc" aria-labelledby="pst-page-navigation-heading-2">
+    <ul class="visible nav section-nav flex-column">
+<li class="toctree-l1 toc-h1 nav-item toc-entry"><a class="reference internal nav-link" href="../index.html">Welcome to pypath!</a></li>
+<li class="toctree-l1 toc-h1 nav-item toc-entry"><a class="reference internal nav-link" href="../webservice.html">Webservice</a></li>
+<li class="toctree-l1 toc-h1 nav-item toc-entry"><a class="reference internal nav-link" href="../releasehistory.html">Release history</a></li>
+<li class="toctree-l1 toc-h1 nav-item toc-entry"><a class="reference internal nav-link" href="../reference.html">Reference</a></li>
+<li class="toctree-l1 toc-h1 nav-item toc-entry"><a class="reference internal nav-link" href="../notebooks/manual.html">The pypath book</a></li>
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\ No newline at end of file
diff --git a/api/pypath.inputs.transmir.html b/api/pypath.inputs.transmir.html
index e788cc5fa..51c4be8e2 100644
--- a/api/pypath.inputs.transmir.html
+++ b/api/pypath.inputs.transmir.html
@@ -48,7 +48,7 @@
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
     <link rel="next" title="pypath.inputs.transmir.transmir_interactions" href="pypath.inputs.transmir.transmir_interactions.html" />
-    <link rel="prev" title="pypath.inputs.switches_elm.get_switches_elm" href="pypath.inputs.switches_elm.get_switches_elm.html" />
+    <link rel="prev" title="pypath.inputs.topdb.topdb_annotations" href="pypath.inputs.topdb.topdb_annotations.html" />
   <meta name="viewport" content="width=device-width, initial-scale=1"/>
   <meta name="docsearch:language" content="en"/>
   </head>
@@ -542,12 +542,12 @@
                   
 <div class="prev-next-area">
     <a class="left-prev"
-       href="pypath.inputs.switches_elm.get_switches_elm.html"
+       href="pypath.inputs.topdb.topdb_annotations.html"
        title="previous page">
       <i class="fa-solid fa-angle-left"></i>
       <div class="prev-next-info">
         <p class="prev-next-subtitle">previous</p>
-        <p class="prev-next-title">pypath.inputs.switches_elm.get_switches_elm</p>
+        <p class="prev-next-title">pypath.inputs.topdb.topdb_annotations</p>
       </div>
     </a>
     <a class="right-next"
diff --git a/api/pypath.inputs.uniprot_db.is_uniprot.html b/api/pypath.inputs.uniprot_db.is_uniprot.html
index 99548dd1b..72f4cac4e 100644
--- a/api/pypath.inputs.uniprot_db.is_uniprot.html
+++ b/api/pypath.inputs.uniprot_db.is_uniprot.html
@@ -47,7 +47,7 @@
     <link rel="icon" href="../_static/omnipath-logo.svg"/>
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   <meta name="viewport" content="width=device-width, initial-scale=1"/>
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diff --git a/api/pypath.inputs.wang.cui_interactions.html b/api/pypath.inputs.wang.cui_interactions.html
new file mode 100644
index 000000000..82d7da436
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@@ -0,0 +1,640 @@
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+  <section id="pypath-inputs-wang-cui-interactions">
+<h1>pypath.inputs.wang.cui_interactions<a class="headerlink" href="#pypath-inputs-wang-cui-interactions" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.inputs.wang.cui_interactions">
+<span class="sig-prename descclassname"><span class="pre">pypath.inputs.wang.</span></span><span class="sig-name descname"><span class="pre">cui_interactions</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><span class="pre">List</span><span class="p"><span class="pre">[</span></span><span class="pre">tuple</span><span class="p"><span class="pre">]</span></span></span></span><a class="reference internal" href="../_modules/pypath/inputs/wang.html#cui_interactions"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.wang.cui_interactions" title="Link to this definition">§</a></dt>
+<dd><p>Interactions from Supplementary Table 9 of Cui et al. 2007
+(<a class="reference external" href="https://www.embopress.org/doi/full/10.1038/msb4100200">https://www.embopress.org/doi/full/10.1038/msb4100200</a>).</p>
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diff --git a/api/pypath.inputs.wang.hsn_interactions.html b/api/pypath.inputs.wang.hsn_interactions.html
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+  <section id="pypath-inputs-wang-hsn-interactions">
+<h1>pypath.inputs.wang.hsn_interactions<a class="headerlink" href="#pypath-inputs-wang-hsn-interactions" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.inputs.wang.hsn_interactions">
+<span class="sig-prename descclassname"><span class="pre">pypath.inputs.wang.</span></span><span class="sig-name descname"><span class="pre">hsn_interactions</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">source</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">Literal</span><span class="p"><span class="pre">[</span></span><span class="s"><span class="pre">'rescued'</span></span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="s"><span class="pre">'researchgate'</span></span><span class="p"><span class="pre">]</span></span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">'rescued'</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><span class="pre">List</span><span class="p"><span class="pre">[</span></span><span class="pre">tuple</span><span class="p"><span class="pre">]</span></span></span></span><a class="reference internal" href="../_modules/pypath/inputs/wang.html#hsn_interactions"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.wang.hsn_interactions" title="Link to this definition">§</a></dt>
+<dd><p>Downloads and processes HumanSignalingNetwork version 6
+(published 2014 Jan by Edwin Wang).</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>source: The same file is available from two domains: the OmniPath</dt><dd><p>rescued repository and Research Gate. These both are secondary
+sources, the dataset is not available any more from its original
+site of publication, which was the old webpage of the Wang Lab.</p>
+</dd>
+</dl>
+</dd>
+<dt>Details:</dt><dd><p>This dataset is identical to the one returned by <cite>wang_interactions</cite>,
+but it does not contain function and localization details.</p>
+</dd>
+</dl>
+</dd></dl>
+
+</section>
+
+
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+                  
+  <section id="module-pypath.inputs.wang">
+<span id="pypath-inputs-wang"></span><h1>pypath.inputs.wang<a class="headerlink" href="#module-pypath.inputs.wang" title="Link to this heading">§</a></h1>
+<dl class="field-list simple">
+<dt class="field-odd">members<span class="colon">:</span></dt>
+<dd class="field-odd"><p></p></dd>
+</dl>
+<p class="rubric">Functions</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.inputs.wang.cui_interactions.html#pypath.inputs.wang.cui_interactions" title="pypath.inputs.wang.cui_interactions"><code class="xref py py-obj docutils literal notranslate"><span class="pre">cui_interactions</span></code></a>()</p></td>
+<td><p>Interactions from Supplementary Table 9 of Cui et al. 2007 (<a class="reference external" href="https://www.embopress.org/doi/full/10.1038/msb4100200">https://www.embopress.org/doi/full/10.1038/msb4100200</a>).</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.inputs.wang.hsn_interactions.html#pypath.inputs.wang.hsn_interactions" title="pypath.inputs.wang.hsn_interactions"><code class="xref py py-obj docutils literal notranslate"><span class="pre">hsn_interactions</span></code></a>([source])</p></td>
+<td><p>Downloads and processes HumanSignalingNetwork version 6 (published 2014 Jan by Edwin Wang).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.inputs.wang.wang_annotations.html#pypath.inputs.wang.wang_annotations" title="pypath.inputs.wang.wang_annotations"><code class="xref py py-obj docutils literal notranslate"><span class="pre">wang_annotations</span></code></a>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.inputs.wang.wang_interactions.html#pypath.inputs.wang.wang_interactions" title="pypath.inputs.wang.wang_interactions"><code class="xref py py-obj docutils literal notranslate"><span class="pre">wang_interactions</span></code></a>()</p></td>
+<td><p>Downloads and processes Wang Lab HumanSignalingNetwork.</p></td>
+</tr>
+</tbody>
+</table>
+</section>
+
+
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diff --git a/api/pypath.inputs.wang.wang_annotations.html b/api/pypath.inputs.wang.wang_annotations.html
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diff --git a/api/pypath.inputs.wang.wang_interactions.html b/api/pypath.inputs.wang.wang_interactions.html
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+<h1>pypath.inputs.wang.wang_interactions<a class="headerlink" href="#pypath-inputs-wang-wang-interactions" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.inputs.wang.wang_interactions">
+<span class="sig-prename descclassname"><span class="pre">pypath.inputs.wang.</span></span><span class="sig-name descname"><span class="pre">wang_interactions</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><span class="pre">List</span><span class="p"><span class="pre">[</span></span><span class="pre">tuple</span><span class="p"><span class="pre">]</span></span></span></span><a class="reference internal" href="../_modules/pypath/inputs/wang.html#wang_interactions"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.wang.wang_interactions" title="Link to this definition">§</a></dt>
+<dd><p>Downloads and processes Wang Lab HumanSignalingNetwork.
+Returns list of interactions as tuples of source, target and effect.</p>
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+
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+
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+  <section id="module-pypath.inputs.wojtowicz2020">
+<span id="pypath-inputs-wojtowicz2020"></span><h1>pypath.inputs.wojtowicz2020<a class="headerlink" href="#module-pypath.inputs.wojtowicz2020" title="Link to this heading">§</a></h1>
+<dl class="field-list simple">
+<dt class="field-odd">members<span class="colon">:</span></dt>
+<dd class="field-odd"><p></p></dd>
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+<p class="rubric">Functions</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.inputs.wojtowicz2020.wojtowicz2020_interactions.html#pypath.inputs.wojtowicz2020.wojtowicz2020_interactions" title="pypath.inputs.wojtowicz2020.wojtowicz2020_interactions"><code class="xref py py-obj docutils literal notranslate"><span class="pre">wojtowicz2020_interactions</span></code></a>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.inputs.wojtowicz2020.wojtowicz2020_raw.html#pypath.inputs.wojtowicz2020.wojtowicz2020_raw" title="pypath.inputs.wojtowicz2020.wojtowicz2020_raw"><code class="xref py py-obj docutils literal notranslate"><span class="pre">wojtowicz2020_raw</span></code></a>()</p></td>
+<td><p>Returns Supplementary Table S4 from 10.1016/j.cell.2020.07.025 (Wojtowicz et al. 2020) as a list of tuples.</p></td>
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+  <section id="pypath-inputs-wojtowicz2020-wojtowicz2020-raw">
+<h1>pypath.inputs.wojtowicz2020.wojtowicz2020_raw<a class="headerlink" href="#pypath-inputs-wojtowicz2020-wojtowicz2020-raw" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.inputs.wojtowicz2020.wojtowicz2020_raw">
+<span class="sig-prename descclassname"><span class="pre">pypath.inputs.wojtowicz2020.</span></span><span class="sig-name descname"><span class="pre">wojtowicz2020_raw</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/inputs/wojtowicz2020.html#wojtowicz2020_raw"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.wojtowicz2020.wojtowicz2020_raw" title="Link to this definition">§</a></dt>
+<dd><p>Returns Supplementary Table S4 from 10.1016/j.cell.2020.07.025
+(Wojtowicz et al. 2020) as a list of tuples.</p>
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+  <section id="module-pypath.inputs.zhong2015">
+<span id="pypath-inputs-zhong2015"></span><h1>pypath.inputs.zhong2015<a class="headerlink" href="#module-pypath.inputs.zhong2015" title="Link to this heading">§</a></h1>
+<dl class="field-list simple">
+<dt class="field-odd">members<span class="colon">:</span></dt>
+<dd class="field-odd"><p></p></dd>
+</dl>
+<p class="rubric">Functions</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.inputs.zhong2015.zhong2015_annotations.html#pypath.inputs.zhong2015.zhong2015_annotations" title="pypath.inputs.zhong2015.zhong2015_annotations"><code class="xref py py-obj docutils literal notranslate"><span class="pre">zhong2015_annotations</span></code></a>()</p></td>
+<td><p>From 10.1111/nyas.12776 (PMID 25988664).</p></td>
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diff --git a/api/pypath.inputs.zhong2015.zhong2015_annotations.html b/api/pypath.inputs.zhong2015.zhong2015_annotations.html
new file mode 100644
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+  <section id="pypath-inputs-zhong2015-zhong2015-annotations">
+<h1>pypath.inputs.zhong2015.zhong2015_annotations<a class="headerlink" href="#pypath-inputs-zhong2015-zhong2015-annotations" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.inputs.zhong2015.zhong2015_annotations">
+<span class="sig-prename descclassname"><span class="pre">pypath.inputs.zhong2015.</span></span><span class="sig-name descname"><span class="pre">zhong2015_annotations</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/inputs/zhong2015.html#zhong2015_annotations"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.inputs.zhong2015.zhong2015_annotations" title="Link to this definition">§</a></dt>
+<dd><p>From 10.1111/nyas.12776 (PMID 25988664).</p>
+</dd></dl>
+
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+
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diff --git a/api/pypath.internals.annot_formats.AnnotDef.html b/api/pypath.internals.annot_formats.AnnotDef.html
new file mode 100644
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+                        Release history
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+                        Reference
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+    
+                    <li class="nav-item">
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+                      </a>
+                    </li>
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+                    <li class="nav-item">
+                      <a class="nav-link nav-internal" href="../webservice.html">
+                        Webservice
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+                      <a class="nav-link nav-internal" href="../notebooks/manual.html">
+                        The pypath book
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+                <article class="bd-article">
+                  
+  <section id="pypath-internals-annot-formats-annotdef">
+<h1>pypath.internals.annot_formats.AnnotDef<a class="headerlink" href="#pypath-internals-annot-formats-annotdef" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.internals.annot_formats.AnnotDef">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.internals.annot_formats.</span></span><span class="sig-name descname"><span class="pre">AnnotDef</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resource</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">parent</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">aspect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'functional'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">scope</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'specific'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">source</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'resource_specific'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">args</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">exclude</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">transmitter</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">receiver</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resource_name</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">limit</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">avoid</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">enabled</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/internals/annot_formats.html#AnnotDef"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.internals.annot_formats.AnnotDef" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">AnnotDefBase</span></code></p>
+<p>Annotations are defined by a <code class="docutils literal notranslate"><span class="pre">name</span></code>, a <code class="docutils literal notranslate"><span class="pre">resource</span></code> and an <code class="docutils literal notranslate"><span class="pre">args</span></code>
+parameter. If the former is a string it will be first looked up among the
+annotation resources in <code class="docutils literal notranslate"><span class="pre">pypath.annot.db</span></code>. Otherwise among the keys of
+the classes in the <code class="docutils literal notranslate"><span class="pre">CustomAnnotation</span></code> object or in the dictionary of
+the class_definitions. If <code class="docutils literal notranslate"><span class="pre">source</span></code> is a <cite>set</cite>, it will be used as a
+category without further processing. If it is callable it will be called
+and should return a <cite>set</cite>. If <code class="docutils literal notranslate"><span class="pre">bool(args)</span></code> is <cite>False</cite>, in case of
+annotations in <code class="docutils literal notranslate"><span class="pre">pypath.annot.db</span></code> the <code class="docutils literal notranslate"><span class="pre">to_set</span></code> method will be called.
+Otherwise <code class="docutils literal notranslate"><span class="pre">args</span></code> will be passed to the <code class="docutils literal notranslate"><span class="pre">get_subset</span></code> method.
+If <code class="docutils literal notranslate"><span class="pre">resource</span></code> is callable, <code class="docutils literal notranslate"><span class="pre">args</span></code> will be passed if available.</p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.internals.annot_formats.AnnotDef.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.internals.annot_formats.AnnotDef.__init__" title="Link to this definition">§</a></dt>
+<dd></dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.internals.annot_formats.AnnotDef.__init__" title="pypath.internals.annot_formats.AnnotDef.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.internals.annot_formats.AnnotDef.count" title="pypath.internals.annot_formats.AnnotDef.count"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count</span></code></a>(value, /)</p></td>
+<td><p>Return number of occurrences of value.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.internals.annot_formats.AnnotDef.index" title="pypath.internals.annot_formats.AnnotDef.index"><code class="xref py py-obj docutils literal notranslate"><span class="pre">index</span></code></a>(value[, start, stop])</p></td>
+<td><p>Return first index of value.</p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Attributes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.internals.annot_formats.AnnotDef.args" title="pypath.internals.annot_formats.AnnotDef.args"><code class="xref py py-obj docutils literal notranslate"><span class="pre">args</span></code></a></p></td>
+<td><p>Alias for field number 6</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.internals.annot_formats.AnnotDef.aspect" title="pypath.internals.annot_formats.AnnotDef.aspect"><code class="xref py py-obj docutils literal notranslate"><span class="pre">aspect</span></code></a></p></td>
+<td><p>Alias for field number 3</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.internals.annot_formats.AnnotDef.avoid" title="pypath.internals.annot_formats.AnnotDef.avoid"><code class="xref py py-obj docutils literal notranslate"><span class="pre">avoid</span></code></a></p></td>
+<td><p>Alias for field number 12</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.internals.annot_formats.AnnotDef.enabled" title="pypath.internals.annot_formats.AnnotDef.enabled"><code class="xref py py-obj docutils literal notranslate"><span class="pre">enabled</span></code></a></p></td>
+<td><p>Alias for field number 13</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.internals.annot_formats.AnnotDef.exclude" title="pypath.internals.annot_formats.AnnotDef.exclude"><code class="xref py py-obj docutils literal notranslate"><span class="pre">exclude</span></code></a></p></td>
+<td><p>Alias for field number 7</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">key</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.internals.annot_formats.AnnotDef.limit" title="pypath.internals.annot_formats.AnnotDef.limit"><code class="xref py py-obj docutils literal notranslate"><span class="pre">limit</span></code></a></p></td>
+<td><p>Alias for field number 11</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.internals.annot_formats.AnnotDef.name" title="pypath.internals.annot_formats.AnnotDef.name"><code class="xref py py-obj docutils literal notranslate"><span class="pre">name</span></code></a></p></td>
+<td><p>Alias for field number 0</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.internals.annot_formats.AnnotDef.parent" title="pypath.internals.annot_formats.AnnotDef.parent"><code class="xref py py-obj docutils literal notranslate"><span class="pre">parent</span></code></a></p></td>
+<td><p>Alias for field number 2</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.internals.annot_formats.AnnotDef.receiver" title="pypath.internals.annot_formats.AnnotDef.receiver"><code class="xref py py-obj docutils literal notranslate"><span class="pre">receiver</span></code></a></p></td>
+<td><p>Alias for field number 9</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.internals.annot_formats.AnnotDef.resource" title="pypath.internals.annot_formats.AnnotDef.resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">resource</span></code></a></p></td>
+<td><p>Alias for field number 1</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.internals.annot_formats.AnnotDef.resource_name" title="pypath.internals.annot_formats.AnnotDef.resource_name"><code class="xref py py-obj docutils literal notranslate"><span class="pre">resource_name</span></code></a></p></td>
+<td><p>Alias for field number 10</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.internals.annot_formats.AnnotDef.scope" title="pypath.internals.annot_formats.AnnotDef.scope"><code class="xref py py-obj docutils literal notranslate"><span class="pre">scope</span></code></a></p></td>
+<td><p>Alias for field number 4</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.internals.annot_formats.AnnotDef.source" title="pypath.internals.annot_formats.AnnotDef.source"><code class="xref py py-obj docutils literal notranslate"><span class="pre">source</span></code></a></p></td>
+<td><p>Alias for field number 5</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.internals.annot_formats.AnnotDef.transmitter" title="pypath.internals.annot_formats.AnnotDef.transmitter"><code class="xref py py-obj docutils literal notranslate"><span class="pre">transmitter</span></code></a></p></td>
+<td><p>Alias for field number 8</p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.internals.annot_formats.AnnotDef.args">
+<span class="sig-name descname"><span class="pre">args</span></span><a class="headerlink" href="#pypath.internals.annot_formats.AnnotDef.args" title="Link to this definition">§</a></dt>
+<dd><p>Alias for field number 6</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.internals.annot_formats.AnnotDef.aspect">
+<span class="sig-name descname"><span class="pre">aspect</span></span><a class="headerlink" href="#pypath.internals.annot_formats.AnnotDef.aspect" title="Link to this definition">§</a></dt>
+<dd><p>Alias for field number 3</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.internals.annot_formats.AnnotDef.avoid">
+<span class="sig-name descname"><span class="pre">avoid</span></span><a class="headerlink" href="#pypath.internals.annot_formats.AnnotDef.avoid" title="Link to this definition">§</a></dt>
+<dd><p>Alias for field number 12</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.internals.annot_formats.AnnotDef.count">
+<span class="sig-name descname"><span class="pre">count</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">value</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">/</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.internals.annot_formats.AnnotDef.count" title="Link to this definition">§</a></dt>
+<dd><p>Return number of occurrences of value.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.internals.annot_formats.AnnotDef.enabled">
+<span class="sig-name descname"><span class="pre">enabled</span></span><a class="headerlink" href="#pypath.internals.annot_formats.AnnotDef.enabled" title="Link to this definition">§</a></dt>
+<dd><p>Alias for field number 13</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.internals.annot_formats.AnnotDef.exclude">
+<span class="sig-name descname"><span class="pre">exclude</span></span><a class="headerlink" href="#pypath.internals.annot_formats.AnnotDef.exclude" title="Link to this definition">§</a></dt>
+<dd><p>Alias for field number 7</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.internals.annot_formats.AnnotDef.index">
+<span class="sig-name descname"><span class="pre">index</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">value</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">start</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">stop</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9223372036854775807</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">/</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.internals.annot_formats.AnnotDef.index" title="Link to this definition">§</a></dt>
+<dd><p>Return first index of value.</p>
+<p>Raises ValueError if the value is not present.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.internals.annot_formats.AnnotDef.limit">
+<span class="sig-name descname"><span class="pre">limit</span></span><a class="headerlink" href="#pypath.internals.annot_formats.AnnotDef.limit" title="Link to this definition">§</a></dt>
+<dd><p>Alias for field number 11</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.internals.annot_formats.AnnotDef.name">
+<span class="sig-name descname"><span class="pre">name</span></span><a class="headerlink" href="#pypath.internals.annot_formats.AnnotDef.name" title="Link to this definition">§</a></dt>
+<dd><p>Alias for field number 0</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.internals.annot_formats.AnnotDef.parent">
+<span class="sig-name descname"><span class="pre">parent</span></span><a class="headerlink" href="#pypath.internals.annot_formats.AnnotDef.parent" title="Link to this definition">§</a></dt>
+<dd><p>Alias for field number 2</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.internals.annot_formats.AnnotDef.receiver">
+<span class="sig-name descname"><span class="pre">receiver</span></span><a class="headerlink" href="#pypath.internals.annot_formats.AnnotDef.receiver" title="Link to this definition">§</a></dt>
+<dd><p>Alias for field number 9</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.internals.annot_formats.AnnotDef.resource">
+<span class="sig-name descname"><span class="pre">resource</span></span><a class="headerlink" href="#pypath.internals.annot_formats.AnnotDef.resource" title="Link to this definition">§</a></dt>
+<dd><p>Alias for field number 1</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.internals.annot_formats.AnnotDef.resource_name">
+<span class="sig-name descname"><span class="pre">resource_name</span></span><a class="headerlink" href="#pypath.internals.annot_formats.AnnotDef.resource_name" title="Link to this definition">§</a></dt>
+<dd><p>Alias for field number 10</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.internals.annot_formats.AnnotDef.scope">
+<span class="sig-name descname"><span class="pre">scope</span></span><a class="headerlink" href="#pypath.internals.annot_formats.AnnotDef.scope" title="Link to this definition">§</a></dt>
+<dd><p>Alias for field number 4</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.internals.annot_formats.AnnotDef.source">
+<span class="sig-name descname"><span class="pre">source</span></span><a class="headerlink" href="#pypath.internals.annot_formats.AnnotDef.source" title="Link to this definition">§</a></dt>
+<dd><p>Alias for field number 5</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.internals.annot_formats.AnnotDef.transmitter">
+<span class="sig-name descname"><span class="pre">transmitter</span></span><a class="headerlink" href="#pypath.internals.annot_formats.AnnotDef.transmitter" title="Link to this definition">§</a></dt>
+<dd><p>Alias for field number 8</p>
+</dd></dl>
+
+</dd></dl>
+
+</section>
+
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diff --git a/api/pypath.internals.annot_formats.AnnotDefKey.html b/api/pypath.internals.annot_formats.AnnotDefKey.html
new file mode 100644
index 000000000..a6b91f399
--- /dev/null
+++ b/api/pypath.internals.annot_formats.AnnotDefKey.html
@@ -0,0 +1,703 @@
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+  <section id="pypath-internals-annot-formats-annotdefkey">
+<h1>pypath.internals.annot_formats.AnnotDefKey<a class="headerlink" href="#pypath-internals-annot-formats-annotdefkey" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.internals.annot_formats.AnnotDefKey">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.internals.annot_formats.</span></span><span class="sig-name descname"><span class="pre">AnnotDefKey</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">parent</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resource</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.internals.annot_formats.AnnotDefKey" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">tuple</span></code></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.internals.annot_formats.AnnotDefKey.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.internals.annot_formats.AnnotDefKey.__init__" title="Link to this definition">§</a></dt>
+<dd></dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.internals.annot_formats.AnnotDefKey.__init__" title="pypath.internals.annot_formats.AnnotDefKey.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.internals.annot_formats.AnnotDefKey.count" title="pypath.internals.annot_formats.AnnotDefKey.count"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count</span></code></a>(value, /)</p></td>
+<td><p>Return number of occurrences of value.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.internals.annot_formats.AnnotDefKey.index" title="pypath.internals.annot_formats.AnnotDefKey.index"><code class="xref py py-obj docutils literal notranslate"><span class="pre">index</span></code></a>(value[, start, stop])</p></td>
+<td><p>Return first index of value.</p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Attributes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.internals.annot_formats.AnnotDefKey.name" title="pypath.internals.annot_formats.AnnotDefKey.name"><code class="xref py py-obj docutils literal notranslate"><span class="pre">name</span></code></a></p></td>
+<td><p>Alias for field number 0</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.internals.annot_formats.AnnotDefKey.parent" title="pypath.internals.annot_formats.AnnotDefKey.parent"><code class="xref py py-obj docutils literal notranslate"><span class="pre">parent</span></code></a></p></td>
+<td><p>Alias for field number 1</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.internals.annot_formats.AnnotDefKey.resource" title="pypath.internals.annot_formats.AnnotDefKey.resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">resource</span></code></a></p></td>
+<td><p>Alias for field number 2</p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.internals.annot_formats.AnnotDefKey.count">
+<span class="sig-name descname"><span class="pre">count</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">value</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">/</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.internals.annot_formats.AnnotDefKey.count" title="Link to this definition">§</a></dt>
+<dd><p>Return number of occurrences of value.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.internals.annot_formats.AnnotDefKey.index">
+<span class="sig-name descname"><span class="pre">index</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">value</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">start</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">stop</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9223372036854775807</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">/</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.internals.annot_formats.AnnotDefKey.index" title="Link to this definition">§</a></dt>
+<dd><p>Return first index of value.</p>
+<p>Raises ValueError if the value is not present.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.internals.annot_formats.AnnotDefKey.name">
+<span class="sig-name descname"><span class="pre">name</span></span><a class="headerlink" href="#pypath.internals.annot_formats.AnnotDefKey.name" title="Link to this definition">§</a></dt>
+<dd><p>Alias for field number 0</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.internals.annot_formats.AnnotDefKey.parent">
+<span class="sig-name descname"><span class="pre">parent</span></span><a class="headerlink" href="#pypath.internals.annot_formats.AnnotDefKey.parent" title="Link to this definition">§</a></dt>
+<dd><p>Alias for field number 1</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.internals.annot_formats.AnnotDefKey.resource">
+<span class="sig-name descname"><span class="pre">resource</span></span><a class="headerlink" href="#pypath.internals.annot_formats.AnnotDefKey.resource" title="Link to this definition">§</a></dt>
+<dd><p>Alias for field number 2</p>
+</dd></dl>
+
+</dd></dl>
+
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+  <section id="pypath-internals-annot-formats-annotop">
+<h1>pypath.internals.annot_formats.AnnotOp<a class="headerlink" href="#pypath-internals-annot-formats-annotop" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.internals.annot_formats.AnnotOp">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.internals.annot_formats.</span></span><span class="sig-name descname"><span class="pre">AnnotOp</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">annots</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">op=&lt;method</span> <span class="pre">'union'</span> <span class="pre">of</span> <span class="pre">'set'</span> <span class="pre">objects&gt;</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/internals/annot_formats.html#AnnotOp"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.internals.annot_formats.AnnotOp" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">AnnotOpBase</span></code></p>
+<p>Annotation operations consist of list of annotation definitions or names as
+they can be looked up in the <code class="docutils literal notranslate"><span class="pre">class_definitions</span></code> of the
+<code class="docutils literal notranslate"><span class="pre">CustomAnnotation</span></code> object and an operator to be called on the sets
+(union, intersection or difference).</p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.internals.annot_formats.AnnotOp.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.internals.annot_formats.AnnotOp.__init__" title="Link to this definition">§</a></dt>
+<dd></dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.internals.annot_formats.AnnotOp.__init__" title="pypath.internals.annot_formats.AnnotOp.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.internals.annot_formats.AnnotOp.count" title="pypath.internals.annot_formats.AnnotOp.count"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count</span></code></a>(value, /)</p></td>
+<td><p>Return number of occurrences of value.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.internals.annot_formats.AnnotOp.index" title="pypath.internals.annot_formats.AnnotOp.index"><code class="xref py py-obj docutils literal notranslate"><span class="pre">index</span></code></a>(value[, start, stop])</p></td>
+<td><p>Return first index of value.</p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Attributes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.internals.annot_formats.AnnotOp.annots" title="pypath.internals.annot_formats.AnnotOp.annots"><code class="xref py py-obj docutils literal notranslate"><span class="pre">annots</span></code></a></p></td>
+<td><p>Alias for field number 0</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.internals.annot_formats.AnnotOp.op" title="pypath.internals.annot_formats.AnnotOp.op"><code class="xref py py-obj docutils literal notranslate"><span class="pre">op</span></code></a></p></td>
+<td><p>Alias for field number 1</p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.internals.annot_formats.AnnotOp.annots">
+<span class="sig-name descname"><span class="pre">annots</span></span><a class="headerlink" href="#pypath.internals.annot_formats.AnnotOp.annots" title="Link to this definition">§</a></dt>
+<dd><p>Alias for field number 0</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.internals.annot_formats.AnnotOp.count">
+<span class="sig-name descname"><span class="pre">count</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">value</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">/</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.internals.annot_formats.AnnotOp.count" title="Link to this definition">§</a></dt>
+<dd><p>Return number of occurrences of value.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.internals.annot_formats.AnnotOp.index">
+<span class="sig-name descname"><span class="pre">index</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">value</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">start</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">stop</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9223372036854775807</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">/</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.internals.annot_formats.AnnotOp.index" title="Link to this definition">§</a></dt>
+<dd><p>Return first index of value.</p>
+<p>Raises ValueError if the value is not present.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.internals.annot_formats.AnnotOp.op">
+<span class="sig-name descname"><span class="pre">op</span></span><a class="headerlink" href="#pypath.internals.annot_formats.AnnotOp.op" title="Link to this definition">§</a></dt>
+<dd><p>Alias for field number 1</p>
+</dd></dl>
+
+</dd></dl>
+
+</section>
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+  <section id="pypath-internals-annot-formats-annotationgroup">
+<h1>pypath.internals.annot_formats.AnnotationGroup<a class="headerlink" href="#pypath-internals-annot-formats-annotationgroup" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.internals.annot_formats.AnnotationGroup">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.internals.annot_formats.</span></span><span class="sig-name descname"><span class="pre">AnnotationGroup</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">members</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">name</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">parent</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">aspect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'functional'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">source</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'resource_specific'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">scope</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'specific'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resource</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">transmitter</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">receiver</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">limit</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">avoid</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">enabled</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/internals/annot_formats.html#AnnotationGroup"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.internals.annot_formats.AnnotationGroup" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">Set</span></code></p>
+<p>Represents a set of molecular entities sharing a custom defined
+annotation. This class behaves like a <code class="docutils literal notranslate"><span class="pre">set</span></code> and set operations on it
+result set objects. Normally this class is instantiated by
+<code class="docutils literal notranslate"><span class="pre">pypath.core.annot.CustomAnnotation</span></code> in the process of populating
+categories and the contents of the groups defined in
+<code class="docutils literal notranslate"><span class="pre">pypath.core.intercell_annot</span></code> in case of annotations of the
+intercellular communication roles.
+For detailed definitions of the parameter values see the Supplementary
+Table S10 in Turei et al. 2020 (in prep).</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>members</strong> (<em>list</em><em>,</em><em>set</em><em>,</em><em>tuple</em>) – The identifiers of the entities in the category.</p></li>
+<li><p><strong>name</strong> (<em>str</em>) – The name of the category.</p></li>
+<li><p><strong>parent</strong> (<em>str</em>) – The name of the parent category; might be the same as <code class="docutils literal notranslate"><span class="pre">name</span></code> in
+case of high level (generic) categories.</p></li>
+<li><p><strong>aspect</strong> (<em>str</em>) – Either <em>functional</em> or <em>locational</em>.</p></li>
+<li><p><strong>source</strong> (<em>str</em>) – Either <em>resource_specific</em> or <em>composite</em>.</p></li>
+<li><p><strong>scope</strong> (<em>str</em>) – Either <em>specific</em> or <em>generic</em>.</p></li>
+<li><p><strong>resource</strong> (<em>str</em>) – The resource (database) name; in case of composite categories it
+should be the name of the database you are actually building, this
+by default is <cite>OmniPath</cite> and you can change by the
+<code class="docutils literal notranslate"><span class="pre">pypath.share.settings</span></code> module using the
+<code class="docutils literal notranslate"><span class="pre">annot_composite_database_name</span></code> key.</p></li>
+<li><p><strong>transmitter</strong> (<em>bool</em>) – Whether the category contains transmitters of signaling information
+from the cell expressing the molecular entities in direction of other
+cells.</p></li>
+<li><p><strong>receiver</strong> (<em>bool</em>) – Whether the category contains receivers of signaling information
+from other cells in direction of the cells expressing the molecular
+entites in the category.</p></li>
+<li><p><strong>limit</strong> (<em>str</em><em>,</em><em>set</em>) – Limit to this or these categories. E.g. if it’s ‘extracellular’
+the result will be the intersection of this category and
+‘extracellular’ i.e. the category will be limited to extracellular
+proteins.</p></li>
+<li><p><strong>avoid</strong> (<em>str</em><em>,</em><em>set</em>) – Avoid elements of this or these categories. E.g. if it’s
+‘cell_surface’ then all cell_surface proteins will be removed from
+this category.</p></li>
+</ul>
+</dd>
+</dl>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.internals.annot_formats.AnnotationGroup.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">members</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">name</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">parent</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">aspect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'functional'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">source</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'resource_specific'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">scope</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'specific'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resource</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">transmitter</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">receiver</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">limit</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">avoid</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">enabled</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/internals/annot_formats.html#AnnotationGroup.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.internals.annot_formats.AnnotationGroup.__init__" title="Link to this definition">§</a></dt>
+<dd></dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.internals.annot_formats.AnnotationGroup.__init__" title="pypath.internals.annot_formats.AnnotationGroup.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>(members[, name, parent, aspect, ...])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">count_entity_type</span></code>([entity_type])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">difference</span></code>(*args)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.internals.annot_formats.AnnotationGroup.filter_entity_type" title="pypath.internals.annot_formats.AnnotationGroup.filter_entity_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">filter_entity_type</span></code></a>([entity_type])</p></td>
+<td><p>Returns a copy of the group with only the selected entity types.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">intersection</span></code>(*args)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.internals.annot_formats.AnnotationGroup.isdisjoint" title="pypath.internals.annot_formats.AnnotationGroup.isdisjoint"><code class="xref py py-obj docutils literal notranslate"><span class="pre">isdisjoint</span></code></a>(*args)</p></td>
+<td><p>Return True if two sets have a null intersection.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">keys</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">sets</span></code>(*args)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">symmetric_difference</span></code>(*args)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">union</span></code>(*args)</p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Attributes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">args</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">complexes</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">key</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">label</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">mirnas</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">n_complexes</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">n_mirnas</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">n_proteins</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">name_label</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">proteins</span></code></p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.internals.annot_formats.AnnotationGroup.filter_entity_type">
+<span class="sig-name descname"><span class="pre">filter_entity_type</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/internals/annot_formats.html#AnnotationGroup.filter_entity_type"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.internals.annot_formats.AnnotationGroup.filter_entity_type" title="Link to this definition">§</a></dt>
+<dd><p>Returns a copy of the group with only the selected entity types.
+If <code class="docutils literal notranslate"><span class="pre">entity_type</span></code> is None returns the object itself.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.internals.annot_formats.AnnotationGroup.isdisjoint">
+<em class="property"><span class="pre">classmethod</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">isdisjoint</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">*</span></span><span class="n"><span class="pre">args</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/internals/annot_formats.html#AnnotationGroup.isdisjoint"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.internals.annot_formats.AnnotationGroup.isdisjoint" title="Link to this definition">§</a></dt>
+<dd><p>Return True if two sets have a null intersection.</p>
+</dd></dl>
+
+</dd></dl>
+
+</section>
+
+
+                </article>
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+  <section id="module-pypath.internals.annot_formats">
+<span id="pypath-internals-annot-formats"></span><h1>pypath.internals.annot_formats<a class="headerlink" href="#module-pypath.internals.annot_formats" title="Link to this heading">§</a></h1>
+<dl class="field-list simple">
+<dt class="field-odd">members<span class="colon">:</span></dt>
+<dd class="field-odd"><p></p></dd>
+</dl>
+<p class="rubric">Classes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.internals.annot_formats.AnnotDef.html#pypath.internals.annot_formats.AnnotDef" title="pypath.internals.annot_formats.AnnotDef"><code class="xref py py-obj docutils literal notranslate"><span class="pre">AnnotDef</span></code></a>(name, resource[, parent, aspect, ...])</p></td>
+<td><p>Annotations are defined by a <code class="docutils literal notranslate"><span class="pre">name</span></code>, a <code class="docutils literal notranslate"><span class="pre">resource</span></code> and an <code class="docutils literal notranslate"><span class="pre">args</span></code> parameter.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.internals.annot_formats.AnnotDefKey.html#pypath.internals.annot_formats.AnnotDefKey" title="pypath.internals.annot_formats.AnnotDefKey"><code class="xref py py-obj docutils literal notranslate"><span class="pre">AnnotDefKey</span></code></a>(name, parent, resource)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.internals.annot_formats.AnnotOp.html#pypath.internals.annot_formats.AnnotOp" title="pypath.internals.annot_formats.AnnotOp"><code class="xref py py-obj docutils literal notranslate"><span class="pre">AnnotOp</span></code></a>(annots[, op])</p></td>
+<td><p>Annotation operations consist of list of annotation definitions or names as they can be looked up in the <code class="docutils literal notranslate"><span class="pre">class_definitions</span></code> of the <code class="docutils literal notranslate"><span class="pre">CustomAnnotation</span></code> object and an operator to be called on the sets (union, intersection or difference).</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.internals.annot_formats.AnnotationGroup.html#pypath.internals.annot_formats.AnnotationGroup" title="pypath.internals.annot_formats.AnnotationGroup"><code class="xref py py-obj docutils literal notranslate"><span class="pre">AnnotationGroup</span></code></a>(members[, name, parent, ...])</p></td>
+<td><p>Represents a set of molecular entities sharing a custom defined annotation.</p></td>
+</tr>
+</tbody>
+</table>
+</section>
+
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diff --git a/api/pypath.internals.html b/api/pypath.internals.html
index fb9b2d387..9c8601964 100644
--- a/api/pypath.internals.html
+++ b/api/pypath.internals.html
@@ -47,8 +47,8 @@
     <link rel="icon" href="../_static/omnipath-logo.svg"/>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
-    <link rel="next" title="pypath.internals.input_formats" href="pypath.internals.input_formats.html" />
-    <link rel="prev" title="pypath.inputs.uniprot_db.is_uniprot" href="pypath.inputs.uniprot_db.is_uniprot.html" />
+    <link rel="next" title="pypath.internals.annot_formats" href="pypath.internals.annot_formats.html" />
+    <link rel="prev" title="pypath.inputs.zhong2015.zhong2015_annotations" href="pypath.inputs.zhong2015.zhong2015_annotations.html" />
   <meta name="viewport" content="width=device-width, initial-scale=1"/>
   <meta name="docsearch:language" content="en"/>
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@@ -519,9 +519,15 @@
 <p class="rubric">Modules</p>
 <table class="autosummary longtable table autosummary">
 <tbody>
-<tr class="row-odd"><td><p><a class="reference internal" href="pypath.internals.input_formats.html#module-pypath.internals.input_formats" title="pypath.internals.input_formats"><code class="xref py py-obj docutils literal notranslate"><span class="pre">pypath.internals.input_formats</span></code></a></p></td>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.internals.annot_formats.html#module-pypath.internals.annot_formats" title="pypath.internals.annot_formats"><code class="xref py py-obj docutils literal notranslate"><span class="pre">pypath.internals.annot_formats</span></code></a></p></td>
 <td><p></p></td>
 </tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.internals.input_formats.html#module-pypath.internals.input_formats" title="pypath.internals.input_formats"><code class="xref py py-obj docutils literal notranslate"><span class="pre">pypath.internals.input_formats</span></code></a></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.internals.intera.html#module-pypath.internals.intera" title="pypath.internals.intera"><code class="xref py py-obj docutils literal notranslate"><span class="pre">pypath.internals.intera</span></code></a></p></td>
+<td><p>This module provides classes to represent and handle structural details of protein interactions i.e. residues, post-translational modifications, short motifs, domains, domain-motifs and domain-motif interactions, binding interfaces.</p></td>
+</tr>
 <tr class="row-even"><td><p><a class="reference internal" href="pypath.internals.license.html#module-pypath.internals.license" title="pypath.internals.license"><code class="xref py py-obj docutils literal notranslate"><span class="pre">pypath.internals.license</span></code></a></p></td>
 <td><p></p></td>
 </tr>
@@ -549,20 +555,20 @@
                   
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+       href="pypath.inputs.zhong2015.zhong2015_annotations.html"
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-        <p class="prev-next-title">pypath.inputs.uniprot_db.is_uniprot</p>
+        <p class="prev-next-title">pypath.inputs.zhong2015.zhong2015_annotations</p>
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diff --git a/api/pypath.internals.input_formats.UniprotMapping.html b/api/pypath.internals.input_formats.UniprotMapping.html
index 416e4b7a5..89168992b 100644
--- a/api/pypath.internals.input_formats.UniprotMapping.html
+++ b/api/pypath.internals.input_formats.UniprotMapping.html
@@ -47,7 +47,7 @@
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+    <link rel="next" title="pypath.internals.intera" href="pypath.internals.intera.html" />
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   <meta name="viewport" content="width=device-width, initial-scale=1"/>
   <meta name="docsearch:language" content="en"/>
@@ -615,11 +615,11 @@ <h1>pypath.internals.input_formats.UniprotMapping<a class="headerlink" href="#py
       </div>
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-        <p class="prev-next-title">pypath.internals.license</p>
+        <p class="prev-next-title">pypath.internals.intera</p>
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diff --git a/api/pypath.internals.input_formats.html b/api/pypath.internals.input_formats.html
index c967cf429..0fc3a25f7 100644
--- a/api/pypath.internals.input_formats.html
+++ b/api/pypath.internals.input_formats.html
@@ -48,7 +48,7 @@
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-    <link rel="prev" title="pypath.internals" href="pypath.internals.html" />
+    <link rel="prev" title="pypath.internals.annot_formats.AnnotationGroup" href="pypath.internals.annot_formats.AnnotationGroup.html" />
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@@ -578,12 +578,12 @@
                   
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+       href="pypath.internals.annot_formats.AnnotationGroup.html"
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+        <p class="prev-next-title">pypath.internals.annot_formats.AnnotationGroup</p>
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@@ -0,0 +1,743 @@
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+  <section id="pypath-internals-intera-complex">
+<h1>pypath.internals.intera.Complex<a class="headerlink" href="#pypath-internals-intera-complex" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.internals.intera.Complex">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.internals.intera.</span></span><span class="sig-name descname"><span class="pre">Complex</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">components</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">name</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ids</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">sources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interactions</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">proteins</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">attrs</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/internals/intera.html#Complex"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.internals.intera.Complex" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.internals.intera.Complex.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">components</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">name</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ids</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">sources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">interactions</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">references</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">proteins</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">attrs</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/internals/intera.html#Complex.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.internals.intera.Complex.__init__" title="Link to this definition">§</a></dt>
+<dd><p>Represents a molecular complex.</p>
+<dl class="simple">
+<dt>components<span class="classifier">list,dict</span></dt><dd><p>Either a list of identifiers or a dict with identifiers as keys
+and stoichiometric coefficients as values. List of identifiers
+also assumed to represent stoichiometry by repetition
+of identifiers.</p>
+</dd>
+<dt>ncbi_tax_id<span class="classifier">int</span></dt><dd><p>NCBI taxonomy identifier of the complex. It implies all members
+of the complex belong to the same organism. Support for multi-
+organism complexes will be implemented in the future.</p>
+</dd>
+<dt>name<span class="classifier">str</span></dt><dd><p>A custom name or identifier of the complex.</p>
+</dd>
+<dt>ids<span class="classifier">dict</span></dt><dd><p>Identifiers. If <code class="docutils literal notranslate"><span class="pre">sources</span></code> is a set, list or tuple it should be
+a dict with database names as keys and set of identifiers as
+values. If <code class="docutils literal notranslate"><span class="pre">sources</span></code> is a string, it can be a set of
+identifiers or a single identifier.</p>
+</dd>
+<dt>sources<span class="classifier">set,str</span></dt><dd><p>Database(s) the complex has been defined in.</p>
+</dd>
+<dt>interactions<span class="classifier">list,dict</span></dt><dd><p>Interactions between the components of the complex. Either
+a list of tuples of component IDs or a dict with tuples as
+keys and custom interaction properties as values.</p>
+</dd>
+<dt>proteins<span class="classifier">list,dict</span></dt><dd><p>Synonym for <cite>components</cite>, kept for compatibility.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.internals.intera.Complex.__init__" title="pypath.internals.intera.Complex.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>(components[, ncbi_tax_id, name, ...])</p></td>
+<td><p>Represents a molecular complex.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.internals.intera.Complex.add_attr" title="pypath.internals.intera.Complex.add_attr"><code class="xref py py-obj docutils literal notranslate"><span class="pre">add_attr</span></code></a>(source, attr)</p></td>
+<td><p>Attributes can store annotations for complexes.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">add_ids</span></code>(ids[, source])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">add_source</span></code>(source)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_interaction</span></code>(component1, component2)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_interaction</span></code>(component1, component2)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">iter_proteins</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.internals.intera.Complex.merge" title="pypath.internals.intera.Complex.merge"><code class="xref py py-obj docutils literal notranslate"><span class="pre">merge</span></code></a>(other)</p></td>
+<td><p>Adds the annotations (sources, references, attrs) of the other <code class="docutils literal notranslate"><span class="pre">Complex</span></code> instance to this one.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">reload</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_interaction</span></code>(component1, component2, ...)</p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Attributes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">genesymbol_str</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">genesymbols</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">have_stoichiometry</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">stoichiometry</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">stoichiometry_str</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">stoichiometry_str_genesymbols</span></code></p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.internals.intera.Complex.add_attr">
+<span class="sig-name descname"><span class="pre">add_attr</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">source</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">attr</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/internals/intera.html#Complex.add_attr"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.internals.intera.Complex.add_attr" title="Link to this definition">§</a></dt>
+<dd><p>Attributes can store annotations for complexes.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.internals.intera.Complex.merge">
+<span class="sig-name descname"><span class="pre">merge</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">other</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/internals/intera.html#Complex.merge"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.internals.intera.Complex.merge" title="Link to this definition">§</a></dt>
+<dd><p>Adds the annotations (sources, references, attrs) of the other
+<code class="docutils literal notranslate"><span class="pre">Complex</span></code> instance to this one. If the other <code class="docutils literal notranslate"><span class="pre">Complex</span></code> has
+different components it does nothing.</p>
+</dd></dl>
+
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+                  
+  <section id="pypath-internals-intera-domain">
+<h1>pypath.internals.intera.Domain<a class="headerlink" href="#pypath-internals-intera-domain" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.internals.intera.Domain">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.internals.intera.</span></span><span class="sig-name descname"><span class="pre">Domain</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">protein</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">id_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'uniprot'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">domain</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">domain_id_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'pfam'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">start</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">end</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">isoform</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">chains</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">{}</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/internals/intera.html#Domain"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.internals.intera.Domain" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.internals.intera.Domain.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">protein</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">id_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'uniprot'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">domain</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">domain_id_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'pfam'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">start</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">end</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">isoform</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">chains</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">{}</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/internals/intera.html#Domain.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.internals.intera.Domain.__init__" title="Link to this definition">§</a></dt>
+<dd></dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.internals.intera.Domain.__init__" title="pypath.internals.intera.Domain.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>(protein[, id_type, ncbi_tax_id, ...])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">add_chains</span></code>(pdb, chain)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_position</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_position</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">merge</span></code>(other)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">range</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">range_str</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">serialize</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+</section>
+
+
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+  <section id="pypath-internals-intera-domaindomain">
+<h1>pypath.internals.intera.DomainDomain<a class="headerlink" href="#pypath-internals-intera-domaindomain" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.internals.intera.DomainDomain">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.internals.intera.</span></span><span class="sig-name descname"><span class="pre">DomainDomain</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">domain_a</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">domain_b</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">pdbs</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">sources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">refs</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">contact_residues</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/internals/intera.html#DomainDomain"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.internals.intera.DomainDomain" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.internals.intera.DomainDomain.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">domain_a</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">domain_b</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">pdbs</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">sources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">refs</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">contact_residues</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/internals/intera.html#DomainDomain.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.internals.intera.DomainDomain.__init__" title="Link to this definition">§</a></dt>
+<dd></dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.internals.intera.DomainDomain.__init__" title="pypath.internals.intera.DomainDomain.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>(domain_a, domain_b[, pdbs, ...])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">add_pdbs</span></code>(pdbs)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">add_refs</span></code>(refs)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">add_sources</span></code>(source)</p></td>
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+  <section id="pypath-internals-intera-domainmotif">
+<h1>pypath.internals.intera.DomainMotif<a class="headerlink" href="#pypath-internals-intera-domainmotif" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.internals.intera.DomainMotif">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.internals.intera.</span></span><span class="sig-name descname"><span class="pre">DomainMotif</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">domain</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ptm</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">evidences</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">pdbs</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/internals/intera.html#DomainMotif"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.internals.intera.DomainMotif" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.internals.intera.DomainMotif.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">domain</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ptm</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">evidences</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">pdbs</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/internals/intera.html#DomainMotif.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.internals.intera.DomainMotif.__init__" title="Link to this definition">§</a></dt>
+<dd></dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.internals.intera.DomainMotif.__init__" title="pypath.internals.intera.DomainMotif.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>(domain, ptm[, evidences, pdbs])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">add_evidences</span></code>(evidences)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">add_pdbs</span></code>(pdbs)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.internals.intera.DomainMotif.get_line" title="pypath.internals.intera.DomainMotif.get_line"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_line</span></code></a>([resources_only_primary])</p></td>
+<td><p>Returns a list intended to be a row in a data frame of enzyme-substrate relationships.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_proteins</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.internals.intera.DomainMotif.key" title="pypath.internals.intera.DomainMotif.key"><code class="xref py py-obj docutils literal notranslate"><span class="pre">key</span></code></a>()</p></td>
+<td><p>Returns a unique key which is a tuple of the proteins, the residue and the modification type.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">merge</span></code>(other)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">print_residues</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">references</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">references_by_resource</span></code>([only_primary])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">references_by_resource_str</span></code>([only_primary])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">resources</span></code>([only_primary])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">serialize</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.internals.intera.DomainMotif.get_line">
+<span class="sig-name descname"><span class="pre">get_line</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">resources_only_primary</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/internals/intera.html#DomainMotif.get_line"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.internals.intera.DomainMotif.get_line" title="Link to this definition">§</a></dt>
+<dd><p>Returns a list intended to be a row in a data frame of
+enzyme-substrate relationships.</p>
+<dl class="simple">
+<dt>Elements of the list:</dt><dd><ul class="simple">
+<li><p>enzyme</p></li>
+<li><p>enzyme_genesymbol</p></li>
+<li><p>substrate</p></li>
+<li><p>substrate_genesymbol</p></li>
+<li><p>isoforms</p></li>
+<li><p>residue_type</p></li>
+<li><p>residue_offset</p></li>
+<li><p>modification</p></li>
+<li><p>sources</p></li>
+<li><p>references</p></li>
+<li><p>curation_effort</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.internals.intera.DomainMotif.key">
+<span class="sig-name descname"><span class="pre">key</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/internals/intera.html#DomainMotif.key"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.internals.intera.DomainMotif.key" title="Link to this definition">§</a></dt>
+<dd><p>Returns a unique key which is a tuple of the proteins, the residue
+and the modification type.</p>
+</dd></dl>
+
+</dd></dl>
+
+</section>
+
+
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+  <section id="pypath-internals-intera-interface">
+<h1>pypath.internals.intera.Interface<a class="headerlink" href="#pypath-internals-intera-interface" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.internals.intera.Interface">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.internals.intera.</span></span><span class="sig-name descname"><span class="pre">Interface</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">id_a</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">id_b</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">source</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">id_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'uniprot'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">pdb</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">css</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">stab_en</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">solv_en</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">area</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">isoform_a</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">isoform_b</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/internals/intera.html#Interface"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.internals.intera.Interface" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.internals.intera.Interface.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">id_a</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">id_b</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">source</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">id_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'uniprot'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">pdb</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">css</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">stab_en</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">solv_en</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">area</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">isoform_a</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">isoform_b</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/internals/intera.html#Interface.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.internals.intera.Interface.__init__" title="Link to this definition">§</a></dt>
+<dd><p>This class is to store residue level information of
+protein-protein interfaces.</p>
+</dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.internals.intera.Interface.__init__" title="pypath.internals.intera.Interface.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>(id_a, id_b, source[, id_type, pdb, ...])</p></td>
+<td><p>This class is to store residue level information of protein-protein interfaces.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.internals.intera.Interface.add_residues" title="pypath.internals.intera.Interface.add_residues"><code class="xref py py-obj docutils literal notranslate"><span class="pre">add_residues</span></code></a>(res_a, res_b[, typ])</p></td>
+<td><p>Adds one pair of residues of type <cite>typ</cite>, where <cite>res_a</cite> and <cite>res_b</cite> are tuples of residue number in sequence and residue type, e.g. (124, 'S') -- (means Serine #124) <cite>typ</cite> can be undefined, hbonds, sbridges, ssbonds or covbonds.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.internals.intera.Interface.bond_types" title="pypath.internals.intera.Interface.bond_types"><code class="xref py py-obj docutils literal notranslate"><span class="pre">bond_types</span></code></a>()</p></td>
+<td><p>Returns the bond types present in this interface</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.internals.intera.Interface.get_bonds" title="pypath.internals.intera.Interface.get_bonds"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_bonds</span></code></a>([typ, mode])</p></td>
+<td><p>Gives a generator to iterate throught bonds in this interface.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.internals.intera.Interface.numof_residues" title="pypath.internals.intera.Interface.numof_residues"><code class="xref py py-obj docutils literal notranslate"><span class="pre">numof_residues</span></code></a>()</p></td>
+<td><p>Returns the number of residue pairs by bound type</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">serialize</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.internals.intera.Interface.add_residues">
+<span class="sig-name descname"><span class="pre">add_residues</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">res_a</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">res_b</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">typ</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'undefined'</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/internals/intera.html#Interface.add_residues"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.internals.intera.Interface.add_residues" title="Link to this definition">§</a></dt>
+<dd><p>Adds one pair of residues of type <cite>typ</cite>,
+where <cite>res_a</cite> and <cite>res_b</cite> are tuples of
+residue number in sequence and residue type,
+e.g. (124, ‘S’) – (means Serine #124)
+<cite>typ</cite> can be undefined, hbonds, sbridges, ssbonds or covbonds</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.internals.intera.Interface.bond_types">
+<span class="sig-name descname"><span class="pre">bond_types</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/internals/intera.html#Interface.bond_types"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.internals.intera.Interface.bond_types" title="Link to this definition">§</a></dt>
+<dd><p>Returns the bond types present in this interface</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.internals.intera.Interface.get_bonds">
+<span class="sig-name descname"><span class="pre">get_bonds</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">typ</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">mode</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/internals/intera.html#Interface.get_bonds"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.internals.intera.Interface.get_bonds" title="Link to this definition">§</a></dt>
+<dd><p>Gives a generator to iterate throught bonds in
+this interface. If no type given, bonds of all types
+returned.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.internals.intera.Interface.numof_residues">
+<span class="sig-name descname"><span class="pre">numof_residues</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/internals/intera.html#Interface.numof_residues"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.internals.intera.Interface.numof_residues" title="Link to this definition">§</a></dt>
+<dd><p>Returns the number of residue pairs by bound type</p>
+</dd></dl>
+
+</dd></dl>
+
+</section>
+
+
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+  <section id="pypath-internals-intera-motif">
+<h1>pypath.internals.intera.Motif<a class="headerlink" href="#pypath-internals-intera-motif" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.internals.intera.Motif">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.internals.intera.</span></span><span class="sig-name descname"><span class="pre">Motif</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">protein</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">start</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">end</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">id_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'uniprot'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">regex</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">instance</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">isoform</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">motif_name</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">prob</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">elm</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">description</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">seq</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">evidences</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/internals/intera.html#Motif"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.internals.intera.Motif" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.internals.intera.Motif.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">protein</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">start</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">end</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">id_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'uniprot'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">regex</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">instance</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">isoform</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">motif_name</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">prob</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">elm</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">description</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">seq</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">evidences</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/internals/intera.html#Motif.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.internals.intera.Motif.__init__" title="Link to this definition">§</a></dt>
+<dd></dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.internals.intera.Motif.__init__" title="pypath.internals.intera.Motif.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>(protein, start, end[, id_type, ...])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">add_evidences</span></code>(evidences)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">in_isoform</span></code>(isoform[, seq])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">merge</span></code>(other)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">print_residues</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">range</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">range_str</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">serialize</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+</tbody>
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+  <section id="pypath-internals-intera-ptm">
+<h1>pypath.internals.intera.Ptm<a class="headerlink" href="#pypath-internals-intera-ptm" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.internals.intera.Ptm">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.internals.intera.</span></span><span class="sig-name descname"><span class="pre">Ptm</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">protein</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">id_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'uniprot'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">typ</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'unknown'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">motif</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">residue</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">isoform</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">evidences</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">seq</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/internals/intera.html#Ptm"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.internals.intera.Ptm" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.internals.intera.Ptm.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">protein</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">id_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'uniprot'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">typ</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'unknown'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">motif</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">residue</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">isoform</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">evidences</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">seq</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/internals/intera.html#Ptm.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.internals.intera.Ptm.__init__" title="Link to this definition">§</a></dt>
+<dd></dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.internals.intera.Ptm.__init__" title="pypath.internals.intera.Ptm.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>(protein[, id_type, ncbi_tax_id, ...])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">add_evidences</span></code>(evidences)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">add_isoform</span></code>(isoform)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_isoforms</span></code>([seq])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">in_isoform</span></code>(isoform[, seq])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">merge</span></code>(other)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">print_residue</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">serialize</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+</tbody>
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+  <section id="pypath-internals-intera-regulation">
+<h1>pypath.internals.intera.Regulation<a class="headerlink" href="#pypath-internals-intera-regulation" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.internals.intera.Regulation">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.internals.intera.</span></span><span class="sig-name descname"><span class="pre">Regulation</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">ptm</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">source</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">target</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">effect</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">sources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">refs</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/internals/intera.html#Regulation"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.internals.intera.Regulation" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.internals.intera.Regulation.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">ptm</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">source</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">target</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">effect</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">sources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">refs</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/internals/intera.html#Regulation.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.internals.intera.Regulation.__init__" title="Link to this definition">§</a></dt>
+<dd></dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.internals.intera.Regulation.__init__" title="pypath.internals.intera.Regulation.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>(ptm, source, target, effect[, ...])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">add_refs</span></code>(refs)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">add_sources</span></code>(source)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">merge</span></code>(other)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">serialize</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+</section>
+
+
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+  <section id="pypath-internals-intera-residue">
+<h1>pypath.internals.intera.Residue<a class="headerlink" href="#pypath-internals-intera-residue" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.internals.intera.Residue">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.internals.intera.</span></span><span class="sig-name descname"><span class="pre">Residue</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">number</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">protein</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">id_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'uniprot'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">isoform</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">mutated</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">seq</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/internals/intera.html#Residue"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.internals.intera.Residue" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.internals.intera.Residue.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">number</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">protein</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">id_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'uniprot'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">isoform</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">mutated</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">seq</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/internals/intera.html#Residue.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.internals.intera.Residue.__init__" title="Link to this definition">§</a></dt>
+<dd></dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.internals.intera.Residue.__init__" title="pypath.internals.intera.Residue.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>(number, name, protein[, id_type, ...])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">in_isoform</span></code>(isoform[, seq])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">serialize</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
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+  <section id="module-pypath.internals.intera">
+<span id="pypath-internals-intera"></span><h1>pypath.internals.intera<a class="headerlink" href="#module-pypath.internals.intera" title="Link to this heading">§</a></h1>
+<p>This module provides classes to represent and handle
+structural details of protein interactions
+i.e. residues, post-translational modifications,
+short motifs, domains, domain-motifs and
+domain-motif interactions, binding interfaces.</p>
+<dl class="field-list simple">
+<dt class="field-odd">members<span class="colon">:</span></dt>
+<dd class="field-odd"><p></p></dd>
+</dl>
+<p class="rubric">Classes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.internals.intera.Complex.html#pypath.internals.intera.Complex" title="pypath.internals.intera.Complex"><code class="xref py py-obj docutils literal notranslate"><span class="pre">Complex</span></code></a>(components[, ncbi_tax_id, name, ...])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.internals.intera.Domain.html#pypath.internals.intera.Domain" title="pypath.internals.intera.Domain"><code class="xref py py-obj docutils literal notranslate"><span class="pre">Domain</span></code></a>(protein[, id_type, ncbi_tax_id, ...])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.internals.intera.DomainDomain.html#pypath.internals.intera.DomainDomain" title="pypath.internals.intera.DomainDomain"><code class="xref py py-obj docutils literal notranslate"><span class="pre">DomainDomain</span></code></a>(domain_a, domain_b[, pdbs, ...])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.internals.intera.DomainMotif.html#pypath.internals.intera.DomainMotif" title="pypath.internals.intera.DomainMotif"><code class="xref py py-obj docutils literal notranslate"><span class="pre">DomainMotif</span></code></a>(domain, ptm[, evidences, pdbs])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.internals.intera.Interface.html#pypath.internals.intera.Interface" title="pypath.internals.intera.Interface"><code class="xref py py-obj docutils literal notranslate"><span class="pre">Interface</span></code></a>(id_a, id_b, source[, id_type, ...])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.internals.intera.Motif.html#pypath.internals.intera.Motif" title="pypath.internals.intera.Motif"><code class="xref py py-obj docutils literal notranslate"><span class="pre">Motif</span></code></a>(protein, start, end[, id_type, ...])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.internals.intera.Ptm.html#pypath.internals.intera.Ptm" title="pypath.internals.intera.Ptm"><code class="xref py py-obj docutils literal notranslate"><span class="pre">Ptm</span></code></a>(protein[, id_type, ncbi_tax_id, typ, ...])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.internals.intera.Regulation.html#pypath.internals.intera.Regulation" title="pypath.internals.intera.Regulation"><code class="xref py py-obj docutils literal notranslate"><span class="pre">Regulation</span></code></a>(ptm, source, target, effect[, ...])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.internals.intera.Residue.html#pypath.internals.intera.Residue" title="pypath.internals.intera.Residue"><code class="xref py py-obj docutils literal notranslate"><span class="pre">Residue</span></code></a>(number, name, protein[, id_type, ...])</p></td>
+<td><p></p></td>
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diff --git a/api/pypath.internals.license.html b/api/pypath.internals.license.html
index f9be9485b..7b1e97f05 100644
--- a/api/pypath.internals.license.html
+++ b/api/pypath.internals.license.html
@@ -48,7 +48,7 @@
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
     <link rel="next" title="pypath.internals.license.License" href="pypath.internals.license.License.html" />
-    <link rel="prev" title="pypath.internals.input_formats.UniprotMapping" href="pypath.internals.input_formats.UniprotMapping.html" />
+    <link rel="prev" title="pypath.internals.intera.Residue" href="pypath.internals.intera.Residue.html" />
   <meta name="viewport" content="width=device-width, initial-scale=1"/>
   <meta name="docsearch:language" content="en"/>
   </head>
@@ -554,12 +554,12 @@
                   
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-       href="pypath.internals.input_formats.UniprotMapping.html"
+       href="pypath.internals.intera.Residue.html"
        title="previous page">
       <i class="fa-solid fa-angle-left"></i>
       <div class="prev-next-info">
         <p class="prev-next-subtitle">previous</p>
-        <p class="prev-next-title">pypath.internals.input_formats.UniprotMapping</p>
+        <p class="prev-next-title">pypath.internals.intera.Residue</p>
       </div>
     </a>
     <a class="right-next"
diff --git a/api/pypath.legacy.db_categories.get_category.html b/api/pypath.legacy.db_categories.get_category.html
index 3ee0ffba1..15ccf7720 100644
--- a/api/pypath.legacy.db_categories.get_category.html
+++ b/api/pypath.legacy.db_categories.get_category.html
@@ -47,7 +47,7 @@
     <link rel="icon" href="../_static/omnipath-logo.svg"/>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
-    <link rel="next" title="pypath.resources" href="pypath.resources.html" />
+    <link rel="next" title="pypath.omnipath" href="pypath.omnipath.html" />
     <link rel="prev" title="pypath.legacy.db_categories.get_categories" href="pypath.legacy.db_categories.get_categories.html" />
   <meta name="viewport" content="width=device-width, initial-scale=1"/>
   <meta name="docsearch:language" content="en"/>
@@ -544,11 +544,11 @@ <h1>pypath.legacy.db_categories.get_category<a class="headerlink" href="#pypath-
       </div>
     </a>
     <a class="right-next"
-       href="pypath.resources.html"
+       href="pypath.omnipath.html"
        title="next page">
       <div class="prev-next-info">
         <p class="prev-next-subtitle">next</p>
-        <p class="prev-next-title">pypath.resources</p>
+        <p class="prev-next-title">pypath.omnipath</p>
       </div>
       <i class="fa-solid fa-angle-right"></i>
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diff --git a/api/pypath.omnipath.app.DatabaseManager.html b/api/pypath.omnipath.app.DatabaseManager.html
new file mode 100644
index 000000000..f6540c667
--- /dev/null
+++ b/api/pypath.omnipath.app.DatabaseManager.html
@@ -0,0 +1,993 @@
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+    document.documentElement.dataset.mode = localStorage.getItem("mode") || "";
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+  <section id="pypath-omnipath-app-databasemanager">
+<h1>pypath.omnipath.app.DatabaseManager<a class="headerlink" href="#pypath-omnipath-app-databasemanager" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.omnipath.app.DatabaseManager">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.omnipath.app.</span></span><span class="sig-name descname"><span class="pre">DatabaseManager</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">rebuild</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/omnipath/app.html#DatabaseManager"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.omnipath.app.DatabaseManager" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">Logger</span></code></p>
+<p>Builds and serves the databases in OmniPath such as various networks,
+enzyme-substrate interactions, protein complexes, annotations and
+inter-cellular communication roles. Saves the databases to and loads
+them from pickle dumps on demand.</p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.omnipath.app.DatabaseManager.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">rebuild</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/omnipath/app.html#DatabaseManager.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.omnipath.app.DatabaseManager.__init__" title="Link to this definition">§</a></dt>
+<dd><p>Make this instance a logger.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>name</strong> – The label of this instance that will be prepended to all
+messages it sends to the logger.</p></li>
+<li><p><strong>module</strong> – Send the messages by the logger of this module.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.omnipath.app.DatabaseManager.__init__" title="pypath.omnipath.app.DatabaseManager.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>([rebuild])</p></td>
+<td><p>Make this instance a logger.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.omnipath.app.DatabaseManager.build" title="pypath.omnipath.app.DatabaseManager.build"><code class="xref py py-obj docutils literal notranslate"><span class="pre">build</span></code></a>()</p></td>
+<td><p>Builds all built-in datasets.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.omnipath.app.DatabaseManager.build_dataset" title="pypath.omnipath.app.DatabaseManager.build_dataset"><code class="xref py py-obj docutils literal notranslate"><span class="pre">build_dataset</span></code></a>(dataset[, ncbi_tax_id])</p></td>
+<td><p>Builds a dataset.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.omnipath.app.DatabaseManager.compile_table" title="pypath.omnipath.app.DatabaseManager.compile_table"><code class="xref py py-obj docutils literal notranslate"><span class="pre">compile_table</span></code></a>(dataset)</p></td>
+<td><p>Compiles the <cite>summaries</cite> table for a dataset.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.omnipath.app.DatabaseManager.compile_tables" title="pypath.omnipath.app.DatabaseManager.compile_tables"><code class="xref py py-obj docutils literal notranslate"><span class="pre">compile_tables</span></code></a>()</p></td>
+<td><p>Compiles the <cite>summaries</cite> table for all datasets.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.omnipath.app.DatabaseManager.dataset_dependencies" title="pypath.omnipath.app.DatabaseManager.dataset_dependencies"><code class="xref py py-obj docutils literal notranslate"><span class="pre">dataset_dependencies</span></code></a>(dataset)</p></td>
+<td><p>Returns the dependencies of a dataset.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.omnipath.app.DatabaseManager.define_dataset" title="pypath.omnipath.app.DatabaseManager.define_dataset"><code class="xref py py-obj docutils literal notranslate"><span class="pre">define_dataset</span></code></a>(name, module[, args, pickle])</p></td>
+<td><p>Add a new dataset definition.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.omnipath.app.DatabaseManager.ensure_dataset" title="pypath.omnipath.app.DatabaseManager.ensure_dataset"><code class="xref py py-obj docutils literal notranslate"><span class="pre">ensure_dataset</span></code></a>(dataset[, force_reload, ...])</p></td>
+<td><p>Makes sure a dataset is loaded. It loads only if it's not loaded yet or <a href="#id1"><span class="problematic" id="id2">:py:arg:`force_reload`</span></a> is <code class="docutils literal notranslate"><span class="pre">True</span></code>. It only builds if it's not availabe as a pickle dump or <a href="#id3"><span class="problematic" id="id4">:py:arg:`force_rebuild`</span></a> is <code class="docutils literal notranslate"><span class="pre">True</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.omnipath.app.DatabaseManager.ensure_dirs" title="pypath.omnipath.app.DatabaseManager.ensure_dirs"><code class="xref py py-obj docutils literal notranslate"><span class="pre">ensure_dirs</span></code></a>()</p></td>
+<td><p>Checks if the directories for tables, figures and pickles exist and creates them if necessary.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.omnipath.app.DatabaseManager.ensure_module" title="pypath.omnipath.app.DatabaseManager.ensure_module"><code class="xref py py-obj docutils literal notranslate"><span class="pre">ensure_module</span></code></a>(dataset[, reset])</p></td>
+<td><p>Makes sure the module providing a particular dataset is available and has no default database loaded yet (<code class="xref py py-attr docutils literal notranslate"><span class="pre">db</span></code> attribute of the module).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.omnipath.app.DatabaseManager.foreach_dataset" title="pypath.omnipath.app.DatabaseManager.foreach_dataset"><code class="xref py py-obj docutils literal notranslate"><span class="pre">foreach_dataset</span></code></a>(method)</p></td>
+<td><p>Applies a method for each dataset.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.omnipath.app.DatabaseManager.get_args_curated" title="pypath.omnipath.app.DatabaseManager.get_args_curated"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_args_curated</span></code></a>()</p></td>
+<td><p>Returns the arguments for building the curated PPI network dataset.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.omnipath.app.DatabaseManager.get_args_lncrna_mrna" title="pypath.omnipath.app.DatabaseManager.get_args_lncrna_mrna"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_args_lncrna_mrna</span></code></a>()</p></td>
+<td><p>Returns the arguments for building the lncRNA-mRNA network dataset.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.omnipath.app.DatabaseManager.get_args_mirna_mrna" title="pypath.omnipath.app.DatabaseManager.get_args_mirna_mrna"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_args_mirna_mrna</span></code></a>()</p></td>
+<td><p>Returns the arguments for building the miRNA-mRNA network dataset.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.omnipath.app.DatabaseManager.get_args_small_molecule" title="pypath.omnipath.app.DatabaseManager.get_args_small_molecule"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_args_small_molecule</span></code></a>()</p></td>
+<td><p>Returns the arguments for building the small molecule-protein network dataset.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.omnipath.app.DatabaseManager.get_args_tf_mirna" title="pypath.omnipath.app.DatabaseManager.get_args_tf_mirna"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_args_tf_mirna</span></code></a>()</p></td>
+<td><p>Returns the arguments for building the TF-miRNA network dataset.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.omnipath.app.DatabaseManager.get_args_tf_target" title="pypath.omnipath.app.DatabaseManager.get_args_tf_target"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_args_tf_target</span></code></a>()</p></td>
+<td><p>Returns the arguments for building the TF-target network dataset.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.omnipath.app.DatabaseManager.get_build_args" title="pypath.omnipath.app.DatabaseManager.get_build_args"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_build_args</span></code></a>(dataset)</p></td>
+<td><p>Retrieves the default database build parameters for a dataset.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.omnipath.app.DatabaseManager.get_db" title="pypath.omnipath.app.DatabaseManager.get_db"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_db</span></code></a>(dataset[, ncbi_tax_id])</p></td>
+<td><p>Returns a dataset object.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.omnipath.app.DatabaseManager.get_param" title="pypath.omnipath.app.DatabaseManager.get_param"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_param</span></code></a>(key)</p></td>
+<td><p>Retrieves a parameter from the <code class="xref py py-attr docutils literal notranslate"><span class="pre">param</span></code> dict of the current object or from the module settings.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.omnipath.app.DatabaseManager.load_dataset" title="pypath.omnipath.app.DatabaseManager.load_dataset"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_dataset</span></code></a>(dataset[, ncbi_tax_id])</p></td>
+<td><p>Loads a dataset, builds it if no pickle dump is available.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.omnipath.app.DatabaseManager.network_df" title="pypath.omnipath.app.DatabaseManager.network_df"><code class="xref py py-obj docutils literal notranslate"><span class="pre">network_df</span></code></a>(dataset[, by_source])</p></td>
+<td><p>Creates a data frame of a network dataset where rows aggregate information from all resources describing an interaction.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.omnipath.app.DatabaseManager.network_df_by_source" title="pypath.omnipath.app.DatabaseManager.network_df_by_source"><code class="xref py py-obj docutils literal notranslate"><span class="pre">network_df_by_source</span></code></a>([dataset])</p></td>
+<td><p>Creates a data frame of a network dataset where each row contains information from one resource.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.omnipath.app.DatabaseManager.pickle_exists" title="pypath.omnipath.app.DatabaseManager.pickle_exists"><code class="xref py py-obj docutils literal notranslate"><span class="pre">pickle_exists</span></code></a>(dataset[, ncbi_tax_id])</p></td>
+<td><p>Tells if a pickle dump of a particular dataset exists.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.omnipath.app.DatabaseManager.pickle_path" title="pypath.omnipath.app.DatabaseManager.pickle_path"><code class="xref py py-obj docutils literal notranslate"><span class="pre">pickle_path</span></code></a>(dataset[, ncbi_tax_id])</p></td>
+<td><p>Returns the path of the pickle dump for a dataset according to the current settings.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.omnipath.app.DatabaseManager.reload" title="pypath.omnipath.app.DatabaseManager.reload"><code class="xref py py-obj docutils literal notranslate"><span class="pre">reload</span></code></a>()</p></td>
+<td><p>Reloads the object from the module level.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.omnipath.app.DatabaseManager.reload_module" title="pypath.omnipath.app.DatabaseManager.reload_module"><code class="xref py py-obj docutils literal notranslate"><span class="pre">reload_module</span></code></a>(dataset)</p></td>
+<td><p>Reloads the module of the database object of a particular dataset.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.omnipath.app.DatabaseManager.remove_all" title="pypath.omnipath.app.DatabaseManager.remove_all"><code class="xref py py-obj docutils literal notranslate"><span class="pre">remove_all</span></code></a>()</p></td>
+<td><p>Removes all loaded datasets.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.omnipath.app.DatabaseManager.remove_db" title="pypath.omnipath.app.DatabaseManager.remove_db"><code class="xref py py-obj docutils literal notranslate"><span class="pre">remove_db</span></code></a>(dataset[, ncbi_tax_id])</p></td>
+<td><p>Removes a dataset.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.omnipath.app.DatabaseManager.set_network" title="pypath.omnipath.app.DatabaseManager.set_network"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_network</span></code></a>(dataset[, by_source])</p></td>
+<td><p>Sets dataset as the default</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.omnipath.app.DatabaseManager.table_path" title="pypath.omnipath.app.DatabaseManager.table_path"><code class="xref py py-obj docutils literal notranslate"><span class="pre">table_path</span></code></a>(dataset)</p></td>
+<td><p>Returns the full path for a table (to be exported or imported).</p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.omnipath.app.DatabaseManager.build">
+<span class="sig-name descname"><span class="pre">build</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/omnipath/app.html#DatabaseManager.build"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.omnipath.app.DatabaseManager.build" title="Link to this definition">§</a></dt>
+<dd><p>Builds all built-in datasets.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.omnipath.app.DatabaseManager.build_dataset">
+<span class="sig-name descname"><span class="pre">build_dataset</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">dataset</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/omnipath/app.html#DatabaseManager.build_dataset"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.omnipath.app.DatabaseManager.build_dataset" title="Link to this definition">§</a></dt>
+<dd><p>Builds a dataset.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.omnipath.app.DatabaseManager.compile_table">
+<span class="sig-name descname"><span class="pre">compile_table</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">dataset</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/omnipath/app.html#DatabaseManager.compile_table"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.omnipath.app.DatabaseManager.compile_table" title="Link to this definition">§</a></dt>
+<dd><p>Compiles the <cite>summaries</cite> table for a dataset. These tables contain
+various quantitative descriptions of the data contents.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.omnipath.app.DatabaseManager.compile_tables">
+<span class="sig-name descname"><span class="pre">compile_tables</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/omnipath/app.html#DatabaseManager.compile_tables"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.omnipath.app.DatabaseManager.compile_tables" title="Link to this definition">§</a></dt>
+<dd><p>Compiles the <cite>summaries</cite> table for all datasets. These tables contain
+various quantitative descriptions of the data contents.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.omnipath.app.DatabaseManager.dataset_dependencies">
+<span class="sig-name descname"><span class="pre">dataset_dependencies</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">dataset</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/omnipath/app.html#DatabaseManager.dataset_dependencies"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.omnipath.app.DatabaseManager.dataset_dependencies" title="Link to this definition">§</a></dt>
+<dd><p>Returns the dependencies of a dataset. E.g. to build <cite>annotations</cite>
+<cite>complexes</cite> must be loaded hence the former is dependent on the
+latter.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.omnipath.app.DatabaseManager.define_dataset">
+<span class="sig-name descname"><span class="pre">define_dataset</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">module</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">Literal</span><span class="p"><span class="pre">[</span></span><span class="s"><span class="pre">'annot'</span></span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="s"><span class="pre">'complex'</span></span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="s"><span class="pre">'enz_sub'</span></span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="s"><span class="pre">'intercell'</span></span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="s"><span class="pre">'network'</span></span><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="n"><span class="pre">args</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">dict</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">pickle</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">param</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/omnipath/app.html#DatabaseManager.define_dataset"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.omnipath.app.DatabaseManager.define_dataset" title="Link to this definition">§</a></dt>
+<dd><p>Add a new dataset definition.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>name:</dt><dd><p>Arbitrary name for the dataset.</p>
+</dd>
+<dt>module:</dt><dd><p>A database builder module: this determines the type of the
+dataset.</p>
+</dd>
+<dt>args:</dt><dd><p>Arguments for the database provider method (typically
+called <code class="docutils literal notranslate"><span class="pre">get_db</span></code>) of the above module.</p>
+</dd>
+<dt>pickle:</dt><dd><p>A name for the pickle file, if not provided it will be
+named as “&lt;name&gt;_&lt;module&gt;.pickle”.</p>
+</dd>
+<dt>param:</dt><dd><p>Further parameters, saved directly into the :attr:<code class="docutils literal notranslate"><span class="pre">param</span></code>
+dict of this object, however the three arguments above
+override values provided this way.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.omnipath.app.DatabaseManager.ensure_dataset">
+<span class="sig-name descname"><span class="pre">ensure_dataset</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">dataset</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">force_reload</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">force_rebuild</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/omnipath/app.html#DatabaseManager.ensure_dataset"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.omnipath.app.DatabaseManager.ensure_dataset" title="Link to this definition">§</a></dt>
+<dd><p>Makes sure a dataset is loaded. It loads only if it’s not loaded
+yet or <a href="#id5"><span class="problematic" id="id6">:py:arg:`force_reload`</span></a> is <code class="docutils literal notranslate"><span class="pre">True</span></code>. It only builds if it’s
+not availabe as a pickle dump or <a href="#id7"><span class="problematic" id="id8">:py:arg:`force_rebuild`</span></a> is <code class="docutils literal notranslate"><span class="pre">True</span></code>.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>dataset</strong> (<em>str</em>) – The name of the dataset.</p></li>
+<li><p><strong>ncbi_tax_id</strong> (<em>int</em>) – NCBI Taxonomy ID of the organism. Considered only if the dataset
+builds for one organism and saved to organism specific pickle
+files.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.omnipath.app.DatabaseManager.ensure_dirs">
+<span class="sig-name descname"><span class="pre">ensure_dirs</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/omnipath/app.html#DatabaseManager.ensure_dirs"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.omnipath.app.DatabaseManager.ensure_dirs" title="Link to this definition">§</a></dt>
+<dd><p>Checks if the directories for tables, figures and pickles exist and
+creates them if necessary.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.omnipath.app.DatabaseManager.ensure_module">
+<span class="sig-name descname"><span class="pre">ensure_module</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">dataset</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">reset</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/omnipath/app.html#DatabaseManager.ensure_module"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.omnipath.app.DatabaseManager.ensure_module" title="Link to this definition">§</a></dt>
+<dd><p>Makes sure the module providing a particular dataset is available
+and has no default database loaded yet (<code class="xref py py-attr docutils literal notranslate"><span class="pre">db</span></code> attribute
+of the module).</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.omnipath.app.DatabaseManager.foreach_dataset">
+<span class="sig-name descname"><span class="pre">foreach_dataset</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/omnipath/app.html#DatabaseManager.foreach_dataset"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.omnipath.app.DatabaseManager.foreach_dataset" title="Link to this definition">§</a></dt>
+<dd><p>Applies a method for each dataset.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.omnipath.app.DatabaseManager.get_args_curated">
+<span class="sig-name descname"><span class="pre">get_args_curated</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/omnipath/app.html#DatabaseManager.get_args_curated"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.omnipath.app.DatabaseManager.get_args_curated" title="Link to this definition">§</a></dt>
+<dd><p>Returns the arguments for building the curated PPI network dataset.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.omnipath.app.DatabaseManager.get_args_lncrna_mrna">
+<span class="sig-name descname"><span class="pre">get_args_lncrna_mrna</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/omnipath/app.html#DatabaseManager.get_args_lncrna_mrna"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.omnipath.app.DatabaseManager.get_args_lncrna_mrna" title="Link to this definition">§</a></dt>
+<dd><p>Returns the arguments for building the lncRNA-mRNA network dataset.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.omnipath.app.DatabaseManager.get_args_mirna_mrna">
+<span class="sig-name descname"><span class="pre">get_args_mirna_mrna</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/omnipath/app.html#DatabaseManager.get_args_mirna_mrna"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.omnipath.app.DatabaseManager.get_args_mirna_mrna" title="Link to this definition">§</a></dt>
+<dd><p>Returns the arguments for building the miRNA-mRNA network dataset.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.omnipath.app.DatabaseManager.get_args_small_molecule">
+<span class="sig-name descname"><span class="pre">get_args_small_molecule</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/omnipath/app.html#DatabaseManager.get_args_small_molecule"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.omnipath.app.DatabaseManager.get_args_small_molecule" title="Link to this definition">§</a></dt>
+<dd><p>Returns the arguments for building the small molecule-protein
+network dataset.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.omnipath.app.DatabaseManager.get_args_tf_mirna">
+<span class="sig-name descname"><span class="pre">get_args_tf_mirna</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/omnipath/app.html#DatabaseManager.get_args_tf_mirna"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.omnipath.app.DatabaseManager.get_args_tf_mirna" title="Link to this definition">§</a></dt>
+<dd><p>Returns the arguments for building the TF-miRNA network dataset.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.omnipath.app.DatabaseManager.get_args_tf_target">
+<span class="sig-name descname"><span class="pre">get_args_tf_target</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/omnipath/app.html#DatabaseManager.get_args_tf_target"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.omnipath.app.DatabaseManager.get_args_tf_target" title="Link to this definition">§</a></dt>
+<dd><p>Returns the arguments for building the TF-target network dataset.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.omnipath.app.DatabaseManager.get_build_args">
+<span class="sig-name descname"><span class="pre">get_build_args</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">dataset</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/omnipath/app.html#DatabaseManager.get_build_args"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.omnipath.app.DatabaseManager.get_build_args" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the default database build parameters for a dataset.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.omnipath.app.DatabaseManager.get_db">
+<span class="sig-name descname"><span class="pre">get_db</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">dataset</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/omnipath/app.html#DatabaseManager.get_db"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.omnipath.app.DatabaseManager.get_db" title="Link to this definition">§</a></dt>
+<dd><p>Returns a dataset object. Loads and builds the dataset if necessary.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><p><strong>ncbi_tax_id</strong> (<em>int</em>) – NCBI Taxonomy ID of the organism. Considered only if the dataset
+builds for one organism and saved to organism specific pickle
+files.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.omnipath.app.DatabaseManager.get_param">
+<span class="sig-name descname"><span class="pre">get_param</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">key</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/omnipath/app.html#DatabaseManager.get_param"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.omnipath.app.DatabaseManager.get_param" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a parameter from the <code class="xref py py-attr docutils literal notranslate"><span class="pre">param</span></code> dict of the current
+object or from the module settings.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.omnipath.app.DatabaseManager.load_dataset">
+<span class="sig-name descname"><span class="pre">load_dataset</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">dataset</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/omnipath/app.html#DatabaseManager.load_dataset"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.omnipath.app.DatabaseManager.load_dataset" title="Link to this definition">§</a></dt>
+<dd><p>Loads a dataset, builds it if no pickle dump is available.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.omnipath.app.DatabaseManager.network_df">
+<span class="sig-name descname"><span class="pre">network_df</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">dataset</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">by_source</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/omnipath/app.html#DatabaseManager.network_df"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.omnipath.app.DatabaseManager.network_df" title="Link to this definition">§</a></dt>
+<dd><p>Creates a data frame of a network dataset where rows aggregate
+information from all resources describing an interaction.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.omnipath.app.DatabaseManager.network_df_by_source">
+<span class="sig-name descname"><span class="pre">network_df_by_source</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">dataset</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'omnipath'</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/omnipath/app.html#DatabaseManager.network_df_by_source"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.omnipath.app.DatabaseManager.network_df_by_source" title="Link to this definition">§</a></dt>
+<dd><p>Creates a data frame of a network dataset where each row contains
+information from one resource.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.omnipath.app.DatabaseManager.pickle_exists">
+<span class="sig-name descname"><span class="pre">pickle_exists</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">dataset</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/omnipath/app.html#DatabaseManager.pickle_exists"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.omnipath.app.DatabaseManager.pickle_exists" title="Link to this definition">§</a></dt>
+<dd><p>Tells if a pickle dump of a particular dataset exists.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.omnipath.app.DatabaseManager.pickle_path">
+<span class="sig-name descname"><span class="pre">pickle_path</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">dataset</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/omnipath/app.html#DatabaseManager.pickle_path"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.omnipath.app.DatabaseManager.pickle_path" title="Link to this definition">§</a></dt>
+<dd><p>Returns the path of the pickle dump for a dataset according to
+the current settings.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.omnipath.app.DatabaseManager.reload">
+<span class="sig-name descname"><span class="pre">reload</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/omnipath/app.html#DatabaseManager.reload"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.omnipath.app.DatabaseManager.reload" title="Link to this definition">§</a></dt>
+<dd><p>Reloads the object from the module level.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.omnipath.app.DatabaseManager.reload_module">
+<span class="sig-name descname"><span class="pre">reload_module</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">dataset</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/omnipath/app.html#DatabaseManager.reload_module"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.omnipath.app.DatabaseManager.reload_module" title="Link to this definition">§</a></dt>
+<dd><p>Reloads the module of the database object of a particular dataset.
+E.g. in case of network datasets the <code class="docutils literal notranslate"><span class="pre">pypath.network</span></code> module
+will be reloaded.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.omnipath.app.DatabaseManager.remove_all">
+<span class="sig-name descname"><span class="pre">remove_all</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/omnipath/app.html#DatabaseManager.remove_all"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.omnipath.app.DatabaseManager.remove_all" title="Link to this definition">§</a></dt>
+<dd><p>Removes all loaded datasets. Deletes the references to the objects
+in the module, however if you have references elsewhere in your
+code they remain in the memory.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.omnipath.app.DatabaseManager.remove_db">
+<span class="sig-name descname"><span class="pre">remove_db</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">dataset</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/omnipath/app.html#DatabaseManager.remove_db"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.omnipath.app.DatabaseManager.remove_db" title="Link to this definition">§</a></dt>
+<dd><p>Removes a dataset. Deletes the references to the object
+in the module, however if you have references elsewhere in your
+code it remains in the memory.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.omnipath.app.DatabaseManager.set_network">
+<span class="sig-name descname"><span class="pre">set_network</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">dataset</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">by_source</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/omnipath/app.html#DatabaseManager.set_network"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.omnipath.app.DatabaseManager.set_network" title="Link to this definition">§</a></dt>
+<dd><p>Sets dataset as the default</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.omnipath.app.DatabaseManager.table_path">
+<span class="sig-name descname"><span class="pre">table_path</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">dataset</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/omnipath/app.html#DatabaseManager.table_path"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.omnipath.app.DatabaseManager.table_path" title="Link to this definition">§</a></dt>
+<dd><p>Returns the full path for a table (to be exported or imported).</p>
+</dd></dl>
+
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+
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+
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+  <section id="module-pypath.omnipath.app">
+<span id="pypath-omnipath-app"></span><h1>pypath.omnipath.app<a class="headerlink" href="#module-pypath.omnipath.app" title="Link to this heading">§</a></h1>
+<dl class="field-list simple">
+<dt class="field-odd">members<span class="colon">:</span></dt>
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+<p class="rubric">Classes</p>
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+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.omnipath.app.DatabaseManager.html#pypath.omnipath.app.DatabaseManager" title="pypath.omnipath.app.DatabaseManager"><code class="xref py py-obj docutils literal notranslate"><span class="pre">DatabaseManager</span></code></a>([rebuild])</p></td>
+<td><p>Builds and serves the databases in OmniPath such as various networks, enzyme-substrate interactions, protein complexes, annotations and inter-cellular communication roles.</p></td>
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+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.omnipath.databases.build">
+<span class="sig-prename descclassname"><span class="pre">pypath.omnipath.databases.</span></span><span class="sig-name descname"><span class="pre">build</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">label</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/omnipath/databases.html#build"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.omnipath.databases.build" title="Link to this definition">§</a></dt>
+<dd><p>Builds a built in database and returns the instance.
+This is not the preferred method to get a database instance.
+Unless there is a strong reason, both built in and user defined databases
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new file mode 100644
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+  <section id="pypath-omnipath-databases-class-and-param">
+<h1>pypath.omnipath.databases.class_and_param<a class="headerlink" href="#pypath-omnipath-databases-class-and-param" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.omnipath.databases.class_and_param">
+<span class="sig-prename descclassname"><span class="pre">pypath.omnipath.databases.</span></span><span class="sig-name descname"><span class="pre">class_and_param</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">label</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/omnipath/databases.html#class_and_param"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.omnipath.databases.class_and_param" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves the database definition of a built in database.</p>
+</dd></dl>
+
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diff --git a/api/pypath.omnipath.databases.define.DatabaseClass.html b/api/pypath.omnipath.databases.define.DatabaseClass.html
new file mode 100644
index 000000000..3a0894642
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+  <section id="pypath-omnipath-databases-define-databaseclass">
+<h1>pypath.omnipath.databases.define.DatabaseClass<a class="headerlink" href="#pypath-omnipath-databases-define-databaseclass" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.omnipath.databases.define.DatabaseClass">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.omnipath.databases.define.</span></span><span class="sig-name descname"><span class="pre">DatabaseClass</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">module</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">method</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">label</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/omnipath/databases/define.html#DatabaseClass"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.omnipath.databases.define.DatabaseClass" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></p>
+<p>Describes a class of databases which can be filled with different data
+but here the module and the class implementing the database are defined.</p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.omnipath.databases.define.DatabaseClass.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">module</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">method</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">label</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/omnipath/databases/define.html#DatabaseClass.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.omnipath.databases.define.DatabaseClass.__init__" title="Link to this definition">§</a></dt>
+<dd></dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.omnipath.databases.define.DatabaseClass.__init__" title="pypath.omnipath.databases.define.DatabaseClass.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>(module, method[, label])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">from_dict</span></code>(dct[, label])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">from_json</span></code>(path[, label])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_class</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+</tbody>
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+  <section id="pypath-omnipath-databases-define-databasedefinition">
+<h1>pypath.omnipath.databases.define.DatabaseDefinition<a class="headerlink" href="#pypath-omnipath-databases-define-databasedefinition" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.omnipath.databases.define.DatabaseDefinition">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.omnipath.databases.define.</span></span><span class="sig-name descname"><span class="pre">DatabaseDefinition</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">label</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/omnipath/databases/define.html#DatabaseDefinition"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.omnipath.databases.define.DatabaseDefinition" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.omnipath.databases.define.DatabaseDefinition.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">label</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/omnipath/databases/define.html#DatabaseDefinition.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.omnipath.databases.define.DatabaseDefinition.__init__" title="Link to this definition">§</a></dt>
+<dd></dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.omnipath.databases.define.DatabaseDefinition.__init__" title="pypath.omnipath.databases.define.DatabaseDefinition.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>(label, **kwargs)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.omnipath.databases.define.DatabaseDefinition.from_dict" title="pypath.omnipath.databases.define.DatabaseDefinition.from_dict"><code class="xref py py-obj docutils literal notranslate"><span class="pre">from_dict</span></code></a>(dct[, label])</p></td>
+<td><p><dl class="field-list simple">
+<dt class="field-odd">param dict dct<span class="colon">:</span></dt>
+<dd class="field-odd"><p></p></dd>
+</dl>
+</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.omnipath.databases.define.DatabaseDefinition.from_json" title="pypath.omnipath.databases.define.DatabaseDefinition.from_json"><code class="xref py py-obj docutils literal notranslate"><span class="pre">from_json</span></code></a>(path[, label])</p></td>
+<td><p><dl class="field-list simple">
+<dt class="field-odd">param str path<span class="colon">:</span></dt>
+<dd class="field-odd"><p></p></dd>
+</dl>
+</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">get</span></code>(attr)</p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.omnipath.databases.define.DatabaseDefinition.from_dict">
+<em class="property"><span class="pre">classmethod</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">from_dict</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">dct</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">label</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/omnipath/databases/define.html#DatabaseDefinition.from_dict"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.omnipath.databases.define.DatabaseDefinition.from_dict" title="Link to this definition">§</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><p><strong>dct</strong> (<em>dict</em>) – Dictionary containing the parameters for the database definition.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.omnipath.databases.define.DatabaseDefinition.from_json">
+<em class="property"><span class="pre">classmethod</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">from_json</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">path</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">label</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/omnipath/databases/define.html#DatabaseDefinition.from_json"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.omnipath.databases.define.DatabaseDefinition.from_json" title="Link to this definition">§</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><p><strong>path</strong> (<em>str</em>) – Path to JSON file with database definition.</p>
+</dd>
+</dl>
+</dd></dl>
+
+</dd></dl>
+
+</section>
+
+
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+  <section id="pypath-omnipath-databases-define-databasedefinitionmanager">
+<h1>pypath.omnipath.databases.define.DatabaseDefinitionManager<a class="headerlink" href="#pypath-omnipath-databases-define-databasedefinitionmanager" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.omnipath.databases.define.DatabaseDefinitionManager">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.omnipath.databases.define.</span></span><span class="sig-name descname"><span class="pre">DatabaseDefinitionManager</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">classes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">databases</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/omnipath/databases/define.html#DatabaseDefinitionManager"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.omnipath.databases.define.DatabaseDefinitionManager" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">Logger</span></code></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.omnipath.databases.define.DatabaseDefinitionManager.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">classes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">databases</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/omnipath/databases/define.html#DatabaseDefinitionManager.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.omnipath.databases.define.DatabaseDefinitionManager.__init__" title="Link to this definition">§</a></dt>
+<dd><p>Make this instance a logger.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>name</strong> – The label of this instance that will be prepended to all
+messages it sends to the logger.</p></li>
+<li><p><strong>module</strong> – Send the messages by the logger of this module.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.omnipath.databases.define.DatabaseDefinitionManager.__init__" title="pypath.omnipath.databases.define.DatabaseDefinitionManager.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>([classes, databases])</p></td>
+<td><p>Make this instance a logger.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.omnipath.databases.define.DatabaseDefinitionManager.build" title="pypath.omnipath.databases.define.DatabaseDefinitionManager.build"><code class="xref py py-obj docutils literal notranslate"><span class="pre">build</span></code></a>(label)</p></td>
+<td><p>For a database definition label returns an instance of the database: creates an instance of the class or calls the method with the arguments in the database definition.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.omnipath.databases.define.DatabaseDefinitionManager.class_and_param" title="pypath.omnipath.databases.define.DatabaseDefinitionManager.class_and_param"><code class="xref py py-obj docutils literal notranslate"><span class="pre">class_and_param</span></code></a>(label)</p></td>
+<td><p>For a database definition label returns the class or method and its arguments which are necessary to build the database according to the definition.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_class</span></code>(label)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_db_class</span></code>(label)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_db_definition</span></code>(label)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">load</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.omnipath.databases.define.DatabaseDefinitionManager.build">
+<span class="sig-name descname"><span class="pre">build</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">label</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/omnipath/databases/define.html#DatabaseDefinitionManager.build"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.omnipath.databases.define.DatabaseDefinitionManager.build" title="Link to this definition">§</a></dt>
+<dd><p>For a database definition label returns an instance of the database:
+creates an instance of the class or calls the method with the
+arguments in the database definition. Returns the database instance.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.omnipath.databases.define.DatabaseDefinitionManager.class_and_param">
+<span class="sig-name descname"><span class="pre">class_and_param</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">label</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/omnipath/databases/define.html#DatabaseDefinitionManager.class_and_param"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.omnipath.databases.define.DatabaseDefinitionManager.class_and_param" title="Link to this definition">§</a></dt>
+<dd><p>For a database definition label returns the class or method and its
+arguments which are necessary to build the database according to
+the definition.</p>
+</dd></dl>
+
+</dd></dl>
+
+</section>
+
+
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+  <section id="module-pypath.omnipath.databases.define">
+<span id="pypath-omnipath-databases-define"></span><h1>pypath.omnipath.databases.define<a class="headerlink" href="#module-pypath.omnipath.databases.define" title="Link to this heading">§</a></h1>
+<dl class="field-list simple">
+<dt class="field-odd">members<span class="colon">:</span></dt>
+<dd class="field-odd"><p></p></dd>
+</dl>
+<p class="rubric">Classes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.omnipath.databases.define.DatabaseClass.html#pypath.omnipath.databases.define.DatabaseClass" title="pypath.omnipath.databases.define.DatabaseClass"><code class="xref py py-obj docutils literal notranslate"><span class="pre">DatabaseClass</span></code></a>(module, method[, label])</p></td>
+<td><p>Describes a class of databases which can be filled with different data but here the module and the class implementing the database are defined.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.omnipath.databases.define.DatabaseDefinition.html#pypath.omnipath.databases.define.DatabaseDefinition" title="pypath.omnipath.databases.define.DatabaseDefinition"><code class="xref py py-obj docutils literal notranslate"><span class="pre">DatabaseDefinition</span></code></a>(label, **kwargs)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.omnipath.databases.define.DatabaseDefinitionManager.html#pypath.omnipath.databases.define.DatabaseDefinitionManager" title="pypath.omnipath.databases.define.DatabaseDefinitionManager"><code class="xref py py-obj docutils literal notranslate"><span class="pre">DatabaseDefinitionManager</span></code></a>([classes, databases])</p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+</section>
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+  <section id="pypath-omnipath-databases-get-manager">
+<h1>pypath.omnipath.databases.get_manager<a class="headerlink" href="#pypath-omnipath-databases-get-manager" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.omnipath.databases.get_manager">
+<span class="sig-prename descclassname"><span class="pre">pypath.omnipath.databases.</span></span><span class="sig-name descname"><span class="pre">get_manager</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/omnipath/databases.html#get_manager"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.omnipath.databases.get_manager" title="Link to this definition">§</a></dt>
+<dd></dd></dl>
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+  <section id="module-pypath.omnipath.databases">
+<span id="pypath-omnipath-databases"></span><h1>pypath.omnipath.databases<a class="headerlink" href="#module-pypath.omnipath.databases" title="Link to this heading">§</a></h1>
+<dl class="field-list simple">
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+<dd class="field-odd"><p></p></dd>
+</dl>
+<p class="rubric">Functions</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.omnipath.databases.build.html#pypath.omnipath.databases.build" title="pypath.omnipath.databases.build"><code class="xref py py-obj docutils literal notranslate"><span class="pre">build</span></code></a>(label)</p></td>
+<td><p>Builds a built in database and returns the instance.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.omnipath.databases.class_and_param.html#pypath.omnipath.databases.class_and_param" title="pypath.omnipath.databases.class_and_param"><code class="xref py py-obj docutils literal notranslate"><span class="pre">class_and_param</span></code></a>(label)</p></td>
+<td><p>Retrieves the database definition of a built in database.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.omnipath.databases.get_manager.html#pypath.omnipath.databases.get_manager" title="pypath.omnipath.databases.get_manager"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_manager</span></code></a>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.omnipath.databases.init_manager.html#pypath.omnipath.databases.init_manager" title="pypath.omnipath.databases.init_manager"><code class="xref py py-obj docutils literal notranslate"><span class="pre">init_manager</span></code></a>()</p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Modules</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.omnipath.databases.define.html#module-pypath.omnipath.databases.define" title="pypath.omnipath.databases.define"><code class="xref py py-obj docutils literal notranslate"><span class="pre">pypath.omnipath.databases.define</span></code></a></p></td>
+<td><p></p></td>
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+          <a href="https://pypi.org/project/pypath-omnipath" title="PyPI" class="nav-link" rel="noopener" target="_blank" data-bs-toggle="tooltip" data-bs-placement="bottom"><span><i class="fa-solid fa-box fa-lg" aria-hidden="true"></i></span>
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+          <a href="https://omnipathdb.org/" title="OmniPath" class="nav-link" rel="noopener" target="_blank" data-bs-toggle="tooltip" data-bs-placement="bottom"><span><i class="fa-solid fa-university fa-lg" aria-hidden="true"></i></span>
+            <span class="sr-only">OmniPath</span></a>
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+            <span class="sr-only">Saez Lab</span></a>
+        </li>
+</ul></div>
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+  <section id="pypath-omnipath-export-export">
+<h1>pypath.omnipath.export.Export<a class="headerlink" href="#pypath-omnipath-export-export" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.omnipath.export.Export">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.omnipath.export.</span></span><span class="sig-name descname"><span class="pre">Export</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">network</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">only_sources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">extra_node_attrs</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">extra_edge_attrs</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">outfile</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">default_vertex_attr_processor</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">default_edge_attr_processor</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">pa</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/omnipath/export.html#Export"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.omnipath.export.Export" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">Logger</span></code></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.omnipath.export.Export.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">network</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">only_sources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">extra_node_attrs</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">extra_edge_attrs</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">outfile</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">default_vertex_attr_processor</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">default_edge_attr_processor</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">pa</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/omnipath/export.html#Export.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.omnipath.export.Export.__init__" title="Link to this definition">§</a></dt>
+<dd><p>Make this instance a logger.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>name</strong> – The label of this instance that will be prepended to all
+messages it sends to the logger.</p></li>
+<li><p><strong>module</strong> – Send the messages by the logger of this module.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.omnipath.export.Export.__init__" title="pypath.omnipath.export.Export.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>([network, only_sources, ...])</p></td>
+<td><p>Make this instance a logger.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.omnipath.export.Export.add_extra_fields" title="pypath.omnipath.export.Export.add_extra_fields"><code class="xref py py-obj docutils literal notranslate"><span class="pre">add_extra_fields</span></code></a>(e, line[, dr])</p></td>
+<td><p>Takes one table row and using the <cite>igraph.Edge</cite> object and the direction provided adds the extra node and edge attribute fields as they are defined in <cite>extra_node_attrs</cite> and <cite>extra_edge_attrs</cite>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">default_edge_attr_processor</span></code>(eattr)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">default_vertex_attr_processor</span></code>(vattr)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.omnipath.export.Export.generic_attr_processor" title="pypath.omnipath.export.Export.generic_attr_processor"><code class="xref py py-obj docutils literal notranslate"><span class="pre">generic_attr_processor</span></code></a>(proc, obj[, dr])</p></td>
+<td><p>Wraps the attribute processor to handle unknown number of arguments.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.omnipath.export.Export.get_header" title="pypath.omnipath.export.Export.get_header"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_header</span></code></a>([unique_pairs])</p></td>
+<td><p>Creates a data frame header (list of field names) according to the data frame type and the extra fields.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.omnipath.export.Export.make_df" title="pypath.omnipath.export.Export.make_df"><code class="xref py py-obj docutils literal notranslate"><span class="pre">make_df</span></code></a>([unique_pairs, extra_node_attrs, ...])</p></td>
+<td><p>Creates a data frame from the network.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">match_consensus</span></code>(consensus, nodes[, effect])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">process_interaction</span></code>(ia)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">reload</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.omnipath.export.Export.sources_table" title="pypath.omnipath.export.Export.sources_table"><code class="xref py py-obj docutils literal notranslate"><span class="pre">sources_table</span></code></a>(pa[, only_sources, ...])</p></td>
+<td><p>Creates a data frame which contains a column for each source database with binary values showing presence-absence of interactions across resources.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">webservice_interactions_df</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">webservice_interactions_df_legacy</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">write</span></code>([outfile])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.omnipath.export.Export.write_tab" title="pypath.omnipath.export.Export.write_tab"><code class="xref py py-obj docutils literal notranslate"><span class="pre">write_tab</span></code></a>([outfile])</p></td>
+<td><p>Writes the data frame into a tab separated file.</p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Attributes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">default_dtypes_bydirs</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">default_dtypes_uniquepairs</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">default_header_bydirs</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">default_header_uniquepairs</span></code></p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.omnipath.export.Export.add_extra_fields">
+<span class="sig-name descname"><span class="pre">add_extra_fields</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">e</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">line</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">dr</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/omnipath/export.html#Export.add_extra_fields"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.omnipath.export.Export.add_extra_fields" title="Link to this definition">§</a></dt>
+<dd><p>Takes one table row and using the <cite>igraph.Edge</cite> object and the
+direction provided adds the extra node and edge attribute fields
+as they are defined in <cite>extra_node_attrs</cite> and <cite>extra_edge_attrs</cite>.</p>
+<p>Returns the row with extra fields added.</p>
+<p>:param : One edge.
+:type : param igraph.Edge e:
+:param : A table row.
+:type : param list line:
+:param : Direction key. A tuple of names (most often UniProt IDs) or</p>
+<blockquote>
+<div><p><cite>undirected</cite>.</p>
+</div></blockquote>
+<p>:type : param tuple,str dr:</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.omnipath.export.Export.generic_attr_processor">
+<em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">generic_attr_processor</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">proc</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">obj</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">dr</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/omnipath/export.html#Export.generic_attr_processor"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.omnipath.export.Export.generic_attr_processor" title="Link to this definition">§</a></dt>
+<dd><p>Wraps the attribute processor to handle unknown number of arguments.</p>
+<p>Not knowing if the attribute processor expects one or two arguments,
+have no better way than try: if calling with 2 arguments fails with
+<cite>TypeError</cite> we call with one argument.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.omnipath.export.Export.get_header">
+<span class="sig-name descname"><span class="pre">get_header</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">unique_pairs</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/omnipath/export.html#Export.get_header"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.omnipath.export.Export.get_header" title="Link to this definition">§</a></dt>
+<dd><p>Creates a data frame header (list of field names) according to the
+data frame type and the extra fields.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.omnipath.export.Export.make_df">
+<span class="sig-name descname"><span class="pre">make_df</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">unique_pairs</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">extra_node_attrs</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">extra_edge_attrs</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/omnipath/export.html#Export.make_df"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.omnipath.export.Export.make_df" title="Link to this definition">§</a></dt>
+<dd><p>Creates a data frame from the network.</p>
+<p>By default UniProt IDs, Gene Symbols, source databases, literature
+references, directionality and sign information and interaction type
+are included.</p>
+<dl>
+<dt>:param<span class="classifier">If <cite>True</cite> each line corresponds to a unique pair of molecules,</span></dt><dd><p>all directionality and sign information are covered in other
+columns. If <cite>False</cite>, order of <cite>A</cite> and <cite>B</cite> IDs corresponds to
+the direction while sign covered in further columns.</p>
+</dd>
+</dl>
+<p>:type : param bool unique_pairs:
+:param : Additional node attributes to be included in the exported table.</p>
+<blockquote>
+<div><p>Keys are column names used in the header while values are names
+of vertex attributes. Values also might be methods which then
+will be called then on each vertex. These should return strings
+or their result will be converted to string.
+In the header <cite>_A</cite> and <cite>_B</cite> suffixes will be appended to the
+column names so the values can be assigned to A and B side
+interaction partners.</p>
+</div></blockquote>
+<p>:type : param dict extra_node_attrs:
+:param : Additional edge attributes to be included in the exported table.</p>
+<blockquote>
+<div><p>Keys are column names used in the header while values are names
+of edge attributes or callables accepting an edge as single
+argument.</p>
+</div></blockquote>
+<p>:type : param dict extra_edge_attrs:
+:param : Name of the output file. If <cite>None</cite> a file name</p>
+<blockquote>
+<div><p>“netrowk-&lt;session id&gt;.tab” is used.</p>
+</div></blockquote>
+<p>:type : param str outfile:</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.omnipath.export.Export.sources_table">
+<em class="property"><span class="pre">classmethod</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">sources_table</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">pa</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">only_sources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">unique_pairs</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">extra_edge_attrs</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">extra_node_attrs</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">outfile</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">default_vertex_attr_processor</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">default_edge_attr_processor</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/omnipath/export.html#Export.sources_table"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.omnipath.export.Export.sources_table" title="Link to this definition">§</a></dt>
+<dd><p>Creates a data frame which contains a column for each source database
+with binary values showing presence-absence of interactions across
+resources.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.omnipath.export.Export.write_tab">
+<span class="sig-name descname"><span class="pre">write_tab</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">outfile</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/omnipath/export.html#Export.write_tab"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.omnipath.export.Export.write_tab" title="Link to this definition">§</a></dt>
+<dd><p>Writes the data frame into a tab separated file.</p>
+<p>:param : Forwarded to <cite>make_df()</cite>.
+:type : param <a href="#id1"><span class="problematic" id="id2">**</span></a>kwargs:</p>
+</dd></dl>
+
+</dd></dl>
+
+</section>
+
+
+                </article>
+              
+              
+              
+              
+              
+                <footer class="prev-next-footer">
+                  
+<div class="prev-next-area">
+    <a class="left-prev"
+       href="pypath.omnipath.export.html"
+       title="previous page">
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+<span id="pypath-omnipath-export"></span><h1>pypath.omnipath.export<a class="headerlink" href="#module-pypath.omnipath.export" title="Link to this heading">§</a></h1>
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+<dl class="field-list simple">
+<dt class="field-odd">members<span class="colon">:</span></dt>
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+<p class="rubric">Functions</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.omnipath.init.html#pypath.omnipath.init" title="pypath.omnipath.init"><code class="xref py py-obj docutils literal notranslate"><span class="pre">init</span></code></a>(**kwargs)</p></td>
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+<p class="rubric">Modules</p>
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+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.omnipath.app.html#module-pypath.omnipath.app" title="pypath.omnipath.app"><code class="xref py py-obj docutils literal notranslate"><span class="pre">pypath.omnipath.app</span></code></a></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.omnipath.databases.html#module-pypath.omnipath.databases" title="pypath.omnipath.databases"><code class="xref py py-obj docutils literal notranslate"><span class="pre">pypath.omnipath.databases</span></code></a></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.omnipath.export.html#module-pypath.omnipath.export" title="pypath.omnipath.export"><code class="xref py py-obj docutils literal notranslate"><span class="pre">pypath.omnipath.export</span></code></a></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.omnipath.param.html#module-pypath.omnipath.param" title="pypath.omnipath.param"><code class="xref py py-obj docutils literal notranslate"><span class="pre">pypath.omnipath.param</span></code></a></p></td>
+<td><p>Contains auxiliary functions for preparation of arguments for building built in databases.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.omnipath.server.html#module-pypath.omnipath.server" title="pypath.omnipath.server"><code class="xref py py-obj docutils literal notranslate"><span class="pre">pypath.omnipath.server</span></code></a></p></td>
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diff --git a/api/pypath.omnipath.param.curated_ppi_resources.html b/api/pypath.omnipath.param.curated_ppi_resources.html
new file mode 100644
index 000000000..2f5cc3920
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@@ -0,0 +1,641 @@
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+  <section id="pypath-omnipath-param-curated-ppi-resources">
+<h1>pypath.omnipath.param.curated_ppi_resources<a class="headerlink" href="#pypath-omnipath-param-curated-ppi-resources" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.omnipath.param.curated_ppi_resources">
+<span class="sig-prename descclassname"><span class="pre">pypath.omnipath.param.</span></span><span class="sig-name descname"><span class="pre">curated_ppi_resources</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/omnipath/param.html#curated_ppi_resources"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.omnipath.param.curated_ppi_resources" title="Link to this definition">§</a></dt>
+<dd><p>Returns a resource set which more or less corresponds to the literature
+curated activity flow resources. It is an union of the literature curated
+activity flow and enzyme-substrate resources.</p>
+</dd></dl>
+
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+
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diff --git a/api/pypath.omnipath.param.tf_target_resources.html b/api/pypath.omnipath.param.tf_target_resources.html
new file mode 100644
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+<h1>pypath.omnipath.param.tf_target_resources<a class="headerlink" href="#pypath-omnipath-param-tf-target-resources" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.omnipath.param.tf_target_resources">
+<span class="sig-prename descclassname"><span class="pre">pypath.omnipath.param.</span></span><span class="sig-name descname"><span class="pre">tf_target_resources</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/omnipath/param.html#tf_target_resources"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.omnipath.param.tf_target_resources" title="Link to this definition">§</a></dt>
+<dd><p>Returns the resource set for building the TF-target network dataset.</p>
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+  <section id="pypath-omnipath-server-build-webservicetables">
+<h1>pypath.omnipath.server.build.WebserviceTables<a class="headerlink" href="#pypath-omnipath-server-build-webservicetables" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.omnipath.server.build.WebserviceTables">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.omnipath.server.build.</span></span><span class="sig-name descname"><span class="pre">WebserviceTables</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">only_human</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">build_dir</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'.'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">outfile_interactions</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'omnipath_webservice_interactions.tsv'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">outfile_enz_sub</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'omnipath_webservice_enz_sub.tsv'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">outfile_complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'omnipath_webservice_complexes.tsv'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">outfile_annotations</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'omnipath_webservice_annotations.tsv'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">outfile_intercell</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'omnipath_webservice_intercell.tsv'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">network_datasets</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/omnipath/server/build.html#WebserviceTables"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.omnipath.server.build.WebserviceTables" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">Logger</span></code></p>
+<p>Creates the data frames which the web service uses to serve the data from.</p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.omnipath.server.build.WebserviceTables.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">only_human</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">build_dir</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'.'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">outfile_interactions</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'omnipath_webservice_interactions.tsv'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">outfile_enz_sub</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'omnipath_webservice_enz_sub.tsv'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">outfile_complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'omnipath_webservice_complexes.tsv'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">outfile_annotations</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'omnipath_webservice_annotations.tsv'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">outfile_intercell</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'omnipath_webservice_intercell.tsv'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">network_datasets</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/omnipath/server/build.html#WebserviceTables.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.omnipath.server.build.WebserviceTables.__init__" title="Link to this definition">§</a></dt>
+<dd><p>Make this instance a logger.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>name</strong> – The label of this instance that will be prepended to all
+messages it sends to the logger.</p></li>
+<li><p><strong>module</strong> – Send the messages by the logger of this module.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.omnipath.server.build.WebserviceTables.__init__" title="pypath.omnipath.server.build.WebserviceTables.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>([only_human, build_dir, ...])</p></td>
+<td><p>Make this instance a logger.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">annotations</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">complexes</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">enz_sub</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">interactions</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">interactions_legacy</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">intercell</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">main</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">reload</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
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+<p>This is a standalone module with the only purpose of
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diff --git a/api/pypath.omnipath.server.generate_about_page.export_licenses.html b/api/pypath.omnipath.server.generate_about_page.export_licenses.html
new file mode 100644
index 000000000..efb4ff521
--- /dev/null
+++ b/api/pypath.omnipath.server.generate_about_page.export_licenses.html
@@ -0,0 +1,638 @@
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diff --git a/api/pypath.omnipath.server.generate_about_page.generate_about_html.html b/api/pypath.omnipath.server.generate_about_page.generate_about_html.html
new file mode 100644
index 000000000..7ecca3d26
--- /dev/null
+++ b/api/pypath.omnipath.server.generate_about_page.generate_about_html.html
@@ -0,0 +1,641 @@
+
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+  <section id="pypath-omnipath-server-generate-about-page-generate-about-html">
+<h1>pypath.omnipath.server.generate_about_page.generate_about_html<a class="headerlink" href="#pypath-omnipath-server-generate-about-page-generate-about-html" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.omnipath.server.generate_about_page.generate_about_html">
+<span class="sig-prename descclassname"><span class="pre">pypath.omnipath.server.generate_about_page.</span></span><span class="sig-name descname"><span class="pre">generate_about_html</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">descriptions</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">format</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'b'</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/omnipath/server/generate_about_page.html#generate_about_html"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.omnipath.server.generate_about_page.generate_about_html" title="Link to this definition">§</a></dt>
+<dd><p>Generates a HTML page from the <cite>descriptions</cite> array.
+This HTML is provided by the webservice under <cite>/info</cite>,
+or can be saved locally with <cite>write_html()</cite>.</p>
+</dd></dl>
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+  <section id="module-pypath.omnipath.server.generate_about_page">
+<span id="pypath-omnipath-server-generate-about-page"></span><h1>pypath.omnipath.server.generate_about_page<a class="headerlink" href="#module-pypath.omnipath.server.generate_about_page" title="Link to this heading">§</a></h1>
+<dl class="field-list simple">
+<dt class="field-odd">members<span class="colon">:</span></dt>
+<dd class="field-odd"><p></p></dd>
+</dl>
+<p class="rubric">Functions</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.omnipath.server.generate_about_page.export_licenses.html#pypath.omnipath.server.generate_about_page.export_licenses" title="pypath.omnipath.server.generate_about_page.export_licenses"><code class="xref py py-obj docutils literal notranslate"><span class="pre">export_licenses</span></code></a>(descriptions[, outfile])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.omnipath.server.generate_about_page.generate_about_html.html#pypath.omnipath.server.generate_about_page.generate_about_html" title="pypath.omnipath.server.generate_about_page.generate_about_html"><code class="xref py py-obj docutils literal notranslate"><span class="pre">generate_about_html</span></code></a>(descriptions[, format])</p></td>
+<td><p>Generates a HTML page from the <cite>descriptions</cite> array.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.omnipath.server.generate_about_page.resource_list_latex.html#pypath.omnipath.server.generate_about_page.resource_list_latex" title="pypath.omnipath.server.generate_about_page.resource_list_latex"><code class="xref py py-obj docutils literal notranslate"><span class="pre">resource_list_latex</span></code></a>(descriptions[, ...])</p></td>
+<td><p>Generates Supplementary Table 3 (The list of the 52 resources considered) for the article.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.omnipath.server.generate_about_page.write_html.html#pypath.omnipath.server.generate_about_page.write_html" title="pypath.omnipath.server.generate_about_page.write_html"><code class="xref py py-obj docutils literal notranslate"><span class="pre">write_html</span></code></a>(descriptions[, filename])</p></td>
+<td><p>Saves the HTML descriptions to custom local file.</p></td>
+</tr>
+</tbody>
+</table>
+</section>
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diff --git a/api/pypath.omnipath.server.generate_about_page.resource_list_latex.html b/api/pypath.omnipath.server.generate_about_page.resource_list_latex.html
new file mode 100644
index 000000000..65727b2ca
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+  <section id="pypath-omnipath-server-generate-about-page-resource-list-latex">
+<h1>pypath.omnipath.server.generate_about_page.resource_list_latex<a class="headerlink" href="#pypath-omnipath-server-generate-about-page-resource-list-latex" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.omnipath.server.generate_about_page.resource_list_latex">
+<span class="sig-prename descclassname"><span class="pre">pypath.omnipath.server.generate_about_page.</span></span><span class="sig-name descname"><span class="pre">resource_list_latex</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">descriptions</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">filename</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'resource-list.tex'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">latex_hdr</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">fontsize</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">8</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">font</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'HelveticaNeueLTStd-LtCn'</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/omnipath/server/generate_about_page.html#resource_list_latex"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.omnipath.server.generate_about_page.resource_list_latex" title="Link to this definition">§</a></dt>
+<dd><p>Generates Supplementary Table 3 (The list of the 52 resources considered) for the article.</p>
+</dd></dl>
+
+</section>
+
+
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+  <section id="pypath-omnipath-server-generate-about-page-write-html">
+<h1>pypath.omnipath.server.generate_about_page.write_html<a class="headerlink" href="#pypath-omnipath-server-generate-about-page-write-html" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.omnipath.server.generate_about_page.write_html">
+<span class="sig-prename descclassname"><span class="pre">pypath.omnipath.server.generate_about_page.</span></span><span class="sig-name descname"><span class="pre">write_html</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">descriptions</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">filename</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'resources.html'</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/omnipath/server/generate_about_page.html#write_html"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.omnipath.server.generate_about_page.write_html" title="Link to this definition">§</a></dt>
+<dd><p>Saves the HTML descriptions to custom local file.</p>
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diff --git a/api/pypath.omnipath.server.html b/api/pypath.omnipath.server.html
new file mode 100644
index 000000000..9f6cbc198
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+<td><p>This is a standalone module with the only purpose of building the tables for the webservice.</p></td>
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+                  
+  <section id="pypath-omnipath-server-legacy-pypathserver">
+<h1>pypath.omnipath.server.legacy.PypathServer<a class="headerlink" href="#pypath-omnipath-server-legacy-pypathserver" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.omnipath.server.legacy.PypathServer">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.omnipath.server.legacy.</span></span><span class="sig-name descname"><span class="pre">PypathServer</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">pypath</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/omnipath/server/legacy.html#PypathServer"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.omnipath.server.legacy.PypathServer" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <a class="reference internal" href="pypath.omnipath.server.run.BaseServer.html#pypath.omnipath.server.run.BaseServer" title="pypath.omnipath.server.run.BaseServer"><code class="xref py py-class docutils literal notranslate"><span class="pre">BaseServer</span></code></a></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.omnipath.server.legacy.PypathServer.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">pypath</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/omnipath/server/legacy.html#PypathServer.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.omnipath.server.legacy.PypathServer.__init__" title="Link to this definition">§</a></dt>
+<dd></dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.omnipath.server.legacy.PypathServer.__init__" title="pypath.omnipath.server.legacy.PypathServer.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>(pypath)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">about</span></code>(req)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">info</span></code>(req)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">interactions</span></code>(req)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">network</span></code>(req)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">ptms</span></code>(req)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">render_GET</span></code>(request)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">render_POST</span></code>(request)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">resources</span></code>(req)</p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Attributes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">recomment</span></code></p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
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+
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+<p>Old server class working from a <code class="docutils literal notranslate"><span class="pre">pypath.legacy.main.PyPath</span></code> object.</p>
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diff --git a/api/pypath.omnipath.server.run.BaseServer.html b/api/pypath.omnipath.server.run.BaseServer.html
new file mode 100644
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+                <article class="bd-article">
+                  
+  <section id="pypath-omnipath-server-run-baseserver">
+<h1>pypath.omnipath.server.run.BaseServer<a class="headerlink" href="#pypath-omnipath-server-run-baseserver" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.omnipath.server.run.BaseServer">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.omnipath.server.run.</span></span><span class="sig-name descname"><span class="pre">BaseServer</span></span><a class="reference internal" href="../_modules/pypath/omnipath/server/run.html#BaseServer"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.omnipath.server.run.BaseServer" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <a class="reference internal" href="pypath.omnipath.server.run.TwistedWebResource.html#pypath.omnipath.server.run.TwistedWebResource" title="pypath.omnipath.server.run.TwistedWebResource"><code class="xref py py-class docutils literal notranslate"><span class="pre">TwistedWebResource</span></code></a>, <code class="xref py py-class docutils literal notranslate"><span class="pre">Logger</span></code></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.omnipath.server.run.BaseServer.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/omnipath/server/run.html#BaseServer.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.omnipath.server.run.BaseServer.__init__" title="Link to this definition">§</a></dt>
+<dd></dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.omnipath.server.run.BaseServer.__init__" title="pypath.omnipath.server.run.BaseServer.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">about</span></code>(req)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">info</span></code>(req)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">render_GET</span></code>(request)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">render_POST</span></code>(request)</p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Attributes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">recomment</span></code></p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
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+
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+<li class="toctree-l1 toc-h1 nav-item toc-entry"><a class="reference internal nav-link" href="../notebooks/manual.html">The pypath book</a></li>
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diff --git a/api/pypath.omnipath.server.run.Rest.html b/api/pypath.omnipath.server.run.Rest.html
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+                  
+  <section id="pypath-omnipath-server-run-rest">
+<h1>pypath.omnipath.server.run.Rest<a class="headerlink" href="#pypath-omnipath-server-run-rest" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.omnipath.server.run.Rest">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.omnipath.server.run.</span></span><span class="sig-name descname"><span class="pre">Rest</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">port</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">serverclass=&lt;class</span> <span class="pre">'pypath.omnipath.server.run.TableServer'&gt;</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">start=True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">**kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/omnipath/server/run.html#Rest"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.omnipath.server.run.Rest" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.omnipath.server.run.Rest.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">port</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">serverclass=&lt;class</span> <span class="pre">'pypath.omnipath.server.run.TableServer'&gt;</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">start=True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">**kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/omnipath/server/run.html#Rest.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.omnipath.server.run.Rest.__init__" title="Link to this definition">§</a></dt>
+<dd><p>Runs a webserver serving a <cite>PyPath</cite> instance listening
+to a custom port.</p>
+<p>:param : The port to listen to.
+:type : param int port:
+:param : The class implementing the server.
+:type : param str serverclass’
+:param : Arguments for initialization of the server class.
+:type : param <a href="#id1"><span class="problematic" id="id2">**</span></a>kwargs:</p>
+</dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.omnipath.server.run.Rest.__init__" title="pypath.omnipath.server.run.Rest.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>(port[, serverclass, start])</p></td>
+<td><p>Runs a webserver serving a <cite>PyPath</cite> instance listening to a custom port.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">start</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+</tbody>
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new file mode 100644
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+  <section id="pypath-omnipath-server-run-tableserver">
+<h1>pypath.omnipath.server.run.TableServer<a class="headerlink" href="#pypath-omnipath-server-run-tableserver" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.omnipath.server.run.TableServer">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.omnipath.server.run.</span></span><span class="sig-name descname"><span class="pre">TableServer</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">input_files</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">only_tables</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">exclude_tables</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/omnipath/server/run.html#TableServer"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.omnipath.server.run.TableServer" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <a class="reference internal" href="pypath.omnipath.server.run.BaseServer.html#pypath.omnipath.server.run.BaseServer" title="pypath.omnipath.server.run.BaseServer"><code class="xref py py-class docutils literal notranslate"><span class="pre">BaseServer</span></code></a></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.omnipath.server.run.TableServer.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">input_files</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">only_tables</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">exclude_tables</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/omnipath/server/run.html#TableServer.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.omnipath.server.run.TableServer.__init__" title="Link to this definition">§</a></dt>
+<dd><p>Server based on <code class="docutils literal notranslate"><span class="pre">pandas</span></code> data frames.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><p><strong>input_files</strong> (<em>dict</em>) – Paths to tables exported by the <code class="docutils literal notranslate"><span class="pre">pypath.websrvtab</span></code> module.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.omnipath.server.run.TableServer.__init__" title="pypath.omnipath.server.run.TableServer.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>([input_files, only_tables, ...])</p></td>
+<td><p>Server based on <code class="docutils literal notranslate"><span class="pre">pandas</span></code> data frames.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">about</span></code>(req)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">annotations</span></code>(req)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">annotations_summary</span></code>(req)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">complexes</span></code>(req)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">databases</span></code>(req)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">datasets</span></code>(req)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">enz_sub</span></code>(req)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">enzsub</span></code>(req[, organisms, enzyme_substrate])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">info</span></code>(req)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">interactions</span></code>(req[, datasets, databases, ...])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">intercell</span></code>(req)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">intercell_summary</span></code>(req)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">ptms</span></code>(req)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">queries</span></code>(req)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">render_GET</span></code>(request)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">render_POST</span></code>(request)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">resources</span></code>(req)</p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Attributes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">args_reference</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">cytoscape_attributes</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">data_query_types</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">dataset2type</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">datasets_</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">default_dtypes</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">default_input_files</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">dorothea_methods</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">enzsub_fields</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">field_synonyms</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">int_list_fields</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">interaction_fields</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">list_fields</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">query_type_synonyms</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">query_types</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">recomment</span></code></p></td>
+<td><p></p></td>
+</tr>
+</tbody>
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+                  
+  <section id="pypath-omnipath-server-run-twistedwebresource">
+<h1>pypath.omnipath.server.run.TwistedWebResource<a class="headerlink" href="#pypath-omnipath-server-run-twistedwebresource" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.omnipath.server.run.TwistedWebResource">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.omnipath.server.run.</span></span><span class="sig-name descname"><span class="pre">TwistedWebResource</span></span><a class="reference internal" href="../_modules/pypath/omnipath/server/run.html#TwistedWebResource"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.omnipath.server.run.TwistedWebResource" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.omnipath.server.run.TwistedWebResource.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.omnipath.server.run.TwistedWebResource.__init__" title="Link to this definition">§</a></dt>
+<dd></dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.omnipath.server.run.TwistedWebResource.__init__" title="pypath.omnipath.server.run.TwistedWebResource.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>()</p></td>
+<td><p></p></td>
+</tr>
+</tbody>
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diff --git a/api/pypath.omnipath.server.run.TwistedWebSite.html b/api/pypath.omnipath.server.run.TwistedWebSite.html
new file mode 100644
index 000000000..95947c378
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@@ -0,0 +1,652 @@
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+      
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+              
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+<div id="searchbox"></div>
+                <article class="bd-article">
+                  
+  <section id="pypath-omnipath-server-run-twistedwebsite">
+<h1>pypath.omnipath.server.run.TwistedWebSite<a class="headerlink" href="#pypath-omnipath-server-run-twistedwebsite" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.omnipath.server.run.TwistedWebSite">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.omnipath.server.run.</span></span><span class="sig-name descname"><span class="pre">TwistedWebSite</span></span><a class="reference internal" href="../_modules/pypath/omnipath/server/run.html#TwistedWebSite"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.omnipath.server.run.TwistedWebSite" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.omnipath.server.run.TwistedWebSite.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.omnipath.server.run.TwistedWebSite.__init__" title="Link to this definition">§</a></dt>
+<dd></dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.omnipath.server.run.TwistedWebSite.__init__" title="pypath.omnipath.server.run.TwistedWebSite.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>()</p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+</section>
+
+
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diff --git a/api/pypath.omnipath.server.run.html b/api/pypath.omnipath.server.run.html
new file mode 100644
index 000000000..242e22640
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@@ -0,0 +1,674 @@
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+<dl class="field-list simple">
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+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.omnipath.server.run.ignore_pandas_copywarn.html#pypath.omnipath.server.run.ignore_pandas_copywarn" title="pypath.omnipath.server.run.ignore_pandas_copywarn"><code class="xref py py-obj docutils literal notranslate"><span class="pre">ignore_pandas_copywarn</span></code></a>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.omnipath.server.run.stop_server.html#pypath.omnipath.server.run.stop_server" title="pypath.omnipath.server.run.stop_server"><code class="xref py py-obj docutils literal notranslate"><span class="pre">stop_server</span></code></a>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.omnipath.server.run.twisted_listen_tcp.html#pypath.omnipath.server.run.twisted_listen_tcp" title="pypath.omnipath.server.run.twisted_listen_tcp"><code class="xref py py-obj docutils literal notranslate"><span class="pre">twisted_listen_tcp</span></code></a>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.omnipath.server.run.twisted_run.html#pypath.omnipath.server.run.twisted_run" title="pypath.omnipath.server.run.twisted_run"><code class="xref py py-obj docutils literal notranslate"><span class="pre">twisted_run</span></code></a>()</p></td>
+<td><p></p></td>
+</tr>
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+</table>
+<p class="rubric">Classes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.omnipath.server.run.BaseServer.html#pypath.omnipath.server.run.BaseServer" title="pypath.omnipath.server.run.BaseServer"><code class="xref py py-obj docutils literal notranslate"><span class="pre">BaseServer</span></code></a>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.omnipath.server.run.Rest.html#pypath.omnipath.server.run.Rest" title="pypath.omnipath.server.run.Rest"><code class="xref py py-obj docutils literal notranslate"><span class="pre">Rest</span></code></a>(port[, serverclass, start])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.omnipath.server.run.TableServer.html#pypath.omnipath.server.run.TableServer" title="pypath.omnipath.server.run.TableServer"><code class="xref py py-obj docutils literal notranslate"><span class="pre">TableServer</span></code></a>([input_files, only_tables, ...])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.omnipath.server.run.TwistedWebResource.html#pypath.omnipath.server.run.TwistedWebResource" title="pypath.omnipath.server.run.TwistedWebResource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">TwistedWebResource</span></code></a>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.omnipath.server.run.TwistedWebSite.html#pypath.omnipath.server.run.TwistedWebSite" title="pypath.omnipath.server.run.TwistedWebSite"><code class="xref py py-obj docutils literal notranslate"><span class="pre">TwistedWebSite</span></code></a>()</p></td>
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diff --git a/api/pypath.omnipath.server.run.ignore_pandas_copywarn.html b/api/pypath.omnipath.server.run.ignore_pandas_copywarn.html
new file mode 100644
index 000000000..330d9ef6b
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diff --git a/api/pypath.omnipath.server.run.stop_server.html b/api/pypath.omnipath.server.run.stop_server.html
new file mode 100644
index 000000000..11c512501
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@@ -0,0 +1,638 @@
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diff --git a/api/pypath.omnipath.server.run.twisted_run.html b/api/pypath.omnipath.server.run.twisted_run.html
new file mode 100644
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diff --git a/api/pypath.resources.data_formats.transcription_deprecated.html b/api/pypath.resources.data_formats.transcription_deprecated.html
index 925126f05..85a770af6 100644
--- a/api/pypath.resources.data_formats.transcription_deprecated.html
+++ b/api/pypath.resources.data_formats.transcription_deprecated.html
@@ -47,7 +47,7 @@
     <link rel="icon" href="../_static/omnipath-logo.svg"/>
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-    <link rel="next" title="pypath.resources.licenses" href="pypath.resources.licenses.html" />
+    <link rel="next" title="pypath.resources.descriptions" href="pypath.resources.descriptions.html" />
     <link rel="prev" title="pypath.resources.data_formats.transcription_onebyone" href="pypath.resources.data_formats.transcription_onebyone.html" />
   <meta name="viewport" content="width=device-width, initial-scale=1"/>
   <meta name="docsearch:language" content="en"/>
@@ -545,11 +545,11 @@ <h1>pypath.resources.data_formats.transcription_deprecated<a class="headerlink"
       </div>
     </a>
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+       href="pypath.resources.descriptions.html"
        title="next page">
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         <p class="prev-next-subtitle">next</p>
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diff --git a/api/pypath.resources.descriptions.export_licenses.html b/api/pypath.resources.descriptions.export_licenses.html
new file mode 100644
index 000000000..f038d6482
--- /dev/null
+++ b/api/pypath.resources.descriptions.export_licenses.html
@@ -0,0 +1,638 @@
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+  <section id="pypath-resources-descriptions-export-licenses">
+<h1>pypath.resources.descriptions.export_licenses<a class="headerlink" href="#pypath-resources-descriptions-export-licenses" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.resources.descriptions.export_licenses">
+<span class="sig-prename descclassname"><span class="pre">pypath.resources.descriptions.</span></span><span class="sig-name descname"><span class="pre">export_licenses</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">outfile</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'licenses.tsv'</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/resources/descriptions.html#export_licenses"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.resources.descriptions.export_licenses" title="Link to this definition">§</a></dt>
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+    <div class="footer-items__start">
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+        <div class="footer-item">
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+    
+      © Copyright 2024, Denes Turei &lt;turei.denes@gmail.com&gt;, Nicolàs Palacio, Sebastian Lobentanzer, Olga Ivanova, Melih Darcan, Erva Ulusoy, Tennur Kilic, Omer Kaan Vural, Ahmet Rifaioglu, Charles Tapley Hoyt.
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+        <div class="footer-item">
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+    Created using <a href="https://www.sphinx-doc.org/">Sphinx</a> 7.2.6.
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+    <div class="footer-items__end">
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+  Built with the <a href="https://pydata-sphinx-theme.readthedocs.io/en/stable/index.html">PyData Sphinx Theme</a> 0.15.2.
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diff --git a/api/pypath.resources.descriptions.gen_html.html b/api/pypath.resources.descriptions.gen_html.html
new file mode 100644
index 000000000..988f094d7
--- /dev/null
+++ b/api/pypath.resources.descriptions.gen_html.html
@@ -0,0 +1,641 @@
+
+<!DOCTYPE html>
+
+
+<html lang="en" data-content_root="../" >
+
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+    <meta charset="utf-8" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="viewport" content="width=device-width, initial-scale=1" />
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+    <title>pypath.resources.descriptions.gen_html &#8212; pypath 0.16.9 documentation</title>
+  
+  
+  
+  <script data-cfasync="false">
+    document.documentElement.dataset.mode = localStorage.getItem("mode") || "";
+    document.documentElement.dataset.theme = localStorage.getItem("theme") || "light";
+  </script>
+  
+  <!-- Loaded before other Sphinx assets -->
+  <link href="../_static/styles/theme.css?digest=8d27b9dea8ad943066ae" rel="stylesheet" />
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+
+  
+  <link href="../_static/vendor/fontawesome/6.5.1/css/all.min.css?digest=8d27b9dea8ad943066ae" rel="stylesheet" />
+  <link rel="preload" as="font" type="font/woff2" crossorigin href="../_static/vendor/fontawesome/6.5.1/webfonts/fa-solid-900.woff2" />
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+<link rel="preload" as="font" type="font/woff2" crossorigin href="../_static/vendor/fontawesome/6.5.1/webfonts/fa-regular-400.woff2" />
+
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+  <!-- Pre-loaded scripts that we'll load fully later -->
+  <link rel="preload" as="script" href="../_static/scripts/bootstrap.js?digest=8d27b9dea8ad943066ae" />
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+  <script src="../_static/vendor/fontawesome/6.5.1/js/all.min.js?digest=8d27b9dea8ad943066ae"></script>
+
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+    <script>DOCUMENTATION_OPTIONS.pagename = 'api/pypath.resources.descriptions.gen_html';</script>
+    <link rel="icon" href="../_static/omnipath-logo.svg"/>
+    <link rel="index" title="Index" href="../genindex.html" />
+    <link rel="search" title="Search" href="../search.html" />
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+  <meta name="viewport" content="width=device-width, initial-scale=1"/>
+  <meta name="docsearch:language" content="en"/>
+  </head>
+  
+  
+  <body data-bs-spy="scroll" data-bs-target=".bd-toc-nav" data-offset="180" data-bs-root-margin="0px 0px -60%" data-default-mode="">
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+  
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+          name="__secondary"
+          id="__secondary"/>
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+<form class="bd-search d-flex align-items-center"
+      action="../search.html"
+      method="get">
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+         class="form-control"
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+         id="search-input"
+         placeholder="Search the docs ..."
+         aria-label="Search the docs ..."
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+         autocapitalize="off"
+         spellcheck="false"/>
+  <span class="search-button__kbd-shortcut"><kbd class="kbd-shortcut__modifier">Ctrl</kbd>+<kbd>K</kbd></span>
+</form></div>
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+<div class="bd-header__inner bd-page-width">
+  <label class="sidebar-toggle primary-toggle" for="__primary">
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+  </label>
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+  <div class=" navbar-header-items__start">
+    
+      <div class="navbar-item">
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+
+<a class="navbar-brand logo" href="../contents.html">
+  
+  
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+  
+  
+    
+    
+      
+    
+    
+    <img src="../_static/omnipath-logo.svg" class="logo__image only-light" alt="Pypath"/>
+    <script>document.write(`<img src="../_static/omnipath-logo.svg" class="logo__image only-dark" alt="Pypath"/>`);</script>
+  
+  
+    <p class="title logo__title">Pypath</p>
+  
+</a></div>
+    
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+    
+                    <li class="nav-item">
+                      <a class="nav-link nav-internal" href="../index.html">
+                        Welcome to pypath!
+                      </a>
+                    </li>
+                
+
+                    <li class="nav-item">
+                      <a class="nav-link nav-internal" href="../webservice.html">
+                        Webservice
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+                    </li>
+                
+
+                    <li class="nav-item">
+                      <a class="nav-link nav-internal" href="../releasehistory.html">
+                        Release history
+                      </a>
+                    </li>
+                
+
+                    <li class="nav-item current active">
+                      <a class="nav-link nav-internal" href="../reference.html">
+                        Reference
+                      </a>
+                    </li>
+                
+
+                    <li class="nav-item">
+                      <a class="nav-link nav-internal" href="../notebooks/manual.html">
+                        The pypath book
+                      </a>
+                    </li>
+                
+  </ul>
+</nav></div>
+      
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+    <div class="navbar-header-items__end">
+      
+        <div class="navbar-item navbar-persistent--container">
+          
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+ <script>
+ document.write(`
+   <button class="btn navbar-btn search-button-field search-button__button" title="Search" aria-label="Search" data-bs-placement="bottom" data-bs-toggle="tooltip">
+    <i class="fa-solid fa-magnifying-glass"></i>
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+    <span class="search-button__kbd-shortcut"><kbd class="kbd-shortcut__modifier">Ctrl</kbd>+<kbd class="kbd-shortcut__modifier">K</kbd></span>
+   </button>
+ `);
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+        </div>
+      
+      
+        <div class="navbar-item">
+
+<script>
+document.write(`
+  <button class="btn btn-sm navbar-btn theme-switch-button" title="light/dark" aria-label="light/dark" data-bs-placement="bottom" data-bs-toggle="tooltip">
+    <span class="theme-switch nav-link" data-mode="light"><i class="fa-solid fa-sun fa-lg"></i></span>
+    <span class="theme-switch nav-link" data-mode="dark"><i class="fa-solid fa-moon fa-lg"></i></span>
+    <span class="theme-switch nav-link" data-mode="auto"><i class="fa-solid fa-circle-half-stroke fa-lg"></i></span>
+  </button>
+`);
+</script></div>
+      
+        <div class="navbar-item"><ul class="navbar-icon-links navbar-nav"
+    aria-label="Icon Links">
+        <li class="nav-item">
+          
+          
+          
+          
+          
+          
+          
+          
+          <a href="https://github.com/saezlab/pypath" title="GitHub" class="nav-link" rel="noopener" target="_blank" data-bs-toggle="tooltip" data-bs-placement="bottom"><span><i class="fa-brands fa-square-github fa-lg" aria-hidden="true"></i></span>
+            <span class="sr-only">GitHub</span></a>
+        </li>
+        <li class="nav-item">
+          
+          
+          
+          
+          
+          
+          
+          
+          <a href="https://twitter.com/omnipathdb" title="Twitter" class="nav-link" rel="noopener" target="_blank" data-bs-toggle="tooltip" data-bs-placement="bottom"><span><i class="fa-brands fa-square-twitter fa-lg" aria-hidden="true"></i></span>
+            <span class="sr-only">Twitter</span></a>
+        </li>
+        <li class="nav-item">
+          
+          
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+          <a href="https://pypi.org/project/pypath-omnipath" title="PyPI" class="nav-link" rel="noopener" target="_blank" data-bs-toggle="tooltip" data-bs-placement="bottom"><span><i class="fa-solid fa-box fa-lg" aria-hidden="true"></i></span>
+            <span class="sr-only">PyPI</span></a>
+        </li>
+        <li class="nav-item">
+          
+          
+          
+          
+          
+          
+          
+          
+          <a href="https://omnipathdb.org/" title="OmniPath" class="nav-link" rel="noopener" target="_blank" data-bs-toggle="tooltip" data-bs-placement="bottom"><span><i class="fa-solid fa-university fa-lg" aria-hidden="true"></i></span>
+            <span class="sr-only">OmniPath</span></a>
+        </li>
+        <li class="nav-item">
+          
+          
+          
+          
+          
+          
+          
+          
+          <a href="https://saezlab.org/" title="Saez Lab" class="nav-link" rel="noopener" target="_blank" data-bs-toggle="tooltip" data-bs-placement="bottom"><span><i class="fa-solid fa-users fa-lg" aria-hidden="true"></i></span>
+            <span class="sr-only">Saez Lab</span></a>
+        </li>
+</ul></div>
+      
+    </div>
+    
+  </div>
+  
+  
+    <div class="navbar-persistent--mobile">
+
+ <script>
+ document.write(`
+   <button class="btn navbar-btn search-button-field search-button__button" title="Search" aria-label="Search" data-bs-placement="bottom" data-bs-toggle="tooltip">
+    <i class="fa-solid fa-magnifying-glass"></i>
+    <span class="search-button__default-text">Search</span>
+    <span class="search-button__kbd-shortcut"><kbd class="kbd-shortcut__modifier">Ctrl</kbd>+<kbd class="kbd-shortcut__modifier">K</kbd></span>
+   </button>
+ `);
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+    </div>
+  
+
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+    <label class="sidebar-toggle secondary-toggle" for="__secondary" tabindex="0">
+      <span class="fa-solid fa-outdent"></span>
+    </label>
+  
+</div>
+
+    </header>
+  
+
+  <div class="bd-container">
+    <div class="bd-container__inner bd-page-width">
+      
+      
+      
+      <div class="bd-sidebar-primary bd-sidebar">
+        
+
+  
+  <div class="sidebar-header-items sidebar-primary__section">
+    
+    
+      <div class="sidebar-header-items__center">
+        
+          <div class="navbar-item">
+<nav class="navbar-nav">
+  <ul class="bd-navbar-elements navbar-nav">
+    
+                    <li class="nav-item">
+                      <a class="nav-link nav-internal" href="../index.html">
+                        Welcome to pypath!
+                      </a>
+                    </li>
+                
+
+                    <li class="nav-item">
+                      <a class="nav-link nav-internal" href="../webservice.html">
+                        Webservice
+                      </a>
+                    </li>
+                
+
+                    <li class="nav-item">
+                      <a class="nav-link nav-internal" href="../releasehistory.html">
+                        Release history
+                      </a>
+                    </li>
+                
+
+                    <li class="nav-item current active">
+                      <a class="nav-link nav-internal" href="../reference.html">
+                        Reference
+                      </a>
+                    </li>
+                
+
+                    <li class="nav-item">
+                      <a class="nav-link nav-internal" href="../notebooks/manual.html">
+                        The pypath book
+                      </a>
+                    </li>
+                
+  </ul>
+</nav></div>
+        
+      </div>
+    
+    
+    
+      <div class="sidebar-header-items__end">
+        
+          <div class="navbar-item">
+
+<script>
+document.write(`
+  <button class="btn btn-sm navbar-btn theme-switch-button" title="light/dark" aria-label="light/dark" data-bs-placement="bottom" data-bs-toggle="tooltip">
+    <span class="theme-switch nav-link" data-mode="light"><i class="fa-solid fa-sun fa-lg"></i></span>
+    <span class="theme-switch nav-link" data-mode="dark"><i class="fa-solid fa-moon fa-lg"></i></span>
+    <span class="theme-switch nav-link" data-mode="auto"><i class="fa-solid fa-circle-half-stroke fa-lg"></i></span>
+  </button>
+`);
+</script></div>
+        
+          <div class="navbar-item"><ul class="navbar-icon-links navbar-nav"
+    aria-label="Icon Links">
+        <li class="nav-item">
+          
+          
+          
+          
+          
+          
+          
+          
+          <a href="https://github.com/saezlab/pypath" title="GitHub" class="nav-link" rel="noopener" target="_blank" data-bs-toggle="tooltip" data-bs-placement="bottom"><span><i class="fa-brands fa-square-github fa-lg" aria-hidden="true"></i></span>
+            <span class="sr-only">GitHub</span></a>
+        </li>
+        <li class="nav-item">
+          
+          
+          
+          
+          
+          
+          
+          
+          <a href="https://twitter.com/omnipathdb" title="Twitter" class="nav-link" rel="noopener" target="_blank" data-bs-toggle="tooltip" data-bs-placement="bottom"><span><i class="fa-brands fa-square-twitter fa-lg" aria-hidden="true"></i></span>
+            <span class="sr-only">Twitter</span></a>
+        </li>
+        <li class="nav-item">
+          
+          
+          
+          
+          
+          
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+          
+          <a href="https://pypi.org/project/pypath-omnipath" title="PyPI" class="nav-link" rel="noopener" target="_blank" data-bs-toggle="tooltip" data-bs-placement="bottom"><span><i class="fa-solid fa-box fa-lg" aria-hidden="true"></i></span>
+            <span class="sr-only">PyPI</span></a>
+        </li>
+        <li class="nav-item">
+          
+          
+          
+          
+          
+          
+          
+          
+          <a href="https://omnipathdb.org/" title="OmniPath" class="nav-link" rel="noopener" target="_blank" data-bs-toggle="tooltip" data-bs-placement="bottom"><span><i class="fa-solid fa-university fa-lg" aria-hidden="true"></i></span>
+            <span class="sr-only">OmniPath</span></a>
+        </li>
+        <li class="nav-item">
+          
+          
+          
+          
+          
+          
+          
+          
+          <a href="https://saezlab.org/" title="Saez Lab" class="nav-link" rel="noopener" target="_blank" data-bs-toggle="tooltip" data-bs-placement="bottom"><span><i class="fa-solid fa-users fa-lg" aria-hidden="true"></i></span>
+            <span class="sr-only">Saez Lab</span></a>
+        </li>
+</ul></div>
+        
+      </div>
+    
+  </div>
+  
+    <div class="sidebar-primary-items__start sidebar-primary__section">
+        <div class="sidebar-primary-item">
+<nav class="bd-docs-nav bd-links"
+     aria-label="Section Navigation">
+  <p class="bd-links__title" role="heading" aria-level="1">Section Navigation</p>
+  <div class="bd-toc-item navbar-nav"></div>
+</nav></div>
+    </div>
+  
+  
+  <div class="sidebar-primary-items__end sidebar-primary__section">
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+  
+  <div id="rtd-footer-container"></div>
+
+
+      </div>
+      
+      <main id="main-content" class="bd-main">
+        
+        
+          <div class="bd-content">
+            <div class="bd-article-container">
+              
+              <div class="bd-header-article">
+<div class="header-article-items header-article__inner">
+  
+    <div class="header-article-items__start">
+      
+        <div class="header-article-item">
+
+
+
+
+
+<nav aria-label="Breadcrumb">
+  <ul class="bd-breadcrumbs">
+    
+    <li class="breadcrumb-item breadcrumb-home">
+      <a href="../contents.html" class="nav-link" aria-label="Home">
+        <i class="fa-solid fa-home"></i>
+      </a>
+    </li>
+    
+    <li class="breadcrumb-item"><a href="../reference.html" class="nav-link">Reference</a></li>
+    
+    
+    <li class="breadcrumb-item"><i class="fa-solid fa-ellipsis"></i></li>
+    
+    
+    <li class="breadcrumb-item"><a href="pypath.resources.descriptions.html" class="nav-link">pypath.resources.descriptions</a></li>
+    
+    <li class="breadcrumb-item active" aria-current="page">pypath.resou...</li>
+  </ul>
+</nav>
+</div>
+      
+    </div>
+  
+  
+</div>
+</div>
+              
+              
+              
+                
+<div id="searchbox"></div>
+                <article class="bd-article">
+                  
+  <section id="pypath-resources-descriptions-gen-html">
+<h1>pypath.resources.descriptions.gen_html<a class="headerlink" href="#pypath-resources-descriptions-gen-html" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.resources.descriptions.gen_html">
+<span class="sig-prename descclassname"><span class="pre">pypath.resources.descriptions.</span></span><span class="sig-name descname"><span class="pre">gen_html</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/resources/descriptions.html#gen_html"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.resources.descriptions.gen_html" title="Link to this definition">§</a></dt>
+<dd><p>Generates a HTML page from the <cite>descriptions</cite> array.
+This HTML is provided by the webservice under <cite>/info</cite>,
+or can be saved locally with <cite>write_html()</cite>.</p>
+</dd></dl>
+
+</section>
+
+
+                </article>
+              
+              
+              
+              
+              
+                <footer class="prev-next-footer">
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+<div class="prev-next-area">
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+       href="pypath.resources.descriptions.export_licenses.html"
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+      <i class="fa-solid fa-angle-left"></i>
+      <div class="prev-next-info">
+        <p class="prev-next-subtitle">previous</p>
+        <p class="prev-next-title">pypath.resources.descriptions.export_licenses</p>
+      </div>
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+    <a class="right-next"
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+    class="page-toc tocsection onthispage">
+    <i class="fa-solid fa-list"></i> On this page
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+  <nav class="bd-toc-nav page-toc" aria-labelledby="pst-page-navigation-heading-2">
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+                  
+  <section id="module-pypath.resources.descriptions">
+<span id="pypath-resources-descriptions"></span><h1>pypath.resources.descriptions<a class="headerlink" href="#module-pypath.resources.descriptions" title="Link to this heading">§</a></h1>
+<dl class="field-list simple">
+<dt class="field-odd">members<span class="colon">:</span></dt>
+<dd class="field-odd"><p></p></dd>
+</dl>
+<p class="rubric">Functions</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.resources.descriptions.export_licenses.html#pypath.resources.descriptions.export_licenses" title="pypath.resources.descriptions.export_licenses"><code class="xref py py-obj docutils literal notranslate"><span class="pre">export_licenses</span></code></a>([outfile])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.resources.descriptions.gen_html.html#pypath.resources.descriptions.gen_html" title="pypath.resources.descriptions.gen_html"><code class="xref py py-obj docutils literal notranslate"><span class="pre">gen_html</span></code></a>()</p></td>
+<td><p>Generates a HTML page from the <cite>descriptions</cite> array.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.resources.descriptions.resource_list_latex.html#pypath.resources.descriptions.resource_list_latex" title="pypath.resources.descriptions.resource_list_latex"><code class="xref py py-obj docutils literal notranslate"><span class="pre">resource_list_latex</span></code></a>([filename, latex_hdr, ...])</p></td>
+<td><p>Generates Supplementary Table 3 (The list of the 52 resources considered) for the article.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.resources.descriptions.write_html.html#pypath.resources.descriptions.write_html" title="pypath.resources.descriptions.write_html"><code class="xref py py-obj docutils literal notranslate"><span class="pre">write_html</span></code></a>([filename])</p></td>
+<td><p>Saves the HTML descriptions to custom local file.</p></td>
+</tr>
+</tbody>
+</table>
+</section>
+
+
+                </article>
+              
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+    Created using <a href="https://www.sphinx-doc.org/">Sphinx</a> 7.2.6.
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diff --git a/api/pypath.resources.descriptions.resource_list_latex.html b/api/pypath.resources.descriptions.resource_list_latex.html
new file mode 100644
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@@ -0,0 +1,639 @@
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+                        Release history
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+                        Reference
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+      
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+  <section id="pypath-resources-descriptions-resource-list-latex">
+<h1>pypath.resources.descriptions.resource_list_latex<a class="headerlink" href="#pypath-resources-descriptions-resource-list-latex" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.resources.descriptions.resource_list_latex">
+<span class="sig-prename descclassname"><span class="pre">pypath.resources.descriptions.</span></span><span class="sig-name descname"><span class="pre">resource_list_latex</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">filename</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'resource-list.tex'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">latex_hdr</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">fontsize</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">8</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">font</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'HelveticaNeueLTStd-LtCn'</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/resources/descriptions.html#resource_list_latex"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.resources.descriptions.resource_list_latex" title="Link to this definition">§</a></dt>
+<dd><p>Generates Supplementary Table 3 (The list of the 52 resources considered) for the article.</p>
+</dd></dl>
+
+</section>
+
+
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+            <span class="sr-only">Saez Lab</span></a>
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+</ul></div>
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+              
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+<div class="header-article-items header-article__inner">
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+
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+  <ul class="bd-breadcrumbs">
+    
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+      <a href="../contents.html" class="nav-link" aria-label="Home">
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+    <li class="breadcrumb-item"><a href="../reference.html" class="nav-link">Reference</a></li>
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+    <li class="breadcrumb-item"><i class="fa-solid fa-ellipsis"></i></li>
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+    <li class="breadcrumb-item"><a href="pypath.resources.descriptions.html" class="nav-link">pypath.resources.descriptions</a></li>
+    
+    <li class="breadcrumb-item active" aria-current="page">pypath.resou...</li>
+  </ul>
+</nav>
+</div>
+      
+    </div>
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+  
+</div>
+</div>
+              
+              
+              
+                
+<div id="searchbox"></div>
+                <article class="bd-article">
+                  
+  <section id="pypath-resources-descriptions-write-html">
+<h1>pypath.resources.descriptions.write_html<a class="headerlink" href="#pypath-resources-descriptions-write-html" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.resources.descriptions.write_html">
+<span class="sig-prename descclassname"><span class="pre">pypath.resources.descriptions.</span></span><span class="sig-name descname"><span class="pre">write_html</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">filename</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'resources.html'</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/resources/descriptions.html#write_html"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.resources.descriptions.write_html" title="Link to this definition">§</a></dt>
+<dd><p>Saves the HTML descriptions to custom local file.</p>
+</dd></dl>
+
+</section>
+
+
+                </article>
+              
+              
+              
+              
+              
+                <footer class="prev-next-footer">
+                  
+<div class="prev-next-area">
+    <a class="left-prev"
+       href="pypath.resources.descriptions.resource_list_latex.html"
+       title="previous page">
+      <i class="fa-solid fa-angle-left"></i>
+      <div class="prev-next-info">
+        <p class="prev-next-subtitle">previous</p>
+        <p class="prev-next-title">pypath.resources.descriptions.resource_list_latex</p>
+      </div>
+    </a>
+    <a class="right-next"
+       href="pypath.resources.licenses.html"
+       title="next page">
+      <div class="prev-next-info">
+        <p class="prev-next-subtitle">next</p>
+        <p class="prev-next-title">pypath.resources.licenses</p>
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+            </div>
+            
+            
+              
+                <div class="bd-sidebar-secondary bd-toc"><div class="sidebar-secondary-items sidebar-secondary__inner">
+
+
+  <div class="sidebar-secondary-item">
+<div
+    id="pst-page-navigation-heading-2"
+    class="page-toc tocsection onthispage">
+    <i class="fa-solid fa-list"></i> On this page
+  </div>
+  <nav class="bd-toc-nav page-toc" aria-labelledby="pst-page-navigation-heading-2">
+    <ul class="visible nav section-nav flex-column">
+<li class="toctree-l1 toc-h1 nav-item toc-entry"><a class="reference internal nav-link" href="../index.html">Welcome to pypath!</a></li>
+<li class="toctree-l1 toc-h1 nav-item toc-entry"><a class="reference internal nav-link" href="../webservice.html">Webservice</a></li>
+<li class="toctree-l1 toc-h1 nav-item toc-entry"><a class="reference internal nav-link" href="../releasehistory.html">Release history</a></li>
+<li class="toctree-l1 toc-h1 nav-item toc-entry"><a class="reference internal nav-link" href="../reference.html">Reference</a></li>
+<li class="toctree-l1 toc-h1 nav-item toc-entry"><a class="reference internal nav-link" href="../notebooks/manual.html">The pypath book</a></li>
+</ul>
+
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+
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+              
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+          </div>
+          <footer class="bd-footer-content">
+            
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+  
+  <!-- Scripts loaded after <body> so the DOM is not blocked -->
+  <script src="../_static/scripts/bootstrap.js?digest=8d27b9dea8ad943066ae"></script>
+<script src="../_static/scripts/pydata-sphinx-theme.js?digest=8d27b9dea8ad943066ae"></script>
+
+  <footer class="bd-footer">
+<div class="bd-footer__inner bd-page-width">
+  
+    <div class="footer-items__start">
+      
+        <div class="footer-item">
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+  <p class="copyright">
+    
+      © Copyright 2024, Denes Turei &lt;turei.denes@gmail.com&gt;, Nicolàs Palacio, Sebastian Lobentanzer, Olga Ivanova, Melih Darcan, Erva Ulusoy, Tennur Kilic, Omer Kaan Vural, Ahmet Rifaioglu, Charles Tapley Hoyt.
+      <br/>
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+      
+        <div class="footer-item">
+
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+    Created using <a href="https://www.sphinx-doc.org/">Sphinx</a> 7.2.6.
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+  
+    <div class="footer-items__end">
+      
+        <div class="footer-item">
+<p class="theme-version">
+  Built with the <a href="https://pydata-sphinx-theme.readthedocs.io/en/stable/index.html">PyData Sphinx Theme</a> 0.15.2.
+</p></div>
+      
+    </div>
+  
+</div>
+
+  </footer>
+  </body>
+</html>
\ No newline at end of file
diff --git a/api/pypath.resources.html b/api/pypath.resources.html
index fbe2611ca..c3e264cc3 100644
--- a/api/pypath.resources.html
+++ b/api/pypath.resources.html
@@ -48,7 +48,7 @@
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
     <link rel="next" title="pypath.resources.get_controller" href="pypath.resources.get_controller.html" />
-    <link rel="prev" title="pypath.legacy.db_categories.get_category" href="pypath.legacy.db_categories.get_category.html" />
+    <link rel="prev" title="pypath.omnipath.server.run.TwistedWebSite" href="pypath.omnipath.server.run.TwistedWebSite.html" />
   <meta name="viewport" content="width=device-width, initial-scale=1"/>
   <meta name="docsearch:language" content="en"/>
   </head>
@@ -536,13 +536,16 @@
 <tr class="row-odd"><td><p><a class="reference internal" href="pypath.resources.data_formats.html#module-pypath.resources.data_formats" title="pypath.resources.data_formats"><code class="xref py py-obj docutils literal notranslate"><span class="pre">pypath.resources.data_formats</span></code></a></p></td>
 <td><p></p></td>
 </tr>
-<tr class="row-even"><td><p><a class="reference internal" href="pypath.resources.licenses.html#module-pypath.resources.licenses" title="pypath.resources.licenses"><code class="xref py py-obj docutils literal notranslate"><span class="pre">pypath.resources.licenses</span></code></a></p></td>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.resources.descriptions.html#module-pypath.resources.descriptions" title="pypath.resources.descriptions"><code class="xref py py-obj docutils literal notranslate"><span class="pre">pypath.resources.descriptions</span></code></a></p></td>
 <td><p></p></td>
 </tr>
-<tr class="row-odd"><td><p><a class="reference internal" href="pypath.resources.network.html#module-pypath.resources.network" title="pypath.resources.network"><code class="xref py py-obj docutils literal notranslate"><span class="pre">pypath.resources.network</span></code></a></p></td>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.resources.licenses.html#module-pypath.resources.licenses" title="pypath.resources.licenses"><code class="xref py py-obj docutils literal notranslate"><span class="pre">pypath.resources.licenses</span></code></a></p></td>
 <td><p></p></td>
 </tr>
-<tr class="row-even"><td><p><a class="reference internal" href="pypath.resources.urls.html#module-pypath.resources.urls" title="pypath.resources.urls"><code class="xref py py-obj docutils literal notranslate"><span class="pre">pypath.resources.urls</span></code></a></p></td>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.resources.network.html#module-pypath.resources.network" title="pypath.resources.network"><code class="xref py py-obj docutils literal notranslate"><span class="pre">pypath.resources.network</span></code></a></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.resources.urls.html#module-pypath.resources.urls" title="pypath.resources.urls"><code class="xref py py-obj docutils literal notranslate"><span class="pre">pypath.resources.urls</span></code></a></p></td>
 <td><p></p></td>
 </tr>
 </tbody>
@@ -560,12 +563,12 @@
                   
 <div class="prev-next-area">
     <a class="left-prev"
-       href="pypath.legacy.db_categories.get_category.html"
+       href="pypath.omnipath.server.run.TwistedWebSite.html"
        title="previous page">
       <i class="fa-solid fa-angle-left"></i>
       <div class="prev-next-info">
         <p class="prev-next-subtitle">previous</p>
-        <p class="prev-next-title">pypath.legacy.db_categories.get_category</p>
+        <p class="prev-next-title">pypath.omnipath.server.run.TwistedWebSite</p>
       </div>
     </a>
     <a class="right-next"
diff --git a/api/pypath.resources.licenses.html b/api/pypath.resources.licenses.html
index 02da19f62..a5e9dfc2e 100644
--- a/api/pypath.resources.licenses.html
+++ b/api/pypath.resources.licenses.html
@@ -48,7 +48,7 @@
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
     <link rel="next" title="pypath.resources.licenses.Licenses" href="pypath.resources.licenses.Licenses.html" />
-    <link rel="prev" title="pypath.resources.data_formats.transcription_deprecated" href="pypath.resources.data_formats.transcription_deprecated.html" />
+    <link rel="prev" title="pypath.resources.descriptions.write_html" href="pypath.resources.descriptions.write_html.html" />
   <meta name="viewport" content="width=device-width, initial-scale=1"/>
   <meta name="docsearch:language" content="en"/>
   </head>
@@ -542,12 +542,12 @@
                   
 <div class="prev-next-area">
     <a class="left-prev"
-       href="pypath.resources.data_formats.transcription_deprecated.html"
+       href="pypath.resources.descriptions.write_html.html"
        title="previous page">
       <i class="fa-solid fa-angle-left"></i>
       <div class="prev-next-info">
         <p class="prev-next-subtitle">previous</p>
-        <p class="prev-next-title">pypath.resources.data_formats.transcription_deprecated</p>
+        <p class="prev-next-title">pypath.resources.descriptions.write_html</p>
       </div>
     </a>
     <a class="right-next"
diff --git a/api/pypath.utils.go.GeneOntology.html b/api/pypath.utils.go.GeneOntology.html
index d05c13221..2e16f55e9 100644
--- a/api/pypath.utils.go.GeneOntology.html
+++ b/api/pypath.utils.go.GeneOntology.html
@@ -47,7 +47,7 @@
     <link rel="icon" href="../_static/omnipath-logo.svg"/>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
-    <link rel="next" title="pypath.utils.pdb" href="pypath.utils.pdb.html" />
+    <link rel="next" title="pypath.utils.mapping" href="pypath.utils.mapping.html" />
     <link rel="prev" title="pypath.utils.go.GOCustomAnnotation" href="pypath.utils.go.GOCustomAnnotation.html" />
   <meta name="viewport" content="width=device-width, initial-scale=1"/>
   <meta name="docsearch:language" content="en"/>
@@ -810,11 +810,11 @@ <h1>pypath.utils.go.GeneOntology<a class="headerlink" href="#pypath-utils-go-gen
       </div>
     </a>
     <a class="right-next"
-       href="pypath.utils.pdb.html"
+       href="pypath.utils.mapping.html"
        title="next page">
       <div class="prev-next-info">
         <p class="prev-next-subtitle">next</p>
-        <p class="prev-next-title">pypath.utils.pdb</p>
+        <p class="prev-next-title">pypath.utils.mapping</p>
       </div>
       <i class="fa-solid fa-angle-right"></i>
     </a>
diff --git a/api/pypath.utils.html b/api/pypath.utils.html
index f55abb6e3..7deaf991a 100644
--- a/api/pypath.utils.html
+++ b/api/pypath.utils.html
@@ -522,10 +522,22 @@
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 <td><p></p></td>
 </tr>
-<tr class="row-even"><td><p><a class="reference internal" href="pypath.utils.pdb.html#module-pypath.utils.pdb" title="pypath.utils.pdb"><code class="xref py py-obj docutils literal notranslate"><span class="pre">pypath.utils.pdb</span></code></a></p></td>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.utils.mapping.html#module-pypath.utils.mapping" title="pypath.utils.mapping"><code class="xref py py-obj docutils literal notranslate"><span class="pre">pypath.utils.mapping</span></code></a></p></td>
 <td><p></p></td>
 </tr>
-<tr class="row-odd"><td><p><a class="reference internal" href="pypath.utils.proteomicsdb.html#module-pypath.utils.proteomicsdb" title="pypath.utils.proteomicsdb"><code class="xref py py-obj docutils literal notranslate"><span class="pre">pypath.utils.proteomicsdb</span></code></a></p></td>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.utils.metabo.html#module-pypath.utils.metabo" title="pypath.utils.metabo"><code class="xref py py-obj docutils literal notranslate"><span class="pre">pypath.utils.metabo</span></code></a></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.utils.orthology.html#module-pypath.utils.orthology" title="pypath.utils.orthology"><code class="xref py py-obj docutils literal notranslate"><span class="pre">pypath.utils.orthology</span></code></a></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.utils.pdb.html#module-pypath.utils.pdb" title="pypath.utils.pdb"><code class="xref py py-obj docutils literal notranslate"><span class="pre">pypath.utils.pdb</span></code></a></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.utils.proteomicsdb.html#module-pypath.utils.proteomicsdb" title="pypath.utils.proteomicsdb"><code class="xref py py-obj docutils literal notranslate"><span class="pre">pypath.utils.proteomicsdb</span></code></a></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.utils.pyreact.html#module-pypath.utils.pyreact" title="pypath.utils.pyreact"><code class="xref py py-obj docutils literal notranslate"><span class="pre">pypath.utils.pyreact</span></code></a></p></td>
 <td><p></p></td>
 </tr>
 <tr class="row-even"><td><p><a class="reference internal" href="pypath.utils.reflists.html#module-pypath.utils.reflists" title="pypath.utils.reflists"><code class="xref py py-obj docutils literal notranslate"><span class="pre">pypath.utils.reflists</span></code></a></p></td>
@@ -543,6 +555,9 @@
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 <td><p></p></td>
 </tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.utils.uniprot.html#module-pypath.utils.uniprot" title="pypath.utils.uniprot"><code class="xref py py-obj docutils literal notranslate"><span class="pre">pypath.utils.uniprot</span></code></a></p></td>
+<td><p></p></td>
+</tr>
 </tbody>
 </table>
 </section>
diff --git a/api/pypath.utils.mapping.MapReader.html b/api/pypath.utils.mapping.MapReader.html
new file mode 100644
index 000000000..59f88ba20
--- /dev/null
+++ b/api/pypath.utils.mapping.MapReader.html
@@ -0,0 +1,901 @@
+
+<!DOCTYPE html>
+
+
+<html lang="en" data-content_root="../" >
+
+  <head>
+    <meta charset="utf-8" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="viewport" content="width=device-width, initial-scale=1" />
+
+    <title>pypath.utils.mapping.MapReader &#8212; pypath 0.16.9 documentation</title>
+  
+  
+  
+  <script data-cfasync="false">
+    document.documentElement.dataset.mode = localStorage.getItem("mode") || "";
+    document.documentElement.dataset.theme = localStorage.getItem("theme") || "light";
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+  
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+<link href="../_static/styles/bootstrap.css?digest=8d27b9dea8ad943066ae" rel="stylesheet" />
+<link href="../_static/styles/pydata-sphinx-theme.css?digest=8d27b9dea8ad943066ae" rel="stylesheet" />
+
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+  <link rel="preload" as="font" type="font/woff2" crossorigin href="../_static/vendor/fontawesome/6.5.1/webfonts/fa-solid-900.woff2" />
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+    <link rel="stylesheet" type="text/css" href="../_static/copybutton.css?v=76b2166b" />
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+  
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+  <link rel="preload" as="script" href="../_static/scripts/bootstrap.js?digest=8d27b9dea8ad943066ae" />
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+    <script src="../_static/doctools.js?v=888ff710"></script>
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+    <script src="../_static/copybutton.js?v=f281be69"></script>
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+    <script>DOCUMENTATION_OPTIONS.pagename = 'api/pypath.utils.mapping.MapReader';</script>
+    <link rel="icon" href="../_static/omnipath-logo.svg"/>
+    <link rel="index" title="Index" href="../genindex.html" />
+    <link rel="search" title="Search" href="../search.html" />
+    <link rel="next" title="pypath.utils.mapping.Mapper" href="pypath.utils.mapping.Mapper.html" />
+    <link rel="prev" title="pypath.utils.mapping.translation_dict" href="pypath.utils.mapping.translation_dict.html" />
+  <meta name="viewport" content="width=device-width, initial-scale=1"/>
+  <meta name="docsearch:language" content="en"/>
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+  <section id="pypath-utils-mapping-mapreader">
+<h1>pypath.utils.mapping.MapReader<a class="headerlink" href="#pypath-utils-mapping-mapreader" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.utils.mapping.MapReader">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.utils.mapping.</span></span><span class="sig-name descname"><span class="pre">MapReader</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">param</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">load_a_to_b</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">load_b_to_a</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">uniprots</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">lifetime</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">300</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resource_id_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/utils/mapping.html#MapReader"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.utils.mapping.MapReader" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">Logger</span></code></p>
+<p>Reads ID translation data and creates <code class="docutils literal notranslate"><span class="pre">MappingTable</span></code> instances.
+When initializing ID conversion tables for the first time
+data is downloaded from UniProt and read into dictionaries.
+It takes a couple of seconds. Data is saved to pickle
+dumps, this way later the tables load much faster.</p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.utils.mapping.MapReader.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">param</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">load_a_to_b</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">load_b_to_a</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">uniprots</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">lifetime</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">300</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resource_id_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/utils/mapping.html#MapReader.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.utils.mapping.MapReader.__init__" title="Link to this definition">§</a></dt>
+<dd><dl>
+<dt>Args</dt><dd><dl class="simple">
+<dt>param (MappingInput): A mapping table definition, any child of</dt><dd><p>the <cite>internals.input_formats.MappingInput</cite> class.</p>
+</dd>
+</dl>
+<p>ncbi_tax_id (int): NCBI Taxonomy identifier of the organism.
+entity_type (str): An optional, custom string showing the type of</p>
+<blockquote>
+<div><p>the entities,  e.g. <cite>protein</cite>. This is not mandatory for the
+identification of mapping tables, hence the same name types
+can’t be used for different entities. E.g. if both proteins
+and miRNAs have Entrez gene IDs then these should be
+different ID types (e.g. <cite>entrez_protein</cite> and <cite>entrez_mirna</cite>)
+or both protein and miRNA IDs can be loaded into one mapping
+table and simply called <cite>entrez</cite>.</p>
+</div></blockquote>
+<dl class="simple">
+<dt>load_a_to_b (bool): Load the mapping table for translation from</dt><dd><p><cite>id_type</cite> to <cite>target_id_type</cite>.</p>
+</dd>
+<dt>load_b_to_a (bool): Load the mapping table for translation from</dt><dd><p><cite>target_id_type</cite> to <cite>id_type</cite>.</p>
+</dd>
+<dt>uniprots (set): UniProt IDs to query in case the source of the</dt><dd><p>mapping table is the UniProt web service.</p>
+</dd>
+<dt>lifetime (int): If this table has not been used for longer than</dt><dd><p>this preiod it is to be removed at next cleanup. Time in
+seconds. Passed to <code class="docutils literal notranslate"><span class="pre">MappingTable</span></code>.</p>
+</dd>
+<dt>resource_id_types: Additional mappings between pypath and resource</dt><dd><p>specific identifier type labels.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.utils.mapping.MapReader.__init__" title="pypath.utils.mapping.MapReader.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>(param[, ncbi_tax_id, entity_type, ...])</p></td>
+<td><p>Args</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.utils.mapping.MapReader.id_type_side" title="pypath.utils.mapping.MapReader.id_type_side"><code class="xref py py-obj docutils literal notranslate"><span class="pre">id_type_side</span></code></a>(id_type)</p></td>
+<td><p>Tells if an ID type is on the &quot;a&quot; or &quot;b&quot; (source or target) side in the current mapping table definition.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.utils.mapping.MapReader.load" title="pypath.utils.mapping.MapReader.load"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load</span></code></a>()</p></td>
+<td><p>The complete process of loading mapping tables.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.utils.mapping.MapReader.read" title="pypath.utils.mapping.MapReader.read"><code class="xref py py-obj docutils literal notranslate"><span class="pre">read</span></code></a>()</p></td>
+<td><p>Reads the ID translation data from the original source.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.utils.mapping.MapReader.read_cache" title="pypath.utils.mapping.MapReader.read_cache"><code class="xref py py-obj docutils literal notranslate"><span class="pre">read_cache</span></code></a>()</p></td>
+<td><p>Reads the ID translation data from a previously saved pickle file.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.utils.mapping.MapReader.read_mapping_array" title="pypath.utils.mapping.MapReader.read_mapping_array"><code class="xref py py-obj docutils literal notranslate"><span class="pre">read_mapping_array</span></code></a>()</p></td>
+<td><p>Loads mapping table between microarray probe IDs and genes.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.utils.mapping.MapReader.read_mapping_biomart" title="pypath.utils.mapping.MapReader.read_mapping_biomart"><code class="xref py py-obj docutils literal notranslate"><span class="pre">read_mapping_biomart</span></code></a>()</p></td>
+<td><p>Loads a mapping table using BioMart data.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.utils.mapping.MapReader.read_mapping_file" title="pypath.utils.mapping.MapReader.read_mapping_file"><code class="xref py py-obj docutils literal notranslate"><span class="pre">read_mapping_file</span></code></a>()</p></td>
+<td><p>Reads a mapping table from a local file or a function.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.utils.mapping.MapReader.read_mapping_hmdb" title="pypath.utils.mapping.MapReader.read_mapping_hmdb"><code class="xref py py-obj docutils literal notranslate"><span class="pre">read_mapping_hmdb</span></code></a>()</p></td>
+<td><p>Loads an ID translation table from th Human Metabolome Database.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">read_mapping_pro</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.utils.mapping.MapReader.read_mapping_ramp" title="pypath.utils.mapping.MapReader.read_mapping_ramp"><code class="xref py py-obj docutils literal notranslate"><span class="pre">read_mapping_ramp</span></code></a>()</p></td>
+<td><p>Loads an ID translation table from RaMP.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.utils.mapping.MapReader.read_mapping_unichem" title="pypath.utils.mapping.MapReader.read_mapping_unichem"><code class="xref py py-obj docutils literal notranslate"><span class="pre">read_mapping_unichem</span></code></a>()</p></td>
+<td><p>Loads an ID translation table from UniChem.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.utils.mapping.MapReader.read_mapping_uniprot" title="pypath.utils.mapping.MapReader.read_mapping_uniprot"><code class="xref py py-obj docutils literal notranslate"><span class="pre">read_mapping_uniprot</span></code></a>()</p></td>
+<td><p>Downloads ID mappings directly from UniProt.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.utils.mapping.MapReader.read_mapping_uniprot_list" title="pypath.utils.mapping.MapReader.read_mapping_uniprot_list"><code class="xref py py-obj docutils literal notranslate"><span class="pre">read_mapping_uniprot_list</span></code></a>()</p></td>
+<td><p>Builds a mapping table by downloading data from UniProt's upload lists service.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">reload</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.utils.mapping.MapReader.resource_id_type" title="pypath.utils.mapping.MapReader.resource_id_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">resource_id_type</span></code></a>([side])</p></td>
+<td><p>Resource specific identifier type.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.utils.mapping.MapReader.set_uniprot_space" title="pypath.utils.mapping.MapReader.set_uniprot_space"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_uniprot_space</span></code></a>([swissprot])</p></td>
+<td><p>Sets up a search space of UniProt IDs.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.utils.mapping.MapReader.setup_cache" title="pypath.utils.mapping.MapReader.setup_cache"><code class="xref py py-obj docutils literal notranslate"><span class="pre">setup_cache</span></code></a>()</p></td>
+<td><p>Constructs the cache file path as md5 hash of the parameters.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.utils.mapping.MapReader.tables_loaded" title="pypath.utils.mapping.MapReader.tables_loaded"><code class="xref py py-obj docutils literal notranslate"><span class="pre">tables_loaded</span></code></a>()</p></td>
+<td><p>Tells if the requested tables have been created.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.utils.mapping.MapReader.write_cache" title="pypath.utils.mapping.MapReader.write_cache"><code class="xref py py-obj docutils literal notranslate"><span class="pre">write_cache</span></code></a>()</p></td>
+<td><p>Exports the ID translation data into pickle files.</p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Attributes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.utils.mapping.MapReader.mapping_table_a_to_b" title="pypath.utils.mapping.MapReader.mapping_table_a_to_b"><code class="xref py py-obj docutils literal notranslate"><span class="pre">mapping_table_a_to_b</span></code></a></p></td>
+<td><p>Returns a <code class="docutils literal notranslate"><span class="pre">MappingTable</span></code> instance created from the already loaded data.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.utils.mapping.MapReader.mapping_table_b_to_a" title="pypath.utils.mapping.MapReader.mapping_table_b_to_a"><code class="xref py py-obj docutils literal notranslate"><span class="pre">mapping_table_b_to_a</span></code></a></p></td>
+<td><p>Returns a <code class="docutils literal notranslate"><span class="pre">MappingTable</span></code> instance created from the already loaded data.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">resource_id_type_a</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">resource_id_type_b</span></code></p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.utils.mapping.MapReader.id_type_side">
+<span class="sig-name descname"><span class="pre">id_type_side</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">id_type</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/utils/mapping.html#MapReader.id_type_side"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.utils.mapping.MapReader.id_type_side" title="Link to this definition">§</a></dt>
+<dd><p>Tells if an ID type is on the “a” or “b” (source or target) side
+in the current mapping table definition.</p>
+<dl class="simple">
+<dt>Args</dt><dd><p>id_type (str): An ID type label.</p>
+</dd>
+<dt>Returns</dt><dd><p>Returns the string “a” if <cite>id_type</cite> is on the source side in
+the mapping table definition, “b” if it is on the target side,
+None if the <cite>id_type</cite> is not in the definition.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.utils.mapping.MapReader.load">
+<span class="sig-name descname"><span class="pre">load</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/utils/mapping.html#MapReader.load"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.utils.mapping.MapReader.load" title="Link to this definition">§</a></dt>
+<dd><p>The complete process of loading mapping tables. First sets up the
+paths of the cache files, then loads the tables from the cache files
+or the original sources if necessary. Upon successful loading from an
+original source writes the results to cache files.</p>
+</dd></dl>
+
+<dl class="py property">
+<dt class="sig sig-object py" id="pypath.utils.mapping.MapReader.mapping_table_a_to_b">
+<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">mapping_table_a_to_b</span></span><a class="headerlink" href="#pypath.utils.mapping.MapReader.mapping_table_a_to_b" title="Link to this definition">§</a></dt>
+<dd><p>Returns a <code class="docutils literal notranslate"><span class="pre">MappingTable</span></code> instance created from the already
+loaded data.</p>
+</dd></dl>
+
+<dl class="py property">
+<dt class="sig sig-object py" id="pypath.utils.mapping.MapReader.mapping_table_b_to_a">
+<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">mapping_table_b_to_a</span></span><a class="headerlink" href="#pypath.utils.mapping.MapReader.mapping_table_b_to_a" title="Link to this definition">§</a></dt>
+<dd><p>Returns a <code class="docutils literal notranslate"><span class="pre">MappingTable</span></code> instance created from the already
+loaded data.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.utils.mapping.MapReader.read">
+<span class="sig-name descname"><span class="pre">read</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/utils/mapping.html#MapReader.read"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.utils.mapping.MapReader.read" title="Link to this definition">§</a></dt>
+<dd><p>Reads the ID translation data from the original source.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.utils.mapping.MapReader.read_cache">
+<span class="sig-name descname"><span class="pre">read_cache</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/utils/mapping.html#MapReader.read_cache"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.utils.mapping.MapReader.read_cache" title="Link to this definition">§</a></dt>
+<dd><p>Reads the ID translation data from a previously saved pickle file.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.utils.mapping.MapReader.read_mapping_array">
+<span class="sig-name descname"><span class="pre">read_mapping_array</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/utils/mapping.html#MapReader.read_mapping_array"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.utils.mapping.MapReader.read_mapping_array" title="Link to this definition">§</a></dt>
+<dd><p>Loads mapping table between microarray probe IDs and genes.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.utils.mapping.MapReader.read_mapping_biomart">
+<span class="sig-name descname"><span class="pre">read_mapping_biomart</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/utils/mapping.html#MapReader.read_mapping_biomart"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.utils.mapping.MapReader.read_mapping_biomart" title="Link to this definition">§</a></dt>
+<dd><p>Loads a mapping table using BioMart data.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.utils.mapping.MapReader.read_mapping_file">
+<span class="sig-name descname"><span class="pre">read_mapping_file</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/utils/mapping.html#MapReader.read_mapping_file"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.utils.mapping.MapReader.read_mapping_file" title="Link to this definition">§</a></dt>
+<dd><p>Reads a mapping table from a local file or a function.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.utils.mapping.MapReader.read_mapping_hmdb">
+<span class="sig-name descname"><span class="pre">read_mapping_hmdb</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/utils/mapping.html#MapReader.read_mapping_hmdb"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.utils.mapping.MapReader.read_mapping_hmdb" title="Link to this definition">§</a></dt>
+<dd><p>Loads an ID translation table from th Human Metabolome Database.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.utils.mapping.MapReader.read_mapping_ramp">
+<span class="sig-name descname"><span class="pre">read_mapping_ramp</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/utils/mapping.html#MapReader.read_mapping_ramp"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.utils.mapping.MapReader.read_mapping_ramp" title="Link to this definition">§</a></dt>
+<dd><p>Loads an ID translation table from RaMP.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.utils.mapping.MapReader.read_mapping_unichem">
+<span class="sig-name descname"><span class="pre">read_mapping_unichem</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/utils/mapping.html#MapReader.read_mapping_unichem"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.utils.mapping.MapReader.read_mapping_unichem" title="Link to this definition">§</a></dt>
+<dd><p>Loads an ID translation table from UniChem.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.utils.mapping.MapReader.read_mapping_uniprot">
+<span class="sig-name descname"><span class="pre">read_mapping_uniprot</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/utils/mapping.html#MapReader.read_mapping_uniprot"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.utils.mapping.MapReader.read_mapping_uniprot" title="Link to this definition">§</a></dt>
+<dd><p>Downloads ID mappings directly from UniProt.
+See the names of possible identifiers here:
+<a class="reference external" href="http://www.uniprot.org/help/programmatic_access">http://www.uniprot.org/help/programmatic_access</a></p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.utils.mapping.MapReader.read_mapping_uniprot_list">
+<span class="sig-name descname"><span class="pre">read_mapping_uniprot_list</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/utils/mapping.html#MapReader.read_mapping_uniprot_list"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.utils.mapping.MapReader.read_mapping_uniprot_list" title="Link to this definition">§</a></dt>
+<dd><p>Builds a mapping table by downloading data from UniProt’s
+upload lists service.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.utils.mapping.MapReader.resource_id_type">
+<span class="sig-name descname"><span class="pre">resource_id_type</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">side</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">typing.Literal['a',</span> <span class="pre">'b']</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span></span><a class="reference internal" href="../_modules/pypath/utils/mapping.html#MapReader.resource_id_type"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.utils.mapping.MapReader.resource_id_type" title="Link to this definition">§</a></dt>
+<dd><p>Resource specific identifier type.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.utils.mapping.MapReader.set_uniprot_space">
+<span class="sig-name descname"><span class="pre">set_uniprot_space</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">swissprot</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/utils/mapping.html#MapReader.set_uniprot_space"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.utils.mapping.MapReader.set_uniprot_space" title="Link to this definition">§</a></dt>
+<dd><p>Sets up a search space of UniProt IDs.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>swissprot (bool): Use only SwissProt IDs, not TrEMBL. True</dt><dd><p>loads only SwissProt IDs, False only TrEMBL IDs, None
+loads both.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.utils.mapping.MapReader.setup_cache">
+<span class="sig-name descname"><span class="pre">setup_cache</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/utils/mapping.html#MapReader.setup_cache"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.utils.mapping.MapReader.setup_cache" title="Link to this definition">§</a></dt>
+<dd><p>Constructs the cache file path as md5 hash of the parameters.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.utils.mapping.MapReader.tables_loaded">
+<span class="sig-name descname"><span class="pre">tables_loaded</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/utils/mapping.html#MapReader.tables_loaded"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.utils.mapping.MapReader.tables_loaded" title="Link to this definition">§</a></dt>
+<dd><p>Tells if the requested tables have been created.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.utils.mapping.MapReader.write_cache">
+<span class="sig-name descname"><span class="pre">write_cache</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/utils/mapping.html#MapReader.write_cache"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.utils.mapping.MapReader.write_cache" title="Link to this definition">§</a></dt>
+<dd><p>Exports the ID translation data into pickle files.</p>
+</dd></dl>
+
+</dd></dl>
+
+</section>
+
+
+                </article>
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+  <section id="pypath-utils-mapping-mapper">
+<h1>pypath.utils.mapping.Mapper<a class="headerlink" href="#pypath-utils-mapping-mapper" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.utils.mapping.Mapper">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.utils.mapping.</span></span><span class="sig-name descname"><span class="pre">Mapper</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cleanup_period</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">10</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">lifetime</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">300</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">translate_deleted_uniprot</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">keep_invalid_uniprot</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">trembl_swissprot_by_genesymbol</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/utils/mapping.html#Mapper"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.utils.mapping.Mapper" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">Logger</span></code></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.utils.mapping.Mapper.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cleanup_period</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">10</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">lifetime</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">300</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">translate_deleted_uniprot</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">keep_invalid_uniprot</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">trembl_swissprot_by_genesymbol</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/utils/mapping.html#Mapper.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.utils.mapping.Mapper.__init__" title="Link to this definition">§</a></dt>
+<dd><dl class="simple">
+<dt>cleanup_period<span class="classifier">int</span></dt><dd><p>Periodically check and remove unused mapping data.
+Time in seconds. If <cite>None</cite> tables kept forever.</p>
+</dd>
+<dt>lifetime<span class="classifier">int</span></dt><dd><p>If a table has not been used for longer than this preiod it is
+to be removed at next cleanup.</p>
+</dd>
+<dt>translate_deleted_uniprot<span class="classifier">bool</span></dt><dd><p>Do an extra attempt to translate deleted or obsolete UniProt IDs
+by retrieving their archived datasheet and use the gene symbol
+to find the corresponding valid UniProt ID?</p>
+</dd>
+<dt>keep_invalid_uniprot<span class="classifier">bool</span></dt><dd><p>If the target ID is UniProt, keep the results if they fit the
+format for UniProt IDs (we won’t check if they are deleted or
+from a different taxon). The alternative is to keep only those
+which are in the list of all UniProt IDs for the given organism.</p>
+</dd>
+<dt>trembl_swissprot_by_genesymbol<span class="classifier">bool</span></dt><dd><p>Attempt to translate TrEMBL IDs to SwissProt by translating to
+gene symbols and then to SwissProt.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.utils.mapping.Mapper.__init__" title="pypath.utils.mapping.Mapper.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>([ncbi_tax_id, cleanup_period, ...])</p></td>
+<td><p>cleanup_period : int</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.utils.mapping.Mapper.chain_map" title="pypath.utils.mapping.Mapper.chain_map"><code class="xref py py-obj docutils literal notranslate"><span class="pre">chain_map</span></code></a>(name, id_type, by_id_type, ...[, ...])</p></td>
+<td><p>Translate IDs which can not be directly translated in two steps: from <cite>id_type</cite> to <cite>via_id_type</cite> and from there to <cite>target_id_type</cite>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.utils.mapping.Mapper.create_reverse" title="pypath.utils.mapping.Mapper.create_reverse"><code class="xref py py-obj docutils literal notranslate"><span class="pre">create_reverse</span></code></a>(key)</p></td>
+<td><p>Creates a mapping table with <code class="docutils literal notranslate"><span class="pre">id_type</span></code> and <code class="docutils literal notranslate"><span class="pre">target_id_type</span></code> (i.e. direction of the ID translation) swapped.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">deleted_uniprot_genesymbol</span></code>(uniprot)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.utils.mapping.Mapper.get_table_key" title="pypath.utils.mapping.Mapper.get_table_key"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_table_key</span></code></a>(id_type, target_id_type[, ...])</p></td>
+<td><p>Returns a tuple unambigously identifying a mapping table.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.utils.mapping.Mapper.guess_type" title="pypath.utils.mapping.Mapper.guess_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">guess_type</span></code></a>(name[, entity_type])</p></td>
+<td><p>From a string, tries to guess the ID type and optionally the entity type.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.utils.mapping.Mapper.has_mapping_table" title="pypath.utils.mapping.Mapper.has_mapping_table"><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_mapping_table</span></code></a>(id_type, target_id_type[, ...])</p></td>
+<td><p>Tells if a mapping table is loaded.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">id_from_label</span></code>(label[, label_id_type, ...])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">id_from_label0</span></code>(label[, label_id_type, ...])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.utils.mapping.Mapper.id_types" title="pypath.utils.mapping.Mapper.id_types"><code class="xref py py-obj docutils literal notranslate"><span class="pre">id_types</span></code></a>()</p></td>
+<td><p>A list of all identifier types that can be handled by any of the resources.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.utils.mapping.Mapper.identifier" title="pypath.utils.mapping.Mapper.identifier"><code class="xref py py-obj docutils literal notranslate"><span class="pre">identifier</span></code></a>(label[, ncbi_tax_id, id_type, ...])</p></td>
+<td><p>For a label returns the corresponding primary identifier.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">identifier0</span></code>(label[, ncbi_tax_id, id_type, ...])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.utils.mapping.Mapper.label" title="pypath.utils.mapping.Mapper.label"><code class="xref py py-obj docutils literal notranslate"><span class="pre">label</span></code></a>(name[, entity_type, id_type, ncbi_tax_id])</p></td>
+<td><p>For any kind of entity, either protein, miRNA or protein complex, returns the preferred human readable label.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.utils.mapping.Mapper.load_genesymbol5" title="pypath.utils.mapping.Mapper.load_genesymbol5"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_genesymbol5</span></code></a>([ncbi_tax_id])</p></td>
+<td><p>Creates a Gene Symbol to UniProt mapping table with the first 5 characters of each Gene Symbol.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.utils.mapping.Mapper.load_mapping" title="pypath.utils.mapping.Mapper.load_mapping"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_mapping</span></code></a>(resource, **kwargs)</p></td>
+<td><p>Loads a single mapping table based on input definition in <code class="docutils literal notranslate"><span class="pre">resource</span></code>.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.utils.mapping.Mapper.load_uniprot_static" title="pypath.utils.mapping.Mapper.load_uniprot_static"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_uniprot_static</span></code></a>(keys[, ncbi_tax_id])</p></td>
+<td><p>Loads mapping tables from the huge static mapping file from UniProt.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.utils.mapping.Mapper.map_name" title="pypath.utils.mapping.Mapper.map_name"><code class="xref py py-obj docutils literal notranslate"><span class="pre">map_name</span></code></a>(name[, id_type, target_id_type, ...])</p></td>
+<td><p>Translates one instance of one ID type to a different one.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.utils.mapping.Mapper.map_name0" title="pypath.utils.mapping.Mapper.map_name0"><code class="xref py py-obj docutils literal notranslate"><span class="pre">map_name0</span></code></a>(name[, id_type, target_id_type, ...])</p></td>
+<td><p>Translates the name and returns only one of the resulted IDs.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.utils.mapping.Mapper.map_names" title="pypath.utils.mapping.Mapper.map_names"><code class="xref py py-obj docutils literal notranslate"><span class="pre">map_names</span></code></a>(names[, id_type, target_id_type, ...])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">map_name</span></code> but translates multiple IDs at once.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.utils.mapping.Mapper.mapping_tables" title="pypath.utils.mapping.Mapper.mapping_tables"><code class="xref py py-obj docutils literal notranslate"><span class="pre">mapping_tables</span></code></a>()</p></td>
+<td><p>List of mapping tables available to load.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.utils.mapping.Mapper.only_uniprot_ac" title="pypath.utils.mapping.Mapper.only_uniprot_ac"><code class="xref py py-obj docutils literal notranslate"><span class="pre">only_uniprot_ac</span></code></a>(uniprots)</p></td>
+<td><p>For one or more strings returns only those which match the format of UniProt accession numbers.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">only_valid_uniprots</span></code>(uniprots[, ncbi_tax_id])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.utils.mapping.Mapper.other_organism_uniprot" title="pypath.utils.mapping.Mapper.other_organism_uniprot"><code class="xref py py-obj docutils literal notranslate"><span class="pre">other_organism_uniprot</span></code></a>(uniprot[, ncbi_tax_id])</p></td>
+<td><p>Tells if <code class="docutils literal notranslate"><span class="pre">uniprot</span></code> is an UniProt ID from some other organism than <code class="docutils literal notranslate"><span class="pre">ncbi_tax_id</span></code>.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.utils.mapping.Mapper.primary_uniprot" title="pypath.utils.mapping.Mapper.primary_uniprot"><code class="xref py py-obj docutils literal notranslate"><span class="pre">primary_uniprot</span></code></a>(uniprots[, ncbi_tax_id])</p></td>
+<td><p>For an iterable of UniProt IDs returns a set with the secondary IDs changed to the corresponding primary IDs.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.utils.mapping.Mapper.reload" title="pypath.utils.mapping.Mapper.reload"><code class="xref py py-obj docutils literal notranslate"><span class="pre">reload</span></code></a>()</p></td>
+<td><p>Reload the class from the module level.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.utils.mapping.Mapper.remove_expired" title="pypath.utils.mapping.Mapper.remove_expired"><code class="xref py py-obj docutils literal notranslate"><span class="pre">remove_expired</span></code></a>()</p></td>
+<td><p>Removes tables last used a longer time ago than their lifetime.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.utils.mapping.Mapper.remove_key" title="pypath.utils.mapping.Mapper.remove_key"><code class="xref py py-obj docutils literal notranslate"><span class="pre">remove_key</span></code></a>(key)</p></td>
+<td><p>Removes the table with key <code class="docutils literal notranslate"><span class="pre">key</span></code> if exists.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.utils.mapping.Mapper.remove_table" title="pypath.utils.mapping.Mapper.remove_table"><code class="xref py py-obj docutils literal notranslate"><span class="pre">remove_table</span></code></a>(id_type, target_id_type, ...)</p></td>
+<td><p>Removes the table defined by the ID types and organism.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.utils.mapping.Mapper.reverse_key" title="pypath.utils.mapping.Mapper.reverse_key"><code class="xref py py-obj docutils literal notranslate"><span class="pre">reverse_key</span></code></a>(key)</p></td>
+<td><p>For a mapping table key returns a new key with the identifiers reversed.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.utils.mapping.Mapper.reverse_mapping" title="pypath.utils.mapping.Mapper.reverse_mapping"><code class="xref py py-obj docutils literal notranslate"><span class="pre">reverse_mapping</span></code></a>(mapping_table)</p></td>
+<td><p>Creates an opposite direction <cite>MappingTable</cite> by swapping the dictionary inside an existing <cite>MappingTable</cite> object.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.utils.mapping.Mapper.swissprots" title="pypath.utils.mapping.Mapper.swissprots"><code class="xref py py-obj docutils literal notranslate"><span class="pre">swissprots</span></code></a>(uniprots[, ncbi_tax_id])</p></td>
+<td><p>Creates a dict translating a set of potentially secondary and non-reviewed UniProt IDs to primary SwissProt IDs (whenever is possible).</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.utils.mapping.Mapper.translate_deleted_uniprot_by_genesymbol" title="pypath.utils.mapping.Mapper.translate_deleted_uniprot_by_genesymbol"><code class="xref py py-obj docutils literal notranslate"><span class="pre">translate_deleted_uniprot_by_genesymbol</span></code></a>(uniprot)</p></td>
+<td><p>Due to potentially ambiguous translation always returns set.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">translate_deleted_uniprots_by_genesymbol</span></code>(...)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.utils.mapping.Mapper.translation_df" title="pypath.utils.mapping.Mapper.translation_df"><code class="xref py py-obj docutils literal notranslate"><span class="pre">translation_df</span></code></a>(id_type, target_id_type[, ...])</p></td>
+<td><p>Translation table as a data frame.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.utils.mapping.Mapper.translation_dict" title="pypath.utils.mapping.Mapper.translation_dict"><code class="xref py py-obj docutils literal notranslate"><span class="pre">translation_dict</span></code></a>(id_type, target_id_type[, ...])</p></td>
+<td><p>Translation table as a dict.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.utils.mapping.Mapper.trembl_swissprot" title="pypath.utils.mapping.Mapper.trembl_swissprot"><code class="xref py py-obj docutils literal notranslate"><span class="pre">trembl_swissprot</span></code></a>(uniprots[, ncbi_tax_id])</p></td>
+<td><p>For an iterable of TrEMBL and SwissProt IDs, returns a set with only SwissProt, mapping from TrEMBL to gene symbols, and then back to SwissProt.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.utils.mapping.Mapper.uniprot_cleanup" title="pypath.utils.mapping.Mapper.uniprot_cleanup"><code class="xref py py-obj docutils literal notranslate"><span class="pre">uniprot_cleanup</span></code></a>(uniprots[, ncbi_tax_id])</p></td>
+<td><p>We use this function as a standard callback when the target ID type is UniProt.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.utils.mapping.Mapper.valid_uniprot" title="pypath.utils.mapping.Mapper.valid_uniprot"><code class="xref py py-obj docutils literal notranslate"><span class="pre">valid_uniprot</span></code></a>(uniprot[, ncbi_tax_id])</p></td>
+<td><p>If the UniProt ID <code class="docutils literal notranslate"><span class="pre">uniprot</span></code> exist in the proteome of the organism <code class="docutils literal notranslate"><span class="pre">ncbi_tax_id</span></code> returns the ID, otherwise returns None.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.utils.mapping.Mapper.which_table" title="pypath.utils.mapping.Mapper.which_table"><code class="xref py py-obj docutils literal notranslate"><span class="pre">which_table</span></code></a>(id_type, target_id_type[, load, ...])</p></td>
+<td><p>Returns the table which is suitable to convert an ID of id_type to target_id_type.</p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Attributes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">default_label_types</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">default_name_types</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">label_type_to_id_type</span></code></p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.utils.mapping.Mapper.chain_map">
+<span class="sig-name descname"><span class="pre">chain_map</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">id_type</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">by_id_type</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">target_id_type</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/utils/mapping.html#Mapper.chain_map"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.utils.mapping.Mapper.chain_map" title="Link to this definition">§</a></dt>
+<dd><p>Translate IDs which can not be directly translated in two steps:
+from <cite>id_type</cite> to <cite>via_id_type</cite> and from there to <cite>target_id_type</cite>.</p>
+<dl>
+<dt>Args</dt><dd><p>name (str): The original name to be converted.
+id_type (str): The type of the name.
+by_id_type (str): The intermediate name type.
+target_id_type (str): The name type to translate to, more or</p>
+<blockquote>
+<div><p>less the same values are available as for <code class="docutils literal notranslate"><span class="pre">id_type</span></code>.</p>
+</div></blockquote>
+<p>ncbi_tax_id (int): The NCBI Taxonomy identifier of the organism.
+kwargs: Passed to <cite>map_name</cite>.</p>
+</dd>
+<dt>Returns</dt><dd><p>Set of IDs of type <cite>target_id_type</cite>.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.utils.mapping.Mapper.create_reverse">
+<span class="sig-name descname"><span class="pre">create_reverse</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">key</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/utils/mapping.html#Mapper.create_reverse"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.utils.mapping.Mapper.create_reverse" title="Link to this definition">§</a></dt>
+<dd><p>Creates a mapping table with <code class="docutils literal notranslate"><span class="pre">id_type</span></code> and <code class="docutils literal notranslate"><span class="pre">target_id_type</span></code>
+(i.e. direction of the ID translation) swapped.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.utils.mapping.Mapper.get_table_key">
+<span class="sig-name descname"><span class="pre">get_table_key</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">id_type</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">target_id_type</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/utils/mapping.html#Mapper.get_table_key"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.utils.mapping.Mapper.get_table_key" title="Link to this definition">§</a></dt>
+<dd><p>Returns a tuple unambigously identifying a mapping table.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.utils.mapping.Mapper.guess_type">
+<span class="sig-name descname"><span class="pre">guess_type</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/utils/mapping.html#Mapper.guess_type"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.utils.mapping.Mapper.guess_type" title="Link to this definition">§</a></dt>
+<dd><p>From a string, tries to guess the ID type and optionally the entity
+type. Returns a tuple of strings: ID type and entity type.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.utils.mapping.Mapper.has_mapping_table">
+<span class="sig-name descname"><span class="pre">has_mapping_table</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">id_type</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">target_id_type</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/utils/mapping.html#Mapper.has_mapping_table"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.utils.mapping.Mapper.has_mapping_table" title="Link to this definition">§</a></dt>
+<dd><p>Tells if a mapping table is loaded. If it’s loaded, it resets the
+expiry timer so the table remains loaded.</p>
+<dl class="simple">
+<dt>Returns</dt><dd><p>(bool): True if the mapping table is loaded.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.utils.mapping.Mapper.id_types">
+<em class="property"><span class="pre">classmethod</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">id_types</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/utils/mapping.html#Mapper.id_types"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.utils.mapping.Mapper.id_types" title="Link to this definition">§</a></dt>
+<dd><p>A list of all identifier types that can be handled by any of the
+resources.</p>
+<dl class="simple">
+<dt>Returns</dt><dd><dl class="simple">
+<dt>(list): A list of tuples with the identifier type labels used</dt><dd><p>in pypath and in the original resource. If the latter is
+None, typically the ID type has no name in the original
+resource.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.utils.mapping.Mapper.identifier">
+<span class="sig-name descname"><span class="pre">identifier</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">label</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">Iterable</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">id_type</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">Literal</span><span class="p"><span class="pre">[</span></span><span class="s"><span class="pre">'drug'</span></span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="s"><span class="pre">'lncrna'</span></span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="s"><span class="pre">'mirna'</span></span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="s"><span class="pre">'protein'</span></span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="s"><span class="pre">'small_molecule'</span></span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><span class="pre">Set</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">List</span><span class="p"><span class="pre">[</span></span><span class="pre">Set</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span></span></span><a class="reference internal" href="../_modules/pypath/utils/mapping.html#Mapper.identifier"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.utils.mapping.Mapper.identifier" title="Link to this definition">§</a></dt>
+<dd><p>For a label returns the corresponding primary identifier. The type
+of default identifiers is determined by the settings module. Note,
+this kind of translation is not always unambigous, one gene symbol
+might correspond to multiple UniProt IDs.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.utils.mapping.Mapper.label">
+<span class="sig-name descname"><span class="pre">label</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">id_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/utils/mapping.html#Mapper.label"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.utils.mapping.Mapper.label" title="Link to this definition">§</a></dt>
+<dd><p>For any kind of entity, either protein, miRNA or protein complex,
+returns the preferred human readable label. For proteins this means
+Gene Symbols, for miRNAs miRNA names, for complexes a series of
+Gene Symbols.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.utils.mapping.Mapper.load_genesymbol5">
+<span class="sig-name descname"><span class="pre">load_genesymbol5</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/utils/mapping.html#Mapper.load_genesymbol5"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.utils.mapping.Mapper.load_genesymbol5" title="Link to this definition">§</a></dt>
+<dd><p>Creates a Gene Symbol to UniProt mapping table with the first
+5 characters of each Gene Symbol.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.utils.mapping.Mapper.load_mapping">
+<span class="sig-name descname"><span class="pre">load_mapping</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">resource</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/utils/mapping.html#Mapper.load_mapping"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.utils.mapping.Mapper.load_mapping" title="Link to this definition">§</a></dt>
+<dd><p>Loads a single mapping table based on input definition in
+<code class="docutils literal notranslate"><span class="pre">resource</span></code>. <code class="docutils literal notranslate"><span class="pre">**kwargs</span></code> passed to <code class="docutils literal notranslate"><span class="pre">MapReader</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.utils.mapping.Mapper.load_uniprot_static">
+<span class="sig-name descname"><span class="pre">load_uniprot_static</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">keys</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/utils/mapping.html#Mapper.load_uniprot_static"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.utils.mapping.Mapper.load_uniprot_static" title="Link to this definition">§</a></dt>
+<dd><p>Loads mapping tables from the huge static mapping file from UniProt.
+Takes long to download and process, also requires more memory. This
+is the last thing we try if everything else failed.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.utils.mapping.Mapper.map_name">
+<span class="sig-name descname"><span class="pre">map_name</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">id_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">target_id_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">strict</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">expand_complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">uniprot_cleanup</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/utils/mapping.html#Mapper.map_name"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.utils.mapping.Mapper.map_name" title="Link to this definition">§</a></dt>
+<dd><p>Translates one instance of one ID type to a different one.
+Returns set of the target ID type.</p>
+<p>This function should be used to convert individual IDs.
+It takes care about everything and ideally you don’t need to
+think on the details.</p>
+<p>How does it work: looks up dictionaries between the original
+and target ID type, if doesn’t find, attempts to load from the
+predefined inputs.
+If the original name is genesymbol, first it looks up among the
+preferred gene names from UniProt, if not found, it takes an
+attempt with the alternative gene names. If the gene symbol
+still couldn’t be found, and strict = False, the last attempt
+only the first 5 characters of the gene symbol matched. If the
+target name type is uniprot, then it converts all the ACs to
+primary. Then, for the Trembl IDs it looks up the preferred gene
+names, and find Swissprot IDs with the same preferred gene name.</p>
+<dl>
+<dt>Args</dt><dd><p>name (str): The original name to be converted.
+id_type (str): The type of the name. Available by default:</p>
+<blockquote>
+<div><ul class="simple">
+<li><p>genesymbol (gene name)</p></li>
+<li><p>entrez (Entrez Gene ID [#])</p></li>
+<li><p>refseqp (NCBI RefSeq Protein ID [NP_*|XP_*])</p></li>
+<li><p>ensp (Ensembl protein ID [ENSP*])</p></li>
+<li><p>enst (Ensembl transcript ID [ENST*])</p></li>
+<li><p>ensg (Ensembl genomic DNA ID [ENSG*])</p></li>
+<li><p>hgnc (HGNC ID [HGNC:#])</p></li>
+<li><p>gi (GI number [#])</p></li>
+<li><p>embl (DDBJ/EMBL/GeneBank CDS accession)</p></li>
+<li><p>embl_id (DDBJ/EMBL/GeneBank accession)</p></li>
+</ul>
+<p>And many more, see the code of
+<code class="docutils literal notranslate"><span class="pre">pypath.internals.input_formats</span></code></p>
+</div></blockquote>
+<dl class="simple">
+<dt>target_id_type (str): The name type to translate to, more or</dt><dd><p>less the same values are available as for <code class="docutils literal notranslate"><span class="pre">id_type</span></code>.</p>
+</dd>
+</dl>
+<p>ncbi_tax_id (int): NCBI Taxonomy ID of the organism.
+strict (bool): In case a Gene Symbol can not be translated,</p>
+<blockquote>
+<div><p>try to add number “1” to the end, or try to match only
+its first five characters. This option is rarely used,
+but it makes possible to translate some non-standard
+gene names typically found in old, unmaintained resources.</p>
+</div></blockquote>
+<dl class="simple">
+<dt>expand_complexes (bool): When encountering complexes,</dt><dd><p>translated the IDs of its components and return a set
+of IDs. The alternative behaviour is to return the
+<cite>Complex</cite> objects.</p>
+</dd>
+<dt>uniprot_cleanup (bool): When the <cite>target_id_type</cite> is UniProt</dt><dd><p>ID, call the <cite>uniprot_cleanup</cite> function at the end.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.utils.mapping.Mapper.map_name0">
+<span class="sig-name descname"><span class="pre">map_name0</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">id_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">target_id_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">strict</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">expand_complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">uniprot_cleanup</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/utils/mapping.html#Mapper.map_name0"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.utils.mapping.Mapper.map_name0" title="Link to this definition">§</a></dt>
+<dd><p>Translates the name and returns only one of the resulted IDs. It
+means in case of ambiguous ID translation, a random one of them
+will be picked and returned. Recommended to use only if the
+translation between the given ID types is mostly unambigous and
+the loss of information can be ignored. See more details at
+<cite>map_name</cite>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.utils.mapping.Mapper.map_names">
+<span class="sig-name descname"><span class="pre">map_names</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">names</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">id_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">target_id_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">strict</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">expand_complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">uniprot_cleanup</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/utils/mapping.html#Mapper.map_names"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.utils.mapping.Mapper.map_names" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">map_name</span></code> but translates multiple IDs at once. These two
+functions could be seamlessly implemented as one, still I created
+separate functions to always make it explicit if a set of translated
+IDs come from multiple original IDs.</p>
+<dl>
+<dt>Args</dt><dd><p>name (str): The original name to be converted.
+id_type (str): The type of the name. Available by default:</p>
+<blockquote>
+<div><ul class="simple">
+<li><p>genesymbol (gene name)</p></li>
+<li><p>entrez (Entrez Gene ID [#])</p></li>
+<li><p>refseqp (NCBI RefSeq Protein ID [NP_*|XP_*])</p></li>
+<li><p>ensp (Ensembl protein ID [ENSP*])</p></li>
+<li><p>enst (Ensembl transcript ID [ENST*])</p></li>
+<li><p>ensg (Ensembl genomic DNA ID [ENSG*])</p></li>
+<li><p>hgnc (HGNC ID [HGNC:#])</p></li>
+<li><p>gi (GI number [#])</p></li>
+<li><p>embl (DDBJ/EMBL/GeneBank CDS accession)</p></li>
+<li><p>embl_id (DDBJ/EMBL/GeneBank accession)</p></li>
+</ul>
+<p>And many more, see the code of
+<code class="docutils literal notranslate"><span class="pre">pypath.internals.input_formats</span></code></p>
+</div></blockquote>
+<dl class="simple">
+<dt>target_id_type (str): The name type to translate to, more or</dt><dd><p>less the same values are available as for <code class="docutils literal notranslate"><span class="pre">id_type</span></code>.</p>
+</dd>
+</dl>
+<p>ncbi_tax_id (int): NCBI Taxonomy ID of the organism.
+strict (bool): In case a Gene Symbol can not be translated,</p>
+<blockquote>
+<div><p>try to add number “1” to the end, or try to match only
+its first five characters. This option is rarely used,
+but it makes possible to translate some non-standard
+gene names typically found in old, unmaintained resources.</p>
+</div></blockquote>
+<dl class="simple">
+<dt>expand_complexes (bool): When encountering complexes,</dt><dd><p>translated the IDs of its components and return a set
+of IDs. The alternative behaviour is to return the
+<cite>Complex</cite> objects.</p>
+</dd>
+<dt>uniprot_cleanup (bool): When the <cite>target_id_type</cite> is UniProt</dt><dd><p>ID, call the <cite>uniprot_cleanup</cite> function at the end.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.utils.mapping.Mapper.mapping_tables">
+<em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">mapping_tables</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/utils/mapping.html#Mapper.mapping_tables"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.utils.mapping.Mapper.mapping_tables" title="Link to this definition">§</a></dt>
+<dd><p>List of mapping tables available to load.</p>
+<dl class="simple">
+<dt>Returns</dt><dd><dl class="simple">
+<dt>(list): A list of tuples, each representing an ID translation</dt><dd><p>table, with the ID types, the data source and the loader
+class.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.utils.mapping.Mapper.only_uniprot_ac">
+<span class="sig-name descname"><span class="pre">only_uniprot_ac</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">uniprots</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/utils/mapping.html#Mapper.only_uniprot_ac"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.utils.mapping.Mapper.only_uniprot_ac" title="Link to this definition">§</a></dt>
+<dd><p>For one or more strings returns only those which match the format
+of UniProt accession numbers.
+The format is defined here:
+<a class="reference external" href="https://www.uniprot.org/help/accession_numbers">https://www.uniprot.org/help/accession_numbers</a></p>
+<p>If string provided, returns string or None.
+If iterable provided, returns set (potentially empty if none of the
+strings are valid).</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.utils.mapping.Mapper.other_organism_uniprot">
+<span class="sig-name descname"><span class="pre">other_organism_uniprot</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">uniprot</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/utils/mapping.html#Mapper.other_organism_uniprot"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.utils.mapping.Mapper.other_organism_uniprot" title="Link to this definition">§</a></dt>
+<dd><p>Tells if <code class="docutils literal notranslate"><span class="pre">uniprot</span></code> is an UniProt ID from some other organism than
+<code class="docutils literal notranslate"><span class="pre">ncbi_tax_id</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.utils.mapping.Mapper.primary_uniprot">
+<span class="sig-name descname"><span class="pre">primary_uniprot</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">uniprots</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/utils/mapping.html#Mapper.primary_uniprot"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.utils.mapping.Mapper.primary_uniprot" title="Link to this definition">§</a></dt>
+<dd><p>For an iterable of UniProt IDs returns a set with the secondary IDs
+changed to the corresponding primary IDs. Anything what is not a
+secondary UniProt ID left intact.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.utils.mapping.Mapper.reload">
+<span class="sig-name descname"><span class="pre">reload</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/utils/mapping.html#Mapper.reload"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.utils.mapping.Mapper.reload" title="Link to this definition">§</a></dt>
+<dd><p>Reload the class from the module level.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.utils.mapping.Mapper.remove_expired">
+<span class="sig-name descname"><span class="pre">remove_expired</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/utils/mapping.html#Mapper.remove_expired"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.utils.mapping.Mapper.remove_expired" title="Link to this definition">§</a></dt>
+<dd><p>Removes tables last used a longer time ago than their lifetime.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.utils.mapping.Mapper.remove_key">
+<span class="sig-name descname"><span class="pre">remove_key</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">key</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/utils/mapping.html#Mapper.remove_key"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.utils.mapping.Mapper.remove_key" title="Link to this definition">§</a></dt>
+<dd><p>Removes the table with key <code class="docutils literal notranslate"><span class="pre">key</span></code> if exists.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.utils.mapping.Mapper.remove_table">
+<span class="sig-name descname"><span class="pre">remove_table</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">id_type</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">target_id_type</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/utils/mapping.html#Mapper.remove_table"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.utils.mapping.Mapper.remove_table" title="Link to this definition">§</a></dt>
+<dd><p>Removes the table defined by the ID types and organism.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.utils.mapping.Mapper.reverse_key">
+<span class="sig-name descname"><span class="pre">reverse_key</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">key</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/utils/mapping.html#Mapper.reverse_key"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.utils.mapping.Mapper.reverse_key" title="Link to this definition">§</a></dt>
+<dd><p>For a mapping table key returns a new key with the identifiers
+reversed.</p>
+<dl class="simple">
+<dt>Args</dt><dd><p>key (tuple): A mapping table key.</p>
+</dd>
+<dt>Returns</dt><dd><p>A tuple representing a mapping table key, identifiers swapped.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.utils.mapping.Mapper.reverse_mapping">
+<em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">reverse_mapping</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">mapping_table</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/utils/mapping.html#Mapper.reverse_mapping"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.utils.mapping.Mapper.reverse_mapping" title="Link to this definition">§</a></dt>
+<dd><p>Creates an opposite direction <cite>MappingTable</cite> by swapping the
+dictionary inside an existing <cite>MappingTable</cite> object.</p>
+<dl class="simple">
+<dt>Args</dt><dd><p>mapping_table (MappingTable): A <cite>MappingTable</cite> object.</p>
+</dd>
+<dt>Returns</dt><dd><p>A new <cite>MappingTable</cite> object.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.utils.mapping.Mapper.swissprots">
+<span class="sig-name descname"><span class="pre">swissprots</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">uniprots</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/utils/mapping.html#Mapper.swissprots"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.utils.mapping.Mapper.swissprots" title="Link to this definition">§</a></dt>
+<dd><p>Creates a dict translating a set of potentially secondary and
+non-reviewed UniProt IDs to primary SwissProt IDs (whenever
+is possible).</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.utils.mapping.Mapper.translate_deleted_uniprot_by_genesymbol">
+<span class="sig-name descname"><span class="pre">translate_deleted_uniprot_by_genesymbol</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">uniprot</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/utils/mapping.html#Mapper.translate_deleted_uniprot_by_genesymbol"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.utils.mapping.Mapper.translate_deleted_uniprot_by_genesymbol" title="Link to this definition">§</a></dt>
+<dd><p>Due to potentially ambiguous translation always returns set.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.utils.mapping.Mapper.translation_df">
+<span class="sig-name descname"><span class="pre">translation_df</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">id_type</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">target_id_type</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><span class="pre">DataFrame</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span></span><a class="reference internal" href="../_modules/pypath/utils/mapping.html#Mapper.translation_df"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.utils.mapping.Mapper.translation_df" title="Link to this definition">§</a></dt>
+<dd><p>Translation table as a data frame.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.utils.mapping.Mapper.translation_dict">
+<span class="sig-name descname"><span class="pre">translation_dict</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">id_type</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">target_id_type</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><a class="reference internal" href="pypath.utils.mapping.MappingTable.html#pypath.utils.mapping.MappingTable" title="pypath.utils.mapping.MappingTable"><span class="pre">MappingTable</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span></span><a class="reference internal" href="../_modules/pypath/utils/mapping.html#Mapper.translation_dict"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.utils.mapping.Mapper.translation_dict" title="Link to this definition">§</a></dt>
+<dd><p>Translation table as a dict.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.utils.mapping.Mapper.trembl_swissprot">
+<span class="sig-name descname"><span class="pre">trembl_swissprot</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">uniprots</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/utils/mapping.html#Mapper.trembl_swissprot"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.utils.mapping.Mapper.trembl_swissprot" title="Link to this definition">§</a></dt>
+<dd><p>For an iterable of TrEMBL and SwissProt IDs, returns a set with
+only SwissProt, mapping from TrEMBL to gene symbols, and
+then back to SwissProt. If this kind of translation is not successful
+for any of the IDs it will be kept in the result, no matter if it’s
+not a SwissProt ID. If the</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.utils.mapping.Mapper.uniprot_cleanup">
+<span class="sig-name descname"><span class="pre">uniprot_cleanup</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">uniprots</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/utils/mapping.html#Mapper.uniprot_cleanup"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.utils.mapping.Mapper.uniprot_cleanup" title="Link to this definition">§</a></dt>
+<dd><p>We use this function as a standard callback when the target ID
+type is UniProt. It checks if the format of the IDs are correct,
+if they are part of the organism proteome, attempts to translate
+secondary and deleted IDs to their primary, recent counterparts.</p>
+<dl class="simple">
+<dt>Args</dt><dd><p>uniprots (str,set): One or more UniProt IDs.
+ncbi_tax_id (int): The NCBI Taxonomy identifier of the organism.</p>
+</dd>
+<dt>Returns</dt><dd><p>Set of checked and potentially translated UniProt iDs. Elements
+which do not fit the criteria will be discarded.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.utils.mapping.Mapper.valid_uniprot">
+<span class="sig-name descname"><span class="pre">valid_uniprot</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">uniprot</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/utils/mapping.html#Mapper.valid_uniprot"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.utils.mapping.Mapper.valid_uniprot" title="Link to this definition">§</a></dt>
+<dd><p>If the UniProt ID <code class="docutils literal notranslate"><span class="pre">uniprot</span></code> exist in the proteome of the organism
+<code class="docutils literal notranslate"><span class="pre">ncbi_tax_id</span></code> returns the ID, otherwise returns None.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.utils.mapping.Mapper.which_table">
+<span class="sig-name descname"><span class="pre">which_table</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">id_type</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">target_id_type</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">load</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/utils/mapping.html#Mapper.which_table"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.utils.mapping.Mapper.which_table" title="Link to this definition">§</a></dt>
+<dd><p>Returns the table which is suitable to convert an ID of
+id_type to target_id_type. If no such table have been loaded
+yet, it attempts to load from UniProt. If all attempts failed
+returns <cite>None</cite>.</p>
+</dd></dl>
+
+</dd></dl>
+
+</section>
+
+
+                </article>
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+  <section id="pypath-utils-mapping-mappingtable">
+<h1>pypath.utils.mapping.MappingTable<a class="headerlink" href="#pypath-utils-mapping-mappingtable" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.utils.mapping.MappingTable">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.utils.mapping.</span></span><span class="sig-name descname"><span class="pre">MappingTable</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">data</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">id_type</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">target_id_type</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">lifetime</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">300</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/utils/mapping.html#MappingTable"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.utils.mapping.MappingTable" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">Logger</span></code></p>
+<p>This is the class directly handling ID translation data.
+It does not care about loading it or what kind of IDs these
+only accepts the translation dictionary.</p>
+<dl class="simple">
+<dt>lifetime<span class="classifier">int</span></dt><dd><p>If this table has not been used for longer than this preiod it is
+to be removed at next cleanup. Time in seconds.</p>
+</dd>
+</dl>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.utils.mapping.MappingTable.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">data</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">id_type</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">target_id_type</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">lifetime</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">300</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/utils/mapping.html#MappingTable.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.utils.mapping.MappingTable.__init__" title="Link to this definition">§</a></dt>
+<dd><p>Wrapper around a dictionary of identifier mapping. The dictionary
+is located in the <cite>data</cite> attribute, keys are the source identifiers,
+values are sets of target identifiers. Most often the mapping is
+unambigous, which means one target identifier for each source
+identifier.</p>
+<dl>
+<dt>Args</dt><dd><p>data (dict): The identifier translation dictionary.
+id_type (str): The source ID type.
+target_id_type (str): The target ID type.
+ncbi_tax_id (int): NCBI Taxonomy identifier of the organism.
+lifetime (int): Time in seconds to keep the table loaded in</p>
+<blockquote>
+<div><p>the memory. If not used, the table will be unloaded after
+this time. Each usage resets the expiry time.</p>
+</div></blockquote>
+</dd>
+</dl>
+</dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.utils.mapping.MappingTable.__init__" title="pypath.utils.mapping.MappingTable.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>(data, id_type, target_id_type, ...)</p></td>
+<td><p>Wrapper around a dictionary of identifier mapping.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.utils.mapping.MappingTable.get_key" title="pypath.utils.mapping.MappingTable.get_key"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_key</span></code></a>()</p></td>
+<td><p>Creates a mapping table key, a tuple with all the defining properties of the mapping table.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">reload</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Attributes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">items</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">key</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">keys</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">values</span></code></p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.utils.mapping.MappingTable.get_key">
+<span class="sig-name descname"><span class="pre">get_key</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/utils/mapping.html#MappingTable.get_key"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.utils.mapping.MappingTable.get_key" title="Link to this definition">§</a></dt>
+<dd><p>Creates a mapping table key, a tuple with all the defining properties
+of the mapping table.</p>
+</dd></dl>
+
+</dd></dl>
+
+</section>
+
+
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+  <section id="pypath-utils-mapping-mappingtablekey">
+<h1>pypath.utils.mapping.MappingTableKey<a class="headerlink" href="#pypath-utils-mapping-mappingtablekey" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.utils.mapping.MappingTableKey">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.utils.mapping.</span></span><span class="sig-name descname"><span class="pre">MappingTableKey</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">id_type</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">target_id_type</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.utils.mapping.MappingTableKey" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">tuple</span></code></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.utils.mapping.MappingTableKey.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.utils.mapping.MappingTableKey.__init__" title="Link to this definition">§</a></dt>
+<dd></dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.utils.mapping.MappingTableKey.__init__" title="pypath.utils.mapping.MappingTableKey.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.utils.mapping.MappingTableKey.count" title="pypath.utils.mapping.MappingTableKey.count"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count</span></code></a>(value, /)</p></td>
+<td><p>Return number of occurrences of value.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.utils.mapping.MappingTableKey.index" title="pypath.utils.mapping.MappingTableKey.index"><code class="xref py py-obj docutils literal notranslate"><span class="pre">index</span></code></a>(value[, start, stop])</p></td>
+<td><p>Return first index of value.</p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Attributes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.utils.mapping.MappingTableKey.id_type" title="pypath.utils.mapping.MappingTableKey.id_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">id_type</span></code></a></p></td>
+<td><p>Alias for field number 0</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.utils.mapping.MappingTableKey.ncbi_tax_id" title="pypath.utils.mapping.MappingTableKey.ncbi_tax_id"><code class="xref py py-obj docutils literal notranslate"><span class="pre">ncbi_tax_id</span></code></a></p></td>
+<td><p>Alias for field number 2</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.utils.mapping.MappingTableKey.target_id_type" title="pypath.utils.mapping.MappingTableKey.target_id_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">target_id_type</span></code></a></p></td>
+<td><p>Alias for field number 1</p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.utils.mapping.MappingTableKey.count">
+<span class="sig-name descname"><span class="pre">count</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">value</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">/</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.utils.mapping.MappingTableKey.count" title="Link to this definition">§</a></dt>
+<dd><p>Return number of occurrences of value.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.utils.mapping.MappingTableKey.id_type">
+<span class="sig-name descname"><span class="pre">id_type</span></span><a class="headerlink" href="#pypath.utils.mapping.MappingTableKey.id_type" title="Link to this definition">§</a></dt>
+<dd><p>Alias for field number 0</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.utils.mapping.MappingTableKey.index">
+<span class="sig-name descname"><span class="pre">index</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">value</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">start</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">stop</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9223372036854775807</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">/</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.utils.mapping.MappingTableKey.index" title="Link to this definition">§</a></dt>
+<dd><p>Return first index of value.</p>
+<p>Raises ValueError if the value is not present.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.utils.mapping.MappingTableKey.ncbi_tax_id">
+<span class="sig-name descname"><span class="pre">ncbi_tax_id</span></span><a class="headerlink" href="#pypath.utils.mapping.MappingTableKey.ncbi_tax_id" title="Link to this definition">§</a></dt>
+<dd><p>Alias for field number 2</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.utils.mapping.MappingTableKey.target_id_type">
+<span class="sig-name descname"><span class="pre">target_id_type</span></span><a class="headerlink" href="#pypath.utils.mapping.MappingTableKey.target_id_type" title="Link to this definition">§</a></dt>
+<dd><p>Alias for field number 1</p>
+</dd></dl>
+
+</dd></dl>
+
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diff --git a/api/pypath.utils.mapping.UNIPROT_ID_TYPES.html b/api/pypath.utils.mapping.UNIPROT_ID_TYPES.html
new file mode 100644
index 000000000..03840676b
--- /dev/null
+++ b/api/pypath.utils.mapping.UNIPROT_ID_TYPES.html
@@ -0,0 +1,641 @@
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+<dl class="py data">
+<dt class="sig sig-object py" id="pypath.utils.mapping.UNIPROT_ID_TYPES">
+<span class="sig-prename descclassname"><span class="pre">pypath.utils.mapping.</span></span><span class="sig-name descname"><span class="pre">UNIPROT_ID_TYPES</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">{'swissprot',</span> <span class="pre">'trembl',</span> <span class="pre">'uniprot',</span> <span class="pre">'uniprot-pri',</span> <span class="pre">'uniprot-sec'}</span></em><a class="headerlink" href="#pypath.utils.mapping.UNIPROT_ID_TYPES" title="Link to this definition">§</a></dt>
+<dd><p>Classes for reading and use serving ID mapping data from custom file,
+function, UniProt, UniProt ID Mapping, Ensembl BioMart,
+PRO (Protein Ontology), miRBase or pickle file.</p>
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+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.utils.mapping.get_mapper">
+<span class="sig-prename descclassname"><span class="pre">pypath.utils.mapping.</span></span><span class="sig-name descname"><span class="pre">get_mapper</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/utils/mapping.html#get_mapper"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.utils.mapping.get_mapper" title="Link to this definition">§</a></dt>
+<dd><p>The module under its <cite>mapper</cite> attribute has an instance of the <cite>Mapper</cite>
+object, which manages the ID translations. This function creates the
+instance if does not exist and returns it.</p>
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+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.utils.mapping.guess_type">
+<span class="sig-prename descclassname"><span class="pre">pypath.utils.mapping.</span></span><span class="sig-name descname"><span class="pre">guess_type</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/utils/mapping.html#guess_type"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.utils.mapping.guess_type" title="Link to this definition">§</a></dt>
+<dd><p>From a string, tries to guess the ID type and optionally the entity
+type. Returns a tuple of strings: ID type and entity type.</p>
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+  <section id="module-pypath.utils.mapping">
+<span id="pypath-utils-mapping"></span><h1>pypath.utils.mapping<a class="headerlink" href="#module-pypath.utils.mapping" title="Link to this heading">§</a></h1>
+<dl class="field-list simple">
+<dt class="field-odd">members<span class="colon">:</span></dt>
+<dd class="field-odd"><p></p></dd>
+</dl>
+<p class="rubric">Module Attributes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.utils.mapping.UNIPROT_ID_TYPES.html#pypath.utils.mapping.UNIPROT_ID_TYPES" title="pypath.utils.mapping.UNIPROT_ID_TYPES"><code class="xref py py-obj docutils literal notranslate"><span class="pre">UNIPROT_ID_TYPES</span></code></a></p></td>
+<td><p>Classes for reading and use serving ID mapping data from custom file, function, UniProt, UniProt ID Mapping, Ensembl BioMart, PRO (Protein Ontology), miRBase or pickle file.</p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Functions</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.utils.mapping.get_mapper.html#pypath.utils.mapping.get_mapper" title="pypath.utils.mapping.get_mapper"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_mapper</span></code></a>(**kwargs)</p></td>
+<td><p>The module under its <cite>mapper</cite> attribute has an instance of the <cite>Mapper</cite> object, which manages the ID translations.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.utils.mapping.guess_type.html#pypath.utils.mapping.guess_type" title="pypath.utils.mapping.guess_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">guess_type</span></code></a>(name[, entity_type])</p></td>
+<td><p>From a string, tries to guess the ID type and optionally the entity type.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.utils.mapping.id_from_label.html#pypath.utils.mapping.id_from_label" title="pypath.utils.mapping.id_from_label"><code class="xref py py-obj docutils literal notranslate"><span class="pre">id_from_label</span></code></a>(label[, label_id_type, ...])</p></td>
+<td><p>For a label (e.g. Gene Symbol) returns the corresponding IDs (e.g. UniProt IDs).</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.utils.mapping.id_from_label0.html#pypath.utils.mapping.id_from_label0" title="pypath.utils.mapping.id_from_label0"><code class="xref py py-obj docutils literal notranslate"><span class="pre">id_from_label0</span></code></a>(label[, label_id_type, ...])</p></td>
+<td><p>For a label (e.g. Gene Symbol) returns a single ID (e.g. UniProt IDs).</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.utils.mapping.id_types.html#pypath.utils.mapping.id_types" title="pypath.utils.mapping.id_types"><code class="xref py py-obj docutils literal notranslate"><span class="pre">id_types</span></code></a>()</p></td>
+<td><p>Identifier types with their labels.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.utils.mapping.init.html#pypath.utils.mapping.init" title="pypath.utils.mapping.init"><code class="xref py py-obj docutils literal notranslate"><span class="pre">init</span></code></a>(**kwargs)</p></td>
+<td><p>Create a new <cite>Mapper</cite> instance under the <cite>mapper</cite> attribute of this module.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.utils.mapping.label.html#pypath.utils.mapping.label" title="pypath.utils.mapping.label"><code class="xref py py-obj docutils literal notranslate"><span class="pre">label</span></code></a>(name[, id_type, entity_type, ncbi_tax_id])</p></td>
+<td><p>For any kind of entity, either protein, miRNA or protein complex, returns the preferred human readable label.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.utils.mapping.map_name.html#pypath.utils.mapping.map_name" title="pypath.utils.mapping.map_name"><code class="xref py py-obj docutils literal notranslate"><span class="pre">map_name</span></code></a>(name, id_type, target_id_type[, ...])</p></td>
+<td><p>Translates one instance of one ID type to a different one.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.utils.mapping.map_name0.html#pypath.utils.mapping.map_name0" title="pypath.utils.mapping.map_name0"><code class="xref py py-obj docutils literal notranslate"><span class="pre">map_name0</span></code></a>(name, id_type, target_id_type[, ...])</p></td>
+<td><p>Translates the name and returns only one of the resulted IDs.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.utils.mapping.map_names.html#pypath.utils.mapping.map_names" title="pypath.utils.mapping.map_names"><code class="xref py py-obj docutils literal notranslate"><span class="pre">map_names</span></code></a>(names[, id_type, target_id_type, ...])</p></td>
+<td><p>Same as <code class="docutils literal notranslate"><span class="pre">map_name</span></code> but translates multiple IDs at once.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.utils.mapping.mapping_tables.html#pypath.utils.mapping.mapping_tables" title="pypath.utils.mapping.mapping_tables"><code class="xref py py-obj docutils literal notranslate"><span class="pre">mapping_tables</span></code></a>()</p></td>
+<td><p>A list of built-in mapping tables.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.utils.mapping.translation_df.html#pypath.utils.mapping.translation_df" title="pypath.utils.mapping.translation_df"><code class="xref py py-obj docutils literal notranslate"><span class="pre">translation_df</span></code></a>(id_type, target_id_type[, ...])</p></td>
+<td><p>Identifier translation table as a <cite>pandas.DataFrame</cite>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.utils.mapping.translation_dict.html#pypath.utils.mapping.translation_dict" title="pypath.utils.mapping.translation_dict"><code class="xref py py-obj docutils literal notranslate"><span class="pre">translation_dict</span></code></a>(id_type, target_id_type[, ...])</p></td>
+<td><p>Identifier translation table as a dict of sets.</p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Classes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.utils.mapping.MapReader.html#pypath.utils.mapping.MapReader" title="pypath.utils.mapping.MapReader"><code class="xref py py-obj docutils literal notranslate"><span class="pre">MapReader</span></code></a>(param[, ncbi_tax_id, entity_type, ...])</p></td>
+<td><p>Reads ID translation data and creates <code class="docutils literal notranslate"><span class="pre">MappingTable</span></code> instances.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.utils.mapping.Mapper.html#pypath.utils.mapping.Mapper" title="pypath.utils.mapping.Mapper"><code class="xref py py-obj docutils literal notranslate"><span class="pre">Mapper</span></code></a>([ncbi_tax_id, cleanup_period, ...])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.utils.mapping.MappingTable.html#pypath.utils.mapping.MappingTable" title="pypath.utils.mapping.MappingTable"><code class="xref py py-obj docutils literal notranslate"><span class="pre">MappingTable</span></code></a>(data, id_type, target_id_type, ...)</p></td>
+<td><p>This is the class directly handling ID translation data.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.utils.mapping.MappingTableKey.html#pypath.utils.mapping.MappingTableKey" title="pypath.utils.mapping.MappingTableKey"><code class="xref py py-obj docutils literal notranslate"><span class="pre">MappingTableKey</span></code></a>(id_type, target_id_type, ...)</p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+</section>
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+<h1>pypath.utils.mapping.id_from_label<a class="headerlink" href="#pypath-utils-mapping-id-from-label" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.utils.mapping.id_from_label">
+<span class="sig-prename descclassname"><span class="pre">pypath.utils.mapping.</span></span><span class="sig-name descname"><span class="pre">id_from_label</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">label</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">label_id_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'genesymbol'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/utils/mapping.html#id_from_label"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.utils.mapping.id_from_label" title="Link to this definition">§</a></dt>
+<dd><p>For a label (e.g. Gene Symbol) returns the corresponding IDs (e.g.
+UniProt IDs).</p>
+</dd></dl>
+
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+
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+  <section id="pypath-utils-mapping-id-from-label0">
+<h1>pypath.utils.mapping.id_from_label0<a class="headerlink" href="#pypath-utils-mapping-id-from-label0" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.utils.mapping.id_from_label0">
+<span class="sig-prename descclassname"><span class="pre">pypath.utils.mapping.</span></span><span class="sig-name descname"><span class="pre">id_from_label0</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">label</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">label_id_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'genesymbol'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/utils/mapping.html#id_from_label0"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.utils.mapping.id_from_label0" title="Link to this definition">§</a></dt>
+<dd><p>For a label (e.g. Gene Symbol) returns a single ID (e.g. UniProt IDs).</p>
+</dd></dl>
+
+</section>
+
+
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diff --git a/api/pypath.utils.mapping.id_types.html b/api/pypath.utils.mapping.id_types.html
new file mode 100644
index 000000000..7106f78e0
--- /dev/null
+++ b/api/pypath.utils.mapping.id_types.html
@@ -0,0 +1,639 @@
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+  <section id="pypath-utils-mapping-id-types">
+<h1>pypath.utils.mapping.id_types<a class="headerlink" href="#pypath-utils-mapping-id-types" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.utils.mapping.id_types">
+<span class="sig-prename descclassname"><span class="pre">pypath.utils.mapping.</span></span><span class="sig-name descname"><span class="pre">id_types</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">IdType</span><span class="p"><span class="pre">]</span></span></span></span><a class="reference internal" href="../_modules/pypath/utils/mapping.html#id_types"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.utils.mapping.id_types" title="Link to this definition">§</a></dt>
+<dd><p>Identifier types with their labels.</p>
+</dd></dl>
+
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+  <section id="pypath-utils-mapping-init">
+<h1>pypath.utils.mapping.init<a class="headerlink" href="#pypath-utils-mapping-init" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.utils.mapping.init">
+<span class="sig-prename descclassname"><span class="pre">pypath.utils.mapping.</span></span><span class="sig-name descname"><span class="pre">init</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/utils/mapping.html#init"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.utils.mapping.init" title="Link to this definition">§</a></dt>
+<dd><p>Create a new <cite>Mapper</cite> instance under the <cite>mapper</cite> attribute of this
+module.</p>
+<dl class="simple">
+<dt>Returns</dt><dd><p>None.</p>
+</dd>
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+  <section id="pypath-utils-mapping-label">
+<h1>pypath.utils.mapping.label<a class="headerlink" href="#pypath-utils-mapping-label" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.utils.mapping.label">
+<span class="sig-prename descclassname"><span class="pre">pypath.utils.mapping.</span></span><span class="sig-name descname"><span class="pre">label</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">id_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entity_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/utils/mapping.html#label"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.utils.mapping.label" title="Link to this definition">§</a></dt>
+<dd><p>For any kind of entity, either protein, miRNA or protein complex,
+returns the preferred human readable label. For proteins this means
+Gene Symbols, for miRNAs miRNA names, for complexes a series of
+Gene Symbols.</p>
+</dd></dl>
+
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+
+
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+  <section id="pypath-utils-mapping-map-name">
+<h1>pypath.utils.mapping.map_name<a class="headerlink" href="#pypath-utils-mapping-map-name" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.utils.mapping.map_name">
+<span class="sig-prename descclassname"><span class="pre">pypath.utils.mapping.</span></span><span class="sig-name descname"><span class="pre">map_name</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">id_type</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">target_id_type</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">strict</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">expand_complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">uniprot_cleanup</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/utils/mapping.html#map_name"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.utils.mapping.map_name" title="Link to this definition">§</a></dt>
+<dd><p>Translates one instance of one ID type to a different one.
+Returns set of the target ID type.</p>
+<p>This function should be used to convert individual IDs.
+It takes care about everything and ideally you don’t need to
+think on the details.</p>
+<p>How does it work: looks up dictionaries between the original
+and target ID type, if doesn’t find, attempts to load from the
+predefined inputs.
+If the original name is genesymbol, first it looks up among the
+preferred gene names from UniProt, if not found, it takes an
+attempt with the alternative gene names. If the gene symbol
+still couldn’t be found, and strict = False, the last attempt
+only the first 5 characters of the gene symbol matched. If the
+target name type is uniprot, then it converts all the ACs to
+primary. Then, for the Trembl IDs it looks up the preferred gene
+names, and find Swissprot IDs with the same preferred gene name.</p>
+<dl>
+<dt>Args</dt><dd><p>name (str): The original name to be converted.
+id_type (str): The type of the name. Available by default:</p>
+<blockquote>
+<div><ul class="simple">
+<li><p>genesymbol (gene name)</p></li>
+<li><p>entrez (Entrez Gene ID [#])</p></li>
+<li><p>refseqp (NCBI RefSeq Protein ID [NP_*|XP_*])</p></li>
+<li><p>ensp (Ensembl protein ID [ENSP*])</p></li>
+<li><p>enst (Ensembl transcript ID [ENST*])</p></li>
+<li><p>ensg (Ensembl genomic DNA ID [ENSG*])</p></li>
+<li><p>hgnc (HGNC ID [HGNC:#])</p></li>
+<li><p>gi (GI number [#])</p></li>
+<li><p>embl (DDBJ/EMBL/GeneBank CDS accession)</p></li>
+<li><p>embl_id (DDBJ/EMBL/GeneBank accession)</p></li>
+</ul>
+<p>And many more, see the code of
+<code class="docutils literal notranslate"><span class="pre">pypath.internals.input_formats</span></code></p>
+</div></blockquote>
+<dl class="simple">
+<dt>target_id_type (str): The name type to translate to, more or</dt><dd><p>less the same values are available as for <code class="docutils literal notranslate"><span class="pre">id_type</span></code>.</p>
+</dd>
+</dl>
+<p>ncbi_tax_id (int): NCBI Taxonomy ID of the organism.
+strict (bool): In case a Gene Symbol can not be translated,</p>
+<blockquote>
+<div><p>try to add number “1” to the end, or try to match only
+its first five characters. This option is rarely used,
+but it makes possible to translate some non-standard
+gene names typically found in old, unmaintained resources.</p>
+</div></blockquote>
+<dl class="simple">
+<dt>expand_complexes (bool): When encountering complexes,</dt><dd><p>translated the IDs of its components and return a set
+of IDs. The alternative behaviour is to return the
+<cite>Complex</cite> objects.</p>
+</dd>
+<dt>uniprot_cleanup (bool): When the <cite>target_id_type</cite> is UniProt</dt><dd><p>ID, call the <cite>uniprot_cleanup</cite> function at the end.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+</section>
+
+
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+  <section id="pypath-utils-mapping-map-name0">
+<h1>pypath.utils.mapping.map_name0<a class="headerlink" href="#pypath-utils-mapping-map-name0" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.utils.mapping.map_name0">
+<span class="sig-prename descclassname"><span class="pre">pypath.utils.mapping.</span></span><span class="sig-name descname"><span class="pre">map_name0</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">id_type</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">target_id_type</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">strict</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">expand_complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">uniprot_cleanup</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/utils/mapping.html#map_name0"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.utils.mapping.map_name0" title="Link to this definition">§</a></dt>
+<dd><p>Translates the name and returns only one of the resulted IDs. It
+means in case of ambiguous ID translation, a random one of them
+will be picked and returned. Recommended to use only if the
+translation between the given ID types is mostly unambigous and
+the loss of information can be ignored. See more details at
+<cite>map_name</cite>.</p>
+</dd></dl>
+
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+
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diff --git a/api/pypath.utils.mapping.map_names.html b/api/pypath.utils.mapping.map_names.html
new file mode 100644
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+  <section id="pypath-utils-mapping-map-names">
+<h1>pypath.utils.mapping.map_names<a class="headerlink" href="#pypath-utils-mapping-map-names" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.utils.mapping.map_names">
+<span class="sig-prename descclassname"><span class="pre">pypath.utils.mapping.</span></span><span class="sig-name descname"><span class="pre">map_names</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">names</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">id_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">target_id_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">strict</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">expand_complexes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">uniprot_cleanup</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/utils/mapping.html#map_names"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.utils.mapping.map_names" title="Link to this definition">§</a></dt>
+<dd><p>Same as <code class="docutils literal notranslate"><span class="pre">map_name</span></code> but translates multiple IDs at once. These two
+functions could be seamlessly implemented as one, still I created
+separate functions to always make it explicit if a set of translated
+IDs come from multiple original IDs.</p>
+<dl>
+<dt>Args</dt><dd><p>name (str): The original name to be converted.
+id_type (str): The type of the name. Available by default:</p>
+<blockquote>
+<div><ul class="simple">
+<li><p>genesymbol (gene name)</p></li>
+<li><p>entrez (Entrez Gene ID [#])</p></li>
+<li><p>refseqp (NCBI RefSeq Protein ID [NP_*|XP_*])</p></li>
+<li><p>ensp (Ensembl protein ID [ENSP*])</p></li>
+<li><p>enst (Ensembl transcript ID [ENST*])</p></li>
+<li><p>ensg (Ensembl genomic DNA ID [ENSG*])</p></li>
+<li><p>hgnc (HGNC ID [HGNC:#])</p></li>
+<li><p>gi (GI number [#])</p></li>
+<li><p>embl (DDBJ/EMBL/GeneBank CDS accession)</p></li>
+<li><p>embl_id (DDBJ/EMBL/GeneBank accession)</p></li>
+</ul>
+<p>And many more, see the code of
+<code class="docutils literal notranslate"><span class="pre">pypath.internals.input_formats</span></code></p>
+</div></blockquote>
+<dl class="simple">
+<dt>target_id_type (str): The name type to translate to, more or</dt><dd><p>less the same values are available as for <code class="docutils literal notranslate"><span class="pre">id_type</span></code>.</p>
+</dd>
+</dl>
+<p>ncbi_tax_id (int): NCBI Taxonomy ID of the organism.
+strict (bool): In case a Gene Symbol can not be translated,</p>
+<blockquote>
+<div><p>try to add number “1” to the end, or try to match only
+its first five characters. This option is rarely used,
+but it makes possible to translate some non-standard
+gene names typically found in old, unmaintained resources.</p>
+</div></blockquote>
+<dl class="simple">
+<dt>expand_complexes (bool): When encountering complexes,</dt><dd><p>translated the IDs of its components and return a set
+of IDs. The alternative behaviour is to return the
+<cite>Complex</cite> objects.</p>
+</dd>
+<dt>uniprot_cleanup (bool): When the <cite>target_id_type</cite> is UniProt</dt><dd><p>ID, call the <cite>Mapper.uniprot_cleanup</cite> function at the end.</p>
+</dd>
+</dl>
+</dd>
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+
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+<dl class="py function">
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+<span class="sig-prename descclassname"><span class="pre">pypath.utils.mapping.</span></span><span class="sig-name descname"><span class="pre">mapping_tables</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">MappingTableDefinition</span><span class="p"><span class="pre">]</span></span></span></span><a class="reference internal" href="../_modules/pypath/utils/mapping.html#mapping_tables"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.utils.mapping.mapping_tables" title="Link to this definition">§</a></dt>
+<dd><p>A list of built-in mapping tables.</p>
+<p>If <cite>id_type_b</cite> is <cite>None</cite>, that means translation to all other ID types
+provided by the same resource is possible.</p>
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+  <section id="pypath-utils-mapping-translation-df">
+<h1>pypath.utils.mapping.translation_df<a class="headerlink" href="#pypath-utils-mapping-translation-df" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.utils.mapping.translation_df">
+<span class="sig-prename descclassname"><span class="pre">pypath.utils.mapping.</span></span><span class="sig-name descname"><span class="pre">translation_df</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">id_type</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">target_id_type</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><a class="reference internal" href="pypath.utils.mapping.MappingTable.html#pypath.utils.mapping.MappingTable" title="pypath.utils.mapping.MappingTable"><span class="pre">MappingTable</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span></span><a class="reference internal" href="../_modules/pypath/utils/mapping.html#translation_df"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.utils.mapping.translation_df" title="Link to this definition">§</a></dt>
+<dd><p>Identifier translation table as a <cite>pandas.DataFrame</cite>.</p>
+</dd></dl>
+
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diff --git a/api/pypath.utils.mapping.translation_dict.html b/api/pypath.utils.mapping.translation_dict.html
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+<span class="sig-prename descclassname"><span class="pre">pypath.utils.mapping.</span></span><span class="sig-name descname"><span class="pre">translation_dict</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">id_type</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">target_id_type</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><a class="reference internal" href="pypath.utils.mapping.MappingTable.html#pypath.utils.mapping.MappingTable" title="pypath.utils.mapping.MappingTable"><span class="pre">MappingTable</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span></span><a class="reference internal" href="../_modules/pypath/utils/mapping.html#translation_dict"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.utils.mapping.translation_dict" title="Link to this definition">§</a></dt>
+<dd><p>Identifier translation table as a dict of sets.</p>
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+
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diff --git a/api/pypath.utils.orthology.EnsemblOrtholog.html b/api/pypath.utils.orthology.EnsemblOrtholog.html
new file mode 100644
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+  <section id="pypath-utils-orthology-ensemblortholog">
+<h1>pypath.utils.orthology.EnsemblOrtholog<a class="headerlink" href="#pypath-utils-orthology-ensemblortholog" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.utils.orthology.EnsemblOrtholog">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.utils.orthology.</span></span><span class="sig-name descname"><span class="pre">EnsemblOrtholog</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">id</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">types</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">hc</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/utils/orthology.html#EnsemblOrtholog"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.utils.orthology.EnsemblOrtholog" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">EnsemblOrthologBase</span></code></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.utils.orthology.EnsemblOrtholog.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.utils.orthology.EnsemblOrtholog.__init__" title="Link to this definition">§</a></dt>
+<dd></dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.utils.orthology.EnsemblOrtholog.__init__" title="pypath.utils.orthology.EnsemblOrtholog.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.utils.orthology.EnsemblOrtholog.count" title="pypath.utils.orthology.EnsemblOrtholog.count"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count</span></code></a>(value, /)</p></td>
+<td><p>Return number of occurrences of value.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.utils.orthology.EnsemblOrtholog.index" title="pypath.utils.orthology.EnsemblOrtholog.index"><code class="xref py py-obj docutils literal notranslate"><span class="pre">index</span></code></a>(value[, start, stop])</p></td>
+<td><p>Return first index of value.</p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Attributes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.utils.orthology.EnsemblOrtholog.hc" title="pypath.utils.orthology.EnsemblOrtholog.hc"><code class="xref py py-obj docutils literal notranslate"><span class="pre">hc</span></code></a></p></td>
+<td><p>Alias for field number 2</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.utils.orthology.EnsemblOrtholog.id" title="pypath.utils.orthology.EnsemblOrtholog.id"><code class="xref py py-obj docutils literal notranslate"><span class="pre">id</span></code></a></p></td>
+<td><p>Alias for field number 0</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.utils.orthology.EnsemblOrtholog.types" title="pypath.utils.orthology.EnsemblOrtholog.types"><code class="xref py py-obj docutils literal notranslate"><span class="pre">types</span></code></a></p></td>
+<td><p>Alias for field number 1</p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.utils.orthology.EnsemblOrtholog.count">
+<span class="sig-name descname"><span class="pre">count</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">value</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">/</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.utils.orthology.EnsemblOrtholog.count" title="Link to this definition">§</a></dt>
+<dd><p>Return number of occurrences of value.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.utils.orthology.EnsemblOrtholog.hc">
+<span class="sig-name descname"><span class="pre">hc</span></span><a class="headerlink" href="#pypath.utils.orthology.EnsemblOrtholog.hc" title="Link to this definition">§</a></dt>
+<dd><p>Alias for field number 2</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.utils.orthology.EnsemblOrtholog.id">
+<span class="sig-name descname"><span class="pre">id</span></span><a class="headerlink" href="#pypath.utils.orthology.EnsemblOrtholog.id" title="Link to this definition">§</a></dt>
+<dd><p>Alias for field number 0</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.utils.orthology.EnsemblOrtholog.index">
+<span class="sig-name descname"><span class="pre">index</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">value</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">start</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">stop</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9223372036854775807</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">/</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.utils.orthology.EnsemblOrtholog.index" title="Link to this definition">§</a></dt>
+<dd><p>Return first index of value.</p>
+<p>Raises ValueError if the value is not present.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.utils.orthology.EnsemblOrtholog.types">
+<span class="sig-name descname"><span class="pre">types</span></span><a class="headerlink" href="#pypath.utils.orthology.EnsemblOrtholog.types" title="Link to this definition">§</a></dt>
+<dd><p>Alias for field number 1</p>
+</dd></dl>
+
+</dd></dl>
+
+</section>
+
+
+                </article>
+              
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+  <section id="pypath-utils-orthology-ensemblorthology">
+<h1>pypath.utils.orthology.EnsemblOrthology<a class="headerlink" href="#pypath-utils-orthology-ensemblorthology" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.utils.orthology.EnsemblOrthology">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.utils.orthology.</span></span><span class="sig-name descname"><span class="pre">EnsemblOrthology</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">target</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">str</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">source</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">str</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">id_type</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">'uniprot'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">only_swissprot</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">hc</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">types</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">Literal</span><span class="p"><span class="pre">[</span></span><span class="s"><span class="pre">'one2one'</span></span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="s"><span class="pre">'one2many'</span></span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="s"><span class="pre">'many2many'</span></span><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/utils/orthology.html#EnsemblOrthology"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.utils.orthology.EnsemblOrthology" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <a class="reference internal" href="pypath.utils.orthology.ProteinOrthology.html#pypath.utils.orthology.ProteinOrthology" title="pypath.utils.orthology.ProteinOrthology"><code class="xref py py-class docutils literal notranslate"><span class="pre">ProteinOrthology</span></code></a></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.utils.orthology.EnsemblOrthology.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">target</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">str</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">source</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">str</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">id_type</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">'uniprot'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">only_swissprot</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">hc</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">types</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">Literal</span><span class="p"><span class="pre">[</span></span><span class="s"><span class="pre">'one2one'</span></span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="s"><span class="pre">'one2many'</span></span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="s"><span class="pre">'many2many'</span></span><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/utils/orthology.html#EnsemblOrthology.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.utils.orthology.EnsemblOrthology.__init__" title="Link to this definition">§</a></dt>
+<dd><p>Orthology translation with Ensembl data.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>target:</dt><dd><p>Name or NCBI Taxonomy ID of the target organism.</p>
+</dd>
+<dt>source:</dt><dd><p>Name or NCBI Taxonomy ID of the source organism.</p>
+</dd>
+<dt>id_type:</dt><dd><p>The identifier type to use.</p>
+</dd>
+<dt>only_swissprot:</dt><dd><p>Use only SwissProt IDs.</p>
+</dd>
+<dt>hc:</dt><dd><p>Use only high confidence orthology relations
+from Ensembl. By default it is True. You can also set it
+by the <cite>ensembl_hc</cite> attribute.</p>
+</dd>
+<dt>types:</dt><dd><p>The Ensembl orthology relationship types
+to use. Possible values are <cite>one2one</cite>, <cite>one2many</cite> and
+<cite>many2many</cite>. By default only <cite>one2one</cite> is used. You can
+also set this parameter by the <cite>ensembl_types</cite> attribute.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.utils.orthology.EnsemblOrthology.__init__" title="pypath.utils.orthology.EnsemblOrthology.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>(target[, source, id_type, ...])</p></td>
+<td><p>Orthology translation with Ensembl data.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.utils.orthology.EnsemblOrthology.asdict" title="pypath.utils.orthology.EnsemblOrthology.asdict"><code class="xref py py-obj docutils literal notranslate"><span class="pre">asdict</span></code></a>([full_records])</p></td>
+<td><p>Create a dictionary from the translation table.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.utils.orthology.EnsemblOrthology.df" title="pypath.utils.orthology.EnsemblOrthology.df"><code class="xref py py-obj docutils literal notranslate"><span class="pre">df</span></code></a>([full_records])</p></td>
+<td><p>Orthologous pairs as data frame.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_taxon</span></code>(protein[, only_swissprot])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_taxon_trembl</span></code>(protein)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_protein</span></code>(protein)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_swissprot</span></code>(protein)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">load</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_proteome</span></code>(taxon[, only_swissprot])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_taxonomy</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.utils.orthology.EnsemblOrthology.match" title="pypath.utils.orthology.EnsemblOrthology.match"><code class="xref py py-obj docutils literal notranslate"><span class="pre">match</span></code></a>(ortholog, **kwargs)</p></td>
+<td><p>Check an ortholog against filtering criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">reload</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.utils.orthology.EnsemblOrthology.translate" title="pypath.utils.orthology.EnsemblOrthology.translate"><code class="xref py py-obj docutils literal notranslate"><span class="pre">translate</span></code></a>(identifier[, full_records])</p></td>
+<td><p>For one UniProt ID of the source organism returns all orthologues from the target organism.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.utils.orthology.EnsemblOrthology.translate_df" title="pypath.utils.orthology.EnsemblOrthology.translate_df"><code class="xref py py-obj docutils literal notranslate"><span class="pre">translate_df</span></code></a>(df[, cols, ortho_df])</p></td>
+<td><p>Translate columns in a data frame.</p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Attributes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">key</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">pickle_path</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">resource</span></code></p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.utils.orthology.EnsemblOrthology.asdict">
+<span class="sig-name descname"><span class="pre">asdict</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">full_records</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">set</span><span class="p"><span class="pre">[</span></span><a class="reference internal" href="pypath.utils.orthology.OrthologBase.html#pypath.utils.orthology.OrthologBase" title="pypath.utils.orthology.OrthologBase"><span class="pre">OrthologBase</span></a><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span></span></span><a class="headerlink" href="#pypath.utils.orthology.EnsemblOrthology.asdict" title="Link to this definition">§</a></dt>
+<dd><p>Create a dictionary from the translation table.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>full_records</strong> – Include not only the identifiers, but also some properties of
+the orthology relationships.</p></li>
+<li><p><strong>kwargs</strong> – Resource specific filtering criteria.</p></li>
+</ul>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p>A dict with identifiers of the source organism as keys, and
+sets of their orthologs as values.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.utils.orthology.EnsemblOrthology.df">
+<span class="sig-name descname"><span class="pre">df</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">full_records</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><span class="pre">DataFrame</span></span></span><a class="headerlink" href="#pypath.utils.orthology.EnsemblOrthology.df" title="Link to this definition">§</a></dt>
+<dd><p>Orthologous pairs as data frame.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>full_records</strong> – Include not only the identifiers, but also some properties of
+the orthology relationships.</p></li>
+<li><p><strong>kwargs</strong> – Resource specific filtering criteria.</p></li>
+</ul>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p>A data frame with pairs of orthologous identifiers,
+in two columns: “source” and “target”.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.utils.orthology.EnsemblOrthology.match">
+<span class="sig-name descname"><span class="pre">match</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">ortholog</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="pypath.utils.orthology.OrthologBase.html#pypath.utils.orthology.OrthologBase" title="pypath.utils.orthology.OrthologBase"><span class="pre">OrthologBase</span></a></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><span class="pre">bool</span></span></span><a class="reference internal" href="../_modules/pypath/utils/orthology.html#EnsemblOrthology.match"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.utils.orthology.EnsemblOrthology.match" title="Link to this definition">§</a></dt>
+<dd><p>Check an ortholog against filtering criteria.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>ortholog</strong> – An ortholog record.</p></li>
+<li><p><strong>kwargs</strong> – Override default filtering parameters.</p></li>
+</ul>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p>True if the ortholog meets the criteria.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.utils.orthology.EnsemblOrthology.translate">
+<span class="sig-name descname"><span class="pre">translate</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">identifier</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">Iterable</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="n"><span class="pre">full_records</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><span class="pre">set</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span></span></span><a class="headerlink" href="#pypath.utils.orthology.EnsemblOrthology.translate" title="Link to this definition">§</a></dt>
+<dd><p>For one UniProt ID of the source organism returns all orthologues
+from the target organism.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>identifier</strong> – An identifier corresponding to the ID type and source organism
+of the instance.</p></li>
+<li><p><strong>full_records</strong> – Include not only the identifiers, but also some properties of
+the orthology relationships.</p></li>
+<li><p><strong>kwargs</strong> – Resource specific translation parameters.</p></li>
+</ul>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p>A set of identifiers of orthologues in the target taxon.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.utils.orthology.EnsemblOrthology.translate_df">
+<span class="sig-name descname"><span class="pre">translate_df</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">df</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">DataFrame</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cols</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ortho_df</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">DataFrame</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.utils.orthology.EnsemblOrthology.translate_df" title="Link to this definition">§</a></dt>
+<dd><p>Translate columns in a data frame.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>df</strong> – A data frame.</p></li>
+<li><p><strong>cols</strong> – One or more columns to be translated. It can be a single
+column name, an iterable of column names or a dict where
+keys are column names and values are ID types. Except this
+last case, identifiers are assumed to be UniProt.</p></li>
+<li><p><strong>ortho_df</strong> – Override the translation data frame. If provided, the
+parameters in <cite>kwargs</cite> won’t have an effect. Must have
+columns “source” and “target”.</p></li>
+<li><p><strong>kwargs</strong> – Resource specific translation parameters.</p></li>
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+  <section id="pypath-utils-orthology-homologeneortholog">
+<h1>pypath.utils.orthology.HomologeneOrtholog<a class="headerlink" href="#pypath-utils-orthology-homologeneortholog" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.utils.orthology.HomologeneOrtholog">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.utils.orthology.</span></span><span class="sig-name descname"><span class="pre">HomologeneOrtholog</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">id</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/utils/orthology.html#HomologeneOrtholog"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.utils.orthology.HomologeneOrtholog" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">HomologeneOrthologBase</span></code></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.utils.orthology.HomologeneOrtholog.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.utils.orthology.HomologeneOrtholog.__init__" title="Link to this definition">§</a></dt>
+<dd></dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.utils.orthology.HomologeneOrtholog.__init__" title="pypath.utils.orthology.HomologeneOrtholog.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.utils.orthology.HomologeneOrtholog.count" title="pypath.utils.orthology.HomologeneOrtholog.count"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count</span></code></a>(value, /)</p></td>
+<td><p>Return number of occurrences of value.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.utils.orthology.HomologeneOrtholog.index" title="pypath.utils.orthology.HomologeneOrtholog.index"><code class="xref py py-obj docutils literal notranslate"><span class="pre">index</span></code></a>(value[, start, stop])</p></td>
+<td><p>Return first index of value.</p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Attributes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.utils.orthology.HomologeneOrtholog.id" title="pypath.utils.orthology.HomologeneOrtholog.id"><code class="xref py py-obj docutils literal notranslate"><span class="pre">id</span></code></a></p></td>
+<td><p>Alias for field number 0</p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.utils.orthology.HomologeneOrtholog.count">
+<span class="sig-name descname"><span class="pre">count</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">value</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">/</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.utils.orthology.HomologeneOrtholog.count" title="Link to this definition">§</a></dt>
+<dd><p>Return number of occurrences of value.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.utils.orthology.HomologeneOrtholog.id">
+<span class="sig-name descname"><span class="pre">id</span></span><a class="headerlink" href="#pypath.utils.orthology.HomologeneOrtholog.id" title="Link to this definition">§</a></dt>
+<dd><p>Alias for field number 0</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.utils.orthology.HomologeneOrtholog.index">
+<span class="sig-name descname"><span class="pre">index</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">value</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">start</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">stop</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9223372036854775807</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">/</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.utils.orthology.HomologeneOrtholog.index" title="Link to this definition">§</a></dt>
+<dd><p>Return first index of value.</p>
+<p>Raises ValueError if the value is not present.</p>
+</dd></dl>
+
+</dd></dl>
+
+</section>
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+  <section id="pypath-utils-orthology-homologeneorthology">
+<h1>pypath.utils.orthology.HomologeneOrthology<a class="headerlink" href="#pypath-utils-orthology-homologeneorthology" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.utils.orthology.HomologeneOrthology">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.utils.orthology.</span></span><span class="sig-name descname"><span class="pre">HomologeneOrthology</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">target</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">int</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">source</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">int</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">id_type</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">'uniprot'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">only_swissprot</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/utils/orthology.html#HomologeneOrthology"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.utils.orthology.HomologeneOrthology" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <a class="reference internal" href="pypath.utils.orthology.ProteinOrthology.html#pypath.utils.orthology.ProteinOrthology" title="pypath.utils.orthology.ProteinOrthology"><code class="xref py py-class docutils literal notranslate"><span class="pre">ProteinOrthology</span></code></a></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.utils.orthology.HomologeneOrthology.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">target</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">int</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">source</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">int</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">id_type</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">'uniprot'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">only_swissprot</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.utils.orthology.HomologeneOrthology.__init__" title="Link to this definition">§</a></dt>
+<dd><p>This class translates between homologous UniProt IDs of two organisms
+based on NCBI HomoloGene and Ensembl data. In case of HomoloGene,
+the UniProt-UniProt translation table is created by translating the
+source organism UniProts to RefSeq and Entrez IDs, finding the
+homologues (orthologues) for these IDs, and then translating them
+to the target organism UniProt IDs. In case of Ensembl, we obtain
+data with Ensembl protein identifiers and translate those to UniProt.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>target:</dt><dd><p>Name or NCBI Taxonomy ID of the target organism.</p>
+</dd>
+<dt>source:</dt><dd><p>Name or NCBI Taxonomy ID of the source organism.</p>
+</dd>
+<dt>id_type:</dt><dd><p>The identifier type to use.</p>
+</dd>
+<dt>only_swissprot:</dt><dd><p>Use only SwissProt IDs.</p>
+</dd>
+<dt>kwargs:</dt><dd><p>Resource specific parameters.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.utils.orthology.HomologeneOrthology.__init__" title="pypath.utils.orthology.HomologeneOrthology.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>(target[, source, id_type, ...])</p></td>
+<td><p>This class translates between homologous UniProt IDs of two organisms based on NCBI HomoloGene and Ensembl data.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.utils.orthology.HomologeneOrthology.asdict" title="pypath.utils.orthology.HomologeneOrthology.asdict"><code class="xref py py-obj docutils literal notranslate"><span class="pre">asdict</span></code></a>([full_records])</p></td>
+<td><p>Create a dictionary from the translation table.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.utils.orthology.HomologeneOrthology.df" title="pypath.utils.orthology.HomologeneOrthology.df"><code class="xref py py-obj docutils literal notranslate"><span class="pre">df</span></code></a>([full_records])</p></td>
+<td><p>Orthologous pairs as data frame.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_taxon</span></code>(protein[, only_swissprot])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_taxon_trembl</span></code>(protein)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_protein</span></code>(protein)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_swissprot</span></code>(protein)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.utils.orthology.HomologeneOrthology.load" title="pypath.utils.orthology.HomologeneOrthology.load"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load</span></code></a>()</p></td>
+<td><p>Load orthology data from NCBI HomoloGene.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_proteome</span></code>(taxon[, only_swissprot])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_taxonomy</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">match</span></code>(ortholog, **kwargs)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">reload</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.utils.orthology.HomologeneOrthology.translate" title="pypath.utils.orthology.HomologeneOrthology.translate"><code class="xref py py-obj docutils literal notranslate"><span class="pre">translate</span></code></a>(identifier[, full_records])</p></td>
+<td><p>For one UniProt ID of the source organism returns all orthologues from the target organism.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.utils.orthology.HomologeneOrthology.translate_df" title="pypath.utils.orthology.HomologeneOrthology.translate_df"><code class="xref py py-obj docutils literal notranslate"><span class="pre">translate_df</span></code></a>(df[, cols, ortho_df])</p></td>
+<td><p>Translate columns in a data frame.</p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Attributes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">key</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">pickle_path</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">resource</span></code></p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.utils.orthology.HomologeneOrthology.asdict">
+<span class="sig-name descname"><span class="pre">asdict</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">full_records</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">set</span><span class="p"><span class="pre">[</span></span><a class="reference internal" href="pypath.utils.orthology.OrthologBase.html#pypath.utils.orthology.OrthologBase" title="pypath.utils.orthology.OrthologBase"><span class="pre">OrthologBase</span></a><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span></span></span><a class="headerlink" href="#pypath.utils.orthology.HomologeneOrthology.asdict" title="Link to this definition">§</a></dt>
+<dd><p>Create a dictionary from the translation table.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>full_records</strong> – Include not only the identifiers, but also some properties of
+the orthology relationships.</p></li>
+<li><p><strong>kwargs</strong> – Resource specific filtering criteria.</p></li>
+</ul>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p>A dict with identifiers of the source organism as keys, and
+sets of their orthologs as values.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.utils.orthology.HomologeneOrthology.df">
+<span class="sig-name descname"><span class="pre">df</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">full_records</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><span class="pre">DataFrame</span></span></span><a class="headerlink" href="#pypath.utils.orthology.HomologeneOrthology.df" title="Link to this definition">§</a></dt>
+<dd><p>Orthologous pairs as data frame.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>full_records</strong> – Include not only the identifiers, but also some properties of
+the orthology relationships.</p></li>
+<li><p><strong>kwargs</strong> – Resource specific filtering criteria.</p></li>
+</ul>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p>A data frame with pairs of orthologous identifiers,
+in two columns: “source” and “target”.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.utils.orthology.HomologeneOrthology.load">
+<span class="sig-name descname"><span class="pre">load</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/utils/orthology.html#HomologeneOrthology.load"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.utils.orthology.HomologeneOrthology.load" title="Link to this definition">§</a></dt>
+<dd><p>Load orthology data from NCBI HomoloGene.</p>
+<p>Builds orthology translation table as dict based on NCBI HomoloGene
+data. If the <cite>id_type</cite> is supported by HomoloGene (Gene Symbol, RefSeq,
+Entrez, GI), the data will be simply loaded. For other ID types it
+translates HomoloGene Gene Symbol, RefSeq and Entrez tables to UniProt
+and then translates the orthologous UniProt pairs to the desired
+ID type.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.utils.orthology.HomologeneOrthology.translate">
+<span class="sig-name descname"><span class="pre">translate</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">identifier</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">Iterable</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="n"><span class="pre">full_records</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><span class="pre">set</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span></span></span><a class="headerlink" href="#pypath.utils.orthology.HomologeneOrthology.translate" title="Link to this definition">§</a></dt>
+<dd><p>For one UniProt ID of the source organism returns all orthologues
+from the target organism.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>identifier</strong> – An identifier corresponding to the ID type and source organism
+of the instance.</p></li>
+<li><p><strong>full_records</strong> – Include not only the identifiers, but also some properties of
+the orthology relationships.</p></li>
+<li><p><strong>kwargs</strong> – Resource specific translation parameters.</p></li>
+</ul>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p>A set of identifiers of orthologues in the target taxon.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.utils.orthology.HomologeneOrthology.translate_df">
+<span class="sig-name descname"><span class="pre">translate_df</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">df</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">DataFrame</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cols</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ortho_df</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">DataFrame</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.utils.orthology.HomologeneOrthology.translate_df" title="Link to this definition">§</a></dt>
+<dd><p>Translate columns in a data frame.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>df</strong> – A data frame.</p></li>
+<li><p><strong>cols</strong> – One or more columns to be translated. It can be a single
+column name, an iterable of column names or a dict where
+keys are column names and values are ID types. Except this
+last case, identifiers are assumed to be UniProt.</p></li>
+<li><p><strong>ortho_df</strong> – Override the translation data frame. If provided, the
+parameters in <cite>kwargs</cite> won’t have an effect. Must have
+columns “source” and “target”.</p></li>
+<li><p><strong>kwargs</strong> – Resource specific translation parameters.</p></li>
+</ul>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p>A data frame with the same column layout as the input, and the
+identifiers translated as demanded. Rows that could not be
+translated are omitted.</p>
+</dd>
+</dl>
+</dd></dl>
+
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+
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+  <section id="pypath-utils-orthology-omaortholog">
+<h1>pypath.utils.orthology.OmaOrtholog<a class="headerlink" href="#pypath-utils-orthology-omaortholog" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.utils.orthology.OmaOrtholog">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.utils.orthology.</span></span><span class="sig-name descname"><span class="pre">OmaOrtholog</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">id</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">rel_type</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">score</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/utils/orthology.html#OmaOrtholog"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.utils.orthology.OmaOrtholog" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">OmaOrthologBase</span></code></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.utils.orthology.OmaOrtholog.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.utils.orthology.OmaOrtholog.__init__" title="Link to this definition">§</a></dt>
+<dd></dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.utils.orthology.OmaOrtholog.__init__" title="pypath.utils.orthology.OmaOrtholog.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.utils.orthology.OmaOrtholog.count" title="pypath.utils.orthology.OmaOrtholog.count"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count</span></code></a>(value, /)</p></td>
+<td><p>Return number of occurrences of value.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.utils.orthology.OmaOrtholog.index" title="pypath.utils.orthology.OmaOrtholog.index"><code class="xref py py-obj docutils literal notranslate"><span class="pre">index</span></code></a>(value[, start, stop])</p></td>
+<td><p>Return first index of value.</p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Attributes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.utils.orthology.OmaOrtholog.id" title="pypath.utils.orthology.OmaOrtholog.id"><code class="xref py py-obj docutils literal notranslate"><span class="pre">id</span></code></a></p></td>
+<td><p>Alias for field number 0</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.utils.orthology.OmaOrtholog.rel_type" title="pypath.utils.orthology.OmaOrtholog.rel_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">rel_type</span></code></a></p></td>
+<td><p>Alias for field number 1</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.utils.orthology.OmaOrtholog.score" title="pypath.utils.orthology.OmaOrtholog.score"><code class="xref py py-obj docutils literal notranslate"><span class="pre">score</span></code></a></p></td>
+<td><p>Alias for field number 2</p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.utils.orthology.OmaOrtholog.count">
+<span class="sig-name descname"><span class="pre">count</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">value</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">/</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.utils.orthology.OmaOrtholog.count" title="Link to this definition">§</a></dt>
+<dd><p>Return number of occurrences of value.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.utils.orthology.OmaOrtholog.id">
+<span class="sig-name descname"><span class="pre">id</span></span><a class="headerlink" href="#pypath.utils.orthology.OmaOrtholog.id" title="Link to this definition">§</a></dt>
+<dd><p>Alias for field number 0</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.utils.orthology.OmaOrtholog.index">
+<span class="sig-name descname"><span class="pre">index</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">value</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">start</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">stop</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9223372036854775807</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">/</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.utils.orthology.OmaOrtholog.index" title="Link to this definition">§</a></dt>
+<dd><p>Return first index of value.</p>
+<p>Raises ValueError if the value is not present.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.utils.orthology.OmaOrtholog.rel_type">
+<span class="sig-name descname"><span class="pre">rel_type</span></span><a class="headerlink" href="#pypath.utils.orthology.OmaOrtholog.rel_type" title="Link to this definition">§</a></dt>
+<dd><p>Alias for field number 1</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.utils.orthology.OmaOrtholog.score">
+<span class="sig-name descname"><span class="pre">score</span></span><a class="headerlink" href="#pypath.utils.orthology.OmaOrtholog.score" title="Link to this definition">§</a></dt>
+<dd><p>Alias for field number 2</p>
+</dd></dl>
+
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+  <section id="pypath-utils-orthology-omaorthology">
+<h1>pypath.utils.orthology.OmaOrthology<a class="headerlink" href="#pypath-utils-orthology-omaorthology" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.utils.orthology.OmaOrthology">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.utils.orthology.</span></span><span class="sig-name descname"><span class="pre">OmaOrthology</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">target</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">str</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">source</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">str</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">id_type</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">'uniprot'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">only_swissprot</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">rel_type</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">set</span><span class="p"><span class="pre">[</span></span><span class="pre">Literal</span><span class="p"><span class="pre">[</span></span><span class="s"><span class="pre">'1:1'</span></span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="s"><span class="pre">'1:n'</span></span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="s"><span class="pre">'m:1'</span></span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="s"><span class="pre">'m:n'</span></span><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">score</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">float</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/utils/orthology.html#OmaOrthology"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.utils.orthology.OmaOrthology" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <a class="reference internal" href="pypath.utils.orthology.ProteinOrthology.html#pypath.utils.orthology.ProteinOrthology" title="pypath.utils.orthology.ProteinOrthology"><code class="xref py py-class docutils literal notranslate"><span class="pre">ProteinOrthology</span></code></a></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.utils.orthology.OmaOrthology.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">target</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">str</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">source</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">str</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">id_type</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">'uniprot'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">only_swissprot</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">rel_type</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">set</span><span class="p"><span class="pre">[</span></span><span class="pre">Literal</span><span class="p"><span class="pre">[</span></span><span class="s"><span class="pre">'1:1'</span></span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="s"><span class="pre">'1:n'</span></span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="s"><span class="pre">'m:1'</span></span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="s"><span class="pre">'m:n'</span></span><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">score</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">float</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/utils/orthology.html#OmaOrthology.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.utils.orthology.OmaOrthology.__init__" title="Link to this definition">§</a></dt>
+<dd><p>Orthology translation with Ensembl data.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>target:</dt><dd><p>Name or NCBI Taxonomy ID of the target organism.</p>
+</dd>
+<dt>source:</dt><dd><p>Name or NCBI Taxonomy ID of the source organism.</p>
+</dd>
+<dt>id_type:</dt><dd><p>The identifier type to use.</p>
+</dd>
+<dt>only_swissprot:</dt><dd><p>Use only SwissProt IDs.</p>
+</dd>
+<dt>rel_type:</dt><dd><p>Restrict relations to certain types.</p>
+</dd>
+<dt>score:</dt><dd><p>Lower threshold for similarity metric.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.utils.orthology.OmaOrthology.__init__" title="pypath.utils.orthology.OmaOrthology.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>(target[, source, id_type, ...])</p></td>
+<td><p>Orthology translation with Ensembl data.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.utils.orthology.OmaOrthology.asdict" title="pypath.utils.orthology.OmaOrthology.asdict"><code class="xref py py-obj docutils literal notranslate"><span class="pre">asdict</span></code></a>([full_records])</p></td>
+<td><p>Create a dictionary from the translation table.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.utils.orthology.OmaOrthology.df" title="pypath.utils.orthology.OmaOrthology.df"><code class="xref py py-obj docutils literal notranslate"><span class="pre">df</span></code></a>([full_records])</p></td>
+<td><p>Orthologous pairs as data frame.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_taxon</span></code>(protein[, only_swissprot])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_taxon_trembl</span></code>(protein)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_protein</span></code>(protein)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_swissprot</span></code>(protein)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">load</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_proteome</span></code>(taxon[, only_swissprot])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_taxonomy</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.utils.orthology.OmaOrthology.match" title="pypath.utils.orthology.OmaOrthology.match"><code class="xref py py-obj docutils literal notranslate"><span class="pre">match</span></code></a>(ortholog, **kwargs)</p></td>
+<td><p>Check an ortholog against filtering criteria.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">reload</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.utils.orthology.OmaOrthology.translate" title="pypath.utils.orthology.OmaOrthology.translate"><code class="xref py py-obj docutils literal notranslate"><span class="pre">translate</span></code></a>(identifier[, full_records])</p></td>
+<td><p>For one UniProt ID of the source organism returns all orthologues from the target organism.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.utils.orthology.OmaOrthology.translate_df" title="pypath.utils.orthology.OmaOrthology.translate_df"><code class="xref py py-obj docutils literal notranslate"><span class="pre">translate_df</span></code></a>(df[, cols, ortho_df])</p></td>
+<td><p>Translate columns in a data frame.</p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Attributes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">key</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">pickle_path</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">resource</span></code></p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.utils.orthology.OmaOrthology.asdict">
+<span class="sig-name descname"><span class="pre">asdict</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">full_records</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">set</span><span class="p"><span class="pre">[</span></span><a class="reference internal" href="pypath.utils.orthology.OrthologBase.html#pypath.utils.orthology.OrthologBase" title="pypath.utils.orthology.OrthologBase"><span class="pre">OrthologBase</span></a><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span></span></span><a class="headerlink" href="#pypath.utils.orthology.OmaOrthology.asdict" title="Link to this definition">§</a></dt>
+<dd><p>Create a dictionary from the translation table.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>full_records</strong> – Include not only the identifiers, but also some properties of
+the orthology relationships.</p></li>
+<li><p><strong>kwargs</strong> – Resource specific filtering criteria.</p></li>
+</ul>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p>A dict with identifiers of the source organism as keys, and
+sets of their orthologs as values.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.utils.orthology.OmaOrthology.df">
+<span class="sig-name descname"><span class="pre">df</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">full_records</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><span class="pre">DataFrame</span></span></span><a class="headerlink" href="#pypath.utils.orthology.OmaOrthology.df" title="Link to this definition">§</a></dt>
+<dd><p>Orthologous pairs as data frame.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>full_records</strong> – Include not only the identifiers, but also some properties of
+the orthology relationships.</p></li>
+<li><p><strong>kwargs</strong> – Resource specific filtering criteria.</p></li>
+</ul>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p>A data frame with pairs of orthologous identifiers,
+in two columns: “source” and “target”.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.utils.orthology.OmaOrthology.match">
+<span class="sig-name descname"><span class="pre">match</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">ortholog</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="pypath.utils.orthology.OrthologBase.html#pypath.utils.orthology.OrthologBase" title="pypath.utils.orthology.OrthologBase"><span class="pre">OrthologBase</span></a></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><span class="pre">bool</span></span></span><a class="reference internal" href="../_modules/pypath/utils/orthology.html#OmaOrthology.match"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.utils.orthology.OmaOrthology.match" title="Link to this definition">§</a></dt>
+<dd><p>Check an ortholog against filtering criteria.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>ortholog</strong> – An ortholog record.</p></li>
+<li><p><strong>kwargs</strong> – Override default filtering parameters.</p></li>
+</ul>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p>True if the ortholog meets the criteria.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.utils.orthology.OmaOrthology.translate">
+<span class="sig-name descname"><span class="pre">translate</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">identifier</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">Iterable</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="n"><span class="pre">full_records</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><span class="pre">set</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span></span></span><a class="headerlink" href="#pypath.utils.orthology.OmaOrthology.translate" title="Link to this definition">§</a></dt>
+<dd><p>For one UniProt ID of the source organism returns all orthologues
+from the target organism.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>identifier</strong> – An identifier corresponding to the ID type and source organism
+of the instance.</p></li>
+<li><p><strong>full_records</strong> – Include not only the identifiers, but also some properties of
+the orthology relationships.</p></li>
+<li><p><strong>kwargs</strong> – Resource specific translation parameters.</p></li>
+</ul>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p>A set of identifiers of orthologues in the target taxon.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.utils.orthology.OmaOrthology.translate_df">
+<span class="sig-name descname"><span class="pre">translate_df</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">df</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">DataFrame</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cols</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ortho_df</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">DataFrame</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.utils.orthology.OmaOrthology.translate_df" title="Link to this definition">§</a></dt>
+<dd><p>Translate columns in a data frame.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>df</strong> – A data frame.</p></li>
+<li><p><strong>cols</strong> – One or more columns to be translated. It can be a single
+column name, an iterable of column names or a dict where
+keys are column names and values are ID types. Except this
+last case, identifiers are assumed to be UniProt.</p></li>
+<li><p><strong>ortho_df</strong> – Override the translation data frame. If provided, the
+parameters in <cite>kwargs</cite> won’t have an effect. Must have
+columns “source” and “target”.</p></li>
+<li><p><strong>kwargs</strong> – Resource specific translation parameters.</p></li>
+</ul>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p>A data frame with the same column layout as the input, and the
+identifiers translated as demanded. Rows that could not be
+translated are omitted.</p>
+</dd>
+</dl>
+</dd></dl>
+
+</dd></dl>
+
+</section>
+
+
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+  <section id="pypath-utils-orthology-orthologbase">
+<h1>pypath.utils.orthology.OrthologBase<a class="headerlink" href="#pypath-utils-orthology-orthologbase" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.utils.orthology.OrthologBase">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.utils.orthology.</span></span><span class="sig-name descname"><span class="pre">OrthologBase</span></span><a class="reference internal" href="../_modules/pypath/utils/orthology.html#OrthologBase"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.utils.orthology.OrthologBase" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.utils.orthology.OrthologBase.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.utils.orthology.OrthologBase.__init__" title="Link to this definition">§</a></dt>
+<dd></dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.utils.orthology.OrthologBase.__init__" title="pypath.utils.orthology.OrthologBase.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>()</p></td>
+<td><p></p></td>
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diff --git a/api/pypath.utils.orthology.OrthologMeta.html b/api/pypath.utils.orthology.OrthologMeta.html
new file mode 100644
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+  <section id="pypath-utils-orthology-orthologmeta">
+<h1>pypath.utils.orthology.OrthologMeta<a class="headerlink" href="#pypath-utils-orthology-orthologmeta" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.utils.orthology.OrthologMeta">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.utils.orthology.</span></span><span class="sig-name descname"><span class="pre">OrthologMeta</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">supercls</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">attrs</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resource</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">fields</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">tuple</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">('id',)</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/utils/orthology.html#OrthologMeta"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.utils.orthology.OrthologMeta" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">ABCMeta</span></code></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.utils.orthology.OrthologMeta.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">*</span></span><span class="n"><span class="pre">args</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.utils.orthology.OrthologMeta.__init__" title="Link to this definition">§</a></dt>
+<dd></dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.utils.orthology.OrthologMeta.__init__" title="pypath.utils.orthology.OrthologMeta.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>(*args, **kwargs)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.utils.orthology.OrthologMeta.mro" title="pypath.utils.orthology.OrthologMeta.mro"><code class="xref py py-obj docutils literal notranslate"><span class="pre">mro</span></code></a>()</p></td>
+<td><p>Return a type's method resolution order.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.utils.orthology.OrthologMeta.register" title="pypath.utils.orthology.OrthologMeta.register"><code class="xref py py-obj docutils literal notranslate"><span class="pre">register</span></code></a>(subclass)</p></td>
+<td><p>Register a virtual subclass of an ABC.</p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.utils.orthology.OrthologMeta.mro">
+<span class="sig-name descname"><span class="pre">mro</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.utils.orthology.OrthologMeta.mro" title="Link to this definition">§</a></dt>
+<dd><p>Return a type’s method resolution order.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.utils.orthology.OrthologMeta.register">
+<span class="sig-name descname"><span class="pre">register</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">subclass</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.utils.orthology.OrthologMeta.register" title="Link to this definition">§</a></dt>
+<dd><p>Register a virtual subclass of an ABC.</p>
+<p>Returns the subclass, to allow usage as a class decorator.</p>
+</dd></dl>
+
+</dd></dl>
+
+</section>
+
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+  <section id="pypath-utils-orthology-orthologymanager">
+<h1>pypath.utils.orthology.OrthologyManager<a class="headerlink" href="#pypath-utils-orthology-orthologymanager" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.utils.orthology.OrthologyManager">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.utils.orthology.</span></span><span class="sig-name descname"><span class="pre">OrthologyManager</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cleanup_period</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">10</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">lifetime</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">300</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/utils/orthology.html#OrthologyManager"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.utils.orthology.OrthologyManager" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">Logger</span></code></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.utils.orthology.OrthologyManager.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cleanup_period</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">10</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">lifetime</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">300</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/utils/orthology.html#OrthologyManager.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.utils.orthology.OrthologyManager.__init__" title="Link to this definition">§</a></dt>
+<dd><p>Make this instance a logger.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>name</strong> – The label of this instance that will be prepended to all
+messages it sends to the logger.</p></li>
+<li><p><strong>module</strong> – Send the messages by the logger of this module.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.utils.orthology.OrthologyManager.__init__" title="pypath.utils.orthology.OrthologyManager.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>([cleanup_period, lifetime])</p></td>
+<td><p>Make this instance a logger.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.utils.orthology.OrthologyManager.get_df" title="pypath.utils.orthology.OrthologyManager.get_df"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_df</span></code></a>(target[, source, id_type, ...])</p></td>
+<td><p>Create a data frame for one source organism and ID type.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.utils.orthology.OrthologyManager.get_dict" title="pypath.utils.orthology.OrthologyManager.get_dict"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_dict</span></code></a>(target[, source, id_type, ...])</p></td>
+<td><p>Create a dictionary for one source organism and ID type.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">load</span></code>(key)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">reload</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.utils.orthology.OrthologyManager.translate" title="pypath.utils.orthology.OrthologyManager.translate"><code class="xref py py-obj docutils literal notranslate"><span class="pre">translate</span></code></a>(identifiers, target[, source, ...])</p></td>
+<td><p>Translate one or more identifiers by orthologous gene pairs.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.utils.orthology.OrthologyManager.translate_df" title="pypath.utils.orthology.OrthologyManager.translate_df"><code class="xref py py-obj docutils literal notranslate"><span class="pre">translate_df</span></code></a>(df, target[, source, cols, ...])</p></td>
+<td><p>Translate columns in a data frame.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">which_table</span></code>(target[, source, ...])</p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Attributes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">RESOURCE_PARAM</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">TRANSLATION_PARAM</span></code></p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.utils.orthology.OrthologyManager.get_df">
+<span class="sig-name descname"><span class="pre">get_df</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">target</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">int</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">source</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">int</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">id_type</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">'uniprot'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">only_swissprot</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">oma</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">homologene</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ensembl</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">oma_rel_type</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">set</span><span class="p"><span class="pre">[</span></span><span class="pre">Literal</span><span class="p"><span class="pre">[</span></span><span class="s"><span class="pre">'1:1'</span></span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="s"><span class="pre">'1:n'</span></span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="s"><span class="pre">'m:1'</span></span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="s"><span class="pre">'m:n'</span></span><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">oma_score</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">float</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ensembl_hc</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ensembl_types</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">Literal</span><span class="p"><span class="pre">[</span></span><span class="s"><span class="pre">'one2one'</span></span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="s"><span class="pre">'one2many'</span></span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="s"><span class="pre">'many2many'</span></span><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">full_records</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><span class="pre">DataFrame</span></span></span><a class="reference internal" href="../_modules/pypath/utils/orthology.html#OrthologyManager.get_df"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.utils.orthology.OrthologyManager.get_df" title="Link to this definition">§</a></dt>
+<dd><p>Create a data frame for one source organism and ID type.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>target</strong> – Name or NCBI Taxonomy ID of the target organism.</p></li>
+<li><p><strong>source</strong> – Name or NCBI Taxonomy ID of the source organism.</p></li>
+<li><p><strong>id_type</strong> – The identifier type to use.</p></li>
+<li><p><strong>only_swissprot</strong> – Use only SwissProt IDs.</p></li>
+<li><p><strong>oma</strong> – Use orthology information from the Orthologous Matrix (OMA).
+Currently this is the recommended source for orthology data.</p></li>
+<li><p><strong>homologene</strong> – Use orthology information from NCBI HomoloGene.</p></li>
+<li><p><strong>ensembl</strong> – Use orthology information from Ensembl.</p></li>
+<li><p><strong>oma_rel_type</strong> – Restrict relations to certain types.</p></li>
+<li><p><strong>oma_score</strong> – Lower threshold for similarity metric.</p></li>
+<li><p><strong>ensembl_hc</strong> – Use only the high confidence orthology relations from Ensembl.</p></li>
+<li><p><strong>ensembl_types</strong> – Ensembl orthology relation types to use. Possible values are
+<cite>one2one</cite>, <cite>one2many</cite> and <cite>many2many</cite>. By default only
+<cite>one2one</cite> is used.</p></li>
+<li><p><strong>full_records</strong> – Include not only the identifiers, but also some properties of
+the orthology relationships.</p></li>
+<li><p><strong>kwargs</strong> – Ignored.</p></li>
+</ul>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p>A data frame with pairs of orthologous identifiers,
+in two columns: “source” and “target”.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.utils.orthology.OrthologyManager.get_dict">
+<span class="sig-name descname"><span class="pre">get_dict</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">target</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">int</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">source</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">int</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">id_type</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">'uniprot'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">only_swissprot</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">oma</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">homologene</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ensembl</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">oma_rel_type</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">set</span><span class="p"><span class="pre">[</span></span><span class="pre">Literal</span><span class="p"><span class="pre">[</span></span><span class="s"><span class="pre">'1:1'</span></span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="s"><span class="pre">'1:n'</span></span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="s"><span class="pre">'m:1'</span></span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="s"><span class="pre">'m:n'</span></span><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">oma_score</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">float</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ensembl_hc</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ensembl_types</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">Literal</span><span class="p"><span class="pre">[</span></span><span class="s"><span class="pre">'one2one'</span></span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="s"><span class="pre">'one2many'</span></span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="s"><span class="pre">'many2many'</span></span><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">full_records</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">set</span><span class="p"><span class="pre">[</span></span><a class="reference internal" href="pypath.utils.orthology.OrthologBase.html#pypath.utils.orthology.OrthologBase" title="pypath.utils.orthology.OrthologBase"><span class="pre">OrthologBase</span></a><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span></span></span><a class="reference internal" href="../_modules/pypath/utils/orthology.html#OrthologyManager.get_dict"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.utils.orthology.OrthologyManager.get_dict" title="Link to this definition">§</a></dt>
+<dd><p>Create a dictionary for one source organism and ID type.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>target</strong> – Name or NCBI Taxonomy ID of the target organism.</p></li>
+<li><p><strong>source</strong> – Name or NCBI Taxonomy ID of the source organism.</p></li>
+<li><p><strong>id_type</strong> – The identifier type to use.</p></li>
+<li><p><strong>only_swissprot</strong> – Use only SwissProt IDs.</p></li>
+<li><p><strong>oma</strong> – Use orthology information from the Orthologous Matrix (OMA).
+Currently this is the recommended source for orthology data.</p></li>
+<li><p><strong>homologene</strong> – Use orthology information from NCBI HomoloGene.</p></li>
+<li><p><strong>ensembl</strong> – Use orthology information from Ensembl.</p></li>
+<li><p><strong>oma_rel_type</strong> – Restrict relations to certain types.</p></li>
+<li><p><strong>oma_score</strong> – Lower threshold for similarity metric.</p></li>
+<li><p><strong>ensembl_hc</strong> – Use only the high confidence orthology relations from Ensembl.</p></li>
+<li><p><strong>ensembl_types</strong> – Ensembl orthology relation types to use. Possible values are
+<cite>one2one</cite>, <cite>one2many</cite> and <cite>many2many</cite>. By default only
+<cite>one2one</cite> is used.</p></li>
+<li><p><strong>full_records</strong> – Include not only the identifiers, but also some properties of
+the orthology relationships.</p></li>
+</ul>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p>A dict with identifiers of the source organism as keys, and
+sets of their orthologs as values.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.utils.orthology.OrthologyManager.translate">
+<span class="sig-name descname"><span class="pre">translate</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">identifiers</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">Iterable</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="n"><span class="pre">target</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">int</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">source</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">int</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">id_type</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">'uniprot'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">only_swissprot</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">oma</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">homologene</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ensembl</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">oma_rel_type</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">set</span><span class="p"><span class="pre">[</span></span><span class="pre">Literal</span><span class="p"><span class="pre">[</span></span><span class="s"><span class="pre">'1:1'</span></span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="s"><span class="pre">'1:n'</span></span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="s"><span class="pre">'m:1'</span></span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="s"><span class="pre">'m:n'</span></span><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">oma_score</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">float</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ensembl_hc</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ensembl_types</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">Literal</span><span class="p"><span class="pre">[</span></span><span class="s"><span class="pre">'one2one'</span></span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="s"><span class="pre">'one2many'</span></span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="s"><span class="pre">'many2many'</span></span><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">full_records</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/utils/orthology.html#OrthologyManager.translate"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.utils.orthology.OrthologyManager.translate" title="Link to this definition">§</a></dt>
+<dd><p>Translate one or more identifiers by orthologous gene pairs.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>identifiers</strong> – One or more identifers of the source organism, of ID type
+<cite>id_type</cite>.</p></li>
+<li><p><strong>target</strong> – Name or NCBI Taxonomy ID of the target organism.</p></li>
+<li><p><strong>source</strong> – Name or NCBI Taxonomy ID of the source organism.</p></li>
+<li><p><strong>id_type</strong> – The identifier type to use.</p></li>
+<li><p><strong>only_swissprot</strong> – Use only SwissProt IDs.</p></li>
+<li><p><strong>oma</strong> – Use orthology information from the Orthologous Matrix (OMA).
+Currently this is the recommended source for orthology data.</p></li>
+<li><p><strong>homologene</strong> – Use orthology information from NCBI HomoloGene.</p></li>
+<li><p><strong>ensembl</strong> – Use orthology information from Ensembl.</p></li>
+<li><p><strong>oma_rel_type</strong> – Restrict relations to certain types.</p></li>
+<li><p><strong>oma_score</strong> – Lower threshold for similarity metric.</p></li>
+<li><p><strong>ensembl_hc</strong> – Use only the high confidence orthology relations from Ensembl.</p></li>
+<li><p><strong>ensembl_types</strong> – Ensembl orthology relation types to use. Possible values are
+<cite>one2one</cite>, <cite>one2many</cite> and <cite>many2many</cite>. By default only
+<cite>one2one</cite> is used.</p></li>
+<li><p><strong>full_records</strong> – Include not only the identifiers, but also some properties of
+the orthology relationships.</p></li>
+</ul>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p>Set of identifiers of orthologous genes or proteins in the
+target taxon.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.utils.orthology.OrthologyManager.translate_df">
+<span class="sig-name descname"><span class="pre">translate_df</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">df</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">DataFrame</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">target</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">int</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">source</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">int</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cols</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">id_type</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">'uniprot'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">only_swissprot</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">oma</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">homologene</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ensembl</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">oma_rel_type</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">set</span><span class="p"><span class="pre">[</span></span><span class="pre">Literal</span><span class="p"><span class="pre">[</span></span><span class="s"><span class="pre">'1:1'</span></span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="s"><span class="pre">'1:n'</span></span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="s"><span class="pre">'m:1'</span></span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="s"><span class="pre">'m:n'</span></span><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">oma_score</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">float</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ensembl_hc</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ensembl_types</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">Literal</span><span class="p"><span class="pre">[</span></span><span class="s"><span class="pre">'one2one'</span></span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="s"><span class="pre">'one2many'</span></span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="s"><span class="pre">'many2many'</span></span><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">tuple</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">str</span><span class="p"><span class="pre">]</span></span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><span class="pre">DataFrame</span></span></span><a class="reference internal" href="../_modules/pypath/utils/orthology.html#OrthologyManager.translate_df"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.utils.orthology.OrthologyManager.translate_df" title="Link to this definition">§</a></dt>
+<dd><p>Translate columns in a data frame.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>df</strong> – A data frame.</p></li>
+<li><p><strong>cols</strong> – One or more columns to be translated. It can be a single
+column name, an iterable of column names or a dict where
+keys are column names and values are ID types. Except this
+last case, identifiers are assumed to be <cite>id_type</cite>.</p></li>
+<li><p><strong>target</strong> – Name or NCBI Taxonomy ID of the target organism.</p></li>
+<li><p><strong>source</strong> – Name or NCBI Taxonomy ID of the source organism.</p></li>
+<li><p><strong>id_type</strong> – The default identifier type to use, will be used for all
+columns where ID type is not specified.</p></li>
+<li><p><strong>only_swissprot</strong> – Use only SwissProt IDs.</p></li>
+<li><p><strong>oma</strong> – Use orthology information from the Orthologous Matrix (OMA).
+Currently this is the recommended source for orthology data.</p></li>
+<li><p><strong>homologene</strong> – Use orthology information from NCBI HomoloGene.</p></li>
+<li><p><strong>ensembl</strong> – Use orthology information from Ensembl.</p></li>
+<li><p><strong>oma_rel_type</strong> – Restrict relations to certain types.</p></li>
+<li><p><strong>oma_score</strong> – Lower threshold for similarity metric.</p></li>
+<li><p><strong>ensembl_hc</strong> – Use only the high confidence orthology relations from Ensembl.</p></li>
+<li><p><strong>ensembl_types</strong> – Ensembl orthology relation types to use. Possible values are
+<cite>one2one</cite>, <cite>one2many</cite> and <cite>many2many</cite>. By default only
+<cite>one2one</cite> is used.</p></li>
+<li><p><strong>kwargs</strong> – Same as providing a dict to <code class="docutils literal notranslate"><span class="pre">cols</span></code>, but beware, keys
+(column names) can not match existing argument names of
+this function.</p></li>
+</ul>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p>A data frame with the same column layout as the input, and the
+identifiers translated as demanded. Rows that could not be
+translated are omitted.</p>
+</dd>
+</dl>
+</dd></dl>
+
+</dd></dl>
+
+</section>
+
+
+                </article>
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+  <section id="pypath-utils-orthology-orthologytablekey">
+<h1>pypath.utils.orthology.OrthologyTableKey<a class="headerlink" href="#pypath-utils-orthology-orthologytablekey" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.utils.orthology.OrthologyTableKey">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.utils.orthology.</span></span><span class="sig-name descname"><span class="pre">OrthologyTableKey</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">source</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">target</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">only_swissprot</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">resource</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">id_type</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.utils.orthology.OrthologyTableKey" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">tuple</span></code></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.utils.orthology.OrthologyTableKey.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.utils.orthology.OrthologyTableKey.__init__" title="Link to this definition">§</a></dt>
+<dd></dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.utils.orthology.OrthologyTableKey.__init__" title="pypath.utils.orthology.OrthologyTableKey.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.utils.orthology.OrthologyTableKey.count" title="pypath.utils.orthology.OrthologyTableKey.count"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count</span></code></a>(value, /)</p></td>
+<td><p>Return number of occurrences of value.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.utils.orthology.OrthologyTableKey.index" title="pypath.utils.orthology.OrthologyTableKey.index"><code class="xref py py-obj docutils literal notranslate"><span class="pre">index</span></code></a>(value[, start, stop])</p></td>
+<td><p>Return first index of value.</p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Attributes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.utils.orthology.OrthologyTableKey.id_type" title="pypath.utils.orthology.OrthologyTableKey.id_type"><code class="xref py py-obj docutils literal notranslate"><span class="pre">id_type</span></code></a></p></td>
+<td><p>Alias for field number 4</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.utils.orthology.OrthologyTableKey.only_swissprot" title="pypath.utils.orthology.OrthologyTableKey.only_swissprot"><code class="xref py py-obj docutils literal notranslate"><span class="pre">only_swissprot</span></code></a></p></td>
+<td><p>Alias for field number 2</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.utils.orthology.OrthologyTableKey.resource" title="pypath.utils.orthology.OrthologyTableKey.resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">resource</span></code></a></p></td>
+<td><p>Alias for field number 3</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.utils.orthology.OrthologyTableKey.source" title="pypath.utils.orthology.OrthologyTableKey.source"><code class="xref py py-obj docutils literal notranslate"><span class="pre">source</span></code></a></p></td>
+<td><p>Alias for field number 0</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.utils.orthology.OrthologyTableKey.target" title="pypath.utils.orthology.OrthologyTableKey.target"><code class="xref py py-obj docutils literal notranslate"><span class="pre">target</span></code></a></p></td>
+<td><p>Alias for field number 1</p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.utils.orthology.OrthologyTableKey.count">
+<span class="sig-name descname"><span class="pre">count</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">value</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">/</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.utils.orthology.OrthologyTableKey.count" title="Link to this definition">§</a></dt>
+<dd><p>Return number of occurrences of value.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.utils.orthology.OrthologyTableKey.id_type">
+<span class="sig-name descname"><span class="pre">id_type</span></span><a class="headerlink" href="#pypath.utils.orthology.OrthologyTableKey.id_type" title="Link to this definition">§</a></dt>
+<dd><p>Alias for field number 4</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.utils.orthology.OrthologyTableKey.index">
+<span class="sig-name descname"><span class="pre">index</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">value</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">start</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">stop</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9223372036854775807</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">/</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.utils.orthology.OrthologyTableKey.index" title="Link to this definition">§</a></dt>
+<dd><p>Return first index of value.</p>
+<p>Raises ValueError if the value is not present.</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.utils.orthology.OrthologyTableKey.only_swissprot">
+<span class="sig-name descname"><span class="pre">only_swissprot</span></span><a class="headerlink" href="#pypath.utils.orthology.OrthologyTableKey.only_swissprot" title="Link to this definition">§</a></dt>
+<dd><p>Alias for field number 2</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.utils.orthology.OrthologyTableKey.resource">
+<span class="sig-name descname"><span class="pre">resource</span></span><a class="headerlink" href="#pypath.utils.orthology.OrthologyTableKey.resource" title="Link to this definition">§</a></dt>
+<dd><p>Alias for field number 3</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.utils.orthology.OrthologyTableKey.source">
+<span class="sig-name descname"><span class="pre">source</span></span><a class="headerlink" href="#pypath.utils.orthology.OrthologyTableKey.source" title="Link to this definition">§</a></dt>
+<dd><p>Alias for field number 0</p>
+</dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="pypath.utils.orthology.OrthologyTableKey.target">
+<span class="sig-name descname"><span class="pre">target</span></span><a class="headerlink" href="#pypath.utils.orthology.OrthologyTableKey.target" title="Link to this definition">§</a></dt>
+<dd><p>Alias for field number 1</p>
+</dd></dl>
+
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+
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diff --git a/api/pypath.utils.orthology.ProteinOrthology.html b/api/pypath.utils.orthology.ProteinOrthology.html
new file mode 100644
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+  <section id="pypath-utils-orthology-proteinorthology">
+<h1>pypath.utils.orthology.ProteinOrthology<a class="headerlink" href="#pypath-utils-orthology-proteinorthology" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.utils.orthology.ProteinOrthology">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.utils.orthology.</span></span><span class="sig-name descname"><span class="pre">ProteinOrthology</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">target</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">int</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">source</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">int</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">id_type</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">'uniprot'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">only_swissprot</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/utils/orthology.html#ProteinOrthology"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.utils.orthology.ProteinOrthology" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <a class="reference internal" href="pypath.utils.orthology.Proteomes.html#pypath.utils.orthology.Proteomes" title="pypath.utils.orthology.Proteomes"><code class="xref py py-class docutils literal notranslate"><span class="pre">Proteomes</span></code></a></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.utils.orthology.ProteinOrthology.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">target</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">int</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">source</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">int</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">id_type</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">'uniprot'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">only_swissprot</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/utils/orthology.html#ProteinOrthology.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.utils.orthology.ProteinOrthology.__init__" title="Link to this definition">§</a></dt>
+<dd><p>This class translates between homologous UniProt IDs of two organisms
+based on NCBI HomoloGene and Ensembl data. In case of HomoloGene,
+the UniProt-UniProt translation table is created by translating the
+source organism UniProts to RefSeq and Entrez IDs, finding the
+homologues (orthologues) for these IDs, and then translating them
+to the target organism UniProt IDs. In case of Ensembl, we obtain
+data with Ensembl protein identifiers and translate those to UniProt.</p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>target:</dt><dd><p>Name or NCBI Taxonomy ID of the target organism.</p>
+</dd>
+<dt>source:</dt><dd><p>Name or NCBI Taxonomy ID of the source organism.</p>
+</dd>
+<dt>id_type:</dt><dd><p>The identifier type to use.</p>
+</dd>
+<dt>only_swissprot:</dt><dd><p>Use only SwissProt IDs.</p>
+</dd>
+<dt>kwargs:</dt><dd><p>Resource specific parameters.</p>
+</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.utils.orthology.ProteinOrthology.__init__" title="pypath.utils.orthology.ProteinOrthology.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>(target[, source, id_type, ...])</p></td>
+<td><p>This class translates between homologous UniProt IDs of two organisms based on NCBI HomoloGene and Ensembl data.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.utils.orthology.ProteinOrthology.asdict" title="pypath.utils.orthology.ProteinOrthology.asdict"><code class="xref py py-obj docutils literal notranslate"><span class="pre">asdict</span></code></a>([full_records])</p></td>
+<td><p>Create a dictionary from the translation table.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.utils.orthology.ProteinOrthology.df" title="pypath.utils.orthology.ProteinOrthology.df"><code class="xref py py-obj docutils literal notranslate"><span class="pre">df</span></code></a>([full_records])</p></td>
+<td><p>Orthologous pairs as data frame.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_taxon</span></code>(protein[, only_swissprot])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_taxon_trembl</span></code>(protein)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_protein</span></code>(protein)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_swissprot</span></code>(protein)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">load</span></code>([source])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_proteome</span></code>(taxon[, only_swissprot])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_taxonomy</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">match</span></code>(ortholog, **kwargs)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">reload</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.utils.orthology.ProteinOrthology.translate" title="pypath.utils.orthology.ProteinOrthology.translate"><code class="xref py py-obj docutils literal notranslate"><span class="pre">translate</span></code></a>(identifier[, full_records])</p></td>
+<td><p>For one UniProt ID of the source organism returns all orthologues from the target organism.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.utils.orthology.ProteinOrthology.translate_df" title="pypath.utils.orthology.ProteinOrthology.translate_df"><code class="xref py py-obj docutils literal notranslate"><span class="pre">translate_df</span></code></a>(df[, cols, ortho_df])</p></td>
+<td><p>Translate columns in a data frame.</p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Attributes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">key</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">pickle_path</span></code></p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.utils.orthology.ProteinOrthology.asdict">
+<span class="sig-name descname"><span class="pre">asdict</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">full_records</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">set</span><span class="p"><span class="pre">[</span></span><a class="reference internal" href="pypath.utils.orthology.OrthologBase.html#pypath.utils.orthology.OrthologBase" title="pypath.utils.orthology.OrthologBase"><span class="pre">OrthologBase</span></a><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span></span></span><a class="reference internal" href="../_modules/pypath/utils/orthology.html#ProteinOrthology.asdict"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.utils.orthology.ProteinOrthology.asdict" title="Link to this definition">§</a></dt>
+<dd><p>Create a dictionary from the translation table.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>full_records</strong> – Include not only the identifiers, but also some properties of
+the orthology relationships.</p></li>
+<li><p><strong>kwargs</strong> – Resource specific filtering criteria.</p></li>
+</ul>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p>A dict with identifiers of the source organism as keys, and
+sets of their orthologs as values.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.utils.orthology.ProteinOrthology.df">
+<span class="sig-name descname"><span class="pre">df</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">full_records</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><span class="pre">DataFrame</span></span></span><a class="reference internal" href="../_modules/pypath/utils/orthology.html#ProteinOrthology.df"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.utils.orthology.ProteinOrthology.df" title="Link to this definition">§</a></dt>
+<dd><p>Orthologous pairs as data frame.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>full_records</strong> – Include not only the identifiers, but also some properties of
+the orthology relationships.</p></li>
+<li><p><strong>kwargs</strong> – Resource specific filtering criteria.</p></li>
+</ul>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p>A data frame with pairs of orthologous identifiers,
+in two columns: “source” and “target”.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.utils.orthology.ProteinOrthology.translate">
+<span class="sig-name descname"><span class="pre">translate</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">identifier</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">Iterable</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="n"><span class="pre">full_records</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><span class="pre">set</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span></span></span><a class="reference internal" href="../_modules/pypath/utils/orthology.html#ProteinOrthology.translate"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.utils.orthology.ProteinOrthology.translate" title="Link to this definition">§</a></dt>
+<dd><p>For one UniProt ID of the source organism returns all orthologues
+from the target organism.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>identifier</strong> – An identifier corresponding to the ID type and source organism
+of the instance.</p></li>
+<li><p><strong>full_records</strong> – Include not only the identifiers, but also some properties of
+the orthology relationships.</p></li>
+<li><p><strong>kwargs</strong> – Resource specific translation parameters.</p></li>
+</ul>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p>A set of identifiers of orthologues in the target taxon.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.utils.orthology.ProteinOrthology.translate_df">
+<span class="sig-name descname"><span class="pre">translate_df</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">df</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">DataFrame</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cols</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ortho_df</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">DataFrame</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/utils/orthology.html#ProteinOrthology.translate_df"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.utils.orthology.ProteinOrthology.translate_df" title="Link to this definition">§</a></dt>
+<dd><p>Translate columns in a data frame.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>df</strong> – A data frame.</p></li>
+<li><p><strong>cols</strong> – One or more columns to be translated. It can be a single
+column name, an iterable of column names or a dict where
+keys are column names and values are ID types. Except this
+last case, identifiers are assumed to be UniProt.</p></li>
+<li><p><strong>ortho_df</strong> – Override the translation data frame. If provided, the
+parameters in <cite>kwargs</cite> won’t have an effect. Must have
+columns “source” and “target”.</p></li>
+<li><p><strong>kwargs</strong> – Resource specific translation parameters.</p></li>
+</ul>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p>A data frame with the same column layout as the input, and the
+identifiers translated as demanded. Rows that could not be
+translated are omitted.</p>
+</dd>
+</dl>
+</dd></dl>
+
+</dd></dl>
+
+</section>
+
+
+                </article>
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+  <section id="pypath-utils-orthology-proteomes">
+<h1>pypath.utils.orthology.Proteomes<a class="headerlink" href="#pypath-utils-orthology-proteomes" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.utils.orthology.Proteomes">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.utils.orthology.</span></span><span class="sig-name descname"><span class="pre">Proteomes</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">preload_prot</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">int</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">only_swissprot</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/utils/orthology.html#Proteomes"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.utils.orthology.Proteomes" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.utils.orthology.Proteomes.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">preload_prot</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">int</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">only_swissprot</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/utils/orthology.html#Proteomes.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.utils.orthology.Proteomes.__init__" title="Link to this definition">§</a></dt>
+<dd></dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.utils.orthology.Proteomes.__init__" title="pypath.utils.orthology.Proteomes.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>([preload_prot, only_swissprot])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_taxon</span></code>(protein[, only_swissprot])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_taxon_trembl</span></code>(protein)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_protein</span></code>(protein)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_swissprot</span></code>(protein)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_proteome</span></code>(taxon[, only_swissprot])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_taxonomy</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
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+  <section id="pypath-utils-orthology-ptmorthology">
+<h1>pypath.utils.orthology.PtmOrthology<a class="headerlink" href="#pypath-utils-orthology-ptmorthology" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.utils.orthology.PtmOrthology">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.utils.orthology.</span></span><span class="sig-name descname"><span class="pre">PtmOrthology</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">target</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">int</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">source</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">int</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">only_swissprot</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">strict</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">orthology_args</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">dict</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/utils/orthology.html#PtmOrthology"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.utils.orthology.PtmOrthology" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <a class="reference internal" href="pypath.utils.orthology.Proteomes.html#pypath.utils.orthology.Proteomes" title="pypath.utils.orthology.Proteomes"><code class="xref py py-class docutils literal notranslate"><span class="pre">Proteomes</span></code></a>, <a class="reference internal" href="pypath.utils.orthology.SequenceContainer.html#pypath.utils.orthology.SequenceContainer" title="pypath.utils.orthology.SequenceContainer"><code class="xref py py-class docutils literal notranslate"><span class="pre">SequenceContainer</span></code></a></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.utils.orthology.PtmOrthology.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">target</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">int</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">source</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">int</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">only_swissprot</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">strict</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">orthology_args</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">dict</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/utils/orthology.html#PtmOrthology.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.utils.orthology.PtmOrthology.__init__" title="Link to this definition">§</a></dt>
+<dd><p>This is an object to store sequences of multiple
+organisms and select the appropriate one.</p>
+</dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.utils.orthology.PtmOrthology.__init__" title="pypath.utils.orthology.PtmOrthology.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>(target[, source, only_swissprot, ...])</p></td>
+<td><p>This is an object to store sequences of multiple organisms and select the appropriate one.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_seq</span></code>(protein[, taxon])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_taxon</span></code>(protein[, only_swissprot])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_taxon_trembl</span></code>(protein)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_protein</span></code>(protein)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_swissprot</span></code>(protein)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_proteome</span></code>(taxon[, only_swissprot])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_seq</span></code>(taxon)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_taxonomy</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.utils.orthology.PtmOrthology.ptm_orthology" title="pypath.utils.orthology.PtmOrthology.ptm_orthology"><code class="xref py py-obj docutils literal notranslate"><span class="pre">ptm_orthology</span></code></a>()</p></td>
+<td><p>Load PTM orthology data from PhosphoSite.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">reload</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.utils.orthology.PtmOrthology.translate" title="pypath.utils.orthology.PtmOrthology.translate"><code class="xref py py-obj docutils literal notranslate"><span class="pre">translate</span></code></a>(x[, return_strings])</p></td>
+<td><p>Translates anything: string notation, intera objects, tuples.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">translate_domain</span></code>(domain)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">translate_domain_motif</span></code>(dmotif)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">translate_ptm</span></code>(ptm)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">translate_residue</span></code>(residue)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.utils.orthology.PtmOrthology.translate_site" title="pypath.utils.orthology.PtmOrthology.translate_site"><code class="xref py py-obj docutils literal notranslate"><span class="pre">translate_site</span></code></a>(protein, res, offset[, ...])</p></td>
+<td><p>Translates one PTM site.</p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.utils.orthology.PtmOrthology.ptm_orthology">
+<span class="sig-name descname"><span class="pre">ptm_orthology</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/utils/orthology.html#PtmOrthology.ptm_orthology"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.utils.orthology.PtmOrthology.ptm_orthology" title="Link to this definition">§</a></dt>
+<dd><p>Load PTM orthology data from PhosphoSite.</p>
+<p>Creates an orthology translation dict of phosphosites
+based on phosphorylation sites table from PhosphoSitePlus.
+In the result all PTMs represented by a tuple of the following
+6 elements: UniProt ID, isoform (int), residue one letter code,
+residue number (int), NCBI Taxonomy ID (int), modification type.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.utils.orthology.PtmOrthology.translate">
+<span class="sig-name descname"><span class="pre">translate</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">x</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">return_strings</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/utils/orthology.html#PtmOrthology.translate"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.utils.orthology.PtmOrthology.translate" title="Link to this definition">§</a></dt>
+<dd><p>Translates anything: string notation, intera objects, tuples.</p>
+<ul class="simple">
+<li><p>one PTM provided as tuple of (UniProt, amino acid, offest)</p></li>
+<li><p>one PTM provided as string (e.g. <cite>P00533_S231</cite>)</p></li>
+<li><p>instance from pypath.intera: DomainMotif, Domain or Ptm</p></li>
+</ul>
+<p>Additional arguments can be isoform and typ (modification type).</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.utils.orthology.PtmOrthology.translate_site">
+<span class="sig-name descname"><span class="pre">translate_site</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">protein</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">intera.Protein</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">res</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">offset</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">isoform</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">typ</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">'phosphorylation'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">source_organism</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">int</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><span class="pre">set</span><span class="p"><span class="pre">[</span></span><span class="pre">tuple</span><span class="p"><span class="pre">]</span></span></span></span><a class="reference internal" href="../_modules/pypath/utils/orthology.html#PtmOrthology.translate_site"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.utils.orthology.PtmOrthology.translate_site" title="Link to this definition">§</a></dt>
+<dd><p>Translates one PTM site.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>protein</strong> – A protein identifier or an intera.Protein object.</p></li>
+<li><p><strong>res</strong> – Single letter code of the residue.</p></li>
+<li><p><strong>offset</strong> – Sequence offset of the site.</p></li>
+<li><p><strong>isoform</strong> – Sequence isoform.</p></li>
+<li><p><strong>typ</strong> – Modification type.</p></li>
+<li><p><strong>source_organism</strong> – Name or NCBI Taxonomy ID of the source organism.</p></li>
+</ul>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p>A list of tuples with the identifier, isoform, residue, offset,
+taxon and modification type of the orthologous PTM sites.</p>
+</dd>
+</dl>
+</dd></dl>
+
+</dd></dl>
+
+</section>
+
+
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+  <section id="pypath-utils-orthology-sequencecontainer">
+<h1>pypath.utils.orthology.SequenceContainer<a class="headerlink" href="#pypath-utils-orthology-sequencecontainer" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.utils.orthology.SequenceContainer">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.utils.orthology.</span></span><span class="sig-name descname"><span class="pre">SequenceContainer</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">preload_seq</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">[]</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">isoforms</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/utils/orthology.html#SequenceContainer"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.utils.orthology.SequenceContainer" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">Logger</span></code></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.utils.orthology.SequenceContainer.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">preload_seq</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">[]</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">isoforms</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/utils/orthology.html#SequenceContainer.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.utils.orthology.SequenceContainer.__init__" title="Link to this definition">§</a></dt>
+<dd><p>This is an object to store sequences of multiple
+organisms and select the appropriate one.</p>
+</dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.utils.orthology.SequenceContainer.__init__" title="pypath.utils.orthology.SequenceContainer.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>([preload_seq, isoforms])</p></td>
+<td><p>This is an object to store sequences of multiple organisms and select the appropriate one.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_seq</span></code>(protein[, taxon])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_seq</span></code>(taxon)</p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+</section>
+
+
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+<h1>pypath.utils.orthology.get_df<a class="headerlink" href="#pypath-utils-orthology-get-df" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.utils.orthology.get_df">
+<span class="sig-prename descclassname"><span class="pre">pypath.utils.orthology.</span></span><span class="sig-name descname"><span class="pre">get_df</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">target</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">int</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">source</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">int</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">id_type</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">'uniprot'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">only_swissprot</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">oma</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">homologene</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ensembl</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">oma_rel_type</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">set</span><span class="p"><span class="pre">[</span></span><span class="pre">Literal</span><span class="p"><span class="pre">[</span></span><span class="s"><span class="pre">'1:1'</span></span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="s"><span class="pre">'1:n'</span></span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="s"><span class="pre">'m:1'</span></span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="s"><span class="pre">'m:n'</span></span><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">oma_score</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">float</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ensembl_hc</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ensembl_types</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">Literal</span><span class="p"><span class="pre">[</span></span><span class="s"><span class="pre">'one2one'</span></span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="s"><span class="pre">'one2many'</span></span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="s"><span class="pre">'many2many'</span></span><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">full_records</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><span class="pre">DataFrame</span></span></span><a class="reference internal" href="../_modules/pypath/utils/orthology.html#get_df"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.utils.orthology.get_df" title="Link to this definition">§</a></dt>
+<dd><p>Create a data frame for one source organism and ID type.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>target</strong> – Name or NCBI Taxonomy ID of the target organism.</p></li>
+<li><p><strong>source</strong> – Name or NCBI Taxonomy ID of the source organism.</p></li>
+<li><p><strong>id_type</strong> – The identifier type to use.</p></li>
+<li><p><strong>only_swissprot</strong> – Use only SwissProt IDs.</p></li>
+<li><p><strong>oma</strong> – Use orthology information from the Orthologous Matrix (OMA).
+Currently this is the recommended source for orthology data.</p></li>
+<li><p><strong>homologene</strong> – Use orthology information from NCBI HomoloGene.</p></li>
+<li><p><strong>ensembl</strong> – Use orthology information from Ensembl.</p></li>
+<li><p><strong>oma_rel_type</strong> – Restrict relations to certain types.</p></li>
+<li><p><strong>oma_score</strong> – Lower threshold for similarity metric.</p></li>
+<li><p><strong>ensembl_hc</strong> – Use only the high confidence orthology relations from Ensembl.</p></li>
+<li><p><strong>ensembl_types</strong> – Ensembl orthology relation types to use. Possible values are
+<cite>one2one</cite>, <cite>one2many</cite> and <cite>many2many</cite>. By default only
+<cite>one2one</cite> is used.</p></li>
+<li><p><strong>full_records</strong> – Include not only the identifiers, but also some properties of
+the orthology relationships.</p></li>
+<li><p><strong>kwargs</strong> – Ignored.</p></li>
+</ul>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p>A data frame with pairs of orthologous identifiers,
+in two columns: “source” and “target”.</p>
+</dd>
+</dl>
+</dd></dl>
+
+</section>
+
+
+                </article>
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+  <section id="pypath-utils-orthology-get-dict">
+<h1>pypath.utils.orthology.get_dict<a class="headerlink" href="#pypath-utils-orthology-get-dict" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.utils.orthology.get_dict">
+<span class="sig-prename descclassname"><span class="pre">pypath.utils.orthology.</span></span><span class="sig-name descname"><span class="pre">get_dict</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">target</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">int</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">source</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">int</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">id_type</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">'uniprot'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">only_swissprot</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">oma</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">homologene</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ensembl</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">oma_rel_type</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">set</span><span class="p"><span class="pre">[</span></span><span class="pre">Literal</span><span class="p"><span class="pre">[</span></span><span class="s"><span class="pre">'1:1'</span></span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="s"><span class="pre">'1:n'</span></span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="s"><span class="pre">'m:1'</span></span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="s"><span class="pre">'m:n'</span></span><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">oma_score</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">float</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ensembl_hc</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ensembl_types</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">Literal</span><span class="p"><span class="pre">[</span></span><span class="s"><span class="pre">'one2one'</span></span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="s"><span class="pre">'one2many'</span></span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="s"><span class="pre">'many2many'</span></span><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">full_records</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">set</span><span class="p"><span class="pre">[</span></span><a class="reference internal" href="pypath.utils.orthology.OrthologBase.html#pypath.utils.orthology.OrthologBase" title="pypath.utils.orthology.OrthologBase"><span class="pre">OrthologBase</span></a><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span></span></span><a class="reference internal" href="../_modules/pypath/utils/orthology.html#get_dict"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.utils.orthology.get_dict" title="Link to this definition">§</a></dt>
+<dd><p>Create a dictionary for one source organism and ID type.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>target</strong> – Name or NCBI Taxonomy ID of the target organism.</p></li>
+<li><p><strong>source</strong> – Name or NCBI Taxonomy ID of the source organism.</p></li>
+<li><p><strong>id_type</strong> – The identifier type to use.</p></li>
+<li><p><strong>only_swissprot</strong> – Use only SwissProt IDs.</p></li>
+<li><p><strong>oma</strong> – Use orthology information from the Orthologous Matrix (OMA).
+Currently this is the recommended source for orthology data.</p></li>
+<li><p><strong>homologene</strong> – Use orthology information from NCBI HomoloGene.</p></li>
+<li><p><strong>ensembl</strong> – Use orthology information from Ensembl.</p></li>
+<li><p><strong>oma_rel_type</strong> – Restrict relations to certain types.</p></li>
+<li><p><strong>oma_score</strong> – Lower threshold for similarity metric.</p></li>
+<li><p><strong>ensembl_hc</strong> – Use only the high confidence orthology relations from Ensembl.</p></li>
+<li><p><strong>ensembl_types</strong> – Ensembl orthology relation types to use. Possible values are
+<cite>one2one</cite>, <cite>one2many</cite> and <cite>many2many</cite>. By default only
+<cite>one2one</cite> is used.</p></li>
+<li><p><strong>full_records</strong> – Include not only the identifiers, but also some properties of
+the orthology relationships.</p></li>
+</ul>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p>A dict with identifiers of the source organism as keys, and
+sets of their orthologs as values.</p>
+</dd>
+</dl>
+</dd></dl>
+
+</section>
+
+
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+<h1>pypath.utils.orthology.get_manager<a class="headerlink" href="#pypath-utils-orthology-get-manager" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.utils.orthology.get_manager">
+<span class="sig-prename descclassname"><span class="pre">pypath.utils.orthology.</span></span><span class="sig-name descname"><span class="pre">get_manager</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/utils/orthology.html#get_manager"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.utils.orthology.get_manager" title="Link to this definition">§</a></dt>
+<dd><p>Access the orthology manager.</p>
+<p>Returns the orthology manager, an object which loads and unloads the
+orthology lookup tables as necessary, and provides the interface for
+querying the orthology data. Normally an instance of the manager
+belongs to the module, and if it does not exist yet, will be created
+automatically.</p>
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diff --git a/api/pypath.utils.orthology.html b/api/pypath.utils.orthology.html
new file mode 100644
index 000000000..8b7559b78
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@@ -0,0 +1,707 @@
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+  <section id="module-pypath.utils.orthology">
+<span id="pypath-utils-orthology"></span><h1>pypath.utils.orthology<a class="headerlink" href="#module-pypath.utils.orthology" title="Link to this heading">§</a></h1>
+<dl class="field-list simple">
+<dt class="field-odd">members<span class="colon">:</span></dt>
+<dd class="field-odd"><p></p></dd>
+</dl>
+<p class="rubric">Functions</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.utils.orthology.get_df.html#pypath.utils.orthology.get_df" title="pypath.utils.orthology.get_df"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_df</span></code></a>(target[, source, id_type, ...])</p></td>
+<td><p>Create a data frame for one source organism and ID type.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.utils.orthology.get_dict.html#pypath.utils.orthology.get_dict" title="pypath.utils.orthology.get_dict"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_dict</span></code></a>(target[, source, id_type, ...])</p></td>
+<td><p>Create a dictionary for one source organism and ID type.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.utils.orthology.get_manager.html#pypath.utils.orthology.get_manager" title="pypath.utils.orthology.get_manager"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_manager</span></code></a>()</p></td>
+<td><p>Access the orthology manager.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.utils.orthology.init.html#pypath.utils.orthology.init" title="pypath.utils.orthology.init"><code class="xref py py-obj docutils literal notranslate"><span class="pre">init</span></code></a>()</p></td>
+<td><p>Initialize the orthology manager.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.utils.orthology.translate.html#pypath.utils.orthology.translate" title="pypath.utils.orthology.translate"><code class="xref py py-obj docutils literal notranslate"><span class="pre">translate</span></code></a>(identifiers, target[, source, ...])</p></td>
+<td><p>Translate one or more identifiers by orthologous gene pairs.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.utils.orthology.translate_df.html#pypath.utils.orthology.translate_df" title="pypath.utils.orthology.translate_df"><code class="xref py py-obj docutils literal notranslate"><span class="pre">translate_df</span></code></a>(df, target[, source, cols, ...])</p></td>
+<td><p>Translate columns in a data frame.</p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Classes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.utils.orthology.EnsemblOrtholog.html#pypath.utils.orthology.EnsemblOrtholog" title="pypath.utils.orthology.EnsemblOrtholog"><code class="xref py py-obj docutils literal notranslate"><span class="pre">EnsemblOrtholog</span></code></a>(id, types, hc)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.utils.orthology.EnsemblOrthology.html#pypath.utils.orthology.EnsemblOrthology" title="pypath.utils.orthology.EnsemblOrthology"><code class="xref py py-obj docutils literal notranslate"><span class="pre">EnsemblOrthology</span></code></a>(target[, source, id_type, ...])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.utils.orthology.HomologeneOrtholog.html#pypath.utils.orthology.HomologeneOrtholog" title="pypath.utils.orthology.HomologeneOrtholog"><code class="xref py py-obj docutils literal notranslate"><span class="pre">HomologeneOrtholog</span></code></a>(id)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.utils.orthology.HomologeneOrthology.html#pypath.utils.orthology.HomologeneOrthology" title="pypath.utils.orthology.HomologeneOrthology"><code class="xref py py-obj docutils literal notranslate"><span class="pre">HomologeneOrthology</span></code></a>(target[, source, ...])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.utils.orthology.OmaOrtholog.html#pypath.utils.orthology.OmaOrtholog" title="pypath.utils.orthology.OmaOrtholog"><code class="xref py py-obj docutils literal notranslate"><span class="pre">OmaOrtholog</span></code></a>(id, rel_type, score)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.utils.orthology.OmaOrthology.html#pypath.utils.orthology.OmaOrthology" title="pypath.utils.orthology.OmaOrthology"><code class="xref py py-obj docutils literal notranslate"><span class="pre">OmaOrthology</span></code></a>(target[, source, id_type, ...])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.utils.orthology.OrthologBase.html#pypath.utils.orthology.OrthologBase" title="pypath.utils.orthology.OrthologBase"><code class="xref py py-obj docutils literal notranslate"><span class="pre">OrthologBase</span></code></a>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.utils.orthology.OrthologMeta.html#pypath.utils.orthology.OrthologMeta" title="pypath.utils.orthology.OrthologMeta"><code class="xref py py-obj docutils literal notranslate"><span class="pre">OrthologMeta</span></code></a>(name, supercls, attrs, resource)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.utils.orthology.OrthologyManager.html#pypath.utils.orthology.OrthologyManager" title="pypath.utils.orthology.OrthologyManager"><code class="xref py py-obj docutils literal notranslate"><span class="pre">OrthologyManager</span></code></a>([cleanup_period, lifetime])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.utils.orthology.OrthologyTableKey.html#pypath.utils.orthology.OrthologyTableKey" title="pypath.utils.orthology.OrthologyTableKey"><code class="xref py py-obj docutils literal notranslate"><span class="pre">OrthologyTableKey</span></code></a>(source, target, ...)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.utils.orthology.ProteinOrthology.html#pypath.utils.orthology.ProteinOrthology" title="pypath.utils.orthology.ProteinOrthology"><code class="xref py py-obj docutils literal notranslate"><span class="pre">ProteinOrthology</span></code></a>(target[, source, id_type, ...])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.utils.orthology.Proteomes.html#pypath.utils.orthology.Proteomes" title="pypath.utils.orthology.Proteomes"><code class="xref py py-obj docutils literal notranslate"><span class="pre">Proteomes</span></code></a>([preload_prot, only_swissprot])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.utils.orthology.PtmOrthology.html#pypath.utils.orthology.PtmOrthology" title="pypath.utils.orthology.PtmOrthology"><code class="xref py py-obj docutils literal notranslate"><span class="pre">PtmOrthology</span></code></a>(target[, source, ...])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.utils.orthology.SequenceContainer.html#pypath.utils.orthology.SequenceContainer" title="pypath.utils.orthology.SequenceContainer"><code class="xref py py-obj docutils literal notranslate"><span class="pre">SequenceContainer</span></code></a>([preload_seq, isoforms])</p></td>
+<td><p></p></td>
+</tr>
+</tbody>
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+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.utils.orthology.init">
+<span class="sig-prename descclassname"><span class="pre">pypath.utils.orthology.</span></span><span class="sig-name descname"><span class="pre">init</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/utils/orthology.html#init"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.utils.orthology.init" title="Link to this definition">§</a></dt>
+<dd><p>Initialize the orthology manager.</p>
+<p>Creates an instance of the orthology manager. Stores it in the module
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+  <section id="pypath-utils-orthology-translate">
+<h1>pypath.utils.orthology.translate<a class="headerlink" href="#pypath-utils-orthology-translate" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.utils.orthology.translate">
+<span class="sig-prename descclassname"><span class="pre">pypath.utils.orthology.</span></span><span class="sig-name descname"><span class="pre">translate</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">identifiers</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">Iterable</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="n"><span class="pre">target</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">int</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">source</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">int</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">id_type</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">'uniprot'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">only_swissprot</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">oma</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">homologene</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ensembl</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">oma_rel_type</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">set</span><span class="p"><span class="pre">[</span></span><span class="pre">Literal</span><span class="p"><span class="pre">[</span></span><span class="s"><span class="pre">'1:1'</span></span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="s"><span class="pre">'1:n'</span></span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="s"><span class="pre">'m:1'</span></span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="s"><span class="pre">'m:n'</span></span><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">oma_score</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">float</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ensembl_hc</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ensembl_types</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">Literal</span><span class="p"><span class="pre">[</span></span><span class="s"><span class="pre">'one2one'</span></span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="s"><span class="pre">'one2many'</span></span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="s"><span class="pre">'many2many'</span></span><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">full_records</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/utils/orthology.html#translate"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.utils.orthology.translate" title="Link to this definition">§</a></dt>
+<dd><p>Translate one or more identifiers by orthologous gene pairs.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>identifiers</strong> – One or more identifers of the source organism, of ID type
+<cite>id_type</cite>.</p></li>
+<li><p><strong>target</strong> – Name or NCBI Taxonomy ID of the target organism.</p></li>
+<li><p><strong>source</strong> – Name or NCBI Taxonomy ID of the source organism.</p></li>
+<li><p><strong>id_type</strong> – The identifier type to use.</p></li>
+<li><p><strong>only_swissprot</strong> – Use only SwissProt IDs.</p></li>
+<li><p><strong>oma</strong> – Use orthology information from the Orthologous Matrix (OMA).
+Currently this is the recommended source for orthology data.</p></li>
+<li><p><strong>homologene</strong> – Use orthology information from NCBI HomoloGene.</p></li>
+<li><p><strong>ensembl</strong> – Use orthology information from Ensembl.</p></li>
+<li><p><strong>oma_rel_type</strong> – Restrict relations to certain types.</p></li>
+<li><p><strong>oma_score</strong> – Lower threshold for similarity metric.</p></li>
+<li><p><strong>ensembl_hc</strong> – Use only the high confidence orthology relations from Ensembl.</p></li>
+<li><p><strong>ensembl_types</strong> – Ensembl orthology relation types to use. Possible values are
+<cite>one2one</cite>, <cite>one2many</cite> and <cite>many2many</cite>. By default only
+<cite>one2one</cite> is used.</p></li>
+<li><p><strong>full_records</strong> – Include not only the identifiers, but also some properties of
+the orthology relationships.</p></li>
+</ul>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p>Set of identifiers of orthologous genes or proteins in the
+target taxon.</p>
+</dd>
+</dl>
+</dd></dl>
+
+</section>
+
+
+                </article>
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+  <section id="pypath-utils-orthology-translate-df">
+<h1>pypath.utils.orthology.translate_df<a class="headerlink" href="#pypath-utils-orthology-translate-df" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.utils.orthology.translate_df">
+<span class="sig-prename descclassname"><span class="pre">pypath.utils.orthology.</span></span><span class="sig-name descname"><span class="pre">translate_df</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">df</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">DataFrame</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">target</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">int</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">source</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">int</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cols</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">id_type</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">'uniprot'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">only_swissprot</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">oma</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">homologene</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ensembl</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">oma_rel_type</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">set</span><span class="p"><span class="pre">[</span></span><span class="pre">Literal</span><span class="p"><span class="pre">[</span></span><span class="s"><span class="pre">'1:1'</span></span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="s"><span class="pre">'1:n'</span></span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="s"><span class="pre">'m:1'</span></span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="s"><span class="pre">'m:n'</span></span><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">oma_score</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">float</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ensembl_hc</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ensembl_types</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">Literal</span><span class="p"><span class="pre">[</span></span><span class="s"><span class="pre">'one2one'</span></span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="s"><span class="pre">'one2many'</span></span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="s"><span class="pre">'many2many'</span></span><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">tuple</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">str</span><span class="p"><span class="pre">]</span></span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><span class="pre">DataFrame</span></span></span><a class="reference internal" href="../_modules/pypath/utils/orthology.html#translate_df"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.utils.orthology.translate_df" title="Link to this definition">§</a></dt>
+<dd><p>Translate columns in a data frame.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>df</strong> – A data frame.</p></li>
+<li><p><strong>target</strong> – Name or NCBI Taxonomy ID of the target organism.</p></li>
+<li><p><strong>source</strong> – Name or NCBI Taxonomy ID of the source organism.</p></li>
+<li><p><strong>cols</strong> – One or more columns to be translated. It can be a single
+column name, an iterable of column names or a dict where
+keys are column names and values are ID types. Except this
+last case, identifiers are assumed to be <cite>id_type</cite>.</p></li>
+<li><p><strong>id_type</strong> – The default identifier type to use, will be used for all
+columns where ID type is not specified.</p></li>
+<li><p><strong>only_swissprot</strong> – Use only SwissProt IDs.</p></li>
+<li><p><strong>oma</strong> – Use orthology information from the Orthologous Matrix (OMA).
+Currently this is the recommended source for orthology data.</p></li>
+<li><p><strong>homologene</strong> – Use orthology information from NCBI HomoloGene.</p></li>
+<li><p><strong>ensembl</strong> – Use orthology information from Ensembl.</p></li>
+<li><p><strong>oma_rel_type</strong> – Restrict relations to certain types.</p></li>
+<li><p><strong>oma_score</strong> – Lower threshold for similarity metric.</p></li>
+<li><p><strong>ensembl_hc</strong> – Use only the high confidence orthology relations from Ensembl.</p></li>
+<li><p><strong>ensembl_types</strong> – Ensembl orthology relation types to use. Possible values are
+<cite>one2one</cite>, <cite>one2many</cite> and <cite>many2many</cite>. By default only
+<cite>one2one</cite> is used.</p></li>
+<li><p><strong>kwargs</strong> – Same as providing a dict to <code class="docutils literal notranslate"><span class="pre">cols</span></code>, but beware, keys
+(column names) can not match existing argument names of
+this function.</p></li>
+</ul>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p>A data frame with the same column layout as the input, and the
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diff --git a/api/pypath.utils.pdb.html b/api/pypath.utils.pdb.html
index 4d662d285..6eb295b6a 100644
--- a/api/pypath.utils.pdb.html
+++ b/api/pypath.utils.pdb.html
@@ -48,7 +48,7 @@
     <link rel="index" title="Index" href="../genindex.html" />
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     <link rel="next" title="pypath.utils.pdb.residue_pdb" href="pypath.utils.pdb.residue_pdb.html" />
-    <link rel="prev" title="pypath.utils.go.GeneOntology" href="pypath.utils.go.GeneOntology.html" />
+    <link rel="prev" title="pypath.utils.orthology.SequenceContainer" href="pypath.utils.orthology.SequenceContainer.html" />
   <meta name="viewport" content="width=device-width, initial-scale=1"/>
   <meta name="docsearch:language" content="en"/>
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@@ -556,12 +556,12 @@
                   
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-       href="pypath.utils.go.GeneOntology.html"
+       href="pypath.utils.orthology.SequenceContainer.html"
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         <p class="prev-next-subtitle">previous</p>
-        <p class="prev-next-title">pypath.utils.go.GeneOntology</p>
+        <p class="prev-next-title">pypath.utils.orthology.SequenceContainer</p>
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diff --git a/api/pypath.utils.proteomicsdb.ProteomicsDB.html b/api/pypath.utils.proteomicsdb.ProteomicsDB.html
index 50512df99..d54e6538b 100644
--- a/api/pypath.utils.proteomicsdb.ProteomicsDB.html
+++ b/api/pypath.utils.proteomicsdb.ProteomicsDB.html
@@ -47,7 +47,7 @@
     <link rel="icon" href="../_static/omnipath-logo.svg"/>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
-    <link rel="next" title="pypath.utils.reflists" href="pypath.utils.reflists.html" />
+    <link rel="next" title="pypath.utils.pyreact" href="pypath.utils.pyreact.html" />
     <link rel="prev" title="pypath.utils.proteomicsdb" href="pypath.utils.proteomicsdb.html" />
   <meta name="viewport" content="width=device-width, initial-scale=1"/>
   <meta name="docsearch:language" content="en"/>
@@ -690,11 +690,11 @@ <h1>pypath.utils.proteomicsdb.ProteomicsDB<a class="headerlink" href="#pypath-ut
       </div>
     </a>
     <a class="right-next"
-       href="pypath.utils.reflists.html"
+       href="pypath.utils.pyreact.html"
        title="next page">
       <div class="prev-next-info">
         <p class="prev-next-subtitle">next</p>
-        <p class="prev-next-title">pypath.utils.reflists</p>
+        <p class="prev-next-title">pypath.utils.pyreact</p>
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new file mode 100644
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--- /dev/null
+++ b/api/pypath.utils.pyreact.AttributeHandler.html
@@ -0,0 +1,661 @@
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+<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></p>
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+  <section id="pypath-utils-pyreact-biopaxreader">
+<h1>pypath.utils.pyreact.BioPaxReader<a class="headerlink" href="#pypath-utils-pyreact-biopaxreader" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.utils.pyreact.BioPaxReader">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.utils.pyreact.</span></span><span class="sig-name descname"><span class="pre">BioPaxReader</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">biopax</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">source</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cleanup_period</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">800</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">file_from_archive</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">silent</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/utils/pyreact.html#BioPaxReader"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.utils.pyreact.BioPaxReader" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">Logger</span></code></p>
+<p>This class parses a BioPAX file and exposes its content easily accessible
+for further processing. First it opens the file, if necessary it extracts
+from the archive. Then an <cite>lxml.etree.iterparse</cite> object is created, so the
+iteration is efficient and memory requirements are minimal. The iterparse
+object is iterated then, and for each tag included in the
+<cite>BioPaxReader.methods</cite> dict, the appropriate method is called. These me-
+thods extract information from the BioPAX entity, and store it in arbit-
+rary data structures: strings, lists or dicts. These are stored in dicts
+where keys are the original IDs of the tags, prefixed with the unique ID
+of the parser object. This is necessary to give a way to merge later the
+result of parsing more BioPAX files. For example, <cite>id42</cite> may identify
+EGFR in one file, but AKT1 in the other. Then, the parser of the first
+file has a unique ID of a 5 letter random string, the second parser a
+different one, and the molecules with the same ID can be distinguished
+at merging, e.g. EGFR will be <cite>ffjh2&#64;id42</cite> and AKT1 will be <cite>tr9gy&#64;id42</cite>.
+The methods and the resulted dicts are named after the BioPAX elements,
+sometimes abbreviated. For example, <cite>BioPaxReader.protein()</cite> processes
+the <cite>&lt;bp:Protein&gt;</cite> elements, and stores the results in
+<cite>BioPaxReader.proteins</cite>.</p>
+<p>In its current state, this class does not parse every information and
+all BioPax entities. For example, nucleic acid related entities and
+interactions are omitted. But these easily can be added with minor mo-
+difications.</p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.utils.pyreact.BioPaxReader.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">biopax</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">source</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cleanup_period</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">800</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">file_from_archive</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">silent</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/utils/pyreact.html#BioPaxReader.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.utils.pyreact.BioPaxReader.__init__" title="Link to this definition">§</a></dt>
+<dd><dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><p><strong>biopax</strong> (<em>str</em><em>,</em><a class="reference internal" href="pypath.share.curl.FileOpener.html#pypath.share.curl.FileOpener" title="pypath.share.curl.FileOpener"><em>FileOpener</em></a>) – either a filename, or a FileOpener</p>
+</dd>
+</dl>
+<p>object; if string is supplied, the FileOpener will be created in-
+ternally</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>source</strong> (<em>str</em>) – the name of the data source, e.g. <em>Reactome</em></p></li>
+<li><p><strong>cleanup_period</strong> (<em>int</em>) – the number of last elements stored</p></li>
+</ul>
+</dd>
+</dl>
+<p>during the iteration of lxml.etree.iterparse; lower number
+results lower memory usage, but might risk that an element is
+deleted before it has been processed. Default is 800, which is
+a safe option.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><p><strong>file_from_archive</strong> (<em>str</em>) – in case of processing an archive</p>
+</dd>
+</dl>
+<p>which may contain multiple files (tar.gz or zip), the path of
+the file to be processed needs to be supplied.
+E.g. <em>BioPax/Homo_sapiens.owl</em>.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><p><strong>silent</strong> (<em>bool</em>) – whether print status messages and progress</p>
+</dd>
+</dl>
+<p>bars during processing. If you process large number of small
+files, better to set False, in case of one large file, True.
+The default is <em>False</em>.</p>
+</dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.utils.pyreact.BioPaxReader.__init__" title="pypath.utils.pyreact.BioPaxReader.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>(biopax, source[, cleanup_period, ...])</p></td>
+<td><p><dl class="field-list simple">
+<dt class="field-odd">param str,FileOpener biopax<span class="colon">:</span></dt>
+<dd class="field-odd"><p>either a filename, or a FileOpener</p>
+</dd>
+</dl>
+</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.utils.pyreact.BioPaxReader.biopax_size" title="pypath.utils.pyreact.BioPaxReader.biopax_size"><code class="xref py py-obj docutils literal notranslate"><span class="pre">biopax_size</span></code></a>()</p></td>
+<td><p>Gets the uncompressed size of the BioPax XML.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">cassembly</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">catalysis</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.utils.pyreact.BioPaxReader.cleanup_hook" title="pypath.utils.pyreact.BioPaxReader.cleanup_hook"><code class="xref py py-obj docutils literal notranslate"><span class="pre">cleanup_hook</span></code></a>()</p></td>
+<td><p>Removes the used elements to free up memory.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.utils.pyreact.BioPaxReader.close_biopax" title="pypath.utils.pyreact.BioPaxReader.close_biopax"><code class="xref py py-obj docutils literal notranslate"><span class="pre">close_biopax</span></code></a>()</p></td>
+<td><p>Deletes the iterator and closes the file object.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">control</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">cplex</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.utils.pyreact.BioPaxReader.extract" title="pypath.utils.pyreact.BioPaxReader.extract"><code class="xref py py-obj docutils literal notranslate"><span class="pre">extract</span></code></a>()</p></td>
+<td><p>Extracts the BioPax file from compressed archive.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">fragfea</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_none</span></code>(something)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.utils.pyreact.BioPaxReader.init_etree" title="pypath.utils.pyreact.BioPaxReader.init_etree"><code class="xref py py-obj docutils literal notranslate"><span class="pre">init_etree</span></code></a>()</p></td>
+<td><p>Creates the <code class="docutils literal notranslate"><span class="pre">lxml.etree.iterparse</span></code> object.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">interaction</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.utils.pyreact.BioPaxReader.iterate" title="pypath.utils.pyreact.BioPaxReader.iterate"><code class="xref py py-obj docutils literal notranslate"><span class="pre">iterate</span></code></a>()</p></td>
+<td><p>Iterates the BioPax XML and calls the appropriate methods for each element.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">modfea</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.utils.pyreact.BioPaxReader.open_biopax" title="pypath.utils.pyreact.BioPaxReader.open_biopax"><code class="xref py py-obj docutils literal notranslate"><span class="pre">open_biopax</span></code></a>()</p></td>
+<td><p>Opens the BioPax file.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">pathway</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">pref</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.utils.pyreact.BioPaxReader.process" title="pypath.utils.pyreact.BioPaxReader.process"><code class="xref py py-obj docutils literal notranslate"><span class="pre">process</span></code></a>([silent])</p></td>
+<td><p>This method executes the total workflow of BioPax processing.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">protein</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">pubref</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">pwstep</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">reaction</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">reload</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">rxref</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">seqint</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">seqmodvoc</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">seqsite</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.utils.pyreact.BioPaxReader.set_progress" title="pypath.utils.pyreact.BioPaxReader.set_progress"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_progress</span></code></a>()</p></td>
+<td><p>Initializes a progress bar.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">stoichiometry</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">uxref</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.utils.pyreact.BioPaxReader.biopax_size">
+<span class="sig-name descname"><span class="pre">biopax_size</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/utils/pyreact.html#BioPaxReader.biopax_size"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.utils.pyreact.BioPaxReader.biopax_size" title="Link to this definition">§</a></dt>
+<dd><p>Gets the uncompressed size of the BioPax XML. This is needed in
+order to have a progress bar. This method should not be called
+directly, <code class="docutils literal notranslate"><span class="pre">BioPaxReader.process()</span></code> calls it.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.utils.pyreact.BioPaxReader.cleanup_hook">
+<span class="sig-name descname"><span class="pre">cleanup_hook</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/utils/pyreact.html#BioPaxReader.cleanup_hook"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.utils.pyreact.BioPaxReader.cleanup_hook" title="Link to this definition">§</a></dt>
+<dd><p>Removes the used elements to free up memory.
+This method should not be called directly,
+<code class="docutils literal notranslate"><span class="pre">BioPaxReader.iterate()</span></code> calls it.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.utils.pyreact.BioPaxReader.close_biopax">
+<span class="sig-name descname"><span class="pre">close_biopax</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/utils/pyreact.html#BioPaxReader.close_biopax"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.utils.pyreact.BioPaxReader.close_biopax" title="Link to this definition">§</a></dt>
+<dd><p>Deletes the iterator and closes the file object.
+This method should not be called directly,
+<code class="docutils literal notranslate"><span class="pre">BioPaxReader.process()</span></code> calls it.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.utils.pyreact.BioPaxReader.extract">
+<span class="sig-name descname"><span class="pre">extract</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/utils/pyreact.html#BioPaxReader.extract"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.utils.pyreact.BioPaxReader.extract" title="Link to this definition">§</a></dt>
+<dd><p>Extracts the BioPax file from compressed archive. Creates a
+temporary file. This is needed to trace the progress of
+processing, which is useful in case of large files.
+This method should not be called directly,
+<code class="docutils literal notranslate"><span class="pre">BioPaxReader.process()</span></code> calls it.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.utils.pyreact.BioPaxReader.init_etree">
+<span class="sig-name descname"><span class="pre">init_etree</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/utils/pyreact.html#BioPaxReader.init_etree"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.utils.pyreact.BioPaxReader.init_etree" title="Link to this definition">§</a></dt>
+<dd><p>Creates the <code class="docutils literal notranslate"><span class="pre">lxml.etree.iterparse</span></code> object.
+This method should not be called directly,
+<code class="docutils literal notranslate"><span class="pre">BioPaxReader.process()</span></code> calls it.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.utils.pyreact.BioPaxReader.iterate">
+<span class="sig-name descname"><span class="pre">iterate</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/utils/pyreact.html#BioPaxReader.iterate"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.utils.pyreact.BioPaxReader.iterate" title="Link to this definition">§</a></dt>
+<dd><p>Iterates the BioPax XML and calls the appropriate methods
+for each element.
+This method should not be called directly,
+<code class="docutils literal notranslate"><span class="pre">BioPaxReader.process()</span></code> calls it.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.utils.pyreact.BioPaxReader.open_biopax">
+<span class="sig-name descname"><span class="pre">open_biopax</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/utils/pyreact.html#BioPaxReader.open_biopax"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.utils.pyreact.BioPaxReader.open_biopax" title="Link to this definition">§</a></dt>
+<dd><p>Opens the BioPax file. This method should not be called directly,
+<code class="docutils literal notranslate"><span class="pre">BioPaxReader.process()</span></code> calls it.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.utils.pyreact.BioPaxReader.process">
+<span class="sig-name descname"><span class="pre">process</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">silent</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/utils/pyreact.html#BioPaxReader.process"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.utils.pyreact.BioPaxReader.process" title="Link to this definition">§</a></dt>
+<dd><p>This method executes the total workflow of BioPax processing.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><p><strong>silent</strong> (<em>bool</em>) – whether to print status messages and progress bars.</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.utils.pyreact.BioPaxReader.set_progress">
+<span class="sig-name descname"><span class="pre">set_progress</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/utils/pyreact.html#BioPaxReader.set_progress"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.utils.pyreact.BioPaxReader.set_progress" title="Link to this definition">§</a></dt>
+<dd><p>Initializes a progress bar.
+This method should not be called directly,
+<code class="docutils literal notranslate"><span class="pre">BioPaxReader.process()</span></code> calls it.</p>
+</dd></dl>
+
+</dd></dl>
+
+</section>
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+  <section id="pypath-utils-pyreact-complex">
+<h1>pypath.utils.pyreact.Complex<a class="headerlink" href="#pypath-utils-pyreact-complex" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.utils.pyreact.Complex">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.utils.pyreact.</span></span><span class="sig-name descname"><span class="pre">Complex</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">members</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">source</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">parent</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/utils/pyreact.html#Complex"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.utils.pyreact.Complex" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <a class="reference internal" href="pypath.utils.pyreact.EntitySet.html#pypath.utils.pyreact.EntitySet" title="pypath.utils.pyreact.EntitySet"><code class="xref py py-class docutils literal notranslate"><span class="pre">EntitySet</span></code></a></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.utils.pyreact.Complex.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">members</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">source</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">parent</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/utils/pyreact.html#Complex.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.utils.pyreact.Complex.__init__" title="Link to this definition">§</a></dt>
+<dd></dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.utils.pyreact.Complex.__init__" title="pypath.utils.pyreact.Complex.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>(members, source[, parent])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">add_source</span></code>(source)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">expand</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_stoichiometries</span></code>(source, cid[, with_pids])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">itermembers</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">key</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">merge_attrs</span></code>(attrs)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">proteins</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">reload</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">update_attr</span></code>(attr)</p></td>
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+</tr>
+</tbody>
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diff --git a/api/pypath.utils.pyreact.ComplexVariations.html b/api/pypath.utils.pyreact.ComplexVariations.html
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+  <section id="pypath-utils-pyreact-complexvariations">
+<h1>pypath.utils.pyreact.ComplexVariations<a class="headerlink" href="#pypath-utils-pyreact-complexvariations" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.utils.pyreact.ComplexVariations">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.utils.pyreact.</span></span><span class="sig-name descname"><span class="pre">ComplexVariations</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">members</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">source</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">parent</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/utils/pyreact.html#ComplexVariations"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.utils.pyreact.ComplexVariations" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <a class="reference internal" href="pypath.utils.pyreact.Intersecting.html#pypath.utils.pyreact.Intersecting" title="pypath.utils.pyreact.Intersecting"><code class="xref py py-class docutils literal notranslate"><span class="pre">Intersecting</span></code></a>, <a class="reference internal" href="pypath.utils.pyreact.EntitySet.html#pypath.utils.pyreact.EntitySet" title="pypath.utils.pyreact.EntitySet"><code class="xref py py-class docutils literal notranslate"><span class="pre">EntitySet</span></code></a></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.utils.pyreact.ComplexVariations.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">members</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">source</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">parent</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/utils/pyreact.html#ComplexVariations.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.utils.pyreact.ComplexVariations.__init__" title="Link to this definition">§</a></dt>
+<dd></dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.utils.pyreact.ComplexVariations.__init__" title="pypath.utils.pyreact.ComplexVariations.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>(members, source[, parent])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">add_source</span></code>(source)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">expand</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.utils.pyreact.ComplexVariations.itermembers" title="pypath.utils.pyreact.ComplexVariations.itermembers"><code class="xref py py-obj docutils literal notranslate"><span class="pre">itermembers</span></code></a>()</p></td>
+<td><p>This is a convenient iterator for the expand methods of higher classes like <code class="docutils literal notranslate"><span class="pre">ReactionSide</span></code> or <code class="docutils literal notranslate"><span class="pre">Control</span></code>.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">key</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">merge_attrs</span></code>(attrs)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">proteins</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">reload</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">update_attr</span></code>(attr)</p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.utils.pyreact.ComplexVariations.itermembers">
+<span class="sig-name descname"><span class="pre">itermembers</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/utils/pyreact.html#ComplexVariations.itermembers"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.utils.pyreact.ComplexVariations.itermembers" title="Link to this definition">§</a></dt>
+<dd><p>This is a convenient iterator for the expand methods
+of higher classes like <code class="docutils literal notranslate"><span class="pre">ReactionSide</span></code> or <code class="docutils literal notranslate"><span class="pre">Control</span></code>.</p>
+</dd></dl>
+
+</dd></dl>
+
+</section>
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+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.utils.pyreact.Control">
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+<dd><p>Bases: <a class="reference internal" href="pypath.utils.pyreact.AttributeHandler.html#pypath.utils.pyreact.AttributeHandler" title="pypath.utils.pyreact.AttributeHandler"><code class="xref py py-class docutils literal notranslate"><span class="pre">AttributeHandler</span></code></a></p>
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+<dt class="sig sig-object py" id="pypath.utils.pyreact.Control.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">er</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ed</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">source</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">[]</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">parent</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/utils/pyreact.html#Control.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.utils.pyreact.Control.__init__" title="Link to this definition">§</a></dt>
+<dd></dd></dl>
+
+<p class="rubric">Methods</p>
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+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.utils.pyreact.Control.__init__" title="pypath.utils.pyreact.Control.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>(er, ed[, source, parent])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">add_source</span></code>(source)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">expand</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">merge_attrs</span></code>(attrs)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">reload</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">update_attr</span></code>(attr)</p></td>
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+</tr>
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+                  
+  <section id="pypath-utils-pyreact-entity">
+<h1>pypath.utils.pyreact.Entity<a class="headerlink" href="#pypath-utils-pyreact-entity" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.utils.pyreact.Entity">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.utils.pyreact.</span></span><span class="sig-name descname"><span class="pre">Entity</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">identifier</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">id_type</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">sources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">[]</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">attrs</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/utils/pyreact.html#Entity"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.utils.pyreact.Entity" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <a class="reference internal" href="pypath.utils.pyreact.AttributeHandler.html#pypath.utils.pyreact.AttributeHandler" title="pypath.utils.pyreact.AttributeHandler"><code class="xref py py-class docutils literal notranslate"><span class="pre">AttributeHandler</span></code></a></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.utils.pyreact.Entity.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">identifier</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">id_type</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">sources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">[]</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">attrs</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/utils/pyreact.html#Entity.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.utils.pyreact.Entity.__init__" title="Link to this definition">§</a></dt>
+<dd></dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.utils.pyreact.Entity.__init__" title="pypath.utils.pyreact.Entity.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>(identifier, id_type[, sources, attrs])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">add_source</span></code>(source)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.utils.pyreact.Entity.expand" title="pypath.utils.pyreact.Entity.expand"><code class="xref py py-obj docutils literal notranslate"><span class="pre">expand</span></code></a>()</p></td>
+<td><p>With this method it is possible to iterate <code class="docutils literal notranslate"><span class="pre">Entity</span></code> objects just like <code class="docutils literal notranslate"><span class="pre">EntitySet</span></code> objects.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">itermembers</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">merge_attrs</span></code>(attrs)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">update_attr</span></code>(attr)</p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.utils.pyreact.Entity.expand">
+<span class="sig-name descname"><span class="pre">expand</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/utils/pyreact.html#Entity.expand"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.utils.pyreact.Entity.expand" title="Link to this definition">§</a></dt>
+<dd><p>With this method it is possible to iterate <code class="docutils literal notranslate"><span class="pre">Entity</span></code> objects
+just like <code class="docutils literal notranslate"><span class="pre">EntitySet</span></code> objects.</p>
+<p>Yields string.</p>
+</dd></dl>
+
+</dd></dl>
+
+</section>
+
+
+                </article>
+              
+              
+              
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+<h1>pypath.utils.pyreact.EntitySet<a class="headerlink" href="#pypath-utils-pyreact-entityset" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.utils.pyreact.EntitySet">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.utils.pyreact.</span></span><span class="sig-name descname"><span class="pre">EntitySet</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">members</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">sources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">[]</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">sep</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">';'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">parent</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/utils/pyreact.html#EntitySet"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.utils.pyreact.EntitySet" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <a class="reference internal" href="pypath.utils.pyreact.AttributeHandler.html#pypath.utils.pyreact.AttributeHandler" title="pypath.utils.pyreact.AttributeHandler"><code class="xref py py-class docutils literal notranslate"><span class="pre">AttributeHandler</span></code></a></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.utils.pyreact.EntitySet.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">members</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">sources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">[]</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">sep</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">';'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">parent</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/utils/pyreact.html#EntitySet.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.utils.pyreact.EntitySet.__init__" title="Link to this definition">§</a></dt>
+<dd></dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.utils.pyreact.EntitySet.__init__" title="pypath.utils.pyreact.EntitySet.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>(members[, sources, sep, parent])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">add_source</span></code>(source)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">merge_attrs</span></code>(attrs)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">update_attr</span></code>(attr)</p></td>
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+</tr>
+</tbody>
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+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.utils.pyreact.Intersecting">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.utils.pyreact.</span></span><span class="sig-name descname"><span class="pre">Intersecting</span></span><a class="reference internal" href="../_modules/pypath/utils/pyreact.html#Intersecting"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.utils.pyreact.Intersecting" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.utils.pyreact.Intersecting.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/utils/pyreact.html#Intersecting.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.utils.pyreact.Intersecting.__init__" title="Link to this definition">§</a></dt>
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+  <section id="pypath-utils-pyreact-protein">
+<h1>pypath.utils.pyreact.Protein<a class="headerlink" href="#pypath-utils-pyreact-protein" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.utils.pyreact.Protein">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.utils.pyreact.</span></span><span class="sig-name descname"><span class="pre">Protein</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">protein_id</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">id_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'uniprot'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">sources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">[]</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">attrs</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/utils/pyreact.html#Protein"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.utils.pyreact.Protein" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <a class="reference internal" href="pypath.utils.pyreact.Entity.html#pypath.utils.pyreact.Entity" title="pypath.utils.pyreact.Entity"><code class="xref py py-class docutils literal notranslate"><span class="pre">Entity</span></code></a></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.utils.pyreact.Protein.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">protein_id</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">id_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'uniprot'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">sources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">[]</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">attrs</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/utils/pyreact.html#Protein.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.utils.pyreact.Protein.__init__" title="Link to this definition">§</a></dt>
+<dd></dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.utils.pyreact.Protein.__init__" title="pypath.utils.pyreact.Protein.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>(protein_id[, id_type, sources, attrs])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">add_source</span></code>(source)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.utils.pyreact.Protein.expand" title="pypath.utils.pyreact.Protein.expand"><code class="xref py py-obj docutils literal notranslate"><span class="pre">expand</span></code></a>()</p></td>
+<td><p>With this method it is possible to iterate <code class="docutils literal notranslate"><span class="pre">Entity</span></code> objects just like <code class="docutils literal notranslate"><span class="pre">EntitySet</span></code> objects.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">itermembers</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">key</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">merge_attrs</span></code>(attrs)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">proteins</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">reload</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">update_attr</span></code>(attr)</p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.utils.pyreact.Protein.expand">
+<span class="sig-name descname"><span class="pre">expand</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.utils.pyreact.Protein.expand" title="Link to this definition">§</a></dt>
+<dd><p>With this method it is possible to iterate <code class="docutils literal notranslate"><span class="pre">Entity</span></code> objects
+just like <code class="docutils literal notranslate"><span class="pre">EntitySet</span></code> objects.</p>
+<p>Yields string.</p>
+</dd></dl>
+
+</dd></dl>
+
+</section>
+
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diff --git a/api/pypath.utils.pyreact.ProteinFamily.html b/api/pypath.utils.pyreact.ProteinFamily.html
new file mode 100644
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+  <section id="pypath-utils-pyreact-proteinfamily">
+<h1>pypath.utils.pyreact.ProteinFamily<a class="headerlink" href="#pypath-utils-pyreact-proteinfamily" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.utils.pyreact.ProteinFamily">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.utils.pyreact.</span></span><span class="sig-name descname"><span class="pre">ProteinFamily</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">members</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">source</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">parent</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/utils/pyreact.html#ProteinFamily"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.utils.pyreact.ProteinFamily" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <a class="reference internal" href="pypath.utils.pyreact.Intersecting.html#pypath.utils.pyreact.Intersecting" title="pypath.utils.pyreact.Intersecting"><code class="xref py py-class docutils literal notranslate"><span class="pre">Intersecting</span></code></a>, <a class="reference internal" href="pypath.utils.pyreact.EntitySet.html#pypath.utils.pyreact.EntitySet" title="pypath.utils.pyreact.EntitySet"><code class="xref py py-class docutils literal notranslate"><span class="pre">EntitySet</span></code></a></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.utils.pyreact.ProteinFamily.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">members</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">source</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">parent</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/utils/pyreact.html#ProteinFamily.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.utils.pyreact.ProteinFamily.__init__" title="Link to this definition">§</a></dt>
+<dd></dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.utils.pyreact.ProteinFamily.__init__" title="pypath.utils.pyreact.ProteinFamily.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>(members, source[, parent])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">add_source</span></code>(source)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">expand</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">itermembers</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">key</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">merge_attrs</span></code>(attrs)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">proteins</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">reload</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">update_attr</span></code>(attr)</p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
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+  <section id="pypath-utils-pyreact-pyreact">
+<h1>pypath.utils.pyreact.PyReact<a class="headerlink" href="#pypath-utils-pyreact-pyreact" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.utils.pyreact.PyReact">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.utils.pyreact.</span></span><span class="sig-name descname"><span class="pre">PyReact</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">default_id_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">{}</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">modifications</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">seq</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">silent</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">max_complex_combinations</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">100</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">max_reaction_combinations</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">100</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/utils/pyreact.html#PyReact"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.utils.pyreact.PyReact" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">Logger</span></code></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.utils.pyreact.PyReact.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">ncbi_tax_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">9606</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">default_id_types</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">{}</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">modifications</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">seq</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">silent</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">max_complex_combinations</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">100</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">max_reaction_combinations</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">100</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/utils/pyreact.html#PyReact.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.utils.pyreact.PyReact.__init__" title="Link to this definition">§</a></dt>
+<dd><p>Make this instance a logger.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>name</strong> – The label of this instance that will be prepended to all
+messages it sends to the logger.</p></li>
+<li><p><strong>module</strong> – Send the messages by the logger of this module.</p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.utils.pyreact.PyReact.__init__" title="pypath.utils.pyreact.PyReact.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>([ncbi_tax_id, default_id_types, ...])</p></td>
+<td><p>Make this instance a logger.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">add_dataset</span></code>(parser[, id_types, process_id])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">add_pfamily</span></code>(proteins, pfid)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">basic_stats</span></code>([exclude_empty])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">co_control</span></code>([by_source])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">complex_get_mods</span></code>(source, complex_elem)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">complex_get_refs</span></code>(source, cplex_elem)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">expand</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">expand_by_source</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.utils.pyreact.PyReact.gen_cvariations" title="pypath.utils.pyreact.PyReact.gen_cvariations"><code class="xref py py-obj docutils literal notranslate"><span class="pre">gen_cvariations</span></code></a>()</p></td>
+<td><p>Because one key from the BioPax file might represent more complexes, <em>complexvariations</em> are created to give a way to represent sets of combinations.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.utils.pyreact.PyReact.in_same_component" title="pypath.utils.pyreact.PyReact.in_same_component"><code class="xref py py-obj docutils literal notranslate"><span class="pre">in_same_component</span></code></a>([by_source])</p></td>
+<td><p>For all complexes connects all members of the complex with each other.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">interacts_with</span></code>([by_source])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">iterate_reactions</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_acsn</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_all</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_kegg</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_netpath</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_panther</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_pid</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_reactome</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_sequences</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_wikipathways</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">merge</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">merge_cassemblies</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">merge_catalyses</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.utils.pyreact.PyReact.merge_complexes" title="pypath.utils.pyreact.PyReact.merge_complexes"><code class="xref py py-obj docutils literal notranslate"><span class="pre">merge_complexes</span></code></a>([this_round])</p></td>
+<td><p>Merges complexes from the active <code class="docutils literal notranslate"><span class="pre">BioPaxReader</span></code> object.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">merge_controls</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.utils.pyreact.PyReact.merge_cvariations" title="pypath.utils.pyreact.PyReact.merge_cvariations"><code class="xref py py-obj docutils literal notranslate"><span class="pre">merge_cvariations</span></code></a>()</p></td>
+<td><p>This processes those complexes which are in fact a set of complex variations.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">merge_modifications</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">merge_pfamilies</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">merge_proteins</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">merge_reactions</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">merge_refs</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">netpath_names</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">preprocess_seqmodvoc</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">protein_get_mods</span></code>(source, protein_elem)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">protein_get_refs</span></code>(source, protein_elem)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">reaction_mod_diff</span></code>(source, reaction[, by_rid])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">reaction_side_get_mods</span></code>(source, rside[, by_rid])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">reload</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">remove_defaults</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">resource_graph_edges</span></code>(etyp)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_corrections</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">simpson_stats</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">state_change</span></code>([by_source])</p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.utils.pyreact.PyReact.gen_cvariations">
+<span class="sig-name descname"><span class="pre">gen_cvariations</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/utils/pyreact.html#PyReact.gen_cvariations"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.utils.pyreact.PyReact.gen_cvariations" title="Link to this definition">§</a></dt>
+<dd><p>Because one key from the BioPax file might represent more complexes,
+<em>complexvariations</em> are created to give a way to represent sets of
+combinations. These are created for all complexes, even with only
+one unambiguous constitution. The keys are the constitutions of
+all the combinations listed in alphabetic order, separated by <code class="docutils literal notranslate"><span class="pre">|</span></code>.
+For example, <code class="docutils literal notranslate"><span class="pre">A,B,C|A,B,D|A,B,E</span></code>.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.utils.pyreact.PyReact.in_same_component">
+<span class="sig-name descname"><span class="pre">in_same_component</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">by_source</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/utils/pyreact.html#PyReact.in_same_component"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.utils.pyreact.PyReact.in_same_component" title="Link to this definition">§</a></dt>
+<dd><p>For all complexes connects all members of the complex with each other.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.utils.pyreact.PyReact.merge_complexes">
+<span class="sig-name descname"><span class="pre">merge_complexes</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">this_round</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/utils/pyreact.html#PyReact.merge_complexes"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.utils.pyreact.PyReact.merge_complexes" title="Link to this definition">§</a></dt>
+<dd><p>Merges complexes from the active <code class="docutils literal notranslate"><span class="pre">BioPaxReader</span></code> object.
+Protein families and subcomplexes are expanded, and all combinations
+are created as separate complexes. The complexes from the same ID
+are added to sets in the <code class="docutils literal notranslate"><span class="pre">rcomplexes</span></code> dict.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.utils.pyreact.PyReact.merge_cvariations">
+<span class="sig-name descname"><span class="pre">merge_cvariations</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/utils/pyreact.html#PyReact.merge_cvariations"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.utils.pyreact.PyReact.merge_cvariations" title="Link to this definition">§</a></dt>
+<dd><p>This processes those complexes which are in fact a set of complex variations.
+As simple complexes also are always extended to complex variations because
+they might have not only simple proteins but protein families as members,
+here we only add new records to the attributes of already existing complexes.
+After <code class="docutils literal notranslate"><span class="pre">merge_complexes</span></code> will be called again, to process those simple
+complexes which have any of the complex variations processed here among their
+subcomplexes.</p>
+</dd></dl>
+
+</dd></dl>
+
+</section>
+
+
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+<h1>pypath.utils.pyreact.Reaction<a class="headerlink" href="#pypath-utils-pyreact-reaction" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.utils.pyreact.Reaction">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.utils.pyreact.</span></span><span class="sig-name descname"><span class="pre">Reaction</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">left</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">right</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">left_attrs</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">right_attrs</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">source</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">[]</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">parent</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/utils/pyreact.html#Reaction"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.utils.pyreact.Reaction" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <a class="reference internal" href="pypath.utils.pyreact.AttributeHandler.html#pypath.utils.pyreact.AttributeHandler" title="pypath.utils.pyreact.AttributeHandler"><code class="xref py py-class docutils literal notranslate"><span class="pre">AttributeHandler</span></code></a></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.utils.pyreact.Reaction.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">left</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">right</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">left_attrs</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">right_attrs</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">source</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">[]</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">parent</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/utils/pyreact.html#Reaction.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.utils.pyreact.Reaction.__init__" title="Link to this definition">§</a></dt>
+<dd></dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.utils.pyreact.Reaction.__init__" title="pypath.utils.pyreact.Reaction.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>(left, right, left_attrs, right_attrs)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">add_source</span></code>(source)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">expand</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">merge_attrs</span></code>(attrs)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">reload</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">update_attr</span></code>(attr)</p></td>
+<td><p></p></td>
+</tr>
+</tbody>
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+  <section id="pypath-utils-pyreact-reactionside">
+<h1>pypath.utils.pyreact.ReactionSide<a class="headerlink" href="#pypath-utils-pyreact-reactionside" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.utils.pyreact.ReactionSide">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.utils.pyreact.</span></span><span class="sig-name descname"><span class="pre">ReactionSide</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">members</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">source</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">[]</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">parent</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/utils/pyreact.html#ReactionSide"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.utils.pyreact.ReactionSide" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <a class="reference internal" href="pypath.utils.pyreact.AttributeHandler.html#pypath.utils.pyreact.AttributeHandler" title="pypath.utils.pyreact.AttributeHandler"><code class="xref py py-class docutils literal notranslate"><span class="pre">AttributeHandler</span></code></a></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.utils.pyreact.ReactionSide.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">members</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">source</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">[]</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">parent</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/utils/pyreact.html#ReactionSide.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.utils.pyreact.ReactionSide.__init__" title="Link to this definition">§</a></dt>
+<dd></dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.utils.pyreact.ReactionSide.__init__" title="pypath.utils.pyreact.ReactionSide.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>(members[, source, parent])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">add_source</span></code>(source)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">equality</span></code>(one, two)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.utils.pyreact.ReactionSide.expand" title="pypath.utils.pyreact.ReactionSide.expand"><code class="xref py py-obj docutils literal notranslate"><span class="pre">expand</span></code></a>()</p></td>
+<td><p>Expands the <code class="docutils literal notranslate"><span class="pre">ReactionSide</span></code> by iterating over all combinations of all <code class="docutils literal notranslate"><span class="pre">ComplexVariation</span></code> and <code class="docutils literal notranslate"><span class="pre">ProteinFamily</span></code> members, so yields <code class="docutils literal notranslate"><span class="pre">ReactionSide</span></code> objects with only <code class="docutils literal notranslate"><span class="pre">Protein</span></code> and <code class="docutils literal notranslate"><span class="pre">Complex</span></code> members.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">merge_attrs</span></code>(attrs)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">proteins</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">reload</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">update_attr</span></code>(attr)</p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.utils.pyreact.ReactionSide.expand">
+<span class="sig-name descname"><span class="pre">expand</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/utils/pyreact.html#ReactionSide.expand"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.utils.pyreact.ReactionSide.expand" title="Link to this definition">§</a></dt>
+<dd><p>Expands the <code class="docutils literal notranslate"><span class="pre">ReactionSide</span></code> by iterating over all combinations
+of all <code class="docutils literal notranslate"><span class="pre">ComplexVariation</span></code> and <code class="docutils literal notranslate"><span class="pre">ProteinFamily</span></code> members, so
+yields <code class="docutils literal notranslate"><span class="pre">ReactionSide</span></code> objects with only <code class="docutils literal notranslate"><span class="pre">Protein</span></code> and <code class="docutils literal notranslate"><span class="pre">Complex</span></code>
+members. Yields tuple, because <code class="docutils literal notranslate"><span class="pre">ReactionSide</span></code> is initialized in
+<code class="docutils literal notranslate"><span class="pre">Reaction</span></code>, the tuple is suitable to serve as <code class="docutils literal notranslate"><span class="pre">members</span></code> and
+<code class="docutils literal notranslate"><span class="pre">attrs</span></code>.</p>
+</dd></dl>
+
+</dd></dl>
+
+</section>
+
+
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+  <section id="pypath-utils-pyreact-reference">
+<h1>pypath.utils.pyreact.Reference<a class="headerlink" href="#pypath-utils-pyreact-reference" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.utils.pyreact.Reference">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.utils.pyreact.</span></span><span class="sig-name descname"><span class="pre">Reference</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">ref_id</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">id_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'pubmed'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">sources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">[]</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/utils/pyreact.html#Reference"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.utils.pyreact.Reference" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <a class="reference internal" href="pypath.utils.pyreact.Entity.html#pypath.utils.pyreact.Entity" title="pypath.utils.pyreact.Entity"><code class="xref py py-class docutils literal notranslate"><span class="pre">Entity</span></code></a></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.utils.pyreact.Reference.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">ref_id</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">id_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'pubmed'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">sources</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">[]</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/utils/pyreact.html#Reference.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.utils.pyreact.Reference.__init__" title="Link to this definition">§</a></dt>
+<dd></dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.utils.pyreact.Reference.__init__" title="pypath.utils.pyreact.Reference.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>(ref_id[, id_type, sources])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">add_source</span></code>(source)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.utils.pyreact.Reference.expand" title="pypath.utils.pyreact.Reference.expand"><code class="xref py py-obj docutils literal notranslate"><span class="pre">expand</span></code></a>()</p></td>
+<td><p>With this method it is possible to iterate <code class="docutils literal notranslate"><span class="pre">Entity</span></code> objects just like <code class="docutils literal notranslate"><span class="pre">EntitySet</span></code> objects.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_ref</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">itermembers</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">merge_attrs</span></code>(attrs)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">update_attr</span></code>(attr)</p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.utils.pyreact.Reference.expand">
+<span class="sig-name descname"><span class="pre">expand</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pypath.utils.pyreact.Reference.expand" title="Link to this definition">§</a></dt>
+<dd><p>With this method it is possible to iterate <code class="docutils literal notranslate"><span class="pre">Entity</span></code> objects
+just like <code class="docutils literal notranslate"><span class="pre">EntitySet</span></code> objects.</p>
+<p>Yields string.</p>
+</dd></dl>
+
+</dd></dl>
+
+</section>
+
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+                <article class="bd-article">
+                  
+  <section id="module-pypath.utils.pyreact">
+<span id="pypath-utils-pyreact"></span><h1>pypath.utils.pyreact<a class="headerlink" href="#module-pypath.utils.pyreact" title="Link to this heading">§</a></h1>
+<dl class="field-list simple">
+<dt class="field-odd">members<span class="colon">:</span></dt>
+<dd class="field-odd"><p></p></dd>
+</dl>
+<p class="rubric">Classes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.utils.pyreact.AttributeHandler.html#pypath.utils.pyreact.AttributeHandler" title="pypath.utils.pyreact.AttributeHandler"><code class="xref py py-obj docutils literal notranslate"><span class="pre">AttributeHandler</span></code></a>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.utils.pyreact.BioPaxReader.html#pypath.utils.pyreact.BioPaxReader" title="pypath.utils.pyreact.BioPaxReader"><code class="xref py py-obj docutils literal notranslate"><span class="pre">BioPaxReader</span></code></a>(biopax, source[, ...])</p></td>
+<td><p>This class parses a BioPAX file and exposes its content easily accessible for further processing.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.utils.pyreact.Complex.html#pypath.utils.pyreact.Complex" title="pypath.utils.pyreact.Complex"><code class="xref py py-obj docutils literal notranslate"><span class="pre">Complex</span></code></a>(members, source[, parent])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.utils.pyreact.ComplexVariations.html#pypath.utils.pyreact.ComplexVariations" title="pypath.utils.pyreact.ComplexVariations"><code class="xref py py-obj docutils literal notranslate"><span class="pre">ComplexVariations</span></code></a>(members, source[, parent])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.utils.pyreact.Control.html#pypath.utils.pyreact.Control" title="pypath.utils.pyreact.Control"><code class="xref py py-obj docutils literal notranslate"><span class="pre">Control</span></code></a>(er, ed[, source, parent])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.utils.pyreact.Entity.html#pypath.utils.pyreact.Entity" title="pypath.utils.pyreact.Entity"><code class="xref py py-obj docutils literal notranslate"><span class="pre">Entity</span></code></a>(identifier, id_type[, sources, attrs])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.utils.pyreact.EntitySet.html#pypath.utils.pyreact.EntitySet" title="pypath.utils.pyreact.EntitySet"><code class="xref py py-obj docutils literal notranslate"><span class="pre">EntitySet</span></code></a>(members[, sources, sep, parent])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.utils.pyreact.Intersecting.html#pypath.utils.pyreact.Intersecting" title="pypath.utils.pyreact.Intersecting"><code class="xref py py-obj docutils literal notranslate"><span class="pre">Intersecting</span></code></a>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.utils.pyreact.Protein.html#pypath.utils.pyreact.Protein" title="pypath.utils.pyreact.Protein"><code class="xref py py-obj docutils literal notranslate"><span class="pre">Protein</span></code></a>(protein_id[, id_type, sources, attrs])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.utils.pyreact.ProteinFamily.html#pypath.utils.pyreact.ProteinFamily" title="pypath.utils.pyreact.ProteinFamily"><code class="xref py py-obj docutils literal notranslate"><span class="pre">ProteinFamily</span></code></a>(members, source[, parent])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.utils.pyreact.PyReact.html#pypath.utils.pyreact.PyReact" title="pypath.utils.pyreact.PyReact"><code class="xref py py-obj docutils literal notranslate"><span class="pre">PyReact</span></code></a>([ncbi_tax_id, default_id_types, ...])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.utils.pyreact.Reaction.html#pypath.utils.pyreact.Reaction" title="pypath.utils.pyreact.Reaction"><code class="xref py py-obj docutils literal notranslate"><span class="pre">Reaction</span></code></a>(left, right, left_attrs, right_attrs)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.utils.pyreact.ReactionSide.html#pypath.utils.pyreact.ReactionSide" title="pypath.utils.pyreact.ReactionSide"><code class="xref py py-obj docutils literal notranslate"><span class="pre">ReactionSide</span></code></a>(members[, source, parent])</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.utils.pyreact.Reference.html#pypath.utils.pyreact.Reference" title="pypath.utils.pyreact.Reference"><code class="xref py py-obj docutils literal notranslate"><span class="pre">Reference</span></code></a>(ref_id[, id_type, sources])</p></td>
+<td><p></p></td>
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diff --git a/api/pypath.utils.reflists.html b/api/pypath.utils.reflists.html
index 23cc94105..07b096f10 100644
--- a/api/pypath.utils.reflists.html
+++ b/api/pypath.utils.reflists.html
@@ -48,7 +48,7 @@
     <link rel="index" title="Index" href="../genindex.html" />
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     <link rel="next" title="pypath.utils.reflists.check" href="pypath.utils.reflists.check.html" />
-    <link rel="prev" title="pypath.utils.proteomicsdb.ProteomicsDB" href="pypath.utils.proteomicsdb.ProteomicsDB.html" />
+    <link rel="prev" title="pypath.utils.pyreact.Reference" href="pypath.utils.pyreact.Reference.html" />
   <meta name="viewport" content="width=device-width, initial-scale=1"/>
   <meta name="docsearch:language" content="en"/>
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@@ -565,12 +565,12 @@
                   
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-       href="pypath.utils.proteomicsdb.ProteomicsDB.html"
+       href="pypath.utils.pyreact.Reference.html"
        title="previous page">
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       <div class="prev-next-info">
         <p class="prev-next-subtitle">previous</p>
-        <p class="prev-next-title">pypath.utils.proteomicsdb.ProteomicsDB</p>
+        <p class="prev-next-title">pypath.utils.pyreact.Reference</p>
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diff --git a/api/pypath.utils.unichem.Unichem.html b/api/pypath.utils.unichem.Unichem.html
index 871016c72..973375269 100644
--- a/api/pypath.utils.unichem.Unichem.html
+++ b/api/pypath.utils.unichem.Unichem.html
@@ -47,7 +47,7 @@
     <link rel="icon" href="../_static/omnipath-logo.svg"/>
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-    <link rel="next" title="pypath.visual" href="pypath.visual.html" />
+    <link rel="next" title="pypath.utils.uniprot" href="pypath.utils.uniprot.html" />
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   <meta name="viewport" content="width=device-width, initial-scale=1"/>
   <meta name="docsearch:language" content="en"/>
@@ -671,11 +671,11 @@ <h1>pypath.utils.unichem.Unichem<a class="headerlink" href="#pypath-utils-uniche
       </div>
     </a>
     <a class="right-next"
-       href="pypath.visual.html"
+       href="pypath.utils.uniprot.html"
        title="next page">
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         <p class="prev-next-subtitle">next</p>
-        <p class="prev-next-title">pypath.visual</p>
+        <p class="prev-next-title">pypath.utils.uniprot</p>
       </div>
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diff --git a/api/pypath.utils.uniprot.UniprotProtein.html b/api/pypath.utils.uniprot.UniprotProtein.html
new file mode 100644
index 000000000..df99e8e2e
--- /dev/null
+++ b/api/pypath.utils.uniprot.UniprotProtein.html
@@ -0,0 +1,873 @@
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+  
+  
+  
+  <script data-cfasync="false">
+    document.documentElement.dataset.mode = localStorage.getItem("mode") || "";
+    document.documentElement.dataset.theme = localStorage.getItem("theme") || "light";
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+    <script>DOCUMENTATION_OPTIONS.pagename = 'api/pypath.utils.uniprot.UniprotProtein';</script>
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+  <section id="pypath-utils-uniprot-uniprotprotein">
+<h1>pypath.utils.uniprot.UniprotProtein<a class="headerlink" href="#pypath-utils-uniprot-uniprotprotein" title="Link to this heading">§</a></h1>
+<dl class="py class">
+<dt class="sig sig-object py" id="pypath.utils.uniprot.UniprotProtein">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">pypath.utils.uniprot.</span></span><span class="sig-name descname"><span class="pre">UniprotProtein</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">uniprot_id</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/utils/uniprot.html#UniprotProtein"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.utils.uniprot.UniprotProtein" title="Link to this definition">§</a></dt>
+<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.utils.uniprot.UniprotProtein.__init__">
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">uniprot_id</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/utils/uniprot.html#UniprotProtein.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.utils.uniprot.UniprotProtein.__init__" title="Link to this definition">§</a></dt>
+<dd></dd></dl>
+
+<p class="rubric">Methods</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.utils.uniprot.UniprotProtein.__init__" title="pypath.utils.uniprot.UniprotProtein.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>(uniprot_id)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_tag</span></code>(tag)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.utils.uniprot.UniprotProtein.info_section" title="pypath.utils.uniprot.UniprotProtein.info_section"><code class="xref py py-obj docutils literal notranslate"><span class="pre">info_section</span></code></a>(title)</p></td>
+<td><p>Retrieves a section from the description.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">itertag</span></code>(tag)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">load</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">reload</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">remove_xrefs</span></code>(value)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">update_databases</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">update_info</span></code>()</p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Attributes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">ac</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">activity_regulation</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">activity_regulation_with_xrefs</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">alternative_products</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">alternative_products_with_xrefs</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">catalytic_activity</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">catalytic_activity_with_xrefs</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.utils.uniprot.UniprotProtein.databases" title="pypath.utils.uniprot.UniprotProtein.databases"><code class="xref py py-obj docutils literal notranslate"><span class="pre">databases</span></code></a></p></td>
+<td><p>Returns the database identifiers (cross-references) as a dict of database names and identifiers.</p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">disease</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">disease_with_xrefs</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">ec</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">full_name</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">function</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">function_genecards</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">function_or_genecards</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">function_with_genecards</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">function_with_xrefs</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">genesymbol</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">id</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">info</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">interaction</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">interaction_with_xrefs</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_reviewed</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.utils.uniprot.UniprotProtein.keywords" title="pypath.utils.uniprot.UniprotProtein.keywords"><code class="xref py py-obj docutils literal notranslate"><span class="pre">keywords</span></code></a></p></td>
+<td><p>Returns the keywords as a list.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.utils.uniprot.UniprotProtein.keywords_with_xrefs" title="pypath.utils.uniprot.UniprotProtein.keywords_with_xrefs"><code class="xref py py-obj docutils literal notranslate"><span class="pre">keywords_with_xrefs</span></code></a></p></td>
+<td><p>Returns the keywords as a list with keeping the cross-references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.utils.uniprot.UniprotProtein.length" title="pypath.utils.uniprot.UniprotProtein.length"><code class="xref py py-obj docutils literal notranslate"><span class="pre">length</span></code></a></p></td>
+<td><p>Returns the length (number of residues) of the canonical sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.utils.uniprot.UniprotProtein.lengths" title="pypath.utils.uniprot.UniprotProtein.lengths"><code class="xref py py-obj docutils literal notranslate"><span class="pre">lengths</span></code></a></p></td>
+<td><p>Returns the length of all isoforms as a list.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">organism</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">ptm</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">ptm_with_xrefs</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.utils.uniprot.UniprotProtein.sequence" title="pypath.utils.uniprot.UniprotProtein.sequence"><code class="xref py py-obj docutils literal notranslate"><span class="pre">sequence</span></code></a></p></td>
+<td><p>Returns the canonical sequence (the first one) as a string of standard capital letter residue symbols.</p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">sequence_caution</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">sequence_caution_with_xrefs</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">similarity</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">similarity_with_xrefs</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">subcellular_location</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">subcellular_location_with_xrefs</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">subunit</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">subunit_with_xrefs</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">tissue_specificity</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">tissue_specificity_with_xrefs</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">web_resource</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">web_resource_with_xrefs</span></code></p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#pypath.utils.uniprot.UniprotProtein.weight" title="pypath.utils.uniprot.UniprotProtein.weight"><code class="xref py py-obj docutils literal notranslate"><span class="pre">weight</span></code></a></p></td>
+<td><p>Returns the molecular weight of the canonical isoform in Daltons.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#pypath.utils.uniprot.UniprotProtein.weights" title="pypath.utils.uniprot.UniprotProtein.weights"><code class="xref py py-obj docutils literal notranslate"><span class="pre">weights</span></code></a></p></td>
+<td><p>Returns the molecular weights of all isoforms as a list.</p></td>
+</tr>
+</tbody>
+</table>
+<dl class="py property">
+<dt class="sig sig-object py" id="pypath.utils.uniprot.UniprotProtein.databases">
+<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">databases</span></span><a class="headerlink" href="#pypath.utils.uniprot.UniprotProtein.databases" title="Link to this definition">§</a></dt>
+<dd><p>Returns the database identifiers (cross-references) as a dict of
+database names and identifiers.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="pypath.utils.uniprot.UniprotProtein.info_section">
+<span class="sig-name descname"><span class="pre">info_section</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">title</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/utils/uniprot.html#UniprotProtein.info_section"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.utils.uniprot.UniprotProtein.info_section" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a section from the description. If the section is not
+availeble, returns <code class="docutils literal notranslate"><span class="pre">None</span></code>.</p>
+</dd></dl>
+
+<dl class="py property">
+<dt class="sig sig-object py" id="pypath.utils.uniprot.UniprotProtein.keywords">
+<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">keywords</span></span><a class="headerlink" href="#pypath.utils.uniprot.UniprotProtein.keywords" title="Link to this definition">§</a></dt>
+<dd><p>Returns the keywords as a list.</p>
+</dd></dl>
+
+<dl class="py property">
+<dt class="sig sig-object py" id="pypath.utils.uniprot.UniprotProtein.keywords_with_xrefs">
+<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">keywords_with_xrefs</span></span><a class="headerlink" href="#pypath.utils.uniprot.UniprotProtein.keywords_with_xrefs" title="Link to this definition">§</a></dt>
+<dd><p>Returns the keywords as a list with keeping the cross-references.</p>
+</dd></dl>
+
+<dl class="py property">
+<dt class="sig sig-object py" id="pypath.utils.uniprot.UniprotProtein.length">
+<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">length</span></span><a class="headerlink" href="#pypath.utils.uniprot.UniprotProtein.length" title="Link to this definition">§</a></dt>
+<dd><p>Returns the length (number of residues) of the canonical sequence.</p>
+</dd></dl>
+
+<dl class="py property">
+<dt class="sig sig-object py" id="pypath.utils.uniprot.UniprotProtein.lengths">
+<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">lengths</span></span><a class="headerlink" href="#pypath.utils.uniprot.UniprotProtein.lengths" title="Link to this definition">§</a></dt>
+<dd><p>Returns the length of all isoforms as a list.</p>
+</dd></dl>
+
+<dl class="py property">
+<dt class="sig sig-object py" id="pypath.utils.uniprot.UniprotProtein.sequence">
+<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">sequence</span></span><a class="headerlink" href="#pypath.utils.uniprot.UniprotProtein.sequence" title="Link to this definition">§</a></dt>
+<dd><p>Returns the canonical sequence (the first one) as a string of
+standard capital letter residue symbols.</p>
+</dd></dl>
+
+<dl class="py property">
+<dt class="sig sig-object py" id="pypath.utils.uniprot.UniprotProtein.weight">
+<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">weight</span></span><a class="headerlink" href="#pypath.utils.uniprot.UniprotProtein.weight" title="Link to this definition">§</a></dt>
+<dd><p>Returns the molecular weight of the canonical isoform in Daltons.</p>
+</dd></dl>
+
+<dl class="py property">
+<dt class="sig sig-object py" id="pypath.utils.uniprot.UniprotProtein.weights">
+<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">weights</span></span><a class="headerlink" href="#pypath.utils.uniprot.UniprotProtein.weights" title="Link to this definition">§</a></dt>
+<dd><p>Returns the molecular weights of all isoforms as a list.</p>
+</dd></dl>
+
+</dd></dl>
+
+</section>
+
+
+                </article>
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+<span class="sig-prename descclassname"><span class="pre">pypath.utils.uniprot.</span></span><span class="sig-name descname"><span class="pre">activity_regulation</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">uniprot_id</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">*</span></span><span class="n"><span class="pre">args</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.utils.uniprot.activity_regulation" title="Link to this definition">§</a></dt>
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+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.utils.uniprot.alternative_products">
+<span class="sig-prename descclassname"><span class="pre">pypath.utils.uniprot.</span></span><span class="sig-name descname"><span class="pre">alternative_products</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">uniprot_id</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">*</span></span><span class="n"><span class="pre">args</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.utils.uniprot.alternative_products" title="Link to this definition">§</a></dt>
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diff --git a/api/pypath.utils.uniprot.alternative_products_with_xrefs.html b/api/pypath.utils.uniprot.alternative_products_with_xrefs.html
new file mode 100644
index 000000000..fa14cab62
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@@ -0,0 +1,638 @@
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+<dl class="py function">
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+<span class="sig-prename descclassname"><span class="pre">pypath.utils.uniprot.</span></span><span class="sig-name descname"><span class="pre">alternative_products_with_xrefs</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">uniprot_id</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">*</span></span><span class="n"><span class="pre">args</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.utils.uniprot.alternative_products_with_xrefs" title="Link to this definition">§</a></dt>
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+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.utils.uniprot.browse">
+<span class="sig-prename descclassname"><span class="pre">pypath.utils.uniprot.</span></span><span class="sig-name descname"><span class="pre">browse</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">groups</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">start</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">fileobj</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/utils/uniprot.html#browse"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.utils.uniprot.browse" title="Link to this definition">§</a></dt>
+<dd><p>Browses through a series of protein groups, printing an information table
+for each group. <code class="docutils literal notranslate"><span class="pre">kwargs</span></code> passed to <code class="docutils literal notranslate"><span class="pre">info</span></code> and then to print_features``.
+Parameters for <code class="docutils literal notranslate"><span class="pre">common.table_format</span></code> can be provided.</p>
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diff --git a/api/pypath.utils.uniprot.catalytic_activity_with_xrefs.html b/api/pypath.utils.uniprot.catalytic_activity_with_xrefs.html
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index 000000000..c17ea4dc8
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new file mode 100644
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+  <section id="pypath-utils-uniprot-collect">
+<h1>pypath.utils.uniprot.collect<a class="headerlink" href="#pypath-utils-uniprot-collect" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.utils.uniprot.collect">
+<span class="sig-prename descclassname"><span class="pre">pypath.utils.uniprot.</span></span><span class="sig-name descname"><span class="pre">collect</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">uniprot_ids</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">*</span></span><span class="n"><span class="pre">features</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/utils/uniprot.html#collect"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.utils.uniprot.collect" title="Link to this definition">§</a></dt>
+<dd><p>Collects data about one or more UniProt IDs.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>uniprot_ids</strong> (<em>str</em><em>,</em><em>list</em>) – One or more UniProt IDs.</p></li>
+<li><p><strong>features</strong> (<em>*str</em><em>,</em><em>list</em>) – <p>Features to query: these must be method (property) names of the
+<code class="docutils literal notranslate"><span class="pre">UniprotProtein</span></code> class. E.g. <code class="docutils literal notranslate"><span class="pre">['ac',</span> <span class="pre">'genesymbol',</span> <span class="pre">'function']</span></code>.</p>
+</p></li>
+</ul>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p>A <code class="docutils literal notranslate"><span class="pre">collections.OrderedDict</span></code> object with feature names as keys and
+list of values for each UniProt ID as values.</p>
+</dd>
+</dl>
+</dd></dl>
+
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+  <section id="pypath-utils-uniprot-databases">
+<h1>pypath.utils.uniprot.databases<a class="headerlink" href="#pypath-utils-uniprot-databases" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.utils.uniprot.databases">
+<span class="sig-prename descclassname"><span class="pre">pypath.utils.uniprot.</span></span><span class="sig-name descname"><span class="pre">databases</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">uniprot_id</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">*</span></span><span class="n"><span class="pre">args</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.utils.uniprot.databases" title="Link to this definition">§</a></dt>
+<dd><p>Returns the database identifiers (cross-references) as a dict of
+database names and identifiers.</p>
+</dd></dl>
+
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+
+
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+  <section id="pypath-utils-uniprot-disease">
+<h1>pypath.utils.uniprot.disease<a class="headerlink" href="#pypath-utils-uniprot-disease" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.utils.uniprot.disease">
+<span class="sig-prename descclassname"><span class="pre">pypath.utils.uniprot.</span></span><span class="sig-name descname"><span class="pre">disease</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">uniprot_id</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">*</span></span><span class="n"><span class="pre">args</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.utils.uniprot.disease" title="Link to this definition">§</a></dt>
+<dd></dd></dl>
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+  <section id="pypath-utils-uniprot-disease-with-xrefs">
+<h1>pypath.utils.uniprot.disease_with_xrefs<a class="headerlink" href="#pypath-utils-uniprot-disease-with-xrefs" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.utils.uniprot.disease_with_xrefs">
+<span class="sig-prename descclassname"><span class="pre">pypath.utils.uniprot.</span></span><span class="sig-name descname"><span class="pre">disease_with_xrefs</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">uniprot_id</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">*</span></span><span class="n"><span class="pre">args</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.utils.uniprot.disease_with_xrefs" title="Link to this definition">§</a></dt>
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+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.utils.uniprot.features_table">
+<span class="sig-prename descclassname"><span class="pre">pypath.utils.uniprot.</span></span><span class="sig-name descname"><span class="pre">features_table</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">uniprot_ids</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">*</span></span><span class="n"><span class="pre">features</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">width</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">40</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">maxlen</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">tablefmt</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'fancy_grid'</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/utils/uniprot.html#features_table"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.utils.uniprot.features_table" title="Link to this definition">§</a></dt>
+<dd><p>Returns a table with the requested features of a list of UniProt IDs.
+The underlying table formatting module is <code class="docutils literal notranslate"><span class="pre">tabulate</span></code>, a versatile
+module to export various ascii tables as well as HTML or LaTeX –
+check the docs for formatting options:
+<a class="github reference external" href="https://github.com/astanin/python-tabulate">astanin/python-tabulate</a></p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>kwargs:</dt><dd><p>Passed to <code class="docutils literal notranslate"><span class="pre">tabulate.tabulate</span></code>.</p>
+</dd>
+</dl>
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+</dd>
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+<dl class="py function">
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+<span class="sig-prename descclassname"><span class="pre">pypath.utils.uniprot.</span></span><span class="sig-name descname"><span class="pre">genesymbol</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">uniprot_id</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">*</span></span><span class="n"><span class="pre">args</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.utils.uniprot.genesymbol" title="Link to this definition">§</a></dt>
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new file mode 100644
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+  <section id="module-pypath.utils.uniprot">
+<span id="pypath-utils-uniprot"></span><h1>pypath.utils.uniprot<a class="headerlink" href="#module-pypath.utils.uniprot" title="Link to this heading">§</a></h1>
+<dl class="field-list simple">
+<dt class="field-odd">members<span class="colon">:</span></dt>
+<dd class="field-odd"><p></p></dd>
+</dl>
+<p class="rubric">Functions</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.utils.uniprot.ac.html#pypath.utils.uniprot.ac" title="pypath.utils.uniprot.ac"><code class="xref py py-obj docutils literal notranslate"><span class="pre">ac</span></code></a>(uniprot_id, *args, **kwargs)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.utils.uniprot.activity_regulation.html#pypath.utils.uniprot.activity_regulation" title="pypath.utils.uniprot.activity_regulation"><code class="xref py py-obj docutils literal notranslate"><span class="pre">activity_regulation</span></code></a>(uniprot_id, *args, **kwargs)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.utils.uniprot.activity_regulation_with_xrefs.html#pypath.utils.uniprot.activity_regulation_with_xrefs" title="pypath.utils.uniprot.activity_regulation_with_xrefs"><code class="xref py py-obj docutils literal notranslate"><span class="pre">activity_regulation_with_xrefs</span></code></a>(uniprot_id, ...)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.utils.uniprot.alternative_products.html#pypath.utils.uniprot.alternative_products" title="pypath.utils.uniprot.alternative_products"><code class="xref py py-obj docutils literal notranslate"><span class="pre">alternative_products</span></code></a>(uniprot_id, *args, **kwargs)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.utils.uniprot.alternative_products_with_xrefs.html#pypath.utils.uniprot.alternative_products_with_xrefs" title="pypath.utils.uniprot.alternative_products_with_xrefs"><code class="xref py py-obj docutils literal notranslate"><span class="pre">alternative_products_with_xrefs</span></code></a>(uniprot_id, ...)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.utils.uniprot.browse.html#pypath.utils.uniprot.browse" title="pypath.utils.uniprot.browse"><code class="xref py py-obj docutils literal notranslate"><span class="pre">browse</span></code></a>(groups[, start, fileobj])</p></td>
+<td><p>Browses through a series of protein groups, printing an information table for each group.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.utils.uniprot.catalytic_activity.html#pypath.utils.uniprot.catalytic_activity" title="pypath.utils.uniprot.catalytic_activity"><code class="xref py py-obj docutils literal notranslate"><span class="pre">catalytic_activity</span></code></a>(uniprot_id, *args, **kwargs)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.utils.uniprot.catalytic_activity_with_xrefs.html#pypath.utils.uniprot.catalytic_activity_with_xrefs" title="pypath.utils.uniprot.catalytic_activity_with_xrefs"><code class="xref py py-obj docutils literal notranslate"><span class="pre">catalytic_activity_with_xrefs</span></code></a>(uniprot_id, ...)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.utils.uniprot.collect.html#pypath.utils.uniprot.collect" title="pypath.utils.uniprot.collect"><code class="xref py py-obj docutils literal notranslate"><span class="pre">collect</span></code></a>(uniprot_ids, *features)</p></td>
+<td><p>Collects data about one or more UniProt IDs.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.utils.uniprot.databases.html#pypath.utils.uniprot.databases" title="pypath.utils.uniprot.databases"><code class="xref py py-obj docutils literal notranslate"><span class="pre">databases</span></code></a>(uniprot_id, *args, **kwargs)</p></td>
+<td><p>Returns the database identifiers (cross-references) as a dict of database names and identifiers.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.utils.uniprot.disease.html#pypath.utils.uniprot.disease" title="pypath.utils.uniprot.disease"><code class="xref py py-obj docutils literal notranslate"><span class="pre">disease</span></code></a>(uniprot_id, *args, **kwargs)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.utils.uniprot.disease_with_xrefs.html#pypath.utils.uniprot.disease_with_xrefs" title="pypath.utils.uniprot.disease_with_xrefs"><code class="xref py py-obj docutils literal notranslate"><span class="pre">disease_with_xrefs</span></code></a>(uniprot_id, *args, **kwargs)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.utils.uniprot.ec.html#pypath.utils.uniprot.ec" title="pypath.utils.uniprot.ec"><code class="xref py py-obj docutils literal notranslate"><span class="pre">ec</span></code></a>(uniprot_id, *args, **kwargs)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.utils.uniprot.features_table.html#pypath.utils.uniprot.features_table" title="pypath.utils.uniprot.features_table"><code class="xref py py-obj docutils literal notranslate"><span class="pre">features_table</span></code></a>(uniprot_ids, *features[, ...])</p></td>
+<td><p>Returns a table with the requested features of a list of UniProt IDs.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.utils.uniprot.full_name.html#pypath.utils.uniprot.full_name" title="pypath.utils.uniprot.full_name"><code class="xref py py-obj docutils literal notranslate"><span class="pre">full_name</span></code></a>(uniprot_id, *args, **kwargs)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.utils.uniprot.function.html#pypath.utils.uniprot.function" title="pypath.utils.uniprot.function"><code class="xref py py-obj docutils literal notranslate"><span class="pre">function</span></code></a>(uniprot_id, *args, **kwargs)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.utils.uniprot.function_genecards.html#pypath.utils.uniprot.function_genecards" title="pypath.utils.uniprot.function_genecards"><code class="xref py py-obj docutils literal notranslate"><span class="pre">function_genecards</span></code></a>(uniprot_id, *args, **kwargs)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.utils.uniprot.function_or_genecards.html#pypath.utils.uniprot.function_or_genecards" title="pypath.utils.uniprot.function_or_genecards"><code class="xref py py-obj docutils literal notranslate"><span class="pre">function_or_genecards</span></code></a>(uniprot_id, *args, ...)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.utils.uniprot.function_with_genecards.html#pypath.utils.uniprot.function_with_genecards" title="pypath.utils.uniprot.function_with_genecards"><code class="xref py py-obj docutils literal notranslate"><span class="pre">function_with_genecards</span></code></a>(uniprot_id, *args, ...)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.utils.uniprot.function_with_xrefs.html#pypath.utils.uniprot.function_with_xrefs" title="pypath.utils.uniprot.function_with_xrefs"><code class="xref py py-obj docutils literal notranslate"><span class="pre">function_with_xrefs</span></code></a>(uniprot_id, *args, **kwargs)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.utils.uniprot.genesymbol.html#pypath.utils.uniprot.genesymbol" title="pypath.utils.uniprot.genesymbol"><code class="xref py py-obj docutils literal notranslate"><span class="pre">genesymbol</span></code></a>(uniprot_id, *args, **kwargs)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.utils.uniprot.has_tag.html#pypath.utils.uniprot.has_tag" title="pypath.utils.uniprot.has_tag"><code class="xref py py-obj docutils literal notranslate"><span class="pre">has_tag</span></code></a>(uniprot_id, *args, **kwargs)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.utils.uniprot.id.html#pypath.utils.uniprot.id" title="pypath.utils.uniprot.id"><code class="xref py py-obj docutils literal notranslate"><span class="pre">id</span></code></a>(uniprot_id, *args, **kwargs)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.utils.uniprot.info.html#pypath.utils.uniprot.info" title="pypath.utils.uniprot.info"><code class="xref py py-obj docutils literal notranslate"><span class="pre">info</span></code></a>(*uniprot_ids[, features, fileobj, header])</p></td>
+<td><p>Prints a table with the most important (or the requested) features of a list of UniProt IDs.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.utils.uniprot.info_section.html#pypath.utils.uniprot.info_section" title="pypath.utils.uniprot.info_section"><code class="xref py py-obj docutils literal notranslate"><span class="pre">info_section</span></code></a>(uniprot_id, *args, **kwargs)</p></td>
+<td><p>Retrieves a section from the description.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.utils.uniprot.interaction.html#pypath.utils.uniprot.interaction" title="pypath.utils.uniprot.interaction"><code class="xref py py-obj docutils literal notranslate"><span class="pre">interaction</span></code></a>(uniprot_id, *args, **kwargs)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.utils.uniprot.interaction_with_xrefs.html#pypath.utils.uniprot.interaction_with_xrefs" title="pypath.utils.uniprot.interaction_with_xrefs"><code class="xref py py-obj docutils literal notranslate"><span class="pre">interaction_with_xrefs</span></code></a>(uniprot_id, *args, ...)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.utils.uniprot.is_reviewed.html#pypath.utils.uniprot.is_reviewed" title="pypath.utils.uniprot.is_reviewed"><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_reviewed</span></code></a>(uniprot_id, *args, **kwargs)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.utils.uniprot.itertag.html#pypath.utils.uniprot.itertag" title="pypath.utils.uniprot.itertag"><code class="xref py py-obj docutils literal notranslate"><span class="pre">itertag</span></code></a>(uniprot_id, *args, **kwargs)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.utils.uniprot.keywords.html#pypath.utils.uniprot.keywords" title="pypath.utils.uniprot.keywords"><code class="xref py py-obj docutils literal notranslate"><span class="pre">keywords</span></code></a>(uniprot_id, *args, **kwargs)</p></td>
+<td><p>Returns the keywords as a list.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.utils.uniprot.keywords_with_xrefs.html#pypath.utils.uniprot.keywords_with_xrefs" title="pypath.utils.uniprot.keywords_with_xrefs"><code class="xref py py-obj docutils literal notranslate"><span class="pre">keywords_with_xrefs</span></code></a>(uniprot_id, *args, **kwargs)</p></td>
+<td><p>Returns the keywords as a list with keeping the cross-references.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.utils.uniprot.length.html#pypath.utils.uniprot.length" title="pypath.utils.uniprot.length"><code class="xref py py-obj docutils literal notranslate"><span class="pre">length</span></code></a>(uniprot_id, *args, **kwargs)</p></td>
+<td><p>Returns the length (number of residues) of the canonical sequence.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.utils.uniprot.lengths.html#pypath.utils.uniprot.lengths" title="pypath.utils.uniprot.lengths"><code class="xref py py-obj docutils literal notranslate"><span class="pre">lengths</span></code></a>(uniprot_id, *args, **kwargs)</p></td>
+<td><p>Returns the length of all isoforms as a list.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.utils.uniprot.load.html#pypath.utils.uniprot.load" title="pypath.utils.uniprot.load"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load</span></code></a>(uniprot_id, *args, **kwargs)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.utils.uniprot.organism.html#pypath.utils.uniprot.organism" title="pypath.utils.uniprot.organism"><code class="xref py py-obj docutils literal notranslate"><span class="pre">organism</span></code></a>(uniprot_id, *args, **kwargs)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.utils.uniprot.print_features.html#pypath.utils.uniprot.print_features" title="pypath.utils.uniprot.print_features"><code class="xref py py-obj docutils literal notranslate"><span class="pre">print_features</span></code></a>(uniprot_ids, *features[, ...])</p></td>
+<td><p>Prints a table with the requested features of a list of UniProt IDs.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.utils.uniprot.ptm.html#pypath.utils.uniprot.ptm" title="pypath.utils.uniprot.ptm"><code class="xref py py-obj docutils literal notranslate"><span class="pre">ptm</span></code></a>(uniprot_id, *args, **kwargs)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.utils.uniprot.ptm_with_xrefs.html#pypath.utils.uniprot.ptm_with_xrefs" title="pypath.utils.uniprot.ptm_with_xrefs"><code class="xref py py-obj docutils literal notranslate"><span class="pre">ptm_with_xrefs</span></code></a>(uniprot_id, *args, **kwargs)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.utils.uniprot.query.html#pypath.utils.uniprot.query" title="pypath.utils.uniprot.query"><code class="xref py py-obj docutils literal notranslate"><span class="pre">query</span></code></a>(*uniprot_ids)</p></td>
+<td><p>Queries the datasheet of one or more UniProt IDs.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.utils.uniprot.reload.html#pypath.utils.uniprot.reload" title="pypath.utils.uniprot.reload"><code class="xref py py-obj docutils literal notranslate"><span class="pre">reload</span></code></a>(uniprot_id, *args, **kwargs)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.utils.uniprot.remove_xrefs.html#pypath.utils.uniprot.remove_xrefs" title="pypath.utils.uniprot.remove_xrefs"><code class="xref py py-obj docutils literal notranslate"><span class="pre">remove_xrefs</span></code></a>(uniprot_id, *args, **kwargs)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.utils.uniprot.sequence.html#pypath.utils.uniprot.sequence" title="pypath.utils.uniprot.sequence"><code class="xref py py-obj docutils literal notranslate"><span class="pre">sequence</span></code></a>(uniprot_id, *args, **kwargs)</p></td>
+<td><p>Returns the canonical sequence (the first one) as a string of standard capital letter residue symbols.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.utils.uniprot.sequence_caution.html#pypath.utils.uniprot.sequence_caution" title="pypath.utils.uniprot.sequence_caution"><code class="xref py py-obj docutils literal notranslate"><span class="pre">sequence_caution</span></code></a>(uniprot_id, *args, **kwargs)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.utils.uniprot.sequence_caution_with_xrefs.html#pypath.utils.uniprot.sequence_caution_with_xrefs" title="pypath.utils.uniprot.sequence_caution_with_xrefs"><code class="xref py py-obj docutils literal notranslate"><span class="pre">sequence_caution_with_xrefs</span></code></a>(uniprot_id, ...)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.utils.uniprot.similarity.html#pypath.utils.uniprot.similarity" title="pypath.utils.uniprot.similarity"><code class="xref py py-obj docutils literal notranslate"><span class="pre">similarity</span></code></a>(uniprot_id, *args, **kwargs)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.utils.uniprot.similarity_with_xrefs.html#pypath.utils.uniprot.similarity_with_xrefs" title="pypath.utils.uniprot.similarity_with_xrefs"><code class="xref py py-obj docutils literal notranslate"><span class="pre">similarity_with_xrefs</span></code></a>(uniprot_id, *args, ...)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.utils.uniprot.subcellular_location.html#pypath.utils.uniprot.subcellular_location" title="pypath.utils.uniprot.subcellular_location"><code class="xref py py-obj docutils literal notranslate"><span class="pre">subcellular_location</span></code></a>(uniprot_id, *args, **kwargs)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.utils.uniprot.subcellular_location_with_xrefs.html#pypath.utils.uniprot.subcellular_location_with_xrefs" title="pypath.utils.uniprot.subcellular_location_with_xrefs"><code class="xref py py-obj docutils literal notranslate"><span class="pre">subcellular_location_with_xrefs</span></code></a>(uniprot_id, ...)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.utils.uniprot.subunit.html#pypath.utils.uniprot.subunit" title="pypath.utils.uniprot.subunit"><code class="xref py py-obj docutils literal notranslate"><span class="pre">subunit</span></code></a>(uniprot_id, *args, **kwargs)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.utils.uniprot.subunit_with_xrefs.html#pypath.utils.uniprot.subunit_with_xrefs" title="pypath.utils.uniprot.subunit_with_xrefs"><code class="xref py py-obj docutils literal notranslate"><span class="pre">subunit_with_xrefs</span></code></a>(uniprot_id, *args, **kwargs)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.utils.uniprot.tissue_specificity.html#pypath.utils.uniprot.tissue_specificity" title="pypath.utils.uniprot.tissue_specificity"><code class="xref py py-obj docutils literal notranslate"><span class="pre">tissue_specificity</span></code></a>(uniprot_id, *args, **kwargs)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.utils.uniprot.tissue_specificity_with_xrefs.html#pypath.utils.uniprot.tissue_specificity_with_xrefs" title="pypath.utils.uniprot.tissue_specificity_with_xrefs"><code class="xref py py-obj docutils literal notranslate"><span class="pre">tissue_specificity_with_xrefs</span></code></a>(uniprot_id, ...)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.utils.uniprot.update_databases.html#pypath.utils.uniprot.update_databases" title="pypath.utils.uniprot.update_databases"><code class="xref py py-obj docutils literal notranslate"><span class="pre">update_databases</span></code></a>(uniprot_id, *args, **kwargs)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.utils.uniprot.update_info.html#pypath.utils.uniprot.update_info" title="pypath.utils.uniprot.update_info"><code class="xref py py-obj docutils literal notranslate"><span class="pre">update_info</span></code></a>(uniprot_id, *args, **kwargs)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.utils.uniprot.web_resource.html#pypath.utils.uniprot.web_resource" title="pypath.utils.uniprot.web_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">web_resource</span></code></a>(uniprot_id, *args, **kwargs)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.utils.uniprot.web_resource_with_xrefs.html#pypath.utils.uniprot.web_resource_with_xrefs" title="pypath.utils.uniprot.web_resource_with_xrefs"><code class="xref py py-obj docutils literal notranslate"><span class="pre">web_resource_with_xrefs</span></code></a>(uniprot_id, *args, ...)</p></td>
+<td><p></p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.utils.uniprot.weight.html#pypath.utils.uniprot.weight" title="pypath.utils.uniprot.weight"><code class="xref py py-obj docutils literal notranslate"><span class="pre">weight</span></code></a>(uniprot_id, *args, **kwargs)</p></td>
+<td><p>Returns the molecular weight of the canonical isoform in Daltons.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="pypath.utils.uniprot.weights.html#pypath.utils.uniprot.weights" title="pypath.utils.uniprot.weights"><code class="xref py py-obj docutils literal notranslate"><span class="pre">weights</span></code></a>(uniprot_id, *args, **kwargs)</p></td>
+<td><p>Returns the molecular weights of all isoforms as a list.</p></td>
+</tr>
+</tbody>
+</table>
+<p class="rubric">Classes</p>
+<table class="autosummary longtable table autosummary">
+<tbody>
+<tr class="row-odd"><td><p><a class="reference internal" href="pypath.utils.uniprot.UniprotProtein.html#pypath.utils.uniprot.UniprotProtein" title="pypath.utils.uniprot.UniprotProtein"><code class="xref py py-obj docutils literal notranslate"><span class="pre">UniprotProtein</span></code></a>(uniprot_id)</p></td>
+<td><p></p></td>
+</tr>
+</tbody>
+</table>
+</section>
+
+
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+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.utils.uniprot.id">
+<span class="sig-prename descclassname"><span class="pre">pypath.utils.uniprot.</span></span><span class="sig-name descname"><span class="pre">id</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">uniprot_id</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">*</span></span><span class="n"><span class="pre">args</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.utils.uniprot.id" title="Link to this definition">§</a></dt>
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new file mode 100644
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+  <section id="pypath-utils-uniprot-info">
+<h1>pypath.utils.uniprot.info<a class="headerlink" href="#pypath-utils-uniprot-info" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.utils.uniprot.info">
+<span class="sig-prename descclassname"><span class="pre">pypath.utils.uniprot.</span></span><span class="sig-name descname"><span class="pre">info</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">*</span></span><span class="n"><span class="pre">uniprot_ids</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">features</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">fileobj</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">header</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/utils/uniprot.html#info"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.utils.uniprot.info" title="Link to this definition">§</a></dt>
+<dd><p>Prints a table with the most important (or the requested) features of a
+list of UniProt IDs.</p>
+</dd></dl>
+
+</section>
+
+
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diff --git a/api/pypath.utils.uniprot.info_section.html b/api/pypath.utils.uniprot.info_section.html
new file mode 100644
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+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.utils.uniprot.info_section">
+<span class="sig-prename descclassname"><span class="pre">pypath.utils.uniprot.</span></span><span class="sig-name descname"><span class="pre">info_section</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">uniprot_id</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">*</span></span><span class="n"><span class="pre">args</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.utils.uniprot.info_section" title="Link to this definition">§</a></dt>
+<dd><p>Retrieves a section from the description. If the section is not
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diff --git a/api/pypath.utils.uniprot.interaction.html b/api/pypath.utils.uniprot.interaction.html
new file mode 100644
index 000000000..9f02f4691
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diff --git a/api/pypath.utils.uniprot.interaction_with_xrefs.html b/api/pypath.utils.uniprot.interaction_with_xrefs.html
new file mode 100644
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+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.utils.uniprot.interaction_with_xrefs">
+<span class="sig-prename descclassname"><span class="pre">pypath.utils.uniprot.</span></span><span class="sig-name descname"><span class="pre">interaction_with_xrefs</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">uniprot_id</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">*</span></span><span class="n"><span class="pre">args</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.utils.uniprot.interaction_with_xrefs" title="Link to this definition">§</a></dt>
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+  <section id="pypath-utils-uniprot-is-reviewed">
+<h1>pypath.utils.uniprot.is_reviewed<a class="headerlink" href="#pypath-utils-uniprot-is-reviewed" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.utils.uniprot.is_reviewed">
+<span class="sig-prename descclassname"><span class="pre">pypath.utils.uniprot.</span></span><span class="sig-name descname"><span class="pre">is_reviewed</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">uniprot_id</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">*</span></span><span class="n"><span class="pre">args</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.utils.uniprot.is_reviewed" title="Link to this definition">§</a></dt>
+<dd></dd></dl>
+
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+  <section id="pypath-utils-uniprot-itertag">
+<h1>pypath.utils.uniprot.itertag<a class="headerlink" href="#pypath-utils-uniprot-itertag" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.utils.uniprot.itertag">
+<span class="sig-prename descclassname"><span class="pre">pypath.utils.uniprot.</span></span><span class="sig-name descname"><span class="pre">itertag</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">uniprot_id</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">*</span></span><span class="n"><span class="pre">args</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.utils.uniprot.itertag" title="Link to this definition">§</a></dt>
+<dd></dd></dl>
+
+</section>
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+  <section id="pypath-utils-uniprot-keywords">
+<h1>pypath.utils.uniprot.keywords<a class="headerlink" href="#pypath-utils-uniprot-keywords" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.utils.uniprot.keywords">
+<span class="sig-prename descclassname"><span class="pre">pypath.utils.uniprot.</span></span><span class="sig-name descname"><span class="pre">keywords</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">uniprot_id</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">*</span></span><span class="n"><span class="pre">args</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.utils.uniprot.keywords" title="Link to this definition">§</a></dt>
+<dd><p>Returns the keywords as a list.</p>
+</dd></dl>
+
+</section>
+
+
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+  <section id="pypath-utils-uniprot-keywords-with-xrefs">
+<h1>pypath.utils.uniprot.keywords_with_xrefs<a class="headerlink" href="#pypath-utils-uniprot-keywords-with-xrefs" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.utils.uniprot.keywords_with_xrefs">
+<span class="sig-prename descclassname"><span class="pre">pypath.utils.uniprot.</span></span><span class="sig-name descname"><span class="pre">keywords_with_xrefs</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">uniprot_id</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">*</span></span><span class="n"><span class="pre">args</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.utils.uniprot.keywords_with_xrefs" title="Link to this definition">§</a></dt>
+<dd><p>Returns the keywords as a list with keeping the cross-references.</p>
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+
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+  <section id="pypath-utils-uniprot-length">
+<h1>pypath.utils.uniprot.length<a class="headerlink" href="#pypath-utils-uniprot-length" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.utils.uniprot.length">
+<span class="sig-prename descclassname"><span class="pre">pypath.utils.uniprot.</span></span><span class="sig-name descname"><span class="pre">length</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">uniprot_id</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">*</span></span><span class="n"><span class="pre">args</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.utils.uniprot.length" title="Link to this definition">§</a></dt>
+<dd><p>Returns the length (number of residues) of the canonical sequence.</p>
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+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.utils.uniprot.lengths">
+<span class="sig-prename descclassname"><span class="pre">pypath.utils.uniprot.</span></span><span class="sig-name descname"><span class="pre">lengths</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">uniprot_id</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">*</span></span><span class="n"><span class="pre">args</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.utils.uniprot.lengths" title="Link to this definition">§</a></dt>
+<dd><p>Returns the length of all isoforms as a list.</p>
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+<h1>pypath.utils.uniprot.print_features<a class="headerlink" href="#pypath-utils-uniprot-print-features" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.utils.uniprot.print_features">
+<span class="sig-prename descclassname"><span class="pre">pypath.utils.uniprot.</span></span><span class="sig-name descname"><span class="pre">print_features</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">uniprot_ids</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">*</span></span><span class="n"><span class="pre">features</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">fileobj</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">width</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">maxlen</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">tablefmt</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'fancy_grid'</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/utils/uniprot.html#print_features"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.utils.uniprot.print_features" title="Link to this definition">§</a></dt>
+<dd><p>Prints a table with the requested features of a list of UniProt IDs.
+The underlying table formatting module is <code class="docutils literal notranslate"><span class="pre">tabulate</span></code>, a versatile
+module to export various ascii tables as well as HTML or LaTeX –
+check the docs for formatting options:
+<a class="github reference external" href="https://github.com/astanin/python-tabulate">astanin/python-tabulate</a></p>
+<dl class="simple">
+<dt>Args</dt><dd><dl class="simple">
+<dt>kwargs:</dt><dd><p>Passed to <code class="docutils literal notranslate"><span class="pre">tabulate.tabulate</span></code>.</p>
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+<dl class="py function">
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new file mode 100644
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+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.utils.uniprot.query">
+<span class="sig-prename descclassname"><span class="pre">pypath.utils.uniprot.</span></span><span class="sig-name descname"><span class="pre">query</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">*</span></span><span class="n"><span class="pre">uniprot_ids</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/pypath/utils/uniprot.html#query"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pypath.utils.uniprot.query" title="Link to this definition">§</a></dt>
+<dd><p>Queries the datasheet of one or more UniProt IDs.
+Returns a single <code class="docutils literal notranslate"><span class="pre">UniprotProtein</span></code> object or a list of those objects.</p>
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+  <section id="pypath-utils-uniprot-sequence">
+<h1>pypath.utils.uniprot.sequence<a class="headerlink" href="#pypath-utils-uniprot-sequence" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.utils.uniprot.sequence">
+<span class="sig-prename descclassname"><span class="pre">pypath.utils.uniprot.</span></span><span class="sig-name descname"><span class="pre">sequence</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">uniprot_id</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">*</span></span><span class="n"><span class="pre">args</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.utils.uniprot.sequence" title="Link to this definition">§</a></dt>
+<dd><p>Returns the canonical sequence (the first one) as a string of
+standard capital letter residue symbols.</p>
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+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.utils.uniprot.similarity">
+<span class="sig-prename descclassname"><span class="pre">pypath.utils.uniprot.</span></span><span class="sig-name descname"><span class="pre">similarity</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">uniprot_id</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">*</span></span><span class="n"><span class="pre">args</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.utils.uniprot.similarity" title="Link to this definition">§</a></dt>
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diff --git a/api/pypath.utils.uniprot.similarity_with_xrefs.html b/api/pypath.utils.uniprot.similarity_with_xrefs.html
new file mode 100644
index 000000000..cbb742922
--- /dev/null
+++ b/api/pypath.utils.uniprot.similarity_with_xrefs.html
@@ -0,0 +1,638 @@
+
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+  <section id="pypath-utils-uniprot-subcellular-location">
+<h1>pypath.utils.uniprot.subcellular_location<a class="headerlink" href="#pypath-utils-uniprot-subcellular-location" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.utils.uniprot.subcellular_location">
+<span class="sig-prename descclassname"><span class="pre">pypath.utils.uniprot.</span></span><span class="sig-name descname"><span class="pre">subcellular_location</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">uniprot_id</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">*</span></span><span class="n"><span class="pre">args</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.utils.uniprot.subcellular_location" title="Link to this definition">§</a></dt>
+<dd></dd></dl>
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+<h1>pypath.utils.uniprot.subcellular_location_with_xrefs<a class="headerlink" href="#pypath-utils-uniprot-subcellular-location-with-xrefs" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.utils.uniprot.subcellular_location_with_xrefs">
+<span class="sig-prename descclassname"><span class="pre">pypath.utils.uniprot.</span></span><span class="sig-name descname"><span class="pre">subcellular_location_with_xrefs</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">uniprot_id</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">*</span></span><span class="n"><span class="pre">args</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.utils.uniprot.subcellular_location_with_xrefs" title="Link to this definition">§</a></dt>
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+  <section id="pypath-utils-uniprot-subunit">
+<h1>pypath.utils.uniprot.subunit<a class="headerlink" href="#pypath-utils-uniprot-subunit" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.utils.uniprot.subunit">
+<span class="sig-prename descclassname"><span class="pre">pypath.utils.uniprot.</span></span><span class="sig-name descname"><span class="pre">subunit</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">uniprot_id</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">*</span></span><span class="n"><span class="pre">args</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.utils.uniprot.subunit" title="Link to this definition">§</a></dt>
+<dd></dd></dl>
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new file mode 100644
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+<h1>pypath.utils.uniprot.subunit_with_xrefs<a class="headerlink" href="#pypath-utils-uniprot-subunit-with-xrefs" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.utils.uniprot.subunit_with_xrefs">
+<span class="sig-prename descclassname"><span class="pre">pypath.utils.uniprot.</span></span><span class="sig-name descname"><span class="pre">subunit_with_xrefs</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">uniprot_id</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">*</span></span><span class="n"><span class="pre">args</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.utils.uniprot.subunit_with_xrefs" title="Link to this definition">§</a></dt>
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new file mode 100644
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diff --git a/api/pypath.utils.uniprot.web_resource.html b/api/pypath.utils.uniprot.web_resource.html
new file mode 100644
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+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.utils.uniprot.web_resource">
+<span class="sig-prename descclassname"><span class="pre">pypath.utils.uniprot.</span></span><span class="sig-name descname"><span class="pre">web_resource</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">uniprot_id</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">*</span></span><span class="n"><span class="pre">args</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.utils.uniprot.web_resource" title="Link to this definition">§</a></dt>
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diff --git a/api/pypath.utils.uniprot.web_resource_with_xrefs.html b/api/pypath.utils.uniprot.web_resource_with_xrefs.html
new file mode 100644
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+<span class="sig-prename descclassname"><span class="pre">pypath.utils.uniprot.</span></span><span class="sig-name descname"><span class="pre">web_resource_with_xrefs</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">uniprot_id</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">*</span></span><span class="n"><span class="pre">args</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.utils.uniprot.web_resource_with_xrefs" title="Link to this definition">§</a></dt>
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+<h1>pypath.utils.uniprot.weight<a class="headerlink" href="#pypath-utils-uniprot-weight" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.utils.uniprot.weight">
+<span class="sig-prename descclassname"><span class="pre">pypath.utils.uniprot.</span></span><span class="sig-name descname"><span class="pre">weight</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">uniprot_id</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">*</span></span><span class="n"><span class="pre">args</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.utils.uniprot.weight" title="Link to this definition">§</a></dt>
+<dd><p>Returns the molecular weight of the canonical isoform in Daltons.</p>
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diff --git a/api/pypath.utils.uniprot.weights.html b/api/pypath.utils.uniprot.weights.html
new file mode 100644
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+          
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+            <span class="sr-only">Twitter</span></a>
+        </li>
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+          
+          
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+            <span class="sr-only">PyPI</span></a>
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+          
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+            <span class="sr-only">OmniPath</span></a>
+        </li>
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+          
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+          
+          <a href="https://saezlab.org/" title="Saez Lab" class="nav-link" rel="noopener" target="_blank" data-bs-toggle="tooltip" data-bs-placement="bottom"><span><i class="fa-solid fa-users fa-lg" aria-hidden="true"></i></span>
+            <span class="sr-only">Saez Lab</span></a>
+        </li>
+</ul></div>
+      
+    </div>
+    
+  </div>
+  
+  
+    <div class="navbar-persistent--mobile">
+
+ <script>
+ document.write(`
+   <button class="btn navbar-btn search-button-field search-button__button" title="Search" aria-label="Search" data-bs-placement="bottom" data-bs-toggle="tooltip">
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+    
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+                        Webservice
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+                    </li>
+                
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+                      <a class="nav-link nav-internal" href="../releasehistory.html">
+                        Release history
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+                
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+                      <a class="nav-link nav-internal" href="../notebooks/manual.html">
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+                      </a>
+                    </li>
+                
+  </ul>
+</nav></div>
+        
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+    
+    
+    
+      <div class="sidebar-header-items__end">
+        
+          <div class="navbar-item">
+
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+document.write(`
+  <button class="btn btn-sm navbar-btn theme-switch-button" title="light/dark" aria-label="light/dark" data-bs-placement="bottom" data-bs-toggle="tooltip">
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+        
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+            <span class="sr-only">Twitter</span></a>
+        </li>
+        <li class="nav-item">
+          
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+            <span class="sr-only">PyPI</span></a>
+        </li>
+        <li class="nav-item">
+          
+          
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+          
+          
+          
+          
+          <a href="https://omnipathdb.org/" title="OmniPath" class="nav-link" rel="noopener" target="_blank" data-bs-toggle="tooltip" data-bs-placement="bottom"><span><i class="fa-solid fa-university fa-lg" aria-hidden="true"></i></span>
+            <span class="sr-only">OmniPath</span></a>
+        </li>
+        <li class="nav-item">
+          
+          
+          
+          
+          
+          
+          
+          
+          <a href="https://saezlab.org/" title="Saez Lab" class="nav-link" rel="noopener" target="_blank" data-bs-toggle="tooltip" data-bs-placement="bottom"><span><i class="fa-solid fa-users fa-lg" aria-hidden="true"></i></span>
+            <span class="sr-only">Saez Lab</span></a>
+        </li>
+</ul></div>
+        
+      </div>
+    
+  </div>
+  
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+
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+        
+        
+          <div class="bd-content">
+            <div class="bd-article-container">
+              
+              <div class="bd-header-article">
+<div class="header-article-items header-article__inner">
+  
+    <div class="header-article-items__start">
+      
+        <div class="header-article-item">
+
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+  <ul class="bd-breadcrumbs">
+    
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+      </a>
+    </li>
+    
+    <li class="breadcrumb-item"><a href="../reference.html" class="nav-link">Reference</a></li>
+    
+    
+    <li class="breadcrumb-item"><i class="fa-solid fa-ellipsis"></i></li>
+    
+    
+    <li class="breadcrumb-item"><a href="pypath.utils.uniprot.html" class="nav-link">pypath.utils.uniprot</a></li>
+    
+    <li class="breadcrumb-item active" aria-current="page">pypath.utils...</li>
+  </ul>
+</nav>
+</div>
+      
+    </div>
+  
+  
+</div>
+</div>
+              
+              
+              
+                
+<div id="searchbox"></div>
+                <article class="bd-article">
+                  
+  <section id="pypath-utils-uniprot-weights">
+<h1>pypath.utils.uniprot.weights<a class="headerlink" href="#pypath-utils-uniprot-weights" title="Link to this heading">§</a></h1>
+<dl class="py function">
+<dt class="sig sig-object py" id="pypath.utils.uniprot.weights">
+<span class="sig-prename descclassname"><span class="pre">pypath.utils.uniprot.</span></span><span class="sig-name descname"><span class="pre">weights</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">uniprot_id</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">*</span></span><span class="n"><span class="pre">args</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#pypath.utils.uniprot.weights" title="Link to this definition">§</a></dt>
+<dd><p>Returns the molecular weights of all isoforms as a list.</p>
+</dd></dl>
+
+</section>
+
+
+                </article>
+              
+              
+              
+              
+              
+                <footer class="prev-next-footer">
+                  
+<div class="prev-next-area">
+    <a class="left-prev"
+       href="pypath.utils.uniprot.weight.html"
+       title="previous page">
+      <i class="fa-solid fa-angle-left"></i>
+      <div class="prev-next-info">
+        <p class="prev-next-subtitle">previous</p>
+        <p class="prev-next-title">pypath.utils.uniprot.weight</p>
+      </div>
+    </a>
+    <a class="right-next"
+       href="pypath.utils.uniprot.UniprotProtein.html"
+       title="next page">
+      <div class="prev-next-info">
+        <p class="prev-next-subtitle">next</p>
+        <p class="prev-next-title">pypath.utils.uniprot.UniprotProtein</p>
+      </div>
+      <i class="fa-solid fa-angle-right"></i>
+    </a>
+</div>
+                </footer>
+              
+            </div>
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+
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+<div
+    id="pst-page-navigation-heading-2"
+    class="page-toc tocsection onthispage">
+    <i class="fa-solid fa-list"></i> On this page
+  </div>
+  <nav class="bd-toc-nav page-toc" aria-labelledby="pst-page-navigation-heading-2">
+    <ul class="visible nav section-nav flex-column">
+<li class="toctree-l1 toc-h1 nav-item toc-entry"><a class="reference internal nav-link" href="../index.html">Welcome to pypath!</a></li>
+<li class="toctree-l1 toc-h1 nav-item toc-entry"><a class="reference internal nav-link" href="../webservice.html">Webservice</a></li>
+<li class="toctree-l1 toc-h1 nav-item toc-entry"><a class="reference internal nav-link" href="../releasehistory.html">Release history</a></li>
+<li class="toctree-l1 toc-h1 nav-item toc-entry"><a class="reference internal nav-link" href="../reference.html">Reference</a></li>
+<li class="toctree-l1 toc-h1 nav-item toc-entry"><a class="reference internal nav-link" href="../notebooks/manual.html">The pypath book</a></li>
+</ul>
+
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+
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+              
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+  
+    <div class="footer-items__start">
+      
+        <div class="footer-item">
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+    
+      © Copyright 2024, Denes Turei &lt;turei.denes@gmail.com&gt;, Nicolàs Palacio, Sebastian Lobentanzer, Olga Ivanova, Melih Darcan, Erva Ulusoy, Tennur Kilic, Omer Kaan Vural, Ahmet Rifaioglu, Charles Tapley Hoyt.
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+        <div class="footer-item">
+
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+    Created using <a href="https://www.sphinx-doc.org/">Sphinx</a> 7.2.6.
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+  
+    <div class="footer-items__end">
+      
+        <div class="footer-item">
+<p class="theme-version">
+  Built with the <a href="https://pydata-sphinx-theme.readthedocs.io/en/stable/index.html">PyData Sphinx Theme</a> 0.15.2.
+</p></div>
+      
+    </div>
+  
+</div>
+
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+  </body>
+</html>
\ No newline at end of file
diff --git a/api/pypath.visual.html b/api/pypath.visual.html
index c3d09d45a..c9c3c4d03 100644
--- a/api/pypath.visual.html
+++ b/api/pypath.visual.html
@@ -48,7 +48,7 @@
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
     <link rel="next" title="pypath.visual.drawing" href="pypath.visual.drawing.html" />
-    <link rel="prev" title="pypath.utils.unichem.Unichem" href="pypath.utils.unichem.Unichem.html" />
+    <link rel="prev" title="pypath.utils.uniprot.UniprotProtein" href="pypath.utils.uniprot.UniprotProtein.html" />
   <meta name="viewport" content="width=device-width, initial-scale=1"/>
   <meta name="docsearch:language" content="en"/>
   </head>
@@ -540,12 +540,12 @@
                   
 <div class="prev-next-area">
     <a class="left-prev"
-       href="pypath.utils.unichem.Unichem.html"
+       href="pypath.utils.uniprot.UniprotProtein.html"
        title="previous page">
       <i class="fa-solid fa-angle-left"></i>
       <div class="prev-next-info">
         <p class="prev-next-subtitle">previous</p>
-        <p class="prev-next-title">pypath.utils.unichem.Unichem</p>
+        <p class="prev-next-title">pypath.utils.uniprot.UniprotProtein</p>
       </div>
     </a>
     <a class="right-next"
diff --git a/genindex.html b/genindex.html
index 683f1e25c..3a4b3c4b5 100644
--- a/genindex.html
+++ b/genindex.html
@@ -495,14 +495,263 @@ <h1 id="index">Index</h1>
  | <a href="#T"><strong>T</strong></a>
  | <a href="#U"><strong>U</strong></a>
  | <a href="#V"><strong>V</strong></a>
+ | <a href="#W"><strong>W</strong></a>
+ | <a href="#Y"><strong>Y</strong></a>
+ | <a href="#Z"><strong>Z</strong></a>
  
 </div>
 <h2 id="_">_</h2>
 <table style="width: 100%" class="indextable genindextable"><tr>
   <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="api/pypath.core.attrs.AttributeHandler.html#pypath.core.attrs.AttributeHandler.__init__">__init__() (pypath.core.attrs.AttributeHandler method)</a>
+      <li><a href="api/pypath.core.annot.Adhesome.html#pypath.core.annot.Adhesome.__init__">__init__() (pypath.core.annot.Adhesome method)</a>
 
       <ul>
+        <li><a href="api/pypath.core.annot.Almen2009.html#pypath.core.annot.Almen2009.__init__">(pypath.core.annot.Almen2009 method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.AnnotationBase.html#pypath.core.annot.AnnotationBase.__init__">(pypath.core.annot.AnnotationBase method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.AnnotationTable.html#pypath.core.annot.AnnotationTable.__init__">(pypath.core.annot.AnnotationTable method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Baccin2019.html#pypath.core.annot.Baccin2019.__init__">(pypath.core.annot.Baccin2019 method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Biogps.html#pypath.core.annot.Biogps.__init__">(pypath.core.annot.Biogps method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cancerdrugsdb.html#pypath.core.annot.Cancerdrugsdb.__init__">(pypath.core.annot.Cancerdrugsdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CancerGeneCensus.html#pypath.core.annot.CancerGeneCensus.__init__">(pypath.core.annot.CancerGeneCensus method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cancersea.html#pypath.core.annot.Cancersea.__init__">(pypath.core.annot.Cancersea method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cellcall.html#pypath.core.annot.Cellcall.__init__">(pypath.core.annot.Cellcall method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cellcellinteractions.html#pypath.core.annot.Cellcellinteractions.__init__">(pypath.core.annot.Cellcellinteractions method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cellchatdb.html#pypath.core.annot.Cellchatdb.__init__">(pypath.core.annot.Cellchatdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CellchatdbComplex.html#pypath.core.annot.CellchatdbComplex.__init__">(pypath.core.annot.CellchatdbComplex method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cellinker.html#pypath.core.annot.Cellinker.__init__">(pypath.core.annot.Cellinker method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CellinkerComplex.html#pypath.core.annot.CellinkerComplex.__init__">(pypath.core.annot.CellinkerComplex method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CellPhoneDB.html#pypath.core.annot.CellPhoneDB.__init__">(pypath.core.annot.CellPhoneDB method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CellPhoneDBComplex.html#pypath.core.annot.CellPhoneDBComplex.__init__">(pypath.core.annot.CellPhoneDBComplex method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CellSurfaceProteinAtlas.html#pypath.core.annot.CellSurfaceProteinAtlas.__init__">(pypath.core.annot.CellSurfaceProteinAtlas method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CellSurfaceProteinAtlasCellType.html#pypath.core.annot.CellSurfaceProteinAtlasCellType.__init__">(pypath.core.annot.CellSurfaceProteinAtlasCellType method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Celltalkdb.html#pypath.core.annot.Celltalkdb.__init__">(pypath.core.annot.Celltalkdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Celltypist.html#pypath.core.annot.Celltypist.__init__">(pypath.core.annot.Celltypist method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Comppi.html#pypath.core.annot.Comppi.__init__">(pypath.core.annot.Comppi method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Connectomedb.html#pypath.core.annot.Connectomedb.__init__">(pypath.core.annot.Connectomedb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Corum.html#pypath.core.annot.Corum.__init__">(pypath.core.annot.Corum method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CorumFuncat.html#pypath.core.annot.CorumFuncat.__init__">(pypath.core.annot.CorumFuncat method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CorumGO.html#pypath.core.annot.CorumGO.__init__">(pypath.core.annot.CorumGO method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cpad.html#pypath.core.annot.Cpad.__init__">(pypath.core.annot.Cpad method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CustomAnnotation.html#pypath.core.annot.CustomAnnotation.__init__">(pypath.core.annot.CustomAnnotation method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cytosig.html#pypath.core.annot.Cytosig.__init__">(pypath.core.annot.Cytosig method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Dgidb.html#pypath.core.annot.Dgidb.__init__">(pypath.core.annot.Dgidb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Disgenet.html#pypath.core.annot.Disgenet.__init__">(pypath.core.annot.Disgenet method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Embrace.html#pypath.core.annot.Embrace.__init__">(pypath.core.annot.Embrace method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Exocarta.html#pypath.core.annot.Exocarta.__init__">(pypath.core.annot.Exocarta method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.GOCustomIntercell.html#pypath.core.annot.GOCustomIntercell.__init__">(pypath.core.annot.GOCustomIntercell method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.GOIntercell.html#pypath.core.annot.GOIntercell.__init__">(pypath.core.annot.GOIntercell method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Gpcrdb.html#pypath.core.annot.Gpcrdb.__init__">(pypath.core.annot.Gpcrdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.GuideToPharmacology.html#pypath.core.annot.GuideToPharmacology.__init__">(pypath.core.annot.GuideToPharmacology method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Hgnc.html#pypath.core.annot.Hgnc.__init__">(pypath.core.annot.Hgnc method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.HpmrComplex.html#pypath.core.annot.HpmrComplex.__init__">(pypath.core.annot.HpmrComplex method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.HPO.html#pypath.core.annot.HPO.__init__">(pypath.core.annot.HPO method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Humancellmap.html#pypath.core.annot.Humancellmap.__init__">(pypath.core.annot.Humancellmap method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.HumanPlasmaMembraneReceptome.html#pypath.core.annot.HumanPlasmaMembraneReceptome.__init__">(pypath.core.annot.HumanPlasmaMembraneReceptome method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.HumanProteinAtlas.html#pypath.core.annot.HumanProteinAtlas.__init__">(pypath.core.annot.HumanProteinAtlas method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.HumanProteinAtlasSecretome.html#pypath.core.annot.HumanProteinAtlasSecretome.__init__">(pypath.core.annot.HumanProteinAtlasSecretome method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.HumanProteinAtlasSubcellular.html#pypath.core.annot.HumanProteinAtlasSubcellular.__init__">(pypath.core.annot.HumanProteinAtlasSubcellular method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Icellnet.html#pypath.core.annot.Icellnet.__init__">(pypath.core.annot.Icellnet method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.IcellnetComplex.html#pypath.core.annot.IcellnetComplex.__init__">(pypath.core.annot.IcellnetComplex method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Integrins.html#pypath.core.annot.Integrins.__init__">(pypath.core.annot.Integrins method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.InterPro.html#pypath.core.annot.InterPro.__init__">(pypath.core.annot.InterPro method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Intogen.html#pypath.core.annot.Intogen.__init__">(pypath.core.annot.Intogen method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Italk.html#pypath.core.annot.Italk.__init__">(pypath.core.annot.Italk method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.KeggPathways.html#pypath.core.annot.KeggPathways.__init__">(pypath.core.annot.KeggPathways method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.KeggPathwaysPC.html#pypath.core.annot.KeggPathwaysPC.__init__">(pypath.core.annot.KeggPathwaysPC method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Kinasedotcom.html#pypath.core.annot.Kinasedotcom.__init__">(pypath.core.annot.Kinasedotcom method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Kirouac2010.html#pypath.core.annot.Kirouac2010.__init__">(pypath.core.annot.Kirouac2010 method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Lambert2018.html#pypath.core.annot.Lambert2018.__init__">(pypath.core.annot.Lambert2018 method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.LigandReceptor.html#pypath.core.annot.LigandReceptor.__init__">(pypath.core.annot.LigandReceptor method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Locate.html#pypath.core.annot.Locate.__init__">(pypath.core.annot.Locate method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Lrdb.html#pypath.core.annot.Lrdb.__init__">(pypath.core.annot.Lrdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Matrisome.html#pypath.core.annot.Matrisome.__init__">(pypath.core.annot.Matrisome method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Matrixdb.html#pypath.core.annot.Matrixdb.__init__">(pypath.core.annot.Matrixdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Mcam.html#pypath.core.annot.Mcam.__init__">(pypath.core.annot.Mcam method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Membranome.html#pypath.core.annot.Membranome.__init__">(pypath.core.annot.Membranome method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Msigdb.html#pypath.core.annot.Msigdb.__init__">(pypath.core.annot.Msigdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.NetpathPathways.html#pypath.core.annot.NetpathPathways.__init__">(pypath.core.annot.NetpathPathways method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Opm.html#pypath.core.annot.Opm.__init__">(pypath.core.annot.Opm method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Panglaodb.html#pypath.core.annot.Panglaodb.__init__">(pypath.core.annot.Panglaodb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Phobius.html#pypath.core.annot.Phobius.__init__">(pypath.core.annot.Phobius method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Phosphatome.html#pypath.core.annot.Phosphatome.__init__">(pypath.core.annot.Phosphatome method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Progeny.html#pypath.core.annot.Progeny.__init__">(pypath.core.annot.Progeny method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Ramilowski2015.html#pypath.core.annot.Ramilowski2015.__init__">(pypath.core.annot.Ramilowski2015 method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Ramilowski2015Location.html#pypath.core.annot.Ramilowski2015Location.__init__">(pypath.core.annot.Ramilowski2015Location method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Scconnect.html#pypath.core.annot.Scconnect.__init__">(pypath.core.annot.Scconnect method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.ScconnectComplex.html#pypath.core.annot.ScconnectComplex.__init__">(pypath.core.annot.ScconnectComplex method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.SignalinkFunctions.html#pypath.core.annot.SignalinkFunctions.__init__">(pypath.core.annot.SignalinkFunctions method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.SignalinkPathways.html#pypath.core.annot.SignalinkPathways.__init__">(pypath.core.annot.SignalinkPathways method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.SignorPathways.html#pypath.core.annot.SignorPathways.__init__">(pypath.core.annot.SignorPathways method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Surfaceome.html#pypath.core.annot.Surfaceome.__init__">(pypath.core.annot.Surfaceome method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Talklr.html#pypath.core.annot.Talklr.__init__">(pypath.core.annot.Talklr method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Tcdb.html#pypath.core.annot.Tcdb.__init__">(pypath.core.annot.Tcdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Tfcensus.html#pypath.core.annot.Tfcensus.__init__">(pypath.core.annot.Tfcensus method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Topdb.html#pypath.core.annot.Topdb.__init__">(pypath.core.annot.Topdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.UniprotFamilies.html#pypath.core.annot.UniprotFamilies.__init__">(pypath.core.annot.UniprotFamilies method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.UniprotKeywords.html#pypath.core.annot.UniprotKeywords.__init__">(pypath.core.annot.UniprotKeywords method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.UniprotLocations.html#pypath.core.annot.UniprotLocations.__init__">(pypath.core.annot.UniprotLocations method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.UniprotTissues.html#pypath.core.annot.UniprotTissues.__init__">(pypath.core.annot.UniprotTissues method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.UniprotTopologies.html#pypath.core.annot.UniprotTopologies.__init__">(pypath.core.annot.UniprotTopologies method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Vesiclepedia.html#pypath.core.annot.Vesiclepedia.__init__">(pypath.core.annot.Vesiclepedia method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Wang.html#pypath.core.annot.Wang.__init__">(pypath.core.annot.Wang method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Zhong2015.html#pypath.core.annot.Zhong2015.__init__">(pypath.core.annot.Zhong2015 method)</a>
+</li>
+        <li><a href="api/pypath.core.attrs.AttributeHandler.html#pypath.core.attrs.AttributeHandler.__init__">(pypath.core.attrs.AttributeHandler method)</a>
+</li>
+        <li><a href="api/pypath.core.complex.AbstractComplexResource.html#pypath.core.complex.AbstractComplexResource.__init__">(pypath.core.complex.AbstractComplexResource method)</a>
+</li>
+        <li><a href="api/pypath.core.complex.Cellchatdb.html#pypath.core.complex.Cellchatdb.__init__">(pypath.core.complex.Cellchatdb method)</a>
+</li>
+        <li><a href="api/pypath.core.complex.Cellinker.html#pypath.core.complex.Cellinker.__init__">(pypath.core.complex.Cellinker method)</a>
+</li>
+        <li><a href="api/pypath.core.complex.CellPhoneDB.html#pypath.core.complex.CellPhoneDB.__init__">(pypath.core.complex.CellPhoneDB method)</a>
+</li>
+        <li><a href="api/pypath.core.complex.Compleat.html#pypath.core.complex.Compleat.__init__">(pypath.core.complex.Compleat method)</a>
+</li>
+        <li><a href="api/pypath.core.complex.ComplexAggregator.html#pypath.core.complex.ComplexAggregator.__init__">(pypath.core.complex.ComplexAggregator method)</a>
+</li>
+        <li><a href="api/pypath.core.complex.ComplexPortal.html#pypath.core.complex.ComplexPortal.__init__">(pypath.core.complex.ComplexPortal method)</a>
+</li>
+        <li><a href="api/pypath.core.complex.Corum.html#pypath.core.complex.Corum.__init__">(pypath.core.complex.Corum method)</a>
+</li>
+        <li><a href="api/pypath.core.complex.GuideToPharmacology.html#pypath.core.complex.GuideToPharmacology.__init__">(pypath.core.complex.GuideToPharmacology method)</a>
+</li>
+        <li><a href="api/pypath.core.complex.Havugimana.html#pypath.core.complex.Havugimana.__init__">(pypath.core.complex.Havugimana method)</a>
+</li>
+        <li><a href="api/pypath.core.complex.Hpmr.html#pypath.core.complex.Hpmr.__init__">(pypath.core.complex.Hpmr method)</a>
+</li>
+        <li><a href="api/pypath.core.complex.Humap.html#pypath.core.complex.Humap.__init__">(pypath.core.complex.Humap method)</a>
+</li>
+        <li><a href="api/pypath.core.complex.Humap2.html#pypath.core.complex.Humap2.__init__">(pypath.core.complex.Humap2 method)</a>
+</li>
+        <li><a href="api/pypath.core.complex.Icellnet.html#pypath.core.complex.Icellnet.__init__">(pypath.core.complex.Icellnet method)</a>
+</li>
+        <li><a href="api/pypath.core.complex.Kegg.html#pypath.core.complex.Kegg.__init__">(pypath.core.complex.Kegg method)</a>
+</li>
+        <li><a href="api/pypath.core.complex.Pdb.html#pypath.core.complex.Pdb.__init__">(pypath.core.complex.Pdb method)</a>
+</li>
+        <li><a href="api/pypath.core.complex.Signor.html#pypath.core.complex.Signor.__init__">(pypath.core.complex.Signor method)</a>
+</li>
+        <li><a href="api/pypath.core.complex.Spike.html#pypath.core.complex.Spike.__init__">(pypath.core.complex.Spike method)</a>
+</li>
+        <li><a href="api/pypath.core.entity.Entity.html#pypath.core.entity.Entity.__init__">(pypath.core.entity.Entity method)</a>
+</li>
+        <li><a href="api/pypath.core.entity.EntityKey.html#pypath.core.entity.EntityKey.__init__">(pypath.core.entity.EntityKey method)</a>
+</li>
+        <li><a href="api/pypath.core.entity.EntityList.html#pypath.core.entity.EntityList.__init__">(pypath.core.entity.EntityList method)</a>
+</li>
+        <li><a href="api/pypath.core.enz_sub.EnzymeSubstrateAggregator.html#pypath.core.enz_sub.EnzymeSubstrateAggregator.__init__">(pypath.core.enz_sub.EnzymeSubstrateAggregator method)</a>
+</li>
+        <li><a href="api/pypath.core.enz_sub.EnzymeSubstrateOrthologyProcessor.html#pypath.core.enz_sub.EnzymeSubstrateOrthologyProcessor.__init__">(pypath.core.enz_sub.EnzymeSubstrateOrthologyProcessor method)</a>
+</li>
+        <li><a href="api/pypath.core.enz_sub.EnzymeSubstrateProcessor.html#pypath.core.enz_sub.EnzymeSubstrateProcessor.__init__">(pypath.core.enz_sub.EnzymeSubstrateProcessor method)</a>
+</li>
+        <li><a href="api/pypath.core.evidence.Evidence.html#pypath.core.evidence.Evidence.__init__">(pypath.core.evidence.Evidence method)</a>
+</li>
+        <li><a href="api/pypath.core.evidence.Evidences.html#pypath.core.evidence.Evidences.__init__">(pypath.core.evidence.Evidences method)</a>
+</li>
+        <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.__init__">(pypath.core.interaction.Interaction method)</a>
+</li>
+        <li><a href="api/pypath.core.interaction.InteractionDataFrameRecord.html#pypath.core.interaction.InteractionDataFrameRecord.__init__">(pypath.core.interaction.InteractionDataFrameRecord method)</a>
+</li>
+        <li><a href="api/pypath.core.interaction.InteractionKey.html#pypath.core.interaction.InteractionKey.__init__">(pypath.core.interaction.InteractionKey method)</a>
+</li>
+        <li><a href="api/pypath.core.intercell.IntercellAnnotation.html#pypath.core.intercell.IntercellAnnotation.__init__">(pypath.core.intercell.IntercellAnnotation method)</a>
+</li>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.__init__">(pypath.core.network.Network method)</a>
+</li>
+        <li><a href="api/pypath.core.network.NetworkEntityCollection.html#pypath.core.network.NetworkEntityCollection.__init__">(pypath.core.network.NetworkEntityCollection method)</a>
+</li>
+        <li><a href="api/pypath.core.network.NetworkStatsRecord.html#pypath.core.network.NetworkStatsRecord.__init__">(pypath.core.network.NetworkStatsRecord method)</a>
+</li>
         <li><a href="api/pypath.inputs.adrecs.AdrecsAdr.html#pypath.inputs.adrecs.AdrecsAdr.__init__">(pypath.inputs.adrecs.AdrecsAdr method)</a>
 </li>
         <li><a href="api/pypath.inputs.adrecs.AdrecsChildParent.html#pypath.inputs.adrecs.AdrecsChildParent.__init__">(pypath.inputs.adrecs.AdrecsChildParent method)</a>
@@ -512,18 +761,40 @@ <h2 id="_">_</h2>
         <li><a href="api/pypath.inputs.adrecs.AdrecsDrugAdr.html#pypath.inputs.adrecs.AdrecsDrugAdr.__init__">(pypath.inputs.adrecs.AdrecsDrugAdr method)</a>
 </li>
         <li><a href="api/pypath.inputs.adrecs.AdrecsTerm.html#pypath.inputs.adrecs.AdrecsTerm.__init__">(pypath.inputs.adrecs.AdrecsTerm method)</a>
+</li>
+        <li><a href="api/pypath.inputs.biogps.BiogpsDataset.html#pypath.inputs.biogps.BiogpsDataset.__init__">(pypath.inputs.biogps.BiogpsDataset method)</a>
+</li>
+        <li><a href="api/pypath.inputs.cellinker.CellinkerInteraction.html#pypath.inputs.cellinker.CellinkerInteraction.__init__">(pypath.inputs.cellinker.CellinkerInteraction method)</a>
+</li>
+        <li><a href="api/pypath.inputs.cellphonedb.CellPhoneDBAnnotation.html#pypath.inputs.cellphonedb.CellPhoneDBAnnotation.__init__">(pypath.inputs.cellphonedb.CellPhoneDBAnnotation method)</a>
 </li>
         <li><a href="api/pypath.inputs.dorothea.DorotheaInteraction.html#pypath.inputs.dorothea.DorotheaInteraction.__init__">(pypath.inputs.dorothea.DorotheaInteraction method)</a>
 </li>
         <li><a href="api/pypath.inputs.drugbank.DrugbankFull.html#pypath.inputs.drugbank.DrugbankFull.__init__">(pypath.inputs.drugbank.DrugbankFull method)</a>
+</li>
+        <li><a href="api/pypath.inputs.gutmgene.GutmgeneAnnotation.html#pypath.inputs.gutmgene.GutmgeneAnnotation.__init__">(pypath.inputs.gutmgene.GutmgeneAnnotation method)</a>
+</li>
+        <li><a href="api/pypath.inputs.gutmgene.GutmgeneRaw.html#pypath.inputs.gutmgene.GutmgeneRaw.__init__">(pypath.inputs.gutmgene.GutmgeneRaw method)</a>
 </li>
         <li><a href="api/pypath.inputs.hmdb.schema.common.Field.html#pypath.inputs.hmdb.schema.common.Field.__init__">(pypath.inputs.hmdb.schema.common.Field method)</a>
+</li>
+        <li><a href="api/pypath.inputs.hpmr.HpmrInteraction.html#pypath.inputs.hpmr.HpmrInteraction.__init__">(pypath.inputs.hpmr.HpmrInteraction method)</a>
+</li>
+        <li><a href="api/pypath.inputs.icellnet.IcellnetRecord.html#pypath.inputs.icellnet.IcellnetRecord.__init__">(pypath.inputs.icellnet.IcellnetRecord method)</a>
+</li>
+        <li><a href="api/pypath.inputs.iptmnet.IptmnetInteraction.html#pypath.inputs.iptmnet.IptmnetInteraction.__init__">(pypath.inputs.iptmnet.IptmnetInteraction method)</a>
+</li>
+        <li><a href="api/pypath.inputs.kegg.KeggPathway.html#pypath.inputs.kegg.KeggPathway.__init__">(pypath.inputs.kegg.KeggPathway method)</a>
+</li>
+        <li><a href="api/pypath.inputs.lrdb.LrdbAnnotation.html#pypath.inputs.lrdb.LrdbAnnotation.__init__">(pypath.inputs.lrdb.LrdbAnnotation method)</a>
 </li>
         <li><a href="api/pypath.inputs.pathophenodb.DiseasePathogen.html#pypath.inputs.pathophenodb.DiseasePathogen.__init__">(pypath.inputs.pathophenodb.DiseasePathogen method)</a>
 </li>
         <li><a href="api/pypath.inputs.pathwaycommons.PathwayCommonsInteraction.html#pypath.inputs.pathwaycommons.PathwayCommonsInteraction.__init__">(pypath.inputs.pathwaycommons.PathwayCommonsInteraction method)</a>
 </li>
         <li><a href="api/pypath.inputs.pathwaycommons.PathwayCommonsResource.html#pypath.inputs.pathwaycommons.PathwayCommonsResource.__init__">(pypath.inputs.pathwaycommons.PathwayCommonsResource method)</a>
+</li>
+        <li><a href="api/pypath.inputs.pisa.PisaBond.html#pypath.inputs.pisa.PisaBond.__init__">(pypath.inputs.pisa.PisaBond method)</a>
 </li>
         <li><a href="api/pypath.inputs.sider.SiderDrug.html#pypath.inputs.sider.SiderDrug.__init__">(pypath.inputs.sider.SiderDrug method)</a>
 </li>
@@ -538,6 +809,14 @@ <h2 id="_">_</h2>
         <li><a href="api/pypath.inputs.uniprot.UniprotQuery.html#pypath.inputs.uniprot.UniprotQuery.__init__">(pypath.inputs.uniprot.UniprotQuery method)</a>
 </li>
         <li><a href="api/pypath.inputs.uniprot.UniprotRecordHistory.html#pypath.inputs.uniprot.UniprotRecordHistory.__init__">(pypath.inputs.uniprot.UniprotRecordHistory method)</a>
+</li>
+        <li><a href="api/pypath.internals.annot_formats.AnnotationGroup.html#pypath.internals.annot_formats.AnnotationGroup.__init__">(pypath.internals.annot_formats.AnnotationGroup method)</a>
+</li>
+        <li><a href="api/pypath.internals.annot_formats.AnnotDef.html#pypath.internals.annot_formats.AnnotDef.__init__">(pypath.internals.annot_formats.AnnotDef method)</a>
+</li>
+        <li><a href="api/pypath.internals.annot_formats.AnnotDefKey.html#pypath.internals.annot_formats.AnnotDefKey.__init__">(pypath.internals.annot_formats.AnnotDefKey method)</a>
+</li>
+        <li><a href="api/pypath.internals.annot_formats.AnnotOp.html#pypath.internals.annot_formats.AnnotOp.__init__">(pypath.internals.annot_formats.AnnotOp method)</a>
 </li>
         <li><a href="api/pypath.internals.input_formats.ArrayMapping.html#pypath.internals.input_formats.ArrayMapping.__init__">(pypath.internals.input_formats.ArrayMapping method)</a>
 </li>
@@ -564,6 +843,24 @@ <h2 id="_">_</h2>
         <li><a href="api/pypath.internals.input_formats.UniprotListMapping.html#pypath.internals.input_formats.UniprotListMapping.__init__">(pypath.internals.input_formats.UniprotListMapping method)</a>
 </li>
         <li><a href="api/pypath.internals.input_formats.UniprotMapping.html#pypath.internals.input_formats.UniprotMapping.__init__">(pypath.internals.input_formats.UniprotMapping method)</a>
+</li>
+        <li><a href="api/pypath.internals.intera.Complex.html#pypath.internals.intera.Complex.__init__">(pypath.internals.intera.Complex method)</a>
+</li>
+        <li><a href="api/pypath.internals.intera.Domain.html#pypath.internals.intera.Domain.__init__">(pypath.internals.intera.Domain method)</a>
+</li>
+        <li><a href="api/pypath.internals.intera.DomainDomain.html#pypath.internals.intera.DomainDomain.__init__">(pypath.internals.intera.DomainDomain method)</a>
+</li>
+        <li><a href="api/pypath.internals.intera.DomainMotif.html#pypath.internals.intera.DomainMotif.__init__">(pypath.internals.intera.DomainMotif method)</a>
+</li>
+        <li><a href="api/pypath.internals.intera.Interface.html#pypath.internals.intera.Interface.__init__">(pypath.internals.intera.Interface method)</a>
+</li>
+        <li><a href="api/pypath.internals.intera.Motif.html#pypath.internals.intera.Motif.__init__">(pypath.internals.intera.Motif method)</a>
+</li>
+        <li><a href="api/pypath.internals.intera.Ptm.html#pypath.internals.intera.Ptm.__init__">(pypath.internals.intera.Ptm method)</a>
+</li>
+        <li><a href="api/pypath.internals.intera.Regulation.html#pypath.internals.intera.Regulation.__init__">(pypath.internals.intera.Regulation method)</a>
+</li>
+        <li><a href="api/pypath.internals.intera.Residue.html#pypath.internals.intera.Residue.__init__">(pypath.internals.intera.Residue method)</a>
 </li>
         <li><a href="api/pypath.internals.license.License.html#pypath.internals.license.License.__init__">(pypath.internals.license.License method)</a>
 </li>
@@ -590,6 +887,30 @@ <h2 id="_">_</h2>
         <li><a href="api/pypath.internals.resource.NetworkResourceKey.html#pypath.internals.resource.NetworkResourceKey.__init__">(pypath.internals.resource.NetworkResourceKey method)</a>
 </li>
         <li><a href="api/pypath.internals.resource.ResourceAttributes.html#pypath.internals.resource.ResourceAttributes.__init__">(pypath.internals.resource.ResourceAttributes method)</a>
+</li>
+        <li><a href="api/pypath.omnipath.app.DatabaseManager.html#pypath.omnipath.app.DatabaseManager.__init__">(pypath.omnipath.app.DatabaseManager method)</a>
+</li>
+        <li><a href="api/pypath.omnipath.databases.define.DatabaseClass.html#pypath.omnipath.databases.define.DatabaseClass.__init__">(pypath.omnipath.databases.define.DatabaseClass method)</a>
+</li>
+        <li><a href="api/pypath.omnipath.databases.define.DatabaseDefinition.html#pypath.omnipath.databases.define.DatabaseDefinition.__init__">(pypath.omnipath.databases.define.DatabaseDefinition method)</a>
+</li>
+        <li><a href="api/pypath.omnipath.databases.define.DatabaseDefinitionManager.html#pypath.omnipath.databases.define.DatabaseDefinitionManager.__init__">(pypath.omnipath.databases.define.DatabaseDefinitionManager method)</a>
+</li>
+        <li><a href="api/pypath.omnipath.export.Export.html#pypath.omnipath.export.Export.__init__">(pypath.omnipath.export.Export method)</a>
+</li>
+        <li><a href="api/pypath.omnipath.server.build.WebserviceTables.html#pypath.omnipath.server.build.WebserviceTables.__init__">(pypath.omnipath.server.build.WebserviceTables method)</a>
+</li>
+        <li><a href="api/pypath.omnipath.server.legacy.PypathServer.html#pypath.omnipath.server.legacy.PypathServer.__init__">(pypath.omnipath.server.legacy.PypathServer method)</a>
+</li>
+        <li><a href="api/pypath.omnipath.server.run.BaseServer.html#pypath.omnipath.server.run.BaseServer.__init__">(pypath.omnipath.server.run.BaseServer method)</a>
+</li>
+        <li><a href="api/pypath.omnipath.server.run.Rest.html#pypath.omnipath.server.run.Rest.__init__">(pypath.omnipath.server.run.Rest method)</a>
+</li>
+        <li><a href="api/pypath.omnipath.server.run.TableServer.html#pypath.omnipath.server.run.TableServer.__init__">(pypath.omnipath.server.run.TableServer method)</a>
+</li>
+        <li><a href="api/pypath.omnipath.server.run.TwistedWebResource.html#pypath.omnipath.server.run.TwistedWebResource.__init__">(pypath.omnipath.server.run.TwistedWebResource method)</a>
+</li>
+        <li><a href="api/pypath.omnipath.server.run.TwistedWebSite.html#pypath.omnipath.server.run.TwistedWebSite.__init__">(pypath.omnipath.server.run.TwistedWebSite method)</a>
 </li>
         <li><a href="api/pypath.resources.controller.ResourceController.html#pypath.resources.controller.ResourceController.__init__">(pypath.resources.controller.ResourceController method)</a>
 </li>
@@ -632,6 +953,42 @@ <h2 id="_">_</h2>
         <li><a href="api/pypath.utils.go.GOAnnotation.html#pypath.utils.go.GOAnnotation.__init__">(pypath.utils.go.GOAnnotation method)</a>
 </li>
         <li><a href="api/pypath.utils.go.GOCustomAnnotation.html#pypath.utils.go.GOCustomAnnotation.__init__">(pypath.utils.go.GOCustomAnnotation method)</a>
+</li>
+        <li><a href="api/pypath.utils.mapping.Mapper.html#pypath.utils.mapping.Mapper.__init__">(pypath.utils.mapping.Mapper method)</a>
+</li>
+        <li><a href="api/pypath.utils.mapping.MappingTable.html#pypath.utils.mapping.MappingTable.__init__">(pypath.utils.mapping.MappingTable method)</a>
+</li>
+        <li><a href="api/pypath.utils.mapping.MappingTableKey.html#pypath.utils.mapping.MappingTableKey.__init__">(pypath.utils.mapping.MappingTableKey method)</a>
+</li>
+        <li><a href="api/pypath.utils.mapping.MapReader.html#pypath.utils.mapping.MapReader.__init__">(pypath.utils.mapping.MapReader method)</a>
+</li>
+        <li><a href="api/pypath.utils.orthology.EnsemblOrtholog.html#pypath.utils.orthology.EnsemblOrtholog.__init__">(pypath.utils.orthology.EnsemblOrtholog method)</a>
+</li>
+        <li><a href="api/pypath.utils.orthology.EnsemblOrthology.html#pypath.utils.orthology.EnsemblOrthology.__init__">(pypath.utils.orthology.EnsemblOrthology method)</a>
+</li>
+        <li><a href="api/pypath.utils.orthology.HomologeneOrtholog.html#pypath.utils.orthology.HomologeneOrtholog.__init__">(pypath.utils.orthology.HomologeneOrtholog method)</a>
+</li>
+        <li><a href="api/pypath.utils.orthology.HomologeneOrthology.html#pypath.utils.orthology.HomologeneOrthology.__init__">(pypath.utils.orthology.HomologeneOrthology method)</a>
+</li>
+        <li><a href="api/pypath.utils.orthology.OmaOrtholog.html#pypath.utils.orthology.OmaOrtholog.__init__">(pypath.utils.orthology.OmaOrtholog method)</a>
+</li>
+        <li><a href="api/pypath.utils.orthology.OmaOrthology.html#pypath.utils.orthology.OmaOrthology.__init__">(pypath.utils.orthology.OmaOrthology method)</a>
+</li>
+        <li><a href="api/pypath.utils.orthology.OrthologBase.html#pypath.utils.orthology.OrthologBase.__init__">(pypath.utils.orthology.OrthologBase method)</a>
+</li>
+        <li><a href="api/pypath.utils.orthology.OrthologMeta.html#pypath.utils.orthology.OrthologMeta.__init__">(pypath.utils.orthology.OrthologMeta method)</a>
+</li>
+        <li><a href="api/pypath.utils.orthology.OrthologyManager.html#pypath.utils.orthology.OrthologyManager.__init__">(pypath.utils.orthology.OrthologyManager method)</a>
+</li>
+        <li><a href="api/pypath.utils.orthology.OrthologyTableKey.html#pypath.utils.orthology.OrthologyTableKey.__init__">(pypath.utils.orthology.OrthologyTableKey method)</a>
+</li>
+        <li><a href="api/pypath.utils.orthology.ProteinOrthology.html#pypath.utils.orthology.ProteinOrthology.__init__">(pypath.utils.orthology.ProteinOrthology method)</a>
+</li>
+        <li><a href="api/pypath.utils.orthology.Proteomes.html#pypath.utils.orthology.Proteomes.__init__">(pypath.utils.orthology.Proteomes method)</a>
+</li>
+        <li><a href="api/pypath.utils.orthology.PtmOrthology.html#pypath.utils.orthology.PtmOrthology.__init__">(pypath.utils.orthology.PtmOrthology method)</a>
+</li>
+        <li><a href="api/pypath.utils.orthology.SequenceContainer.html#pypath.utils.orthology.SequenceContainer.__init__">(pypath.utils.orthology.SequenceContainer method)</a>
 </li>
         <li><a href="api/pypath.utils.pdb.Residue.html#pypath.utils.pdb.Residue.__init__">(pypath.utils.pdb.Residue method)</a>
 </li>
@@ -640,6 +997,34 @@ <h2 id="_">_</h2>
         <li><a href="api/pypath.utils.pdb.Segment.html#pypath.utils.pdb.Segment.__init__">(pypath.utils.pdb.Segment method)</a>
 </li>
         <li><a href="api/pypath.utils.proteomicsdb.ProteomicsDB.html#pypath.utils.proteomicsdb.ProteomicsDB.__init__">(pypath.utils.proteomicsdb.ProteomicsDB method)</a>
+</li>
+        <li><a href="api/pypath.utils.pyreact.AttributeHandler.html#pypath.utils.pyreact.AttributeHandler.__init__">(pypath.utils.pyreact.AttributeHandler method)</a>
+</li>
+        <li><a href="api/pypath.utils.pyreact.BioPaxReader.html#pypath.utils.pyreact.BioPaxReader.__init__">(pypath.utils.pyreact.BioPaxReader method)</a>
+</li>
+        <li><a href="api/pypath.utils.pyreact.Complex.html#pypath.utils.pyreact.Complex.__init__">(pypath.utils.pyreact.Complex method)</a>
+</li>
+        <li><a href="api/pypath.utils.pyreact.ComplexVariations.html#pypath.utils.pyreact.ComplexVariations.__init__">(pypath.utils.pyreact.ComplexVariations method)</a>
+</li>
+        <li><a href="api/pypath.utils.pyreact.Control.html#pypath.utils.pyreact.Control.__init__">(pypath.utils.pyreact.Control method)</a>
+</li>
+        <li><a href="api/pypath.utils.pyreact.Entity.html#pypath.utils.pyreact.Entity.__init__">(pypath.utils.pyreact.Entity method)</a>
+</li>
+        <li><a href="api/pypath.utils.pyreact.EntitySet.html#pypath.utils.pyreact.EntitySet.__init__">(pypath.utils.pyreact.EntitySet method)</a>
+</li>
+        <li><a href="api/pypath.utils.pyreact.Intersecting.html#pypath.utils.pyreact.Intersecting.__init__">(pypath.utils.pyreact.Intersecting method)</a>
+</li>
+        <li><a href="api/pypath.utils.pyreact.Protein.html#pypath.utils.pyreact.Protein.__init__">(pypath.utils.pyreact.Protein method)</a>
+</li>
+        <li><a href="api/pypath.utils.pyreact.ProteinFamily.html#pypath.utils.pyreact.ProteinFamily.__init__">(pypath.utils.pyreact.ProteinFamily method)</a>
+</li>
+        <li><a href="api/pypath.utils.pyreact.PyReact.html#pypath.utils.pyreact.PyReact.__init__">(pypath.utils.pyreact.PyReact method)</a>
+</li>
+        <li><a href="api/pypath.utils.pyreact.Reaction.html#pypath.utils.pyreact.Reaction.__init__">(pypath.utils.pyreact.Reaction method)</a>
+</li>
+        <li><a href="api/pypath.utils.pyreact.ReactionSide.html#pypath.utils.pyreact.ReactionSide.__init__">(pypath.utils.pyreact.ReactionSide method)</a>
+</li>
+        <li><a href="api/pypath.utils.pyreact.Reference.html#pypath.utils.pyreact.Reference.__init__">(pypath.utils.pyreact.Reference method)</a>
 </li>
         <li><a href="api/pypath.utils.reflists.ReferenceListManager.html#pypath.utils.reflists.ReferenceListManager.__init__">(pypath.utils.reflists.ReferenceListManager method)</a>
 </li>
@@ -652,6 +1037,8 @@ <h2 id="_">_</h2>
         <li><a href="api/pypath.utils.seq.Seq.html#pypath.utils.seq.Seq.__init__">(pypath.utils.seq.Seq method)</a>
 </li>
         <li><a href="api/pypath.utils.unichem.Unichem.html#pypath.utils.unichem.Unichem.__init__">(pypath.utils.unichem.Unichem method)</a>
+</li>
+        <li><a href="api/pypath.utils.uniprot.UniprotProtein.html#pypath.utils.uniprot.UniprotProtein.__init__">(pypath.utils.uniprot.UniprotProtein method)</a>
 </li>
         <li><a href="api/pypath.visual.drawing.InterSet.html#pypath.visual.drawing.InterSet.__init__">(pypath.visual.drawing.InterSet method)</a>
 </li>
@@ -701,6 +1088,8 @@ <h2 id="A">A</h2>
       <li><a href="api/pypath.visual.igraph_drawing.AbstractCairoGraphDrawer.html#pypath.visual.igraph_drawing.AbstractCairoGraphDrawer">AbstractCairoGraphDrawer (class in pypath.visual.igraph_drawing)</a>
 </li>
       <li><a href="api/pypath.visual.igraph_drawing.vertex.AbstractCairoVertexDrawer.html#pypath.visual.igraph_drawing.vertex.AbstractCairoVertexDrawer">AbstractCairoVertexDrawer (class in pypath.visual.igraph_drawing.vertex)</a>
+</li>
+      <li><a href="api/pypath.core.complex.AbstractComplexResource.html#pypath.core.complex.AbstractComplexResource">AbstractComplexResource (class in pypath.core.complex)</a>
 </li>
       <li><a href="api/pypath.visual.igraph_drawing.vertex.AbstractDrawer.html#pypath.visual.igraph_drawing.vertex.AbstractDrawer">AbstractDrawer (class in pypath.visual.igraph_drawing.vertex)</a>
 </li>
@@ -709,6 +1098,8 @@ <h2 id="A">A</h2>
       <li><a href="api/pypath.internals.resource.AbstractResource.html#pypath.internals.resource.AbstractResource">AbstractResource (class in pypath.internals.resource)</a>
 </li>
       <li><a href="api/pypath.visual.igraph_drawing.vertex.AbstractVertexDrawer.html#pypath.visual.igraph_drawing.vertex.AbstractVertexDrawer">AbstractVertexDrawer (class in pypath.visual.igraph_drawing.vertex)</a>
+</li>
+      <li><a href="api/pypath.utils.uniprot.ac.html#pypath.utils.uniprot.ac">ac() (in module pypath.utils.uniprot)</a>
 </li>
       <li><a href="api/pypath.inputs.reaction.acsn_biopax.html#pypath.inputs.reaction.acsn_biopax">acsn_biopax() (in module pypath.inputs.reaction)</a>
 </li>
@@ -717,3105 +1108,15233 @@ <h2 id="A">A</h2>
       <li><a href="api/pypath.inputs.reaction.acsn_interactions_2.html#pypath.inputs.reaction.acsn_interactions_2">acsn_interactions_2() (in module pypath.inputs.reaction)</a>
 </li>
       <li><a href="api/pypath.inputs.acsn.acsn_interactions_sif.html#pypath.inputs.acsn.acsn_interactions_sif">acsn_interactions_sif() (in module pypath.inputs.acsn)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.activated_by">activated_by (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.activates">activates (pypath.core.network.Network attribute)</a>
 </li>
       <li><a href="api/pypath.resources.data_formats.activity_flow.html#pypath.resources.data_formats.activity_flow">activity_flow (in module pypath.resources.data_formats)</a>
 </li>
-      <li><a href="api/pypath.resources.controller.ResourceController.html#pypath.resources.controller.ResourceController.add_resource_attrs">add_resource_attrs() (pypath.resources.controller.ResourceController method)</a>
+      <li><a href="api/pypath.utils.uniprot.activity_regulation.html#pypath.utils.uniprot.activity_regulation">activity_regulation() (in module pypath.utils.uniprot)</a>
 </li>
-      <li><a href="api/pypath.inputs.adrecs.AdrecsDrugAdr.html#pypath.inputs.adrecs.AdrecsDrugAdr.adr">adr (pypath.inputs.adrecs.AdrecsDrugAdr attribute)</a>
+      <li><a href="api/pypath.utils.uniprot.activity_regulation_with_xrefs.html#pypath.utils.uniprot.activity_regulation_with_xrefs">activity_regulation_with_xrefs() (in module pypath.utils.uniprot)</a>
 </li>
-      <li><a href="api/pypath.inputs.adrecs.AdrecsDrugAdr.html#pypath.inputs.adrecs.AdrecsDrugAdr.adr_badd">adr_badd (pypath.inputs.adrecs.AdrecsDrugAdr attribute)</a>
+      <li><a href="api/pypath.internals.intera.Complex.html#pypath.internals.intera.Complex.add_attr">add_attr() (pypath.internals.intera.Complex method)</a>
 </li>
-      <li><a href="api/pypath.inputs.adrecs.AdrecsAdr.html#pypath.inputs.adrecs.AdrecsAdr.adr_class">adr_class (pypath.inputs.adrecs.AdrecsAdr attribute)</a>
+      <li><a href="api/pypath.core.annot.Adhesome.html#pypath.core.annot.Adhesome.add_complexes_by_inference">add_complexes_by_inference() (pypath.core.annot.Adhesome method)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.annot.Almen2009.html#pypath.core.annot.Almen2009.add_complexes_by_inference">(pypath.core.annot.Almen2009 method)</a>
 </li>
-      <li><a href="api/pypath.inputs.adrecs.adrecs_adr_ontology.html#pypath.inputs.adrecs.adrecs_adr_ontology">adrecs_adr_ontology() (in module pypath.inputs.adrecs)</a>
+        <li><a href="api/pypath.core.annot.AnnotationBase.html#pypath.core.annot.AnnotationBase.add_complexes_by_inference">(pypath.core.annot.AnnotationBase method)</a>
 </li>
-      <li><a href="api/pypath.inputs.adrecs.AdrecsTerm.html#pypath.inputs.adrecs.AdrecsTerm.adrecs_class">adrecs_class (pypath.inputs.adrecs.AdrecsTerm attribute)</a>
+        <li><a href="api/pypath.core.annot.Baccin2019.html#pypath.core.annot.Baccin2019.add_complexes_by_inference">(pypath.core.annot.Baccin2019 method)</a>
 </li>
-      <li><a href="api/pypath.inputs.adrecs.adrecs_drug_adr.html#pypath.inputs.adrecs.adrecs_drug_adr">adrecs_drug_adr() (in module pypath.inputs.adrecs)</a>
+        <li><a href="api/pypath.core.annot.Biogps.html#pypath.core.annot.Biogps.add_complexes_by_inference">(pypath.core.annot.Biogps method)</a>
 </li>
-      <li><a href="api/pypath.inputs.adrecs.adrecs_drug_identifiers.html#pypath.inputs.adrecs.adrecs_drug_identifiers">adrecs_drug_identifiers() (in module pypath.inputs.adrecs)</a>
+        <li><a href="api/pypath.core.annot.Cancerdrugsdb.html#pypath.core.annot.Cancerdrugsdb.add_complexes_by_inference">(pypath.core.annot.Cancerdrugsdb method)</a>
 </li>
-  </ul></td>
-  <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="api/pypath.inputs.adrecs.adrecs_hierarchy.html#pypath.inputs.adrecs.adrecs_hierarchy">adrecs_hierarchy() (in module pypath.inputs.adrecs)</a>
+        <li><a href="api/pypath.core.annot.CancerGeneCensus.html#pypath.core.annot.CancerGeneCensus.add_complexes_by_inference">(pypath.core.annot.CancerGeneCensus method)</a>
 </li>
-      <li><a href="api/pypath.inputs.adrecs.AdrecsAdr.html#pypath.inputs.adrecs.AdrecsAdr">AdrecsAdr (class in pypath.inputs.adrecs)</a>
+        <li><a href="api/pypath.core.annot.Cancersea.html#pypath.core.annot.Cancersea.add_complexes_by_inference">(pypath.core.annot.Cancersea method)</a>
 </li>
-      <li><a href="api/pypath.inputs.adrecs.AdrecsChildParent.html#pypath.inputs.adrecs.AdrecsChildParent">AdrecsChildParent (class in pypath.inputs.adrecs)</a>
+        <li><a href="api/pypath.core.annot.Cellcall.html#pypath.core.annot.Cellcall.add_complexes_by_inference">(pypath.core.annot.Cellcall method)</a>
 </li>
-      <li><a href="api/pypath.inputs.adrecs.AdrecsDrug.html#pypath.inputs.adrecs.AdrecsDrug">AdrecsDrug (class in pypath.inputs.adrecs)</a>
+        <li><a href="api/pypath.core.annot.Cellcellinteractions.html#pypath.core.annot.Cellcellinteractions.add_complexes_by_inference">(pypath.core.annot.Cellcellinteractions method)</a>
 </li>
-      <li><a href="api/pypath.inputs.adrecs.AdrecsDrugAdr.html#pypath.inputs.adrecs.AdrecsDrugAdr">AdrecsDrugAdr (class in pypath.inputs.adrecs)</a>
+        <li><a href="api/pypath.core.annot.Cellchatdb.html#pypath.core.annot.Cellchatdb.add_complexes_by_inference">(pypath.core.annot.Cellchatdb method)</a>
 </li>
-      <li><a href="api/pypath.inputs.adrecs.AdrecsTerm.html#pypath.inputs.adrecs.AdrecsTerm">AdrecsTerm (class in pypath.inputs.adrecs)</a>
+        <li><a href="api/pypath.core.annot.CellchatdbComplex.html#pypath.core.annot.CellchatdbComplex.add_complexes_by_inference">(pypath.core.annot.CellchatdbComplex method)</a>
 </li>
-      <li><a href="api/pypath.utils.go.GeneOntology.html#pypath.utils.go.GeneOntology.all_from_aspect">all_from_aspect() (pypath.utils.go.GeneOntology method)</a>
+        <li><a href="api/pypath.core.annot.Cellinker.html#pypath.core.annot.Cellinker.add_complexes_by_inference">(pypath.core.annot.Cellinker method)</a>
 </li>
-      <li><a href="api/pypath.inputs.dorothea.DorotheaInteraction.html#pypath.inputs.dorothea.DorotheaInteraction.all_sources">all_sources (pypath.inputs.dorothea.DorotheaInteraction attribute)</a>
+        <li><a href="api/pypath.core.annot.CellinkerComplex.html#pypath.core.annot.CellinkerComplex.add_complexes_by_inference">(pypath.core.annot.CellinkerComplex method)</a>
 </li>
-      <li><a href="api/pypath.inputs.uniprot_db.all_swissprots.html#pypath.inputs.uniprot_db.all_swissprots">all_swissprots() (in module pypath.inputs.uniprot_db)</a>
+        <li><a href="api/pypath.core.annot.CellPhoneDB.html#pypath.core.annot.CellPhoneDB.add_complexes_by_inference">(pypath.core.annot.CellPhoneDB method)</a>
 </li>
-      <li><a href="api/pypath.inputs.uniprot_db.all_trembls.html#pypath.inputs.uniprot_db.all_trembls">all_trembls() (in module pypath.inputs.uniprot_db)</a>
+        <li><a href="api/pypath.core.annot.CellPhoneDBComplex.html#pypath.core.annot.CellPhoneDBComplex.add_complexes_by_inference">(pypath.core.annot.CellPhoneDBComplex method)</a>
 </li>
-      <li><a href="api/pypath.inputs.uniprot_db.all_uniprots.html#pypath.inputs.uniprot_db.all_uniprots">all_uniprots() (in module pypath.inputs.uniprot_db)</a>
-
-      <ul>
-        <li><a href="api/pypath.utils.go.GOAnnotation.html#pypath.utils.go.GOAnnotation.all_uniprots">(pypath.utils.go.GOAnnotation method)</a>
+        <li><a href="api/pypath.core.annot.CellSurfaceProteinAtlas.html#pypath.core.annot.CellSurfaceProteinAtlas.add_complexes_by_inference">(pypath.core.annot.CellSurfaceProteinAtlas method)</a>
 </li>
-      </ul></li>
-      <li><a href="api/pypath.visual.igraph_drawing.edge.AlphaVaryingEdgeDrawer.html#pypath.visual.igraph_drawing.edge.AlphaVaryingEdgeDrawer">AlphaVaryingEdgeDrawer (class in pypath.visual.igraph_drawing.edge)</a>
+        <li><a href="api/pypath.core.annot.CellSurfaceProteinAtlasCellType.html#pypath.core.annot.CellSurfaceProteinAtlasCellType.add_complexes_by_inference">(pypath.core.annot.CellSurfaceProteinAtlasCellType method)</a>
 </li>
-      <li><a href="api/pypath.utils.go.annotate.html#pypath.utils.go.annotate">annotate() (in module pypath.utils.go)</a>
+        <li><a href="api/pypath.core.annot.Celltalkdb.html#pypath.core.annot.Celltalkdb.add_complexes_by_inference">(pypath.core.annot.Celltalkdb method)</a>
 </li>
-      <li><a href="api/pypath.inputs.netbiol.arn_interactions.html#pypath.inputs.netbiol.arn_interactions">arn_interactions() (in module pypath.inputs.netbiol)</a>
+        <li><a href="api/pypath.core.annot.Celltypist.html#pypath.core.annot.Celltypist.add_complexes_by_inference">(pypath.core.annot.Celltypist method)</a>
 </li>
-      <li><a href="api/pypath.internals.input_formats.ArrayMapping.html#pypath.internals.input_formats.ArrayMapping">ArrayMapping (class in pypath.internals.input_formats)</a>
+        <li><a href="api/pypath.core.annot.Comppi.html#pypath.core.annot.Comppi.add_complexes_by_inference">(pypath.core.annot.Comppi method)</a>
 </li>
-      <li><a href="api/pypath.visual.igraph_drawing.edge.ArrowEdgeDrawer.html#pypath.visual.igraph_drawing.edge.ArrowEdgeDrawer">ArrowEdgeDrawer (class in pypath.visual.igraph_drawing.edge)</a>
-
-      <ul>
-        <li><a href="api/pypath.visual.igraph_drawing.ArrowEdgeDrawer.html#pypath.visual.igraph_drawing.ArrowEdgeDrawer">(in module pypath.visual.igraph_drawing)</a>
+        <li><a href="api/pypath.core.annot.Connectomedb.html#pypath.core.annot.Connectomedb.add_complexes_by_inference">(pypath.core.annot.Connectomedb method)</a>
 </li>
-      </ul></li>
-      <li><a href="api/pypath.utils.go.GeneOntology.html#pypath.utils.go.GeneOntology.aspect_from_name">aspect_from_name() (pypath.utils.go.GeneOntology method)</a>
+        <li><a href="api/pypath.core.annot.Corum.html#pypath.core.annot.Corum.add_complexes_by_inference">(pypath.core.annot.Corum method)</a>
 </li>
-      <li><a href="api/pypath.inputs.sider.SiderDrug.html#pypath.inputs.sider.SiderDrug.atc">atc (pypath.inputs.sider.SiderDrug attribute)</a>
+        <li><a href="api/pypath.core.annot.CorumFuncat.html#pypath.core.annot.CorumFuncat.add_complexes_by_inference">(pypath.core.annot.CorumFuncat method)</a>
 </li>
-      <li><a href="api/pypath.core.attrs.AttributeHandler.html#pypath.core.attrs.AttributeHandler">AttributeHandler (class in pypath.core.attrs)</a>
+        <li><a href="api/pypath.core.annot.CorumGO.html#pypath.core.annot.CorumGO.add_complexes_by_inference">(pypath.core.annot.CorumGO method)</a>
 </li>
-  </ul></td>
-</tr></table>
-
-<h2 id="B">B</h2>
-<table style="width: 100%" class="indextable genindextable"><tr>
-  <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="api/pypath.inputs.adrecs.AdrecsAdr.html#pypath.inputs.adrecs.AdrecsAdr.badd">badd (pypath.inputs.adrecs.AdrecsAdr attribute)</a>
-
-      <ul>
-        <li><a href="api/pypath.inputs.adrecs.AdrecsDrug.html#pypath.inputs.adrecs.AdrecsDrug.badd">(pypath.inputs.adrecs.AdrecsDrug attribute)</a>
+        <li><a href="api/pypath.core.annot.Cpad.html#pypath.core.annot.Cpad.add_complexes_by_inference">(pypath.core.annot.Cpad method)</a>
 </li>
-        <li><a href="api/pypath.inputs.adrecs.AdrecsTerm.html#pypath.inputs.adrecs.AdrecsTerm.badd">(pypath.inputs.adrecs.AdrecsTerm attribute)</a>
+        <li><a href="api/pypath.core.annot.Cytosig.html#pypath.core.annot.Cytosig.add_complexes_by_inference">(pypath.core.annot.Cytosig method)</a>
 </li>
-      </ul></li>
-      <li><a href="api/pypath.inputs.biogrid.biogrid_all_interactions.html#pypath.inputs.biogrid.biogrid_all_interactions">biogrid_all_interactions() (in module pypath.inputs.biogrid)</a>
+        <li><a href="api/pypath.core.annot.Dgidb.html#pypath.core.annot.Dgidb.add_complexes_by_inference">(pypath.core.annot.Dgidb method)</a>
 </li>
-      <li><a href="api/pypath.inputs.biogrid.biogrid_interactions.html#pypath.inputs.biogrid.biogrid_interactions">biogrid_interactions() (in module pypath.inputs.biogrid)</a>
+        <li><a href="api/pypath.core.annot.Disgenet.html#pypath.core.annot.Disgenet.add_complexes_by_inference">(pypath.core.annot.Disgenet method)</a>
 </li>
-  </ul></td>
-  <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="api/pypath.inputs.biomart.biomart_homology.html#pypath.inputs.biomart.biomart_homology">biomart_homology() (in module pypath.inputs.biomart)</a>
+        <li><a href="api/pypath.core.annot.Embrace.html#pypath.core.annot.Embrace.add_complexes_by_inference">(pypath.core.annot.Embrace method)</a>
 </li>
-      <li><a href="api/pypath.inputs.biomart.biomart_microarray.html#pypath.inputs.biomart.biomart_microarray">biomart_microarray() (in module pypath.inputs.biomart)</a>
+        <li><a href="api/pypath.core.annot.Exocarta.html#pypath.core.annot.Exocarta.add_complexes_by_inference">(pypath.core.annot.Exocarta method)</a>
 </li>
-      <li><a href="api/pypath.inputs.biomart.biomart_microarray_types.html#pypath.inputs.biomart.biomart_microarray_types">biomart_microarray_types() (in module pypath.inputs.biomart)</a>
+        <li><a href="api/pypath.core.annot.GOIntercell.html#pypath.core.annot.GOIntercell.add_complexes_by_inference">(pypath.core.annot.GOIntercell method)</a>
 </li>
-      <li><a href="api/pypath.inputs.biomart.biomart_microarrays.html#pypath.inputs.biomart.biomart_microarrays">biomart_microarrays() (in module pypath.inputs.biomart)</a>
+        <li><a href="api/pypath.core.annot.Gpcrdb.html#pypath.core.annot.Gpcrdb.add_complexes_by_inference">(pypath.core.annot.Gpcrdb method)</a>
 </li>
-      <li><a href="api/pypath.inputs.biomart.biomart_query.html#pypath.inputs.biomart.biomart_query">biomart_query() (in module pypath.inputs.biomart)</a>
+        <li><a href="api/pypath.core.annot.GuideToPharmacology.html#pypath.core.annot.GuideToPharmacology.add_complexes_by_inference">(pypath.core.annot.GuideToPharmacology method)</a>
 </li>
-      <li><a href="api/pypath.internals.input_formats.BiomartMapping.html#pypath.internals.input_formats.BiomartMapping">BiomartMapping (class in pypath.internals.input_formats)</a>
+        <li><a href="api/pypath.core.annot.Hgnc.html#pypath.core.annot.Hgnc.add_complexes_by_inference">(pypath.core.annot.Hgnc method)</a>
 </li>
-  </ul></td>
-</tr></table>
-
-<h2 id="C">C</h2>
-<table style="width: 100%" class="indextable genindextable"><tr>
-  <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="api/pypath.inputs.ca1.ca1_interactions.html#pypath.inputs.ca1.ca1_interactions">ca1_interactions() (in module pypath.inputs.ca1)</a>
+        <li><a href="api/pypath.core.annot.HpmrComplex.html#pypath.core.annot.HpmrComplex.add_complexes_by_inference">(pypath.core.annot.HpmrComplex method)</a>
 </li>
-      <li><a href="api/pypath.share.curl.cache_delete_off.html#pypath.share.curl.cache_delete_off">cache_delete_off (class in pypath.share.curl)</a>
+        <li><a href="api/pypath.core.annot.HPO.html#pypath.core.annot.HPO.add_complexes_by_inference">(pypath.core.annot.HPO method)</a>
 </li>
-      <li><a href="api/pypath.share.curl.cache_delete_on.html#pypath.share.curl.cache_delete_on">cache_delete_on (class in pypath.share.curl)</a>
+        <li><a href="api/pypath.core.annot.Humancellmap.html#pypath.core.annot.Humancellmap.add_complexes_by_inference">(pypath.core.annot.Humancellmap method)</a>
 </li>
-      <li><a href="api/pypath.share.cache.cache_item.html#pypath.share.cache.cache_item">cache_item() (in module pypath.share.cache)</a>
+        <li><a href="api/pypath.core.annot.HumanPlasmaMembraneReceptome.html#pypath.core.annot.HumanPlasmaMembraneReceptome.add_complexes_by_inference">(pypath.core.annot.HumanPlasmaMembraneReceptome method)</a>
 </li>
-      <li><a href="api/pypath.share.curl.cache_off.html#pypath.share.curl.cache_off">cache_off (class in pypath.share.curl)</a>
+        <li><a href="api/pypath.core.annot.HumanProteinAtlas.html#pypath.core.annot.HumanProteinAtlas.add_complexes_by_inference">(pypath.core.annot.HumanProteinAtlas method)</a>
 </li>
-      <li><a href="api/pypath.share.curl.cache_on.html#pypath.share.curl.cache_on">cache_on (class in pypath.share.curl)</a>
+        <li><a href="api/pypath.core.annot.HumanProteinAtlasSecretome.html#pypath.core.annot.HumanProteinAtlasSecretome.add_complexes_by_inference">(pypath.core.annot.HumanProteinAtlasSecretome method)</a>
 </li>
-      <li><a href="api/pypath.share.cache.cache_path.html#pypath.share.cache.cache_path">cache_path() (in module pypath.share.cache)</a>
-
-      <ul>
-        <li><a href="api/pypath.share.curl.Curl.html#pypath.share.curl.Curl.cache_path">(pypath.share.curl.Curl class method)</a>
+        <li><a href="api/pypath.core.annot.HumanProteinAtlasSubcellular.html#pypath.core.annot.HumanProteinAtlasSubcellular.add_complexes_by_inference">(pypath.core.annot.HumanProteinAtlasSubcellular method)</a>
 </li>
-      </ul></li>
-      <li><a href="api/pypath.share.curl.cache_print_off.html#pypath.share.curl.cache_print_off">cache_print_off (class in pypath.share.curl)</a>
+        <li><a href="api/pypath.core.annot.Icellnet.html#pypath.core.annot.Icellnet.add_complexes_by_inference">(pypath.core.annot.Icellnet method)</a>
 </li>
-      <li><a href="api/pypath.share.curl.cache_print_on.html#pypath.share.curl.cache_print_on">cache_print_on (class in pypath.share.curl)</a>
+        <li><a href="api/pypath.core.annot.IcellnetComplex.html#pypath.core.annot.IcellnetComplex.add_complexes_by_inference">(pypath.core.annot.IcellnetComplex method)</a>
 </li>
-      <li><a href="api/pypath.inputs.cancercellmap.ccmap_interactions.html#pypath.inputs.cancercellmap.ccmap_interactions">ccmap_interactions() (in module pypath.inputs.cancercellmap)</a>
+        <li><a href="api/pypath.core.annot.Integrins.html#pypath.core.annot.Integrins.add_complexes_by_inference">(pypath.core.annot.Integrins method)</a>
 </li>
-      <li><a href="api/pypath.inputs.cell.cell_supplementary.html#pypath.inputs.cell.cell_supplementary">cell_supplementary() (in module pypath.inputs.cell)</a>
+        <li><a href="api/pypath.core.annot.InterPro.html#pypath.core.annot.InterPro.add_complexes_by_inference">(pypath.core.annot.InterPro method)</a>
 </li>
-      <li><a href="api/pypath.utils.pdb.Residue.html#pypath.utils.pdb.Residue.chain">chain (pypath.utils.pdb.Residue attribute)</a>
+        <li><a href="api/pypath.core.annot.Intogen.html#pypath.core.annot.Intogen.add_complexes_by_inference">(pypath.core.annot.Intogen method)</a>
 </li>
-      <li><a href="api/pypath.utils.reflists.check.html#pypath.utils.reflists.check">check() (in module pypath.utils.reflists)</a>
-
-      <ul>
-        <li><a href="api/pypath.utils.reflists.ReferenceListManager.html#pypath.utils.reflists.ReferenceListManager.check">(pypath.utils.reflists.ReferenceListManager method)</a>
+        <li><a href="api/pypath.core.annot.Italk.html#pypath.core.annot.Italk.add_complexes_by_inference">(pypath.core.annot.Italk method)</a>
 </li>
-      </ul></li>
-      <li><a href="api/pypath.internals.license.LicenseAttrib.html#pypath.internals.license.LicenseAttrib.check_level">check_level() (pypath.internals.license.LicenseAttrib class method)</a>
-
-      <ul>
-        <li><a href="api/pypath.internals.license.LicenseFeature.html#pypath.internals.license.LicenseFeature.check_level">(pypath.internals.license.LicenseFeature class method)</a>
+        <li><a href="api/pypath.core.annot.KeggPathways.html#pypath.core.annot.KeggPathways.add_complexes_by_inference">(pypath.core.annot.KeggPathways method)</a>
 </li>
-        <li><a href="api/pypath.internals.license.LicensePurpose.html#pypath.internals.license.LicensePurpose.check_level">(pypath.internals.license.LicensePurpose class method)</a>
+        <li><a href="api/pypath.core.annot.KeggPathwaysPC.html#pypath.core.annot.KeggPathwaysPC.add_complexes_by_inference">(pypath.core.annot.KeggPathwaysPC method)</a>
 </li>
-        <li><a href="api/pypath.internals.license.LicenseSharing.html#pypath.internals.license.LicenseSharing.check_level">(pypath.internals.license.LicenseSharing class method)</a>
+        <li><a href="api/pypath.core.annot.Kinasedotcom.html#pypath.core.annot.Kinasedotcom.add_complexes_by_inference">(pypath.core.annot.Kinasedotcom method)</a>
 </li>
-      </ul></li>
-      <li><a href="api/pypath.inputs.chembl.chembl_activities.html#pypath.inputs.chembl.chembl_activities">chembl_activities() (in module pypath.inputs.chembl)</a>
+        <li><a href="api/pypath.core.annot.Kirouac2010.html#pypath.core.annot.Kirouac2010.add_complexes_by_inference">(pypath.core.annot.Kirouac2010 method)</a>
 </li>
-      <li><a href="api/pypath.inputs.chembl.chembl_assays.html#pypath.inputs.chembl.chembl_assays">chembl_assays() (in module pypath.inputs.chembl)</a>
+        <li><a href="api/pypath.core.annot.Lambert2018.html#pypath.core.annot.Lambert2018.add_complexes_by_inference">(pypath.core.annot.Lambert2018 method)</a>
 </li>
-      <li><a href="api/pypath.inputs.chembl.chembl_documents.html#pypath.inputs.chembl.chembl_documents">chembl_documents() (in module pypath.inputs.chembl)</a>
+        <li><a href="api/pypath.core.annot.LigandReceptor.html#pypath.core.annot.LigandReceptor.add_complexes_by_inference">(pypath.core.annot.LigandReceptor method)</a>
 </li>
-      <li><a href="api/pypath.inputs.chembl.chembl_drug_indications.html#pypath.inputs.chembl.chembl_drug_indications">chembl_drug_indications() (in module pypath.inputs.chembl)</a>
+        <li><a href="api/pypath.core.annot.Locate.html#pypath.core.annot.Locate.add_complexes_by_inference">(pypath.core.annot.Locate method)</a>
 </li>
-      <li><a href="api/pypath.inputs.chembl.chembl_mechanisms.html#pypath.inputs.chembl.chembl_mechanisms">chembl_mechanisms() (in module pypath.inputs.chembl)</a>
+        <li><a href="api/pypath.core.annot.Lrdb.html#pypath.core.annot.Lrdb.add_complexes_by_inference">(pypath.core.annot.Lrdb method)</a>
 </li>
-      <li><a href="api/pypath.inputs.chembl.chembl_molecules.html#pypath.inputs.chembl.chembl_molecules">chembl_molecules() (in module pypath.inputs.chembl)</a>
+        <li><a href="api/pypath.core.annot.Matrisome.html#pypath.core.annot.Matrisome.add_complexes_by_inference">(pypath.core.annot.Matrisome method)</a>
 </li>
-      <li><a href="api/pypath.inputs.chembl.chembl_targets.html#pypath.inputs.chembl.chembl_targets">chembl_targets() (in module pypath.inputs.chembl)</a>
+        <li><a href="api/pypath.core.annot.Matrixdb.html#pypath.core.annot.Matrixdb.add_complexes_by_inference">(pypath.core.annot.Matrixdb method)</a>
 </li>
-      <li><a href="api/pypath.inputs.adrecs.AdrecsChildParent.html#pypath.inputs.adrecs.AdrecsChildParent.child">child (pypath.inputs.adrecs.AdrecsChildParent attribute)</a>
+        <li><a href="api/pypath.core.annot.Mcam.html#pypath.core.annot.Mcam.add_complexes_by_inference">(pypath.core.annot.Mcam method)</a>
 </li>
-      <li><a href="api/pypath.inputs.dorothea.DorotheaInteraction.html#pypath.inputs.dorothea.DorotheaInteraction.chipseq">chipseq (pypath.inputs.dorothea.DorotheaInteraction attribute)</a>
+        <li><a href="api/pypath.core.annot.Membranome.html#pypath.core.annot.Membranome.add_complexes_by_inference">(pypath.core.annot.Membranome method)</a>
 </li>
-      <li><a href="api/pypath.inputs.dorothea.DorotheaInteraction.html#pypath.inputs.dorothea.DorotheaInteraction.chipseq_sources">chipseq_sources (pypath.inputs.dorothea.DorotheaInteraction attribute)</a>
+        <li><a href="api/pypath.core.annot.Msigdb.html#pypath.core.annot.Msigdb.add_complexes_by_inference">(pypath.core.annot.Msigdb method)</a>
 </li>
-      <li><a href="api/pypath.resources.network.choose_dataset.html#pypath.resources.network.choose_dataset">choose_dataset() (in module pypath.resources.network)</a>
+        <li><a href="api/pypath.core.annot.NetpathPathways.html#pypath.core.annot.NetpathPathways.add_complexes_by_inference">(pypath.core.annot.NetpathPathways method)</a>
 </li>
-      <li><a href="api/pypath.inputs.sider.SiderSideeffectMeddra.html#pypath.inputs.sider.SiderSideeffectMeddra.cid">cid (pypath.inputs.sider.SiderSideeffectMeddra attribute)</a>
+        <li><a href="api/pypath.core.annot.Opm.html#pypath.core.annot.Opm.add_complexes_by_inference">(pypath.core.annot.Opm method)</a>
 </li>
-      <li><a href="api/pypath.utils.pdb.ResidueMapper.html#pypath.utils.pdb.ResidueMapper.clean">clean() (pypath.utils.pdb.ResidueMapper method)</a>
-
-      <ul>
-        <li><a href="api/pypath.utils.residues.ResidueMapper.html#pypath.utils.residues.ResidueMapper.clean">(pypath.utils.residues.ResidueMapper method)</a>
+        <li><a href="api/pypath.core.annot.Panglaodb.html#pypath.core.annot.Panglaodb.add_complexes_by_inference">(pypath.core.annot.Panglaodb method)</a>
 </li>
-      </ul></li>
-      <li><a href="api/pypath.internals.resource.NetworkDataset.html#pypath.internals.resource.NetworkDataset.clear">clear() (pypath.internals.resource.NetworkDataset method)</a>
+        <li><a href="api/pypath.core.annot.Phobius.html#pypath.core.annot.Phobius.add_complexes_by_inference">(pypath.core.annot.Phobius method)</a>
 </li>
-      <li><a href="api/pypath.inputs.clinvar.clinvar_citations.html#pypath.inputs.clinvar.clinvar_citations">clinvar_citations() (in module pypath.inputs.clinvar)</a>
+        <li><a href="api/pypath.core.annot.Phosphatome.html#pypath.core.annot.Phosphatome.add_complexes_by_inference">(pypath.core.annot.Phosphatome method)</a>
 </li>
-      <li><a href="api/pypath.inputs.clinvar.clinvar_raw.html#pypath.inputs.clinvar.clinvar_raw">clinvar_raw() (in module pypath.inputs.clinvar)</a>
+        <li><a href="api/pypath.core.annot.Progeny.html#pypath.core.annot.Progeny.add_complexes_by_inference">(pypath.core.annot.Progeny method)</a>
 </li>
-  </ul></td>
-  <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="api/pypath.share.curl.Curl.html#pypath.share.curl.Curl.close">close() (pypath.share.curl.Curl method)</a>
+        <li><a href="api/pypath.core.annot.Ramilowski2015.html#pypath.core.annot.Ramilowski2015.add_complexes_by_inference">(pypath.core.annot.Ramilowski2015 method)</a>
 </li>
-      <li><a href="api/pypath.inputs.dorothea.DorotheaInteraction.html#pypath.inputs.dorothea.DorotheaInteraction.coexp">coexp (pypath.inputs.dorothea.DorotheaInteraction attribute)</a>
+        <li><a href="api/pypath.core.annot.Ramilowski2015Location.html#pypath.core.annot.Ramilowski2015Location.add_complexes_by_inference">(pypath.core.annot.Ramilowski2015Location method)</a>
 </li>
-      <li><a href="api/pypath.inputs.dorothea.DorotheaInteraction.html#pypath.inputs.dorothea.DorotheaInteraction.coexp_sources">coexp_sources (pypath.inputs.dorothea.DorotheaInteraction attribute)</a>
+        <li><a href="api/pypath.core.annot.Scconnect.html#pypath.core.annot.Scconnect.add_complexes_by_inference">(pypath.core.annot.Scconnect method)</a>
 </li>
-      <li><a href="api/pypath.resources.controller.ResourceController.html#pypath.resources.controller.ResourceController.collect_interaction">collect_interaction() (pypath.resources.controller.ResourceController method)</a>
+        <li><a href="api/pypath.core.annot.ScconnectComplex.html#pypath.core.annot.ScconnectComplex.add_complexes_by_inference">(pypath.core.annot.ScconnectComplex method)</a>
 </li>
-      <li><a href="api/pypath.resources.controller.ResourceController.html#pypath.resources.controller.ResourceController.collect_network">collect_network() (pypath.resources.controller.ResourceController method)</a>
+        <li><a href="api/pypath.core.annot.SignalinkFunctions.html#pypath.core.annot.SignalinkFunctions.add_complexes_by_inference">(pypath.core.annot.SignalinkFunctions method)</a>
 </li>
-      <li><a href="api/pypath.inputs.compath.compath_mappings.html#pypath.inputs.compath.compath_mappings">compath_mappings() (in module pypath.inputs.compath)</a>
+        <li><a href="api/pypath.core.annot.SignalinkPathways.html#pypath.core.annot.SignalinkPathways.add_complexes_by_inference">(pypath.core.annot.SignalinkPathways method)</a>
 </li>
-      <li><a href="api/pypath.utils.unichem.Unichem.html#pypath.utils.unichem.Unichem.connectivity_search">connectivity_search() (pypath.utils.unichem.Unichem method)</a>
+        <li><a href="api/pypath.core.annot.SignorPathways.html#pypath.core.annot.SignorPathways.add_complexes_by_inference">(pypath.core.annot.SignorPathways method)</a>
 </li>
-      <li><a href="api/pypath.share.curl.Curl.html#pypath.share.curl.Curl.construct_binary_data">construct_binary_data() (pypath.share.curl.Curl method)</a>
+        <li><a href="api/pypath.core.annot.Surfaceome.html#pypath.core.annot.Surfaceome.add_complexes_by_inference">(pypath.core.annot.Surfaceome method)</a>
 </li>
-      <li><a href="api/pypath.inputs.adrecs.AdrecsAdr.html#pypath.inputs.adrecs.AdrecsAdr.count">count() (pypath.inputs.adrecs.AdrecsAdr method)</a>
-
-      <ul>
-        <li><a href="api/pypath.inputs.adrecs.AdrecsChildParent.html#pypath.inputs.adrecs.AdrecsChildParent.count">(pypath.inputs.adrecs.AdrecsChildParent method)</a>
+        <li><a href="api/pypath.core.annot.Talklr.html#pypath.core.annot.Talklr.add_complexes_by_inference">(pypath.core.annot.Talklr method)</a>
 </li>
-        <li><a href="api/pypath.inputs.adrecs.AdrecsDrug.html#pypath.inputs.adrecs.AdrecsDrug.count">(pypath.inputs.adrecs.AdrecsDrug method)</a>
+        <li><a href="api/pypath.core.annot.Tcdb.html#pypath.core.annot.Tcdb.add_complexes_by_inference">(pypath.core.annot.Tcdb method)</a>
 </li>
-        <li><a href="api/pypath.inputs.adrecs.AdrecsDrugAdr.html#pypath.inputs.adrecs.AdrecsDrugAdr.count">(pypath.inputs.adrecs.AdrecsDrugAdr method)</a>
+        <li><a href="api/pypath.core.annot.Tfcensus.html#pypath.core.annot.Tfcensus.add_complexes_by_inference">(pypath.core.annot.Tfcensus method)</a>
 </li>
-        <li><a href="api/pypath.inputs.adrecs.AdrecsTerm.html#pypath.inputs.adrecs.AdrecsTerm.count">(pypath.inputs.adrecs.AdrecsTerm method)</a>
+        <li><a href="api/pypath.core.annot.Topdb.html#pypath.core.annot.Topdb.add_complexes_by_inference">(pypath.core.annot.Topdb method)</a>
 </li>
-        <li><a href="api/pypath.inputs.dorothea.DorotheaInteraction.html#pypath.inputs.dorothea.DorotheaInteraction.count">(pypath.inputs.dorothea.DorotheaInteraction method)</a>
+        <li><a href="api/pypath.core.annot.UniprotFamilies.html#pypath.core.annot.UniprotFamilies.add_complexes_by_inference">(pypath.core.annot.UniprotFamilies method)</a>
 </li>
-        <li><a href="api/pypath.inputs.pathophenodb.DiseasePathogen.html#pypath.inputs.pathophenodb.DiseasePathogen.count">(pypath.inputs.pathophenodb.DiseasePathogen method)</a>
+        <li><a href="api/pypath.core.annot.UniprotKeywords.html#pypath.core.annot.UniprotKeywords.add_complexes_by_inference">(pypath.core.annot.UniprotKeywords method)</a>
 </li>
-        <li><a href="api/pypath.inputs.pathwaycommons.PathwayCommonsInteraction.html#pypath.inputs.pathwaycommons.PathwayCommonsInteraction.count">(pypath.inputs.pathwaycommons.PathwayCommonsInteraction method)</a>
+        <li><a href="api/pypath.core.annot.UniprotLocations.html#pypath.core.annot.UniprotLocations.add_complexes_by_inference">(pypath.core.annot.UniprotLocations method)</a>
 </li>
-        <li><a href="api/pypath.inputs.pathwaycommons.PathwayCommonsResource.html#pypath.inputs.pathwaycommons.PathwayCommonsResource.count">(pypath.inputs.pathwaycommons.PathwayCommonsResource method)</a>
+        <li><a href="api/pypath.core.annot.UniprotTissues.html#pypath.core.annot.UniprotTissues.add_complexes_by_inference">(pypath.core.annot.UniprotTissues method)</a>
 </li>
-        <li><a href="api/pypath.inputs.sider.SiderDrug.html#pypath.inputs.sider.SiderDrug.count">(pypath.inputs.sider.SiderDrug method)</a>
+        <li><a href="api/pypath.core.annot.UniprotTopologies.html#pypath.core.annot.UniprotTopologies.add_complexes_by_inference">(pypath.core.annot.UniprotTopologies method)</a>
 </li>
-        <li><a href="api/pypath.inputs.sider.SiderSideeffect.html#pypath.inputs.sider.SiderSideeffect.count">(pypath.inputs.sider.SiderSideeffect method)</a>
+        <li><a href="api/pypath.core.annot.Vesiclepedia.html#pypath.core.annot.Vesiclepedia.add_complexes_by_inference">(pypath.core.annot.Vesiclepedia method)</a>
 </li>
-        <li><a href="api/pypath.inputs.sider.SiderSideeffectMeddra.html#pypath.inputs.sider.SiderSideeffectMeddra.count">(pypath.inputs.sider.SiderSideeffectMeddra method)</a>
+        <li><a href="api/pypath.core.annot.Wang.html#pypath.core.annot.Wang.add_complexes_by_inference">(pypath.core.annot.Wang method)</a>
 </li>
-        <li><a href="api/pypath.inputs.sider.SiderSideeffetFrequency.html#pypath.inputs.sider.SiderSideeffetFrequency.count">(pypath.inputs.sider.SiderSideeffetFrequency method)</a>
+        <li><a href="api/pypath.core.annot.Zhong2015.html#pypath.core.annot.Zhong2015.add_complexes_by_inference">(pypath.core.annot.Zhong2015 method)</a>
 </li>
-        <li><a href="api/pypath.inputs.uniprot.Taxon.html#pypath.inputs.uniprot.Taxon.count">(pypath.inputs.uniprot.Taxon method)</a>
+      </ul></li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.add_evidence">add_evidence() (pypath.core.interaction.Interaction method)</a>
 </li>
-        <li><a href="api/pypath.inputs.uniprot.UniprotRecordHistory.html#pypath.inputs.uniprot.UniprotRecordHistory.count">(pypath.inputs.uniprot.UniprotRecordHistory method)</a>
+      <li><a href="api/pypath.omnipath.export.Export.html#pypath.omnipath.export.Export.add_extra_fields">add_extra_fields() (pypath.omnipath.export.Export method)</a>
 </li>
-        <li><a href="api/pypath.internals.resource.EnzymeSubstrateResourceKey.html#pypath.internals.resource.EnzymeSubstrateResourceKey.count">(pypath.internals.resource.EnzymeSubstrateResourceKey method)</a>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.add_interaction">add_interaction() (pypath.core.network.Network method)</a>
 </li>
-        <li><a href="api/pypath.internals.resource.NetworkResourceKey.html#pypath.internals.resource.NetworkResourceKey.count">(pypath.internals.resource.NetworkResourceKey method)</a>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.add_node">add_node() (pypath.core.network.Network method)</a>
 </li>
-        <li><a href="api/pypath.utils.pdb.Residue.html#pypath.utils.pdb.Residue.count">(pypath.utils.pdb.Residue method)</a>
+      <li><a href="api/pypath.internals.intera.Interface.html#pypath.internals.intera.Interface.add_residues">add_residues() (pypath.internals.intera.Interface method)</a>
 </li>
-        <li><a href="api/pypath.utils.pdb.Segment.html#pypath.utils.pdb.Segment.count">(pypath.utils.pdb.Segment method)</a>
+      <li><a href="api/pypath.resources.controller.ResourceController.html#pypath.resources.controller.ResourceController.add_resource_attrs">add_resource_attrs() (pypath.resources.controller.ResourceController method)</a>
 </li>
-      </ul></li>
-      <li><a href="api/pypath.inputs.cpdb.cpdb_interactions.html#pypath.inputs.cpdb.cpdb_interactions">cpdb_interactions() (in module pypath.inputs.cpdb)</a>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.add_sign">add_sign() (pypath.core.interaction.Interaction method)</a>
 </li>
-      <li><a href="api/pypath.inputs.cpdb.cpdb_interactions_ltp.html#pypath.inputs.cpdb.cpdb_interactions_ltp">cpdb_interactions_ltp() (in module pypath.inputs.cpdb)</a>
+      <li><a href="api/pypath.core.annot.Adhesome.html#pypath.core.annot.Adhesome">Adhesome (class in pypath.core.annot)</a>
 </li>
-      <li><a href="api/pypath.inputs.credentials.credentials.html#pypath.inputs.credentials.credentials">credentials() (in module pypath.inputs.credentials)</a>
+      <li><a href="api/pypath.inputs.adhesome.adhesome_annotations.html#pypath.inputs.adhesome.adhesome_annotations">adhesome_annotations() (in module pypath.inputs.adhesome)</a>
 </li>
-      <li><a href="api/pypath.inputs.common.csv_sep_change.html#pypath.inputs.common.csv_sep_change">csv_sep_change() (in module pypath.inputs.common)</a>
+      <li><a href="api/pypath.inputs.adhesome.adhesome_interactions.html#pypath.inputs.adhesome.adhesome_interactions">adhesome_interactions() (in module pypath.inputs.adhesome)</a>
 </li>
-      <li><a href="api/pypath.inputs.ctdbase.ctdbase_relations.html#pypath.inputs.ctdbase.ctdbase_relations">ctdbase_relations() (in module pypath.inputs.ctdbase)</a>
+      <li><a href="api/pypath.inputs.adrecs.AdrecsDrugAdr.html#pypath.inputs.adrecs.AdrecsDrugAdr.adr">adr (pypath.inputs.adrecs.AdrecsDrugAdr attribute)</a>
 </li>
-      <li><a href="api/pypath.inputs.ctdbase.ctdbase_vocabulary.html#pypath.inputs.ctdbase.ctdbase_vocabulary">ctdbase_vocabulary() (in module pypath.inputs.ctdbase)</a>
+      <li><a href="api/pypath.inputs.adrecs.AdrecsDrugAdr.html#pypath.inputs.adrecs.AdrecsDrugAdr.adr_badd">adr_badd (pypath.inputs.adrecs.AdrecsDrugAdr attribute)</a>
 </li>
-      <li><a href="api/pypath.inputs.dorothea.DorotheaInteraction.html#pypath.inputs.dorothea.DorotheaInteraction.curated">curated (pypath.inputs.dorothea.DorotheaInteraction attribute)</a>
+      <li><a href="api/pypath.inputs.adrecs.AdrecsAdr.html#pypath.inputs.adrecs.AdrecsAdr.adr_class">adr_class (pypath.inputs.adrecs.AdrecsAdr attribute)</a>
 </li>
-      <li><a href="api/pypath.inputs.dorothea.DorotheaInteraction.html#pypath.inputs.dorothea.DorotheaInteraction.curated_sources">curated_sources (pypath.inputs.dorothea.DorotheaInteraction attribute)</a>
+      <li><a href="api/pypath.inputs.adrecs.adrecs_adr_ontology.html#pypath.inputs.adrecs.adrecs_adr_ontology">adrecs_adr_ontology() (in module pypath.inputs.adrecs)</a>
 </li>
-      <li><a href="api/pypath.share.curl.Curl.html#pypath.share.curl.Curl">Curl (class in pypath.share.curl)</a>
+      <li><a href="api/pypath.inputs.adrecs.AdrecsTerm.html#pypath.inputs.adrecs.AdrecsTerm.adrecs_class">adrecs_class (pypath.inputs.adrecs.AdrecsTerm attribute)</a>
 </li>
-  </ul></td>
-</tr></table>
-
-<h2 id="D">D</h2>
-<table style="width: 100%" class="indextable genindextable"><tr>
-  <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="api/pypath.visual.igraph_drawing.edge.DarkToLightEdgeDrawer.html#pypath.visual.igraph_drawing.edge.DarkToLightEdgeDrawer">DarkToLightEdgeDrawer (class in pypath.visual.igraph_drawing.edge)</a>
+      <li><a href="api/pypath.inputs.adrecs.adrecs_drug_adr.html#pypath.inputs.adrecs.adrecs_drug_adr">adrecs_drug_adr() (in module pypath.inputs.adrecs)</a>
 </li>
-      <li><a href="api/pypath.internals.resource.NetworkResourceKey.html#pypath.internals.resource.NetworkResourceKey.data_model">data_model (pypath.internals.resource.NetworkResourceKey attribute)</a>
+      <li><a href="api/pypath.inputs.adrecs.adrecs_drug_identifiers.html#pypath.inputs.adrecs.adrecs_drug_identifiers">adrecs_drug_identifiers() (in module pypath.inputs.adrecs)</a>
 </li>
-      <li><a href="api/pypath.internals.resource.EnzymeSubstrateResourceKey.html#pypath.internals.resource.EnzymeSubstrateResourceKey.data_type">data_type (pypath.internals.resource.EnzymeSubstrateResourceKey attribute)</a>
-
-      <ul>
-        <li><a href="api/pypath.internals.resource.NetworkResourceKey.html#pypath.internals.resource.NetworkResourceKey.data_type">(pypath.internals.resource.NetworkResourceKey attribute)</a>
+      <li><a href="api/pypath.inputs.adrecs.adrecs_hierarchy.html#pypath.inputs.adrecs.adrecs_hierarchy">adrecs_hierarchy() (in module pypath.inputs.adrecs)</a>
 </li>
-      </ul></li>
-      <li><a href="api/pypath.inputs.uniprot.UniprotRecordHistory.html#pypath.inputs.uniprot.UniprotRecordHistory.database">database (pypath.inputs.uniprot.UniprotRecordHistory attribute)</a>
+      <li><a href="api/pypath.inputs.adrecs.AdrecsAdr.html#pypath.inputs.adrecs.AdrecsAdr">AdrecsAdr (class in pypath.inputs.adrecs)</a>
 </li>
-      <li><a href="api/pypath.resources.network.dataset_priority.html#pypath.resources.network.dataset_priority">dataset_priority() (in module pypath.resources.network)</a>
+      <li><a href="api/pypath.inputs.adrecs.AdrecsChildParent.html#pypath.inputs.adrecs.AdrecsChildParent">AdrecsChildParent (class in pypath.inputs.adrecs)</a>
 </li>
-      <li><a href="api/pypath.inputs.uniprot.UniprotRecordHistory.html#pypath.inputs.uniprot.UniprotRecordHistory.date">date (pypath.inputs.uniprot.UniprotRecordHistory attribute)</a>
+      <li><a href="api/pypath.inputs.adrecs.AdrecsDrug.html#pypath.inputs.adrecs.AdrecsDrug">AdrecsDrug (class in pypath.inputs.adrecs)</a>
 </li>
-      <li><a href="api/pypath.inputs.dbptm.dbptm_enzyme_substrate.html#pypath.inputs.dbptm.dbptm_enzyme_substrate">dbptm_enzyme_substrate() (in module pypath.inputs.dbptm)</a>
+      <li><a href="api/pypath.inputs.adrecs.AdrecsDrugAdr.html#pypath.inputs.adrecs.AdrecsDrugAdr">AdrecsDrugAdr (class in pypath.inputs.adrecs)</a>
 </li>
-      <li><a href="api/pypath.inputs.dbptm.dbptm_enzyme_substrate_old.html#pypath.inputs.dbptm.dbptm_enzyme_substrate_old">dbptm_enzyme_substrate_old() (in module pypath.inputs.dbptm)</a>
+      <li><a href="api/pypath.inputs.adrecs.AdrecsTerm.html#pypath.inputs.adrecs.AdrecsTerm">AdrecsTerm (class in pypath.inputs.adrecs)</a>
 </li>
-      <li><a href="api/pypath.inputs.dbptm.dbptm_interactions.html#pypath.inputs.dbptm.dbptm_interactions">dbptm_interactions() (in module pypath.inputs.dbptm)</a>
+      <li><a href="api/pypath.core.annot.AnnotationTable.html#pypath.core.annot.AnnotationTable.all_annotations">all_annotations() (pypath.core.annot.AnnotationTable method)</a>
 </li>
-      <li><a href="api/pypath.inputs.ddinter.ddinter_drug_interactions.html#pypath.inputs.ddinter.ddinter_drug_interactions">ddinter_drug_interactions() (in module pypath.inputs.ddinter)</a>
+      <li><a href="api/pypath.core.annot.AnnotationTable.html#pypath.core.annot.AnnotationTable.all_annotations_str">all_annotations_str() (pypath.core.annot.AnnotationTable method)</a>
 </li>
-      <li><a href="api/pypath.inputs.ddinter.ddinter_identifiers.html#pypath.inputs.ddinter.ddinter_identifiers">ddinter_identifiers() (in module pypath.inputs.ddinter)</a>
+      <li><a href="api/pypath.core.complex.all_complexes.html#pypath.core.complex.all_complexes">all_complexes() (in module pypath.core.complex)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.annot.Adhesome.html#pypath.core.annot.Adhesome.all_complexes">(pypath.core.annot.Adhesome method)</a>
 </li>
-      <li><a href="api/pypath.inputs.ddinter.ddinter_interactions.html#pypath.inputs.ddinter.ddinter_interactions">ddinter_interactions() (in module pypath.inputs.ddinter)</a>
+        <li><a href="api/pypath.core.annot.Almen2009.html#pypath.core.annot.Almen2009.all_complexes">(pypath.core.annot.Almen2009 method)</a>
 </li>
-      <li><a href="api/pypath.inputs.ddinter.ddinter_mappings.html#pypath.inputs.ddinter.ddinter_mappings">ddinter_mappings() (in module pypath.inputs.ddinter)</a>
+        <li><a href="api/pypath.core.annot.AnnotationBase.html#pypath.core.annot.AnnotationBase.all_complexes">(pypath.core.annot.AnnotationBase method)</a>
 </li>
-      <li><a href="api/pypath.inputs.ddinter.ddinter_n_drugs.html#pypath.inputs.ddinter.ddinter_n_drugs">ddinter_n_drugs() (in module pypath.inputs.ddinter)</a>
+        <li><a href="api/pypath.core.annot.Baccin2019.html#pypath.core.annot.Baccin2019.all_complexes">(pypath.core.annot.Baccin2019 method)</a>
 </li>
-      <li><a href="api/pypath.inputs.deathdomain.deathdomain_interactions.html#pypath.inputs.deathdomain.deathdomain_interactions">deathdomain_interactions() (in module pypath.inputs.deathdomain)</a>
+        <li><a href="api/pypath.core.annot.Biogps.html#pypath.core.annot.Biogps.all_complexes">(pypath.core.annot.Biogps method)</a>
 </li>
-      <li><a href="api/pypath.inputs.deathdomain.deathdomain_interactions_rescued.html#pypath.inputs.deathdomain.deathdomain_interactions_rescued">deathdomain_interactions_rescued() (in module pypath.inputs.deathdomain)</a>
+        <li><a href="api/pypath.core.annot.Cancerdrugsdb.html#pypath.core.annot.Cancerdrugsdb.all_complexes">(pypath.core.annot.Cancerdrugsdb method)</a>
 </li>
-      <li><a href="api/pypath.share.curl.debug_off.html#pypath.share.curl.debug_off">debug_off (class in pypath.share.curl)</a>
+        <li><a href="api/pypath.core.annot.CancerGeneCensus.html#pypath.core.annot.CancerGeneCensus.all_complexes">(pypath.core.annot.CancerGeneCensus method)</a>
 </li>
-      <li><a href="api/pypath.share.curl.debug_on.html#pypath.share.curl.debug_on">debug_on (class in pypath.share.curl)</a>
+        <li><a href="api/pypath.core.annot.Cancersea.html#pypath.core.annot.Cancersea.all_complexes">(pypath.core.annot.Cancersea method)</a>
 </li>
-      <li><a href="api/pypath.visual.igraph_drawing.DefaultGraphDrawerFFsupport.html#pypath.visual.igraph_drawing.DefaultGraphDrawerFFsupport">DefaultGraphDrawerFFsupport (class in pypath.visual.igraph_drawing)</a>
+        <li><a href="api/pypath.core.annot.Cellcall.html#pypath.core.annot.Cellcall.all_complexes">(pypath.core.annot.Cellcall method)</a>
 </li>
-      <li><a href="api/pypath.visual.igraph_drawing.vertex.DefaultVertexDrawer.html#pypath.visual.igraph_drawing.vertex.DefaultVertexDrawer">DefaultVertexDrawer (class in pypath.visual.igraph_drawing.vertex)</a>
-
-      <ul>
-        <li><a href="api/pypath.visual.igraph_drawing.DefaultVertexDrawer.html#pypath.visual.igraph_drawing.DefaultVertexDrawer">(in module pypath.visual.igraph_drawing)</a>
+        <li><a href="api/pypath.core.annot.Cellcellinteractions.html#pypath.core.annot.Cellcellinteractions.all_complexes">(pypath.core.annot.Cellcellinteractions method)</a>
 </li>
-      </ul></li>
-      <li><a href="api/pypath.inputs.uniprot.deleted_uniprot_genesymbol.html#pypath.inputs.uniprot.deleted_uniprot_genesymbol">deleted_uniprot_genesymbol() (in module pypath.inputs.uniprot)</a>
+        <li><a href="api/pypath.core.annot.Cellchatdb.html#pypath.core.annot.Cellchatdb.all_complexes">(pypath.core.annot.Cellchatdb method)</a>
 </li>
-      <li><a href="api/pypath.inputs.dip.dip_interactions.html#pypath.inputs.dip.dip_interactions">dip_interactions() (in module pypath.inputs.dip)</a>
+        <li><a href="api/pypath.core.annot.CellchatdbComplex.html#pypath.core.annot.CellchatdbComplex.all_complexes">(pypath.core.annot.CellchatdbComplex method)</a>
 </li>
-      <li><a href="api/pypath.inputs.dip.dip_login.html#pypath.inputs.dip.dip_login">dip_login() (in module pypath.inputs.dip)</a>
+        <li><a href="api/pypath.core.annot.Cellinker.html#pypath.core.annot.Cellinker.all_complexes">(pypath.core.annot.Cellinker method)</a>
 </li>
-      <li><a href="api/pypath.disclaimer.html#pypath.disclaimer">disclaimer() (in module pypath)</a>
+        <li><a href="api/pypath.core.annot.CellinkerComplex.html#pypath.core.annot.CellinkerComplex.all_complexes">(pypath.core.annot.CellinkerComplex method)</a>
 </li>
-      <li><a href="api/pypath.inputs.pathophenodb.DiseasePathogen.html#pypath.inputs.pathophenodb.DiseasePathogen.disease">disease (pypath.inputs.pathophenodb.DiseasePathogen attribute)</a>
+        <li><a href="api/pypath.core.annot.CellPhoneDB.html#pypath.core.annot.CellPhoneDB.all_complexes">(pypath.core.annot.CellPhoneDB method)</a>
 </li>
-      <li><a href="api/pypath.inputs.pathophenodb.DiseasePathogen.html#pypath.inputs.pathophenodb.DiseasePathogen.disease_id">disease_id (pypath.inputs.pathophenodb.DiseasePathogen attribute)</a>
+        <li><a href="api/pypath.core.annot.CellPhoneDBComplex.html#pypath.core.annot.CellPhoneDBComplex.all_complexes">(pypath.core.annot.CellPhoneDBComplex method)</a>
 </li>
-      <li><a href="api/pypath.inputs.pathophenodb.disease_pathogen_interactions.html#pypath.inputs.pathophenodb.disease_pathogen_interactions">disease_pathogen_interactions() (in module pypath.inputs.pathophenodb)</a>
+        <li><a href="api/pypath.core.annot.CellSurfaceProteinAtlas.html#pypath.core.annot.CellSurfaceProteinAtlas.all_complexes">(pypath.core.annot.CellSurfaceProteinAtlas method)</a>
 </li>
-      <li><a href="api/pypath.inputs.kegg_api.disease_to_drug.html#pypath.inputs.kegg_api.disease_to_drug">disease_to_drug() (in module pypath.inputs.kegg_api)</a>
+        <li><a href="api/pypath.core.annot.CellSurfaceProteinAtlasCellType.html#pypath.core.annot.CellSurfaceProteinAtlasCellType.all_complexes">(pypath.core.annot.CellSurfaceProteinAtlasCellType method)</a>
 </li>
-      <li><a href="api/pypath.inputs.kegg_api.disease_to_gene.html#pypath.inputs.kegg_api.disease_to_gene">disease_to_gene() (in module pypath.inputs.kegg_api)</a>
+        <li><a href="api/pypath.core.annot.Celltalkdb.html#pypath.core.annot.Celltalkdb.all_complexes">(pypath.core.annot.Celltalkdb method)</a>
 </li>
-      <li><a href="api/pypath.inputs.kegg_api.disease_to_pathway.html#pypath.inputs.kegg_api.disease_to_pathway">disease_to_pathway() (in module pypath.inputs.kegg_api)</a>
+        <li><a href="api/pypath.core.annot.Celltypist.html#pypath.core.annot.Celltypist.all_complexes">(pypath.core.annot.Celltypist method)</a>
 </li>
-      <li><a href="api/pypath.inputs.pathophenodb.DiseasePathogen.html#pypath.inputs.pathophenodb.DiseasePathogen">DiseasePathogen (class in pypath.inputs.pathophenodb)</a>
+        <li><a href="api/pypath.core.annot.Comppi.html#pypath.core.annot.Comppi.all_complexes">(pypath.core.annot.Comppi method)</a>
 </li>
-      <li><a href="api/pypath.inputs.diseases.diseases_general.html#pypath.inputs.diseases.diseases_general">diseases_general() (in module pypath.inputs.diseases)</a>
+        <li><a href="api/pypath.core.annot.Connectomedb.html#pypath.core.annot.Connectomedb.all_complexes">(pypath.core.annot.Connectomedb method)</a>
 </li>
-      <li><a href="api/pypath.resources.network.dorothea_expand_levels.html#pypath.resources.network.dorothea_expand_levels">dorothea_expand_levels() (in module pypath.resources.network)</a>
+        <li><a href="api/pypath.core.annot.Corum.html#pypath.core.annot.Corum.all_complexes">(pypath.core.annot.Corum method)</a>
 </li>
-      <li><a href="api/pypath.inputs.dorothea.dorothea_full_raw.html#pypath.inputs.dorothea.dorothea_full_raw">dorothea_full_raw() (in module pypath.inputs.dorothea)</a>
+        <li><a href="api/pypath.core.annot.CorumFuncat.html#pypath.core.annot.CorumFuncat.all_complexes">(pypath.core.annot.CorumFuncat method)</a>
 </li>
-      <li><a href="api/pypath.inputs.dorothea.dorothea_interactions.html#pypath.inputs.dorothea.dorothea_interactions">dorothea_interactions() (in module pypath.inputs.dorothea)</a>
+        <li><a href="api/pypath.core.annot.CorumGO.html#pypath.core.annot.CorumGO.all_complexes">(pypath.core.annot.CorumGO method)</a>
 </li>
-      <li><a href="api/pypath.inputs.dorothea.dorothea_interactions_old.html#pypath.inputs.dorothea.dorothea_interactions_old">dorothea_interactions_old() (in module pypath.inputs.dorothea)</a>
+        <li><a href="api/pypath.core.annot.Cpad.html#pypath.core.annot.Cpad.all_complexes">(pypath.core.annot.Cpad method)</a>
 </li>
-      <li><a href="api/pypath.inputs.dorothea.dorothea_old_csv.html#pypath.inputs.dorothea.dorothea_old_csv">dorothea_old_csv() (in module pypath.inputs.dorothea)</a>
+        <li><a href="api/pypath.core.annot.Cytosig.html#pypath.core.annot.Cytosig.all_complexes">(pypath.core.annot.Cytosig method)</a>
 </li>
-      <li><a href="api/pypath.inputs.dorothea.dorothea_rda_raw.html#pypath.inputs.dorothea.dorothea_rda_raw">dorothea_rda_raw() (in module pypath.inputs.dorothea)</a>
+        <li><a href="api/pypath.core.annot.Dgidb.html#pypath.core.annot.Dgidb.all_complexes">(pypath.core.annot.Dgidb method)</a>
 </li>
-      <li><a href="api/pypath.inputs.dorothea.DorotheaInteraction.html#pypath.inputs.dorothea.DorotheaInteraction">DorotheaInteraction (class in pypath.inputs.dorothea)</a>
+        <li><a href="api/pypath.core.annot.Disgenet.html#pypath.core.annot.Disgenet.all_complexes">(pypath.core.annot.Disgenet method)</a>
 </li>
-      <li><a href="api/pypath.inputs.biomodels.download_single_model.html#pypath.inputs.biomodels.download_single_model">download_single_model() (in module pypath.inputs.biomodels)</a>
+        <li><a href="api/pypath.core.annot.Embrace.html#pypath.core.annot.Embrace.all_complexes">(pypath.core.annot.Embrace method)</a>
 </li>
-      <li><a href="api/pypath.visual.drawing.InterSet.html#pypath.visual.drawing.InterSet.draw">draw() (pypath.visual.drawing.InterSet method)</a>
-
-      <ul>
-        <li><a href="api/pypath.visual.igraph_drawing.vertex.AbstractCairoVertexDrawer.html#pypath.visual.igraph_drawing.vertex.AbstractCairoVertexDrawer.draw">(pypath.visual.igraph_drawing.vertex.AbstractCairoVertexDrawer method)</a>
+        <li><a href="api/pypath.core.annot.Exocarta.html#pypath.core.annot.Exocarta.all_complexes">(pypath.core.annot.Exocarta method)</a>
 </li>
-        <li><a href="api/pypath.visual.igraph_drawing.vertex.AbstractVertexDrawer.html#pypath.visual.igraph_drawing.vertex.AbstractVertexDrawer.draw">(pypath.visual.igraph_drawing.vertex.AbstractVertexDrawer method)</a>
+        <li><a href="api/pypath.core.annot.GOIntercell.html#pypath.core.annot.GOIntercell.all_complexes">(pypath.core.annot.GOIntercell method)</a>
 </li>
-        <li><a href="api/pypath.visual.igraph_drawing.vertex.DefaultVertexDrawer.html#pypath.visual.igraph_drawing.vertex.DefaultVertexDrawer.draw">(pypath.visual.igraph_drawing.vertex.DefaultVertexDrawer method)</a>
+        <li><a href="api/pypath.core.annot.Gpcrdb.html#pypath.core.annot.Gpcrdb.all_complexes">(pypath.core.annot.Gpcrdb method)</a>
 </li>
-      </ul></li>
-  </ul></td>
-  <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="api/pypath.visual.igraph_drawing.edge.AbstractEdgeDrawer.html#pypath.visual.igraph_drawing.edge.AbstractEdgeDrawer.draw_directed_edge">draw_directed_edge() (pypath.visual.igraph_drawing.edge.AbstractEdgeDrawer method)</a>
-
-      <ul>
-        <li><a href="api/pypath.visual.igraph_drawing.edge.AlphaVaryingEdgeDrawer.html#pypath.visual.igraph_drawing.edge.AlphaVaryingEdgeDrawer.draw_directed_edge">(pypath.visual.igraph_drawing.edge.AlphaVaryingEdgeDrawer method)</a>
+        <li><a href="api/pypath.core.annot.GuideToPharmacology.html#pypath.core.annot.GuideToPharmacology.all_complexes">(pypath.core.annot.GuideToPharmacology method)</a>
 </li>
-        <li><a href="api/pypath.visual.igraph_drawing.edge.ArrowEdgeDrawer.html#pypath.visual.igraph_drawing.edge.ArrowEdgeDrawer.draw_directed_edge">(pypath.visual.igraph_drawing.edge.ArrowEdgeDrawer method)</a>
+        <li><a href="api/pypath.core.annot.Hgnc.html#pypath.core.annot.Hgnc.all_complexes">(pypath.core.annot.Hgnc method)</a>
 </li>
-        <li><a href="api/pypath.visual.igraph_drawing.edge.DarkToLightEdgeDrawer.html#pypath.visual.igraph_drawing.edge.DarkToLightEdgeDrawer.draw_directed_edge">(pypath.visual.igraph_drawing.edge.DarkToLightEdgeDrawer method)</a>
+        <li><a href="api/pypath.core.annot.HpmrComplex.html#pypath.core.annot.HpmrComplex.all_complexes">(pypath.core.annot.HpmrComplex method)</a>
 </li>
-        <li><a href="api/pypath.visual.igraph_drawing.edge.LightToDarkEdgeDrawer.html#pypath.visual.igraph_drawing.edge.LightToDarkEdgeDrawer.draw_directed_edge">(pypath.visual.igraph_drawing.edge.LightToDarkEdgeDrawer method)</a>
+        <li><a href="api/pypath.core.annot.HPO.html#pypath.core.annot.HPO.all_complexes">(pypath.core.annot.HPO method)</a>
 </li>
-        <li><a href="api/pypath.visual.igraph_drawing.edge.TaperedEdgeDrawer.html#pypath.visual.igraph_drawing.edge.TaperedEdgeDrawer.draw_directed_edge">(pypath.visual.igraph_drawing.edge.TaperedEdgeDrawer method)</a>
+        <li><a href="api/pypath.core.annot.Humancellmap.html#pypath.core.annot.Humancellmap.all_complexes">(pypath.core.annot.Humancellmap method)</a>
 </li>
-      </ul></li>
-      <li><a href="api/pypath.visual.igraph_drawing.edge.AbstractEdgeDrawer.html#pypath.visual.igraph_drawing.edge.AbstractEdgeDrawer.draw_loop_edge">draw_loop_edge() (pypath.visual.igraph_drawing.edge.AbstractEdgeDrawer method)</a>
-
-      <ul>
-        <li><a href="api/pypath.visual.igraph_drawing.edge.AlphaVaryingEdgeDrawer.html#pypath.visual.igraph_drawing.edge.AlphaVaryingEdgeDrawer.draw_loop_edge">(pypath.visual.igraph_drawing.edge.AlphaVaryingEdgeDrawer method)</a>
+        <li><a href="api/pypath.core.annot.HumanPlasmaMembraneReceptome.html#pypath.core.annot.HumanPlasmaMembraneReceptome.all_complexes">(pypath.core.annot.HumanPlasmaMembraneReceptome method)</a>
 </li>
-        <li><a href="api/pypath.visual.igraph_drawing.edge.ArrowEdgeDrawer.html#pypath.visual.igraph_drawing.edge.ArrowEdgeDrawer.draw_loop_edge">(pypath.visual.igraph_drawing.edge.ArrowEdgeDrawer method)</a>
+        <li><a href="api/pypath.core.annot.HumanProteinAtlas.html#pypath.core.annot.HumanProteinAtlas.all_complexes">(pypath.core.annot.HumanProteinAtlas method)</a>
 </li>
-        <li><a href="api/pypath.visual.igraph_drawing.edge.DarkToLightEdgeDrawer.html#pypath.visual.igraph_drawing.edge.DarkToLightEdgeDrawer.draw_loop_edge">(pypath.visual.igraph_drawing.edge.DarkToLightEdgeDrawer method)</a>
+        <li><a href="api/pypath.core.annot.HumanProteinAtlasSecretome.html#pypath.core.annot.HumanProteinAtlasSecretome.all_complexes">(pypath.core.annot.HumanProteinAtlasSecretome method)</a>
 </li>
-        <li><a href="api/pypath.visual.igraph_drawing.edge.LightToDarkEdgeDrawer.html#pypath.visual.igraph_drawing.edge.LightToDarkEdgeDrawer.draw_loop_edge">(pypath.visual.igraph_drawing.edge.LightToDarkEdgeDrawer method)</a>
+        <li><a href="api/pypath.core.annot.HumanProteinAtlasSubcellular.html#pypath.core.annot.HumanProteinAtlasSubcellular.all_complexes">(pypath.core.annot.HumanProteinAtlasSubcellular method)</a>
 </li>
-        <li><a href="api/pypath.visual.igraph_drawing.edge.TaperedEdgeDrawer.html#pypath.visual.igraph_drawing.edge.TaperedEdgeDrawer.draw_loop_edge">(pypath.visual.igraph_drawing.edge.TaperedEdgeDrawer method)</a>
+        <li><a href="api/pypath.core.annot.Icellnet.html#pypath.core.annot.Icellnet.all_complexes">(pypath.core.annot.Icellnet method)</a>
 </li>
-      </ul></li>
-      <li><a href="api/pypath.visual.igraph_drawing.edge.AbstractEdgeDrawer.html#pypath.visual.igraph_drawing.edge.AbstractEdgeDrawer.draw_undirected_edge">draw_undirected_edge() (pypath.visual.igraph_drawing.edge.AbstractEdgeDrawer method)</a>
-
-      <ul>
-        <li><a href="api/pypath.visual.igraph_drawing.edge.AlphaVaryingEdgeDrawer.html#pypath.visual.igraph_drawing.edge.AlphaVaryingEdgeDrawer.draw_undirected_edge">(pypath.visual.igraph_drawing.edge.AlphaVaryingEdgeDrawer method)</a>
+        <li><a href="api/pypath.core.annot.IcellnetComplex.html#pypath.core.annot.IcellnetComplex.all_complexes">(pypath.core.annot.IcellnetComplex method)</a>
 </li>
-        <li><a href="api/pypath.visual.igraph_drawing.edge.ArrowEdgeDrawer.html#pypath.visual.igraph_drawing.edge.ArrowEdgeDrawer.draw_undirected_edge">(pypath.visual.igraph_drawing.edge.ArrowEdgeDrawer method)</a>
+        <li><a href="api/pypath.core.annot.Integrins.html#pypath.core.annot.Integrins.all_complexes">(pypath.core.annot.Integrins method)</a>
 </li>
-        <li><a href="api/pypath.visual.igraph_drawing.edge.DarkToLightEdgeDrawer.html#pypath.visual.igraph_drawing.edge.DarkToLightEdgeDrawer.draw_undirected_edge">(pypath.visual.igraph_drawing.edge.DarkToLightEdgeDrawer method)</a>
+        <li><a href="api/pypath.core.annot.InterPro.html#pypath.core.annot.InterPro.all_complexes">(pypath.core.annot.InterPro method)</a>
 </li>
-        <li><a href="api/pypath.visual.igraph_drawing.edge.LightToDarkEdgeDrawer.html#pypath.visual.igraph_drawing.edge.LightToDarkEdgeDrawer.draw_undirected_edge">(pypath.visual.igraph_drawing.edge.LightToDarkEdgeDrawer method)</a>
+        <li><a href="api/pypath.core.annot.Intogen.html#pypath.core.annot.Intogen.all_complexes">(pypath.core.annot.Intogen method)</a>
 </li>
-        <li><a href="api/pypath.visual.igraph_drawing.edge.TaperedEdgeDrawer.html#pypath.visual.igraph_drawing.edge.TaperedEdgeDrawer.draw_undirected_edge">(pypath.visual.igraph_drawing.edge.TaperedEdgeDrawer method)</a>
+        <li><a href="api/pypath.core.annot.Italk.html#pypath.core.annot.Italk.all_complexes">(pypath.core.annot.Italk method)</a>
 </li>
-      </ul></li>
-      <li><a href="api/pypath.inputs.adrecs.AdrecsDrug.html#pypath.inputs.adrecs.AdrecsDrug.drug">drug (pypath.inputs.adrecs.AdrecsDrug attribute)</a>
-
-      <ul>
-        <li><a href="api/pypath.inputs.adrecs.AdrecsDrugAdr.html#pypath.inputs.adrecs.AdrecsDrugAdr.drug">(pypath.inputs.adrecs.AdrecsDrugAdr attribute)</a>
+        <li><a href="api/pypath.core.annot.KeggPathways.html#pypath.core.annot.KeggPathways.all_complexes">(pypath.core.annot.KeggPathways method)</a>
 </li>
-      </ul></li>
-      <li><a href="api/pypath.inputs.adrecs.AdrecsDrugAdr.html#pypath.inputs.adrecs.AdrecsDrugAdr.drug_badd">drug_badd (pypath.inputs.adrecs.AdrecsDrugAdr attribute)</a>
+        <li><a href="api/pypath.core.annot.KeggPathwaysPC.html#pypath.core.annot.KeggPathwaysPC.all_complexes">(pypath.core.annot.KeggPathwaysPC method)</a>
 </li>
-      <li><a href="api/pypath.inputs.kegg_api.drug_to_disease.html#pypath.inputs.kegg_api.drug_to_disease">drug_to_disease() (in module pypath.inputs.kegg_api)</a>
+        <li><a href="api/pypath.core.annot.Kinasedotcom.html#pypath.core.annot.Kinasedotcom.all_complexes">(pypath.core.annot.Kinasedotcom method)</a>
 </li>
-      <li><a href="api/pypath.inputs.kegg_api.drug_to_drug.html#pypath.inputs.kegg_api.drug_to_drug">drug_to_drug() (in module pypath.inputs.kegg_api)</a>
+        <li><a href="api/pypath.core.annot.Kirouac2010.html#pypath.core.annot.Kirouac2010.all_complexes">(pypath.core.annot.Kirouac2010 method)</a>
 </li>
-      <li><a href="api/pypath.inputs.kegg_api.drug_to_gene.html#pypath.inputs.kegg_api.drug_to_gene">drug_to_gene() (in module pypath.inputs.kegg_api)</a>
+        <li><a href="api/pypath.core.annot.Lambert2018.html#pypath.core.annot.Lambert2018.all_complexes">(pypath.core.annot.Lambert2018 method)</a>
 </li>
-      <li><a href="api/pypath.inputs.kegg_api.drug_to_pathway.html#pypath.inputs.kegg_api.drug_to_pathway">drug_to_pathway() (in module pypath.inputs.kegg_api)</a>
+        <li><a href="api/pypath.core.annot.LigandReceptor.html#pypath.core.annot.LigandReceptor.all_complexes">(pypath.core.annot.LigandReceptor method)</a>
 </li>
-      <li><a href="api/pypath.inputs.adrecs.AdrecsDrug.html#pypath.inputs.adrecs.AdrecsDrug.drugbank">drugbank (pypath.inputs.adrecs.AdrecsDrug attribute)</a>
+        <li><a href="api/pypath.core.annot.Locate.html#pypath.core.annot.Locate.all_complexes">(pypath.core.annot.Locate method)</a>
 </li>
-      <li><a href="api/pypath.inputs.drugbank.drugbank_annotations.html#pypath.inputs.drugbank.drugbank_annotations">drugbank_annotations() (in module pypath.inputs.drugbank)</a>
+        <li><a href="api/pypath.core.annot.Lrdb.html#pypath.core.annot.Lrdb.all_complexes">(pypath.core.annot.Lrdb method)</a>
 </li>
-      <li><a href="api/pypath.inputs.drugbank.drugbank_drugs.html#pypath.inputs.drugbank.drugbank_drugs">drugbank_drugs() (in module pypath.inputs.drugbank)</a>
+        <li><a href="api/pypath.core.annot.Matrisome.html#pypath.core.annot.Matrisome.all_complexes">(pypath.core.annot.Matrisome method)</a>
 </li>
-      <li><a href="api/pypath.inputs.drugbank.DrugbankFull.html#pypath.inputs.drugbank.DrugbankFull.drugbank_drugs_full">drugbank_drugs_full() (pypath.inputs.drugbank.DrugbankFull method)</a>
+        <li><a href="api/pypath.core.annot.Matrixdb.html#pypath.core.annot.Matrixdb.all_complexes">(pypath.core.annot.Matrixdb method)</a>
 </li>
-      <li><a href="api/pypath.inputs.drugbank.DrugbankFull.html#pypath.inputs.drugbank.DrugbankFull.drugbank_external_ids_full">drugbank_external_ids_full() (pypath.inputs.drugbank.DrugbankFull method)</a>
+        <li><a href="api/pypath.core.annot.Mcam.html#pypath.core.annot.Mcam.all_complexes">(pypath.core.annot.Mcam method)</a>
 </li>
-      <li><a href="api/pypath.inputs.drugbank.drugbank_interactions.html#pypath.inputs.drugbank.drugbank_interactions">drugbank_interactions() (in module pypath.inputs.drugbank)</a>
+        <li><a href="api/pypath.core.annot.Membranome.html#pypath.core.annot.Membranome.all_complexes">(pypath.core.annot.Membranome method)</a>
 </li>
-      <li><a href="api/pypath.inputs.drugbank.drugbank_mapping.html#pypath.inputs.drugbank.drugbank_mapping">drugbank_mapping() (in module pypath.inputs.drugbank)</a>
+        <li><a href="api/pypath.core.annot.Msigdb.html#pypath.core.annot.Msigdb.all_complexes">(pypath.core.annot.Msigdb method)</a>
 </li>
-      <li><a href="api/pypath.inputs.drugbank.DrugbankFull.html#pypath.inputs.drugbank.DrugbankFull.drugbank_properties_full">drugbank_properties_full() (pypath.inputs.drugbank.DrugbankFull method)</a>
+        <li><a href="api/pypath.core.annot.NetpathPathways.html#pypath.core.annot.NetpathPathways.all_complexes">(pypath.core.annot.NetpathPathways method)</a>
 </li>
-      <li><a href="api/pypath.inputs.drugbank.drugbank_raw_interactions.html#pypath.inputs.drugbank.drugbank_raw_interactions">drugbank_raw_interactions() (in module pypath.inputs.drugbank)</a>
+        <li><a href="api/pypath.core.annot.Opm.html#pypath.core.annot.Opm.all_complexes">(pypath.core.annot.Opm method)</a>
 </li>
-      <li><a href="api/pypath.inputs.drugbank.DrugbankFull.html#pypath.inputs.drugbank.DrugbankFull.drugbank_targets_full">drugbank_targets_full() (pypath.inputs.drugbank.DrugbankFull method)</a>
+        <li><a href="api/pypath.core.annot.Panglaodb.html#pypath.core.annot.Panglaodb.all_complexes">(pypath.core.annot.Panglaodb method)</a>
 </li>
-      <li><a href="api/pypath.inputs.drugbank.DrugbankFull.html#pypath.inputs.drugbank.DrugbankFull">DrugbankFull (class in pypath.inputs.drugbank)</a>
+        <li><a href="api/pypath.core.annot.Phobius.html#pypath.core.annot.Phobius.all_complexes">(pypath.core.annot.Phobius method)</a>
 </li>
-      <li><a href="api/pypath.inputs.drugcentral.drugcentral_drugs.html#pypath.inputs.drugcentral.drugcentral_drugs">drugcentral_drugs() (in module pypath.inputs.drugcentral)</a>
+        <li><a href="api/pypath.core.annot.Phosphatome.html#pypath.core.annot.Phosphatome.all_complexes">(pypath.core.annot.Phosphatome method)</a>
 </li>
-      <li><a href="api/pypath.inputs.drugcentral.drugcentral_interactions.html#pypath.inputs.drugcentral.drugcentral_interactions">drugcentral_interactions() (in module pypath.inputs.drugcentral)</a>
+        <li><a href="api/pypath.core.annot.Progeny.html#pypath.core.annot.Progeny.all_complexes">(pypath.core.annot.Progeny method)</a>
 </li>
-      <li><a href="api/pypath.inputs.drugcentral.drugcentral_mapping.html#pypath.inputs.drugcentral.drugcentral_mapping">drugcentral_mapping() (in module pypath.inputs.drugcentral)</a>
+        <li><a href="api/pypath.core.annot.Ramilowski2015.html#pypath.core.annot.Ramilowski2015.all_complexes">(pypath.core.annot.Ramilowski2015 method)</a>
 </li>
-      <li><a href="api/pypath.share.curl.dryrun_off.html#pypath.share.curl.dryrun_off">dryrun_off (class in pypath.share.curl)</a>
+        <li><a href="api/pypath.core.annot.Ramilowski2015Location.html#pypath.core.annot.Ramilowski2015Location.all_complexes">(pypath.core.annot.Ramilowski2015Location method)</a>
 </li>
-      <li><a href="api/pypath.share.curl.dryrun_on.html#pypath.share.curl.dryrun_on">dryrun_on (class in pypath.share.curl)</a>
+        <li><a href="api/pypath.core.annot.Scconnect.html#pypath.core.annot.Scconnect.all_complexes">(pypath.core.annot.Scconnect method)</a>
 </li>
-  </ul></td>
-</tr></table>
-
-<h2 id="E">E</h2>
-<table style="width: 100%" class="indextable genindextable"><tr>
-  <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="api/pypath.inputs.ebi.ebi_rest.html#pypath.inputs.ebi.ebi_rest">ebi_rest() (in module pypath.inputs.ebi)</a>
+        <li><a href="api/pypath.core.annot.ScconnectComplex.html#pypath.core.annot.ScconnectComplex.all_complexes">(pypath.core.annot.ScconnectComplex method)</a>
 </li>
-      <li><a href="api/pypath.inputs.dorothea.DorotheaInteraction.html#pypath.inputs.dorothea.DorotheaInteraction.effect">effect (pypath.inputs.dorothea.DorotheaInteraction attribute)</a>
+        <li><a href="api/pypath.core.annot.SignalinkFunctions.html#pypath.core.annot.SignalinkFunctions.all_complexes">(pypath.core.annot.SignalinkFunctions method)</a>
 </li>
-      <li><a href="api/pypath.inputs.elm.elm_classes.html#pypath.inputs.elm.elm_classes">elm_classes() (in module pypath.inputs.elm)</a>
+        <li><a href="api/pypath.core.annot.SignalinkPathways.html#pypath.core.annot.SignalinkPathways.all_complexes">(pypath.core.annot.SignalinkPathways method)</a>
 </li>
-      <li><a href="api/pypath.inputs.elm.elm_domains.html#pypath.inputs.elm.elm_domains">elm_domains() (in module pypath.inputs.elm)</a>
+        <li><a href="api/pypath.core.annot.SignorPathways.html#pypath.core.annot.SignorPathways.all_complexes">(pypath.core.annot.SignorPathways method)</a>
 </li>
-      <li><a href="api/pypath.inputs.elm.elm_instances.html#pypath.inputs.elm.elm_instances">elm_instances() (in module pypath.inputs.elm)</a>
+        <li><a href="api/pypath.core.annot.Surfaceome.html#pypath.core.annot.Surfaceome.all_complexes">(pypath.core.annot.Surfaceome method)</a>
 </li>
-      <li><a href="api/pypath.inputs.elm.elm_interactions.html#pypath.inputs.elm.elm_interactions">elm_interactions() (in module pypath.inputs.elm)</a>
+        <li><a href="api/pypath.core.annot.Talklr.html#pypath.core.annot.Talklr.all_complexes">(pypath.core.annot.Talklr method)</a>
 </li>
-      <li><a href="api/pypath.inputs.embopress.embopress_supplementary.html#pypath.inputs.embopress.embopress_supplementary">embopress_supplementary() (in module pypath.inputs.embopress)</a>
+        <li><a href="api/pypath.core.annot.Tcdb.html#pypath.core.annot.Tcdb.all_complexes">(pypath.core.annot.Tcdb method)</a>
 </li>
-      <li><a href="api/pypath.internals.license.License.html#pypath.internals.license.License.enables">enables() (pypath.internals.license.License method)</a>
+        <li><a href="api/pypath.core.annot.Tfcensus.html#pypath.core.annot.Tfcensus.all_complexes">(pypath.core.annot.Tfcensus method)</a>
 </li>
-      <li><a href="api/pypath.inputs.encode.encode_tf_mirna_interactions.html#pypath.inputs.encode.encode_tf_mirna_interactions">encode_tf_mirna_interactions() (in module pypath.inputs.encode)</a>
+        <li><a href="api/pypath.core.annot.Topdb.html#pypath.core.annot.Topdb.all_complexes">(pypath.core.annot.Topdb method)</a>
 </li>
-      <li><a href="api/pypath.inputs.uniprot.Taxon.html#pypath.inputs.uniprot.Taxon.english">english (pypath.inputs.uniprot.Taxon attribute)</a>
+        <li><a href="api/pypath.core.annot.UniprotFamilies.html#pypath.core.annot.UniprotFamilies.all_complexes">(pypath.core.annot.UniprotFamilies method)</a>
 </li>
-      <li><a href="api/pypath.inputs.ensembl.ensembl_organisms.html#pypath.inputs.ensembl.ensembl_organisms">ensembl_organisms() (in module pypath.inputs.ensembl)</a>
+        <li><a href="api/pypath.core.annot.UniprotKeywords.html#pypath.core.annot.UniprotKeywords.all_complexes">(pypath.core.annot.UniprotKeywords method)</a>
 </li>
-      <li><a href="api/pypath.utils.taxonomy.ensure_common_name.html#pypath.utils.taxonomy.ensure_common_name">ensure_common_name() (in module pypath.utils.taxonomy)</a>
+        <li><a href="api/pypath.core.annot.UniprotLocations.html#pypath.core.annot.UniprotLocations.all_complexes">(pypath.core.annot.UniprotLocations method)</a>
 </li>
-      <li><a href="api/pypath.utils.taxonomy.ensure_ensembl_name.html#pypath.utils.taxonomy.ensure_ensembl_name">ensure_ensembl_name() (in module pypath.utils.taxonomy)</a>
+        <li><a href="api/pypath.core.annot.UniprotTissues.html#pypath.core.annot.UniprotTissues.all_complexes">(pypath.core.annot.UniprotTissues method)</a>
 </li>
-      <li><a href="api/pypath.utils.taxonomy.ensure_latin_name.html#pypath.utils.taxonomy.ensure_latin_name">ensure_latin_name() (in module pypath.utils.taxonomy)</a>
+        <li><a href="api/pypath.core.annot.UniprotTopologies.html#pypath.core.annot.UniprotTopologies.all_complexes">(pypath.core.annot.UniprotTopologies method)</a>
 </li>
-  </ul></td>
-  <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="api/pypath.utils.taxonomy.ensure_ncbi_tax_id.html#pypath.utils.taxonomy.ensure_ncbi_tax_id">ensure_ncbi_tax_id() (in module pypath.utils.taxonomy)</a>
+        <li><a href="api/pypath.core.annot.Vesiclepedia.html#pypath.core.annot.Vesiclepedia.all_complexes">(pypath.core.annot.Vesiclepedia method)</a>
 </li>
-      <li><a href="api/pypath.inputs.uniprot.UniprotRecordHistory.html#pypath.inputs.uniprot.UniprotRecordHistory.entry_name">entry_name (pypath.inputs.uniprot.UniprotRecordHistory attribute)</a>
+        <li><a href="api/pypath.core.annot.Wang.html#pypath.core.annot.Wang.all_complexes">(pypath.core.annot.Wang method)</a>
 </li>
-      <li><a href="api/pypath.inputs.uniprot.UniprotRecordHistory.html#pypath.inputs.uniprot.UniprotRecordHistory.entry_version">entry_version (pypath.inputs.uniprot.UniprotRecordHistory attribute)</a>
+        <li><a href="api/pypath.core.annot.Zhong2015.html#pypath.core.annot.Zhong2015.all_complexes">(pypath.core.annot.Zhong2015 method)</a>
 </li>
-      <li><a href="api/pypath.resources.data_formats.enzyme_substrate.html#pypath.resources.data_formats.enzyme_substrate">enzyme_substrate (in module pypath.resources.data_formats)</a>
+      </ul></li>
+      <li><a href="api/pypath.core.annot.Adhesome.html#pypath.core.annot.Adhesome.all_entities">all_entities() (pypath.core.annot.Adhesome method)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.annot.Almen2009.html#pypath.core.annot.Almen2009.all_entities">(pypath.core.annot.Almen2009 method)</a>
 </li>
-      <li><a href="api/pypath.internals.resource.EnzymeSubstrateResource.html#pypath.internals.resource.EnzymeSubstrateResource">EnzymeSubstrateResource (class in pypath.internals.resource)</a>
+        <li><a href="api/pypath.core.annot.AnnotationBase.html#pypath.core.annot.AnnotationBase.all_entities">(pypath.core.annot.AnnotationBase method)</a>
 </li>
-      <li><a href="api/pypath.internals.resource.EnzymeSubstrateResourceKey.html#pypath.internals.resource.EnzymeSubstrateResourceKey">EnzymeSubstrateResourceKey (class in pypath.internals.resource)</a>
+        <li><a href="api/pypath.core.annot.Baccin2019.html#pypath.core.annot.Baccin2019.all_entities">(pypath.core.annot.Baccin2019 method)</a>
 </li>
-      <li><a href="api/pypath.inputs.eutils.esummary.html#pypath.inputs.eutils.esummary">esummary() (in module pypath.inputs.eutils)</a>
+        <li><a href="api/pypath.core.annot.Biogps.html#pypath.core.annot.Biogps.all_entities">(pypath.core.annot.Biogps method)</a>
 </li>
-      <li><a href="api/pypath.inputs.pathophenodb.DiseasePathogen.html#pypath.inputs.pathophenodb.DiseasePathogen.evidence">evidence (pypath.inputs.pathophenodb.DiseasePathogen attribute)</a>
+        <li><a href="api/pypath.core.annot.Cancerdrugsdb.html#pypath.core.annot.Cancerdrugsdb.all_entities">(pypath.core.annot.Cancerdrugsdb method)</a>
 </li>
-      <li><a href="api/pypath.inputs.expasy.expasy_enzyme_classes.html#pypath.inputs.expasy.expasy_enzyme_classes">expasy_enzyme_classes() (in module pypath.inputs.expasy)</a>
+        <li><a href="api/pypath.core.annot.CancerGeneCensus.html#pypath.core.annot.CancerGeneCensus.all_entities">(pypath.core.annot.CancerGeneCensus method)</a>
 </li>
-      <li><a href="api/pypath.inputs.expasy.expasy_enzymes.html#pypath.inputs.expasy.expasy_enzymes">expasy_enzymes() (in module pypath.inputs.expasy)</a>
+        <li><a href="api/pypath.core.annot.Cancersea.html#pypath.core.annot.Cancersea.all_entities">(pypath.core.annot.Cancersea method)</a>
 </li>
-      <li><a href="api/pypath.inputs.diseases.experiments_filtered.html#pypath.inputs.diseases.experiments_filtered">experiments_filtered() (in module pypath.inputs.diseases)</a>
+        <li><a href="api/pypath.core.annot.Cellcall.html#pypath.core.annot.Cellcall.all_entities">(pypath.core.annot.Cellcall method)</a>
 </li>
-      <li><a href="api/pypath.inputs.diseases.experiments_full.html#pypath.inputs.diseases.experiments_full">experiments_full() (in module pypath.inputs.diseases)</a>
+        <li><a href="api/pypath.core.annot.Cellcellinteractions.html#pypath.core.annot.Cellcellinteractions.all_entities">(pypath.core.annot.Cellcellinteractions method)</a>
 </li>
-      <li><a href="api/pypath.utils.go.GOAnnotation.html#pypath.utils.go.GOAnnotation.expr_names_to_terms">expr_names_to_terms() (pypath.utils.go.GOAnnotation method)</a>
+        <li><a href="api/pypath.core.annot.Cellchatdb.html#pypath.core.annot.Cellchatdb.all_entities">(pypath.core.annot.Cellchatdb method)</a>
 </li>
-      <li><a href="api/pypath.share.curl.Curl.html#pypath.share.curl.Curl.extract">extract() (pypath.share.curl.Curl method)</a>
-
-      <ul>
-        <li><a href="api/pypath.share.curl.FileOpener.html#pypath.share.curl.FileOpener.extract">(pypath.share.curl.FileOpener method)</a>
+        <li><a href="api/pypath.core.annot.CellchatdbComplex.html#pypath.core.annot.CellchatdbComplex.all_entities">(pypath.core.annot.CellchatdbComplex method)</a>
 </li>
-      </ul></li>
-  </ul></td>
-</tr></table>
-
-<h2 id="F">F</h2>
-<table style="width: 100%" class="indextable genindextable"><tr>
-  <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="api/pypath.inputs.uniprot.UniprotQuery.html#pypath.inputs.uniprot.UniprotQuery.fail_on_empty">fail_on_empty (pypath.inputs.uniprot.UniprotQuery attribute)</a>
+        <li><a href="api/pypath.core.annot.Cellinker.html#pypath.core.annot.Cellinker.all_entities">(pypath.core.annot.Cellinker method)</a>
 </li>
-      <li><a href="api/pypath.inputs.hmdb.schema.common.Field.html#pypath.inputs.hmdb.schema.common.Field">Field (class in pypath.inputs.hmdb.schema.common)</a>
+        <li><a href="api/pypath.core.annot.CellinkerComplex.html#pypath.core.annot.CellinkerComplex.all_entities">(pypath.core.annot.CellinkerComplex method)</a>
 </li>
-      <li><a href="api/pypath.internals.input_formats.FileMapping.html#pypath.internals.input_formats.FileMapping">FileMapping (class in pypath.internals.input_formats)</a>
+        <li><a href="api/pypath.core.annot.CellPhoneDB.html#pypath.core.annot.CellPhoneDB.all_entities">(pypath.core.annot.CellPhoneDB method)</a>
 </li>
-      <li><a href="api/pypath.share.curl.FileOpener.html#pypath.share.curl.FileOpener">FileOpener (class in pypath.share.curl)</a>
+        <li><a href="api/pypath.core.annot.CellPhoneDBComplex.html#pypath.core.annot.CellPhoneDBComplex.all_entities">(pypath.core.annot.CellPhoneDBComplex method)</a>
 </li>
-  </ul></td>
-  <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="api/pypath.core.common.filter_network_df.html#pypath.core.common.filter_network_df">filter_network_df() (in module pypath.core.common)</a>
+        <li><a href="api/pypath.core.annot.CellSurfaceProteinAtlas.html#pypath.core.annot.CellSurfaceProteinAtlas.all_entities">(pypath.core.annot.CellSurfaceProteinAtlas method)</a>
 </li>
-      <li><a href="api/pypath.utils.seq.Seq.html#pypath.utils.seq.Seq.findall">findall() (pypath.utils.seq.Seq method)</a>
+        <li><a href="api/pypath.core.annot.CellSurfaceProteinAtlasCellType.html#pypath.core.annot.CellSurfaceProteinAtlasCellType.all_entities">(pypath.core.annot.CellSurfaceProteinAtlasCellType method)</a>
 </li>
-      <li><a href="api/pypath.utils.go.GeneOntology.html#pypath.utils.go.GeneOntology.flatten">flatten() (pypath.utils.go.GeneOntology method)</a>
+        <li><a href="api/pypath.core.annot.Celltalkdb.html#pypath.core.annot.Celltalkdb.all_entities">(pypath.core.annot.Celltalkdb method)</a>
 </li>
-      <li><a href="api/pypath.inputs.sider.SiderSideeffetFrequency.html#pypath.inputs.sider.SiderSideeffetFrequency.frequency">frequency (pypath.inputs.sider.SiderSideeffetFrequency attribute)</a>
+        <li><a href="api/pypath.core.annot.Celltypist.html#pypath.core.annot.Celltypist.all_entities">(pypath.core.annot.Celltypist method)</a>
 </li>
-  </ul></td>
-</tr></table>
-
-<h2 id="G">G</h2>
-<table style="width: 100%" class="indextable genindextable"><tr>
-  <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="api/pypath.inputs.kegg_api.gene_to_disease.html#pypath.inputs.kegg_api.gene_to_disease">gene_to_disease() (in module pypath.inputs.kegg_api)</a>
+        <li><a href="api/pypath.core.annot.Comppi.html#pypath.core.annot.Comppi.all_entities">(pypath.core.annot.Comppi method)</a>
 </li>
-      <li><a href="api/pypath.inputs.kegg_api.gene_to_drug.html#pypath.inputs.kegg_api.gene_to_drug">gene_to_drug() (in module pypath.inputs.kegg_api)</a>
+        <li><a href="api/pypath.core.annot.Connectomedb.html#pypath.core.annot.Connectomedb.all_entities">(pypath.core.annot.Connectomedb method)</a>
 </li>
-      <li><a href="api/pypath.inputs.kegg_api.gene_to_pathway.html#pypath.inputs.kegg_api.gene_to_pathway">gene_to_pathway() (in module pypath.inputs.kegg_api)</a>
+        <li><a href="api/pypath.core.annot.Corum.html#pypath.core.annot.Corum.all_entities">(pypath.core.annot.Corum method)</a>
 </li>
-      <li><a href="api/pypath.inputs.genecards.genecards_datasheet.html#pypath.inputs.genecards.genecards_datasheet">genecards_datasheet() (in module pypath.inputs.genecards)</a>
+        <li><a href="api/pypath.core.annot.CorumFuncat.html#pypath.core.annot.CorumFuncat.all_entities">(pypath.core.annot.CorumFuncat method)</a>
 </li>
-      <li><a href="api/pypath.inputs.genecards.genecards_soup.html#pypath.inputs.genecards.genecards_soup">genecards_soup() (in module pypath.inputs.genecards)</a>
+        <li><a href="api/pypath.core.annot.CorumGO.html#pypath.core.annot.CorumGO.all_entities">(pypath.core.annot.CorumGO method)</a>
 </li>
-      <li><a href="api/pypath.inputs.genecards.genecards_summaries.html#pypath.inputs.genecards.genecards_summaries">genecards_summaries() (in module pypath.inputs.genecards)</a>
+        <li><a href="api/pypath.core.annot.Cpad.html#pypath.core.annot.Cpad.all_entities">(pypath.core.annot.Cpad method)</a>
 </li>
-      <li><a href="api/pypath.utils.go.GeneOntology.html#pypath.utils.go.GeneOntology">GeneOntology (class in pypath.utils.go)</a>
+        <li><a href="api/pypath.core.annot.Cytosig.html#pypath.core.annot.Cytosig.all_entities">(pypath.core.annot.Cytosig method)</a>
 </li>
-      <li><a href="api/pypath.internals.resource.NetworkDataset.html#pypath.internals.resource.NetworkDataset.get">get() (pypath.internals.resource.NetworkDataset method)</a>
+        <li><a href="api/pypath.core.annot.Dgidb.html#pypath.core.annot.Dgidb.all_entities">(pypath.core.annot.Dgidb method)</a>
 </li>
-      <li><a href="api/pypath.inputs.reaction.get_acsn_effects.html#pypath.inputs.reaction.get_acsn_effects">get_acsn_effects() (in module pypath.inputs.reaction)</a>
+        <li><a href="api/pypath.core.annot.Disgenet.html#pypath.core.annot.Disgenet.all_entities">(pypath.core.annot.Disgenet method)</a>
 </li>
-      <li><a href="api/pypath.utils.go.GeneOntology.html#pypath.utils.go.GeneOntology.get_all_ancestors">get_all_ancestors() (pypath.utils.go.GeneOntology method)</a>
+        <li><a href="api/pypath.core.annot.Embrace.html#pypath.core.annot.Embrace.all_entities">(pypath.core.annot.Embrace method)</a>
 </li>
-      <li><a href="api/pypath.utils.go.GeneOntology.html#pypath.utils.go.GeneOntology.get_all_descendants">get_all_descendants() (pypath.utils.go.GeneOntology method)</a>
+        <li><a href="api/pypath.core.annot.Exocarta.html#pypath.core.annot.Exocarta.all_entities">(pypath.core.annot.Exocarta method)</a>
 </li>
-      <li><a href="api/pypath.inputs.biomodels.get_all_models.html#pypath.inputs.biomodels.get_all_models">get_all_models() (in module pypath.inputs.biomodels)</a>
+        <li><a href="api/pypath.core.annot.GOIntercell.html#pypath.core.annot.GOIntercell.all_entities">(pypath.core.annot.GOIntercell method)</a>
 </li>
-      <li><a href="api/pypath.utils.go.GOAnnotation.html#pypath.utils.go.GOAnnotation.get_annot">get_annot() (pypath.utils.go.GOAnnotation method)</a>
+        <li><a href="api/pypath.core.annot.Gpcrdb.html#pypath.core.annot.Gpcrdb.all_entities">(pypath.core.annot.Gpcrdb method)</a>
 </li>
-      <li><a href="api/pypath.utils.go.GOAnnotation.html#pypath.utils.go.GOAnnotation.get_annot_ancestors">get_annot_ancestors() (pypath.utils.go.GOAnnotation method)</a>
+        <li><a href="api/pypath.core.annot.GuideToPharmacology.html#pypath.core.annot.GuideToPharmacology.all_entities">(pypath.core.annot.GuideToPharmacology method)</a>
 </li>
-      <li><a href="api/pypath.utils.go.GOCustomAnnotation.html#pypath.utils.go.GOCustomAnnotation.get_annotation">get_annotation() (pypath.utils.go.GOCustomAnnotation method)</a>
+        <li><a href="api/pypath.core.annot.Hgnc.html#pypath.core.annot.Hgnc.all_entities">(pypath.core.annot.Hgnc method)</a>
 </li>
-      <li><a href="api/pypath.utils.go.GOCustomAnnotation.html#pypath.utils.go.GOCustomAnnotation.get_annotations">get_annotations() (pypath.utils.go.GOCustomAnnotation method)</a>
+        <li><a href="api/pypath.core.annot.HpmrComplex.html#pypath.core.annot.HpmrComplex.all_entities">(pypath.core.annot.HpmrComplex method)</a>
 </li>
-      <li><a href="api/pypath.utils.go.GOAnnotation.html#pypath.utils.go.GOAnnotation.get_annots">get_annots() (pypath.utils.go.GOAnnotation method)</a>
+        <li><a href="api/pypath.core.annot.HPO.html#pypath.core.annot.HPO.all_entities">(pypath.core.annot.HPO method)</a>
 </li>
-      <li><a href="api/pypath.utils.go.GOAnnotation.html#pypath.utils.go.GOAnnotation.get_annots_ancestors">get_annots_ancestors() (pypath.utils.go.GOAnnotation method)</a>
+        <li><a href="api/pypath.core.annot.Humancellmap.html#pypath.core.annot.Humancellmap.all_entities">(pypath.core.annot.Humancellmap method)</a>
 </li>
-      <li><a href="api/pypath.utils.go.GeneOntology.html#pypath.utils.go.GeneOntology.get_aspect">get_aspect() (pypath.utils.go.GeneOntology method)</a>
+        <li><a href="api/pypath.core.annot.HumanPlasmaMembraneReceptome.html#pypath.core.annot.HumanPlasmaMembraneReceptome.all_entities">(pypath.core.annot.HumanPlasmaMembraneReceptome method)</a>
 </li>
-      <li><a href="api/pypath.inputs.biomodels.get_biomodels.html#pypath.inputs.biomodels.get_biomodels">get_biomodels() (in module pypath.inputs.biomodels)</a>
+        <li><a href="api/pypath.core.annot.HumanProteinAtlas.html#pypath.core.annot.HumanProteinAtlas.all_entities">(pypath.core.annot.HumanProteinAtlas method)</a>
 </li>
-      <li><a href="api/pypath.inputs.biomodels.get_biomodels_req.html#pypath.inputs.biomodels.get_biomodels_req">get_biomodels_req() (in module pypath.inputs.biomodels)</a>
+        <li><a href="api/pypath.core.annot.HumanProteinAtlasSecretome.html#pypath.core.annot.HumanProteinAtlasSecretome.all_entities">(pypath.core.annot.HumanProteinAtlasSecretome method)</a>
 </li>
-      <li><a href="api/pypath.share.cache.get_cachedir.html#pypath.share.cache.get_cachedir">get_cachedir() (in module pypath.share.cache)</a>
+        <li><a href="api/pypath.core.annot.HumanProteinAtlasSubcellular.html#pypath.core.annot.HumanProteinAtlasSubcellular.all_entities">(pypath.core.annot.HumanProteinAtlasSubcellular method)</a>
 </li>
-      <li><a href="api/pypath.legacy.db_categories.get_categories.html#pypath.legacy.db_categories.get_categories">get_categories() (in module pypath.legacy.db_categories)</a>
+        <li><a href="api/pypath.core.annot.Icellnet.html#pypath.core.annot.Icellnet.all_entities">(pypath.core.annot.Icellnet method)</a>
 </li>
-      <li><a href="api/pypath.legacy.db_categories.get_category.html#pypath.legacy.db_categories.get_category">get_category() (in module pypath.legacy.db_categories)</a>
+        <li><a href="api/pypath.core.annot.IcellnetComplex.html#pypath.core.annot.IcellnetComplex.all_entities">(pypath.core.annot.IcellnetComplex method)</a>
 </li>
-      <li><a href="api/pypath.resources.get_controller.html#pypath.resources.get_controller">get_controller() (in module pypath.resources)</a>
+        <li><a href="api/pypath.core.annot.Integrins.html#pypath.core.annot.Integrins.all_entities">(pypath.core.annot.Integrins method)</a>
 </li>
-      <li><a href="api/pypath.inputs.reaction.get_controls.html#pypath.inputs.reaction.get_controls">get_controls() (in module pypath.inputs.reaction)</a>
+        <li><a href="api/pypath.core.annot.InterPro.html#pypath.core.annot.InterPro.all_entities">(pypath.core.annot.InterPro method)</a>
 </li>
-      <li><a href="api/pypath.inputs.uniprot_db.get_db.html#pypath.inputs.uniprot_db.get_db">get_db() (in module pypath.inputs.uniprot_db)</a>
-
-      <ul>
-        <li><a href="api/pypath.utils.go.get_db.html#pypath.utils.go.get_db">(in module pypath.utils.go)</a>
+        <li><a href="api/pypath.core.annot.Intogen.html#pypath.core.annot.Intogen.all_entities">(pypath.core.annot.Intogen method)</a>
 </li>
-        <li><a href="api/pypath.utils.taxonomy.get_db.html#pypath.utils.taxonomy.get_db">(in module pypath.utils.taxonomy)</a>
+        <li><a href="api/pypath.core.annot.Italk.html#pypath.core.annot.Italk.all_entities">(pypath.core.annot.Italk method)</a>
 </li>
-      </ul></li>
-      <li><a href="api/pypath.share.progress.Progress.html#pypath.share.progress.Progress.get_desc">get_desc() (pypath.share.progress.Progress method)</a>
+        <li><a href="api/pypath.core.annot.KeggPathways.html#pypath.core.annot.KeggPathways.all_entities">(pypath.core.annot.KeggPathways method)</a>
 </li>
-      <li><a href="api/pypath.inputs.dorothea.get_dorothea_old.html#pypath.inputs.dorothea.get_dorothea_old">get_dorothea_old() (in module pypath.inputs.dorothea)</a>
+        <li><a href="api/pypath.core.annot.KeggPathwaysPC.html#pypath.core.annot.KeggPathwaysPC.all_entities">(pypath.core.annot.KeggPathwaysPC method)</a>
 </li>
-      <li><a href="api/pypath.inputs.exocarta.get_exocarta.html#pypath.inputs.exocarta.get_exocarta">get_exocarta() (in module pypath.inputs.exocarta)</a>
+        <li><a href="api/pypath.core.annot.Kinasedotcom.html#pypath.core.annot.Kinasedotcom.all_entities">(pypath.core.annot.Kinasedotcom method)</a>
 </li>
-      <li><a href="api/pypath.utils.proteomicsdb.ProteomicsDB.html#pypath.utils.proteomicsdb.ProteomicsDB.get_expression">get_expression() (pypath.utils.proteomicsdb.ProteomicsDB method)</a>
+        <li><a href="api/pypath.core.annot.Kirouac2010.html#pypath.core.annot.Kirouac2010.all_entities">(pypath.core.annot.Kirouac2010 method)</a>
 </li>
-      <li><a href="api/pypath.inputs.go.get_go_desc.html#pypath.inputs.go.get_go_desc">get_go_desc() (in module pypath.inputs.go)</a>
+        <li><a href="api/pypath.core.annot.Lambert2018.html#pypath.core.annot.Lambert2018.all_entities">(pypath.core.annot.Lambert2018 method)</a>
 </li>
-      <li><a href="api/pypath.inputs.go.get_go_quick.html#pypath.inputs.go.get_go_quick">get_go_quick() (in module pypath.inputs.go)</a>
+        <li><a href="api/pypath.core.annot.LigandReceptor.html#pypath.core.annot.LigandReceptor.all_entities">(pypath.core.annot.LigandReceptor method)</a>
 </li>
-      <li><a href="api/pypath.inputs.go.get_goslim.html#pypath.inputs.go.get_goslim">get_goslim() (in module pypath.inputs.go)</a>
+        <li><a href="api/pypath.core.annot.Locate.html#pypath.core.annot.Locate.all_entities">(pypath.core.annot.Locate method)</a>
 </li>
-      <li><a href="api/pypath.inputs.hprd.get_hprd.html#pypath.inputs.hprd.get_hprd">get_hprd() (in module pypath.inputs.hprd)</a>
+        <li><a href="api/pypath.core.annot.Lrdb.html#pypath.core.annot.Lrdb.all_entities">(pypath.core.annot.Lrdb method)</a>
 </li>
-      <li><a href="api/pypath.inputs.i3d.get_i3d.html#pypath.inputs.i3d.get_i3d">get_i3d() (in module pypath.inputs.i3d)</a>
+        <li><a href="api/pypath.core.annot.Matrisome.html#pypath.core.annot.Matrisome.all_entities">(pypath.core.annot.Matrisome method)</a>
 </li>
-      <li><a href="api/pypath.inputs.ielm.get_ielm.html#pypath.inputs.ielm.get_ielm">get_ielm() (in module pypath.inputs.ielm)</a>
+        <li><a href="api/pypath.core.annot.Matrixdb.html#pypath.core.annot.Matrixdb.all_entities">(pypath.core.annot.Matrixdb method)</a>
 </li>
-      <li><a href="api/pypath.inputs.ielm.get_ielm_huge.html#pypath.inputs.ielm.get_ielm_huge">get_ielm_huge() (in module pypath.inputs.ielm)</a>
+        <li><a href="api/pypath.core.annot.Mcam.html#pypath.core.annot.Mcam.all_entities">(pypath.core.annot.Mcam method)</a>
 </li>
-      <li><a href="api/pypath.inputs.imweb.get_imweb.html#pypath.inputs.imweb.get_imweb">get_imweb() (in module pypath.inputs.imweb)</a>
+        <li><a href="api/pypath.core.annot.Membranome.html#pypath.core.annot.Membranome.all_entities">(pypath.core.annot.Membranome method)</a>
 </li>
-      <li><a href="api/pypath.inputs.imweb.get_imweb_req.html#pypath.inputs.imweb.get_imweb_req">get_imweb_req() (in module pypath.inputs.imweb)</a>
+        <li><a href="api/pypath.core.annot.Msigdb.html#pypath.core.annot.Msigdb.all_entities">(pypath.core.annot.Msigdb method)</a>
 </li>
-      <li><a href="api/pypath.inputs.instruct.get_instruct.html#pypath.inputs.instruct.get_instruct">get_instruct() (in module pypath.inputs.instruct)</a>
+        <li><a href="api/pypath.core.annot.NetpathPathways.html#pypath.core.annot.NetpathPathways.all_entities">(pypath.core.annot.NetpathPathways method)</a>
 </li>
-      <li><a href="api/pypath.inputs.instruct.get_instruct_offsets.html#pypath.inputs.instruct.get_instruct_offsets">get_instruct_offsets() (in module pypath.inputs.instruct)</a>
+        <li><a href="api/pypath.core.annot.Opm.html#pypath.core.annot.Opm.all_entities">(pypath.core.annot.Opm method)</a>
 </li>
-      <li><a href="api/pypath.inputs.reaction.get_interactions.html#pypath.inputs.reaction.get_interactions">get_interactions() (in module pypath.inputs.reaction)</a>
+        <li><a href="api/pypath.core.annot.Panglaodb.html#pypath.core.annot.Panglaodb.all_entities">(pypath.core.annot.Panglaodb method)</a>
 </li>
-      <li><a href="api/pypath.utils.seq.get_isoforms.html#pypath.utils.seq.get_isoforms">get_isoforms() (in module pypath.utils.seq)</a>
+        <li><a href="api/pypath.core.annot.Phobius.html#pypath.core.annot.Phobius.all_entities">(pypath.core.annot.Phobius method)</a>
 </li>
-      <li><a href="api/pypath.inputs.mimp.get_kinase_class.html#pypath.inputs.mimp.get_kinase_class">get_kinase_class() (in module pypath.inputs.mimp)</a>
+        <li><a href="api/pypath.core.annot.Phosphatome.html#pypath.core.annot.Phosphatome.all_entities">(pypath.core.annot.Phosphatome method)</a>
 </li>
-      <li><a href="api/pypath.visual.igraph_drawing.edge.AbstractEdgeDrawer.html#pypath.visual.igraph_drawing.edge.AbstractEdgeDrawer.get_label_position">get_label_position() (pypath.visual.igraph_drawing.edge.AbstractEdgeDrawer method)</a>
-
-      <ul>
-        <li><a href="api/pypath.visual.igraph_drawing.edge.AlphaVaryingEdgeDrawer.html#pypath.visual.igraph_drawing.edge.AlphaVaryingEdgeDrawer.get_label_position">(pypath.visual.igraph_drawing.edge.AlphaVaryingEdgeDrawer method)</a>
+        <li><a href="api/pypath.core.annot.Progeny.html#pypath.core.annot.Progeny.all_entities">(pypath.core.annot.Progeny method)</a>
 </li>
-        <li><a href="api/pypath.visual.igraph_drawing.edge.ArrowEdgeDrawer.html#pypath.visual.igraph_drawing.edge.ArrowEdgeDrawer.get_label_position">(pypath.visual.igraph_drawing.edge.ArrowEdgeDrawer method)</a>
+        <li><a href="api/pypath.core.annot.Ramilowski2015.html#pypath.core.annot.Ramilowski2015.all_entities">(pypath.core.annot.Ramilowski2015 method)</a>
 </li>
-        <li><a href="api/pypath.visual.igraph_drawing.edge.DarkToLightEdgeDrawer.html#pypath.visual.igraph_drawing.edge.DarkToLightEdgeDrawer.get_label_position">(pypath.visual.igraph_drawing.edge.DarkToLightEdgeDrawer method)</a>
+        <li><a href="api/pypath.core.annot.Ramilowski2015Location.html#pypath.core.annot.Ramilowski2015Location.all_entities">(pypath.core.annot.Ramilowski2015Location method)</a>
 </li>
-        <li><a href="api/pypath.visual.igraph_drawing.edge.LightToDarkEdgeDrawer.html#pypath.visual.igraph_drawing.edge.LightToDarkEdgeDrawer.get_label_position">(pypath.visual.igraph_drawing.edge.LightToDarkEdgeDrawer method)</a>
+        <li><a href="api/pypath.core.annot.Scconnect.html#pypath.core.annot.Scconnect.all_entities">(pypath.core.annot.Scconnect method)</a>
 </li>
-        <li><a href="api/pypath.visual.igraph_drawing.edge.TaperedEdgeDrawer.html#pypath.visual.igraph_drawing.edge.TaperedEdgeDrawer.get_label_position">(pypath.visual.igraph_drawing.edge.TaperedEdgeDrawer method)</a>
+        <li><a href="api/pypath.core.annot.ScconnectComplex.html#pypath.core.annot.ScconnectComplex.all_entities">(pypath.core.annot.ScconnectComplex method)</a>
 </li>
-      </ul></li>
-  </ul></td>
-  <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="api/pypath.utils.reflists.get_manager.html#pypath.utils.reflists.get_manager">get_manager() (in module pypath.utils.reflists)</a>
+        <li><a href="api/pypath.core.annot.SignalinkFunctions.html#pypath.core.annot.SignalinkFunctions.all_entities">(pypath.core.annot.SignalinkFunctions method)</a>
 </li>
-      <li><a href="api/pypath.inputs.get_method.html#pypath.inputs.get_method">get_method() (in module pypath.inputs)</a>
+        <li><a href="api/pypath.core.annot.SignalinkPathways.html#pypath.core.annot.SignalinkPathways.all_entities">(pypath.core.annot.SignalinkPathways method)</a>
 </li>
-      <li><a href="api/pypath.inputs.mirbase.get_mirbase_aliases.html#pypath.inputs.mirbase.get_mirbase_aliases">get_mirbase_aliases() (in module pypath.inputs.mirbase)</a>
+        <li><a href="api/pypath.core.annot.SignorPathways.html#pypath.core.annot.SignorPathways.all_entities">(pypath.core.annot.SignorPathways method)</a>
 </li>
-      <li><a href="api/pypath.utils.go.GeneOntology.html#pypath.utils.go.GeneOntology.get_name">get_name() (pypath.utils.go.GeneOntology method)</a>
-
-      <ul>
-        <li><a href="api/pypath.utils.go.GOAnnotation.html#pypath.utils.go.GOAnnotation.get_name">(pypath.utils.go.GOAnnotation method)</a>
+        <li><a href="api/pypath.core.annot.Surfaceome.html#pypath.core.annot.Surfaceome.all_entities">(pypath.core.annot.Surfaceome method)</a>
 </li>
-      </ul></li>
-      <li><a href="api/pypath.utils.proteomicsdb.ProteomicsDB.html#pypath.utils.proteomicsdb.ProteomicsDB.get_pieces">get_pieces() (pypath.utils.proteomicsdb.ProteomicsDB method)</a>
+        <li><a href="api/pypath.core.annot.Talklr.html#pypath.core.annot.Talklr.all_entities">(pypath.core.annot.Talklr method)</a>
 </li>
-      <li><a href="api/pypath.inputs.pubmed.get_pmid.html#pypath.inputs.pubmed.get_pmid">get_pmid() (in module pypath.inputs.pubmed)</a>
+        <li><a href="api/pypath.core.annot.Tcdb.html#pypath.core.annot.Tcdb.all_entities">(pypath.core.annot.Tcdb method)</a>
 </li>
-      <li><a href="api/pypath.inputs.pro.get_pro.html#pypath.inputs.pro.get_pro">get_pro() (in module pypath.inputs.pro)</a>
+        <li><a href="api/pypath.core.annot.Tfcensus.html#pypath.core.annot.Tfcensus.all_entities">(pypath.core.annot.Tfcensus method)</a>
 </li>
-      <li><a href="api/pypath.utils.proteomicsdb.ProteomicsDB.html#pypath.utils.proteomicsdb.ProteomicsDB.get_proteins">get_proteins() (pypath.utils.proteomicsdb.ProteomicsDB method)</a>
+        <li><a href="api/pypath.core.annot.Topdb.html#pypath.core.annot.Topdb.all_entities">(pypath.core.annot.Topdb method)</a>
 </li>
-      <li><a href="api/pypath.inputs.protmapper.get_protmapper.html#pypath.inputs.protmapper.get_protmapper">get_protmapper() (in module pypath.inputs.protmapper)</a>
+        <li><a href="api/pypath.core.annot.UniprotFamilies.html#pypath.core.annot.UniprotFamilies.all_entities">(pypath.core.annot.UniprotFamilies method)</a>
 </li>
-      <li><a href="api/pypath.internals.refs.get_pubmed_data.html#pypath.internals.refs.get_pubmed_data">get_pubmed_data() (in module pypath.internals.refs)</a>
+        <li><a href="api/pypath.core.annot.UniprotKeywords.html#pypath.core.annot.UniprotKeywords.all_entities">(pypath.core.annot.UniprotKeywords method)</a>
 </li>
-      <li><a href="api/pypath.inputs.pubmed.get_pubmeds.html#pypath.inputs.pubmed.get_pubmeds">get_pubmeds() (in module pypath.inputs.pubmed)</a>
+        <li><a href="api/pypath.core.annot.UniprotLocations.html#pypath.core.annot.UniprotLocations.all_entities">(pypath.core.annot.UniprotLocations method)</a>
 </li>
-      <li><a href="api/pypath.inputs.reaction.get_reactions.html#pypath.inputs.reaction.get_reactions">get_reactions() (in module pypath.inputs.reaction)</a>
+        <li><a href="api/pypath.core.annot.UniprotTissues.html#pypath.core.annot.UniprotTissues.all_entities">(pypath.core.annot.UniprotTissues method)</a>
 </li>
-      <li><a href="api/pypath.utils.reflists.get_reflist.html#pypath.utils.reflists.get_reflist">get_reflist() (in module pypath.utils.reflists)</a>
+        <li><a href="api/pypath.core.annot.UniprotTopologies.html#pypath.core.annot.UniprotTopologies.all_entities">(pypath.core.annot.UniprotTopologies method)</a>
 </li>
-      <li><a href="api/pypath.utils.pdb.ResidueMapper.html#pypath.utils.pdb.ResidueMapper.get_residue">get_residue() (pypath.utils.pdb.ResidueMapper method)</a>
+        <li><a href="api/pypath.core.annot.Vesiclepedia.html#pypath.core.annot.Vesiclepedia.all_entities">(pypath.core.annot.Vesiclepedia method)</a>
 </li>
-      <li><a href="api/pypath.inputs.biomodels.get_single_model.html#pypath.inputs.biomodels.get_single_model">get_single_model() (in module pypath.inputs.biomodels)</a>
+        <li><a href="api/pypath.core.annot.Wang.html#pypath.core.annot.Wang.all_entities">(pypath.core.annot.Wang method)</a>
 </li>
-      <li><a href="api/pypath.inputs.reaction.get_soup.html#pypath.inputs.reaction.get_soup">get_soup() (in module pypath.inputs.reaction)</a>
+        <li><a href="api/pypath.core.annot.Zhong2015.html#pypath.core.annot.Zhong2015.all_entities">(pypath.core.annot.Zhong2015 method)</a>
 </li>
-      <li><a href="api/pypath.inputs.switches_elm.get_switches_elm.html#pypath.inputs.switches_elm.get_switches_elm">get_switches_elm() (in module pypath.inputs.switches_elm)</a>
+      </ul></li>
+      <li><a href="api/pypath.utils.go.GeneOntology.html#pypath.utils.go.GeneOntology.all_from_aspect">all_from_aspect() (pypath.utils.go.GeneOntology method)</a>
 </li>
-      <li><a href="api/pypath.utils.go.GeneOntology.html#pypath.utils.go.GeneOntology.get_term">get_term() (pypath.utils.go.GeneOntology method)</a>
+      <li><a href="api/pypath.core.annot.Adhesome.html#pypath.core.annot.Adhesome.all_mirnas">all_mirnas() (pypath.core.annot.Adhesome method)</a>
 
       <ul>
-        <li><a href="api/pypath.utils.go.GOAnnotation.html#pypath.utils.go.GOAnnotation.get_term">(pypath.utils.go.GOAnnotation method)</a>
+        <li><a href="api/pypath.core.annot.Almen2009.html#pypath.core.annot.Almen2009.all_mirnas">(pypath.core.annot.Almen2009 method)</a>
 </li>
-      </ul></li>
-      <li><a href="api/pypath.inputs.dorothea.get_tfregulons.html#pypath.inputs.dorothea.get_tfregulons">get_tfregulons() (in module pypath.inputs.dorothea)</a>
+        <li><a href="api/pypath.core.annot.AnnotationBase.html#pypath.core.annot.AnnotationBase.all_mirnas">(pypath.core.annot.AnnotationBase method)</a>
 </li>
-      <li><a href="api/pypath.utils.proteomicsdb.ProteomicsDB.html#pypath.utils.proteomicsdb.ProteomicsDB.get_tissues">get_tissues() (pypath.utils.proteomicsdb.ProteomicsDB method)</a>
+        <li><a href="api/pypath.core.annot.Baccin2019.html#pypath.core.annot.Baccin2019.all_mirnas">(pypath.core.annot.Baccin2019 method)</a>
 </li>
-      <li><a href="api/pypath.inputs.uniprot.get_uniprot_sec.html#pypath.inputs.uniprot.get_uniprot_sec">get_uniprot_sec() (in module pypath.inputs.uniprot)</a>
+        <li><a href="api/pypath.core.annot.Biogps.html#pypath.core.annot.Biogps.all_mirnas">(pypath.core.annot.Biogps method)</a>
 </li>
-      <li><a href="api/pypath.inputs.exocarta.get_vesiclepedia.html#pypath.inputs.exocarta.get_vesiclepedia">get_vesiclepedia() (in module pypath.inputs.exocarta)</a>
+        <li><a href="api/pypath.core.annot.Cancerdrugsdb.html#pypath.core.annot.Cancerdrugsdb.all_mirnas">(pypath.core.annot.Cancerdrugsdb method)</a>
 </li>
-      <li><a href="api/pypath.internals.resource.EnzymeSubstrateResource.html#pypath.internals.resource.EnzymeSubstrateResource.get_via">get_via() (pypath.internals.resource.EnzymeSubstrateResource method)</a>
+        <li><a href="api/pypath.core.annot.CancerGeneCensus.html#pypath.core.annot.CancerGeneCensus.all_mirnas">(pypath.core.annot.CancerGeneCensus method)</a>
 </li>
-      <li><a href="api/pypath.inputs.common.glom_fields.html#pypath.inputs.common.glom_fields">glom_fields() (in module pypath.inputs.common)</a>
+        <li><a href="api/pypath.core.annot.Cancersea.html#pypath.core.annot.Cancersea.all_mirnas">(pypath.core.annot.Cancersea method)</a>
 </li>
-      <li><a href="api/pypath.inputs.go.go_ancestors.html#pypath.inputs.go.go_ancestors">go_ancestors() (in module pypath.inputs.go)</a>
+        <li><a href="api/pypath.core.annot.Cellcall.html#pypath.core.annot.Cellcall.all_mirnas">(pypath.core.annot.Cellcall method)</a>
 </li>
-      <li><a href="api/pypath.inputs.go.go_ancestors_goose.html#pypath.inputs.go.go_ancestors_goose">go_ancestors_goose() (in module pypath.inputs.go)</a>
+        <li><a href="api/pypath.core.annot.Cellcellinteractions.html#pypath.core.annot.Cellcellinteractions.all_mirnas">(pypath.core.annot.Cellcellinteractions method)</a>
 </li>
-      <li><a href="api/pypath.inputs.go.go_ancestors_quickgo.html#pypath.inputs.go.go_ancestors_quickgo">go_ancestors_quickgo() (in module pypath.inputs.go)</a>
+        <li><a href="api/pypath.core.annot.Cellchatdb.html#pypath.core.annot.Cellchatdb.all_mirnas">(pypath.core.annot.Cellchatdb method)</a>
 </li>
-      <li><a href="api/pypath.inputs.go.go_annotations.html#pypath.inputs.go.go_annotations">go_annotations() (in module pypath.inputs.go)</a>
+        <li><a href="api/pypath.core.annot.CellchatdbComplex.html#pypath.core.annot.CellchatdbComplex.all_mirnas">(pypath.core.annot.CellchatdbComplex method)</a>
 </li>
-      <li><a href="api/pypath.inputs.go.go_annotations_all.html#pypath.inputs.go.go_annotations_all">go_annotations_all() (in module pypath.inputs.go)</a>
+        <li><a href="api/pypath.core.annot.Cellinker.html#pypath.core.annot.Cellinker.all_mirnas">(pypath.core.annot.Cellinker method)</a>
 </li>
-      <li><a href="api/pypath.inputs.go.go_annotations_goa.html#pypath.inputs.go.go_annotations_goa">go_annotations_goa() (in module pypath.inputs.go)</a>
+        <li><a href="api/pypath.core.annot.CellinkerComplex.html#pypath.core.annot.CellinkerComplex.all_mirnas">(pypath.core.annot.CellinkerComplex method)</a>
 </li>
-      <li><a href="api/pypath.inputs.go.go_annotations_goose.html#pypath.inputs.go.go_annotations_goose">go_annotations_goose() (in module pypath.inputs.go)</a>
+        <li><a href="api/pypath.core.annot.CellPhoneDB.html#pypath.core.annot.CellPhoneDB.all_mirnas">(pypath.core.annot.CellPhoneDB method)</a>
 </li>
-      <li><a href="api/pypath.inputs.go.go_annotations_quickgo.html#pypath.inputs.go.go_annotations_quickgo">go_annotations_quickgo() (in module pypath.inputs.go)</a>
+        <li><a href="api/pypath.core.annot.CellPhoneDBComplex.html#pypath.core.annot.CellPhoneDBComplex.all_mirnas">(pypath.core.annot.CellPhoneDBComplex method)</a>
 </li>
-      <li><a href="api/pypath.inputs.go.go_annotations_solr.html#pypath.inputs.go.go_annotations_solr">go_annotations_solr() (in module pypath.inputs.go)</a>
+        <li><a href="api/pypath.core.annot.CellSurfaceProteinAtlas.html#pypath.core.annot.CellSurfaceProteinAtlas.all_mirnas">(pypath.core.annot.CellSurfaceProteinAtlas method)</a>
 </li>
-      <li><a href="api/pypath.inputs.go.go_annotations_uniprot.html#pypath.inputs.go.go_annotations_uniprot">go_annotations_uniprot() (in module pypath.inputs.go)</a>
+        <li><a href="api/pypath.core.annot.CellSurfaceProteinAtlasCellType.html#pypath.core.annot.CellSurfaceProteinAtlasCellType.all_mirnas">(pypath.core.annot.CellSurfaceProteinAtlasCellType method)</a>
 </li>
-      <li><a href="api/pypath.inputs.go.go_descendants.html#pypath.inputs.go.go_descendants">go_descendants() (in module pypath.inputs.go)</a>
+        <li><a href="api/pypath.core.annot.Celltalkdb.html#pypath.core.annot.Celltalkdb.all_mirnas">(pypath.core.annot.Celltalkdb method)</a>
 </li>
-      <li><a href="api/pypath.inputs.go.go_descendants_goose.html#pypath.inputs.go.go_descendants_goose">go_descendants_goose() (in module pypath.inputs.go)</a>
+        <li><a href="api/pypath.core.annot.Celltypist.html#pypath.core.annot.Celltypist.all_mirnas">(pypath.core.annot.Celltypist method)</a>
 </li>
-      <li><a href="api/pypath.inputs.go.go_descendants_quickgo.html#pypath.inputs.go.go_descendants_quickgo">go_descendants_quickgo() (in module pypath.inputs.go)</a>
+        <li><a href="api/pypath.core.annot.Comppi.html#pypath.core.annot.Comppi.all_mirnas">(pypath.core.annot.Comppi method)</a>
 </li>
-      <li><a href="api/pypath.inputs.go.go_descendants_to_ancestors.html#pypath.inputs.go.go_descendants_to_ancestors">go_descendants_to_ancestors() (in module pypath.inputs.go)</a>
+        <li><a href="api/pypath.core.annot.Connectomedb.html#pypath.core.annot.Connectomedb.all_mirnas">(pypath.core.annot.Connectomedb method)</a>
 </li>
-      <li><a href="api/pypath.inputs.go.go_terms.html#pypath.inputs.go.go_terms">go_terms() (in module pypath.inputs.go)</a>
+        <li><a href="api/pypath.core.annot.Corum.html#pypath.core.annot.Corum.all_mirnas">(pypath.core.annot.Corum method)</a>
 </li>
-      <li><a href="api/pypath.inputs.go.go_terms_goose.html#pypath.inputs.go.go_terms_goose">go_terms_goose() (in module pypath.inputs.go)</a>
+        <li><a href="api/pypath.core.annot.CorumFuncat.html#pypath.core.annot.CorumFuncat.all_mirnas">(pypath.core.annot.CorumFuncat method)</a>
 </li>
-      <li><a href="api/pypath.inputs.go.go_terms_quickgo.html#pypath.inputs.go.go_terms_quickgo">go_terms_quickgo() (in module pypath.inputs.go)</a>
+        <li><a href="api/pypath.core.annot.CorumGO.html#pypath.core.annot.CorumGO.all_mirnas">(pypath.core.annot.CorumGO method)</a>
 </li>
-      <li><a href="api/pypath.inputs.go.go_terms_solr.html#pypath.inputs.go.go_terms_solr">go_terms_solr() (in module pypath.inputs.go)</a>
+        <li><a href="api/pypath.core.annot.Cpad.html#pypath.core.annot.Cpad.all_mirnas">(pypath.core.annot.Cpad method)</a>
 </li>
-      <li><a href="api/pypath.utils.go.GOAnnotation.html#pypath.utils.go.GOAnnotation">GOAnnotation (class in pypath.utils.go)</a>
+        <li><a href="api/pypath.core.annot.Cytosig.html#pypath.core.annot.Cytosig.all_mirnas">(pypath.core.annot.Cytosig method)</a>
 </li>
-      <li><a href="api/pypath.utils.go.GOCustomAnnotation.html#pypath.utils.go.GOCustomAnnotation">GOCustomAnnotation (class in pypath.utils.go)</a>
+        <li><a href="api/pypath.core.annot.Dgidb.html#pypath.core.annot.Dgidb.all_mirnas">(pypath.core.annot.Dgidb method)</a>
 </li>
-      <li><a href="api/pypath.inputs.gpcrdb.gpcrdb_annotations.html#pypath.inputs.gpcrdb.gpcrdb_annotations">gpcrdb_annotations() (in module pypath.inputs.gpcrdb)</a>
+        <li><a href="api/pypath.core.annot.Disgenet.html#pypath.core.annot.Disgenet.all_mirnas">(pypath.core.annot.Disgenet method)</a>
 </li>
-      <li><a href="api/pypath.inputs.graphviz.graphviz_attrs.html#pypath.inputs.graphviz.graphviz_attrs">graphviz_attrs() (in module pypath.inputs.graphviz)</a>
+        <li><a href="api/pypath.core.annot.Embrace.html#pypath.core.annot.Embrace.all_mirnas">(pypath.core.annot.Embrace method)</a>
 </li>
-  </ul></td>
-</tr></table>
-
-<h2 id="H">H</h2>
-<table style="width: 100%" class="indextable genindextable"><tr>
-  <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="api/pypath.utils.go.GOAnnotation.html#pypath.utils.go.GOAnnotation.has_any_term">has_any_term() (pypath.utils.go.GOAnnotation method)</a>
+        <li><a href="api/pypath.core.annot.Exocarta.html#pypath.core.annot.Exocarta.all_mirnas">(pypath.core.annot.Exocarta method)</a>
 </li>
-      <li><a href="api/pypath.utils.go.GOAnnotation.html#pypath.utils.go.GOAnnotation.has_term">has_term() (pypath.utils.go.GOAnnotation method)</a>
+        <li><a href="api/pypath.core.annot.GOIntercell.html#pypath.core.annot.GOIntercell.all_mirnas">(pypath.core.annot.GOIntercell method)</a>
 </li>
-      <li><a href="api/pypath.utils.go.GeneOntology.html#pypath.utils.go.GeneOntology.highest">highest() (pypath.utils.go.GeneOntology method)</a>
+        <li><a href="api/pypath.core.annot.Gpcrdb.html#pypath.core.annot.Gpcrdb.all_mirnas">(pypath.core.annot.Gpcrdb method)</a>
 </li>
-      <li><a href="api/pypath.inputs.hmdb.xml.hmdb_xml.html#pypath.inputs.hmdb.xml.hmdb_xml">hmdb_xml() (in module pypath.inputs.hmdb.xml)</a>
+        <li><a href="api/pypath.core.annot.GuideToPharmacology.html#pypath.core.annot.GuideToPharmacology.all_mirnas">(pypath.core.annot.GuideToPharmacology method)</a>
 </li>
-  </ul></td>
-  <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="api/pypath.internals.input_formats.HmdbMapping.html#pypath.internals.input_formats.HmdbMapping">HmdbMapping (class in pypath.internals.input_formats)</a>
+        <li><a href="api/pypath.core.annot.Hgnc.html#pypath.core.annot.Hgnc.all_mirnas">(pypath.core.annot.Hgnc method)</a>
 </li>
-      <li><a href="api/pypath.inputs.hprd.hprd_enzyme_substrate.html#pypath.inputs.hprd.hprd_enzyme_substrate">hprd_enzyme_substrate() (in module pypath.inputs.hprd)</a>
+        <li><a href="api/pypath.core.annot.HpmrComplex.html#pypath.core.annot.HpmrComplex.all_mirnas">(pypath.core.annot.HpmrComplex method)</a>
 </li>
-      <li><a href="api/pypath.inputs.hprd.hprd_interactions.html#pypath.inputs.hprd.hprd_interactions">hprd_interactions() (in module pypath.inputs.hprd)</a>
+        <li><a href="api/pypath.core.annot.HPO.html#pypath.core.annot.HPO.all_mirnas">(pypath.core.annot.HPO method)</a>
 </li>
-      <li><a href="api/pypath.inputs.hprd.hprd_interactions_htp.html#pypath.inputs.hprd.hprd_interactions_htp">hprd_interactions_htp() (in module pypath.inputs.hprd)</a>
+        <li><a href="api/pypath.core.annot.Humancellmap.html#pypath.core.annot.Humancellmap.all_mirnas">(pypath.core.annot.Humancellmap method)</a>
 </li>
-      <li><a href="api/pypath.inputs.htri.htri_interactions.html#pypath.inputs.htri.htri_interactions">htri_interactions() (in module pypath.inputs.htri)</a>
+        <li><a href="api/pypath.core.annot.HumanPlasmaMembraneReceptome.html#pypath.core.annot.HumanPlasmaMembraneReceptome.all_mirnas">(pypath.core.annot.HumanPlasmaMembraneReceptome method)</a>
 </li>
-  </ul></td>
-</tr></table>
-
-<h2 id="I">I</h2>
-<table style="width: 100%" class="indextable genindextable"><tr>
-  <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="api/pypath.utils.go.GOAnnotation.html#pypath.utils.go.GOAnnotation.i_select_by_term">i_select_by_term() (pypath.utils.go.GOAnnotation method)</a>
+        <li><a href="api/pypath.core.annot.HumanProteinAtlas.html#pypath.core.annot.HumanProteinAtlas.all_mirnas">(pypath.core.annot.HumanProteinAtlas method)</a>
 </li>
-      <li><a href="api/pypath.inputs.pathwaycommons.PathwayCommonsInteraction.html#pypath.inputs.pathwaycommons.PathwayCommonsInteraction.id_a">id_a (pypath.inputs.pathwaycommons.PathwayCommonsInteraction attribute)</a>
+        <li><a href="api/pypath.core.annot.HumanProteinAtlasSecretome.html#pypath.core.annot.HumanProteinAtlasSecretome.all_mirnas">(pypath.core.annot.HumanProteinAtlasSecretome method)</a>
 </li>
-      <li><a href="api/pypath.inputs.pathwaycommons.PathwayCommonsInteraction.html#pypath.inputs.pathwaycommons.PathwayCommonsInteraction.id_b">id_b (pypath.inputs.pathwaycommons.PathwayCommonsInteraction attribute)</a>
+        <li><a href="api/pypath.core.annot.HumanProteinAtlasSubcellular.html#pypath.core.annot.HumanProteinAtlasSubcellular.all_mirnas">(pypath.core.annot.HumanProteinAtlasSubcellular method)</a>
 </li>
-      <li><a href="api/pypath.inputs.uniprot.idmapping_idtypes.html#pypath.inputs.uniprot.idmapping_idtypes">idmapping_idtypes() (in module pypath.inputs.uniprot)</a>
+        <li><a href="api/pypath.core.annot.Icellnet.html#pypath.core.annot.Icellnet.all_mirnas">(pypath.core.annot.Icellnet method)</a>
 </li>
-      <li><a href="api/pypath.utils.unichem.Unichem.html#pypath.utils.unichem.Unichem.inchikey2anything">inchikey2anything() (pypath.utils.unichem.Unichem method)</a>
+        <li><a href="api/pypath.core.annot.IcellnetComplex.html#pypath.core.annot.IcellnetComplex.all_mirnas">(pypath.core.annot.IcellnetComplex method)</a>
 </li>
-      <li><a href="api/pypath.inputs.adrecs.AdrecsAdr.html#pypath.inputs.adrecs.AdrecsAdr.index">index() (pypath.inputs.adrecs.AdrecsAdr method)</a>
-
-      <ul>
-        <li><a href="api/pypath.inputs.adrecs.AdrecsChildParent.html#pypath.inputs.adrecs.AdrecsChildParent.index">(pypath.inputs.adrecs.AdrecsChildParent method)</a>
+        <li><a href="api/pypath.core.annot.Integrins.html#pypath.core.annot.Integrins.all_mirnas">(pypath.core.annot.Integrins method)</a>
 </li>
-        <li><a href="api/pypath.inputs.adrecs.AdrecsDrug.html#pypath.inputs.adrecs.AdrecsDrug.index">(pypath.inputs.adrecs.AdrecsDrug method)</a>
+        <li><a href="api/pypath.core.annot.InterPro.html#pypath.core.annot.InterPro.all_mirnas">(pypath.core.annot.InterPro method)</a>
 </li>
-        <li><a href="api/pypath.inputs.adrecs.AdrecsDrugAdr.html#pypath.inputs.adrecs.AdrecsDrugAdr.index">(pypath.inputs.adrecs.AdrecsDrugAdr method)</a>
+        <li><a href="api/pypath.core.annot.Intogen.html#pypath.core.annot.Intogen.all_mirnas">(pypath.core.annot.Intogen method)</a>
 </li>
-        <li><a href="api/pypath.inputs.adrecs.AdrecsTerm.html#pypath.inputs.adrecs.AdrecsTerm.index">(pypath.inputs.adrecs.AdrecsTerm method)</a>
+        <li><a href="api/pypath.core.annot.Italk.html#pypath.core.annot.Italk.all_mirnas">(pypath.core.annot.Italk method)</a>
 </li>
-        <li><a href="api/pypath.inputs.dorothea.DorotheaInteraction.html#pypath.inputs.dorothea.DorotheaInteraction.index">(pypath.inputs.dorothea.DorotheaInteraction method)</a>
+        <li><a href="api/pypath.core.annot.KeggPathways.html#pypath.core.annot.KeggPathways.all_mirnas">(pypath.core.annot.KeggPathways method)</a>
 </li>
-        <li><a href="api/pypath.inputs.pathophenodb.DiseasePathogen.html#pypath.inputs.pathophenodb.DiseasePathogen.index">(pypath.inputs.pathophenodb.DiseasePathogen method)</a>
+        <li><a href="api/pypath.core.annot.KeggPathwaysPC.html#pypath.core.annot.KeggPathwaysPC.all_mirnas">(pypath.core.annot.KeggPathwaysPC method)</a>
 </li>
-        <li><a href="api/pypath.inputs.pathwaycommons.PathwayCommonsInteraction.html#pypath.inputs.pathwaycommons.PathwayCommonsInteraction.index">(pypath.inputs.pathwaycommons.PathwayCommonsInteraction method)</a>
+        <li><a href="api/pypath.core.annot.Kinasedotcom.html#pypath.core.annot.Kinasedotcom.all_mirnas">(pypath.core.annot.Kinasedotcom method)</a>
 </li>
-        <li><a href="api/pypath.inputs.pathwaycommons.PathwayCommonsResource.html#pypath.inputs.pathwaycommons.PathwayCommonsResource.index">(pypath.inputs.pathwaycommons.PathwayCommonsResource method)</a>
+        <li><a href="api/pypath.core.annot.Kirouac2010.html#pypath.core.annot.Kirouac2010.all_mirnas">(pypath.core.annot.Kirouac2010 method)</a>
 </li>
-        <li><a href="api/pypath.inputs.sider.SiderDrug.html#pypath.inputs.sider.SiderDrug.index">(pypath.inputs.sider.SiderDrug method)</a>
+        <li><a href="api/pypath.core.annot.Lambert2018.html#pypath.core.annot.Lambert2018.all_mirnas">(pypath.core.annot.Lambert2018 method)</a>
 </li>
-        <li><a href="api/pypath.inputs.sider.SiderSideeffect.html#pypath.inputs.sider.SiderSideeffect.index">(pypath.inputs.sider.SiderSideeffect method)</a>
+        <li><a href="api/pypath.core.annot.LigandReceptor.html#pypath.core.annot.LigandReceptor.all_mirnas">(pypath.core.annot.LigandReceptor method)</a>
 </li>
-        <li><a href="api/pypath.inputs.sider.SiderSideeffectMeddra.html#pypath.inputs.sider.SiderSideeffectMeddra.index">(pypath.inputs.sider.SiderSideeffectMeddra method)</a>
+        <li><a href="api/pypath.core.annot.Locate.html#pypath.core.annot.Locate.all_mirnas">(pypath.core.annot.Locate method)</a>
 </li>
-        <li><a href="api/pypath.inputs.sider.SiderSideeffetFrequency.html#pypath.inputs.sider.SiderSideeffetFrequency.index">(pypath.inputs.sider.SiderSideeffetFrequency method)</a>
+        <li><a href="api/pypath.core.annot.Lrdb.html#pypath.core.annot.Lrdb.all_mirnas">(pypath.core.annot.Lrdb method)</a>
 </li>
-        <li><a href="api/pypath.inputs.uniprot.Taxon.html#pypath.inputs.uniprot.Taxon.index">(pypath.inputs.uniprot.Taxon method)</a>
+        <li><a href="api/pypath.core.annot.Matrisome.html#pypath.core.annot.Matrisome.all_mirnas">(pypath.core.annot.Matrisome method)</a>
 </li>
-        <li><a href="api/pypath.inputs.uniprot.UniprotRecordHistory.html#pypath.inputs.uniprot.UniprotRecordHistory.index">(pypath.inputs.uniprot.UniprotRecordHistory method)</a>
+        <li><a href="api/pypath.core.annot.Matrixdb.html#pypath.core.annot.Matrixdb.all_mirnas">(pypath.core.annot.Matrixdb method)</a>
 </li>
-        <li><a href="api/pypath.internals.resource.EnzymeSubstrateResourceKey.html#pypath.internals.resource.EnzymeSubstrateResourceKey.index">(pypath.internals.resource.EnzymeSubstrateResourceKey method)</a>
+        <li><a href="api/pypath.core.annot.Mcam.html#pypath.core.annot.Mcam.all_mirnas">(pypath.core.annot.Mcam method)</a>
 </li>
-        <li><a href="api/pypath.internals.resource.NetworkResourceKey.html#pypath.internals.resource.NetworkResourceKey.index">(pypath.internals.resource.NetworkResourceKey method)</a>
+        <li><a href="api/pypath.core.annot.Membranome.html#pypath.core.annot.Membranome.all_mirnas">(pypath.core.annot.Membranome method)</a>
 </li>
-        <li><a href="api/pypath.utils.pdb.Residue.html#pypath.utils.pdb.Residue.index">(pypath.utils.pdb.Residue method)</a>
+        <li><a href="api/pypath.core.annot.Msigdb.html#pypath.core.annot.Msigdb.all_mirnas">(pypath.core.annot.Msigdb method)</a>
 </li>
-        <li><a href="api/pypath.utils.pdb.Segment.html#pypath.utils.pdb.Segment.index">(pypath.utils.pdb.Segment method)</a>
+        <li><a href="api/pypath.core.annot.NetpathPathways.html#pypath.core.annot.NetpathPathways.all_mirnas">(pypath.core.annot.NetpathPathways method)</a>
 </li>
-      </ul></li>
-      <li><a href="api/pypath.info.html#pypath.info">info() (in module pypath)</a>
-
-      <ul>
-        <li><a href="api/pypath.inputs.unichem.info.html#pypath.inputs.unichem.info">(in module pypath.inputs.unichem)</a>
+        <li><a href="api/pypath.core.annot.Opm.html#pypath.core.annot.Opm.all_mirnas">(pypath.core.annot.Opm method)</a>
 </li>
-        <li><a href="api/pypath.utils.unichem.Unichem.html#pypath.utils.unichem.Unichem.info">(pypath.utils.unichem.Unichem static method)</a>
+        <li><a href="api/pypath.core.annot.Panglaodb.html#pypath.core.annot.Panglaodb.all_mirnas">(pypath.core.annot.Panglaodb method)</a>
 </li>
-      </ul></li>
-      <li><a href="api/pypath.utils.reflists.init.html#pypath.utils.reflists.init">init() (in module pypath.utils.reflists)</a>
+        <li><a href="api/pypath.core.annot.Phobius.html#pypath.core.annot.Phobius.all_mirnas">(pypath.core.annot.Phobius method)</a>
 </li>
-      <li><a href="api/pypath.inputs.uniprot_db.init_db.html#pypath.inputs.uniprot_db.init_db">init_db() (in module pypath.inputs.uniprot_db)</a>
-
-      <ul>
-        <li><a href="api/pypath.utils.go.init_db.html#pypath.utils.go.init_db">(in module pypath.utils.go)</a>
+        <li><a href="api/pypath.core.annot.Phosphatome.html#pypath.core.annot.Phosphatome.all_mirnas">(pypath.core.annot.Phosphatome method)</a>
 </li>
-        <li><a href="api/pypath.utils.taxonomy.init_db.html#pypath.utils.taxonomy.init_db">(in module pypath.utils.taxonomy)</a>
+        <li><a href="api/pypath.core.annot.Progeny.html#pypath.core.annot.Progeny.all_mirnas">(pypath.core.annot.Progeny method)</a>
 </li>
-      </ul></li>
-      <li><a href="api/pypath.share.progress.Progress.html#pypath.share.progress.Progress.init_tqdm">init_tqdm() (pypath.share.progress.Progress method)</a>
+        <li><a href="api/pypath.core.annot.Ramilowski2015.html#pypath.core.annot.Ramilowski2015.all_mirnas">(pypath.core.annot.Ramilowski2015 method)</a>
 </li>
-      <li><a href="api/pypath.inputs.innatedb.innatedb_interactions.html#pypath.inputs.innatedb.innatedb_interactions">innatedb_interactions() (in module pypath.inputs.innatedb)</a>
+        <li><a href="api/pypath.core.annot.Ramilowski2015Location.html#pypath.core.annot.Ramilowski2015Location.all_mirnas">(pypath.core.annot.Ramilowski2015Location method)</a>
 </li>
-  </ul></td>
-  <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="api/pypath.internals.license.LicenseAttrib.html#pypath.internals.license.LicenseAttrib.int_to_level">int_to_level() (pypath.internals.license.LicenseAttrib class method)</a>
-
-      <ul>
-        <li><a href="api/pypath.internals.license.LicenseFeature.html#pypath.internals.license.LicenseFeature.int_to_level">(pypath.internals.license.LicenseFeature class method)</a>
+        <li><a href="api/pypath.core.annot.Scconnect.html#pypath.core.annot.Scconnect.all_mirnas">(pypath.core.annot.Scconnect method)</a>
 </li>
-        <li><a href="api/pypath.internals.license.LicensePurpose.html#pypath.internals.license.LicensePurpose.int_to_level">(pypath.internals.license.LicensePurpose class method)</a>
+        <li><a href="api/pypath.core.annot.ScconnectComplex.html#pypath.core.annot.ScconnectComplex.all_mirnas">(pypath.core.annot.ScconnectComplex method)</a>
 </li>
-        <li><a href="api/pypath.internals.license.LicenseSharing.html#pypath.internals.license.LicenseSharing.int_to_level">(pypath.internals.license.LicenseSharing class method)</a>
+        <li><a href="api/pypath.core.annot.SignalinkFunctions.html#pypath.core.annot.SignalinkFunctions.all_mirnas">(pypath.core.annot.SignalinkFunctions method)</a>
 </li>
-      </ul></li>
-      <li><a href="api/pypath.inputs.intact.intact_interactions.html#pypath.inputs.intact.intact_interactions">intact_interactions() (in module pypath.inputs.intact)</a>
+        <li><a href="api/pypath.core.annot.SignalinkPathways.html#pypath.core.annot.SignalinkPathways.all_mirnas">(pypath.core.annot.SignalinkPathways method)</a>
 </li>
-      <li><a href="api/pypath.resources.data_formats.interaction.html#pypath.resources.data_formats.interaction">interaction (in module pypath.resources.data_formats)</a>
+        <li><a href="api/pypath.core.annot.SignorPathways.html#pypath.core.annot.SignorPathways.all_mirnas">(pypath.core.annot.SignorPathways method)</a>
 </li>
-      <li><a href="api/pypath.resources.data_formats.interaction_htp.html#pypath.resources.data_formats.interaction_htp">interaction_htp (in module pypath.resources.data_formats)</a>
+        <li><a href="api/pypath.core.annot.Surfaceome.html#pypath.core.annot.Surfaceome.all_mirnas">(pypath.core.annot.Surfaceome method)</a>
 </li>
-      <li><a href="api/pypath.inputs.pathwaycommons.PathwayCommonsInteraction.html#pypath.inputs.pathwaycommons.PathwayCommonsInteraction.interaction_type">interaction_type (pypath.inputs.pathwaycommons.PathwayCommonsInteraction attribute)</a>
-
-      <ul>
-        <li><a href="api/pypath.internals.resource.NetworkResourceKey.html#pypath.internals.resource.NetworkResourceKey.interaction_type">(pypath.internals.resource.NetworkResourceKey attribute)</a>
+        <li><a href="api/pypath.core.annot.Talklr.html#pypath.core.annot.Talklr.all_mirnas">(pypath.core.annot.Talklr method)</a>
 </li>
-      </ul></li>
-      <li><a href="api/pypath.inputs.interpro.interpro2go_annotations.html#pypath.inputs.interpro.interpro2go_annotations">interpro2go_annotations() (in module pypath.inputs.interpro)</a>
+        <li><a href="api/pypath.core.annot.Tcdb.html#pypath.core.annot.Tcdb.all_mirnas">(pypath.core.annot.Tcdb method)</a>
 </li>
-      <li><a href="api/pypath.inputs.interpro.interpro_annotations.html#pypath.inputs.interpro.interpro_annotations">interpro_annotations() (in module pypath.inputs.interpro)</a>
+        <li><a href="api/pypath.core.annot.Tfcensus.html#pypath.core.annot.Tfcensus.all_mirnas">(pypath.core.annot.Tfcensus method)</a>
 </li>
-      <li><a href="api/pypath.inputs.interpro.interpro_entries.html#pypath.inputs.interpro.interpro_entries">interpro_entries() (in module pypath.inputs.interpro)</a>
+        <li><a href="api/pypath.core.annot.Topdb.html#pypath.core.annot.Topdb.all_mirnas">(pypath.core.annot.Topdb method)</a>
 </li>
-      <li><a href="api/pypath.inputs.interpro.interpro_xrefs.html#pypath.inputs.interpro.interpro_xrefs">interpro_xrefs() (in module pypath.inputs.interpro)</a>
+        <li><a href="api/pypath.core.annot.UniprotFamilies.html#pypath.core.annot.UniprotFamilies.all_mirnas">(pypath.core.annot.UniprotFamilies method)</a>
 </li>
-      <li><a href="api/pypath.visual.drawing.InterSet.html#pypath.visual.drawing.InterSet">InterSet (class in pypath.visual.drawing)</a>
+        <li><a href="api/pypath.core.annot.UniprotKeywords.html#pypath.core.annot.UniprotKeywords.all_mirnas">(pypath.core.annot.UniprotKeywords method)</a>
 </li>
-      <li><a href="api/pypath.inputs.ipi.ipi_uniprot.html#pypath.inputs.ipi.ipi_uniprot">ipi_uniprot() (in module pypath.inputs.ipi)</a>
+        <li><a href="api/pypath.core.annot.UniprotLocations.html#pypath.core.annot.UniprotLocations.all_mirnas">(pypath.core.annot.UniprotLocations method)</a>
 </li>
-      <li><a href="api/pypath.utils.go.GeneOntology.html#pypath.utils.go.GeneOntology.is_leaf">is_leaf() (pypath.utils.go.GeneOntology method)</a>
+        <li><a href="api/pypath.core.annot.UniprotTissues.html#pypath.core.annot.UniprotTissues.all_mirnas">(pypath.core.annot.UniprotTissues method)</a>
 </li>
-      <li><a href="api/pypath.utils.go.GeneOntology.html#pypath.utils.go.GeneOntology.is_name">is_name() (pypath.utils.go.GeneOntology method)</a>
+        <li><a href="api/pypath.core.annot.UniprotTopologies.html#pypath.core.annot.UniprotTopologies.all_mirnas">(pypath.core.annot.UniprotTopologies method)</a>
 </li>
-      <li><a href="api/pypath.utils.reflists.is_not.html#pypath.utils.reflists.is_not">is_not() (in module pypath.utils.reflists)</a>
+        <li><a href="api/pypath.core.annot.Vesiclepedia.html#pypath.core.annot.Vesiclepedia.all_mirnas">(pypath.core.annot.Vesiclepedia method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Wang.html#pypath.core.annot.Wang.all_mirnas">(pypath.core.annot.Wang method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Zhong2015.html#pypath.core.annot.Zhong2015.all_mirnas">(pypath.core.annot.Zhong2015 method)</a>
+</li>
+      </ul></li>
+  </ul></td>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="api/pypath.core.annot.Adhesome.html#pypath.core.annot.Adhesome.all_proteins">all_proteins() (pypath.core.annot.Adhesome method)</a>
 
       <ul>
-        <li><a href="api/pypath.utils.reflists.ReferenceListManager.html#pypath.utils.reflists.ReferenceListManager.is_not">(pypath.utils.reflists.ReferenceListManager method)</a>
+        <li><a href="api/pypath.core.annot.Almen2009.html#pypath.core.annot.Almen2009.all_proteins">(pypath.core.annot.Almen2009 method)</a>
 </li>
-      </ul></li>
-      <li><a href="api/pypath.share.curl.Curl.html#pypath.share.curl.Curl.is_quoted">is_quoted() (pypath.share.curl.Curl method)</a>
+        <li><a href="api/pypath.core.annot.AnnotationBase.html#pypath.core.annot.AnnotationBase.all_proteins">(pypath.core.annot.AnnotationBase method)</a>
 </li>
-      <li><a href="api/pypath.utils.go.GeneOntology.html#pypath.utils.go.GeneOntology.is_root">is_root() (pypath.utils.go.GeneOntology method)</a>
+        <li><a href="api/pypath.core.annot.Baccin2019.html#pypath.core.annot.Baccin2019.all_proteins">(pypath.core.annot.Baccin2019 method)</a>
 </li>
-      <li><a href="api/pypath.inputs.uniprot_db.is_swissprot.html#pypath.inputs.uniprot_db.is_swissprot">is_swissprot() (in module pypath.inputs.uniprot_db)</a>
+        <li><a href="api/pypath.core.annot.Biogps.html#pypath.core.annot.Biogps.all_proteins">(pypath.core.annot.Biogps method)</a>
 </li>
-      <li><a href="api/pypath.utils.go.GeneOntology.html#pypath.utils.go.GeneOntology.is_term">is_term() (pypath.utils.go.GeneOntology method)</a>
+        <li><a href="api/pypath.core.annot.Cancerdrugsdb.html#pypath.core.annot.Cancerdrugsdb.all_proteins">(pypath.core.annot.Cancerdrugsdb method)</a>
 </li>
-      <li><a href="api/pypath.inputs.uniprot_db.is_trembl.html#pypath.inputs.uniprot_db.is_trembl">is_trembl() (in module pypath.inputs.uniprot_db)</a>
+        <li><a href="api/pypath.core.annot.CancerGeneCensus.html#pypath.core.annot.CancerGeneCensus.all_proteins">(pypath.core.annot.CancerGeneCensus method)</a>
 </li>
-      <li><a href="api/pypath.inputs.uniprot_db.is_uniprot.html#pypath.inputs.uniprot_db.is_uniprot">is_uniprot() (in module pypath.inputs.uniprot_db)</a>
+        <li><a href="api/pypath.core.annot.Cancersea.html#pypath.core.annot.Cancersea.all_proteins">(pypath.core.annot.Cancersea method)</a>
 </li>
-      <li><a href="api/pypath.share.curl.is_url.html#pypath.share.curl.is_url">is_url() (in module pypath.share.curl)</a>
+        <li><a href="api/pypath.core.annot.Cellcall.html#pypath.core.annot.Cellcall.all_proteins">(pypath.core.annot.Cellcall method)</a>
 </li>
-      <li><a href="api/pypath.internals.resource.NetworkDataset.html#pypath.internals.resource.NetworkDataset.items">items() (pypath.internals.resource.NetworkDataset method)</a>
+        <li><a href="api/pypath.core.annot.Cellcellinteractions.html#pypath.core.annot.Cellcellinteractions.all_proteins">(pypath.core.annot.Cellcellinteractions method)</a>
 </li>
-      <li><a href="api/pypath.inputs.hmdb.common.iter.html#pypath.inputs.hmdb.common.iter">iter() (in module pypath.inputs.hmdb.common)</a>
-
-      <ul>
-        <li><a href="api/pypath.inputs.hmdb.metabolites.iter.html#pypath.inputs.hmdb.metabolites.iter">(in module pypath.inputs.hmdb.metabolites)</a>
+        <li><a href="api/pypath.core.annot.Cellchatdb.html#pypath.core.annot.Cellchatdb.all_proteins">(pypath.core.annot.Cellchatdb method)</a>
 </li>
-        <li><a href="api/pypath.inputs.hmdb.proteins.iter.html#pypath.inputs.hmdb.proteins.iter">(in module pypath.inputs.hmdb.proteins)</a>
+        <li><a href="api/pypath.core.annot.CellchatdbComplex.html#pypath.core.annot.CellchatdbComplex.all_proteins">(pypath.core.annot.CellchatdbComplex method)</a>
 </li>
-      </ul></li>
-      <li><a href="api/pypath.utils.seq.Pfam.html#pypath.utils.seq.Pfam.iterdb">iterdb() (pypath.utils.seq.Pfam method)</a>
-
-      <ul>
-        <li><a href="api/pypath.utils.seq.Resource.html#pypath.utils.seq.Resource.iterdb">(pypath.utils.seq.Resource method)</a>
+        <li><a href="api/pypath.core.annot.Cellinker.html#pypath.core.annot.Cellinker.all_proteins">(pypath.core.annot.Cellinker method)</a>
 </li>
-      </ul></li>
-      <li><a href="api/pypath.utils.seq.Pfam.html#pypath.utils.seq.Pfam.iterprotein">iterprotein() (pypath.utils.seq.Pfam method)</a>
-
-      <ul>
-        <li><a href="api/pypath.utils.seq.Resource.html#pypath.utils.seq.Resource.iterprotein">(pypath.utils.seq.Resource method)</a>
+        <li><a href="api/pypath.core.annot.CellinkerComplex.html#pypath.core.annot.CellinkerComplex.all_proteins">(pypath.core.annot.CellinkerComplex method)</a>
 </li>
-      </ul></li>
-  </ul></td>
-</tr></table>
-
-<h2 id="J">J</h2>
-<table style="width: 100%" class="indextable genindextable"><tr>
-  <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="api/pypath.inputs.common.json_extract.html#pypath.inputs.common.json_extract">json_extract() (in module pypath.inputs.common)</a>
+        <li><a href="api/pypath.core.annot.CellPhoneDB.html#pypath.core.annot.CellPhoneDB.all_proteins">(pypath.core.annot.CellPhoneDB method)</a>
 </li>
-  </ul></td>
-  <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="api/pypath.inputs.common.json_read.html#pypath.inputs.common.json_read">json_read() (in module pypath.inputs.common)</a>
+        <li><a href="api/pypath.core.annot.CellPhoneDBComplex.html#pypath.core.annot.CellPhoneDBComplex.all_proteins">(pypath.core.annot.CellPhoneDBComplex method)</a>
 </li>
-  </ul></td>
-</tr></table>
-
-<h2 id="K">K</h2>
-<table style="width: 100%" class="indextable genindextable"><tr>
-  <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="api/pypath.inputs.adrecs.AdrecsDrug.html#pypath.inputs.adrecs.AdrecsDrug.kegg">kegg (pypath.inputs.adrecs.AdrecsDrug attribute)</a>
+        <li><a href="api/pypath.core.annot.CellSurfaceProteinAtlas.html#pypath.core.annot.CellSurfaceProteinAtlas.all_proteins">(pypath.core.annot.CellSurfaceProteinAtlas method)</a>
 </li>
-      <li><a href="api/pypath.inputs.kegg_api.kegg_drug_to_chebi.html#pypath.inputs.kegg_api.kegg_drug_to_chebi">kegg_drug_to_chebi() (in module pypath.inputs.kegg_api)</a>
+        <li><a href="api/pypath.core.annot.CellSurfaceProteinAtlasCellType.html#pypath.core.annot.CellSurfaceProteinAtlasCellType.all_proteins">(pypath.core.annot.CellSurfaceProteinAtlasCellType method)</a>
 </li>
-      <li><a href="api/pypath.inputs.kegg_api.kegg_gene_to_ncbi_geneid.html#pypath.inputs.kegg_api.kegg_gene_to_ncbi_geneid">kegg_gene_to_ncbi_geneid() (in module pypath.inputs.kegg_api)</a>
+        <li><a href="api/pypath.core.annot.Celltalkdb.html#pypath.core.annot.Celltalkdb.all_proteins">(pypath.core.annot.Celltalkdb method)</a>
 </li>
-      <li><a href="api/pypath.inputs.kegg_api.kegg_gene_to_uniprot.html#pypath.inputs.kegg_api.kegg_gene_to_uniprot">kegg_gene_to_uniprot() (in module pypath.inputs.kegg_api)</a>
+        <li><a href="api/pypath.core.annot.Celltypist.html#pypath.core.annot.Celltypist.all_proteins">(pypath.core.annot.Celltypist method)</a>
 </li>
-  </ul></td>
-  <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="api/pypath.inputs.dorothea.DorotheaInteraction.html#pypath.inputs.dorothea.DorotheaInteraction.kegg_pathways">kegg_pathways (pypath.inputs.dorothea.DorotheaInteraction attribute)</a>
+        <li><a href="api/pypath.core.annot.Comppi.html#pypath.core.annot.Comppi.all_proteins">(pypath.core.annot.Comppi method)</a>
 </li>
-      <li><a href="api/pypath.internals.resource.NetworkDataset.html#pypath.internals.resource.NetworkDataset.keys">keys() (pypath.internals.resource.NetworkDataset method)</a>
+        <li><a href="api/pypath.core.annot.Connectomedb.html#pypath.core.annot.Connectomedb.all_proteins">(pypath.core.annot.Connectomedb method)</a>
 </li>
-      <li><a href="api/pypath.inputs.kirouac2010.kirouac2010_interactions.html#pypath.inputs.kirouac2010.kirouac2010_interactions">kirouac2010_interactions() (in module pypath.inputs.kirouac2010)</a>
+        <li><a href="api/pypath.core.annot.Corum.html#pypath.core.annot.Corum.all_proteins">(pypath.core.annot.Corum method)</a>
 </li>
-      <li><a href="api/pypath.inputs.diseases.knowledge_filtered.html#pypath.inputs.diseases.knowledge_filtered">knowledge_filtered() (in module pypath.inputs.diseases)</a>
+        <li><a href="api/pypath.core.annot.CorumFuncat.html#pypath.core.annot.CorumFuncat.all_proteins">(pypath.core.annot.CorumFuncat method)</a>
 </li>
-      <li><a href="api/pypath.inputs.diseases.knowledge_full.html#pypath.inputs.diseases.knowledge_full">knowledge_full() (in module pypath.inputs.diseases)</a>
+        <li><a href="api/pypath.core.annot.CorumGO.html#pypath.core.annot.CorumGO.all_proteins">(pypath.core.annot.CorumGO method)</a>
 </li>
-  </ul></td>
-</tr></table>
-
-<h2 id="L">L</h2>
-<table style="width: 100%" class="indextable genindextable"><tr>
-  <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="api/pypath.internals.resource.NetworkResourceKey.html#pypath.internals.resource.NetworkResourceKey.label">label (pypath.internals.resource.NetworkResourceKey property)</a>
+        <li><a href="api/pypath.core.annot.Cpad.html#pypath.core.annot.Cpad.all_proteins">(pypath.core.annot.Cpad method)</a>
 </li>
-      <li><a href="api/pypath.internals.resource.NetworkResourceKey.html#pypath.internals.resource.NetworkResourceKey.last">last (pypath.internals.resource.NetworkResourceKey property)</a>
+        <li><a href="api/pypath.core.annot.Cytosig.html#pypath.core.annot.Cytosig.all_proteins">(pypath.core.annot.Cytosig method)</a>
 </li>
-      <li><a href="api/pypath.inputs.uniprot.Taxon.html#pypath.inputs.uniprot.Taxon.latin">latin (pypath.inputs.uniprot.Taxon attribute)</a>
+        <li><a href="api/pypath.core.annot.Dgidb.html#pypath.core.annot.Dgidb.all_proteins">(pypath.core.annot.Dgidb method)</a>
 </li>
-      <li><a href="api/pypath.inputs.uniprot.Taxon.html#pypath.inputs.uniprot.Taxon.latin_synonym">latin_synonym (pypath.inputs.uniprot.Taxon attribute)</a>
+        <li><a href="api/pypath.core.annot.Disgenet.html#pypath.core.annot.Disgenet.all_proteins">(pypath.core.annot.Disgenet method)</a>
 </li>
-      <li><a href="api/pypath.inputs.laudanna.laudanna_directions.html#pypath.inputs.laudanna.laudanna_directions">laudanna_directions() (in module pypath.inputs.laudanna)</a>
+        <li><a href="api/pypath.core.annot.Embrace.html#pypath.core.annot.Embrace.all_proteins">(pypath.core.annot.Embrace method)</a>
 </li>
-      <li><a href="api/pypath.inputs.laudanna.laudanna_effects.html#pypath.inputs.laudanna.laudanna_effects">laudanna_effects() (in module pypath.inputs.laudanna)</a>
+        <li><a href="api/pypath.core.annot.Exocarta.html#pypath.core.annot.Exocarta.all_proteins">(pypath.core.annot.Exocarta method)</a>
 </li>
-      <li><a href="api/pypath.inputs.dorothea.DorotheaInteraction.html#pypath.inputs.dorothea.DorotheaInteraction.level">level (pypath.inputs.dorothea.DorotheaInteraction attribute)</a>
+        <li><a href="api/pypath.core.annot.GOIntercell.html#pypath.core.annot.GOIntercell.all_proteins">(pypath.core.annot.GOIntercell method)</a>
 </li>
-      <li><a href="api/pypath.internals.license.LicenseAttrib.html#pypath.internals.license.LicenseAttrib.level_to_int">level_to_int() (pypath.internals.license.LicenseAttrib class method)</a>
-
-      <ul>
-        <li><a href="api/pypath.internals.license.LicenseFeature.html#pypath.internals.license.LicenseFeature.level_to_int">(pypath.internals.license.LicenseFeature class method)</a>
+        <li><a href="api/pypath.core.annot.Gpcrdb.html#pypath.core.annot.Gpcrdb.all_proteins">(pypath.core.annot.Gpcrdb method)</a>
 </li>
-        <li><a href="api/pypath.internals.license.LicensePurpose.html#pypath.internals.license.LicensePurpose.level_to_int">(pypath.internals.license.LicensePurpose class method)</a>
+        <li><a href="api/pypath.core.annot.GuideToPharmacology.html#pypath.core.annot.GuideToPharmacology.all_proteins">(pypath.core.annot.GuideToPharmacology method)</a>
 </li>
-        <li><a href="api/pypath.internals.license.LicenseSharing.html#pypath.internals.license.LicenseSharing.level_to_int">(pypath.internals.license.LicenseSharing class method)</a>
+        <li><a href="api/pypath.core.annot.Hgnc.html#pypath.core.annot.Hgnc.all_proteins">(pypath.core.annot.Hgnc method)</a>
 </li>
-      </ul></li>
-      <li><a href="api/pypath.internals.license.License.html#pypath.internals.license.License">License (class in pypath.internals.license)</a>
+        <li><a href="api/pypath.core.annot.HpmrComplex.html#pypath.core.annot.HpmrComplex.all_proteins">(pypath.core.annot.HpmrComplex method)</a>
 </li>
-      <li><a href="api/pypath.resources.controller.ResourceController.html#pypath.resources.controller.ResourceController.license_filter">license_filter() (pypath.resources.controller.ResourceController method)</a>
+        <li><a href="api/pypath.core.annot.HPO.html#pypath.core.annot.HPO.all_proteins">(pypath.core.annot.HPO method)</a>
 </li>
-      <li><a href="api/pypath.internals.license.LicenseAttrib.html#pypath.internals.license.LicenseAttrib">LicenseAttrib (class in pypath.internals.license)</a>
+        <li><a href="api/pypath.core.annot.Humancellmap.html#pypath.core.annot.Humancellmap.all_proteins">(pypath.core.annot.Humancellmap method)</a>
 </li>
-      <li><a href="api/pypath.internals.license.LicenseFeature.html#pypath.internals.license.LicenseFeature">LicenseFeature (class in pypath.internals.license)</a>
+        <li><a href="api/pypath.core.annot.HumanPlasmaMembraneReceptome.html#pypath.core.annot.HumanPlasmaMembraneReceptome.all_proteins">(pypath.core.annot.HumanPlasmaMembraneReceptome method)</a>
 </li>
-  </ul></td>
-  <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="api/pypath.internals.license.LicensePurpose.html#pypath.internals.license.LicensePurpose">LicensePurpose (class in pypath.internals.license)</a>
+        <li><a href="api/pypath.core.annot.HumanProteinAtlas.html#pypath.core.annot.HumanProteinAtlas.all_proteins">(pypath.core.annot.HumanProteinAtlas method)</a>
 </li>
-      <li><a href="api/pypath.resources.licenses.Licenses.html#pypath.resources.licenses.Licenses">Licenses (class in pypath.resources.licenses)</a>
+        <li><a href="api/pypath.core.annot.HumanProteinAtlasSecretome.html#pypath.core.annot.HumanProteinAtlasSecretome.all_proteins">(pypath.core.annot.HumanProteinAtlasSecretome method)</a>
 </li>
-      <li><a href="api/pypath.internals.license.LicenseSharing.html#pypath.internals.license.LicenseSharing">LicenseSharing (class in pypath.internals.license)</a>
+        <li><a href="api/pypath.core.annot.HumanProteinAtlasSubcellular.html#pypath.core.annot.HumanProteinAtlasSubcellular.all_proteins">(pypath.core.annot.HumanProteinAtlasSubcellular method)</a>
 </li>
-      <li><a href="api/pypath.visual.igraph_drawing.edge.LightToDarkEdgeDrawer.html#pypath.visual.igraph_drawing.edge.LightToDarkEdgeDrawer">LightToDarkEdgeDrawer (class in pypath.visual.igraph_drawing.edge)</a>
+        <li><a href="api/pypath.core.annot.Icellnet.html#pypath.core.annot.Icellnet.all_proteins">(pypath.core.annot.Icellnet method)</a>
 </li>
-      <li><a href="api/pypath.inputs.lincs.lincs_compounds.html#pypath.inputs.lincs.lincs_compounds">lincs_compounds() (in module pypath.inputs.lincs)</a>
+        <li><a href="api/pypath.core.annot.IcellnetComplex.html#pypath.core.annot.IcellnetComplex.all_proteins">(pypath.core.annot.IcellnetComplex method)</a>
 </li>
-      <li><a href="api/pypath.inputs.ontology.listof_ontologies.html#pypath.inputs.ontology.listof_ontologies">listof_ontologies() (in module pypath.inputs.ontology)</a>
+        <li><a href="api/pypath.core.annot.Integrins.html#pypath.core.annot.Integrins.all_proteins">(pypath.core.annot.Integrins method)</a>
 </li>
-      <li><a href="api/pypath.inputs.lncdisease.lncdisease_interactions.html#pypath.inputs.lncdisease.lncdisease_interactions">lncdisease_interactions() (in module pypath.inputs.lncdisease)</a>
+        <li><a href="api/pypath.core.annot.InterPro.html#pypath.core.annot.InterPro.all_proteins">(pypath.core.annot.InterPro method)</a>
 </li>
-      <li><a href="api/pypath.inputs.lncrnadb.lncrnadb_interactions.html#pypath.inputs.lncrnadb.lncrnadb_interactions">lncrnadb_interactions() (in module pypath.inputs.lncrnadb)</a>
+        <li><a href="api/pypath.core.annot.Intogen.html#pypath.core.annot.Intogen.all_proteins">(pypath.core.annot.Intogen method)</a>
 </li>
-      <li><a href="api/pypath.utils.seq.Pfam.html#pypath.utils.seq.Pfam.load">load() (pypath.utils.seq.Pfam method)</a>
-
-      <ul>
-        <li><a href="api/pypath.utils.seq.Resource.html#pypath.utils.seq.Resource.load">(pypath.utils.seq.Resource method)</a>
+        <li><a href="api/pypath.core.annot.Italk.html#pypath.core.annot.Italk.all_proteins">(pypath.core.annot.Italk method)</a>
 </li>
-      </ul></li>
-      <li><a href="api/pypath.internals.resource.AbstractResource.html#pypath.internals.resource.AbstractResource.load_data">load_data() (pypath.internals.resource.AbstractResource method)</a>
+        <li><a href="api/pypath.core.annot.KeggPathways.html#pypath.core.annot.KeggPathways.all_proteins">(pypath.core.annot.KeggPathways method)</a>
 </li>
-      <li><a href="api/pypath.utils.go.load_go.html#pypath.utils.go.load_go">load_go() (in module pypath.utils.go)</a>
+        <li><a href="api/pypath.core.annot.KeggPathwaysPC.html#pypath.core.annot.KeggPathwaysPC.all_proteins">(pypath.core.annot.KeggPathwaysPC method)</a>
 </li>
-      <li><a href="api/pypath.utils.pdb.ResidueMapper.html#pypath.utils.pdb.ResidueMapper.load_mapping">load_mapping() (pypath.utils.pdb.ResidueMapper method)</a>
+        <li><a href="api/pypath.core.annot.Kinasedotcom.html#pypath.core.annot.Kinasedotcom.all_proteins">(pypath.core.annot.Kinasedotcom method)</a>
 </li>
-      <li><a href="api/pypath.log.html#pypath.log">log() (in module pypath)</a>
+        <li><a href="api/pypath.core.annot.Kirouac2010.html#pypath.core.annot.Kirouac2010.all_proteins">(pypath.core.annot.Kirouac2010 method)</a>
 </li>
-      <li><a href="api/pypath.utils.go.GeneOntology.html#pypath.utils.go.GeneOntology.lowest">lowest() (pypath.utils.go.GeneOntology method)</a>
+        <li><a href="api/pypath.core.annot.Lambert2018.html#pypath.core.annot.Lambert2018.all_proteins">(pypath.core.annot.Lambert2018 method)</a>
 </li>
-  </ul></td>
-</tr></table>
-
-<h2 id="M">M</h2>
-<table style="width: 100%" class="indextable genindextable"><tr>
-  <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="api/pypath.inputs.macrophage.macrophage_interactions.html#pypath.inputs.macrophage.macrophage_interactions">macrophage_interactions() (in module pypath.inputs.macrophage)</a>
+        <li><a href="api/pypath.core.annot.LigandReceptor.html#pypath.core.annot.LigandReceptor.all_proteins">(pypath.core.annot.LigandReceptor method)</a>
 </li>
-      <li><a href="api/pypath.inputs.hmdb.common.mapping.html#pypath.inputs.hmdb.common.mapping">mapping() (in module pypath.inputs.hmdb.common)</a>
-
-      <ul>
-        <li><a href="api/pypath.inputs.hmdb.metabolites.mapping.html#pypath.inputs.hmdb.metabolites.mapping">(in module pypath.inputs.hmdb.metabolites)</a>
+        <li><a href="api/pypath.core.annot.Locate.html#pypath.core.annot.Locate.all_proteins">(pypath.core.annot.Locate method)</a>
 </li>
-        <li><a href="api/pypath.inputs.hmdb.proteins.mapping.html#pypath.inputs.hmdb.proteins.mapping">(in module pypath.inputs.hmdb.proteins)</a>
+        <li><a href="api/pypath.core.annot.Lrdb.html#pypath.core.annot.Lrdb.all_proteins">(pypath.core.annot.Lrdb method)</a>
 </li>
-      </ul></li>
-      <li><a href="api/pypath.internals.input_formats.MappingInput.html#pypath.internals.input_formats.MappingInput">MappingInput (class in pypath.internals.input_formats)</a>
+        <li><a href="api/pypath.core.annot.Matrisome.html#pypath.core.annot.Matrisome.all_proteins">(pypath.core.annot.Matrisome method)</a>
 </li>
-      <li><a href="api/pypath.inputs.adrecs.AdrecsTerm.html#pypath.inputs.adrecs.AdrecsTerm.meddra">meddra (pypath.inputs.adrecs.AdrecsTerm attribute)</a>
+        <li><a href="api/pypath.core.annot.Matrixdb.html#pypath.core.annot.Matrixdb.all_proteins">(pypath.core.annot.Matrixdb method)</a>
 </li>
-      <li><a href="api/pypath.inputs.sider.SiderSideeffectMeddra.html#pypath.inputs.sider.SiderSideeffectMeddra.meddra_id">meddra_id (pypath.inputs.sider.SiderSideeffectMeddra attribute)</a>
+        <li><a href="api/pypath.core.annot.Mcam.html#pypath.core.annot.Mcam.all_proteins">(pypath.core.annot.Mcam method)</a>
 </li>
-      <li><a href="api/pypath.inputs.adrecs.AdrecsDrug.html#pypath.inputs.adrecs.AdrecsDrug.mesh">mesh (pypath.inputs.adrecs.AdrecsDrug attribute)</a>
+        <li><a href="api/pypath.core.annot.Membranome.html#pypath.core.annot.Membranome.all_proteins">(pypath.core.annot.Membranome method)</a>
 </li>
-      <li><a href="api/pypath.inputs.mimp.mimp_enzyme_substrate.html#pypath.inputs.mimp.mimp_enzyme_substrate">mimp_enzyme_substrate() (in module pypath.inputs.mimp)</a>
+        <li><a href="api/pypath.core.annot.Msigdb.html#pypath.core.annot.Msigdb.all_proteins">(pypath.core.annot.Msigdb method)</a>
 </li>
-      <li><a href="api/pypath.inputs.mimp.mimp_interactions.html#pypath.inputs.mimp.mimp_interactions">mimp_interactions() (in module pypath.inputs.mimp)</a>
+        <li><a href="api/pypath.core.annot.NetpathPathways.html#pypath.core.annot.NetpathPathways.all_proteins">(pypath.core.annot.NetpathPathways method)</a>
 </li>
-      <li><a href="api/pypath.inputs.mir2disease.mir2disease_interactions.html#pypath.inputs.mir2disease.mir2disease_interactions">mir2disease_interactions() (in module pypath.inputs.mir2disease)</a>
+        <li><a href="api/pypath.core.annot.Opm.html#pypath.core.annot.Opm.all_proteins">(pypath.core.annot.Opm method)</a>
 </li>
-      <li><a href="api/pypath.inputs.mirbase.mirbase_ids.html#pypath.inputs.mirbase.mirbase_ids">mirbase_ids() (in module pypath.inputs.mirbase)</a>
+        <li><a href="api/pypath.core.annot.Panglaodb.html#pypath.core.annot.Panglaodb.all_proteins">(pypath.core.annot.Panglaodb method)</a>
 </li>
-      <li><a href="api/pypath.inputs.mirbase.mirbase_mature.html#pypath.inputs.mirbase.mirbase_mature">mirbase_mature() (in module pypath.inputs.mirbase)</a>
+        <li><a href="api/pypath.core.annot.Phobius.html#pypath.core.annot.Phobius.all_proteins">(pypath.core.annot.Phobius method)</a>
 </li>
-      <li><a href="api/pypath.inputs.mirbase.mirbase_mature_all.html#pypath.inputs.mirbase.mirbase_mature_all">mirbase_mature_all() (in module pypath.inputs.mirbase)</a>
+        <li><a href="api/pypath.core.annot.Phosphatome.html#pypath.core.annot.Phosphatome.all_proteins">(pypath.core.annot.Phosphatome method)</a>
 </li>
-      <li><a href="api/pypath.inputs.mirbase.mirbase_precursor.html#pypath.inputs.mirbase.mirbase_precursor">mirbase_precursor() (in module pypath.inputs.mirbase)</a>
+        <li><a href="api/pypath.core.annot.Progeny.html#pypath.core.annot.Progeny.all_proteins">(pypath.core.annot.Progeny method)</a>
 </li>
-      <li><a href="api/pypath.inputs.mirbase.mirbase_precursor_all.html#pypath.inputs.mirbase.mirbase_precursor_all">mirbase_precursor_all() (in module pypath.inputs.mirbase)</a>
+        <li><a href="api/pypath.core.annot.Ramilowski2015.html#pypath.core.annot.Ramilowski2015.all_proteins">(pypath.core.annot.Ramilowski2015 method)</a>
 </li>
-      <li><a href="api/pypath.inputs.mirbase.mirbase_precursor_to_mature.html#pypath.inputs.mirbase.mirbase_precursor_to_mature">mirbase_precursor_to_mature() (in module pypath.inputs.mirbase)</a>
+        <li><a href="api/pypath.core.annot.Ramilowski2015Location.html#pypath.core.annot.Ramilowski2015Location.all_proteins">(pypath.core.annot.Ramilowski2015Location method)</a>
 </li>
-      <li><a href="api/pypath.inputs.mirdeathdb.mirdeathdb_interactions.html#pypath.inputs.mirdeathdb.mirdeathdb_interactions">mirdeathdb_interactions() (in module pypath.inputs.mirdeathdb)</a>
+        <li><a href="api/pypath.core.annot.Scconnect.html#pypath.core.annot.Scconnect.all_proteins">(pypath.core.annot.Scconnect method)</a>
 </li>
-      <li><a href="api/pypath.inputs.mirecords.mirecords_interactions.html#pypath.inputs.mirecords.mirecords_interactions">mirecords_interactions() (in module pypath.inputs.mirecords)</a>
+        <li><a href="api/pypath.core.annot.ScconnectComplex.html#pypath.core.annot.ScconnectComplex.all_proteins">(pypath.core.annot.ScconnectComplex method)</a>
 </li>
-      <li><a href="api/pypath.inputs.mirtarbase.mirtarbase_interactions.html#pypath.inputs.mirtarbase.mirtarbase_interactions">mirtarbase_interactions() (in module pypath.inputs.mirtarbase)</a>
+        <li><a href="api/pypath.core.annot.SignalinkFunctions.html#pypath.core.annot.SignalinkFunctions.all_proteins">(pypath.core.annot.SignalinkFunctions method)</a>
 </li>
-      <li><a href="api/pypath.inputs.mitab.mitab_field_list.html#pypath.inputs.mitab.mitab_field_list">mitab_field_list() (in module pypath.inputs.mitab)</a>
+        <li><a href="api/pypath.core.annot.SignalinkPathways.html#pypath.core.annot.SignalinkPathways.all_proteins">(pypath.core.annot.SignalinkPathways method)</a>
 </li>
-      <li><a href="api/pypath.inputs.mitab.mitab_field_uniprot.html#pypath.inputs.mitab.mitab_field_uniprot">mitab_field_uniprot() (in module pypath.inputs.mitab)</a>
+        <li><a href="api/pypath.core.annot.SignorPathways.html#pypath.core.annot.SignorPathways.all_proteins">(pypath.core.annot.SignorPathways method)</a>
 </li>
-      <li>
-    module
-
-      <ul>
-        <li><a href="api/pypath.html#module-pypath">pypath</a>
+        <li><a href="api/pypath.core.annot.Surfaceome.html#pypath.core.annot.Surfaceome.all_proteins">(pypath.core.annot.Surfaceome method)</a>
 </li>
-        <li><a href="api/pypath.core.html#module-pypath.core">pypath.core</a>
+        <li><a href="api/pypath.core.annot.Talklr.html#pypath.core.annot.Talklr.all_proteins">(pypath.core.annot.Talklr method)</a>
 </li>
-        <li><a href="api/pypath.core.attrs.html#module-pypath.core.attrs">pypath.core.attrs</a>
+        <li><a href="api/pypath.core.annot.Tcdb.html#pypath.core.annot.Tcdb.all_proteins">(pypath.core.annot.Tcdb method)</a>
 </li>
-        <li><a href="api/pypath.core.common.html#module-pypath.core.common">pypath.core.common</a>
+        <li><a href="api/pypath.core.annot.Tfcensus.html#pypath.core.annot.Tfcensus.all_proteins">(pypath.core.annot.Tfcensus method)</a>
 </li>
-        <li><a href="api/pypath.data.html#module-pypath.data">pypath.data</a>
+        <li><a href="api/pypath.core.annot.Topdb.html#pypath.core.annot.Topdb.all_proteins">(pypath.core.annot.Topdb method)</a>
 </li>
-        <li><a href="api/pypath.inputs.html#module-pypath.inputs">pypath.inputs</a>
+        <li><a href="api/pypath.core.annot.UniprotFamilies.html#pypath.core.annot.UniprotFamilies.all_proteins">(pypath.core.annot.UniprotFamilies method)</a>
 </li>
-        <li><a href="api/pypath.inputs.abs.html#module-pypath.inputs.abs">pypath.inputs.abs</a>
+        <li><a href="api/pypath.core.annot.UniprotKeywords.html#pypath.core.annot.UniprotKeywords.all_proteins">(pypath.core.annot.UniprotKeywords method)</a>
 </li>
-        <li><a href="api/pypath.inputs.acsn.html#module-pypath.inputs.acsn">pypath.inputs.acsn</a>
+        <li><a href="api/pypath.core.annot.UniprotLocations.html#pypath.core.annot.UniprotLocations.all_proteins">(pypath.core.annot.UniprotLocations method)</a>
 </li>
-        <li><a href="api/pypath.inputs.adrecs.html#module-pypath.inputs.adrecs">pypath.inputs.adrecs</a>
+        <li><a href="api/pypath.core.annot.UniprotTissues.html#pypath.core.annot.UniprotTissues.all_proteins">(pypath.core.annot.UniprotTissues method)</a>
 </li>
-        <li><a href="api/pypath.inputs.biogrid.html#module-pypath.inputs.biogrid">pypath.inputs.biogrid</a>
+        <li><a href="api/pypath.core.annot.UniprotTopologies.html#pypath.core.annot.UniprotTopologies.all_proteins">(pypath.core.annot.UniprotTopologies method)</a>
 </li>
-        <li><a href="api/pypath.inputs.biomart.html#module-pypath.inputs.biomart">pypath.inputs.biomart</a>
+        <li><a href="api/pypath.core.annot.Vesiclepedia.html#pypath.core.annot.Vesiclepedia.all_proteins">(pypath.core.annot.Vesiclepedia method)</a>
 </li>
-        <li><a href="api/pypath.inputs.biomodels.html#module-pypath.inputs.biomodels">pypath.inputs.biomodels</a>
+        <li><a href="api/pypath.core.annot.Wang.html#pypath.core.annot.Wang.all_proteins">(pypath.core.annot.Wang method)</a>
 </li>
-        <li><a href="api/pypath.inputs.ca1.html#module-pypath.inputs.ca1">pypath.inputs.ca1</a>
+        <li><a href="api/pypath.core.annot.Zhong2015.html#pypath.core.annot.Zhong2015.all_proteins">(pypath.core.annot.Zhong2015 method)</a>
 </li>
-        <li><a href="api/pypath.inputs.cancercellmap.html#module-pypath.inputs.cancercellmap">pypath.inputs.cancercellmap</a>
+      </ul></li>
+      <li><a href="api/pypath.core.annot.Adhesome.html#pypath.core.annot.Adhesome.all_refs">all_refs() (pypath.core.annot.Adhesome method)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.annot.Almen2009.html#pypath.core.annot.Almen2009.all_refs">(pypath.core.annot.Almen2009 method)</a>
 </li>
-        <li><a href="api/pypath.inputs.cell.html#module-pypath.inputs.cell">pypath.inputs.cell</a>
+        <li><a href="api/pypath.core.annot.AnnotationBase.html#pypath.core.annot.AnnotationBase.all_refs">(pypath.core.annot.AnnotationBase method)</a>
 </li>
-        <li><a href="api/pypath.inputs.chembl.html#module-pypath.inputs.chembl">pypath.inputs.chembl</a>
+        <li><a href="api/pypath.core.annot.Baccin2019.html#pypath.core.annot.Baccin2019.all_refs">(pypath.core.annot.Baccin2019 method)</a>
 </li>
-        <li><a href="api/pypath.inputs.clinvar.html#module-pypath.inputs.clinvar">pypath.inputs.clinvar</a>
+        <li><a href="api/pypath.core.annot.Biogps.html#pypath.core.annot.Biogps.all_refs">(pypath.core.annot.Biogps method)</a>
 </li>
-        <li><a href="api/pypath.inputs.common.html#module-pypath.inputs.common">pypath.inputs.common</a>
+        <li><a href="api/pypath.core.annot.Cancerdrugsdb.html#pypath.core.annot.Cancerdrugsdb.all_refs">(pypath.core.annot.Cancerdrugsdb method)</a>
 </li>
-        <li><a href="api/pypath.inputs.compath.html#module-pypath.inputs.compath">pypath.inputs.compath</a>
+        <li><a href="api/pypath.core.annot.CancerGeneCensus.html#pypath.core.annot.CancerGeneCensus.all_refs">(pypath.core.annot.CancerGeneCensus method)</a>
 </li>
-        <li><a href="api/pypath.inputs.cpdb.html#module-pypath.inputs.cpdb">pypath.inputs.cpdb</a>
+        <li><a href="api/pypath.core.annot.Cancersea.html#pypath.core.annot.Cancersea.all_refs">(pypath.core.annot.Cancersea method)</a>
 </li>
-        <li><a href="api/pypath.inputs.credentials.html#module-pypath.inputs.credentials">pypath.inputs.credentials</a>
+        <li><a href="api/pypath.core.annot.Cellcall.html#pypath.core.annot.Cellcall.all_refs">(pypath.core.annot.Cellcall method)</a>
 </li>
-        <li><a href="api/pypath.inputs.ctdbase.html#module-pypath.inputs.ctdbase">pypath.inputs.ctdbase</a>
+        <li><a href="api/pypath.core.annot.Cellcellinteractions.html#pypath.core.annot.Cellcellinteractions.all_refs">(pypath.core.annot.Cellcellinteractions method)</a>
 </li>
-        <li><a href="api/pypath.inputs.dbptm.html#module-pypath.inputs.dbptm">pypath.inputs.dbptm</a>
+        <li><a href="api/pypath.core.annot.Cellchatdb.html#pypath.core.annot.Cellchatdb.all_refs">(pypath.core.annot.Cellchatdb method)</a>
 </li>
-        <li><a href="api/pypath.inputs.ddinter.html#module-pypath.inputs.ddinter">pypath.inputs.ddinter</a>
+        <li><a href="api/pypath.core.annot.CellchatdbComplex.html#pypath.core.annot.CellchatdbComplex.all_refs">(pypath.core.annot.CellchatdbComplex method)</a>
 </li>
-        <li><a href="api/pypath.inputs.deathdomain.html#module-pypath.inputs.deathdomain">pypath.inputs.deathdomain</a>
+        <li><a href="api/pypath.core.annot.Cellinker.html#pypath.core.annot.Cellinker.all_refs">(pypath.core.annot.Cellinker method)</a>
 </li>
-        <li><a href="api/pypath.inputs.dip.html#module-pypath.inputs.dip">pypath.inputs.dip</a>
+        <li><a href="api/pypath.core.annot.CellinkerComplex.html#pypath.core.annot.CellinkerComplex.all_refs">(pypath.core.annot.CellinkerComplex method)</a>
 </li>
-        <li><a href="api/pypath.inputs.diseases.html#module-pypath.inputs.diseases">pypath.inputs.diseases</a>
+        <li><a href="api/pypath.core.annot.CellPhoneDB.html#pypath.core.annot.CellPhoneDB.all_refs">(pypath.core.annot.CellPhoneDB method)</a>
 </li>
-        <li><a href="api/pypath.inputs.dorothea.html#module-pypath.inputs.dorothea">pypath.inputs.dorothea</a>
+        <li><a href="api/pypath.core.annot.CellPhoneDBComplex.html#pypath.core.annot.CellPhoneDBComplex.all_refs">(pypath.core.annot.CellPhoneDBComplex method)</a>
 </li>
-        <li><a href="api/pypath.inputs.drugbank.html#module-pypath.inputs.drugbank">pypath.inputs.drugbank</a>
+        <li><a href="api/pypath.core.annot.CellSurfaceProteinAtlas.html#pypath.core.annot.CellSurfaceProteinAtlas.all_refs">(pypath.core.annot.CellSurfaceProteinAtlas method)</a>
 </li>
-        <li><a href="api/pypath.inputs.drugcentral.html#module-pypath.inputs.drugcentral">pypath.inputs.drugcentral</a>
+        <li><a href="api/pypath.core.annot.CellSurfaceProteinAtlasCellType.html#pypath.core.annot.CellSurfaceProteinAtlasCellType.all_refs">(pypath.core.annot.CellSurfaceProteinAtlasCellType method)</a>
 </li>
-        <li><a href="api/pypath.inputs.ebi.html#module-pypath.inputs.ebi">pypath.inputs.ebi</a>
+        <li><a href="api/pypath.core.annot.Celltalkdb.html#pypath.core.annot.Celltalkdb.all_refs">(pypath.core.annot.Celltalkdb method)</a>
 </li>
-        <li><a href="api/pypath.inputs.elm.html#module-pypath.inputs.elm">pypath.inputs.elm</a>
+        <li><a href="api/pypath.core.annot.Celltypist.html#pypath.core.annot.Celltypist.all_refs">(pypath.core.annot.Celltypist method)</a>
 </li>
-        <li><a href="api/pypath.inputs.embopress.html#module-pypath.inputs.embopress">pypath.inputs.embopress</a>
+        <li><a href="api/pypath.core.annot.Comppi.html#pypath.core.annot.Comppi.all_refs">(pypath.core.annot.Comppi method)</a>
 </li>
-        <li><a href="api/pypath.inputs.encode.html#module-pypath.inputs.encode">pypath.inputs.encode</a>
+        <li><a href="api/pypath.core.annot.Connectomedb.html#pypath.core.annot.Connectomedb.all_refs">(pypath.core.annot.Connectomedb method)</a>
 </li>
-        <li><a href="api/pypath.inputs.ensembl.html#module-pypath.inputs.ensembl">pypath.inputs.ensembl</a>
+        <li><a href="api/pypath.core.annot.Corum.html#pypath.core.annot.Corum.all_refs">(pypath.core.annot.Corum method)</a>
 </li>
-        <li><a href="api/pypath.inputs.eutils.html#module-pypath.inputs.eutils">pypath.inputs.eutils</a>
+        <li><a href="api/pypath.core.annot.CorumFuncat.html#pypath.core.annot.CorumFuncat.all_refs">(pypath.core.annot.CorumFuncat method)</a>
 </li>
-        <li><a href="api/pypath.inputs.exocarta.html#module-pypath.inputs.exocarta">pypath.inputs.exocarta</a>
+        <li><a href="api/pypath.core.annot.CorumGO.html#pypath.core.annot.CorumGO.all_refs">(pypath.core.annot.CorumGO method)</a>
 </li>
-        <li><a href="api/pypath.inputs.expasy.html#module-pypath.inputs.expasy">pypath.inputs.expasy</a>
+        <li><a href="api/pypath.core.annot.Cpad.html#pypath.core.annot.Cpad.all_refs">(pypath.core.annot.Cpad method)</a>
 </li>
-        <li><a href="api/pypath.inputs.genecards.html#module-pypath.inputs.genecards">pypath.inputs.genecards</a>
+        <li><a href="api/pypath.core.annot.Cytosig.html#pypath.core.annot.Cytosig.all_refs">(pypath.core.annot.Cytosig method)</a>
 </li>
-        <li><a href="api/pypath.inputs.go.html#module-pypath.inputs.go">pypath.inputs.go</a>
+        <li><a href="api/pypath.core.annot.Dgidb.html#pypath.core.annot.Dgidb.all_refs">(pypath.core.annot.Dgidb method)</a>
 </li>
-        <li><a href="api/pypath.inputs.gpcrdb.html#module-pypath.inputs.gpcrdb">pypath.inputs.gpcrdb</a>
+        <li><a href="api/pypath.core.annot.Disgenet.html#pypath.core.annot.Disgenet.all_refs">(pypath.core.annot.Disgenet method)</a>
 </li>
-        <li><a href="api/pypath.inputs.graphviz.html#module-pypath.inputs.graphviz">pypath.inputs.graphviz</a>
+        <li><a href="api/pypath.core.annot.Embrace.html#pypath.core.annot.Embrace.all_refs">(pypath.core.annot.Embrace method)</a>
 </li>
-        <li><a href="api/pypath.inputs.hmdb.html#module-pypath.inputs.hmdb">pypath.inputs.hmdb</a>
+        <li><a href="api/pypath.core.annot.Exocarta.html#pypath.core.annot.Exocarta.all_refs">(pypath.core.annot.Exocarta method)</a>
 </li>
-        <li><a href="api/pypath.inputs.hmdb.common.html#module-pypath.inputs.hmdb.common">pypath.inputs.hmdb.common</a>
+        <li><a href="api/pypath.core.annot.GOIntercell.html#pypath.core.annot.GOIntercell.all_refs">(pypath.core.annot.GOIntercell method)</a>
 </li>
-        <li><a href="api/pypath.inputs.hmdb.metabolites.html#module-pypath.inputs.hmdb.metabolites">pypath.inputs.hmdb.metabolites</a>
+        <li><a href="api/pypath.core.annot.Gpcrdb.html#pypath.core.annot.Gpcrdb.all_refs">(pypath.core.annot.Gpcrdb method)</a>
 </li>
-        <li><a href="api/pypath.inputs.hmdb.proteins.html#module-pypath.inputs.hmdb.proteins">pypath.inputs.hmdb.proteins</a>
+        <li><a href="api/pypath.core.annot.GuideToPharmacology.html#pypath.core.annot.GuideToPharmacology.all_refs">(pypath.core.annot.GuideToPharmacology method)</a>
 </li>
-        <li><a href="api/pypath.inputs.hmdb.schema.html#module-pypath.inputs.hmdb.schema">pypath.inputs.hmdb.schema</a>
+        <li><a href="api/pypath.core.annot.Hgnc.html#pypath.core.annot.Hgnc.all_refs">(pypath.core.annot.Hgnc method)</a>
 </li>
-        <li><a href="api/pypath.inputs.hmdb.schema.common.html#module-pypath.inputs.hmdb.schema.common">pypath.inputs.hmdb.schema.common</a>
+        <li><a href="api/pypath.core.annot.HpmrComplex.html#pypath.core.annot.HpmrComplex.all_refs">(pypath.core.annot.HpmrComplex method)</a>
 </li>
-        <li><a href="api/pypath.inputs.hmdb.schema.metabolites.html#module-pypath.inputs.hmdb.schema.metabolites">pypath.inputs.hmdb.schema.metabolites</a>
+        <li><a href="api/pypath.core.annot.HPO.html#pypath.core.annot.HPO.all_refs">(pypath.core.annot.HPO method)</a>
 </li>
-        <li><a href="api/pypath.inputs.hmdb.schema.proteins.html#module-pypath.inputs.hmdb.schema.proteins">pypath.inputs.hmdb.schema.proteins</a>
+        <li><a href="api/pypath.core.annot.Humancellmap.html#pypath.core.annot.Humancellmap.all_refs">(pypath.core.annot.Humancellmap method)</a>
 </li>
-        <li><a href="api/pypath.inputs.hmdb.structures.html#module-pypath.inputs.hmdb.structures">pypath.inputs.hmdb.structures</a>
+        <li><a href="api/pypath.core.annot.HumanPlasmaMembraneReceptome.html#pypath.core.annot.HumanPlasmaMembraneReceptome.all_refs">(pypath.core.annot.HumanPlasmaMembraneReceptome method)</a>
 </li>
-        <li><a href="api/pypath.inputs.hmdb.visual.html#module-pypath.inputs.hmdb.visual">pypath.inputs.hmdb.visual</a>
+        <li><a href="api/pypath.core.annot.HumanProteinAtlas.html#pypath.core.annot.HumanProteinAtlas.all_refs">(pypath.core.annot.HumanProteinAtlas method)</a>
 </li>
-        <li><a href="api/pypath.inputs.hmdb.xml.html#module-pypath.inputs.hmdb.xml">pypath.inputs.hmdb.xml</a>
+        <li><a href="api/pypath.core.annot.HumanProteinAtlasSecretome.html#pypath.core.annot.HumanProteinAtlasSecretome.all_refs">(pypath.core.annot.HumanProteinAtlasSecretome method)</a>
 </li>
-        <li><a href="api/pypath.inputs.hprd.html#module-pypath.inputs.hprd">pypath.inputs.hprd</a>
+        <li><a href="api/pypath.core.annot.HumanProteinAtlasSubcellular.html#pypath.core.annot.HumanProteinAtlasSubcellular.all_refs">(pypath.core.annot.HumanProteinAtlasSubcellular method)</a>
 </li>
-        <li><a href="api/pypath.inputs.htri.html#module-pypath.inputs.htri">pypath.inputs.htri</a>
+        <li><a href="api/pypath.core.annot.Icellnet.html#pypath.core.annot.Icellnet.all_refs">(pypath.core.annot.Icellnet method)</a>
 </li>
-        <li><a href="api/pypath.inputs.humsavar.html#module-pypath.inputs.humsavar">pypath.inputs.humsavar</a>
+        <li><a href="api/pypath.core.annot.IcellnetComplex.html#pypath.core.annot.IcellnetComplex.all_refs">(pypath.core.annot.IcellnetComplex method)</a>
 </li>
-        <li><a href="api/pypath.inputs.i3d.html#module-pypath.inputs.i3d">pypath.inputs.i3d</a>
+        <li><a href="api/pypath.core.annot.Integrins.html#pypath.core.annot.Integrins.all_refs">(pypath.core.annot.Integrins method)</a>
 </li>
-        <li><a href="api/pypath.inputs.ielm.html#module-pypath.inputs.ielm">pypath.inputs.ielm</a>
+        <li><a href="api/pypath.core.annot.InterPro.html#pypath.core.annot.InterPro.all_refs">(pypath.core.annot.InterPro method)</a>
 </li>
-        <li><a href="api/pypath.inputs.imweb.html#module-pypath.inputs.imweb">pypath.inputs.imweb</a>
+        <li><a href="api/pypath.core.annot.Intogen.html#pypath.core.annot.Intogen.all_refs">(pypath.core.annot.Intogen method)</a>
 </li>
-        <li><a href="api/pypath.inputs.innatedb.html#module-pypath.inputs.innatedb">pypath.inputs.innatedb</a>
+        <li><a href="api/pypath.core.annot.Italk.html#pypath.core.annot.Italk.all_refs">(pypath.core.annot.Italk method)</a>
 </li>
-        <li><a href="api/pypath.inputs.instruct.html#module-pypath.inputs.instruct">pypath.inputs.instruct</a>
+        <li><a href="api/pypath.core.annot.KeggPathways.html#pypath.core.annot.KeggPathways.all_refs">(pypath.core.annot.KeggPathways method)</a>
 </li>
-        <li><a href="api/pypath.inputs.intact.html#module-pypath.inputs.intact">pypath.inputs.intact</a>
+        <li><a href="api/pypath.core.annot.KeggPathwaysPC.html#pypath.core.annot.KeggPathwaysPC.all_refs">(pypath.core.annot.KeggPathwaysPC method)</a>
 </li>
-        <li><a href="api/pypath.inputs.interpro.html#module-pypath.inputs.interpro">pypath.inputs.interpro</a>
+        <li><a href="api/pypath.core.annot.Kinasedotcom.html#pypath.core.annot.Kinasedotcom.all_refs">(pypath.core.annot.Kinasedotcom method)</a>
 </li>
-        <li><a href="api/pypath.inputs.ipi.html#module-pypath.inputs.ipi">pypath.inputs.ipi</a>
+        <li><a href="api/pypath.core.annot.Kirouac2010.html#pypath.core.annot.Kirouac2010.all_refs">(pypath.core.annot.Kirouac2010 method)</a>
 </li>
-        <li><a href="api/pypath.inputs.kegg_api.html#module-pypath.inputs.kegg_api">pypath.inputs.kegg_api</a>
+        <li><a href="api/pypath.core.annot.Lambert2018.html#pypath.core.annot.Lambert2018.all_refs">(pypath.core.annot.Lambert2018 method)</a>
 </li>
-        <li><a href="api/pypath.inputs.kirouac2010.html#module-pypath.inputs.kirouac2010">pypath.inputs.kirouac2010</a>
+        <li><a href="api/pypath.core.annot.LigandReceptor.html#pypath.core.annot.LigandReceptor.all_refs">(pypath.core.annot.LigandReceptor method)</a>
 </li>
-        <li><a href="api/pypath.inputs.laudanna.html#module-pypath.inputs.laudanna">pypath.inputs.laudanna</a>
+        <li><a href="api/pypath.core.annot.Locate.html#pypath.core.annot.Locate.all_refs">(pypath.core.annot.Locate method)</a>
 </li>
-        <li><a href="api/pypath.inputs.lincs.html#module-pypath.inputs.lincs">pypath.inputs.lincs</a>
+        <li><a href="api/pypath.core.annot.Lrdb.html#pypath.core.annot.Lrdb.all_refs">(pypath.core.annot.Lrdb method)</a>
 </li>
-        <li><a href="api/pypath.inputs.lncdisease.html#module-pypath.inputs.lncdisease">pypath.inputs.lncdisease</a>
+        <li><a href="api/pypath.core.annot.Matrisome.html#pypath.core.annot.Matrisome.all_refs">(pypath.core.annot.Matrisome method)</a>
 </li>
-        <li><a href="api/pypath.inputs.lncrnadb.html#module-pypath.inputs.lncrnadb">pypath.inputs.lncrnadb</a>
+        <li><a href="api/pypath.core.annot.Matrixdb.html#pypath.core.annot.Matrixdb.all_refs">(pypath.core.annot.Matrixdb method)</a>
 </li>
-        <li><a href="api/pypath.inputs.macrophage.html#module-pypath.inputs.macrophage">pypath.inputs.macrophage</a>
+        <li><a href="api/pypath.core.annot.Mcam.html#pypath.core.annot.Mcam.all_refs">(pypath.core.annot.Mcam method)</a>
 </li>
-        <li><a href="api/pypath.inputs.main.html#module-pypath.inputs.main">pypath.inputs.main</a>
+        <li><a href="api/pypath.core.annot.Membranome.html#pypath.core.annot.Membranome.all_refs">(pypath.core.annot.Membranome method)</a>
 </li>
-        <li><a href="api/pypath.inputs.mimp.html#module-pypath.inputs.mimp">pypath.inputs.mimp</a>
+        <li><a href="api/pypath.core.annot.Msigdb.html#pypath.core.annot.Msigdb.all_refs">(pypath.core.annot.Msigdb method)</a>
 </li>
-        <li><a href="api/pypath.inputs.mir2disease.html#module-pypath.inputs.mir2disease">pypath.inputs.mir2disease</a>
+        <li><a href="api/pypath.core.annot.NetpathPathways.html#pypath.core.annot.NetpathPathways.all_refs">(pypath.core.annot.NetpathPathways method)</a>
 </li>
-        <li><a href="api/pypath.inputs.mirbase.html#module-pypath.inputs.mirbase">pypath.inputs.mirbase</a>
+        <li><a href="api/pypath.core.annot.Opm.html#pypath.core.annot.Opm.all_refs">(pypath.core.annot.Opm method)</a>
 </li>
-        <li><a href="api/pypath.inputs.mirdeathdb.html#module-pypath.inputs.mirdeathdb">pypath.inputs.mirdeathdb</a>
+        <li><a href="api/pypath.core.annot.Panglaodb.html#pypath.core.annot.Panglaodb.all_refs">(pypath.core.annot.Panglaodb method)</a>
 </li>
-        <li><a href="api/pypath.inputs.mirecords.html#module-pypath.inputs.mirecords">pypath.inputs.mirecords</a>
+        <li><a href="api/pypath.core.annot.Phobius.html#pypath.core.annot.Phobius.all_refs">(pypath.core.annot.Phobius method)</a>
 </li>
-        <li><a href="api/pypath.inputs.mirtarbase.html#module-pypath.inputs.mirtarbase">pypath.inputs.mirtarbase</a>
+        <li><a href="api/pypath.core.annot.Phosphatome.html#pypath.core.annot.Phosphatome.all_refs">(pypath.core.annot.Phosphatome method)</a>
 </li>
-        <li><a href="api/pypath.inputs.mitab.html#module-pypath.inputs.mitab">pypath.inputs.mitab</a>
+        <li><a href="api/pypath.core.annot.Progeny.html#pypath.core.annot.Progeny.all_refs">(pypath.core.annot.Progeny method)</a>
 </li>
-        <li><a href="api/pypath.inputs.mppi.html#module-pypath.inputs.mppi">pypath.inputs.mppi</a>
+        <li><a href="api/pypath.core.annot.Ramilowski2015.html#pypath.core.annot.Ramilowski2015.all_refs">(pypath.core.annot.Ramilowski2015 method)</a>
 </li>
-        <li><a href="api/pypath.inputs.ncrdeathdb.html#module-pypath.inputs.ncrdeathdb">pypath.inputs.ncrdeathdb</a>
+        <li><a href="api/pypath.core.annot.Ramilowski2015Location.html#pypath.core.annot.Ramilowski2015Location.all_refs">(pypath.core.annot.Ramilowski2015Location method)</a>
 </li>
-        <li><a href="api/pypath.inputs.negatome.html#module-pypath.inputs.negatome">pypath.inputs.negatome</a>
+        <li><a href="api/pypath.core.annot.Scconnect.html#pypath.core.annot.Scconnect.all_refs">(pypath.core.annot.Scconnect method)</a>
 </li>
-        <li><a href="api/pypath.inputs.netbiol.html#module-pypath.inputs.netbiol">pypath.inputs.netbiol</a>
+        <li><a href="api/pypath.core.annot.ScconnectComplex.html#pypath.core.annot.ScconnectComplex.all_refs">(pypath.core.annot.ScconnectComplex method)</a>
 </li>
-        <li><a href="api/pypath.inputs.offsides.html#module-pypath.inputs.offsides">pypath.inputs.offsides</a>
+        <li><a href="api/pypath.core.annot.SignalinkFunctions.html#pypath.core.annot.SignalinkFunctions.all_refs">(pypath.core.annot.SignalinkFunctions method)</a>
 </li>
-        <li><a href="api/pypath.inputs.ontology.html#module-pypath.inputs.ontology">pypath.inputs.ontology</a>
+        <li><a href="api/pypath.core.annot.SignalinkPathways.html#pypath.core.annot.SignalinkPathways.all_refs">(pypath.core.annot.SignalinkPathways method)</a>
 </li>
-        <li><a href="api/pypath.inputs.opentargets.html#module-pypath.inputs.opentargets">pypath.inputs.opentargets</a>
+        <li><a href="api/pypath.core.annot.SignorPathways.html#pypath.core.annot.SignorPathways.all_refs">(pypath.core.annot.SignorPathways method)</a>
 </li>
-        <li><a href="api/pypath.inputs.oreganno.html#module-pypath.inputs.oreganno">pypath.inputs.oreganno</a>
+        <li><a href="api/pypath.core.annot.Surfaceome.html#pypath.core.annot.Surfaceome.all_refs">(pypath.core.annot.Surfaceome method)</a>
 </li>
-        <li><a href="api/pypath.inputs.pathophenodb.html#module-pypath.inputs.pathophenodb">pypath.inputs.pathophenodb</a>
+        <li><a href="api/pypath.core.annot.Talklr.html#pypath.core.annot.Talklr.all_refs">(pypath.core.annot.Talklr method)</a>
 </li>
-        <li><a href="api/pypath.inputs.pathwaycommons.html#module-pypath.inputs.pathwaycommons">pypath.inputs.pathwaycommons</a>
+        <li><a href="api/pypath.core.annot.Tcdb.html#pypath.core.annot.Tcdb.all_refs">(pypath.core.annot.Tcdb method)</a>
 </li>
-        <li><a href="api/pypath.inputs.pazar.html#module-pypath.inputs.pazar">pypath.inputs.pazar</a>
+        <li><a href="api/pypath.core.annot.Tfcensus.html#pypath.core.annot.Tfcensus.all_refs">(pypath.core.annot.Tfcensus method)</a>
 </li>
-        <li><a href="api/pypath.inputs.pdzbase.html#module-pypath.inputs.pdzbase">pypath.inputs.pdzbase</a>
+        <li><a href="api/pypath.core.annot.Topdb.html#pypath.core.annot.Topdb.all_refs">(pypath.core.annot.Topdb method)</a>
 </li>
-        <li><a href="api/pypath.inputs.pepcyber.html#module-pypath.inputs.pepcyber">pypath.inputs.pepcyber</a>
+        <li><a href="api/pypath.core.annot.UniprotFamilies.html#pypath.core.annot.UniprotFamilies.all_refs">(pypath.core.annot.UniprotFamilies method)</a>
 </li>
-        <li><a href="api/pypath.inputs.pfam.html#module-pypath.inputs.pfam">pypath.inputs.pfam</a>
+        <li><a href="api/pypath.core.annot.UniprotKeywords.html#pypath.core.annot.UniprotKeywords.all_refs">(pypath.core.annot.UniprotKeywords method)</a>
 </li>
-        <li><a href="api/pypath.inputs.pharos.html#module-pypath.inputs.pharos">pypath.inputs.pharos</a>
+        <li><a href="api/pypath.core.annot.UniprotLocations.html#pypath.core.annot.UniprotLocations.all_refs">(pypath.core.annot.UniprotLocations method)</a>
 </li>
-        <li><a href="api/pypath.inputs.phobius.html#module-pypath.inputs.phobius">pypath.inputs.phobius</a>
+        <li><a href="api/pypath.core.annot.UniprotTissues.html#pypath.core.annot.UniprotTissues.all_refs">(pypath.core.annot.UniprotTissues method)</a>
 </li>
-        <li><a href="api/pypath.inputs.phosphoelm.html#module-pypath.inputs.phosphoelm">pypath.inputs.phosphoelm</a>
+        <li><a href="api/pypath.core.annot.UniprotTopologies.html#pypath.core.annot.UniprotTopologies.all_refs">(pypath.core.annot.UniprotTopologies method)</a>
 </li>
-        <li><a href="api/pypath.inputs.phosphonetworks.html#module-pypath.inputs.phosphonetworks">pypath.inputs.phosphonetworks</a>
+        <li><a href="api/pypath.core.annot.Vesiclepedia.html#pypath.core.annot.Vesiclepedia.all_refs">(pypath.core.annot.Vesiclepedia method)</a>
 </li>
-        <li><a href="api/pypath.inputs.phosphopoint.html#module-pypath.inputs.phosphopoint">pypath.inputs.phosphopoint</a>
+        <li><a href="api/pypath.core.annot.Wang.html#pypath.core.annot.Wang.all_refs">(pypath.core.annot.Wang method)</a>
 </li>
-        <li><a href="api/pypath.inputs.pro.html#module-pypath.inputs.pro">pypath.inputs.pro</a>
+        <li><a href="api/pypath.core.annot.Zhong2015.html#pypath.core.annot.Zhong2015.all_refs">(pypath.core.annot.Zhong2015 method)</a>
 </li>
-        <li><a href="api/pypath.inputs.proteins.html#module-pypath.inputs.proteins">pypath.inputs.proteins</a>
+      </ul></li>
+      <li><a href="api/pypath.inputs.dorothea.DorotheaInteraction.html#pypath.inputs.dorothea.DorotheaInteraction.all_sources">all_sources (pypath.inputs.dorothea.DorotheaInteraction attribute)</a>
 </li>
-        <li><a href="api/pypath.inputs.protmapper.html#module-pypath.inputs.protmapper">pypath.inputs.protmapper</a>
+      <li><a href="api/pypath.inputs.uniprot_db.all_swissprots.html#pypath.inputs.uniprot_db.all_swissprots">all_swissprots() (in module pypath.inputs.uniprot_db)</a>
 </li>
-        <li><a href="api/pypath.inputs.pubchem.html#module-pypath.inputs.pubchem">pypath.inputs.pubchem</a>
+      <li><a href="api/pypath.inputs.uniprot_db.all_trembls.html#pypath.inputs.uniprot_db.all_trembls">all_trembls() (in module pypath.inputs.uniprot_db)</a>
 </li>
-        <li><a href="api/pypath.inputs.pubmed.html#module-pypath.inputs.pubmed">pypath.inputs.pubmed</a>
+      <li><a href="api/pypath.inputs.uniprot_db.all_uniprots.html#pypath.inputs.uniprot_db.all_uniprots">all_uniprots() (in module pypath.inputs.uniprot_db)</a>
+
+      <ul>
+        <li><a href="api/pypath.utils.go.GOAnnotation.html#pypath.utils.go.GOAnnotation.all_uniprots">(pypath.utils.go.GOAnnotation method)</a>
 </li>
-        <li><a href="api/pypath.inputs.ramp.html#module-pypath.inputs.ramp">pypath.inputs.ramp</a>
+      </ul></li>
+      <li><a href="api/pypath.core.annot.Almen2009.html#pypath.core.annot.Almen2009">Almen2009 (class in pypath.core.annot)</a>
 </li>
-        <li><a href="api/pypath.inputs.rdata.html#module-pypath.inputs.rdata">pypath.inputs.rdata</a>
+      <li><a href="api/pypath.inputs.almen2009.almen2009_annotations.html#pypath.inputs.almen2009.almen2009_annotations">almen2009_annotations() (in module pypath.inputs.almen2009)</a>
 </li>
-        <li><a href="api/pypath.inputs.reaction.html#module-pypath.inputs.reaction">pypath.inputs.reaction</a>
+      <li><a href="api/pypath.visual.igraph_drawing.edge.AlphaVaryingEdgeDrawer.html#pypath.visual.igraph_drawing.edge.AlphaVaryingEdgeDrawer">AlphaVaryingEdgeDrawer (class in pypath.visual.igraph_drawing.edge)</a>
 </li>
-        <li><a href="api/pypath.inputs.reactome.html#module-pypath.inputs.reactome">pypath.inputs.reactome</a>
+      <li><a href="api/pypath.utils.uniprot.alternative_products.html#pypath.utils.uniprot.alternative_products">alternative_products() (in module pypath.utils.uniprot)</a>
 </li>
-        <li><a href="api/pypath.inputs.science.html#module-pypath.inputs.science">pypath.inputs.science</a>
+      <li><a href="api/pypath.utils.uniprot.alternative_products_with_xrefs.html#pypath.utils.uniprot.alternative_products_with_xrefs">alternative_products_with_xrefs() (in module pypath.utils.uniprot)</a>
 </li>
-        <li><a href="api/pypath.inputs.sider.html#module-pypath.inputs.sider">pypath.inputs.sider</a>
+      <li><a href="api/pypath.utils.go.annotate.html#pypath.utils.go.annotate">annotate() (in module pypath.utils.go)</a>
 </li>
-        <li><a href="api/pypath.inputs.stitch.html#module-pypath.inputs.stitch">pypath.inputs.stitch</a>
+      <li><a href="api/pypath.core.annot.Adhesome.html#pypath.core.annot.Adhesome.annotate_complex">annotate_complex() (pypath.core.annot.Adhesome method)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.annot.Almen2009.html#pypath.core.annot.Almen2009.annotate_complex">(pypath.core.annot.Almen2009 method)</a>
 </li>
-        <li><a href="api/pypath.inputs.string.html#module-pypath.inputs.string">pypath.inputs.string</a>
+        <li><a href="api/pypath.core.annot.AnnotationBase.html#pypath.core.annot.AnnotationBase.annotate_complex">(pypath.core.annot.AnnotationBase method)</a>
 </li>
-        <li><a href="api/pypath.inputs.switches_elm.html#module-pypath.inputs.switches_elm">pypath.inputs.switches_elm</a>
+        <li><a href="api/pypath.core.annot.Baccin2019.html#pypath.core.annot.Baccin2019.annotate_complex">(pypath.core.annot.Baccin2019 method)</a>
 </li>
-        <li><a href="api/pypath.inputs.transmir.html#module-pypath.inputs.transmir">pypath.inputs.transmir</a>
+        <li><a href="api/pypath.core.annot.Biogps.html#pypath.core.annot.Biogps.annotate_complex">(pypath.core.annot.Biogps method)</a>
 </li>
-        <li><a href="api/pypath.inputs.trip.html#module-pypath.inputs.trip">pypath.inputs.trip</a>
+        <li><a href="api/pypath.core.annot.Cancerdrugsdb.html#pypath.core.annot.Cancerdrugsdb.annotate_complex">(pypath.core.annot.Cancerdrugsdb method)</a>
 </li>
-        <li><a href="api/pypath.inputs.trrust.html#module-pypath.inputs.trrust">pypath.inputs.trrust</a>
+        <li><a href="api/pypath.core.annot.CancerGeneCensus.html#pypath.core.annot.CancerGeneCensus.annotate_complex">(pypath.core.annot.CancerGeneCensus method)</a>
 </li>
-        <li><a href="api/pypath.inputs.twosides.html#module-pypath.inputs.twosides">pypath.inputs.twosides</a>
+        <li><a href="api/pypath.core.annot.Cancersea.html#pypath.core.annot.Cancersea.annotate_complex">(pypath.core.annot.Cancersea method)</a>
 </li>
-        <li><a href="api/pypath.inputs.unichem.html#module-pypath.inputs.unichem">pypath.inputs.unichem</a>
+        <li><a href="api/pypath.core.annot.Cellcall.html#pypath.core.annot.Cellcall.annotate_complex">(pypath.core.annot.Cellcall method)</a>
 </li>
-        <li><a href="api/pypath.inputs.uniprot.html#module-pypath.inputs.uniprot">pypath.inputs.uniprot</a>
+        <li><a href="api/pypath.core.annot.Cellcellinteractions.html#pypath.core.annot.Cellcellinteractions.annotate_complex">(pypath.core.annot.Cellcellinteractions method)</a>
 </li>
-        <li><a href="api/pypath.inputs.uniprot_db.html#module-pypath.inputs.uniprot_db">pypath.inputs.uniprot_db</a>
+        <li><a href="api/pypath.core.annot.Cellchatdb.html#pypath.core.annot.Cellchatdb.annotate_complex">(pypath.core.annot.Cellchatdb method)</a>
 </li>
-        <li><a href="api/pypath.internals.html#module-pypath.internals">pypath.internals</a>
+        <li><a href="api/pypath.core.annot.CellchatdbComplex.html#pypath.core.annot.CellchatdbComplex.annotate_complex">(pypath.core.annot.CellchatdbComplex method)</a>
 </li>
-        <li><a href="api/pypath.internals.input_formats.html#module-pypath.internals.input_formats">pypath.internals.input_formats</a>
+        <li><a href="api/pypath.core.annot.Cellinker.html#pypath.core.annot.Cellinker.annotate_complex">(pypath.core.annot.Cellinker method)</a>
 </li>
-        <li><a href="api/pypath.internals.license.html#module-pypath.internals.license">pypath.internals.license</a>
+        <li><a href="api/pypath.core.annot.CellinkerComplex.html#pypath.core.annot.CellinkerComplex.annotate_complex">(pypath.core.annot.CellinkerComplex method)</a>
 </li>
-        <li><a href="api/pypath.internals.maps.html#module-pypath.internals.maps">pypath.internals.maps</a>
+        <li><a href="api/pypath.core.annot.CellPhoneDB.html#pypath.core.annot.CellPhoneDB.annotate_complex">(pypath.core.annot.CellPhoneDB method)</a>
 </li>
-        <li><a href="api/pypath.internals.refs.html#module-pypath.internals.refs">pypath.internals.refs</a>
+        <li><a href="api/pypath.core.annot.CellPhoneDBComplex.html#pypath.core.annot.CellPhoneDBComplex.annotate_complex">(pypath.core.annot.CellPhoneDBComplex method)</a>
 </li>
-        <li><a href="api/pypath.internals.resource.html#module-pypath.internals.resource">pypath.internals.resource</a>
+        <li><a href="api/pypath.core.annot.CellSurfaceProteinAtlas.html#pypath.core.annot.CellSurfaceProteinAtlas.annotate_complex">(pypath.core.annot.CellSurfaceProteinAtlas method)</a>
 </li>
-        <li><a href="api/pypath.legacy.html#module-pypath.legacy">pypath.legacy</a>
+        <li><a href="api/pypath.core.annot.CellSurfaceProteinAtlasCellType.html#pypath.core.annot.CellSurfaceProteinAtlasCellType.annotate_complex">(pypath.core.annot.CellSurfaceProteinAtlasCellType method)</a>
 </li>
-        <li><a href="api/pypath.legacy.db_categories.html#module-pypath.legacy.db_categories">pypath.legacy.db_categories</a>
+        <li><a href="api/pypath.core.annot.Celltalkdb.html#pypath.core.annot.Celltalkdb.annotate_complex">(pypath.core.annot.Celltalkdb method)</a>
 </li>
-        <li><a href="api/pypath.resources.html#module-pypath.resources">pypath.resources</a>
+        <li><a href="api/pypath.core.annot.Celltypist.html#pypath.core.annot.Celltypist.annotate_complex">(pypath.core.annot.Celltypist method)</a>
 </li>
-        <li><a href="api/pypath.resources.controller.html#module-pypath.resources.controller">pypath.resources.controller</a>
+        <li><a href="api/pypath.core.annot.Comppi.html#pypath.core.annot.Comppi.annotate_complex">(pypath.core.annot.Comppi method)</a>
 </li>
-        <li><a href="api/pypath.resources.data.html#module-pypath.resources.data">pypath.resources.data</a>
+        <li><a href="api/pypath.core.annot.Connectomedb.html#pypath.core.annot.Connectomedb.annotate_complex">(pypath.core.annot.Connectomedb method)</a>
 </li>
-        <li><a href="api/pypath.resources.data_formats.html#module-pypath.resources.data_formats">pypath.resources.data_formats</a>
+        <li><a href="api/pypath.core.annot.Corum.html#pypath.core.annot.Corum.annotate_complex">(pypath.core.annot.Corum method)</a>
 </li>
-        <li><a href="api/pypath.resources.licenses.html#module-pypath.resources.licenses">pypath.resources.licenses</a>
+        <li><a href="api/pypath.core.annot.CorumFuncat.html#pypath.core.annot.CorumFuncat.annotate_complex">(pypath.core.annot.CorumFuncat method)</a>
 </li>
-        <li><a href="api/pypath.resources.network.html#module-pypath.resources.network">pypath.resources.network</a>
+        <li><a href="api/pypath.core.annot.CorumGO.html#pypath.core.annot.CorumGO.annotate_complex">(pypath.core.annot.CorumGO method)</a>
 </li>
-        <li><a href="api/pypath.resources.urls.html#module-pypath.resources.urls">pypath.resources.urls</a>
+        <li><a href="api/pypath.core.annot.Cpad.html#pypath.core.annot.Cpad.annotate_complex">(pypath.core.annot.Cpad method)</a>
 </li>
-        <li><a href="api/pypath.share.html#module-pypath.share">pypath.share</a>
+        <li><a href="api/pypath.core.annot.Cytosig.html#pypath.core.annot.Cytosig.annotate_complex">(pypath.core.annot.Cytosig method)</a>
 </li>
-        <li><a href="api/pypath.share.cache.html#module-pypath.share.cache">pypath.share.cache</a>
+        <li><a href="api/pypath.core.annot.Dgidb.html#pypath.core.annot.Dgidb.annotate_complex">(pypath.core.annot.Dgidb method)</a>
 </li>
-        <li><a href="api/pypath.share.common.html#module-pypath.share.common">pypath.share.common</a>
+        <li><a href="api/pypath.core.annot.Disgenet.html#pypath.core.annot.Disgenet.annotate_complex">(pypath.core.annot.Disgenet method)</a>
 </li>
-        <li><a href="api/pypath.share.constants.html#module-pypath.share.constants">pypath.share.constants</a>
+        <li><a href="api/pypath.core.annot.Embrace.html#pypath.core.annot.Embrace.annotate_complex">(pypath.core.annot.Embrace method)</a>
 </li>
-        <li><a href="api/pypath.share.curl.html#module-pypath.share.curl">pypath.share.curl</a>
+        <li><a href="api/pypath.core.annot.Exocarta.html#pypath.core.annot.Exocarta.annotate_complex">(pypath.core.annot.Exocarta method)</a>
 </li>
-        <li><a href="api/pypath.share.progress.html#module-pypath.share.progress">pypath.share.progress</a>
+        <li><a href="api/pypath.core.annot.GOIntercell.html#pypath.core.annot.GOIntercell.annotate_complex">(pypath.core.annot.GOIntercell method)</a>
 </li>
-        <li><a href="api/pypath.share.session.html#module-pypath.share.session">pypath.share.session</a>
+        <li><a href="api/pypath.core.annot.Gpcrdb.html#pypath.core.annot.Gpcrdb.annotate_complex">(pypath.core.annot.Gpcrdb method)</a>
 </li>
-        <li><a href="api/pypath.share.settings.html#module-pypath.share.settings">pypath.share.settings</a>
+        <li><a href="api/pypath.core.annot.GuideToPharmacology.html#pypath.core.annot.GuideToPharmacology.annotate_complex">(pypath.core.annot.GuideToPharmacology method)</a>
 </li>
-        <li><a href="api/pypath.utils.html#module-pypath.utils">pypath.utils</a>
+        <li><a href="api/pypath.core.annot.Hgnc.html#pypath.core.annot.Hgnc.annotate_complex">(pypath.core.annot.Hgnc method)</a>
 </li>
-        <li><a href="api/pypath.utils.go.html#module-pypath.utils.go">pypath.utils.go</a>
+        <li><a href="api/pypath.core.annot.HpmrComplex.html#pypath.core.annot.HpmrComplex.annotate_complex">(pypath.core.annot.HpmrComplex method)</a>
 </li>
-        <li><a href="api/pypath.utils.pdb.html#module-pypath.utils.pdb">pypath.utils.pdb</a>
+        <li><a href="api/pypath.core.annot.HPO.html#pypath.core.annot.HPO.annotate_complex">(pypath.core.annot.HPO method)</a>
 </li>
-        <li><a href="api/pypath.utils.proteomicsdb.html#module-pypath.utils.proteomicsdb">pypath.utils.proteomicsdb</a>
+        <li><a href="api/pypath.core.annot.Humancellmap.html#pypath.core.annot.Humancellmap.annotate_complex">(pypath.core.annot.Humancellmap method)</a>
 </li>
-        <li><a href="api/pypath.utils.reflists.html#module-pypath.utils.reflists">pypath.utils.reflists</a>
+        <li><a href="api/pypath.core.annot.HumanPlasmaMembraneReceptome.html#pypath.core.annot.HumanPlasmaMembraneReceptome.annotate_complex">(pypath.core.annot.HumanPlasmaMembraneReceptome method)</a>
 </li>
-        <li><a href="api/pypath.utils.residues.html#module-pypath.utils.residues">pypath.utils.residues</a>
+        <li><a href="api/pypath.core.annot.HumanProteinAtlas.html#pypath.core.annot.HumanProteinAtlas.annotate_complex">(pypath.core.annot.HumanProteinAtlas method)</a>
 </li>
-        <li><a href="api/pypath.utils.seq.html#module-pypath.utils.seq">pypath.utils.seq</a>
+        <li><a href="api/pypath.core.annot.HumanProteinAtlasSecretome.html#pypath.core.annot.HumanProteinAtlasSecretome.annotate_complex">(pypath.core.annot.HumanProteinAtlasSecretome method)</a>
 </li>
-        <li><a href="api/pypath.utils.taxonomy.html#module-pypath.utils.taxonomy">pypath.utils.taxonomy</a>
+        <li><a href="api/pypath.core.annot.HumanProteinAtlasSubcellular.html#pypath.core.annot.HumanProteinAtlasSubcellular.annotate_complex">(pypath.core.annot.HumanProteinAtlasSubcellular method)</a>
 </li>
-        <li><a href="api/pypath.utils.unichem.html#module-pypath.utils.unichem">pypath.utils.unichem</a>
+        <li><a href="api/pypath.core.annot.Icellnet.html#pypath.core.annot.Icellnet.annotate_complex">(pypath.core.annot.Icellnet method)</a>
 </li>
-        <li><a href="api/pypath.visual.html#module-pypath.visual">pypath.visual</a>
+        <li><a href="api/pypath.core.annot.IcellnetComplex.html#pypath.core.annot.IcellnetComplex.annotate_complex">(pypath.core.annot.IcellnetComplex method)</a>
 </li>
-        <li><a href="api/pypath.visual.drawing.html#module-pypath.visual.drawing">pypath.visual.drawing</a>
+        <li><a href="api/pypath.core.annot.Integrins.html#pypath.core.annot.Integrins.annotate_complex">(pypath.core.annot.Integrins method)</a>
 </li>
-        <li><a href="api/pypath.visual.igraph_drawing.html#module-pypath.visual.igraph_drawing">pypath.visual.igraph_drawing</a>
+        <li><a href="api/pypath.core.annot.InterPro.html#pypath.core.annot.InterPro.annotate_complex">(pypath.core.annot.InterPro method)</a>
 </li>
-        <li><a href="api/pypath.visual.igraph_drawing.edge.html#module-pypath.visual.igraph_drawing.edge">pypath.visual.igraph_drawing.edge</a>
+        <li><a href="api/pypath.core.annot.Intogen.html#pypath.core.annot.Intogen.annotate_complex">(pypath.core.annot.Intogen method)</a>
 </li>
-        <li><a href="api/pypath.visual.igraph_drawing.vertex.html#module-pypath.visual.igraph_drawing.vertex">pypath.visual.igraph_drawing.vertex</a>
+        <li><a href="api/pypath.core.annot.Italk.html#pypath.core.annot.Italk.annotate_complex">(pypath.core.annot.Italk method)</a>
 </li>
-      </ul></li>
-  </ul></td>
-  <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="api/pypath.inputs.mppi.mppi_interactions.html#pypath.inputs.mppi.mppi_interactions">mppi_interactions() (in module pypath.inputs.mppi)</a>
+        <li><a href="api/pypath.core.annot.KeggPathways.html#pypath.core.annot.KeggPathways.annotate_complex">(pypath.core.annot.KeggPathways method)</a>
 </li>
-  </ul></td>
-</tr></table>
-
-<h2 id="N">N</h2>
-<table style="width: 100%" class="indextable genindextable"><tr>
-  <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="api/pypath.inputs.adrecs.AdrecsTerm.html#pypath.inputs.adrecs.AdrecsTerm.name">name (pypath.inputs.adrecs.AdrecsTerm attribute)</a>
-
-      <ul>
-        <li><a href="api/pypath.inputs.pathwaycommons.PathwayCommonsResource.html#pypath.inputs.pathwaycommons.PathwayCommonsResource.name">(pypath.inputs.pathwaycommons.PathwayCommonsResource attribute)</a>
+        <li><a href="api/pypath.core.annot.KeggPathwaysPC.html#pypath.core.annot.KeggPathwaysPC.annotate_complex">(pypath.core.annot.KeggPathwaysPC method)</a>
 </li>
-        <li><a href="api/pypath.inputs.sider.SiderDrug.html#pypath.inputs.sider.SiderDrug.name">(pypath.inputs.sider.SiderDrug attribute)</a>
+        <li><a href="api/pypath.core.annot.Kinasedotcom.html#pypath.core.annot.Kinasedotcom.annotate_complex">(pypath.core.annot.Kinasedotcom method)</a>
 </li>
-        <li><a href="api/pypath.internals.resource.EnzymeSubstrateResourceKey.html#pypath.internals.resource.EnzymeSubstrateResourceKey.name">(pypath.internals.resource.EnzymeSubstrateResourceKey attribute)</a>
+        <li><a href="api/pypath.core.annot.Kirouac2010.html#pypath.core.annot.Kirouac2010.annotate_complex">(pypath.core.annot.Kirouac2010 method)</a>
 </li>
-        <li><a href="api/pypath.internals.resource.NetworkResourceKey.html#pypath.internals.resource.NetworkResourceKey.name">(pypath.internals.resource.NetworkResourceKey attribute)</a>
+        <li><a href="api/pypath.core.annot.Lambert2018.html#pypath.core.annot.Lambert2018.annotate_complex">(pypath.core.annot.Lambert2018 method)</a>
 </li>
-      </ul></li>
-      <li><a href="api/pypath.inputs.uniprot.UniprotQuery.html#pypath.inputs.uniprot.UniprotQuery.name_process">name_process (pypath.inputs.uniprot.UniprotQuery attribute)</a>
+        <li><a href="api/pypath.core.annot.LigandReceptor.html#pypath.core.annot.LigandReceptor.annotate_complex">(pypath.core.annot.LigandReceptor method)</a>
 </li>
-      <li><a href="api/pypath.utils.go.GeneOntology.html#pypath.utils.go.GeneOntology.names_to_terms">names_to_terms() (pypath.utils.go.GeneOntology method)</a>
+        <li><a href="api/pypath.core.annot.Locate.html#pypath.core.annot.Locate.annotate_complex">(pypath.core.annot.Locate method)</a>
 </li>
-      <li><a href="api/pypath.utils.go.GeneOntology.html#pypath.utils.go.GeneOntology.names_to_terms_aspects">names_to_terms_aspects() (pypath.utils.go.GeneOntology method)</a>
+        <li><a href="api/pypath.core.annot.Lrdb.html#pypath.core.annot.Lrdb.annotate_complex">(pypath.core.annot.Lrdb method)</a>
 </li>
-  </ul></td>
-  <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="api/pypath.inputs.uniprot.Taxon.html#pypath.inputs.uniprot.Taxon.ncbi_id">ncbi_id (pypath.inputs.uniprot.Taxon attribute)</a>
+        <li><a href="api/pypath.core.annot.Matrisome.html#pypath.core.annot.Matrisome.annotate_complex">(pypath.core.annot.Matrisome method)</a>
 </li>
-      <li><a href="api/pypath.inputs.ncrdeathdb.ncrdeathdb_interactions.html#pypath.inputs.ncrdeathdb.ncrdeathdb_interactions">ncrdeathdb_interactions() (in module pypath.inputs.ncrdeathdb)</a>
+        <li><a href="api/pypath.core.annot.Matrixdb.html#pypath.core.annot.Matrixdb.annotate_complex">(pypath.core.annot.Matrixdb method)</a>
 </li>
-      <li><a href="api/pypath.inputs.negatome.negatome_interactions.html#pypath.inputs.negatome.negatome_interactions">negatome_interactions() (in module pypath.inputs.negatome)</a>
+        <li><a href="api/pypath.core.annot.Mcam.html#pypath.core.annot.Mcam.annotate_complex">(pypath.core.annot.Mcam method)</a>
 </li>
-      <li><a href="api/pypath.internals.resource.NetworkDataset.html#pypath.internals.resource.NetworkDataset">NetworkDataset (class in pypath.internals.resource)</a>
+        <li><a href="api/pypath.core.annot.Membranome.html#pypath.core.annot.Membranome.annotate_complex">(pypath.core.annot.Membranome method)</a>
 </li>
-      <li><a href="api/pypath.internals.input_formats.NetworkInput.html#pypath.internals.input_formats.NetworkInput">NetworkInput (class in pypath.internals.input_formats)</a>
+        <li><a href="api/pypath.core.annot.Msigdb.html#pypath.core.annot.Msigdb.annotate_complex">(pypath.core.annot.Msigdb method)</a>
 </li>
-      <li><a href="api/pypath.internals.resource.NetworkResource.html#pypath.internals.resource.NetworkResource">NetworkResource (class in pypath.internals.resource)</a>
+        <li><a href="api/pypath.core.annot.NetpathPathways.html#pypath.core.annot.NetpathPathways.annotate_complex">(pypath.core.annot.NetpathPathways method)</a>
 </li>
-      <li><a href="api/pypath.internals.resource.NetworkResourceKey.html#pypath.internals.resource.NetworkResourceKey">NetworkResourceKey (class in pypath.internals.resource)</a>
+        <li><a href="api/pypath.core.annot.Opm.html#pypath.core.annot.Opm.annotate_complex">(pypath.core.annot.Opm method)</a>
 </li>
-      <li><a href="api/pypath.inputs.netbiol.nrf2ome_interactions.html#pypath.inputs.netbiol.nrf2ome_interactions">nrf2ome_interactions() (in module pypath.inputs.netbiol)</a>
+        <li><a href="api/pypath.core.annot.Panglaodb.html#pypath.core.annot.Panglaodb.annotate_complex">(pypath.core.annot.Panglaodb method)</a>
 </li>
-      <li><a href="api/pypath.inputs.uniprot.UniprotRecordHistory.html#pypath.inputs.uniprot.UniprotRecordHistory.number">number (pypath.inputs.uniprot.UniprotRecordHistory attribute)</a>
+        <li><a href="api/pypath.core.annot.Phobius.html#pypath.core.annot.Phobius.annotate_complex">(pypath.core.annot.Phobius method)</a>
 </li>
-  </ul></td>
-</tr></table>
-
-<h2 id="O">O</h2>
-<table style="width: 100%" class="indextable genindextable"><tr>
-  <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="api/pypath.utils.pdb.Residue.html#pypath.utils.pdb.Residue.offset">offset (pypath.utils.pdb.Residue attribute)</a>
+        <li><a href="api/pypath.core.annot.Phosphatome.html#pypath.core.annot.Phosphatome.annotate_complex">(pypath.core.annot.Phosphatome method)</a>
 </li>
-      <li><a href="api/pypath.inputs.offsides.offsides_side_effects.html#pypath.inputs.offsides.offsides_side_effects">offsides_side_effects() (in module pypath.inputs.offsides)</a>
+        <li><a href="api/pypath.core.annot.Progeny.html#pypath.core.annot.Progeny.annotate_complex">(pypath.core.annot.Progeny method)</a>
 </li>
-      <li><a href="api/pypath.inputs.pubmed.only_pmids.html#pypath.inputs.pubmed.only_pmids">only_pmids() (in module pypath.inputs.pubmed)</a>
+        <li><a href="api/pypath.core.annot.Ramilowski2015.html#pypath.core.annot.Ramilowski2015.annotate_complex">(pypath.core.annot.Ramilowski2015 method)</a>
 </li>
-      <li><a href="api/pypath.inputs.ontology.ontology.html#pypath.inputs.ontology.ontology">ontology() (in module pypath.inputs.ontology)</a>
+        <li><a href="api/pypath.core.annot.Ramilowski2015Location.html#pypath.core.annot.Ramilowski2015Location.annotate_complex">(pypath.core.annot.Ramilowski2015Location method)</a>
 </li>
-      <li><a href="api/pypath.share.curl.Curl.html#pypath.share.curl.Curl.open">open() (pypath.share.curl.Curl method)</a>
+        <li><a href="api/pypath.core.annot.Scconnect.html#pypath.core.annot.Scconnect.annotate_complex">(pypath.core.annot.Scconnect method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.ScconnectComplex.html#pypath.core.annot.ScconnectComplex.annotate_complex">(pypath.core.annot.ScconnectComplex method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.SignalinkFunctions.html#pypath.core.annot.SignalinkFunctions.annotate_complex">(pypath.core.annot.SignalinkFunctions method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.SignalinkPathways.html#pypath.core.annot.SignalinkPathways.annotate_complex">(pypath.core.annot.SignalinkPathways method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.SignorPathways.html#pypath.core.annot.SignorPathways.annotate_complex">(pypath.core.annot.SignorPathways method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Surfaceome.html#pypath.core.annot.Surfaceome.annotate_complex">(pypath.core.annot.Surfaceome method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Talklr.html#pypath.core.annot.Talklr.annotate_complex">(pypath.core.annot.Talklr method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Tcdb.html#pypath.core.annot.Tcdb.annotate_complex">(pypath.core.annot.Tcdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Tfcensus.html#pypath.core.annot.Tfcensus.annotate_complex">(pypath.core.annot.Tfcensus method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Topdb.html#pypath.core.annot.Topdb.annotate_complex">(pypath.core.annot.Topdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.UniprotFamilies.html#pypath.core.annot.UniprotFamilies.annotate_complex">(pypath.core.annot.UniprotFamilies method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.UniprotKeywords.html#pypath.core.annot.UniprotKeywords.annotate_complex">(pypath.core.annot.UniprotKeywords method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.UniprotLocations.html#pypath.core.annot.UniprotLocations.annotate_complex">(pypath.core.annot.UniprotLocations method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.UniprotTissues.html#pypath.core.annot.UniprotTissues.annotate_complex">(pypath.core.annot.UniprotTissues method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.UniprotTopologies.html#pypath.core.annot.UniprotTopologies.annotate_complex">(pypath.core.annot.UniprotTopologies method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Vesiclepedia.html#pypath.core.annot.Vesiclepedia.annotate_complex">(pypath.core.annot.Vesiclepedia method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Wang.html#pypath.core.annot.Wang.annotate_complex">(pypath.core.annot.Wang method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Zhong2015.html#pypath.core.annot.Zhong2015.annotate_complex">(pypath.core.annot.Zhong2015 method)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.annot.AnnotationBase.html#pypath.core.annot.AnnotationBase">AnnotationBase (class in pypath.core.annot)</a>
+</li>
+      <li><a href="api/pypath.internals.annot_formats.AnnotationGroup.html#pypath.internals.annot_formats.AnnotationGroup">AnnotationGroup (class in pypath.internals.annot_formats)</a>
+</li>
+      <li><a href="api/pypath.core.annot.AnnotationTable.html#pypath.core.annot.AnnotationTable">AnnotationTable (class in pypath.core.annot)</a>
+</li>
+      <li><a href="api/pypath.internals.annot_formats.AnnotDef.html#pypath.internals.annot_formats.AnnotDef">AnnotDef (class in pypath.internals.annot_formats)</a>
+</li>
+      <li><a href="api/pypath.internals.annot_formats.AnnotDefKey.html#pypath.internals.annot_formats.AnnotDefKey">AnnotDefKey (class in pypath.internals.annot_formats)</a>
+</li>
+      <li><a href="api/pypath.internals.annot_formats.AnnotOp.html#pypath.internals.annot_formats.AnnotOp">AnnotOp (class in pypath.internals.annot_formats)</a>
+</li>
+      <li><a href="api/pypath.internals.annot_formats.AnnotOp.html#pypath.internals.annot_formats.AnnotOp.annots">annots (pypath.internals.annot_formats.AnnotOp attribute)</a>
+</li>
+      <li><a href="api/pypath.internals.annot_formats.AnnotDef.html#pypath.internals.annot_formats.AnnotDef.args">args (pypath.internals.annot_formats.AnnotDef attribute)</a>
+</li>
+      <li><a href="api/pypath.inputs.netbiol.arn_interactions.html#pypath.inputs.netbiol.arn_interactions">arn_interactions() (in module pypath.inputs.netbiol)</a>
+</li>
+      <li><a href="api/pypath.internals.input_formats.ArrayMapping.html#pypath.internals.input_formats.ArrayMapping">ArrayMapping (class in pypath.internals.input_formats)</a>
+</li>
+      <li><a href="api/pypath.visual.igraph_drawing.edge.ArrowEdgeDrawer.html#pypath.visual.igraph_drawing.edge.ArrowEdgeDrawer">ArrowEdgeDrawer (class in pypath.visual.igraph_drawing.edge)</a>
 
       <ul>
-        <li><a href="api/pypath.share.curl.FileOpener.html#pypath.share.curl.FileOpener.open">(pypath.share.curl.FileOpener method)</a>
+        <li><a href="api/pypath.visual.igraph_drawing.ArrowEdgeDrawer.html#pypath.visual.igraph_drawing.ArrowEdgeDrawer">(in module pypath.visual.igraph_drawing)</a>
 </li>
       </ul></li>
-      <li><a href="api/pypath.inputs.pubmed.open_pubmed.html#pypath.inputs.pubmed.open_pubmed">open_pubmed() (in module pypath.inputs.pubmed)</a>
-</li>
-      <li><a href="api/pypath.share.curl.Curl.html#pypath.share.curl.Curl.open_tgz">open_tgz() (pypath.share.curl.Curl method)</a>
+      <li><a href="api/pypath.core.evidence.Evidence.html#pypath.core.evidence.Evidence.asdict">asdict() (pypath.core.evidence.Evidence method)</a>
 
       <ul>
-        <li><a href="api/pypath.share.curl.FileOpener.html#pypath.share.curl.FileOpener.open_tgz">(pypath.share.curl.FileOpener method)</a>
+        <li><a href="api/pypath.core.evidence.Evidences.html#pypath.core.evidence.Evidences.asdict">(pypath.core.evidence.Evidences method)</a>
+</li>
+        <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.asdict">(pypath.core.interaction.Interaction method)</a>
+</li>
+        <li><a href="api/pypath.utils.orthology.EnsemblOrthology.html#pypath.utils.orthology.EnsemblOrthology.asdict">(pypath.utils.orthology.EnsemblOrthology method)</a>
+</li>
+        <li><a href="api/pypath.utils.orthology.HomologeneOrthology.html#pypath.utils.orthology.HomologeneOrthology.asdict">(pypath.utils.orthology.HomologeneOrthology method)</a>
+</li>
+        <li><a href="api/pypath.utils.orthology.OmaOrthology.html#pypath.utils.orthology.OmaOrthology.asdict">(pypath.utils.orthology.OmaOrthology method)</a>
+</li>
+        <li><a href="api/pypath.utils.orthology.ProteinOrthology.html#pypath.utils.orthology.ProteinOrthology.asdict">(pypath.utils.orthology.ProteinOrthology method)</a>
 </li>
       </ul></li>
-  </ul></td>
-  <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="api/pypath.inputs.opentargets.opentargets_adverse_reactions.html#pypath.inputs.opentargets.opentargets_adverse_reactions">opentargets_adverse_reactions() (in module pypath.inputs.opentargets)</a>
+      <li><a href="api/pypath.internals.annot_formats.AnnotDef.html#pypath.internals.annot_formats.AnnotDef.aspect">aspect (pypath.internals.annot_formats.AnnotDef attribute)</a>
 </li>
-      <li><a href="api/pypath.inputs.opentargets.opentargets_baseline_expression.html#pypath.inputs.opentargets.opentargets_baseline_expression">opentargets_baseline_expression() (in module pypath.inputs.opentargets)</a>
+      <li><a href="api/pypath.utils.go.GeneOntology.html#pypath.utils.go.GeneOntology.aspect_from_name">aspect_from_name() (pypath.utils.go.GeneOntology method)</a>
 </li>
-      <li><a href="api/pypath.inputs.opentargets.opentargets_direct_score.html#pypath.inputs.opentargets.opentargets_direct_score">opentargets_direct_score() (in module pypath.inputs.opentargets)</a>
+      <li><a href="api/pypath.core.enz_sub.EnzymeSubstrateAggregator.html#pypath.core.enz_sub.EnzymeSubstrateAggregator.assign_to_network">assign_to_network() (pypath.core.enz_sub.EnzymeSubstrateAggregator method)</a>
 </li>
-      <li><a href="api/pypath.inputs.opentargets.opentargets_general.html#pypath.inputs.opentargets.opentargets_general">opentargets_general() (in module pypath.inputs.opentargets)</a>
+      <li><a href="api/pypath.inputs.sider.SiderDrug.html#pypath.inputs.sider.SiderDrug.atc">atc (pypath.inputs.sider.SiderDrug attribute)</a>
 </li>
-      <li><a href="api/pypath.inputs.opentargets.opentargets_indirect_score.html#pypath.inputs.opentargets.opentargets_indirect_score">opentargets_indirect_score() (in module pypath.inputs.opentargets)</a>
+      <li><a href="api/pypath.core.attrs.AttributeHandler.html#pypath.core.attrs.AttributeHandler">AttributeHandler (class in pypath.core.attrs)</a>
+
+      <ul>
+        <li><a href="api/pypath.utils.pyreact.AttributeHandler.html#pypath.utils.pyreact.AttributeHandler">(class in pypath.utils.pyreact)</a>
 </li>
-      <li><a href="api/pypath.inputs.oreganno.oreganno_interactions.html#pypath.inputs.oreganno.oreganno_interactions">oreganno_interactions() (in module pypath.inputs.oreganno)</a>
+      </ul></li>
+      <li><a href="api/pypath.core.evidence.Evidences.html#pypath.core.evidence.Evidences.attrs">attrs (pypath.core.evidence.Evidences property)</a>
 </li>
-      <li><a href="api/pypath.inputs.oreganno.oreganno_raw.html#pypath.inputs.oreganno.oreganno_raw">oreganno_raw() (in module pypath.inputs.oreganno)</a>
+      <li><a href="api/pypath.internals.annot_formats.AnnotDef.html#pypath.internals.annot_formats.AnnotDef.avoid">avoid (pypath.internals.annot_formats.AnnotDef attribute)</a>
 </li>
   </ul></td>
 </tr></table>
 
-<h2 id="P">P</h2>
+<h2 id="B">B</h2>
 <table style="width: 100%" class="indextable genindextable"><tr>
   <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="api/pypath.utils.proteomicsdb.ProteomicsDB.html#pypath.utils.proteomicsdb.ProteomicsDB.pandas_matrix">pandas_matrix() (pypath.utils.proteomicsdb.ProteomicsDB method)</a>
+      <li><a href="api/pypath.core.annot.Baccin2019.html#pypath.core.annot.Baccin2019">Baccin2019 (class in pypath.core.annot)</a>
 </li>
-      <li><a href="api/pypath.inputs.reaction.panther_biopax.html#pypath.inputs.reaction.panther_biopax">panther_biopax() (in module pypath.inputs.reaction)</a>
+      <li><a href="api/pypath.inputs.baccin2019.baccin2019_annotations.html#pypath.inputs.baccin2019.baccin2019_annotations">baccin2019_annotations() (in module pypath.inputs.baccin2019)</a>
 </li>
-      <li><a href="api/pypath.inputs.reaction.panther_interactions.html#pypath.inputs.reaction.panther_interactions">panther_interactions() (in module pypath.inputs.reaction)</a>
+      <li><a href="api/pypath.inputs.baccin2019.baccin2019_interactions.html#pypath.inputs.baccin2019.baccin2019_interactions">baccin2019_interactions() (in module pypath.inputs.baccin2019)</a>
 </li>
-      <li><a href="api/pypath.inputs.adrecs.AdrecsChildParent.html#pypath.inputs.adrecs.AdrecsChildParent.parent">parent (pypath.inputs.adrecs.AdrecsChildParent attribute)</a>
+      <li><a href="api/pypath.inputs.adrecs.AdrecsAdr.html#pypath.inputs.adrecs.AdrecsAdr.badd">badd (pypath.inputs.adrecs.AdrecsAdr attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.inputs.adrecs.AdrecsDrug.html#pypath.inputs.adrecs.AdrecsDrug.badd">(pypath.inputs.adrecs.AdrecsDrug attribute)</a>
 </li>
-      <li><a href="api/pypath.inputs.pathophenodb.DiseasePathogen.html#pypath.inputs.pathophenodb.DiseasePathogen.pathogen">pathogen (pypath.inputs.pathophenodb.DiseasePathogen attribute)</a>
+        <li><a href="api/pypath.inputs.adrecs.AdrecsTerm.html#pypath.inputs.adrecs.AdrecsTerm.badd">(pypath.inputs.adrecs.AdrecsTerm attribute)</a>
 </li>
-      <li><a href="api/pypath.inputs.pathophenodb.DiseasePathogen.html#pypath.inputs.pathophenodb.DiseasePathogen.pathogen_taxid">pathogen_taxid (pypath.inputs.pathophenodb.DiseasePathogen attribute)</a>
+      </ul></li>
+      <li><a href="api/pypath.omnipath.server.run.BaseServer.html#pypath.omnipath.server.run.BaseServer">BaseServer (class in pypath.omnipath.server.run)</a>
 </li>
-      <li><a href="api/pypath.resources.data_formats.pathway_bad.html#pypath.resources.data_formats.pathway_bad">pathway_bad (in module pypath.resources.data_formats)</a>
+      <li><a href="api/pypath.core.annot.Biogps.html#pypath.core.annot.Biogps">Biogps (class in pypath.core.annot)</a>
 </li>
-      <li><a href="api/pypath.inputs.kegg_api.pathway_to_disease.html#pypath.inputs.kegg_api.pathway_to_disease">pathway_to_disease() (in module pypath.inputs.kegg_api)</a>
+      <li><a href="api/pypath.inputs.biogps.biogps_annotations.html#pypath.inputs.biogps.biogps_annotations">biogps_annotations() (in module pypath.inputs.biogps)</a>
 </li>
-      <li><a href="api/pypath.inputs.kegg_api.pathway_to_drug.html#pypath.inputs.kegg_api.pathway_to_drug">pathway_to_drug() (in module pypath.inputs.kegg_api)</a>
+      <li><a href="api/pypath.inputs.biogps.biogps_datasets.html#pypath.inputs.biogps.biogps_datasets">biogps_datasets() (in module pypath.inputs.biogps)</a>
 </li>
-      <li><a href="api/pypath.inputs.kegg_api.pathway_to_gene.html#pypath.inputs.kegg_api.pathway_to_gene">pathway_to_gene() (in module pypath.inputs.kegg_api)</a>
+      <li><a href="api/pypath.inputs.biogps.biogps_download.html#pypath.inputs.biogps.biogps_download">biogps_download() (in module pypath.inputs.biogps)</a>
 </li>
-      <li><a href="api/pypath.inputs.pathwaycommons.pathwaycommons_bind_interactions.html#pypath.inputs.pathwaycommons.pathwaycommons_bind_interactions">pathwaycommons_bind_interactions() (in module pypath.inputs.pathwaycommons)</a>
+      <li><a href="api/pypath.inputs.biogps.biogps_download_all.html#pypath.inputs.biogps.biogps_download_all">biogps_download_all() (in module pypath.inputs.biogps)</a>
 </li>
-      <li><a href="api/pypath.inputs.pathwaycommons.pathwaycommons_biogrid_interactions.html#pypath.inputs.pathwaycommons.pathwaycommons_biogrid_interactions">pathwaycommons_biogrid_interactions() (in module pypath.inputs.pathwaycommons)</a>
+      <li><a href="api/pypath.inputs.biogps.BiogpsDataset.html#pypath.inputs.biogps.BiogpsDataset">BiogpsDataset (class in pypath.inputs.biogps)</a>
 </li>
-      <li><a href="api/pypath.inputs.pathwaycommons.pathwaycommons_corum_interactions.html#pypath.inputs.pathwaycommons.pathwaycommons_corum_interactions">pathwaycommons_corum_interactions() (in module pypath.inputs.pathwaycommons)</a>
+      <li><a href="api/pypath.inputs.biogrid.biogrid_all_interactions.html#pypath.inputs.biogrid.biogrid_all_interactions">biogrid_all_interactions() (in module pypath.inputs.biogrid)</a>
 </li>
-      <li><a href="api/pypath.inputs.pathwaycommons.pathwaycommons_dip_interactions.html#pypath.inputs.pathwaycommons.pathwaycommons_dip_interactions">pathwaycommons_dip_interactions() (in module pypath.inputs.pathwaycommons)</a>
+      <li><a href="api/pypath.inputs.biogrid.biogrid_interactions.html#pypath.inputs.biogrid.biogrid_interactions">biogrid_interactions() (in module pypath.inputs.biogrid)</a>
 </li>
-      <li><a href="api/pypath.inputs.pathwaycommons.pathwaycommons_hprd_interactions.html#pypath.inputs.pathwaycommons.pathwaycommons_hprd_interactions">pathwaycommons_hprd_interactions() (in module pypath.inputs.pathwaycommons)</a>
+      <li><a href="api/pypath.inputs.biomart.biomart_homology.html#pypath.inputs.biomart.biomart_homology">biomart_homology() (in module pypath.inputs.biomart)</a>
 </li>
-      <li><a href="api/pypath.inputs.pathwaycommons.pathwaycommons_inoh_interactions.html#pypath.inputs.pathwaycommons.pathwaycommons_inoh_interactions">pathwaycommons_inoh_interactions() (in module pypath.inputs.pathwaycommons)</a>
+      <li><a href="api/pypath.inputs.biomart.biomart_microarray.html#pypath.inputs.biomart.biomart_microarray">biomart_microarray() (in module pypath.inputs.biomart)</a>
 </li>
-      <li><a href="api/pypath.inputs.pathwaycommons.pathwaycommons_intact_interactions.html#pypath.inputs.pathwaycommons.pathwaycommons_intact_interactions">pathwaycommons_intact_interactions() (in module pypath.inputs.pathwaycommons)</a>
+      <li><a href="api/pypath.inputs.biomart.biomart_microarray_types.html#pypath.inputs.biomart.biomart_microarray_types">biomart_microarray_types() (in module pypath.inputs.biomart)</a>
 </li>
-      <li><a href="api/pypath.inputs.pathwaycommons.pathwaycommons_interactions.html#pypath.inputs.pathwaycommons.pathwaycommons_interactions">pathwaycommons_interactions() (in module pypath.inputs.pathwaycommons)</a>
+      <li><a href="api/pypath.inputs.biomart.biomart_microarrays.html#pypath.inputs.biomart.biomart_microarrays">biomart_microarrays() (in module pypath.inputs.biomart)</a>
 </li>
-      <li><a href="api/pypath.inputs.pathwaycommons.pathwaycommons_kegg_interactions.html#pypath.inputs.pathwaycommons.pathwaycommons_kegg_interactions">pathwaycommons_kegg_interactions() (in module pypath.inputs.pathwaycommons)</a>
+      <li><a href="api/pypath.inputs.biomart.biomart_query.html#pypath.inputs.biomart.biomart_query">biomart_query() (in module pypath.inputs.biomart)</a>
 </li>
-      <li><a href="api/pypath.inputs.pathwaycommons.pathwaycommons_netpath_interactions.html#pypath.inputs.pathwaycommons.pathwaycommons_netpath_interactions">pathwaycommons_netpath_interactions() (in module pypath.inputs.pathwaycommons)</a>
+      <li><a href="api/pypath.internals.input_formats.BiomartMapping.html#pypath.internals.input_formats.BiomartMapping">BiomartMapping (class in pypath.internals.input_formats)</a>
 </li>
-      <li><a href="api/pypath.inputs.pathwaycommons.pathwaycommons_panther_interactions.html#pypath.inputs.pathwaycommons.pathwaycommons_panther_interactions">pathwaycommons_panther_interactions() (in module pypath.inputs.pathwaycommons)</a>
+      <li><a href="api/pypath.utils.pyreact.BioPaxReader.html#pypath.utils.pyreact.BioPaxReader.biopax_size">biopax_size() (pypath.utils.pyreact.BioPaxReader method)</a>
 </li>
-      <li><a href="api/pypath.inputs.pathwaycommons.pathwaycommons_phosphosite_interactions.html#pypath.inputs.pathwaycommons.pathwaycommons_phosphosite_interactions">pathwaycommons_phosphosite_interactions() (in module pypath.inputs.pathwaycommons)</a>
+      <li><a href="api/pypath.utils.pyreact.BioPaxReader.html#pypath.utils.pyreact.BioPaxReader">BioPaxReader (class in pypath.utils.pyreact)</a>
 </li>
-      <li><a href="api/pypath.inputs.pathwaycommons.pathwaycommons_reactome_interactions.html#pypath.inputs.pathwaycommons.pathwaycommons_reactome_interactions">pathwaycommons_reactome_interactions() (in module pypath.inputs.pathwaycommons)</a>
+      <li><a href="api/pypath.internals.intera.Interface.html#pypath.internals.intera.Interface.bond_types">bond_types() (pypath.internals.intera.Interface method)</a>
 </li>
-      <li><a href="api/pypath.inputs.pathwaycommons.pathwaycommons_wikipathways_interactions.html#pypath.inputs.pathwaycommons.pathwaycommons_wikipathways_interactions">pathwaycommons_wikipathways_interactions() (in module pypath.inputs.pathwaycommons)</a>
+      <li><a href="api/pypath.utils.uniprot.browse.html#pypath.utils.uniprot.browse">browse() (in module pypath.utils.uniprot)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.annot.Adhesome.html#pypath.core.annot.Adhesome.browse">(pypath.core.annot.Adhesome method)</a>
 </li>
-      <li><a href="api/pypath.inputs.pathwaycommons.PathwayCommonsInteraction.html#pypath.inputs.pathwaycommons.PathwayCommonsInteraction">PathwayCommonsInteraction (class in pypath.inputs.pathwaycommons)</a>
+        <li><a href="api/pypath.core.annot.Almen2009.html#pypath.core.annot.Almen2009.browse">(pypath.core.annot.Almen2009 method)</a>
 </li>
-      <li><a href="api/pypath.inputs.pathwaycommons.PathwayCommonsResource.html#pypath.inputs.pathwaycommons.PathwayCommonsResource">PathwayCommonsResource (class in pypath.inputs.pathwaycommons)</a>
+        <li><a href="api/pypath.core.annot.AnnotationBase.html#pypath.core.annot.AnnotationBase.browse">(pypath.core.annot.AnnotationBase method)</a>
 </li>
-      <li><a href="api/pypath.inputs.pazar.pazar_interactions.html#pypath.inputs.pazar.pazar_interactions">pazar_interactions() (in module pypath.inputs.pazar)</a>
+        <li><a href="api/pypath.core.annot.Baccin2019.html#pypath.core.annot.Baccin2019.browse">(pypath.core.annot.Baccin2019 method)</a>
 </li>
-      <li><a href="api/pypath.inputs.pathwaycommons.PathwayCommonsResource.html#pypath.inputs.pathwaycommons.PathwayCommonsResource.pc_label">pc_label (pypath.inputs.pathwaycommons.PathwayCommonsResource attribute)</a>
+        <li><a href="api/pypath.core.annot.Biogps.html#pypath.core.annot.Biogps.browse">(pypath.core.annot.Biogps method)</a>
 </li>
-      <li><a href="api/pypath.utils.pdb.Segment.html#pypath.utils.pdb.Segment.pdb_end">pdb_end (pypath.utils.pdb.Segment attribute)</a>
+        <li><a href="api/pypath.core.annot.Cancerdrugsdb.html#pypath.core.annot.Cancerdrugsdb.browse">(pypath.core.annot.Cancerdrugsdb method)</a>
 </li>
-      <li><a href="api/pypath.utils.pdb.Segment.html#pypath.utils.pdb.Segment.pdb_start">pdb_start (pypath.utils.pdb.Segment attribute)</a>
+        <li><a href="api/pypath.core.annot.CancerGeneCensus.html#pypath.core.annot.CancerGeneCensus.browse">(pypath.core.annot.CancerGeneCensus method)</a>
 </li>
-      <li><a href="api/pypath.inputs.pdzbase.pdzbase_interactions.html#pypath.inputs.pdzbase.pdzbase_interactions">pdzbase_interactions() (in module pypath.inputs.pdzbase)</a>
+        <li><a href="api/pypath.core.annot.Cancersea.html#pypath.core.annot.Cancersea.browse">(pypath.core.annot.Cancersea method)</a>
 </li>
-      <li><a href="api/pypath.inputs.pepcyber.pepcyber_details.html#pypath.inputs.pepcyber.pepcyber_details">pepcyber_details() (in module pypath.inputs.pepcyber)</a>
+        <li><a href="api/pypath.core.annot.Cellcall.html#pypath.core.annot.Cellcall.browse">(pypath.core.annot.Cellcall method)</a>
 </li>
-      <li><a href="api/pypath.inputs.pepcyber.pepcyber_interactions.html#pypath.inputs.pepcyber.pepcyber_interactions">pepcyber_interactions() (in module pypath.inputs.pepcyber)</a>
+        <li><a href="api/pypath.core.annot.Cellcellinteractions.html#pypath.core.annot.Cellcellinteractions.browse">(pypath.core.annot.Cellcellinteractions method)</a>
 </li>
-      <li><a href="api/pypath.inputs.uniprot.UniprotQuery.html#pypath.inputs.uniprot.UniprotQuery.perform">perform() (pypath.inputs.uniprot.UniprotQuery method)</a>
+        <li><a href="api/pypath.core.annot.Cellchatdb.html#pypath.core.annot.Cellchatdb.browse">(pypath.core.annot.Cellchatdb method)</a>
 </li>
-      <li><a href="api/pypath.utils.seq.Pfam.html#pypath.utils.seq.Pfam">Pfam (class in pypath.utils.seq)</a>
+        <li><a href="api/pypath.core.annot.CellchatdbComplex.html#pypath.core.annot.CellchatdbComplex.browse">(pypath.core.annot.CellchatdbComplex method)</a>
 </li>
-      <li><a href="api/pypath.inputs.pfam.pfam_names.html#pypath.inputs.pfam.pfam_names">pfam_names() (in module pypath.inputs.pfam)</a>
+        <li><a href="api/pypath.core.annot.Cellinker.html#pypath.core.annot.Cellinker.browse">(pypath.core.annot.Cellinker method)</a>
 </li>
-      <li><a href="api/pypath.inputs.pfam.pfam_pdb.html#pypath.inputs.pfam.pfam_pdb">pfam_pdb() (in module pypath.inputs.pfam)</a>
+        <li><a href="api/pypath.core.annot.CellinkerComplex.html#pypath.core.annot.CellinkerComplex.browse">(pypath.core.annot.CellinkerComplex method)</a>
 </li>
-      <li><a href="api/pypath.inputs.pfam.pfam_regions.html#pypath.inputs.pfam.pfam_regions">pfam_regions() (in module pypath.inputs.pfam)</a>
+        <li><a href="api/pypath.core.annot.CellPhoneDB.html#pypath.core.annot.CellPhoneDB.browse">(pypath.core.annot.CellPhoneDB method)</a>
 </li>
-      <li><a href="api/pypath.inputs.pfam.pfam_uniprot.html#pypath.inputs.pfam.pfam_uniprot">pfam_uniprot() (in module pypath.inputs.pfam)</a>
+        <li><a href="api/pypath.core.annot.CellPhoneDBComplex.html#pypath.core.annot.CellPhoneDBComplex.browse">(pypath.core.annot.CellPhoneDBComplex method)</a>
 </li>
-      <li><a href="api/pypath.inputs.pharos.pharos_diseases.html#pypath.inputs.pharos.pharos_diseases">pharos_diseases() (in module pypath.inputs.pharos)</a>
+        <li><a href="api/pypath.core.annot.CellSurfaceProteinAtlas.html#pypath.core.annot.CellSurfaceProteinAtlas.browse">(pypath.core.annot.CellSurfaceProteinAtlas method)</a>
 </li>
-      <li><a href="api/pypath.inputs.pharos.pharos_expression.html#pypath.inputs.pharos.pharos_expression">pharos_expression() (in module pypath.inputs.pharos)</a>
+        <li><a href="api/pypath.core.annot.CellSurfaceProteinAtlasCellType.html#pypath.core.annot.CellSurfaceProteinAtlasCellType.browse">(pypath.core.annot.CellSurfaceProteinAtlasCellType method)</a>
 </li>
-      <li><a href="api/pypath.inputs.pharos.pharos_general.html#pypath.inputs.pharos.pharos_general">pharos_general() (in module pypath.inputs.pharos)</a>
+        <li><a href="api/pypath.core.annot.Celltalkdb.html#pypath.core.annot.Celltalkdb.browse">(pypath.core.annot.Celltalkdb method)</a>
 </li>
-      <li><a href="api/pypath.inputs.pharos.pharos_gtex.html#pypath.inputs.pharos.pharos_gtex">pharos_gtex() (in module pypath.inputs.pharos)</a>
+        <li><a href="api/pypath.core.annot.Celltypist.html#pypath.core.annot.Celltypist.browse">(pypath.core.annot.Celltypist method)</a>
 </li>
-      <li><a href="api/pypath.inputs.pharos.pharos_ligands.html#pypath.inputs.pharos.pharos_ligands">pharos_ligands() (in module pypath.inputs.pharos)</a>
+        <li><a href="api/pypath.core.annot.Comppi.html#pypath.core.annot.Comppi.browse">(pypath.core.annot.Comppi method)</a>
 </li>
-      <li><a href="api/pypath.inputs.pharos.pharos_orthologs.html#pypath.inputs.pharos.pharos_orthologs">pharos_orthologs() (in module pypath.inputs.pharos)</a>
+        <li><a href="api/pypath.core.annot.Connectomedb.html#pypath.core.annot.Connectomedb.browse">(pypath.core.annot.Connectomedb method)</a>
 </li>
-      <li><a href="api/pypath.inputs.pharos.pharos_targets.html#pypath.inputs.pharos.pharos_targets">pharos_targets() (in module pypath.inputs.pharos)</a>
+        <li><a href="api/pypath.core.annot.Corum.html#pypath.core.annot.Corum.browse">(pypath.core.annot.Corum method)</a>
 </li>
-      <li><a href="api/pypath.inputs.pharos.pharos_xrefs.html#pypath.inputs.pharos.pharos_xrefs">pharos_xrefs() (in module pypath.inputs.pharos)</a>
+        <li><a href="api/pypath.core.annot.CorumFuncat.html#pypath.core.annot.CorumFuncat.browse">(pypath.core.annot.CorumFuncat method)</a>
 </li>
-      <li><a href="api/pypath.inputs.phobius.phobius_annotations.html#pypath.inputs.phobius.phobius_annotations">phobius_annotations() (in module pypath.inputs.phobius)</a>
+        <li><a href="api/pypath.core.annot.CorumGO.html#pypath.core.annot.CorumGO.browse">(pypath.core.annot.CorumGO method)</a>
 </li>
-      <li><a href="api/pypath.inputs.phosphoelm.phosphoelm_enzyme_substrate.html#pypath.inputs.phosphoelm.phosphoelm_enzyme_substrate">phosphoelm_enzyme_substrate() (in module pypath.inputs.phosphoelm)</a>
+        <li><a href="api/pypath.core.annot.Cpad.html#pypath.core.annot.Cpad.browse">(pypath.core.annot.Cpad method)</a>
 </li>
-      <li><a href="api/pypath.inputs.phosphoelm.phosphoelm_interactions.html#pypath.inputs.phosphoelm.phosphoelm_interactions">phosphoelm_interactions() (in module pypath.inputs.phosphoelm)</a>
+        <li><a href="api/pypath.core.annot.CustomAnnotation.html#pypath.core.annot.CustomAnnotation.browse">(pypath.core.annot.CustomAnnotation method)</a>
 </li>
-      <li><a href="api/pypath.inputs.phosphoelm.phosphoelm_kinases.html#pypath.inputs.phosphoelm.phosphoelm_kinases">phosphoelm_kinases() (in module pypath.inputs.phosphoelm)</a>
+        <li><a href="api/pypath.core.annot.Cytosig.html#pypath.core.annot.Cytosig.browse">(pypath.core.annot.Cytosig method)</a>
 </li>
-      <li><a href="api/pypath.inputs.phosphonetworks.phosphonetworks_enzyme_substrate.html#pypath.inputs.phosphonetworks.phosphonetworks_enzyme_substrate">phosphonetworks_enzyme_substrate() (in module pypath.inputs.phosphonetworks)</a>
+        <li><a href="api/pypath.core.annot.Dgidb.html#pypath.core.annot.Dgidb.browse">(pypath.core.annot.Dgidb method)</a>
 </li>
-      <li><a href="api/pypath.inputs.phosphonetworks.phosphonetworks_interactions.html#pypath.inputs.phosphonetworks.phosphonetworks_interactions">phosphonetworks_interactions() (in module pypath.inputs.phosphonetworks)</a>
+        <li><a href="api/pypath.core.annot.Disgenet.html#pypath.core.annot.Disgenet.browse">(pypath.core.annot.Disgenet method)</a>
 </li>
-      <li><a href="api/pypath.inputs.phosphopoint.phosphopoint_directions.html#pypath.inputs.phosphopoint.phosphopoint_directions">phosphopoint_directions() (in module pypath.inputs.phosphopoint)</a>
+        <li><a href="api/pypath.core.annot.Embrace.html#pypath.core.annot.Embrace.browse">(pypath.core.annot.Embrace method)</a>
 </li>
-      <li><a href="api/pypath.inputs.phosphopoint.phosphopoint_interactions.html#pypath.inputs.phosphopoint.phosphopoint_interactions">phosphopoint_interactions() (in module pypath.inputs.phosphopoint)</a>
+        <li><a href="api/pypath.core.annot.Exocarta.html#pypath.core.annot.Exocarta.browse">(pypath.core.annot.Exocarta method)</a>
 </li>
-      <li><a href="api/pypath.internals.input_formats.PickleMapping.html#pypath.internals.input_formats.PickleMapping">PickleMapping (class in pypath.internals.input_formats)</a>
+        <li><a href="api/pypath.core.annot.GOIntercell.html#pypath.core.annot.GOIntercell.browse">(pypath.core.annot.GOIntercell method)</a>
 </li>
-      <li><a href="api/pypath.inputs.reaction.pid_biopax.html#pypath.inputs.reaction.pid_biopax">pid_biopax() (in module pypath.inputs.reaction)</a>
+        <li><a href="api/pypath.core.annot.Gpcrdb.html#pypath.core.annot.Gpcrdb.browse">(pypath.core.annot.Gpcrdb method)</a>
 </li>
-      <li><a href="api/pypath.inputs.reaction.pid_interactions.html#pypath.inputs.reaction.pid_interactions">pid_interactions() (in module pypath.inputs.reaction)</a>
+        <li><a href="api/pypath.core.annot.GuideToPharmacology.html#pypath.core.annot.GuideToPharmacology.browse">(pypath.core.annot.GuideToPharmacology method)</a>
 </li>
-      <li><a href="api/pypath.visual.drawing.Plot.html#pypath.visual.drawing.Plot">Plot (class in pypath.visual.drawing)</a>
+        <li><a href="api/pypath.core.annot.Hgnc.html#pypath.core.annot.Hgnc.browse">(pypath.core.annot.Hgnc method)</a>
 </li>
-      <li><a href="api/pypath.inputs.pubmed.pmids_dict.html#pypath.inputs.pubmed.pmids_dict">pmids_dict() (in module pypath.inputs.pubmed)</a>
+        <li><a href="api/pypath.core.annot.HpmrComplex.html#pypath.core.annot.HpmrComplex.browse">(pypath.core.annot.HpmrComplex method)</a>
 </li>
-      <li><a href="api/pypath.inputs.pubmed.pmids_list.html#pypath.inputs.pubmed.pmids_list">pmids_list() (in module pypath.inputs.pubmed)</a>
+        <li><a href="api/pypath.core.annot.HPO.html#pypath.core.annot.HPO.browse">(pypath.core.annot.HPO method)</a>
 </li>
-      <li><a href="api/pypath.internals.resource.NetworkDataset.html#pypath.internals.resource.NetworkDataset.pop">pop() (pypath.internals.resource.NetworkDataset method)</a>
+        <li><a href="api/pypath.core.annot.Humancellmap.html#pypath.core.annot.Humancellmap.browse">(pypath.core.annot.Humancellmap method)</a>
 </li>
-      <li><a href="api/pypath.internals.resource.NetworkDataset.html#pypath.internals.resource.NetworkDataset.popitem">popitem() (pypath.internals.resource.NetworkDataset method)</a>
+        <li><a href="api/pypath.core.annot.HumanPlasmaMembraneReceptome.html#pypath.core.annot.HumanPlasmaMembraneReceptome.browse">(pypath.core.annot.HumanPlasmaMembraneReceptome method)</a>
 </li>
-      <li><a href="api/pypath.inputs.dorothea.DorotheaInteraction.html#pypath.inputs.dorothea.DorotheaInteraction.predicted">predicted (pypath.inputs.dorothea.DorotheaInteraction attribute)</a>
+        <li><a href="api/pypath.core.annot.HumanProteinAtlas.html#pypath.core.annot.HumanProteinAtlas.browse">(pypath.core.annot.HumanProteinAtlas method)</a>
 </li>
-      <li><a href="api/pypath.inputs.dorothea.DorotheaInteraction.html#pypath.inputs.dorothea.DorotheaInteraction.predicted_sources">predicted_sources (pypath.inputs.dorothea.DorotheaInteraction attribute)</a>
+        <li><a href="api/pypath.core.annot.HumanProteinAtlasSecretome.html#pypath.core.annot.HumanProteinAtlasSecretome.browse">(pypath.core.annot.HumanProteinAtlasSecretome method)</a>
 </li>
-      <li><a href="api/pypath.share.curl.preserve_off.html#pypath.share.curl.preserve_off">preserve_off (class in pypath.share.curl)</a>
+        <li><a href="api/pypath.core.annot.HumanProteinAtlasSubcellular.html#pypath.core.annot.HumanProteinAtlasSubcellular.browse">(pypath.core.annot.HumanProteinAtlasSubcellular method)</a>
 </li>
-      <li><a href="api/pypath.share.curl.preserve_on.html#pypath.share.curl.preserve_on">preserve_on (class in pypath.share.curl)</a>
+        <li><a href="api/pypath.core.annot.Icellnet.html#pypath.core.annot.Icellnet.browse">(pypath.core.annot.Icellnet method)</a>
 </li>
-      <li><a href="api/pypath.inputs.pro.pro_mapping.html#pypath.inputs.pro.pro_mapping">pro_mapping() (in module pypath.inputs.pro)</a>
+        <li><a href="api/pypath.core.annot.IcellnetComplex.html#pypath.core.annot.IcellnetComplex.browse">(pypath.core.annot.IcellnetComplex method)</a>
 </li>
-      <li><a href="api/pypath.internals.resource.AbstractResource.html#pypath.internals.resource.AbstractResource.process">process() (pypath.internals.resource.AbstractResource method)</a>
+        <li><a href="api/pypath.core.annot.Integrins.html#pypath.core.annot.Integrins.browse">(pypath.core.annot.Integrins method)</a>
 </li>
-      <li><a href="api/pypath.utils.go.GOCustomAnnotation.html#pypath.utils.go.GOCustomAnnotation.process_categories">process_categories() (pypath.utils.go.GOCustomAnnotation method)</a>
+        <li><a href="api/pypath.core.annot.InterPro.html#pypath.core.annot.InterPro.browse">(pypath.core.annot.InterPro method)</a>
 </li>
-      <li><a href="api/pypath.inputs.reaction.process_complex.html#pypath.inputs.reaction.process_complex">process_complex() (in module pypath.inputs.reaction)</a>
+        <li><a href="api/pypath.core.annot.Intogen.html#pypath.core.annot.Intogen.browse">(pypath.core.annot.Intogen method)</a>
 </li>
-      <li><a href="api/pypath.inputs.reaction.process_controls.html#pypath.inputs.reaction.process_controls">process_controls() (in module pypath.inputs.reaction)</a>
+        <li><a href="api/pypath.core.annot.Italk.html#pypath.core.annot.Italk.browse">(pypath.core.annot.Italk method)</a>
 </li>
-      <li><a href="api/pypath.inputs.reaction.process_reactions.html#pypath.inputs.reaction.process_reactions">process_reactions() (in module pypath.inputs.reaction)</a>
+        <li><a href="api/pypath.core.annot.KeggPathways.html#pypath.core.annot.KeggPathways.browse">(pypath.core.annot.KeggPathways method)</a>
 </li>
-      <li><a href="api/pypath.utils.seq.Pfam.html#pypath.utils.seq.Pfam.processor">processor() (pypath.utils.seq.Pfam method)</a>
-
-      <ul>
-        <li><a href="api/pypath.utils.seq.Resource.html#pypath.utils.seq.Resource.processor">(pypath.utils.seq.Resource method)</a>
+        <li><a href="api/pypath.core.annot.KeggPathwaysPC.html#pypath.core.annot.KeggPathwaysPC.browse">(pypath.core.annot.KeggPathwaysPC method)</a>
 </li>
-      </ul></li>
-      <li><a href="api/pypath.share.progress.Progress.html#pypath.share.progress.Progress">Progress (class in pypath.share.progress)</a>
+        <li><a href="api/pypath.core.annot.Kinasedotcom.html#pypath.core.annot.Kinasedotcom.browse">(pypath.core.annot.Kinasedotcom method)</a>
 </li>
-      <li><a href="api/pypath.internals.input_formats.ProMapping.html#pypath.internals.input_formats.ProMapping">ProMapping (class in pypath.internals.input_formats)</a>
+        <li><a href="api/pypath.core.annot.Kirouac2010.html#pypath.core.annot.Kirouac2010.browse">(pypath.core.annot.Kirouac2010 method)</a>
 </li>
-      <li><a href="api/pypath.inputs.uniprot.protein_datasheet.html#pypath.inputs.uniprot.protein_datasheet">protein_datasheet() (in module pypath.inputs.uniprot)</a>
+        <li><a href="api/pypath.core.annot.Lambert2018.html#pypath.core.annot.Lambert2018.browse">(pypath.core.annot.Lambert2018 method)</a>
 </li>
-      <li><a href="api/pypath.utils.proteomicsdb.ProteomicsDB.html#pypath.utils.proteomicsdb.ProteomicsDB">ProteomicsDB (class in pypath.utils.proteomicsdb)</a>
+        <li><a href="api/pypath.core.annot.LigandReceptor.html#pypath.core.annot.LigandReceptor.browse">(pypath.core.annot.LigandReceptor method)</a>
 </li>
-      <li><a href="api/pypath.inputs.protmapper.protmapper_enzyme_substrate.html#pypath.inputs.protmapper.protmapper_enzyme_substrate">protmapper_enzyme_substrate() (in module pypath.inputs.protmapper)</a>
+        <li><a href="api/pypath.core.annot.Locate.html#pypath.core.annot.Locate.browse">(pypath.core.annot.Locate method)</a>
 </li>
-      <li><a href="api/pypath.inputs.protmapper.protmapper_interactions.html#pypath.inputs.protmapper.protmapper_interactions">protmapper_interactions() (in module pypath.inputs.protmapper)</a>
+        <li><a href="api/pypath.core.annot.Lrdb.html#pypath.core.annot.Lrdb.browse">(pypath.core.annot.Lrdb method)</a>
 </li>
-      <li><a href="api/pypath.inputs.adrecs.AdrecsDrug.html#pypath.inputs.adrecs.AdrecsDrug.pubchem_cid">pubchem_cid (pypath.inputs.adrecs.AdrecsDrug attribute)</a>
+        <li><a href="api/pypath.core.annot.Matrisome.html#pypath.core.annot.Matrisome.browse">(pypath.core.annot.Matrisome method)</a>
 </li>
-      <li><a href="api/pypath.inputs.pubchem.pubchem_mapping.html#pypath.inputs.pubchem.pubchem_mapping">pubchem_mapping() (in module pypath.inputs.pubchem)</a>
+        <li><a href="api/pypath.core.annot.Matrixdb.html#pypath.core.annot.Matrixdb.browse">(pypath.core.annot.Matrixdb method)</a>
 </li>
-      <li><a href="api/pypath.inputs.dorothea.DorotheaInteraction.html#pypath.inputs.dorothea.DorotheaInteraction.pubmed">pubmed (pypath.inputs.dorothea.DorotheaInteraction attribute)</a>
+        <li><a href="api/pypath.core.annot.Mcam.html#pypath.core.annot.Mcam.browse">(pypath.core.annot.Mcam method)</a>
 </li>
-      <li>
-    pypath
-
-      <ul>
-        <li><a href="api/pypath.html#module-pypath">module</a>
+        <li><a href="api/pypath.core.annot.Membranome.html#pypath.core.annot.Membranome.browse">(pypath.core.annot.Membranome method)</a>
 </li>
-      </ul></li>
-      <li>
-    pypath.core
-
-      <ul>
-        <li><a href="api/pypath.core.html#module-pypath.core">module</a>
+        <li><a href="api/pypath.core.annot.Msigdb.html#pypath.core.annot.Msigdb.browse">(pypath.core.annot.Msigdb method)</a>
 </li>
-      </ul></li>
-      <li>
-    pypath.core.attrs
-
-      <ul>
-        <li><a href="api/pypath.core.attrs.html#module-pypath.core.attrs">module</a>
+        <li><a href="api/pypath.core.annot.NetpathPathways.html#pypath.core.annot.NetpathPathways.browse">(pypath.core.annot.NetpathPathways method)</a>
 </li>
-      </ul></li>
-      <li>
-    pypath.core.common
-
-      <ul>
-        <li><a href="api/pypath.core.common.html#module-pypath.core.common">module</a>
+        <li><a href="api/pypath.core.annot.Opm.html#pypath.core.annot.Opm.browse">(pypath.core.annot.Opm method)</a>
 </li>
-      </ul></li>
-      <li>
-    pypath.data
-
-      <ul>
-        <li><a href="api/pypath.data.html#module-pypath.data">module</a>
+        <li><a href="api/pypath.core.annot.Panglaodb.html#pypath.core.annot.Panglaodb.browse">(pypath.core.annot.Panglaodb method)</a>
 </li>
-      </ul></li>
-      <li>
-    pypath.inputs
-
-      <ul>
-        <li><a href="api/pypath.inputs.html#module-pypath.inputs">module</a>
+        <li><a href="api/pypath.core.annot.Phobius.html#pypath.core.annot.Phobius.browse">(pypath.core.annot.Phobius method)</a>
 </li>
-      </ul></li>
-      <li>
-    pypath.inputs.abs
-
-      <ul>
-        <li><a href="api/pypath.inputs.abs.html#module-pypath.inputs.abs">module</a>
+        <li><a href="api/pypath.core.annot.Phosphatome.html#pypath.core.annot.Phosphatome.browse">(pypath.core.annot.Phosphatome method)</a>
 </li>
-      </ul></li>
-      <li>
-    pypath.inputs.acsn
-
-      <ul>
-        <li><a href="api/pypath.inputs.acsn.html#module-pypath.inputs.acsn">module</a>
+        <li><a href="api/pypath.core.annot.Progeny.html#pypath.core.annot.Progeny.browse">(pypath.core.annot.Progeny method)</a>
 </li>
-      </ul></li>
-      <li>
-    pypath.inputs.adrecs
-
-      <ul>
-        <li><a href="api/pypath.inputs.adrecs.html#module-pypath.inputs.adrecs">module</a>
+        <li><a href="api/pypath.core.annot.Ramilowski2015.html#pypath.core.annot.Ramilowski2015.browse">(pypath.core.annot.Ramilowski2015 method)</a>
 </li>
-      </ul></li>
-      <li>
-    pypath.inputs.biogrid
-
-      <ul>
-        <li><a href="api/pypath.inputs.biogrid.html#module-pypath.inputs.biogrid">module</a>
+        <li><a href="api/pypath.core.annot.Ramilowski2015Location.html#pypath.core.annot.Ramilowski2015Location.browse">(pypath.core.annot.Ramilowski2015Location method)</a>
 </li>
-      </ul></li>
-      <li>
-    pypath.inputs.biomart
-
-      <ul>
-        <li><a href="api/pypath.inputs.biomart.html#module-pypath.inputs.biomart">module</a>
+        <li><a href="api/pypath.core.annot.Scconnect.html#pypath.core.annot.Scconnect.browse">(pypath.core.annot.Scconnect method)</a>
 </li>
-      </ul></li>
-      <li>
-    pypath.inputs.biomodels
-
-      <ul>
-        <li><a href="api/pypath.inputs.biomodels.html#module-pypath.inputs.biomodels">module</a>
+        <li><a href="api/pypath.core.annot.ScconnectComplex.html#pypath.core.annot.ScconnectComplex.browse">(pypath.core.annot.ScconnectComplex method)</a>
 </li>
-      </ul></li>
-      <li>
-    pypath.inputs.ca1
-
-      <ul>
-        <li><a href="api/pypath.inputs.ca1.html#module-pypath.inputs.ca1">module</a>
+        <li><a href="api/pypath.core.annot.SignalinkFunctions.html#pypath.core.annot.SignalinkFunctions.browse">(pypath.core.annot.SignalinkFunctions method)</a>
 </li>
-      </ul></li>
-      <li>
-    pypath.inputs.cancercellmap
-
-      <ul>
-        <li><a href="api/pypath.inputs.cancercellmap.html#module-pypath.inputs.cancercellmap">module</a>
+        <li><a href="api/pypath.core.annot.SignalinkPathways.html#pypath.core.annot.SignalinkPathways.browse">(pypath.core.annot.SignalinkPathways method)</a>
 </li>
-      </ul></li>
-      <li>
-    pypath.inputs.cell
-
-      <ul>
-        <li><a href="api/pypath.inputs.cell.html#module-pypath.inputs.cell">module</a>
+        <li><a href="api/pypath.core.annot.SignorPathways.html#pypath.core.annot.SignorPathways.browse">(pypath.core.annot.SignorPathways method)</a>
 </li>
-      </ul></li>
-      <li>
-    pypath.inputs.chembl
-
-      <ul>
-        <li><a href="api/pypath.inputs.chembl.html#module-pypath.inputs.chembl">module</a>
+        <li><a href="api/pypath.core.annot.Surfaceome.html#pypath.core.annot.Surfaceome.browse">(pypath.core.annot.Surfaceome method)</a>
 </li>
-      </ul></li>
-      <li>
-    pypath.inputs.clinvar
-
-      <ul>
-        <li><a href="api/pypath.inputs.clinvar.html#module-pypath.inputs.clinvar">module</a>
+        <li><a href="api/pypath.core.annot.Talklr.html#pypath.core.annot.Talklr.browse">(pypath.core.annot.Talklr method)</a>
 </li>
-      </ul></li>
-      <li>
-    pypath.inputs.common
-
-      <ul>
-        <li><a href="api/pypath.inputs.common.html#module-pypath.inputs.common">module</a>
+        <li><a href="api/pypath.core.annot.Tcdb.html#pypath.core.annot.Tcdb.browse">(pypath.core.annot.Tcdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Tfcensus.html#pypath.core.annot.Tfcensus.browse">(pypath.core.annot.Tfcensus method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Topdb.html#pypath.core.annot.Topdb.browse">(pypath.core.annot.Topdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.UniprotFamilies.html#pypath.core.annot.UniprotFamilies.browse">(pypath.core.annot.UniprotFamilies method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.UniprotKeywords.html#pypath.core.annot.UniprotKeywords.browse">(pypath.core.annot.UniprotKeywords method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.UniprotLocations.html#pypath.core.annot.UniprotLocations.browse">(pypath.core.annot.UniprotLocations method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.UniprotTissues.html#pypath.core.annot.UniprotTissues.browse">(pypath.core.annot.UniprotTissues method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.UniprotTopologies.html#pypath.core.annot.UniprotTopologies.browse">(pypath.core.annot.UniprotTopologies method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Vesiclepedia.html#pypath.core.annot.Vesiclepedia.browse">(pypath.core.annot.Vesiclepedia method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Wang.html#pypath.core.annot.Wang.browse">(pypath.core.annot.Wang method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Zhong2015.html#pypath.core.annot.Zhong2015.browse">(pypath.core.annot.Zhong2015 method)</a>
+</li>
+        <li><a href="api/pypath.core.intercell.IntercellAnnotation.html#pypath.core.intercell.IntercellAnnotation.browse">(pypath.core.intercell.IntercellAnnotation method)</a>
 </li>
       </ul></li>
-      <li>
-    pypath.inputs.compath
+  </ul></td>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="api/pypath.omnipath.databases.build.html#pypath.omnipath.databases.build">build() (in module pypath.omnipath.databases)</a>
 
       <ul>
-        <li><a href="api/pypath.inputs.compath.html#module-pypath.inputs.compath">module</a>
+        <li><a href="api/pypath.omnipath.app.DatabaseManager.html#pypath.omnipath.app.DatabaseManager.build">(pypath.omnipath.app.DatabaseManager method)</a>
+</li>
+        <li><a href="api/pypath.omnipath.databases.define.DatabaseDefinitionManager.html#pypath.omnipath.databases.define.DatabaseDefinitionManager.build">(pypath.omnipath.databases.define.DatabaseDefinitionManager method)</a>
 </li>
       </ul></li>
-      <li>
-    pypath.inputs.cpdb
+      <li><a href="api/pypath.omnipath.app.DatabaseManager.html#pypath.omnipath.app.DatabaseManager.build_dataset">build_dataset() (pypath.omnipath.app.DatabaseManager method)</a>
+</li>
+      <li><a href="api/pypath.core.enz_sub.EnzymeSubstrateAggregator.html#pypath.core.enz_sub.EnzymeSubstrateAggregator.build_list">build_list() (pypath.core.enz_sub.EnzymeSubstrateAggregator method)</a>
+</li>
+      <li><a href="api/pypath.core.network.NetworkStatsRecord.html#pypath.core.network.NetworkStatsRecord.by_category">by_category (pypath.core.network.NetworkStatsRecord attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.NetworkStatsRecord.html#pypath.core.network.NetworkStatsRecord.by_resource">by_resource (pypath.core.network.NetworkStatsRecord attribute)</a>
+</li>
+  </ul></td>
+</tr></table>
 
-      <ul>
-        <li><a href="api/pypath.inputs.cpdb.html#module-pypath.inputs.cpdb">module</a>
+<h2 id="C">C</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="api/pypath.inputs.ca1.ca1_interactions.html#pypath.inputs.ca1.ca1_interactions">ca1_interactions() (in module pypath.inputs.ca1)</a>
 </li>
-      </ul></li>
-      <li>
-    pypath.inputs.credentials
+      <li><a href="api/pypath.share.curl.cache_delete_off.html#pypath.share.curl.cache_delete_off">cache_delete_off (class in pypath.share.curl)</a>
+</li>
+      <li><a href="api/pypath.share.curl.cache_delete_on.html#pypath.share.curl.cache_delete_on">cache_delete_on (class in pypath.share.curl)</a>
+</li>
+      <li><a href="api/pypath.share.cache.cache_item.html#pypath.share.cache.cache_item">cache_item() (in module pypath.share.cache)</a>
+</li>
+      <li><a href="api/pypath.share.curl.cache_off.html#pypath.share.curl.cache_off">cache_off (class in pypath.share.curl)</a>
+</li>
+      <li><a href="api/pypath.share.curl.cache_on.html#pypath.share.curl.cache_on">cache_on (class in pypath.share.curl)</a>
+</li>
+      <li><a href="api/pypath.share.cache.cache_path.html#pypath.share.cache.cache_path">cache_path() (in module pypath.share.cache)</a>
 
       <ul>
-        <li><a href="api/pypath.inputs.credentials.html#module-pypath.inputs.credentials">module</a>
+        <li><a href="api/pypath.share.curl.Curl.html#pypath.share.curl.Curl.cache_path">(pypath.share.curl.Curl class method)</a>
 </li>
       </ul></li>
-      <li>
-    pypath.inputs.ctdbase
+      <li><a href="api/pypath.share.curl.cache_print_off.html#pypath.share.curl.cache_print_off">cache_print_off (class in pypath.share.curl)</a>
+</li>
+      <li><a href="api/pypath.share.curl.cache_print_on.html#pypath.share.curl.cache_print_on">cache_print_on (class in pypath.share.curl)</a>
+</li>
+      <li><a href="api/pypath.inputs.cosmic.cancer_gene_census_annotations.html#pypath.inputs.cosmic.cancer_gene_census_annotations">cancer_gene_census_annotations() (in module pypath.inputs.cosmic)</a>
+</li>
+      <li><a href="api/pypath.core.annot.Cancerdrugsdb.html#pypath.core.annot.Cancerdrugsdb">Cancerdrugsdb (class in pypath.core.annot)</a>
+</li>
+      <li><a href="api/pypath.inputs.cancerdrugsdb.cancerdrugsdb_annotations.html#pypath.inputs.cancerdrugsdb.cancerdrugsdb_annotations">cancerdrugsdb_annotations() (in module pypath.inputs.cancerdrugsdb)</a>
+</li>
+      <li><a href="api/pypath.inputs.cancerdrugsdb.cancerdrugsdb_download.html#pypath.inputs.cancerdrugsdb.cancerdrugsdb_download">cancerdrugsdb_download() (in module pypath.inputs.cancerdrugsdb)</a>
+</li>
+      <li><a href="api/pypath.inputs.cancerdrugsdb.cancerdrugsdb_interactions.html#pypath.inputs.cancerdrugsdb.cancerdrugsdb_interactions">cancerdrugsdb_interactions() (in module pypath.inputs.cancerdrugsdb)</a>
+</li>
+      <li><a href="api/pypath.core.annot.CancerGeneCensus.html#pypath.core.annot.CancerGeneCensus">CancerGeneCensus (class in pypath.core.annot)</a>
+</li>
+      <li><a href="api/pypath.core.annot.Cancersea.html#pypath.core.annot.Cancersea">Cancersea (class in pypath.core.annot)</a>
+</li>
+      <li><a href="api/pypath.inputs.cancersea.cancersea_annotations.html#pypath.inputs.cancersea.cancersea_annotations">cancersea_annotations() (in module pypath.inputs.cancersea)</a>
+</li>
+      <li><a href="api/pypath.core.network.NetworkStatsRecord.html#pypath.core.network.NetworkStatsRecord.cat_resource">cat_resource (pypath.core.network.NetworkStatsRecord attribute)</a>
+</li>
+      <li><a href="api/pypath.utils.uniprot.catalytic_activity.html#pypath.utils.uniprot.catalytic_activity">catalytic_activity() (in module pypath.utils.uniprot)</a>
+</li>
+      <li><a href="api/pypath.utils.uniprot.catalytic_activity_with_xrefs.html#pypath.utils.uniprot.catalytic_activity_with_xrefs">catalytic_activity_with_xrefs() (in module pypath.utils.uniprot)</a>
+</li>
+      <li><a href="api/pypath.inputs.cancercellmap.ccmap_interactions.html#pypath.inputs.cancercellmap.ccmap_interactions">ccmap_interactions() (in module pypath.inputs.cancercellmap)</a>
+</li>
+      <li><a href="api/pypath.inputs.cell.cell_supplementary.html#pypath.inputs.cell.cell_supplementary">cell_supplementary() (in module pypath.inputs.cell)</a>
+</li>
+      <li><a href="api/pypath.inputs.lrdb.LrdbAnnotation.html#pypath.inputs.lrdb.LrdbAnnotation.cell_type">cell_type (pypath.inputs.lrdb.LrdbAnnotation attribute)</a>
+</li>
+      <li><a href="api/pypath.core.annot.Cellcall.html#pypath.core.annot.Cellcall">Cellcall (class in pypath.core.annot)</a>
+</li>
+      <li><a href="api/pypath.inputs.cellcall.cellcall_annotations.html#pypath.inputs.cellcall.cellcall_annotations">cellcall_annotations() (in module pypath.inputs.cellcall)</a>
+</li>
+      <li><a href="api/pypath.inputs.cellcall.cellcall_download.html#pypath.inputs.cellcall.cellcall_download">cellcall_download() (in module pypath.inputs.cellcall)</a>
+</li>
+      <li><a href="api/pypath.inputs.cellcall.cellcall_download_all.html#pypath.inputs.cellcall.cellcall_download_all">cellcall_download_all() (in module pypath.inputs.cellcall)</a>
+</li>
+      <li><a href="api/pypath.inputs.cellcall.cellcall_interactions.html#pypath.inputs.cellcall.cellcall_interactions">cellcall_interactions() (in module pypath.inputs.cellcall)</a>
+</li>
+      <li><a href="api/pypath.core.annot.Cellcellinteractions.html#pypath.core.annot.Cellcellinteractions">Cellcellinteractions (class in pypath.core.annot)</a>
+</li>
+      <li><a href="api/pypath.inputs.cellcellinteractions.cellcellinteractions_annotations.html#pypath.inputs.cellcellinteractions.cellcellinteractions_annotations">cellcellinteractions_annotations() (in module pypath.inputs.cellcellinteractions)</a>
+</li>
+      <li><a href="api/pypath.core.annot.Cellchatdb.html#pypath.core.annot.Cellchatdb">Cellchatdb (class in pypath.core.annot)</a>
 
       <ul>
-        <li><a href="api/pypath.inputs.ctdbase.html#module-pypath.inputs.ctdbase">module</a>
+        <li><a href="api/pypath.core.complex.Cellchatdb.html#pypath.core.complex.Cellchatdb">(class in pypath.core.complex)</a>
 </li>
       </ul></li>
-      <li>
-    pypath.inputs.dbptm
+      <li><a href="api/pypath.inputs.cellchatdb.cellchatdb_annotations.html#pypath.inputs.cellchatdb.cellchatdb_annotations">cellchatdb_annotations() (in module pypath.inputs.cellchatdb)</a>
+</li>
+      <li><a href="api/pypath.inputs.cellchatdb.cellchatdb_cofactors.html#pypath.inputs.cellchatdb.cellchatdb_cofactors">cellchatdb_cofactors() (in module pypath.inputs.cellchatdb)</a>
+</li>
+      <li><a href="api/pypath.inputs.cellchatdb.cellchatdb_complexes.html#pypath.inputs.cellchatdb.cellchatdb_complexes">cellchatdb_complexes() (in module pypath.inputs.cellchatdb)</a>
+</li>
+      <li><a href="api/pypath.inputs.cellchatdb.cellchatdb_download.html#pypath.inputs.cellchatdb.cellchatdb_download">cellchatdb_download() (in module pypath.inputs.cellchatdb)</a>
+</li>
+      <li><a href="api/pypath.inputs.cellchatdb.cellchatdb_interactions.html#pypath.inputs.cellchatdb.cellchatdb_interactions">cellchatdb_interactions() (in module pypath.inputs.cellchatdb)</a>
+</li>
+      <li><a href="api/pypath.core.annot.CellchatdbComplex.html#pypath.core.annot.CellchatdbComplex">CellchatdbComplex (class in pypath.core.annot)</a>
+</li>
+      <li><a href="api/pypath.core.annot.Cellinker.html#pypath.core.annot.Cellinker">Cellinker (class in pypath.core.annot)</a>
 
       <ul>
-        <li><a href="api/pypath.inputs.dbptm.html#module-pypath.inputs.dbptm">module</a>
+        <li><a href="api/pypath.core.complex.Cellinker.html#pypath.core.complex.Cellinker">(class in pypath.core.complex)</a>
 </li>
       </ul></li>
-      <li>
-    pypath.inputs.ddinter
+      <li><a href="api/pypath.inputs.cellinker.cellinker_annotations.html#pypath.inputs.cellinker.cellinker_annotations">cellinker_annotations() (in module pypath.inputs.cellinker)</a>
+</li>
+      <li><a href="api/pypath.inputs.cellinker.cellinker_complex_annotations.html#pypath.inputs.cellinker.cellinker_complex_annotations">cellinker_complex_annotations() (in module pypath.inputs.cellinker)</a>
+</li>
+      <li><a href="api/pypath.inputs.cellinker.cellinker_complexes.html#pypath.inputs.cellinker.cellinker_complexes">cellinker_complexes() (in module pypath.inputs.cellinker)</a>
+</li>
+      <li><a href="api/pypath.inputs.cellinker.cellinker_complexes_raw.html#pypath.inputs.cellinker.cellinker_complexes_raw">cellinker_complexes_raw() (in module pypath.inputs.cellinker)</a>
+</li>
+      <li><a href="api/pypath.inputs.cellinker.cellinker_lr_interactions.html#pypath.inputs.cellinker.cellinker_lr_interactions">cellinker_lr_interactions() (in module pypath.inputs.cellinker)</a>
+</li>
+      <li><a href="api/pypath.inputs.cellinker.cellinker_lr_interactions_raw.html#pypath.inputs.cellinker.cellinker_lr_interactions_raw">cellinker_lr_interactions_raw() (in module pypath.inputs.cellinker)</a>
+</li>
+      <li><a href="api/pypath.inputs.cellinker.cellinker_protein_annotations.html#pypath.inputs.cellinker.cellinker_protein_annotations">cellinker_protein_annotations() (in module pypath.inputs.cellinker)</a>
+</li>
+      <li><a href="api/pypath.inputs.cellinker.cellinker_smol_interactions.html#pypath.inputs.cellinker.cellinker_smol_interactions">cellinker_smol_interactions() (in module pypath.inputs.cellinker)</a>
+</li>
+      <li><a href="api/pypath.inputs.cellinker.cellinker_smol_interactions_raw.html#pypath.inputs.cellinker.cellinker_smol_interactions_raw">cellinker_smol_interactions_raw() (in module pypath.inputs.cellinker)</a>
+</li>
+      <li><a href="api/pypath.core.annot.CellinkerComplex.html#pypath.core.annot.CellinkerComplex">CellinkerComplex (class in pypath.core.annot)</a>
+</li>
+      <li><a href="api/pypath.inputs.cellinker.CellinkerInteraction.html#pypath.inputs.cellinker.CellinkerInteraction">CellinkerInteraction (class in pypath.inputs.cellinker)</a>
+</li>
+      <li><a href="api/pypath.core.annot.CellPhoneDB.html#pypath.core.annot.CellPhoneDB">CellPhoneDB (class in pypath.core.annot)</a>
 
       <ul>
-        <li><a href="api/pypath.inputs.ddinter.html#module-pypath.inputs.ddinter">module</a>
+        <li><a href="api/pypath.core.complex.CellPhoneDB.html#pypath.core.complex.CellPhoneDB">(class in pypath.core.complex)</a>
 </li>
       </ul></li>
-      <li>
-    pypath.inputs.deathdomain
+      <li><a href="api/pypath.inputs.cellphonedb.cellphonedb_complex_annotations.html#pypath.inputs.cellphonedb.cellphonedb_complex_annotations">cellphonedb_complex_annotations() (in module pypath.inputs.cellphonedb)</a>
+</li>
+      <li><a href="api/pypath.inputs.cellphonedb.cellphonedb_complexes.html#pypath.inputs.cellphonedb.cellphonedb_complexes">cellphonedb_complexes() (in module pypath.inputs.cellphonedb)</a>
+</li>
+      <li><a href="api/pypath.inputs.cellphonedb.cellphonedb_interactions.html#pypath.inputs.cellphonedb.cellphonedb_interactions">cellphonedb_interactions() (in module pypath.inputs.cellphonedb)</a>
+</li>
+      <li><a href="api/pypath.inputs.cellphonedb.cellphonedb_ligands_receptors.html#pypath.inputs.cellphonedb.cellphonedb_ligands_receptors">cellphonedb_ligands_receptors() (in module pypath.inputs.cellphonedb)</a>
+</li>
+      <li><a href="api/pypath.inputs.cellphonedb.cellphonedb_protein_annotations.html#pypath.inputs.cellphonedb.cellphonedb_protein_annotations">cellphonedb_protein_annotations() (in module pypath.inputs.cellphonedb)</a>
+</li>
+      <li><a href="api/pypath.inputs.cellphonedb.CellPhoneDBAnnotation.html#pypath.inputs.cellphonedb.CellPhoneDBAnnotation">CellPhoneDBAnnotation (class in pypath.inputs.cellphonedb)</a>
+</li>
+      <li><a href="api/pypath.core.annot.CellPhoneDBComplex.html#pypath.core.annot.CellPhoneDBComplex">CellPhoneDBComplex (class in pypath.core.annot)</a>
+</li>
+      <li><a href="api/pypath.core.annot.CellSurfaceProteinAtlas.html#pypath.core.annot.CellSurfaceProteinAtlas">CellSurfaceProteinAtlas (class in pypath.core.annot)</a>
+</li>
+      <li><a href="api/pypath.core.annot.CellSurfaceProteinAtlasCellType.html#pypath.core.annot.CellSurfaceProteinAtlasCellType">CellSurfaceProteinAtlasCellType (class in pypath.core.annot)</a>
+</li>
+      <li><a href="api/pypath.core.annot.Celltalkdb.html#pypath.core.annot.Celltalkdb">Celltalkdb (class in pypath.core.annot)</a>
+</li>
+      <li><a href="api/pypath.inputs.celltalkdb.celltalkdb_annotations.html#pypath.inputs.celltalkdb.celltalkdb_annotations">celltalkdb_annotations() (in module pypath.inputs.celltalkdb)</a>
+</li>
+      <li><a href="api/pypath.inputs.celltalkdb.celltalkdb_download.html#pypath.inputs.celltalkdb.celltalkdb_download">celltalkdb_download() (in module pypath.inputs.celltalkdb)</a>
+</li>
+      <li><a href="api/pypath.inputs.celltalkdb.celltalkdb_interactions.html#pypath.inputs.celltalkdb.celltalkdb_interactions">celltalkdb_interactions() (in module pypath.inputs.celltalkdb)</a>
+</li>
+      <li><a href="api/pypath.core.annot.Celltypist.html#pypath.core.annot.Celltypist">Celltypist (class in pypath.core.annot)</a>
+</li>
+      <li><a href="api/pypath.inputs.celltypist.celltypist_annotations.html#pypath.inputs.celltypist.celltypist_annotations">celltypist_annotations() (in module pypath.inputs.celltypist)</a>
+</li>
+      <li><a href="api/pypath.utils.pdb.Residue.html#pypath.utils.pdb.Residue.chain">chain (pypath.utils.pdb.Residue attribute)</a>
+</li>
+      <li><a href="api/pypath.inputs.pisa.PisaBond.html#pypath.inputs.pisa.PisaBond.chain_1">chain_1 (pypath.inputs.pisa.PisaBond attribute)</a>
+</li>
+      <li><a href="api/pypath.inputs.pisa.PisaBond.html#pypath.inputs.pisa.PisaBond.chain_2">chain_2 (pypath.inputs.pisa.PisaBond attribute)</a>
+</li>
+      <li><a href="api/pypath.utils.mapping.Mapper.html#pypath.utils.mapping.Mapper.chain_map">chain_map() (pypath.utils.mapping.Mapper method)</a>
+</li>
+      <li><a href="api/pypath.utils.reflists.check.html#pypath.utils.reflists.check">check() (in module pypath.utils.reflists)</a>
 
       <ul>
-        <li><a href="api/pypath.inputs.deathdomain.html#module-pypath.inputs.deathdomain">module</a>
+        <li><a href="api/pypath.utils.reflists.ReferenceListManager.html#pypath.utils.reflists.ReferenceListManager.check">(pypath.utils.reflists.ReferenceListManager method)</a>
 </li>
       </ul></li>
-      <li>
-    pypath.inputs.dip
+      <li><a href="api/pypath.internals.license.LicenseAttrib.html#pypath.internals.license.LicenseAttrib.check_level">check_level() (pypath.internals.license.LicenseAttrib class method)</a>
 
       <ul>
-        <li><a href="api/pypath.inputs.dip.html#module-pypath.inputs.dip">module</a>
+        <li><a href="api/pypath.internals.license.LicenseFeature.html#pypath.internals.license.LicenseFeature.check_level">(pypath.internals.license.LicenseFeature class method)</a>
+</li>
+        <li><a href="api/pypath.internals.license.LicensePurpose.html#pypath.internals.license.LicensePurpose.check_level">(pypath.internals.license.LicensePurpose class method)</a>
+</li>
+        <li><a href="api/pypath.internals.license.LicenseSharing.html#pypath.internals.license.LicenseSharing.check_level">(pypath.internals.license.LicenseSharing class method)</a>
 </li>
       </ul></li>
-      <li>
-    pypath.inputs.diseases
+      <li><a href="api/pypath.inputs.chembl.chembl_activities.html#pypath.inputs.chembl.chembl_activities">chembl_activities() (in module pypath.inputs.chembl)</a>
+</li>
+      <li><a href="api/pypath.inputs.chembl.chembl_assays.html#pypath.inputs.chembl.chembl_assays">chembl_assays() (in module pypath.inputs.chembl)</a>
+</li>
+      <li><a href="api/pypath.inputs.chembl.chembl_documents.html#pypath.inputs.chembl.chembl_documents">chembl_documents() (in module pypath.inputs.chembl)</a>
+</li>
+      <li><a href="api/pypath.inputs.chembl.chembl_drug_indications.html#pypath.inputs.chembl.chembl_drug_indications">chembl_drug_indications() (in module pypath.inputs.chembl)</a>
+</li>
+      <li><a href="api/pypath.inputs.chembl.chembl_mechanisms.html#pypath.inputs.chembl.chembl_mechanisms">chembl_mechanisms() (in module pypath.inputs.chembl)</a>
+</li>
+      <li><a href="api/pypath.inputs.chembl.chembl_molecules.html#pypath.inputs.chembl.chembl_molecules">chembl_molecules() (in module pypath.inputs.chembl)</a>
+</li>
+      <li><a href="api/pypath.inputs.chembl.chembl_targets.html#pypath.inputs.chembl.chembl_targets">chembl_targets() (in module pypath.inputs.chembl)</a>
+</li>
+      <li><a href="api/pypath.inputs.adrecs.AdrecsChildParent.html#pypath.inputs.adrecs.AdrecsChildParent.child">child (pypath.inputs.adrecs.AdrecsChildParent attribute)</a>
+</li>
+      <li><a href="api/pypath.inputs.dorothea.DorotheaInteraction.html#pypath.inputs.dorothea.DorotheaInteraction.chipseq">chipseq (pypath.inputs.dorothea.DorotheaInteraction attribute)</a>
+</li>
+      <li><a href="api/pypath.inputs.dorothea.DorotheaInteraction.html#pypath.inputs.dorothea.DorotheaInteraction.chipseq_sources">chipseq_sources (pypath.inputs.dorothea.DorotheaInteraction attribute)</a>
+</li>
+      <li><a href="api/pypath.resources.network.choose_dataset.html#pypath.resources.network.choose_dataset">choose_dataset() (in module pypath.resources.network)</a>
+</li>
+      <li><a href="api/pypath.inputs.sider.SiderSideeffectMeddra.html#pypath.inputs.sider.SiderSideeffectMeddra.cid">cid (pypath.inputs.sider.SiderSideeffectMeddra attribute)</a>
+</li>
+      <li><a href="api/pypath.omnipath.databases.class_and_param.html#pypath.omnipath.databases.class_and_param">class_and_param() (in module pypath.omnipath.databases)</a>
 
       <ul>
-        <li><a href="api/pypath.inputs.diseases.html#module-pypath.inputs.diseases">module</a>
+        <li><a href="api/pypath.omnipath.databases.define.DatabaseDefinitionManager.html#pypath.omnipath.databases.define.DatabaseDefinitionManager.class_and_param">(pypath.omnipath.databases.define.DatabaseDefinitionManager method)</a>
 </li>
       </ul></li>
-      <li>
-    pypath.inputs.dorothea
+      <li><a href="api/pypath.core.annot.CustomAnnotation.html#pypath.core.annot.CustomAnnotation.class_to_class_connections">class_to_class_connections() (pypath.core.annot.CustomAnnotation method)</a>
 
       <ul>
-        <li><a href="api/pypath.inputs.dorothea.html#module-pypath.inputs.dorothea">module</a>
+        <li><a href="api/pypath.core.intercell.IntercellAnnotation.html#pypath.core.intercell.IntercellAnnotation.class_to_class_connections">(pypath.core.intercell.IntercellAnnotation method)</a>
 </li>
       </ul></li>
-      <li>
-    pypath.inputs.drugbank
+      <li><a href="api/pypath.core.annot.CustomAnnotation.html#pypath.core.annot.CustomAnnotation.classes_by_entity">classes_by_entity() (pypath.core.annot.CustomAnnotation method)</a>
 
       <ul>
-        <li><a href="api/pypath.inputs.drugbank.html#module-pypath.inputs.drugbank">module</a>
+        <li><a href="api/pypath.core.intercell.IntercellAnnotation.html#pypath.core.intercell.IntercellAnnotation.classes_by_entity">(pypath.core.intercell.IntercellAnnotation method)</a>
 </li>
       </ul></li>
-      <li>
-    pypath.inputs.drugcentral
+      <li><a href="api/pypath.inputs.gutmgene.GutmgeneAnnotation.html#pypath.inputs.gutmgene.GutmgeneAnnotation.classification">classification (pypath.inputs.gutmgene.GutmgeneAnnotation attribute)</a>
 
       <ul>
-        <li><a href="api/pypath.inputs.drugcentral.html#module-pypath.inputs.drugcentral">module</a>
+        <li><a href="api/pypath.inputs.gutmgene.GutmgeneRaw.html#pypath.inputs.gutmgene.GutmgeneRaw.classification">(pypath.inputs.gutmgene.GutmgeneRaw attribute)</a>
+</li>
+        <li><a href="api/pypath.inputs.icellnet.IcellnetRecord.html#pypath.inputs.icellnet.IcellnetRecord.classification">(pypath.inputs.icellnet.IcellnetRecord attribute)</a>
 </li>
       </ul></li>
-      <li>
-    pypath.inputs.ebi
+      <li><a href="api/pypath.utils.pdb.ResidueMapper.html#pypath.utils.pdb.ResidueMapper.clean">clean() (pypath.utils.pdb.ResidueMapper method)</a>
 
       <ul>
-        <li><a href="api/pypath.inputs.ebi.html#module-pypath.inputs.ebi">module</a>
+        <li><a href="api/pypath.utils.residues.ResidueMapper.html#pypath.utils.residues.ResidueMapper.clean">(pypath.utils.residues.ResidueMapper method)</a>
 </li>
       </ul></li>
-      <li>
+      <li><a href="api/pypath.utils.pyreact.BioPaxReader.html#pypath.utils.pyreact.BioPaxReader.cleanup_hook">cleanup_hook() (pypath.utils.pyreact.BioPaxReader method)</a>
+</li>
+      <li><a href="api/pypath.internals.resource.NetworkDataset.html#pypath.internals.resource.NetworkDataset.clear">clear() (pypath.internals.resource.NetworkDataset method)</a>
+</li>
+      <li><a href="api/pypath.inputs.clinvar.clinvar_citations.html#pypath.inputs.clinvar.clinvar_citations">clinvar_citations() (in module pypath.inputs.clinvar)</a>
+</li>
+      <li><a href="api/pypath.inputs.clinvar.clinvar_raw.html#pypath.inputs.clinvar.clinvar_raw">clinvar_raw() (in module pypath.inputs.clinvar)</a>
+</li>
+      <li><a href="api/pypath.share.curl.Curl.html#pypath.share.curl.Curl.close">close() (pypath.share.curl.Curl method)</a>
+</li>
+      <li><a href="api/pypath.utils.pyreact.BioPaxReader.html#pypath.utils.pyreact.BioPaxReader.close_biopax">close_biopax() (pypath.utils.pyreact.BioPaxReader method)</a>
+</li>
+      <li><a href="api/pypath.inputs.dorothea.DorotheaInteraction.html#pypath.inputs.dorothea.DorotheaInteraction.coexp">coexp (pypath.inputs.dorothea.DorotheaInteraction attribute)</a>
+</li>
+      <li><a href="api/pypath.inputs.dorothea.DorotheaInteraction.html#pypath.inputs.dorothea.DorotheaInteraction.coexp_sources">coexp_sources (pypath.inputs.dorothea.DorotheaInteraction attribute)</a>
+</li>
+      <li><a href="api/pypath.utils.uniprot.collect.html#pypath.utils.uniprot.collect">collect() (in module pypath.utils.uniprot)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.collect_complex_identifiers">collect_complex_identifiers (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.collect_complex_labels">collect_complex_labels (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.collect_complexes">collect_complexes (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.collect_curation_effort">collect_curation_effort (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.collect_data_models">collect_data_models (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.collect_datasets">collect_datasets (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.collect_degrees_directed">collect_degrees_directed (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.collect_degrees_directed_in">collect_degrees_directed_in (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.collect_degrees_directed_out">collect_degrees_directed_out (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.collect_degrees_negative">collect_degrees_negative (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.collect_degrees_negative_in">collect_degrees_negative_in (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.collect_degrees_negative_out">collect_degrees_negative_out (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.collect_degrees_non_directed">collect_degrees_non_directed (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.collect_degrees_positive">collect_degrees_positive (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.collect_degrees_positive_in">collect_degrees_positive_in (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.collect_degrees_positive_out">collect_degrees_positive_out (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.collect_degrees_signed">collect_degrees_signed (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.collect_degrees_signed_in">collect_degrees_signed_in (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.collect_degrees_signed_out">collect_degrees_signed_out (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.collect_degrees_undirected">collect_degrees_undirected (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.collect_entities">collect_entities (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.collect_evidences">collect_evidences (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.collect_identifiers">collect_identifiers (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.resources.controller.ResourceController.html#pypath.resources.controller.ResourceController.collect_interaction">collect_interaction() (pypath.resources.controller.ResourceController method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.collect_interaction_types">collect_interaction_types (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.collect_interactions">collect_interactions (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.collect_interactions_0">collect_interactions_0 (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.collect_interactions_directed">collect_interactions_directed (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.collect_interactions_mutual">collect_interactions_mutual (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.collect_interactions_negative">collect_interactions_negative (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.collect_interactions_non_directed">collect_interactions_non_directed (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.collect_interactions_non_directed_0">collect_interactions_non_directed_0 (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.collect_interactions_positive">collect_interactions_positive (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.collect_interactions_signed">collect_interactions_signed (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.collect_interactions_undirected">collect_interactions_undirected (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.collect_interactions_undirected_0">collect_interactions_undirected_0 (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.collect_labels">collect_labels (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.collect_lncrna_identifiers">collect_lncrna_identifiers (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.collect_lncrna_labels">collect_lncrna_labels (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.collect_lncrnas">collect_lncrnas (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.collect_mirna_identifiers">collect_mirna_identifiers (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.collect_mirna_labels">collect_mirna_labels (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.collect_mirnas">collect_mirnas (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.resources.controller.ResourceController.html#pypath.resources.controller.ResourceController.collect_network">collect_network() (pypath.resources.controller.ResourceController method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.collect_protein_identifiers">collect_protein_identifiers (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.collect_protein_labels">collect_protein_labels (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.collect_proteins">collect_proteins (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.collect_references">collect_references (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.collect_resource_names">collect_resource_names (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.collect_resource_names_via">collect_resource_names_via (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.collect_resources">collect_resources (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.collect_resources_via">collect_resources_via (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.collect_small_molecule_identifiers">collect_small_molecule_identifiers (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.collect_small_molecule_labels">collect_small_molecule_labels (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.collect_small_molecules">collect_small_molecules (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.collectri">collectri() (pypath.core.network.Network class method)</a>
+</li>
+      <li><a href="api/pypath.inputs.collectri.collectri_interactions.html#pypath.inputs.collectri.collectri_interactions">collectri_interactions() (in module pypath.inputs.collectri)</a>
+</li>
+      <li><a href="api/pypath.inputs.collectri.collectri_raw.html#pypath.inputs.collectri.collectri_raw">collectri_raw() (in module pypath.inputs.collectri)</a>
+</li>
+      <li><a href="api/pypath.inputs.compath.compath_mappings.html#pypath.inputs.compath.compath_mappings">compath_mappings() (in module pypath.inputs.compath)</a>
+</li>
+      <li><a href="api/pypath.omnipath.app.DatabaseManager.html#pypath.omnipath.app.DatabaseManager.compile_table">compile_table() (pypath.omnipath.app.DatabaseManager method)</a>
+</li>
+      <li><a href="api/pypath.omnipath.app.DatabaseManager.html#pypath.omnipath.app.DatabaseManager.compile_tables">compile_tables() (pypath.omnipath.app.DatabaseManager method)</a>
+</li>
+      <li><a href="api/pypath.core.complex.Compleat.html#pypath.core.complex.Compleat">Compleat (class in pypath.core.complex)</a>
+</li>
+      <li><a href="api/pypath.inputs.compleat.compleat_complexes.html#pypath.inputs.compleat.compleat_complexes">compleat_complexes() (in module pypath.inputs.compleat)</a>
+</li>
+      <li><a href="api/pypath.inputs.compleat.compleat_raw.html#pypath.inputs.compleat.compleat_raw">compleat_raw() (in module pypath.inputs.compleat)</a>
+</li>
+      <li><a href="api/pypath.internals.intera.Complex.html#pypath.internals.intera.Complex">Complex (class in pypath.internals.intera)</a>
+
+      <ul>
+        <li><a href="api/pypath.utils.pyreact.Complex.html#pypath.utils.pyreact.Complex">(class in pypath.utils.pyreact)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.complex_identifiers_by_data_model">complex_identifiers_by_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.complex_identifiers_by_data_model">complex_identifiers_by_data_model() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.complex_identifiers_by_interaction_type">complex_identifiers_by_interaction_type (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.complex_identifiers_by_interaction_type">complex_identifiers_by_interaction_type() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.complex_identifiers_by_interaction_type_and_data_model">complex_identifiers_by_interaction_type_and_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.complex_identifiers_by_interaction_type_and_data_model">complex_identifiers_by_interaction_type_and_data_model() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.complex_identifiers_by_interaction_type_and_data_model_and_resource">complex_identifiers_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.complex_identifiers_by_interaction_type_and_data_model_and_resource">complex_identifiers_by_interaction_type_and_data_model_and_resource() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.complex_identifiers_by_reference">complex_identifiers_by_reference (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.complex_identifiers_by_reference">complex_identifiers_by_reference() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.complex_identifiers_by_resource">complex_identifiers_by_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.complex_identifiers_by_resource">complex_identifiers_by_resource() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.annot.Adhesome.html#pypath.core.annot.Adhesome.complex_inference">complex_inference() (pypath.core.annot.Adhesome method)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.annot.Almen2009.html#pypath.core.annot.Almen2009.complex_inference">(pypath.core.annot.Almen2009 method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.AnnotationBase.html#pypath.core.annot.AnnotationBase.complex_inference">(pypath.core.annot.AnnotationBase method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Baccin2019.html#pypath.core.annot.Baccin2019.complex_inference">(pypath.core.annot.Baccin2019 method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Biogps.html#pypath.core.annot.Biogps.complex_inference">(pypath.core.annot.Biogps method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cancerdrugsdb.html#pypath.core.annot.Cancerdrugsdb.complex_inference">(pypath.core.annot.Cancerdrugsdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CancerGeneCensus.html#pypath.core.annot.CancerGeneCensus.complex_inference">(pypath.core.annot.CancerGeneCensus method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cancersea.html#pypath.core.annot.Cancersea.complex_inference">(pypath.core.annot.Cancersea method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cellcall.html#pypath.core.annot.Cellcall.complex_inference">(pypath.core.annot.Cellcall method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cellcellinteractions.html#pypath.core.annot.Cellcellinteractions.complex_inference">(pypath.core.annot.Cellcellinteractions method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cellchatdb.html#pypath.core.annot.Cellchatdb.complex_inference">(pypath.core.annot.Cellchatdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CellchatdbComplex.html#pypath.core.annot.CellchatdbComplex.complex_inference">(pypath.core.annot.CellchatdbComplex method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cellinker.html#pypath.core.annot.Cellinker.complex_inference">(pypath.core.annot.Cellinker method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CellinkerComplex.html#pypath.core.annot.CellinkerComplex.complex_inference">(pypath.core.annot.CellinkerComplex method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CellPhoneDB.html#pypath.core.annot.CellPhoneDB.complex_inference">(pypath.core.annot.CellPhoneDB method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CellPhoneDBComplex.html#pypath.core.annot.CellPhoneDBComplex.complex_inference">(pypath.core.annot.CellPhoneDBComplex method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CellSurfaceProteinAtlas.html#pypath.core.annot.CellSurfaceProteinAtlas.complex_inference">(pypath.core.annot.CellSurfaceProteinAtlas method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CellSurfaceProteinAtlasCellType.html#pypath.core.annot.CellSurfaceProteinAtlasCellType.complex_inference">(pypath.core.annot.CellSurfaceProteinAtlasCellType method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Celltalkdb.html#pypath.core.annot.Celltalkdb.complex_inference">(pypath.core.annot.Celltalkdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Celltypist.html#pypath.core.annot.Celltypist.complex_inference">(pypath.core.annot.Celltypist method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Comppi.html#pypath.core.annot.Comppi.complex_inference">(pypath.core.annot.Comppi method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Connectomedb.html#pypath.core.annot.Connectomedb.complex_inference">(pypath.core.annot.Connectomedb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Corum.html#pypath.core.annot.Corum.complex_inference">(pypath.core.annot.Corum method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CorumFuncat.html#pypath.core.annot.CorumFuncat.complex_inference">(pypath.core.annot.CorumFuncat method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CorumGO.html#pypath.core.annot.CorumGO.complex_inference">(pypath.core.annot.CorumGO method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cpad.html#pypath.core.annot.Cpad.complex_inference">(pypath.core.annot.Cpad method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cytosig.html#pypath.core.annot.Cytosig.complex_inference">(pypath.core.annot.Cytosig method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Dgidb.html#pypath.core.annot.Dgidb.complex_inference">(pypath.core.annot.Dgidb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Disgenet.html#pypath.core.annot.Disgenet.complex_inference">(pypath.core.annot.Disgenet method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Embrace.html#pypath.core.annot.Embrace.complex_inference">(pypath.core.annot.Embrace method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Exocarta.html#pypath.core.annot.Exocarta.complex_inference">(pypath.core.annot.Exocarta method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.GOIntercell.html#pypath.core.annot.GOIntercell.complex_inference">(pypath.core.annot.GOIntercell method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Gpcrdb.html#pypath.core.annot.Gpcrdb.complex_inference">(pypath.core.annot.Gpcrdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.GuideToPharmacology.html#pypath.core.annot.GuideToPharmacology.complex_inference">(pypath.core.annot.GuideToPharmacology method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Hgnc.html#pypath.core.annot.Hgnc.complex_inference">(pypath.core.annot.Hgnc method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.HpmrComplex.html#pypath.core.annot.HpmrComplex.complex_inference">(pypath.core.annot.HpmrComplex method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.HPO.html#pypath.core.annot.HPO.complex_inference">(pypath.core.annot.HPO method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Humancellmap.html#pypath.core.annot.Humancellmap.complex_inference">(pypath.core.annot.Humancellmap method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.HumanPlasmaMembraneReceptome.html#pypath.core.annot.HumanPlasmaMembraneReceptome.complex_inference">(pypath.core.annot.HumanPlasmaMembraneReceptome method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.HumanProteinAtlas.html#pypath.core.annot.HumanProteinAtlas.complex_inference">(pypath.core.annot.HumanProteinAtlas method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.HumanProteinAtlasSecretome.html#pypath.core.annot.HumanProteinAtlasSecretome.complex_inference">(pypath.core.annot.HumanProteinAtlasSecretome method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.HumanProteinAtlasSubcellular.html#pypath.core.annot.HumanProteinAtlasSubcellular.complex_inference">(pypath.core.annot.HumanProteinAtlasSubcellular method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Icellnet.html#pypath.core.annot.Icellnet.complex_inference">(pypath.core.annot.Icellnet method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.IcellnetComplex.html#pypath.core.annot.IcellnetComplex.complex_inference">(pypath.core.annot.IcellnetComplex method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Integrins.html#pypath.core.annot.Integrins.complex_inference">(pypath.core.annot.Integrins method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.InterPro.html#pypath.core.annot.InterPro.complex_inference">(pypath.core.annot.InterPro method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Intogen.html#pypath.core.annot.Intogen.complex_inference">(pypath.core.annot.Intogen method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Italk.html#pypath.core.annot.Italk.complex_inference">(pypath.core.annot.Italk method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.KeggPathways.html#pypath.core.annot.KeggPathways.complex_inference">(pypath.core.annot.KeggPathways method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.KeggPathwaysPC.html#pypath.core.annot.KeggPathwaysPC.complex_inference">(pypath.core.annot.KeggPathwaysPC method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Kinasedotcom.html#pypath.core.annot.Kinasedotcom.complex_inference">(pypath.core.annot.Kinasedotcom method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Kirouac2010.html#pypath.core.annot.Kirouac2010.complex_inference">(pypath.core.annot.Kirouac2010 method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Lambert2018.html#pypath.core.annot.Lambert2018.complex_inference">(pypath.core.annot.Lambert2018 method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.LigandReceptor.html#pypath.core.annot.LigandReceptor.complex_inference">(pypath.core.annot.LigandReceptor method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Locate.html#pypath.core.annot.Locate.complex_inference">(pypath.core.annot.Locate method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Lrdb.html#pypath.core.annot.Lrdb.complex_inference">(pypath.core.annot.Lrdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Matrisome.html#pypath.core.annot.Matrisome.complex_inference">(pypath.core.annot.Matrisome method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Matrixdb.html#pypath.core.annot.Matrixdb.complex_inference">(pypath.core.annot.Matrixdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Mcam.html#pypath.core.annot.Mcam.complex_inference">(pypath.core.annot.Mcam method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Membranome.html#pypath.core.annot.Membranome.complex_inference">(pypath.core.annot.Membranome method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Msigdb.html#pypath.core.annot.Msigdb.complex_inference">(pypath.core.annot.Msigdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.NetpathPathways.html#pypath.core.annot.NetpathPathways.complex_inference">(pypath.core.annot.NetpathPathways method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Opm.html#pypath.core.annot.Opm.complex_inference">(pypath.core.annot.Opm method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Panglaodb.html#pypath.core.annot.Panglaodb.complex_inference">(pypath.core.annot.Panglaodb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Phobius.html#pypath.core.annot.Phobius.complex_inference">(pypath.core.annot.Phobius method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Phosphatome.html#pypath.core.annot.Phosphatome.complex_inference">(pypath.core.annot.Phosphatome method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Progeny.html#pypath.core.annot.Progeny.complex_inference">(pypath.core.annot.Progeny method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Ramilowski2015.html#pypath.core.annot.Ramilowski2015.complex_inference">(pypath.core.annot.Ramilowski2015 method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Ramilowski2015Location.html#pypath.core.annot.Ramilowski2015Location.complex_inference">(pypath.core.annot.Ramilowski2015Location method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Scconnect.html#pypath.core.annot.Scconnect.complex_inference">(pypath.core.annot.Scconnect method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.ScconnectComplex.html#pypath.core.annot.ScconnectComplex.complex_inference">(pypath.core.annot.ScconnectComplex method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.SignalinkFunctions.html#pypath.core.annot.SignalinkFunctions.complex_inference">(pypath.core.annot.SignalinkFunctions method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.SignalinkPathways.html#pypath.core.annot.SignalinkPathways.complex_inference">(pypath.core.annot.SignalinkPathways method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.SignorPathways.html#pypath.core.annot.SignorPathways.complex_inference">(pypath.core.annot.SignorPathways method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Surfaceome.html#pypath.core.annot.Surfaceome.complex_inference">(pypath.core.annot.Surfaceome method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Talklr.html#pypath.core.annot.Talklr.complex_inference">(pypath.core.annot.Talklr method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Tcdb.html#pypath.core.annot.Tcdb.complex_inference">(pypath.core.annot.Tcdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Tfcensus.html#pypath.core.annot.Tfcensus.complex_inference">(pypath.core.annot.Tfcensus method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Topdb.html#pypath.core.annot.Topdb.complex_inference">(pypath.core.annot.Topdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.UniprotFamilies.html#pypath.core.annot.UniprotFamilies.complex_inference">(pypath.core.annot.UniprotFamilies method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.UniprotKeywords.html#pypath.core.annot.UniprotKeywords.complex_inference">(pypath.core.annot.UniprotKeywords method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.UniprotLocations.html#pypath.core.annot.UniprotLocations.complex_inference">(pypath.core.annot.UniprotLocations method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.UniprotTissues.html#pypath.core.annot.UniprotTissues.complex_inference">(pypath.core.annot.UniprotTissues method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.UniprotTopologies.html#pypath.core.annot.UniprotTopologies.complex_inference">(pypath.core.annot.UniprotTopologies method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Vesiclepedia.html#pypath.core.annot.Vesiclepedia.complex_inference">(pypath.core.annot.Vesiclepedia method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Wang.html#pypath.core.annot.Wang.complex_inference">(pypath.core.annot.Wang method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Zhong2015.html#pypath.core.annot.Zhong2015.complex_inference">(pypath.core.annot.Zhong2015 method)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.complex_labels_by_data_model">complex_labels_by_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.complex_labels_by_data_model">complex_labels_by_data_model() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.complex_labels_by_interaction_type">complex_labels_by_interaction_type (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.complex_labels_by_interaction_type">complex_labels_by_interaction_type() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.complex_labels_by_interaction_type_and_data_model">complex_labels_by_interaction_type_and_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.complex_labels_by_interaction_type_and_data_model">complex_labels_by_interaction_type_and_data_model() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.complex_labels_by_interaction_type_and_data_model_and_resource">complex_labels_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.complex_labels_by_interaction_type_and_data_model_and_resource">complex_labels_by_interaction_type_and_data_model_and_resource() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.complex_labels_by_reference">complex_labels_by_reference (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.complex_labels_by_reference">complex_labels_by_reference() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.complex_labels_by_resource">complex_labels_by_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.complex_labels_by_resource">complex_labels_by_resource() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.complex.ComplexAggregator.html#pypath.core.complex.ComplexAggregator">ComplexAggregator (class in pypath.core.complex)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.complexes_by_data_model">complexes_by_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.complexes_by_data_model">complexes_by_data_model() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.complexes_by_interaction_type">complexes_by_interaction_type (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.complexes_by_interaction_type">complexes_by_interaction_type() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.complexes_by_interaction_type_and_data_model">complexes_by_interaction_type_and_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.complexes_by_interaction_type_and_data_model">complexes_by_interaction_type_and_data_model() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.complexes_by_interaction_type_and_data_model_and_resource">complexes_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.complexes_by_interaction_type_and_data_model_and_resource">complexes_by_interaction_type_and_data_model_and_resource() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.complexes_by_reference">complexes_by_reference (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.complexes_by_reference">complexes_by_reference() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.complexes_by_resource">complexes_by_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.complexes_by_resource">complexes_by_resource() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.complex.ComplexPortal.html#pypath.core.complex.ComplexPortal">ComplexPortal (class in pypath.core.complex)</a>
+</li>
+      <li><a href="api/pypath.inputs.complexportal.complexportal_complexes.html#pypath.inputs.complexportal.complexportal_complexes">complexportal_complexes() (in module pypath.inputs.complexportal)</a>
+</li>
+      <li><a href="api/pypath.utils.pyreact.ComplexVariations.html#pypath.utils.pyreact.ComplexVariations">ComplexVariations (class in pypath.utils.pyreact)</a>
+</li>
+      <li><a href="api/pypath.inputs.cellinker.components_to_complex.html#pypath.inputs.cellinker.components_to_complex">components_to_complex() (in module pypath.inputs.cellinker)</a>
+</li>
+      <li><a href="api/pypath.core.annot.Comppi.html#pypath.core.annot.Comppi">Comppi (class in pypath.core.annot)</a>
+</li>
+      <li><a href="api/pypath.inputs.comppi.comppi_interaction_locations.html#pypath.inputs.comppi.comppi_interaction_locations">comppi_interaction_locations() (in module pypath.inputs.comppi)</a>
+</li>
+      <li><a href="api/pypath.inputs.comppi.comppi_locations.html#pypath.inputs.comppi.comppi_locations">comppi_locations() (in module pypath.inputs.comppi)</a>
+</li>
+      <li><a href="api/pypath.utils.unichem.Unichem.html#pypath.utils.unichem.Unichem.connectivity_search">connectivity_search() (pypath.utils.unichem.Unichem method)</a>
+</li>
+      <li><a href="api/pypath.core.annot.Connectomedb.html#pypath.core.annot.Connectomedb">Connectomedb (class in pypath.core.annot)</a>
+</li>
+      <li><a href="api/pypath.inputs.connectomedb.connectomedb_annotations.html#pypath.inputs.connectomedb.connectomedb_annotations">connectomedb_annotations() (in module pypath.inputs.connectomedb)</a>
+</li>
+      <li><a href="api/pypath.inputs.connectomedb.connectomedb_interactions.html#pypath.inputs.connectomedb.connectomedb_interactions">connectomedb_interactions() (in module pypath.inputs.connectomedb)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.consensus">consensus() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.consensus_edges">consensus_edges() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.share.curl.Curl.html#pypath.share.curl.Curl.construct_binary_data">construct_binary_data() (pypath.share.curl.Curl method)</a>
+</li>
+      <li><a href="api/pypath.utils.pyreact.Control.html#pypath.utils.pyreact.Control">Control (class in pypath.utils.pyreact)</a>
+</li>
+      <li><a href="api/pypath.core.annot.Corum.html#pypath.core.annot.Corum">Corum (class in pypath.core.annot)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.complex.Corum.html#pypath.core.complex.Corum">(class in pypath.core.complex)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.inputs.corum.corum_complexes.html#pypath.inputs.corum.corum_complexes">corum_complexes() (in module pypath.inputs.corum)</a>
+</li>
+      <li><a href="api/pypath.core.annot.CorumFuncat.html#pypath.core.annot.CorumFuncat">CorumFuncat (class in pypath.core.annot)</a>
+</li>
+      <li><a href="api/pypath.core.annot.CorumGO.html#pypath.core.annot.CorumGO">CorumGO (class in pypath.core.annot)</a>
+</li>
+      <li><a href="api/pypath.core.entity.EntityKey.html#pypath.core.entity.EntityKey.count">count() (pypath.core.entity.EntityKey method)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.interaction.InteractionDataFrameRecord.html#pypath.core.interaction.InteractionDataFrameRecord.count">(pypath.core.interaction.InteractionDataFrameRecord method)</a>
+</li>
+        <li><a href="api/pypath.core.interaction.InteractionKey.html#pypath.core.interaction.InteractionKey.count">(pypath.core.interaction.InteractionKey method)</a>
+</li>
+        <li><a href="api/pypath.core.network.NetworkStatsRecord.html#pypath.core.network.NetworkStatsRecord.count">(pypath.core.network.NetworkStatsRecord method)</a>
+</li>
+        <li><a href="api/pypath.inputs.adrecs.AdrecsAdr.html#pypath.inputs.adrecs.AdrecsAdr.count">(pypath.inputs.adrecs.AdrecsAdr method)</a>
+</li>
+        <li><a href="api/pypath.inputs.adrecs.AdrecsChildParent.html#pypath.inputs.adrecs.AdrecsChildParent.count">(pypath.inputs.adrecs.AdrecsChildParent method)</a>
+</li>
+        <li><a href="api/pypath.inputs.adrecs.AdrecsDrug.html#pypath.inputs.adrecs.AdrecsDrug.count">(pypath.inputs.adrecs.AdrecsDrug method)</a>
+</li>
+        <li><a href="api/pypath.inputs.adrecs.AdrecsDrugAdr.html#pypath.inputs.adrecs.AdrecsDrugAdr.count">(pypath.inputs.adrecs.AdrecsDrugAdr method)</a>
+</li>
+        <li><a href="api/pypath.inputs.adrecs.AdrecsTerm.html#pypath.inputs.adrecs.AdrecsTerm.count">(pypath.inputs.adrecs.AdrecsTerm method)</a>
+</li>
+        <li><a href="api/pypath.inputs.biogps.BiogpsDataset.html#pypath.inputs.biogps.BiogpsDataset.count">(pypath.inputs.biogps.BiogpsDataset method)</a>
+</li>
+        <li><a href="api/pypath.inputs.cellinker.CellinkerInteraction.html#pypath.inputs.cellinker.CellinkerInteraction.count">(pypath.inputs.cellinker.CellinkerInteraction method)</a>
+</li>
+        <li><a href="api/pypath.inputs.cellphonedb.CellPhoneDBAnnotation.html#pypath.inputs.cellphonedb.CellPhoneDBAnnotation.count">(pypath.inputs.cellphonedb.CellPhoneDBAnnotation method)</a>
+</li>
+        <li><a href="api/pypath.inputs.dorothea.DorotheaInteraction.html#pypath.inputs.dorothea.DorotheaInteraction.count">(pypath.inputs.dorothea.DorotheaInteraction method)</a>
+</li>
+        <li><a href="api/pypath.inputs.gutmgene.GutmgeneAnnotation.html#pypath.inputs.gutmgene.GutmgeneAnnotation.count">(pypath.inputs.gutmgene.GutmgeneAnnotation method)</a>
+</li>
+        <li><a href="api/pypath.inputs.gutmgene.GutmgeneRaw.html#pypath.inputs.gutmgene.GutmgeneRaw.count">(pypath.inputs.gutmgene.GutmgeneRaw method)</a>
+</li>
+        <li><a href="api/pypath.inputs.hpmr.HpmrInteraction.html#pypath.inputs.hpmr.HpmrInteraction.count">(pypath.inputs.hpmr.HpmrInteraction method)</a>
+</li>
+        <li><a href="api/pypath.inputs.icellnet.IcellnetRecord.html#pypath.inputs.icellnet.IcellnetRecord.count">(pypath.inputs.icellnet.IcellnetRecord method)</a>
+</li>
+        <li><a href="api/pypath.inputs.iptmnet.IptmnetInteraction.html#pypath.inputs.iptmnet.IptmnetInteraction.count">(pypath.inputs.iptmnet.IptmnetInteraction method)</a>
+</li>
+        <li><a href="api/pypath.inputs.kegg.KeggPathway.html#pypath.inputs.kegg.KeggPathway.count">(pypath.inputs.kegg.KeggPathway method)</a>
+</li>
+        <li><a href="api/pypath.inputs.lrdb.LrdbAnnotation.html#pypath.inputs.lrdb.LrdbAnnotation.count">(pypath.inputs.lrdb.LrdbAnnotation method)</a>
+</li>
+        <li><a href="api/pypath.inputs.pathophenodb.DiseasePathogen.html#pypath.inputs.pathophenodb.DiseasePathogen.count">(pypath.inputs.pathophenodb.DiseasePathogen method)</a>
+</li>
+        <li><a href="api/pypath.inputs.pathwaycommons.PathwayCommonsInteraction.html#pypath.inputs.pathwaycommons.PathwayCommonsInteraction.count">(pypath.inputs.pathwaycommons.PathwayCommonsInteraction method)</a>
+</li>
+        <li><a href="api/pypath.inputs.pathwaycommons.PathwayCommonsResource.html#pypath.inputs.pathwaycommons.PathwayCommonsResource.count">(pypath.inputs.pathwaycommons.PathwayCommonsResource method)</a>
+</li>
+        <li><a href="api/pypath.inputs.pisa.PisaBond.html#pypath.inputs.pisa.PisaBond.count">(pypath.inputs.pisa.PisaBond method)</a>
+</li>
+        <li><a href="api/pypath.inputs.sider.SiderDrug.html#pypath.inputs.sider.SiderDrug.count">(pypath.inputs.sider.SiderDrug method)</a>
+</li>
+        <li><a href="api/pypath.inputs.sider.SiderSideeffect.html#pypath.inputs.sider.SiderSideeffect.count">(pypath.inputs.sider.SiderSideeffect method)</a>
+</li>
+        <li><a href="api/pypath.inputs.sider.SiderSideeffectMeddra.html#pypath.inputs.sider.SiderSideeffectMeddra.count">(pypath.inputs.sider.SiderSideeffectMeddra method)</a>
+</li>
+        <li><a href="api/pypath.inputs.sider.SiderSideeffetFrequency.html#pypath.inputs.sider.SiderSideeffetFrequency.count">(pypath.inputs.sider.SiderSideeffetFrequency method)</a>
+</li>
+        <li><a href="api/pypath.inputs.uniprot.Taxon.html#pypath.inputs.uniprot.Taxon.count">(pypath.inputs.uniprot.Taxon method)</a>
+</li>
+        <li><a href="api/pypath.inputs.uniprot.UniprotRecordHistory.html#pypath.inputs.uniprot.UniprotRecordHistory.count">(pypath.inputs.uniprot.UniprotRecordHistory method)</a>
+</li>
+        <li><a href="api/pypath.internals.annot_formats.AnnotDef.html#pypath.internals.annot_formats.AnnotDef.count">(pypath.internals.annot_formats.AnnotDef method)</a>
+</li>
+        <li><a href="api/pypath.internals.annot_formats.AnnotDefKey.html#pypath.internals.annot_formats.AnnotDefKey.count">(pypath.internals.annot_formats.AnnotDefKey method)</a>
+</li>
+        <li><a href="api/pypath.internals.annot_formats.AnnotOp.html#pypath.internals.annot_formats.AnnotOp.count">(pypath.internals.annot_formats.AnnotOp method)</a>
+</li>
+        <li><a href="api/pypath.internals.resource.EnzymeSubstrateResourceKey.html#pypath.internals.resource.EnzymeSubstrateResourceKey.count">(pypath.internals.resource.EnzymeSubstrateResourceKey method)</a>
+</li>
+        <li><a href="api/pypath.internals.resource.NetworkResourceKey.html#pypath.internals.resource.NetworkResourceKey.count">(pypath.internals.resource.NetworkResourceKey method)</a>
+</li>
+        <li><a href="api/pypath.utils.mapping.MappingTableKey.html#pypath.utils.mapping.MappingTableKey.count">(pypath.utils.mapping.MappingTableKey method)</a>
+</li>
+        <li><a href="api/pypath.utils.orthology.EnsemblOrtholog.html#pypath.utils.orthology.EnsemblOrtholog.count">(pypath.utils.orthology.EnsemblOrtholog method)</a>
+</li>
+        <li><a href="api/pypath.utils.orthology.HomologeneOrtholog.html#pypath.utils.orthology.HomologeneOrtholog.count">(pypath.utils.orthology.HomologeneOrtholog method)</a>
+</li>
+        <li><a href="api/pypath.utils.orthology.OmaOrtholog.html#pypath.utils.orthology.OmaOrtholog.count">(pypath.utils.orthology.OmaOrtholog method)</a>
+</li>
+        <li><a href="api/pypath.utils.orthology.OrthologyTableKey.html#pypath.utils.orthology.OrthologyTableKey.count">(pypath.utils.orthology.OrthologyTableKey method)</a>
+</li>
+        <li><a href="api/pypath.utils.pdb.Residue.html#pypath.utils.pdb.Residue.count">(pypath.utils.pdb.Residue method)</a>
+</li>
+        <li><a href="api/pypath.utils.pdb.Segment.html#pypath.utils.pdb.Segment.count">(pypath.utils.pdb.Segment method)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_activated_by">count_activated_by (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_activates">count_activates (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_complex_identifiers">count_complex_identifiers (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.count_complex_identifiers">count_complex_identifiers() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_complex_identifiers_by_data_model">count_complex_identifiers_by_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_complex_identifiers_by_interaction_type">count_complex_identifiers_by_interaction_type (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_complex_identifiers_by_interaction_type_and_data_model">count_complex_identifiers_by_interaction_type_and_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_complex_identifiers_by_interaction_type_and_data_model_and_resource">count_complex_identifiers_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_complex_identifiers_by_reference">count_complex_identifiers_by_reference (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_complex_identifiers_by_resource">count_complex_identifiers_by_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_complex_labels">count_complex_labels (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.count_complex_labels">count_complex_labels() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_complex_labels_by_data_model">count_complex_labels_by_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_complex_labels_by_interaction_type">count_complex_labels_by_interaction_type (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_complex_labels_by_interaction_type_and_data_model">count_complex_labels_by_interaction_type_and_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_complex_labels_by_interaction_type_and_data_model_and_resource">count_complex_labels_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_complex_labels_by_reference">count_complex_labels_by_reference (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_complex_labels_by_resource">count_complex_labels_by_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_complexes">count_complexes (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.count_complexes">count_complexes() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_complexes_by_data_model">count_complexes_by_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_complexes_by_interaction_type">count_complexes_by_interaction_type (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_complexes_by_interaction_type_and_data_model">count_complexes_by_interaction_type_and_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_complexes_by_interaction_type_and_data_model_and_resource">count_complexes_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_complexes_by_reference">count_complexes_by_reference (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_complexes_by_resource">count_complexes_by_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_curation_effort">count_curation_effort (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_curation_effort_by_data_model">count_curation_effort_by_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_curation_effort_by_interaction_type">count_curation_effort_by_interaction_type (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_curation_effort_by_interaction_type_and_data_model">count_curation_effort_by_interaction_type_and_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_curation_effort_by_interaction_type_and_data_model_and_resource">count_curation_effort_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_curation_effort_by_reference">count_curation_effort_by_reference (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_curation_effort_by_resource">count_curation_effort_by_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.count_data_models">count_data_models (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_data_models">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_data_models_by_data_model">count_data_models_by_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_data_models_by_interaction_type">count_data_models_by_interaction_type (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_data_models_by_interaction_type_and_data_model">count_data_models_by_interaction_type_and_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_data_models_by_interaction_type_and_data_model_and_resource">count_data_models_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_data_models_by_reference">count_data_models_by_reference (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_data_models_by_resource">count_data_models_by_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_datasets">count_datasets (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_datasets_by_data_model">count_datasets_by_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_datasets_by_interaction_type">count_datasets_by_interaction_type (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_datasets_by_interaction_type_and_data_model">count_datasets_by_interaction_type_and_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_datasets_by_interaction_type_and_data_model_and_resource">count_datasets_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_datasets_by_reference">count_datasets_by_reference (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_datasets_by_resource">count_datasets_by_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.count_degrees_directed">count_degrees_directed (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_degrees_directed">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_degrees_directed_by_data_model">count_degrees_directed_by_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_degrees_directed_by_interaction_type">count_degrees_directed_by_interaction_type (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_degrees_directed_by_interaction_type_and_data_model">count_degrees_directed_by_interaction_type_and_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_degrees_directed_by_interaction_type_and_data_model_and_resource">count_degrees_directed_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_degrees_directed_by_reference">count_degrees_directed_by_reference (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_degrees_directed_by_resource">count_degrees_directed_by_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.count_degrees_directed_in">count_degrees_directed_in (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_degrees_directed_in">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_degrees_directed_in_by_data_model">count_degrees_directed_in_by_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_degrees_directed_in_by_interaction_type">count_degrees_directed_in_by_interaction_type (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_degrees_directed_in_by_interaction_type_and_data_model">count_degrees_directed_in_by_interaction_type_and_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_degrees_directed_in_by_interaction_type_and_data_model_and_resource">count_degrees_directed_in_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_degrees_directed_in_by_reference">count_degrees_directed_in_by_reference (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_degrees_directed_in_by_resource">count_degrees_directed_in_by_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.count_degrees_directed_out">count_degrees_directed_out (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_degrees_directed_out">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_degrees_directed_out_by_data_model">count_degrees_directed_out_by_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_degrees_directed_out_by_interaction_type">count_degrees_directed_out_by_interaction_type (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_degrees_directed_out_by_interaction_type_and_data_model">count_degrees_directed_out_by_interaction_type_and_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_degrees_directed_out_by_interaction_type_and_data_model_and_resource">count_degrees_directed_out_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_degrees_directed_out_by_reference">count_degrees_directed_out_by_reference (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_degrees_directed_out_by_resource">count_degrees_directed_out_by_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.count_degrees_negative">count_degrees_negative (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_degrees_negative">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_degrees_negative_by_data_model">count_degrees_negative_by_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_degrees_negative_by_interaction_type">count_degrees_negative_by_interaction_type (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_degrees_negative_by_interaction_type_and_data_model">count_degrees_negative_by_interaction_type_and_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_degrees_negative_by_interaction_type_and_data_model_and_resource">count_degrees_negative_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_degrees_negative_by_reference">count_degrees_negative_by_reference (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_degrees_negative_by_resource">count_degrees_negative_by_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.count_degrees_negative_in">count_degrees_negative_in (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_degrees_negative_in">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_degrees_negative_in_by_data_model">count_degrees_negative_in_by_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_degrees_negative_in_by_interaction_type">count_degrees_negative_in_by_interaction_type (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_degrees_negative_in_by_interaction_type_and_data_model">count_degrees_negative_in_by_interaction_type_and_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_degrees_negative_in_by_interaction_type_and_data_model_and_resource">count_degrees_negative_in_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_degrees_negative_in_by_reference">count_degrees_negative_in_by_reference (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_degrees_negative_in_by_resource">count_degrees_negative_in_by_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.count_degrees_negative_out">count_degrees_negative_out (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_degrees_negative_out">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_degrees_negative_out_by_data_model">count_degrees_negative_out_by_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_degrees_negative_out_by_interaction_type">count_degrees_negative_out_by_interaction_type (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_degrees_negative_out_by_interaction_type_and_data_model">count_degrees_negative_out_by_interaction_type_and_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_degrees_negative_out_by_interaction_type_and_data_model_and_resource">count_degrees_negative_out_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_degrees_negative_out_by_reference">count_degrees_negative_out_by_reference (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_degrees_negative_out_by_resource">count_degrees_negative_out_by_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.count_degrees_non_directed">count_degrees_non_directed (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_degrees_non_directed">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_degrees_non_directed_by_data_model">count_degrees_non_directed_by_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_degrees_non_directed_by_interaction_type">count_degrees_non_directed_by_interaction_type (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_degrees_non_directed_by_interaction_type_and_data_model">count_degrees_non_directed_by_interaction_type_and_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_degrees_non_directed_by_interaction_type_and_data_model_and_resource">count_degrees_non_directed_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_degrees_non_directed_by_reference">count_degrees_non_directed_by_reference (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_degrees_non_directed_by_resource">count_degrees_non_directed_by_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.count_degrees_positive">count_degrees_positive (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_degrees_positive">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_degrees_positive_by_data_model">count_degrees_positive_by_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_degrees_positive_by_interaction_type">count_degrees_positive_by_interaction_type (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_degrees_positive_by_interaction_type_and_data_model">count_degrees_positive_by_interaction_type_and_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_degrees_positive_by_interaction_type_and_data_model_and_resource">count_degrees_positive_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_degrees_positive_by_reference">count_degrees_positive_by_reference (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_degrees_positive_by_resource">count_degrees_positive_by_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.count_degrees_positive_in">count_degrees_positive_in (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_degrees_positive_in">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_degrees_positive_in_by_data_model">count_degrees_positive_in_by_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_degrees_positive_in_by_interaction_type">count_degrees_positive_in_by_interaction_type (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_degrees_positive_in_by_interaction_type_and_data_model">count_degrees_positive_in_by_interaction_type_and_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_degrees_positive_in_by_interaction_type_and_data_model_and_resource">count_degrees_positive_in_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_degrees_positive_in_by_reference">count_degrees_positive_in_by_reference (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_degrees_positive_in_by_resource">count_degrees_positive_in_by_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.count_degrees_positive_out">count_degrees_positive_out (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_degrees_positive_out">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_degrees_positive_out_by_data_model">count_degrees_positive_out_by_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_degrees_positive_out_by_interaction_type">count_degrees_positive_out_by_interaction_type (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_degrees_positive_out_by_interaction_type_and_data_model">count_degrees_positive_out_by_interaction_type_and_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_degrees_positive_out_by_interaction_type_and_data_model_and_resource">count_degrees_positive_out_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_degrees_positive_out_by_reference">count_degrees_positive_out_by_reference (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_degrees_positive_out_by_resource">count_degrees_positive_out_by_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.count_degrees_signed">count_degrees_signed (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_degrees_signed">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_degrees_signed_by_data_model">count_degrees_signed_by_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_degrees_signed_by_interaction_type">count_degrees_signed_by_interaction_type (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_degrees_signed_by_interaction_type_and_data_model">count_degrees_signed_by_interaction_type_and_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_degrees_signed_by_interaction_type_and_data_model_and_resource">count_degrees_signed_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_degrees_signed_by_reference">count_degrees_signed_by_reference (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_degrees_signed_by_resource">count_degrees_signed_by_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.count_degrees_signed_in">count_degrees_signed_in (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_degrees_signed_in">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_degrees_signed_in_by_data_model">count_degrees_signed_in_by_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_degrees_signed_in_by_interaction_type">count_degrees_signed_in_by_interaction_type (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_degrees_signed_in_by_interaction_type_and_data_model">count_degrees_signed_in_by_interaction_type_and_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_degrees_signed_in_by_interaction_type_and_data_model_and_resource">count_degrees_signed_in_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_degrees_signed_in_by_reference">count_degrees_signed_in_by_reference (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_degrees_signed_in_by_resource">count_degrees_signed_in_by_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.count_degrees_signed_out">count_degrees_signed_out (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_degrees_signed_out">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+  </ul></td>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_degrees_signed_out_by_data_model">count_degrees_signed_out_by_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_degrees_signed_out_by_interaction_type">count_degrees_signed_out_by_interaction_type (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_degrees_signed_out_by_interaction_type_and_data_model">count_degrees_signed_out_by_interaction_type_and_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_degrees_signed_out_by_interaction_type_and_data_model_and_resource">count_degrees_signed_out_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_degrees_signed_out_by_reference">count_degrees_signed_out_by_reference (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_degrees_signed_out_by_resource">count_degrees_signed_out_by_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.count_degrees_undirected">count_degrees_undirected (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_degrees_undirected">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_degrees_undirected_by_data_model">count_degrees_undirected_by_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_degrees_undirected_by_interaction_type">count_degrees_undirected_by_interaction_type (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_degrees_undirected_by_interaction_type_and_data_model">count_degrees_undirected_by_interaction_type_and_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_degrees_undirected_by_interaction_type_and_data_model_and_resource">count_degrees_undirected_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_degrees_undirected_by_reference">count_degrees_undirected_by_reference (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_degrees_undirected_by_resource">count_degrees_undirected_by_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_entities">count_entities (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.count_entities">count_entities() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_entities_by_data_model">count_entities_by_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_entities_by_interaction_type">count_entities_by_interaction_type (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_entities_by_interaction_type_and_data_model">count_entities_by_interaction_type_and_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_entities_by_interaction_type_and_data_model_and_resource">count_entities_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_entities_by_reference">count_entities_by_reference (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_entities_by_resource">count_entities_by_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.entity.Entity.html#pypath.core.entity.Entity.count_entity_type">count_entity_type() (pypath.core.entity.Entity class method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_evidences">count_evidences (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_evidences_by_data_model">count_evidences_by_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_evidences_by_interaction_type">count_evidences_by_interaction_type (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_evidences_by_interaction_type_and_data_model">count_evidences_by_interaction_type_and_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_evidences_by_interaction_type_and_data_model_and_resource">count_evidences_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_evidences_by_reference">count_evidences_by_reference (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_evidences_by_resource">count_evidences_by_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_identifiers">count_identifiers (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.count_identifiers">count_identifiers() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_identifiers_by_data_model">count_identifiers_by_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_identifiers_by_interaction_type">count_identifiers_by_interaction_type (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_identifiers_by_interaction_type_and_data_model">count_identifiers_by_interaction_type_and_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_identifiers_by_interaction_type_and_data_model_and_resource">count_identifiers_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_identifiers_by_reference">count_identifiers_by_reference (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_identifiers_by_resource">count_identifiers_by_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.count_interaction_types">count_interaction_types (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_interaction_types">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_interaction_types_by_data_model">count_interaction_types_by_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_interaction_types_by_interaction_type">count_interaction_types_by_interaction_type (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_interaction_types_by_interaction_type_and_data_model">count_interaction_types_by_interaction_type_and_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_interaction_types_by_interaction_type_and_data_model_and_resource">count_interaction_types_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_interaction_types_by_reference">count_interaction_types_by_reference (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_interaction_types_by_resource">count_interaction_types_by_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_interactions">count_interactions (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.count_interactions">count_interactions() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_interactions_0">count_interactions_0 (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.count_interactions_0">count_interactions_0() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_interactions_0_by_data_model">count_interactions_0_by_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_interactions_0_by_interaction_type">count_interactions_0_by_interaction_type (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_interactions_0_by_interaction_type_and_data_model">count_interactions_0_by_interaction_type_and_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_interactions_0_by_interaction_type_and_data_model_and_resource">count_interactions_0_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_interactions_0_by_reference">count_interactions_0_by_reference (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_interactions_0_by_resource">count_interactions_0_by_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_interactions_by_data_model">count_interactions_by_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_interactions_by_interaction_type">count_interactions_by_interaction_type (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_interactions_by_interaction_type_and_data_model">count_interactions_by_interaction_type_and_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_interactions_by_interaction_type_and_data_model_and_resource">count_interactions_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_interactions_by_reference">count_interactions_by_reference (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_interactions_by_resource">count_interactions_by_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_interactions_directed">count_interactions_directed (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.count_interactions_directed">count_interactions_directed() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_interactions_directed_by_data_model">count_interactions_directed_by_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_interactions_directed_by_interaction_type">count_interactions_directed_by_interaction_type (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_interactions_directed_by_interaction_type_and_data_model">count_interactions_directed_by_interaction_type_and_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_interactions_directed_by_interaction_type_and_data_model_and_resource">count_interactions_directed_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_interactions_directed_by_reference">count_interactions_directed_by_reference (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_interactions_directed_by_resource">count_interactions_directed_by_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_interactions_mutual">count_interactions_mutual (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.count_interactions_mutual">count_interactions_mutual() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_interactions_mutual_by_data_model">count_interactions_mutual_by_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_interactions_mutual_by_interaction_type">count_interactions_mutual_by_interaction_type (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_interactions_mutual_by_interaction_type_and_data_model">count_interactions_mutual_by_interaction_type_and_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_interactions_mutual_by_interaction_type_and_data_model_and_resource">count_interactions_mutual_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_interactions_mutual_by_reference">count_interactions_mutual_by_reference (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_interactions_mutual_by_resource">count_interactions_mutual_by_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_interactions_negative">count_interactions_negative (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.count_interactions_negative">count_interactions_negative() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_interactions_negative_by_data_model">count_interactions_negative_by_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_interactions_negative_by_interaction_type">count_interactions_negative_by_interaction_type (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_interactions_negative_by_interaction_type_and_data_model">count_interactions_negative_by_interaction_type_and_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_interactions_negative_by_interaction_type_and_data_model_and_resource">count_interactions_negative_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_interactions_negative_by_reference">count_interactions_negative_by_reference (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_interactions_negative_by_resource">count_interactions_negative_by_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_interactions_non_directed">count_interactions_non_directed (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.count_interactions_non_directed">count_interactions_non_directed() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_interactions_non_directed_0">count_interactions_non_directed_0 (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_interactions_non_directed_0_by_data_model">count_interactions_non_directed_0_by_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_interactions_non_directed_0_by_interaction_type">count_interactions_non_directed_0_by_interaction_type (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_interactions_non_directed_0_by_interaction_type_and_data_model">count_interactions_non_directed_0_by_interaction_type_and_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_interactions_non_directed_0_by_interaction_type_and_data_model_and_resource">count_interactions_non_directed_0_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_interactions_non_directed_0_by_reference">count_interactions_non_directed_0_by_reference (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_interactions_non_directed_0_by_resource">count_interactions_non_directed_0_by_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_interactions_non_directed_by_data_model">count_interactions_non_directed_by_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_interactions_non_directed_by_interaction_type">count_interactions_non_directed_by_interaction_type (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_interactions_non_directed_by_interaction_type_and_data_model">count_interactions_non_directed_by_interaction_type_and_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_interactions_non_directed_by_interaction_type_and_data_model_and_resource">count_interactions_non_directed_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_interactions_non_directed_by_reference">count_interactions_non_directed_by_reference (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_interactions_non_directed_by_resource">count_interactions_non_directed_by_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_interactions_positive">count_interactions_positive (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.count_interactions_positive">count_interactions_positive() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_interactions_positive_by_data_model">count_interactions_positive_by_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_interactions_positive_by_interaction_type">count_interactions_positive_by_interaction_type (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_interactions_positive_by_interaction_type_and_data_model">count_interactions_positive_by_interaction_type_and_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_interactions_positive_by_interaction_type_and_data_model_and_resource">count_interactions_positive_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_interactions_positive_by_reference">count_interactions_positive_by_reference (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_interactions_positive_by_resource">count_interactions_positive_by_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_interactions_signed">count_interactions_signed (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.count_interactions_signed">count_interactions_signed() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_interactions_signed_by_data_model">count_interactions_signed_by_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_interactions_signed_by_interaction_type">count_interactions_signed_by_interaction_type (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_interactions_signed_by_interaction_type_and_data_model">count_interactions_signed_by_interaction_type_and_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_interactions_signed_by_interaction_type_and_data_model_and_resource">count_interactions_signed_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_interactions_signed_by_reference">count_interactions_signed_by_reference (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_interactions_signed_by_resource">count_interactions_signed_by_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_interactions_undirected">count_interactions_undirected (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.count_interactions_undirected">count_interactions_undirected() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_interactions_undirected_0">count_interactions_undirected_0 (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_interactions_undirected_0_by_data_model">count_interactions_undirected_0_by_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_interactions_undirected_0_by_interaction_type">count_interactions_undirected_0_by_interaction_type (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_interactions_undirected_0_by_interaction_type_and_data_model">count_interactions_undirected_0_by_interaction_type_and_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_interactions_undirected_0_by_interaction_type_and_data_model_and_resource">count_interactions_undirected_0_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_interactions_undirected_0_by_reference">count_interactions_undirected_0_by_reference (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_interactions_undirected_0_by_resource">count_interactions_undirected_0_by_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_interactions_undirected_by_data_model">count_interactions_undirected_by_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_interactions_undirected_by_interaction_type">count_interactions_undirected_by_interaction_type (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_interactions_undirected_by_interaction_type_and_data_model">count_interactions_undirected_by_interaction_type_and_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_interactions_undirected_by_interaction_type_and_data_model_and_resource">count_interactions_undirected_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_interactions_undirected_by_reference">count_interactions_undirected_by_reference (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_interactions_undirected_by_resource">count_interactions_undirected_by_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_labels">count_labels (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.count_labels">count_labels() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_labels_by_data_model">count_labels_by_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_labels_by_interaction_type">count_labels_by_interaction_type (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_labels_by_interaction_type_and_data_model">count_labels_by_interaction_type_and_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_labels_by_interaction_type_and_data_model_and_resource">count_labels_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_labels_by_reference">count_labels_by_reference (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_labels_by_resource">count_labels_by_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_lncrna_identifiers">count_lncrna_identifiers (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.count_lncrna_identifiers">count_lncrna_identifiers() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_lncrna_identifiers_by_data_model">count_lncrna_identifiers_by_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_lncrna_identifiers_by_interaction_type">count_lncrna_identifiers_by_interaction_type (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_lncrna_identifiers_by_interaction_type_and_data_model">count_lncrna_identifiers_by_interaction_type_and_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_lncrna_identifiers_by_interaction_type_and_data_model_and_resource">count_lncrna_identifiers_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_lncrna_identifiers_by_reference">count_lncrna_identifiers_by_reference (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_lncrna_identifiers_by_resource">count_lncrna_identifiers_by_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_lncrna_labels">count_lncrna_labels (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.count_lncrna_labels">count_lncrna_labels() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_lncrna_labels_by_data_model">count_lncrna_labels_by_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_lncrna_labels_by_interaction_type">count_lncrna_labels_by_interaction_type (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_lncrna_labels_by_interaction_type_and_data_model">count_lncrna_labels_by_interaction_type_and_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_lncrna_labels_by_interaction_type_and_data_model_and_resource">count_lncrna_labels_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_lncrna_labels_by_reference">count_lncrna_labels_by_reference (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_lncrna_labels_by_resource">count_lncrna_labels_by_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_lncrnas">count_lncrnas (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.count_lncrnas">count_lncrnas() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_lncrnas_by_data_model">count_lncrnas_by_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_lncrnas_by_interaction_type">count_lncrnas_by_interaction_type (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_lncrnas_by_interaction_type_and_data_model">count_lncrnas_by_interaction_type_and_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_lncrnas_by_interaction_type_and_data_model_and_resource">count_lncrnas_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_lncrnas_by_reference">count_lncrnas_by_reference (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_lncrnas_by_resource">count_lncrnas_by_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_mirna_identifiers">count_mirna_identifiers (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.count_mirna_identifiers">count_mirna_identifiers() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_mirna_identifiers_by_data_model">count_mirna_identifiers_by_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_mirna_identifiers_by_interaction_type">count_mirna_identifiers_by_interaction_type (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_mirna_identifiers_by_interaction_type_and_data_model">count_mirna_identifiers_by_interaction_type_and_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_mirna_identifiers_by_interaction_type_and_data_model_and_resource">count_mirna_identifiers_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_mirna_identifiers_by_reference">count_mirna_identifiers_by_reference (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_mirna_identifiers_by_resource">count_mirna_identifiers_by_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_mirna_labels">count_mirna_labels (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.count_mirna_labels">count_mirna_labels() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_mirna_labels_by_data_model">count_mirna_labels_by_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_mirna_labels_by_interaction_type">count_mirna_labels_by_interaction_type (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_mirna_labels_by_interaction_type_and_data_model">count_mirna_labels_by_interaction_type_and_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_mirna_labels_by_interaction_type_and_data_model_and_resource">count_mirna_labels_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_mirna_labels_by_reference">count_mirna_labels_by_reference (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_mirna_labels_by_resource">count_mirna_labels_by_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_mirnas">count_mirnas (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.count_mirnas">count_mirnas() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_mirnas_by_data_model">count_mirnas_by_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_mirnas_by_interaction_type">count_mirnas_by_interaction_type (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_mirnas_by_interaction_type_and_data_model">count_mirnas_by_interaction_type_and_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_mirnas_by_interaction_type_and_data_model_and_resource">count_mirnas_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_mirnas_by_reference">count_mirnas_by_reference (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_mirnas_by_resource">count_mirnas_by_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_partners">count_partners() (pypath.core.network.Network method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_post_transcriptionally_activated_by">count_post_transcriptionally_activated_by (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_post_transcriptionally_activates">count_post_transcriptionally_activates (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_post_transcriptionally_regulated_by">count_post_transcriptionally_regulated_by (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_post_transcriptionally_regulates">count_post_transcriptionally_regulates (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_post_transcriptionally_suppressed_by">count_post_transcriptionally_suppressed_by (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_post_transcriptionally_suppresses">count_post_transcriptionally_suppresses (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_post_translationally_activated_by">count_post_translationally_activated_by (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_post_translationally_activates">count_post_translationally_activates (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_post_translationally_regulated_by">count_post_translationally_regulated_by (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_post_translationally_regulates">count_post_translationally_regulates (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_post_translationally_suppressed_by">count_post_translationally_suppressed_by (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_post_translationally_suppresses">count_post_translationally_suppresses (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_protein_identifiers">count_protein_identifiers (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.count_protein_identifiers">count_protein_identifiers() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_protein_identifiers_by_data_model">count_protein_identifiers_by_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_protein_identifiers_by_interaction_type">count_protein_identifiers_by_interaction_type (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_protein_identifiers_by_interaction_type_and_data_model">count_protein_identifiers_by_interaction_type_and_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_protein_identifiers_by_interaction_type_and_data_model_and_resource">count_protein_identifiers_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_protein_identifiers_by_reference">count_protein_identifiers_by_reference (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_protein_identifiers_by_resource">count_protein_identifiers_by_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_protein_labels">count_protein_labels (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.count_protein_labels">count_protein_labels() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_protein_labels_by_data_model">count_protein_labels_by_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_protein_labels_by_interaction_type">count_protein_labels_by_interaction_type (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_protein_labels_by_interaction_type_and_data_model">count_protein_labels_by_interaction_type_and_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_protein_labels_by_interaction_type_and_data_model_and_resource">count_protein_labels_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_protein_labels_by_reference">count_protein_labels_by_reference (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_protein_labels_by_resource">count_protein_labels_by_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_proteins">count_proteins (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.count_proteins">count_proteins() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_proteins_by_data_model">count_proteins_by_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_proteins_by_interaction_type">count_proteins_by_interaction_type (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_proteins_by_interaction_type_and_data_model">count_proteins_by_interaction_type_and_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_proteins_by_interaction_type_and_data_model_and_resource">count_proteins_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_proteins_by_reference">count_proteins_by_reference (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_proteins_by_resource">count_proteins_by_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.count_references">count_references (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_references">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_references_by_data_model">count_references_by_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_references_by_interaction_type">count_references_by_interaction_type (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_references_by_interaction_type_and_data_model">count_references_by_interaction_type_and_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_references_by_interaction_type_and_data_model_and_resource">count_references_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_references_by_reference">count_references_by_reference (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_references_by_resource">count_references_by_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_regulated_by">count_regulated_by (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_regulates">count_regulates (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.count_resource_names">count_resource_names (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_resource_names">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_resource_names_by_data_model">count_resource_names_by_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_resource_names_by_interaction_type">count_resource_names_by_interaction_type (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_resource_names_by_interaction_type_and_data_model">count_resource_names_by_interaction_type_and_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_resource_names_by_interaction_type_and_data_model_and_resource">count_resource_names_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_resource_names_by_reference">count_resource_names_by_reference (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_resource_names_by_resource">count_resource_names_by_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.count_resource_names_via">count_resource_names_via (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_resource_names_via">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_resource_names_via_by_data_model">count_resource_names_via_by_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_resource_names_via_by_interaction_type">count_resource_names_via_by_interaction_type (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_resource_names_via_by_interaction_type_and_data_model">count_resource_names_via_by_interaction_type_and_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_resource_names_via_by_interaction_type_and_data_model_and_resource">count_resource_names_via_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_resource_names_via_by_reference">count_resource_names_via_by_reference (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_resource_names_via_by_resource">count_resource_names_via_by_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.count_resources">count_resources (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_resources">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_resources_by_data_model">count_resources_by_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_resources_by_interaction_type">count_resources_by_interaction_type (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_resources_by_interaction_type_and_data_model">count_resources_by_interaction_type_and_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_resources_by_interaction_type_and_data_model_and_resource">count_resources_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_resources_by_reference">count_resources_by_reference (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_resources_by_resource">count_resources_by_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.count_resources_via">count_resources_via (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_resources_via">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_resources_via_by_data_model">count_resources_via_by_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_resources_via_by_interaction_type">count_resources_via_by_interaction_type (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_resources_via_by_interaction_type_and_data_model">count_resources_via_by_interaction_type_and_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_resources_via_by_interaction_type_and_data_model_and_resource">count_resources_via_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_resources_via_by_reference">count_resources_via_by_reference (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_resources_via_by_resource">count_resources_via_by_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_small_molecule_identifiers">count_small_molecule_identifiers (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.count_small_molecule_identifiers">count_small_molecule_identifiers() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_small_molecule_identifiers_by_data_model">count_small_molecule_identifiers_by_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_small_molecule_identifiers_by_interaction_type">count_small_molecule_identifiers_by_interaction_type (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_small_molecule_identifiers_by_interaction_type_and_data_model">count_small_molecule_identifiers_by_interaction_type_and_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_small_molecule_identifiers_by_interaction_type_and_data_model_and_resource">count_small_molecule_identifiers_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_small_molecule_identifiers_by_reference">count_small_molecule_identifiers_by_reference (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_small_molecule_identifiers_by_resource">count_small_molecule_identifiers_by_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_small_molecule_labels">count_small_molecule_labels (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.count_small_molecule_labels">count_small_molecule_labels() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_small_molecule_labels_by_data_model">count_small_molecule_labels_by_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_small_molecule_labels_by_interaction_type">count_small_molecule_labels_by_interaction_type (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_small_molecule_labels_by_interaction_type_and_data_model">count_small_molecule_labels_by_interaction_type_and_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_small_molecule_labels_by_interaction_type_and_data_model_and_resource">count_small_molecule_labels_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_small_molecule_labels_by_reference">count_small_molecule_labels_by_reference (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_small_molecule_labels_by_resource">count_small_molecule_labels_by_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_small_molecules">count_small_molecules (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.count_small_molecules">count_small_molecules() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_small_molecules_by_data_model">count_small_molecules_by_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_small_molecules_by_interaction_type">count_small_molecules_by_interaction_type (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_small_molecules_by_interaction_type_and_data_model">count_small_molecules_by_interaction_type_and_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_small_molecules_by_interaction_type_and_data_model_and_resource">count_small_molecules_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_small_molecules_by_reference">count_small_molecules_by_reference (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_small_molecules_by_resource">count_small_molecules_by_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_suppressed_by">count_suppressed_by (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_suppresses">count_suppresses (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_transcriptionally_activated_by">count_transcriptionally_activated_by (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_transcriptionally_activates">count_transcriptionally_activates (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_transcriptionally_regulated_by">count_transcriptionally_regulated_by (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_transcriptionally_regulates">count_transcriptionally_regulates (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_transcriptionally_suppressed_by">count_transcriptionally_suppressed_by (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.count_transcriptionally_suppresses">count_transcriptionally_suppresses (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.annot.CustomAnnotation.html#pypath.core.annot.CustomAnnotation.counts">counts() (pypath.core.annot.CustomAnnotation method)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.intercell.IntercellAnnotation.html#pypath.core.intercell.IntercellAnnotation.counts">(pypath.core.intercell.IntercellAnnotation method)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.annot.CustomAnnotation.html#pypath.core.annot.CustomAnnotation.counts_by_class">counts_by_class() (pypath.core.annot.CustomAnnotation method)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.intercell.IntercellAnnotation.html#pypath.core.intercell.IntercellAnnotation.counts_by_class">(pypath.core.intercell.IntercellAnnotation method)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.annot.Adhesome.html#pypath.core.annot.Adhesome.coverage">coverage() (pypath.core.annot.Adhesome method)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.annot.Almen2009.html#pypath.core.annot.Almen2009.coverage">(pypath.core.annot.Almen2009 method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.AnnotationBase.html#pypath.core.annot.AnnotationBase.coverage">(pypath.core.annot.AnnotationBase method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Baccin2019.html#pypath.core.annot.Baccin2019.coverage">(pypath.core.annot.Baccin2019 method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Biogps.html#pypath.core.annot.Biogps.coverage">(pypath.core.annot.Biogps method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cancerdrugsdb.html#pypath.core.annot.Cancerdrugsdb.coverage">(pypath.core.annot.Cancerdrugsdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CancerGeneCensus.html#pypath.core.annot.CancerGeneCensus.coverage">(pypath.core.annot.CancerGeneCensus method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cancersea.html#pypath.core.annot.Cancersea.coverage">(pypath.core.annot.Cancersea method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cellcall.html#pypath.core.annot.Cellcall.coverage">(pypath.core.annot.Cellcall method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cellcellinteractions.html#pypath.core.annot.Cellcellinteractions.coverage">(pypath.core.annot.Cellcellinteractions method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cellchatdb.html#pypath.core.annot.Cellchatdb.coverage">(pypath.core.annot.Cellchatdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CellchatdbComplex.html#pypath.core.annot.CellchatdbComplex.coverage">(pypath.core.annot.CellchatdbComplex method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cellinker.html#pypath.core.annot.Cellinker.coverage">(pypath.core.annot.Cellinker method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CellinkerComplex.html#pypath.core.annot.CellinkerComplex.coverage">(pypath.core.annot.CellinkerComplex method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CellPhoneDB.html#pypath.core.annot.CellPhoneDB.coverage">(pypath.core.annot.CellPhoneDB method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CellPhoneDBComplex.html#pypath.core.annot.CellPhoneDBComplex.coverage">(pypath.core.annot.CellPhoneDBComplex method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CellSurfaceProteinAtlas.html#pypath.core.annot.CellSurfaceProteinAtlas.coverage">(pypath.core.annot.CellSurfaceProteinAtlas method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CellSurfaceProteinAtlasCellType.html#pypath.core.annot.CellSurfaceProteinAtlasCellType.coverage">(pypath.core.annot.CellSurfaceProteinAtlasCellType method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Celltalkdb.html#pypath.core.annot.Celltalkdb.coverage">(pypath.core.annot.Celltalkdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Celltypist.html#pypath.core.annot.Celltypist.coverage">(pypath.core.annot.Celltypist method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Comppi.html#pypath.core.annot.Comppi.coverage">(pypath.core.annot.Comppi method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Connectomedb.html#pypath.core.annot.Connectomedb.coverage">(pypath.core.annot.Connectomedb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Corum.html#pypath.core.annot.Corum.coverage">(pypath.core.annot.Corum method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CorumFuncat.html#pypath.core.annot.CorumFuncat.coverage">(pypath.core.annot.CorumFuncat method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CorumGO.html#pypath.core.annot.CorumGO.coverage">(pypath.core.annot.CorumGO method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cpad.html#pypath.core.annot.Cpad.coverage">(pypath.core.annot.Cpad method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cytosig.html#pypath.core.annot.Cytosig.coverage">(pypath.core.annot.Cytosig method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Dgidb.html#pypath.core.annot.Dgidb.coverage">(pypath.core.annot.Dgidb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Disgenet.html#pypath.core.annot.Disgenet.coverage">(pypath.core.annot.Disgenet method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Embrace.html#pypath.core.annot.Embrace.coverage">(pypath.core.annot.Embrace method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Exocarta.html#pypath.core.annot.Exocarta.coverage">(pypath.core.annot.Exocarta method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.GOIntercell.html#pypath.core.annot.GOIntercell.coverage">(pypath.core.annot.GOIntercell method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Gpcrdb.html#pypath.core.annot.Gpcrdb.coverage">(pypath.core.annot.Gpcrdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.GuideToPharmacology.html#pypath.core.annot.GuideToPharmacology.coverage">(pypath.core.annot.GuideToPharmacology method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Hgnc.html#pypath.core.annot.Hgnc.coverage">(pypath.core.annot.Hgnc method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.HpmrComplex.html#pypath.core.annot.HpmrComplex.coverage">(pypath.core.annot.HpmrComplex method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.HPO.html#pypath.core.annot.HPO.coverage">(pypath.core.annot.HPO method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Humancellmap.html#pypath.core.annot.Humancellmap.coverage">(pypath.core.annot.Humancellmap method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.HumanPlasmaMembraneReceptome.html#pypath.core.annot.HumanPlasmaMembraneReceptome.coverage">(pypath.core.annot.HumanPlasmaMembraneReceptome method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.HumanProteinAtlas.html#pypath.core.annot.HumanProteinAtlas.coverage">(pypath.core.annot.HumanProteinAtlas method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.HumanProteinAtlasSecretome.html#pypath.core.annot.HumanProteinAtlasSecretome.coverage">(pypath.core.annot.HumanProteinAtlasSecretome method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.HumanProteinAtlasSubcellular.html#pypath.core.annot.HumanProteinAtlasSubcellular.coverage">(pypath.core.annot.HumanProteinAtlasSubcellular method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Icellnet.html#pypath.core.annot.Icellnet.coverage">(pypath.core.annot.Icellnet method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.IcellnetComplex.html#pypath.core.annot.IcellnetComplex.coverage">(pypath.core.annot.IcellnetComplex method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Integrins.html#pypath.core.annot.Integrins.coverage">(pypath.core.annot.Integrins method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.InterPro.html#pypath.core.annot.InterPro.coverage">(pypath.core.annot.InterPro method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Intogen.html#pypath.core.annot.Intogen.coverage">(pypath.core.annot.Intogen method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Italk.html#pypath.core.annot.Italk.coverage">(pypath.core.annot.Italk method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.KeggPathways.html#pypath.core.annot.KeggPathways.coverage">(pypath.core.annot.KeggPathways method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.KeggPathwaysPC.html#pypath.core.annot.KeggPathwaysPC.coverage">(pypath.core.annot.KeggPathwaysPC method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Kinasedotcom.html#pypath.core.annot.Kinasedotcom.coverage">(pypath.core.annot.Kinasedotcom method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Kirouac2010.html#pypath.core.annot.Kirouac2010.coverage">(pypath.core.annot.Kirouac2010 method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Lambert2018.html#pypath.core.annot.Lambert2018.coverage">(pypath.core.annot.Lambert2018 method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.LigandReceptor.html#pypath.core.annot.LigandReceptor.coverage">(pypath.core.annot.LigandReceptor method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Locate.html#pypath.core.annot.Locate.coverage">(pypath.core.annot.Locate method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Lrdb.html#pypath.core.annot.Lrdb.coverage">(pypath.core.annot.Lrdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Matrisome.html#pypath.core.annot.Matrisome.coverage">(pypath.core.annot.Matrisome method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Matrixdb.html#pypath.core.annot.Matrixdb.coverage">(pypath.core.annot.Matrixdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Mcam.html#pypath.core.annot.Mcam.coverage">(pypath.core.annot.Mcam method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Membranome.html#pypath.core.annot.Membranome.coverage">(pypath.core.annot.Membranome method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Msigdb.html#pypath.core.annot.Msigdb.coverage">(pypath.core.annot.Msigdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.NetpathPathways.html#pypath.core.annot.NetpathPathways.coverage">(pypath.core.annot.NetpathPathways method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Opm.html#pypath.core.annot.Opm.coverage">(pypath.core.annot.Opm method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Panglaodb.html#pypath.core.annot.Panglaodb.coverage">(pypath.core.annot.Panglaodb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Phobius.html#pypath.core.annot.Phobius.coverage">(pypath.core.annot.Phobius method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Phosphatome.html#pypath.core.annot.Phosphatome.coverage">(pypath.core.annot.Phosphatome method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Progeny.html#pypath.core.annot.Progeny.coverage">(pypath.core.annot.Progeny method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Ramilowski2015.html#pypath.core.annot.Ramilowski2015.coverage">(pypath.core.annot.Ramilowski2015 method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Ramilowski2015Location.html#pypath.core.annot.Ramilowski2015Location.coverage">(pypath.core.annot.Ramilowski2015Location method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Scconnect.html#pypath.core.annot.Scconnect.coverage">(pypath.core.annot.Scconnect method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.ScconnectComplex.html#pypath.core.annot.ScconnectComplex.coverage">(pypath.core.annot.ScconnectComplex method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.SignalinkFunctions.html#pypath.core.annot.SignalinkFunctions.coverage">(pypath.core.annot.SignalinkFunctions method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.SignalinkPathways.html#pypath.core.annot.SignalinkPathways.coverage">(pypath.core.annot.SignalinkPathways method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.SignorPathways.html#pypath.core.annot.SignorPathways.coverage">(pypath.core.annot.SignorPathways method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Surfaceome.html#pypath.core.annot.Surfaceome.coverage">(pypath.core.annot.Surfaceome method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Talklr.html#pypath.core.annot.Talklr.coverage">(pypath.core.annot.Talklr method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Tcdb.html#pypath.core.annot.Tcdb.coverage">(pypath.core.annot.Tcdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Tfcensus.html#pypath.core.annot.Tfcensus.coverage">(pypath.core.annot.Tfcensus method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Topdb.html#pypath.core.annot.Topdb.coverage">(pypath.core.annot.Topdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.UniprotFamilies.html#pypath.core.annot.UniprotFamilies.coverage">(pypath.core.annot.UniprotFamilies method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.UniprotKeywords.html#pypath.core.annot.UniprotKeywords.coverage">(pypath.core.annot.UniprotKeywords method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.UniprotLocations.html#pypath.core.annot.UniprotLocations.coverage">(pypath.core.annot.UniprotLocations method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.UniprotTissues.html#pypath.core.annot.UniprotTissues.coverage">(pypath.core.annot.UniprotTissues method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.UniprotTopologies.html#pypath.core.annot.UniprotTopologies.coverage">(pypath.core.annot.UniprotTopologies method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Vesiclepedia.html#pypath.core.annot.Vesiclepedia.coverage">(pypath.core.annot.Vesiclepedia method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Wang.html#pypath.core.annot.Wang.coverage">(pypath.core.annot.Wang method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Zhong2015.html#pypath.core.annot.Zhong2015.coverage">(pypath.core.annot.Zhong2015 method)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.annot.Cpad.html#pypath.core.annot.Cpad">Cpad (class in pypath.core.annot)</a>
+</li>
+      <li><a href="api/pypath.inputs.cpad.cpad_annotations.html#pypath.inputs.cpad.cpad_annotations">cpad_annotations() (in module pypath.inputs.cpad)</a>
+</li>
+      <li><a href="api/pypath.inputs.cpad.cpad_pathway_cancer.html#pypath.inputs.cpad.cpad_pathway_cancer">cpad_pathway_cancer() (in module pypath.inputs.cpad)</a>
+</li>
+      <li><a href="api/pypath.inputs.cpdb.cpdb_interactions.html#pypath.inputs.cpdb.cpdb_interactions">cpdb_interactions() (in module pypath.inputs.cpdb)</a>
+</li>
+      <li><a href="api/pypath.inputs.cpdb.cpdb_interactions_ltp.html#pypath.inputs.cpdb.cpdb_interactions_ltp">cpdb_interactions_ltp() (in module pypath.inputs.cpdb)</a>
+</li>
+      <li><a href="api/pypath.core.annot.CustomAnnotation.html#pypath.core.annot.CustomAnnotation.create_class">create_class() (pypath.core.annot.CustomAnnotation method)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.intercell.IntercellAnnotation.html#pypath.core.intercell.IntercellAnnotation.create_class">(pypath.core.intercell.IntercellAnnotation method)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.utils.mapping.Mapper.html#pypath.utils.mapping.Mapper.create_reverse">create_reverse() (pypath.utils.mapping.Mapper method)</a>
+</li>
+      <li><a href="api/pypath.inputs.credentials.credentials.html#pypath.inputs.credentials.credentials">credentials() (in module pypath.inputs.credentials)</a>
+</li>
+      <li><a href="api/pypath.inputs.cspa.cspa_annotations.html#pypath.inputs.cspa.cspa_annotations">cspa_annotations() (in module pypath.inputs.cspa)</a>
+</li>
+      <li><a href="api/pypath.inputs.cspa.cspa_cell_type_annotations.html#pypath.inputs.cspa.cspa_cell_type_annotations">cspa_cell_type_annotations() (in module pypath.inputs.cspa)</a>
+</li>
+      <li><a href="api/pypath.inputs.cspa.cspa_cell_types.html#pypath.inputs.cspa.cspa_cell_types">cspa_cell_types() (in module pypath.inputs.cspa)</a>
+</li>
+      <li><a href="api/pypath.inputs.common.csv_sep_change.html#pypath.inputs.common.csv_sep_change">csv_sep_change() (in module pypath.inputs.common)</a>
+</li>
+      <li><a href="api/pypath.inputs.ctdbase.ctdbase_relations.html#pypath.inputs.ctdbase.ctdbase_relations">ctdbase_relations() (in module pypath.inputs.ctdbase)</a>
+</li>
+      <li><a href="api/pypath.inputs.ctdbase.ctdbase_vocabulary.html#pypath.inputs.ctdbase.ctdbase_vocabulary">ctdbase_vocabulary() (in module pypath.inputs.ctdbase)</a>
+</li>
+      <li><a href="api/pypath.inputs.wang.cui_interactions.html#pypath.inputs.wang.cui_interactions">cui_interactions() (in module pypath.inputs.wang)</a>
+</li>
+      <li><a href="api/pypath.inputs.dorothea.DorotheaInteraction.html#pypath.inputs.dorothea.DorotheaInteraction.curated">curated (pypath.inputs.dorothea.DorotheaInteraction attribute)</a>
+</li>
+      <li><a href="api/pypath.omnipath.param.curated_ppi_resources.html#pypath.omnipath.param.curated_ppi_resources">curated_ppi_resources() (in module pypath.omnipath.param)</a>
+</li>
+      <li><a href="api/pypath.inputs.dorothea.DorotheaInteraction.html#pypath.inputs.dorothea.DorotheaInteraction.curated_sources">curated_sources (pypath.inputs.dorothea.DorotheaInteraction attribute)</a>
+</li>
+      <li><a href="api/pypath.core.annot.Adhesome.html#pypath.core.annot.Adhesome.curation_effort">curation_effort() (pypath.core.annot.Adhesome method)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.annot.Almen2009.html#pypath.core.annot.Almen2009.curation_effort">(pypath.core.annot.Almen2009 method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.AnnotationBase.html#pypath.core.annot.AnnotationBase.curation_effort">(pypath.core.annot.AnnotationBase method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Baccin2019.html#pypath.core.annot.Baccin2019.curation_effort">(pypath.core.annot.Baccin2019 method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Biogps.html#pypath.core.annot.Biogps.curation_effort">(pypath.core.annot.Biogps method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cancerdrugsdb.html#pypath.core.annot.Cancerdrugsdb.curation_effort">(pypath.core.annot.Cancerdrugsdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CancerGeneCensus.html#pypath.core.annot.CancerGeneCensus.curation_effort">(pypath.core.annot.CancerGeneCensus method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cancersea.html#pypath.core.annot.Cancersea.curation_effort">(pypath.core.annot.Cancersea method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cellcall.html#pypath.core.annot.Cellcall.curation_effort">(pypath.core.annot.Cellcall method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cellcellinteractions.html#pypath.core.annot.Cellcellinteractions.curation_effort">(pypath.core.annot.Cellcellinteractions method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cellchatdb.html#pypath.core.annot.Cellchatdb.curation_effort">(pypath.core.annot.Cellchatdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CellchatdbComplex.html#pypath.core.annot.CellchatdbComplex.curation_effort">(pypath.core.annot.CellchatdbComplex method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cellinker.html#pypath.core.annot.Cellinker.curation_effort">(pypath.core.annot.Cellinker method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CellinkerComplex.html#pypath.core.annot.CellinkerComplex.curation_effort">(pypath.core.annot.CellinkerComplex method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CellPhoneDB.html#pypath.core.annot.CellPhoneDB.curation_effort">(pypath.core.annot.CellPhoneDB method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CellPhoneDBComplex.html#pypath.core.annot.CellPhoneDBComplex.curation_effort">(pypath.core.annot.CellPhoneDBComplex method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CellSurfaceProteinAtlas.html#pypath.core.annot.CellSurfaceProteinAtlas.curation_effort">(pypath.core.annot.CellSurfaceProteinAtlas method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CellSurfaceProteinAtlasCellType.html#pypath.core.annot.CellSurfaceProteinAtlasCellType.curation_effort">(pypath.core.annot.CellSurfaceProteinAtlasCellType method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Celltalkdb.html#pypath.core.annot.Celltalkdb.curation_effort">(pypath.core.annot.Celltalkdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Celltypist.html#pypath.core.annot.Celltypist.curation_effort">(pypath.core.annot.Celltypist method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Comppi.html#pypath.core.annot.Comppi.curation_effort">(pypath.core.annot.Comppi method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Connectomedb.html#pypath.core.annot.Connectomedb.curation_effort">(pypath.core.annot.Connectomedb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Corum.html#pypath.core.annot.Corum.curation_effort">(pypath.core.annot.Corum method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CorumFuncat.html#pypath.core.annot.CorumFuncat.curation_effort">(pypath.core.annot.CorumFuncat method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CorumGO.html#pypath.core.annot.CorumGO.curation_effort">(pypath.core.annot.CorumGO method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cpad.html#pypath.core.annot.Cpad.curation_effort">(pypath.core.annot.Cpad method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cytosig.html#pypath.core.annot.Cytosig.curation_effort">(pypath.core.annot.Cytosig method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Dgidb.html#pypath.core.annot.Dgidb.curation_effort">(pypath.core.annot.Dgidb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Disgenet.html#pypath.core.annot.Disgenet.curation_effort">(pypath.core.annot.Disgenet method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Embrace.html#pypath.core.annot.Embrace.curation_effort">(pypath.core.annot.Embrace method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Exocarta.html#pypath.core.annot.Exocarta.curation_effort">(pypath.core.annot.Exocarta method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.GOIntercell.html#pypath.core.annot.GOIntercell.curation_effort">(pypath.core.annot.GOIntercell method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Gpcrdb.html#pypath.core.annot.Gpcrdb.curation_effort">(pypath.core.annot.Gpcrdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.GuideToPharmacology.html#pypath.core.annot.GuideToPharmacology.curation_effort">(pypath.core.annot.GuideToPharmacology method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Hgnc.html#pypath.core.annot.Hgnc.curation_effort">(pypath.core.annot.Hgnc method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.HpmrComplex.html#pypath.core.annot.HpmrComplex.curation_effort">(pypath.core.annot.HpmrComplex method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.HPO.html#pypath.core.annot.HPO.curation_effort">(pypath.core.annot.HPO method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Humancellmap.html#pypath.core.annot.Humancellmap.curation_effort">(pypath.core.annot.Humancellmap method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.HumanPlasmaMembraneReceptome.html#pypath.core.annot.HumanPlasmaMembraneReceptome.curation_effort">(pypath.core.annot.HumanPlasmaMembraneReceptome method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.HumanProteinAtlas.html#pypath.core.annot.HumanProteinAtlas.curation_effort">(pypath.core.annot.HumanProteinAtlas method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.HumanProteinAtlasSecretome.html#pypath.core.annot.HumanProteinAtlasSecretome.curation_effort">(pypath.core.annot.HumanProteinAtlasSecretome method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.HumanProteinAtlasSubcellular.html#pypath.core.annot.HumanProteinAtlasSubcellular.curation_effort">(pypath.core.annot.HumanProteinAtlasSubcellular method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Icellnet.html#pypath.core.annot.Icellnet.curation_effort">(pypath.core.annot.Icellnet method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.IcellnetComplex.html#pypath.core.annot.IcellnetComplex.curation_effort">(pypath.core.annot.IcellnetComplex method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Integrins.html#pypath.core.annot.Integrins.curation_effort">(pypath.core.annot.Integrins method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.InterPro.html#pypath.core.annot.InterPro.curation_effort">(pypath.core.annot.InterPro method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Intogen.html#pypath.core.annot.Intogen.curation_effort">(pypath.core.annot.Intogen method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Italk.html#pypath.core.annot.Italk.curation_effort">(pypath.core.annot.Italk method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.KeggPathways.html#pypath.core.annot.KeggPathways.curation_effort">(pypath.core.annot.KeggPathways method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.KeggPathwaysPC.html#pypath.core.annot.KeggPathwaysPC.curation_effort">(pypath.core.annot.KeggPathwaysPC method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Kinasedotcom.html#pypath.core.annot.Kinasedotcom.curation_effort">(pypath.core.annot.Kinasedotcom method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Kirouac2010.html#pypath.core.annot.Kirouac2010.curation_effort">(pypath.core.annot.Kirouac2010 method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Lambert2018.html#pypath.core.annot.Lambert2018.curation_effort">(pypath.core.annot.Lambert2018 method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.LigandReceptor.html#pypath.core.annot.LigandReceptor.curation_effort">(pypath.core.annot.LigandReceptor method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Locate.html#pypath.core.annot.Locate.curation_effort">(pypath.core.annot.Locate method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Lrdb.html#pypath.core.annot.Lrdb.curation_effort">(pypath.core.annot.Lrdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Matrisome.html#pypath.core.annot.Matrisome.curation_effort">(pypath.core.annot.Matrisome method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Matrixdb.html#pypath.core.annot.Matrixdb.curation_effort">(pypath.core.annot.Matrixdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Mcam.html#pypath.core.annot.Mcam.curation_effort">(pypath.core.annot.Mcam method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Membranome.html#pypath.core.annot.Membranome.curation_effort">(pypath.core.annot.Membranome method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Msigdb.html#pypath.core.annot.Msigdb.curation_effort">(pypath.core.annot.Msigdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.NetpathPathways.html#pypath.core.annot.NetpathPathways.curation_effort">(pypath.core.annot.NetpathPathways method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Opm.html#pypath.core.annot.Opm.curation_effort">(pypath.core.annot.Opm method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Panglaodb.html#pypath.core.annot.Panglaodb.curation_effort">(pypath.core.annot.Panglaodb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Phobius.html#pypath.core.annot.Phobius.curation_effort">(pypath.core.annot.Phobius method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Phosphatome.html#pypath.core.annot.Phosphatome.curation_effort">(pypath.core.annot.Phosphatome method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Progeny.html#pypath.core.annot.Progeny.curation_effort">(pypath.core.annot.Progeny method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Ramilowski2015.html#pypath.core.annot.Ramilowski2015.curation_effort">(pypath.core.annot.Ramilowski2015 method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Ramilowski2015Location.html#pypath.core.annot.Ramilowski2015Location.curation_effort">(pypath.core.annot.Ramilowski2015Location method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Scconnect.html#pypath.core.annot.Scconnect.curation_effort">(pypath.core.annot.Scconnect method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.ScconnectComplex.html#pypath.core.annot.ScconnectComplex.curation_effort">(pypath.core.annot.ScconnectComplex method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.SignalinkFunctions.html#pypath.core.annot.SignalinkFunctions.curation_effort">(pypath.core.annot.SignalinkFunctions method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.SignalinkPathways.html#pypath.core.annot.SignalinkPathways.curation_effort">(pypath.core.annot.SignalinkPathways method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.SignorPathways.html#pypath.core.annot.SignorPathways.curation_effort">(pypath.core.annot.SignorPathways method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Surfaceome.html#pypath.core.annot.Surfaceome.curation_effort">(pypath.core.annot.Surfaceome method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Talklr.html#pypath.core.annot.Talklr.curation_effort">(pypath.core.annot.Talklr method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Tcdb.html#pypath.core.annot.Tcdb.curation_effort">(pypath.core.annot.Tcdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Tfcensus.html#pypath.core.annot.Tfcensus.curation_effort">(pypath.core.annot.Tfcensus method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Topdb.html#pypath.core.annot.Topdb.curation_effort">(pypath.core.annot.Topdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.UniprotFamilies.html#pypath.core.annot.UniprotFamilies.curation_effort">(pypath.core.annot.UniprotFamilies method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.UniprotKeywords.html#pypath.core.annot.UniprotKeywords.curation_effort">(pypath.core.annot.UniprotKeywords method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.UniprotLocations.html#pypath.core.annot.UniprotLocations.curation_effort">(pypath.core.annot.UniprotLocations method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.UniprotTissues.html#pypath.core.annot.UniprotTissues.curation_effort">(pypath.core.annot.UniprotTissues method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.UniprotTopologies.html#pypath.core.annot.UniprotTopologies.curation_effort">(pypath.core.annot.UniprotTopologies method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Vesiclepedia.html#pypath.core.annot.Vesiclepedia.curation_effort">(pypath.core.annot.Vesiclepedia method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Wang.html#pypath.core.annot.Wang.curation_effort">(pypath.core.annot.Wang method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Zhong2015.html#pypath.core.annot.Zhong2015.curation_effort">(pypath.core.annot.Zhong2015 method)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.curation_effort_by_data_model">curation_effort_by_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.curation_effort_by_interaction_type">curation_effort_by_interaction_type (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.curation_effort_by_interaction_type_and_data_model">curation_effort_by_interaction_type_and_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.curation_effort_by_interaction_type_and_data_model_and_resource">curation_effort_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.curation_effort_by_reference">curation_effort_by_reference (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.curation_effort_by_resource">curation_effort_by_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.share.curl.Curl.html#pypath.share.curl.Curl">Curl (class in pypath.share.curl)</a>
+</li>
+      <li><a href="api/pypath.core.annot.CustomAnnotation.html#pypath.core.annot.CustomAnnotation">CustomAnnotation (class in pypath.core.annot)</a>
+</li>
+      <li><a href="api/pypath.core.annot.Cytosig.html#pypath.core.annot.Cytosig">Cytosig (class in pypath.core.annot)</a>
+</li>
+      <li><a href="api/pypath.inputs.cytosig.cytosig_annotations.html#pypath.inputs.cytosig.cytosig_annotations">cytosig_annotations() (in module pypath.inputs.cytosig)</a>
+</li>
+      <li><a href="api/pypath.inputs.cytosig.cytosig_df.html#pypath.inputs.cytosig.cytosig_df">cytosig_df() (in module pypath.inputs.cytosig)</a>
+</li>
+  </ul></td>
+</tr></table>
+
+<h2 id="D">D</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="api/pypath.visual.igraph_drawing.edge.DarkToLightEdgeDrawer.html#pypath.visual.igraph_drawing.edge.DarkToLightEdgeDrawer">DarkToLightEdgeDrawer (class in pypath.visual.igraph_drawing.edge)</a>
+</li>
+      <li><a href="api/pypath.internals.resource.NetworkResourceKey.html#pypath.internals.resource.NetworkResourceKey.data_model">data_model (pypath.internals.resource.NetworkResourceKey attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.data_models_by_data_model">data_models_by_data_model (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.data_models_by_data_model">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.data_models_by_interaction_type">data_models_by_interaction_type (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.data_models_by_interaction_type">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.data_models_by_interaction_type_and_data_model">data_models_by_interaction_type_and_data_model (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.data_models_by_interaction_type_and_data_model">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.data_models_by_interaction_type_and_data_model_and_resource">data_models_by_interaction_type_and_data_model_and_resource (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.data_models_by_interaction_type_and_data_model_and_resource">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.data_models_by_reference">data_models_by_reference (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.data_models_by_reference">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.data_models_by_resource">data_models_by_resource (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.data_models_by_resource">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.internals.resource.EnzymeSubstrateResourceKey.html#pypath.internals.resource.EnzymeSubstrateResourceKey.data_type">data_type (pypath.internals.resource.EnzymeSubstrateResourceKey attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.internals.resource.NetworkResourceKey.html#pypath.internals.resource.NetworkResourceKey.data_type">(pypath.internals.resource.NetworkResourceKey attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.inputs.uniprot.UniprotRecordHistory.html#pypath.inputs.uniprot.UniprotRecordHistory.database">database (pypath.inputs.uniprot.UniprotRecordHistory attribute)</a>
+</li>
+      <li><a href="api/pypath.omnipath.databases.define.DatabaseClass.html#pypath.omnipath.databases.define.DatabaseClass">DatabaseClass (class in pypath.omnipath.databases.define)</a>
+</li>
+      <li><a href="api/pypath.omnipath.databases.define.DatabaseDefinition.html#pypath.omnipath.databases.define.DatabaseDefinition">DatabaseDefinition (class in pypath.omnipath.databases.define)</a>
+</li>
+      <li><a href="api/pypath.omnipath.databases.define.DatabaseDefinitionManager.html#pypath.omnipath.databases.define.DatabaseDefinitionManager">DatabaseDefinitionManager (class in pypath.omnipath.databases.define)</a>
+</li>
+      <li><a href="api/pypath.omnipath.app.DatabaseManager.html#pypath.omnipath.app.DatabaseManager">DatabaseManager (class in pypath.omnipath.app)</a>
+</li>
+      <li><a href="api/pypath.utils.uniprot.UniprotProtein.html#pypath.utils.uniprot.UniprotProtein.databases">databases (pypath.utils.uniprot.UniprotProtein property)</a>
+</li>
+      <li><a href="api/pypath.utils.uniprot.databases.html#pypath.utils.uniprot.databases">databases() (in module pypath.utils.uniprot)</a>
+</li>
+      <li><a href="api/pypath.omnipath.app.DatabaseManager.html#pypath.omnipath.app.DatabaseManager.dataset_dependencies">dataset_dependencies() (pypath.omnipath.app.DatabaseManager method)</a>
+</li>
+      <li><a href="api/pypath.resources.network.dataset_priority.html#pypath.resources.network.dataset_priority">dataset_priority() (in module pypath.resources.network)</a>
+</li>
+      <li><a href="api/pypath.core.evidence.Evidences.html#pypath.core.evidence.Evidences.datasets">datasets (pypath.core.evidence.Evidences property)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.datasets_by_data_model">datasets_by_data_model (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.datasets_by_data_model">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.datasets_by_interaction_type">datasets_by_interaction_type (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.datasets_by_interaction_type">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.datasets_by_interaction_type_and_data_model">datasets_by_interaction_type_and_data_model (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.datasets_by_interaction_type_and_data_model">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.datasets_by_interaction_type_and_data_model_and_resource">datasets_by_interaction_type_and_data_model_and_resource (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.datasets_by_interaction_type_and_data_model_and_resource">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.datasets_by_reference">datasets_by_reference (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.datasets_by_reference">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.datasets_by_resource">datasets_by_resource (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.datasets_by_resource">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.inputs.uniprot.UniprotRecordHistory.html#pypath.inputs.uniprot.UniprotRecordHistory.date">date (pypath.inputs.uniprot.UniprotRecordHistory attribute)</a>
+</li>
+      <li><a href="api/pypath.inputs.dbptm.dbptm_enzyme_substrate.html#pypath.inputs.dbptm.dbptm_enzyme_substrate">dbptm_enzyme_substrate() (in module pypath.inputs.dbptm)</a>
+</li>
+      <li><a href="api/pypath.inputs.dbptm.dbptm_enzyme_substrate_old.html#pypath.inputs.dbptm.dbptm_enzyme_substrate_old">dbptm_enzyme_substrate_old() (in module pypath.inputs.dbptm)</a>
+</li>
+      <li><a href="api/pypath.inputs.dbptm.dbptm_interactions.html#pypath.inputs.dbptm.dbptm_interactions">dbptm_interactions() (in module pypath.inputs.dbptm)</a>
+</li>
+      <li><a href="api/pypath.inputs.ddinter.ddinter_drug_interactions.html#pypath.inputs.ddinter.ddinter_drug_interactions">ddinter_drug_interactions() (in module pypath.inputs.ddinter)</a>
+</li>
+      <li><a href="api/pypath.inputs.ddinter.ddinter_identifiers.html#pypath.inputs.ddinter.ddinter_identifiers">ddinter_identifiers() (in module pypath.inputs.ddinter)</a>
+</li>
+      <li><a href="api/pypath.inputs.ddinter.ddinter_interactions.html#pypath.inputs.ddinter.ddinter_interactions">ddinter_interactions() (in module pypath.inputs.ddinter)</a>
+</li>
+      <li><a href="api/pypath.inputs.ddinter.ddinter_mappings.html#pypath.inputs.ddinter.ddinter_mappings">ddinter_mappings() (in module pypath.inputs.ddinter)</a>
+</li>
+      <li><a href="api/pypath.inputs.ddinter.ddinter_n_drugs.html#pypath.inputs.ddinter.ddinter_n_drugs">ddinter_n_drugs() (in module pypath.inputs.ddinter)</a>
+</li>
+      <li><a href="api/pypath.inputs.deathdomain.deathdomain_interactions.html#pypath.inputs.deathdomain.deathdomain_interactions">deathdomain_interactions() (in module pypath.inputs.deathdomain)</a>
+</li>
+      <li><a href="api/pypath.inputs.deathdomain.deathdomain_interactions_rescued.html#pypath.inputs.deathdomain.deathdomain_interactions_rescued">deathdomain_interactions_rescued() (in module pypath.inputs.deathdomain)</a>
+</li>
+      <li><a href="api/pypath.share.curl.debug_off.html#pypath.share.curl.debug_off">debug_off (class in pypath.share.curl)</a>
+</li>
+      <li><a href="api/pypath.share.curl.debug_on.html#pypath.share.curl.debug_on">debug_on (class in pypath.share.curl)</a>
+</li>
+      <li><a href="api/pypath.visual.igraph_drawing.DefaultGraphDrawerFFsupport.html#pypath.visual.igraph_drawing.DefaultGraphDrawerFFsupport">DefaultGraphDrawerFFsupport (class in pypath.visual.igraph_drawing)</a>
+</li>
+      <li><a href="api/pypath.visual.igraph_drawing.vertex.DefaultVertexDrawer.html#pypath.visual.igraph_drawing.vertex.DefaultVertexDrawer">DefaultVertexDrawer (class in pypath.visual.igraph_drawing.vertex)</a>
+
+      <ul>
+        <li><a href="api/pypath.visual.igraph_drawing.DefaultVertexDrawer.html#pypath.visual.igraph_drawing.DefaultVertexDrawer">(in module pypath.visual.igraph_drawing)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.omnipath.app.DatabaseManager.html#pypath.omnipath.app.DatabaseManager.define_dataset">define_dataset() (pypath.omnipath.app.DatabaseManager method)</a>
+</li>
+      <li><a href="api/pypath.core.annot.CustomAnnotation.html#pypath.core.annot.CustomAnnotation.degree_inter_class_network">degree_inter_class_network() (pypath.core.annot.CustomAnnotation method)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.intercell.IntercellAnnotation.html#pypath.core.intercell.IntercellAnnotation.degree_inter_class_network">(pypath.core.intercell.IntercellAnnotation method)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.degrees_directed_by_data_model">degrees_directed_by_data_model (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.degrees_directed_by_data_model">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.degrees_directed_by_interaction_type">degrees_directed_by_interaction_type (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.degrees_directed_by_interaction_type">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.degrees_directed_by_interaction_type_and_data_model">degrees_directed_by_interaction_type_and_data_model (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.degrees_directed_by_interaction_type_and_data_model">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.degrees_directed_by_interaction_type_and_data_model_and_resource">degrees_directed_by_interaction_type_and_data_model_and_resource (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.degrees_directed_by_interaction_type_and_data_model_and_resource">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.degrees_directed_by_reference">degrees_directed_by_reference (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.degrees_directed_by_reference">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.degrees_directed_by_resource">degrees_directed_by_resource (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.degrees_directed_by_resource">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.degrees_directed_in_by_data_model">degrees_directed_in_by_data_model (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.degrees_directed_in_by_data_model">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.degrees_directed_in_by_interaction_type">degrees_directed_in_by_interaction_type (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.degrees_directed_in_by_interaction_type">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.degrees_directed_in_by_interaction_type_and_data_model">degrees_directed_in_by_interaction_type_and_data_model (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.degrees_directed_in_by_interaction_type_and_data_model">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.degrees_directed_in_by_interaction_type_and_data_model_and_resource">degrees_directed_in_by_interaction_type_and_data_model_and_resource (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.degrees_directed_in_by_interaction_type_and_data_model_and_resource">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.degrees_directed_in_by_reference">degrees_directed_in_by_reference (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.degrees_directed_in_by_reference">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.degrees_directed_in_by_resource">degrees_directed_in_by_resource (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.degrees_directed_in_by_resource">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.degrees_directed_out_by_data_model">degrees_directed_out_by_data_model (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.degrees_directed_out_by_data_model">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.degrees_directed_out_by_interaction_type">degrees_directed_out_by_interaction_type (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.degrees_directed_out_by_interaction_type">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.degrees_directed_out_by_interaction_type_and_data_model">degrees_directed_out_by_interaction_type_and_data_model (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.degrees_directed_out_by_interaction_type_and_data_model">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.degrees_directed_out_by_interaction_type_and_data_model_and_resource">degrees_directed_out_by_interaction_type_and_data_model_and_resource (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.degrees_directed_out_by_interaction_type_and_data_model_and_resource">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.degrees_directed_out_by_reference">degrees_directed_out_by_reference (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.degrees_directed_out_by_reference">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.degrees_directed_out_by_resource">degrees_directed_out_by_resource (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.degrees_directed_out_by_resource">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.degrees_negative_by_data_model">degrees_negative_by_data_model (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.degrees_negative_by_data_model">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.degrees_negative_by_interaction_type">degrees_negative_by_interaction_type (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.degrees_negative_by_interaction_type">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.degrees_negative_by_interaction_type_and_data_model">degrees_negative_by_interaction_type_and_data_model (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.degrees_negative_by_interaction_type_and_data_model">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.degrees_negative_by_interaction_type_and_data_model_and_resource">degrees_negative_by_interaction_type_and_data_model_and_resource (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.degrees_negative_by_interaction_type_and_data_model_and_resource">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.degrees_negative_by_reference">degrees_negative_by_reference (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.degrees_negative_by_reference">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.degrees_negative_by_resource">degrees_negative_by_resource (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.degrees_negative_by_resource">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.degrees_negative_in_by_data_model">degrees_negative_in_by_data_model (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.degrees_negative_in_by_data_model">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.degrees_negative_in_by_interaction_type">degrees_negative_in_by_interaction_type (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.degrees_negative_in_by_interaction_type">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.degrees_negative_in_by_interaction_type_and_data_model">degrees_negative_in_by_interaction_type_and_data_model (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.degrees_negative_in_by_interaction_type_and_data_model">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.degrees_negative_in_by_interaction_type_and_data_model_and_resource">degrees_negative_in_by_interaction_type_and_data_model_and_resource (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.degrees_negative_in_by_interaction_type_and_data_model_and_resource">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.degrees_negative_in_by_reference">degrees_negative_in_by_reference (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.degrees_negative_in_by_reference">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.degrees_negative_in_by_resource">degrees_negative_in_by_resource (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.degrees_negative_in_by_resource">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.degrees_negative_out_by_data_model">degrees_negative_out_by_data_model (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.degrees_negative_out_by_data_model">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.degrees_negative_out_by_interaction_type">degrees_negative_out_by_interaction_type (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.degrees_negative_out_by_interaction_type">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.degrees_negative_out_by_interaction_type_and_data_model">degrees_negative_out_by_interaction_type_and_data_model (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.degrees_negative_out_by_interaction_type_and_data_model">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.degrees_negative_out_by_interaction_type_and_data_model_and_resource">degrees_negative_out_by_interaction_type_and_data_model_and_resource (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.degrees_negative_out_by_interaction_type_and_data_model_and_resource">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.degrees_negative_out_by_reference">degrees_negative_out_by_reference (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.degrees_negative_out_by_reference">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.degrees_negative_out_by_resource">degrees_negative_out_by_resource (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.degrees_negative_out_by_resource">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.degrees_non_directed_by_data_model">degrees_non_directed_by_data_model (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.degrees_non_directed_by_data_model">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.degrees_non_directed_by_interaction_type">degrees_non_directed_by_interaction_type (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.degrees_non_directed_by_interaction_type">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.degrees_non_directed_by_interaction_type_and_data_model">degrees_non_directed_by_interaction_type_and_data_model (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.degrees_non_directed_by_interaction_type_and_data_model">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.degrees_non_directed_by_interaction_type_and_data_model_and_resource">degrees_non_directed_by_interaction_type_and_data_model_and_resource (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.degrees_non_directed_by_interaction_type_and_data_model_and_resource">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.degrees_non_directed_by_reference">degrees_non_directed_by_reference (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.degrees_non_directed_by_reference">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.degrees_non_directed_by_resource">degrees_non_directed_by_resource (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.degrees_non_directed_by_resource">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.degrees_positive_by_data_model">degrees_positive_by_data_model (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.degrees_positive_by_data_model">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.degrees_positive_by_interaction_type">degrees_positive_by_interaction_type (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.degrees_positive_by_interaction_type">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.degrees_positive_by_interaction_type_and_data_model">degrees_positive_by_interaction_type_and_data_model (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.degrees_positive_by_interaction_type_and_data_model">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.degrees_positive_by_interaction_type_and_data_model_and_resource">degrees_positive_by_interaction_type_and_data_model_and_resource (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.degrees_positive_by_interaction_type_and_data_model_and_resource">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.degrees_positive_by_reference">degrees_positive_by_reference (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.degrees_positive_by_reference">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.degrees_positive_by_resource">degrees_positive_by_resource (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.degrees_positive_by_resource">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.degrees_positive_in_by_data_model">degrees_positive_in_by_data_model (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.degrees_positive_in_by_data_model">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.degrees_positive_in_by_interaction_type">degrees_positive_in_by_interaction_type (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.degrees_positive_in_by_interaction_type">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+  </ul></td>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.degrees_positive_in_by_interaction_type_and_data_model">degrees_positive_in_by_interaction_type_and_data_model (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.degrees_positive_in_by_interaction_type_and_data_model">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.degrees_positive_in_by_interaction_type_and_data_model_and_resource">degrees_positive_in_by_interaction_type_and_data_model_and_resource (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.degrees_positive_in_by_interaction_type_and_data_model_and_resource">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.degrees_positive_in_by_reference">degrees_positive_in_by_reference (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.degrees_positive_in_by_reference">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.degrees_positive_in_by_resource">degrees_positive_in_by_resource (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.degrees_positive_in_by_resource">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.degrees_positive_out_by_data_model">degrees_positive_out_by_data_model (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.degrees_positive_out_by_data_model">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.degrees_positive_out_by_interaction_type">degrees_positive_out_by_interaction_type (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.degrees_positive_out_by_interaction_type">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.degrees_positive_out_by_interaction_type_and_data_model">degrees_positive_out_by_interaction_type_and_data_model (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.degrees_positive_out_by_interaction_type_and_data_model">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.degrees_positive_out_by_interaction_type_and_data_model_and_resource">degrees_positive_out_by_interaction_type_and_data_model_and_resource (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.degrees_positive_out_by_interaction_type_and_data_model_and_resource">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.degrees_positive_out_by_reference">degrees_positive_out_by_reference (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.degrees_positive_out_by_reference">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.degrees_positive_out_by_resource">degrees_positive_out_by_resource (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.degrees_positive_out_by_resource">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.degrees_signed_by_data_model">degrees_signed_by_data_model (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.degrees_signed_by_data_model">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.degrees_signed_by_interaction_type">degrees_signed_by_interaction_type (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.degrees_signed_by_interaction_type">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.degrees_signed_by_interaction_type_and_data_model">degrees_signed_by_interaction_type_and_data_model (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.degrees_signed_by_interaction_type_and_data_model">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.degrees_signed_by_interaction_type_and_data_model_and_resource">degrees_signed_by_interaction_type_and_data_model_and_resource (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.degrees_signed_by_interaction_type_and_data_model_and_resource">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.degrees_signed_by_reference">degrees_signed_by_reference (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.degrees_signed_by_reference">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.degrees_signed_by_resource">degrees_signed_by_resource (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.degrees_signed_by_resource">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.degrees_signed_in_by_data_model">degrees_signed_in_by_data_model (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.degrees_signed_in_by_data_model">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.degrees_signed_in_by_interaction_type">degrees_signed_in_by_interaction_type (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.degrees_signed_in_by_interaction_type">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.degrees_signed_in_by_interaction_type_and_data_model">degrees_signed_in_by_interaction_type_and_data_model (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.degrees_signed_in_by_interaction_type_and_data_model">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.degrees_signed_in_by_interaction_type_and_data_model_and_resource">degrees_signed_in_by_interaction_type_and_data_model_and_resource (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.degrees_signed_in_by_interaction_type_and_data_model_and_resource">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.degrees_signed_in_by_reference">degrees_signed_in_by_reference (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.degrees_signed_in_by_reference">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.degrees_signed_in_by_resource">degrees_signed_in_by_resource (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.degrees_signed_in_by_resource">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.degrees_signed_out_by_data_model">degrees_signed_out_by_data_model (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.degrees_signed_out_by_data_model">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.degrees_signed_out_by_interaction_type">degrees_signed_out_by_interaction_type (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.degrees_signed_out_by_interaction_type">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.degrees_signed_out_by_interaction_type_and_data_model">degrees_signed_out_by_interaction_type_and_data_model (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.degrees_signed_out_by_interaction_type_and_data_model">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.degrees_signed_out_by_interaction_type_and_data_model_and_resource">degrees_signed_out_by_interaction_type_and_data_model_and_resource (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.degrees_signed_out_by_interaction_type_and_data_model_and_resource">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.degrees_signed_out_by_reference">degrees_signed_out_by_reference (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.degrees_signed_out_by_reference">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.degrees_signed_out_by_resource">degrees_signed_out_by_resource (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.degrees_signed_out_by_resource">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.degrees_undirected_by_data_model">degrees_undirected_by_data_model (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.degrees_undirected_by_data_model">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.degrees_undirected_by_interaction_type">degrees_undirected_by_interaction_type (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.degrees_undirected_by_interaction_type">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.degrees_undirected_by_interaction_type_and_data_model">degrees_undirected_by_interaction_type_and_data_model (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.degrees_undirected_by_interaction_type_and_data_model">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.degrees_undirected_by_interaction_type_and_data_model_and_resource">degrees_undirected_by_interaction_type_and_data_model_and_resource (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.degrees_undirected_by_interaction_type_and_data_model_and_resource">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.degrees_undirected_by_reference">degrees_undirected_by_reference (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.degrees_undirected_by_reference">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.degrees_undirected_by_resource">degrees_undirected_by_resource (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.degrees_undirected_by_resource">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.inputs.uniprot.deleted_uniprot_genesymbol.html#pypath.inputs.uniprot.deleted_uniprot_genesymbol">deleted_uniprot_genesymbol() (in module pypath.inputs.uniprot)</a>
+</li>
+      <li><a href="api/pypath.inputs.depod.depod_enzyme_substrate.html#pypath.inputs.depod.depod_enzyme_substrate">depod_enzyme_substrate() (in module pypath.inputs.depod)</a>
+</li>
+      <li><a href="api/pypath.inputs.depod.depod_interactions.html#pypath.inputs.depod.depod_interactions">depod_interactions() (in module pypath.inputs.depod)</a>
+</li>
+      <li><a href="api/pypath.utils.orthology.EnsemblOrthology.html#pypath.utils.orthology.EnsemblOrthology.df">df() (pypath.utils.orthology.EnsemblOrthology method)</a>
+
+      <ul>
+        <li><a href="api/pypath.utils.orthology.HomologeneOrthology.html#pypath.utils.orthology.HomologeneOrthology.df">(pypath.utils.orthology.HomologeneOrthology method)</a>
+</li>
+        <li><a href="api/pypath.utils.orthology.OmaOrthology.html#pypath.utils.orthology.OmaOrthology.df">(pypath.utils.orthology.OmaOrthology method)</a>
+</li>
+        <li><a href="api/pypath.utils.orthology.ProteinOrthology.html#pypath.utils.orthology.ProteinOrthology.df">(pypath.utils.orthology.ProteinOrthology method)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.annot.Dgidb.html#pypath.core.annot.Dgidb">Dgidb (class in pypath.core.annot)</a>
+</li>
+      <li><a href="api/pypath.inputs.dgidb.dgidb_annotations.html#pypath.inputs.dgidb.dgidb_annotations">dgidb_annotations() (in module pypath.inputs.dgidb)</a>
+</li>
+      <li><a href="api/pypath.inputs.dgidb.dgidb_interactions.html#pypath.inputs.dgidb.dgidb_interactions">dgidb_interactions() (in module pypath.inputs.dgidb)</a>
+</li>
+      <li><a href="api/pypath.inputs.dip.dip_interactions.html#pypath.inputs.dip.dip_interactions">dip_interactions() (in module pypath.inputs.dip)</a>
+</li>
+      <li><a href="api/pypath.inputs.dip.dip_login.html#pypath.inputs.dip.dip_login">dip_login() (in module pypath.inputs.dip)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.InteractionDataFrameRecord.html#pypath.core.interaction.InteractionDataFrameRecord.directed">directed (pypath.core.interaction.InteractionDataFrameRecord attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.direction_consistency">direction_consistency() (pypath.core.network.Network method)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.direction_key">direction_key() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.disclaimer.html#pypath.disclaimer">disclaimer() (in module pypath)</a>
+</li>
+      <li><a href="api/pypath.inputs.pathophenodb.DiseasePathogen.html#pypath.inputs.pathophenodb.DiseasePathogen.disease">disease (pypath.inputs.pathophenodb.DiseasePathogen attribute)</a>
+</li>
+      <li><a href="api/pypath.utils.uniprot.disease.html#pypath.utils.uniprot.disease">disease() (in module pypath.utils.uniprot)</a>
+</li>
+      <li><a href="api/pypath.inputs.pathophenodb.DiseasePathogen.html#pypath.inputs.pathophenodb.DiseasePathogen.disease_id">disease_id (pypath.inputs.pathophenodb.DiseasePathogen attribute)</a>
+</li>
+      <li><a href="api/pypath.inputs.pathophenodb.disease_pathogen_interactions.html#pypath.inputs.pathophenodb.disease_pathogen_interactions">disease_pathogen_interactions() (in module pypath.inputs.pathophenodb)</a>
+</li>
+      <li><a href="api/pypath.inputs.kegg_api.disease_to_drug.html#pypath.inputs.kegg_api.disease_to_drug">disease_to_drug() (in module pypath.inputs.kegg_api)</a>
+</li>
+      <li><a href="api/pypath.inputs.kegg_api.disease_to_gene.html#pypath.inputs.kegg_api.disease_to_gene">disease_to_gene() (in module pypath.inputs.kegg_api)</a>
+</li>
+      <li><a href="api/pypath.inputs.kegg_api.disease_to_pathway.html#pypath.inputs.kegg_api.disease_to_pathway">disease_to_pathway() (in module pypath.inputs.kegg_api)</a>
+</li>
+      <li><a href="api/pypath.utils.uniprot.disease_with_xrefs.html#pypath.utils.uniprot.disease_with_xrefs">disease_with_xrefs() (in module pypath.utils.uniprot)</a>
+</li>
+      <li><a href="api/pypath.inputs.pathophenodb.DiseasePathogen.html#pypath.inputs.pathophenodb.DiseasePathogen">DiseasePathogen (class in pypath.inputs.pathophenodb)</a>
+</li>
+      <li><a href="api/pypath.inputs.diseases.diseases_general.html#pypath.inputs.diseases.diseases_general">diseases_general() (in module pypath.inputs.diseases)</a>
+</li>
+      <li><a href="api/pypath.core.annot.Disgenet.html#pypath.core.annot.Disgenet">Disgenet (class in pypath.core.annot)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.InteractionDataFrameRecord.html#pypath.core.interaction.InteractionDataFrameRecord.dmodel">dmodel (pypath.core.interaction.InteractionDataFrameRecord attribute)</a>
+</li>
+      <li><a href="api/pypath.internals.intera.Domain.html#pypath.internals.intera.Domain">Domain (class in pypath.internals.intera)</a>
+</li>
+      <li><a href="api/pypath.internals.intera.DomainDomain.html#pypath.internals.intera.DomainDomain">DomainDomain (class in pypath.internals.intera)</a>
+</li>
+      <li><a href="api/pypath.internals.intera.DomainMotif.html#pypath.internals.intera.DomainMotif">DomainMotif (class in pypath.internals.intera)</a>
+</li>
+      <li><a href="api/pypath.inputs.domino.domino_ddi.html#pypath.inputs.domino.domino_ddi">domino_ddi() (in module pypath.inputs.domino)</a>
+</li>
+      <li><a href="api/pypath.inputs.domino.domino_enzsub.html#pypath.inputs.domino.domino_enzsub">domino_enzsub() (in module pypath.inputs.domino)</a>
+</li>
+      <li><a href="api/pypath.inputs.domino.domino_interactions.html#pypath.inputs.domino.domino_interactions">domino_interactions() (in module pypath.inputs.domino)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.dorothea">dorothea() (pypath.core.network.Network class method)</a>
+</li>
+      <li><a href="api/pypath.resources.network.dorothea_expand_levels.html#pypath.resources.network.dorothea_expand_levels">dorothea_expand_levels() (in module pypath.resources.network)</a>
+</li>
+      <li><a href="api/pypath.inputs.dorothea.dorothea_full_raw.html#pypath.inputs.dorothea.dorothea_full_raw">dorothea_full_raw() (in module pypath.inputs.dorothea)</a>
+</li>
+      <li><a href="api/pypath.inputs.dorothea.dorothea_interactions.html#pypath.inputs.dorothea.dorothea_interactions">dorothea_interactions() (in module pypath.inputs.dorothea)</a>
+</li>
+      <li><a href="api/pypath.inputs.dorothea.dorothea_interactions_old.html#pypath.inputs.dorothea.dorothea_interactions_old">dorothea_interactions_old() (in module pypath.inputs.dorothea)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.dorothea_level">dorothea_level() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.dorothea_levels">dorothea_levels() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.inputs.dorothea.dorothea_old_csv.html#pypath.inputs.dorothea.dorothea_old_csv">dorothea_old_csv() (in module pypath.inputs.dorothea)</a>
+</li>
+      <li><a href="api/pypath.inputs.dorothea.dorothea_rda_raw.html#pypath.inputs.dorothea.dorothea_rda_raw">dorothea_rda_raw() (in module pypath.inputs.dorothea)</a>
+</li>
+      <li><a href="api/pypath.inputs.dorothea.DorotheaInteraction.html#pypath.inputs.dorothea.DorotheaInteraction">DorotheaInteraction (class in pypath.inputs.dorothea)</a>
+</li>
+      <li><a href="api/pypath.inputs.biomodels.download_single_model.html#pypath.inputs.biomodels.download_single_model">download_single_model() (in module pypath.inputs.biomodels)</a>
+</li>
+      <li><a href="api/pypath.visual.drawing.InterSet.html#pypath.visual.drawing.InterSet.draw">draw() (pypath.visual.drawing.InterSet method)</a>
+
+      <ul>
+        <li><a href="api/pypath.visual.igraph_drawing.vertex.AbstractCairoVertexDrawer.html#pypath.visual.igraph_drawing.vertex.AbstractCairoVertexDrawer.draw">(pypath.visual.igraph_drawing.vertex.AbstractCairoVertexDrawer method)</a>
+</li>
+        <li><a href="api/pypath.visual.igraph_drawing.vertex.AbstractVertexDrawer.html#pypath.visual.igraph_drawing.vertex.AbstractVertexDrawer.draw">(pypath.visual.igraph_drawing.vertex.AbstractVertexDrawer method)</a>
+</li>
+        <li><a href="api/pypath.visual.igraph_drawing.vertex.DefaultVertexDrawer.html#pypath.visual.igraph_drawing.vertex.DefaultVertexDrawer.draw">(pypath.visual.igraph_drawing.vertex.DefaultVertexDrawer method)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.visual.igraph_drawing.edge.AbstractEdgeDrawer.html#pypath.visual.igraph_drawing.edge.AbstractEdgeDrawer.draw_directed_edge">draw_directed_edge() (pypath.visual.igraph_drawing.edge.AbstractEdgeDrawer method)</a>
+
+      <ul>
+        <li><a href="api/pypath.visual.igraph_drawing.edge.AlphaVaryingEdgeDrawer.html#pypath.visual.igraph_drawing.edge.AlphaVaryingEdgeDrawer.draw_directed_edge">(pypath.visual.igraph_drawing.edge.AlphaVaryingEdgeDrawer method)</a>
+</li>
+        <li><a href="api/pypath.visual.igraph_drawing.edge.ArrowEdgeDrawer.html#pypath.visual.igraph_drawing.edge.ArrowEdgeDrawer.draw_directed_edge">(pypath.visual.igraph_drawing.edge.ArrowEdgeDrawer method)</a>
+</li>
+        <li><a href="api/pypath.visual.igraph_drawing.edge.DarkToLightEdgeDrawer.html#pypath.visual.igraph_drawing.edge.DarkToLightEdgeDrawer.draw_directed_edge">(pypath.visual.igraph_drawing.edge.DarkToLightEdgeDrawer method)</a>
+</li>
+        <li><a href="api/pypath.visual.igraph_drawing.edge.LightToDarkEdgeDrawer.html#pypath.visual.igraph_drawing.edge.LightToDarkEdgeDrawer.draw_directed_edge">(pypath.visual.igraph_drawing.edge.LightToDarkEdgeDrawer method)</a>
+</li>
+        <li><a href="api/pypath.visual.igraph_drawing.edge.TaperedEdgeDrawer.html#pypath.visual.igraph_drawing.edge.TaperedEdgeDrawer.draw_directed_edge">(pypath.visual.igraph_drawing.edge.TaperedEdgeDrawer method)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.visual.igraph_drawing.edge.AbstractEdgeDrawer.html#pypath.visual.igraph_drawing.edge.AbstractEdgeDrawer.draw_loop_edge">draw_loop_edge() (pypath.visual.igraph_drawing.edge.AbstractEdgeDrawer method)</a>
+
+      <ul>
+        <li><a href="api/pypath.visual.igraph_drawing.edge.AlphaVaryingEdgeDrawer.html#pypath.visual.igraph_drawing.edge.AlphaVaryingEdgeDrawer.draw_loop_edge">(pypath.visual.igraph_drawing.edge.AlphaVaryingEdgeDrawer method)</a>
+</li>
+        <li><a href="api/pypath.visual.igraph_drawing.edge.ArrowEdgeDrawer.html#pypath.visual.igraph_drawing.edge.ArrowEdgeDrawer.draw_loop_edge">(pypath.visual.igraph_drawing.edge.ArrowEdgeDrawer method)</a>
+</li>
+        <li><a href="api/pypath.visual.igraph_drawing.edge.DarkToLightEdgeDrawer.html#pypath.visual.igraph_drawing.edge.DarkToLightEdgeDrawer.draw_loop_edge">(pypath.visual.igraph_drawing.edge.DarkToLightEdgeDrawer method)</a>
+</li>
+        <li><a href="api/pypath.visual.igraph_drawing.edge.LightToDarkEdgeDrawer.html#pypath.visual.igraph_drawing.edge.LightToDarkEdgeDrawer.draw_loop_edge">(pypath.visual.igraph_drawing.edge.LightToDarkEdgeDrawer method)</a>
+</li>
+        <li><a href="api/pypath.visual.igraph_drawing.edge.TaperedEdgeDrawer.html#pypath.visual.igraph_drawing.edge.TaperedEdgeDrawer.draw_loop_edge">(pypath.visual.igraph_drawing.edge.TaperedEdgeDrawer method)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.visual.igraph_drawing.edge.AbstractEdgeDrawer.html#pypath.visual.igraph_drawing.edge.AbstractEdgeDrawer.draw_undirected_edge">draw_undirected_edge() (pypath.visual.igraph_drawing.edge.AbstractEdgeDrawer method)</a>
+
+      <ul>
+        <li><a href="api/pypath.visual.igraph_drawing.edge.AlphaVaryingEdgeDrawer.html#pypath.visual.igraph_drawing.edge.AlphaVaryingEdgeDrawer.draw_undirected_edge">(pypath.visual.igraph_drawing.edge.AlphaVaryingEdgeDrawer method)</a>
+</li>
+        <li><a href="api/pypath.visual.igraph_drawing.edge.ArrowEdgeDrawer.html#pypath.visual.igraph_drawing.edge.ArrowEdgeDrawer.draw_undirected_edge">(pypath.visual.igraph_drawing.edge.ArrowEdgeDrawer method)</a>
+</li>
+        <li><a href="api/pypath.visual.igraph_drawing.edge.DarkToLightEdgeDrawer.html#pypath.visual.igraph_drawing.edge.DarkToLightEdgeDrawer.draw_undirected_edge">(pypath.visual.igraph_drawing.edge.DarkToLightEdgeDrawer method)</a>
+</li>
+        <li><a href="api/pypath.visual.igraph_drawing.edge.LightToDarkEdgeDrawer.html#pypath.visual.igraph_drawing.edge.LightToDarkEdgeDrawer.draw_undirected_edge">(pypath.visual.igraph_drawing.edge.LightToDarkEdgeDrawer method)</a>
+</li>
+        <li><a href="api/pypath.visual.igraph_drawing.edge.TaperedEdgeDrawer.html#pypath.visual.igraph_drawing.edge.TaperedEdgeDrawer.draw_undirected_edge">(pypath.visual.igraph_drawing.edge.TaperedEdgeDrawer method)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.inputs.adrecs.AdrecsDrug.html#pypath.inputs.adrecs.AdrecsDrug.drug">drug (pypath.inputs.adrecs.AdrecsDrug attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.inputs.adrecs.AdrecsDrugAdr.html#pypath.inputs.adrecs.AdrecsDrugAdr.drug">(pypath.inputs.adrecs.AdrecsDrugAdr attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.inputs.adrecs.AdrecsDrugAdr.html#pypath.inputs.adrecs.AdrecsDrugAdr.drug_badd">drug_badd (pypath.inputs.adrecs.AdrecsDrugAdr attribute)</a>
+</li>
+      <li><a href="api/pypath.inputs.kegg_api.drug_to_disease.html#pypath.inputs.kegg_api.drug_to_disease">drug_to_disease() (in module pypath.inputs.kegg_api)</a>
+</li>
+      <li><a href="api/pypath.inputs.kegg_api.drug_to_drug.html#pypath.inputs.kegg_api.drug_to_drug">drug_to_drug() (in module pypath.inputs.kegg_api)</a>
+</li>
+      <li><a href="api/pypath.inputs.kegg_api.drug_to_gene.html#pypath.inputs.kegg_api.drug_to_gene">drug_to_gene() (in module pypath.inputs.kegg_api)</a>
+</li>
+      <li><a href="api/pypath.inputs.kegg_api.drug_to_pathway.html#pypath.inputs.kegg_api.drug_to_pathway">drug_to_pathway() (in module pypath.inputs.kegg_api)</a>
+</li>
+      <li><a href="api/pypath.inputs.adrecs.AdrecsDrug.html#pypath.inputs.adrecs.AdrecsDrug.drugbank">drugbank (pypath.inputs.adrecs.AdrecsDrug attribute)</a>
+</li>
+      <li><a href="api/pypath.inputs.drugbank.drugbank_annotations.html#pypath.inputs.drugbank.drugbank_annotations">drugbank_annotations() (in module pypath.inputs.drugbank)</a>
+</li>
+      <li><a href="api/pypath.inputs.drugbank.drugbank_drugs.html#pypath.inputs.drugbank.drugbank_drugs">drugbank_drugs() (in module pypath.inputs.drugbank)</a>
+</li>
+      <li><a href="api/pypath.inputs.drugbank.DrugbankFull.html#pypath.inputs.drugbank.DrugbankFull.drugbank_drugs_full">drugbank_drugs_full() (pypath.inputs.drugbank.DrugbankFull method)</a>
+</li>
+      <li><a href="api/pypath.inputs.drugbank.DrugbankFull.html#pypath.inputs.drugbank.DrugbankFull.drugbank_external_ids_full">drugbank_external_ids_full() (pypath.inputs.drugbank.DrugbankFull method)</a>
+</li>
+      <li><a href="api/pypath.inputs.drugbank.drugbank_interactions.html#pypath.inputs.drugbank.drugbank_interactions">drugbank_interactions() (in module pypath.inputs.drugbank)</a>
+</li>
+      <li><a href="api/pypath.inputs.drugbank.drugbank_mapping.html#pypath.inputs.drugbank.drugbank_mapping">drugbank_mapping() (in module pypath.inputs.drugbank)</a>
+</li>
+      <li><a href="api/pypath.inputs.drugbank.DrugbankFull.html#pypath.inputs.drugbank.DrugbankFull.drugbank_properties_full">drugbank_properties_full() (pypath.inputs.drugbank.DrugbankFull method)</a>
+</li>
+      <li><a href="api/pypath.inputs.drugbank.drugbank_raw_interactions.html#pypath.inputs.drugbank.drugbank_raw_interactions">drugbank_raw_interactions() (in module pypath.inputs.drugbank)</a>
+</li>
+      <li><a href="api/pypath.inputs.drugbank.DrugbankFull.html#pypath.inputs.drugbank.DrugbankFull.drugbank_targets_full">drugbank_targets_full() (pypath.inputs.drugbank.DrugbankFull method)</a>
+</li>
+      <li><a href="api/pypath.inputs.drugbank.DrugbankFull.html#pypath.inputs.drugbank.DrugbankFull">DrugbankFull (class in pypath.inputs.drugbank)</a>
+</li>
+      <li><a href="api/pypath.inputs.drugcentral.drugcentral_drugs.html#pypath.inputs.drugcentral.drugcentral_drugs">drugcentral_drugs() (in module pypath.inputs.drugcentral)</a>
+</li>
+      <li><a href="api/pypath.inputs.drugcentral.drugcentral_interactions.html#pypath.inputs.drugcentral.drugcentral_interactions">drugcentral_interactions() (in module pypath.inputs.drugcentral)</a>
+</li>
+      <li><a href="api/pypath.inputs.drugcentral.drugcentral_mapping.html#pypath.inputs.drugcentral.drugcentral_mapping">drugcentral_mapping() (in module pypath.inputs.drugcentral)</a>
+</li>
+      <li><a href="api/pypath.share.curl.dryrun_off.html#pypath.share.curl.dryrun_off">dryrun_off (class in pypath.share.curl)</a>
+</li>
+      <li><a href="api/pypath.share.curl.dryrun_on.html#pypath.share.curl.dryrun_on">dryrun_on (class in pypath.share.curl)</a>
+</li>
+  </ul></td>
+</tr></table>
+
+<h2 id="E">E</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="api/pypath.inputs.ebi.ebi_rest.html#pypath.inputs.ebi.ebi_rest">ebi_rest() (in module pypath.inputs.ebi)</a>
+</li>
+      <li><a href="api/pypath.utils.uniprot.ec.html#pypath.utils.uniprot.ec">ec() (in module pypath.utils.uniprot)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.InteractionDataFrameRecord.html#pypath.core.interaction.InteractionDataFrameRecord.effect">effect (pypath.core.interaction.InteractionDataFrameRecord attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.inputs.dorothea.DorotheaInteraction.html#pypath.inputs.dorothea.DorotheaInteraction.effect">(pypath.inputs.dorothea.DorotheaInteraction attribute)</a>
+</li>
+        <li><a href="api/pypath.inputs.gutmgene.GutmgeneAnnotation.html#pypath.inputs.gutmgene.GutmgeneAnnotation.effect">(pypath.inputs.gutmgene.GutmgeneAnnotation attribute)</a>
+</li>
+        <li><a href="api/pypath.inputs.gutmgene.GutmgeneRaw.html#pypath.inputs.gutmgene.GutmgeneRaw.effect">(pypath.inputs.gutmgene.GutmgeneRaw attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.inputs.elm.elm_classes.html#pypath.inputs.elm.elm_classes">elm_classes() (in module pypath.inputs.elm)</a>
+</li>
+      <li><a href="api/pypath.inputs.elm.elm_domains.html#pypath.inputs.elm.elm_domains">elm_domains() (in module pypath.inputs.elm)</a>
+</li>
+      <li><a href="api/pypath.inputs.elm.elm_instances.html#pypath.inputs.elm.elm_instances">elm_instances() (in module pypath.inputs.elm)</a>
+</li>
+      <li><a href="api/pypath.inputs.elm.elm_interactions.html#pypath.inputs.elm.elm_interactions">elm_interactions() (in module pypath.inputs.elm)</a>
+</li>
+      <li><a href="api/pypath.inputs.embopress.embopress_supplementary.html#pypath.inputs.embopress.embopress_supplementary">embopress_supplementary() (in module pypath.inputs.embopress)</a>
+</li>
+      <li><a href="api/pypath.core.annot.Embrace.html#pypath.core.annot.Embrace">Embrace (class in pypath.core.annot)</a>
+</li>
+      <li><a href="api/pypath.inputs.embrace.embrace_annotations.html#pypath.inputs.embrace.embrace_annotations">embrace_annotations() (in module pypath.inputs.embrace)</a>
+</li>
+      <li><a href="api/pypath.inputs.embrace.embrace_interactions.html#pypath.inputs.embrace.embrace_interactions">embrace_interactions() (in module pypath.inputs.embrace)</a>
+</li>
+      <li><a href="api/pypath.inputs.embrace.embrace_raw.html#pypath.inputs.embrace.embrace_raw">embrace_raw() (in module pypath.inputs.embrace)</a>
+</li>
+      <li><a href="api/pypath.inputs.embrace.embrace_translated.html#pypath.inputs.embrace.embrace_translated">embrace_translated() (in module pypath.inputs.embrace)</a>
+</li>
+      <li><a href="api/pypath.internals.annot_formats.AnnotDef.html#pypath.internals.annot_formats.AnnotDef.enabled">enabled (pypath.internals.annot_formats.AnnotDef attribute)</a>
+</li>
+      <li><a href="api/pypath.internals.license.License.html#pypath.internals.license.License.enables">enables() (pypath.internals.license.License method)</a>
+</li>
+      <li><a href="api/pypath.inputs.encode.encode_tf_mirna_interactions.html#pypath.inputs.encode.encode_tf_mirna_interactions">encode_tf_mirna_interactions() (in module pypath.inputs.encode)</a>
+</li>
+      <li><a href="api/pypath.inputs.uniprot.Taxon.html#pypath.inputs.uniprot.Taxon.english">english (pypath.inputs.uniprot.Taxon attribute)</a>
+</li>
+      <li><a href="api/pypath.inputs.ensembl.ensembl_organisms.html#pypath.inputs.ensembl.ensembl_organisms">ensembl_organisms() (in module pypath.inputs.ensembl)</a>
+</li>
+      <li><a href="api/pypath.utils.orthology.EnsemblOrtholog.html#pypath.utils.orthology.EnsemblOrtholog">EnsemblOrtholog (class in pypath.utils.orthology)</a>
+</li>
+      <li><a href="api/pypath.utils.orthology.EnsemblOrthology.html#pypath.utils.orthology.EnsemblOrthology">EnsemblOrthology (class in pypath.utils.orthology)</a>
+</li>
+      <li><a href="api/pypath.utils.taxonomy.ensure_common_name.html#pypath.utils.taxonomy.ensure_common_name">ensure_common_name() (in module pypath.utils.taxonomy)</a>
+</li>
+      <li><a href="api/pypath.omnipath.app.DatabaseManager.html#pypath.omnipath.app.DatabaseManager.ensure_dataset">ensure_dataset() (pypath.omnipath.app.DatabaseManager method)</a>
+</li>
+      <li><a href="api/pypath.omnipath.app.DatabaseManager.html#pypath.omnipath.app.DatabaseManager.ensure_dirs">ensure_dirs() (pypath.omnipath.app.DatabaseManager method)</a>
+</li>
+      <li><a href="api/pypath.utils.taxonomy.ensure_ensembl_name.html#pypath.utils.taxonomy.ensure_ensembl_name">ensure_ensembl_name() (in module pypath.utils.taxonomy)</a>
+</li>
+      <li><a href="api/pypath.utils.taxonomy.ensure_latin_name.html#pypath.utils.taxonomy.ensure_latin_name">ensure_latin_name() (in module pypath.utils.taxonomy)</a>
+</li>
+      <li><a href="api/pypath.omnipath.app.DatabaseManager.html#pypath.omnipath.app.DatabaseManager.ensure_module">ensure_module() (pypath.omnipath.app.DatabaseManager method)</a>
+</li>
+      <li><a href="api/pypath.utils.taxonomy.ensure_ncbi_tax_id.html#pypath.utils.taxonomy.ensure_ncbi_tax_id">ensure_ncbi_tax_id() (in module pypath.utils.taxonomy)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.entities_by_data_model">entities_by_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.entities_by_data_model">entities_by_data_model() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.entities_by_interaction_type">entities_by_interaction_type (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.entities_by_interaction_type">entities_by_interaction_type() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.entities_by_interaction_type_and_data_model">entities_by_interaction_type_and_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.entities_by_interaction_type_and_data_model">entities_by_interaction_type_and_data_model() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.entities_by_interaction_type_and_data_model_and_resource">entities_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.entities_by_interaction_type_and_data_model_and_resource">entities_by_interaction_type_and_data_model_and_resource() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.entities_by_reference">entities_by_reference (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.entities_by_reference">entities_by_reference() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.entities_by_resource">entities_by_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.entities_by_resource">entities_by_resource() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.entity.Entity.html#pypath.core.entity.Entity">Entity (class in pypath.core.entity)</a>
+
+      <ul>
+        <li><a href="api/pypath.utils.pyreact.Entity.html#pypath.utils.pyreact.Entity">(class in pypath.utils.pyreact)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.interaction.InteractionKey.html#pypath.core.interaction.InteractionKey.entity_a">entity_a (pypath.core.interaction.InteractionKey attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.InteractionKey.html#pypath.core.interaction.InteractionKey.entity_b">entity_b (pypath.core.interaction.InteractionKey attribute)</a>
+</li>
+  </ul></td>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.entity_by_id">entity_by_id() (pypath.core.network.Network method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.entity_by_label">entity_by_label() (pypath.core.network.Network method)</a>
+</li>
+      <li><a href="api/pypath.core.entity.EntityKey.html#pypath.core.entity.EntityKey.entity_type">entity_type (pypath.core.entity.EntityKey attribute)</a>
+</li>
+      <li><a href="api/pypath.core.entity.EntityKey.html#pypath.core.entity.EntityKey">EntityKey (class in pypath.core.entity)</a>
+</li>
+      <li><a href="api/pypath.core.entity.EntityList.html#pypath.core.entity.EntityList">EntityList (class in pypath.core.entity)</a>
+</li>
+      <li><a href="api/pypath.utils.pyreact.EntitySet.html#pypath.utils.pyreact.EntitySet">EntitySet (class in pypath.utils.pyreact)</a>
+</li>
+      <li><a href="api/pypath.inputs.gutmgene.GutmgeneRaw.html#pypath.inputs.gutmgene.GutmgeneRaw.entrez">entrez (pypath.inputs.gutmgene.GutmgeneRaw attribute)</a>
+</li>
+      <li><a href="api/pypath.inputs.uniprot.UniprotRecordHistory.html#pypath.inputs.uniprot.UniprotRecordHistory.entry_name">entry_name (pypath.inputs.uniprot.UniprotRecordHistory attribute)</a>
+</li>
+      <li><a href="api/pypath.inputs.uniprot.UniprotRecordHistory.html#pypath.inputs.uniprot.UniprotRecordHistory.entry_version">entry_version (pypath.inputs.uniprot.UniprotRecordHistory attribute)</a>
+</li>
+      <li><a href="api/pypath.inputs.iptmnet.IptmnetInteraction.html#pypath.inputs.iptmnet.IptmnetInteraction.enzyme">enzyme (pypath.inputs.iptmnet.IptmnetInteraction attribute)</a>
+</li>
+      <li><a href="api/pypath.inputs.iptmnet.IptmnetInteraction.html#pypath.inputs.iptmnet.IptmnetInteraction.enzyme_isoform">enzyme_isoform (pypath.inputs.iptmnet.IptmnetInteraction attribute)</a>
+</li>
+      <li><a href="api/pypath.resources.data_formats.enzyme_substrate.html#pypath.resources.data_formats.enzyme_substrate">enzyme_substrate (in module pypath.resources.data_formats)</a>
+</li>
+      <li><a href="api/pypath.core.enz_sub.EnzymeSubstrateAggregator.html#pypath.core.enz_sub.EnzymeSubstrateAggregator">EnzymeSubstrateAggregator (class in pypath.core.enz_sub)</a>
+</li>
+      <li><a href="api/pypath.core.enz_sub.EnzymeSubstrateOrthologyProcessor.html#pypath.core.enz_sub.EnzymeSubstrateOrthologyProcessor">EnzymeSubstrateOrthologyProcessor (class in pypath.core.enz_sub)</a>
+</li>
+      <li><a href="api/pypath.core.enz_sub.EnzymeSubstrateProcessor.html#pypath.core.enz_sub.EnzymeSubstrateProcessor">EnzymeSubstrateProcessor (class in pypath.core.enz_sub)</a>
+</li>
+      <li><a href="api/pypath.internals.resource.EnzymeSubstrateResource.html#pypath.internals.resource.EnzymeSubstrateResource">EnzymeSubstrateResource (class in pypath.internals.resource)</a>
+</li>
+      <li><a href="api/pypath.internals.resource.EnzymeSubstrateResourceKey.html#pypath.internals.resource.EnzymeSubstrateResourceKey">EnzymeSubstrateResourceKey (class in pypath.internals.resource)</a>
+</li>
+      <li><a href="api/pypath.inputs.eutils.esummary.html#pypath.inputs.eutils.esummary">esummary() (in module pypath.inputs.eutils)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.evaluate_evidences">evaluate_evidences() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.evidence.Evidence.html#pypath.core.evidence.Evidence">Evidence (class in pypath.core.evidence)</a>
+</li>
+      <li><a href="api/pypath.inputs.pathophenodb.DiseasePathogen.html#pypath.inputs.pathophenodb.DiseasePathogen.evidence">evidence (pypath.inputs.pathophenodb.DiseasePathogen attribute)</a>
+</li>
+      <li><a href="api/pypath.core.evidence.Evidences.html#pypath.core.evidence.Evidences">Evidences (class in pypath.core.evidence)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.evidences_by_data_model">evidences_by_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.evidences_by_interaction_type">evidences_by_interaction_type (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.evidences_by_interaction_type_and_data_model">evidences_by_interaction_type_and_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.evidences_by_interaction_type_and_data_model_and_resource">evidences_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.evidences_by_reference">evidences_by_reference (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.evidences_by_resource">evidences_by_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.internals.annot_formats.AnnotDef.html#pypath.internals.annot_formats.AnnotDef.exclude">exclude (pypath.internals.annot_formats.AnnotDef attribute)</a>
+</li>
+      <li><a href="api/pypath.core.intercell_annot.excludes.html#pypath.core.intercell_annot.excludes">excludes (in module pypath.core.intercell_annot)</a>
+</li>
+      <li><a href="api/pypath.core.annot.Exocarta.html#pypath.core.annot.Exocarta">Exocarta (class in pypath.core.annot)</a>
+</li>
+      <li><a href="api/pypath.utils.pyreact.Entity.html#pypath.utils.pyreact.Entity.expand">expand() (pypath.utils.pyreact.Entity method)</a>
+
+      <ul>
+        <li><a href="api/pypath.utils.pyreact.Protein.html#pypath.utils.pyreact.Protein.expand">(pypath.utils.pyreact.Protein method)</a>
+</li>
+        <li><a href="api/pypath.utils.pyreact.ReactionSide.html#pypath.utils.pyreact.ReactionSide.expand">(pypath.utils.pyreact.ReactionSide method)</a>
+</li>
+        <li><a href="api/pypath.utils.pyreact.Reference.html#pypath.utils.pyreact.Reference.expand">(pypath.utils.pyreact.Reference method)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.inputs.expasy.expasy_enzyme_classes.html#pypath.inputs.expasy.expasy_enzyme_classes">expasy_enzyme_classes() (in module pypath.inputs.expasy)</a>
+</li>
+      <li><a href="api/pypath.inputs.expasy.expasy_enzymes.html#pypath.inputs.expasy.expasy_enzymes">expasy_enzymes() (in module pypath.inputs.expasy)</a>
+</li>
+      <li><a href="api/pypath.inputs.diseases.experiments_filtered.html#pypath.inputs.diseases.experiments_filtered">experiments_filtered() (in module pypath.inputs.diseases)</a>
+</li>
+      <li><a href="api/pypath.inputs.diseases.experiments_full.html#pypath.inputs.diseases.experiments_full">experiments_full() (in module pypath.inputs.diseases)</a>
+</li>
+      <li><a href="api/pypath.omnipath.export.Export.html#pypath.omnipath.export.Export">Export (class in pypath.omnipath.export)</a>
+</li>
+      <li><a href="api/pypath.omnipath.server.generate_about_page.export_licenses.html#pypath.omnipath.server.generate_about_page.export_licenses">export_licenses() (in module pypath.omnipath.server.generate_about_page)</a>
+
+      <ul>
+        <li><a href="api/pypath.resources.descriptions.export_licenses.html#pypath.resources.descriptions.export_licenses">(in module pypath.resources.descriptions)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.utils.go.GOAnnotation.html#pypath.utils.go.GOAnnotation.expr_names_to_terms">expr_names_to_terms() (pypath.utils.go.GOAnnotation method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.extra_directions">extra_directions() (pypath.core.network.Network method)</a>
+</li>
+      <li><a href="api/pypath.share.curl.Curl.html#pypath.share.curl.Curl.extract">extract() (pypath.share.curl.Curl method)</a>
+
+      <ul>
+        <li><a href="api/pypath.share.curl.FileOpener.html#pypath.share.curl.FileOpener.extract">(pypath.share.curl.FileOpener method)</a>
+</li>
+        <li><a href="api/pypath.utils.pyreact.BioPaxReader.html#pypath.utils.pyreact.BioPaxReader.extract">(pypath.utils.pyreact.BioPaxReader method)</a>
+</li>
+      </ul></li>
+  </ul></td>
+</tr></table>
+
+<h2 id="F">F</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="api/pypath.inputs.uniprot.UniprotQuery.html#pypath.inputs.uniprot.UniprotQuery.fail_on_empty">fail_on_empty (pypath.inputs.uniprot.UniprotQuery attribute)</a>
+</li>
+      <li><a href="api/pypath.inputs.icellnet.IcellnetRecord.html#pypath.inputs.icellnet.IcellnetRecord.family">family (pypath.inputs.icellnet.IcellnetRecord attribute)</a>
+</li>
+      <li><a href="api/pypath.utils.uniprot.features_table.html#pypath.utils.uniprot.features_table">features_table() (in module pypath.utils.uniprot)</a>
+</li>
+      <li><a href="api/pypath.inputs.hmdb.schema.common.Field.html#pypath.inputs.hmdb.schema.common.Field">Field (class in pypath.inputs.hmdb.schema.common)</a>
+</li>
+      <li><a href="api/pypath.internals.input_formats.FileMapping.html#pypath.internals.input_formats.FileMapping">FileMapping (class in pypath.internals.input_formats)</a>
+</li>
+      <li><a href="api/pypath.share.curl.FileOpener.html#pypath.share.curl.FileOpener">FileOpener (class in pypath.share.curl)</a>
+</li>
+      <li><a href="api/pypath.core.annot.CustomAnnotation.html#pypath.core.annot.CustomAnnotation.filter">filter() (pypath.core.annot.CustomAnnotation method)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.intercell.IntercellAnnotation.html#pypath.core.intercell.IntercellAnnotation.filter">(pypath.core.intercell.IntercellAnnotation method)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.annot.CustomAnnotation.html#pypath.core.annot.CustomAnnotation.filter_classes">filter_classes() (pypath.core.annot.CustomAnnotation static method)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.intercell.IntercellAnnotation.html#pypath.core.intercell.IntercellAnnotation.filter_classes">(pypath.core.intercell.IntercellAnnotation static method)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.entity.Entity.html#pypath.core.entity.Entity.filter_entity_type">filter_entity_type() (pypath.core.entity.Entity class method)</a>
+
+      <ul>
+        <li><a href="api/pypath.internals.annot_formats.AnnotationGroup.html#pypath.internals.annot_formats.AnnotationGroup.filter_entity_type">(pypath.internals.annot_formats.AnnotationGroup method)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.annot.CustomAnnotation.html#pypath.core.annot.CustomAnnotation.filter_interclass_network">filter_interclass_network() (pypath.core.annot.CustomAnnotation method)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.intercell.IntercellAnnotation.html#pypath.core.intercell.IntercellAnnotation.filter_interclass_network">(pypath.core.intercell.IntercellAnnotation method)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.common.filter_network_df.html#pypath.core.common.filter_network_df">filter_network_df() (in module pypath.core.common)</a>
+</li>
+  </ul></td>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.find_paths">find_paths() (pypath.core.network.Network method)</a>
+</li>
+      <li><a href="api/pypath.utils.seq.Seq.html#pypath.utils.seq.Seq.findall">findall() (pypath.utils.seq.Seq method)</a>
+</li>
+      <li><a href="api/pypath.utils.go.GeneOntology.html#pypath.utils.go.GeneOntology.flatten">flatten() (pypath.utils.go.GeneOntology method)</a>
+</li>
+      <li><a href="api/pypath.omnipath.app.DatabaseManager.html#pypath.omnipath.app.DatabaseManager.foreach_dataset">foreach_dataset() (pypath.omnipath.app.DatabaseManager method)</a>
+</li>
+      <li><a href="api/pypath.inputs.sider.SiderSideeffetFrequency.html#pypath.inputs.sider.SiderSideeffetFrequency.frequency">frequency (pypath.inputs.sider.SiderSideeffetFrequency attribute)</a>
+</li>
+      <li><a href="api/pypath.omnipath.databases.define.DatabaseDefinition.html#pypath.omnipath.databases.define.DatabaseDefinition.from_dict">from_dict() (pypath.omnipath.databases.define.DatabaseDefinition class method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.from_igraph">from_igraph() (pypath.core.network.Network class method)</a>
+</li>
+      <li><a href="api/pypath.omnipath.databases.define.DatabaseDefinition.html#pypath.omnipath.databases.define.DatabaseDefinition.from_json">from_json() (pypath.omnipath.databases.define.DatabaseDefinition class method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.from_pickle">from_pickle() (pypath.core.network.Network class method)</a>
+</li>
+      <li><a href="api/pypath.utils.uniprot.full_name.html#pypath.utils.uniprot.full_name">full_name() (in module pypath.utils.uniprot)</a>
+</li>
+      <li><a href="api/pypath.utils.uniprot.function.html#pypath.utils.uniprot.function">function() (in module pypath.utils.uniprot)</a>
+</li>
+      <li><a href="api/pypath.utils.uniprot.function_genecards.html#pypath.utils.uniprot.function_genecards">function_genecards() (in module pypath.utils.uniprot)</a>
+</li>
+      <li><a href="api/pypath.utils.uniprot.function_or_genecards.html#pypath.utils.uniprot.function_or_genecards">function_or_genecards() (in module pypath.utils.uniprot)</a>
+</li>
+      <li><a href="api/pypath.utils.uniprot.function_with_genecards.html#pypath.utils.uniprot.function_with_genecards">function_with_genecards() (in module pypath.utils.uniprot)</a>
+</li>
+      <li><a href="api/pypath.utils.uniprot.function_with_xrefs.html#pypath.utils.uniprot.function_with_xrefs">function_with_xrefs() (in module pypath.utils.uniprot)</a>
+</li>
+  </ul></td>
+</tr></table>
+
+<h2 id="G">G</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="api/pypath.utils.pyreact.PyReact.html#pypath.utils.pyreact.PyReact.gen_cvariations">gen_cvariations() (pypath.utils.pyreact.PyReact method)</a>
+</li>
+      <li><a href="api/pypath.resources.descriptions.gen_html.html#pypath.resources.descriptions.gen_html">gen_html() (in module pypath.resources.descriptions)</a>
+</li>
+      <li><a href="api/pypath.inputs.kegg_api.gene_to_disease.html#pypath.inputs.kegg_api.gene_to_disease">gene_to_disease() (in module pypath.inputs.kegg_api)</a>
+</li>
+      <li><a href="api/pypath.inputs.kegg_api.gene_to_drug.html#pypath.inputs.kegg_api.gene_to_drug">gene_to_drug() (in module pypath.inputs.kegg_api)</a>
+</li>
+      <li><a href="api/pypath.inputs.kegg_api.gene_to_pathway.html#pypath.inputs.kegg_api.gene_to_pathway">gene_to_pathway() (in module pypath.inputs.kegg_api)</a>
+</li>
+      <li><a href="api/pypath.inputs.genecards.genecards_datasheet.html#pypath.inputs.genecards.genecards_datasheet">genecards_datasheet() (in module pypath.inputs.genecards)</a>
+</li>
+      <li><a href="api/pypath.inputs.genecards.genecards_soup.html#pypath.inputs.genecards.genecards_soup">genecards_soup() (in module pypath.inputs.genecards)</a>
+</li>
+      <li><a href="api/pypath.inputs.genecards.genecards_summaries.html#pypath.inputs.genecards.genecards_summaries">genecards_summaries() (in module pypath.inputs.genecards)</a>
+</li>
+      <li><a href="api/pypath.utils.go.GeneOntology.html#pypath.utils.go.GeneOntology">GeneOntology (class in pypath.utils.go)</a>
+</li>
+      <li><a href="api/pypath.omnipath.server.generate_about_page.generate_about_html.html#pypath.omnipath.server.generate_about_page.generate_about_html">generate_about_html() (in module pypath.omnipath.server.generate_about_page)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.generate_df_records">generate_df_records() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.omnipath.export.Export.html#pypath.omnipath.export.Export.generic_attr_processor">generic_attr_processor() (pypath.omnipath.export.Export static method)</a>
+</li>
+      <li><a href="api/pypath.inputs.gutmgene.GutmgeneRaw.html#pypath.inputs.gutmgene.GutmgeneRaw.genesymbol">genesymbol (pypath.inputs.gutmgene.GutmgeneRaw attribute)</a>
+</li>
+      <li><a href="api/pypath.utils.uniprot.genesymbol.html#pypath.utils.uniprot.genesymbol">genesymbol() (in module pypath.utils.uniprot)</a>
+</li>
+      <li><a href="api/pypath.internals.resource.NetworkDataset.html#pypath.internals.resource.NetworkDataset.get">get() (pypath.internals.resource.NetworkDataset method)</a>
+</li>
+      <li><a href="api/pypath.inputs.threedid.get_3did.html#pypath.inputs.threedid.get_3did">get_3did() (in module pypath.inputs.threedid)</a>
+</li>
+      <li><a href="api/pypath.inputs.threedid.get_3did_ddi.html#pypath.inputs.threedid.get_3did_ddi">get_3did_ddi() (in module pypath.inputs.threedid)</a>
+</li>
+      <li><a href="api/pypath.inputs.threedid.get_3did_dmi.html#pypath.inputs.threedid.get_3did_dmi">get_3did_dmi() (in module pypath.inputs.threedid)</a>
+</li>
+      <li><a href="api/pypath.inputs.reaction.get_acsn_effects.html#pypath.inputs.reaction.get_acsn_effects">get_acsn_effects() (in module pypath.inputs.reaction)</a>
+</li>
+      <li><a href="api/pypath.utils.go.GeneOntology.html#pypath.utils.go.GeneOntology.get_all_ancestors">get_all_ancestors() (pypath.utils.go.GeneOntology method)</a>
+</li>
+      <li><a href="api/pypath.utils.go.GeneOntology.html#pypath.utils.go.GeneOntology.get_all_descendants">get_all_descendants() (pypath.utils.go.GeneOntology method)</a>
+</li>
+      <li><a href="api/pypath.inputs.biomodels.get_all_models.html#pypath.inputs.biomodels.get_all_models">get_all_models() (in module pypath.inputs.biomodels)</a>
+</li>
+      <li><a href="api/pypath.utils.go.GOAnnotation.html#pypath.utils.go.GOAnnotation.get_annot">get_annot() (pypath.utils.go.GOAnnotation method)</a>
+</li>
+      <li><a href="api/pypath.utils.go.GOAnnotation.html#pypath.utils.go.GOAnnotation.get_annot_ancestors">get_annot_ancestors() (pypath.utils.go.GOAnnotation method)</a>
+</li>
+      <li><a href="api/pypath.core.annot.GOCustomIntercell.html#pypath.core.annot.GOCustomIntercell.get_annotation">get_annotation() (pypath.core.annot.GOCustomIntercell method)</a>
+
+      <ul>
+        <li><a href="api/pypath.utils.go.GOCustomAnnotation.html#pypath.utils.go.GOCustomAnnotation.get_annotation">(pypath.utils.go.GOCustomAnnotation method)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.annot.GOCustomIntercell.html#pypath.core.annot.GOCustomIntercell.get_annotations">get_annotations() (pypath.core.annot.GOCustomIntercell method)</a>
+
+      <ul>
+        <li><a href="api/pypath.utils.go.GOCustomAnnotation.html#pypath.utils.go.GOCustomAnnotation.get_annotations">(pypath.utils.go.GOCustomAnnotation method)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.utils.go.GOAnnotation.html#pypath.utils.go.GOAnnotation.get_annots">get_annots() (pypath.utils.go.GOAnnotation method)</a>
+</li>
+      <li><a href="api/pypath.utils.go.GOAnnotation.html#pypath.utils.go.GOAnnotation.get_annots_ancestors">get_annots_ancestors() (pypath.utils.go.GOAnnotation method)</a>
+</li>
+      <li><a href="api/pypath.omnipath.app.DatabaseManager.html#pypath.omnipath.app.DatabaseManager.get_args_curated">get_args_curated() (pypath.omnipath.app.DatabaseManager method)</a>
+</li>
+      <li><a href="api/pypath.omnipath.app.DatabaseManager.html#pypath.omnipath.app.DatabaseManager.get_args_lncrna_mrna">get_args_lncrna_mrna() (pypath.omnipath.app.DatabaseManager method)</a>
+</li>
+      <li><a href="api/pypath.omnipath.app.DatabaseManager.html#pypath.omnipath.app.DatabaseManager.get_args_mirna_mrna">get_args_mirna_mrna() (pypath.omnipath.app.DatabaseManager method)</a>
+</li>
+      <li><a href="api/pypath.omnipath.app.DatabaseManager.html#pypath.omnipath.app.DatabaseManager.get_args_small_molecule">get_args_small_molecule() (pypath.omnipath.app.DatabaseManager method)</a>
+</li>
+      <li><a href="api/pypath.omnipath.app.DatabaseManager.html#pypath.omnipath.app.DatabaseManager.get_args_tf_mirna">get_args_tf_mirna() (pypath.omnipath.app.DatabaseManager method)</a>
+</li>
+      <li><a href="api/pypath.omnipath.app.DatabaseManager.html#pypath.omnipath.app.DatabaseManager.get_args_tf_target">get_args_tf_target() (pypath.omnipath.app.DatabaseManager method)</a>
+</li>
+      <li><a href="api/pypath.utils.go.GeneOntology.html#pypath.utils.go.GeneOntology.get_aspect">get_aspect() (pypath.utils.go.GeneOntology method)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.get_attr">get_attr() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.inputs.biomodels.get_biomodels.html#pypath.inputs.biomodels.get_biomodels">get_biomodels() (in module pypath.inputs.biomodels)</a>
+</li>
+      <li><a href="api/pypath.inputs.biomodels.get_biomodels_req.html#pypath.inputs.biomodels.get_biomodels_req">get_biomodels_req() (in module pypath.inputs.biomodels)</a>
+</li>
+      <li><a href="api/pypath.internals.intera.Interface.html#pypath.internals.intera.Interface.get_bonds">get_bonds() (pypath.internals.intera.Interface method)</a>
+</li>
+      <li><a href="api/pypath.omnipath.app.DatabaseManager.html#pypath.omnipath.app.DatabaseManager.get_build_args">get_build_args() (pypath.omnipath.app.DatabaseManager method)</a>
+</li>
+      <li><a href="api/pypath.share.cache.get_cachedir.html#pypath.share.cache.get_cachedir">get_cachedir() (in module pypath.share.cache)</a>
+</li>
+      <li><a href="api/pypath.legacy.db_categories.get_categories.html#pypath.legacy.db_categories.get_categories">get_categories() (in module pypath.legacy.db_categories)</a>
+</li>
+      <li><a href="api/pypath.legacy.db_categories.get_category.html#pypath.legacy.db_categories.get_category">get_category() (in module pypath.legacy.db_categories)</a>
+</li>
+      <li><a href="api/pypath.core.annot.CustomAnnotation.html#pypath.core.annot.CustomAnnotation.get_class">get_class() (pypath.core.annot.CustomAnnotation method)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.intercell.IntercellAnnotation.html#pypath.core.intercell.IntercellAnnotation.get_class">(pypath.core.intercell.IntercellAnnotation method)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.get_complex_identifiers">get_complex_identifiers (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.get_complex_identifiers">get_complex_identifiers() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.get_complex_labels">get_complex_labels (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.get_complex_labels">get_complex_labels() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.get_complexes">get_complexes (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.get_complexes">get_complexes() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.resources.get_controller.html#pypath.resources.get_controller">get_controller() (in module pypath.resources)</a>
+</li>
+      <li><a href="api/pypath.inputs.reaction.get_controls.html#pypath.inputs.reaction.get_controls">get_controls() (in module pypath.inputs.reaction)</a>
+</li>
+      <li><a href="api/pypath.inputs.cpad.get_cpad.html#pypath.inputs.cpad.get_cpad">get_cpad() (in module pypath.inputs.cpad)</a>
+</li>
+      <li><a href="api/pypath.inputs.csa.get_csa.html#pypath.inputs.csa.get_csa">get_csa() (in module pypath.inputs.csa)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.get_curation_effort">get_curation_effort (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.get_data_models">get_data_models (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.get_data_models">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.get_datasets">get_datasets (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.get_datasets">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.annot.get_db.html#pypath.core.annot.get_db">get_db() (in module pypath.core.annot)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.complex.get_db.html#pypath.core.complex.get_db">(in module pypath.core.complex)</a>
+</li>
+        <li><a href="api/pypath.core.enz_sub.get_db.html#pypath.core.enz_sub.get_db">(in module pypath.core.enz_sub)</a>
+</li>
+        <li><a href="api/pypath.core.intercell.get_db.html#pypath.core.intercell.get_db">(in module pypath.core.intercell)</a>
+</li>
+        <li><a href="api/pypath.core.network.get_db.html#pypath.core.network.get_db">(in module pypath.core.network)</a>
+</li>
+        <li><a href="api/pypath.inputs.uniprot_db.get_db.html#pypath.inputs.uniprot_db.get_db">(in module pypath.inputs.uniprot_db)</a>
+</li>
+        <li><a href="api/pypath.utils.go.get_db.html#pypath.utils.go.get_db">(in module pypath.utils.go)</a>
+</li>
+        <li><a href="api/pypath.utils.taxonomy.get_db.html#pypath.utils.taxonomy.get_db">(in module pypath.utils.taxonomy)</a>
+</li>
+        <li><a href="api/pypath.omnipath.app.DatabaseManager.html#pypath.omnipath.app.DatabaseManager.get_db">(pypath.omnipath.app.DatabaseManager method)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.get_degrees">get_degrees() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.get_degrees_directed">get_degrees_directed (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.get_degrees_directed">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.get_degrees_directed_in">get_degrees_directed_in (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.get_degrees_directed_in">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.get_degrees_directed_out">get_degrees_directed_out (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.get_degrees_directed_out">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.get_degrees_negative">get_degrees_negative (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.get_degrees_negative">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.get_degrees_negative_in">get_degrees_negative_in (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.get_degrees_negative_in">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.get_degrees_negative_out">get_degrees_negative_out (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.get_degrees_negative_out">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.get_degrees_non_directed">get_degrees_non_directed (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.get_degrees_non_directed">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.get_degrees_positive">get_degrees_positive (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.get_degrees_positive">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.get_degrees_positive_in">get_degrees_positive_in (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.get_degrees_positive_in">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.get_degrees_positive_out">get_degrees_positive_out (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.get_degrees_positive_out">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.get_degrees_signed">get_degrees_signed (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.get_degrees_signed">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.get_degrees_signed_in">get_degrees_signed_in (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.get_degrees_signed_in">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.get_degrees_signed_out">get_degrees_signed_out (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.get_degrees_signed_out">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.get_degrees_undirected">get_degrees_undirected (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.get_degrees_undirected">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.share.progress.Progress.html#pypath.share.progress.Progress.get_desc">get_desc() (pypath.share.progress.Progress method)</a>
+</li>
+      <li><a href="api/pypath.utils.orthology.get_df.html#pypath.utils.orthology.get_df">get_df() (in module pypath.utils.orthology)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.annot.CustomAnnotation.html#pypath.core.annot.CustomAnnotation.get_df">(pypath.core.annot.CustomAnnotation method)</a>
+</li>
+        <li><a href="api/pypath.core.intercell.IntercellAnnotation.html#pypath.core.intercell.IntercellAnnotation.get_df">(pypath.core.intercell.IntercellAnnotation method)</a>
+</li>
+        <li><a href="api/pypath.utils.orthology.OrthologyManager.html#pypath.utils.orthology.OrthologyManager.get_df">(pypath.utils.orthology.OrthologyManager method)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.inputs.dgidb.get_dgidb_old.html#pypath.inputs.dgidb.get_dgidb_old">get_dgidb_old() (in module pypath.inputs.dgidb)</a>
+</li>
+      <li><a href="api/pypath.utils.orthology.get_dict.html#pypath.utils.orthology.get_dict">get_dict() (in module pypath.utils.orthology)</a>
+
+      <ul>
+        <li><a href="api/pypath.utils.orthology.OrthologyManager.html#pypath.utils.orthology.OrthologyManager.get_dict">(pypath.utils.orthology.OrthologyManager method)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.get_direction">get_direction() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.get_directions">get_directions() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.inputs.domino.get_domino.html#pypath.inputs.domino.get_domino">get_domino() (in module pypath.inputs.domino)</a>
+</li>
+      <li><a href="api/pypath.inputs.dorothea.get_dorothea_old.html#pypath.inputs.dorothea.get_dorothea_old">get_dorothea_old() (in module pypath.inputs.dorothea)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.get_entities">get_entities (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.get_entities">get_entities() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.get_evidences">get_evidences (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.inputs.exocarta.get_exocarta.html#pypath.inputs.exocarta.get_exocarta">get_exocarta() (in module pypath.inputs.exocarta)</a>
+</li>
+      <li><a href="api/pypath.utils.proteomicsdb.ProteomicsDB.html#pypath.utils.proteomicsdb.ProteomicsDB.get_expression">get_expression() (pypath.utils.proteomicsdb.ProteomicsDB method)</a>
+</li>
+      <li><a href="api/pypath.inputs.go.get_go_desc.html#pypath.inputs.go.get_go_desc">get_go_desc() (in module pypath.inputs.go)</a>
+</li>
+      <li><a href="api/pypath.inputs.go.get_go_quick.html#pypath.inputs.go.get_go_quick">get_go_quick() (in module pypath.inputs.go)</a>
+</li>
+      <li><a href="api/pypath.inputs.go.get_goslim.html#pypath.inputs.go.get_goslim">get_goslim() (in module pypath.inputs.go)</a>
+</li>
+      <li><a href="api/pypath.inputs.havugimana.get_havugimana.html#pypath.inputs.havugimana.get_havugimana">get_havugimana() (in module pypath.inputs.havugimana)</a>
+</li>
+      <li><a href="api/pypath.omnipath.export.Export.html#pypath.omnipath.export.Export.get_header">get_header() (pypath.omnipath.export.Export method)</a>
+</li>
+      <li><a href="api/pypath.inputs.homologene.get_homologene.html#pypath.inputs.homologene.get_homologene">get_homologene() (in module pypath.inputs.homologene)</a>
+</li>
+      <li><a href="api/pypath.inputs.hpmr.get_hpmr.html#pypath.inputs.hpmr.get_hpmr">get_hpmr() (in module pypath.inputs.hpmr)</a>
+</li>
+      <li><a href="api/pypath.inputs.hprd.get_hprd.html#pypath.inputs.hprd.get_hprd">get_hprd() (in module pypath.inputs.hprd)</a>
+</li>
+      <li><a href="api/pypath.inputs.i3d.get_i3d.html#pypath.inputs.i3d.get_i3d">get_i3d() (in module pypath.inputs.i3d)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.get_identifiers">get_identifiers (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.get_identifiers">get_identifiers() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.inputs.ielm.get_ielm.html#pypath.inputs.ielm.get_ielm">get_ielm() (in module pypath.inputs.ielm)</a>
+</li>
+      <li><a href="api/pypath.inputs.ielm.get_ielm_huge.html#pypath.inputs.ielm.get_ielm_huge">get_ielm_huge() (in module pypath.inputs.ielm)</a>
+</li>
+      <li><a href="api/pypath.inputs.imweb.get_imweb.html#pypath.inputs.imweb.get_imweb">get_imweb() (in module pypath.inputs.imweb)</a>
+</li>
+      <li><a href="api/pypath.inputs.imweb.get_imweb_req.html#pypath.inputs.imweb.get_imweb_req">get_imweb_req() (in module pypath.inputs.imweb)</a>
+</li>
+      <li><a href="api/pypath.inputs.instruct.get_instruct.html#pypath.inputs.instruct.get_instruct">get_instruct() (in module pypath.inputs.instruct)</a>
+</li>
+      <li><a href="api/pypath.inputs.instruct.get_instruct_offsets.html#pypath.inputs.instruct.get_instruct_offsets">get_instruct_offsets() (in module pypath.inputs.instruct)</a>
+</li>
+      <li><a href="api/pypath.inputs.integrins.get_integrins.html#pypath.inputs.integrins.get_integrins">get_integrins() (in module pypath.inputs.integrins)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.get_interaction_types">get_interaction_types (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.get_interaction_types">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.get_interactions">get_interactions (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.inputs.reaction.get_interactions.html#pypath.inputs.reaction.get_interactions">get_interactions() (in module pypath.inputs.reaction)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.get_interactions">(pypath.core.interaction.Interaction method)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.get_interactions_0">get_interactions_0 (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.get_interactions_0">get_interactions_0() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.get_interactions_directed">get_interactions_directed (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.get_interactions_directed">get_interactions_directed() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.get_interactions_mutual">get_interactions_mutual (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.get_interactions_mutual">get_interactions_mutual() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.get_interactions_negative">get_interactions_negative (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.get_interactions_negative">get_interactions_negative() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.get_interactions_non_directed">get_interactions_non_directed (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.get_interactions_non_directed">get_interactions_non_directed() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.get_interactions_non_directed_0">get_interactions_non_directed_0 (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.get_interactions_non_directed_0">get_interactions_non_directed_0() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.get_interactions_positive">get_interactions_positive (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.get_interactions_positive">get_interactions_positive() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.get_interactions_signed">get_interactions_signed (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.get_interactions_signed">get_interactions_signed() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.get_interactions_undirected">get_interactions_undirected (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.get_interactions_undirected">get_interactions_undirected() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.get_interactions_undirected_0">get_interactions_undirected_0 (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.get_interactions_undirected_0">get_interactions_undirected_0() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.annot.CustomAnnotation.html#pypath.core.annot.CustomAnnotation.get_interclass_network_df">get_interclass_network_df() (pypath.core.annot.CustomAnnotation method)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.intercell.IntercellAnnotation.html#pypath.core.intercell.IntercellAnnotation.get_interclass_network_df">(pypath.core.intercell.IntercellAnnotation method)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.utils.seq.get_isoforms.html#pypath.utils.seq.get_isoforms">get_isoforms() (in module pypath.utils.seq)</a>
+</li>
+      <li><a href="api/pypath.utils.mapping.MappingTable.html#pypath.utils.mapping.MappingTable.get_key">get_key() (pypath.utils.mapping.MappingTable method)</a>
+</li>
+      <li><a href="api/pypath.inputs.mimp.get_kinase_class.html#pypath.inputs.mimp.get_kinase_class">get_kinase_class() (in module pypath.inputs.mimp)</a>
+</li>
+      <li><a href="api/pypath.visual.igraph_drawing.edge.AbstractEdgeDrawer.html#pypath.visual.igraph_drawing.edge.AbstractEdgeDrawer.get_label_position">get_label_position() (pypath.visual.igraph_drawing.edge.AbstractEdgeDrawer method)</a>
+
+      <ul>
+        <li><a href="api/pypath.visual.igraph_drawing.edge.AlphaVaryingEdgeDrawer.html#pypath.visual.igraph_drawing.edge.AlphaVaryingEdgeDrawer.get_label_position">(pypath.visual.igraph_drawing.edge.AlphaVaryingEdgeDrawer method)</a>
+</li>
+        <li><a href="api/pypath.visual.igraph_drawing.edge.ArrowEdgeDrawer.html#pypath.visual.igraph_drawing.edge.ArrowEdgeDrawer.get_label_position">(pypath.visual.igraph_drawing.edge.ArrowEdgeDrawer method)</a>
+</li>
+        <li><a href="api/pypath.visual.igraph_drawing.edge.DarkToLightEdgeDrawer.html#pypath.visual.igraph_drawing.edge.DarkToLightEdgeDrawer.get_label_position">(pypath.visual.igraph_drawing.edge.DarkToLightEdgeDrawer method)</a>
+</li>
+        <li><a href="api/pypath.visual.igraph_drawing.edge.LightToDarkEdgeDrawer.html#pypath.visual.igraph_drawing.edge.LightToDarkEdgeDrawer.get_label_position">(pypath.visual.igraph_drawing.edge.LightToDarkEdgeDrawer method)</a>
+</li>
+        <li><a href="api/pypath.visual.igraph_drawing.edge.TaperedEdgeDrawer.html#pypath.visual.igraph_drawing.edge.TaperedEdgeDrawer.get_label_position">(pypath.visual.igraph_drawing.edge.TaperedEdgeDrawer method)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.get_labels">get_labels (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.get_labels">get_labels() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.inputs.li2012.get_li2012.html#pypath.inputs.li2012.get_li2012">get_li2012() (in module pypath.inputs.li2012)</a>
+</li>
+      <li><a href="api/pypath.internals.intera.DomainMotif.html#pypath.internals.intera.DomainMotif.get_line">get_line() (pypath.internals.intera.DomainMotif method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.get_lncrna_identifiers">get_lncrna_identifiers (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.get_lncrna_identifiers">get_lncrna_identifiers() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.get_lncrna_labels">get_lncrna_labels (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.get_lncrna_labels">get_lncrna_labels() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.get_lncrnas">get_lncrnas (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.get_lncrnas">get_lncrnas() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.omnipath.databases.get_manager.html#pypath.omnipath.databases.get_manager">get_manager() (in module pypath.omnipath.databases)</a>
+
+      <ul>
+        <li><a href="api/pypath.utils.orthology.get_manager.html#pypath.utils.orthology.get_manager">(in module pypath.utils.orthology)</a>
+</li>
+        <li><a href="api/pypath.utils.reflists.get_manager.html#pypath.utils.reflists.get_manager">(in module pypath.utils.reflists)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.utils.mapping.get_mapper.html#pypath.utils.mapping.get_mapper">get_mapper() (in module pypath.utils.mapping)</a>
+</li>
+      <li><a href="api/pypath.inputs.get_method.html#pypath.inputs.get_method">get_method() (in module pypath.inputs)</a>
+</li>
+      <li><a href="api/pypath.inputs.mirbase.get_mirbase_aliases.html#pypath.inputs.mirbase.get_mirbase_aliases">get_mirbase_aliases() (in module pypath.inputs.mirbase)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.get_mirna_identifiers">get_mirna_identifiers (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.get_mirna_identifiers">get_mirna_identifiers() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.get_mirna_labels">get_mirna_labels (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.get_mirna_labels">get_mirna_labels() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.get_mirnas">get_mirnas (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.get_mirnas">get_mirnas() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.utils.go.GeneOntology.html#pypath.utils.go.GeneOntology.get_name">get_name() (pypath.utils.go.GeneOntology method)</a>
+
+      <ul>
+        <li><a href="api/pypath.utils.go.GOAnnotation.html#pypath.utils.go.GOAnnotation.get_name">(pypath.utils.go.GOAnnotation method)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.annot.Adhesome.html#pypath.core.annot.Adhesome.get_names">get_names() (pypath.core.annot.Adhesome method)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.annot.Almen2009.html#pypath.core.annot.Almen2009.get_names">(pypath.core.annot.Almen2009 method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.AnnotationBase.html#pypath.core.annot.AnnotationBase.get_names">(pypath.core.annot.AnnotationBase method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Baccin2019.html#pypath.core.annot.Baccin2019.get_names">(pypath.core.annot.Baccin2019 method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Biogps.html#pypath.core.annot.Biogps.get_names">(pypath.core.annot.Biogps method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cancerdrugsdb.html#pypath.core.annot.Cancerdrugsdb.get_names">(pypath.core.annot.Cancerdrugsdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CancerGeneCensus.html#pypath.core.annot.CancerGeneCensus.get_names">(pypath.core.annot.CancerGeneCensus method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cancersea.html#pypath.core.annot.Cancersea.get_names">(pypath.core.annot.Cancersea method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cellcall.html#pypath.core.annot.Cellcall.get_names">(pypath.core.annot.Cellcall method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cellcellinteractions.html#pypath.core.annot.Cellcellinteractions.get_names">(pypath.core.annot.Cellcellinteractions method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cellchatdb.html#pypath.core.annot.Cellchatdb.get_names">(pypath.core.annot.Cellchatdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CellchatdbComplex.html#pypath.core.annot.CellchatdbComplex.get_names">(pypath.core.annot.CellchatdbComplex method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cellinker.html#pypath.core.annot.Cellinker.get_names">(pypath.core.annot.Cellinker method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CellinkerComplex.html#pypath.core.annot.CellinkerComplex.get_names">(pypath.core.annot.CellinkerComplex method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CellPhoneDB.html#pypath.core.annot.CellPhoneDB.get_names">(pypath.core.annot.CellPhoneDB method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CellPhoneDBComplex.html#pypath.core.annot.CellPhoneDBComplex.get_names">(pypath.core.annot.CellPhoneDBComplex method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CellSurfaceProteinAtlas.html#pypath.core.annot.CellSurfaceProteinAtlas.get_names">(pypath.core.annot.CellSurfaceProteinAtlas method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CellSurfaceProteinAtlasCellType.html#pypath.core.annot.CellSurfaceProteinAtlasCellType.get_names">(pypath.core.annot.CellSurfaceProteinAtlasCellType method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Celltalkdb.html#pypath.core.annot.Celltalkdb.get_names">(pypath.core.annot.Celltalkdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Celltypist.html#pypath.core.annot.Celltypist.get_names">(pypath.core.annot.Celltypist method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Comppi.html#pypath.core.annot.Comppi.get_names">(pypath.core.annot.Comppi method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Connectomedb.html#pypath.core.annot.Connectomedb.get_names">(pypath.core.annot.Connectomedb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Corum.html#pypath.core.annot.Corum.get_names">(pypath.core.annot.Corum method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CorumFuncat.html#pypath.core.annot.CorumFuncat.get_names">(pypath.core.annot.CorumFuncat method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CorumGO.html#pypath.core.annot.CorumGO.get_names">(pypath.core.annot.CorumGO method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cpad.html#pypath.core.annot.Cpad.get_names">(pypath.core.annot.Cpad method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cytosig.html#pypath.core.annot.Cytosig.get_names">(pypath.core.annot.Cytosig method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Dgidb.html#pypath.core.annot.Dgidb.get_names">(pypath.core.annot.Dgidb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Disgenet.html#pypath.core.annot.Disgenet.get_names">(pypath.core.annot.Disgenet method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Embrace.html#pypath.core.annot.Embrace.get_names">(pypath.core.annot.Embrace method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Exocarta.html#pypath.core.annot.Exocarta.get_names">(pypath.core.annot.Exocarta method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.GOIntercell.html#pypath.core.annot.GOIntercell.get_names">(pypath.core.annot.GOIntercell method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Gpcrdb.html#pypath.core.annot.Gpcrdb.get_names">(pypath.core.annot.Gpcrdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.GuideToPharmacology.html#pypath.core.annot.GuideToPharmacology.get_names">(pypath.core.annot.GuideToPharmacology method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Hgnc.html#pypath.core.annot.Hgnc.get_names">(pypath.core.annot.Hgnc method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.HpmrComplex.html#pypath.core.annot.HpmrComplex.get_names">(pypath.core.annot.HpmrComplex method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.HPO.html#pypath.core.annot.HPO.get_names">(pypath.core.annot.HPO method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Humancellmap.html#pypath.core.annot.Humancellmap.get_names">(pypath.core.annot.Humancellmap method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.HumanPlasmaMembraneReceptome.html#pypath.core.annot.HumanPlasmaMembraneReceptome.get_names">(pypath.core.annot.HumanPlasmaMembraneReceptome method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.HumanProteinAtlas.html#pypath.core.annot.HumanProteinAtlas.get_names">(pypath.core.annot.HumanProteinAtlas method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.HumanProteinAtlasSecretome.html#pypath.core.annot.HumanProteinAtlasSecretome.get_names">(pypath.core.annot.HumanProteinAtlasSecretome method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.HumanProteinAtlasSubcellular.html#pypath.core.annot.HumanProteinAtlasSubcellular.get_names">(pypath.core.annot.HumanProteinAtlasSubcellular method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Icellnet.html#pypath.core.annot.Icellnet.get_names">(pypath.core.annot.Icellnet method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.IcellnetComplex.html#pypath.core.annot.IcellnetComplex.get_names">(pypath.core.annot.IcellnetComplex method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Integrins.html#pypath.core.annot.Integrins.get_names">(pypath.core.annot.Integrins method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.InterPro.html#pypath.core.annot.InterPro.get_names">(pypath.core.annot.InterPro method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Intogen.html#pypath.core.annot.Intogen.get_names">(pypath.core.annot.Intogen method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Italk.html#pypath.core.annot.Italk.get_names">(pypath.core.annot.Italk method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.KeggPathways.html#pypath.core.annot.KeggPathways.get_names">(pypath.core.annot.KeggPathways method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.KeggPathwaysPC.html#pypath.core.annot.KeggPathwaysPC.get_names">(pypath.core.annot.KeggPathwaysPC method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Kinasedotcom.html#pypath.core.annot.Kinasedotcom.get_names">(pypath.core.annot.Kinasedotcom method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Kirouac2010.html#pypath.core.annot.Kirouac2010.get_names">(pypath.core.annot.Kirouac2010 method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Lambert2018.html#pypath.core.annot.Lambert2018.get_names">(pypath.core.annot.Lambert2018 method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.LigandReceptor.html#pypath.core.annot.LigandReceptor.get_names">(pypath.core.annot.LigandReceptor method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Locate.html#pypath.core.annot.Locate.get_names">(pypath.core.annot.Locate method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Lrdb.html#pypath.core.annot.Lrdb.get_names">(pypath.core.annot.Lrdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Matrisome.html#pypath.core.annot.Matrisome.get_names">(pypath.core.annot.Matrisome method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Matrixdb.html#pypath.core.annot.Matrixdb.get_names">(pypath.core.annot.Matrixdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Mcam.html#pypath.core.annot.Mcam.get_names">(pypath.core.annot.Mcam method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Membranome.html#pypath.core.annot.Membranome.get_names">(pypath.core.annot.Membranome method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Msigdb.html#pypath.core.annot.Msigdb.get_names">(pypath.core.annot.Msigdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.NetpathPathways.html#pypath.core.annot.NetpathPathways.get_names">(pypath.core.annot.NetpathPathways method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Opm.html#pypath.core.annot.Opm.get_names">(pypath.core.annot.Opm method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Panglaodb.html#pypath.core.annot.Panglaodb.get_names">(pypath.core.annot.Panglaodb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Phobius.html#pypath.core.annot.Phobius.get_names">(pypath.core.annot.Phobius method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Phosphatome.html#pypath.core.annot.Phosphatome.get_names">(pypath.core.annot.Phosphatome method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Progeny.html#pypath.core.annot.Progeny.get_names">(pypath.core.annot.Progeny method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Ramilowski2015.html#pypath.core.annot.Ramilowski2015.get_names">(pypath.core.annot.Ramilowski2015 method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Ramilowski2015Location.html#pypath.core.annot.Ramilowski2015Location.get_names">(pypath.core.annot.Ramilowski2015Location method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Scconnect.html#pypath.core.annot.Scconnect.get_names">(pypath.core.annot.Scconnect method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.ScconnectComplex.html#pypath.core.annot.ScconnectComplex.get_names">(pypath.core.annot.ScconnectComplex method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.SignalinkFunctions.html#pypath.core.annot.SignalinkFunctions.get_names">(pypath.core.annot.SignalinkFunctions method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.SignalinkPathways.html#pypath.core.annot.SignalinkPathways.get_names">(pypath.core.annot.SignalinkPathways method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.SignorPathways.html#pypath.core.annot.SignorPathways.get_names">(pypath.core.annot.SignorPathways method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Surfaceome.html#pypath.core.annot.Surfaceome.get_names">(pypath.core.annot.Surfaceome method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Talklr.html#pypath.core.annot.Talklr.get_names">(pypath.core.annot.Talklr method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Tcdb.html#pypath.core.annot.Tcdb.get_names">(pypath.core.annot.Tcdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Tfcensus.html#pypath.core.annot.Tfcensus.get_names">(pypath.core.annot.Tfcensus method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Topdb.html#pypath.core.annot.Topdb.get_names">(pypath.core.annot.Topdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.UniprotFamilies.html#pypath.core.annot.UniprotFamilies.get_names">(pypath.core.annot.UniprotFamilies method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.UniprotKeywords.html#pypath.core.annot.UniprotKeywords.get_names">(pypath.core.annot.UniprotKeywords method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.UniprotLocations.html#pypath.core.annot.UniprotLocations.get_names">(pypath.core.annot.UniprotLocations method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.UniprotTissues.html#pypath.core.annot.UniprotTissues.get_names">(pypath.core.annot.UniprotTissues method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.UniprotTopologies.html#pypath.core.annot.UniprotTopologies.get_names">(pypath.core.annot.UniprotTopologies method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Vesiclepedia.html#pypath.core.annot.Vesiclepedia.get_names">(pypath.core.annot.Vesiclepedia method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Wang.html#pypath.core.annot.Wang.get_names">(pypath.core.annot.Wang method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Zhong2015.html#pypath.core.annot.Zhong2015.get_names">(pypath.core.annot.Zhong2015 method)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.get_organisms">get_organisms() (pypath.core.network.Network method)</a>
+</li>
+      <li><a href="api/pypath.omnipath.app.DatabaseManager.html#pypath.omnipath.app.DatabaseManager.get_param">get_param() (pypath.omnipath.app.DatabaseManager method)</a>
+</li>
+      <li><a href="api/pypath.core.annot.CustomAnnotation.html#pypath.core.annot.CustomAnnotation.get_parents">get_parents() (pypath.core.annot.CustomAnnotation method)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.intercell.IntercellAnnotation.html#pypath.core.intercell.IntercellAnnotation.get_parents">(pypath.core.intercell.IntercellAnnotation method)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.utils.proteomicsdb.ProteomicsDB.html#pypath.utils.proteomicsdb.ProteomicsDB.get_pieces">get_pieces() (pypath.utils.proteomicsdb.ProteomicsDB method)</a>
+</li>
+      <li><a href="api/pypath.inputs.pubmed.get_pmid.html#pypath.inputs.pubmed.get_pmid">get_pmid() (in module pypath.inputs.pubmed)</a>
+</li>
+      <li><a href="api/pypath.inputs.pro.get_pro.html#pypath.inputs.pro.get_pro">get_pro() (in module pypath.inputs.pro)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.get_protein_identifiers">get_protein_identifiers (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.get_protein_identifiers">get_protein_identifiers() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.get_protein_labels">get_protein_labels (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.get_protein_labels">get_protein_labels() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.inputs.proteinatlas.get_proteinatlas.html#pypath.inputs.proteinatlas.get_proteinatlas">get_proteinatlas() (in module pypath.inputs.proteinatlas)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.get_proteins">get_proteins (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.get_proteins">get_proteins() (pypath.core.interaction.Interaction method)</a>
+
+      <ul>
+        <li><a href="api/pypath.utils.proteomicsdb.ProteomicsDB.html#pypath.utils.proteomicsdb.ProteomicsDB.get_proteins">(pypath.utils.proteomicsdb.ProteomicsDB method)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.inputs.protmapper.get_protmapper.html#pypath.inputs.protmapper.get_protmapper">get_protmapper() (in module pypath.inputs.protmapper)</a>
+</li>
+      <li><a href="api/pypath.internals.refs.get_pubmed_data.html#pypath.internals.refs.get_pubmed_data">get_pubmed_data() (in module pypath.internals.refs)</a>
+</li>
+      <li><a href="api/pypath.inputs.pubmed.get_pubmeds.html#pypath.inputs.pubmed.get_pubmeds">get_pubmeds() (in module pypath.inputs.pubmed)</a>
+</li>
+      <li><a href="api/pypath.inputs.reaction.get_reactions.html#pypath.inputs.reaction.get_reactions">get_reactions() (in module pypath.inputs.reaction)</a>
+</li>
+      <li><a href="api/pypath.core.annot.Adhesome.html#pypath.core.annot.Adhesome.get_reference_set">get_reference_set() (pypath.core.annot.Adhesome static method)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.annot.Almen2009.html#pypath.core.annot.Almen2009.get_reference_set">(pypath.core.annot.Almen2009 static method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.AnnotationBase.html#pypath.core.annot.AnnotationBase.get_reference_set">(pypath.core.annot.AnnotationBase static method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Baccin2019.html#pypath.core.annot.Baccin2019.get_reference_set">(pypath.core.annot.Baccin2019 static method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Biogps.html#pypath.core.annot.Biogps.get_reference_set">(pypath.core.annot.Biogps static method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cancerdrugsdb.html#pypath.core.annot.Cancerdrugsdb.get_reference_set">(pypath.core.annot.Cancerdrugsdb static method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CancerGeneCensus.html#pypath.core.annot.CancerGeneCensus.get_reference_set">(pypath.core.annot.CancerGeneCensus static method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cancersea.html#pypath.core.annot.Cancersea.get_reference_set">(pypath.core.annot.Cancersea static method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cellcall.html#pypath.core.annot.Cellcall.get_reference_set">(pypath.core.annot.Cellcall static method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cellcellinteractions.html#pypath.core.annot.Cellcellinteractions.get_reference_set">(pypath.core.annot.Cellcellinteractions static method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cellchatdb.html#pypath.core.annot.Cellchatdb.get_reference_set">(pypath.core.annot.Cellchatdb static method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CellchatdbComplex.html#pypath.core.annot.CellchatdbComplex.get_reference_set">(pypath.core.annot.CellchatdbComplex static method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cellinker.html#pypath.core.annot.Cellinker.get_reference_set">(pypath.core.annot.Cellinker static method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CellinkerComplex.html#pypath.core.annot.CellinkerComplex.get_reference_set">(pypath.core.annot.CellinkerComplex static method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CellPhoneDB.html#pypath.core.annot.CellPhoneDB.get_reference_set">(pypath.core.annot.CellPhoneDB static method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CellPhoneDBComplex.html#pypath.core.annot.CellPhoneDBComplex.get_reference_set">(pypath.core.annot.CellPhoneDBComplex static method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CellSurfaceProteinAtlas.html#pypath.core.annot.CellSurfaceProteinAtlas.get_reference_set">(pypath.core.annot.CellSurfaceProteinAtlas static method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CellSurfaceProteinAtlasCellType.html#pypath.core.annot.CellSurfaceProteinAtlasCellType.get_reference_set">(pypath.core.annot.CellSurfaceProteinAtlasCellType static method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Celltalkdb.html#pypath.core.annot.Celltalkdb.get_reference_set">(pypath.core.annot.Celltalkdb static method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Celltypist.html#pypath.core.annot.Celltypist.get_reference_set">(pypath.core.annot.Celltypist static method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Comppi.html#pypath.core.annot.Comppi.get_reference_set">(pypath.core.annot.Comppi static method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Connectomedb.html#pypath.core.annot.Connectomedb.get_reference_set">(pypath.core.annot.Connectomedb static method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Corum.html#pypath.core.annot.Corum.get_reference_set">(pypath.core.annot.Corum static method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CorumFuncat.html#pypath.core.annot.CorumFuncat.get_reference_set">(pypath.core.annot.CorumFuncat static method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CorumGO.html#pypath.core.annot.CorumGO.get_reference_set">(pypath.core.annot.CorumGO static method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cpad.html#pypath.core.annot.Cpad.get_reference_set">(pypath.core.annot.Cpad static method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cytosig.html#pypath.core.annot.Cytosig.get_reference_set">(pypath.core.annot.Cytosig static method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Dgidb.html#pypath.core.annot.Dgidb.get_reference_set">(pypath.core.annot.Dgidb static method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Disgenet.html#pypath.core.annot.Disgenet.get_reference_set">(pypath.core.annot.Disgenet static method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Embrace.html#pypath.core.annot.Embrace.get_reference_set">(pypath.core.annot.Embrace static method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Exocarta.html#pypath.core.annot.Exocarta.get_reference_set">(pypath.core.annot.Exocarta static method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.GOIntercell.html#pypath.core.annot.GOIntercell.get_reference_set">(pypath.core.annot.GOIntercell static method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Gpcrdb.html#pypath.core.annot.Gpcrdb.get_reference_set">(pypath.core.annot.Gpcrdb static method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.GuideToPharmacology.html#pypath.core.annot.GuideToPharmacology.get_reference_set">(pypath.core.annot.GuideToPharmacology static method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Hgnc.html#pypath.core.annot.Hgnc.get_reference_set">(pypath.core.annot.Hgnc static method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.HpmrComplex.html#pypath.core.annot.HpmrComplex.get_reference_set">(pypath.core.annot.HpmrComplex static method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.HPO.html#pypath.core.annot.HPO.get_reference_set">(pypath.core.annot.HPO static method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Humancellmap.html#pypath.core.annot.Humancellmap.get_reference_set">(pypath.core.annot.Humancellmap static method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.HumanPlasmaMembraneReceptome.html#pypath.core.annot.HumanPlasmaMembraneReceptome.get_reference_set">(pypath.core.annot.HumanPlasmaMembraneReceptome static method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.HumanProteinAtlas.html#pypath.core.annot.HumanProteinAtlas.get_reference_set">(pypath.core.annot.HumanProteinAtlas static method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.HumanProteinAtlasSecretome.html#pypath.core.annot.HumanProteinAtlasSecretome.get_reference_set">(pypath.core.annot.HumanProteinAtlasSecretome static method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.HumanProteinAtlasSubcellular.html#pypath.core.annot.HumanProteinAtlasSubcellular.get_reference_set">(pypath.core.annot.HumanProteinAtlasSubcellular static method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Icellnet.html#pypath.core.annot.Icellnet.get_reference_set">(pypath.core.annot.Icellnet static method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.IcellnetComplex.html#pypath.core.annot.IcellnetComplex.get_reference_set">(pypath.core.annot.IcellnetComplex static method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Integrins.html#pypath.core.annot.Integrins.get_reference_set">(pypath.core.annot.Integrins static method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.InterPro.html#pypath.core.annot.InterPro.get_reference_set">(pypath.core.annot.InterPro static method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Intogen.html#pypath.core.annot.Intogen.get_reference_set">(pypath.core.annot.Intogen static method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Italk.html#pypath.core.annot.Italk.get_reference_set">(pypath.core.annot.Italk static method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.KeggPathways.html#pypath.core.annot.KeggPathways.get_reference_set">(pypath.core.annot.KeggPathways static method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.KeggPathwaysPC.html#pypath.core.annot.KeggPathwaysPC.get_reference_set">(pypath.core.annot.KeggPathwaysPC static method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Kinasedotcom.html#pypath.core.annot.Kinasedotcom.get_reference_set">(pypath.core.annot.Kinasedotcom static method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Kirouac2010.html#pypath.core.annot.Kirouac2010.get_reference_set">(pypath.core.annot.Kirouac2010 static method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Lambert2018.html#pypath.core.annot.Lambert2018.get_reference_set">(pypath.core.annot.Lambert2018 static method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.LigandReceptor.html#pypath.core.annot.LigandReceptor.get_reference_set">(pypath.core.annot.LigandReceptor static method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Locate.html#pypath.core.annot.Locate.get_reference_set">(pypath.core.annot.Locate static method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Lrdb.html#pypath.core.annot.Lrdb.get_reference_set">(pypath.core.annot.Lrdb static method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Matrisome.html#pypath.core.annot.Matrisome.get_reference_set">(pypath.core.annot.Matrisome static method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Matrixdb.html#pypath.core.annot.Matrixdb.get_reference_set">(pypath.core.annot.Matrixdb static method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Mcam.html#pypath.core.annot.Mcam.get_reference_set">(pypath.core.annot.Mcam static method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Membranome.html#pypath.core.annot.Membranome.get_reference_set">(pypath.core.annot.Membranome static method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Msigdb.html#pypath.core.annot.Msigdb.get_reference_set">(pypath.core.annot.Msigdb static method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.NetpathPathways.html#pypath.core.annot.NetpathPathways.get_reference_set">(pypath.core.annot.NetpathPathways static method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Opm.html#pypath.core.annot.Opm.get_reference_set">(pypath.core.annot.Opm static method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Panglaodb.html#pypath.core.annot.Panglaodb.get_reference_set">(pypath.core.annot.Panglaodb static method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Phobius.html#pypath.core.annot.Phobius.get_reference_set">(pypath.core.annot.Phobius static method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Phosphatome.html#pypath.core.annot.Phosphatome.get_reference_set">(pypath.core.annot.Phosphatome static method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Progeny.html#pypath.core.annot.Progeny.get_reference_set">(pypath.core.annot.Progeny static method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Ramilowski2015.html#pypath.core.annot.Ramilowski2015.get_reference_set">(pypath.core.annot.Ramilowski2015 static method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Ramilowski2015Location.html#pypath.core.annot.Ramilowski2015Location.get_reference_set">(pypath.core.annot.Ramilowski2015Location static method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Scconnect.html#pypath.core.annot.Scconnect.get_reference_set">(pypath.core.annot.Scconnect static method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.ScconnectComplex.html#pypath.core.annot.ScconnectComplex.get_reference_set">(pypath.core.annot.ScconnectComplex static method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.SignalinkFunctions.html#pypath.core.annot.SignalinkFunctions.get_reference_set">(pypath.core.annot.SignalinkFunctions static method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.SignalinkPathways.html#pypath.core.annot.SignalinkPathways.get_reference_set">(pypath.core.annot.SignalinkPathways static method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.SignorPathways.html#pypath.core.annot.SignorPathways.get_reference_set">(pypath.core.annot.SignorPathways static method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Surfaceome.html#pypath.core.annot.Surfaceome.get_reference_set">(pypath.core.annot.Surfaceome static method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Talklr.html#pypath.core.annot.Talklr.get_reference_set">(pypath.core.annot.Talklr static method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Tcdb.html#pypath.core.annot.Tcdb.get_reference_set">(pypath.core.annot.Tcdb static method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Tfcensus.html#pypath.core.annot.Tfcensus.get_reference_set">(pypath.core.annot.Tfcensus static method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Topdb.html#pypath.core.annot.Topdb.get_reference_set">(pypath.core.annot.Topdb static method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.UniprotFamilies.html#pypath.core.annot.UniprotFamilies.get_reference_set">(pypath.core.annot.UniprotFamilies static method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.UniprotKeywords.html#pypath.core.annot.UniprotKeywords.get_reference_set">(pypath.core.annot.UniprotKeywords static method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.UniprotLocations.html#pypath.core.annot.UniprotLocations.get_reference_set">(pypath.core.annot.UniprotLocations static method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.UniprotTissues.html#pypath.core.annot.UniprotTissues.get_reference_set">(pypath.core.annot.UniprotTissues static method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.UniprotTopologies.html#pypath.core.annot.UniprotTopologies.get_reference_set">(pypath.core.annot.UniprotTopologies static method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Vesiclepedia.html#pypath.core.annot.Vesiclepedia.get_reference_set">(pypath.core.annot.Vesiclepedia static method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Wang.html#pypath.core.annot.Wang.get_reference_set">(pypath.core.annot.Wang static method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Zhong2015.html#pypath.core.annot.Zhong2015.get_reference_set">(pypath.core.annot.Zhong2015 static method)</a>
+</li>
+      </ul></li>
+  </ul></td>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.get_references">get_references (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.get_references">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.utils.reflists.get_reflist.html#pypath.utils.reflists.get_reflist">get_reflist() (in module pypath.utils.reflists)</a>
+</li>
+      <li><a href="api/pypath.utils.pdb.ResidueMapper.html#pypath.utils.pdb.ResidueMapper.get_residue">get_residue() (pypath.utils.pdb.ResidueMapper method)</a>
+</li>
+      <li><a href="api/pypath.core.annot.CustomAnnotation.html#pypath.core.annot.CustomAnnotation.get_resource">get_resource() (pypath.core.annot.CustomAnnotation method)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.intercell.IntercellAnnotation.html#pypath.core.intercell.IntercellAnnotation.get_resource">(pypath.core.intercell.IntercellAnnotation method)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.get_resource_names">get_resource_names (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.get_resource_names">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.get_resource_names_via">get_resource_names_via (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.get_resource_names_via">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.get_resources">get_resources (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.get_resources">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.annot.CustomAnnotation.html#pypath.core.annot.CustomAnnotation.get_resources">get_resources() (pypath.core.annot.CustomAnnotation method)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.intercell.IntercellAnnotation.html#pypath.core.intercell.IntercellAnnotation.get_resources">(pypath.core.intercell.IntercellAnnotation method)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.get_resources_via">get_resources_via (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.get_resources_via">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.get_sign">get_sign() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.inputs.biomodels.get_single_model.html#pypath.inputs.biomodels.get_single_model">get_single_model() (in module pypath.inputs.biomodels)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.get_small_molecule_identifiers">get_small_molecule_identifiers (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.get_small_molecule_identifiers">get_small_molecule_identifiers() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.get_small_molecule_labels">get_small_molecule_labels (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.get_small_molecule_labels">get_small_molecule_labels() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.get_small_molecules">get_small_molecules (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.get_small_molecules">get_small_molecules() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.inputs.reaction.get_soup.html#pypath.inputs.reaction.get_soup">get_soup() (in module pypath.inputs.reaction)</a>
+</li>
+      <li><a href="api/pypath.core.annot.Adhesome.html#pypath.core.annot.Adhesome.get_subset">get_subset() (pypath.core.annot.Adhesome method)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.annot.Almen2009.html#pypath.core.annot.Almen2009.get_subset">(pypath.core.annot.Almen2009 method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.AnnotationBase.html#pypath.core.annot.AnnotationBase.get_subset">(pypath.core.annot.AnnotationBase method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Baccin2019.html#pypath.core.annot.Baccin2019.get_subset">(pypath.core.annot.Baccin2019 method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Biogps.html#pypath.core.annot.Biogps.get_subset">(pypath.core.annot.Biogps method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cancerdrugsdb.html#pypath.core.annot.Cancerdrugsdb.get_subset">(pypath.core.annot.Cancerdrugsdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CancerGeneCensus.html#pypath.core.annot.CancerGeneCensus.get_subset">(pypath.core.annot.CancerGeneCensus method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cancersea.html#pypath.core.annot.Cancersea.get_subset">(pypath.core.annot.Cancersea method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cellcall.html#pypath.core.annot.Cellcall.get_subset">(pypath.core.annot.Cellcall method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cellcellinteractions.html#pypath.core.annot.Cellcellinteractions.get_subset">(pypath.core.annot.Cellcellinteractions method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cellchatdb.html#pypath.core.annot.Cellchatdb.get_subset">(pypath.core.annot.Cellchatdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CellchatdbComplex.html#pypath.core.annot.CellchatdbComplex.get_subset">(pypath.core.annot.CellchatdbComplex method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cellinker.html#pypath.core.annot.Cellinker.get_subset">(pypath.core.annot.Cellinker method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CellinkerComplex.html#pypath.core.annot.CellinkerComplex.get_subset">(pypath.core.annot.CellinkerComplex method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CellPhoneDB.html#pypath.core.annot.CellPhoneDB.get_subset">(pypath.core.annot.CellPhoneDB method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CellPhoneDBComplex.html#pypath.core.annot.CellPhoneDBComplex.get_subset">(pypath.core.annot.CellPhoneDBComplex method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CellSurfaceProteinAtlas.html#pypath.core.annot.CellSurfaceProteinAtlas.get_subset">(pypath.core.annot.CellSurfaceProteinAtlas method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CellSurfaceProteinAtlasCellType.html#pypath.core.annot.CellSurfaceProteinAtlasCellType.get_subset">(pypath.core.annot.CellSurfaceProteinAtlasCellType method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Celltalkdb.html#pypath.core.annot.Celltalkdb.get_subset">(pypath.core.annot.Celltalkdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Celltypist.html#pypath.core.annot.Celltypist.get_subset">(pypath.core.annot.Celltypist method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Comppi.html#pypath.core.annot.Comppi.get_subset">(pypath.core.annot.Comppi method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Connectomedb.html#pypath.core.annot.Connectomedb.get_subset">(pypath.core.annot.Connectomedb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Corum.html#pypath.core.annot.Corum.get_subset">(pypath.core.annot.Corum method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CorumFuncat.html#pypath.core.annot.CorumFuncat.get_subset">(pypath.core.annot.CorumFuncat method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CorumGO.html#pypath.core.annot.CorumGO.get_subset">(pypath.core.annot.CorumGO method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cpad.html#pypath.core.annot.Cpad.get_subset">(pypath.core.annot.Cpad method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cytosig.html#pypath.core.annot.Cytosig.get_subset">(pypath.core.annot.Cytosig method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Dgidb.html#pypath.core.annot.Dgidb.get_subset">(pypath.core.annot.Dgidb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Disgenet.html#pypath.core.annot.Disgenet.get_subset">(pypath.core.annot.Disgenet method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Embrace.html#pypath.core.annot.Embrace.get_subset">(pypath.core.annot.Embrace method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Exocarta.html#pypath.core.annot.Exocarta.get_subset">(pypath.core.annot.Exocarta method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.GOIntercell.html#pypath.core.annot.GOIntercell.get_subset">(pypath.core.annot.GOIntercell method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Gpcrdb.html#pypath.core.annot.Gpcrdb.get_subset">(pypath.core.annot.Gpcrdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.GuideToPharmacology.html#pypath.core.annot.GuideToPharmacology.get_subset">(pypath.core.annot.GuideToPharmacology method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Hgnc.html#pypath.core.annot.Hgnc.get_subset">(pypath.core.annot.Hgnc method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.HpmrComplex.html#pypath.core.annot.HpmrComplex.get_subset">(pypath.core.annot.HpmrComplex method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.HPO.html#pypath.core.annot.HPO.get_subset">(pypath.core.annot.HPO method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Humancellmap.html#pypath.core.annot.Humancellmap.get_subset">(pypath.core.annot.Humancellmap method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.HumanPlasmaMembraneReceptome.html#pypath.core.annot.HumanPlasmaMembraneReceptome.get_subset">(pypath.core.annot.HumanPlasmaMembraneReceptome method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.HumanProteinAtlas.html#pypath.core.annot.HumanProteinAtlas.get_subset">(pypath.core.annot.HumanProteinAtlas method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.HumanProteinAtlasSecretome.html#pypath.core.annot.HumanProteinAtlasSecretome.get_subset">(pypath.core.annot.HumanProteinAtlasSecretome method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.HumanProteinAtlasSubcellular.html#pypath.core.annot.HumanProteinAtlasSubcellular.get_subset">(pypath.core.annot.HumanProteinAtlasSubcellular method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Icellnet.html#pypath.core.annot.Icellnet.get_subset">(pypath.core.annot.Icellnet method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.IcellnetComplex.html#pypath.core.annot.IcellnetComplex.get_subset">(pypath.core.annot.IcellnetComplex method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Integrins.html#pypath.core.annot.Integrins.get_subset">(pypath.core.annot.Integrins method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.InterPro.html#pypath.core.annot.InterPro.get_subset">(pypath.core.annot.InterPro method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Intogen.html#pypath.core.annot.Intogen.get_subset">(pypath.core.annot.Intogen method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Italk.html#pypath.core.annot.Italk.get_subset">(pypath.core.annot.Italk method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.KeggPathways.html#pypath.core.annot.KeggPathways.get_subset">(pypath.core.annot.KeggPathways method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.KeggPathwaysPC.html#pypath.core.annot.KeggPathwaysPC.get_subset">(pypath.core.annot.KeggPathwaysPC method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Kinasedotcom.html#pypath.core.annot.Kinasedotcom.get_subset">(pypath.core.annot.Kinasedotcom method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Kirouac2010.html#pypath.core.annot.Kirouac2010.get_subset">(pypath.core.annot.Kirouac2010 method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Lambert2018.html#pypath.core.annot.Lambert2018.get_subset">(pypath.core.annot.Lambert2018 method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.LigandReceptor.html#pypath.core.annot.LigandReceptor.get_subset">(pypath.core.annot.LigandReceptor method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Locate.html#pypath.core.annot.Locate.get_subset">(pypath.core.annot.Locate method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Lrdb.html#pypath.core.annot.Lrdb.get_subset">(pypath.core.annot.Lrdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Matrisome.html#pypath.core.annot.Matrisome.get_subset">(pypath.core.annot.Matrisome method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Matrixdb.html#pypath.core.annot.Matrixdb.get_subset">(pypath.core.annot.Matrixdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Mcam.html#pypath.core.annot.Mcam.get_subset">(pypath.core.annot.Mcam method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Membranome.html#pypath.core.annot.Membranome.get_subset">(pypath.core.annot.Membranome method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Msigdb.html#pypath.core.annot.Msigdb.get_subset">(pypath.core.annot.Msigdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.NetpathPathways.html#pypath.core.annot.NetpathPathways.get_subset">(pypath.core.annot.NetpathPathways method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Opm.html#pypath.core.annot.Opm.get_subset">(pypath.core.annot.Opm method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Panglaodb.html#pypath.core.annot.Panglaodb.get_subset">(pypath.core.annot.Panglaodb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Phobius.html#pypath.core.annot.Phobius.get_subset">(pypath.core.annot.Phobius method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Phosphatome.html#pypath.core.annot.Phosphatome.get_subset">(pypath.core.annot.Phosphatome method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Progeny.html#pypath.core.annot.Progeny.get_subset">(pypath.core.annot.Progeny method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Ramilowski2015.html#pypath.core.annot.Ramilowski2015.get_subset">(pypath.core.annot.Ramilowski2015 method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Ramilowski2015Location.html#pypath.core.annot.Ramilowski2015Location.get_subset">(pypath.core.annot.Ramilowski2015Location method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Scconnect.html#pypath.core.annot.Scconnect.get_subset">(pypath.core.annot.Scconnect method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.ScconnectComplex.html#pypath.core.annot.ScconnectComplex.get_subset">(pypath.core.annot.ScconnectComplex method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.SignalinkFunctions.html#pypath.core.annot.SignalinkFunctions.get_subset">(pypath.core.annot.SignalinkFunctions method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.SignalinkPathways.html#pypath.core.annot.SignalinkPathways.get_subset">(pypath.core.annot.SignalinkPathways method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.SignorPathways.html#pypath.core.annot.SignorPathways.get_subset">(pypath.core.annot.SignorPathways method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Surfaceome.html#pypath.core.annot.Surfaceome.get_subset">(pypath.core.annot.Surfaceome method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Talklr.html#pypath.core.annot.Talklr.get_subset">(pypath.core.annot.Talklr method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Tcdb.html#pypath.core.annot.Tcdb.get_subset">(pypath.core.annot.Tcdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Tfcensus.html#pypath.core.annot.Tfcensus.get_subset">(pypath.core.annot.Tfcensus method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Topdb.html#pypath.core.annot.Topdb.get_subset">(pypath.core.annot.Topdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.UniprotFamilies.html#pypath.core.annot.UniprotFamilies.get_subset">(pypath.core.annot.UniprotFamilies method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.UniprotKeywords.html#pypath.core.annot.UniprotKeywords.get_subset">(pypath.core.annot.UniprotKeywords method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.UniprotLocations.html#pypath.core.annot.UniprotLocations.get_subset">(pypath.core.annot.UniprotLocations method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.UniprotTissues.html#pypath.core.annot.UniprotTissues.get_subset">(pypath.core.annot.UniprotTissues method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.UniprotTopologies.html#pypath.core.annot.UniprotTopologies.get_subset">(pypath.core.annot.UniprotTopologies method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Vesiclepedia.html#pypath.core.annot.Vesiclepedia.get_subset">(pypath.core.annot.Vesiclepedia method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Wang.html#pypath.core.annot.Wang.get_subset">(pypath.core.annot.Wang method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Zhong2015.html#pypath.core.annot.Zhong2015.get_subset">(pypath.core.annot.Zhong2015 method)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.annot.Adhesome.html#pypath.core.annot.Adhesome.get_subset_bool_array">get_subset_bool_array() (pypath.core.annot.Adhesome method)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.annot.Almen2009.html#pypath.core.annot.Almen2009.get_subset_bool_array">(pypath.core.annot.Almen2009 method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.AnnotationBase.html#pypath.core.annot.AnnotationBase.get_subset_bool_array">(pypath.core.annot.AnnotationBase method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Baccin2019.html#pypath.core.annot.Baccin2019.get_subset_bool_array">(pypath.core.annot.Baccin2019 method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Biogps.html#pypath.core.annot.Biogps.get_subset_bool_array">(pypath.core.annot.Biogps method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cancerdrugsdb.html#pypath.core.annot.Cancerdrugsdb.get_subset_bool_array">(pypath.core.annot.Cancerdrugsdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CancerGeneCensus.html#pypath.core.annot.CancerGeneCensus.get_subset_bool_array">(pypath.core.annot.CancerGeneCensus method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cancersea.html#pypath.core.annot.Cancersea.get_subset_bool_array">(pypath.core.annot.Cancersea method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cellcall.html#pypath.core.annot.Cellcall.get_subset_bool_array">(pypath.core.annot.Cellcall method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cellcellinteractions.html#pypath.core.annot.Cellcellinteractions.get_subset_bool_array">(pypath.core.annot.Cellcellinteractions method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cellchatdb.html#pypath.core.annot.Cellchatdb.get_subset_bool_array">(pypath.core.annot.Cellchatdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CellchatdbComplex.html#pypath.core.annot.CellchatdbComplex.get_subset_bool_array">(pypath.core.annot.CellchatdbComplex method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cellinker.html#pypath.core.annot.Cellinker.get_subset_bool_array">(pypath.core.annot.Cellinker method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CellinkerComplex.html#pypath.core.annot.CellinkerComplex.get_subset_bool_array">(pypath.core.annot.CellinkerComplex method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CellPhoneDB.html#pypath.core.annot.CellPhoneDB.get_subset_bool_array">(pypath.core.annot.CellPhoneDB method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CellPhoneDBComplex.html#pypath.core.annot.CellPhoneDBComplex.get_subset_bool_array">(pypath.core.annot.CellPhoneDBComplex method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CellSurfaceProteinAtlas.html#pypath.core.annot.CellSurfaceProteinAtlas.get_subset_bool_array">(pypath.core.annot.CellSurfaceProteinAtlas method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CellSurfaceProteinAtlasCellType.html#pypath.core.annot.CellSurfaceProteinAtlasCellType.get_subset_bool_array">(pypath.core.annot.CellSurfaceProteinAtlasCellType method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Celltalkdb.html#pypath.core.annot.Celltalkdb.get_subset_bool_array">(pypath.core.annot.Celltalkdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Celltypist.html#pypath.core.annot.Celltypist.get_subset_bool_array">(pypath.core.annot.Celltypist method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Comppi.html#pypath.core.annot.Comppi.get_subset_bool_array">(pypath.core.annot.Comppi method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Connectomedb.html#pypath.core.annot.Connectomedb.get_subset_bool_array">(pypath.core.annot.Connectomedb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Corum.html#pypath.core.annot.Corum.get_subset_bool_array">(pypath.core.annot.Corum method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CorumFuncat.html#pypath.core.annot.CorumFuncat.get_subset_bool_array">(pypath.core.annot.CorumFuncat method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CorumGO.html#pypath.core.annot.CorumGO.get_subset_bool_array">(pypath.core.annot.CorumGO method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cpad.html#pypath.core.annot.Cpad.get_subset_bool_array">(pypath.core.annot.Cpad method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cytosig.html#pypath.core.annot.Cytosig.get_subset_bool_array">(pypath.core.annot.Cytosig method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Dgidb.html#pypath.core.annot.Dgidb.get_subset_bool_array">(pypath.core.annot.Dgidb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Disgenet.html#pypath.core.annot.Disgenet.get_subset_bool_array">(pypath.core.annot.Disgenet method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Embrace.html#pypath.core.annot.Embrace.get_subset_bool_array">(pypath.core.annot.Embrace method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Exocarta.html#pypath.core.annot.Exocarta.get_subset_bool_array">(pypath.core.annot.Exocarta method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.GOIntercell.html#pypath.core.annot.GOIntercell.get_subset_bool_array">(pypath.core.annot.GOIntercell method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Gpcrdb.html#pypath.core.annot.Gpcrdb.get_subset_bool_array">(pypath.core.annot.Gpcrdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.GuideToPharmacology.html#pypath.core.annot.GuideToPharmacology.get_subset_bool_array">(pypath.core.annot.GuideToPharmacology method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Hgnc.html#pypath.core.annot.Hgnc.get_subset_bool_array">(pypath.core.annot.Hgnc method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.HpmrComplex.html#pypath.core.annot.HpmrComplex.get_subset_bool_array">(pypath.core.annot.HpmrComplex method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.HPO.html#pypath.core.annot.HPO.get_subset_bool_array">(pypath.core.annot.HPO method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Humancellmap.html#pypath.core.annot.Humancellmap.get_subset_bool_array">(pypath.core.annot.Humancellmap method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.HumanPlasmaMembraneReceptome.html#pypath.core.annot.HumanPlasmaMembraneReceptome.get_subset_bool_array">(pypath.core.annot.HumanPlasmaMembraneReceptome method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.HumanProteinAtlas.html#pypath.core.annot.HumanProteinAtlas.get_subset_bool_array">(pypath.core.annot.HumanProteinAtlas method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.HumanProteinAtlasSecretome.html#pypath.core.annot.HumanProteinAtlasSecretome.get_subset_bool_array">(pypath.core.annot.HumanProteinAtlasSecretome method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.HumanProteinAtlasSubcellular.html#pypath.core.annot.HumanProteinAtlasSubcellular.get_subset_bool_array">(pypath.core.annot.HumanProteinAtlasSubcellular method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Icellnet.html#pypath.core.annot.Icellnet.get_subset_bool_array">(pypath.core.annot.Icellnet method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.IcellnetComplex.html#pypath.core.annot.IcellnetComplex.get_subset_bool_array">(pypath.core.annot.IcellnetComplex method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Integrins.html#pypath.core.annot.Integrins.get_subset_bool_array">(pypath.core.annot.Integrins method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.InterPro.html#pypath.core.annot.InterPro.get_subset_bool_array">(pypath.core.annot.InterPro method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Intogen.html#pypath.core.annot.Intogen.get_subset_bool_array">(pypath.core.annot.Intogen method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Italk.html#pypath.core.annot.Italk.get_subset_bool_array">(pypath.core.annot.Italk method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.KeggPathways.html#pypath.core.annot.KeggPathways.get_subset_bool_array">(pypath.core.annot.KeggPathways method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.KeggPathwaysPC.html#pypath.core.annot.KeggPathwaysPC.get_subset_bool_array">(pypath.core.annot.KeggPathwaysPC method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Kinasedotcom.html#pypath.core.annot.Kinasedotcom.get_subset_bool_array">(pypath.core.annot.Kinasedotcom method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Kirouac2010.html#pypath.core.annot.Kirouac2010.get_subset_bool_array">(pypath.core.annot.Kirouac2010 method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Lambert2018.html#pypath.core.annot.Lambert2018.get_subset_bool_array">(pypath.core.annot.Lambert2018 method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.LigandReceptor.html#pypath.core.annot.LigandReceptor.get_subset_bool_array">(pypath.core.annot.LigandReceptor method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Locate.html#pypath.core.annot.Locate.get_subset_bool_array">(pypath.core.annot.Locate method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Lrdb.html#pypath.core.annot.Lrdb.get_subset_bool_array">(pypath.core.annot.Lrdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Matrisome.html#pypath.core.annot.Matrisome.get_subset_bool_array">(pypath.core.annot.Matrisome method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Matrixdb.html#pypath.core.annot.Matrixdb.get_subset_bool_array">(pypath.core.annot.Matrixdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Mcam.html#pypath.core.annot.Mcam.get_subset_bool_array">(pypath.core.annot.Mcam method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Membranome.html#pypath.core.annot.Membranome.get_subset_bool_array">(pypath.core.annot.Membranome method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Msigdb.html#pypath.core.annot.Msigdb.get_subset_bool_array">(pypath.core.annot.Msigdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.NetpathPathways.html#pypath.core.annot.NetpathPathways.get_subset_bool_array">(pypath.core.annot.NetpathPathways method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Opm.html#pypath.core.annot.Opm.get_subset_bool_array">(pypath.core.annot.Opm method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Panglaodb.html#pypath.core.annot.Panglaodb.get_subset_bool_array">(pypath.core.annot.Panglaodb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Phobius.html#pypath.core.annot.Phobius.get_subset_bool_array">(pypath.core.annot.Phobius method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Phosphatome.html#pypath.core.annot.Phosphatome.get_subset_bool_array">(pypath.core.annot.Phosphatome method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Progeny.html#pypath.core.annot.Progeny.get_subset_bool_array">(pypath.core.annot.Progeny method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Ramilowski2015.html#pypath.core.annot.Ramilowski2015.get_subset_bool_array">(pypath.core.annot.Ramilowski2015 method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Ramilowski2015Location.html#pypath.core.annot.Ramilowski2015Location.get_subset_bool_array">(pypath.core.annot.Ramilowski2015Location method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Scconnect.html#pypath.core.annot.Scconnect.get_subset_bool_array">(pypath.core.annot.Scconnect method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.ScconnectComplex.html#pypath.core.annot.ScconnectComplex.get_subset_bool_array">(pypath.core.annot.ScconnectComplex method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.SignalinkFunctions.html#pypath.core.annot.SignalinkFunctions.get_subset_bool_array">(pypath.core.annot.SignalinkFunctions method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.SignalinkPathways.html#pypath.core.annot.SignalinkPathways.get_subset_bool_array">(pypath.core.annot.SignalinkPathways method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.SignorPathways.html#pypath.core.annot.SignorPathways.get_subset_bool_array">(pypath.core.annot.SignorPathways method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Surfaceome.html#pypath.core.annot.Surfaceome.get_subset_bool_array">(pypath.core.annot.Surfaceome method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Talklr.html#pypath.core.annot.Talklr.get_subset_bool_array">(pypath.core.annot.Talklr method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Tcdb.html#pypath.core.annot.Tcdb.get_subset_bool_array">(pypath.core.annot.Tcdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Tfcensus.html#pypath.core.annot.Tfcensus.get_subset_bool_array">(pypath.core.annot.Tfcensus method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Topdb.html#pypath.core.annot.Topdb.get_subset_bool_array">(pypath.core.annot.Topdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.UniprotFamilies.html#pypath.core.annot.UniprotFamilies.get_subset_bool_array">(pypath.core.annot.UniprotFamilies method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.UniprotKeywords.html#pypath.core.annot.UniprotKeywords.get_subset_bool_array">(pypath.core.annot.UniprotKeywords method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.UniprotLocations.html#pypath.core.annot.UniprotLocations.get_subset_bool_array">(pypath.core.annot.UniprotLocations method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.UniprotTissues.html#pypath.core.annot.UniprotTissues.get_subset_bool_array">(pypath.core.annot.UniprotTissues method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.UniprotTopologies.html#pypath.core.annot.UniprotTopologies.get_subset_bool_array">(pypath.core.annot.UniprotTopologies method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Vesiclepedia.html#pypath.core.annot.Vesiclepedia.get_subset_bool_array">(pypath.core.annot.Vesiclepedia method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Wang.html#pypath.core.annot.Wang.get_subset_bool_array">(pypath.core.annot.Wang method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Zhong2015.html#pypath.core.annot.Zhong2015.get_subset_bool_array">(pypath.core.annot.Zhong2015 method)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.inputs.switches_elm.get_switches_elm.html#pypath.inputs.switches_elm.get_switches_elm">get_switches_elm() (in module pypath.inputs.switches_elm)</a>
+</li>
+      <li><a href="api/pypath.utils.mapping.Mapper.html#pypath.utils.mapping.Mapper.get_table_key">get_table_key() (pypath.utils.mapping.Mapper method)</a>
+</li>
+      <li><a href="api/pypath.utils.go.GeneOntology.html#pypath.utils.go.GeneOntology.get_term">get_term() (pypath.utils.go.GeneOntology method)</a>
+
+      <ul>
+        <li><a href="api/pypath.utils.go.GOAnnotation.html#pypath.utils.go.GOAnnotation.get_term">(pypath.utils.go.GOAnnotation method)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.inputs.dorothea.get_tfregulons.html#pypath.inputs.dorothea.get_tfregulons">get_tfregulons() (in module pypath.inputs.dorothea)</a>
+</li>
+      <li><a href="api/pypath.utils.proteomicsdb.ProteomicsDB.html#pypath.utils.proteomicsdb.ProteomicsDB.get_tissues">get_tissues() (pypath.utils.proteomicsdb.ProteomicsDB method)</a>
+</li>
+      <li><a href="api/pypath.inputs.uniprot.get_uniprot_sec.html#pypath.inputs.uniprot.get_uniprot_sec">get_uniprot_sec() (in module pypath.inputs.uniprot)</a>
+</li>
+      <li><a href="api/pypath.core.annot.Adhesome.html#pypath.core.annot.Adhesome.get_values">get_values() (pypath.core.annot.Adhesome method)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.annot.Almen2009.html#pypath.core.annot.Almen2009.get_values">(pypath.core.annot.Almen2009 method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.AnnotationBase.html#pypath.core.annot.AnnotationBase.get_values">(pypath.core.annot.AnnotationBase method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Baccin2019.html#pypath.core.annot.Baccin2019.get_values">(pypath.core.annot.Baccin2019 method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Biogps.html#pypath.core.annot.Biogps.get_values">(pypath.core.annot.Biogps method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cancerdrugsdb.html#pypath.core.annot.Cancerdrugsdb.get_values">(pypath.core.annot.Cancerdrugsdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CancerGeneCensus.html#pypath.core.annot.CancerGeneCensus.get_values">(pypath.core.annot.CancerGeneCensus method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cancersea.html#pypath.core.annot.Cancersea.get_values">(pypath.core.annot.Cancersea method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cellcall.html#pypath.core.annot.Cellcall.get_values">(pypath.core.annot.Cellcall method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cellcellinteractions.html#pypath.core.annot.Cellcellinteractions.get_values">(pypath.core.annot.Cellcellinteractions method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cellchatdb.html#pypath.core.annot.Cellchatdb.get_values">(pypath.core.annot.Cellchatdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CellchatdbComplex.html#pypath.core.annot.CellchatdbComplex.get_values">(pypath.core.annot.CellchatdbComplex method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cellinker.html#pypath.core.annot.Cellinker.get_values">(pypath.core.annot.Cellinker method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CellinkerComplex.html#pypath.core.annot.CellinkerComplex.get_values">(pypath.core.annot.CellinkerComplex method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CellPhoneDB.html#pypath.core.annot.CellPhoneDB.get_values">(pypath.core.annot.CellPhoneDB method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CellPhoneDBComplex.html#pypath.core.annot.CellPhoneDBComplex.get_values">(pypath.core.annot.CellPhoneDBComplex method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CellSurfaceProteinAtlas.html#pypath.core.annot.CellSurfaceProteinAtlas.get_values">(pypath.core.annot.CellSurfaceProteinAtlas method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CellSurfaceProteinAtlasCellType.html#pypath.core.annot.CellSurfaceProteinAtlasCellType.get_values">(pypath.core.annot.CellSurfaceProteinAtlasCellType method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Celltalkdb.html#pypath.core.annot.Celltalkdb.get_values">(pypath.core.annot.Celltalkdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Celltypist.html#pypath.core.annot.Celltypist.get_values">(pypath.core.annot.Celltypist method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Comppi.html#pypath.core.annot.Comppi.get_values">(pypath.core.annot.Comppi method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Connectomedb.html#pypath.core.annot.Connectomedb.get_values">(pypath.core.annot.Connectomedb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Corum.html#pypath.core.annot.Corum.get_values">(pypath.core.annot.Corum method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CorumFuncat.html#pypath.core.annot.CorumFuncat.get_values">(pypath.core.annot.CorumFuncat method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CorumGO.html#pypath.core.annot.CorumGO.get_values">(pypath.core.annot.CorumGO method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cpad.html#pypath.core.annot.Cpad.get_values">(pypath.core.annot.Cpad method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cytosig.html#pypath.core.annot.Cytosig.get_values">(pypath.core.annot.Cytosig method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Dgidb.html#pypath.core.annot.Dgidb.get_values">(pypath.core.annot.Dgidb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Disgenet.html#pypath.core.annot.Disgenet.get_values">(pypath.core.annot.Disgenet method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Embrace.html#pypath.core.annot.Embrace.get_values">(pypath.core.annot.Embrace method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Exocarta.html#pypath.core.annot.Exocarta.get_values">(pypath.core.annot.Exocarta method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.GOIntercell.html#pypath.core.annot.GOIntercell.get_values">(pypath.core.annot.GOIntercell method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Gpcrdb.html#pypath.core.annot.Gpcrdb.get_values">(pypath.core.annot.Gpcrdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.GuideToPharmacology.html#pypath.core.annot.GuideToPharmacology.get_values">(pypath.core.annot.GuideToPharmacology method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Hgnc.html#pypath.core.annot.Hgnc.get_values">(pypath.core.annot.Hgnc method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.HpmrComplex.html#pypath.core.annot.HpmrComplex.get_values">(pypath.core.annot.HpmrComplex method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.HPO.html#pypath.core.annot.HPO.get_values">(pypath.core.annot.HPO method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Humancellmap.html#pypath.core.annot.Humancellmap.get_values">(pypath.core.annot.Humancellmap method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.HumanPlasmaMembraneReceptome.html#pypath.core.annot.HumanPlasmaMembraneReceptome.get_values">(pypath.core.annot.HumanPlasmaMembraneReceptome method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.HumanProteinAtlas.html#pypath.core.annot.HumanProteinAtlas.get_values">(pypath.core.annot.HumanProteinAtlas method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.HumanProteinAtlasSecretome.html#pypath.core.annot.HumanProteinAtlasSecretome.get_values">(pypath.core.annot.HumanProteinAtlasSecretome method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.HumanProteinAtlasSubcellular.html#pypath.core.annot.HumanProteinAtlasSubcellular.get_values">(pypath.core.annot.HumanProteinAtlasSubcellular method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Icellnet.html#pypath.core.annot.Icellnet.get_values">(pypath.core.annot.Icellnet method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.IcellnetComplex.html#pypath.core.annot.IcellnetComplex.get_values">(pypath.core.annot.IcellnetComplex method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Integrins.html#pypath.core.annot.Integrins.get_values">(pypath.core.annot.Integrins method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.InterPro.html#pypath.core.annot.InterPro.get_values">(pypath.core.annot.InterPro method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Intogen.html#pypath.core.annot.Intogen.get_values">(pypath.core.annot.Intogen method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Italk.html#pypath.core.annot.Italk.get_values">(pypath.core.annot.Italk method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.KeggPathways.html#pypath.core.annot.KeggPathways.get_values">(pypath.core.annot.KeggPathways method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.KeggPathwaysPC.html#pypath.core.annot.KeggPathwaysPC.get_values">(pypath.core.annot.KeggPathwaysPC method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Kinasedotcom.html#pypath.core.annot.Kinasedotcom.get_values">(pypath.core.annot.Kinasedotcom method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Kirouac2010.html#pypath.core.annot.Kirouac2010.get_values">(pypath.core.annot.Kirouac2010 method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Lambert2018.html#pypath.core.annot.Lambert2018.get_values">(pypath.core.annot.Lambert2018 method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.LigandReceptor.html#pypath.core.annot.LigandReceptor.get_values">(pypath.core.annot.LigandReceptor method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Locate.html#pypath.core.annot.Locate.get_values">(pypath.core.annot.Locate method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Lrdb.html#pypath.core.annot.Lrdb.get_values">(pypath.core.annot.Lrdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Matrisome.html#pypath.core.annot.Matrisome.get_values">(pypath.core.annot.Matrisome method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Matrixdb.html#pypath.core.annot.Matrixdb.get_values">(pypath.core.annot.Matrixdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Mcam.html#pypath.core.annot.Mcam.get_values">(pypath.core.annot.Mcam method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Membranome.html#pypath.core.annot.Membranome.get_values">(pypath.core.annot.Membranome method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Msigdb.html#pypath.core.annot.Msigdb.get_values">(pypath.core.annot.Msigdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.NetpathPathways.html#pypath.core.annot.NetpathPathways.get_values">(pypath.core.annot.NetpathPathways method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Opm.html#pypath.core.annot.Opm.get_values">(pypath.core.annot.Opm method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Panglaodb.html#pypath.core.annot.Panglaodb.get_values">(pypath.core.annot.Panglaodb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Phobius.html#pypath.core.annot.Phobius.get_values">(pypath.core.annot.Phobius method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Phosphatome.html#pypath.core.annot.Phosphatome.get_values">(pypath.core.annot.Phosphatome method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Progeny.html#pypath.core.annot.Progeny.get_values">(pypath.core.annot.Progeny method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Ramilowski2015.html#pypath.core.annot.Ramilowski2015.get_values">(pypath.core.annot.Ramilowski2015 method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Ramilowski2015Location.html#pypath.core.annot.Ramilowski2015Location.get_values">(pypath.core.annot.Ramilowski2015Location method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Scconnect.html#pypath.core.annot.Scconnect.get_values">(pypath.core.annot.Scconnect method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.ScconnectComplex.html#pypath.core.annot.ScconnectComplex.get_values">(pypath.core.annot.ScconnectComplex method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.SignalinkFunctions.html#pypath.core.annot.SignalinkFunctions.get_values">(pypath.core.annot.SignalinkFunctions method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.SignalinkPathways.html#pypath.core.annot.SignalinkPathways.get_values">(pypath.core.annot.SignalinkPathways method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.SignorPathways.html#pypath.core.annot.SignorPathways.get_values">(pypath.core.annot.SignorPathways method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Surfaceome.html#pypath.core.annot.Surfaceome.get_values">(pypath.core.annot.Surfaceome method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Talklr.html#pypath.core.annot.Talklr.get_values">(pypath.core.annot.Talklr method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Tcdb.html#pypath.core.annot.Tcdb.get_values">(pypath.core.annot.Tcdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Tfcensus.html#pypath.core.annot.Tfcensus.get_values">(pypath.core.annot.Tfcensus method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Topdb.html#pypath.core.annot.Topdb.get_values">(pypath.core.annot.Topdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.UniprotFamilies.html#pypath.core.annot.UniprotFamilies.get_values">(pypath.core.annot.UniprotFamilies method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.UniprotKeywords.html#pypath.core.annot.UniprotKeywords.get_values">(pypath.core.annot.UniprotKeywords method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.UniprotLocations.html#pypath.core.annot.UniprotLocations.get_values">(pypath.core.annot.UniprotLocations method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.UniprotTissues.html#pypath.core.annot.UniprotTissues.get_values">(pypath.core.annot.UniprotTissues method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.UniprotTopologies.html#pypath.core.annot.UniprotTopologies.get_values">(pypath.core.annot.UniprotTopologies method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Vesiclepedia.html#pypath.core.annot.Vesiclepedia.get_values">(pypath.core.annot.Vesiclepedia method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Wang.html#pypath.core.annot.Wang.get_values">(pypath.core.annot.Wang method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Zhong2015.html#pypath.core.annot.Zhong2015.get_values">(pypath.core.annot.Zhong2015 method)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.inputs.exocarta.get_vesiclepedia.html#pypath.inputs.exocarta.get_vesiclepedia">get_vesiclepedia() (in module pypath.inputs.exocarta)</a>
+</li>
+      <li><a href="api/pypath.internals.resource.EnzymeSubstrateResource.html#pypath.internals.resource.EnzymeSubstrateResource.get_via">get_via() (pypath.internals.resource.EnzymeSubstrateResource method)</a>
+</li>
+      <li><a href="api/pypath.inputs.common.glom_fields.html#pypath.inputs.common.glom_fields">glom_fields() (in module pypath.inputs.common)</a>
+</li>
+      <li><a href="api/pypath.inputs.go.go_ancestors.html#pypath.inputs.go.go_ancestors">go_ancestors() (in module pypath.inputs.go)</a>
+</li>
+      <li><a href="api/pypath.inputs.go.go_ancestors_goose.html#pypath.inputs.go.go_ancestors_goose">go_ancestors_goose() (in module pypath.inputs.go)</a>
+</li>
+      <li><a href="api/pypath.inputs.go.go_ancestors_quickgo.html#pypath.inputs.go.go_ancestors_quickgo">go_ancestors_quickgo() (in module pypath.inputs.go)</a>
+</li>
+      <li><a href="api/pypath.inputs.go.go_annotations.html#pypath.inputs.go.go_annotations">go_annotations() (in module pypath.inputs.go)</a>
+</li>
+      <li><a href="api/pypath.inputs.go.go_annotations_all.html#pypath.inputs.go.go_annotations_all">go_annotations_all() (in module pypath.inputs.go)</a>
+</li>
+      <li><a href="api/pypath.inputs.go.go_annotations_goa.html#pypath.inputs.go.go_annotations_goa">go_annotations_goa() (in module pypath.inputs.go)</a>
+</li>
+      <li><a href="api/pypath.inputs.go.go_annotations_goose.html#pypath.inputs.go.go_annotations_goose">go_annotations_goose() (in module pypath.inputs.go)</a>
+</li>
+      <li><a href="api/pypath.inputs.go.go_annotations_quickgo.html#pypath.inputs.go.go_annotations_quickgo">go_annotations_quickgo() (in module pypath.inputs.go)</a>
+</li>
+      <li><a href="api/pypath.inputs.go.go_annotations_solr.html#pypath.inputs.go.go_annotations_solr">go_annotations_solr() (in module pypath.inputs.go)</a>
+</li>
+      <li><a href="api/pypath.inputs.go.go_annotations_uniprot.html#pypath.inputs.go.go_annotations_uniprot">go_annotations_uniprot() (in module pypath.inputs.go)</a>
+</li>
+      <li><a href="api/pypath.inputs.go.go_descendants.html#pypath.inputs.go.go_descendants">go_descendants() (in module pypath.inputs.go)</a>
+</li>
+      <li><a href="api/pypath.inputs.go.go_descendants_goose.html#pypath.inputs.go.go_descendants_goose">go_descendants_goose() (in module pypath.inputs.go)</a>
+</li>
+      <li><a href="api/pypath.inputs.go.go_descendants_quickgo.html#pypath.inputs.go.go_descendants_quickgo">go_descendants_quickgo() (in module pypath.inputs.go)</a>
+</li>
+      <li><a href="api/pypath.inputs.go.go_descendants_to_ancestors.html#pypath.inputs.go.go_descendants_to_ancestors">go_descendants_to_ancestors() (in module pypath.inputs.go)</a>
+</li>
+      <li><a href="api/pypath.inputs.go.go_terms.html#pypath.inputs.go.go_terms">go_terms() (in module pypath.inputs.go)</a>
+</li>
+      <li><a href="api/pypath.inputs.go.go_terms_goose.html#pypath.inputs.go.go_terms_goose">go_terms_goose() (in module pypath.inputs.go)</a>
+</li>
+      <li><a href="api/pypath.inputs.go.go_terms_quickgo.html#pypath.inputs.go.go_terms_quickgo">go_terms_quickgo() (in module pypath.inputs.go)</a>
+</li>
+      <li><a href="api/pypath.inputs.go.go_terms_solr.html#pypath.inputs.go.go_terms_solr">go_terms_solr() (in module pypath.inputs.go)</a>
+</li>
+      <li><a href="api/pypath.utils.go.GOAnnotation.html#pypath.utils.go.GOAnnotation">GOAnnotation (class in pypath.utils.go)</a>
+</li>
+      <li><a href="api/pypath.utils.go.GOCustomAnnotation.html#pypath.utils.go.GOCustomAnnotation">GOCustomAnnotation (class in pypath.utils.go)</a>
+</li>
+      <li><a href="api/pypath.core.annot.GOCustomIntercell.html#pypath.core.annot.GOCustomIntercell">GOCustomIntercell (class in pypath.core.annot)</a>
+</li>
+      <li><a href="api/pypath.core.annot.GOIntercell.html#pypath.core.annot.GOIntercell">GOIntercell (class in pypath.core.annot)</a>
+</li>
+      <li><a href="api/pypath.core.annot.Gpcrdb.html#pypath.core.annot.Gpcrdb">Gpcrdb (class in pypath.core.annot)</a>
+</li>
+      <li><a href="api/pypath.inputs.gpcrdb.gpcrdb_annotations.html#pypath.inputs.gpcrdb.gpcrdb_annotations">gpcrdb_annotations() (in module pypath.inputs.gpcrdb)</a>
+</li>
+      <li><a href="api/pypath.inputs.graphviz.graphviz_attrs.html#pypath.inputs.graphviz.graphviz_attrs">graphviz_attrs() (in module pypath.inputs.graphviz)</a>
+</li>
+      <li><a href="api/pypath.utils.mapping.guess_type.html#pypath.utils.mapping.guess_type">guess_type() (in module pypath.utils.mapping)</a>
+
+      <ul>
+        <li><a href="api/pypath.utils.mapping.Mapper.html#pypath.utils.mapping.Mapper.guess_type">(pypath.utils.mapping.Mapper method)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.inputs.guide2pharma.guide2pharma_complexes.html#pypath.inputs.guide2pharma.guide2pharma_complexes">guide2pharma_complexes() (in module pypath.inputs.guide2pharma)</a>
+</li>
+      <li><a href="api/pypath.inputs.guide2pharma.guide2pharma_download.html#pypath.inputs.guide2pharma.guide2pharma_download">guide2pharma_download() (in module pypath.inputs.guide2pharma)</a>
+</li>
+      <li><a href="api/pypath.inputs.guide2pharma.guide2pharma_interactions.html#pypath.inputs.guide2pharma.guide2pharma_interactions">guide2pharma_interactions() (in module pypath.inputs.guide2pharma)</a>
+</li>
+      <li><a href="api/pypath.core.annot.GuideToPharmacology.html#pypath.core.annot.GuideToPharmacology">GuideToPharmacology (class in pypath.core.annot)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.complex.GuideToPharmacology.html#pypath.core.complex.GuideToPharmacology">(class in pypath.core.complex)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.inputs.gutmgene.GutmgeneAnnotation.html#pypath.inputs.gutmgene.GutmgeneAnnotation.gut_microbiota_id">gut_microbiota_id (pypath.inputs.gutmgene.GutmgeneAnnotation attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.inputs.gutmgene.GutmgeneRaw.html#pypath.inputs.gutmgene.GutmgeneRaw.gut_microbiota_id">(pypath.inputs.gutmgene.GutmgeneRaw attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.inputs.gutmgene.gutmgene_annotations.html#pypath.inputs.gutmgene.gutmgene_annotations">gutmgene_annotations() (in module pypath.inputs.gutmgene)</a>
+</li>
+      <li><a href="api/pypath.inputs.gutmgene.gutmgene_raw.html#pypath.inputs.gutmgene.gutmgene_raw">gutmgene_raw() (in module pypath.inputs.gutmgene)</a>
+</li>
+      <li><a href="api/pypath.inputs.gutmgene.GutmgeneAnnotation.html#pypath.inputs.gutmgene.GutmgeneAnnotation">GutmgeneAnnotation (class in pypath.inputs.gutmgene)</a>
+</li>
+      <li><a href="api/pypath.inputs.gutmgene.GutmgeneRaw.html#pypath.inputs.gutmgene.GutmgeneRaw">GutmgeneRaw (class in pypath.inputs.gutmgene)</a>
+</li>
+  </ul></td>
+</tr></table>
+
+<h2 id="H">H</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="api/pypath.utils.go.GOAnnotation.html#pypath.utils.go.GOAnnotation.has_any_term">has_any_term() (pypath.utils.go.GOAnnotation method)</a>
+</li>
+      <li><a href="api/pypath.core.evidence.Evidences.html#pypath.core.evidence.Evidences.has_dataset">has_dataset() (pypath.core.evidence.Evidences method)</a>
+</li>
+      <li><a href="api/pypath.core.evidence.Evidence.html#pypath.core.evidence.Evidence.has_interaction_type">has_interaction_type() (pypath.core.evidence.Evidence method)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.evidence.Evidences.html#pypath.core.evidence.Evidences.has_interaction_type">(pypath.core.evidence.Evidences method)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.utils.mapping.Mapper.html#pypath.utils.mapping.Mapper.has_mapping_table">has_mapping_table() (pypath.utils.mapping.Mapper method)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.has_sign">has_sign() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.utils.uniprot.has_tag.html#pypath.utils.uniprot.has_tag">has_tag() (in module pypath.utils.uniprot)</a>
+</li>
+      <li><a href="api/pypath.utils.go.GOAnnotation.html#pypath.utils.go.GOAnnotation.has_term">has_term() (pypath.utils.go.GOAnnotation method)</a>
+</li>
+      <li><a href="api/pypath.core.complex.Havugimana.html#pypath.core.complex.Havugimana">Havugimana (class in pypath.core.complex)</a>
+</li>
+      <li><a href="api/pypath.inputs.havugimana.havugimana_complexes.html#pypath.inputs.havugimana.havugimana_complexes">havugimana_complexes() (in module pypath.inputs.havugimana)</a>
+</li>
+      <li><a href="api/pypath.utils.orthology.EnsemblOrtholog.html#pypath.utils.orthology.EnsemblOrtholog.hc">hc (pypath.utils.orthology.EnsemblOrtholog attribute)</a>
+</li>
+      <li><a href="api/pypath.core.annot.Hgnc.html#pypath.core.annot.Hgnc">Hgnc (class in pypath.core.annot)</a>
+</li>
+      <li><a href="api/pypath.inputs.hgnc.hgnc_genegroups.html#pypath.inputs.hgnc.hgnc_genegroups">hgnc_genegroups() (in module pypath.inputs.hgnc)</a>
+</li>
+      <li><a href="api/pypath.inputs.huri.hi_i_interactions.html#pypath.inputs.huri.hi_i_interactions">hi_i_interactions() (in module pypath.inputs.huri)</a>
+</li>
+      <li><a href="api/pypath.inputs.huri.hi_ii_interactions.html#pypath.inputs.huri.hi_ii_interactions">hi_ii_interactions() (in module pypath.inputs.huri)</a>
+</li>
+      <li><a href="api/pypath.inputs.huri.hi_iii_old.html#pypath.inputs.huri.hi_iii_old">hi_iii_old() (in module pypath.inputs.huri)</a>
+</li>
+      <li><a href="api/pypath.inputs.huri.hi_union_interactions.html#pypath.inputs.huri.hi_union_interactions">hi_union_interactions() (in module pypath.inputs.huri)</a>
+</li>
+      <li><a href="api/pypath.utils.go.GeneOntology.html#pypath.utils.go.GeneOntology.highest">highest() (pypath.utils.go.GeneOntology method)</a>
+</li>
+      <li><a href="api/pypath.inputs.hippie.hippie_interactions.html#pypath.inputs.hippie.hippie_interactions">hippie_interactions() (in module pypath.inputs.hippie)</a>
+</li>
+      <li><a href="api/pypath.inputs.hmdb.xml.hmdb_xml.html#pypath.inputs.hmdb.xml.hmdb_xml">hmdb_xml() (in module pypath.inputs.hmdb.xml)</a>
+</li>
+      <li><a href="api/pypath.internals.input_formats.HmdbMapping.html#pypath.internals.input_formats.HmdbMapping">HmdbMapping (class in pypath.internals.input_formats)</a>
+</li>
+      <li><a href="api/pypath.inputs.homologene.homologene_dict.html#pypath.inputs.homologene.homologene_dict">homologene_dict() (in module pypath.inputs.homologene)</a>
+</li>
+      <li><a href="api/pypath.inputs.homologene.homologene_uniprot_dict.html#pypath.inputs.homologene.homologene_uniprot_dict">homologene_uniprot_dict() (in module pypath.inputs.homologene)</a>
+</li>
+      <li><a href="api/pypath.utils.orthology.HomologeneOrtholog.html#pypath.utils.orthology.HomologeneOrtholog">HomologeneOrtholog (class in pypath.utils.orthology)</a>
+</li>
+      <li><a href="api/pypath.utils.orthology.HomologeneOrthology.html#pypath.utils.orthology.HomologeneOrthology">HomologeneOrthology (class in pypath.utils.orthology)</a>
+</li>
+      <li><a href="api/pypath.core.complex.Hpmr.html#pypath.core.complex.Hpmr">Hpmr (class in pypath.core.complex)</a>
+</li>
+      <li><a href="api/pypath.inputs.hpmr.hpmr_annotations.html#pypath.inputs.hpmr.hpmr_annotations">hpmr_annotations() (in module pypath.inputs.hpmr)</a>
+</li>
+  </ul></td>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="api/pypath.inputs.hpmr.hpmr_complexes.html#pypath.inputs.hpmr.hpmr_complexes">hpmr_complexes() (in module pypath.inputs.hpmr)</a>
+</li>
+      <li><a href="api/pypath.inputs.hpmr.hpmr_interactions.html#pypath.inputs.hpmr.hpmr_interactions">hpmr_interactions() (in module pypath.inputs.hpmr)</a>
+</li>
+      <li><a href="api/pypath.core.annot.HpmrComplex.html#pypath.core.annot.HpmrComplex">HpmrComplex (class in pypath.core.annot)</a>
+</li>
+      <li><a href="api/pypath.inputs.hpmr.HpmrInteraction.html#pypath.inputs.hpmr.HpmrInteraction">HpmrInteraction (class in pypath.inputs.hpmr)</a>
+</li>
+      <li><a href="api/pypath.core.annot.HPO.html#pypath.core.annot.HPO">HPO (class in pypath.core.annot)</a>
+</li>
+      <li><a href="api/pypath.inputs.hpo.hpo_annotations.html#pypath.inputs.hpo.hpo_annotations">hpo_annotations() (in module pypath.inputs.hpo)</a>
+</li>
+      <li><a href="api/pypath.inputs.hpo.hpo_diseases.html#pypath.inputs.hpo.hpo_diseases">hpo_diseases() (in module pypath.inputs.hpo)</a>
+</li>
+      <li><a href="api/pypath.inputs.hpo.hpo_ontology.html#pypath.inputs.hpo.hpo_ontology">hpo_ontology() (in module pypath.inputs.hpo)</a>
+</li>
+      <li><a href="api/pypath.inputs.hpo.hpo_terms.html#pypath.inputs.hpo.hpo_terms">hpo_terms() (in module pypath.inputs.hpo)</a>
+</li>
+      <li><a href="api/pypath.inputs.hprd.hprd_enzyme_substrate.html#pypath.inputs.hprd.hprd_enzyme_substrate">hprd_enzyme_substrate() (in module pypath.inputs.hprd)</a>
+</li>
+      <li><a href="api/pypath.inputs.hprd.hprd_interactions.html#pypath.inputs.hprd.hprd_interactions">hprd_interactions() (in module pypath.inputs.hprd)</a>
+</li>
+      <li><a href="api/pypath.inputs.hprd.hprd_interactions_htp.html#pypath.inputs.hprd.hprd_interactions_htp">hprd_interactions_htp() (in module pypath.inputs.hprd)</a>
+</li>
+      <li><a href="api/pypath.inputs.wang.hsn_interactions.html#pypath.inputs.wang.hsn_interactions">hsn_interactions() (in module pypath.inputs.wang)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.htp_interactions">htp_interactions() (pypath.core.network.Network method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.htp_references">htp_references() (pypath.core.network.Network method)</a>
+</li>
+      <li><a href="api/pypath.inputs.htri.htri_interactions.html#pypath.inputs.htri.htri_interactions">htri_interactions() (in module pypath.inputs.htri)</a>
+</li>
+      <li><a href="api/pypath.core.annot.Humancellmap.html#pypath.core.annot.Humancellmap">Humancellmap (class in pypath.core.annot)</a>
+</li>
+      <li><a href="api/pypath.inputs.humancellmap.humancellmap_annotations.html#pypath.inputs.humancellmap.humancellmap_annotations">humancellmap_annotations() (in module pypath.inputs.humancellmap)</a>
+</li>
+      <li><a href="api/pypath.core.annot.HumanPlasmaMembraneReceptome.html#pypath.core.annot.HumanPlasmaMembraneReceptome">HumanPlasmaMembraneReceptome (class in pypath.core.annot)</a>
+</li>
+      <li><a href="api/pypath.core.annot.HumanProteinAtlas.html#pypath.core.annot.HumanProteinAtlas">HumanProteinAtlas (class in pypath.core.annot)</a>
+</li>
+      <li><a href="api/pypath.core.annot.HumanProteinAtlasSecretome.html#pypath.core.annot.HumanProteinAtlasSecretome">HumanProteinAtlasSecretome (class in pypath.core.annot)</a>
+</li>
+      <li><a href="api/pypath.core.annot.HumanProteinAtlasSubcellular.html#pypath.core.annot.HumanProteinAtlasSubcellular">HumanProteinAtlasSubcellular (class in pypath.core.annot)</a>
+</li>
+      <li><a href="api/pypath.core.complex.Humap.html#pypath.core.complex.Humap">Humap (class in pypath.core.complex)</a>
+</li>
+      <li><a href="api/pypath.core.complex.Humap2.html#pypath.core.complex.Humap2">Humap2 (class in pypath.core.complex)</a>
+</li>
+      <li><a href="api/pypath.inputs.humap.humap2_complexes.html#pypath.inputs.humap.humap2_complexes">humap2_complexes() (in module pypath.inputs.humap)</a>
+</li>
+      <li><a href="api/pypath.inputs.humap.humap_complexes.html#pypath.inputs.humap.humap_complexes">humap_complexes() (in module pypath.inputs.humap)</a>
+</li>
+      <li><a href="api/pypath.inputs.huri.huri_interactions.html#pypath.inputs.huri.huri_interactions">huri_interactions() (in module pypath.inputs.huri)</a>
+</li>
+  </ul></td>
+</tr></table>
+
+<h2 id="I">I</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="api/pypath.utils.go.GOAnnotation.html#pypath.utils.go.GOAnnotation.i_select_by_term">i_select_by_term() (pypath.utils.go.GOAnnotation method)</a>
+</li>
+      <li><a href="api/pypath.core.annot.Icellnet.html#pypath.core.annot.Icellnet">Icellnet (class in pypath.core.annot)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.complex.Icellnet.html#pypath.core.complex.Icellnet">(class in pypath.core.complex)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.inputs.icellnet.icellnet_annotations.html#pypath.inputs.icellnet.icellnet_annotations">icellnet_annotations() (in module pypath.inputs.icellnet)</a>
+</li>
+      <li><a href="api/pypath.inputs.icellnet.icellnet_complexes.html#pypath.inputs.icellnet.icellnet_complexes">icellnet_complexes() (in module pypath.inputs.icellnet)</a>
+</li>
+      <li><a href="api/pypath.inputs.icellnet.icellnet_interactions.html#pypath.inputs.icellnet.icellnet_interactions">icellnet_interactions() (in module pypath.inputs.icellnet)</a>
+</li>
+      <li><a href="api/pypath.core.annot.IcellnetComplex.html#pypath.core.annot.IcellnetComplex">IcellnetComplex (class in pypath.core.annot)</a>
+</li>
+      <li><a href="api/pypath.inputs.icellnet.IcellnetRecord.html#pypath.inputs.icellnet.IcellnetRecord">IcellnetRecord (class in pypath.inputs.icellnet)</a>
+</li>
+      <li><a href="api/pypath.utils.orthology.EnsemblOrtholog.html#pypath.utils.orthology.EnsemblOrtholog.id">id (pypath.utils.orthology.EnsemblOrtholog attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.utils.orthology.HomologeneOrtholog.html#pypath.utils.orthology.HomologeneOrtholog.id">(pypath.utils.orthology.HomologeneOrtholog attribute)</a>
+</li>
+        <li><a href="api/pypath.utils.orthology.OmaOrtholog.html#pypath.utils.orthology.OmaOrtholog.id">(pypath.utils.orthology.OmaOrtholog attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.utils.uniprot.id.html#pypath.utils.uniprot.id">id() (in module pypath.utils.uniprot)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.InteractionDataFrameRecord.html#pypath.core.interaction.InteractionDataFrameRecord.id_a">id_a (pypath.core.interaction.InteractionDataFrameRecord attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.inputs.pathwaycommons.PathwayCommonsInteraction.html#pypath.inputs.pathwaycommons.PathwayCommonsInteraction.id_a">(pypath.inputs.pathwaycommons.PathwayCommonsInteraction attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.interaction.InteractionDataFrameRecord.html#pypath.core.interaction.InteractionDataFrameRecord.id_b">id_b (pypath.core.interaction.InteractionDataFrameRecord attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.inputs.pathwaycommons.PathwayCommonsInteraction.html#pypath.inputs.pathwaycommons.PathwayCommonsInteraction.id_b">(pypath.inputs.pathwaycommons.PathwayCommonsInteraction attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.utils.mapping.id_from_label.html#pypath.utils.mapping.id_from_label">id_from_label() (in module pypath.utils.mapping)</a>
+</li>
+      <li><a href="api/pypath.utils.mapping.id_from_label0.html#pypath.utils.mapping.id_from_label0">id_from_label0() (in module pypath.utils.mapping)</a>
+</li>
+      <li><a href="api/pypath.core.entity.EntityKey.html#pypath.core.entity.EntityKey.id_type">id_type (pypath.core.entity.EntityKey attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.utils.mapping.MappingTableKey.html#pypath.utils.mapping.MappingTableKey.id_type">(pypath.utils.mapping.MappingTableKey attribute)</a>
+</li>
+        <li><a href="api/pypath.utils.orthology.OrthologyTableKey.html#pypath.utils.orthology.OrthologyTableKey.id_type">(pypath.utils.orthology.OrthologyTableKey attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.utils.mapping.MapReader.html#pypath.utils.mapping.MapReader.id_type_side">id_type_side() (pypath.utils.mapping.MapReader method)</a>
+</li>
+      <li><a href="api/pypath.utils.mapping.id_types.html#pypath.utils.mapping.id_types">id_types() (in module pypath.utils.mapping)</a>
+
+      <ul>
+        <li><a href="api/pypath.utils.mapping.Mapper.html#pypath.utils.mapping.Mapper.id_types">(pypath.utils.mapping.Mapper class method)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.entity.EntityKey.html#pypath.core.entity.EntityKey.identifier">identifier (pypath.core.entity.EntityKey attribute)</a>
+</li>
+      <li><a href="api/pypath.utils.mapping.Mapper.html#pypath.utils.mapping.Mapper.identifier">identifier() (pypath.utils.mapping.Mapper method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.identifiers_by_data_model">identifiers_by_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.identifiers_by_data_model">identifiers_by_data_model() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.identifiers_by_interaction_type">identifiers_by_interaction_type (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.identifiers_by_interaction_type">identifiers_by_interaction_type() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.identifiers_by_interaction_type_and_data_model">identifiers_by_interaction_type_and_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.identifiers_by_interaction_type_and_data_model">identifiers_by_interaction_type_and_data_model() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.identifiers_by_interaction_type_and_data_model_and_resource">identifiers_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.identifiers_by_interaction_type_and_data_model_and_resource">identifiers_by_interaction_type_and_data_model_and_resource() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.identifiers_by_reference">identifiers_by_reference (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.identifiers_by_reference">identifiers_by_reference() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.identifiers_by_resource">identifiers_by_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.identifiers_by_resource">identifiers_by_resource() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.inputs.uniprot.idmapping_idtypes.html#pypath.inputs.uniprot.idmapping_idtypes">idmapping_idtypes() (in module pypath.inputs.uniprot)</a>
+</li>
+      <li><a href="api/pypath.omnipath.server.run.ignore_pandas_copywarn.html#pypath.omnipath.server.run.ignore_pandas_copywarn">ignore_pandas_copywarn() (in module pypath.omnipath.server.run)</a>
+</li>
+      <li><a href="api/pypath.utils.pyreact.PyReact.html#pypath.utils.pyreact.PyReact.in_same_component">in_same_component() (pypath.utils.pyreact.PyReact method)</a>
+</li>
+      <li><a href="api/pypath.utils.unichem.Unichem.html#pypath.utils.unichem.Unichem.inchikey2anything">inchikey2anything() (pypath.utils.unichem.Unichem method)</a>
+</li>
+      <li><a href="api/pypath.core.entity.EntityKey.html#pypath.core.entity.EntityKey.index">index() (pypath.core.entity.EntityKey method)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.interaction.InteractionDataFrameRecord.html#pypath.core.interaction.InteractionDataFrameRecord.index">(pypath.core.interaction.InteractionDataFrameRecord method)</a>
+</li>
+        <li><a href="api/pypath.core.interaction.InteractionKey.html#pypath.core.interaction.InteractionKey.index">(pypath.core.interaction.InteractionKey method)</a>
+</li>
+        <li><a href="api/pypath.core.network.NetworkStatsRecord.html#pypath.core.network.NetworkStatsRecord.index">(pypath.core.network.NetworkStatsRecord method)</a>
+</li>
+        <li><a href="api/pypath.inputs.adrecs.AdrecsAdr.html#pypath.inputs.adrecs.AdrecsAdr.index">(pypath.inputs.adrecs.AdrecsAdr method)</a>
+</li>
+        <li><a href="api/pypath.inputs.adrecs.AdrecsChildParent.html#pypath.inputs.adrecs.AdrecsChildParent.index">(pypath.inputs.adrecs.AdrecsChildParent method)</a>
+</li>
+        <li><a href="api/pypath.inputs.adrecs.AdrecsDrug.html#pypath.inputs.adrecs.AdrecsDrug.index">(pypath.inputs.adrecs.AdrecsDrug method)</a>
+</li>
+        <li><a href="api/pypath.inputs.adrecs.AdrecsDrugAdr.html#pypath.inputs.adrecs.AdrecsDrugAdr.index">(pypath.inputs.adrecs.AdrecsDrugAdr method)</a>
+</li>
+        <li><a href="api/pypath.inputs.adrecs.AdrecsTerm.html#pypath.inputs.adrecs.AdrecsTerm.index">(pypath.inputs.adrecs.AdrecsTerm method)</a>
+</li>
+        <li><a href="api/pypath.inputs.biogps.BiogpsDataset.html#pypath.inputs.biogps.BiogpsDataset.index">(pypath.inputs.biogps.BiogpsDataset method)</a>
+</li>
+        <li><a href="api/pypath.inputs.cellinker.CellinkerInteraction.html#pypath.inputs.cellinker.CellinkerInteraction.index">(pypath.inputs.cellinker.CellinkerInteraction method)</a>
+</li>
+        <li><a href="api/pypath.inputs.cellphonedb.CellPhoneDBAnnotation.html#pypath.inputs.cellphonedb.CellPhoneDBAnnotation.index">(pypath.inputs.cellphonedb.CellPhoneDBAnnotation method)</a>
+</li>
+        <li><a href="api/pypath.inputs.dorothea.DorotheaInteraction.html#pypath.inputs.dorothea.DorotheaInteraction.index">(pypath.inputs.dorothea.DorotheaInteraction method)</a>
+</li>
+        <li><a href="api/pypath.inputs.gutmgene.GutmgeneAnnotation.html#pypath.inputs.gutmgene.GutmgeneAnnotation.index">(pypath.inputs.gutmgene.GutmgeneAnnotation method)</a>
+</li>
+        <li><a href="api/pypath.inputs.gutmgene.GutmgeneRaw.html#pypath.inputs.gutmgene.GutmgeneRaw.index">(pypath.inputs.gutmgene.GutmgeneRaw method)</a>
+</li>
+        <li><a href="api/pypath.inputs.hpmr.HpmrInteraction.html#pypath.inputs.hpmr.HpmrInteraction.index">(pypath.inputs.hpmr.HpmrInteraction method)</a>
+</li>
+        <li><a href="api/pypath.inputs.icellnet.IcellnetRecord.html#pypath.inputs.icellnet.IcellnetRecord.index">(pypath.inputs.icellnet.IcellnetRecord method)</a>
+</li>
+        <li><a href="api/pypath.inputs.iptmnet.IptmnetInteraction.html#pypath.inputs.iptmnet.IptmnetInteraction.index">(pypath.inputs.iptmnet.IptmnetInteraction method)</a>
+</li>
+        <li><a href="api/pypath.inputs.kegg.KeggPathway.html#pypath.inputs.kegg.KeggPathway.index">(pypath.inputs.kegg.KeggPathway method)</a>
+</li>
+        <li><a href="api/pypath.inputs.lrdb.LrdbAnnotation.html#pypath.inputs.lrdb.LrdbAnnotation.index">(pypath.inputs.lrdb.LrdbAnnotation method)</a>
+</li>
+        <li><a href="api/pypath.inputs.pathophenodb.DiseasePathogen.html#pypath.inputs.pathophenodb.DiseasePathogen.index">(pypath.inputs.pathophenodb.DiseasePathogen method)</a>
+</li>
+        <li><a href="api/pypath.inputs.pathwaycommons.PathwayCommonsInteraction.html#pypath.inputs.pathwaycommons.PathwayCommonsInteraction.index">(pypath.inputs.pathwaycommons.PathwayCommonsInteraction method)</a>
+</li>
+        <li><a href="api/pypath.inputs.pathwaycommons.PathwayCommonsResource.html#pypath.inputs.pathwaycommons.PathwayCommonsResource.index">(pypath.inputs.pathwaycommons.PathwayCommonsResource method)</a>
+</li>
+        <li><a href="api/pypath.inputs.pisa.PisaBond.html#pypath.inputs.pisa.PisaBond.index">(pypath.inputs.pisa.PisaBond method)</a>
+</li>
+        <li><a href="api/pypath.inputs.sider.SiderDrug.html#pypath.inputs.sider.SiderDrug.index">(pypath.inputs.sider.SiderDrug method)</a>
+</li>
+        <li><a href="api/pypath.inputs.sider.SiderSideeffect.html#pypath.inputs.sider.SiderSideeffect.index">(pypath.inputs.sider.SiderSideeffect method)</a>
+</li>
+        <li><a href="api/pypath.inputs.sider.SiderSideeffectMeddra.html#pypath.inputs.sider.SiderSideeffectMeddra.index">(pypath.inputs.sider.SiderSideeffectMeddra method)</a>
+</li>
+        <li><a href="api/pypath.inputs.sider.SiderSideeffetFrequency.html#pypath.inputs.sider.SiderSideeffetFrequency.index">(pypath.inputs.sider.SiderSideeffetFrequency method)</a>
+</li>
+        <li><a href="api/pypath.inputs.uniprot.Taxon.html#pypath.inputs.uniprot.Taxon.index">(pypath.inputs.uniprot.Taxon method)</a>
+</li>
+        <li><a href="api/pypath.inputs.uniprot.UniprotRecordHistory.html#pypath.inputs.uniprot.UniprotRecordHistory.index">(pypath.inputs.uniprot.UniprotRecordHistory method)</a>
+</li>
+        <li><a href="api/pypath.internals.annot_formats.AnnotDef.html#pypath.internals.annot_formats.AnnotDef.index">(pypath.internals.annot_formats.AnnotDef method)</a>
+</li>
+        <li><a href="api/pypath.internals.annot_formats.AnnotDefKey.html#pypath.internals.annot_formats.AnnotDefKey.index">(pypath.internals.annot_formats.AnnotDefKey method)</a>
+</li>
+        <li><a href="api/pypath.internals.annot_formats.AnnotOp.html#pypath.internals.annot_formats.AnnotOp.index">(pypath.internals.annot_formats.AnnotOp method)</a>
+</li>
+        <li><a href="api/pypath.internals.resource.EnzymeSubstrateResourceKey.html#pypath.internals.resource.EnzymeSubstrateResourceKey.index">(pypath.internals.resource.EnzymeSubstrateResourceKey method)</a>
+</li>
+        <li><a href="api/pypath.internals.resource.NetworkResourceKey.html#pypath.internals.resource.NetworkResourceKey.index">(pypath.internals.resource.NetworkResourceKey method)</a>
+</li>
+        <li><a href="api/pypath.utils.mapping.MappingTableKey.html#pypath.utils.mapping.MappingTableKey.index">(pypath.utils.mapping.MappingTableKey method)</a>
+</li>
+        <li><a href="api/pypath.utils.orthology.EnsemblOrtholog.html#pypath.utils.orthology.EnsemblOrtholog.index">(pypath.utils.orthology.EnsemblOrtholog method)</a>
+</li>
+        <li><a href="api/pypath.utils.orthology.HomologeneOrtholog.html#pypath.utils.orthology.HomologeneOrtholog.index">(pypath.utils.orthology.HomologeneOrtholog method)</a>
+</li>
+        <li><a href="api/pypath.utils.orthology.OmaOrtholog.html#pypath.utils.orthology.OmaOrtholog.index">(pypath.utils.orthology.OmaOrtholog method)</a>
+</li>
+        <li><a href="api/pypath.utils.orthology.OrthologyTableKey.html#pypath.utils.orthology.OrthologyTableKey.index">(pypath.utils.orthology.OrthologyTableKey method)</a>
+</li>
+        <li><a href="api/pypath.utils.pdb.Residue.html#pypath.utils.pdb.Residue.index">(pypath.utils.pdb.Residue method)</a>
+</li>
+        <li><a href="api/pypath.utils.pdb.Segment.html#pypath.utils.pdb.Segment.index">(pypath.utils.pdb.Segment method)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.info.html#pypath.info">info() (in module pypath)</a>
+
+      <ul>
+        <li><a href="api/pypath.inputs.unichem.info.html#pypath.inputs.unichem.info">(in module pypath.inputs.unichem)</a>
+</li>
+        <li><a href="api/pypath.utils.uniprot.info.html#pypath.utils.uniprot.info">(in module pypath.utils.uniprot)</a>
+</li>
+        <li><a href="api/pypath.utils.unichem.Unichem.html#pypath.utils.unichem.Unichem.info">(pypath.utils.unichem.Unichem static method)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.utils.uniprot.info_section.html#pypath.utils.uniprot.info_section">info_section() (in module pypath.utils.uniprot)</a>
+
+      <ul>
+        <li><a href="api/pypath.utils.uniprot.UniprotProtein.html#pypath.utils.uniprot.UniprotProtein.info_section">(pypath.utils.uniprot.UniprotProtein method)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.omnipath.init.html#pypath.omnipath.init">init() (in module pypath.omnipath)</a>
+
+      <ul>
+        <li><a href="api/pypath.utils.mapping.init.html#pypath.utils.mapping.init">(in module pypath.utils.mapping)</a>
+</li>
+        <li><a href="api/pypath.utils.orthology.init.html#pypath.utils.orthology.init">(in module pypath.utils.orthology)</a>
+</li>
+        <li><a href="api/pypath.utils.reflists.init.html#pypath.utils.reflists.init">(in module pypath.utils.reflists)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.annot.init_db.html#pypath.core.annot.init_db">init_db() (in module pypath.core.annot)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.complex.init_db.html#pypath.core.complex.init_db">(in module pypath.core.complex)</a>
+</li>
+        <li><a href="api/pypath.core.enz_sub.init_db.html#pypath.core.enz_sub.init_db">(in module pypath.core.enz_sub)</a>
+</li>
+        <li><a href="api/pypath.core.intercell.init_db.html#pypath.core.intercell.init_db">(in module pypath.core.intercell)</a>
+</li>
+        <li><a href="api/pypath.core.network.init_db.html#pypath.core.network.init_db">(in module pypath.core.network)</a>
+</li>
+        <li><a href="api/pypath.inputs.uniprot_db.init_db.html#pypath.inputs.uniprot_db.init_db">(in module pypath.inputs.uniprot_db)</a>
+</li>
+        <li><a href="api/pypath.utils.go.init_db.html#pypath.utils.go.init_db">(in module pypath.utils.go)</a>
+</li>
+        <li><a href="api/pypath.utils.taxonomy.init_db.html#pypath.utils.taxonomy.init_db">(in module pypath.utils.taxonomy)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.utils.pyreact.BioPaxReader.html#pypath.utils.pyreact.BioPaxReader.init_etree">init_etree() (pypath.utils.pyreact.BioPaxReader method)</a>
+</li>
+      <li><a href="api/pypath.omnipath.databases.init_manager.html#pypath.omnipath.databases.init_manager">init_manager() (in module pypath.omnipath.databases)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.init_network">init_network() (pypath.core.network.Network method)</a>
+</li>
+      <li><a href="api/pypath.share.progress.Progress.html#pypath.share.progress.Progress.init_tqdm">init_tqdm() (pypath.share.progress.Progress method)</a>
+</li>
+      <li><a href="api/pypath.inputs.innatedb.innatedb_interactions.html#pypath.inputs.innatedb.innatedb_interactions">innatedb_interactions() (in module pypath.inputs.innatedb)</a>
+</li>
+      <li><a href="api/pypath.internals.license.LicenseAttrib.html#pypath.internals.license.LicenseAttrib.int_to_level">int_to_level() (pypath.internals.license.LicenseAttrib class method)</a>
+
+      <ul>
+        <li><a href="api/pypath.internals.license.LicenseFeature.html#pypath.internals.license.LicenseFeature.int_to_level">(pypath.internals.license.LicenseFeature class method)</a>
+</li>
+        <li><a href="api/pypath.internals.license.LicensePurpose.html#pypath.internals.license.LicensePurpose.int_to_level">(pypath.internals.license.LicensePurpose class method)</a>
+</li>
+        <li><a href="api/pypath.internals.license.LicenseSharing.html#pypath.internals.license.LicenseSharing.int_to_level">(pypath.internals.license.LicenseSharing class method)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.inputs.intact.intact_interactions.html#pypath.inputs.intact.intact_interactions">intact_interactions() (in module pypath.inputs.intact)</a>
+</li>
+      <li><a href="api/pypath.inputs.cellphonedb.CellPhoneDBAnnotation.html#pypath.inputs.cellphonedb.CellPhoneDBAnnotation.integrin">integrin (pypath.inputs.cellphonedb.CellPhoneDBAnnotation attribute)</a>
+</li>
+      <li><a href="api/pypath.core.annot.Integrins.html#pypath.core.annot.Integrins">Integrins (class in pypath.core.annot)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction">Interaction (class in pypath.core.interaction)</a>
+</li>
+      <li><a href="api/pypath.resources.data_formats.interaction.html#pypath.resources.data_formats.interaction">interaction (in module pypath.resources.data_formats)</a>
+</li>
+      <li><a href="api/pypath.utils.uniprot.interaction.html#pypath.utils.uniprot.interaction">interaction() (in module pypath.utils.uniprot)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.interaction">(pypath.core.network.Network method)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.interaction_by_id">interaction_by_id() (pypath.core.network.Network method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.interaction_by_label">interaction_by_label() (pypath.core.network.Network method)</a>
+</li>
+      <li><a href="api/pypath.resources.data_formats.interaction_htp.html#pypath.resources.data_formats.interaction_htp">interaction_htp (in module pypath.resources.data_formats)</a>
+</li>
+      <li><a href="api/pypath.inputs.pathwaycommons.PathwayCommonsInteraction.html#pypath.inputs.pathwaycommons.PathwayCommonsInteraction.interaction_type">interaction_type (pypath.inputs.pathwaycommons.PathwayCommonsInteraction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.internals.resource.NetworkResourceKey.html#pypath.internals.resource.NetworkResourceKey.interaction_type">(pypath.internals.resource.NetworkResourceKey attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.interaction_types_by_data_model">interaction_types_by_data_model (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.interaction_types_by_data_model">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.interaction_types_by_interaction_type">interaction_types_by_interaction_type (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.interaction_types_by_interaction_type">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.interaction_types_by_interaction_type_and_data_model">interaction_types_by_interaction_type_and_data_model (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.interaction_types_by_interaction_type_and_data_model">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.interaction_types_by_interaction_type_and_data_model_and_resource">interaction_types_by_interaction_type_and_data_model_and_resource (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.interaction_types_by_interaction_type_and_data_model_and_resource">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.interaction_types_by_reference">interaction_types_by_reference (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.interaction_types_by_reference">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.interaction_types_by_resource">interaction_types_by_resource (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.interaction_types_by_resource">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.utils.uniprot.interaction_with_xrefs.html#pypath.utils.uniprot.interaction_with_xrefs">interaction_with_xrefs() (in module pypath.utils.uniprot)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.InteractionDataFrameRecord.html#pypath.core.interaction.InteractionDataFrameRecord">InteractionDataFrameRecord (class in pypath.core.interaction)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.InteractionKey.html#pypath.core.interaction.InteractionKey">InteractionKey (class in pypath.core.interaction)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.interactions_0_by_data_model">interactions_0_by_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.interactions_0_by_data_model">interactions_0_by_data_model() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.interactions_0_by_interaction_type">interactions_0_by_interaction_type (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.interactions_0_by_interaction_type">interactions_0_by_interaction_type() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.interactions_0_by_interaction_type_and_data_model">interactions_0_by_interaction_type_and_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.interactions_0_by_interaction_type_and_data_model">interactions_0_by_interaction_type_and_data_model() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.interactions_0_by_interaction_type_and_data_model_and_resource">interactions_0_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.interactions_0_by_interaction_type_and_data_model_and_resource">interactions_0_by_interaction_type_and_data_model_and_resource() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.interactions_0_by_reference">interactions_0_by_reference (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.interactions_0_by_reference">interactions_0_by_reference() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.interactions_0_by_resource">interactions_0_by_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.interactions_0_by_resource">interactions_0_by_resource() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.interactions_by_data_model">interactions_by_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.interactions_by_data_model">interactions_by_data_model() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.interactions_by_interaction_type">interactions_by_interaction_type (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.interactions_by_interaction_type">interactions_by_interaction_type() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.interactions_by_interaction_type_and_data_model">interactions_by_interaction_type_and_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.interactions_by_interaction_type_and_data_model">interactions_by_interaction_type_and_data_model() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.interactions_by_interaction_type_and_data_model_and_resource">interactions_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.interactions_by_interaction_type_and_data_model_and_resource">interactions_by_interaction_type_and_data_model_and_resource() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.interactions_by_reference">interactions_by_reference (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.interactions_by_reference">interactions_by_reference() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.interactions_by_resource">interactions_by_resource (pypath.core.network.Network attribute)</a>
+</li>
+  </ul></td>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.interactions_by_resource">interactions_by_resource() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.interactions_directed_by_data_model">interactions_directed_by_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.interactions_directed_by_data_model">interactions_directed_by_data_model() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.interactions_directed_by_interaction_type">interactions_directed_by_interaction_type (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.interactions_directed_by_interaction_type">interactions_directed_by_interaction_type() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.interactions_directed_by_interaction_type_and_data_model">interactions_directed_by_interaction_type_and_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.interactions_directed_by_interaction_type_and_data_model">interactions_directed_by_interaction_type_and_data_model() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.interactions_directed_by_interaction_type_and_data_model_and_resource">interactions_directed_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.interactions_directed_by_interaction_type_and_data_model_and_resource">interactions_directed_by_interaction_type_and_data_model_and_resource() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.interactions_directed_by_reference">interactions_directed_by_reference (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.interactions_directed_by_reference">interactions_directed_by_reference() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.interactions_directed_by_resource">interactions_directed_by_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.interactions_directed_by_resource">interactions_directed_by_resource() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.interactions_mutual_by_data_model">interactions_mutual_by_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.interactions_mutual_by_data_model">interactions_mutual_by_data_model() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.interactions_mutual_by_interaction_type">interactions_mutual_by_interaction_type (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.interactions_mutual_by_interaction_type">interactions_mutual_by_interaction_type() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.interactions_mutual_by_interaction_type_and_data_model">interactions_mutual_by_interaction_type_and_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.interactions_mutual_by_interaction_type_and_data_model">interactions_mutual_by_interaction_type_and_data_model() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.interactions_mutual_by_interaction_type_and_data_model_and_resource">interactions_mutual_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.interactions_mutual_by_interaction_type_and_data_model_and_resource">interactions_mutual_by_interaction_type_and_data_model_and_resource() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.interactions_mutual_by_reference">interactions_mutual_by_reference (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.interactions_mutual_by_reference">interactions_mutual_by_reference() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.interactions_mutual_by_resource">interactions_mutual_by_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.interactions_mutual_by_resource">interactions_mutual_by_resource() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.interactions_negative_by_data_model">interactions_negative_by_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.interactions_negative_by_data_model">interactions_negative_by_data_model() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.interactions_negative_by_interaction_type">interactions_negative_by_interaction_type (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.interactions_negative_by_interaction_type">interactions_negative_by_interaction_type() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.interactions_negative_by_interaction_type_and_data_model">interactions_negative_by_interaction_type_and_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.interactions_negative_by_interaction_type_and_data_model">interactions_negative_by_interaction_type_and_data_model() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.interactions_negative_by_interaction_type_and_data_model_and_resource">interactions_negative_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.interactions_negative_by_interaction_type_and_data_model_and_resource">interactions_negative_by_interaction_type_and_data_model_and_resource() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.interactions_negative_by_reference">interactions_negative_by_reference (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.interactions_negative_by_reference">interactions_negative_by_reference() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.interactions_negative_by_resource">interactions_negative_by_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.interactions_negative_by_resource">interactions_negative_by_resource() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.interactions_non_directed_0_by_data_model">interactions_non_directed_0_by_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.interactions_non_directed_0_by_data_model">interactions_non_directed_0_by_data_model() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.interactions_non_directed_0_by_interaction_type">interactions_non_directed_0_by_interaction_type (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.interactions_non_directed_0_by_interaction_type">interactions_non_directed_0_by_interaction_type() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.interactions_non_directed_0_by_interaction_type_and_data_model">interactions_non_directed_0_by_interaction_type_and_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.interactions_non_directed_0_by_interaction_type_and_data_model">interactions_non_directed_0_by_interaction_type_and_data_model() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.interactions_non_directed_0_by_interaction_type_and_data_model_and_resource">interactions_non_directed_0_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.interactions_non_directed_0_by_interaction_type_and_data_model_and_resource">interactions_non_directed_0_by_interaction_type_and_data_model_and_resource() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.interactions_non_directed_0_by_reference">interactions_non_directed_0_by_reference (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.interactions_non_directed_0_by_reference">interactions_non_directed_0_by_reference() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.interactions_non_directed_0_by_resource">interactions_non_directed_0_by_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.interactions_non_directed_0_by_resource">interactions_non_directed_0_by_resource() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.interactions_non_directed_by_data_model">interactions_non_directed_by_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.interactions_non_directed_by_data_model">interactions_non_directed_by_data_model() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.interactions_non_directed_by_interaction_type">interactions_non_directed_by_interaction_type (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.interactions_non_directed_by_interaction_type">interactions_non_directed_by_interaction_type() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.interactions_non_directed_by_interaction_type_and_data_model">interactions_non_directed_by_interaction_type_and_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.interactions_non_directed_by_interaction_type_and_data_model">interactions_non_directed_by_interaction_type_and_data_model() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.interactions_non_directed_by_interaction_type_and_data_model_and_resource">interactions_non_directed_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.interactions_non_directed_by_interaction_type_and_data_model_and_resource">interactions_non_directed_by_interaction_type_and_data_model_and_resource() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.interactions_non_directed_by_reference">interactions_non_directed_by_reference (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.interactions_non_directed_by_reference">interactions_non_directed_by_reference() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.interactions_non_directed_by_resource">interactions_non_directed_by_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.interactions_non_directed_by_resource">interactions_non_directed_by_resource() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.interactions_positive_by_data_model">interactions_positive_by_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.interactions_positive_by_data_model">interactions_positive_by_data_model() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.interactions_positive_by_interaction_type">interactions_positive_by_interaction_type (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.interactions_positive_by_interaction_type">interactions_positive_by_interaction_type() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.interactions_positive_by_interaction_type_and_data_model">interactions_positive_by_interaction_type_and_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.interactions_positive_by_interaction_type_and_data_model">interactions_positive_by_interaction_type_and_data_model() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.interactions_positive_by_interaction_type_and_data_model_and_resource">interactions_positive_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.interactions_positive_by_interaction_type_and_data_model_and_resource">interactions_positive_by_interaction_type_and_data_model_and_resource() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.interactions_positive_by_reference">interactions_positive_by_reference (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.interactions_positive_by_reference">interactions_positive_by_reference() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.interactions_positive_by_resource">interactions_positive_by_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.interactions_positive_by_resource">interactions_positive_by_resource() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.interactions_signed_by_data_model">interactions_signed_by_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.interactions_signed_by_data_model">interactions_signed_by_data_model() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.interactions_signed_by_interaction_type">interactions_signed_by_interaction_type (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.interactions_signed_by_interaction_type">interactions_signed_by_interaction_type() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.interactions_signed_by_interaction_type_and_data_model">interactions_signed_by_interaction_type_and_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.interactions_signed_by_interaction_type_and_data_model">interactions_signed_by_interaction_type_and_data_model() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.interactions_signed_by_interaction_type_and_data_model_and_resource">interactions_signed_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.interactions_signed_by_interaction_type_and_data_model_and_resource">interactions_signed_by_interaction_type_and_data_model_and_resource() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.interactions_signed_by_reference">interactions_signed_by_reference (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.interactions_signed_by_reference">interactions_signed_by_reference() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.interactions_signed_by_resource">interactions_signed_by_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.interactions_signed_by_resource">interactions_signed_by_resource() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.interactions_undirected_0_by_data_model">interactions_undirected_0_by_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.interactions_undirected_0_by_data_model">interactions_undirected_0_by_data_model() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.interactions_undirected_0_by_interaction_type">interactions_undirected_0_by_interaction_type (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.interactions_undirected_0_by_interaction_type">interactions_undirected_0_by_interaction_type() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.interactions_undirected_0_by_interaction_type_and_data_model">interactions_undirected_0_by_interaction_type_and_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.interactions_undirected_0_by_interaction_type_and_data_model">interactions_undirected_0_by_interaction_type_and_data_model() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.interactions_undirected_0_by_interaction_type_and_data_model_and_resource">interactions_undirected_0_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.interactions_undirected_0_by_interaction_type_and_data_model_and_resource">interactions_undirected_0_by_interaction_type_and_data_model_and_resource() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.interactions_undirected_0_by_reference">interactions_undirected_0_by_reference (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.interactions_undirected_0_by_reference">interactions_undirected_0_by_reference() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.interactions_undirected_0_by_resource">interactions_undirected_0_by_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.interactions_undirected_0_by_resource">interactions_undirected_0_by_resource() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.interactions_undirected_by_data_model">interactions_undirected_by_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.interactions_undirected_by_data_model">interactions_undirected_by_data_model() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.interactions_undirected_by_interaction_type">interactions_undirected_by_interaction_type (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.interactions_undirected_by_interaction_type">interactions_undirected_by_interaction_type() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.interactions_undirected_by_interaction_type_and_data_model">interactions_undirected_by_interaction_type_and_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.interactions_undirected_by_interaction_type_and_data_model">interactions_undirected_by_interaction_type_and_data_model() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.interactions_undirected_by_interaction_type_and_data_model_and_resource">interactions_undirected_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.interactions_undirected_by_interaction_type_and_data_model_and_resource">interactions_undirected_by_interaction_type_and_data_model_and_resource() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.interactions_undirected_by_reference">interactions_undirected_by_reference (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.interactions_undirected_by_reference">interactions_undirected_by_reference() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.interactions_undirected_by_resource">interactions_undirected_by_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.interactions_undirected_by_resource">interactions_undirected_by_resource() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.intercell.IntercellAnnotation.html#pypath.core.intercell.IntercellAnnotation">IntercellAnnotation (class in pypath.core.intercell)</a>
+</li>
+      <li><a href="api/pypath.internals.intera.Interface.html#pypath.internals.intera.Interface">Interface (class in pypath.internals.intera)</a>
+</li>
+      <li><a href="api/pypath.core.annot.InterPro.html#pypath.core.annot.InterPro">InterPro (class in pypath.core.annot)</a>
+</li>
+      <li><a href="api/pypath.inputs.interpro.interpro2go_annotations.html#pypath.inputs.interpro.interpro2go_annotations">interpro2go_annotations() (in module pypath.inputs.interpro)</a>
+</li>
+      <li><a href="api/pypath.inputs.interpro.interpro_annotations.html#pypath.inputs.interpro.interpro_annotations">interpro_annotations() (in module pypath.inputs.interpro)</a>
+</li>
+      <li><a href="api/pypath.inputs.interpro.interpro_entries.html#pypath.inputs.interpro.interpro_entries">interpro_entries() (in module pypath.inputs.interpro)</a>
+</li>
+      <li><a href="api/pypath.inputs.interpro.interpro_xrefs.html#pypath.inputs.interpro.interpro_xrefs">interpro_xrefs() (in module pypath.inputs.interpro)</a>
+</li>
+      <li><a href="api/pypath.utils.pyreact.Intersecting.html#pypath.utils.pyreact.Intersecting">Intersecting (class in pypath.utils.pyreact)</a>
+</li>
+      <li><a href="api/pypath.visual.drawing.InterSet.html#pypath.visual.drawing.InterSet">InterSet (class in pypath.visual.drawing)</a>
+</li>
+      <li><a href="api/pypath.core.annot.Intogen.html#pypath.core.annot.Intogen">Intogen (class in pypath.core.annot)</a>
+</li>
+      <li><a href="api/pypath.inputs.intogen.intogen_annotations.html#pypath.inputs.intogen.intogen_annotations">intogen_annotations() (in module pypath.inputs.intogen)</a>
+</li>
+      <li><a href="api/pypath.inputs.ipi.ipi_uniprot.html#pypath.inputs.ipi.ipi_uniprot">ipi_uniprot() (in module pypath.inputs.ipi)</a>
+</li>
+      <li><a href="api/pypath.inputs.iptmnet.iptmnet_interactions.html#pypath.inputs.iptmnet.iptmnet_interactions">iptmnet_interactions() (in module pypath.inputs.iptmnet)</a>
+</li>
+      <li><a href="api/pypath.inputs.iptmnet.IptmnetInteraction.html#pypath.inputs.iptmnet.IptmnetInteraction">IptmnetInteraction (class in pypath.inputs.iptmnet)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.is_directed">is_directed() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.is_directed_by_resources">is_directed_by_resources() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.is_inhibition">is_inhibition() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.utils.go.GeneOntology.html#pypath.utils.go.GeneOntology.is_leaf">is_leaf() (pypath.utils.go.GeneOntology method)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.is_loop">is_loop() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.is_mutual">is_mutual() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.is_mutual_by_resources">is_mutual_by_resources() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.utils.go.GeneOntology.html#pypath.utils.go.GeneOntology.is_name">is_name() (pypath.utils.go.GeneOntology method)</a>
+</li>
+      <li><a href="api/pypath.utils.reflists.is_not.html#pypath.utils.reflists.is_not">is_not() (in module pypath.utils.reflists)</a>
+
+      <ul>
+        <li><a href="api/pypath.utils.reflists.ReferenceListManager.html#pypath.utils.reflists.ReferenceListManager.is_not">(pypath.utils.reflists.ReferenceListManager method)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.share.curl.Curl.html#pypath.share.curl.Curl.is_quoted">is_quoted() (pypath.share.curl.Curl method)</a>
+</li>
+      <li><a href="api/pypath.utils.uniprot.is_reviewed.html#pypath.utils.uniprot.is_reviewed">is_reviewed() (in module pypath.utils.uniprot)</a>
+</li>
+      <li><a href="api/pypath.utils.go.GeneOntology.html#pypath.utils.go.GeneOntology.is_root">is_root() (pypath.utils.go.GeneOntology method)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.is_stimulation">is_stimulation() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.inputs.uniprot_db.is_swissprot.html#pypath.inputs.uniprot_db.is_swissprot">is_swissprot() (in module pypath.inputs.uniprot_db)</a>
+</li>
+      <li><a href="api/pypath.utils.go.GeneOntology.html#pypath.utils.go.GeneOntology.is_term">is_term() (pypath.utils.go.GeneOntology method)</a>
+</li>
+      <li><a href="api/pypath.inputs.uniprot_db.is_trembl.html#pypath.inputs.uniprot_db.is_trembl">is_trembl() (in module pypath.inputs.uniprot_db)</a>
+</li>
+      <li><a href="api/pypath.inputs.uniprot_db.is_uniprot.html#pypath.inputs.uniprot_db.is_uniprot">is_uniprot() (in module pypath.inputs.uniprot_db)</a>
+</li>
+      <li><a href="api/pypath.share.curl.is_url.html#pypath.share.curl.is_url">is_url() (in module pypath.share.curl)</a>
+</li>
+      <li><a href="api/pypath.internals.annot_formats.AnnotationGroup.html#pypath.internals.annot_formats.AnnotationGroup.isdisjoint">isdisjoint() (pypath.internals.annot_formats.AnnotationGroup class method)</a>
+</li>
+      <li><a href="api/pypath.core.annot.Italk.html#pypath.core.annot.Italk">Italk (class in pypath.core.annot)</a>
+</li>
+      <li><a href="api/pypath.inputs.italk.italk_annotations.html#pypath.inputs.italk.italk_annotations">italk_annotations() (in module pypath.inputs.italk)</a>
+</li>
+      <li><a href="api/pypath.inputs.italk.italk_interactions.html#pypath.inputs.italk.italk_interactions">italk_interactions() (in module pypath.inputs.italk)</a>
+</li>
+      <li><a href="api/pypath.inputs.italk.italk_raw.html#pypath.inputs.italk.italk_raw">italk_raw() (in module pypath.inputs.italk)</a>
+</li>
+      <li><a href="api/pypath.core.evidence.Evidences.html#pypath.core.evidence.Evidences.items">items() (pypath.core.evidence.Evidences method)</a>
+
+      <ul>
+        <li><a href="api/pypath.internals.resource.NetworkDataset.html#pypath.internals.resource.NetworkDataset.items">(pypath.internals.resource.NetworkDataset method)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.inputs.hmdb.common.iter.html#pypath.inputs.hmdb.common.iter">iter() (in module pypath.inputs.hmdb.common)</a>
+
+      <ul>
+        <li><a href="api/pypath.inputs.hmdb.metabolites.iter.html#pypath.inputs.hmdb.metabolites.iter">(in module pypath.inputs.hmdb.metabolites)</a>
+</li>
+        <li><a href="api/pypath.inputs.hmdb.proteins.iter.html#pypath.inputs.hmdb.proteins.iter">(in module pypath.inputs.hmdb.proteins)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.iter_evidences">iter_evidences() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.iter_match_evidences">iter_match_evidences() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.utils.pyreact.BioPaxReader.html#pypath.utils.pyreact.BioPaxReader.iterate">iterate() (pypath.utils.pyreact.BioPaxReader method)</a>
+</li>
+      <li><a href="api/pypath.utils.seq.Pfam.html#pypath.utils.seq.Pfam.iterdb">iterdb() (pypath.utils.seq.Pfam method)</a>
+
+      <ul>
+        <li><a href="api/pypath.utils.seq.Resource.html#pypath.utils.seq.Resource.iterdb">(pypath.utils.seq.Resource method)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.utils.pyreact.ComplexVariations.html#pypath.utils.pyreact.ComplexVariations.itermembers">itermembers() (pypath.utils.pyreact.ComplexVariations method)</a>
+</li>
+      <li><a href="api/pypath.utils.seq.Pfam.html#pypath.utils.seq.Pfam.iterprotein">iterprotein() (pypath.utils.seq.Pfam method)</a>
+
+      <ul>
+        <li><a href="api/pypath.utils.seq.Resource.html#pypath.utils.seq.Resource.iterprotein">(pypath.utils.seq.Resource method)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.utils.uniprot.itertag.html#pypath.utils.uniprot.itertag">itertag() (in module pypath.utils.uniprot)</a>
+</li>
+  </ul></td>
+</tr></table>
+
+<h2 id="J">J</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="api/pypath.inputs.common.json_extract.html#pypath.inputs.common.json_extract">json_extract() (in module pypath.inputs.common)</a>
+</li>
+  </ul></td>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="api/pypath.inputs.common.json_read.html#pypath.inputs.common.json_read">json_read() (in module pypath.inputs.common)</a>
+</li>
+  </ul></td>
+</tr></table>
+
+<h2 id="K">K</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="api/pypath.inputs.kea.kea_enzyme_substrate.html#pypath.inputs.kea.kea_enzyme_substrate">kea_enzyme_substrate() (in module pypath.inputs.kea)</a>
+</li>
+      <li><a href="api/pypath.inputs.kea.kea_interactions.html#pypath.inputs.kea.kea_interactions">kea_interactions() (in module pypath.inputs.kea)</a>
+</li>
+      <li><a href="api/pypath.core.complex.Kegg.html#pypath.core.complex.Kegg">Kegg (class in pypath.core.complex)</a>
+</li>
+      <li><a href="api/pypath.inputs.adrecs.AdrecsDrug.html#pypath.inputs.adrecs.AdrecsDrug.kegg">kegg (pypath.inputs.adrecs.AdrecsDrug attribute)</a>
+</li>
+      <li><a href="api/pypath.inputs.kegg.kegg_dbget.html#pypath.inputs.kegg.kegg_dbget">kegg_dbget() (in module pypath.inputs.kegg)</a>
+</li>
+      <li><a href="api/pypath.inputs.kegg_api.kegg_drug_to_chebi.html#pypath.inputs.kegg_api.kegg_drug_to_chebi">kegg_drug_to_chebi() (in module pypath.inputs.kegg_api)</a>
+</li>
+      <li><a href="api/pypath.inputs.kegg_api.kegg_gene_to_ncbi_geneid.html#pypath.inputs.kegg_api.kegg_gene_to_ncbi_geneid">kegg_gene_to_ncbi_geneid() (in module pypath.inputs.kegg_api)</a>
+</li>
+      <li><a href="api/pypath.inputs.kegg_api.kegg_gene_to_uniprot.html#pypath.inputs.kegg_api.kegg_gene_to_uniprot">kegg_gene_to_uniprot() (in module pypath.inputs.kegg_api)</a>
+</li>
+      <li><a href="api/pypath.inputs.kegg.kegg_interactions.html#pypath.inputs.kegg.kegg_interactions">kegg_interactions() (in module pypath.inputs.kegg)</a>
+</li>
+      <li><a href="api/pypath.inputs.kegg.kegg_medicus.html#pypath.inputs.kegg.kegg_medicus">kegg_medicus() (in module pypath.inputs.kegg)</a>
+</li>
+      <li><a href="api/pypath.inputs.kegg.kegg_medicus_complexes.html#pypath.inputs.kegg.kegg_medicus_complexes">kegg_medicus_complexes() (in module pypath.inputs.kegg)</a>
+</li>
+      <li><a href="api/pypath.inputs.kegg.kegg_medicus_interactions.html#pypath.inputs.kegg.kegg_medicus_interactions">kegg_medicus_interactions() (in module pypath.inputs.kegg)</a>
+</li>
+      <li><a href="api/pypath.inputs.kegg.kegg_pathway_annotations.html#pypath.inputs.kegg.kegg_pathway_annotations">kegg_pathway_annotations() (in module pypath.inputs.kegg)</a>
+</li>
+      <li><a href="api/pypath.inputs.kegg.kegg_pathway_annotations_pathwaycommons.html#pypath.inputs.kegg.kegg_pathway_annotations_pathwaycommons">kegg_pathway_annotations_pathwaycommons() (in module pypath.inputs.kegg)</a>
+</li>
+      <li><a href="api/pypath.inputs.dorothea.DorotheaInteraction.html#pypath.inputs.dorothea.DorotheaInteraction.kegg_pathways">kegg_pathways (pypath.inputs.dorothea.DorotheaInteraction attribute)</a>
+</li>
+      <li><a href="api/pypath.inputs.kegg.kegg_pathways.html#pypath.inputs.kegg.kegg_pathways">kegg_pathways() (in module pypath.inputs.kegg)</a>
+</li>
+  </ul></td>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="api/pypath.inputs.kegg.KeggPathway.html#pypath.inputs.kegg.KeggPathway">KeggPathway (class in pypath.inputs.kegg)</a>
+</li>
+      <li><a href="api/pypath.core.annot.KeggPathways.html#pypath.core.annot.KeggPathways">KeggPathways (class in pypath.core.annot)</a>
+</li>
+      <li><a href="api/pypath.core.annot.KeggPathwaysPC.html#pypath.core.annot.KeggPathwaysPC">KeggPathwaysPC (class in pypath.core.annot)</a>
+</li>
+      <li><a href="api/pypath.internals.intera.DomainMotif.html#pypath.internals.intera.DomainMotif.key">key() (pypath.internals.intera.DomainMotif method)</a>
+</li>
+      <li><a href="api/pypath.core.evidence.Evidences.html#pypath.core.evidence.Evidences.keys">keys() (pypath.core.evidence.Evidences method)</a>
+
+      <ul>
+        <li><a href="api/pypath.internals.resource.NetworkDataset.html#pypath.internals.resource.NetworkDataset.keys">(pypath.internals.resource.NetworkDataset method)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.utils.uniprot.UniprotProtein.html#pypath.utils.uniprot.UniprotProtein.keywords">keywords (pypath.utils.uniprot.UniprotProtein property)</a>
+</li>
+      <li><a href="api/pypath.utils.uniprot.keywords.html#pypath.utils.uniprot.keywords">keywords() (in module pypath.utils.uniprot)</a>
+</li>
+      <li><a href="api/pypath.utils.uniprot.UniprotProtein.html#pypath.utils.uniprot.UniprotProtein.keywords_with_xrefs">keywords_with_xrefs (pypath.utils.uniprot.UniprotProtein property)</a>
+</li>
+      <li><a href="api/pypath.utils.uniprot.keywords_with_xrefs.html#pypath.utils.uniprot.keywords_with_xrefs">keywords_with_xrefs() (in module pypath.utils.uniprot)</a>
+</li>
+      <li><a href="api/pypath.core.annot.Kinasedotcom.html#pypath.core.annot.Kinasedotcom">Kinasedotcom (class in pypath.core.annot)</a>
+</li>
+      <li><a href="api/pypath.inputs.kinasedotcom.kinasedotcom_annotations.html#pypath.inputs.kinasedotcom.kinasedotcom_annotations">kinasedotcom_annotations() (in module pypath.inputs.kinasedotcom)</a>
+</li>
+      <li><a href="api/pypath.core.annot.Kirouac2010.html#pypath.core.annot.Kirouac2010">Kirouac2010 (class in pypath.core.annot)</a>
+</li>
+      <li><a href="api/pypath.inputs.kirouac2010.kirouac2010_interactions.html#pypath.inputs.kirouac2010.kirouac2010_interactions">kirouac2010_interactions() (in module pypath.inputs.kirouac2010)</a>
+</li>
+      <li><a href="api/pypath.inputs.diseases.knowledge_filtered.html#pypath.inputs.diseases.knowledge_filtered">knowledge_filtered() (in module pypath.inputs.diseases)</a>
+</li>
+      <li><a href="api/pypath.inputs.diseases.knowledge_full.html#pypath.inputs.diseases.knowledge_full">knowledge_full() (in module pypath.inputs.diseases)</a>
+</li>
+  </ul></td>
+</tr></table>
+
+<h2 id="L">L</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="api/pypath.core.network.NetworkStatsRecord.html#pypath.core.network.NetworkStatsRecord.label">label (pypath.core.network.NetworkStatsRecord attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.inputs.biogps.BiogpsDataset.html#pypath.inputs.biogps.BiogpsDataset.label">(pypath.inputs.biogps.BiogpsDataset attribute)</a>
+</li>
+        <li><a href="api/pypath.internals.resource.NetworkResourceKey.html#pypath.internals.resource.NetworkResourceKey.label">(pypath.internals.resource.NetworkResourceKey property)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.utils.mapping.label.html#pypath.utils.mapping.label">label() (in module pypath.utils.mapping)</a>
+
+      <ul>
+        <li><a href="api/pypath.utils.mapping.Mapper.html#pypath.utils.mapping.Mapper.label">(pypath.utils.mapping.Mapper method)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.annot.Adhesome.html#pypath.core.annot.Adhesome.labels">labels() (pypath.core.annot.Adhesome method)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.annot.Almen2009.html#pypath.core.annot.Almen2009.labels">(pypath.core.annot.Almen2009 method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.AnnotationBase.html#pypath.core.annot.AnnotationBase.labels">(pypath.core.annot.AnnotationBase method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Baccin2019.html#pypath.core.annot.Baccin2019.labels">(pypath.core.annot.Baccin2019 method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Biogps.html#pypath.core.annot.Biogps.labels">(pypath.core.annot.Biogps method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cancerdrugsdb.html#pypath.core.annot.Cancerdrugsdb.labels">(pypath.core.annot.Cancerdrugsdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CancerGeneCensus.html#pypath.core.annot.CancerGeneCensus.labels">(pypath.core.annot.CancerGeneCensus method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cancersea.html#pypath.core.annot.Cancersea.labels">(pypath.core.annot.Cancersea method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cellcall.html#pypath.core.annot.Cellcall.labels">(pypath.core.annot.Cellcall method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cellcellinteractions.html#pypath.core.annot.Cellcellinteractions.labels">(pypath.core.annot.Cellcellinteractions method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cellchatdb.html#pypath.core.annot.Cellchatdb.labels">(pypath.core.annot.Cellchatdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CellchatdbComplex.html#pypath.core.annot.CellchatdbComplex.labels">(pypath.core.annot.CellchatdbComplex method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cellinker.html#pypath.core.annot.Cellinker.labels">(pypath.core.annot.Cellinker method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CellinkerComplex.html#pypath.core.annot.CellinkerComplex.labels">(pypath.core.annot.CellinkerComplex method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CellPhoneDB.html#pypath.core.annot.CellPhoneDB.labels">(pypath.core.annot.CellPhoneDB method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CellPhoneDBComplex.html#pypath.core.annot.CellPhoneDBComplex.labels">(pypath.core.annot.CellPhoneDBComplex method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CellSurfaceProteinAtlas.html#pypath.core.annot.CellSurfaceProteinAtlas.labels">(pypath.core.annot.CellSurfaceProteinAtlas method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CellSurfaceProteinAtlasCellType.html#pypath.core.annot.CellSurfaceProteinAtlasCellType.labels">(pypath.core.annot.CellSurfaceProteinAtlasCellType method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Celltalkdb.html#pypath.core.annot.Celltalkdb.labels">(pypath.core.annot.Celltalkdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Celltypist.html#pypath.core.annot.Celltypist.labels">(pypath.core.annot.Celltypist method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Comppi.html#pypath.core.annot.Comppi.labels">(pypath.core.annot.Comppi method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Connectomedb.html#pypath.core.annot.Connectomedb.labels">(pypath.core.annot.Connectomedb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Corum.html#pypath.core.annot.Corum.labels">(pypath.core.annot.Corum method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CorumFuncat.html#pypath.core.annot.CorumFuncat.labels">(pypath.core.annot.CorumFuncat method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CorumGO.html#pypath.core.annot.CorumGO.labels">(pypath.core.annot.CorumGO method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cpad.html#pypath.core.annot.Cpad.labels">(pypath.core.annot.Cpad method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CustomAnnotation.html#pypath.core.annot.CustomAnnotation.labels">(pypath.core.annot.CustomAnnotation method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cytosig.html#pypath.core.annot.Cytosig.labels">(pypath.core.annot.Cytosig method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Dgidb.html#pypath.core.annot.Dgidb.labels">(pypath.core.annot.Dgidb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Disgenet.html#pypath.core.annot.Disgenet.labels">(pypath.core.annot.Disgenet method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Embrace.html#pypath.core.annot.Embrace.labels">(pypath.core.annot.Embrace method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Exocarta.html#pypath.core.annot.Exocarta.labels">(pypath.core.annot.Exocarta method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.GOIntercell.html#pypath.core.annot.GOIntercell.labels">(pypath.core.annot.GOIntercell method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Gpcrdb.html#pypath.core.annot.Gpcrdb.labels">(pypath.core.annot.Gpcrdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.GuideToPharmacology.html#pypath.core.annot.GuideToPharmacology.labels">(pypath.core.annot.GuideToPharmacology method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Hgnc.html#pypath.core.annot.Hgnc.labels">(pypath.core.annot.Hgnc method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.HpmrComplex.html#pypath.core.annot.HpmrComplex.labels">(pypath.core.annot.HpmrComplex method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.HPO.html#pypath.core.annot.HPO.labels">(pypath.core.annot.HPO method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Humancellmap.html#pypath.core.annot.Humancellmap.labels">(pypath.core.annot.Humancellmap method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.HumanPlasmaMembraneReceptome.html#pypath.core.annot.HumanPlasmaMembraneReceptome.labels">(pypath.core.annot.HumanPlasmaMembraneReceptome method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.HumanProteinAtlas.html#pypath.core.annot.HumanProteinAtlas.labels">(pypath.core.annot.HumanProteinAtlas method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.HumanProteinAtlasSecretome.html#pypath.core.annot.HumanProteinAtlasSecretome.labels">(pypath.core.annot.HumanProteinAtlasSecretome method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.HumanProteinAtlasSubcellular.html#pypath.core.annot.HumanProteinAtlasSubcellular.labels">(pypath.core.annot.HumanProteinAtlasSubcellular method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Icellnet.html#pypath.core.annot.Icellnet.labels">(pypath.core.annot.Icellnet method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.IcellnetComplex.html#pypath.core.annot.IcellnetComplex.labels">(pypath.core.annot.IcellnetComplex method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Integrins.html#pypath.core.annot.Integrins.labels">(pypath.core.annot.Integrins method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.InterPro.html#pypath.core.annot.InterPro.labels">(pypath.core.annot.InterPro method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Intogen.html#pypath.core.annot.Intogen.labels">(pypath.core.annot.Intogen method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Italk.html#pypath.core.annot.Italk.labels">(pypath.core.annot.Italk method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.KeggPathways.html#pypath.core.annot.KeggPathways.labels">(pypath.core.annot.KeggPathways method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.KeggPathwaysPC.html#pypath.core.annot.KeggPathwaysPC.labels">(pypath.core.annot.KeggPathwaysPC method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Kinasedotcom.html#pypath.core.annot.Kinasedotcom.labels">(pypath.core.annot.Kinasedotcom method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Kirouac2010.html#pypath.core.annot.Kirouac2010.labels">(pypath.core.annot.Kirouac2010 method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Lambert2018.html#pypath.core.annot.Lambert2018.labels">(pypath.core.annot.Lambert2018 method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.LigandReceptor.html#pypath.core.annot.LigandReceptor.labels">(pypath.core.annot.LigandReceptor method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Locate.html#pypath.core.annot.Locate.labels">(pypath.core.annot.Locate method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Lrdb.html#pypath.core.annot.Lrdb.labels">(pypath.core.annot.Lrdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Matrisome.html#pypath.core.annot.Matrisome.labels">(pypath.core.annot.Matrisome method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Matrixdb.html#pypath.core.annot.Matrixdb.labels">(pypath.core.annot.Matrixdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Mcam.html#pypath.core.annot.Mcam.labels">(pypath.core.annot.Mcam method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Membranome.html#pypath.core.annot.Membranome.labels">(pypath.core.annot.Membranome method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Msigdb.html#pypath.core.annot.Msigdb.labels">(pypath.core.annot.Msigdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.NetpathPathways.html#pypath.core.annot.NetpathPathways.labels">(pypath.core.annot.NetpathPathways method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Opm.html#pypath.core.annot.Opm.labels">(pypath.core.annot.Opm method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Panglaodb.html#pypath.core.annot.Panglaodb.labels">(pypath.core.annot.Panglaodb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Phobius.html#pypath.core.annot.Phobius.labels">(pypath.core.annot.Phobius method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Phosphatome.html#pypath.core.annot.Phosphatome.labels">(pypath.core.annot.Phosphatome method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Progeny.html#pypath.core.annot.Progeny.labels">(pypath.core.annot.Progeny method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Ramilowski2015.html#pypath.core.annot.Ramilowski2015.labels">(pypath.core.annot.Ramilowski2015 method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Ramilowski2015Location.html#pypath.core.annot.Ramilowski2015Location.labels">(pypath.core.annot.Ramilowski2015Location method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Scconnect.html#pypath.core.annot.Scconnect.labels">(pypath.core.annot.Scconnect method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.ScconnectComplex.html#pypath.core.annot.ScconnectComplex.labels">(pypath.core.annot.ScconnectComplex method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.SignalinkFunctions.html#pypath.core.annot.SignalinkFunctions.labels">(pypath.core.annot.SignalinkFunctions method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.SignalinkPathways.html#pypath.core.annot.SignalinkPathways.labels">(pypath.core.annot.SignalinkPathways method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.SignorPathways.html#pypath.core.annot.SignorPathways.labels">(pypath.core.annot.SignorPathways method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Surfaceome.html#pypath.core.annot.Surfaceome.labels">(pypath.core.annot.Surfaceome method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Talklr.html#pypath.core.annot.Talklr.labels">(pypath.core.annot.Talklr method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Tcdb.html#pypath.core.annot.Tcdb.labels">(pypath.core.annot.Tcdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Tfcensus.html#pypath.core.annot.Tfcensus.labels">(pypath.core.annot.Tfcensus method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Topdb.html#pypath.core.annot.Topdb.labels">(pypath.core.annot.Topdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.UniprotFamilies.html#pypath.core.annot.UniprotFamilies.labels">(pypath.core.annot.UniprotFamilies method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.UniprotKeywords.html#pypath.core.annot.UniprotKeywords.labels">(pypath.core.annot.UniprotKeywords method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.UniprotLocations.html#pypath.core.annot.UniprotLocations.labels">(pypath.core.annot.UniprotLocations method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.UniprotTissues.html#pypath.core.annot.UniprotTissues.labels">(pypath.core.annot.UniprotTissues method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.UniprotTopologies.html#pypath.core.annot.UniprotTopologies.labels">(pypath.core.annot.UniprotTopologies method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Vesiclepedia.html#pypath.core.annot.Vesiclepedia.labels">(pypath.core.annot.Vesiclepedia method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Wang.html#pypath.core.annot.Wang.labels">(pypath.core.annot.Wang method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Zhong2015.html#pypath.core.annot.Zhong2015.labels">(pypath.core.annot.Zhong2015 method)</a>
+</li>
+        <li><a href="api/pypath.core.intercell.IntercellAnnotation.html#pypath.core.intercell.IntercellAnnotation.labels">(pypath.core.intercell.IntercellAnnotation method)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.labels_by_data_model">labels_by_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.labels_by_data_model">labels_by_data_model() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.labels_by_interaction_type">labels_by_interaction_type (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.labels_by_interaction_type">labels_by_interaction_type() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.labels_by_interaction_type_and_data_model">labels_by_interaction_type_and_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.labels_by_interaction_type_and_data_model">labels_by_interaction_type_and_data_model() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.labels_by_interaction_type_and_data_model_and_resource">labels_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.labels_by_interaction_type_and_data_model_and_resource">labels_by_interaction_type_and_data_model_and_resource() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.labels_by_reference">labels_by_reference (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.labels_by_reference">labels_by_reference() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.labels_by_resource">labels_by_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.labels_by_resource">labels_by_resource() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.annot.Lambert2018.html#pypath.core.annot.Lambert2018">Lambert2018 (class in pypath.core.annot)</a>
+</li>
+      <li><a href="api/pypath.inputs.lambert2018.lambert2018_annotations.html#pypath.inputs.lambert2018.lambert2018_annotations">lambert2018_annotations() (in module pypath.inputs.lambert2018)</a>
+</li>
+      <li><a href="api/pypath.inputs.lambert2018.lambert2018_s1_raw.html#pypath.inputs.lambert2018.lambert2018_s1_raw">lambert2018_s1_raw() (in module pypath.inputs.lambert2018)</a>
+</li>
+      <li><a href="api/pypath.internals.resource.NetworkResourceKey.html#pypath.internals.resource.NetworkResourceKey.last">last (pypath.internals.resource.NetworkResourceKey property)</a>
+</li>
+      <li><a href="api/pypath.inputs.uniprot.Taxon.html#pypath.inputs.uniprot.Taxon.latin">latin (pypath.inputs.uniprot.Taxon attribute)</a>
+</li>
+      <li><a href="api/pypath.inputs.uniprot.Taxon.html#pypath.inputs.uniprot.Taxon.latin_synonym">latin_synonym (pypath.inputs.uniprot.Taxon attribute)</a>
+</li>
+      <li><a href="api/pypath.inputs.laudanna.laudanna_directions.html#pypath.inputs.laudanna.laudanna_directions">laudanna_directions() (in module pypath.inputs.laudanna)</a>
+</li>
+      <li><a href="api/pypath.inputs.laudanna.laudanna_effects.html#pypath.inputs.laudanna.laudanna_effects">laudanna_effects() (in module pypath.inputs.laudanna)</a>
+</li>
+      <li><a href="api/pypath.utils.uniprot.UniprotProtein.html#pypath.utils.uniprot.UniprotProtein.length">length (pypath.utils.uniprot.UniprotProtein property)</a>
+</li>
+      <li><a href="api/pypath.utils.uniprot.length.html#pypath.utils.uniprot.length">length() (in module pypath.utils.uniprot)</a>
+</li>
+      <li><a href="api/pypath.utils.uniprot.UniprotProtein.html#pypath.utils.uniprot.UniprotProtein.lengths">lengths (pypath.utils.uniprot.UniprotProtein property)</a>
+</li>
+      <li><a href="api/pypath.utils.uniprot.lengths.html#pypath.utils.uniprot.lengths">lengths() (in module pypath.utils.uniprot)</a>
+</li>
+      <li><a href="api/pypath.inputs.dorothea.DorotheaInteraction.html#pypath.inputs.dorothea.DorotheaInteraction.level">level (pypath.inputs.dorothea.DorotheaInteraction attribute)</a>
+</li>
+      <li><a href="api/pypath.internals.license.LicenseAttrib.html#pypath.internals.license.LicenseAttrib.level_to_int">level_to_int() (pypath.internals.license.LicenseAttrib class method)</a>
+
+      <ul>
+        <li><a href="api/pypath.internals.license.LicenseFeature.html#pypath.internals.license.LicenseFeature.level_to_int">(pypath.internals.license.LicenseFeature class method)</a>
+</li>
+        <li><a href="api/pypath.internals.license.LicensePurpose.html#pypath.internals.license.LicensePurpose.level_to_int">(pypath.internals.license.LicensePurpose class method)</a>
+</li>
+        <li><a href="api/pypath.internals.license.LicenseSharing.html#pypath.internals.license.LicenseSharing.level_to_int">(pypath.internals.license.LicenseSharing class method)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.inputs.li2012.li2012_dmi.html#pypath.inputs.li2012.li2012_dmi">li2012_dmi() (in module pypath.inputs.li2012)</a>
+</li>
+      <li><a href="api/pypath.inputs.li2012.li2012_enzyme_substrate.html#pypath.inputs.li2012.li2012_enzyme_substrate">li2012_enzyme_substrate() (in module pypath.inputs.li2012)</a>
+</li>
+      <li><a href="api/pypath.inputs.li2012.li2012_interactions.html#pypath.inputs.li2012.li2012_interactions">li2012_interactions() (in module pypath.inputs.li2012)</a>
+</li>
+      <li><a href="api/pypath.internals.license.License.html#pypath.internals.license.License">License (class in pypath.internals.license)</a>
+</li>
+      <li><a href="api/pypath.resources.controller.ResourceController.html#pypath.resources.controller.ResourceController.license_filter">license_filter() (pypath.resources.controller.ResourceController method)</a>
+</li>
+      <li><a href="api/pypath.internals.license.LicenseAttrib.html#pypath.internals.license.LicenseAttrib">LicenseAttrib (class in pypath.internals.license)</a>
+</li>
+      <li><a href="api/pypath.internals.license.LicenseFeature.html#pypath.internals.license.LicenseFeature">LicenseFeature (class in pypath.internals.license)</a>
+</li>
+      <li><a href="api/pypath.internals.license.LicensePurpose.html#pypath.internals.license.LicensePurpose">LicensePurpose (class in pypath.internals.license)</a>
+</li>
+      <li><a href="api/pypath.resources.licenses.Licenses.html#pypath.resources.licenses.Licenses">Licenses (class in pypath.resources.licenses)</a>
+</li>
+      <li><a href="api/pypath.internals.license.LicenseSharing.html#pypath.internals.license.LicenseSharing">LicenseSharing (class in pypath.internals.license)</a>
+</li>
+      <li><a href="api/pypath.inputs.cellinker.CellinkerInteraction.html#pypath.inputs.cellinker.CellinkerInteraction.ligand">ligand (pypath.inputs.cellinker.CellinkerInteraction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.inputs.icellnet.IcellnetRecord.html#pypath.inputs.icellnet.IcellnetRecord.ligand">(pypath.inputs.icellnet.IcellnetRecord attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.inputs.cellinker.CellinkerInteraction.html#pypath.inputs.cellinker.CellinkerInteraction.ligand_location">ligand_location (pypath.inputs.cellinker.CellinkerInteraction attribute)</a>
+</li>
+      <li><a href="api/pypath.core.annot.LigandReceptor.html#pypath.core.annot.LigandReceptor">LigandReceptor (class in pypath.core.annot)</a>
+</li>
+      <li><a href="api/pypath.visual.igraph_drawing.edge.LightToDarkEdgeDrawer.html#pypath.visual.igraph_drawing.edge.LightToDarkEdgeDrawer">LightToDarkEdgeDrawer (class in pypath.visual.igraph_drawing.edge)</a>
+</li>
+      <li><a href="api/pypath.internals.annot_formats.AnnotDef.html#pypath.internals.annot_formats.AnnotDef.limit">limit (pypath.internals.annot_formats.AnnotDef attribute)</a>
+</li>
+      <li><a href="api/pypath.inputs.lincs.lincs_compounds.html#pypath.inputs.lincs.lincs_compounds">lincs_compounds() (in module pypath.inputs.lincs)</a>
+</li>
+      <li><a href="api/pypath.inputs.ontology.listof_ontologies.html#pypath.inputs.ontology.listof_ontologies">listof_ontologies() (in module pypath.inputs.ontology)</a>
+</li>
+      <li><a href="api/pypath.inputs.huri.lit_bm_13_interactions.html#pypath.inputs.huri.lit_bm_13_interactions">lit_bm_13_interactions() (in module pypath.inputs.huri)</a>
+</li>
+      <li><a href="api/pypath.inputs.huri.lit_bm_17_interactions.html#pypath.inputs.huri.lit_bm_17_interactions">lit_bm_17_interactions() (in module pypath.inputs.huri)</a>
+</li>
+      <li><a href="api/pypath.inputs.huri.lit_bm_interactions.html#pypath.inputs.huri.lit_bm_interactions">lit_bm_interactions() (in module pypath.inputs.huri)</a>
+</li>
+      <li><a href="api/pypath.inputs.lmpid.lmpid_dmi.html#pypath.inputs.lmpid.lmpid_dmi">lmpid_dmi() (in module pypath.inputs.lmpid)</a>
+</li>
+      <li><a href="api/pypath.inputs.lmpid.lmpid_interactions.html#pypath.inputs.lmpid.lmpid_interactions">lmpid_interactions() (in module pypath.inputs.lmpid)</a>
+</li>
+      <li><a href="api/pypath.inputs.lncdisease.lncdisease_interactions.html#pypath.inputs.lncdisease.lncdisease_interactions">lncdisease_interactions() (in module pypath.inputs.lncdisease)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.lncrna_identifiers_by_data_model">lncrna_identifiers_by_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.lncrna_identifiers_by_data_model">lncrna_identifiers_by_data_model() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.lncrna_identifiers_by_interaction_type">lncrna_identifiers_by_interaction_type (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.lncrna_identifiers_by_interaction_type">lncrna_identifiers_by_interaction_type() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.lncrna_identifiers_by_interaction_type_and_data_model">lncrna_identifiers_by_interaction_type_and_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.lncrna_identifiers_by_interaction_type_and_data_model">lncrna_identifiers_by_interaction_type_and_data_model() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.lncrna_identifiers_by_interaction_type_and_data_model_and_resource">lncrna_identifiers_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.lncrna_identifiers_by_interaction_type_and_data_model_and_resource">lncrna_identifiers_by_interaction_type_and_data_model_and_resource() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.lncrna_identifiers_by_reference">lncrna_identifiers_by_reference (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.lncrna_identifiers_by_reference">lncrna_identifiers_by_reference() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.lncrna_identifiers_by_resource">lncrna_identifiers_by_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.lncrna_identifiers_by_resource">lncrna_identifiers_by_resource() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.lncrna_labels_by_data_model">lncrna_labels_by_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.lncrna_labels_by_data_model">lncrna_labels_by_data_model() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.lncrna_labels_by_interaction_type">lncrna_labels_by_interaction_type (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.lncrna_labels_by_interaction_type">lncrna_labels_by_interaction_type() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.lncrna_labels_by_interaction_type_and_data_model">lncrna_labels_by_interaction_type_and_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.lncrna_labels_by_interaction_type_and_data_model">lncrna_labels_by_interaction_type_and_data_model() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.lncrna_labels_by_interaction_type_and_data_model_and_resource">lncrna_labels_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.lncrna_labels_by_interaction_type_and_data_model_and_resource">lncrna_labels_by_interaction_type_and_data_model_and_resource() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.lncrna_labels_by_reference">lncrna_labels_by_reference (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.lncrna_labels_by_reference">lncrna_labels_by_reference() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.lncrna_labels_by_resource">lncrna_labels_by_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.lncrna_labels_by_resource">lncrna_labels_by_resource() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.inputs.lncrnadb.lncrnadb_interactions.html#pypath.inputs.lncrnadb.lncrnadb_interactions">lncrnadb_interactions() (in module pypath.inputs.lncrnadb)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.lncrnas_by_data_model">lncrnas_by_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.lncrnas_by_data_model">lncrnas_by_data_model() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.lncrnas_by_interaction_type">lncrnas_by_interaction_type (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.lncrnas_by_interaction_type">lncrnas_by_interaction_type() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.lncrnas_by_interaction_type_and_data_model">lncrnas_by_interaction_type_and_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.lncrnas_by_interaction_type_and_data_model">lncrnas_by_interaction_type_and_data_model() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.lncrnas_by_interaction_type_and_data_model_and_resource">lncrnas_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.lncrnas_by_interaction_type_and_data_model_and_resource">lncrnas_by_interaction_type_and_data_model_and_resource() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.lncrnas_by_reference">lncrnas_by_reference (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.lncrnas_by_reference">lncrnas_by_reference() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.lncrnas_by_resource">lncrnas_by_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.lncrnas_by_resource">lncrnas_by_resource() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.utils.uniprot.load.html#pypath.utils.uniprot.load">load() (in module pypath.utils.uniprot)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.annot.Adhesome.html#pypath.core.annot.Adhesome.load">(pypath.core.annot.Adhesome method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Almen2009.html#pypath.core.annot.Almen2009.load">(pypath.core.annot.Almen2009 method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.AnnotationBase.html#pypath.core.annot.AnnotationBase.load">(pypath.core.annot.AnnotationBase method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Baccin2019.html#pypath.core.annot.Baccin2019.load">(pypath.core.annot.Baccin2019 method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Biogps.html#pypath.core.annot.Biogps.load">(pypath.core.annot.Biogps method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cancerdrugsdb.html#pypath.core.annot.Cancerdrugsdb.load">(pypath.core.annot.Cancerdrugsdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CancerGeneCensus.html#pypath.core.annot.CancerGeneCensus.load">(pypath.core.annot.CancerGeneCensus method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cancersea.html#pypath.core.annot.Cancersea.load">(pypath.core.annot.Cancersea method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cellcall.html#pypath.core.annot.Cellcall.load">(pypath.core.annot.Cellcall method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cellcellinteractions.html#pypath.core.annot.Cellcellinteractions.load">(pypath.core.annot.Cellcellinteractions method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cellchatdb.html#pypath.core.annot.Cellchatdb.load">(pypath.core.annot.Cellchatdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CellchatdbComplex.html#pypath.core.annot.CellchatdbComplex.load">(pypath.core.annot.CellchatdbComplex method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cellinker.html#pypath.core.annot.Cellinker.load">(pypath.core.annot.Cellinker method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CellinkerComplex.html#pypath.core.annot.CellinkerComplex.load">(pypath.core.annot.CellinkerComplex method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CellPhoneDB.html#pypath.core.annot.CellPhoneDB.load">(pypath.core.annot.CellPhoneDB method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CellPhoneDBComplex.html#pypath.core.annot.CellPhoneDBComplex.load">(pypath.core.annot.CellPhoneDBComplex method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CellSurfaceProteinAtlas.html#pypath.core.annot.CellSurfaceProteinAtlas.load">(pypath.core.annot.CellSurfaceProteinAtlas method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CellSurfaceProteinAtlasCellType.html#pypath.core.annot.CellSurfaceProteinAtlasCellType.load">(pypath.core.annot.CellSurfaceProteinAtlasCellType method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Celltalkdb.html#pypath.core.annot.Celltalkdb.load">(pypath.core.annot.Celltalkdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Celltypist.html#pypath.core.annot.Celltypist.load">(pypath.core.annot.Celltypist method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Comppi.html#pypath.core.annot.Comppi.load">(pypath.core.annot.Comppi method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Connectomedb.html#pypath.core.annot.Connectomedb.load">(pypath.core.annot.Connectomedb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Corum.html#pypath.core.annot.Corum.load">(pypath.core.annot.Corum method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CorumFuncat.html#pypath.core.annot.CorumFuncat.load">(pypath.core.annot.CorumFuncat method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CorumGO.html#pypath.core.annot.CorumGO.load">(pypath.core.annot.CorumGO method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cpad.html#pypath.core.annot.Cpad.load">(pypath.core.annot.Cpad method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cytosig.html#pypath.core.annot.Cytosig.load">(pypath.core.annot.Cytosig method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Dgidb.html#pypath.core.annot.Dgidb.load">(pypath.core.annot.Dgidb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Disgenet.html#pypath.core.annot.Disgenet.load">(pypath.core.annot.Disgenet method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Embrace.html#pypath.core.annot.Embrace.load">(pypath.core.annot.Embrace method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Exocarta.html#pypath.core.annot.Exocarta.load">(pypath.core.annot.Exocarta method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.GOIntercell.html#pypath.core.annot.GOIntercell.load">(pypath.core.annot.GOIntercell method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Gpcrdb.html#pypath.core.annot.Gpcrdb.load">(pypath.core.annot.Gpcrdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.GuideToPharmacology.html#pypath.core.annot.GuideToPharmacology.load">(pypath.core.annot.GuideToPharmacology method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Hgnc.html#pypath.core.annot.Hgnc.load">(pypath.core.annot.Hgnc method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.HpmrComplex.html#pypath.core.annot.HpmrComplex.load">(pypath.core.annot.HpmrComplex method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.HPO.html#pypath.core.annot.HPO.load">(pypath.core.annot.HPO method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Humancellmap.html#pypath.core.annot.Humancellmap.load">(pypath.core.annot.Humancellmap method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.HumanPlasmaMembraneReceptome.html#pypath.core.annot.HumanPlasmaMembraneReceptome.load">(pypath.core.annot.HumanPlasmaMembraneReceptome method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.HumanProteinAtlas.html#pypath.core.annot.HumanProteinAtlas.load">(pypath.core.annot.HumanProteinAtlas method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.HumanProteinAtlasSecretome.html#pypath.core.annot.HumanProteinAtlasSecretome.load">(pypath.core.annot.HumanProteinAtlasSecretome method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.HumanProteinAtlasSubcellular.html#pypath.core.annot.HumanProteinAtlasSubcellular.load">(pypath.core.annot.HumanProteinAtlasSubcellular method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Icellnet.html#pypath.core.annot.Icellnet.load">(pypath.core.annot.Icellnet method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.IcellnetComplex.html#pypath.core.annot.IcellnetComplex.load">(pypath.core.annot.IcellnetComplex method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Integrins.html#pypath.core.annot.Integrins.load">(pypath.core.annot.Integrins method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.InterPro.html#pypath.core.annot.InterPro.load">(pypath.core.annot.InterPro method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Intogen.html#pypath.core.annot.Intogen.load">(pypath.core.annot.Intogen method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Italk.html#pypath.core.annot.Italk.load">(pypath.core.annot.Italk method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.KeggPathways.html#pypath.core.annot.KeggPathways.load">(pypath.core.annot.KeggPathways method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.KeggPathwaysPC.html#pypath.core.annot.KeggPathwaysPC.load">(pypath.core.annot.KeggPathwaysPC method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Kinasedotcom.html#pypath.core.annot.Kinasedotcom.load">(pypath.core.annot.Kinasedotcom method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Kirouac2010.html#pypath.core.annot.Kirouac2010.load">(pypath.core.annot.Kirouac2010 method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Lambert2018.html#pypath.core.annot.Lambert2018.load">(pypath.core.annot.Lambert2018 method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.LigandReceptor.html#pypath.core.annot.LigandReceptor.load">(pypath.core.annot.LigandReceptor method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Locate.html#pypath.core.annot.Locate.load">(pypath.core.annot.Locate method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Lrdb.html#pypath.core.annot.Lrdb.load">(pypath.core.annot.Lrdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Matrisome.html#pypath.core.annot.Matrisome.load">(pypath.core.annot.Matrisome method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Matrixdb.html#pypath.core.annot.Matrixdb.load">(pypath.core.annot.Matrixdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Mcam.html#pypath.core.annot.Mcam.load">(pypath.core.annot.Mcam method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Membranome.html#pypath.core.annot.Membranome.load">(pypath.core.annot.Membranome method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Msigdb.html#pypath.core.annot.Msigdb.load">(pypath.core.annot.Msigdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.NetpathPathways.html#pypath.core.annot.NetpathPathways.load">(pypath.core.annot.NetpathPathways method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Opm.html#pypath.core.annot.Opm.load">(pypath.core.annot.Opm method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Panglaodb.html#pypath.core.annot.Panglaodb.load">(pypath.core.annot.Panglaodb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Phobius.html#pypath.core.annot.Phobius.load">(pypath.core.annot.Phobius method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Phosphatome.html#pypath.core.annot.Phosphatome.load">(pypath.core.annot.Phosphatome method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Progeny.html#pypath.core.annot.Progeny.load">(pypath.core.annot.Progeny method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Ramilowski2015.html#pypath.core.annot.Ramilowski2015.load">(pypath.core.annot.Ramilowski2015 method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Ramilowski2015Location.html#pypath.core.annot.Ramilowski2015Location.load">(pypath.core.annot.Ramilowski2015Location method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Scconnect.html#pypath.core.annot.Scconnect.load">(pypath.core.annot.Scconnect method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.ScconnectComplex.html#pypath.core.annot.ScconnectComplex.load">(pypath.core.annot.ScconnectComplex method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.SignalinkFunctions.html#pypath.core.annot.SignalinkFunctions.load">(pypath.core.annot.SignalinkFunctions method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.SignalinkPathways.html#pypath.core.annot.SignalinkPathways.load">(pypath.core.annot.SignalinkPathways method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.SignorPathways.html#pypath.core.annot.SignorPathways.load">(pypath.core.annot.SignorPathways method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Surfaceome.html#pypath.core.annot.Surfaceome.load">(pypath.core.annot.Surfaceome method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Talklr.html#pypath.core.annot.Talklr.load">(pypath.core.annot.Talklr method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Tcdb.html#pypath.core.annot.Tcdb.load">(pypath.core.annot.Tcdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Tfcensus.html#pypath.core.annot.Tfcensus.load">(pypath.core.annot.Tfcensus method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Topdb.html#pypath.core.annot.Topdb.load">(pypath.core.annot.Topdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.UniprotFamilies.html#pypath.core.annot.UniprotFamilies.load">(pypath.core.annot.UniprotFamilies method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.UniprotKeywords.html#pypath.core.annot.UniprotKeywords.load">(pypath.core.annot.UniprotKeywords method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.UniprotLocations.html#pypath.core.annot.UniprotLocations.load">(pypath.core.annot.UniprotLocations method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.UniprotTissues.html#pypath.core.annot.UniprotTissues.load">(pypath.core.annot.UniprotTissues method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.UniprotTopologies.html#pypath.core.annot.UniprotTopologies.load">(pypath.core.annot.UniprotTopologies method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Vesiclepedia.html#pypath.core.annot.Vesiclepedia.load">(pypath.core.annot.Vesiclepedia method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Wang.html#pypath.core.annot.Wang.load">(pypath.core.annot.Wang method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Zhong2015.html#pypath.core.annot.Zhong2015.load">(pypath.core.annot.Zhong2015 method)</a>
+</li>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.load">(pypath.core.network.Network method)</a>
+</li>
+        <li><a href="api/pypath.utils.mapping.MapReader.html#pypath.utils.mapping.MapReader.load">(pypath.utils.mapping.MapReader method)</a>
+</li>
+        <li><a href="api/pypath.utils.orthology.HomologeneOrthology.html#pypath.utils.orthology.HomologeneOrthology.load">(pypath.utils.orthology.HomologeneOrthology method)</a>
+</li>
+        <li><a href="api/pypath.utils.seq.Pfam.html#pypath.utils.seq.Pfam.load">(pypath.utils.seq.Pfam method)</a>
+</li>
+        <li><a href="api/pypath.utils.seq.Resource.html#pypath.utils.seq.Resource.load">(pypath.utils.seq.Resource method)</a>
+</li>
+      </ul></li>
+  </ul></td>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="api/pypath.core.annot.Adhesome.html#pypath.core.annot.Adhesome.load_data">load_data() (pypath.core.annot.Adhesome method)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.annot.Almen2009.html#pypath.core.annot.Almen2009.load_data">(pypath.core.annot.Almen2009 method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.AnnotationBase.html#pypath.core.annot.AnnotationBase.load_data">(pypath.core.annot.AnnotationBase method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Baccin2019.html#pypath.core.annot.Baccin2019.load_data">(pypath.core.annot.Baccin2019 method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Biogps.html#pypath.core.annot.Biogps.load_data">(pypath.core.annot.Biogps method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cancerdrugsdb.html#pypath.core.annot.Cancerdrugsdb.load_data">(pypath.core.annot.Cancerdrugsdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CancerGeneCensus.html#pypath.core.annot.CancerGeneCensus.load_data">(pypath.core.annot.CancerGeneCensus method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cancersea.html#pypath.core.annot.Cancersea.load_data">(pypath.core.annot.Cancersea method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cellcall.html#pypath.core.annot.Cellcall.load_data">(pypath.core.annot.Cellcall method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cellcellinteractions.html#pypath.core.annot.Cellcellinteractions.load_data">(pypath.core.annot.Cellcellinteractions method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cellchatdb.html#pypath.core.annot.Cellchatdb.load_data">(pypath.core.annot.Cellchatdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CellchatdbComplex.html#pypath.core.annot.CellchatdbComplex.load_data">(pypath.core.annot.CellchatdbComplex method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cellinker.html#pypath.core.annot.Cellinker.load_data">(pypath.core.annot.Cellinker method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CellinkerComplex.html#pypath.core.annot.CellinkerComplex.load_data">(pypath.core.annot.CellinkerComplex method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CellPhoneDB.html#pypath.core.annot.CellPhoneDB.load_data">(pypath.core.annot.CellPhoneDB method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CellPhoneDBComplex.html#pypath.core.annot.CellPhoneDBComplex.load_data">(pypath.core.annot.CellPhoneDBComplex method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CellSurfaceProteinAtlas.html#pypath.core.annot.CellSurfaceProteinAtlas.load_data">(pypath.core.annot.CellSurfaceProteinAtlas method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CellSurfaceProteinAtlasCellType.html#pypath.core.annot.CellSurfaceProteinAtlasCellType.load_data">(pypath.core.annot.CellSurfaceProteinAtlasCellType method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Celltalkdb.html#pypath.core.annot.Celltalkdb.load_data">(pypath.core.annot.Celltalkdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Celltypist.html#pypath.core.annot.Celltypist.load_data">(pypath.core.annot.Celltypist method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Comppi.html#pypath.core.annot.Comppi.load_data">(pypath.core.annot.Comppi method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Connectomedb.html#pypath.core.annot.Connectomedb.load_data">(pypath.core.annot.Connectomedb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Corum.html#pypath.core.annot.Corum.load_data">(pypath.core.annot.Corum method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CorumFuncat.html#pypath.core.annot.CorumFuncat.load_data">(pypath.core.annot.CorumFuncat method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CorumGO.html#pypath.core.annot.CorumGO.load_data">(pypath.core.annot.CorumGO method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cpad.html#pypath.core.annot.Cpad.load_data">(pypath.core.annot.Cpad method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cytosig.html#pypath.core.annot.Cytosig.load_data">(pypath.core.annot.Cytosig method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Dgidb.html#pypath.core.annot.Dgidb.load_data">(pypath.core.annot.Dgidb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Disgenet.html#pypath.core.annot.Disgenet.load_data">(pypath.core.annot.Disgenet method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Embrace.html#pypath.core.annot.Embrace.load_data">(pypath.core.annot.Embrace method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Exocarta.html#pypath.core.annot.Exocarta.load_data">(pypath.core.annot.Exocarta method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.GOIntercell.html#pypath.core.annot.GOIntercell.load_data">(pypath.core.annot.GOIntercell method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Gpcrdb.html#pypath.core.annot.Gpcrdb.load_data">(pypath.core.annot.Gpcrdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.GuideToPharmacology.html#pypath.core.annot.GuideToPharmacology.load_data">(pypath.core.annot.GuideToPharmacology method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Hgnc.html#pypath.core.annot.Hgnc.load_data">(pypath.core.annot.Hgnc method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.HpmrComplex.html#pypath.core.annot.HpmrComplex.load_data">(pypath.core.annot.HpmrComplex method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.HPO.html#pypath.core.annot.HPO.load_data">(pypath.core.annot.HPO method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Humancellmap.html#pypath.core.annot.Humancellmap.load_data">(pypath.core.annot.Humancellmap method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.HumanPlasmaMembraneReceptome.html#pypath.core.annot.HumanPlasmaMembraneReceptome.load_data">(pypath.core.annot.HumanPlasmaMembraneReceptome method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.HumanProteinAtlas.html#pypath.core.annot.HumanProteinAtlas.load_data">(pypath.core.annot.HumanProteinAtlas method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.HumanProteinAtlasSecretome.html#pypath.core.annot.HumanProteinAtlasSecretome.load_data">(pypath.core.annot.HumanProteinAtlasSecretome method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.HumanProteinAtlasSubcellular.html#pypath.core.annot.HumanProteinAtlasSubcellular.load_data">(pypath.core.annot.HumanProteinAtlasSubcellular method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Icellnet.html#pypath.core.annot.Icellnet.load_data">(pypath.core.annot.Icellnet method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.IcellnetComplex.html#pypath.core.annot.IcellnetComplex.load_data">(pypath.core.annot.IcellnetComplex method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Integrins.html#pypath.core.annot.Integrins.load_data">(pypath.core.annot.Integrins method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.InterPro.html#pypath.core.annot.InterPro.load_data">(pypath.core.annot.InterPro method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Intogen.html#pypath.core.annot.Intogen.load_data">(pypath.core.annot.Intogen method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Italk.html#pypath.core.annot.Italk.load_data">(pypath.core.annot.Italk method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.KeggPathways.html#pypath.core.annot.KeggPathways.load_data">(pypath.core.annot.KeggPathways method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.KeggPathwaysPC.html#pypath.core.annot.KeggPathwaysPC.load_data">(pypath.core.annot.KeggPathwaysPC method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Kinasedotcom.html#pypath.core.annot.Kinasedotcom.load_data">(pypath.core.annot.Kinasedotcom method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Kirouac2010.html#pypath.core.annot.Kirouac2010.load_data">(pypath.core.annot.Kirouac2010 method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Lambert2018.html#pypath.core.annot.Lambert2018.load_data">(pypath.core.annot.Lambert2018 method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.LigandReceptor.html#pypath.core.annot.LigandReceptor.load_data">(pypath.core.annot.LigandReceptor method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Locate.html#pypath.core.annot.Locate.load_data">(pypath.core.annot.Locate method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Lrdb.html#pypath.core.annot.Lrdb.load_data">(pypath.core.annot.Lrdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Matrisome.html#pypath.core.annot.Matrisome.load_data">(pypath.core.annot.Matrisome method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Matrixdb.html#pypath.core.annot.Matrixdb.load_data">(pypath.core.annot.Matrixdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Mcam.html#pypath.core.annot.Mcam.load_data">(pypath.core.annot.Mcam method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Membranome.html#pypath.core.annot.Membranome.load_data">(pypath.core.annot.Membranome method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Msigdb.html#pypath.core.annot.Msigdb.load_data">(pypath.core.annot.Msigdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.NetpathPathways.html#pypath.core.annot.NetpathPathways.load_data">(pypath.core.annot.NetpathPathways method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Opm.html#pypath.core.annot.Opm.load_data">(pypath.core.annot.Opm method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Panglaodb.html#pypath.core.annot.Panglaodb.load_data">(pypath.core.annot.Panglaodb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Phobius.html#pypath.core.annot.Phobius.load_data">(pypath.core.annot.Phobius method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Phosphatome.html#pypath.core.annot.Phosphatome.load_data">(pypath.core.annot.Phosphatome method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Progeny.html#pypath.core.annot.Progeny.load_data">(pypath.core.annot.Progeny method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Ramilowski2015.html#pypath.core.annot.Ramilowski2015.load_data">(pypath.core.annot.Ramilowski2015 method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Ramilowski2015Location.html#pypath.core.annot.Ramilowski2015Location.load_data">(pypath.core.annot.Ramilowski2015Location method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Scconnect.html#pypath.core.annot.Scconnect.load_data">(pypath.core.annot.Scconnect method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.ScconnectComplex.html#pypath.core.annot.ScconnectComplex.load_data">(pypath.core.annot.ScconnectComplex method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.SignalinkFunctions.html#pypath.core.annot.SignalinkFunctions.load_data">(pypath.core.annot.SignalinkFunctions method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.SignalinkPathways.html#pypath.core.annot.SignalinkPathways.load_data">(pypath.core.annot.SignalinkPathways method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.SignorPathways.html#pypath.core.annot.SignorPathways.load_data">(pypath.core.annot.SignorPathways method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Surfaceome.html#pypath.core.annot.Surfaceome.load_data">(pypath.core.annot.Surfaceome method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Talklr.html#pypath.core.annot.Talklr.load_data">(pypath.core.annot.Talklr method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Tcdb.html#pypath.core.annot.Tcdb.load_data">(pypath.core.annot.Tcdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Tfcensus.html#pypath.core.annot.Tfcensus.load_data">(pypath.core.annot.Tfcensus method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Topdb.html#pypath.core.annot.Topdb.load_data">(pypath.core.annot.Topdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.UniprotFamilies.html#pypath.core.annot.UniprotFamilies.load_data">(pypath.core.annot.UniprotFamilies method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.UniprotKeywords.html#pypath.core.annot.UniprotKeywords.load_data">(pypath.core.annot.UniprotKeywords method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.UniprotLocations.html#pypath.core.annot.UniprotLocations.load_data">(pypath.core.annot.UniprotLocations method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.UniprotTissues.html#pypath.core.annot.UniprotTissues.load_data">(pypath.core.annot.UniprotTissues method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.UniprotTopologies.html#pypath.core.annot.UniprotTopologies.load_data">(pypath.core.annot.UniprotTopologies method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Vesiclepedia.html#pypath.core.annot.Vesiclepedia.load_data">(pypath.core.annot.Vesiclepedia method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Wang.html#pypath.core.annot.Wang.load_data">(pypath.core.annot.Wang method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Zhong2015.html#pypath.core.annot.Zhong2015.load_data">(pypath.core.annot.Zhong2015 method)</a>
+</li>
+        <li><a href="api/pypath.core.complex.AbstractComplexResource.html#pypath.core.complex.AbstractComplexResource.load_data">(pypath.core.complex.AbstractComplexResource method)</a>
+</li>
+        <li><a href="api/pypath.core.complex.Cellchatdb.html#pypath.core.complex.Cellchatdb.load_data">(pypath.core.complex.Cellchatdb method)</a>
+</li>
+        <li><a href="api/pypath.core.complex.Cellinker.html#pypath.core.complex.Cellinker.load_data">(pypath.core.complex.Cellinker method)</a>
+</li>
+        <li><a href="api/pypath.core.complex.CellPhoneDB.html#pypath.core.complex.CellPhoneDB.load_data">(pypath.core.complex.CellPhoneDB method)</a>
+</li>
+        <li><a href="api/pypath.core.complex.Compleat.html#pypath.core.complex.Compleat.load_data">(pypath.core.complex.Compleat method)</a>
+</li>
+        <li><a href="api/pypath.core.complex.ComplexAggregator.html#pypath.core.complex.ComplexAggregator.load_data">(pypath.core.complex.ComplexAggregator method)</a>
+</li>
+        <li><a href="api/pypath.core.complex.ComplexPortal.html#pypath.core.complex.ComplexPortal.load_data">(pypath.core.complex.ComplexPortal method)</a>
+</li>
+        <li><a href="api/pypath.core.complex.Corum.html#pypath.core.complex.Corum.load_data">(pypath.core.complex.Corum method)</a>
+</li>
+        <li><a href="api/pypath.core.complex.GuideToPharmacology.html#pypath.core.complex.GuideToPharmacology.load_data">(pypath.core.complex.GuideToPharmacology method)</a>
+</li>
+        <li><a href="api/pypath.core.complex.Havugimana.html#pypath.core.complex.Havugimana.load_data">(pypath.core.complex.Havugimana method)</a>
+</li>
+        <li><a href="api/pypath.core.complex.Hpmr.html#pypath.core.complex.Hpmr.load_data">(pypath.core.complex.Hpmr method)</a>
+</li>
+        <li><a href="api/pypath.core.complex.Humap.html#pypath.core.complex.Humap.load_data">(pypath.core.complex.Humap method)</a>
+</li>
+        <li><a href="api/pypath.core.complex.Humap2.html#pypath.core.complex.Humap2.load_data">(pypath.core.complex.Humap2 method)</a>
+</li>
+        <li><a href="api/pypath.core.complex.Icellnet.html#pypath.core.complex.Icellnet.load_data">(pypath.core.complex.Icellnet method)</a>
+</li>
+        <li><a href="api/pypath.core.complex.Kegg.html#pypath.core.complex.Kegg.load_data">(pypath.core.complex.Kegg method)</a>
+</li>
+        <li><a href="api/pypath.core.complex.Pdb.html#pypath.core.complex.Pdb.load_data">(pypath.core.complex.Pdb method)</a>
+</li>
+        <li><a href="api/pypath.core.complex.Signor.html#pypath.core.complex.Signor.load_data">(pypath.core.complex.Signor method)</a>
+</li>
+        <li><a href="api/pypath.core.complex.Spike.html#pypath.core.complex.Spike.load_data">(pypath.core.complex.Spike method)</a>
+</li>
+        <li><a href="api/pypath.core.enz_sub.EnzymeSubstrateOrthologyProcessor.html#pypath.core.enz_sub.EnzymeSubstrateOrthologyProcessor.load_data">(pypath.core.enz_sub.EnzymeSubstrateOrthologyProcessor method)</a>
+</li>
+        <li><a href="api/pypath.core.enz_sub.EnzymeSubstrateProcessor.html#pypath.core.enz_sub.EnzymeSubstrateProcessor.load_data">(pypath.core.enz_sub.EnzymeSubstrateProcessor method)</a>
+</li>
+        <li><a href="api/pypath.internals.resource.AbstractResource.html#pypath.internals.resource.AbstractResource.load_data">(pypath.internals.resource.AbstractResource method)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.omnipath.app.DatabaseManager.html#pypath.omnipath.app.DatabaseManager.load_dataset">load_dataset() (pypath.omnipath.app.DatabaseManager method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.load_from_pickle">load_from_pickle() (pypath.core.network.Network method)</a>
+</li>
+      <li><a href="api/pypath.utils.mapping.Mapper.html#pypath.utils.mapping.Mapper.load_genesymbol5">load_genesymbol5() (pypath.utils.mapping.Mapper method)</a>
+</li>
+      <li><a href="api/pypath.utils.go.load_go.html#pypath.utils.go.load_go">load_go() (in module pypath.utils.go)</a>
+</li>
+      <li><a href="api/pypath.inputs.lmpid.load_lmpid.html#pypath.inputs.lmpid.load_lmpid">load_lmpid() (in module pypath.inputs.lmpid)</a>
+</li>
+      <li><a href="api/pypath.utils.mapping.Mapper.html#pypath.utils.mapping.Mapper.load_mapping">load_mapping() (pypath.utils.mapping.Mapper method)</a>
+
+      <ul>
+        <li><a href="api/pypath.utils.pdb.ResidueMapper.html#pypath.utils.pdb.ResidueMapper.load_mapping">(pypath.utils.pdb.ResidueMapper method)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.annot.Adhesome.html#pypath.core.annot.Adhesome.load_proteins">load_proteins() (pypath.core.annot.Adhesome method)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.annot.Almen2009.html#pypath.core.annot.Almen2009.load_proteins">(pypath.core.annot.Almen2009 method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.AnnotationBase.html#pypath.core.annot.AnnotationBase.load_proteins">(pypath.core.annot.AnnotationBase method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Baccin2019.html#pypath.core.annot.Baccin2019.load_proteins">(pypath.core.annot.Baccin2019 method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Biogps.html#pypath.core.annot.Biogps.load_proteins">(pypath.core.annot.Biogps method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cancerdrugsdb.html#pypath.core.annot.Cancerdrugsdb.load_proteins">(pypath.core.annot.Cancerdrugsdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CancerGeneCensus.html#pypath.core.annot.CancerGeneCensus.load_proteins">(pypath.core.annot.CancerGeneCensus method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cancersea.html#pypath.core.annot.Cancersea.load_proteins">(pypath.core.annot.Cancersea method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cellcall.html#pypath.core.annot.Cellcall.load_proteins">(pypath.core.annot.Cellcall method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cellcellinteractions.html#pypath.core.annot.Cellcellinteractions.load_proteins">(pypath.core.annot.Cellcellinteractions method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cellchatdb.html#pypath.core.annot.Cellchatdb.load_proteins">(pypath.core.annot.Cellchatdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CellchatdbComplex.html#pypath.core.annot.CellchatdbComplex.load_proteins">(pypath.core.annot.CellchatdbComplex method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cellinker.html#pypath.core.annot.Cellinker.load_proteins">(pypath.core.annot.Cellinker method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CellinkerComplex.html#pypath.core.annot.CellinkerComplex.load_proteins">(pypath.core.annot.CellinkerComplex method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CellPhoneDB.html#pypath.core.annot.CellPhoneDB.load_proteins">(pypath.core.annot.CellPhoneDB method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CellPhoneDBComplex.html#pypath.core.annot.CellPhoneDBComplex.load_proteins">(pypath.core.annot.CellPhoneDBComplex method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CellSurfaceProteinAtlas.html#pypath.core.annot.CellSurfaceProteinAtlas.load_proteins">(pypath.core.annot.CellSurfaceProteinAtlas method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CellSurfaceProteinAtlasCellType.html#pypath.core.annot.CellSurfaceProteinAtlasCellType.load_proteins">(pypath.core.annot.CellSurfaceProteinAtlasCellType method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Celltalkdb.html#pypath.core.annot.Celltalkdb.load_proteins">(pypath.core.annot.Celltalkdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Celltypist.html#pypath.core.annot.Celltypist.load_proteins">(pypath.core.annot.Celltypist method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Comppi.html#pypath.core.annot.Comppi.load_proteins">(pypath.core.annot.Comppi method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Connectomedb.html#pypath.core.annot.Connectomedb.load_proteins">(pypath.core.annot.Connectomedb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Corum.html#pypath.core.annot.Corum.load_proteins">(pypath.core.annot.Corum method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CorumFuncat.html#pypath.core.annot.CorumFuncat.load_proteins">(pypath.core.annot.CorumFuncat method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CorumGO.html#pypath.core.annot.CorumGO.load_proteins">(pypath.core.annot.CorumGO method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cpad.html#pypath.core.annot.Cpad.load_proteins">(pypath.core.annot.Cpad method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cytosig.html#pypath.core.annot.Cytosig.load_proteins">(pypath.core.annot.Cytosig method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Dgidb.html#pypath.core.annot.Dgidb.load_proteins">(pypath.core.annot.Dgidb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Disgenet.html#pypath.core.annot.Disgenet.load_proteins">(pypath.core.annot.Disgenet method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Embrace.html#pypath.core.annot.Embrace.load_proteins">(pypath.core.annot.Embrace method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Exocarta.html#pypath.core.annot.Exocarta.load_proteins">(pypath.core.annot.Exocarta method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.GOIntercell.html#pypath.core.annot.GOIntercell.load_proteins">(pypath.core.annot.GOIntercell method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Gpcrdb.html#pypath.core.annot.Gpcrdb.load_proteins">(pypath.core.annot.Gpcrdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.GuideToPharmacology.html#pypath.core.annot.GuideToPharmacology.load_proteins">(pypath.core.annot.GuideToPharmacology method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Hgnc.html#pypath.core.annot.Hgnc.load_proteins">(pypath.core.annot.Hgnc method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.HpmrComplex.html#pypath.core.annot.HpmrComplex.load_proteins">(pypath.core.annot.HpmrComplex method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.HPO.html#pypath.core.annot.HPO.load_proteins">(pypath.core.annot.HPO method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Humancellmap.html#pypath.core.annot.Humancellmap.load_proteins">(pypath.core.annot.Humancellmap method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.HumanPlasmaMembraneReceptome.html#pypath.core.annot.HumanPlasmaMembraneReceptome.load_proteins">(pypath.core.annot.HumanPlasmaMembraneReceptome method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.HumanProteinAtlas.html#pypath.core.annot.HumanProteinAtlas.load_proteins">(pypath.core.annot.HumanProteinAtlas method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.HumanProteinAtlasSecretome.html#pypath.core.annot.HumanProteinAtlasSecretome.load_proteins">(pypath.core.annot.HumanProteinAtlasSecretome method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.HumanProteinAtlasSubcellular.html#pypath.core.annot.HumanProteinAtlasSubcellular.load_proteins">(pypath.core.annot.HumanProteinAtlasSubcellular method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Icellnet.html#pypath.core.annot.Icellnet.load_proteins">(pypath.core.annot.Icellnet method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.IcellnetComplex.html#pypath.core.annot.IcellnetComplex.load_proteins">(pypath.core.annot.IcellnetComplex method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Integrins.html#pypath.core.annot.Integrins.load_proteins">(pypath.core.annot.Integrins method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.InterPro.html#pypath.core.annot.InterPro.load_proteins">(pypath.core.annot.InterPro method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Intogen.html#pypath.core.annot.Intogen.load_proteins">(pypath.core.annot.Intogen method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Italk.html#pypath.core.annot.Italk.load_proteins">(pypath.core.annot.Italk method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.KeggPathways.html#pypath.core.annot.KeggPathways.load_proteins">(pypath.core.annot.KeggPathways method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.KeggPathwaysPC.html#pypath.core.annot.KeggPathwaysPC.load_proteins">(pypath.core.annot.KeggPathwaysPC method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Kinasedotcom.html#pypath.core.annot.Kinasedotcom.load_proteins">(pypath.core.annot.Kinasedotcom method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Kirouac2010.html#pypath.core.annot.Kirouac2010.load_proteins">(pypath.core.annot.Kirouac2010 method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Lambert2018.html#pypath.core.annot.Lambert2018.load_proteins">(pypath.core.annot.Lambert2018 method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.LigandReceptor.html#pypath.core.annot.LigandReceptor.load_proteins">(pypath.core.annot.LigandReceptor method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Locate.html#pypath.core.annot.Locate.load_proteins">(pypath.core.annot.Locate method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Lrdb.html#pypath.core.annot.Lrdb.load_proteins">(pypath.core.annot.Lrdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Matrisome.html#pypath.core.annot.Matrisome.load_proteins">(pypath.core.annot.Matrisome method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Matrixdb.html#pypath.core.annot.Matrixdb.load_proteins">(pypath.core.annot.Matrixdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Mcam.html#pypath.core.annot.Mcam.load_proteins">(pypath.core.annot.Mcam method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Membranome.html#pypath.core.annot.Membranome.load_proteins">(pypath.core.annot.Membranome method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Msigdb.html#pypath.core.annot.Msigdb.load_proteins">(pypath.core.annot.Msigdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.NetpathPathways.html#pypath.core.annot.NetpathPathways.load_proteins">(pypath.core.annot.NetpathPathways method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Opm.html#pypath.core.annot.Opm.load_proteins">(pypath.core.annot.Opm method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Panglaodb.html#pypath.core.annot.Panglaodb.load_proteins">(pypath.core.annot.Panglaodb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Phobius.html#pypath.core.annot.Phobius.load_proteins">(pypath.core.annot.Phobius method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Phosphatome.html#pypath.core.annot.Phosphatome.load_proteins">(pypath.core.annot.Phosphatome method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Progeny.html#pypath.core.annot.Progeny.load_proteins">(pypath.core.annot.Progeny method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Ramilowski2015.html#pypath.core.annot.Ramilowski2015.load_proteins">(pypath.core.annot.Ramilowski2015 method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Ramilowski2015Location.html#pypath.core.annot.Ramilowski2015Location.load_proteins">(pypath.core.annot.Ramilowski2015Location method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Scconnect.html#pypath.core.annot.Scconnect.load_proteins">(pypath.core.annot.Scconnect method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.ScconnectComplex.html#pypath.core.annot.ScconnectComplex.load_proteins">(pypath.core.annot.ScconnectComplex method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.SignalinkFunctions.html#pypath.core.annot.SignalinkFunctions.load_proteins">(pypath.core.annot.SignalinkFunctions method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.SignalinkPathways.html#pypath.core.annot.SignalinkPathways.load_proteins">(pypath.core.annot.SignalinkPathways method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.SignorPathways.html#pypath.core.annot.SignorPathways.load_proteins">(pypath.core.annot.SignorPathways method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Surfaceome.html#pypath.core.annot.Surfaceome.load_proteins">(pypath.core.annot.Surfaceome method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Talklr.html#pypath.core.annot.Talklr.load_proteins">(pypath.core.annot.Talklr method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Tcdb.html#pypath.core.annot.Tcdb.load_proteins">(pypath.core.annot.Tcdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Tfcensus.html#pypath.core.annot.Tfcensus.load_proteins">(pypath.core.annot.Tfcensus method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Topdb.html#pypath.core.annot.Topdb.load_proteins">(pypath.core.annot.Topdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.UniprotFamilies.html#pypath.core.annot.UniprotFamilies.load_proteins">(pypath.core.annot.UniprotFamilies method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.UniprotKeywords.html#pypath.core.annot.UniprotKeywords.load_proteins">(pypath.core.annot.UniprotKeywords method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.UniprotLocations.html#pypath.core.annot.UniprotLocations.load_proteins">(pypath.core.annot.UniprotLocations method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.UniprotTissues.html#pypath.core.annot.UniprotTissues.load_proteins">(pypath.core.annot.UniprotTissues method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.UniprotTopologies.html#pypath.core.annot.UniprotTopologies.load_proteins">(pypath.core.annot.UniprotTopologies method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Vesiclepedia.html#pypath.core.annot.Vesiclepedia.load_proteins">(pypath.core.annot.Vesiclepedia method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Wang.html#pypath.core.annot.Wang.load_proteins">(pypath.core.annot.Wang method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Zhong2015.html#pypath.core.annot.Zhong2015.load_proteins">(pypath.core.annot.Zhong2015 method)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.load_resource">load_resource() (pypath.core.network.Network method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.load_resources">load_resources() (pypath.core.network.Network method)</a>
+</li>
+      <li><a href="api/pypath.utils.mapping.Mapper.html#pypath.utils.mapping.Mapper.load_uniprot_static">load_uniprot_static() (pypath.utils.mapping.Mapper method)</a>
+</li>
+      <li><a href="api/pypath.core.annot.Locate.html#pypath.core.annot.Locate">Locate (class in pypath.core.annot)</a>
+</li>
+      <li><a href="api/pypath.inputs.locate.locate_localizations.html#pypath.inputs.locate.locate_localizations">locate_localizations() (in module pypath.inputs.locate)</a>
+</li>
+      <li><a href="api/pypath.log.html#pypath.log">log() (in module pypath)</a>
+</li>
+      <li><a href="api/pypath.utils.go.GeneOntology.html#pypath.utils.go.GeneOntology.lowest">lowest() (pypath.utils.go.GeneOntology method)</a>
+</li>
+      <li><a href="api/pypath.core.annot.Lrdb.html#pypath.core.annot.Lrdb">Lrdb (class in pypath.core.annot)</a>
+</li>
+      <li><a href="api/pypath.inputs.lrdb.lrdb_annotations.html#pypath.inputs.lrdb.lrdb_annotations">lrdb_annotations() (in module pypath.inputs.lrdb)</a>
+</li>
+      <li><a href="api/pypath.inputs.lrdb.lrdb_interactions.html#pypath.inputs.lrdb.lrdb_interactions">lrdb_interactions() (in module pypath.inputs.lrdb)</a>
+</li>
+      <li><a href="api/pypath.inputs.lrdb.LrdbAnnotation.html#pypath.inputs.lrdb.LrdbAnnotation">LrdbAnnotation (class in pypath.inputs.lrdb)</a>
+</li>
+  </ul></td>
+</tr></table>
+
+<h2 id="M">M</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="api/pypath.inputs.macrophage.macrophage_interactions.html#pypath.inputs.macrophage.macrophage_interactions">macrophage_interactions() (in module pypath.inputs.macrophage)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.majority_dir">majority_dir() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.majority_sign">majority_sign() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.annot.Adhesome.html#pypath.core.annot.Adhesome.make_df">make_df() (pypath.core.annot.Adhesome method)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.annot.Almen2009.html#pypath.core.annot.Almen2009.make_df">(pypath.core.annot.Almen2009 method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.AnnotationBase.html#pypath.core.annot.AnnotationBase.make_df">(pypath.core.annot.AnnotationBase method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Baccin2019.html#pypath.core.annot.Baccin2019.make_df">(pypath.core.annot.Baccin2019 method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Biogps.html#pypath.core.annot.Biogps.make_df">(pypath.core.annot.Biogps method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cancerdrugsdb.html#pypath.core.annot.Cancerdrugsdb.make_df">(pypath.core.annot.Cancerdrugsdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CancerGeneCensus.html#pypath.core.annot.CancerGeneCensus.make_df">(pypath.core.annot.CancerGeneCensus method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cancersea.html#pypath.core.annot.Cancersea.make_df">(pypath.core.annot.Cancersea method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cellcall.html#pypath.core.annot.Cellcall.make_df">(pypath.core.annot.Cellcall method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cellcellinteractions.html#pypath.core.annot.Cellcellinteractions.make_df">(pypath.core.annot.Cellcellinteractions method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cellchatdb.html#pypath.core.annot.Cellchatdb.make_df">(pypath.core.annot.Cellchatdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CellchatdbComplex.html#pypath.core.annot.CellchatdbComplex.make_df">(pypath.core.annot.CellchatdbComplex method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cellinker.html#pypath.core.annot.Cellinker.make_df">(pypath.core.annot.Cellinker method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CellinkerComplex.html#pypath.core.annot.CellinkerComplex.make_df">(pypath.core.annot.CellinkerComplex method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CellPhoneDB.html#pypath.core.annot.CellPhoneDB.make_df">(pypath.core.annot.CellPhoneDB method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CellPhoneDBComplex.html#pypath.core.annot.CellPhoneDBComplex.make_df">(pypath.core.annot.CellPhoneDBComplex method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CellSurfaceProteinAtlas.html#pypath.core.annot.CellSurfaceProteinAtlas.make_df">(pypath.core.annot.CellSurfaceProteinAtlas method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CellSurfaceProteinAtlasCellType.html#pypath.core.annot.CellSurfaceProteinAtlasCellType.make_df">(pypath.core.annot.CellSurfaceProteinAtlasCellType method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Celltalkdb.html#pypath.core.annot.Celltalkdb.make_df">(pypath.core.annot.Celltalkdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Celltypist.html#pypath.core.annot.Celltypist.make_df">(pypath.core.annot.Celltypist method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Comppi.html#pypath.core.annot.Comppi.make_df">(pypath.core.annot.Comppi method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Connectomedb.html#pypath.core.annot.Connectomedb.make_df">(pypath.core.annot.Connectomedb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Corum.html#pypath.core.annot.Corum.make_df">(pypath.core.annot.Corum method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CorumFuncat.html#pypath.core.annot.CorumFuncat.make_df">(pypath.core.annot.CorumFuncat method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CorumGO.html#pypath.core.annot.CorumGO.make_df">(pypath.core.annot.CorumGO method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cpad.html#pypath.core.annot.Cpad.make_df">(pypath.core.annot.Cpad method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CustomAnnotation.html#pypath.core.annot.CustomAnnotation.make_df">(pypath.core.annot.CustomAnnotation method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cytosig.html#pypath.core.annot.Cytosig.make_df">(pypath.core.annot.Cytosig method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Dgidb.html#pypath.core.annot.Dgidb.make_df">(pypath.core.annot.Dgidb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Disgenet.html#pypath.core.annot.Disgenet.make_df">(pypath.core.annot.Disgenet method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Embrace.html#pypath.core.annot.Embrace.make_df">(pypath.core.annot.Embrace method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Exocarta.html#pypath.core.annot.Exocarta.make_df">(pypath.core.annot.Exocarta method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.GOIntercell.html#pypath.core.annot.GOIntercell.make_df">(pypath.core.annot.GOIntercell method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Gpcrdb.html#pypath.core.annot.Gpcrdb.make_df">(pypath.core.annot.Gpcrdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.GuideToPharmacology.html#pypath.core.annot.GuideToPharmacology.make_df">(pypath.core.annot.GuideToPharmacology method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Hgnc.html#pypath.core.annot.Hgnc.make_df">(pypath.core.annot.Hgnc method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.HpmrComplex.html#pypath.core.annot.HpmrComplex.make_df">(pypath.core.annot.HpmrComplex method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.HPO.html#pypath.core.annot.HPO.make_df">(pypath.core.annot.HPO method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Humancellmap.html#pypath.core.annot.Humancellmap.make_df">(pypath.core.annot.Humancellmap method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.HumanPlasmaMembraneReceptome.html#pypath.core.annot.HumanPlasmaMembraneReceptome.make_df">(pypath.core.annot.HumanPlasmaMembraneReceptome method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.HumanProteinAtlas.html#pypath.core.annot.HumanProteinAtlas.make_df">(pypath.core.annot.HumanProteinAtlas method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.HumanProteinAtlasSecretome.html#pypath.core.annot.HumanProteinAtlasSecretome.make_df">(pypath.core.annot.HumanProteinAtlasSecretome method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.HumanProteinAtlasSubcellular.html#pypath.core.annot.HumanProteinAtlasSubcellular.make_df">(pypath.core.annot.HumanProteinAtlasSubcellular method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Icellnet.html#pypath.core.annot.Icellnet.make_df">(pypath.core.annot.Icellnet method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.IcellnetComplex.html#pypath.core.annot.IcellnetComplex.make_df">(pypath.core.annot.IcellnetComplex method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Integrins.html#pypath.core.annot.Integrins.make_df">(pypath.core.annot.Integrins method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.InterPro.html#pypath.core.annot.InterPro.make_df">(pypath.core.annot.InterPro method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Intogen.html#pypath.core.annot.Intogen.make_df">(pypath.core.annot.Intogen method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Italk.html#pypath.core.annot.Italk.make_df">(pypath.core.annot.Italk method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.KeggPathways.html#pypath.core.annot.KeggPathways.make_df">(pypath.core.annot.KeggPathways method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.KeggPathwaysPC.html#pypath.core.annot.KeggPathwaysPC.make_df">(pypath.core.annot.KeggPathwaysPC method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Kinasedotcom.html#pypath.core.annot.Kinasedotcom.make_df">(pypath.core.annot.Kinasedotcom method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Kirouac2010.html#pypath.core.annot.Kirouac2010.make_df">(pypath.core.annot.Kirouac2010 method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Lambert2018.html#pypath.core.annot.Lambert2018.make_df">(pypath.core.annot.Lambert2018 method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.LigandReceptor.html#pypath.core.annot.LigandReceptor.make_df">(pypath.core.annot.LigandReceptor method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Locate.html#pypath.core.annot.Locate.make_df">(pypath.core.annot.Locate method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Lrdb.html#pypath.core.annot.Lrdb.make_df">(pypath.core.annot.Lrdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Matrisome.html#pypath.core.annot.Matrisome.make_df">(pypath.core.annot.Matrisome method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Matrixdb.html#pypath.core.annot.Matrixdb.make_df">(pypath.core.annot.Matrixdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Mcam.html#pypath.core.annot.Mcam.make_df">(pypath.core.annot.Mcam method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Membranome.html#pypath.core.annot.Membranome.make_df">(pypath.core.annot.Membranome method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Msigdb.html#pypath.core.annot.Msigdb.make_df">(pypath.core.annot.Msigdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.NetpathPathways.html#pypath.core.annot.NetpathPathways.make_df">(pypath.core.annot.NetpathPathways method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Opm.html#pypath.core.annot.Opm.make_df">(pypath.core.annot.Opm method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Panglaodb.html#pypath.core.annot.Panglaodb.make_df">(pypath.core.annot.Panglaodb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Phobius.html#pypath.core.annot.Phobius.make_df">(pypath.core.annot.Phobius method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Phosphatome.html#pypath.core.annot.Phosphatome.make_df">(pypath.core.annot.Phosphatome method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Progeny.html#pypath.core.annot.Progeny.make_df">(pypath.core.annot.Progeny method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Ramilowski2015.html#pypath.core.annot.Ramilowski2015.make_df">(pypath.core.annot.Ramilowski2015 method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Ramilowski2015Location.html#pypath.core.annot.Ramilowski2015Location.make_df">(pypath.core.annot.Ramilowski2015Location method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Scconnect.html#pypath.core.annot.Scconnect.make_df">(pypath.core.annot.Scconnect method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.ScconnectComplex.html#pypath.core.annot.ScconnectComplex.make_df">(pypath.core.annot.ScconnectComplex method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.SignalinkFunctions.html#pypath.core.annot.SignalinkFunctions.make_df">(pypath.core.annot.SignalinkFunctions method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.SignalinkPathways.html#pypath.core.annot.SignalinkPathways.make_df">(pypath.core.annot.SignalinkPathways method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.SignorPathways.html#pypath.core.annot.SignorPathways.make_df">(pypath.core.annot.SignorPathways method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Surfaceome.html#pypath.core.annot.Surfaceome.make_df">(pypath.core.annot.Surfaceome method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Talklr.html#pypath.core.annot.Talklr.make_df">(pypath.core.annot.Talklr method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Tcdb.html#pypath.core.annot.Tcdb.make_df">(pypath.core.annot.Tcdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Tfcensus.html#pypath.core.annot.Tfcensus.make_df">(pypath.core.annot.Tfcensus method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Topdb.html#pypath.core.annot.Topdb.make_df">(pypath.core.annot.Topdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.UniprotFamilies.html#pypath.core.annot.UniprotFamilies.make_df">(pypath.core.annot.UniprotFamilies method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.UniprotKeywords.html#pypath.core.annot.UniprotKeywords.make_df">(pypath.core.annot.UniprotKeywords method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.UniprotLocations.html#pypath.core.annot.UniprotLocations.make_df">(pypath.core.annot.UniprotLocations method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.UniprotTissues.html#pypath.core.annot.UniprotTissues.make_df">(pypath.core.annot.UniprotTissues method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.UniprotTopologies.html#pypath.core.annot.UniprotTopologies.make_df">(pypath.core.annot.UniprotTopologies method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Vesiclepedia.html#pypath.core.annot.Vesiclepedia.make_df">(pypath.core.annot.Vesiclepedia method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Wang.html#pypath.core.annot.Wang.make_df">(pypath.core.annot.Wang method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Zhong2015.html#pypath.core.annot.Zhong2015.make_df">(pypath.core.annot.Zhong2015 method)</a>
+</li>
+        <li><a href="api/pypath.core.intercell.IntercellAnnotation.html#pypath.core.intercell.IntercellAnnotation.make_df">(pypath.core.intercell.IntercellAnnotation method)</a>
+</li>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.make_df">(pypath.core.network.Network method)</a>
+</li>
+        <li><a href="api/pypath.omnipath.export.Export.html#pypath.omnipath.export.Export.make_df">(pypath.omnipath.export.Export method)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.utils.mapping.map_name.html#pypath.utils.mapping.map_name">map_name() (in module pypath.utils.mapping)</a>
+
+      <ul>
+        <li><a href="api/pypath.utils.mapping.Mapper.html#pypath.utils.mapping.Mapper.map_name">(pypath.utils.mapping.Mapper method)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.utils.mapping.map_name0.html#pypath.utils.mapping.map_name0">map_name0() (in module pypath.utils.mapping)</a>
+
+      <ul>
+        <li><a href="api/pypath.utils.mapping.Mapper.html#pypath.utils.mapping.Mapper.map_name0">(pypath.utils.mapping.Mapper method)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.utils.mapping.map_names.html#pypath.utils.mapping.map_names">map_names() (in module pypath.utils.mapping)</a>
+
+      <ul>
+        <li><a href="api/pypath.utils.mapping.Mapper.html#pypath.utils.mapping.Mapper.map_names">(pypath.utils.mapping.Mapper method)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.utils.mapping.Mapper.html#pypath.utils.mapping.Mapper">Mapper (class in pypath.utils.mapping)</a>
+</li>
+      <li><a href="api/pypath.inputs.hmdb.common.mapping.html#pypath.inputs.hmdb.common.mapping">mapping() (in module pypath.inputs.hmdb.common)</a>
+
+      <ul>
+        <li><a href="api/pypath.inputs.hmdb.metabolites.mapping.html#pypath.inputs.hmdb.metabolites.mapping">(in module pypath.inputs.hmdb.metabolites)</a>
+</li>
+        <li><a href="api/pypath.inputs.hmdb.proteins.mapping.html#pypath.inputs.hmdb.proteins.mapping">(in module pypath.inputs.hmdb.proteins)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.utils.mapping.MapReader.html#pypath.utils.mapping.MapReader.mapping_table_a_to_b">mapping_table_a_to_b (pypath.utils.mapping.MapReader property)</a>
+</li>
+      <li><a href="api/pypath.utils.mapping.MapReader.html#pypath.utils.mapping.MapReader.mapping_table_b_to_a">mapping_table_b_to_a (pypath.utils.mapping.MapReader property)</a>
+</li>
+      <li><a href="api/pypath.utils.mapping.mapping_tables.html#pypath.utils.mapping.mapping_tables">mapping_tables() (in module pypath.utils.mapping)</a>
+
+      <ul>
+        <li><a href="api/pypath.utils.mapping.Mapper.html#pypath.utils.mapping.Mapper.mapping_tables">(pypath.utils.mapping.Mapper static method)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.internals.input_formats.MappingInput.html#pypath.internals.input_formats.MappingInput">MappingInput (class in pypath.internals.input_formats)</a>
+</li>
+      <li><a href="api/pypath.utils.mapping.MappingTable.html#pypath.utils.mapping.MappingTable">MappingTable (class in pypath.utils.mapping)</a>
+</li>
+      <li><a href="api/pypath.utils.mapping.MappingTableKey.html#pypath.utils.mapping.MappingTableKey">MappingTableKey (class in pypath.utils.mapping)</a>
+</li>
+      <li><a href="api/pypath.utils.mapping.MapReader.html#pypath.utils.mapping.MapReader">MapReader (class in pypath.utils.mapping)</a>
+</li>
+      <li><a href="api/pypath.utils.orthology.EnsemblOrthology.html#pypath.utils.orthology.EnsemblOrthology.match">match() (pypath.utils.orthology.EnsemblOrthology method)</a>
+
+      <ul>
+        <li><a href="api/pypath.utils.orthology.OmaOrthology.html#pypath.utils.orthology.OmaOrthology.match">(pypath.utils.orthology.OmaOrthology method)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.annot.Matrisome.html#pypath.core.annot.Matrisome">Matrisome (class in pypath.core.annot)</a>
+</li>
+      <li><a href="api/pypath.inputs.matrisome.matrisome_annotations.html#pypath.inputs.matrisome.matrisome_annotations">matrisome_annotations() (in module pypath.inputs.matrisome)</a>
+</li>
+      <li><a href="api/pypath.core.annot.Matrixdb.html#pypath.core.annot.Matrixdb">Matrixdb (class in pypath.core.annot)</a>
+</li>
+      <li><a href="api/pypath.inputs.matrixdb.matrixdb_annotations.html#pypath.inputs.matrixdb.matrixdb_annotations">matrixdb_annotations() (in module pypath.inputs.matrixdb)</a>
+</li>
+      <li><a href="api/pypath.inputs.matrixdb.matrixdb_ecm_proteins.html#pypath.inputs.matrixdb.matrixdb_ecm_proteins">matrixdb_ecm_proteins() (in module pypath.inputs.matrixdb)</a>
+</li>
+      <li><a href="api/pypath.inputs.matrixdb.matrixdb_interactions.html#pypath.inputs.matrixdb.matrixdb_interactions">matrixdb_interactions() (in module pypath.inputs.matrixdb)</a>
+</li>
+      <li><a href="api/pypath.inputs.matrixdb.matrixdb_membrane_proteins.html#pypath.inputs.matrixdb.matrixdb_membrane_proteins">matrixdb_membrane_proteins() (in module pypath.inputs.matrixdb)</a>
+</li>
+      <li><a href="api/pypath.inputs.matrixdb.matrixdb_secreted_proteins.html#pypath.inputs.matrixdb.matrixdb_secreted_proteins">matrixdb_secreted_proteins() (in module pypath.inputs.matrixdb)</a>
+</li>
+      <li><a href="api/pypath.core.annot.Mcam.html#pypath.core.annot.Mcam">Mcam (class in pypath.core.annot)</a>
+</li>
+      <li><a href="api/pypath.inputs.mcam.mcam_cell_adhesion_molecules.html#pypath.inputs.mcam.mcam_cell_adhesion_molecules">mcam_cell_adhesion_molecules() (in module pypath.inputs.mcam)</a>
+</li>
+      <li><a href="api/pypath.inputs.adrecs.AdrecsTerm.html#pypath.inputs.adrecs.AdrecsTerm.meddra">meddra (pypath.inputs.adrecs.AdrecsTerm attribute)</a>
+</li>
+      <li><a href="api/pypath.inputs.sider.SiderSideeffectMeddra.html#pypath.inputs.sider.SiderSideeffectMeddra.meddra_id">meddra_id (pypath.inputs.sider.SiderSideeffectMeddra attribute)</a>
+</li>
+      <li><a href="api/pypath.core.annot.Membranome.html#pypath.core.annot.Membranome">Membranome (class in pypath.core.annot)</a>
+</li>
+      <li><a href="api/pypath.inputs.membranome.membranome_annotations.html#pypath.inputs.membranome.membranome_annotations">membranome_annotations() (in module pypath.inputs.membranome)</a>
+</li>
+      <li><a href="api/pypath.core.evidence.Evidence.html#pypath.core.evidence.Evidence.merge">merge() (pypath.core.evidence.Evidence method)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.merge">(pypath.core.interaction.Interaction method)</a>
+</li>
+        <li><a href="api/pypath.internals.intera.Complex.html#pypath.internals.intera.Complex.merge">(pypath.internals.intera.Complex method)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.utils.pyreact.PyReact.html#pypath.utils.pyreact.PyReact.merge_complexes">merge_complexes() (pypath.utils.pyreact.PyReact method)</a>
+</li>
+      <li><a href="api/pypath.utils.pyreact.PyReact.html#pypath.utils.pyreact.PyReact.merge_cvariations">merge_cvariations() (pypath.utils.pyreact.PyReact method)</a>
+</li>
+      <li><a href="api/pypath.inputs.adrecs.AdrecsDrug.html#pypath.inputs.adrecs.AdrecsDrug.mesh">mesh (pypath.inputs.adrecs.AdrecsDrug attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.NetworkStatsRecord.html#pypath.core.network.NetworkStatsRecord.method">method (pypath.core.network.NetworkStatsRecord attribute)</a>
+</li>
+      <li><a href="api/pypath.inputs.gutmgene.GutmgeneAnnotation.html#pypath.inputs.gutmgene.GutmgeneAnnotation.microbe_ncbi_tax_id">microbe_ncbi_tax_id (pypath.inputs.gutmgene.GutmgeneAnnotation attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.inputs.gutmgene.GutmgeneRaw.html#pypath.inputs.gutmgene.GutmgeneRaw.microbe_ncbi_tax_id">(pypath.inputs.gutmgene.GutmgeneRaw attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.inputs.gutmgene.GutmgeneAnnotation.html#pypath.inputs.gutmgene.GutmgeneAnnotation.microbe_taxon">microbe_taxon (pypath.inputs.gutmgene.GutmgeneAnnotation attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.inputs.gutmgene.GutmgeneRaw.html#pypath.inputs.gutmgene.GutmgeneRaw.microbe_taxon">(pypath.inputs.gutmgene.GutmgeneRaw attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.inputs.mimp.mimp_enzyme_substrate.html#pypath.inputs.mimp.mimp_enzyme_substrate">mimp_enzyme_substrate() (in module pypath.inputs.mimp)</a>
+</li>
+      <li><a href="api/pypath.inputs.mimp.mimp_interactions.html#pypath.inputs.mimp.mimp_interactions">mimp_interactions() (in module pypath.inputs.mimp)</a>
+</li>
+      <li><a href="api/pypath.inputs.mir2disease.mir2disease_interactions.html#pypath.inputs.mir2disease.mir2disease_interactions">mir2disease_interactions() (in module pypath.inputs.mir2disease)</a>
+</li>
+      <li><a href="api/pypath.inputs.mirbase.mirbase_ids.html#pypath.inputs.mirbase.mirbase_ids">mirbase_ids() (in module pypath.inputs.mirbase)</a>
+</li>
+      <li><a href="api/pypath.inputs.mirbase.mirbase_mature.html#pypath.inputs.mirbase.mirbase_mature">mirbase_mature() (in module pypath.inputs.mirbase)</a>
+</li>
+      <li><a href="api/pypath.inputs.mirbase.mirbase_mature_all.html#pypath.inputs.mirbase.mirbase_mature_all">mirbase_mature_all() (in module pypath.inputs.mirbase)</a>
+</li>
+      <li><a href="api/pypath.inputs.mirbase.mirbase_precursor.html#pypath.inputs.mirbase.mirbase_precursor">mirbase_precursor() (in module pypath.inputs.mirbase)</a>
+</li>
+      <li><a href="api/pypath.inputs.mirbase.mirbase_precursor_all.html#pypath.inputs.mirbase.mirbase_precursor_all">mirbase_precursor_all() (in module pypath.inputs.mirbase)</a>
+</li>
+      <li><a href="api/pypath.inputs.mirbase.mirbase_precursor_to_mature.html#pypath.inputs.mirbase.mirbase_precursor_to_mature">mirbase_precursor_to_mature() (in module pypath.inputs.mirbase)</a>
+</li>
+      <li><a href="api/pypath.inputs.mirdeathdb.mirdeathdb_interactions.html#pypath.inputs.mirdeathdb.mirdeathdb_interactions">mirdeathdb_interactions() (in module pypath.inputs.mirdeathdb)</a>
+</li>
+      <li><a href="api/pypath.inputs.mirecords.mirecords_interactions.html#pypath.inputs.mirecords.mirecords_interactions">mirecords_interactions() (in module pypath.inputs.mirecords)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.mirna_identifiers_by_data_model">mirna_identifiers_by_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.mirna_identifiers_by_data_model">mirna_identifiers_by_data_model() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.mirna_identifiers_by_interaction_type">mirna_identifiers_by_interaction_type (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.mirna_identifiers_by_interaction_type">mirna_identifiers_by_interaction_type() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.mirna_identifiers_by_interaction_type_and_data_model">mirna_identifiers_by_interaction_type_and_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.mirna_identifiers_by_interaction_type_and_data_model">mirna_identifiers_by_interaction_type_and_data_model() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.mirna_identifiers_by_interaction_type_and_data_model_and_resource">mirna_identifiers_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.mirna_identifiers_by_interaction_type_and_data_model_and_resource">mirna_identifiers_by_interaction_type_and_data_model_and_resource() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.mirna_identifiers_by_reference">mirna_identifiers_by_reference (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.mirna_identifiers_by_reference">mirna_identifiers_by_reference() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.mirna_identifiers_by_resource">mirna_identifiers_by_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.mirna_identifiers_by_resource">mirna_identifiers_by_resource() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.mirna_labels_by_data_model">mirna_labels_by_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.mirna_labels_by_data_model">mirna_labels_by_data_model() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.mirna_labels_by_interaction_type">mirna_labels_by_interaction_type (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.mirna_labels_by_interaction_type">mirna_labels_by_interaction_type() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.mirna_labels_by_interaction_type_and_data_model">mirna_labels_by_interaction_type_and_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.mirna_labels_by_interaction_type_and_data_model">mirna_labels_by_interaction_type_and_data_model() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.mirna_labels_by_interaction_type_and_data_model_and_resource">mirna_labels_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.mirna_labels_by_interaction_type_and_data_model_and_resource">mirna_labels_by_interaction_type_and_data_model_and_resource() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.mirna_labels_by_reference">mirna_labels_by_reference (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.mirna_labels_by_reference">mirna_labels_by_reference() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.mirna_labels_by_resource">mirna_labels_by_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.mirna_labels_by_resource">mirna_labels_by_resource() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.mirna_target">mirna_target() (pypath.core.network.Network class method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.mirnas_by_data_model">mirnas_by_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.mirnas_by_data_model">mirnas_by_data_model() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.mirnas_by_interaction_type">mirnas_by_interaction_type (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.mirnas_by_interaction_type">mirnas_by_interaction_type() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.mirnas_by_interaction_type_and_data_model">mirnas_by_interaction_type_and_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.mirnas_by_interaction_type_and_data_model">mirnas_by_interaction_type_and_data_model() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.mirnas_by_interaction_type_and_data_model_and_resource">mirnas_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.mirnas_by_interaction_type_and_data_model_and_resource">mirnas_by_interaction_type_and_data_model_and_resource() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.mirnas_by_reference">mirnas_by_reference (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.mirnas_by_reference">mirnas_by_reference() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.mirnas_by_resource">mirnas_by_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.mirnas_by_resource">mirnas_by_resource() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.inputs.mirtarbase.mirtarbase_interactions.html#pypath.inputs.mirtarbase.mirtarbase_interactions">mirtarbase_interactions() (in module pypath.inputs.mirtarbase)</a>
+</li>
+      <li><a href="api/pypath.inputs.mitab.mitab_field_list.html#pypath.inputs.mitab.mitab_field_list">mitab_field_list() (in module pypath.inputs.mitab)</a>
+</li>
+      <li><a href="api/pypath.inputs.mitab.mitab_field_uniprot.html#pypath.inputs.mitab.mitab_field_uniprot">mitab_field_uniprot() (in module pypath.inputs.mitab)</a>
+</li>
+      <li>
+    module
+
+      <ul>
+        <li><a href="api/pypath.html#module-pypath">pypath</a>
+</li>
+        <li><a href="api/pypath.core.html#module-pypath.core">pypath.core</a>
+</li>
+        <li><a href="api/pypath.core.annot.html#module-pypath.core.annot">pypath.core.annot</a>
+</li>
+        <li><a href="api/pypath.core.attrs.html#module-pypath.core.attrs">pypath.core.attrs</a>
+</li>
+        <li><a href="api/pypath.core.common.html#module-pypath.core.common">pypath.core.common</a>
+</li>
+        <li><a href="api/pypath.core.complex.html#module-pypath.core.complex">pypath.core.complex</a>
+</li>
+        <li><a href="api/pypath.core.entity.html#module-pypath.core.entity">pypath.core.entity</a>
+</li>
+        <li><a href="api/pypath.core.enz_sub.html#module-pypath.core.enz_sub">pypath.core.enz_sub</a>
+</li>
+        <li><a href="api/pypath.core.evidence.html#module-pypath.core.evidence">pypath.core.evidence</a>
+</li>
+        <li><a href="api/pypath.core.interaction.html#module-pypath.core.interaction">pypath.core.interaction</a>
+</li>
+        <li><a href="api/pypath.core.intercell.html#module-pypath.core.intercell">pypath.core.intercell</a>
+</li>
+        <li><a href="api/pypath.core.intercell_annot.html#module-pypath.core.intercell_annot">pypath.core.intercell_annot</a>
+</li>
+        <li><a href="api/pypath.core.network.html#module-pypath.core.network">pypath.core.network</a>
+</li>
+        <li><a href="api/pypath.data.html#module-pypath.data">pypath.data</a>
+</li>
+        <li><a href="api/pypath.inputs.html#module-pypath.inputs">pypath.inputs</a>
+</li>
+        <li><a href="api/pypath.inputs.abs.html#module-pypath.inputs.abs">pypath.inputs.abs</a>
+</li>
+        <li><a href="api/pypath.inputs.acsn.html#module-pypath.inputs.acsn">pypath.inputs.acsn</a>
+</li>
+        <li><a href="api/pypath.inputs.adhesome.html#module-pypath.inputs.adhesome">pypath.inputs.adhesome</a>
+</li>
+        <li><a href="api/pypath.inputs.adrecs.html#module-pypath.inputs.adrecs">pypath.inputs.adrecs</a>
+</li>
+        <li><a href="api/pypath.inputs.almen2009.html#module-pypath.inputs.almen2009">pypath.inputs.almen2009</a>
+</li>
+        <li><a href="api/pypath.inputs.baccin2019.html#module-pypath.inputs.baccin2019">pypath.inputs.baccin2019</a>
+</li>
+        <li><a href="api/pypath.inputs.biogps.html#module-pypath.inputs.biogps">pypath.inputs.biogps</a>
+</li>
+        <li><a href="api/pypath.inputs.biogrid.html#module-pypath.inputs.biogrid">pypath.inputs.biogrid</a>
+</li>
+        <li><a href="api/pypath.inputs.biomart.html#module-pypath.inputs.biomart">pypath.inputs.biomart</a>
+</li>
+        <li><a href="api/pypath.inputs.biomodels.html#module-pypath.inputs.biomodels">pypath.inputs.biomodels</a>
+</li>
+        <li><a href="api/pypath.inputs.ca1.html#module-pypath.inputs.ca1">pypath.inputs.ca1</a>
+</li>
+        <li><a href="api/pypath.inputs.cancercellmap.html#module-pypath.inputs.cancercellmap">pypath.inputs.cancercellmap</a>
+</li>
+        <li><a href="api/pypath.inputs.cancerdrugsdb.html#module-pypath.inputs.cancerdrugsdb">pypath.inputs.cancerdrugsdb</a>
+</li>
+        <li><a href="api/pypath.inputs.cancersea.html#module-pypath.inputs.cancersea">pypath.inputs.cancersea</a>
+</li>
+        <li><a href="api/pypath.inputs.cell.html#module-pypath.inputs.cell">pypath.inputs.cell</a>
+</li>
+        <li><a href="api/pypath.inputs.cellcall.html#module-pypath.inputs.cellcall">pypath.inputs.cellcall</a>
+</li>
+        <li><a href="api/pypath.inputs.cellcellinteractions.html#module-pypath.inputs.cellcellinteractions">pypath.inputs.cellcellinteractions</a>
+</li>
+        <li><a href="api/pypath.inputs.cellchatdb.html#module-pypath.inputs.cellchatdb">pypath.inputs.cellchatdb</a>
+</li>
+        <li><a href="api/pypath.inputs.cellinker.html#module-pypath.inputs.cellinker">pypath.inputs.cellinker</a>
+</li>
+        <li><a href="api/pypath.inputs.cellphonedb.html#module-pypath.inputs.cellphonedb">pypath.inputs.cellphonedb</a>
+</li>
+        <li><a href="api/pypath.inputs.celltalkdb.html#module-pypath.inputs.celltalkdb">pypath.inputs.celltalkdb</a>
+</li>
+        <li><a href="api/pypath.inputs.celltypist.html#module-pypath.inputs.celltypist">pypath.inputs.celltypist</a>
+</li>
+        <li><a href="api/pypath.inputs.chembl.html#module-pypath.inputs.chembl">pypath.inputs.chembl</a>
+</li>
+        <li><a href="api/pypath.inputs.clinvar.html#module-pypath.inputs.clinvar">pypath.inputs.clinvar</a>
+</li>
+        <li><a href="api/pypath.inputs.collectri.html#module-pypath.inputs.collectri">pypath.inputs.collectri</a>
+</li>
+        <li><a href="api/pypath.inputs.common.html#module-pypath.inputs.common">pypath.inputs.common</a>
+</li>
+        <li><a href="api/pypath.inputs.compath.html#module-pypath.inputs.compath">pypath.inputs.compath</a>
+</li>
+        <li><a href="api/pypath.inputs.compleat.html#module-pypath.inputs.compleat">pypath.inputs.compleat</a>
+</li>
+        <li><a href="api/pypath.inputs.complexportal.html#module-pypath.inputs.complexportal">pypath.inputs.complexportal</a>
+</li>
+        <li><a href="api/pypath.inputs.comppi.html#module-pypath.inputs.comppi">pypath.inputs.comppi</a>
+</li>
+        <li><a href="api/pypath.inputs.connectomedb.html#module-pypath.inputs.connectomedb">pypath.inputs.connectomedb</a>
+</li>
+        <li><a href="api/pypath.inputs.corum.html#module-pypath.inputs.corum">pypath.inputs.corum</a>
+</li>
+        <li><a href="api/pypath.inputs.cosmic.html#module-pypath.inputs.cosmic">pypath.inputs.cosmic</a>
+</li>
+        <li><a href="api/pypath.inputs.cpad.html#module-pypath.inputs.cpad">pypath.inputs.cpad</a>
+</li>
+        <li><a href="api/pypath.inputs.cpdb.html#module-pypath.inputs.cpdb">pypath.inputs.cpdb</a>
+</li>
+        <li><a href="api/pypath.inputs.credentials.html#module-pypath.inputs.credentials">pypath.inputs.credentials</a>
+</li>
+        <li><a href="api/pypath.inputs.csa.html#module-pypath.inputs.csa">pypath.inputs.csa</a>
+</li>
+        <li><a href="api/pypath.inputs.cspa.html#module-pypath.inputs.cspa">pypath.inputs.cspa</a>
+</li>
+        <li><a href="api/pypath.inputs.ctdbase.html#module-pypath.inputs.ctdbase">pypath.inputs.ctdbase</a>
+</li>
+        <li><a href="api/pypath.inputs.cytosig.html#module-pypath.inputs.cytosig">pypath.inputs.cytosig</a>
+</li>
+        <li><a href="api/pypath.inputs.dbptm.html#module-pypath.inputs.dbptm">pypath.inputs.dbptm</a>
+</li>
+        <li><a href="api/pypath.inputs.ddinter.html#module-pypath.inputs.ddinter">pypath.inputs.ddinter</a>
+</li>
+        <li><a href="api/pypath.inputs.deathdomain.html#module-pypath.inputs.deathdomain">pypath.inputs.deathdomain</a>
+</li>
+        <li><a href="api/pypath.inputs.depod.html#module-pypath.inputs.depod">pypath.inputs.depod</a>
+</li>
+        <li><a href="api/pypath.inputs.dgidb.html#module-pypath.inputs.dgidb">pypath.inputs.dgidb</a>
+</li>
+        <li><a href="api/pypath.inputs.dip.html#module-pypath.inputs.dip">pypath.inputs.dip</a>
+</li>
+        <li><a href="api/pypath.inputs.diseases.html#module-pypath.inputs.diseases">pypath.inputs.diseases</a>
+</li>
+        <li><a href="api/pypath.inputs.domino.html#module-pypath.inputs.domino">pypath.inputs.domino</a>
+</li>
+        <li><a href="api/pypath.inputs.dorothea.html#module-pypath.inputs.dorothea">pypath.inputs.dorothea</a>
+</li>
+        <li><a href="api/pypath.inputs.drugbank.html#module-pypath.inputs.drugbank">pypath.inputs.drugbank</a>
+</li>
+        <li><a href="api/pypath.inputs.drugcentral.html#module-pypath.inputs.drugcentral">pypath.inputs.drugcentral</a>
+</li>
+        <li><a href="api/pypath.inputs.ebi.html#module-pypath.inputs.ebi">pypath.inputs.ebi</a>
+</li>
+        <li><a href="api/pypath.inputs.elm.html#module-pypath.inputs.elm">pypath.inputs.elm</a>
+</li>
+        <li><a href="api/pypath.inputs.embopress.html#module-pypath.inputs.embopress">pypath.inputs.embopress</a>
+</li>
+        <li><a href="api/pypath.inputs.embrace.html#module-pypath.inputs.embrace">pypath.inputs.embrace</a>
+</li>
+        <li><a href="api/pypath.inputs.encode.html#module-pypath.inputs.encode">pypath.inputs.encode</a>
+</li>
+        <li><a href="api/pypath.inputs.ensembl.html#module-pypath.inputs.ensembl">pypath.inputs.ensembl</a>
+</li>
+        <li><a href="api/pypath.inputs.eutils.html#module-pypath.inputs.eutils">pypath.inputs.eutils</a>
+</li>
+        <li><a href="api/pypath.inputs.exocarta.html#module-pypath.inputs.exocarta">pypath.inputs.exocarta</a>
+</li>
+        <li><a href="api/pypath.inputs.expasy.html#module-pypath.inputs.expasy">pypath.inputs.expasy</a>
+</li>
+        <li><a href="api/pypath.inputs.genecards.html#module-pypath.inputs.genecards">pypath.inputs.genecards</a>
+</li>
+        <li><a href="api/pypath.inputs.go.html#module-pypath.inputs.go">pypath.inputs.go</a>
+</li>
+        <li><a href="api/pypath.inputs.gpcrdb.html#module-pypath.inputs.gpcrdb">pypath.inputs.gpcrdb</a>
+</li>
+        <li><a href="api/pypath.inputs.graphviz.html#module-pypath.inputs.graphviz">pypath.inputs.graphviz</a>
+</li>
+        <li><a href="api/pypath.inputs.guide2pharma.html#module-pypath.inputs.guide2pharma">pypath.inputs.guide2pharma</a>
+</li>
+        <li><a href="api/pypath.inputs.gutmgene.html#module-pypath.inputs.gutmgene">pypath.inputs.gutmgene</a>
+</li>
+        <li><a href="api/pypath.inputs.havugimana.html#module-pypath.inputs.havugimana">pypath.inputs.havugimana</a>
+</li>
+        <li><a href="api/pypath.inputs.hgnc.html#module-pypath.inputs.hgnc">pypath.inputs.hgnc</a>
+</li>
+        <li><a href="api/pypath.inputs.hippie.html#module-pypath.inputs.hippie">pypath.inputs.hippie</a>
+</li>
+        <li><a href="api/pypath.inputs.hmdb.html#module-pypath.inputs.hmdb">pypath.inputs.hmdb</a>
+</li>
+        <li><a href="api/pypath.inputs.hmdb.common.html#module-pypath.inputs.hmdb.common">pypath.inputs.hmdb.common</a>
+</li>
+        <li><a href="api/pypath.inputs.hmdb.metabolites.html#module-pypath.inputs.hmdb.metabolites">pypath.inputs.hmdb.metabolites</a>
+</li>
+        <li><a href="api/pypath.inputs.hmdb.proteins.html#module-pypath.inputs.hmdb.proteins">pypath.inputs.hmdb.proteins</a>
+</li>
+        <li><a href="api/pypath.inputs.hmdb.schema.html#module-pypath.inputs.hmdb.schema">pypath.inputs.hmdb.schema</a>
+</li>
+        <li><a href="api/pypath.inputs.hmdb.schema.common.html#module-pypath.inputs.hmdb.schema.common">pypath.inputs.hmdb.schema.common</a>
+</li>
+        <li><a href="api/pypath.inputs.hmdb.schema.metabolites.html#module-pypath.inputs.hmdb.schema.metabolites">pypath.inputs.hmdb.schema.metabolites</a>
+</li>
+        <li><a href="api/pypath.inputs.hmdb.schema.proteins.html#module-pypath.inputs.hmdb.schema.proteins">pypath.inputs.hmdb.schema.proteins</a>
+</li>
+        <li><a href="api/pypath.inputs.hmdb.structures.html#module-pypath.inputs.hmdb.structures">pypath.inputs.hmdb.structures</a>
+</li>
+        <li><a href="api/pypath.inputs.hmdb.visual.html#module-pypath.inputs.hmdb.visual">pypath.inputs.hmdb.visual</a>
+</li>
+        <li><a href="api/pypath.inputs.hmdb.xml.html#module-pypath.inputs.hmdb.xml">pypath.inputs.hmdb.xml</a>
+</li>
+        <li><a href="api/pypath.inputs.homologene.html#module-pypath.inputs.homologene">pypath.inputs.homologene</a>
+</li>
+        <li><a href="api/pypath.inputs.hpmr.html#module-pypath.inputs.hpmr">pypath.inputs.hpmr</a>
+</li>
+        <li><a href="api/pypath.inputs.hpo.html#module-pypath.inputs.hpo">pypath.inputs.hpo</a>
+</li>
+        <li><a href="api/pypath.inputs.hprd.html#module-pypath.inputs.hprd">pypath.inputs.hprd</a>
+</li>
+        <li><a href="api/pypath.inputs.htri.html#module-pypath.inputs.htri">pypath.inputs.htri</a>
+</li>
+        <li><a href="api/pypath.inputs.humancellmap.html#module-pypath.inputs.humancellmap">pypath.inputs.humancellmap</a>
+</li>
+        <li><a href="api/pypath.inputs.humap.html#module-pypath.inputs.humap">pypath.inputs.humap</a>
+</li>
+        <li><a href="api/pypath.inputs.humsavar.html#module-pypath.inputs.humsavar">pypath.inputs.humsavar</a>
+</li>
+        <li><a href="api/pypath.inputs.huri.html#module-pypath.inputs.huri">pypath.inputs.huri</a>
+</li>
+        <li><a href="api/pypath.inputs.i3d.html#module-pypath.inputs.i3d">pypath.inputs.i3d</a>
+</li>
+        <li><a href="api/pypath.inputs.icellnet.html#module-pypath.inputs.icellnet">pypath.inputs.icellnet</a>
+</li>
+        <li><a href="api/pypath.inputs.ielm.html#module-pypath.inputs.ielm">pypath.inputs.ielm</a>
+</li>
+        <li><a href="api/pypath.inputs.imweb.html#module-pypath.inputs.imweb">pypath.inputs.imweb</a>
+</li>
+        <li><a href="api/pypath.inputs.innatedb.html#module-pypath.inputs.innatedb">pypath.inputs.innatedb</a>
+</li>
+        <li><a href="api/pypath.inputs.instruct.html#module-pypath.inputs.instruct">pypath.inputs.instruct</a>
+</li>
+        <li><a href="api/pypath.inputs.intact.html#module-pypath.inputs.intact">pypath.inputs.intact</a>
+</li>
+        <li><a href="api/pypath.inputs.integrins.html#module-pypath.inputs.integrins">pypath.inputs.integrins</a>
+</li>
+        <li><a href="api/pypath.inputs.interpro.html#module-pypath.inputs.interpro">pypath.inputs.interpro</a>
+</li>
+        <li><a href="api/pypath.inputs.intogen.html#module-pypath.inputs.intogen">pypath.inputs.intogen</a>
+</li>
+        <li><a href="api/pypath.inputs.ipi.html#module-pypath.inputs.ipi">pypath.inputs.ipi</a>
+</li>
+        <li><a href="api/pypath.inputs.iptmnet.html#module-pypath.inputs.iptmnet">pypath.inputs.iptmnet</a>
+</li>
+        <li><a href="api/pypath.inputs.italk.html#module-pypath.inputs.italk">pypath.inputs.italk</a>
+</li>
+        <li><a href="api/pypath.inputs.kea.html#module-pypath.inputs.kea">pypath.inputs.kea</a>
+</li>
+        <li><a href="api/pypath.inputs.kegg.html#module-pypath.inputs.kegg">pypath.inputs.kegg</a>
+</li>
+        <li><a href="api/pypath.inputs.kegg_api.html#module-pypath.inputs.kegg_api">pypath.inputs.kegg_api</a>
+</li>
+        <li><a href="api/pypath.inputs.kinasedotcom.html#module-pypath.inputs.kinasedotcom">pypath.inputs.kinasedotcom</a>
+</li>
+        <li><a href="api/pypath.inputs.kirouac2010.html#module-pypath.inputs.kirouac2010">pypath.inputs.kirouac2010</a>
+</li>
+        <li><a href="api/pypath.inputs.lambert2018.html#module-pypath.inputs.lambert2018">pypath.inputs.lambert2018</a>
+</li>
+        <li><a href="api/pypath.inputs.laudanna.html#module-pypath.inputs.laudanna">pypath.inputs.laudanna</a>
+</li>
+        <li><a href="api/pypath.inputs.li2012.html#module-pypath.inputs.li2012">pypath.inputs.li2012</a>
+</li>
+        <li><a href="api/pypath.inputs.lincs.html#module-pypath.inputs.lincs">pypath.inputs.lincs</a>
+</li>
+        <li><a href="api/pypath.inputs.lmpid.html#module-pypath.inputs.lmpid">pypath.inputs.lmpid</a>
+</li>
+        <li><a href="api/pypath.inputs.lncdisease.html#module-pypath.inputs.lncdisease">pypath.inputs.lncdisease</a>
+</li>
+        <li><a href="api/pypath.inputs.lncrnadb.html#module-pypath.inputs.lncrnadb">pypath.inputs.lncrnadb</a>
+</li>
+        <li><a href="api/pypath.inputs.locate.html#module-pypath.inputs.locate">pypath.inputs.locate</a>
+</li>
+        <li><a href="api/pypath.inputs.lrdb.html#module-pypath.inputs.lrdb">pypath.inputs.lrdb</a>
+</li>
+        <li><a href="api/pypath.inputs.macrophage.html#module-pypath.inputs.macrophage">pypath.inputs.macrophage</a>
+</li>
+        <li><a href="api/pypath.inputs.main.html#module-pypath.inputs.main">pypath.inputs.main</a>
+</li>
+        <li><a href="api/pypath.inputs.matrisome.html#module-pypath.inputs.matrisome">pypath.inputs.matrisome</a>
+</li>
+        <li><a href="api/pypath.inputs.matrixdb.html#module-pypath.inputs.matrixdb">pypath.inputs.matrixdb</a>
+</li>
+        <li><a href="api/pypath.inputs.mcam.html#module-pypath.inputs.mcam">pypath.inputs.mcam</a>
+</li>
+        <li><a href="api/pypath.inputs.membranome.html#module-pypath.inputs.membranome">pypath.inputs.membranome</a>
+</li>
+        <li><a href="api/pypath.inputs.mimp.html#module-pypath.inputs.mimp">pypath.inputs.mimp</a>
+</li>
+        <li><a href="api/pypath.inputs.mir2disease.html#module-pypath.inputs.mir2disease">pypath.inputs.mir2disease</a>
+</li>
+        <li><a href="api/pypath.inputs.mirbase.html#module-pypath.inputs.mirbase">pypath.inputs.mirbase</a>
+</li>
+        <li><a href="api/pypath.inputs.mirdeathdb.html#module-pypath.inputs.mirdeathdb">pypath.inputs.mirdeathdb</a>
+</li>
+        <li><a href="api/pypath.inputs.mirecords.html#module-pypath.inputs.mirecords">pypath.inputs.mirecords</a>
+</li>
+        <li><a href="api/pypath.inputs.mirtarbase.html#module-pypath.inputs.mirtarbase">pypath.inputs.mirtarbase</a>
+</li>
+        <li><a href="api/pypath.inputs.mitab.html#module-pypath.inputs.mitab">pypath.inputs.mitab</a>
+</li>
+        <li><a href="api/pypath.inputs.mppi.html#module-pypath.inputs.mppi">pypath.inputs.mppi</a>
+</li>
+        <li><a href="api/pypath.inputs.msigdb.html#module-pypath.inputs.msigdb">pypath.inputs.msigdb</a>
+</li>
+        <li><a href="api/pypath.inputs.ncrdeathdb.html#module-pypath.inputs.ncrdeathdb">pypath.inputs.ncrdeathdb</a>
+</li>
+        <li><a href="api/pypath.inputs.negatome.html#module-pypath.inputs.negatome">pypath.inputs.negatome</a>
+</li>
+        <li><a href="api/pypath.inputs.netbiol.html#module-pypath.inputs.netbiol">pypath.inputs.netbiol</a>
+</li>
+        <li><a href="api/pypath.inputs.netpath.html#module-pypath.inputs.netpath">pypath.inputs.netpath</a>
+</li>
+        <li><a href="api/pypath.inputs.offsides.html#module-pypath.inputs.offsides">pypath.inputs.offsides</a>
+</li>
+        <li><a href="api/pypath.inputs.oma.html#module-pypath.inputs.oma">pypath.inputs.oma</a>
+</li>
+        <li><a href="api/pypath.inputs.ontology.html#module-pypath.inputs.ontology">pypath.inputs.ontology</a>
+</li>
+        <li><a href="api/pypath.inputs.opentargets.html#module-pypath.inputs.opentargets">pypath.inputs.opentargets</a>
+</li>
+        <li><a href="api/pypath.inputs.opm.html#module-pypath.inputs.opm">pypath.inputs.opm</a>
+</li>
+        <li><a href="api/pypath.inputs.oreganno.html#module-pypath.inputs.oreganno">pypath.inputs.oreganno</a>
+</li>
+        <li><a href="api/pypath.inputs.panglaodb.html#module-pypath.inputs.panglaodb">pypath.inputs.panglaodb</a>
+</li>
+        <li><a href="api/pypath.inputs.pathophenodb.html#module-pypath.inputs.pathophenodb">pypath.inputs.pathophenodb</a>
+</li>
+        <li><a href="api/pypath.inputs.pathwaycommons.html#module-pypath.inputs.pathwaycommons">pypath.inputs.pathwaycommons</a>
+</li>
+        <li><a href="api/pypath.inputs.pazar.html#module-pypath.inputs.pazar">pypath.inputs.pazar</a>
+</li>
+        <li><a href="api/pypath.inputs.pdb.html#module-pypath.inputs.pdb">pypath.inputs.pdb</a>
+</li>
+        <li><a href="api/pypath.inputs.pdzbase.html#module-pypath.inputs.pdzbase">pypath.inputs.pdzbase</a>
+</li>
+        <li><a href="api/pypath.inputs.pepcyber.html#module-pypath.inputs.pepcyber">pypath.inputs.pepcyber</a>
+</li>
+        <li><a href="api/pypath.inputs.pfam.html#module-pypath.inputs.pfam">pypath.inputs.pfam</a>
+</li>
+        <li><a href="api/pypath.inputs.pharos.html#module-pypath.inputs.pharos">pypath.inputs.pharos</a>
+</li>
+        <li><a href="api/pypath.inputs.phobius.html#module-pypath.inputs.phobius">pypath.inputs.phobius</a>
+</li>
+        <li><a href="api/pypath.inputs.phosphatome.html#module-pypath.inputs.phosphatome">pypath.inputs.phosphatome</a>
+</li>
+        <li><a href="api/pypath.inputs.phosphoelm.html#module-pypath.inputs.phosphoelm">pypath.inputs.phosphoelm</a>
+</li>
+        <li><a href="api/pypath.inputs.phosphonetworks.html#module-pypath.inputs.phosphonetworks">pypath.inputs.phosphonetworks</a>
+</li>
+        <li><a href="api/pypath.inputs.phosphopoint.html#module-pypath.inputs.phosphopoint">pypath.inputs.phosphopoint</a>
+</li>
+        <li><a href="api/pypath.inputs.phosphosite.html#module-pypath.inputs.phosphosite">pypath.inputs.phosphosite</a>
+</li>
+        <li><a href="api/pypath.inputs.pisa.html#module-pypath.inputs.pisa">pypath.inputs.pisa</a>
+</li>
+        <li><a href="api/pypath.inputs.pro.html#module-pypath.inputs.pro">pypath.inputs.pro</a>
+</li>
+        <li><a href="api/pypath.inputs.progeny.html#module-pypath.inputs.progeny">pypath.inputs.progeny</a>
+</li>
+        <li><a href="api/pypath.inputs.proteinatlas.html#module-pypath.inputs.proteinatlas">pypath.inputs.proteinatlas</a>
+</li>
+        <li><a href="api/pypath.inputs.proteins.html#module-pypath.inputs.proteins">pypath.inputs.proteins</a>
+</li>
+        <li><a href="api/pypath.inputs.protmapper.html#module-pypath.inputs.protmapper">pypath.inputs.protmapper</a>
+</li>
+        <li><a href="api/pypath.inputs.pubchem.html#module-pypath.inputs.pubchem">pypath.inputs.pubchem</a>
+</li>
+        <li><a href="api/pypath.inputs.pubmed.html#module-pypath.inputs.pubmed">pypath.inputs.pubmed</a>
+</li>
+        <li><a href="api/pypath.inputs.ramilowski2015.html#module-pypath.inputs.ramilowski2015">pypath.inputs.ramilowski2015</a>
+</li>
+        <li><a href="api/pypath.inputs.ramp.html#module-pypath.inputs.ramp">pypath.inputs.ramp</a>
+</li>
+        <li><a href="api/pypath.inputs.rdata.html#module-pypath.inputs.rdata">pypath.inputs.rdata</a>
+</li>
+        <li><a href="api/pypath.inputs.reaction.html#module-pypath.inputs.reaction">pypath.inputs.reaction</a>
+</li>
+        <li><a href="api/pypath.inputs.reactome.html#module-pypath.inputs.reactome">pypath.inputs.reactome</a>
+</li>
+        <li><a href="api/pypath.inputs.scconnect.html#module-pypath.inputs.scconnect">pypath.inputs.scconnect</a>
+</li>
+        <li><a href="api/pypath.inputs.science.html#module-pypath.inputs.science">pypath.inputs.science</a>
+</li>
+        <li><a href="api/pypath.inputs.sider.html#module-pypath.inputs.sider">pypath.inputs.sider</a>
+</li>
+        <li><a href="api/pypath.inputs.signalink.html#module-pypath.inputs.signalink">pypath.inputs.signalink</a>
+</li>
+        <li><a href="api/pypath.inputs.signor.html#module-pypath.inputs.signor">pypath.inputs.signor</a>
+</li>
+        <li><a href="api/pypath.inputs.spike.html#module-pypath.inputs.spike">pypath.inputs.spike</a>
+</li>
+        <li><a href="api/pypath.inputs.stitch.html#module-pypath.inputs.stitch">pypath.inputs.stitch</a>
+</li>
+        <li><a href="api/pypath.inputs.string.html#module-pypath.inputs.string">pypath.inputs.string</a>
+</li>
+        <li><a href="api/pypath.inputs.surfaceome.html#module-pypath.inputs.surfaceome">pypath.inputs.surfaceome</a>
+</li>
+        <li><a href="api/pypath.inputs.switches_elm.html#module-pypath.inputs.switches_elm">pypath.inputs.switches_elm</a>
+</li>
+        <li><a href="api/pypath.inputs.talklr.html#module-pypath.inputs.talklr">pypath.inputs.talklr</a>
+</li>
+        <li><a href="api/pypath.inputs.tcdb.html#module-pypath.inputs.tcdb">pypath.inputs.tcdb</a>
+</li>
+        <li><a href="api/pypath.inputs.tfcensus.html#module-pypath.inputs.tfcensus">pypath.inputs.tfcensus</a>
+</li>
+        <li><a href="api/pypath.inputs.threedcomplex.html#module-pypath.inputs.threedcomplex">pypath.inputs.threedcomplex</a>
+</li>
+        <li><a href="api/pypath.inputs.threedid.html#module-pypath.inputs.threedid">pypath.inputs.threedid</a>
+</li>
+        <li><a href="api/pypath.inputs.topdb.html#module-pypath.inputs.topdb">pypath.inputs.topdb</a>
+</li>
+        <li><a href="api/pypath.inputs.transmir.html#module-pypath.inputs.transmir">pypath.inputs.transmir</a>
+</li>
+        <li><a href="api/pypath.inputs.trip.html#module-pypath.inputs.trip">pypath.inputs.trip</a>
+</li>
+        <li><a href="api/pypath.inputs.trrust.html#module-pypath.inputs.trrust">pypath.inputs.trrust</a>
+</li>
+        <li><a href="api/pypath.inputs.twosides.html#module-pypath.inputs.twosides">pypath.inputs.twosides</a>
+</li>
+        <li><a href="api/pypath.inputs.unichem.html#module-pypath.inputs.unichem">pypath.inputs.unichem</a>
+</li>
+        <li><a href="api/pypath.inputs.uniprot.html#module-pypath.inputs.uniprot">pypath.inputs.uniprot</a>
+</li>
+        <li><a href="api/pypath.inputs.uniprot_db.html#module-pypath.inputs.uniprot_db">pypath.inputs.uniprot_db</a>
+</li>
+        <li><a href="api/pypath.inputs.wang.html#module-pypath.inputs.wang">pypath.inputs.wang</a>
+</li>
+        <li><a href="api/pypath.inputs.wojtowicz2020.html#module-pypath.inputs.wojtowicz2020">pypath.inputs.wojtowicz2020</a>
+</li>
+        <li><a href="api/pypath.inputs.zhong2015.html#module-pypath.inputs.zhong2015">pypath.inputs.zhong2015</a>
+</li>
+        <li><a href="api/pypath.internals.html#module-pypath.internals">pypath.internals</a>
+</li>
+        <li><a href="api/pypath.internals.annot_formats.html#module-pypath.internals.annot_formats">pypath.internals.annot_formats</a>
+</li>
+        <li><a href="api/pypath.internals.input_formats.html#module-pypath.internals.input_formats">pypath.internals.input_formats</a>
+</li>
+        <li><a href="api/pypath.internals.intera.html#module-pypath.internals.intera">pypath.internals.intera</a>
+</li>
+        <li><a href="api/pypath.internals.license.html#module-pypath.internals.license">pypath.internals.license</a>
+</li>
+        <li><a href="api/pypath.internals.maps.html#module-pypath.internals.maps">pypath.internals.maps</a>
+</li>
+        <li><a href="api/pypath.internals.refs.html#module-pypath.internals.refs">pypath.internals.refs</a>
+</li>
+        <li><a href="api/pypath.internals.resource.html#module-pypath.internals.resource">pypath.internals.resource</a>
+</li>
+        <li><a href="api/pypath.legacy.html#module-pypath.legacy">pypath.legacy</a>
+</li>
+        <li><a href="api/pypath.legacy.db_categories.html#module-pypath.legacy.db_categories">pypath.legacy.db_categories</a>
+</li>
+        <li><a href="api/pypath.omnipath.html#module-pypath.omnipath">pypath.omnipath</a>
+</li>
+        <li><a href="api/pypath.omnipath.app.html#module-pypath.omnipath.app">pypath.omnipath.app</a>
+</li>
+        <li><a href="api/pypath.omnipath.databases.html#module-pypath.omnipath.databases">pypath.omnipath.databases</a>
+</li>
+        <li><a href="api/pypath.omnipath.databases.define.html#module-pypath.omnipath.databases.define">pypath.omnipath.databases.define</a>
+</li>
+        <li><a href="api/pypath.omnipath.export.html#module-pypath.omnipath.export">pypath.omnipath.export</a>
+</li>
+        <li><a href="api/pypath.omnipath.param.html#module-pypath.omnipath.param">pypath.omnipath.param</a>
+</li>
+        <li><a href="api/pypath.omnipath.server.html#module-pypath.omnipath.server">pypath.omnipath.server</a>
+</li>
+        <li><a href="api/pypath.omnipath.server.build.html#module-pypath.omnipath.server.build">pypath.omnipath.server.build</a>
+</li>
+        <li><a href="api/pypath.omnipath.server.generate_about_page.html#module-pypath.omnipath.server.generate_about_page">pypath.omnipath.server.generate_about_page</a>
+</li>
+        <li><a href="api/pypath.omnipath.server.legacy.html#module-pypath.omnipath.server.legacy">pypath.omnipath.server.legacy</a>
+</li>
+        <li><a href="api/pypath.omnipath.server.run.html#module-pypath.omnipath.server.run">pypath.omnipath.server.run</a>
+</li>
+        <li><a href="api/pypath.resources.html#module-pypath.resources">pypath.resources</a>
+</li>
+        <li><a href="api/pypath.resources.controller.html#module-pypath.resources.controller">pypath.resources.controller</a>
+</li>
+        <li><a href="api/pypath.resources.data.html#module-pypath.resources.data">pypath.resources.data</a>
+</li>
+        <li><a href="api/pypath.resources.data_formats.html#module-pypath.resources.data_formats">pypath.resources.data_formats</a>
+</li>
+        <li><a href="api/pypath.resources.descriptions.html#module-pypath.resources.descriptions">pypath.resources.descriptions</a>
+</li>
+        <li><a href="api/pypath.resources.licenses.html#module-pypath.resources.licenses">pypath.resources.licenses</a>
+</li>
+        <li><a href="api/pypath.resources.network.html#module-pypath.resources.network">pypath.resources.network</a>
+</li>
+        <li><a href="api/pypath.resources.urls.html#module-pypath.resources.urls">pypath.resources.urls</a>
+</li>
+        <li><a href="api/pypath.share.html#module-pypath.share">pypath.share</a>
+</li>
+        <li><a href="api/pypath.share.cache.html#module-pypath.share.cache">pypath.share.cache</a>
+</li>
+        <li><a href="api/pypath.share.common.html#module-pypath.share.common">pypath.share.common</a>
+</li>
+        <li><a href="api/pypath.share.constants.html#module-pypath.share.constants">pypath.share.constants</a>
+</li>
+        <li><a href="api/pypath.share.curl.html#module-pypath.share.curl">pypath.share.curl</a>
+</li>
+        <li><a href="api/pypath.share.progress.html#module-pypath.share.progress">pypath.share.progress</a>
+</li>
+        <li><a href="api/pypath.share.session.html#module-pypath.share.session">pypath.share.session</a>
+</li>
+        <li><a href="api/pypath.share.settings.html#module-pypath.share.settings">pypath.share.settings</a>
+</li>
+        <li><a href="api/pypath.utils.html#module-pypath.utils">pypath.utils</a>
+</li>
+        <li><a href="api/pypath.utils.go.html#module-pypath.utils.go">pypath.utils.go</a>
+</li>
+        <li><a href="api/pypath.utils.mapping.html#module-pypath.utils.mapping">pypath.utils.mapping</a>
+</li>
+        <li><a href="api/pypath.utils.metabo.html#module-pypath.utils.metabo">pypath.utils.metabo</a>
+</li>
+        <li><a href="api/pypath.utils.orthology.html#module-pypath.utils.orthology">pypath.utils.orthology</a>
+</li>
+        <li><a href="api/pypath.utils.pdb.html#module-pypath.utils.pdb">pypath.utils.pdb</a>
+</li>
+        <li><a href="api/pypath.utils.proteomicsdb.html#module-pypath.utils.proteomicsdb">pypath.utils.proteomicsdb</a>
+</li>
+        <li><a href="api/pypath.utils.pyreact.html#module-pypath.utils.pyreact">pypath.utils.pyreact</a>
+</li>
+        <li><a href="api/pypath.utils.reflists.html#module-pypath.utils.reflists">pypath.utils.reflists</a>
+</li>
+        <li><a href="api/pypath.utils.residues.html#module-pypath.utils.residues">pypath.utils.residues</a>
+</li>
+        <li><a href="api/pypath.utils.seq.html#module-pypath.utils.seq">pypath.utils.seq</a>
+</li>
+        <li><a href="api/pypath.utils.taxonomy.html#module-pypath.utils.taxonomy">pypath.utils.taxonomy</a>
+</li>
+        <li><a href="api/pypath.utils.unichem.html#module-pypath.utils.unichem">pypath.utils.unichem</a>
+</li>
+        <li><a href="api/pypath.utils.uniprot.html#module-pypath.utils.uniprot">pypath.utils.uniprot</a>
+</li>
+        <li><a href="api/pypath.visual.html#module-pypath.visual">pypath.visual</a>
+</li>
+        <li><a href="api/pypath.visual.drawing.html#module-pypath.visual.drawing">pypath.visual.drawing</a>
+</li>
+        <li><a href="api/pypath.visual.igraph_drawing.html#module-pypath.visual.igraph_drawing">pypath.visual.igraph_drawing</a>
+</li>
+        <li><a href="api/pypath.visual.igraph_drawing.edge.html#module-pypath.visual.igraph_drawing.edge">pypath.visual.igraph_drawing.edge</a>
+</li>
+        <li><a href="api/pypath.visual.igraph_drawing.vertex.html#module-pypath.visual.igraph_drawing.vertex">pypath.visual.igraph_drawing.vertex</a>
+</li>
+      </ul></li>
+  </ul></td>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="api/pypath.internals.intera.Motif.html#pypath.internals.intera.Motif">Motif (class in pypath.internals.intera)</a>
+</li>
+      <li><a href="api/pypath.inputs.mppi.mppi_interactions.html#pypath.inputs.mppi.mppi_interactions">mppi_interactions() (in module pypath.inputs.mppi)</a>
+</li>
+      <li><a href="api/pypath.utils.orthology.OrthologMeta.html#pypath.utils.orthology.OrthologMeta.mro">mro() (pypath.utils.orthology.OrthologMeta method)</a>
+</li>
+      <li><a href="api/pypath.core.annot.Msigdb.html#pypath.core.annot.Msigdb">Msigdb (class in pypath.core.annot)</a>
+</li>
+      <li><a href="api/pypath.inputs.msigdb.msigdb_annotations.html#pypath.inputs.msigdb.msigdb_annotations">msigdb_annotations() (in module pypath.inputs.msigdb)</a>
+</li>
+      <li><a href="api/pypath.inputs.msigdb.msigdb_download.html#pypath.inputs.msigdb.msigdb_download">msigdb_download() (in module pypath.inputs.msigdb)</a>
+</li>
+      <li><a href="api/pypath.inputs.msigdb.msigdb_download_collections.html#pypath.inputs.msigdb.msigdb_download_collections">msigdb_download_collections() (in module pypath.inputs.msigdb)</a>
+</li>
+  </ul></td>
+</tr></table>
+
+<h2 id="N">N</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="api/pypath.inputs.adrecs.AdrecsTerm.html#pypath.inputs.adrecs.AdrecsTerm.name">name (pypath.inputs.adrecs.AdrecsTerm attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.inputs.pathwaycommons.PathwayCommonsResource.html#pypath.inputs.pathwaycommons.PathwayCommonsResource.name">(pypath.inputs.pathwaycommons.PathwayCommonsResource attribute)</a>
+</li>
+        <li><a href="api/pypath.inputs.sider.SiderDrug.html#pypath.inputs.sider.SiderDrug.name">(pypath.inputs.sider.SiderDrug attribute)</a>
+</li>
+        <li><a href="api/pypath.internals.annot_formats.AnnotDef.html#pypath.internals.annot_formats.AnnotDef.name">(pypath.internals.annot_formats.AnnotDef attribute)</a>
+</li>
+        <li><a href="api/pypath.internals.annot_formats.AnnotDefKey.html#pypath.internals.annot_formats.AnnotDefKey.name">(pypath.internals.annot_formats.AnnotDefKey attribute)</a>
+</li>
+        <li><a href="api/pypath.internals.resource.EnzymeSubstrateResourceKey.html#pypath.internals.resource.EnzymeSubstrateResourceKey.name">(pypath.internals.resource.EnzymeSubstrateResourceKey attribute)</a>
+</li>
+        <li><a href="api/pypath.internals.resource.NetworkResourceKey.html#pypath.internals.resource.NetworkResourceKey.name">(pypath.internals.resource.NetworkResourceKey attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.inputs.uniprot.UniprotQuery.html#pypath.inputs.uniprot.UniprotQuery.name_process">name_process (pypath.inputs.uniprot.UniprotQuery attribute)</a>
+</li>
+      <li><a href="api/pypath.utils.go.GeneOntology.html#pypath.utils.go.GeneOntology.names_to_terms">names_to_terms() (pypath.utils.go.GeneOntology method)</a>
+</li>
+      <li><a href="api/pypath.utils.go.GeneOntology.html#pypath.utils.go.GeneOntology.names_to_terms_aspects">names_to_terms_aspects() (pypath.utils.go.GeneOntology method)</a>
+</li>
+      <li><a href="api/pypath.inputs.uniprot.Taxon.html#pypath.inputs.uniprot.Taxon.ncbi_id">ncbi_id (pypath.inputs.uniprot.Taxon attribute)</a>
+</li>
+      <li><a href="api/pypath.utils.mapping.MappingTableKey.html#pypath.utils.mapping.MappingTableKey.ncbi_tax_id">ncbi_tax_id (pypath.utils.mapping.MappingTableKey attribute)</a>
+</li>
+      <li><a href="api/pypath.inputs.ncrdeathdb.ncrdeathdb_interactions.html#pypath.inputs.ncrdeathdb.ncrdeathdb_interactions">ncrdeathdb_interactions() (in module pypath.inputs.ncrdeathdb)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.negative_a_b">negative_a_b() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.negative_b_a">negative_b_a() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.negative_resources_a_b">negative_resources_a_b() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.negative_resources_b_a">negative_resources_b_a() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.negative_reverse">negative_reverse() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.negative_straight">negative_straight() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.inputs.negatome.negatome_interactions.html#pypath.inputs.negatome.negatome_interactions">negatome_interactions() (in module pypath.inputs.negatome)</a>
+</li>
+      <li><a href="api/pypath.inputs.netpath.netpath_interactions.html#pypath.inputs.netpath.netpath_interactions">netpath_interactions() (in module pypath.inputs.netpath)</a>
+</li>
+      <li><a href="api/pypath.inputs.netpath.netpath_names.html#pypath.inputs.netpath.netpath_names">netpath_names() (in module pypath.inputs.netpath)</a>
+</li>
+      <li><a href="api/pypath.inputs.netpath.netpath_pathway_annotations.html#pypath.inputs.netpath.netpath_pathway_annotations">netpath_pathway_annotations() (in module pypath.inputs.netpath)</a>
+</li>
+      <li><a href="api/pypath.core.annot.NetpathPathways.html#pypath.core.annot.NetpathPathways">NetpathPathways (class in pypath.core.annot)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network">Network (class in pypath.core.network)</a>
+</li>
+      <li><a href="api/pypath.core.annot.CustomAnnotation.html#pypath.core.annot.CustomAnnotation.network_df">network_df() (pypath.core.annot.CustomAnnotation method)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.intercell.IntercellAnnotation.html#pypath.core.intercell.IntercellAnnotation.network_df">(pypath.core.intercell.IntercellAnnotation method)</a>
+</li>
+        <li><a href="api/pypath.omnipath.app.DatabaseManager.html#pypath.omnipath.app.DatabaseManager.network_df">(pypath.omnipath.app.DatabaseManager method)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.omnipath.app.DatabaseManager.html#pypath.omnipath.app.DatabaseManager.network_df_by_source">network_df_by_source() (pypath.omnipath.app.DatabaseManager method)</a>
+</li>
+      <li><a href="api/pypath.internals.resource.NetworkDataset.html#pypath.internals.resource.NetworkDataset">NetworkDataset (class in pypath.internals.resource)</a>
+</li>
+      <li><a href="api/pypath.core.network.NetworkEntityCollection.html#pypath.core.network.NetworkEntityCollection">NetworkEntityCollection (class in pypath.core.network)</a>
+</li>
+      <li><a href="api/pypath.internals.input_formats.NetworkInput.html#pypath.internals.input_formats.NetworkInput">NetworkInput (class in pypath.internals.input_formats)</a>
+</li>
+      <li><a href="api/pypath.internals.resource.NetworkResource.html#pypath.internals.resource.NetworkResource">NetworkResource (class in pypath.internals.resource)</a>
+</li>
+      <li><a href="api/pypath.internals.resource.NetworkResourceKey.html#pypath.internals.resource.NetworkResourceKey">NetworkResourceKey (class in pypath.internals.resource)</a>
+</li>
+      <li><a href="api/pypath.core.network.NetworkStatsRecord.html#pypath.core.network.NetworkStatsRecord">NetworkStatsRecord (class in pypath.core.network)</a>
+</li>
+      <li><a href="api/pypath.inputs.netbiol.nrf2ome_interactions.html#pypath.inputs.netbiol.nrf2ome_interactions">nrf2ome_interactions() (in module pypath.inputs.netbiol)</a>
+</li>
+      <li><a href="api/pypath.inputs.uniprot.UniprotRecordHistory.html#pypath.inputs.uniprot.UniprotRecordHistory.number">number (pypath.inputs.uniprot.UniprotRecordHistory attribute)</a>
+</li>
+      <li><a href="api/pypath.core.annot.Adhesome.html#pypath.core.annot.Adhesome.numof_entities">numof_entities() (pypath.core.annot.Adhesome method)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.annot.Almen2009.html#pypath.core.annot.Almen2009.numof_entities">(pypath.core.annot.Almen2009 method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.AnnotationBase.html#pypath.core.annot.AnnotationBase.numof_entities">(pypath.core.annot.AnnotationBase method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Baccin2019.html#pypath.core.annot.Baccin2019.numof_entities">(pypath.core.annot.Baccin2019 method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Biogps.html#pypath.core.annot.Biogps.numof_entities">(pypath.core.annot.Biogps method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cancerdrugsdb.html#pypath.core.annot.Cancerdrugsdb.numof_entities">(pypath.core.annot.Cancerdrugsdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CancerGeneCensus.html#pypath.core.annot.CancerGeneCensus.numof_entities">(pypath.core.annot.CancerGeneCensus method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cancersea.html#pypath.core.annot.Cancersea.numof_entities">(pypath.core.annot.Cancersea method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cellcall.html#pypath.core.annot.Cellcall.numof_entities">(pypath.core.annot.Cellcall method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cellcellinteractions.html#pypath.core.annot.Cellcellinteractions.numof_entities">(pypath.core.annot.Cellcellinteractions method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cellchatdb.html#pypath.core.annot.Cellchatdb.numof_entities">(pypath.core.annot.Cellchatdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CellchatdbComplex.html#pypath.core.annot.CellchatdbComplex.numof_entities">(pypath.core.annot.CellchatdbComplex method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cellinker.html#pypath.core.annot.Cellinker.numof_entities">(pypath.core.annot.Cellinker method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CellinkerComplex.html#pypath.core.annot.CellinkerComplex.numof_entities">(pypath.core.annot.CellinkerComplex method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CellPhoneDB.html#pypath.core.annot.CellPhoneDB.numof_entities">(pypath.core.annot.CellPhoneDB method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CellPhoneDBComplex.html#pypath.core.annot.CellPhoneDBComplex.numof_entities">(pypath.core.annot.CellPhoneDBComplex method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CellSurfaceProteinAtlas.html#pypath.core.annot.CellSurfaceProteinAtlas.numof_entities">(pypath.core.annot.CellSurfaceProteinAtlas method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CellSurfaceProteinAtlasCellType.html#pypath.core.annot.CellSurfaceProteinAtlasCellType.numof_entities">(pypath.core.annot.CellSurfaceProteinAtlasCellType method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Celltalkdb.html#pypath.core.annot.Celltalkdb.numof_entities">(pypath.core.annot.Celltalkdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Celltypist.html#pypath.core.annot.Celltypist.numof_entities">(pypath.core.annot.Celltypist method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Comppi.html#pypath.core.annot.Comppi.numof_entities">(pypath.core.annot.Comppi method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Connectomedb.html#pypath.core.annot.Connectomedb.numof_entities">(pypath.core.annot.Connectomedb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Corum.html#pypath.core.annot.Corum.numof_entities">(pypath.core.annot.Corum method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CorumFuncat.html#pypath.core.annot.CorumFuncat.numof_entities">(pypath.core.annot.CorumFuncat method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CorumGO.html#pypath.core.annot.CorumGO.numof_entities">(pypath.core.annot.CorumGO method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cpad.html#pypath.core.annot.Cpad.numof_entities">(pypath.core.annot.Cpad method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cytosig.html#pypath.core.annot.Cytosig.numof_entities">(pypath.core.annot.Cytosig method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Dgidb.html#pypath.core.annot.Dgidb.numof_entities">(pypath.core.annot.Dgidb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Disgenet.html#pypath.core.annot.Disgenet.numof_entities">(pypath.core.annot.Disgenet method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Embrace.html#pypath.core.annot.Embrace.numof_entities">(pypath.core.annot.Embrace method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Exocarta.html#pypath.core.annot.Exocarta.numof_entities">(pypath.core.annot.Exocarta method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.GOIntercell.html#pypath.core.annot.GOIntercell.numof_entities">(pypath.core.annot.GOIntercell method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Gpcrdb.html#pypath.core.annot.Gpcrdb.numof_entities">(pypath.core.annot.Gpcrdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.GuideToPharmacology.html#pypath.core.annot.GuideToPharmacology.numof_entities">(pypath.core.annot.GuideToPharmacology method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Hgnc.html#pypath.core.annot.Hgnc.numof_entities">(pypath.core.annot.Hgnc method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.HpmrComplex.html#pypath.core.annot.HpmrComplex.numof_entities">(pypath.core.annot.HpmrComplex method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.HPO.html#pypath.core.annot.HPO.numof_entities">(pypath.core.annot.HPO method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Humancellmap.html#pypath.core.annot.Humancellmap.numof_entities">(pypath.core.annot.Humancellmap method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.HumanPlasmaMembraneReceptome.html#pypath.core.annot.HumanPlasmaMembraneReceptome.numof_entities">(pypath.core.annot.HumanPlasmaMembraneReceptome method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.HumanProteinAtlas.html#pypath.core.annot.HumanProteinAtlas.numof_entities">(pypath.core.annot.HumanProteinAtlas method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.HumanProteinAtlasSecretome.html#pypath.core.annot.HumanProteinAtlasSecretome.numof_entities">(pypath.core.annot.HumanProteinAtlasSecretome method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.HumanProteinAtlasSubcellular.html#pypath.core.annot.HumanProteinAtlasSubcellular.numof_entities">(pypath.core.annot.HumanProteinAtlasSubcellular method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Icellnet.html#pypath.core.annot.Icellnet.numof_entities">(pypath.core.annot.Icellnet method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.IcellnetComplex.html#pypath.core.annot.IcellnetComplex.numof_entities">(pypath.core.annot.IcellnetComplex method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Integrins.html#pypath.core.annot.Integrins.numof_entities">(pypath.core.annot.Integrins method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.InterPro.html#pypath.core.annot.InterPro.numof_entities">(pypath.core.annot.InterPro method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Intogen.html#pypath.core.annot.Intogen.numof_entities">(pypath.core.annot.Intogen method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Italk.html#pypath.core.annot.Italk.numof_entities">(pypath.core.annot.Italk method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.KeggPathways.html#pypath.core.annot.KeggPathways.numof_entities">(pypath.core.annot.KeggPathways method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.KeggPathwaysPC.html#pypath.core.annot.KeggPathwaysPC.numof_entities">(pypath.core.annot.KeggPathwaysPC method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Kinasedotcom.html#pypath.core.annot.Kinasedotcom.numof_entities">(pypath.core.annot.Kinasedotcom method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Kirouac2010.html#pypath.core.annot.Kirouac2010.numof_entities">(pypath.core.annot.Kirouac2010 method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Lambert2018.html#pypath.core.annot.Lambert2018.numof_entities">(pypath.core.annot.Lambert2018 method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.LigandReceptor.html#pypath.core.annot.LigandReceptor.numof_entities">(pypath.core.annot.LigandReceptor method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Locate.html#pypath.core.annot.Locate.numof_entities">(pypath.core.annot.Locate method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Lrdb.html#pypath.core.annot.Lrdb.numof_entities">(pypath.core.annot.Lrdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Matrisome.html#pypath.core.annot.Matrisome.numof_entities">(pypath.core.annot.Matrisome method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Matrixdb.html#pypath.core.annot.Matrixdb.numof_entities">(pypath.core.annot.Matrixdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Mcam.html#pypath.core.annot.Mcam.numof_entities">(pypath.core.annot.Mcam method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Membranome.html#pypath.core.annot.Membranome.numof_entities">(pypath.core.annot.Membranome method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Msigdb.html#pypath.core.annot.Msigdb.numof_entities">(pypath.core.annot.Msigdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.NetpathPathways.html#pypath.core.annot.NetpathPathways.numof_entities">(pypath.core.annot.NetpathPathways method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Opm.html#pypath.core.annot.Opm.numof_entities">(pypath.core.annot.Opm method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Panglaodb.html#pypath.core.annot.Panglaodb.numof_entities">(pypath.core.annot.Panglaodb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Phobius.html#pypath.core.annot.Phobius.numof_entities">(pypath.core.annot.Phobius method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Phosphatome.html#pypath.core.annot.Phosphatome.numof_entities">(pypath.core.annot.Phosphatome method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Progeny.html#pypath.core.annot.Progeny.numof_entities">(pypath.core.annot.Progeny method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Ramilowski2015.html#pypath.core.annot.Ramilowski2015.numof_entities">(pypath.core.annot.Ramilowski2015 method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Ramilowski2015Location.html#pypath.core.annot.Ramilowski2015Location.numof_entities">(pypath.core.annot.Ramilowski2015Location method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Scconnect.html#pypath.core.annot.Scconnect.numof_entities">(pypath.core.annot.Scconnect method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.ScconnectComplex.html#pypath.core.annot.ScconnectComplex.numof_entities">(pypath.core.annot.ScconnectComplex method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.SignalinkFunctions.html#pypath.core.annot.SignalinkFunctions.numof_entities">(pypath.core.annot.SignalinkFunctions method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.SignalinkPathways.html#pypath.core.annot.SignalinkPathways.numof_entities">(pypath.core.annot.SignalinkPathways method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.SignorPathways.html#pypath.core.annot.SignorPathways.numof_entities">(pypath.core.annot.SignorPathways method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Surfaceome.html#pypath.core.annot.Surfaceome.numof_entities">(pypath.core.annot.Surfaceome method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Talklr.html#pypath.core.annot.Talklr.numof_entities">(pypath.core.annot.Talklr method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Tcdb.html#pypath.core.annot.Tcdb.numof_entities">(pypath.core.annot.Tcdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Tfcensus.html#pypath.core.annot.Tfcensus.numof_entities">(pypath.core.annot.Tfcensus method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Topdb.html#pypath.core.annot.Topdb.numof_entities">(pypath.core.annot.Topdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.UniprotFamilies.html#pypath.core.annot.UniprotFamilies.numof_entities">(pypath.core.annot.UniprotFamilies method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.UniprotKeywords.html#pypath.core.annot.UniprotKeywords.numof_entities">(pypath.core.annot.UniprotKeywords method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.UniprotLocations.html#pypath.core.annot.UniprotLocations.numof_entities">(pypath.core.annot.UniprotLocations method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.UniprotTissues.html#pypath.core.annot.UniprotTissues.numof_entities">(pypath.core.annot.UniprotTissues method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.UniprotTopologies.html#pypath.core.annot.UniprotTopologies.numof_entities">(pypath.core.annot.UniprotTopologies method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Vesiclepedia.html#pypath.core.annot.Vesiclepedia.numof_entities">(pypath.core.annot.Vesiclepedia method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Wang.html#pypath.core.annot.Wang.numof_entities">(pypath.core.annot.Wang method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Zhong2015.html#pypath.core.annot.Zhong2015.numof_entities">(pypath.core.annot.Zhong2015 method)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.numof_interactions_per_reference">numof_interactions_per_reference() (pypath.core.network.Network method)</a>
+</li>
+      <li><a href="api/pypath.core.annot.Adhesome.html#pypath.core.annot.Adhesome.numof_records">numof_records() (pypath.core.annot.Adhesome method)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.annot.Almen2009.html#pypath.core.annot.Almen2009.numof_records">(pypath.core.annot.Almen2009 method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.AnnotationBase.html#pypath.core.annot.AnnotationBase.numof_records">(pypath.core.annot.AnnotationBase method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Baccin2019.html#pypath.core.annot.Baccin2019.numof_records">(pypath.core.annot.Baccin2019 method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Biogps.html#pypath.core.annot.Biogps.numof_records">(pypath.core.annot.Biogps method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cancerdrugsdb.html#pypath.core.annot.Cancerdrugsdb.numof_records">(pypath.core.annot.Cancerdrugsdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CancerGeneCensus.html#pypath.core.annot.CancerGeneCensus.numof_records">(pypath.core.annot.CancerGeneCensus method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cancersea.html#pypath.core.annot.Cancersea.numof_records">(pypath.core.annot.Cancersea method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cellcall.html#pypath.core.annot.Cellcall.numof_records">(pypath.core.annot.Cellcall method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cellcellinteractions.html#pypath.core.annot.Cellcellinteractions.numof_records">(pypath.core.annot.Cellcellinteractions method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cellchatdb.html#pypath.core.annot.Cellchatdb.numof_records">(pypath.core.annot.Cellchatdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CellchatdbComplex.html#pypath.core.annot.CellchatdbComplex.numof_records">(pypath.core.annot.CellchatdbComplex method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cellinker.html#pypath.core.annot.Cellinker.numof_records">(pypath.core.annot.Cellinker method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CellinkerComplex.html#pypath.core.annot.CellinkerComplex.numof_records">(pypath.core.annot.CellinkerComplex method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CellPhoneDB.html#pypath.core.annot.CellPhoneDB.numof_records">(pypath.core.annot.CellPhoneDB method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CellPhoneDBComplex.html#pypath.core.annot.CellPhoneDBComplex.numof_records">(pypath.core.annot.CellPhoneDBComplex method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CellSurfaceProteinAtlas.html#pypath.core.annot.CellSurfaceProteinAtlas.numof_records">(pypath.core.annot.CellSurfaceProteinAtlas method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CellSurfaceProteinAtlasCellType.html#pypath.core.annot.CellSurfaceProteinAtlasCellType.numof_records">(pypath.core.annot.CellSurfaceProteinAtlasCellType method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Celltalkdb.html#pypath.core.annot.Celltalkdb.numof_records">(pypath.core.annot.Celltalkdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Celltypist.html#pypath.core.annot.Celltypist.numof_records">(pypath.core.annot.Celltypist method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Comppi.html#pypath.core.annot.Comppi.numof_records">(pypath.core.annot.Comppi method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Connectomedb.html#pypath.core.annot.Connectomedb.numof_records">(pypath.core.annot.Connectomedb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Corum.html#pypath.core.annot.Corum.numof_records">(pypath.core.annot.Corum method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CorumFuncat.html#pypath.core.annot.CorumFuncat.numof_records">(pypath.core.annot.CorumFuncat method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CorumGO.html#pypath.core.annot.CorumGO.numof_records">(pypath.core.annot.CorumGO method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cpad.html#pypath.core.annot.Cpad.numof_records">(pypath.core.annot.Cpad method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cytosig.html#pypath.core.annot.Cytosig.numof_records">(pypath.core.annot.Cytosig method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Dgidb.html#pypath.core.annot.Dgidb.numof_records">(pypath.core.annot.Dgidb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Disgenet.html#pypath.core.annot.Disgenet.numof_records">(pypath.core.annot.Disgenet method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Embrace.html#pypath.core.annot.Embrace.numof_records">(pypath.core.annot.Embrace method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Exocarta.html#pypath.core.annot.Exocarta.numof_records">(pypath.core.annot.Exocarta method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.GOIntercell.html#pypath.core.annot.GOIntercell.numof_records">(pypath.core.annot.GOIntercell method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Gpcrdb.html#pypath.core.annot.Gpcrdb.numof_records">(pypath.core.annot.Gpcrdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.GuideToPharmacology.html#pypath.core.annot.GuideToPharmacology.numof_records">(pypath.core.annot.GuideToPharmacology method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Hgnc.html#pypath.core.annot.Hgnc.numof_records">(pypath.core.annot.Hgnc method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.HpmrComplex.html#pypath.core.annot.HpmrComplex.numof_records">(pypath.core.annot.HpmrComplex method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.HPO.html#pypath.core.annot.HPO.numof_records">(pypath.core.annot.HPO method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Humancellmap.html#pypath.core.annot.Humancellmap.numof_records">(pypath.core.annot.Humancellmap method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.HumanPlasmaMembraneReceptome.html#pypath.core.annot.HumanPlasmaMembraneReceptome.numof_records">(pypath.core.annot.HumanPlasmaMembraneReceptome method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.HumanProteinAtlas.html#pypath.core.annot.HumanProteinAtlas.numof_records">(pypath.core.annot.HumanProteinAtlas method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.HumanProteinAtlasSecretome.html#pypath.core.annot.HumanProteinAtlasSecretome.numof_records">(pypath.core.annot.HumanProteinAtlasSecretome method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.HumanProteinAtlasSubcellular.html#pypath.core.annot.HumanProteinAtlasSubcellular.numof_records">(pypath.core.annot.HumanProteinAtlasSubcellular method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Icellnet.html#pypath.core.annot.Icellnet.numof_records">(pypath.core.annot.Icellnet method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.IcellnetComplex.html#pypath.core.annot.IcellnetComplex.numof_records">(pypath.core.annot.IcellnetComplex method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Integrins.html#pypath.core.annot.Integrins.numof_records">(pypath.core.annot.Integrins method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.InterPro.html#pypath.core.annot.InterPro.numof_records">(pypath.core.annot.InterPro method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Intogen.html#pypath.core.annot.Intogen.numof_records">(pypath.core.annot.Intogen method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Italk.html#pypath.core.annot.Italk.numof_records">(pypath.core.annot.Italk method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.KeggPathways.html#pypath.core.annot.KeggPathways.numof_records">(pypath.core.annot.KeggPathways method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.KeggPathwaysPC.html#pypath.core.annot.KeggPathwaysPC.numof_records">(pypath.core.annot.KeggPathwaysPC method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Kinasedotcom.html#pypath.core.annot.Kinasedotcom.numof_records">(pypath.core.annot.Kinasedotcom method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Kirouac2010.html#pypath.core.annot.Kirouac2010.numof_records">(pypath.core.annot.Kirouac2010 method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Lambert2018.html#pypath.core.annot.Lambert2018.numof_records">(pypath.core.annot.Lambert2018 method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.LigandReceptor.html#pypath.core.annot.LigandReceptor.numof_records">(pypath.core.annot.LigandReceptor method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Locate.html#pypath.core.annot.Locate.numof_records">(pypath.core.annot.Locate method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Lrdb.html#pypath.core.annot.Lrdb.numof_records">(pypath.core.annot.Lrdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Matrisome.html#pypath.core.annot.Matrisome.numof_records">(pypath.core.annot.Matrisome method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Matrixdb.html#pypath.core.annot.Matrixdb.numof_records">(pypath.core.annot.Matrixdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Mcam.html#pypath.core.annot.Mcam.numof_records">(pypath.core.annot.Mcam method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Membranome.html#pypath.core.annot.Membranome.numof_records">(pypath.core.annot.Membranome method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Msigdb.html#pypath.core.annot.Msigdb.numof_records">(pypath.core.annot.Msigdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.NetpathPathways.html#pypath.core.annot.NetpathPathways.numof_records">(pypath.core.annot.NetpathPathways method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Opm.html#pypath.core.annot.Opm.numof_records">(pypath.core.annot.Opm method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Panglaodb.html#pypath.core.annot.Panglaodb.numof_records">(pypath.core.annot.Panglaodb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Phobius.html#pypath.core.annot.Phobius.numof_records">(pypath.core.annot.Phobius method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Phosphatome.html#pypath.core.annot.Phosphatome.numof_records">(pypath.core.annot.Phosphatome method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Progeny.html#pypath.core.annot.Progeny.numof_records">(pypath.core.annot.Progeny method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Ramilowski2015.html#pypath.core.annot.Ramilowski2015.numof_records">(pypath.core.annot.Ramilowski2015 method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Ramilowski2015Location.html#pypath.core.annot.Ramilowski2015Location.numof_records">(pypath.core.annot.Ramilowski2015Location method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Scconnect.html#pypath.core.annot.Scconnect.numof_records">(pypath.core.annot.Scconnect method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.ScconnectComplex.html#pypath.core.annot.ScconnectComplex.numof_records">(pypath.core.annot.ScconnectComplex method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.SignalinkFunctions.html#pypath.core.annot.SignalinkFunctions.numof_records">(pypath.core.annot.SignalinkFunctions method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.SignalinkPathways.html#pypath.core.annot.SignalinkPathways.numof_records">(pypath.core.annot.SignalinkPathways method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.SignorPathways.html#pypath.core.annot.SignorPathways.numof_records">(pypath.core.annot.SignorPathways method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Surfaceome.html#pypath.core.annot.Surfaceome.numof_records">(pypath.core.annot.Surfaceome method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Talklr.html#pypath.core.annot.Talklr.numof_records">(pypath.core.annot.Talklr method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Tcdb.html#pypath.core.annot.Tcdb.numof_records">(pypath.core.annot.Tcdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Tfcensus.html#pypath.core.annot.Tfcensus.numof_records">(pypath.core.annot.Tfcensus method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Topdb.html#pypath.core.annot.Topdb.numof_records">(pypath.core.annot.Topdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.UniprotFamilies.html#pypath.core.annot.UniprotFamilies.numof_records">(pypath.core.annot.UniprotFamilies method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.UniprotKeywords.html#pypath.core.annot.UniprotKeywords.numof_records">(pypath.core.annot.UniprotKeywords method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.UniprotLocations.html#pypath.core.annot.UniprotLocations.numof_records">(pypath.core.annot.UniprotLocations method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.UniprotTissues.html#pypath.core.annot.UniprotTissues.numof_records">(pypath.core.annot.UniprotTissues method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.UniprotTopologies.html#pypath.core.annot.UniprotTopologies.numof_records">(pypath.core.annot.UniprotTopologies method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Vesiclepedia.html#pypath.core.annot.Vesiclepedia.numof_records">(pypath.core.annot.Vesiclepedia method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Wang.html#pypath.core.annot.Wang.numof_records">(pypath.core.annot.Wang method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Zhong2015.html#pypath.core.annot.Zhong2015.numof_records">(pypath.core.annot.Zhong2015 method)</a>
+</li>
+      </ul></li>
+  </ul></td>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="api/pypath.core.annot.Adhesome.html#pypath.core.annot.Adhesome.numof_references">numof_references() (pypath.core.annot.Adhesome method)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.annot.Almen2009.html#pypath.core.annot.Almen2009.numof_references">(pypath.core.annot.Almen2009 method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.AnnotationBase.html#pypath.core.annot.AnnotationBase.numof_references">(pypath.core.annot.AnnotationBase method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Baccin2019.html#pypath.core.annot.Baccin2019.numof_references">(pypath.core.annot.Baccin2019 method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Biogps.html#pypath.core.annot.Biogps.numof_references">(pypath.core.annot.Biogps method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cancerdrugsdb.html#pypath.core.annot.Cancerdrugsdb.numof_references">(pypath.core.annot.Cancerdrugsdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CancerGeneCensus.html#pypath.core.annot.CancerGeneCensus.numof_references">(pypath.core.annot.CancerGeneCensus method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cancersea.html#pypath.core.annot.Cancersea.numof_references">(pypath.core.annot.Cancersea method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cellcall.html#pypath.core.annot.Cellcall.numof_references">(pypath.core.annot.Cellcall method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cellcellinteractions.html#pypath.core.annot.Cellcellinteractions.numof_references">(pypath.core.annot.Cellcellinteractions method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cellchatdb.html#pypath.core.annot.Cellchatdb.numof_references">(pypath.core.annot.Cellchatdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CellchatdbComplex.html#pypath.core.annot.CellchatdbComplex.numof_references">(pypath.core.annot.CellchatdbComplex method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cellinker.html#pypath.core.annot.Cellinker.numof_references">(pypath.core.annot.Cellinker method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CellinkerComplex.html#pypath.core.annot.CellinkerComplex.numof_references">(pypath.core.annot.CellinkerComplex method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CellPhoneDB.html#pypath.core.annot.CellPhoneDB.numof_references">(pypath.core.annot.CellPhoneDB method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CellPhoneDBComplex.html#pypath.core.annot.CellPhoneDBComplex.numof_references">(pypath.core.annot.CellPhoneDBComplex method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CellSurfaceProteinAtlas.html#pypath.core.annot.CellSurfaceProteinAtlas.numof_references">(pypath.core.annot.CellSurfaceProteinAtlas method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CellSurfaceProteinAtlasCellType.html#pypath.core.annot.CellSurfaceProteinAtlasCellType.numof_references">(pypath.core.annot.CellSurfaceProteinAtlasCellType method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Celltalkdb.html#pypath.core.annot.Celltalkdb.numof_references">(pypath.core.annot.Celltalkdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Celltypist.html#pypath.core.annot.Celltypist.numof_references">(pypath.core.annot.Celltypist method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Comppi.html#pypath.core.annot.Comppi.numof_references">(pypath.core.annot.Comppi method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Connectomedb.html#pypath.core.annot.Connectomedb.numof_references">(pypath.core.annot.Connectomedb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Corum.html#pypath.core.annot.Corum.numof_references">(pypath.core.annot.Corum method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CorumFuncat.html#pypath.core.annot.CorumFuncat.numof_references">(pypath.core.annot.CorumFuncat method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CorumGO.html#pypath.core.annot.CorumGO.numof_references">(pypath.core.annot.CorumGO method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cpad.html#pypath.core.annot.Cpad.numof_references">(pypath.core.annot.Cpad method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cytosig.html#pypath.core.annot.Cytosig.numof_references">(pypath.core.annot.Cytosig method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Dgidb.html#pypath.core.annot.Dgidb.numof_references">(pypath.core.annot.Dgidb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Disgenet.html#pypath.core.annot.Disgenet.numof_references">(pypath.core.annot.Disgenet method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Embrace.html#pypath.core.annot.Embrace.numof_references">(pypath.core.annot.Embrace method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Exocarta.html#pypath.core.annot.Exocarta.numof_references">(pypath.core.annot.Exocarta method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.GOIntercell.html#pypath.core.annot.GOIntercell.numof_references">(pypath.core.annot.GOIntercell method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Gpcrdb.html#pypath.core.annot.Gpcrdb.numof_references">(pypath.core.annot.Gpcrdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.GuideToPharmacology.html#pypath.core.annot.GuideToPharmacology.numof_references">(pypath.core.annot.GuideToPharmacology method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Hgnc.html#pypath.core.annot.Hgnc.numof_references">(pypath.core.annot.Hgnc method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.HpmrComplex.html#pypath.core.annot.HpmrComplex.numof_references">(pypath.core.annot.HpmrComplex method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.HPO.html#pypath.core.annot.HPO.numof_references">(pypath.core.annot.HPO method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Humancellmap.html#pypath.core.annot.Humancellmap.numof_references">(pypath.core.annot.Humancellmap method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.HumanPlasmaMembraneReceptome.html#pypath.core.annot.HumanPlasmaMembraneReceptome.numof_references">(pypath.core.annot.HumanPlasmaMembraneReceptome method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.HumanProteinAtlas.html#pypath.core.annot.HumanProteinAtlas.numof_references">(pypath.core.annot.HumanProteinAtlas method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.HumanProteinAtlasSecretome.html#pypath.core.annot.HumanProteinAtlasSecretome.numof_references">(pypath.core.annot.HumanProteinAtlasSecretome method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.HumanProteinAtlasSubcellular.html#pypath.core.annot.HumanProteinAtlasSubcellular.numof_references">(pypath.core.annot.HumanProteinAtlasSubcellular method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Icellnet.html#pypath.core.annot.Icellnet.numof_references">(pypath.core.annot.Icellnet method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.IcellnetComplex.html#pypath.core.annot.IcellnetComplex.numof_references">(pypath.core.annot.IcellnetComplex method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Integrins.html#pypath.core.annot.Integrins.numof_references">(pypath.core.annot.Integrins method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.InterPro.html#pypath.core.annot.InterPro.numof_references">(pypath.core.annot.InterPro method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Intogen.html#pypath.core.annot.Intogen.numof_references">(pypath.core.annot.Intogen method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Italk.html#pypath.core.annot.Italk.numof_references">(pypath.core.annot.Italk method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.KeggPathways.html#pypath.core.annot.KeggPathways.numof_references">(pypath.core.annot.KeggPathways method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.KeggPathwaysPC.html#pypath.core.annot.KeggPathwaysPC.numof_references">(pypath.core.annot.KeggPathwaysPC method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Kinasedotcom.html#pypath.core.annot.Kinasedotcom.numof_references">(pypath.core.annot.Kinasedotcom method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Kirouac2010.html#pypath.core.annot.Kirouac2010.numof_references">(pypath.core.annot.Kirouac2010 method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Lambert2018.html#pypath.core.annot.Lambert2018.numof_references">(pypath.core.annot.Lambert2018 method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.LigandReceptor.html#pypath.core.annot.LigandReceptor.numof_references">(pypath.core.annot.LigandReceptor method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Locate.html#pypath.core.annot.Locate.numof_references">(pypath.core.annot.Locate method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Lrdb.html#pypath.core.annot.Lrdb.numof_references">(pypath.core.annot.Lrdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Matrisome.html#pypath.core.annot.Matrisome.numof_references">(pypath.core.annot.Matrisome method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Matrixdb.html#pypath.core.annot.Matrixdb.numof_references">(pypath.core.annot.Matrixdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Mcam.html#pypath.core.annot.Mcam.numof_references">(pypath.core.annot.Mcam method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Membranome.html#pypath.core.annot.Membranome.numof_references">(pypath.core.annot.Membranome method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Msigdb.html#pypath.core.annot.Msigdb.numof_references">(pypath.core.annot.Msigdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.NetpathPathways.html#pypath.core.annot.NetpathPathways.numof_references">(pypath.core.annot.NetpathPathways method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Opm.html#pypath.core.annot.Opm.numof_references">(pypath.core.annot.Opm method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Panglaodb.html#pypath.core.annot.Panglaodb.numof_references">(pypath.core.annot.Panglaodb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Phobius.html#pypath.core.annot.Phobius.numof_references">(pypath.core.annot.Phobius method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Phosphatome.html#pypath.core.annot.Phosphatome.numof_references">(pypath.core.annot.Phosphatome method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Progeny.html#pypath.core.annot.Progeny.numof_references">(pypath.core.annot.Progeny method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Ramilowski2015.html#pypath.core.annot.Ramilowski2015.numof_references">(pypath.core.annot.Ramilowski2015 method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Ramilowski2015Location.html#pypath.core.annot.Ramilowski2015Location.numof_references">(pypath.core.annot.Ramilowski2015Location method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Scconnect.html#pypath.core.annot.Scconnect.numof_references">(pypath.core.annot.Scconnect method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.ScconnectComplex.html#pypath.core.annot.ScconnectComplex.numof_references">(pypath.core.annot.ScconnectComplex method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.SignalinkFunctions.html#pypath.core.annot.SignalinkFunctions.numof_references">(pypath.core.annot.SignalinkFunctions method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.SignalinkPathways.html#pypath.core.annot.SignalinkPathways.numof_references">(pypath.core.annot.SignalinkPathways method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.SignorPathways.html#pypath.core.annot.SignorPathways.numof_references">(pypath.core.annot.SignorPathways method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Surfaceome.html#pypath.core.annot.Surfaceome.numof_references">(pypath.core.annot.Surfaceome method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Talklr.html#pypath.core.annot.Talklr.numof_references">(pypath.core.annot.Talklr method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Tcdb.html#pypath.core.annot.Tcdb.numof_references">(pypath.core.annot.Tcdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Tfcensus.html#pypath.core.annot.Tfcensus.numof_references">(pypath.core.annot.Tfcensus method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Topdb.html#pypath.core.annot.Topdb.numof_references">(pypath.core.annot.Topdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.UniprotFamilies.html#pypath.core.annot.UniprotFamilies.numof_references">(pypath.core.annot.UniprotFamilies method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.UniprotKeywords.html#pypath.core.annot.UniprotKeywords.numof_references">(pypath.core.annot.UniprotKeywords method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.UniprotLocations.html#pypath.core.annot.UniprotLocations.numof_references">(pypath.core.annot.UniprotLocations method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.UniprotTissues.html#pypath.core.annot.UniprotTissues.numof_references">(pypath.core.annot.UniprotTissues method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.UniprotTopologies.html#pypath.core.annot.UniprotTopologies.numof_references">(pypath.core.annot.UniprotTopologies method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Vesiclepedia.html#pypath.core.annot.Vesiclepedia.numof_references">(pypath.core.annot.Vesiclepedia method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Wang.html#pypath.core.annot.Wang.numof_references">(pypath.core.annot.Wang method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Zhong2015.html#pypath.core.annot.Zhong2015.numof_references">(pypath.core.annot.Zhong2015 method)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.internals.intera.Interface.html#pypath.internals.intera.Interface.numof_residues">numof_residues() (pypath.internals.intera.Interface method)</a>
+</li>
+  </ul></td>
+</tr></table>
+
+<h2 id="O">O</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="api/pypath.utils.pdb.Residue.html#pypath.utils.pdb.Residue.offset">offset (pypath.utils.pdb.Residue attribute)</a>
+</li>
+      <li><a href="api/pypath.inputs.offsides.offsides_side_effects.html#pypath.inputs.offsides.offsides_side_effects">offsides_side_effects() (in module pypath.inputs.offsides)</a>
+</li>
+      <li><a href="api/pypath.inputs.oma.oma_orthologs.html#pypath.inputs.oma.oma_orthologs">oma_orthologs() (in module pypath.inputs.oma)</a>
+</li>
+      <li><a href="api/pypath.inputs.oma.oma_table.html#pypath.inputs.oma.oma_table">oma_table() (in module pypath.inputs.oma)</a>
+</li>
+      <li><a href="api/pypath.utils.orthology.OmaOrtholog.html#pypath.utils.orthology.OmaOrtholog">OmaOrtholog (class in pypath.utils.orthology)</a>
+</li>
+      <li><a href="api/pypath.utils.orthology.OmaOrthology.html#pypath.utils.orthology.OmaOrthology">OmaOrthology (class in pypath.utils.orthology)</a>
+</li>
+      <li><a href="api/pypath.inputs.pubmed.only_pmids.html#pypath.inputs.pubmed.only_pmids">only_pmids() (in module pypath.inputs.pubmed)</a>
+</li>
+      <li><a href="api/pypath.utils.orthology.OrthologyTableKey.html#pypath.utils.orthology.OrthologyTableKey.only_swissprot">only_swissprot (pypath.utils.orthology.OrthologyTableKey attribute)</a>
+</li>
+      <li><a href="api/pypath.utils.mapping.Mapper.html#pypath.utils.mapping.Mapper.only_uniprot_ac">only_uniprot_ac() (pypath.utils.mapping.Mapper method)</a>
+</li>
+      <li><a href="api/pypath.inputs.ontology.ontology.html#pypath.inputs.ontology.ontology">ontology() (in module pypath.inputs.ontology)</a>
+</li>
+      <li><a href="api/pypath.internals.annot_formats.AnnotOp.html#pypath.internals.annot_formats.AnnotOp.op">op (pypath.internals.annot_formats.AnnotOp attribute)</a>
+</li>
+      <li><a href="api/pypath.share.curl.Curl.html#pypath.share.curl.Curl.open">open() (pypath.share.curl.Curl method)</a>
+
+      <ul>
+        <li><a href="api/pypath.share.curl.FileOpener.html#pypath.share.curl.FileOpener.open">(pypath.share.curl.FileOpener method)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.utils.pyreact.BioPaxReader.html#pypath.utils.pyreact.BioPaxReader.open_biopax">open_biopax() (pypath.utils.pyreact.BioPaxReader method)</a>
+</li>
+      <li><a href="api/pypath.inputs.pubmed.open_pubmed.html#pypath.inputs.pubmed.open_pubmed">open_pubmed() (in module pypath.inputs.pubmed)</a>
+</li>
+      <li><a href="api/pypath.share.curl.Curl.html#pypath.share.curl.Curl.open_tgz">open_tgz() (pypath.share.curl.Curl method)</a>
+
+      <ul>
+        <li><a href="api/pypath.share.curl.FileOpener.html#pypath.share.curl.FileOpener.open_tgz">(pypath.share.curl.FileOpener method)</a>
+</li>
+      </ul></li>
+  </ul></td>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="api/pypath.inputs.opentargets.opentargets_adverse_reactions.html#pypath.inputs.opentargets.opentargets_adverse_reactions">opentargets_adverse_reactions() (in module pypath.inputs.opentargets)</a>
+</li>
+      <li><a href="api/pypath.inputs.opentargets.opentargets_baseline_expression.html#pypath.inputs.opentargets.opentargets_baseline_expression">opentargets_baseline_expression() (in module pypath.inputs.opentargets)</a>
+</li>
+      <li><a href="api/pypath.inputs.opentargets.opentargets_direct_score.html#pypath.inputs.opentargets.opentargets_direct_score">opentargets_direct_score() (in module pypath.inputs.opentargets)</a>
+</li>
+      <li><a href="api/pypath.inputs.opentargets.opentargets_general.html#pypath.inputs.opentargets.opentargets_general">opentargets_general() (in module pypath.inputs.opentargets)</a>
+</li>
+      <li><a href="api/pypath.inputs.opentargets.opentargets_indirect_score.html#pypath.inputs.opentargets.opentargets_indirect_score">opentargets_indirect_score() (in module pypath.inputs.opentargets)</a>
+</li>
+      <li><a href="api/pypath.core.annot.Opm.html#pypath.core.annot.Opm">Opm (class in pypath.core.annot)</a>
+</li>
+      <li><a href="api/pypath.inputs.opm.opm_annotations.html#pypath.inputs.opm.opm_annotations">opm_annotations() (in module pypath.inputs.opm)</a>
+</li>
+      <li><a href="api/pypath.inputs.oreganno.oreganno_interactions.html#pypath.inputs.oreganno.oreganno_interactions">oreganno_interactions() (in module pypath.inputs.oreganno)</a>
+</li>
+      <li><a href="api/pypath.inputs.oreganno.oreganno_raw.html#pypath.inputs.oreganno.oreganno_raw">oreganno_raw() (in module pypath.inputs.oreganno)</a>
+</li>
+      <li><a href="api/pypath.inputs.biogps.BiogpsDataset.html#pypath.inputs.biogps.BiogpsDataset.organism">organism (pypath.inputs.biogps.BiogpsDataset attribute)</a>
+</li>
+      <li><a href="api/pypath.utils.uniprot.organism.html#pypath.utils.uniprot.organism">organism() (in module pypath.utils.uniprot)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.organisms_check">organisms_check() (pypath.core.network.Network method)</a>
+</li>
+      <li><a href="api/pypath.utils.orthology.OrthologBase.html#pypath.utils.orthology.OrthologBase">OrthologBase (class in pypath.utils.orthology)</a>
+</li>
+      <li><a href="api/pypath.utils.orthology.OrthologMeta.html#pypath.utils.orthology.OrthologMeta">OrthologMeta (class in pypath.utils.orthology)</a>
+</li>
+      <li><a href="api/pypath.utils.orthology.OrthologyManager.html#pypath.utils.orthology.OrthologyManager">OrthologyManager (class in pypath.utils.orthology)</a>
+</li>
+      <li><a href="api/pypath.utils.orthology.OrthologyTableKey.html#pypath.utils.orthology.OrthologyTableKey">OrthologyTableKey (class in pypath.utils.orthology)</a>
+</li>
+      <li><a href="api/pypath.utils.mapping.Mapper.html#pypath.utils.mapping.Mapper.other_organism_uniprot">other_organism_uniprot() (pypath.utils.mapping.Mapper method)</a>
+</li>
+  </ul></td>
+</tr></table>
+
+<h2 id="P">P</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="api/pypath.utils.proteomicsdb.ProteomicsDB.html#pypath.utils.proteomicsdb.ProteomicsDB.pandas_matrix">pandas_matrix() (pypath.utils.proteomicsdb.ProteomicsDB method)</a>
+</li>
+      <li><a href="api/pypath.core.annot.Panglaodb.html#pypath.core.annot.Panglaodb">Panglaodb (class in pypath.core.annot)</a>
+</li>
+      <li><a href="api/pypath.inputs.panglaodb.panglaodb_annotations.html#pypath.inputs.panglaodb.panglaodb_annotations">panglaodb_annotations() (in module pypath.inputs.panglaodb)</a>
+</li>
+      <li><a href="api/pypath.inputs.panglaodb.panglaodb_raw.html#pypath.inputs.panglaodb.panglaodb_raw">panglaodb_raw() (in module pypath.inputs.panglaodb)</a>
+</li>
+      <li><a href="api/pypath.inputs.reaction.panther_biopax.html#pypath.inputs.reaction.panther_biopax">panther_biopax() (in module pypath.inputs.reaction)</a>
+</li>
+      <li><a href="api/pypath.inputs.reaction.panther_interactions.html#pypath.inputs.reaction.panther_interactions">panther_interactions() (in module pypath.inputs.reaction)</a>
+</li>
+      <li><a href="api/pypath.inputs.adrecs.AdrecsChildParent.html#pypath.inputs.adrecs.AdrecsChildParent.parent">parent (pypath.inputs.adrecs.AdrecsChildParent attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.internals.annot_formats.AnnotDef.html#pypath.internals.annot_formats.AnnotDef.parent">(pypath.internals.annot_formats.AnnotDef attribute)</a>
+</li>
+        <li><a href="api/pypath.internals.annot_formats.AnnotDefKey.html#pypath.internals.annot_formats.AnnotDefKey.parent">(pypath.internals.annot_formats.AnnotDefKey attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.inputs.hpmr.HpmrInteraction.html#pypath.inputs.hpmr.HpmrInteraction.partner">partner (pypath.inputs.hpmr.HpmrInteraction attribute)</a>
+</li>
+      <li><a href="api/pypath.inputs.hpmr.HpmrInteraction.html#pypath.inputs.hpmr.HpmrInteraction.partner_role">partner_role (pypath.inputs.hpmr.HpmrInteraction attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.partners">partners() (pypath.core.network.Network method)</a>
+</li>
+      <li><a href="api/pypath.inputs.pathophenodb.DiseasePathogen.html#pypath.inputs.pathophenodb.DiseasePathogen.pathogen">pathogen (pypath.inputs.pathophenodb.DiseasePathogen attribute)</a>
+</li>
+      <li><a href="api/pypath.inputs.pathophenodb.DiseasePathogen.html#pypath.inputs.pathophenodb.DiseasePathogen.pathogen_taxid">pathogen_taxid (pypath.inputs.pathophenodb.DiseasePathogen attribute)</a>
+</li>
+      <li><a href="api/pypath.inputs.kegg.KeggPathway.html#pypath.inputs.kegg.KeggPathway.pathway">pathway (pypath.inputs.kegg.KeggPathway attribute)</a>
+</li>
+      <li><a href="api/pypath.resources.data_formats.pathway_bad.html#pypath.resources.data_formats.pathway_bad">pathway_bad (in module pypath.resources.data_formats)</a>
+</li>
+      <li><a href="api/pypath.inputs.kegg_api.pathway_to_disease.html#pypath.inputs.kegg_api.pathway_to_disease">pathway_to_disease() (in module pypath.inputs.kegg_api)</a>
+</li>
+      <li><a href="api/pypath.inputs.kegg_api.pathway_to_drug.html#pypath.inputs.kegg_api.pathway_to_drug">pathway_to_drug() (in module pypath.inputs.kegg_api)</a>
+</li>
+      <li><a href="api/pypath.inputs.kegg_api.pathway_to_gene.html#pypath.inputs.kegg_api.pathway_to_gene">pathway_to_gene() (in module pypath.inputs.kegg_api)</a>
+</li>
+      <li><a href="api/pypath.inputs.pathwaycommons.pathwaycommons_bind_interactions.html#pypath.inputs.pathwaycommons.pathwaycommons_bind_interactions">pathwaycommons_bind_interactions() (in module pypath.inputs.pathwaycommons)</a>
+</li>
+      <li><a href="api/pypath.inputs.pathwaycommons.pathwaycommons_biogrid_interactions.html#pypath.inputs.pathwaycommons.pathwaycommons_biogrid_interactions">pathwaycommons_biogrid_interactions() (in module pypath.inputs.pathwaycommons)</a>
+</li>
+      <li><a href="api/pypath.inputs.pathwaycommons.pathwaycommons_corum_interactions.html#pypath.inputs.pathwaycommons.pathwaycommons_corum_interactions">pathwaycommons_corum_interactions() (in module pypath.inputs.pathwaycommons)</a>
+</li>
+      <li><a href="api/pypath.inputs.pathwaycommons.pathwaycommons_dip_interactions.html#pypath.inputs.pathwaycommons.pathwaycommons_dip_interactions">pathwaycommons_dip_interactions() (in module pypath.inputs.pathwaycommons)</a>
+</li>
+      <li><a href="api/pypath.inputs.pathwaycommons.pathwaycommons_hprd_interactions.html#pypath.inputs.pathwaycommons.pathwaycommons_hprd_interactions">pathwaycommons_hprd_interactions() (in module pypath.inputs.pathwaycommons)</a>
+</li>
+      <li><a href="api/pypath.inputs.pathwaycommons.pathwaycommons_inoh_interactions.html#pypath.inputs.pathwaycommons.pathwaycommons_inoh_interactions">pathwaycommons_inoh_interactions() (in module pypath.inputs.pathwaycommons)</a>
+</li>
+      <li><a href="api/pypath.inputs.pathwaycommons.pathwaycommons_intact_interactions.html#pypath.inputs.pathwaycommons.pathwaycommons_intact_interactions">pathwaycommons_intact_interactions() (in module pypath.inputs.pathwaycommons)</a>
+</li>
+      <li><a href="api/pypath.inputs.pathwaycommons.pathwaycommons_interactions.html#pypath.inputs.pathwaycommons.pathwaycommons_interactions">pathwaycommons_interactions() (in module pypath.inputs.pathwaycommons)</a>
+</li>
+      <li><a href="api/pypath.inputs.pathwaycommons.pathwaycommons_kegg_interactions.html#pypath.inputs.pathwaycommons.pathwaycommons_kegg_interactions">pathwaycommons_kegg_interactions() (in module pypath.inputs.pathwaycommons)</a>
+</li>
+      <li><a href="api/pypath.inputs.pathwaycommons.pathwaycommons_netpath_interactions.html#pypath.inputs.pathwaycommons.pathwaycommons_netpath_interactions">pathwaycommons_netpath_interactions() (in module pypath.inputs.pathwaycommons)</a>
+</li>
+      <li><a href="api/pypath.inputs.pathwaycommons.pathwaycommons_panther_interactions.html#pypath.inputs.pathwaycommons.pathwaycommons_panther_interactions">pathwaycommons_panther_interactions() (in module pypath.inputs.pathwaycommons)</a>
+</li>
+      <li><a href="api/pypath.inputs.pathwaycommons.pathwaycommons_phosphosite_interactions.html#pypath.inputs.pathwaycommons.pathwaycommons_phosphosite_interactions">pathwaycommons_phosphosite_interactions() (in module pypath.inputs.pathwaycommons)</a>
+</li>
+      <li><a href="api/pypath.inputs.pathwaycommons.pathwaycommons_reactome_interactions.html#pypath.inputs.pathwaycommons.pathwaycommons_reactome_interactions">pathwaycommons_reactome_interactions() (in module pypath.inputs.pathwaycommons)</a>
+</li>
+      <li><a href="api/pypath.inputs.pathwaycommons.pathwaycommons_wikipathways_interactions.html#pypath.inputs.pathwaycommons.pathwaycommons_wikipathways_interactions">pathwaycommons_wikipathways_interactions() (in module pypath.inputs.pathwaycommons)</a>
+</li>
+      <li><a href="api/pypath.inputs.pathwaycommons.PathwayCommonsInteraction.html#pypath.inputs.pathwaycommons.PathwayCommonsInteraction">PathwayCommonsInteraction (class in pypath.inputs.pathwaycommons)</a>
+</li>
+      <li><a href="api/pypath.inputs.pathwaycommons.PathwayCommonsResource.html#pypath.inputs.pathwaycommons.PathwayCommonsResource">PathwayCommonsResource (class in pypath.inputs.pathwaycommons)</a>
+</li>
+      <li><a href="api/pypath.inputs.pazar.pazar_interactions.html#pypath.inputs.pazar.pazar_interactions">pazar_interactions() (in module pypath.inputs.pazar)</a>
+</li>
+      <li><a href="api/pypath.inputs.pathwaycommons.PathwayCommonsResource.html#pypath.inputs.pathwaycommons.PathwayCommonsResource.pc_label">pc_label (pypath.inputs.pathwaycommons.PathwayCommonsResource attribute)</a>
+</li>
+      <li><a href="api/pypath.core.complex.Pdb.html#pypath.core.complex.Pdb">Pdb (class in pypath.core.complex)</a>
+</li>
+      <li><a href="api/pypath.inputs.pdb.pdb_chains.html#pypath.inputs.pdb.pdb_chains">pdb_chains() (in module pypath.inputs.pdb)</a>
+</li>
+      <li><a href="api/pypath.inputs.pdb.pdb_complexes.html#pypath.inputs.pdb.pdb_complexes">pdb_complexes() (in module pypath.inputs.pdb)</a>
+</li>
+      <li><a href="api/pypath.utils.pdb.Segment.html#pypath.utils.pdb.Segment.pdb_end">pdb_end (pypath.utils.pdb.Segment attribute)</a>
+</li>
+      <li><a href="api/pypath.utils.pdb.Segment.html#pypath.utils.pdb.Segment.pdb_start">pdb_start (pypath.utils.pdb.Segment attribute)</a>
+</li>
+      <li><a href="api/pypath.inputs.pdb.pdb_uniprot.html#pypath.inputs.pdb.pdb_uniprot">pdb_uniprot() (in module pypath.inputs.pdb)</a>
+</li>
+      <li><a href="api/pypath.inputs.pdzbase.pdzbase_interactions.html#pypath.inputs.pdzbase.pdzbase_interactions">pdzbase_interactions() (in module pypath.inputs.pdzbase)</a>
+</li>
+      <li><a href="api/pypath.inputs.pepcyber.pepcyber_details.html#pypath.inputs.pepcyber.pepcyber_details">pepcyber_details() (in module pypath.inputs.pepcyber)</a>
+</li>
+      <li><a href="api/pypath.inputs.pepcyber.pepcyber_interactions.html#pypath.inputs.pepcyber.pepcyber_interactions">pepcyber_interactions() (in module pypath.inputs.pepcyber)</a>
+</li>
+      <li><a href="api/pypath.core.network.NetworkStatsRecord.html#pypath.core.network.NetworkStatsRecord.percent">percent (pypath.core.network.NetworkStatsRecord attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.NetworkStatsRecord.html#pypath.core.network.NetworkStatsRecord.percent_cat">percent_cat (pypath.core.network.NetworkStatsRecord attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.NetworkStatsRecord.html#pypath.core.network.NetworkStatsRecord.percent_res_cat">percent_res_cat (pypath.core.network.NetworkStatsRecord attribute)</a>
+</li>
+      <li><a href="api/pypath.inputs.uniprot.UniprotQuery.html#pypath.inputs.uniprot.UniprotQuery.perform">perform() (pypath.inputs.uniprot.UniprotQuery method)</a>
+</li>
+      <li><a href="api/pypath.inputs.cellphonedb.CellPhoneDBAnnotation.html#pypath.inputs.cellphonedb.CellPhoneDBAnnotation.peripheral">peripheral (pypath.inputs.cellphonedb.CellPhoneDBAnnotation attribute)</a>
+</li>
+      <li><a href="api/pypath.utils.seq.Pfam.html#pypath.utils.seq.Pfam">Pfam (class in pypath.utils.seq)</a>
+</li>
+      <li><a href="api/pypath.inputs.pfam.pfam_names.html#pypath.inputs.pfam.pfam_names">pfam_names() (in module pypath.inputs.pfam)</a>
+</li>
+      <li><a href="api/pypath.inputs.pfam.pfam_pdb.html#pypath.inputs.pfam.pfam_pdb">pfam_pdb() (in module pypath.inputs.pfam)</a>
+</li>
+      <li><a href="api/pypath.inputs.pfam.pfam_regions.html#pypath.inputs.pfam.pfam_regions">pfam_regions() (in module pypath.inputs.pfam)</a>
+</li>
+      <li><a href="api/pypath.inputs.pfam.pfam_uniprot.html#pypath.inputs.pfam.pfam_uniprot">pfam_uniprot() (in module pypath.inputs.pfam)</a>
+</li>
+      <li><a href="api/pypath.inputs.pharos.pharos_diseases.html#pypath.inputs.pharos.pharos_diseases">pharos_diseases() (in module pypath.inputs.pharos)</a>
+</li>
+      <li><a href="api/pypath.inputs.pharos.pharos_expression.html#pypath.inputs.pharos.pharos_expression">pharos_expression() (in module pypath.inputs.pharos)</a>
+</li>
+      <li><a href="api/pypath.inputs.pharos.pharos_general.html#pypath.inputs.pharos.pharos_general">pharos_general() (in module pypath.inputs.pharos)</a>
+</li>
+      <li><a href="api/pypath.inputs.pharos.pharos_gtex.html#pypath.inputs.pharos.pharos_gtex">pharos_gtex() (in module pypath.inputs.pharos)</a>
+</li>
+      <li><a href="api/pypath.inputs.pharos.pharos_ligands.html#pypath.inputs.pharos.pharos_ligands">pharos_ligands() (in module pypath.inputs.pharos)</a>
+</li>
+      <li><a href="api/pypath.inputs.pharos.pharos_orthologs.html#pypath.inputs.pharos.pharos_orthologs">pharos_orthologs() (in module pypath.inputs.pharos)</a>
+</li>
+      <li><a href="api/pypath.inputs.pharos.pharos_targets.html#pypath.inputs.pharos.pharos_targets">pharos_targets() (in module pypath.inputs.pharos)</a>
+</li>
+      <li><a href="api/pypath.inputs.pharos.pharos_xrefs.html#pypath.inputs.pharos.pharos_xrefs">pharos_xrefs() (in module pypath.inputs.pharos)</a>
+</li>
+      <li><a href="api/pypath.core.annot.Phobius.html#pypath.core.annot.Phobius">Phobius (class in pypath.core.annot)</a>
+</li>
+      <li><a href="api/pypath.inputs.phobius.phobius_annotations.html#pypath.inputs.phobius.phobius_annotations">phobius_annotations() (in module pypath.inputs.phobius)</a>
+</li>
+      <li><a href="api/pypath.core.annot.Phosphatome.html#pypath.core.annot.Phosphatome">Phosphatome (class in pypath.core.annot)</a>
+</li>
+      <li><a href="api/pypath.inputs.phosphatome.phosphatome_annotations.html#pypath.inputs.phosphatome.phosphatome_annotations">phosphatome_annotations() (in module pypath.inputs.phosphatome)</a>
+</li>
+      <li><a href="api/pypath.inputs.phosphoelm.phosphoelm_enzyme_substrate.html#pypath.inputs.phosphoelm.phosphoelm_enzyme_substrate">phosphoelm_enzyme_substrate() (in module pypath.inputs.phosphoelm)</a>
+</li>
+      <li><a href="api/pypath.inputs.phosphoelm.phosphoelm_interactions.html#pypath.inputs.phosphoelm.phosphoelm_interactions">phosphoelm_interactions() (in module pypath.inputs.phosphoelm)</a>
+</li>
+      <li><a href="api/pypath.inputs.phosphoelm.phosphoelm_kinases.html#pypath.inputs.phosphoelm.phosphoelm_kinases">phosphoelm_kinases() (in module pypath.inputs.phosphoelm)</a>
+</li>
+      <li><a href="api/pypath.inputs.phosphonetworks.phosphonetworks_enzyme_substrate.html#pypath.inputs.phosphonetworks.phosphonetworks_enzyme_substrate">phosphonetworks_enzyme_substrate() (in module pypath.inputs.phosphonetworks)</a>
+</li>
+      <li><a href="api/pypath.inputs.phosphonetworks.phosphonetworks_interactions.html#pypath.inputs.phosphonetworks.phosphonetworks_interactions">phosphonetworks_interactions() (in module pypath.inputs.phosphonetworks)</a>
+</li>
+      <li><a href="api/pypath.inputs.phosphopoint.phosphopoint_directions.html#pypath.inputs.phosphopoint.phosphopoint_directions">phosphopoint_directions() (in module pypath.inputs.phosphopoint)</a>
+</li>
+      <li><a href="api/pypath.inputs.phosphopoint.phosphopoint_interactions.html#pypath.inputs.phosphopoint.phosphopoint_interactions">phosphopoint_interactions() (in module pypath.inputs.phosphopoint)</a>
+</li>
+      <li><a href="api/pypath.inputs.phosphosite.phosphosite_directions.html#pypath.inputs.phosphosite.phosphosite_directions">phosphosite_directions() (in module pypath.inputs.phosphosite)</a>
+</li>
+      <li><a href="api/pypath.inputs.phosphosite.phosphosite_enzyme_substrate.html#pypath.inputs.phosphosite.phosphosite_enzyme_substrate">phosphosite_enzyme_substrate() (in module pypath.inputs.phosphosite)</a>
+</li>
+      <li><a href="api/pypath.inputs.phosphosite.phosphosite_interactions.html#pypath.inputs.phosphosite.phosphosite_interactions">phosphosite_interactions() (in module pypath.inputs.phosphosite)</a>
+</li>
+      <li><a href="api/pypath.inputs.phosphosite.phosphosite_interactions_all.html#pypath.inputs.phosphosite.phosphosite_interactions_all">phosphosite_interactions_all() (in module pypath.inputs.phosphosite)</a>
+</li>
+      <li><a href="api/pypath.inputs.phosphosite.phosphosite_interactions_curated.html#pypath.inputs.phosphosite.phosphosite_interactions_curated">phosphosite_interactions_curated() (in module pypath.inputs.phosphosite)</a>
+</li>
+      <li><a href="api/pypath.inputs.phosphosite.phosphosite_interactions_new.html#pypath.inputs.phosphosite.phosphosite_interactions_new">phosphosite_interactions_new() (in module pypath.inputs.phosphosite)</a>
+</li>
+      <li><a href="api/pypath.inputs.phosphosite.phosphosite_interactions_noref.html#pypath.inputs.phosphosite.phosphosite_interactions_noref">phosphosite_interactions_noref() (in module pypath.inputs.phosphosite)</a>
+</li>
+      <li><a href="api/pypath.inputs.phosphosite.phosphosite_ptm_orthology.html#pypath.inputs.phosphosite.phosphosite_ptm_orthology">phosphosite_ptm_orthology() (in module pypath.inputs.phosphosite)</a>
+</li>
+      <li><a href="api/pypath.inputs.phosphosite.phosphosite_ptms.html#pypath.inputs.phosphosite.phosphosite_ptms">phosphosite_ptms() (in module pypath.inputs.phosphosite)</a>
+</li>
+      <li><a href="api/pypath.inputs.phosphosite.phosphosite_regsites.html#pypath.inputs.phosphosite.phosphosite_regsites">phosphosite_regsites() (in module pypath.inputs.phosphosite)</a>
+</li>
+      <li><a href="api/pypath.inputs.phosphosite.phosphosite_regsites_one_organism.html#pypath.inputs.phosphosite.phosphosite_regsites_one_organism">phosphosite_regsites_one_organism() (in module pypath.inputs.phosphosite)</a>
+</li>
+      <li><a href="api/pypath.omnipath.app.DatabaseManager.html#pypath.omnipath.app.DatabaseManager.pickle_exists">pickle_exists() (pypath.omnipath.app.DatabaseManager method)</a>
+</li>
+      <li><a href="api/pypath.omnipath.app.DatabaseManager.html#pypath.omnipath.app.DatabaseManager.pickle_path">pickle_path() (pypath.omnipath.app.DatabaseManager method)</a>
+</li>
+      <li><a href="api/pypath.internals.input_formats.PickleMapping.html#pypath.internals.input_formats.PickleMapping">PickleMapping (class in pypath.internals.input_formats)</a>
+</li>
+      <li><a href="api/pypath.inputs.reaction.pid_biopax.html#pypath.inputs.reaction.pid_biopax">pid_biopax() (in module pypath.inputs.reaction)</a>
+</li>
+      <li><a href="api/pypath.inputs.reaction.pid_interactions.html#pypath.inputs.reaction.pid_interactions">pid_interactions() (in module pypath.inputs.reaction)</a>
+</li>
+      <li><a href="api/pypath.inputs.pisa.pisa_bonds.html#pypath.inputs.pisa.pisa_bonds">pisa_bonds() (in module pypath.inputs.pisa)</a>
+</li>
+      <li><a href="api/pypath.inputs.pisa.pisa_interfaces.html#pypath.inputs.pisa.pisa_interfaces">pisa_interfaces() (in module pypath.inputs.pisa)</a>
+</li>
+      <li><a href="api/pypath.inputs.pisa.PisaBond.html#pypath.inputs.pisa.PisaBond">PisaBond (class in pypath.inputs.pisa)</a>
+</li>
+      <li><a href="api/pypath.visual.drawing.Plot.html#pypath.visual.drawing.Plot">Plot (class in pypath.visual.drawing)</a>
+</li>
+      <li><a href="api/pypath.inputs.cellinker.CellinkerInteraction.html#pypath.inputs.cellinker.CellinkerInteraction.pmids">pmids (pypath.inputs.cellinker.CellinkerInteraction attribute)</a>
+</li>
+      <li><a href="api/pypath.inputs.pubmed.pmids_dict.html#pypath.inputs.pubmed.pmids_dict">pmids_dict() (in module pypath.inputs.pubmed)</a>
+</li>
+      <li><a href="api/pypath.inputs.pubmed.pmids_list.html#pypath.inputs.pubmed.pmids_list">pmids_list() (in module pypath.inputs.pubmed)</a>
+</li>
+      <li><a href="api/pypath.internals.resource.NetworkDataset.html#pypath.internals.resource.NetworkDataset.pop">pop() (pypath.internals.resource.NetworkDataset method)</a>
+</li>
+      <li><a href="api/pypath.internals.resource.NetworkDataset.html#pypath.internals.resource.NetworkDataset.popitem">popitem() (pypath.internals.resource.NetworkDataset method)</a>
+</li>
+      <li><a href="api/pypath.core.annot.CustomAnnotation.html#pypath.core.annot.CustomAnnotation.populate_classes">populate_classes() (pypath.core.annot.CustomAnnotation method)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.intercell.IntercellAnnotation.html#pypath.core.intercell.IntercellAnnotation.populate_classes">(pypath.core.intercell.IntercellAnnotation method)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.annot.CustomAnnotation.html#pypath.core.annot.CustomAnnotation.populate_scores">populate_scores() (pypath.core.annot.CustomAnnotation method)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.intercell.IntercellAnnotation.html#pypath.core.intercell.IntercellAnnotation.populate_scores">(pypath.core.intercell.IntercellAnnotation method)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.positive_a_b">positive_a_b() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.positive_b_a">positive_b_a() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.positive_resources_a_b">positive_resources_a_b() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.positive_resources_b_a">positive_resources_b_a() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.positive_reverse">positive_reverse() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.positive_straight">positive_straight() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.post_transcriptionally_activated_by">post_transcriptionally_activated_by (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.post_transcriptionally_activates">post_transcriptionally_activates (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.post_transcriptionally_regulated_by">post_transcriptionally_regulated_by (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.post_transcriptionally_regulates">post_transcriptionally_regulates (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.post_transcriptionally_suppressed_by">post_transcriptionally_suppressed_by (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.post_transcriptionally_suppresses">post_transcriptionally_suppresses (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.post_translationally_activated_by">post_translationally_activated_by (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.post_translationally_activates">post_translationally_activates (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.post_translationally_regulated_by">post_translationally_regulated_by (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.post_translationally_regulates">post_translationally_regulates (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.post_translationally_suppressed_by">post_translationally_suppressed_by (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.post_translationally_suppresses">post_translationally_suppresses (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.inputs.dorothea.DorotheaInteraction.html#pypath.inputs.dorothea.DorotheaInteraction.predicted">predicted (pypath.inputs.dorothea.DorotheaInteraction attribute)</a>
+</li>
+      <li><a href="api/pypath.inputs.dorothea.DorotheaInteraction.html#pypath.inputs.dorothea.DorotheaInteraction.predicted_sources">predicted_sources (pypath.inputs.dorothea.DorotheaInteraction attribute)</a>
+</li>
+      <li><a href="api/pypath.share.curl.preserve_off.html#pypath.share.curl.preserve_off">preserve_off (class in pypath.share.curl)</a>
+</li>
+      <li><a href="api/pypath.share.curl.preserve_on.html#pypath.share.curl.preserve_on">preserve_on (class in pypath.share.curl)</a>
+</li>
+      <li><a href="api/pypath.utils.mapping.Mapper.html#pypath.utils.mapping.Mapper.primary_uniprot">primary_uniprot() (pypath.utils.mapping.Mapper method)</a>
+</li>
+      <li><a href="api/pypath.utils.uniprot.print_features.html#pypath.utils.uniprot.print_features">print_features() (in module pypath.utils.uniprot)</a>
+</li>
+      <li><a href="api/pypath.inputs.pro.pro_mapping.html#pypath.inputs.pro.pro_mapping">pro_mapping() (in module pypath.inputs.pro)</a>
+</li>
+      <li><a href="api/pypath.core.annot.Adhesome.html#pypath.core.annot.Adhesome.process">process() (pypath.core.annot.Adhesome method)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.annot.Almen2009.html#pypath.core.annot.Almen2009.process">(pypath.core.annot.Almen2009 method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.AnnotationBase.html#pypath.core.annot.AnnotationBase.process">(pypath.core.annot.AnnotationBase method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Baccin2019.html#pypath.core.annot.Baccin2019.process">(pypath.core.annot.Baccin2019 method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Biogps.html#pypath.core.annot.Biogps.process">(pypath.core.annot.Biogps method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cancerdrugsdb.html#pypath.core.annot.Cancerdrugsdb.process">(pypath.core.annot.Cancerdrugsdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CancerGeneCensus.html#pypath.core.annot.CancerGeneCensus.process">(pypath.core.annot.CancerGeneCensus method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cancersea.html#pypath.core.annot.Cancersea.process">(pypath.core.annot.Cancersea method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cellcall.html#pypath.core.annot.Cellcall.process">(pypath.core.annot.Cellcall method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cellcellinteractions.html#pypath.core.annot.Cellcellinteractions.process">(pypath.core.annot.Cellcellinteractions method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cellchatdb.html#pypath.core.annot.Cellchatdb.process">(pypath.core.annot.Cellchatdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CellchatdbComplex.html#pypath.core.annot.CellchatdbComplex.process">(pypath.core.annot.CellchatdbComplex method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cellinker.html#pypath.core.annot.Cellinker.process">(pypath.core.annot.Cellinker method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CellinkerComplex.html#pypath.core.annot.CellinkerComplex.process">(pypath.core.annot.CellinkerComplex method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CellPhoneDB.html#pypath.core.annot.CellPhoneDB.process">(pypath.core.annot.CellPhoneDB method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CellPhoneDBComplex.html#pypath.core.annot.CellPhoneDBComplex.process">(pypath.core.annot.CellPhoneDBComplex method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CellSurfaceProteinAtlas.html#pypath.core.annot.CellSurfaceProteinAtlas.process">(pypath.core.annot.CellSurfaceProteinAtlas method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CellSurfaceProteinAtlasCellType.html#pypath.core.annot.CellSurfaceProteinAtlasCellType.process">(pypath.core.annot.CellSurfaceProteinAtlasCellType method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Celltalkdb.html#pypath.core.annot.Celltalkdb.process">(pypath.core.annot.Celltalkdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Celltypist.html#pypath.core.annot.Celltypist.process">(pypath.core.annot.Celltypist method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Comppi.html#pypath.core.annot.Comppi.process">(pypath.core.annot.Comppi method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Connectomedb.html#pypath.core.annot.Connectomedb.process">(pypath.core.annot.Connectomedb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Corum.html#pypath.core.annot.Corum.process">(pypath.core.annot.Corum method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CorumFuncat.html#pypath.core.annot.CorumFuncat.process">(pypath.core.annot.CorumFuncat method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CorumGO.html#pypath.core.annot.CorumGO.process">(pypath.core.annot.CorumGO method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cpad.html#pypath.core.annot.Cpad.process">(pypath.core.annot.Cpad method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cytosig.html#pypath.core.annot.Cytosig.process">(pypath.core.annot.Cytosig method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Dgidb.html#pypath.core.annot.Dgidb.process">(pypath.core.annot.Dgidb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Disgenet.html#pypath.core.annot.Disgenet.process">(pypath.core.annot.Disgenet method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Embrace.html#pypath.core.annot.Embrace.process">(pypath.core.annot.Embrace method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Exocarta.html#pypath.core.annot.Exocarta.process">(pypath.core.annot.Exocarta method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.GOIntercell.html#pypath.core.annot.GOIntercell.process">(pypath.core.annot.GOIntercell method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Gpcrdb.html#pypath.core.annot.Gpcrdb.process">(pypath.core.annot.Gpcrdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.GuideToPharmacology.html#pypath.core.annot.GuideToPharmacology.process">(pypath.core.annot.GuideToPharmacology method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Hgnc.html#pypath.core.annot.Hgnc.process">(pypath.core.annot.Hgnc method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.HpmrComplex.html#pypath.core.annot.HpmrComplex.process">(pypath.core.annot.HpmrComplex method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.HPO.html#pypath.core.annot.HPO.process">(pypath.core.annot.HPO method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Humancellmap.html#pypath.core.annot.Humancellmap.process">(pypath.core.annot.Humancellmap method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.HumanPlasmaMembraneReceptome.html#pypath.core.annot.HumanPlasmaMembraneReceptome.process">(pypath.core.annot.HumanPlasmaMembraneReceptome method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.HumanProteinAtlas.html#pypath.core.annot.HumanProteinAtlas.process">(pypath.core.annot.HumanProteinAtlas method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.HumanProteinAtlasSecretome.html#pypath.core.annot.HumanProteinAtlasSecretome.process">(pypath.core.annot.HumanProteinAtlasSecretome method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.HumanProteinAtlasSubcellular.html#pypath.core.annot.HumanProteinAtlasSubcellular.process">(pypath.core.annot.HumanProteinAtlasSubcellular method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Icellnet.html#pypath.core.annot.Icellnet.process">(pypath.core.annot.Icellnet method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.IcellnetComplex.html#pypath.core.annot.IcellnetComplex.process">(pypath.core.annot.IcellnetComplex method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Integrins.html#pypath.core.annot.Integrins.process">(pypath.core.annot.Integrins method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.InterPro.html#pypath.core.annot.InterPro.process">(pypath.core.annot.InterPro method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Intogen.html#pypath.core.annot.Intogen.process">(pypath.core.annot.Intogen method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Italk.html#pypath.core.annot.Italk.process">(pypath.core.annot.Italk method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.KeggPathways.html#pypath.core.annot.KeggPathways.process">(pypath.core.annot.KeggPathways method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.KeggPathwaysPC.html#pypath.core.annot.KeggPathwaysPC.process">(pypath.core.annot.KeggPathwaysPC method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Kinasedotcom.html#pypath.core.annot.Kinasedotcom.process">(pypath.core.annot.Kinasedotcom method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Kirouac2010.html#pypath.core.annot.Kirouac2010.process">(pypath.core.annot.Kirouac2010 method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Lambert2018.html#pypath.core.annot.Lambert2018.process">(pypath.core.annot.Lambert2018 method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.LigandReceptor.html#pypath.core.annot.LigandReceptor.process">(pypath.core.annot.LigandReceptor method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Locate.html#pypath.core.annot.Locate.process">(pypath.core.annot.Locate method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Lrdb.html#pypath.core.annot.Lrdb.process">(pypath.core.annot.Lrdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Matrisome.html#pypath.core.annot.Matrisome.process">(pypath.core.annot.Matrisome method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Matrixdb.html#pypath.core.annot.Matrixdb.process">(pypath.core.annot.Matrixdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Mcam.html#pypath.core.annot.Mcam.process">(pypath.core.annot.Mcam method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Membranome.html#pypath.core.annot.Membranome.process">(pypath.core.annot.Membranome method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Msigdb.html#pypath.core.annot.Msigdb.process">(pypath.core.annot.Msigdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.NetpathPathways.html#pypath.core.annot.NetpathPathways.process">(pypath.core.annot.NetpathPathways method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Opm.html#pypath.core.annot.Opm.process">(pypath.core.annot.Opm method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Panglaodb.html#pypath.core.annot.Panglaodb.process">(pypath.core.annot.Panglaodb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Phobius.html#pypath.core.annot.Phobius.process">(pypath.core.annot.Phobius method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Phosphatome.html#pypath.core.annot.Phosphatome.process">(pypath.core.annot.Phosphatome method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Progeny.html#pypath.core.annot.Progeny.process">(pypath.core.annot.Progeny method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Ramilowski2015.html#pypath.core.annot.Ramilowski2015.process">(pypath.core.annot.Ramilowski2015 method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Ramilowski2015Location.html#pypath.core.annot.Ramilowski2015Location.process">(pypath.core.annot.Ramilowski2015Location method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Scconnect.html#pypath.core.annot.Scconnect.process">(pypath.core.annot.Scconnect method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.ScconnectComplex.html#pypath.core.annot.ScconnectComplex.process">(pypath.core.annot.ScconnectComplex method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.SignalinkFunctions.html#pypath.core.annot.SignalinkFunctions.process">(pypath.core.annot.SignalinkFunctions method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.SignalinkPathways.html#pypath.core.annot.SignalinkPathways.process">(pypath.core.annot.SignalinkPathways method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.SignorPathways.html#pypath.core.annot.SignorPathways.process">(pypath.core.annot.SignorPathways method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Surfaceome.html#pypath.core.annot.Surfaceome.process">(pypath.core.annot.Surfaceome method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Talklr.html#pypath.core.annot.Talklr.process">(pypath.core.annot.Talklr method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Tcdb.html#pypath.core.annot.Tcdb.process">(pypath.core.annot.Tcdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Tfcensus.html#pypath.core.annot.Tfcensus.process">(pypath.core.annot.Tfcensus method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Topdb.html#pypath.core.annot.Topdb.process">(pypath.core.annot.Topdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.UniprotFamilies.html#pypath.core.annot.UniprotFamilies.process">(pypath.core.annot.UniprotFamilies method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.UniprotKeywords.html#pypath.core.annot.UniprotKeywords.process">(pypath.core.annot.UniprotKeywords method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.UniprotLocations.html#pypath.core.annot.UniprotLocations.process">(pypath.core.annot.UniprotLocations method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.UniprotTissues.html#pypath.core.annot.UniprotTissues.process">(pypath.core.annot.UniprotTissues method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.UniprotTopologies.html#pypath.core.annot.UniprotTopologies.process">(pypath.core.annot.UniprotTopologies method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Vesiclepedia.html#pypath.core.annot.Vesiclepedia.process">(pypath.core.annot.Vesiclepedia method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Wang.html#pypath.core.annot.Wang.process">(pypath.core.annot.Wang method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Zhong2015.html#pypath.core.annot.Zhong2015.process">(pypath.core.annot.Zhong2015 method)</a>
+</li>
+        <li><a href="api/pypath.core.complex.AbstractComplexResource.html#pypath.core.complex.AbstractComplexResource.process">(pypath.core.complex.AbstractComplexResource method)</a>
+</li>
+        <li><a href="api/pypath.core.complex.Cellchatdb.html#pypath.core.complex.Cellchatdb.process">(pypath.core.complex.Cellchatdb method)</a>
+</li>
+        <li><a href="api/pypath.core.complex.Cellinker.html#pypath.core.complex.Cellinker.process">(pypath.core.complex.Cellinker method)</a>
+</li>
+        <li><a href="api/pypath.core.complex.CellPhoneDB.html#pypath.core.complex.CellPhoneDB.process">(pypath.core.complex.CellPhoneDB method)</a>
+</li>
+        <li><a href="api/pypath.core.complex.Compleat.html#pypath.core.complex.Compleat.process">(pypath.core.complex.Compleat method)</a>
+</li>
+        <li><a href="api/pypath.core.complex.ComplexAggregator.html#pypath.core.complex.ComplexAggregator.process">(pypath.core.complex.ComplexAggregator method)</a>
+</li>
+        <li><a href="api/pypath.core.complex.ComplexPortal.html#pypath.core.complex.ComplexPortal.process">(pypath.core.complex.ComplexPortal method)</a>
+</li>
+        <li><a href="api/pypath.core.complex.Corum.html#pypath.core.complex.Corum.process">(pypath.core.complex.Corum method)</a>
+</li>
+        <li><a href="api/pypath.core.complex.GuideToPharmacology.html#pypath.core.complex.GuideToPharmacology.process">(pypath.core.complex.GuideToPharmacology method)</a>
+</li>
+        <li><a href="api/pypath.core.complex.Havugimana.html#pypath.core.complex.Havugimana.process">(pypath.core.complex.Havugimana method)</a>
+</li>
+        <li><a href="api/pypath.core.complex.Hpmr.html#pypath.core.complex.Hpmr.process">(pypath.core.complex.Hpmr method)</a>
+</li>
+        <li><a href="api/pypath.core.complex.Humap.html#pypath.core.complex.Humap.process">(pypath.core.complex.Humap method)</a>
+</li>
+        <li><a href="api/pypath.core.complex.Humap2.html#pypath.core.complex.Humap2.process">(pypath.core.complex.Humap2 method)</a>
+</li>
+        <li><a href="api/pypath.core.complex.Icellnet.html#pypath.core.complex.Icellnet.process">(pypath.core.complex.Icellnet method)</a>
+</li>
+        <li><a href="api/pypath.core.complex.Kegg.html#pypath.core.complex.Kegg.process">(pypath.core.complex.Kegg method)</a>
+</li>
+        <li><a href="api/pypath.core.complex.Pdb.html#pypath.core.complex.Pdb.process">(pypath.core.complex.Pdb method)</a>
+</li>
+        <li><a href="api/pypath.core.complex.Signor.html#pypath.core.complex.Signor.process">(pypath.core.complex.Signor method)</a>
+</li>
+        <li><a href="api/pypath.core.complex.Spike.html#pypath.core.complex.Spike.process">(pypath.core.complex.Spike method)</a>
+</li>
+        <li><a href="api/pypath.internals.resource.AbstractResource.html#pypath.internals.resource.AbstractResource.process">(pypath.internals.resource.AbstractResource method)</a>
+</li>
+        <li><a href="api/pypath.utils.pyreact.BioPaxReader.html#pypath.utils.pyreact.BioPaxReader.process">(pypath.utils.pyreact.BioPaxReader method)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.inputs.threedid.process_3did_dmi.html#pypath.inputs.threedid.process_3did_dmi">process_3did_dmi() (in module pypath.inputs.threedid)</a>
+</li>
+      <li><a href="api/pypath.core.annot.CustomAnnotation.html#pypath.core.annot.CustomAnnotation.process_annot">process_annot() (pypath.core.annot.CustomAnnotation method)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.intercell.IntercellAnnotation.html#pypath.core.intercell.IntercellAnnotation.process_annot">(pypath.core.intercell.IntercellAnnotation method)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.annot.GOCustomIntercell.html#pypath.core.annot.GOCustomIntercell.process_categories">process_categories() (pypath.core.annot.GOCustomIntercell method)</a>
+
+      <ul>
+        <li><a href="api/pypath.utils.go.GOCustomAnnotation.html#pypath.utils.go.GOCustomAnnotation.process_categories">(pypath.utils.go.GOCustomAnnotation method)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.inputs.reaction.process_complex.html#pypath.inputs.reaction.process_complex">process_complex() (in module pypath.inputs.reaction)</a>
+</li>
+      <li><a href="api/pypath.inputs.reaction.process_controls.html#pypath.inputs.reaction.process_controls">process_controls() (in module pypath.inputs.reaction)</a>
+</li>
+      <li><a href="api/pypath.inputs.reaction.process_reactions.html#pypath.inputs.reaction.process_reactions">process_reactions() (in module pypath.inputs.reaction)</a>
+</li>
+      <li><a href="api/pypath.utils.seq.Pfam.html#pypath.utils.seq.Pfam.processor">processor() (pypath.utils.seq.Pfam method)</a>
+
+      <ul>
+        <li><a href="api/pypath.utils.seq.Resource.html#pypath.utils.seq.Resource.processor">(pypath.utils.seq.Resource method)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.annot.Progeny.html#pypath.core.annot.Progeny">Progeny (class in pypath.core.annot)</a>
+</li>
+      <li><a href="api/pypath.inputs.progeny.progeny_annotations.html#pypath.inputs.progeny.progeny_annotations">progeny_annotations() (in module pypath.inputs.progeny)</a>
+</li>
+      <li><a href="api/pypath.inputs.progeny.progeny_raw.html#pypath.inputs.progeny.progeny_raw">progeny_raw() (in module pypath.inputs.progeny)</a>
+</li>
+      <li><a href="api/pypath.share.progress.Progress.html#pypath.share.progress.Progress">Progress (class in pypath.share.progress)</a>
+</li>
+      <li><a href="api/pypath.internals.input_formats.ProMapping.html#pypath.internals.input_formats.ProMapping">ProMapping (class in pypath.internals.input_formats)</a>
+</li>
+      <li><a href="api/pypath.utils.pyreact.Protein.html#pypath.utils.pyreact.Protein">Protein (class in pypath.utils.pyreact)</a>
+</li>
+      <li><a href="api/pypath.inputs.uniprot.protein_datasheet.html#pypath.inputs.uniprot.protein_datasheet">protein_datasheet() (in module pypath.inputs.uniprot)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.protein_identifiers_by_data_model">protein_identifiers_by_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.protein_identifiers_by_data_model">protein_identifiers_by_data_model() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.protein_identifiers_by_interaction_type">protein_identifiers_by_interaction_type (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.protein_identifiers_by_interaction_type">protein_identifiers_by_interaction_type() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.protein_identifiers_by_interaction_type_and_data_model">protein_identifiers_by_interaction_type_and_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.protein_identifiers_by_interaction_type_and_data_model">protein_identifiers_by_interaction_type_and_data_model() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.protein_identifiers_by_interaction_type_and_data_model_and_resource">protein_identifiers_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.protein_identifiers_by_interaction_type_and_data_model_and_resource">protein_identifiers_by_interaction_type_and_data_model_and_resource() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.protein_identifiers_by_reference">protein_identifiers_by_reference (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.protein_identifiers_by_reference">protein_identifiers_by_reference() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.protein_identifiers_by_resource">protein_identifiers_by_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.protein_identifiers_by_resource">protein_identifiers_by_resource() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.protein_labels_by_data_model">protein_labels_by_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.protein_labels_by_data_model">protein_labels_by_data_model() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.protein_labels_by_interaction_type">protein_labels_by_interaction_type (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.protein_labels_by_interaction_type">protein_labels_by_interaction_type() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.protein_labels_by_interaction_type_and_data_model">protein_labels_by_interaction_type_and_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.protein_labels_by_interaction_type_and_data_model">protein_labels_by_interaction_type_and_data_model() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.protein_labels_by_interaction_type_and_data_model_and_resource">protein_labels_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.protein_labels_by_interaction_type_and_data_model_and_resource">protein_labels_by_interaction_type_and_data_model_and_resource() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.protein_labels_by_reference">protein_labels_by_reference (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.protein_labels_by_reference">protein_labels_by_reference() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.protein_labels_by_resource">protein_labels_by_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.protein_labels_by_resource">protein_labels_by_resource() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.inputs.proteinatlas.proteinatlas_annotations.html#pypath.inputs.proteinatlas.proteinatlas_annotations">proteinatlas_annotations() (in module pypath.inputs.proteinatlas)</a>
+</li>
+      <li><a href="api/pypath.inputs.proteinatlas.proteinatlas_secretome_annotations.html#pypath.inputs.proteinatlas.proteinatlas_secretome_annotations">proteinatlas_secretome_annotations() (in module pypath.inputs.proteinatlas)</a>
+</li>
+      <li><a href="api/pypath.inputs.proteinatlas.proteinatlas_subcellular_annotations.html#pypath.inputs.proteinatlas.proteinatlas_subcellular_annotations">proteinatlas_subcellular_annotations() (in module pypath.inputs.proteinatlas)</a>
+</li>
+      <li><a href="api/pypath.utils.pyreact.ProteinFamily.html#pypath.utils.pyreact.ProteinFamily">ProteinFamily (class in pypath.utils.pyreact)</a>
+</li>
+      <li><a href="api/pypath.utils.orthology.ProteinOrthology.html#pypath.utils.orthology.ProteinOrthology">ProteinOrthology (class in pypath.utils.orthology)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.proteins_by_data_model">proteins_by_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.proteins_by_data_model">proteins_by_data_model() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.proteins_by_interaction_type">proteins_by_interaction_type (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.proteins_by_interaction_type">proteins_by_interaction_type() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.proteins_by_interaction_type_and_data_model">proteins_by_interaction_type_and_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.proteins_by_interaction_type_and_data_model">proteins_by_interaction_type_and_data_model() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.proteins_by_interaction_type_and_data_model_and_resource">proteins_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.proteins_by_interaction_type_and_data_model_and_resource">proteins_by_interaction_type_and_data_model_and_resource() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.proteins_by_reference">proteins_by_reference (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.proteins_by_reference">proteins_by_reference() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.proteins_by_resource">proteins_by_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.proteins_by_resource">proteins_by_resource() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.utils.orthology.Proteomes.html#pypath.utils.orthology.Proteomes">Proteomes (class in pypath.utils.orthology)</a>
+</li>
+      <li><a href="api/pypath.utils.proteomicsdb.ProteomicsDB.html#pypath.utils.proteomicsdb.ProteomicsDB">ProteomicsDB (class in pypath.utils.proteomicsdb)</a>
+</li>
+      <li><a href="api/pypath.inputs.protmapper.protmapper_enzyme_substrate.html#pypath.inputs.protmapper.protmapper_enzyme_substrate">protmapper_enzyme_substrate() (in module pypath.inputs.protmapper)</a>
+</li>
+      <li><a href="api/pypath.inputs.protmapper.protmapper_interactions.html#pypath.inputs.protmapper.protmapper_interactions">protmapper_interactions() (in module pypath.inputs.protmapper)</a>
+</li>
+      <li><a href="api/pypath.internals.intera.Ptm.html#pypath.internals.intera.Ptm">Ptm (class in pypath.internals.intera)</a>
+</li>
+      <li><a href="api/pypath.utils.uniprot.ptm.html#pypath.utils.uniprot.ptm">ptm() (in module pypath.utils.uniprot)</a>
+</li>
+      <li><a href="api/pypath.core.enz_sub.EnzymeSubstrateOrthologyProcessor.html#pypath.core.enz_sub.EnzymeSubstrateOrthologyProcessor.ptm_orthology">ptm_orthology() (pypath.core.enz_sub.EnzymeSubstrateOrthologyProcessor method)</a>
+
+      <ul>
+        <li><a href="api/pypath.utils.orthology.PtmOrthology.html#pypath.utils.orthology.PtmOrthology.ptm_orthology">(pypath.utils.orthology.PtmOrthology method)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.inputs.iptmnet.IptmnetInteraction.html#pypath.inputs.iptmnet.IptmnetInteraction.ptm_type">ptm_type (pypath.inputs.iptmnet.IptmnetInteraction attribute)</a>
+</li>
+      <li><a href="api/pypath.utils.uniprot.ptm_with_xrefs.html#pypath.utils.uniprot.ptm_with_xrefs">ptm_with_xrefs() (in module pypath.utils.uniprot)</a>
+</li>
+      <li><a href="api/pypath.utils.orthology.PtmOrthology.html#pypath.utils.orthology.PtmOrthology">PtmOrthology (class in pypath.utils.orthology)</a>
+</li>
+      <li><a href="api/pypath.inputs.adrecs.AdrecsDrug.html#pypath.inputs.adrecs.AdrecsDrug.pubchem_cid">pubchem_cid (pypath.inputs.adrecs.AdrecsDrug attribute)</a>
+</li>
+      <li><a href="api/pypath.inputs.pubchem.pubchem_mapping.html#pypath.inputs.pubchem.pubchem_mapping">pubchem_mapping() (in module pypath.inputs.pubchem)</a>
+</li>
+      <li><a href="api/pypath.inputs.dorothea.DorotheaInteraction.html#pypath.inputs.dorothea.DorotheaInteraction.pubmed">pubmed (pypath.inputs.dorothea.DorotheaInteraction attribute)</a>
+</li>
+      <li><a href="api/pypath.core.evidence.Evidence.html#pypath.core.evidence.Evidence.pubmeds">pubmeds (pypath.core.evidence.Evidence property)</a>
+</li>
+      <li>
+    pypath
+
+      <ul>
+        <li><a href="api/pypath.html#module-pypath">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.core
+
+      <ul>
+        <li><a href="api/pypath.core.html#module-pypath.core">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.core.annot
+
+      <ul>
+        <li><a href="api/pypath.core.annot.html#module-pypath.core.annot">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.core.attrs
+
+      <ul>
+        <li><a href="api/pypath.core.attrs.html#module-pypath.core.attrs">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.core.common
+
+      <ul>
+        <li><a href="api/pypath.core.common.html#module-pypath.core.common">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.core.complex
+
+      <ul>
+        <li><a href="api/pypath.core.complex.html#module-pypath.core.complex">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.core.entity
+
+      <ul>
+        <li><a href="api/pypath.core.entity.html#module-pypath.core.entity">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.core.enz_sub
+
+      <ul>
+        <li><a href="api/pypath.core.enz_sub.html#module-pypath.core.enz_sub">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.core.evidence
+
+      <ul>
+        <li><a href="api/pypath.core.evidence.html#module-pypath.core.evidence">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.core.interaction
+
+      <ul>
+        <li><a href="api/pypath.core.interaction.html#module-pypath.core.interaction">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.core.intercell
+
+      <ul>
+        <li><a href="api/pypath.core.intercell.html#module-pypath.core.intercell">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.core.intercell_annot
+
+      <ul>
+        <li><a href="api/pypath.core.intercell_annot.html#module-pypath.core.intercell_annot">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.core.network
+
+      <ul>
+        <li><a href="api/pypath.core.network.html#module-pypath.core.network">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.data
+
+      <ul>
+        <li><a href="api/pypath.data.html#module-pypath.data">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs
+
+      <ul>
+        <li><a href="api/pypath.inputs.html#module-pypath.inputs">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.abs
+
+      <ul>
+        <li><a href="api/pypath.inputs.abs.html#module-pypath.inputs.abs">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.acsn
+
+      <ul>
+        <li><a href="api/pypath.inputs.acsn.html#module-pypath.inputs.acsn">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.adhesome
+
+      <ul>
+        <li><a href="api/pypath.inputs.adhesome.html#module-pypath.inputs.adhesome">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.adrecs
+
+      <ul>
+        <li><a href="api/pypath.inputs.adrecs.html#module-pypath.inputs.adrecs">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.almen2009
+
+      <ul>
+        <li><a href="api/pypath.inputs.almen2009.html#module-pypath.inputs.almen2009">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.baccin2019
+
+      <ul>
+        <li><a href="api/pypath.inputs.baccin2019.html#module-pypath.inputs.baccin2019">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.biogps
+
+      <ul>
+        <li><a href="api/pypath.inputs.biogps.html#module-pypath.inputs.biogps">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.biogrid
+
+      <ul>
+        <li><a href="api/pypath.inputs.biogrid.html#module-pypath.inputs.biogrid">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.biomart
+
+      <ul>
+        <li><a href="api/pypath.inputs.biomart.html#module-pypath.inputs.biomart">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.biomodels
+
+      <ul>
+        <li><a href="api/pypath.inputs.biomodels.html#module-pypath.inputs.biomodels">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.ca1
+
+      <ul>
+        <li><a href="api/pypath.inputs.ca1.html#module-pypath.inputs.ca1">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.cancercellmap
+
+      <ul>
+        <li><a href="api/pypath.inputs.cancercellmap.html#module-pypath.inputs.cancercellmap">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.cancerdrugsdb
+
+      <ul>
+        <li><a href="api/pypath.inputs.cancerdrugsdb.html#module-pypath.inputs.cancerdrugsdb">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.cancersea
+
+      <ul>
+        <li><a href="api/pypath.inputs.cancersea.html#module-pypath.inputs.cancersea">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.cell
+
+      <ul>
+        <li><a href="api/pypath.inputs.cell.html#module-pypath.inputs.cell">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.cellcall
+
+      <ul>
+        <li><a href="api/pypath.inputs.cellcall.html#module-pypath.inputs.cellcall">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.cellcellinteractions
+
+      <ul>
+        <li><a href="api/pypath.inputs.cellcellinteractions.html#module-pypath.inputs.cellcellinteractions">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.cellchatdb
+
+      <ul>
+        <li><a href="api/pypath.inputs.cellchatdb.html#module-pypath.inputs.cellchatdb">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.cellinker
+
+      <ul>
+        <li><a href="api/pypath.inputs.cellinker.html#module-pypath.inputs.cellinker">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.cellphonedb
+
+      <ul>
+        <li><a href="api/pypath.inputs.cellphonedb.html#module-pypath.inputs.cellphonedb">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.celltalkdb
+
+      <ul>
+        <li><a href="api/pypath.inputs.celltalkdb.html#module-pypath.inputs.celltalkdb">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.celltypist
+
+      <ul>
+        <li><a href="api/pypath.inputs.celltypist.html#module-pypath.inputs.celltypist">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.chembl
+
+      <ul>
+        <li><a href="api/pypath.inputs.chembl.html#module-pypath.inputs.chembl">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.clinvar
+
+      <ul>
+        <li><a href="api/pypath.inputs.clinvar.html#module-pypath.inputs.clinvar">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.collectri
+
+      <ul>
+        <li><a href="api/pypath.inputs.collectri.html#module-pypath.inputs.collectri">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.common
+
+      <ul>
+        <li><a href="api/pypath.inputs.common.html#module-pypath.inputs.common">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.compath
+
+      <ul>
+        <li><a href="api/pypath.inputs.compath.html#module-pypath.inputs.compath">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.compleat
+
+      <ul>
+        <li><a href="api/pypath.inputs.compleat.html#module-pypath.inputs.compleat">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.complexportal
+
+      <ul>
+        <li><a href="api/pypath.inputs.complexportal.html#module-pypath.inputs.complexportal">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.comppi
+
+      <ul>
+        <li><a href="api/pypath.inputs.comppi.html#module-pypath.inputs.comppi">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.connectomedb
+
+      <ul>
+        <li><a href="api/pypath.inputs.connectomedb.html#module-pypath.inputs.connectomedb">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.corum
+
+      <ul>
+        <li><a href="api/pypath.inputs.corum.html#module-pypath.inputs.corum">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.cosmic
+
+      <ul>
+        <li><a href="api/pypath.inputs.cosmic.html#module-pypath.inputs.cosmic">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.cpad
+
+      <ul>
+        <li><a href="api/pypath.inputs.cpad.html#module-pypath.inputs.cpad">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.cpdb
+
+      <ul>
+        <li><a href="api/pypath.inputs.cpdb.html#module-pypath.inputs.cpdb">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.credentials
+
+      <ul>
+        <li><a href="api/pypath.inputs.credentials.html#module-pypath.inputs.credentials">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.csa
+
+      <ul>
+        <li><a href="api/pypath.inputs.csa.html#module-pypath.inputs.csa">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.cspa
+
+      <ul>
+        <li><a href="api/pypath.inputs.cspa.html#module-pypath.inputs.cspa">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.ctdbase
+
+      <ul>
+        <li><a href="api/pypath.inputs.ctdbase.html#module-pypath.inputs.ctdbase">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.cytosig
+
+      <ul>
+        <li><a href="api/pypath.inputs.cytosig.html#module-pypath.inputs.cytosig">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.dbptm
+
+      <ul>
+        <li><a href="api/pypath.inputs.dbptm.html#module-pypath.inputs.dbptm">module</a>
+</li>
+      </ul></li>
+  </ul></td>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li>
+    pypath.inputs.ddinter
+
+      <ul>
+        <li><a href="api/pypath.inputs.ddinter.html#module-pypath.inputs.ddinter">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.deathdomain
+
+      <ul>
+        <li><a href="api/pypath.inputs.deathdomain.html#module-pypath.inputs.deathdomain">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.depod
+
+      <ul>
+        <li><a href="api/pypath.inputs.depod.html#module-pypath.inputs.depod">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.dgidb
+
+      <ul>
+        <li><a href="api/pypath.inputs.dgidb.html#module-pypath.inputs.dgidb">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.dip
+
+      <ul>
+        <li><a href="api/pypath.inputs.dip.html#module-pypath.inputs.dip">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.diseases
+
+      <ul>
+        <li><a href="api/pypath.inputs.diseases.html#module-pypath.inputs.diseases">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.domino
+
+      <ul>
+        <li><a href="api/pypath.inputs.domino.html#module-pypath.inputs.domino">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.dorothea
+
+      <ul>
+        <li><a href="api/pypath.inputs.dorothea.html#module-pypath.inputs.dorothea">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.drugbank
+
+      <ul>
+        <li><a href="api/pypath.inputs.drugbank.html#module-pypath.inputs.drugbank">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.drugcentral
+
+      <ul>
+        <li><a href="api/pypath.inputs.drugcentral.html#module-pypath.inputs.drugcentral">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.ebi
+
+      <ul>
+        <li><a href="api/pypath.inputs.ebi.html#module-pypath.inputs.ebi">module</a>
+</li>
+      </ul></li>
+      <li>
     pypath.inputs.elm
 
       <ul>
-        <li><a href="api/pypath.inputs.elm.html#module-pypath.inputs.elm">module</a>
+        <li><a href="api/pypath.inputs.elm.html#module-pypath.inputs.elm">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.embopress
+
+      <ul>
+        <li><a href="api/pypath.inputs.embopress.html#module-pypath.inputs.embopress">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.embrace
+
+      <ul>
+        <li><a href="api/pypath.inputs.embrace.html#module-pypath.inputs.embrace">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.encode
+
+      <ul>
+        <li><a href="api/pypath.inputs.encode.html#module-pypath.inputs.encode">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.ensembl
+
+      <ul>
+        <li><a href="api/pypath.inputs.ensembl.html#module-pypath.inputs.ensembl">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.eutils
+
+      <ul>
+        <li><a href="api/pypath.inputs.eutils.html#module-pypath.inputs.eutils">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.exocarta
+
+      <ul>
+        <li><a href="api/pypath.inputs.exocarta.html#module-pypath.inputs.exocarta">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.expasy
+
+      <ul>
+        <li><a href="api/pypath.inputs.expasy.html#module-pypath.inputs.expasy">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.genecards
+
+      <ul>
+        <li><a href="api/pypath.inputs.genecards.html#module-pypath.inputs.genecards">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.go
+
+      <ul>
+        <li><a href="api/pypath.inputs.go.html#module-pypath.inputs.go">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.gpcrdb
+
+      <ul>
+        <li><a href="api/pypath.inputs.gpcrdb.html#module-pypath.inputs.gpcrdb">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.graphviz
+
+      <ul>
+        <li><a href="api/pypath.inputs.graphviz.html#module-pypath.inputs.graphviz">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.guide2pharma
+
+      <ul>
+        <li><a href="api/pypath.inputs.guide2pharma.html#module-pypath.inputs.guide2pharma">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.gutmgene
+
+      <ul>
+        <li><a href="api/pypath.inputs.gutmgene.html#module-pypath.inputs.gutmgene">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.havugimana
+
+      <ul>
+        <li><a href="api/pypath.inputs.havugimana.html#module-pypath.inputs.havugimana">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.hgnc
+
+      <ul>
+        <li><a href="api/pypath.inputs.hgnc.html#module-pypath.inputs.hgnc">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.hippie
+
+      <ul>
+        <li><a href="api/pypath.inputs.hippie.html#module-pypath.inputs.hippie">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.hmdb
+
+      <ul>
+        <li><a href="api/pypath.inputs.hmdb.html#module-pypath.inputs.hmdb">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.hmdb.common
+
+      <ul>
+        <li><a href="api/pypath.inputs.hmdb.common.html#module-pypath.inputs.hmdb.common">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.hmdb.metabolites
+
+      <ul>
+        <li><a href="api/pypath.inputs.hmdb.metabolites.html#module-pypath.inputs.hmdb.metabolites">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.hmdb.proteins
+
+      <ul>
+        <li><a href="api/pypath.inputs.hmdb.proteins.html#module-pypath.inputs.hmdb.proteins">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.hmdb.schema
+
+      <ul>
+        <li><a href="api/pypath.inputs.hmdb.schema.html#module-pypath.inputs.hmdb.schema">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.hmdb.schema.common
+
+      <ul>
+        <li><a href="api/pypath.inputs.hmdb.schema.common.html#module-pypath.inputs.hmdb.schema.common">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.hmdb.schema.metabolites
+
+      <ul>
+        <li><a href="api/pypath.inputs.hmdb.schema.metabolites.html#module-pypath.inputs.hmdb.schema.metabolites">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.hmdb.schema.proteins
+
+      <ul>
+        <li><a href="api/pypath.inputs.hmdb.schema.proteins.html#module-pypath.inputs.hmdb.schema.proteins">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.hmdb.structures
+
+      <ul>
+        <li><a href="api/pypath.inputs.hmdb.structures.html#module-pypath.inputs.hmdb.structures">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.hmdb.visual
+
+      <ul>
+        <li><a href="api/pypath.inputs.hmdb.visual.html#module-pypath.inputs.hmdb.visual">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.hmdb.xml
+
+      <ul>
+        <li><a href="api/pypath.inputs.hmdb.xml.html#module-pypath.inputs.hmdb.xml">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.homologene
+
+      <ul>
+        <li><a href="api/pypath.inputs.homologene.html#module-pypath.inputs.homologene">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.hpmr
+
+      <ul>
+        <li><a href="api/pypath.inputs.hpmr.html#module-pypath.inputs.hpmr">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.hpo
+
+      <ul>
+        <li><a href="api/pypath.inputs.hpo.html#module-pypath.inputs.hpo">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.hprd
+
+      <ul>
+        <li><a href="api/pypath.inputs.hprd.html#module-pypath.inputs.hprd">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.htri
+
+      <ul>
+        <li><a href="api/pypath.inputs.htri.html#module-pypath.inputs.htri">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.humancellmap
+
+      <ul>
+        <li><a href="api/pypath.inputs.humancellmap.html#module-pypath.inputs.humancellmap">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.humap
+
+      <ul>
+        <li><a href="api/pypath.inputs.humap.html#module-pypath.inputs.humap">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.humsavar
+
+      <ul>
+        <li><a href="api/pypath.inputs.humsavar.html#module-pypath.inputs.humsavar">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.huri
+
+      <ul>
+        <li><a href="api/pypath.inputs.huri.html#module-pypath.inputs.huri">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.i3d
+
+      <ul>
+        <li><a href="api/pypath.inputs.i3d.html#module-pypath.inputs.i3d">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.icellnet
+
+      <ul>
+        <li><a href="api/pypath.inputs.icellnet.html#module-pypath.inputs.icellnet">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.ielm
+
+      <ul>
+        <li><a href="api/pypath.inputs.ielm.html#module-pypath.inputs.ielm">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.imweb
+
+      <ul>
+        <li><a href="api/pypath.inputs.imweb.html#module-pypath.inputs.imweb">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.innatedb
+
+      <ul>
+        <li><a href="api/pypath.inputs.innatedb.html#module-pypath.inputs.innatedb">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.instruct
+
+      <ul>
+        <li><a href="api/pypath.inputs.instruct.html#module-pypath.inputs.instruct">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.intact
+
+      <ul>
+        <li><a href="api/pypath.inputs.intact.html#module-pypath.inputs.intact">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.integrins
+
+      <ul>
+        <li><a href="api/pypath.inputs.integrins.html#module-pypath.inputs.integrins">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.interpro
+
+      <ul>
+        <li><a href="api/pypath.inputs.interpro.html#module-pypath.inputs.interpro">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.intogen
+
+      <ul>
+        <li><a href="api/pypath.inputs.intogen.html#module-pypath.inputs.intogen">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.ipi
+
+      <ul>
+        <li><a href="api/pypath.inputs.ipi.html#module-pypath.inputs.ipi">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.iptmnet
+
+      <ul>
+        <li><a href="api/pypath.inputs.iptmnet.html#module-pypath.inputs.iptmnet">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.italk
+
+      <ul>
+        <li><a href="api/pypath.inputs.italk.html#module-pypath.inputs.italk">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.kea
+
+      <ul>
+        <li><a href="api/pypath.inputs.kea.html#module-pypath.inputs.kea">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.kegg
+
+      <ul>
+        <li><a href="api/pypath.inputs.kegg.html#module-pypath.inputs.kegg">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.kegg_api
+
+      <ul>
+        <li><a href="api/pypath.inputs.kegg_api.html#module-pypath.inputs.kegg_api">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.kinasedotcom
+
+      <ul>
+        <li><a href="api/pypath.inputs.kinasedotcom.html#module-pypath.inputs.kinasedotcom">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.kirouac2010
+
+      <ul>
+        <li><a href="api/pypath.inputs.kirouac2010.html#module-pypath.inputs.kirouac2010">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.lambert2018
+
+      <ul>
+        <li><a href="api/pypath.inputs.lambert2018.html#module-pypath.inputs.lambert2018">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.laudanna
+
+      <ul>
+        <li><a href="api/pypath.inputs.laudanna.html#module-pypath.inputs.laudanna">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.li2012
+
+      <ul>
+        <li><a href="api/pypath.inputs.li2012.html#module-pypath.inputs.li2012">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.lincs
+
+      <ul>
+        <li><a href="api/pypath.inputs.lincs.html#module-pypath.inputs.lincs">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.lmpid
+
+      <ul>
+        <li><a href="api/pypath.inputs.lmpid.html#module-pypath.inputs.lmpid">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.lncdisease
+
+      <ul>
+        <li><a href="api/pypath.inputs.lncdisease.html#module-pypath.inputs.lncdisease">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.lncrnadb
+
+      <ul>
+        <li><a href="api/pypath.inputs.lncrnadb.html#module-pypath.inputs.lncrnadb">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.locate
+
+      <ul>
+        <li><a href="api/pypath.inputs.locate.html#module-pypath.inputs.locate">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.lrdb
+
+      <ul>
+        <li><a href="api/pypath.inputs.lrdb.html#module-pypath.inputs.lrdb">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.macrophage
+
+      <ul>
+        <li><a href="api/pypath.inputs.macrophage.html#module-pypath.inputs.macrophage">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.main
+
+      <ul>
+        <li><a href="api/pypath.inputs.main.html#module-pypath.inputs.main">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.matrisome
+
+      <ul>
+        <li><a href="api/pypath.inputs.matrisome.html#module-pypath.inputs.matrisome">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.matrixdb
+
+      <ul>
+        <li><a href="api/pypath.inputs.matrixdb.html#module-pypath.inputs.matrixdb">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.mcam
+
+      <ul>
+        <li><a href="api/pypath.inputs.mcam.html#module-pypath.inputs.mcam">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.membranome
+
+      <ul>
+        <li><a href="api/pypath.inputs.membranome.html#module-pypath.inputs.membranome">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.mimp
+
+      <ul>
+        <li><a href="api/pypath.inputs.mimp.html#module-pypath.inputs.mimp">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.mir2disease
+
+      <ul>
+        <li><a href="api/pypath.inputs.mir2disease.html#module-pypath.inputs.mir2disease">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.mirbase
+
+      <ul>
+        <li><a href="api/pypath.inputs.mirbase.html#module-pypath.inputs.mirbase">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.mirdeathdb
+
+      <ul>
+        <li><a href="api/pypath.inputs.mirdeathdb.html#module-pypath.inputs.mirdeathdb">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.mirecords
+
+      <ul>
+        <li><a href="api/pypath.inputs.mirecords.html#module-pypath.inputs.mirecords">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.mirtarbase
+
+      <ul>
+        <li><a href="api/pypath.inputs.mirtarbase.html#module-pypath.inputs.mirtarbase">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.mitab
+
+      <ul>
+        <li><a href="api/pypath.inputs.mitab.html#module-pypath.inputs.mitab">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.mppi
+
+      <ul>
+        <li><a href="api/pypath.inputs.mppi.html#module-pypath.inputs.mppi">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.msigdb
+
+      <ul>
+        <li><a href="api/pypath.inputs.msigdb.html#module-pypath.inputs.msigdb">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.ncrdeathdb
+
+      <ul>
+        <li><a href="api/pypath.inputs.ncrdeathdb.html#module-pypath.inputs.ncrdeathdb">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.negatome
+
+      <ul>
+        <li><a href="api/pypath.inputs.negatome.html#module-pypath.inputs.negatome">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.netbiol
+
+      <ul>
+        <li><a href="api/pypath.inputs.netbiol.html#module-pypath.inputs.netbiol">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.netpath
+
+      <ul>
+        <li><a href="api/pypath.inputs.netpath.html#module-pypath.inputs.netpath">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.offsides
+
+      <ul>
+        <li><a href="api/pypath.inputs.offsides.html#module-pypath.inputs.offsides">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.oma
+
+      <ul>
+        <li><a href="api/pypath.inputs.oma.html#module-pypath.inputs.oma">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.ontology
+
+      <ul>
+        <li><a href="api/pypath.inputs.ontology.html#module-pypath.inputs.ontology">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.opentargets
+
+      <ul>
+        <li><a href="api/pypath.inputs.opentargets.html#module-pypath.inputs.opentargets">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.opm
+
+      <ul>
+        <li><a href="api/pypath.inputs.opm.html#module-pypath.inputs.opm">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.oreganno
+
+      <ul>
+        <li><a href="api/pypath.inputs.oreganno.html#module-pypath.inputs.oreganno">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.panglaodb
+
+      <ul>
+        <li><a href="api/pypath.inputs.panglaodb.html#module-pypath.inputs.panglaodb">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.pathophenodb
+
+      <ul>
+        <li><a href="api/pypath.inputs.pathophenodb.html#module-pypath.inputs.pathophenodb">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.pathwaycommons
+
+      <ul>
+        <li><a href="api/pypath.inputs.pathwaycommons.html#module-pypath.inputs.pathwaycommons">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.pazar
+
+      <ul>
+        <li><a href="api/pypath.inputs.pazar.html#module-pypath.inputs.pazar">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.pdb
+
+      <ul>
+        <li><a href="api/pypath.inputs.pdb.html#module-pypath.inputs.pdb">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.pdzbase
+
+      <ul>
+        <li><a href="api/pypath.inputs.pdzbase.html#module-pypath.inputs.pdzbase">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.pepcyber
+
+      <ul>
+        <li><a href="api/pypath.inputs.pepcyber.html#module-pypath.inputs.pepcyber">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.pfam
+
+      <ul>
+        <li><a href="api/pypath.inputs.pfam.html#module-pypath.inputs.pfam">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.pharos
+
+      <ul>
+        <li><a href="api/pypath.inputs.pharos.html#module-pypath.inputs.pharos">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.phobius
+
+      <ul>
+        <li><a href="api/pypath.inputs.phobius.html#module-pypath.inputs.phobius">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.phosphatome
+
+      <ul>
+        <li><a href="api/pypath.inputs.phosphatome.html#module-pypath.inputs.phosphatome">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.phosphoelm
+
+      <ul>
+        <li><a href="api/pypath.inputs.phosphoelm.html#module-pypath.inputs.phosphoelm">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.phosphonetworks
+
+      <ul>
+        <li><a href="api/pypath.inputs.phosphonetworks.html#module-pypath.inputs.phosphonetworks">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.phosphopoint
+
+      <ul>
+        <li><a href="api/pypath.inputs.phosphopoint.html#module-pypath.inputs.phosphopoint">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.phosphosite
+
+      <ul>
+        <li><a href="api/pypath.inputs.phosphosite.html#module-pypath.inputs.phosphosite">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.pisa
+
+      <ul>
+        <li><a href="api/pypath.inputs.pisa.html#module-pypath.inputs.pisa">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.pro
+
+      <ul>
+        <li><a href="api/pypath.inputs.pro.html#module-pypath.inputs.pro">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.progeny
+
+      <ul>
+        <li><a href="api/pypath.inputs.progeny.html#module-pypath.inputs.progeny">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.proteinatlas
+
+      <ul>
+        <li><a href="api/pypath.inputs.proteinatlas.html#module-pypath.inputs.proteinatlas">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.proteins
+
+      <ul>
+        <li><a href="api/pypath.inputs.proteins.html#module-pypath.inputs.proteins">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.protmapper
+
+      <ul>
+        <li><a href="api/pypath.inputs.protmapper.html#module-pypath.inputs.protmapper">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.pubchem
+
+      <ul>
+        <li><a href="api/pypath.inputs.pubchem.html#module-pypath.inputs.pubchem">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.pubmed
+
+      <ul>
+        <li><a href="api/pypath.inputs.pubmed.html#module-pypath.inputs.pubmed">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.ramilowski2015
+
+      <ul>
+        <li><a href="api/pypath.inputs.ramilowski2015.html#module-pypath.inputs.ramilowski2015">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.ramp
+
+      <ul>
+        <li><a href="api/pypath.inputs.ramp.html#module-pypath.inputs.ramp">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.rdata
+
+      <ul>
+        <li><a href="api/pypath.inputs.rdata.html#module-pypath.inputs.rdata">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.reaction
+
+      <ul>
+        <li><a href="api/pypath.inputs.reaction.html#module-pypath.inputs.reaction">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.reactome
+
+      <ul>
+        <li><a href="api/pypath.inputs.reactome.html#module-pypath.inputs.reactome">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.scconnect
+
+      <ul>
+        <li><a href="api/pypath.inputs.scconnect.html#module-pypath.inputs.scconnect">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.science
+
+      <ul>
+        <li><a href="api/pypath.inputs.science.html#module-pypath.inputs.science">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.sider
+
+      <ul>
+        <li><a href="api/pypath.inputs.sider.html#module-pypath.inputs.sider">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.signalink
+
+      <ul>
+        <li><a href="api/pypath.inputs.signalink.html#module-pypath.inputs.signalink">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.signor
+
+      <ul>
+        <li><a href="api/pypath.inputs.signor.html#module-pypath.inputs.signor">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.spike
+
+      <ul>
+        <li><a href="api/pypath.inputs.spike.html#module-pypath.inputs.spike">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.stitch
+
+      <ul>
+        <li><a href="api/pypath.inputs.stitch.html#module-pypath.inputs.stitch">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.string
+
+      <ul>
+        <li><a href="api/pypath.inputs.string.html#module-pypath.inputs.string">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.surfaceome
+
+      <ul>
+        <li><a href="api/pypath.inputs.surfaceome.html#module-pypath.inputs.surfaceome">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.switches_elm
+
+      <ul>
+        <li><a href="api/pypath.inputs.switches_elm.html#module-pypath.inputs.switches_elm">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.talklr
+
+      <ul>
+        <li><a href="api/pypath.inputs.talklr.html#module-pypath.inputs.talklr">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.tcdb
+
+      <ul>
+        <li><a href="api/pypath.inputs.tcdb.html#module-pypath.inputs.tcdb">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.tfcensus
+
+      <ul>
+        <li><a href="api/pypath.inputs.tfcensus.html#module-pypath.inputs.tfcensus">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.threedcomplex
+
+      <ul>
+        <li><a href="api/pypath.inputs.threedcomplex.html#module-pypath.inputs.threedcomplex">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.threedid
+
+      <ul>
+        <li><a href="api/pypath.inputs.threedid.html#module-pypath.inputs.threedid">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.topdb
+
+      <ul>
+        <li><a href="api/pypath.inputs.topdb.html#module-pypath.inputs.topdb">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.transmir
+
+      <ul>
+        <li><a href="api/pypath.inputs.transmir.html#module-pypath.inputs.transmir">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.trip
+
+      <ul>
+        <li><a href="api/pypath.inputs.trip.html#module-pypath.inputs.trip">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.trrust
+
+      <ul>
+        <li><a href="api/pypath.inputs.trrust.html#module-pypath.inputs.trrust">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.twosides
+
+      <ul>
+        <li><a href="api/pypath.inputs.twosides.html#module-pypath.inputs.twosides">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.unichem
+
+      <ul>
+        <li><a href="api/pypath.inputs.unichem.html#module-pypath.inputs.unichem">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.uniprot
+
+      <ul>
+        <li><a href="api/pypath.inputs.uniprot.html#module-pypath.inputs.uniprot">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.uniprot_db
+
+      <ul>
+        <li><a href="api/pypath.inputs.uniprot_db.html#module-pypath.inputs.uniprot_db">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.wang
+
+      <ul>
+        <li><a href="api/pypath.inputs.wang.html#module-pypath.inputs.wang">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.wojtowicz2020
+
+      <ul>
+        <li><a href="api/pypath.inputs.wojtowicz2020.html#module-pypath.inputs.wojtowicz2020">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.inputs.zhong2015
+
+      <ul>
+        <li><a href="api/pypath.inputs.zhong2015.html#module-pypath.inputs.zhong2015">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.internals
+
+      <ul>
+        <li><a href="api/pypath.internals.html#module-pypath.internals">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.internals.annot_formats
+
+      <ul>
+        <li><a href="api/pypath.internals.annot_formats.html#module-pypath.internals.annot_formats">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.internals.input_formats
+
+      <ul>
+        <li><a href="api/pypath.internals.input_formats.html#module-pypath.internals.input_formats">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.internals.intera
+
+      <ul>
+        <li><a href="api/pypath.internals.intera.html#module-pypath.internals.intera">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.internals.license
+
+      <ul>
+        <li><a href="api/pypath.internals.license.html#module-pypath.internals.license">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.internals.maps
+
+      <ul>
+        <li><a href="api/pypath.internals.maps.html#module-pypath.internals.maps">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.internals.refs
+
+      <ul>
+        <li><a href="api/pypath.internals.refs.html#module-pypath.internals.refs">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.internals.resource
+
+      <ul>
+        <li><a href="api/pypath.internals.resource.html#module-pypath.internals.resource">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.legacy
+
+      <ul>
+        <li><a href="api/pypath.legacy.html#module-pypath.legacy">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.legacy.db_categories
+
+      <ul>
+        <li><a href="api/pypath.legacy.db_categories.html#module-pypath.legacy.db_categories">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.omnipath
+
+      <ul>
+        <li><a href="api/pypath.omnipath.html#module-pypath.omnipath">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.omnipath.app
+
+      <ul>
+        <li><a href="api/pypath.omnipath.app.html#module-pypath.omnipath.app">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.omnipath.databases
+
+      <ul>
+        <li><a href="api/pypath.omnipath.databases.html#module-pypath.omnipath.databases">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.omnipath.databases.define
+
+      <ul>
+        <li><a href="api/pypath.omnipath.databases.define.html#module-pypath.omnipath.databases.define">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.omnipath.export
+
+      <ul>
+        <li><a href="api/pypath.omnipath.export.html#module-pypath.omnipath.export">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.omnipath.param
+
+      <ul>
+        <li><a href="api/pypath.omnipath.param.html#module-pypath.omnipath.param">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.omnipath.server
+
+      <ul>
+        <li><a href="api/pypath.omnipath.server.html#module-pypath.omnipath.server">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.omnipath.server.build
+
+      <ul>
+        <li><a href="api/pypath.omnipath.server.build.html#module-pypath.omnipath.server.build">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.omnipath.server.generate_about_page
+
+      <ul>
+        <li><a href="api/pypath.omnipath.server.generate_about_page.html#module-pypath.omnipath.server.generate_about_page">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.omnipath.server.legacy
+
+      <ul>
+        <li><a href="api/pypath.omnipath.server.legacy.html#module-pypath.omnipath.server.legacy">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.omnipath.server.run
+
+      <ul>
+        <li><a href="api/pypath.omnipath.server.run.html#module-pypath.omnipath.server.run">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.resources
+
+      <ul>
+        <li><a href="api/pypath.resources.html#module-pypath.resources">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.resources.controller
+
+      <ul>
+        <li><a href="api/pypath.resources.controller.html#module-pypath.resources.controller">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.resources.data
+
+      <ul>
+        <li><a href="api/pypath.resources.data.html#module-pypath.resources.data">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.resources.data_formats
+
+      <ul>
+        <li><a href="api/pypath.resources.data_formats.html#module-pypath.resources.data_formats">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.resources.descriptions
+
+      <ul>
+        <li><a href="api/pypath.resources.descriptions.html#module-pypath.resources.descriptions">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.resources.licenses
+
+      <ul>
+        <li><a href="api/pypath.resources.licenses.html#module-pypath.resources.licenses">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.resources.network
+
+      <ul>
+        <li><a href="api/pypath.resources.network.html#module-pypath.resources.network">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.resources.urls
+
+      <ul>
+        <li><a href="api/pypath.resources.urls.html#module-pypath.resources.urls">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.share
+
+      <ul>
+        <li><a href="api/pypath.share.html#module-pypath.share">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.share.cache
+
+      <ul>
+        <li><a href="api/pypath.share.cache.html#module-pypath.share.cache">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.share.common
+
+      <ul>
+        <li><a href="api/pypath.share.common.html#module-pypath.share.common">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.share.constants
+
+      <ul>
+        <li><a href="api/pypath.share.constants.html#module-pypath.share.constants">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.share.curl
+
+      <ul>
+        <li><a href="api/pypath.share.curl.html#module-pypath.share.curl">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.share.progress
+
+      <ul>
+        <li><a href="api/pypath.share.progress.html#module-pypath.share.progress">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.share.session
+
+      <ul>
+        <li><a href="api/pypath.share.session.html#module-pypath.share.session">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.share.settings
+
+      <ul>
+        <li><a href="api/pypath.share.settings.html#module-pypath.share.settings">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.utils
+
+      <ul>
+        <li><a href="api/pypath.utils.html#module-pypath.utils">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.utils.go
+
+      <ul>
+        <li><a href="api/pypath.utils.go.html#module-pypath.utils.go">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.utils.mapping
+
+      <ul>
+        <li><a href="api/pypath.utils.mapping.html#module-pypath.utils.mapping">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.utils.metabo
+
+      <ul>
+        <li><a href="api/pypath.utils.metabo.html#module-pypath.utils.metabo">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.utils.orthology
+
+      <ul>
+        <li><a href="api/pypath.utils.orthology.html#module-pypath.utils.orthology">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.utils.pdb
+
+      <ul>
+        <li><a href="api/pypath.utils.pdb.html#module-pypath.utils.pdb">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.utils.proteomicsdb
+
+      <ul>
+        <li><a href="api/pypath.utils.proteomicsdb.html#module-pypath.utils.proteomicsdb">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.utils.pyreact
+
+      <ul>
+        <li><a href="api/pypath.utils.pyreact.html#module-pypath.utils.pyreact">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.utils.reflists
+
+      <ul>
+        <li><a href="api/pypath.utils.reflists.html#module-pypath.utils.reflists">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.utils.residues
+
+      <ul>
+        <li><a href="api/pypath.utils.residues.html#module-pypath.utils.residues">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.utils.seq
+
+      <ul>
+        <li><a href="api/pypath.utils.seq.html#module-pypath.utils.seq">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.utils.taxonomy
+
+      <ul>
+        <li><a href="api/pypath.utils.taxonomy.html#module-pypath.utils.taxonomy">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.utils.unichem
+
+      <ul>
+        <li><a href="api/pypath.utils.unichem.html#module-pypath.utils.unichem">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.utils.uniprot
+
+      <ul>
+        <li><a href="api/pypath.utils.uniprot.html#module-pypath.utils.uniprot">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.visual
+
+      <ul>
+        <li><a href="api/pypath.visual.html#module-pypath.visual">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.visual.drawing
+
+      <ul>
+        <li><a href="api/pypath.visual.drawing.html#module-pypath.visual.drawing">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.visual.igraph_drawing
+
+      <ul>
+        <li><a href="api/pypath.visual.igraph_drawing.html#module-pypath.visual.igraph_drawing">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.visual.igraph_drawing.edge
+
+      <ul>
+        <li><a href="api/pypath.visual.igraph_drawing.edge.html#module-pypath.visual.igraph_drawing.edge">module</a>
+</li>
+      </ul></li>
+      <li>
+    pypath.visual.igraph_drawing.vertex
+
+      <ul>
+        <li><a href="api/pypath.visual.igraph_drawing.vertex.html#module-pypath.visual.igraph_drawing.vertex">module</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.omnipath.server.legacy.PypathServer.html#pypath.omnipath.server.legacy.PypathServer">PypathServer (class in pypath.omnipath.server.legacy)</a>
+</li>
+      <li><a href="api/pypath.utils.pyreact.PyReact.html#pypath.utils.pyreact.PyReact">PyReact (class in pypath.utils.pyreact)</a>
+</li>
+  </ul></td>
+</tr></table>
+
+<h2 id="Q">Q</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="api/pypath.core.annot.CustomAnnotation.html#pypath.core.annot.CustomAnnotation.quality_check_table">quality_check_table() (pypath.core.annot.CustomAnnotation method)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.intercell.IntercellAnnotation.html#pypath.core.intercell.IntercellAnnotation.quality_check_table">(pypath.core.intercell.IntercellAnnotation method)</a>
+</li>
+      </ul></li>
+  </ul></td>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="api/pypath.utils.uniprot.query.html#pypath.utils.uniprot.query">query() (in module pypath.utils.uniprot)</a>
+
+      <ul>
+        <li><a href="api/pypath.utils.proteomicsdb.ProteomicsDB.html#pypath.utils.proteomicsdb.ProteomicsDB.query">(pypath.utils.proteomicsdb.ProteomicsDB method)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.inputs.uniprot.query_builder.html#pypath.inputs.uniprot.query_builder">query_builder() (in module pypath.inputs.uniprot)</a>
+</li>
+  </ul></td>
+</tr></table>
+
+<h2 id="R">R</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="api/pypath.core.annot.Ramilowski2015.html#pypath.core.annot.Ramilowski2015">Ramilowski2015 (class in pypath.core.annot)</a>
+</li>
+      <li><a href="api/pypath.core.annot.Ramilowski2015Location.html#pypath.core.annot.Ramilowski2015Location">Ramilowski2015Location (class in pypath.core.annot)</a>
+</li>
+      <li><a href="api/pypath.inputs.ramilowski2015.ramilowski_interactions.html#pypath.inputs.ramilowski2015.ramilowski_interactions">ramilowski_interactions() (in module pypath.inputs.ramilowski2015)</a>
+</li>
+      <li><a href="api/pypath.inputs.ramilowski2015.ramilowski_locations.html#pypath.inputs.ramilowski2015.ramilowski_locations">ramilowski_locations() (in module pypath.inputs.ramilowski2015)</a>
+</li>
+      <li><a href="api/pypath.inputs.ramp.ramp_id_types.html#pypath.inputs.ramp.ramp_id_types">ramp_id_types() (in module pypath.inputs.ramp)</a>
+</li>
+      <li><a href="api/pypath.inputs.ramp.ramp_id_types_2.html#pypath.inputs.ramp.ramp_id_types_2">ramp_id_types_2() (in module pypath.inputs.ramp)</a>
+</li>
+      <li><a href="api/pypath.inputs.ramp.ramp_list_tables.html#pypath.inputs.ramp.ramp_list_tables">ramp_list_tables() (in module pypath.inputs.ramp)</a>
+</li>
+      <li><a href="api/pypath.inputs.ramp.ramp_mapping.html#pypath.inputs.ramp.ramp_mapping">ramp_mapping() (in module pypath.inputs.ramp)</a>
+</li>
+      <li><a href="api/pypath.inputs.ramp.ramp_raw.html#pypath.inputs.ramp.ramp_raw">ramp_raw() (in module pypath.inputs.ramp)</a>
+</li>
+      <li><a href="api/pypath.inputs.ramp.ramp_show_tables.html#pypath.inputs.ramp.ramp_show_tables">ramp_show_tables() (in module pypath.inputs.ramp)</a>
+</li>
+      <li><a href="api/pypath.internals.input_formats.RampMapping.html#pypath.internals.input_formats.RampMapping">RampMapping (class in pypath.internals.input_formats)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.random_interaction">random_interaction() (pypath.core.network.Network method)</a>
+</li>
+      <li><a href="api/pypath.inputs.hmdb.common.raw.html#pypath.inputs.hmdb.common.raw">raw() (in module pypath.inputs.hmdb.common)</a>
+
+      <ul>
+        <li><a href="api/pypath.inputs.hmdb.metabolites.raw.html#pypath.inputs.hmdb.metabolites.raw">(in module pypath.inputs.hmdb.metabolites)</a>
+</li>
+        <li><a href="api/pypath.inputs.hmdb.proteins.raw.html#pypath.inputs.hmdb.proteins.raw">(in module pypath.inputs.hmdb.proteins)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.utils.pyreact.Reaction.html#pypath.utils.pyreact.Reaction">Reaction (class in pypath.utils.pyreact)</a>
+</li>
+      <li><a href="api/pypath.resources.data_formats.reaction_pc.html#pypath.resources.data_formats.reaction_pc">reaction_pc (in module pypath.resources.data_formats)</a>
+</li>
+      <li><a href="api/pypath.inputs.reaction.reactions_biopax.html#pypath.inputs.reaction.reactions_biopax">reactions_biopax() (in module pypath.inputs.reaction)</a>
+</li>
+      <li><a href="api/pypath.utils.pyreact.ReactionSide.html#pypath.utils.pyreact.ReactionSide">ReactionSide (class in pypath.utils.pyreact)</a>
+</li>
+      <li><a href="api/pypath.inputs.reaction.reactome_biopax.html#pypath.inputs.reaction.reactome_biopax">reactome_biopax() (in module pypath.inputs.reaction)</a>
+</li>
+      <li><a href="api/pypath.inputs.reaction.reactome_bs.html#pypath.inputs.reaction.reactome_bs">reactome_bs() (in module pypath.inputs.reaction)</a>
+</li>
+      <li><a href="api/pypath.inputs.reactome.reactome_chebis.html#pypath.inputs.reactome.reactome_chebis">reactome_chebis() (in module pypath.inputs.reactome)</a>
+</li>
+      <li><a href="api/pypath.inputs.reaction.reactome_interactions.html#pypath.inputs.reaction.reactome_interactions">reactome_interactions() (in module pypath.inputs.reaction)</a>
+</li>
+      <li><a href="api/pypath.inputs.reactome.reactome_pathway_relations.html#pypath.inputs.reactome.reactome_pathway_relations">reactome_pathway_relations() (in module pypath.inputs.reactome)</a>
+</li>
+      <li><a href="api/pypath.inputs.reactome.reactome_pathways.html#pypath.inputs.reactome.reactome_pathways">reactome_pathways() (in module pypath.inputs.reactome)</a>
+</li>
+      <li><a href="api/pypath.inputs.reaction.reactome_sbml.html#pypath.inputs.reaction.reactome_sbml">reactome_sbml() (in module pypath.inputs.reaction)</a>
+</li>
+      <li><a href="api/pypath.inputs.reactome.reactome_uniprots.html#pypath.inputs.reactome.reactome_uniprots">reactome_uniprots() (in module pypath.inputs.reactome)</a>
+</li>
+      <li><a href="api/pypath.utils.mapping.MapReader.html#pypath.utils.mapping.MapReader.read">read() (pypath.utils.mapping.MapReader method)</a>
+</li>
+      <li><a href="api/pypath.utils.mapping.MapReader.html#pypath.utils.mapping.MapReader.read_cache">read_cache() (pypath.utils.mapping.MapReader method)</a>
+</li>
+      <li><a href="api/pypath.utils.seq.read_fasta.html#pypath.utils.seq.read_fasta">read_fasta() (in module pypath.utils.seq)</a>
+</li>
+      <li><a href="api/pypath.utils.mapping.MapReader.html#pypath.utils.mapping.MapReader.read_mapping_array">read_mapping_array() (pypath.utils.mapping.MapReader method)</a>
+</li>
+      <li><a href="api/pypath.utils.mapping.MapReader.html#pypath.utils.mapping.MapReader.read_mapping_biomart">read_mapping_biomart() (pypath.utils.mapping.MapReader method)</a>
+</li>
+      <li><a href="api/pypath.utils.mapping.MapReader.html#pypath.utils.mapping.MapReader.read_mapping_file">read_mapping_file() (pypath.utils.mapping.MapReader method)</a>
+</li>
+      <li><a href="api/pypath.utils.mapping.MapReader.html#pypath.utils.mapping.MapReader.read_mapping_hmdb">read_mapping_hmdb() (pypath.utils.mapping.MapReader method)</a>
+</li>
+      <li><a href="api/pypath.utils.mapping.MapReader.html#pypath.utils.mapping.MapReader.read_mapping_ramp">read_mapping_ramp() (pypath.utils.mapping.MapReader method)</a>
+</li>
+      <li><a href="api/pypath.utils.mapping.MapReader.html#pypath.utils.mapping.MapReader.read_mapping_unichem">read_mapping_unichem() (pypath.utils.mapping.MapReader method)</a>
+</li>
+      <li><a href="api/pypath.utils.mapping.MapReader.html#pypath.utils.mapping.MapReader.read_mapping_uniprot">read_mapping_uniprot() (pypath.utils.mapping.MapReader method)</a>
+</li>
+      <li><a href="api/pypath.utils.mapping.MapReader.html#pypath.utils.mapping.MapReader.read_mapping_uniprot_list">read_mapping_uniprot_list() (pypath.utils.mapping.MapReader method)</a>
+</li>
+      <li><a href="api/pypath.inputs.common.read_table.html#pypath.inputs.common.read_table">read_table() (in module pypath.inputs.common)</a>
+</li>
+      <li><a href="api/pypath.inputs.common.read_xls.html#pypath.inputs.common.read_xls">read_xls() (in module pypath.inputs.common)</a>
+</li>
+      <li><a href="api/pypath.internals.input_formats.ReadList.html#pypath.internals.input_formats.ReadList">ReadList (class in pypath.internals.input_formats)</a>
+</li>
+      <li><a href="api/pypath.internals.annot_formats.AnnotDef.html#pypath.internals.annot_formats.AnnotDef.receiver">receiver (pypath.internals.annot_formats.AnnotDef attribute)</a>
+</li>
+      <li><a href="api/pypath.inputs.cellinker.CellinkerInteraction.html#pypath.inputs.cellinker.CellinkerInteraction.receptor">receptor (pypath.inputs.cellinker.CellinkerInteraction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.inputs.cellphonedb.CellPhoneDBAnnotation.html#pypath.inputs.cellphonedb.CellPhoneDBAnnotation.receptor">(pypath.inputs.cellphonedb.CellPhoneDBAnnotation attribute)</a>
+</li>
+        <li><a href="api/pypath.inputs.hpmr.HpmrInteraction.html#pypath.inputs.hpmr.HpmrInteraction.receptor">(pypath.inputs.hpmr.HpmrInteraction attribute)</a>
+</li>
+        <li><a href="api/pypath.inputs.icellnet.IcellnetRecord.html#pypath.inputs.icellnet.IcellnetRecord.receptor">(pypath.inputs.icellnet.IcellnetRecord attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.inputs.cellphonedb.CellPhoneDBAnnotation.html#pypath.inputs.cellphonedb.CellPhoneDBAnnotation.receptor_class">receptor_class (pypath.inputs.cellphonedb.CellPhoneDBAnnotation attribute)</a>
+</li>
+      <li><a href="api/pypath.inputs.cellinker.CellinkerInteraction.html#pypath.inputs.cellinker.CellinkerInteraction.receptor_location">receptor_location (pypath.inputs.cellinker.CellinkerInteraction attribute)</a>
+</li>
+      <li><a href="api/pypath.internals.refs.Reference.html#pypath.internals.refs.Reference">Reference (class in pypath.internals.refs)</a>
+
+      <ul>
+        <li><a href="api/pypath.utils.pyreact.Reference.html#pypath.utils.pyreact.Reference">(class in pypath.utils.pyreact)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.utils.reflists.ReferenceListManager.html#pypath.utils.reflists.ReferenceListManager">ReferenceListManager (class in pypath.utils.reflists)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.InteractionDataFrameRecord.html#pypath.core.interaction.InteractionDataFrameRecord.references">references (pypath.core.interaction.InteractionDataFrameRecord attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.inputs.hpmr.HpmrInteraction.html#pypath.inputs.hpmr.HpmrInteraction.references">(pypath.inputs.hpmr.HpmrInteraction attribute)</a>
+</li>
+        <li><a href="api/pypath.inputs.icellnet.IcellnetRecord.html#pypath.inputs.icellnet.IcellnetRecord.references">(pypath.inputs.icellnet.IcellnetRecord attribute)</a>
+</li>
+        <li><a href="api/pypath.inputs.iptmnet.IptmnetInteraction.html#pypath.inputs.iptmnet.IptmnetInteraction.references">(pypath.inputs.iptmnet.IptmnetInteraction attribute)</a>
+</li>
+        <li><a href="api/pypath.inputs.lrdb.LrdbAnnotation.html#pypath.inputs.lrdb.LrdbAnnotation.references">(pypath.inputs.lrdb.LrdbAnnotation attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.references_by_data_model">references_by_data_model (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.references_by_data_model">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.references_by_interaction_type">references_by_interaction_type (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.references_by_interaction_type">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.references_by_interaction_type_and_data_model">references_by_interaction_type_and_data_model (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.references_by_interaction_type_and_data_model">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.references_by_interaction_type_and_data_model_and_resource">references_by_interaction_type_and_data_model_and_resource (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.references_by_interaction_type_and_data_model_and_resource">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.references_by_reference">references_by_reference (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.references_by_reference">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.references_by_resource">references_by_resource (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.references_by_resource">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.utils.orthology.OrthologMeta.html#pypath.utils.orthology.OrthologMeta.register">register() (pypath.utils.orthology.OrthologMeta method)</a>
+</li>
+      <li><a href="api/pypath.core.annot.CustomAnnotation.html#pypath.core.annot.CustomAnnotation.register_network">register_network() (pypath.core.annot.CustomAnnotation method)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.intercell.IntercellAnnotation.html#pypath.core.intercell.IntercellAnnotation.register_network">(pypath.core.intercell.IntercellAnnotation method)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.inputs.phosphosite.regsites_tab.html#pypath.inputs.phosphosite.regsites_tab">regsites_tab() (in module pypath.inputs.phosphosite)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.regulated_by">regulated_by (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.regulates">regulates (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.internals.intera.Regulation.html#pypath.internals.intera.Regulation">Regulation (class in pypath.internals.intera)</a>
+</li>
+      <li><a href="api/pypath.utils.orthology.OmaOrtholog.html#pypath.utils.orthology.OmaOrtholog.rel_type">rel_type (pypath.utils.orthology.OmaOrtholog attribute)</a>
+</li>
+      <li><a href="api/pypath.utils.uniprot.reload.html#pypath.utils.uniprot.reload">reload() (in module pypath.utils.uniprot)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.annot.Adhesome.html#pypath.core.annot.Adhesome.reload">(pypath.core.annot.Adhesome method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Almen2009.html#pypath.core.annot.Almen2009.reload">(pypath.core.annot.Almen2009 method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.AnnotationBase.html#pypath.core.annot.AnnotationBase.reload">(pypath.core.annot.AnnotationBase method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.AnnotationTable.html#pypath.core.annot.AnnotationTable.reload">(pypath.core.annot.AnnotationTable method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Baccin2019.html#pypath.core.annot.Baccin2019.reload">(pypath.core.annot.Baccin2019 method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Biogps.html#pypath.core.annot.Biogps.reload">(pypath.core.annot.Biogps method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cancerdrugsdb.html#pypath.core.annot.Cancerdrugsdb.reload">(pypath.core.annot.Cancerdrugsdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CancerGeneCensus.html#pypath.core.annot.CancerGeneCensus.reload">(pypath.core.annot.CancerGeneCensus method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cancersea.html#pypath.core.annot.Cancersea.reload">(pypath.core.annot.Cancersea method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cellcall.html#pypath.core.annot.Cellcall.reload">(pypath.core.annot.Cellcall method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cellcellinteractions.html#pypath.core.annot.Cellcellinteractions.reload">(pypath.core.annot.Cellcellinteractions method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cellchatdb.html#pypath.core.annot.Cellchatdb.reload">(pypath.core.annot.Cellchatdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CellchatdbComplex.html#pypath.core.annot.CellchatdbComplex.reload">(pypath.core.annot.CellchatdbComplex method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cellinker.html#pypath.core.annot.Cellinker.reload">(pypath.core.annot.Cellinker method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CellinkerComplex.html#pypath.core.annot.CellinkerComplex.reload">(pypath.core.annot.CellinkerComplex method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CellPhoneDB.html#pypath.core.annot.CellPhoneDB.reload">(pypath.core.annot.CellPhoneDB method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CellPhoneDBComplex.html#pypath.core.annot.CellPhoneDBComplex.reload">(pypath.core.annot.CellPhoneDBComplex method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CellSurfaceProteinAtlas.html#pypath.core.annot.CellSurfaceProteinAtlas.reload">(pypath.core.annot.CellSurfaceProteinAtlas method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CellSurfaceProteinAtlasCellType.html#pypath.core.annot.CellSurfaceProteinAtlasCellType.reload">(pypath.core.annot.CellSurfaceProteinAtlasCellType method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Celltalkdb.html#pypath.core.annot.Celltalkdb.reload">(pypath.core.annot.Celltalkdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Celltypist.html#pypath.core.annot.Celltypist.reload">(pypath.core.annot.Celltypist method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Comppi.html#pypath.core.annot.Comppi.reload">(pypath.core.annot.Comppi method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Connectomedb.html#pypath.core.annot.Connectomedb.reload">(pypath.core.annot.Connectomedb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Corum.html#pypath.core.annot.Corum.reload">(pypath.core.annot.Corum method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CorumFuncat.html#pypath.core.annot.CorumFuncat.reload">(pypath.core.annot.CorumFuncat method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CorumGO.html#pypath.core.annot.CorumGO.reload">(pypath.core.annot.CorumGO method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cpad.html#pypath.core.annot.Cpad.reload">(pypath.core.annot.Cpad method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CustomAnnotation.html#pypath.core.annot.CustomAnnotation.reload">(pypath.core.annot.CustomAnnotation method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cytosig.html#pypath.core.annot.Cytosig.reload">(pypath.core.annot.Cytosig method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Dgidb.html#pypath.core.annot.Dgidb.reload">(pypath.core.annot.Dgidb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Disgenet.html#pypath.core.annot.Disgenet.reload">(pypath.core.annot.Disgenet method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Embrace.html#pypath.core.annot.Embrace.reload">(pypath.core.annot.Embrace method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Exocarta.html#pypath.core.annot.Exocarta.reload">(pypath.core.annot.Exocarta method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.GOCustomIntercell.html#pypath.core.annot.GOCustomIntercell.reload">(pypath.core.annot.GOCustomIntercell method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.GOIntercell.html#pypath.core.annot.GOIntercell.reload">(pypath.core.annot.GOIntercell method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Gpcrdb.html#pypath.core.annot.Gpcrdb.reload">(pypath.core.annot.Gpcrdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.GuideToPharmacology.html#pypath.core.annot.GuideToPharmacology.reload">(pypath.core.annot.GuideToPharmacology method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Hgnc.html#pypath.core.annot.Hgnc.reload">(pypath.core.annot.Hgnc method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.HpmrComplex.html#pypath.core.annot.HpmrComplex.reload">(pypath.core.annot.HpmrComplex method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.HPO.html#pypath.core.annot.HPO.reload">(pypath.core.annot.HPO method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Humancellmap.html#pypath.core.annot.Humancellmap.reload">(pypath.core.annot.Humancellmap method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.HumanPlasmaMembraneReceptome.html#pypath.core.annot.HumanPlasmaMembraneReceptome.reload">(pypath.core.annot.HumanPlasmaMembraneReceptome method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.HumanProteinAtlas.html#pypath.core.annot.HumanProteinAtlas.reload">(pypath.core.annot.HumanProteinAtlas method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.HumanProteinAtlasSecretome.html#pypath.core.annot.HumanProteinAtlasSecretome.reload">(pypath.core.annot.HumanProteinAtlasSecretome method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.HumanProteinAtlasSubcellular.html#pypath.core.annot.HumanProteinAtlasSubcellular.reload">(pypath.core.annot.HumanProteinAtlasSubcellular method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Icellnet.html#pypath.core.annot.Icellnet.reload">(pypath.core.annot.Icellnet method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.IcellnetComplex.html#pypath.core.annot.IcellnetComplex.reload">(pypath.core.annot.IcellnetComplex method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Integrins.html#pypath.core.annot.Integrins.reload">(pypath.core.annot.Integrins method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.InterPro.html#pypath.core.annot.InterPro.reload">(pypath.core.annot.InterPro method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Intogen.html#pypath.core.annot.Intogen.reload">(pypath.core.annot.Intogen method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Italk.html#pypath.core.annot.Italk.reload">(pypath.core.annot.Italk method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.KeggPathways.html#pypath.core.annot.KeggPathways.reload">(pypath.core.annot.KeggPathways method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.KeggPathwaysPC.html#pypath.core.annot.KeggPathwaysPC.reload">(pypath.core.annot.KeggPathwaysPC method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Kinasedotcom.html#pypath.core.annot.Kinasedotcom.reload">(pypath.core.annot.Kinasedotcom method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Kirouac2010.html#pypath.core.annot.Kirouac2010.reload">(pypath.core.annot.Kirouac2010 method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Lambert2018.html#pypath.core.annot.Lambert2018.reload">(pypath.core.annot.Lambert2018 method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.LigandReceptor.html#pypath.core.annot.LigandReceptor.reload">(pypath.core.annot.LigandReceptor method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Locate.html#pypath.core.annot.Locate.reload">(pypath.core.annot.Locate method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Lrdb.html#pypath.core.annot.Lrdb.reload">(pypath.core.annot.Lrdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Matrisome.html#pypath.core.annot.Matrisome.reload">(pypath.core.annot.Matrisome method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Matrixdb.html#pypath.core.annot.Matrixdb.reload">(pypath.core.annot.Matrixdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Mcam.html#pypath.core.annot.Mcam.reload">(pypath.core.annot.Mcam method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Membranome.html#pypath.core.annot.Membranome.reload">(pypath.core.annot.Membranome method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Msigdb.html#pypath.core.annot.Msigdb.reload">(pypath.core.annot.Msigdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.NetpathPathways.html#pypath.core.annot.NetpathPathways.reload">(pypath.core.annot.NetpathPathways method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Opm.html#pypath.core.annot.Opm.reload">(pypath.core.annot.Opm method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Panglaodb.html#pypath.core.annot.Panglaodb.reload">(pypath.core.annot.Panglaodb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Phobius.html#pypath.core.annot.Phobius.reload">(pypath.core.annot.Phobius method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Phosphatome.html#pypath.core.annot.Phosphatome.reload">(pypath.core.annot.Phosphatome method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Progeny.html#pypath.core.annot.Progeny.reload">(pypath.core.annot.Progeny method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Ramilowski2015.html#pypath.core.annot.Ramilowski2015.reload">(pypath.core.annot.Ramilowski2015 method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Ramilowski2015Location.html#pypath.core.annot.Ramilowski2015Location.reload">(pypath.core.annot.Ramilowski2015Location method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Scconnect.html#pypath.core.annot.Scconnect.reload">(pypath.core.annot.Scconnect method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.ScconnectComplex.html#pypath.core.annot.ScconnectComplex.reload">(pypath.core.annot.ScconnectComplex method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.SignalinkFunctions.html#pypath.core.annot.SignalinkFunctions.reload">(pypath.core.annot.SignalinkFunctions method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.SignalinkPathways.html#pypath.core.annot.SignalinkPathways.reload">(pypath.core.annot.SignalinkPathways method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.SignorPathways.html#pypath.core.annot.SignorPathways.reload">(pypath.core.annot.SignorPathways method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Surfaceome.html#pypath.core.annot.Surfaceome.reload">(pypath.core.annot.Surfaceome method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Talklr.html#pypath.core.annot.Talklr.reload">(pypath.core.annot.Talklr method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Tcdb.html#pypath.core.annot.Tcdb.reload">(pypath.core.annot.Tcdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Tfcensus.html#pypath.core.annot.Tfcensus.reload">(pypath.core.annot.Tfcensus method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Topdb.html#pypath.core.annot.Topdb.reload">(pypath.core.annot.Topdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.UniprotFamilies.html#pypath.core.annot.UniprotFamilies.reload">(pypath.core.annot.UniprotFamilies method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.UniprotKeywords.html#pypath.core.annot.UniprotKeywords.reload">(pypath.core.annot.UniprotKeywords method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.UniprotLocations.html#pypath.core.annot.UniprotLocations.reload">(pypath.core.annot.UniprotLocations method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.UniprotTissues.html#pypath.core.annot.UniprotTissues.reload">(pypath.core.annot.UniprotTissues method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.UniprotTopologies.html#pypath.core.annot.UniprotTopologies.reload">(pypath.core.annot.UniprotTopologies method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Vesiclepedia.html#pypath.core.annot.Vesiclepedia.reload">(pypath.core.annot.Vesiclepedia method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Wang.html#pypath.core.annot.Wang.reload">(pypath.core.annot.Wang method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Zhong2015.html#pypath.core.annot.Zhong2015.reload">(pypath.core.annot.Zhong2015 method)</a>
+</li>
+        <li><a href="api/pypath.core.complex.ComplexAggregator.html#pypath.core.complex.ComplexAggregator.reload">(pypath.core.complex.ComplexAggregator method)</a>
+</li>
+        <li><a href="api/pypath.core.evidence.Evidence.html#pypath.core.evidence.Evidence.reload">(pypath.core.evidence.Evidence method)</a>
+</li>
+        <li><a href="api/pypath.core.evidence.Evidences.html#pypath.core.evidence.Evidences.reload">(pypath.core.evidence.Evidences method)</a>
+</li>
+        <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.reload">(pypath.core.interaction.Interaction method)</a>
+</li>
+        <li><a href="api/pypath.core.intercell.IntercellAnnotation.html#pypath.core.intercell.IntercellAnnotation.reload">(pypath.core.intercell.IntercellAnnotation method)</a>
+</li>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.reload">(pypath.core.network.Network method)</a>
+</li>
+        <li><a href="api/pypath.omnipath.app.DatabaseManager.html#pypath.omnipath.app.DatabaseManager.reload">(pypath.omnipath.app.DatabaseManager method)</a>
+</li>
+        <li><a href="api/pypath.utils.go.GeneOntology.html#pypath.utils.go.GeneOntology.reload">(pypath.utils.go.GeneOntology method)</a>
+</li>
+        <li><a href="api/pypath.utils.go.GOAnnotation.html#pypath.utils.go.GOAnnotation.reload">(pypath.utils.go.GOAnnotation method)</a>
+</li>
+        <li><a href="api/pypath.utils.go.GOCustomAnnotation.html#pypath.utils.go.GOCustomAnnotation.reload">(pypath.utils.go.GOCustomAnnotation method)</a>
+</li>
+        <li><a href="api/pypath.utils.mapping.Mapper.html#pypath.utils.mapping.Mapper.reload">(pypath.utils.mapping.Mapper method)</a>
+</li>
+      </ul></li>
+  </ul></td>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="api/pypath.omnipath.app.DatabaseManager.html#pypath.omnipath.app.DatabaseManager.reload_module">reload_module() (pypath.omnipath.app.DatabaseManager method)</a>
+</li>
+      <li><a href="api/pypath.share.curl.RemoteFile.html#pypath.share.curl.RemoteFile">RemoteFile (class in pypath.share.curl)</a>
+</li>
+      <li><a href="api/pypath.omnipath.app.DatabaseManager.html#pypath.omnipath.app.DatabaseManager.remove_all">remove_all() (pypath.omnipath.app.DatabaseManager method)</a>
+</li>
+      <li><a href="api/pypath.omnipath.app.DatabaseManager.html#pypath.omnipath.app.DatabaseManager.remove_db">remove_db() (pypath.omnipath.app.DatabaseManager method)</a>
+</li>
+      <li><a href="api/pypath.utils.mapping.Mapper.html#pypath.utils.mapping.Mapper.remove_expired">remove_expired() (pypath.utils.mapping.Mapper method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.remove_interaction">remove_interaction() (pypath.core.network.Network method)</a>
+</li>
+      <li><a href="api/pypath.utils.mapping.Mapper.html#pypath.utils.mapping.Mapper.remove_key">remove_key() (pypath.utils.mapping.Mapper method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.remove_loops">remove_loops() (pypath.core.network.Network method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.remove_node">remove_node() (pypath.core.network.Network method)</a>
+</li>
+      <li><a href="api/pypath.utils.mapping.Mapper.html#pypath.utils.mapping.Mapper.remove_table">remove_table() (pypath.utils.mapping.Mapper method)</a>
+</li>
+      <li><a href="api/pypath.utils.uniprot.remove_xrefs.html#pypath.utils.uniprot.remove_xrefs">remove_xrefs() (in module pypath.utils.uniprot)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.remove_zero_degree">remove_zero_degree() (pypath.core.network.Network method)</a>
+</li>
+      <li><a href="api/pypath.share.curl.Curl.html#pypath.share.curl.Curl.replace_forbidden">replace_forbidden() (pypath.share.curl.Curl class method)</a>
+</li>
+      <li><a href="api/pypath.inputs.uniprot.UniprotRecordHistory.html#pypath.inputs.uniprot.UniprotRecordHistory.replaced_by">replaced_by (pypath.inputs.uniprot.UniprotRecordHistory attribute)</a>
+</li>
+      <li><a href="api/pypath.inputs.uniprot.UniprotRecordHistory.html#pypath.inputs.uniprot.UniprotRecordHistory.replaces">replaces (pypath.inputs.uniprot.UniprotRecordHistory attribute)</a>
+</li>
+      <li><a href="api/pypath.inputs.iptmnet.IptmnetInteraction.html#pypath.inputs.iptmnet.IptmnetInteraction.resaa">resaa (pypath.inputs.iptmnet.IptmnetInteraction attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.reset">reset() (pypath.core.network.Network method)</a>
+</li>
+      <li><a href="api/pypath.internals.intera.Residue.html#pypath.internals.intera.Residue">Residue (class in pypath.internals.intera)</a>
+
+      <ul>
+        <li><a href="api/pypath.utils.pdb.Residue.html#pypath.utils.pdb.Residue">(class in pypath.utils.pdb)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.inputs.pisa.PisaBond.html#pypath.inputs.pisa.PisaBond.residue_1">residue_1 (pypath.inputs.pisa.PisaBond attribute)</a>
+</li>
+      <li><a href="api/pypath.inputs.pisa.PisaBond.html#pypath.inputs.pisa.PisaBond.residue_2">residue_2 (pypath.inputs.pisa.PisaBond attribute)</a>
+</li>
+      <li><a href="api/pypath.utils.pdb.residue_pdb.html#pypath.utils.pdb.residue_pdb">residue_pdb() (in module pypath.utils.pdb)</a>
+</li>
+      <li><a href="api/pypath.utils.pdb.ResidueMapper.html#pypath.utils.pdb.ResidueMapper">ResidueMapper (class in pypath.utils.pdb)</a>
+
+      <ul>
+        <li><a href="api/pypath.utils.residues.ResidueMapper.html#pypath.utils.residues.ResidueMapper">(class in pypath.utils.residues)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.inputs.iptmnet.IptmnetInteraction.html#pypath.inputs.iptmnet.IptmnetInteraction.resnum">resnum (pypath.inputs.iptmnet.IptmnetInteraction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.utils.pdb.Residue.html#pypath.utils.pdb.Residue.resnum">(pypath.utils.pdb.Residue attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.utils.seq.Resource.html#pypath.utils.seq.Resource">Resource (class in pypath.utils.seq)</a>
+</li>
+      <li><a href="api/pypath.inputs.pathwaycommons.PathwayCommonsInteraction.html#pypath.inputs.pathwaycommons.PathwayCommonsInteraction.resource">resource (pypath.inputs.pathwaycommons.PathwayCommonsInteraction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.internals.annot_formats.AnnotDef.html#pypath.internals.annot_formats.AnnotDef.resource">(pypath.internals.annot_formats.AnnotDef attribute)</a>
+</li>
+        <li><a href="api/pypath.internals.annot_formats.AnnotDefKey.html#pypath.internals.annot_formats.AnnotDefKey.resource">(pypath.internals.annot_formats.AnnotDefKey attribute)</a>
+</li>
+        <li><a href="api/pypath.utils.orthology.OrthologyTableKey.html#pypath.utils.orthology.OrthologyTableKey.resource">(pypath.utils.orthology.OrthologyTableKey attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.network.NetworkStatsRecord.html#pypath.core.network.NetworkStatsRecord.resource_cat">resource_cat (pypath.core.network.NetworkStatsRecord attribute)</a>
+</li>
+      <li><a href="api/pypath.internals.input_formats.UniprotMapping.html#pypath.internals.input_formats.UniprotMapping.resource_id_type">resource_id_type() (pypath.internals.input_formats.UniprotMapping static method)</a>
+
+      <ul>
+        <li><a href="api/pypath.utils.mapping.MapReader.html#pypath.utils.mapping.MapReader.resource_id_type">(pypath.utils.mapping.MapReader method)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.omnipath.server.generate_about_page.resource_list_latex.html#pypath.omnipath.server.generate_about_page.resource_list_latex">resource_list_latex() (in module pypath.omnipath.server.generate_about_page)</a>
+
+      <ul>
+        <li><a href="api/pypath.resources.descriptions.resource_list_latex.html#pypath.resources.descriptions.resource_list_latex">(in module pypath.resources.descriptions)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.internals.annot_formats.AnnotDef.html#pypath.internals.annot_formats.AnnotDef.resource_name">resource_name (pypath.internals.annot_formats.AnnotDef attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.resource_names">resource_names (pypath.core.network.Network property)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.resource_names_by_data_model">resource_names_by_data_model (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.resource_names_by_data_model">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.resource_names_by_interaction_type">resource_names_by_interaction_type (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.resource_names_by_interaction_type">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.resource_names_by_interaction_type_and_data_model">resource_names_by_interaction_type_and_data_model (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.resource_names_by_interaction_type_and_data_model">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.resource_names_by_interaction_type_and_data_model_and_resource">resource_names_by_interaction_type_and_data_model_and_resource (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.resource_names_by_interaction_type_and_data_model_and_resource">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.resource_names_by_reference">resource_names_by_reference (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.resource_names_by_reference">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.resource_names_by_resource">resource_names_by_resource (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.resource_names_by_resource">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.resource_names_via_by_data_model">resource_names_via_by_data_model (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.resource_names_via_by_data_model">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.resource_names_via_by_interaction_type">resource_names_via_by_interaction_type (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.resource_names_via_by_interaction_type">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.resource_names_via_by_interaction_type_and_data_model">resource_names_via_by_interaction_type_and_data_model (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.resource_names_via_by_interaction_type_and_data_model">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.resource_names_via_by_interaction_type_and_data_model_and_resource">resource_names_via_by_interaction_type_and_data_model_and_resource (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.resource_names_via_by_interaction_type_and_data_model_and_resource">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.resource_names_via_by_reference">resource_names_via_by_reference (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.resource_names_via_by_reference">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.resource_names_via_by_resource">resource_names_via_by_resource (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.resource_names_via_by_resource">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.internals.resource.ResourceAttributes.html#pypath.internals.resource.ResourceAttributes">ResourceAttributes (class in pypath.internals.resource)</a>
+</li>
+      <li><a href="api/pypath.resources.controller.ResourceController.html#pypath.resources.controller.ResourceController">ResourceController (class in pypath.resources.controller)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.resources">resources (pypath.core.network.Network property)</a>
+
+      <ul>
+        <li><a href="api/pypath.inputs.cellinker.CellinkerInteraction.html#pypath.inputs.cellinker.CellinkerInteraction.resources">(pypath.inputs.cellinker.CellinkerInteraction attribute)</a>
+</li>
+        <li><a href="api/pypath.inputs.icellnet.IcellnetRecord.html#pypath.inputs.icellnet.IcellnetRecord.resources">(pypath.inputs.icellnet.IcellnetRecord attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.resources_a_b">resources_a_b() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.resources_b_a">resources_b_a() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.resources_by_data_model">resources_by_data_model (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.resources_by_data_model">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.resources_by_interaction_type">resources_by_interaction_type (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.resources_by_interaction_type">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.resources_by_interaction_type_and_data_model">resources_by_interaction_type_and_data_model (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.resources_by_interaction_type_and_data_model">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.resources_by_interaction_type_and_data_model_and_resource">resources_by_interaction_type_and_data_model_and_resource (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.resources_by_interaction_type_and_data_model_and_resource">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.resources_by_reference">resources_by_reference (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.resources_by_reference">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.resources_by_resource">resources_by_resource (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.resources_by_resource">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.annot.CustomAnnotation.html#pypath.core.annot.CustomAnnotation.resources_in_category">resources_in_category() (pypath.core.annot.CustomAnnotation method)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.intercell.IntercellAnnotation.html#pypath.core.intercell.IntercellAnnotation.resources_in_category">(pypath.core.intercell.IntercellAnnotation method)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.resources_undirected">resources_undirected() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.resources_via_by_data_model">resources_via_by_data_model (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.resources_via_by_data_model">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.resources_via_by_interaction_type">resources_via_by_interaction_type (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.resources_via_by_interaction_type">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.resources_via_by_interaction_type_and_data_model">resources_via_by_interaction_type_and_data_model (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.resources_via_by_interaction_type_and_data_model">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.resources_via_by_interaction_type_and_data_model_and_resource">resources_via_by_interaction_type_and_data_model_and_resource (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.resources_via_by_interaction_type_and_data_model_and_resource">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.resources_via_by_reference">resources_via_by_reference (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.resources_via_by_reference">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.resources_via_by_resource">resources_via_by_resource (pypath.core.interaction.Interaction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.resources_via_by_resource">(pypath.core.network.Network attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.omnipath.server.run.Rest.html#pypath.omnipath.server.run.Rest">Rest (class in pypath.omnipath.server.run)</a>
+</li>
+      <li><a href="api/pypath.utils.mapping.Mapper.html#pypath.utils.mapping.Mapper.reverse_key">reverse_key() (pypath.utils.mapping.Mapper method)</a>
+</li>
+      <li><a href="api/pypath.utils.mapping.Mapper.html#pypath.utils.mapping.Mapper.reverse_mapping">reverse_mapping() (pypath.utils.mapping.Mapper static method)</a>
+</li>
+      <li><a href="api/pypath.inputs.lrdb.LrdbAnnotation.html#pypath.inputs.lrdb.LrdbAnnotation.role">role (pypath.inputs.lrdb.LrdbAnnotation attribute)</a>
+</li>
+      <li><a href="api/pypath.inputs.huri.rolland_hi_ii_14.html#pypath.inputs.huri.rolland_hi_ii_14">rolland_hi_ii_14() (in module pypath.inputs.huri)</a>
+</li>
+  </ul></td>
+</tr></table>
+
+<h2 id="S">S</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.save_to_pickle">save_to_pickle() (pypath.core.network.Network method)</a>
+</li>
+      <li><a href="api/pypath.core.annot.Scconnect.html#pypath.core.annot.Scconnect">Scconnect (class in pypath.core.annot)</a>
+</li>
+      <li><a href="api/pypath.inputs.scconnect.scconnect_annotations.html#pypath.inputs.scconnect.scconnect_annotations">scconnect_annotations() (in module pypath.inputs.scconnect)</a>
+</li>
+      <li><a href="api/pypath.inputs.scconnect.scconnect_complexes.html#pypath.inputs.scconnect.scconnect_complexes">scconnect_complexes() (in module pypath.inputs.scconnect)</a>
+</li>
+      <li><a href="api/pypath.inputs.scconnect.scconnect_interactions.html#pypath.inputs.scconnect.scconnect_interactions">scconnect_interactions() (in module pypath.inputs.scconnect)</a>
+</li>
+      <li><a href="api/pypath.core.annot.ScconnectComplex.html#pypath.core.annot.ScconnectComplex">ScconnectComplex (class in pypath.core.annot)</a>
+</li>
+      <li><a href="api/pypath.inputs.science.science_download.html#pypath.inputs.science.science_download">science_download() (in module pypath.inputs.science)</a>
+</li>
+      <li><a href="api/pypath.internals.annot_formats.AnnotDef.html#pypath.internals.annot_formats.AnnotDef.scope">scope (pypath.internals.annot_formats.AnnotDef attribute)</a>
+</li>
+      <li><a href="api/pypath.inputs.iptmnet.IptmnetInteraction.html#pypath.inputs.iptmnet.IptmnetInteraction.score">score (pypath.inputs.iptmnet.IptmnetInteraction attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.utils.orthology.OmaOrtholog.html#pypath.utils.orthology.OmaOrtholog.score">(pypath.utils.orthology.OmaOrtholog attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.inputs.hmdb.structures.sdf.html#pypath.inputs.hmdb.structures.sdf">sdf() (in module pypath.inputs.hmdb.structures)</a>
+</li>
+      <li><a href="api/pypath.core.annot.AnnotationTable.html#pypath.core.annot.AnnotationTable.search">search() (pypath.core.annot.AnnotationTable method)</a>
+</li>
+      <li><a href="api/pypath.resources.controller.ResourceController.html#pypath.resources.controller.ResourceController.secondary_resources">secondary_resources() (pypath.resources.controller.ResourceController method)</a>
+</li>
+      <li><a href="api/pypath.inputs.cellphonedb.CellPhoneDBAnnotation.html#pypath.inputs.cellphonedb.CellPhoneDBAnnotation.secreted">secreted (pypath.inputs.cellphonedb.CellPhoneDBAnnotation attribute)</a>
+</li>
+      <li><a href="api/pypath.inputs.cellphonedb.CellPhoneDBAnnotation.html#pypath.inputs.cellphonedb.CellPhoneDBAnnotation.secreted_class">secreted_class (pypath.inputs.cellphonedb.CellPhoneDBAnnotation attribute)</a>
+</li>
+      <li><a href="api/pypath.utils.pdb.Segment.html#pypath.utils.pdb.Segment">Segment (class in pypath.utils.pdb)</a>
+</li>
+      <li><a href="api/pypath.utils.reflists.select.html#pypath.utils.reflists.select">select() (in module pypath.utils.reflists)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.annot.Adhesome.html#pypath.core.annot.Adhesome.select">(pypath.core.annot.Adhesome method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Almen2009.html#pypath.core.annot.Almen2009.select">(pypath.core.annot.Almen2009 method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.AnnotationBase.html#pypath.core.annot.AnnotationBase.select">(pypath.core.annot.AnnotationBase method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Baccin2019.html#pypath.core.annot.Baccin2019.select">(pypath.core.annot.Baccin2019 method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Biogps.html#pypath.core.annot.Biogps.select">(pypath.core.annot.Biogps method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cancerdrugsdb.html#pypath.core.annot.Cancerdrugsdb.select">(pypath.core.annot.Cancerdrugsdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CancerGeneCensus.html#pypath.core.annot.CancerGeneCensus.select">(pypath.core.annot.CancerGeneCensus method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cancersea.html#pypath.core.annot.Cancersea.select">(pypath.core.annot.Cancersea method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cellcall.html#pypath.core.annot.Cellcall.select">(pypath.core.annot.Cellcall method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cellcellinteractions.html#pypath.core.annot.Cellcellinteractions.select">(pypath.core.annot.Cellcellinteractions method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cellchatdb.html#pypath.core.annot.Cellchatdb.select">(pypath.core.annot.Cellchatdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CellchatdbComplex.html#pypath.core.annot.CellchatdbComplex.select">(pypath.core.annot.CellchatdbComplex method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cellinker.html#pypath.core.annot.Cellinker.select">(pypath.core.annot.Cellinker method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CellinkerComplex.html#pypath.core.annot.CellinkerComplex.select">(pypath.core.annot.CellinkerComplex method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CellPhoneDB.html#pypath.core.annot.CellPhoneDB.select">(pypath.core.annot.CellPhoneDB method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CellPhoneDBComplex.html#pypath.core.annot.CellPhoneDBComplex.select">(pypath.core.annot.CellPhoneDBComplex method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CellSurfaceProteinAtlas.html#pypath.core.annot.CellSurfaceProteinAtlas.select">(pypath.core.annot.CellSurfaceProteinAtlas method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CellSurfaceProteinAtlasCellType.html#pypath.core.annot.CellSurfaceProteinAtlasCellType.select">(pypath.core.annot.CellSurfaceProteinAtlasCellType method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Celltalkdb.html#pypath.core.annot.Celltalkdb.select">(pypath.core.annot.Celltalkdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Celltypist.html#pypath.core.annot.Celltypist.select">(pypath.core.annot.Celltypist method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Comppi.html#pypath.core.annot.Comppi.select">(pypath.core.annot.Comppi method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Connectomedb.html#pypath.core.annot.Connectomedb.select">(pypath.core.annot.Connectomedb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Corum.html#pypath.core.annot.Corum.select">(pypath.core.annot.Corum method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CorumFuncat.html#pypath.core.annot.CorumFuncat.select">(pypath.core.annot.CorumFuncat method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CorumGO.html#pypath.core.annot.CorumGO.select">(pypath.core.annot.CorumGO method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cpad.html#pypath.core.annot.Cpad.select">(pypath.core.annot.Cpad method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CustomAnnotation.html#pypath.core.annot.CustomAnnotation.select">(pypath.core.annot.CustomAnnotation method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cytosig.html#pypath.core.annot.Cytosig.select">(pypath.core.annot.Cytosig method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Dgidb.html#pypath.core.annot.Dgidb.select">(pypath.core.annot.Dgidb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Disgenet.html#pypath.core.annot.Disgenet.select">(pypath.core.annot.Disgenet method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Embrace.html#pypath.core.annot.Embrace.select">(pypath.core.annot.Embrace method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Exocarta.html#pypath.core.annot.Exocarta.select">(pypath.core.annot.Exocarta method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.GOIntercell.html#pypath.core.annot.GOIntercell.select">(pypath.core.annot.GOIntercell method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Gpcrdb.html#pypath.core.annot.Gpcrdb.select">(pypath.core.annot.Gpcrdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.GuideToPharmacology.html#pypath.core.annot.GuideToPharmacology.select">(pypath.core.annot.GuideToPharmacology method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Hgnc.html#pypath.core.annot.Hgnc.select">(pypath.core.annot.Hgnc method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.HpmrComplex.html#pypath.core.annot.HpmrComplex.select">(pypath.core.annot.HpmrComplex method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.HPO.html#pypath.core.annot.HPO.select">(pypath.core.annot.HPO method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Humancellmap.html#pypath.core.annot.Humancellmap.select">(pypath.core.annot.Humancellmap method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.HumanPlasmaMembraneReceptome.html#pypath.core.annot.HumanPlasmaMembraneReceptome.select">(pypath.core.annot.HumanPlasmaMembraneReceptome method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.HumanProteinAtlas.html#pypath.core.annot.HumanProteinAtlas.select">(pypath.core.annot.HumanProteinAtlas method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.HumanProteinAtlasSecretome.html#pypath.core.annot.HumanProteinAtlasSecretome.select">(pypath.core.annot.HumanProteinAtlasSecretome method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.HumanProteinAtlasSubcellular.html#pypath.core.annot.HumanProteinAtlasSubcellular.select">(pypath.core.annot.HumanProteinAtlasSubcellular method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Icellnet.html#pypath.core.annot.Icellnet.select">(pypath.core.annot.Icellnet method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.IcellnetComplex.html#pypath.core.annot.IcellnetComplex.select">(pypath.core.annot.IcellnetComplex method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Integrins.html#pypath.core.annot.Integrins.select">(pypath.core.annot.Integrins method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.InterPro.html#pypath.core.annot.InterPro.select">(pypath.core.annot.InterPro method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Intogen.html#pypath.core.annot.Intogen.select">(pypath.core.annot.Intogen method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Italk.html#pypath.core.annot.Italk.select">(pypath.core.annot.Italk method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.KeggPathways.html#pypath.core.annot.KeggPathways.select">(pypath.core.annot.KeggPathways method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.KeggPathwaysPC.html#pypath.core.annot.KeggPathwaysPC.select">(pypath.core.annot.KeggPathwaysPC method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Kinasedotcom.html#pypath.core.annot.Kinasedotcom.select">(pypath.core.annot.Kinasedotcom method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Kirouac2010.html#pypath.core.annot.Kirouac2010.select">(pypath.core.annot.Kirouac2010 method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Lambert2018.html#pypath.core.annot.Lambert2018.select">(pypath.core.annot.Lambert2018 method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.LigandReceptor.html#pypath.core.annot.LigandReceptor.select">(pypath.core.annot.LigandReceptor method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Locate.html#pypath.core.annot.Locate.select">(pypath.core.annot.Locate method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Lrdb.html#pypath.core.annot.Lrdb.select">(pypath.core.annot.Lrdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Matrisome.html#pypath.core.annot.Matrisome.select">(pypath.core.annot.Matrisome method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Matrixdb.html#pypath.core.annot.Matrixdb.select">(pypath.core.annot.Matrixdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Mcam.html#pypath.core.annot.Mcam.select">(pypath.core.annot.Mcam method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Membranome.html#pypath.core.annot.Membranome.select">(pypath.core.annot.Membranome method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Msigdb.html#pypath.core.annot.Msigdb.select">(pypath.core.annot.Msigdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.NetpathPathways.html#pypath.core.annot.NetpathPathways.select">(pypath.core.annot.NetpathPathways method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Opm.html#pypath.core.annot.Opm.select">(pypath.core.annot.Opm method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Panglaodb.html#pypath.core.annot.Panglaodb.select">(pypath.core.annot.Panglaodb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Phobius.html#pypath.core.annot.Phobius.select">(pypath.core.annot.Phobius method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Phosphatome.html#pypath.core.annot.Phosphatome.select">(pypath.core.annot.Phosphatome method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Progeny.html#pypath.core.annot.Progeny.select">(pypath.core.annot.Progeny method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Ramilowski2015.html#pypath.core.annot.Ramilowski2015.select">(pypath.core.annot.Ramilowski2015 method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Ramilowski2015Location.html#pypath.core.annot.Ramilowski2015Location.select">(pypath.core.annot.Ramilowski2015Location method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Scconnect.html#pypath.core.annot.Scconnect.select">(pypath.core.annot.Scconnect method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.ScconnectComplex.html#pypath.core.annot.ScconnectComplex.select">(pypath.core.annot.ScconnectComplex method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.SignalinkFunctions.html#pypath.core.annot.SignalinkFunctions.select">(pypath.core.annot.SignalinkFunctions method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.SignalinkPathways.html#pypath.core.annot.SignalinkPathways.select">(pypath.core.annot.SignalinkPathways method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.SignorPathways.html#pypath.core.annot.SignorPathways.select">(pypath.core.annot.SignorPathways method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Surfaceome.html#pypath.core.annot.Surfaceome.select">(pypath.core.annot.Surfaceome method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Talklr.html#pypath.core.annot.Talklr.select">(pypath.core.annot.Talklr method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Tcdb.html#pypath.core.annot.Tcdb.select">(pypath.core.annot.Tcdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Tfcensus.html#pypath.core.annot.Tfcensus.select">(pypath.core.annot.Tfcensus method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Topdb.html#pypath.core.annot.Topdb.select">(pypath.core.annot.Topdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.UniprotFamilies.html#pypath.core.annot.UniprotFamilies.select">(pypath.core.annot.UniprotFamilies method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.UniprotKeywords.html#pypath.core.annot.UniprotKeywords.select">(pypath.core.annot.UniprotKeywords method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.UniprotLocations.html#pypath.core.annot.UniprotLocations.select">(pypath.core.annot.UniprotLocations method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.UniprotTissues.html#pypath.core.annot.UniprotTissues.select">(pypath.core.annot.UniprotTissues method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.UniprotTopologies.html#pypath.core.annot.UniprotTopologies.select">(pypath.core.annot.UniprotTopologies method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Vesiclepedia.html#pypath.core.annot.Vesiclepedia.select">(pypath.core.annot.Vesiclepedia method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Wang.html#pypath.core.annot.Wang.select">(pypath.core.annot.Wang method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Zhong2015.html#pypath.core.annot.Zhong2015.select">(pypath.core.annot.Zhong2015 method)</a>
+</li>
+        <li><a href="api/pypath.core.intercell.IntercellAnnotation.html#pypath.core.intercell.IntercellAnnotation.select">(pypath.core.intercell.IntercellAnnotation method)</a>
+</li>
+        <li><a href="api/pypath.utils.go.GOAnnotation.html#pypath.utils.go.GOAnnotation.select">(pypath.utils.go.GOAnnotation method)</a>
+</li>
+        <li><a href="api/pypath.utils.reflists.ReferenceListManager.html#pypath.utils.reflists.ReferenceListManager.select">(pypath.utils.reflists.ReferenceListManager method)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.utils.go.GOAnnotation.html#pypath.utils.go.GOAnnotation.select_by_all">select_by_all() (pypath.utils.go.GOAnnotation method)</a>
+</li>
+      <li><a href="api/pypath.utils.go.GOAnnotation.html#pypath.utils.go.GOAnnotation.select_by_expr">select_by_expr() (pypath.utils.go.GOAnnotation method)</a>
+</li>
+      <li><a href="api/pypath.utils.go.GOAnnotation.html#pypath.utils.go.GOAnnotation.select_by_expr_terms">select_by_expr_terms() (pypath.utils.go.GOAnnotation method)</a>
+</li>
+      <li><a href="api/pypath.utils.go.GOAnnotation.html#pypath.utils.go.GOAnnotation.select_by_name">select_by_name() (pypath.utils.go.GOAnnotation method)</a>
+</li>
+      <li><a href="api/pypath.utils.go.GOAnnotation.html#pypath.utils.go.GOAnnotation.select_by_term">select_by_term() (pypath.utils.go.GOAnnotation method)</a>
+</li>
+      <li><a href="api/pypath.utils.seq.Seq.html#pypath.utils.seq.Seq">Seq (class in pypath.utils.seq)</a>
+</li>
+      <li><a href="api/pypath.inputs.pisa.PisaBond.html#pypath.inputs.pisa.PisaBond.seqnum_1">seqnum_1 (pypath.inputs.pisa.PisaBond attribute)</a>
+</li>
+      <li><a href="api/pypath.inputs.pisa.PisaBond.html#pypath.inputs.pisa.PisaBond.seqnum_2">seqnum_2 (pypath.inputs.pisa.PisaBond attribute)</a>
+</li>
+      <li><a href="api/pypath.utils.uniprot.UniprotProtein.html#pypath.utils.uniprot.UniprotProtein.sequence">sequence (pypath.utils.uniprot.UniprotProtein property)</a>
+</li>
+      <li><a href="api/pypath.utils.uniprot.sequence.html#pypath.utils.uniprot.sequence">sequence() (in module pypath.utils.uniprot)</a>
+</li>
+      <li><a href="api/pypath.utils.uniprot.sequence_caution.html#pypath.utils.uniprot.sequence_caution">sequence_caution() (in module pypath.utils.uniprot)</a>
+</li>
+      <li><a href="api/pypath.utils.uniprot.sequence_caution_with_xrefs.html#pypath.utils.uniprot.sequence_caution_with_xrefs">sequence_caution_with_xrefs() (in module pypath.utils.uniprot)</a>
+</li>
+      <li><a href="api/pypath.inputs.uniprot.UniprotRecordHistory.html#pypath.inputs.uniprot.UniprotRecordHistory.sequence_version">sequence_version (pypath.inputs.uniprot.UniprotRecordHistory attribute)</a>
+</li>
+      <li><a href="api/pypath.utils.orthology.SequenceContainer.html#pypath.utils.orthology.SequenceContainer">SequenceContainer (class in pypath.utils.orthology)</a>
+</li>
+      <li><a href="api/pypath.core.attrs.AttributeHandler.html#pypath.core.attrs.AttributeHandler.serialize">serialize() (pypath.core.attrs.AttributeHandler method)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.entity.Entity.html#pypath.core.entity.Entity.serialize">(pypath.core.entity.Entity method)</a>
+</li>
+        <li><a href="api/pypath.core.evidence.Evidence.html#pypath.core.evidence.Evidence.serialize">(pypath.core.evidence.Evidence method)</a>
+</li>
+        <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.serialize">(pypath.core.interaction.Interaction method)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.evidence.Evidences.html#pypath.core.evidence.Evidences.serialize_attrs">serialize_attrs() (pypath.core.evidence.Evidences method)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.serialize_attrs">(pypath.core.interaction.Interaction method)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.serialize_evidences">serialize_evidences() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.share.curl.Curl.html#pypath.share.curl.Curl.set_binary_data">set_binary_data() (pypath.share.curl.Curl method)</a>
+</li>
+      <li><a href="api/pypath.share.progress.Progress.html#pypath.share.progress.Progress.set_done">set_done() (pypath.share.progress.Progress method)</a>
+</li>
+      <li><a href="api/pypath.core.enz_sub.EnzymeSubstrateOrthologyProcessor.html#pypath.core.enz_sub.EnzymeSubstrateOrthologyProcessor.set_inputargs">set_inputargs() (pypath.core.enz_sub.EnzymeSubstrateOrthologyProcessor method)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.enz_sub.EnzymeSubstrateProcessor.html#pypath.core.enz_sub.EnzymeSubstrateProcessor.set_inputargs">(pypath.core.enz_sub.EnzymeSubstrateProcessor method)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.annot.CustomAnnotation.html#pypath.core.annot.CustomAnnotation.set_interclass_network_df">set_interclass_network_df() (pypath.core.annot.CustomAnnotation method)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.intercell.IntercellAnnotation.html#pypath.core.intercell.IntercellAnnotation.set_interclass_network_df">(pypath.core.intercell.IntercellAnnotation method)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.annot.Adhesome.html#pypath.core.annot.Adhesome.set_method">set_method() (pypath.core.annot.Adhesome method)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.annot.Almen2009.html#pypath.core.annot.Almen2009.set_method">(pypath.core.annot.Almen2009 method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.AnnotationBase.html#pypath.core.annot.AnnotationBase.set_method">(pypath.core.annot.AnnotationBase method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Baccin2019.html#pypath.core.annot.Baccin2019.set_method">(pypath.core.annot.Baccin2019 method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Biogps.html#pypath.core.annot.Biogps.set_method">(pypath.core.annot.Biogps method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cancerdrugsdb.html#pypath.core.annot.Cancerdrugsdb.set_method">(pypath.core.annot.Cancerdrugsdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CancerGeneCensus.html#pypath.core.annot.CancerGeneCensus.set_method">(pypath.core.annot.CancerGeneCensus method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cancersea.html#pypath.core.annot.Cancersea.set_method">(pypath.core.annot.Cancersea method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cellcall.html#pypath.core.annot.Cellcall.set_method">(pypath.core.annot.Cellcall method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cellcellinteractions.html#pypath.core.annot.Cellcellinteractions.set_method">(pypath.core.annot.Cellcellinteractions method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cellchatdb.html#pypath.core.annot.Cellchatdb.set_method">(pypath.core.annot.Cellchatdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CellchatdbComplex.html#pypath.core.annot.CellchatdbComplex.set_method">(pypath.core.annot.CellchatdbComplex method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cellinker.html#pypath.core.annot.Cellinker.set_method">(pypath.core.annot.Cellinker method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CellinkerComplex.html#pypath.core.annot.CellinkerComplex.set_method">(pypath.core.annot.CellinkerComplex method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CellPhoneDB.html#pypath.core.annot.CellPhoneDB.set_method">(pypath.core.annot.CellPhoneDB method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CellPhoneDBComplex.html#pypath.core.annot.CellPhoneDBComplex.set_method">(pypath.core.annot.CellPhoneDBComplex method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CellSurfaceProteinAtlas.html#pypath.core.annot.CellSurfaceProteinAtlas.set_method">(pypath.core.annot.CellSurfaceProteinAtlas method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CellSurfaceProteinAtlasCellType.html#pypath.core.annot.CellSurfaceProteinAtlasCellType.set_method">(pypath.core.annot.CellSurfaceProteinAtlasCellType method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Celltalkdb.html#pypath.core.annot.Celltalkdb.set_method">(pypath.core.annot.Celltalkdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Celltypist.html#pypath.core.annot.Celltypist.set_method">(pypath.core.annot.Celltypist method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Comppi.html#pypath.core.annot.Comppi.set_method">(pypath.core.annot.Comppi method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Connectomedb.html#pypath.core.annot.Connectomedb.set_method">(pypath.core.annot.Connectomedb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Corum.html#pypath.core.annot.Corum.set_method">(pypath.core.annot.Corum method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CorumFuncat.html#pypath.core.annot.CorumFuncat.set_method">(pypath.core.annot.CorumFuncat method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CorumGO.html#pypath.core.annot.CorumGO.set_method">(pypath.core.annot.CorumGO method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cpad.html#pypath.core.annot.Cpad.set_method">(pypath.core.annot.Cpad method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cytosig.html#pypath.core.annot.Cytosig.set_method">(pypath.core.annot.Cytosig method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Dgidb.html#pypath.core.annot.Dgidb.set_method">(pypath.core.annot.Dgidb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Disgenet.html#pypath.core.annot.Disgenet.set_method">(pypath.core.annot.Disgenet method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Embrace.html#pypath.core.annot.Embrace.set_method">(pypath.core.annot.Embrace method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Exocarta.html#pypath.core.annot.Exocarta.set_method">(pypath.core.annot.Exocarta method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.GOIntercell.html#pypath.core.annot.GOIntercell.set_method">(pypath.core.annot.GOIntercell method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Gpcrdb.html#pypath.core.annot.Gpcrdb.set_method">(pypath.core.annot.Gpcrdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.GuideToPharmacology.html#pypath.core.annot.GuideToPharmacology.set_method">(pypath.core.annot.GuideToPharmacology method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Hgnc.html#pypath.core.annot.Hgnc.set_method">(pypath.core.annot.Hgnc method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.HpmrComplex.html#pypath.core.annot.HpmrComplex.set_method">(pypath.core.annot.HpmrComplex method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.HPO.html#pypath.core.annot.HPO.set_method">(pypath.core.annot.HPO method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Humancellmap.html#pypath.core.annot.Humancellmap.set_method">(pypath.core.annot.Humancellmap method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.HumanPlasmaMembraneReceptome.html#pypath.core.annot.HumanPlasmaMembraneReceptome.set_method">(pypath.core.annot.HumanPlasmaMembraneReceptome method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.HumanProteinAtlas.html#pypath.core.annot.HumanProteinAtlas.set_method">(pypath.core.annot.HumanProteinAtlas method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.HumanProteinAtlasSecretome.html#pypath.core.annot.HumanProteinAtlasSecretome.set_method">(pypath.core.annot.HumanProteinAtlasSecretome method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.HumanProteinAtlasSubcellular.html#pypath.core.annot.HumanProteinAtlasSubcellular.set_method">(pypath.core.annot.HumanProteinAtlasSubcellular method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Icellnet.html#pypath.core.annot.Icellnet.set_method">(pypath.core.annot.Icellnet method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.IcellnetComplex.html#pypath.core.annot.IcellnetComplex.set_method">(pypath.core.annot.IcellnetComplex method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Integrins.html#pypath.core.annot.Integrins.set_method">(pypath.core.annot.Integrins method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.InterPro.html#pypath.core.annot.InterPro.set_method">(pypath.core.annot.InterPro method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Intogen.html#pypath.core.annot.Intogen.set_method">(pypath.core.annot.Intogen method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Italk.html#pypath.core.annot.Italk.set_method">(pypath.core.annot.Italk method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.KeggPathways.html#pypath.core.annot.KeggPathways.set_method">(pypath.core.annot.KeggPathways method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.KeggPathwaysPC.html#pypath.core.annot.KeggPathwaysPC.set_method">(pypath.core.annot.KeggPathwaysPC method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Kinasedotcom.html#pypath.core.annot.Kinasedotcom.set_method">(pypath.core.annot.Kinasedotcom method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Kirouac2010.html#pypath.core.annot.Kirouac2010.set_method">(pypath.core.annot.Kirouac2010 method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Lambert2018.html#pypath.core.annot.Lambert2018.set_method">(pypath.core.annot.Lambert2018 method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.LigandReceptor.html#pypath.core.annot.LigandReceptor.set_method">(pypath.core.annot.LigandReceptor method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Locate.html#pypath.core.annot.Locate.set_method">(pypath.core.annot.Locate method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Lrdb.html#pypath.core.annot.Lrdb.set_method">(pypath.core.annot.Lrdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Matrisome.html#pypath.core.annot.Matrisome.set_method">(pypath.core.annot.Matrisome method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Matrixdb.html#pypath.core.annot.Matrixdb.set_method">(pypath.core.annot.Matrixdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Mcam.html#pypath.core.annot.Mcam.set_method">(pypath.core.annot.Mcam method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Membranome.html#pypath.core.annot.Membranome.set_method">(pypath.core.annot.Membranome method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Msigdb.html#pypath.core.annot.Msigdb.set_method">(pypath.core.annot.Msigdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.NetpathPathways.html#pypath.core.annot.NetpathPathways.set_method">(pypath.core.annot.NetpathPathways method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Opm.html#pypath.core.annot.Opm.set_method">(pypath.core.annot.Opm method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Panglaodb.html#pypath.core.annot.Panglaodb.set_method">(pypath.core.annot.Panglaodb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Phobius.html#pypath.core.annot.Phobius.set_method">(pypath.core.annot.Phobius method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Phosphatome.html#pypath.core.annot.Phosphatome.set_method">(pypath.core.annot.Phosphatome method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Progeny.html#pypath.core.annot.Progeny.set_method">(pypath.core.annot.Progeny method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Ramilowski2015.html#pypath.core.annot.Ramilowski2015.set_method">(pypath.core.annot.Ramilowski2015 method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Ramilowski2015Location.html#pypath.core.annot.Ramilowski2015Location.set_method">(pypath.core.annot.Ramilowski2015Location method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Scconnect.html#pypath.core.annot.Scconnect.set_method">(pypath.core.annot.Scconnect method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.ScconnectComplex.html#pypath.core.annot.ScconnectComplex.set_method">(pypath.core.annot.ScconnectComplex method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.SignalinkFunctions.html#pypath.core.annot.SignalinkFunctions.set_method">(pypath.core.annot.SignalinkFunctions method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.SignalinkPathways.html#pypath.core.annot.SignalinkPathways.set_method">(pypath.core.annot.SignalinkPathways method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.SignorPathways.html#pypath.core.annot.SignorPathways.set_method">(pypath.core.annot.SignorPathways method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Surfaceome.html#pypath.core.annot.Surfaceome.set_method">(pypath.core.annot.Surfaceome method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Talklr.html#pypath.core.annot.Talklr.set_method">(pypath.core.annot.Talklr method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Tcdb.html#pypath.core.annot.Tcdb.set_method">(pypath.core.annot.Tcdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Tfcensus.html#pypath.core.annot.Tfcensus.set_method">(pypath.core.annot.Tfcensus method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Topdb.html#pypath.core.annot.Topdb.set_method">(pypath.core.annot.Topdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.UniprotFamilies.html#pypath.core.annot.UniprotFamilies.set_method">(pypath.core.annot.UniprotFamilies method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.UniprotKeywords.html#pypath.core.annot.UniprotKeywords.set_method">(pypath.core.annot.UniprotKeywords method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.UniprotLocations.html#pypath.core.annot.UniprotLocations.set_method">(pypath.core.annot.UniprotLocations method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.UniprotTissues.html#pypath.core.annot.UniprotTissues.set_method">(pypath.core.annot.UniprotTissues method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.UniprotTopologies.html#pypath.core.annot.UniprotTopologies.set_method">(pypath.core.annot.UniprotTopologies method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Vesiclepedia.html#pypath.core.annot.Vesiclepedia.set_method">(pypath.core.annot.Vesiclepedia method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Wang.html#pypath.core.annot.Wang.set_method">(pypath.core.annot.Wang method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Zhong2015.html#pypath.core.annot.Zhong2015.set_method">(pypath.core.annot.Zhong2015 method)</a>
+</li>
+        <li><a href="api/pypath.core.complex.AbstractComplexResource.html#pypath.core.complex.AbstractComplexResource.set_method">(pypath.core.complex.AbstractComplexResource method)</a>
+</li>
+        <li><a href="api/pypath.core.complex.Cellchatdb.html#pypath.core.complex.Cellchatdb.set_method">(pypath.core.complex.Cellchatdb method)</a>
+</li>
+        <li><a href="api/pypath.core.complex.Cellinker.html#pypath.core.complex.Cellinker.set_method">(pypath.core.complex.Cellinker method)</a>
+</li>
+        <li><a href="api/pypath.core.complex.CellPhoneDB.html#pypath.core.complex.CellPhoneDB.set_method">(pypath.core.complex.CellPhoneDB method)</a>
+</li>
+        <li><a href="api/pypath.core.complex.Compleat.html#pypath.core.complex.Compleat.set_method">(pypath.core.complex.Compleat method)</a>
+</li>
+        <li><a href="api/pypath.core.complex.ComplexAggregator.html#pypath.core.complex.ComplexAggregator.set_method">(pypath.core.complex.ComplexAggregator method)</a>
+</li>
+        <li><a href="api/pypath.core.complex.ComplexPortal.html#pypath.core.complex.ComplexPortal.set_method">(pypath.core.complex.ComplexPortal method)</a>
+</li>
+        <li><a href="api/pypath.core.complex.Corum.html#pypath.core.complex.Corum.set_method">(pypath.core.complex.Corum method)</a>
+</li>
+        <li><a href="api/pypath.core.complex.GuideToPharmacology.html#pypath.core.complex.GuideToPharmacology.set_method">(pypath.core.complex.GuideToPharmacology method)</a>
+</li>
+        <li><a href="api/pypath.core.complex.Havugimana.html#pypath.core.complex.Havugimana.set_method">(pypath.core.complex.Havugimana method)</a>
+</li>
+        <li><a href="api/pypath.core.complex.Hpmr.html#pypath.core.complex.Hpmr.set_method">(pypath.core.complex.Hpmr method)</a>
+</li>
+        <li><a href="api/pypath.core.complex.Humap.html#pypath.core.complex.Humap.set_method">(pypath.core.complex.Humap method)</a>
+</li>
+        <li><a href="api/pypath.core.complex.Humap2.html#pypath.core.complex.Humap2.set_method">(pypath.core.complex.Humap2 method)</a>
+</li>
+        <li><a href="api/pypath.core.complex.Icellnet.html#pypath.core.complex.Icellnet.set_method">(pypath.core.complex.Icellnet method)</a>
+</li>
+        <li><a href="api/pypath.core.complex.Kegg.html#pypath.core.complex.Kegg.set_method">(pypath.core.complex.Kegg method)</a>
+</li>
+        <li><a href="api/pypath.core.complex.Pdb.html#pypath.core.complex.Pdb.set_method">(pypath.core.complex.Pdb method)</a>
+</li>
+        <li><a href="api/pypath.core.complex.Signor.html#pypath.core.complex.Signor.set_method">(pypath.core.complex.Signor method)</a>
+</li>
+        <li><a href="api/pypath.core.complex.Spike.html#pypath.core.complex.Spike.set_method">(pypath.core.complex.Spike method)</a>
+</li>
+        <li><a href="api/pypath.core.enz_sub.EnzymeSubstrateOrthologyProcessor.html#pypath.core.enz_sub.EnzymeSubstrateOrthologyProcessor.set_method">(pypath.core.enz_sub.EnzymeSubstrateOrthologyProcessor method)</a>
+</li>
+        <li><a href="api/pypath.core.enz_sub.EnzymeSubstrateProcessor.html#pypath.core.enz_sub.EnzymeSubstrateProcessor.set_method">(pypath.core.enz_sub.EnzymeSubstrateProcessor method)</a>
+</li>
+        <li><a href="api/pypath.internals.resource.AbstractResource.html#pypath.internals.resource.AbstractResource.set_method">(pypath.internals.resource.AbstractResource method)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.omnipath.app.DatabaseManager.html#pypath.omnipath.app.DatabaseManager.set_network">set_network() (pypath.omnipath.app.DatabaseManager method)</a>
+</li>
+      <li><a href="api/pypath.utils.go.GeneOntology.html#pypath.utils.go.GeneOntology.set_of">set_of() (pypath.utils.go.GeneOntology method)</a>
+</li>
+      <li><a href="api/pypath.utils.go.GeneOntology.html#pypath.utils.go.GeneOntology.set_of_names">set_of_names() (pypath.utils.go.GeneOntology method)</a>
+</li>
+      <li><a href="api/pypath.utils.go.GeneOntology.html#pypath.utils.go.GeneOntology.set_of_terms">set_of_terms() (pypath.utils.go.GeneOntology method)</a>
+</li>
+      <li><a href="api/pypath.utils.pyreact.BioPaxReader.html#pypath.utils.pyreact.BioPaxReader.set_progress">set_progress() (pypath.utils.pyreact.BioPaxReader method)</a>
+</li>
+      <li><a href="api/pypath.core.annot.Adhesome.html#pypath.core.annot.Adhesome.set_reference_set">set_reference_set() (pypath.core.annot.Adhesome method)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.annot.Almen2009.html#pypath.core.annot.Almen2009.set_reference_set">(pypath.core.annot.Almen2009 method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.AnnotationBase.html#pypath.core.annot.AnnotationBase.set_reference_set">(pypath.core.annot.AnnotationBase method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Baccin2019.html#pypath.core.annot.Baccin2019.set_reference_set">(pypath.core.annot.Baccin2019 method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Biogps.html#pypath.core.annot.Biogps.set_reference_set">(pypath.core.annot.Biogps method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cancerdrugsdb.html#pypath.core.annot.Cancerdrugsdb.set_reference_set">(pypath.core.annot.Cancerdrugsdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CancerGeneCensus.html#pypath.core.annot.CancerGeneCensus.set_reference_set">(pypath.core.annot.CancerGeneCensus method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cancersea.html#pypath.core.annot.Cancersea.set_reference_set">(pypath.core.annot.Cancersea method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cellcall.html#pypath.core.annot.Cellcall.set_reference_set">(pypath.core.annot.Cellcall method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cellcellinteractions.html#pypath.core.annot.Cellcellinteractions.set_reference_set">(pypath.core.annot.Cellcellinteractions method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cellchatdb.html#pypath.core.annot.Cellchatdb.set_reference_set">(pypath.core.annot.Cellchatdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CellchatdbComplex.html#pypath.core.annot.CellchatdbComplex.set_reference_set">(pypath.core.annot.CellchatdbComplex method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cellinker.html#pypath.core.annot.Cellinker.set_reference_set">(pypath.core.annot.Cellinker method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CellinkerComplex.html#pypath.core.annot.CellinkerComplex.set_reference_set">(pypath.core.annot.CellinkerComplex method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CellPhoneDB.html#pypath.core.annot.CellPhoneDB.set_reference_set">(pypath.core.annot.CellPhoneDB method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CellPhoneDBComplex.html#pypath.core.annot.CellPhoneDBComplex.set_reference_set">(pypath.core.annot.CellPhoneDBComplex method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CellSurfaceProteinAtlas.html#pypath.core.annot.CellSurfaceProteinAtlas.set_reference_set">(pypath.core.annot.CellSurfaceProteinAtlas method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CellSurfaceProteinAtlasCellType.html#pypath.core.annot.CellSurfaceProteinAtlasCellType.set_reference_set">(pypath.core.annot.CellSurfaceProteinAtlasCellType method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Celltalkdb.html#pypath.core.annot.Celltalkdb.set_reference_set">(pypath.core.annot.Celltalkdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Celltypist.html#pypath.core.annot.Celltypist.set_reference_set">(pypath.core.annot.Celltypist method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Comppi.html#pypath.core.annot.Comppi.set_reference_set">(pypath.core.annot.Comppi method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Connectomedb.html#pypath.core.annot.Connectomedb.set_reference_set">(pypath.core.annot.Connectomedb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Corum.html#pypath.core.annot.Corum.set_reference_set">(pypath.core.annot.Corum method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CorumFuncat.html#pypath.core.annot.CorumFuncat.set_reference_set">(pypath.core.annot.CorumFuncat method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CorumGO.html#pypath.core.annot.CorumGO.set_reference_set">(pypath.core.annot.CorumGO method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cpad.html#pypath.core.annot.Cpad.set_reference_set">(pypath.core.annot.Cpad method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cytosig.html#pypath.core.annot.Cytosig.set_reference_set">(pypath.core.annot.Cytosig method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Dgidb.html#pypath.core.annot.Dgidb.set_reference_set">(pypath.core.annot.Dgidb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Disgenet.html#pypath.core.annot.Disgenet.set_reference_set">(pypath.core.annot.Disgenet method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Embrace.html#pypath.core.annot.Embrace.set_reference_set">(pypath.core.annot.Embrace method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Exocarta.html#pypath.core.annot.Exocarta.set_reference_set">(pypath.core.annot.Exocarta method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.GOIntercell.html#pypath.core.annot.GOIntercell.set_reference_set">(pypath.core.annot.GOIntercell method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Gpcrdb.html#pypath.core.annot.Gpcrdb.set_reference_set">(pypath.core.annot.Gpcrdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.GuideToPharmacology.html#pypath.core.annot.GuideToPharmacology.set_reference_set">(pypath.core.annot.GuideToPharmacology method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Hgnc.html#pypath.core.annot.Hgnc.set_reference_set">(pypath.core.annot.Hgnc method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.HpmrComplex.html#pypath.core.annot.HpmrComplex.set_reference_set">(pypath.core.annot.HpmrComplex method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.HPO.html#pypath.core.annot.HPO.set_reference_set">(pypath.core.annot.HPO method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Humancellmap.html#pypath.core.annot.Humancellmap.set_reference_set">(pypath.core.annot.Humancellmap method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.HumanPlasmaMembraneReceptome.html#pypath.core.annot.HumanPlasmaMembraneReceptome.set_reference_set">(pypath.core.annot.HumanPlasmaMembraneReceptome method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.HumanProteinAtlas.html#pypath.core.annot.HumanProteinAtlas.set_reference_set">(pypath.core.annot.HumanProteinAtlas method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.HumanProteinAtlasSecretome.html#pypath.core.annot.HumanProteinAtlasSecretome.set_reference_set">(pypath.core.annot.HumanProteinAtlasSecretome method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.HumanProteinAtlasSubcellular.html#pypath.core.annot.HumanProteinAtlasSubcellular.set_reference_set">(pypath.core.annot.HumanProteinAtlasSubcellular method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Icellnet.html#pypath.core.annot.Icellnet.set_reference_set">(pypath.core.annot.Icellnet method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.IcellnetComplex.html#pypath.core.annot.IcellnetComplex.set_reference_set">(pypath.core.annot.IcellnetComplex method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Integrins.html#pypath.core.annot.Integrins.set_reference_set">(pypath.core.annot.Integrins method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.InterPro.html#pypath.core.annot.InterPro.set_reference_set">(pypath.core.annot.InterPro method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Intogen.html#pypath.core.annot.Intogen.set_reference_set">(pypath.core.annot.Intogen method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Italk.html#pypath.core.annot.Italk.set_reference_set">(pypath.core.annot.Italk method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.KeggPathways.html#pypath.core.annot.KeggPathways.set_reference_set">(pypath.core.annot.KeggPathways method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.KeggPathwaysPC.html#pypath.core.annot.KeggPathwaysPC.set_reference_set">(pypath.core.annot.KeggPathwaysPC method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Kinasedotcom.html#pypath.core.annot.Kinasedotcom.set_reference_set">(pypath.core.annot.Kinasedotcom method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Kirouac2010.html#pypath.core.annot.Kirouac2010.set_reference_set">(pypath.core.annot.Kirouac2010 method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Lambert2018.html#pypath.core.annot.Lambert2018.set_reference_set">(pypath.core.annot.Lambert2018 method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.LigandReceptor.html#pypath.core.annot.LigandReceptor.set_reference_set">(pypath.core.annot.LigandReceptor method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Locate.html#pypath.core.annot.Locate.set_reference_set">(pypath.core.annot.Locate method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Lrdb.html#pypath.core.annot.Lrdb.set_reference_set">(pypath.core.annot.Lrdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Matrisome.html#pypath.core.annot.Matrisome.set_reference_set">(pypath.core.annot.Matrisome method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Matrixdb.html#pypath.core.annot.Matrixdb.set_reference_set">(pypath.core.annot.Matrixdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Mcam.html#pypath.core.annot.Mcam.set_reference_set">(pypath.core.annot.Mcam method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Membranome.html#pypath.core.annot.Membranome.set_reference_set">(pypath.core.annot.Membranome method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Msigdb.html#pypath.core.annot.Msigdb.set_reference_set">(pypath.core.annot.Msigdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.NetpathPathways.html#pypath.core.annot.NetpathPathways.set_reference_set">(pypath.core.annot.NetpathPathways method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Opm.html#pypath.core.annot.Opm.set_reference_set">(pypath.core.annot.Opm method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Panglaodb.html#pypath.core.annot.Panglaodb.set_reference_set">(pypath.core.annot.Panglaodb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Phobius.html#pypath.core.annot.Phobius.set_reference_set">(pypath.core.annot.Phobius method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Phosphatome.html#pypath.core.annot.Phosphatome.set_reference_set">(pypath.core.annot.Phosphatome method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Progeny.html#pypath.core.annot.Progeny.set_reference_set">(pypath.core.annot.Progeny method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Ramilowski2015.html#pypath.core.annot.Ramilowski2015.set_reference_set">(pypath.core.annot.Ramilowski2015 method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Ramilowski2015Location.html#pypath.core.annot.Ramilowski2015Location.set_reference_set">(pypath.core.annot.Ramilowski2015Location method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Scconnect.html#pypath.core.annot.Scconnect.set_reference_set">(pypath.core.annot.Scconnect method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.ScconnectComplex.html#pypath.core.annot.ScconnectComplex.set_reference_set">(pypath.core.annot.ScconnectComplex method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.SignalinkFunctions.html#pypath.core.annot.SignalinkFunctions.set_reference_set">(pypath.core.annot.SignalinkFunctions method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.SignalinkPathways.html#pypath.core.annot.SignalinkPathways.set_reference_set">(pypath.core.annot.SignalinkPathways method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.SignorPathways.html#pypath.core.annot.SignorPathways.set_reference_set">(pypath.core.annot.SignorPathways method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Surfaceome.html#pypath.core.annot.Surfaceome.set_reference_set">(pypath.core.annot.Surfaceome method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Talklr.html#pypath.core.annot.Talklr.set_reference_set">(pypath.core.annot.Talklr method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Tcdb.html#pypath.core.annot.Tcdb.set_reference_set">(pypath.core.annot.Tcdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Tfcensus.html#pypath.core.annot.Tfcensus.set_reference_set">(pypath.core.annot.Tfcensus method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Topdb.html#pypath.core.annot.Topdb.set_reference_set">(pypath.core.annot.Topdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.UniprotFamilies.html#pypath.core.annot.UniprotFamilies.set_reference_set">(pypath.core.annot.UniprotFamilies method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.UniprotKeywords.html#pypath.core.annot.UniprotKeywords.set_reference_set">(pypath.core.annot.UniprotKeywords method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.UniprotLocations.html#pypath.core.annot.UniprotLocations.set_reference_set">(pypath.core.annot.UniprotLocations method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.UniprotTissues.html#pypath.core.annot.UniprotTissues.set_reference_set">(pypath.core.annot.UniprotTissues method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.UniprotTopologies.html#pypath.core.annot.UniprotTopologies.set_reference_set">(pypath.core.annot.UniprotTopologies method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Vesiclepedia.html#pypath.core.annot.Vesiclepedia.set_reference_set">(pypath.core.annot.Vesiclepedia method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Wang.html#pypath.core.annot.Wang.set_reference_set">(pypath.core.annot.Wang method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Zhong2015.html#pypath.core.annot.Zhong2015.set_reference_set">(pypath.core.annot.Zhong2015 method)</a>
+</li>
+      </ul></li>
+  </ul></td>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="api/pypath.share.progress.Progress.html#pypath.share.progress.Progress.set_status">set_status() (pypath.share.progress.Progress method)</a>
+</li>
+      <li><a href="api/pypath.share.progress.Progress.html#pypath.share.progress.Progress.set_total">set_total() (pypath.share.progress.Progress method)</a>
+</li>
+      <li><a href="api/pypath.utils.mapping.MapReader.html#pypath.utils.mapping.MapReader.set_uniprot_space">set_uniprot_space() (pypath.utils.mapping.MapReader method)</a>
+</li>
+      <li><a href="api/pypath.internals.resource.NetworkDataset.html#pypath.internals.resource.NetworkDataset.setdefault">setdefault() (pypath.internals.resource.NetworkDataset method)</a>
+</li>
+      <li><a href="api/pypath.utils.mapping.MapReader.html#pypath.utils.mapping.MapReader.setup_cache">setup_cache() (pypath.utils.mapping.MapReader method)</a>
+</li>
+      <li><a href="api/pypath.core.network.NetworkStatsRecord.html#pypath.core.network.NetworkStatsRecord.shared">shared (pypath.core.network.NetworkStatsRecord attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.NetworkStatsRecord.html#pypath.core.network.NetworkStatsRecord.shared_cat">shared_cat (pypath.core.network.NetworkStatsRecord attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.NetworkStatsRecord.html#pypath.core.network.NetworkStatsRecord.shared_res_cat">shared_res_cat (pypath.core.network.NetworkStatsRecord attribute)</a>
+</li>
+      <li><a href="api/pypath.utils.taxonomy.short_latin_names.html#pypath.utils.taxonomy.short_latin_names">short_latin_names() (in module pypath.utils.taxonomy)</a>
+</li>
+      <li><a href="api/pypath.utils.taxonomy.shorten_latin_name.html#pypath.utils.taxonomy.shorten_latin_name">shorten_latin_name() (in module pypath.utils.taxonomy)</a>
+</li>
+      <li><a href="api/pypath.core.annot.Adhesome.html#pypath.core.annot.Adhesome.show">show() (pypath.core.annot.Adhesome method)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.annot.Almen2009.html#pypath.core.annot.Almen2009.show">(pypath.core.annot.Almen2009 method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.AnnotationBase.html#pypath.core.annot.AnnotationBase.show">(pypath.core.annot.AnnotationBase method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Baccin2019.html#pypath.core.annot.Baccin2019.show">(pypath.core.annot.Baccin2019 method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Biogps.html#pypath.core.annot.Biogps.show">(pypath.core.annot.Biogps method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cancerdrugsdb.html#pypath.core.annot.Cancerdrugsdb.show">(pypath.core.annot.Cancerdrugsdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CancerGeneCensus.html#pypath.core.annot.CancerGeneCensus.show">(pypath.core.annot.CancerGeneCensus method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cancersea.html#pypath.core.annot.Cancersea.show">(pypath.core.annot.Cancersea method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cellcall.html#pypath.core.annot.Cellcall.show">(pypath.core.annot.Cellcall method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cellcellinteractions.html#pypath.core.annot.Cellcellinteractions.show">(pypath.core.annot.Cellcellinteractions method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cellchatdb.html#pypath.core.annot.Cellchatdb.show">(pypath.core.annot.Cellchatdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CellchatdbComplex.html#pypath.core.annot.CellchatdbComplex.show">(pypath.core.annot.CellchatdbComplex method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cellinker.html#pypath.core.annot.Cellinker.show">(pypath.core.annot.Cellinker method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CellinkerComplex.html#pypath.core.annot.CellinkerComplex.show">(pypath.core.annot.CellinkerComplex method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CellPhoneDB.html#pypath.core.annot.CellPhoneDB.show">(pypath.core.annot.CellPhoneDB method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CellPhoneDBComplex.html#pypath.core.annot.CellPhoneDBComplex.show">(pypath.core.annot.CellPhoneDBComplex method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CellSurfaceProteinAtlas.html#pypath.core.annot.CellSurfaceProteinAtlas.show">(pypath.core.annot.CellSurfaceProteinAtlas method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CellSurfaceProteinAtlasCellType.html#pypath.core.annot.CellSurfaceProteinAtlasCellType.show">(pypath.core.annot.CellSurfaceProteinAtlasCellType method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Celltalkdb.html#pypath.core.annot.Celltalkdb.show">(pypath.core.annot.Celltalkdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Celltypist.html#pypath.core.annot.Celltypist.show">(pypath.core.annot.Celltypist method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Comppi.html#pypath.core.annot.Comppi.show">(pypath.core.annot.Comppi method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Connectomedb.html#pypath.core.annot.Connectomedb.show">(pypath.core.annot.Connectomedb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Corum.html#pypath.core.annot.Corum.show">(pypath.core.annot.Corum method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CorumFuncat.html#pypath.core.annot.CorumFuncat.show">(pypath.core.annot.CorumFuncat method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CorumGO.html#pypath.core.annot.CorumGO.show">(pypath.core.annot.CorumGO method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cpad.html#pypath.core.annot.Cpad.show">(pypath.core.annot.Cpad method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CustomAnnotation.html#pypath.core.annot.CustomAnnotation.show">(pypath.core.annot.CustomAnnotation method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cytosig.html#pypath.core.annot.Cytosig.show">(pypath.core.annot.Cytosig method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Dgidb.html#pypath.core.annot.Dgidb.show">(pypath.core.annot.Dgidb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Disgenet.html#pypath.core.annot.Disgenet.show">(pypath.core.annot.Disgenet method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Embrace.html#pypath.core.annot.Embrace.show">(pypath.core.annot.Embrace method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Exocarta.html#pypath.core.annot.Exocarta.show">(pypath.core.annot.Exocarta method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.GOIntercell.html#pypath.core.annot.GOIntercell.show">(pypath.core.annot.GOIntercell method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Gpcrdb.html#pypath.core.annot.Gpcrdb.show">(pypath.core.annot.Gpcrdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.GuideToPharmacology.html#pypath.core.annot.GuideToPharmacology.show">(pypath.core.annot.GuideToPharmacology method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Hgnc.html#pypath.core.annot.Hgnc.show">(pypath.core.annot.Hgnc method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.HpmrComplex.html#pypath.core.annot.HpmrComplex.show">(pypath.core.annot.HpmrComplex method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.HPO.html#pypath.core.annot.HPO.show">(pypath.core.annot.HPO method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Humancellmap.html#pypath.core.annot.Humancellmap.show">(pypath.core.annot.Humancellmap method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.HumanPlasmaMembraneReceptome.html#pypath.core.annot.HumanPlasmaMembraneReceptome.show">(pypath.core.annot.HumanPlasmaMembraneReceptome method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.HumanProteinAtlas.html#pypath.core.annot.HumanProteinAtlas.show">(pypath.core.annot.HumanProteinAtlas method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.HumanProteinAtlasSecretome.html#pypath.core.annot.HumanProteinAtlasSecretome.show">(pypath.core.annot.HumanProteinAtlasSecretome method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.HumanProteinAtlasSubcellular.html#pypath.core.annot.HumanProteinAtlasSubcellular.show">(pypath.core.annot.HumanProteinAtlasSubcellular method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Icellnet.html#pypath.core.annot.Icellnet.show">(pypath.core.annot.Icellnet method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.IcellnetComplex.html#pypath.core.annot.IcellnetComplex.show">(pypath.core.annot.IcellnetComplex method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Integrins.html#pypath.core.annot.Integrins.show">(pypath.core.annot.Integrins method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.InterPro.html#pypath.core.annot.InterPro.show">(pypath.core.annot.InterPro method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Intogen.html#pypath.core.annot.Intogen.show">(pypath.core.annot.Intogen method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Italk.html#pypath.core.annot.Italk.show">(pypath.core.annot.Italk method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.KeggPathways.html#pypath.core.annot.KeggPathways.show">(pypath.core.annot.KeggPathways method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.KeggPathwaysPC.html#pypath.core.annot.KeggPathwaysPC.show">(pypath.core.annot.KeggPathwaysPC method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Kinasedotcom.html#pypath.core.annot.Kinasedotcom.show">(pypath.core.annot.Kinasedotcom method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Kirouac2010.html#pypath.core.annot.Kirouac2010.show">(pypath.core.annot.Kirouac2010 method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Lambert2018.html#pypath.core.annot.Lambert2018.show">(pypath.core.annot.Lambert2018 method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.LigandReceptor.html#pypath.core.annot.LigandReceptor.show">(pypath.core.annot.LigandReceptor method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Locate.html#pypath.core.annot.Locate.show">(pypath.core.annot.Locate method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Lrdb.html#pypath.core.annot.Lrdb.show">(pypath.core.annot.Lrdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Matrisome.html#pypath.core.annot.Matrisome.show">(pypath.core.annot.Matrisome method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Matrixdb.html#pypath.core.annot.Matrixdb.show">(pypath.core.annot.Matrixdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Mcam.html#pypath.core.annot.Mcam.show">(pypath.core.annot.Mcam method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Membranome.html#pypath.core.annot.Membranome.show">(pypath.core.annot.Membranome method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Msigdb.html#pypath.core.annot.Msigdb.show">(pypath.core.annot.Msigdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.NetpathPathways.html#pypath.core.annot.NetpathPathways.show">(pypath.core.annot.NetpathPathways method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Opm.html#pypath.core.annot.Opm.show">(pypath.core.annot.Opm method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Panglaodb.html#pypath.core.annot.Panglaodb.show">(pypath.core.annot.Panglaodb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Phobius.html#pypath.core.annot.Phobius.show">(pypath.core.annot.Phobius method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Phosphatome.html#pypath.core.annot.Phosphatome.show">(pypath.core.annot.Phosphatome method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Progeny.html#pypath.core.annot.Progeny.show">(pypath.core.annot.Progeny method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Ramilowski2015.html#pypath.core.annot.Ramilowski2015.show">(pypath.core.annot.Ramilowski2015 method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Ramilowski2015Location.html#pypath.core.annot.Ramilowski2015Location.show">(pypath.core.annot.Ramilowski2015Location method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Scconnect.html#pypath.core.annot.Scconnect.show">(pypath.core.annot.Scconnect method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.ScconnectComplex.html#pypath.core.annot.ScconnectComplex.show">(pypath.core.annot.ScconnectComplex method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.SignalinkFunctions.html#pypath.core.annot.SignalinkFunctions.show">(pypath.core.annot.SignalinkFunctions method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.SignalinkPathways.html#pypath.core.annot.SignalinkPathways.show">(pypath.core.annot.SignalinkPathways method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.SignorPathways.html#pypath.core.annot.SignorPathways.show">(pypath.core.annot.SignorPathways method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Surfaceome.html#pypath.core.annot.Surfaceome.show">(pypath.core.annot.Surfaceome method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Talklr.html#pypath.core.annot.Talklr.show">(pypath.core.annot.Talklr method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Tcdb.html#pypath.core.annot.Tcdb.show">(pypath.core.annot.Tcdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Tfcensus.html#pypath.core.annot.Tfcensus.show">(pypath.core.annot.Tfcensus method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Topdb.html#pypath.core.annot.Topdb.show">(pypath.core.annot.Topdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.UniprotFamilies.html#pypath.core.annot.UniprotFamilies.show">(pypath.core.annot.UniprotFamilies method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.UniprotKeywords.html#pypath.core.annot.UniprotKeywords.show">(pypath.core.annot.UniprotKeywords method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.UniprotLocations.html#pypath.core.annot.UniprotLocations.show">(pypath.core.annot.UniprotLocations method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.UniprotTissues.html#pypath.core.annot.UniprotTissues.show">(pypath.core.annot.UniprotTissues method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.UniprotTopologies.html#pypath.core.annot.UniprotTopologies.show">(pypath.core.annot.UniprotTopologies method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Vesiclepedia.html#pypath.core.annot.Vesiclepedia.show">(pypath.core.annot.Vesiclepedia method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Wang.html#pypath.core.annot.Wang.show">(pypath.core.annot.Wang method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Zhong2015.html#pypath.core.annot.Zhong2015.show">(pypath.core.annot.Zhong2015 method)</a>
+</li>
+        <li><a href="api/pypath.core.intercell.IntercellAnnotation.html#pypath.core.intercell.IntercellAnnotation.show">(pypath.core.intercell.IntercellAnnotation method)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.inputs.hmdb.visual.show_structure.html#pypath.inputs.hmdb.visual.show_structure">show_structure() (in module pypath.inputs.hmdb.visual)</a>
+</li>
+      <li><a href="api/pypath.inputs.sider.SiderSideeffect.html#pypath.inputs.sider.SiderSideeffect.side_effect">side_effect (pypath.inputs.sider.SiderSideeffect attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.inputs.sider.SiderSideeffetFrequency.html#pypath.inputs.sider.SiderSideeffetFrequency.side_effect">(pypath.inputs.sider.SiderSideeffetFrequency attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.inputs.sider.SiderSideeffectMeddra.html#pypath.inputs.sider.SiderSideeffectMeddra.side_effect_name">side_effect_name (pypath.inputs.sider.SiderSideeffectMeddra attribute)</a>
+</li>
+      <li><a href="api/pypath.inputs.sider.sider_drug_names.html#pypath.inputs.sider.sider_drug_names">sider_drug_names() (in module pypath.inputs.sider)</a>
+</li>
+      <li><a href="api/pypath.inputs.sider.sider_meddra_side_effects.html#pypath.inputs.sider.sider_meddra_side_effects">sider_meddra_side_effects() (in module pypath.inputs.sider)</a>
+</li>
+      <li><a href="api/pypath.inputs.sider.sider_side_effect_frequencies.html#pypath.inputs.sider.sider_side_effect_frequencies">sider_side_effect_frequencies() (in module pypath.inputs.sider)</a>
+</li>
+      <li><a href="api/pypath.inputs.sider.sider_side_effects.html#pypath.inputs.sider.sider_side_effects">sider_side_effects() (in module pypath.inputs.sider)</a>
+</li>
+      <li><a href="api/pypath.inputs.sider.SiderDrug.html#pypath.inputs.sider.SiderDrug">SiderDrug (class in pypath.inputs.sider)</a>
+</li>
+      <li><a href="api/pypath.inputs.sider.SiderSideeffect.html#pypath.inputs.sider.SiderSideeffect">SiderSideeffect (class in pypath.inputs.sider)</a>
+</li>
+      <li><a href="api/pypath.inputs.sider.SiderSideeffectMeddra.html#pypath.inputs.sider.SiderSideeffectMeddra">SiderSideeffectMeddra (class in pypath.inputs.sider)</a>
+</li>
+      <li><a href="api/pypath.inputs.sider.SiderSideeffetFrequency.html#pypath.inputs.sider.SiderSideeffetFrequency">SiderSideeffetFrequency (class in pypath.inputs.sider)</a>
+</li>
+      <li><a href="api/pypath.inputs.signalink.signalink_annotations.html#pypath.inputs.signalink.signalink_annotations">signalink_annotations() (in module pypath.inputs.signalink)</a>
+</li>
+      <li><a href="api/pypath.inputs.signalink.signalink_function_annotations.html#pypath.inputs.signalink.signalink_function_annotations">signalink_function_annotations() (in module pypath.inputs.signalink)</a>
+</li>
+      <li><a href="api/pypath.inputs.signalink.signalink_interactions.html#pypath.inputs.signalink.signalink_interactions">signalink_interactions() (in module pypath.inputs.signalink)</a>
+</li>
+      <li><a href="api/pypath.inputs.signalink.signalink_pathway_annotations.html#pypath.inputs.signalink.signalink_pathway_annotations">signalink_pathway_annotations() (in module pypath.inputs.signalink)</a>
+</li>
+      <li><a href="api/pypath.core.annot.SignalinkFunctions.html#pypath.core.annot.SignalinkFunctions">SignalinkFunctions (class in pypath.core.annot)</a>
+</li>
+      <li><a href="api/pypath.core.annot.SignalinkPathways.html#pypath.core.annot.SignalinkPathways">SignalinkPathways (class in pypath.core.annot)</a>
+</li>
+      <li><a href="api/pypath.core.complex.Signor.html#pypath.core.complex.Signor">Signor (class in pypath.core.complex)</a>
+</li>
+      <li><a href="api/pypath.inputs.signor.signor_complexes.html#pypath.inputs.signor.signor_complexes">signor_complexes() (in module pypath.inputs.signor)</a>
+</li>
+      <li><a href="api/pypath.inputs.signor.signor_enzyme_substrate.html#pypath.inputs.signor.signor_enzyme_substrate">signor_enzyme_substrate() (in module pypath.inputs.signor)</a>
+</li>
+      <li><a href="api/pypath.inputs.signor.signor_interactions.html#pypath.inputs.signor.signor_interactions">signor_interactions() (in module pypath.inputs.signor)</a>
+</li>
+      <li><a href="api/pypath.inputs.signor.signor_pathway_annotations.html#pypath.inputs.signor.signor_pathway_annotations">signor_pathway_annotations() (in module pypath.inputs.signor)</a>
+</li>
+      <li><a href="api/pypath.inputs.signor.signor_pathways.html#pypath.inputs.signor.signor_pathways">signor_pathways() (in module pypath.inputs.signor)</a>
+</li>
+      <li><a href="api/pypath.inputs.signor.signor_protein_families.html#pypath.inputs.signor.signor_protein_families">signor_protein_families() (in module pypath.inputs.signor)</a>
+</li>
+      <li><a href="api/pypath.core.annot.SignorPathways.html#pypath.core.annot.SignorPathways">SignorPathways (class in pypath.core.annot)</a>
+</li>
+      <li><a href="api/pypath.utils.uniprot.similarity.html#pypath.utils.uniprot.similarity">similarity() (in module pypath.utils.uniprot)</a>
+</li>
+      <li><a href="api/pypath.utils.uniprot.similarity_with_xrefs.html#pypath.utils.uniprot.similarity_with_xrefs">similarity_with_xrefs() (in module pypath.utils.uniprot)</a>
+</li>
+      <li><a href="api/pypath.core.evidence.Evidences.html#pypath.core.evidence.Evidences.simple_dict">simple_dict (pypath.core.evidence.Evidences property)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.small_molecule_identifiers_by_data_model">small_molecule_identifiers_by_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.small_molecule_identifiers_by_data_model">small_molecule_identifiers_by_data_model() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.small_molecule_identifiers_by_interaction_type">small_molecule_identifiers_by_interaction_type (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.small_molecule_identifiers_by_interaction_type">small_molecule_identifiers_by_interaction_type() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.small_molecule_identifiers_by_interaction_type_and_data_model">small_molecule_identifiers_by_interaction_type_and_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.small_molecule_identifiers_by_interaction_type_and_data_model">small_molecule_identifiers_by_interaction_type_and_data_model() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.small_molecule_identifiers_by_interaction_type_and_data_model_and_resource">small_molecule_identifiers_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.small_molecule_identifiers_by_interaction_type_and_data_model_and_resource">small_molecule_identifiers_by_interaction_type_and_data_model_and_resource() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.small_molecule_identifiers_by_reference">small_molecule_identifiers_by_reference (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.small_molecule_identifiers_by_reference">small_molecule_identifiers_by_reference() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.small_molecule_identifiers_by_resource">small_molecule_identifiers_by_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.small_molecule_identifiers_by_resource">small_molecule_identifiers_by_resource() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.small_molecule_labels_by_data_model">small_molecule_labels_by_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.small_molecule_labels_by_data_model">small_molecule_labels_by_data_model() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.small_molecule_labels_by_interaction_type">small_molecule_labels_by_interaction_type (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.small_molecule_labels_by_interaction_type">small_molecule_labels_by_interaction_type() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.small_molecule_labels_by_interaction_type_and_data_model">small_molecule_labels_by_interaction_type_and_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.small_molecule_labels_by_interaction_type_and_data_model">small_molecule_labels_by_interaction_type_and_data_model() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.small_molecule_labels_by_interaction_type_and_data_model_and_resource">small_molecule_labels_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.small_molecule_labels_by_interaction_type_and_data_model_and_resource">small_molecule_labels_by_interaction_type_and_data_model_and_resource() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.small_molecule_labels_by_reference">small_molecule_labels_by_reference (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.small_molecule_labels_by_reference">small_molecule_labels_by_reference() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.small_molecule_labels_by_resource">small_molecule_labels_by_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.small_molecule_labels_by_resource">small_molecule_labels_by_resource() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.small_molecules_by_data_model">small_molecules_by_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.small_molecules_by_data_model">small_molecules_by_data_model() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.small_molecules_by_interaction_type">small_molecules_by_interaction_type (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.small_molecules_by_interaction_type">small_molecules_by_interaction_type() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.small_molecules_by_interaction_type_and_data_model">small_molecules_by_interaction_type_and_data_model (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.small_molecules_by_interaction_type_and_data_model">small_molecules_by_interaction_type_and_data_model() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.small_molecules_by_interaction_type_and_data_model_and_resource">small_molecules_by_interaction_type_and_data_model_and_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.small_molecules_by_interaction_type_and_data_model_and_resource">small_molecules_by_interaction_type_and_data_model_and_resource() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.small_molecules_by_reference">small_molecules_by_reference (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.small_molecules_by_reference">small_molecules_by_reference() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.small_molecules_by_resource">small_molecules_by_resource (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.small_molecules_by_resource">small_molecules_by_resource() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.utils.unichem.Unichem.html#pypath.utils.unichem.Unichem.smiles2chembl">smiles2chembl() (pypath.utils.unichem.Unichem method)</a>
+</li>
+      <li><a href="api/pypath.internals.annot_formats.AnnotDef.html#pypath.internals.annot_formats.AnnotDef.source">source (pypath.internals.annot_formats.AnnotDef attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.utils.orthology.OrthologyTableKey.html#pypath.utils.orthology.OrthologyTableKey.source">(pypath.utils.orthology.OrthologyTableKey attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.source">source() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.InteractionDataFrameRecord.html#pypath.core.interaction.InteractionDataFrameRecord.sources">sources (pypath.core.interaction.InteractionDataFrameRecord attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.inputs.lrdb.LrdbAnnotation.html#pypath.inputs.lrdb.LrdbAnnotation.sources">(pypath.inputs.lrdb.LrdbAnnotation attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.sources_reverse">sources_reverse() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.sources_straight">sources_straight() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.omnipath.export.Export.html#pypath.omnipath.export.Export.sources_table">sources_table() (pypath.omnipath.export.Export class method)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.sources_undirected">sources_undirected() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.complex.Spike.html#pypath.core.complex.Spike">Spike (class in pypath.core.complex)</a>
+</li>
+      <li><a href="api/pypath.inputs.spike.spike_complexes.html#pypath.inputs.spike.spike_complexes">spike_complexes() (in module pypath.inputs.spike)</a>
+</li>
+      <li><a href="api/pypath.inputs.spike.spike_interactions.html#pypath.inputs.spike.spike_interactions">spike_interactions() (in module pypath.inputs.spike)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.src">src() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.src_by_resource">src_by_resource() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.share.progress.Progress.html#pypath.share.progress.Progress.step">step() (pypath.share.progress.Progress method)</a>
+</li>
+      <li><a href="api/pypath.inputs.stitch.stitch_actions_interactions.html#pypath.inputs.stitch.stitch_actions_interactions">stitch_actions_interactions() (in module pypath.inputs.stitch)</a>
+</li>
+      <li><a href="api/pypath.inputs.stitch.stitch_links_interactions.html#pypath.inputs.stitch.stitch_links_interactions">stitch_links_interactions() (in module pypath.inputs.stitch)</a>
+</li>
+      <li><a href="api/pypath.omnipath.server.run.stop_server.html#pypath.omnipath.server.run.stop_server">stop_server() (in module pypath.omnipath.server.run)</a>
+</li>
+      <li><a href="api/pypath.inputs.string.string_effects.html#pypath.inputs.string.string_effects">string_effects() (in module pypath.inputs.string)</a>
+</li>
+      <li><a href="api/pypath.inputs.string.string_links_interactions.html#pypath.inputs.string.string_links_interactions">string_links_interactions() (in module pypath.inputs.string)</a>
+</li>
+      <li><a href="api/pypath.inputs.string.string_physical_interactions.html#pypath.inputs.string.string_physical_interactions">string_physical_interactions() (in module pypath.inputs.string)</a>
+</li>
+      <li><a href="api/pypath.inputs.string.string_species.html#pypath.inputs.string.string_species">string_species() (in module pypath.inputs.string)</a>
+</li>
+      <li><a href="api/pypath.inputs.hmdb.visual.structure_svg.html#pypath.inputs.hmdb.visual.structure_svg">structure_svg() (in module pypath.inputs.hmdb.visual)</a>
+</li>
+      <li><a href="api/pypath.utils.uniprot.subcellular_location.html#pypath.utils.uniprot.subcellular_location">subcellular_location() (in module pypath.utils.uniprot)</a>
+</li>
+      <li><a href="api/pypath.utils.uniprot.subcellular_location_with_xrefs.html#pypath.utils.uniprot.subcellular_location_with_xrefs">subcellular_location_with_xrefs() (in module pypath.utils.uniprot)</a>
+</li>
+      <li><a href="api/pypath.inputs.icellnet.IcellnetRecord.html#pypath.inputs.icellnet.IcellnetRecord.subfamily">subfamily (pypath.inputs.icellnet.IcellnetRecord attribute)</a>
+</li>
+      <li><a href="api/pypath.utils.go.GeneOntology.html#pypath.utils.go.GeneOntology.subgraph_nodes">subgraph_nodes() (pypath.utils.go.GeneOntology method)</a>
+</li>
+      <li><a href="api/pypath.core.annot.Adhesome.html#pypath.core.annot.Adhesome.subset_intersection">subset_intersection() (pypath.core.annot.Adhesome method)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.annot.Almen2009.html#pypath.core.annot.Almen2009.subset_intersection">(pypath.core.annot.Almen2009 method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.AnnotationBase.html#pypath.core.annot.AnnotationBase.subset_intersection">(pypath.core.annot.AnnotationBase method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Baccin2019.html#pypath.core.annot.Baccin2019.subset_intersection">(pypath.core.annot.Baccin2019 method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Biogps.html#pypath.core.annot.Biogps.subset_intersection">(pypath.core.annot.Biogps method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cancerdrugsdb.html#pypath.core.annot.Cancerdrugsdb.subset_intersection">(pypath.core.annot.Cancerdrugsdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CancerGeneCensus.html#pypath.core.annot.CancerGeneCensus.subset_intersection">(pypath.core.annot.CancerGeneCensus method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cancersea.html#pypath.core.annot.Cancersea.subset_intersection">(pypath.core.annot.Cancersea method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cellcall.html#pypath.core.annot.Cellcall.subset_intersection">(pypath.core.annot.Cellcall method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cellcellinteractions.html#pypath.core.annot.Cellcellinteractions.subset_intersection">(pypath.core.annot.Cellcellinteractions method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cellchatdb.html#pypath.core.annot.Cellchatdb.subset_intersection">(pypath.core.annot.Cellchatdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CellchatdbComplex.html#pypath.core.annot.CellchatdbComplex.subset_intersection">(pypath.core.annot.CellchatdbComplex method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cellinker.html#pypath.core.annot.Cellinker.subset_intersection">(pypath.core.annot.Cellinker method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CellinkerComplex.html#pypath.core.annot.CellinkerComplex.subset_intersection">(pypath.core.annot.CellinkerComplex method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CellPhoneDB.html#pypath.core.annot.CellPhoneDB.subset_intersection">(pypath.core.annot.CellPhoneDB method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CellPhoneDBComplex.html#pypath.core.annot.CellPhoneDBComplex.subset_intersection">(pypath.core.annot.CellPhoneDBComplex method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CellSurfaceProteinAtlas.html#pypath.core.annot.CellSurfaceProteinAtlas.subset_intersection">(pypath.core.annot.CellSurfaceProteinAtlas method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CellSurfaceProteinAtlasCellType.html#pypath.core.annot.CellSurfaceProteinAtlasCellType.subset_intersection">(pypath.core.annot.CellSurfaceProteinAtlasCellType method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Celltalkdb.html#pypath.core.annot.Celltalkdb.subset_intersection">(pypath.core.annot.Celltalkdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Celltypist.html#pypath.core.annot.Celltypist.subset_intersection">(pypath.core.annot.Celltypist method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Comppi.html#pypath.core.annot.Comppi.subset_intersection">(pypath.core.annot.Comppi method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Connectomedb.html#pypath.core.annot.Connectomedb.subset_intersection">(pypath.core.annot.Connectomedb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Corum.html#pypath.core.annot.Corum.subset_intersection">(pypath.core.annot.Corum method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CorumFuncat.html#pypath.core.annot.CorumFuncat.subset_intersection">(pypath.core.annot.CorumFuncat method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CorumGO.html#pypath.core.annot.CorumGO.subset_intersection">(pypath.core.annot.CorumGO method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cpad.html#pypath.core.annot.Cpad.subset_intersection">(pypath.core.annot.Cpad method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cytosig.html#pypath.core.annot.Cytosig.subset_intersection">(pypath.core.annot.Cytosig method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Dgidb.html#pypath.core.annot.Dgidb.subset_intersection">(pypath.core.annot.Dgidb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Disgenet.html#pypath.core.annot.Disgenet.subset_intersection">(pypath.core.annot.Disgenet method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Embrace.html#pypath.core.annot.Embrace.subset_intersection">(pypath.core.annot.Embrace method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Exocarta.html#pypath.core.annot.Exocarta.subset_intersection">(pypath.core.annot.Exocarta method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.GOIntercell.html#pypath.core.annot.GOIntercell.subset_intersection">(pypath.core.annot.GOIntercell method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Gpcrdb.html#pypath.core.annot.Gpcrdb.subset_intersection">(pypath.core.annot.Gpcrdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.GuideToPharmacology.html#pypath.core.annot.GuideToPharmacology.subset_intersection">(pypath.core.annot.GuideToPharmacology method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Hgnc.html#pypath.core.annot.Hgnc.subset_intersection">(pypath.core.annot.Hgnc method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.HpmrComplex.html#pypath.core.annot.HpmrComplex.subset_intersection">(pypath.core.annot.HpmrComplex method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.HPO.html#pypath.core.annot.HPO.subset_intersection">(pypath.core.annot.HPO method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Humancellmap.html#pypath.core.annot.Humancellmap.subset_intersection">(pypath.core.annot.Humancellmap method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.HumanPlasmaMembraneReceptome.html#pypath.core.annot.HumanPlasmaMembraneReceptome.subset_intersection">(pypath.core.annot.HumanPlasmaMembraneReceptome method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.HumanProteinAtlas.html#pypath.core.annot.HumanProteinAtlas.subset_intersection">(pypath.core.annot.HumanProteinAtlas method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.HumanProteinAtlasSecretome.html#pypath.core.annot.HumanProteinAtlasSecretome.subset_intersection">(pypath.core.annot.HumanProteinAtlasSecretome method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.HumanProteinAtlasSubcellular.html#pypath.core.annot.HumanProteinAtlasSubcellular.subset_intersection">(pypath.core.annot.HumanProteinAtlasSubcellular method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Icellnet.html#pypath.core.annot.Icellnet.subset_intersection">(pypath.core.annot.Icellnet method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.IcellnetComplex.html#pypath.core.annot.IcellnetComplex.subset_intersection">(pypath.core.annot.IcellnetComplex method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Integrins.html#pypath.core.annot.Integrins.subset_intersection">(pypath.core.annot.Integrins method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.InterPro.html#pypath.core.annot.InterPro.subset_intersection">(pypath.core.annot.InterPro method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Intogen.html#pypath.core.annot.Intogen.subset_intersection">(pypath.core.annot.Intogen method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Italk.html#pypath.core.annot.Italk.subset_intersection">(pypath.core.annot.Italk method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.KeggPathways.html#pypath.core.annot.KeggPathways.subset_intersection">(pypath.core.annot.KeggPathways method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.KeggPathwaysPC.html#pypath.core.annot.KeggPathwaysPC.subset_intersection">(pypath.core.annot.KeggPathwaysPC method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Kinasedotcom.html#pypath.core.annot.Kinasedotcom.subset_intersection">(pypath.core.annot.Kinasedotcom method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Kirouac2010.html#pypath.core.annot.Kirouac2010.subset_intersection">(pypath.core.annot.Kirouac2010 method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Lambert2018.html#pypath.core.annot.Lambert2018.subset_intersection">(pypath.core.annot.Lambert2018 method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.LigandReceptor.html#pypath.core.annot.LigandReceptor.subset_intersection">(pypath.core.annot.LigandReceptor method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Locate.html#pypath.core.annot.Locate.subset_intersection">(pypath.core.annot.Locate method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Lrdb.html#pypath.core.annot.Lrdb.subset_intersection">(pypath.core.annot.Lrdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Matrisome.html#pypath.core.annot.Matrisome.subset_intersection">(pypath.core.annot.Matrisome method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Matrixdb.html#pypath.core.annot.Matrixdb.subset_intersection">(pypath.core.annot.Matrixdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Mcam.html#pypath.core.annot.Mcam.subset_intersection">(pypath.core.annot.Mcam method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Membranome.html#pypath.core.annot.Membranome.subset_intersection">(pypath.core.annot.Membranome method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Msigdb.html#pypath.core.annot.Msigdb.subset_intersection">(pypath.core.annot.Msigdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.NetpathPathways.html#pypath.core.annot.NetpathPathways.subset_intersection">(pypath.core.annot.NetpathPathways method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Opm.html#pypath.core.annot.Opm.subset_intersection">(pypath.core.annot.Opm method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Panglaodb.html#pypath.core.annot.Panglaodb.subset_intersection">(pypath.core.annot.Panglaodb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Phobius.html#pypath.core.annot.Phobius.subset_intersection">(pypath.core.annot.Phobius method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Phosphatome.html#pypath.core.annot.Phosphatome.subset_intersection">(pypath.core.annot.Phosphatome method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Progeny.html#pypath.core.annot.Progeny.subset_intersection">(pypath.core.annot.Progeny method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Ramilowski2015.html#pypath.core.annot.Ramilowski2015.subset_intersection">(pypath.core.annot.Ramilowski2015 method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Ramilowski2015Location.html#pypath.core.annot.Ramilowski2015Location.subset_intersection">(pypath.core.annot.Ramilowski2015Location method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Scconnect.html#pypath.core.annot.Scconnect.subset_intersection">(pypath.core.annot.Scconnect method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.ScconnectComplex.html#pypath.core.annot.ScconnectComplex.subset_intersection">(pypath.core.annot.ScconnectComplex method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.SignalinkFunctions.html#pypath.core.annot.SignalinkFunctions.subset_intersection">(pypath.core.annot.SignalinkFunctions method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.SignalinkPathways.html#pypath.core.annot.SignalinkPathways.subset_intersection">(pypath.core.annot.SignalinkPathways method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.SignorPathways.html#pypath.core.annot.SignorPathways.subset_intersection">(pypath.core.annot.SignorPathways method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Surfaceome.html#pypath.core.annot.Surfaceome.subset_intersection">(pypath.core.annot.Surfaceome method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Talklr.html#pypath.core.annot.Talklr.subset_intersection">(pypath.core.annot.Talklr method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Tcdb.html#pypath.core.annot.Tcdb.subset_intersection">(pypath.core.annot.Tcdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Tfcensus.html#pypath.core.annot.Tfcensus.subset_intersection">(pypath.core.annot.Tfcensus method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Topdb.html#pypath.core.annot.Topdb.subset_intersection">(pypath.core.annot.Topdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.UniprotFamilies.html#pypath.core.annot.UniprotFamilies.subset_intersection">(pypath.core.annot.UniprotFamilies method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.UniprotKeywords.html#pypath.core.annot.UniprotKeywords.subset_intersection">(pypath.core.annot.UniprotKeywords method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.UniprotLocations.html#pypath.core.annot.UniprotLocations.subset_intersection">(pypath.core.annot.UniprotLocations method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.UniprotTissues.html#pypath.core.annot.UniprotTissues.subset_intersection">(pypath.core.annot.UniprotTissues method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.UniprotTopologies.html#pypath.core.annot.UniprotTopologies.subset_intersection">(pypath.core.annot.UniprotTopologies method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Vesiclepedia.html#pypath.core.annot.Vesiclepedia.subset_intersection">(pypath.core.annot.Vesiclepedia method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Wang.html#pypath.core.annot.Wang.subset_intersection">(pypath.core.annot.Wang method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Zhong2015.html#pypath.core.annot.Zhong2015.subset_intersection">(pypath.core.annot.Zhong2015 method)</a>
 </li>
       </ul></li>
-      <li>
-    pypath.inputs.embopress
+      <li><a href="api/pypath.inputs.iptmnet.IptmnetInteraction.html#pypath.inputs.iptmnet.IptmnetInteraction.substrate">substrate (pypath.inputs.iptmnet.IptmnetInteraction attribute)</a>
+</li>
+      <li><a href="api/pypath.inputs.iptmnet.IptmnetInteraction.html#pypath.inputs.iptmnet.IptmnetInteraction.substrate_isoform">substrate_isoform (pypath.inputs.iptmnet.IptmnetInteraction attribute)</a>
+</li>
+      <li><a href="api/pypath.utils.uniprot.subunit.html#pypath.utils.uniprot.subunit">subunit() (in module pypath.utils.uniprot)</a>
+</li>
+      <li><a href="api/pypath.utils.uniprot.subunit_with_xrefs.html#pypath.utils.uniprot.subunit_with_xrefs">subunit_with_xrefs() (in module pypath.utils.uniprot)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.summaries_tab">summaries_tab() (pypath.core.network.Network method)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.suppressed_by">suppressed_by (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.suppresses">suppresses (pypath.core.network.Network attribute)</a>
+</li>
+      <li><a href="api/pypath.core.annot.Surfaceome.html#pypath.core.annot.Surfaceome">Surfaceome (class in pypath.core.annot)</a>
+</li>
+      <li><a href="api/pypath.inputs.surfaceome.surfaceome_annotations.html#pypath.inputs.surfaceome.surfaceome_annotations">surfaceome_annotations() (in module pypath.inputs.surfaceome)</a>
+</li>
+      <li><a href="api/pypath.inputs.uniprot.swissprot_deleted.html#pypath.inputs.uniprot.swissprot_deleted">swissprot_deleted() (in module pypath.inputs.uniprot)</a>
+</li>
+      <li><a href="api/pypath.utils.seq.swissprot_seq.html#pypath.utils.seq.swissprot_seq">swissprot_seq() (in module pypath.utils.seq)</a>
+</li>
+      <li><a href="api/pypath.utils.mapping.Mapper.html#pypath.utils.mapping.Mapper.swissprots">swissprots() (pypath.utils.mapping.Mapper method)</a>
+</li>
+      <li><a href="api/pypath.inputs.adrecs.AdrecsDrug.html#pypath.inputs.adrecs.AdrecsDrug.synonyms">synonyms (pypath.inputs.adrecs.AdrecsDrug attribute)</a>
 
       <ul>
-        <li><a href="api/pypath.inputs.embopress.html#module-pypath.inputs.embopress">module</a>
+        <li><a href="api/pypath.inputs.adrecs.AdrecsTerm.html#pypath.inputs.adrecs.AdrecsTerm.synonyms">(pypath.inputs.adrecs.AdrecsTerm attribute)</a>
 </li>
       </ul></li>
-      <li>
-    pypath.inputs.encode
+  </ul></td>
+</tr></table>
+
+<h2 id="T">T</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="api/pypath.inputs.hmdb.common.table.html#pypath.inputs.hmdb.common.table">table() (in module pypath.inputs.hmdb.common)</a>
 
       <ul>
-        <li><a href="api/pypath.inputs.encode.html#module-pypath.inputs.encode">module</a>
+        <li><a href="api/pypath.inputs.hmdb.metabolites.table.html#pypath.inputs.hmdb.metabolites.table">(in module pypath.inputs.hmdb.metabolites)</a>
+</li>
+        <li><a href="api/pypath.inputs.hmdb.proteins.table.html#pypath.inputs.hmdb.proteins.table">(in module pypath.inputs.hmdb.proteins)</a>
 </li>
       </ul></li>
-      <li>
-    pypath.inputs.ensembl
+      <li><a href="api/pypath.omnipath.app.DatabaseManager.html#pypath.omnipath.app.DatabaseManager.table_path">table_path() (pypath.omnipath.app.DatabaseManager method)</a>
+</li>
+      <li><a href="api/pypath.utils.mapping.MapReader.html#pypath.utils.mapping.MapReader.tables_loaded">tables_loaded() (pypath.utils.mapping.MapReader method)</a>
+</li>
+      <li><a href="api/pypath.omnipath.server.run.TableServer.html#pypath.omnipath.server.run.TableServer">TableServer (class in pypath.omnipath.server.run)</a>
+</li>
+      <li><a href="api/pypath.inputs.trip.take_a_trip.html#pypath.inputs.trip.take_a_trip">take_a_trip() (in module pypath.inputs.trip)</a>
+</li>
+      <li><a href="api/pypath.core.annot.Talklr.html#pypath.core.annot.Talklr">Talklr (class in pypath.core.annot)</a>
+</li>
+      <li><a href="api/pypath.inputs.talklr.talklr_annotations.html#pypath.inputs.talklr.talklr_annotations">talklr_annotations() (in module pypath.inputs.talklr)</a>
+</li>
+      <li><a href="api/pypath.inputs.talklr.talklr_interactions.html#pypath.inputs.talklr.talklr_interactions">talklr_interactions() (in module pypath.inputs.talklr)</a>
+</li>
+      <li><a href="api/pypath.inputs.talklr.talklr_raw.html#pypath.inputs.talklr.talklr_raw">talklr_raw() (in module pypath.inputs.talklr)</a>
+</li>
+      <li><a href="api/pypath.visual.igraph_drawing.edge.TaperedEdgeDrawer.html#pypath.visual.igraph_drawing.edge.TaperedEdgeDrawer">TaperedEdgeDrawer (class in pypath.visual.igraph_drawing.edge)</a>
+</li>
+      <li><a href="api/pypath.inputs.dorothea.DorotheaInteraction.html#pypath.inputs.dorothea.DorotheaInteraction.target">target (pypath.inputs.dorothea.DorotheaInteraction attribute)</a>
 
       <ul>
-        <li><a href="api/pypath.inputs.ensembl.html#module-pypath.inputs.ensembl">module</a>
+        <li><a href="api/pypath.utils.orthology.OrthologyTableKey.html#pypath.utils.orthology.OrthologyTableKey.target">(pypath.utils.orthology.OrthologyTableKey attribute)</a>
 </li>
       </ul></li>
-      <li>
-    pypath.inputs.eutils
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.target">target() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.utils.mapping.MappingTableKey.html#pypath.utils.mapping.MappingTableKey.target_id_type">target_id_type (pypath.utils.mapping.MappingTableKey attribute)</a>
+</li>
+      <li><a href="api/pypath.utils.taxonomy.taxid_from_common_name.html#pypath.utils.taxonomy.taxid_from_common_name">taxid_from_common_name() (in module pypath.utils.taxonomy)</a>
+</li>
+      <li><a href="api/pypath.utils.taxonomy.taxid_from_dbptm_taxon_name.html#pypath.utils.taxonomy.taxid_from_dbptm_taxon_name">taxid_from_dbptm_taxon_name() (in module pypath.utils.taxonomy)</a>
+</li>
+      <li><a href="api/pypath.utils.taxonomy.taxid_from_ensembl_name.html#pypath.utils.taxonomy.taxid_from_ensembl_name">taxid_from_ensembl_name() (in module pypath.utils.taxonomy)</a>
+</li>
+      <li><a href="api/pypath.utils.taxonomy.taxid_from_latin_name.html#pypath.utils.taxonomy.taxid_from_latin_name">taxid_from_latin_name() (in module pypath.utils.taxonomy)</a>
+</li>
+      <li><a href="api/pypath.utils.taxonomy.taxid_from_nonstandard.html#pypath.utils.taxonomy.taxid_from_nonstandard">taxid_from_nonstandard() (in module pypath.utils.taxonomy)</a>
+</li>
+      <li><a href="api/pypath.inputs.uniprot.Taxon.html#pypath.inputs.uniprot.Taxon">Taxon (class in pypath.inputs.uniprot)</a>
+</li>
+      <li><a href="api/pypath.core.entity.EntityKey.html#pypath.core.entity.EntityKey.taxon">taxon (pypath.core.entity.EntityKey attribute)</a>
+</li>
+      <li><a href="api/pypath.core.annot.Tcdb.html#pypath.core.annot.Tcdb">Tcdb (class in pypath.core.annot)</a>
+</li>
+      <li><a href="api/pypath.inputs.tcdb.tcdb_annotations.html#pypath.inputs.tcdb.tcdb_annotations">tcdb_annotations() (in module pypath.inputs.tcdb)</a>
+</li>
+      <li><a href="api/pypath.inputs.tcdb.tcdb_classes.html#pypath.inputs.tcdb.tcdb_classes">tcdb_classes() (in module pypath.inputs.tcdb)</a>
+</li>
+      <li><a href="api/pypath.inputs.tcdb.tcdb_families.html#pypath.inputs.tcdb.tcdb_families">tcdb_families() (in module pypath.inputs.tcdb)</a>
+</li>
+      <li><a href="api/pypath.inputs.adrecs.AdrecsDrug.html#pypath.inputs.adrecs.AdrecsDrug.tdd">tdd (pypath.inputs.adrecs.AdrecsDrug attribute)</a>
+</li>
+      <li><a href="api/pypath.share.progress.Progress.html#pypath.share.progress.Progress.terminate">terminate() (pypath.share.progress.Progress method)</a>
+</li>
+      <li><a href="api/pypath.utils.go.GeneOntology.html#pypath.utils.go.GeneOntology.terms_to_names">terms_to_names() (pypath.utils.go.GeneOntology method)</a>
+</li>
+      <li><a href="api/pypath.utils.go.GeneOntology.html#pypath.utils.go.GeneOntology.terms_to_names_aspects">terms_to_names_aspects() (pypath.utils.go.GeneOntology method)</a>
+</li>
+      <li><a href="api/pypath.visual.igraph_drawing.TextDrawer.html#pypath.visual.igraph_drawing.TextDrawer">TextDrawer (in module pypath.visual.igraph_drawing)</a>
+</li>
+      <li><a href="api/pypath.inputs.diseases.textmining_filtered.html#pypath.inputs.diseases.textmining_filtered">textmining_filtered() (in module pypath.inputs.diseases)</a>
+</li>
+      <li><a href="api/pypath.inputs.diseases.textmining_full.html#pypath.inputs.diseases.textmining_full">textmining_full() (in module pypath.inputs.diseases)</a>
+</li>
+      <li><a href="api/pypath.inputs.dorothea.DorotheaInteraction.html#pypath.inputs.dorothea.DorotheaInteraction.tf">tf (pypath.inputs.dorothea.DorotheaInteraction attribute)</a>
+</li>
+      <li><a href="api/pypath.omnipath.param.tf_target_resources.html#pypath.omnipath.param.tf_target_resources">tf_target_resources() (in module pypath.omnipath.param)</a>
+</li>
+      <li><a href="api/pypath.core.annot.Tfcensus.html#pypath.core.annot.Tfcensus">Tfcensus (class in pypath.core.annot)</a>
+</li>
+      <li><a href="api/pypath.inputs.tfcensus.tfcensus_annotations.html#pypath.inputs.tfcensus.tfcensus_annotations">tfcensus_annotations() (in module pypath.inputs.tfcensus)</a>
+</li>
+      <li><a href="api/pypath.inputs.dorothea.tfregulons_interactions.html#pypath.inputs.dorothea.tfregulons_interactions">tfregulons_interactions() (in module pypath.inputs.dorothea)</a>
+</li>
+      <li><a href="api/pypath.inputs.dorothea.tfregulons_interactions_old.html#pypath.inputs.dorothea.tfregulons_interactions_old">tfregulons_interactions_old() (in module pypath.inputs.dorothea)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.tgt">tgt() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.tgt_by_resource">tgt_by_resource() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.inputs.threedcomplex.threedcomplex_chains.html#pypath.inputs.threedcomplex.threedcomplex_chains">threedcomplex_chains() (in module pypath.inputs.threedcomplex)</a>
+</li>
+      <li><a href="api/pypath.inputs.threedcomplex.threedcomplex_complexes.html#pypath.inputs.threedcomplex.threedcomplex_complexes">threedcomplex_complexes() (in module pypath.inputs.threedcomplex)</a>
+</li>
+      <li><a href="api/pypath.inputs.threedcomplex.threedcomplex_contacts.html#pypath.inputs.threedcomplex.threedcomplex_contacts">threedcomplex_contacts() (in module pypath.inputs.threedcomplex)</a>
+</li>
+      <li><a href="api/pypath.inputs.threedcomplex.threedcomplex_ddi.html#pypath.inputs.threedcomplex.threedcomplex_ddi">threedcomplex_ddi() (in module pypath.inputs.threedcomplex)</a>
+</li>
+      <li><a href="api/pypath.inputs.threedcomplex.threedcomplex_nresidues.html#pypath.inputs.threedcomplex.threedcomplex_nresidues">threedcomplex_nresidues() (in module pypath.inputs.threedcomplex)</a>
+</li>
+      <li><a href="api/pypath.inputs.gutmgene.GutmgeneAnnotation.html#pypath.inputs.gutmgene.GutmgeneAnnotation.throughput">throughput (pypath.inputs.gutmgene.GutmgeneAnnotation attribute)</a>
 
       <ul>
-        <li><a href="api/pypath.inputs.eutils.html#module-pypath.inputs.eutils">module</a>
+        <li><a href="api/pypath.inputs.gutmgene.GutmgeneRaw.html#pypath.inputs.gutmgene.GutmgeneRaw.throughput">(pypath.inputs.gutmgene.GutmgeneRaw attribute)</a>
 </li>
       </ul></li>
-      <li>
-    pypath.inputs.exocarta
+      <li><a href="api/pypath.utils.uniprot.tissue_specificity.html#pypath.utils.uniprot.tissue_specificity">tissue_specificity() (in module pypath.utils.uniprot)</a>
+</li>
+      <li><a href="api/pypath.utils.uniprot.tissue_specificity_with_xrefs.html#pypath.utils.uniprot.tissue_specificity_with_xrefs">tissue_specificity_with_xrefs() (in module pypath.utils.uniprot)</a>
+</li>
+      <li><a href="api/pypath.utils.proteomicsdb.ProteomicsDB.html#pypath.utils.proteomicsdb.ProteomicsDB.tissues_x_proteins">tissues_x_proteins() (pypath.utils.proteomicsdb.ProteomicsDB method)</a>
+</li>
+      <li><a href="api/pypath.core.annot.Adhesome.html#pypath.core.annot.Adhesome.to_array">to_array() (pypath.core.annot.Adhesome method)</a>
 
       <ul>
-        <li><a href="api/pypath.inputs.exocarta.html#module-pypath.inputs.exocarta">module</a>
+        <li><a href="api/pypath.core.annot.Almen2009.html#pypath.core.annot.Almen2009.to_array">(pypath.core.annot.Almen2009 method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.AnnotationBase.html#pypath.core.annot.AnnotationBase.to_array">(pypath.core.annot.AnnotationBase method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Baccin2019.html#pypath.core.annot.Baccin2019.to_array">(pypath.core.annot.Baccin2019 method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Biogps.html#pypath.core.annot.Biogps.to_array">(pypath.core.annot.Biogps method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cancerdrugsdb.html#pypath.core.annot.Cancerdrugsdb.to_array">(pypath.core.annot.Cancerdrugsdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CancerGeneCensus.html#pypath.core.annot.CancerGeneCensus.to_array">(pypath.core.annot.CancerGeneCensus method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cancersea.html#pypath.core.annot.Cancersea.to_array">(pypath.core.annot.Cancersea method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cellcall.html#pypath.core.annot.Cellcall.to_array">(pypath.core.annot.Cellcall method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cellcellinteractions.html#pypath.core.annot.Cellcellinteractions.to_array">(pypath.core.annot.Cellcellinteractions method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cellchatdb.html#pypath.core.annot.Cellchatdb.to_array">(pypath.core.annot.Cellchatdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CellchatdbComplex.html#pypath.core.annot.CellchatdbComplex.to_array">(pypath.core.annot.CellchatdbComplex method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cellinker.html#pypath.core.annot.Cellinker.to_array">(pypath.core.annot.Cellinker method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CellinkerComplex.html#pypath.core.annot.CellinkerComplex.to_array">(pypath.core.annot.CellinkerComplex method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CellPhoneDB.html#pypath.core.annot.CellPhoneDB.to_array">(pypath.core.annot.CellPhoneDB method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CellPhoneDBComplex.html#pypath.core.annot.CellPhoneDBComplex.to_array">(pypath.core.annot.CellPhoneDBComplex method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CellSurfaceProteinAtlas.html#pypath.core.annot.CellSurfaceProteinAtlas.to_array">(pypath.core.annot.CellSurfaceProteinAtlas method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CellSurfaceProteinAtlasCellType.html#pypath.core.annot.CellSurfaceProteinAtlasCellType.to_array">(pypath.core.annot.CellSurfaceProteinAtlasCellType method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Celltalkdb.html#pypath.core.annot.Celltalkdb.to_array">(pypath.core.annot.Celltalkdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Celltypist.html#pypath.core.annot.Celltypist.to_array">(pypath.core.annot.Celltypist method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Comppi.html#pypath.core.annot.Comppi.to_array">(pypath.core.annot.Comppi method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Connectomedb.html#pypath.core.annot.Connectomedb.to_array">(pypath.core.annot.Connectomedb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Corum.html#pypath.core.annot.Corum.to_array">(pypath.core.annot.Corum method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CorumFuncat.html#pypath.core.annot.CorumFuncat.to_array">(pypath.core.annot.CorumFuncat method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.CorumGO.html#pypath.core.annot.CorumGO.to_array">(pypath.core.annot.CorumGO method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cpad.html#pypath.core.annot.Cpad.to_array">(pypath.core.annot.Cpad method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Cytosig.html#pypath.core.annot.Cytosig.to_array">(pypath.core.annot.Cytosig method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Dgidb.html#pypath.core.annot.Dgidb.to_array">(pypath.core.annot.Dgidb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Disgenet.html#pypath.core.annot.Disgenet.to_array">(pypath.core.annot.Disgenet method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Embrace.html#pypath.core.annot.Embrace.to_array">(pypath.core.annot.Embrace method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Exocarta.html#pypath.core.annot.Exocarta.to_array">(pypath.core.annot.Exocarta method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.GOIntercell.html#pypath.core.annot.GOIntercell.to_array">(pypath.core.annot.GOIntercell method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Gpcrdb.html#pypath.core.annot.Gpcrdb.to_array">(pypath.core.annot.Gpcrdb method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.GuideToPharmacology.html#pypath.core.annot.GuideToPharmacology.to_array">(pypath.core.annot.GuideToPharmacology method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Hgnc.html#pypath.core.annot.Hgnc.to_array">(pypath.core.annot.Hgnc method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.HpmrComplex.html#pypath.core.annot.HpmrComplex.to_array">(pypath.core.annot.HpmrComplex method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.HPO.html#pypath.core.annot.HPO.to_array">(pypath.core.annot.HPO method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Humancellmap.html#pypath.core.annot.Humancellmap.to_array">(pypath.core.annot.Humancellmap method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.HumanPlasmaMembraneReceptome.html#pypath.core.annot.HumanPlasmaMembraneReceptome.to_array">(pypath.core.annot.HumanPlasmaMembraneReceptome method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.HumanProteinAtlas.html#pypath.core.annot.HumanProteinAtlas.to_array">(pypath.core.annot.HumanProteinAtlas method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.HumanProteinAtlasSecretome.html#pypath.core.annot.HumanProteinAtlasSecretome.to_array">(pypath.core.annot.HumanProteinAtlasSecretome method)</a>
 </li>
-      </ul></li>
-      <li>
-    pypath.inputs.expasy
-
-      <ul>
-        <li><a href="api/pypath.inputs.expasy.html#module-pypath.inputs.expasy">module</a>
+        <li><a href="api/pypath.core.annot.HumanProteinAtlasSubcellular.html#pypath.core.annot.HumanProteinAtlasSubcellular.to_array">(pypath.core.annot.HumanProteinAtlasSubcellular method)</a>
 </li>
-      </ul></li>
-      <li>
-    pypath.inputs.genecards
-
-      <ul>
-        <li><a href="api/pypath.inputs.genecards.html#module-pypath.inputs.genecards">module</a>
+        <li><a href="api/pypath.core.annot.Icellnet.html#pypath.core.annot.Icellnet.to_array">(pypath.core.annot.Icellnet method)</a>
 </li>
-      </ul></li>
-      <li>
-    pypath.inputs.go
-
-      <ul>
-        <li><a href="api/pypath.inputs.go.html#module-pypath.inputs.go">module</a>
+        <li><a href="api/pypath.core.annot.IcellnetComplex.html#pypath.core.annot.IcellnetComplex.to_array">(pypath.core.annot.IcellnetComplex method)</a>
 </li>
-      </ul></li>
-      <li>
-    pypath.inputs.gpcrdb
-
-      <ul>
-        <li><a href="api/pypath.inputs.gpcrdb.html#module-pypath.inputs.gpcrdb">module</a>
+        <li><a href="api/pypath.core.annot.Integrins.html#pypath.core.annot.Integrins.to_array">(pypath.core.annot.Integrins method)</a>
 </li>
-      </ul></li>
-      <li>
-    pypath.inputs.graphviz
-
-      <ul>
-        <li><a href="api/pypath.inputs.graphviz.html#module-pypath.inputs.graphviz">module</a>
+        <li><a href="api/pypath.core.annot.InterPro.html#pypath.core.annot.InterPro.to_array">(pypath.core.annot.InterPro method)</a>
 </li>
-      </ul></li>
-      <li>
-    pypath.inputs.hmdb
-
-      <ul>
-        <li><a href="api/pypath.inputs.hmdb.html#module-pypath.inputs.hmdb">module</a>
+        <li><a href="api/pypath.core.annot.Intogen.html#pypath.core.annot.Intogen.to_array">(pypath.core.annot.Intogen method)</a>
 </li>
-      </ul></li>
-      <li>
-    pypath.inputs.hmdb.common
-
-      <ul>
-        <li><a href="api/pypath.inputs.hmdb.common.html#module-pypath.inputs.hmdb.common">module</a>
+        <li><a href="api/pypath.core.annot.Italk.html#pypath.core.annot.Italk.to_array">(pypath.core.annot.Italk method)</a>
 </li>
-      </ul></li>
-      <li>
-    pypath.inputs.hmdb.metabolites
-
-      <ul>
-        <li><a href="api/pypath.inputs.hmdb.metabolites.html#module-pypath.inputs.hmdb.metabolites">module</a>
+        <li><a href="api/pypath.core.annot.KeggPathways.html#pypath.core.annot.KeggPathways.to_array">(pypath.core.annot.KeggPathways method)</a>
 </li>
-      </ul></li>
-      <li>
-    pypath.inputs.hmdb.proteins
-
-      <ul>
-        <li><a href="api/pypath.inputs.hmdb.proteins.html#module-pypath.inputs.hmdb.proteins">module</a>
+        <li><a href="api/pypath.core.annot.KeggPathwaysPC.html#pypath.core.annot.KeggPathwaysPC.to_array">(pypath.core.annot.KeggPathwaysPC method)</a>
 </li>
-      </ul></li>
-      <li>
-    pypath.inputs.hmdb.schema
-
-      <ul>
-        <li><a href="api/pypath.inputs.hmdb.schema.html#module-pypath.inputs.hmdb.schema">module</a>
+        <li><a href="api/pypath.core.annot.Kinasedotcom.html#pypath.core.annot.Kinasedotcom.to_array">(pypath.core.annot.Kinasedotcom method)</a>
 </li>
-      </ul></li>
-      <li>
-    pypath.inputs.hmdb.schema.common
-
-      <ul>
-        <li><a href="api/pypath.inputs.hmdb.schema.common.html#module-pypath.inputs.hmdb.schema.common">module</a>
+        <li><a href="api/pypath.core.annot.Kirouac2010.html#pypath.core.annot.Kirouac2010.to_array">(pypath.core.annot.Kirouac2010 method)</a>
 </li>
-      </ul></li>
-      <li>
-    pypath.inputs.hmdb.schema.metabolites
-
-      <ul>
-        <li><a href="api/pypath.inputs.hmdb.schema.metabolites.html#module-pypath.inputs.hmdb.schema.metabolites">module</a>
+        <li><a href="api/pypath.core.annot.Lambert2018.html#pypath.core.annot.Lambert2018.to_array">(pypath.core.annot.Lambert2018 method)</a>
 </li>
-      </ul></li>
-      <li>
-    pypath.inputs.hmdb.schema.proteins
-
-      <ul>
-        <li><a href="api/pypath.inputs.hmdb.schema.proteins.html#module-pypath.inputs.hmdb.schema.proteins">module</a>
+        <li><a href="api/pypath.core.annot.LigandReceptor.html#pypath.core.annot.LigandReceptor.to_array">(pypath.core.annot.LigandReceptor method)</a>
 </li>
-      </ul></li>
-      <li>
-    pypath.inputs.hmdb.structures
-
-      <ul>
-        <li><a href="api/pypath.inputs.hmdb.structures.html#module-pypath.inputs.hmdb.structures">module</a>
+        <li><a href="api/pypath.core.annot.Locate.html#pypath.core.annot.Locate.to_array">(pypath.core.annot.Locate method)</a>
 </li>
-      </ul></li>
-      <li>
-    pypath.inputs.hmdb.visual
-
-      <ul>
-        <li><a href="api/pypath.inputs.hmdb.visual.html#module-pypath.inputs.hmdb.visual">module</a>
+        <li><a href="api/pypath.core.annot.Lrdb.html#pypath.core.annot.Lrdb.to_array">(pypath.core.annot.Lrdb method)</a>
 </li>
-      </ul></li>
-      <li>
-    pypath.inputs.hmdb.xml
-
-      <ul>
-        <li><a href="api/pypath.inputs.hmdb.xml.html#module-pypath.inputs.hmdb.xml">module</a>
+        <li><a href="api/pypath.core.annot.Matrisome.html#pypath.core.annot.Matrisome.to_array">(pypath.core.annot.Matrisome method)</a>
 </li>
-      </ul></li>
-      <li>
-    pypath.inputs.hprd
-
-      <ul>
-        <li><a href="api/pypath.inputs.hprd.html#module-pypath.inputs.hprd">module</a>
+        <li><a href="api/pypath.core.annot.Matrixdb.html#pypath.core.annot.Matrixdb.to_array">(pypath.core.annot.Matrixdb method)</a>
 </li>
-      </ul></li>
-      <li>
-    pypath.inputs.htri
-
-      <ul>
-        <li><a href="api/pypath.inputs.htri.html#module-pypath.inputs.htri">module</a>
+        <li><a href="api/pypath.core.annot.Mcam.html#pypath.core.annot.Mcam.to_array">(pypath.core.annot.Mcam method)</a>
 </li>
-      </ul></li>
-      <li>
-    pypath.inputs.humsavar
-
-      <ul>
-        <li><a href="api/pypath.inputs.humsavar.html#module-pypath.inputs.humsavar">module</a>
+        <li><a href="api/pypath.core.annot.Membranome.html#pypath.core.annot.Membranome.to_array">(pypath.core.annot.Membranome method)</a>
 </li>
-      </ul></li>
-      <li>
-    pypath.inputs.i3d
-
-      <ul>
-        <li><a href="api/pypath.inputs.i3d.html#module-pypath.inputs.i3d">module</a>
+        <li><a href="api/pypath.core.annot.Msigdb.html#pypath.core.annot.Msigdb.to_array">(pypath.core.annot.Msigdb method)</a>
 </li>
-      </ul></li>
-  </ul></td>
-  <td style="width: 33%; vertical-align: top;"><ul>
-      <li>
-    pypath.inputs.ielm
-
-      <ul>
-        <li><a href="api/pypath.inputs.ielm.html#module-pypath.inputs.ielm">module</a>
+        <li><a href="api/pypath.core.annot.NetpathPathways.html#pypath.core.annot.NetpathPathways.to_array">(pypath.core.annot.NetpathPathways method)</a>
 </li>
-      </ul></li>
-      <li>
-    pypath.inputs.imweb
-
-      <ul>
-        <li><a href="api/pypath.inputs.imweb.html#module-pypath.inputs.imweb">module</a>
+        <li><a href="api/pypath.core.annot.Opm.html#pypath.core.annot.Opm.to_array">(pypath.core.annot.Opm method)</a>
 </li>
-      </ul></li>
-      <li>
-    pypath.inputs.innatedb
-
-      <ul>
-        <li><a href="api/pypath.inputs.innatedb.html#module-pypath.inputs.innatedb">module</a>
+        <li><a href="api/pypath.core.annot.Panglaodb.html#pypath.core.annot.Panglaodb.to_array">(pypath.core.annot.Panglaodb method)</a>
 </li>
-      </ul></li>
-      <li>
-    pypath.inputs.instruct
-
-      <ul>
-        <li><a href="api/pypath.inputs.instruct.html#module-pypath.inputs.instruct">module</a>
+        <li><a href="api/pypath.core.annot.Phobius.html#pypath.core.annot.Phobius.to_array">(pypath.core.annot.Phobius method)</a>
 </li>
-      </ul></li>
-      <li>
-    pypath.inputs.intact
-
-      <ul>
-        <li><a href="api/pypath.inputs.intact.html#module-pypath.inputs.intact">module</a>
+        <li><a href="api/pypath.core.annot.Phosphatome.html#pypath.core.annot.Phosphatome.to_array">(pypath.core.annot.Phosphatome method)</a>
 </li>
-      </ul></li>
-      <li>
-    pypath.inputs.interpro
-
-      <ul>
-        <li><a href="api/pypath.inputs.interpro.html#module-pypath.inputs.interpro">module</a>
+        <li><a href="api/pypath.core.annot.Progeny.html#pypath.core.annot.Progeny.to_array">(pypath.core.annot.Progeny method)</a>
 </li>
-      </ul></li>
-      <li>
-    pypath.inputs.ipi
-
-      <ul>
-        <li><a href="api/pypath.inputs.ipi.html#module-pypath.inputs.ipi">module</a>
+        <li><a href="api/pypath.core.annot.Ramilowski2015.html#pypath.core.annot.Ramilowski2015.to_array">(pypath.core.annot.Ramilowski2015 method)</a>
 </li>
-      </ul></li>
-      <li>
-    pypath.inputs.kegg_api
-
-      <ul>
-        <li><a href="api/pypath.inputs.kegg_api.html#module-pypath.inputs.kegg_api">module</a>
+        <li><a href="api/pypath.core.annot.Ramilowski2015Location.html#pypath.core.annot.Ramilowski2015Location.to_array">(pypath.core.annot.Ramilowski2015Location method)</a>
 </li>
-      </ul></li>
-      <li>
-    pypath.inputs.kirouac2010
-
-      <ul>
-        <li><a href="api/pypath.inputs.kirouac2010.html#module-pypath.inputs.kirouac2010">module</a>
+        <li><a href="api/pypath.core.annot.Scconnect.html#pypath.core.annot.Scconnect.to_array">(pypath.core.annot.Scconnect method)</a>
 </li>
-      </ul></li>
-      <li>
-    pypath.inputs.laudanna
-
-      <ul>
-        <li><a href="api/pypath.inputs.laudanna.html#module-pypath.inputs.laudanna">module</a>
+        <li><a href="api/pypath.core.annot.ScconnectComplex.html#pypath.core.annot.ScconnectComplex.to_array">(pypath.core.annot.ScconnectComplex method)</a>
 </li>
-      </ul></li>
-      <li>
-    pypath.inputs.lincs
-
-      <ul>
-        <li><a href="api/pypath.inputs.lincs.html#module-pypath.inputs.lincs">module</a>
+        <li><a href="api/pypath.core.annot.SignalinkFunctions.html#pypath.core.annot.SignalinkFunctions.to_array">(pypath.core.annot.SignalinkFunctions method)</a>
 </li>
-      </ul></li>
-      <li>
-    pypath.inputs.lncdisease
-
-      <ul>
-        <li><a href="api/pypath.inputs.lncdisease.html#module-pypath.inputs.lncdisease">module</a>
+        <li><a href="api/pypath.core.annot.SignalinkPathways.html#pypath.core.annot.SignalinkPathways.to_array">(pypath.core.annot.SignalinkPathways method)</a>
 </li>
-      </ul></li>
-      <li>
-    pypath.inputs.lncrnadb
-
-      <ul>
-        <li><a href="api/pypath.inputs.lncrnadb.html#module-pypath.inputs.lncrnadb">module</a>
+        <li><a href="api/pypath.core.annot.SignorPathways.html#pypath.core.annot.SignorPathways.to_array">(pypath.core.annot.SignorPathways method)</a>
 </li>
-      </ul></li>
-      <li>
-    pypath.inputs.macrophage
-
-      <ul>
-        <li><a href="api/pypath.inputs.macrophage.html#module-pypath.inputs.macrophage">module</a>
+        <li><a href="api/pypath.core.annot.Surfaceome.html#pypath.core.annot.Surfaceome.to_array">(pypath.core.annot.Surfaceome method)</a>
 </li>
-      </ul></li>
-      <li>
-    pypath.inputs.main
-
-      <ul>
-        <li><a href="api/pypath.inputs.main.html#module-pypath.inputs.main">module</a>
+        <li><a href="api/pypath.core.annot.Talklr.html#pypath.core.annot.Talklr.to_array">(pypath.core.annot.Talklr method)</a>
 </li>
-      </ul></li>
-      <li>
-    pypath.inputs.mimp
-
-      <ul>
-        <li><a href="api/pypath.inputs.mimp.html#module-pypath.inputs.mimp">module</a>
+        <li><a href="api/pypath.core.annot.Tcdb.html#pypath.core.annot.Tcdb.to_array">(pypath.core.annot.Tcdb method)</a>
 </li>
-      </ul></li>
-      <li>
-    pypath.inputs.mir2disease
-
-      <ul>
-        <li><a href="api/pypath.inputs.mir2disease.html#module-pypath.inputs.mir2disease">module</a>
+        <li><a href="api/pypath.core.annot.Tfcensus.html#pypath.core.annot.Tfcensus.to_array">(pypath.core.annot.Tfcensus method)</a>
 </li>
-      </ul></li>
-      <li>
-    pypath.inputs.mirbase
-
-      <ul>
-        <li><a href="api/pypath.inputs.mirbase.html#module-pypath.inputs.mirbase">module</a>
+        <li><a href="api/pypath.core.annot.Topdb.html#pypath.core.annot.Topdb.to_array">(pypath.core.annot.Topdb method)</a>
 </li>
-      </ul></li>
-      <li>
-    pypath.inputs.mirdeathdb
-
-      <ul>
-        <li><a href="api/pypath.inputs.mirdeathdb.html#module-pypath.inputs.mirdeathdb">module</a>
+        <li><a href="api/pypath.core.annot.UniprotFamilies.html#pypath.core.annot.UniprotFamilies.to_array">(pypath.core.annot.UniprotFamilies method)</a>
 </li>
-      </ul></li>
-      <li>
-    pypath.inputs.mirecords
-
-      <ul>
-        <li><a href="api/pypath.inputs.mirecords.html#module-pypath.inputs.mirecords">module</a>
+        <li><a href="api/pypath.core.annot.UniprotKeywords.html#pypath.core.annot.UniprotKeywords.to_array">(pypath.core.annot.UniprotKeywords method)</a>
 </li>
-      </ul></li>
-      <li>
-    pypath.inputs.mirtarbase
-
-      <ul>
-        <li><a href="api/pypath.inputs.mirtarbase.html#module-pypath.inputs.mirtarbase">module</a>
+        <li><a href="api/pypath.core.annot.UniprotLocations.html#pypath.core.annot.UniprotLocations.to_array">(pypath.core.annot.UniprotLocations method)</a>
 </li>
-      </ul></li>
-      <li>
-    pypath.inputs.mitab
-
-      <ul>
-        <li><a href="api/pypath.inputs.mitab.html#module-pypath.inputs.mitab">module</a>
+        <li><a href="api/pypath.core.annot.UniprotTissues.html#pypath.core.annot.UniprotTissues.to_array">(pypath.core.annot.UniprotTissues method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.UniprotTopologies.html#pypath.core.annot.UniprotTopologies.to_array">(pypath.core.annot.UniprotTopologies method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Vesiclepedia.html#pypath.core.annot.Vesiclepedia.to_array">(pypath.core.annot.Vesiclepedia method)</a>
 </li>
-      </ul></li>
-      <li>
-    pypath.inputs.mppi
-
-      <ul>
-        <li><a href="api/pypath.inputs.mppi.html#module-pypath.inputs.mppi">module</a>
+        <li><a href="api/pypath.core.annot.Wang.html#pypath.core.annot.Wang.to_array">(pypath.core.annot.Wang method)</a>
 </li>
-      </ul></li>
-      <li>
-    pypath.inputs.ncrdeathdb
-
-      <ul>
-        <li><a href="api/pypath.inputs.ncrdeathdb.html#module-pypath.inputs.ncrdeathdb">module</a>
+        <li><a href="api/pypath.core.annot.Zhong2015.html#pypath.core.annot.Zhong2015.to_array">(pypath.core.annot.Zhong2015 method)</a>
 </li>
       </ul></li>
-      <li>
-    pypath.inputs.negatome
+      <li><a href="api/pypath.core.annot.Adhesome.html#pypath.core.annot.Adhesome.to_bool_array">to_bool_array() (pypath.core.annot.Adhesome method)</a>
 
       <ul>
-        <li><a href="api/pypath.inputs.negatome.html#module-pypath.inputs.negatome">module</a>
+        <li><a href="api/pypath.core.annot.Almen2009.html#pypath.core.annot.Almen2009.to_bool_array">(pypath.core.annot.Almen2009 method)</a>
 </li>
-      </ul></li>
-      <li>
-    pypath.inputs.netbiol
-
-      <ul>
-        <li><a href="api/pypath.inputs.netbiol.html#module-pypath.inputs.netbiol">module</a>
+        <li><a href="api/pypath.core.annot.AnnotationBase.html#pypath.core.annot.AnnotationBase.to_bool_array">(pypath.core.annot.AnnotationBase method)</a>
 </li>
-      </ul></li>
-      <li>
-    pypath.inputs.offsides
-
-      <ul>
-        <li><a href="api/pypath.inputs.offsides.html#module-pypath.inputs.offsides">module</a>
+        <li><a href="api/pypath.core.annot.Baccin2019.html#pypath.core.annot.Baccin2019.to_bool_array">(pypath.core.annot.Baccin2019 method)</a>
 </li>
-      </ul></li>
-      <li>
-    pypath.inputs.ontology
-
-      <ul>
-        <li><a href="api/pypath.inputs.ontology.html#module-pypath.inputs.ontology">module</a>
+        <li><a href="api/pypath.core.annot.Biogps.html#pypath.core.annot.Biogps.to_bool_array">(pypath.core.annot.Biogps method)</a>
 </li>
-      </ul></li>
-      <li>
-    pypath.inputs.opentargets
-
-      <ul>
-        <li><a href="api/pypath.inputs.opentargets.html#module-pypath.inputs.opentargets">module</a>
+        <li><a href="api/pypath.core.annot.Cancerdrugsdb.html#pypath.core.annot.Cancerdrugsdb.to_bool_array">(pypath.core.annot.Cancerdrugsdb method)</a>
 </li>
-      </ul></li>
-      <li>
-    pypath.inputs.oreganno
-
-      <ul>
-        <li><a href="api/pypath.inputs.oreganno.html#module-pypath.inputs.oreganno">module</a>
+        <li><a href="api/pypath.core.annot.CancerGeneCensus.html#pypath.core.annot.CancerGeneCensus.to_bool_array">(pypath.core.annot.CancerGeneCensus method)</a>
 </li>
-      </ul></li>
-      <li>
-    pypath.inputs.pathophenodb
-
-      <ul>
-        <li><a href="api/pypath.inputs.pathophenodb.html#module-pypath.inputs.pathophenodb">module</a>
+        <li><a href="api/pypath.core.annot.Cancersea.html#pypath.core.annot.Cancersea.to_bool_array">(pypath.core.annot.Cancersea method)</a>
 </li>
-      </ul></li>
-      <li>
-    pypath.inputs.pathwaycommons
-
-      <ul>
-        <li><a href="api/pypath.inputs.pathwaycommons.html#module-pypath.inputs.pathwaycommons">module</a>
+        <li><a href="api/pypath.core.annot.Cellcall.html#pypath.core.annot.Cellcall.to_bool_array">(pypath.core.annot.Cellcall method)</a>
 </li>
-      </ul></li>
-      <li>
-    pypath.inputs.pazar
-
-      <ul>
-        <li><a href="api/pypath.inputs.pazar.html#module-pypath.inputs.pazar">module</a>
+        <li><a href="api/pypath.core.annot.Cellcellinteractions.html#pypath.core.annot.Cellcellinteractions.to_bool_array">(pypath.core.annot.Cellcellinteractions method)</a>
 </li>
-      </ul></li>
-      <li>
-    pypath.inputs.pdzbase
-
-      <ul>
-        <li><a href="api/pypath.inputs.pdzbase.html#module-pypath.inputs.pdzbase">module</a>
+        <li><a href="api/pypath.core.annot.Cellchatdb.html#pypath.core.annot.Cellchatdb.to_bool_array">(pypath.core.annot.Cellchatdb method)</a>
 </li>
-      </ul></li>
-      <li>
-    pypath.inputs.pepcyber
-
-      <ul>
-        <li><a href="api/pypath.inputs.pepcyber.html#module-pypath.inputs.pepcyber">module</a>
+        <li><a href="api/pypath.core.annot.CellchatdbComplex.html#pypath.core.annot.CellchatdbComplex.to_bool_array">(pypath.core.annot.CellchatdbComplex method)</a>
 </li>
-      </ul></li>
-      <li>
-    pypath.inputs.pfam
-
-      <ul>
-        <li><a href="api/pypath.inputs.pfam.html#module-pypath.inputs.pfam">module</a>
+        <li><a href="api/pypath.core.annot.Cellinker.html#pypath.core.annot.Cellinker.to_bool_array">(pypath.core.annot.Cellinker method)</a>
 </li>
-      </ul></li>
-      <li>
-    pypath.inputs.pharos
-
-      <ul>
-        <li><a href="api/pypath.inputs.pharos.html#module-pypath.inputs.pharos">module</a>
+        <li><a href="api/pypath.core.annot.CellinkerComplex.html#pypath.core.annot.CellinkerComplex.to_bool_array">(pypath.core.annot.CellinkerComplex method)</a>
 </li>
-      </ul></li>
-      <li>
-    pypath.inputs.phobius
-
-      <ul>
-        <li><a href="api/pypath.inputs.phobius.html#module-pypath.inputs.phobius">module</a>
+        <li><a href="api/pypath.core.annot.CellPhoneDB.html#pypath.core.annot.CellPhoneDB.to_bool_array">(pypath.core.annot.CellPhoneDB method)</a>
 </li>
-      </ul></li>
-      <li>
-    pypath.inputs.phosphoelm
-
-      <ul>
-        <li><a href="api/pypath.inputs.phosphoelm.html#module-pypath.inputs.phosphoelm">module</a>
+        <li><a href="api/pypath.core.annot.CellPhoneDBComplex.html#pypath.core.annot.CellPhoneDBComplex.to_bool_array">(pypath.core.annot.CellPhoneDBComplex method)</a>
 </li>
-      </ul></li>
-      <li>
-    pypath.inputs.phosphonetworks
-
-      <ul>
-        <li><a href="api/pypath.inputs.phosphonetworks.html#module-pypath.inputs.phosphonetworks">module</a>
+        <li><a href="api/pypath.core.annot.CellSurfaceProteinAtlas.html#pypath.core.annot.CellSurfaceProteinAtlas.to_bool_array">(pypath.core.annot.CellSurfaceProteinAtlas method)</a>
 </li>
-      </ul></li>
-      <li>
-    pypath.inputs.phosphopoint
-
-      <ul>
-        <li><a href="api/pypath.inputs.phosphopoint.html#module-pypath.inputs.phosphopoint">module</a>
+        <li><a href="api/pypath.core.annot.CellSurfaceProteinAtlasCellType.html#pypath.core.annot.CellSurfaceProteinAtlasCellType.to_bool_array">(pypath.core.annot.CellSurfaceProteinAtlasCellType method)</a>
 </li>
-      </ul></li>
-      <li>
-    pypath.inputs.pro
-
-      <ul>
-        <li><a href="api/pypath.inputs.pro.html#module-pypath.inputs.pro">module</a>
+        <li><a href="api/pypath.core.annot.Celltalkdb.html#pypath.core.annot.Celltalkdb.to_bool_array">(pypath.core.annot.Celltalkdb method)</a>
 </li>
-      </ul></li>
-      <li>
-    pypath.inputs.proteins
-
-      <ul>
-        <li><a href="api/pypath.inputs.proteins.html#module-pypath.inputs.proteins">module</a>
+        <li><a href="api/pypath.core.annot.Celltypist.html#pypath.core.annot.Celltypist.to_bool_array">(pypath.core.annot.Celltypist method)</a>
 </li>
-      </ul></li>
-      <li>
-    pypath.inputs.protmapper
-
-      <ul>
-        <li><a href="api/pypath.inputs.protmapper.html#module-pypath.inputs.protmapper">module</a>
+        <li><a href="api/pypath.core.annot.Comppi.html#pypath.core.annot.Comppi.to_bool_array">(pypath.core.annot.Comppi method)</a>
 </li>
-      </ul></li>
-      <li>
-    pypath.inputs.pubchem
-
-      <ul>
-        <li><a href="api/pypath.inputs.pubchem.html#module-pypath.inputs.pubchem">module</a>
+        <li><a href="api/pypath.core.annot.Connectomedb.html#pypath.core.annot.Connectomedb.to_bool_array">(pypath.core.annot.Connectomedb method)</a>
 </li>
-      </ul></li>
-      <li>
-    pypath.inputs.pubmed
-
-      <ul>
-        <li><a href="api/pypath.inputs.pubmed.html#module-pypath.inputs.pubmed">module</a>
+        <li><a href="api/pypath.core.annot.Corum.html#pypath.core.annot.Corum.to_bool_array">(pypath.core.annot.Corum method)</a>
 </li>
-      </ul></li>
-      <li>
-    pypath.inputs.ramp
-
-      <ul>
-        <li><a href="api/pypath.inputs.ramp.html#module-pypath.inputs.ramp">module</a>
+        <li><a href="api/pypath.core.annot.CorumFuncat.html#pypath.core.annot.CorumFuncat.to_bool_array">(pypath.core.annot.CorumFuncat method)</a>
 </li>
-      </ul></li>
-      <li>
-    pypath.inputs.rdata
-
-      <ul>
-        <li><a href="api/pypath.inputs.rdata.html#module-pypath.inputs.rdata">module</a>
+        <li><a href="api/pypath.core.annot.CorumGO.html#pypath.core.annot.CorumGO.to_bool_array">(pypath.core.annot.CorumGO method)</a>
 </li>
-      </ul></li>
-      <li>
-    pypath.inputs.reaction
-
-      <ul>
-        <li><a href="api/pypath.inputs.reaction.html#module-pypath.inputs.reaction">module</a>
+        <li><a href="api/pypath.core.annot.Cpad.html#pypath.core.annot.Cpad.to_bool_array">(pypath.core.annot.Cpad method)</a>
 </li>
-      </ul></li>
-      <li>
-    pypath.inputs.reactome
-
-      <ul>
-        <li><a href="api/pypath.inputs.reactome.html#module-pypath.inputs.reactome">module</a>
+        <li><a href="api/pypath.core.annot.Cytosig.html#pypath.core.annot.Cytosig.to_bool_array">(pypath.core.annot.Cytosig method)</a>
 </li>
-      </ul></li>
-      <li>
-    pypath.inputs.science
-
-      <ul>
-        <li><a href="api/pypath.inputs.science.html#module-pypath.inputs.science">module</a>
+        <li><a href="api/pypath.core.annot.Dgidb.html#pypath.core.annot.Dgidb.to_bool_array">(pypath.core.annot.Dgidb method)</a>
 </li>
-      </ul></li>
-      <li>
-    pypath.inputs.sider
-
-      <ul>
-        <li><a href="api/pypath.inputs.sider.html#module-pypath.inputs.sider">module</a>
+        <li><a href="api/pypath.core.annot.Disgenet.html#pypath.core.annot.Disgenet.to_bool_array">(pypath.core.annot.Disgenet method)</a>
 </li>
-      </ul></li>
-      <li>
-    pypath.inputs.stitch
-
-      <ul>
-        <li><a href="api/pypath.inputs.stitch.html#module-pypath.inputs.stitch">module</a>
+        <li><a href="api/pypath.core.annot.Embrace.html#pypath.core.annot.Embrace.to_bool_array">(pypath.core.annot.Embrace method)</a>
 </li>
-      </ul></li>
-      <li>
-    pypath.inputs.string
-
-      <ul>
-        <li><a href="api/pypath.inputs.string.html#module-pypath.inputs.string">module</a>
+        <li><a href="api/pypath.core.annot.Exocarta.html#pypath.core.annot.Exocarta.to_bool_array">(pypath.core.annot.Exocarta method)</a>
 </li>
-      </ul></li>
-      <li>
-    pypath.inputs.switches_elm
-
-      <ul>
-        <li><a href="api/pypath.inputs.switches_elm.html#module-pypath.inputs.switches_elm">module</a>
+        <li><a href="api/pypath.core.annot.GOIntercell.html#pypath.core.annot.GOIntercell.to_bool_array">(pypath.core.annot.GOIntercell method)</a>
 </li>
-      </ul></li>
-      <li>
-    pypath.inputs.transmir
-
-      <ul>
-        <li><a href="api/pypath.inputs.transmir.html#module-pypath.inputs.transmir">module</a>
+        <li><a href="api/pypath.core.annot.Gpcrdb.html#pypath.core.annot.Gpcrdb.to_bool_array">(pypath.core.annot.Gpcrdb method)</a>
 </li>
-      </ul></li>
-      <li>
-    pypath.inputs.trip
-
-      <ul>
-        <li><a href="api/pypath.inputs.trip.html#module-pypath.inputs.trip">module</a>
+        <li><a href="api/pypath.core.annot.GuideToPharmacology.html#pypath.core.annot.GuideToPharmacology.to_bool_array">(pypath.core.annot.GuideToPharmacology method)</a>
 </li>
-      </ul></li>
-      <li>
-    pypath.inputs.trrust
-
-      <ul>
-        <li><a href="api/pypath.inputs.trrust.html#module-pypath.inputs.trrust">module</a>
+        <li><a href="api/pypath.core.annot.Hgnc.html#pypath.core.annot.Hgnc.to_bool_array">(pypath.core.annot.Hgnc method)</a>
 </li>
-      </ul></li>
-      <li>
-    pypath.inputs.twosides
-
-      <ul>
-        <li><a href="api/pypath.inputs.twosides.html#module-pypath.inputs.twosides">module</a>
+        <li><a href="api/pypath.core.annot.HpmrComplex.html#pypath.core.annot.HpmrComplex.to_bool_array">(pypath.core.annot.HpmrComplex method)</a>
 </li>
-      </ul></li>
-      <li>
-    pypath.inputs.unichem
-
-      <ul>
-        <li><a href="api/pypath.inputs.unichem.html#module-pypath.inputs.unichem">module</a>
+        <li><a href="api/pypath.core.annot.HPO.html#pypath.core.annot.HPO.to_bool_array">(pypath.core.annot.HPO method)</a>
 </li>
-      </ul></li>
-      <li>
-    pypath.inputs.uniprot
-
-      <ul>
-        <li><a href="api/pypath.inputs.uniprot.html#module-pypath.inputs.uniprot">module</a>
+        <li><a href="api/pypath.core.annot.Humancellmap.html#pypath.core.annot.Humancellmap.to_bool_array">(pypath.core.annot.Humancellmap method)</a>
 </li>
-      </ul></li>
-      <li>
-    pypath.inputs.uniprot_db
-
-      <ul>
-        <li><a href="api/pypath.inputs.uniprot_db.html#module-pypath.inputs.uniprot_db">module</a>
+        <li><a href="api/pypath.core.annot.HumanPlasmaMembraneReceptome.html#pypath.core.annot.HumanPlasmaMembraneReceptome.to_bool_array">(pypath.core.annot.HumanPlasmaMembraneReceptome method)</a>
 </li>
-      </ul></li>
-      <li>
-    pypath.internals
-
-      <ul>
-        <li><a href="api/pypath.internals.html#module-pypath.internals">module</a>
+        <li><a href="api/pypath.core.annot.HumanProteinAtlas.html#pypath.core.annot.HumanProteinAtlas.to_bool_array">(pypath.core.annot.HumanProteinAtlas method)</a>
 </li>
-      </ul></li>
-      <li>
-    pypath.internals.input_formats
-
-      <ul>
-        <li><a href="api/pypath.internals.input_formats.html#module-pypath.internals.input_formats">module</a>
+        <li><a href="api/pypath.core.annot.HumanProteinAtlasSecretome.html#pypath.core.annot.HumanProteinAtlasSecretome.to_bool_array">(pypath.core.annot.HumanProteinAtlasSecretome method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.HumanProteinAtlasSubcellular.html#pypath.core.annot.HumanProteinAtlasSubcellular.to_bool_array">(pypath.core.annot.HumanProteinAtlasSubcellular method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Icellnet.html#pypath.core.annot.Icellnet.to_bool_array">(pypath.core.annot.Icellnet method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.IcellnetComplex.html#pypath.core.annot.IcellnetComplex.to_bool_array">(pypath.core.annot.IcellnetComplex method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Integrins.html#pypath.core.annot.Integrins.to_bool_array">(pypath.core.annot.Integrins method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.InterPro.html#pypath.core.annot.InterPro.to_bool_array">(pypath.core.annot.InterPro method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Intogen.html#pypath.core.annot.Intogen.to_bool_array">(pypath.core.annot.Intogen method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Italk.html#pypath.core.annot.Italk.to_bool_array">(pypath.core.annot.Italk method)</a>
 </li>
-      </ul></li>
-      <li>
-    pypath.internals.license
-
-      <ul>
-        <li><a href="api/pypath.internals.license.html#module-pypath.internals.license">module</a>
+        <li><a href="api/pypath.core.annot.KeggPathways.html#pypath.core.annot.KeggPathways.to_bool_array">(pypath.core.annot.KeggPathways method)</a>
 </li>
-      </ul></li>
-      <li>
-    pypath.internals.maps
-
-      <ul>
-        <li><a href="api/pypath.internals.maps.html#module-pypath.internals.maps">module</a>
+        <li><a href="api/pypath.core.annot.KeggPathwaysPC.html#pypath.core.annot.KeggPathwaysPC.to_bool_array">(pypath.core.annot.KeggPathwaysPC method)</a>
 </li>
-      </ul></li>
-      <li>
-    pypath.internals.refs
-
-      <ul>
-        <li><a href="api/pypath.internals.refs.html#module-pypath.internals.refs">module</a>
+        <li><a href="api/pypath.core.annot.Kinasedotcom.html#pypath.core.annot.Kinasedotcom.to_bool_array">(pypath.core.annot.Kinasedotcom method)</a>
 </li>
-      </ul></li>
-      <li>
-    pypath.internals.resource
-
-      <ul>
-        <li><a href="api/pypath.internals.resource.html#module-pypath.internals.resource">module</a>
+        <li><a href="api/pypath.core.annot.Kirouac2010.html#pypath.core.annot.Kirouac2010.to_bool_array">(pypath.core.annot.Kirouac2010 method)</a>
 </li>
-      </ul></li>
-      <li>
-    pypath.legacy
-
-      <ul>
-        <li><a href="api/pypath.legacy.html#module-pypath.legacy">module</a>
+        <li><a href="api/pypath.core.annot.Lambert2018.html#pypath.core.annot.Lambert2018.to_bool_array">(pypath.core.annot.Lambert2018 method)</a>
 </li>
-      </ul></li>
-      <li>
-    pypath.legacy.db_categories
-
-      <ul>
-        <li><a href="api/pypath.legacy.db_categories.html#module-pypath.legacy.db_categories">module</a>
+        <li><a href="api/pypath.core.annot.LigandReceptor.html#pypath.core.annot.LigandReceptor.to_bool_array">(pypath.core.annot.LigandReceptor method)</a>
 </li>
-      </ul></li>
-      <li>
-    pypath.resources
-
-      <ul>
-        <li><a href="api/pypath.resources.html#module-pypath.resources">module</a>
+        <li><a href="api/pypath.core.annot.Locate.html#pypath.core.annot.Locate.to_bool_array">(pypath.core.annot.Locate method)</a>
 </li>
-      </ul></li>
-      <li>
-    pypath.resources.controller
-
-      <ul>
-        <li><a href="api/pypath.resources.controller.html#module-pypath.resources.controller">module</a>
+        <li><a href="api/pypath.core.annot.Lrdb.html#pypath.core.annot.Lrdb.to_bool_array">(pypath.core.annot.Lrdb method)</a>
 </li>
-      </ul></li>
-      <li>
-    pypath.resources.data
-
-      <ul>
-        <li><a href="api/pypath.resources.data.html#module-pypath.resources.data">module</a>
+        <li><a href="api/pypath.core.annot.Matrisome.html#pypath.core.annot.Matrisome.to_bool_array">(pypath.core.annot.Matrisome method)</a>
 </li>
-      </ul></li>
-      <li>
-    pypath.resources.data_formats
-
-      <ul>
-        <li><a href="api/pypath.resources.data_formats.html#module-pypath.resources.data_formats">module</a>
+        <li><a href="api/pypath.core.annot.Matrixdb.html#pypath.core.annot.Matrixdb.to_bool_array">(pypath.core.annot.Matrixdb method)</a>
 </li>
-      </ul></li>
-      <li>
-    pypath.resources.licenses
-
-      <ul>
-        <li><a href="api/pypath.resources.licenses.html#module-pypath.resources.licenses">module</a>
+        <li><a href="api/pypath.core.annot.Mcam.html#pypath.core.annot.Mcam.to_bool_array">(pypath.core.annot.Mcam method)</a>
 </li>
-      </ul></li>
-      <li>
-    pypath.resources.network
-
-      <ul>
-        <li><a href="api/pypath.resources.network.html#module-pypath.resources.network">module</a>
+        <li><a href="api/pypath.core.annot.Membranome.html#pypath.core.annot.Membranome.to_bool_array">(pypath.core.annot.Membranome method)</a>
 </li>
-      </ul></li>
-      <li>
-    pypath.resources.urls
-
-      <ul>
-        <li><a href="api/pypath.resources.urls.html#module-pypath.resources.urls">module</a>
+        <li><a href="api/pypath.core.annot.Msigdb.html#pypath.core.annot.Msigdb.to_bool_array">(pypath.core.annot.Msigdb method)</a>
 </li>
-      </ul></li>
-      <li>
-    pypath.share
-
-      <ul>
-        <li><a href="api/pypath.share.html#module-pypath.share">module</a>
+        <li><a href="api/pypath.core.annot.NetpathPathways.html#pypath.core.annot.NetpathPathways.to_bool_array">(pypath.core.annot.NetpathPathways method)</a>
 </li>
-      </ul></li>
-      <li>
-    pypath.share.cache
-
-      <ul>
-        <li><a href="api/pypath.share.cache.html#module-pypath.share.cache">module</a>
+        <li><a href="api/pypath.core.annot.Opm.html#pypath.core.annot.Opm.to_bool_array">(pypath.core.annot.Opm method)</a>
 </li>
-      </ul></li>
-      <li>
-    pypath.share.common
-
-      <ul>
-        <li><a href="api/pypath.share.common.html#module-pypath.share.common">module</a>
+        <li><a href="api/pypath.core.annot.Panglaodb.html#pypath.core.annot.Panglaodb.to_bool_array">(pypath.core.annot.Panglaodb method)</a>
 </li>
-      </ul></li>
-      <li>
-    pypath.share.constants
-
-      <ul>
-        <li><a href="api/pypath.share.constants.html#module-pypath.share.constants">module</a>
+        <li><a href="api/pypath.core.annot.Phobius.html#pypath.core.annot.Phobius.to_bool_array">(pypath.core.annot.Phobius method)</a>
 </li>
-      </ul></li>
-      <li>
-    pypath.share.curl
-
-      <ul>
-        <li><a href="api/pypath.share.curl.html#module-pypath.share.curl">module</a>
+        <li><a href="api/pypath.core.annot.Phosphatome.html#pypath.core.annot.Phosphatome.to_bool_array">(pypath.core.annot.Phosphatome method)</a>
 </li>
-      </ul></li>
-      <li>
-    pypath.share.progress
-
-      <ul>
-        <li><a href="api/pypath.share.progress.html#module-pypath.share.progress">module</a>
+        <li><a href="api/pypath.core.annot.Progeny.html#pypath.core.annot.Progeny.to_bool_array">(pypath.core.annot.Progeny method)</a>
 </li>
-      </ul></li>
-      <li>
-    pypath.share.session
-
-      <ul>
-        <li><a href="api/pypath.share.session.html#module-pypath.share.session">module</a>
+        <li><a href="api/pypath.core.annot.Ramilowski2015.html#pypath.core.annot.Ramilowski2015.to_bool_array">(pypath.core.annot.Ramilowski2015 method)</a>
 </li>
-      </ul></li>
-      <li>
-    pypath.share.settings
-
-      <ul>
-        <li><a href="api/pypath.share.settings.html#module-pypath.share.settings">module</a>
+        <li><a href="api/pypath.core.annot.Ramilowski2015Location.html#pypath.core.annot.Ramilowski2015Location.to_bool_array">(pypath.core.annot.Ramilowski2015Location method)</a>
 </li>
-      </ul></li>
-      <li>
-    pypath.utils
-
-      <ul>
-        <li><a href="api/pypath.utils.html#module-pypath.utils">module</a>
+        <li><a href="api/pypath.core.annot.Scconnect.html#pypath.core.annot.Scconnect.to_bool_array">(pypath.core.annot.Scconnect method)</a>
 </li>
-      </ul></li>
-      <li>
-    pypath.utils.go
-
-      <ul>
-        <li><a href="api/pypath.utils.go.html#module-pypath.utils.go">module</a>
+        <li><a href="api/pypath.core.annot.ScconnectComplex.html#pypath.core.annot.ScconnectComplex.to_bool_array">(pypath.core.annot.ScconnectComplex method)</a>
 </li>
-      </ul></li>
-      <li>
-    pypath.utils.pdb
-
-      <ul>
-        <li><a href="api/pypath.utils.pdb.html#module-pypath.utils.pdb">module</a>
+        <li><a href="api/pypath.core.annot.SignalinkFunctions.html#pypath.core.annot.SignalinkFunctions.to_bool_array">(pypath.core.annot.SignalinkFunctions method)</a>
 </li>
-      </ul></li>
-      <li>
-    pypath.utils.proteomicsdb
-
-      <ul>
-        <li><a href="api/pypath.utils.proteomicsdb.html#module-pypath.utils.proteomicsdb">module</a>
+        <li><a href="api/pypath.core.annot.SignalinkPathways.html#pypath.core.annot.SignalinkPathways.to_bool_array">(pypath.core.annot.SignalinkPathways method)</a>
 </li>
-      </ul></li>
-      <li>
-    pypath.utils.reflists
-
-      <ul>
-        <li><a href="api/pypath.utils.reflists.html#module-pypath.utils.reflists">module</a>
+        <li><a href="api/pypath.core.annot.SignorPathways.html#pypath.core.annot.SignorPathways.to_bool_array">(pypath.core.annot.SignorPathways method)</a>
 </li>
-      </ul></li>
-      <li>
-    pypath.utils.residues
-
-      <ul>
-        <li><a href="api/pypath.utils.residues.html#module-pypath.utils.residues">module</a>
+        <li><a href="api/pypath.core.annot.Surfaceome.html#pypath.core.annot.Surfaceome.to_bool_array">(pypath.core.annot.Surfaceome method)</a>
 </li>
-      </ul></li>
-      <li>
-    pypath.utils.seq
-
-      <ul>
-        <li><a href="api/pypath.utils.seq.html#module-pypath.utils.seq">module</a>
+        <li><a href="api/pypath.core.annot.Talklr.html#pypath.core.annot.Talklr.to_bool_array">(pypath.core.annot.Talklr method)</a>
 </li>
-      </ul></li>
-      <li>
-    pypath.utils.taxonomy
-
-      <ul>
-        <li><a href="api/pypath.utils.taxonomy.html#module-pypath.utils.taxonomy">module</a>
+        <li><a href="api/pypath.core.annot.Tcdb.html#pypath.core.annot.Tcdb.to_bool_array">(pypath.core.annot.Tcdb method)</a>
 </li>
-      </ul></li>
-      <li>
-    pypath.utils.unichem
-
-      <ul>
-        <li><a href="api/pypath.utils.unichem.html#module-pypath.utils.unichem">module</a>
+        <li><a href="api/pypath.core.annot.Tfcensus.html#pypath.core.annot.Tfcensus.to_bool_array">(pypath.core.annot.Tfcensus method)</a>
 </li>
-      </ul></li>
-      <li>
-    pypath.visual
-
-      <ul>
-        <li><a href="api/pypath.visual.html#module-pypath.visual">module</a>
+        <li><a href="api/pypath.core.annot.Topdb.html#pypath.core.annot.Topdb.to_bool_array">(pypath.core.annot.Topdb method)</a>
 </li>
-      </ul></li>
-      <li>
-    pypath.visual.drawing
-
-      <ul>
-        <li><a href="api/pypath.visual.drawing.html#module-pypath.visual.drawing">module</a>
+        <li><a href="api/pypath.core.annot.UniprotFamilies.html#pypath.core.annot.UniprotFamilies.to_bool_array">(pypath.core.annot.UniprotFamilies method)</a>
 </li>
-      </ul></li>
-      <li>
-    pypath.visual.igraph_drawing
-
-      <ul>
-        <li><a href="api/pypath.visual.igraph_drawing.html#module-pypath.visual.igraph_drawing">module</a>
+        <li><a href="api/pypath.core.annot.UniprotKeywords.html#pypath.core.annot.UniprotKeywords.to_bool_array">(pypath.core.annot.UniprotKeywords method)</a>
 </li>
-      </ul></li>
-      <li>
-    pypath.visual.igraph_drawing.edge
-
-      <ul>
-        <li><a href="api/pypath.visual.igraph_drawing.edge.html#module-pypath.visual.igraph_drawing.edge">module</a>
+        <li><a href="api/pypath.core.annot.UniprotLocations.html#pypath.core.annot.UniprotLocations.to_bool_array">(pypath.core.annot.UniprotLocations method)</a>
 </li>
-      </ul></li>
-      <li>
-    pypath.visual.igraph_drawing.vertex
-
-      <ul>
-        <li><a href="api/pypath.visual.igraph_drawing.vertex.html#module-pypath.visual.igraph_drawing.vertex">module</a>
+        <li><a href="api/pypath.core.annot.UniprotTissues.html#pypath.core.annot.UniprotTissues.to_bool_array">(pypath.core.annot.UniprotTissues method)</a>
 </li>
-      </ul></li>
-  </ul></td>
-</tr></table>
-
-<h2 id="Q">Q</h2>
-<table style="width: 100%" class="indextable genindextable"><tr>
-  <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="api/pypath.utils.proteomicsdb.ProteomicsDB.html#pypath.utils.proteomicsdb.ProteomicsDB.query">query() (pypath.utils.proteomicsdb.ProteomicsDB method)</a>
+        <li><a href="api/pypath.core.annot.UniprotTopologies.html#pypath.core.annot.UniprotTopologies.to_bool_array">(pypath.core.annot.UniprotTopologies method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Vesiclepedia.html#pypath.core.annot.Vesiclepedia.to_bool_array">(pypath.core.annot.Vesiclepedia method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Wang.html#pypath.core.annot.Wang.to_bool_array">(pypath.core.annot.Wang method)</a>
+</li>
+        <li><a href="api/pypath.core.annot.Zhong2015.html#pypath.core.annot.Zhong2015.to_bool_array">(pypath.core.annot.Zhong2015 method)</a>
 </li>
+      </ul></li>
   </ul></td>
   <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="api/pypath.inputs.uniprot.query_builder.html#pypath.inputs.uniprot.query_builder">query_builder() (in module pypath.inputs.uniprot)</a>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.to_igraph">to_igraph() (pypath.core.network.Network method)</a>
 </li>
-  </ul></td>
-</tr></table>
+      <li><a href="api/pypath.internals.license.LicenseAttrib.html#pypath.internals.license.LicenseAttrib.to_int">to_int() (pypath.internals.license.LicenseAttrib method)</a>
 
-<h2 id="R">R</h2>
-<table style="width: 100%" class="indextable genindextable"><tr>
-  <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="api/pypath.inputs.ramp.ramp_id_types.html#pypath.inputs.ramp.ramp_id_types">ramp_id_types() (in module pypath.inputs.ramp)</a>
+      <ul>
+        <li><a href="api/pypath.internals.license.LicenseFeature.html#pypath.internals.license.LicenseFeature.to_int">(pypath.internals.license.LicenseFeature method)</a>
 </li>
-      <li><a href="api/pypath.inputs.ramp.ramp_id_types_2.html#pypath.inputs.ramp.ramp_id_types_2">ramp_id_types_2() (in module pypath.inputs.ramp)</a>
+        <li><a href="api/pypath.internals.license.LicensePurpose.html#pypath.internals.license.LicensePurpose.to_int">(pypath.internals.license.LicensePurpose method)</a>
 </li>
-      <li><a href="api/pypath.inputs.ramp.ramp_list_tables.html#pypath.inputs.ramp.ramp_list_tables">ramp_list_tables() (in module pypath.inputs.ramp)</a>
+        <li><a href="api/pypath.internals.license.LicenseSharing.html#pypath.internals.license.LicenseSharing.to_int">(pypath.internals.license.LicenseSharing method)</a>
 </li>
-      <li><a href="api/pypath.inputs.ramp.ramp_mapping.html#pypath.inputs.ramp.ramp_mapping">ramp_mapping() (in module pypath.inputs.ramp)</a>
+      </ul></li>
+      <li><a href="api/pypath.core.annot.Adhesome.html#pypath.core.annot.Adhesome.to_set">to_set() (pypath.core.annot.Adhesome method)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.annot.Almen2009.html#pypath.core.annot.Almen2009.to_set">(pypath.core.annot.Almen2009 method)</a>
 </li>
-      <li><a href="api/pypath.inputs.ramp.ramp_raw.html#pypath.inputs.ramp.ramp_raw">ramp_raw() (in module pypath.inputs.ramp)</a>
+        <li><a href="api/pypath.core.annot.AnnotationBase.html#pypath.core.annot.AnnotationBase.to_set">(pypath.core.annot.AnnotationBase method)</a>
 </li>
-      <li><a href="api/pypath.inputs.ramp.ramp_show_tables.html#pypath.inputs.ramp.ramp_show_tables">ramp_show_tables() (in module pypath.inputs.ramp)</a>
+        <li><a href="api/pypath.core.annot.Baccin2019.html#pypath.core.annot.Baccin2019.to_set">(pypath.core.annot.Baccin2019 method)</a>
 </li>
-      <li><a href="api/pypath.internals.input_formats.RampMapping.html#pypath.internals.input_formats.RampMapping">RampMapping (class in pypath.internals.input_formats)</a>
+        <li><a href="api/pypath.core.annot.Biogps.html#pypath.core.annot.Biogps.to_set">(pypath.core.annot.Biogps method)</a>
 </li>
-      <li><a href="api/pypath.inputs.hmdb.common.raw.html#pypath.inputs.hmdb.common.raw">raw() (in module pypath.inputs.hmdb.common)</a>
-
-      <ul>
-        <li><a href="api/pypath.inputs.hmdb.metabolites.raw.html#pypath.inputs.hmdb.metabolites.raw">(in module pypath.inputs.hmdb.metabolites)</a>
+        <li><a href="api/pypath.core.annot.Cancerdrugsdb.html#pypath.core.annot.Cancerdrugsdb.to_set">(pypath.core.annot.Cancerdrugsdb method)</a>
 </li>
-        <li><a href="api/pypath.inputs.hmdb.proteins.raw.html#pypath.inputs.hmdb.proteins.raw">(in module pypath.inputs.hmdb.proteins)</a>
+        <li><a href="api/pypath.core.annot.CancerGeneCensus.html#pypath.core.annot.CancerGeneCensus.to_set">(pypath.core.annot.CancerGeneCensus method)</a>
 </li>
-      </ul></li>
-      <li><a href="api/pypath.resources.data_formats.reaction_pc.html#pypath.resources.data_formats.reaction_pc">reaction_pc (in module pypath.resources.data_formats)</a>
+        <li><a href="api/pypath.core.annot.Cancersea.html#pypath.core.annot.Cancersea.to_set">(pypath.core.annot.Cancersea method)</a>
 </li>
-      <li><a href="api/pypath.inputs.reaction.reactions_biopax.html#pypath.inputs.reaction.reactions_biopax">reactions_biopax() (in module pypath.inputs.reaction)</a>
+        <li><a href="api/pypath.core.annot.Cellcall.html#pypath.core.annot.Cellcall.to_set">(pypath.core.annot.Cellcall method)</a>
 </li>
-      <li><a href="api/pypath.inputs.reaction.reactome_biopax.html#pypath.inputs.reaction.reactome_biopax">reactome_biopax() (in module pypath.inputs.reaction)</a>
+        <li><a href="api/pypath.core.annot.Cellcellinteractions.html#pypath.core.annot.Cellcellinteractions.to_set">(pypath.core.annot.Cellcellinteractions method)</a>
 </li>
-      <li><a href="api/pypath.inputs.reaction.reactome_bs.html#pypath.inputs.reaction.reactome_bs">reactome_bs() (in module pypath.inputs.reaction)</a>
+        <li><a href="api/pypath.core.annot.Cellchatdb.html#pypath.core.annot.Cellchatdb.to_set">(pypath.core.annot.Cellchatdb method)</a>
 </li>
-      <li><a href="api/pypath.inputs.reactome.reactome_chebis.html#pypath.inputs.reactome.reactome_chebis">reactome_chebis() (in module pypath.inputs.reactome)</a>
+        <li><a href="api/pypath.core.annot.CellchatdbComplex.html#pypath.core.annot.CellchatdbComplex.to_set">(pypath.core.annot.CellchatdbComplex method)</a>
 </li>
-      <li><a href="api/pypath.inputs.reaction.reactome_interactions.html#pypath.inputs.reaction.reactome_interactions">reactome_interactions() (in module pypath.inputs.reaction)</a>
+        <li><a href="api/pypath.core.annot.Cellinker.html#pypath.core.annot.Cellinker.to_set">(pypath.core.annot.Cellinker method)</a>
 </li>
-      <li><a href="api/pypath.inputs.reactome.reactome_pathway_relations.html#pypath.inputs.reactome.reactome_pathway_relations">reactome_pathway_relations() (in module pypath.inputs.reactome)</a>
+        <li><a href="api/pypath.core.annot.CellinkerComplex.html#pypath.core.annot.CellinkerComplex.to_set">(pypath.core.annot.CellinkerComplex method)</a>
 </li>
-      <li><a href="api/pypath.inputs.reactome.reactome_pathways.html#pypath.inputs.reactome.reactome_pathways">reactome_pathways() (in module pypath.inputs.reactome)</a>
+        <li><a href="api/pypath.core.annot.CellPhoneDB.html#pypath.core.annot.CellPhoneDB.to_set">(pypath.core.annot.CellPhoneDB method)</a>
 </li>
-      <li><a href="api/pypath.inputs.reaction.reactome_sbml.html#pypath.inputs.reaction.reactome_sbml">reactome_sbml() (in module pypath.inputs.reaction)</a>
+        <li><a href="api/pypath.core.annot.CellPhoneDBComplex.html#pypath.core.annot.CellPhoneDBComplex.to_set">(pypath.core.annot.CellPhoneDBComplex method)</a>
 </li>
-      <li><a href="api/pypath.inputs.reactome.reactome_uniprots.html#pypath.inputs.reactome.reactome_uniprots">reactome_uniprots() (in module pypath.inputs.reactome)</a>
+        <li><a href="api/pypath.core.annot.CellSurfaceProteinAtlas.html#pypath.core.annot.CellSurfaceProteinAtlas.to_set">(pypath.core.annot.CellSurfaceProteinAtlas method)</a>
 </li>
-      <li><a href="api/pypath.utils.seq.read_fasta.html#pypath.utils.seq.read_fasta">read_fasta() (in module pypath.utils.seq)</a>
+        <li><a href="api/pypath.core.annot.CellSurfaceProteinAtlasCellType.html#pypath.core.annot.CellSurfaceProteinAtlasCellType.to_set">(pypath.core.annot.CellSurfaceProteinAtlasCellType method)</a>
 </li>
-  </ul></td>
-  <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="api/pypath.inputs.common.read_table.html#pypath.inputs.common.read_table">read_table() (in module pypath.inputs.common)</a>
+        <li><a href="api/pypath.core.annot.Celltalkdb.html#pypath.core.annot.Celltalkdb.to_set">(pypath.core.annot.Celltalkdb method)</a>
 </li>
-      <li><a href="api/pypath.inputs.common.read_xls.html#pypath.inputs.common.read_xls">read_xls() (in module pypath.inputs.common)</a>
+        <li><a href="api/pypath.core.annot.Celltypist.html#pypath.core.annot.Celltypist.to_set">(pypath.core.annot.Celltypist method)</a>
 </li>
-      <li><a href="api/pypath.internals.input_formats.ReadList.html#pypath.internals.input_formats.ReadList">ReadList (class in pypath.internals.input_formats)</a>
+        <li><a href="api/pypath.core.annot.Comppi.html#pypath.core.annot.Comppi.to_set">(pypath.core.annot.Comppi method)</a>
 </li>
-      <li><a href="api/pypath.internals.refs.Reference.html#pypath.internals.refs.Reference">Reference (class in pypath.internals.refs)</a>
+        <li><a href="api/pypath.core.annot.Connectomedb.html#pypath.core.annot.Connectomedb.to_set">(pypath.core.annot.Connectomedb method)</a>
 </li>
-      <li><a href="api/pypath.utils.reflists.ReferenceListManager.html#pypath.utils.reflists.ReferenceListManager">ReferenceListManager (class in pypath.utils.reflists)</a>
+        <li><a href="api/pypath.core.annot.Corum.html#pypath.core.annot.Corum.to_set">(pypath.core.annot.Corum method)</a>
 </li>
-      <li><a href="api/pypath.utils.go.GeneOntology.html#pypath.utils.go.GeneOntology.reload">reload() (pypath.utils.go.GeneOntology method)</a>
-
-      <ul>
-        <li><a href="api/pypath.utils.go.GOAnnotation.html#pypath.utils.go.GOAnnotation.reload">(pypath.utils.go.GOAnnotation method)</a>
+        <li><a href="api/pypath.core.annot.CorumFuncat.html#pypath.core.annot.CorumFuncat.to_set">(pypath.core.annot.CorumFuncat method)</a>
 </li>
-        <li><a href="api/pypath.utils.go.GOCustomAnnotation.html#pypath.utils.go.GOCustomAnnotation.reload">(pypath.utils.go.GOCustomAnnotation method)</a>
+        <li><a href="api/pypath.core.annot.CorumGO.html#pypath.core.annot.CorumGO.to_set">(pypath.core.annot.CorumGO method)</a>
 </li>
-      </ul></li>
-      <li><a href="api/pypath.share.curl.RemoteFile.html#pypath.share.curl.RemoteFile">RemoteFile (class in pypath.share.curl)</a>
+        <li><a href="api/pypath.core.annot.Cpad.html#pypath.core.annot.Cpad.to_set">(pypath.core.annot.Cpad method)</a>
 </li>
-      <li><a href="api/pypath.share.curl.Curl.html#pypath.share.curl.Curl.replace_forbidden">replace_forbidden() (pypath.share.curl.Curl class method)</a>
+        <li><a href="api/pypath.core.annot.Cytosig.html#pypath.core.annot.Cytosig.to_set">(pypath.core.annot.Cytosig method)</a>
 </li>
-      <li><a href="api/pypath.inputs.uniprot.UniprotRecordHistory.html#pypath.inputs.uniprot.UniprotRecordHistory.replaced_by">replaced_by (pypath.inputs.uniprot.UniprotRecordHistory attribute)</a>
+        <li><a href="api/pypath.core.annot.Dgidb.html#pypath.core.annot.Dgidb.to_set">(pypath.core.annot.Dgidb method)</a>
 </li>
-      <li><a href="api/pypath.inputs.uniprot.UniprotRecordHistory.html#pypath.inputs.uniprot.UniprotRecordHistory.replaces">replaces (pypath.inputs.uniprot.UniprotRecordHistory attribute)</a>
+        <li><a href="api/pypath.core.annot.Disgenet.html#pypath.core.annot.Disgenet.to_set">(pypath.core.annot.Disgenet method)</a>
 </li>
-      <li><a href="api/pypath.utils.pdb.Residue.html#pypath.utils.pdb.Residue">Residue (class in pypath.utils.pdb)</a>
+        <li><a href="api/pypath.core.annot.Embrace.html#pypath.core.annot.Embrace.to_set">(pypath.core.annot.Embrace method)</a>
 </li>
-      <li><a href="api/pypath.utils.pdb.residue_pdb.html#pypath.utils.pdb.residue_pdb">residue_pdb() (in module pypath.utils.pdb)</a>
+        <li><a href="api/pypath.core.annot.Exocarta.html#pypath.core.annot.Exocarta.to_set">(pypath.core.annot.Exocarta method)</a>
 </li>
-      <li><a href="api/pypath.utils.pdb.ResidueMapper.html#pypath.utils.pdb.ResidueMapper">ResidueMapper (class in pypath.utils.pdb)</a>
-
-      <ul>
-        <li><a href="api/pypath.utils.residues.ResidueMapper.html#pypath.utils.residues.ResidueMapper">(class in pypath.utils.residues)</a>
+        <li><a href="api/pypath.core.annot.GOIntercell.html#pypath.core.annot.GOIntercell.to_set">(pypath.core.annot.GOIntercell method)</a>
 </li>
-      </ul></li>
-      <li><a href="api/pypath.utils.pdb.Residue.html#pypath.utils.pdb.Residue.resnum">resnum (pypath.utils.pdb.Residue attribute)</a>
+        <li><a href="api/pypath.core.annot.Gpcrdb.html#pypath.core.annot.Gpcrdb.to_set">(pypath.core.annot.Gpcrdb method)</a>
 </li>
-      <li><a href="api/pypath.utils.seq.Resource.html#pypath.utils.seq.Resource">Resource (class in pypath.utils.seq)</a>
+        <li><a href="api/pypath.core.annot.GuideToPharmacology.html#pypath.core.annot.GuideToPharmacology.to_set">(pypath.core.annot.GuideToPharmacology method)</a>
 </li>
-      <li><a href="api/pypath.inputs.pathwaycommons.PathwayCommonsInteraction.html#pypath.inputs.pathwaycommons.PathwayCommonsInteraction.resource">resource (pypath.inputs.pathwaycommons.PathwayCommonsInteraction attribute)</a>
+        <li><a href="api/pypath.core.annot.Hgnc.html#pypath.core.annot.Hgnc.to_set">(pypath.core.annot.Hgnc method)</a>
 </li>
-      <li><a href="api/pypath.internals.input_formats.UniprotMapping.html#pypath.internals.input_formats.UniprotMapping.resource_id_type">resource_id_type() (pypath.internals.input_formats.UniprotMapping static method)</a>
+        <li><a href="api/pypath.core.annot.HpmrComplex.html#pypath.core.annot.HpmrComplex.to_set">(pypath.core.annot.HpmrComplex method)</a>
 </li>
-      <li><a href="api/pypath.internals.resource.ResourceAttributes.html#pypath.internals.resource.ResourceAttributes">ResourceAttributes (class in pypath.internals.resource)</a>
+        <li><a href="api/pypath.core.annot.HPO.html#pypath.core.annot.HPO.to_set">(pypath.core.annot.HPO method)</a>
 </li>
-      <li><a href="api/pypath.resources.controller.ResourceController.html#pypath.resources.controller.ResourceController">ResourceController (class in pypath.resources.controller)</a>
+        <li><a href="api/pypath.core.annot.Humancellmap.html#pypath.core.annot.Humancellmap.to_set">(pypath.core.annot.Humancellmap method)</a>
 </li>
-  </ul></td>
-</tr></table>
-
-<h2 id="S">S</h2>
-<table style="width: 100%" class="indextable genindextable"><tr>
-  <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="api/pypath.inputs.science.science_download.html#pypath.inputs.science.science_download">science_download() (in module pypath.inputs.science)</a>
+        <li><a href="api/pypath.core.annot.HumanPlasmaMembraneReceptome.html#pypath.core.annot.HumanPlasmaMembraneReceptome.to_set">(pypath.core.annot.HumanPlasmaMembraneReceptome method)</a>
 </li>
-      <li><a href="api/pypath.inputs.hmdb.structures.sdf.html#pypath.inputs.hmdb.structures.sdf">sdf() (in module pypath.inputs.hmdb.structures)</a>
+        <li><a href="api/pypath.core.annot.HumanProteinAtlas.html#pypath.core.annot.HumanProteinAtlas.to_set">(pypath.core.annot.HumanProteinAtlas method)</a>
 </li>
-      <li><a href="api/pypath.resources.controller.ResourceController.html#pypath.resources.controller.ResourceController.secondary_resources">secondary_resources() (pypath.resources.controller.ResourceController method)</a>
+        <li><a href="api/pypath.core.annot.HumanProteinAtlasSecretome.html#pypath.core.annot.HumanProteinAtlasSecretome.to_set">(pypath.core.annot.HumanProteinAtlasSecretome method)</a>
 </li>
-      <li><a href="api/pypath.utils.pdb.Segment.html#pypath.utils.pdb.Segment">Segment (class in pypath.utils.pdb)</a>
+        <li><a href="api/pypath.core.annot.HumanProteinAtlasSubcellular.html#pypath.core.annot.HumanProteinAtlasSubcellular.to_set">(pypath.core.annot.HumanProteinAtlasSubcellular method)</a>
 </li>
-      <li><a href="api/pypath.utils.reflists.select.html#pypath.utils.reflists.select">select() (in module pypath.utils.reflists)</a>
-
-      <ul>
-        <li><a href="api/pypath.utils.go.GOAnnotation.html#pypath.utils.go.GOAnnotation.select">(pypath.utils.go.GOAnnotation method)</a>
+        <li><a href="api/pypath.core.annot.Icellnet.html#pypath.core.annot.Icellnet.to_set">(pypath.core.annot.Icellnet method)</a>
 </li>
-        <li><a href="api/pypath.utils.reflists.ReferenceListManager.html#pypath.utils.reflists.ReferenceListManager.select">(pypath.utils.reflists.ReferenceListManager method)</a>
+        <li><a href="api/pypath.core.annot.IcellnetComplex.html#pypath.core.annot.IcellnetComplex.to_set">(pypath.core.annot.IcellnetComplex method)</a>
 </li>
-      </ul></li>
-      <li><a href="api/pypath.utils.go.GOAnnotation.html#pypath.utils.go.GOAnnotation.select_by_all">select_by_all() (pypath.utils.go.GOAnnotation method)</a>
+        <li><a href="api/pypath.core.annot.Integrins.html#pypath.core.annot.Integrins.to_set">(pypath.core.annot.Integrins method)</a>
 </li>
-      <li><a href="api/pypath.utils.go.GOAnnotation.html#pypath.utils.go.GOAnnotation.select_by_expr">select_by_expr() (pypath.utils.go.GOAnnotation method)</a>
+        <li><a href="api/pypath.core.annot.InterPro.html#pypath.core.annot.InterPro.to_set">(pypath.core.annot.InterPro method)</a>
 </li>
-      <li><a href="api/pypath.utils.go.GOAnnotation.html#pypath.utils.go.GOAnnotation.select_by_expr_terms">select_by_expr_terms() (pypath.utils.go.GOAnnotation method)</a>
+        <li><a href="api/pypath.core.annot.Intogen.html#pypath.core.annot.Intogen.to_set">(pypath.core.annot.Intogen method)</a>
 </li>
-      <li><a href="api/pypath.utils.go.GOAnnotation.html#pypath.utils.go.GOAnnotation.select_by_name">select_by_name() (pypath.utils.go.GOAnnotation method)</a>
+        <li><a href="api/pypath.core.annot.Italk.html#pypath.core.annot.Italk.to_set">(pypath.core.annot.Italk method)</a>
 </li>
-      <li><a href="api/pypath.utils.go.GOAnnotation.html#pypath.utils.go.GOAnnotation.select_by_term">select_by_term() (pypath.utils.go.GOAnnotation method)</a>
+        <li><a href="api/pypath.core.annot.KeggPathways.html#pypath.core.annot.KeggPathways.to_set">(pypath.core.annot.KeggPathways method)</a>
 </li>
-      <li><a href="api/pypath.utils.seq.Seq.html#pypath.utils.seq.Seq">Seq (class in pypath.utils.seq)</a>
+        <li><a href="api/pypath.core.annot.KeggPathwaysPC.html#pypath.core.annot.KeggPathwaysPC.to_set">(pypath.core.annot.KeggPathwaysPC method)</a>
 </li>
-      <li><a href="api/pypath.inputs.uniprot.UniprotRecordHistory.html#pypath.inputs.uniprot.UniprotRecordHistory.sequence_version">sequence_version (pypath.inputs.uniprot.UniprotRecordHistory attribute)</a>
+        <li><a href="api/pypath.core.annot.Kinasedotcom.html#pypath.core.annot.Kinasedotcom.to_set">(pypath.core.annot.Kinasedotcom method)</a>
 </li>
-      <li><a href="api/pypath.core.attrs.AttributeHandler.html#pypath.core.attrs.AttributeHandler.serialize">serialize() (pypath.core.attrs.AttributeHandler method)</a>
+        <li><a href="api/pypath.core.annot.Kirouac2010.html#pypath.core.annot.Kirouac2010.to_set">(pypath.core.annot.Kirouac2010 method)</a>
 </li>
-      <li><a href="api/pypath.share.curl.Curl.html#pypath.share.curl.Curl.set_binary_data">set_binary_data() (pypath.share.curl.Curl method)</a>
+        <li><a href="api/pypath.core.annot.Lambert2018.html#pypath.core.annot.Lambert2018.to_set">(pypath.core.annot.Lambert2018 method)</a>
 </li>
-      <li><a href="api/pypath.share.progress.Progress.html#pypath.share.progress.Progress.set_done">set_done() (pypath.share.progress.Progress method)</a>
+        <li><a href="api/pypath.core.annot.LigandReceptor.html#pypath.core.annot.LigandReceptor.to_set">(pypath.core.annot.LigandReceptor method)</a>
 </li>
-      <li><a href="api/pypath.internals.resource.AbstractResource.html#pypath.internals.resource.AbstractResource.set_method">set_method() (pypath.internals.resource.AbstractResource method)</a>
+        <li><a href="api/pypath.core.annot.Locate.html#pypath.core.annot.Locate.to_set">(pypath.core.annot.Locate method)</a>
 </li>
-      <li><a href="api/pypath.utils.go.GeneOntology.html#pypath.utils.go.GeneOntology.set_of">set_of() (pypath.utils.go.GeneOntology method)</a>
+        <li><a href="api/pypath.core.annot.Lrdb.html#pypath.core.annot.Lrdb.to_set">(pypath.core.annot.Lrdb method)</a>
 </li>
-      <li><a href="api/pypath.utils.go.GeneOntology.html#pypath.utils.go.GeneOntology.set_of_names">set_of_names() (pypath.utils.go.GeneOntology method)</a>
+        <li><a href="api/pypath.core.annot.Matrisome.html#pypath.core.annot.Matrisome.to_set">(pypath.core.annot.Matrisome method)</a>
 </li>
-      <li><a href="api/pypath.utils.go.GeneOntology.html#pypath.utils.go.GeneOntology.set_of_terms">set_of_terms() (pypath.utils.go.GeneOntology method)</a>
+        <li><a href="api/pypath.core.annot.Matrixdb.html#pypath.core.annot.Matrixdb.to_set">(pypath.core.annot.Matrixdb method)</a>
 </li>
-      <li><a href="api/pypath.share.progress.Progress.html#pypath.share.progress.Progress.set_status">set_status() (pypath.share.progress.Progress method)</a>
+        <li><a href="api/pypath.core.annot.Mcam.html#pypath.core.annot.Mcam.to_set">(pypath.core.annot.Mcam method)</a>
 </li>
-      <li><a href="api/pypath.share.progress.Progress.html#pypath.share.progress.Progress.set_total">set_total() (pypath.share.progress.Progress method)</a>
+        <li><a href="api/pypath.core.annot.Membranome.html#pypath.core.annot.Membranome.to_set">(pypath.core.annot.Membranome method)</a>
 </li>
-      <li><a href="api/pypath.internals.resource.NetworkDataset.html#pypath.internals.resource.NetworkDataset.setdefault">setdefault() (pypath.internals.resource.NetworkDataset method)</a>
+        <li><a href="api/pypath.core.annot.Msigdb.html#pypath.core.annot.Msigdb.to_set">(pypath.core.annot.Msigdb method)</a>
 </li>
-      <li><a href="api/pypath.utils.taxonomy.short_latin_names.html#pypath.utils.taxonomy.short_latin_names">short_latin_names() (in module pypath.utils.taxonomy)</a>
+        <li><a href="api/pypath.core.annot.NetpathPathways.html#pypath.core.annot.NetpathPathways.to_set">(pypath.core.annot.NetpathPathways method)</a>
 </li>
-      <li><a href="api/pypath.utils.taxonomy.shorten_latin_name.html#pypath.utils.taxonomy.shorten_latin_name">shorten_latin_name() (in module pypath.utils.taxonomy)</a>
+        <li><a href="api/pypath.core.annot.Opm.html#pypath.core.annot.Opm.to_set">(pypath.core.annot.Opm method)</a>
 </li>
-  </ul></td>
-  <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="api/pypath.inputs.hmdb.visual.show_structure.html#pypath.inputs.hmdb.visual.show_structure">show_structure() (in module pypath.inputs.hmdb.visual)</a>
+        <li><a href="api/pypath.core.annot.Panglaodb.html#pypath.core.annot.Panglaodb.to_set">(pypath.core.annot.Panglaodb method)</a>
 </li>
-      <li><a href="api/pypath.inputs.sider.SiderSideeffect.html#pypath.inputs.sider.SiderSideeffect.side_effect">side_effect (pypath.inputs.sider.SiderSideeffect attribute)</a>
-
-      <ul>
-        <li><a href="api/pypath.inputs.sider.SiderSideeffetFrequency.html#pypath.inputs.sider.SiderSideeffetFrequency.side_effect">(pypath.inputs.sider.SiderSideeffetFrequency attribute)</a>
+        <li><a href="api/pypath.core.annot.Phobius.html#pypath.core.annot.Phobius.to_set">(pypath.core.annot.Phobius method)</a>
 </li>
-      </ul></li>
-      <li><a href="api/pypath.inputs.sider.SiderSideeffectMeddra.html#pypath.inputs.sider.SiderSideeffectMeddra.side_effect_name">side_effect_name (pypath.inputs.sider.SiderSideeffectMeddra attribute)</a>
+        <li><a href="api/pypath.core.annot.Phosphatome.html#pypath.core.annot.Phosphatome.to_set">(pypath.core.annot.Phosphatome method)</a>
 </li>
-      <li><a href="api/pypath.inputs.sider.sider_drug_names.html#pypath.inputs.sider.sider_drug_names">sider_drug_names() (in module pypath.inputs.sider)</a>
+        <li><a href="api/pypath.core.annot.Progeny.html#pypath.core.annot.Progeny.to_set">(pypath.core.annot.Progeny method)</a>
 </li>
-      <li><a href="api/pypath.inputs.sider.sider_meddra_side_effects.html#pypath.inputs.sider.sider_meddra_side_effects">sider_meddra_side_effects() (in module pypath.inputs.sider)</a>
+        <li><a href="api/pypath.core.annot.Ramilowski2015.html#pypath.core.annot.Ramilowski2015.to_set">(pypath.core.annot.Ramilowski2015 method)</a>
 </li>
-      <li><a href="api/pypath.inputs.sider.sider_side_effect_frequencies.html#pypath.inputs.sider.sider_side_effect_frequencies">sider_side_effect_frequencies() (in module pypath.inputs.sider)</a>
+        <li><a href="api/pypath.core.annot.Ramilowski2015Location.html#pypath.core.annot.Ramilowski2015Location.to_set">(pypath.core.annot.Ramilowski2015Location method)</a>
 </li>
-      <li><a href="api/pypath.inputs.sider.sider_side_effects.html#pypath.inputs.sider.sider_side_effects">sider_side_effects() (in module pypath.inputs.sider)</a>
+        <li><a href="api/pypath.core.annot.Scconnect.html#pypath.core.annot.Scconnect.to_set">(pypath.core.annot.Scconnect method)</a>
 </li>
-      <li><a href="api/pypath.inputs.sider.SiderDrug.html#pypath.inputs.sider.SiderDrug">SiderDrug (class in pypath.inputs.sider)</a>
+        <li><a href="api/pypath.core.annot.ScconnectComplex.html#pypath.core.annot.ScconnectComplex.to_set">(pypath.core.annot.ScconnectComplex method)</a>
 </li>
-      <li><a href="api/pypath.inputs.sider.SiderSideeffect.html#pypath.inputs.sider.SiderSideeffect">SiderSideeffect (class in pypath.inputs.sider)</a>
+        <li><a href="api/pypath.core.annot.SignalinkFunctions.html#pypath.core.annot.SignalinkFunctions.to_set">(pypath.core.annot.SignalinkFunctions method)</a>
 </li>
-      <li><a href="api/pypath.inputs.sider.SiderSideeffectMeddra.html#pypath.inputs.sider.SiderSideeffectMeddra">SiderSideeffectMeddra (class in pypath.inputs.sider)</a>
+        <li><a href="api/pypath.core.annot.SignalinkPathways.html#pypath.core.annot.SignalinkPathways.to_set">(pypath.core.annot.SignalinkPathways method)</a>
 </li>
-      <li><a href="api/pypath.inputs.sider.SiderSideeffetFrequency.html#pypath.inputs.sider.SiderSideeffetFrequency">SiderSideeffetFrequency (class in pypath.inputs.sider)</a>
+        <li><a href="api/pypath.core.annot.SignorPathways.html#pypath.core.annot.SignorPathways.to_set">(pypath.core.annot.SignorPathways method)</a>
 </li>
-      <li><a href="api/pypath.utils.unichem.Unichem.html#pypath.utils.unichem.Unichem.smiles2chembl">smiles2chembl() (pypath.utils.unichem.Unichem method)</a>
+        <li><a href="api/pypath.core.annot.Surfaceome.html#pypath.core.annot.Surfaceome.to_set">(pypath.core.annot.Surfaceome method)</a>
 </li>
-      <li><a href="api/pypath.share.progress.Progress.html#pypath.share.progress.Progress.step">step() (pypath.share.progress.Progress method)</a>
+        <li><a href="api/pypath.core.annot.Talklr.html#pypath.core.annot.Talklr.to_set">(pypath.core.annot.Talklr method)</a>
 </li>
-      <li><a href="api/pypath.inputs.stitch.stitch_actions_interactions.html#pypath.inputs.stitch.stitch_actions_interactions">stitch_actions_interactions() (in module pypath.inputs.stitch)</a>
+        <li><a href="api/pypath.core.annot.Tcdb.html#pypath.core.annot.Tcdb.to_set">(pypath.core.annot.Tcdb method)</a>
 </li>
-      <li><a href="api/pypath.inputs.stitch.stitch_links_interactions.html#pypath.inputs.stitch.stitch_links_interactions">stitch_links_interactions() (in module pypath.inputs.stitch)</a>
+        <li><a href="api/pypath.core.annot.Tfcensus.html#pypath.core.annot.Tfcensus.to_set">(pypath.core.annot.Tfcensus method)</a>
 </li>
-      <li><a href="api/pypath.inputs.string.string_effects.html#pypath.inputs.string.string_effects">string_effects() (in module pypath.inputs.string)</a>
+        <li><a href="api/pypath.core.annot.Topdb.html#pypath.core.annot.Topdb.to_set">(pypath.core.annot.Topdb method)</a>
 </li>
-      <li><a href="api/pypath.inputs.string.string_links_interactions.html#pypath.inputs.string.string_links_interactions">string_links_interactions() (in module pypath.inputs.string)</a>
+        <li><a href="api/pypath.core.annot.UniprotFamilies.html#pypath.core.annot.UniprotFamilies.to_set">(pypath.core.annot.UniprotFamilies method)</a>
 </li>
-      <li><a href="api/pypath.inputs.string.string_physical_interactions.html#pypath.inputs.string.string_physical_interactions">string_physical_interactions() (in module pypath.inputs.string)</a>
+        <li><a href="api/pypath.core.annot.UniprotKeywords.html#pypath.core.annot.UniprotKeywords.to_set">(pypath.core.annot.UniprotKeywords method)</a>
 </li>
-      <li><a href="api/pypath.inputs.string.string_species.html#pypath.inputs.string.string_species">string_species() (in module pypath.inputs.string)</a>
+        <li><a href="api/pypath.core.annot.UniprotLocations.html#pypath.core.annot.UniprotLocations.to_set">(pypath.core.annot.UniprotLocations method)</a>
 </li>
-      <li><a href="api/pypath.inputs.hmdb.visual.structure_svg.html#pypath.inputs.hmdb.visual.structure_svg">structure_svg() (in module pypath.inputs.hmdb.visual)</a>
+        <li><a href="api/pypath.core.annot.UniprotTissues.html#pypath.core.annot.UniprotTissues.to_set">(pypath.core.annot.UniprotTissues method)</a>
 </li>
-      <li><a href="api/pypath.utils.go.GeneOntology.html#pypath.utils.go.GeneOntology.subgraph_nodes">subgraph_nodes() (pypath.utils.go.GeneOntology method)</a>
+        <li><a href="api/pypath.core.annot.UniprotTopologies.html#pypath.core.annot.UniprotTopologies.to_set">(pypath.core.annot.UniprotTopologies method)</a>
 </li>
-      <li><a href="api/pypath.inputs.uniprot.swissprot_deleted.html#pypath.inputs.uniprot.swissprot_deleted">swissprot_deleted() (in module pypath.inputs.uniprot)</a>
+        <li><a href="api/pypath.core.annot.Vesiclepedia.html#pypath.core.annot.Vesiclepedia.to_set">(pypath.core.annot.Vesiclepedia method)</a>
 </li>
-      <li><a href="api/pypath.utils.seq.swissprot_seq.html#pypath.utils.seq.swissprot_seq">swissprot_seq() (in module pypath.utils.seq)</a>
+        <li><a href="api/pypath.core.annot.Wang.html#pypath.core.annot.Wang.to_set">(pypath.core.annot.Wang method)</a>
 </li>
-      <li><a href="api/pypath.inputs.adrecs.AdrecsDrug.html#pypath.inputs.adrecs.AdrecsDrug.synonyms">synonyms (pypath.inputs.adrecs.AdrecsDrug attribute)</a>
-
-      <ul>
-        <li><a href="api/pypath.inputs.adrecs.AdrecsTerm.html#pypath.inputs.adrecs.AdrecsTerm.synonyms">(pypath.inputs.adrecs.AdrecsTerm attribute)</a>
+        <li><a href="api/pypath.core.annot.Zhong2015.html#pypath.core.annot.Zhong2015.to_set">(pypath.core.annot.Zhong2015 method)</a>
 </li>
       </ul></li>
-  </ul></td>
-</tr></table>
-
-<h2 id="T">T</h2>
-<table style="width: 100%" class="indextable genindextable"><tr>
-  <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="api/pypath.inputs.hmdb.common.table.html#pypath.inputs.hmdb.common.table">table() (in module pypath.inputs.hmdb.common)</a>
-
-      <ul>
-        <li><a href="api/pypath.inputs.hmdb.metabolites.table.html#pypath.inputs.hmdb.metabolites.table">(in module pypath.inputs.hmdb.metabolites)</a>
+      <li><a href="api/pypath.core.annot.Topdb.html#pypath.core.annot.Topdb">Topdb (class in pypath.core.annot)</a>
 </li>
-        <li><a href="api/pypath.inputs.hmdb.proteins.table.html#pypath.inputs.hmdb.proteins.table">(in module pypath.inputs.hmdb.proteins)</a>
+      <li><a href="api/pypath.inputs.topdb.topdb_annotations.html#pypath.inputs.topdb.topdb_annotations">topdb_annotations() (in module pypath.inputs.topdb)</a>
 </li>
-      </ul></li>
-      <li><a href="api/pypath.inputs.trip.take_a_trip.html#pypath.inputs.trip.take_a_trip">take_a_trip() (in module pypath.inputs.trip)</a>
+      <li><a href="api/pypath.core.network.NetworkStatsRecord.html#pypath.core.network.NetworkStatsRecord.total">total (pypath.core.network.NetworkStatsRecord attribute)</a>
 </li>
-      <li><a href="api/pypath.visual.igraph_drawing.edge.TaperedEdgeDrawer.html#pypath.visual.igraph_drawing.edge.TaperedEdgeDrawer">TaperedEdgeDrawer (class in pypath.visual.igraph_drawing.edge)</a>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.transcription">transcription() (pypath.core.network.Network class method)</a>
 </li>
-      <li><a href="api/pypath.inputs.dorothea.DorotheaInteraction.html#pypath.inputs.dorothea.DorotheaInteraction.target">target (pypath.inputs.dorothea.DorotheaInteraction attribute)</a>
+      <li><a href="api/pypath.resources.data_formats.transcription_deprecated.html#pypath.resources.data_formats.transcription_deprecated">transcription_deprecated (in module pypath.resources.data_formats)</a>
 </li>
-      <li><a href="api/pypath.utils.taxonomy.taxid_from_common_name.html#pypath.utils.taxonomy.taxid_from_common_name">taxid_from_common_name() (in module pypath.utils.taxonomy)</a>
+      <li><a href="api/pypath.resources.data_formats.transcription_onebyone.html#pypath.resources.data_formats.transcription_onebyone">transcription_onebyone (in module pypath.resources.data_formats)</a>
 </li>
-      <li><a href="api/pypath.utils.taxonomy.taxid_from_dbptm_taxon_name.html#pypath.utils.taxonomy.taxid_from_dbptm_taxon_name">taxid_from_dbptm_taxon_name() (in module pypath.utils.taxonomy)</a>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.transcriptionally_activated_by">transcriptionally_activated_by (pypath.core.network.Network attribute)</a>
 </li>
-      <li><a href="api/pypath.utils.taxonomy.taxid_from_ensembl_name.html#pypath.utils.taxonomy.taxid_from_ensembl_name">taxid_from_ensembl_name() (in module pypath.utils.taxonomy)</a>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.transcriptionally_activates">transcriptionally_activates (pypath.core.network.Network attribute)</a>
 </li>
-      <li><a href="api/pypath.utils.taxonomy.taxid_from_latin_name.html#pypath.utils.taxonomy.taxid_from_latin_name">taxid_from_latin_name() (in module pypath.utils.taxonomy)</a>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.transcriptionally_regulated_by">transcriptionally_regulated_by (pypath.core.network.Network attribute)</a>
 </li>
-      <li><a href="api/pypath.utils.taxonomy.taxid_from_nonstandard.html#pypath.utils.taxonomy.taxid_from_nonstandard">taxid_from_nonstandard() (in module pypath.utils.taxonomy)</a>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.transcriptionally_regulates">transcriptionally_regulates (pypath.core.network.Network attribute)</a>
 </li>
-      <li><a href="api/pypath.inputs.uniprot.Taxon.html#pypath.inputs.uniprot.Taxon">Taxon (class in pypath.inputs.uniprot)</a>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.transcriptionally_suppressed_by">transcriptionally_suppressed_by (pypath.core.network.Network attribute)</a>
 </li>
-      <li><a href="api/pypath.inputs.adrecs.AdrecsDrug.html#pypath.inputs.adrecs.AdrecsDrug.tdd">tdd (pypath.inputs.adrecs.AdrecsDrug attribute)</a>
+      <li><a href="api/pypath.core.network.Network.html#pypath.core.network.Network.transcriptionally_suppresses">transcriptionally_suppresses (pypath.core.network.Network attribute)</a>
 </li>
-      <li><a href="api/pypath.share.progress.Progress.html#pypath.share.progress.Progress.terminate">terminate() (pypath.share.progress.Progress method)</a>
+      <li><a href="api/pypath.utils.orthology.translate.html#pypath.utils.orthology.translate">translate() (in module pypath.utils.orthology)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.enz_sub.EnzymeSubstrateOrthologyProcessor.html#pypath.core.enz_sub.EnzymeSubstrateOrthologyProcessor.translate">(pypath.core.enz_sub.EnzymeSubstrateOrthologyProcessor method)</a>
 </li>
-      <li><a href="api/pypath.utils.go.GeneOntology.html#pypath.utils.go.GeneOntology.terms_to_names">terms_to_names() (pypath.utils.go.GeneOntology method)</a>
+        <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.translate">(pypath.core.interaction.Interaction method)</a>
 </li>
-      <li><a href="api/pypath.utils.go.GeneOntology.html#pypath.utils.go.GeneOntology.terms_to_names_aspects">terms_to_names_aspects() (pypath.utils.go.GeneOntology method)</a>
+        <li><a href="api/pypath.utils.orthology.EnsemblOrthology.html#pypath.utils.orthology.EnsemblOrthology.translate">(pypath.utils.orthology.EnsemblOrthology method)</a>
 </li>
-      <li><a href="api/pypath.visual.igraph_drawing.TextDrawer.html#pypath.visual.igraph_drawing.TextDrawer">TextDrawer (in module pypath.visual.igraph_drawing)</a>
+        <li><a href="api/pypath.utils.orthology.HomologeneOrthology.html#pypath.utils.orthology.HomologeneOrthology.translate">(pypath.utils.orthology.HomologeneOrthology method)</a>
 </li>
-      <li><a href="api/pypath.inputs.diseases.textmining_filtered.html#pypath.inputs.diseases.textmining_filtered">textmining_filtered() (in module pypath.inputs.diseases)</a>
+        <li><a href="api/pypath.utils.orthology.OmaOrthology.html#pypath.utils.orthology.OmaOrthology.translate">(pypath.utils.orthology.OmaOrthology method)</a>
 </li>
-      <li><a href="api/pypath.inputs.diseases.textmining_full.html#pypath.inputs.diseases.textmining_full">textmining_full() (in module pypath.inputs.diseases)</a>
+        <li><a href="api/pypath.utils.orthology.OrthologyManager.html#pypath.utils.orthology.OrthologyManager.translate">(pypath.utils.orthology.OrthologyManager method)</a>
 </li>
-      <li><a href="api/pypath.inputs.dorothea.DorotheaInteraction.html#pypath.inputs.dorothea.DorotheaInteraction.tf">tf (pypath.inputs.dorothea.DorotheaInteraction attribute)</a>
+        <li><a href="api/pypath.utils.orthology.ProteinOrthology.html#pypath.utils.orthology.ProteinOrthology.translate">(pypath.utils.orthology.ProteinOrthology method)</a>
 </li>
-  </ul></td>
-  <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="api/pypath.inputs.dorothea.tfregulons_interactions.html#pypath.inputs.dorothea.tfregulons_interactions">tfregulons_interactions() (in module pypath.inputs.dorothea)</a>
+        <li><a href="api/pypath.utils.orthology.PtmOrthology.html#pypath.utils.orthology.PtmOrthology.translate">(pypath.utils.orthology.PtmOrthology method)</a>
 </li>
-      <li><a href="api/pypath.inputs.dorothea.tfregulons_interactions_old.html#pypath.inputs.dorothea.tfregulons_interactions_old">tfregulons_interactions_old() (in module pypath.inputs.dorothea)</a>
+        <li><a href="api/pypath.utils.unichem.Unichem.html#pypath.utils.unichem.Unichem.translate">(pypath.utils.unichem.Unichem method)</a>
 </li>
-      <li><a href="api/pypath.utils.proteomicsdb.ProteomicsDB.html#pypath.utils.proteomicsdb.ProteomicsDB.tissues_x_proteins">tissues_x_proteins() (pypath.utils.proteomicsdb.ProteomicsDB method)</a>
+      </ul></li>
+      <li><a href="api/pypath.utils.mapping.Mapper.html#pypath.utils.mapping.Mapper.translate_deleted_uniprot_by_genesymbol">translate_deleted_uniprot_by_genesymbol() (pypath.utils.mapping.Mapper method)</a>
 </li>
-      <li><a href="api/pypath.internals.license.LicenseAttrib.html#pypath.internals.license.LicenseAttrib.to_int">to_int() (pypath.internals.license.LicenseAttrib method)</a>
+      <li><a href="api/pypath.utils.orthology.translate_df.html#pypath.utils.orthology.translate_df">translate_df() (in module pypath.utils.orthology)</a>
 
       <ul>
-        <li><a href="api/pypath.internals.license.LicenseFeature.html#pypath.internals.license.LicenseFeature.to_int">(pypath.internals.license.LicenseFeature method)</a>
+        <li><a href="api/pypath.utils.orthology.EnsemblOrthology.html#pypath.utils.orthology.EnsemblOrthology.translate_df">(pypath.utils.orthology.EnsemblOrthology method)</a>
 </li>
-        <li><a href="api/pypath.internals.license.LicensePurpose.html#pypath.internals.license.LicensePurpose.to_int">(pypath.internals.license.LicensePurpose method)</a>
+        <li><a href="api/pypath.utils.orthology.HomologeneOrthology.html#pypath.utils.orthology.HomologeneOrthology.translate_df">(pypath.utils.orthology.HomologeneOrthology method)</a>
 </li>
-        <li><a href="api/pypath.internals.license.LicenseSharing.html#pypath.internals.license.LicenseSharing.to_int">(pypath.internals.license.LicenseSharing method)</a>
+        <li><a href="api/pypath.utils.orthology.OmaOrthology.html#pypath.utils.orthology.OmaOrthology.translate_df">(pypath.utils.orthology.OmaOrthology method)</a>
+</li>
+        <li><a href="api/pypath.utils.orthology.OrthologyManager.html#pypath.utils.orthology.OrthologyManager.translate_df">(pypath.utils.orthology.OrthologyManager method)</a>
+</li>
+        <li><a href="api/pypath.utils.orthology.ProteinOrthology.html#pypath.utils.orthology.ProteinOrthology.translate_df">(pypath.utils.orthology.ProteinOrthology method)</a>
 </li>
       </ul></li>
-      <li><a href="api/pypath.resources.data_formats.transcription_deprecated.html#pypath.resources.data_formats.transcription_deprecated">transcription_deprecated (in module pypath.resources.data_formats)</a>
+      <li><a href="api/pypath.core.enz_sub.EnzymeSubstrateOrthologyProcessor.html#pypath.core.enz_sub.EnzymeSubstrateOrthologyProcessor.translate_site">translate_site() (pypath.core.enz_sub.EnzymeSubstrateOrthologyProcessor method)</a>
+
+      <ul>
+        <li><a href="api/pypath.utils.orthology.PtmOrthology.html#pypath.utils.orthology.PtmOrthology.translate_site">(pypath.utils.orthology.PtmOrthology method)</a>
 </li>
-      <li><a href="api/pypath.resources.data_formats.transcription_onebyone.html#pypath.resources.data_formats.transcription_onebyone">transcription_onebyone (in module pypath.resources.data_formats)</a>
+      </ul></li>
+      <li><a href="api/pypath.utils.mapping.translation_df.html#pypath.utils.mapping.translation_df">translation_df() (in module pypath.utils.mapping)</a>
+
+      <ul>
+        <li><a href="api/pypath.utils.mapping.Mapper.html#pypath.utils.mapping.Mapper.translation_df">(pypath.utils.mapping.Mapper method)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.utils.mapping.translation_dict.html#pypath.utils.mapping.translation_dict">translation_dict() (in module pypath.utils.mapping)</a>
+
+      <ul>
+        <li><a href="api/pypath.utils.mapping.Mapper.html#pypath.utils.mapping.Mapper.translation_dict">(pypath.utils.mapping.Mapper method)</a>
 </li>
-      <li><a href="api/pypath.utils.unichem.Unichem.html#pypath.utils.unichem.Unichem.translate">translate() (pypath.utils.unichem.Unichem method)</a>
+      </ul></li>
+      <li><a href="api/pypath.inputs.cellphonedb.CellPhoneDBAnnotation.html#pypath.inputs.cellphonedb.CellPhoneDBAnnotation.transmembrane">transmembrane (pypath.inputs.cellphonedb.CellPhoneDBAnnotation attribute)</a>
 </li>
       <li><a href="api/pypath.inputs.transmir.transmir_interactions.html#pypath.inputs.transmir.transmir_interactions">transmir_interactions() (in module pypath.inputs.transmir)</a>
+</li>
+      <li><a href="api/pypath.internals.annot_formats.AnnotDef.html#pypath.internals.annot_formats.AnnotDef.transmitter">transmitter (pypath.internals.annot_formats.AnnotDef attribute)</a>
 </li>
       <li><a href="api/pypath.inputs.uniprot.trembl_deleted.html#pypath.inputs.uniprot.trembl_deleted">trembl_deleted() (in module pypath.inputs.uniprot)</a>
+</li>
+      <li><a href="api/pypath.utils.mapping.Mapper.html#pypath.utils.mapping.Mapper.trembl_swissprot">trembl_swissprot() (pypath.utils.mapping.Mapper method)</a>
 </li>
       <li><a href="api/pypath.inputs.trip.trip_find_uniprot.html#pypath.inputs.trip.trip_find_uniprot">trip_find_uniprot() (in module pypath.inputs.trip)</a>
 </li>
@@ -3832,8 +16351,28 @@ <h2 id="T">T</h2>
       <li><a href="api/pypath.inputs.trrust.trrust_interactions.html#pypath.inputs.trrust.trrust_interactions">trrust_interactions() (in module pypath.inputs.trrust)</a>
 </li>
       <li><a href="api/pypath.inputs.trrust.trrust_mouse.html#pypath.inputs.trrust.trrust_mouse">trrust_mouse() (in module pypath.inputs.trrust)</a>
+</li>
+      <li><a href="api/pypath.omnipath.server.run.twisted_listen_tcp.html#pypath.omnipath.server.run.twisted_listen_tcp">twisted_listen_tcp() (in module pypath.omnipath.server.run)</a>
+</li>
+      <li><a href="api/pypath.omnipath.server.run.twisted_run.html#pypath.omnipath.server.run.twisted_run">twisted_run() (in module pypath.omnipath.server.run)</a>
+</li>
+      <li><a href="api/pypath.omnipath.server.run.TwistedWebResource.html#pypath.omnipath.server.run.TwistedWebResource">TwistedWebResource (class in pypath.omnipath.server.run)</a>
+</li>
+      <li><a href="api/pypath.omnipath.server.run.TwistedWebSite.html#pypath.omnipath.server.run.TwistedWebSite">TwistedWebSite (class in pypath.omnipath.server.run)</a>
 </li>
       <li><a href="api/pypath.inputs.twosides.twosides_interactions.html#pypath.inputs.twosides.twosides_interactions">twosides_interactions() (in module pypath.inputs.twosides)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.InteractionDataFrameRecord.html#pypath.core.interaction.InteractionDataFrameRecord.type">type (pypath.core.interaction.InteractionDataFrameRecord attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.inputs.cellinker.CellinkerInteraction.html#pypath.inputs.cellinker.CellinkerInteraction.type">(pypath.inputs.cellinker.CellinkerInteraction attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.core.interaction.InteractionDataFrameRecord.html#pypath.core.interaction.InteractionDataFrameRecord.type_a">type_a (pypath.core.interaction.InteractionDataFrameRecord attribute)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.InteractionDataFrameRecord.html#pypath.core.interaction.InteractionDataFrameRecord.type_b">type_b (pypath.core.interaction.InteractionDataFrameRecord attribute)</a>
+</li>
+      <li><a href="api/pypath.utils.orthology.EnsemblOrtholog.html#pypath.utils.orthology.EnsemblOrtholog.types">types (pypath.utils.orthology.EnsemblOrtholog attribute)</a>
 </li>
   </ul></td>
 </tr></table>
@@ -3853,6 +16392,8 @@ <h2 id="U">U</h2>
         <li><a href="api/pypath.inputs.sider.SiderSideeffetFrequency.html#pypath.inputs.sider.SiderSideeffetFrequency.umls_concept_on_label">(pypath.inputs.sider.SiderSideeffetFrequency attribute)</a>
 </li>
       </ul></li>
+      <li><a href="api/pypath.inputs.hpmr.HpmrInteraction.html#pypath.inputs.hpmr.HpmrInteraction.unambiguous">unambiguous (pypath.inputs.hpmr.HpmrInteraction attribute)</a>
+</li>
       <li><a href="api/pypath.utils.unichem.Unichem.html#pypath.utils.unichem.Unichem">Unichem (class in pypath.utils.unichem)</a>
 </li>
       <li><a href="api/pypath.inputs.unichem.unichem_info.html#pypath.inputs.unichem.unichem_info">unichem_info() (in module pypath.inputs.unichem)</a>
@@ -3869,6 +16410,12 @@ <h2 id="U">U</h2>
         <li><a href="api/pypath.utils.pdb.Segment.html#pypath.utils.pdb.Segment.uniprot">(pypath.utils.pdb.Segment attribute)</a>
 </li>
       </ul></li>
+      <li><a href="api/pypath.inputs.pisa.PisaBond.html#pypath.inputs.pisa.PisaBond.uniprot_1">uniprot_1 (pypath.inputs.pisa.PisaBond attribute)</a>
+</li>
+      <li><a href="api/pypath.inputs.pisa.PisaBond.html#pypath.inputs.pisa.PisaBond.uniprot_2">uniprot_2 (pypath.inputs.pisa.PisaBond attribute)</a>
+</li>
+      <li><a href="api/pypath.utils.mapping.Mapper.html#pypath.utils.mapping.Mapper.uniprot_cleanup">uniprot_cleanup() (pypath.utils.mapping.Mapper method)</a>
+</li>
       <li><a href="api/pypath.inputs.uniprot.uniprot_data.html#pypath.inputs.uniprot.uniprot_data">uniprot_data() (in module pypath.inputs.uniprot)</a>
 </li>
       <li><a href="api/pypath.inputs.uniprot.uniprot_deleted.html#pypath.inputs.uniprot.uniprot_deleted">uniprot_deleted() (in module pypath.inputs.uniprot)</a>
@@ -3880,6 +16427,8 @@ <h2 id="U">U</h2>
       <li><a href="api/pypath.inputs.uniprot.uniprot_history.html#pypath.inputs.uniprot.uniprot_history">uniprot_history() (in module pypath.inputs.uniprot)</a>
 </li>
       <li><a href="api/pypath.inputs.uniprot.uniprot_history_recent_datasheet.html#pypath.inputs.uniprot.uniprot_history_recent_datasheet">uniprot_history_recent_datasheet() (in module pypath.inputs.uniprot)</a>
+</li>
+      <li><a href="api/pypath.utils.mapping.UNIPROT_ID_TYPES.html#pypath.utils.mapping.UNIPROT_ID_TYPES">UNIPROT_ID_TYPES (in module pypath.utils.mapping)</a>
 </li>
       <li><a href="api/pypath.inputs.uniprot.uniprot_keywords.html#pypath.inputs.uniprot.uniprot_keywords">uniprot_keywords() (in module pypath.inputs.uniprot)</a>
 </li>
@@ -3889,8 +16438,6 @@ <h2 id="U">U</h2>
 </li>
       <li><a href="api/pypath.inputs.uniprot.uniprot_ncbi_taxids_2.html#pypath.inputs.uniprot.uniprot_ncbi_taxids_2">uniprot_ncbi_taxids_2() (in module pypath.inputs.uniprot)</a>
 </li>
-  </ul></td>
-  <td style="width: 33%; vertical-align: top;"><ul>
       <li><a href="api/pypath.inputs.uniprot.uniprot_preprocess.html#pypath.inputs.uniprot.uniprot_preprocess">uniprot_preprocess() (in module pypath.inputs.uniprot)</a>
 </li>
       <li><a href="api/pypath.inputs.uniprot.uniprot_query.html#pypath.inputs.uniprot.uniprot_query">uniprot_query() (in module pypath.inputs.uniprot)</a>
@@ -3908,14 +16455,36 @@ <h2 id="U">U</h2>
       <li><a href="api/pypath.inputs.uniprot.uniprot_topology.html#pypath.inputs.uniprot.uniprot_topology">uniprot_topology() (in module pypath.inputs.uniprot)</a>
 </li>
       <li><a href="api/pypath.inputs.humsavar.uniprot_variants.html#pypath.inputs.humsavar.uniprot_variants">uniprot_variants() (in module pypath.inputs.humsavar)</a>
+</li>
+  </ul></td>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="api/pypath.core.annot.UniprotFamilies.html#pypath.core.annot.UniprotFamilies">UniprotFamilies (class in pypath.core.annot)</a>
+</li>
+      <li><a href="api/pypath.core.annot.UniprotKeywords.html#pypath.core.annot.UniprotKeywords">UniprotKeywords (class in pypath.core.annot)</a>
 </li>
       <li><a href="api/pypath.internals.input_formats.UniprotListMapping.html#pypath.internals.input_formats.UniprotListMapping">UniprotListMapping (class in pypath.internals.input_formats)</a>
+</li>
+      <li><a href="api/pypath.core.annot.UniprotLocations.html#pypath.core.annot.UniprotLocations">UniprotLocations (class in pypath.core.annot)</a>
 </li>
       <li><a href="api/pypath.internals.input_formats.UniprotMapping.html#pypath.internals.input_formats.UniprotMapping">UniprotMapping (class in pypath.internals.input_formats)</a>
+</li>
+      <li><a href="api/pypath.utils.uniprot.UniprotProtein.html#pypath.utils.uniprot.UniprotProtein">UniprotProtein (class in pypath.utils.uniprot)</a>
 </li>
       <li><a href="api/pypath.inputs.uniprot.UniprotQuery.html#pypath.inputs.uniprot.UniprotQuery">UniprotQuery (class in pypath.inputs.uniprot)</a>
 </li>
       <li><a href="api/pypath.inputs.uniprot.UniprotRecordHistory.html#pypath.inputs.uniprot.UniprotRecordHistory">UniprotRecordHistory (class in pypath.inputs.uniprot)</a>
+</li>
+      <li><a href="api/pypath.core.annot.UniprotTissues.html#pypath.core.annot.UniprotTissues">UniprotTissues (class in pypath.core.annot)</a>
+</li>
+      <li><a href="api/pypath.core.annot.UniprotTopologies.html#pypath.core.annot.UniprotTopologies">UniprotTopologies (class in pypath.core.annot)</a>
+</li>
+      <li><a href="api/pypath.core.network.NetworkStatsRecord.html#pypath.core.network.NetworkStatsRecord.unique">unique (pypath.core.network.NetworkStatsRecord attribute)</a>
+</li>
+      <li><a href="api/pypath.core.enz_sub.EnzymeSubstrateAggregator.html#pypath.core.enz_sub.EnzymeSubstrateAggregator.unique">unique() (pypath.core.enz_sub.EnzymeSubstrateAggregator method)</a>
+</li>
+      <li><a href="api/pypath.core.network.NetworkStatsRecord.html#pypath.core.network.NetworkStatsRecord.unique_cat">unique_cat (pypath.core.network.NetworkStatsRecord attribute)</a>
+</li>
+      <li><a href="api/pypath.core.network.NetworkStatsRecord.html#pypath.core.network.NetworkStatsRecord.unique_res_cat">unique_res_cat (pypath.core.network.NetworkStatsRecord attribute)</a>
 </li>
       <li><a href="api/pypath.utils.seq.Pfam.html#pypath.utils.seq.Pfam.unload">unload() (pypath.utils.seq.Pfam method)</a>
 
@@ -3923,6 +16492,14 @@ <h2 id="U">U</h2>
         <li><a href="api/pypath.utils.seq.Resource.html#pypath.utils.seq.Resource.unload">(pypath.utils.seq.Resource method)</a>
 </li>
       </ul></li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.unset_dir">unset_dir() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.unset_direction">unset_direction() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.unset_interaction_type">unset_interaction_type() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.unset_sign">unset_sign() (pypath.core.interaction.Interaction method)</a>
+</li>
       <li><a href="api/pypath.internals.resource.NetworkDataset.html#pypath.internals.resource.NetworkDataset.update">update() (pypath.internals.resource.NetworkDataset method)</a>
 
       <ul>
@@ -3930,9 +16507,31 @@ <h2 id="U">U</h2>
 </li>
       </ul></li>
       <li><a href="api/pypath.core.attrs.AttributeHandler.html#pypath.core.attrs.AttributeHandler.update_attrs">update_attrs() (pypath.core.attrs.AttributeHandler method)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.entity.Entity.html#pypath.core.entity.Entity.update_attrs">(pypath.core.entity.Entity method)</a>
 </li>
-      <li><a href="api/pypath.inputs.uniprot.UniprotQuery.html#pypath.inputs.uniprot.UniprotQuery.url">url (pypath.inputs.uniprot.UniprotQuery property)</a>
+        <li><a href="api/pypath.core.evidence.Evidence.html#pypath.core.evidence.Evidence.update_attrs">(pypath.core.evidence.Evidence method)</a>
 </li>
+        <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.update_attrs">(pypath.core.interaction.Interaction method)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.utils.uniprot.update_databases.html#pypath.utils.uniprot.update_databases">update_databases() (in module pypath.utils.uniprot)</a>
+</li>
+      <li><a href="api/pypath.utils.uniprot.update_info.html#pypath.utils.uniprot.update_info">update_info() (in module pypath.utils.uniprot)</a>
+</li>
+      <li><a href="api/pypath.core.annot.CustomAnnotation.html#pypath.core.annot.CustomAnnotation.update_parents">update_parents() (pypath.core.annot.CustomAnnotation method)</a>
+
+      <ul>
+        <li><a href="api/pypath.core.intercell.IntercellAnnotation.html#pypath.core.intercell.IntercellAnnotation.update_parents">(pypath.core.intercell.IntercellAnnotation method)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.inputs.biogps.BiogpsDataset.html#pypath.inputs.biogps.BiogpsDataset.url">url (pypath.inputs.biogps.BiogpsDataset attribute)</a>
+
+      <ul>
+        <li><a href="api/pypath.inputs.uniprot.UniprotQuery.html#pypath.inputs.uniprot.UniprotQuery.url">(pypath.inputs.uniprot.UniprotQuery property)</a>
+</li>
+      </ul></li>
       <li><a href="api/pypath.share.curl.Curl.html#pypath.share.curl.Curl.url_fix">url_fix() (pypath.share.curl.Curl method)</a>
 </li>
       <li><a href="api/pypath.inputs.uniprot.UniprotQuery.html#pypath.inputs.uniprot.UniprotQuery.url_plain">url_plain (pypath.inputs.uniprot.UniprotQuery property)</a>
@@ -3946,7 +16545,11 @@ <h2 id="V">V</h2>
 <table style="width: 100%" class="indextable genindextable"><tr>
   <td style="width: 33%; vertical-align: top;"><ul>
       <li><a href="api/pypath.inputs.uniprot.valid_uniprot.html#pypath.inputs.uniprot.valid_uniprot">valid_uniprot() (in module pypath.inputs.uniprot)</a>
+
+      <ul>
+        <li><a href="api/pypath.utils.mapping.Mapper.html#pypath.utils.mapping.Mapper.valid_uniprot">(pypath.utils.mapping.Mapper method)</a>
 </li>
+      </ul></li>
       <li><a href="api/pypath.internals.resource.NetworkDataset.html#pypath.internals.resource.NetworkDataset.values">values() (pypath.internals.resource.NetworkDataset method)</a>
 </li>
       <li><a href="api/pypath.inputs.proteins.variants.html#pypath.inputs.proteins.variants">variants() (in module pypath.inputs.proteins)</a>
@@ -3954,6 +16557,8 @@ <h2 id="V">V</h2>
   </ul></td>
   <td style="width: 33%; vertical-align: top;"><ul>
       <li><a href="api/pypath.inputs.pathwaycommons.PathwayCommonsResource.html#pypath.inputs.pathwaycommons.PathwayCommonsResource.version">version (pypath.inputs.pathwaycommons.PathwayCommonsResource attribute)</a>
+</li>
+      <li><a href="api/pypath.core.annot.Vesiclepedia.html#pypath.core.annot.Vesiclepedia">Vesiclepedia (class in pypath.core.annot)</a>
 </li>
       <li><a href="api/pypath.internals.resource.EnzymeSubstrateResourceKey.html#pypath.internals.resource.EnzymeSubstrateResourceKey.via">via (pypath.internals.resource.EnzymeSubstrateResourceKey attribute)</a>
 
@@ -3961,6 +16566,82 @@ <h2 id="V">V</h2>
         <li><a href="api/pypath.internals.resource.NetworkResourceKey.html#pypath.internals.resource.NetworkResourceKey.via">(pypath.internals.resource.NetworkResourceKey attribute)</a>
 </li>
       </ul></li>
+      <li><a href="api/pypath.inputs.huri.vidal_hi_iii_old.html#pypath.inputs.huri.vidal_hi_iii_old">vidal_hi_iii_old() (in module pypath.inputs.huri)</a>
+</li>
+  </ul></td>
+</tr></table>
+
+<h2 id="W">W</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="api/pypath.core.annot.Wang.html#pypath.core.annot.Wang">Wang (class in pypath.core.annot)</a>
+</li>
+      <li><a href="api/pypath.inputs.wang.wang_annotations.html#pypath.inputs.wang.wang_annotations">wang_annotations() (in module pypath.inputs.wang)</a>
+</li>
+      <li><a href="api/pypath.inputs.wang.wang_interactions.html#pypath.inputs.wang.wang_interactions">wang_interactions() (in module pypath.inputs.wang)</a>
+</li>
+      <li><a href="api/pypath.utils.uniprot.web_resource.html#pypath.utils.uniprot.web_resource">web_resource() (in module pypath.utils.uniprot)</a>
+</li>
+      <li><a href="api/pypath.utils.uniprot.web_resource_with_xrefs.html#pypath.utils.uniprot.web_resource_with_xrefs">web_resource_with_xrefs() (in module pypath.utils.uniprot)</a>
+</li>
+      <li><a href="api/pypath.omnipath.server.build.WebserviceTables.html#pypath.omnipath.server.build.WebserviceTables">WebserviceTables (class in pypath.omnipath.server.build)</a>
+</li>
+      <li><a href="api/pypath.utils.uniprot.UniprotProtein.html#pypath.utils.uniprot.UniprotProtein.weight">weight (pypath.utils.uniprot.UniprotProtein property)</a>
+</li>
+      <li><a href="api/pypath.utils.uniprot.weight.html#pypath.utils.uniprot.weight">weight() (in module pypath.utils.uniprot)</a>
+</li>
+      <li><a href="api/pypath.utils.uniprot.UniprotProtein.html#pypath.utils.uniprot.UniprotProtein.weights">weights (pypath.utils.uniprot.UniprotProtein property)</a>
+</li>
+      <li><a href="api/pypath.utils.uniprot.weights.html#pypath.utils.uniprot.weights">weights() (in module pypath.utils.uniprot)</a>
+</li>
+  </ul></td>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.which_directions">which_directions() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.which_dirs">which_dirs() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.core.interaction.Interaction.html#pypath.core.interaction.Interaction.which_signs">which_signs() (pypath.core.interaction.Interaction method)</a>
+</li>
+      <li><a href="api/pypath.utils.mapping.Mapper.html#pypath.utils.mapping.Mapper.which_table">which_table() (pypath.utils.mapping.Mapper method)</a>
+</li>
+      <li><a href="api/pypath.inputs.wojtowicz2020.wojtowicz2020_interactions.html#pypath.inputs.wojtowicz2020.wojtowicz2020_interactions">wojtowicz2020_interactions() (in module pypath.inputs.wojtowicz2020)</a>
+</li>
+      <li><a href="api/pypath.inputs.wojtowicz2020.wojtowicz2020_raw.html#pypath.inputs.wojtowicz2020.wojtowicz2020_raw">wojtowicz2020_raw() (in module pypath.inputs.wojtowicz2020)</a>
+</li>
+      <li><a href="api/pypath.utils.mapping.MapReader.html#pypath.utils.mapping.MapReader.write_cache">write_cache() (pypath.utils.mapping.MapReader method)</a>
+</li>
+      <li><a href="api/pypath.omnipath.server.generate_about_page.write_html.html#pypath.omnipath.server.generate_about_page.write_html">write_html() (in module pypath.omnipath.server.generate_about_page)</a>
+
+      <ul>
+        <li><a href="api/pypath.resources.descriptions.write_html.html#pypath.resources.descriptions.write_html">(in module pypath.resources.descriptions)</a>
+</li>
+      </ul></li>
+      <li><a href="api/pypath.omnipath.export.Export.html#pypath.omnipath.export.Export.write_tab">write_tab() (pypath.omnipath.export.Export method)</a>
+</li>
+  </ul></td>
+</tr></table>
+
+<h2 id="Y">Y</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="api/pypath.inputs.huri.yang2016_interactions.html#pypath.inputs.huri.yang2016_interactions">yang2016_interactions() (in module pypath.inputs.huri)</a>
+</li>
+  </ul></td>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="api/pypath.inputs.huri.yu2011_interactions.html#pypath.inputs.huri.yu2011_interactions">yu2011_interactions() (in module pypath.inputs.huri)</a>
+</li>
+  </ul></td>
+</tr></table>
+
+<h2 id="Z">Z</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="api/pypath.core.annot.Zhong2015.html#pypath.core.annot.Zhong2015">Zhong2015 (class in pypath.core.annot)</a>
+</li>
+  </ul></td>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="api/pypath.inputs.zhong2015.zhong2015_annotations.html#pypath.inputs.zhong2015.zhong2015_annotations">zhong2015_annotations() (in module pypath.inputs.zhong2015)</a>
+</li>
   </ul></td>
 </tr></table>
 
diff --git a/objects.inv b/objects.inv
index c6d10eef5..822fd5120 100644
Binary files a/objects.inv and b/objects.inv differ
diff --git a/py-modindex.html b/py-modindex.html
index cbefd238a..99f6c2a0f 100644
--- a/py-modindex.html
+++ b/py-modindex.html
@@ -493,6 +493,11 @@ <h1>Python Module Index</h1>
        <td>&#160;&#160;&#160;
        <a href="api/pypath.core.html#module-pypath.core"><code class="xref">pypath.core</code></a></td><td>
        <em></em></td></tr>
+     <tr class="cg-1">
+       <td></td>
+       <td>&#160;&#160;&#160;
+       <a href="api/pypath.core.annot.html#module-pypath.core.annot"><code class="xref">pypath.core.annot</code></a></td><td>
+       <em></em></td></tr>
      <tr class="cg-1">
        <td></td>
        <td>&#160;&#160;&#160;
@@ -503,6 +508,46 @@ <h1>Python Module Index</h1>
        <td>&#160;&#160;&#160;
        <a href="api/pypath.core.common.html#module-pypath.core.common"><code class="xref">pypath.core.common</code></a></td><td>
        <em></em></td></tr>
+     <tr class="cg-1">
+       <td></td>
+       <td>&#160;&#160;&#160;
+       <a href="api/pypath.core.complex.html#module-pypath.core.complex"><code class="xref">pypath.core.complex</code></a></td><td>
+       <em></em></td></tr>
+     <tr class="cg-1">
+       <td></td>
+       <td>&#160;&#160;&#160;
+       <a href="api/pypath.core.entity.html#module-pypath.core.entity"><code class="xref">pypath.core.entity</code></a></td><td>
+       <em></em></td></tr>
+     <tr class="cg-1">
+       <td></td>
+       <td>&#160;&#160;&#160;
+       <a href="api/pypath.core.enz_sub.html#module-pypath.core.enz_sub"><code class="xref">pypath.core.enz_sub</code></a></td><td>
+       <em></em></td></tr>
+     <tr class="cg-1">
+       <td></td>
+       <td>&#160;&#160;&#160;
+       <a href="api/pypath.core.evidence.html#module-pypath.core.evidence"><code class="xref">pypath.core.evidence</code></a></td><td>
+       <em></em></td></tr>
+     <tr class="cg-1">
+       <td></td>
+       <td>&#160;&#160;&#160;
+       <a href="api/pypath.core.interaction.html#module-pypath.core.interaction"><code class="xref">pypath.core.interaction</code></a></td><td>
+       <em></em></td></tr>
+     <tr class="cg-1">
+       <td></td>
+       <td>&#160;&#160;&#160;
+       <a href="api/pypath.core.intercell.html#module-pypath.core.intercell"><code class="xref">pypath.core.intercell</code></a></td><td>
+       <em></em></td></tr>
+     <tr class="cg-1">
+       <td></td>
+       <td>&#160;&#160;&#160;
+       <a href="api/pypath.core.intercell_annot.html#module-pypath.core.intercell_annot"><code class="xref">pypath.core.intercell_annot</code></a></td><td>
+       <em></em></td></tr>
+     <tr class="cg-1">
+       <td></td>
+       <td>&#160;&#160;&#160;
+       <a href="api/pypath.core.network.html#module-pypath.core.network"><code class="xref">pypath.core.network</code></a></td><td>
+       <em></em></td></tr>
      <tr class="cg-1">
        <td></td>
        <td>&#160;&#160;&#160;
@@ -523,11 +568,31 @@ <h1>Python Module Index</h1>
        <td>&#160;&#160;&#160;
        <a href="api/pypath.inputs.acsn.html#module-pypath.inputs.acsn"><code class="xref">pypath.inputs.acsn</code></a></td><td>
        <em></em></td></tr>
+     <tr class="cg-1">
+       <td></td>
+       <td>&#160;&#160;&#160;
+       <a href="api/pypath.inputs.adhesome.html#module-pypath.inputs.adhesome"><code class="xref">pypath.inputs.adhesome</code></a></td><td>
+       <em></em></td></tr>
      <tr class="cg-1">
        <td></td>
        <td>&#160;&#160;&#160;
        <a href="api/pypath.inputs.adrecs.html#module-pypath.inputs.adrecs"><code class="xref">pypath.inputs.adrecs</code></a></td><td>
        <em></em></td></tr>
+     <tr class="cg-1">
+       <td></td>
+       <td>&#160;&#160;&#160;
+       <a href="api/pypath.inputs.almen2009.html#module-pypath.inputs.almen2009"><code class="xref">pypath.inputs.almen2009</code></a></td><td>
+       <em></em></td></tr>
+     <tr class="cg-1">
+       <td></td>
+       <td>&#160;&#160;&#160;
+       <a href="api/pypath.inputs.baccin2019.html#module-pypath.inputs.baccin2019"><code class="xref">pypath.inputs.baccin2019</code></a></td><td>
+       <em></em></td></tr>
+     <tr class="cg-1">
+       <td></td>
+       <td>&#160;&#160;&#160;
+       <a href="api/pypath.inputs.biogps.html#module-pypath.inputs.biogps"><code class="xref">pypath.inputs.biogps</code></a></td><td>
+       <em></em></td></tr>
      <tr class="cg-1">
        <td></td>
        <td>&#160;&#160;&#160;
@@ -553,11 +618,56 @@ <h1>Python Module Index</h1>
        <td>&#160;&#160;&#160;
        <a href="api/pypath.inputs.cancercellmap.html#module-pypath.inputs.cancercellmap"><code class="xref">pypath.inputs.cancercellmap</code></a></td><td>
        <em></em></td></tr>
+     <tr class="cg-1">
+       <td></td>
+       <td>&#160;&#160;&#160;
+       <a href="api/pypath.inputs.cancerdrugsdb.html#module-pypath.inputs.cancerdrugsdb"><code class="xref">pypath.inputs.cancerdrugsdb</code></a></td><td>
+       <em></em></td></tr>
+     <tr class="cg-1">
+       <td></td>
+       <td>&#160;&#160;&#160;
+       <a href="api/pypath.inputs.cancersea.html#module-pypath.inputs.cancersea"><code class="xref">pypath.inputs.cancersea</code></a></td><td>
+       <em></em></td></tr>
      <tr class="cg-1">
        <td></td>
        <td>&#160;&#160;&#160;
        <a href="api/pypath.inputs.cell.html#module-pypath.inputs.cell"><code class="xref">pypath.inputs.cell</code></a></td><td>
        <em></em></td></tr>
+     <tr class="cg-1">
+       <td></td>
+       <td>&#160;&#160;&#160;
+       <a href="api/pypath.inputs.cellcall.html#module-pypath.inputs.cellcall"><code class="xref">pypath.inputs.cellcall</code></a></td><td>
+       <em></em></td></tr>
+     <tr class="cg-1">
+       <td></td>
+       <td>&#160;&#160;&#160;
+       <a href="api/pypath.inputs.cellcellinteractions.html#module-pypath.inputs.cellcellinteractions"><code class="xref">pypath.inputs.cellcellinteractions</code></a></td><td>
+       <em></em></td></tr>
+     <tr class="cg-1">
+       <td></td>
+       <td>&#160;&#160;&#160;
+       <a href="api/pypath.inputs.cellchatdb.html#module-pypath.inputs.cellchatdb"><code class="xref">pypath.inputs.cellchatdb</code></a></td><td>
+       <em></em></td></tr>
+     <tr class="cg-1">
+       <td></td>
+       <td>&#160;&#160;&#160;
+       <a href="api/pypath.inputs.cellinker.html#module-pypath.inputs.cellinker"><code class="xref">pypath.inputs.cellinker</code></a></td><td>
+       <em></em></td></tr>
+     <tr class="cg-1">
+       <td></td>
+       <td>&#160;&#160;&#160;
+       <a href="api/pypath.inputs.cellphonedb.html#module-pypath.inputs.cellphonedb"><code class="xref">pypath.inputs.cellphonedb</code></a></td><td>
+       <em></em></td></tr>
+     <tr class="cg-1">
+       <td></td>
+       <td>&#160;&#160;&#160;
+       <a href="api/pypath.inputs.celltalkdb.html#module-pypath.inputs.celltalkdb"><code class="xref">pypath.inputs.celltalkdb</code></a></td><td>
+       <em></em></td></tr>
+     <tr class="cg-1">
+       <td></td>
+       <td>&#160;&#160;&#160;
+       <a href="api/pypath.inputs.celltypist.html#module-pypath.inputs.celltypist"><code class="xref">pypath.inputs.celltypist</code></a></td><td>
+       <em></em></td></tr>
      <tr class="cg-1">
        <td></td>
        <td>&#160;&#160;&#160;
@@ -568,6 +678,11 @@ <h1>Python Module Index</h1>
        <td>&#160;&#160;&#160;
        <a href="api/pypath.inputs.clinvar.html#module-pypath.inputs.clinvar"><code class="xref">pypath.inputs.clinvar</code></a></td><td>
        <em></em></td></tr>
+     <tr class="cg-1">
+       <td></td>
+       <td>&#160;&#160;&#160;
+       <a href="api/pypath.inputs.collectri.html#module-pypath.inputs.collectri"><code class="xref">pypath.inputs.collectri</code></a></td><td>
+       <em></em></td></tr>
      <tr class="cg-1">
        <td></td>
        <td>&#160;&#160;&#160;
@@ -578,6 +693,41 @@ <h1>Python Module Index</h1>
        <td>&#160;&#160;&#160;
        <a href="api/pypath.inputs.compath.html#module-pypath.inputs.compath"><code class="xref">pypath.inputs.compath</code></a></td><td>
        <em></em></td></tr>
+     <tr class="cg-1">
+       <td></td>
+       <td>&#160;&#160;&#160;
+       <a href="api/pypath.inputs.compleat.html#module-pypath.inputs.compleat"><code class="xref">pypath.inputs.compleat</code></a></td><td>
+       <em></em></td></tr>
+     <tr class="cg-1">
+       <td></td>
+       <td>&#160;&#160;&#160;
+       <a href="api/pypath.inputs.complexportal.html#module-pypath.inputs.complexportal"><code class="xref">pypath.inputs.complexportal</code></a></td><td>
+       <em></em></td></tr>
+     <tr class="cg-1">
+       <td></td>
+       <td>&#160;&#160;&#160;
+       <a href="api/pypath.inputs.comppi.html#module-pypath.inputs.comppi"><code class="xref">pypath.inputs.comppi</code></a></td><td>
+       <em></em></td></tr>
+     <tr class="cg-1">
+       <td></td>
+       <td>&#160;&#160;&#160;
+       <a href="api/pypath.inputs.connectomedb.html#module-pypath.inputs.connectomedb"><code class="xref">pypath.inputs.connectomedb</code></a></td><td>
+       <em></em></td></tr>
+     <tr class="cg-1">
+       <td></td>
+       <td>&#160;&#160;&#160;
+       <a href="api/pypath.inputs.corum.html#module-pypath.inputs.corum"><code class="xref">pypath.inputs.corum</code></a></td><td>
+       <em></em></td></tr>
+     <tr class="cg-1">
+       <td></td>
+       <td>&#160;&#160;&#160;
+       <a href="api/pypath.inputs.cosmic.html#module-pypath.inputs.cosmic"><code class="xref">pypath.inputs.cosmic</code></a></td><td>
+       <em></em></td></tr>
+     <tr class="cg-1">
+       <td></td>
+       <td>&#160;&#160;&#160;
+       <a href="api/pypath.inputs.cpad.html#module-pypath.inputs.cpad"><code class="xref">pypath.inputs.cpad</code></a></td><td>
+       <em></em></td></tr>
      <tr class="cg-1">
        <td></td>
        <td>&#160;&#160;&#160;
@@ -588,11 +738,26 @@ <h1>Python Module Index</h1>
        <td>&#160;&#160;&#160;
        <a href="api/pypath.inputs.credentials.html#module-pypath.inputs.credentials"><code class="xref">pypath.inputs.credentials</code></a></td><td>
        <em></em></td></tr>
+     <tr class="cg-1">
+       <td></td>
+       <td>&#160;&#160;&#160;
+       <a href="api/pypath.inputs.csa.html#module-pypath.inputs.csa"><code class="xref">pypath.inputs.csa</code></a></td><td>
+       <em></em></td></tr>
+     <tr class="cg-1">
+       <td></td>
+       <td>&#160;&#160;&#160;
+       <a href="api/pypath.inputs.cspa.html#module-pypath.inputs.cspa"><code class="xref">pypath.inputs.cspa</code></a></td><td>
+       <em></em></td></tr>
      <tr class="cg-1">
        <td></td>
        <td>&#160;&#160;&#160;
        <a href="api/pypath.inputs.ctdbase.html#module-pypath.inputs.ctdbase"><code class="xref">pypath.inputs.ctdbase</code></a></td><td>
        <em></em></td></tr>
+     <tr class="cg-1">
+       <td></td>
+       <td>&#160;&#160;&#160;
+       <a href="api/pypath.inputs.cytosig.html#module-pypath.inputs.cytosig"><code class="xref">pypath.inputs.cytosig</code></a></td><td>
+       <em></em></td></tr>
      <tr class="cg-1">
        <td></td>
        <td>&#160;&#160;&#160;
@@ -608,6 +773,16 @@ <h1>Python Module Index</h1>
        <td>&#160;&#160;&#160;
        <a href="api/pypath.inputs.deathdomain.html#module-pypath.inputs.deathdomain"><code class="xref">pypath.inputs.deathdomain</code></a></td><td>
        <em></em></td></tr>
+     <tr class="cg-1">
+       <td></td>
+       <td>&#160;&#160;&#160;
+       <a href="api/pypath.inputs.depod.html#module-pypath.inputs.depod"><code class="xref">pypath.inputs.depod</code></a></td><td>
+       <em></em></td></tr>
+     <tr class="cg-1">
+       <td></td>
+       <td>&#160;&#160;&#160;
+       <a href="api/pypath.inputs.dgidb.html#module-pypath.inputs.dgidb"><code class="xref">pypath.inputs.dgidb</code></a></td><td>
+       <em></em></td></tr>
      <tr class="cg-1">
        <td></td>
        <td>&#160;&#160;&#160;
@@ -618,6 +793,11 @@ <h1>Python Module Index</h1>
        <td>&#160;&#160;&#160;
        <a href="api/pypath.inputs.diseases.html#module-pypath.inputs.diseases"><code class="xref">pypath.inputs.diseases</code></a></td><td>
        <em></em></td></tr>
+     <tr class="cg-1">
+       <td></td>
+       <td>&#160;&#160;&#160;
+       <a href="api/pypath.inputs.domino.html#module-pypath.inputs.domino"><code class="xref">pypath.inputs.domino</code></a></td><td>
+       <em></em></td></tr>
      <tr class="cg-1">
        <td></td>
        <td>&#160;&#160;&#160;
@@ -648,6 +828,11 @@ <h1>Python Module Index</h1>
        <td>&#160;&#160;&#160;
        <a href="api/pypath.inputs.embopress.html#module-pypath.inputs.embopress"><code class="xref">pypath.inputs.embopress</code></a></td><td>
        <em></em></td></tr>
+     <tr class="cg-1">
+       <td></td>
+       <td>&#160;&#160;&#160;
+       <a href="api/pypath.inputs.embrace.html#module-pypath.inputs.embrace"><code class="xref">pypath.inputs.embrace</code></a></td><td>
+       <em></em></td></tr>
      <tr class="cg-1">
        <td></td>
        <td>&#160;&#160;&#160;
@@ -693,6 +878,31 @@ <h1>Python Module Index</h1>
        <td>&#160;&#160;&#160;
        <a href="api/pypath.inputs.graphviz.html#module-pypath.inputs.graphviz"><code class="xref">pypath.inputs.graphviz</code></a></td><td>
        <em></em></td></tr>
+     <tr class="cg-1">
+       <td></td>
+       <td>&#160;&#160;&#160;
+       <a href="api/pypath.inputs.guide2pharma.html#module-pypath.inputs.guide2pharma"><code class="xref">pypath.inputs.guide2pharma</code></a></td><td>
+       <em></em></td></tr>
+     <tr class="cg-1">
+       <td></td>
+       <td>&#160;&#160;&#160;
+       <a href="api/pypath.inputs.gutmgene.html#module-pypath.inputs.gutmgene"><code class="xref">pypath.inputs.gutmgene</code></a></td><td>
+       <em></em></td></tr>
+     <tr class="cg-1">
+       <td></td>
+       <td>&#160;&#160;&#160;
+       <a href="api/pypath.inputs.havugimana.html#module-pypath.inputs.havugimana"><code class="xref">pypath.inputs.havugimana</code></a></td><td>
+       <em></em></td></tr>
+     <tr class="cg-1">
+       <td></td>
+       <td>&#160;&#160;&#160;
+       <a href="api/pypath.inputs.hgnc.html#module-pypath.inputs.hgnc"><code class="xref">pypath.inputs.hgnc</code></a></td><td>
+       <em></em></td></tr>
+     <tr class="cg-1">
+       <td></td>
+       <td>&#160;&#160;&#160;
+       <a href="api/pypath.inputs.hippie.html#module-pypath.inputs.hippie"><code class="xref">pypath.inputs.hippie</code></a></td><td>
+       <em></em></td></tr>
      <tr class="cg-1">
        <td></td>
        <td>&#160;&#160;&#160;
@@ -748,6 +958,21 @@ <h1>Python Module Index</h1>
        <td>&#160;&#160;&#160;
        <a href="api/pypath.inputs.hmdb.xml.html#module-pypath.inputs.hmdb.xml"><code class="xref">pypath.inputs.hmdb.xml</code></a></td><td>
        <em></em></td></tr>
+     <tr class="cg-1">
+       <td></td>
+       <td>&#160;&#160;&#160;
+       <a href="api/pypath.inputs.homologene.html#module-pypath.inputs.homologene"><code class="xref">pypath.inputs.homologene</code></a></td><td>
+       <em></em></td></tr>
+     <tr class="cg-1">
+       <td></td>
+       <td>&#160;&#160;&#160;
+       <a href="api/pypath.inputs.hpmr.html#module-pypath.inputs.hpmr"><code class="xref">pypath.inputs.hpmr</code></a></td><td>
+       <em></em></td></tr>
+     <tr class="cg-1">
+       <td></td>
+       <td>&#160;&#160;&#160;
+       <a href="api/pypath.inputs.hpo.html#module-pypath.inputs.hpo"><code class="xref">pypath.inputs.hpo</code></a></td><td>
+       <em></em></td></tr>
      <tr class="cg-1">
        <td></td>
        <td>&#160;&#160;&#160;
@@ -758,16 +983,36 @@ <h1>Python Module Index</h1>
        <td>&#160;&#160;&#160;
        <a href="api/pypath.inputs.htri.html#module-pypath.inputs.htri"><code class="xref">pypath.inputs.htri</code></a></td><td>
        <em></em></td></tr>
+     <tr class="cg-1">
+       <td></td>
+       <td>&#160;&#160;&#160;
+       <a href="api/pypath.inputs.humancellmap.html#module-pypath.inputs.humancellmap"><code class="xref">pypath.inputs.humancellmap</code></a></td><td>
+       <em></em></td></tr>
+     <tr class="cg-1">
+       <td></td>
+       <td>&#160;&#160;&#160;
+       <a href="api/pypath.inputs.humap.html#module-pypath.inputs.humap"><code class="xref">pypath.inputs.humap</code></a></td><td>
+       <em></em></td></tr>
      <tr class="cg-1">
        <td></td>
        <td>&#160;&#160;&#160;
        <a href="api/pypath.inputs.humsavar.html#module-pypath.inputs.humsavar"><code class="xref">pypath.inputs.humsavar</code></a></td><td>
        <em></em></td></tr>
+     <tr class="cg-1">
+       <td></td>
+       <td>&#160;&#160;&#160;
+       <a href="api/pypath.inputs.huri.html#module-pypath.inputs.huri"><code class="xref">pypath.inputs.huri</code></a></td><td>
+       <em></em></td></tr>
      <tr class="cg-1">
        <td></td>
        <td>&#160;&#160;&#160;
        <a href="api/pypath.inputs.i3d.html#module-pypath.inputs.i3d"><code class="xref">pypath.inputs.i3d</code></a></td><td>
        <em></em></td></tr>
+     <tr class="cg-1">
+       <td></td>
+       <td>&#160;&#160;&#160;
+       <a href="api/pypath.inputs.icellnet.html#module-pypath.inputs.icellnet"><code class="xref">pypath.inputs.icellnet</code></a></td><td>
+       <em></em></td></tr>
      <tr class="cg-1">
        <td></td>
        <td>&#160;&#160;&#160;
@@ -793,36 +1038,86 @@ <h1>Python Module Index</h1>
        <td>&#160;&#160;&#160;
        <a href="api/pypath.inputs.intact.html#module-pypath.inputs.intact"><code class="xref">pypath.inputs.intact</code></a></td><td>
        <em></em></td></tr>
+     <tr class="cg-1">
+       <td></td>
+       <td>&#160;&#160;&#160;
+       <a href="api/pypath.inputs.integrins.html#module-pypath.inputs.integrins"><code class="xref">pypath.inputs.integrins</code></a></td><td>
+       <em></em></td></tr>
      <tr class="cg-1">
        <td></td>
        <td>&#160;&#160;&#160;
        <a href="api/pypath.inputs.interpro.html#module-pypath.inputs.interpro"><code class="xref">pypath.inputs.interpro</code></a></td><td>
        <em></em></td></tr>
+     <tr class="cg-1">
+       <td></td>
+       <td>&#160;&#160;&#160;
+       <a href="api/pypath.inputs.intogen.html#module-pypath.inputs.intogen"><code class="xref">pypath.inputs.intogen</code></a></td><td>
+       <em></em></td></tr>
      <tr class="cg-1">
        <td></td>
        <td>&#160;&#160;&#160;
        <a href="api/pypath.inputs.ipi.html#module-pypath.inputs.ipi"><code class="xref">pypath.inputs.ipi</code></a></td><td>
        <em></em></td></tr>
+     <tr class="cg-1">
+       <td></td>
+       <td>&#160;&#160;&#160;
+       <a href="api/pypath.inputs.iptmnet.html#module-pypath.inputs.iptmnet"><code class="xref">pypath.inputs.iptmnet</code></a></td><td>
+       <em></em></td></tr>
+     <tr class="cg-1">
+       <td></td>
+       <td>&#160;&#160;&#160;
+       <a href="api/pypath.inputs.italk.html#module-pypath.inputs.italk"><code class="xref">pypath.inputs.italk</code></a></td><td>
+       <em></em></td></tr>
+     <tr class="cg-1">
+       <td></td>
+       <td>&#160;&#160;&#160;
+       <a href="api/pypath.inputs.kea.html#module-pypath.inputs.kea"><code class="xref">pypath.inputs.kea</code></a></td><td>
+       <em></em></td></tr>
+     <tr class="cg-1">
+       <td></td>
+       <td>&#160;&#160;&#160;
+       <a href="api/pypath.inputs.kegg.html#module-pypath.inputs.kegg"><code class="xref">pypath.inputs.kegg</code></a></td><td>
+       <em></em></td></tr>
      <tr class="cg-1">
        <td></td>
        <td>&#160;&#160;&#160;
        <a href="api/pypath.inputs.kegg_api.html#module-pypath.inputs.kegg_api"><code class="xref">pypath.inputs.kegg_api</code></a></td><td>
        <em></em></td></tr>
+     <tr class="cg-1">
+       <td></td>
+       <td>&#160;&#160;&#160;
+       <a href="api/pypath.inputs.kinasedotcom.html#module-pypath.inputs.kinasedotcom"><code class="xref">pypath.inputs.kinasedotcom</code></a></td><td>
+       <em></em></td></tr>
      <tr class="cg-1">
        <td></td>
        <td>&#160;&#160;&#160;
        <a href="api/pypath.inputs.kirouac2010.html#module-pypath.inputs.kirouac2010"><code class="xref">pypath.inputs.kirouac2010</code></a></td><td>
        <em></em></td></tr>
+     <tr class="cg-1">
+       <td></td>
+       <td>&#160;&#160;&#160;
+       <a href="api/pypath.inputs.lambert2018.html#module-pypath.inputs.lambert2018"><code class="xref">pypath.inputs.lambert2018</code></a></td><td>
+       <em></em></td></tr>
      <tr class="cg-1">
        <td></td>
        <td>&#160;&#160;&#160;
        <a href="api/pypath.inputs.laudanna.html#module-pypath.inputs.laudanna"><code class="xref">pypath.inputs.laudanna</code></a></td><td>
        <em></em></td></tr>
+     <tr class="cg-1">
+       <td></td>
+       <td>&#160;&#160;&#160;
+       <a href="api/pypath.inputs.li2012.html#module-pypath.inputs.li2012"><code class="xref">pypath.inputs.li2012</code></a></td><td>
+       <em></em></td></tr>
      <tr class="cg-1">
        <td></td>
        <td>&#160;&#160;&#160;
        <a href="api/pypath.inputs.lincs.html#module-pypath.inputs.lincs"><code class="xref">pypath.inputs.lincs</code></a></td><td>
        <em></em></td></tr>
+     <tr class="cg-1">
+       <td></td>
+       <td>&#160;&#160;&#160;
+       <a href="api/pypath.inputs.lmpid.html#module-pypath.inputs.lmpid"><code class="xref">pypath.inputs.lmpid</code></a></td><td>
+       <em></em></td></tr>
      <tr class="cg-1">
        <td></td>
        <td>&#160;&#160;&#160;
@@ -833,6 +1128,16 @@ <h1>Python Module Index</h1>
        <td>&#160;&#160;&#160;
        <a href="api/pypath.inputs.lncrnadb.html#module-pypath.inputs.lncrnadb"><code class="xref">pypath.inputs.lncrnadb</code></a></td><td>
        <em></em></td></tr>
+     <tr class="cg-1">
+       <td></td>
+       <td>&#160;&#160;&#160;
+       <a href="api/pypath.inputs.locate.html#module-pypath.inputs.locate"><code class="xref">pypath.inputs.locate</code></a></td><td>
+       <em></em></td></tr>
+     <tr class="cg-1">
+       <td></td>
+       <td>&#160;&#160;&#160;
+       <a href="api/pypath.inputs.lrdb.html#module-pypath.inputs.lrdb"><code class="xref">pypath.inputs.lrdb</code></a></td><td>
+       <em></em></td></tr>
      <tr class="cg-1">
        <td></td>
        <td>&#160;&#160;&#160;
@@ -843,6 +1148,26 @@ <h1>Python Module Index</h1>
        <td>&#160;&#160;&#160;
        <a href="api/pypath.inputs.main.html#module-pypath.inputs.main"><code class="xref">pypath.inputs.main</code></a></td><td>
        <em></em></td></tr>
+     <tr class="cg-1">
+       <td></td>
+       <td>&#160;&#160;&#160;
+       <a href="api/pypath.inputs.matrisome.html#module-pypath.inputs.matrisome"><code class="xref">pypath.inputs.matrisome</code></a></td><td>
+       <em></em></td></tr>
+     <tr class="cg-1">
+       <td></td>
+       <td>&#160;&#160;&#160;
+       <a href="api/pypath.inputs.matrixdb.html#module-pypath.inputs.matrixdb"><code class="xref">pypath.inputs.matrixdb</code></a></td><td>
+       <em></em></td></tr>
+     <tr class="cg-1">
+       <td></td>
+       <td>&#160;&#160;&#160;
+       <a href="api/pypath.inputs.mcam.html#module-pypath.inputs.mcam"><code class="xref">pypath.inputs.mcam</code></a></td><td>
+       <em></em></td></tr>
+     <tr class="cg-1">
+       <td></td>
+       <td>&#160;&#160;&#160;
+       <a href="api/pypath.inputs.membranome.html#module-pypath.inputs.membranome"><code class="xref">pypath.inputs.membranome</code></a></td><td>
+       <em></em></td></tr>
      <tr class="cg-1">
        <td></td>
        <td>&#160;&#160;&#160;
@@ -883,6 +1208,11 @@ <h1>Python Module Index</h1>
        <td>&#160;&#160;&#160;
        <a href="api/pypath.inputs.mppi.html#module-pypath.inputs.mppi"><code class="xref">pypath.inputs.mppi</code></a></td><td>
        <em></em></td></tr>
+     <tr class="cg-1">
+       <td></td>
+       <td>&#160;&#160;&#160;
+       <a href="api/pypath.inputs.msigdb.html#module-pypath.inputs.msigdb"><code class="xref">pypath.inputs.msigdb</code></a></td><td>
+       <em></em></td></tr>
      <tr class="cg-1">
        <td></td>
        <td>&#160;&#160;&#160;
@@ -898,11 +1228,21 @@ <h1>Python Module Index</h1>
        <td>&#160;&#160;&#160;
        <a href="api/pypath.inputs.netbiol.html#module-pypath.inputs.netbiol"><code class="xref">pypath.inputs.netbiol</code></a></td><td>
        <em></em></td></tr>
+     <tr class="cg-1">
+       <td></td>
+       <td>&#160;&#160;&#160;
+       <a href="api/pypath.inputs.netpath.html#module-pypath.inputs.netpath"><code class="xref">pypath.inputs.netpath</code></a></td><td>
+       <em></em></td></tr>
      <tr class="cg-1">
        <td></td>
        <td>&#160;&#160;&#160;
        <a href="api/pypath.inputs.offsides.html#module-pypath.inputs.offsides"><code class="xref">pypath.inputs.offsides</code></a></td><td>
        <em></em></td></tr>
+     <tr class="cg-1">
+       <td></td>
+       <td>&#160;&#160;&#160;
+       <a href="api/pypath.inputs.oma.html#module-pypath.inputs.oma"><code class="xref">pypath.inputs.oma</code></a></td><td>
+       <em></em></td></tr>
      <tr class="cg-1">
        <td></td>
        <td>&#160;&#160;&#160;
@@ -913,11 +1253,21 @@ <h1>Python Module Index</h1>
        <td>&#160;&#160;&#160;
        <a href="api/pypath.inputs.opentargets.html#module-pypath.inputs.opentargets"><code class="xref">pypath.inputs.opentargets</code></a></td><td>
        <em></em></td></tr>
+     <tr class="cg-1">
+       <td></td>
+       <td>&#160;&#160;&#160;
+       <a href="api/pypath.inputs.opm.html#module-pypath.inputs.opm"><code class="xref">pypath.inputs.opm</code></a></td><td>
+       <em></em></td></tr>
      <tr class="cg-1">
        <td></td>
        <td>&#160;&#160;&#160;
        <a href="api/pypath.inputs.oreganno.html#module-pypath.inputs.oreganno"><code class="xref">pypath.inputs.oreganno</code></a></td><td>
        <em></em></td></tr>
+     <tr class="cg-1">
+       <td></td>
+       <td>&#160;&#160;&#160;
+       <a href="api/pypath.inputs.panglaodb.html#module-pypath.inputs.panglaodb"><code class="xref">pypath.inputs.panglaodb</code></a></td><td>
+       <em></em></td></tr>
      <tr class="cg-1">
        <td></td>
        <td>&#160;&#160;&#160;
@@ -933,6 +1283,11 @@ <h1>Python Module Index</h1>
        <td>&#160;&#160;&#160;
        <a href="api/pypath.inputs.pazar.html#module-pypath.inputs.pazar"><code class="xref">pypath.inputs.pazar</code></a></td><td>
        <em></em></td></tr>
+     <tr class="cg-1">
+       <td></td>
+       <td>&#160;&#160;&#160;
+       <a href="api/pypath.inputs.pdb.html#module-pypath.inputs.pdb"><code class="xref">pypath.inputs.pdb</code></a></td><td>
+       <em></em></td></tr>
      <tr class="cg-1">
        <td></td>
        <td>&#160;&#160;&#160;
@@ -958,6 +1313,11 @@ <h1>Python Module Index</h1>
        <td>&#160;&#160;&#160;
        <a href="api/pypath.inputs.phobius.html#module-pypath.inputs.phobius"><code class="xref">pypath.inputs.phobius</code></a></td><td>
        <em></em></td></tr>
+     <tr class="cg-1">
+       <td></td>
+       <td>&#160;&#160;&#160;
+       <a href="api/pypath.inputs.phosphatome.html#module-pypath.inputs.phosphatome"><code class="xref">pypath.inputs.phosphatome</code></a></td><td>
+       <em></em></td></tr>
      <tr class="cg-1">
        <td></td>
        <td>&#160;&#160;&#160;
@@ -973,11 +1333,31 @@ <h1>Python Module Index</h1>
        <td>&#160;&#160;&#160;
        <a href="api/pypath.inputs.phosphopoint.html#module-pypath.inputs.phosphopoint"><code class="xref">pypath.inputs.phosphopoint</code></a></td><td>
        <em></em></td></tr>
+     <tr class="cg-1">
+       <td></td>
+       <td>&#160;&#160;&#160;
+       <a href="api/pypath.inputs.phosphosite.html#module-pypath.inputs.phosphosite"><code class="xref">pypath.inputs.phosphosite</code></a></td><td>
+       <em></em></td></tr>
+     <tr class="cg-1">
+       <td></td>
+       <td>&#160;&#160;&#160;
+       <a href="api/pypath.inputs.pisa.html#module-pypath.inputs.pisa"><code class="xref">pypath.inputs.pisa</code></a></td><td>
+       <em></em></td></tr>
      <tr class="cg-1">
        <td></td>
        <td>&#160;&#160;&#160;
        <a href="api/pypath.inputs.pro.html#module-pypath.inputs.pro"><code class="xref">pypath.inputs.pro</code></a></td><td>
        <em></em></td></tr>
+     <tr class="cg-1">
+       <td></td>
+       <td>&#160;&#160;&#160;
+       <a href="api/pypath.inputs.progeny.html#module-pypath.inputs.progeny"><code class="xref">pypath.inputs.progeny</code></a></td><td>
+       <em></em></td></tr>
+     <tr class="cg-1">
+       <td></td>
+       <td>&#160;&#160;&#160;
+       <a href="api/pypath.inputs.proteinatlas.html#module-pypath.inputs.proteinatlas"><code class="xref">pypath.inputs.proteinatlas</code></a></td><td>
+       <em></em></td></tr>
      <tr class="cg-1">
        <td></td>
        <td>&#160;&#160;&#160;
@@ -998,6 +1378,11 @@ <h1>Python Module Index</h1>
        <td>&#160;&#160;&#160;
        <a href="api/pypath.inputs.pubmed.html#module-pypath.inputs.pubmed"><code class="xref">pypath.inputs.pubmed</code></a></td><td>
        <em></em></td></tr>
+     <tr class="cg-1">
+       <td></td>
+       <td>&#160;&#160;&#160;
+       <a href="api/pypath.inputs.ramilowski2015.html#module-pypath.inputs.ramilowski2015"><code class="xref">pypath.inputs.ramilowski2015</code></a></td><td>
+       <em></em></td></tr>
      <tr class="cg-1">
        <td></td>
        <td>&#160;&#160;&#160;
@@ -1018,6 +1403,11 @@ <h1>Python Module Index</h1>
        <td>&#160;&#160;&#160;
        <a href="api/pypath.inputs.reactome.html#module-pypath.inputs.reactome"><code class="xref">pypath.inputs.reactome</code></a></td><td>
        <em></em></td></tr>
+     <tr class="cg-1">
+       <td></td>
+       <td>&#160;&#160;&#160;
+       <a href="api/pypath.inputs.scconnect.html#module-pypath.inputs.scconnect"><code class="xref">pypath.inputs.scconnect</code></a></td><td>
+       <em></em></td></tr>
      <tr class="cg-1">
        <td></td>
        <td>&#160;&#160;&#160;
@@ -1028,6 +1418,21 @@ <h1>Python Module Index</h1>
        <td>&#160;&#160;&#160;
        <a href="api/pypath.inputs.sider.html#module-pypath.inputs.sider"><code class="xref">pypath.inputs.sider</code></a></td><td>
        <em></em></td></tr>
+     <tr class="cg-1">
+       <td></td>
+       <td>&#160;&#160;&#160;
+       <a href="api/pypath.inputs.signalink.html#module-pypath.inputs.signalink"><code class="xref">pypath.inputs.signalink</code></a></td><td>
+       <em></em></td></tr>
+     <tr class="cg-1">
+       <td></td>
+       <td>&#160;&#160;&#160;
+       <a href="api/pypath.inputs.signor.html#module-pypath.inputs.signor"><code class="xref">pypath.inputs.signor</code></a></td><td>
+       <em></em></td></tr>
+     <tr class="cg-1">
+       <td></td>
+       <td>&#160;&#160;&#160;
+       <a href="api/pypath.inputs.spike.html#module-pypath.inputs.spike"><code class="xref">pypath.inputs.spike</code></a></td><td>
+       <em></em></td></tr>
      <tr class="cg-1">
        <td></td>
        <td>&#160;&#160;&#160;
@@ -1038,11 +1443,46 @@ <h1>Python Module Index</h1>
        <td>&#160;&#160;&#160;
        <a href="api/pypath.inputs.string.html#module-pypath.inputs.string"><code class="xref">pypath.inputs.string</code></a></td><td>
        <em></em></td></tr>
+     <tr class="cg-1">
+       <td></td>
+       <td>&#160;&#160;&#160;
+       <a href="api/pypath.inputs.surfaceome.html#module-pypath.inputs.surfaceome"><code class="xref">pypath.inputs.surfaceome</code></a></td><td>
+       <em></em></td></tr>
      <tr class="cg-1">
        <td></td>
        <td>&#160;&#160;&#160;
        <a href="api/pypath.inputs.switches_elm.html#module-pypath.inputs.switches_elm"><code class="xref">pypath.inputs.switches_elm</code></a></td><td>
        <em></em></td></tr>
+     <tr class="cg-1">
+       <td></td>
+       <td>&#160;&#160;&#160;
+       <a href="api/pypath.inputs.talklr.html#module-pypath.inputs.talklr"><code class="xref">pypath.inputs.talklr</code></a></td><td>
+       <em></em></td></tr>
+     <tr class="cg-1">
+       <td></td>
+       <td>&#160;&#160;&#160;
+       <a href="api/pypath.inputs.tcdb.html#module-pypath.inputs.tcdb"><code class="xref">pypath.inputs.tcdb</code></a></td><td>
+       <em></em></td></tr>
+     <tr class="cg-1">
+       <td></td>
+       <td>&#160;&#160;&#160;
+       <a href="api/pypath.inputs.tfcensus.html#module-pypath.inputs.tfcensus"><code class="xref">pypath.inputs.tfcensus</code></a></td><td>
+       <em></em></td></tr>
+     <tr class="cg-1">
+       <td></td>
+       <td>&#160;&#160;&#160;
+       <a href="api/pypath.inputs.threedcomplex.html#module-pypath.inputs.threedcomplex"><code class="xref">pypath.inputs.threedcomplex</code></a></td><td>
+       <em></em></td></tr>
+     <tr class="cg-1">
+       <td></td>
+       <td>&#160;&#160;&#160;
+       <a href="api/pypath.inputs.threedid.html#module-pypath.inputs.threedid"><code class="xref">pypath.inputs.threedid</code></a></td><td>
+       <em></em></td></tr>
+     <tr class="cg-1">
+       <td></td>
+       <td>&#160;&#160;&#160;
+       <a href="api/pypath.inputs.topdb.html#module-pypath.inputs.topdb"><code class="xref">pypath.inputs.topdb</code></a></td><td>
+       <em></em></td></tr>
      <tr class="cg-1">
        <td></td>
        <td>&#160;&#160;&#160;
@@ -1078,16 +1518,41 @@ <h1>Python Module Index</h1>
        <td>&#160;&#160;&#160;
        <a href="api/pypath.inputs.uniprot_db.html#module-pypath.inputs.uniprot_db"><code class="xref">pypath.inputs.uniprot_db</code></a></td><td>
        <em></em></td></tr>
+     <tr class="cg-1">
+       <td></td>
+       <td>&#160;&#160;&#160;
+       <a href="api/pypath.inputs.wang.html#module-pypath.inputs.wang"><code class="xref">pypath.inputs.wang</code></a></td><td>
+       <em></em></td></tr>
+     <tr class="cg-1">
+       <td></td>
+       <td>&#160;&#160;&#160;
+       <a href="api/pypath.inputs.wojtowicz2020.html#module-pypath.inputs.wojtowicz2020"><code class="xref">pypath.inputs.wojtowicz2020</code></a></td><td>
+       <em></em></td></tr>
+     <tr class="cg-1">
+       <td></td>
+       <td>&#160;&#160;&#160;
+       <a href="api/pypath.inputs.zhong2015.html#module-pypath.inputs.zhong2015"><code class="xref">pypath.inputs.zhong2015</code></a></td><td>
+       <em></em></td></tr>
      <tr class="cg-1">
        <td></td>
        <td>&#160;&#160;&#160;
        <a href="api/pypath.internals.html#module-pypath.internals"><code class="xref">pypath.internals</code></a></td><td>
        <em></em></td></tr>
+     <tr class="cg-1">
+       <td></td>
+       <td>&#160;&#160;&#160;
+       <a href="api/pypath.internals.annot_formats.html#module-pypath.internals.annot_formats"><code class="xref">pypath.internals.annot_formats</code></a></td><td>
+       <em></em></td></tr>
      <tr class="cg-1">
        <td></td>
        <td>&#160;&#160;&#160;
        <a href="api/pypath.internals.input_formats.html#module-pypath.internals.input_formats"><code class="xref">pypath.internals.input_formats</code></a></td><td>
        <em></em></td></tr>
+     <tr class="cg-1">
+       <td></td>
+       <td>&#160;&#160;&#160;
+       <a href="api/pypath.internals.intera.html#module-pypath.internals.intera"><code class="xref">pypath.internals.intera</code></a></td><td>
+       <em></em></td></tr>
      <tr class="cg-1">
        <td></td>
        <td>&#160;&#160;&#160;
@@ -1118,6 +1583,61 @@ <h1>Python Module Index</h1>
        <td>&#160;&#160;&#160;
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        <em></em></td></tr>
+     <tr class="cg-1">
+       <td></td>
+       <td>&#160;&#160;&#160;
+       <a href="api/pypath.omnipath.html#module-pypath.omnipath"><code class="xref">pypath.omnipath</code></a></td><td>
+       <em></em></td></tr>
+     <tr class="cg-1">
+       <td></td>
+       <td>&#160;&#160;&#160;
+       <a href="api/pypath.omnipath.app.html#module-pypath.omnipath.app"><code class="xref">pypath.omnipath.app</code></a></td><td>
+       <em></em></td></tr>
+     <tr class="cg-1">
+       <td></td>
+       <td>&#160;&#160;&#160;
+       <a href="api/pypath.omnipath.databases.html#module-pypath.omnipath.databases"><code class="xref">pypath.omnipath.databases</code></a></td><td>
+       <em></em></td></tr>
+     <tr class="cg-1">
+       <td></td>
+       <td>&#160;&#160;&#160;
+       <a href="api/pypath.omnipath.databases.define.html#module-pypath.omnipath.databases.define"><code class="xref">pypath.omnipath.databases.define</code></a></td><td>
+       <em></em></td></tr>
+     <tr class="cg-1">
+       <td></td>
+       <td>&#160;&#160;&#160;
+       <a href="api/pypath.omnipath.export.html#module-pypath.omnipath.export"><code class="xref">pypath.omnipath.export</code></a></td><td>
+       <em></em></td></tr>
+     <tr class="cg-1">
+       <td></td>
+       <td>&#160;&#160;&#160;
+       <a href="api/pypath.omnipath.param.html#module-pypath.omnipath.param"><code class="xref">pypath.omnipath.param</code></a></td><td>
+       <em></em></td></tr>
+     <tr class="cg-1">
+       <td></td>
+       <td>&#160;&#160;&#160;
+       <a href="api/pypath.omnipath.server.html#module-pypath.omnipath.server"><code class="xref">pypath.omnipath.server</code></a></td><td>
+       <em></em></td></tr>
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418, 440, 454, 455, 456, 491, 492, 493, 494, 495, 496, 497, 498, 499, 500, 501, 502, 503, 505, 506, 507, 508, 509, 512, 515, 516, 517, 518, 519, 520, 521, 529, 542, 556, 557, 558, 559, 560, 561, 562, 563, 564, 565, 566, 567, 568, 570, 571, 573, 578, 579, 580, 586, 587, 588, 591, 593, 601, 603, 604, 605, 625, 628, 629, 631, 633, 637, 638, 639, 640, 641, 642, 644, 645, 646, 647, 648, 650, 651, 653], "serial": 3, "gener": [3, 22, 59, 62, 63, 65, 91, 92, 93, 94, 95, 96, 97, 102, 103, 108, 295, 300, 301, 302, 303, 304, 408, 409, 410, 411, 447, 467, 515, 529, 591, 651, 653, 654], "json": [3, 60, 61, 121, 343, 459, 529, 591, 651], "string": [3, 60, 61, 62, 70, 121, 142, 177, 182, 187, 197, 371, 404, 449, 451, 455, 461, 464, 474, 551, 556, 573, 578, 591, 625, 651], "full": [3, 30, 91, 93, 95, 97, 110, 176, 181, 186, 297, 298, 451, 591, 640, 641, 649, 650, 653], "content": [3, 132, 367, 384, 459, 529, 556, 650, 652, 653], "without": [3, 4, 47, 421, 529, 532, 556, 649, 654], "ani": [3, 61, 62, 70, 156, 161, 338, 551, 578, 581, 584, 633, 649, 650, 653, 654], "whitespac": 3, "line": [3, 62, 101, 102, 103, 105, 107, 108, 455, 637, 638, 639, 640, 641, 642, 651], "break": [3, 213], "return": [3, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 29, 30, 32, 33, 36, 39, 41, 43, 45, 47, 48, 49, 50, 51, 52, 53, 55, 56, 62, 63, 65, 70, 72, 73, 75, 76, 79, 80, 81, 82, 91, 92, 93, 94, 95, 96, 97, 99, 100, 104, 106, 110, 111, 112, 113, 114, 115, 117, 118, 119, 121, 132, 139, 140, 142, 143, 144, 145, 148, 150, 151, 152, 156, 157, 158, 160, 161, 162, 164, 165, 166, 167, 171, 175, 176, 180, 181, 185, 186, 197, 202, 203, 208, 225, 226, 227, 228, 236, 251, 252, 254, 297, 300, 301, 302, 303, 304, 309, 310, 312, 313, 331, 333, 334, 336, 337, 338, 339, 341, 342, 343, 344, 345, 346, 347, 348, 352, 367, 371, 375, 383, 384, 390, 403, 406, 408, 409, 410, 411, 413, 415, 416, 417, 418, 419, 420, 421, 422, 430, 437, 439, 440, 450, 451, 452, 454, 455, 456, 457, 459, 461, 464, 467, 474, 476, 486, 487, 503, 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202, 203, 381, 402, 405, 459, 556, 557, 591, 651], "integr": [35, 539, 649, 651, 653], "should": [35, 47, 147, 148, 157, 159, 221, 441, 529, 579, 637, 638, 639, 640, 641, 642, 650, 651, 654], "cach": [35, 134, 212, 213, 334, 338, 374, 381, 403, 441, 556, 559, 560, 561, 562, 563, 564, 567, 568, 587, 601, 649, 650], "fetch": [36, 347, 373, 503, 630, 651], "smbl": 36, "being": [36, 645, 647, 648], "most": [36, 156, 161, 467, 537, 562, 650, 651], "submiss": 36, "modif": [36, 604, 651], "date": [36, 102, 103, 108, 157, 161, 456, 625, 651], "author": [36, 651], "verbos": [37, 215, 563, 564, 651, 653], "get": [39, 156, 158, 161, 210, 503, 518, 556, 580, 591, 649, 651, 654], "contain": [39, 65, 110, 121, 176, 181, 186, 210, 220, 337, 375, 420, 428, 432, 441, 520, 591, 630, 637, 638, 639, 640, 641, 642, 650, 651, 654], "specif": [39, 60, 121, 233, 237, 239, 240, 241, 243, 244, 247, 254, 613, 650, 651, 654], "eg": 39, "descript": [39, 368, 573, 651, 653], "associ": [39, 302, 304, 428, 633, 645, 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529, 651, 653, 654], "assai": 48, "document": [49, 650, 651, 652], "pubm": [49, 99, 134, 158, 333, 513, 651], "convers": [49, 503, 649, 651, 653], "max_phase_threshold": 50, "indic": [50, 429, 556, 578, 637, 638, 639, 640, 641, 642, 645, 647, 648, 651], "threshold": [50, 424, 651], "maximum": 50, "phase": 50, "mechan": [51, 432, 651], "molecul": [52, 111, 136, 137, 650, 654], "variant": [54, 55, 56, 208, 650, 651], "citat": 55, "csv": [58, 63, 102, 103, 108, 367, 368, 651], "old": [58, 102, 103, 108, 529, 573, 650, 651], "callabl": [59, 121, 365, 515, 529], "glom": [59, 60, 121, 298], "spec": [59, 60, 121, 298], "protect": 59, "coalesc": 59, "io": [60, 61, 121], "arbitrari": [60, 651, 654], "depth": [60, 399], "like": [60, 62, 176, 181, 186, 341, 342, 344, 345, 346, 347, 348, 503, 518, 546, 650, 651], "read": [61, 62, 63, 121, 334, 343, 367, 529, 557, 560, 567, 568, 591, 625, 649, 650, 653], "pass": [61, 439, 455, 461, 464, 474, 503, 591, 651], "through": [61, 513, 650, 651], "col": 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"across": [65, 651], "specifi": [65, 440, 518, 638, 645, 647, 648], "direct": [65, 251, 302, 338, 496, 534, 537, 578, 580, 637, 638, 639, 640, 641, 642, 649], "consensuspathdb": [67, 68], "cpdb_interact": 68, "hprd": [68, 535, 651], "biogrid": [68, 534, 535, 651], "phosphopoint": 68, "mint": 68, "bind": [68, 334, 425, 428, 578, 651], "intact": [68, 534, 535, 651], "from_fil": 70, "requir": [70, 405, 425, 428, 429, 479, 650, 651], "restrict": [70, 111, 176, 181, 186, 464, 651], "two": [70, 110, 175, 180, 185, 383, 633, 637, 638, 639, 640, 641, 642, 650, 651], "password": [70, 110, 111, 112, 113, 114, 115, 591], "apart": [70, 297, 298, 650, 651], "rest": [70, 121, 150, 152, 157, 160, 162, 164, 166, 455, 461, 464, 474, 654], "ignor": [70, 520, 529], "_credenti": 70, "exist": [70, 290, 384, 436, 550, 552, 556, 557, 561, 582, 651], "its": [70, 112, 145, 157, 337, 455, 461, 464, 474, 550, 552, 563, 564, 578, 580, 581, 584, 617, 623, 645, 647, 648, 651, 653], "locat": [70, 650, 651, 653, 654], "": [70, 110, 236, 295, 297, 447, 503, 518, 520, 566, 650, 651, 653], "default": [70, 110, 134, 156, 157, 158, 176, 181, 186, 213, 297, 298, 300, 301, 302, 303, 304, 347, 374, 384, 436, 455, 461, 464, 474, 518, 529, 539, 540, 545, 559, 560, 561, 562, 563, 564, 565, 566, 567, 568, 570, 571, 578, 591, 605, 608, 610, 633, 637, 638, 639, 640, 641, 642, 643, 648, 650, 651, 654], "secret": [70, 556, 651, 654], "directori": [70, 338, 552, 650, 651, 653], "unchang": [70, 375, 580], "explicit": 70, "runtimeerror": 70, "relation_typ": 72, "diseas": [72, 73, 232, 233, 234, 235, 236, 239, 245, 302, 304, 309, 310, 341, 347, 365], "those": [72, 375, 578, 651], "directevid": 72, "non": [72, 290, 529, 580, 651], "too": [72, 651], "larg": [72, 405, 534, 556, 557, 591, 650, 651, 653, 654], "follow": [72, 73, 420, 518, 556, 650, 651], "chemical_gen": 72, "chemical_diseas": 72, "disease_pathwai": 72, "chemical_phenotyp": 72, "gene_diseas": 72, "vocabulary_typ": 73, "vocabulari": 73, "chemic": [73, 425, 625], "anatomi": 73, "phenotyp": 73, "enzym": [75, 76, 139, 140, 529, 649, 650, 653], "substrat": [75, 76, 202, 352, 529, 649, 650, 653], "level": [79, 81, 99, 101, 102, 103, 105, 107, 108, 164, 165, 166, 167, 177, 182, 187, 300, 301, 302, 303, 304, 432, 455, 464, 474, 506, 507, 508, 509, 529, 539, 546, 559, 560, 561, 562, 563, 564, 565, 566, 567, 568, 570, 571, 578, 579, 580, 587, 601, 650, 654], "action": [79, 81], "chembl": [80, 82, 114, 254, 625, 651, 653], "pubchem": [80, 82, 254, 419, 420, 422, 651], "html": [85, 121, 142, 331, 441, 591, 651, 654], "load": [86, 148, 213, 223, 436, 515, 529, 539, 550, 578, 580, 587, 603, 604, 606, 608, 649, 650, 653], "rescu": 86, "core_onli": 88, "direct_onli": 88, "small_scale_onli": 88, "passwd": [89, 110, 111, 112, 113, 114, 115, 558], "doe": [89, 213, 436, 518, 550, 560, 565, 570, 580, 582, 650, 651], "unknown": [89, 496, 500, 651], "reason": [89, 213, 650, 651], "In": [89, 156, 157, 158, 518, 529, 546, 556, 591, 617, 650, 651], "addit": [89, 104, 106, 213, 297, 298, 455, 461, 464, 474, 529, 556, 578, 651, 654], "binary_data": [89, 556], "curl": [89, 591, 654], "ha": [89, 156, 161, 254, 518, 529, 539, 556, 580, 591, 650, 651, 653, 654], "been": [89, 156, 158, 161, 529, 560, 650, 651, 653, 654], "chang": [89, 455, 461, 464, 474, 559, 562, 573, 650, 651], "below": [89, 208, 455, 461, 464, 474, 650, 651], "necessari": [89, 515, 650, 651], "data_origin": 91, "textmin": [91, 96, 97], "knowledg": [91, 94, 95, 290, 367], "experi": [91, 92, 93, 290, 651], "jensen": [91, 92, 93, 94, 95, 96, 97], "lab": [91, 92, 93, 94, 95, 96, 97, 251, 252, 650, 651], "warn": [91, 96, 97, 651], "enorm": [91, 96, 97], "instead": [91, 175, 180, 185, 334, 383, 384, 551, 560, 651, 652, 654], "chipseq": 99, "predict": [99, 101, 102, 103, 105, 107, 108, 213, 439, 440], "coexp": 99, "curated_sourc": 99, "chipseq_sourc": 99, "predicted_sourc": 99, "coexp_sourc": 99, "all_sourc": 99, "kegg_pathwai": [99, 101, 107], "12": [99, 321, 649, 651], "11": [99, 649, 651], "8": [99, 556, 557, 649, 650, 651], "14": [99, 529, 649, 651], "10": [99, 134, 182, 187, 249, 367, 374, 591, 593, 629, 649, 651, 654], "13": [99, 649, 651], "r": [100, 556, 557, 650, 651, 654], "packag": [100, 650, 651], "complet": [100, 347, 455, 461, 464, 474, 617, 650, 651, 653], "detail": [100, 104, 106, 110, 121, 227, 333, 425, 450, 455, 461, 464, 474, 650, 651], "origin": [100, 516, 649, 650, 653], "b": [101, 102, 103, 105, 107, 108, 539, 651], "c": [101, 107, 148, 150, 151, 152, 156, 157, 158, 160, 161, 162, 164, 165, 166, 167, 539, 581, 584, 637, 638, 639, 640, 641, 642, 651], "d": [101, 107, 518, 539, 651], "only_cur": [101, 102, 103, 105, 107, 108], "confidence_pairwis": [101, 107], "regulon": [101, 107, 654], "confid": [101, 102, 103, 105, 107, 108, 425, 428, 429, 539, 546, 651, 654], "literatur": [101, 102, 103, 105, 107, 108, 267, 277, 279, 290, 292, 293, 306, 529, 532, 536, 537, 649, 654], "comprehens": [101, 102, 103, 105, 107, 108, 591, 650, 651, 653, 654], "evid": [101, 102, 103, 105, 107, 108, 153, 155, 309, 333, 368, 425, 428, 651, 653], "chip": [101, 102, 103, 105, 107, 108], "seq": [101, 102, 103, 105, 107, 108, 651], "pwm": [101, 102, 103, 105, 107, 108], "hocomoco": [101, 102, 103, 105, 107, 108], "jaspar": [101, 102, 103, 105, 107, 108], "matric": [101, 102, 103, 105, 107, 108], "gtex": [101, 102, 103, 105, 107, 108, 344, 347], "express": [101, 102, 103, 105, 107, 108, 301, 342, 347, 427, 578, 579, 591, 650, 651, 654], "aracn": [101, 102, 103, 105, 107, 108], "As": [101, 107, 562, 563, 651, 654], "longer": [101, 107, 651], "version": [101, 102, 103, 107, 108, 313, 321, 529, 617, 650, 651, 653], "alwai": [101, 107, 546, 651], "empti": [101, 107, 455, 518, 650, 651], "saezlab": [101, 102, 103, 105, 107, 108, 650], "2018": [102, 103, 108], "up": [102, 103, 108, 157, 161, 437, 438, 441, 515, 587, 601, 603, 604, 605, 625, 651], "pleas": [102, 103, 108, 213, 578, 650, 651], "dorothea_interact": [102, 103, 108], "mous": [104, 106, 169, 444, 649, 650, 651], "support": [104, 106, 156, 161, 169, 220, 650, 651, 653], "credentials_fnam": [110, 111, 112, 113, 114, 115], "wrapper": [110, 518, 556, 573, 591, 651], "around": [110, 337, 338, 339, 518, 556, 573, 649, 650], "xml": [110, 176, 181, 186, 591, 651], "drugbank_drugs_ful": 110, "drugbank_targets_ful": 110, "second": [110, 213, 336, 337, 339, 383, 651], "mail": [110, 111, 112, 113, 114, 115, 591], "address": [110, 111, 112, 113, 114, 115, 591, 651], "regist": [110, 111, 112, 113, 114, 115, 551, 591], "account": [110, 111, 112, 113, 114, 115, 651], "drugbank_external_ids_ful": 110, "extern": [110, 228, 651], "drugbank_properties_ful": 110, "calcul": [110, 220], "statu": [111, 556, 573, 651], "variou": [112, 132, 177, 182, 187, 476, 613, 636, 650, 651], "pharma_act": [113, 115], "pharmacolog": [113, 115], "id_typ": [114, 119, 212, 213, 500, 503, 593, 594, 596, 598, 599, 625, 651], "target_id_typ": [114, 119, 363, 503, 651], "group": [114, 300, 301, 302, 303, 304, 591, 629, 650, 651, 653], "ca": [114, 119, 651], "inchikei": [114, 119, 651], "inchi": [114, 119, 254, 371, 625, 651], "smile": [114, 119, 182, 187, 254, 371, 625, 651], "formula": 114, "kegg_compound": 114, "kegg_drug": 114, "pubchem_compound": 114, "pubchem_subst": 114, "chebi": [114, 242, 254, 408, 651], "pharmgkb": 114, "het": [114, 651], "login": 114, "credenti": 114, "central": [117, 118, 119, 529, 651], "comment": [118, 651], "retain": 118, "inn": 119, "q": [121, 365], "pagin": [121, 651], "page_length": 121, "500": [121, 160, 162, 212, 213, 455, 461, 464, 474, 651], "size_param": 121, "size": [121, 213, 557, 591, 629, 651], "page_param": 121, "offset": [121, 210, 220, 221, 586, 587, 605, 651], "by_pag": 121, "page_field": 121, "total_field": 121, "totalpag": 121, "record_nam": 121, "append": [121, 529], "until": [121, 651, 652], "end": [121, 337, 651], "per": [121, 428, 429, 591], "item": [121, 518, 550, 551, 573, 651], "total": [121, 573, 640, 641], "readthedoc": 121, "en": [121, 651], "latest": [121, 651], "tutori": [121, 650, 651], "downlod": 126, "manual": [126, 536, 537, 651], "gold": 126, "init_url": [128, 556], "taxon": [132, 476, 613, 651], "metadata": [132, 374, 513, 518, 651], "db": [134, 583, 650, 651], "cache_smal": [134, 374], "metainform": 134, "client": [134, 464, 474, 625, 650, 651], "api": [134, 150, 152, 157, 160, 162, 164, 166, 381, 455, 461, 464, 474, 503, 591, 650, 653, 654], "endpoint": [134, 651], "nlm": 134, "nih": [134, 340, 343, 347, 375], "gov": [134, 343], "book": [134, 649, 650], "nbk25499": 134, "chapter4": 134, "interst": 134, "understand": [134, 213, 651], "letter": [134, 156, 157, 158, 164, 165, 166, 167, 651], "strip": [134, 455, 651], "geoprofil": [134, 651], "small": [134, 374, 381, 629, 637, 638, 639, 640, 641, 642, 650, 653], "less": [134, 374, 651], "except": [134, 374, 654], "lower": [134, 164, 165, 166, 167, 374, 422, 610, 651], "mrna": [136, 137, 653, 654], "classif": 139, "digit": 139, "ec": [139, 651], "datasheet": [142, 143, 144, 457], "symbol": [142, 143, 144, 177, 182, 187, 333, 457, 491, 498, 502, 650, 651, 654], "uniprot": [142, 143, 144, 148, 153, 155, 156, 157, 158, 210, 220, 221, 226, 230, 244, 333, 338, 339, 365, 402, 411, 437, 438, 441, 488, 496, 500, 502, 503, 516, 578, 579, 581, 584, 586, 587, 588, 601, 603, 604, 606, 608, 623, 649, 650, 653, 654], "bs4": [143, 404, 437, 441], "beautifulsoup": [143, 404, 437], "summari": [144, 651, 653], "text": [144, 367, 455, 461, 464, 474, 651], "module_nam": 145, "method_nam": 145, "submodul": [145, 650, 651, 653], "uniprot_db": 145, "all_uniprot": [145, 578, 651], "go_id": [147, 651], "deprec": [147, 148, 159], "soon": [147, 148, 159, 651], "slim": 148, "names_onli": 148, "aspect": [148, 150, 151, 152, 156, 157, 158, 160, 161, 162, 164, 165, 166, 167, 578, 580, 581, 584, 651, 654], "f": [148, 150, 151, 152, 156, 157, 158, 160, 161, 162, 164, 165, 166, 167, 518, 581, 584], "p": [148, 150, 151, 152, 156, 157, 158, 160, 161, 162, 164, 165, 166, 167, 581, 584, 651], "quickgo": [148, 150, 152, 157, 160, 161, 162, 164, 166], "ancestor": [150, 151, 152, 163, 578, 580], "where": [150, 151, 152, 160, 161, 162, 164, 165, 166, 167, 228, 520, 556, 637, 638, 639, 640, 641, 642, 651, 654], "cellular_compon": [150, 151, 152, 156, 157, 158, 160, 161, 162, 164, 165, 166, 167], "molecular_funct": [150, 151, 152, 156, 157, 158, 160, 161, 162, 164, 165, 166, 167], "biological_process": [150, 151, 152, 156, 157, 158, 160, 161, 162, 164, 165, 166, 167], "respect": [150, 151, 152, 156, 157, 158, 160, 161, 162, 164, 165, 166, 167, 651], "amigo": [151, 156, 158, 161, 165, 167], "evidence_cod": [153, 155], "goa": [153, 155, 157, 651], "output": [153, 155, 175, 180, 185, 381, 428, 625, 651], "prefer": [156, 157, 158, 161, 371, 650, 651], "recent": [156, 157, 161, 467, 650, 651], "go_annotations_solr": 156, "mysql": [156, 161, 381, 651, 653], "instanc": [156, 161, 437, 529, 540, 542, 556, 557, 571, 573, 582, 587, 593, 598, 629, 633, 650, 651, 654], "sinc": [156, 161, 651], "dec": [156, 161], "2016": [156, 161], "unfortun": [156, 161, 651], "ceas": [156, 161], "flexibl": [156, 161, 529, 651], "highest": [156, 161, 580, 654], "perform": [156, 161, 212, 213, 300, 301, 302, 303, 304, 455, 461, 464, 474, 556, 567, 568, 651], "solr": [156, 158, 161, 167], "far": [156, 161], "same": [156, 161, 175, 177, 180, 182, 185, 187, 212, 381, 441, 451, 455, 461, 464, 474, 491, 496, 498, 502, 516, 529, 651], "featur": [156, 161, 506, 507, 508, 509, 603, 604, 649, 651], "is_a": 157, "part_of": 157, "go_annotations_goa": 157, "contrari": 157, "super": 157, "slow": [157, 381, 556, 651], "otherwis": [157, 226, 228, 297, 459, 518, 651], "befor": [158, 529, 573, 651], "now": [158, 573, 591, 651], "implement": [158, 236, 573, 591, 633, 637, 638, 639, 640, 641, 642, 643, 647, 648, 650, 653, 654], "swissprot": [159, 338, 464, 476, 483, 484, 485, 486, 487, 488, 502, 503, 608, 650, 651], "ye": [159, 503], "quickgo_download_s": [160, 162], "descend": [160, 161, 162, 163, 578, 580], "go_terms_solr": [160, 162], "go_descendants_quickgo": 161, "exampl": [161, 182, 187, 455, 461, 464, 474, 505, 539, 559, 560, 561, 562, 563, 564, 565, 566, 567, 568, 570, 571, 578, 625, 649, 650], "unabl": 161, "graph": [161, 580, 581, 584, 629, 630, 633, 636, 643, 645, 647, 648, 651, 653], "nice": [161, 651], "desc": 163, "turn": [163, 560, 561, 562], "swap": 163, "upper": [164, 165, 166, 167], "graph_attr": 171, "vertex_attr": 171, "edge_attr": 171, "metabolit": [174, 175, 176, 177, 186, 196, 197, 199, 651, 653], "itert": [174, 179, 184], "over": [174, 179, 184, 455, 467, 603, 604, 653], "id_type_a": [175, 180, 185, 383, 451, 491, 492, 493, 494, 495, 496, 497, 498, 499, 501, 502, 503, 651], "id_type_b": [175, 180, 185, 383, 451, 491, 492, 493, 494, 495, 496, 497, 498, 499, 501, 502, 503, 651], "head": [175, 176, 177, 180, 181, 182, 185, 186, 187, 651], "purpos": [175, 180, 185, 505, 529, 651], "weight": [175, 180, 185, 651], "though": [175, 180, 185, 651, 654], "guarante": [175, 180, 185, 651], "meaning": [175, 180, 185], "id_field": [175, 180, 185], "simple_field": [175, 180, 185], "anoth": [175, 177, 180, 182, 185, 187, 578, 625, 650, 651, 654], "n": [175, 176, 177, 180, 181, 182, 185, 186, 187, 651], "peek": [175, 176, 177, 180, 181, 182, 185, 186, 187, 651], "schema": [176, 177, 181, 182, 186, 187, 651], "either": [176, 303, 338, 371, 384, 451, 518, 556, 580, 591, 625, 651, 654], "defin": [176, 181, 186, 337, 425, 428, 429, 503, 529, 637, 638, 639, 640, 641, 642, 645, 647, 648, 649, 650, 654], "By": [176, 181, 186, 436, 455, 529, 565, 570, 578, 580, 591, 651, 654], "cover": [176, 181, 186, 464, 650, 651], "nearli": [176, 181, 186], "don": [176, 181, 186, 650, 651, 652, 654], "within": [176, 181, 186, 455, 461, 464, 474, 518, 573, 633, 645, 648, 650, 651, 654], "task": [176, 181, 186, 573], "case": [176, 177, 181, 182, 186, 187, 213, 518, 537, 557, 579, 591, 650, 651, 654], "metabolite_schema": 176, "proteins_schema": [176, 186, 651], "creat": [176, 181, 186, 496, 529, 546, 556, 573, 578, 650], "your": [176, 181, 186, 591, 651, 654], "own": [176, 181, 186, 651, 653], "interest": [176, 181, 186, 503, 649, 650, 652], "These": [176, 177, 181, 182, 186, 187, 221, 290, 455, 461, 464, 474, 491, 498, 502, 503, 534, 536, 537, 550, 651, 654], "deepli": [176, 181, 186], "nest": [176, 177, 181, 182, 186, 187, 455, 461, 464, 474, 651], "named_field": [177, 182, 187], "simpl": [177, 182, 187, 455, 461, 464, 474, 529, 650, 651, 654], "altern": [177, 182, 187, 213, 455, 461, 464, 474, 579, 650, 651, 654], "sequeti": [177, 182, 187], "step": [177, 182, 187, 529, 568, 573, 651], "special": [177, 182, 187, 333, 529, 651, 653], "sub": [177, 182, 187], "while": [177, 182, 187, 338, 381, 384, 529, 556, 573, 650, 651], "expand": [177, 182, 187, 651], "row": [177, 182, 187, 421, 651, 654], "Be": [177, 182, 187], "care": [177, 182, 187, 651], "latter": [177, 182, 187, 503, 651], "becaus": [177, 182, 187, 341, 342, 344, 345, 346, 347, 348, 533, 651, 654], "appli": [177, 182, 187, 405, 455, 529, 567, 651], "combinatori": [177, 182, 187, 651], "rown": [177, 182, 187], "alreadi": [177, 182, 187, 381, 441, 529, 539, 580, 651], "35": [177, 182, 187, 651], "excess": [177, 182, 187], "memori": [177, 182, 187, 223, 384, 405, 587, 601, 603, 604, 650, 651, 653], "time": [177, 182, 187, 213, 226, 436, 529, 650, 651], "differ": [177, 182, 187, 455, 503, 529, 546, 650, 651, 653, 654], "top": [177, 182, 187, 300, 301, 302, 303, 304, 455, 464, 474, 524, 651], "metabolites_schema": [181, 651], "block": [182, 187], "hmdb_metabolites_t": 182, "state": [182, 187, 651], "substitu": [182, 187, 651], "proteins_t": [187, 651], "definit": [190, 439, 529, 546, 649, 650, 653], "hmdb_id": [196, 197], "show": [196, 385, 556, 651, 654], "2d": [196, 197, 633], "given": [196, 210, 220, 300, 301, 302, 303, 304, 338, 518, 578, 591, 593, 598, 603, 604, 633, 637, 638, 639, 640, 641, 642, 645, 647, 648, 651], "browser": [196, 376, 651, 654], "pictur": 197, "svg": 197, "save": [197, 436, 649, 650], "iterpars": 199, "in_vivo": [201, 202, 203], "preprocess": [201, 362, 436, 455, 603, 604, 650], "ptm": [202, 529, 533, 534, 651, 653, 654], "kinas": [202, 352, 455, 461, 464, 474, 651, 654], "missens": 208, "uniprotkb": [208, 226, 363, 651], "swiss": [208, 651], "prot": [208, 651], "interaction3d": 210, "residu": [210, 220, 587, 589, 605, 651], "chain": [210, 220, 337, 586, 587, 589, 651], "pdb": [210, 220, 221, 337, 601, 651, 654], "stuctur": 210, "so": [210, 441, 559, 565, 567, 570, 650, 651], "we": [210, 425, 428, 633, 645, 648, 650, 651, 652, 654], "obtain": [210, 439, 503, 513, 651], "instruct": [210, 651], "pfam": [210, 651], "ppi": [212, 213, 519, 650, 651], "uniprotkb_ac": [212, 213], "mydomain": [212, 213], "hmm": [212, 213], "maxwait": [212, 213], "180": [212, 213], "part_siz": [212, 213], "get_ielm_hug": 212, "domain": [213, 220, 337, 432, 441, 603, 604, 651, 654], "motif": [213, 432, 604, 651], "chunk": [213, 347], "retri": 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"Integrated databases": [[650, "integrated-databases"]], "Database management": [[650, "database-management"]], "Further modules in pypath": [[650, "further-modules-in-pypath"]], "ID conversion": [[650, "id-conversion"]], "Homology translation": [[650, "homology-translation"]], "FAQ": [[650, "faq"]], "Contact": [[650, "contact"]], "Impressum": [[650, "impressum"]], "History and releases": [[650, "history-and-releases"]], "The pypath book": [[651, "The-pypath-book"]], "Introduction": [[651, "Introduction"]], "Build, load and save databases": [[651, "Build,-load-and-save-databases"]], "The OmniPath app": [[651, "The-OmniPath-app"]], "Built-in database definitions": [[651, "Built-in-database-definitions"]], "Networks": [[651, "Networks"]], "Strictly literature curated network": [[651, "Strictly-literature-curated-network"]], "The OmniPath network with extra activity flow, enzyme-substrate and ligand-receptor interactions": [[651, 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"Is it failing only for you?": [[651, "Is-it-failing-only-for-you?"]], "Read the log": [[651, "Read-the-log"]], "TLS (SSL, HTTPS) errors": [[651, "TLS-(SSL,-HTTPS)-errors"]], "Resources": [[651, "Resources"]], "Licenses": [[651, "Licenses"]], "Example: build a network for commercial use": [[651, "Example:-build-a-network-for-commercial-use"]], "Resource information": [[651, "Resource-information"]], "Resource definitions for a certain database or dataset": [[651, "Resource-definitions-for-a-certain-database-or-dataset"]], "Building networks": [[651, "Building-networks"]], "Which network datasets are pre-defined in pypath?": [[651, "Which-network-datasets-are-pre-defined-in-pypath?"]], "The Network object": [[651, "The-Network-object"]], "Network in pandas.DataFrame": [[651, "Network-in-pandas.DataFrame"]], "Self interactions (loop edges) in the network": [[651, "Self-interactions-(loop-edges)-in-the-network"]], "Molecular complexes in the network": [[651, 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manager": [[651, "Load-the-full-annotations-database-by-the-database-manager"]], "Load only selected annotations": [[651, "Load-only-selected-annotations"]], "Data frames of annotations": [[651, "Data-frames-of-annotations"]], "Inter-cellular signaling roles": [[651, "Inter-cellular-signaling-roles"]], "Build an intercellular communication network": [[651, "Build-an-intercellular-communication-network"]], "Quantitative overview of intercell annotations": [[651, "Quantitative-overview-of-intercell-annotations"]], "Intercell database as data frame": [[651, "Intercell-database-as-data-frame"]], "Browse intercell categories": [[651, "Browse-intercell-categories"]], "Gene Ontology": [[651, "Gene-Ontology"]], "Protein complex objects": [[651, "Protein-complex-objects"]], "Protein complex data frame": [[651, "Protein-complex-data-frame"]], "Saving datasets as pickles": [[651, "Saving-datasets-as-pickles"]], "Log messages and sessions": [[651, "Log-messages-and-sessions"]], "Basic info about 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"api/pypath.inputs.encode", "api/pypath.inputs.encode.encode_tf_mirna_interactions", "api/pypath.inputs.ensembl", "api/pypath.inputs.ensembl.ensembl_organisms", "api/pypath.inputs.eutils", "api/pypath.inputs.eutils.esummary", "api/pypath.inputs.exocarta", "api/pypath.inputs.exocarta.get_exocarta", "api/pypath.inputs.exocarta.get_vesiclepedia", "api/pypath.inputs.expasy", "api/pypath.inputs.expasy.expasy_enzyme_classes", "api/pypath.inputs.expasy.expasy_enzymes", "api/pypath.inputs.genecards", "api/pypath.inputs.genecards.genecards_datasheet", "api/pypath.inputs.genecards.genecards_soup", "api/pypath.inputs.genecards.genecards_summaries", "api/pypath.inputs.get_method", "api/pypath.inputs.go", "api/pypath.inputs.go.get_go_desc", "api/pypath.inputs.go.get_go_quick", "api/pypath.inputs.go.get_goslim", "api/pypath.inputs.go.go_ancestors", "api/pypath.inputs.go.go_ancestors_goose", "api/pypath.inputs.go.go_ancestors_quickgo", "api/pypath.inputs.go.go_annotations", "api/pypath.inputs.go.go_annotations_all", "api/pypath.inputs.go.go_annotations_goa", "api/pypath.inputs.go.go_annotations_goose", "api/pypath.inputs.go.go_annotations_quickgo", "api/pypath.inputs.go.go_annotations_solr", "api/pypath.inputs.go.go_annotations_uniprot", "api/pypath.inputs.go.go_descendants", "api/pypath.inputs.go.go_descendants_goose", "api/pypath.inputs.go.go_descendants_quickgo", "api/pypath.inputs.go.go_descendants_to_ancestors", "api/pypath.inputs.go.go_terms", "api/pypath.inputs.go.go_terms_goose", "api/pypath.inputs.go.go_terms_quickgo", "api/pypath.inputs.go.go_terms_solr", "api/pypath.inputs.gpcrdb", "api/pypath.inputs.gpcrdb.gpcrdb_annotations", "api/pypath.inputs.graphviz", "api/pypath.inputs.graphviz.graphviz_attrs", "api/pypath.inputs.guide2pharma", "api/pypath.inputs.guide2pharma.guide2pharma_complexes", "api/pypath.inputs.guide2pharma.guide2pharma_download", "api/pypath.inputs.guide2pharma.guide2pharma_interactions", "api/pypath.inputs.gutmgene", "api/pypath.inputs.gutmgene.GutmgeneAnnotation", "api/pypath.inputs.gutmgene.GutmgeneRaw", "api/pypath.inputs.gutmgene.gutmgene_annotations", "api/pypath.inputs.gutmgene.gutmgene_raw", "api/pypath.inputs.havugimana", "api/pypath.inputs.havugimana.get_havugimana", "api/pypath.inputs.havugimana.havugimana_complexes", "api/pypath.inputs.hgnc", "api/pypath.inputs.hgnc.hgnc_genegroups", "api/pypath.inputs.hippie", "api/pypath.inputs.hippie.hippie_interactions", "api/pypath.inputs.hmdb", "api/pypath.inputs.hmdb.common", "api/pypath.inputs.hmdb.common.iter", "api/pypath.inputs.hmdb.common.mapping", "api/pypath.inputs.hmdb.common.raw", "api/pypath.inputs.hmdb.common.table", "api/pypath.inputs.hmdb.metabolites", "api/pypath.inputs.hmdb.metabolites.iter", "api/pypath.inputs.hmdb.metabolites.mapping", "api/pypath.inputs.hmdb.metabolites.raw", "api/pypath.inputs.hmdb.metabolites.table", "api/pypath.inputs.hmdb.proteins", "api/pypath.inputs.hmdb.proteins.iter", "api/pypath.inputs.hmdb.proteins.mapping", "api/pypath.inputs.hmdb.proteins.raw", "api/pypath.inputs.hmdb.proteins.table", "api/pypath.inputs.hmdb.schema", "api/pypath.inputs.hmdb.schema.common", "api/pypath.inputs.hmdb.schema.common.Field", "api/pypath.inputs.hmdb.schema.metabolites", "api/pypath.inputs.hmdb.schema.proteins", "api/pypath.inputs.hmdb.structures", "api/pypath.inputs.hmdb.structures.sdf", "api/pypath.inputs.hmdb.visual", "api/pypath.inputs.hmdb.visual.show_structure", "api/pypath.inputs.hmdb.visual.structure_svg", "api/pypath.inputs.hmdb.xml", "api/pypath.inputs.hmdb.xml.hmdb_xml", "api/pypath.inputs.homologene", "api/pypath.inputs.homologene.get_homologene", "api/pypath.inputs.homologene.homologene_dict", "api/pypath.inputs.homologene.homologene_uniprot_dict", "api/pypath.inputs.hpmr", "api/pypath.inputs.hpmr.HpmrInteraction", "api/pypath.inputs.hpmr.get_hpmr", "api/pypath.inputs.hpmr.hpmr_annotations", "api/pypath.inputs.hpmr.hpmr_complexes", "api/pypath.inputs.hpmr.hpmr_interactions", "api/pypath.inputs.hpo", "api/pypath.inputs.hpo.hpo_annotations", "api/pypath.inputs.hpo.hpo_diseases", "api/pypath.inputs.hpo.hpo_ontology", "api/pypath.inputs.hpo.hpo_terms", "api/pypath.inputs.hprd", "api/pypath.inputs.hprd.get_hprd", "api/pypath.inputs.hprd.hprd_enzyme_substrate", "api/pypath.inputs.hprd.hprd_interactions", "api/pypath.inputs.hprd.hprd_interactions_htp", "api/pypath.inputs.htri", "api/pypath.inputs.htri.htri_interactions", "api/pypath.inputs.humancellmap", "api/pypath.inputs.humancellmap.humancellmap_annotations", "api/pypath.inputs.humap", "api/pypath.inputs.humap.humap2_complexes", "api/pypath.inputs.humap.humap_complexes", "api/pypath.inputs.humsavar", "api/pypath.inputs.humsavar.uniprot_variants", "api/pypath.inputs.huri", "api/pypath.inputs.huri.hi_i_interactions", "api/pypath.inputs.huri.hi_ii_interactions", "api/pypath.inputs.huri.hi_iii_old", "api/pypath.inputs.huri.hi_union_interactions", "api/pypath.inputs.huri.huri_interactions", "api/pypath.inputs.huri.lit_bm_13_interactions", "api/pypath.inputs.huri.lit_bm_17_interactions", "api/pypath.inputs.huri.lit_bm_interactions", "api/pypath.inputs.huri.rolland_hi_ii_14", "api/pypath.inputs.huri.vidal_hi_iii_old", "api/pypath.inputs.huri.yang2016_interactions", "api/pypath.inputs.huri.yu2011_interactions", "api/pypath.inputs.i3d", "api/pypath.inputs.i3d.get_i3d", "api/pypath.inputs.icellnet", "api/pypath.inputs.icellnet.IcellnetRecord", "api/pypath.inputs.icellnet.icellnet_annotations", "api/pypath.inputs.icellnet.icellnet_complexes", "api/pypath.inputs.icellnet.icellnet_interactions", "api/pypath.inputs.ielm", "api/pypath.inputs.ielm.get_ielm", "api/pypath.inputs.ielm.get_ielm_huge", "api/pypath.inputs.imweb", "api/pypath.inputs.imweb.get_imweb", "api/pypath.inputs.imweb.get_imweb_req", "api/pypath.inputs.innatedb", "api/pypath.inputs.innatedb.innatedb_interactions", "api/pypath.inputs.instruct", "api/pypath.inputs.instruct.get_instruct", "api/pypath.inputs.instruct.get_instruct_offsets", "api/pypath.inputs.intact", "api/pypath.inputs.intact.intact_interactions", "api/pypath.inputs.integrins", "api/pypath.inputs.integrins.get_integrins", "api/pypath.inputs.interpro", "api/pypath.inputs.interpro.interpro2go_annotations", "api/pypath.inputs.interpro.interpro_annotations", "api/pypath.inputs.interpro.interpro_entries", "api/pypath.inputs.interpro.interpro_xrefs", "api/pypath.inputs.intogen", "api/pypath.inputs.intogen.intogen_annotations", "api/pypath.inputs.ipi", "api/pypath.inputs.ipi.ipi_uniprot", "api/pypath.inputs.iptmnet", "api/pypath.inputs.iptmnet.IptmnetInteraction", "api/pypath.inputs.iptmnet.iptmnet_interactions", "api/pypath.inputs.italk", "api/pypath.inputs.italk.italk_annotations", "api/pypath.inputs.italk.italk_interactions", "api/pypath.inputs.italk.italk_raw", "api/pypath.inputs.kea", "api/pypath.inputs.kea.kea_enzyme_substrate", "api/pypath.inputs.kea.kea_interactions", "api/pypath.inputs.kegg", "api/pypath.inputs.kegg.KeggPathway", "api/pypath.inputs.kegg.kegg_dbget", "api/pypath.inputs.kegg.kegg_interactions", "api/pypath.inputs.kegg.kegg_medicus", "api/pypath.inputs.kegg.kegg_medicus_complexes", "api/pypath.inputs.kegg.kegg_medicus_interactions", "api/pypath.inputs.kegg.kegg_pathway_annotations", "api/pypath.inputs.kegg.kegg_pathway_annotations_pathwaycommons", "api/pypath.inputs.kegg.kegg_pathways", "api/pypath.inputs.kegg_api", "api/pypath.inputs.kegg_api.disease_to_drug", "api/pypath.inputs.kegg_api.disease_to_gene", "api/pypath.inputs.kegg_api.disease_to_pathway", "api/pypath.inputs.kegg_api.drug_to_disease", "api/pypath.inputs.kegg_api.drug_to_drug", "api/pypath.inputs.kegg_api.drug_to_gene", "api/pypath.inputs.kegg_api.drug_to_pathway", "api/pypath.inputs.kegg_api.gene_to_disease", "api/pypath.inputs.kegg_api.gene_to_drug", "api/pypath.inputs.kegg_api.gene_to_pathway", "api/pypath.inputs.kegg_api.kegg_drug_to_chebi", "api/pypath.inputs.kegg_api.kegg_gene_to_ncbi_geneid", "api/pypath.inputs.kegg_api.kegg_gene_to_uniprot", "api/pypath.inputs.kegg_api.pathway_to_disease", "api/pypath.inputs.kegg_api.pathway_to_drug", "api/pypath.inputs.kegg_api.pathway_to_gene", "api/pypath.inputs.kinasedotcom", "api/pypath.inputs.kinasedotcom.kinasedotcom_annotations", "api/pypath.inputs.kirouac2010", "api/pypath.inputs.kirouac2010.kirouac2010_interactions", "api/pypath.inputs.lambert2018", "api/pypath.inputs.lambert2018.lambert2018_annotations", "api/pypath.inputs.lambert2018.lambert2018_s1_raw", "api/pypath.inputs.laudanna", "api/pypath.inputs.laudanna.laudanna_directions", "api/pypath.inputs.laudanna.laudanna_effects", "api/pypath.inputs.li2012", "api/pypath.inputs.li2012.get_li2012", "api/pypath.inputs.li2012.li2012_dmi", "api/pypath.inputs.li2012.li2012_enzyme_substrate", "api/pypath.inputs.li2012.li2012_interactions", "api/pypath.inputs.lincs", "api/pypath.inputs.lincs.lincs_compounds", "api/pypath.inputs.lmpid", "api/pypath.inputs.lmpid.lmpid_dmi", "api/pypath.inputs.lmpid.lmpid_interactions", "api/pypath.inputs.lmpid.load_lmpid", "api/pypath.inputs.lncdisease", "api/pypath.inputs.lncdisease.lncdisease_interactions", "api/pypath.inputs.lncrnadb", "api/pypath.inputs.lncrnadb.lncrnadb_interactions", "api/pypath.inputs.locate", "api/pypath.inputs.locate.locate_localizations", "api/pypath.inputs.lrdb", "api/pypath.inputs.lrdb.LrdbAnnotation", "api/pypath.inputs.lrdb.lrdb_annotations", "api/pypath.inputs.lrdb.lrdb_interactions", "api/pypath.inputs.macrophage", "api/pypath.inputs.macrophage.macrophage_interactions", "api/pypath.inputs.main", "api/pypath.inputs.matrisome", "api/pypath.inputs.matrisome.matrisome_annotations", "api/pypath.inputs.matrixdb", "api/pypath.inputs.matrixdb.matrixdb_annotations", "api/pypath.inputs.matrixdb.matrixdb_ecm_proteins", "api/pypath.inputs.matrixdb.matrixdb_interactions", "api/pypath.inputs.matrixdb.matrixdb_membrane_proteins", "api/pypath.inputs.matrixdb.matrixdb_secreted_proteins", "api/pypath.inputs.mcam", "api/pypath.inputs.mcam.mcam_cell_adhesion_molecules", "api/pypath.inputs.membranome", "api/pypath.inputs.membranome.membranome_annotations", "api/pypath.inputs.mimp", "api/pypath.inputs.mimp.get_kinase_class", "api/pypath.inputs.mimp.mimp_enzyme_substrate", "api/pypath.inputs.mimp.mimp_interactions", "api/pypath.inputs.mir2disease", "api/pypath.inputs.mir2disease.mir2disease_interactions", "api/pypath.inputs.mirbase", "api/pypath.inputs.mirbase.get_mirbase_aliases", "api/pypath.inputs.mirbase.mirbase_ids", "api/pypath.inputs.mirbase.mirbase_mature", "api/pypath.inputs.mirbase.mirbase_mature_all", "api/pypath.inputs.mirbase.mirbase_precursor", "api/pypath.inputs.mirbase.mirbase_precursor_all", "api/pypath.inputs.mirbase.mirbase_precursor_to_mature", "api/pypath.inputs.mirdeathdb", "api/pypath.inputs.mirdeathdb.mirdeathdb_interactions", "api/pypath.inputs.mirecords", "api/pypath.inputs.mirecords.mirecords_interactions", "api/pypath.inputs.mirtarbase", "api/pypath.inputs.mirtarbase.mirtarbase_interactions", "api/pypath.inputs.mitab", "api/pypath.inputs.mitab.mitab_field_list", "api/pypath.inputs.mitab.mitab_field_uniprot", "api/pypath.inputs.mppi", "api/pypath.inputs.mppi.mppi_interactions", "api/pypath.inputs.msigdb", "api/pypath.inputs.msigdb.msigdb_annotations", "api/pypath.inputs.msigdb.msigdb_download", "api/pypath.inputs.msigdb.msigdb_download_collections", "api/pypath.inputs.ncrdeathdb", "api/pypath.inputs.ncrdeathdb.ncrdeathdb_interactions", "api/pypath.inputs.negatome", "api/pypath.inputs.negatome.negatome_interactions", "api/pypath.inputs.netbiol", "api/pypath.inputs.netbiol.arn_interactions", "api/pypath.inputs.netbiol.nrf2ome_interactions", "api/pypath.inputs.netpath", "api/pypath.inputs.netpath.netpath_interactions", "api/pypath.inputs.netpath.netpath_names", "api/pypath.inputs.netpath.netpath_pathway_annotations", "api/pypath.inputs.offsides", "api/pypath.inputs.offsides.offsides_side_effects", "api/pypath.inputs.oma", "api/pypath.inputs.oma.oma_orthologs", "api/pypath.inputs.oma.oma_table", "api/pypath.inputs.ontology", "api/pypath.inputs.ontology.listof_ontologies", "api/pypath.inputs.ontology.ontology", "api/pypath.inputs.opentargets", "api/pypath.inputs.opentargets.opentargets_adverse_reactions", "api/pypath.inputs.opentargets.opentargets_baseline_expression", "api/pypath.inputs.opentargets.opentargets_direct_score", "api/pypath.inputs.opentargets.opentargets_general", "api/pypath.inputs.opentargets.opentargets_indirect_score", "api/pypath.inputs.opm", "api/pypath.inputs.opm.opm_annotations", "api/pypath.inputs.oreganno", "api/pypath.inputs.oreganno.oreganno_interactions", "api/pypath.inputs.oreganno.oreganno_raw", "api/pypath.inputs.panglaodb", "api/pypath.inputs.panglaodb.panglaodb_annotations", "api/pypath.inputs.panglaodb.panglaodb_raw", "api/pypath.inputs.pathophenodb", "api/pypath.inputs.pathophenodb.DiseasePathogen", "api/pypath.inputs.pathophenodb.disease_pathogen_interactions", "api/pypath.inputs.pathwaycommons", "api/pypath.inputs.pathwaycommons.PathwayCommonsInteraction", "api/pypath.inputs.pathwaycommons.PathwayCommonsResource", "api/pypath.inputs.pathwaycommons.pathwaycommons_bind_interactions", "api/pypath.inputs.pathwaycommons.pathwaycommons_biogrid_interactions", "api/pypath.inputs.pathwaycommons.pathwaycommons_corum_interactions", "api/pypath.inputs.pathwaycommons.pathwaycommons_dip_interactions", "api/pypath.inputs.pathwaycommons.pathwaycommons_hprd_interactions", "api/pypath.inputs.pathwaycommons.pathwaycommons_inoh_interactions", "api/pypath.inputs.pathwaycommons.pathwaycommons_intact_interactions", "api/pypath.inputs.pathwaycommons.pathwaycommons_interactions", "api/pypath.inputs.pathwaycommons.pathwaycommons_kegg_interactions", "api/pypath.inputs.pathwaycommons.pathwaycommons_netpath_interactions", "api/pypath.inputs.pathwaycommons.pathwaycommons_panther_interactions", "api/pypath.inputs.pathwaycommons.pathwaycommons_phosphosite_interactions", "api/pypath.inputs.pathwaycommons.pathwaycommons_reactome_interactions", "api/pypath.inputs.pathwaycommons.pathwaycommons_wikipathways_interactions", "api/pypath.inputs.pazar", "api/pypath.inputs.pazar.pazar_interactions", "api/pypath.inputs.pdb", "api/pypath.inputs.pdb.pdb_chains", "api/pypath.inputs.pdb.pdb_complexes", "api/pypath.inputs.pdb.pdb_uniprot", "api/pypath.inputs.pdzbase", "api/pypath.inputs.pdzbase.pdzbase_interactions", "api/pypath.inputs.pepcyber", "api/pypath.inputs.pepcyber.pepcyber_details", "api/pypath.inputs.pepcyber.pepcyber_interactions", "api/pypath.inputs.pfam", "api/pypath.inputs.pfam.pfam_names", "api/pypath.inputs.pfam.pfam_pdb", "api/pypath.inputs.pfam.pfam_regions", "api/pypath.inputs.pfam.pfam_uniprot", "api/pypath.inputs.pharos", "api/pypath.inputs.pharos.pharos_diseases", "api/pypath.inputs.pharos.pharos_expression", "api/pypath.inputs.pharos.pharos_general", "api/pypath.inputs.pharos.pharos_gtex", "api/pypath.inputs.pharos.pharos_ligands", "api/pypath.inputs.pharos.pharos_orthologs", "api/pypath.inputs.pharos.pharos_targets", "api/pypath.inputs.pharos.pharos_xrefs", "api/pypath.inputs.phobius", "api/pypath.inputs.phobius.phobius_annotations", "api/pypath.inputs.phosphatome", "api/pypath.inputs.phosphatome.phosphatome_annotations", "api/pypath.inputs.phosphoelm", "api/pypath.inputs.phosphoelm.phosphoelm_enzyme_substrate", "api/pypath.inputs.phosphoelm.phosphoelm_interactions", "api/pypath.inputs.phosphoelm.phosphoelm_kinases", "api/pypath.inputs.phosphonetworks", "api/pypath.inputs.phosphonetworks.phosphonetworks_enzyme_substrate", "api/pypath.inputs.phosphonetworks.phosphonetworks_interactions", "api/pypath.inputs.phosphopoint", "api/pypath.inputs.phosphopoint.phosphopoint_directions", "api/pypath.inputs.phosphopoint.phosphopoint_interactions", "api/pypath.inputs.phosphosite", "api/pypath.inputs.phosphosite.phosphosite_directions", "api/pypath.inputs.phosphosite.phosphosite_enzyme_substrate", "api/pypath.inputs.phosphosite.phosphosite_interactions", "api/pypath.inputs.phosphosite.phosphosite_interactions_all", "api/pypath.inputs.phosphosite.phosphosite_interactions_curated", "api/pypath.inputs.phosphosite.phosphosite_interactions_new", "api/pypath.inputs.phosphosite.phosphosite_interactions_noref", "api/pypath.inputs.phosphosite.phosphosite_ptm_orthology", "api/pypath.inputs.phosphosite.phosphosite_ptms", "api/pypath.inputs.phosphosite.phosphosite_regsites", "api/pypath.inputs.phosphosite.phosphosite_regsites_one_organism", "api/pypath.inputs.phosphosite.regsites_tab", "api/pypath.inputs.pisa", "api/pypath.inputs.pisa.PisaBond", "api/pypath.inputs.pisa.pisa_bonds", "api/pypath.inputs.pisa.pisa_interfaces", "api/pypath.inputs.pro", "api/pypath.inputs.pro.get_pro", "api/pypath.inputs.pro.pro_mapping", "api/pypath.inputs.progeny", "api/pypath.inputs.progeny.progeny_annotations", "api/pypath.inputs.progeny.progeny_raw", "api/pypath.inputs.proteinatlas", "api/pypath.inputs.proteinatlas.get_proteinatlas", "api/pypath.inputs.proteinatlas.proteinatlas_annotations", "api/pypath.inputs.proteinatlas.proteinatlas_secretome_annotations", "api/pypath.inputs.proteinatlas.proteinatlas_subcellular_annotations", "api/pypath.inputs.proteins", "api/pypath.inputs.proteins.variants", "api/pypath.inputs.protmapper", "api/pypath.inputs.protmapper.get_protmapper", "api/pypath.inputs.protmapper.protmapper_enzyme_substrate", "api/pypath.inputs.protmapper.protmapper_interactions", "api/pypath.inputs.pubchem", "api/pypath.inputs.pubchem.pubchem_mapping", "api/pypath.inputs.pubmed", "api/pypath.inputs.pubmed.get_pmid", "api/pypath.inputs.pubmed.get_pubmeds", "api/pypath.inputs.pubmed.only_pmids", "api/pypath.inputs.pubmed.open_pubmed", "api/pypath.inputs.pubmed.pmids_dict", "api/pypath.inputs.pubmed.pmids_list", "api/pypath.inputs.ramilowski2015", "api/pypath.inputs.ramilowski2015.ramilowski_interactions", "api/pypath.inputs.ramilowski2015.ramilowski_locations", "api/pypath.inputs.ramp", "api/pypath.inputs.ramp.ramp_id_types", "api/pypath.inputs.ramp.ramp_id_types_2", "api/pypath.inputs.ramp.ramp_list_tables", "api/pypath.inputs.ramp.ramp_mapping", "api/pypath.inputs.ramp.ramp_raw", "api/pypath.inputs.ramp.ramp_show_tables", "api/pypath.inputs.rdata", "api/pypath.inputs.reaction", "api/pypath.inputs.reaction.acsn_biopax", "api/pypath.inputs.reaction.acsn_interactions_2", "api/pypath.inputs.reaction.get_acsn_effects", "api/pypath.inputs.reaction.get_controls", "api/pypath.inputs.reaction.get_interactions", "api/pypath.inputs.reaction.get_reactions", "api/pypath.inputs.reaction.get_soup", "api/pypath.inputs.reaction.panther_biopax", "api/pypath.inputs.reaction.panther_interactions", "api/pypath.inputs.reaction.pid_biopax", "api/pypath.inputs.reaction.pid_interactions", "api/pypath.inputs.reaction.process_complex", "api/pypath.inputs.reaction.process_controls", "api/pypath.inputs.reaction.process_reactions", "api/pypath.inputs.reaction.reactions_biopax", "api/pypath.inputs.reaction.reactome_biopax", "api/pypath.inputs.reaction.reactome_bs", "api/pypath.inputs.reaction.reactome_interactions", "api/pypath.inputs.reaction.reactome_sbml", "api/pypath.inputs.reactome", "api/pypath.inputs.reactome.reactome_chebis", "api/pypath.inputs.reactome.reactome_pathway_relations", "api/pypath.inputs.reactome.reactome_pathways", "api/pypath.inputs.reactome.reactome_uniprots", "api/pypath.inputs.scconnect", "api/pypath.inputs.scconnect.scconnect_annotations", "api/pypath.inputs.scconnect.scconnect_complexes", "api/pypath.inputs.scconnect.scconnect_interactions", "api/pypath.inputs.science", "api/pypath.inputs.science.science_download", "api/pypath.inputs.sider", "api/pypath.inputs.sider.SiderDrug", "api/pypath.inputs.sider.SiderSideeffect", "api/pypath.inputs.sider.SiderSideeffectMeddra", "api/pypath.inputs.sider.SiderSideeffetFrequency", "api/pypath.inputs.sider.sider_drug_names", "api/pypath.inputs.sider.sider_meddra_side_effects", "api/pypath.inputs.sider.sider_side_effect_frequencies", "api/pypath.inputs.sider.sider_side_effects", "api/pypath.inputs.signalink", "api/pypath.inputs.signalink.signalink_annotations", "api/pypath.inputs.signalink.signalink_function_annotations", "api/pypath.inputs.signalink.signalink_interactions", "api/pypath.inputs.signalink.signalink_pathway_annotations", "api/pypath.inputs.signor", "api/pypath.inputs.signor.signor_complexes", "api/pypath.inputs.signor.signor_enzyme_substrate", "api/pypath.inputs.signor.signor_interactions", "api/pypath.inputs.signor.signor_pathway_annotations", "api/pypath.inputs.signor.signor_pathways", "api/pypath.inputs.signor.signor_protein_families", "api/pypath.inputs.spike", "api/pypath.inputs.spike.spike_complexes", "api/pypath.inputs.spike.spike_interactions", "api/pypath.inputs.stitch", "api/pypath.inputs.stitch.stitch_actions_interactions", "api/pypath.inputs.stitch.stitch_links_interactions", "api/pypath.inputs.string", "api/pypath.inputs.string.string_effects", "api/pypath.inputs.string.string_links_interactions", "api/pypath.inputs.string.string_physical_interactions", "api/pypath.inputs.string.string_species", "api/pypath.inputs.surfaceome", "api/pypath.inputs.surfaceome.surfaceome_annotations", "api/pypath.inputs.switches_elm", "api/pypath.inputs.switches_elm.get_switches_elm", "api/pypath.inputs.talklr", "api/pypath.inputs.talklr.talklr_annotations", "api/pypath.inputs.talklr.talklr_interactions", "api/pypath.inputs.talklr.talklr_raw", "api/pypath.inputs.tcdb", "api/pypath.inputs.tcdb.tcdb_annotations", "api/pypath.inputs.tcdb.tcdb_classes", "api/pypath.inputs.tcdb.tcdb_families", "api/pypath.inputs.tfcensus", "api/pypath.inputs.tfcensus.tfcensus_annotations", "api/pypath.inputs.threedcomplex", "api/pypath.inputs.threedcomplex.threedcomplex_chains", "api/pypath.inputs.threedcomplex.threedcomplex_complexes", "api/pypath.inputs.threedcomplex.threedcomplex_contacts", "api/pypath.inputs.threedcomplex.threedcomplex_ddi", "api/pypath.inputs.threedcomplex.threedcomplex_nresidues", "api/pypath.inputs.threedid", "api/pypath.inputs.threedid.get_3did", "api/pypath.inputs.threedid.get_3did_ddi", "api/pypath.inputs.threedid.get_3did_dmi", "api/pypath.inputs.threedid.process_3did_dmi", "api/pypath.inputs.topdb", "api/pypath.inputs.topdb.topdb_annotations", "api/pypath.inputs.transmir", "api/pypath.inputs.transmir.transmir_interactions", "api/pypath.inputs.trip", "api/pypath.inputs.trip.take_a_trip", "api/pypath.inputs.trip.trip_find_uniprot", "api/pypath.inputs.trip.trip_get_uniprot", "api/pypath.inputs.trip.trip_interactions", "api/pypath.inputs.trip.trip_process", "api/pypath.inputs.trip.trip_process_table", "api/pypath.inputs.trrust", "api/pypath.inputs.trrust.trrust_human", "api/pypath.inputs.trrust.trrust_interactions", "api/pypath.inputs.trrust.trrust_mouse", "api/pypath.inputs.twosides", "api/pypath.inputs.twosides.twosides_interactions", "api/pypath.inputs.unichem", "api/pypath.inputs.unichem.info", "api/pypath.inputs.unichem.unichem_info", "api/pypath.inputs.unichem.unichem_mapping", "api/pypath.inputs.unichem.unichem_sources", "api/pypath.inputs.uniprot", "api/pypath.inputs.uniprot.Taxon", "api/pypath.inputs.uniprot.UniprotQuery", "api/pypath.inputs.uniprot.UniprotRecordHistory", "api/pypath.inputs.uniprot.deleted_uniprot_genesymbol", "api/pypath.inputs.uniprot.get_uniprot_sec", "api/pypath.inputs.uniprot.idmapping_idtypes", "api/pypath.inputs.uniprot.protein_datasheet", "api/pypath.inputs.uniprot.query_builder", "api/pypath.inputs.uniprot.swissprot_deleted", "api/pypath.inputs.uniprot.trembl_deleted", "api/pypath.inputs.uniprot.uniprot_data", "api/pypath.inputs.uniprot.uniprot_deleted", "api/pypath.inputs.uniprot.uniprot_families", "api/pypath.inputs.uniprot.uniprot_history", "api/pypath.inputs.uniprot.uniprot_history_recent_datasheet", "api/pypath.inputs.uniprot.uniprot_keywords", "api/pypath.inputs.uniprot.uniprot_locations", "api/pypath.inputs.uniprot.uniprot_ncbi_taxids", "api/pypath.inputs.uniprot.uniprot_ncbi_taxids_2", "api/pypath.inputs.uniprot.uniprot_preprocess", "api/pypath.inputs.uniprot.uniprot_query", "api/pypath.inputs.uniprot.uniprot_recent_version", "api/pypath.inputs.uniprot.uniprot_taxonomy", "api/pypath.inputs.uniprot.uniprot_tissues", "api/pypath.inputs.uniprot.uniprot_topology", "api/pypath.inputs.uniprot.valid_uniprot", "api/pypath.inputs.uniprot_db", "api/pypath.inputs.uniprot_db.all_swissprots", "api/pypath.inputs.uniprot_db.all_trembls", "api/pypath.inputs.uniprot_db.all_uniprots", "api/pypath.inputs.uniprot_db.get_db", "api/pypath.inputs.uniprot_db.init_db", "api/pypath.inputs.uniprot_db.is_swissprot", "api/pypath.inputs.uniprot_db.is_trembl", "api/pypath.inputs.uniprot_db.is_uniprot", "api/pypath.inputs.wang", "api/pypath.inputs.wang.cui_interactions", "api/pypath.inputs.wang.hsn_interactions", "api/pypath.inputs.wang.wang_annotations", "api/pypath.inputs.wang.wang_interactions", "api/pypath.inputs.wojtowicz2020", "api/pypath.inputs.wojtowicz2020.wojtowicz2020_interactions", "api/pypath.inputs.wojtowicz2020.wojtowicz2020_raw", "api/pypath.inputs.zhong2015", "api/pypath.inputs.zhong2015.zhong2015_annotations", "api/pypath.internals", "api/pypath.internals.annot_formats", "api/pypath.internals.annot_formats.AnnotDef", "api/pypath.internals.annot_formats.AnnotDefKey", "api/pypath.internals.annot_formats.AnnotOp", "api/pypath.internals.annot_formats.AnnotationGroup", "api/pypath.internals.input_formats", "api/pypath.internals.input_formats.ArrayMapping", "api/pypath.internals.input_formats.BiomartMapping", "api/pypath.internals.input_formats.FileMapping", "api/pypath.internals.input_formats.HmdbMapping", "api/pypath.internals.input_formats.MappingInput", "api/pypath.internals.input_formats.NetworkInput", "api/pypath.internals.input_formats.PickleMapping", "api/pypath.internals.input_formats.ProMapping", "api/pypath.internals.input_formats.RampMapping", "api/pypath.internals.input_formats.ReadList", "api/pypath.internals.input_formats.UnichemMapping", "api/pypath.internals.input_formats.UniprotListMapping", "api/pypath.internals.input_formats.UniprotMapping", "api/pypath.internals.intera", "api/pypath.internals.intera.Complex", "api/pypath.internals.intera.Domain", "api/pypath.internals.intera.DomainDomain", "api/pypath.internals.intera.DomainMotif", "api/pypath.internals.intera.Interface", "api/pypath.internals.intera.Motif", "api/pypath.internals.intera.Ptm", "api/pypath.internals.intera.Regulation", "api/pypath.internals.intera.Residue", "api/pypath.internals.license", "api/pypath.internals.license.License", "api/pypath.internals.license.LicenseAttrib", "api/pypath.internals.license.LicenseFeature", "api/pypath.internals.license.LicensePurpose", "api/pypath.internals.license.LicenseSharing", "api/pypath.internals.maps", "api/pypath.internals.refs", "api/pypath.internals.refs.Reference", "api/pypath.internals.refs.get_pubmed_data", "api/pypath.internals.resource", "api/pypath.internals.resource.AbstractResource", "api/pypath.internals.resource.EnzymeSubstrateResource", "api/pypath.internals.resource.EnzymeSubstrateResourceKey", "api/pypath.internals.resource.NetworkDataset", "api/pypath.internals.resource.NetworkResource", "api/pypath.internals.resource.NetworkResourceKey", "api/pypath.internals.resource.ResourceAttributes", "api/pypath.legacy", "api/pypath.legacy.db_categories", "api/pypath.legacy.db_categories.get_categories", "api/pypath.legacy.db_categories.get_category", "api/pypath.log", "api/pypath.omnipath", "api/pypath.omnipath.app", "api/pypath.omnipath.app.DatabaseManager", "api/pypath.omnipath.databases", "api/pypath.omnipath.databases.build", "api/pypath.omnipath.databases.class_and_param", "api/pypath.omnipath.databases.define", "api/pypath.omnipath.databases.define.DatabaseClass", "api/pypath.omnipath.databases.define.DatabaseDefinition", "api/pypath.omnipath.databases.define.DatabaseDefinitionManager", "api/pypath.omnipath.databases.get_manager", "api/pypath.omnipath.databases.init_manager", "api/pypath.omnipath.export", "api/pypath.omnipath.export.Export", "api/pypath.omnipath.init", "api/pypath.omnipath.param", "api/pypath.omnipath.param.curated_ppi_resources", "api/pypath.omnipath.param.tf_target_resources", "api/pypath.omnipath.server", "api/pypath.omnipath.server.build", "api/pypath.omnipath.server.build.WebserviceTables", "api/pypath.omnipath.server.generate_about_page", "api/pypath.omnipath.server.generate_about_page.export_licenses", "api/pypath.omnipath.server.generate_about_page.generate_about_html", "api/pypath.omnipath.server.generate_about_page.resource_list_latex", "api/pypath.omnipath.server.generate_about_page.write_html", "api/pypath.omnipath.server.legacy", "api/pypath.omnipath.server.legacy.PypathServer", "api/pypath.omnipath.server.run", "api/pypath.omnipath.server.run.BaseServer", "api/pypath.omnipath.server.run.Rest", "api/pypath.omnipath.server.run.TableServer", "api/pypath.omnipath.server.run.TwistedWebResource", "api/pypath.omnipath.server.run.TwistedWebSite", "api/pypath.omnipath.server.run.ignore_pandas_copywarn", "api/pypath.omnipath.server.run.stop_server", "api/pypath.omnipath.server.run.twisted_listen_tcp", "api/pypath.omnipath.server.run.twisted_run", "api/pypath.resources", "api/pypath.resources.controller", "api/pypath.resources.controller.ResourceController", "api/pypath.resources.data", "api/pypath.resources.data_formats", "api/pypath.resources.data_formats.activity_flow", "api/pypath.resources.data_formats.enzyme_substrate", "api/pypath.resources.data_formats.interaction", "api/pypath.resources.data_formats.interaction_htp", "api/pypath.resources.data_formats.pathway_bad", "api/pypath.resources.data_formats.reaction_pc", "api/pypath.resources.data_formats.transcription_deprecated", "api/pypath.resources.data_formats.transcription_onebyone", "api/pypath.resources.descriptions", "api/pypath.resources.descriptions.export_licenses", "api/pypath.resources.descriptions.gen_html", "api/pypath.resources.descriptions.resource_list_latex", "api/pypath.resources.descriptions.write_html", "api/pypath.resources.get_controller", "api/pypath.resources.licenses", "api/pypath.resources.licenses.Licenses", "api/pypath.resources.network", "api/pypath.resources.network.choose_dataset", "api/pypath.resources.network.dataset_priority", "api/pypath.resources.network.dorothea_expand_levels", "api/pypath.resources.urls", "api/pypath.share", "api/pypath.share.cache", "api/pypath.share.cache.cache_item", "api/pypath.share.cache.cache_path", "api/pypath.share.cache.get_cachedir", "api/pypath.share.common", "api/pypath.share.constants", "api/pypath.share.curl", "api/pypath.share.curl.Curl", "api/pypath.share.curl.FileOpener", "api/pypath.share.curl.RemoteFile", "api/pypath.share.curl.cache_delete_off", "api/pypath.share.curl.cache_delete_on", "api/pypath.share.curl.cache_off", "api/pypath.share.curl.cache_on", "api/pypath.share.curl.cache_print_off", "api/pypath.share.curl.cache_print_on", "api/pypath.share.curl.debug_off", "api/pypath.share.curl.debug_on", "api/pypath.share.curl.dryrun_off", "api/pypath.share.curl.dryrun_on", "api/pypath.share.curl.is_url", "api/pypath.share.curl.preserve_off", "api/pypath.share.curl.preserve_on", "api/pypath.share.progress", "api/pypath.share.progress.Progress", "api/pypath.share.session", "api/pypath.share.settings", "api/pypath.utils", "api/pypath.utils.go", "api/pypath.utils.go.GOAnnotation", "api/pypath.utils.go.GOCustomAnnotation", "api/pypath.utils.go.GeneOntology", "api/pypath.utils.go.annotate", "api/pypath.utils.go.get_db", "api/pypath.utils.go.init_db", "api/pypath.utils.go.load_go", "api/pypath.utils.mapping", "api/pypath.utils.mapping.MapReader", "api/pypath.utils.mapping.Mapper", "api/pypath.utils.mapping.MappingTable", "api/pypath.utils.mapping.MappingTableKey", "api/pypath.utils.mapping.UNIPROT_ID_TYPES", "api/pypath.utils.mapping.get_mapper", "api/pypath.utils.mapping.guess_type", "api/pypath.utils.mapping.id_from_label", "api/pypath.utils.mapping.id_from_label0", "api/pypath.utils.mapping.id_types", "api/pypath.utils.mapping.init", "api/pypath.utils.mapping.label", "api/pypath.utils.mapping.map_name", "api/pypath.utils.mapping.map_name0", "api/pypath.utils.mapping.map_names", "api/pypath.utils.mapping.mapping_tables", "api/pypath.utils.mapping.translation_df", "api/pypath.utils.mapping.translation_dict", "api/pypath.utils.metabo", "api/pypath.utils.orthology", "api/pypath.utils.orthology.EnsemblOrtholog", "api/pypath.utils.orthology.EnsemblOrthology", "api/pypath.utils.orthology.HomologeneOrtholog", "api/pypath.utils.orthology.HomologeneOrthology", "api/pypath.utils.orthology.OmaOrtholog", "api/pypath.utils.orthology.OmaOrthology", "api/pypath.utils.orthology.OrthologBase", "api/pypath.utils.orthology.OrthologMeta", "api/pypath.utils.orthology.OrthologyManager", "api/pypath.utils.orthology.OrthologyTableKey", "api/pypath.utils.orthology.ProteinOrthology", "api/pypath.utils.orthology.Proteomes", "api/pypath.utils.orthology.PtmOrthology", "api/pypath.utils.orthology.SequenceContainer", "api/pypath.utils.orthology.get_df", "api/pypath.utils.orthology.get_dict", "api/pypath.utils.orthology.get_manager", "api/pypath.utils.orthology.init", "api/pypath.utils.orthology.translate", "api/pypath.utils.orthology.translate_df", "api/pypath.utils.pdb", "api/pypath.utils.pdb.Residue", "api/pypath.utils.pdb.ResidueMapper", "api/pypath.utils.pdb.Segment", "api/pypath.utils.pdb.residue_pdb", "api/pypath.utils.proteomicsdb", "api/pypath.utils.proteomicsdb.ProteomicsDB", "api/pypath.utils.pyreact", "api/pypath.utils.pyreact.AttributeHandler", "api/pypath.utils.pyreact.BioPaxReader", "api/pypath.utils.pyreact.Complex", "api/pypath.utils.pyreact.ComplexVariations", "api/pypath.utils.pyreact.Control", "api/pypath.utils.pyreact.Entity", "api/pypath.utils.pyreact.EntitySet", "api/pypath.utils.pyreact.Intersecting", "api/pypath.utils.pyreact.Protein", "api/pypath.utils.pyreact.ProteinFamily", "api/pypath.utils.pyreact.PyReact", "api/pypath.utils.pyreact.Reaction", "api/pypath.utils.pyreact.ReactionSide", "api/pypath.utils.pyreact.Reference", "api/pypath.utils.reflists", "api/pypath.utils.reflists.ReferenceListManager", "api/pypath.utils.reflists.check", "api/pypath.utils.reflists.get_manager", "api/pypath.utils.reflists.get_reflist", "api/pypath.utils.reflists.init", "api/pypath.utils.reflists.is_not", "api/pypath.utils.reflists.select", 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1062, 1068, 1072, 1074, 1078, 1079, 1095, 1100, 1101, 1102, 1108, 1109, 1111, 1113, 1114, 1115, 1116, 1118, 1119, 1120, 1121, 1122, 1128, 1129, 1130, 1131, 1132, 1133, 1135, 1136, 1137, 1138, 1140, 1142, 1143, 1144, 1146, 1147, 1149, 1150, 1151, 1154, 1171, 1176, 1185, 1186, 1188, 1191, 1194, 1195, 1201, 1203, 1205, 1214, 1215, 1219, 1230, 1235, 1236, 1237, 1238, 1244, 1247, 1262, 1263, 1271, 1275, 1276, 1277, 1278, 1279, 1280, 1288, 1289, 1292], "dict": [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 96, 122, 126, 127, 128, 132, 133, 135, 139, 145, 179, 182, 194, 197, 203, 204, 211, 212, 213, 225, 226, 227, 230, 231, 233, 251, 264, 265, 266, 267, 285, 288, 294, 305, 308, 309, 340, 355, 356, 359, 364, 366, 375, 384, 390, 394, 398, 400, 401, 402, 404, 406, 407, 408, 410, 411, 412, 413, 414, 415, 416, 417, 421, 424, 429, 441, 442, 443, 446, 447, 448, 451, 452, 453, 468, 469, 472, 474, 477, 478, 479, 480, 494, 531, 532, 534, 554, 564, 570, 571, 572, 589, 592, 611, 649, 650, 666, 668, 669, 671, 672, 673, 674, 675, 707, 708, 713, 717, 718, 719, 721, 722, 723, 724, 725, 726, 727, 728, 734, 751, 759, 764, 772, 778, 781, 792, 793, 794, 816, 833, 836, 844, 845, 850, 859, 861, 873, 877, 879, 894, 895, 905, 906, 909, 913, 915, 918, 928, 930, 974, 997, 1008, 1014, 1019, 1037, 1046, 1068, 1101, 1109, 1110, 1125, 1129, 1131, 1133, 1136, 1138, 1140, 1143, 1147, 1154, 1157, 1166, 1185, 1186, 1194, 1205, 1215, 1289, 1291], "uniprot": [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 122, 127, 128, 135, 139, 145, 179, 205, 211, 225, 229, 231, 232, 243, 244, 260, 296, 375, 376, 378, 392, 393, 394, 398, 403, 405, 406, 407, 408, 429, 469, 509, 524, 525, 529, 532, 538, 572, 588, 611, 614, 616, 617, 665, 666, 707, 709, 713, 718, 719, 751, 754, 755, 759, 764, 772, 812, 821, 825, 861, 873, 877, 879, 891, 892, 895, 942, 965, 969, 971, 972, 975, 978, 979, 980, 982, 995, 1019, 1100, 1101, 1103, 1106, 1108, 1109, 1112, 1115, 1116, 1120, 1122, 1129, 1131, 1133, 1136, 1138, 1140, 1142, 1143, 1146, 1147, 1149, 1150, 1151, 1164, 1179, 1181, 1182, 1184, 1186, 1201, 1287, 1288, 1291, 1292], "kei": [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 96, 122, 132, 133, 135, 139, 145, 179, 182, 188, 190, 194, 203, 211, 225, 226, 227, 231, 243, 251, 267, 294, 359, 364, 366, 375, 390, 394, 400, 401, 402, 406, 407, 408, 410, 411, 412, 413, 414, 415, 416, 417, 429, 441, 443, 446, 448, 451, 453, 468, 469, 477, 479, 531, 532, 534, 564, 592, 611, 649, 650, 666, 668, 669, 671, 672, 673, 674, 675, 707, 708, 709, 713, 718, 759, 764, 778, 794, 859, 861, 873, 879, 905, 906, 909, 915, 918, 928, 930, 955, 958, 974, 977, 985, 986, 987, 988, 997, 1008, 1019, 1046, 1072, 1073, 1078, 1101, 1109, 1110, 1129, 1131, 1133, 1136, 1138, 1143, 1147, 1157, 1166, 1185, 1186, 1192, 1193, 1203, 1214, 1289, 1292], "an": [3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 96, 122, 127, 132, 133, 135, 139, 145, 188, 189, 190, 191, 230, 233, 347, 348, 353, 359, 364, 366, 441, 443, 446, 448, 451, 453, 474, 498, 509, 538, 551, 648, 649, 650, 668, 669, 707, 713, 714, 719, 721, 722, 724, 725, 726, 728, 751, 794, 836, 905, 909, 915, 918, 928, 955, 957, 972, 985, 986, 987, 988, 997, 999, 1008, 1015, 1019, 1022, 1046, 1056, 1073, 1100, 1102, 1108, 1109, 1113, 1120, 1129, 1131, 1133, 1135, 1136, 1138, 1140, 1141, 1144, 1145, 1147, 1154, 1157, 1186, 1188, 1203, 1211, 1268, 1271, 1275, 1276, 1277, 1278, 1279, 1280, 1287, 1288, 1292], "object": [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 96, 97, 105, 122, 124, 127, 132, 133, 134, 135, 139, 145, 146, 181, 221, 225, 226, 227, 229, 232, 234, 260, 265, 267, 355, 393, 456, 588, 594, 708, 759, 813, 814, 816, 876, 878, 909, 955, 957, 958, 964, 965, 969, 974, 975, 976, 977, 978, 979, 980, 981, 982, 984, 986, 991, 992, 997, 1000, 1008, 1013, 1014, 1019, 1032, 1036, 1038, 1039, 1046, 1049, 1050, 1051, 1052, 1053, 1054, 1055, 1056, 1068, 1078, 1080, 1095, 1100, 1101, 1102, 1103, 1106, 1109, 1113, 1120, 1122, 1134, 1139, 1140, 1141, 1144, 1154, 1156, 1157, 1161, 1163, 1164, 1166, 1168, 1169, 1179, 1182, 1183, 1186, 1203, 1205, 1214, 1244, 1266, 1269, 1271, 1275, 1276, 1277, 1278, 1279, 1280, 1282, 1283, 1284, 1285, 1286, 1287, 1288, 1290], "suitabl": [3, 4, 5, 7, 8, 9, 11, 12, 13, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 33, 34, 35, 39, 41, 42, 44, 45, 46, 48, 49, 50, 52, 53, 57, 59, 60, 61, 62, 65, 66, 68, 70, 73, 74, 75, 76, 80, 81, 84, 90, 92, 909, 1109, 1168, 1289], "process_method": [3, 4, 5, 7, 8, 9, 11, 12, 13, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 33, 34, 35, 39, 41, 42, 44, 45, 46, 48, 49, 50, 52, 53, 57, 59, 60, 61, 62, 65, 66, 68, 70, 73, 74, 75, 76, 80, 81, 84, 90, 92, 100, 101, 102, 103, 104, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117], "input_arg": [3, 4, 5, 7, 8, 9, 11, 12, 13, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 33, 34, 35, 39, 41, 42, 44, 45, 46, 48, 49, 50, 52, 53, 57, 59, 60, 61, 62, 65, 66, 68, 70, 73, 74, 75, 76, 80, 81, 84, 90, 92, 100, 102, 103, 104, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 965, 994, 1056], "argument": [3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 96, 122, 127, 128, 132, 135, 139, 145, 212, 443, 448, 453, 893, 960, 967, 971, 1008, 1015, 1019, 1021, 1036, 1078, 1136, 1140, 1147, 1271, 1289], "attribut": [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 94, 96, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 120, 122, 123, 124, 126, 132, 133, 135, 136, 137, 139, 142, 145, 146, 147, 163, 164, 165, 166, 167, 178, 191, 194, 224, 236, 249, 344, 421, 427, 428, 471, 494, 511, 540, 550, 553, 584, 585, 604, 685, 688, 689, 757, 829, 830, 831, 832, 908, 909, 910, 918, 928, 955, 956, 957, 958, 965, 972, 974, 984, 985, 986, 987, 988, 991, 995, 996, 997, 998, 999, 1000, 1008, 1019, 1033, 1035, 1037, 1046, 1048, 1078, 1079, 1100, 1102, 1103, 1105, 1106, 1107, 1108, 1109, 1110, 1111, 1113, 1118, 1128, 1129, 1130, 1131, 1132, 1133, 1136, 1137, 1138, 1149, 1151, 1166, 1203, 1205, 1275, 1276, 1277, 1278, 1279, 1280, 1289, 1292], "add_complexes_by_infer": [3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92], "complex": [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 132, 133, 135, 139, 145, 157, 220, 225, 226, 227, 228, 229, 232, 234, 241, 260, 272, 273, 275, 433, 474, 512, 553, 554, 555, 708, 809, 824, 825, 850, 857, 858, 875, 876, 877, 909, 915, 918, 928, 1008, 1101, 1109, 1119, 1120, 1122, 1166, 1168, 1287, 1288, 1291], "none": [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 96, 98, 100, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 122, 126, 127, 128, 132, 133, 135, 139, 145, 146, 149, 179, 182, 184, 185, 190, 191, 203, 204, 205, 225, 234, 249, 264, 267, 268, 270, 285, 291, 294, 296, 328, 342, 349, 351, 355, 356, 357, 358, 359, 360, 363, 366, 373, 375, 386, 387, 395, 399, 404, 406, 407, 410, 412, 437, 441, 442, 443, 446, 447, 448, 451, 452, 453, 462, 463, 472, 473, 474, 475, 512, 516, 517, 564, 648, 649, 650, 665, 666, 668, 669, 697, 707, 708, 718, 719, 723, 755, 772, 775, 790, 791, 794, 795, 801, 803, 815, 853, 873, 877, 878, 881, 882, 883, 890, 909, 915, 918, 928, 937, 938, 939, 942, 955, 958, 961, 962, 964, 965, 966, 967, 969, 971, 972, 974, 975, 976, 977, 978, 979, 980, 981, 982, 984, 992, 994, 995, 997, 998, 1000, 1008, 1013, 1014, 1015, 1019, 1026, 1037, 1046, 1064, 1068, 1074, 1078, 1079, 1083, 1084, 1095, 1100, 1101, 1102, 1104, 1105, 1108, 1109, 1114, 1115, 1116, 1118, 1119, 1120, 1121, 1122, 1123, 1124, 1125, 1129, 1131, 1133, 1136, 1138, 1139, 1140, 1142, 1143, 1146, 1147, 1150, 1154, 1157, 1158, 1159, 1160, 1161, 1162, 1164, 1165, 1166, 1167, 1168, 1171, 1172, 1174, 1176, 1177, 1181, 1182, 1188, 1203, 1205, 1211, 1219, 1229, 1230, 1241, 1266, 1267, 1289], "creat": [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 127, 128, 132, 133, 135, 139, 145, 442, 447, 452, 877, 965, 1008, 1015, 1019, 1026, 1046, 1068, 1078, 1095, 1100, 1108, 1109, 1110, 1113, 1118, 1122, 1129, 1131, 1133, 1136, 1138, 1140, 1142, 1143, 1144, 1145, 1157, 1166, 1288], "silico": [3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 861], "infer": [3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 135, 212, 213, 893, 894, 1289], "add": [3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 135, 145, 170, 509, 974, 978, 1008, 1019, 1046, 1103, 1106, 1109, 1120, 1122, 1166, 1288, 1289, 1291, 1292], "them": [3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 127, 135, 139, 145, 564, 648, 845, 1008, 1046, 1109, 1121, 1131, 1138, 1154, 1288, 1289, 1292], "thi": [3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 94, 105, 120, 122, 126, 132, 133, 135, 139, 145, 179, 182, 184, 185, 192, 204, 212, 277, 294, 296, 306, 329, 347, 348, 353, 355, 371, 384, 395, 406, 408, 411, 413, 441, 442, 443, 446, 447, 448, 451, 452, 453, 463, 474, 498, 517, 553, 554, 555, 648, 649, 650, 665, 666, 718, 753, 754, 758, 759, 778, 781, 794, 835, 836, 845, 873, 890, 895, 909, 915, 918, 928, 945, 958, 960, 965, 967, 971, 973, 974, 978, 985, 986, 987, 988, 995, 997, 1008, 1010, 1015, 1019, 1025, 1026, 1029, 1046, 1059, 1064, 1078, 1079, 1081, 1082, 1083, 1084, 1085, 1086, 1087, 1088, 1089, 1090, 1092, 1093, 1101, 1105, 1108, 1109, 1110, 1113, 1118, 1119, 1120, 1122, 1129, 1131, 1133, 1136, 1138, 1140, 1141, 1142, 1143, 1146, 1147, 1150, 1154, 1157, 1159, 1161, 1164, 1166, 1169, 1171, 1179, 1183, 1203, 1266, 1267, 1268, 1271, 1275, 1276, 1277, 1278, 1279, 1280, 1281, 1288, 1289, 1291, 1292], "all_complex": [3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92], "all": [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 118, 122, 126, 127, 133, 135, 139, 145, 182, 184, 190, 192, 213, 315, 326, 345, 355, 363, 366, 406, 407, 441, 442, 443, 446, 447, 448, 451, 452, 453, 460, 494, 532, 553, 641, 648, 649, 650, 665, 666, 718, 751, 755, 759, 778, 794, 873, 893, 909, 915, 918, 928, 958, 974, 978, 992, 997, 1008, 1015, 1019, 1026, 1046, 1064, 1078, 1079, 1090, 1100, 1101, 1102, 1109, 1110, 1120, 1123, 1129, 1131, 1133, 1136, 1138, 1140, 1147, 1150, 1154, 1157, 1166, 1168, 1171, 1181, 1182, 1184, 1186, 1194, 1205, 1238, 1263, 1267, 1275, 1285, 1288, 1291, 1292], "all_ent": [3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92], "entity_typ": [3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 98, 122, 123, 135, 139, 225, 790, 791, 958, 962, 969, 1108, 1109, 1114, 1119, 1289], "entiti": [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 98, 135, 139, 145, 553, 554, 555, 958, 1108, 1109, 1114, 1119, 1157, 1164, 1169, 1289, 1291, 1292], "all_mirna": [3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92], "mirna": [3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 122, 135, 139, 145, 260, 261, 627, 637, 639, 641, 888, 1008, 1055, 1108, 1109, 1119, 1288, 1291, 1292], "all_protein": [3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92], "all_ref": [3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92], "some": [3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 135, 139, 145, 553, 648, 650, 972, 997, 1088, 1093, 1102, 1109, 1120, 1122, 1129, 1131, 1133, 1136, 1138, 1142, 1143, 1146, 1154, 1288, 1289, 1292], "contain": [3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 126, 133, 135, 139, 145, 197, 270, 340, 355, 366, 430, 442, 447, 452, 474, 509, 524, 649, 717, 782, 834, 857, 863, 895, 945, 958, 999, 1008, 1014, 1019, 1021, 1154, 1157, 1268, 1275, 1276, 1277, 1278, 1279, 1280, 1288, 1289, 1292], "refer": [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 118, 122, 126, 131, 132, 135, 136, 145, 184, 185, 212, 213, 342, 357, 408, 437, 471, 479, 511, 517, 534, 540, 604, 648, 649, 650, 654, 679, 713, 787, 909, 915, 918, 928, 965, 974, 977, 992, 1008, 1019, 1046, 1049, 1050, 1053, 1054, 1092, 1093, 1171, 1172, 1177, 1205, 1215, 1236, 1287, 1288, 1292], "The": [3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 94, 96, 120, 122, 127, 128, 131, 132, 133, 134, 135, 139, 145, 188, 209, 211, 212, 213, 214, 225, 226, 229, 231, 232, 244, 252, 270, 306, 331, 336, 337, 340, 345, 355, 356, 359, 364, 366, 384, 406, 411, 442, 447, 452, 463, 479, 505, 517, 592, 596, 649, 669, 707, 708, 718, 719, 723, 727, 759, 778, 791, 793, 815, 819, 820, 827, 845, 854, 857, 858, 891, 892, 903, 909, 913, 915, 918, 928, 945, 958, 972, 992, 999, 1008, 1015, 1019, 1026, 1030, 1036, 1046, 1060, 1062, 1064, 1073, 1078, 1079, 1095, 1101, 1102, 1105, 1108, 1109, 1110, 1113, 1120, 1122, 1129, 1131, 1133, 1136, 1138, 1142, 1143, 1146, 1147, 1150, 1157, 1166, 1171, 1203, 1219, 1241, 1267, 1271, 1275, 1276, 1277, 1278, 1279, 1280, 1286, 1287, 1288, 1291, 1292], "field": [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 123, 135, 136, 137, 147, 163, 164, 165, 166, 167, 178, 187, 224, 236, 264, 265, 267, 294, 302, 342, 344, 346, 352, 355, 357, 366, 404, 427, 428, 442, 443, 447, 448, 452, 453, 471, 511, 540, 550, 604, 643, 644, 668, 669, 685, 688, 689, 757, 772, 829, 830, 831, 832, 834, 845, 908, 909, 910, 915, 918, 927, 928, 955, 956, 957, 996, 999, 1019, 1078, 1111, 1128, 1130, 1132, 1135, 1137, 1149, 1151, 1289, 1292], "alwai": [3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 346, 352, 474, 479, 1068, 1109, 1122, 1166, 1289], "pmid": [3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 224, 780, 781, 782, 783, 952, 991, 1289], "pubm": [3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 132, 251, 344, 384, 408, 496, 497, 713, 992, 1169, 1289], "collect": [3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 121, 131, 133, 135, 145, 146, 150, 192, 288, 331, 359, 364, 366, 441, 446, 451, 503, 648, 649, 650, 1046, 1289, 1292], "across": [3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 135, 145, 270, 1019, 1289], "record": [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 135, 139, 145, 191, 204, 212, 213, 230, 233, 244, 249, 250, 254, 255, 260, 288, 316, 342, 366, 384, 440, 441, 442, 443, 445, 446, 447, 448, 450, 451, 452, 453, 478, 527, 553, 665, 671, 672, 673, 675, 680, 721, 722, 724, 725, 726, 727, 728, 764, 774, 781, 783, 845, 921, 1129, 1133, 1166, 1292], "list": [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 105, 122, 126, 127, 128, 132, 133, 135, 139, 145, 157, 168, 169, 170, 180, 181, 184, 185, 187, 188, 189, 191, 194, 199, 201, 204, 205, 212, 213, 214, 222, 228, 230, 233, 245, 249, 250, 252, 253, 254, 255, 257, 258, 260, 261, 264, 265, 266, 267, 268, 285, 302, 303, 308, 309, 312, 313, 314, 315, 325, 326, 342, 355, 356, 357, 358, 360, 362, 363, 366, 373, 377, 382, 384, 389, 404, 406, 407, 421, 424, 430, 442, 447, 452, 483, 484, 494, 501, 502, 504, 505, 517, 527, 533, 534, 536, 552, 555, 564, 579, 584, 585, 587, 588, 589, 590, 594, 595, 596, 665, 666, 668, 669, 671, 672, 673, 674, 675, 686, 707, 711, 713, 714, 721, 722, 724, 725, 726, 727, 728, 732, 734, 744, 746, 748, 749, 750, 759, 772, 780, 781, 782, 787, 790, 791, 792, 794, 800, 820, 825, 833, 834, 835, 840, 845, 851, 853, 854, 856, 857, 858, 859, 873, 878, 879, 893, 894, 898, 904, 905, 909, 913, 915, 918, 928, 944, 945, 947, 950, 957, 958, 971, 972, 974, 977, 997, 1019, 1030, 1046, 1060, 1078, 1100, 1101, 1102, 1108, 1109, 1117, 1123, 1129, 1131, 1133, 1136, 1138, 1139, 1140, 1142, 1143, 1146, 1147, 1150, 1154, 1157, 1166, 1171, 1172, 1177, 1203, 1205, 1214, 1219, 1229, 1235, 1236, 1238, 1241, 1244, 1263, 1288, 1289, 1291, 1292], "annotate_complex": [3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92], "cplex": [3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 809, 1289], "singl": [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 127, 135, 139, 145, 193, 197, 204, 212, 312, 313, 443, 448, 453, 553, 554, 555, 782, 974, 1019, 1100, 1101, 1102, 1109, 1116, 1129, 1131, 1133, 1136, 1138, 1140, 1147, 1244, 1287], "brows": [3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 139, 1005, 1287], "start": [3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 123, 136, 137, 139, 145, 147, 163, 164, 165, 166, 167, 178, 224, 236, 344, 427, 428, 471, 511, 540, 550, 604, 648, 650, 685, 688, 689, 707, 717, 757, 829, 830, 831, 832, 908, 910, 955, 956, 957, 975, 979, 996, 999, 1036, 1111, 1128, 1130, 1132, 1137, 1149, 1151, 1154, 1211, 1288, 1289, 1291], "0": [3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 122, 123, 135, 136, 137, 139, 147, 163, 164, 165, 166, 167, 178, 195, 224, 236, 252, 268, 278, 344, 427, 428, 437, 471, 491, 511, 519, 527, 540, 550, 604, 611, 685, 688, 689, 757, 829, 830, 831, 832, 845, 856, 908, 910, 955, 956, 957, 962, 965, 969, 996, 999, 1095, 1111, 1128, 1130, 1132, 1137, 1149, 1151, 1154, 1203, 1211, 1267, 1287, 1288, 1289], "print": [3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 139, 151, 152, 903, 1083, 1084, 1085, 1086, 1087, 1088, 1157, 1203, 1211, 1229, 1241, 1289], "inform": [3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 100, 131, 135, 139, 145, 151, 152, 192, 227, 257, 355, 430, 533, 663, 713, 753, 774, 833, 834, 835, 836, 903, 904, 906, 958, 978, 1008, 1019, 1046, 1087, 1088, 1095, 1109, 1121, 1136, 1142, 1143, 1146, 1147, 1157, 1203, 1211, 1287, 1292], "tabl": [3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 127, 139, 145, 267, 318, 359, 364, 375, 376, 377, 378, 432, 433, 441, 446, 451, 468, 469, 509, 529, 587, 588, 589, 590, 629, 666, 711, 732, 751, 775, 787, 792, 794, 795, 845, 861, 891, 892, 895, 944, 950, 958, 960, 963, 967, 968, 971, 972, 1008, 1019, 1025, 1030, 1037, 1060, 1108, 1109, 1110, 1123, 1124, 1125, 1129, 1131, 1133, 1138, 1140, 1144, 1211, 1219, 1229, 1241, 1287, 1288, 1290, 1291], "present": [3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 123, 135, 136, 137, 139, 145, 147, 163, 164, 165, 166, 167, 171, 178, 224, 236, 344, 384, 427, 428, 471, 511, 540, 550, 604, 685, 688, 689, 757, 829, 830, 831, 832, 908, 910, 955, 956, 957, 978, 996, 997, 999, 1111, 1128, 1130, 1132, 1137, 1149, 1151, 1288, 1289], "categori": [3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 139, 713, 863, 955, 958, 1101, 1287, 1291, 1292], "ascii": [3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 139, 267, 1219, 1241], "termin": [3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 139, 1095, 1289], "If": [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 128, 132, 133, 135, 139, 145, 212, 225, 267, 294, 349, 351, 355, 363, 406, 407, 410, 412, 534, 564, 648, 649, 650, 665, 666, 668, 671, 672, 673, 674, 675, 718, 758, 759, 794, 845, 877, 878, 890, 909, 942, 955, 958, 972, 974, 978, 997, 1019, 1100, 1101, 1102, 1108, 1109, 1110, 1120, 1123, 1129, 1131, 1133, 1138, 1154, 1157, 1205, 1230, 1288, 1289, 1292], "one": [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 127, 132, 133, 134, 135, 139, 145, 179, 181, 190, 268, 294, 296, 312, 366, 406, 407, 408, 414, 415, 416, 417, 442, 443, 447, 448, 452, 453, 479, 516, 517, 533, 553, 554, 555, 649, 721, 722, 724, 725, 726, 727, 728, 751, 754, 782, 845, 892, 895, 903, 904, 909, 918, 928, 945, 960, 963, 967, 968, 970, 971, 972, 974, 978, 992, 1008, 1019, 1046, 1100, 1102, 1108, 1109, 1110, 1120, 1121, 1122, 1129, 1131, 1133, 1136, 1138, 1140, 1141, 1142, 1143, 1146, 1150, 1154, 1157, 1166, 1181, 1182, 1186, 1203, 1205, 1214, 1244, 1247, 1271, 1278, 1279, 1288, 1292], "multipl": [3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 105, 127, 132, 135, 139, 190, 212, 346, 347, 348, 350, 352, 353, 443, 448, 453, 517, 1101, 1109, 1122, 1140, 1141, 1157, 1288, 1289, 1292], "each": [3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 126, 132, 133, 135, 139, 145, 191, 204, 205, 212, 213, 214, 228, 229, 230, 232, 233, 241, 264, 267, 355, 357, 362, 442, 443, 447, 448, 452, 453, 478, 517, 533, 534, 553, 668, 707, 709, 713, 717, 727, 754, 764, 765, 825, 904, 909, 1008, 1019, 1068, 1101, 1109, 1110, 1154, 1157, 1166, 1211, 1214, 1288, 1289, 1291, 1292], "proceed": [3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 139], "next": [3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 139, 505, 890, 1072, 1108, 1109, 1110, 1289], "onc": [3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 135, 139, 179, 1062, 1078, 1109, 1122, 1154, 1288, 1289], "hit": [3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 139], "goe": [3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 139, 1289], "through": [3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 139, 266, 992, 1211, 1288, 1289], "level": [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 105, 132, 133, 135, 139, 143, 145, 312, 314, 344, 346, 347, 348, 350, 352, 353, 414, 415, 416, 417, 429, 443, 448, 453, 650, 671, 672, 673, 674, 675, 707, 759, 851, 863, 879, 909, 918, 928, 958, 978, 985, 986, 987, 988, 1008, 1046, 1056, 1068, 1081, 1082, 1083, 1084, 1085, 1086, 1087, 1088, 1089, 1090, 1092, 1093, 1100, 1101, 1102, 1109, 1150, 1179, 1288, 1292], "primari": [3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 132, 133, 135, 912, 999, 1046, 1109, 1120, 1288, 1289], "arg": [3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 128, 135, 145, 179, 181, 182, 184, 185, 188, 189, 190, 191, 197, 203, 204, 205, 209, 211, 212, 213, 214, 225, 226, 227, 228, 229, 230, 231, 232, 233, 234, 249, 252, 265, 291, 292, 294, 306, 345, 355, 356, 357, 358, 359, 360, 363, 364, 366, 468, 469, 472, 532, 534, 561, 564, 565, 567, 568, 569, 571, 572, 575, 668, 669, 714, 718, 719, 759, 764, 765, 778, 823, 824, 827, 845, 851, 854, 857, 858, 877, 878, 903, 905, 945, 955, 958, 999, 1008, 1072, 1102, 1108, 1109, 1110, 1120, 1122, 1129, 1131, 1133, 1135, 1138, 1150, 1203, 1206, 1207, 1208, 1209, 1210, 1212, 1213, 1215, 1216, 1217, 1218, 1219, 1220, 1221, 1222, 1223, 1224, 1225, 1226, 1227, 1228, 1230, 1231, 1232, 1233, 1234, 1235, 1236, 1237, 1238, 1239, 1240, 1241, 1242, 1243, 1245, 1246, 1247, 1248, 1249, 1250, 1251, 1252, 1253, 1254, 1255, 1256, 1257, 1258, 1259, 1260, 1261, 1262, 1263], "select": [3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 127, 128, 135, 139, 145, 213, 958, 1079, 1100, 1140, 1141, 1171, 1287, 1292], "doesn": [3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 145, 1109, 1120, 1288, 1289], "t": [3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 145, 267, 442, 447, 452, 553, 554, 555, 649, 861, 1080, 1081, 1084, 1085, 1108, 1109, 1120, 1129, 1131, 1133, 1138, 1288, 1289, 1290, 1292], "have": [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 127, 135, 139, 145, 187, 408, 648, 650, 854, 857, 958, 972, 1008, 1019, 1046, 1053, 1082, 1088, 1093, 1100, 1108, 1109, 1129, 1131, 1133, 1138, 1154, 1157, 1166, 1288, 1289, 1291, 1292], "string": [3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 96, 122, 127, 132, 133, 135, 139, 145, 227, 265, 266, 267, 294, 366, 392, 443, 448, 453, 463, 648, 650, 708, 778, 814, 903, 905, 909, 915, 918, 928, 955, 974, 1019, 1073, 1078, 1095, 1100, 1108, 1109, 1114, 1140, 1154, 1157, 1161, 1164, 1169, 1203, 1205, 1219, 1247, 1289], "consid": [3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 132, 133, 135, 139, 145, 474, 942, 992, 1008, 1030, 1060, 1100, 1289], "tupl": [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 122, 123, 127, 133, 135, 136, 137, 139, 145, 147, 167, 168, 169, 170, 171, 178, 179, 180, 184, 185, 187, 190, 191, 205, 214, 222, 224, 225, 226, 228, 229, 231, 232, 234, 236, 239, 240, 244, 245, 249, 250, 252, 253, 254, 255, 257, 258, 260, 261, 264, 270, 294, 302, 303, 312, 313, 314, 315, 325, 331, 332, 333, 334, 335, 336, 337, 344, 355, 356, 357, 358, 360, 362, 363, 366, 375, 377, 382, 389, 390, 400, 401, 402, 404, 406, 407, 408, 410, 411, 412, 414, 415, 416, 417, 424, 429, 430, 443, 448, 453, 471, 477, 478, 494, 511, 527, 531, 533, 540, 550, 564, 579, 592, 604, 611, 648, 650, 663, 665, 666, 668, 669, 679, 680, 685, 686, 688, 689, 709, 711, 714, 718, 751, 757, 759, 772, 814, 818, 819, 820, 821, 825, 833, 834, 835, 836, 845, 851, 853, 854, 856, 857, 858, 861, 879, 901, 904, 908, 909, 910, 913, 915, 918, 928, 944, 945, 947, 950, 956, 958, 974, 977, 978, 996, 997, 1019, 1073, 1078, 1100, 1102, 1109, 1110, 1111, 1114, 1135, 1136, 1137, 1140, 1147, 1149, 1150, 1151, 1154, 1168, 1183, 1271, 1275, 1276, 1277, 1278, 1279, 1280, 1283, 1286, 1289], "valu": [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 123, 133, 135, 136, 137, 139, 145, 147, 163, 164, 165, 166, 167, 178, 179, 181, 182, 188, 190, 194, 203, 211, 220, 221, 222, 224, 227, 236, 243, 244, 245, 249, 251, 266, 267, 294, 344, 359, 364, 375, 386, 387, 394, 400, 401, 402, 406, 407, 408, 410, 411, 412, 413, 414, 415, 416, 417, 427, 428, 443, 448, 453, 468, 469, 471, 477, 511, 531, 532, 534, 540, 550, 564, 592, 604, 611, 649, 650, 666, 668, 685, 688, 689, 707, 708, 709, 713, 717, 718, 723, 754, 757, 759, 764, 765, 778, 794, 829, 830, 831, 832, 854, 857, 858, 859, 861, 873, 879, 905, 906, 908, 909, 910, 915, 918, 928, 930, 955, 956, 957, 958, 972, 974, 985, 986, 987, 988, 996, 997, 999, 1008, 1019, 1046, 1078, 1081, 1082, 1083, 1084, 1085, 1086, 1087, 1088, 1089, 1090, 1092, 1093, 1095, 1101, 1102, 1109, 1110, 1111, 1120, 1122, 1128, 1129, 1130, 1131, 1132, 1133, 1136, 1137, 1138, 1142, 1143, 1146, 1147, 1149, 1151, 1154, 1185, 1186, 1214, 1276, 1278, 1279, 1289, 1292], "In": [3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 127, 135, 145, 329, 406, 407, 408, 553, 554, 555, 751, 754, 759, 861, 997, 1019, 1046, 1068, 1078, 1109, 1120, 1122, 1131, 1138, 1140, 1154, 1157, 1195, 1288, 1289], "former": [3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 791, 955, 972, 1008, 1289, 1291], "case": [3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 135, 243, 244, 245, 442, 443, 447, 448, 452, 453, 517, 759, 955, 958, 997, 1008, 1054, 1079, 1101, 1108, 1109, 1120, 1121, 1122, 1129, 1131, 1133, 1136, 1138, 1147, 1154, 1157, 1288, 1289, 1292], "latter": [3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 135, 340, 443, 448, 453, 708, 972, 1008, 1109, 1289], "limit": [3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 135, 139, 190, 498, 517, 553, 554, 555, 648, 650, 854, 857, 858, 955, 958, 1289], "ar": [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 96, 122, 126, 127, 131, 132, 133, 135, 139, 145, 179, 181, 182, 190, 203, 211, 213, 214, 220, 221, 222, 225, 226, 227, 228, 229, 230, 231, 232, 233, 234, 249, 267, 296, 302, 306, 325, 329, 331, 336, 337, 349, 351, 355, 356, 384, 398, 400, 401, 402, 406, 407, 408, 410, 411, 412, 414, 415, 416, 417, 419, 429, 430, 441, 446, 451, 468, 469, 479, 516, 524, 532, 534, 553, 554, 555, 561, 565, 567, 568, 569, 571, 572, 575, 611, 650, 665, 666, 668, 707, 708, 709, 754, 758, 759, 764, 765, 778, 781, 782, 794, 815, 823, 824, 825, 845, 858, 879, 893, 898, 905, 909, 915, 918, 928, 945, 955, 958, 960, 967, 971, 978, 1013, 1015, 1019, 1046, 1050, 1053, 1054, 1072, 1078, 1100, 1102, 1109, 1110, 1120, 1122, 1129, 1131, 1133, 1136, 1138, 1142, 1143, 1146, 1147, 1154, 1157, 1166, 1171, 1176, 1177, 1203, 1275, 1276, 1277, 1278, 1279, 1280, 1285, 1287, 1288, 1290, 1291, 1292], "suppos": [3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 1095], "us": [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 96, 97, 122, 127, 128, 132, 135, 139, 145, 179, 191, 192, 194, 197, 211, 213, 214, 260, 346, 347, 348, 350, 352, 353, 359, 364, 441, 442, 443, 446, 447, 448, 451, 452, 453, 468, 469, 472, 498, 517, 648, 649, 650, 665, 666, 669, 671, 672, 673, 674, 675, 758, 759, 774, 778, 782, 794, 854, 857, 858, 894, 955, 958, 960, 967, 971, 972, 984, 1019, 1021, 1026, 1046, 1050, 1072, 1073, 1078, 1084, 1088, 1093, 1100, 1101, 1108, 1109, 1110, 1112, 1120, 1121, 1122, 1129, 1131, 1133, 1136, 1138, 1142, 1143, 1146, 1147, 1150, 1157, 1179, 1203, 1268, 1271, 1275, 1276, 1277, 1278, 1279, 1280, 1281, 1283, 1285, 1286, 1288, 1292], "e": [3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 122, 127, 128, 135, 139, 145, 267, 302, 355, 356, 357, 358, 359, 360, 395, 424, 441, 443, 446, 448, 451, 453, 551, 553, 648, 649, 650, 775, 782, 894, 918, 958, 973, 978, 992, 997, 1008, 1019, 1046, 1100, 1102, 1108, 1109, 1115, 1116, 1140, 1154, 1157, 1166, 1182, 1214, 1271, 1281, 1283, 1286, 1287, 1288, 1291, 1292], "g": [3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 122, 127, 128, 135, 139, 145, 267, 395, 424, 441, 446, 451, 551, 553, 648, 649, 650, 775, 894, 918, 958, 978, 1008, 1046, 1100, 1108, 1115, 1116, 1140, 1157, 1182, 1214, 1288, 1289, 1291, 1292], "500": [3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 366, 410, 412, 516, 517, 909, 915, 918, 928, 1289], "250": [3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92], "skip": [3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 909, 1266], "everyth": [3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 517, 1109, 1120, 1289], "befor": [3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 408, 1046, 1095, 1157, 1289], "250th": [3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92], "pass": [3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 135, 139, 145, 266, 893, 909, 915, 918, 928, 955, 972, 1108, 1109, 1154, 1211, 1219, 1241, 1289], "info": [3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 139, 1029, 1046, 1059, 1203, 1211, 1287, 1292], "complex_infer": [3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92], "default": [3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 122, 135, 139, 145, 213, 294, 306, 355, 384, 406, 407, 408, 442, 447, 452, 517, 648, 649, 650, 665, 666, 668, 669, 671, 672, 673, 674, 675, 727, 781, 794, 890, 909, 915, 918, 928, 958, 997, 1008, 1019, 1046, 1056, 1062, 1067, 1081, 1082, 1083, 1084, 1085, 1086, 1087, 1088, 1089, 1090, 1092, 1093, 1100, 1109, 1120, 1122, 1129, 1133, 1136, 1142, 1143, 1146, 1147, 1154, 1157, 1183, 1186, 1188, 1271, 1275, 1276, 1277, 1278, 1279, 1280, 1281, 1286, 1288, 1289, 1292], "exist": [3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 119, 135, 139, 145, 294, 654, 794, 890, 1008, 1072, 1074, 1078, 1079, 1083, 1104, 1109, 1113, 1136, 1144, 1147, 1166, 1289], "gener": [3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 96, 122, 128, 132, 135, 139, 169, 244, 264, 267, 268, 270, 331, 332, 333, 334, 335, 336, 337, 347, 348, 353, 663, 671, 672, 673, 674, 675, 744, 818, 819, 820, 821, 901, 921, 958, 978, 994, 1029, 1030, 1046, 1059, 1060, 1154, 1289, 1291, 1292], "demand": [3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 1008, 1062, 1129, 1131, 1133, 1136, 1138, 1147, 1289], "accord": [3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 135, 139, 145, 536, 863, 984, 1008, 1015, 1019, 1154, 1271, 1289], "": [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 122, 133, 135, 139, 145, 294, 355, 564, 663, 668, 861, 901, 958, 972, 974, 978, 997, 999, 1008, 1088, 1108, 1109, 1135, 1288, 1289, 1291], "current": [3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 119, 135, 145, 152, 366, 408, 985, 986, 987, 988, 1005, 1008, 1095, 1104, 1108, 1136, 1142, 1143, 1146, 1147, 1157, 1268, 1288, 1289, 1292], "valid": [3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 135, 145, 185, 252, 509, 641, 775, 909, 985, 986, 987, 988, 1109], "won": [3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 145, 553, 554, 555, 649, 1081, 1084, 1085, 1109, 1129, 1131, 1133, 1138, 1289], "iter": [3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 122, 128, 133, 145, 187, 384, 856, 909, 918, 921, 928, 978, 997, 1046, 1095, 1102, 1109, 1129, 1131, 1133, 1136, 1138, 1146, 1147, 1157, 1159, 1161, 1164, 1168, 1169, 1181, 1182, 1289], "yield": [3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 100, 101, 102, 103, 104, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 122, 135, 191, 239, 244, 407, 443, 448, 453, 553, 554, 555, 663, 679, 680, 814, 815, 901, 909, 912, 1161, 1164, 1168, 1169, 1183, 1289], "coverag": [3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 836, 1056, 1292], "calcul": [3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 355, 524], "proport": [3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92], "least": [3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 135, 139, 1289], "arbitrari": [3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 265, 1008, 1289, 1292], "curation_effort": [3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 145, 977, 1289], "count": [3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 122, 123, 135, 136, 137, 139, 145, 147, 163, 164, 165, 166, 167, 178, 224, 236, 344, 427, 428, 471, 511, 540, 550, 604, 685, 688, 689, 757, 829, 830, 831, 832, 908, 910, 955, 956, 957, 996, 999, 1111, 1128, 1130, 1132, 1137, 1149, 1151, 1289], "pair": [3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 126, 127, 135, 139, 145, 169, 270, 294, 527, 553, 579, 654, 666, 716, 717, 719, 879, 912, 913, 978, 997, 1019, 1078, 1129, 1131, 1133, 1136, 1138, 1142, 1146, 1289, 1292], "get_nam": [3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 1100, 1102, 1289], "consist": [3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 132, 145, 727, 957, 1095, 1288, 1289], "uniform": [3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 139], "might": [3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 97, 126, 135, 139, 442, 443, 447, 448, 452, 453, 553, 554, 555, 721, 722, 724, 725, 726, 728, 791, 958, 1019, 1046, 1109, 1157, 1166, 1289, 1292], "exampl": [3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 127, 131, 145, 411, 448, 453, 909, 915, 918, 928, 984, 1056, 1081, 1082, 1083, 1084, 1085, 1086, 1087, 1088, 1089, 1090, 1092, 1093, 1100, 1157, 1166, 1203, 1287, 1288], "cell_typ": [3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 604], "expression_level": [3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92], "score": [3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 139, 277, 540, 665, 666, 673, 675, 854, 857, 858, 861, 1132, 1133, 1289], "static": [3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 139, 972, 1019, 1109, 1203], "get_reference_set": [3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92], "use_complex": [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94], "fals": [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 98, 126, 127, 128, 132, 133, 135, 139, 145, 149, 168, 169, 170, 188, 190, 191, 211, 212, 214, 241, 249, 260, 261, 268, 275, 287, 306, 312, 314, 315, 331, 332, 333, 334, 335, 336, 337, 342, 346, 347, 348, 350, 352, 353, 358, 360, 363, 366, 389, 390, 398, 403, 405, 408, 437, 441, 446, 451, 516, 527, 555, 564, 602, 641, 649, 665, 666, 668, 671, 672, 673, 674, 675, 697, 714, 727, 759, 762, 775, 787, 788, 793, 794, 818, 819, 820, 821, 836, 845, 882, 893, 894, 913, 918, 930, 940, 941, 955, 961, 965, 969, 977, 982, 995, 1003, 1008, 1019, 1026, 1046, 1062, 1078, 1081, 1082, 1083, 1085, 1086, 1087, 1088, 1089, 1090, 1092, 1093, 1095, 1100, 1102, 1108, 1109, 1120, 1121, 1122, 1129, 1131, 1133, 1136, 1138, 1140, 1142, 1143, 1146, 1154, 1157, 1166, 1186, 1188, 1289], "9606": [3, 4, 5, 6, 7, 8, 9, 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212, 213, 222, 260, 261, 272, 306, 328, 346, 352, 366, 384, 424, 437, 469, 482, 483, 484, 516, 517, 532, 564, 602, 641, 665, 666, 671, 672, 673, 674, 675, 714, 718, 734, 745, 746, 749, 767, 768, 781, 782, 802, 810, 812, 813, 815, 840, 845, 854, 857, 865, 866, 867, 881, 909, 913, 915, 917, 918, 919, 920, 923, 924, 927, 928, 931, 932, 955, 958, 965, 972, 1003, 1008, 1019, 1030, 1036, 1060, 1078, 1079, 1080, 1082, 1084, 1086, 1088, 1090, 1093, 1095, 1100, 1102, 1104, 1105, 1108, 1109, 1120, 1121, 1122, 1129, 1131, 1133, 1136, 1138, 1139, 1140, 1141, 1142, 1143, 1146, 1147, 1154, 1157, 1166, 1186, 1195, 1289], "retriev": [3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 119, 135, 139, 145, 158, 181, 187, 189, 190, 207, 212, 220, 221, 222, 240, 243, 245, 249, 250, 251, 252, 253, 254, 255, 257, 258, 272, 280, 281, 285, 302, 303, 316, 325, 331, 346, 347, 348, 350, 352, 353, 357, 360, 363, 366, 386, 387, 392, 393, 394, 395, 408, 433, 463, 494, 538, 551, 553, 555, 614, 616, 617, 627, 637, 639, 641, 663, 665, 686, 713, 720, 721, 722, 723, 724, 725, 726, 727, 728, 793, 794, 833, 834, 835, 836, 901, 911, 918, 921, 972, 1008, 1011, 1100, 1104, 1109, 1154, 1205, 1230, 1289], "which": [3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 96, 97, 100, 118, 126, 127, 128, 134, 135, 139, 145, 249, 252, 296, 355, 406, 411, 553, 649, 665, 666, 707, 753, 782, 854, 857, 945, 977, 1013, 1015, 1019, 1022, 1026, 1046, 1050, 1081, 1082, 1085, 1086, 1087, 1088, 1089, 1090, 1092, 1093, 1100, 1102, 1109, 1110, 1113, 1144, 1154, 1157, 1166, 1171, 1176, 1177, 1271, 1275, 1276, 1277, 1278, 1279, 1280, 1283, 1285, 1286, 1287, 1288, 1291, 1292], "potenti": [3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 1046, 1109, 1289], "typic": [3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 1008, 1072, 1109, 1120, 1122, 1288, 1289], "proteom": [3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 118, 128, 1109, 1138, 1140, 1289], "organ": [3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 127, 128, 131, 145, 178, 179, 180, 182, 184, 185, 187, 188, 189, 190, 201, 211, 213, 214, 218, 219, 220, 221, 222, 225, 226, 227, 228, 229, 230, 231, 232, 233, 234, 243, 244, 245, 275, 277, 278, 283, 298, 299, 300, 308, 309, 321, 322, 328, 345, 346, 349, 351, 352, 363, 375, 376, 378, 382, 386, 387, 397, 398, 403, 404, 405, 406, 407, 408, 409, 419, 424, 429, 430, 437, 468, 469, 522, 527, 541, 560, 561, 562, 563, 565, 566, 567, 568, 569, 570, 571, 572, 573, 574, 575, 594, 595, 596, 602, 611, 613, 614, 615, 616, 617, 629, 630, 631, 632, 633, 634, 635, 646, 648, 649, 650, 665, 666, 677, 679, 708, 718, 719, 734, 735, 744, 745, 752, 754, 764, 765, 772, 812, 813, 823, 824, 838, 839, 840, 841, 843, 844, 845, 848, 859, 869, 881, 882, 894, 898, 909, 912, 915, 918, 920, 923, 924, 927, 928, 930, 931, 932, 935, 936, 937, 938, 939, 940, 941, 942, 972, 974, 995, 1008, 1100, 1103, 1104, 1105, 1106, 1108, 1109, 1110, 1120, 1122, 1129, 1131, 1133, 1136, 1138, 1140, 1141, 1142, 1143, 1146, 1147, 1171, 1172, 1176, 1177, 1181, 1182, 1184, 1186, 1188, 1287, 1288, 1291, 1292], "option": [3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 127, 132, 135, 139, 145, 190, 234, 406, 407, 441, 443, 446, 448, 451, 453, 463, 553, 554, 555, 794, 1108, 1109, 1114, 1120, 1122, 1150, 1154, 1157, 1183, 1186, 1219, 1241, 1289, 1292], "get_subset": [3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 955, 1289], "subset": [3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 1053], "filter": [3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 98, 122, 131, 133, 139, 145, 187, 191, 331, 332, 334, 336, 1046, 1129, 1131, 1133, 1138, 1289], "element": [3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 122, 126, 127, 134, 135, 139, 145, 267, 340, 472, 751, 759, 782, 787, 895, 909, 915, 918, 928, 958, 977, 1100, 1109, 1140, 1157, 1289], "get_subset_bool_arrai": [3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92], "reference_set": [3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92], "boolean": [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 135, 723, 965, 1289], "vector": [3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92], "presenc": [3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 135, 1019], "absenc": [3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 135, 1019], "simplest": [3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92], "kind": [3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 135, 139, 909, 918, 928, 1109, 1110, 1119, 1289, 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973, 977, 1140, 1181, 1182, 1289, 1292], "transmembran": [82, 89, 236, 1289, 1292], "segment": [82, 89, 1154, 1289], "transcript": [83, 135, 145, 155, 181, 182, 188, 190, 191, 555, 873, 961, 1046, 1052, 1056, 1109, 1120, 1122, 1288, 1292], "factor": [83, 145, 873, 1289, 1292], "tf": [83, 155, 212, 213, 260, 261, 344, 345, 346, 347, 348, 350, 352, 353, 679, 680, 873, 888, 1008, 1023, 1289, 1291, 1292], "censu": [83, 285, 873], "vaqueriza": [83, 873], "2009": [83, 873, 1289], "tissu": [86, 88, 181, 182, 1154, 1289, 1292], "subcellular": [87, 788], "exocarta": 90, "cytosig": [91, 1289], "dedic": [96, 1289], "json": [96, 122, 132, 133, 135, 265, 266, 366, 723, 913, 1014, 1046, 1154, 1289], "full": [96, 122, 126, 132, 135, 188, 275, 331, 333, 335, 337, 355, 442, 447, 452, 668, 669, 845, 905, 944, 1008, 1154, 1278, 1279, 1287, 1288, 1291], "whitespac": [96, 122, 132, 135], "line": [96, 122, 132, 135, 181, 182, 267, 346, 347, 348, 350, 352, 353, 909, 1019, 1275, 1276, 1277, 1278, 1279, 1280, 1289], "break": [96, 122, 132, 135, 517], "update_attr": [96, 122, 132, 135], "store": [96, 122, 132, 135, 974, 978, 1046, 1062, 1140, 1141, 1145, 1150, 1154, 1157, 1179, 1203, 1288, 1289, 1291], "ident": [96, 122, 132, 135, 407, 945, 1046, 1289], "share": [96, 122, 132, 135, 145, 147, 958, 984, 1046, 1289, 1291], "common": [96, 122, 132, 135, 194, 1188, 1191, 1211, 1287], "combine_attr": [96, 122, 132, 135], "new": [96, 122, 128, 132, 135, 145, 263, 794, 1008, 1046, 1056, 1109, 1118, 1166, 1288, 1289, 1291, 1292], "three": [96, 122, 132, 135, 709, 1008, 1271], "wai": [96, 122, 132, 133, 135, 145, 294, 411, 413, 443, 448, 453, 717, 718, 719, 794, 905, 909, 915, 918, 928, 960, 967, 971, 1008, 1019, 1108, 1157, 1166, 1289], "keyword": [96, 122, 132, 135, 1205, 1236, 1271, 1289], "work": [97, 329, 366, 441, 446, 451, 754, 791, 1032, 1046, 1109, 1120, 1180, 1288, 1289, 1292], "import": [97, 145, 406, 407, 411, 448, 453, 845, 1008, 1056, 1081, 1082, 1083, 1084, 1085, 1086, 1087, 1088, 1089, 1090, 1092, 1093, 1229, 1288, 1289], "main": [97, 126, 132, 135, 145, 193, 1032, 1266, 1288, 1289, 1292], "data_model": [98, 135, 145, 965, 998, 999, 1046], "interaction_typ": [98, 132, 133, 135, 145, 688, 965, 998, 999, 1046, 1289], "source_ent": 98, "target_ent": 98, "remove_loop": [98, 145], "intera": [100, 101, 102, 103, 104, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 127, 227, 234, 588, 594, 708, 759, 876, 1140, 1289], "abstractcomplexresourc": [101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117], "mani": [118, 479, 553, 554, 555, 1046, 1078, 1109, 1120, 1122, 1288, 1289, 1291, 1292], "just": [118, 145, 960, 967, 971, 1068, 1161, 1164, 1169, 1287], "like": [118, 135, 145, 265, 267, 442, 447, 452, 721, 722, 724, 725, 726, 727, 728, 958, 972, 997, 1068, 1159, 1161, 1164, 1169, 1288, 1289], "uniprot_db": [118, 395], "all_uniprot": [118, 395, 1100, 1289], "taxon": [121, 122, 123, 127, 135, 145, 382, 751, 930, 1109, 1129, 1131, 1133, 1136, 1138, 1140, 1146, 1191, 1289], "id_typ": [122, 123, 135, 359, 364, 468, 516, 517, 649, 650, 665, 666, 969, 972, 975, 978, 979, 980, 982, 1108, 1109, 1110, 1111, 1119, 1120, 1121, 1122, 1124, 1125, 1129, 1131, 1133, 1136, 1137, 1138, 1142, 1143, 1146, 1147, 1161, 1164, 1169, 1171, 1172, 1174, 1176, 1177, 1203, 1289], "attributehandl": [122, 132, 135, 1160, 1161, 1162, 1167, 1168], "lncrna": [122, 145, 1008, 1109], "non": [122, 128, 145, 302, 654, 1021, 1046, 1102, 1109, 1120, 1122, 1289], "metabolit": [122, 145, 440, 441, 442, 443, 452, 462, 463, 465, 1289, 1291], "compound": [122, 145, 551, 592, 790, 791, 1203, 1289, 1291], "nonetyp": [122, 132, 135, 145, 648, 649, 650, 775, 1046], "addit": [122, 127, 145, 329, 349, 351, 517, 668, 669, 909, 915, 918, 928, 1019, 1046, 1078, 1100, 1108, 1140, 1289, 1292], "prepend": [122, 145, 1008, 1015, 1019, 1026, 1046, 1064, 1078, 1079, 1136, 1150, 1166, 1171, 1267], "messag": [122, 145, 1008, 1015, 1019, 1026, 1046, 1064, 1078, 1079, 1082, 1085, 1086, 1136, 1150, 1157, 1166, 1171, 1267, 1287, 1292], "send": [122, 145, 517, 1008, 1015, 1019, 1026, 1046, 1064, 1078, 1079, 1136, 1150, 1166, 1171, 1267, 1268], "classmethod": [122, 145, 958, 985, 986, 987, 988, 1014, 1019, 1078, 1109], "count_entity_typ": 122, "filter_entity_typ": [122, 958], "ones": [122, 135, 145, 668, 669, 707, 1102, 1150, 1179, 1289], "occurr": [123, 136, 137, 147, 163, 164, 165, 166, 167, 178, 224, 236, 277, 344, 427, 428, 471, 511, 540, 550, 604, 685, 688, 689, 757, 829, 830, 831, 832, 908, 910, 955, 956, 957, 996, 999, 1111, 1128, 1130, 1132, 1137, 1149, 1151], "alia": [123, 136, 137, 147, 163, 164, 165, 166, 167, 178, 224, 236, 344, 427, 428, 471, 511, 540, 550, 604, 685, 688, 689, 757, 829, 830, 831, 832, 908, 910, 955, 956, 957, 996, 999, 1111, 1128, 1130, 1132, 1137, 1149, 1151, 1270, 1272, 1273], "2": [123, 136, 145, 147, 165, 166, 167, 178, 224, 236, 267, 344, 398, 427, 428, 471, 511, 540, 553, 604, 611, 685, 688, 689, 713, 757, 787, 830, 831, 832, 850, 851, 908, 910, 955, 956, 996, 997, 999, 1019, 1111, 1128, 1132, 1137, 1149, 1151, 1154, 1271, 1283, 1286, 1287], "index": [123, 136, 137, 147, 163, 164, 165, 166, 167, 170, 178, 224, 236, 243, 245, 306, 344, 427, 428, 471, 511, 540, 550, 604, 641, 682, 683, 685, 688, 689, 757, 829, 830, 831, 832, 908, 910, 955, 956, 957, 996, 999, 1111, 1128, 1130, 1132, 1137, 1149, 1151, 1289], "stop": [123, 136, 137, 147, 163, 164, 165, 166, 167, 178, 224, 236, 344, 427, 428, 471, 511, 540, 550, 604, 685, 688, 689, 757, 829, 830, 831, 832, 908, 910, 955, 956, 957, 996, 999, 1081, 1085, 1111, 1128, 1130, 1132, 1137, 1149, 1151, 1289], "9223372036854775807": [123, 136, 137, 147, 163, 164, 165, 166, 167, 178, 224, 236, 344, 427, 428, 471, 511, 540, 550, 604, 685, 688, 689, 757, 829, 830, 831, 832, 908, 910, 955, 956, 957, 996, 999, 1111, 1128, 1130, 1132, 1137, 1149, 1151], "rais": [123, 136, 137, 147, 163, 164, 165, 166, 167, 178, 224, 236, 294, 344, 427, 428, 471, 511, 540, 550, 604, 685, 688, 689, 757, 829, 830, 831, 832, 908, 909, 910, 955, 956, 957, 996, 997, 999, 1111, 1128, 1130, 1132, 1137, 1149, 1151], "valueerror": [123, 136, 137, 147, 163, 164, 165, 166, 167, 178, 224, 236, 344, 427, 428, 471, 511, 540, 550, 604, 685, 688, 689, 757, 829, 830, 831, 832, 908, 910, 955, 956, 957, 996, 999, 1111, 1128, 1130, 1132, 1137, 1149, 1151], "3": [123, 136, 145, 147, 165, 166, 167, 224, 236, 267, 342, 344, 389, 421, 427, 428, 471, 511, 540, 553, 604, 685, 688, 757, 832, 908, 909, 910, 915, 918, 928, 955, 999, 1030, 1060, 1137, 1149, 1151, 1266, 1287, 1288, 1289], "input_param": [126, 127, 128], "map_by_orthology_from": [126, 127], "trace": [126, 127, 128, 1157], "orthology_only_swissprot": [126, 127], "ptm_orthology_strict": [126, 127], "nonhuman_direct_lookup": [126, 128], "inputarg": [126, 127, 128], "doc": [126, 135, 145, 1219, 1241, 1287, 1291], "written": [126, 1154, 1289], "assign_to_network": 126, "pa": [126, 145, 1019, 1056, 1081, 1082, 1083, 1084, 1085, 1086, 1087, 1088, 1089, 1090, 1092, 1093, 1289], "enzym": [126, 127, 128, 132, 133, 308, 309, 389, 390, 540, 977, 1008, 1022, 1046, 1287, 1288, 1291], "substrat": [126, 127, 128, 308, 309, 483, 540, 589, 734, 977, 1008, 1022, 1046, 1287, 1288, 1291], "edg": [126, 135, 145, 584, 585, 1019, 1271, 1287], "legaci": [126, 145, 1287], "build_list": 126, "request": [126, 135, 191, 366, 375, 376, 378, 384, 517, 668, 781, 1078, 1079, 1108, 1219, 1229, 1241, 1289, 1292], "redund": [126, 135, 1102, 1289], "organis": [126, 997], "effici": [126, 1157, 1289], "thei": [126, 131, 135, 139, 532, 845, 957, 1008, 1019, 1021, 1109, 1166, 1288, 1289, 1291], "agre": [126, 1289], "except": [126, 135, 145, 384, 781, 1129, 1131, 1133, 1136, 1138, 1147, 1292], "isoform": [126, 127, 751, 975, 977, 979, 980, 982, 1140, 1141, 1183, 1184, 1186, 1205, 1238, 1262, 1263, 1289, 1292], "id_type_enzym": [127, 128, 995, 1289], "id_type_substr": [127, 128, 995], "ptmorthologi": 127, "enzymesubstrateprocessor": 127, "unifi": 127, "differ": [127, 135, 443, 448, 453, 909, 957, 972, 974, 1013, 1046, 1068, 1108, 1109, 1120, 1157, 1288, 1289, 1291, 1292], "chosen": 127, "mous": [127, 182, 211, 212, 213, 214, 220, 221, 222, 225, 226, 227, 228, 229, 230, 231, 232, 233, 234, 243, 244, 245, 349, 351, 419, 429, 430, 650, 665, 666, 754, 764, 765, 823, 824, 845, 898, 1287, 1288, 1289], "rat": [127, 182, 754, 845, 1287], "To": [127, 758, 759, 876, 972, 1154, 1289, 1292], "get": [127, 197, 406, 408, 411, 509, 972, 997, 1010, 1078, 1102, 1154, 1157, 1287, 1289, 1292], "themselv": 127, "both": [127, 135, 145, 171, 225, 406, 407, 408, 718, 835, 836, 857, 918, 942, 945, 1010, 1078, 1108, 1288, 1289, 1292], "whatmor": 127, "enzymesubstrateaggreg": [127, 1289], "swissprot": [127, 409, 469, 718, 918, 930, 937, 938, 939, 940, 941, 942, 971, 972, 1108, 1109, 1112, 1120, 1129, 1131, 1133, 1136, 1138, 1142, 1143, 1146, 1147, 1186, 1288, 1289], "trembl": [127, 918, 940, 941, 942, 972, 1108, 1109, 1112, 1120, 1288, 1289], "those": [127, 302, 782, 1100, 1109, 1131, 1138, 1166, 1244, 1289], "homolog": [127, 1131, 1138, 1289, 1292], "ptm": [127, 128, 132, 133, 340, 483, 751, 753, 844, 977, 981, 1046, 1050, 1051, 1140, 1289, 1291, 1292], "phosphosit": [127, 128, 774, 1140, 1289, 1291, 1292], "do": [127, 145, 654, 793, 895, 1046, 1087, 1090, 1092, 1109, 1287, 1292], "residu": [127, 296, 509, 524, 751, 754, 759, 882, 973, 977, 978, 980, 1140, 1150, 1152, 1183, 1205, 1237, 1247, 1289], "offset": [127, 366, 509, 524, 525, 707, 1140, 1149, 1150, 1183, 1289], "see": [127, 135, 145, 181, 188, 212, 275, 346, 347, 348, 350, 352, 353, 441, 442, 446, 447, 451, 452, 775, 893, 904, 905, 906, 909, 915, 918, 928, 958, 1088, 1100, 1108, 1109, 1120, 1121, 1122, 1203, 1268, 1271, 1283, 1285, 1286, 1288, 1289, 1292], "further": [127, 151, 294, 524, 553, 894, 955, 1008, 1019, 1150, 1154, 1157, 1179, 1287, 1289, 1292], "ptm_orthologi": [127, 1140], "phosphoryl": [127, 745, 751, 752, 1140, 1289], "site": [127, 296, 745, 751, 752, 753, 754, 755, 915, 945, 1140, 1182, 1289, 1291], "phosphositeplu": [127, 745, 751, 752, 753, 754, 1140], "follow": [127, 135, 302, 303, 342, 751, 834, 997, 1078, 1140, 1288, 1289], "6": [127, 136, 147, 165, 224, 236, 344, 428, 511, 527, 540, 553, 751, 757, 910, 945, 955, 1140, 1287, 1289], "letter": [127, 135, 384, 406, 407, 408, 414, 415, 416, 417, 751, 1140, 1157, 1205, 1247, 1289], "code": [127, 188, 260, 261, 403, 405, 406, 407, 408, 414, 415, 416, 417, 448, 453, 751, 906, 1008, 1021, 1109, 1120, 1122, 1140, 1283, 1285, 1286, 1289, 1291], "modif": [127, 194, 751, 973, 977, 1140, 1166, 1182, 1289], "set_inputarg": [127, 128], "x": [127, 145, 1140, 1275, 1276, 1277, 1278, 1279, 1280, 1283, 1285, 1286], "return_str": [127, 1140], "anyth": [127, 1073, 1081, 1084, 1102, 1109, 1140, 1271, 1283, 1286, 1289], "notat": [127, 1140, 1289], "amino": [127, 707, 879, 1140, 1289], "acid": [127, 707, 879, 1140, 1157, 1289], "offest": [127, 1140], "p00533_s231": [127, 1140], "domainmotif": [127, 588, 594, 1140, 1289], "typ": [127, 978, 980, 1140, 1289], "translate_sit": [127, 1140], "re": [127, 145, 881, 1140], "source_organ": [127, 187, 1140], "ortholog": [127, 665, 666, 726, 727, 754, 1129, 1131, 1133, 1136, 1138, 1140, 1142, 1143, 1146, 1147, 1288, 1289], "allow_mixed_organ": 128, "organisms_support": [128, 995], "sequencecontain": [128, 1140, 1289], "variou": [128, 145, 277, 357, 382, 443, 448, 453, 930, 1008, 1191, 1219, 1241, 1274, 1288, 1289], "obtain": [128, 135, 468, 469, 509, 847, 877, 878, 893, 972, 992, 1131, 1138, 1289], "lookup": [128, 668, 669, 1144], "ambigu": [128, 135, 1109, 1121, 1289], "map": [128, 133, 188, 190, 270, 313, 315, 479, 480, 509, 538, 629, 665, 666, 707, 709, 716, 717, 718, 719, 759, 793, 818, 821, 875, 877, 878, 912, 913, 960, 967, 971, 972, 997, 1150, 1179, 1275, 1276, 1277, 1278, 1279, 1280, 1283, 1285, 1286, 1288, 1289, 1291], "mismatch": 128, "mapper": [128, 1113, 1118, 1122, 1289], "speci": [128, 468, 469, 754, 893, 894, 1289, 1291], "forward": [128, 1019], "support": [131, 132, 133, 135, 145, 211, 214, 243, 244, 245, 349, 351, 406, 411, 419, 524, 764, 765, 974, 1131, 1288, 1289, 1291], "relationship": [131, 132, 133, 171, 288, 363, 411, 413, 429, 478, 665, 686, 977, 1129, 1131, 1133, 1136, 1138, 1142, 1143, 1146, 1287, 1288], "hold": [131, 713, 1154], "avail": [131, 180, 181, 182, 188, 189, 192, 194, 204, 220, 221, 222, 225, 226, 227, 228, 229, 230, 231, 232, 233, 234, 294, 345, 346, 352, 359, 364, 429, 430, 648, 649, 650, 668, 669, 714, 746, 748, 749, 750, 791, 823, 824, 845, 898, 909, 915, 918, 928, 945, 955, 972, 1008, 1109, 1120, 1122, 1154, 1203, 1288, 1289, 1292], "two": [132, 135, 145, 294, 340, 355, 441, 446, 451, 472, 665, 666, 707, 709, 793, 945, 958, 1019, 1109, 1122, 1129, 1131, 1133, 1136, 1138, 1142, 1271, 1275, 1276, 1277, 1278, 1279, 1280, 1288, 1289], "part": [132, 204, 213, 249, 346, 352, 516, 858, 1046, 1109, 1289, 1291, 1292], "resourceattribut": [132, 995, 998], "deriv": [132, 1046, 1275, 1285, 1289, 1292], "prefer": [132, 135, 406, 407, 408, 411, 778, 1010, 1109, 1119, 1120, 1288, 1289], "asdict": [132, 133, 135, 1129, 1131, 1133, 1138], "represent": [132, 135, 227, 1289], "has_interaction_typ": [132, 133], "depend": [132, 135, 190, 442, 447, 452, 1008, 1289, 1291], "comprehens": [133, 145, 346, 347, 348, 350, 352, 353, 1154, 1288, 1289, 1291, 1292], "It": [133, 135, 145, 974, 1008, 1022, 1046, 1072, 1078, 1079, 1108, 1109, 1110, 1120, 1121, 1129, 1131, 1133, 1136, 1138, 1147, 1268, 1288, 1289, 1292], "certain": [133, 135, 145, 665, 666, 1078, 1079, 1133, 1136, 1142, 1143, 1146, 1147, 1154, 1287], "ha": [133, 135, 145, 212, 213, 329, 406, 411, 592, 707, 974, 997, 1008, 1046, 1056, 1078, 1102, 1108, 1109, 1110, 1113, 1154, 1157, 1288, 1289, 1291, 1292], "within": [133, 442, 447, 452, 909, 915, 918, 928, 997, 1095, 1271, 1283, 1286, 1288, 1289, 1292], "has_dataset": 133, "meet": [133, 1129, 1133], "item": [133, 145, 366, 997, 1072, 1073, 1095, 1289], "dict_item": 133, 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1078, 1182], "evid": [135, 145, 346, 347, 348, 350, 352, 353, 403, 405, 685, 713, 775, 854, 857, 977, 979, 980, 1289, 1291], "detail": [135, 145, 345, 349, 351, 355, 366, 533, 713, 854, 904, 909, 915, 918, 928, 945, 958, 973, 1109, 1120, 1121, 1288, 1289], "henc": [135, 474, 1008, 1108, 1289, 1291, 1292], "becom": 135, "add_evid": 135, "direction": [135, 145, 1019], "self": [135, 1154, 1287], "dir": [135, 1289], "networkresourc": [135, 145, 1046, 1068, 1289], "separ": [135, 267, 443, 448, 453, 553, 962, 965, 969, 999, 1019, 1046, 1068, 1109, 1122, 1166, 1289, 1291], "Or": [135, 145, 1289, 1292], "causal": [135, 1287, 1292], "stimul": [135, 856, 1289], "stimulatori": [135, 1289], "inhibit": [135, 856, 1289], "inhibitori": [135, 1289], "unknown": [135, 329, 965, 969, 980, 1019, 1289], "neutral": 135, "been": [135, 145, 329, 406, 408, 411, 974, 1046, 1082, 1108, 1109, 1110, 1157, 1288, 1289, 1291, 1292], "add_sign": 135, "sign": [135, 139, 145, 965, 1019, 1054], "resource_nam": [135, 145, 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